{"query_id": "scaleup_9632387_8100163", "query": "How to achieve a clear color response for reliable determination of phenolic content despite reagent turbidity", "pos": ["ON TYROSINE AND TRYPTOPHANE DETERMINATIONS IN PROTEINS. The article summarizes research into the existing methods for the quantitative determination of tyrosine and tryptophane in proteins. Limitations to the accuracy of the Folin-Looney method (reaction of a phosphotungstic phosphomolybdic acid in a phenol solution, evaluated using colorimetry) have been solved by an improved method detailed in the text. The hydrolysis of proteinaceous material to allow chemical analysis of tryptophane has also been improved; the method is based on digestion with sodium hydroxide for 18-20 hours, followed by rapid neutralization and acidification with sulfuric acid. A more accurate test for tyrosine based on Millon's reaction has been developed; acidified mercuric sulfate solution is used to dissolve precipitated tyrosine and sodium nitrite is added to produce the colored product which is assessed colorimetrically. Two types of casein analyzed by these methods contained 1.4% tryptophane and 6.37-6.55% tyrosine. Tryptophane and tyrosine content of various materials were: casein 1.4%, 6.4-6.6%; egg albumin 1.3%, 4.0%; edestin 1.5%, 4.5%; gliadin 0.84%, 3.1%; zein 0.17%, 5.9%. A method for preparation of the pure mercuric sulfate reagent is described."], "field": "Agricultural and Biological Sciences", "q_year": 2013, "q_cid": "9632387", "pos_cid": 8100163, "source": "eval20x26"}
{"query_id": "scaleup_19816819_21124355", "query": "How to reliably characterize flowering-time variation in common bean landraces across different growing conditions", "pos": ["Assessment of genetic diversity and yield performance in Jordanian barley (Hordeum vulgare L.) landraces grown under Rainfed conditions. BackgroundBarley (Hordeum vulgare L.) is a major cereal crop, which is cultivated under variable environmental conditions and abiotic stresses in marginal areas around the globe. In this study, we evaluated 150 Jordanian landraces obtained from ICARDA Gene Bank and four local checks for yield and yield components related-traits in two locations across Jordan for three growing seasons under rainfed conditions. The study aims to identify superior Jordanian barley genotypes under dry conditions, to understand the genotype × environment (G × E) interactions, to analyze stability parameters and to identify markers associated with yield and yield components under rainfed conditions.ResultsThe barley accessions exhibited significant variation for all traits studied. Three accessions with high yield, cultivar superiority and stability under specific environments were identified with accession G69 is the highest yielding and superior for Madaba and overall environments and G144 is the highest yielding at Ramtha. Accession G123 was high yielding in all environments and was stable across different environments. At the genetic level, the Jordanian landraces were found to be diverse with a clustering that was based on row-type. The GWAS analysis identified 77 significant markers-traits associations for multiple traits including grain yield (GY) with three significant QTLs located at 1H, 2H and 7H, which seem important for dry environments.ConclusionUtilizing Jordanian barley landraces can effectively improve and adapt the current barley cultivars for cultivation under environmental stresses in dry regions. Utilization of markers associated with important agronomical traits and their incorporation in breeding using marker assisted selection can improve barley tolerance to drought stress."], "field": "Agricultural and Biological Sciences", "q_year": 2019, "q_cid": "198168198", "pos_cid": 21124355, "source": "eval20x26"}
{"query_id": "scaleup_67750566_10906134", "query": "How to increase tumor accumulation despite immune clearance and macrophage uptake", "pos": ["Geometry and Surface Characteristics of Gold Nanoparticles Influence their Biodistribution and Uptake by Macrophages. Spherical and rod-shaped gold nanoparticles with surface poly (ethylene glycol) (PEG) chains were characterized for size, shape, charge, poly dispersity and surface plasmon resonance. The nanoparticles were injected intravenously to 6–8 weeks old female nu/nu mice bearing orthotopic ovarian tumors and their biodistribution in vital organs was compared. Gold nanorods were taken up to a lesser extent by the liver, had longer circulation time in the blood, and higher accumulation in the tumors, compared with their spherical counterparts. The cellular uptake of PEGylated gold nanoparticles by a murine macrophage-like cell line as a function of geometry was examined. Compared to nanospheres, PEGylated gold nanorods were taken up to a lesser extent by macrophages. These studies point to the importance of gold nanoparticle geometry and surface properties on transport across biological barriers."], "field": "Agricultural and Biological Sciences", "q_year": 2019, "q_cid": "67750566", "pos_cid": 10906134, "source": "eval20x26"}
{"query_id": "scaleup_19664096_1767710", "query": "How to identify a reference among candidates that remains stable across samples for reliable measurement normalization", "pos": ["Normalization of Real-Time Quantitative Reverse Transcription-PCR Data: A Model-Based Variance Estimation Approach to Identify Genes Suited for Normalization, Applied to Bladder and Colon Cancer Data Sets. Accurate normalization is an absolute prerequisite for correct measurement of gene expression. For quantitative real-time reverse transcription-PCR (RT-PCR), the most commonly used normalization strategy involves standardization to a single constitutively expressed control gene. However, in recent years, it has become clear that no single gene is constitutively expressed in all cell types and under all experimental conditions, implying that the expression stability of the intended control gene has to be verified before each experiment. We outline a novel, innovative, and robust strategy to identify stably expressed genes among a set of candidate normalization genes. The strategy is rooted in a mathematical model of gene expression that enables estimation not only of the overall variation of the candidate normalization genes but also of the variation between sample subgroups of the sample set. Notably, the strategy provides a direct measure for the estimated expression variation, enabling the user to evaluate the systematic error introduced when using the gene. In a side-by-side comparison with a previously published strategy, our model-based approach performed in a more robust manner and showed less sensitivity toward coregulation of the candidate normalization genes. We used the model-based strategy to identify genes suited to normalize quantitative RT-PCR data from colon cancer and bladder cancer. These genes are UBC, GAPD, and TPT1 for the colon and HSPCB, TEGT, and ATP5B for the bladder. The presented strategy can be applied to evaluate the suitability of any normalization gene candidate in any kind of experimental design and should allow more reliable normalization of RT-PCR data."], "field": "Agricultural and Biological Sciences", "q_year": 2017, "q_cid": "19664096", "pos_cid": 1767710, "source": "eval20x26"}
{"query_id": "scaleup_20271129_51727195", "query": "How to identify which secondary metabolites in Buddleia indica leaves interact most favorably with TNF-α and may explain the extract’s hepatoprotective activity", "pos": ["Verification of the anti-inflammatory activity of the polyphenolic-rich fraction of Araucaria bidwillii Hook. using phytohaemagglutinin-stimulated human peripheral blood mononuclear cells and virtual screening.. ETHNOPHARMACOLOGICAL RELEVANCE Araucaria bidwillii Hook., the bunya pine, is an evergreen plant belonging to family Araucariaceae. Traditionally, its leaves and oleoresins have been used as herbal remedies to alleviate pain and inflammation. Based upon the frequent adverse effects accompanying synthetic anti-inflammatory drugs, this study will assess the anti-inflammatory activity of both the total methanol extract and the polyphenolic-rich fraction of A. bidwillii leaves. MATERIALS AND METHODS The anti-inflammatory activity was assessed in vitro using phytohaemagglutinin-stimulated human peripheral blood mononuclear cells (PBMCs). Isolation of the major compounds was conducted using various chromatographic techniques. Molecular modelling studies are performed on tumor necrosis factor-α (TNF-α), cyclooxygenase-II (COX-II) and 5-lipooxygenase (5-LOX). RESULTS Both the total methanol extract of Araucaria bidwillii leaves and its fraction revealed a dose-dependent manner in lowering the levels of IL-1β, IL-6 and TNF-α with an equivalent activity to that of indomethacin. In addition, the phytochemical investigation of the polyphenolic-rich fraction results in identification of agathisflavone-4',7''-dimethyl ether (1), 7-O-methyl-6-hydroxyapigenin (2) and 4',4'-di-O-methylamentoflavone (3) as the main components. In silico molecular modelling showed that agathisflavone-4',7''-dimethyl ether (1) exhibited the fittest binding in TNF-α active sites, while 7-O-methyl-6-hydroxyapigenin (2) showed the highest inhibition in COX-II whereas 4',4'-di-O-methylamentoflavone (3) is the most potent 5-LOX inhibitor. CONCLUSION Thus, the leaves of Araucaria bidwillii could afford a potent anti-inflammatory agent that effectively ameliorates inflammation and its related hazards. This in turn consolidates the fact of using the leaves of Araucaria bidwillii to sooth inflammation in traditional medicine."], "field": "Agricultural and Biological Sciences", "q_year": 2019, "q_cid": "202711299", "pos_cid": 51727195, "source": "eval20x26"}
{"query_id": "scaleup_582163_14008061", "query": "How to explain the higher fraction of root water uptake from dry sand compartments and determine whether local dryness alone accounts for it or moisture conditions elsewhere in the root zone also matter", "pos": ["Accounting for sap flow from different parts of the root system improves the prediction of xylem ABA concentration in plants grown with heterogeneous soil moisture. When soil moisture is heterogeneous, sap flow from, and ABA status of, different parts of the root system impact on leaf xylem ABA concentration ([X-ABA]leaf). The robustness of a model for predicting [X-ABA]leaf was assessed. ‘Two root-one shoot’ grafted sunflower (Helianthus annuus L.) plants received either deficit irrigation (DI, each root system received the same irrigation volumes) or partial rootzone drying (PRD, only one root system was watered and the other dried the soil). Irrespective of whether relative sap flow was assessed using sap flow sensors in vivo or by pressurization of de-topped roots, each root system contributed similarly to total sap flow during DI, while sap flow from roots in drying soil declined linearly with soil water potential (Ψsoil) during PRD. Although Ψsoil of the irrigated pot determined the threshold Ψsoil at which sap flow from roots in drying soil decreased, the slope of this decrease was independent of the wet pot Ψsoil. Irrespective of whether sap was collected from the wet or dry root system of PRD plants, or a DI plant, root xylem ABA concentration increased as Ψsoil declined. The model, which weighted ABA contributions of each root system according to the sap flow from each, almost perfectly explained [X-ABA] immediately above the graft union. That the model overestimated measured [X-ABA]leaf may result from changes in [X-ABA] along the transport pathway or an artefact of collecting xylem sap from detached leaves. The implications of declining sap flow through partially dry roots during PRD for the control of stomatal behaviour and irrigation scheduling are discussed."], "field": "Agricultural and Biological Sciences", "q_year": 2014, "q_cid": "582163", "pos_cid": 14008061, "source": "eval20x26"}
{"query_id": "scaleup_67750566_18839988", "query": "How to control the ratio of modified to unmodified proteins in engineered nanoparticles", "pos": ["Protein Coexpression Using FMDV 2A: Effect of “Linker” Residues. Many biomedical applications absolutely require, or are substantially enhanced by, coexpression of multiple proteins from a single vector. Foot-and-mouth disease virus 2A (F2A) and “2A-like” sequences (e.g., Thosea asigna virus 2A; T2A) are used widely for this purpose since multiple proteins can be coexpressed by linking open reading frames (ORFs) to form a single cistron. The activity of F2A “cleavage” may, however, be compromised by both the use of shorter versions of F2A and the sequences (derived from multiple-purpose cloning sites) used to link F2A to the upstream protein. To characterise these effects, different lengths of F2A and T2A were inserted between green and cherry fluorescent proteins. Mutations were introduced in the linker region immediately upstream of both F2A- and T2A-based constructs and activities determined using both cell-free translation systems and transfected cells. In shorter versions of F2A, activity may be affected by both the C-terminal sequence of the protein upstream and, equally strikingly, the residues immediately upstream introduced during cloning. Mutations significantly improved activity for shorter versions of F2A but could decrease activity in the case of T2A. These data will aid the design of cloning strategies for the co-expression of multiple proteins in biomedical/biotechnological applications."], "field": "Agricultural and Biological Sciences", "q_year": 2019, "q_cid": "67750566", "pos_cid": 18839988, "source": "eval20x26"}
{"query_id": "scaleup_9147286_10324129", "query": "How to determine whether NSm in the pellet fraction truly associates with membranes or is merely trapped within the lumen of closed microsomes", "pos": ["Isolation of intracellular membranes by means of sodium carbonate treatment: application to endoplasmic reticulum. A rapid and simple method for the isolation of membranes from subcellular organelles is described. The procedure consists of diluting the organelles in ice-cold 100 mM Na2CO3 followed by centrifugation to pellet the membranes. Closed vesicles are converted to open membrane sheets, and content proteins and peripheral membrane proteins are released in soluble form. Here we document the method by applying it to various subfractions of a rat liver microsomal fraction, prepared by continuous density gradient centrifugation according to Beaufay et al. (1974, J. Cell Biol. 61:213-231). The results confirm and extend those of previous investigators on the distribution of enzymes and proteins among the membranes of the smooth and rough endoplasmic reticulum. In the accompanying paper (1982, J. Cell Biol. 93:103-110) the procedure is applied to peroxisomes and mitochondria."], "field": "Agricultural and Biological Sciences", "q_year": 2014, "q_cid": "9147286", "pos_cid": 10324129, "source": "eval20x26"}
{"query_id": "scaleup_19896791_10716717", "query": "How to reliably detect and segment individual grape clusters of varying sizes and shapes across different scales in field images", "pos": ["Feature Pyramid Networks for Object Detection. Feature pyramids are a basic component in recognition systems for detecting objects at different scales. But pyramid representations have been avoided in recent object detectors that are based on deep convolutional networks, partially because they are slow to compute and memory intensive. In this paper, we exploit the inherent multi-scale, pyramidal hierarchy of deep convolutional networks to construct feature pyramids with marginal extra cost. A top-down architecture with lateral connections is developed for building high-level semantic feature maps at all scales. This architecture, called a Feature Pyramid Network (FPN), shows significant improvement as a generic feature extractor in several applications. Using a basic Faster R-CNN system, our method achieves state-of-the-art single-model results on the COCO detection benchmark without bells and whistles, surpassing all existing single-model entries including those from the COCO 2016 challenge winners. In addition, our method can run at 5 FPS on a GPU and thus is a practical and accurate solution to multi-scale object detection. Code will be made publicly available."], "field": "Agricultural and Biological Sciences", "q_year": 2019, "q_cid": "198967918", "pos_cid": 10716717, "source": "eval20x26"}
{"query_id": "scaleup_22235444_21885725", "query": "How to distinguish flavonols and ellagic acid glycosides and locate their distributions across ripe strawberry fruit tissues at microscopic resolution", "pos": ["Localization of Flavan-3-ol Species in Peanut Testa by Mass Spectrometry Imaging. Flavan-3-ols, procyanidins and their monomers are major flavonoids present in peanuts that show a wide range of biological properties and health benefits, based on their potent antioxidant activity. Procyanidin oligomers, especially A-type, are reportedly abundant in peanut skin; however, their localization in the raw peanut testa remains poorly understood. Therefore, we performed matrix-assisted laser desorption/ionization-mass spectrometry imaging (MALDI-MSI) to investigate the localization of flavan-3-ols in peanut testa. 1,5-Diaminonaphthalene was coated onto the peanut section by matrix vapor deposition/recrystallization, and MALDI-MSI measurements were performed in the negative-ion mode. Peaks matching the m/z values of flavan-3-ol [M − H]− ions were observed in the mass spectrum extracted from the outer epidermis of the peanut testa, using the region of interest function. Catechin and/or epicatechin, five A-type, and one B-type procyanidins were assigned by the fragment ions generated by retro-Diels-Alder, heterocyclic ring fission, and quinone methide reactions detected in MALDI-tandem MS spectra. These flavan-3-ols were localized in the outer epidermis of the peanut testa. This information will contribute to improving the extraction and purification efficiencies of flavan-3-ols from peanut testa. As flavan-3-ols display anti-microbial activity, it is speculated that flavan-3-ols present in the outer epidermis of peanut testa act to prevent pathogen infection."], "field": "Agricultural and Biological Sciences", "q_year": 2020, "q_cid": "222354440", "pos_cid": 218857259, "source": "eval_collection"}
{"query_id": "scaleup_25596871_22625466", "query": "How to limit water loss in Bermuda grass leaves in hot, dry environments", "pos": ["Structure‐function analysis of the maize bulliform cell cuticle and its potential role in dehydration and leaf rolling. Abstract The hydrophobic cuticle of plant shoots serves as an important interaction interface with the environment. It consists of the lipid polymer cutin, embedded with and covered by waxes, and provides protection against stresses including desiccation, UV radiation, and pathogen attack. Bulliform cells form in longitudinal strips on the adaxial leaf surface, and have been implicated in the leaf rolling response observed in drought‐stressed grass leaves. In this study, we show that bulliform cells of the adult maize leaf epidermis have a specialized cuticle, and we investigate its function along with that of bulliform cells themselves. Bulliform cells displayed increased shrinkage compared to other epidermal cell types during dehydration of the leaf, providing a potential mechanism to facilitate leaf rolling. Analysis of natural variation was used to relate bulliform strip patterning to leaf rolling rate, providing further evidence of a role for bulliform cells in leaf rolling. Bulliform cell cuticles showed a distinct ultrastructure with increased cuticle thickness compared to other leaf epidermal cells. Comparisons of cuticular conductance between adaxial and abaxial leaf surfaces, and between bulliform‐enriched mutants versus wild‐type siblings, showed a correlation between elevated water loss rates and presence or increased density of bulliform cells, suggesting that bulliform cuticles are more water‐permeable. Biochemical analysis revealed altered cutin composition and increased cutin monomer content in bulliform‐enriched tissues. In particular, our findings suggest that an increase in 9,10‐epoxy‐18‐hydroxyoctadecanoic acid content, and a lower proportion of ferulate, are characteristics of bulliform cuticles. We hypothesize that elevated water permeability of the bulliform cell cuticle contributes to the differential shrinkage of these cells during leaf dehydration, thereby facilitating the function of bulliform cells in stress‐induced leaf rolling observed in grasses."], "field": "Agricultural and Biological Sciences", "q_year": 2023, "q_cid": "255968716", "pos_cid": 226254666, "source": "eval_collection"}
{"query_id": "scaleup_23632386_20874764", "query": "How to identify the most relevant metabolites in plant volatile profiles as potential markers distinguishing experimental conditions", "pos": ["Multivariate optimization of headspace solid-phase microextraction coupled to gas chromatography-mass spectrometry for the analysis of terpenoids in sparkling wines.. A headspace solid-phase microextraction coupled to gas-chromatography and mass spectrometry (HS-SPME-GC-MS) was developed and validated for the determination of 26 terpenes in sparkling wines. The use of a Box-Behnken experimental design, together with the desirability function D, allowed the extraction conditions of the method to be optimized. The optimal extraction conditions were found at a dilution ratio of 2:3, the addition of 3.5 g of NaCl, an extraction temperature of 46 °C and an extraction time of 52 min, using the DVB/CAR/PDMS fibre. Afterwards, the analytical method was successfully validated in terms of linearity, matrix effect, limit of detection and quantification, precision and accuracy. To test the developed method, 35 commercial sparkling wines from different grape varieties, geographical regions and ageing times were analysed and their terpenoid profile was monitored. The use of multivariate statistical tools made it possible to highlight differences in the samples related to the terpene profile. Finally, the most important compounds involved in the discrimination of the samples were identified by means of iterative variable selection procedures."], "field": "Agricultural and Biological Sciences", "q_year": 2021, "q_cid": "236323868", "pos_cid": 208747641, "source": "eval_collection"}
{"query_id": "scaleup_23521416_20953198", "query": "How to accurately identify weed leaf age and plant centres in complex field environments while preserving individual distinctions and fine-grained detail for precise targeted spraying", "pos": ["BlendMask: Top-Down Meets Bottom-Up for Instance Segmentation. Instance segmentation is one of the fundamental vision tasks. Recently, fully convolutional instance segmentation methods have drawn much attention as they are often simpler and more efficient than two-stage approaches like Mask R-CNN. To date, almost all such approaches fall behind the two-stage Mask R-CNN method in mask precision when models have similar computation complexity, leaving great room for improvement. In this work, we achieve improved mask prediction by effectively combining instance-level information with semantic information with lower-level fine-granularity. Our main contribution is a blender module which draws inspiration from both top-down and bottom-up instance segmentation approaches. The proposed BlendMask can effectively predict dense per-pixel position-sensitive instance features with very few channels, and learn attention maps for each instance with merely one convolution layer, thus being fast in inference. BlendMask can be easily incorporate with the state-of-the-art one-stage detection frameworks and outperforms Mask R-CNN under the same training schedule while being faster. A light-weight version of BlendMask achieves 36.0 mAP at 27 FPS evaluated on a single 1080Ti. Because of its simplicity and efficacy, we hope that our BlendMask could serve as a simple yet strong baseline for a wide range of instance-wise prediction tasks."], "field": "Agricultural and Biological Sciences", "q_year": 2021, "q_cid": "235214162", "pos_cid": 209531988, "source": "eval_collection"}
{"query_id": "scaleup_25658568_24776994", "query": "How to characterize water and oil absorption, solubility, and swelling of okra residues after pectin extraction and assess their suitability as food ingredients in products such as pastries", "pos": ["Physicochemical and pasting properties of flour and starch from two new cassava accessions. ABSTRACT Some new cassava accessions have been developed and released because of their high yield, resistance to disease, adaptability to wider ecological environment, and less cost of production. However, their flour and starch properties have not been characterized for potential food applications. In the present study, starch and flour were produced from two new cassava accessions (Sika Bankye and Bankye Hemaa) and evaluated for their physicochemical and pasting properties. The flour samples recorded higher values for the various functional parameters compared to their starch counterparts. Both flour samples had a similar water absorption capacity (WAC) of ~263% but the associated starch from Bankye Hemaa recorded the lowest value of 38.6%. Bankye Hemaa flour recorded the highest oil absorption capacity (OAC) (121%) and could be exploited as potential flavor retainer in products. Flour from Bankye Hemaa also recorded the highest swelling power (882 ± 29%), which was indicative of their good thickening and stabilizing functionalities. Sika Bankye starch had the highest setback viscosity (723 ± 32 RVU), which was indicative of its lower susceptibility to retrogradation and potential use in products that require highly viscous paste and processed at high temperatures."], "field": "Agricultural and Biological Sciences", "q_year": 2023, "q_cid": "256585680", "pos_cid": 247769949, "source": "eval_collection"}
{"query_id": "scaleup_26501293_14944573", "query": "How to predict the effects of biopolymers, surfactants, co-surfactants, and fabrication conditions on the performance and controlled release of encapsulated essential-oil formulations", "pos": ["The significance of artificial intelligence in drug delivery system design.. Over the last decade, increasing interest has been attracted towards the application of artificial intelligence (AI) technology for analyzing and interpreting the biological or genetic information, accelerated drug discovery, and identification of the selective small-molecule modulators or rare molecules and prediction of their behavior. Application of the automated workflows and databases for rapid analysis of the huge amounts of data and artificial neural networks (ANNs) for development of the novel hypotheses and treatment strategies, prediction of disease progression, and evaluation of the pharmacological profiles of drug candidates may significantly improve treatment outcomes. Target fishing (TF) by rapid prediction or identification of the biological targets might be of great help for linking targets to the novel compounds. AI and TF methods in association with human expertise may indeed revolutionize the current theranostic strategies, meanwhile, validation approaches are necessary to overcome the potential challenges and ensure higher accuracy. In this review, the significance of AI and TF in the development of drugs and delivery systems and the potential challenging issues have been highlighted."], "field": "Agricultural and Biological Sciences", "q_year": 2023, "q_cid": "265012933", "pos_cid": 149445737, "source": "eval_collection"}
{"query_id": "scaleup_26562688_10297531", "query": "How to achieve practical, selective oxidation and carbon–oxygen bond formation in hydrazones without a complicated reagent system or additional additives", "pos": ["Selective cross-dehydrogenative C–O coupling of N-hydroxy compounds with pyrazolones. Introduction of the diacetyliminoxyl radical into the practice of organic synthesis. Oxidative C–O coupling of pyrazolones with N-hydroxy compounds of different classes (N-hydroxyphthalimide, N-hydroxybenzotriazole, oximes) was achieved; both one-electron oxidants (Fe(ClO4)3, (NH4)2Ce(NO3)6) and two-electron oxidants (PhI(OAc)2, Pb(OAc)4) are applicable, and the yields reach 91%. Apparently, the coupling proceeds via the formation of N-oxyl radicals from N-hydroxy compounds. One of the N-oxyl intermediates, the diacetyliminoxyl radical, was found to be exclusively stable in solution in spite of being sterically unhindered; it was isolated from an oxidant and used as a new reagent for the synthesis and mechanism study. The products of C–O coupling of pyrazolones with N-hydroxyphthalimide can be easily transformed into aminooxy compounds, valuable substances for combinatorial chemistry."], "field": "Agricultural and Biological Sciences", "q_year": 2023, "q_cid": "265626887", "pos_cid": 102975318, "source": "eval_collection"}
{"query_id": "scaleup_22112868_91559649", "query": "How to analyze genetic variation and construct linkage maps in biocontrol agents at low cost with incomplete genome information", "pos": ["Microsatellite markers developed using a next‐generation sequencing technique for Neotrogla spp. (Psocodea: Prionoglarididae), cave dwelling insects with sex‐reversed genitalia. The genus Neotrogla (Psocodea: Prinoglarididae) comprises four named species from Brazil. Females of this cave‐dwelling insect are characterized by a conspicuous penis‐like intromittent organ, termed a gynosome, which is inserted into the vagina‐like male genitalia during copulation. Another evolutionarily novel structure, the spermathecal plate, enables a female to simultaneously store two freshly deposited spermatophores (consisting of sperm and possibly nutritious substances) in her sperm storage organ (spermatheca). It is unknown whether the two spermatophores are derived from two different males. To investigate the mating ecology and population genetic structures of these insects with sex‐reversed genitalia, 16 novel highly polymorphic microsatellite loci were isolated and characterized based on ~2,275 Mbp genomic sequences from an undescribed Neotrogla species. Our first screening detected 99,888 candidate loci. Similar to other hemipteroid insects studied thus far, AAT motif microsatellites were conspicuously dominant. We further screened 99 sequences, for which 50 pairs of polymerase chain reaction primers were successfully designed. Sixteen of these primers successfully amplified products of the expected size in the 11 Neotrogla sp. individuals collected from two caves. The number of alleles per loci varied from two to nine, with no significant deviation from the Hardy–Weinberg equilibrium in either population. Although the caves sampled were only approximately 1 km apart, significant genetic differentiation was detected between the two populations. In total, 13, 12, 13 and 11 loci were cross‐amplified in N. aurora, N. brasiliensis, N. curvata and N. truncata, respectively, indicating the applicability of these microsatellite loci for metapopulation genetic studies in multiple Neotrogla species."], "field": "Agricultural and Biological Sciences", "q_year": 2020, "q_cid": "221128686", "pos_cid": 91559649, "source": "eval_collection"}
{"query_id": "scaleup_26073438_248525", "query": "How to determine whether shared features of root-nodule symbiosis have a common origin or arose independently without overestimating how often similarities arose independently", "pos": ["Genome-wide signatures of convergent evolution in echolocating mammals. Evolution is typically thought to proceed through divergence of genes, proteins and ultimately phenotypes. However, similar traits might also evolve convergently in unrelated taxa owing to similar selection pressures. Adaptive phenotypic convergence is widespread in nature, and recent results from several genes have suggested that this phenomenon is powerful enough to also drive recurrent evolution at the sequence level. Where homoplasious substitutions do occur these have long been considered the result of neutral processes. However, recent studies have demonstrated that adaptive convergent sequence evolution can be detected in vertebrates using statistical methods that model parallel evolution, although the extent to which sequence convergence between genera occurs across genomes is unknown. Here we analyse genomic sequence data in mammals that have independently evolved echolocation and show that convergence is not a rare process restricted to several loci but is instead widespread, continuously distributed and commonly driven by natural selection acting on a small number of sites per locus. Systematic analyses of convergent sequence evolution in 805,053 amino acids within 2,326 orthologous coding gene sequences compared across 22 mammals (including four newly sequenced bat genomes) revealed signatures consistent with convergence in nearly 200 loci. Strong and significant support for convergence among bats and the bottlenose dolphin was seen in numerous genes linked to hearing or deafness, consistent with an involvement in echolocation. Unexpectedly, we also found convergence in many genes linked to vision: the convergent signal of many sensory genes was robustly correlated with the strength of natural selection. This first attempt to detect genome-wide convergent sequence evolution across divergent taxa reveals the phenomenon to be much more pervasive than previously recognized."], "field": "Agricultural and Biological Sciences", "q_year": 2023, "q_cid": "260734381", "pos_cid": 248525, "source": "eval_collection"}
{"query_id": "scaleup_27149489_84183649", "query": "How to determine the lowest chlorpyrifos residue level in tea that different quantitative models can reliably detect", "pos": ["A Simple Procedure to Assess Limit of Detection for Multisensor Systems. Currently, there are no established procedures for limit of detection (LOD) evaluation in multisensor system studies, which complicates their correct comparison with other analytical techniques and hinders further development of the method. In this study we propose a simple and visually comprehensible approach for LOD estimation in multisensor analysis. The suggested approach is based on the assessment of evolution of mean relative error values in calibration series with growing analyte concentration. The LOD value is estimated as the concentration starting from which MRE values become stable from sample to sample. This intuitive procedure was successfully tested with a variety of real data from potentiometric multisensor systems."], "field": "Agricultural and Biological Sciences", "q_year": 2024, "q_cid": "271494898", "pos_cid": 84183649, "source": "eval_collection"}
{"query_id": "scaleup_28054212_25665492", "query": "How to reduce the adverse effects of antibiotic treatment", "pos": ["Antibiotic-Therapy-Induced Gut Dysbiosis Affecting Gut Microbiota—Brain Axis and Cognition: Restoration by Intake of Probiotics and Synbiotics. Antibiotic therapy through short-term or repeated long-term prescriptions can have several damaging effects on the normal microbiota of the gastrointestinal tract. Changes in microbiota could be multiple including decreased diversity of species in gut microbiota, changed metabolic activity, and the occurrence of antibiotic-resistant strains. Antibiotic-induced gut dysbiosis in turn can induce antibiotic-associated diarrhoea and recurrent infections caused by Clostridioides difficile. There is also evidence that the use of different chemical classes of antibiotics for the treatment of a variety of ailments can lead to several health issues including gastrointestinal, immunologic, and neurocognitive conditions. This review discusses gut dysbiosis, its symptoms and one important cause, which is antibiotic therapy for the induction of gut dysbiosis. Since the maintenance of good gut health is important for the well-being and functioning of physiological and cognitive activities through the normal gut-microbiota–brain relationship, the condition of dysbiosis is not desirable. Specific therapies are prescribed by medical practitioners for the cure of a variety of ailments, and, if the prescription of antibiotics becomes unavoidable, there is a possibility of the onset of gut dysbiosis as the side or after effects. Therefore, the restoration of imbalanced gut microbiota to its balanced condition becomes necessary. A healthy relationship between gut microbiota and the brain can be achieved with the introduction of probiotic strains into the gut in a practical and consumer-friendly way, such as consumption of food and beverages prepared with the use of characterised probiotic species, fermented foods as the potential biotics, or synbiotic supplements."], "field": "Agricultural and Biological Sciences", "q_year": 2025, "q_cid": "280542126", "pos_cid": 256654923, "source": "eval_collection"}
{"query_id": "scaleup_27632704_22079550", "query": "How to achieve favorable pharmacokinetics, efficient delivery to target cells, and sustained local activity while limiting systemic toxicity", "pos": ["Lipidation Approaches Potentiate Adjuvant-Pulsed Immune Surveillance: A Design Rationale for Cancer Nanovaccine. Adjuvant-pulsed peptide vaccines hold great promise for the prevention and treatment of different diseases including cancer. However, it has been difficult to maximize vaccine efficacy due to numerous obstacles including the unfavorable tolerability profile of adjuvants, instability of peptide antigens, limited cellular uptake, and fast diffusion from the injection site, as well as systemic adverse effects. Here we describe a robust lipidation approach for effective nanoparticle co-delivery of low-molecular weight immunomodulators (TLR7/8 agonists) and peptides (SIINFEKL) with a potent in vivo prophylactic effect. The lipidation approaches (C16-R848 and C16-SIINFEKL) increased their hydrophobicity that is intended not only to improve drug encapsulation efficiency but also to facilitate the membrane association, intracellular trafficking, and subcellular localization. The polymer–lipid hybrid nanoparticles (PLNs) are designed to sustain antigen/adjuvant levels with less systemic exposure. Our results demonstrated that a lipidated nanovaccine can induce effective immunity by enhancing the expansion and activation of antigen-specific CD8+ T cells. This adaptive immune response led to substantial tumor suppression with improved overall survival in a prophylactic setting. Our new methodology enhances the potential of nanovaccines for anti-tumor therapy."], "field": "Agricultural and Biological Sciences", "q_year": 2025, "q_cid": "276327046", "pos_cid": 220795504, "source": "eval_collection"}
{"query_id": "scaleup_27675149_26708363", "query": "How to quantify the matrix-embedded organisms remaining after treatment to assess formulation efficacy", "pos": ["A Three-Dimensional Model of Bacterial Biofilms and Its Use in Antimicrobial Susceptibility Testing. (1) Background: The discrepant antimicrobial susceptibility between planktonic and biofilm bacterial modes poses a problem for clinical microbiology laboratories and necessitates a relevant 3D experimental model allowing bacteria to grow in biofilm mode, in vitro, for use in anti-biofilm susceptibility testing. (2) Methods: This work develops a 3D biofilm model consisting of alginate beads containing S. aureus biofilm and encased within two thick layers of alginate matrix. The constructed model was placed on a thin Boyden chamber insert suspended on a 24-well culture plate containing the culture medium. The antibacterial activity of bacitracin and chlorhexidine digluconate (CD), either combined or separately, against 2D S. aureus culture was compared to that in the 3D biofilm model. Quantitative analysis and imaging analysis were performed by assessing the bacterial load within the matrix as well as measuring the optical density of the culture medium nourishing the matrix. (3) Results: The 3D biofilm model represented the typical complex characteristics of biofilm with greater insusceptibility to the tested antimicrobials than the 2D culture. Only bacitracin and CD in combination at 100× the concentration found to be successful against 2D culture were able to completely eliminate the 3D biofilm matrix. (4) Conclusions: The 3D biofilm model, designed to be more clinically relevant, exhibits higher antimicrobial insusceptibility than the 2D culture, demonstrating that the model might be useful for testing and discovering new antimicrobial therapies. The data also support the view that combination therapy might be the optimal approach to combat biofilm infections."], "field": "Agricultural and Biological Sciences", "q_year": 2025, "q_cid": "276751494", "pos_cid": 267083638, "source": "eval_collection"}
{"query_id": "scaleup_23522795_22089159", "query": "How to identify and determine the relative amounts of organic compounds in peat and sapropel extracts to characterize their organic-acid composition", "pos": ["Investigation of Organic Acids in Saffron Stigmas (Crocus sativus L.) Extract by Derivatization Method and Determination by GC/MS. The beneficial health properties of organic acids make them target compounds in multiple studies. This is the reason why developing a simple and sensitive determination and investigation method of organic acids is a priority. In this study, an effective method has been established for the determination of organic (lactic, glycolic, and malic) acids in saffron stigmas. N-(tert-butyldimethylsilyl)-N-methyltrifluoroacetamide (MTBSTFA) was used as a derivatization reagent in gas chromatography combined with mass spectrometric detection (GC/MS). The saffron stigmas extract was evaporated to dryness with a stream of nitrogen gas. The derivatization procedure: 0.1 g of dried extract was diluted into 0.1 mL of tetrahydrofuran, then 0.1 mL MTBSTFA was orderly and successively added into a vial. Two different techniques were used to obtain the highest amount of organic acid derivatives from saffron stigmas. To the best of our knowledge, this is the first report of the quantitative and qualitative GC/MS detection of organic acids in saffron stigmas using MTBSTFA reagent, also comparing different derivatization conditions, such as time, temperature and the effect of reagent amount on derivatization process. The identification of these derivatives was performed via GC-electron impact ionization mass spectrometry in positive-ion detection mode. Under optimal conditions, excellent linearity for all organic acids was obtained with determination coefficients of R2 > 0.9955. The detection limits (LODs) and quantitation limits (LOQs) ranged from 0.317 to 0.410 µg/mL and 0.085 to 1.53 µg/mL, respectively. The results showed that the highest yield of organic acids was conducted by using 0.1 mL of MTBSTFA and derivatization method with a conventional heating process at 130 °C for 90 min. This method has been successfully applied to the quantitative analysis of organic acids in saffron stigmas."], "field": "Agricultural and Biological Sciences", "q_year": 2021, "q_cid": "235227959", "pos_cid": 220891598, "source": "eval_collection"}
{"query_id": "scaleup_23571111_23213550", "query": "How to develop a carvacrol-loaded nanoemulsion with nanoscale oil droplets that remain stable over time", "pos": ["New insights into the mechanisms of ultrasonic emulsification in the oil–water system and the role of gas bubbles. Highlights • In situ observations of bubble dynamics in ultrasonic emulsification (USE).• Role of gas bubbles with different cavitation modes in USE is revealed.• The chaotic oscillation of gas bubbles is the governing cavitation mode in USE.• Increasing gas content in USE generates smaller and more stable emulsion droplets."], "field": "Agricultural and Biological Sciences", "q_year": 2021, "q_cid": "235711110", "pos_cid": 232135507, "source": "eval_collection"}
{"query_id": "scaleup_25554447_73434206", "query": "How to understand gene expression dynamics and biological process transitions underlying organic acid accumulation during peach ripening across time, fruit acidity phenotypes, and peach varieties", "pos": ["Comparative transcriptomics method to infer gene coexpression networks and its applications to maize and rice leaf transcriptomes. Significance Time-series transcriptomes of a biological process are useful for identifying the regulators of the process. To analyze such data, we developed a method that avoids time-point alignment and normalization between two conditions. We applied it to analyze time-series transcriptomes of developing maize leaves under light–dark cycles and under total darkness and obtained a time-ordered gene coexpression network (TO-GCN) that likely includes all genes involved in the development of Kranz anatomy, a structure crucial for the high efficiency of C4 photosynthesis. Using this TO-GCN, we predicted and experimentally validated a regulatory cascade of Kranz anatomy development. Moreover, we applied the method to compare transcriptomes from maize and rice leaf segments and identified regulators of C4 enzyme genes, demonstrating its broad utility. Time-series transcriptomes of a biological process obtained under different conditions are useful for identifying the regulators of the process and their regulatory networks. However, such data are 3D (gene expression, time, and condition), and there is currently no method that can deal with their full complexity. Here, we developed a method that avoids time-point alignment and normalization between conditions. We applied it to analyze time-series transcriptomes of developing maize leaves under light–dark cycles and under total darkness and obtained eight time-ordered gene coexpression networks (TO-GCNs), which can be used to predict upstream regulators of any genes in the GCNs. One of the eight TO-GCNs is light-independent and likely includes all genes involved in the development of Kranz anatomy, which is a structure crucial for the high efficiency of photosynthesis in C4 plants. Using this TO-GCN, we predicted and experimentally validated a regulatory cascade upstream of SHORTROOT1, a key Kranz anatomy regulator. Moreover, we applied the method to compare transcriptomes from maize and rice leaf segments and identified regulators of maize C4 enzyme genes and RUBISCO SMALL SUBUNIT2. Our study provides not only a powerful method but also novel insights into the regulatory networks underlying Kranz anatomy development and C4 photosynthesis."], "field": "Agricultural and Biological Sciences", "q_year": 2023, "q_cid": "255544473", "pos_cid": 73434206, "source": "eval_collection"}
{"query_id": "scaleup_27109450_22626908", "query": "How to effectively protect crop growth, development, and tissue water status and prevent oxidative damage under drought and other abiotic stresses while ensuring environmental safety, economic viability, and consumer acceptance", "pos": ["Thiourea supplementation mediated reduction of grain arsenic in rice (Oryza sativa L.) cultivars: A two year field study.. The present study delineates the interactions of arsenic (As), a carcinogenic metalloid, and thiourea (TU), a non-physiological reactive oxygen species (ROS) scavenger, in rice plants grown in As contaminated fields in West Bengal, India. The study was performed for four consecutive seasons (two boro and two aman) in 2016 and 2017 with two local rice cultivars; Gosai and Satabdi (IET-4786) in a control and two As contaminated experimental fields. Thiourea (0.05% wt/vol) treatment was given in the form of seed priming and foliar spray. Thiourea significantly improved growth and yield of rice plants and reduced As concentration in root, shoot, husk and grains in both cultivars and fields. The reduction in As concentration ranged from 10.3% to 27.5% in four seasons in different fields. The average (four seasons) increase in yield was recorded about ~8.1% and ~11.5% in control, ~20.2% and ~18.6% in experimental field 1, and ~16.2% and ~24.1% in experimental field 2, for gosai and satabdi, respectively. Mean hazard quotient (HQ) and incremental lifetime cancer risk (ILCR) values of As reduced upon TU supplementation for both cultivars as compared to that of non-TU plants. Hence, TU can be effectively used to cultivate rice safely in As contaminated fields."], "field": "Agricultural and Biological Sciences", "q_year": 2024, "q_cid": "271094501", "pos_cid": 226269085, "source": "eval_collection"}
{"query_id": "scaleup_25132602_21464734", "query": "How to prevent ETEC attachment to the small intestine in weaned pigs", "pos": ["Anti-adhesion activity of phytochemicals to prevent Campylobacter jejuni biofilm formation on abiotic surfaces. Biofilms provide a protective environment for pathogens such as Campylobacter jejuni, the most prevalent foodborne pathogen, and biofilm formation can enhance bacterial survival in hostile environments. Adhesion of bacteria to the different materials of industrial surfaces is the first step in biofilm formation. Modulation of bacterial adhesion and biofilm formation thus represent important targets in alternative control strategies for reduction of pathogens in food-processing environments. With the high prevalence of C. jejuni and the lack of effective control measures, new control strategies are needed to block adhesion and biofilm formation on food contact surfaces in the food industry, with a focus here on natural antimicrobial phytochemicals. Plants remain a poorly recognized yet vast source of such antimicrobials. Valuable phytochemicals can be obtained directly from plant materials but also from agro-food by-products and waste materials. These materials represent a source of important plant bioactive phytochemicals that are effective for prevention of bacterial adhesion. In this review, we will focus on the anti-adhesion activities of phytochemicals targeted against C. jejuni, on the appropriate methodologies to determine anti-adhesion effects of phytochemicals, on the mechanisms of C. jejuni adhesion, and thus possible targets for reduction and control of this foodborne pathogen in food processing environments."], "field": "Agricultural and Biological Sciences", "q_year": 2022, "q_cid": "251326028", "pos_cid": 214647343, "source": "eval_collection"}
{"query_id": "scaleup_28354369_22179718", "query": "How to determine how concurrent salt exposure and Phoma medicaginis infection affect membrane properties in Medicago truncatula and how these changes relate to its ability to cope with both conditions", "pos": ["Membrane dynamics during individual and combined abiotic stresses in plants and tools to study the same.. The plasma membrane (PM) is possibly the most diverse biological membrane of the plant cell, it separates and guards the cell against its external environment. It has an extremely complex structure comprising a mosaic of lipids and proteins. The PM lipids are responsible for maintaining fluidity, permeability, and integrity of the membrane and also influence the functioning of membrane proteins. However, the PM is a primary target of environmental stress, which affects its conformation and properties, thereby disturbing the cellular homeostasis. Maintenance of integrity and fluidity of the PM is a prerequisite for ensuring the survival of plants during adverse environmental conditions. The ability of plants to remodel membrane lipid and protein composition plays a crucial role in the adaptation to varying abiotic environmental cues, including heat, cold, drought, salt, heavy metals stress. The dynamic changes in lipid composition affect the functioning of membrane transporters and ultimately regulate the physical properties of the membrane. Plant membrane transport systems play a significant role in stress adaptation by cooperating with the membrane lipidome to maintain the membrane integrity under stressful conditions. The present review provides a holistic view of stress responses and adaptation of plants by highlighting the changes in the lipidome of PM under individual and combined abiotic stresses, which cause alterations in the activity of membrane transporters and modifies the fluidity of the PM. The tools to study the varying lipidome and proteome of the PM are also discussed. This article is protected by copyright. All rights reserved."], "field": "Agricultural and Biological Sciences", "q_year": 2025, "q_cid": "283543693", "pos_cid": 221797182, "source": "eval_collection"}
{"query_id": "scaleup_22560696_20206852", "query": "How to reliably distinguish metabolic responses of different Cichorium spinosum ecotypes to nitrogen supply levels and sources and relate these patterns to changes in major metabolic functions", "pos": ["Assessment of the effects of metribuzin, glyphosate, and their mixtures on the metabolism of the model plant Lemna minor L. applying metabolomics.. Chemical plant protection products (PPPs) is a major group of xenobiotics that are being released in the environment. Although the effects of individual active ingredients (a.i.) on organisms have been studied, information on those of mixtures, is fragmented. Aquatic environments are being polluted by PPPs, posing serious risks for the environment, human, and other organisms. Based on the potential of the model aquatic plant Lemna minor L. in the assessment of PPPs-caused stresses, we have undertaken the task of developing a metabolomics approach for the study of the effects of metribuzin and glyphosate, and their mixtures. Bioassays revealed that metribuzin exhibit higher toxicity than glyphosate and metabolomics highlighted corresponding changes in its metabolome. Treatments had a substantial impact on plants' amino acid pool, resulting in elevated levels of the majority of the identified amino acids. Results indicate that the increased proteolytic activity is a common effect of the a.i. and their mixtures. Additionally, the activation of salicylate-signaling pathways was recorded as a response to the toxicity caused by mixtures. Among the identified metabolites that were discovered as biomarkers were γ-aminobutyric acid (GABA), salicylate, caffeate, α,α-trehalose, and squalene, which play multiple roles in plants' metabolism such as, signaling, antioxidant, and structure protection. No reports exist on the combined effects of PPPs on Lemna and results confirm the applicability of Lemna metabolomics in the study of the combined effects of herbicides and its potential in the monitoring of the environmental health of aquatic environments based on fluctuations of the plant's metabolism."], "field": "Agricultural and Biological Sciences", "q_year": 2020, "q_cid": "225606969", "pos_cid": 202068521, "source": "eval_collection"}
{"query_id": "scaleup_26073438_25381033", "query": "How to distinguish broadly shared plant regulatory features potentially involved in root-nodule symbiosis from those specific to the nitrogen-fixing nodulation group", "pos": ["Single-Base Resolution Map of Evolutionary Constraints and Annotation of Conserved Elements across Major Grass Genomes. Abstract Conserved noncoding sequences (CNSs) are evolutionarily conserved DNA sequences that do not encode proteins but may have potential regulatory roles in gene expression. CNS in crop genomes could be linked to many important agronomic traits and ecological adaptations. Compared with the relatively mature exon annotation protocols, efficient methods are lacking to predict the location of noncoding sequences in the plant genomes. We implemented a computational pipeline that is tailored to the comparisons of plant genomes, yielding a large number of conserved sequences using rice genome as the reference. In this study, we used 17 published grass genomes, along with five monocot genomes as well as the basal angiosperm genome of Amborella trichopoda. Genome alignments among these genomes suggest that at least 12.05% of the rice genome appears to be evolving under constraints in the Poaceae lineage, with close to half of the evolutionarily constrained sequences located outside protein-coding regions. We found evidence for purifying selection acting on the conserved sequences by analyzing segregating SNPs within the rice population. Furthermore, we found that known functional motifs were significantly enriched within CNS, with many motifs associated with the preferred binding of ubiquitous transcription factors. The conserved elements that we have curated are accessible through our public database and the JBrowse server. In-depth functional annotations and evolutionary dynamics of the identified conserved sequences provide a solid foundation for studying gene regulation, genome evolution, as well as to inform gene isolation for cereal biologists."], "field": "Agricultural and Biological Sciences", "q_year": 2023, "q_cid": "260734381", "pos_cid": 25381033, "source": "eval_collection"}
{"query_id": "scaleup_21015813_20628573", "query": "How to determine whether myostatin coordinates muscle and bone remodeling in fish during refeeding", "pos": ["Molecular bases of the crosstalk between bone and muscle. Exercise is an evolutionary conserved survival function that nowadays has beneficial health effects. The increased metabolic activity of contracting skeletal muscle affects the biology of many organs involved in regulating muscle functions. The discovery of hormones and cytokines secreted by bone and skeletal muscle during exercise, has recently added experimental credence to the notion that a crosstalk exists between these organs. Bone through the hormone osteocalcin, promotes exercise capacity in the mouse. After binding to a G-coupled protein receptor, Gprc6a, osteocalcin increases nutrients uptake and catabolism in myofibers during exercise. The catabolic aspect of osteocalcin distinguishes it from insulin signaling. In addition, osteocalcin regulates the endocrine function of skeletal muscle because it enhances the expression of interleukin-6 (IL-6). IL-6 is produced and secreted by contracting skeletal muscle and exerts autocrine, paracrine and systemic effects. One of the systemic functions of IL-6 is to drive the generation of bioactive osteocalcin. Altogether, these studies have revealed a feed-forward loop between bone and skeletal muscle that are necessary and sufficient for optimum exercise capacity. This endocrine regulation of exercise biology, suggest novel and adapted strategies for the prevention or treatment of age related muscle loss."], "field": "Agricultural and Biological Sciences", "q_year": 2020, "q_cid": "210158130", "pos_cid": 206285734, "source": "eval_collection"}
{"query_id": "scaleup_28307437_24971523", "query": "How to quantitatively assess H. helix adaptation and urban habitat conditions across multiple traits and environmental gradients amid habitat heterogeneity, multiple abiotic stresses, and limited understanding of its multilevel responses", "pos": ["Developing an Enhanced Ecological Evaluation Index (EEEI) Based on Remotely Sensed Data and Assessing Spatiotemporal Ecological Quality in Guangdong-Hong Kong-Macau Greater Bay Area, China. Ecological changes affected by increasing human activities have highlighted the importance of ecological quality assessments. An appropriate and efficient selection of ecological parameters is fundamental for ecological quality assessments. On the basis of remote sensing data and methods, this study developed an enhanced ecological evaluation index (EEEI) with five integrated ecological parameters by containing pixel and sub-pixel information: normalized difference vegetation index, impervious surface coverage, soil coverage, land surface temperature, and wetness component of tasseled cap transformation. Significantly, the EEEI simultaneously considered the five aspects of land surface ecological conditions (i.e., greenness, human activities, dryness, heat, and moisture), which provided an effective guide for the systematic selection of ecological parameters. The EEEI has a clear theoretical framework, and all the parameters can be obtained quickly on the basis of the remote sensing datasets and methods, which is suitable for the promotion and application of ecological quality assessments to various areas and scales. Furthermore, the EEEI was applied to assess and detect the ecological quality of the Guangdong–Hong Kong–Macau Greater Bay Area (GBA) of China. Assessment results indicated that the ecological quality of the GBA is currently facing great challenges with a degradation trend from 2000 to 2020, which emphasizes the significance and urgency for eco-environmental protection of the GBA. This provided evidence that the EEEI can be used as an effective index for scientific, objective, quantitative, and comprehensive ecological quality assessment, which can also aid regional environmental management and ecological protection."], "field": "Agricultural and Biological Sciences", "q_year": 2025, "q_cid": "283074371", "pos_cid": 249715235, "source": "eval_collection"}
{"query_id": "scaleup_23632386_5395639", "query": "How to determine whether observed differences reliably distinguish experimental plant groups rather than reflect overfitting to the analyzed samples", "pos": ["Double-check: validation of diagnostic statistics for PLS-DA models in metabolomics studies. Partial Least Squares-Discriminant Analysis (PLS-DA) is a PLS regression method with a special binary ‘dummy’ y-variable and it is commonly used for classification purposes and biomarker selection in metabolomics studies. Several statistical approaches are currently in use to validate outcomes of PLS-DA analyses e.g. double cross validation procedures or permutation testing. However, there is a great inconsistency in the optimization and the assessment of performance of PLS-DA models due to many different diagnostic statistics currently employed in metabolomics data analyses. In this paper, properties of four diagnostic statistics of PLS-DA, namely the number of misclassifications (NMC), the Area Under the Receiver Operating Characteristic (AUROC), Q2 and Discriminant Q2 (DQ2) are discussed. All four diagnostic statistics are used in the optimization and the performance assessment of PLS-DA models of three different-size metabolomics data sets obtained with two different types of analytical platforms and with different levels of known differences between two groups: control and case groups. Statistical significance of obtained PLS-DA models was evaluated with permutation testing. PLS-DA models obtained with NMC and AUROC are more powerful in detecting very small differences between groups than models obtained with Q2 and Discriminant Q2 (DQ2). Reproducibility of obtained PLS-DA models outcomes, models complexity and permutation test distributions are also investigated to explain this phenomenon. DQ2 and Q2 (in contrary to NMC and AUROC) prefer PLS-DA models with lower complexity and require higher number of permutation tests and submodels to accurately estimate statistical significance of the model performance. NMC and AUROC seem more efficient and more reliable diagnostic statistics and should be recommended in two group discrimination metabolomic studies."], "field": "Agricultural and Biological Sciences", "q_year": 2021, "q_cid": "236323868", "pos_cid": 5395639, "source": "eval_collection"}
{"query_id": "scaleup_25132602_4389112", "query": "How to control ETEC infection, protect the intestinal epithelial barrier, and limit harmful inflammation in newly weaned pigs without antibiotics", "pos": ["From bacterial killing to immune modulation: Recent insights into the functions of lysozyme. Lysozyme is a cornerstone of innate immunity. The canonical mechanism for bacterial killing by lysozyme occurs through the hydrolysis of cell wall peptidoglycan (PG). Conventional type (c-type) lysozymes are also highly cationic and can kill certain bacteria independently of PG hydrolytic activity. Reflecting the ongoing arms race between host and invading microorganisms, both gram-positive and gram-negative bacteria have evolved mechanisms to thwart killing by lysozyme. In addition to its direct antimicrobial role, more recent evidence has shown that lysozyme modulates the host immune response to infection. The degradation and lysis of bacteria by lysozyme enhance the release of bacterial products, including PG, that activate pattern recognition receptors in host cells. Yet paradoxically, lysozyme is important for the resolution of inflammation at mucosal sites. This review will highlight recent advances in our understanding of the diverse mechanisms that bacteria use to protect themselves against lysozyme, the intriguing immunomodulatory function of lysozyme, and the relationship between these features in the context of infection."], "field": "Agricultural and Biological Sciences", "q_year": 2022, "q_cid": "251326028", "pos_cid": 4389112, "source": "eval_collection"}
{"query_id": "scaleup_22112868_16258169", "query": "How to obtain sufficiently detailed information to accurately track fine-scale variation in biocontrol agents under contrasting ecological conditions", "pos": ["Rapid SNP Discovery and Genetic Mapping Using Sequenced RAD Markers. Single nucleotide polymorphism (SNP) discovery and genotyping are essential to genetic mapping. There remains a need for a simple, inexpensive platform that allows high-density SNP discovery and genotyping in large populations. Here we describe the sequencing of restriction-site associated DNA (RAD) tags, which identified more than 13,000 SNPs, and mapped three traits in two model organisms, using less than half the capacity of one Illumina sequencing run. We demonstrated that different marker densities can be attained by choice of restriction enzyme. Furthermore, we developed a barcoding system for sample multiplexing and fine mapped the genetic basis of lateral plate armor loss in threespine stickleback by identifying recombinant breakpoints in F2 individuals. Barcoding also facilitated mapping of a second trait, a reduction of pelvic structure, by in silico re-sorting of individuals. To further demonstrate the ease of the RAD sequencing approach we identified polymorphic markers and mapped an induced mutation in Neurospora crassa. Sequencing of RAD markers is an integrated platform for SNP discovery and genotyping. This approach should be widely applicable to genetic mapping in a variety of organisms."], "field": "Agricultural and Biological Sciences", "q_year": 2020, "q_cid": "221128686", "pos_cid": 16258169, "source": "eval_collection"}
{"query_id": "scaleup_28273788_91975558", "query": "How to determine whether crop fields or agroforestry habitats meet the species-specific overwintering needs of ground-dwelling spiders found there", "pos": ["Both woody and herbaceous semi-natural habitats are essential for spider overwintering in European farmland. Abstract Semi-natural habitats (SNH) support biodiversity and associated ecosystem services on farmland, thereby contributing to sustainable agriculture. However, little is known about the specific suitability of different types of SNH as overwintering habitat for predatory arthropods, despite the crucial role of such knowledge for conservation biological control. We used ground photoeclectors to sample spiders in 65 habitats comprising crop fields and four major SNH types (herbaceous areal, herbaceous linear, woody areal, woody linear) across two study regions in Switzerland and Germany to identify the most important overwintering habitats for spiders. Spider emergence started in February and over half of the individuals of the most common spiders had already emerged by late April. SNH supported on average 146% higher species richness and 194% higher densities of spiders than crop fields. Woody and herbaceous SNH supported distinct spider communities, with individual species exhibiting marked preferences for either woody or herbaceous SNH. Habitat shape (areal or linear) had no significant effects on spider overwintering. Woody SNH hosted more species, whereas herbaceous SNH had higher densities of agrobiont species (i.e. species known to reach high densities in crops in the growing season). Given the higher number of overwintering agrobionts in herbaceous SNH, this habitat type has potential to promote pest control by spill-over of spiders into nearby crops early in the season. In contrast, woody SNH seem to be more important for the conservation of diverse spider communities that are highly distinct from those inhabiting open land. Hence, creating and preserving a variety of SNH is key to provide suitable overwintering sites for species in agricultural landscapes."], "field": "Agricultural and Biological Sciences", "q_year": 2025, "q_cid": "282737886", "pos_cid": 91975558, "source": "eval_collection"}
{"query_id": "scaleup_27297897_8778942", "query": "How to address the basic knowledge gap about G. littoralis needed to support research on its conservation and sustainable utilization", "pos": ["Estimation of genomic characteristics by analyzing k-mer frequency in de novo genome projects. Background: With the fast development of next generation sequencing technologies, increasing numbers of genomes are being de novo sequenced and assembled. However, most are in fragmental and incomplete draft status, and thus it is often difficult to know the accurate genome size and repeat content. Furthermore, many genomes are highly repetitive or heterozygous, posing problems to current assemblers utilizing short reads. Therefore, it is necessary to develop efficient assembly-independent methods for accurate estimation of these genomic characteristics. Results: Here we present a framework for modeling the distribution of k-mer frequency from sequencing data and estimating the genomic characteristics such as genome size, repeat structure and heterozygous rate. By introducing novel techniques of k-mer individuals, float precision estimation, and proper treatment of sequencing error and coverage bias, the estimation accuracy of our method is significantly improved over existing methods. We also studied how the various genomic and sequencing characteristics affect the estimation accuracy using simulated sequencing data, and discussed the limitations on applying our method to real sequencing data. Conclusion: Based on this research, we show that the k-mer frequency analysis can be used as a general and assembly-independent method for estimating genomic characteristics, which can improve our understanding of a species genome, help design the sequencing strategy of genome projects, and guide the development of assembly algorithms. The programs developed in this research are written using C/C++, and freely accessible at Github URL (this https URL) or BGI ftp ( this ftp URL)."], "field": "Agricultural and Biological Sciences", "q_year": 2024, "q_cid": "272978972", "pos_cid": 8778942, "source": "eval_collection"}
{"query_id": "scaleup_25649791_51711192", "query": "How to assess the in vivo immunomodulatory effects of phytochemicals given limited evidence, a narrow range of models, and the unsuitability of human models in nude mice for studying immune modulation", "pos": ["Murine models of melanoma.. Melanoma is an aggressive and highly metastatic skin cancer, carrying a poor prognosis with a median survival time of 5.3-10 months depending on the stage of disease. Research has advanced our understanding of the underlying pathology of melanoma and strategies to prevent and treat melanoma. Mouse models have been developed to elucidate the molecular, immunological, and cellular mechanisms contributing to proliferation and metastasis of melanoma. This review article aims to provide an overview of various types of murine melanoma models, including xenograft and syngeneic transplantation models, genetically modified models, ultraviolent radiation models, and chemically induced models, and discuss the advantages and limitations of each model."], "field": "Agricultural and Biological Sciences", "q_year": 2023, "q_cid": "256497917", "pos_cid": 51711192, "source": "eval_collection"}
{"query_id": "scaleup_22112868_713208", "query": "How to pinpoint the basis of phenotypic differences in biocontrol agents with sufficient resolution to improve target traits", "pos": ["A Genome-Wide, Fine-Scale Map of Natural Pigmentation Variation in Drosophila melanogaster. Various approaches can be applied to uncover the genetic basis of natural phenotypic variation, each with their specific strengths and limitations. Here, we use a replicated genome-wide association approach (Pool-GWAS) to fine-scale map genomic regions contributing to natural variation in female abdominal pigmentation in Drosophila melanogaster, a trait that is highly variable in natural populations and highly heritable in the laboratory. We examined abdominal pigmentation phenotypes in approximately 8000 female European D. melanogaster, isolating 1000 individuals with extreme phenotypes. We then used whole-genome Illumina sequencing to identify single nucleotide polymorphisms (SNPs) segregating in our sample, and tested these for associations with pigmentation by contrasting allele frequencies between replicate pools of light and dark individuals. We identify two small regions near the pigmentation genes tan and bric-à-brac 1, both corresponding to known cis-regulatory regions, which contain SNPs showing significant associations with pigmentation variation. While the Pool-GWAS approach suffers some limitations, its cost advantage facilitates replication and it can be applied to any non-model system with an available reference genome."], "field": "Agricultural and Biological Sciences", "q_year": 2020, "q_cid": "221128686", "pos_cid": 713208, "source": "eval_collection"}
{"query_id": "scaleup_25832350_25466636", "query": "How to improve citrus fruit yield, quality, size, and diameter under nutrient deficiency", "pos": ["Nanocomposite-based smart fertilizers: A boon to agricultural and environmental sustainability.. Fertilizers are indispensable agri-inputs to accomplish the growing food demand. The injudicious use of conventional fertilizer products has resulted in several environmental and human health complications. To mitigate these problems, nanocomposite-based fertilizers are viable alternative options. Nanocomposites, a novel class of materials having improved mechanical strength, barrier properties, and mechanical and thermal stability, are suitable candidates to develop eco-friendly slow/controlled release fertilizer formulations. In this review, the use of different nanocomposite materials developed for nutrient management in agriculture has been summarized with a major focus on their synthesis and characterization techniques, and application aspects in plant nutrition, along with addressing constraints and future opportunities of this domain. Further detailed studies on nanocomposite-based fertilizers are required to evaluate the cost-effective synthesis methods, in-depth field efficacy, environmental fate, stability, etc. before commercialization in the field of agriculture. The present review is expected to help the policy makers and all the stakeholders in the large-scale commercialization and application of nanocomposite-based smart fertilizer products with greater societal acceptance and environmental sustainability in near future."], "field": "Agricultural and Biological Sciences", "q_year": 2023, "q_cid": "258323507", "pos_cid": 254666361, "source": "eval_collection"}
{"query_id": "scaleup_23435904_16852620", "query": "How to distinguish genuine variation from deterioration-related artifacts in archived samples when variation can naturally be high, so population-size comparisons remain valid across different storage times and sample conditions", "pos": ["Temporal Patterns of Nucleotide Misincorporations and DNA Fragmentation in Ancient DNA. DNA that survives in museum specimens, bones and other tissues recovered by archaeologists is invariably fragmented and chemically modified. The extent to which such modifications accumulate over time is largely unknown but could potentially be used to differentiate between endogenous old DNA and present-day DNA contaminating specimens and experiments. Here we examine mitochondrial DNA sequences from tissue remains that vary in age between 18 and 60,000 years with respect to three molecular features: fragment length, base composition at strand breaks, and apparent C to T substitutions. We find that fragment length does not decrease consistently over time and that strand breaks occur preferentially before purine residues by what may be at least two different molecular mechanisms that are not yet understood. In contrast, the frequency of apparent C to T substitutions towards the 5′-ends of molecules tends to increase over time. These nucleotide misincorporations are thus a useful tool to distinguish recent from ancient DNA sources in specimens that have not been subjected to unusual or harsh treatments."], "field": "Agricultural and Biological Sciences", "q_year": 2021, "q_cid": "234359045", "pos_cid": 16852620, "source": "eval_collection"}
{"query_id": "scaleup_23906740_86645261", "query": "How to quantify the phenolic content of Pseudocaryopteris foetida leaf extracts and fractions to investigate their antioxidant potential", "pos": ["Colorimetry of Total Phenolics with Phosphomolybdic-Phosphotungstic Acid Reagents. Several details of the assay of total phenolic substances have been investigated and an improved procedure developed. The improvements include the use of Folin-Ciocalteu reagent rather than the Folin-Denis reagent, gallic acid as a reference standard, and a more reproducible time-temperature color development period. The values obtained are less subject to variation and interference from several nonphenols, yet are directly comparable to the \"tannin\" values obtained by the previously standard method."], "field": "Agricultural and Biological Sciences", "q_year": 2021, "q_cid": "239067405", "pos_cid": 86645261, "source": "eval_collection"}
{"query_id": "scaleup_24621898_20958387", "query": "How to achieve reliable comparisons among I. batatas, I. trifida, and other entities despite unequal sample sizes", "pos": ["Efficient toolkit implementing best practices for principal component analysis of population genetic data. Principal Component Analysis (PCA) of genetic data is routinely used to infer ancestry and control for population structure in various genetic analyses. However, conducting PCA analyses can be complicated and has several potential pitfalls. These pitfalls include (1) capturing Linkage Disequilibrium (LD) structure instead of population structure, (2) projected PCs that suffer from shrinkage bias when projecting PCA from a reference dataset to another independent dataset, (3) detecting sample outliers, and (4) uneven population sizes. In this work, we explore these potential issues when using PCA, and present efficient solutions to these. Following applications to the UK Biobank and the 1000 Genomes project datasets, we make recommendations for best practices and provide efficient and user-friendly implementations of the proposed solutions in R packages bigsnpr and bigutilsr. For example, we show that PC19 to PC40 in the UK Biobank capture LD structure. Using our automatic algorithm for removing long-range LD regions, we recover 16 PCs that capture population structure only. Therefore, we recommend using only 16-18 PCs from the UK Biobank. We provide evidence for a shrinkage bias when projecting PCs computed with data from the 1000 Genomes project. Although PC1 to PC4 suffer from only moderate shrinkage (1.01-1.09), PC5 (resp. PC10) for example suffers from a shrinkage factor of 1.50 (resp. 3.14). We provide a fast way to project new individuals that is not affected by this shrinkage bias. We also show how to use PCA to restrict analyses to individuals of homogeneous ancestry. Overall, we believe this work would be of interest for anyone using PCA in their analyses of genetic data, as well as for other omics data."], "field": "Agricultural and Biological Sciences", "q_year": 2022, "q_cid": "246218981", "pos_cid": 209583871, "source": "eval_collection"}
{"query_id": "scaleup_25132602_31630424", "query": "How to clarify the potential protective effects of β-glucans against ETEC infection in newly weaned pigs", "pos": ["β-glucan Recognition by the Innate Immune System. Summary: β‐glucans are recognized by the innate immune system. This recognition plays important roles in host defense and presents specific opportunities for clinical modulation of the host immune response. Neutrophils, macrophages, and dendritic cells among others express several receptors capable of recognizing β‐glucan in its various forms. This review explores what is currently known about β‐glucan recognition and how this recognition stimulates immune responses. Special emphasis is placed on Dectin‐1, as we know the most about how this key β‐glucan receptor translates recognition into intracellular signaling, stimulates cellular responses, and participates in orchestrating the adaptive immune response."], "field": "Agricultural and Biological Sciences", "q_year": 2022, "q_cid": "251326028", "pos_cid": 31630424, "source": "eval_collection"}
{"query_id": "scaleup_21426302_25439272", "query": "How to assess differences between test-strip measurements and other analytical methods, test-strip suitability for soil and plant tissue analysis, and the need to modify existing testing procedures", "pos": ["Method Comparison (Agreement) Studies: Myths and Rationale.. Unprecedented technological growth in the last quarter of twentieth century has resulted in improved health care and opened new domains of health care research. This technological leap also facilitated the paradigm shift from hospital care to home care through development of 'point of care' devices. As early diagnoses and timely referral is a key to health management, these devices play an important role in improving health. Validation of the new technology in different settings is necessary before adopting it to practice. For a binary result like pregnancy test, it is trivial to use statistical tools like sensitivity, specificity etc. For a continuous variable like blood glucose level the analysis is not straightforward. Many of us misinterpret 'association' as 'agreement'. This misinterpretation is reflected in studies which have compared two different technologies. The findings of well conducted studies do not contribute to the evidence base just because of wrong analysis strategy. We delineate on finer nuances of analysis and interpretation of method comparison studies."], "field": "Agricultural and Biological Sciences", "q_year": 2020, "q_cid": "214263026", "pos_cid": 25439272, "source": "eval_collection"}
{"query_id": "scaleup_23343293_53477903", "query": "How to determine whether social groups genuinely possess psychological properties beyond individual members’ cognition rather than merely receiving metaphorical labels, when repeated group differences and collective self-organization alone are insufficient", "pos": ["An Organizational Account of Biological Functions. In this paper, we develop an organizational account that defines biological functions as causal relations subject to closure in living systems, interpreted as the most typical example of organizationally closed and differentiated self-maintaining systems. We argue that this account adequately grounds the teleological and normative dimensions of functions in the current organization of a system, insofar as it provides an explanation for the existence of the function bearer and, at the same time, identifies in a non-arbitrary way the norms that functions are supposed to obey. Accordingly, we suggest that the organizational account combines the etiological and dispositional perspectives in an integrated theoretical framework. 1. Introduction2. Dispositional Approaches3. Etiological Theories4. Biological Self-maintenance 4.1. Closure, teleology, and normativity4.2. Organizational differentiation5. Functions 5.1. C1: Contributing to the maintenance of the organization5.2. C2: Producing the functional trait6. Implications and Objections 6.1. Functional versus useful6.2. Dysfunctions, side effects, and accidental contributions6.3. Proper functions and selected effects6.4. Reproduction6.5. Relation with other ‘unitarian’ approaches7. Conclusions Introduction Dispositional Approaches Etiological Theories Biological Self-maintenance 4.1. Closure, teleology, and normativity4.2. Organizational differentiation Closure, teleology, and normativity Organizational differentiation Functions 5.1. C1: Contributing to the maintenance of the organization5.2. C2: Producing the functional trait C1: Contributing to the maintenance of the organization C2: Producing the functional trait Implications and Objections 6.1. Functional versus useful6.2. Dysfunctions, side effects, and accidental contributions6.3. Proper functions and selected effects6.4. Reproduction6.5. Relation with other ‘unitarian’ approaches Functional versus useful Dysfunctions, side effects, and accidental contributions Proper functions and selected effects Reproduction Relation with other ‘unitarian’ approaches Conclusions"], "field": "Agricultural and Biological Sciences", "q_year": 2021, "q_cid": "233432933", "pos_cid": 53477903, "source": "eval_collection"}
{"query_id": "scaleup_24495476_4868248", "query": "How to accurately recognise fruits and estimate suitable grasping poses for harvesting robots in natural orchards where branches and leaves occlude fruits and create a complex workspace", "pos": ["Frustum PointNets for 3D Object Detection from RGB-D Data. In this work, we study 3D object detection from RGBD data in both indoor and outdoor scenes. While previous methods focus on images or 3D voxels, often obscuring natural 3D patterns and invariances of 3D data, we directly operate on raw point clouds by popping up RGB-D scans. However, a key challenge of this approach is how to efficiently localize objects in point clouds of large-scale scenes (region proposal). Instead of solely relying on 3D proposals, our method leverages both mature 2D object detectors and advanced 3D deep learning for object localization, achieving efficiency as well as high recall for even small objects. Benefited from learning directly in raw point clouds, our method is also able to precisely estimate 3D bounding boxes even under strong occlusion or with very sparse points. Evaluated on KITTI and SUN RGB-D 3D detection benchmarks, our method outperforms the state of the art by remarkable margins while having real-time capability."], "field": "Agricultural and Biological Sciences", "q_year": 2021, "q_cid": "244954760", "pos_cid": 4868248, "source": "train_step3"}
{"query_id": "scaleup_27835624_22164129", "query": "How to align production with market demand and manage crop health despite uncertain yields and crop threats while minimizing food waste and loss", "pos": ["Field-scale soil moisture bridges the spatial-scale gap between drought monitoring and agricultural yields. Abstract. Soil moisture is highly variable in space and time, and deficits (i.e., droughts) play an important role in modulating crop yields. Limited hydroclimate and yield data, however, hamper drought impact monitoring and assessment at the farm field scale. This study demonstrates the potential of using field-scale soil moisture simulations to support high-resolution agricultural yield prediction and drought monitoring at the smallholder farm field scale. We present a multiscale modeling approach that combines HydroBlocks – a physically based hyper-resolution land surface model (LSM) – with machine learning. We used HydroBlocks to simulate root zone soil moisture and soil temperature in Zambia at 3 h 30 m resolution. These simulations, along with remotely sensed vegetation indices, meteorological data, and descriptors of the physical landscape (related to topography, land cover, and soils) were combined with district-level maize data to train a random forest (RF) model to predict maize yields at district and field scales (250 m). Our model predicted yields with an average testing coefficient of determination (R2) of 0.57 and mean absolute error (MAE) of 310 kg ha−1 using year-based cross-validation. Our predicted maize losses due to the 2015–2016 El Niño drought agreed well with losses reported by the Food and Agriculture Organization (FAO). Our results reveal that soil moisture is the strongest and most reliable predictor of maize yield, driving its spatial and temporal variability. Soil moisture was also a more effective indicator of drought impacts on crops than precipitation, soil and air temperatures, and remotely sensed normalized difference vegetation index (NDVI)-based drought indices. This study demonstrates how field-scale modeling can help bridge the spatial-scale gap between drought monitoring and agricultural impacts."], "field": "Agricultural and Biological Sciences", "q_year": 2025, "q_cid": "278356240", "pos_cid": 221641290, "source": "train_step3"}
{"query_id": "scaleup_23742597_53983605", "query": "How to rapidly, affordably, and reliably characterize nuclear repeat content and obtain comparable plastid phylogenetic evidence in the same bamboo species to resolve conflicting nuclear and plastid phylogenies", "pos": ["Genomic Characterization for Parasitic Weeds of the Genus Striga by Sample Sequence Analysis. Generation of ∼2200 Sanger sequence reads or ∼10,000 454 reads for seven Striga Lour. DNA samples (five species) allowed identification of the highly repetitive DNA content in these genomes. The 14 most abundant repeats in these Striga species were identified and partially assembled. Annotation indicated that they represent nine long terminal repeat (LTR) retrotransposon families, three tandem satellite repeats, one long interspersed element (LINE) retroelement, and one DNA transposon. All of these repeats are most closely related to repetitive elements in other closely related plants and are not products of horizontal transfer from their host species. These repeats were differentially abundant in each species, with the LTR retrotransposons and satellite repeats most responsible for variation in genome size. Each species had some repetitive elements that were more abundant and some less abundant than the other Striga species examined, indicating that no single element or any unilateral growth or decrease trend in genome behavior was responsible for variation in genome size and composition. Genome sizes were determined by flow sorting, and the values of 615 Mb [S. asiatica (L.) Kuntze], 1330 Mb [S. gesnerioides (Willd.) Vatke], 1425 Mb [S. hermonthica (Delile) Benth.] and 2460 Mb (S. forbesii Benth.) suggest a ploidy series, a prediction supported by repetitive DNA sequence analysis. Phylogenetic analysis using six chloroplast loci indicated the ancestral relationships of the five most agriculturally important Striga species, with the unexpected result that the one parasite of dicotyledonous plants (S. gesnerioides) was found to be more closely related to some of the grass parasites than many of the grass parasites are to each other."], "field": "Agricultural and Biological Sciences", "q_year": 2021, "q_cid": "237425972", "pos_cid": 53983605, "source": "train_step3"}
{"query_id": "scaleup_25824399_17923718", "query": "How to establish whether grape pomace can reduce ultraviolet radiation-induced damage in human cells and offer value beyond waste disposal", "pos": ["Vitis vinifera seeds extract for the modulation of cytosolic factors BAX-α and NF-kB involved in UVB-induced oxidative stress and apoptosis of human skin cells. Background and aims The depletion of the ozone layer allows overexposure of the skin to UV radiation, which is prolonged due to the increasing life expectancy, together with inappropriate life habits contribute to the increasing incidence of cutaneous malignancies. Plant extracts with antioxidant capacities are frequently employed as a means to protect skin against ultraviolet (UV) radiations, thus preventing skin cancers. In the present study we assessed a red grape seed extract (GSE) potential capacities to reduce ultraviolet B (UVB) radiation-induced reactive oxygen species (ROS) and subsequent apoptosis in a human keratinocytes cell line (HaCaT). We identified molecules and pathways modulated by the GSE through which this may exert its photoprotective effect. Methods The GSE was standardized according to its polyphenolic content and the most important biologically active compounds, such as epigallocatechin and epicatechin, catechin hydrate, procyanidin B and gallic acid were evidenced by high-performance liquid chromatography. According to the plant extract cytotoxicity on the HaCaT cell line, two concentrations were selected for testing from the non-toxic range: GSE1 (37.5 μgEqGA/ml) and GSE2 (75 μgEqGA/ml). The level of ROS was evaluated with CM-H2DCFDA assay, while apoptosis, Bax-α and NF-kβ p65 proteins with ELISA and confirmed by western-blot. Results Both concentrations of the extract decreased the level of ROS in UVB-irradiated keratinocytes (p<0.001), whereas apoptosis and Bax-α pro-apoptotic protein were only reduced by the higher concentration (GSE2). The NF-kB p65 protein level registered increasing values in time after UVB exposure of the cells, while the tested plant extract re-established its level when its smaller concentration was used (GSE1). Conclusion These results encourage further studies on this extract in order to identify other molecules and pathways through which this extract might exert its beneficial effects and also recommend its use as a potential photoprotective agent."], "field": "Agricultural and Biological Sciences", "q_year": 2023, "q_cid": "258243999", "pos_cid": 17923718, "source": "train_step3"}
{"query_id": "scaleup_51710297_53539074", "query": "How to establish reliable age–depth chronologies for fossil records despite potential outliers in radiocarbon ages", "pos": ["Flexible paleoclimate age-depth models using an autoregressive gamma process. Radiocarbon dating is routinely used in paleoecology to build chronolo- gies of lake and peat sediments, aiming at inferring a model that would relate the sediment depth with its age. We present a new approach for chronology building (called \\Bacon\") that has received enthusiastic attention by paleoecologists. Our methodology is based on controlling core accumulation rates using a gamma au- toregressive semiparametric model with an arbitrary number of subdivisions along the sediment. Using prior knowledge about accumulation rates is crucial and in- formative priors are routinely used. Since many sediment cores are currently ana- lyzed, using difierent data sets and prior distributions, a robust (adaptive) MCMC is very useful. We use the t-walk (Christen and Fox, 2010), a self adjusting, robust MCMC sampling algorithm, that works acceptably well in many situations. Out- liers are also addressed using a recent approach that considers a Student-t model for radiocarbon data. Two examples are presented here, that of a peat core and a core from a lake, and our results are compared with other approaches. Past climates and environments can be reconstructed from deposits such as ocean or lake sediments, ice sheets and peat bogs. Within a vertical sediment proflle (core), mea- surements of microfossils, macrofossils, isotopes and other variables at a range of depths serve as proxy estimates or \\proxies\" of climate and environmental conditions when the sediment of those depths was deposited. It is crucial to establish reliable relationships between these depths and their ages. Age-depth relationships are used to study the evolution of climate/environmental proxies along sediment depth and therefore through time (e.g., Lowe and Walker 1997). Age-depth models are constructed in various ways. For sediment depths containing organic matter, and for ages younger than c. 50,000 years, radiocarbon dating is often used to create an age-depth model. Cores are divided into slices and some of these are radiocarbon dated. A curve is fltted to the radiocarbon data and interpolated to obtain an age estimate for every depth of the core. The flrst restriction to be considered is that age should be increasing monotonically with depth, because sediment can never have accumulated backwards in time (extraordinary events leading to mixed or reversed sediments are, most of the time, noticeable in the stratigraphy and therefore such cores are ruled out from further analyses). Moreover, cores may have missing sections, leading to ∞at parts in the age depth models."], "field": "Arts and Humanities", "q_year": 2018, "q_cid": "51710297", "pos_cid": 53539074, "source": "eval20x26"}
{"query_id": "scaleup_20521330_23657874", "query": "How to recognize successful communication when a child cooperates in one respect but does not meet another expectation, especially when success differs from everyday ideas of good communication", "pos": ["Experts and 'knowledge that counts': a study into the world of brain cancer diagnosis.. This paper provides a close, in situ look into the life of a neuro-oncology (brain cancer) clinic of a large hospital in Israel, based on a six-month participant observation. It points to the many challenges involved in the solidification of brain tumour diagnoses by different experts, and presents these epistemological and practical complexities as they uncover in daily routine. The paper's task is two-fold: first, to underline the technological and epistemological grounds of 'expertise' in the medicoscientific practice of diagnosis, and their roles in the assertion of expert authoritativeness; and second, to provide analytical tools to approach the complexity of diagnostic processes, the potential frictions it may create, and the related mechanisms of resolution. These mechanisms include Hierarchisation: ranking the relative validity and reliability of the different sources of information, eventually prioritising reports from more authoritative expertises (e.g. imaging reports would be considered more reliable than patients' accounts); Sequencing: relying upon the temporal dimension, and defining the discrepancy itself as a diagnostic sign (e.g. the degradation or amelioration of the disease); Negotiation: adjusting diagnoses via a preliminary exchange between experts and a consequent \"fine tuning\" of the reports (e.g. radiologists being aware of clinical evaluations before finalising their reports); Peripheralising: turning to other expertises to \"explain away\" symptoms that do not fit with a well established initial diagnosis (e.g. asserting that a symptom's source was orthopaedic rather than neurological); and pragmatism: using information only as far as it provided sufficient grounds for treatment decisions, leaving ambiguities unresolved. These five mechanisms are presented here in the context of the daily work of the clinic."], "field": "Arts and Humanities", "q_year": 2013, "q_cid": "205213301", "pos_cid": 23657874, "source": "eval20x26"}
{"query_id": "scaleup_15031500_18036764", "query": "How to account for the equal ontological standing and dynamic relations of what is present, absent, or incomplete in intentionality, information, and ethics despite the limitations of binary logic", "pos": ["The Logical Dynamics of Information; Deacon's \"Incomplete Nature\". In his Incomplete Nature, Deacon extends a thermodynamic concept of energy to yield a description of complex processes in which absence plays a critical role in their emergence and evolution. Starting from a quantum-mechanical picture of energy as an energy-matter duality, the critical role of potential as well as actual properties of processes is also described in the new extension of logic to real phenomena, Logic in Reality (LIR), which I have proposed. Deacon shows how an interactive operation of both Shannon entropy and Boltzmann entropy must be taken into account in information. Here, I demonstrate the complementarity of our two approaches to what is not, or not fully, present for an understanding of the dynamics of complex phenomena, especially, of intentionality, information and meaning. Deacon shows that the hallmark of information is its absent content, and LIR shows that presence (actuality) and absence (potentiality) in such processes are related dynamically. Deacon’s approach and LIR ground and extend Logan’s concepts of biotic information and the relativity of information vs. meaning. Their conjunction constitutes a new conceptual structure for exploring the relationship of information to materiality, that is, to the matter-energy that constitutes it as its carrier and/or substrate."], "field": "Arts and Humanities", "q_year": 2018, "q_cid": "150315004", "pos_cid": 18036764, "source": "eval20x26"}
{"query_id": "scaleup_24435125_6190287", "query": "How to determine whether vocabulary in scientific texts intended for lay readers is sufficiently familiar to support understanding", "pos": ["Lexical threshold revisited: Lexical text coverage, learners’ vocabulary size and reading comprehension. We explore the relationship between second language (L2) learners’ vocabulary size, lexical text coverage that their vocabulary provides and their reading comprehension. We also conceptualize “adequate reading comprehension” and look for the lexical threshold for such reading in terms of coverage and vocabulary size. Vocabulary size was measured by the Levels Test, lexical coverage by the newest version of Vocabulary Profile and reading comprehension by a standardized national test. Results show that small increments of vocabulary knowledge contribute to reading comprehension even though they hardly improve text coverage. We suggest two thresholds: an optimal one, which is the knowledge of 8,000 word families yielding the coverage of 98% (including proper nouns) and a minimal one, which is 4,000–5,000 word families resulting in the coverage of 95% (including proper nouns)."], "field": "Arts and Humanities", "q_year": 2017, "q_cid": "24435125", "pos_cid": 6190287, "source": "eval20x26"}
{"query_id": "scaleup_2286619_46450348", "query": "How to distinguish normal social behavior from mental disorder across differing cultural norms and determine whether culture-specific conditions such as taijin kyofusho are distinct disorders or expressions of disorders recognized in western settings", "pos": ["Cultural Aspects in Social Anxiety and Social Anxiety Disorder. To examine cultural aspects in social anxiety and social anxiety disorder (SAD), we reviewed the literature on the prevalence rates, expressions, and treatments of social anxiety/SAD as they relate to culture, race, and ethnicity. We further reviewed factors that contribute to the differences in social anxiety/SAD between different cultures, including individualism/collectivism, perception of social norms, self‐construal, gender roles, and gender role identification. Our review suggests that the prevalence and expression of social anxiety/SAD depends on the particular culture. Asian cultures typically show the lowest rates, whereas Russian and US samples show the highest rates, of SAD. Taijin kyofusho is discussed as a possible culture‐specific expression of social anxiety, although the empirical evidence concerning the validity of this syndrome has been mixed. It is concluded that the individual's social concerns need to be examined in the context of the person's cultural, racial, and ethnic background in order to adequately assess the degree and expression of social anxiety and SAD. This has direct relevance for the upcoming DSM‐V. Depression and Anxiety, 2010. © 2010 Wiley‐Liss, Inc."], "field": "Arts and Humanities", "q_year": 2013, "q_cid": "2286619", "pos_cid": 46450348, "source": "eval20x26"}
{"query_id": "scaleup_25709482_46455659", "query": "How to account for limits on self-control as a component of autonomy when distractions and contextual demands heavily burden an agent’s mental capacities", "pos": ["Situational Strategies for Self-Control. Exercising self-control is often difficult, whether declining a drink in order to drive home safely, passing on the chocolate cake to stay on a diet, or ignoring text messages to finish reading an important paper. But enacting self-control is not always difficult, particularly when it takes the form of proactively choosing or changing situations in ways that weaken undesirable impulses or potentiate desirable ones. Examples of situational self-control include the partygoer who chooses a seat far from where drinks are being poured, the dieter who asks the waiter not to bring around the dessert cart, and the student who goes to the library without a cell phone. Using the process model of self-control, we argue that the full range of self-control strategies can be organized by considering the timeline of the developing tempting impulse. Because impulses tend to grow stronger over time, situational self-control strategies—which can nip a tempting impulse in the bud—may be especially effective in preventing undesirable action. Ironically, we may underappreciate situational self-control for the same reason it is so effective—namely, that by manipulating our circumstances to advantage, we are often able to minimize the in-the-moment experience of intrapsychic struggle typically associated with exercising self-control."], "field": "Arts and Humanities", "q_year": 2021, "q_cid": "257094822", "pos_cid": 46455659, "source": "eval_collection"}
{"query_id": "scaleup_27274681_14207664", "query": "How to overcome ideological and identity-based divisions among political adversaries that hinder collaboration on societal issues", "pos": ["Working Through Conflict. Introduction: Conflict Interaction. 1. Communication and Conflict. 2. The Inner Experience of Conflict. 3. Theories of Conflict Interaction. 4. Power: The Architecture of Conflict. 5. Face-Saving. 6. Climate and Conflict Interaction. 7. Doing Conflict: Styles, Strategies, And Tactics. 8. Changing Conflict Dynamics. 9. Third Party Intervention."], "field": "Arts and Humanities", "q_year": 2024, "q_cid": "272746811", "pos_cid": 142076647, "source": "eval_collection"}
{"query_id": "scaleup_25062532_22559746", "query": "How to determine at scale whether the perspective of earlier descriptions persists in later descriptions, including their emphases, omissions, and balance of description, interpretation, and evaluation", "pos": ["Curatorial labour, voice and legacy: Mary Dorothy George and the Catalogue of Political and Personal Satires, 1930–54*. Between 1930 and 1954 Mary Dorothy George wrote catalogue entries for 12,553 ‘Golden Age’ satirical prints. This article examines George as a curatorial voice, an interlocutor between the archived past and her readers. It examines the labour processes that produced George’s contributions to the British Museum’s Catalogue of Political and Personal Satires, her writing as a corpus, and her interpretations therein. We argue that George’s linguistic and procedural choices have trouble the legacy of the catalogue, a system of knowledge organisation increasingly uncoupled from its circumstances of production whilst remaining foundational to the historiography of long eighteenth century British history."], "field": "Arts and Humanities", "q_year": 2022, "q_cid": "250625324", "pos_cid": 225597469, "source": "eval_collection"}
{"query_id": "scaleup_27827554_17917984", "query": "How to deliberately foster serendipity in fiction research to generate valuable creative insights and advance narratives", "pos": ["Investigating serendipity: How it unfolds and what may influence it. Serendipity is not an easy word to define. Its meaning has been stretched to apply to experiences ranging from the mundane to the exceptional. Serendipity, however, is consistently associated with unexpected and positive personal, scholarly, scientific, organizational, and societal events and discoveries. Diverse serendipitous experiences share a conceptual space; therefore, what lessons can we draw from an exploration of how serendipity unfolds and what may influence it? This article describes an investigation of work‐related serendipity. Twelve professionals and academics from a variety of fields were interviewed. The core of the semi‐structured interviews focused on participants' own work‐related experiences that could be recalled and discussed in depth. This research validated and augmented prior research while consolidating previous models of serendipity into a single model of the process of serendipity, consisting of: Trigger, Connection, Follow‐up, and Valuable Outcome, and an Unexpected Thread that runs through 1 or more of the first 4 elements. Together, the elements influence the Perception of Serendipity. Furthermore, this research identified what factors relating to the individual and their environment may facilitate the main elements of serendipity and further influence its perception."], "field": "Arts and Humanities", "q_year": 2025, "q_cid": "278275547", "pos_cid": 17917984, "source": "eval_collection"}
{"query_id": "scaleup_23620309_21971991", "query": "How to improve users’ awareness of represented and missing viewpoints in conversational argument search systems and reduce assumptions aligned with their cognitive biases", "pos": ["Enabling News Consumers to View and Understand Biased News Coverage: A Study on the Perception and Visualization of Media Bias. Traditional media outlets are known to report political news in a biased way, potentially affecting the political beliefs of the audience and even altering their voting behaviors. Many researchers focus on automatically detecting and identifying media bias in the news, but only very few studies exist that systematically analyze how theses biases can be best visualized and communicated. We create three manually annotated datasets and test varying visualization strategies. The results show no strong effects of becoming aware of the bias of the treatment groups compared to the control group, although a visualization of hand-annotated bias communicated bias in-stances more effectively than a framing visualization. Showing participants an overview page, which opposes different viewpoints on the same topic, does not yield differences in respondents' bias perception. Using a multilevel model, we find that perceived journalist bias is significantly related to perceived political extremeness and impartiality of the article."], "field": "Arts and Humanities", "q_year": 2021, "q_cid": "236203094", "pos_cid": 219719916, "source": "eval_collection"}
{"query_id": "scaleup_25780392_20736569", "query": "How to clarify the extent and origins of Slavic population influence in Mesa and Exo Mani, distinguishing direct intermarriage with the Melingoi from later contact with other Greek-speaking populations", "pos": ["Genetics of the peloponnesean populations and the theory of extinction of the medieval peloponnesean Greeks. Peloponnese has been one of the cradles of the Classical European civilization and an important contributor to the ancient European history. It has also been the subject of a controversy about the ancestry of its population. In a theory hotly debated by scholars for over 170 years, the German historian Jacob Philipp Fallmerayer proposed that the medieval Peloponneseans were totally extinguished by Slavic and Avar invaders and replaced by Slavic settlers during the 6th century CE. Here we use 2.5 million single-nucleotide polymorphisms to investigate the genetic structure of Peloponnesean populations in a sample of 241 individuals originating from all districts of the peninsula and to examine predictions of the theory of replacement of the medieval Peloponneseans by Slavs. We find considerable heterogeneity of Peloponnesean populations exemplified by genetically distinct subpopulations and by gene flow gradients within Peloponnese. By principal component analysis (PCA) and ADMIXTURE analysis the Peloponneseans are clearly distinguishable from the populations of the Slavic homeland and are very similar to Sicilians and Italians. Using a novel method of quantitative analysis of ADMIXTURE output we find that the Slavic ancestry of Peloponnesean subpopulations ranges from 0.2 to 14.4%. Subpopulations considered by Fallmerayer to be Slavic tribes or to have Near Eastern origin, have no significant ancestry of either. This study rejects the theory of extinction of medieval Peloponneseans and illustrates how genetics can clarify important aspects of the history of a human population."], "field": "Arts and Humanities", "q_year": 2023, "q_cid": "257803929", "pos_cid": 20736569, "source": "eval_collection"}
{"query_id": "scaleup_26963168_3433748", "query": "How to clarify how bodily movements make expected next actions recognizable and normatively organized, and how participants distinguish intended actions and negotiate agency when passing food to request a taste", "pos": ["Exchanging implements: the micro-materialities of multidisciplinary work in the operating theatre.. Surgical procedures rely upon an array of commonplace tools, implements and materials that mediate practice and disciplinary collaboration within the operating theatre. Substantial time is dedicated to the issue and provision of these artefacts and their timely exchange is critical to the successful accomplishment of surgical procedures. In this article, we consider the practice, knowledge and agency that informs how particular implements and materials are passed by the scrub nurse to the surgeon that in turn enables their deployment with regard to the particular procedure and the contingencies 'at hand'. We address the technicalities of these 'non-technical skills' and examine how they rely upon a disciplinary vision and interactional organisation that informs both the scrutiny of action and the ways in which implements and materials are handled and exchanged. We explore the implications of our analysis for our understanding of agency in action and the growing interest in developing robots or autonomous agents to support work and collaboration in health care."], "field": "Arts and Humanities", "q_year": 2024, "q_cid": "269631685", "pos_cid": 3433748, "source": "eval_collection"}
{"query_id": "scaleup_24807823_56115452", "query": "How to ensure equal access, participation and opportunities for church members across languages without unfair discrimination", "pos": ["Language as a barrier to ministry of the Word with special reference to sign language in ministry: Human dignity perspective. This article is born out of my participation in the General Synod Ministerial Formation for theological training of Uniting Reformed Church in Southern Africa (URCSA), when a decision was taken to license a student with a disability to be a minister of the Word in URCSA. Furthermore, my experience and observation of the licensing of the two candidates with hearing impairments to the ministry of the Word and Sacrament in URCSA and Dutch Reformed Church in South Africa (DRCSA) has encouraged me to conduct this research. This article is made up of four important parts: Firstly, the researcher will discuss Belhar Confession as the confession that emphasises unity (inclusivity), reconciliation and justice. Secondly, Belhar Confession and disability from the human dignity perspective will be discussed. Thirdly, the ecclesiological practices and shortcomings from the human dignity perspective will be highlighted. Fourthly, pastoral care as the affirmation of human dignity will be discussed. Interdisciplinary and/or interdisciplinary implications: The fields involved in this article are Systematic Theology, Sociology and Psychology. The author challenges classification of people with a disability under the category of limited competence by the Dutch Reformed Church when they license the ministerial candidates. The future results will reveal the inclusivity in terms of licensing and calling of ministers in the Dutch Reformed Church Family. This research calls for the change in the traditional discourse within ecclesiological, sociological and psychological fields, which exclude the people with a disability from the ministry of the Word and Sacraments."], "field": "Arts and Humanities", "q_year": 2022, "q_cid": "248078239", "pos_cid": 56115452, "source": "eval_collection"}
{"query_id": "scaleup_24477890_16802939", "query": "How to ensure exergame avatars accurately represent fit users’ bodies without reinforcing a narrow ideal body type despite body mass index limitations regarding individual differences in lean mass and fat distribution", "pos": ["Competing for ideal bodies: a study of exergames used as teaching aids in schools. Since the development of the welfare state, the Swedish school subject Health and Physical Education (HPE) has been regarded as an important site for public health work, and still assumes a central role in promoting the health of the coming generation. A specific type of health intervention, promoted by researchers in recent years, is the use of so-called exergames. In some countries, these fitness games are used as teaching aids in physical education classes and can be seen as examples of how public health issues and popular culture are shaping HPE in schools. The aim of the study reported in this paper is to examine which messages about health and body are offered, and how these are expressed in some of the fitness games used as teaching aids in school. The results of the study highlight the dangers of using exergames in the teaching of HPE in schools. The messages communicated by the games have a number of potentially harmful consequences, particularly with regard to the creation of specific health and bodily norms based on a measurable ideal. The use of this tool in education is thus far from value free, and the problems that might be solved when using the games are not necessarily the ones that education should privilege."], "field": "Arts and Humanities", "q_year": 2021, "q_cid": "244778907", "pos_cid": 16802939, "source": "eval_collection"}
{"query_id": "scaleup_25780392_21899756", "query": "How to clarify the relationship between regional variation in Greek toad names and Greece’s linguistic and demographic patterns", "pos": ["On the Slavic Immigration in the Byzantine Balkans. The Balkans have a complex ethnic and linguistic structure owing to migrations from the North which took place in waves of varying intensity and changed the regions demographic character from the antiquity onwards, when it was inhabitated by Illyrian and Greek tribes.1 The Slavic immigration from the late 6th century onwards was the most important for the present ethnic composition of the populations in southeastern Europe. It has been a matter of great debate since Jacob Philipp Fallmerayer (1790–1861) published his notorious thesis, stating that “not the slightest drop of undiluted Hellenic blood flows in the veins of the Christian population of present-day Greece”.2 Already since the 12th century Byzantine historians like Nikephoros Bryennios (12th century), George Pachymeres (13th century), Nikephoros Gregoras (14th century), Michael Kritoboulos and especially Laonikos Chalkokondyles (15th century) discussed the ethnic identities of the medieval Balkan populations and their alledged Illyrian origin. They used the ethnonyms Albanoi, Akarnanoi, Bosnoi, Bulgaroi, Dalmatai, Illyrioi, Makedones, Mysoi, Sarmatai, Skythai, Thrakes, Thessaloi and Triballoi.3 The collective names of the Slavs,"], "field": "Arts and Humanities", "q_year": 2023, "q_cid": "257803929", "pos_cid": 218997565, "source": "eval_collection"}
{"query_id": "scaleup_27363084_23387669", "query": "How to predict when oxygen-depleted deep water reaches the surface near shore and what happens to it as winds weaken on a rotating Earth", "pos": ["The setup and relaxation of spring upwelling in a deep, rotationally influenced lake. Strong and sustained winds can drive dramatic hydrodynamic responses in density‐stratified lakes, with the associated transport and mixing impacting water quality, ecosystem function, and the stratification itself. Analytical expressions offer insight into the dynamics of stratified lakes during severe wind events. However, it can be difficult to predict the aggregate response of a natural system to the superposition of hydrodynamic phenomena in the presence of complex bathymetry and when forced by variable wind patterns. Using an array of current, temperature, and water quality measurements at the upwind shore, we detail the hydrodynamic response of deep, rotationally influenced Lake Tahoe to three strong wind events during late spring. Sustained southwesterly winds in excess of 10 m s−1 drove upwelling at the upwind shore (characteristic of non‐rotational upwelling setup), with upward excursions of deep water exceeding 70 m for the strongest event. Hypolimnetic water, with elevated concentrations of chlorophyll a and nitrate, was advected toward the nearshore, but this water rapidly returned to depth with the relaxation of upwelling after the winds subsided. The relaxation of upwelling exhibited rotational influence, highlighted by an along‐shore, cyclonic front characteristic of a Kelvin wave‐driven coastal jet, with velocities exceeding 25 cm s−1. The rotational front also produced downwelling to 100 m, transporting dissolved oxygen to depth. More complex internal wave features followed the passage of these powerful internal waves. Results emphasize the complexity of these superimposed hydrodynamic phenomena in natural systems, providing a conceptual reference for the role upwelling events may play in lake ecosystems."], "field": "Arts and Humanities", "q_year": 2024, "q_cid": "273630842", "pos_cid": 233876691, "source": "eval_collection"}
{"query_id": "scaleup_25709482_14626890", "query": "How to determine whether a financially incentivized choice reflects authentic intrinsic motivation, accounting for when financial incentives threaten that motivation and how context matters", "pos": ["When Do Financial Incentives Reduce Intrinsic Motivation? Comparing Behaviors Studied in Psychological and Economic Literatures. Objective: To review existing evidence on the potential of incentives to undermine or “crowd out” intrinsic motivation, in order to establish whether and when it predicts financial incentives to crowd out motivation for health-related behaviors. Method: We conducted a conceptual analysis to compare definitions and operationalizations of the effect, and reviewed existing evidence to identify potential moderators of the effect. Results: In the psychological literature, we find strong evidence for an undermining effect of tangible rewards on intrinsic motivation for simple tasks when motivation manifest in behavior is initially high. In the economic literature, evidence for undermining effects exists for a broader variety of behaviors, in settings that involve a conflict of interest between parties. By contrast, for health related behaviors, baseline levels of incentivized behaviors are usually low, and only a subset involve an interpersonal conflict of interest. Correspondingly, we find no evidence for crowding out of incentivized health behaviors. Conclusion: The existing evidence does not warrant a priori predictions that an undermining effect would be found for health-related behaviors. Health-related behaviors and incentives schemes differ greatly in moderating characteristics, which should be the focus of future research."], "field": "Arts and Humanities", "q_year": 2021, "q_cid": "257094822", "pos_cid": 146268901, "source": "eval_collection"}
{"query_id": "scaleup_26942110_27953955", "query": "How to assess whether climate information is understandable for people with cognitive disabilities and reading difficulties and identify remaining barriers from complex sentence structures and jargon", "pos": ["Audio description from an easy-to-understand language perspective: A corpus-based study in Catalan. Providing accessible audiovisual content which caters for diverse user needs is one of the challenges of today’s digitised society. Audio description (AD) has been recently proposed to adopt the principles of easy-to-understand language (E2U) to reach larger audiences (Bernabé-Caro and Orero 2020). A focus group developed in the context of the EASIT project (Arias-Badia and Matamala 2020) showed that some professionals were reluctant to accept easy AD, arguing that AD addresses persons who cannot see, rather than persons who cannot understand. Comments were also made indicating that current audio descriptions may already be easy to understand. Given the lack of research in this area, this article presents results of a corpus study conducted on nine AD scripts in Catalan and provides data on the extent to which current audio descriptions are already “easy” taking into account existing parameters linked to easy-to-understand language principles. The features under analysis are part of speech distribution, sentence complexity, the use of (in)frequent lexicon, word length, and lexical variation. The results show that audio description scripts in Catalan do hold features typically attributed to easy-to-understand language."], "field": "Arts and Humanities", "q_year": 2024, "q_cid": "269421102", "pos_cid": 279539557, "source": "eval_collection"}
{"query_id": "scaleup_24955125_23436618", "query": "How to establish the original form and structural design of a church’s apse despite missing documented elements, while communicating complex historical knowledge without allowing hypothetical representations to mislead interpretation or analysis", "pos": ["Virtual Restoration and Virtual Reconstruction in Cultural Heritage: Terminology, Methodologies, Visual Representation Techniques and Cognitive Models. Today, the practice of making digital replicas of artworks and restoring and recontextualizing them within artificial simulations is widespread in the virtual heritage domain. Virtual reconstructions have achieved results of great realistic and aesthetic impact. Alongside the practice, a growing methodological awareness has developed of the extent to which, and how, it is permissible to virtually operate in the field of restoration, avoid a false sense of reality, and preserve the reliability of the original content. However, there is not yet a full sharing of meanings in virtual restoration and reconstruction domains. Therefore, this article aims to clarify and define concepts, functions, fields of application, and methodologies. The goal of virtual heritage is not only producing digital replicas. In the absence of materiality, what emerges as a fundamental value are the interaction processes, the semantic values that can be attributed to the model itself. The cognitive process originates from this interaction. The theoretical discussion is supported by exemplar case studies carried out by the authors over almost twenty years. Finally, the concepts of uniqueness and authenticity need to be again pondered in light of the digital era. Indeed, real and virtual should be considered as a continuum, as they exchange information favoring new processes of interaction and critical thinking."], "field": "Arts and Humanities", "q_year": 2022, "q_cid": "249551251", "pos_cid": 234366187, "source": "eval_collection"}
{"query_id": "scaleup_22197934_73477447", "query": "How to maintain responsiveness to self without harmful self-directed reactions while distinguishing self-related signals from external inputs in the developing brain", "pos": ["Rethinking Thymic Tolerance: Lessons from Mice.. In the thymus, distinct cortex and medulla areas emphasize the division of labor in selection events shaping the αβT cell receptor repertoire. For example, MHC restriction via positive selection is a unique property of epithelial cells in the thymic cortex. Far less clear are the events controlling tolerance induction in the medulla. By acting in concert through multiple roles, including antigen production/presentation and chemokine-mediated control of migration, we propose that medullary epithelium and dendritic cells collectively enable the medulla to balance T cell production with negative selection and Foxp3+ regulatory T cell (Treg) development. We examine here the features of these medullary resident cells and their roles in T cell tolerance, and discuss how imbalance in the thymus can result in loss of T cell tolerance."], "field": "Arts and Humanities", "q_year": 2020, "q_cid": "221979347", "pos_cid": 73477447, "source": "eval_collection"}
{"query_id": "scaleup_25709482_3464632", "query": "How to determine whether attentional flexibility can be improved in children", "pos": ["The Attention Training Technique improves Children's ability to delay gratification: A controlled comparison with progressive relaxation.. The ability to delay gratification at a young age is a predictor of psychological, cognitive, health, and academic later-life outcomes. This study aimed to extend earlier research and explore whether a metacognitive intervention, Wells' (1990) Attention Training Technique (ATT), could improve young children's ability to delay gratification compared to an active-control (Progressive Muscle Relaxation: PMR), and no-intervention group. One hundred and one children aged 5-6 years old were recruited from schools. Classes of children were randomly allocated to receive the ATT, PMR or no-intervention and tested at pre- and post-intervention on measures of delay of gratification (the Marshmallow Test) and verbal inhibition (Day/Night Task). Results showed that, even when covariates were controlled for, following ATT, children delayed gratification significantly longer than after PMR or no-intervention. ATT also improved verbal inhibition compared with the no-intervention group, whilst PMR did not. The results add to earlier findings; ATT appears to provide a simple and effective way of improving young children's ability to delay gratification which has previously been shown to predict positive outcomes in later-life."], "field": "Arts and Humanities", "q_year": 2021, "q_cid": "257094822", "pos_cid": 3464632, "source": "eval_collection"}
{"query_id": "scaleup_28037168_14290586", "query": "How to understand how student teachers of English as a foreign language experience and respond to feeling uneasy during online and in-person practicums, particularly in online classrooms", "pos": ["Stress: Appraisal and Coping. Here is a monumental work that continues in the tradition pioneered by co-author Richard Lazarus in his classic book Psychological Stress and the Coping Process. Dr. Lazarus and his collaborator, Dr. Susan Folkman, present here a detailed theory of psychological stress, building on the concepts of cognitive appraisal and coping which have become major themes of theory and investigation. As an integrative theoretical analysis, this volume pulls together two decades of research and thought on issues in behavioral medicine, emotion, stress management, treatment, and life span development. A selective review of the most pertinent literature is included in each chapter. The total reference listing for the book extends to 60 pages. This work is necessarily multidisciplinary, reflecting the many dimensions of stress-related problems and their situation within a complex social context. While the emphasis is on psychological aspects of stress, the book is oriented towards professionals in various disciplines, as well as advanced students and educated laypersons. The intended audience ranges from psychiatrists, clinical psychologists, nurses, and social workers to sociologists, anthropologists, medical researchers, and physiologists."], "field": "Arts and Humanities", "q_year": 2025, "q_cid": "280371687", "pos_cid": 142905864, "source": "eval_collection"}
{"query_id": "scaleup_23672604_14480108", "query": "How to determine how an artist’s death and access to trading networks affect different parts of the artwork price distribution despite selection in observed sales prices and increased price variability after death", "pos": ["Earnings and Consumption Dynamics: A Nonlinear Panel Data Framework. We develop a new quantile-based panel data framework to study the nature of income persistence and the transmission of income shocks to consumption. Log-earnings are the sum of a general Markovian persistent component and a transitory innovation. The persistence of past shocks to earnings is allowed to vary according to the size and sign of the current shock. Consumption is modeled as an age-dependent nonlinear function of assets and the two earnings components. We establish the nonparametric identification of the nonlinear earnings process and the consumption policy rule. Exploiting the enhanced consumption and asset data in recent waves of the Panel Study of Income Dynamics, we find nonlinear persistence and conditional skewness to be key features of the earnings process. We show that the impact of earnings shocks varies substantially across earnings histories, and that this nonlinearity drives heterogeneous consumption responses. The transmission of shocks is found to vary systematically with assets."], "field": "Arts and Humanities", "q_year": 2021, "q_cid": "236726041", "pos_cid": 14480108, "source": "eval_collection"}
{"query_id": "scaleup_25632669_25860789", "query": "How to help patients facing negative reputations, imposed identities, and intersecting forms of oppression have their symptoms believed, obtain diagnoses, navigate health care, and manage illness", "pos": ["A Second Chance at Health. Abstract:Mass incarceration and the aging prison population in the United States is an ethical crisis, understudied in empirical bioethics research. In this article, I share one woman’s narrative to illustrate how older Black women describe accessing healthcare while incarcerated and identify sites for bioethical exploration. I argue that, due to the punitive nature of prison healthcare interactions, wherein women are seen as inmates first and patients second, healthcare providers are caught in a trap of competing ethical commitments to their patients and the state. As the prison population ages, these challenges will become more acute. Feminist bioethics has a critical role to play in imagining new possibilities for accessing, giving, and receiving care in the carceral context."], "field": "Arts and Humanities", "q_year": 2023, "q_cid": "256326690", "pos_cid": 258607896, "source": "eval_collection"}
{"query_id": "scaleup_23946675_73679971", "query": "How to determine what air quality messages need to convey to encourage protective action when people evaluate their ability to act and the likely effectiveness of recommended actions", "pos": ["Yes, we can: motivate Dutch citizens to engage in self-protective behavior with regard to flood risks. Although the risk of flooding poses a serious threat to the Dutch public, citizens are not very inclined to engage in self-protective behaviors. Current risk communication tries to enhance these self-protective behaviors among citizens, but is nonetheless not very successful. The level of citizens engaging in self-protective actions remains rather low. Therefore, this research strives to determine the factors that might enhance or lessen the intention to engage in self-protection among citizens. The study was a 2 (flood risk: high vs low) × 2 (efficacy beliefs: high vs low) between subject experiment. It was conducted to test how varying levels of flood risk and efficacy beliefs influence two different self-protective behaviors, namely information seeking and the intention to engage in risk mitigating or preventive behaviors. Furthermore, the relationship between information seeking and the intention to take self-protective actions was discussed. Results showed that high levels of flood risk lead to higher levels of both information seeking and the intention to engage in self-protective behaviors than low levels of flood risk. For efficacy beliefs, the same trend occurred. Also, results showed that information seeking seems to coincide with the intention to take preventive actions and acted as a mediator between the levels of perceived risk and efficacy and the intention to take self-protective actions."], "field": "Arts and Humanities", "q_year": 2021, "q_cid": "239466758", "pos_cid": 73679971, "source": "eval_collection"}
{"query_id": "scaleup_26525481_42091903", "query": "How to characterize non-fungible token price changes whose variability may change over time despite stable overall patterns and little correlation between successive changes", "pos": ["A multivariate generalized ARCH approach to modeling risk premia in forward foreign exchange rate markets. Assuming that daily spot exchange rates follow a martingale process. we derive the implied time series process for the vector of 30-day forward rate forecast errors from using weekly data. The conditional second moment matrix of this vector is modeled as a multivariate generalized ARCH process. The estimated model is used to test the hypothesis that the risk premium is a linear function of the conditional variances and covariances as suggested by the standard asset pricing theory literature. Little support is found for this theory; instead lagged changes in the forward rate appear to be correlated with the ‘risk premium.’ This study examines spot and forward exchange rates at a weekly level for four different currencies. It is shown that the vector of forward market forecast errors can be parameterized as a vector moving average (MA) process where the MA coefficients can be theoretically determined from knowledge of the martingale behavior of exchange rates. The conditional covariance matrix is then estimated by assuming a multivariate GARCH structure which depends on a relatively small number of parameters. A range of LM tests confirms that the model provides an adequate description of the first- and second-order moments of the conditional density of the data. The vector MA process is then used to provide some bounds on the magnitude of the risk premium. Series of tests are also applied to the estimated model to test for the inclusion of terms that would be implied by a time varying risk premium. The results are not consistent with any standard model of asset pricing, but do provide evidence for the existence of this type of effect."], "field": "Arts and Humanities", "q_year": 2023, "q_cid": "265254814", "pos_cid": 42091903, "source": "eval_collection"}
{"query_id": "scaleup_25700431_14563620", "query": "How to ensure minority voices and concerns count as legitimate in political debates over heritage despite presumed otherness, non-belonging, or dismissal as unworthy of political consideration", "pos": ["Schooling and social justice through the lenses of Nancy Fraser. This review essay draws on Nancy Fraser's work as featured in Adding insult to injury: Nancy Fraser debates her critics to explore issues of schooling and social justice. The review focuses on the applicability and usefulness of Fraser's three-dimensional model for understanding matters of justice in education. It begins with an overview of the principles of economic, cultural and political justice as they are reflected in specific examples of equity and schooling policy and practice. This is followed by (1) a consideration of Fraser's concerns that current forms of identity politics are reifying group identity and displacing matters of distributive justice and (2) with an account of her concerns about the political justice issues of representation and misframing in the contemporary global era. With reference to the sphere of Indigenous education, the review examines some of the problematics involved in pursuing distributive, recognitive and representative justice. Fraser's ‘status model’ is presented as a way through these problematics because it engages with a politics that begins with overcoming status subordination rather than with a politics of group identity. Against this theoretical backdrop, the final section of the review briefly considers some of the future challenges for schooling and social justice."], "field": "Arts and Humanities", "q_year": 2023, "q_cid": "257004312", "pos_cid": 145636202, "source": "eval_collection"}
{"query_id": "scaleup_25848586_13779319", "query": "How to assess whether dog tissue isotopes reliably represent human diets given possible human feces consumption by dogs and fecal carbon and nitrogen content", "pos": ["Anthropogenic Food Subsidy to a Commensal Carnivore: The Value and Supply of Human Faeces in the Diet of Free-Ranging Dogs. Simple Summary Free-ranging dog populations are growing worldwide, posing threats to human health and wildlife conservation. Dog population management requires a better understanding of the supply and quality of human-derived food. We studied the diet of free-ranging dogs in a remote area of Zimbabwe to explore the relationships between human waste, dog condition, and fertility, with a focus on the value of human faeces. We found that mammal remains, ‘sadza’ (maize porridge, the human staple) and human faeces were the most important food items, and unlike other items, faeces and sadza were consistently available. Nutritional analysis showed that human faeces was comparatively high in protein and energy content, exceeding that of sadza, and equivalent to mammal remains. Adult female dog condition was good throughout the year, indicating a diet sufficient to maintain fertility, and dogs largely fed alone, suggesting that food was abundant. We conclude that the lack of sanitation allows an important food subsidy to free-ranging dogs, but improved sanitation is unlikely to limit population growth as long as alternative human waste is available. Reproductive control by owners is more likely to reduce fertility rates. Abstract As the global population of free-ranging domestic dogs grows, there is increasing concern about impacts on human health and wildlife conservation. Effective management of dog populations requires reliable information on their diet, feeding behavior, and social ecology. Free-ranging dogs are reliant on humans, but anthropogenic food subsidies, particularly human faeces (i.e., coprophagy) have not previously been fully quantified. In this study we assess the contributions of different food types to the diet, and their influences on the social behaviour of free-ranging dogs in communal lands of rural Zimbabwe, with a focus on coprophagy. Free-ranging dog diets, body condition, and sociology were studied amongst 72 dogs over 18 months using scat analysis and direct observations. Human faeces constituted the fourth most common item in scats (56% occurrence) and contributed 21% by mass to the observed diet. Human faeces represented a valuable resource because relative to other food items it was consistently available, and of higher nutritional value than ‘sadza’ (maize porridge, the human staple and primary human-derived food), yielding 18.7% crude protein and 18.7 KJ/kg gross energy, compared to 8.3% and 18.5 KJ/kg for sadza, respectively. Human faeces had protein and energy values equivalent to mammal remains, another important food item. Dog condition was generally good, with 64% of adult females and 74% of adult males in the highest two body condition scores (on a five point scale), suggesting a plentiful and high quality food supply. Dogs largely fed alone, perhaps as a consequence of the small, inert, and spatially dispersed items that comprise their diet, and its abundance. We discuss the relationships between sanitation, human development, the supply of human faeces, female dog fertility, and population control."], "field": "Arts and Humanities", "q_year": 2023, "q_cid": "258485869", "pos_cid": 13779319, "source": "eval_collection"}
{"query_id": "scaleup_24529530_16761507", "query": "How to explain views of criminals, victims, and criminal acts and why particular responses to crime seem appropriate", "pos": ["Metaphors We Think With: The Role of Metaphor in Reasoning. The way we talk about complex and abstract ideas is suffused with metaphor. In five experiments, we explore how these metaphors influence the way that we reason about complex issues and forage for further information about them. We find that even the subtlest instantiation of a metaphor (via a single word) can have a powerful influence over how people attempt to solve social problems like crime and how they gather information to make “well-informed” decisions. Interestingly, we find that the influence of the metaphorical framing effect is covert: people do not recognize metaphors as influential in their decisions; instead they point to more “substantive” (often numerical) information as the motivation for their problem-solving decision. Metaphors in language appear to instantiate frame-consistent knowledge structures and invite structurally consistent inferences. Far from being mere rhetorical flourishes, metaphors have profound influences on how we conceptualize and act with respect to important societal issues. We find that exposure to even a single metaphor can induce substantial differences in opinion about how to solve social problems: differences that are larger, for example, than pre-existing differences in opinion between Democrats and Republicans."], "field": "Arts and Humanities", "q_year": 2021, "q_cid": "245295306", "pos_cid": 16761507, "source": "eval_collection"}
{"query_id": "scaleup_26641992_14855916", "query": "How to coherently structure learning activities in initial music-teacher training to support creativity, sound exploration, digital competencies and contemporary approaches to musical learning", "pos": ["Project-based learning: A review of the literature. Project-based learning (PBL) is an active student-centred form of instruction which is characterised by students’ autonomy, constructive investigations, goal-setting, collaboration, communication and reflection within real-world practices. It has been explored in various contexts and in different phases of schooling, from primary to higher education. The majority of the reviewed studies were based on a quasi-experimental pretest–posttest design with some baseline equivalence established but no random allocation of participants to control and experimental groups, and as a result, a causal link between PBL instruction and positive student outcomes cannot be established with certainty. Modern digital technology, group processes of high quality, teachers’ ability to effectively scaffold students’ learning and provide guidance and support, the balance between didactic instruction with in-depth inquiry methods and well-aligned assessment have been identified in the literature as facilitating factors in the implementation of PBL. The article concludes with six key recommendations considered to be essential for the successful adoption of a PBL approach in the mainstream school setting."], "field": "Arts and Humanities", "q_year": 2023, "q_cid": "266419922", "pos_cid": 148559169, "source": "eval_collection"}
{"query_id": "scaleup_27191521_27099554", "query": "How to address an online culture that rewards abuse and pressures victims to stay silent or stop participating while preserving people's ability to speak freely", "pos": ["Expressive Law and the Americans with Disabilities Act.. The question of why people follow the law has long been a subject of scholarly consideration. Prevailing accounts of how law changes behavior coalesce around two major themes: legitimacy and deterrence. Advocates of legitimacy argue that law is obeyed when it is created through a legitimate process and its substance comports with community mores. Others emphasize deterrence, particularly those who subscribe to law-and-economics theories. These scholars argue that law makes certain socially undesirable behaviors more costly, and thus individuals are less likely to undertake them."], "field": "Arts and Humanities", "q_year": 2024, "q_cid": "271915215", "pos_cid": 27099554, "source": "eval_collection"}
{"query_id": "scaleup_23946675_10234753", "query": "How to reliably assess participants’ preferences for learning about health risks in a visual format", "pos": ["Development and validation of the Health Visual Information Preference Scale.. OBJECTIVE Patients are likely to have individual preferences for learning about health, which may influence their comprehension and utilization of health information. Some patients may prefer visual health information, which can make complex health information easier to understand. Aligning health information presentation with preferences may increase understanding and improve health outcomes, yet no scale measures preferences for visual health information. DESIGN Two studies examined the psychometric properties of the Health Visual Information Preference Scale (Health VIPS), a new measure designed to assess preferences for visual health information. METHODS In Study 1, 103 undergraduate students and 97 patients undergoing colorectal and gynaecological oncology surgery completed the Health VIPS. Exploratory factor analyses (EFA) were conducted for both samples. Internal consistency, test-retest reliability, and validity were assessed in the student sample. In Study 2, 196 outpatients completed the Health VIPS. Confirmatory factor analysis (CFA) was performed on this sample, in addition to measures of reliability and validity. RESULTS In Study 1, EFA analysis suggested a two-factor structure. The Health VIPS demonstrated good internal consistency in both the student sample (α = .70-.80) and patient sample (α = .80), and good test-retest reliability in the student sample (r = .63, p < .001). Convergent validity and discriminant validity were also established. In Study 2, the CFA confirmed a two-factor structure is the best model fit for the Health VIPS. The Health VIPS also demonstrated discriminant and convergent validity. Scale item means in all samples were positively skewed, suggesting a general preference for visual health information. CONCLUSIONS Initial evidence suggests the Health VIPS has good psychometric properties. This scale could identify patients who would benefit from additional visual aids when receiving health information. Statement of contribution What is already known on this subject? Poor comprehension of health information can lead to misunderstandings of illness and treatment, and potentially non-adherence. It is likely that patients have distinct preferences for how they would choose to receive health information, including information format. Visual health information is becoming more widely used to communicate information about health and illness to patients, although there is no measure to identify those who prefer this information format to standard written health materials. What does this study add? This study describes the first scale to assess preferences for visual health information. This scale could identify patients who would benefit from supplementary visual information in consultations."], "field": "Arts and Humanities", "q_year": 2021, "q_cid": "239466758", "pos_cid": 102347531, "source": "eval_collection"}
{"query_id": "scaleup_27682198_22174850", "query": "How to assess the strength of evidence on group arts interventions amid quality and bias concerns in randomized and non-randomized controlled trials", "pos": ["Assessing the quality of studies in meta‐research: Review/guidelines on the most important quality assessment tools. Systematic reviews and meta‐analyses pool data from individual studies to generate a higher level of evidence to be evaluated by guidelines. These reviews ultimately guide clinicians and stakeholders in health‐related decisions. However, the informativeness and quality of evidence synthesis inherently depend on the quality of what has been pooled into meta‐research projects. Moreover, beyond the quality of included individual studies, only a methodologically correct process, in relation to systematic reviews and meta‐analyses themselves, can produce a reliable and valid evidence synthesis. Hence, quality of meta‐research projects also affects evidence synthesis reliability. In this overview, the authors provide a synthesis of advantages and disadvantages and main characteristics of some of the most frequently used tools to assess quality of individual studies, systematic reviews, and meta‐analyses. Specifically, the tools considered in this work are the Newcastle‐Ottawa scale (NOS) and the Strengthening the Reporting of Observational Studies in Epidemiology (STROBE) for observational studies, the Consolidated Standards of Reporting Trials (CONSORT), the Jadad scale, the Cochrane risk of bias tool 2 (RoB2) for randomized controlled trials, the Preferred Reporting Items for Systematic Reviews and Meta‐analysis (PRISMA) and the Assessment of Multiple Systematic Reviews 2 (AMSTAR2), and AMSTAR‐PLUS for meta‐analyses."], "field": "Arts and Humanities", "q_year": 2025, "q_cid": "276821984", "pos_cid": 221748504, "source": "eval_collection"}
{"query_id": "scaleup_25709482_8148729", "query": "How to clarify the practical meaning and assess the value of an abstract, static concept in particular circumstances while accommodating experiential and empirical knowledge without circular justification", "pos": ["A Proposal for a Scientifically-Informed and Instrumentalist Account of Free Will and Voluntary Action. The ability to choose freely is captured under the umbrella concept of “free will,” which designates an ability that plays a crucial role in most understandings of autonomy and responsibility and, thus, bears significance for moral practice and moral theory. Some claim that neuroscience research challenges the existence of free will/voluntary action while some who adopt stronger eliminativist stances have gone as far as describing free will as an illusion. Contrary to that, those relying on realist stances have restated the foundational value and role of folk psychological concepts of voluntary action and free will in, for example, the domains of ethics and law. An emerging body of research in cognitive science and social psychology has generated results suggesting that the phenomena captured by the concepts describing free will and voluntary action are dynamic and responsive to priming and framing effects. We propose that this body of research suggests the existence of dynamic and consequential properties of free will better captured following pragmatist theory and instrumentalist epistemology. This contrasts the simpler static concept of free will and the related metaphysics that was at the basis of earlier debates and structured around the poles of realism and eliminativism. This paper contextualizes ontological and epistemological debates about free will, describes a scientifically-informed and instrumentalist account of the concept of free will and voluntary action consistent with recent research in cognitive science, and discusses its implications for research (e.g., theoretical assumptions of research paradigms, interdisciplinary research) and practice (e.g., impact on self-image and social behavior)."], "field": "Arts and Humanities", "q_year": 2021, "q_cid": "257094822", "pos_cid": 8148729, "source": "eval_collection"}
{"query_id": "scaleup_25775185_12090811", "query": "How to determine whether BoneXpert versions 2 and 3 differ significantly in accuracy relative to manual bone age assessment rather than due to chance", "pos": ["Comparing Predictive Accuracy. We propose and evaluate explicit tests of the null hypothesis of no difference in the accuracy of two competing forecasts. In contrast to previously developed tests, a wide variety of accuracy measures can be used (in particular, the loss of function need not be quadratic and need not even be symmetric), and forecast errors can be non-Gaussian, nonzero mean, serially correlated, and contemporaneously correlated. Asymptotic and exact finite-sample tests are proposed, evaluated, and illustrated."], "field": "Arts and Humanities", "q_year": 2023, "q_cid": "257751850", "pos_cid": 12090811, "source": "eval_collection"}
{"query_id": "scaleup_22197934_44108206", "query": "How to understand the coordination of survival and death across opposing cell populations to establish balanced developing networks, given the rapid expansion of one population in primates", "pos": ["Pyramidal cell regulation of interneuron survival sculpts cortical networks. Complex neuronal circuitries such as those found in the mammalian cerebral cortex have evolved as balanced networks of excitatory and inhibitory neurons. Although the establishment of appropriate numbers of these cells is essential for brain function and behaviour, our understanding of this fundamental process is limited. Here we show that the survival of interneurons in mice depends on the activity of pyramidal cells in a critical window of postnatal development, during which excitatory synaptic input to individual interneurons predicts their survival or death. Pyramidal cells regulate interneuron survival through the negative modulation of PTEN signalling, which effectively drives interneuron cell death during this period. Our findings indicate that activity-dependent mechanisms dynamically adjust the number of inhibitory cells in nascent local cortical circuits, ultimately establishing the appropriate proportions of excitatory and inhibitory neurons in the cerebral cortex. Excitatory input onto inhibitory interneurons in the developing mouse cortex acts through PTEN to protect interneurons from cell death and thus regulate the balance between excitation and inhibition."], "field": "Arts and Humanities", "q_year": 2020, "q_cid": "221979347", "pos_cid": 44108206, "source": "eval_collection"}
{"query_id": "scaleup_22028485_15817532", "query": "How to achieve precise conversational turn-taking despite language production demands and variability in timing", "pos": ["The role of shared visual information for joint action coordination. Highlights • In joint action tasks, co-actors have a choice between different coordination mechanisms.• How joint actions are coordinated depends on shared perceptual information.• In the absence of shared visual information, co-actors rely on a general heuristic strategy.• When shared visual information is available, co-actors switch to a communicative strategy."], "field": "Arts and Humanities", "q_year": 2020, "q_cid": "220284851", "pos_cid": 15817532, "source": "eval_collection"}
{"query_id": "scaleup_27422643_10619071", "query": "How to help volunteers with little preparation or background information develop shared understanding and exchange tacit knowledge about contemporary art in heritage settings without mandating or managing a community into existence", "pos": ["Thinking together: What makes Communities of Practice work?. In this article, we develop the founding elements of the concept of Communities of Practice by elaborating on the learning processes happening at the heart of such communities. In particular, we provide a consistent perspective on the notions of knowledge, knowing and knowledge sharing that is compatible with the essence of this concept – that learning entails an investment of identity and a social formation of a person. We do so by drawing richly from the work of Michael Polanyi and his conception of personal knowledge, and thereby we clarify the scope of Communities of Practice and offer a number of new insights into how to make such social structures perform well in professional settings. The conceptual discussion is substantiated by findings of a qualitative empirical study in the UK National Health Service. As a result, the process of ‘thinking together’ is conceptualized as a key part of meaningful Communities of Practice where people mutually guide each other through their understandings of the same problems in their area of mutual interest, and this way indirectly share tacit knowledge. The collaborative learning process of ‘thinking together’, we argue, is what essentially brings Communities of Practice to life and not the other way round."], "field": "Arts and Humanities", "q_year": 2024, "q_cid": "274226435", "pos_cid": 10619071, "source": "eval_collection"}
{"query_id": "scaleup_25394104_21653517", "query": "How to explain the effects of mobile-assisted language learning on students’ voluntary engagement rather than participation under external pressure, and on language-learning outcomes", "pos": ["Intrinsic and extrinsic motivation from a self-determination theory perspective: Definitions, theory, practices, and future directions. Abstract Self-determination theory (SDT) is a broad framework for understanding factors that facilitate or undermine intrinsic motivation, autonomous extrinsic motivation, and psychological wellness, all issues of direct relevance to educational settings. We review research from SDT showing that both intrinsic motivation and well-internalized (and thus autonomous) forms of extrinsic motivation predict an array of positive outcomes across varied educational levels and cultural contexts and are enhanced by supports for students’ basic psychological needs for autonomy, competence, and relatedness. Findings also show a dynamic link between teacher and student motivation, as teachers are themselves impacted and constrained by controlling mandates, institutional pressures, and leadership styles. Ironically, despite substantial evidence for the importance of psychological need satisfactions in learning contexts, many current educational policies and practices around the globe remain anchored in traditional motivational models that fail to support students’ and teachers’ needs, a knowledge versus policy gap we should aspire to close."], "field": "Arts and Humanities", "q_year": 2022, "q_cid": "253941042", "pos_cid": 216535176, "source": "eval_collection"}
{"query_id": "scaleup_22028485_21463273", "query": "How to determine whether speakers make conversational turns more predictable in timing and content to support coordination, beyond patterns also present in individual speech", "pos": ["Expectancy effects in the EEG during joint and spontaneous word-by-word sentence production in German. Our aim in the present study is to measure neural correlates during spontaneous interactive sentence production. We present a novel approach using the word-by-word technique from improvisational theatre, in which two speakers jointly produce one sentence. This paradigm allows the assessment of behavioural aspects, such as turn-times, and electrophysiological responses, such as event-related-potentials (ERPs). Twenty-five participants constructed a cued but spontaneous four-word German sentence together with a confederate, taking turns for each word of the sentence. In 30% of the trials, the confederate uttered an unexpected gender-marked article. To complete the sentence in a meaningful way, the participant had to detect the violation and retrieve and utter a new fitting response. We found significant increases in response times after unexpected words and – despite allowing unscripted language production and naturally varying speech material – successfully detected significant N400 and P600 ERP effects for the unexpected word. The N400 EEG activity further significantly predicted the response time of the subsequent turn. Our results show that combining behavioural and neuroscientific measures of verbal interactions while retaining sufficient experimental control is possible, and that this combination provides promising insights into the mechanisms of spontaneous spoken dialogue."], "field": "Arts and Humanities", "q_year": 2020, "q_cid": "220284851", "pos_cid": 214632737, "source": "eval_collection"}
{"query_id": "scaleup_25709482_9438136", "query": "How to clarify how sleep-related conditions affect the capacity for self-control in an account of autonomy", "pos": ["Interactions between sleep habits and self-control. Good sleep habits and effective self-control are important components of successful functioning. Unfortunately chronic sleep loss and impaired self-control are common occurrences for many individuals which can lead to difficulty with daily self-control issues such as resisting impulses and maintaining attentive behavior. Understanding how self-control is depleted and how good sleep habits may help replenish and maintain the capacity for self-control is an important issue. A sleep-deprived individual who has expended the necessary resources for self-control is at an increased risk for succumbing to impulsive desires, poor attentional capacity, and compromised decision making. To date, few studies have investigated how sleep and self-control are inter-related. The goal of this mini-review is to explore the intersection between sleep habits and self-control and encourage researchers to focus on a new area of research that integrates what are at present largely separate areas in psychology and human neurosciences."], "field": "Arts and Humanities", "q_year": 2021, "q_cid": "257094822", "pos_cid": 9438136, "source": "eval_collection"}
{"query_id": "scaleup_23338293_98807409", "query": "How to characterize the compounds in vinegar and white wine used for gall extraction and their role in iron-gall ink composition", "pos": ["Total phenolic content, antioxidant capacity and phytochemical profiling of grape and pomegranate wines. The object of this study was to determine the phenolic profile, the total phenolic content and antioxidant capacity of pomegranate wine and compare to multi-varietalVitisspp. red wine using different spectrophotometric and spectrometric techniques."], "field": "Arts and Humanities", "q_year": 2021, "q_cid": "233382938", "pos_cid": 98807409, "source": "eval_collection"}
{"query_id": "scaleup_25830204_12048422", "query": "How to assess the relationship between schizotypy and highly variable mixed activation–deactivation pixel counts when most pixels are uncolored or marked only for activation or deactivation", "pos": ["Regression Models for Count Data in R. The classical Poisson, geometric and negative binomial regression models for count data belong to the family of generalized linear models and are available at the core of the statistics toolbox in the R system for statistical computing. After reviewing the conceptual and computational features of these methods, a new implementation of zero-inflated and hurdle regression models in the functions zeroinfl() and hurdle() from the package pscl is introduced. It re-uses design and functionality of the basic R functions just as the underlying conceptual tools extend the classical models. Both model classes are able to incorporate over-dispersion and excess zeros - two problems that typically occur in count data sets in economics and the social and political sciences - better than their classical counterparts. Using cross-section data on the demand for medical care, it is illustrated how the classical as well as the zero-augmented models can be fitted, inspected and tested in practice."], "field": "Arts and Humanities", "q_year": 2023, "q_cid": "258302042", "pos_cid": 120484228, "source": "train_step3"}
{"query_id": "scaleup_27210130_25967309", "query": "How to ensure recognition and support for newly arrived learners’ existing knowledge, experiences, and linguistic resources in Swedish-language learning despite diverse language backgrounds and limited Swedish proficiency", "pos": ["SCAFFOLDING IN TEACHING WRITING NEWS ITEM TEXT, ITS BENEFITS AND CHALLENGES. The research aimed at investigating types of scaffolding, the ways a teacher provides scaffolding, and benefits and challenges of scaffolding in teaching writing News Item text in tenth graders in a senior high school in Bandung. This research employed a qualitative research design, embracing characteristic of a case study. The data were obtained from non-participant classroom observation for six meetings, and one interview. The data collected from classroom observation and interview were transcribed and then analyzed by using framework of types of scaffolding (e.g Roehler and Cantlon (1997), Hammond (2001), Gibbons, (2002), and Walqui (2006)). The findings revealed that seven types of scaffolding were provided by the teacher during teaching writing News Item text. The most intensive scaffolding was given in the Modeling stage, while scaffolding was removed in the Independent Writing stage. Regarding the benefits and challenges of providing scaffolding, this research found out the benefits of scaffolding such as to connect students’ prior knowledge with a new concept, to engage students, to minimize the level confusion of students, and to build students‟ self-confidence. Meanwhile, the challenges of providing scaffolding are the number of students in the classroom, time constraints, and demands on teacher."], "field": "Arts and Humanities", "q_year": 2024, "q_cid": "272101300", "pos_cid": 259673090, "source": "train_step3"}
{"query_id": "scaleup_27988019_24566640", "query": "How to explain persistent difficulties adapting to change in former coal-mining communities with strong solidarity and inherited traditions", "pos": ["The role of powerful incumbent firms: shaping regional industrial path development through change and maintenance agency. ABSTRACT This article seeks to advance perspectives on powerful incumbent firms in (new) regional industrial path development. Drawing on recent insights from transition studies, it is argued that this actor group – hitherto often portrayed in a rather one-sided manner – plays a crucial role in shaping the pace and direction of regional path development through agency oriented towards both change and maintenance. Building on systemic perspectives at the intersection of evolutionary economic geography and innovation studies, a particular emphasis is placed on incumbent firms’ interventions to reconfigure or stabilize their surrounding regional innovation system to support their intentions. To this end, this article examines how incumbents exert their influence through various forms of power as means by which they promote or hinder regional industrial change. Empirically, the role of incumbent firms in three traditional automotive regions in Austria is investigated. It is shown how they leverage their power to propel the industry’s digitalization and suppress its decarbonization."], "field": "Arts and Humanities", "q_year": 2025, "q_cid": "279880197", "pos_cid": 245666401, "source": "train_step3"}
{"query_id": "scaleup_26977294_24800618", "query": "How to recover motion information from noisy representations for dance videos that depict a specified person and match the guiding music", "pos": ["Video Diffusion Models. Generating temporally coherent high fidelity video is an important milestone in generative modeling research. We make progress towards this milestone by proposing a diffusion model for video generation that shows very promising initial results. Our model is a natural extension of the standard image diffusion architecture, and it enables jointly training from image and video data, which we find to reduce the variance of minibatch gradients and speed up optimization. To generate long and higher resolution videos we introduce a new conditional sampling technique for spatial and temporal video extension that performs better than previously proposed methods. We present the first results on a large text-conditioned video generation task, as well as state-of-the-art results on established benchmarks for video prediction and unconditional video generation. Supplementary material is available at https://video-diffusion.github.io/"], "field": "Arts and Humanities", "q_year": 2024, "q_cid": "269772949", "pos_cid": 248006185, "source": "train_step3"}
{"query_id": "scaleup_26493543_24398598", "query": "How to achieve sample-efficient reinforcement learning and generalization to unseen objects in robotic manipulation with raw visual and tactile observations, beyond what either sense alone supports", "pos": ["Masked Autoencoders Are Scalable Vision Learners. This paper shows that masked autoencoders (MAE) are scalable self-supervised learners for computer vision. Our MAE approach is simple: we mask random patches of the input image and reconstruct the missing pixels. It is based on two core designs. First, we develop an asymmetric encoder-decoder architecture, with an encoder that operates only on the visible subset of patches (without mask tokens), along with a lightweight decoder that reconstructs the original image from the latent representation and mask tokens. Second, we find that masking a high proportion of the input image, e.g., 75%, yields a nontrivial and meaningful self-supervisory task. Coupling these two designs enables us to train large models efficiently and effectively: we accelerate training (by 3× or more) and improve accuracy. Our scalable approach allows for learning high-capacity models that generalize well: e.g., a vanilla ViT-Huge model achieves the best accuracy (87.8%) among methods that use only ImageNet-1K data. Transfer performance in downstream tasks outperforms supervised pretraining and shows promising scaling behavior."], "field": "Arts and Humanities", "q_year": 2023, "q_cid": "264935434", "pos_cid": 243985980, "source": "train_step3"}
{"query_id": "scaleup_25777080_19874280", "query": "How to determine whether children are progressing as expected in how they put words together in two languages when parents’ assessments differ and may be less favorable in one language than the other", "pos": ["Equitable Evaluation Of Bilingual Children's Language Knowledge Using the CDI. The parent report or rating instrument commonly known as the CDI is an effective and fast method for evaluating, among other things, young children’s early comprehension and production vocabulary. It is widely used with both monolingual and bilingual populations. However, when the CDI is used with bilingual populations, methodological issues arise as to how the instrument can best be employed so that the evaluation is as complete and equitable as possible. It is commonly agreed that children need to be evaluated in both their languages. Who should provide these dual language data is less clear, and there is little attention to how data should be evaluated. Based on a detailed case study, this article focuses on some of these issues, with particular consideration given to (1) the added value of engaging more than a single rater per language in CDI data collection, and (2) the way ratings are processed. Given appropriate methodological attention, the CDI can effectively screen young bilingual children for a possible language delay. The article ends with a proposal for how one could do so in clinical practice."], "field": "Arts and Humanities", "q_year": 2023, "q_cid": "257770802", "pos_cid": 198742802, "source": "train_step3"}
{"query_id": "scaleup_27951361_34787820", "query": "How to explain the relationship between losses of bodily agency, ownership, emotionality, thinking, self-reflection, and personal narrative and the overall absence of experiential content in profound disruptions of selfhood", "pos": ["Looking for the Self: Phenomenology, Neurophysiology and Philosophical Significance of Drug-induced Ego Dissolution. There is converging evidence that high doses of hallucinogenic drugs can produce significant alterations of self-experience, described as the dissolution of the sense of self and the loss of boundaries between self and world. This article discusses the relevance of this phenomenon, known as “drug-induced ego dissolution (DIED)”, for cognitive neuroscience, psychology and philosophy of mind. Data from self-report questionnaires suggest that three neuropharmacological classes of drugs can induce ego dissolution: classical psychedelics, dissociative anesthetics and agonists of the kappa opioid receptor (KOR). While these substances act on different neurotransmitter receptors, they all produce strong subjective effects that can be compared to the symptoms of acute psychosis, including ego dissolution. It has been suggested that neuroimaging of DIED can indirectly shed light on the neural correlates of the self. While this line of inquiry is promising, its results must be interpreted with caution. First, neural correlates of ego dissolution might reveal the necessary neurophysiological conditions for the maintenance of the sense of self, but it is more doubtful that this method can reveal its minimally sufficient conditions. Second, it is necessary to define the relevant notion of self at play in the phenomenon of DIED. This article suggests that DIED consists in the disruption of subpersonal processes underlying the “minimal” or “embodied” self, i.e., the basic experience of being a self rooted in multimodal integration of self-related stimuli. This hypothesis is consistent with Bayesian models of phenomenal selfhood, according to which the subjective structure of conscious experience ultimately results from the optimization of predictions in perception and action. Finally, it is argued that DIED is also of particular interest for philosophy of mind. On the one hand, it challenges theories according to which consciousness always involves self-awareness. On the other hand, it suggests that ordinary conscious experience might involve a minimal kind of self-awareness rooted in multisensory processing, which is what appears to fade away during DIED."], "field": "Arts and Humanities", "q_year": 2025, "q_cid": "279513614", "pos_cid": 34787820, "source": "train_step3"}
{"query_id": "scaleup_24972433_29729561", "query": "How to understand how students negotiate university learning spaces that suit their immediate needs as digital technologies shape their experiences beyond physical surroundings", "pos": ["No Dead Air! The iPod and the Culture of Mobile Listening. Abstract In this paper I investigate the manner in which Apple iPod users re‐inscribe their experiences of commuting through the use of music. I argue that the new technology of MP3 players gives users unprecedented power of control over their experience of time and space. They do so by managing their mood and orientation to space through the micro‐management of personalised music. The paper analyses iPod users’ management of daily urban experience through the use of empirical examples, locating the impulse to use mobile media such as the iPod in patterns of domestic media consumption. It draws upon a variety of urban and social theorists ranging from Sennett, Adorno and Lefebvre."], "field": "Arts and Humanities", "q_year": 2022, "q_cid": "249724330", "pos_cid": 29729561, "source": "train_step3"}
{"query_id": "scaleup_22693577_34754739", "query": "How to measure catalytic activity while tracking product formation and accounting for possible side products", "pos": ["Widespread occurrence of glyceryl ether monooxygenase activity in rat tissues detected by a novel assay. An assay was set up for glyceryl ether monooxygenase activity in tissue samples using the novel substrate 1-O-pyrenedecyl-sn-glycerol and high-performance liquid chromatographic analysis of reaction mixtures with fluorescence detection, allowing robust detection of enzymatic activity in microgram amounts of tissue homogenates. The activity partially purified from rat liver strictly depended on the presence of a tetrahydropteridine. Tetrahydrobiopterin-dependent glyceryl ether monooxygenase activity was observed in all rat tissues tested except female heart, with highest activities in liver, intestine, and cerebellum. Activity was not uniformly distributed in brain: it was higher in cerebellum than in striatum or cortex. These data demonstrate that tetrahydrobiopterin-dependent glyceryl ether monooxygenase is found not only in liver and the gastrointestinal tract but also in brain and other organs of the rat and provide an additional goal for tetrahydrobiopterin biosynthesis in these organs."], "field": "Biochemistry, Genetics and Molecular Biology", "q_year": 2010, "q_cid": "22693577", "pos_cid": 34754739, "source": "eval20x26"}
{"query_id": "scaleup_11065387_23177457", "query": "How to determine whether markers associated with yellow rind identify the locus responsible for rind color", "pos": ["A Kelch Domain-Containing F-Box Coding Gene Negatively Regulates Flavonoid Accumulation in Muskmelon1[OPEN]. Posttranscriptional regulation shifts the metabolic flux of flavonoids toward coumarin and general phenylpropanoids. The flavonoids are phenylpropanoid-derived metabolites that are ubiquitous in plants, playing many roles in growth and development. Recently, we observed that fruit rinds of yellow casaba muskmelons (Cucumis melo ‘Inodorous Group’) accumulate naringenin chalcone, a yellow flavonoid pigment. With RNA-sequencing analysis of bulked segregants representing the tails of a population segregating for naringenin chalcone accumulation followed by fine mapping and genetic transformation, we identified a Kelch domain-containing F-box protein coding (CmKFB) gene that, when expressed, negatively regulates naringenin chalcone accumulation. Additional metabolite analysis indicated that downstream flavonoids are accumulated together with naringenin chalcone, whereas CmKFB expression diverts the biochemical flux toward coumarins and general phenylpropanoids. These results show that CmKFB functions as a posttranscriptional regulator that diverts flavonoid metabolic flux."], "field": "Biochemistry, Genetics and Molecular Biology", "q_year": 2017, "q_cid": "11065387", "pos_cid": 23177457, "source": "eval20x26"}
{"query_id": "scaleup_83458994_17781757", "query": "How to distinguish the effects of individual proteins in nk cell-derived extracellular vesicles on cancer cells", "pos": ["Granzyme A activates another way to die. Summary: Granzyme A (GzmA) is the most abundant serine protease in killer cell cytotoxic granules. GzmA activates a novel programed cell death pathway that begins in the mitochondrion, where cleavage of NDUFS3 in electron transport complex I disrupts mitochondrial metabolism and generates reactive oxygen species (ROS). ROS drives the endoplasmic reticulum‐associated SET complex into the nucleus, where it activates single‐stranded DNA damage. GzmA also targets other important nuclear proteins for degradation, including histones, the lamins that maintain the nuclear envelope, and several key DNA damage repair proteins (Ku70, PARP‐1). Cells that are resistant to the caspases or GzmB by overexpressing bcl‐2 family anti‐apoptotic proteins or caspase or GzmB protease inhibitors are sensitive to GzmA. By activating multiple cell death pathways, killer cells provide better protection against a variety of intracellular pathogens and tumors. GzmA also has proinflammatory activity; it activates pro‐interleukin‐1β and may also have other proinflammatory effects that remain to be elucidated."], "field": "Biochemistry, Genetics and Molecular Biology", "q_year": 2019, "q_cid": "83458994", "pos_cid": 17781757, "source": "eval20x26"}
{"query_id": "scaleup_13172729_5891514", "query": "How to identify the molecular mediators of apoptosis in small cell carcinoma of the ovary, hypercalcemic type", "pos": ["EZH2 promotes E2F driven SCLC tumorigenesis through modulation of apoptosis and cell cycle regulation. Introduction: Although enhancer of zeste homolog 2 (EZH2) has been associated with both non-small cell and small-cell lung cancers (SCLCs), current observations suggest different mechanisms of EZH2 activation and overexpression in these lung cancer types. Globally, SCLC kills 200,000 people yearly. New clinical approaches for SCLC treatment are required to improve the poor survival rate. Given the therapeutic potential of EZH2 as a target, we sought to delineate the downstream consequences of EZH2 disruption to identify the cellular mechanisms by which EZH2 promotes tumorigenesis in SCLC. Methods: We generated cells with stable expression of short hairpin RNA targeting EZH2 and corresponding controls (pLKO.1) and determined the consequences of EZH2 knockdown on the cell cycle and apoptosis by means of propidium iodide staining and fluorescence-activated cell sorting, Western blot, quantitative reverse transcriptase-polymerase chain reaction as well as cell viability assessment using methylthiazol tetrazolium assays. Results: We discovered that EZH2 inhibition (1) increased apoptotic activity by up-regulating the proapoptotic factors Puma and Bad, (2) decreased the fraction of cells in S or G2/M phases, and (3) elevated p21 protein levels, implicating EZH2 in cell death and cell-cycle control in SCLC. Conclusion: Our findings present evidence for the role of EZH2 in the regulation of cell cycle and apoptosis, providing a biological mechanism to explain the tumorigenicity of EZH2 in SCLC. Our work points to the great potential of EZH2 as a therapeutic target in SCLC."], "field": "Biochemistry, Genetics and Molecular Biology", "q_year": 2017, "q_cid": "13172729", "pos_cid": 5891514, "source": "eval20x26"}
{"query_id": "scaleup_4405098_4390344", "query": "How to clarify how ptpn11 mutations in the bone marrow microenvironment disrupt cell dormancy and niche retention, worsen myeloproliferative disease, or promote disease in wild-type cells", "pos": ["Arteriolar niches maintain haematopoietic stem cell quiescence. Cell cycle quiescence is a critical feature contributing to haematopoietic stem cell (HSC) maintenance. Although various candidate stromal cells have been identified as potential HSC niches, the spatial localization of quiescent HSCs in the bone marrow remains unclear. Here, using a novel approach that combines whole-mount confocal immunofluorescence imaging techniques and computational modelling to analyse significant three-dimensional associations in the mouse bone marrow among vascular structures, stromal cells and HSCs, we show that quiescent HSCs associate specifically with small arterioles that are preferentially found in endosteal bone marrow. These arterioles are ensheathed exclusively by rare NG2 (also known as CSPG4)+ pericytes, distinct from sinusoid-associated leptin receptor (LEPR)+ cells. Pharmacological or genetic activation of the HSC cell cycle alters the distribution of HSCs from NG2+ periarteriolar niches to LEPR+ perisinusoidal niches. Conditional depletion of NG2+ cells induces HSC cycling and reduces functional long-term repopulating HSCs in the bone marrow. These results thus indicate that arteriolar niches are indispensable for maintaining HSC quiescence."], "field": "Biochemistry, Genetics and Molecular Biology", "q_year": 2016, "q_cid": "4405098", "pos_cid": 4390344, "source": "eval20x26"}
{"query_id": "scaleup_20109447_13278838", "query": "How to clarify the link between Rab23 signaling and cancer and whether primary cilia signaling contributes to this link", "pos": ["Dopamine receptors reveal an essential role of IFT-B, KIF17, and Rab23 in delivering specific receptors to primary cilia. Appropriate physiological signaling by primary cilia depends on the specific targeting of particular receptors to the ciliary membrane, but how this occurs remains poorly understood. In this study, we show that D1-type dopaminergic receptors are delivered to cilia from the extra-ciliary plasma membrane by a mechanism requiring the receptor cytoplasmic tail, the intraflagellar transport complex-B (IFT-B), and ciliary kinesin KIF17. This targeting mechanism critically depends on Rab23, a small guanine nucleotide binding protein that has important effects on physiological signaling from cilia but was not known previously to be essential for ciliary delivery of any cargo. Depleting Rab23 prevents dopamine receptors from accessing the ciliary membrane. Conversely, fusion of Rab23 to a non-ciliary receptor is sufficient to drive robust, nucleotide-dependent mis-localization to the ciliary membrane. Dopamine receptors thus reveal a previously unrecognized mechanism of ciliary receptor targeting and functional role of Rab23 in promoting this process. DOI: http://dx.doi.org/10.7554/eLife.06996.001"], "field": "Biochemistry, Genetics and Molecular Biology", "q_year": 2019, "q_cid": "201094476", "pos_cid": 13278838, "source": "eval20x26"}
{"query_id": "scaleup_3871126_1655544", "query": "How to determine whether ancient Bavarians and modern Dutch individuals show population continuity while accounting for recent population growth", "pos": ["Neutral genomic regions refine models of recent rapid human population growth. Significance Recent rapid growth of human populations predicts that a large number of genetic variants in populations today are very rare, i.e., appear in a small number of individuals. This effect is similar to that of purifying selection, which drives deleterious alleles to become rarer. Recent studies of the genetic signature left by rapid growth were confounded by purifying selection since they focused on genes. Here, to study recent human history with minimal confounding by selection, we sequenced and examined genetic variants far from genes. These data point to the human population size growing by about 3.4% per generation over the last 3,000–4,000 y, resulting in a greater than 100-fold increase in population size over that epoch. Human populations have experienced dramatic growth since the Neolithic revolution. Recent studies that sequenced a very large number of individuals observed an extreme excess of rare variants and provided clear evidence of recent rapid growth in effective population size, although estimates have varied greatly among studies. All these studies were based on protein-coding genes, in which variants are also impacted by natural selection. In this study, we introduce targeted sequencing data for studying recent human history with minimal confounding by natural selection. We sequenced loci far from genes that meet a wide array of additional criteria such that mutations in these loci are putatively neutral. As population structure also skews allele frequencies, we sequenced 500 individuals of relatively homogeneous ancestry by first analyzing the population structure of 9,716 European Americans. We used very high coverage sequencing to reliably call rare variants and fit an extensive array of models of recent European demographic history to the site frequency spectrum. The best-fit model estimates ∼3.4% growth per generation during the last ∼140 generations, resulting in a population size increase of two orders of magnitude. This model fits the data very well, largely due to our observation that assumptions of more ancient demography can impact estimates of recent growth. This observation and results also shed light on the discrepancy in demographic estimates among recent studies."], "field": "Biochemistry, Genetics and Molecular Biology", "q_year": 2018, "q_cid": "3871126", "pos_cid": 1655544, "source": "eval20x26"}
{"query_id": "scaleup_14090759_7730587", "query": "How to explain cationic amphiphilic drug–induced detachment of curved membrane structures from the cell surface", "pos": ["The BAR Domain Superfamily: Membrane-Molding Macromolecules. Membrane-shaping proteins of the BAR domain superfamily are determinants of organelle biogenesis, membrane trafficking, cell division, and cell migration. An upsurge of research now reveals new principles of BAR domain-mediated membrane remodeling, enhancing our understanding of membrane curvature-mediated information processing."], "field": "Biochemistry, Genetics and Molecular Biology", "q_year": 2016, "q_cid": "14090759", "pos_cid": 7730587, "source": "eval20x26"}
{"query_id": "scaleup_3871126_6461795", "query": "How to determine the geographic origins of ancient individuals relative to multiple potential modern source populations despite substantial variation", "pos": ["Inference of Population Structure using Dense Haplotype Data. The advent of genome-wide dense variation data provides an opportunity to investigate ancestry in unprecedented detail, but presents new statistical challenges. We propose a novel inference framework that aims to efficiently capture information on population structure provided by patterns of haplotype similarity. Each individual in a sample is considered in turn as a recipient, whose chromosomes are reconstructed using chunks of DNA donated by the other individuals. Results of this “chromosome painting” can be summarized as a “coancestry matrix,” which directly reveals key information about ancestral relationships among individuals. If markers are viewed as independent, we show that this matrix almost completely captures the information used by both standard Principal Components Analysis (PCA) and model-based approaches such as STRUCTURE in a unified manner. Furthermore, when markers are in linkage disequilibrium, the matrix combines information across successive markers to increase the ability to discern fine-scale population structure using PCA. In parallel, we have developed an efficient model-based approach to identify discrete populations using this matrix, which offers advantages over PCA in terms of interpretability and over existing clustering algorithms in terms of speed, number of separable populations, and sensitivity to subtle population structure. We analyse Human Genome Diversity Panel data for 938 individuals and 641,000 markers, and we identify 226 populations reflecting differences on continental, regional, local, and family scales. We present multiple lines of evidence that, while many methods capture similar information among strongly differentiated groups, more subtle population structure in human populations is consistently present at a much finer level than currently available geographic labels and is only captured by the haplotype-based approach. The software used for this article, ChromoPainter and fineSTRUCTURE, is available from http://www.paintmychromosomes.com/."], "field": "Biochemistry, Genetics and Molecular Biology", "q_year": 2018, "q_cid": "3871126", "pos_cid": 6461795, "source": "eval20x26"}
{"query_id": "scaleup_53285_12129320", "query": "How to determine whether BARD1 isoforms promote tumorigenesis and cancer cell proliferation in colon cancer and how their functions relate to full-length BARD1", "pos": ["Common Variation at BARD1 Results in the Expression of an Oncogenic Isoform that Influences Neuroblastoma Susceptibility and Oncogenicity. The mechanisms underlying genetic susceptibility at loci discovered by genome-wide association study (GWAS) approaches in human cancer remain largely undefined. In this study we characterized the high-risk neuroblastoma association at the BRCA1-related locus, BARD1, showing that disease-associated variations correlate with increased expression of the oncogenically activated isoform, BARD1β. In neuroblastoma cells, silencing of BARD1β showed genotype-specific cytotoxic effects, including decreased substrate-adherent, anchorage-independent, and foci growth. In established murine fibroblasts, overexpression of BARD1β was sufficient for neoplastic transformation. BARD1β stabilized the Aurora family of kinases in neuroblastoma cells, suggesting both a mechanism for the observed effect and a potential therapeutic strategy. Together, our findings identify BARD1β as an oncogenic driver of high-risk neuroblastoma tumorigenesis, and more generally, they illustrate how robust GWAS signals offer genomic landmarks to identify molecular mechanisms involved in both tumor initiation and malignant progression. The interaction of BARD1β with the Aurora family of kinases lends strong support to the ongoing work to develop Aurora kinase inhibitors for clinically aggressive neuroblastoma."], "field": "Biochemistry, Genetics and Molecular Biology", "q_year": 2012, "q_cid": "53285", "pos_cid": 12129320, "source": "eval20x26"}
{"query_id": "scaleup_20109447_46897925", "query": "How to clarify the role of neurodegeneration-associated LRRK2 in phagosome maturation and innate immune defenses", "pos": ["LRRK2 is a negative regulator of Mycobacterium tuberculosis phagosome maturation in macrophages. Mutations in the leucine‐rich repeat kinase 2 (LRRK2) are associated with Parkinson's disease, chronic inflammation and mycobacterial infections. Although there is evidence supporting the idea that LRRK2 has an immune function, the cellular function of this kinase is still largely unknown. By using genetic, pharmacological and proteomics approaches, we show that LRRK2 kinase activity negatively regulates phagosome maturation via the recruitment of the Class III phosphatidylinositol‐3 kinase complex and Rubicon to the phagosome in macrophages. Moreover, inhibition of LRRK2 kinase activity in mouse and human macrophages enhanced Mycobacterium tuberculosis phagosome maturation and mycobacterial control independently of autophagy. In vivo, LRRK2 deficiency in mice resulted in a significant decrease in M. tuberculosis burdens early during the infection. Collectively, our findings provide a molecular mechanism explaining genetic evidence linking LRRK2 to mycobacterial diseases and establish an LRRK2‐dependent cellular pathway that controls M. tuberculosis replication by regulating phagosome maturation."], "field": "Biochemistry, Genetics and Molecular Biology", "q_year": 2019, "q_cid": "201094476", "pos_cid": 46897925, "source": "eval20x26"}
{"query_id": "scaleup_28513733_28022000", "query": "How to determine how phosphate-binding loop conformations affect active-site hydration energetics and how these differences relate to catalytic cysteine ionization and the enzyme’s active or inactive state", "pos": ["Quantifying Spatially Resolved Hydration Thermodynamics Using Grid Inhomogeneous Solvation Theory [Article v1.0]. Grid Inhomogeneous Solvation Theory (GIST) is a method to compute the free energy of solvation of a solute molecule on a three-dimensional grid based on sampling from molecular dynamics (MD) simulations. The high spatial resolution of the GIST output, as well as the decomposition into energy and entropy contributions, allow for highly detailed analyses of solvation around both proteins and small molecules. However, this versatility also comes with a significant entry barrier for new users. In this tutorial, we aim to guide the reader through the most common steps involved in a GIST analysis using the streptavidin-biotin complex as a demonstrative system. To this end, Jupyter notebooks and a Python package (gisttools) are provided to simplify the analysis. Furthermore, we discuss the theory of GIST with a focus on practical aspects. We highlight potential pitfalls and provide strategies to avoid technical difficulties. This tutorial assumes familiarity with molecular dynamics simulations and the AmberTools package."], "field": "Biochemistry, Genetics and Molecular Biology", "q_year": 2025, "q_cid": "285137334", "pos_cid": 280220004, "source": "eval_collection"}
{"query_id": "scaleup_24533416_15398307", "query": "How to distinguish genuine microbial colonization in fetal sheep samples from control contamination", "pos": ["Large-scale contamination of microbial isolate genomes by Illumina PhiX control. With the rapid growth and development of sequencing technologies, genomes have become the new go-to for exploring solutions to some of the world’s biggest challenges such as searching for alternative energy sources and exploration of genomic dark matter. However, progress in sequencing has been accompanied by its share of errors that can occur during template or library preparation, sequencing, imaging or data analysis. In this study we screened over 18,000 publicly available microbial isolate genome sequences in the Integrated Microbial Genomes database and identified more than 1000 genomes that are contaminated with PhiX, a control frequently used during Illumina sequencing runs. Approximately 10% of these genomes have been published in literature and 129 contaminated genomes were sequenced under the Human Microbiome Project. Raw sequence reads are prone to contamination from various sources and are usually eliminated during downstream quality control steps. Detection of PhiX contaminated genomes indicates a lapse in either the application or effectiveness of proper quality control measures. The presence of PhiX contamination in several publicly available isolate genomes can result in additional errors when such data are used in comparative genomics analyses. Such contamination of public databases have far-reaching consequences in the form of erroneous data interpretation and analyses, and necessitates better measures to proofread raw sequences before releasing them to the broader scientific community."], "field": "Biochemistry, Genetics and Molecular Biology", "q_year": 2021, "q_cid": "245334161", "pos_cid": 15398307, "source": "eval_collection"}
{"query_id": "scaleup_25325952_1438097", "query": "How to identify proteins that directly bind BTBD7_hsa_circ_0000563 with sensitivity and specificity to clarify its possible role in coronary artery disease", "pos": ["Systematic discovery of Xist RNA binding proteins. Summary Noncoding RNAs (ncRNAs) function with associated proteins to effect complex structural and regulatory outcomes. To reveal the composition and dynamics of specific noncoding RNA- protein complexes (RNPs) in vivo, we developed comprehensive identification of RNA-binding proteins by mass spectrometry (ChIRP-MS). ChIRP-MS analysis of four ncRNAs captures key protein interactors, including a U1-specific link to the 3′ RNA processing machinery. Xist, an essential lncRNA for X-chromosome inactivation (XCI), interacts with 81 proteins from chromatin modification, nuclear matrix, and RNA remodeling pathways. The Xist RNA-protein particle assembles in two steps coupled with the transition from pluripotency to differentiation. Specific interactors include HnrnpK that participates in Xist-mediated gene silencing and histone modifications, but not Xist localization and Drosophila Split ends homolog Spen that interacts via the A-repeat domain of Xist and is required for gene silencing. Thus, Xist lncRNA engages with proteins in a modular and developmentally controlled manner to coordinate chromatin spreading and silencing."], "field": "Biochemistry, Genetics and Molecular Biology", "q_year": 2022, "q_cid": "253259522", "pos_cid": 1438097, "source": "eval_collection"}
{"query_id": "scaleup_28513733_25785569", "query": "How to reliably compare catalytic cysteine acidity across protein tyrosine phosphatases to understand differences in oxidation susceptibility despite high computational costs, large prediction errors, and interacting effects of the protein environment", "pos": ["Benchmarking In Silico Tools for Cysteine pKa Prediction. Accurate estimation of the pKa's of cysteine residues in proteins could inform targeted approaches in hit discovery. The pKa of a targetable cysteine residue in a disease-related protein is an important physiochemical parameter in covalent drug discovery, as it influences the fraction of nucleophilic thiolate amenable to chemical protein modification. Traditional structure-based in silico tools are limited in their predictive accuracy of cysteine pKa's relative to other titratable residues. Additionally, there are limited comprehensive benchmark assessments for cysteine pKa predictive tools. This raises the need for extensive assessment and evaluation of methods for cysteine pKa prediction. Here, we report the performance of several computational pKa methods, including single-structure and ensemble-based approaches, on a diverse test set of experimental cysteine pKa's retrieved from the PKAD database. The dataset consisted of 16 wildtype and 10 mutant proteins with experimentally measured cysteine pKa values. Our results highlight that these methods are varied in their overall predictive accuracies. Among the test set of wildtype proteins evaluated, the best method (MOE) yielded a mean absolute error of 2.3 pK units, highlighting the need for improvement of existing pKa methods for accurate cysteine pKa estimation. Given the limited accuracy of these methods, further development is needed before these approaches can be routinely employed to drive design decisions in early drug discovery efforts."], "field": "Biochemistry, Genetics and Molecular Biology", "q_year": 2025, "q_cid": "285137334", "pos_cid": 257855693, "source": "eval_collection"}
{"query_id": "scaleup_23571517_71289101", "query": "How to reduce uncertainty about whether findings on marine alkaloids will translate to human clinical trials", "pos": ["Animal models in translational medicine: Validation and prediction. Despite large investments in drug development, the overall success rate of drugs during clinical development remains low. One prominent explanation is flawed preclinical research, in which the use and outcome of animal models is pivotal to bridge the translational gap to the clinic. Therefore, the selection of a validated and predictive animal model is essential to address the clinical question. In this review, the current challenges and limitations of animal models are discussed, with a focus on the fit-for-purpose validation. Moreover, guidance is provided on the selection, design and conduct of an animal model, including the recommendation of assessing both efficacy and safety endpoints. In order to improve the clinical translation, the use of humanized mouse models and preclinical applications of clinical features are discussed. On top, the translational value of animal models could be further enhanced when combined with emerging alternative translational approaches. Focal points: • Bedside Animal models are essential for translation of drug findings from bench to bedside. Hence, critical evaluation of the face and predictive validity of these models is important. Reversely, clinical bedside findings that were not predicted by animal testing should be back translated and used to refine the animal models. • Benchside Proper design, execution and reporting of animal model results help to make preclinical data more reproducible and translatable to the clinic. • Industry Design of an animal model strategy is part of the translational plan rather than (a) single experiment(s). Data from animal models are essential in predicting the clinical outcome for a specific drug in development. • Community Review, standardization and refinement of animal models by disease expert groups helps to improve rigor of animal model testing. It is important that the applied animal models are validated fit-for-purpose according to stringent criteria and reproducible. • Governments As during drug development fit-for-purpose animal models are key for success in clinical translation, financial investments and support from the government to develop, optimize, validate and run such translation tools are important. Over time, this will be of benefit for patients and healthcare institutions. • Regulatory agencies Preclinical testing of a drug in an animal model is not a prerequisite for regulatory agencies before entering clinical trials, but does unquestionably provide valuable data on the expected clinical performance of the drug. Hence, testing in animal models is largely recommended from both a business and patient perspective. In addition, inclusion of safety parameters in animal models will help to build the required safety data package of drugs in development."], "field": "Biochemistry, Genetics and Molecular Biology", "q_year": 2021, "q_cid": "235715178", "pos_cid": 71289101, "source": "eval_collection"}
{"query_id": "scaleup_27121556_4359205", "query": "How to identify targets for brain rejuvenation that address age-related impairments in hippocampal synaptic plasticity and cognition", "pos": ["A novel pathway regulates memory and plasticity via SIRT1 and miR-134. The NAD-dependent deacetylase Sir2 was initially identified as a mediator of replicative lifespan in budding yeast and was subsequently shown to modulate longevity in worms and flies. Its mammalian homologue, SIRT1, seems to have evolved complex systemic roles in cardiac function, DNA repair and genomic stability. Recent studies suggest a functional relevance of SIRT1 in normal brain physiology and neurological disorders. However, it is unknown if SIRT1 has a role in higher-order brain functions. We report that SIRT1 modulates synaptic plasticity and memory formation via a microRNA-mediated mechanism. Activation of SIRT1 enhances, whereas its loss-of-function impairs, synaptic plasticity. Surprisingly, these effects were mediated via post-transcriptional regulation of cAMP response binding protein (CREB) expression by a brain-specific microRNA, miR-134. SIRT1 normally functions to limit expression of miR-134 via a repressor complex containing the transcription factor YY1, and unchecked miR-134 expression following SIRT1 deficiency results in the downregulated expression of CREB and brain-derived neurotrophic factor (BDNF), thereby impairing synaptic plasticity. These findings demonstrate a new role for SIRT1 in cognition and a previously unknown microRNA-based mechanism by which SIRT1 regulates these processes. Furthermore, these results describe a separate branch of SIRT1 signalling, in which SIRT1 has a direct role in regulating normal brain function in a manner that is disparate from its cell survival functions, demonstrating its value as a potential therapeutic target for the treatment of central nervous system disorders."], "field": "Biochemistry, Genetics and Molecular Biology", "q_year": 2024, "q_cid": "271215564", "pos_cid": 4359205, "source": "eval_collection"}
{"query_id": "scaleup_26430392_1592684", "query": "How to clarify what regulates collagen breakdown and scarring in aged lungs during influenza infection and whether factors implicated in kidney scarring have comparable roles in the lung", "pos": ["Identification of Human Epididymis Protein-4 as a Novel Fibroblast-Derived Mediator of Fibrosis. The functional contribution of myofibroblasts in fibrosis is not well understood. Using a new genetic mouse model to track and isolate myofibroblasts, we performed gene expression profiling followed by biological validation to identify HE4 (encoding human epididymis protein 4, also known as WAP 4-disulfide core domain-2 or Wfdc2) as the most upregulated gene in fibrosis-associated myofibroblasts. The HE4 gene encodes for a putative serine protease inhibitor that is upregulated in human and mouse fibrotic kidneys and is elevated in the serum of patients with kidney fibrosis. HE4 suppresses the activity of multiple proteases, including serine proteases and matrix metalloproteinases, and specifically inhibits their capacity to degrade type I collagen. In particular, we identified two serine proteases, Prss35 and Prss23, as HE4 targets with functional relevance in kidney fibrosis. Administration of HE4-neutralizing antibodies accelerated collagen I degradation and inhibited fibrosis in three different mouse models of renal disease. Collectively these studies suggest that HE4 is a potential biomarker of renal fibrosis and a new therapeutic target."], "field": "Biochemistry, Genetics and Molecular Biology", "q_year": 2023, "q_cid": "264303924", "pos_cid": 1592684, "source": "eval_collection"}
{"query_id": "scaleup_27412783_20200767", "query": "How to meet UniProt’s required evidence standard for reliably verifying the existence of individual proteins", "pos": ["Human Proteome Project Mass Spectrometry Data Interpretation Guidelines 3.0. The Human Proteome Organization’s (HUPO) Human Proteome Project (HPP) developed Mass Spectrometry (MS) Data Interpretation Guidelines that have been applied since 2016. These guidelines have helped ensure that the emerging draft of the complete human proteome is highly accurate and with low numbers of false-positive protein identifications. Here, we describe an update to these guidelines based on consensus-reaching discussions with the wider HPP community over the past year. The revised 3.0 guidelines address several major and minor identified gaps. We have added guidelines for emerging data independent acquisition (DIA) MS workflows and for use of the new Universal Spectrum Identifier (USI) system being developed by the HUPO Proteomics Standards Initiative (PSI). In addition, we discuss updates to the standard HPP pipeline for collecting MS evidence for all proteins in the HPP, including refinements to minimum evidence. We present a new plan for incorporating MassIVE-KB into the HPP pipeline for the next (HPP 2020) cycle in order to obtain more comprehensive coverage of public MS data sets. The main checklist has been reorganized under headings and subitems and related guidelines have been grouped. In sum, Version 2.1 of the HPP MS Data Interpretation Guidelines has served well and this timely update to version 3.0 will aid the HPP as it approaches its goal of collecting and curating MS evidence of translation and expression for all predicted ∼20,000 human proteins encoded by the human genome."], "field": "Biochemistry, Genetics and Molecular Biology", "q_year": 2024, "q_cid": "274127839", "pos_cid": 202007672, "source": "eval_collection"}
{"query_id": "scaleup_28028436_11065420", "query": "How to select an optimal subset of approximately a desired number of hybrids while accounting for differences among them", "pos": ["Dissimilarity-Based Sparse Subset Selection. Finding an informative subset of a large collection of data points or models is at the center of many problems in computer vision, recommender systems, bio/health informatics as well as image and natural language processing. Given pairwise dissimilarities between the elements of a `source set' and a `target set,' we consider the problem of finding a subset of the source set, called representatives or exemplars, that can efficiently describe the target set. We formulate the problem as a row-sparsity regularized trace minimization problem. Since the proposed formulation is, in general, NP-hard, we consider a convex relaxation. The solution of our optimization finds representatives and the assignment of each element of the target set to each representative, hence, obtaining a clustering. We analyze the solution of our proposed optimization as a function of the regularization parameter. We show that when the two sets jointly partition into multiple groups, our algorithm finds representatives from all groups and reveals clustering of the sets. In addition, we show that the proposed framework can effectively deal with outliers. Our algorithm works with arbitrary dissimilarities, which can be asymmetric or violate the triangle inequality. To efficiently implement our algorithm, we consider an Alternating Direction Method of Multipliers (ADMM) framework, which results in quadratic complexity in the problem size. We show that the ADMM implementation allows to parallelize the algorithm, hence further reducing the computational time. Finally, by experiments on real-world datasets, we show that our proposed algorithm improves the state of the art on the two problems of scene categorization using representative images and time-series modeling and segmentation using representative models."], "field": "Biochemistry, Genetics and Molecular Biology", "q_year": 2025, "q_cid": "280284364", "pos_cid": 11065420, "source": "eval_collection"}
{"query_id": "scaleup_23730869_21564657", "query": "How to determine how enterococcal peptidoglycan fragments affect host immune signaling and which sensing pathways are required for improved checkpoint inhibitor responses", "pos": ["NOD1 and NOD2: Signaling, Host Defense, and Inflammatory Disease. Summary The nucleotide-binding oligomerization domain (NOD) proteins, NOD1 and NOD2, the founding members of the intracellular NOD-like receptor family, sense conserved motifs in bacterial peptidoglycan and induce pro-inflammatory and anti-microbial responses. Here we discuss recent developments about the mechanisms by which NOD1 and NOD2 are activated by bacterial ligands, the regulation of their signaling pathways, and their role in host defense and inflammatory disease. Several routes for the entry of peptidoglycan ligands to the host cytosol to trigger activation of NOD1 and NOD2 have been elucidated. Furthermore, genetic screens and biochemical analyses have revealed mechanisms that regulate NOD1 and NOD2 signaling. Finally, recent studies suggest several mechanisms to account for the link between NOD2 mutations and susceptibility to Crohn’s disease. Further understanding of NOD1 and NOD2 should provide new insight into the pathogenesis of disease and the development of new strategies to treat inflammatory and infectious disorders."], "field": "Biochemistry, Genetics and Molecular Biology", "q_year": 2021, "q_cid": "237308692", "pos_cid": 21564657, "source": "eval_collection"}
{"query_id": "scaleup_23374222_20723898", "query": "How to learn informative term embeddings that preserve neighborhood relationships and broader structure when different sources encode different relationships among terms", "pos": ["node2vec: Scalable Feature Learning for Networks. Prediction tasks over nodes and edges in networks require careful effort in engineering features used by learning algorithms. Recent research in the broader field of representation learning has led to significant progress in automating prediction by learning the features themselves. However, present feature learning approaches are not expressive enough to capture the diversity of connectivity patterns observed in networks. Here we propose node2vec, an algorithmic framework for learning continuous feature representations for nodes in networks. In node2vec, we learn a mapping of nodes to a low-dimensional space of features that maximizes the likelihood of preserving network neighborhoods of nodes. We define a flexible notion of a node's network neighborhood and design a biased random walk procedure, which efficiently explores diverse neighborhoods. Our algorithm generalizes prior work which is based on rigid notions of network neighborhoods, and we argue that the added flexibility in exploring neighborhoods is the key to learning richer representations. We demonstrate the efficacy of node2vec over existing state-of-the-art techniques on multi-label classification and link prediction in several real-world networks from diverse domains. Taken together, our work represents a new way for efficiently learning state-of-the-art task-independent representations in complex networks."], "field": "Biochemistry, Genetics and Molecular Biology", "q_year": 2021, "q_cid": "233742223", "pos_cid": 207238980, "source": "eval_collection"}
{"query_id": "scaleup_27687100_14602729", "query": "How to enhance phenolic production in P. graveolens callus cultures to strengthen antioxidant and skin-protective activity", "pos": ["Salicylic Acid–Mediated Defense Mechanisms to Abiotic Stress Tolerance. Abstract In the current era due to climate change plants are facing multitudinous environmental challenges from seeding to maturity stages. Salicylic acid (SA) is a phenolic compound involved in the regulation of growth and development of plants, and their responses to abiotic stress factors. SA is linked with regulation of dynamic physiological responses such as photosynthesis, nitrogen, and proline metabolism; introduction of cell reinforcement protection framework (antioxidant defense system); and plant–water associations under stress environments, and hence delivers operative defense in plants contrary to stress. SA has been known to improve tolerance to major abiotic stresses such as salinity, drought, osmotic, metal, heat and chilling, and radiation stress. Modern molecular research has illustrated that SA is a key regulator in controlling numerous physiognomies in plants at the gene level. SA was recounted to stimulate number of genes accountable for encoding chaperone, heat shock proteins (HSPs), antioxidants, and secondary metabolites sinapyl alcohol dehydrogenase (SAD), cinnamyl alcohol dehydrogenase (CAD), and cytochrome P450. Furthermore, SA contribution in mitogen activated protein kinase (MAPK) modulation has also been researched. Nonetheless, the transcriptional reprogramming that takes place through defense action counter to abiotic strain was reported to be controlled by SA, where the transcription factors of diverse arrays of defensive genes can be meticulous in a spatiotemporal manner via SA mediated mechanisms. In previous study, interaction of phytohormone such as abscisic acid, jasmonic acid, ethylene, and SA have been researched in signaling pathways involved in different plant defense mechanisms. This chapter summarizes the potential and prospective role of the SA in defense mechanisms for the improvement of plant resistance against abiotic stresses."], "field": "Biochemistry, Genetics and Molecular Biology", "q_year": 2025, "q_cid": "276871001", "pos_cid": 146027290, "source": "eval_collection"}
{"query_id": "scaleup_25921097_4402788", "query": "How to clarify ancestral monocot chromosome organization and the changes shaping the Acorus karyotype to place its complex genome history within broader monocot evolution", "pos": ["Oil palm genome sequence reveals divergence of interfertile species in old and new worlds. Oil palm is the most productive oil-bearing crop. Although it is planted on only 5% of the total world vegetable oil acreage, palm oil accounts for 33% of vegetable oil and 45% of edible oil worldwide, but increased cultivation competes with dwindling rainforest reserves. We report the 1.8-gigabase (Gb) genome sequence of the African oil palm Elaeis guineensis, the predominant source of worldwide oil production. A total of 1.535 Gb of assembled sequence and transcriptome data from 30 tissue types were used to predict at least 34,802 genes, including oil biosynthesis genes and homologues of WRINKLED1 (WRI1), and other transcriptional regulators, which are highly expressed in the kernel. We also report the draft sequence of the South American oil palm Elaeis oleifera, which has the same number of chromosomes (2n = 32) and produces fertile interspecific hybrids with E. guineensis but seems to have diverged in the New World. Segmental duplications of chromosome arms define the palaeotetraploid origin of palm trees. The oil palm sequence enables the discovery of genes for important traits as well as somaclonal epigenetic alterations that restrict the use of clones in commercial plantings, and should therefore help to achieve sustainability for biofuels and edible oils, reducing the rainforest footprint of this tropical plantation crop."], "field": "Biochemistry, Genetics and Molecular Biology", "q_year": 2023, "q_cid": "259210972", "pos_cid": 4402788, "source": "eval_collection"}
{"query_id": "scaleup_28513733_20021955", "query": "How to determine whether the oxidation susceptibility of protein tyrosine phosphatase active-site cysteines is an incidental chemical vulnerability or reflects a broader catalytic capacity for redox chemistry", "pos": ["Adventitious Arsenate Reductase Activity of the Catalytic Domain of the Human Cdc25B and Cdc25C Phosphatases. A number of eukaryotic enzymes that function as arsenate reductases are homologues of the catalytic domain of the human Cdc25 phosphatase. For example, the Leishmania major enzyme LmACR2 is both a phosphatase and an arsenate reductase, and its structure bears similarity to the structure of the catalytic domain of human Cdc25 phosphatase. These reductases contain an active site C-X5-R signature motif, where C is the catalytic cysteine, the five X residues form a phosphate binding loop, and R is a highly conserved arginine, which is also present in human Cdc25 phosphatases. We therefore investigated the possibility that the three human Cdc25 isoforms might have adventitious arsenate reductase activity. The sequences for the catalytic domains of Cdc25A, -B, and -C were cloned individually into a prokaryotic expression vector, and their gene products were purified from a bacterial host using nickel affinity chromatography. While each of the three Cdc25 catalytic domains exhibited phosphatase activity, arsenate reductase activity was observed only with Cdc25B and -C. These two enzymes reduced inorganic arsenate but not methylated pentavalent arsenicals. Alteration of either the cysteine and arginine residues of the Cys-X5-Arg motif led to the loss of both reductase and phosphatase activities. Our observations suggest that Cdc25B and -C may adventitiously reduce arsenate to the more toxic arsenite and may also provide a framework for identifying other human protein tyrosine phosphatases containing the active site Cys-X5-Arg loop that might moonlight as arsenate reductases."], "field": "Biochemistry, Genetics and Molecular Biology", "q_year": 2025, "q_cid": "285137334", "pos_cid": 20021955, "source": "eval_collection"}
{"query_id": "scaleup_28125905_13752891", "query": "How to validate whether predicted FGFR1 inhibitor binding geometries match experimentally observed binding geometries", "pos": ["Is It Reliable to Take the Molecular Docking Top Scoring Position as the Best Solution without Considering Available Structural Data?. Molecular docking is the most frequently used computational method for studying the interactions between organic molecules and biological macromolecules. In this context, docking allows predicting the preferred pose of a ligand inside a receptor binding site. However, the selection of the “best” solution is not a trivial task, despite the widely accepted selection criterion that the best pose corresponds to the best energy score. Here, several rigid-target docking methods were evaluated on the same dataset with respect to their ability to reproduce crystallographic binding orientations, to test if the best energy score is a reliable criterion for selecting the best solution. For this, two experiments were performed: (A) to reconstruct the ligand-receptor complex by performing docking of the ligand in its own crystal structure receptor (defined as self-docking), and (B) to reconstruct the ligand-receptor complex by performing docking of the ligand in a crystal structure receptor that contains other ligand (defined as cross-docking). Root-mean square deviation (RMSD) was used to evaluate how different the obtained docking orientation is from the corresponding co-crystallized pose of the same ligand molecule. We found that docking score function is capable of predicting crystallographic binding orientations, but the best ranked solution according to the docking energy is not always the pose that reproduces the experimental binding orientation. This happened when self-docking was achieved, but it was critical in cross-docking. Taking into account that docking is typically used with predictive purposes, during cross-docking experiments, our results indicate that the best energy score is not a reliable criterion to select the best solution in common docking applications. It is strongly recommended to choose the best docking solution according to the scoring function along with additional structural criteria described for analogue ligands to assure the selection of a correct docking solution."], "field": "Biochemistry, Genetics and Molecular Biology", "q_year": 2025, "q_cid": "281259053", "pos_cid": 13752891, "source": "eval_collection"}
{"query_id": "scaleup_24504207_13926751", "query": "How to determine whether loss of specific alleles is associated with poor response to breast cancer therapy independently of genome-wide loss of heterozygosity and copy-number instability", "pos": ["Allele-Specific HLA Loss and Immune Escape in Lung Cancer Evolution. Summary Immune evasion is a hallmark of cancer. Losing the ability to present neoantigens through human leukocyte antigen (HLA) loss may facilitate immune evasion. However, the polymorphic nature of the locus has precluded accurate HLA copy-number analysis. Here, we present loss of heterozygosity in human leukocyte antigen (LOHHLA), a computational tool to determine HLA allele-specific copy number from sequencing data. Using LOHHLA, we find that HLA LOH occurs in 40% of non-small-cell lung cancers (NSCLCs) and is associated with a high subclonal neoantigen burden, APOBEC-mediated mutagenesis, upregulation of cytolytic activity, and PD-L1 positivity. The focal nature of HLA LOH alterations, their subclonal frequencies, enrichment in metastatic sites, and occurrence as parallel events suggests that HLA LOH is an immune escape mechanism that is subject to strong microenvironmental selection pressures later in tumor evolution. Characterizing HLA LOH with LOHHLA refines neoantigen prediction and may have implications for our understanding of resistance mechanisms and immunotherapeutic approaches targeting neoantigens. Video Abstract"], "field": "Biochemistry, Genetics and Molecular Biology", "q_year": 2021, "q_cid": "245042076", "pos_cid": 13926751, "source": "eval_collection"}
{"query_id": "scaleup_28028436_51912402", "query": "How to jointly understand hybrids, genes, and their relationships to identify regulatory genes and select desirable hybrids while meeting interactivity requirements and preserving neighborhood relationships", "pos": ["SIRIUS: Dual, Symmetric, Interactive Dimension Reductions. Much research has been done regarding how to visualize and interact with observations and attributes of high-dimensional data for exploratory data analysis. From the analyst's perceptual and cognitive perspective, current visualization approaches typically treat the observations of the high-dimensional dataset very differently from the attributes. Often, the attributes are treated as inputs (e.g., sliders), and observations as outputs (e.g., projection plots), thus emphasizing investigation of the observations. However, there are many cases in which analysts wish to investigate both the observations and the attributes of the dataset, suggesting a symmetry between how analysts think about attributes and observations. To address this, we define SIRIUS (Symmetric Interactive Representations In a Unified System), a symmetric, dual projection technique to support exploratory data analysis of high-dimensional data. We provide an example implementation of SIRIUS and demonstrate how this symmetry affords additional insights."], "field": "Biochemistry, Genetics and Molecular Biology", "q_year": 2025, "q_cid": "280284364", "pos_cid": 51912402, "source": "eval_collection"}
{"query_id": "scaleup_27412783_5739389", "query": "How to expand reliable functional annotation coverage for unreviewed UniProtKB entries of unstudied proteins", "pos": ["RefSeq: an update on prokaryotic genome annotation and curation. Abstract The Reference Sequence (RefSeq) project at the National Center for Biotechnology Information (NCBI) provides annotation for over 95 000 prokaryotic genomes that meet standards for sequence quality, completeness, and freedom from contamination. Genomes are annotated by a single Prokaryotic Genome Annotation Pipeline (PGAP) to provide users with a resource that is as consistent and accurate as possible. Notable recent changes include the development of a hierarchical evidence scheme, a new focus on curating annotation evidence sources, the addition and curation of protein profile hidden Markov models (HMMs), release of an updated pipeline (PGAP-4), and comprehensive re-annotation of RefSeq prokaryotic genomes. Antimicrobial resistance proteins have been reannotated comprehensively, improved structural annotation of insertion sequence transposases and selenoproteins is provided, curated complex domain architectures have given upgraded names to millions of multidomain proteins, and we introduce a new kind of annotation rule—BlastRules. Continual curation of supporting evidence, and propagation of improved names onto RefSeq proteins ensures that the functional annotation of genomes is kept current. An increasing share of our annotation now derives from HMMs and other sets of annotation rules that are portable by nature, and available for download and for reuse by other investigators. RefSeq is found at https://www.ncbi.nlm.nih.gov/refseq/."], "field": "Biochemistry, Genetics and Molecular Biology", "q_year": 2024, "q_cid": "274127839", "pos_cid": 5739389, "source": "eval_collection"}
{"query_id": "scaleup_25921097_22604305", "query": "How to assign each of the 22 chromosomes in tetraploid Ac. calamus to one of its two homoeologous subgenomes", "pos": ["Genome biology of the paleotetraploid perennial biomass crop Miscanthus. Miscanthus is a perennial wild grass that is of global importance for paper production, roofing, horticultural plantings, and an emerging highly productive temperate biomass crop. We report a chromosome-scale assembly of the paleotetraploid M. sinensis genome, providing a resource for Miscanthus that links its chromosomes to the related diploid Sorghum and complex polyploid sugarcanes. The asymmetric distribution of transposons across the two homoeologous subgenomes proves Miscanthus paleo-allotetraploidy and identifies several balanced reciprocal homoeologous exchanges. Analysis of M. sinensis and M. sacchariflorus populations demonstrates extensive interspecific admixture and hybridization, and documents the origin of the highly productive triploid bioenergy crop M. × giganteus. Transcriptional profiling of leaves, stem, and rhizomes over growing seasons provides insight into rhizome development and nutrient recycling, processes critical for sustainable biomass accumulation in a perennial temperate grass. The Miscanthus genome expands the power of comparative genomics to understand traits of importance to Andropogoneae grasses. The perennial grass Miscanthus is a promising biomass crop. Here, via genomics and transcriptomics, the authors reveal its allotetraploid origin, characterize gene expression associated with rhizome development and nutrient recycling, and describe the hybrid origin of the triploid M. x giganteus."], "field": "Biochemistry, Genetics and Molecular Biology", "q_year": 2023, "q_cid": "259210972", "pos_cid": 226043056, "source": "eval_collection"}
{"query_id": "scaleup_24745441_4340692", "query": "How to clarify the relationship between injury-related mitochondrial damage, intestinal barrier disruption, and multiple-organ dysfunction", "pos": ["Circulating Mitochondrial DAMPs Cause Inflammatory Responses to Injury. Injury causes a systemic inflammatory response syndrome (SIRS) that is clinically much like sepsis. Microbial pathogen-associated molecular patterns (PAMPs) activate innate immunocytes through pattern recognition receptors. Similarly, cellular injury can release endogenous ‘damage’-associated molecular patterns (DAMPs) that activate innate immunity. Mitochondria are evolutionary endosymbionts that were derived from bacteria and so might bear bacterial molecular motifs. Here we show that injury releases mitochondrial DAMPs (MTDs) into the circulation with functionally important immune consequences. MTDs include formyl peptides and mitochondrial DNA. These activate human polymorphonuclear neutrophils (PMNs) through formyl peptide receptor-1 and Toll-like receptor (TLR) 9, respectively. MTDs promote PMN Ca2+ flux and phosphorylation of mitogen-activated protein (MAP) kinases, thus leading to PMN migration and degranulation in vitro and in vivo. Circulating MTDs can elicit neutrophil-mediated organ injury. Cellular disruption by trauma releases mitochondrial DAMPs with evolutionarily conserved similarities to bacterial PAMPs into the circulation. These signal through innate immune pathways identical to those activated in sepsis to create a sepsis-like state. The release of such mitochondrial ‘enemies within’ by cellular injury is a key link between trauma, inflammation and SIRS."], "field": "Biochemistry, Genetics and Molecular Biology", "q_year": 2022, "q_cid": "247454415", "pos_cid": 4340692, "source": "eval_collection"}
{"query_id": "scaleup_23345863_16720890", "query": "How to determine whether symptom severity affects emotional eating and whether reported food choices accurately reflect associated changes in energy intake, particularly from sugary foods", "pos": ["'Dis-comfort eating': An investigation into the use of food as a coping strategy for the management of chronic pain.. OBJECTIVES Chronic pain and obesity are major public health concerns. Animal and human models have demonstrated that eating high-sugar nutrient-dense foods confers analgesic effects. Moreover, recent research suggests that people with chronic pain may \"comfort eat\" to cope with their pain. Given the harmful impact of obesity on chronic pain, it is critical to determine whether pain elicits comfort eating amongst individuals with chronic pain to ensure that this potentially maladaptive pain coping strategy is not overlooked in chronic pain treatment. Therefore, this study aimed to: determine whether chronic pain intensity predicts pain-induced comfort eating and identify mediators of this relationship; to determine whether pain-induced comfort eating predicts elevated BMI; and to establish whether BMI predicts chronic pain interference. METHODS This study utilised a cross-sectional online survey design and a sample of 151 adults with chronic pain. RESULTS Over three-quarters of this chronic pain sample reported engaging in pain-induced comfort eating. Chronic pain intensity did not significantly predict pain-induced comfort eating. However, there was a significant indirect effect of chronic pain intensity on pain-induced comfort eating through stress-but not experiential avoidance or pain catastrophising. As predicted, pain-induced comfort eating significantly predicted increased BMI, and BMI in turn significantly predicted greater chronic pain interference. DISCUSSION This study indicates that pain-induced comfort eating is both common and harmful amongst individuals with chronic pain, across the entire BMI spectrum. Pain-induced comfort eating and stress have emerged as promising chronic pain treatment targets. The findings are discussed and interpreted in light of extant research and theory, as well as limitations of the current study. Future research directions and clinical implications are also considered."], "field": "Biochemistry, Genetics and Molecular Biology", "q_year": 2021, "q_cid": "233458639", "pos_cid": 167208903, "source": "eval_collection"}
{"query_id": "scaleup_23613670_7785281", "query": "How to determine how the etiology of cirrhosis influences pyroptosis-related inflammation", "pos": ["The Sterile Inflammation in the Exacerbation of HBV-Associated Liver Injury. Exacerbation of hepatitis B virus-associated liver injury is characterized by abnormal immune response which not only mobilizes specific antiviral effects but also poses a potentially lethal nonspecific sterile inflammation to the host. How nonspecific sterile inflammation is triggered after the preexisting injury caused by specific immune injury remains elusive. In the setting of sterile inflammation, endogenous damage-associated molecular patterns are released by stressed and dying hepatocytes, which alarm the immune system through their potential pattern recognition receptors and related signaling pathways, orchestrate the influx of diverse cytokines, and ultimately amplify liver destruction. This review highlights current knowledge about the sterile hepatic inflammation in the exacerbation of chronic hepatitis B."], "field": "Biochemistry, Genetics and Molecular Biology", "q_year": 2021, "q_cid": "236136703", "pos_cid": 7785281, "source": "eval_collection"}
{"query_id": "scaleup_22041306_28196376", "query": "How to determine the requirements for BMP-induced miR-101 transcription in vascular smooth muscle cells", "pos": ["Control of Phenotypic Plasticity of Smooth Muscle Cells by Bone Morphogenetic Protein Signaling through the Myocardin-related Transcription Factors*. Vascular smooth muscle cells (VSMCs), unlike other muscle cells, do not terminally differentiate. In response to injury, VSMCs change phenotype, proliferate, and migrate as part of the repair process. Dysregulation of this plasticity program contributes to the pathogenesis of several vascular disorders, such as atherosclerosis, restenosis, and hypertension. The discovery of mutations in the gene encoding BMPRII, the type II subunit of the receptor for bone morphogenetic proteins (BMPs), in patients with pulmonary arterial hypertension (PAH) provided an indication that BMP signaling may affect the homeostasis of VSMCs and their phenotype modulation. Here we report that BMP signaling potently induces SMC-specific genes in pluripotent cells and prevents dedifferentiation of arterial SMCs. The BMP-induced phenotype switch requires intact RhoA/ROCK signaling but is not blocked by inhibitors of the TGFβ and PI3K/Akt pathways. Furthermore, nuclear localization and recruitment of the myocardin-related transcription factors (MRTF-A and MRTF-B) to a smooth muscle α-actin promoter is observed in response to BMP treatment. Thus, BMP signaling modulates VSMC phenotype via cross-talk with the RhoA/MRTFs pathway, and may contribute to the development of the pathological characteristics observed in patients with PAH and other obliterative vascular diseases."], "field": "Biochemistry, Genetics and Molecular Biology", "q_year": 2020, "q_cid": "220413062", "pos_cid": 28196376, "source": "eval_collection"}
{"query_id": "scaleup_21017297_16728001", "query": "How to explain oridonin’s antitumor activity and selective cytotoxicity toward p53-mutant esophageal carcinoma cells", "pos": ["Inhibiting the system xC−/glutathione axis selectively targets cancers with mutant-p53 accumulation. TP53, a critical tumour suppressor gene, is mutated in over half of all cancers resulting in mutant-p53 protein accumulation and poor patient survival. Therapeutic strategies to target mutant-p53 cancers are urgently needed. We show that accumulated mutant-p53 protein suppresses the expression of SLC7A11, a component of the cystine/glutamate antiporter, system xC−, through binding to the master antioxidant transcription factor NRF2. This diminishes glutathione synthesis, rendering mutant-p53 tumours susceptible to oxidative damage. System xC− inhibitors specifically exploit this vulnerability to preferentially kill cancer cells with stabilized mutant-p53 protein. Moreover, we demonstrate that SLC7A11 expression is a novel and robust predictive biomarker for APR-246, a first-in-class mutant-p53 reactivator that also binds and depletes glutathione in tumours, triggering lipid peroxidative cell death. Importantly, system xC− antagonism strongly synergizes with APR-246 to induce apoptosis in mutant-p53 tumours. We propose a new paradigm for targeting cancers that accumulate mutant-p53 protein by inhibiting the SLC7A11–glutathione axis. Efficient therapeutic strategies to target mutant-p53 cancers are needed. Here, the authors demonstrate the molecular mechanism through which mutant-p53 tumours are susceptible to oxidative damage and propose a potential strategy for targeting such cancers by inhibiting the SLC7A11-glutathione axis."], "field": "Biochemistry, Genetics and Molecular Biology", "q_year": 2020, "q_cid": "210172972", "pos_cid": 16728001, "source": "eval_collection"}
{"query_id": "scaleup_23762754_58602295", "query": "How to distinguish inherited predisposition to a lower trait level from inherited susceptibility to a condition that can itself lower that trait", "pos": ["Chronic diseases and objectively monitored physical activity profile among aged individuals – a cross-sectional twin cohort study. Abstract Introduction: High physical activity (PA) at old age indicates good functional capacity enabling independent living. We investigated how different disease conditions are associated with measured PA indicators in old women and men, and whether they recognize this association. Materials and methods: This cross-sectional twin cohort study in Finland comprised 779 individuals (276 complete twin pairs, including 117 monozygotic pairs), who participated in hip-worn accelerometer monitoring of PA and responded to questions on diseases and mobility limitations at mean age of 73 (range 71–75). Results: Of the participants, 23.2% reported having a disease restricting mobility. With sex and age in the regression model, the reported disease restricting mobility explained 11.8% of the variation in moderate-to-vigorous PA (MVPA) and 10.4% of the variation in daily steps. Adding stepwise other self-reported diseases and body mass index to the model increased the explanatory power for MVPA up to 18.5% and 25.5%, and for daily steps up to 16.0% and 20.7%, respectively. In the co-twin control analysis the PA differences were smaller in disease-discordant monozygotic than dizygotic pairs. Conclusions: Chronic disease conditions are associated with low PA, which individuals may not always recognize. Shared genetic factors may explain part of the associations. Key messages Among community-dwelling older men and women one-fourth of the variation in objectively measured moderate-to-vigorous physical activity is accounted for by age, sex, body mass index and self-reported diseases. Occurrence of chronic diseases is associated with low physical activity and individuals do not always recognize this. Healthcare professionals should pay attention to the low physical activity and mobility of individuals with chronic disease conditions before these result in limitations in independent living."], "field": "Biochemistry, Genetics and Molecular Biology", "q_year": 2021, "q_cid": "237627542", "pos_cid": 58602295, "source": "eval_collection"}
{"query_id": "scaleup_27121556_24752428", "query": "How to clarify the effects of physical activity on neuronal epigenetic regulation and its potential to counter age-related deterioration of brain function", "pos": ["Exerkines in health, resilience and disease. The health benefits of exercise are well-recognized and are observed across multiple organ systems. These beneficial effects enhance overall resilience, healthspan and longevity. The molecular mechanisms that underlie the beneficial effects of exercise, however, remain poorly understood. Since the discovery in 2000 that muscle contraction releases IL-6, the number of exercise-associated signalling molecules that have been identified has multiplied. Exerkines are defined as signalling moieties released in response to acute and/or chronic exercise, which exert their effects through endocrine, paracrine and/or autocrine pathways. A multitude of organs, cells and tissues release these factors, including skeletal muscle (myokines), the heart (cardiokines), liver (hepatokines), white adipose tissue (adipokines), brown adipose tissue (baptokines) and neurons (neurokines). Exerkines have potential roles in improving cardiovascular, metabolic, immune and neurological health. As such, exerkines have potential for the treatment of cardiovascular disease, type 2 diabetes mellitus and obesity, and possibly in the facilitation of healthy ageing. This Review summarizes the importance and current state of exerkine research, prevailing challenges and future directions. Exerkines are signalling moieties that are released in response to acute and/or chronic exercise that exert their effects through endocrine, paracrine and/or autocrine pathways. This Review summarizes the importance and current state of exerkine research, prevailing challenges and future directions. Although the benefits of exercise in enhancing health and treating disease are well-acknowledged, the molecular mechanisms underlying exercise-associated benefits remain ill-defined and are actively being investigated. ‘Exerkines’ encompass a broad variety of signalling moieties released in response to acute and/or chronic exercise that exert their effects through endocrine, paracrine and/or autocrine pathways. Exerkines can come in many forms, such as hormones, metabolites, proteins and nucleic acids; interest is increasing in moving beyond singular changes of specific factors to profiling exerkine alterations using ‘omics’ platforms. There is burgeoning interest in the role of extracellular vesicles, which are membranous structures released from cells, in serving as important carriers of molecular signals and drivers of inter-organ crosstalk related to exercise. Multiple organ systems, including the cardiometabolic system, nervous system and immune system, produce exerkines and are influenced by exerkines, which probably contributes to the pleiotropic and variable response to exercise. Emerging research on exerkines suggests multiple promising avenues for translational research and therapeutic modulation to capture exercise-associated benefits; enhanced rigour in experimental design will facilitate comparison between studies. Although the benefits of exercise in enhancing health and treating disease are well-acknowledged, the molecular mechanisms underlying exercise-associated benefits remain ill-defined and are actively being investigated. ‘Exerkines’ encompass a broad variety of signalling moieties released in response to acute and/or chronic exercise that exert their effects through endocrine, paracrine and/or autocrine pathways. Exerkines can come in many forms, such as hormones, metabolites, proteins and nucleic acids; interest is increasing in moving beyond singular changes of specific factors to profiling exerkine alterations using ‘omics’ platforms. There is burgeoning interest in the role of extracellular vesicles, which are membranous structures released from cells, in serving as important carriers of molecular signals and drivers of inter-organ crosstalk related to exercise. Multiple organ systems, including the cardiometabolic system, nervous system and immune system, produce exerkines and are influenced by exerkines, which probably contributes to the pleiotropic and variable response to exercise. Emerging research on exerkines suggests multiple promising avenues for translational research and therapeutic modulation to capture exercise-associated benefits; enhanced rigour in experimental design will facilitate comparison between studies."], "field": "Biochemistry, Genetics and Molecular Biology", "q_year": 2024, "q_cid": "271215564", "pos_cid": 247524287, "source": "eval_collection"}
{"query_id": "scaleup_27376926_6952470", "query": "How to identify what influences variation in sweet potato storage-root traits", "pos": ["The bHLH transcription factor SPATULA regulates root growth by controlling the size of the root meristem. The Arabidopsis thaliana gene SPATULA (SPT), encoding a bHLH transcription factor, was originally identified for its role in pistil development. SPT is necessary for the growth and development of all carpel margin tissues including the style, stigma, septum and transmitting tract. Since then, it has been shown to have pleiotropic roles during development, including restricting the meristematic region of the leaf primordia and cotyledon expansion. Although SPT is expressed in roots, its role in this organ has not been investigated. An analysis of embryo and root development showed that loss of SPT function causes an increase in quiescent center size in both the embryonic and postembryonic stem cell niches. In addition, root meristem size is larger due to increased division, which leads to a longer primary root. spt mutants exhibit other pleiotropic developmental phenotypes, including more flowers, shorter internodes and an extended flowering period. Genetic and molecular analysis suggests that SPT regulates cell proliferation in parallel to gibberellic acid as well as affecting auxin accumulation or transport. Our data suggest that SPT functions in growth control throughout sporophytic growth of Arabidopsis, but is not necessary for cell fate decisions except during carpel development. SPT functions independently of gibberellic acid during root development, but may play a role in regulating auxin transport or accumulation. Our data suggests that SPT plays a role in control of root growth, similar to its roles in above ground tissues."], "field": "Biochemistry, Genetics and Molecular Biology", "q_year": 2024, "q_cid": "273769263", "pos_cid": 6952470, "source": "eval_collection"}
{"query_id": "scaleup_27412783_24035655", "query": "How to represent proteins in their functional environment, including the groups they participate in", "pos": ["Complex Portal 2022: new curation frontiers. Abstract The Complex Portal (www.ebi.ac.uk/complexportal) is a manually curated, encyclopaedic database of macromolecular complexes with known function from a range of model organisms. It summarizes complex composition, topology and function along with links to a large range of domain-specific resources (i.e. wwPDB, EMDB and Reactome). Since the last update in 2019, we have produced a first draft complexome for Escherichia coli, maintained and updated that of Saccharomyces cerevisiae, added over 40 coronavirus complexes and increased the human complexome to over 1100 complexes that include approximately 200 complexes that act as targets for viral proteins or are part of the immune system. The display of protein features in ComplexViewer has been improved and the participant table is now colour-coordinated with the nodes in ComplexViewer. Community collaboration has expanded, for example by contributing to an analysis of putative transcription cofactors and providing data accessible to semantic web tools through Wikidata which is now populated with manually curated Complex Portal content through a new bot. Our data license is now CC0 to encourage data reuse. Users are encouraged to get in touch, provide us with feedback and send curation requests through the ‘Support’ link."], "field": "Biochemistry, Genetics and Molecular Biology", "q_year": 2024, "q_cid": "274127839", "pos_cid": 240356559, "source": "eval_collection"}
{"query_id": "scaleup_24533416_21472355", "query": "How to determine whether metatranscriptomic sequences from the prenatal fetal lamb gut indicate active microbes rather than contaminating DNA", "pos": ["A high-resolution map of bacteriophage øX174 transcription. Bacteriophage øX174 is a model virus for studies across the fields of structural biology, genetics, gut microbiome, and synthetic biology, but did not have a high-resolution transcriptome until this work. In this study we used next-generation sequencing to measure the RNA produced from øX174 while infecting its host E. coli C. We broadly confirm the past transcriptome model while revealing several interesting deviations from previous knowledge. Additionally, we measure the strength of canonical øX174 promoters and terminators and discover both a putative new promoter that may be activated by heat shock sigma factors, as well as rediscover a controversial Rho-dependent terminator. We also provide evidence for the first antisense transcription observed in the Microviridae family, identify two promoters that may be involved in generating this transcriptional activity, and discuss possible reasons why this RNA may be produced."], "field": "Biochemistry, Genetics and Molecular Biology", "q_year": 2021, "q_cid": "245334161", "pos_cid": 214723552, "source": "eval_collection"}
{"query_id": "scaleup_24763797_18748286", "query": "How to resolve uncertainty about the spatial arrangements of compounds 2 and 10, with a reliable assignment for compound 10 needed to evaluate compound 3", "pos": ["Determination of absolute structure using Bayesian statistics on Bijvoet differences. A description is given of a maximum-likelihood approach to absolute structure determinations of biologically active molecules."], "field": "Biochemistry, Genetics and Molecular Biology", "q_year": 2022, "q_cid": "247637974", "pos_cid": 18748286, "source": "eval_collection"}
{"query_id": "scaleup_24403850_1876478", "query": "How to determine how individual genetic loci affect diverse human brain cell types in neural development and neuropsychiatric disease despite limited access to human tissue", "pos": ["Applications of CRISPR-Cas systems in neuroscience. Genome-editing tools, and in particular those based on CRISPR–Cas (clustered regularly interspaced short palindromic repeat (CRISPR)–CRISPR-associated protein) systems, are accelerating the pace of biological research and enabling targeted genetic interrogation in almost any organism and cell type. These tools have opened the door to the development of new model systems for studying the complexity of the nervous system, including animal models and stem cell-derived in vitro models. Precise and efficient gene editing using CRISPR–Cas systems has the potential to advance both basic and translational neuroscience research."], "field": "Biochemistry, Genetics and Molecular Biology", "q_year": 2021, "q_cid": "244038503", "pos_cid": 1876478, "source": "eval_collection"}
{"query_id": "scaleup_27376926_53211514", "query": "How to identify genes underlying sweet potato flesh color variation, particularly those regulating pigment biosynthesis", "pos": ["Identification of transcription factor genes involved in anthocyanin biosynthesis in carrot (Daucus carota L.) using RNA-Seq. Anthocyanins are water-soluble colored flavonoids present in multiple organs of various plant species including flowers, fruits, leaves, stems and roots. DNA-binding R2R3-MYB transcription factors, basic helix–loop–helix (bHLH) transcription factors, and WD40 repeat proteins are known to form MYB-bHLH-WD repeat (MBW) complexes, which activates the transcription of structural genes in the anthocyanin pathway. Although black cultivars of carrots (Daucus carota L.) can accumulate large quantities of anthocyanin in their storage roots, the regulatory genes responsible for their biosynthesis are not well characterized. The current study aimed to analyze global transcription profiles based on RNA sequencing (RNA-Seq), and mine MYB, bHLH and WD40 genes that may function as positive or negative regulators in the carrot anthocyanin biosynthesis pathways. RNA was isolated from differently colored calli, as well as tissue samples from taproots of various black carrot cultivars across the course of development, and gene expression levels of colored and non-colored tissue and callus samples were compared. The expression of 32 MYB, bHLH and WD40 genes were significantly correlated with anthocyanin content in black carrot taproot. Of those, 11 genes were consistently up- or downregulated in a purple color-specific manner across various calli and cultivar comparisons. The expression of 10 out of these 11 genes was validated using real-time quantitative reverse transcriptase polymerase chain reaction (qRT-PCR). The results of this study provide insights into regulatory genes that may be responsible for carrot anthocyanin biosynthesis, and suggest that future focus on them may help improve our overall understanding of the anthocyanin synthesis pathway."], "field": "Biochemistry, Genetics and Molecular Biology", "q_year": 2024, "q_cid": "273769263", "pos_cid": 53211514, "source": "eval_collection"}
{"query_id": "scaleup_23325843_543742", "query": "How to identify a small set of relevant links between transcription factors and histone modifications while accounting for the expectation that related features have similar effects", "pos": ["Efficient Implementations of the Generalized Lasso Dual Path Algorithm. We consider efficient implementations of the generalized lasso dual path algorithm given by Tibshirani and Taylor in 2011. We first describe a generic approach that covers any penalty matrix D and any (full column rank) matrix X of predictor variables. We then describe fast implementations for the special cases of trend filtering problems, fused lasso problems, and sparse fused lasso problems, both with X = I and a general matrix X. These specialized implementations offer a considerable improvement over the generic implementation, both in terms of numerical stability and efficiency of the solution path computation. These algorithms are all available for use in the genlasso R package, which can be found in the CRAN repository."], "field": "Biochemistry, Genetics and Molecular Biology", "q_year": 2021, "q_cid": "233258435", "pos_cid": 543742, "source": "eval_collection"}
{"query_id": "scaleup_24650129_20398410", "query": "How to identify the exact binding sites between long noncoding ribonucleic acids and the protein responsible for their selective sorting into small extracellular vesicles and clarify how their recognition during loading differs from that of micrornas", "pos": ["Exosomal long noncoding RNA LNMAT2 promotes lymphatic metastasis in bladder cancer.. Patients with bladder cancer (BCa) with clinical lymph node (LN) metastasis have extremely poor prognosis. VEGF-C has been demonstrated to play vital roles in LN metastasis in BCa. However, approximately 20% of BCa with LN metastasis exhibits low VEGF-C expression, suggesting a VEGF-C-independent mechanism for LN metastasis of BCa. Herein, we demonstrated that BCa cell-secreted exosomes-mediated lymphangiogenesis promoted LN metastasis in BCa, which was in a VEGF-C-independent manner. We identified an exosomal long noncoding RNA (lncRNA), termed lymph node metastasis-associated transcript 2 (LNMAT2), stimulated HLEC tube formation and migration in vitro and enhanced tumor lymphangiogenesis and LN metastasis in vivo. Mechanistically, LNMAT2 was loaded to BCa cell-secreted exosomes by directly interacting with heterogeneous nuclear ribonucleoprotein A2B1 (hnRNPA2B1). Subsequently, exosomal LNMAT2 was internalized by HLECs and epigenetically upregulated prospero homeobox 1 (PROX1) expression by recruitment of hnRNPA2B1 and increasing the H3K4 trimethylation level in the PROX1 promoter, ultimately resulting in lymphangiogenesis and lymphatic metastasis. Therefore, our findings highlight a VEGF-C-independent mechanism of exosomal lncRNA-mediated LN metastasis and identify LNMAT2 as a therapeutic target for LN metastasis in BCa."], "field": "Biochemistry, Genetics and Molecular Biology", "q_year": 2022, "q_cid": "246501297", "pos_cid": 203984108, "source": "eval_collection"}
{"query_id": "scaleup_24763797_8563254", "query": "How to quantify structural similarities among sesquiterpenes with different molecular skeletons to identify relationships relevant to finding candidate anti-HBV compounds in herbs", "pos": ["ChemmineR: a compound mining framework for R. Motivation: Software applications for structural similarity searching and clustering of small molecules play an important role in drug discovery and chemical genomics. Here, we present the first open-source compound mining framework for the popularstatistical programming environment R. The integration with a powerful statistical environment maximizes the flexibility, expandability and programmability of the provided analysis functions. Results: We discuss the algorithms and compound mining utilities provided by the R package ChemmineR. It contains functions for structural similarity searching, clustering of compound libraries with a wide spectrum of classification algorithms and various utilities for managing complex compound data. It also offers a wide range of visualization functions for compound clusters and chemical structures. The package is well integrated with the online ChemMine environment and allows bidirectional communications between the two services. Availability: ChemmineR is freely available as an R package from the ChemMine project site: http://bioweb.ucr.edu/ChemMineV2/chemminer Contact: thomas.girke@ucr.edu"], "field": "Biochemistry, Genetics and Molecular Biology", "q_year": 2022, "q_cid": "247637974", "pos_cid": 8563254, "source": "eval_collection"}
{"query_id": "scaleup_25919629_31999426", "query": "How to explain and prevent persistent transmission of carbapenemase-producing Enterobacterales from contaminated hospital toilets to patients", "pos": ["Bioaerosol concentrations generated from toilet flushing in a hospital-based patient care setting. In the United States, 1.7 million immunocompromised patients contract a healthcare-associated infection, annually. These infections increase morbidity, mortality and costs of care. A relatively unexplored route of transmission is the generation of bioaerosols during patient care. Transmission of pathogenic microorganisms may result from inhalation or surface contamination of bioaerosols. The toilet flushing of patient fecal waste may be a source of bioaerosols. To date, no study has investigated bioaerosol concentrations from flushing fecal wastes during patient care. Particle and bioaerosol concentrations were measured in hospital bathrooms across three sampling conditions; no waste no flush, no waste with flush, and fecal waste with flush. Particle and bioaerosol concentrations were measured with a particle counter bioaerosol sampler both before after a toilet flushing event at distances of 0.15, 0.5, and 1 m from the toilet for 5, 10, 15 min. Particle concentrations measured before and after the flush were found to be significantly different (0.3–10 μm). Bioaerosol concentrations when flushing fecal waste were found to be significantly greater than background concentrations (p-value = 0.005). However, the bioaerosol concentrations were not different across time (p-value = 0.977) or distance (p-value = 0.911) from the toilet, suggesting that aerosols generated may remain for longer than 30 min post flush. Toilets produce aerosol particles when flushed, with the majority of the particles being 0.3 μm in diameter. The particles aerosolized include microorganisms remaining from previous use or from fecal wastes. Differences in bioaerosol concentrations across conditions also suggest that toilet flushing is a source of bioaerosols that may result in transmission of pathogenic microorganisms. This study is the first to quantify particles and bioaerosols produced from flushing a hospital toilet during routine patient care. Future studies are needed targeting pathogens associated with gastrointestinal illness and evaluating aerosol exposure reduction interventions."], "field": "Biochemistry, Genetics and Molecular Biology", "q_year": 2023, "q_cid": "259196292", "pos_cid": 31999426, "source": "eval_collection"}
{"query_id": "scaleup_28125905_27272541", "query": "How to identify more selective and potent FGFR1 inhibitor candidates that address drug resistance among millions of compounds under limited time and resources", "pos": ["Identification of lead inhibitors for 3CLpro of SARS-CoV-2 target using machine learning based virtual screening, ADMET analysis, molecular docking and molecular dynamics simulations. The SARS-CoV-2 3CLpro is a critical target for COVID-19 therapeutics due to its role in viral replication. We employed a screening pipeline to identify novel inhibitors by combining machine learning classification with similarity checks of approved medications. A voting classifier, integrating three machine learning classifiers, was used to filter a large database (∼10 million compounds) for potential inhibitors. This ensemble-based machine learning technique enhances overall performance and robustness compared to individual classifiers. From the screening, three compounds M1, M2 and M3 were selected for further analysis. Absorption, distribution, metabolism, excretion, and toxicity (ADMET) analysis compared these candidates to nirmatrelvir and azvudine. Molecular docking followed by 200 ns MD simulations showed that only M1 (6-[2,4-bis(dimethylamino)-6,8-dihydro-5H-pyrido[3,4-d]pyrimidine-7-carbonyl]-1H-pyrimidine-2,4-dione) remained stable. For azvudine and M1, the estimated median lethal doses are 1000 and 550 mg kg−1, respectively, with maximum tolerated doses of 0.289 and 0.614 log mg per kg per day. The predicted inhibitory activity of M1 is 7.35, similar to that of nirmatrelvir. The binding free energy based on Molecular Mechanics Poisson-Boltzmann Surface Area (MM-PBSA) of M1 is −18.86 ± 4.38 kcal mol−1, indicating strong binding interactions. These findings suggest that M1 merits further investigation as a potential SARS-CoV-2 treatment."], "field": "Biochemistry, Genetics and Molecular Biology", "q_year": 2025, "q_cid": "281259053", "pos_cid": 272725414, "source": "eval_collection"}
{"query_id": "scaleup_21017297_7093900", "query": "How to explain the cellular response to oridonin", "pos": ["Molecular chaperones as HSF1-specific transcriptional repressors.. The rapid yet transient transcriptional activation of heat shock genes is mediated by the reversible conversion of HSF1 from an inert negatively regulated monomer to a transcriptionally active DNA-binding trimer. During attenuation of the heat shock response, transcription of heat shock genes returns to basal levels and HSF1 reverts to an inert monomer. These events coincide with elevated levels of Hsp70 and other heat shock proteins (molecular chaperones). Here, we show that the molecular chaperone Hsp70 and the cochaperone Hdj1 interact directly with the transactivation domain of HSF1 and repress heat shock gene transcription. Overexpression of either chaperone represses the transcriptional activity of a transfected GAL4-HSF1 activation domain fusion protein and endogenous HSF1. As neither the activation of HSF1 DNA binding nor inducible phosphorylation of HSF1 was affected, the primary autoregulatory role of Hsp70 is to negatively regulate HSF1 transcriptional activity. These results reveal that the repression of heat shock gene transcription, which occurs during attenuation, is due to the association of Hsp70 with the HSF1 transactivation domain, thus providing a plausible explanation for the role of molecular chaperones in at least one key step in the autoregulation of the heat shock response."], "field": "Biochemistry, Genetics and Molecular Biology", "q_year": 2020, "q_cid": "210172972", "pos_cid": 7093900, "source": "eval_collection"}
{"query_id": "scaleup_27710652_25964634", "query": "How to determine the prognostic value of serum cell division cycle 42 levels, their changes during treatment, and their relationship to treatment-related immune responses in patients with metastatic castration-resistant prostate cancer receiving abiraterone plus prednisone", "pos": ["CDC42—A promising immune-related target in glioma. Glioma is the worst prognostic neoplasm in the central nervous system. A polarity-regulating GTPase in cells, known as cell division cycle 42 (CdC42), has been proven to have its overactivation tightly connected to high tumor malignancy. The RNA-seq and protein expression of CDC42 in tumor and comparison tissues were analyzed based on the online tools; CDC42 was remarkably boosted in tumor tissues compared to normal controls. A total of 600 patients in the analysis set from The Cancer Genome Atlas (TCGA) database and 657 patients in the validation set from the Chinese Glioma Genome Atlas (CGGA) database were adopted. The expression of CDC42 in clinical features and biological functions of glioma was analyzed, including differential expression analysis, survival analysis, Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, and immune infiltration analysis. The enrichment of CDC42 was shown to be strongly associated with poor prognosis and terrible clinical indexes of glioma, including higher World Health Organization scale grade, wild-type isocitrate dehydrogenase 1 expression, O6-methylguanine-DNA methyltransferase non-methylated status, and 1p19q non-codeletion status (p < 0.0001). Functional enrichment analysis showed that CDC42 was highly correlated with immune and inflammatory responses in glioma. Additionally, the concentration extent of CDC42 was closely related to immune infiltration, immune checkpoints, and regulatory T (Treg) cell markers (CD4, CD25, and CD127). All evidence suggested that CDC42 may be a potential target for glioma immunotherapy."], "field": "Biochemistry, Genetics and Molecular Biology", "q_year": 2025, "q_cid": "277106525", "pos_cid": 259646349, "source": "eval_collection"}
{"query_id": "scaleup_21134740_16980580", "query": "How to balance economic cost and carbon dioxide emissions in logistics center location and allocation while identifying trade-offs between these objectives", "pos": ["Weighted-Sum Approach for Bi-objective Optimization of Fleet Size with Environmental Aspects. Abstract In this chapter, four bi-objective vehicle routing problems are considered. Weighted-sum approach optimization models are formulated with the use of mixed-integer programming. In presented optimization models, maximization of capacity of truck versus minimization of utilization of fuel, carbon emission, and production of noise are taken into account. The problems deal with real data for green logistics for routes crossing the Western Pyrenees in Navarre, Basque Country, and La Rioja, Spain. Heterogeneous fleet of trucks is considered. Different types of trucks have not only different capacities, but also require different amounts of fuel for operations. Consequently, the amount of carbon emission and noise vary as well. Modern logistic companies planning delivery routes must consider the trade-off between the financial and environmental aspects of transportation. Efficiency of delivery routes is impacted by truck size and the possibility of dividing long delivery routes into smaller ones. The results of computational experiments modeled after real data from a Spanish food distribution company are reported. Computational results based on formulated optimization models show some balance between fleet size, truck types, and utilization of fuel, carbon emission, and production of noise. As a result, the company could consider a mixture of trucks sizes and divided routes for smaller trucks. Analyses of obtained results could help logistics managers lead the initiative in environmental conservation by saving fuel and consequently minimizing pollution. The computational experiments were performed using the AMPL programming language and the CPLEX solver."], "field": "Business, Management and Accounting", "q_year": 2019, "q_cid": "211347409", "pos_cid": 169805806, "source": "eval20x26"}
{"query_id": "scaleup_1056637_15278498", "query": "How to protect public health from risk commodities while attracting and retaining investment and jobs from politically influential corporations that are among the largest firms in low- and middle-income countries", "pos": ["Business Power in Global Governance. Has the political power of big business, particularly transnational corporations (TNCs), increased in our globalizing world? What, if anything, constrains TNCs? Analyzing the role of business in the global arena, this systematic and theoretically grounded book addresses these questions. Fuchs considers the implications of expanded lobbying efforts by businesses and business associations, the impact of capital mobility, and developments in the area of self-regulation and public-private partnerships. She also highlights the role of business in framing policy issues and influencing public debate. Clearly identifying the sources of the marked increase in the political power of TNCs, she also provides ample evidence of the limitations and vulnerabilities that rein them in."], "field": "Business, Management and Accounting", "q_year": 2014, "q_cid": "1056637", "pos_cid": 152784985, "source": "eval20x26"}
{"query_id": "scaleup_30497438_22470481", "query": "How to understand how expectations within an industry and the plans of those in charge affect the choices of new businesses pursuing new ideas", "pos": ["THE IRON CAGE REVISITED:. Instead of examining why organizations are dissimilar, this study explores why organizations tend to be increasingly and inevitably homogenous in their forms and practices. Organizations in a similar line of work are structured into an organizational field by powerful forces that lead them to become similar. Rather than the causes of rationalization and bureaucratization suggested by Max Weber, including competition and the need for efficiency, institutional similarity is due to the structuration of organizational fields, a process caused largely by the state and the professions, which are the great rationalizers of the late 20th century. In highly structured organizational fields, rational efforts of individuals aggregately lead to structural, cultural, and output homogeneity. Homogenization is best captured by the concept of isomorphism, the process whereby one element in a population resembles others that confront the same environmental conditions. The two types of isomorphism are competitive and institutional. Three processes lead to organizational similarity: (1) coercive isomorphism stemming from political influence and the problem of legitimacy; (2) mimetic isomorphism resulting from uniform responses to uncertainty; and (3) normative isomorphism associated with professionalism. While these isomorphic processes improve organizational transactions, they do not necessarily increase internal efficiency. Twelve hypotheses are offered for further research about which organizational fields will be most homogenous. These hypotheses relate the impact of resource centralization and dependency, goal ambiguity and technical uncertainty, and professionalism and structuration on isomorphic change. Finally, useful implications of the study for theories of organizations and social change are offered. (TNM)"], "field": "Business, Management and Accounting", "q_year": 2015, "q_cid": "30497438", "pos_cid": 22470481, "source": "eval20x26"}
{"query_id": "scaleup_16929929_55396735", "query": "How to understand how employees balance flexibility and formalisation while preserving agency across different knowledge-intensive business service processes, with local contextual detail and sufficient breadth for theoretical development", "pos": ["Building theories from case study research. - This paper describes the process of inducting theory using case studies from specifying the research questions to reaching closure. Some features of the process, such as problem definition and construct validation, are similar to hypothesis-testing research. Others, such as within-case analysis and replication logic, are unique to the inductive, case-oriented process. Overall, the process described here is highly iterative and tightly linked to data. This research approach is especially appropriate in new topic areas. The resultant theory is often novel, testable, and empirically valid. Finally, framebreaking insights, the tests of good theory (e.g., parsimony, logical coherence), and convincing grounding in the evidence are the key criteria for evaluating this type of research."], "field": "Business, Management and Accounting", "q_year": 2019, "q_cid": "169299292", "pos_cid": 55396735, "source": "eval20x26"}
{"query_id": "scaleup_25438300_6922193", "query": "How to identify the conditions under which leaders make self-serving accounting choices to enhance perceptions of their performance", "pos": ["The performance of narcissists rises and falls with perceived opportunity for glory.. Narcissists consider themselves to be exceptional performers, but past research has found no consistent relationship between narcissism and performance. The present research tested the hypothesis that the relationship between subclinical narcissism and performance is moderated by a motivational factor: perceived self-enhancement opportunity. Four experiments were conducted, each using different manipulations of self-enhancement opportunity and different performance tasks. In each study, narcissists performed better when self-enhancement opportunity was high rather than low. In contrast, the performance of participants with low narcissism was relatively unaffected by self-enhancement opportunity. Other findings suggested that narcissists' self-enhancement motivation stems more from a desire to garner admiration than from a desire to self-evaluate. Implications and directions for future research are discussed."], "field": "Business, Management and Accounting", "q_year": 2019, "q_cid": "254383009", "pos_cid": 6922193, "source": "eval20x26"}
{"query_id": "scaleup_22493439_62790982", "query": "How to ensure boards and management have sufficient insight and adaptability to make effective development decisions", "pos": ["Intellectual Capital and Its Impact on the Financial Performance of Russian Manufacturing Companies. Intellectual Capital (IC) has been argued to be the key element of value creation in the contemporary economy. According to the results obtained in [Molnar, 2004] in the 1980s the share of tangible assets accounted for about 62% of market capitalization of companies on developed markets. However, by the start of the 2000s, their share fell to 16%. This has been widely supported by empirical research, but mainly based on the data from developed markets. The questions of how IC and its elements work on emerging markets remains under-researched due to a lack of empirical research devoted to this topic. The aim of the study is to provide empirical insight into the relationship between three main elements of IC (human, relational and organisational) and organisational performance of Russian companies, such as asset profitability, net sales growth and market share. The sample includes 240 Russian companies. Information about different elements of intellectual capital has been gathered with the help of a questionnaire that has been answered by the executive management of the companies included in the sample over the course of January-March 2015. The data is collected with the survey using the scales that have been already internationally. The findings based on regression analysis demonstrate that structural and human capital positively influence organisational performance, while relational capital does not. We can assume that the results that we obtained can be explained by the specific features of the analyzed industries. For manufacturing companies the organizational structure and the effectiveness of internal processes play a much more important role in company value creation than relations with customers and other stakeholders. The core managerial implication of this study is that building the structural capital, providing employees with efficient and relevant information systems and tools to support cooperation between employees, as well as carefully documenting organizational knowledge and making it easily accessible for employees, should be in the focus of the managers of manufacturing companies. The concept of IC management in our article is developed within the international context and focuses on emerging markets. At the end of the paper, the main areas for further research are presented."], "field": "Business, Management and Accounting", "q_year": 2020, "q_cid": "224934395", "pos_cid": 62790982, "source": "eval_collection"}
{"query_id": "scaleup_23902613_11652043", "query": "How to predict COVID-19 outcomes and plan proactive responses amid uncertainty across interdependent factors and evolving pandemic information", "pos": ["Applications of Bayesian networks and Petri nets in safety, reliability, and risk assessments: A review. Abstract System safety, reliability and risk analysis are important tasks that are performed throughout the system life-cycle to ensure the dependability of safety-critical systems. Probabilistic risk assessment (PRA) approaches are comprehensive, structured and logical methods widely used for this purpose. PRA approaches include, but not limited to, Fault Tree Analysis (FTA), Failure Mode and Effects Analysis (FMEA), and Event Tree Analysis (ETA). Growing complexity of modern systems and their capability of behaving dynamically make it challenging for classical PRA techniques to analyse such systems accurately. For a comprehensive and accurate analysis of complex systems, different characteristics such as functional dependencies among components, temporal behaviour of systems, multiple failure modes/states for components/systems, and uncertainty in system behaviour and failure data are needed to be considered. Unfortunately, classical approaches are not capable of accounting for these aspects. Bayesian networks (BNs) have gained popularity in risk assessment applications due to their flexible structure and capability of incorporating most of the above mentioned aspects during analysis. Furthermore, BNs have the ability to perform diagnostic analysis. Petri Nets are another formal graphical and mathematical tool capable of modelling and analysing dynamic behaviour of systems. They are also increasingly used for system safety, reliability and risk evaluation. This paper presents a review of the applications of Bayesian networks and Petri nets in system safety, reliability and risk assessments. The review highlights the potential usefulness of the BN and PN based approaches over other classical approaches, and relative strengths and weaknesses in different practical application scenarios."], "field": "Business, Management and Accounting", "q_year": 2021, "q_cid": "239026131", "pos_cid": 116520430, "source": "eval_collection"}
{"query_id": "scaleup_27813133_26500791", "query": "How to improve knowledge sharing and cooperation among participants with knowledge boundaries and gaps and differing motives, resources, and characteristics", "pos": ["The role of knowledge boundary resources for platform ecosystems – insights and design implications from SAP's Business Technology Platform. Platform ecosystems shift the locus of innovation from internal departments to third‐party developers, leading to knowledge boundaries between the platform owner and these external developers. Whereas traditional knowledge management approaches focus on intra‐organizational knowledge sharing, platform owners have to adopt an inter‐organizational approach to integrate knowledge across firm boundaries. Platform owners thus rely on knowledge boundary resources such as technical documentation, information portals, training materials, sample code, blogs, and online communities to overcome knowledge boundaries in their ecosystems. Existing research has identified different types of knowledge boundaries and knowledge boundary resources, but further research is needed to clarify how they influence third‐party application development. Against this background, we study how third‐party developers integrate knowledge boundary resources into their development practices. To derive an in‐depth understanding of the phenomenon, we used cognitive fit theory and conducted a single case study of SAP's Business Technology Platform. Based on 23 interviews, we developed a process model and distilled two primary purposes why third‐party developers use knowledge boundary resources: learning and problem‐solving. Based on these purposes, we explain the emergence of a knowledge boundary resource‐purpose fit that shapes the selection, evaluation, and usage of knowledge boundary resources. We then draw upon various knowledge boundary resource characteristics to condense four cases with a particularly favorable knowledge boundary resource‐purpose fit. Based on our results, we derive five propositions to help platform owners design effective knowledge boundary resources."], "field": "Business, Management and Accounting", "q_year": 2025, "q_cid": "278131339", "pos_cid": 265007914, "source": "eval_collection"}
{"query_id": "scaleup_28192050_14533403", "query": "How to enable external stakeholders facing information asymmetry to distinguish firms’ strategic alliances aligned with actual environmental performance from symbolic efforts misaligned with environmental outcomes", "pos": ["Signaling Theory: A Review and Assessment. Signaling theory is useful for describing behavior when two parties (individuals or organizations) have access to different information. Typically, one party, the sender, must choose whether and how to communicate (or signal) that information, and the other party, the receiver, must choose how to interpret the signal. Accordingly, signaling theory holds a prominent position in a variety of management literatures, including strategic management, entrepreneurship, and human resource management. While the use of signaling theory has gained momentum in recent years, its central tenets have become blurred as it has been applied to organizational concerns. The authors, therefore, provide a concise synthesis of the theory and its key concepts, review its use in the management literature, and put forward directions for future research that will encourage scholars to use signaling theory in new ways and to develop more complex formulations and nuanced variations of the theory."], "field": "Business, Management and Accounting", "q_year": 2025, "q_cid": "281920500", "pos_cid": 145334039, "source": "eval_collection"}
{"query_id": "scaleup_23902613_21642846", "query": "How to identify the factors that most strongly influence multidimensional COVID-19 risk despite their interdependencies, to prioritize proactive national policy responses", "pos": ["Evaluation of natural hazard risk for coastal districts of Bangladesh using the INFORM approach. Abstract Coastal districts of Bangladesh are increasingly suffering from climatic hazards (e.g., cyclone, flood, saltwater intrusion). Tropical cyclones and floods particularly affect millions of people almost every year. Massive property damages and life losses are a common scenario when these disasters hit the coastal belt. Moreover, due to climate change impact, saltwater intrusion is increasing significantly in the coastal districts, especially during dry seasons impacting crop production and drinking water sources. The amount of asset and population exposed to natural hazards have increased significantly in the coastal belt, which has exacerbated the risk of natural hazards. Previous studies on the disaster risk of coastal districts of Bangladesh did not explicitly account for the key vulnerability and lack of coping capacity parameters that are crucial for a comprehensive risk assessment. This study assesses the disaster risk of 19 coastal districts of Bangladesh using the Index for Risk Management (INFORM) model. The multi-layered INFORM framework particularly assesses the risk of coastal communities considering socioeconomic vulnerabilities and vulnerable groups as well as institutional and infrastructural coping capacity under multiple hazards. Forty-five core risk indicators are used to evaluate the final risk score of the communities. The outcome of the study shows that 11 districts are facing moderate to very high level of risk in the coastal belt. The island district, Bhola, has the highest level of risk among the coastal districts, whereas Cox's Bazar, Chandpur, and Feni districts fall into the lowest risk region. In addition to hazard susceptibility, poverty & development, vulnerable health condition and access to the health care system are key vulnerable factors that potentially increase the overall risk. The outcome of this study is expected to be useful for preparing an effective disaster risk mitigation plan by decision-makers."], "field": "Business, Management and Accounting", "q_year": 2021, "q_cid": "239026131", "pos_cid": 216428469, "source": "eval_collection"}
{"query_id": "scaleup_28013973_26104913", "query": "How to understand consumer attitudes and intentions toward home-appliance leasing in developing countries such as Ecuador, where lack of trust and a strong culture of ownership hinder adoption", "pos": ["Green or greedy: the relationship between perceived benefits and homeowners’ intention to adopt residential low-carbon technologies. Transitioning to a net-zero economy requires a nuanced understanding of homeowners decision-making pathways when considering the adoption of Low Carbon Technologies (LCTs). These LCTs present both personal and collective benefits, with positive perceptions critically influencing attitudes and intentions. Our study analyses the relationship between two primary benefits: the household-level financial gain and the broader environmental advantage. Focusing on the intention to adopt Rooftop Photovoltaic Systems, Energy Efficient Appliances, and Green Electricity Tariffs, we employ Partial Least Squares Structural Equation Modeling to demonstrate that the adoption intention of the LCTs is underpinned by the Theory of Planned Behaviour. Attitudes toward the LCTs are more strongly related to product-specific benefits than affective constructs. In terms of evaluative benefits, environmental benefits exhibit a higher positive association with attitude formation compared to financial benefits. However, this relationship switches as homeowners move through the decision process with the financial benefits of selected LCTs having a consistently higher association with adoption intention. At the same time, financial benefits also positively affect attitudes. Observing this trend across both low- and high-cost LCTs, we recommend that policymakers amplify homeowners' recognition of the individual benefits intrinsic to LCTs and enact measures that ensure these financial benefits."], "field": "Business, Management and Accounting", "q_year": 2025, "q_cid": "280139730", "pos_cid": 261049132, "source": "eval_collection"}
{"query_id": "scaleup_28350077_28097529", "query": "How to obtain a comprehensive overview of the extent, nature, and gaps in scientific knowledge on modern slavery in the context of the 2030 Agenda", "pos": ["Best practices of judicial governance: A scoping review protocol. Background Enhancing performance in the public sector is closely tied to institutional structures, governance models, and the behavior of public officials. In the Judiciary, these factors significantly affect the effectiveness of court administration and justice delivery. Judicial governance is a complex and evolving concept encompassing standards and practices related to accountability, independence, resource management, and institutional performance, progressively integrating principles from public management reforms. Despite its growing relevance, the field remains fragmented, with limited evidence connecting international standards to best governance practices in judicial administration. Objective This protocol outlines a scoping review designed to identify, map, and synthesize evidence on best practices in judicial governance, examining their relationship with the effective administration of justice and identifying research gaps to propose a future research agenda. Method This review will follow the JBI methodology and the PRISMA-ScR guidelines. A comprehensive search will be conducted in databases such as Scopus, Web of Science, DOAJ, and JSTOR, as well as additional searches in grey literature. The PCC (Population, Concept, and Context) framework guided the eligibility criteria, and the PRESS 2015 checklist was used to validate the search strategy. The PRISMA-S checklist will inform the reporting of the search process. Studies of all designs and publication statuses will be considered, with no restrictions on language or publication date. Two reviewers will independently screen using Rayyan software, with a third reviewer resolving any disagreements. Data extraction will occur at two levels: general source information and specific content related to the review scope. Qualitative data will be analyzed using NVivo software, enabling categorization, descriptive synthesis, gap identification, and the development of a research agenda. Discussion This scoping review aims to generate key evidence that can inform institutional standards and best governance practices to support evidence-based policymaking; while it does not assess the risk of bias, its systematic methodology and inclusion of grey literature enhance its relevance for future research and innovations in the justice sector. Through this scoping review, key evidence will generate insights that can enhance institutional standards and best practices in governance, enabling evidence-based policymaking. Although the review does not assess the risk of bias, its systematic approach and inclusion of grey literature strengthen its potential to support future research and governance innovations in the justice sector. Trial registration OSF Registries, Jan 21, 2024: https://doi.org/10.17605/osf.io/agv3b."], "field": "Business, Management and Accounting", "q_year": 2025, "q_cid": "283500775", "pos_cid": 280975295, "source": "eval_collection"}
{"query_id": "scaleup_28271703_27888337", "query": "How to measure adaptability to crises to support sound comparisons across industries and crisis types", "pos": ["Formative versus reflective measurement models: two applications of formative measurement | NOVA. The University of Newcastle's Digital Repository. This paper presents a framework that helps researchers to design and validate both formative and reflective measurement models. The framework draws from the existing literature and includes both theoretical and empirical considerations. Two important examples, one from international business and one from marketing, illustrate the use of the framework. Both examples concern constructs that are fundamental to theory-building in these disciplines, and constructs that most scholars measure reflectively. In contrast, applying the framework suggests that a formative measurement model may be more appropriate. These results reinforce the need for all researchers to justify, both theoretically and empirically, their choice of measurement model. Use of an incorrect measurement model undermines the content validity of constructs, misrepresents the structural relationships between them, and ultimately lowers the usefulness of management theories for business researchers and practitioners. The main contribution of this paper is to question the unthinking assumption of reflective measurement seen in much of the business literature."], "field": "Business, Management and Accounting", "q_year": 2025, "q_cid": "282717036", "pos_cid": 27888337, "source": "eval_collection"}
{"query_id": "scaleup_28192050_27692671", "query": "How to ensure firms’ alliances under strong environmental requirements effectively utilize acquired resources and deliver environmental benefits", "pos": ["The role of high-tech certification in enterprise green innovation: from the perspectives of substantive innovation and strategic innovation. Sustainable development comes from a balance between economic growth and environmental protection, with due consideration of long-term impacts on environment. Leveraging policy tools to promote green innovation is a critical strategy for achieving this objective. This paper examines the impact of high-tech certification on corporate green innovation, distinguishing between substantive and strategic green innovation. It develops a theoretical framework to analyze how high-tech certification influences enterprise green innovation through mechanisms such as tax preferences, government subsidies, financing constraints, and leveraging capital market attention. The study employs a zero-inflated negative binomial regression model and utilizes data of A-share listed companies from 2006 to 2023 to systematically assess the impact of high-tech certification on enterprise green innovation strategies, underlying mechanisms, and their heterogeneity. The research discovers that in general, high-tech certification significantly promotes enterprise green innovation, having a more prominent facilitating effect on strategic green innovation, resulting in a certain degree of green patent false prosperity. From the perspective of underlying mechanisms, high-tech certification increases the resources actually obtained by enterprises through tax preferences and government subsidies and alleviates financing constraints, thereby guiding enterprises to undertake more substantive green innovation; while enhancing capital market attention increases the expected resources obtained by enterprises, prompting enterprises to be more inclined towards strategic green innovation. Further analysis reveals that the impact of high-tech certification on corporate green innovation varies significantly across different ownership structures, industries, and regions. Specifically, in state-owned enterprises, technology-intensive sectors, and enterprises located in the central regions, the positive effect on substantive green innovation is particularly pronounced. This study contributes to the literature on policy tools and corporate green innovation strategies by offering robust empirical evidence to optimizing policy design, mitigating policy arbitrage, and preventing patent bubbles."], "field": "Business, Management and Accounting", "q_year": 2025, "q_cid": "281920500", "pos_cid": 276926712, "source": "eval_collection"}
{"query_id": "scaleup_23061037_334423", "query": "How to organize related terms from large volumes of unstructured m-commerce documents into coherent topics to identify and interpret business and technological trends", "pos": ["Fast unfolding of communities in large networks. We propose a simple method to extract the community structure of large networks. Our method is a heuristic method that is based on modularity optimization. It is shown to outperform all other known community detection methods in terms of computation time. Moreover, the quality of the communities detected is very good, as measured by the so-called modularity. This is shown first by identifying language communities in a Belgian mobile phone network of 2 million customers and by analysing a web graph of 118 million nodes and more than one billion links. The accuracy of our algorithm is also verified on ad hoc modular networks."], "field": "Business, Management and Accounting", "q_year": 2021, "q_cid": "230610379", "pos_cid": 334423, "source": "eval_collection"}
{"query_id": "scaleup_26702525_9295376", "query": "How to determine whether reduced agency conflicts explain the effect of green credit policy on heavily polluting enterprises’ excess cash holdings", "pos": ["Identification, Inference and Sensitivity Analysis for Causal Mediation Effects. Causal mediation analysis is routinely conducted by applied researchers in a variety of disciplines. The goal of such an analysis is to investigate alternative causal mechanisms by examining the roles of intermediate variables that lie in the causal paths between the treat- ment and outcome variables. In this paper we first prove that under a particular version of sequential ignorability assumption, the aver- age causal mediation effect (ACME) is nonparametrically identified. We compare our identification assumption with those proposed in the literature. Some practical implications of our identification result are also discussed. In particular, the popular estimator based on the linear structural equation model (LSEM) can be interpreted as an ACME estimator once additional parametric assumptions are made. We show that these assumptions can easily be relaxed within and outside of the LSEM framework and propose simple nonparametric estimation strate- gies. Second, and perhaps most importantly, we propose a new sensi- tivity analysis that can be easily implemented by applied researchers within the LSEM framework. Like the existing identifying assumptions, the proposed sequential ignorability assumption may be too strong in many applied settings. Thus, sensitivity analysis is essential in order to examine the robustness of empirical findings to the possible existence of an unmeasured confounder. Finally, we apply the proposed methods to a randomized experiment from political psychology. We also make easy-to-use software available to implement the proposed methods."], "field": "Business, Management and Accounting", "q_year": 2024, "q_cid": "267025252", "pos_cid": 9295376, "source": "eval_collection"}
{"query_id": "scaleup_28350077_3534564", "query": "How to clearly and concisely present findings on modern slavery and the SDGs, accounting for quantitative evidence and making patterns and knowledge gaps apparent", "pos": ["Convergent and sequential synthesis designs: implications for conducting and reporting systematic reviews of qualitative and quantitative evidence. BackgroundSystematic reviews of qualitative and quantitative evidence can provide a rich understanding of complex phenomena. This type of review is increasingly popular, has been used to provide a landscape of existing knowledge, and addresses the types of questions not usually covered in reviews relying solely on either quantitative or qualitative evidence. Although several typologies of synthesis designs have been developed, none have been tested on a large sample of reviews. The aim of this review of reviews was to identify and develop a typology of synthesis designs and methods that have been used and to propose strategies for synthesizing qualitative and quantitative evidence.MethodsA review of systematic reviews combining qualitative and quantitative evidence was performed. Six databases were searched from inception to December 2014. Reviews were included if they were systematic reviews combining qualitative and quantitative evidence. The included reviews were analyzed according to three concepts of synthesis processes: (a) synthesis methods, (b) sequence of data synthesis, and (c) integration of data and synthesis results.ResultsA total of 459 reviews were included. The analysis of this literature highlighted a lack of transparency in reporting how evidence was synthesized and a lack of consistency in the terminology used. Two main types of synthesis designs were identified: convergent and sequential synthesis designs. Within the convergent synthesis design, three subtypes were found: (a) data-based convergent synthesis design, where qualitative and quantitative evidence is analyzed together using the same synthesis method, (b) results-based convergent synthesis design, where qualitative and quantitative evidence is analyzed separately using different synthesis methods and results of both syntheses are integrated during a final synthesis, and (c) parallel-results convergent synthesis design consisting of independent syntheses of qualitative and quantitative evidence and an interpretation of the results in the discussion.ConclusionsPerforming systematic reviews of qualitative and quantitative evidence is challenging because of the multiple synthesis options. The findings provide guidance on how to combine qualitative and quantitative evidence. Also, recommendations are made to improve the conducting and reporting of this type of review."], "field": "Business, Management and Accounting", "q_year": 2025, "q_cid": "283500775", "pos_cid": 3534564, "source": "eval_collection"}
{"query_id": "scaleup_23208628_22568245", "query": "How to ensure smaller and more vulnerable entities are adequately represented in circular economy and global supply chain management", "pos": ["Technology for Social Good Foundations: A Perspective From the Smallholder Farmer in Sustainable Supply Chains. The livelihood of smallholder farmers in emerging economies’ cocoa supply chain is substandard because of fraud, exploitation, corruption, deceit, child labor, and financial exclusion, usually perpetrated by influential actors. This situation creates a social sustainability problem which needs urgent attention. Digital technologies such as sensors, drones, satellites, and blockchain show promise toward fostering social sustainability deep into the supply chain. This innovation is consistent with the United Nations 2030 sustainable development goals of transforming world economies toward a more sustainable future vision by reducing poverty and inequality. As our contribution, we adopt a traditional approach in our perspective article to initiate a scholarly curiosity to discuss and develop research needs on how to use technology to address this current and critical sustainability and supply chain concern. Blockchain can solve the inefficiencies, complexities, and other social issues of smallholder farmers in the supply chain. This article identifies some blockchain technologies in emerging economies, such as Hara Technology in Indonesia and Cellulant Agrikore Blockchain Solution in Nigeria. Again, we observed that the promise of using technology to improve smallholders' vulnerability in the cocoa supply chain remains underexploited in Africa and other emerging economies. Therefore, rigorous research on smallholders' social sustainability is needed to make sound policy recommendations. This short perspective article describes issues facing these smallholder farmers and how technology can play a role for them and their supply chains to alleviate various social and environmental concerns. Accordingly, we propose some research questions for technology, innovation, and engineering management researchers."], "field": "Business, Management and Accounting", "q_year": 2021, "q_cid": "232086283", "pos_cid": 225682453, "source": "eval_collection"}
{"query_id": "scaleup_27839951_23406029", "query": "How to measure whether family firms achieve both economic and ecological success as a single performance outcome rather than separate competing goals", "pos": ["Performance implications of the buyer-supplier market orientation fit. Abstract Extant research examining the link between market orientation and performance offers few insights into how the interplay between a firm's market orientation (MO) and its key supplier's MO influences the firm's performance. Using archival and survey dyadic data from 876 firms (438 firm-supplier dyads), we explore the impact of MO fit (i.e., fit between the focal firm's MO and its supplier's MO) on the focal firm's performance (ROA). The findings indicate a direct and positive relationship between MO fit and ROA. This highlights the need for firms to focus both on their own MO and their key supplier's MO as sources of competitive advantage in today's business environment. The strength of the relationship between MO fit and ROA increases when the exchanged business volume increases between the focal firm and its supplier and when the respective relationship progresses in age. Furthermore, firms with MO fit perform best, followed by firms with higher supplier MO misfit (firm's MO is lower than its key supplier's MO), while firms with lower supplier MO misfit (firm's MO is higher than its key supplier's MO) are the laggards."], "field": "Business, Management and Accounting", "q_year": 2025, "q_cid": "278399519", "pos_cid": 234060291, "source": "eval_collection"}
{"query_id": "scaleup_24442945_18825441", "query": "How to understand subjectivity and emergence in organizing while accounting for interconnected, co-emergent human and nonhuman modes of being", "pos": ["Staying with the Trouble. In the midst of spiraling ecological devastation, multispecies feminist theorist Donna J. Haraway offers provocative new ways to reconfigure our relations to the earth and all its inhabitants. She eschews referring to our current epoch as the Anthropocene, preferring to conceptualize it as what she calls the Chthulucene, as it more aptly and fully describes our epoch as one in which the human and nonhuman are inextricably linked in tentacular practices. The Chthulucene, Haraway explains, requires sym-poiesis, or making-with, rather than auto-poiesis, or self-making. Learning to stay with the trouble of living and dying together on a damaged earth will prove more conducive to the kind of thinking that would provide the means to building more livable futures. Theoretically and methodologically driven by the signifier SF—string figures, science fact, science fiction, speculative feminism, speculative fabulation, so far— Staying with the Trouble further cements Haraway's reputation as one of the most daring and original thinkers of our time."], "field": "Business, Management and Accounting", "q_year": 2021, "q_cid": "244429455", "pos_cid": 188254413, "source": "eval_collection"}
{"query_id": "scaleup_28103765_22538613", "query": "How to capture contextual relationships and meaning in the analyzed literature", "pos": ["Monolingual and multilingual topic analysis using LDA and BERT embeddings. Abstract Analyzing research topics offers potential insights into the direction of scientific development. In particular, analyzing multilingual research topics can help researchers grasp the evolution of topics globally, revealing topic similarity among scientific publications written in different languages. Most studies to date on topic analysis have been based on English-language publications and have relied heavily on citation-based topic evolution analysis. However, since it can be challenging for English publications to cite non-English sources and since many languages do not offer English translations of abstracts, citation-based methodologies are not suitable for analyzing multilingual research topic relations. Since multilingual sentence embeddings can effectively preserve word semantics in multilingual translation tasks, a topic model based on multilingual sentence embeddings could potentially generate topic–word distributions for publications in multilingual analysis. In this paper, which is situated in the field of library and information science, we use multilingual pretrained Bidirectional Encoder Representations from Transformers (BERT) embeddings and the Latent Dirichlet Allocation (LDA) topic model to analyze topic evolution in monolingual and multilingual topic similarity settings. For each topic, we multiply its LDA probability value by the averaged tensor similarity of BERT embeddings to explore the evolution of the topic in scientific publications. As our proposed method does not rely on a machine translator or the author's subjective translation, it avoids confusion and misusages caused by either machine error or the author's subjectively chosen English keywords. Our results show that the proposed approach is well-suited to analyzing the scientific evolutions in monolingual and scientific multilingual topic similarity relations."], "field": "Business, Management and Accounting", "q_year": 2025, "q_cid": "281037650", "pos_cid": 225386135, "source": "eval_collection"}
{"query_id": "scaleup_25183149_23514775", "query": "How to make technical scientific evidence engaging to policymakers given how they frame and interpret new information", "pos": ["How can we use the ‘science of stories’ to produce persuasive scientific stories?. The core goal of the science communicator is to convey accurate scientific information—to help people update existing understandings of the world and to change those understandings when necessary. However, science communicators, with their often extensive scientific training and educations, are often socialized into educating with information derived from scientific works in a way that mirrors the values of science itself. They do this by primarily relying on an approach termed the Knowledge Deficit Model, a model of communicating that emphasizes the repetition of emotionless objectively sterile information to increase understanding. The problem with this approach is that people do not actually make decisions or process information based on only objective scientific evidence. Their personal beliefs and emotional understandings of the world also play a powerful role. In this article we argue that to better connect with audiences communicators would do well to recognize themselves as storytellers–not to distort the truth, but to help people to connect with problems and issues on a more human level in terms of what matters to them. We reference extant narrative persuasion scholarship in public policy and elsewhere to offer a step-by-step guide to narrating scientific evidence. We argue that through understanding the structure of a narrative, science communicators can engage in the policy process, remaining true to the tenets of science and maintaining the integrity of the evidence, but doing so in a way that is compelling and thus also effective in helping solve problems."], "field": "Business, Management and Accounting", "q_year": 2022, "q_cid": "251831490", "pos_cid": 23514775, "source": "eval_collection"}
{"query_id": "scaleup_23714516_21315629", "query": "How to identify core–periphery structure across multiple sectoral networks while ensuring each sector contributes equally despite differing numbers of connections between countries?", "pos": ["Multiplex core–periphery organization of the human connectome. What is the core of the human brain is a fundamental question that has been mainly addressed by studying the anatomical connections between differently specialized areas, thus neglecting the possible contributions from their functional interactions. While many methods are available to identify the core of a network when connections between nodes are all of the same type, a principled approach to define the core when multiple types of connectivity are allowed is still lacking. Here, we introduce a general framework to define and extract the core–periphery structure of multi-layer networks by explicitly taking into account the connectivity patterns at each layer. We first validate our algorithm on synthetic networks of different size and density, and with tunable overlap between the cores at different layers. We then use our method to merge information from structural and functional brain networks, obtaining in this way an integrated description of the core of the human connectome. Results confirm the role of the main known cortical and subcortical hubs, but also suggest the presence of new areas in the sensori-motor cortex that are crucial for intrinsic brain functioning. Taken together these findings provide fresh evidence on a fundamental question in modern neuroscience and offer new opportunities to explore the mesoscale properties of multimodal brain networks."], "field": "Business, Management and Accounting", "q_year": 2021, "q_cid": "237145165", "pos_cid": 21315629, "source": "eval_collection"}
{"query_id": "scaleup_24637243_14948481", "query": "How to reconcile entrepreneurship’s implications for positive wellbeing and mental illbeing without treating them as a single outcome", "pos": ["The job demands-resources model: A meta-analytic review of longitudinal studies. ABSTRACT The job demands-resources (JD-R) model is an influential framework to understand how job characteristics foster employee well-being. Differing from the cross-sectional focus of most JD-R model reviews, this meta-analytic review uses longitudinal evidence to validate the essential assumptions within the JD-R model. We highlight two aspects: (1) The assessment of the methodological quality of the available longitudinal studies, and (2) the examination of the essential assumptions – the impact of job characteristics on well-being, and vice-versa – with meta-analytic structural equation modelling (metaSEM). We included 74 studies and evaluated their quality. Eighteen studies suffered from serious methodological shortcomings, whereas 29 studies (39%) were considered high-quality studies. Our meta-analytic structural equation models confirmed the essential assumptions simultaneously. The quality of the studies also had an influence on the goodness-of-fit indices. The models with reciprocal assumptions between job characteristics and well-being fitted the data best. The findings of this meta-analytic review suggest that the JD-R model is an excellent theoretical basis to assess employee well-being for a broad range of organisations. However, more research is needed to clarify the reciprocal relationships between job characteristics and employee well-being, as well as the different influences of challenging and hindering job demands on work engagement."], "field": "Business, Management and Accounting", "q_year": 2022, "q_cid": "246372432", "pos_cid": 149484817, "source": "eval_collection"}
{"query_id": "scaleup_27813133_23872406", "query": "How to adapt entrepreneurial ecosystems to crises while sustaining innovation, securing critical resources, and making rapid, well-informed decisions under uncertainty for organizational survival", "pos": ["Synergistic triad of crisis management: leadership, knowledge management and organizational learning. Purpose The prevalence of instability and crises in organizational ecosystems seems to be on the increase, with an upward trend in the occurrence of, for example, natural disasters, such as tornadoes in America, bushfires in Australia and the widespread outbreak of diseases, e.g., Covid-19. As contexts of crisis increase in frequency, the ability of organizations to adapt and effectively respond to crises has become a key necessity for organizational survival and continuity. The purpose of this paper is to explore how the repercussions of crises may be curtailed through a multidimensional crisis management approach. Design/methodology/approach This paper applies a narrative literature review and concept mapping to synthesize and establish relationships between the literature in the domains of leadership, knowledge management, learning and contexts of crisis. The output of this methodological orientation is the Integrated Crisis Management Framework, presenting a conceptualized overview of the symbiotic and intertwined manner through which leadership, knowledge management and learning contribute towards effective crisis management. Findings According to the analysis and the conceptual underpinnings of this paper, in contexts of crisis, leadership is generally responsible for aggregating crisis management strategies and establishing employee motivation. Knowledge management, on the other hand, provides the infrastructure necessary for calculated yet rapid decision-making. Similarly, in times of crisis, learning is a prerequisite for the development of a “learningful” organization, which contributes towards crisis management by serving as the organization's “memory” – where lessons learned from previous crises suffice to guide future crisis response. Originality/value The literature in crisis management reveals that existing crisis management models and frameworks generally consider crisis from a unidimensional perspective, neglecting to account for the multifaceted nature of crises, and the numerous attributes necessary to overcome contexts of crisis. To address this gap in the literature, this paper proposes a multidimensional conceptualization of crisis management through combining three core elements, including leadership, learning and knowledge management. The novelty of this paper is an Integrated Crisis Management Framework, and eight empirical propositions, which act as an impetus for future research."], "field": "Business, Management and Accounting", "q_year": 2025, "q_cid": "278131339", "pos_cid": 238724069, "source": "eval_collection"}
{"query_id": "scaleup_28192050_26713371", "query": "How to achieve substantive environmental benefits in firms with weak internal capabilities and strategic-alliance resources", "pos": ["Technology transfer challenges in asymmetric alliances between high-technology and low-technology firms. Low-technology firms face an increasingly disruptive innovation landscape as new legislation and changing market demands force them to dramatically reduce emission levels to become more sustainable. However, successfully developing and implementing sustainable technologies frequently presupposes alliances between low-technology firms (such as process industry companies) and high-tech firms (such as their specialized technology providers). Such alliances are asymmetric and problematic because of differences in approaches to learning, knowledge bases, collaboration routines, and high cognitive distance between high-and low-technology firms. Against this background, we performed a multiple case study of six asymmetric alliances operating in the food and food packaging sectors in the UK. The analysis reveals that technology distance asymmetry, technology integration complexity, and innovation capability incompatibilities prohibit technology transfer effectiveness. By mapping these themes across three phases of technology transfer, we identified a total of nine unique problems that hamper technology transfer effectiveness and, therefore, risk delaying or distorting the implementation of novel sustainable technology. The paper provides theoretical implications for the literature on innovation in LMT firms and for the literature on sustainability alliances along with practical implications for improving technology transfer between high-tech and low-tech firms considering climate change."], "field": "Business, Management and Accounting", "q_year": 2025, "q_cid": "281920500", "pos_cid": 267133718, "source": "eval_collection"}
{"query_id": "scaleup_25430375_20132190", "query": "How to clarify relationships among theories, concepts, and findings on Chinese multinational enterprises’ corporate social responsibility and identify gaps for future research", "pos": ["Literature review as a research methodology: An overview and guidelines. Abstract Knowledge production within the field of business research is accelerating at a tremendous speed while at the same time remaining fragmented and interdisciplinary. This makes it hard to keep up with state-of-the-art and to be at the forefront of research, as well as to assess the collective evidence in a particular area of business research. This is why the literature review as a research method is more relevant than ever. Traditional literature reviews often lack thoroughness and rigor and are conducted ad hoc, rather than following a specific methodology. Therefore, questions can be raised about the quality and trustworthiness of these types of reviews. This paper discusses literature review as a methodology for conducting research and offers an overview of different types of reviews, as well as some guidelines to how to both conduct and evaluate a literature review paper. It also discusses common pitfalls and how to get literature reviews published."], "field": "Business, Management and Accounting", "q_year": 2022, "q_cid": "254303750", "pos_cid": 201321905, "source": "eval_collection"}
{"query_id": "scaleup_22510790_17847434", "query": "How to clarify parents’ role in developing successors’ skills and commitments to renew family-firm routines and sustain the firm across generations", "pos": ["Deliberate Learning and the Evolution of Dynamic Capabilities. This paper investigates the mechanisms through which organizations develop dynamic capabilities, defined as routinized activities directed to the development and adaptation of operating routines. It addresses the role of (1) experience accumulation, (2) knowledge articulation, and (3) knowledge codifi- cation processes in the evolution of dynamic, as well as operational, routines. The argument is made that dynamic capabilities are shaped by the coevolution of these learning mechanisms. At any point in time, firms adopt a mix of learning behaviors constituted by a semiautomatic accumulation of experience and by deliberate investments in knowledge articulation and codification activities. The relative effectiveness of these capability-building mechanisms is analyzed here as contingent upon selected features of the task to be learned, such as its frequency, homogeneity, and degree of causal ambiguity. Testable hypotheses about these effects are derived. Somewhat counterintuitive implications of the analysis include the relatively superior effectiveness of highly deliberate learning processes such as knowledge codification at lower levels of frequency and homogeneity of the organizational task, in contrast with common managerial practice."], "field": "Business, Management and Accounting", "q_year": 2020, "q_cid": "225107906", "pos_cid": 17847434, "source": "eval_collection"}
{"query_id": "scaleup_23552089_20307015", "query": "How to understand how firms’ resources and managerial capabilities affect their ability to pursue cross-border digital opportunities that meet customer needs in an evolving digital business context", "pos": ["Gearing Up For Successful Digital Transformation. Business success depends on understanding how external forces such as globalization, demographics, and sustainability impact a company’s competitive strategy and position.2 Success also depends on exploiting powerful and reasonably priced digital infrastructures that include mobile technologies, especially smartphones; cloud computing, especially softwareas-a-service for such applications as artificial intelligence and machine learning; wired and wireless networks; and the Internet of things. In fact, digital technology platforms have become the foundation for an increasing share of economic growth. Digital technologies enable the development of new or enhanced products and services delivered to customers more efficiently. These technologies also enable fundamentally new ways to organize business.3 Digital transformation is the reinvention of the company— its vision and strategy, organizational structure, processes, capabilities, and culture. Such transformations not only change companies, but also markets and entire industries."], "field": "Business, Management and Accounting", "q_year": 2021, "q_cid": "235520895", "pos_cid": 203070154, "source": "eval_collection"}
{"query_id": "scaleup_23714516_13931603", "query": "How to determine how countries’ prominence in international ownership varies across industry sectors and relates to their overall prominence, distinguishing sector-specific patterns from broader global economic relationships", "pos": ["Structural measures for multiplex networks.. Many real-world complex systems consist of a set of elementary units connected by relationships of different kinds. All such systems are better described in terms of multiplex networks, where the links at each layer represent a different type of interaction between the same set of nodes rather than in terms of (single-layer) networks. In this paper we present a general framework to describe and study multiplex networks, whose links are either unweighted or weighted. In particular, we propose a series of measures to characterize the multiplexicity of the systems in terms of (i) basic node and link properties such as the node degree, and the edge overlap and reinforcement, (ii) local properties such as the clustering coefficient and the transitivity, and (iii) global properties related to the navigability of the multiplex across the different layers. The measures we introduce are validated on a genuinely multiplex data set of Indonesian terrorists, where information among 78 individuals are recorded with respect to mutual trust, common operations, exchanged communications, and business relationships."], "field": "Business, Management and Accounting", "q_year": 2021, "q_cid": "237145165", "pos_cid": 13931603, "source": "eval_collection"}
{"query_id": "scaleup_23552089_26249739", "query": "How to identify the expertise firms need for digital export given technology and online measurement requirements distinct from traditional export", "pos": ["The digital marketing skills gap: Developing a Digital Marketer Model for the communication industries. We explore digital marketing skills gaps in the communication industry.We find digital marketing skills gaps across the communication industry.The industry needs best practice guidance.Blending digital skills with current marketing approaches is a key strategic challenge.We construct a Digital Marketer Model summarising core skills. Scholarly literature suggests digital marketing skills gaps in industry, but these skills gaps are not clearly identified. The research aims to specify any digital marketing skills gaps encountered by professionals working in communication industries. In-depth interviews were undertaken with 20 communication industry professionals. A focus group followed, testing the rigour of the data.We find that a lack of specific technical skills; a need for best practice guidance on evaluation metrics, and a lack of intelligent futureproofing for dynamic technological change and development are skills gaps currently challenging the communication industry. However, the challenge of integrating digital marketing approaches with established marketing practice emerges as the key skills gap.Emerging from the key findings, a Digital Marketer Model was developed, highlighting the key competencies and skills needed by an excellent digital marketer.The research concludes that guidance on best practice, focusing upon evaluation metrics, futureproofing and strategic integration, needs to be developed for the communication industry. The Digital Marketing Model should be subject to further testing in industry and academia. Suggestions for further research are discussed."], "field": "Business, Management and Accounting", "q_year": 2021, "q_cid": "235520895", "pos_cid": 262497396, "source": "eval_collection"}
{"query_id": "scaleup_24051768_58912049", "query": "How to determine which entrepreneurial businesses warrant government support when many are home-based, low-income operations with no employees", "pos": ["Why encouraging more people to become entrepreneurs is bad public policy. Policy makers often think that creating more start-up companies will transform depressed economic regions, generate innovation, and create jobs. This belief is flawed because the typical start-up is not innovative, creates few jobs, and generates little wealth. Getting economic growth and jobs creation from entrepreneurs is not a numbers game. It is about encouraging the formation of high quality, high growth companies. Policy makers should stop subsidizing the formation of the typical start-up and focus on the subset of businesses with growth potential. While government officials will not be able to “pick winners,” they can identify start-ups with a low probability of generating jobs and enhancing economic growth. By eliminating incentives to create these low probability companies, policy makers can improve the average performance of new businesses."], "field": "Business, Management and Accounting", "q_year": 2021, "q_cid": "240517682", "pos_cid": 58912049, "source": "eval_collection"}
{"query_id": "scaleup_27878952_26789753", "query": "How to understand competition between human creators and GenAI when relative content quality affects user traffic and creator utility, and creators’ quality investments and content-sharing decisions interact with platform incentives to reward sharing", "pos": ["Human vs. Generative AI in Content Creation Competition: Symbiosis or Conflict?. The advent of generative AI (GenAI) technology produces transformative impact on the content creation landscape, offering alternative approaches to produce diverse, high-quality content across media, thereby reshaping online ecosystems but also raising concerns about market over-saturation and the potential marginalization of human creativity. Our work introduces a competition model generalized from the Tullock contest to analyze the tension between human creators and GenAI. Our theory and simulations suggest that despite challenges, a stable equilibrium between human and AI-generated content is possible. Our work contributes to understanding the competitive dynamics in the content creation industry, offering insights into the future interplay between human creativity and technological advancements in GenAI."], "field": "Business, Management and Accounting", "q_year": 2025, "q_cid": "278789521", "pos_cid": 267897530, "source": "eval_collection"}
{"query_id": "scaleup_28350077_26504052", "query": "How to ensure complete, reproducible search documentation covering database selection, limits, filters, and handling of retrieved and duplicate records", "pos": ["PRISMA-S: an extension to the PRISMA Statement for Reporting Literature Searches in Systematic Reviews. Background Literature searches underlie the foundations of systematic reviews and related review types. Yet, the literature searching component of systematic reviews and related review types is often poorly reported. Guidance for literature search reporting has been diverse, and, in many cases, does not offer enough detail to authors who need more specific information about reporting search methods and information sources in a clear, reproducible way. This document presents the PRISMA-S (Preferred Reporting Items for Systematic reviews and Meta-Analyses literature search extension) checklist, and explanation and elaboration. Methods The checklist was developed using a 3-stage Delphi survey process, followed by a consensus conference and public review process. Results The final checklist includes 16 reporting items, each of which is detailed with exemplar reporting and rationale. Conclusions The intent of PRISMA-S is to complement the PRISMA Statement and its extensions by providing a checklist that could be used by interdisciplinary authors, editors, and peer reviewers to verify that each component of a search is completely reported and therefore reproducible."], "field": "Business, Management and Accounting", "q_year": 2025, "q_cid": "283500775", "pos_cid": 265040525, "source": "eval_collection"}
{"query_id": "scaleup_23714516_3805712", "query": "How to determine where the densely interconnected central region ends and the loosely connected outer region begins in each layer", "pos": ["Rich-Cores in Networks. A core comprises of a group of central and densely connected nodes which governs the overall behaviour of a network. It is recognised as one of the key meso-scale structures in complex networks. Profiling this meso-scale structure currently relies on a limited number of methods which are often complex and parameter dependent or require a null model. As a result, scalability issues are likely to arise when dealing with very large networks together with the need for subjective adjustment of parameters. The notion of a rich-club describes nodes which are essentially the hub of a network, as they play a dominating role in structural and functional properties. The definition of a rich-club naturally emphasises high degree nodes and divides a network into two subgroups. Here, we develop a method to characterise a rich-core in networks by theoretically coupling the underlying principle of a rich-club with the escape time of a random walker. The method is fast, scalable to large networks and completely parameter free. In particular, we show that the evolution of the core in World Trade and C. elegans networks correspond to responses to historical events and key stages in their physical development, respectively."], "field": "Business, Management and Accounting", "q_year": 2021, "q_cid": "237145165", "pos_cid": 3805712, "source": "eval_collection"}
{"query_id": "scaleup_23728966_12781230", "query": "How to assess the effects of disruption-related stock-outs on subsequent customers’ willingness to order and rationing profitability, beyond immediate lost sales", "pos": ["Managing a supply chain under the impact of customer reviews: A two-period game analysis. Abstract We investigate a two-period problem for a supply chain involving a manufacturer and a retailer, who serve early and late customers in the first and second periods, respectively. In each period, customers make their purchase decisions and also provide their review ratings. The manufacturer determines his quality and wholesale price, and the retailer then decides on her retail price. We perform a game-theoretic analysis and find Stackelberg equilibrium for the supply chain in each period. When early customers overrate the actual quality in their ratings, the sales in the second period are higher than those when the average review rating reflects the actual quality, and the quality levels as well as the wholesale and retail prices in the two periods are no smaller than those when the actual quality is truly rated. Moreover, in both periods, the quality overstatement increases the retailer’s expected profits in the two periods but may reduce the manufacturer’s expected profits. We also show that the supply chain can achieve a higher profit if customers gain a greater utility per quality level. A larger value of customers’ unit quality-deviation-based rating can raise the quality level as well as the expected sales and the two firms’ expected profits in the second period. The supply chain can obtain a higher profit in the first period if the variance of early customers’ quality expectations is larger, and it can achieve a higher profit in the second period if the variance of later customers’ quality perceptions is smaller."], "field": "Business, Management and Accounting", "q_year": 2021, "q_cid": "237289664", "pos_cid": 127812305, "source": "eval_collection"}
{"query_id": "scaleup_27205051_23419876", "query": "How to clarify the relationship between responsible leadership, employees’ harmonious environmental passion, and voluntary environmental behavior", "pos": ["Birds of a feather flock together: the relationship between managers’ and employees’ perceptions of HR practices. Abstract Human resource (HR) scholars argue that employees perform better when their perceptions of HR practices are consistent with those of their managers. However, few studies have examined the circumstances under which employees are likely to develop consistent perceptions of HR practices as their managers. Drawing on social information processing theory, we investigate the relationship between managers’ and employees’ perceptions of HR practices and explore the factors that moderate this relationship. Cross-level analyses of data from 380 employees matched to 32 department managers in 23 Chinese state-owned enterprises reveal a positive relationship between managers’ and employees’ perceptions of HR practices. This relationship is stronger when managers and employees report similar levels of power distance, long-term orientation, and collectivism. In addition, the moderating effect of long-term orientation similarity is stronger for employees with a high level of cognitive cultural intelligence."], "field": "Business, Management and Accounting", "q_year": 2024, "q_cid": "272050511", "pos_cid": 234198766, "source": "eval_collection"}
{"query_id": "scaleup_23904848_15210228", "query": "How to clarify the role of commercial rankers’ social media activity and apparently technical ranking materials in forming and circulating emotions and influencing higher education policy", "pos": ["Affect theory and policy mobility: challenges and possibilities for critical policy research. ABSTRACT This article contributes to a growing literature on policy mobilities by proposing that affect be considered in analyses of the movements and transformations of policy over time and space. In particular, collective affective conditions, the role of affect in terms of infrastructures and actors of policy apparatuses and the mediating influences of affective bodily encounters are discussed in relation to why and how policies move. The article suggests that policy mobilities research could be strengthened by further examining how affect is inherent in familiar considerations of policy actors and networks, and tools and infrastructures such as policy documents, meetings, and data, and their contributions to policy flows. In addition, encompassing affective atmospheres and structures of feeling, as well as affect in the specific relationships between people and with place, are indicated as important for the study of policy mobility and immobility, including in shaping policy uptake and resistance. Examples from educational research are used to elaborate these considerations of affect for policy mobilities and to suggest possible topical and methodological implications for critical policy research."], "field": "Business, Management and Accounting", "q_year": 2021, "q_cid": "239048482", "pos_cid": 152102289, "source": "eval_collection"}
{"query_id": "scaleup_27786655_14373933", "query": "How to clarify how highly intercorrelated work-related flow dimensions and distinct, weakly intercorrelated employability competencies relate to their respective overall constructs", "pos": ["Recommendations for improving the construct clarity of higher-order multidimensional constructs. Abstract In recent decades, there has been a proliferation of higher-order multidimensional constructs in the management and psychology literatures. Unfortunately, few guidelines have been presented for assessing the appropriateness of these constructs. In the current paper, the authors present seven recommendations for evaluating the construct clarity of multidimensional constructs. As an example, these guidelines are applied to existing multidimensional constructs, such as core self-evaluation and work engagement. The guidelines presented in this paper provide a roadmap for researchers interested in developing multidimensional constructs and identifying aspects of existing multidimensional constructs that are in need of improvement."], "field": "Business, Management and Accounting", "q_year": 2025, "q_cid": "277866557", "pos_cid": 143739330, "source": "eval_collection"}
{"query_id": "scaleup_23714516_15186389", "query": "How to compare industries in terms of whether entities with many international economic relationships tend to engage with entities with many or few such relationships", "pos": ["Mixing patterns in networks.. We study assortative mixing in networks, the tendency for vertices in networks to be connected to other vertices that are like (or unlike) them in some way. We consider mixing according to discrete characteristics such as language or race in social networks and scalar characteristics such as age. As a special example of the latter we consider mixing according to vertex degree, i.e., according to the number of connections vertices have to other vertices: do gregarious people tend to associate with other gregarious people? We propose a number of measures of assortative mixing appropriate to the various mixing types, and apply them to a variety of real-world networks, showing that assortative mixing is a pervasive phenomenon found in many networks. We also propose several models of assortatively mixed networks, both analytic ones based on generating function methods, and numerical ones based on Monte Carlo graph generation techniques. We use these models to probe the properties of networks as their level of assortativity is varied. In the particular case of mixing by degree, we find strong variation with assortativity in the connectivity of the network and in the resilience of the network to the removal of vertices."], "field": "Business, Management and Accounting", "q_year": 2021, "q_cid": "237145165", "pos_cid": 15186389, "source": "eval_collection"}
{"query_id": "scaleup_28013973_14413458", "query": "How to explain the role of perceived peer approval in consumers’ willingness to accept leasing when distrust and a strong culture of ownership hinder adoption", "pos": ["A Model of Green Consumption Behavior Constructed by the Theory of Planned Behavior. In recent years, global warming has become a widespread well-publicized issue. As the general public have become aware of the importance of protecting the environment, consumers have started to evidence a marked preference for green products. This study constructed a model describing the relationships among perceived benefit of green consumption behavior, perceived risk, moral responsibility, normative belief, control strength, control belief, attitude, subjective norms, behavior control, behavior intention, and actual behavior. An analysis of 560 valid questionnaires resulted in six main findings: (1) Perceived benefit of green consumption has a significantly positive impact on consumer attitude. (2) Perceived risk of green consumption has a significantly negative impact on consumer attitude. (3) Normative belief and moral responsibility both have significantly positive impacts on consumer subjective norms. (4) Control strength and control belief both have significantly positive impacts on consumer behavior control. (5) Attitude, subjective norms and behavior control both have significantly positive impacts on consumer behavior intention. (6) Behavioral intention and behavior control both have significantly positive impacts on actual consumer behavior. The results of this study provide reference to industry managers in the formulation of green marketing strategy."], "field": "Business, Management and Accounting", "q_year": 2025, "q_cid": "280139730", "pos_cid": 144134588, "source": "eval_collection"}
{"query_id": "scaleup_23714516_10557200", "query": "How to understand sector-specific variation in the structure and intensity of international economic relationships that aggregate accounts of globalisation do not adequately capture", "pos": ["World Input-Output Network. Production systems, traditionally analyzed as almost independent national systems, are increasingly connected on a global scale. Only recently becoming available, the World Input-Output Database (WIOD) is one of the first efforts to construct the global multi-regional input-output (GMRIO) tables. By viewing the world input-output system as an interdependent network where the nodes are the individual industries in different economies and the edges are the monetary goods flows between industries, we analyze respectively the global, regional, and local network properties of the so-called world input-output network (WION) and document its evolution over time. At global level, we find that the industries are highly but asymmetrically connected, which implies that micro shocks can lead to macro fluctuations. At regional level, we find that the world production is still operated nationally or at most regionally as the communities detected are either individual economies or geographically well defined regions. Finally, at local level, for each industry we compare the network-based measures with the traditional methods of backward linkages. We find that the network-based measures such as PageRank centrality and community coreness measure can give valuable insights into identifying the key industries."], "field": "Business, Management and Accounting", "q_year": 2021, "q_cid": "237145165", "pos_cid": 10557200, "source": "eval_collection"}
{"query_id": "scaleup_27060728_51958536", "query": "How to integrate findings on Brazil’s e-commerce sector into a coherent understanding that supports theoretical development despite differing conceptualizations across research communities", "pos": ["Concern over cost of and access to cancer treatments: A meta-narrative review of nivolumab and pembrolizumab studies.. BACKGROUND A better understanding of the modulation of the immune system has resulted in the development of new classes of antitumor agents such as nivolumab and pembrolizumab. Despite the proven effectiveness and tolerability of these new drugs for specific types of cancer, the high cost of treatment has affected their accessibility. OBJECTIVE The aim of this study is to conduct a meta-narrative review of studies that have addressed the concerns that have been voiced regarding the cost of and access to nivolumab and pembrolizumab in oncology health care. This meta-narrative review attempts to answer the following questions: (1) which papers have considered this broad topic area?; (2) what are the main empirical/theoretical findings?; and (3) what insights can be drawn by combining and comparing findings from different papers? METHODS AND DATA SOURCE A meta-narrative review has been conducted in 5 research databases (Web of Science, Science Direct, Scopus, Embase and Pubmed) without time limitations up to January of 2017 to address concerns related to the cost of and access to nivolumab and pembrolizumab in oncology health care. From each research base, articles were selected that had a key word related to the theme of pharmacoeconomics and nivolumab or pembrolizumab in any field of scientific work. The research questions were analyzed through the application of a meta-narrative review approach and the use of a convergence-coding matrix to summarize similarities and differences directly related to the research topic between the different papers. KEY FINDINGS The first contribution of this meta-narrative review is that it summarizes economic-based works on the use of nivolumab and pembrolizumab, particularly for three therapeutic indications: melanoma, NSCLC and RCC. In general, despite the clinical benefit of nivolumab and pembrolizumab being well accepted and proven by scientific works, the published studies show that there are contradictory results with regard to the cost-effectiveness of these anti-PD-1s. The regulatory, economic and epidemiological variations mean that healthcare costs for cancer patients vary greatly from country to country and according to the type of tumor. The second contribution has to do with the recommendations for the development of high quality process for pharmacoeconomic analyses, especially in the new field of immuno-oncology. Finally, the third contribution is with regard to recommendations for the sustainable use of immunotherapies. CONCLUSIONS Given the revolution in cancer therapy in recent years, the efficient allocation of existing resources is essential for healthcare systems to meet the evolving needs of populations and remain sustainable in the long term. The application of high quality information that stems from scientific evidence and economic modeling can help considerably to make the healthcare system sustainable over time mainly due to a higher number of therapeutic indications or more countries giving regulatory approval for the use of new and expensive cancer drugs."], "field": "Business, Management and Accounting", "q_year": 2024, "q_cid": "270607282", "pos_cid": 51958536, "source": "eval_collection"}
{"query_id": "scaleup_28350077_15885583", "query": "How to clarify the influence and structure of scientific evidence on modern slavery in the context of the 2030 Agenda, including key research actors, collaboration patterns, and thematic trends, to inform public policies and future research priorities", "pos": ["Supply chain finance: A systematic literature review and bibliometric analysis. Abstract Supply Chain Finance (SCF) is an effective method to lower financing costs and improve financing efficiency and effectiveness, and it has gained research momentum in recent years. This paper adopts a systematic literature review methodology combined with bibliometric, network and content analysis based on 348 papers identified from mainstream academic databases. This review provides insights not previously fully captured or evaluated by other reviews on this topic, including key authors, key journals and the prestige of the reviewed papers. Using rigorous bibliometric and visualisation tools, we identified four research clusters, including deteriorating inventory models under trade credit policy based on the EOQ/EPQ model; inventory decisions with trade credit policy under more complex situations; interaction between replenishment decisions and delay payment strategies in the supply chain and roles of financing service in the supply chain. Based on the clusters identified, we carried out a further content analysis of 112 papers, identifying research gaps and proposing seven actionable directions for future research. The findings provide a robust roadmap for further investigation in this field."], "field": "Business, Management and Accounting", "q_year": 2025, "q_cid": "283500775", "pos_cid": 158855830, "source": "eval_collection"}
{"query_id": "scaleup_28350077_27831546", "query": "How to comprehensively identify eligible evidence on modern slavery in the context of the 2030 Agenda", "pos": ["Legal Reforms and Outcomes of the Action of Police Institutions in Combating Violence Against Women: A Systematic Review Protocol. Domestic violence (DV) against women in intimate relationships is a global public health issue with significant legal and institutional challenges. While legal reforms seek to enhance victim protection and perpetrator accountability, their implementation faces barriers within the criminal justice system, particularly in police and judicial institutions. A multi-agency approach—coordinating police, courts, social services, and NGOs—has emerged to improve institutional responses. This systematic review protocol follows PRISMA-P 2015 guidelines to assess the impact of legal reforms on DV policies within police institutions. A qualitative synthesis will analyse contextual factors, with searches conducted in Web of Science, Scopus, and MEDLINE/PubMed, complemented by citation mapping via Litmaps. The PICo framework and validated using the PRESS 2015 guided the search strategy, while PRISMA-S will inform data extraction and Rayyan will manage references. Independent reviewers will assess studies, resolving disagreements with a senior researcher. The review will evaluate legal reforms’ effects on DV recidivism, their effectiveness across contexts, and perceptions of punitive versus restorative approaches. Key challenges include resource constraints, institutional resistance, and program sustainability. Findings will support policymakers in refining legislative measures and strengthening institutional responses."], "field": "Business, Management and Accounting", "q_year": 2025, "q_cid": "283500775", "pos_cid": 278315469, "source": "eval_collection"}
{"query_id": "scaleup_23531872_11513786", "query": "How to assess the effects of macroeconomic shocks and policy responses on disposable household incomes across the income distribution when not all eligible households claim means-tested benefits", "pos": ["Endogenizing take-up of social assistance in a microsimulation model: a case study for Germany. \"Microsimulation studies typically assume that all entitlements to means-tested benefits are actually claimed by eligible households, despite a large body of research that suggests that take-up rates are substantially below 100%. The assumption of full take-up tends to exaggerate the simulated increase in caseloads and fiscal costs of a social policy reform. This paper investigates the impact of non-take-up for two hypothetical scenarios, namely increasing and decreasing the base amount of social assistance in Germany by EURO 100 per month. We find a substantial effect of considering non-take-up on the simulated change in fiscal costs and in particular on the change in caseloads, where the full take-up assumption exaggerates the latter change by a factor of about two.\" (Author's abstract, IAB-Doku) ((en))"], "field": "Business, Management and Accounting", "q_year": 2021, "q_cid": "235318726", "pos_cid": 115137862, "source": "eval_collection"}
{"query_id": "scaleup_27574660_21909249", "query": "How to determine whether a service-learning experience increases service orientation rather than the increase reflecting group differences or changes over time", "pos": ["Use of Quasi-Experimental Research Designs in Education Research: Growth, Promise, and Challenges. In the past few decades, we have seen a rapid proliferation in the use of quasi-experimental research designs in education research. This trend, stemming in part from the “credibility revolution” in the social sciences, particularly economics, is notable along with the increasing use of randomized controlled trials in the strive toward rigorous causal inference. The overarching purpose of this chapter is to explore and document the growth, applicability, promise, and limitations of quasi-experimental research designs in education research. We first provide an overview of widely used quasi-experimental research methods in this growing literature, with particular emphasis on articles from the top ranked education research journals, including those published by the American Educational Research Association. Next, we demonstrate the applicability and promise of these methods in enhancing our understanding of the causal effects of education policies and interventions using key examples and case studies culled from the extant literature across the pre-K–16 education spectrum. Finally, we explore the limitations of these methods and conclude with thoughts on how education researchers can adapt these innovative, interdisciplinary techniques to further our understanding of some of the most enduring questions in educational policy and practice."], "field": "Business, Management and Accounting", "q_year": 2025, "q_cid": "275746602", "pos_cid": 219092495, "source": "eval_collection"}
{"query_id": "scaleup_25802877_17476227", "query": "How to determine whether the indirect relationship between ceo narcissism and innovation involving top management teams’ strategic decision comprehensiveness is statistically supported in family firms", "pos": ["Causal Mediation Analysis. Estimating the mechanisms that connect explanatory variables with the explained variable, also known as “mediation analysis,” is central to a variety of social-science fields, especially psychology, and increasingly to fields like epidemiology. Recent work on the statistical methodology behind mediation analysis points to limitations in earlier methods. We implement in Stata computational approaches based on recent developments in the statistical methodology of mediation analysis. In particular, we provide functions for the correct calculation of causal mediation effects using several different types of parametric models, as well as the calculation of sensitivity analyses for violations to the key identifying assumption required for interpreting mediation results causally."], "field": "Business, Management and Accounting", "q_year": 2022, "q_cid": "258028779", "pos_cid": 17476227, "source": "eval_collection"}
{"query_id": "scaleup_21947458_15878242", "query": "How to assess relationships among quality management practices, innovation and organizational performance involving many constructs, indicators and structural paths while ensuring valid and reliable construct measures", "pos": ["When to use and how to report the results of PLS-SEM. Purpose The purpose of this paper is to provide a comprehensive, yet concise, overview of the considerations and metrics required for partial least squares structural equation modeling (PLS-SEM) analysis and result reporting. Preliminary considerations are summarized first, including reasons for choosing PLS-SEM, recommended sample size in selected contexts, distributional assumptions, use of secondary data, statistical power and the need for goodness-of-fit testing. Next, the metrics as well as the rules of thumb that should be applied to assess the PLS-SEM results are covered. Besides presenting established PLS-SEM evaluation criteria, the overview includes the following new guidelines: PLSpredict (i.e., a novel approach for assessing a model’s out-of-sample prediction), metrics for model comparisons, and several complementary methods for checking the results’ robustness. Design/methodology/approach This paper provides an overview of previously and recently proposed metrics as well as rules of thumb for evaluating the research results based on the application of PLS-SEM. Findings Most of the previously applied metrics for evaluating PLS-SEM results are still relevant. Nevertheless, scholars need to be knowledgeable about recently proposed metrics (e.g. model comparison criteria) and methods (e.g. endogeneity assessment, latent class analysis and PLSpredict), and when and how to apply them to extend their analyses. Research limitations/implications Methodological developments associated with PLS-SEM are rapidly emerging. The metrics reported in this paper are useful for current applications, but must always be up to date with the latest developments in the PLS-SEM method. Originality/value In light of more recent research and methodological developments in the PLS-SEM domain, guidelines for the method’s use need to be continuously extended and updated. This paper is the most current and comprehensive summary of the PLS-SEM method and the metrics applied to assess its solutions."], "field": "Business, Management and Accounting", "q_year": 2020, "q_cid": "219474582", "pos_cid": 158782424, "source": "eval_collection"}
{"query_id": "scaleup_24637243_55829368", "query": "How to clarify how entrepreneurs’ wellbeing and exposure to stressful injustices vary with legal fairness and rights protection in democratic and autocratic settings", "pos": ["Why Nations Fail: The Origins of Power, Prosperity, and Poverty. In the West are the 'haves', while much of the rest of the world are the 'have-nots'. The extent of inequality today is unprecedented. Drawing on an extraordinary range of contemporary and historical examples, Why Nations Fail looks at the root of the problems facing some nations. Economists and scientists have offered useful insights into the reasons for certain aspects of poverty, such as Jeffrey Sachs (it's geography and the weather), and Jared Diamond (it's technology and species). But most theories ignore the incentives and institutions that populations need to invest and prosper: they need to know that if they work hard, they can make money and actually keep it - and the key to ensuring these incentives is sound institutions. Incentives and institutions are what separate the have and have-nots. Based on fifteen years of research, and stepping boldly into the territory of Ian Morris's Why the West Rules - For Now, Daron Acemoglu and James Robinson blend economics, politics, history and current affairs to provide a new, persuasive way of understanding wealth and poverty. And, perhaps most importantly, they provide a pragmatic basis for the hope that those mired in poverty can be placed on the path to prosperity."], "field": "Business, Management and Accounting", "q_year": 2022, "q_cid": "246372432", "pos_cid": 55829368, "source": "eval_collection"}
{"query_id": "scaleup_52921372_73686026", "query": "How to achieve low-cost, reproducible, scalable production of colloidal metal sulfide nanocrystals without resource-intensive precursor preparation or excessive labor demands", "pos": ["Synthesis cost dictates the commercial viability of lead sulfide and perovskite quantum dot photovoltaics. Any new solar photovoltaic (PV) technology must reach low production costs to compete with today's market-leading crystalline silicon and commercial thin-film PV technologies. Colloidal quantum dots (QDs) could open up new applications by enabling lightweight and flexible PV modules. However, the cost of synthesizing nanocrystals at the large scale needed for PV module production has not previously been investigated. Based on our experience with commercial QD scale-up, we develop a Monte Carlo model to analyze the cost of synthesizing lead sulfide and metal halide perovskite QDs using 8 different reported synthetic methods. We also analyze the cost of solution-phase ligand exchange for preparing deposition-ready PbS QD inks, as well as the manufacturing cost for roll-to-roll solution-processed PV modules using these materials. We find that present QD synthesis costs are prohibitively high for PV applications, with median costs of 11 to 59 $ per g for PbS QDs (0.15 to 0.84 $ per W for a 20% efficient cell) and 73 $ per g for CsPbI3 QDs (0.74 $ per W). QD ink preparation adds 6.3 $ per g (0.09 $ per W). In total, QD materials contribute up to 55% of the total module cost, making even roll-to-roll-processed QDPV modules significantly more expensive than silicon PV modules. These results suggest that the development of new low-cost synthetic methods is critically important for the commercial relevance of QD photovoltaics. Using our cost model, we identify strategies for reducing synthetic cost and propose a cost target of 5 $ per g to move QD solar cells closer to commercial viability."], "field": "Chemical Engineering", "q_year": 2018, "q_cid": "52921372", "pos_cid": 73686026, "source": "eval20x26"}
{"query_id": "scaleup_49669829_94072790", "query": "How to determine LiTFSI’s effects on the local molecular environment around methyl groups when vitrification creates diverse local environments that prevent experimental observation of quantum tunneling", "pos": ["Prediction of the crystal structures of axitinib, a polymorphic pharmaceutical molecule. Abstract Organic molecules can crystallize in multiple structures or polymorphs, yielding crystals with very different physical and mechanical properties. The prediction of the polymorphs that may appear in nature is a challenge with great potential benefits for the development of new products and processes. A multistage crystal structure prediction (CSP) methodology is applied to axitinib, a pharmaceutical molecule with significant polymorphism arising from molecular flexibility. The CSP study is focused on those polymorphs with one molecule in the asymmetric unit. The approach successfully identifies all four known polymorphs within this class, as well as a large number of other low-energy structures. The important role of conformational flexibility is highlighted. The performance of the approach is discussed in terms of both the quality of the results and various algorithmic and computational aspects, and some key priorities for further work in this area are identified."], "field": "Chemical Engineering", "q_year": 2018, "q_cid": "49669829", "pos_cid": 94072790, "source": "eval20x26"}
{"query_id": "scaleup_53692566_33018896", "query": "How to determine reaction energies and barriers in ionic liquids with long-range electrostatic effects and a finite simulation interaction cutoff", "pos": ["Long-range electrostatic corrections in multipolar/polarizable QM/MM simulations. Taking long-range electrostatic effects into account in classical and hybrid quantum mechanics–molecular mechanics (QM/MM) simulations is necessary for an accurate description of the system under study. We have recently developed a method, termed long-range electrostatic corrections (LREC), for monopolar QM/MM calculations. Here, we present an extension of LREC for multipolar/polarizable QM/MM simulations within the LICHEM software package. Reaction barriers and QM–MM interaction energies converge with a LREC cutoff between 20 and 25 Å, in agreement with our previous results. Additionally, the LREC approach for the QM–MM interactions can be smoothly combined with standard shifting or Ewald summation methods in the MM calculations. We recommend the use of QM(LREC)/MM(PME), where the QM region is treated with LREC and the MM region is treated with particle mesh Ewald (PME) summation. This combination is an excellent compromise between simplicity, speed, and accuracy for large QM/MM simulations."], "field": "Chemical Engineering", "q_year": 2018, "q_cid": "53692566", "pos_cid": 33018896, "source": "eval20x26"}
{"query_id": "scaleup_46888761_3222621", "query": "How to select microbes that can supply enough metabolic energy for energy-intensive chemical production from carbon monoxide", "pos": ["Pathways and Bioenergetics of Anaerobic Carbon Monoxide Fermentation. Carbon monoxide can act as a substrate for different modes of fermentative anaerobic metabolism. The trait of utilizing CO is spread among a diverse group of microorganisms, including members of bacteria as well as archaea. Over the last decade this metabolism has gained interest due to the potential of converting CO-rich gas, such as synthesis gas, into bio-based products. Three main types of fermentative CO metabolism can be distinguished: hydrogenogenesis, methanogenesis, and acetogenesis, generating hydrogen, methane and acetate, respectively. Here, we review the current knowledge on these three variants of microbial CO metabolism with an emphasis on the potential enzymatic routes and bio-energetics involved."], "field": "Chemical Engineering", "q_year": 2018, "q_cid": "46888761", "pos_cid": 3222621, "source": "eval20x26"}
{"query_id": "scaleup_28161574_27298941", "query": "How to efficiently convert dilute nitric oxide into ammonia in neutral media", "pos": ["Electronic Metal-Support Interaction Induces Hydrogen Spillover and Platinum Utilization in Hydrogen Evolution Reaction.. The substantial promotion of hydrogen evolution reaction (HER) catalytic performance relies on the breakup of the Sabatier principle, which can be achieved by the alternation of the support and electronic metal support interaction (EMSI) is noticed. Due to the utilization of tungsten disulfides as support for platinum (Pt@WS2), surprisingly, Pt@WS2 demands only 31 mV overpotential to attain 10 mA cm-2 in acidic HER test, corresponding to a 2.5-fold higher mass activity than benchmarked Pt/C. The pH dependent electrochemical measurements associated with H2-TPD and in-situ Raman spectroscopy indicate a hydrogen spillover involved HER mechanism is confirmed. The WS2 support triggers a higher hydrogen binding strength for Pt leading to the increment in hydrogen concentration at Pt sites proved by upshifted d band center as well as lower Gibbs free energy of hydrogen, favourable for hydrogen spillover. Besides, the WS2 shows a comparably lower effect on Gibbs free energy for different Pt layers (-0.50 eV layer-1) than carbon black (-0.88 eV layer-1) contributing to a better Pt utilization. Also, the theoretical calculation suggests the hydrogen spillover occurs on the 3rd Pt layer in Pt@WS2; moreover, the energy barrier is lowered with increment in hydrogen coverage on Pt."], "field": "Chemical Engineering", "q_year": 2025, "q_cid": "281615741", "pos_cid": 272989410, "source": "eval_collection"}
{"query_id": "scaleup_24826305_1168783", "query": "How to achieve sub-femtomolar detection of nucleic acids from dilute solutions without amplification despite inefficient surface capture", "pos": ["Aqueous two-phase system patterning of detection antibody solutions for cross-reaction-free multiplex ELISA. Accurate disease diagnosis, patient stratification and biomarker validation require the analysis of multiple biomarkers. This paper describes cross-reactivity-free multiplexing of enzyme-linked immunosorbent assays (ELISAs) using aqueous two-phase systems (ATPSs) to confine detection antibodies at specific locations in fully aqueous environments. Antibody cross-reactions are eliminated because the detection antibody solutions are co-localized only to corresponding surface-immobilized capture antibody spots. This multiplexing technique is validated using plasma samples from allogeneic bone marrow recipients. Patients with acute graft versus host disease (GVHD), a common and serious condition associated with allogeneic bone marrow transplantation, display higher mean concentrations for four multiplexed biomarkers (HGF, elafin, ST2 and TNFR1) relative to healthy donors and transplant patients without GVHD. The antibody co-localization capability of this technology is particularly useful when using inherently cross-reactive reagents such as polyclonal antibodies, although monoclonal antibody cross-reactivity can also be reduced. Because ATPS-ELISA adapts readily available antibody reagents, plate materials and detection instruments, it should be easily transferable into other research and clinical settings."], "field": "Chemical Engineering", "q_year": 2022, "q_cid": "248263058", "pos_cid": 1168783, "source": "eval_collection"}
{"query_id": "scaleup_24492630_18981583", "query": "How to characterize protein–impregnated resin interactions and interpret experimental sorption data", "pos": ["Adsorption of Direct Blue 78 Using Chitosan and Cyclodextrins as Adsorbents. The dyeing industry is one of the most polluting in the world. The adsorption of dyes by polymeric matrixes can be used to minimize the discharge of dyes into the environment. In the present study, chitosan-NaOH and β-cyclodextrin-epichlorohydrin polymers were used to remove the dye Direct Blue 78 from a wastewater model. To understand the adsorption behavior of Direct Blue 78 onto the polymers, adsorption rate and maximum adsorption capacity were calculated using kinetic tests and isotherm curves respectively. The kinetic data and mechanism of the adsorption process were analyzed by three models and the equilibrium data by three adsorption isotherms; also the different thermodynamic parameters were calculated. Results showed that the adsorption process follows pseudo-second-order kinetics in both polymers and the Langmuir isotherm best-fitted data for chitosan-NaOH polymer and the Freundlich isotherm for the β-CDs-EPI polymer. The adsorption process is exothermic in both cases and spontaneous for the β-CDs-EPI polymer to a certain temperature and not spontaneous for the chitosan-NaOH polymer and β-CDs-EPI polymer at higher temperatures. The complementary action of an advanced oxidation process eliminated >99% of the dye from water. The coupled process seems to be suitable for reducing the environmental impact of the dyeing industry."], "field": "Chemical Engineering", "q_year": 2021, "q_cid": "244926301", "pos_cid": 189815834, "source": "eval_collection"}
{"query_id": "scaleup_26372728_13667156", "query": "How to explain observed ion-selective electrode responses and the role of interactions between cations and solid-contact materials", "pos": ["Two-dimensional Na–Cl crystals of unconventional stoichiometries on graphene surface from dilute solution at ambient conditions. AbstractNaCl in a 1:1 stoichiometry is the only known stable form of the Na–Cl crystal under ambient conditions, and non-1:1 Na–Cl species can only form under extreme conditions, such as high pressures. Here we report the direct observation, under ambient conditions, of Na2Cl and Na3Cl as two-dimensional (2D) Na–Cl crystals, together with regular NaCl, on reduced graphene oxide membranes and on the surfaces of natural graphite powders from salt solutions far below the saturated concentration. Molecular dynamics and density functional theory calculations suggest that this unconventional crystallization process originates from the cation–π interaction between the ions and the π-conjugated system in the graphitic surface, which promotes the ion–surface adsorption. The strong Na+–π interaction and charge transfer lead to stoichiometries with an excess of Na+. With unique electron and spin distributions and bonding, the resulting 2D crystals may have unusual electronic, magnetic, optical and mechanical properties.The common form of salt has a 1:1 ratio of Na+ and Cl−; however, species that deviate from this can be found under extreme conditions, such as high pressure. Now, as a result of cation–π interactions that promote ion–surface adsorption, Na2Cl and Na3Cl have been observed as two-dimensional crystals on graphene at ambient conditions."], "field": "Chemical Engineering", "q_year": 2023, "q_cid": "263727285", "pos_cid": 13667156, "source": "eval_collection"}
{"query_id": "scaleup_27657842_51893137", "query": "How to efficiently convert nitrite to ammonia", "pos": ["Defect Sites in Ultrathin Pd Nanowires Facilitate the Highly Efficient Electrochemical Hydrodechlorination of Pollutants by H*ads.. Adsorbed atomic H (H*ads) facilitates indirect pathways playing a major role in the electrochemical removal of various priority pollutants. It is crucial to identify the atomic sites responsible for the provision of H*ads. Herein, through a systematic study of the distribution of H*ads on Pd nanocatalysts with different sizes and, more importantly, deliberately controlled relative abundance of surface defects, we uncovered the central role of defects in the provision of H*ads. Specifically, the H*ads generated on Pd in an electrochemical process increased markedly upon introducing defect sites by changing the morphology to ultrathin polycrystalline Pd nanowires (NWs), while dramatically reducing upon decreasing the number of surface defects through an annealing treatment. Benefiting from a proportion of H*ads up to 40% of the total H* species, the Pd NWs showed an electrochemical active surface area normalized rate constant of 13.8 ± 0.8 h-1 m-2, which is 8-9 times higher than its Pd/C counterparts. The pivotal role of defect sites for the generation of H*ads was further verified by blocking such sites with Rh and Pt atoms, while theoretical calculation also confirms that the adsorption energy of H*ads on these sites is much higher than that on the Pd{111} facet."], "field": "Chemical Engineering", "q_year": 2025, "q_cid": "276578425", "pos_cid": 51893137, "source": "eval_collection"}
{"query_id": "scaleup_28151382_27071784", "query": "How to improve soil-salinity prediction accuracy while ensuring rapid convergence to a high-quality solution", "pos": ["Secure Task Offloading and Resource Allocation Strategies in Mobile Applications Using Probit Mish-Gated Recurrent Unit and an Enhanced-Searching-Based Serval Optimization Algorithm. Today, with the presence of 5G communication systems, including Internet of Things (IoT) technology, there is a high demand for mobile devices (especially smartphones, tablets, wearable technology, and so on). Regarding this proliferation and high demand, the massive adoption of mobile devices (MDs) has led to an exponential increase in network latency; the heavy demand for cloud servers causes the degradation of data traffic, which considerably impacts the real-time communication and computing aspects of mobile devices. As a result, mobile edge computing (MEC), an efficient framework capable of enhancing processing, optimizing energy usage, and offloading computation tasks, is considered a promising solution. In current research, numerous models have been implemented to achieve resource allocation and task offloading. However, these techniques are ineffective due to privacy issues and a lack of sufficient resources. Hence, this study proposes secure task offloading and resource allocation strategies in mobile devices using the Probit Mish–Gated Recurrent Unit (PM-GRU) and Entropic Linear Interpolation-Serval Optimization Algorithm (ELI-SOA). Primarily, the tasks to be offloaded and their attributes are gathered from mobile users and passed to a local computing model to identify the edge server. Here, the task attributes and the server attributes are compared with a cache table using the Sorensen–Dice coefficient. If the attributes match, then details about the appropriate edge server are produced. If the attributes do not match, then they are inputted into a global scheme that analyzes the attributes and predicts the edge server based on the Probit Mish-Gated Recurrent Unit (PM-GRU). Then, the server information is preserved and updated in the cache table in the local scheme. Further, the attributes, along with the predicted edge server, are inputted into a system for privacy-preserving smart contract creation by using Exponential Earth Mover’s Distance Matrix-Based K-Anonymity (EEMDM-KA) to develop a secure smart contract. Subsequently, the traffic attributes in the smart contract are extracted, and the request load is balanced by using HCD-KM. Load-balanced requests are assigned to the edge server, and the optimal resources are allocated in the cloud server by using the Entropic Linear Interpolation-Serval Optimization Algorithm (ELI-SOA). Finally, the created smart contract is hashed based on KECCAK-512 and stored in the blockchain. With a high accuracy of 99.84%, the evaluation results showed that the proposed approach framework performed better than those used in previous efforts."], "field": "Chemical Engineering", "q_year": 2025, "q_cid": "281513823", "pos_cid": 270717846, "source": "eval_collection"}
{"query_id": "scaleup_24722162_23227127", "query": "How to convert nitrate to ammonia rapidly and selectively", "pos": ["Tandem In2O3-Pt/Al2O3 catalyst for coupling of propane dehydrogenation to selective H2 combustion. Overcoming propylene oxidation Catalysts for the oxidative dehydrogenation of propane to propylene and water become less selective with increasing conversion because propylene itself is more readily oxidized than propane. Yan et al. created nanoscale tandem catalysts by growing an ∼2-nanometer shell of indium oxide, a selective hydrogen combustion catalyst, over a propane dehydrogenation catalyst, platinum nanoparticles supported on alumina spheres (see the Perspective by Pei and Gong). This overcoat exposed the platinum nanoparticles for propane dehydrogenation. Surface hydrogen atoms were oxidized at the indium oxide–platinum interface. This approach boosted yields of propylene to up to 30%. Science, this issue p. 1257; see also p. 1203 Tight kinetic coupling of propane dehydrogenation and selective hydrogen combustion enable propylene yields up to 30%. Tandem catalysis couples multiple reactions and promises to improve chemical processing, but precise spatiotemporal control over reactive intermediates remains elusive. We used atomic layer deposition to grow In2O3 over Pt/Al2O3, and this nanostructure kinetically couples the domains through surface hydrogen atom transfer, resulting in propane dehydrogenation (PDH) to propylene by platinum, then selective hydrogen combustion by In2O3, without excessive hydrocarbon combustion. Other nanostructures, including platinum on In2O3 or platinum mixed with In2O3, favor propane combustion because they cannot organize the reactions sequentially. The net effect is rapid and stable oxidative dehydrogenation of propane at high per-pass yields exceeding the PDH equilibrium. Tandem catalysis using this nanoscale overcoating geometry is validated as an opportunity for highly selective catalytic performance in a grand challenge reaction."], "field": "Chemical Engineering", "q_year": 2022, "q_cid": "247221624", "pos_cid": 232271275, "source": "eval_collection"}
{"query_id": "scaleup_26931207_16937343", "query": "How to clarify organisational change challenges within their broader strategic context and determine which alternative options to pursue", "pos": ["Strategizing Before Strategic Decision Making. Processes of strategic problem formulation are not only core to strategic decision making, but may be paramount. Indeed, one cannot even assess whether a situation is strategic until the problem ha..."], "field": "Chemical Engineering", "q_year": 2024, "q_cid": "269312075", "pos_cid": 169373431, "source": "eval_collection"}
{"query_id": "scaleup_28388257_25831090", "query": "How to understand how workers’ chemical safety knowledge and awareness relate to safe behavior and how their risk perceptions shape their interpretation of and responses to potential hazards", "pos": ["The influence of risk awareness and government trust on risk perception and preparedness for natural hazards. Risk perception is considered the primary motivator for taking preparedness actions. But people with prior experience and a high‐risk perception are not necessarily more prepared. This relationship is even more complex when assessing preparedness levels for hazards with different characteristics. These inconsistent findings can be explained by how preparedness has been measured and the influence of other factors, such as trust and risk awareness. Thus, the main goal of this study was to analyze the role of risk awareness and trust in authorities on risk perception and intention to prepare for natural hazards in a coastal city in Chile. A representative sample of the city of Concepción, located in the center‐south zone of Chile (n = 585), completed a survey. We measured risk awareness, risk perception, trust in authorities, and intention to prepare for two hazards: earthquakes/tsunamis and floods. Through structural equation models, we tested five hypotheses. We found that the perception of risk maintained a direct and positive influence on the intention to prepare for both hazards. The results showed that awareness and risk perception influence the intention to prepare and should be considered different concepts. Finally, trust did not significantly influence risk perception when faced with known hazards for the population. Implications for understanding the relationship between risk perception and direct experience are discussed."], "field": "Chemical Engineering", "q_year": 2025, "q_cid": "283882570", "pos_cid": 258310903, "source": "eval_collection"}
{"query_id": "scaleup_25532196_23907900", "query": "How to assess how closely predicted ph values match actual values and compare the accuracy of different regression models", "pos": ["Cricket Match Analytics Using the Big Data Approach. Cricket is one of the most liked, played, encouraged, and exciting sports in today’s time that requires a proper advancement with machine learning and artificial intelligence (AI) to attain more accuracy. With the increasing number of matches with time, the data related to cricket matches and the individual player are increasing rapidly. Moreover, the need of using big data analytics and the opportunities of utilizing this big data effectively in many beneficial ways are also increasing, such as the selection process of players in the team, predicting the winner of the match, and many more future predictions using some machine learning models or big data techniques. We applied the machine learning linear regression model to predict the team scores without big data and the big data framework Spark ML. The experimental results are measured through accuracy, the root mean square error (RMSE), mean square error (MSE), and mean absolute error (MAE), respectively 95%, 30.2, 1350.34, and 28.2 after applying linear regression in Spark ML. Furthermore, our approach can be applied to other sports."], "field": "Chemical Engineering", "q_year": 2022, "q_cid": "255321962", "pos_cid": 239079005, "source": "eval_collection"}
{"query_id": "scaleup_27959165_22152485", "query": "How to clarify how interfacial water orientation and hydrogen-bond organization affect ammonia oxidation rates and intermediate stability despite the water’s intrinsic disorder", "pos": ["Interfacial structure of water as a new descriptor of hydrogen evolution reaction.. Driven by the persisting poor understanding of the sluggish kinetics of the hydrogen evolution reaction (HER) on Pt in alkaline media, a direct correlation of the interfacial water structure and activity is still yet to be established. Here, we first demonstrated a strong dependence of the proton donor structure on the HER activity and pH. The structure of the first layer evolutes from the proton acceptors to the donors with increasing pH. In the base, the reactivity of the interfacial water varied with their structure, and the activation energies of water dissociation increased in the sequence: the dangling O-H bonds < the trihedrally coordinated water < the tetrahedrally coordinated water. Moreover, optimizing the adsorption of H and OH intermediate can re-orient the interfacial water molecules with their H atoms pointing towards the electrode surface, thereby enhancing the kinetics of HER. Our results clarified the dynamic role of the water structure at the electrode-electrolyte interface during HER and the design of highly efficient HER catalysts."], "field": "Chemical Engineering", "q_year": 2025, "q_cid": "279591652", "pos_cid": 221524852, "source": "eval_collection"}
{"query_id": "scaleup_26108450_12282156", "query": "How to establish reliable criteria for identifying and characterizing the behavior of free fatty acid carboxylic groups in solution with other fatty acids or the solvent", "pos": ["Hydrogen Atomic Positions of O–H···O Hydrogen Bonds in Solution and in the Solid State: The Synergy of Quantum Chemical Calculations with 1H-NMR Chemical Shifts and X-ray Diffraction Methods. The exact knowledge of hydrogen atomic positions of O–H···O hydrogen bonds in solution and in the solid state has been a major challenge in structural and physical organic chemistry. The objective of this review article is to summarize recent developments in the refinement of labile hydrogen positions with the use of: (i) density functional theory (DFT) calculations after a structure has been determined by X-ray from single crystals or from powders; (ii) 1H-NMR chemical shifts as constraints in DFT calculations, and (iii) use of root-mean-square deviation between experimentally determined and DFT calculated 1H-NMR chemical shifts considering the great sensitivity of 1H-NMR shielding to hydrogen bonding properties."], "field": "Chemical Engineering", "q_year": 2023, "q_cid": "261084506", "pos_cid": 12282156, "source": "eval_collection"}
{"query_id": "scaleup_26958029_20874250", "query": "How to achieve efficient urea synthesis from carbon dioxide and nitrogen despite weak reactant binding and poor activation", "pos": ["An Interfacial Electron Transfer on Tetrahedral NiS2 /NiSe2 Heterocages with Dual-Phase Synergy for Efficiently Triggering the Oxygen Evolution Reaction.. Tetrahedral NiS2 /NiSe2 heterocages with rich-phase boundaries are synthesized through a simultaneous sulfuration/selenylation process using Ni-based acetate hydroxide prisms as precursor. Such a nanocage-like NiS2 /NiSe2 heterostructure can expose more active sites, accelerate the mass transport of the ions/gas, and optimize the interfacial electronic structure, which shows a significantly lower overpotential of 290 mV at 20 mA cm-2 than those of NiS/NiS2 and NiSe2 as counterparts. The experimental characterizations and theoretical density functional theory (DFT) calculations unveil that the interfacial electron transfer from NiSe2 to NiS2 at the heterointerface can modulate the electronic structure of NiS2 /NiSe2 , which further cooperates synergistically to change the Gibbs free energy of oxygen-containing intermediates as the rate-determining step (RDS) from 2.16 eV (NiSe2 ) and 2.10 eV (NiS2 ) to 1.86 eV (NiS2 /NiSe2 heterostructures) during the oxygen evolution reaction (OER) process. And as a result, tetrahedral NiS2 /NiSe2 heterocages with dual-phase synergy efficiently trigger the OER process, and accelerate the OER kinetics. This work provides insights into the roles of the interfacial electron transfer in electrocatalysis, and can be an admirable strategy to modulate the electronic structure for developing highly active electrocatalysts."], "field": "Chemical Engineering", "q_year": 2024, "q_cid": "269580294", "pos_cid": 208742509, "source": "eval_collection"}
{"query_id": "scaleup_23520761_11528611", "query": "How to reduce the dependence of phase-fluorometric dissolved oxygen sensors on particular chemiluminescent films despite limited excitation-frequency flexibility", "pos": ["A 0.052 mm2, <0.4% THD, Sinusoidal Current Generator for Bio-Impedance Measurement Using a Recursive Digital Oscillator and Current-Domain FIR Filter. This brief presents a low-power, low-area and low total harmonic distortion (THD) sinusoidal current stimulator circuit for bio-impedance measurement. Proposed current generator includes recursive digital oscillator for sine wave generation and delta-sigma modulated 1 bit current source with embedded finite impulse response filter for high resolution digital-to-current conversion. The proposed circuit implemented in 0.18-<inline-formula> <tex-math notation=\"LaTeX\">$ {\\mu }\\text{m}$ </tex-math></inline-formula> CMOS process occupies 0.052 mm<sup>2</sup>, and consumes 55.6 <inline-formula> <tex-math notation=\"LaTeX\">$ {\\mu }\\text{W}$ </tex-math></inline-formula> for 20 kHz, 40 <inline-formula> <tex-math notation=\"LaTeX\">$ {\\mu }\\text{A}_{{{ \\text{p}- \\text{p}}}}$ </tex-math></inline-formula>, 0.17% THD sine current generation."], "field": "Chemical Engineering", "q_year": 2021, "q_cid": "235207616", "pos_cid": 115286110, "source": "eval_collection"}
{"query_id": "scaleup_26450854_25201050", "query": "How to compare production costs of green and conventional gray ammonia when the monetary cost of carbon dioxide emissions is taken into account", "pos": ["Comprehensive evidence implies a higher social cost of CO2. The social cost of carbon dioxide (SC-CO2) measures the monetized value of the damages to society caused by an incremental metric tonne of CO2 emissions and is a key metric informing climate policy. Used by governments and other decision-makers in benefit–cost analysis for over a decade, SC-CO2 estimates draw on climate science, economics, demography and other disciplines. However, a 2017 report by the US National Academies of Sciences, Engineering, and Medicine1 (NASEM) highlighted that current SC-CO2 estimates no longer reflect the latest research. The report provided a series of recommendations for improving the scientific basis, transparency and uncertainty characterization of SC-CO2 estimates. Here we show that improved probabilistic socioeconomic projections, climate models, damage functions, and discounting methods that collectively reflect theoretically consistent valuation of risk, substantially increase estimates of the SC-CO2. Our preferred mean SC-CO2 estimate is $185 per tonne of CO2 ($44–$413 per tCO2: 5%–95% range, 2020 US dollars) at a near-term risk-free discount rate of 2%, a value 3.6 times higher than the US government’s current value of $51 per tCO2. Our estimates incorporate updated scientific understanding throughout all components of SC-CO2 estimation in the new open-source Greenhouse Gas Impact Value Estimator (GIVE) model, in a manner fully responsive to the near-term NASEM recommendations. Our higher SC-CO2 values, compared with estimates currently used in policy evaluation, substantially increase the estimated benefits of greenhouse gas mitigation and thereby increase the expected net benefits of more stringent climate policies. Coupling advances in socioeconomic projections, climate models, damage functions and discounting methods yields an estimate of the social cost of carbon of US$185 per tonne of CO2—triple the widely used value published by the US government."], "field": "Chemical Engineering", "q_year": 2023, "q_cid": "264508543", "pos_cid": 252010506, "source": "eval_collection"}
{"query_id": "scaleup_27554261_22724257", "query": "How to identify the energetic constraints limiting nitrate reduction to ammonia across metal catalysts, given coupled intermediate adsorption energies and distinct adsorption and desorption requirements", "pos": ["Bayesian learning of chemisorption for bridging the complexity of electronic descriptors. Building upon the d-band reactivity theory in surface chemistry and catalysis, we develop a Bayesian learning approach to probing chemisorption processes at atomically tailored metal sites. With representative species, e.g., *O and *OH, Bayesian models trained with ab initio adsorption properties of transition metals predict site reactivity at a diverse range of intermetallics and near-surface alloys while naturally providing uncertainty quantification from posterior sampling. More importantly, this conceptual framework sheds light on the orbitalwise nature of chemical bonding at adsorption sites with d-states characteristics ranging from bulk-like semi-elliptic bands to free-atom-like discrete energy levels, bridging the complexity of electronic descriptors for the prediction of novel catalytic materials. Developing a generalizable model to describe adsorption processes at metal surfaces can be extremely challenging due to complex phenomena involved. Here the authors introduce a Bayesian learning approach based on ab initio data and the d-band model to capture the essential physics of adsorbate–substrate interactions."], "field": "Chemical Engineering", "q_year": 2025, "q_cid": "275542616", "pos_cid": 227242574, "source": "eval_collection"}
{"query_id": "scaleup_27338201_59406552", "query": "How to ensure a sufficiently stable three-dimensional structure in glucose-based non-isocyanate polyurethane foams to maintain complete, intact cell morphologies", "pos": ["Reactions with Wood Carbohydrates and Lignin of Citric Acid as a Bond Promoter of Wood Veneer Panels. The reaction of citric acid with wood veneers was studied by Cross Polarization Magic Angle Spinning Nuclear Magnetic Resonance (CP MAS 13C NMR) and matrix assisted laser desorption ionization time of flight (MALDI ToF) mass spectrometry. The analysis showed that reactions of citric acid occurred with both lignin and carbohydrate constituents of wood. The reactions occurring are esterifications between the carboxylic acid functions of citric acid and the numerous aromatic and aliphatic hydroxyl groups of the main wood constituents. Reaction of citric acid with glucose as a simple model compound of carbohydrates hydroxyl groups also yielded reactions leading to linear and branched oligomers by esterification. The result indicate that the reactions of esterification are accompanied in parallel by some internal rearrangements of lignin. The applied results on bonding wide flat wood surfaces such as veneers to obtain LVL panels yielded excellent strength results even if the conditions of pressing were more drastic than what is usual for this application. The applied bonding results have shown that citric acid has great potential to be used as a bio-binder for wood veneers."], "field": "Chemical Engineering", "q_year": 2024, "q_cid": "273382010", "pos_cid": 59406552, "source": "eval_collection"}
{"query_id": "scaleup_25674255_21889700", "query": "How to connect predicted reactivity at individual metal sites to their chemical characteristics", "pos": ["A Unified Approach to Interpreting Model Predictions. Understanding why a model makes a certain prediction can be as crucial as the prediction's accuracy in many applications. However, the highest accuracy for large modern datasets is often achieved by complex models that even experts struggle to interpret, such as ensemble or deep learning models, creating a tension between accuracy and interpretability. In response, various methods have recently been proposed to help users interpret the predictions of complex models, but it is often unclear how these methods are related and when one method is preferable over another. To address this problem, we present a unified framework for interpreting predictions, SHAP (SHapley Additive exPlanations). SHAP assigns each feature an importance value for a particular prediction. Its novel components include: (1) the identification of a new class of additive feature importance measures, and (2) theoretical results showing there is a unique solution in this class with a set of desirable properties. The new class unifies six existing methods, notable because several recent methods in the class lack the proposed desirable properties. Based on insights from this unification, we present new methods that show improved computational performance and/or better consistency with human intuition than previous approaches."], "field": "Chemical Engineering", "q_year": 2023, "q_cid": "256742556", "pos_cid": 21889700, "source": "eval_collection"}
{"query_id": "scaleup_26360716_22518444", "query": "How to improve ammonia production in electrocatalysts with limited porosity and active-site accessibility", "pos": ["Facile directions for synthesis, modification and activation of MOFs. Abstract This review focuses on the description of typical procedures to prepare MOFs. The updated known methods of synthesis, essential modifications and reliable activation are all briefly elucidated and discussed. Synthesis procedures via Liquid phase synthesis or solid phase synthesis procedures were intensively studied. The liquid phase synthesis methods includes the slow evaporation method, hydrothermal/solvothermal procedure, electrochemical method, sonochemical method, microwave method, spray-drying method, flow chemistry method and ionothermal method while the solid phase method was represented by mechanochemical method. Among of them, the most reliable method used by researchers was the hydrothermal or solvothermal method. The modification by the direct synthesis procedure and post-synthesis procedure are briefly discussed. It has been found that the direct synthesis procedure is broadly used however it was not always preferred due to the difficulty to synthesise some functionalised MOFs. Activation procedures are essentially explained. The solvent exchange activation method was mostly used. This review will provide a comprehensive background of MOF synthesis for the beginners in this area."], "field": "Chemical Engineering", "q_year": 2023, "q_cid": "263607163", "pos_cid": 225184446, "source": "eval_collection"}
{"query_id": "scaleup_25355132_21123156", "query": "How to identify the spatial organization responsible for the new low-q prepeak in LaCl3–NaCl mixtures as LaCl3 is diluted with NaCl", "pos": ["A Pictorial View of Viscosity in Ionic Liquids and the Link to Nanostructural Heterogeneity.. Prototypical ionic liquids (ILs) are characterized by three structural motifs associated with (1) vicinal interactions, (2) the formation of positive-negative charge alternating chains or networks and (3) the alternation of these networks with apolar domains. In recent articles, we highlighted that friction and mobility in these systems are nowhere close to being spatially homogeneous. This results in what one could call mechanical heterogeneity where charge networks are intrinsically stiff and charge depleted regions are softer, flexible and mobile. This letter attempts to provide a clear and visual connection between friction --associated with the dynamics of the structural motifs (in particular the charge network)-- and recent theoretical work by Yamaguchi linking the time-dependent viscosity of ILs to the decay of the charge alternation peak in the dynamic structure function. We propose that charge-blurring associated with the loss of memory of where positive and negative charges are within networks is the key mechanism associated with viscosity in ILs. An IL will have low viscosity if a characteristic charge blurring decorrelation time tcharge is low. With this in mind, engineering new low viscosity ILs reduces to understanding how to minimize this quantity."], "field": "Chemical Engineering", "q_year": 2022, "q_cid": "253551329", "pos_cid": 211231560, "source": "eval_collection"}
{"query_id": "scaleup_24722162_23214053", "query": "How to understand the evolving active phases of transition-metal catalysts and their roles in specific nitrate electroreduction steps for selective ammonia production", "pos": ["Linking dynamic chemical state of catalysts with product profile of electrocatalytic CO2 reduction.. Direct electrochemical reduction of CO 2 (CO 2 RR) is a promising route to capture CO 2 waste and store renewable electricity to generate chemical energy in fuels and feedstocks. Nowadays, in most studies, the promoted activity and enhanced selectivity of various electrocatalysts are commonly ascribed to their specific structural features present in metallic form, such as surface facet, morphology, and atomic defects. However, unraveling the factors that really govern CO 2 RR still faces great challenges due to a fact that the surface state of electrocatalysts is dynamic and challenging to predict under working conditions. Moreover, it has to note that, in a variety of studies , the theoretical predictions from a viewpoint of thermodynamics only may fail to precisely state the actual configuration of a catalyst for the dynamic CO 2 RR process, resulting in numerous inappropriate claims . Herein, we re-survey recent studies with the emphasis on revealing the dynamic chemical state of Cu sites under CO 2 RR conditions extracted by in situ/operando characterizations, and further validate a critical link between the chemical state of Cu and product profile of CO 2 RR. The Cu catalyst surface with a mixed valence of Cu + and Cu 0 substantially manifests a high selectivity for C-C coupling toward ethylene/ethanol, while the oxidized Cu + - and metallic Cu 0 -dominated surface promote the selective production of CO/formic acid and methane, respectively, suggesting the promising potential of dynamic Cu chemical state as a direct and precise descriptor for CO 2 RR selectivity on Cu electrodes. This point of view provides a generalizable concept of dynamic chemical state-driven CO 2 RR selectivity that has been disregarded in the community and offers an inspiration in both fundamental understanding and efficient electrocatalysts design."], "field": "Chemical Engineering", "q_year": 2022, "q_cid": "247221624", "pos_cid": 232140537, "source": "eval_collection"}
{"query_id": "scaleup_28073351_24542645", "query": "How to determine the stationary shape and maximum volume of viscoplastic material that an oblique barrier can support on an inclined plane, with nonzero layer thickness far from the barrier", "pos": ["Subcritical and supercritical granular flow around an obstacle on a rough inclined plane. Abstract A blunt obstacle in the path of a rapid granular avalanche generates a bow shock (a jump in the avalanche thickness and velocity), a region of static grains upstream of the obstacle, and a grain-free region downstream. Here, it is shown that this interaction is qualitatively altered if the incline on which the avalanche is flowing is changed from smooth to rough. On a rough incline, the friction between the grains and the incline depends on the flow thickness and speed, which allows both rapid (supercritical) and slow (subcritical) steady uniform avalanches. For supercritical experimental flows, the material is diverted around a blunt obstacle by the formation of a bow shock and a static dead zone upstream of the obstacle. Downslope, a grain-free vacuum region forms, but, in contrast to flows on smooth beds, static levees form at the boundary between the vacuum region and the flow. In slower, subcritical, flows the flow is diverted smoothly around the dead zone and the obstacle without forming a bow shock. After the avalanche stops, signatures of the dead zone, levees and (in subcritical flows) a deeper region upslope of the obstacle are frozen into the deposit. To capture this behaviour, numerical simulations are performed with a depth-averaged avalanche model that includes frictional hysteresis and depth-averaged viscous terms, which are needed to accurately model the flowing and deposited regions. These results may be directly relevant to geophysical mass flows and snow avalanches, which flow over rough terrain and may impact barriers or other infrastructure."], "field": "Chemical Engineering", "q_year": 2025, "q_cid": "280733517", "pos_cid": 245426451, "source": "eval_collection"}
{"query_id": "scaleup_26372728_20364104", "query": "How to increase the double-layer capacitance and response slope of ion-selective electrodes to improve their sensitivity to changes in ion concentration", "pos": ["Tuning the Electrochemical Performance of Titanium Carbide MXene by Controllable in situ Anodic Oxidation.. MXenes are a class of two-dimensional (2D) transition metal carbides, nitrides and carbonitrides that have shown promise for high-rate pseudocapacitive energy storage. However, the effects that irreversible oxidation have on the surface chemistry and electrochemical properties of MXenes are still not understood. Here we report on a controlled anodic oxidation method which improves the rate performance of titanium carbide MXene (Ti 3 C 2 T x, T x refers to -F, =O, -Cl and -OH) electrodes in acidic electrolytes. The capacitance retention at 2000 mV/s (with respect to the lowest scan rate of 5 mV/s) increases gradually from 38% to 66% by tuning the degree of anodic oxidation. At the same time, a loss in the redox behavior of Ti 3 C 2 is evident at high anodic potentials after oxidation. Several analysis methods were employed to reveal that preserving the structure and surface chemistry while simultaneously introducing defects, without compromising electrochemically active sites, are key factors for improving the rate performance of Ti 3 C 2 T x . This study demonstrates improvement of the electrochemical performance of MXene electrodes by controlling the surface chemistry and transition metal stoichiometry."], "field": "Chemical Engineering", "q_year": 2023, "q_cid": "263727285", "pos_cid": 203641047, "source": "eval_collection"}
{"query_id": "scaleup_26450854_25916293", "query": "How to clarify the effects of variations in economic and environmental inputs on estimates of ammonia production costs and global warming impacts", "pos": ["Environmental and economic evaluation of implementing membrane technologies and struvite crystallisation to recover nutrients from anaerobic digestion supernatant.. The present study investigates the environmental and economic feasibility of implementing membrane technologies and struvite crystallisation (SC) for nutrient recovery from the anaerobic digestion supernatant. To this end, one scenario combining partial-nitritation/Anammox and SC was compared with three scenarios combining membrane technologies and SC. The combination of ultrafiltration, SC and liquid-liquid membrane contactor (LLMC) was the less environmentally impactful scenario. SC and LLMC were the most important environmental and economic contributors in those scenarios using membrane technologies. The economic evaluation illustrated that combining ultrafiltration, SC and LLMC (with or without reverse osmosis pre-concentration) featured the lowest net cost. The sensitivity analysis highlighted that the consumption of chemicals for nutrient recovery and the ammonium sulphate recovered had a large impact on environmental and economic balances. Overall, these results demonstrate that implementing membrane technologies and SC for nutrient recovery can improve the economic and environmental implications of future municipal wastewater treatment plants."], "field": "Chemical Engineering", "q_year": 2023, "q_cid": "264508543", "pos_cid": 259162932, "source": "eval_collection"}
{"query_id": "scaleup_24878526_17371154", "query": "How to rapidly obtain lanthanide-containing nano-assemblies under mild, neutral aqueous conditions with controllable size, uniform size distribution, and solvent dispersibility suitable for ratiometric fluorescence sensing", "pos": ["Biomimetic mineralization of metal-organic frameworks as protective coatings for biomacromolecules. Enhancing the robustness of functional biomacromolecules is a critical challenge in biotechnology, which if addressed would enhance their use in pharmaceuticals, chemical processing and biostorage. Here we report a novel method, inspired by natural biomineralization processes, which provides unprecedented protection of biomacromolecules by encapsulating them within a class of porous materials termed metal-organic frameworks. We show that proteins, enzymes and DNA rapidly induce the formation of protective metal-organic framework coatings under physiological conditions by concentrating the framework building blocks and facilitating crystallization around the biomacromolecules. The resulting biocomposite is stable under conditions that would normally decompose many biological macromolecules. For example, urease and horseradish peroxidase protected within a metal-organic framework shell are found to retain bioactivity after being treated at 80 °C and boiled in dimethylformamide (153 °C), respectively. This rapid, low-cost biomimetic mineralization process gives rise to new possibilities for the exploitation of biomacromolecules. Robust biomacromolecules could be used for a wide range of biotechnological applications. Here the authors report a biomimetic mineralization process, in which biomolecules are encapsulated within metal-organic frameworks, and their stability is subsequently increased without significant bioactivity loss."], "field": "Chemical Engineering", "q_year": 2022, "q_cid": "248785264", "pos_cid": 17371154, "source": "eval_collection"}
{"query_id": "scaleup_26108450_96099437", "query": "How to determine the hydrogen-bond geometry and relative molecular orientations of free fatty acids in different solvents, their relationship to solid-state structures, and their association into low-molecular-weight aggregates", "pos": ["Die Strukturen der essentiellen ungesättigten Fettsäuren, Kristallstruktur der Linolsäure sowie Hinweise auf die Kristallstrukturen der α-Linolensäure und der Arachidonsäure / The Structures of the Essential Unsaturated Fatty Acids. Crystal Structure of Linoleic Acid and Evidence for the Crystal Str. Abstract The essential fatty acids linoleic, α-linolenic and arachidonic acid have been crystallized for the first time. The crystal and molecular structures have been elucidated by X-ray analysis. Linoleic acid crystallizes monoclinic P21/c with a = 4298(3), b = 463.2(3), c = 937.7(6) pm, β = 109.38(8)°, Z = 4. The closely packed molecules are stretched with a tttttts̄CssCs̄tt conformationa. By comparison of the unit-cell constants and calculated densities of the unsaturated fatty acids it may be shown that both α-linolenic acid and arachidonic acid also possess stretched structures in the crystal lattice, α-linolenic acid must display a tttttts̄CssCs̄s̄Cs and arachidonic acid a tts̄CssCs̄s̄CssCs̄ttt conformation."], "field": "Chemical Engineering", "q_year": 2023, "q_cid": "261084506", "pos_cid": 96099437, "source": "eval_collection"}
{"query_id": "scaleup_24747439_54071288", "query": "How to interpret a sensor’s response when its sensing area is in contact with a liquid electrolyte", "pos": ["Electrical impedance spectroscopy (EIS) for biological analysis and food characterization: a review. Abstract. Electrical impedance spectroscopy (EIS), in which a sinusoidal test voltage or current is applied to the sample under test to measure its impedance over a suitable frequency range, is a powerful technique to investigate the electrical properties of a large variety of materials. In practice, the measured impedance spectra, usually fitted with an equivalent electrical model, represent an electrical fingerprint of the sample providing an insight into its properties and behavior. EIS is used in a broad range of applications as a quick and easily automated technique to characterize solid, liquid, semiliquid, organic as well as inorganic materials. This paper presents an updated review of EIS main implementations and applications."], "field": "Chemical Engineering", "q_year": 2022, "q_cid": "247474390", "pos_cid": 54071288, "source": "eval_collection"}
{"query_id": "scaleup_26450854_11593086", "query": "How to secure the critical raw materials required for ammonia production under economic and environmental constraints", "pos": ["Global material requirements for the energy transition. An exergy flow analysis of decarbonisation pathways. Abstract Moving towards a low-carbon economy will imply a considerable increase in the deployment of green technologies, which will in turn increase the demand of certain raw materials. In this paper, the material requirements for 2050 scenarios are assessed in terms of exergy to analyze the impact in natural resources in each scenario and identify which technologies are going to demand more resources. Renewable energy technologies are more mineral intensive than current energy sources. Using the International Energy Agency scenarios, from 2025 to 2050, total raw material demand is going to increase by 30%, being the transport sector the one that experiences the highest increase. Aluminum, iron, copper and potassium are those elements that present a higher share of the material needs for green technologies. Besides, there are five elements that experience at least a six-fold increase in demand in that period: cobalt, lithium, magnesium, titanium and zinc. Comparing those results with Greenpeace's AE [R] scenario, which considers a 100% renewable supply by 2050, this increase is even higher. Therefore, avoiding the dependency on fossil fuels will imply to accept the dependency on raw materials."], "field": "Chemical Engineering", "q_year": 2023, "q_cid": "264508543", "pos_cid": 115930864, "source": "eval_collection"}
{"query_id": "scaleup_26360716_24954470", "query": "How to improve the intrinsic catalytic performance of an iron-based catalyst for nitrate-to-ammonia conversion without complex material modifications or very high temperatures", "pos": ["Evaluation of Iron-Based Metal-Organic Framework Activation Temperatures in Acetylene Adsorption.. One of the major issues regarding long-term human space exploration is the need for a breathable atmosphere. A major component toward achieving this goal is both the removal of exhaled carbon dioxide (CO2) and the generation or recovery of oxygen (O2). NASA's current technology only operates at about 50% efficiency due to the need to vent the methane that is produced during the CO2 reduction process. One method of improving the efficiency of this process is through plasma pyrolysis, wherein the methane is pyrolyzed to produce hydrogen and various dehydrogenated carbon byproducts. In this process, acetylene is one of the main components of this byproduct stream. Unfortunately, while the concentration of this effluent is generally high in hydrogen (>90% typically), the presence of the acetylene waste product can act as a poison for the ruthenium-alumina catalyst used in the CO2-reducing Sabatier process, requiring a removal step. Metal-organic frameworks (MOFs) represent a valuable method for removing these unsaturated hydrocarbons due to their high tunability, particularly through the incorporation of open metal sites. In this study, two common iron-based MOFs, MIL-100 and PCN-250, were studied for their ability to adsorb acetylene. A combination of gas adsorption analysis and density functional theory calculation results shows the ability of these materials to undergo a thermal-induced reduction event, which results in an improvement in gas adsorption performance. This improvement in gas performance appears to be at least partially due to the increased presence of π-backbonding toward the acetylene molecules."], "field": "Chemical Engineering", "q_year": 2023, "q_cid": "263607163", "pos_cid": 249544701, "source": "eval_collection"}
{"query_id": "scaleup_25312004_19690179", "query": "How to create a geometrically ordered, fully three-dimensional porous medium of cubically packed glass spheres for studying elastic turbulence across a volume", "pos": ["3D-printed glass microfluidics for fluid dynamics and rheology. Abstract Microfluidics provides a versatile platform for handling small volumes of fluids at small length scales. From a fluid dynamics perspective, microfluidics gives access to a regime of very high deformation rates γ ˙ at moderate to negligible Reynolds numbers R e . For viscoelastic fluid flows, the resulting high Weissenberg numbers W i = τ γ ˙ , where τ is the fluid characteristic time, means the flow occurs at high elasticity number E l = W i / R e . Consequently, microfluidics supports a burgeoning interest in the experimental study of purely elastic flow instabilities and elastic turbulence. However, for rheological studies, typical microfluidic fabrications by soft lithography in poly (dimethyl siloxane) suffer from a number of limitations arising from the low elastic modulus and poor optical properties of the material. In this review, we summarise a few recent studies from our group in which we have experimented with microdevice fabrications using the subtractive three-dimensional (3D)-printing technique of selective laser-induced etching (SLE). SLE can be used to fabricate arbitrary 3D geometries with micron precision in fused silica: a high modulus, highly transparent material, which is robust and resistant to organic solvents. Apart from high elasticity number flows, we have found that SLE fabricated devices can sustain very high deformation rates without device failure, providing new access to little-explored inertio-elastic regimes in extremely dilute polymer solutions. Furthermore, it is possible to visualize flows from multiple planes of observation, allowing the quantitative study of 3D flow instabilities and vortex dynamics in both Newtonian and non-Newtonian fluids. SLE fabrication offers many new opportunities to those involved in fluid dynamics and rheology research at the microscale, and we highlight what we perceive as potentially fruitful ideas for future studies using this technique."], "field": "Chemical Engineering", "q_year": 2022, "q_cid": "253120046", "pos_cid": 196901790, "source": "eval_collection"}
{"query_id": "scaleup_21895002_20214265", "query": "How to reduce the computational cost of calculating an aggregate’s sedimentation orbit when its translational and angular velocities depend on its changing orientation", "pos": ["Numerical simulations of a stick-slip spherical particle in Poiseuille flow. The dynamics of a stick-slip “Janus” spherical particle suspended in a Newtonian fluid flowing in a cylindrical microchannel is studied by direct numerical simulations. Partial slip is imposed on half of the particle surface, whereas the no-slip boundary condition is present on the other half. The finite element method is used to solve the balance equations under creeping flow conditions. The translational and rotational velocities of the particle are evaluated at several orientations and distances from the tube centerline. The trajectories are then reconstructed by solving the kinematic equations where the velocities are taken by interpolating the simulation data. The particle dynamics is investigated by varying the initial position and orientation, the slip parameter, and the confinement ratio. The results, presented in terms of particle trajectories and phase portraits, highlight the existence of two relevant regimes: a periodic oscillation or a migration toward the tube axis for particle positions sufficiently far from or near the centerline, respectively. The basin of attraction of the tube axis grows with particle confinement and slip coefficient although the dynamics is qualitatively unaffected.The dynamics of a stick-slip “Janus” spherical particle suspended in a Newtonian fluid flowing in a cylindrical microchannel is studied by direct numerical simulations. Partial slip is imposed on half of the particle surface, whereas the no-slip boundary condition is present on the other half. The finite element method is used to solve the balance equations under creeping flow conditions. The translational and rotational velocities of the particle are evaluated at several orientations and distances from the tube centerline. The trajectories are then reconstructed by solving the kinematic equations where the velocities are taken by interpolating the simulation data. The particle dynamics is investigated by varying the initial position and orientation, the slip parameter, and the confinement ratio. The results, presented in terms of particle trajectories and phase portraits, highlight the existence of two relevant regimes: a periodic oscillation or a migration toward the tube axis for particle positions suf..."], "field": "Chemical Engineering", "q_year": 2020, "q_cid": "218950024", "pos_cid": 202142650, "source": "train_step3"}
{"query_id": "scaleup_25282896_96444996", "query": "How to efficiently solve the coupled mass, momentum, constitutive, and energy equations for incompressible non-isothermal viscoelastic flows while avoiding slow convergence of the discretized system", "pos": ["A coupled finite-volume solver for numerical simulation of electrically-driven flows. Abstract The accuracy and stability of implicit CFD codes are frequently impaired by the decoupling between variables, which can ultimately lead to numerical divergence. Coupled solvers, which solve all the governing equations simultaneously, have the potential to fix this problem. In this work, we report the implementation of coupled solvers for transient and steady-state electrically-driven flow simulations in the finite-volumes framework. The numerical method, developed in OpenFOAM®, is generic for Newtonian and viscoelastic fluids and is formulated for the Poisson–Nernst–Planck and Poisson–Boltzmann models. The resulting coupled systems of equations are solved efficiently with PETSc library. The performance of the coupled solvers is assessed in two test cases: induced-charge electroosmosis of a Newtonian fluid around a cylinder; electroosmotic flow of a PTT viscoelastic fluid in a contraction/expansion microchannel. The coupled solvers are more accurate in transient simulations and allow the use of larger time-steps without numerical divergence. For steady-state simulations, the coupled solvers converge in fewer iterations than segregated solvers. Although coupled solvers are much slower in a per time-step basis, the overall speedup factor obtained in this study reached a maximum value of ∼100, where the highest factors have been obtained with semi-coupled solvers, which drop some coupling terms between equations. While further research is needed to improve the efficiency of the matrix solving stage, coupled solvers are already superior to segregated solvers in a number of cases."], "field": "Chemical Engineering", "q_year": 2022, "q_cid": "252828969", "pos_cid": 96444996, "source": "train_step3"}
{"query_id": "scaleup_26119496_33661271", "query": "How to reliably form all-aqueous droplets in aqueous two-phase systems with sufficient control to obtain suitable templates", "pos": ["Forced generation of simple and double emulsions in all-aqueous systems. We report an easy-to-implement method that allows the direct generation of water-in-water (w/w) single emulsions. The method relies on direct perturbation of the pressure that drives the flow of the dispersed phase of the emulsions. The resultant inner jet is induced to break up into droplets due to the growth of the perturbation through Rayleigh-Plateau instability [L. Rayleigh, Proc. R. Soc. London 29, 71–97 (1879)]; this leads to the formation of monodisperse droplets. By implementing this method on a modified microfluidic device, we directly generate water-in-water-in-water (w/w/w) double emulsions with good control over the size and the number of encapsulated droplets. Our approach suggests a route to apply droplet-based microfluidics to completely water-based systems."], "field": "Chemical Engineering", "q_year": 2023, "q_cid": "261194966", "pos_cid": 33661271, "source": "train_step3"}
{"query_id": "scaleup_21460179_7690594", "query": "How to increase biomolecule detection sensitivity despite sensing-interface thickness and leakage constraints", "pos": ["Silicon Nanowires with High-k Hafnium Oxide Dielectrics for Sensitive Detection of Small Nucleic Acid Oligomers. Nanobiosensors based on silicon nanowire field effect transistors offer advantages of low cost, label-free detection, and potential for massive parallelization. As a result, these sensors have often been suggested as an attractive option for applications in Point-of-care (POC) medical diagnostics. Unfortunately, a number of performance issues such as gate leakage and current instability due to fluid contact, have prevented widespread adoption of the technology for routine use. High-k dielectrics, such as hafnium oxide (HfO2), have the known ability to address these challenges by passivating the exposed surfaces against destabilizing concerns of ion transport. With these fundamental stability issues addressed, a promising target for POC diagnostics and SiNWFET’s has been small oligonucleotides, more specifically microRNA (miRNA). MicroRNA’s are small RNA oligonucleotides which bind to messenger RNA’s, causing translational repression of proteins, gene silencing, and expressions are typically altered in several forms of cancer. In this paper, we describe a process for fabricating stable HfO2 dielectric based silicon nanowires for biosensing applications. Here we demonstrate sensing of single stranded DNA analogues to their microRNA cousins using miR-10b and miR-21 as templates, both known to be upregulated in breast cancer. We characterize the effect of surface functionalization on device performance using the miR-10b DNA analogue as the target sequence and different molecular weight poly-l-lysine as the functionalization layer. By optimizing the surface functionalization and fabrication protocol, we were able to achieve <100fM detection levels of miR-10b DNA analogue, with a theoretical limit of detection of 1fM. Moreover, the non-complementary DNA target strand, based on miR-21, showed very little response, indicating a highly sensitive and highly selective biosensing platform."], "field": "Chemical Engineering", "q_year": 2020, "q_cid": "214601791", "pos_cid": 7690594, "source": "train_step3"}
{"query_id": "scaleup_26107419_21908956", "query": "How to make a suitable copper catalyst available for coupling ammonia with arylboronic acids during nitrite electroreduction while limiting alkalinity and phenol formation", "pos": ["Steady-state electrochemical synthesis of HKUST-1 with polarity reversal. Abstract Metal-organic frameworks (MOFs) are commonly synthesised in batch processes that are limited in size. Electrochemical synthesis is a promising method for producing MOFs on an industrial scale, however when using direct current (DC) product films can build up on electrodes causing passivation. This work investigates electrosynthesis of HKUST-1 using periodic polarity reversal (PR). The system was studied using electrochemical impedance spectroscopy (EIS); and scanning electron microscopy (SEM), and X-ray diffraction (XRD) were used to examine the product and electrode surfaces. PR experiments ran continuously for up to 60 h and demonstrated less electrode passivation than DC experiments. A conductive precipitate bridge formed between anode and cathode in DC experiments after 30 min, limiting further electrosynthesis. Between 3 h and 10 h synthesis times, PR achieved a production rate per electrode surface area of 1.83 mg h-1 cm-2 compared to 0.11 mg h-1 cm-2 from DC. Product produced using PR for 10 h and 60 h synthesis times resulted in BET surface areas of 1303 m2 g-1 and 1063 m2 g-1 respectively. PR outperformed DC electrosynthesis in this work, and may be beneficial for increasing the scale of MOF production if integrated into a continuous system."], "field": "Chemical Engineering", "q_year": 2023, "q_cid": "261074195", "pos_cid": 219089566, "source": "train_step3"}
{"query_id": "scaleup_27793776_26498186", "query": "How to determine how heating temperature affects the distribution and size of tungsten on a support when smaller clusters may fall below available detection limits", "pos": ["Impact of Calcination Temperature on Tungsten‐based Composite Catalysts for Olefins Metathesis. The thermal treatment is one of the key procedures for the distribution and transformation of active sites for the supported metal oxide catalysts. However, the underlying impacts of thermal treatment on composite supported catalysts receives limited attention due to the additional complexity of the composite support. In this work, the progressive gradient in the metathesis activity, as the function of enhanced calcination temperature, has been observed for the tungsten‐based catalysts supported on the hierarchical ZSM‐5 zeolite‐alumina composite. The metathesis activity, reflected by ethene conversion, undergoes a stepwise growth from 24.2 % to 38.9 % along with the enhanced calcination temperature from 723 K to 923 K. The supported W‐oxo species share high similarity in structural states except their interaction with the Brønsted acidic bridge hydroxyl groups in zeolite. The density of bridge hydroxyl groups is reduced as the function of enhanced calcination temperatures, which reflects the intensified anchoring of surface W‐oxo species. It should be noted that such dependence is not observed for their counterparts based on microporous ZSM‐5 zeolite‐alumina. These sharp comparisons highlight the critical routes of thermal migration of W‐oxo species along the intrazeolite‐alumina interface in the evolution of active sites for the olefins cross‐metathesis reaction."], "field": "Chemical Engineering", "q_year": 2025, "q_cid": "277937762", "pos_cid": 264981863, "source": "train_step3"}
{"query_id": "scaleup_23370669_10436408", "query": "How to achieve high-yield anthraquinone extraction from Rhei Radix et Rhizoma while accounting for both tissue disruption and solvent dissolving capacity", "pos": ["Polyol-Based Deep Eutectic Solvents for Extraction of Natural Polyphenolic Antioxidants from Chlorella vulgaris. Due to increasing demand of natural antioxidants for pharmaceutical, food and cosmetic applications, extraction of polyphenols from natural resources has received enormous attention. In this regard, microalgae biomass exhibits great potential for target bioactive compounds accumulation. Conventionally, petroleum-derived volatile organic solvents (VOCs) and water have been used to recover polyphenols from biomass; however, VOCs are hazardous, nonenvironmentally friendly solvents while water suffers from coextraction of other impurities. Therefore, the goal of this work is to evaluate renewable deep eutectic solvents (DES) as alternative to conventional solvents for recovering polyphenols from microalgal biomass. In particular, Chlorella vulgaris was subjected to solvent extraction using 12 DES systems composed of choline chloride (ChCl) and polyols including glycerol (Gly), ethylene glycol (EG), 1,3-propanediol (PDO) and 1,4-butanediol (BDO) and two benchmark conventional solvents, namely ethyl acetate and..."], "field": "Chemical Engineering", "q_year": 2021, "q_cid": "233706696", "pos_cid": 104364080, "source": "train_step3"}
{"query_id": "scaleup_23189972_22114419", "query": "How to quantify the difference in inward ion permeation kinetics between R207Q mutant and wild-type Kv7.2 voltage sensor domains to assess whether the mutation favors the experimentally observed anomalous inward current", "pos": ["Thermodynamics and Kinetics of Ion Permeation in Wild-Type and Mutated Open Active Conformation of the Human α7 Nicotinic Receptor. Molecular studies of human pentameric ligand-gated ion channels (LGICs) expressed in neurons and at neuromuscular junctions are of utmost importance in the development of therapeutic strategies for neurological disorders. We focus here on the nicotinic acetylcholine receptor nAChR-α7, a homopentameric channel widely expressed in the human brain, with a proven role in a wide spectrum of disorders including schizophrenia and Alzheimer’s disease. By exploiting an all-atom structural model of the full (transmembrane and extracellular) protein in the open, agonist-bound conformation we recently developed, we evaluate the free energy and the mean first passage time of single-ion permeation using molecular dynamics simulations and the milestoning method with Voronoi tessellation. The results for the wild-type channel provide the first available mapping of the potential of mean force in the full-length α7 nAChR, reveal its expected cationic nature, and are in good agreement with simulation data for other channels of the LGIC family and with experimental data on nAChRs. We then investigate the role of a specific mutation directly related to ion selectivity in LGICs, the E-1′ → A-1′ substitution at the cytoplasmatic selectivity filter. We find that the mutation strongly affects sodium and chloride permeation in opposite directions, leading to a complete inversion of selectivity, at variance with the limited experimental results available that classify this mutant as cationic. We thus provide structural determinants for the observed cationic-to-anionic inversion, revealing a key role of the protonation state of residue rings far from the mutation, in the proximity of the hydrophobic channel gate."], "field": "Chemical Engineering", "q_year": 2021, "q_cid": "231899720", "pos_cid": 221144199, "source": "train_step3"}
{"query_id": "scaleup_26972851_96699031", "query": "How to model surfactant-stabilised concentrated emulsions in which droplets do not coalesce when their interfaces come into close contact", "pos": ["Mesoscopic lattice Boltzmann modeling of soft-glassy systems: Theory and simulations. A multicomponent lattice Boltzmann model recently introduced [R. Benzi et al., Phys. Rev. Lett. 102, 026002 (2009)] to describe some dynamical behaviors of soft-flowing materials is theoretically analyzed. Equilibrium and transport properties are derived within the framework of a continuum free-energy formulation and checked against numerical simulations. Due to the competition between short-range interspecies repulsion and midrange intraspecies attraction, the model is shown to give rise to a very rich configurational dynamics of the density field, exhibiting numerous features of soft-flowing materials such as long-time relaxation due to caging effects, enhanced viscosity and structural arrest, aging under moderate shear, and shear-thinning flow above a critical shear threshold."], "field": "Chemical Engineering", "q_year": 2024, "q_cid": "269728514", "pos_cid": 96699031, "source": "train_step3"}
{"query_id": "scaleup_27255174_26773985", "query": "How to attach two alkyl groups to a difluoromethylene unit in a single step with modularity, broad functional group compatibility, and no complicated substrate synthesis sequences", "pos": ["Iron-catalyzed fluoroalkylative alkylsulfonylation of alkenes via radical-anion relay. Transition metal-catalyzed reductive difunctionalization of alkenes with alkyl halides is a powerful method for upgrading commodity chemicals into densely functionalized molecules. However, super stoichiometric amounts of metal reductant and the requirement of installing a directing group into alkenes to suppress the inherent β-H elimination bring great limitations to this type of reaction. We demonstrate herein that the difunctionalization of alkenes with two different alkyl halides is accessible via a radical-anion relay with Na2S2O4 as both reductant and sulfone-source. The Na2S2O4 together with the electron-shuttle catalyst is crucial to divert the mechanistic pathway toward the formation of alkyl sulfone anion instead of the previously reported alkylmetal intermediates. Mechanistic studies allow the identification of carbon-centered alkyl radical and sulfur-centered alkyl sulfone radical, which are in equilibrium via capture or extrusion of SO2 and could be converted to alkyl sulfone anion accelerated by iron electron-shuttle catalysis, leading to the observed high chemoselectivity."], "field": "Chemical Engineering", "q_year": 2024, "q_cid": "272551744", "pos_cid": 267739852, "source": "train_step3"}
{"query_id": "scaleup_27106198_55692776", "query": "How to determine the explicit relationship between the spatially varying shape of a two-dimensional channel and its average pressure difference", "pos": ["Symplectic Exact Solution for Stokes Flow in the Thin Film Coating Applications. The symplectic analytical method is introduced to solve the problem of the stokes flow in the thin film coating applications. Based on the variational principle, the Lagrangian function of the stokes flow is established. By using the Legendre transformation, the dual variables of velocities and the Hamiltonian function are derived. Considering velocities and stresses as the basic variables, the equations of stokes flow problems are transformed into Hamiltonian system. The method of separation of variables and expansion of eigenfunctions are developed to solve the governing equations in Hamiltonian system, and the analytical solutions of the stokes flow are obtained. Several numerical simulations are carried out to verify the analytical solutions in the present study and discuss the effects of the driven lids of the square cavity on the dynamic behavior of the flow structure."], "field": "Chemical Engineering", "q_year": 2024, "q_cid": "271061980", "pos_cid": 55692776, "source": "train_step3"}
{"query_id": "scaleup_24383493_117257", "query": "How to improve timely awareness of chemical hazards, their frequency, and associated exposures to support incident management and protect public health", "pos": ["Use of Unstructured Event-Based Reports for Global Infectious Disease Surveillance. Free or low-cost unstructured reports offer an alternative to traditional indicator-based outbreak reporting."], "field": "Chemical Engineering", "q_year": 2021, "q_cid": "243834936", "pos_cid": 117257, "source": "train_step3"}
{"query_id": "scaleup_25911094_58649375", "query": "How to increase direct electrochemical nitrogen-reduction currents while minimizing competing hydrogen evolution and matching proton supply to the stoichiometric requirements of nitrogen reduction", "pos": ["Superwettability‐Based Interfacial Chemical Reactions. Superwetting interfaces arising from the cooperation of surface energy and multiscale micro/nanostructures are extensively studied in biological systems. Fundamental understandings gained from biological interfaces boost the control of wettability under different dimensionalities, such as 2D surfaces, 1D fibers and channels, and 3D architectures, thus permitting manipulation of the transport physics of liquids, gases, and ions, which profoundly impacts chemical reactions and material fabrication. In this context, the progress of new chemistry based on superwetting interfaces is highlighted, beginning with mass transport dynamics, including liquid, gas, and ion transport. In the following sections, the impacts of the superwettability‐mediated transport dynamics on chemical reactions and material fabrication is discussed. Superwettability science has greatly enhanced the efficiency of chemical reactions, including photocatalytic, bioelectronic, electrochemical, and organic catalytic reactions, by realizing efficient mass transport. For material fabrication, superwetting interfaces are pivotal in the manipulation of the transport and microfluidic dynamics of liquids on solid surfaces, leading to the spatially regulated growth of low‐dimensional single‐crystalline arrays and high‐quality polymer films. Finally, a perspective on future directions is presented."], "field": "Chemical Engineering", "q_year": 2023, "q_cid": "259110940", "pos_cid": 58649375, "source": "train_step3"}
{"query_id": "scaleup_23651326_20136294", "query": "How to improve mass transfer and heating energy efficiency in a reaction involving immiscible liquids and a solid catalyst", "pos": ["Simple and effective technology for sustainable biodiesel production using high-power household fruit blender. Abstract A commercial household fruit blender is proposed as a simple, less time-consuming, and effective biodiesel production technique in this research work. Biodiesel was successfully produced in a 1200 W commercial household fruit blender. Due to the synergistic effect derived from the very high rotational speed of the blender blades integrated with micro-mixing level from cavitation phenomena, heat and mass transfer became greatly enhanced. The vigorous stirring inherently increased the temperature of the methanol-oil mixture to greater than 60 °C in less than 3 min, thus, a provision of external heating was not required. With a methanol to fresh refined palm oil molar ratio of 6:1 and 1 wt% sodium hydroxide catalyst, the FAME yield of 94.5% can be achieved in less than 3 min with the yield efficiency of 33.8 × 10−4 g/J for 500 mL of reaction volume. For 1000 mL of reaction volume at 1 min of reaction time, the FAME yield of 79.9% can be achieved with the yield efficiency of 122.3 × 10−4 g/J. Properties of the produced FAME comply with the EN 14214 and ASTM D 6751 standards. In conclusion, these results indicate that a high-power commercial household fruit blender can be utilized to produce biodiesel economically and effectively."], "field": "Chemical Engineering", "q_year": 2021, "q_cid": "236513262", "pos_cid": 201362942, "source": "train_step3"}
{"query_id": "scaleup_25927281_4787764", "query": "How to keep ibuprofen amorphous at room temperature", "pos": ["Influence of Solvent Composition on the Performance of Spray-Dried Co-Amorphous Formulations. Ball-milling is usually used to prepare co-amorphous drug–amino acid (AA) mixtures. In this study, co-amorphous drug–AA mixtures were produced using spray-drying, a scalable industrially preferred preparation method. The influence of the solvent type and solvent composition was investigated. Mixtures of indomethacin (IND) and each of the three AAs arginine, histidine, and lysine were ball-milled and spray-dried at a 1:1 molar ratio, respectively. Spray-drying was performed at different solvent ratios in (a) ethanol and water mixtures and (b) acetone and water mixtures. Different ratios of these solvents were chosen to study the effect of solvent mixtures on co-amorphous formulation. Residual crystallinity, thermal properties, salt/partial salt formation, and powder dissolution profiles of the IND–AA mixtures were investigated and compared to pure crystalline and amorphous IND. It was found that using spray-drying as a preparation method, all IND–AA mixtures could be successfully converted into the respective co-amorphous forms, irrespective of the type of solvent used, but depending on the solvent mixture ratios. Both ball-milled and spray-dried co-amorphous samples showed an enhanced dissolution rate and maintained supersaturation compared to the crystalline and amorphous IND itself. The spray-dried samples resulting in co-amorphous samples were stable for at least seven months of storage."], "field": "Chemical Engineering", "q_year": 2023, "q_cid": "259272812", "pos_cid": 4787764, "source": "train_step3"}
{"query_id": "scaleup_27734140_23629996", "query": "How to predict respiratory irritation and sensitization from molecular structure without supplied molecular descriptors when respiratory toxicity testing of all chemicals in use is infeasible", "pos": ["Implementing graph neural networks with TensorFlow-Keras. Abstract Graph neural networks are a versatile machine learning architecture that received a lot of attention recently due to its wide range of applications. In this technical report, we present an implementation of graph convolution and graph pooling layers for TensorFlow-Keras models, which allows a seamless and flexible integration into standard Keras layers to set up graph models in a functional way. We developed the Keras Graph Convolutional Neural Network Python package kgcnn based on TensorFlow-Keras which focus on a transparent tensor structure passed between layers and an ease-of-use mindset."], "field": "Chemical Engineering", "q_year": 2025, "q_cid": "277341408", "pos_cid": 236299966, "source": "train_step3"}
{"query_id": "scaleup_22168761_1595420", "query": "How to identify PP1-related pyrazolopyrimidine derivatives that suppress breast cancer cell growth without indiscriminate kinase inhibition", "pos": ["Targeted polypharmacology: Discovery of dual inhibitors of tyrosine and phosphoinositide kinases. The clinical success of multitargeted kinase inhibitors has stimulated efforts to identify promiscuous drugs with optimal selectivity profiles. It remains unclear to what extent such drugs can be rationally designed, particularly for combinations of targets that are structurally divergent. Here we report the systematic discovery of molecules that potently inhibit both tyrosine kinases and PI3-Ks, two protein families that are among the most intensely pursued cancer drug targets. Through iterative chemical synthesis, X-ray crystallography, and kinome-level biochemical profiling, we identify compounds that inhibit a spectrum of novel target combinations in these two families. Crystal structures reveal that the dual selectivity of these molecules is controlled by a hydrophobic pocket conserved in both enzyme classes and accessible through a rotatable bond in the drug skeleton. We show that one compound, PP121, blocks the proliferation of tumor cells by direct inhibition of oncogenic tyrosine kinases and PI3-Ks. These molecules demonstrate the feasibility of accessing a chemical space that intersects two families of oncogenes."], "field": "Chemistry", "q_year": 2016, "q_cid": "22168761", "pos_cid": 1595420, "source": "eval20x26"}
{"query_id": "scaleup_11196186_45595055", "query": "How to identify the lowest-energy geometries of multimetallic clusters with highly flexible atomic coordination to understand cluster formation intermediates and pathways", "pos": ["Molecular geometry optimization with a genetic algorithm.. We present a method for reliably determining the lowest energy structure of an atomic cluster in an arbitrary model potential. The method is based on a genetic algorithm, which operates on a population of candidate structures to produce new candidates with lower energies. Our method dramatically outperforms simulated annealing, which we demonstrate by applying the genetic algorithm to a tight-binding model potential for carbon. With this potential, the algorithm efficiently finds fullerene cluster structures up to ${\\mathrm{C}}_{60}$ starting from random atomic coordinates."], "field": "Chemistry", "q_year": 2016, "q_cid": "11196186", "pos_cid": 45595055, "source": "eval20x26"}
{"query_id": "scaleup_11359902_95474407", "query": "How to explain an unexpected rearrangement leading to 2-dialkylaminopyridines with no known precedent", "pos": ["Chitosan as an eco-friendly heterogeneous catalyst for Michael type addition reactions. A simple and efficient route to pyridones and phthalazines. Depending on their nature, nitrile activated methylene compounds add readily to β-enaminones in presence of chitosan to yield dienamides, pyridones or pyridine thiones. The dienamides, formed in this manner, can be readily converted to pyridones by stirring in refluxing acetic acid. Reaction of pyridazinones with a mixture containing benzaldehyde, malononitrile and chitosan affords phthalazines that are also produced by reaction of pyridazinone with benzylidene-malononitrile."], "field": "Chemistry", "q_year": 2012, "q_cid": "11359902", "pos_cid": 95474407, "source": "eval20x26"}
{"query_id": "scaleup_4318156_98427203", "query": "How to characterize the Lewis and Brønsted acidities of plant-derived polymetallic materials for comparison with classical metal chlorides", "pos": ["In situ FTIR spectra of pyridine adsorbed on SiO2-Al2O3, TiO2, ZrO2 and CeO2: general considerations for the identification of acid sites on surfaces of finely divided metal oxides. Abstract Exposure of strong Lewis (coordinatively unsaturated metal atoms) and Bronsted (proton donor OH-groups) acid sites on solid surfaces is a prime demand for potential adsorptive and catalytic applications. In situ FTIR spectroscopy of small adsorbed base molecules, often NH 3 , pyridine, CH 3 CN, NO or CO molecules, has been well established as a powerful surface analytical technique for characterization of nature, strength and concentration of acid sites. Pyridine (Py) has been preferred as an IR probe molecule of finely divided metal oxide surfaces at room (RT) and higher temperature regimes, since it is (i) more selective and stable than NH 3 ; (ii) much more strongly adsorbed than CO and CH 3 CN; and (iii) relatively more sensitive to the strength of Lewis acid sites than NO. In the present work, in situ IR spectra of Py adsorbed at ≥RT on characterized alumina, silica, silica–alumina, titania, zirconia and ceria were measured, and compared with RT-spectra of liquid and gas phase Py obtained under identical spectroscopic conditions, in order to characterize spectral consequences of mutual Py–Py interactions in the adsorbed phase. It has been concluded that the availability of Lewis acid sites can be unequivocally monitored by formation of coordinated Py molecules giving rise to IR-absorption(s) due to the ν 8a mode of ν CCN vibrations at 1630–1600 cm −1 , where the higher the frequency assumed, the stronger the acidity of the site. Formation of pyridinium surface species (PyH + ) is identifiable by (i) an ν 8a -absorption at ≥1630 cm −1 ; (ii) an ν 19b -absorption at 1550–1530 cm −1 ; as well as (iii) ν N + H and δ N + H absorptions occurring, respectively, near 2450 and 1580 cm −1 , and, thus, the availability of Bronsted acid sites. Moreover, products and IR-characteristics of Py surface reactions at >RT have been identified, and used to imply nature of surface base sites (OH − and O 2− ) involved in formation of acid–base site pairs."], "field": "Chemistry", "q_year": 2018, "q_cid": "4318156", "pos_cid": 98427203, "source": "eval20x26"}
{"query_id": "scaleup_22168761_12348638", "query": "How to identify effective and safe SRC inhibitors in a living vertebrate while avoiding ABL inhibition and associated cardiac risks", "pos": ["Phenotype-driven chemical screening in zebrafish for compounds that inhibit collective cell migration identifies multiple pathways potentially involved in metastatic invasion. ABSTRACT In the last decade, high-throughput chemical screening has become the dominant approach for discovering novel compounds with therapeutic properties. Automated screening using in vitro or cultured cell assays have yielded thousands of candidate drugs for a variety of biological targets, but these approaches have not resulted in an increase in drug discovery despite major increases in expenditures. In contrast, phenotype-driven screens have shown a much stronger success rate, which is why we developed an in vivo assay using transgenic zebrafish with a GFP-marked migrating posterior lateral line primordium (PLLp) to identify compounds that influence collective cell migration. We then conducted a high-throughput screen using a compound library of 2160 annotated bioactive synthetic compounds and 800 natural products to identify molecules that block normal PLLp migration. We identified 165 compounds that interfere with primordium migration without overt toxicity in vivo. Selected compounds were confirmed in their migration-blocking activity by using additional assays for cell migration. We then proved the screen to be successful in identifying anti-metastatic compounds active in vivo by performing orthotopic tumor implantation assays in mice. We demonstrated that the Src inhibitor SU6656, identified in our screen, can be used to suppress the metastatic capacity of a highly aggressive mammary tumor cell line. Finally, we used CRISPR/Cas9-targeted mutagenesis in zebrafish to genetically validate predicted targets of compounds. This approach demonstrates that the migrating PLLp in zebrafish can be used for large-scale, high-throughput screening for compounds that inhibit collective cell migration and, potentially, anti-metastatic compounds. Summary: We have developed a phenotype-driven screen for identifying new inhibitors of collective cell migration and demonstrated the screen can successfully identify compounds active in vivo and potentially new pathways for targeting cancer metastasis."], "field": "Chemistry", "q_year": 2016, "q_cid": "22168761", "pos_cid": 12348638, "source": "eval20x26"}
{"query_id": "scaleup_36723044_95882047", "query": "How to establish the identity of the malononitrile reaction product previously assigned as a thiocyanatoethylidene malononitrile derivative and reassess the structures of its subsequent reaction products", "pos": ["Polyfunctional heteroaromatics: a route to dicyanomethylene thiazoles based on the reaction of α-thiocyanatoketones with malononitrile. Reactions of α-S-cyanothioketones 6a-c with malononitrile were observed to form 2-(thiazol- 2(3H)-ylidene)malononitrile derivatives 7a-c. The thiazole products readily react with aromatic diazonium salts to yield 2-(5-phenylazo-3H-thiazol-2-ylidene)-malononitrile derivatives 8a-c. The malononitrile derivative 8c undergoes a condensation with DMF/DMA to yield thiazolo(5,4- c)pyridazine 12. Reactions of 7a-c with hydrazine hydrate leads to the generation of diaminopyrazoles 9a-c, which react with enaminone 13 to yield the corresponding thiazolylpyrazolo(1,5-a)pyrimidines 14. In addition, reaction of the malononitrile derivative 8a with benzenediazonium chloride readily affords the coupling product 10."], "field": "Chemistry", "q_year": 2011, "q_cid": "36723044", "pos_cid": 95882047, "source": "eval20x26"}
{"query_id": "scaleup_27675242_25277563", "query": "How to determine whether the methylation-site preference of norbelladine methyltransferase in Leucojum aestivum depends on metal-ion conditions", "pos": ["Regioselectivity Inversion of an O‐Methyltransferase via Semi‐rational Mutagenesis Combined with Metal Ion Substitution. S‐adenosyl‐L‐methionine (SAM)‐dependent O‐methyltransferases (O‐MTs) are a class of valuable and attractive biocatalysts for alkylation of catechols. In this work, an O‐methyltransferase (GeOMT) from the plant Galanthus elwesii was identified and characterised. GeOMT methylated a series of catechols with excellent regioselectivity. Moreover, a strategy was developed that combines structure‐directed protein engineering and metal ion substitution for regioselective inversion of GeOMT. The resultant W50M/A53N/Y186K triple variant preferentially coordinated Ni2+ instead of Mg2+ and displayed almost complete inversion in regioselectivity from 1 : 99 to 94 : 6 (para/meta) for 4‐nitrocatechol, the para‐methylated product of which is a vital plant growth regulator. This represents a promising strategy for regioselectivity improvement of O‐MTs."], "field": "Chemistry", "q_year": 2025, "q_cid": "276752425", "pos_cid": 252775639, "source": "eval_collection"}
{"query_id": "scaleup_27197470_3766791", "query": "How to efficiently obtain correlation functions and thermodynamic properties beyond equilibrium density profiles", "pos": ["Automatic differentiation in machine learning: a survey. Derivatives, mostly in the form of gradients and Hessians, are ubiquitous in machine learning. Automatic differentiation (AD), also called algorithmic differentiation or simply “auto-diff”, is a family of techniques similar to but more general than backpropagation for efficiently and accurately evaluating derivatives of numeric functions expressed as computer programs. AD is a small but established field with applications in areas including computational fluid dynamics, atmospheric sciences, and engineering design optimization. Until very recently, the fields of machine learning and AD have largely been unaware of each other and, in some cases, have independently discovered each other’s results. Despite its relevance, general-purpose AD has been missing from the machine learning toolbox, a situation slowly changing with its ongoing adoption under the names “dynamic computational graphs” and “differentiable programming”. We survey the intersection of AD and machine learning, cover applications where AD has direct relevance, and address the main imple- mentation techniques. By precisely defining the main differentiation techniques and their interrelationships, we aim to bring clarity to the usage of the terms “autodiff”, “automatic differentiation”, and “symbolic differentiation” as these are encountered more and more in machine learning settings."], "field": "Chemistry", "q_year": 2024, "q_cid": "271974703", "pos_cid": 3766791, "source": "eval_collection"}
{"query_id": "scaleup_27798761_32500187", "query": "How to directly activate phenolic C–O bonds in the solid phase for cross-coupling without prior derivatization", "pos": ["18F-Deoxyfluorination of Phenols via Ru π-Complexes. The deficiency of robust and practical methods for 18F-radiofluorination is a bottleneck for positron emission tomography (PET) tracer development. Here, we report the first transition-metal-assisted 18F-deoxyfluorination of phenols. The transformation benefits from readily available phenols as starting materials, tolerance of moisture and ambient atmosphere, large substrate scope, and translatability to generate doses appropriate for PET imaging."], "field": "Chemistry", "q_year": 2025, "q_cid": "277987618", "pos_cid": 32500187, "source": "eval_collection"}
{"query_id": "scaleup_21929660_6485378", "query": "How to explain the low fraction of gold remaining on the substrate and the decreased electroactive surface area after nanoparticle formation during laser treatment?", "pos": ["Jumping Nanodroplets. Flat gold nanostructures on inert substrates like glass or graphite were illuminated by single intensive laser pulses with fluences above the gold melting threshold. The liquid structures produced in this way are far from their equilibrium shape, and a dewetting process sets in. On a time scale of a few nanoseconds, the liquid contracted toward a sphere. During this contraction, the center of mass moved upward, which could lead to detachment of droplets from the surface due to inertia. The resulting velocities were on the order of 10 meters per second for droplets with radii in the range of 100 nanometers."], "field": "Chemistry", "q_year": 2020, "q_cid": "219296608", "pos_cid": 6485378, "source": "eval_collection"}
{"query_id": "scaleup_27339180_10430085", "query": "How to distinguish the effects of dissolved inorganic salts and internal microstructure on hydrogel crystallization temperatures", "pos": ["Antifreeze Hydrogels from Amphiphilic Statistical Copolymers. Prevention of ice formation is a critical issue for many applications, but routes to overcome the large thermodynamic driving force for crystallization of water at significant supercooling are limited. Here, we demonstrate that supramolecular hydrogels formed from statistical copolymers of 2-hydroxyethyl acrylate (HEA) and 2-(N-ethylperfluorooctane sulfonamido)ethyl methacrylate (FOSM) exhibit a degree of ice formation suppression unprecedented in a synthetic material. The mechanisms of ice prevention by these hydrogels mimic two methods used by nature: (1) hydrogen bonding of water to highly hydrophilic macromolecular chains and (2) nanoconfinement of water between hydrophobic moieties. From systematic variation in the copolymer composition to control the nanoscale (<4 nm) separation of the self-assembled hydrophobic nanodomains, the main mechanism by which these supramolecular hydrogels inhibit large amounts of water from freezing appears to be soft nanoconfinement. Nearly complete ice inhibition was ac..."], "field": "Chemistry", "q_year": 2024, "q_cid": "273391802", "pos_cid": 104300857, "source": "eval_collection"}
{"query_id": "scaleup_25738817_22496654", "query": "How to improve montmorillonite’s textural and surface properties for stable support of Pd catalysts", "pos": ["Progress and perspectives for the use of pillared clays as adsorbents for organic compounds in aqueous solution. Abstract The world is faced with several problems as regards water pollution. This is due to several factors, including the discharge of effluents into the environment with no prior treatment. This wastewater, therefore, contains significant levels of pollutants, including numerous toxic organic contaminants and others that are similarly undesirable. Several studies have attempted to find ways of removing wastewater contaminants using pillared interlayered clays (PILC) as adsorbents. In this work, we present a summary of those studies that have used PILC as adsorbents for the removal of organic compounds from aqueous solutions while simultaneously illustrating their potential for this purpose. A general overview is provided so that the reader can acquire a basic understanding of the PILC and their modified counterparts that have been used, and some of the characteristics that can directly affect their adsorption behavior, especially their textural and surface properties."], "field": "Chemistry", "q_year": 2023, "q_cid": "257388174", "pos_cid": 224966546, "source": "eval_collection"}
{"query_id": "scaleup_21011881_26101905", "query": "How to determine whether a new urinary biomarker improves prediction of one-year mortality after intensive care discharge beyond clinical risk factors and existing biomarkers, rather than merely showing an association with mortality", "pos": ["Extensions of net reclassification improvement calculations to measure usefulness of new biomarkers. Appropriate quantification of added usefulness offered by new markers included in risk prediction algorithms is a problem of active research and debate. Standard methods, including statistical significance and c statistic are useful but not sufficient. Net reclassification improvement (NRI) offers a simple intuitive way of quantifying improvement offered by new markers and has been gaining popularity among researchers. However, several aspects of the NRI have not been studied in sufficient detail."], "field": "Chemistry", "q_year": 2020, "q_cid": "210118810", "pos_cid": 26101905, "source": "eval_collection"}
{"query_id": "scaleup_26500146_21928725", "query": "How to improve the degradation resistance, stability, solubility, and bioavailability of α-tomatine and tomatidine to enhance their therapeutic effectiveness and specificity", "pos": ["Natural Product-Based Nanomedicine in Treatment of Inflammatory Bowel Disease. Many synthetic drugs and monoclonal antibodies are currently in use to treat Inflammatory Bowel Disease (IBD). However, they all are implicated in causing severe side effects and long-term use results in many complications. Numerous in vitro and in vivo experiments demonstrate that phytochemicals and natural macromolecules from plants and animals reduce IBD-related complications with encouraging results. Additionally, many of them modify enzymatic activity, alleviate oxidative stress, and downregulate pro-inflammatory transcriptional factors and cytokine secretion. Translational significance of natural nanomedicine and strategies to investigate future natural product-based nanomedicine is discussed. Our focus in this review is to summarize the use of phytochemicals and macromolecules encapsulated in nanoparticles for the treatment of IBD and IBD-associated colorectal cancer."], "field": "Chemistry", "q_year": 2023, "q_cid": "265001462", "pos_cid": 219287259, "source": "eval_collection"}
{"query_id": "scaleup_27675242_5387498", "query": "How to explain lycorine formation in N. benthamiana, including the required additional oxygen bridge and hydroxyl groups", "pos": ["Nicotiana benthamiana as a Production Platform for Artemisinin Precursors. Background Production of pharmaceuticals in plants provides an alternative for chemical synthesis, fermentation or natural sources. Nicotiana benthamiana is deployed at commercial scale for production of therapeutic proteins. Here the potential of this plant is explored for rapid production of precursors of artemisinin, a sesquiterpenoid compound that is used for malaria treatment. Methodology/Principal Findings Biosynthetic genes leading to artemisinic acid, a precursor of artemisinin, were combined and expressed in N. benthamiana by agro-infiltration. The first committed precursor of artemisinin, amorpha-4,11-diene, was produced upon infiltration of a construct containing amorpha-4,11-diene synthase, accompanied by 3-hydroxy-3-methylglutaryl-CoA reductase and farnesyl diphosphate synthase. Amorpha-4,11-diene was detected both in extracts and in the headspace of the N. benthamiana leaves. When the amorphadiene oxidase CYP71AV1 was co-infiltrated with the amorphadiene-synthesizing construct, the amorpha-4,11-diene levels strongly decreased, suggesting it was oxidized. Surprisingly, no anticipated oxidation products, such as artemisinic acid, were detected upon GC-MS analysis. However, analysis of leaf extracts with a non-targeted metabolomics approach, using LC-QTOF-MS, revealed the presence of another compound, which was identified as artemisinic acid-12-β-diglucoside. This compound accumulated to 39.5 mg.kg−1 fwt. Apparently the product of the heterologous pathway that was introduced, artemisinic acid, is further metabolized efficiently by glycosyl transferases that are endogenous to N. benthamiana. Conclusion/Significance This work shows that agroinfiltration of N. bentamiana can be used as a model to study the production of sesquiterpenoid pharmaceutical compounds. The interaction between the ectopically introduced pathway and the endogenous metabolism of the plant is discussed."], "field": "Chemistry", "q_year": 2025, "q_cid": "276752425", "pos_cid": 5387498, "source": "eval_collection"}
{"query_id": "scaleup_28094786_11529661", "query": "How to quantify Penicillin G loaded into synthesized materials to establish initial drug content and determine the percentage subsequently released", "pos": ["Quantification of Unknown Nanoscale Biomolecules Using the Average-Weight-Difference Method. In order to quantify the amount of drug molecules in drug delivery systems, analytical techniques such as high-performance liquid chromatography are used due to their accuracy and reliability. However, the instruments required for such techniques are expensive and not available in all laboratories. Therefore, in this study, we introduce a method that can be a relatively inexpensive and easy to perform drug analysis in almost any laboratory set-up. We have devised the “average-weight-difference method” within the limits of existing spectral analyses. By employing this method, we quantitatively analyzed the amount of isoniazid or doxorubicin molecules loaded onto β-glucan nanoparticles. This proved to be a relatively simple and reliable method and can be used to estimate the amount of nanoscale biomolecules before their analysis through expensive equipment in an environment where the instruments are not readily available."], "field": "Chemistry", "q_year": 2025, "q_cid": "280947865", "pos_cid": 115296618, "source": "eval_collection"}
{"query_id": "scaleup_25268156_22112754", "query": "How to assess the importance of differences in oil composition for diet, particularly their implications for the heart and blood vessels", "pos": ["Nutritional Indices for Assessing Fatty Acids: A Mini-Review. Dietary fats are generally fatty acids that may play positive or negative roles in the prevention and treatment of diseases. In nature, fatty acids occur in the form of mixtures of saturated fatty acid (SFA), monounsaturated fatty acid (MUFA), and polyunsaturated fatty acid (PUFA), so their nutritional and/or medicinal values must be determined. Herein, we do not consider the classic indices, such as ∑SFA, ∑MUFA, ∑PUFA, ∑n-6 PUFA, ∑n-3 PUFA, and n-6 PUFA/n-3 PUFA; instead, we summarize and review the definitions, implications, and applications of indices used in recent years, including the PUFA/SFA, index of atherogenicity (IA), the index of thrombogenicity (IT), the hypocholesterolemic/hypercholesterolemic ratio (HH), the health-promoting index (HPI), the unsaturation index (UI), the sum of eicosapentaenoic acid and docosahexaenoic acid (EPA + DHA), fish lipid quality/flesh lipid quality (FLQ), the linoleic acid/α-linolenic acid (LA/ALA) ratio, and trans fatty acid (TFA). Of these nutritional indices, IA and IT are the most commonly used to assess the composition of fatty acids as they outline significant implications and provide clear evidence. EPA + DHA is commonly used to assess the nutritional quality of marine animal products. All indices have their advantages and disadvantages; hence, a rational choice of which to use is critical."], "field": "Chemistry", "q_year": 2022, "q_cid": "252681565", "pos_cid": 221127545, "source": "eval_collection"}
{"query_id": "scaleup_24634679_10275318", "query": "How to minimize background fluorescence from fluorescent probes in aqueous media for cell staining", "pos": ["Solvatochromic isocyanonaphthalene dyes as ligands for silver(I) complexes, their applicability in silver(I) detection and background reduction in biolabelling. Abstract The complexation behavior of reactive and nonreactive N-substituted 1-amino-5-isocyanonaphthalene (ICAN) derivatives was studied in the presence of Ag(I) ions by UV–vis, steady-state and time resolved fluorescence measurements. The effect of ligand, solvent and counterion is covered. The equilibrium constants were found to be K AgL ∼ 10 6 M −1 in dioxane and water. Complex formation results a significant, solvent dependent (30–59 nm) batochromic shift of the emission maximum. This shift is accompanied by a switch-off effect in the case of the unreactive ligands, while in the case of the acrylated derivative (ACAIN) significant intensity enhancement was detected. Based on spectroscopic results only 1:1 AgL complex could be detected in solution at low concentrations c AgL −4 M, while at higher concentrations pure 1:2 AgL 2 formed which was characterized by ESI–MS, IR and NMR methods The structure and optical behavior of the complexes are discussed based on high-level quantum chemical calculations. It is shown that the complexation of ACAIN can be used for the selective detection and quantification of silver(I) ions from aqueous media. In addition, the fluorescene switch-off in the case of MICAN yields a significant contrast enhancement in biolabeling applications as is shown on fixated HaCat cells.s"], "field": "Chemistry", "q_year": 2022, "q_cid": "246346790", "pos_cid": 102753189, "source": "eval_collection"}
{"query_id": "scaleup_26846234_5011414", "query": "How to clarify the relationship between CPT1A inhibition and amiodarone-associated changes in triglyceride and palmitic-acid levels in ovarian cancer, given differing effects on short- and long-chain fatty acids", "pos": ["Effect of Toxicants on Fatty Acid Metabolism in HepG2 Cells. Impairment of hepatic fatty acid metabolism can lead to liver steatosis and injury. Testing drugs for interference with hepatic fatty acid metabolism is therefore important. To find out whether HepG2 cells are suitable for this purpose, we investigated the effect of three established fatty acid metabolism inhibitors and of three test compounds on triglyceride accumulation, palmitate metabolism, the acylcarnitine pool and dicarboxylic acid accumulation in the cell supernatant and on ApoB-100 excretion in HepG2 cells. The three established inhibitors [etomoxir, methylenecyclopropylacetic acid (MCPA), and 4-bromocrotonic acid (4-BCA)] depleted mitochondrial ATP at lower concentrations than cytotoxicity occurred, suggesting mitochondrial toxicity. They inhibited palmitate metabolism at similar or lower concentrations than ATP depletion, and 4-BCA was associated with cellular fat accumulation. They caused specific changes in the acylcarnitine pattern and etomoxir an increase of thapsic (C18 dicarboxylic) acid in the cell supernatant, and did not interfere with ApoB-100 excretion (marker of VLDL export). The three test compounds (amiodarone, tamoxifen, and the cannabinoid WIN 55,212-2) depleted the cellular ATP content at lower concentrations than cytotoxicity occurred. They all caused cellular fat accumulation and inhibited palmitate metabolism at similar or higher concentrations than ATP depletion. They suppressed medium-chain acylcarnitines in the cell supernatant and amiodarone and tamoxifen impaired thapsic acid production. Tamoxifen and WIN 55,212-2 decreased cellular ApoB-100 excretion. In conclusion, the established inhibitors of fatty acid metabolism caused the expected effects in HepG2 cells. HepG cells proved to be useful for the detection of drug-associated toxicities on hepatocellular fatty acid metabolism."], "field": "Chemistry", "q_year": 2024, "q_cid": "268462342", "pos_cid": 5011414, "source": "eval_collection"}
{"query_id": "scaleup_28039797_25018937", "query": "How to determine whether compounds are active against both immature and mature reproductive forms rather than only asexual forms", "pos": ["Streamlined and Robust Stage-Specific Profiling of Gametocytocidal Compounds Against Plasmodium falciparum. Malaria elimination is dependent on the ability to target both the pathogenic and transmissible stages of the human malaria parasite, Plasmodium falciparum. These forms of the parasite are differentiated by unique developmental stages, each with their own biological mechanisms and processes. These individual stages therefore also respond differently to inhibitory compounds, and this complicates the discovery of multistage active antimalarial agents. The search for compounds with transmission-blocking activity has focused on screening for activity on mature gametocytes, with only limited descriptions available for the activity of such compounds on immature stage gametocytes. This therefore poses a gap in the profiling of antimalarial agents for pan-reactive, multistage activity to antimalarial leads. Here, we optimized an effective and robust strategy for the simple and cost-effective description of the stage-specific action of gametocytocidal antimalarial compounds."], "field": "Chemistry", "q_year": 2025, "q_cid": "280397970", "pos_cid": 250189379, "source": "eval_collection"}
{"query_id": "scaleup_27197470_27028590", "query": "How to accurately describe interacting many-body systems under inhomogeneous conditions, including liquid–gas coexistence and associated bulk and interfacial phenomena, even for states beyond available simulation data", "pos": ["Neural force functional for non-equilibrium many-body colloidal systems. We combine power functional theory and machine learning to study non-equilibrium overdamped many-body systems of colloidal particles at the level of one-body fields. We first sample in steady state the one-body fields relevant for the dynamics from computer simulations of Brownian particles under the influence of randomly generated external fields. A neural network is then trained with this data to represent locally in space the formally exact functional mapping from the one-body density and velocity profiles to the one-body internal force field. The trained network is used to analyse the non-equilibrium superadiabatic force field and the transport coefficients such as shear and bulk viscosities. Due to the local learning approach, the network can be applied to systems much larger than the original simulation box in which the one-body fields are sampled. Complemented with the exact non-equilibrium one-body force balance equation and a continuity equation, the network yields viable predictions of the dynamics in time-dependent situations. Even though training is based on steady states only, the predicted dynamics is in good agreement with simulation results. A neural dynamical density functional theory can be straightforwardly implemented as a limiting case in which the internal force field is that of an equilibrium system. The framework is general and directly applicable to other many-body systems of interacting particles following Brownian dynamics."], "field": "Chemistry", "q_year": 2024, "q_cid": "271974703", "pos_cid": 270285902, "source": "eval_collection"}
{"query_id": "scaleup_24660238_20942588", "query": "How to control the dissolution of inorganic colloids over time", "pos": ["Transient supramolecular assembly of a functional perylene diimide controlled by a programmable pH cycle.. Self-regulating materials require embedded control systems. Active networks of enzymes fulfill this function in living organisms, and the development of chemical controls for synthetic systems is still in its infancy. While previous work has focused on enzymatic controls, small-molecule networks have unexplored potential. We describe a simple small-molecule network that is able to produce transient pH cycles with tunable lagtimes and lifetimes, based on coupling the acid-to-alkali methylene glycol-sulfite reaction to 1,3-propanesultone, a slow acid generator. Applied to transient pH-driven supramolecular self-assembly of a perylene diimide, our system matches the flexibility of in vitro enzymatic systems, including the ability to perform repeated cycles of assembly and disassembly."], "field": "Chemistry", "q_year": 2022, "q_cid": "246602388", "pos_cid": 209425887, "source": "eval_collection"}
{"query_id": "scaleup_27675242_25019053", "query": "How to clarify LaNRII's proposed role in Amaryllidaceae alkaloid biosynthesis", "pos": ["Critical Residues for Structure and Catalysis in Short-chain Dehydrogenases/Reductases*. Short-chain dehydrogenases/reductases form a large, evolutionarily old family of NAD(P)(H)-dependent enzymes with over 60 genes found in the human genome. Despite low levels of sequence identity (often 10–30%), the three-dimensional structures display a highly similar α/β folding pattern. We have analyzed the role of several conserved residues regarding folding, stability, steady-state kinetics, and coenzyme binding using bacterial 3β/17β-hydroxysteroid dehydrogenase and selected mutants. Structure determination of the wild-type enzyme at 1.2-Å resolution by x-ray crystallography and docking analysis was used to interpret the biochemical data. Enzyme kinetic data from mutagenetic replacements emphasize the critical role of residues Thr-12, Asp-60, Asn-86, Asn-87, and Ala-88 in coenzyme binding and catalysis. The data also demonstrate essential interactions of Asn-111 with active site residues. A general role of its side chain interactions for maintenance of the active site configuration to build up a proton relay system is proposed. This extends the previously recognized catalytic triad of Ser-Tyr-Lys residues to form a tetrad of Asn-Ser-Tyr-Lys in the majority of characterized short-chain dehydrogenases/reductase enzymes."], "field": "Chemistry", "q_year": 2025, "q_cid": "276752425", "pos_cid": 25019053, "source": "eval_collection"}
{"query_id": "scaleup_27667780_22118807", "query": "How to quantify and predict the effect of bentonite selection on the pour point of processed vegetable oil?", "pos": ["Investigation of the Interaction of Herbal Ingredients Contained in Triphala Recipe Using Simplex Lattice Design: Chemical Analysis Point of View. The aim of this work was to investigate the interaction of herbal ingredients contained in Triphala recipe (Terminalia chebula, Terminalia bellirica, and Phyllanthus emblica in equal proportion) using simplex lattice design. This work focused on chemical analysis of four phenolic compounds including gallic acid, corilagin, chebulagic acid, and chebulinic acid by validated high-performance liquid chromatography. The effect of the extraction technique (decoction vs. infusion) and gamma irradiation was also examined. The combination index was used as a tool for determination of interaction of the ingredients contained in the herbal recipe. Results showed that the extraction technique and gamma irradiation slightly altered the content of some phenolic compounds as well as the combination index. The positive interaction seems to be found at the equal proportion of the three plants. This work scientifically supported the suitable formula of the Triphala recipe in the traditional use."], "field": "Chemistry", "q_year": 2025, "q_cid": "276677807", "pos_cid": 221188074, "source": "eval_collection"}
{"query_id": "scaleup_28344560_28139783", "query": "How to rapidly and reliably identify low-abundance interactions in cells across chemically diverse surfaces while preserving short, precise distance constraints", "pos": ["In Cellulo Cysteine Umpolung for Protein Structure Probing. Proteome-wide intramolecular cross-linking of amino acids allows for protein structure probing and is often achieved by reactive intermediates generated in situ. For example, carbene insertion chemistry forms versatile products but relies on two-step protocols that first introduce a photoreactive group and then generate a reactive intermediate via UV light irradiation. Alternatively, direct cross-linking with bifunctional electrophilic reagents enables modification of natural amino acids in a single transformation but proceeds via intermediates with a sufficiently long half-life in solution to capture unfavorable protein conformations. Herein, we report the use of commercially available vinyl thianthrenium tetrafluoroborate (VTT) for a single-step cross-linking strategy based on the umpolung of native cysteinyl thiols to electrophilic episulfonium ions in cells. We demonstrate that the umpolung reaction proceeds within minutes in various cell types. Even when competing with cysteine-reactive maleimide or iodoacetamide reagents, the fast cellular uptake of VTT enables efficient intracellular labeling and ensures the formation of products with a short and stable ethylene linker between cysteine and nucleophilic natural amino acids. We anticipate that the fast generation of episulfonium ions, which enable cross-linking without exogenous activation, will assist researchers in predicting protein structures based on quantitative proteome-wide information generated in cellulo."], "field": "Chemistry", "q_year": 2025, "q_cid": "283445609", "pos_cid": 281397833, "source": "eval_collection"}
{"query_id": "scaleup_23793949_6784372", "query": "How to determine whether ferrocene derivatives inhibit t cell acute lymphoblastic leukemia cell proliferation and explain arrest in the resting or initial growth phase", "pos": ["Multiple degradation pathways regulate versatile CIP/KIP CDK inhibitors. The mammalian CIP/KIP family of cyclin-dependent kinase (CDK) inhibitors (CKIs) comprises three proteins – p21Cip1/WAF1, p27Kip1, and p57Kip2 – that bind and inhibit cyclin–CDK complexes, which are key regulators of the cell cycle. CIP/KIP CKIs have additional independent functions in regulating transcription, apoptosis and actin cytoskeletal dynamics. These divergent functions are performed in distinct cellular compartments and contribute to the seemingly contradictory observation that the CKIs can both suppress and promote cancer. Multiple ubiquitin ligases (E3s) direct the proteasome-mediated degradation of p21, p27 and p57. This review analyzes recent data highlighting our current understanding of how distinct E3 pathways regulate subpopulations of the CKIs to control their diverse functions."], "field": "Chemistry", "q_year": 2021, "q_cid": "237939490", "pos_cid": 6784372, "source": "eval_collection"}
{"query_id": "scaleup_25552371_21846958", "query": "How to clarify the relationship between the molecular structures of Evodiae fructus compounds and their anti-liver cancer activity to predict which compounds are biologically active", "pos": ["QSAR without borders. Prediction of chemical bioactivity and physical properties has been one of the most important applications of statistical and more recently, machine learning and artificial intelligence methods in chemical sciences. This field of research, broadly known as Quantitative Structure-Activity Relationships (QSAR) modeling, has developed many important algorithms and has found a broad range of applications in physical organic and medicinal chemistry in the past 55+ years. This Perspective summarizes recent technological advances in QSAR modeling. Importantly, it also highlights the applicability of algorithms, modeling methods, and validation practices developed in QSAR to a wide range of research areas beyond traditional QSAR fields. These fields include nanotechnology, materials science, biomaterials, clinical informatics, and others. As modern research methods generate rapidly increasing amounts of data, knowledge of robust data-driven modelling methods is becoming essential for scientists in many disciplines both within and outside of chemical research. We hope that this contribution will serve to address this challenge."], "field": "Chemistry", "q_year": 2023, "q_cid": "255523719", "pos_cid": 218469582, "source": "eval_collection"}
{"query_id": "scaleup_24927745_42097132", "query": "How to confirm the three-dimensional arrangements around silicon centers in the products", "pos": ["Determination of Absolute Configuration of Natural Products: Theoretical Calculation of Electronic Circular Dichroism as a Tool. Determination of absolute configuration (AC) is one of the most challenging features in the structure elucidation of chiral natural products, especially those with complex structures. With revolutionary advancements in the area of quantum chemical calculations of chiroptical spectroscopy over the past decade, the time dependent density functional theory (TDDFT) calculation of electronic circular dichroism (ECD) spectra has emerged as a very promising tool. The principle is simply based on the comparison of the calculated and experimental ECD spectra: the more closely they match, the more reliable conclusion for the AC assignment can be drawn. This review attempts to use several examples representing monomeric flavonoids, rotationally restricted biflavonoids, complex hexahydroxydiphenoyl-containing flavonoids, conformationally flexible and restrained sesquiterpenoids, cembrane-africanene terpenoids, dihydropyranocoumarins, alkaloids, and dihydroxanthones to illustrate the applicability of this approach in determining the AC of structurally diverse natural products. The findings clearly indicate that the TDDFT calculation of ECD spectra can quantify the contribution of individual conformers and the interaction of multiple chromophores, making it possible to determine the AC of complex chiral molecules. The calculated electronic transitions and molecular orbitals provide new insight into the interpretation of ECD spectra at the molecular level."], "field": "Chemistry", "q_year": 2022, "q_cid": "249277451", "pos_cid": 42097132, "source": "eval_collection"}
{"query_id": "scaleup_24838203_4376643", "query": "How to determine the effects of FeNi alloy nanoparticle preparation conditions on SALDI-MS sensitivity and reproducibility for poison detection", "pos": ["Chemical Synthesis of High-Stable Amorphous FeCo Nanoalloys with Good Magnetic Properties. It is difficult to fabricate high-purity amorphous FeCo alloys by traditional physical methods due to their weak glass forming ability. In this work, the fully amorphous FeCo nanoalloys with high purity and good stability have been prepared by a direct chemical reduction of Fe2+ and Co2+ ions with NaBH4 as the reducing agent and polyvinylpyrrolidone (PVP) as the surfactant. The morphologies, surface compositions and particle sizes with their distribution of these amorphous samples can be effectively tuned by the suitable PVP additions. High crystallization temperature up to 468 °C, high saturation magnetization of 196.2 A·m2·kg−1 and low coercivity of 83.3 Oe are obtained in amorphous FeCo nanoalloys due to their uniform distribution, weak surface oxidation and low surface B concentration. Good frequency-dependent magnetic properties can be also achieved in the fully compacted amorphous sample with a high density of 7.20 g/cm3. The simple chemical method, high stability and good magnetic properties for these amorphous FeCo nanoalloys promise their significant potential applications in high-power magnetic devices."], "field": "Chemistry", "q_year": 2022, "q_cid": "248382039", "pos_cid": 4376643, "source": "eval_collection"}
{"query_id": "scaleup_28310695_21267842", "query": "How to preserve circular polarization in an oled’s emitted light despite cancellation from back cathode reflection", "pos": ["Circularly polarized light at the mirror: Caveats and opportunities.. Moving from the simple concept that reflection onto a mirror surface changes the handedness of circularly polarized light, we describe what happens to the emergent polarization in two different cases after reflection on a back mirror. In the first case, a regular emitter is taken into account, where reflection has the effect to destroy the emergent polarization. In the second case, we show what could happen when a hypothetical apparently non-reciprocal emitting material undergoes a similar experiment. These simple concepts have important implications in the design of efficient circularly polarized emitting devices."], "field": "Chemistry", "q_year": 2025, "q_cid": "283106951", "pos_cid": 212678424, "source": "eval_collection"}
{"query_id": "scaleup_22896618_23466226", "query": "How to determine how aryl substituents on the ligand and substrate affect the stability of the turnover-limiting migratory insertion transition state", "pos": ["Origin of Substituent Effects in Edge-to-Face Aryl-Aryl Interactions. Substituent effects in the edge-to-face configuration of the benzene dimer have been studied using modern density functional theory. An accurate interaction potential energy curve has been computed for the unsubstituted dimer using ab initio methods with large basis sets. The recommended binding energy for the edge-to-face benzene dimer is 2.31 kcal mol−1, estimated at the counterpoise-corrected CCSD(T)/aug-cc-pVTZ level of theory. For both edge-ring and face-ring-substituted dimers, interaction energies correlate with σm for the substituents, indicating that substituent effects can be understood qualitatively in terms of simple electrostatic effects, although in the latter case dispersion results in some scatter in the data. In contrast to prevailing models of substituent effects in benzene dimers, polarization of the π-system of the substituted ring does not induce substituent effects. For edge-ring-substituted dimers, substituent effects arise from differential electrostatic interactions between the hydrogens on the substituted ring and the π-cloud of the face ring and direct interactions of the substituents with the unsubstituted ring. For face-ring-substituted dimers, substituent effects arise from direct electrostatic and dispersion interactions of the substituents with the edge ring. Substituents with σm > 0.12 favour edge ring substitution while for σm < 0.12 substitution on the face ring is preferred."], "field": "Chemistry", "q_year": 2020, "q_cid": "228966185", "pos_cid": 23466226, "source": "eval_collection"}
{"query_id": "scaleup_27339180_22038900", "query": "How to achieve sufficient mechanical robustness, stretchability, and self-healing ability in biocompatible hydrogels to meet the tissue-like mechanical demands of wound care", "pos": ["H-Bonding Supramolecular Hydrogels with Promising Mechanical Strength and Shape Memory Property for Postoperative Anti-adhesion Application.. Development of a physical barrier with mechanical properties similar to human smooth muscle and on-demand degradation profile is crucial for the clinical prevention of postoperative adhesion. Herein, a series of supramolecular hydrogels (PMI hydrogels) composed of poly(ethylene glycol) (PEG), methylenediphenyl 4, 4-diisocyanate (MDI) and imidazolidinyl urea (IU, hydrogen bonding reinforced factor) with biodegradability and high toughness are reported to serve as physical barriers for abdominal adhesion prevention. The tensile fracture strength and strain of the PMI hydrogels could be adjusted in the ranges of 0.6-2.3 MPa and 100%-440%, respectively, and Young's moduli (0.2-1.6 MPa) are close to human soft tissues like smooth muscle and skin tissue as well as outstanding shape memory property. The PMI hydrogels show good cell and tissue biocompatibility, and the in vivo retention time is in accord with the needs for the postoperative anti-adhesion physical barriers. Through an abdominal defect model on mice, this study shows that PMI hydrogel can completely prevent the tissue adhesion compared to the commercialized Seprafilm® with high safety. Owing to the promising mechanical properties and good biocompatibility, the PMI hydrogels may be extended for various biomedical applications and the development of advanced flexible electronic devices."], "field": "Chemistry", "q_year": 2024, "q_cid": "273391802", "pos_cid": 220389008, "source": "eval_collection"}
{"query_id": "scaleup_25184240_77503573", "query": "How to protect against tartrazine-induced neurotoxicity", "pos": ["Advancing role of melatonin in the treatment of neuropsychiatric disorders. Abstract Melatonin is a pineal neurohormone whose secretion is influenced by circadian changes of 24 hour night and day cycle. Over the recent past, several studies have highlighted the ubiquitous influence of the circadian timing in almost all the physiologic functions. An altered/deficient sleep–wake cycle has been correlated with physiological imbalances which are linked to the development of various disorders, viz depression, anxiety, psychosis, attention deficits, sleep deprivation and others. Melatonin and its oxidation products, viz cyclic 3-hydroxymelatonin, N1-acetyl-N2-formyl-5-methoxykinuramine and N1-acetyl-5-methoxykinuramine possess excellent antioxidant properties. Melatonin's beneficial neuroprotective properties are mostly attributed to excellent free radical scavenging properties. A gathering body of evidence has shown that besides strong antioxidant activities, melatonin is a pleiotropic regulator molecule which orchestrates multiple functions through all the three melatonin receptors, i.e. MT1, MT2, and MT3. For example, MT2 receptor agonistic activity is attributed to neuroprotective, hypnotic and anxiolytic properties while MT1 and MT2 agonistic activity is associated with the clinical efficacy of agomelatine. The third melatonin receptor has been identified as quinone reductase (QR) 2, an enzyme involved in detoxification. MT3 agonist has been linked to strong hypotensive effects in preclinical study. In conclusion, the gathering body of evidence both from preclinical and clinical literatures suggests strong antioxidant activities and diverse pleiotropic mechanisms of melatonin for potential neuroprotective role in diverse neuropsychiatric disorders. However, there is still a lack of melatonergic ligands with high selectivity and specificity to precisely target any particular neuropsychiatric disorders for which limited therapeutic options are currently available clinically."], "field": "Chemistry", "q_year": 2022, "q_cid": "251842405", "pos_cid": 77503573, "source": "eval_collection"}
{"query_id": "scaleup_27073598_7427304", "query": "How to identify new chemotherapeutic candidates with activity against drug-resistant tuberculosis", "pos": ["Medicinal plants used for the treatment of tuberculosis by Bapedi traditional healers in three districts of the Limpopo Province, South Africa.. The present study was aimed at documenting medicinal plants used for the treatment of tuberculosis (TB) by the Bapedi traditional healers in three districts of the Limpopo Province, South Africa. Fifty two traditional healers from 17 municipalities covering Capricorn, Sekhukhune and Waterberg districts were interviewed between January and July 2011. Twenty one medicinal plant species belonging to 20 genera and 18 families were documented. The majority (61.9%) are indigenous and the rest are exotics, found near homes as weeds or cultivated in home gardens as ornamentals or food plants. Hyacinthaceae, Moraceae and Rutaceae families were the most represented families in terms of species numbers (9.5% each). Herbs and trees (38% each) constituted the largest proportion of the growth forms of the medicinal plants used. Tuberculosis remedies were mostly prepared from leaves (34%) followed by roots (21%). The therapeutic claims made on medicinal plants used to treat TB by the Bapedi traditional healers are well supported by literature, with 71.4% of the species having antimicrobial properties or have similar ethno medicinal uses in other countries. This study therefore, illustrates the importance of medicinal plants in the treatment and management of TB in the Limpopo Province, South Africa."], "field": "Chemistry", "q_year": 2024, "q_cid": "270735984", "pos_cid": 7427304, "source": "eval_collection"}
{"query_id": "scaleup_21574808_57825911", "query": "How to obtain structurally well-defined molecules that allow the effects of nitrogen substitution on molecular and electronic properties to be distinguished from those of the unsubstituted framework", "pos": ["Finite phenine nanotubes with periodic vacancy defects. Toward nanotubes with periodic gaps Carbon nanotubes consist of a continuous array of benzene rings fused along their edges. It is not straightforward to excise regular fragments in a top-down fashion to produce periodic gaps. Sun et al. showcase the beginnings of a bottom-up strategy toward this end. They used borylations and catalytic cross-coupling chemistry to prepare a discrete cylindrical carbon compound composed of 40 benzene rings bonded to one another at the 1, 3, and 5 positions to leave regular void spaces in the walls. Catenation of multiple similar segments could ultimately lead to an extended nanotube with periodic wall defects. Science, this issue p. 151 A discrete porous tube-shaped compound composed of 40 benzene rings has been rationally synthesized. Discrete graphitic carbon compounds serve as tunable models for the properties of extended macromolecular structures such as nanotubes. Here, we report synthesis and characterization of a cylindrical C304H264 molecule composed of 40 benzene (phenine) units mutually bonded at the 1, 3, and 5 positions. The concise nine-step synthesis featuring successive borylations and couplings proceeded with an average yield for each benzene-benzene bond formation of 91%. The molecular structure of the nanometer-sized cylinder with periodic vacancy defects was confirmed spectroscopically and crystallographically. The nanoporous nature of the compound further enabled inclusion of multiple fullerene guests. Computations suggest that fusing many such cylinders could produce carbon nanotubes with electronic properties modulated by the periodic vacancy defects."], "field": "Chemistry", "q_year": 2020, "q_cid": "215748088", "pos_cid": 57825911, "source": "eval_collection"}
{"query_id": "scaleup_25738817_11699614", "query": "How to determine the dimensions of sub-nanoscale catalyst defects and assess their potential role in material loss during repeated recycling", "pos": ["Void Shapes and o-Ps Lifetime in Molecular Crystals. The size and shape of the free volume in molecular crystals was estimated from crystallographic data. The o-Ps lifetime values were calculated from respective models and compared with the experimental data. The best agreement for channel-like voids has been obtained for the value of DR parameter equal 0.19 nm. The threshold value of radius allowing Ps trapping in the void was found to be (0.12-0.13) nm. PACS numbers: 78.70.Bj"], "field": "Chemistry", "q_year": 2023, "q_cid": "257388174", "pos_cid": 116996145, "source": "eval_collection"}
{"query_id": "scaleup_27667780_23638735", "query": "How to distinguish subtle differences in bentonite composition and structure that affect retention of specific chemical groups during vegetable oil recycling despite the limited selectivity of conventional x-ray diffraction", "pos": ["Swelling layered minerals applications: A solid state NMR overview.. Swelling layered clay minerals form an important sub-group of the phyllosilicate family. They are characterized by their ability to expand or contract in the presence or absence of water. This property makes them useful for a variety of applications, ranging from environmental technologies to heterogeneous catalysis, and including pharmaceutical and industrial applications. Solid State Nuclear Magnetic Resonance (SS-NMR) has been extensively applied in the characterization of these materials, providing useful information on their dynamics and structure that is inaccessible using other characterization methods such as X-ray diffraction. In this review, we present the key contributions of SS-NMR to the understanding of the mechanisms that govern some of the main applications associated to swelling clay minerals. The article is divided in two parts. The first part presents SS-NMR conventional applications to layered clay minerals, while the second part comprises an in-depth review of the information that SS-NMR can provide about the different properties of swelling layered clay minerals."], "field": "Chemistry", "q_year": 2025, "q_cid": "276677807", "pos_cid": 236387356, "source": "eval_collection"}
{"query_id": "scaleup_27133867_24863783", "query": "How to produce particles with consistent, precisely controlled size and shape while avoiding surfactant-related impurities", "pos": ["Precipitation Polymerization: A Powerful Tool for Preparation of Uniform Polymer Particles. Precipitation polymerization (PP) is a powerful tool to prepare various types of uniform polymer particles owing to its outstanding advantages of easy operation and the absence of any surfactant. Several PP approaches have been developed up to now, including traditional thermo-induced precipitation polymerization (TRPP), distillation precipitation polymerization (DPP), reflux precipitation polymerization (RPP), photoinduced precipitation polymerization (PPP), solvothermal precipitation polymerization (SPP), controlled/‘‘living’’ radical precipitation polymerization (CRPP) and self-stabilized precipitation polymerization (2SPP). In this review, a general introduction to the categories, mechanisms, and applications of precipitation polymerization and the recent developments are presented, proving that PP has great potential to become one of the most attractive polymerization techniques in materials science and bio-medical areas."], "field": "Chemistry", "q_year": 2024, "q_cid": "271338671", "pos_cid": 248637834, "source": "eval_collection"}
{"query_id": "scaleup_21851904_1205165", "query": "How to obtain high-cis polymer networks with controlled molecular architecture and sufficient crosslinking to withstand solvent-induced swelling", "pos": ["Copolymerization of Norbornene and Norbornadiene Using a cis-Selective Bimetallic W-Based Catalytic System. The bimetallic cluster Na[W2(μ-Cl)3Cl4(THF)2]·(THF)3 ({W2}, {W 3 W}6+, a′2e′4), which features a triple metal-metal bond, is a highly efficient room-temperature initiator for ring opening metathesis polymerization (ROMP) of norbornene (NBE) and norbornadiene (NBD), providing high-cis polymers. In this work, {W2} was used for the copolymerization of the aforementioned monomers, yielding statistical poly(norbornene)/poly(norbornadiene) PNBE/PNBD copolymers of high molecular weight and high-cis content. The composition of the polymer chain was estimated by 13C CPMAS NMR data and it was found that the ratio of PNBE/PNBD segments in the polymer chain was relative to the monomer molar ratio in the reaction mixture. The thermal properties of all copolymers were similar, resembled the properties of PNBD homopolymer and indicated a high degree of cross-linking. The morphology of all materials in this study was smooth and non-porous; copolymers with higher PNBE content featured a corrugated morphology. Glass transition temperatures were lower for the copolymers than for the homopolymers, providing a strong indication that those materials featured a branched-shaped structure. This conclusion was further supported by viscosity measurements of copolymers solutions in THF. The molecular structure of those materials can be controlled, potentially leading to well-defined star polymers via the “core-first” synthesis method. Therefore, {W2} is not only a cost-efficient, practical, highly active, and cis-stereoselective ROMP-initiator, but it can also be used for the synthesis of more complex macromolecular structures."], "field": "Chemistry", "q_year": 2020, "q_cid": "218519045", "pos_cid": 1205165, "source": "eval_collection"}
{"query_id": "scaleup_23948886_23218698", "query": "How to fabricate high-performance polyimide aerogels with complex three-dimensional structures while maintaining suitable precursor viscosity and sufficient working time to complete fabrication", "pos": ["3D Printing of Lightweight Polyimide Honeycombs with the High Specific Strength and Temperature Resistance.. Lightweight structures are often used for applications requiring higher strength-to-weight ratios and lower densities, such as in aircraft, vehicles, and various engine components. Three-dimensional (3D) printing technology has been widely used for lightweight polymer structures because of the superior flexibility, personalized design, and ease of operation offered by it. However, synthesis of lightweight polymeric structures that possess both high specific strength and glass transfer temperature (Tg) remains an elusive goal, because 3D printed polymers with these properties are still very few in the market. For example, 3,3',4,4'-biphenyl tetracarboxylic dianhydride (BPDA) and p-phenylenediamine (PDA)-type (UPILEX-S type) polyimides show exceptional thermal stability (Tg up to ≈400 °C) and mechanical properties (tensile strength exceeding 500 MPa) and are the first choice if extremely high temperatures of 400 °C or even higher (depending on the duration) are required, which hampers their processing using existing 3D printing techniques. However, their processing using existing 3D printing techniques is hampered due to their thermal resistance. Herein, a 3D printing approach was demonstrated for generating complex lightweight BPDA-PDA polyimide geometries with unprecedented specific strength and thermal resistance. The simple aqueous polymerization reaction of BPDA with water-soluble PDA and triethylamine (TEA) afforded the poly(amic acid) ammonium salt (PAAS) hydrogels. These PAAS solutions showed clear shear thinning and thermo-reversibility, along with high G' gel-state moduli, which ensured self-supporting features and shape fidelity in the gel state. Postprinting thermal treatment transformed the PAAS precursor to BPDA-PDA polyimide (UPILEX-S type). The resulting layer-by-layer deposition onto lightweight polyimide honeycombs in the form of triangular, square, and hexagonal structures showed tailorable mechanical strength, exceptional compressive strength-to-weight ratio (highest up to 0.127 MPa (kg m-3)-1), and remarkable thermoresistance (Tg approximately 380 °C). These high-performance 3D printed polyimide honeycombs and unique synthetic techniques with general structures are potentially useful in fields ranging from automotive to aerospace technologies."], "field": "Chemistry", "q_year": 2021, "q_cid": "239488862", "pos_cid": 232186986, "source": "eval_collection"}
{"query_id": "scaleup_24843203_53645536", "query": "How to understand how L. ferriphilum adapts to salt conditions toxic to most acidophilic microorganisms", "pos": ["Review on fatty acid desaturases and their roles in temperature acclimatisation. Carbohydrates and proteins are polymers of polysaccharides and polypeptide residues, respectively. Conversely, lipids are made up of a wide range of compounds with tremendous differences in structures and lack building blocks. Therefore, fatty acids constitute the major components of various lipid classes such as glycerides and sphingolipids. Fatty acids are organic compounds containing a carboxylic acid group mostly at the end of an aliphatic chain and are categorized into saturated and unsaturated. Most fatty acids especially the so-called polyunsaturated fatty acids (PUFAs) and their derivatives play key biological roles in inflammatory response, cell division, control of lipid metabolism, as signaling molecules, supply of energy and protecting the biological membranes structure and function. In this study, a general overview of fatty acids, their biosynthesis mechanisms as well as biological importance have been discussed. Fatty acid desaturase enzymes and their sources have also been reviewed. Recent studies on the functional expression of different types of desaturase enzymes have also been discussed."], "field": "Chemistry", "q_year": 2022, "q_cid": "248432039", "pos_cid": 53645536, "source": "train_step3"}
{"query_id": "scaleup_23820121_99499118", "query": "How to reliably assess antibacterial surface efficacy under intended end-use conditions despite temperature-dependent effects on microbial survival and antimicrobial release?", "pos": ["Novel antimicrobial zein film for controlled release of lauroyl arginate (LAE). Abstract Novel antimicrobial biopolymer films based on the incorporation of ethyl-Nα-dodecanoyl- l -arginate hydrochloride (LAE) in zein matrices were manufactured and characterized as materials for LAE controlled released applications such as active food packaging. Characterization of the films’ functional properties revealed that incorporation of LAE (5 and 10%) in the biopolymer matrix did not cause substantial changes in morphological, optical, thermal, mechanical and barrier properties. As the mechanism of action of these films is mainly based on release of the antimicrobial, this process was characterized when the active biofilms were exposed to three food simulants (water, 3% acetic acid, and 10% alcohol) at three temperatures (4, 23, and 37 °C). The data obtained revealed that, with the exception of exposure to water at 4 °C which achieved a release of more than 80% of the LAE incorporated, the agent was almost completely extracted in all conditions. Release of LAE was faster at higher temperatures, and the diffusion coefficient values varied according to the Arrhenius law, and increased with temperature. Antibacterial activity of films was assayed against Listeria monocytogenes and Escherichia coli. Zein films with 5% LAE produced 2.02 and 3.07 log reduction against L. monocytogenes and E. coli, respectively, after 5 days of storage at 4 °C. Greater antibacterial activity was observed with films containing 10% LAE (5 log reduction) at 37 °C. This work highlighted that LAE incorporation in a packaging film constructed with renewable polymer materials offers an interesting and efficient hurdle for control of bacterial contamination in foods."], "field": "Chemistry", "q_year": 2021, "q_cid": "238201215", "pos_cid": 99499118, "source": "train_step3"}
{"query_id": "scaleup_25283975_21575619", "query": "How to enhance microbial reduction of nitrous oxide in engineered systems while maintaining material activity", "pos": ["Humic Substances Mediate Anaerobic Methane Oxidation Linked to Nitrous Oxide Reduction in Wetland Sediments. Humic substances are redox-active organic molecules, which play pivotal roles in several biogeochemical cycles due to their electron-transferring capacity involving multiple abiotic and microbial transformations. Based on the redox properties of humic substances, and the metabolic capabilities of microorganisms to reduce and oxidize them, we hypothesized that they could mediate the anaerobic oxidation of methane (AOM) coupled to the reduction of nitrous oxide (N2O) in wetland sediments. This study provides several lines of evidence indicating the coupling between AOM and the reduction of N2O through an extracellular electron transfer mechanism mediated by the redox active functional groups in humic substances (e.g., quinones). We found that the microbiota of a sediment collected from the Sisal wetland (Yucatán Peninsula, southeastern Mexico) was able to reduce N2O (4.6 ± 0.5 μmol N2O g sed.–1 day–1) when reduced humic substances were provided as electron donor in a close stoichiometric relationship. Furthermore, a microbial enrichment derived from the wetland sediment achieved simultaneous 13CH4 oxidation (1.3 ± 0.1 μmol 13CO2 g sed.–1 day–1) and N2O reduction (25.2 ± 0.5 μmol N2O g sed.–1 day–1), which was significantly dependent on the presence of humic substances as an extracellular electron shuttle. Taxonomic characterization based on 16S rRNA gene sequencing revealed Acinetobacter (a ɣ-proteobacterium), the Rice Cluster I from the Methanocellaceae and an uncultured archaeon from the Methanomicrobiaceae family as the microbes potentially involved in AOM linked to N2O reduction mediated by humic substances. The findings reported here suggest that humic substances might play an important role to prevent the emission of greenhouse gases (CH4 and N2O) from wetland sediments. Further efforts to evaluate the feasibility of this novel mechanism under the natural conditions prevailing in ecosystems must be considered in future studies."], "field": "Chemistry", "q_year": 2022, "q_cid": "252839754", "pos_cid": 215756196, "source": "train_step3"}
{"query_id": "scaleup_28406270_22951757", "query": "How to detect surface residues when differences from a clean baseline may involve multiple aspects of color", "pos": ["The Applicability of Total Color Difference ΔE for Determining the Blooming Time in Longissimus Lumborum and Semimembranosus Muscles from Holstein-Friesian Bulls at Different Ageing Times. This study was conducted to determine the optimal blooming time in beef muscles based on ΔE, and to analyze the effects of muscle type and ageing time on beef color and blooming. Beef color was determined on freshly cut longissimus lumborum (LL, n = 8) and semimembranosus (SM, n = 8) muscles on days 1, 9, and 14 of ageing during 60 min blooming at 5 min intervals. It was found that ΔE0, representing the difference in color between freshly cut muscles and subsequently analyzed samples, supported the determination of the optimal blooming time, which varied across ageing times (15, 20, 25 min for the LL muscle, and 10, 15, 20 min for the SM muscle on days 1, 9, and 14 of ageing, respectively). Beef color was affected by both muscle type and ageing. The values of color parameters increased between days 1 and 9 of ageing. The results may have practical applications because beef should be presented to consumers and restaurant owners approximately 25 min after cutting, when its color has fully developed."], "field": "Chemistry", "q_year": 2025, "q_cid": "284062706", "pos_cid": 229517572, "source": "train_step3"}
{"query_id": "scaleup_22146506_17373985", "query": "How to clarify the molecular basis of the activity of compounds 9c and 9e and their binding to the target protein", "pos": ["Structural biology contributions to the discovery of drugs to treat chronic myelogenous leukaemia. A case study showing how the determination of multiple cocrystal structures of the protein tyrosine kinase c-Abl was used to support drug discovery, resulting in a compound effective in the treatment of chronic myelogenous leukaemia."], "field": "Chemistry", "q_year": 2020, "q_cid": "221465069", "pos_cid": 17373985, "source": "train_step3"}
{"query_id": "scaleup_28053534_55751528", "query": "How to synthesize 1,2,3-triazole derivatives rapidly under mild conditions while minimizing energy consumption", "pos": ["SONOCHEMISTRY (APPLICATIONS OF ULTRASOUND IN CHEMICAL SYNTHESIS AND REACTIONS): A REVIEW PART I. Sonochemistry is a powerful and green approach which is being used to accelerate synthesis of organic compounds, and involves the use of ultrasound technique to promote chemical reactions. Ultrasound is the part of the sonic spectrum, which ranges from about 20 KHz to 10 MHz. A large number of organic reactions can be carried out under ultrasonic irradiation in high yields, short reaction times, and mild conditions. Ultrasonic irradiation of liquids causes high energy chemical reactions to occur, often with the emission of light. The origin of sonochemistry and sonoluminescence is acoustic cavitation which is the formation, growth, and implosive collapse of bubbles. The collapse of bubbles caused by cavitation produces intense local heating and high pressures, with very short lifetimes (Hot spots). These hot-spots have an equivalent temperatures of roughly 5,000 K, pressures of about 1,000 atm, and increase reactivity by nearly million-fold using the radical mechanism. A variety of devices have been used for ultrasonic irradiation of solutions."], "field": "Chemistry", "q_year": 2025, "q_cid": "280535343", "pos_cid": 55751528, "source": "train_step3"}
{"query_id": "scaleup_26940811_27719950", "query": "How to interpret the temperature-dependent rheology of covalent polymer networks when the linear polymer can also become elastic as temperature changes", "pos": ["Phase behavior and dynamics of a micelle-forming triblock copolymer system.. Synperonic F-108 (generic name, \"pluronic\") is a micelle forming triblock copolymer of type ABA , where A is polyethylene oxide (PEO) and B is polypropylene oxide (PPO). At high temperatures, the hydrophobicity of the PPO chains increase, and the pluronic molecules, when dissolved in an aqueous medium, self-associate into spherical micelles with dense PPO cores and hydrated PEO coronas. At appropriately high concentrations, these micelles arrange in a face centered cubic lattice to show inverse crystallization, with the samples exhibiting high-temperature crystalline and low-temperature fluidlike phases. By studying the evolution of the elastic and viscous moduli as temperature is increased at a fixed rate, we construct the concentration-temperature phase diagram of Synperonic F-108. For a certain range of temperatures and at appropriate sample concentrations, we observe a predominantly elastic response. Oscillatory strain amplitude sweep measurements on these samples show pronounced peaks in the loss moduli, a typical feature of soft solids. The soft solidlike nature of these materials is further demonstrated by measuring their frequency-dependent mechanical moduli. The storage moduli are significantly larger than the loss moduli and are almost independent of the applied angular frequency. Finally, we perform strain rate frequency superposition experiments to measure the slow relaxation dynamics of this soft solid."], "field": "Chemistry", "q_year": 2024, "q_cid": "269408114", "pos_cid": 27719950, "source": "train_step3"}
{"query_id": "scaleup_27150147_23340921", "query": "How to clarify the effect of counterions on glycosyl cation behaviour and the role of these intermediates in the stereoselectivity of benzylidene-directed glycosylation reactions", "pos": ["Gas-Phase Structural Analysis of Supramolecular Assemblies.. ConspectusIon mobility spectrometry and gas-phase IR action spectroscopy are two structure-sensitive mass-spectrometric methods becoming more popular recently. While ion mobility spectrometry provides collision cross sections as a size and shape dependent parameter of an ion of interest, gas-phase spectroscopy identifies functional groups and is capable of distinguishing different isomers. Both methods have recently found application for the investigation of supramolecular assemblies. We here highlight several aspects.Starting with the characterization of switching states in azobenzene photoswitches as well as redox-switchable lasso-type pseudorotaxanes, structures of isomers can be distinguished and mechanistic details analyzed. Ion mobility mass spectrometry in combination with gas-phase H/D-exchange reactions unravels subtle structural details as described for the chiral recognition of crown ether amino acid complexes. Gas-phase IR spectroscopy allows identification of details of the binding patterns in dimeric amino acid clusters as well as the serine octamer. This research can be extended into the analysis of peptide assemblies that are of medical relevance, for example, in Alzheimer's disease, and into a general hydrophobicity scale for natural as well as synthetic amino acids. The development of ultracold gas-phase spectroscopy that for example makes use of ions trapped in liquid helium droplets provides access to very well resolved spectra. The combination of ion mobility separation of ions with subsequent spectroscopic analysis even permits separation of different isomers and studying them separately with respect to their structure. This represents a great advantage of these gas-phase methods over solution experiments, in which the supramolecular complexes under study typically equilibrate and thus prevent a separate investigation of different isomers. At the end of this overview, we will discuss larger and more complex supramolecules, among them giant halogen-bonded cages and complex intertwined topologies such as molecular knots and Solomon links."], "field": "Chemistry", "q_year": 2024, "q_cid": "271501473", "pos_cid": 233409215, "source": "train_step3"}
{"query_id": "scaleup_23357875_14032460", "query": "How to selectively access either syn- or anti-1,2-diamines with high enantioselectivity and control over both relative and absolute stereochemistry", "pos": ["Copper(I)-Catalyzed Enantio- and Diastereodivergent Borylative Coupling of Styrenes and Imines.. We report copper(I)-catalyzed enantio- and diastereodivergent borylative coupling of styrenes and imines to produce enantiomerically-enriched α,β-dibranched γ-boryl amine derivatives. Each of the four possible stereoisomers of the products, derived from the two contiguous stereocenters, was selectively accessible by choosing a proper chiral ligand for the copper catalyst. This method, which combines catalyst-controlled stereodivergency and constitutional divergency derived from the lynchpin motif (i.e., the C-B bond), offers a strategy for addressing the construction of molecular structural diversity concomitant with precise chirality control."], "field": "Chemistry", "q_year": 2021, "q_cid": "233578753", "pos_cid": 14032460, "source": "train_step3"}
{"query_id": "scaleup_28099595_25845069", "query": "How to obtain indolizine scaffolds bearing bromine or ethyl ester substituents on the pyridine ring for evaluation as potential anticancer agents", "pos": ["Benzoquinoline Derivatives: An Attractive Approach to Newly Small Molecules with Anticancer Activity. This study presents the synthesis, structural characterization, and in vitro evaluation of anticancer activity of some newly benzo[f]quinoline derivatives. The synthesis is facile and efficient, involving two steps: quaternization of nitrogen heterocycle followed by a [3+2] dipolar cycloaddition reaction. The synthesized compounds were characterized by FTIR, NMR, and X-ray diffraction on monocrystal in the case of compounds 6c and 7c. An in vitro single-dose anticancer assay of eighteen benzo[f]quinoline compounds, quaternary salts, and cycloadducts, was performed. The results showed that the most active compounds were quaternary salts 3d and 3f with aromatic R substituents. Quaternary salt 3d revealed non-selective activity against all types of cancer cells, while salt 3f exhibited a highly selective activity against leukemia cells. Compound 3d also presented remarkable cytotoxic efficiency against four distinct types of cancer cells—namely, non-small cell lung cancer HOP–92, melanoma LOX IMVI, melanoma SK–MEL–5, and breast cancer MDA–MB–468. Compound 3f was selected for five-dose screening. The study also includes SAR correlations."], "field": "Chemistry", "q_year": 2025, "q_cid": "280995954", "pos_cid": 258450695, "source": "train_step3"}
{"query_id": "scaleup_21086119_15556973", "query": "How to balance finding new candidate plans and finding feasible parameter values for existing plans under tight, complex continuous constraints", "pos": ["Some aspects of the sequential design of experiments. Until recently, statistical theory has been restricted to the design and analysis of sampling experiments in which the size and composition of the samples are completely determined before the experimentation begins. The reasons for this are partly historical, dating back to the time when the statistician was consulted, if at all, only after the experiment was over, and partly intrinsic in the mathematical difficulty of working with anything but a fixed number of independent random variables. A major advance now appears to be in the making with the creation of a theory of the sequential design of experiments, in which the size and composition of the samples are not fixed in advance but are functions of the observations themselves."], "field": "Computer Science", "q_year": 2018, "q_cid": "210861196", "pos_cid": 15556973, "source": "eval20x26"}
{"query_id": "scaleup_12325031_12922309", "query": "How to make effective wireless network decisions under constraints when network dynamics may be unknown and the network state is only partially observable", "pos": ["Reinforcement Learning in POMDP's via Direct Gradient Ascent. This paper discusses theoretical and experimental aspects of gradient-based approaches to the direct optimization of policy performance in controlled POMDPs. We introduce GPOMDP, a REINFORCE-like algorithm for estimating an approximation to the gradient of the average reward as a function of the parameters of a stochastic policy. The algorithm’s chief advantages are that it requires only a single sample path of the underlying Markov chain, it uses only one free parameter 2 [0; 1), which has a natural interpretation in terms of bias-variance trade-off, and it requires no knowledge of the underlying state. We prove convergence of GPOMDP and show how the gradient estimates produced by GPOMDP can be used in a conjugate-gradient procedure to find local optima of the average reward."], "field": "Computer Science", "q_year": 2015, "q_cid": "12325031", "pos_cid": 12922309, "source": "eval20x26"}
{"query_id": "scaleup_17169677_89141", "query": "How to reduce tree construction cost in time series classification while retaining useful classification features from a large candidate set at each node", "pos": ["Random Forests. Random forests are a combination of tree predictors such that each tree depends on the values of a random vector sampled independently and with the same distribution for all trees in the forest. The generalization error for forests converges a.s. to a limit as the number of trees in the forest becomes large. The generalization error of a forest of tree classifiers depends on the strength of the individual trees in the forest and the correlation between them. Using a random selection of features to split each node yields error rates that compare favorably to Adaboost (Y. Freund & R. Schapire, Machine Learning: Proceedings of the Thirteenth International conference, ***, 148–156), but are more robust with respect to noise. Internal estimates monitor error, strength, and correlation and these are used to show the response to increasing the number of features used in the splitting. Internal estimates are also used to measure variable importance. These ideas are also applicable to regression."], "field": "Computer Science", "q_year": 2013, "q_cid": "17169677", "pos_cid": 89141, "source": "eval20x26"}
{"query_id": "scaleup_49584957_740063", "query": "How to generate informative code summaries that capture api knowledge without heavily depending on the availability and similarity of retrieved code snippets", "pos": ["A Survey on Transfer Learning. A major assumption in many machine learning and data mining algorithms is that the training and future data must be in the same feature space and have the same distribution. However, in many real-world applications, this assumption may not hold. For example, we sometimes have a classification task in one domain of interest, but we only have sufficient training data in another domain of interest, where the latter data may be in a different feature space or follow a different data distribution. In such cases, knowledge transfer, if done successfully, would greatly improve the performance of learning by avoiding much expensive data-labeling efforts. In recent years, transfer learning has emerged as a new learning framework to address this problem. This survey focuses on categorizing and reviewing the current progress on transfer learning for classification, regression, and clustering problems. In this survey, we discuss the relationship between transfer learning and other related machine learning techniques such as domain adaptation, multitask learning and sample selection bias, as well as covariate shift. We also explore some potential future issues in transfer learning research."], "field": "Computer Science", "q_year": 2018, "q_cid": "49584957", "pos_cid": 740063, "source": "eval20x26"}
{"query_id": "scaleup_21028129_11934207", "query": "How to make physics-based eruption prediction computationally feasible for Bayesian ensemble forecasting requiring many model evaluations", "pos": ["Enabling large‐scale viscoelastic calculations via neural network acceleration. One of the most significant challenges involved in efforts to understand the effects of repeated earthquake cycle activity is the computational costs of large‐scale viscoelastic earthquake cycle models. Computationally intensive viscoelastic codes must be evaluated at thousands of times and locations, and as a result, studies tend to adopt a few fixed rheological structures and model geometries and examine the predicted time‐dependent deformation over short (<10 years) time periods at a given depth after a large earthquake. Training a deep neural network to learn a computationally efficient representation of viscoelastic solutions, at any time, location, and for a large range of rheological structures, allows these calculations to be done quickly and reliably, with high spatial and temporal resolutions. We demonstrate that this machine learning approach accelerates viscoelastic calculations by more than 50,000%. This magnitude of acceleration will enable the modeling of geometrically complex faults over thousands of earthquake cycles across wider ranges of model parameters and at larger spatial and temporal scales than have been previously possible."], "field": "Computer Science", "q_year": 2020, "q_cid": "210281298", "pos_cid": 119342074, "source": "eval_collection"}
{"query_id": "scaleup_26928255_24535385", "query": "How to improve neural semantic parsers’ handling of unseen concepts while keeping incorrect predictions semantically close to the intended concepts", "pos": ["Encoding Hierarchical Information in Neural Networks Helps in Subpopulation Shift. Over the past decade, deep neural networks have proven to be adept in image classification tasks, often surpassing humans in terms of accuracy. However, standard neural networks often fail to understand the concept of hierarchical structures and dependencies among different classes for vision-related tasks. Humans on the other hand, seem to intuitively learn categories conceptually, progressively growing from understanding high-level concepts down to granular levels of categories. One of the issues arising from the inability of neural networks to encode such dependencies within its learned structure is that of subpopulation shift—where models are queried with novel unseen classes taken from a shifted population of the training set categories. Since the neural network treats each class as independent from all others, it struggles to categorize shifting populations that are dependent at higher levels of the hierarchy. In this work, we study the aforementioned problems through the lens of a novel conditional supervised training framework. We tackle subpopulation shift by a structured learning procedure that incorporates hierarchical information conditionally through labels. Furthermore, we introduce a notion of hierarchical distance to model the catastrophic effect of mispredictions. We show that learning in this structured hierarchical manner results in networks that are more robust against subpopulation shifts, with an improvement up to 3% in terms of accuracy and up to 11% in terms of hierarchical distance over standard models on subpopulation shift benchmarks."], "field": "Computer Science", "q_year": 2024, "q_cid": "269282559", "pos_cid": 245353852, "source": "eval_collection"}
{"query_id": "scaleup_26885681_3488815", "query": "How to reliably assess ImageNet image recognition on deliberately altered images and determine whether shape and frequency preferences explain performance on altered and new images", "pos": ["Towards Deep Learning Models Resistant to Adversarial Attacks. Recent work has demonstrated that deep neural networks are vulnerable to adversarial examples---inputs that are almost indistinguishable from natural data and yet classified incorrectly by the network. In fact, some of the latest findings suggest that the existence of adversarial attacks may be an inherent weakness of deep learning models. To address this problem, we study the adversarial robustness of neural networks through the lens of robust optimization. This approach provides us with a broad and unifying view on much of the prior work on this topic. Its principled nature also enables us to identify methods for both training and attacking neural networks that are reliable and, in a certain sense, universal. In particular, they specify a concrete security guarantee that would protect against any adversary. These methods let us train networks with significantly improved resistance to a wide range of adversarial attacks. They also suggest the notion of security against a first-order adversary as a natural and broad security guarantee. We believe that robustness against such well-defined classes of adversaries is an important stepping stone towards fully resistant deep learning models. Code and pre-trained models are available at this https URL and this https URL."], "field": "Computer Science", "q_year": 2024, "q_cid": "268856816", "pos_cid": 3488815, "source": "eval_collection"}
{"query_id": "scaleup_24512415_3144218", "query": "How to classify documents while accounting for dependencies between non-consecutive words, sentence-level context, word ambiguity, synonymity, and context-dependent relationships", "pos": ["Semi-Supervised Classification with Graph Convolutional Networks. We present a scalable approach for semi-supervised learning on graph-structured data that is based on an efficient variant of convolutional neural networks which operate directly on graphs. We motivate the choice of our convolutional architecture via a localized first-order approximation of spectral graph convolutions. Our model scales linearly in the number of graph edges and learns hidden layer representations that encode both local graph structure and features of nodes. In a number of experiments on citation networks and on a knowledge graph dataset we demonstrate that our approach outperforms related methods by a significant margin."], "field": "Computer Science", "q_year": 2021, "q_cid": "245124151", "pos_cid": 3144218, "source": "eval_collection"}
{"query_id": "scaleup_26089983_24826661", "query": "How to predict volumetric-video viewports while accounting for gaze information and the user’s viewport context", "pos": ["GIMO: Gaze-Informed Human Motion Prediction in Context. Predicting human motion is critical for assistive robots and AR/VR applications, where the interaction with humans needs to be safe and comfortable. Meanwhile, an accurate prediction depends on understanding both the scene context and human intentions. Even though many works study scene-aware human motion prediction, the latter is largely underexplored due to the lack of ego-centric views that disclose human intent and the limited diversity in motion and scenes. To reduce the gap, we propose a large-scale human motion dataset that delivers high-quality body pose sequences, scene scans, as well as ego-centric views with the eye gaze that serves as a surrogate for inferring human intent. By employing inertial sensors for motion capture, our data collection is not tied to specific scenes, which further boosts the motion dynamics observed from our subjects. We perform an extensive study of the benefits of leveraging the eye gaze for ego-centric human motion prediction with various state-of-the-art architectures. Moreover, to realize the full potential of the gaze, we propose a novel network architecture that enables bidirectional communication between the gaze and motion branches. Our network achieves the top performance in human motion prediction on the proposed dataset, thanks to the intent information from eye gaze and the denoised gaze feature modulated by the motion. Code and data can be found at https://github.com/y-zheng18/GIMO."], "field": "Computer Science", "q_year": 2023, "q_cid": "260899830", "pos_cid": 248266616, "source": "eval_collection"}
{"query_id": "scaleup_25873863_20649172", "query": "How to find energy-efficient sensor covers and sleep–wakeup schedules that maintain coverage of all targets and maximize network lifetime", "pos": ["Cuckoo Search via Lévy flights. In this paper, we intend to formulate a new meta-heuristic algorithm, called Cuckoo Search (CS), for solving optimization problems. This algorithm is based on the obligate brood parasitic behaviour of some cuckoo species in combination with the Lévy flight behaviour of some birds and fruit flies. We validate the proposed algorithm against test functions and then compare its performance with those of genetic algorithms and particle swarm optimization. Finally, we discuss the implication of the results and suggestion for further research."], "field": "Computer Science", "q_year": 2023, "q_cid": "258738632", "pos_cid": 206491725, "source": "eval_collection"}
{"query_id": "scaleup_25987257_8977721", "query": "How to identify groups among sparsely connected entities while keeping computational costs manageable", "pos": ["Finding community structure in very large networks.. The discovery and analysis of community structure in networks is a topic of considerable recent interest within the physics community, but most methods proposed so far are unsuitable for very large networks because of their computational cost. Here we present a hierarchical agglomeration algorithm for detecting community structure which is faster than many competing algorithms: its running time on a network with n vertices and m edges is O (md log n) where d is the depth of the dendrogram describing the community structure. Many real-world networks are sparse and hierarchical, with m approximately n and d approximately log n, in which case our algorithm runs in essentially linear time, O (n log(2) n). As an example of the application of this algorithm we use it to analyze a network of items for sale on the web site of a large on-line retailer, items in the network being linked if they are frequently purchased by the same buyer. The network has more than 400 000 vertices and 2 x 10(6) edges. We show that our algorithm can extract meaningful communities from this network, revealing large-scale patterns present in the purchasing habits of customers."], "field": "Computer Science", "q_year": 2023, "q_cid": "259872572", "pos_cid": 8977721, "source": "eval_collection"}
{"query_id": "scaleup_28205708_25409636", "query": "How to reduce autoregressive llm serving latency and support multiple users on resource-constrained edge nodes with wireless communication", "pos": ["Fast Inference from Transformers via Speculative Decoding. Inference from large autoregressive models like Transformers is slow - decoding K tokens takes K serial runs of the model. In this work we introduce speculative decoding - an algorithm to sample from autoregressive models faster without any changes to the outputs, by computing several tokens in parallel. At the heart of our approach lie the observations that (1) hard language-modeling tasks often include easier subtasks that can be approximated well by more efficient models, and (2) using speculative execution and a novel sampling method, we can make exact decoding from the large models faster, by running them in parallel on the outputs of the approximation models, potentially generating several tokens concurrently, and without changing the distribution. Our method can accelerate existing off-the-shelf models without retraining or architecture changes. We demonstrate it on T5-XXL and show a 2X-3X acceleration compared to the standard T5X implementation, with identical outputs."], "field": "Computer Science", "q_year": 2025, "q_cid": "282057086", "pos_cid": 254096365, "source": "eval_collection"}
{"query_id": "scaleup_25987257_59337586", "query": "How to organize activity events into meaningful groups that can be related across source and target domains despite differences in sensor modalities", "pos": ["Chameleon 2. Traditional clustering algorithms fail to produce human-like results when confronted with data of variable density, complex distributions, or in the presence of noise. We propose an improved graph-based clustering algorithm called Chameleon 2, which overcomes several drawbacks of state-of-the-art clustering approaches. We modified the internal cluster quality measure and added an extra step to ensure algorithm robustness. Our results reveal a significant positive impact on the clustering quality measured by Normalized Mutual Information on 32 artificial datasets used in the clustering literature. This significant improvement is also confirmed on real-world datasets. The performance of clustering algorithms such as DBSCAN is extremely parameter sensitive, and exhaustive manual parameter tuning is necessary to obtain a meaningful result. All hierarchical clustering methods are very sensitive to cutoff selection, and a human expert is often required to find the true cutoff for each clustering result. We present an automated cutoff selection method that enables the Chameleon 2 algorithm to generate high-quality clustering in autonomous mode."], "field": "Computer Science", "q_year": 2023, "q_cid": "259872572", "pos_cid": 59337586, "source": "eval_collection"}
{"query_id": "scaleup_26735287_15793574", "query": "How to identify which school organizational indicators need improvement and which should be maintained for educational management planning", "pos": ["The development of scientific identification theory to conduct operation research in education management. Operations research is a general method used in the study and optimization of a system through modeling of the system. In the field of education, especially in education management, operations research has not been widely used. This paper gives an exposition of ideas about how operations research can be used to conduct research and optimization in the field of education management by developing SITOREM (Scientific Identification Theory for Operation Research in Education Management). To clarify the intent of the idea, an example of applying SITOREM to enhance the professional commitment of lecturers associated with achieving the vision of university will be described."], "field": "Computer Science", "q_year": 2024, "q_cid": "267352874", "pos_cid": 157935748, "source": "eval_collection"}
{"query_id": "scaleup_28206419_26736478", "query": "How to ensure an iterative learning scheme generalizes beyond its training data", "pos": ["Multi-group Learning for Hierarchical Groups. The multi-group learning model formalizes the learning scenario in which a single predictor must generalize well on multiple, possibly overlapping subgroups of interest. We extend the study of multi-group learning to the natural case where the groups are hierarchically structured. We design an algorithm for this setting that outputs an interpretable and deterministic decision tree predictor with near-optimal sample complexity. We then conduct an empirical evaluation of our algorithm and find that it achieves attractive generalization properties on real datasets with hierarchical group structure."], "field": "Computer Science", "q_year": 2025, "q_cid": "282064199", "pos_cid": 267364786, "source": "eval_collection"}
{"query_id": "scaleup_27848148_25888793", "query": "How to achieve fine-grained control of medical images while preserving morphological fidelity and accommodating both exemplar-image and mask guidance", "pos": ["Prompt-Free Diffusion: Taking “Text” Out of Text-to-Image Diffusion Models. Text-to-image (T2I) research has grown explosively in the past year, owing to the large-scale pre-trained diffusion models and many emerging personalization and editing approaches. Yet, one pain point persists: the text prompt engineering, and searching high-quality text prompts for customized results is more art than science. Moreover, as commonly argued: “an image is worth a thousand words” - the attempt to describe a desired image with texts often ends up being ambiguous and cannot comprehensively cover delicate visual details, hence necessitating more additional controls from the visual domain. In this paper, we take a bold step forward: taking “Text” out of a pretrained T2I diffusion model, to reduce the burdensome prompt engineering efforts for users. Our proposed frame-work, Prompt-Free Diffusion, relies on only visual inputs to generate new images: it takes a reference image as “context”, an optional image structural conditioning, and an initial noise, with absolutely no text prompt. The core architecture behind the scene is Semantic Context Encoder (SeeCoder), substituting the commonly used CLIP-based or LLM-based text encoder. The reusability of SeeCoder also makes it a convenient drop-in component: one can also pre-train a SeeCoder in one T2I model and reuse it for another. Through extensive experiments, Prompt-Free Diffusion is experimentally found to (i) outperform prior exemplar-based image synthesis approaches; (ii) perform on par with state-of-the-art T2I models using prompts following the best practice; and (iii) be naturally extensible to other downstream applications such as anime figure generation and virtual try-on, with promising quality. Our code and models will be open-sourced."], "field": "Computer Science", "q_year": 2025, "q_cid": "278481484", "pos_cid": 258887939, "source": "eval_collection"}
{"query_id": "scaleup_26043914_4028864", "query": "How to efficiently refine depth completion with very sparse depth input while avoiding irrelevant or unhelpful spatial information", "pos": ["Deformable Convolutional Networks. Convolutional neural networks (CNNs) are inherently limited to model geometric transformations due to the fixed geometric structures in their building modules. In this work, we introduce two new modules to enhance the transformation modeling capability of CNNs, namely, deformable convolution and deformable RoI pooling. Both are based on the idea of augmenting the spatial sampling locations in the modules with additional offsets and learning the offsets from the target tasks, without additional supervision. The new modules can readily replace their plain counterparts in existing CNNs and can be easily trained end-to-end by standard back-propagation, giving rise to deformable convolutional networks. Extensive experiments validate the performance of our approach. For the first time, we show that learning dense spatial transformation in deep CNNs is effective for sophisticated vision tasks such as object detection and semantic segmentation. The code is released at https://github.com/msracver/Deformable-ConvNets."], "field": "Computer Science", "q_year": 2023, "q_cid": "260439143", "pos_cid": 4028864, "source": "eval_collection"}
{"query_id": "scaleup_26853247_13468104", "query": "How to reliably represent and distinguish dynamic actions in event-based action recognition despite their complex and ambiguous meanings", "pos": ["Word Representations via Gaussian Embedding. Current work in lexical distributed representations maps each word to a point vector in low-dimensional space. Mapping instead to a density provides many interesting advantages, including better capturing uncertainty about a representation and its relationships, expressing asymmetries more naturally than dot product or cosine similarity, and enabling more expressive parameterization of decision boundaries. This paper advocates for density-based distributed embeddings and presents a method for learning representations in the space of Gaussian distributions. We compare performance on various word embedding benchmarks, investigate the ability of these embeddings to model entailment and other asymmetric relationships, and explore novel properties of the representation."], "field": "Computer Science", "q_year": 2024, "q_cid": "268532476", "pos_cid": 13468104, "source": "eval_collection"}
{"query_id": "scaleup_25263339_14924561", "query": "How to reduce the computational burden of finding optimal values for each input sample", "pos": ["Generative Visual Manipulation on the Natural Image Manifold. Realistic image manipulation is challenging because it requires modifying the image appearance in a user-controlled way, while preserving the realism of the result. Unless the user has considerable artistic skill, it is easy to “fall off” the manifold of natural images while editing. In this paper, we propose to learn the natural image manifold directly from data using a generative adversarial neural network. We then define a class of image editing operations, and constrain their output to lie on that learned manifold at all times. The model automatically adjusts the output keeping all edits as realistic as possible. All our manipulations are expressed in terms of constrained optimization and are applied in near-real time. We evaluate our algorithm on the task of realistic photo manipulation of shape and color. The presented method can further be used for changing one image to look like the other, as well as generating novel imagery from scratch based on user’s scribbles."], "field": "Computer Science", "q_year": 2022, "q_cid": "252633398", "pos_cid": 14924561, "source": "eval_collection"}
{"query_id": "scaleup_25763161_24745067", "query": "How to ensure a well-defined, lower semicontinuous cost for trajectories with limited regularity under degenerate and unbounded dynamics", "pos": ["Non-equilibrium large deviations and parabolic-hyperbolic PDE with irregular drift. Large deviations of conservative interacting particle systems, such as the zero range process, about their hydrodynamic limit and their respective rate functions lead to the analysis of the skeleton equation; a degenerate parabolic-hyperbolic PDE with irregular drift. We develop a robust well-posedness theory for such PDEs in energy-critical spaces based on concepts of renormalized solutions and the equation’s kinetic form. We establish these properties by proving that renormalized solutions are equivalent to classical weak solutions, extending concepts of (DiPerna and Lions in Invent. Math. 98(3):511–547, 1989; Ambrosio in Invent. Math. 158(2):227–260, 2004) to the nonlinear setting. The relevance of the results toward large deviations in interacting particle systems is demonstrated by applications to the identification of l.s.c. envelopes of restricted rate functions, to zero noise large deviations for conservative SPDE, and to the Γ\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$\\Gamma $\\end{document}-convergence of rate functions. The first of these solves a long-standing open problem in the large deviations for zero range processes. The second makes rigorous an informal link between the non-equilibrium statistical mechanics approaches of macroscopic fluctuation theory and fluctuating hydrodynamics."], "field": "Computer Science", "q_year": 2023, "q_cid": "257631618", "pos_cid": 247450677, "source": "eval_collection"}
{"query_id": "scaleup_25883352_21995566", "query": "How to predict diverse, plausible human motion futures that preserve spatial-temporal structure, remain physically realistic and consistent with observed poses, and avoid complex, multi-stage training", "pos": ["Denoising Diffusion Probabilistic Models. We present high quality image synthesis results using diffusion probabilistic models, a class of latent variable models inspired by considerations from nonequilibrium thermodynamics. Our best results are obtained by training on a weighted variational bound designed according to a novel connection between diffusion probabilistic models and denoising score matching with Langevin dynamics, and our models naturally admit a progressive lossy decompression scheme that can be interpreted as a generalization of autoregressive decoding. On the unconditional CIFAR10 dataset, we obtain an Inception score of 9.46 and a state-of-the-art FID score of 3.17. On 256x256 LSUN, we obtain sample quality similar to ProgressiveGAN. Our implementation is available at this https URL"], "field": "Computer Science", "q_year": 2023, "q_cid": "258833522", "pos_cid": 219955663, "source": "eval_collection"}
{"query_id": "scaleup_28053195_24642690", "query": "How to align open-source models for climate-adaptation question answering with human judgments beyond expert sentiment assessment", "pos": ["Training language models to follow instructions with human feedback. Making language models bigger does not inherently make them better at following a user's intent. For example, large language models can generate outputs that are untruthful, toxic, or simply not helpful to the user. In other words, these models are not aligned with their users. In this paper, we show an avenue for aligning language models with user intent on a wide range of tasks by fine-tuning with human feedback. Starting with a set of labeler-written prompts and prompts submitted through the OpenAI API, we collect a dataset of labeler demonstrations of the desired model behavior, which we use to fine-tune GPT-3 using supervised learning. We then collect a dataset of rankings of model outputs, which we use to further fine-tune this supervised model using reinforcement learning from human feedback. We call the resulting models InstructGPT. In human evaluations on our prompt distribution, outputs from the 1.3B parameter InstructGPT model are preferred to outputs from the 175B GPT-3, despite having 100x fewer parameters. Moreover, InstructGPT models show improvements in truthfulness and reductions in toxic output generation while having minimal performance regressions on public NLP datasets. Even though InstructGPT still makes simple mistakes, our results show that fine-tuning with human feedback is a promising direction for aligning language models with human intent."], "field": "Computer Science", "q_year": 2025, "q_cid": "280531951", "pos_cid": 246426909, "source": "eval_collection"}
{"query_id": "scaleup_26107626_25594252", "query": "How to add fine-grained control over timing, pitch, and energy to existing pre-trained text-to-audio models while preserving text conditioning and generation diversity", "pos": ["GLIGEN: Open-Set Grounded Text-to-Image Generation. Large-scale text-to-image diffusion models have made amazing advances. However, the status quo is to use text input alone, which can impede controllability. In this work, we propose GLIGEN, Grounded-Language-to-Image Generation, a novel approach that builds upon and extends the functionality of existing pre-trained text-to-image diffusion models by enabling them to also be conditioned on grounding inputs. To preserve the vast concept knowledge of the pre-trained model, we freeze all of its weights and inject the grounding information into new trainable layers via a gated mechanism. Our model achieves open-world grounded text2img generation with caption and bounding box condition inputs, and the grounding ability generalizes well to novel spatial configurations and concepts. GLIGEN's zero-shot performance on COCO and LVIS outperforms existing supervised layout-to-image baselines by a large margin."], "field": "Computer Science", "q_year": 2023, "q_cid": "261076264", "pos_cid": 255942528, "source": "eval_collection"}
{"query_id": "scaleup_26170672_16808655", "query": "How to provide practice support suited to learners’ prior mistakes, current knowledge, and cognitive ability as their skills develop", "pos": ["Methods and techniques of adaptive hypermedia. Adaptive hypermedia is a new direction of research within the area of adaptive and user model-based interfaces. Adaptive hypermedia (AH) systems build a model of the individual user and apply it for adaptation to that user, for example, to adapt the content of a hypermedia page to the user's knowledge and goals, or to suggest the most relevant links to follow. AH systems are used now in several application areas where the hyperspace is reasonably large and where a hypermedia application is expected to be used by individuals with different goals, knowledge and backgrounds. This paper is a review of existing work on adaptive hypermedia. The paper is centered around a set of identified methods and techniques of AH. It introduces several dimensions of classification of AH systems, methods and techniques and describes the most important of them."], "field": "Computer Science", "q_year": 2023, "q_cid": "261706727", "pos_cid": 16808655, "source": "eval_collection"}
{"query_id": "scaleup_26697824_19576688", "query": "How to preserve fine-grained local context and accurately capture strong long-range dependencies under memory constraints", "pos": ["Enhancing the Locality and Breaking the Memory Bottleneck of Transformer on Time Series Forecasting. Time series forecasting is an important problem across many domains, including predictions of solar plant energy output, electricity consumption, and traffic jam situation. In this paper, we propose to tackle such forecasting problem with Transformer [1]. Although impressed by its performance in our preliminary study, we found its two major weaknesses: (1) locality-agnostics: the point-wise dot-product self-attention in canonical Transformer architecture is insensitive to local context, which can make the model prone to anomalies in time series; (2) memory bottleneck: space complexity of canonical Transformer grows quadratically with sequence length $L$, making directly modeling long time series infeasible. In order to solve these two issues, we first propose convolutional self-attention by producing queries and keys with causal convolution so that local context can be better incorporated into attention mechanism. Then, we propose LogSparse Transformer with only $O(L(\\log L)^{2})$ memory cost, improving forecasting accuracy for time series with fine granularity and strong long-term dependencies under constrained memory budget. Our experiments on both synthetic data and real-world datasets show that it compares favorably to the state-of-the-art."], "field": "Computer Science", "q_year": 2024, "q_cid": "266978240", "pos_cid": 195766887, "source": "eval_collection"}
{"query_id": "scaleup_27423401_11929587", "query": "How to achieve robust two-state spin encoding and readout in optical Ising machines without phase-sensitive measurements, intricate phase stabilization, or vulnerability to drift and bias", "pos": ["Asymmetric balance in symmetry breaking. Spontaneous symmetry breaking is central to our understanding of physics and explains many natural phenomena, from cosmic scales to subatomic particles. Its use for applications requires devices with a high level of symmetry, but engineered systems are always imperfect. Surprisingly, the impact of such imperfections has barely been studied, and restricted to a single asymmetry. Here, we experimentally study spontaneous symmetry breaking with two controllable asymmetries. We remarkably find that features typical of spontaneous symmetry breaking, while destroyed by one asymmetry, can be restored by introducing a second asymmetry. In essence, asymmetries are found to balance each other. Our study illustrates aspects of the universal unfolding of the pitchfork bifurcation, and provides insights into a key fundamental process. It also has practical implications, showing that asymmetry can be exploited as an additional degree of freedom. In particular, it could enable sensors based on symmetry breaking or exceptional points to reach divergent sensitivity even in presence of imperfections. Our experimental implementation built around an optical fiber ring additionally constitutes observation of the polarization symmetry breaking of passive driven nonlinear resonators."], "field": "Computer Science", "q_year": 2024, "q_cid": "274234018", "pos_cid": 119295872, "source": "eval_collection"}
{"query_id": "scaleup_25719326_24057756", "query": "How to detect emotions in short, informal tweets while accounting for linguistic, stylistic, and other nonlinguistic cues and limiting feature dimensionality", "pos": ["Latent Personality Traits Assessment From Social Network Activity Using Contextual Language Embedding. Recognizing author identity from digital footprints without having a large corpus of documents from an individual is of keen interest to security researchers and government agencies. Users reveal aspects of their personality via the content they share with their social media followers and through the patterns in their interactions on online networking platforms. This study examines the potency of emerging natural language processing (NLP) methods in analyzing social network activity. A linguostylistic personality traits assessment (LPTA) system is developed to estimate Twitter users’ personality traits based on their tweets using the Myers-Briggs-type indicator (MBTI) and big-five personality scales. A novel input representation mechanism is proposed to process tweets by converting them into real-valued vectors using frequency, co-occurrence, and context (FCC) measures. Other prevalent text representation schemes, such as one-hot encoding, count-based vectorization, and pretrained language model representations are used as comparators. A genetic algorithm (GA) approach is proposed to reduce the feature set and increase the efficacy of the features extracted. The developed system outperforms the state-of-the-art research by reliably estimating the user’s latent personality traits while using 50 or fewer tweets per user."], "field": "Computer Science", "q_year": 2023, "q_cid": "257193265", "pos_cid": 240577567, "source": "eval_collection"}
{"query_id": "scaleup_28069237_51975610", "query": "How to select diverse, informative, representative negative examples from clustered items without overrepresenting dense regions while keeping selection computationally efficient?", "pos": ["Determinantal Point Processes for Machine Learning. Determinantal point processes (DPPs) are elegant probabilistic models of repulsion that arise in quantum physics and random matrix theory. In contrast to traditional structured models like Markov random fields, which become intractable and hard to approximate in the presence of negative correlations, DPPs offer efficient and exact algorithms for sampling, marginalization, conditioning, and other inference tasks. While they have been studied extensively by mathematicians, giving rise to a deep and beautiful theory, DPPs are relatively new in machine learning. Determinantal Point Processes for Machine Learning provides a comprehensible introduction to DPPs, focusing on the intuitions, algorithms, and extensions that are most relevant to the machine learning community, and shows how DPPs can be applied to real-world applications like finding diverse sets of high-quality search results, building informative summaries by selecting diverse sentences from documents, modeling non-overlapping human poses in images or video, and automatically building timelines of important news stories. It presents the general mathematical background to DPPs along with a range of modeling extensions, efficient algorithms, and theoretical results that aim to enable practical modeling and learning."], "field": "Computer Science", "q_year": 2025, "q_cid": "280692375", "pos_cid": 51975610, "source": "eval_collection"}
{"query_id": "scaleup_28206419_88520704", "query": "How to find a single simple, unrandomized predictor that simultaneously minimizes many proper losses for different decision makers’ utilities with low sample requirements", "pos": ["Of quantiles and expectiles: consistent scoring functions, Choquet representations and forecast rankings. In the practice of point prediction, it is desirable that forecasters receive a directive in the form of a statistical functional. For example, forecasters might be asked to report the mean or a quantile of their predictive distributions. When evaluating and comparing competing forecasts, it is then critical that the scoring function used for these purposes be consistent for the functional at hand, in the sense that the expected score is minimized when following the directive. We show that any scoring function that is consistent for a quantile or an expectile functional can be represented as a mixture of elementary or extremal scoring functions that form a linearly parameterized family. Scoring functions for the mean value and probability forecasts of binary events constitute important examples. The extremal scoring functions admit appealing economic interpretations of quantiles and expectiles in the context of betting and investment problems. The Choquet‐type mixture representations give rise to simple checks of whether a forecast dominates another in the sense that it is preferable under any consistent scoring function. In empirical settings it suffices to compare the average scores for only a finite number of extremal elements. Plots of the average scores with respect to the extremal scoring functions, which we call Murphy diagrams, permit detailed comparisons of the relative merits of competing forecasts."], "field": "Computer Science", "q_year": 2025, "q_cid": "282064199", "pos_cid": 88520704, "source": "eval_collection"}
{"query_id": "scaleup_23634728_12784424", "query": "How to obtain clear images suitable for digital image correlation for full-field deformation measurement at high temperatures despite intense thermal radiation", "pos": ["In-situ 3D shape and recession measurements of ablative materials in an arc-heated wind tunnel by UV stereo-digital image correlation. Abstract In-situ three-dimensional (3D) ablation shape and recession measurements of ablative materials of hypersonic vehicles in high-temperature wind tunnel tests are essential to understand the ablation performance of these materials, which can provide necessary information for better thermal protection system (TPS) design. In this work, a novel ultraviolet stereo-digital image correlation (UV stereo-DIC) technique is proposed for in-situ measurements of 3D ablation shapes and recession in ablation tests. Specifically, a self-developed UV stereo-DIC system, combing a monochromatic UV illumination, two bandpass filters and two UV cameras, is first established. Using the UV stereo-DIC system, strong thermal radiation emitted from the heated sample and the heating device can be effectively suppressed. Natural textures formed from illuminating the rough sample surface by UV light are used as speckle patterns in stereo-correlation. In-situ 3D ablation shapes of a blunt cone subjected to arc heating were measured with a temperature range of 1000 °C to 1868 °C, and the UV stereo-DIC measurements showed good agreement with post-test measurement of the recession of the test articles. Based on the experimentally measured 3D shapes, several key parameters, such as full-field recession, dynamic recession rate, were calculated. The results demonstrate the efficacy and potential of UV stereo-DIC for 3D shape and recession measurements in ablation tests."], "field": "Computer Science", "q_year": 2021, "q_cid": "236347283", "pos_cid": 127844243, "source": "eval_collection"}
{"query_id": "scaleup_26361957_20817554", "query": "How to accurately segment cervical nuclei in images with overlapping cells, color variation, noise, and fuzzy or blurred boundaries", "pos": ["EfficientDet: Scalable and Efficient Object Detection. Model efficiency has become increasingly important in computer vision. In this paper, we systematically study neural network architecture design choices for object detection and propose several key optimizations to improve efficiency. First, we propose a weighted bi-directional feature pyramid network (BiFPN), which allows easy and fast multi-scale feature fusion; Second, we propose a compound scaling method that uniformly scales the resolution, depth, and width for all backbone, feature network, and box/class prediction networks at the same time. Based on these optimizations and EfficientNet backbones, we have developed a new family of object detectors, called EfficientDet, which consistently achieve much better efficiency than prior art across a wide spectrum of resource constraints. In particular, with single-model and single-scale, our EfficientDetD7 achieves state-of-the-art 52.2 AP on COCO test-dev with 52M parameters and 325B FLOPs, being 4x – 9x smaller and using 13x – 42x fewer FLOPs than previous detector."], "field": "Computer Science", "q_year": 2023, "q_cid": "263619571", "pos_cid": 208175544, "source": "eval_collection"}
{"query_id": "scaleup_25873863_10224699", "query": "How to maximize network lifetime while maintaining coverage of all targets in discrete directional-sensor scheduling?", "pos": ["Genetic Algorithm for Traveling Salesman Problem with Modified Cycle Crossover Operator. Genetic algorithms are evolutionary techniques used for optimization purposes according to survival of the fittest idea. These methods do not ensure optimal solutions; however, they give good approximation usually in time. The genetic algorithms are useful for NP-hard problems, especially the traveling salesman problem. The genetic algorithm depends on selection criteria, crossover, and mutation operators. To tackle the traveling salesman problem using genetic algorithms, there are various representations such as binary, path, adjacency, ordinal, and matrix representations. In this article, we propose a new crossover operator for traveling salesman problem to minimize the total distance. This approach has been linked with path representation, which is the most natural way to represent a legal tour. Computational results are also reported with some traditional path representation methods like partially mapped and order crossovers along with new cycle crossover operator for some benchmark TSPLIB instances and found improvements."], "field": "Computer Science", "q_year": 2023, "q_cid": "258738632", "pos_cid": 10224699, "source": "eval_collection"}
{"query_id": "scaleup_28071121_21109673", "query": "How to distinguish normal from anomalous human actions with scarce normal examples across action categories despite variation within each category", "pos": ["A Simple Framework for Contrastive Learning of Visual Representations. This paper presents SimCLR: a simple framework for contrastive learning of visual representations. We simplify recently proposed contrastive self-supervised learning algorithms without requiring specialized architectures or a memory bank. In order to understand what enables the contrastive prediction tasks to learn useful representations, we systematically study the major components of our framework. We show that (1) composition of data augmentations plays a critical role in defining effective predictive tasks, (2) introducing a learnable nonlinear transformation between the representation and the contrastive loss substantially improves the quality of the learned representations, and (3) contrastive learning benefits from larger batch sizes and more training steps compared to supervised learning. By combining these findings, we are able to considerably outperform previous methods for self-supervised and semi-supervised learning on ImageNet. A linear classifier trained on self-supervised representations learned by SimCLR achieves 76.5% top-1 accuracy, which is a 7% relative improvement over previous state-of-the-art, matching the performance of a supervised ResNet-50. When fine-tuned on only 1% of the labels, we achieve 85.8% top-5 accuracy, outperforming AlexNet with 100X fewer labels."], "field": "Computer Science", "q_year": 2025, "q_cid": "280711210", "pos_cid": 211096730, "source": "eval_collection"}
{"query_id": "scaleup_27832816_23474175", "query": "How to determine whether conditional disclosure of secrets admits a large resource advantage while requiring perfect correctness and allowing security errors", "pos": ["Communication Complexity of Private Simultaneous Quantum Messages Protocols. The private simultaneous messages model is a non-interactive version of the multiparty secure computation, which has been intensively studied to examine the communication cost of the secure computation. We consider its quantum counterpart, the private simultaneous quantum messages (PSQM) model, and examine the advantages of quantum communication and prior entanglement of this model. In the PSQM model, $k$ parties $P_1,\\ldots,P_k$ initially share a common random string (or entangled states in a stronger setting), and they have private classical inputs $x_1,\\ldots, x_k$. Every $P_i$ generates a quantum message from the private input $x_i$ and the shared random string (entangled states), and then sends it to the referee $R$. Receiving the messages, $R$ computes $F(x_1,\\ldots,x_k)$. Then, $R$ learns nothing except for $F(x_1,\\ldots,x_k)$ as the privacy condition. We obtain the following results for this PSQM model. (1) We demonstrate that the privacy condition inevitably increases the communication cost in the two-party PSQM model as well as in the classical case presented by Applebaum, Holenstein, Mishra, and Shayevitz. In particular, we prove a lower bound $(3-o(1))n$ of the communication complexity in PSQM protocols with a shared random string for random Boolean functions of $2n$-bit input, which is larger than the trivial upper bound $2n$ of the communication complexity without the privacy condition. (2) We demonstrate a factor two gap between the communication complexity of PSQM protocols with shared entangled states and with shared random strings by designing a multiparty PSQM protocol with shared entangled states for a total function that extends the two-party equality function. (3) We demonstrate an exponential gap between the communication complexity of PSQM protocols with shared entangled states and with shared random strings for a two-party partial function."], "field": "Computer Science", "q_year": 2025, "q_cid": "278328163", "pos_cid": 234741754, "source": "eval_collection"}
{"query_id": "scaleup_21480728_15161999", "query": "How to determine whether noticing implausibility in a virtual environment reduces the sense of being there, and whether this depends on mental capacity limited by other tasks", "pos": ["Rational Versus Intuitive Processing: The Impact of Cognitive Load and Moral Salience on In-Game Aggression and Feelings of Guilt. This study explored two main theoretical propositions. First, we tested Hartmann’s (2011, 2012) notion that video games are processed via two separate cognitive systems: System 1, the automatic system, and System 2, the rational system. Specifically, we used a cognitive load manipulation to test if intuitive moral responses such as guilt and anthropomorphism are processed in System 1. Second, we utilized moral foundations theory to test the effect of care salience on guilt and in-game aggression. Using an experimental design (n = 94), the results indicate that under conditions of cognitive load, players had somewhat lower in-game aggression. Effects on guilt and anthropomorphism were in the same direction, albeit with small effects. In terms of moral foundations, we found that care salience was not negatively related to in-game aggression but was directly related to guilt, indicating that greater emphasis on the moral foundation of care resulted in greater guilt. Also, anthropomorphism was positively related to experienced guilt and negatively related to in-game aggression."], "field": "Computer Science", "q_year": 2020, "q_cid": "214807288", "pos_cid": 151619998, "source": "eval_collection"}
{"query_id": "scaleup_27677602_27442270", "query": "How to help code language models learn meaningful error-correction patterns when preference learning compares entire solutions based on test pass rates without identifying specific errors", "pos": ["Critical Tokens Matter: Token-Level Contrastive Estimation Enhances LLM's Reasoning Capability. Mathematical reasoning tasks pose significant challenges for large language models (LLMs) because they require precise logical deduction and sequence analysis. In this work, we introduce the concept of critical tokens -- elements within reasoning trajectories that significantly influence incorrect outcomes. We present a novel framework for identifying these tokens through rollout sampling and demonstrate their substantial divergence from traditional error tokens. Through extensive experiments on datasets such as GSM8K and MATH500, we show that identifying and replacing critical tokens significantly improves model accuracy. We propose an efficient methodology for pinpointing these tokens in large-scale datasets using contrastive estimation and extend this framework to enhance model training processes with direct preference optimization (DPO). Experimental results on GSM8K and MATH500 benchmarks with the widely used models Llama-3 (8B and 70B) and Deepseek-math (7B) demonstrate the effectiveness of the proposed approach, cDPO. Our results underscore the potential of leveraging critical tokens to reduce errors in reasoning tasks, advancing the development of AI systems capable of robust logical deduction. Our code, annotated datasets, and trained models are available at https://github.com/chenzhiling9954/Critical-Tokens-Matter to support and encourage future research in this promising field."], "field": "Computer Science", "q_year": 2025, "q_cid": "276776025", "pos_cid": 274422705, "source": "eval_collection"}
{"query_id": "scaleup_27832816_16599608", "query": "How to establish a substantial efficiency separation between resource models for conditional disclosure of secrets when both correctness and security errors are allowed", "pos": ["Forrelation: A Problem that Optimally Separates Quantum from Classical Computing. We achieve essentially the largest possible separation between quantum and classical query complexities. We do so using a property-testing problem called Forrelation, where one needs to decide whether one Boolean function is highly correlated with the Fourier transform of a second function. This problem can be solved using 1 quantum query, yet we show that any randomized algorithm needs Ω(√(N)log(N)) queries (improving an Ω(N1/4) lower bound of Aaronson). Conversely, we show that this 1 versus Ω(√(N)) separation is optimal: indeed, any t-query quantum algorithm whatsoever can be simulated by an O(N1-1/2t)-query randomized algorithm. Thus, resolving an open question of Buhrman et al. from 2002, there is no partial Boolean function whose quantum query complexity is constant and whose randomized query complexity is linear. We conjecture that a natural generalization of Forrelation achieves the optimal t versus Ω(N1-1/2t) separation for all t. As a bonus, we show that this generalization is BQP-complete. This yields what's arguably the simplest BQP-complete problem yet known, and gives a second sense in which Forrelation \"captures the maximum power of quantum computation.\""], "field": "Computer Science", "q_year": 2025, "q_cid": "278328163", "pos_cid": 16599608, "source": "eval_collection"}
{"query_id": "scaleup_25069892_21979306", "query": "How to preserve the rich information of an original dataset in a tiny training set for effective network training", "pos": ["Differentiable Augmentation for Data-Efficient GAN Training. The performance of generative adversarial networks (GANs) heavily deteriorates given a limited amount of training data. This is mainly because the discriminator is memorizing the exact training set. To combat it, we propose Differentiable Augmentation (DiffAugment), a simple method that improves the data efficiency of GANs by imposing various types of differentiable augmentations on both real and fake samples. Previous attempts to directly augment the training data manipulate the distribution of real images, yielding little benefit; DiffAugment enables us to adopt the differentiable augmentation for the generated samples, effectively stabilizes training, and leads to better convergence. Experiments demonstrate consistent gains of our method over a variety of GAN architectures and loss functions for both unconditional and class-conditional generation. With DiffAugment, we achieve a state-of-the-art FID of 6.80 with an IS of 100.8 on ImageNet 128x128. Furthermore, with only 20% training data, we can match the top performance on CIFAR-10 and CIFAR-100. Finally, our method can generate high-fidelity images using only 100 images without pre-training, while being on par with existing transfer learning algorithms. Code is available at this https URL."], "field": "Computer Science", "q_year": 2022, "q_cid": "250698926", "pos_cid": 219793068, "source": "eval_collection"}
{"query_id": "scaleup_27423401_25225122", "query": "How to achieve stable, unbiased artificial spins in optical Ising machines with equal probability of selecting either state and reliable readout", "pos": ["Random number generation using spontaneous symmetry breaking in a Kerr resonator. We present an all-optical random number generator based on polarization symmetry breaking in a passive, nonlinear Kerr cavity. The system generates numbers with statistically confirmed randomness at MHz rates with no post-processing."], "field": "Computer Science", "q_year": 2024, "q_cid": "274234018", "pos_cid": 252251229, "source": "eval_collection"}
{"query_id": "scaleup_27204951_22092855", "query": "How to understand the existing literature and clarify the essential pillars of artificial intelligence in university science education, where research remains incipient and these pillars lack a coherent, systematic structure", "pos": ["Impact of Interprofessional Primary Care Practice on Patient Outcomes: A Scoping Review. Systematic reviews have provided some insight into the impact of interprofessional collaborative practice on patient outcomes. Despite strong interest in interprofessional collaborative practice, relatively little is known about its impact in primary care settings. This scoping literature review describes the essential elements of an interprofessional primary care practice and explores what is known about its impact on patient care including clinical, humanistic, and economic outcomes. We completed a review of the literature examining the breadth of knowledge related to interprofessional collaborative practice in primary care settings. A search was conducted to identify studies based on predefined criteria. A total of 51 studies met the criteria. A total of 27 studies reported a significantly positive clinical outcome with the interprofessional collaborative practice model, 27 studies reported no difference, and one study reported negative outcome in mortality. A total of 15 studies reported a significantly positive humanistic outcome. There was little to no difference in economic outcomes. This study provides new insights for future research that examines the impact of interprofessional primary care practice."], "field": "Computer Science", "q_year": 2024, "q_cid": "272049514", "pos_cid": 220928551, "source": "eval_collection"}
{"query_id": "scaleup_27778191_26699955", "query": "How to achieve accurate, high-recall multi-glomerular segmentation in immunofluorescence images while reducing labor-intensive annotation requirements", "pos": ["UV-SAM: Adapting Segment Anything Model for Urban Village Identification. Urban villages, defined as informal residential areas in or around urban centers, are characterized by inadequate infrastructures and poor living conditions, closely related to the Sustainable Development Goals (SDGs) on poverty, adequate housing, and sustainable cities. Traditionally, governments heavily depend on field survey methods to monitor the urban villages, which however are time-consuming, labor-intensive, and possibly delayed. Thanks to widely available and timely updated satellite images, recent studies develop computer vision techniques to detect urban villages efficiently. However, existing studies either focus on simple urban village image classification or fail to provide accurate boundary information. To accurately identify urban village boundaries from satellite images, we harness the power of the vision foundation model and adapt the Segment Anything Model (SAM) to urban village segmentation, named UV-SAM. Specifically, UV-SAM first leverages a small-sized semantic segmentation model to produce mixed prompts for urban villages, including mask, bounding box, and image representations, which are then fed into SAM for fine-grained boundary identification. Extensive experimental results on two datasets in China demonstrate that UV-SAM outperforms existing baselines, and identification results over multiple years show that both the number and area of urban villages are decreasing over time, providing deeper insights into the development trends of urban villages and sheds light on the vision foundation models for sustainable cities. The dataset and codes of this study are available at https://github.com/tsinghua-fib-lab/UV-SAM."], "field": "Computer Science", "q_year": 2025, "q_cid": "277781919", "pos_cid": 266999554, "source": "eval_collection"}
{"query_id": "scaleup_22626222_20166850", "query": "How to make existing semantic information in pre-trained BERT sentence embeddings accessible for sentence comparison despite their non-smooth, anisotropic distribution", "pos": ["Normalizing Flows: Introduction and Ideas. Normalizing Flows are generative models which produce tractable distributions where both sampling and density evaluation can be efficient and exact. The goal of this survey article is to give a coherent and comprehensive review of the literature around the construction and use of Normalizing Flows for distribution learning. We aim to provide context and explanation of the models, review current state-of-the-art literature, and identify open questions and promising future directions."], "field": "Computer Science", "q_year": 2020, "q_cid": "226262227", "pos_cid": 201668500, "source": "eval_collection"}
{"query_id": "scaleup_21242500_12323615", "query": "How to safely reclaim released memory when references may remain and accessibility can change, without interrupting ongoing activity or imposing excessive overhead", "pos": ["Mostly parallel garbage collection. We present a method for adapting garbage collectors designed to run sequentially with the client, so that they may run concurrently with it. We rely on virtual memory hardware to provide information about pages that have been updated or “dirtied” during a given period of time. This method has been used to construct a mostly parallel trace-and-sweep collector that exhibits very short pause times. Performance measurements are given."], "field": "Computer Science", "q_year": 2020, "q_cid": "212425000", "pos_cid": 12323615, "source": "eval_collection"}
{"query_id": "scaleup_27683798_11879708", "query": "How to understand how anxiety about artificial intelligence affects people’s views of paid knowledge products amid uncertainty about future job security and skill relevance", "pos": ["All Negative Moods Are Not Equal: Motivational Influences of Anxiety and Sadness on Decision Making.. Affective states of the same valence may have distinct, yet predictable, influences on decision processes. Results from three experiments show that, in gambling decisions, as well as in job-selection decisions, sad individuals are biased in favor of high-risk/high-reward options, whereas anxious individuals are biased in favor of low-risk/low-reward options. We argue that these biases occur because anxiety and sadness convey distinct types of information to the decision-maker and prime different goals. While anxiety primes an implicit goal of uncertainty reduction, sadness primes an implicit goal of reward replacement. We offer that these motivational influences operate through an active process of feeling monitoring, whereby anxious or sad individuals think about the options and ask themselves, \"What would I feel better about ellipsis?\" Copyright 1999 Academic Press."], "field": "Computer Science", "q_year": 2025, "q_cid": "276837984", "pos_cid": 11879708, "source": "eval_collection"}
{"query_id": "scaleup_27355890_16224674", "query": "How to reliably estimate knee flexion and ankle dorsiflexion from single-camera two-dimensional gait images without complex body modelling or a more demanding camera setup", "pos": ["Realtime Multi-person 2D Pose Estimation Using Part Affinity Fields. We present an approach to efficiently detect the 2D pose of multiple people in an image. The approach uses a nonparametric representation, which we refer to as Part Affinity Fields (PAFs), to learn to associate body parts with individuals in the image. The architecture encodes global context, allowing a greedy bottom-up parsing step that maintains high accuracy while achieving realtime performance, irrespective of the number of people in the image. The architecture is designed to jointly learn part locations and their association via two branches of the same sequential prediction process. Our method placed first in the inaugural COCO 2016 keypoints challenge, and significantly exceeds the previous state-of-the-art result on the MPII Multi-Person benchmark, both in performance and efficiency."], "field": "Computer Science", "q_year": 2024, "q_cid": "273558905", "pos_cid": 16224674, "source": "train_step3"}
{"query_id": "scaleup_21167797_57761158", "query": "How to estimate crowd density at each pixel across varying scales with less manual design effort and lower computational cost", "pos": ["Auto-DeepLab: Hierarchical Neural Architecture Search for Semantic Image Segmentation. Recently, Neural Architecture Search (NAS) has successfully identified neural network architectures that exceed human designed ones on large-scale image classification. In this paper, we study NAS for semantic image segmentation. Existing works often focus on searching the repeatable cell structure, while hand-designing the outer network structure that controls the spatial resolution changes. This choice simplifies the search space, but becomes increasingly problematic for dense image prediction which exhibits a lot more network level architectural variations. Therefore, we propose to search the network level structure in addition to the cell level structure, which forms a hierarchical architecture search space. We present a network level search space that includes many popular designs, and develop a formulation that allows efficient gradient-based architecture search (3 P100 GPU days on Cityscapes images). We demonstrate the effectiveness of the proposed method on the challenging Cityscapes, PASCAL VOC 2012, and ADE20K datasets. Auto-DeepLab, our architecture searched specifically for semantic image segmentation, attains state-of-the-art performance without any ImageNet pretraining."], "field": "Computer Science", "q_year": 2020, "q_cid": "211677970", "pos_cid": 57761158, "source": "train_step3"}
{"query_id": "scaleup_26763675_5519060", "query": "How to obtain reliable semantic relatedness scores for sentence pairs with a manageable number of annotation comparisons", "pos": ["Best-Worst Scaling More Reliable than Rating Scales: A Case Study on Sentiment Intensity Annotation. Rating scales are a widely used method for data annotation; however, they present several challenges, such as difficulty in maintaining inter- and intra-annotator consistency. Best–worst scaling (BWS) is an alternative method of annotation that is claimed to produce high-quality annotations while keeping the required number of annotations similar to that of rating scales. However, the veracity of this claim has never been systematically established. Here for the first time, we set up an experiment that directly compares the rating scale method with BWS. We show that with the same total number of annotations, BWS produces significantly more reliable results than the rating scale."], "field": "Computer Science", "q_year": 2024, "q_cid": "267636752", "pos_cid": 5519060, "source": "train_step3"}
{"query_id": "scaleup_27590688_25930929", "query": "How to reduce social media users’ exposure to harmful content in engagement-focused rankings while scaling and adapting to new forms of harm without extensive human-annotated data", "pos": ["Large Language Models are Effective Text Rankers with Pairwise Ranking Prompting. Ranking documents using Large Language Models (LLMs) by directly feeding the query and candidate documents into the prompt is an interesting and practical problem. However, researchers have found it difficult to outperform fine-tuned baseline rankers on benchmark datasets. We analyze pointwise and listwise ranking prompts used by existing methods and argue that off-the-shelf LLMs do not fully understand these challenging ranking formulations. In this paper, we propose to significantly reduce the burden on LLMs by using a new technique called Pairwise Ranking Prompting (PRP). Our results are the first in the literature to achieve state-of-the-art ranking performance on standard benchmarks using moderate-sized open-sourced LLMs. On TREC-DL 2019&2020, PRP based on the Flan-UL2 model with 20B parameters performs favorably with the previous best approach in the literature, which is based on the blackbox commercial GPT-4 that has 50x (estimated) model size, while outperforming other LLM-based solutions, such as InstructGPT which has 175B parameters, by over 10% for all ranking metrics. By using the same prompt template on seven BEIR tasks, PRP outperforms supervised baselines and outperforms the blackbox commercial ChatGPT solution by 4.2% and pointwise LLM-based solutions by more than 10% on average NDCG@10. Furthermore, we propose several variants of PRP to improve efficiency and show that it is possible to achieve competitive results even with linear complexity."], "field": "Computer Science", "q_year": 2025, "q_cid": "275906887", "pos_cid": 259309299, "source": "train_step3"}
{"query_id": "scaleup_23532480_52912260", "query": "How to predict scores for unlabeled essays with only one manually scored essay available per distinct score", "pos": ["Learning to Propagate Labels: Transductive Propagation Network for Few-Shot Learning. The goal of few-shot learning is to learn a classifier that generalizes well even when trained with a limited number of training instances per class. The recently introduced meta-learning approaches tackle this problem by learning a generic classifier across a large number of multiclass classification tasks and generalizing the model to a new task. Yet, even with such meta-learning, the low-data problem in the novel classification task still remains. In this paper, we propose Transductive Propagation Network (TPN), a novel meta-learning framework for transductive inference that classifies the entire test set at once to alleviate the low-data problem. Specifically, we propose to learn to propagate labels from labeled instances to unlabeled test instances, by learning a graph construction module that exploits the manifold structure in the data. TPN jointly learns both the parameters of feature embedding and the graph construction in an end-to-end manner. We validate TPN on multiple benchmark datasets, on which it largely outperforms existing few-shot learning approaches and achieves the state-of-the-art results."], "field": "Computer Science", "q_year": 2021, "q_cid": "235324805", "pos_cid": 52912260, "source": "train_step3"}
{"query_id": "scaleup_21578616_14604520", "query": "How to determine whether a generated response is consistent with the speaker’s stated persona text", "pos": ["A large annotated corpus for learning natural language inference. Understanding entailment and contradiction is fundamental to understanding natural language, and inference about entailment and contradiction is a valuable testing ground for the development of semantic representations. However, machine learning research in this area has been dramatically limited by the lack of large-scale resources. To address this, we introduce the Stanford Natural Language Inference corpus, a new, freely available collection of labeled sentence pairs, written by humans doing a novel grounded task based on image captioning. At 570K pairs, it is two orders of magnitude larger than all other resources of its type. This increase in scale allows lexicalized classifiers to outperform some sophisticated existing entailment models, and it allows a neural network-based model to perform competitively on natural language inference benchmarks for the first time."], "field": "Computer Science", "q_year": 2020, "q_cid": "215786161", "pos_cid": 14604520, "source": "train_step3"}
{"query_id": "scaleup_3371871_7214363", "query": "How to select initial users or marketing actions to maximize expected influence in a social network despite uncertainty about who becomes influenced and how influence spreads", "pos": ["Maximizing the spread of influence through a social network. Models for the processes by which ideas and influence propagate through a social network have been studied in a number of domains, including the diffusion of medical and technological innovations, the sudden and widespread adoption of various strategies in game-theoretic settings, and the effects of \"word of mouth\" in the promotion of new products. Recently, motivated by the design of viral marketing strategies, Domingos and Richardson posed a fundamental algorithmic problem for such social network processes: if we can try to convince a subset of individuals to adopt a new product or innovation, and the goal is to trigger a large cascade of further adoptions, which set of individuals should we target?We consider this problem in several of the most widely studied models in social network analysis. The optimization problem of selecting the most influential nodes is NP-hard here, and we provide the first provable approximation guarantees for efficient algorithms. Using an analysis framework based on submodular functions, we show that a natural greedy strategy obtains a solution that is provably within 63% of optimal for several classes of models; our framework suggests a general approach for reasoning about the performance guarantees of algorithms for these types of influence problems in social networks.We also provide computational experiments on large collaboration networks, showing that in addition to their provable guarantees, our approximation algorithms significantly out-perform node-selection heuristics based on the well-studied notions of degree centrality and distance centrality from the field of social networks."], "field": "Decision Sciences", "q_year": 2017, "q_cid": "3371871", "pos_cid": 7214363, "source": "eval20x26"}
{"query_id": "scaleup_51987568_1145074", "query": "How to efficiently compute query result probabilities involving arbitrary Boolean formulas in conjunctive normal form", "pos": ["An Improved Decision-DNNF Compiler. We present and evaluate a new compiler, called D4 , targeting the Decision-DNNF language. As the state-of-the-art compilers C2D and Dsharp targeting the same language, D4 is a top-down tree-search algorithm exploring the space of propositional interpretations. D4 is based on the same ingredients as those considered in C2D and Dsharp (mainly, disjoint component analysis, conflict analysis and non-chronological backtracking, component caching). D4 takes advantage of a dynamic decomposition approach based on hypergraph partitioning, used sparingly. Some simplification rules are also used to minimize the time spent in the partitioning steps and to promote the quality of the decompositions. Experiments show that the compilation times and the sizes of the Decision-DNNF representations computed by D4 are in many cases significantly lower than the ones obtained by C2D and Dsharp ."], "field": "Decision Sciences", "q_year": 2018, "q_cid": "51987568", "pos_cid": 1145074, "source": "eval20x26"}
{"query_id": "scaleup_17480282_52804752", "query": "How to estimate a nonlinear reward function when only context distributions are observed and rewards cannot be paired with their realized contexts", "pos": ["Kernel Mean Embedding of Distributions: A Review and Beyonds. A Hilbert space embedding of a distribution---in short, a kernel mean embedding---has recently emerged as a powerful tool for machine learning and inference. The basic idea behind this framework is to map distributions into a reproducing kernel Hilbert space (RKHS) in which the whole arsenal of kernel methods can be extended to probability measures. It can be viewed as a generalization of the original \"feature map\" common to support vector machines (SVMs) and other kernel methods. While initially closely associated with the latter, it has meanwhile found application in fields ranging from kernel machines and probabilistic modeling to statistical inference, causal discovery, and deep learning. The goal of this survey is to give a comprehensive review of existing work and recent advances in this research area, and to discuss the most challenging issues and open problems that could lead to new research directions. The survey begins with a brief introduction to the RKHS and positive definite kernels which forms the backbone of this survey, followed by a thorough discussion of the Hilbert space embedding of marginal distributions, theoretical guarantees, and a review of its applications. The embedding of distributions enables us to apply RKHS methods to probability measures which prompts a wide range of applications such as kernel two-sample testing, independent testing, and learning on distributional data. Next, we discuss the Hilbert space embedding for conditional distributions, give theoretical insights, and review some applications. The conditional mean embedding enables us to perform sum, product, and Bayes' rules---which are ubiquitous in graphical model, probabilistic inference, and reinforcement learning---in a non-parametric way. We then discuss relationships between this framework and other related areas. Lastly, we give some suggestions on future research directions."], "field": "Decision Sciences", "q_year": 2019, "q_cid": "174802823", "pos_cid": 52804752, "source": "eval20x26"}
{"query_id": "scaleup_28073057_21302090", "query": "How to gain support and reduce negative reactions across consumer groups whose values conflict with brands’ sociopolitical stances, without compromising those stances, and clarify what makes these appeals persuasive?", "pos": ["Moral reframing: A technique for effective and persuasive communication across political divides. Correspondence Matthew Feinberg, Rotman School of Management, University of Toronto. Email: matthew.feinberg@rotman.utoronto.ca Abstract The political landscape in the US and many other countries is characterized by policy impasses and animosity between rival political groups. Research finds that these divisions are fueled in part by disparate moral concerns and convictions that undermine communication and understanding between liberals and conservatives. This “moral empathy gap” is particularly evident in the moral underpinnings of the political arguments members of each side employ when trying to persuade one another. Both liberals and conservatives typically craft arguments based on their own moral convictions rather than the convictions of the people they target for persuasion. As a result, these moral arguments tend to be unpersuasive, even offensive, to their recipients. The technique of moral reframing—whereby a position an individual would not normally support is framed in a way that is consistent with that individual's moral values—can be an effective means for political communication and persuasion. Over the last decade, studies of moral reframing have shown its effectiveness across a wide range of polarized topics, including views of economic inequality, environmental protection, same-sex marriage, and major party candidates for the US presidency. In this article, we review the moral reframing literature, examining potential mediators and moderators of the effect, and discuss important questions that remain unanswered about this phenomenon. DOI: 10.1111/spc3.12501"], "field": "Decision Sciences", "q_year": 2025, "q_cid": "280730572", "pos_cid": 213020906, "source": "eval_collection"}
{"query_id": "scaleup_26312415_23850459", "query": "How to ensure valid comparisons across cultural or language groups when identical ratings may reflect different interpretations of response categories rather than comparable experiences", "pos": ["Using Anchoring Vignettes to Assess Group Differences in General Self-Rated Health. This article addresses a potentially serious problem with the widely used self-rated health (SRH) survey item: that different groups have systematically different ways of using the item’s response categories. Analyses based on unadjusted SRH may thus yield misleading results. The authors evaluate anchoring vignettes as a possible solution to this problem. Using vignettes specifically designed to calibrate the SRH item and data from the Wisconsin Longitudinal Study (WLS; N = 2,625), the authors show how demographic and health-related factors, including sex and education, predict differences in rating styles. Such differences, when not adjusted for statistically, may be sufficiently large to lead to mistakes in rank orderings of groups. In the present sample, unadjusted models show that women have better SRH than men, but this difference disappears in models adjusting for women’s greater health-optimism. Anchoring vignettes appear a promising tool for improving intergroup comparability of SRH."], "field": "Decision Sciences", "q_year": 2023, "q_cid": "263124156", "pos_cid": 23850459, "source": "eval_collection"}
{"query_id": "scaleup_28048249_21889700", "query": "How to identify which individual asset-pricing characteristics matter most for predicting stock returns across different models", "pos": ["A Unified Approach to Interpreting Model Predictions. Understanding why a model makes a certain prediction can be as crucial as the prediction's accuracy in many applications. However, the highest accuracy for large modern datasets is often achieved by complex models that even experts struggle to interpret, such as ensemble or deep learning models, creating a tension between accuracy and interpretability. In response, various methods have recently been proposed to help users interpret the predictions of complex models, but it is often unclear how these methods are related and when one method is preferable over another. To address this problem, we present a unified framework for interpreting predictions, SHAP (SHapley Additive exPlanations). SHAP assigns each feature an importance value for a particular prediction. Its novel components include: (1) the identification of a new class of additive feature importance measures, and (2) theoretical results showing there is a unique solution in this class with a set of desirable properties. The new class unifies six existing methods, notable because several recent methods in the class lack the proposed desirable properties. Based on insights from this unification, we present new methods that show improved computational performance and/or better consistency with human intuition than previous approaches."], "field": "Decision Sciences", "q_year": 2025, "q_cid": "280482490", "pos_cid": 21889700, "source": "eval_collection"}
{"query_id": "scaleup_27672836_24624235", "query": "How to determine whether fear of COVID-19 influences Generation Z consumers’ intentions to continue shopping on mobile apps during and after the pandemic", "pos": ["Predicting Consumer Green Product Purchase Attitudes and Behavioral Intention During COVID-19 Pandemic. This work has aimed to investigate the consumers’ green product purchase attitudes and behavioral intention during COVID-19 pandemic. Data was collected through a survey method of 503 consumers in Malaysia. Data were analyzed using the partial least square method. The findings revealed that fear of COVID-19 pandemic has a significant impact on green product behavioral intention. Green product literacy, green product orientation, and social influence have a significant influence on green product purchase attitudes. The results also indicated that consumers’ green product purchase attitudes mediate the effect of green product literacy, green product orientation, and social influence on behavioral intention. The findings of this work will provide strategically relevant references to green marketers and retail managers in the understanding of consumers’ green product purchase attitudes and green product behavioral intention during the ongoing uncertainty of the COVID-19 pandemic."], "field": "Decision Sciences", "q_year": 2025, "q_cid": "276728363", "pos_cid": 246242354, "source": "eval_collection"}
{"query_id": "scaleup_25064436_257219", "query": "How to reconcile probabilistic count forecasts into a joint distribution that incorporates multiple uncertain upper-level base forecasts, with the same result regardless of incorporation order", "pos": ["On the revision of probabilistic beliefs using uncertain evidence. We revisit the problem of revising probabilistic beliefs using uncertain evidence, and report results on several major issues relating to this problem: how should one specify uncertain evidence? How should one revise a probability distribution? How should one interpret informal evidential statements? Should, and do, iterated belief revisions commute? And what guarantees can be offered on the amount of belief change induced by a particular revision? Our discussion is focused on two main methods for probabilistic revision: Jeffrey's rule of probability kinematics and Pearl's method of virtual evidence, where we analyze and unify these methods from the perspective of the questions posed above."], "field": "Decision Sciences", "q_year": 2022, "q_cid": "250644364", "pos_cid": 257219, "source": "eval_collection"}
{"query_id": "scaleup_26544841_3051291", "query": "How to estimate mutual fund performance while accounting for connections among funds and related entities", "pos": ["DeepWalk: online learning of social representations. We present DeepWalk, a novel approach for learning latent representations of vertices in a network. These latent representations encode social relations in a continuous vector space, which is easily exploited by statistical models. DeepWalk generalizes recent advancements in language modeling and unsupervised feature learning (or deep learning) from sequences of words to graphs. DeepWalk uses local information obtained from truncated random walks to learn latent representations by treating walks as the equivalent of sentences. We demonstrate DeepWalk's latent representations on several multi-label network classification tasks for social networks such as BlogCatalog, Flickr, and YouTube. Our results show that DeepWalk outperforms challenging baselines which are allowed a global view of the network, especially in the presence of missing information. DeepWalk's representations can provide F1 scores up to 10% higher than competing methods when labeled data is sparse. In some experiments, DeepWalk's representations are able to outperform all baseline methods while using 60% less training data. DeepWalk is also scalable. It is an online learning algorithm which builds useful incremental results, and is trivially parallelizable. These qualities make it suitable for a broad class of real world applications such as network classification, and anomaly detection."], "field": "Decision Sciences", "q_year": 2023, "q_cid": "265448416", "pos_cid": 3051291, "source": "eval_collection"}
{"query_id": "scaleup_27704789_26206733", "query": "How to understand consumer-level psychological processes linking corporate apologies to brand trust repair, particularly the role of perceived warmth in forgiveness-based recovery", "pos": ["Why do we feel close to a person who expresses gratitude? Exploring mediating roles of perceived warmth, conscientiousness, and agreeableness. The literature suggests that expressed gratitude improves the interpersonal relationship between a beneficiary and a benefactor. However, there is little research that has explored why thanking provides these positive effects, so this study investigated thanking mechanisms to explain reasons why people feel close to a beneficiary who expresses gratitude. This study also examines the effects of apologies, which are sometimes used to show gratitude in Japan. In this experimental study, 671 Japanese participants reported their perceived closeness, warmth, conscientiousness, and agreeableness to a hypothetical beneficiary who expressed gratitude, apologies, or both after a benefit was provided. The results revealed that benefactors who received a message indicating gratitude and both gratitude and apologies reported higher levels of closeness toward a beneficiary than those who received a message with only apologies and a message without either gratitude or apologies. A structural equation model further indicated that warmth and conscientiousness mediated the link between expressed gratitude/apologies and perceived closeness."], "field": "Decision Sciences", "q_year": 2025, "q_cid": "277047896", "pos_cid": 262067334, "source": "eval_collection"}
{"query_id": "scaleup_25269567_18541623", "query": "How to shift from protecting formerly scarce entities to limiting their overabundance despite existing protective goals and legal safeguards", "pos": ["Threatened species to super-abundance: The unexpected international implications of successful goose conservation. Wild geese wintering in western Europe were declining by the 1930s probably due to loss of natural habitat and over exploitation through hunting, although the causes will never be known. Refuge provision and hunting restrictions from the 1950s enabled numbers to recover. Improved monitoring systems enabled the description of progressive increases and extensions of wintering range since that time, especially amongst those goose populations that increasingly exploited agricultural landscapes. This introductory article sets the scene for the special issue on the increasing interactions and conflicts created by recent increases in the range and abundance of wild geese throughout the northern hemisphere, especially with regard to agricultural damage, but including issues associated with air flight safety, human and animal health, ecosystem effects and conflicts with other biodiversity objectives. It also provides the context for finding common solutions to problems, presenting experiences from regional-, national- and flyway-coordinated management to find solutions to conflict."], "field": "Decision Sciences", "q_year": 2022, "q_cid": "252695674", "pos_cid": 18541623, "source": "eval_collection"}
{"query_id": "scaleup_27890457_25936066", "query": "How to ensure model outputs reflect updated facts and crucial contextual information in document-level model editing", "pos": ["Lost in the Middle: How Language Models Use Long Contexts. While recent language models have the ability to take long contexts as input, relatively little is known about how well they use longer context. We analyze the performance of language models on two tasks that require identifying relevant information in their input contexts: multi-document question answering and key-value retrieval. We find that performance can degrade significantly when changing the position of relevant information, indicating that current language models do not robustly make use of information in long input contexts. In particular, we observe that performance is often highest when relevant information occurs at the beginning or end of the input context, and significantly degrades when models must access relevant information in the middle of long contexts, even for explicitly long-context models. Our analysis provides a better understanding of how language models use their input context and provides new evaluation protocols for future long-context language models."], "field": "Decision Sciences", "q_year": 2025, "q_cid": "278904570", "pos_cid": 259360665, "source": "eval_collection"}
{"query_id": "scaleup_26515064_15054167", "query": "How to determine production at different relative output ranks for arbitrary input levels to assess alternative resource allocations, given only unit-specific estimates and the requirement of a concave production relationship", "pos": ["Representation theorem for convex nonparametric least squares. Summary We examine a nonparametric least-squares regression model that endogenously selects the functional form of the regression function from the family of continuous, monotonic increasing and globally concave functions that can be nondifferentiable. We show that this family of functions can be characterized without a loss of generality by a subset of continuous, piece-wise linear functions whose intercept and slope coefficients are constrained to satisfy the required monotonicity and concavity conditions. This representation theorem is useful at least in three respects. First, it enables us to derive an explicit representation for the regression function, which can be used for assessing marginal properties and for the purposes of forecasting and ex post economic modelling. Second, it enables us to transform the infinite dimensional regression problem into a tractable quadratic programming (QP) form, which can be solved by standard QP algorithms and solver software. Importantly, the QP formulation applies to the general multiple regression setting. Third, an operational computational procedure enables us to apply bootstrap techniques to draw statistical inference."], "field": "Decision Sciences", "q_year": 2023, "q_cid": "265150643", "pos_cid": 15054167, "source": "eval_collection"}
{"query_id": "scaleup_23066951_334423", "query": "How to distinguish collaborative groupings of disciplines and their characteristics in precision medicine?", "pos": ["Fast unfolding of communities in large networks. We propose a simple method to extract the community structure of large networks. Our method is a heuristic method that is based on modularity optimization. It is shown to outperform all other known community detection methods in terms of computation time. Moreover, the quality of the communities detected is very good, as measured by the so-called modularity. This is shown first by identifying language communities in a Belgian mobile phone network of 2 million customers and by analysing a web graph of 118 million nodes and more than one billion links. The accuracy of our algorithm is also verified on ad hoc modular networks."], "field": "Decision Sciences", "q_year": 2020, "q_cid": "230669518", "pos_cid": 334423, "source": "eval_collection"}
{"query_id": "scaleup_27869991_96445194", "query": "How to improve latent variable reliability and the precision, consistency, and applicability of structural equation modelling estimates across contexts or populations despite measurement error, common method bias, and endogeneity", "pos": ["Endogeneity bias in marketing research: Problem, causes and remedies. Endogeneity bias represents a critical issue for the analysis of cause and effect relationships. Although the existence of endogeneity can produce severely biased results, it has hitherto received only limited attention from researchers in marketing and related disciplines. Thus, this article aims to sensitize researchers intending to publish in the Industrial Marketing Management (IMM) journal to the topic of endogeneity. It outlines the problem of endogeneity bias, and provides an overview of potential sources, i.e. omission of variables, errors-in-variables, and simultaneous causality. Furthermore, the article shows ways to deal with endogeneity, including techniques based on instrumental variables as well as instrument-free approaches. Our methodological contribution relates to providing researchers aiming to publish in IMM with an initial overview of the causes of and remedies for endogeneity bias, which should be considered in designing research projects as well as when analysing data to obtain insights into cause and effect relationships (causal models)."], "field": "Decision Sciences", "q_year": 2025, "q_cid": "278699915", "pos_cid": 96445194, "source": "eval_collection"}
{"query_id": "scaleup_25626572_20660690", "query": "How to determine how academic self-concept and achievement affect each other when some data are missing", "pos": ["Propensity score analysis with partially observed covariates: How should multiple imputation be used?. Inverse probability of treatment weighting is a popular propensity score-based approach to estimate marginal treatment effects in observational studies at risk of confounding bias. A major issue when estimating the propensity score is the presence of partially observed covariates. Multiple imputation is a natural approach to handle missing data on covariates: covariates are imputed and a propensity score analysis is performed in each imputed dataset to estimate the treatment effect. The treatment effect estimates from each imputed dataset are then combined to obtain an overall estimate. We call this method MIte. However, an alternative approach has been proposed, in which the propensity scores are combined across the imputed datasets (MIps). Therefore, there are remaining uncertainties about how to implement multiple imputation for propensity score analysis: (a) should we apply Rubin’s rules to the inverse probability of treatment weighting treatment effect estimates or to the propensity score estimates themselves? (b) does the outcome have to be included in the imputation model? (c) how should we estimate the variance of the inverse probability of treatment weighting estimator after multiple imputation? We studied the consistency and balancing properties of the MIte and MIps estimators and performed a simulation study to empirically assess their performance for the analysis of a binary outcome. We also compared the performance of these methods to complete case analysis and the missingness pattern approach, which uses a different propensity score model for each pattern of missingness, and a third multiple imputation approach in which the propensity score parameters are combined rather than the propensity scores themselves (MIpar). Under a missing at random mechanism, complete case and missingness pattern analyses were biased in most cases for estimating the marginal treatment effect, whereas multiple imputation approaches were approximately unbiased as long as the outcome was included in the imputation model. Only MIte was unbiased in all the studied scenarios and Rubin’s rules provided good variance estimates for MIte. The propensity score estimated in the MIte approach showed good balancing properties. In conclusion, when using multiple imputation in the inverse probability of treatment weighting context, MIte with the outcome included in the imputation model is the preferred approach."], "field": "Decision Sciences", "q_year": 2023, "q_cid": "256265728", "pos_cid": 206606906, "source": "eval_collection"}
{"query_id": "scaleup_25602257_8511322", "query": "How to make critical zone science and education responsive to communities, attentive to relationships, trust, and human experiences, and grounded in diversity and equity as foundational priorities", "pos": ["Achieving Research Impact Through Co‐creation in Community‐Based Health Services: Literature Review and Case Study. POLICY POINTS Co-creation-collaborative knowledge generation by academics working alongside other stakeholders-is an increasingly popular approach to aligning research and service development. It has potential for \"moving beyond the ivory towers\" to deliver significant societal impact via dynamic, locally adaptive community-academic partnerships. Principles of successful co-creation include a systems perspective, a creative approach to research focused on improving human experience, and careful attention to governance and process. If these principles are not followed, co-creation efforts may fail. CONTEXT Co-creation-collaborative knowledge generation by academics working alongside other stakeholders-reflects a \"Mode 2\" relationship (knowledge production rather than knowledge translation) between universities and society. Co-creation is widely believed to increase research impact. METHODS We undertook a narrative review of different models of co-creation relevant to community-based health services. We contrasted their diverse disciplinary roots and highlighted their common philosophical assumptions, principles of success, and explanations for failures. We applied these to an empirical case study of a community-based research-service partnership led by the Centre of Research Excellence in Quality and Safety in Integrated Primary-Secondary Care at the University of Queensland, Australia. FINDINGS Co-creation emerged independently in several fields, including business studies (\"value co-creation\"), design science (\"experience-based co-design\"), computer science (\"technology co-design\"), and community development (\"participatory research\"). These diverse models share some common features, which were also evident in the case study. Key success principles included (1) a systems perspective (assuming emergence, local adaptation, and nonlinearity); (2) the framing of research as a creative enterprise with human experience at its core; and (3) an emphasis on process (the framing of the program, the nature of relationships, and governance and facilitation arrangements, especially the style of leadership and how conflict is managed). In both the literature review and the case study, co-creation \"failures\" could often be tracked back to abandoning (or never adopting) these principles. All co-creation models made strong claims for significant and sustainable societal impacts as a result of the adaptive and developmental research process; these were illustrated in the case study. CONCLUSIONS Co-creation models have high potential for societal impact but depend critically on key success principles. To capture the nonlinear chains of causation in the co-creation pathway, impact metrics must reflect the dynamic nature and complex interdependencies of health research systems and address processes as well as outcomes."], "field": "Decision Sciences", "q_year": 2023, "q_cid": "256022574", "pos_cid": 8511322, "source": "eval_collection"}
{"query_id": "scaleup_25626572_71146453", "query": "How to estimate the effects of academic self-concept and achievement on each other when the relevance of other factors depends on assumptions that cannot be formally tested", "pos": ["Principles of confounder selection. Selecting an appropriate set of confounders for which to control is critical for reliable causal inference. Recent theoretical and methodological developments have helped clarify a number of principles of confounder selection. When complete knowledge of a causal diagram relating all covariates to each other is available, graphical rules can be used to make decisions about covariate control. Unfortunately, such complete knowledge is often unavailable. This paper puts forward a practical approach to confounder selection decisions when the somewhat less stringent assumption is made that knowledge is available for each covariate whether it is a cause of the exposure, and whether it is a cause of the outcome. Based on recent theoretically justified developments in the causal inference literature, the following proposal is made for covariate control decisions: control for each covariate that is a cause of the exposure, or of the outcome, or of both; exclude from this set any variable known to be an instrumental variable; and include as a covariate any proxy for an unmeasured variable that is a common cause of both the exposure and the outcome. Various principles of confounder selection are then further related to statistical covariate selection methods."], "field": "Decision Sciences", "q_year": 2023, "q_cid": "256265728", "pos_cid": 71146453, "source": "eval_collection"}
{"query_id": "scaleup_25626821_26590874", "query": "How to determine whether a model adequately fits observed patient data for estimating treatment effectiveness", "pos": ["Visualization in Bayesian workflow. Bayesian data analysis is about more than just computing a posterior distribution, and Bayesian visualization is about more than trace plots of Markov chains. Practical Bayesian data analysis, like all data analysis, is an iterative process of model building, inference, model checking and evaluation, and model expansion. Visualization is helpful in each of these stages of the Bayesian workflow and it is indispensable when drawing inferences from the types of modern, high dimensional models that are used by applied researchers."], "field": "Decision Sciences", "q_year": 2023, "q_cid": "256268214", "pos_cid": 26590874, "source": "eval_collection"}
{"query_id": "scaleup_25602257_22547779", "query": "How to ensure accountability among educational institutions and funding agencies and sustain changes needed to address racial and ethnic underrepresentation in critical zone science and education", "pos": ["Anti-racist actions and accountability: not more empty promises. PurposeThe current piece summarizes five critical points about racism from the point of view of Black scholars and allies: (1) Black people are experiencing exhaustion from and physiological effects of racism, (2) racism extends far beyond police brutality and into most societal structures, (3) despite being the targets of racism, Black people are often blamed for their oppression and retaliated against for their response to it, (4) everyone must improve their awareness and knowledge (through both formal education and individual motivation) to fight racism and (5) anti-racist policies and accountability are key to enact structural reformation.FindingsThe first three of these points detail the depths of the problem from the perspectives of the authors and the final two lay out a call to action.Practical implicationsThis viewpoint is the joint effort of 14 authors who provided a unified perspective.Originality/valueThis was one of the most original experiences the authors have had – working with 13 former/current students on joint perspectives about police brutality and racism more generally. The authors thank for the opportunity."], "field": "Decision Sciences", "q_year": 2023, "q_cid": "256022574", "pos_cid": 225477797, "source": "eval_collection"}
{"query_id": "scaleup_27233454_22004729", "query": "How to avoid privileging dominant perspectives when assumptions, social positions, and team power relations remain unexamined and a focus on shared meanings limits attention to context and differences in marginalization across intersecting identities", "pos": ["Considerations for Employing Intersectionality in Qualitative Health Research. Intersectionality theory has recently emerged in the health sciences as a critical theoretical and methodical approach. Though some scholars have outlined explicit guidelines for applying intersectionality in research using quantitative methods, others have cited epistemological concerns and additive thinking to advocate for the analysis of intersectionality with qualitative methods. Thus, there remains a need for additional guidance and support for utilizing and applying intersectionality theory throughout the qualitative research process. With the goal of demystifying the process of utilizing intersectionality as a methodological approach in qualitative research in the health sciences, this paper provides researchers with recommendations, specific examples, and important considerations for incorporating intersectional approaches into study conceptualization, participant recruitment, data collection, and data analysis. Additionally, this paper reviews challenges that researchers may experience in conducting research using intersectional approaches and offers suggestions for overcoming challenges. This paper offers timely and relevant information that can be used to strengthen the theoretical and methodological rigor of qualitative health research, especially studies that seek to advance health equity."], "field": "Decision Sciences", "q_year": 2024, "q_cid": "272334543", "pos_cid": 220047297, "source": "eval_collection"}
{"query_id": "scaleup_23398580_2180281", "query": "How to make a meta-analysis sufficiently transparent for readers to reproduce it", "pos": ["Ten Simple Rules for Reproducible Computational Research. Replication is the cornerstone of a cumulative science [1]. However, new tools and technologies, massive amounts of data, interdisciplinary approaches, and the complexity of the questions being asked are complicating replication efforts, as are increased pressures on scientists to advance their research [2]. As full replication of studies on independently collected data is often not feasible, there has recently been a call for reproducible research as an attainable minimum standard for assessing the value of scientific claims [3]. This requires that papers in experimental science describe the results and provide a sufficiently clear protocol to allow successful repetition and extension of analyses based on original data [4]. The importance of replication and reproducibility has recently been exemplified through studies showing that scientific papers commonly leave out experimental details essential for reproduction [5], studies showing difficulties with replicating published experimental results [6], an increase in retracted papers [7], and through a high number of failing clinical trials [8], [9]. This has led to discussions on how individual researchers, institutions, funding bodies, and journals can establish routines that increase transparency and reproducibility. In order to foster such aspects, it has been suggested that the scientific community needs to develop a “culture of reproducibility” for computational science, and to require it for published claims [3]. We want to emphasize that reproducibility is not only a moral responsibility with respect to the scientific field, but that a lack of reproducibility can also be a burden for you as an individual researcher. As an example, a good practice of reproducibility is necessary in order to allow previously developed methodology to be effectively applied on new data, or to allow reuse of code and results for new projects. In other words, good habits of reproducibility may actually turn out to be a time-saver in the longer run. We further note that reproducibility is just as much about the habits that ensure reproducible research as the technologies that can make these processes efficient and realistic. Each of the following ten rules captures a specific aspect of reproducibility, and discusses what is needed in terms of information handling and tracking of procedures. If you are taking a bare-bones approach to bioinformatics analysis, i.e., running various custom scripts from the command line, you will probably need to handle each rule explicitly. If you are instead performing your analyses through an integrated framework (such as GenePattern [10], Galaxy [11], LONI pipeline [12], or Taverna [13]), the system may already provide full or partial support for most of the rules. What is needed on your part is then merely the knowledge of how to exploit these existing possibilities. In a pragmatic setting, with publication pressure and deadlines, one may face the need to make a trade-off between the ideals of reproducibility and the need to get the research out while it is still relevant. This trade-off becomes more important when considering that a large part of the analyses being tried out never end up yielding any results. However, frequently one will, with the wisdom of hindsight, contemplate the missed opportunity to ensure reproducibility, as it may already be too late to take the necessary notes from memory (or at least much more difficult than to do it while underway). We believe that the rewards of reproducibility will compensate for the risk of having spent valuable time developing an annotated catalog of analyses that turned out as blind alleys. As a minimal requirement, you should at least be able to reproduce the results yourself. This would satisfy the most basic requirements of sound research, allowing any substantial future questioning of the research to be met with a precise explanation. Although it may sound like a very weak requirement, even this level of reproducibility will often require a certain level of care in order to be met. There will for a given analysis be an exponential number of possible combinations of software versions, parameter values, pre-processing steps, and so on, meaning that a failure to take notes may make exact reproduction essentially impossible. With this basic level of reproducibility in place, there is much more that can be wished for. An obvious extension is to go from a level where you can reproduce results in case of a critical situation to a level where you can practically and routinely reuse your previous work and increase your productivity. A second extension is to ensure that peers have a practical possibility of reproducing your results, which can lead to increased trust in, interest for, and citations of your work [6], [14]. We here present ten simple rules for reproducibility of computational research. These rules can be at your disposal for whenever you want to make your research more accessible—be it for peers or for your future self."], "field": "Decision Sciences", "q_year": 2021, "q_cid": "233985805", "pos_cid": 2180281, "source": "eval_collection"}
{"query_id": "scaleup_26762754_25686837", "query": "How to streamline communication between vehicles while preserving the information needed to predict their complete three-dimensional surroundings", "pos": ["Tri-Perspective View for Vision-Based 3D Semantic Occupancy Prediction. Modern methods for vision-centric autonomous driving perception widely adopt the bird's-eye-view (BEV) representation to describe a 3D scene. Despite its better efficiency than voxel representation, it has difficulty describing the fine-grained 3D structure of a scene with a single plane. To address this, we propose a tri-perspective view (TPV) representation which accompanies BEV with two additional perpendicular planes. We model each point in the 3D space by summing its projected features on the three planes. To lift image features to the 3D TPV space, we further propose a transformer-based TPV encoder (TPVFormer) to obtain the TPV features effectively. We employ the attention mechanism to aggregate the image features corresponding to each query in each TPV plane. Experiments show that our model trained with sparse supervision effectively predicts the semantic occupancy for all voxels. We demonstrate for the first time that using only camera inputs can achieve comparable performance with LiDAR-based methods on the LiDAR segmentation task on nuScenes. Code: https://github.com/wzzheng/TPVFormer."], "field": "Decision Sciences", "q_year": 2024, "q_cid": "267627547", "pos_cid": 256868375, "source": "eval_collection"}
{"query_id": "scaleup_28033401_21113001", "query": "How to determine whether task-based exploration measures and self-reported exploration tendencies capture the same underlying construct, interpret their weak correlations, and establish their external validity", "pos": ["Why Are Self-Report and Behavioral Measures Weakly Correlated?. Accumulating evidence indicates weak correlations between self-report and behavioral measures of the same construct. We suggest that these weak correlations result from the poor reliability of many behavioral measures and the distinct response processes involved in the two measurement types. We also describe how researchers can benefit from appropriate use of these measures."], "field": "Decision Sciences", "q_year": 2025, "q_cid": "280334014", "pos_cid": 211130019, "source": "eval_collection"}
{"query_id": "scaleup_26515064_21905074", "query": "How to estimate achievable outputs across the conditional output distribution for units with differing performance and characteristics despite random noise and unequal variability", "pos": ["Forward-looking assessment of the GHG abatement cost: Application to China. Abstract Evaluation of abatement costs is critical in setting reduction goals and devising climate policy. However, reliable forward-looking assessment of the short-term effects of climate policy remains a major challenge. Using panel data of 30 Chinese provinces during 1997–2015, we first estimate the marginal CO2 abatement costs using a novel data-driven approach, convex quantile regression. Based on the marginal abatement cost estimates and China's plans regarding carbon intensity reduction and economic growth, we present a forward-looking assessment of the abatement costs for Chinese provinces for 2016–2020. Our main finding is that all the Chinese provinces have a negative abatement cost, which means these provinces can benefit from an increase in the absolute level of CO2 emissions despite the constraint on carbon intensity. The magnitudes of economic benefits exhibit a significant regional disparity because some provinces can increase more CO2 emissions than others. However, there is still costly carbon intensity abatement relative to a counterfactual where the provinces meet their economic growth targets but in the absence of the intensity reduction constraints. Policy implications have been proposed to enhance the efficiency and fairness of climate policy in China."], "field": "Decision Sciences", "q_year": 2023, "q_cid": "265150643", "pos_cid": 219050742, "source": "eval_collection"}
{"query_id": "scaleup_26482035_25534068", "query": "How to find and sample from continuous worst-case distributions in Wasserstein distributionally robust optimization at larger dataset scales with limited memory and computational resources", "pos": ["Normalizing flow neural networks by JKO scheme. Normalizing flow is a class of deep generative models for efficient sampling and likelihood estimation, which achieves attractive performance, particularly in high dimensions. The flow is often implemented using a sequence of invertible residual blocks. Existing works adopt special network architectures and regularization of flow trajectories. In this paper, we develop a neural ODE flow network called JKO-iFlow, inspired by the Jordan-Kinderleherer-Otto (JKO) scheme, which unfolds the discrete-time dynamic of the Wasserstein gradient flow. The proposed method stacks residual blocks one after another, allowing efficient block-wise training of the residual blocks, avoiding sampling SDE trajectories and score matching or variational learning, thus reducing the memory load and difficulty in end-to-end training. We also develop adaptive time reparameterization of the flow network with a progressive refinement of the induced trajectory in probability space to improve the model accuracy further. Experiments with synthetic and real data show that the proposed JKO-iFlow network achieves competitive performance compared with existing flow and diffusion models at a significantly reduced computational and memory cost."], "field": "Decision Sciences", "q_year": 2023, "q_cid": "264820357", "pos_cid": 255340683, "source": "eval_collection"}
{"query_id": "scaleup_26762754_22220863", "query": "How to relate image content to locations in a three-dimensional scene for a coherent representation of what occupies each location", "pos": ["Deformable DETR: Deformable Transformers for End-to-End Object Detection. DETR has been recently proposed to eliminate the need for many hand-designed components in object detection while demonstrating good performance. However, it suffers from slow convergence and limited feature spatial resolution, due to the limitation of Transformer attention modules in processing image feature maps. To mitigate these issues, we proposed Deformable DETR, whose attention modules only attend to a small set of key sampling points around a reference. Deformable DETR can achieve better performance than DETR (especially on small objects) with 10$\\times$ less training epochs. Extensive experiments on the COCO benchmark demonstrate the effectiveness of our approach. Code shall be released."], "field": "Decision Sciences", "q_year": 2024, "q_cid": "267627547", "pos_cid": 222208633, "source": "eval_collection"}
{"query_id": "scaleup_27832728_20390233", "query": "How to capture long-range spatial dependencies and global relationships among spectral features?", "pos": ["ECA-Net: Efficient Channel Attention for Deep Convolutional Neural Networks. Recently, channel attention mechanism has demonstrated to offer great potential in improving the performance of deep convolutional neural networks (CNNs). However, most existing methods dedicate to developing more sophisticated attention modules for achieving better performance, which inevitably increase model complexity. To overcome the paradox of performance and complexity trade-off, this paper proposes an Efficient Channel Attention (ECA) module, which only involves a handful of parameters while bringing clear performance gain. By dissecting the channel attention module in SENet, we empirically show avoiding dimensionality reduction is important for learning channel attention, and appropriate cross-channel interaction can preserve performance while significantly decreasing model complexity. Therefore, we propose a local cross-channel interaction strategy without dimensionality reduction, which can be efficiently implemented via 1D convolution. Furthermore, we develop a method to adaptively select kernel size of 1D convolution, determining coverage of local cross-channel interaction. The proposed ECA module is both efficient and effective, e.g., the parameters and computations of our modules against backbone of ResNet50 are 80 vs. 24.37M and 4.7e-4 GFlops vs. 3.86 GFlops, respectively, and the performance boost is more than 2% in terms of Top-1 accuracy. We extensively evaluate our ECA module on image classification, object detection and instance segmentation with backbones of ResNets and MobileNetV2. The experimental results show our module is more efficient while performing favorably against its counterparts."], "field": "Decision Sciences", "q_year": 2025, "q_cid": "278327287", "pos_cid": 203902337, "source": "eval_collection"}
{"query_id": "scaleup_26841737_21573717", "query": "How to enable generic pretrained language models to efficiently capture sparse signals about a company’s future prospects across long financial reports containing specialized jargon and extensive boilerplate", "pos": ["Longformer: The Long-Document Transformer. Transformer-based models are unable to process long sequences due to their self-attention operation, which scales quadratically with the sequence length. To address this limitation, we introduce the Longformer with an attention mechanism that scales linearly with sequence length, making it easy to process documents of thousands of tokens or longer. Longformer's attention mechanism is a drop-in replacement for the standard self-attention and combines a local windowed attention with a task motivated global attention. Following prior work on long-sequence transformers, we evaluate Longformer on character-level language modeling and achieve state-of-the-art results on text8 and enwik8. In contrast to most prior work, we also pretrain Longformer and finetune it on a variety of downstream tasks. Our pretrained Longformer consistently outperforms RoBERTa on long document tasks and sets new state-of-the-art results on WikiHop and TriviaQA. We finally introduce the Longformer-Encoder-Decoder (LED), a Longformer variant for supporting long document generative sequence-to-sequence tasks, and demonstrate its effectiveness on the arXiv summarization dataset."], "field": "Decision Sciences", "q_year": 2024, "q_cid": "268417377", "pos_cid": 215737171, "source": "eval_collection"}
{"query_id": "scaleup_27997987_6669381", "query": "How to clarify how patient absorptive capacity and hospital mobile health portal innovativeness relate to portal use and why high portal adoption can coexist with low usage", "pos": ["Introduction to mediation analysis with structural equation modeling. In mediation, we consider an intermediate variable, called the mediator, that helps explain how or why an independent variable influences an outcome. In the context of a treatment study, it is often of great interest to identify and study the mechanisms by which an intervention achieves its effect. By investigating mediational processes that clarify how the treatment achieves the study outcome, not only can we further our understanding of the pathology of the disease and the mechanisms of treatment, but we may also be able to identify alternative, more efficient, intervention strategies. For example, a tobacco prevention program may teach participants how to stop taking smoking breaks at work (the intervention) which changes their social norms about tobacco use (the intermediate mediator) and subsequently leads to a reduction in smoking behavior (study outcome)."], "field": "Decision Sciences", "q_year": 2025, "q_cid": "279979874", "pos_cid": 6669381, "source": "eval_collection"}
{"query_id": "scaleup_27890457_24521892", "query": "How to obtain reliable, supported, accurately annotated factual changes across documents for document-level model editing and evaluate edits separately from unchanged text", "pos": ["FRUIT: Faithfully Reflecting Updated Information in Text. Textual knowledge bases such as Wikipedia require considerable effort to keep up to date and consistent. While automated writing assistants could potentially ease this burden, the problem of suggesting edits grounded in external knowledge has been under-explored. In this paper, we introduce the novel generation task of *faithfully reflecting updated information in text* (FRUIT) where the goal is to update an existing article given new evidence. We release the FRUIT-WIKI dataset, a collection of over 170K distantly supervised data produced from pairs of Wikipedia snapshots, along with our data generation pipeline and a gold evaluation set of 914 instances whose edits are guaranteed to be supported by the evidence. We provide benchmark results for popular generation systems as well as EDIT5 – a T5-based approach tailored to editing we introduce that establishes the state of the art. Our analysis shows that developing models that can update articles faithfully requires new capabilities for neural generation models, and opens doors to many new applications."], "field": "Decision Sciences", "q_year": 2025, "q_cid": "278904570", "pos_cid": 245218924, "source": "eval_collection"}
{"query_id": "scaleup_27870265_13473158", "query": "How to optimize sensor placement in large-scale function-space inverse problems when evaluating the design objective and its derivatives is computationally demanding", "pos": ["A Computational Framework for Infinite-Dimensional Bayesian Inverse Problems Part I: The Linearized Case, with Application to Global Seismic Inversion. We present a computational framework for estimating the uncertainty in the numerical solution of linearized infinite-dimensional statistical inverse problems. We adopt the Bayesian inference formulation: given observational data and their uncertainty, the governing forward problem and its uncertainty, and a prior probability distribution describing uncertainty in the parameter field, find the posterior probability distribution over the parameter field. The prior must be chosen appropriately in order to guarantee well-posedness of the infinite-dimensional inverse problem and facilitate computation of the posterior. Furthermore, straightforward discretizations may not lead to convergent approximations of the infinite-dimensional problem. And finally, solution of the discretized inverse problem via explicit construction of the covariance matrix is prohibitive due to the need to solve the forward problem as many times as there are parameters. Our computational framework builds on the infinite-dimensional formulation proposed by Stuart (A. M. Stuart, Inverse problems: A Bayesian perspective, Acta Numerica, 19 (2010), pp. 451-559), and incorporates a number of components aimed at ensuring a convergent discretization of the underlying infinite-dimensional inverse problem. The framework additionally incorporates algorithms for manipulating the prior, constructing a low rank approximation of the data-informed component of the posterior covariance operator, and exploring the posterior that together ensure scalability of the entire framework to very high parameter dimensions. We demonstrate this computational framework on the Bayesian solution of an inverse problem in 3D global seismic wave propagation with hundreds of thousands of parameters."], "field": "Decision Sciences", "q_year": 2024, "q_cid": "278702659", "pos_cid": 13473158, "source": "eval_collection"}
{"query_id": "scaleup_27086939_20882842", "query": "How to set a per-item price for a fixed quantity of perishable goods when the quantity people will buy is uncertain and decreases as the price rises", "pos": ["The price-setting newsvendor: review and extensions. The newsvendor problem is a staple of operations management research, pedagogy and practice. From its humble roots as a single-period problem for a price-taking newspaper seller, this problem (and its solutions) has inspired generations of researchers and students while contributing to inventory management at countless firms. One major extension of the newsvendor problem was the extension of the decision variables to include price as well as quantity. This extension has been known for decades, but recently gained new life, as researchers have expended considerable energy in analysing and exploring this scenario. We trace major developments in the single-period, price- and quantity-setting newsvendor problem in the recent past and propose extensions of these developments. We also extend a relatively unexplored model describing a price-setting newsvendor faced with a fixed stock level to show that there is a unique optimising price and that, as in the price- and quantity-setting newsvendor problem, the optimal price depends heavily on the form of the demand uncertainty."], "field": "Decision Sciences", "q_year": 2024, "q_cid": "270869396", "pos_cid": 208828426, "source": "eval_collection"}
{"query_id": "scaleup_28219326_26142255", "query": "How to clarify the role of users’ confidence in their ability to use teleconsultation in shaping perceived ease of use, perceived usefulness, and adoption intention", "pos": ["Relationship between technology acceptance model, self-regulation strategies, and academic self-efficacy with academic performance and perceived learning among college students during remote education. Introduction The aim of this study was to examine the relationship between the technology acceptance model, self-regulation strategies, and academic self-efficacy with academic performance and perceived learning among college students during remote education. Methods The participants were 301 university students from Lima. Structural equation model was used to test the proposed theoretical relationships between the variables. On the one hand, the study sought to explore the relationship between academic self-efficacy and self-regulation strategies with the technology acceptance model. On the other hand, it sought to determine whether the three dimensions of the technology acceptance model are positively related to perceived learning and academic performance. Results The results suggest the importance of improving psychological variables such as self-efficacy and self-regulation strategies to improve the acceptance of technology, which would also improve the academic performance and perceived learning of students in a virtual environment. Discussion The discussion highlights the significance of self-efficacy and metacognitive strategies in influencing technology perception and attitudes, ultimately impacting perceived learning and academic performance in virtual education."], "field": "Decision Sciences", "q_year": 2025, "q_cid": "282193266", "pos_cid": 261422557, "source": "eval_collection"}
{"query_id": "scaleup_26841737_20164630", "query": "How to predict company risk and correlation from long, jargon-heavy financial reports dominated by boilerplate and containing few meaningful signals about future prospects", "pos": ["Sentence-BERT: Sentence Embeddings using Siamese BERT-Networks. BERT (Devlin et al., 2018) and RoBERTa (Liu et al., 2019) has set a new state-of-the-art performance on sentence-pair regression tasks like semantic textual similarity (STS). However, it requires that both sentences are fed into the network, which causes a massive computational overhead: Finding the most similar pair in a collection of 10,000 sentences requires about 50 million inference computations (~65 hours) with BERT. The construction of BERT makes it unsuitable for semantic similarity search as well as for unsupervised tasks like clustering. In this publication, we present Sentence-BERT (SBERT), a modification of the pretrained BERT network that use siamese and triplet network structures to derive semantically meaningful sentence embeddings that can be compared using cosine-similarity. This reduces the effort for finding the most similar pair from 65 hours with BERT / RoBERTa to about 5 seconds with SBERT, while maintaining the accuracy from BERT. We evaluate SBERT and SRoBERTa on common STS tasks and transfer learning tasks, where it outperforms other state-of-the-art sentence embeddings methods."], "field": "Decision Sciences", "q_year": 2024, "q_cid": "268417377", "pos_cid": 201646309, "source": "eval_collection"}
{"query_id": "scaleup_27704789_21694946", "query": "How to understand consumer trust recovery following a corporate apology after a brand crisis", "pos": ["Stereotype Content: Warmth and Competence Endure. Two dimensions persist in social cognition when people are making sense of individuals or groups. The stereotype content model (SCM) terms these two basic dimensions perceived warmth (trustworthiness, friendliness) and competence (capability, assertiveness). Measured reliably and validly, these Big Two dimensions converge across survey, cultural, laboratory, and biobehavioral approaches. Generality across place, levels, and time further support the framework. Similar dimensions have emerged repeatedly over the history of psychology and in current theories. The SCM proposes and tests a comprehensive causal theory: Perceived social structure (cooperation, status) predicts stereotypes (warmth, competence), which in turn predict emotional prejudices (pride, pity, contempt, envy), and finally, the emotions predict discrimination (active and passive help and harm). The SCM uncovers systematic content and dynamics of stereotypes, which has practical implications."], "field": "Decision Sciences", "q_year": 2025, "q_cid": "277047896", "pos_cid": 21694946, "source": "eval_collection"}
{"query_id": "scaleup_23963188_15439476", "query": "How to establish the relative importance of time, cost, and quality in construction scheduling to reflect experts’ judgments and decision-makers’ preferences", "pos": ["Selection of rational dispute resolution method by applying new step‐wise weight assessment ratio analysis (Swara). Abstract The paper considers major principles of application of the multi‐attribute systems to solve legislative tasks. In order to assess dispute resolution methods from economic, social and other points of view, it is necessary to apply methods for assessing solutions according to multiple attributes. All known multi‐attribute methods cannot value the atribute weights as one weight of attribute is higher or lower significant than the other attribute. The new step‐wise weight assessment ratio analysis method (SWARA) allows including experts, lawyers or dispute parties opinion about significance ratio of the attributes in the process of rational decision determination. SWARA method could be applied in practical implementation of specialised decision support systems and alternative dispute resolution in virtual environment. Starting with principles and established approaches, a problem‐structuring methodology was developed which would condition the problem to allow a more thoughtful application of existing..."], "field": "Decision Sciences", "q_year": 2021, "q_cid": "239631888", "pos_cid": 154394761, "source": "eval_collection"}
{"query_id": "scaleup_23535818_1671874", "query": "How to identify hierarchical and equal-level relationships between table cells based on their meanings", "pos": ["WordNet: A Lexical Database for English. Because meaningful sentences are composed of meaningful words, any system that hopes to process natural languages as people do must have information about words and their meanings. This information is traditionally provided through dictionaries, and machine-readable dictionaries are now widely available. But dictionary entries evolved for the convenience of human readers, not for machines. WordNet1 provides a more effective combination of traditional lexicographic information and modern computing. WordNet is an online lexical database designed for use under program control. English nouns, verbs, adjectives, and adverbs are organized into sets of synonyms, each representing a lexicalized concept. Semantic relations link the synonym sets [4]."], "field": "Decision Sciences", "q_year": 2021, "q_cid": "235358189", "pos_cid": 1671874, "source": "eval_collection"}
{"query_id": "scaleup_27596027_29692856", "query": "How to coordinate participation among researchers and other contributors in developing an environmental credentials platform", "pos": ["Coordination and Participation in Living Lab Networks. Previous research on living labs has emphasized the importance of users and a real-life environment. However, the existing scholarly discourse lacks understanding of innovation mechanisms in diverse living lab networks, especially from the perspectives of coordination and participation. This study addresses the research gaps by constructing a framework for analyzing coordination (i.e., top-down versus bottom-up) and participation (i.e., inhalation-dominated versus exhalation-dominated) approaches in living lab networks. The classification is based on a literature review and an analysis of 26 living labs in four countries. Given that inhalation and exhalation dominance have not been discussed previously in the innovation literature, the study provides novel ways for both scholars and managers wishing to exploit or explore innovations in living labs. The framework reveals the opportunities for practitioners of innovation with respect to coordination and participation in living lab networks. To raise new questions, new possibilities, to regard old problems from a new angle, requires creative imagination and marks real advance in science."], "field": "Decision Sciences", "q_year": 2024, "q_cid": "275960276", "pos_cid": 29692856, "source": "train_step3"}
{"query_id": "scaleup_25925189_24056009", "query": "How to estimate the effect of early arXiving while ensuring early-arXived and non-early-arXived papers are comparable in author count, submission year, and overall topic distribution", "pos": ["Matching One Sample According to Two Criteria in Observational Studies. Abstract Multivariate matching has two goals (i) to construct treated and control groups that have similar distributions of observed covariates, and (ii) to produce matched pairs or sets that are homogeneous in a few key covariates. When there are only a few binary covariates, both goals may be achieved by matching exactly for these few covariates. Commonly, however, there are many covariates, so goals (i) and (ii) come apart, and must be achieved by different means. As is also true in a randomized experiment, similar distributions can be achieved for a high-dimensional covariate, but close pairs can be achieved for only a few covariates. We introduce a new polynomial-time method for achieving both goals that substantially generalizes several existing methods; in particular, it can minimize the earthmover distance between two marginal distributions. The method involves minimum cost flow optimization in a network built around a tripartite graph, unlike the usual network built around a bipartite graph. In the tripartite graph, treated subjects appear twice, on the far left and the far right, with controls sandwiched between them, and efforts to balance covariates are represented on the right, while efforts to find close individual pairs are represented on the left. In this way, the two efforts may be pursued simultaneously without conflict. The method is applied to our on-going study in the Medicare population of the relationship between superior nursing and sepsis mortality. The match2C package in R implements the method. Supplementary materials for this article are available online."], "field": "Decision Sciences", "q_year": 2023, "q_cid": "259251893", "pos_cid": 240560096, "source": "train_step3"}
{"query_id": "scaleup_25406949_19521869", "query": "How to align entities while ensuring compatible predictions for interdependent entities when fitting labelled alignments alone is insufficient", "pos": ["Probabilistic Logic Neural Networks for Reasoning. Knowledge graph reasoning, which aims at predicting the missing facts through reasoning with the observed facts, is critical to many applications. Such a problem has been widely explored by traditional logic rule-based approaches and recent knowledge graph embedding methods. A principled logic rule-based approach is the Markov Logic Network (MLN), which is able to leverage domain knowledge with first-order logic and meanwhile handle their uncertainty. However, the inference of MLNs is usually very difficult due to the complicated graph structures. Different from MLNs, knowledge graph embedding methods (e.g. TransE, DistMult) learn effective entity and relation embeddings for reasoning, which are much more effective and efficient. However, they are unable to leverage domain knowledge. In this paper, we propose the probabilistic Logic Neural Network (pLogicNet), which combines the advantages of both methods. A pLogicNet defines the joint distribution of all possible triplets by using a Markov logic network with first-order logic, which can be efficiently optimized with the variational EM algorithm. In the E-step, a knowledge graph embedding model is used for inferring the missing triplets, while in the M-step, the weights of logic rules are updated based on both the observed and predicted triplets. Experiments on multiple knowledge graphs prove the effectiveness of pLogicNet over many competitive baselines."], "field": "Decision Sciences", "q_year": 2022, "q_cid": "254069490", "pos_cid": 195218696, "source": "train_step3"}
{"query_id": "scaleup_22497726_46997957", "query": "How to distinguish closely interconnected nodes within the same communities in a scientific-literature citation network and completely map the technology evolution path", "pos": ["Relation extraction for biological pathway construction using node2vec. Systems biology is an important field for understanding whole biological mechanisms composed of interactions between biological components. One approach for understanding complex and diverse mechanisms is to analyze biological pathways. However, because these pathways consist of important interactions and information on these interactions is disseminated in a large number of biomedical reports, text-mining techniques are essential for extracting these relationships automatically. In this study, we applied node2vec, an algorithmic framework for feature learning in networks, for relationship extraction. To this end, we extracted genes from paper abstracts using pkde4j, a text-mining tool for detecting entities and relationships. Using the extracted genes, a co-occurrence network was constructed and node2vec was used with the network to generate a latent representation. To demonstrate the efficacy of node2vec in extracting relationships between genes, performance was evaluated for gene-gene interactions involved in a type 2 diabetes pathway. Moreover, we compared the results of node2vec to those of baseline methods such as co-occurrence and DeepWalk. Node2vec outperformed existing methods in detecting relationships in the type 2 diabetes pathway, demonstrating that this method is appropriate for capturing the relatedness between pairs of biological entities involved in biological pathways. The results demonstrated that node2vec is useful for automatic pathway construction."], "field": "Decision Sciences", "q_year": 2020, "q_cid": "224977262", "pos_cid": 46997957, "source": "train_step3"}
{"query_id": "scaleup_27035776_26020284", "query": "How to accelerate action synthesis in diffusion-based robotic policies for faster responses to new observations without sacrificing accuracy or action diversity", "pos": ["TEDi: Temporally-Entangled Diffusion for Long-Term Motion Synthesis. The gradual nature of a diffusion process that synthesizes samples in small increments constitutes a key ingredient of Denoising Diffusion Probabilistic Models (DDPM), which have presented unprecedented quality in image synthesis and been recently explored in the motion domain. In this work, we propose to adapt the gradual diffusion concept (operating along a diffusion time-axis) into the temporal-axis of the motion sequence. Our key idea is to extend the DDPM framework to support temporally varying denoising, thereby entangling the two axes. Using our special formulation, we iteratively denoise a motion buffer that contains a set of increasingly-noised poses, which auto-regressively produces an arbitrarily long stream of frames. With a stationary diffusion time-axis, in each diffusion step we increment only the temporal-axis of the motion such that the framework produces a new, clean frame which is removed from the beginning of the buffer, followed by a newly drawn noise vector that is appended to it. This new mechanism paves the way towards a new framework for long-term motion synthesis with applications to character animation and other domains."], "field": "Decision Sciences", "q_year": 2024, "q_cid": "270357764", "pos_cid": 260202842, "source": "train_step3"}
{"query_id": "scaleup_23544240_20584435", "query": "How to determine the number of studies needed per examined factor to avoid false links with treatment effects in combined study-level findings", "pos": ["The number of subjects per variable required in linear regression analyses.. OBJECTIVES To determine the number of independent variables that can be included in a linear regression model. STUDY DESIGN AND SETTING We used a series of Monte Carlo simulations to examine the impact of the number of subjects per variable (SPV) on the accuracy of estimated regression coefficients and standard errors, on the empirical coverage of estimated confidence intervals, and on the accuracy of the estimated R(2) of the fitted model. RESULTS A minimum of approximately two SPV tended to result in estimation of regression coefficients with relative bias of less than 10%. Furthermore, with this minimum number of SPV, the standard errors of the regression coefficients were accurately estimated and estimated confidence intervals had approximately the advertised coverage rates. A much higher number of SPV were necessary to minimize bias in estimating the model R(2), although adjusted R(2) estimates behaved well. The bias in estimating the model R(2) statistic was inversely proportional to the magnitude of the proportion of variation explained by the population regression model. CONCLUSION Linear regression models require only two SPV for adequate estimation of regression coefficients, standard errors, and confidence intervals."], "field": "Decision Sciences", "q_year": 2021, "q_cid": "235442403", "pos_cid": 205844358, "source": "train_step3"}
{"query_id": "scaleup_27298798_13693120", "query": "How to establish sufficiently comparable groups of Reddit users who do and do not receive positive feedback for a credible causal assessment of behavioral changes", "pos": ["Using Longitudinal Social Media Analysis to Understand the Effects of Early College Alcohol Use. While college completion is predictive of individual career happiness and economic achievement, many factors, such as excessive alcohol usage, jeopardize college success. In this paper, we propose a method for analyzing large-scale, longitudinal social media timelines to provide fine-grained visibility into how the behaviors and trajectories of alcohol-mentioning students differ from their peers. Using propensity score stratification to reduce bias from confounding factors, we analyze the Twitter data of 63k college students over 5 years to study the effect of early alcohol usage on topics linked to college success. We find multi-year effects, including lower mentions of study habits, increased mentions of potentially risky behaviors, and decreases in mentions of positive emotions. We conclude with a discussion of social media data's role in the study of the risky behaviors of college students and other individual behaviors with long-term effects."], "field": "Decision Sciences", "q_year": 2024, "q_cid": "272987983", "pos_cid": 13693120, "source": "train_step3"}
{"query_id": "scaleup_27337519_24779385", "query": "How to obtain disentangled representations of individual-specific exogenous noise for correct causal effect identification in counterfactual generative modeling when paired outcomes under different interventions are unavailable", "pos": ["Weakly supervised causal representation learning. Learning high-level causal representations together with a causal model from unstructured low-level data such as pixels is impossible from observational data alone. We prove under mild assumptions that this representation is however identifiable in a weakly supervised setting. This involves a dataset with paired samples before and after random, unknown interventions, but no further labels. We then introduce implicit latent causal models, variational autoencoders that represent causal variables and causal structure without having to optimize an explicit discrete graph structure. On simple image data, including a novel dataset of simulated robotic manipulation, we demonstrate that such models can reliably identify the causal structure and disentangle causal variables."], "field": "Decision Sciences", "q_year": 2024, "q_cid": "273375194", "pos_cid": 247793853, "source": "train_step3"}
{"query_id": "scaleup_25947825_19788564", "query": "How to achieve a more parsimonious representation of overlapping innovation characteristics while retaining information fidelity and addressing excessive relationships between lower-order and dependent constructs and collinearity concerns among formative indicators", "pos": ["How to Specify, Estimate, and Validate Higher-Order Constructs in PLS-SEM. Higher-order constructs, which facilitate modeling a construct on a more abstract higher-level dimension and its more concrete lower-order subdimensions, have become an increasingly visible trend in applications of partial least squares structural equation modeling (PLS-SEM). Unfortunately, researchers frequently confuse the specification, estimation, and validation of higher-order constructs, for example, when it comes to assessing their reliability and validity. Addressing this concern, this paper explains how to evaluate the results of higher-order constructs in PLS-SEM using the repeated indicators and the two-stage approaches, which feature prominently in applied social sciences research. Focusing on the reflective-reflective and reflective-formative types of higher-order constructs, we use the well-known corporate reputation model example to illustrate their specification, estimation, and validation. Thereby, we provide the guidance that scholars, marketing researchers, and practitioners need when using higher-order constructs in their studies."], "field": "Decision Sciences", "q_year": 2023, "q_cid": "259478259", "pos_cid": 197885643, "source": "train_step3"}
{"query_id": "scaleup_25351037_15475452", "query": "How to select among multiple candidate inconsistency factors while accounting for the number of candidates", "pos": ["Bayes and empirical-Bayes multiplicity adjustment in the variable-selection problem. This paper studies the multiplicity-correction effect of standard Bayesian variable-selection priors in linear regression. Our first goal is to clarify when, and how, multiplicity correction happens automatically in Bayesian analysis, and to distinguish this correction from the Bayesian Ockham's-razor effect. Our second goal is to contrast empirical-Bayes and fully Bayesian approaches to variable selection through examples, theoretical results and simulations. Considerable differences between the two approaches are found. In particular, we prove a theorem that characterizes a surprising aymptotic discrepancy between fully Bayes and empirical Bayes. This discrepancy arises from a different source than the failure to account for hyperparameter uncertainty in the empirical-Bayes estimate. Indeed, even at the extreme, when the empirical-Bayes estimate converges asymptotically to the true variable-inclusion probability, the potential for a serious difference remains."], "field": "Decision Sciences", "q_year": 2022, "q_cid": "253510375", "pos_cid": 15475452, "source": "train_step3"}
{"query_id": "scaleup_28282126_23569777", "query": "How to identify which risky choices are relevant in everyday life and matter to a large number of citizens in a complex, fast-changing world", "pos": ["Human social sensing is an untapped resource for computational social science. The ability to ‘sense’ the social environment and thereby to understand the thoughts and actions of others allows humans to fit into their social worlds, communicate and cooperate, and learn from others’ experiences. Here we argue that, through the lens of computational social science, this ability can be used to advance research into human sociality. When strategically selected to represent a specific population of interest, human social sensors can help to describe and predict societal trends. In addition, their reports of how they experience their social worlds can help to build models of social dynamics that are constrained by the empirical reality of human social systems. The ability of people to understand the thoughts and actions of others—known as social sensing—can be combined with computational social science to advance research into human sociality."], "field": "Decision Sciences", "q_year": 2025, "q_cid": "282821265", "pos_cid": 235697772, "source": "train_step3"}
{"query_id": "scaleup_26976353_20711327", "query": "How to determine how contextual changes affect each individual’s willingness to delegate decisions to an algorithm, apart from differences associated with personal characteristics", "pos": ["Ensemble methods for uplift modeling. Uplift modeling is a branch of machine learning which aims at predicting the causal effect of an action such as a marketing campaign or a medical treatment on a given individual by taking into account responses in a treatment group, containing individuals subject to the action, and a control group serving as a background. The resulting model can then be used to select individuals for whom the action will be most profitable. This paper analyzes the use of ensemble methods: bagging and random forests in uplift modeling. We perform an extensive experimental evaluation to demonstrate that the application of those methods often results in spectacular gains in model performance, turning almost useless single models into highly capable uplift ensembles. The gains are much larger than those achieved in case of standard classification. We show that those gains are a result of high ensemble diversity, which in turn is a result of the differences between class probabilities in the treatment and control groups being harder to model than the class probabilities themselves. The feature of uplift modeling which makes it difficult thus also makes it amenable to the application of ensemble methods. As a result, bagging and random forests emerge from our evaluation as key tools in the uplift modeling toolbox."], "field": "Decision Sciences", "q_year": 2024, "q_cid": "269763534", "pos_cid": 207113272, "source": "train_step3"}
{"query_id": "scaleup_4086615_14415824", "query": "How to determine how long fixed tooth-supported restorations last without underestimating their longevity", "pos": ["Survival Analysis Part I: Basic concepts and first analyses. Survival analysis is a collection of statistical procedures for data analysis where the outcome variable of interest is time until an event occurs. Because of censoring–the nonobservation of the event of interest after a period of follow-up–a proportion of the survival times of interest will often be unknown. It is assumed that those patients who are censored have the same survival prospects as those who continue to be followed, that is, the censoring is uninformative. Survival data are generally described and modelled in terms of two related functions, the survivor function and the hazard function. The survivor function represents the probability that an individual survives from the time of origin to some time beyond time t. It directly describes the survival experience of a study cohort, and is usually estimated by the KM method. The logrank test may be used to test for differences between survival curves for groups, such as treatment arms. The hazard function gives the instantaneous potential of having an event at a time, given survival up to that time. It is used primarily as a diagnostic tool or for specifying a mathematical model for survival analysis. In comparing treatments or prognostic groups in terms of survival, it is often necessary to adjust for patient-related factors that could potentially affect the survival time of a patient. Failure to adjust for confounders may result in spurious effects. Multivariate survival analysis, a form of multiple regression, provides a way of doing this adjustment, and is the subject the next paper in this series."], "field": "Dentistry", "q_year": 2014, "q_cid": "4086615", "pos_cid": 14415824, "source": "eval20x26"}
{"query_id": "scaleup_12522998_1843083", "query": "How to identify statistically significant differences in relative abundance across classification levels between two groups of children", "pos": ["Statistical Methods for Detecting Differentially Abundant Features in Clinical Metagenomic Samples. Numerous studies are currently underway to characterize the microbial communities inhabiting our world. These studies aim to dramatically expand our understanding of the microbial biosphere and, more importantly, hope to reveal the secrets of the complex symbiotic relationship between us and our commensal bacterial microflora. An important prerequisite for such discoveries are computational tools that are able to rapidly and accurately compare large datasets generated from complex bacterial communities to identify features that distinguish them. We present a statistical method for comparing clinical metagenomic samples from two treatment populations on the basis of count data (e.g. as obtained through sequencing) to detect differentially abundant features. Our method, Metastats, employs the false discovery rate to improve specificity in high-complexity environments, and separately handles sparsely-sampled features using Fisher's exact test. Under a variety of simulations, we show that Metastats performs well compared to previously used methods, and significantly outperforms other methods for features with sparse counts. We demonstrate the utility of our method on several datasets including a 16S rRNA survey of obese and lean human gut microbiomes, COG functional profiles of infant and mature gut microbiomes, and bacterial and viral metabolic subsystem data inferred from random sequencing of 85 metagenomes. The application of our method to the obesity dataset reveals differences between obese and lean subjects not reported in the original study. For the COG and subsystem datasets, we provide the first statistically rigorous assessment of the differences between these populations. The methods described in this paper are the first to address clinical metagenomic datasets comprising samples from multiple subjects. Our methods are robust across datasets of varied complexity and sampling level. While designed for metagenomic applications, our software can also be applied to digital gene expression studies (e.g. SAGE). A web server implementation of our methods and freely available source code can be found at http://metastats.cbcb.umd.edu/."], "field": "Dentistry", "q_year": 2014, "q_cid": "12522998", "pos_cid": 1843083, "source": "eval20x26"}
{"query_id": "scaleup_15706695_10184700", "query": "How to fully account for socioeconomic position’s contribution to ethnic inequalities in health and avoid residual confounding when it may be inadequately captured across ethnic groups", "pos": ["The applicability of measures of socioeconomic position to different ethnic groups within the UK. BackgroundIn this paper we seek to tease out differences in socioeconomic position between ethnic groups. There are 3 main reasons why conventional socioeconomic indicators and asset based measures may not be equally applicable to all ethnic groups:1) Differences in response rate to conventional socioeconomic indicators2) Cultural and social differences in economic priorities/opportunities3) Differences in housing quality, assets and debt within socioeconomic strataMethodsThe sample consisted of White (n = 227), African-Caribbean (n = 213) and Indian and Pakistani (n = 233) adults aged between 18 and 59 years living in Leeds as measured in a stratified population survey. Measures included income, education, employment, car ownership, home ownership, housing quality, household assets, investments, debt, perceived ability to obtain various sums and perceived level of financial support given and received.ResultsResponse rates to education and income questions were similar for the different ethnic groups. Overall response rates for income were much lower than those for education and biased towards wealthier people. There were differences between ethnic groups in economic priorities/opportunities particularly in relation to car ownership, home ownership, investment and debt. Differences in living conditions, household assets and debt between ethnic groups were dependent on differences in education; however differences in car ownership, home ownership, ability to obtain £10 000, and loaning money to family/friends and income from employment/self employment persisted after adjustment for education.ConclusionIn the UK, education appears to be an effective variable for measuring variation in SEP across ethnic groups but the ability to account for SEP differences may be improved by the addition of car and home ownership, ability to obtain £10 000, loaning money to family/friends and income from employment/self employment. Further research is required to establish the degree to which results of this study are generalisable."], "field": "Dentistry", "q_year": 2019, "q_cid": "157066951", "pos_cid": 10184700, "source": "eval20x26"}
{"query_id": "scaleup_52179461_21369860", "query": "How to explain the embedding of an auxiliary device’s pointed tips in newly formed bone at the cortical surface", "pos": ["Vertical osteoconductive characteristics of titanium implants with calcium-phosphate-coated surfaces - a pilot study in rabbits.. INTRODUCTION Osteoconductive characteristics of different implant surface coatings are in the focus of current interest. The aim of the present study was to compare the vertical osteoconductivity at the implant shoulder of supracrestal inserted calcium-phosphate coated implants (SLA-CaP) with conventional sand-blasted/acid-etched (SLA) implants in a rabbit model. MATERIALS AND METHODS SLA-CaP and SLA implants were inserted bilaterally in the mandible of four rabbits in a split-mouth design. The implants were placed 2 mm supracrestal. After 3 weeks, at the left and right implant shoulder, the percentage of linear bone fill (PLF) as well as bone-implant contact (BIC-D) were determined. RESULTS After 3 weeks, newly formed woven bone could be found at the shoulder of the most of both surface-treated implants (75%). PLF was significantly higher in SLA-CaP implants (11.2% vs. 46.5%; n = 8, p = .008). BIC-D was significantly increased in the SLA-CaP implants (13.0% vs. 71.4%; n = 8, p < .001) as well. CONCLUSION The results of this study show for the first time that calcium-phosphate coated surfaces on supracrestal inserted implants have vertical osteoconductive characteristics and increase the bone-implant contact at the implant shoulder significantly in a rabbit model. In clinical long-term settings, these implants may contribute to a better vertical bone height."], "field": "Dentistry", "q_year": 2018, "q_cid": "52179461", "pos_cid": 21369860, "source": "eval20x26"}
{"query_id": "scaleup_3105394_13670028", "query": "How to compare the extent of silane grafting on differently treated denture-base surfaces to clarify chemical interactions underlying bonding to a silicone soft liner", "pos": ["EFFECT OF POLYMER STRUCTURE AND ADDITIVES ON SILANE GRAFTING OF POLYETHYLENE. Silane method is a preferred method in crosslinking polyethylene to modify its properties. Here, the silane graft- ing reactions of low density (LDPE), linear low density (LLDPE) and high density polyethylene (HDPE) were compared, all with a fixed amount of silane (vinyltrimethoxysilane) and peroxide (dicumylperoxide). Processing for silane grafting was carried out in an internal mixer, and FTIR spectra were used for comparing the silane grafting efficiencies. The effect of polymer physical form and pre-mixing the components was also determined. Molecular structure parameters were ana- lyzed to investigate their effect on silane grafting efficiency. In case of LDPE and LLDPE, the probable interfering effect of two types of antioxidants on silane grafting reactions was studied. Ethylene propylene diene monomer (EPDM) was added to LDPE to evaluate its effect on silane grafting efficiency. Amongst different grades of polyethylene, LLDPE had a better efficiency in silane grafting. Branchings, PDI, Mw, and MFI are all determining factors and should be considered in comparing the silane grafting efficiency between different grades of polyethylene. In case of incorporating antioxidant, dif- ferent results were observed when the polymer under study was different. EPDM as an additive would enhance silane graft- ing efficiency."], "field": "Dentistry", "q_year": 2013, "q_cid": "3105394", "pos_cid": 13670028, "source": "eval20x26"}
{"query_id": "scaleup_18429344_23782947", "query": "How to limit inflammatory responses in P. gingivalis–infected cells while preserving their tissue-forming capacity", "pos": ["IL-6 is produced by osteoblasts and induces bone resorption.. To examine the possible involvement of IL-6 in bone metabolism, a mouse osteoblastic cell line (MC3T3-E1) and primary osteoblast-like cells from fetal mouse calvaria were cultured with several systemic and local bone-resorbing agents and their expression of IL-6 mRNA was determined. Local bone-resorbing agents such as IL-1 alpha, IL-1 beta, TNF-alpha, and LPS greatly induced IL-6 mRNA expression in both MC3T3-E1 cells and primary osteoblast-like cells. Parathyroid hormone slightly increased expression of IL-6 mRNA in primary osteoblast-like cells but not in MC3T3-E1 cells. Neither IL-6 nor 1 alpha,25-dihydroxyvitamin D3 increased expression of IL-6 mRNA in either of the osteoblast-like cells. In agreement with the expression of IL-6 mRNA, biologically active IL-6 was produced in response to the treatment with IL-1 alpha, TNF-alpha, and LPS in MC3T3-E1 cells. Adding IL-6 dose dependently stimulated the release of 45Ca from prelabeled fetal mouse calvaria. Simultaneously adding suboptimal concentrations of IL-6 and IL-1 alpha induced bone resorption cooperatively. In accord with the increase in the release of 45Ca by IL-6, there were three times as many osteoclasts in the bone sections of calvaria cultured with IL-6 for 5 days as in the controls. IL-6 slightly suppressed alkaline phosphatase activity and collagen synthesis in MC3T3-E1 cells. These results indicate that IL-6 is also produced by osteoblasts, preferentially in response to local bone-resorbing agents, and it induces bone resorption both alone and in concert with other bone-resorbing agents."], "field": "Dentistry", "q_year": 2017, "q_cid": "18429344", "pos_cid": 23782947, "source": "eval20x26"}
{"query_id": "scaleup_52179461_55133097", "query": "How to distinguish the effects of auxiliary-device presence and implantation duration on miniscrew displacement under lateral loading across multiple experimental groups and time points", "pos": ["Nonparametric analysis of longitudinal data in factorial experiments. Preface. Acknowledgments. Introduction. Models. Effects and Hypotheses. Estimators for Relative Effects. Test Statistics. Software. Experiments for One Group of Subjects. Experiements for Several Groups of Subjects. Dependent Replications. Multifactorial Experiments. Numerous Time Points. References. Appendix A: Original Data. Appendix B: Results from the SAS Macros. Glossary. Index."], "field": "Dentistry", "q_year": 2018, "q_cid": "52179461", "pos_cid": 55133097, "source": "eval20x26"}
{"query_id": "scaleup_23698357_12463037", "query": "How to determine where epinephrine is stored in human neutrophils and what is required for its release in response to A. actinomycetemcomitans", "pos": ["Exocytosis of Neutrophil Granule Subsets and Activation of Prolyl Isomerase 1 are required for Respiratory Burst Priming. This study tested the hypothesis that priming the neutrophil respiratory burst requires both granule exocytosis and activation of the prolyl isomerase Pin1. Fusion proteins containing the TAT cell permeability sequence and either the SNARE domain of syntaxin-4 or the N-terminal SNARE domain of SNAP-23 were used to examine the role of granule subsets in TNF-mediated respiratory burst priming using human neutrophils. Concentration-inhibition curves for exocytosis of individual granule subsets and for priming of fMLF-stimulated superoxide release and phagocytosis-stimulated H2O2 production were generated. Maximal inhibition of priming ranged from 72 to 88%. Linear regression lines for inhibition of priming versus inhibition of exocytosis did not differ from the line of identity for secretory vesicles and gelatinase granules, while the slopes or the y-intercepts were different from the line of identity for specific and azurophilic granules. Inhibition of Pin1 reduced priming by 56%, while exocytosis of secretory vesicles and specific granules was not affected. These findings indicate that exocytosis of secretory vesicles and gelatinase granules and activation of Pin1 are independent events required for TNF-mediated priming of neutrophil respiratory burst."], "field": "Dentistry", "q_year": 2021, "q_cid": "236983573", "pos_cid": 12463037, "source": "eval_collection"}
{"query_id": "scaleup_24712967_15706359", "query": "How to assess the effects of polyphenolic-coated titanium on host immune responses and blood compatibility", "pos": ["Complement System Part I – Molecular Mechanisms of Activation and Regulation. Complement is a complex innate immune surveillance system, playing a key role in defense against pathogens and in host homeostasis. The complement system is initiated by conformational changes in recognition molecular complexes upon sensing danger signals. The subsequent cascade of enzymatic reactions is tightly regulated to assure that complement is activated only at specific locations requiring defense against pathogens, thus avoiding host tissue damage. Here, we discuss the recent advances describing the molecular and structural basis of activation and regulation of the complement pathways and their implication on physiology and pathology. This article will review the mechanisms of activation of alternative, classical, and lectin pathways, the formation of C3 and C5 convertases, the action of anaphylatoxins, and the membrane-attack-complex. We will also discuss the importance of structure–function relationships using the example of atypical hemolytic uremic syndrome. Lastly, we will discuss the development and benefits of therapies using complement inhibitors."], "field": "Dentistry", "q_year": 2022, "q_cid": "247129671", "pos_cid": 15706359, "source": "eval_collection"}
{"query_id": "scaleup_24708176_21577436", "query": "How to understand what drives or limits parents’ and caregivers’ online searches for early childhood caries information when disease burden alone may not explain their motivation", "pos": ["Online Health Information Seeking: A Review and Meta-Analysis. ABSTRACT Online health information, as an emerging field in health communication research, has attracted close attention from researchers. To identify major determinants of why individuals seek health information online, we conducted a meta-analysis that systematically accumulates the existing research findings. To that end, by integrating three theories or models for examining information-seeking behavior, we developed a theoretical framework for the current meta-analysis that emphasizing psychosocial, instrumental, contextual, and demographic factors. By analyzing the effect sizes from 44 articles representing 54 empirical samples, we found that the quality, trustworthiness, and utility of online health information were the dominant predictors of seeking it and that instrumental factors were more important than psychological ones in determining whether individuals did so. Moreover, the development of information and communication technology, the sampling method, and the type of information sought significantly moderated pairwise relationships between determinants and seeking behavior, whereas culture did not. Herein, we discuss the theoretical implications of our findings as well as directions for future research."], "field": "Dentistry", "q_year": 2022, "q_cid": "247081764", "pos_cid": 215774367, "source": "eval_collection"}
{"query_id": "scaleup_23521439_36473197", "query": "How to achieve high polymer conversion and resistance to hydrolysis and solvent exposure in dental composite resins in the oral environment", "pos": ["Ester-free Thiol-X Resins: New Materials with Enhanced Mechanical Behavior and Solvent Resistance. A series of thiol-Michael and radical thiol-ene network polymers were successfully prepared from ester-free as well as ester-containing monomer formulations. Polymerization reaction rates, dynamic mechanical analysis, and solvent resistance experiments were performed and compared between compositions with varied ester loading. The incorporation of ester-free alkyl thiol, vinyl sulfone and allylic monomers significantly improved the mechanical properties when compared with commercial, mercaptopropionate-based thiol-ene or thiol-Michael networks. For polymers with no hydrolytically degradable esters, glass transition temperatures (Tg's) as high as 100 °C were achieved. Importantly, solvent resistance tests demonstrated enhanced stability of ester-free formulations over PETMP-based polymers, especially in concentrated basic solutions. Kinetic analysis showed that glassy step-growth polymers are readily formed at ambient conditions with conversions reaching 80% and higher."], "field": "Dentistry", "q_year": 2021, "q_cid": "235214391", "pos_cid": 36473197, "source": "eval_collection"}
{"query_id": "scaleup_25726447_71144645", "query": "How to clarify whether the oral microbiome merely reflects dietary intake or also influences taste preferences and eating habits", "pos": ["New insights into the relationship between taste perception and oral microbiota composition. Fairly poor data are available on the relationship between taste perception, food preferences and oral microbiota. In the present study, we investigated the hypothesis that subjects with higher responsiveness to 6-n-propylthiuracil (PROP) might be characterized by a different taste sensitivity and tongue microbiota composition. Indeed, the bacterial metabolism may modulate/enhance the concentration of tastants near the taste receptors, modifying taste perception through a sensorial adaptation mechanism or by a broad range of microbial metabolic pathways. The detection thresholds of sweet, sour, salty and bitter, the Fungiform Papillae Density (FPD) and the composition of bacteria lining the tongue were determined in Supertasters (high PROP responsiveness, ST) and Non-tasters (low PROP responsiveness, NT). An important inter-individual variability was found for all taste stimuli and FPD between the two groups, with NT subjects showing significant higher threshold values and a lower FPD than with STs. We found five bacterial genera whose relative abundances were significantly higher in STs than NTs. This study opens new avenues of research by highlighting associations between parameters usually studied independently."], "field": "Dentistry", "q_year": 2023, "q_cid": "257264472", "pos_cid": 71144645, "source": "eval_collection"}
{"query_id": "scaleup_24776644_5914432", "query": "How to understand why initiatives succeed or fail as they develop over time and inform future implementation and planning", "pos": ["‘Doing’ health policy analysis: methodological and conceptual reflections and challenges. The case for undertaking policy analysis has been made by a number of scholars and practitioners. However, there has been much less attention given to how to do policy analysis, what research designs, theories or methods best inform policy analysis. This paper begins by looking at the health policy environment, and some of the challenges to researching this highly complex phenomenon. It focuses on research in middle and low income countries, drawing on some of the frameworks and theories, methodologies and designs that can be used in health policy analysis, giving examples from recent studies. The implications of case studies and of temporality in research design are explored. Attention is drawn to the roles of the policy researcher and the importance of reflexivity and researcher positionality in the research process. The final section explores ways of advancing the field of health policy analysis with recommendations on theory, methodology and researcher reflexivity."], "field": "Dentistry", "q_year": 2022, "q_cid": "247766443", "pos_cid": 5914432, "source": "eval_collection"}
{"query_id": "scaleup_25724100_23374340", "query": "How to achieve effective local decontamination and control microbial biofilms and inflammation without antimicrobial side effects", "pos": ["The Treatment of Peri-Implant Diseases: A New Approach Using HYBENX® as a Decontaminant for Implant Surface and Oral Tissues. Background: Peri-implantitis is a pathological condition characterized by an inflammatory process involving soft and hard tissues surrounding dental implants. The management of peri-implant disease has several protocols, among which is the chemical method HYBENX®. The aim of this study is to demonstrate the efficacy of HYBENX® in the treatment of peri-implantitis and to compare HYBENX® with other chemical agents used in the surgical treatment of peri-implantitis. Methods: The present study included a population of ten subjects with severe peri-implantitis. The procedure used in the study involves the application of HYBENX® after open-flap debridement. Each patient has been followed for 12 months after a single application of the decontaminant agent. Clinical and radiographical parameters were recorded at baseline, 3 months, and 12 months after treatment completion. Results: At baseline, a mean pocket probing depth (PPD) of 7.3 ± 0.5 mm and a mean clinical attachment level (CAL) of 8.8 ± 0.8 mm was recorded. An average residual PPD of 4.2 ± 0.5 mm and a mean CAL of 5.2 ± 0.8 mm were observed after 1 year. Additionally, the average of bone gain was about 3.4 mm, with a mean marginal bone level (MBL) change from 5.8 mm (baseline) to 2.4 mm (12 months). In total, 90% of the treated implants reached the success rate after the 1-year follow-up. Only in one case out of ten treated implants was resolution of the disease not achieved. Conclusion: Clinical improvements highlight that the procedure of open-flap debridement (OFD) + HYBENX® may be considered an effective technique in the treatment of peri-implantitis. From the results obtained, it can be concluded that the use of HYBENX® in the surgical treatment of peri-implantitis is promising. Overall, this protocol demands further studies to better understand the role and potential benefits of HYBENX® in the treatment of peri-implantitis."], "field": "Dentistry", "q_year": 2023, "q_cid": "257241006", "pos_cid": 233743401, "source": "eval_collection"}
{"query_id": "scaleup_28096264_37520619", "query": "How to sustain long-term antimicrobial release at dental restoration bonded interfaces to prevent secondary caries and treatment failure without particle destruction, void formation, or loss of interfacial integrity", "pos": ["Drug self-assembly for synthesis of highly-loaded antimicrobial drug-silica particles. Antimicrobial drug release from biomaterials for orthopedic repair and dental restorations can prevent biofilm growth and caries formation. Carriers for drug incorporation would benefit from long-term drug storage, controlled release, and structural stability. Mesoporous silica, synthesized through a co-assembly of silica and surfactant template, is an ideal drug encapsulation scaffold that maintains structural integrity upon release. However, conventional loading of drug within meso-silica pores via concentration-gradient diffusion limits the overall payload, concentration uniformity, and drug release control. Herein we demonstrate the co-assembly of an antimicrobial drug (octenidine dihydrochloride, OCT), and silica, to form highly-loaded (35% wt.) OCT-silica nanocomposite spheres of 500 nm diameter. Drug release significantly outlasted conventional OCT-loaded mesoporous silica, closely fit Higuchi models of diffusive release, and was visualized via electron microscopy. Extension of this concept to the broad collection of self-assembling drugs grants biomedical community a powerful tool for synthesizing drug-loaded inorganic nanomaterials from the bottom-up."], "field": "Dentistry", "q_year": 2025, "q_cid": "280962644", "pos_cid": 37520619, "source": "eval_collection"}
{"query_id": "scaleup_23698357_1374971", "query": "How to identify the host source of catecholamines available to A. actinomycetemcomitans for iron acquisition, growth, and survival in the anaerobic periodontal pocket", "pos": ["Aggregatibacter actinomycetemcomitans QseBC is activated by catecholamines and iron and regulates genes encoding proteins associated with anaerobic respiration and metabolism. Aggregatibacter actinomycetemcomitans QseBC regulates its own expression and is essential for biofilm growth and virulence. However, the signal that activates the QseC sensor has not been identified and the qseBC regulon has not been defined. In this study, we show that QseC is activated by catecholamine hormones and iron but not by either component alone. Activation of QseC requires an EYRDD motif in the periplasmic domain of the sensor and site-specific mutations in EYRDD or the deletion of the periplasmic domain inhibits catecholamine/iron-dependent induction of the ygiW-qseBC operon. Catecholamine/iron-dependent induction of transcription also requires interaction of the QseB response regulator with its binding site in the ygiW-qseBC promoter. Whole genome microarrays were used to compare gene expression profiles of A. actinomycetemcomitans grown in a chemically defined medium with and without catecholamine and iron supplementation. Approximately 11.5% of the A. actinomycetemcomitans genome was differentially expressed by at least two-fold upon exposure to catecholamines and iron. The expression of ferritin was strongly induced, suggesting that intracellular iron storage capacity is increased upon QseBC activation. Consistent with this, genes encoding iron binding and transport proteins were down-regulated by QseBC. Strikingly, 57% of the QseBC up-regulated genes (56/99) encode proteins associated with anaerobic metabolism and respiration. Most of these up-regulated genes were recently reported to be induced during in vivo growth of A. actinomycetemcomitans. These results suggest that detection of catecholamines and iron by QseBC may alter the cellular metabolism of A. actinomycetemcomitans for increased fitness and growth in an anaerobic host environment."], "field": "Dentistry", "q_year": 2021, "q_cid": "236983573", "pos_cid": 1374971, "source": "eval_collection"}
{"query_id": "scaleup_27123150_26934298", "query": "How to achieve sufficient antibacterial activity in dental resins without compromising aesthetics or harming human cells", "pos": ["Silver Nanoparticles: Multifunctional Tool in Environmental Water Remediation. Water pollution is a worldwide environmental and health problem that requires the development of sustainable, efficient, and accessible technologies. Nanotechnology is a very attractive alternative in environmental remediation processes due to the multiple properties that are conferred on a material when it is at the nanometric scale. This present review focuses on the understanding of the structure–physicochemical properties–performance relationships of silver nanoparticles, with the objective of guiding the selection of physicochemical properties that promote greater performance and are key factors in their use as antibacterial agents, surface modifiers, colorimetric sensors, signal amplifiers, and plasmonic photocatalysts. Silver nanoparticles with a size of less than 10 nm, morphology with a high percentage of reactive facets {111}, and positive surface charge improve the interaction of the nanoparticles with bacterial cells and induce a greater antibacterial effect. Adsorbent materials functionalized with an optimal concentration of silver nanoparticles increase their contact area and enhance adsorbent capacity. The use of stabilizing agents in silver nanoparticles promotes selective adsorption of contaminants by modifying the surface charge and type of active sites in an adsorbent material, in addition to inducing selective complexation and providing stability in their use as colorimetric sensors. Silver nanoparticles with complex morphologies allow the formation of hot spots or chemical or electromagnetic bonds between substrate and analyte, promoting a greater amplification factor. Controlled doping with nanoparticles in photocatalytic materials produces improvements in their electronic structural properties, promotes changes in charge transfer and bandgap, and improves and expands their photocatalytic properties. Silver nanoparticles have potential use as a tool in water remediation, where by selecting appropriate physicochemical properties for each application, their performance and efficiency are improved."], "field": "Dentistry", "q_year": 2024, "q_cid": "271231504", "pos_cid": 269342988, "source": "eval_collection"}
{"query_id": "scaleup_24567180_22359910", "query": "How to clarify the role of C. albicans surface proteins in mixed oral biofilms, including their structure, function, and antigen presentation and recognition", "pos": ["Autoantigenesis: The evolution of protein modifications in autoimmune disease. Protein targets in autoimmune disease vary in location, originating within cells as in SLE, or found on cell surfaces or in extracellular spaces. The term “autoantigenesis” is first defined here as the changes that arise in self-proteins as they break self tolerance and trigger autoimmune B and/or T cell responses. As illustrated in many studies, between 50 and 90% of the proteins in the human body acquire posttranslational modification. In some cases, it may be that these modifications are necessary for the biological functions of proteins of the cells in which they reside or as extracellular mediators. Summarized herein, it is clear that some posttranslational modifications can create new self-antigens by altering immunologic processing and presentation. While many protein modifications exist, we will focus on those created, amplified, or altered in the context of inflammation or other immune system responses. Finally, we will address how posttranslational modifications in self-antigens may affect the analyses of B and T cell specificity, current diagnostic techniques, and/or the development of immunotherapies for autoimmune diseases."], "field": "Dentistry", "q_year": 2022, "q_cid": "245671808", "pos_cid": 22359910, "source": "eval_collection"}
{"query_id": "scaleup_24712967_20274810", "query": "How to determine whether tannic acid released from implant coatings reaches concentrations that could cause adverse responses", "pos": ["Effect of tannic acid on blood components and functions.. Tannic acid (TA) has become increasingly important as a biomaterial because of its ability to capture free radicals and form complexes with metal ions. Nevertheless, a systematic evaluation of the blood safety of TA has not been done. Therefore, we studied the effect of TA on erythrocyte morphology and hemolysis at different time points, and the fluorescence and circular dichroism (CD) spectroscopy of TA and fibrinogen. The blood coagulation time of TA was measured by the activated partial thromboplastin time (APTT), plasma prothrombin time (PT), and thrombelastogram (TEG) experiments. We found that higher concentrations of TA could lead to crinkling and hemolysis of erythrocytes, which may have been mediated by the hydrogen bond in TA. Spectroscopic results showed that TA influenced the structure and conformation of fibrinogen. Higher concentrations of TA could shorten the activated partial thromboplastin and plasma prothrombin times, and various concentrations of TA could affect the reaction time, clotting time, clot aggregation speed, and maximum clot strength of whole blood coagulation. These findings provide a basis for the design of TA molecules and the possible application of TA in biomedicine."], "field": "Dentistry", "q_year": 2022, "q_cid": "247129671", "pos_cid": 202748107, "source": "eval_collection"}
{"query_id": "scaleup_28096264_14520353", "query": "How to compare the effects of localized antimicrobial interventions under equivalent conditions without differences in the surrounding environment confounding the comparison", "pos": ["Effect of Propolis on Dentin Regeneration and the Potential Role of Dental Pulp Stem Cell in Guinea Pigs. Objective: Evaluation of the effect of Propolis as a bioactive material on quality of dentin and presence of dental pulp stem cells. Materials and Methods: For conducting this experimental split-mouth study,a total of 48 maxillary and mandibular incisors of male guinea pigs were randomly divided into an experimental Propolis group and a control calcium hydroxide group. Cutting the crowns and using Propolis or calcium hydroxide to cap the pulp, all of the cavities were sealed. Sections of the teeth were obtained after sacrificing 4 guinea pigs from each group on the 10th, 15th and 30th day. After they had been stained by hematoxylin and eosin (H&E), specimens underwent a histological evaluation under a light microscope for identification of the presence of odontoblast-like cells, pulp vitality, congestion, inflammation of the pulp and the presence of remnants of the material used. The immunohistochemistry (IHC) method using CD29 and CD146 was performed to evaluate the presence of stem cells and the results were statistically evaluated by Kruskal-Wallis, Chi Square and Fisher tests. Results: In H&E stained specimens, there was no difference between the two groups in the presence of odontoblast-like cells, pulp vitality, congestion, inflammation of the pulp and the presence of remnants of used material(p>0.05). There was a significant difference between the quality of regenerative dentin on the 15th and 30th days (p<0.05): all of the Propolis cases presented tubular dentin while 14% of the calcium hydroxide cases produced porous dentin. There was no significant difference between Propolis and calcium hydroxide in stimulation of dental pulp stem cells (DPSCs). Conclusion: This study which is the first one that documented the stimulation of stem cells by Propolis, provides evidence that this material has advantages over calcium hydroxide as a capping agent in vital pulp therapy. In addition to producing no pulpal inflammation, infection or necrosis this material induces the production of high quality tubular dentin."], "field": "Dentistry", "q_year": 2025, "q_cid": "280962644", "pos_cid": 14520353, "source": "eval_collection"}
{"query_id": "scaleup_24616499_21717467", "query": "How to explain pulp stone formation and variation in morphology and composition across locations in the pulp cavity", "pos": ["Characterisation of matrix vesicles in skeletal and soft tissue mineralisation.. The importance of matrix vesicles (MVs) has been repeatedly highlighted in the formation of cartilage, bone, and dentin since their discovery in 1967. These nano-vesicular structures, which are found in the extracellular matrix, are believed to be one of the sites of mineral nucleation that occurs in the organic matrix of the skeletal tissues. In the more recent years, there have been numerous reports on the observation of MV-like particles in calcified vascular tissues that could be playing a similar role. Therefore, here, we review the characteristics MVs possess that enable them to participate in mineral deposition. Additionally, we outline the content of skeletal tissue- and soft tissue-derived MVs, and discuss their key mineralisation mediators that could be targeted for future therapeutic use."], "field": "Dentistry", "q_year": 2021, "q_cid": "246164997", "pos_cid": 21717467, "source": "eval_collection"}
{"query_id": "scaleup_27292542_21092369", "query": "How to maintain sufficient moisture around glass embedded in a hydrophobic resin matrix for direct pulp capping", "pos": ["Bioactive Pore‐Forming Bone Adhesives Facilitating Cell Ingrowth for Fracture Healing. The effectiveness of commercial bone adhesives is known to be hampered by the weak efficacy of cell ingrowth. The strategy of macropore‐forming, especially bioactive macropores, holds considerable promise to circumvent this problem, thereby promoting fracture healing. Herein, a class of bioactive glass‐involved macropore‐embedded bone adhesives is developed, which is capable of facilitating the migration of bone‐derived mesenchymal stromal cells into the adhesive layer and differentiation into osteocytes. The integration of bioactive glass‐particle‐encapsulated porogens in the bone adhesives is key to this approach. A robust instant bonding on the bone adhesive and a high efficiency of bone regeneration on a mouse skull are observed, both of which are vital for clinical applications and personalized surgical procedures. This work represents a general strategy to design biomaterials with high cell‐ingrowth efficacy."], "field": "Dentistry", "q_year": 2024, "q_cid": "272925426", "pos_cid": 210923694, "source": "eval_collection"}
{"query_id": "scaleup_24712967_45317154", "query": "How to limit inflammation and microbial colonization on implant surfaces and oxidative stress during wound healing to support tissue integration in patients with chronic inflammation or impaired wound healing", "pos": ["Dietary Polyphenols and Their Biological Significance. Dietary polyphenols represent a wide variety of compounds that occur in fruits, vegetables, wine, tea, extra virgin olive oil, chocolate and other cocoa products. They are mostly derivatives and/or isomers of flavones, isoflavones, flavonols, catechins and phenolic acids, and possess diverse biological properties such as antioxidant, antiapoptosis, anti-aging, anticarcinogen, anti-inflammation, anti-atherosclerosis, cardiovascular protection, improvement of the endothelial function, as well as inhibition of angiogenesis and cell proliferation activity. Most of these biological actions have been attributed to their intrinsic reducing capabilities. They may also offer indirect protection by activating endogenous defense systems and by modulating cellular signaling processes such as nuclear factor-kappa B (NF-κB) activation, activator protein-1(AP-1) DNA binding, glutathione biosynthesis, phosphoinositide 3 (PI3)-kinase/protein kinase B (Akt) pathway, mitogen-activated protein kinase (MAPK) proteins [extracellular signal-regulated protein kinase (ERK), c-jun N-terminal kinase (JNK) and P38 ] activation, and the translocation into the nucleus of nuclear factor erythroid 2 related factor 2 (Nrf2). This paper covers the most recent literature on the subject, and describes the biological mechanisms of action and protective effects of dietary polyphenols."], "field": "Dentistry", "q_year": 2022, "q_cid": "247129671", "pos_cid": 45317154, "source": "eval_collection"}
{"query_id": "scaleup_22097810_2939479", "query": "How to improve resin-based dental sealants’ resistance to protein adsorption and cariogenic bacterial adhesion for better caries prevention", "pos": ["Zwitteration: Coating Surfaces with Zwitterionic Functionality to Reduce Nonspecific Adsorption. Coating surfaces with thin or thick films of zwitterionic material is an effective way to reduce or eliminate nonspecific adsorption to the solid/liquid interface. This review tracks the various approaches to zwitteration, such as monolayer assemblies and polymeric brush coatings, on micro- to macroscopic surfaces. A critical summary of the mechanisms responsible for antifouling shows how zwitterions are ideally suited to this task."], "field": "Dentistry", "q_year": 2020, "q_cid": "220978104", "pos_cid": 2939479, "source": "eval_collection"}
{"query_id": "scaleup_25358422_20493971", "query": "How to clarify the basis of antimicrobial activity against microorganisms within biofilms", "pos": ["Antibacterial and immunomodulator activities of virgin coconut oil (VCO) against Staphylococcus aureus. Antibiotics have components to inhibit infections against Staphylococcus aureus, but they depend on judicious use to minimize the incidence of resistance forms. Strategies to improve the current situation include research in finding a new antimicrobial from virgin coconut oil (VCO). The saturated fatty acid, lauric acid (LA) (C12) contain in VCO was reported to have antibacterial activities. This study developed antimicrobial of VCO as an antimicrobial and immunomodulatory agent. Staphylococcus aureus used in this study had been isolated and identified from the mastitis milk crossbreed Etawa goat from Riau, Indonesia. The susceptibility of S. aureus to VCO was tested using the broth dilution method. The inhibition mechanisms of S. aureus had been studied by scanning electron microscopy (SEM) after treatment with VCO, and potential of VCO, which is known in phagocytosis macrophage. In vitro test confirmed the inhibitory effect of VCO on the growth of S. aureus at the concentration of 200 μl (equal to 0.102 % LA). Based on the result of the phagocytosing assay, VCO could increase the ability of the macrophage cells to phagocyte S. aureus significantly at a concentration of 200 μL (equal to 0.102% LA). This study concluded that the VCO could inhibit the growth of S. aureus with destructive mechanisms of bacterial cell walls and increase the ability of the phagocytic immune cells."], "field": "Dentistry", "q_year": 2022, "q_cid": "253584227", "pos_cid": 204939715, "source": "eval_collection"}
{"query_id": "scaleup_25358422_20490938", "query": "How to eliminate biofilms within the contact times recommended for oral care", "pos": ["Comparison of bactericidal and fungicidal efficacy of antiseptic formulations according to EN 13727 and EN 13624 standards. Background/aim In this study, the antibacterial and antifungal properties of the five most commonly used antiseptic formulations were evaluated in terms of different contact times and organic conditions. Materials and methods Solutions of chlorhexidine digluconate, povidone iodine, isopropyl alcohol, hydrogen peroxide, and tincture of iodine were prepared and tested according to European standards EN 13727 and EN 13624 with different parameters. Results The results showed that isopropyl alcohol (70% v/v) and tincture of iodine (2%) had greater bactericidal and fungicidal activity against the four tested bacteria and two fungi in all conditions. Conclusion When the results of the five different active substances were quantitatively evaluated regarding their bactericidal and fungicidal activities, it was found that contact time and organic load significantly affected the antiseptic efficacy."], "field": "Dentistry", "q_year": 2022, "q_cid": "253584227", "pos_cid": 204909383, "source": "eval_collection"}
{"query_id": "scaleup_26802926_23157279", "query": "How to reliably number teeth and detect caries in bitewing radiographs in real time to support clinicians during assessment", "pos": ["RepVGG: Making VGG-style ConvNets Great Again. We present a simple but powerful architecture of convolutional neural network, which has a VGG-like inference-time body composed of nothing but a stack of 3 × 3 convolution and ReLU, while the training-time model has a multi-branch topology. Such decoupling of the training-time and inference-time architecture is realized by a structural re-parameterization technique so that the model is named RepVGG. On ImageNet, RepVGG reaches over 80% top-1 accuracy, which is the first time for a plain model, to the best of our knowledge. On NVIDIA 1080Ti GPU, RepVGG models run 83% faster than ResNet-50 or 101% faster than ResNet-101 with higher accuracy and show favorable accuracy-speed trade-off compared to the state-of-the-art models like EfficientNet and RegNet. The code and trained models are available at https://github.com/megvii-model/RepVGG."], "field": "Dentistry", "q_year": 2024, "q_cid": "268029260", "pos_cid": 231572790, "source": "eval_collection"}
{"query_id": "scaleup_25344912_17826093", "query": "How to determine whether the oral microbiome causes anxiety and depression rather than merely being associated with them", "pos": ["Mendelian Randomization Analysis With Multiple Genetic Variants Using Summarized Data. Genome‐wide association studies, which typically report regression coefficients summarizing the associations of many genetic variants with various traits, are potentially a powerful source of data for Mendelian randomization investigations. We demonstrate how such coefficients from multiple variants can be combined in a Mendelian randomization analysis to estimate the causal effect of a risk factor on an outcome. The bias and efficiency of estimates based on summarized data are compared to those based on individual‐level data in simulation studies. We investigate the impact of gene–gene interactions, linkage disequilibrium, and ‘weak instruments’ on these estimates. Both an inverse‐variance weighted average of variant‐specific associations and a likelihood‐based approach for summarized data give similar estimates and precision to the two‐stage least squares method for individual‐level data, even when there are gene–gene interactions. However, these summarized data methods overstate precision when variants are in linkage disequilibrium. If the P‐value in a linear regression of the risk factor for each variant is less than 1×10−5 , then weak instrument bias will be small. We use these methods to estimate the causal association of low‐density lipoprotein cholesterol (LDL‐C) on coronary artery disease using published data on five genetic variants. A 30% reduction in LDL‐C is estimated to reduce coronary artery disease risk by 67% (95% CI: 54% to 76%). We conclude that Mendelian randomization investigations using summarized data from uncorrelated variants are similarly efficient to those using individual‐level data, although the necessary assumptions cannot be so fully assessed."], "field": "Dentistry", "q_year": 2022, "q_cid": "253449125", "pos_cid": 17826093, "source": "eval_collection"}
{"query_id": "scaleup_25884003_337036", "query": "How to explain why Mfa1 fimbriae are shorter in strain Ando than in strain JI-1 and determine whether Mfa2 is expressed and functional in Ando", "pos": ["A Distinct Type of Pilus from the Human Microbiome. Summary Pili are proteinaceous polymers of linked pilins that protrude from the cell surface of many bacteria and often mediate adherence and virulence. We investigated a set of 20 Bacteroidia pilins from the human microbiome whose structures and mechanism of assembly were unknown. Crystal structures and biochemical data revealed a diverse protein superfamily with a common Greek-key β-sandwich fold with two transthyretin-like repeats that polymerize into a pilus through a strand-exchange mechanism. The assembly mechanism of the central, structural pilins involves proteinase-assisted removal of their N-terminal β-strand, creating an extended hydrophobic groove that binds the C-terminal donor strands of the incoming pilin. Accessory pilins at the tip and base have unique structural features specific to their location, allowing initiation or termination of the assembly. The bacteroidia pilus therefore has a biogenesis mechanism that is distinct from other known pili and likely represents a different type of bacterial pilus."], "field": "Dentistry", "q_year": 2023, "q_cid": "258840030", "pos_cid": 337036, "source": "eval_collection"}
{"query_id": "scaleup_25892627_9420316", "query": "How to clarify the causal relationship between oral changes, immune responses, inflammation, and cancer development", "pos": ["Dietary Gut Microbial Metabolites, Short-chain Fatty Acids, and Host Metabolic Regulation. During feeding, the gut microbiota contributes to the host energy acquisition and metabolic regulation thereby influencing the development of metabolic disorders such as obesity and diabetes. Short-chain fatty acids (SCFAs) such as acetate, butyrate, and propionate, which are produced by gut microbial fermentation of dietary fiber, are recognized as essential host energy sources and act as signal transduction molecules via G-protein coupled receptors (FFAR2, FFAR3, OLFR78, GPR109A) and as epigenetic regulators of gene expression by the inhibition of histone deacetylase (HDAC). Recent evidence suggests that dietary fiber and the gut microbial-derived SCFAs exert multiple beneficial effects on the host energy metabolism not only by improving the intestinal environment, but also by directly affecting various host peripheral tissues. In this review, we summarize the roles of gut microbial SCFAs in the host energy regulation and present an overview of the current understanding of its physiological functions."], "field": "Dentistry", "q_year": 2023, "q_cid": "258926275", "pos_cid": 9420316, "source": "eval_collection"}
{"query_id": "scaleup_24712967_2250965", "query": "How to compare the antioxidant capacity of tannic acid and pyrogallol coatings on titanium while accounting for differences in their thickness and chemistry", "pos": ["Deposition Kinetics of Bioinspired Phenolic Coatings on Titanium Surfaces. Polyphenols can form functional coatings on a variety of different materials through auto-oxidative surface polymerization in a manner similar to polydopamine coatings. However, the mechanisms behind the coating deposition are poorly understood. We report the coating deposition kinetics of the polyphenol tannic acid (TA) and the simple phenolic compound pyrogallol (PG) on titanium surfaces. The coating deposition was followed in real time over a period of 24 h using a quartz crystal microbalance with dissipation monitoring (QCM-D). TA coatings revealed a multiphasic layer formation: the deposition of an initial rigid layer was followed by the buildup of an increasingly dissipative layer, before mass adsorption stopped after approximately 5 h of coating time. The PG deposition was biphasic, starting with the adsorption of a nonrigid viscoelastic layer which was followed by layer stiffening upon further mass adsorption. Coating evaluation by ellipsometry and AFM confirmed the deposition kinetics determined by QCM-D and revealed maximum coating thicknesses of approximately 50 and 75 nm for TA and PG, respectively. Chemical characterization of the coatings and polymerized polyphenol particles indicated the involvement of both physical and chemical interactions in the auto-oxidation reactions."], "field": "Dentistry", "q_year": 2022, "q_cid": "247129671", "pos_cid": 2250965, "source": "eval_collection"}
{"query_id": "scaleup_25330365_21906248", "query": "How to determine whether pain differences between maxillary expanders are related to sensitivity differences between deciduous teeth and permanent molars serving as anchors", "pos": ["The distribution of nerves in human deciduous and permanent teeth.. Human permanent teeth without caries, obtained from 10-16 year old males and females and noncarious human deciduous teeth in which roots remained intact or were only poorly resorbed, were studied histologically. The distribution of sensory nerves in deciduous teeth were compared with that in permanent teeth by means of the silver-nitrate technique. 1. In radicular pulp, the sensory nerve fiber bundles accompany blood vessels in the axial area and several nerve single-fibers occur in the peripheral area of the pulp. 2. The subodontoblastic nerve plexus is formed in or beneath the cell-rich zone of the coronal pulp, and further, the marginal nerve plexus is built up near the pulpo-predentinal border. 3. The nerve fibers entering the predentin can be classified into 3 types by their courses. In the first type, nerve fibers pass directly toward the calcification front along the dentinal tubules in the predentin. In the second type, nerve fibers run obliquely or transversely in the predentin. The transversal fibers form a plexus-like structure by dividing and interlacing at various levels of predentin. The third type nerve fibers pass along the dentinal tubules in the predentin and, after reaching the predentino-dentinal border, reverse the odontoblast layer, thus forming a looped course. 4. There is no essential difference between the nerve supply in the deciduous and in the permanent teeth, but the nerves in the deciduous teeth are less dense in distribution and lower in amount than in the permanent teeth. Moreover, a typical marginal nerve plexus, which occurs constantly in the permanent teeth, is only occasionally found in the deciduous teeth; and no nerve fiber was observed to penetrate into the calcified dentin in the deciduous teeth. This finding seems to account for the fact that the deciduous teeth are less sensitive than their permanent successors."], "field": "Dentistry", "q_year": 2022, "q_cid": "253303651", "pos_cid": 21906248, "source": "eval_collection"}
{"query_id": "scaleup_23521458_22079799", "query": "How to safely resume routine dental care and determine when preventive measures can be relaxed amid unequal vaccine availability, uncertain vaccine protection, and the risk of recurrent outbreaks with unpredictable severity", "pos": ["With Risk of Reinfection, Is COVID-19 Here to Stay?. Many factors have served the swift transformation of the coronavirus disease (COVID-19) from an endemic to a pandemic.1 Some can be attributed to characteristics of the virus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), such as high basic reproducing number (R0) of about 2 to 6 and transmissibility despite absence of clinical manifestations.2 However, our assumptions about the pandemic, most of which are falsified or questioned, at this point, also played a major role. One such assumption was that SARS-CoV-2, similar to H1N1 virus, will attenuate in high temperatures, while we are now observing the second wave of the pandemic in some countries, despite rising temperatures. Another assumption was reaching herd immunity for SARSCoV-2 as the number of the affected individuals would rise, thus restrict the transmission of virus due to the increased number of immune hosts and decreased number of susceptible ones.2 However, a key concept in establishing and maintaining herd immunity is a strong immunization against the pathogens which lasts long enough so that the fraction of the population immune to the virus surpasses the herd immunity threshold. Therefore, persistence of immunoglobulin concentrations is one of the factors that determines the possibility of reaching herd immunity or periodic outbreaks.2"], "field": "Dentistry", "q_year": 2021, "q_cid": "235214583", "pos_cid": 220797993, "source": "eval_collection"}
{"query_id": "scaleup_26887406_21974421", "query": "How to establish the precise mechanical properties of optimized silica-reinforced dental resin and reliably predict the behavior of a crown made from it under oblique loading", "pos": ["A novel approach to determining piezoelectric properties of nanogenerators based on PVDF nanofibers using iterative finite element simulation for walking energy harvesting. This study presents the experimental characterization and finite element investigation of a piezoelectric nanogenerator based on electrospun poly(vinylidene difluoride) (PVDF) nanofibers walking energy harvesting applications. The piezoelectric response of nanogenerator device was experimentally evaluated under low frequency cyclic impacts using PiezoTester. The impact test was then simulated and the obtained experimental applied force-time curve is implemented into the finite element model as the impactor external force. Based on mentioned procedure, a novel iterative finite element simulation was then introduced to determine the piezoelectric properties of PVDF nanofibers to avoid any redundant experiments. The experimental voltage-time was compared with voltage time obtained from optimized finite element model and a reasonable agreement was achieved between the numerical and experimental curves. Thereinafter, as a case study, a PVDF nanofibers nanogenerator integrated foam (PNIF) was simulated to use as an energy harvester in the shoe insole. The validated finite element model was then constructed to optimize the PNIF elasticity modulus to reach the maximum efficiency of energy harvester during human walking. The results showed that the best efficiency of the energy harvesting is achieved for 211.27 kPa PNIF modulus, which can generate 15.1 V. These results lead to the establishment of engineering design rules in the industrial scale for wearable power harvesting devices in the footwear industry."], "field": "Dentistry", "q_year": 2024, "q_cid": "268874064", "pos_cid": 219744217, "source": "eval_collection"}
{"query_id": "scaleup_25724100_18380656", "query": "How to control local inflammation and support tissue recovery in mild disease involving contamination, bleeding, deepened tissue pockets, and bone defects", "pos": ["Decontamination Using a Desiccant with Air Powder Abrasion Followed by Biphasic Calcium Sulfate Grafting: A New Treatment for Peri-Implantitis. Peri‐implantitis is characterized by inflammation and crestal bone loss in the tissues surrounding implants. Contamination by deleterious bacteria in the peri‐implant microenvironment is believed to be a major factor in the etiology of peri‐implantitis. Prior to any therapeutic regenerative treatment, adequate decontamination of the peri‐implant microenvironment must occur. Herein we present a novel approach to the treatment of peri‐implantitis that incorporates the use of a topical desiccant (HYBENX), along with air powder abrasives as a means of decontamination, followed by the application of biphasic calcium sulfate combined with inorganic bovine bone material to augment the intrabony defect. We highlight the case of a 62‐year‐old man presenting peri‐implantitis at two neighboring implants in positions 12 and 13, who underwent access flap surgery, followed by our procedure. After an uneventful 2‐year healing period, both implants showed an absence of bleeding on probing, near complete regeneration of the missing bone, probing pocket depth reduction, and clinical attachment gain. While we observed a slight mucosal recession, there was no reduction in keratinized tissue. Based on the results described within, we conclude that the use of HYBENX and air powder abrasives, followed by bone defect grafting, represents a viable option in the treatment of peri‐implantitis."], "field": "Dentistry", "q_year": 2023, "q_cid": "257241006", "pos_cid": 18380656, "source": "eval_collection"}
{"query_id": "scaleup_24482439_13990985", "query": "How to explain differences in coatings’ ability to inhibit bacterial attachment at different fabrication powers", "pos": ["Biodegradable optically transparent terpinen-4-ol thin films for marine antifouling applications. Abstract Sustainable marine antifouling strategies aim to minimize long term environmental impacts while effectively preventing surface colonization. In this study, we report upon a biodegradable antifouling coating for marine applications. In two stages, thin bilayers were produced using plasma-enhanced chemical vapor deposition of terpinen-4-ol, at applied powers of 100 W initially and then 10 or 25 W. The resulting coatings were characterized for solubility, surface energy, surface roughness and optical transmission. Both coatings exhibited similar solubility over the initial 14 days of observation, though structures deposited at 25 W were significantly more stable after 14 days. Coatings were smoother than the control surface upon which they were deposited and had higher hydrophobicity with transmission efficiencies >90% (400–1000 nm). Field assessments of the samples were carried out in Curralea Lake (Townsville, Australia) to assess their real world performance. Results indicate that the environmentally friendly coatings, terpinen-4-ol plasma polymer influenced antifouling. The proposed mechanism for this effect is the dissolution of the coating coupled with possible antimicrobial properties of the terpinen-4-ol. These results point to the potential usefulness of developing multilayer coatings for extended deployments."], "field": "Dentistry", "q_year": 2021, "q_cid": "244824391", "pos_cid": 139909856, "source": "eval_collection"}
{"query_id": "scaleup_24743980_19823906", "query": "How to identify surface conditions that support attachment and stable single-subspecies biofilm formation across different F. nucleatum subspecies", "pos": ["Imaging live bacteria at the nanoscale: comparison of immobilisation strategies. Atomic force microscopy (AFM) provides an effective, label-free technique enabling the imaging of live bacteria under physiological conditions with nanometre precision. However, AFM is a surface scanning technique, and the accuracy of its performance requires the effective and reliable immobilisation of bacterial cells onto substrates. Here, we compare the effectiveness of various chemical approaches to facilitate the immobilisation of Escherichia coli onto glass cover slips in terms of bacterial adsorption, viability and compatibility with correlative imaging by fluorescence microscopy. We assess surface functionalisation using gelatin, poly-L-lysine, Cell-Tak™, and Vectabond®. We describe how bacterial immobilisation, viability and suitability for AFM experiments depend on bacterial strain, buffer conditions and surface functionalisation. We demonstrate the use of such immobilisation by AFM images that resolve the porin lattice on the bacterial surface; local degradation of the bacterial cell envelope by an antimicrobial peptide (Cecropin B); and the formation of membrane attack complexes on the bacterial membrane."], "field": "Dentistry", "q_year": 2022, "q_cid": "247439805", "pos_cid": 198239062, "source": "eval_collection"}
{"query_id": "scaleup_25344912_8457187", "query": "How to verify the reliability and stability of estimated causal effects of the oral microbiome on anxiety and depression", "pos": ["Consistent Estimation in Mendelian Randomization with Some Invalid Instruments Using a Weighted Median Estimator. Developments in genome‐wide association studies and the increasing availability of summary genetic association data have made application of Mendelian randomization relatively straightforward. However, obtaining reliable results from a Mendelian randomization investigation remains problematic, as the conventional inverse‐variance weighted method only gives consistent estimates if all of the genetic variants in the analysis are valid instrumental variables. We present a novel weighted median estimator for combining data on multiple genetic variants into a single causal estimate. This estimator is consistent even when up to 50% of the information comes from invalid instrumental variables. In a simulation analysis, it is shown to have better finite‐sample Type 1 error rates than the inverse‐variance weighted method, and is complementary to the recently proposed MR‐Egger (Mendelian randomization‐Egger) regression method. In analyses of the causal effects of low‐density lipoprotein cholesterol and high‐density lipoprotein cholesterol on coronary artery disease risk, the inverse‐variance weighted method suggests a causal effect of both lipid fractions, whereas the weighted median and MR‐Egger regression methods suggest a null effect of high‐density lipoprotein cholesterol that corresponds with the experimental evidence. Both median‐based and MR‐Egger regression methods should be considered as sensitivity analyses for Mendelian randomization investigations with multiple genetic variants."], "field": "Dentistry", "q_year": 2022, "q_cid": "253449125", "pos_cid": 8457187, "source": "eval_collection"}
{"query_id": "scaleup_24818478_4833863", "query": "How to quantify cumulative aerosol exposure over the duration of dental treatments?", "pos": ["Brand Cigarillos — A Cheap and Less Harmful Alternative to Cigarettes? Particulate Matter Emissions Suggest Otherwise. Background: Environmental tobacco smoke (ETS)-associated particulate matter (PM) constitutes a considerable health risk for passive smokers. It ought to be assessed separately from the other known toxic compounds of tobacco smoke. Brand-specific differences between cigarettes and particularly between cigarettes and favorably taxed cigarillos, are of public interest and therefore worth being investigated. Methods: An automatic environmental tobacco smoke emitter (AETSE) was developed to generate cigarette and cigarillo smoke in a reliable and reproducible way. John Player Special (JPS) Red cigarettes, JPS filter cigarillos and 3R4F standard research cigarettes were smoked automatically in a 2.88 m3 glass chamber according to a standardized protocol until 5 cm from the top were burned down. Results: Mean concentrations (Cmean) and area of the curve (AUC) of PM2.5 were measured and compared. Cmean PM2.5 were found to be 804 µg/m3 for 3R4F reference cigarettes, 1633 µg/m3 for JPS cigarettes, and 1059 µg/m3 for JPS filter cigarillos. AUC PM2.5-values are 433,873 µg/m3×s for 3R4F reference cigarettes, 534,267 µg/m3×s for JPS Red cigarettes and 782,850 µg/m3×s for JPS filter cigarillos. Conclusion: Potential brand-specific differences of ETS-associated PM emissions among brands of cigarettes, and between cigarettes and cigarillos of the same brand and size should be investigated and published. Information about relative PM-emissions should be printed on the package."], "field": "Dentistry", "q_year": 2022, "q_cid": "248184782", "pos_cid": 4833863, "source": "eval_collection"}
{"query_id": "scaleup_27653382_13906415", "query": "How to establish whether each isolate is S. mutans with sufficient confidence to support a species-specific comparison between adults with high and low caries risk", "pos": ["Ribosomal Multi-Locus Sequence Typing: universal characterisation of bacteria from domain to strain. Summary No single characterisation scheme currently encompasses all levels of bacterial diversity, from domain to strain. We propose Ribosomal Multi Locus Sequence Typing (rMLST), an approach which indexes variation of the 53 genes encoding the bacterial ribosome protein subunits (rps genes), as a means of integrated microbial taxonomy and typing. As with MLST, rMLST employs curated reference sequences to identify gene variants efficiently and rapidly. The rps loci are ideal targets for a universal characterization scheme as they are: (i) present in all bacteria; (ii) distributed around the chromosome; and (iii) encode proteins which are under stabilising selection for functional conservation. Collectively, the rps loci exhibit variation that resolves bacteria in to groups at all taxonomic and most typing levels providing significantly more resolution than 16S small subunit rRNA gene phylogenies. A web-accessible expandable database, comprising whole genome data from more than 1900 bacterial isolates, including 28 draft genomes assembled de novo from the EBI sequence read archive, has been assembled. The rps gene variation catalogued in this database permits rapid and computationally non-intensive identification of the phylogenetic position of any bacterial sequence at the domain, phylum, class, order, family, genus, species and strain levels. The groupings generated with rMLST data are consistent with current nomenclature schemes and independent of the clustering algorithm used. This approach is applicable to the other domains of life, potentially providing a rational and universal approach to the classification of life that is based on one of its fundamental features, the translation mechanism."], "field": "Dentistry", "q_year": 2025, "q_cid": "276533827", "pos_cid": 13906415, "source": "train_step3"}
{"query_id": "scaleup_25966734_4964783", "query": "How to improve resin cement wetting and bonding on chemically inert ceramic surfaces", "pos": ["Time-dependent effects of ultraviolet and nonthermal atmospheric pressure plasma on the biological activity of titanium. Here, we evaluated time-dependent changes in the effects of ultraviolet (UV) and nonthermal atmospheric pressure plasma (NTAPPJ) on the biological activity of titanium compared with that of untreated titanium. Grade IV machined surface titanium discs (12-mm diameter) were used immediately and stored up to 28 days after 15-min UV or 10-min NTAPPJ treatment. Changes of surface characteristics over time were evaluated using scanning electron microscopy, surface profiling, contact angle analysis, X-ray photoelectron spectroscopy, and surface zeta-potential. Changes in biological activity over time were as determined by analysing bovine serum albumin adsorption, MC3T3-E1 early adhesion and morphometry, and alkaline phosphatase (ALP) activity between groups. We found no differences in the effects of treatment on titanium between UV or NTAPPJ over time; both treatments resulted in changes from negatively charged hydrophobic (bioinert) to positively charged hydrophilic (bioactive) surfaces, allowing enhancement of albumin adsorption, osteoblastic cell attachment, and cytoskeleton development. Although this effect may not be prolonged for promotion of cell adhesion until 4 weeks, the effects were sufficient to maintain ALP activity after 7 days of incubation. This positive effect of UV and NTAPPJ treatment can enhance the biological activity of titanium over time."], "field": "Dentistry", "q_year": 2023, "q_cid": "259667344", "pos_cid": 4964783, "source": "train_step3"}
{"query_id": "scaleup_23337126_22212634", "query": "How to identify the microorganisms driving a recurrent, multifactorial disease and determine whether associated devices sustain tissue reinfection", "pos": ["Etiological factors related to denture stomatitis: A meta-analysis. Denture stomatitis (DS) is a very common disorder that affects upper denture wearers. Clinically, DS presents erythema and inflammation of the palatal mucosa covered by the denture. The objective of the study was to assess the etiological factors related to DS. A search for articles on etiological factors related to DS was performed in the following electronic databases: PubMed (MEDLINE, Cochrane Library), Web of Science (WoS), and Spanish Medical Index (IME). One thousand five hundred thirty-two articles were found (683 in PubMed, 829 in WoS, and 19 in IME), 340 of them were duplicates. From 330 articles with full-text availability, 306 were excluded for several reasons. Finally, 24 studies were included in this meta-analysis. For dichotomous outcomes, the estimates of effects of an intervention were expressed as odds ratios (ORs) using Mantel–Haenszel method with 95% confidence intervals. Data were processed using the statistical software RevMan 5.3. The most important risk factors for DS were Candida species infection (OR: 5.64,P < 0.001), denture age over 10 years (OR: 5.36, P = 0.02), the existence of denture trauma related to ill-fitting denture (OR: 4.30, P = 0.02), night sleeping with the denture (OR: 4.09,P < 0.001), poor denture cleaning (OR: 2.81, P = 0.02), high carbohydrate intake (OR: 1.83, P = 0.01), and female gender (OR: 1.42, P = 0.02). The most common microorganisms in DS were the Candida albicans fungus and the Stafilococcus aureus bacteria. Infection by species of the genus Candida seems to be the main etiological factor of DS."], "field": "Dentistry", "q_year": 2021, "q_cid": "233371263", "pos_cid": 222126345, "source": "train_step3"}
{"query_id": "scaleup_24467938_21968803", "query": "How to prevent dual-species cariogenic biofilms while addressing bacterial and fungal virulence factors and accommodating multiple antibiofilm drugs without compromising their affinity for and retention on tooth and biofilm surfaces", "pos": ["Electrostatic Interactions Enable Nanoparticle Delivery of the Flavonoid Myricetin. Flavonoids are natural polyphenolic compounds with myriad biological activities and potential as prophylactic and therapeutic agents. However, poor aqueous solubility and low bioavailability have limited the clinical utility of flavonoids, suggesting that drug delivery systems (DDSs) may improve their clinical relevance. Therefore, loading of a representative flavonoid (i.e., myricetin) into a diblock, polymeric nanoparticle carrier (NPC) DDS with a cationic corona and hydrophobic core was investigated. Absorbance and fluorescence spectroscopy results revealed association constants and standard Gibbs free energy values that align with previously reported values (Ka = ∼1–3 × 104 M–1; ΔG° = −5.4 to −6.0 kcal mol–1), suggesting that NPCs load myricetin via electrostatic interactions. The zeta potential and gel electrophoresis analysis confirmed this loading mechanism and indicated that NPCs improve myricetin solubility >25-fold compared to myricetin alone. Finally, the dual-drug loading of NPCs was tested using a combination of myricetin and a hydrophobic drug (i.e., farnesol). Electrostatic loading of NPCs with myricetin at concentrations ≤1.2 mM did not affect NPC core loading and release of farnesol, thus demonstrating a novel formulation strategy for the dual-drug-loaded NPC. These findings offer key insights into the NPC DDS design that may enhance the clinical relevance of flavonoid-based therapeutic approaches."], "field": "Dentistry", "q_year": 2021, "q_cid": "244679382", "pos_cid": 219688033, "source": "train_step3"}
{"query_id": "scaleup_24657193_59600605", "query": "How to reliably identify individuals at risk of periodontal disease early from multiple non-invasive patient characteristics readily collected in a clinic", "pos": ["Implementation of a Web Application to Predict Diabetes Disease: An Approach Using Machine Learning Algorithm. Diabetes is caused due to the excessive amount of sugar condensed into the blood. Currently, it is considered as one of the lethal diseases in the world. People all around the globe are affected by this severe disease knowingly or unknowingly. Other diseases like heart attack, paralyzed, kidney disease, blindness etc. are also caused by diabetes. Numerous computer-based detection systems were designed and outlined for anticipating and analyzing diabetes. Usual identifying process for diabetic patients needs more time and money. But with the rise of machine learning, we have that ability to develop a solution to this intense issue. Therefore we have developed an architecture which has the capability to predict where the patient has diabetes or not. Our main aim of this exploration is to build a web application based on the higher prediction accuracy of some powerful machine learning algorithm. We have used a benchmark dataset namely Pima Indian which is capable of predicting the onset of diabetes based on diagnostics manner. With an accuracy of 82.35% prediction rate Artificial Neural Network (ANN) shows a significant improvement of accuracy which drives us to develop an Interactive Web Application for Diabetes Prediction."], "field": "Dentistry", "q_year": 2022, "q_cid": "246571931", "pos_cid": 59600605, "source": "train_step3"}
{"query_id": "scaleup_24699801_11949094", "query": "How to reduce entrenched, long-standing fear in individuals with high trait anxiety", "pos": ["High Trait Anxiety: A Challenge for Disrupting Fear Memory Reconsolidation. Disrupting reconsolidation may be promising in the treatment of anxiety disorders but the fear-reducing effects are thus far solely demonstrated in the average organism. A relevant question is whether disrupting fear memory reconsolidation is less effective in individuals who are vulnerable to develop an anxiety disorder. By collapsing data from six previous human fear conditioning studies we tested whether trait anxiety was related to the fear-reducing effects of a pharmacological agent targeting the process of memory reconsolidation - n = 107. Testing included different phases across three consecutive days each separated by 24 h. Fear responding was measured by the eye-blink startle reflex. Disrupting the process of fear memory reconsolidation was manipulated by administering the β-adrenergic receptor antagonist propranolol HCl either before or after memory retrieval. Trait anxiety uniquely predicted the fear-reducing effects of disrupting memory reconsolidation: the higher the trait anxiety, the less fear reduction. Vulnerable individuals with the propensity to develop anxiety disorders may need higher dosages of propranolol HCl or more retrieval trials for targeting and changing fear memory. Our finding clearly demonstrates that we cannot simply translate observations from fundamental research on fear reduction in the average organism to clinical practice."], "field": "Dentistry", "q_year": 2022, "q_cid": "246998016", "pos_cid": 11949094, "source": "train_step3"}
{"query_id": "scaleup_26890830_5421278", "query": "How to determine whether an endodontist and an oral and maxillofacial radiologist identify the same apical periodontitis status for the same teeth on radiographs", "pos": ["Interrater reliability: the kappa statistic. The kappa statistic is frequently used to test interrater reliability. The importance of rater reliability lies in the fact that it represents the extent to which the data collected in the study are correct representations of the variables measured. Measurement of the extent to which data collectors (raters) assign the same score to the same variable is called interrater reliability. While there have been a variety of methods to measure interrater reliability, traditionally it was measured as percent agreement, calculated as the number of agreement scores divided by the total number of scores. In 1960, Jacob Cohen critiqued use of percent agreement due to its inability to account for chance agreement. He introduced the Cohen’s kappa, developed to account for the possibility that raters actually guess on at least some variables due to uncertainty. Like most correlation statistics, the kappa can range from −1 to +1. While the kappa is one of the most commonly used statistics to test interrater reliability, it has limitations. Judgments about what level of kappa should be acceptable for health research are questioned. Cohen’s suggested interpretation may be too lenient for health related studies because it implies that a score as low as 0.41 might be acceptable. Kappa and percent agreement are compared, and levels for both kappa and percent agreement that should be demanded in healthcare studies are suggested."], "field": "Dentistry", "q_year": 2024, "q_cid": "268908304", "pos_cid": 5421278, "source": "train_step3"}
{"query_id": "scaleup_23902750_21256857", "query": "How to clarify the association between overweight/obesity and oral health in Mexican children and adolescents when available studies are observational and findings vary with sociodemographic factors and outcome measures", "pos": ["Challenges in meta-analyses with observational studies. Objective Meta-analyses of observational studies are frequently published in the literature, but they are generally considered suboptimal to those involving randomised controlled trials (RCTs) only. This is due to the increased risk of biases that observational studies may entail as well as because of the high heterogeneity that might be present. In this article, we highlight aspects of meta-analyses with observational studies that need more careful consideration in comparison to meta-analyses of RCTs. Methods We present an overview of recommendations from the literature with respect to how the different steps of a meta-analysis involving observational studies should be comprehensively conducted. We focus more on issues arising at the step of the quantitative synthesis, in terms of handling heterogeneity and biases. We briefly describe some sophisticated synthesis methods, which may allow for more flexible modelling approaches than common meta-analysis models. We illustrate the issues encountered in the presence of observational studies using an example from mental health, which assesses the risk of myocardial infarction in antipsychotic drug users. Results The increased heterogeneity observed among studies challenges the interpretation of the diamond, while the inclusion of short exposure studies may lead to an exaggerated risk for myocardial infarction in this population. Conclusions In the presence of observational study designs, prior to synthesis, investigators should carefully consider whether all studies at hand are able to answer the same clinical question. The potential for a quantitative synthesis should be guided through examination of the amount of clinical and methodological heterogeneity and assessment of possible biases."], "field": "Dentistry", "q_year": 2021, "q_cid": "239027508", "pos_cid": 212568570, "source": "train_step3"}
{"query_id": "scaleup_23475278_20856585", "query": "How to distinguish incorrectly assigned fragments from genuine group content to avoid misrepresenting population composition and changes over time", "pos": ["Accurate and complete genomes from metagenomes. Genomes are an integral component of the biological information about an organism and, logically, the more complete the genome, the more informative it is. Historically, bacterial and archaeal genomes were reconstructed from pure (monoclonal) cultures and the first reported sequences were manually curated to completion. However, the bottleneck imposed by the requirement for isolates precluded genomic insights for the vast majority of microbial life. Shotgun sequencing of microbial communities, referred to initially as community genomics and subsequently as genome-resolved metagenomics, can circumvent this limitation by obtaining metagenome-assembled genomes (MAGs), but gaps, local assembly errors, chimeras and contamination by fragments from other genomes limit the value of these genomes. Here, we discuss genome curation to improve and in some cases achieve complete (circularized, no gaps) MAGs (CMAGs). To date, few CMAGs have been generated, although notably some are from very complex systems such as soil and sediment. Through analysis of ~7000 published complete bacterial isolate genomes, we verify the value of cumulative GC skew in combination with other metrics to establish bacterial genome sequence accuracy. Interestingly, analysis of cumulative GC skew identified potential mis-assemblies in some reference genomes of isolated bacteria and the repeat sequences that likely gave rise to them. We discuss methods that could be implemented in bioinformatic approaches for curation to ensure that metabolic and evolutionary analyses can be based on very high-quality genomes."], "field": "Dentistry", "q_year": 2022, "q_cid": "234752783", "pos_cid": 208565852, "source": "train_step3"}
{"query_id": "scaleup_23564034_2099459", "query": "How to distinguish oral sample subgroups with different caries status and oral microhabitats", "pos": ["Metagenomic biomarker discovery and explanation. This study describes and validates a new method for metagenomic biomarker discovery by way of class comparison, tests of biological consistency and effect size estimation. This addresses the challenge of finding organisms, genes, or pathways that consistently explain the differences between two or more microbial communities, which is a central problem to the study of metagenomics. We extensively validate our method on several microbiomes and a convenient online interface for the method is provided at http://huttenhower.sph.harvard.edu/lefse/."], "field": "Dentistry", "q_year": 2021, "q_cid": "235640348", "pos_cid": 2099459, "source": "train_step3"}
{"query_id": "scaleup_23740588_20563857", "query": "How to determine whether antidiabetic drugs can control macrophage inflammatory responses and shared inflammation in periodontitis–diabetes comorbidity when antibiotic treatment of periodontitis is unsatisfactory", "pos": ["Glyburide and retinoic acid synergize to promote wound healing by anti-inflammation and RIP140 degradation. Chronic inflammation underlies the development of metabolic diseases and individuals with metabolic disease often also suffer from delayed wound healing due to prolonged inflammation. Resolving inflammation provides a therapeutic strategy in treating metabolic diseases. We previously showed that during an anti-inflammatory response when macrophages were alternatively (M2) polarized, retinoic acid (RA) dramatically activated arginase 1 gene (Arg1), a gene crucial for wound healing. Here we report that a widely used sulfonylurea drug for type 2 diabetes mellitus (T2DM), glyburide, enhances the anti-inflammatory response and synergizes with RA to promote wound healing. Our data also delineate the mechanism underlying glyburide’s anti-inflammatory effect, which is to stimulate the degradation of a pro-inflammatory regulator, Receptor Interacting Protein 140 (RIP140), by activating Ca2+/calmodulin-dependent protein kinase II (CamKII) that triggers specific ubiquitination of RIP140 for degradation. By stimulating RIP140 degradation, glyburide enhances M2 polarization and anti-inflammation. Using a high-fat diet induced obesity mouse model to monitor wound healing effects, we provide a proof-of-concept for a therapeutic strategy that combining glyburide and RA can significantly improve wound healing. Mechanistically, this study uncovers a new mechanism of action of glyburide and a new pathway modulating RIP140 protein degradation that is mediated by CamKII signaling."], "field": "Dentistry", "q_year": 2021, "q_cid": "237405885", "pos_cid": 205638575, "source": "train_step3"}
{"query_id": "scaleup_13452703_54744686", "query": "How to assess the sensitivity of predicted crystal preferred orientations in deforming mantle aggregates to numerical choices", "pos": ["Improving the Self-Consistent Predictions of Texture Development of Polycrystals Incorporating Intragranular Field Fluctuations. In this contribution we present how to implement the calculation of average field fluctuations inside the grains of a thermoelastic aggregate in terms of the derivatives of the stress potential given by the standard linear self-consistent (SC) model, and how this statistical information can be used to generate second-order estimates for the mechanical behavior of nonlinear viscoplastic polycrystals, by means of a rigorous non-linear homogenization procedure. To illustrate the differences between this second-order (SO) self-consistent approach and the classical first-order SC approximations, we compare them in terms of their predictions of the effective behavior of random fcc polycrystals as a function of their rate-sensitivity, and of the texture evolution in hcp ice polycrystals under uniaxial compression. In the latter case, the SO approximation is the only one able to predict a substantial accommodation of deformation by basal slip, even when the basal poles become strongly aligned with the compression direction and the basal slip systems became unfavorably oriented."], "field": "Earth and Planetary Sciences", "q_year": 2018, "q_cid": "134527038", "pos_cid": 54744686, "source": "eval20x26"}
{"query_id": "scaleup_13460266_13400443", "query": "How to determine whether reported rapid sea-level rise corresponds to destabilization of Pacific atolls when local records are too short and unreliable to establish accurate sea-level rise rates", "pos": ["A global assessment of atoll island planform changes over the past decades. Over the past decades, atoll islands exhibited no widespread sign of physical destabilization in the face of sea‐level rise. A reanalysis of available data, which cover 30 Pacific and Indian Ocean atolls including 709 islands, reveals that no atoll lost land area and that 88.6% of islands were either stable or increased in area, while only 11.4% contracted. Atoll islands affected by rapid sea‐level rise did not show a distinct behavior compared to islands on other atolls. Island behavior correlated with island size, and no island larger than 10 ha decreased in size. This threshold could be used to define the minimum island size required for human occupancy and to assess atoll countries and territories' vulnerability to climate change. Beyond emphasizing the major role of climate drivers in causing substantial changes in the configuration of islands, this reanalysis of available data indicates that these drivers explain subregional variations in atoll behavior and within‐atoll variations in island and shoreline (lagoon vs. ocean) behavior, following atoll‐specific patterns. Increasing human disturbances, especially land reclamation and human structure construction, operated on atoll‐to‐shoreline spatial scales, explaining marked within‐atoll variations in island and shoreline behavior. Collectively, these findings highlight the heterogeneity of atoll situations. Further research needs include addressing geographical gaps (Indian Ocean, Caribbean, north‐western Pacific atolls), using standardized protocols to allow comparative analyses of island and shoreline behavior across ocean regions, investigating the role of ecological drivers, and promoting interdisciplinary approaches. Such efforts would assist in anticipating potential future changes in the contributions and interactions of key drivers."], "field": "Earth and Planetary Sciences", "q_year": 2019, "q_cid": "134602663", "pos_cid": 134004433, "source": "eval20x26"}
{"query_id": "scaleup_20875063_1650181", "query": "How to assess future sulfate aerosol radiative forcing over Europe under different future emission conditions within and outside Europe", "pos": ["The Shared Socioeconomic Pathways and their energy, land use, and greenhouse gas emissions implications: An overview. Abstract This paper presents the overview of the Shared Socioeconomic Pathways (SSPs) and their energy, land use, and emissions implications. The SSPs are part of a new scenario framework, established by the climate change research community in order to facilitate the integrated analysis of future climate impacts, vulnerabilities, adaptation, and mitigation. The pathways were developed over the last years as a joint community effort and describe plausible major global developments that together would lead in the future to different challenges for mitigation and adaptation to climate change. The SSPs are based on five narratives describing alternative socio-economic developments, including sustainable development, regional rivalry, inequality, fossil-fueled development, and middle-of-the-road development. The long-term demographic and economic projections of the SSPs depict a wide uncertainty range consistent with the scenario literature. A multi-model approach was used for the elaboration of the energy, land-use and the emissions trajectories of SSP-based scenarios. The baseline scenarios lead to global energy consumption of 400–1200 EJ in 2100, and feature vastly different land-use dynamics, ranging from a possible reduction in cropland area up to a massive expansion by more than 700 million hectares by 2100. The associated annual CO 2 emissions of the baseline scenarios range from about 25 GtCO 2 to more than 120 GtCO 2 per year by 2100. With respect to mitigation, we find that associated costs strongly depend on three factors: (1) the policy assumptions, (2) the socio-economic narrative, and (3) the stringency of the target. The carbon price for reaching the target of 2.6 W/m 2 that is consistent with a temperature change limit of 2 °C, differs in our analysis thus by about a factor of three across the SSP marker scenarios. Moreover, many models could not reach this target from the SSPs with high mitigation challenges. While the SSPs were designed to represent different mitigation and adaptation challenges, the resulting narratives and quantifications span a wide range of different futures broadly representative of the current literature. This allows their subsequent use and development in new assessments and research projects. Critical next steps for the community scenario process will, among others, involve regional and sectoral extensions, further elaboration of the adaptation and impacts dimension, as well as employing the SSP scenarios with the new generation of earth system models as part of the 6th climate model intercomparison project (CMIP6)."], "field": "Earth and Planetary Sciences", "q_year": 2019, "q_cid": "208750631", "pos_cid": 1650181, "source": "eval20x26"}
{"query_id": "scaleup_52110583_11930184", "query": "How to determine whether the atmospheric anomaly of 774 had a solar origin and how its intensity varied with latitude", "pos": ["Production of cosmogenic isotopes 7Be, 10Be, 14C, 22Na, and 36Cl in the atmosphere: Altitudinal profiles of yield functions. New consistent and precise computations of the production of five cosmogenic radioisotopes, 7Be, 10Be, 14C, 22Na, and 36Cl, in the Earth's atmosphere by cosmic rays are presented in the form of tabulated yield functions. For the first time, a detailed set of the altitude profiles of the production functions is provided which makes it possible to apply the results directly as input for atmospheric transport models. Good agreement with most of the earlier published works for columnar and global isotopic production rates is shown. Altitude profiles of the production are important, in particular for such tasks as studies of strong solar particle events in the past, precise reconstructions of solar activity on long‐term scale, tracing air mass dynamics using cosmogenic radioisotopes, etc. As an example, computations of the 10Be deposition flux in the polar region are shown for the last decades and also for a period around 780 A.D. and confronted with the actual measurements in Greenland and Antarctic ice cores."], "field": "Earth and Planetary Sciences", "q_year": 2018, "q_cid": "52110583", "pos_cid": 119301845, "source": "eval20x26"}
{"query_id": "scaleup_13527454_12374605", "query": "How to explain why dune sand remains largely immobile during autumn and winter despite winds favorable for sand movement", "pos": ["Likely frost events at Gale crater: Analysis from MSL/REMS measurements. Abstract We provide indirect evidence for the formation of frost at the surface of Gale crater by analyzing the highest confidence data from simultaneous measurements of relative humidity and ground temperature during the first 1000 sols of the Mars Science Laboratory (MSL) mission. We find that except for sol 44, frost events could have occurred only between sols 400 and 710, corresponding to the most humid and coldest time of the year (from early fall to late winter). In particular, measurements at Dingo Gap during sols 529–535, at an unnamed place during sols 554–560, at Kimberley during sols 609–617 and at an unnamed place during sols 673–676 showed the largest likelihood of the occurrence of frost events. At these four locations, the terrain is composed of fine-grained and loosely packed material with thermal inertia values of ∼200 SI units, much lower than the 365 ± 50 SI units value found at the landing ellipse. This is important because terrains with exceptionally low thermal inertia favor the formation of frost by lowering minimum daily ground temperatures. An order-of-magnitude calculation to determine the thickness of the frost layer at these four locations results in values of tenths of µm, while the precipitable water content is a few pr-µm. Therefore, surface frost events can have important implications for the local water cycle at Gale crater. In addition, frost is the most likely type of water that can be temporarily found in bulk amounts on the surface of Mars at low latitudes and therefore can cause weathering, influencing the geology of Gale crater."], "field": "Earth and Planetary Sciences", "q_year": 2018, "q_cid": "135274540", "pos_cid": 123746057, "source": "eval20x26"}
{"query_id": "scaleup_56447530_5692281", "query": "How to efficiently generate high-quality computational meshes that satisfy spatially varying cell-spacing or data-based density requirements", "pos": ["Locally-orthogonal, unstructured grid-generation for general circulation modelling on the sphere. Abstract. An algorithm for the generation of non-uniform, locally orthogonal staggered unstructured spheroidal grids is described. This technique is designed to generate very high-quality staggered Voronoi–Delaunay meshes appropriate for general circulation modelling on the sphere, including applications to atmospheric simulation, ocean-modelling and numerical weather prediction. Using a recently developed Frontal-Delaunay refinement technique, a method for the construction of high-quality unstructured spheroidal Delaunay triangulations is introduced. A locally orthogonal polygonal grid, derived from the associated Voronoi diagram, is computed as the staggered dual. It is shown that use of the Frontal-Delaunay refinement technique allows for the generation of very high-quality unstructured triangulations, satisfying a priori bounds on element size and shape. Grid quality is further improved through the application of hill-climbing-type optimisation techniques. Overall, the algorithm is shown to produce grids with very high element quality and smooth grading characteristics, while imposing relatively low computational expense. A selection of uniform and non-uniform spheroidal grids appropriate for high-resolution, multi-scale general circulation modelling are presented. These grids are shown to satisfy the geometric constraints associated with contemporary unstructured C-grid-type finite-volume models, including the Model for Prediction Across Scales (MPAS-O). The use of user-defined mesh-spacing functions to generate smoothly graded, non-uniform grids for multi-resolution-type studies is discussed in detail."], "field": "Earth and Planetary Sciences", "q_year": 2018, "q_cid": "56447530", "pos_cid": 5692281, "source": "eval20x26"}
{"query_id": "scaleup_52665_26422754", "query": "How to determine when seawater conditions will become unfavorable for larval shellfish production before aragonite dissolution becomes possible", "pos": ["The representative concentration pathways: an overview. This paper summarizes the development process and main characteristics of the Representative Concentration Pathways (RCPs), a set of four new pathways developed for the climate modeling community as a basis for long-term and near-term modeling experiments. The four RCPs together span the range of year 2100 radiative forcing values found in the open literature, i.e. from 2.6 to 8.5 W/m2. The RCPs are the product of an innovative collaboration between integrated assessment modelers, climate modelers, terrestrial ecosystem modelers and emission inventory experts. The resulting product forms a comprehensive data set with high spatial and sectoral resolutions for the period extending to 2100. Land use and emissions of air pollutants and greenhouse gases are reported mostly at a 0.5 × 0.5 degree spatial resolution, with air pollutants also provided per sector (for well-mixed gases, a coarser resolution is used). The underlying integrated assessment model outputs for land use, atmospheric emissions and concentration data were harmonized across models and scenarios to ensure consistency with historical observations while preserving individual scenario trends. For most variables, the RCPs cover a wide range of the existing literature. The RCPs are supplemented with extensions (Extended Concentration Pathways, ECPs), which allow climate modeling experiments through the year 2300. The RCPs are an important development in climate research and provide a potential foundation for further research and assessment, including emissions mitigation and impact analysis."], "field": "Earth and Planetary Sciences", "q_year": 2015, "q_cid": "52665", "pos_cid": 264227544, "source": "eval20x26"}
{"query_id": "scaleup_92044903_73565461", "query": "How to predict when geodiversity is strongly associated with biodiversity within and between locations across spatial scales", "pos": ["The spatial scaling of beta diversity. Beta diversity is an important concept used to describe turnover in species composition across a wide range of spatial and temporal scales, and it underpins much of conservation theory and practice. Although substantial progress has been made in the mathematical and terminological treatment of different measures of beta diversity, there has been little conceptual synthesis of potential scale dependence of beta diversity with increasing spatial grain and geographic extent of sampling. Here, we evaluate different conceptual approaches to the spatial scaling of beta diversity, interpreted from ‘fixed’ and ‘varying’ perspectives of spatial grain and extent. We argue that a ‘sliding window’ perspective, in which spatial grain and extent covary, is an informative way to conceptualize community differentiation across scales. This concept more realistically reflects the varying empirical approaches that researchers adopt in field sampling and the varying scales of landscape perception by different organisms. Scale dependence in beta diversity has broad implications for emerging fields in ecology and biogeography, such as the integration of fine-resolution ecogenomic data with large-scale macroecological studies, as well as for guiding appropriate management responses to threats to biodiversity operating at different spatial scales."], "field": "Earth and Planetary Sciences", "q_year": 2019, "q_cid": "92044903", "pos_cid": 73565461, "source": "eval20x26"}
{"query_id": "scaleup_25106824_21426550", "query": "How to disentangle individual environmental factors’ contributions to Arctic aerosol concentration variations when relationships are nonlinear and depend on particle size and source", "pos": ["From Local Explanations to Global Understanding with Explainable AI for Trees. Tree-based machine learning models such as random forests, decision trees and gradient boosted trees are popular nonlinear predictive models, yet comparatively little attention has been paid to explaining their predictions. Here we improve the interpretability of tree-based models through three main contributions. (1) A polynomial time algorithm to compute optimal explanations based on game theory. (2) A new type of explanation that directly measures local feature interaction effects. (3) A new set of tools for understanding global model structure based on combining many local explanations of each prediction. We apply these tools to three medical machine learning problems and show how combining many high-quality local explanations allows us to represent global structure while retaining local faithfulness to the original model. These tools enable us to (1) identify high-magnitude but low-frequency nonlinear mortality risk factors in the US population, (2) highlight distinct population subgroups with shared risk characteristics, (3) identify nonlinear interaction effects among risk factors for chronic kidney disease and (4) monitor a machine learning model deployed in a hospital by identifying which features are degrading the model’s performance over time. Given the popularity of tree-based machine learning models, these improvements to their interpretability have implications across a broad set of domains. Tree-based machine learning models are widely used in domains such as healthcare, finance and public services. The authors present an explanation method for trees that enables the computation of optimal local explanations for individual predictions, and demonstrate their method on three medical datasets."], "field": "Earth and Planetary Sciences", "q_year": 2022, "q_cid": "251068242", "pos_cid": 214265509, "source": "eval_collection"}
{"query_id": "scaleup_22807663_4810729", "query": "How to assess shrub nutrient acquisition without conflating resource uptake with transport and storage", "pos": ["Redefining fine roots improves understanding of below-ground contributions to terrestrial biosphere processes.. Fine roots acquire essential soil resources and mediate biogeochemical cycling in terrestrial ecosystems. Estimates of carbon and nutrient allocation to build and maintain these structures remain uncertain because of the challenges of consistently measuring and interpreting fine-root systems. Traditionally, fine roots have been defined as all roots ≤ 2 mm in diameter, yet it is now recognized that this approach fails to capture the diversity of form and function observed among fine-root orders. Here, we demonstrate how order-based and functional classification frameworks improve our understanding of dynamic root processes in ecosystems dominated by perennial plants. In these frameworks, fine roots are either separated into individual root orders or functionally defined into a shorter-lived absorptive pool and a longer-lived transport fine-root pool. Using these frameworks, we estimate that fine-root production and turnover represent 22% of terrestrial net primary production globally - a c. 30% reduction from previous estimates assuming a single fine-root pool. Future work developing tools to rapidly differentiate functional fine-root classes, explicit incorporation of mycorrhizal fungi into fine-root studies, and wider adoption of a two-pool approach to model fine roots provide opportunities to better understand below-ground processes in the terrestrial biosphere."], "field": "Earth and Planetary Sciences", "q_year": 2020, "q_cid": "228076634", "pos_cid": 4810729, "source": "eval_collection"}
{"query_id": "scaleup_22809050_54931100", "query": "How to assess the effects of glacial north pacific circulation on atmospheric carbon dioxide under nutrient and iron availability constraints", "pos": ["How well do global ocean biogeochemistry models simulate dissolved iron distributions?. Numerical models of ocean biogeochemistry are relied upon to make projections about the impact of climate change on marine resources and test hypotheses regarding the drivers of past changes in climate and ecosystems. In large areas of the ocean, iron availability regulates the functioning of marine ecosystems and hence the ocean carbon cycle. Accordingly, our ability to quantify the drivers and impacts of fluctuations in ocean ecosystems and carbon cycling in space and time relies on first achieving an appropriate representation of the modern marine iron cycle in models. When the iron distributions from 13 global ocean biogeochemistry models are compared against the latest oceanic sections from the GEOTRACES program, we find that all models struggle to reproduce many aspects of the observed spatial patterns. Models that reflect the emerging evidence for multiple iron sources or subtleties of its internal cycling perform much better in capturing observed features than their simpler contemporaries, particularly in the ocean interior. We show that the substantial uncertainty in the input fluxes of iron results in a very wide range of residence times across models, which has implications for the response of ecosystems and global carbon cycling to perturbations. Given this large uncertainty, iron fertilization experiments based on any single current generation model should be interpreted with caution. Improvements to how such models represent iron scavenging and also biological cycling are needed to raise confidence in their projections of global biogeochemical change in the ocean."], "field": "Earth and Planetary Sciences", "q_year": 2020, "q_cid": "228090508", "pos_cid": 54931100, "source": "eval_collection"}
{"query_id": "scaleup_28415420_25937571", "query": "How to describe the fine-grained attributes of a specific marine organism in an image, rather than the whole scene, with domain-specific detail despite morphological overlap among species", "pos": ["GPT4RoI: Instruction Tuning Large Language Model on Region-of-Interest. Visual instruction tuning large language model(LLM) on image-text pairs has achieved general-purpose vision-language abilities. However, the lack of region-text pairs limits their advancements to fine-grained multimodal understanding. In this paper, we propose spatial instruction tuning, which introduces the reference to the region-of-interest(RoI) in the instruction. Before sending to LLM, the reference is replaced by RoI features and interleaved with language embeddings as a sequence. Our model GPT4RoI, trained on 7 region-text pair datasets, brings an unprecedented interactive and conversational experience compared to previous image-level models. (1) Interaction beyond language: Users can interact with our model by both language and drawing bounding boxes to flexibly adjust the referring granularity. (2) Versatile multimodal abilities: A variety of attribute information within each RoI can be mined by GPT4RoI, e.g., color, shape, material, action, etc. Furthermore, it can reason about multiple RoIs based on common sense. On the Visual Commonsense Reasoning(VCR) dataset, GPT4RoI achieves a remarkable accuracy of 81.6%, surpassing all existing models by a significant margin (the second place is 75.6%) and almost reaching human-level performance of 85.0%. The code and model can be found at https://github.com/jshilong/GPT4RoI."], "field": "Earth and Planetary Sciences", "q_year": 2025, "q_cid": "284154201", "pos_cid": 259375716, "source": "eval_collection"}
{"query_id": "scaleup_26560998_24747629", "query": "How to capture grouping relationships reflected in image masks when the grouping of scene elements is ambiguous across physical scales", "pos": ["Unsupervised Semantic Segmentation by Distilling Feature Correspondences. Unsupervised semantic segmentation aims to discover and localize semantically meaningful categories within image corpora without any form of annotation. To solve this task, algorithms must produce features for every pixel that are both semantically meaningful and compact enough to form distinct clusters. Unlike previous works which achieve this with a single end-to-end framework, we propose to separate feature learning from cluster compactification. Empirically, we show that current unsupervised feature learning frameworks already generate dense features whose correlations are semantically consistent. This observation motivates us to design STEGO ($\\textbf{S}$elf-supervised $\\textbf{T}$ransformer with $\\textbf{E}$nergy-based $\\textbf{G}$raph $\\textbf{O}$ptimization), a novel framework that distills unsupervised features into high-quality discrete semantic labels. At the core of STEGO is a novel contrastive loss function that encourages features to form compact clusters while preserving their relationships across the corpora. STEGO yields a significant improvement over the prior state of the art, on both the CocoStuff ($\\textbf{+14 mIoU}$) and Cityscapes ($\\textbf{+9 mIoU}$) semantic segmentation challenges."], "field": "Earth and Planetary Sciences", "q_year": 2023, "q_cid": "265609986", "pos_cid": 247476291, "source": "eval_collection"}
{"query_id": "scaleup_21389900_12058674", "query": "How to determine whether the asymmetric pattern behind Guadalupe Island requires Earth’s rotation or can also arise from the island’s asymmetric shape", "pos": ["VORTEX SHEDDING IN FLOW PAST AN INCLINED FLAT PLATE AT HIGH INCIDENCE. The properties of asymmetric wake patterns behind a flat plate inclined at angles of attack 20°, 25°, and 30° are investigated. The Reynolds number based on the inflow velocity and the plate width is 1000. Both two-dimensional and three-dimensional calculations are performed by direct numerical simulations. Compared to the three-dimensional simulations, the two-dimensional calculations predict a significantly lower pressure on the rear surface of the plate, which consequently leads to very high drag and lift forces on the plate. The asymmetric mean wake flow, turbulence properties, and coherent patterns in the three-dimensional simulations are analysed by time- and phase-averaged techniques. Unlike the symmetric wake flow, the vortices shed from the leading and trailing edges of an inclined plate possess unequal strength with the trailing edge vortex having higher strength. It is observed that the present three-dimensional simulations predict results which compare well with the experimental data. In addit..."], "field": "Earth and Planetary Sciences", "q_year": 2020, "q_cid": "213899006", "pos_cid": 120586746, "source": "eval_collection"}
{"query_id": "scaleup_21019332_33617316", "query": "How to estimate extreme sea-level event probabilities where tide-gauge records are sparse or absent while accounting for relationships between events at different locations and differences in local conditions", "pos": ["A HIERARCHICAL MAX-STABLE SPATIAL MODEL FOR EXTREME PRECIPITATION. Extreme environmental phenomena such as major precipitation events manifestly exhibit spatial dependence. Max-stable processes are a class of asymptotically-justified models that are capable of representing spatial dependence among extreme values. While these models satisfy modeling requirements, they are limited in their utility because their corresponding joint likelihoods are unknown for more than a trivial number of spatial locations, preventing, in particular, Bayesian analyses. In this paper, we propose a new random effects model to account for spatial dependence. We show that our specification of the random effect distribution leads to a max-stable process that has the popular Gaussian extreme value process (GEVP) as a limiting case. The proposed model is used to analyze the yearly maximum precipitation from a regional climate model."], "field": "Earth and Planetary Sciences", "q_year": 2020, "q_cid": "210193323", "pos_cid": 33617316, "source": "eval_collection"}
{"query_id": "scaleup_21575019_8755162", "query": "How to track climate-induced range shifts in marine species when distribution records are scattered across diverse sources and have inconsistent formats", "pos": ["The FAIR Guiding Principles for scientific data management and stewardship. There is an urgent need to improve the infrastructure supporting the reuse of scholarly data. A diverse set of stakeholders—representing academia, industry, funding agencies, and scholarly publishers—have come together to design and jointly endorse a concise and measureable set of principles that we refer to as the FAIR Data Principles. The intent is that these may act as a guideline for those wishing to enhance the reusability of their data holdings. Distinct from peer initiatives that focus on the human scholar, the FAIR Principles put specific emphasis on enhancing the ability of machines to automatically find and use the data, in addition to supporting its reuse by individuals. This Comment is the first formal publication of the FAIR Principles, and includes the rationale behind them, and some exemplar implementations in the community."], "field": "Earth and Planetary Sciences", "q_year": 2020, "q_cid": "215750191", "pos_cid": 8755162, "source": "eval_collection"}
{"query_id": "scaleup_23401299_64247539", "query": "How to enable users to explore, evaluate, and analyze spatial information in environmental research databases in relation to real-world environments", "pos": ["Managing the Scalability of Visual Exploration Using Game Engines to Analyse UHI Scenarios. Abstract Large data sets have proven valuable to reveal behaviour phenomena in multidimensional problem spaces. As two-dimensional scientific visualizations are often limited in such scenarios, 4D spatial-temporal visualizations are increasingly raising interest. The huge data size often hinder loading of larger simulation scenes or longer animation sequences. This leads often to performance degrades and thus hinder the broad acceptance of such visualization techniques. We propose a visual pre-processing approach to overcome this challenge. In our research we study how domain knowledge can help to reduce data, guide exploration and the keep scene reloading effort to a minimum. We conduct a feasibility study for the visual pre-processing on heat emission data from cars using cellular automata for simulation and the Unity3D game engine for visualization. The results show a data reduction rate of more than 90% in the model/file size that leads without loss of the visual quality to significantly smoother scene change during urban heat island exploration."], "field": "Earth and Planetary Sciences", "q_year": 2021, "q_cid": "234012999", "pos_cid": 64247539, "source": "eval_collection"}
{"query_id": "scaleup_26516010_13395208", "query": "How to isolate seasonal variations in a corrected vertical displacement time series containing step changes and transient signals of unknown timing and number", "pos": ["Greedy Automatic Signal Decomposition and Its Application to Daily GPS Time Series. The recognition of transient motion in terrestrial continuous Global Positioning System (GPS) time series implies the knowledge of certain time functions that we assume to be ever present in the time series. By assuming that the permanent time functions are the long‐term secular velocity of the Earth and the seasonal oscillations, we define the total remaining signal as transient motion. Here we adopt the multitransient as a versatile function for modeling transient motion over a range of time scales. We define the multitransient as the sum of two or more transient decaying functions with different characteristic time scales and identical onset times. We then demonstrate the greedy approach to fitting the time series by using a minimum number of multitransients (sparse functions) in addition to the permanent time functions in a linear regression. The Greedy Automatic Signal Decomposition algorithm decomposes the signal into three parts: (1) background seasonal motion, (2) secular and transient motion, and (3) a residual (noise). We describe the greedy algorithm with synthetic examples before demonstrating its application to time series of daily GPS solutions. The implementation of the multitransient allows for a more realistic plate‐trajectory model, whereby a full range of transient signal time scales, from short‐duration slow slip to longer‐duration processes such as postseismic slab accelerations or postseismic decay, can all be estimated with the same function. Since Greedy Automatic Signal Decomposition algorithm automatically estimates trend, its application to a GPS network allows for the common mode filter to be applied seamlessly."], "field": "Earth and Planetary Sciences", "q_year": 2023, "q_cid": "265160108", "pos_cid": 133952086, "source": "eval_collection"}
{"query_id": "scaleup_27701559_25320269", "query": "How to determine when cooling igneous sills can admit surrounding fluids and sustain their circulation", "pos": ["Impact of permeability evolution in igneous sills on hydrothermal flow and hydrocarbon transport in volcanic sedimentary basins. Abstract. Sills emplaced in organic-rich sedimentary rocks trigger the generation and migration of hydrocarbons in volcanic sedimentary basins. Based on seismic and geological observations, numerical modeling studies of hydrothermal flow around sills show that thermogenic methane is channeled below the intrusion towards its tip, where hydrothermal vents nucleate and transport methane to the surface. However, these models typically assume impermeable sills and ignore potential effects of permeability evolution in cooling sills, e.g., due to fracturing. Here, we combine a geological field study of a volcanic basin (Neuquén Basin, Argentina) with a hybrid finite-element–finite-volume method (FEM–FVM) of numerical modeling of hydrothermal flow around a sill, including hydrocarbon generation and transport. Our field observations show widespread veins within sills composed of graphitized bitumen and cooling joints filled with solid bitumen or fluidized shale. Raman spectroscopy indicates graphitization at temperatures between 350 and 500 ∘C, suggesting fluid flow within the intrusions during cooling. This finding motivates our modeling setup, which investigates flow patterns around and through intrusions that become porous and permeable upon solidification. The results show three flow phases affecting the transport of hydrocarbons generated in the contact aureole: (1) contact-parallel flow toward the sill tip prior to solidification, (2) upon complete solidification, sudden vertical “flushing” of overpressured hydrocarbon-rich fluids from the lower contact aureole towards and into the hot sill along its entire length, and (3) stabilization of hydrocarbon distribution and fading hydrothermal flow. In low-permeability host rocks, hydraulic fracturing facilitates flow and hydrocarbon migration toward the sill by temporarily elevating porosity and permeability. Up to 7.5 % of the generated methane is exposed to temperatures >400 ∘C in the simulations and may thus be permanently stored as graphite in or near the sill. Porosity and permeability creation within cooling sills may impact hydrothermal flow, hydrocarbon transport, and venting in volcanic basins, as it considerably alters the fluid pressure configuration, provides vertical flow paths, and helps to dissipate overpressure below the sills."], "field": "Earth and Planetary Sciences", "q_year": 2025, "q_cid": "277015591", "pos_cid": 253202692, "source": "eval_collection"}
{"query_id": "scaleup_27945605_12072406", "query": "How to reconstruct past rainfall amounts in northern Africa without confounding effects from temperature, altitude, or moisture source", "pos": ["Stable isotopes in precipitation. In chapter 2 the isotopic fractionation of water in some simple condensation-evaporation processes are considered quantitatively on the basis of the fractionation factors given in section 1.2. The condensation temperature is an important parameter, which has got some glaciological applications. The temperature effect (the δ's decreasing with temperature) together with varying evaporation and exchange appear in the “amount effect” as high δ's in sparse rain. The relative deuterium-oxygen-18 fractionation is not quite simple. If the relative deviations from the standard water (S.M.O.W.) are called δ D and δ 18 , the best linear approximation is δ D = 8 δ 18 . Chapter 3 gives some qualitative considerations on non-equilibrium (fast) processes. Kinetic effects have heavy bearings upon the effective fractionation factors. Such effects have only been demonstrated clearly in evaporation processes, but may also influence condensation processes. The quantity d = δ D −8 δ 18 is used as an index for non-equilibrium conditions. The stable isotope data from the world wide I.A.E.A.-W.M.O. precipitation survey are discussed in chapter 4. The unweighted mean annual composition of rain at tropical island stations fits the line δ D = 4.6 δ 18 indicating a first stage equilibrium condensation from vapour evaporated in a non-equilibrium process. Regional characteristics appear in the weighted means. The Northern hemisphere continental stations, except African and Near East, fit the line δ D = 8.0 δ 18 + 10 as far as the weighted means are concerned (δ D = 8.1 δ 18 + 11 for the unweighted) corresponding to an equilibrium Rayleigh condensation from vapour, evaporated in a non-equilibrium process from S.M.O.W. The departure from equilibrium vapour seems even higher in the rest of the investigated part of the world. At most stations the δ D and varies linearily with δ 18 with a slope close to 8, only at two stations higher than 8, at several lower than 8 (mainly connected with relatively dry climates). Considerable variations in the isotopic composition of monthly precipitation occur at most stations. At low latitudes the amount effect accounts for the variations, whereas seasonal variation at high latitudes is ascribed to the temperature effect. Tokyo is an example of a mid latitude station influenced by both effects. Some possible hydrological applications are outlined in chapter 5. DOI: 10.1111/j.2153-3490.1964.tb00181.x"], "field": "Earth and Planetary Sciences", "q_year": 2025, "q_cid": "279456050", "pos_cid": 120724062, "source": "eval_collection"}
{"query_id": "scaleup_26076016_24953680", "query": "How to simplify counting small Wolffia fronds to measure growth inhibition when assessing contaminant toxicity in duckweed", "pos": ["Performance Comparison of Five Methods for Tetrahymena Number Counting on the ImageJ Platform: Assessing the Built-in Tool and Machine-Learning-Based Extension. Previous methods to measure protozoan numbers mostly rely on manual counting, which suffers from high variation and poor efficiency. Although advanced counting devices are available, the specialized and usually expensive machinery precludes their prevalent utilization in the regular laboratory routine. In this study, we established the ImageJ-based workflow to quantify ciliate numbers in a high-throughput manner. We conducted Tetrahymena number measurement using five different methods: particle analyzer method (PAM), find maxima method (FMM), trainable WEKA segmentation method (TWS), watershed segmentation method (WSM) and StarDist method (SDM), and compared their results with the data obtained from the manual counting. Among the five methods tested, all of them could yield decent results, but the deep-learning-based SDM displayed the best performance for Tetrahymena cell counting. The optimized methods reported in this paper provide scientists with a convenient tool to perform cell counting for Tetrahymena ecotoxicity assessment."], "field": "Earth and Planetary Sciences", "q_year": 2023, "q_cid": "260760162", "pos_cid": 249536804, "source": "eval_collection"}
{"query_id": "scaleup_28000372_12491331", "query": "How to accurately determine ground motion without underestimating its magnitude due to spatial averaging", "pos": ["Vector-based approach for combining ascending and descending persistent scatterers interferometric point measurements. Abstract The combination of ascending and descending persistent scatterers interferometric (PSI) data by means of resampling and/or spatial interpolation, separately for each synthetic aperture radar geometry, is a commonly followed procedure, limited though by the reduced spatial coverage and the introduced uncertainties from multiple rasterization steps. Herein, an alternative approach is proposed for combining different PSI line-of-sight observables in the vector domain, based on the geographic proximity of PS point targets. In the proposed nearest neighbour vector approach all necessary analysis steps are performed by means of attributes transfer and calculations between features geodatabases, prior to any rasterization. By increasing the number of input point vectors during subsequent interpolation, the overall error budget coming from spatial interpolation is being reduced. The advantages of the proposed vector-based approach compared to the commonly used grid-based procedure are being demonstrated using real data."], "field": "Earth and Planetary Sciences", "q_year": 2025, "q_cid": "280003721", "pos_cid": 124913316, "source": "eval_collection"}
{"query_id": "scaleup_28000372_55926158", "query": "How to determine whether the volume involved in the current episode is consistent with accumulation over the 14 years since the previous episode, given the available supply", "pos": ["The emergence and growth of a submarine volcano : the Kameni islands, Santorini (Greece).. The morphology of a volcanic edifice reflects the integrated eruptive and evolutionary history of that system, and can be used to reconstruct the time-series of prior eruptions. We present a new high-resolution merged LiDAR-bathymetry grid, which has enabled detailed mapping of both onshore and offshore historic lava flows of the Kameni islands, emplaced in the centre of the Santorini caldera since at least AD 46. We identify three new submarine lava flows: two flows, of unknown age, lie to the east of Nea Kameni and a third submarine flow, located north of Nea Kameni appears to predate the 1925–1928 lava flows but was emplaced subsequent to the 1707–1711 lava flows. Yield strength estimates derived from the morphology of the 1570/1573 lobe suggest that submarine lava strengths are approximately two times greater than those derived from the onshore flows. To our knowledge this is the first documented yield strength estimate for submarine flows. This increase in strength is likely related to cooling and thickening of the dacite lava flows as they displace sea water. Improved lava volume estimates derived from the merged LiDAR-Bathymetry grid suggest typical lava extrusion rates of ∼2–3 m3 s−1 during four of the historic eruptions on Nea Kameni (1707–1711, 1866–1870, 1925–1928 and 1939–1941). They also reveal a linear relationship between the pre-eruption interval and the volume of extruded lava. These observations may be used to estimate the size of future dome-building eruptions at Santorini volcano, based on the time interval since the last significant eruption."], "field": "Earth and Planetary Sciences", "q_year": 2025, "q_cid": "280003721", "pos_cid": 55926158, "source": "eval_collection"}
{"query_id": "scaleup_28372271_21426550", "query": "How to determine how much each meteorological factor contributes to predicted oxidant responses for individual observations while remaining computationally feasible across the full data set", "pos": ["From Local Explanations to Global Understanding with Explainable AI for Trees. Tree-based machine learning models such as random forests, decision trees and gradient boosted trees are popular nonlinear predictive models, yet comparatively little attention has been paid to explaining their predictions. Here we improve the interpretability of tree-based models through three main contributions. (1) A polynomial time algorithm to compute optimal explanations based on game theory. (2) A new type of explanation that directly measures local feature interaction effects. (3) A new set of tools for understanding global model structure based on combining many local explanations of each prediction. We apply these tools to three medical machine learning problems and show how combining many high-quality local explanations allows us to represent global structure while retaining local faithfulness to the original model. These tools enable us to (1) identify high-magnitude but low-frequency nonlinear mortality risk factors in the US population, (2) highlight distinct population subgroups with shared risk characteristics, (3) identify nonlinear interaction effects among risk factors for chronic kidney disease and (4) monitor a machine learning model deployed in a hospital by identifying which features are degrading the model’s performance over time. Given the popularity of tree-based machine learning models, these improvements to their interpretability have implications across a broad set of domains. Tree-based machine learning models are widely used in domains such as healthcare, finance and public services. The authors present an explanation method for trees that enables the computation of optimal local explanations for individual predictions, and demonstrate their method on three medical datasets."], "field": "Earth and Planetary Sciences", "q_year": 2025, "q_cid": "283722710", "pos_cid": 214265509, "source": "eval_collection"}
{"query_id": "scaleup_26718679_10958663", "query": "How to estimate the volume of potential landslide material between a ground surface and a subsurface slipping plane with varying elevations", "pos": ["Application of Surfer in Quality Inspection of Waterway Dredging. GPSRTK and depth sounder technology provides a foundation for outdoor digital sampling of waterway dredging quality inspection. The gathered sample data can be used by Surfer to develop a 3D underwater topography model. Surfer can create 3D visualization through 3D space analysis, makes precise calculation of underwater earthwork load possible. Based on the Hangzhou-Ningbo canal dredging project, this paper describes the applied work principle and procedure of Surfer in quality inspection of waterway dredging. The technical aspect of cross section surveying and quality inspection is also analyzed. Surfer can adopt Trapezoidal Rule, Simpson’s Rule and Simpson’s 3/8 Rule to calculate volume. This paper performs error analysis on the results of each algorithm and proves the accuracy, reliability and efficiency of Surfer in waterway dredging quality inspection."], "field": "Earth and Planetary Sciences", "q_year": 2024, "q_cid": "267186797", "pos_cid": 109586638, "source": "eval_collection"}
{"query_id": "scaleup_23580797_2159031", "query": "How to explain why some genes in marine plants are constitutively expressed while others respond flexibly to environmental stress", "pos": ["Is There a Relationship between DNA Methylation and Phenotypic Plasticity in Invertebrates?. There is a significant amount of variation in DNA methylation characteristics across organisms. Likewise, the biological role of DNA methylation varies across taxonomic lineages. The complexity of DNA methylation patterns in invertebrates has only recently begun to be characterized in-depth. In some invertebrate species that have been examined to date, methylated DNA is found primarily within coding regions and patterning is closely associated with gene function. Here we provide a perspective on the potential role of DNA methylation in these invertebrates with a focus on how limited methylation may contribute to increased phenotypic plasticity in highly fluctuating environments. Specifically, limited methylation could facilitate a variety of transcriptional opportunities including access to alternative transcription start sites, increasing sequence mutations, exon skipping, and transient methylation."], "field": "Earth and Planetary Sciences", "q_year": 2021, "q_cid": "235807976", "pos_cid": 2159031, "source": "eval_collection"}
{"query_id": "scaleup_26718679_13486619", "query": "How to identify weak subsurface materials, potential slipping regions, and slope-failure triggers in residual soils under heavy rainfall", "pos": ["The use of cross-plots in lithology delineation and petrophysical evaluation of some wells in the western Coastal Swamp, Niger Delta. The inaccurate delineation of the sand intervals in well logs can significantly affect the porosity, permeability, pore-size geometry and net-to-gross ratio of the reservoir units. This study utilized well log cross-plots to accurately delineate the lithologic units and also used petrophysical evaluation methods to determine the reservoir properties of the sandstone intervals in three wells (L, M, N wells) of the Daura field, Niger Delta. The cross-plots of the gamma ray with density, gamma ray with sonic and gamma ray with depth were generated using the Hampson Russel software. The result of the cross-plot clusters shows two major lithologies of sandstone and shale with occasional intercalation of sand and shale units. Fluid detection analysis shows that reservoirs L3 (well L), M4–M5 (well M), and N2–N3 (well N) were found to contain oil, while reservoir M2 (well M) contains gas. The rest of the reservoir intervals in the three wells contain water, and the average porosity ranges from 14.23 to 28.01%. This study has shown that the cross-plots approach can be used to accurately delineate reservoirs for further formation evaluation. It therefore means that an outright estimation of petrophysical properties on wrongly delineated reservoirs can significantly affect the porosity, permeability, pore-size geometry and net-to-gross ratio of the reservoir units."], "field": "Earth and Planetary Sciences", "q_year": 2024, "q_cid": "267186797", "pos_cid": 134866192, "source": "eval_collection"}
{"query_id": "scaleup_26718209_25592001", "query": "How to reduce organic matter inputs from rivers into coastal waters during periods of elevated river discharge", "pos": ["Capturing of organic carbon and nitrogen in eelgrass sediments of southern Scandinavia. The ability of seagrass meadows to filter nutrients and capture and store CO2 and nutrients in the form of organic carbon (OC) and nitrogen (N) in their sediments may help to mitigate local eutrophication as well as climate change via meadow restoration and protection. This study assesses OC and N sediment stocks (top 50 cm) and sequestration rates within Danish eelgrass meadows. At four locations, eelgrass‐vegetated and nearby unvegetated plots were studied in protected and exposed areas. The average OC and N sediment 50 cm stocks were 2.6 ± 0.3 kg OC m−2 and 0.23 ± 0.01 kg N m−2, including vegetated and unvegetated plots. In general, OC and N stocks did not differ significantly between eelgrass meadows and unvegetated sediments. Lack of accumulation of excess 210Pb suggested sediment erosion or low rates of sediment accumulation at most sites. OC accumulation rates ranged from 6 to 134 g m−2 yr−1 and N from 0.7 to 14 g m−2 yr−1. Generalized additive models showed that ≥ 80% of the variation in sediment OC and N stocks was explained by sediment grain size, organic matter source, and hydrodynamic exposure. Long cores, dated with 210Pb, showed declining OC and N densities toward present time, suggesting long‐term declines in eelgrass OC and N pools. Estimates of potential nation‐wide OC and N accumulation in eelgrass sediments show that they could annually capture up to 0.7% ± 0.5% of CO2 emissions and 6.9% ± 5.2% of the total terrestrial N load."], "field": "Earth and Planetary Sciences", "q_year": 2024, "q_cid": "267182096", "pos_cid": 255920018, "source": "eval_collection"}
{"query_id": "scaleup_27952720_23420862", "query": "How to clarify Aluto’s shallow reservoir physical state, fluid origins and roles, seismic activity and unrest, magmatic–hydrothermal connections, and geothermal reservoir sensitivity to small stress changes", "pos": ["Integrated magnetotelluric and petrological analysis of felsic magma reservoirs: Insights from Ethiopian rift volcanoes. Geophysical and petrological probes are key to understanding the structure and the thermochemical state of active magmatic systems. Recent advances in laboratory analyses, field investigations and numerical methods have allowed increasingly complex data-constraint models with new insights into magma plumbing systems and melt evolution. However, there is still a need for methods to quantitatively link geophysical and petrological observables for a more consistent description of magmatic processes at both micro- and macro-scales. Whilst modern geophysical studies provide detailed 3-D subsurface images that help to characterize magma reservoirs by relating state variables with physical material properties, constraints from on-site petrological analyses and thermodynamic modelling of melt evolution are at best incorporated qualitatively. Here, we combine modelling of phase equilibria in cooling magma and laboratory measurements of electrical properties of melt to derive the evolution of electrical conductivity in a crystallizing silicic magmatic system. We apply this framework to 3-D electrical conductivity images from magnetotelluric studies of two volcanoes in the Ethiopian Rift. The presented approach enables us to constrain key variables such as melt content, temperature and magmatic volatile abundance at depth. Our study shows that accounting for magmatic volatiles as an independent phase is crucial for understanding electrical conductivity structures in magma reservoirs at an advanced state of crystallization. Furthermore, our results deepen the understanding of the mechanisms behind volcanic unrest and help assess the long-term potential of hydrothermal reservoirs for geothermal energy production."], "field": "Earth and Planetary Sciences", "q_year": 2025, "q_cid": "279527204", "pos_cid": 234208627, "source": "eval_collection"}
{"query_id": "scaleup_24383518_24434848", "query": "How to consistently compare dental complexity across dinosaurs and living saurians despite differences in tooth size, surface morphology, scanner resolution, and fossil damage", "pos": ["The Application of Dental Complexity Metrics on Extant Saurians. Abstract: Quantifying morphology has become increasingly popular with the advent of widely available high-powered computing. Orientation patch count rotated (OPCR) is an important measurement of dental surface complexity and has been shown to relate to diet, with carnivores possessing simple teeth and herbivores exhibiting complex dentitions. This method, however, has primarily been applied to mammals with comparatively little research focusing on dentigerous reptiles. Three methods are currently used to measure dental complexity (Surfer Manipulator, molaR, and MorphoTester), and the comparability of these methods remains untested in saurian datasets. Here, we test for differences among the three dental complexity methods using a dataset comprising lepidosaur and crocodylian teeth. Additionally, we seek to test the hypothesis that phenotypic dental complexity is related to dietary ecology using the molaR and MorphoTester OPCR methods. We find that Surfer Manipulator and 3D-OPCR methods (molaR and MorphoTester) generate different complexities, with molaR and MorphoTester consistently producing higher complexity values. The relationship between diet and dental complexity was recovered using molaR and MorphoTester, with carnivores possessing simple teeth and herbivores exhibiting significantly more-complex teeth, but this trend was not as distinct as when using Surfer Manipulator. Dental complexities were highly dependent on model preparation, in particular the triangle count of each 3D model, with surfaces that possess a greater number of faces exhibiting higher complexities. We present a series of recommendations that will help guide future studies of nonmammalian dentitions. Ultimately, 3D-OPCR methods are a fruitful area of research and represent a relatively untapped avenue of quantitative herpetology."], "field": "Earth and Planetary Sciences", "q_year": 2021, "q_cid": "243835180", "pos_cid": 244348484, "source": "eval_collection"}
{"query_id": "scaleup_27945605_26415834", "query": "How to determine how the relationship between two records with differing temporal resolutions varies over time and across periodicities", "pos": ["Application of the cross wavelet transform and wavelet coherence to geophysical time series. Many scientists have made use of the wavelet method in analyzing time series, often using popular free software. However, at present there are no similar easy to use wavelet packages for analyzing two time series together. We discuss the cross wavelet transform and wavelet coher- ence for examining relationships in time frequency space be- tween two time series. We demonstrate how phase angle statistics can be used to gain confidence in causal relation- ships and test mechanistic models of physical relationships between the time series. As an example of typical data where such analyses have proven useful, we apply the methods to the Arctic Oscillation index and the Baltic maximum sea ice extent record. Monte Carlo methods are used to assess the statistical significance against red noise backgrounds. A software package has been developed that allows users to perform the cross wavelet transform and wavelet coherence (http://www.pol.ac.uk/home/research/waveletcoherence/). As we are interested in extracting low s/n ratio signals in time series we discuss only CWT in this paper. While CWT is a common tool for analyzing localized intermittent os- cillations in a time series, it is very often desirable to ex- amine two time series together that may be expected to be linked in some way. In particular, to examine whether re- gions in time frequency space with large common power have a consistent phase relationship and therefore are sug- gestive of causality between the time series. Many geophys- ical time series are not Normally distributed and we suggest methods of applying the CWT to such time series. From two CWTs we construct the Cross Wavelet Transform (XWT) which will expose their common power and relative phase in time-frequency space. We will further define a measure of Wavelet Coherence (WTC) between two CWT, which can find significant coherence even though the common power is low, and show how confidence levels against red noise back- grounds are calculated. We will present the basic CWT theory before we move on to XWT and WTC. New developments such as quanti- fying the phase relationship and calculating the WTC sig- nificance level will be treated more fully. When using the methods on time series it is important to have solid mecha- nistic foundations on which to base any relationships found, and we caution against using the methods in a \"scatter-gun\" approach (particularly if the time series probability density functions are modified). To illustrate how the various meth- ods are used we apply them to two data sets from meteo- rology and glaciology. Finally, we will provide links to a MatLab software package."], "field": "Earth and Planetary Sciences", "q_year": 2025, "q_cid": "279456050", "pos_cid": 264158349, "source": "eval_collection"}
{"query_id": "scaleup_23876925_99152845", "query": "How to identify phenolic compounds in C. officinalis and G. pulchellum extracts despite weak spectra and poorly defined bands", "pos": ["Surface enhanced Raman spectroscopy of phenolic antioxidants: A systematic evaluation of ferulic acid, p-coumaric acid, caffeic acid and sinapic acid. Abstract Surface-Enhanced Raman Spectroscopy (SERS) is a powerful surface-sensitive technique to study the vibrational properties of analytes at very low levels of concentration. In particular, detection of bioactive molecules, specifically antioxidants, is an area of interest to gain insights into the reproducible and quantitative SERS-determination. In this study, SERS measurements were systematically evaluated for ferulic acid, p -coumaric acid, caffeic acid and sinapic acid. The study objective in this research was to: 1) prepare and characterize SERS-active silver colloids; 2) cluster the as-obtained colloids through Principal Component Analysis on the basis of concentration and nanoparticle size; and 3) develop a highly sensitive SERS-based method for phenolic antioxidant detection. The reliability of the proposed method was demonstrated through detection of the phenolic antioxidants evaluated at low levels of concentration. In particular, sinapic acid was evaluated for the first time, with a limit of detection of 2.5 × 10 −9 M."], "field": "Earth and Planetary Sciences", "q_year": 2021, "q_cid": "238769255", "pos_cid": 99152845, "source": "eval_collection"}
{"query_id": "scaleup_27892147_18182893", "query": "How to quantitatively validate automated calving-front positions against manually delineated fronts for reliable characterization of rapid calving processes", "pos": ["Metrics for evaluating 3D medical image segmentation: analysis, selection, and tool. BackgroundMedical Image segmentation is an important image processing step. Comparing images to evaluate the quality of segmentation is an essential part of measuring progress in this research area. Some of the challenges in evaluating medical segmentation are: metric selection, the use in the literature of multiple definitions for certain metrics, inefficiency of the metric calculation implementations leading to difficulties with large volumes, and lack of support for fuzzy segmentation by existing metrics.ResultFirst we present an overview of 20 evaluation metrics selected based on a comprehensive literature review. For fuzzy segmentation, which shows the level of membership of each voxel to multiple classes, fuzzy definitions of all metrics are provided. We present a discussion about metric properties to provide a guide for selecting evaluation metrics. Finally, we propose an efficient evaluation tool implementing the 20 selected metrics. The tool is optimized to perform efficiently in terms of speed and required memory, also if the image size is extremely large as in the case of whole body MRI or CT volume segmentation. An implementation of this tool is available as an open source project.ConclusionWe propose an efficient evaluation tool for 3D medical image segmentation using 20 evaluation metrics and provide guidelines for selecting a subset of these metrics that is suitable for the data and the segmentation task."], "field": "Earth and Planetary Sciences", "q_year": 2025, "q_cid": "278921473", "pos_cid": 18182893, "source": "eval_collection"}
{"query_id": "scaleup_21389900_20313854", "query": "How to quantitatively characterize evolving atmospheric island wakes with reliable winds at accurate cloud-top altitudes despite insufficient spatial and temporal detail in satellite wind data", "pos": ["Joint 3D-Wind Retrievals with Stereoscopic Views from MODIS and GOES. Atmospheric motion vectors (AMVs), derived by tracking patterns, represent the winds in a layer characteristic of the pattern. AMV height (or pressure), important for applications in atmospheric research and operational meteorology, is usually assigned using observed IR brightness temperatures with a modeled atmosphere and can be inaccurate. Stereoscopic tracking provides a direct geometric height measurement of the pattern that an AMV represents. We extend our previous work with multi-angle imaging spectro–radiometer (MISR) and GOES to moderate resolution imaging spectroradiometer (MODIS) and the GOES-R series advanced baseline imager (ABI). MISR is a unique satellite instrument for stereoscopy with nine angular views along track, but its images have a narrow (380 km) swath and no thermal IR channels. MODIS provides a much wider (2330 km) swath and eight thermal IR channels that pair well with all but two ABI channels, offering a rich set of potential applications. Given the similarities between MODIS and VIIRS, our methods should also yield similar performance with VIIRS. Our methods, as enabled by advanced sensors like MODIS and ABI, require high-accuracy geographic registration in both systems but no synchronization of observations. AMVs are retrieved jointly with their heights from the disparities between triplets of ABI scenes and the paired MODIS granule. We validate our retrievals against MISR-GOES retrievals, operational GOES wind products, and by tracking clear-sky terrain. We demonstrate that the 3D-wind algorithm can produce high-quality AMV and height measurements for applications from the planetary boundary layer (PBL) to the upper troposphere, including cold-air outbreaks, wildfire smoke plumes, and hurricanes."], "field": "Earth and Planetary Sciences", "q_year": 2020, "q_cid": "213899006", "pos_cid": 203138546, "source": "eval_collection"}
{"query_id": "scaleup_28389104_16981129", "query": "How to reduce organ-specific damage and persistent rare earth element burden in exposed patients when chelation options are limited and standardized treatment protocols are lacking", "pos": ["Structural, chemical and biological aspects of antioxidants for strategies against metal and metalloid exposure. Oxidative stress contributes to the pathophysiology of exposure to heavy metals/metalloid. Beneficial renal effects of some medications, such as chelation therapy depend at least partially on the ability to alleviate oxidative stress. The administration of various natural or synthetic antioxidants has been shown to be of benefit in the prevention and attenuation of metal induced biochemical alterations. These include vitamins, N-acetylcysteine, α-lipoic acid, melatonin, dietary flavonoids and many others. Human studies are limited in this regard. Under certain conditions, surprisingly, the antioxidant supplements may exhibit pro-oxidant properties and even worsen metal induced toxic damage. To date, the evidence is insufficient to recommend antioxidant supplements in subject with exposure to metals. Prospective, controlled clinical trials on safety and effectiveness of different therapeutic antioxidant strategies either individually or in combination with chelating agent are indispensable. The present review focuses on structural, chemical and biological aspects of antioxidants particularly related to their chelating properties."], "field": "Earth and Planetary Sciences", "q_year": 2025, "q_cid": "283891043", "pos_cid": 16981129, "source": "eval_collection"}
{"query_id": "scaleup_27892147_25928701", "query": "How to monitor rapid glacier calving-front changes with sufficient temporal resolution and positional accuracy while minimizing computational and operational burdens", "pos": ["The Segment Anything Model (SAM) for Remote Sensing Applications: From Zero to One Shot. Segmentation is an essential step for remote sensing image processing. This study aims to advance the application of the Segment Anything Model (SAM), an innovative image segmentation model by Meta AI, in the field of remote sensing image analysis. SAM is known for its exceptional generalization capabilities and zero-shot learning, making it a promising approach to processing aerial and orbital images from diverse geographical contexts. Our exploration involved testing SAM across multi-scale datasets using various input prompts, such as bounding boxes, individual points, and text descriptors. To enhance the model's performance, we implemented a novel automated technique that combines a text-prompt-derived general example with one-shot training. This adjustment resulted in an improvement in accuracy, underscoring SAM's potential for deployment in remote sensing imagery and reducing the need for manual annotation. Despite the limitations encountered with lower spatial resolution images, SAM exhibits promising adaptability to remote sensing data analysis. We recommend future research to enhance the model's proficiency through integration with supplementary fine-tuning techniques and other networks. Furthermore, we provide the open-source code of our modifications on online repositories, encouraging further and broader adaptations of SAM to the remote sensing domain."], "field": "Earth and Planetary Sciences", "q_year": 2025, "q_cid": "278921473", "pos_cid": 259287018, "source": "eval_collection"}
{"query_id": "scaleup_28036885_26208415", "query": "How to detect small and indistinct vessels in satellite imagery as data arrive in a stream without losing previously learned information", "pos": ["RMT: Retentive Networks Meet Vision Transformers. Vision Transformer (ViT) has gained increasing attention in the computer vision community in recent years. How-ever, the core component of ViT, Self-Attention, lacks ex-plicit spatial priors and bears a quadratic computational complexity, thereby constraining the applicability of ViT. To alleviate these issues, we draw inspiration from the re-cent Retentive Network (RetNet) in the field of NLP, and propose RMT, a strong vision backbone with explicit spa-tial prior for general purposes. Specifically, we extend the RetNet's temporal decay mechanism to the spatial do-main, and propose a spatial decay matrix based on the Manhattan distance to introduce the explicit spatial prior to Self-Attention. Additionally, an attention decomposition form that adeptly adapts to explicit spatial prior is proposed, aiming to reduce the computational burden of modeling global information without disrupting the spa-tial decay matrix. Based on the spatial decay matrix and the attention decomposition form, we can flexibly integrate explicit spatial prior into the vision backbone with lin-ear complexity. Extensive experiments demonstrate that RMT exhibits exceptional performance across various vision tasks. Specifically, without extra training data, RMT achieves 84.8% and 86.1% top-l acc on ImageNet-lk with 27MI4.5GFLOPs and 96M/18.2GFLOPs. For downstream tasks, RMT achieves 54.5 box AP and 47.2 mask AP on the COCO detection task, and 52.8 mloU on the ADE20K se-mantic segmentation task."], "field": "Earth and Planetary Sciences", "q_year": 2025, "q_cid": "280368853", "pos_cid": 262084150, "source": "eval_collection"}
{"query_id": "scaleup_22807663_21441747", "query": "How to predict how expansion of different arctic shrub genera will affect belowground nutrient cycling in nutrient-poor tundra soils", "pos": ["The fungal collaboration gradient dominates the root economics space in plants. Collaboration broadens the “root economics space” ranging from “do-it-yourself” to “outsourcing” to mycorrhizal partners. Plant economics run on carbon and nutrients instead of money. Leaf strategies aboveground span an economic spectrum from “live fast and die young” to “slow and steady,” but the economy defined by root strategies belowground remains unclear. Here, we take a holistic view of the belowground economy and show that root-mycorrhizal collaboration can short circuit a one-dimensional economic spectrum, providing an entire space of economic possibilities. Root trait data from 1810 species across the globe confirm a classical fast-slow “conservation” gradient but show that most variation is explained by an orthogonal “collaboration” gradient, ranging from “do-it-yourself” resource uptake to “outsourcing” of resource uptake to mycorrhizal fungi. This broadened “root economics space” provides a solid foundation for predictive understanding of belowground responses to changing environmental conditions."], "field": "Earth and Planetary Sciences", "q_year": 2020, "q_cid": "228076634", "pos_cid": 214417473, "source": "eval_collection"}
{"query_id": "scaleup_26442154_18645782", "query": "How to represent the brightness of Arctic snow, white ice, and melt ponds under low solar elevation and varying satellite viewing angles", "pos": ["Geometrical considerations and nomenclature for reflectance. Report issued by the U.S. National Bureau of Standards discussing specifications of reflectance and proposed nomenclature. As stated in the introduction, \"this monograph presents a unified approach to the specification of reflectance in relation to the beam geometry of both the incident and the reflected flux in any reflectometer or in any application of measured reflectance data\" (p. 1). This report includes illustrations."], "field": "Earth and Planetary Sciences", "q_year": 2024, "q_cid": "264421540", "pos_cid": 18645782, "source": "eval_collection"}
{"query_id": "scaleup_22176103_51852421", "query": "How to identify biological particles potentially responsible for seasonal variations in ice-nucleating particle abundance despite fluorescence from both biological and nonbiological materials", "pos": ["Systematic characterization and fluorescence threshold strategies for the wideband integrated bioaerosol sensor ( WIBS ) using size-resolved biological and interfering particles. Atmospheric particles of biological origin, also referred to as bioaerosols or primary biological aerosol particles (PBAP), are important to various human health and environmental systems. There has been a recent steep increase in the frequency of published studies utilizing commercial instrumentation based on ultraviolet laser/light-induced fluorescence (UV-LIF), such as the WIBS (wideband integrated bioaerosol sensor) or UV-APS (ultraviolet aerodynamic particle sizer), for bioaerosol detection both outdoors and in the built environment. Significant work over several decades supported the development of the general technologies, but efforts to systematically characterize the operation of new commercial sensors have remained lacking. Specifically, there have been gaps in the understanding of how different classes of biological and non-biological particles can influence the detection ability of LIF instrumentation. Here we present a systematic characterization of the WIBS4A instrument using 69 types of aerosol materials, including a representative list of pollen, fungal spores, and bacteria as well as the most important groups of non-biological materials reported to exhibit interfering fluorescent properties. Broad separation can be seen between the biological and non-biological particles directly using the five WIBS output parameters and by taking advantage of the particle classification analysis introduced by Perring et al. (2015). We highlight the importance that particle size plays on observed fluorescence properties and thus in the Perring-style particle classification. We also discuss several particle analysis strategies, including the commonly used fluorescence threshold defined as the mean instrument background (forced trigger; FT) plus 3 standard deviations (σ) of the measurement. Changing the particle fluorescence threshold was shown to have a significant impact on fluorescence fraction and particle type classification. We conclude that raising the fluorescence threshold from FT + 3σ to FT + 9σ does little to reduce the relative fraction of biological material considered fluorescent but can significantly reduce the interference from mineral dust and other non-biological aerosols. We discuss examples of highly fluorescent interfering particles, such as brown carbon, diesel soot, and cotton fibers, and how these may impact WIBS analysis and data interpretation in various indoor and outdoor environments. The performance of the particle asymmetry factor (AF) reported by the instrument was assessed across particle types as a function of particle size, and comments on the reliability of this parameter are given. A comprehensive online supplement is provided, which includes size distributions broken down by fluorescent particle type for all 69 aerosol materials and comparing threshold strategies. Lastly, the study was designed to propose analysis strategies that may be useful to the broader community of UV-LIF instrumentation users in order to promote deeper discussions about how best to continue improving UV-LIF instrumentation and results. Published by Copernicus Publications on behalf of the European Geosciences Union. 4280 N. J. Savage et al.: Characterization and fluorescence threshold strategies for the WIBS-4A"], "field": "Earth and Planetary Sciences", "q_year": 2020, "q_cid": "221761033", "pos_cid": 51852421, "source": "eval_collection"}
{"query_id": "scaleup_19192435_15500228", "query": "How to select appropriate responses to mountain cryosphere change given varying socio-economic conditions and climate stresses, limited knowledge and institutional support, and weak coordination across scales, without overlooking connections to other sectors and downstream adaptation", "pos": ["The nexus approach to water–energy–food security: an option for adaptation to climate change. Developing countries face a difficult challenge in meeting the growing demands for food, water, and energy, which is further compounded by climate change. Effective adaptation to change requires the efficient use of land, water, energy, and other vital resources, and coordinated efforts to minimize trade-offs and maximize synergies. However, as in many developing countries, the policy process in South Asia generally follows a sectoral approach that does not take into account the interconnections and interdependence among the three sectors. Although the concept of a water–energy–food nexus is gaining currency, and adaptation to climate change has become an urgent need, little effort has been made so far to understand the linkages between the nexus perspective and adaptation to climate change. Using the Hindu Kush Himalayan region as an example, this article seeks to increase understanding of the interlinkages in the water, energy, and food nexus, explains why it is important to consider this nexus in the context of adaptation responses, and argues that focusing on trade-offs and synergies using a nexus approach could facilitate greater climate change adaptation and help ensure food, water, and energy security by enhancing resource use efficiency and encouraging greater policy coherence. It concludes that a nexus-based adaption approach – which integrates a nexus perspective into climate change adaptation plans and an adaptation perspective into development plans – is crucial for effective adaptation. The article provides a conceptual framework for considering the nexus approach in relation to climate change adaptation, discusses the potential synergies, trade-offs, and offers a broader framework for making adaptation responses more effective. Policy relevance This article draws attention to the importance of the interlinkages in the water, energy, and food nexus, and the implications for sustainable development and adaptation. The potential synergies and complementarities among the sectors should be used to guide formulation of effective adaptation options. The issues highlight the need for a shift in policy approaches from a sectoral focus, which can result in competing and counterproductive actions, to an integrated approach with policy coherence among the sectors that uses knowledge of the interlinkages to maximize gain, optimize trade-offs, and avoid negative impacts."], "field": "Earth and Planetary Sciences", "q_year": 2020, "q_cid": "191924355", "pos_cid": 155002286, "source": "train_step3"}
{"query_id": "scaleup_26730117_25376129", "query": "How to explain fluid pressure changes in rock away from a fault during sliding failure", "pos": ["Micromechanical controls on the brittle-plastic transition in rocks. The rheology of rocks transitions from a cataclastic brittle behaviour to plastic flow with increasing pressure and temperature. This brittle-plastic transition is empirically observed to occur when the material strength becomes lower than the confining stress, which is termed Goetze’s criterion. Such a criterion works well for most silicates but is not universal for all materials. We aim to determine the microphysical controls and stress-strain behaviour of rocks in the brittle-plastic transition. We use a micro-mechanical approach due to Horii and Nemat-Nasser, and consider representative volume elements containing sliding wing-cracks and plastic zones. We find solutions for frictional slip, plastic deformation and crack opening at constant confining pressure, and obtain stress-strain evolution. We show that the brittle-plastic transition depends on the confining stress, fracture toughness and plastic yield stress but also critically on the friction coefficient on preexisting defects. Materials with low friction are expected to be more brittle, and experience transition to fully plastic flow at higher pressure than anticipated from Goetze’s criterion. The overall success of Goetze’s criterion for the brittle-plastic transition in rocks is likely arising from the low toughness, high strength, and medium friction coefficient character of most rock forming minerals."], "field": "Earth and Planetary Sciences", "q_year": 2024, "q_cid": "267301174", "pos_cid": 253761296, "source": "train_step3"}
{"query_id": "scaleup_25496707_21990962", "query": "How to resolve molecular and ion-pair motions during crystal nucleation at angstrom spatial and millisecond temporal resolution to characterize metastable intermediate dynamics and the role of vibration in confined motion", "pos": ["Real-Time Video Imaging of Mechanical Motions of a Single Molecular Shuttle with Sub-Millisecond Sub-Angstrom Precision. Miniaturized machines have open up a new dimension of chemistry, studied usually as an average over numerous molecules or for a single molecule bound on a robust substrate. Mechanical motions at a ..."], "field": "Earth and Planetary Sciences", "q_year": 2022, "q_cid": "254967077", "pos_cid": 219909620, "source": "train_step3"}
{"query_id": "scaleup_23382033_12947716", "query": "How to determine whether the studied structures were exposed to air shortly after growth and clarify their relationship to changing water levels", "pos": ["Early Vadose Silt in Townsend Mound (Reef), New Mexico: ABSTRACT. Vugs, fractures, interstices, and other voids in the Townsend carbonate mound (reef) are floored with internal sediment composed of well sorted calcite silt. Internal sedimentation predates precipitation of blocky cement, and post-dates both precipitation of early drusy cement and early internal erosion. The crystal silt differs from associated marine sediment in its scarcity of clay-size particles, sand-size particles, and recognizable skeletal debris. The age relationships and texture of crystal silt seem best explained by sedimentation inside pre-existing crumbly rock in the vadose zone during early emergence. If the explanation is valid, similar internal sediment might be a valuable clue to previously unrecognized subaerial stages in other carbonate mounds. End_of_Article - Last_Page 356------------"], "field": "Earth and Planetary Sciences", "q_year": 2021, "q_cid": "233820331", "pos_cid": 129477162, "source": "train_step3"}
{"query_id": "scaleup_21956221_15643057", "query": "How to assess variation in pollen-isotope distributions and average values across sampling sites and years", "pos": ["Beanplot: A Boxplot Alternative for Visual Comparison of Distributions. Boxplots and variants thereof are frequently used to compare univariate data. Boxplots have the disadvantage that they are not easy to explain to non-mathematicians, and that some information is not visible. A beanplot is an alternative to the boxplot for visual comparison of univariate data between groups. In a beanplot, the individual observations are shown as small lines in a one-dimensional scatter plot. Next to that, the estimated density of the distributions is visible and the average is shown. It is easy to compare different groups of data in a beanplot and to see if a group contains enough observations to make the group interesting from a statistical point of view. Anomalies in the data, such as bimodal distributions and duplicate measurements, are easily spotted in a beanplot. For groups with two subgroups (e.g., male and female), there is a special asymmetric beanplot. For easy usage, an implementation was made in R."], "field": "Earth and Planetary Sciences", "q_year": 2020, "q_cid": "219562215", "pos_cid": 15643057, "source": "train_step3"}
{"query_id": "scaleup_26707519_14030986", "query": "How to integrate information across channels while accommodating one-dimensional representations in data assimilation", "pos": ["Squeeze-and-Excitation Networks. Convolutional neural networks are built upon the convolution operation, which extracts informative features by fusing spatial and channel-wise information together within local receptive fields. In order to boost the representational power of a network, several recent approaches have shown the benefit of enhancing spatial encoding. In this work, we focus on the channel relationship and propose a novel architectural unit, which we term the \"Squeeze-and-Excitation\" (SE) block, that adaptively recalibrates channel-wise feature responses by explicitly modelling interdependencies between channels. We demonstrate that by stacking these blocks together, we can construct SENet architectures that generalise extremely well across challenging datasets. Crucially, we find that SE blocks produce significant performance improvements for existing state-of-the-art deep architectures at minimal additional computational cost. SENets formed the foundation of our ILSVRC 2017 classification submission which won first place and significantly reduced the top-5 error to 2.251%, achieving a ~25% relative improvement over the winning entry of 2016. Code and models are available at https://github.com/hujie-frank/SENet."], "field": "Earth and Planetary Sciences", "q_year": 2024, "q_cid": "267075191", "pos_cid": 140309863, "source": "train_step3"}
{"query_id": "scaleup_25749916_19950483", "query": "How to determine the structure of calcium phosphite in fulgurite, including what surrounds each calcium atom and how the phosphite units are arranged and connected", "pos": ["Synthesis and crystal structure of calcium hydrogen phosphite, CaHPO3. The title compound is built up from CaO7 polyhedra and HPO3 pseudo tetrahedra sharing corners and edges to generate a three-dimensional network."], "field": "Earth and Planetary Sciences", "q_year": 2023, "q_cid": "257499163", "pos_cid": 199504834, "source": "train_step3"}
{"query_id": "scaleup_27754859_26812931", "query": "How to achieve computationally efficient error correction for stable autoregressive forecasts on the sphere despite spherical distortions", "pos": ["MgNet: A unified framework of multigrid and convolutional neural network. We develop a unified model, known as MgNet, that simultaneously recovers some convolutional neural networks (CNN) for image classification and multigrid (MG) methods for solving discretized partial differential equations (PDEs). This model is based on close connections that we have observed and uncovered between the CNN and MG methodologies. For example, pooling operation and feature extraction in CNN correspond directly to restriction operation and iterative smoothers in MG, respectively. As the solution space is often the dual of the data space in PDEs, the analogous concept of feature space and data space (which are dual to each other) is introduced in CNN. With such connections and new concept in the unified model, the function of various convolution operations and pooling used in CNN can be better understood. As a result, modified CNN models (with fewer weights and hyperparameters) are developed that exhibit competitive and sometimes better performance in comparison with existing CNN models when applied to both CIFAR-10 and CIFAR-100 data sets."], "field": "Earth and Planetary Sciences", "q_year": 2025, "q_cid": "277548592", "pos_cid": 268129312, "source": "train_step3"}
{"query_id": "scaleup_27754859_24824219", "query": "How to account for high-frequency components lost when truncating spherical harmonic representations for spherical convolution without the computational cost of retaining them explicitly?", "pos": ["SPHARM-Net: Spherical Harmonics-Based Convolution for Cortical Parcellation. We present a spherical harmonics-based convolutional neural network (CNN) for cortical parcellation, which we call SPHARM-Net. Recent advances in CNNs offer cortical parcellation on a fine-grained triangle mesh of the cortex. Yet, most CNNs designed for cortical parcellation employ spatial convolution that depends on extensive data augmentation and allows only predefined neighborhoods of specific spherical tessellation. On the other hand, a rotation-equivariant convolutional filter avoids data augmentation, and rotational equivariance can be achieved in spectral convolution independent of a neighborhood definition. Nevertheless, the limited resources of a modern machine enable only a finite set of spectral components that might lose geometric details. In this paper, we propose (1) a constrained spherical convolutional filter that supports an infinite set of spectral components and (2) an end-to-end framework without data augmentation. The proposed filter encodes all the spectral components without the full expansion of spherical harmonics. We show that rotational equivariance drastically reduces the training time while achieving accurate cortical parcellation. Furthermore, the proposed convolution is fully composed of matrix transformations, which offers efficient and fast spectral processing. In the experiments, we validate SPHARM-Net on two public datasets with manual labels: Mindboggle-101 (N=101) and NAMIC (N=39). The experimental results show that the proposed method outperforms the state-of-the-art methods on both datasets even with fewer learnable parameters without rigid alignment and data augmentation. Our code is publicly available at https://github.com/Shape-Lab/SPHARM-Net."], "field": "Earth and Planetary Sciences", "q_year": 2025, "q_cid": "277548592", "pos_cid": 248242190, "source": "train_step3"}
{"query_id": "scaleup_26506692_12556379", "query": "How to distinguish physically different internal density models consistent with the same measurements when only differences between aggregate properties are constrained and exhaustive exploration may be infeasible", "pos": ["Signature of Phobos’ interior structure in its gravity field and libration. Abstract The interior of the Martian moon Phobos has not been precisely determined yet, in spite of space missions sent at close distance to the body. The current measurements (imagery, astrometric, etc.) lead to controversial conclusions about the level of heterogeneity inside Phobos. Yet, the inside mass distribution is a signature of the conditions prevailing at its formation as well as of its evolution. Here, we study possible heterogenous mass distributions based on internal models built from surface observables and available bulk density and shape measurements. We identify four different families of mass distribution involving rocky material, (macro-)porosity and ice. Mass heterogeneities correspond to either an excess of porosity or a compaction of material under Stickney crater, or a deficit of porosity in the upper layers of Phobos, or a concentration of ice either in depth inside Phobos or in shallow layers. We then discretize the shape of Phobos using 500m-length cubes to fit its volume and total mass. We compute the possible distribution of these cubes for each family of internal mass heterogeneity model. We deduce the possible values of the principal moments of inertia as well as of the geodetic observables such as the libration amplitude and the gravity field anomalies (up to degree and order 10) associated with these models. A comparison of these computed observables between the different heterogeneity models and with their expected homogenous mass distribution values allow us to quantify the possible heterogeneity degree within Phobos. The computed heterogeneity observables can depart by tens of percent from the homogenous values. The most striking departures are from the interior model with mass excess (less porosity) or deficit (more porosity) beneath Stickney crater. In turn, measurements of libration amplitude and low degree coefficients of the gravity field at a precision better than 5% can allow to identify such kinds of heterogeneities mainly located beneath Stickney. Mass excess or deficit can therefore be also distinguished, which is of importance to identify whether Phobos was already porous or monolithic before the formation of Stickney. The current measurements of libration amplitude and degree-two gravity coefficient are quite uncertain, but seem to reject models with higher porosity under Stickney, favoring a pre-impact porous body. The icy models depart less from the homogenous signatures, hence requiring more precise measurements of the geodetic observables and of the shape of Phobos. The improvement of these measurements by the Mars Moon Explorer mission for instance could thus allow for better constraining our model of Phobos’ interior and bring further constraints for its formation."], "field": "Earth and Planetary Sciences", "q_year": 2023, "q_cid": "265066929", "pos_cid": 125563790, "source": "train_step3"}
{"query_id": "scaleup_23999839_1957433", "query": "How to improve asset pricing while accounting for long-term relationships among stocks and cross-sectional effects", "pos": ["GloVe: Global Vectors for Word Representation. Recent methods for learning vector space representations of words have succeeded in capturing fine-grained semantic and syntactic regularities using vector arithmetic, but the origin of these regularities has remained opaque. We analyze and make explicit the model properties needed for such regularities to emerge in word vectors. The result is a new global logbilinear regression model that combines the advantages of the two major model families in the literature: global matrix factorization and local context window methods. Our model efficiently leverages statistical information by training only on the nonzero elements in a word-word cooccurrence matrix, rather than on the entire sparse matrix or on individual context windows in a large corpus. The model produces a vector space with meaningful substructure, as evidenced by its performance of 75% on a recent word analogy task. It also outperforms related models on similarity tasks and named entity recognition."], "field": "Economics, Econometrics and Finance", "q_year": 2019, "q_cid": "239998396", "pos_cid": 1957433, "source": "eval20x26"}
{"query_id": "scaleup_39890515_40833313", "query": "How to achieve accurate and efficient finite-sample inference in dynamic panel data estimation under heteroskedasticity and weak instruments", "pos": ["Efficiency Gains by Modifying GMM Estimation in Linear Models Under Heteroskedasticity. While coping with nonsphericality of the disturbances, standard GMM suffers from a blind spot for exploiting the most effective instruments when these are obtained directly from unconditional rather than conditional moment assumptions. For instance, standard GMM counteracts that exogenous regressors are used as their own optimal instruments. This is easily seen after transmuting GMM for linear models into IV in terms of transformed variables. It is demonstrated that modified GMM (MGMM), exploiting straight-forward modifications of the instruments, can achieve substantial efficiency gains and bias reductions, even under mild heteroskedasticity. Feasible MGMM implementations and their standard error estimates are examined and compared with standard GMM and IV for a range of typical models for cross-section data, both by simulation and by empirical illustration."], "field": "Economics, Econometrics and Finance", "q_year": 2017, "q_cid": "39890515", "pos_cid": 40833313, "source": "eval20x26"}
{"query_id": "scaleup_17035837_14345049", "query": "How to determine future pharmaceutical purchase prices over time", "pos": ["Automatic Time Series Forecasting: The forecast Package for R. Automatic forecasts of large numbers of univariate time series are often needed in business and other contexts. We describe two automatic forecasting algorithms that have been implemented in the forecast package for R. The first is based on innovations state space models that underly exponential smoothing methods. The second is a step-wise algorithm for forecasting with ARIMA models. The algorithms are applicable to both seasonal and non-seasonal data, and are compared and illustrated using four real time series. We also briefly describe some of the other functionality available in the forecast package."], "field": "Economics, Econometrics and Finance", "q_year": 2015, "q_cid": "17035837", "pos_cid": 14345049, "source": "eval20x26"}
{"query_id": "scaleup_5044504_20514930", "query": "How to establish confidence in responsible and safe pharmacy provision of medicines after a switch to non-prescription access", "pos": ["Five years of non-prescription oseltamivir: effects on resistance, immunization and stockpiling. Abstract Objectives In 2007 New Zealand (NZ) became the first country to make oseltamivir (Tamiflu®) available off-prescription. This study investigated the extent of pharmacist supply of oseltamivir over 5 years, including during the influenza A(H1N1) pandemic, and the impact of pharmacist supply of oseltamivir on influenza virus oseltamivir susceptibility, personal stockpiling and influenza vaccine uptake. Methods Randomly selected community pharmacies in NZ reported oseltamivir provision by prescription and through pharmacist supply from 1 January 2007 to 15 September 2011. Oseltamivir resistance data on influenza viruses isolated during influenza surveillance from 2008 to 2011 were obtained, along with influenza vaccine uptake data from 2005 to 2011 and influenza detection data. Results Seventy of 85 eligible pharmacies completed the study (82% response rate). Most supplies of oseltamivir throughout the 5 years were dispensed against a prescription rather than pharmacist supplied, with pharmacist supply responsible for 11% of supplies during the pandemic years (2009–10) versus 27% and 31% during 2007 and 2008, respectively. Pharmacist-supplied oseltamivir did not appear to be associated with the development of resistance, with identified likely stockpiling or with a decline in influenza immunization. Pharmacist supplies largely matched the timing of influenza in the community and peaked in June 2009, as did prescription supplies. Conclusions Five years of non-prescription oseltamivir in NZ has resulted in no significant change in the development of resistance or rates of influenza immunization. Supplies remained modest and significant consumer stockpiling through pharmacist supply has not occurred, even during the influenza A(H1N1)pdm09 pandemic in 2009 and 2010. Pharmacists could be better utilized in ensuring fast distribution of antivirals to influenza sufferers during a pandemic."], "field": "Economics, Econometrics and Finance", "q_year": 2015, "q_cid": "5044504", "pos_cid": 205149306, "source": "eval20x26"}
{"query_id": "scaleup_26729500_45835", "query": "How to determine whether standard rational expectations in macroeconomic models are consistent with observed behavior in how people form and revise their forecasts", "pos": ["Information Rigidity and the Expectations Formation Process: A Simple Framework and New Facts. We propose a new approach to test of the null of full-information rational expectations which is informative about whether rejections of the null reflect departures from rationality or full-information. This approach can also quantify the economic significance of departures from the null by mapping them into the underlying degree of information rigidity faced by economic agents. Applying this approach to both U.S. and cross-country data of professional forecasters and other economic agents yields pervasive evidence of informational rigidities that can be explained by models of imperfect information. Furthermore, the proposed approach sheds new light on the implications of policies such as inflation-targeting and those leading to the Great Moderation on expectations. Finally, we document evidence of state-dependence in the expectations formation process."], "field": "Economics, Econometrics and Finance", "q_year": 2023, "q_cid": "267295009", "pos_cid": 45835, "source": "eval_collection"}
{"query_id": "scaleup_27847747_22036556", "query": "How to determine how policy instruments and institutional conditions affect the probability of a fiscal crisis in decentralized fiscal systems", "pos": ["Macroprudential policy and the probability of a banking crisis. The ultimate purpose of macroprudential policy is to avoid financial instability, such as banking crises, which have a long-lasting and devastating effect on the economy. Although a growing number of studies have examined the effects of macroprudential policy on credit growth, few empirical studies have analyzed its effect on the probability of a banking crisis. Does macroprudential policy actually affect the probability of a banking crisis? Do other macroeconomic policies matter for the effectiveness of macroprudential policy? To answer these questions, this paper empirically investigates the effect of macroprudential policy on the probability of a banking crisis and its relationship with other macroeconomic policies. Specifically, using data on 65 countries from 2000 to 2016, we employ a probit model to analyze the effect of changes in the loan-to-value (LTV) ratio on crisis probability. Our results show that macroprudential policy is effective in changing the probability of a banking crisis via a credit channel and that its effectiveness depends on other macroeconomic policies. Changes in the LTV ratio are found to be effective in influencing the probability of a banking crisis in countries that have inflation targeting frameworks, floating exchange rate regimes, and/or no capital controls. Our results underscore the importance of policy coordination among different government bodies to design an appropriate macroprudential policy, especially in the current context of the Covid-19 crisis."], "field": "Economics, Econometrics and Finance", "q_year": 2025, "q_cid": "278477474", "pos_cid": 220365569, "source": "eval_collection"}
{"query_id": "scaleup_23946007_15807062", "query": "How to assess the combined effects of environmental and pandemic disruptions on overall economic activity and finances, and how borrowing and employment constraints affect government spending’s ability to support recovery", "pos": ["The EIRIN Flow-of-funds Behavioural Model of Green Fiscal Policies and Green Sovereign Bonds. Fiscal and monetary policies, as well as new financial instruments, could play a key role to meet the Paris Agreement. However, deep uncertainty characterizes their design and their potential effects on growth, financial and credit market stability, and inequality. We develop the EIRIN flow-of-funds behavioural model to simulate the introduction of green fiscal policies and green sovereign bonds, and we display their effects on firms' investments in the brown and green sector, on unemployment, on the credit and bonds market. EIRIN is Stock-Flow Consistent and is rooted on a balance sheet approach. It adopts a Leontief production function with no substitution of the production factors, i.e., Labour, Capital, and Raw Materials. Its sectors are endowed with adaptive behaviours and expectations, and interact with the others and the foreign sector through a set of markets. Simulations show that green public policies can promote green growth by influencing firms’ expectations and the credit market. Green sovereign bonds represent a short-term win-win solution, while green fiscal measures have higher immediate distributive effects that induce negative feedbacks on the economy. These results are influenced by the conditions (fiscal, budgetary and public debt/GDP) in which both measures are implemented."], "field": "Economics, Econometrics and Finance", "q_year": 2021, "q_cid": "239460077", "pos_cid": 158070623, "source": "eval_collection"}
{"query_id": "scaleup_24891791_23414778", "query": "How to predict future Saudi stock-market values amid oil-price changes and COVID-19 conditions and quantify how closely predictions match actual market values?", "pos": ["Assessment of predicting hourly global solar radiation in Jordan based on Rules, Trees, Meta, Lazy and Function prediction methods. Abstract Nowadays, predicting solar radiation is widely increased to maximize the efficiency of solar systems globally. Meteorological data from metrological stations is used to implement the intelligent prediction systems. Unfortunately, uncertainty in the used solar variables and the selected prediction models would increase the difficulties in using intelligent models to predict solar radiation. Several studies perfectly estimated solar radiation using only time and date variables. The main objective of this study is to review different prediction methods in predicting the solar radiation of Jordan. To achieve this target, five main methods including Rules, Trees, Meta, Lazy and Function Methods are selected, and then the most important and used algorithms in each method are selected to build a prediction model. The study shows that M5Rule, Random forest, Random committee, Instance Based Learning with Parameter K and multi-layer perceptron are the best algorithms in Rules, Trees, Meta, Lazy, and Function Methods respectively. Random forest algorithm performed better than other algorithms in predicting global solar radiation. The results of the analysis found that the accuracy of prediction depends on the used category, training algorithm and variables combinations."], "field": "Economics, Econometrics and Finance", "q_year": 2022, "q_cid": "248917910", "pos_cid": 234147780, "source": "eval_collection"}
{"query_id": "scaleup_25617776_15864510", "query": "How to understand which aspects of project teams’ perceived complexity change during publicly co-funded research and development projects", "pos": ["A framework for understanding managerial responses to supply chain complexity. The purpose of this paper is to examine the nature of supply chain complexity and extend this with literature developed within the project domain. The authors use the lens of ambidexterity (the ability both to exploit and explore) to analyse responses to complexity, since this enables the authors to understand the application of known solutions in conjunction with innovative ones to resolve difficulties. This research also seeks to investigate how managers respond to supply chain complexities that can either be operationally deleterious or strategically beneficial.,The authors develop a descriptive framework based on the project management (PM) literature to understand response options to complexity, and then use interviews with supply chain managers in six organisations to examine the utility of this framework in practice. The authors ask the research question “How do managers in supply chains respond to complexities”?,The case study data show first that managers faced with structural, socio-political, or emergent supply chain complexities use a wide range of responses. Second, over a third of the instances of complexity coded were actually accommodated, rather than reduced, by the study firms, suggesting that adapting to supply chain complexity in certain instances may be strategically appropriate. Third, the lens of ambidexterity allows a more explicit assessment of whether existing PM solutions can be considered or if novel methods are required to address supply chain complexities.,The descriptive framework can aid managers in conceptualising and addressing supply chain complexity. Through exploiting current knowledge, managers can lessen the impact of complexity while exploring other innovative approaches to solve new problems and challenges that evolve from complexity growth driven by business strategy.,This study addresses a gap in the literature through the development of a framework which provides a structure on ways to address supply chain complexity. The authors evaluate an existing project complexity concept and demonstrate that it is both applicable and valuable in non-project, ongoing operations. The authors then extend it using the lens of ambidexterity, and develop a framework that can support practitioners in analysing and addressing both strategically necessary supply complexities, together with unwanted, negative complexities within the organisation and across the supply chain."], "field": "Economics, Econometrics and Finance", "q_year": 2023, "q_cid": "256177763", "pos_cid": 158645109, "source": "eval_collection"}
{"query_id": "scaleup_23579538_20278613", "query": "How to align parameter calibration and risk-budgeting portfolio optimization with the investor’s reward–risk objective while limiting estimation-error amplification", "pos": ["Differentiable Convex Optimization Layers. Recent work has shown how to embed differentiable optimization problems (that is, problems whose solutions can be backpropagated through) as layers within deep learning architectures. This method provides a useful inductive bias for certain problems, but existing software for differentiable optimization layers is rigid and difficult to apply to new settings. In this paper, we propose an approach to differentiating through disciplined convex programs, a subclass of convex optimization problems used by domain-specific languages (DSLs) for convex optimization. We introduce disciplined parametrized programming, a subset of disciplined convex programming, and we show that every disciplined parametrized program can be represented as the composition of an affine map from parameters to problem data, a solver, and an affine map from the solver’s solution to a solution of the original problem (a new form we refer to as affine-solver-affine form). We then demonstrate how to efficiently differentiate through each of these components, allowing for end-to-end analytical differentiation through the entire convex program. We implement our methodology in version 1.1 of CVXPY, a popular Python-embedded DSL for convex optimization, and additionally implement differentiable layers for disciplined convex programs in PyTorch and TensorFlow 2.0. Our implementation significantly lowers the barrier to using convex optimization problems in differentiable programs. We present applications in linear machine learning models and in stochastic control, and we show that our layer is competitive (in execution time) compared to specialized differentiable solvers from past work."], "field": "Economics, Econometrics and Finance", "q_year": 2021, "q_cid": "235795388", "pos_cid": 202786139, "source": "eval_collection"}
{"query_id": "scaleup_25668483_12023913", "query": "How to isolate a policy’s effect on eco-innovation when cities’ observed characteristics may influence whether they receive the policy intervention", "pos": ["Reducing Bias in Observational Studies Using Subclassification on the Propensity Score. Abstract The propensity score is the conditional probability of assignment to a particular treatment given a vector of observed covariates. Previous theoretical arguments have shown that subclassification on the propensity score will balance all observed covariates. Subclassification on an estimated propensity score is illustrated, using observational data on treatments for coronary artery disease. Five subclasses defined by the estimated propensity score are constructed that balance 74 covariates, and thereby provide estimates of treatment effects using direct adjustment. These subclasses are applied within sub-populations, and model-based adjustments are then used to provide estimates of treatment effects within these sub-populations. Two appendixes address theoretical issues related to the application: the effectiveness of subclassification on the propensity score in removing bias, and balancing properties of propensity scores with incomplete data."], "field": "Economics, Econometrics and Finance", "q_year": 2023, "q_cid": "256684838", "pos_cid": 120239136, "source": "eval_collection"}
{"query_id": "scaleup_25488285_36804682", "query": "How to understand organizations’ and specialist enterprises’ perceptions of their alignment and relationship governance, including trust and context", "pos": ["Grounded Theory and Sensitizing Concepts. Grounded theory is a qualitative research approach that uses inductive analysis as a principal technique. Yet, researchers who embrace this approach often use sensitizing concepts to guide their analysis. In this article, the author examines the relationship between sensitizing concepts and grounded theory. Furthermore, he illustrates the application of sensitizing concepts in a study of community-based antipoverty projects in Jamaica. The article contains commentary about trustworthiness techniques, the coding process, and the constant comparative method of analysis, as well as a synopsis of study findings."], "field": "Economics, Econometrics and Finance", "q_year": 2023, "q_cid": "254882857", "pos_cid": 36804682, "source": "eval_collection"}
{"query_id": "scaleup_26894522_19771114", "query": "How to understand the relationships among research themes and their evolution over time in the literature on capital markets’ green financial instrument issuances", "pos": ["Conceptual structure and perspectives on entrepreneurship education research: A bibliometric review. This study aims to review the field of Entrepreneurship Education (EE). The review examines 325 scientific articles published in refereed scientific journals from 1987 to 2017. The SciMat software was used to conduct an analysis of performance indicators and science mapping visualizations. The performance analysis results identified some of the field's most active and influential articles, journals, and authors. The science mapping visualization of co-word analysis results revealed EE research evolution. In general, we found that EE research has evolved from EE as part of an economic development strategy to the EE academic perspective. Furthermore, research themes showed that students, rather than teachers, have become the main agents of the educational process. The results of this bibliometric analysis enhance understanding of the evolution of EE research with a global overview of the relevant literature and its authors"], "field": "Economics, Econometrics and Finance", "q_year": 2024, "q_cid": "268945228", "pos_cid": 197711149, "source": "eval_collection"}
{"query_id": "scaleup_27535650_21123140", "query": "How to identify gaps in the registration of essential medicines when national drug registers and essential medicines lists lack common data variables and standards", "pos": ["WHODrug: A Global, Validated and Updated Dictionary for Medicinal Information. The WHODrug medicinal information dictionary is a worldwide source of global medicinal information with the aim to facilitate the coding of medications in clinical trials as well as identification of medication-related problems when monitoring patient safety, thereby supporting the development and usage of effective and safe medications. WHODrug contains individual trade names, active ingredients and additional information such as marketing authorisation holder, country of sale, pharmaceutical form and strength. All related medications are linked using a structured WHODrug alphanumeric code, connecting trade names and variation of the ingredient with the active moiety of the ingredient. Medications in WHODrug are classified using the ATC system and clustered into Standardised Drug Groupings, to allow for grouping of medications with one or more properties in common. The built-in data structure and the classification of medications in WHODrug facilitate various ways of aggregating medications for identification and analysis of possible adverse drug reactions. The different information levels in WHODrug are used to explore the relationship between a medication or a class of medications and an adverse event. By using WHODrug in clinical trials and post-marketing safety, accurate and standardised medication information can be achieved globally and allow easy information exchange. To meet the demands of WHODrug users from the pharmaceutical industry, academia and regulatory authorities, it is relevant to keep the dictionary comprehensive, validated and constantly updated on a global scale."], "field": "Economics, Econometrics and Finance", "q_year": 2024, "q_cid": "275356502", "pos_cid": 211231403, "source": "eval_collection"}
{"query_id": "scaleup_26729500_15738916", "query": "How to choose among alternative filters for an empirical analysis", "pos": ["What cycles? Data detrending in DSGE models. Abstract It is widely-known that different methods of detrending data yield different business cycle features. The choice of the detrending method, however, is usually arbitrarily made. This paper aims at revealing potential pitfalls of different detrending methods for the estimation of a standard medium-scale DSGE model. By comparing nine popular detrending methods, we find that model parameter estimates, variance decompositions, optimal monetary policies, and out-of-sample forecasting performances of the model are all sensitive to how the data are detrended. We also discuss some possible criteria to choose among different methods."], "field": "Economics, Econometrics and Finance", "q_year": 2023, "q_cid": "267295009", "pos_cid": 157389165, "source": "eval_collection"}
{"query_id": "scaleup_26894522_26064102", "query": "How to assess a research field’s publication patterns and whether they conform to established bibliometric regularities", "pos": ["Technical Analysis, Fundamental Analysis, and Ichimoku Dynamics: A Bibliometric Analysis. This article aims to contribute to the academic knowledge in the field of scientific production regarding decision support tools for investments in the capital market, specifically focusing on fundamental analysis, technical analysis, and Ichimoku dynamics. Bibliometric analysis, following the three main laws (Bradford’s Law, Lotka’s Law, and Zipf’s Law), was employed to evaluate scientific production, identify publication patterns, and uncover gaps and collaboration networks over the last thirty years. To achieve these objectives, 1710 relevant academic publications on the topic were analyzed and retrieved from the Web of Science (WOS) database, pertaining to the last 30 years, between 1990 and 22 May 2023. The significance of this article lies in the contributions of the findings, which advance scientific knowledge by identifying gaps in the knowledge and research, particularly in the limited literature on Ichimoku; our review reveals a growing trend of research in this area. Another notable conclusion is the emergence of new research topics and areas of interest, as well as the identification of collaboration networks among authors, institutions, and countries. Moreover, the article provides valuable insights for financial professionals and investors who are interested in applying these methodologies as methods for price forecasting. The highlighted results support investment decision making, trading strategies, and portfolio management."], "field": "Economics, Econometrics and Finance", "q_year": 2024, "q_cid": "268945228", "pos_cid": 260641021, "source": "eval_collection"}
{"query_id": "scaleup_23923924_15439476", "query": "How to select green bonds based on environmental performance and financial indicators rather than solely on opinions", "pos": ["Selection of rational dispute resolution method by applying new step‐wise weight assessment ratio analysis (Swara). Abstract The paper considers major principles of application of the multi‐attribute systems to solve legislative tasks. In order to assess dispute resolution methods from economic, social and other points of view, it is necessary to apply methods for assessing solutions according to multiple attributes. All known multi‐attribute methods cannot value the atribute weights as one weight of attribute is higher or lower significant than the other attribute. The new step‐wise weight assessment ratio analysis method (SWARA) allows including experts, lawyers or dispute parties opinion about significance ratio of the attributes in the process of rational decision determination. SWARA method could be applied in practical implementation of specialised decision support systems and alternative dispute resolution in virtual environment. Starting with principles and established approaches, a problem‐structuring methodology was developed which would condition the problem to allow a more thoughtful application of existing..."], "field": "Economics, Econometrics and Finance", "q_year": 2021, "q_cid": "239239245", "pos_cid": 154394761, "source": "eval_collection"}
{"query_id": "scaleup_27679778_23629059", "query": "How to determine whether international and regional organisations cooperate or compete in supporting emerging national pricing initiatives in sub-Saharan Africa", "pos": ["Competition, cooperation, and adaptation: The organizational ecology of international organizations in global energy governance. Abstract In policy domains characterised by complexity, international organizations (IOs) with overlapping mandates and governance functions regularly interact in ways that have important implications for global governance. Yet the dynamics of IO interactions remain understudied. This article breaks new ground by building on the theoretical insights of organizational ecology to examine IO competition, cooperation, and adaptation in the domain of energy. Drawing on original empirical data, I consider three related hypotheses: (1) competition between IOs in the same population is likely to centre on material resources; (2) IOs are more likely to cooperate when they have a shared governance goal; and (3) individual IOs can adapt by changing their goals and boundaries. In considering these hypotheses, this article highlights the limits of the organizational ecology approach and the need to broaden it to account for the possibility that IOs do cooperate, and that individual IOs, such as the International Energy Agency, have the capacity to adapt to changes in their environment."], "field": "Economics, Econometrics and Finance", "q_year": 2024, "q_cid": "276797786", "pos_cid": 236290595, "source": "eval_collection"}
{"query_id": "scaleup_27721179_3279702", "query": "How to assess the effects of geopolitical uncertainty on economic growth in selected Turkic republics and neighboring states", "pos": ["Measuring Geopolitical Risk. We present a news-based measure of adverse geopolitical events and associated risks. The geopolitical risk (GPR) index spikes around the two world wars, at the beginning of the Korean War, during the Cuban Missile Crisis, and after 9/11. Higher geopolitical risk foreshadows lower investment and employment and is associated with higher disaster probability and larger downside risks. The adverse consequences of the GPR index are driven by both the threat and the realization of adverse geopolitical events. We complement our aggregate measures with industry- and firm-level indicators of geopolitical risk. Investment drops more in industries that are exposed to aggregate geopolitical risk. Higher firm-level geopolitical risk is associated with lower firm-level investment."], "field": "Economics, Econometrics and Finance", "q_year": 2025, "q_cid": "277211792", "pos_cid": 3279702, "source": "eval_collection"}
{"query_id": "scaleup_25165232_22149537", "query": "How to clarify the relationship between construction workers’ perceptions of their organization’s pandemic response, their ability to cope with work pressures, and their perceived availability of adequate resources and support", "pos": ["Coping strategies as mediators in the relation between perceived social support and job burnout among Chinese firefighters. Perceived social support is a known factor in preventing job burnout in many professions. However, the influence of coping strategies on perceived social support and job burnout remains unclear. The current study investigated firefighters using data from a two-wave study to fill this gap in knowledge. Chinese firefighters (N = 340) participated in the study for 3-months. Results indicated that perceived social support at baseline predicted job burnout at the 3-month follow-up through coping strategies. We concluded that perceived social support acts through positive coping strategies to reduce job burnout in Chinese firefighters."], "field": "Economics, Econometrics and Finance", "q_year": 2022, "q_cid": "251652323", "pos_cid": 221495375, "source": "eval_collection"}
{"query_id": "scaleup_25100661_22620638", "query": "How to assess the relationship between private medical insurance and pediatric healthcare access while accounting for children’s underlying health differences despite missing four-character diagnostic subcategories in KHP data", "pos": ["Development and Validation of a Pediatric Comorbidity Index.. Comorbidity scores are widely used to help address confounding bias in nonrandomized studies conducted within healthcare databases, but existing scores were developed to predict all-cause mortality in adults and may not be appropriate for use in pediatric studies. We developed and validated a pediatric comorbidity index, using healthcare utilization data from the tenth revision of the International Classification of Diseases. Within the MarketScan database, pediatric patients (<18 years) continuously enrolled between October 1, 2015-September 30, 2017 were identified. Logistic regression was used to predict the 1-year risk of hospitalization based on 27 predefined conditions and empirically-identified conditions derived from the most prevalent diagnoses among patients with the outcome. A single numerical index was created by assigning weights to each condition based on its beta coefficient. We conducted internal validation of the index and compared its performance to existing adult scores. The pediatric comorbidity index consisted of 24 conditions and achieved a c-statistic of 0.718 (95% confidence interval [CI] 0.714, 0.723). The index oasutperformed existing adult scores in a pediatric population (c-statistics ranging from 0.522 to 0.640). The pediatric comorbidity index provides a summary measure of disease burden and can be used for risk adjustment in epidemiologic studies of pediatric patients."], "field": "Economics, Econometrics and Finance", "q_year": 2022, "q_cid": "251006614", "pos_cid": 226206383, "source": "eval_collection"}
{"query_id": "scaleup_23946007_20884633", "query": "How to anticipate the economic consequences of compounding shocks across interconnected sectors and borders amid nonlinear responses, hard-to-identify tipping points, and uncertain relationships between triggers and impacts", "pos": ["Governance of systemic risks for disaster prevention and mitigation. Purpose Systemic risks originate in tightly coupled systems. They are characterised by complexity, transboundary cascading effects, non-linear stochastic developments, tipping points, and lag in perception and regulation. Disasters need to be analysed in the context of vulnerabilities of infrastructure, industrial activities, structural developments and behavioural patterns which amplify or attenuate the impact of hazards. In particular, disasters are triggered by chains of events that often amplify and also multiply damages. The paper aims to discuss these issues. Design/methodology/approach The paper applies the concept of systemic risks to disasters more precisely to the combination of natural and human-induced disasters. The paper refers to the International Risk Governance Council’s Risk Governance Framework and applies this framework to the systemic aspects of disaster risks. Findings The paper maps out strategies for inclusive governance of systemic risks for disaster prevention and mitigation. Furthermore, the paper highlights policy implications of these strategies and calls out for an integrated, inclusive and adaptive management approach for the systemic aspects of disaster risks. Originality/value The paper fulfils the identified need to analyse disaster risks in the context of vulnerabilities of infrastructure, industrial activities, structural developments and behavioural patterns which amplify or attenuate the impact of hazards."], "field": "Economics, Econometrics and Finance", "q_year": 2021, "q_cid": "239460077", "pos_cid": 208846331, "source": "eval_collection"}
{"query_id": "scaleup_23635026_19762530", "query": "How to capture complex nonlinear relationships and asymmetric lower- and upper-tail comovements across financial markets", "pos": ["Reliability analysis of stochastic structure with multi-failure modes based on mixed Copula. Abstract In view of that there exist complicated correlations among failure modes of the stochastic structure because of the same uncertain variables that are contained in different failure modes, many reliability analysis methods based on empirical probability model have been developed to calculate and assess the structural reliability. However, the empirical distributions of uncertain variables are not always available or not accurate. Thus, based on the available sample data of random variables of the stochastic structural system to be analyzed, this paper presents a new reliability analysis method in which the mixed Copula is constructed to describe the correlations among multi-failure modes. First, the Gumbel Copula and Clayton Copula, which have the upper and lower tail dependence separately, are utilized to construct a mixed Copula so as to describe the correlations among multi-failure modes. Then, the sample data of the random variables is substituted into the performance functions of failure modes to calculate the sequence values thereof, and the probability density function (PDF) and cumulative distribution function (CDF) of each performance function of the structure are estimated by using the nonparametric kernel density estimation (NKDE) technique. Subsequently, the Canonical Maximum Likelihood (CML) method is applied to estimate the correlation parameters in the mixed Copula. Finally, the main girder structure of an overhead traveling crane is investigated by using the proposed method, and the results indicate that the new reliability analysis method is effective and valid. Compared with traditional reliability analysis methods, the new method, in which the available sample data of random variables is directly used to calculate the values of performance functions so as to avoid the errors caused by empirical distributions, provides some important theories and engineering contributions for the reliability design analyses and safety assessments of actual engineering structures, especially these with complex correlations among multi-failure modes."], "field": "Economics, Econometrics and Finance", "q_year": 2021, "q_cid": "236350260", "pos_cid": 197625305, "source": "eval_collection"}
{"query_id": "scaleup_27619202_11430517", "query": "How to identify feasible and desirable options given cost-effectiveness, decision-maker and public acceptance, and value-based trade-offs in distributing benefits and burdens within and across generations", "pos": ["Integrated approach to the assessment of CO2e-mitigation measures for the road passenger transport sector in Bahrain. The transport sector is one of the fastest-growing energy-consuming sectors in the world and it contributes greatly to emissions of carbon dioxide equivalent (CO2e). In Bahrain, CO2e emissions from the transport sector grew by an average of 8% annually between 1994 and 2006. The aim of this research was to develop an integrated approach to assess the measures adopted to reduce CO2e emissions by the transport sector within the context of climate change mitigation. This approach used the multi-criteria analysis methodology of the Analytic Hierarchy Process (AHP) to embed conventional assessment methods and a participatory approach. Three extensions to the original AHP methodology were developed: multi-AHP models, scenario packaging, and the examination of the plausibility of the results. The AHP results showed that certain fuel economy standards achieved the highest scores against five qualitative and quantitative criteria. Using socially and politically acceptable options, an integrated approach to CO2e mitigation could achieve a reduction in emissions of around 22% by 2030 (compared with 2010), at a cost of USD 112 per metric tonne of avoided CO2e emissions. Results from surveys of policymakers, experts, and the general public indicated that the outcomes of scenario packaging were plausible. The contributions of this research are two-fold. First, for the first time in Bahrain, the preferences of the general public have been considered and integrated with both the preferences of policymakers and experts and the results obtained from conventional assessment methods. Second, a structured approach for the integration of different assessment methods, transferable to other contexts, was developed and examined. Furthermore, multi-AHP models were introduced that can reflect the preferences of different concerned groups. Applications of this approach include assessment of the implementation of mitigation measures that could affect a number of concerned groups, decision making in energy-consuming sectors, and development of mitigation policy packages."], "field": "Economics, Econometrics and Finance", "q_year": 2025, "q_cid": "276192021", "pos_cid": 114305170, "source": "eval_collection"}
{"query_id": "scaleup_26976042_24880073", "query": "How to maintain stable alignment between manufacturing enterprises and supervisory departments in carbon emission supervision under static incentives despite periodic shifts between incentive-compatible and incentive-incompatible states", "pos": ["Supervision for the Public Health Services for Older Adults Under the Background of Government Purchasing: An Evolutionary Game Analysis Framework. As an important measure to involve services for older adults, the government procurement practices have become a key link for public health services. However, the information asymmetry between public health service purchasers and public health service undertakers triggers a supervision dilemma. Based on this background, this study uses the evolutionary game theory to analyze the symbiotic evolution between local governments and public health service institutions under different reward and punishment mechanisms, explore game evolution, strategy adjustment, and influencing factors of different game subjects, and analyze the necessity and appropriate intensity of dynamic rewards and punishment mechanisms. The results show that: under the static condition, the penalty can change the strategies of local governments to a certain extent, but it is still difficult to achieve complete self-discipline management of public health service institutions. If local governments implement a dynamic reward or penalty mechanism in the supervision process of public health services for older adults, the equilibrium between them tends to be evolutionary stable. For three dynamic mechanisms, a dynamic reward mechanism is more conducive to adopting a self-discipline behavior of public health service institutions, which is helpful to realize the supervision of public health services for older adults. Also, there is a positive correlation between the proportion of public health service institutions who adopt a “self-discipline behavior” strategy and the maximum punishment intensity, and a negative correlation with the reward intensity. This study provides theoretical and decision-making references for governments to explore the promotion and implementation of public health services in older adults."], "field": "Economics, Econometrics and Finance", "q_year": 2024, "q_cid": "269760423", "pos_cid": 248800738, "source": "eval_collection"}
{"query_id": "scaleup_21352341_38659192", "query": "How to clarify how individual preferences, cultural housing expectations, and institutional programmes interact in shaping housing choices across the life course", "pos": ["A life-course approach to fertility. Background: The life-course approach as a methodological framework for the empirical analysis of longitudinal individual-level data has fundamentally changed the agenda of demographic research. However, these methodological innovations have not been paralleled by a similarly successful theoretical integration in the life-course field. Objective: We aim to show that the life course is an indispensable framework for demographic research. Social forces, both structural and cultural, are articulated in the life-course dimension, and the individuals who act under their influence conceive of their actions in life-course terms. Thus, theories of fertility need to be set in these terms as well. Results: In substantive terms, the life-course approach promises to integrate the extra- and intra-individual levels of relevant processes in a system of interdependent dynamics that unfolds over time; to conceptualize fertility and family formation as part of a multidimensional process of welfare production which requires complex decisions on the proper allocation of time and resources to the different life domains; to examine how cultural scripts and institutional programs shape and interact with intentions and preferences; and to highlight the impact of the past and anticipation of the future as a framework for the number, timing and spacing of births. In methodological terms, the life-course approach requires a shift in the efforts to identify complex causal mechanisms in empirical research. Conclusions: Even though the life-course approach still lacks the status of a systematic theory, several hypotheses can already be drawn from it, which extend the scope of fertility research, and demonstrate it to be an indispensable framework for studying fertility decisions."], "field": "Economics, Econometrics and Finance", "q_year": 2020, "q_cid": "213523418", "pos_cid": 38659192, "source": "eval_collection"}
{"query_id": "scaleup_25661615_940696", "query": "How to quantify international economic uncertainty spillovers accurately and promptly when cross-country dependencies change abruptly or gradually and historical data may no longer represent current conditions", "pos": ["Multiscale local change point detection with applications to value-at-risk. This paper offers a new approach to modeling and forecasting of nonstationary time series with applications to volatility modeling for financial data. The approach is based on the assumption of local homogeneity: for every time point, there exists a historical interval of homogeneity, in which the volatility parameter can be well approximated by a constant. The proposed procedure recovers this interval from the data using the local change point (LCP) analysis. Afterward, the estimate of the volatility can be simply obtained by local averaging. The approach carefully addresses the question of choosing the tuning parameters of the procedure using the so-called ``propagation'' condition. The main result claims a new ``oracle'' inequality in terms of the modeling bias which measures the quality of the local constant approximation. This result yields the optimal rate of estimation for smooth and piecewise constant volatility functions. Then, the new procedure is applied to some data sets and a comparison with a standard GARCH model is also provided. Finally, we discuss applications of the new method to the Value at Risk problem. The numerical results demonstrate a very reasonable performance of the new method."], "field": "Economics, Econometrics and Finance", "q_year": 2023, "q_cid": "256616159", "pos_cid": 940696, "source": "eval_collection"}
{"query_id": "scaleup_26937839_11992992", "query": "How to determine whether the relationships between green economic growth and its determinants are the same across G7 countries or differ across countries", "pos": ["Testing Slope Homogeneity in Large Panels. This paper proposes a modi?ed version of Swamy’s test of slope homogeneity for panel data models where the cross section dimension (N) could be large relative to the time series dimension (T). The proposed test exploits the cross section dispersion of individual slopes weighted by their relative precision. In the case of models with strictly exogenous regressors and normally distributed errors, the test is shown to have a standard normal distribution as (N, T) j ? 8. Under non-normal errors and in the case of stationary dynamic models, the condition on the relative expansion rates of N and T for the test to be valid is given by vN/T ? 0, as (N, T) j ? 8. Using Monte Carlo experiments, it is shown that the test has the correct size and satisfactory power in panels with strictly exogenous regressors for various combinations of N and T. For autoregressive (AR) models the proposed test performs well for moderate values of the root of the autoregressive process. But for AR models with roots near unity a bias-corrected bootstrapped version of the test is proposed which performs well even if N is large relative to T. The proposed cross section dispersion tests are applied to testing the homogeneity of slopes in autoregressive models of individual earnings using the PSID data. The results show statistically signi?cant evidence of slope heterogeneity in the earnings dynamics, even when individuals with similar educational backgrounds are considered as sub-sets."], "field": "Economics, Econometrics and Finance", "q_year": 2024, "q_cid": "269378394", "pos_cid": 119929921, "source": "eval_collection"}
{"query_id": "scaleup_27633386_22884117", "query": "How to explain why industrial policies achieve backward integration in Nigeria’s cement industry but fail to revive its textile industry", "pos": ["The Learning Trap in Late Industrialisation: Local Firms and Capability Building in Ethiopia’s Apparel Export Industry. Abstract Local firms in new supplier countries face major challenges in entering manufacturing global value chains (GVCs) in the context of increased competition and requirements. To understand these challenges, we argue for the importance of looking more closely at local firm capability building, which is a costly and uncertain process and in the early stage of industrialisation was historically facilitated by industrial policy and leveraging foreign knowledge. This article examines the opportunities and constraints that Ethiopian-owned firms faced in building capabilities to enter apparel GVCs, using a survey designed to measure firms’ capabilities and firm histories to understand learning paths. We find that local export firms had a large capability gap between their existing capabilities and what is required to enter apparel GVCs, leading to high learning costs and risks, while the profit margins were very low, and there were limited learning channels. Industrial policy evolved taking into account these constraints, but faced challenges in providing learning channels for local firms in the context of a weak manufacturing class and hyper-competitive apparel GVCs. This resulted in a learning trap where local firms do not even try to enter manufacturing GVCs, or enter but fail to remain."], "field": "Economics, Econometrics and Finance", "q_year": 2025, "q_cid": "276333862", "pos_cid": 228841175, "source": "eval_collection"}
{"query_id": "scaleup_26415431_29248468", "query": "How to distinguish genuine long-run relationships from no long-run relationship and cases where either the dependent variable or the independent variables are absent from that relationship", "pos": ["Bootstrapping the autoregressive distributed lag test for cointegration. ABSTRACT We propose a bootstrap autoregressive-distributed lag (ARDL) test. By applying the appropriate bootstrap method, some weaknesses underlying the Pesaran, Shin and Smith ARDL bounds test are addressed including size and power properties and the elimination of inconclusive inferences. In addition, inferences based solely on the significance of the F-test and single t-test from the ARDL bounds test are not sufficient to avoid degenerate cases. The bootstrap ARDL test provides an additional test on the significance of coefficients on lagged levels of the regressors, which provides a better insight into the cointegration status of the model."], "field": "Economics, Econometrics and Finance", "q_year": 2023, "q_cid": "264154319", "pos_cid": 29248468, "source": "eval_collection"}
{"query_id": "scaleup_25910896_22049640", "query": "How to support inference for data with dependence both over time and across observed units", "pos": ["Sharp connections between Berry-Esseen characteristics and Edgeworth expansions for stationary processes. Given a weakly dependent stationary process, we describe the transition between a Berry-Esseen bound and a second order Edgeworth expansion in terms of the Berry-Esseen characteristic. This characteristic is sharp: We show that Edgeworth expansions are valid if and only if the Berry-Esseen characteristic is of a certain magnitude. If this is not the case, we still get an optimal Berry-Esseen bound, thus describing the exact transition. We also obtain (fractional) expansions given $3 < p \\leq 4$ moments, where a similar transition occurs. Corresponding results also hold for the Wasserstein metric $W_1$, where a related, integrated characteristic turns out to be optimal. As an application, we establish novel weak Edgeworth expansion and CLTs in $L^p$ and $W_1$. As another application, we show that a large class of high dimensional linear statistics admit Edgeworth expansions without any smoothness constraints, that is, no non-lattice condition or related is necessary. In all results, the necessary weak-dependence assumptions are very mild. In particular, we show that many prominent dynamical systems and models from time series analysis are within our framework, giving rise to many new results in these areas."], "field": "Economics, Econometrics and Finance", "q_year": 2022, "q_cid": "259108967", "pos_cid": 220496404, "source": "eval_collection"}
{"query_id": "scaleup_26870603_13315673", "query": "How to select high-quality loan-approval rules that maintain the target bad rate, account for approval criteria beyond credit scores, and remain understandable to risk analysts and customers", "pos": ["Submodular Optimization with Submodular Cover and Submodular Knapsack Constraints. We investigate two new optimization problems — minimizing a submodular function subject to a submodular lower bound constraint (submodular cover) and maximizing a submodular function subject to a submodular upper bound constraint (submodular knapsack). We are motivated by a number of real-world applications in machine learning including sensor placement and data subset selection, which require maximizing a certain submodular function (like coverage or diversity) while simultaneously minimizing another (like cooperative cost). These problems are often posed as minimizing the difference between submodular functions [9, 25] which is in the worst case inapproximable. We show, however, that by phrasing these problems as constrained optimization, which is more natural for many applications, we achieve a number of bounded approximation guarantees. We also show that both these problems are closely related and an approximation algorithm solving one can be used to obtain an approximation guarantee for the other. We provide hardness results for both problems thus showing that our approximation factors are tight up to log-factors. Finally, we empirically demonstrate the performance and good scalability properties of our algorithms."], "field": "Economics, Econometrics and Finance", "q_year": 2024, "q_cid": "268706037", "pos_cid": 13315673, "source": "eval_collection"}
{"query_id": "scaleup_25668483_15818774", "query": "How to understand how different types of interventions interact to support innovation in cities in developing economies", "pos": ["The co-evolution of policy mixes and socio-technical systems: Towards a conceptual framework of policy mix feedback in sustainability transitions. Abstract Understanding how policymaking processes can influence the rate and direction of socio-technical change towards sustainability is an important, yet underexplored research agenda in the field of sustainability transitions. Some studies have sought to explain how individual policy instruments can influence transitions, and the politics surrounding this process. We argue that such individual policy instruments can cause wider feedback mechanisms that influence not only their own future development, but also other instruments in the same area. Consequently, by extending the scope of analysis to that of a policy mix allows us to account for multiple policy effects on socio-technical change and resultant feedback mechanisms influencing the policy processes that underpin further policy mix change. This paper takes a first step in this regard by combining policy studies and innovation studies literatures to conceptualise the co-evolutionary dynamics of policy mixes and socio-technical systems. We focus on policy processes to help explain how policy mixes influence socio-technical change, and how changes in the socio-technical system also shape the evolution of the policy mix. To do so we draw on insights from the policy feedback literature, and propose a novel conceptual framework. The framework highlights that policy mixes aiming to foster sustainability transitions need to be designed to create incentives for beneficiaries to mobilise further support, while overcoming a number of prevailing challenges which may undermine political support over time. In the paper, we illustrate the framework using the example of the zero carbon homes policy mix in the UK. We conclude with deriving research and policy implications for analysing and designing dynamic policy mixes for sustainability transitions."], "field": "Economics, Econometrics and Finance", "q_year": 2023, "q_cid": "256684838", "pos_cid": 158187741, "source": "eval_collection"}
{"query_id": "scaleup_27619202_25475789", "query": "How to ensure carbon dioxide removal policy deliberation accounts for diverse stakeholder views and value judgments while upholding procedural fairness", "pos": ["An environmental justice perspective on ecosystem services. Mainstreaming of ecosystem service approaches has been proposed as one path toward sustainable development. Meanwhile, critics of ecosystem services question if the approach can account for the multiple values of ecosystems to diverse groups of people, or for aspects of inter- and intra-generational justice. In particular, an ecosystem service approach often overlooks power dimensions and capabilities that are core to environmental justice. This article addresses the need for greater guidance on incorporating justice into ecosystem services research and practice. We point to the importance of deep engagement with stakeholders and rights holders to disentangle contextual factors that moderate justice outcomes on ecosystem service attribution and appropriation in socio-political interventions. Such a holistic perspective enables the integration of values and knowledge plurality for enhancing justice in ecosystem services research. This broadened perspective paves a way for transformative ecosystem service assessments, management, and research, which can help inform and design governance structures that nourish human agency to sustainably identify, manage, and enjoy ecosystem services for human wellbeing."], "field": "Economics, Econometrics and Finance", "q_year": 2025, "q_cid": "276192021", "pos_cid": 254757899, "source": "eval_collection"}
{"query_id": "scaleup_24798600_21769801", "query": "How to clarify the effects of global economic crises on Nigeria’s foreign investment flows and the relationship between disrupted flows, reduced domestic economic activity, and economic growth", "pos": ["The 2008/2009 Banking Crisis in Nigeria: The Hidden Trigger of the Financial Crash. It is observed that, while existing literature on the 2008/2009 Nigerian banking crisis has emphasised causal factors, which can be classified as remote causes, it is silent on the immediate cause of the financial crash. Therefore, this study seeks to identify the trigger of events that culminated to the 2008/2009 banking crisis in Nigeria. The paper makes a conjecture that the trigger, lies hidden in the remote causes which, although regarded as causes of the banking crisis, do not make a definite specification of the trigger. Thus, this study sets out to examine the data of FDI and FPI inflows to Nigeria during the years of financial liberalisation. Using the applicable logic in Minsky’s financial instability hypothesis, it concludes that the sudden divestment of FPI in 2009 from the Nigerian economy, was the trigger of the financial crash."], "field": "Economics, Econometrics and Finance", "q_year": 2022, "q_cid": "247986008", "pos_cid": 217698018, "source": "eval_collection"}
{"query_id": "scaleup_27679778_21968186", "query": "How to clarify the need for new organisations and their relationship to existing actors when carbon-pricing governance may not adequately address emerging issues and specialised needs", "pos": ["Coordination or conflict? The causes and consequences of institutional overlap in a disaggregated world order. Abstract Institutional overlap emerges not only as an unintended by-product of purposive state action but also as its deliberate result. In two ways, this article expands existing research on the causes and consequences of institutional overlap. First, we establish that three different types of dissatisfaction may lead states to deliberately create institutional overlap: dissatisfaction with substantive norms and rules, dissatisfaction with decision-making rules and dissatisfaction with the institutional fit of an existing governance arrangement for a given cooperation problem. Each type of dissatisfaction triggers a distinct motivation for the creation of institutional overlap: to induce policy change, to increase influence on collective decision-making or to enhance governance effectiveness. Second, we demonstrate that whereas the motivation to induce policy change leads to interface conflicts, the motivations to increase influence on collective decision-making and to enhance governance effectiveness give rise to inter-institutional coordination. Three empirical case studies on global energy governance, the governance of global development banking and global environmental governance probe these analytical claims."], "field": "Economics, Econometrics and Finance", "q_year": 2024, "q_cid": "276797786", "pos_cid": 219681869, "source": "eval_collection"}
{"query_id": "scaleup_23635026_15901352", "query": "How to characterize outcome distributions with changing asymmetry and tail heaviness to assess how adverse effects spread under changing conditions", "pos": ["A new GARCH model with higher moments for stock return predictability. The main purpose of the paper is to propose a new GARCH-SK predictive regression model that accommodates higher order moments (skewness and kurtosis) in testing the null hypothesis of no predictability. Using an extensive and well-known time-series dataset on stock returns and 19 predictors for the United States, we show that our proposed GARCH-SK model outperforms a model without these higher moments. The superior performance of our proposed model holds both statistically and economically and is robust to different data frequencies."], "field": "Economics, Econometrics and Finance", "q_year": 2021, "q_cid": "236350260", "pos_cid": 159013528, "source": "eval_collection"}
{"query_id": "scaleup_26459147_24881158", "query": "How to assess the informational value of each data owner’s privately held data for joint parameter estimation when owners may require monetary incentives to share it", "pos": ["On the Convergence of the Shapley Value in Parametric Bayesian Learning Games. Measuring contributions is a classical problem in cooperative game theory where the Shapley value is the most well-known solution concept. In this paper, we establish the convergence property of the Shapley value in parametric Bayesian learning games where players perform a Bayesian inference using their combined data, and the posterior-prior KL divergence is used as the characteristic function. We show that for any two players, under some regularity conditions, their difference in Shapley value converges in probability to the difference in Shapley value of a limiting game whose characteristic function is proportional to the log-determinant of the joint Fisher information. As an application, we present an online collaborative learning framework that is asymptotically Shapley-fair. Our result enables this to be achieved without any costly computations of posterior-prior KL divergences. Only a consistent estimator of the Fisher information is needed. The effectiveness of our framework is demonstrated with experiments using real-world data."], "field": "Economics, Econometrics and Finance", "q_year": 2023, "q_cid": "264591474", "pos_cid": 248811584, "source": "eval_collection"}
{"query_id": "scaleup_25433782_22197040", "query": "How to comprehensively account for economic activities and interactions within cities, including retail and other service sectors, in analyses of economic relatedness and complexity", "pos": ["The amenity mix of urban neighborhoods. Abstract Advances in computational urbanism have stimulated the rise of generative and parametric approaches to urban design. Yet, most generative and parametric approaches focus on physical characteristics, such as a neighborhoods walkability, energy efficiency, and urban form. Here, we study the colocation patterns of more than one million amenities in 47 U.S. cities to model the amenity mix of neighborhoods, and to identify the amenities that are over- or under-supplied in a neighborhood. We build this model by combining a clustering algorithm, designed to identify amenity-dense neighborhoods, and a network, connecting amenities that are likely to collocate. Our findings extend generative and parametric urban design approaches to the amenity mix of neighborhoods, by leveraging the idea of relatedness from the economic geography literature, to evaluate and optimize a neighborhood's amenity mix."], "field": "Economics, Econometrics and Finance", "q_year": 2023, "q_cid": "254337826", "pos_cid": 221970400, "source": "eval_collection"}
{"query_id": "scaleup_25492462_23963831", "query": "How to understand firms’ responses outside the market to economic policy uncertainty affecting regulatory compliance and access to government-controlled benefits in emerging economies such as China", "pos": ["Corruption, Bribery and Innovation in CEE: Where is the Link?. This study investigates the influence of formal and informal institutions on firm innovation in transitional economies of Central and Eastern Europe (CEEs) by explicitly differentiating between corruption and bribery as distinct informal institutions. We integrate institutional theory and legitimacy theory to explain that the failure of formal institutions creates an environment of corruption which encourages firms to use bribes to facilitate economic exchange. We test our hypotheses on the innovation performance of a sample (n = 1603) of firms in 11 CEEs. The results show that weak rule of law and ineffective business regulations in CEEs propagate the perception of corruption that inhibits firm innovation. However, the use of bribery enables firms to transform this environment of corruption into innovation outcomes. The policy and managerial implications of our research for differentiating between corruption and bribery and our findings that bribery acts as the glue that binds formal and informal institutions are fully discussed."], "field": "Economics, Econometrics and Finance", "q_year": 2022, "q_cid": "254924622", "pos_cid": 239638313, "source": "eval_collection"}
{"query_id": "scaleup_26894522_49409049", "query": "How to identify core journals containing the most pertinent and extensively referenced research on capital markets’ green financial instrument issuances", "pos": ["Using Bradford's law of scattering to identify the core journals of pediatric surgery.. BACKGROUND Bradford's law of scattering defines an exponentially diminishing return when extending a search for references in journals and can be used to identify the \"core\" journals in a field. The purpose of this study was to identify the core journals of pediatric surgery. METHODS With Institutional Review Board approval, we developed bibliometric profiles for the top academically productive pediatric surgeons in the United States. These profiles included the total number of publications, journals in which those authors published their manuscripts, and identification of all articles cited by those surgeons, along with the journals those references were drawn from. Bradford's law of scattering was applied to identify the core journals of pediatric surgery. RESULTS We identified n = 69 pediatric surgeons (10 ± 0.2 5-year h-index). These authors published 10,031 articles (145 ± 90 per surgeon), which were cited 250841 times (3635 ± 413 per surgeon). Pediatric surgeons' articles contained 199507 references (2891 ± 176 per surgeon). We analyzed 58,310 references (top 20 journals) cited by pediatric surgeons. Bradford's Law identified a single core journal for p = 3-10 zones, with P = 3, providing the best correlation between predicted and actual values (Rˆ2 = 0.9996). The core journal for pediatric surgery is Journal of Pediatric Surgery. CONCLUSIONS We used Bradford's Law to identify the core journals of pediatric surgery. These core journals include the two leading pediatric surgery-specific journals and the highest impact factor journals in surgery (Annals of Surgery) and medicine (NEJM). These findings can help busy pediatric surgeons focus their reading to stay updated in a rapidly evolving field."], "field": "Economics, Econometrics and Finance", "q_year": 2024, "q_cid": "268945228", "pos_cid": 49409049, "source": "eval_collection"}
{"query_id": "scaleup_27178566_22150759", "query": "How to determine the war’s effect on grain futures prices despite differences in pre-invasion price trends", "pos": ["The Role of Parallel Trends in Event Study Settings: An Application to Environmental Economics. Difference-in-differences (DID) research designs usually rely on variation of treatment timing such that, after making an appropriate parallel trends assumption, one can identify, estimate, and make inference about causal effects. In practice, however, different DID procedures rely on different parallel trends assumptions (PTAs), and recover different causal parameters. In this paper, we focus on staggered DID (also referred as event studies) and discuss the role played by the PTA in terms of identification and estimation of causal parameters. We document a “robustness” versus “efficiency” trade-off in terms of the strength of the underlying PTA and argue that practitioners should be explicit about these trade-offs whenever using DID procedures. We propose new DID estimators that reflect these trade-offs and derive their large sample properties. We illustrate the practical relevance of these results by assessing whether the transition from federal to state management of the Clean Water Act affects compliance rates."], "field": "Economics, Econometrics and Finance", "q_year": 2024, "q_cid": "271785662", "pos_cid": 221507592, "source": "eval_collection"}
{"query_id": "scaleup_26732640_20262738", "query": "How to classify local government investments when generating financial income is not their only purpose", "pos": ["The rise of transnational state capital: state-led foreign investment in the 21st century. Abstract Cross-border state-led investment is a recently rising, but understudied phenomenon of the global political economy. Existing research employs an anecdotal and case-oriented perspective that does not engage in a systemic, large-scale analysis of this rise of transnational state investment and its consequences for the transformation of state power in 21st century capitalism. We take a first step at filling this gap and offer two original contributions: Conceptually, we operationalize transnational foreign state-led investment on the basis of weighted ownership ties. These state capital ties are created by states as investors in corporations around the world. Empirically, we demonstrate our approach by setting up and analyzing the largest dataset on transnational state capital up to date. We show which different outward strategies states as owners employ and classify states according to their relative positions within the global network of transnational state capital. Our results illustrate a crucial aspect of the ongoing transformation of state power and sovereignty within globalization and we demonstrate how a careful and data-driven approach is able to identify different pathways and dimensions of this transformation."], "field": "Economics, Econometrics and Finance", "q_year": 2024, "q_cid": "267326403", "pos_cid": 202627384, "source": "eval_collection"}
{"query_id": "scaleup_23760750_12216584", "query": "How to quantify socioeconomic inequalities in health outcomes and forgone care and identify the socioeconomic and health-system factors associated with them", "pos": ["On Decomposing the Causes of Health Sector Inequalities with an Application to Malnutrition Inequalities in Vietnam. A method for decomposing inequalities in the health sector into their causes is developed and applied to data on child malnutrition in Vietnam. Wagstaff, van Doorslaer, and Watanabe propose a method for decomposing inequalities in the health sector into their causes, by coupling the concentration index with a regression framework. They also show how changes in inequality over time, and differences across countries, can be decomposed into the following: - Changes due to changing inequalities in the determinants of the variable of interest. - Changes in the means of the determinants. - Changes in the effects of the determinants on the variable of interest. The authors illustrate the method using data on child malnutrition in Vietnam. They find that inequalities in height-for-age in 1993 and 1998 are accounted for largely by inequalities in household consumption and by unobserved influences at the commune level. And they find that an increase in such inequalities is accounted for largely by changes in these two influences. In the case of household consumption, rising inequalities play a part, but more important have been the inequality - increasing effects of rising average consumption and the increased protective effect of consumption on nutritional status. In the case of unobserved commune-level influences, rising inequality and general improvements seem to have been roughly equally important in accounting for rising inequality in malnutrition. This paper - a joint product of Public Services for Human Development, Development Research Group, and the Development Data Group - is part of a larger effort in the Bank to investigate the links between health and poverty. The authors may be contacted at awagstaff@worldbank.org, vandoorslaer@econ.bmg.eur.nl., or nwatanabe@worldbank.org."], "field": "Economics, Econometrics and Finance", "q_year": 2021, "q_cid": "237607508", "pos_cid": 122165846, "source": "eval_collection"}
{"query_id": "scaleup_22208146_16904309", "query": "How to anticipate which restaurant firms are more vulnerable to stock-market declines during an unexpected crisis such as COVID-19", "pos": ["Macroeconomic factors, firm characteristics and financial performance. PurposeThe purpose of this paper is to explore the interrelationship between macroeconomic factors, firm characteristics and financial performance of quoted manufacturing firms in Nigeria. Specifically, the study investigates the effect of interest rate, inflation rate, exchange rate and the gross domestic product (GDP) growth rate, while the firm characteristics were size, leverage and liquidity. The dependent variable financial performance is measured as return on assets (ROA).Design/methodology/approachThe study used theex post factoresearch design. The population comprised all quoted manufacturing firms on the Nigerian Stock Exchange. The sample was restricted to companies in the consumer goods sector, selected using non-probability sampling method. The study used multiple linear regression as the method of validating the hypotheses.FindingsThe study finds no significant effect for interest rate and exchange rate, but a significant effect for inflation rate and GDP growth rate on ROA. Second, the firm characteristics showed that firm size, leverage and liquidity were significant.Practical implicationsThe study has implications for regulators and policy makers in formulating policy decisions. In addition, managers may better understand the interplay between macroeconomic factors, firm characteristics and profitability of firms.Originality/valueFew studies have addressed the interplay of macroeconomic factors and firm characteristics in determining the profitability of manufacturing firms in the country and developing countries in general."], "field": "Economics, Econometrics and Finance", "q_year": 2020, "q_cid": "222081463", "pos_cid": 169043091, "source": "eval_collection"}
{"query_id": "scaleup_23404905_20949930", "query": "How to determine how strongly reference-group expectations and others’ opinions influence intentions to dine out in China and Korea during COVID-19", "pos": ["Some Key Factors Affecting Consumers’ Intentions to Purchase Functional Foods: A Case Study of Functional Yogurts in Vietnam. The development of functional foods is key to promoting a healthy diet and preventing certain diseases. This study aims to examine several key factors that affect consumer attitude and intention with respect to purchasing functional foods in an emerging market economy. A research model was developed by extension of the Theory of Reasoned Action (TRA), and then validated through obtaining data from 596 Vietnamese consumers who were interested in functional yogurts using an interviewer-administered questionnaire. Multivariate data analysis reveals that while health consciousness and subjective norm significantly enhance consumers’ attitudes towards purchasing functional yogurts, perceived price of functional yogurts exerts a negative impact on such attitudes. Moreover, subjective norm and attitude appear to be key predictors of consumers’ intentions to buy functional yogurts. These findings extend the extant literature relating to functional food purchase and consumption in emerging markets, and they have several important practical implications for functional yogurt manufacturers, retailers, and policymakers. A major implication is that education and communication programs that aim at increasing consumers’ health consciousness and their awareness of functional foods’ health benefits play an integral role in the success of functional food products such as functional yogurts. Research limitations and future research directions are also presented."], "field": "Economics, Econometrics and Finance", "q_year": 2021, "q_cid": "234049053", "pos_cid": 209499302, "source": "train_step3"}
{"query_id": "scaleup_24641234_16916329", "query": "How to explain panic buying during COVID-19", "pos": ["‘Should I Buy, Hoard, or Hide?’- Consumers’ responses to perceived scarcity. ABSTRACT Scarce shopping situations often seem to have a greater value for consumers and trigger extreme behaviors. This study examines the effects of scarcity that is strategically created by the marketer in influencing consumer behavior. Drawing from reactance theory, it is suggested that, when scarcity is perceived to be strategically created by the retailer, consumers tend to exhibit deviant and competitive behaviors. The mediating role of emotions like anticipated regret is also examined. Further, the role of human traits like competitiveness and hedonic motivations in moderating the relationships between perceived scarcity and behaviors is also examined. The results of the study suggest that, under the conditions of perceived scarcity, consumers tend to exhibit behaviors like in-store hoarding, and in-store hiding, due in part to the increased urgency to buy. Also, the findings suggest a pertinent role of emotions and human traits in influencing the decision making under the condition of strategically-created scarcity."], "field": "Economics, Econometrics and Finance", "q_year": 2022, "q_cid": "246412349", "pos_cid": 169163293, "source": "train_step3"}
{"query_id": "scaleup_26526483_21621324", "query": "How to assess how well restaurants are doing when it is unclear whether gains from borrowed money justify its cost", "pos": ["The Impact of Capital Structure on Firm Performance: Evidence from Vietnam. This paper explores the impact of capital structure on firm performance in the context of Vietnam. The paper investigates the different effect of capital structure on firm performance in state-owned and non-state enterprises listed on the Vietnam stock market. The panel data of research sample includes 488 non-financial listed companies on the Vietnam stock market for a period of six years, from 2013 to 2018. The Generalized Least Square (GLS) is employed to address econometric issues and to improve the accuracy of the regression coefficients. In this research, firm performance is measured by return on equity (ROE), return on assets (ROA), and earnings per share (EPS). The ratios of short-term liabilities, long-term liabilities, and total liabilities to total assets are proxy for capital structure. Firm sizes, growth rate, liquidity, and ratio of fixed assets to total assets are control variables in the study. The empirical results show that capital structure has a statistically significant negative effect on the firm performance. The result also shows this effect is stronger in state-owned enterprises than non-state enterprises in Vietnam. These evidences provide a new insight to managers of both state-owned and non-state enterprises on how to improve the firm ’ s performance with capital structure."], "field": "Economics, Econometrics and Finance", "q_year": 2023, "q_cid": "265264837", "pos_cid": 216213245, "source": "train_step3"}
{"query_id": "scaleup_25409692_7742072", "query": "How to determine what leads employees to pursue creative goals and generate, share, and implement ideas", "pos": ["Self-efficacy: toward a unifying theory of behavioral change.. The present article presents an integrative theoretical framework to explain and to predict psychological changes achieved by different modes of treatment. This theory states that psychological procedures, whatever their form, alter the level and strength of self-efficacy. It is hypothesized that expectations of personal efficacy determine whether coping behavior will be initiated, how much effort will be expended, and how long it will be sustained in the face of obstacles and aversive experiences. Persistence in activities that are subjectively threatening but in fact relatively safe produces, through experiences of mastery, further enhancement of self-efficacy and corresponding reductions in defensive behavior. In the proposed model, expectations of personal efficacy are derived from four principal sources of information: performance accomplishments, vicarious experience, verbal persuasion, and physiological states. The more dependable the experiential sources, the greater are the changes in perceived selfefficacy. A number of factors are identified as influencing the cognitive processing of efficacy information arising from enactive, vicarious, exhortative, and emotive sources. The differential power of diverse therapeutic procedures is analyzed in terms of the postulated cognitive mechanism of operation. Findings are reported from microanalyses of enactive, vicarious, and emotive modes of treatment that support the hypothesized relationship between perceived self-efficacy and behavioral changes. Possible directions for further research are discussed."], "field": "Economics, Econometrics and Finance", "q_year": 2022, "q_cid": "254096927", "pos_cid": 7742072, "source": "train_step3"}
{"query_id": "scaleup_23485197_55496542", "query": "How to determine whether a nationwide cut in mandatory charges on pay affects pay differences across cities, especially for people paid near the legal minimum", "pos": ["The Impact of Lowering the Payroll Tax on Informality in Colombia. In 2012, the Colombian Government reduced employer payroll contributions from 29.5 to 16.0 percent. Two years later, the informality rate had diminished by about 4.0 percentage points. This paper attempts to estimate how much of this reduction was due to the tax reform, isolating the impact of other macroeconomic variables. A natural approach to performing this task is to apply a difference-in-differences methodology using a household survey panel. Since the Colombian survey does not have a panel structure, we simulated one using a matching difference-in-differences methodology. According to the results, the tax reform is associated with a 4.8-percentage-point decrease in the informality of workers affected by the reform in the thirteen main metropolitan areas. This represents approximately half the reduction of the relevant informality rate during that period, affecting mostly salaried men and workers in general with low levels of education."], "field": "Economics, Econometrics and Finance", "q_year": 2021, "q_cid": "234851976", "pos_cid": 55496542, "source": "train_step3"}
{"query_id": "scaleup_14582077_23981835", "query": "How to determine the biosynthetic origin of c30–32 alkenols in Nannochloropsis and whether twenty-carbon hydroxy fatty acids can supply their unsaturated precursors", "pos": ["Roles of the FabA and FabZ β-Hydroxyacyl-Acyl Carrier Protein Dehydratases in Escherichia coli Fatty Acid Biosynthesis*. There are two genes, fabA and fabZ, encoding β-hydroxyacyl-acyl carrier protein (ACP) dehydratases that function in the dissociated, type II fatty acid synthase system of Escherichia coli. We have investigated their roles in fatty acid synthesis by purifying the two proteins and reconstituting cycles of fatty acid synthesis in vitro using five other purified proteins. FabA and FabZ exhibited broad, overlapping chain length specificities. The FabZ dehydratase efficiently catalyzed the dehydration of short chain β-hydroxyacyl-ACPs and long chain saturated and unsaturated β-hydroxyacyl-ACPs. FabA was most active on intermediate chain length β-hydroxyacyl-ACPs and also possessed significant activity toward both short and long chain saturated β-hydroxyacyl-ACPs. Significantly, FabA was virtually inactive in the dehydration of long chain unsaturated β-hydroxyacyl-ACP. The introduction of the double bond at the 10-carbon stage of fatty acid synthesis by FabA was only detected in the presence of β-ketoacyl-ACP synthase I (FabB). A yeast two-hybrid analysis failed to detect an interaction between FabA and FabB, therefore the channeling of intermediates toward unsaturated fatty acid synthesis by FabB was attributed to the affinity of the condensing enzyme for cis-decenoyl-ACP. The broad substrate specificity of FabZ coupled with the inactivity of FabA toward a long chain unsaturated β-hydroxyacyl-ACP provides a biochemical explanation for the phenotypes of cells with genetically altered levels of the two dehydratases."], "field": "Energy", "q_year": 2019, "q_cid": "145820773", "pos_cid": 23981835, "source": "eval20x26"}
{"query_id": "scaleup_44116795_1531438", "query": "How to accurately visualize and quantify intracellular metabolites in individual live, motile microalgae with spatial and temporal resolution", "pos": ["Photoporation of Biomolecules into Single Cells in Living Vertebrate Embryos Induced by a Femtosecond Laser Amplifier. Introduction of biomolecules into cells in living animals is one of the most important techniques in molecular and developmental biology research, and has potentially broad biomedical implications. Here we report that biomolecules can be introduced into single cells in living vertebrate embryos by photoporation using a femtosecond laser amplifier with a high pulse energy and a low repetition rate. First, we confirmed the efficiency of this photoporation technique by introducing dextran, morpholino oligonucleotides, or DNA plasmids into targeted single cells of zebrafish, chick, shark, and mouse embryos. Second, we demonstrated that femtosecond laser irradiation efficiently delivered DNA plasmids into single neurons of chick embryos. Finally, we successfully manipulated the fate of single neurons in zebrafish embryos by delivering mRNA. Our observations suggest that photoporation using a femtosecond laser with a high pulse energy and low repetition rate offers a novel way to manipulate the function(s) of individual cells in a wide range of vertebrate embryos by introduction of selected biomolecules."], "field": "Energy", "q_year": 2018, "q_cid": "44116795", "pos_cid": 1531438, "source": "eval20x26"}
{"query_id": "scaleup_1211280_23770747", "query": "How to determine the origin of the modification at the fourth carbon of nosiheptide’s indole ring", "pos": ["Nosiheptide Biosynthesis Featuring a Unique Indole Side Ring Formation on the Characteristic Thiopeptide Framework. Nosiheptide (NOS), belonging to the e series of thiopeptide antibiotics that exhibit potent activity against various bacterial pathogens, bears a unique indole side ring system and regiospecific hydroxyl groups on the characteristic macrocyclic core. Here, cloning, sequencing and characterization of the nos gene cluster from Streptomyces actuosus ATCC 25421 as a model for this series of thiopeptides has unveiled new insights into their biosynthesis. Bioinformatics-based sequence analysis and in vivo investigation into the gene functions show that NOS biosynthesis shares a common strategy with recently characterized b or c series thiopeptides for forming the characteristic macrocyclic core, which features a ribosomally synthesized precursor peptide with conserved posttranslational modifications. However, it apparently proceeds via a different route for tailoring the thiopeptide framework, allowing the final product to exhibit the distinct structural characteristics of e series thiopeptides, such as the indole side ring system. Chemical complementation supports the notion that the S-adenosylmethionine (AdoMet)-dependent protein NosL may play a central role in converting Trp to the key 3-methylindole moiety by an unusual carbon side chain rearrangement, most likely via a radical-initiated mechanism. Characterization of the indole side ring-opened analog of NOS from the nosN mutant strain is consistent with the proposed methyltransferase activity of its encoded protein, shedding light into the timing of the individual steps for indole side ring biosynthesis. These results also suggest the feasibility of engineering novel thiopeptides for drug discovery by manipulating the NOS biosynthetic machinery."], "field": "Energy", "q_year": 2011, "q_cid": "1211280", "pos_cid": 23770747, "source": "eval20x26"}
{"query_id": "scaleup_1211280_39638203", "query": "How to clarify methyl-group acquisition and regeneration of the proposed cofactor in class B radical SAM methyltransferases, including SAM’s role and the source of the required reducing electron", "pos": ["COBALAMIN- AND COBAMIDE-DEPENDENT METHYLTRANSFERASES. Methyltransferases that employ cobalamin cofactors, or their analogues the cobamides, as intermediates in catalysis of methyl transfer play vital roles in energy generation in anaerobic unicellular organisms. In a broader range of organisms they are involved in the conversion of homocysteine to methionine. Although the individual methyl transfer reactions catalyzed are simple SN2 displacements, the required change in coordination at the cobalt of the cobalamin or cobamide cofactors and the lability of the reduced Co+1 intermediates introduces the necessity for complex conformational changes during the catalytic cycle. Recent spectroscopic and structural studies on several of these methyltransferases have helped to reveal the strategies by which these conformational changes are facilitated and controlled."], "field": "Energy", "q_year": 2011, "q_cid": "1211280", "pos_cid": 39638203, "source": "eval20x26"}
{"query_id": "scaleup_15858843_4462224", "query": "How to explain precise site selection across variable peptide sequences with conserved leading segments and determine whether a common recognition principle applies?", "pos": ["Structure and Mechanism of the tRNA-Dependent Lantibiotic Dehydratase NisB. Lantibiotics are a class of peptide antibiotics that contain one or more thioether bonds. The lantibiotic nisin is an antimicrobial peptide that is widely used as a food preservative to combat food-borne pathogens. Nisin contains dehydroalanine and dehydrobutyrine residues that are formed by the dehydration of Ser/Thr by the lantibiotic dehydratase NisB (ref. 2). Recent biochemical studies revealed that NisB glutamylates Ser/Thr side chains as part of the dehydration process. However, the molecular mechanism by which NisB uses glutamate to catalyse dehydration remains unresolved. Here we show that this process involves glutamyl-tRNAGlu to activate Ser/Thr residues. In addition, the 2.9-Å crystal structure of NisB in complex with its substrate peptide NisA reveals the presence of two separate domains that catalyse the Ser/Thr glutamylation and glutamate elimination steps. The co-crystal structure also provides insights into substrate recognition by lantibiotic dehydratases. Our findings demonstrate an unexpected role for aminoacyl-tRNA in the formation of dehydroamino acids in lantibiotics, and serve as a basis for the functional characterization of the many lantibiotic-like dehydratases involved in the biosynthesis of other classes of natural products."], "field": "Energy", "q_year": 2015, "q_cid": "15858843", "pos_cid": 4462224, "source": "eval20x26"}
{"query_id": "scaleup_20557895_24763098", "query": "How to achieve efficient solar hydrogen generation with effective charge separation and sufficiently favorable electronic energetics for hydrogen evolution", "pos": ["Catalysis with TiO2/gold nanocomposites. Effect of metal particle size on the Fermi level equilibration.. Photoexcited semiconductor nanoparticles undergo charge equilibration when they are in contact with metal nanoparticles. Such a charge distribution has direct influence in dictating the energetics of the composite by shifting the Fermi level to more negative potentials. The transfer of electrons to Au nanoparticles has now been probed by exciting TiO(2) nanoparticles under steady-state and laser pulse excitation. Equilibration with the C(60)/C(60)(-) redox couple provides a means to determine the apparent Fermi level of the TiO(2)-Au composite system. The size-dependent shift in the apparent Fermi level of the TiO(2)-Au composite (20 mV for 8-nm diameter and 40 mV for 5-nm and 60 mV for 3-nm gold nanoparticles) shows the ability of Au nanoparticles to influence the energetics by improving the photoinduced charge separation. Isolation of individual charge-transfer steps from UV-excited TiO(2) --> Au --> C(60) has provided mechanistic and kinetic information on the role of metal in semiconductor-assisted photocatalysis and size-dependent catalytic activity of metal-semiconductor nanocomposites."], "field": "Energy", "q_year": 2017, "q_cid": "205578954", "pos_cid": 24763098, "source": "eval20x26"}
{"query_id": "scaleup_17086375_2821800", "query": "How to establish whether NFS1 interacts with MOCS3 in the cytosol of human cells", "pos": ["Formation and Toxicity of Soluble Polyglutamine Oligomers in Living Cells. Background Aggregation and cytotoxicity of mutant proteins containing an expanded number of polyglutamine (polyQ) repeats is a hallmark of several diseases, including Huntington's disease (HD). Within cells, mutant Huntingtin (mHtt) and other polyglutamine expansion mutant proteins exist as monomers, soluble oligomers, and insoluble inclusion bodies (IBs). Determining which of these forms constitute a toxic species has proven difficult. Recent studies support a role for IBs as a cellular coping mechanism to sequester levels of potentially toxic soluble monomeric and oligomeric species of mHtt. Methodology/Principal Findings When fused to a fluorescent reporter (GFP) and expressed in cells, the soluble monomeric and oligomeric polyglutamine species are visually indistinguishable. Here, we describe two complementary biophysical fluorescence microscopy techniques to directly detect soluble polyglutamine oligomers (using Htt exon 1 or Httex1) and monitor their fates in live cells. Photobleaching analyses revealed a significant reduction in the mobilities of mHttex1 variants consistent with their incorporation into soluble microcomplexes. Similarly, when fused to split-GFP constructs, both wildtype and mHttex1 formed oligomers, as evidenced by the formation of a fluorescent reporter. Only the mHttex1 split-GFP oligomers assembled into IBs. Both FRAP and split-GFP approaches confirmed the ability of mHttex1 to bind and incorporate wildtype Htt into soluble oligomers. We exploited the irreversible binding of split-GFP fragments to forcibly increase levels of soluble oligomeric mHttex1. A corresponding increase in the rate of IBs formation and the number formed was observed. Importantly, higher levels of soluble mHttex1 oligomers significantly correlated with increased mutant cytotoxicity, independent of the presence of IBs. Conclusions/Significance Our study describes powerful and sensitive tools for investigating soluble oligomeric forms of expanded polyglutamine proteins, and their impact on cell viability. Moreover, these methods should be applicable for the detection of soluble oligomers of a wide variety of aggregation prone proteins."], "field": "Energy", "q_year": 2013, "q_cid": "17086375", "pos_cid": 2821800, "source": "eval20x26"}
{"query_id": "scaleup_25198108_23732920", "query": "How to distinguish solar-panel observations suitable for assessing long-term degradation from periods of capped output, outages, or abnormal sunlight or temperature", "pos": ["Performance Comparison of Clipping Detection Techniques in AC Power Time Series. In this research, a variety of methods were developed to detect clipping periods in AC power time series. AC power data streams associated with 36 unique systems across the United States were collected, and data points representing clipping periods were manually labeled by experts. Using this data set for training and validation, novel logic-based and machine learning (ML) approaches were developed to classify time series values as clipping or non-clipping. These approaches were compared to the RdTools method for detecting clipping periods. The logic-based and ML XGBoost approaches achieved F-scores of 85.0 and 77.6, respectively, when cross-validated against the manually labeled data, as compared to the current RdTools approach (F-score of 56.4), indicating a significant improvement at detecting clipping periods. Additionally, the effects of each clipping filter when evaluating system degradation rates were assessed, using 31 unique systems across the United States. Results indicate that estimated system degradation rate can vary based on the type of clipping filter used, by up to 0.6% degradation rate for some cases."], "field": "Energy", "q_year": 2022, "q_cid": "251981081", "pos_cid": 237329205, "source": "eval_collection"}
{"query_id": "scaleup_25839408_23481016", "query": "How to prevent clumping and maintain an even distribution for high, long-lasting activity in peroxide activation", "pos": ["Pomegranate-like Core–Shell Ni-NSs@MSNSs as a High Activity, Good Stability, Rapid Magnetic Separation, and Multiple Recyclability Nanocatalyst for DCPD Hydrogenation. A novel pomegranate-like Ni-NSs@MSNSs nanocatalyst was successfully synthesized via a modified Stöber method, and its application in the hydrogenation of dicyclopentadiene (DCPD) was firstly reported. The Ni-NSs@MSNSs possessed a high specific area (658 m2/g) and mesoporous structure (1.7–3.3 nm). The reaction of hydrogenation of DCPD to endo-tetrahydrodicyclopentadiene (endo-THDCPD) was used to evaluate the catalytic performance of the prepared materials. The distinctive pomegranate-like Ni-NSs@MSNSs core–shell nanocomposite exhibited superior catalytic activity (TOF = 106.0 h–1 and STY = 112.7 g·L–1·h–1) and selectivity (98.9%) than conventional Ni-based catalysts (experimental conditions: Ni/DCPD/cyclohexane = 1/100/1000 (w/w), 150 °C, and 2.5 MPa). Moreover, the Ni-NSs@MSNSs nanocatalyst could be rapidly and conveniently recycled by magnetic separation without appreciable loss. The Ni-NSs@MSNSs also exhibited excellent thermal stability (≥750 °C) and good recycling performance (without an activity and selectivity decrease in four runs). The superior application performance of the Ni-NSs@MSNSs nanocatalyst was mainly owing to its unique pomegranate-like structure and core–shell synergistic confinement effect."], "field": "Energy", "q_year": 2023, "q_cid": "258394082", "pos_cid": 234810164, "source": "eval_collection"}
{"query_id": "scaleup_23517295_418071", "query": "How to selectively inactivate MgAOX1 in Microchloropsis gaditana to clarify its role in respiration and mixotrophic growth", "pos": ["A Transcription Activator-Like Effector (TALE) Toolbox for Genome Engineering. Transcription activator-like effectors (TALEs) are a class of naturally occurring DNA-binding proteins found in the plant pathogen Xanthomonas sp. The DNA-binding domain of each TALE consists of tandem 34–amino acid repeat modules that can be rearranged according to a simple cipher to target new DNA sequences. Customized TALEs can be used for a wide variety of genome engineering applications, including transcriptional modulation and genome editing. Here we describe a toolbox for rapid construction of custom TALE transcription factors (TALE-TFs) and nucleases (TALENs) using a hierarchical ligation procedure. This toolbox facilitates affordable and rapid construction of custom TALE-TFs and TALENs within 1 week and can be easily scaled up to construct TALEs for multiple targets in parallel. We also provide details for testing the activity in mammalian cells of custom TALE-TFs and TALENs using quantitative reverse-transcription PCR and Surveyor nuclease, respectively. The TALE toolbox described here will enable a broad range of biological applications."], "field": "Energy", "q_year": 2021, "q_cid": "235172952", "pos_cid": 418071, "source": "eval_collection"}
{"query_id": "scaleup_23868322_23729710", "query": "How to accurately estimate the electrical parameters of solar photovoltaic systems with complex, nonlinear current–voltage and power–voltage relationships", "pos": ["Artificial gorilla troops optimizer: A new nature‐inspired metaheuristic algorithm for global optimization problems. Metaheuristics play a critical role in solving optimization problems, and most of them have been inspired by the collective intelligence of natural organisms in nature. This paper proposes a new metaheuristic algorithm inspired by gorilla troops' social intelligence in nature, called Artificial Gorilla Troops Optimizer (GTO). In this algorithm, gorillas' collective life is mathematically formulated, and new mechanisms are designed to perform exploration and exploitation. To evaluate the GTO, we apply it to 52 standard benchmark functions and seven engineering problems. Friedman's test and Wilcoxon rank‐sum statistical tests statistically compared the proposed method with several existing metaheuristics. The results demonstrate that the GTO performs better than comparative algorithms on most benchmark functions, particularly on high‐dimensional problems. The results demonstrate that the GTO can provide superior results compared with other metaheuristics."], "field": "Energy", "q_year": 2021, "q_cid": "238683229", "pos_cid": 237297101, "source": "eval_collection"}
{"query_id": "scaleup_25380191_189900", "query": "How to determine the appropriate number of distinct coal-county groups for a recovery-oriented classification", "pos": ["Silhouettes: a graphical aid to the interpretation and validation of cluster analysis. A new graphical display is proposed for partitioning techniques. Each cluster is represented by a so-called silhouette, which is based on the comparison of its tightness and separation. This silhouette shows which objects lie well within their cluster, and which ones are merely somewhere in between clusters. The entire clustering is displayed by combining the silhouettes into a single plot, allowing an appreciation of the relative quality of the clusters and an overview of the data configuration. The average silhouette width provides an evaluation of clustering validity, and might be used to select an ‘appropriate’ number of clusters."], "field": "Energy", "q_year": 2022, "q_cid": "253801915", "pos_cid": 189900, "source": "eval_collection"}
{"query_id": "scaleup_25765822_15571777", "query": "How to maintain an uninterrupted energy supply despite unexpected fluctuations in demand for fuel and energy resources", "pos": ["Demand-side management for energy in the region. The article deals with a promising approach to solving the problem of investment in the regional electric power industry — the application of demand-side management, the essence of which lies in proactive interaction of energy companies with customers, based on the balance of economic interests. The features of the concept and its tools are revealed, positive results of its implementation for energy market players and the region are shown, and examples of demand-side management programs are given. Institutional and mental barriers to effective implementation of demand-side management tools in power generation are analyzed. The article also proposes algorithms for implementing demand-side management programs in the region, and a mix of motivational activities that combines methods of administrative enforcement and economic stimulus for energy companies and consumers of energy and power, as well as guidelines on project funding and effectiveness evaluation."], "field": "Energy", "q_year": 2023, "q_cid": "257658220", "pos_cid": 155717772, "source": "eval_collection"}
{"query_id": "scaleup_25911967_10584818", "query": "How to select a support that provides sufficient molecular modification sites, limits trapping of active species in pores, and accommodates modifications to the molecular component", "pos": ["Comparative study on the effects of different structural Ti substrates on the properties of SnO2 electrodes. Abstract To investigate the influence of substrate structure on the properties of titanium-based tin oxide electrodes, Ti/SnO2 with porous titanium, planar titanium, titanium mesh, and titanium-copper alloy as substrates was prepared by a thermal decomposition method. Electrodes were characterized and tested by scanning electron microscopy (SEM), X-ray diffraction (XRD), electrochemical techniques, and accelerated life tests. The surface morphology, phase composition, electrochemical performance, and service life of the electrodes were studied and analysed. With phenol as the target pollutant, the effects of different substrates on the electrocatalytic degradation performance of the electrodes were investigated. The porous Ti/SnO2-Sb-La electrode prepared by the porous titanium substrate has finer surface grains and a larger specific surface area. The phenomena of “cracking” and “agglomeration” are obviously improved. At the same time, the oxygen evolution potential increased to 2.09 V, and the membrane impedance decreased to 5.722 Ω. The degradation experiment of simulated phenol wastewater reveals that the porous Ti/SnO2-Sb-La electrode has the highest phenol degradation rate of 90.8% and a removal rate of COD of 79.9% within 120 min. Additionally, the porous Ti/SnO2-Sb-La electrode has the longest accelerated service lifetime of 105 min, which is 5 times that of the planar Ti/SnO2-Sb-La electrode. It can be seen from the experimental results that the electrode prepared by using the novel porous titanium as the matrix has obvious electrochemical performance, service life and current utilization efficiency advantages in the degradation process. At the same time, it is further proved that the electrode substrate has a significant effect on the electrode performance in the electrochemical treatment of phenol-containing water."], "field": "Energy", "q_year": 2023, "q_cid": "259119672", "pos_cid": 105848181, "source": "eval_collection"}
{"query_id": "scaleup_24714386_21013360", "query": "How to safely and affordably support immune function and sustain host health during the COVID-19 pandemic", "pos": ["Health benefits and bioavailability of marine resources components that contribute to health – what’s new?. Abstract The strict connection between nutritional intake and health leads to a necessity of understanding the beneficial and protective role of healthy nutrients and foods. The marine environment is a source of a plethora of many organisms with unique properties, extremely rich in bioactive compounds and with remarkable potential for medical, industrial and biotechnological applications. Marine organisms are an extreme valuable source of functional ingredients such as polysaccharides, vitamins, minerals, pigments, enzymes, proteins and peptides, polyunsaturated fatty acids (PUFA), phenolic compounds and other secondary metabolites that prevent or have the potential to treat several diseases given their cardiovascular protective, anti-inflammatory, anti-hypertensive, anti-oxidant, anti-coagulant, anti-proliferative and anti-diabetic activities. This review provides an overview on the current advances regarding health benefits of marine bioactive compounds on several diseases and on human gut microbiota. In addition, it is discussed a crucial factor that is related to the effectiveness of these compounds on human organism namely its real bioavailability."], "field": "Energy", "q_year": 2022, "q_cid": "247143865", "pos_cid": 210133601, "source": "eval_collection"}
{"query_id": "scaleup_27555756_15105787", "query": "How to identify peptides released from N. gaditana proteins during gastric and gastrointestinal digestion that are promising candidates for biological effects", "pos": ["Towards the Improved Discovery and Design of Functional Peptides: Common Features of Diverse Classes Permit Generalized Prediction of Bioactivity. The conventional wisdom is that certain classes of bioactive peptides have specific structural features that endow their particular functions. Accordingly, predictions of bioactivity have focused on particular subgroups, such as antimicrobial peptides. We hypothesized that bioactive peptides may share more general features, and assessed this by contrasting the predictive power of existing antimicrobial predictors as well as a novel general predictor, PeptideRanker, across different classes of peptides. We observed that existing antimicrobial predictors had reasonable predictive power to identify peptides of certain other classes i.e. toxin and venom peptides. We trained two general predictors of peptide bioactivity, one focused on short peptides (4–20 amino acids) and one focused on long peptides ( amino acids). These general predictors had performance that was typically as good as, or better than, that of specific predictors. We noted some striking differences in the features of short peptide and long peptide predictions, in particular, high scoring short peptides favour phenylalanine. This is consistent with the hypothesis that short and long peptides have different functional constraints, perhaps reflecting the difficulty for typical short peptides in supporting independent tertiary structure. We conclude that there are general shared features of bioactive peptides across different functional classes, indicating that computational prediction may accelerate the discovery of novel bioactive peptides and aid in the improved design of existing peptides, across many functional classes. An implementation of the predictive method, PeptideRanker, may be used to identify among a set of peptides those that may be more likely to be bioactive."], "field": "Energy", "q_year": 2025, "q_cid": "275557561", "pos_cid": 15105787, "source": "eval_collection"}
{"query_id": "scaleup_27714962_23507483", "query": "How to incorporate fragile photocatalysts into polymer networks while preserving their structures and controlling their loading for efficient photocatalysis", "pos": ["When polymerization meets coordination-driven self-assembly: metallo-supramolecular polymers based on supramolecular coordination complexes.. Polymers have greatly changed and are still changing the way we live ever since, and the construction of novel polymers as functional materials remains an attractive topic in polymer science and related areas. During the past few years, the marriage of discrete supramolecular coordination complexes (SCCs), including two-dimensional (2D) metallacycles and three-dimensional (3D) metallacages, and polymers gave rise to two novel types of metallo-supramolecular polymers, i.e., metallacycle/metallacage-cored star polymers (MSPs) and metallacycle/metallacage-crosslinked polymer networks (MPNs), which has attracted increasing attention and emerged as an exciting new research direction in polymer chemistry. Attributed to their well-defined and diverse topological architectures as well as the unique dynamic features of metallacycles/metallacages as cores or crosslinks, these novel polymers have shown extensive applications. In this review, aiming at providing a practical guide to this emerging area, the introduction of synthetic strategies towards MSPs and MPNs will be presented. In addition, their wide applications in areas such as functional materials, molecular sieving, drug delivery, bacterial killing and bioimaging are also discussed."], "field": "Energy", "q_year": 2025, "q_cid": "277149621", "pos_cid": 235074832, "source": "eval_collection"}
{"query_id": "scaleup_25110272_21382871", "query": "How to quantify lipids, proteins, and polysaccharides at the microalgal cell-wall surface", "pos": ["Monitoring Surface Chemical Changes in the Bacterial Cell Wall. Gram-negative bacteria can alter the composition of the lipopolysaccharide (LPS) layer of the outer membrane as a response to different growth conditions and external stimuli. These alterations can, for example, promote attachment to surfaces and biofilm formation. The changes occur in the outermost layer of the cell and may consequently influence interactions between bacterial cells and surrounding host tissue, as well as other surfaces. Microscopic analyses, fractionation of bacterial cells, or other traditional microbiological assays have previously been used to study these alterations. These methods can, however, be time consuming and do not always give detailed chemical information about the bacterial cell surface. We here present an analytical method that provides chemical information on the outermost portion of bacterial cells with respect to protein, peptidoglycan, lipid, and polysaccharide content. The method involves cryo-x-ray photoelectron spectroscopy analyses of the outermost portion (within ∼10 nm of the surface) of intact bacterial cells followed by a multivariate curve resolution analysis of carbon spectra. It can be used as a tool for characterizing and monitoring variations in the chemical composition of bacterial cell walls or of isolated outer membrane vesicles, variations that result from e.g. mutations or external stimuli. The method enabled us to predict accurately the alterations in polysaccharide content and surface chemistries of a set of well characterized Escherichia coli LPS mutants. The described approach may moreover be applied to monitor surface chemical composition of other biological samples."], "field": "Energy", "q_year": 2022, "q_cid": "251102727", "pos_cid": 21382871, "source": "eval_collection"}
{"query_id": "scaleup_25911967_20596158", "query": "How to attach metal-containing materials to carbon-based electrodes while preserving their activity and lifetime and avoiding unintended metal-ion adsorption", "pos": ["The advantages of covalently attaching organometallic catalysts to a carbon black support: recyclable Rh(i) complexes that deliver enhanced conversion and product selectivity.. Pure carbon black (CB) was covalently attached to a bidentate nitrogen coordination motif with a carbon-carbon bond by spontaneous reaction with an in situ generated ligand precursor. The functionalized support was treated with [Rh(CO)2(μ-Cl)]2 to form a heterogeneous carbon-based support covalently linked to a well defined Rh(i) coordination complex. The hybrid material was characterized using X-ray photoelectron spectroscopy (XPS), thermogravimetric analysis (TGA), Infrared (IR) spectroscopy and inductively coupled plasma mass spectrometry (ICP-MS). The CB-supported Rh(i) catalyst was active in both hydroamination and dihydroalkoxylation reactions achieving turnover numbers approaching 1000 and was readily recycled. The selectivity of an intramolecular dihydroalkoxylation reaction was significantly improved by covalently anchoring the catalyst to the CB surface."], "field": "Energy", "q_year": 2023, "q_cid": "259119672", "pos_cid": 205961584, "source": "eval_collection"}
{"query_id": "scaleup_24599441_20178668", "query": "How to determine how isolated copper atoms change structurally under operating conditions and whether those changes are reversible", "pos": ["Electroreduction of CO2 on Single-Site Copper-Nitrogen-Doped Carbon Material: Selective Formation of Ethanol and Reversible Restructuration of the Metal Sites.. It is generally believed that CO2 electroreduction to multi-carbon products such as ethanol or ethylene may be catalyzed with significant yield only on metallic copper surfaces, implying large ensembles of copper atoms. Here, we report on an inexpensive Cu-N-C material prepared via a simple pyrolytic route that exclusively feature single copper atoms with a CuN4 coordination environment, atomically dispersed in a nitrogen-doped conductive carbon matrix. This material achieves aqueous CO2 electroreduction to ethanol at a Faradaic yield of 55% under optimized conditions (electrolyte: 0.1 M CsHCO3 , potential: -1.2V vs. RHE and gas-phase recycling set up), as well as CO electroreduction to C2-products (ethanol and ethylene) with a Faradaic yield of 80%. During electrolysis the isolated sites transiently convert into metallic copper nanoparticles, as shown by operando XAS analysis, which are likely to be the catalytically active species. Remarkably, this process is reversible and the initial material is recovered intact after electrolysis."], "field": "Energy", "q_year": 2022, "q_cid": "245994412", "pos_cid": 201786681, "source": "eval_collection"}
{"query_id": "scaleup_25135455_23056490", "query": "How to quantify the light reaching reaction channels under solar illumination", "pos": ["Laboratory protocols for measuring and reporting the performance of luminescent solar concentrators. Recommendation of standardised experiments for adoption by all researchers on luminescent solar concentrators to unify reporting and legitimise the field."], "field": "Energy", "q_year": 2022, "q_cid": "251354554", "pos_cid": 230564902, "source": "eval_collection"}
{"query_id": "scaleup_24349801_15921775", "query": "How to ensure energy security and environmental sustainability amid reliance on exhaustible resources without compromising future generations’ ability to meet their energy needs", "pos": ["Choices and the value of natural capital. Sustainability requires maintaining opportunities for future generations, so they can meet their needs. Opportunities are passed to future generations through a set of capital assets. Nature provides an important class of these assets, but markets seldom reveal the marginal value of natural capital. Rather, the marginal social worth or asset price must be imputed based on intertemporal exchange. In the context of assessing whether intertemporal allocation rules lead to sustainable development, appropriate asset prices must be based on the actual allocations and trade-offs society makes. Therefore, measuring economic programmes that enable the measurement of asset prices is an important empirical task. We review the theory of measuring natural capital asset prices and discuss the key elements of measuring economic programmes that enable the measurement of natural capital asset prices. We place the measurement of economic programmes and natural capital asset prices in the context of wealth-based sustainability metrics."], "field": "Energy", "q_year": 2021, "q_cid": "243498014", "pos_cid": 159217755, "source": "eval_collection"}
{"query_id": "scaleup_25353887_44339535", "query": "How to understand the disruption of epithelial cell adhesion to the extracellular matrix following cylindrospermopsin exposure", "pos": ["Tissue inhibitor of metalloproteinase (TIMP-2). A new member of the metalloproteinase inhibitor family.. Human melanoma cells secret a 21-kDa protein, termed CSC-21K, which binds with 1:1 molar stoichiometry to the matrix metalloproteinase type IV collagenase proenzyme (70-kDa gelatinase) secreted by the same cells. This binding protein has been purified and its complete primary structure determined by sequencing overlapping peptides which span the entire protein. The amino acid sequence demonstrates that this protein shares significant homology with human TIMP (tissue inhibitor of metalloproteinase), including conservation of the positions of the 12 cysteine residues and 3 of 4 tryptophan residues. The identification of CSC-21K now indicates that a family of TIMP-related proteins exists. Individual members of this family may possess selective affinities for different members of the matrix metalloproteinase family. CSC-21K produced by tumor cells is isolated as a 1:1 molar complex with type IV procollagenase, as demonstrated by amino acid composition analysis. Addition of purified CSC-21K to the activated metalloproteinase results in inhibition of the collagenolytic activity in a stoichiometric fashion. Based on its sequence homology to TIMP and ability to inhibit type IV collagenolysis we propose the name TIMP-2 for this inhibitor."], "field": "Energy", "q_year": 2022, "q_cid": "253538870", "pos_cid": 44339535, "source": "eval_collection"}
{"query_id": "scaleup_24616844_15439476", "query": "How to establish the relative importance of technical, economic, and environmental considerations for comparing locations for wind- and solar-based hydrogen production", "pos": ["Selection of rational dispute resolution method by applying new step‐wise weight assessment ratio analysis (Swara). Abstract The paper considers major principles of application of the multi‐attribute systems to solve legislative tasks. In order to assess dispute resolution methods from economic, social and other points of view, it is necessary to apply methods for assessing solutions according to multiple attributes. All known multi‐attribute methods cannot value the atribute weights as one weight of attribute is higher or lower significant than the other attribute. The new step‐wise weight assessment ratio analysis method (SWARA) allows including experts, lawyers or dispute parties opinion about significance ratio of the attributes in the process of rational decision determination. SWARA method could be applied in practical implementation of specialised decision support systems and alternative dispute resolution in virtual environment. Starting with principles and established approaches, a problem‐structuring methodology was developed which would condition the problem to allow a more thoughtful application of existing..."], "field": "Energy", "q_year": 2022, "q_cid": "246168447", "pos_cid": 154394761, "source": "eval_collection"}
{"query_id": "scaleup_23346179_94824233", "query": "How to increase the accessible surface area of carbon nanotube and graphene catalyst supports to improve iron sulfide nanoparticle contact with the electrolyte and oxygen reduction reaction performance", "pos": ["Graphene–carbon nanotube composite as an effective conducting scaffold to enhance the photoelectrochemical water oxidation activity of a hematite film. The iron oxide photoanode was modified with a graphene–carbon nanotube (CNT) composite conducting scaffold for efficient charge transfer from Fe2O3 particles to transparent conducting oxide substrate in photoelectrochemical water splitting cells. The Fe2O3–composite photoanode showed a photocurrent increase of 530% compared with to the bare Fe2O3 photoanode at 1.23 V vs. RHE, while the increase was only 200 and 240% for Fe2O3–CNT and Fe2O3–graphene photoanodes, respectively. This remarkable performance enhancement by the composite scaffold was attributed to synergistic effects induced by the formation of a 3D-like architecture from 1D CNT and 2D graphene. They become a spacer for each other forming a more open and highly exposed structure, in which both 2D graphene and 1D CNT can exist in the forms with much less self-agglomeration, thus not only enlarging the contact area between the conducting scaffold and Fe2O3 particles but also recovering in part the intrinsic conducting ability of graphene and CNT."], "field": "Energy", "q_year": 2021, "q_cid": "233461793", "pos_cid": 94824233, "source": "eval_collection"}
{"query_id": "scaleup_25260971_21304176", "query": "How to assess whether oxalic acid production from carbon dioxide can be profitable and compete with fossil-fuel-based production", "pos": ["Calculate the production costs of your own process. Abstract Establishing the cost of production, € per ton of a dedicated product, is a fundamental piece of information to carry out the assessment on the economic viability of a project, in particular for a novel process. The scope of this chapter is to make an overview of the major steps involved in the calculation of the total production cost of the product of interest, with particular focus on the key elements to be considered when the production scheme is based on an innovative technology. A case study related to economic viability of a novel technology studied by KT is also reported."], "field": "Energy", "q_year": 2022, "q_cid": "252609714", "pos_cid": 213041760, "source": "eval_collection"}
{"query_id": "scaleup_25839408_21954900", "query": "How to achieve high reactivity and resistance to deactivation in metal catalysts for peroxide activation in advanced oxidation processes while overcoming bulk catalyst limitations in metal dispersion, metastable phase stability, and thermal stability", "pos": ["Nanoconfinement Mediated Water Treatment: from Fundamental to Application.. Safe and clean water is of pivotal importance to all living species and the ecosystem on earth. However, the accelerating economy and industrialization of mankind generate water pollutants with much larger quantity and higher complexity than ever before, challenging the efficacy of traditional water treatment technologies. The flourishing researches on nanomaterials and nanotechnologies in the past decade have generated new understandings on many fundamental processes and brought revolutionary upgrades to various traditional technologies in almost all areas, including water treatment. An indispensable step towards the real application of nanomaterials in water treatment is to confine them in large processable substrate, in order to address various inherent issues such as spontaneous aggregation, difficult operation and potential environmental risks. Strikingly, when the size of the spatial restriction provided by the substrate is on the order of only one or several nanometers, referred to as nanoconfinement, the phase behavior of matter and the energy diagram of a chemical reaction could be utterly changed. Nevertheless, the relationship between such changes under nanoconfinement and their implications for water treatment is rarely elucidated systematically. In this perspective review, we will briefly summarize the current state-of-the-art of the nanomaterials as well as the nanoconfined analogues (i.e., nanocomposites) developed for water treatment. Afterwards, we will put emphasis on the effects of nanoconfinement from three aspects, i.e., on the structure and behavior of water molecules, on the formation (e.g., crystallization) of confined nanomaterials, and on the nano-enabled chemical reactions. For each aspect, we will build the correlation between the nanoconfinement effects and the current studies for water treatment. More importantly, we will make proposals for future studies based on the missing links between some of the nanoconfinement effects and the water treatment technologies. Through this review, we aim to raise the research attention on using nanoconfinement as a fundamental guide or even tool to advance water treatment technologies."], "field": "Energy", "q_year": 2023, "q_cid": "258394082", "pos_cid": 219549002, "source": "eval_collection"}
{"query_id": "scaleup_21303834_28488626", "query": "How to select an economically viable option suited to Deokjeok-do’s extreme winds, airflow variability, and local geography", "pos": ["Techno-Economic Assessment of Wind Energy Potential at Three Locations in South Korea Using Long-Term Measured Wind Data. The present study deals with wind energy analysis and the selection of an optimum type of wind turbine in terms of the feasibility of installing wind power system at three locations in South Korea: Deokjeok-do, Baengnyeong-do and Seo-San. The wind data measurements were conducted during 2005–2015 at Deokjeok-do, 2001–2016 at Baengnyeong-do and 1997–2016 at Seo-San. In the first part of this paper wind conditions, like mean wind speed, wind rose diagrams and Weibull shape and scale parameters are presented, so that the wind potential of all the locations could be assessed. It was found that the prevailing wind directions at all locations was either southeast or southwest in which the latter one being more dominant. After analyzing the wind conditions, 50-year and 1-year extreme wind speeds (EWS) were estimated using the graphical method of Gumbel distribution. Finally, according to the wind conditions at each site and international electro-technical commission (IEC) guidelines, a set of five different wind turbines best suited for each location were shortlisted. Each wind turbine was evaluated on the basis of technical parameters like monthly energy production, annual energy production (AEP) and capacity factors (CF). Similarly, economical parameters including net present value (NPV), internal rate of return (IRR), payback period (PBP) and levelized cost of electricity (LCOE) were considered. The analysis shows that a Doosan model WinDS134/3000 wind turbine is the most suitable for Deokjeok-do and Baengnyeong-do, whereas a Hanjin model HJWT 87/2000 is the most suitable wind turbine for Seo-San. Economic sensitivity analysis is also included and discussed in detail to analyze the impact on economics of wind power by varying turbine’s hub height."], "field": "Energy", "q_year": 2020, "q_cid": "213038346", "pos_cid": 28488626, "source": "eval_collection"}
{"query_id": "scaleup_25911967_4864963", "query": "How to advance electrostatic control of catalytic activity in synthetic chemistry", "pos": ["Electric Fields and Enzyme Catalysis. What happens inside an enzyme’s active site to allow slow and difficult chemical reactions to occur so rapidly? This question has occupied biochemists’ attention for a long time. Computer models of increasing sophistication have predicted an important role for electrostatic interactions in enzymatic reactions, yet this hypothesis has proved vexingly difficult to test experimentally. Recent experiments utilizing the vibrational Stark effect make it possible to measure the electric field a substrate molecule experiences when bound inside its enzyme’s active site. These experiments have provided compelling evidence supporting a major electrostatic contribution to enzymatic catalysis. Here, we review these results and develop a simple model for electrostatic catalysis that enables us to incorporate disparate concepts introduced by many investigators to describe how enzymes work into a more unified framework stressing the importance of electric fields at the active site."], "field": "Energy", "q_year": 2023, "q_cid": "259119672", "pos_cid": 4864963, "source": "eval_collection"}
{"query_id": "scaleup_24599441_20934139", "query": "How to improve catalyst stability and catalytic activity for electrochemical carbon dioxide reduction beyond the limits of simple single-metal compositions", "pos": ["Hard-Sphere Random Close-Packed Au47Cd2(TBBT)31 Nanoclusters with a Faradaic Efficiency of Up to 96% for Electrocatalytic CO2 Reduction to CO.. Metal nanoclusters have recently attracted considerable attention, not only because of their special size range but also due to their well-defined compositions and structures. However, subtly tailoring the compositions and structures of metal nanoclusters for potential applications remains challenging. In this report, we present a two-phase anti-galvanic reduction (AGR) method for precisely tailoring Au 44 (TBBT) 28 to produce Au 47 Cd 2 (TBBT) 31 nanoclusters with a hard-sphere random close-packed structure, which exhibit Faradaic efficiencies of up to 96% at -0.57 V for the electrocatalytic reduction of CO 2 to CO."], "field": "Energy", "q_year": 2022, "q_cid": "245994412", "pos_cid": 209341395, "source": "eval_collection"}
{"query_id": "scaleup_27165312_14896394", "query": "How to ensure comprehensive coverage of high-quality studies relevant to the EU’s current energy-security context and consistent judgments about study inclusion", "pos": ["Guidance on Conducting a Systematic Literature Review. Literature reviews establish the foundation of academic inquires. However, in the planning field, we lack rigorous systematic reviews. In this article, through a systematic search on the methodology of literature review, we categorize a typology of literature reviews, discuss steps in conducting a systematic literature review, and provide suggestions on how to enhance rigor in literature reviews in planning education and research."], "field": "Energy", "q_year": 2024, "q_cid": "271653126", "pos_cid": 148963947, "source": "eval_collection"}
{"query_id": "scaleup_25110272_23522037", "query": "How to quantify lipids, proteins, and polysaccharides specifically at the outer surface of hydrated microalgal cells without interference from bulk-cell signals", "pos": ["Applying Cryo-X-ray Photoelectron Spectroscopy to Study the Surface Chemical Composition of Fungi and Viruses. Interaction between microorganisms and their surroundings are generally mediated via the cell wall or cell envelope. An understanding of the overall chemical composition of these surface layers may give clues on how these interactions occur and suggest mechanisms to manipulate them. This knowledge is key, for instance, in research aiming to reduce colonization of medical devices and device-related infections from different types of microorganisms. In this context, X-ray photoelectron spectroscopy (XPS) is a powerful technique as its analysis depth below 10 nm enables studies of the outermost surface structures of microorganism. Of specific interest for the study of biological systems is cryogenic XPS (cryo-XPS). This technique allows studies of intact fast-frozen hydrated samples without the need for pre-treatment procedures that may cause the cell structure to collapse or change due to the loss of water. Previously, cryo-XPS has been applied to study bacterial and algal surfaces with respect to their composition of lipids, polysaccharides and peptide (protein and/or peptidoglycan). This contribution focuses onto two other groups of microorganisms with widely different architecture and modes of life, namely fungi and viruses. It evaluates to what extent existing models for data treatment of XPS spectra can be applied to understand the chemical composition of their very different surface layers. XPS data from model organisms as well as reference substances representing specific building blocks of their surface were collected and are presented. These results aims to guide future analysis of the surface chemical composition of biological systems."], "field": "Energy", "q_year": 2022, "q_cid": "251102727", "pos_cid": 235220378, "source": "eval_collection"}
{"query_id": "scaleup_24714386_20392480", "query": "How to find natural antiviral agents with demonstrated activity to prevent coronavirus infection, fewer side effects, and lower costs than synthetic drugs", "pos": ["Griffithsin, a Highly Potent Broad-Spectrum Antiviral Lectin from Red Algae: From Discovery to Clinical Application. Virus entry into a susceptible host cell is the first step in the formation of all viral diseases. Controlling viral infections by disrupting viral entry is advantageous for antibody-mediated neutralization by the host’s immune system and as a preventive and therapeutic antiviral strategy. Recently, several plant-derived carbohydrate-binding proteins (lectins) have emerged as a new class of antiviral biologics by taking advantage of a unique glycosylation pattern only found on the surface of viruses. In particular, a red algae-derived griffithsin (GRFT) protein has demonstrated superior in vitro and in vivo antiviral activity with minimum host toxicity against a variety of clinically relevant, enveloped viruses. This review examines the structural characteristics of GRFT, focusing on its carbohydrate-binding capability. Its in vitro antiviral profiles against human immunodeficiency virus (HIV) are also discussed followed by a description of the results from a combination study using anti-HIV drugs. The results of several studies regarding its novel antiviral mechanism of action are provided in conjunction with an explanation of viral resistance profiles to GRFT. In addition, its in vitro and in vivo host toxicity profiles are summarized with its pharmacokinetic behavior using in vivo efficacy study results. Also, a large-scale production and formulation strategy, as well as a drug delivery strategy, for GRFT as a new class of broad-spectrum microbicides is discussed. Finally, results from two ongoing clinical studies examining GRFT’s effects on viruses are presented."], "field": "Energy", "q_year": 2022, "q_cid": "247143865", "pos_cid": 203924806, "source": "eval_collection"}
{"query_id": "scaleup_26656020_23692477", "query": "How to determine how temperature affects charge distribution, iron charge states, and electrical conduction in Sr3Fe2O7", "pos": ["Hidden Charge Order in an Iron Oxide Square-Lattice Compound.. Since the discovery of charge disproportionation in the FeO_{2} square-lattice compound Sr_{3}Fe_{2}O_{7} by Mössbauer spectroscopy more than fifty years ago, the spatial ordering pattern of the disproportionated charges has remained \"hidden\" to conventional diffraction probes, despite numerous x-ray and neutron scattering studies. We have used neutron Larmor diffraction and Fe K-edge resonant x-ray scattering to demonstrate checkerboard charge order in the FeO_{2} planes that vanishes at a sharp second-order phase transition upon heating above 332 K. Stacking disorder of the checkerboard pattern due to frustrated interlayer interactions broadens the corresponding superstructure reflections and greatly reduces their amplitude, thus explaining the difficulty of detecting them by conventional probes. We discuss the implications of these findings for research on \"hidden order\" in other materials."], "field": "Energy", "q_year": 2023, "q_cid": "266560209", "pos_cid": 236924770, "source": "eval_collection"}
{"query_id": "scaleup_23173369_6318044", "query": "How to clarify the effect of living cells in wet algal biomass on nutrient availability to wheat roots compared with dried algal fertilizers", "pos": ["Competition between roots and microorganisms for nitrogen: mechanisms and ecological relevance.. Demand of all living organisms on the same nutrients forms the basis for interspecific competition between plants and microorganisms in soils. This competition is especially strong in the rhizosphere. To evaluate competitive and mutualistic interactions between plants and microorganisms and to analyse ecological consequences of these interactions, we analysed 424 data pairs from 41 (15)N-labelling studies that investigated (15)N redistribution between roots and microorganisms. Calculated Michaelis-Menten kinetics based on K(m) (Michaelis constant) and V(max) (maximum uptake capacity) values from 77 studies on the uptake of nitrate, ammonia, and amino acids by roots and microorganisms clearly showed that, shortly after nitrogen (N) mobilization from soil organic matter and litter, microorganisms take up most N. Lower K(m) values of microorganisms suggest that they are especially efficient at low N concentrations, but can also acquire more N at higher N concentrations (V(max)) compared with roots. Because of the unidirectional flow of nutrients from soil to roots, plants are the winners for N acquisition in the long run. Therefore, despite strong competition between roots and microorganisms for N, a temporal niche differentiation reflecting their generation times leads to mutualistic relationships in the rhizosphere. This temporal niche differentiation is highly relevant ecologically because it: protects ecosystems from N losses by leaching during periods of slow or no root uptake; continuously provides roots with available N according to plant demand; and contributes to the evolutionary development of mutualistic interactions between roots and microorganisms."], "field": "Energy", "q_year": 2021, "q_cid": "231733692", "pos_cid": 6318044, "source": "eval_collection"}
{"query_id": "scaleup_23542250_20820195", "query": "How to determine an interface’s full differential response under a fixed driving condition and a zero-net-balance constraint when some fluctuations are suppressed", "pos": ["Charge fluctuations from molecular simulations in the constant-potential ensemble.. We revisit the statistical mechanics of charge fluctuations in capacitors. In constant-potential classical molecular simulations, the atomic charges of electrode atoms are treated as additional degrees of freedom which evolve in time so as to satisfy the constraint of fixed electrostatic potential for each configuration of the electrolyte. The present work clarifies the role of the overall electroneutrality constraint, as well as the link between the averages computed within the Born-Oppenheimer approximation and that of the full constant-potential ensemble. This allows us in particular to derive a complete fluctuation-dissipation relation for the differential capacitance, that includes a contribution from the charge fluctuations (around the charges satisfying the constant-potential and electroneutrality constraints) also present in the absence of an electrolyte. We provide a simple expression for this contribution from the elements of the inverse of the matrix defining the quadratic form of the fluctuating charges in the energy. We then illustrate numerically the validity of our results, and recover the expected continuum result for an empty capacitor with structureless electrodes at large inter-electrode distances. By considering a variety of liquids between graphite electrodes, we confirm that this contribution to the total differential capacitance is small compared to that induced by the thermal fluctuations of the electrolyte."], "field": "Energy", "q_year": 2021, "q_cid": "235422501", "pos_cid": 208201958, "source": "eval_collection"}
{"query_id": "scaleup_27165312_627405", "query": "How to ensure rigor and academic acceptability in a synthesis of literature on the EU’s international economic relations and energy security", "pos": ["Lessons from applying the systematic literature review process within the software engineering domain. A consequence of the growing number of empirical studies in software engineering is the need to adopt systematic approaches to assessing and aggregating research outcomes in order to provide a balanced and objective summary of research evidence for a particular topic. The paper reports experiences with applying one such approach, the practice of systematic literature review, to the published studies relevant to topics within the software engineering domain. The systematic literature review process is summarised, a number of reviews being undertaken by the authors and others are described and some lessons about the applicability of this practice to software engineering are extracted.The basic systematic literature review process seems appropriate to software engineering and the preparation and validation of a review protocol in advance of a review activity is especially valuable. The paper highlights areas where some adaptation of the process to accommodate the domain-specific characteristics of software engineering is needed as well as areas where improvements to current software engineering infrastructure and practices would enhance its applicability. In particular, infrastructure support provided by software engineering indexing databases is inadequate. Also, the quality of abstracts is poor; it is usually not possible to judge the relevance of a study from a review of the abstract alone."], "field": "Energy", "q_year": 2024, "q_cid": "271653126", "pos_cid": 627405, "source": "eval_collection"}
{"query_id": "scaleup_26505808_15436224", "query": "How to determine necessary business model changes and strategic priorities for municipal district heating companies facing digitalization’s effects on customer value creation and delivery, given differing managerial views of current and future markets and owners’ willingness to accept risk", "pos": ["Business Models, Business Strategy and Innovation. Whenever a business enterprise is established, it either explicitly or implicitly employs a particular business model that describes the design or architecture of the value creation, delivery, and capture mechanisms it employs. The essence of a business model is in defining the manner by which the enterprise delivers value to customers, entices customers to pay for value, and converts those payments to profit. It thus reflects management's hypothesis about what customers want, how they want it, and how the enterprise can organize to best meet those needs, get paid for doing so, and make a profit. The purpose of this article is to understand the significance of business models and explore their connections with business strategy, innovation management, and economic theory."], "field": "Energy", "q_year": 2023, "q_cid": "265058089", "pos_cid": 154362245, "source": "eval_collection"}
{"query_id": "scaleup_25911967_21152464", "query": "How to predict the effects of ligand substituents on reactivity when electron-donating or electron-withdrawing properties alone are insufficient", "pos": ["Oriented (local) Electric Fields Drive the Millionfold Enhancement of the H-Abstraction Catalysis Observed for Synthetic Metalloenzyme Analogues.. This contribution follows the recent remarkable catalysis observed by Groves et al. in hydrogen abstraction reactions by, (a) an oxoferryl porphyrin radical cation complex [Por•+FeIV(O)Lax], and (b) a hydroxoiron porphyrazine ferric complex [PyPzFeIII(OH)Lax]; both of which involve positively charged substituents on the outer circumference of the respective macrocyclic ligands. These charge-coronated complexes are analogues of the biologically important Compound I (Cpd I), and synthetic hydroxo-ferric species respectively. We demonstrate that the observed enhancement of the H-abstraction catalysis for these systems is a purely electrostatic effect, elicited by the local charges embedded on the peripheries of the respective macrocyclic ligands. Our findings provide new insights into how electrostatics can be employed to tune the catalytic activity of metalloenzymes and can thus contribute to the future design of new and highly efficient hydrogen abstraction catalysts."], "field": "Energy", "q_year": 2023, "q_cid": "259119672", "pos_cid": 211524643, "source": "eval_collection"}
{"query_id": "scaleup_24714386_16878981", "query": "How to identify safe, effective, and affordable antiviral options for COVID-19 despite limited trial evidence", "pos": ["Griffithsin: An Antiviral Lectin with Outstanding Therapeutic Potential. Griffithsin (GRFT), an algae-derived lectin, is one of the most potent viral entry inhibitors discovered to date. It is currently being developed as a microbicide with broad-spectrum activity against several enveloped viruses. GRFT can inhibit human immunodeficiency virus (HIV) infection at picomolar concentrations, surpassing the ability of most anti-HIV agents. The potential to inhibit other viruses as well as parasites has also been demonstrated. Griffithsin’s antiviral activity stems from its ability to bind terminal mannoses present in high-mannose oligosaccharides and crosslink these glycans on the surface of the viral envelope glycoproteins. Here, we review structural and biochemical studies that established mode of action and facilitated construction of GRFT analogs, mechanisms that may lead to resistance, and in vitro and pre-clinical results that support the therapeutic potential of this lectin."], "field": "Energy", "q_year": 2022, "q_cid": "247143865", "pos_cid": 16878981, "source": "eval_collection"}
{"query_id": "scaleup_23318402_19943524", "query": "How to establish suitable conditions for S. marinoi growth under varying light and temperature", "pos": ["Friends With Benefits: Exploring the Phycosphere of the Marine Diatom Skeletonema marinoi. Marine diatoms are the dominant phytoplankton in the temperate oceans and coastal regions, contributing to global photosynthesis, biogeochemical cycling of key nutrients and minerals and aquatic food chains. Integral to the success of marine diatoms is a diverse array of bacterial species that closely interact within the diffusive boundary layer, or phycosphere, surrounding the diatom partner. Recently, we isolated seven distinct bacterial species from cultures of Skeletonema marinoi, a chain-forming, centric diatom that dominates the coastal regions of the temperate oceans. Genomes of all seven bacteria were sequenced revealing many unusual characteristics such as the existence of numerous plasmids of widely varying sizes. Here we have investigated the characteristics of the bacterial interactions with S. marinoi, demonstrating that several strains (Arenibacter algicola strain SMS7, Marinobacter salarius strain SMR5, Sphingorhabdus flavimaris strain SMR4y, Sulfitobacter pseudonitzschiae strain SMR1, Yoonia vestfoldensis strain SMR4r and Roseovarius mucosus strain SMR3) stimulate growth of the diatom partner. Testing of many different environmental factors including low iron concentration, high and low temperatures, and chemical signals showed variable effects on this growth enhancement by each bacterial species, with the most significant being light quality in which green and blue but not red light enhanced the stimulatory effect on S. marinoi growth by all bacteria. Several of the bacteria also inhibited growth of one or more of the other bacterial strains to different extents when mixed together. This study highlights the complex interactions between diatoms and their associated bacteria within the phycosphere, and that further studies are needed to resolve the underlying mechanisms for these relationships and how they might influence the global success of marine diatoms."], "field": "Energy", "q_year": 2021, "q_cid": "233184020", "pos_cid": 199435245, "source": "eval_collection"}
{"query_id": "scaleup_28176443_24492475", "query": "How to control ordered nucleation and growth of inorganic nanoparticles with precise structural control and tight interfacial integration in environmentally friendly composite systems", "pos": ["Advances in biomineralization-inspired materials for hard tissue repair. Biomineralization is the process by which organisms form mineralized tissues with hierarchical structures and excellent properties, including the bones and teeth in vertebrates. The underlying mechanisms and pathways of biomineralization provide inspiration for designing and constructing materials to repair hard tissues. In particular, the formation processes of minerals can be partly replicated by utilizing bioinspired artificial materials to mimic the functions of biomolecules or stabilize intermediate mineral phases involved in biomineralization. Here, we review recent advances in biomineralization-inspired materials developed for hard tissue repair. Biomineralization-inspired materials are categorized into different types based on their specific applications, which include bone repair, dentin remineralization, and enamel remineralization. Finally, the advantages and limitations of these materials are summarized, and several perspectives on future directions are discussed."], "field": "Energy", "q_year": 2025, "q_cid": "281764436", "pos_cid": 244924750, "source": "eval_collection"}
{"query_id": "scaleup_28310707_21098244", "query": "How to assess the efficacy and safety of microalgal supplementation for improving anemia-related blood parameters and iron status across different physiological and inflammatory contexts", "pos": ["Protective effects of spirulina against hemato-biochemical alterations, nephrotoxicity, and DNA damage upon lead exposition. The current study was aimed at exploring the protective efficacy of spirulina against the hemato-biochemical alterations and nephrotoxicity induced by lead (Pb). Female rats aged 12 weeks were treated for 4 weeks with Pb (0.344 g kg−1 bw) associated or not with spirulina (5.3 g kg−1 bw). Renal damage induced by Pb was related to a severe anemia, increases of oxidative stress-related parameters (thiobarbituric acid reactive substances (TBARS) (+29%), protein carbonyl (PCO) (+66.3%), and advanced oxidation protein product (AOPP) (+110%)), plasma lactate dehydrogenase (LDH) (+80%), creatinine and urea levels in plasma, and uric acid concentration in urine, as well as genotoxic changes (+89.3% and +60% for DNA and mRNA levels, respectively). Conversely, LDH and antioxidant enzyme activities in kidney were decreased, as well as the levels of plasma uric acid, and urinary creatinine and urea levels. Spirulina-supplemented rats exhibited normal peripheral blood and renal parameters and renal histology. It can be suggested that Arthrospira platensis alleviates damages induced by Pb, thanks to its high phenolic content and antioxidant capacity."], "field": "Energy", "q_year": 2025, "q_cid": "283107074", "pos_cid": 210982440, "source": "train_step3"}
{"query_id": "scaleup_24895942_3938611", "query": "How to increase oil productivity and oil content in crypthecodinium cohnii to narrow the price gap between its docosahexaenoic acid and the fish-oil-derived counterpart", "pos": ["Genetic Engineering of Crypthecodinium cohnii to Increase Growth and Lipid Accumulation. In this study, we evaluated suitable selected markers and optimized transformation protocols to develop a new genetic transformation methodology for DHA-producing Crypthecodinium cohnii. Additionally, ribulose 1,5-bisphosphate carboxylase/oxygenase (RuBisCO), potentially involved in CO2 fixation under autotrophic conditions, was selected as the target for construction of a gene knockdown mutant. Our results show that the constructs were successfully inserted into the C. cohnii chromosome by homologous recombination. Comparative analysis showed that deletion of the RuBisCO gene promoted cell growth and increased the lipid content of C. cohnii under heterotrophic conditions compared with those of the wild-type. The liquid chromatography-mass spectrometry (LC-MS) based metabolomic analysis showed that the metabolites involved in energy metabolism were upregulated, suggesting that the deletion of the RuBisCO gene may contribute to the re-direction of more carbon or energy toward growth and lipid accumulation under heterotrophic conditions."], "field": "Energy", "q_year": 2022, "q_cid": "248959426", "pos_cid": 3938611, "source": "train_step3"}
{"query_id": "scaleup_26932777_24666807", "query": "How to explain dmp’s photocatalytic degradation", "pos": ["Molecular electrostatic potential analysis: A powerful tool to interpret and predict chemical reactivity. The molecular electrostatic potential (MESP) V(r) data derived from a reliable quantum chemical method has been widely used for the interpretation and prediction of various aspects of chemical reactivity. A rigorous mapping of the MESP topology is achieved by computing both ∇V(r) data and the elements of the Hessian matrix at the critical points where ∇V(r) = 0. In the MESP topology, intra‐ and inter‐molecular bonded regions show the characteristic (3, −1) bond critical points (BCPs) while the electron‐rich regions such as lone pair and π‐bonds show (3, +3) minimum (Vmin) CPs. The Vmin analysis provides a simple and powerful technique to characterize the electron‐rich region in a molecular system as it corresponds to the condensed information of the wave function at this point due to the nuclei and electronic distribution through the Coulomb's law. The Vmin analysis has been successfully applied to explain the phenomena related to chemical reactivity such as π‐conjugation, aromaticity, substituent effect, ligand electronic effects, trans‐influence, redox potential, activation energy, cooperativity, noncovalent interactions, and so on. The MESP parameters ∆Vmin and ∆Vn, derived for arene systems have been used as powerful measures of substituent effects while Vmin at the lone pair region of ligands has been used as a reliable electronic parameter to assess their σ‐donating ability to metal centers. Furthermore, strong predictions on the intermolecular interactive behavior of molecular systems can be made from MESP topology studies. This review summarizes the chemical reactivity applications offered by MESP topology analysis for a large variety of organic, organometallic, and inorganic molecular systems."], "field": "Energy", "q_year": 2024, "q_cid": "269327771", "pos_cid": 246668070, "source": "train_step3"}
{"query_id": "scaleup_23842126_11980073", "query": "How to reliably identify a newly isolated strain", "pos": ["Pan-eukaryote ITS2 homologies revealed by RNA secondary structure. For evolutionary comparisons, phylogenetics and evaluation of potential interbreeding taxa of a species, various loci have served for animals and plants and protistans. One [second internal transcribed spacer (ITS2) of the nuclear ribosomal DNA] is highly suitable for all. Its sequence is species specific. It has already been used extensively and very successfully for plants and some protistans, and a few animals (where historically, the mitochondrial genes have dominated species studies). Despite initial impressions that ITS2 is too variable, it has proven to provide useful biological information at higher taxonomic levels, even across all eukaryotes, thanks to the conserved aspects of its transcript secondary structure. The review of all eukaryote groups reveals that ITS2 is expandable, but always retains in its RNA transcript a common core structure of two helices with hallmark characteristics important for ribosomal RNA processing. This aspect of its RNA transcript secondary structure can rescue difficult alignment problems, making the ITS2 a more powerful tool for phylogenetics. Equally important, the recognition of eukaryote-wide homology regions provides extensive and detailed information to test experimental studies of ribosomal rRNA processing."], "field": "Energy", "q_year": 2021, "q_cid": "238421268", "pos_cid": 11980073, "source": "train_step3"}
{"query_id": "scaleup_27564697_24796288", "query": "How to assess wind power’s life-cycle greenhouse-gas emissions with up-to-date accounting of Chinese rare-earth permanent-magnet supply-chain emissions attributable to an individual wind turbine", "pos": ["Global environmental cost of using rare earth elements in green energy technologies.. Decarbonization of economy is intended to reduce the consumption of non-renewable energy sources and emissions from them. One of the major components of decarbonization are \"green energy\" technologies, e.g. wind turbines and electric vehicles. However, they themselves create new sustainability challenges, e.g. use of green energy contributes to the reduction of consumption of fossil fuels, on one hand, but at the same time it increases demand for permanent magnets containing considerable amounts of rare earth elements (REEs). This article provides the first global analysis of environmental impact of using rare earth elements in green energy technologies. The analysis was performed applying system dynamics modelling methodology integrated with life cycle assessment and geometallurgical approach. We provide evidence that an increase by 1% of green energy production causes a depletion of REEs reserves by 0.18% and increases GHG emissions in the exploitation phase by 0.90%. Our results demonstrate that between 2010 and 2020, the use of permanent magnets has resulted cumulatively in 32 billion tonnes CO2-equivalent of GHG emissions globally. It shows that new approaches to decarbonization are still needed, in order to ensure sustainability of the process. The finding highlights a need to design and implement various measures intended to increase REEs reuse, recycling (currently below 1%), limit their dematerialization, increase substitution and develop new elimination technologies. Such measures would support the development of appropriate strategies for decarbonization and environmentally sustainable development of green energy technologies."], "field": "Energy", "q_year": 2025, "q_cid": "275646975", "pos_cid": 247962880, "source": "train_step3"}
{"query_id": "scaleup_27174247_10557813", "query": "How to form a stable, single-phase oxide containing multiple elements in significant proportions with differing atomic sizes, without phase separation or elemental segregation", "pos": ["Entropy contributions to phase stability in binary random solid solutions. High entropy alloys contain multiple elements in large proportions that make them prone to phase separation. These alloys generally have shallow enthalpy of mixing which makes the entropy contributions of similar magnitude. As a result, the phase stability of these alloys is equally dependent on enthalpy and entropy of mixing and understanding the individual contribution of thermodynamic properties is critical. In the overall vision of designing high entropy alloys, in this work, using density functional theory calculations, we elucidate the contributions of various entropies, i.e., vibrational, electronic and configurational towards the phase stability of binary alloys. We show that the contribution of electronic entropy is very small compared to the vibrational and configurational entropies, and does not play a significant role in the phase stability of alloys. The configurational and vibrational entropies can either destabilize or can collectively contribute to stabilize the solid solutions. As a result, even those systems that have negative mixing enthalpy can show phase instability, revealed as a miscibility gap; conversely, systems with positive mixing enthalpy can be phase stable due to entropic contributions. We suggest that including entropic contributions are critical in the development of theoretical framework for the computational prediction of stable, single-phase high entropy alloys that have shallow mixing enthalpies, unlike ordered intermetallics.Phase stability: entropy enabled predictionsConfigurational and vibrational entropies, while conventionally neglected, can determine an alloy’s phase stability. A team led by Dilpuneet Aidhy at the University of Wyoming in U.S.A. used density functional theory calculations to examine the contribution of different types of entropy in seven binary metallic alloys with shallow enthalpies of mixing. They found that relying on the enthalpy of mixing to predict solid solution stability was insufficient. While electronic entropy did not meaningfully contribute to phase stability in any of the alloys, configurational entropy stabilized solid solutions, while vibrational entropy either stabilized or destabilized solid solutions depending on the alloy system. Vibrational entropy is a measure of the softness of atomic bonds, and research into how it varies in different systems may help us better predict single-phase multicomponent alloy stability."], "field": "Energy", "q_year": 2024, "q_cid": "271742474", "pos_cid": 105578130, "source": "train_step3"}
{"query_id": "scaleup_27468476_3645744", "query": "How to determine why cancer cells die and how far this process has progressed", "pos": ["Dual AO/EB Staining to Detect Apoptosis in Osteosarcoma Cells Compared with Flow Cytometry. Background The aim of this study was to evaluate the ability of dual acridine orange/ethidium bromide (AO/EB) staining to detect tumor cell apoptosis. According to apoptosis-associated changes of cell membranes during the process of apoptosis, a clear distinction is made between normal cells, early and late apoptotic cells, and necrotic cells. Material/Method We cultured human osteosarcoma cells with 30, 60, and 120 μg/ml kappa-selenocarrageenan. To assess the rates of cell proliferation and apoptosis, cells were fluorescently stained with acridine orange/ethidium bromide (AO/EB) or stained with propidium iodide (PI) and analyzed by flow cytometry. All experiments were repeated at least 3 times. Result Normal tumor cells, early and late apoptotic cells, and necrotic cells were examined using fluorescent microscopy. Early-stage apoptotic cells were marked by crescent-shaped or granular yellow-green acridine orange nuclear staining. Late-stage apoptotic cells were marked with concentrated and asymmetrically localized orange nuclear ethidium bromide staining. Necrotic cells increased in volume and showed uneven orange-red fluorescence at their periphery. Cells appeared to be in the process of disintegrating. The percentage of apoptotic osteosarcoma cells detected by dual acridine orange/ethidium bromide (AO/EB) staining was not significantly different from that detected using flow cytometry (P>0.05). Conclusions Our results suggest that dual acridine orange/ethidium bromide staining is an economic and convenient method to detect apoptosis in tumor cells and to test tumor chemosensitivity compared with flow cytometry."], "field": "Energy", "q_year": 2024, "q_cid": "274684768", "pos_cid": 3645744, "source": "train_step3"}
{"query_id": "scaleup_27174648_10407622", "query": "How to explain differences in elemental composition, graphitic structure, and photodegradation ability between particles and bulk material across preparation temperatures and reaction conditions", "pos": ["A review of the hydrothermal carbonization of biomass waste for hydrochar formation: Process conditions, fundamentals, and physicochemical properties. Abstract Hydrothermal carbonization (HTC) is a thermochemical conversion technique which is attractive due to its ability to transform wet biomass into energy and chemicals without predrying. The solid product, known as hydrochar, has received attention because of its ability to prepare precursors of activated carbon in wastewater pollution remediation, soil remediation applications, solid fuels, and other carbonaceous materials. Besides the generally lignocellulose biomass used as sustainable feedstock, HTC has been applied to a wide range of derived waste, including sewage sludge, algae, and municipal solid waste to solve practical problems and generate desirable carbonaceous products. This review presented the critical hydrothermal parameters of HTC, including temperature, residence time, heating rate, reactant concentration, and aqueous quality. The chemical reaction mechanisms involved in the formation of hydrochar derived from single components and representative feedstock, lignocellulose, and sludge termed as N-free and N-rich biomass, were elucidated and summarized to better understand the hydrochar formation process. Specifically, hydrochar physicochemical characteristics such as surface chemistry and structure were investigated. Current knowledge gaps, and new perspectives with corresponding recommendations were provided to further exploit the great potential of the HTC technique and more practical applications for hydrochar in the future."], "field": "Energy", "q_year": 2024, "q_cid": "271746486", "pos_cid": 104076225, "source": "train_step3"}
{"query_id": "scaleup_16074598_1708582", "query": "How to decide when a self-interested device should provide relay services for tokens to maximize its utility over time given its token holdings, remaining relay energy budget, and network conditions", "pos": ["Reinforcement Learning: A Survey. This paper surveys the field of reinforcement learning from a computer-science perspective. It is written to be accessible to researchers familiar with machine learning. Both the historical basis of the field and a broad selection of current work are summarized. Reinforcement learning is the problem faced by an agent that learns behavior through trial-and-error interactions with a dynamic environment. The work described here has a resemblance to work in psychology, but differs considerably in the details and in the use of the word \"reinforcement.\" The paper discusses central issues of reinforcement learning, including trading off exploration and exploitation, establishing the foundations of the field via Markov decision theory, learning from delayed reinforcement, constructing empirical models to accelerate learning, making use of generalization and hierarchy, and coping with hidden state. It concludes with a survey of some implemented systems and an assessment of the practical utility of current methods for reinforcement learning."], "field": "Engineering", "q_year": 2013, "q_cid": "16074598", "pos_cid": 1708582, "source": "eval20x26"}
{"query_id": "scaleup_20274866_14507452", "query": "How to provide effective rehabilitation support for patients who struggle to relate their current orientation to an environment’s spatial layout and navigate it", "pos": ["What is the role of spatial processing in the decline of episodic memory in Alzheimer’s disease? The “mental frame syncing” hypothesis. The current theories on episodic memory suggest a crucial role of spatial processing for an effective retrieval. For a successful episodic recall, the long-term allocentric scene has to be translated into an egocentric scene. Here, we argue that a crucial role for an episodic retrieval is played by a “mental frame syncing” between two kinds of allocentric representations. This neurocognitive process allows an effective retrieval of our past experiences by synchronizing the allocentric view-point independent representation with the allocentric view-point dependent representation. If the “mental frame syncing” stops, even momentarily, it is difficult to reconstruct a coherent spatial scaffold upon which to effectively retrieve our previous events within an egocentric perspective. This is what apparently happens in Alzheimer’s disease: a break in the “mental frame syncing” between these two kinds of allocentric representations, underpinned by damage to the hippocampus, may contribute significantly to the early deficit in episodic memory."], "field": "Engineering", "q_year": 2019, "q_cid": "202748667", "pos_cid": 14507452, "source": "eval20x26"}
{"query_id": "scaleup_16622877_10445513", "query": "How to minimize total power consumption for an unmanned aerial vehicle on a two-dimensional trajectory under uncertain departure angles, user locations, and wind speeds while respecting polygonal no-fly zones", "pos": ["Multi-Objective Optimization for Robust Power Efficient and Secure Full-Duplex Wireless Communication Systems. In this paper, we investigate the power efficient resource allocation algorithm design for secure multiuser wireless communication systems employing a full-duplex (FD) base station (BS) for serving multiple half-duplex (HD) downlink (DL) and uplink (UL) users simultaneously. We propose a multi-objective optimization framework to study two conflicting yet desirable design objectives, i.e., total DL transmit power minimization and total UL transmit power minimization. To this end, the weighed Tchebycheff method is adopted to formulate the resource allocation algorithm design as a multi-objective optimization problem (MOOP). The considered MOOP takes into account the quality-of-service requirements of all legitimate users for guaranteeing secure DL and UL transmission in the presence of potential eavesdroppers. Thereby, secure UL transmission is enabled by the FD BS and would not be possible with an HD BS. The imperfectness of the channel state information of the eavesdropping channels and the inter-user interference channels is incorporated for robust resource allocation algorithm design. Although the considered MOOP is non-convex, we solve it optimally by semidefinite programming relaxation. Simulation results not only unveil the trade-off between the total DL transmit power and the total UL transmit power, but also confirm the robustness of the proposed algorithm against potential eavesdroppers."], "field": "Engineering", "q_year": 2019, "q_cid": "166228773", "pos_cid": 10445513, "source": "eval20x26"}
{"query_id": "scaleup_20490912_5834217", "query": "How to recover fractionally sampled pulse-position-modulated signals without channel knowledge in shallow-water acoustic links with severe inter-symbol interference, time-varying multipath, large delay spreads, and short channel coherence times", "pos": ["Blind Image Deblurring Driven by Nonlinear Processing in the Edge Domain. This work addresses the problem of blind image deblurring, that is, of recovering an original image observed through one or more unknown linear channels and corrupted by additive noise. We resort to an iterative algorithm, belonging to the class of Bussgang algorithms, based on alternating a linear and a nonlinear image estimation stage. In detail, we investigate the design of a novel nonlinear processing acting on the Radon transform of the image edges. This choice is motivated by the fact that the Radon transform of the image edges well describes the structural image features and the effect of blur, thus simplifying the nonlinearity design. The effect of the nonlinear processing is to thin the blurred image edges and to drive the overall blind restoration algorithm to a sharp, focused image. The performance of the algorithm is assessed by experimental results pertaining to restoration of blurred natural images."], "field": "Engineering", "q_year": 2019, "q_cid": "204909122", "pos_cid": 5834217, "source": "eval20x26"}
{"query_id": "scaleup_20486572_5590763", "query": "How to estimate heart rate from a video sequence while accounting for dependencies between measurements from adjacent clips", "pos": ["Learning Phrase Representations using RNN Encoder–Decoder for Statistical Machine Translation. In this paper, we propose a novel neural network model called RNN Encoder‐ Decoder that consists of two recurrent neural networks (RNN). One RNN encodes a sequence of symbols into a fixedlength vector representation, and the other decodes the representation into another sequence of symbols. The encoder and decoder of the proposed model are jointly trained to maximize the conditional probability of a target sequence given a source sequence. The performance of a statistical machine translation system is empirically found to improve by using the conditional probabilities of phrase pairs computed by the RNN Encoder‐Decoder as an additional feature in the existing log-linear model. Qualitatively, we show that the proposed model learns a semantically and syntactically meaningful representation of linguistic phrases."], "field": "Engineering", "q_year": 2019, "q_cid": "204865728", "pos_cid": 5590763, "source": "eval20x26"}
{"query_id": "scaleup_24958253_583827", "query": "How to identify which structural features of the tested eco-friendly compounds account for differences in antifouling activity", "pos": ["Unravelling the Structural and Molecular Basis Responsible for the Anti-Biofilm Activity of Zosteric Acid. The natural compound zosteric acid, or p-(sulfoxy)cinnamic acid (ZA), is proposed as an alternative biocide-free agent suitable for preventive or integrative anti-biofilm approaches. Despite its potential, the lack of information concerning the structural and molecular mechanism of action involved in its anti-biofilm activity has limited efforts to generate more potent anti-biofilm strategies. In this study a 43-member library of small molecules based on ZA scaffold diversity was designed and screened against Escherichia coli to understand the structural requirements necessary for biofilm inhibition at sub-lethal concentrations. Considerations concerning the relationship between structure and anti-biofilm activity revealed that i) the para-sulfoxy ester group is not needed to exploit the anti-biofilm activity of the molecule, it is the cinnamic acid scaffold that is responsible for anti-biofilm performance; ii) the anti-biofilm activity of ZA derivatives depends on the presence of a carboxylate anion and, consequently, on its hydrogen-donating ability; iii) the conjugated aromatic system is instrumental to the anti-biofilm activities of ZA and its analogues. Using a protein pull-down approach, combined with mass spectrometry, the herein-defined active structure of ZA was matrix-immobilized, and was proved to interact with the E. coli NADH:quinone reductase, WrbA, suggesting a possible role of this protein in the biofilm formation process."], "field": "Engineering", "q_year": 2022, "q_cid": "249582539", "pos_cid": 583827, "source": "eval_collection"}
{"query_id": "scaleup_28273906_53985596", "query": "How to accurately detect collar boundaries in ccl logs despite noise, perturbations, uncertain boundary locations, and rigid single-point labels, while retaining sufficient local waveform context", "pos": ["Generalized Seismic Phase Detection with Deep Learning. To optimally monitor earthquake‐generating processes, seismologists have sought to lower detection sensitivities ever since instrumental seismic networks were started about a century ago. Recently, it has become possible to search continuous waveform archives for replicas of previously recorded events (i.e., template matching), which has led to at least an order of magnitude increase in the number of detected earthquakes and greatly sharpened our view of geological structures. Earthquake catalogs produced in this fashion, however, are heavily biased in that they are completely blind to events for which no templates are available, such as in previously quiet regions or for very large‐magnitude events. Here, we show that with deep learning, we can overcome such biases without sacrificing detection sensitivity. We trained a convolutional neural network (ConvNet) on the vast hand‐labeled data archives of the Southern California Seismic Network to detect seismic body‐wave phases. We show that the ConvNet is extremely sensitive and robust in detecting phases even when masked by high background noise and when the ConvNet is applied to new data that are not represented in the training set (in particular, very large‐magnitude events). This generalized phase detection framework will significantly improve earthquake monitoring and catalogs, which form the underlying basis for a wide range of basic and applied seismological research."], "field": "Engineering", "q_year": 2025, "q_cid": "282739063", "pos_cid": 53985596, "source": "eval_collection"}
{"query_id": "scaleup_26489760_13351447", "query": "How to understand where LEED-certified projects are clustered or sparse and how these spatial patterns evolve over time", "pos": ["The human cost of global warming: Deadly landslides and their triggers (1995-2014).. Worldwide, landslides incur catastrophic and significant economic and human losses. Previous studies have characterized the patterns in landslides' fatalities, from all kinds of triggering causes, at a continental or global scale, but they were based on data from periods of <10 years. The research herein presented hypothesizes that climate change associated with extreme rainfall and population distribution is contributing to a higher number of deadly landslides worldwide. This study maps and identified deadly landslides in 128 countries and it encompasses their role, for a 20 years' period from January/1995 to December/2014, considered representative for establishing a relationship between landslides and their meteorological triggers. A database of georeferenced landslides, their date, and casualties' information, duly validated, was implemented. A hot spot analysis for the daily record of landslide locations was performed, as well as a percentile-based approach to evaluate the trend of extreme rainfall events for each occurrence. The relationship between casualty, population distribution, and rainfall was also evaluated. For 20 years, 3876 landslides caused a total of 163,658 deaths and 11,689 injuries globally. They occurred most frequently between June and December in the Northern Hemisphere, and between December and February in the Southern Hemisphere. A significant global rise in the number of deadly landslides and hotspots across the studied period was observed. Analysis of daily rainfall confirmed that more than half of the events were in areas exposed to the risk of extreme rainfall. The relationships established between extreme rainfall, population distribution, seasonality, and landslides provide a useful basis for efforts to model the adverse impacts of extreme rainfall due to climate change and human activities and thus contribute towards a more resilient society."], "field": "Engineering", "q_year": 2023, "q_cid": "264897603", "pos_cid": 133514476, "source": "eval_collection"}
{"query_id": "scaleup_28273906_23457970", "query": "How to improve neural network training and convergence under unstable input distributions and vanishing or exploding gradients", "pos": ["Effect of Data Normalization on Neural Networks for the Forward Modelling of Transient Electromagnetic Data. Summary Inversion of geophysical data is often challenging and time-consuming, particularly for large scale surveys. The solution of the inverse problem requires numerous calculations of the forward problem, especially when calculating partial derivatives required for most linearized inversion schemes. The forward model is usually calculated numerically using accurate equations, but often less accurate and faster equations are used. In recent years, neural networks have become increasingly popular to replace the numerical forward modelling, as this may lead to a significant speed-up. Data normalization, prior to the training of neural networks, is crucial to obtain good results and faster convergence rate. This is especially true for geophysical data, as numerical data values may span over several orders of magnitude. In this abstract, we investigate several normalization approaches for TEM data, with a special focus on towed TEM data. Through extensive experimentations, we show that data normalization substantially affects the performance of neural networks when surrogating forward models. We also demonstrate the effect of normalized data variation on neural network’s performance and provide insights into which normalization approaches may be better than others. A significant improvement in performance accuracy is achieved when the appropriate data normalization technique is employed."], "field": "Engineering", "q_year": 2025, "q_cid": "282739063", "pos_cid": 234579706, "source": "eval_collection"}
{"query_id": "scaleup_25881328_17479939", "query": "How to maintain training stability as network depth increases", "pos": ["Learning Deep Transformer Models for Machine Translation. Transformer is the state-of-the-art model in recent machine translation evaluations. Two strands of research are promising to improve models of this kind: the first uses wide networks (a.k.a. Transformer-Big) and has been the de facto standard for development of the Transformer system, and the other uses deeper language representation but faces the difficulty arising from learning deep networks. Here, we continue the line of research on the latter. We claim that a truly deep Transformer model can surpass the Transformer-Big counterpart by 1) proper use of layer normalization and 2) a novel way of passing the combination of previous layers to the next. On WMT’16 English-German and NIST OpenMT’12 Chinese-English tasks, our deep system (30/25-layer encoder) outperforms the shallow Transformer-Big/Base baseline (6-layer encoder) by 0.4-2.4 BLEU points. As another bonus, the deep model is 1.6X smaller in size and 3X faster in training than Transformer-Big."], "field": "Engineering", "q_year": 2023, "q_cid": "258813282", "pos_cid": 174799399, "source": "eval_collection"}
{"query_id": "scaleup_25923525_2375110", "query": "How to reduce the parameter count and computational overhead of convolutional local feature extraction in MPViT’s multi-path structure while retaining local feature capture", "pos": ["Xception: Deep Learning with Depthwise Separable Convolutions. We present an interpretation of Inception modules in convolutional neural networks as being an intermediate step in-between regular convolution and the depthwise separable convolution operation (a depthwise convolution followed by a pointwise convolution). In this light, a depthwise separable convolution can be understood as an Inception module with a maximally large number of towers. This observation leads us to propose a novel deep convolutional neural network architecture inspired by Inception, where Inception modules have been replaced with depthwise separable convolutions. We show that this architecture, dubbed Xception, slightly outperforms Inception V3 on the ImageNet dataset (which Inception V3 was designed for), and significantly outperforms Inception V3 on a larger image classification dataset comprising 350 million images and 17,000 classes. Since the Xception architecture has the same number of parameters as Inception V3, the performance gains are not due to increased capacity but rather to a more efficient use of model parameters."], "field": "Engineering", "q_year": 2023, "q_cid": "259235256", "pos_cid": 2375110, "source": "eval_collection"}
{"query_id": "scaleup_27499599_52169462", "query": "How to improve the compressive and tensile strength of sustainable porous materials", "pos": ["Effect of bio-additives on physico-chemical properties of fly ash-ground granulated blast furnace slag based self cured geopolymer mortars.. Heat curing catalyzed the geopolymerization reaction in geopolymers whereas the practical challenges in applying heat curing process limited the applications of geopolymers to precast elements alone. Bio-additives inclusion could facilitate ambient temperature curing that lead to environment friendly self cured geopolymers. Natural sugars (molasses/palm jaggery/honey) and terminalia chebula were used as bio-additives in fly ash (FA) and ground granulated blast furnace slag (GGBS) based geopolymer mortars. X-ray diffraction (XRD), Fourier transform infrared spectral (FTIR), thermogravimetric (TG/DTG) and scanning electron microscopic (SEM) studies were used for the characterization for all geopolymer mortar samples. Physico-chemical test results of bio-additives added FA-GGBS based self cured geopolymer mortar samples showed XRD peaks at 2θ = 20°, 26°, 39°, 48°, 66° and 75°, FTIR bands at 3430, 2922, 1390, 1270, 1120 and 881cm-1, DTG peaks at 120 °C, 126 °C and 134 °C that led to the conclusion that development of differences in geopolymer reaction products, intense structural reorganization leading to stable geopolymer matrix and more ordered geopolymer gels. Further SEM observations revealed compact and dense microstructure development in bio-additives added FA-GGBS based self cured geopolymer mortar samples."], "field": "Engineering", "q_year": 2024, "q_cid": "274995999", "pos_cid": 52169462, "source": "eval_collection"}
{"query_id": "scaleup_27585202_23572357", "query": "How to control the mechanical properties of enzyme hydrogels while preserving catalytic activity", "pos": ["Control of Nanoscale In Situ Protein Unfolding Defines Network Architecture and Mechanics of Protein Hydrogels. Hierarchical assemblies of proteins exhibit a wide-range of material properties that are exploited both in nature and by artificially by humankind. However, little is understood about the importance of protein unfolding on the network assembly, severely limiting opportunities to utilize this nanoscale transition in the development of biomimetic and bioinspired materials. Here we control the force lability of a single protein building block, bovine serum albumin (BSA), and demonstrate that protein unfolding plays a critical role in defining the architecture and mechanics of a photochemically cross-linked native protein network. The internal nanoscale structure of BSA contains “molecular reinforcement” in the form of 17 covalent disulphide “nanostaples”, preventing force-induced unfolding. Upon addition of reducing agents, these nanostaples are broken rendering the protein force labile. Employing a combination of circular dichroism (CD) spectroscopy, small-angle scattering (SAS), rheology, and modeling, we show that stapled protein forms reasonably homogeneous networks of cross-linked fractal-like clusters connected by an intercluster region of folded protein. Conversely, in situ protein unfolding results in more heterogeneous networks of denser fractal-like clusters connected by an intercluster region populated by unfolded protein. In addition, gelation-induced protein unfolding and cross-linking in the intercluster region changes the hydrogel mechanics, as measured by a 3-fold enhancement of the storage modulus, an increase in both the loss ratio and energy dissipation, and markedly different relaxation behavior. By controlling the protein’s ability to unfold through nanoscale (un)stapling, we demonstrate the importance of in situ unfolding in defining both network architecture and mechanics, providing insight into fundamental hierarchical mechanics and a route to tune biomaterials for future applications."], "field": "Engineering", "q_year": 2025, "q_cid": "275852025", "pos_cid": 235723573, "source": "eval_collection"}
{"query_id": "scaleup_27011781_23232439", "query": "How to reliably assess intrinsic contractile ability under markedly altered loading conditions when conventional performance measures are strongly load-dependent", "pos": ["Myocardial work index: a marker of left ventricular contractility in pressure‐ or volume overload‐induced heart failure. While global longitudinal strain (GLS) is considered to be a sensitive marker of left ventricular (LV) function, it is significantly influenced by loading conditions. We hypothesized that global myocardial work index (GMWI), a novel marker of LV function, may show better correlation with load‐independent markers of LV contractility in rat models of pressure‐induced or volume overload‐induced heart failure."], "field": "Engineering", "q_year": 2024, "q_cid": "270117816", "pos_cid": 232324394, "source": "eval_collection"}
{"query_id": "scaleup_25903104_20450953", "query": "How to select suitable settings for bearing fault diagnosis without a theoretical basis for selection and with limited task-specific empirical guidance", "pos": ["On Empirical Comparisons of Optimizers for Deep Learning. Selecting an optimizer is a central step in the contemporary deep learning pipeline. In this paper, we demonstrate the sensitivity of optimizer comparisons to the hyperparameter tuning protocol. Our findings suggest that the hyperparameter search space may be the single most important factor explaining the rankings obtained by recent empirical comparisons in the literature. In fact, we show that these results can be contradicted when hyperparameter search spaces are changed. As tuning effort grows without bound, more general optimizers should never underperform the ones they can approximate (i.e., Adam should never perform worse than momentum), but recent attempts to compare optimizers either assume these inclusion relationships are not practically relevant or restrict the hyperparameters in ways that break the inclusions. In our experiments, we find that inclusion relationships between optimizers matter in practice and always predict optimizer comparisons. In particular, we find that the popular adaptive gradient methods never underperform momentum or gradient descent. We also report practical tips around tuning often ignored hyperparameters of adaptive gradient methods and raise concerns about fairly benchmarking optimizers for neural network training."], "field": "Engineering", "q_year": 2023, "q_cid": "259031048", "pos_cid": 204509533, "source": "eval_collection"}
{"query_id": "scaleup_22495138_11537005", "query": "How to provide practical, financially feasible charging electricity for daily urban electric vehicle use without storage equipment, energy-intensive high-pressure storage, or a dedicated supply network", "pos": ["Comparison of the solid oxide fuel cell system for micro CHP using natural gas with a system using a mixture of natural gas and hydrogen. Solid oxide fuel cell systems for combined heat and power production (SOFC μCHP) fueled by natural gas are attractive because of their high electrical and total efficiency even at small scale. The development of a hydrogen economy will increase the availability of distributed hydrogen as a pure gas. Alternatively, hydrogen may be blended with natural gas in the grid. This study investigates the performance of SOFC μCHP systems, while using a fuel varying from pure hydrogen to pure methane via mixtures of hydrogen and methane called Hythane. Flowsheet models of external as well as internal reforming fuel cell systems were developed in Cycle-Tempo simulation software. Results show that both the external as well as the internal reforming system can operated on all fuel gas compositions varying from pure hydrogen to pure methane, thus allowing for a transition towards a hydrogen economy via the mixing of hydrogen into the natural gas grid. Although the natural gas based systems have a higher electrical efficiency, the introduction of hydrogen into the gas leads to a higher total efficiency of the combined heat and power system. The addition of hydrogen into the fuel minimizes the problems of thermal stress and thermal shock associated with the use of methane in internal reforming fuel cell systems. The internal reforming system showed a higher performance compared to the external reforming system for all Hythane gas mixtures in terms of not only electrical efficiency but also in terms of thermal and total efficiency."], "field": "Engineering", "q_year": 2020, "q_cid": "224951389", "pos_cid": 115370050, "source": "eval_collection"}
{"query_id": "scaleup_22495138_19745198", "query": "How to evaluate and optimize a charging station’s energy performance while ensuring consistent energy balances across its individual devices", "pos": ["Solid Oxide Fuel Cell systems for electricity generation: An optimization prospect. Abstract The present study concerns with an optimization method of Solid Oxide Fuel Cell (SOFC) systems for electricity generation, directly fed by CH4 (methane) or C2H5OH (ethanol). By considering a detailed thermodynamic analysis, an innovative simulation model, namely THERMAS (THERmodynamic MAthematical Simulation), was designed and implemented. A specific SOFC-based system was selected to be the reference simulation, which is assumed to be equipped with heat exchangers (preheaters), a reformer, a SOFC-stack system and an afterburner. THERMAS allows for an extended parametric analysis in terms of energy and exergy and offers the opportunity to investigate all the operational characteristics that affect system's efficiency. The optimization process relies on the difference between the energy and exergy efficiency, where an OPF (OPtimization Factor) has been introduced and particularly estimated for each simulated scenario, based on several operational parameters, such as fuel composition, extension of chemical reactions and temperatures. The introduction of this OPF is actually an innovative improvement towards an easy-to-use optimization of SOFC systems. It is found that the design of a SOFC-based power plant fueled by pure hydrocarbons, has to be carefully simulated before its, otherwise the purification of fuels sounds meaningless."], "field": "Engineering", "q_year": 2020, "q_cid": "224951389", "pos_cid": 197451984, "source": "eval_collection"}
{"query_id": "scaleup_28273906_20659388", "query": "How to reduce overconfident casing collar recognition predictions and improve performance on unseen casing collar locator data", "pos": ["Rethinking the Inception Architecture for Computer Vision. Convolutional networks are at the core of most state of-the-art computer vision solutions for a wide variety of tasks. Since 2014 very deep convolutional networks started to become mainstream, yielding substantial gains in various benchmarks. Although increased model size and computational cost tend to translate to immediate quality gains for most tasks (as long as enough labeled data is provided for training), computational efficiency and low parameter count are still enabling factors for various use cases such as mobile vision and big-data scenarios. Here we are exploring ways to scale up networks in ways that aim at utilizing the added computation as efficiently as possible by suitably factorized convolutions and aggressive regularization. We benchmark our methods on the ILSVRC 2012 classification challenge validation set demonstrate substantial gains over the state of the art: 21:2% top-1 and 5:6% top-5 error for single frame evaluation using a network with a computational cost of 5 billion multiply-adds per inference and with using less than 25 million parameters. With an ensemble of 4 models and multi-crop evaluation, we report 3:5% top-5 error and 17:3% top-1 error on the validation set and 3:6% top-5 error on the official test set."], "field": "Engineering", "q_year": 2025, "q_cid": "282739063", "pos_cid": 206593880, "source": "eval_collection"}
{"query_id": "scaleup_25726745_62141856", "query": "How to assess future local water availability and crop needs for reliable irrigated agriculture planning", "pos": ["Design of a regional climate modelling projection ensemble experiment - NARCliM. Abstract. Including the impacts of climate change in decision making and planning processes is a challenge facing many regional governments including the New South Wales (NSW) and Australian Capital Territory (ACT) governments in Australia. NARCliM (NSW/ACT Regional Climate Modelling project) is a regional climate modelling project that aims to provide a comprehensive and consistent set of climate projections that can be used by all relevant government departments when considering climate change. To maximise end user engagement and ensure outputs are relevant to the planning process, a series of stakeholder workshops were run to define key aspects of the model experiment including spatial resolution, time slices, and output variables. As with all such experiments, practical considerations limit the number of ensemble members that can be simulated such that choices must be made concerning which global climate models (GCMs) to downscale from, and which regional climate models (RCMs) to downscale with. Here a methodology for making these choices is proposed that aims to sample the uncertainty in both GCM and RCM ensembles, as well as spanning the range of future climate projections present in the GCM ensemble. The RCM selection process uses performance evaluation metrics to eliminate poor performing models from consideration, followed by explicit consideration of model independence in order to retain as much information as possible in a small model subset. In addition to these two steps the GCM selection process also considers the future change in temperature and precipitation projected by each GCM. The final GCM selection is based on a subjective consideration of the GCM independence and future change. The created ensemble provides a more robust view of future regional climate changes. Future research is required to determine objective criteria that could replace the subjective aspects of the selection process."], "field": "Engineering", "q_year": 2023, "q_cid": "257267455", "pos_cid": 62141856, "source": "eval_collection"}
{"query_id": "scaleup_27830058_23168397", "query": "How to reliably determine whether an object is present at a given location despite background disturbances and unknown random responses, while accounting for available statistical information about its reflectivity", "pos": ["MAP Ratio Test Detector for Radar System. In some radar applications, neither the channel parameters nor the transmitted signal are known a-priori at the radar receiver. As such, both the transmitted signal as well as the channel parameters are random variables. Given the knowledge of distributions of the unknown parameters, we propose a maximum a-posteriori (MAP) ratio test (MAPRT) detector that incorporates this knowledge into its decision making process. This MAP approach is a generalization of past approaches such as the generalized likelihood ratio test (GLRT) detectors, where the estimates of the unknown parameters are obtained using maximum likelihood (ML) estimation. Assuming no knowledge of transmit waveforms, we derive the test statistics for bi-static and multi-static radar systems, when the noise power is both known and unknown. For the case of known noise variance in the bi-static radar system, we derive an exact closed-form expression for the probability of false alarm (PFA) and an approximate expression for the probability of detection (PD). For the multi-static case with known noise power, we derive upper bounds on PFA and PD. Numerical simulations verify the accuracy of the derived expressions and demonstrate that the proposed MAPRT detector performs significantly better than the GLRT-based detectors, especially when the signal-to-noise ratio (SNR) associated with the surveillance channel or sample size assumes small values."], "field": "Engineering", "q_year": 2025, "q_cid": "278300581", "pos_cid": 231683977, "source": "eval_collection"}
{"query_id": "scaleup_25752093_3504045", "query": "How to achieve efficient amplification at physiological temperature with limited magnesium availability under low-temperature conditions", "pos": ["Excess dNTPs minimize RNA hydrolysis during reverse transcription.. Divalent Mg2+-catalyzed degradation of RNA is a welldocumented phenomenon (1,3) that is not widely recognized in the molecular biology laboratory. At temperatures above 37°C (1) and at pH 7.5 and above in Tris-HCl buffers (3), the rate of RNA breakdown is directly proportional to Mg2+ concentration between 1 and 10 mM. Other buffer systems such as glycine (1) or sodium citrate (3) reduce the detrimental effects of Mg2+. Free Mg2+ (1–3.5 mM) and alkaline pH (8.4) in Tris-HCl buffers are present during cDNA synthesis with murine and avian retroviral reverse transcriptases (8,14), creating conditions under which Mg2+-catalyzed RNA breakdown occurs. One significant difficulty with retroviral reverse transcriptase-catalyzed cDNA synthesis is the tendency of the enzyme to pause at regions of secondary structure in mRNA (5,10,20), resulting in the generation of truncated products. As the result, more thermal stable reverse transcriptases are being sought and used that function at temperatures high enough to denature RNA (18), and protocols are being developed that employ RNA heating steps at high temperatures in the presence of Mg2+ (11). To define the stability of RNA under reaction conditions used to synthesize cDNA, we determined the rate of degradation and half-life of a 7.5-kb cRNA at various temperatures under reaction conditions optimal for Moloney murine leukemia virus (MMLV) reverse transcriptase (8). We found that the rate of Mg2+-catalyzed RNA degradation is quite rapid at higher temperatures and that RNA breakdown can be reduced by the addition of excess dNTPs to chelate free Mg2+. The protocol used to measure RNA breakdown was as follows. RNA (7.5 kb; Invitrogen, Carlsbad, CA, USA) was used unlabeled or labeled at the 3′end with [α-32P]ddATP and yeast poly(A) polymerase (Amersham Biosciences, Piscataway, NJ, USA). The results obtained with labeled and unlabeled RNA were similar. RNA was heated at various temperatures in a 0.5mL tube in a thermal cycler equipped with a heated lid. The heating solution (20 μL) mimicking MMLV reverse transcriptase reaction conditions contained 50 mM Tris-HCl, pH 8.4, 75 mM KCl, 3 mM MgCl2, 500 μM each dCTP, dGTP, dTTP, and dATP, and 10 μg unlabeled or 3′-end-labeled 7.5-kb RNA. At various times, 2-μL aliquots were removed and placed on ice in separate tubes containing 1 μL 100 mM EDTA. Gel loading buffer (30 mM MOPS, pH 7.0, 0.6 mM EDTA, 27 mg/mL sucrose, 2.9 M formaldehyde, 57% formamide, 1.3 mg/mL bromocresol green, and 7 μL 70 μg/mL ethidium bromide) was added, and the RNA was heated at 65°C for 5 min. When testing avian reverse transcriptase reaction conditions, the MgCl2 concentration was increased to 7.5 mM and the concentration of each dNTP was increased to 1 mM in heating mixtures. Heated RNA was subjected to denaturing formaldehyde agarose gel electrophoresis as described previously (7). Gels contained 1.5% agarose, 50 mM MOPS, pH 7.0, 1 mM EDTA, and 2.2 M formaldehyde and were run in 50 mM MOPS (pH 7.0)-1 mM EDTA. A digitized image of ethidium bromidestained, unlabeled RNA was captured during transillumination of gels with short-wave UV light with a Lynx 5000 Gel Imaging System (Applied Imaging, Santa Clara, CA, USA). The system software was used to quantify the fraction of intact 7.5-kb RNA present in a lane of the gel. When labeled RNA was used, the gel was dried and exposed to X-ray film. Using an exposed film as a guide, the intact 7.5-kb RNA and any breakdown products were excised separately and counted in a scintillation counter to determine the fraction of intact RNA. cDNA synthesis with MMLV Hreverse transcriptase (SuperScript II reverse transcriptase; Invitrogen) was carried out in reaction mixtures (20 μL) containing 50 mM Tris-HCl, pH 8.4, 75 mM KCl, 3 mM MgCl2, 10 mM DTT, 500 μM each dATP, dTTP, dGTP, and [α-32P]dCTP (400 cpm/pmol), 1750 U/mL RNase Inhibitor, 62 nM 5.2-kb MAP-4 cRNA with a 3′-poly(A) tail (4), 575 nM p(dT)25-30, and 430 nM MMLV Hreverse transcriptase. In some cases, the concentration of each dNTP was increased to 1 mM. Reaction mixtures for Rous sarcoma virus (RSV) Hreverse transcriptase (80 nM ThermoScript reverse transcriptase; Invitrogen) were the same, except the MgCl2 and individual dNTP concentraBenchmarks"], "field": "Engineering", "q_year": 2023, "q_cid": "257520936", "pos_cid": 3504045, "source": "eval_collection"}
{"query_id": "scaleup_27196571_23186544", "query": "How to determine whether pain during movement preparation and execution affects motor learning differently, with pain-induced changes in motor-pathway responsiveness confined to one phase rather than spanning both?", "pos": ["The effect of experimental pain on the excitability of the corticospinal tract in humans: A systematic review and meta‐analysis. Pain influences motor control. Previous reviews observed that pain reduces the excitability of corticospinal projections to muscles tested with transcranial magnetic stimulation. However, the independent effect of the type of pain models (tonic, phasic), pain location and tissues targeted (e.g. muscle, skin) remains unexplored. The objective of this review was to determine the influence of experimental pain and of different methodological factors on the corticospinal excitability."], "field": "Engineering", "q_year": 2024, "q_cid": "271965713", "pos_cid": 231865441, "source": "eval_collection"}
{"query_id": "scaleup_27585202_24395174", "query": "How to quantify the reduction in solute diffusion at the concentration used for enzyme kinetic measurements", "pos": ["High-Throughput FRAP Analysis of Solute Diffusion in Hydrogels. Increasingly accurate mathematical models have been developed to relate solute and hydrogel properties to solute diffusion coefficients in hydrogels, primarily by comparing solute sizes and hydrogel mesh sizes. Here, we use a standardized, high-throughput method for fluorescence recovery after photobleaching (FRAP) experiments and analysis to characterize the diffusion coefficients of fluorescein, three sizes of FITC-dextran, and three sizes of FITC-conjugated poly(ethylene glycol) (PEG) through 18 structurally varied poly(vinyl alcohol) (PVA) hydrogel formulations. Increasing the hydrogel mesh radii increased the diffusivities of all the tested solutes within the hydrogels. While the diffusivity of FITC-dextrans in hydrogels decreased with increasing solute size, the diffusivity of FITC-PEGs increased with increasing solute size, suggesting that a generalized hydrodynamic radius-based model is not universally applicable for solute diffusion in hydrogels. The high-throughput characterization method for solute diffusion in hydrogels described here facilitates precise hydrogel design for biomedical applications."], "field": "Engineering", "q_year": 2025, "q_cid": "275852025", "pos_cid": 243951740, "source": "eval_collection"}
{"query_id": "scaleup_28414366_14681110", "query": "How to improve the mechanical strength of highly porous polycaprolactone scaffolds to meet the demands of natural bone for effective bone repair", "pos": ["Embedding magnesium metallic particles in polycaprolactone nanofiber mesh improves applicability for biomedical applications.. Magnesium (Mg) metal is of great interest in biomedical applications, especially in tissue engineering. Mg exhibits excellent in vivo biocompatibility, biodegradability and, during degradation, releases Mg ions (Mg2+) with the potential to improve tissue repair. We used electrospinning technology to incorporate Mg particles into nanofibers. Various ratios of Mg metal microparticles (<44 µm diameter) were incorporated into nanofiber polycaprolactone (PCL) meshes. Physicochemical properties of the meshes were analyzed by scanning electron microscopy (SEM), Fourier-transform infrared spectroscopy (FTIR), mechanical tensile testing, X-ray diffractometry and UV-VIS spectrophotometry. Biological properties of meshes were evaluated in vitro and in vivo. Under mammalian cell culture conditions, Mg-containing meshes released hydrogen gas and relative amounts of free Mg2+ that reflected the Mg/PCL ratios. All meshes were non-cytotoxic for 3T3 fibroblasts and PC-12 pheochromocytoma cells. In vivo implantation under the skin of mice for 3, 8 and 28 days showed that Mg-containing meshes were well vascularized, with improved measures of inflammation and healing compared to meshes without Mg. Evidence included an earlier appearance and infiltration of tissue repairing macrophages and, after 28 days, evidence of more mature tissue remodeling. Thus, these new composite nanofiber meshes have promising material properties that mitigated inflammatory tissue responses to PCL alone and improved tissue healing, thus providing a suitable matrix for use in clinically relevant tissue engineering applications. STATEMENT OF SIGNIFICANCE: The biodegradable metal, magnesium, safely biodegrades in the body, releasing beneficial byproducts. To improve tissue delivery, magnesium metal particles were incorporated into electrospun nanofiber meshes composed of a biodegradable, biocompatible polymer, polycaprolactone (PCL). Magnesium addition, at several concentrations, did not alter PCL chemistry, but did alter physical properties. Under cell culture conditions, meshes released magnesium ions and hydrogen gas and were not cytotoxic for two cell types. After implantation in mice, the mesh with magnesium resulted in earlier appearance of M2-like, reparative macrophages and improved tissue healing versus mesh alone. This is in agreement with other studies showing beneficial effects of magnesium metal and provides a new type of scaffold material that will be useful in clinically relevant tissue engineering applications."], "field": "Engineering", "q_year": 2025, "q_cid": "284143667", "pos_cid": 146811106, "source": "eval_collection"}
{"query_id": "scaleup_25923525_23241778", "query": "How to improve fine-grained and coarse-grained visual token utilization in transformer-based weld defect detection with weaker local than global feature capture", "pos": ["CvT: Introducing Convolutions to Vision Transformers. We present in this paper a new architecture, named Convolutional vision Transformer (CvT), that improves Vision Transformer (ViT) in performance and efficiency by introducing convolutions into ViT to yield the best of both de-signs. This is accomplished through two primary modifications: a hierarchy of Transformers containing a new convolutional token embedding, and a convolutional Transformer block leveraging a convolutional projection. These changes introduce desirable properties of convolutional neural networks (CNNs) to the ViT architecture (i.e. shift, scale, and distortion invariance) while maintaining the merits of Transformers (i.e. dynamic attention, global context, and better generalization). We validate CvT by conducting extensive experiments, showing that this approach achieves state-of-the-art performance over other Vision Transformers and ResNets on ImageNet-1k, with fewer parameters and lower FLOPs. In addition, performance gains are maintained when pretrained on larger datasets (e.g. ImageNet-22k) and fine-tuned to downstream tasks. Pretrained on ImageNet-22k, our CvT-W24 obtains a top-1 accuracy of 87.7% on the ImageNet-1k val set. Finally, our results show that the positional encoding, a crucial component in existing Vision Transformers, can be safely re-moved in our model, simplifying the design for higher resolution vision tasks. Code will be released at https://github.com/microsoft/CvT."], "field": "Engineering", "q_year": 2023, "q_cid": "259235256", "pos_cid": 232417787, "source": "eval_collection"}
{"query_id": "scaleup_23644741_15228290", "query": "How to reduce overfitting and redundant complexity in system identification, select relevant input variables, and quantify parameter and prediction uncertainty while accounting for related parameter groups under computational constraints", "pos": ["BayesNAS: A Bayesian Approach for Neural Architecture Search. One-Shot Neural Architecture Search (NAS) is a promising method to significantly reduce search time without any separate training. It can be treated as a Network Compression problem on the architecture parameters from an over-parameterized network. However, there are two issues associated with most one-shot NAS methods. First, dependencies between a node and its predecessors and successors are often disregarded which result in improper treatment over zero operations. Second, architecture parameters pruning based on their magnitude is questionable. In this paper, we employ the classic Bayesian learning approach to alleviate these two issues by modeling architecture parameters using hierarchical automatic relevance determination (HARD) priors. Unlike other NAS methods, we train the over-parameterized network for only one epoch then update the architecture. Impressively, this enabled us to find the architecture on CIFAR-10 within only 0.2 GPU days using a single GPU. Competitive performance can be also achieved by transferring to ImageNet. As a byproduct, our approach can be applied directly to compress convolutional neural networks by enforcing structural sparsity which achieves extremely sparse networks without accuracy deterioration."], "field": "Engineering", "q_year": 2021, "q_cid": "236447411", "pos_cid": 152282904, "source": "train_step3"}
{"query_id": "scaleup_21121024_20659248", "query": "How to preserve spectral and spatial fidelity in pan-sharpening while retaining coarse structures and high-frequency details", "pos": ["Going deeper with convolutions. We propose a deep convolutional neural network architecture codenamed Inception that achieves the new state of the art for classification and detection in the ImageNet Large-Scale Visual Recognition Challenge 2014 (ILSVRC14). The main hallmark of this architecture is the improved utilization of the computing resources inside the network. By a carefully crafted design, we increased the depth and width of the network while keeping the computational budget constant. To optimize quality, the architectural decisions were based on the Hebbian principle and the intuition of multi-scale processing. One particular incarnation used in our submission for ILSVRC14 is called GoogLeNet, a 22 layers deep network, the quality of which is assessed in the context of classification and detection."], "field": "Engineering", "q_year": 2020, "q_cid": "211210249", "pos_cid": 206592484, "source": "train_step3"}
{"query_id": "scaleup_25256582_9889571", "query": "How to predict acute brain injury risk in va-ecmo patients", "pos": ["Prognostic value of systolic short-term blood pressure variability in systolic heart failure. BackgroundTraditional cardiovascular risk factors in the general population are usually correlated to a better prognosis in patients with chronic heart failure (HF). Most of the studies show that blood pressure variability (BPV) has noxious effect on general population but data are missing for patients with systolic HF. The aim of this study was to assess the prognostic impact of short-term blood pressure variability (BPV) in systolic HF.Methods and resultsWe retrospectively studied 288 patients (60 ± 12 years-old; 79 % male) referred to our tertiary center of HF for the management of their systolic HF (left ventricular ejection fraction was 28 ± 9 %). All patients underwent ambulatory blood pressure monitoring (systolic BP: 110 ± 15; diastolic BP: 68 ± 10 and pulse pressure: 42 ± 11 mmHg) and the prognostic impact of BPV was collected with a mean follow-up of 4.4 ± 3.1 years. Twenty-five (9 %) patients were missing for follow-up. Among the others patients, 70 (27 %) cardiovascular events (cardiac deaths: 24 %; heart transplantation: 2 %) were recorded. By multivariate analysis BPV daytime (OR = 0.963, p = 0.033) and severe NYHA class (OR = 5.2, p < 0.0001) were found as independent predictors of cardiac event. Patients with a systolic daytime BPV under a cut-off value of 19 mmHg had the poorest prognosis with an OR for cumulative events of 1.65 (IC95 % 1.1–2.7; p < 0.04).ConclusionBPV is simple tool and a predictor of cardiac events in patients with systolic HF."], "field": "Engineering", "q_year": 2022, "q_cid": "252565824", "pos_cid": 9889571, "source": "train_step3"}
{"query_id": "scaleup_25855728_22970272", "query": "How to achieve two-state phase control at individual elements of a reconfigurable intelligent surface in practical hardware", "pos": ["A Programmable Binary Metasurface for Wireless Power Transfer Application. This paper proposes a 1-bit programmable metasurface which is capable of an adaptive beam focusing according to the receiver position. By doing so, the electromagnetic (EM) wireless power transfer (WPT) efficiency can be increased. The metasurface is designed to work at 5.8GHz and consists of 16 x 16 square unicell. Each of the unicells is connected with one pin diode that enables \"ON\" and \"OFF\" states with 1800 reflected signal phase change. The \"ON\" (0) and \"OFF\" (1) states correspond to the states of the pin diode. By adjusting the ON/OFF pattern of the metasurface appropriately, we can control the reflected impinging wave. Then, as a radio frequency (RF) choke, a butterfly stub has been designed. We also fabricate and implement a metasurface prototype to verify the ability of the metasurface. The results show that the metasurface is capable of steering and focusing the beam towards the receiver position."], "field": "Engineering", "q_year": 2023, "q_cid": "258557280", "pos_cid": 229702722, "source": "train_step3"}
{"query_id": "scaleup_26521917_21611020", "query": "How to determine the bleeding safety of calcium channel blockers in patients with continuous-flow left ventricular assist devices who already face heightened bleeding risk", "pos": ["Association of Oral Anticoagulants and Verapamil or Diltiazem With Adverse Bleeding Events in Patients With Nonvalvular Atrial Fibrillation and Normal Kidney Function. Key Points Question What is the association of oral anticoagulants and verapamil hydrochloride or diltiazem hydrochloride with adverse bleeding events in patients with no kidney disease? Findings In this comparative effectiveness study using data from 48 442 patients, rates of bleeding were increased for patients receiving dabigatran etexilate with concomitant verapamil or diltiazem compared with those who were receiving concomitant amlodipine or metoprolol therapy. Other direct oral anticoagulants had no evidence of these drug-drug interactions. Meaning These findings suggest that prescribers may need to avoid P-glycoprotein–related drug-drug interactions with dabigatran regardless of kidney function."], "field": "Engineering", "q_year": 2023, "q_cid": "265219175", "pos_cid": 216110202, "source": "train_step3"}
{"query_id": "scaleup_25379087_21998192", "query": "How to predict modular integrated construction installation productivity from resource inputs for project planning and establish that predictions accurately reflect actual outcomes", "pos": ["Prediction Algorithm of Bridge Construction Cost Based on Regression Analysis. ABSTRACT Yang, Z. and Qiu, H., 2020. Prediction algorithm of bridge construction cost based on regression analysis. In: Yang, Y.; Mi, C.; Zhao, L., and Lam, S. (eds.), Global Topics and New Trends in Coastal Research: Port, Coastal and Ocean Engineering. Journal of Coastal Research, Special Issue No. 103, pp. 979–982. Coconut Creek (Florida), ISSN 0749-0208. In the prediction of bridge construction cost, the correlation between the variables that affect the construction cost is an important factor that affects the prediction results. In the previous prediction algorithm, there is the problem of low Pearson correlation coefficient. Therefore, the prediction algorithm of bridge construction cost based on regression analysis is designed. According to the structure of the bridge entity and the various costs in the project, the influencing factors of the construction cost of the bridge project are determined, and the determinable coefficients among the influencing factors are calculated by regression analysis, then the predicted value of the construction cost of the bridge project is calculated, and the average relative error method and the mean square deviation ratio method are set to ensure the reliability of the predicted value. The experimental results show that the Pearson correlation coefficient of the designed prediction algorithm based on regression analysis is higher than that of the traditional prediction algorithm, which shows that the algorithm is suitable for practical bridge engineering projects."], "field": "Engineering", "q_year": 2022, "q_cid": "253790877", "pos_cid": 219981923, "source": "train_step3"}
{"query_id": "scaleup_27600966_10438761", "query": "How to determine whether an antibacterial material can also support bone regrowth", "pos": ["Strontium Ranelate Incorporated Enzyme-Cross-Linked Gelatin Nanoparticle/Silk Fibroin Aerogel for Osteogenesis in OVX-Induced Osteoporosis.. Osteoporosis is a wide-range disease with a negative impact on bone defect healing. Strontium ranelate (SR) has promising osteogenic potential for its dual function on stimulating osteoblasts and inhibiting osteoclast activity. However, it has limitations for its dose-dependent effect and side effects on systemic applications. Here, a sequentially cross-linking strategy including enzyme-cross-linking through tyrosinase from mushroom and physical folding is acquired to create SR loaded gelatin nanoparticle/silk fibroin aerogel (abbreviated as S/G-Sr-MT) with drug release controlling capacity. The results showed successful enzyme-cross-linking, excellent spatial structure, and enhanced mechanical properties of S/G-Sr-MT. Even Sr2+ loading and stable release with markedly inhibited initial burst release were detected. The biomineralization investigation showed rapid deposition of hydroxyapatite on the surface of S/G-Sr-MT. In vitro, spreading morphology and higher osteogenic gene expression of MC3T3-E1 seeded on S/G-Sr-MT were observed compared to other groups after 7 day culturing. In vivo, S/G-Sr-MT showed an obvious osteogenic capacity in calvaria defects of ovariectomized rats in which high Runx2 expression and inhibited TRAP activity were observed. Such results suggested the S/G-Sr-MT scaffold could stimulate osteogenic differentiation of osteoblasts while inhibiting osteoclast behaviors in vivo. These findings highlight the potential osteogenic ability and clinical application of SR incorporated enzyme-cross-linked scaffold in ovariectomized (OVX) bone healing."], "field": "Engineering", "q_year": 2025, "q_cid": "276009665", "pos_cid": 104387611, "source": "train_step3"}
{"query_id": "scaleup_23319650_16646795", "query": "How to determine whether gait measurements from IR-UWB and Kinect agree sufficiently to establish their comparability", "pos": ["Understanding Bland Altman analysis. In a contemporary clinical laboratory it is very common to have to assess the agreement between two quantitative methods of measurement. The correct statistical approach to assess this degree of agreement is not obvious. Correlation and regression studies are frequently proposed. However, correlation studies the relationship between one variable and another, not the differences, and it is not recommended as a method for assessing the comparability between methods. In 1983 Altman and Bland (B&A) proposed an alternative analysis, based on the quantification of the agreement between two quantitative measurements by studying the mean difference and constructing limits of agreement. The B&A plot analysis is a simple way to evaluate a bias between the mean differences, and to estimate an agreement interval, within which 95% of the differences of the second method, compared to the first one, fall. Data can be analyzed both as unit differences plot and as percentage differences plot. The B&A plot method only defines the intervals of agreements, it does not say whether those limits are acceptable or not. Acceptable limits must be defined a priori, based on clinical necessity, biological considerations or other goals. The aim of this article is to provide guidance on the use and interpretation of Bland Altman analysis in method comparison studies."], "field": "Engineering", "q_year": 2021, "q_cid": "233196507", "pos_cid": 16646795, "source": "train_step3"}
{"query_id": "scaleup_27235518_19757191", "query": "how to obtain high-quality reference data for training artificial intelligence models in earth science when available data quality is insufficient", "pos": ["Key issues in rigorous accuracy assessment of land cover products. Abstract Accuracy assessment and land cover mapping have been inexorably linked throughout the first 50 years of publication of Remote Sensing of Environment. The earliest developers of land-cover maps recognized the importance of evaluating the quality of their maps, and the methods and reporting format of these early accuracy assessments included features that would be familiar to practitioners today. Specifically, practitioners have consistently recognized the importance of obtaining high quality reference data to which the map is compared, the need for sampling to collect these reference data, and the role of an error matrix and accuracy measures derived from the error matrix to summarize the accuracy information. Over the past half century these techniques have undergone refinements to place accuracy assessment on a more scientifically credible footing. We describe the current status of accuracy assessment that has emerged from nearly 50 years of practice and identify opportunities for future advances. The article is organized by the three major components of accuracy assessment, the sampling design, response design, and analysis, focusing on good practice methodology that contributes to a rigorous, informative, and honest assessment. The long history of research and applications underlying the current practice of accuracy assessment has advanced the field to a mature state. However, documentation of accuracy assessment methods needs to be improved to enhance reproducibility and transparency, and improved methods are required to address new challenges created by advanced technology that has expanded the capacity to map land cover extensively in space and intensively in time."], "field": "Engineering", "q_year": 2024, "q_cid": "272355185", "pos_cid": 197571915, "source": "train_step3"}
{"query_id": "scaleup_26824823_23324104", "query": "How to distinguish fine-grained urban building categories from low-resolution satellite images lacking metre-scale building details", "pos": ["Image Super-Resolution via Iterative Refinement. We present SR3, an approach to image Super-Resolution via Repeated Refinement. SR3 adapts denoising diffusion probabilistic models (Ho et al. 2020), (Sohl-Dickstein et al. 2015) to image-to-image translation, and performs super-resolution through a stochastic iterative denoising process. Output images are initialized with pure Gaussian noise and iteratively refined using a U-Net architecture that is trained on denoising at various noise levels, conditioned on a low-resolution input image. SR3 exhibits strong performance on super-resolution tasks at different magnification factors, on faces and natural images. We conduct human evaluation on a standard 8× face super-resolution task on CelebA-HQ for which SR3 achieves a fool rate close to 50%, suggesting photo-realistic outputs, while GAN baselines do not exceed a fool rate of 34%. We evaluate SR3 on a 4× super-resolution task on ImageNet, where SR3 outperforms baselines in human evaluation and classification accuracy of a ResNet-50 classifier trained on high-resolution images. We further show the effectiveness of SR3 in cascaded image generation, where a generative model is chained with super-resolution models to synthesize high-resolution images with competitive FID scores on the class-conditional 256×256 ImageNet generation challenge."], "field": "Engineering", "q_year": 2024, "q_cid": "268248236", "pos_cid": 233241040, "source": "train_step3"}
{"query_id": "scaleup_27867506_23899520", "query": "How to distinguish informative content from irrelevant information in complex, multi-scale remote sensing images while balancing overall image understanding and local detail", "pos": ["U-Net combined with multi-scale attention mechanism for liver segmentation in CT images. Background The liver is an important organ that undertakes the metabolic function of the human body. Liver cancer has become one of the cancers with the highest mortality. In clinic, it is an important work to extract the liver region accurately before the diagnosis and treatment of liver lesions. However, manual liver segmentation is a time-consuming and boring process. Not only that, but the segmentation results usually varies from person to person due to different work experience. In order to assist in clinical automatic liver segmentation, this paper proposes a U-shaped network with multi-scale attention mechanism for liver organ segmentation in CT images, which is called MSA-UNet. Our method makes a new design of U-Net encoder, decoder, skip connection, and context transition structure. These structures greatly enhance the feature extraction ability of encoder and the efficiency of decoder to recover spatial location information. We have designed many experiments on publicly available datasets to show the effectiveness of MSA-UNet. Compared with some other advanced segmentation methods, MSA-UNet finally achieved the best segmentation effect, reaching 98.00% dice similarity coefficient (DSC) and 96.08% intersection over union (IOU)."], "field": "Engineering", "q_year": 2025, "q_cid": "278675062", "pos_cid": 238995204, "source": "train_step3"}
{"query_id": "scaleup_26164830_59540952", "query": "How to explain the effects of prior cold rolling reduction levels on austenite transformation, resulting phase proportions, and microstructural size in quenching and partitioning steel with an initial ferrite-pearlite structure", "pos": ["Effect of Cold Rolling on the Phase Transformation Kinetics of an Al0.5CoCrFeNi High-Entropy Alloy. The solid state phase transformation kinetics of as-cast and cold rolling deformed Al0.5CoCrFeNi high-entropy alloys have been investigated by the thermal expansion method. The phase transformed volume fractions are determined from the thermal expansion curve using the lever rule method, and the deformed sample exhibits a much higher transformation rate. Two kinetic parameters, activation energy (E) and kinetic exponent (n) are determined using Kissinger– Akahira–Sunose (KAS) and Johnson–Mehl–Avrami (JMA) method, respectively. Results show that a pre-deformed sample shows a much lower activation energy and higher kinetic exponent compared with the as-cast sample, which are interpreted based on the deformation induced defects that can promote the nucleation and growth process during phase transformation."], "field": "Engineering", "q_year": 2023, "q_cid": "261648309", "pos_cid": 59540952, "source": "train_step3"}
{"query_id": "scaleup_26202468_25602922", "query": "How to explain differences in osteogenesis-related gene expression in bone mesenchymal stem cells across hydrogel matrices", "pos": ["Mechanosensitive miR-99b mediates the regulatory effect of matrix stiffness on bone marrow mesenchymal stem cell fate both in vitro and in vivo. Mechanical signals from extracellular matrix stiffness are important cues that regulate the proliferation and differentiation of bone marrow mesenchymal stem cells (BMSCs). However, the incorporation of BMSCs into soft hydrogels and the dominance of soft matrices for BMSC growth and differentiation limit the directed differentiation of BMSCs incorporated into hydrogels for tissue engineering, especially osteogenesis. Here, we found that the expression of miR-99b increased with increasing hydrogel stiffness and that miR-99b regulated the proliferation and differentiation of BMSCs seeded on the surface of substrates with different stiffnesses. Furthermore, miR-99b significantly promoted the migration of BMSCs in 3D hydrogels. Mechanistically, we demonstrated that matrix stiffness-sensitive miR-99b targets the mammalian target of the rapamycin signaling pathway to regulate the adipogenic and osteogenic differentiation of BMSCs. In addition, by modulating the expression of miR-99b, the osteogenic differentiation of BMSCs in soft 3D hydrogels was promoted. Consistently, the flexible BMSC-GelMA hydrogel transfected with miR-99b significantly promoted bone regeneration in the rat calvarial defect area. These results suggest that miR-99b plays a key role in the mechanotransduction and phenotypic transformation of BMSCs and may inspire new tissue engineering applications with MSCs as key components."], "field": "Engineering", "q_year": 2023, "q_cid": "262024689", "pos_cid": 256029226, "source": "train_step3"}
{"query_id": "scaleup_25509662_86526816", "query": "How to identify multiple distinct structures that produce the same target mechanical response", "pos": ["Probabilistic Representation and Inverse Design of Metamaterials Based on a Deep Generative Model with Semi‐Supervised Learning Strategy. The research of metamaterials has achieved enormous success in the manipulation of light in a prescribed manner using delicately designed subwavelength structures, so‐called meta‐atoms. Even though modern numerical methods allow for the accurate calculation of the optical response of complex structures, the inverse design of metamaterials, which aims to retrieve the optimal structure according to given requirements, is still a challenging task owing to the nonintuitive and nonunique relationship between physical structures and optical responses. To better unveil this implicit relationship and thus facilitate metamaterial designs, it is proposed to represent metamaterials and model the inverse design problem in a probabilistically generative manner, enabling to elegantly investigate the complex structure–performance relationship in an interpretable way, and solve the one‐to‐many mapping issue that is intractable in a deterministic model. Moreover, to alleviate the burden of numerical calculations when collecting data, a semisupervised learning strategy is developed that allows the model to utilize unlabeled data in addition to labeled data in an end‐to‐end training. On a data‐driven basis, the proposed deep generative model can serve as a comprehensive and efficient tool that accelerates the design, characterization, and even new discovery in the research domain of metamaterials, and photonics in general."], "field": "Engineering", "q_year": 2022, "q_cid": "255096621", "pos_cid": 86526816, "source": "train_step3"}
{"query_id": "scaleup_24427047_46897706", "query": "How to minimize total economic dispatch cost with only local information and noisy, direction-limited communication while avoiding detrimental decisions and instability", "pos": ["A Linear Algorithm for Optimization Over Directed Graphs With Geometric Convergence. In this letter, we study distributed optimization, where a network of agents, abstracted as a directed graph, collaborates to minimize the average of locally known convex functions. Most of the existing approaches over directed graphs are based on push-sum (type) techniques, which use an independent algorithm to asymptotically learn either the left or right eigenvector of the underlying weight matrices. This strategy causes additional computation, communication, and nonlinearity in the algorithm. In contrast, we propose a linear algorithm based on an inexact gradient method and a gradient estimation technique. Under the assumptions that each local function is strongly convex with Lipschitz-continuous gradients, we show that the proposed algorithm geometrically converges to the global minimizer with a sufficiently small step-size. We present simulations to illustrate the theoretical findings."], "field": "Engineering", "q_year": 2021, "q_cid": "244270477", "pos_cid": 46897706, "source": "train_step3"}
{"query_id": "scaleup_23215047_17258616", "query": "How to reconcile independent household scheduling decisions with shared neighborhood objectives without a central operator while preventing rebound surges, instability, and strain on shared infrastructure", "pos": ["Multi-Area Unit Scheduling and Reserve Allocation Under Wind Power Uncertainty. This paper proposes a decentralized methodology to optimally schedule generating units while simultaneously determining the geographical allocation of the required reserve. We consider an interconnected multi-area power system with cross-border trading in the presence of wind power uncertainty. The multi-area market-clearing model is represented as a two-stage stochastic programming model. The proposed decentralized procedure relies on an augmented Lagrangian algorithm that requires no central operator intervention but just moderate interchanges of information among neighboring regions. The methodology proposed is illustrated using an example and a realistic case study."], "field": "Engineering", "q_year": 2021, "q_cid": "232150473", "pos_cid": 17258616, "source": "train_step3"}
{"query_id": "scaleup_23215047_52073652", "query": "How to achieve reliable convergence, fast coordination, and high accuracy among agents in non-convex, nonlinear problems with limited iterations and communication", "pos": ["Toward Distributed OPF Using ALADIN. This paper discusses the application of the recently proposed augmented Lagrangian alternating direction inexact Newton (<sc>aladin</sc>) method to non-convex ac optimal power flow problems (<sc>ac</sc>-<sc>opf</sc>) in a distributed fashion. In contrast to the often used alternating direction of multipliers method (<sc>admm</sc>), <sc>aladin</sc> guarantees locally quadratic convergence for <sc>ac</sc>-<sc>opf</sc>. Numerical results for 5–300 bus test cases indicate that <sc>aladin</sc> is able to outperform the <sc>admm</sc> and to reduce the number of iterations by about one order of magnitude. We compare <sc>aladin</sc> to numerical results for the <sc>admm</sc> documented in the literature. The improved convergence speed comes at the cost of increasing the communication effort per iteration. Therefore, we propose a variant of <sc>aladin</sc> that uses inexact Hessians to reduce communication. Additionally, we provide a detailed comparison of these <sc>aladin</sc> variants to the <sc>admm</sc> from an algorithmic and communication perspective. Moreover, we prove that <sc>aladin</sc> converges locally at a quadratic rate even for the relevant case of suboptimally solved local nonlinear programs."], "field": "Engineering", "q_year": 2021, "q_cid": "232150473", "pos_cid": 52073652, "source": "train_step3"}
{"query_id": "scaleup_24955439_23430673", "query": "How to improve traffic management decision reliability while reducing computation time", "pos": ["Conditional Support-Vector-Machine-Based Shared Adaptive Computing Model for Smart City Traffic Management. Smart connected vehicles are becoming standardized with the incorporation of information and communication technology. Connected vehicles are employed for surveillance and management of road traffic, navigation assistance, etc., by inheriting different analytical and communication techniques. With the Social Internet of Things (SIoT), interogrowthperable and shared computing models are adopted by the connected vehicles to perform application-specific decisions. By considering the need for computation models in smart connected vehicle networks, this article introduces a shared adaptive computing model (SACM) for improving the reliability of vehicle control and traffic management. This computing model considers multiple features of the in-range vehicles in detecting traffic and providing guided solutions for reliable routing in a smart city environment. This computing model is aided by the conditional support vector machine (SVM) for differentiating the complexity of multiflow data processing from the neighboring vehicles. The physical and connectivity-based factors from the smart vehicle using SVM classification learning improve the decision reliability and reduce the computing time and complexity."], "field": "Engineering", "q_year": 2022, "q_cid": "249554391", "pos_cid": 234306734, "source": "train_step3"}
{"query_id": "scaleup_28042188_12542391", "query": "How to compare two-stage and single-stage pose estimation performance when image quality degrades", "pos": ["Benchmarking Neural Network Robustness to Common Corruptions and Surface Variations. In this paper we establish rigorous benchmarks for image classifier robustness. Our first benchmark, ImageNet-C, standardizes and expands the corruption robustness topic, while showing which classifiers are preferable in safety-critical applications. Unlike recent robustness research, this benchmark evaluates performance on commonplace corruptions not worst-case adversarial corruptions. We find that there are negligible changes in relative corruption robustness from AlexNet to ResNet classifiers, and we discover ways to enhance corruption robustness. Then we propose a new dataset called Icons-50 which opens research on a new kind of robustness, surface variation robustness. With this dataset we evaluate the frailty of classifiers on new styles of known objects and unexpected instances of known classes. We also demonstrate two methods that improve surface variation robustness. Together our benchmarks may aid future work toward networks that learn fundamental class structure and also robustly generalize."], "field": "Engineering", "q_year": 2025, "q_cid": "280421889", "pos_cid": 125423918, "source": "train_step3"}
{"query_id": "scaleup_26455110_41442380", "query": "How to update system states despite bad measurement data and uncertain measurement-noise covariance without further reducing measurement redundancy", "pos": ["A Novel Adaptive Kalman Filter With Inaccurate Process and Measurement Noise Covariance Matrices. In this paper, a novel variational Bayesian (VB)-based adaptive Kalman filter (VBAKF) for linear Gaussian state-space models with inaccurate process and measurement noise covariance matrices is proposed. By choosing inverse Wishart priors, the state together with the predicted error and measurement noise covariance matrices are inferred based on the VB approach. Simulation results for a target tracking example illustrate that the proposed VBAKF has better robustness to resist the uncertainties of process and measurement noise covariance matrices than existing state-of-the-art filters."], "field": "Engineering", "q_year": 2024, "q_cid": "264551109", "pos_cid": 41442380, "source": "train_step3"}
{"query_id": "scaleup_28363068_62782910", "query": "How to recover embedded glass fibers from wind turbine blade waste containing a crosslinked polyester matrix", "pos": ["Recent Developments in the Chemical Recycling of PET. Poly(ethylene terephthalate), more commonly known as PET in the packaging industry and generally referred to as ‘polyester‘ in the textile industry, is an indispensable material with immense applications owing to its excellent physical and chemical properties. On the other hand, due to its increasing consumption and non-biodegradability, PET waste disposal has created serious environmental and economic concerns. Thus, management of PET waste has become an important social issue. In view of the increasing environmental awareness in the society, recycling remains the most viable option for the treatment of waste PET. Among the various methods of PET recycling (primary or ‘in-plant’, secondary or mechanical, tertiary or chemical, quaternary involving energy recovery), only chemical recycling conforms to the principles of sustainable development because it leads to the formation of the raw materials from which PET is originally made. Chemical recycling utilizes processes such as hydrolysis, methanolysis, glycloysis, ammonolysis and aminolysis. In a large collection of researches for the chemical recycling of PET, the primary objective is to increase the monomer yield while reducing the reaction time and/or carrying out the reaction under mild conditions. Continuous efforts of researchers have brought great improvements in the chemical recycling processes. This paper reviews methods for the chemical recycling of PET with special emphasis on glycolytic depolymerization with ethylene glycol. It covers the researches, including the works by the authors, on various processes and introduces recent developments to increase monomer yield. Processes including suband supercritical, catalytic, and microwave-assisted depolymerization are discussed. This paper also presents the impact of the new technologies such as nanotechnology on the future developments in the chemical recycling of PET."], "field": "Engineering", "q_year": 2025, "q_cid": "283630687", "pos_cid": 62782910, "source": "train_step3"}
{"query_id": "scaleup_27923228_16973894", "query": "How to balance network operators’ revenue with users’ quality of service and fairness requirements in bandwidth pricing under varying network conditions and visual-data demands, including compression, latency sensitivity, and content priority", "pos": ["Optimal Pricing for Spectrum Allocation in Cognitive Radio Networks. In this paper, we investigate the problem of spectrum allocation in Cognitive Radio Networks (CRNs) where a primary user (PU) leases its idle spectrums to a number of secondary users (SUs) who may have different willing to pay for these spectrums. For the PU, its main objective is to gain profit from selling the idle spectrums, and from the perspective of the Sus, they aim to maximize their utility from using spectrums. We model the interaction between the PU and SUs as a two-stage Stackelberg game, where the PU sets the prices for its spectrum in the first stage, and SUs make their spectrum demands decisions in the second stage. We use the backward induction method to solve this game. The numerical results show that the proposed solution method can increase revenue of the PU compared with the uniform pricing scheme."], "field": "Engineering", "q_year": 2025, "q_cid": "279232286", "pos_cid": 169738942, "source": "train_step3"}
{"query_id": "scaleup_28259224_3292002", "query": "How to infer motion hierarchies from data with unknown parent–child dependencies, determining relevant neighboring motion elements and their influence strengths while generalizing across tasks", "pos": ["Graph Attention Networks. We present graph attention networks (GATs), novel neural network architectures that operate on graph-structured data, leveraging masked self-attentional layers to address the shortcomings of prior methods based on graph convolutions or their approximations. By stacking layers in which nodes are able to attend over their neighborhoods' features, we enable (implicitly) specifying different weights to different nodes in a neighborhood, without requiring any kind of costly matrix operation (such as inversion) or depending on knowing the graph structure upfront. In this way, we address several key challenges of spectral-based graph neural networks simultaneously, and make our model readily applicable to inductive as well as transductive problems. Our GAT models have achieved or matched state-of-the-art results across four established transductive and inductive graph benchmarks: the Cora, Citeseer and Pubmed citation network datasets, as well as a protein-protein interaction dataset (wherein test graphs remain unseen during training)."], "field": "Engineering", "q_year": 2025, "q_cid": "282592241", "pos_cid": 3292002, "source": "train_step3"}
{"query_id": "scaleup_24555149_28894554", "query": "How to determine which nanoscale surface features influence stem-cell self-renewal and differentiation", "pos": ["Nanotopography Influences Adhesion, Spreading, and Self-renewal of Human Embryonic Stem Cells. Human embryonic stem cells (hESCs) have great potentials for future cell-based therapeutics. However, their mechanosensitivity to biophysical signals from the cellular microenvironment is not well characterized. Here we introduced an effective microfabrication strategy for accurate control and patterning of nanoroughness on glass surfaces. Our results demonstrated that nanotopography could provide a potent regulatory signal over different hESC behaviors, including cell morphology, adhesion, proliferation, clonal expansion, and self-renewal. Our results indicated that topological sensing of hESCs might include feedback regulation involving mechanosensory integrin-mediated cell-matrix adhesion, myosin II, and E-cadherin. Our results also demonstrated that cellular responses to nanotopography were cell-type specific and as such, we could generate a spatially segregated co-culture system for hESCs and NIH/3T3 fibroblasts using patterned nanorough glass surfaces."], "field": "Engineering", "q_year": 2021, "q_cid": "245551497", "pos_cid": 28894554, "source": "train_step3"}
{"query_id": "scaleup_26969224_5442606", "query": "How to achieve strong, durable adhesion of hydrogel coatings to nonporous substrates for long-term protection under diverse underwater conditions, including harsh marine environments?", "pos": ["Tough Bonding of Hydrogels to Diverse Nonporous Surfaces. In many animals, the bonding of tendon and cartilage to bone is extremely tough (for example, interfacial toughness ∼800 J m(-2); refs ,), yet such tough interfaces have not been achieved between synthetic hydrogels and non-porous surfaces of engineered solids. Here, we report a strategy to design tough transparent and conductive bonding of synthetic hydrogels containing 90% water to non-porous surfaces of diverse solids, including glass, silicon, ceramics, titanium and aluminium. The design strategy is to anchor the long-chain polymer networks of tough hydrogels covalently to non-porous solid surfaces, which can be achieved by the silanation of such surfaces. Compared with physical interactions, the chemical anchorage results in a higher intrinsic work of adhesion and in significant energy dissipation of bulk hydrogel during detachment, which lead to interfacial toughness values over 1,000 J m(-2). We also demonstrate applications of robust hydrogel-solid hybrids, including hydrogel superglues, mechanically protective hydrogel coatings, hydrogel joints for robotic structures and robust hydrogel-metal conductors."], "field": "Engineering", "q_year": 2024, "q_cid": "269692241", "pos_cid": 5442606, "source": "train_step3"}
{"query_id": "scaleup_21138750_3833089", "query": "How to distinguish spatial clusters, atypical locations, and patterns of association in uneven ecological conditions across a heritage site", "pos": ["Spatial-temporal patterns of PM2.5 concentrations for 338 Chinese cities.. Air pollution has become a major concern in cities worldwide. The present study explores the spatial-temporal patterns of PM2.5 (particles with an aerodynamic diameters ≤2.5μm) and the variation in the attainment rate (the number of cities attaining the national PM2.5 standard each day) at different time-scales based on PM2.5 concentrations. One-year of monitoring was conducted in 338 cities at or above the prefectural level in China. Spatial hot spots of PM2.5 were analyzed using exploratory spatial data analysis. Meteorological factors affecting PM2.5 distributions were analyzed. The results indicate the following: (1) Diurnal variations of PM2.5 exhibited a W-shaped trend, with the lowest value observed in the afternoon. The peak concentrations occurred after the ends of the morning and evening rush hours. (2) Out of 338 cities, 235 exceeded the national annual PM2.5 standards (≤35μg/m3), with slightly polluted (75-115μg/m3) cities occupying the greatest proportion. (3) The attainment rate showed an inverted U-shape, while there was a U-shaped pattern observed for daily and monthly mean PM2.5. (4) The spatial distribution of PM2.5 concentrations varied greatly, PM2.5 has significant spatial autocorrelation and clustering characteristics. Hot spots for pollution were mainly concentrated in the Beijing-Tianjin-Hebei area and neighboring regions, in part because of the large amount of smoke and dust emissions in this region. However, weather factors (temperature, humidity, and wind speed) also had an effect. In addition, southwest Xinjiang experienced heavy PM2.5 pollution that was mainly caused by the frequent occurrence of sandstorms, although no significant relationship was observed between PM2.5 and meteorological elements in this region."], "field": "Environmental Science", "q_year": 2019, "q_cid": "211387502", "pos_cid": 3833089, "source": "eval20x26"}
{"query_id": "scaleup_1261495_7555200", "query": "How to determine whether sampling solutions compromise genetic amplification and subsequent genetic identification in ways not reflected in dna yield or apparent quality", "pos": ["Mutation spectrum of copper-induced DNA damage.. The ability of metal ions to damage DNA and cause mutagenesis has been analyzed with reversion and forward mutation assays using single-stranded DNA templates. We previously reported that incubation of phi X174 am3 DNA with Fe2+ in vitro results in mutagenesis when the treated DNA is transfected into Escherichia coli spheroplasts (Loeb, L. A., James, E. A., Waltersdorph, A. M., and Klebanoff, S. J. (1988) Proc. Natl. Acad. Sci. U.S.A. 85, 3918-3922, 1988). We now extend these studies to other metal ions. Of the metal ions tested, copper ions were the most mutagenic; the frequency of mutants produced was equal to or greater than that produced by Fe2+. Mutagenesis by Cu+ was diminished by catalase, mannitol, and superoxide dismutase suggesting the involvement of H2O2, hydroxyl ions, and superoxide, respectively. However, the findings that Cu+ and Cu2+ are nearly equally mutagenic and that the mutagenic activities are not completely inhibited by oxygen free radical scavengers make it unlikely that the mechanism for mutagenesis is simply the production of hydroxyl free radicals. The spectra of mutations produced by either copper ion using the lacZ gene as a target are very similar and differ from those reported with other agents. The predominant mutagenic sequence changes are single-base substitutions, the most frequent being replacement of a template C by a T. This transition presumably results from mispairing of an altered C with deoxyadenosine. Copper-induced mutations are not randomly distributed. Instead, they are found predominantly in clusters suggesting direct interaction of copper ions with specific nucleotide sequences in DNA. Evidence is considered that the high frequency of C----T transitions may be a common manifestation of DNA damage by oxygen radicals."], "field": "Environmental Science", "q_year": 2016, "q_cid": "1261495", "pos_cid": 7555200, "source": "eval20x26"}
{"query_id": "scaleup_3865954_20537748", "query": "How to characterize T. circumcincta larval antigens, particularly those associated with immune suppression, and their interactions with host immunity to assess their suitability as protective vaccine targets", "pos": ["A macrophage migration inhibitory factor-like tautomerase from Teladorsagia circumcincta (Nematoda: Strongylida). A macrophage migration inhibitory factor (MIF)‐like molecule, Tci‐MIF‐1, was isolated from Teladorsagia circumcincta and subjected to detailed characterization. A cDNA representing Tci‐mif‐1 was isolated following its identification in third‐stage larvae (L3)‐enriched cDNA population. Sequencing of the cDNA indicated a 348‐bp open reading frame (ORF) with the closest orthologue being a MIF derived from the human hookworm Ancylostoma ceylanicum. Messenger RNA (mRNA) representing the Tci‐MIF‐1 transcript was detected in eggs, L3 and adult stages of T. circumcincta. The transcript was also present, but to a lesser extent in fourth‐stage larvae (L4). Detection of Tci‐MIF‐1 protein in T. circumcincta developmental stages reflected the transcript levels identified by reverse transcriptase‐PCR. Using immunohistochemistry, the Tci‐MIF‐1 protein was shown to have a diffuse distribution in L3 tissue, and in L4 and adult stages, the protein was localized to the nematode gut. A recombinant version of Tci‐MIF‐1 was produced, and enzymic assays indicated that this recombinant protein and a somatic extract of L3 possessed dopachrome tautomerase activity as has been observed previously in other MIF‐like molecules. Neither native, purified Tci‐MIF nor recombinant Tci‐MIF‐1 dramatically influenced the in vitro migration of sheep monocytes."], "field": "Environmental Science", "q_year": 2018, "q_cid": "3865954", "pos_cid": 205377480, "source": "eval20x26"}
{"query_id": "scaleup_17875277_5765186", "query": "How to explain disrupted and masculinized reproductive development following early perchlorate exposure", "pos": ["Sex Reversal in Zebrafish fancl Mutants Is Caused by Tp53-Mediated Germ Cell Apoptosis. The molecular genetic mechanisms of sex determination are not known for most vertebrates, including zebrafish. We identified a mutation in the zebrafish fancl gene that causes homozygous mutants to develop as fertile males due to female-to-male sex reversal. Fancl is a member of the Fanconi Anemia/BRCA DNA repair pathway. Experiments showed that zebrafish fancl was expressed in developing germ cells in bipotential gonads at the critical time of sexual fate determination. Caspase-3 immunoassays revealed increased germ cell apoptosis in fancl mutants that compromised oocyte survival. In the absence of oocytes surviving through meiosis, somatic cells of mutant gonads did not maintain expression of the ovary gene cyp19a1a and did not down-regulate expression of the early testis gene amh; consequently, gonads masculinized and became testes. Remarkably, results showed that the introduction of a tp53 (p53) mutation into fancl mutants rescued the sex-reversal phenotype by reducing germ cell apoptosis and, thus, allowed fancl mutants to become fertile females. Our results show that Fancl function is not essential for spermatogonia and oogonia to become sperm or mature oocytes, but instead suggest that Fancl function is involved in the survival of developing oocytes through meiosis. This work reveals that Tp53-mediated germ cell apoptosis induces sex reversal after the mutation of a DNA–repair pathway gene by compromising the survival of oocytes and suggests the existence of an oocyte-derived signal that biases gonad fate towards the female developmental pathway and thereby controls zebrafish sex determination."], "field": "Environmental Science", "q_year": 2016, "q_cid": "17875277", "pos_cid": 5765186, "source": "eval20x26"}
{"query_id": "scaleup_2150399_26779040", "query": "How to distinguish genuine differences between two samples from biases caused by highly abundant components dominating counts and obscuring less abundant components", "pos": ["A scaling normalization method for differential expression analysis of RNA-seq data. The fine detail provided by sequencing-based transcriptome surveys suggests that RNA-seq is likely to become the platform of choice for interrogating steady state RNA. In order to discover biologically important changes in expression, we show that normalization continues to be an essential step in the analysis. We outline a simple and effective method for performing normalization and show dramatically improved results for inferring differential expression in simulated and publicly available data sets."], "field": "Environmental Science", "q_year": 2015, "q_cid": "2150399", "pos_cid": 267790402, "source": "eval20x26"}
{"query_id": "scaleup_6598661_17977055", "query": "How to obtain ecological results that are reproducible across laboratories under stringently controlled experimental conditions", "pos": ["Effect of Population Heterogenization on the Reproducibility of Mouse Behavior: A Multi-Laboratory Study. In animal experiments, animals, husbandry and test procedures are traditionally standardized to maximize test sensitivity and minimize animal use, assuming that this will also guarantee reproducibility. However, by reducing within-experiment variation, standardization may limit inference to the specific experimental conditions. Indeed, we have recently shown in mice that standardization may generate spurious results in behavioral tests, accounting for poor reproducibility, and that this can be avoided by population heterogenization through systematic variation of experimental conditions. Here, we examined whether a simple form of heterogenization effectively improves reproducibility of test results in a multi-laboratory situation. Each of six laboratories independently ordered 64 female mice of two inbred strains (C57BL/6NCrl, DBA/2NCrl) and examined them for strain differences in five commonly used behavioral tests under two different experimental designs. In the standardized design, experimental conditions were standardized as much as possible in each laboratory, while they were systematically varied with respect to the animals' test age and cage enrichment in the heterogenized design. Although heterogenization tended to improve reproducibility by increasing within-experiment variation relative to between-experiment variation, the effect was too weak to account for the large variation between laboratories. However, our findings confirm the potential of systematic heterogenization for improving reproducibility of animal experiments and highlight the need for effective and practicable heterogenization strategies."], "field": "Environmental Science", "q_year": 2016, "q_cid": "6598661", "pos_cid": 17977055, "source": "eval20x26"}
{"query_id": "scaleup_26875301_24641138", "query": "How to identify a minimal set of streamflow features that retain catchment landscape information without meteorological forcing or noise and, together with meteorological drivers, contain enough information to reconstruct the full streamflow time series", "pos": ["Learning Summary Statistics for Bayesian Inference with Autoencoders. For stochastic models with intractable likelihood functions, approximate Bayesian computation offers a way of approximating the true posterior through repeated comparisons of observations with simulated model outputs in terms of a small set of summary statistics. These statistics need to retain the information that is relevant for constraining the parameters but cancel out the noise. They can thus be seen as thermodynamic state variables, for general stochastic models. For many scientific applications, we need strictly more summary statistics than model parameters to reach a satisfactory approximation of the posterior. Therefore, we propose to use a latent representation of deep neural networks based on Autoencoders as summary statistics. To create an incentive for the encoder to encode all the parameter-related information but not the noise, we give the decoder access to explicit or implicit information on the noise that has been used to generate the training data. We validate the approach empirically on two types of stochastic models."], "field": "Environmental Science", "q_year": 2024, "q_cid": "268753018", "pos_cid": 246411381, "source": "eval_collection"}
{"query_id": "scaleup_26960277_52952069", "query": "How to assess whether arrangements supporting low trophic mariculture expansion are effective, equitable, responsive, and robust", "pos": ["Environmental governance: A practical framework to guide design, evaluation, and analysis. Governance is one of the most important factors for ensuring effective environmental management and conservation actions. Yet, there is still a relative paucity of comprehensive and practicable guidance that can be used to frame the evaluation, design, and analysis of systems of environmental governance. This conceptual review and synthesis article seeks to addresses this problem through resituating the broad body of governance literature into a practical framework for environmental governance. Our framework builds on a rich history of governance scholarship to propose that environmental governance has four general aims or objectives – to be effective, to be equitable, to be responsive, and to be robust. Each of these four objectives need to be considered simultaneously across the institutional, structural, and procedural elements of environmental governance. Through a review of the literature, we developed a set of attributes for each of these objectives and relate these to the overall capacity, functioning, and performance of environmental governance. Our aim is to provide a practical and adaptable framework that can be applied to the design, evaluation, and analysis of environmental governance in different social and political contexts, to diverse environmental problems and modes of governance, and at a range of scales."], "field": "Environmental Science", "q_year": 2024, "q_cid": "269602777", "pos_cid": 52952069, "source": "eval_collection"}
{"query_id": "scaleup_27672768_21853805", "query": "How to recover multispectral information from ordinary drone color images for field vegetation segmentation without dedicated spectral acquisition equipment", "pos": ["NTIRE 2020 Challenge on Spectral Reconstruction from an RGB Image. This paper reviews the second challenge on spectral reconstruction from RGB images, i.e., the recovery of whole- scene hyperspectral (HS) information from a 3-channel RGB image. As in the previous challenge, two tracks were provided: (i) a \"Clean\" track where HS images are estimated from noise-free RGBs, the RGB images are themselves calculated numerically using the ground-truth HS images and supplied spectral sensitivity functions (ii) a \"Real World\" track, simulating capture by an uncalibrated and unknown camera, where the HS images are recovered from noisy JPEG-compressed RGB images. A new, larger-than-ever, natural hyperspectral image data set is presented, containing a total of 510 HS images. The Clean and Real World tracks had 103 and 78 registered participants respectively, with 14 teams competing in the final testing phase. A description of the proposed methods, alongside their challenge scores and an extensive evaluation of top performing methods is also provided. They gauge the state-of-the-art in spectral reconstruction from an RGB image."], "field": "Environmental Science", "q_year": 2025, "q_cid": "276727689", "pos_cid": 218538055, "source": "eval_collection"}
{"query_id": "scaleup_26890084_52048869", "query": "How to distinguish individual component associations from the overall mixture’s association with trajectory parameters while accounting for the other components and characterizing uncertainty in these associations", "pos": ["Statistical software for analyzing the health effects of multiple concurrent exposures via Bayesian kernel machine regression. BackgroundEstimating the health effects of multi-pollutant mixtures is of increasing interest in environmental epidemiology. Recently, a new approach for estimating the health effects of mixtures, Bayesian kernel machine regression (BKMR), has been developed. This method estimates the multivariable exposure-response function in a flexible and parsimonious way, conducts variable selection on the (potentially high-dimensional) vector of exposures, and allows for a grouped variable selection approach that can accommodate highly correlated exposures. However, the application of this novel method has been limited by a lack of available software, the need to derive interpretable output in a computationally efficient manner, and the inability to apply the method to non-continuous outcome variables.MethodsThis paper addresses these limitations by (i) introducing an open-source software package in the R programming language, the bkmr R package, (ii) demonstrating methods for visualizing high-dimensional exposure-response functions, and for estimating scientifically relevant summaries, (iii) illustrating a probit regression implementation of BKMR for binary outcomes, and (iv) describing a fast version of BKMR that utilizes a Gaussian predictive process approach. All of the methods are illustrated using fully reproducible examples with the provided R code.ResultsApplying the methods to a continuous outcome example illustrated the ability of the BKMR implementation to estimate the health effects of multi-pollutant mixtures in the context of a highly nonlinear, biologically-based dose-response function, and to estimate overall, single-exposure, and interactive health effects. The Gaussian predictive process method led to a substantial reduction in the runtime, without a major decrease in accuracy. In the setting of a larger number of exposures and a dichotomous outcome, the probit BKMR implementation was able to correctly identify the variables included in the exposure-response function and yielded interpretable quantities on the scale of a latent continuous outcome or on the scale of the outcome probability.ConclusionsThis newly developed software, integrated suite of tools, and extended methodology makes BKMR accessible for use across a broad range of epidemiological applications in which multiple risk factors have complex effects on health."], "field": "Environmental Science", "q_year": 2024, "q_cid": "268900847", "pos_cid": 52048869, "source": "eval_collection"}
{"query_id": "scaleup_21479030_20116499", "query": "How to establish whether the RIH Tool consistently assesses the same health innovations across different raters for fulfillment of responsible innovation requirements", "pos": ["Principles and methods of validity and reliability testing of questionnaires used in social and health science researches. The importance of measuring the accuracy and consistency of research instruments (especially questionnaires) known as validity and reliability, respectively, have been documented in several studies, but their measure is not commonly carried out among health and social science researchers in developing countries. This has been linked to the dearth of knowledge of these tests. This is a review article which comprehensively explores and describes the validity and reliability of a research instrument (with special reference to questionnaire). It further discusses various forms of validity and reliability tests with concise examples and finally explains various methods of analysing these tests with scientific principles guiding such analysis."], "field": "Environmental Science", "q_year": 2020, "q_cid": "214790301", "pos_cid": 20116499, "source": "eval_collection"}
{"query_id": "scaleup_22525332_91865577", "query": "How to reliably measure household energy-source diversity and validly capture differences across households and family groups with varying energy-use patterns and income levels", "pos": ["Measuring species diversity in the tropics: a review of methodological approaches and framework for future studies. The analysis of species diversity has benefited from multiple methodological approaches that are changing not only the way we measure biodiversity, but also our general conceptualization of it. We review the concepts and methods for measuring species diversity, including a report on how species diversity has been measured in tropical ecosystems, and summarize current methodological approaches that can be used to achieve more comprehensive analyses of species diversity. We reviewed papers dealing with species diversity published in Biotropica over the last 28 yr. Most of the studies were carried out in the Neotropics. The most popular methods for reporting alpha diversity were species accumulation curves, rarefaction curves, and the Shannon–Wiener index, while beta diversity assessments mainly relied on the Sørensen, Jaccard or Bray–Curtis indices. We offer a general framework for comprehensive biodiversity assessments that includes the alpha and beta components, and taxonomic, functional, and phylogenetic dimensions. We briefly describe the conceptual background, relevant methods, and examples of the components, and dimensions described in this framework. To improve our knowledge of tropical biodiversity and its regulatory processes, we encourage researchers to carry out more complete assessments, and to take advantage of the wide variety of methods available; methods that are perhaps especially useful in human‐disturbed and human‐managed landscapes."], "field": "Environmental Science", "q_year": 2020, "q_cid": "225253328", "pos_cid": 91865577, "source": "eval_collection"}
{"query_id": "scaleup_22118826_19581386", "query": "How to expand awareness and adoption of consumer actions beyond individuals across people and community groups", "pos": ["Improving Environmental Interventions by Understanding Information Flows.. Conservationists are increasingly interested in changing human behaviour. One understudied aspect of such interventions is information flow. Different patterns of interpersonal communication and social structures within communities influence the adoption of behavioural changes through social influence and social reinforcement. Understanding the structure of information flow in a group, using tools such as social network analysis, can therefore offer important insights for interventions. For example, communications may be targeted to highly connected opinion leaders to leverage their influence, or communication may be facilitated between distinct subgroups to promote peer learning. Incorporating these approaches into conservation interventions can promote more effective behaviour change. This review introduces conservation researchers and practitioners to key concepts underpinning information flows for interventions targeting networks of individuals."], "field": "Environmental Science", "q_year": 2020, "q_cid": "221188265", "pos_cid": 195813866, "source": "eval_collection"}
{"query_id": "scaleup_26861830_255583", "query": "How to obtain consistent results across laboratories despite differences in their underlying environments", "pos": ["An introduction to Docker for reproducible research. As computational work becomes more and more integral to many aspects of scientific research, computational reproducibility has become an issue of increasing importance to computer systems researchers and domain scientists alike. Though computational reproducibility seems more straight forward than replicating physical experiments, the complex and rapidly changing nature of computer environments makes being able to reproduce and extend such work a serious challenge. In this paper, I explore common reasons that code developed for one research project cannot be successfully executed or extended by subsequent researchers. I review current approaches to these issues, including virtual machines and workflow systems, and their limitations. I then examine how the popular emerging technology Docker combines several areas from systems research - such as operating system virtualization, cross-platform portability, modular re-usable elements, versioning, and a 'DevOps' philosophy, to address these challenges. I illustrate this with several examples of Docker use with a focus on the R statistical environment."], "field": "Environmental Science", "q_year": 2024, "q_cid": "268618305", "pos_cid": 255583, "source": "eval_collection"}
{"query_id": "scaleup_27056289_25829882", "query": "How to assess the usefulness of a large collection of unlabelled insect dna barcodes for tasks beyond species- and genus-level identification", "pos": ["A Cookbook of Self-Supervised Learning. Self-supervised learning, dubbed the dark matter of intelligence, is a promising path to advance machine learning. Yet, much like cooking, training SSL methods is a delicate art with a high barrier to entry. While many components are familiar, successfully training a SSL method involves a dizzying set of choices from the pretext tasks to training hyper-parameters. Our goal is to lower the barrier to entry into SSL research by laying the foundations and latest SSL recipes in the style of a cookbook. We hope to empower the curious researcher to navigate the terrain of methods, understand the role of the various knobs, and gain the know-how required to explore how delicious SSL can be."], "field": "Environmental Science", "q_year": 2024, "q_cid": "270562895", "pos_cid": 258298825, "source": "eval_collection"}
{"query_id": "scaleup_25614486_4943877", "query": "How to estimate energy consumption per sample on each battery-powered sensor and assess how assigned workloads affect system lifetime under limited energy resources", "pos": ["Minimum energy quantized neural networks. This work targets the automated minimum-energy optimization of Quantized Neural Networks (QNNs) — networks using low precision weights and activations. These networks are trained from scratch at an arbitrary fixed point precision. At iso-accuracy, QNNs using fewer bits require deeper and wider network architectures than networks using higher precision operators, while they require less complex arithmetic and less bits per weights. This fundamental trade-off is analyzed and quantified to find the minimum energy QNN for any benchmark and hence optimize energy-efficiency. To this end, the energy consumption of inference is modeled for a generic hardware platform. This allows drawing several conclusions across different benchmarks. First, energy consumption varies orders of magnitude at iso-accuracy depending on the number of bits used in the QNN. Second, in a typical system, BinaryNets or int4 implementations lead to the minimum energy solution, outperforming int8 networks up to 2–10× at iso-accuracy. All code used for QNN training is available from https://github.com/BertMoons/."], "field": "Environmental Science", "q_year": 2024, "q_cid": "256144860", "pos_cid": 4943877, "source": "eval_collection"}
{"query_id": "scaleup_28081502_53409389", "query": "How to account for the effects of solid boulders and bed spheres on fluid flow while satisfying boundary conditions at their curved surfaces", "pos": ["An immersed boundary method with direct forcing for the simulation of particulate flows. We present an improved method for computing incompressible viscous flow around suspended rigid particles using a fixed and uniform computational grid. The main idea is to incorporate Peskin's regularized delta function approach [Acta Numerica 11 (2002) 1] into a direct formulation of the fluid-solid interaction force in order to allow for a smooth transfer between Eulerian and Lagrangian representations while at the same time avoiding strong restrictions of the time step. This technique was implemented in a finite-difference and fractional-step context. A variety of two- and three-dimensional simulations are presented, ranging from the flow around a single cylinder to the sedimentation of 1000 spherical particles. The accuracy and efficiency of the current method are clearly demonstrated."], "field": "Environmental Science", "q_year": 2025, "q_cid": "280815023", "pos_cid": 53409389, "source": "eval_collection"}
{"query_id": "scaleup_21012286_54174614", "query": "How to explain conflicts over ocean overuse and control and why expanding conservation-related tourism can yield little benefit for local households", "pos": ["Environmental fixes and historical trajectories of marine resource use in Southeast Asia. This paper emphasises the long-term historical trajectories of marine resource use in the Philippines through an examination of successive environmental fixes. Based on fieldwork from coastal Mindoro province, the paper shows how the technological intensification and geographical expansion of fisheries, the development of aquaculture and the promotion of tourism represent three forms of environmental fixes that aim to address the problems caused by marine resource declines and subsequent lack of availability of means of production. All three fixes have struggled to reduce environmental pressure or provide a long-term basis for livelihoods. The paper argues that viewing how successive types of environmental fixes unfold over long periods of time highlights how marine resource declines are part of much wider economic and historical processes, with consequent implications for livelihoods and governance."], "field": "Environmental Science", "q_year": 2020, "q_cid": "210122861", "pos_cid": 54174614, "source": "eval_collection"}
{"query_id": "scaleup_23167741_18376389", "query": "How to reliably assess prenatal anti-androgen exposure in infants despite size and measurement-boundary limitations and establish the assessment’s relevance to later reproductive function", "pos": ["Anogenital Distance and Penile Length in Infants with Hypospadias or Cryptorchidism: Comparison with Normative Data. Background: Anogenital distance (AGD) in animals is a sensitive biomarker of fetal endocrine disruption and the associated testicular dysgenesis syndrome (TDS). However, AGD in human infants with cryptorchidism and hypospadias, which are potential manifestations of TDS during childhood, is not clearly described. Objective: Our aim was to compare AGD in boys with cryptorchidism or hypospadias against normative data. Methods: Boys with isolated cryptorchidism (n = 71, age 13.4 ± 5.8 months) or hypospadias (n = 81, age 11.4 ± 6.2 months) were recruited from a tertiary center for measurement of AGD and penile length; they were compared with 487 healthy full-term boys from a birth cohort by deriving age-specific standard deviation scores (SDS). Results: Boys with cryptorchidism were older (p = 0.048) compared with boys with hypospadias. Boys with hypospadias had shorter mean AGD and penile length SDS than healthy boys (both p < 0.0001). Mean AGD and penile length SDS values in boys with cryptorchidism were longer than mean values in boys with hypospadias (both p < 0.01) and shorter than mean values in healthy boys (both p < 0.0001). Mean penile length SDS decreased as the severity of hypospadias increased (ptrend = 0.078). Conclusions: In the study population, AGD and penile length were reduced in boys with hypospadias or cryptorchidism relative to normative data derived from a longitudinal birth cohort. The findings support the use of AGD as a quantitative biomarker to examine the prenatal effects of exposure to endocrine disruptors on the development of the male reproductive tract. Citation: Thankamony A, Lek N, Carroll D, Williams M, Dunger DB, Acerini CL, Ong KK, Hughes IA. 2014. Anogenital distance and penile length in infants with hypospadias or cryptorchidism: comparison with normative data. Environ Health Perspect 122:207–211; http://dx.doi.org/10.1289/ehp.1307178"], "field": "Environmental Science", "q_year": 2021, "q_cid": "231677414", "pos_cid": 18376389, "source": "eval_collection"}
{"query_id": "scaleup_26083533_8678472", "query": "How to assess foliar fertilizer efficacy when evidence of uptake and assimilation is insufficient and leaf traits and material size may limit uptake", "pos": ["Interaction of Nanomaterials with Plants: What Do We Need for Real Applications in Agriculture?. The number of published researching works related with applications of nanomaterials in agriculture is increasing every year. Most of such works focus on the synthesis of nanodevices, their characteristics as nanocarriers for controlled release of active substances, and their interaction (either positive or negative) with plants or microorganisms under controlled conditions. Important knowledge has been gained about the uptake and distribution of nanomaterials in plants, although there are still gaps regarding internalization inside plant cells. Nanoparticle traits and plant species greatly affect the interaction, and nanodevices can enter and move through different pathways (apoplast vs. symplast), what influences their effectiveness and their final fate. Depending on the effect we are expecting for a nanocarrier, the application method might be critical. However, in order to get that research used in the field, some problems must be addressed. First, the cost for escalating the production of nanodevices must be affordable with the current production cost of agricultural goods. Second, we need to be sure that a technology is safe before spreading it into the environment. Third, consumers will distrust a technology unfamiliar for them in the same way that happened with transgenic crops. We need to broaden our horizons and start looking for real practical approaches, filling the main gaps that hamper our jump from laboratory research into field applications."], "field": "Environmental Science", "q_year": 2023, "q_cid": "260835335", "pos_cid": 8678472, "source": "eval_collection"}
{"query_id": "scaleup_25318458_84493875", "query": "How to understand microplastic removal from the surface and transport to greater depths", "pos": ["The role of particulate carbohydrate exudates in the flocculation of diatom blooms. Diatom blooms are frequently terminated by mass aggregation of cells into large, rapidly sinking aggregates. It has been hypothesized that transparent exopolymer particles (TEP), abundant particles formed from the polysaccharides exuded by living cells, may be essential for this mass flocculation processes. We investigated the abundance of TEP and their role in the aggregation of diatoms in laboratory cultures and during a natural diatom bloom off California. TEP and dissolved carbohydrates accumulated appreciably over the growth cycle of Chaetoceros gracilis in the laboratory. The flocculation of C. gracilis in a laboratory flocculator was dominated by TEP, not cells, and large flocs, consisting predominantly of particulate polysaccharides, formed at a rate more than an order of magnitude higher than predicted by coagulation theory for cells alone. The frequency of interparticle attachment was three orders of magnitude higher for TEP than for cells. The pattern of flocculation of a natural diatom bloom was similar to that of laboratory cultures. Prior to bloom flocculation the abundance and total quantity of TEP and the concentration of particulate carbohydrates increased, while dissolved carbohydrate concentrations decreased. During the flocculation stage TEP aggregated into fewer, but much larger particles and concentrations of dissolved carbohydrates decreased further. The percentage of diatom cells which were attached to TEP increased during the flocculation period from 3 to 90% and TEP formed the matrix of all the natural diatom aggregates observed. During the late flocculation stage the quantity of TEP and TEP aggregates did not increase further and concentrations of diatoms decreased, presumably because large flocs sank out. Our findings indicate that TEP should be included in models of particle aggregation in the ocean. The abundance, large size and high sticking coefficient of TEP make them essential to the aggregation of diatom blooms. The extracellular release of polysaccharides by growing cells may be an adaptation for aggregation. The abiotic formation of particulate organic matter (TEP) from dissolved organic matter (DOC) may help to explain the extremely high turnover rates of DOC observed during blooms."], "field": "Environmental Science", "q_year": 2022, "q_cid": "253184581", "pos_cid": 84493875, "source": "eval_collection"}
{"query_id": "scaleup_25300196_23060348", "query": "How to accurately compare predictive performance for type 2 diabetes when cases are rare relative to non-cases and evaluation metrics may not adequately reflect performance under this imbalance", "pos": ["On selecting a probabilistic classifier for appointment no-show prediction. Abstract Appointment no-shows are disruptive to healthcare clinics, and may increase patient waiting time and clinic overtime, resulting in increased clinic costs. Appointment scheduling models typically mitigate the negative effects of no-shows through appointment overbooking. Recent work has proposed a predictive overbooking framework, where a probabilisitic classifier predicts the no-show probability of individual appointment requests, and a scheduling algorithm uses those predictions to optimally schedule appointments. Because predicting no-shows is typically an imbalanced classification problem, the preferred classifier is often chosen based upon the area under the receiver operator characteristic curve (AUC), which is a commonly used metric for many other imbalanced classification problems. Contrary to intuition, in this paper we show that employing the AUC to select a classifier results in significantly lower schedule efficiency than using other metrics such as Log Loss or Brier Score. Our computational experiments, validated on large real-world appointment data, suggest that by using Log Loss or Brier Score instead of AUC, practitioners can improve the schedule quality by 3–7%."], "field": "Environmental Science", "q_year": 2022, "q_cid": "253001969", "pos_cid": 230603482, "source": "eval_collection"}
{"query_id": "scaleup_26083533_22972001", "query": "How to scientifically validate fertilizer claims of improved nutrient uptake, reduced nutrient losses, enhanced plant stress tolerance, and environmental benefits despite missing product details and limited supporting evidence", "pos": ["Nano-Fertilization as an Emerging Fertilization Technique: Why Can Modern Agriculture Benefit from Its Use?. There is a need for a more innovative fertilizer approach that can increase the productivity of agricultural systems and be more environmentally friendly than synthetic fertilizers. In this article, we reviewed the recent development and potential benefits derived from the use of nanofertilizers (NFs) in modern agriculture. NFs have the potential to promote sustainable agriculture and increase overall crop productivity, mainly by increasing the nutrient use efficiency (NUE) of field and greenhouse crops. NFs can release their nutrients at a slow and steady pace, either when applied alone or in combination with synthetic or organic fertilizers. They can release their nutrients in 40–50 days, while synthetic fertilizers do the same in 4–10 days. Moreover, NFs can increase the tolerance of plants against biotic and abiotic stresses. Here, the advantages of NFs over synthetic fertilizers, as well as the different types of macro and micro NFs, are discussed in detail. Furthermore, the application of NFs in smart sustainable agriculture and the role of NFs in the mitigation of biotic and abiotic stress on plants is presented. Though NF applications may have many benefits for sustainable agriculture, there are some concerns related to the release of nanoparticles (NPs) from NFs into the environment, with the subsequent detrimental effects that this could have on both human and animal health. Future research should explore green synthesized and biosynthesized NFs, their safe use, bioavailability, and toxicity concerns."], "field": "Environmental Science", "q_year": 2023, "q_cid": "260835335", "pos_cid": 229720015, "source": "eval_collection"}
{"query_id": "scaleup_24568965_20127605", "query": "How to establish the risks of Korean school cooking fumes under short-term exposure or low average concentrations", "pos": ["Ambient Particulate Air Pollution and Daily Mortality in 652 Cities. BACKGROUND The systematic evaluation of the results of time-series studies of air pollution is challenged by differences in model specification and publication bias. METHODS We evaluated the associations of inhalable particulate matter (PM) with an aerodynamic diameter of 10 μm or less (PM10) and fine PM with an aerodynamic diameter of 2.5 μm or less (PM2.5) with daily all-cause, cardiovascular, and respiratory mortality across multiple countries or regions. Daily data on mortality and air pollution were collected from 652 cities in 24 countries or regions. We used overdispersed generalized additive models with random-effects meta-analysis to investigate the associations. Two-pollutant models were fitted to test the robustness of the associations. Concentration–response curves from each city were pooled to allow global estimates to be derived. RESULTS On average, an increase of 10 μg per cubic meter in the 2-day moving average of PM10 concentration, which represents the average over the current and previous day, was associated with increases of 0.44% (95% confidence interval [CI], 0.39 to 0.50) in daily all-cause mortality, 0.36% (95% CI, 0.30 to 0.43) in daily cardiovascular mortality, and 0.47% (95% CI, 0.35 to 0.58) in daily respiratory mortality. The corresponding increases in daily mortality for the same change in PM2.5 concentration were 0.68% (95% CI, 0.59 to 0.77), 0.55% (95% CI, 0.45 to 0.66), and 0.74% (95% CI, 0.53 to 0.95). These associations remained significant after adjustment for gaseous pollutants. Associations were stronger in locations with lower annual mean PM concentrations and higher annual mean temperatures. The pooled concentration–response curves showed a consistent increase in daily mortality with increasing PM concentration, with steeper slopes at lower PM concentrations. CONCLUSIONS Our data show independent associations between short-term exposure to PM10 and PM2.5 and daily all-cause, cardiovascular, and respiratory mortality in more than 600 cities across the globe. These data reinforce the evidence of a link between mortality and PM concentration established in regional and local studies. (Funded by the National Natural Science Foundation of China and others.)"], "field": "Environmental Science", "q_year": 2022, "q_cid": "245689654", "pos_cid": 201276053, "source": "eval_collection"}
{"query_id": "scaleup_21479030_2913866", "query": "How to consistently assess how closely different evaluators’ judgments match without unexpectedly low scores when most judgments match", "pos": ["A comparison of Cohen’s Kappa and Gwet’s AC1 when calculating inter-rater reliability coefficients: a study conducted with personality disorder samples. BackgroundRater agreement is important in clinical research, and Cohen’s Kappa is a widely used method for assessing inter-rater reliability; however, there are well documented statistical problems associated with the measure. In order to assess its utility, we evaluated it against Gwet’s AC1 and compared the results.MethodsThis study was carried out across 67 patients (56% males) aged 18 to 67, with a mean SD of 44.13 ± 12.68 years. Nine raters (7 psychiatrists, a psychiatry resident and a social worker) participated as interviewers, either for the first or the second interviews, which were held 4 to 6 weeks apart. The interviews were held in order to establish a personality disorder (PD) diagnosis using DSM-IV criteria. Cohen’s Kappa and Gwet’s AC1 were used and the level of agreement between raters was assessed in terms of a simple categorical diagnosis (i.e., the presence or absence of a disorder). Data were also compared with a previous analysis in order to evaluate the effects of trait prevalence.ResultsGwet’s AC1 was shown to have higher inter-rater reliability coefficients for all the PD criteria, ranging from .752 to 1.000, whereas Cohen’s Kappa ranged from 0 to 1.00. Cohen’s Kappa values were high and close to the percentage of agreement when the prevalence was high, whereas Gwet’s AC1 values appeared not to change much with a change in prevalence, but remained close to the percentage of agreement. For example a Schizoid sample revealed a mean Cohen’s Kappa of .726 and a Gwet’s AC1of .853 , which fell within the different level of agreement according to criteria developed by Landis and Koch, and Altman and Fleiss.ConclusionsBased on the different formulae used to calculate the level of chance-corrected agreement, Gwet’s AC1 was shown to provide a more stable inter-rater reliability coefficient than Cohen’s Kappa. It was also found to be less affected by prevalence and marginal probability than that of Cohen’s Kappa, and therefore should be considered for use with inter-rater reliability analysis."], "field": "Environmental Science", "q_year": 2020, "q_cid": "214790301", "pos_cid": 2913866, "source": "eval_collection"}
{"query_id": "scaleup_26540158_43862413", "query": "How to identify exposure–outcome associations in outcome-wide exposome analysis with many correlated exposures and interdependent health outcomes, including weak associations and exposures associated with multiple outcomes?", "pos": ["A regularized multivariate regression approach for eQTL analysis. Expression quantitative trait loci (eQTLs) are genomic loci that regulate expression levels of mRNAs or proteins. Understanding these regulatory provides important clues to biological pathways that underlie diseases. In this paper, we propose a new statistical method, GroupRemMap, for identifying eQTLs. We model the relationship between gene expression and single nucleotide variants (SNVs) through multivariate linear regression models, in which gene expression levels are responses and SNV genotypes are predictors. To handle the high dimensionality as well as to incorporate the intrinsic group structure of SNVs, we introduce a new regularization scheme to (1) control the overall sparsity of the model; (2) encourage the group selection of SNVs from the same gene; and (3) facilitate the detection of trans-hub-eQTLs. We apply the proposed method to the colorectal and breast cancer data sets from The Cancer Genome Atlas (TCGA), and identify several biologically interesting eQTLs. These findings may provide insight into biological processes associated with cancers and generate hypotheses for future studies."], "field": "Environmental Science", "q_year": 2023, "q_cid": "265401588", "pos_cid": 43862413, "source": "eval_collection"}
{"query_id": "scaleup_23192678_15328826", "query": "How to determine whether exchanges of habitat losses and gains are ecologically equivalent, reflect relevant social and ecological values, and align with broader environmental goals", "pos": ["Currencies and the Commodification of Environmental Law. If one compares environmental trading markets (ETMs), they all seem to share a basic feature--they all exchange commodities that are fungible. A CFC molecule, kilo of herring, or ton of sulfur dioxide seems much the same as another, both in terms of its identity and impact. It's trading apples for apples. Indeed ETMs must assume fungibility--that the things exchanged are sufficiently similar in ways important to the goals of environmental protection and resource allocation efficiency. Otherwise, there would be no assurance that exchanges were equivalent, that trading ensured environmental protection. This core assumption of fungibility, however, turns out to be less obvious and more problematic than first appears.In this Article we develop a comprehensive analytical framework for evaluating ETMs from the perspective of commodity nonfungibility and explore the challenges that nonfungibilities (trading apples for oranges) present. We argue that in order for ETMs to deliver on their promise of environmental protection, they must satisfy three standards of adequacy. \"Instrumental adequacy\" involves the choice of \"currency\" with which we value the traded commodities and carry out the exchange. A perfect ETM currency would accurately reflect ecological and social values and allow us to compare the exchanged commodities regardless of differences across the three dimensions of nonfungibility--type, space, and time. But nonfungibilities are present in almost all ETMs, most strongly in those trading habitat, and the perfect currency becomes simply too expensive to mint given time, knowledge, and financial constraints. Thus ETMs usually resort to using a crude currency--such as counting acres of wetlands--that will surely fail to reflect important values being exchanged or avoid negative externalities.\"Procedural adequacy\" refers to ETM trading constraints adopted to compensate for less-than-perfect currencies. For example, if counting acres of wetland fails to account for the services delivered by different types of wetlands, we can restrict the ETM to in-kind trades. Naturally, increasing trading restrictions of type, space, and time decreases the volume of trading. ETMs using crude currencies thus must balance the desire to control externalities with the need to keep the trading market robust, or \"fat.\" Through a case study of the wetland mitigation banking ETM, we demonstrate the inverse relation between currency adequacy and market restriction--i.e., the pressure on ETMs to keep markets fat even when it means sloppy accounting.Our discussion of \"substantive adequacy\" explores measures ETMs can take to police themselves when the combination of inadequate currencies and inadequate market procedures leaves the door open to trades that lead to loss of social welfare. We argue that the presence of significant nonfungibilities shifts the model of an ETM from a commodity market to a barter market, where discretion matters. We, therefore, call for use of ex post approval measures, in part to ensure meaningful valuation of the public goods exchanged and in part to counteract the agencies' and trading parties' inherent biases to encourage nonfungible trades. We further argue that it is inappropriate to use the conventional permitting process to carry out habitat trades and explore options for new institutional design of a \"permit-plus\" system that preserves the efficiency benefits of ETMs, while more clearly acknowledging the inherent costs in trading nonfungible commodities."], "field": "Environmental Science", "q_year": 2021, "q_cid": "231926783", "pos_cid": 153288260, "source": "eval_collection"}
{"query_id": "scaleup_21479030_55550334", "query": "How to assess whether health innovations are ethically acceptable, sustainable and socially desirable amid emerging knowledge, outcomes and shifting contexts, while accounting for risks, unintended consequences and broader societal challenges", "pos": ["Developing a framework for responsible innovation*. The governance of emerging science and innovation is a major challenge for contemporary democracies. In this paper we present a framework for understanding and supporting efforts aimed at ‘responsible innovation’. The framework was developed in part through work with one of the first major research projects in the controversial area of geoengineering, funded by the UK Research Councils. We describe this case study, and how this became a location to articulate and explore four integrated dimensions of responsible innovation: anticipation, reflexivity, inclusion and responsiveness. Although the framework for responsible innovation was designed for use by the UK Research Councils and the scientific communities they support, we argue that it has more general application and relevance."], "field": "Environmental Science", "q_year": 2020, "q_cid": "214790301", "pos_cid": 55550334, "source": "eval_collection"}
{"query_id": "scaleup_26902602_15597679", "query": "How to determine how land-surface changes affect moisture movement and rainfall over southeastern South America, and how these effects depend on the location of soil moisture changes", "pos": ["Isolating the Observed Influence of Vegetation Variability on the Climate of La Plata River Basin. This work aims to isolate and quantify the local and remote biogeophysical influences of slowly varying vegetation variability on the climate of La Plata basin (LPB) in the austral spring season (September–November) using observational records. Past studies have shown strong land–atmosphere coupling in LPB during this season. The analysis uses a 34-yr record (1981–2014) of the modified enhanced vegetation index (EVI2) from the NASA Making Earth System Data Records for Use in Research Environments (MEaSUREs) Vegetation Index and Phenology dataset and the third-generation normalized difference vegetation index (NDVI) from Global Inventory Modeling and Mapping Studies. The dominant patterns of vegetation index variability in space and time are assessed using empirical orthogonal function/principal component analysis over the LPB. The dominant mode in the austral spring is a vegetation dipole, with greening (browning) or positive (negative) vegetation index anomalies in the northeastern (southwestern) part of the basin. Using the stepwise generalized equilibrium feedback assessment (SGEFA), the effect of the vegetation variability on the atmosphere is then isolated. The dominant mode of LPB vegetation variability in austral spring is related to warmer temperatures in the southwest LPB and enhanced precipitation over the central and southern parts of the basin. A mechanism is proposed for the increase in latent heat flux and cooler temperatures in the northeastern LPB due to greening, and the increase in sensible heat flux, warmer temperatures, and decrease in surface pressure in southwestern LPB due to browning. The geostrophic response to this induced pressure gradient leads to anomalous northerly enhancement of moisture-laden winds, deeper penetration of moisture into LPB, and increased precipitation over the central and southern parts of the basin."], "field": "Environmental Science", "q_year": 2024, "q_cid": "269026027", "pos_cid": 155976796, "source": "eval_collection"}
{"query_id": "scaleup_25856552_26145332", "query": "How to explain differences among bird species in rates of recent physical change and determine whether body size affects these rates independently of the time between generations", "pos": ["What factors shape rates of phenotypic evolution? A comparative study of cranial morphology of four mammalian clades. Understanding why rates of morphological evolution vary is a major goal in evolutionary biology. Classical work suggests that body size, interspecific competition, geographic range size and specialization may all be important, and each may increase or decrease rates of evolution. Here, we investigate correlates of proportional evolutionary rates in phalangeriform possums, phyllostomid bats, platyrrhine monkeys and marmotine squirrels, using phylogenetic comparative methods. We find that the most important correlate is body size. Large species evolve the fastest in all four clades, and there is a nonlinear relationship in platyrrhines and phalangeriformes, with the slowest evolution in species of intermediate size. We also find significant increases in rate with high environmental temperature in phyllostomids, and low mass‐specific metabolic rate in marmotine squirrels. The mechanisms underlying these correlations are uncertain and appear to be size specific. We conclude that there is significant variation in rates of evolution, but that its meaning is not yet clear."], "field": "Environmental Science", "q_year": 2023, "q_cid": "258565524", "pos_cid": 26145332, "source": "eval_collection"}
{"query_id": "scaleup_26083533_22223805", "query": "How to interpret measurements when essential details about sampling position, age, and time since application are missing", "pos": ["Spad value varies with age and leaf of maize plant and its relationship with grain yield. A field experiment was conducted to evaluate Soil Plant Analysis Development (SPAD) value in different age and leaf of maize hybrid and correlating with grain yield. Ten maize hybrids were replicated thricely under Randomized Complete Block Design (RCBD) during winter of 2018. SPAD value was measured by SPAD 502 plus meter. At 30 days interval during vegetative stage SPAD measurement were taken from T1 (top most leaf) and T3 (2nd leaf from top leaf) leaves of five randomly selected plants from one plot and they were averaged. For reproductive phase data taken from eo (leaf attached to ear) and e2 (2nd leaf from eo leaf) leaves at 10 days intervals. Same leaves were used for entire data collection. Significantly different SPAD value was observed for different age and leaves of maize during pre and post anthesis. SPAD value increase with increase in age and decrease at the time of maturity. During vegetative phase T3 leaves has more SPAD value than T1. During reproductive stage eo leaves had more SPAD than e2 leaves, so center leaf of maize contributes more to grain yield. Correlation showed that there is strong positive correlation between different stage of SPAD with grain yield."], "field": "Environmental Science", "q_year": 2023, "q_cid": "260835335", "pos_cid": 222238056, "source": "eval_collection"}
{"query_id": "scaleup_27930902_32960112", "query": "How to obtain valid, precise estimates of medication–mortality associations compatible with a machine learning model that cannot accommodate conditional analyses", "pos": ["Analysis of matched case-control studies. There are two common misconceptions about case-control studies: that matching in itself eliminates (controls) confounding by the matching factors, and that if matching has been performed, then a “matched analysis” is required. However, matching in a case-control study does not control for confounding by the matching factors; in fact it can introduce confounding by the matching factors even when it did not exist in the source population. Thus, a matched design may require controlling for the matching factors in the analysis. However, it is not the case that a matched design requires a matched analysis. Provided that there are no problems of sparse data, control for the matching factors can be obtained, with no loss of validity and a possible increase in precision, using a “standard” (unconditional) analysis, and a “matched” (conditional) analysis may not be required or appropriate."], "field": "Environmental Science", "q_year": 2025, "q_cid": "279309023", "pos_cid": 32960112, "source": "eval_collection"}
{"query_id": "scaleup_28346199_21088011", "query": "How to determine how much individual chemicals and mixtures, especially polycyclic aromatic hydrocarbons and toxic metals, contribute to oxidative stress toxicity from fine particulate matter", "pos": ["Tracking complex mixtures of chemicals in our changing environment. Chemicals have improved our quality of life, but the resulting environmental pollution has the potential to cause detrimental effects on humans and the environment. People and biota are chronically exposed to thousands of chemicals from various environmental sources through multiple pathways. Environmental chemists and toxicologists have moved beyond detecting and quantifying single chemicals to characterizing complex mixtures of chemicals in indoor and outdoor environments and biological matrices. We highlight analytical and bioanalytical approaches to isolating, characterizing, and tracking groups of chemicals of concern in complex matrices. Techniques that combine chemical analysis and bioassays have the potential to facilitate the identification of mixtures of chemicals that pose a combined risk."], "field": "Environmental Science", "q_year": 2025, "q_cid": "283461997", "pos_cid": 210880119, "source": "eval_collection"}
{"query_id": "scaleup_26540158_53185823", "query": "How to improve prediction and relationship plausibility for interdependent outcomes and high-dimensional inputs", "pos": ["Comparative Evaluation of Machine Learning Strategies for Analyzing Big Data in Psychiatry. The requirement of innovative big data analytics has become a critical success factor for research in biological psychiatry. Integrative analyses across distributed data resources are considered essential for untangling the biological complexity of mental illnesses. However, little is known about algorithm properties for such integrative machine learning. Here, we performed a comparative analysis of eight machine learning algorithms for identification of reproducible biological fingerprints across data sources, using five transcriptome-wide expression datasets of schizophrenia patients and controls as a use case. We found that multi-task learning (MTL) with network structure (MTL_NET) showed superior accuracy compared to other MTL formulations as well as single task learning, and tied performance with support vector machines (SVM). Compared to SVM, MTL_NET showed significant benefits regarding the variability of accuracy estimates, as well as its robustness to cross-dataset and sampling variability. These results support the utility of this algorithm as a flexible tool for integrative machine learning in psychiatry."], "field": "Environmental Science", "q_year": 2023, "q_cid": "265401588", "pos_cid": 53185823, "source": "eval_collection"}
{"query_id": "scaleup_26890084_28827543", "query": "How to assess associations between early exposure to per- and polyfluoroalkyl substances and individual differences in the overall magnitude and rate of change of repeated measurements", "pos": ["SITAR—a useful instrument for growth curve analysis. Background Growth curve analysis is a statistical issue in life course epidemiology. Height in puberty involves a growth spurt, the timing and intensity of which varies between individuals. Such data can be summarized with individual Preece–Baines (PB) curves, and their five parameters then related to earlier exposures or later outcomes. But it involves fitting many curves. Methods We present an alternative SuperImposition by Translation And Rotation (SITAR) model, a shape invariant model with a single fitted curve. Curves for individuals are matched to the mean curve by shifting their curve up–down (representing differences in mean size) and left–right (for differences in growth tempo), and the age scale is also shrunk or stretched to indicate how fast time passes in the individual (i.e. velocity). These three parameters per individual are estimated as random effects while fitting the curve. The outcome is a mean curve plus triplets of parameters per individual (size, tempo and velocity) that summarize the individual growth patterns. The data are heights for Christ’s Hospital School (CHS) boys aged 9–19 years (N = 3245, n = 129 508), and girls with Turner syndrome (TS) aged 9–18 years from the UK Turner Study (N = 105, n = 1321). Results The SITAR model explained 99% of the variance in both datasets [residual standard deviation (RSD) 6–7 mm], matching the fit of individually-fitted PB curves. In CHS, growth tempo was associated with insulin-like growth factor-1 measured 50 years later (P = 0.01, N = 1009). For the girls with TS randomized to receive oxandrolone from 9 years, velocity was substantially increased compared with placebo (P = 10−8). Conclusions The SITAR growth curve model is a useful epidemiological instrument for the analysis of height in puberty."], "field": "Environmental Science", "q_year": 2024, "q_cid": "268900847", "pos_cid": 288275431, "source": "eval_collection"}
{"query_id": "scaleup_26770006_20655385", "query": "How to determine whether dissolved organic matter release under oxygen-free conditions and precipitation when oxygen returns are fully reversible or permanently alter its molecular composition and reactivity, and clarify the implications for carbon cycling across interconnected aquatic networks", "pos": ["Molecular-Scale Investigation with ESI-FT-ICR-MS on Fractionation of Dissolved Organic Matter Induced by Adsorption on Iron Oxyhydroxides.. Adsorption by minerals is a common geochemical process of dissolved organic matter (DOM) which may induce fractionation of DOM at the mineral-water interface. Here, we examine the molecular fractionation of DOM induced by adsorption onto three common iron oxyhydroxides using electrospray ionization coupled with Fourier-transform ion cyclotron resonance mass spectrometry (ESI-FT-ICR-MS). Ferrihydrite exhibited higher affinity to DOM and induced more pronounced molecular fractionation of DOM than did goethite or lepidocrocite. High molecular weight (>500 Da) compounds and compounds high in unsaturation or rich in oxygen including polycyclic aromatics, polyphenols and carboxylic compounds had higher affinity to iron oxyhydroxides and especially to ferrihydrite. Low molecular weight compounds and compounds low in unsaturation or containing few oxygenated groups (mainly alcohols and ethers) were preferentially maintained in solution. This study confirms that the double bond equivalence and the number of oxygen atoms are valuable parameters indicating the selective fractionation of DOM at mineral and water interfaces. The results of this study provide important information for further understanding the behavior of DOM in the natural environment."], "field": "Environmental Science", "q_year": 2024, "q_cid": "267700069", "pos_cid": 206553851, "source": "eval_collection"}
{"query_id": "scaleup_22938850_21342699", "query": "How to address long-term sustainability problems and future generations’ needs despite present-generation priorities and entrenched assumptions about available options", "pos": ["Taking a Future Generation’s Perspective as a Facilitator of Insight Problem-Solving: Sustainable Water Supply Management. Human societies face various unsustainability problems, often characterized as “wicked” in the sense that they have no single definitive formulation. Thus, the role of creativity or insight in solving such problems has attracted a lot of attention from scholars. Therefore, this study investigated how an emerging methodology, Future Design (and its unique intervention of asking problem solvers to take a future generation’s perspective), can facilitate insight problem solving (IPS) and the generation of sustainable solutions. In a municipality in Japan, nine officers from a bureau responsible for water supply management participated in a series of seven Future Design workshops. In two groups, these officers created visions of water supply management 30 years into the future, taking the perspective of a future generation working in the same municipality. On the basis of in-depth transcription analyses of these workshops, we obtained a hypothetical framework demonstrating that four factors mediate the influence of perspective taking on IPS: (a) Discounting the present generation’s cost, (b) contrasting the future with the present, (c) deconstructing hierarchy, and (d) intellectual joy. While the first three mediators (a, b, and c) were considered to be contributors to the problem reframing and IPS via constraint relaxation, the fourth (d) was considered to do so via positive interpretation. Further, the reason why taking a future generation’s perspective is likely to lead to sustainable solutions, useful for the future—rather than the present—generation, is also discussed."], "field": "Environmental Science", "q_year": 2020, "q_cid": "229388500", "pos_cid": 213426995, "source": "eval_collection"}
{"query_id": "scaleup_27644717_18005520", "query": "How to assess whether adaptation to human-altered habitats increases the risk of relocated urban populations surviving transport and becoming established elsewhere, especially in other urban environments", "pos": ["Anthropogenically induced adaptation to invade (AIAI): contemporary adaptation to human-altered habitats within the native range can promote invasions. Adaptive evolution is currently accepted as playing a significant role in biological invasions. Adaptations relevant to invasions are typically thought to occur either recently within the introduced range, as an evolutionary response to novel selection regimes, or within the native range, because of long‐term adaptation to the local environment. We propose that recent adaptation within the native range, in particular adaptations to human‐altered habitat, could also contribute to the evolution of invasive populations. Populations adapted to human‐altered habitats in the native range are likely to increase in abundance within areas frequented by humans and associated with human transport mechanisms, thus enhancing the likelihood of transport to a novel range. Given that habitats are altered by humans in similar ways worldwide, as evidenced by global environmental homogenization, propagules from populations adapted to human‐altered habitats in the native range should perform well within similarly human‐altered habitats in the novel range. We label this scenario ‘Anthropogenically Induced Adaptation to Invade’. We illustrate how it differs from other evolutionary processes that may occur during invasions, and how it can help explain accelerating rates of invasions."], "field": "Environmental Science", "q_year": 2025, "q_cid": "276447171", "pos_cid": 18005520, "source": "eval_collection"}
{"query_id": "scaleup_26367259_46927633", "query": "How to assess the association between fine particulate matter exposure and diabetes onset while accounting for other factors related to both exposure and diabetes risk", "pos": ["Assessing the performance of the generalized propensity score for estimating the effect of quantitative or continuous exposures on survival or time-to-event outcomes. Propensity score methods are frequently used to estimate the effects of interventions using observational data. The propensity score was originally developed for use with binary exposures. The generalized propensity score (GPS) is an extension of the propensity score for use with quantitative or continuous exposures (e.g. pack-years of cigarettes smoked, dose of medication, or years of education). We describe how the GPS can be used to estimate the effect of continuous exposures on survival or time-to-event outcomes. To do so we modified the concept of the dose–response function for use with time-to-event outcomes. We used Monte Carlo simulations to examine the performance of different methods of using the GPS to estimate the effect of quantitative exposures on survival or time-to-event outcomes. We examined covariate adjustment using the GPS and weighting using weights based on the inverse of the GPS. The use of methods based on the GPS was compared with the use of conventional G-computation and weighted G-computation. Conventional G-computation resulted in estimates of the dose–response function that displayed the lowest bias and the lowest variability. Amongst the two GPS-based methods, covariate adjustment using the GPS tended to have the better performance. We illustrate the application of these methods by estimating the effect of average neighbourhood income on the probability of survival following hospitalization for an acute myocardial infarction."], "field": "Environmental Science", "q_year": 2023, "q_cid": "263672599", "pos_cid": 46927633, "source": "eval_collection"}
{"query_id": "scaleup_24483154_53248868", "query": "How to determine whether two successive life-cycle stages require the same number of FGDF motifs", "pos": ["Conserved motifs in the hypervariable domain of chikungunya virus nsP3 required for transmission by Aedes aegypti mosquitoes. Background Chikungunya virus (CHIKV) is a re-emerging arthropod-borne (arbo)virus that causes chikungunya fever in humans and is predominantly transmitted by Aedes aegypti mosquitoes. The CHIKV replication machinery consists of four non-structural proteins (nsP1-4) that additionally require the presence of a number of host proteins for replication of the viral RNA. NsP3 is essential for CHIKV replication and has a conserved macro, central and C-terminal hypervariable domain (HVD). The HVD is intrinsically disordered and interacts with various host proteins via conserved short peptide motifs: A proline-rich (P-rich) motif that has affinity for SH3-domain containing proteins and duplicate FGDF motifs with affinity for G3BP and its mosquito homologue Rasputin. The importance of these motifs for infection of mammalian cells has previously been implicated. However, their role during CHIKV infection of mosquito cells and transmission by mosquitoes remains unclear. Methodology / Principal findings Here, we show that in-frame deletion of the P-rich motif is lethal for CHIKV replication in both mosquito and mammalian cells. However, while mutagenesis of the P-rich motif negatively affects replication both in mammalian and mosquito cells, it did not compromise the infection and transmission of CHIKV by Ae. aegypti mosquitoes. Mutagenesis of both FGDF motifs together completely inactivated CHIKV replication in both mammalian and mosquito cells. Importantly, mutation of a single FGDF motif attenuated CHIKV replication in mammalian cells, while replication in mosquito cells was similar to wild type. Surprisingly, CHIKV mutants containing only a single FGDF motif were efficiently transmitted by Ae. aegypti. Conclusions / Significance The P-rich motif in CHIKV nsP3 is dispensable for transmission by mosquitoes. A single FGDF motif is sufficient for infection and dissemination in mosquitoes, but duplicate FGDF motifs are required for the efficient infection from the mosquito saliva to a vertebrate host. These results contribute to understanding the dynamics of the alphavirus transmission cycle and may help the development of arboviral intervention strategies."], "field": "Environmental Science", "q_year": 2021, "q_cid": "244831541", "pos_cid": 53248868, "source": "eval_collection"}
{"query_id": "scaleup_25585071_72333549", "query": "How to assess whether chronic exposure to plastic-associated heavy metals contributes to hypertension and metabolic disorders", "pos": ["Chronic exposure to inorganic mercury alters stress responses in male prairie voles (Microtus ochrogaster). &NA; Male, but not female, prairie voles that experience chronic exposure to inorganic mercury display aberrant social behavior ‐ avoiding unfamiliar conspecifics rather than approaching them. The mechanisms that underlie such behavioral changes are unknown, but likely involve the hypothalamus‐pituitary‐adrenal (HPA) axis. We tested this hypothesis by providing voles of both sexes with mercury chloride in their drinking water for ten weeks and then staging same‐sex dyadic encounters after which plasma was assayed for corticosterone as an index of HPA activity. Consistent with sex‐specific behavioral responses previously reported, mercury‐treated males had lower plasma corticosterone after social encounters than did similarly‐treated females or males that consumed normal drinking water. The results suggest that mercury‐treated males may be less inclined toward social engagement with conspecifics due to reduced HPA activity."], "field": "Environmental Science", "q_year": 2023, "q_cid": "255850719", "pos_cid": 72333549, "source": "eval_collection"}
{"query_id": "scaleup_28346299_3331118", "query": "How to reliably quantify each feature’s contribution to predictions of individuals’ dietary water footprints while satisfying local accuracy, missingness, and consistency", "pos": ["Consistent feature attribution for tree ensembles. Note that a newer expanded version of this paper is now available at: arXiv:1802.03888 It is critical in many applications to understand what features are important for a model, and why individual predictions were made. For tree ensemble methods these questions are usually answered by attributing importance values to input features, either globally or for a single prediction. Here we show that current feature attribution methods are inconsistent, which means changing the model to rely more on a given feature can actually decrease the importance assigned to that feature. To address this problem we develop fast exact solutions for SHAP (SHapley Additive exPlanation) values, which were recently shown to be the unique additive feature attribution method based on conditional expectations that is both consistent and locally accurate. We integrate these improvements into the latest version of XGBoost, demonstrate the inconsistencies of current methods, and show how using SHAP values results in significantly improved supervised clustering performance. Feature importance values are a key part of understanding widely used models such as gradient boosting trees and random forests, so improvements to them have broad practical implications."], "field": "Environmental Science", "q_year": 2025, "q_cid": "283462997", "pos_cid": 3331118, "source": "eval_collection"}
{"query_id": "scaleup_25318458_21931100", "query": "How to reconcile estimated plastic inputs with observed floating plastic and clarify the link between microplastic transport and the carbon cycle despite sparse observations", "pos": ["Marvelous Marine Microgels: On the Distribution and Impact of Gel-Like Particles in the Oceanic Water-Column. Three-dimensional hydrogels of organic polymers have been suggested to affect a variety of processes in the ocean, including element cycling, microbial ecology, food-web dynamics, and air-sea exchange. However, their abundance and distribution in the ocean are hardly known, strongly limiting an assessment of their global significance. As a consequence, marine gels are often disregarded in biogeochemical or ecosystem models. Here, we demonstrate the widespread abundance of microgels in the ocean, from the surface to the deep sea. We exhibit size spectra of two major classes of marine gels, transparent exopolymer particles (TEP) and Coomassie stainable particles (CSP) for three different ocean regimes: (a) Polar Seas, (b) Eastern Boundary Upwelling Systems, and (c) the oligotrophic open ocean. We show the variations of TEP and CSP over the water-column, and compare them to dissolved organic carbon (DOC). We also discuss how the observed distributional patterns inform about productivity and particle dynamics of these distinct oceanic regimes. Finally, we exploit current research topics, where consideration of microgels may give new insight into the role of organic matter for marine biogeochemical processes."], "field": "Environmental Science", "q_year": 2022, "q_cid": "253184581", "pos_cid": 219311001, "source": "eval_collection"}
{"query_id": "scaleup_23409575_25763703", "query": "How to accurately estimate statistical parameters in populations whose distributions differ from that of the observed data", "pos": ["Tailored inference for finite populations: conditional validity and transfer across distributions. Parameters of sub-populations can be more relevant than those of super-populations. For example, a healthcare provider may be interested in the effect of a treatment plan for a specific subset of their patients; policymakers may be concerned with the impact of a policy in a particular state within a given population. In these cases, the focus is on a specific finite population, as opposed to an infinite super-population. Such a population can be characterized by fixing some attributes that are intrinsic to them, leaving unexplained variations like measurement error as random. Inference for a population with fixed attributes can then be modelled as inferring parameters of a conditional distribution. Accordingly, it is desirable that confidence intervals are conditionally valid for the realized population, instead of marginalizing over many possible draws of populations. We provide a statistical inference framework for parameters of finite populations with known attributes. Leveraging the attribute information, our estimators and confidence intervals closely target a specific finite population. When the data is from the population of interest, our confidence intervals attain asymptotic conditional validity given the attributes, and are shorter than those for super-population inference. In addition, we develop procedures to infer parameters of new populations with differing covariate distributions; the confidence intervals are also conditionally valid for the new populations under mild conditions. Our methods extend to situations where the fixed information has a weaker structure or is only partially observed. We demonstrate the validity and applicability of our methods using simulated and real-world data."], "field": "Environmental Science", "q_year": 2021, "q_cid": "234095751", "pos_cid": 257637033, "source": "eval_collection"}
{"query_id": "scaleup_27208950_23649717", "query": "How to make hyperspectral data from spaceborne and airborne missions accessible for visualization and analysis in coastal environments", "pos": ["Leafmap: A Python package for interactive mapping and geospatial analysis with minimal coding in a Jupyter environment. Leafmap is a Python package for interactive mapping and geospatial analysis with minimal coding in a Jupyter environment. It is a spin-off project of the geemap Python package (Wu, 2020), which was designed specifically to work with Google Earth Engine (GEE) (Gorelick et al., 2017). However, not everyone in the geospatial community has access to the GEE cloud computing platform. Leafmap is designed to fill this gap for non-GEE users. It is a free and open-source Python package that enables users to analyze and visualize geospatial data with minimal coding in a Jupyter environment, such as Google Colab, Jupyter Notebook, and JupyterLab. Leafmap is built upon several open-source packages, such as folium (Filipe et al., 2021)and ipyleaflet (Renou et al., 2021) (for creating interactive maps), WhiteboxTools (Lindsay, 2018) and whiteboxgui (for analyzing geospatial data), and ipywidgets (Grout & et al., 2021) (for designing interactive graphical user interface [GUI]). Leafmap has a toolset with various interactive tools that allow users to load vector and raster data onto the map without coding. In addition, users can use the powerful analytical backend (i.e., WhiteboxTools) to perform geospatial analysis directly within the leafmap user interface without writing a single line of code. The WhiteboxTools library currently contains 468 tools for advanced geospatial analysis, such as GIS Analysis, Geomorphometric Analysis, Hydrological Analysis, LiDAR Data Analysis, Mathematical and Statistical Analysis, and Stream Network Analysis."], "field": "Environmental Science", "q_year": 2024, "q_cid": "272089503", "pos_cid": 236497171, "source": "eval_collection"}
{"query_id": "scaleup_25107943_22491673", "query": "How to identify the psychological factors that most strongly motivate Malaysian consumers’ intentions and sustained behavior toward responsibly handling unwanted electronics", "pos": ["Waste separation at source behaviour among Malaysian households: The Theory of Planned Behaviour with moral norm. Abstract Background Malaysia, as one of the countries that intend to achieve the 17 Sustainable Development Goals (SDGs) by the United Nations (UN). Under the responsible consumption and production goals category, Malaysian households should take part by practising waste separation at home when the Separation at Source Initiative (SSI) under Solid Waste and Public Cleansing Management Act 2007 (Act 672) launched and effective in September 2015. However, many households in Malaysia is unwilling to participate. As the local authority has taken an extrinsic motivation thru SSI, this paper will study the impact of intrinsic motivation among the households. This paper purpose is to emphasise the part of intrinsic motivation thru extended Theory of Planned Behaviour in influencing households waste separation behaviour. A questionnaire survey was conducted towards high-rise residential units in Kuala Lumpur, Malaysia and obtained a total of 900 valid questionnaires. Data are analysed using the Smart PLS software. The results show that all the determinants from the model that consists of attitude towards behaviour, subjective norm, perceived behaviour control, and moral norm are significant. All the determinants positively influence the waste separation behaviour with the moral norm as the most influential determinant in improving households intrinsic motivation to engage with the waste separation at source behaviour. This paper result with the suggestions to foster waste separation behaviour among households based on the findings. Objectives To identify the factors that could positively influence the waste separation at source behaviour among high-rise residents in Kuala Lumpur. This paper intends to discover the application of the Theory of Planned Behaviour (TPB) extended with Moral Norm (MN) element in influencing the Waste Separation at Source Behaviour (WSB) among households. As this research focuses on intrinsic motivation, the MN element is included as it is one of the elements that represent a person intrinsic motivation. The result will support the application of moral norm together with TPB determinants. Furthermore, it shows the significance of the extended TPB. Originality/value Most past papers studied the recycling intentions and behaviour among households. This paper is the first study that applying the extended TPB in investigating the WSB among high-rise residents in Kuala Lumpur, Malaysia. The implication of the findings is useful for the local authority to encourage waste separation at source behaviour among households."], "field": "Environmental Science", "q_year": 2022, "q_cid": "251079439", "pos_cid": 224916736, "source": "eval_collection"}
{"query_id": "scaleup_27930902_21889700", "query": "How to identify which medications are most important to machine-learning predictions of mortality risk during an extreme heat event", "pos": ["A Unified Approach to Interpreting Model Predictions. Understanding why a model makes a certain prediction can be as crucial as the prediction's accuracy in many applications. However, the highest accuracy for large modern datasets is often achieved by complex models that even experts struggle to interpret, such as ensemble or deep learning models, creating a tension between accuracy and interpretability. In response, various methods have recently been proposed to help users interpret the predictions of complex models, but it is often unclear how these methods are related and when one method is preferable over another. To address this problem, we present a unified framework for interpreting predictions, SHAP (SHapley Additive exPlanations). SHAP assigns each feature an importance value for a particular prediction. Its novel components include: (1) the identification of a new class of additive feature importance measures, and (2) theoretical results showing there is a unique solution in this class with a set of desirable properties. The new class unifies six existing methods, notable because several recent methods in the class lack the proposed desirable properties. Based on insights from this unification, we present new methods that show improved computational performance and/or better consistency with human intuition than previous approaches."], "field": "Environmental Science", "q_year": 2025, "q_cid": "279309023", "pos_cid": 21889700, "source": "eval_collection"}
{"query_id": "scaleup_26890084_73439446", "query": "How to characterize nonlinear changes over time with interpretable, meaningful trajectory measures that support association analyses without arbitrarily chosen intervals", "pos": ["A discussion of statistical methods to characterize early growth and its impact on bone mineral content later in childhood. Abstract Background: Many statistical methods are available to model longitudinal growth data and relate derived summary measures to later outcomes. Aim: To apply and compare commonly used methods to a realistic scenario including pre- and postnatal data, missing data, and confounders. Subjects and methods: Data were collected from 753 offspring in the Southampton Women’s Survey with measurements of bone mineral content (BMC) at age 6 years. Ultrasound measures included crown-rump length (11 weeks’ gestation) and femur length (19 and 34 weeks’ gestation); postnatally, infant length (birth, 6 and 12 months) and height (2 and 3 years) were measured. A residual growth model, two-stage multilevel linear spline model, joint multilevel linear spline model, SITAR and a growth mixture model were used to relate growth to 6-year BMC. Results: Results from the residual growth, two-stage and joint multilevel linear spline models were most comparable: an increase in length at all ages was positively associated with BMC, the strongest association being with later growth. Both SITAR and the growth mixture model demonstrated that length was positively associated with BMC. Conclusions: Similarities and differences in results from a variety of analytic strategies need to be understood in the context of each statistical methodology."], "field": "Environmental Science", "q_year": 2024, "q_cid": "268900847", "pos_cid": 73439446, "source": "eval_collection"}
{"query_id": "scaleup_26861830_18797375", "query": "How to distinguish real sequence variants from sequencing noise in environmental sequencing reads while retaining sufficient overlap between forward and reverse reads", "pos": ["DADA2: High resolution sample inference from Illumina amplicon data. We present the open-source software package DADA2 for modeling and correcting Illumina-sequenced amplicon errors (https://github.com/benjjneb/dada2). DADA2 infers sample sequences exactly and resolves differences of as little as 1 nucleotide. In several mock communities, DADA2 identified more real variants and output fewer spurious sequences than other methods. We applied DADA2 to vaginal samples from a cohort of pregnant women, revealing a diversity of previously undetected Lactobacillus crispatus variants."], "field": "Environmental Science", "q_year": 2024, "q_cid": "268618305", "pos_cid": 18797375, "source": "eval_collection"}
{"query_id": "scaleup_26773319_86863466", "query": "How to maintain reliable biological performance and effluent quality in wastewater treatment while limiting operating costs", "pos": ["Anaerobic Membrane Bioreactor as Highly Efficient and Reliable Technology for Wastewater Treatment—A Review. In this review paper, Anaerobic Membrane Bioreactor (AnMBR) is considering as highly efficient and reliable technology for organic material removal from wastewater with no additional energy requirement for aeration. AnMBR is a combination of conventional anaerobic technology and modern membrane system. AnMBR is cost effective alternative technology with pros of anaerobic microbial activity because Methogenic microorganism can convert organic pollutant load of wastewater into renewable energy in the form of methane rich biogas, this conversion is mainly done by transformation of organic matter into energy by high chemical oxygen demand (COD), total suspended solid (TSS) and pathogens removal. Methane rich biogas can be used as a storable source of supplemental energy for the production of heat or power thus AnMBR technology provides improved effluent quality, reliability, and efficiency over the other traditional technologies. This review paper is included the overview of AnMBR, the advantages over other wastewater treatment technology, operational constraints and the concerned factors that has affected the performances of implemented systems, applications of AnMBR for various types of wastewaters, research and development summary and future perspective for further research."], "field": "Environmental Science", "q_year": 2024, "q_cid": "267733194", "pos_cid": 86863466, "source": "eval_collection"}
{"query_id": "scaleup_14342529_19470601", "query": "How to ensure cancer screening education materials address patients’ screening barriers when meaningful patient input requires support and the number of participants is limited", "pos": ["Co-Creation With TickiT: Designing and Evaluating a Clinical eHealth Platform for Youth. Background All youth are susceptible to mental health issues and engaging in risky behavior, and for youth with chronic health conditions, the consequences can be more significant than in their healthy peers. Standardized paper-based questionnaires are recommended by the American Academy of Pediatrics in community practice to screen for health risks. In hospitals, psychosocial screening is traditionally undertaken using the Home Education, Eating, Activities, Drugs, Depression, Sex, Safety (HEEADDSS) interview. However, time constraints and patient/provider discomfort reduce implementation. We report findings from an eHealth initiative undertaken to improve uptake of psychosocial screening among youth. Objective Youth are sophisticated “technology natives.” Our objective was to leverage youth’s comfort with technology, creating a youth-friendly interactive mobile eHealth psychosocial screening tool, TickiT. Patients enter data into the mobile application prior to a clinician visit. Response data is recorded in a report, which generates alerts for clinicians, shifting the clinical focus from collecting information to focused management. Design goals included improving the patient experience, improving efficiency through electronic patient based data entry, and supporting the collection of aggregated data for research. Methods This paper describes the iterative design and evaluation processes undertaken to develop TickiT including co-creation processes, and a pilot study utilizing mixed qualitative and quantitative methods. A collaborative industry/academic partnership engaged stakeholders (youth, health care providers, and administrators) in the co-creation development process. An independent descriptive study conducted in 2 Canadian pediatric teaching hospitals evaluated the feasibility of the platform in both inpatient and ambulatory clinical settings, evaluating both providers and patient responses to the platform. Results The independent pilot feasibility study included 80 adolescents, 12-18 years, and 38 medical staff-residents, inpatient and outpatient pediatricians, and surgeons. Youth uptake was 99% (79/80), and survey completion 99% (78/79; 90 questions). Youth found it easy to understand (92%, 72/78), easy to use (92%, 72/78), and efficient (80%, 63/79 with completion rate < 10 minutes). Residents were most positive about the application and surgeons were least positive. All inpatient providers obtained new patient information. Conclusions Co-creative design methodology with stakeholders was effective for informing design and development processes to leverage effective eHealth opportunities. Continuing stakeholder engagement has further fostered platform development. The platform has the potential to meet IHI Triple Aim goals. Clinical adaptation requires planning, training, and support for health care providers to adjust their practices."], "field": "Health Professions", "q_year": 2019, "q_cid": "143425297", "pos_cid": 19470601, "source": "eval20x26"}
{"query_id": "scaleup_4268986_18783913", "query": "How to support people with dementia in deciding when to retire from driving while ensuring balanced, well-presented information and support that meets validated quality standards", "pos": ["Developing a quality criteria framework for patient decision aids: online international Delphi consensus process. Abstract Objective To develop a set of quality criteria for patient decision support technologies (decision aids). Design and setting Two stage web based Delphi process using online rating process to enable international collaboration. Participants Individuals from four stakeholder groups (researchers, practitioners, patients, policy makers) representing 14 countries reviewed evidence summaries and rated the importance of 80 criteria in 12 quality domains ona1to9 scale. Second round participants received feedback from the first round and repeated their assessment of the 80 criteria plus three new ones. Main outcome measure Aggregate ratings for each criterion calculated using medians weighted to compensate for different numbers in stakeholder groups; criteria rated between 7 and 9 were retained. Results 212 nominated people were invited to participate. Of those invited, 122 participated in the first round (77 researchers, 21 patients, 10 practitioners, 14 policy makers); 104/122 (85%) participated in the second round. 74 of 83 criteria were retained in the following domains: systematic development process (9/9 criteria); providing information about options (13/13); presenting probabilities (11/13); clarifying and expressing values (3/3); using patient stories (2/5); guiding/coaching (3/5); disclosing conflicts of interest (5/5); providing internet access (6/6); balanced presentation of options (3/3); using plain language (4/6); basing information on up to date evidence (7/7); and establishing effectiveness (8/8). Conclusions Criteria were given the highest ratings where evidence existed, and these were retained. Gaps in research were highlighted. Developers, users, and purchasers of patient decision aids now have a checklist for appraising quality. An instrument for measuring quality of decision aids is being developed."], "field": "Health Professions", "q_year": 2014, "q_cid": "4268986", "pos_cid": 18783913, "source": "eval20x26"}
{"query_id": "scaleup_4772304_41645208", "query": "How to establish whether items within each scale measure a single dimension without inter-item dependence and can be summed into valid scores for older adults after a fall", "pos": ["Application of Rasch analysis in the development and application of quality of life instruments.. This paper discusses recent advances that have been made in the field of psychometrics, specifically, the application of Rasch analysis to the instrument development process. It emphasizes the importance of assessing the fundamental scaling properties of an instrument prior to consideration of traditional psychometric indicators. The paper introduces Rasch analysis and shows how it has been applied in the development of needs-based measures in order to ensure that they provide unidimensional measurement. By ensuring that scales are based on the same measurement model and that they fit the Rasch model it is possible for QoL scores to be compared across diseases by means of cocalibration and item banking."], "field": "Health Professions", "q_year": 2017, "q_cid": "4772304", "pos_cid": 41645208, "source": "eval20x26"}
{"query_id": "scaleup_23692885_6233865", "query": "How to identify what influenced participants’ diet and physical activity changes in a complex weight loss programme, while distinguishing those influences from the programme’s roles and activities in participants’ accounts", "pos": ["Validation of the theoretical domains framework for use in behaviour change and implementation research. BackgroundAn integrative theoretical framework, developed for cross-disciplinary implementation and other behaviour change research, has been applied across a wide range of clinical situations. This study tests the validity of this framework.MethodsValidity was investigated by behavioural experts sorting 112 unique theoretical constructs using closed and open sort tasks. The extent of replication was tested by Discriminant Content Validation and Fuzzy Cluster Analysis.ResultsThere was good support for a refinement of the framework comprising 14 domains of theoretical constructs (average silhouette value 0.29): ‘Knowledge’, ‘Skills’, ‘Social/Professional Role and Identity’, ‘Beliefs about Capabilities’, ‘Optimism’, ‘Beliefs about Consequences’, ‘Reinforcement’, ‘Intentions’, ‘Goals’, ‘Memory, Attention and Decision Processes’, ‘Environmental Context and Resources’, ‘Social Influences’, ‘Emotions’, and ‘Behavioural Regulation’.ConclusionsThe refined Theoretical Domains Framework has a strengthened empirical base and provides a method for theoretically assessing implementation problems, as well as professional and other health-related behaviours as a basis for intervention development."], "field": "Health Professions", "q_year": 2016, "q_cid": "23692885", "pos_cid": 6233865, "source": "eval20x26"}
{"query_id": "scaleup_38535768_8631455", "query": "How to determine how water immersion affects variation in movement during common recovery exercises and whether these changes are beneficial, particularly regarding harm from repeated activity", "pos": ["Coordinative variability and overuse injury. Overuse injuries are generally defined as a repetitive micro-trauma to tissue. Many researchers have associated particular biomechanical parameters as an indicator of such injuries. However, while these parameters have been reported in single studies, in many instances, it has been difficult to verify these parameters as causative to the injury. We have investigated overuse injuries, such as patella-femoral pain syndrome, using a dynamical systems approach. Using such methods, the importance of the structure of coordinative variability (i.e. the variability of the interaction between segments or joints) becomes apparent. We view coordinative variability as functionally important to the movement and different from end-point or goal variability. Using concepts derived from the work of Bernstein, we conducted studies using a continuous relative phase and/or modified vector coding approaches to investigate the coordinative variability of overuse injuries. Consistently, we have found that the higher variability state of a coordinative structure is the healthy state while the lower variability state is the unhealthy or pathological state. It is clear that very high coordinative variability could also result in injury and that there must be a window of ‘higher variability’ in which non-injured athletes function. While this finding that coordinative variability is functional has been shown in several studies, it is still not clear if reduced variability contributes to or results from the injury. Studies are currently underway to determine the potential reasons for the reduced variability in injured athletes. Nevertheless, our laboratory believes that this understanding of how joints interact can be important in understanding overuse injuries."], "field": "Health Professions", "q_year": 2017, "q_cid": "38535768", "pos_cid": 8631455, "source": "eval20x26"}
{"query_id": "scaleup_20470210_4835904", "query": "How to determine which changes can improve an already established condition without causing harm when clinical evidence is sparse", "pos": ["Gut Microbiota Regulate Motor Deficits and Neuroinflammation in a Model of Parkinson's Disease. Summary The intestinal microbiota influence neurodevelopment, modulate behavior, and contribute to neurological disorders. However, a functional link between gut bacteria and neurodegenerative diseases remains unexplored. Synucleinopathies are characterized by aggregation of the protein α-synuclein (αSyn), often resulting in motor dysfunction as exemplified by Parkinson's disease (PD). Using mice that overexpress αSyn, we report herein that gut microbiota are required for motor deficits, microglia activation, and αSyn pathology. Antibiotic treatment ameliorates, while microbial re-colonization promotes, pathophysiology in adult animals, suggesting postnatal signaling between the gut and the brain modulates disease. Indeed, oral administration of specific microbial metabolites to germ-free mice promotes neuroinflammation and motor symptoms. Remarkably, colonization of αSyn-overexpressing mice with microbiota from PD patients enhances physical impairments compared to microbiota transplants from healthy human donors. These findings reveal that gut bacteria regulate movement disorders in mice, and suggest that alterations in the human microbiome represent a risk factor for PD."], "field": "Health Professions", "q_year": 2019, "q_cid": "204702109", "pos_cid": 4835904, "source": "eval20x26"}
{"query_id": "scaleup_9519814_10117932", "query": "How to identify text-messaging features with theoretical or empirical support relevant to physical activity barriers among low-income Latino patients with diabetes", "pos": ["A taxonomy of behavior change techniques used in interventions.. OBJECTIVE Without standardized definitions of the techniques included in behavior change interventions, it is difficult to faithfully replicate effective interventions and challenging to identify techniques contributing to effectiveness across interventions. This research aimed to develop and test a theory-linked taxonomy of generally applicable behavior change techniques (BCTs). DESIGN Twenty-six BCTs were defined. Two psychologists used a 5-page coding manual to independently judge the presence or absence of each technique in published intervention descriptions and in intervention manuals. RESULTS Three systematic reviews yielded 195 published descriptions. Across 78 reliability tests (i.e., 26 techniques applied to 3 reviews), the average kappa per technique was 0.79, with 93% of judgments being agreements. Interventions were found to vary widely in the range and type of techniques used, even when targeting the same behavior among similar participants. The average agreement for intervention manuals was 85%, and a comparison of BCTs identified in 13 manuals and 13 published articles describing the same interventions generated a technique correspondence rate of 74%, with most mismatches (73%) arising from identification of a technique in the manual but not in the article. CONCLUSIONS These findings demonstrate the feasibility of developing standardized definitions of BCTs included in behavioral interventions and highlight problematic variability in the reporting of intervention content."], "field": "Health Professions", "q_year": 2016, "q_cid": "9519814", "pos_cid": 10117932, "source": "eval20x26"}
{"query_id": "scaleup_25864944_1221398", "query": "How to determine whether applying signature character strengths is associated with better outcomes among professionals", "pos": ["The job demands-resources model : state of the art. Purpose – The purpose of this paper is to give a state‐of‐the art overview of the Job Demands‐Resources (JD‐R) modelDesign/methodology/approach – The strengths and weaknesses of the demand‐control model and the effort‐reward imbalance model regarding their predictive value for employee well being are discussed. The paper then introduces the more flexible JD‐R model and discusses its basic premises.Findings – The paper provides an overview of the studies that have been conducted with the JD‐R model. It discusses evidence for each of the model's main propositions. The JD‐R model can be used as a tool for human resource management. A two‐stage approach can highlight the strengths and weaknesses of individuals, work groups, departments, and organizations at large.Originality/value – This paper challenges existing stress models, and focuses on both negative and positive indicators of employee well being. In addition, it outlines how the JD‐R model can be applied to a wide range of occupations, and be used to i..."], "field": "Health Professions", "q_year": 2017, "q_cid": "25864944", "pos_cid": 1221398, "source": "eval20x26"}
{"query_id": "scaleup_27288178_20758901", "query": "How to better understand the tension between capitalism’s materialistic values and wealth-oriented goals and people’s basic needs", "pos": ["The relationship between materialism and personal well-being: A meta-analysis.. This meta-analysis investigates the relationship between individuals' materialistic orientation and their personal well-being. Theoretical approaches in psychology agree that prioritizing money and associated aims is negatively associated with individuals' well-being but differ in their implications for whether this is invariably the case. To address these and other questions, we examined 753 effect sizes from 259 independent samples. Materialism was associated with significantly lower well-being for the most widely used, multifaceted measures (materialist values and beliefs, r = -.19, ρ = -.24; relative importance of materialist goals, r = -.16, ρ = -.21), more than for measures assessing emphasis on money alone (rs = -.08 to -.11, ρs = -.09 to -.14). The relationship also depended on type of well-being outcome, with largest effects for risky health and consumer behaviors and for negative self-appraisals (rs = -.28 to -.44, ρs = -.32 to -.53) and weakest effects for life satisfaction and negative affect (rs = -.13 to -.15, ρs = -.17 to -.18). Moderator analyses revealed that the strength of the effect depended on certain demographic factors (gender and age), on value context (study/work environments that support materialistic values and cultures that emphasize affective autonomy), and on cultural economic indicators (economic growth and wealth differentials). Mediation analyses suggested that the negative link may be explained by poor psychological need satisfaction. We discuss implications for the measurement of materialist values and the need for theoretical and empirical advances to explore underlying processes, which likely will require more experimental, longitudinal, and developmental research."], "field": "Health Professions", "q_year": 2024, "q_cid": "272881789", "pos_cid": 207589010, "source": "eval_collection"}
{"query_id": "scaleup_23741829_14683425", "query": "How to clarify the role of social media in supporting dialogue and fostering questioning", "pos": ["The Socratic method: adult education theories. Postgraduate students need to explore their research question(s) from different angles, take ownership of the research process, and develop their own scholarly voice. Supervisors are often ill-equipped to guide students in a strategic and learner-centred manner. The Socratic method draws on strategies to elicit learning through uncertainty in the question-and-answer technique employed. Based on a qualitative study, various adult education theories are used to formulate a rationale for the application of the Socratic method as a tool to facilitate learning in the supervisor-student relationship. Theoretical perspectives which emerged as themes through this study include experiential learning, ontological coaching and empowerment. This article provides a conceptual framework for postgraduate supervisors which could act as a guide to enhance their supervisory practice and facilitate independent student learning."], "field": "Health Professions", "q_year": 2021, "q_cid": "237418293", "pos_cid": 146834250, "source": "eval_collection"}
{"query_id": "scaleup_27889920_25011614", "query": "How to address multiple factors comprehensively while meeting each person’s specific needs", "pos": ["Life’s Essential 8: Updating and Enhancing the American Heart Association’s Construct of Cardiovascular Health: A Presidential Advisory From the American Heart Association. In 2010, the American Heart Association defined a novel construct of cardiovascular health to promote a paradigm shift from a focus solely on disease treatment to one inclusive of positive health promotion and preservation across the life course in populations and individuals. Extensive subsequent evidence has provided insights into strengths and limitations of the original approach to defining and quantifying cardiovascular health. In response, the American Heart Association convened a writing group to recommend enhancements and updates. The definition and quantification of each of the original metrics (Life’s Simple 7) were evaluated for responsiveness to interindividual variation and intraindividual change. New metrics were considered, and the age spectrum was expanded to include the entire life course. The foundational contexts of social determinants of health and psychological health were addressed as crucial factors in optimizing and preserving cardiovascular health. This presidential advisory introduces an enhanced approach to assessing cardiovascular health: Life’s Essential 8. The components of Life’s Essential 8 include diet (updated), physical activity, nicotine exposure (updated), sleep health (new), body mass index, blood lipids (updated), blood glucose (updated), and blood pressure. Each metric has a new scoring algorithm ranging from 0 to 100 points, allowing generation of a new composite cardiovascular health score (the unweighted average of all components) that also varies from 0 to 100 points. Methods for implementing cardiovascular health assessment and longitudinal monitoring are discussed, as are potential data sources and tools to promote widespread adoption in policy, public health, clinical, institutional, and community settings."], "field": "Health Professions", "q_year": 2025, "q_cid": "278899207", "pos_cid": 250116145, "source": "eval_collection"}
{"query_id": "scaleup_21126270_17380916", "query": "How to understand compulsive behaviour and distress amid personal vulnerability and cultural expectations of perfection and autonomy within education", "pos": ["Show what you know and deal with stress yourself: a qualitative interview study of medical interns’ perceptions of stress and gender. BackgroundMedical students report high stress levels and in particular, the clinical phase is a demanding one. The field of medicine is still described as having a patriarchal culture which favors aspects like a physicians’ perceived certainty and rationalism. Also, the Effort-Recovery Model explains stress as coming from a discrepancy between job demands, job control, and perceived work potential. Gendered differences in stress are reported, but not much is known about medical interns’ perceptions of how gender plays in relation to stress. The aim of this study is to explore how medical interns experience and cope with stress, as well as how they reflect on the gendered aspects of stress.MethodsIn order to do this, we have performed a qualitative study. In 2010–2011, semi-structured qualitative interviews were conducted with seventeen medical interns across all three years of the Masters programme (6 male, 11 female) at a Dutch medical school. The interview guide is based on gender theory, the Effort-Recovery Model, and empirical literature. Transcribed interviews have been analyzed thematically.ResultsFirst, stress mainly evolves from having to prove one’s self and show off competencies and motivation (“Show What You Know…”). Second, interns seek own solutions for handling stress because it is not open for discussion (… “And Deal With Stress Yourself”). Patient encounters are a source of pride and satisfaction rather than a source of stress. But interns report having to present themselves as ‘professional and self-confident’, remaining silent about experiencing stress. Female students are perceived to have more stress and to study harder in order to live up to expectations.ConclusionsThe implicit message interns hear is to remain silent about insecurities and stress, and, in particular, female students might face disadvantages. Students who feel less able to manifest the ‘masculine protest’ may benefit from a culture that embraces more collaborative styles, such as having open conversation about stress."], "field": "Health Professions", "q_year": 2020, "q_cid": "211262705", "pos_cid": 17380916, "source": "eval_collection"}
{"query_id": "scaleup_27940564_25750776", "query": "How to help family caregivers sustain positive appraisals of caregiving while reducing its negative aspects to support their quality of life", "pos": ["“Out of the clear blue sky she tells me she loves me”: Connection experiences between caregivers and people with dementia. Dementia can impede the relationship and connection between the person with dementia (PWD) and their caregiver. Yet, caregiving in dementia also offers opportunities for connection, which has implications for caregiver and PWD well‐being. In this qualitative study, we describe and characterize ways caregivers felt connected to the person with dementia they care for."], "field": "Health Professions", "q_year": 2025, "q_cid": "279405649", "pos_cid": 257507764, "source": "eval_collection"}
{"query_id": "scaleup_28003619_3162051", "query": "How to reduce overfitting and improve generalization to unseen wound images with a small, imbalanced wound image dataset", "pos": ["mixup: Beyond Empirical Risk Minimization. Large deep neural networks are powerful, but exhibit undesirable behaviors such as memorization and sensitivity to adversarial examples. In this work, we propose mixup, a simple learning principle to alleviate these issues. In essence, mixup trains a neural network on convex combinations of pairs of examples and their labels. By doing so, mixup regularizes the neural network to favor simple linear behavior in-between training examples. Our experiments on the ImageNet-2012, CIFAR-10, CIFAR-100, Google commands and UCI datasets show that mixup improves the generalization of state-of-the-art neural network architectures. We also find that mixup reduces the memorization of corrupt labels, increases the robustness to adversarial examples, and stabilizes the training of generative adversarial networks."], "field": "Health Professions", "q_year": 2025, "q_cid": "280036191", "pos_cid": 3162051, "source": "eval_collection"}
{"query_id": "scaleup_25072076_53493286", "query": "How to develop a coherent, consistent, transparent, and trustworthy understanding of conversational participation from interview responses while accounting for researcher bias", "pos": ["Theme development in qualitative content analysis and thematic analysis. Sufficient knowledge is available about the definition, details and differences of qualitative content and thematic analysis as two approaches of qualitative descriptive research. However, identifying the main features of theme as the data analysis product and the method of its development remain unclear. The purpose of this study was to describe the meaning of theme and offer a method on theme construction that can be used by qualitative content analysis and thematic analysis researchers in line with the underpinning specific approach to data analysis. This methodological paper comprises an analytical overview of qualitative descriptive research products and the meaning of theme. Also, our practical experiences of qualitative analysis supported by relevant published literature informed the generation of a stage like model of theme construction for qualitative content analysis and thematic analysis. This paper comprises: (i) analytical importance of theme, (ii) meaning of theme, (iii) meaning of category, (iv) theme and category in terms of level of content, and (v) theme development. This paper offers a conceptual clarification and a pragmatic step by step method of theme development that has the capacity of assisting nurse researchers understand how theme is developed. As nursing is a pragmatic discipline, nurse researchers have tried to develop practical findings and devise some way to “do something” with findings to enhance the action and impact of nursing. The application of a precise method of theme development for qualitative descriptive data analysis suggested in this paper helps yield meaningful, credible and practical results for nursing."], "field": "Health Professions", "q_year": 2022, "q_cid": "250720768", "pos_cid": 53493286, "source": "eval_collection"}
{"query_id": "scaleup_25072076_7742072", "query": "How to help people with Parkinson’s be ready to address communication difficulties when needed during conversations", "pos": ["Self-efficacy: toward a unifying theory of behavioral change.. The present article presents an integrative theoretical framework to explain and to predict psychological changes achieved by different modes of treatment. This theory states that psychological procedures, whatever their form, alter the level and strength of self-efficacy. It is hypothesized that expectations of personal efficacy determine whether coping behavior will be initiated, how much effort will be expended, and how long it will be sustained in the face of obstacles and aversive experiences. Persistence in activities that are subjectively threatening but in fact relatively safe produces, through experiences of mastery, further enhancement of self-efficacy and corresponding reductions in defensive behavior. In the proposed model, expectations of personal efficacy are derived from four principal sources of information: performance accomplishments, vicarious experience, verbal persuasion, and physiological states. The more dependable the experiential sources, the greater are the changes in perceived selfefficacy. A number of factors are identified as influencing the cognitive processing of efficacy information arising from enactive, vicarious, exhortative, and emotive sources. The differential power of diverse therapeutic procedures is analyzed in terms of the postulated cognitive mechanism of operation. Findings are reported from microanalyses of enactive, vicarious, and emotive modes of treatment that support the hypothesized relationship between perceived self-efficacy and behavioral changes. Possible directions for further research are discussed."], "field": "Health Professions", "q_year": 2022, "q_cid": "250720768", "pos_cid": 7742072, "source": "eval_collection"}
{"query_id": "scaleup_21126270_14524423", "query": "How to understand a person’s experience and the interplay of social and intrapsychic dimensions in case study research when the researcher’s position shapes what is noticed and personal motives and experiences receive insufficient attention", "pos": ["Whose Science? Whose Knowledge?: Thinking from Women's Lives. Introduction - after the science question in feminism. Part 1 Science: feminism confronts the sciences how the women's movement benefits science - two views why \"physics\" is a bad model for physics. Part 2 Epistemology: what is feminist epistemology \"strong objectivity\" and socially situated knowledge feminist epistemology in and after the enlightenment. Part 3 \"Others\": \"...and race?\" - the science question in global feminism common histories, common destinies - science in the first and third worlds \"real science\" thinking from the perspective of lesbian lives reinventing ourselves as other Conclusion - what is a feminist science."], "field": "Health Professions", "q_year": 2020, "q_cid": "211262705", "pos_cid": 145244236, "source": "eval_collection"}
{"query_id": "scaleup_22090915_6464878", "query": "How to determine how quickly balance control adapts to changing information during continuous stance perturbations, accounting for task demands and limited time per cycle at higher perturbation frequencies", "pos": ["Time-interval for integration of stabilizing haptic and visual information in subjects balancing under static and dynamic conditions. Maintaining equilibrium is basically a sensorimotor integration task. The central nervous system (CNS) continually and selectively weights and rapidly integrates sensory inputs from multiple sources, and coordinates multiple outputs. The weighting process is based on the availability and accuracy of afferent signals at a given instant, on the time-period required to process each input, and possibly on the plasticity of the relevant pathways. The likelihood that sensory inflow changes while balancing under static or dynamic conditions is high, because subjects can pass from a dark to a well-lit environment or from a tactile-guided stabilization to loss of haptic inflow. This review article presents recent data on the temporal events accompanying sensory transition, on which basic information is fragmentary. The processing time from sensory shift to reaching a new steady state includes the time to (a) subtract or integrate sensory inputs; (b) move from allocentric to egocentric reference or vice versa; and (c) adjust the calibration of motor activity in time and amplitude to the new sensory set. We present examples of processes of integration of posture-stabilizing information, and of the respective sensorimotor time-intervals while allowing or occluding vision or adding or subtracting tactile information. These intervals are short, in the order of 1–2 s for different postural conditions, modalities and deliberate or passive shift. They are just longer for haptic than visual shift, just shorter on withdrawal than on addition of stabilizing input, and on deliberate than unexpected mode. The delays are the shortest (for haptic shift) in blind subjects. Since automatic balance stabilization may be vulnerable to sensory-integration delays and to interference from concurrent cognitive tasks in patients with sensorimotor problems, insight into the processing time for balance control represents a critical step in the design of new balance- and locomotion training devices."], "field": "Health Professions", "q_year": 2020, "q_cid": "220909155", "pos_cid": 6464878, "source": "eval_collection"}
{"query_id": "scaleup_24879622_23160430", "query": "How to improve outcomes for low-income women and their babies during an economic recession", "pos": ["Postpartum Medicaid Extension to Address Racial Inequity in Maternal Mortality.. The US pregnancy-related mortality ratio, defined as the number of deaths of women while pregnant or up to one year after delivery from any cause related to or aggravated by the pregnancy or its management, has increased from 14 5 pregnancy-related deaths per 100 000 live births in 2007 to 16 9 per 100 000 in 2016 1 Nearly a quarter of pregnancyrelated deaths occur between 43 days and one-year postpartum, with cardiovascular conditions being the leading cause of death Expansion states decreased the uninsured rate among women who gave birth in the past year, increased preconception Medicaid enrollment among low-income women, reduced racial disparities in preterm birth and low birth weight,6 and decreased infant mortality Research examining differences in maternal and perinatal outcomes after the implementation of postpartum Medicaid extension as well as the impact of innovative health care delivery mechanisms on inequities in postpartum care will provide critical data that can guide the state-level adoption and implementation of postpartum Medicaid extension Other proposed solutions-including improved maternal death reporting, sustainable support for perinatal quality collaboratives and maternal mortality review committees, increased pregnancy and postpartum support (e g , doulas, patient navigators, breastfeeding peer counselors, home visits, and case management), pregnancy-centered medical homes, and implicit bias training-have been well characterized in the literature 7 Increased access to postpartum health care via Medicaid extension could allow safer birth spacing via improved access to contraception, increased provision of mental health care, improved access to medication-assisted treatment and recovery services, and longer follow-up for medical complications that occur during pregnancy as well as chronic diseases"], "field": "Health Professions", "q_year": 2022, "q_cid": "248796221", "pos_cid": 231604307, "source": "eval_collection"}
{"query_id": "scaleup_25515532_55425380", "query": "How to connect students’ cultural perspectives with astronomy knowledge and strengthen their ability to understand and communicate it in English while still learning the language", "pos": ["Indigenous sky stories: Reframing how we introduce primary school students to astronomy - A Type II case study of implementation. The Indigenous Sky Stories Program may have the potential to deliver significant and long-lasting changes to the way science is taught to Year 5 and 6 primary school students. The context for this article is informed by research that shows that educational outcomes can be strengthened when Indigenous knowledge is given the space to co-exist with the hegemony of current western science concepts. This research presents a case study of one primary school involved in the Indigenous Sky Stories Program. It showcases how teachers and students worked in conjunction with their local community to implement the program. The results suggest that introducing cultural sky stories into the science program, engaged and primed Year 5 and 6 students to seek out additional sky stories and to investigate the astronomical content mapped to the National Science Curriculum. The involvement of Aboriginal elders and community enriched the experience for all involved. The integrated science program appears to generate positive engagement for both Indigenous students and their non-Indigenous peers. Additionally, the program provided a valuable template for teachers to emulate and which can act as a model for the requirement to include Indigenous perspectives in the new National Science Curriculum."], "field": "Health Professions", "q_year": 2020, "q_cid": "255155321", "pos_cid": 55425380, "source": "eval_collection"}
{"query_id": "scaleup_24987353_16954911", "query": "How to understand the institutional, political, organizational, and governance influences on BC’s COVID-19 policy decisions while accounting for existing ideas and relevant unanticipated insights", "pos": ["Demonstrating Rigor Using Thematic Analysis: A Hybrid Approach of Inductive and Deductive Coding and Theme Development. In this article, the authors describe how they used a hybrid process of inductive and deductive thematic analysis to interpret raw data in a doctoral study on the role of performance feedback in the self-assessment of nursing practice. The methodological approach integrated data-driven codes with theory-driven ones based on the tenets of social phenomenology. The authors present a detailed exemplar of the staged process of data coding and identification of themes. This process demonstrates how analysis of the raw data from interview transcripts and organizational documents progressed toward the identification of overarching themes that captured the phenomenon of performance feedback as described by participants in the study."], "field": "Health Professions", "q_year": 2022, "q_cid": "249873530", "pos_cid": 16954911, "source": "eval_collection"}
{"query_id": "scaleup_28165210_21472361", "query": "How to explain shifts from over-responsiveness to under-responsiveness, cumulative strain, and maladaptive outcomes under prolonged demands during military training", "pos": ["A new model for the HPA axis explains dysregulation of stress hormones on the timescale of weeks. Stress activates a complex network of hormones known as the Hypothalamic-Pituitary-Adrenal (HPA) axis. The HPA axis is dysregulated in chronic stress and psychiatric disorders, but the origin of this dysregulation is unclear and cannot be explained by current HPA models. To address this, we developed a new mathematical model for the HPA axis that incorporates changes in the total functional mass of the HPA hormone-secreting glands. The mass changes are caused by the HPA hormones which act as growth factors for the glands in the axis. We find that the HPA axis shows the property of dynamical compensation, where gland masses adjust over weeks to buffer variation in physiological parameters. These mass changes explain the experimental findings on dysregulation of cortisol and ACTH dynamics in alcoholism, anorexia and postpartum. Dysregulation occurs for a wide range of parameters, and is exacerbated by impaired glucocorticoid receptor (GR) feedback, providing an explanation for the implication of GR in mood disorders. These findings suggest that gland-mass dynamics may play an important role in the pathophysiology of stress-related disorders. Author Summary The HPA axis is a neuroendocrine axis that is activated in response to stressors. The classical description of this axis includes three hormones that act in a cascade, with the final hormone cortisol inhibiting the two upstream hormones, ACTH and CRH. This classical picture has timescales of hours due to hormone half-lives, and cannot explain phenomena on the scale of weeks to months associated with this axis, such as the dysregulation observed in depression, alcohol addiction, postpartum, and other conditions. Here, we use a minimal-model approach to add to the classical model two known interactions in which CRH and ACTH not only regulate downstream hormones, but also act as growth factors for the cells that secrete these hormones. This creates a physiological circuit that can maintain total cell mass and buffer parameter changes. It has a fragility in which after prolonged stress, the total cell functional masses grow and take weeks to return to baseline. This is sufficient to explain the specific dynamics of hormone dysregulation found in several contexts. It also quantifies the effect of the cortisol (glucocorticoid) receptor on resilience to prolonged stress. Our findings suggest that interactions between hormones and cell functional mass may play an important role in HPA axis regulation on the timescale of weeks to months. Synopsis The HPA axis helps the body adapt to stress, but becomes dysregulated after prolonged activation, with clinical consequences. The origin of this dysregulation is unclear. We provide a mechanism for dysregulation based on the effect of the HPA hormones as growth factors for their downstream glands. A mathematical model that includes gland functional mass dynamics, introduces a new slow timescale of weeks to the HPA axis; previous models had only fast timescales of hours. The gland masses grow during prolonged activation, providing dynamical compensation, and recover with overshoots over weeks after withdrawal of activation. These overshoots are sufficient to explain the observed HPA dysregulation in pathological conditions, and clarify the role of glucocorticoid receptors in resilience to prolonged stress."], "field": "Health Professions", "q_year": 2025, "q_cid": "281652102", "pos_cid": 214723616, "source": "eval_collection"}
{"query_id": "scaleup_27634438_16373812", "query": "How to determine whether weight stigmatization in middle childhood impairs the development of appetite self-regulation and whether this impairment helps explain its association with adolescent weight", "pos": ["Stress and the Development of Self-Regulation in Context. This article considers the effects of psychosocial stress on child development and describes mechanisms through which early stress in the context of poverty affects the functioning of neural networks that underlie executive functions and self-regulation. It examines the effects of early experience on glucocorticoid and catecholamine levels that influence neural activity in areas of the brain associated with executive functions, primarily as studied in animal models. Finally, it considers the strengths and limitations of this research, its relevance to understanding stress reactivity from the perspective of biological sensitivity to context, and the implications for the study of risk and resilience processes and early intervention to prevent developmental delays."], "field": "Health Professions", "q_year": 2025, "q_cid": "276344384", "pos_cid": 16373812, "source": "eval_collection"}
{"query_id": "scaleup_28165210_49484691", "query": "How to determine which consumer wrist-worn wearable signals are suitable for assessing cumulative stress in military training environments", "pos": ["A Critical Review of Consumer Wearables, Mobile Applications, and Equipment for Providing Biofeedback, Monitoring Stress, and Sleep in Physically Active Populations. The commercial market for technologies to monitor and improve personal health and sports performance is ever expanding. A wide range of smart watches, bands, garments, and patches with embedded sensors, small portable devices and mobile applications now exist to record and provide users with feedback on many different physical performance variables. These variables include cardiorespiratory function, movement patterns, sweat analysis, tissue oxygenation, sleep, emotional state, and changes in cognitive function following concussion. In this review, we have summarized the features and evaluated the characteristics of a cross-section of technologies for health and sports performance according to what the technology is claimed to do, whether it has been validated and is reliable, and if it is suitable for general consumer use. Consumers who are choosing new technology should consider whether it (1) produces desirable (or non-desirable) outcomes, (2) has been developed based on real-world need, and (3) has been tested and proven effective in applied studies in different settings. Among the technologies included in this review, more than half have not been validated through independent research. Only 5% of the technologies have been formally validated. Around 10% of technologies have been developed for and used in research. The value of such technologies for consumer use is debatable, however, because they may require extra time to set up and interpret the data they produce. Looking to the future, the rapidly expanding market of health and sports performance technology has much to offer consumers. To create a competitive advantage, companies producing health and performance technologies should consult with consumers to identify real-world need, and invest in research to prove the effectiveness of their products. To get the best value, consumers should carefully select such products, not only based on their personal needs, but also according to the strength of supporting evidence and effectiveness of the products."], "field": "Health Professions", "q_year": 2025, "q_cid": "281652102", "pos_cid": 49484691, "source": "eval_collection"}
{"query_id": "scaleup_22090915_75135422", "query": "How to explain why focusing on a limited, prominent visual target may delay reaching steady balance during continuous disturbances to standing", "pos": ["Getting rid of visual distractors: the why, when, how, and where.. Distractor suppression, or the ability to disregard salient distractors while dealing with task-relevant information, is a key component of selective attention. Recent research has shown that distractor suppression can take place in different circumstances and present itself in different guises, which is presumably paralleled by a multiplicity of underlying neural mechanisms. In this review article, we discuss a number of central themes concerning distractor suppression and the underlying neural mechanisms, and also highlight several unresolved issues that will have to be addressed in future investigations."], "field": "Health Professions", "q_year": 2020, "q_cid": "220909155", "pos_cid": 75135422, "source": "eval_collection"}
{"query_id": "scaleup_28194600_25966627", "query": "How to understand healthcare access when migration status, socio-economic position, and social isolation interact amid overlapping identities and structural inequities", "pos": ["Intersectionality as a theoretical framework for researching health inequities in chronic pain. Chronic pain is experienced unequally by different population groups; we outline examples from the pain literature of inequities related to gender, ethnicity, socioeconomic and migration status. Health inequities are systematic, avoidable and unfair differences in health outcomes between groups of people, with the fundamental ‘causes of causes’ recognised as unequal distribution of income, power and wealth. Intersectionality can add further theory to health inequities literature; collective social identities including class/socioeconomic status, race/ethnicity, gender, migration status, age, sexuality and disabled status intersect in multiple interconnected systems of power leading to differing experiences of privilege and oppression which can be understood as axes of health inequities. The process of knowledge creation in pain research is shaped by these interconnected systems of power, and may perpetuate inequities in pain care as it is largely based on majority white, middle class, Eurocentric populations. Intersectionality can inform research epistemology (ways of knowing), priorities, methodology and methods. We give examples from the literature where intersectionality has informed a justice oriented approach across different research methods and we offer suggestions for further development. The use of a reductionist frame can force unachievable objectivity on to complex health concepts, and we note increasing realisation in the field of the need to understand the individuals within their social world, and recognise the fluid and contextual nature of this."], "field": "Health Professions", "q_year": 2025, "q_cid": "281946002", "pos_cid": 259666271, "source": "eval_collection"}
{"query_id": "scaleup_21126270_7617754", "query": "How to remain aware of and make clear how one’s position, perspective, and relationship shape understanding of a person’s case when closely involved with them", "pos": ["Researcher–researched relationship in qualitative research: Shifts in positions and researcher vulnerability. Background The researcher role is highly debated in qualitative research. This article concerns the researcher-researched relationship. Methods A group of health science researchers anchored in various qualitative research traditions gathered in reflective group discussions over a period of two years. Results Efforts to establish an anti-authoritarian relationship between researcher and researched, negotiation of who actually “rules” the research agenda, and experiences of shifts in “inferior” and “superior” knowledge positions emerged as central and intertwined themes throughout the discussions. The dual role as both insider and outsider, characteristic of qualitative approaches, seemed to lead to power relations and researcher vulnerability which manifested in tangible ways. Conclusion Shifting positions and vulnerability surfaced in various ways in the projects. They nonetheless indicated a number of similar experiences which can shed light on the researcher-researched relationship. These issues could benefit from further discussion in the qualitative health research literature."], "field": "Health Professions", "q_year": 2020, "q_cid": "211262705", "pos_cid": 7617754, "source": "eval_collection"}
{"query_id": "scaleup_26760783_28766187", "query": "How to address ethical dilemmas as they arise in qualitative researchers’ interactions with participants while maintaining research rigor and credibility", "pos": ["Reflexivity and the Capacity to Think. Reflexivity is fundamental to qualitative health research, yet notoriously difficult to unpack. Drawing on Wilfred Bion’s work on the development of the capacity to think and to learn, I show how the capacity to think is an impermanent and fallible capacity, with the potential to materialize or evaporate at any number of different points. I use this conceptualization together with examples from published interview data to illustrate the difficulties for researchers attempting to sustain a reflexive approach, and to direct attention toward the possibilities for recovering and supporting the capacity to think. I counter some of the criticisms suggesting that reflexivity can be self-indulgent, and suggest instead that self-indulgence constitutes a failure of reflexivity. In the concluding discussions I acknowledge tensions accompanying the use of psychoanalytic theories for research purposes, and point to emerging psychosocial approaches as one way of negotiating these."], "field": "Health Professions", "q_year": 2024, "q_cid": "267607834", "pos_cid": 28766187, "source": "eval_collection"}
{"query_id": "scaleup_28317483_25010723", "query": "How to explain why companies with the same legal obligations differ in which occupational health and safety issues they consider important and how much detail they make public", "pos": ["Stakeholder or Legitimacy Theory? The Rationale behind a Company’s Materiality Analysis: Evidence from Indonesia. Recently, more and more research has examined sustainability reports, including how to process materiality analysis in sustainability reports. However, the motivation for why and how companies prepare materiality analysis has not received much attention from researchers. This study fills a gap in the sustainability literature related to materiality analysis by identifying the theoretical motivations of companies in conducting materiality analysis. The literature review on materiality analysis also showed that the existing measurements have not used the GRI 102-46 and 102-47, which are guidelines for companies in conducting materiality analysis based on the GRI. Therefore, this study developed a measurement of materiality analysis based on GRI 102-46 and 102-47. This study aimed to assess materiality analysis in sustainability reports based on the perspectives of legitimacy theory and stakeholder theory. The research sample was 150 sustainability reports of company listed on the Indonesia Stock Exchange from 2018 to 2020. The researcher developed an index using the GRI approach to measure the quality of materiality analysis. This study proves that the legitimacy theory perspective is mainly the basis for the company in conducting materiality analysis. This study also found no significant improvement in the quality of materiality topic analysis from 2018 to 2020. Of the four financial characteristics, only DER has a significant relationship with materiality analysis, which indicates that the disclosure of materiality analysis tends to be related to the company’s debt condition. The study fills a gap in the literature by contributing to research on sustainability reporting quality, specifically on materiality analysis."], "field": "Health Professions", "q_year": 2025, "q_cid": "283174832", "pos_cid": 250107231, "source": "eval_collection"}
{"query_id": "scaleup_27877058_26503564", "query": "How to achieve sustained, equitable cervical screening promotion with inclusive language amid organizational demands, regulatory environments, political pressures, and socio-cultural norms", "pos": ["Revisiting the policy ecology framework for implementation of evidence-based practices in mental health settings. Background Over the past three decades, policy actors and actions have been highly influential in supporting the implementation of evidence-based practices (EBPs) in mental health settings. An early examination of these actions resulted in the Policy Ecology Framework (PEF), which was originally developed as a tactical primer for state and local mental health regulators in the field of child mental health. However, the policy landscape for implementation has evolved significantly since the original PEF was published. An interrogation of the strategies originally proposed in the PEF is necessary to provide an updated menu of strategies to improve our understanding of the mechanisms of policy action and promote system improvement. Objectives This paper builds upon the original PEF to address changes in the policy landscape for the implementation of mental health EBPs between 2009 and 2022. We review the current state of policy strategies that support the implementation of EBPs in mental health care and outline key areas for policy-oriented implementation research. Our review identifies policy strategies at federal, state, agency, and organizational levels, and highlights developments in the social context in which EBPs are implemented. Furthermore, our review is organized around some key changes that occurred across each PEF domain that span organizational, agency, political, and social contexts along with subdomains within each area. Discussion We present an updated menu of policy strategies to support the implementation of EBPs in mental health settings. This updated menu of strategies considers the broad range of conceptual developments and changes in the policy landscape. These developments have occurred across the organizational, agency, political, and social contexts and are important for policymakers to consider in the context of supporting the implementation of EBPs. Summary The updated PEF expands and enhances the specification of policy levers currently available, and identifies policy targets that are underdeveloped (e.g., de-implementation and sustainment) but are becoming visible opportunities for policy to support system improvement. The updated PEF clarifies current policy efforts within the field of implementation science in health to conceptualize and better operationalize the role of policy in the implementation of EBPs."], "field": "Health Professions", "q_year": 2025, "q_cid": "278770589", "pos_cid": 265035642, "source": "eval_collection"}
{"query_id": "scaleup_27288178_24750778", "query": "How to understand the psychological costs of capitalism’s promotion of wealth, image, and material success for self-esteem and self-worth", "pos": ["The effects of consumption on self-esteem.. Research on the effect of consumption on self-esteem is relatively scarce and related evidence is fragmented. We review articles from the literature on consumption, advertising, materialism, mass media, and social media as they relate - directly or indirectly - to consumer self-esteem. We introduce a taxonomy of eight types of processes through which consumption affects self-esteem: self-discrepancy, self-congruency, self-enhancement, self-determination, compensatory consumption, self-verification, self-object association, and market-mediated relationships. Based on this taxonomy, we highlight consumption domains and recent consumer trends that impact self-esteem. Moreover, we suggest priorities for further research."], "field": "Health Professions", "q_year": 2024, "q_cid": "272881789", "pos_cid": 247507787, "source": "eval_collection"}
{"query_id": "scaleup_23758876_21939983", "query": "How to identify non-clinical practitioner and practice factors influencing whether general dentists perceive specialists as colleagues or competitors", "pos": ["What influences the clinical decision-making of dentists? A cross-sectional study. Clinical decision-making is a complex process influenced by clinical and non-clinical factors. The aim of this study was to investigate the association between provider, patient, and practice factors with clinical decision-making among dentists in Ontario, Canada’s most populated province and its largest dental care market. This was a cross-sectional, self-administered survey of a random sample of general dentists in Ontario (n = 3,201). The 46-item survey collected demographic, professional, and practice information. The outcome (treatment intensity) was measured using a set of clinical scenarios, which categorized dentists as either relatively aggressive or conservative in their treatment decisions. Associations were assessed using bivariate analysis and logistic regressions. One thousand and seventy-five dentists responded (33.6% response rate). Age (p = 0.001), place of initial training (p<0.001), number of dependents (p = 0.001), number of hygienists employed (p = 0.001), and perceptions of practice loans (p = 0.020) were associated with treatment intensity. Dentists who were <40-years old (OR = 2.06, 95% CI:1.39–3.06, p<0.001), American-trained (OR = 2.48, 95% CI:1.51–4.06, p<0.001), and perceived their practice loans as large (OR = 1.57, 95% CI:1.02–2.42, p = 0.039), were relatively more aggressive in their treatment decisions. Various non-clinical factors appear to influence the clinical decision-making of dentists in Ontario."], "field": "Health Professions", "q_year": 2021, "q_cid": "237588767", "pos_cid": 219399831, "source": "eval_collection"}
{"query_id": "scaleup_22630237_3515507", "query": "How to protect the health and psychological well-being of anesthetists caring for COVID-19 patients to support optimal patient care", "pos": ["Evidence-Based Guidelines for Fatigue Risk Management in Emergency Medical Services. Abstract Background: Administrators of Emergency Medical Services (EMS) operations lack guidance on how to mitigate workplace fatigue, which affects greater than half of all EMS personnel. The primary objective of the Fatigue in EMS Project was to create an evidence-based guideline for fatigue risk management tailored to EMS operations. Methods: Systematic searches were conducted from 1980 to September 2016 and guided by seven research questions framed in the Population, Intervention, Comparison, Outcome (PICO) framework. Teams of investigators applied inclusion criteria, which included limiting the retained literature to EMS personnel or similar shift worker groups. The expert panel reviewed summaries of the evidence based on the Grading of Recommendations, Assessment, Development and Evaluation (GRADE) methodology. The panel evaluated the quality of evidence for each PICO question separately, considered the balance between benefits and harms, considered the values and preferences of the targeted population, and evaluated the resource requirements/needs. The GRADE Evidence-to-Decision (EtD) Framework was used to prepare draft recommendations based on the evidence, and the Content Validity Index (CVI) was used to quantify the panel's agreement on the relevance and clarity of each recommendation. CVI scores for relevance and clarity were measured separately on a 1–4 scale to indicate consensus/agreement among panel members and conclusion of recommendation development. Results: The EtD framework was applied to all 7 PICO questions, and the panel created 5 recommendations. PICO1: The panel recommends using fatigue/sleepiness survey instruments to measure and monitor fatigue in EMS personnel. PICO2: The panel recommends that EMS personnel work shifts shorter than 24 hours in duration. PICO3: The panel recommends that EMS personnel have access to caffeine as a fatigue countermeasure. PICO4: The panel recommends that, EMS personnel have the opportunity to nap while on duty to mitigate fatigue. PICO5: The panel recommends that EMS personnel receive education and training to mitigate fatigue and fatigue-related risks. The panel referenced insufficient evidence as the reason for making no recommendation linked to 2 PICO questions. Conclusions: Based on a review of the evidence, the panel developed a guideline with 5 recommendations for fatigue risk management in EMS operations."], "field": "Health Professions", "q_year": 2020, "q_cid": "226302372", "pos_cid": 3515507, "source": "eval_collection"}
{"query_id": "scaleup_26163399_41218016", "query": "How to ensure frontline healthcare professionals in underserved or remote communities have timely, reliable clinical guidance and the knowledge, confidence, and motivation to apply it, especially nurses with limited training in concurrent disorder management", "pos": ["Outcomes of Hepatitis C Treatment by Primary Care Providers. Background The Extension for Community Healthcare Outcomes (ECHO) model was developed to improve access to care for complex health problems such as hepatitis C virus (HCV) infection for underserved populations. Using videoconferencing technology, ECHO trains primary care providers to treat complex diseases. Methods A prospective cohort study compared treatment of HCV at the University of New Mexico (UNM) HCV clinic to treatment by primary care clinicians at 21 ECHO sites in rural areas and prisons in New Mexico. A total of 407 treatment naive patients with chronic HCV were enrolled. The primary end point was a sustained viral response (SVR). Results The rate of SVR was 57.5% (84/146) for patients treated at UNM and 58.2% (152 /261) at ECHO sites (P=0.89); difference between SVR rates 0.7% (95% CI -9.2%, 10.7%). In genotype 1 infection the SVR rate was 45.8% (38 /83) at UNM and 49.7% (73 /147) at ECHO sites (P=0.57). Serious adverse events occurred in 13.7% of the UNM HCV clinic cohort and 6.9% of the ECHO cohort. Conclusions This study demonstrates that the ECHO model is an effective way to treat HCV in underserved communities. Implementation of this model would allow other states and nations to treat more patients with HCV."], "field": "Health Professions", "q_year": 2023, "q_cid": "261633990", "pos_cid": 41218016, "source": "eval_collection"}
{"query_id": "scaleup_25811521_1837377", "query": "How to determine whether Turkish Safety Climate Survey scores are sufficiently stable over time", "pos": ["A Guideline of Selecting and Reporting Intraclass Correlation Coefficients for Reliability Research.. OBJECTIVE Intraclass correlation coefficient (ICC) is a widely used reliability index in test-retest, intrarater, and interrater reliability analyses. This article introduces the basic concept of ICC in the content of reliability analysis. DISCUSSION FOR RESEARCHERS There are 10 forms of ICCs. Because each form involves distinct assumptions in their calculation and will lead to different interpretations, researchers should explicitly specify the ICC form they used in their calculation. A thorough review of the research design is needed in selecting the appropriate form of ICC to evaluate reliability. The best practice of reporting ICC should include software information, \"model,\" \"type,\" and \"definition\" selections. DISCUSSION FOR READERS When coming across an article that includes ICC, readers should first check whether information about the ICC form has been reported and if an appropriate ICC form was used. Based on the 95% confident interval of the ICC estimate, values less than 0.5, between 0.5 and 0.75, between 0.75 and 0.9, and greater than 0.90 are indicative of poor, moderate, good, and excellent reliability, respectively. CONCLUSION This article provides a practical guideline for clinical researchers to choose the correct form of ICC and suggests the best practice of reporting ICC parameters in scientific publications. This article also gives readers an appreciation for what to look for when coming across ICC while reading an article."], "field": "Health Professions", "q_year": 2023, "q_cid": "258115219", "pos_cid": 1837377, "source": "eval_collection"}
{"query_id": "scaleup_24987353_55740", "query": "How to understand institutional, political, organizational, and governance influences on BC’s COVID-19 policy decisions when a single evidence source may provide only a partial picture", "pos": ["The case study approach. The case study approach allows in-depth, multi-faceted explorations of complex issues in their real-life settings. The value of the case study approach is well recognised in the fields of business, law and policy, but somewhat less so in health services research. Based on our experiences of conducting several health-related case studies, we reflect on the different types of case study design, the specific research questions this approach can help answer, the data sources that tend to be used, and the particular advantages and disadvantages of employing this methodological approach. The paper concludes with key pointers to aid those designing and appraising proposals for conducting case study research, and a checklist to help readers assess the quality of case study reports."], "field": "Health Professions", "q_year": 2022, "q_cid": "249873530", "pos_cid": 55740, "source": "eval_collection"}
{"query_id": "scaleup_25903751_60285653", "query": "How to explain what young pupils can do when jointly creating texts in different forms, given teachers’ planned activities, pupils’ own choices, and available resources", "pos": ["Designs for learning : A theoretical perspective. In this article, I will introduce a perspective on learning as complex processes of transformations of signs, by way of modes and media in different institutional settings. I will also discuss a design theoretic perspective in relation to different framings of knowledge and learning practices."], "field": "Health Professions", "q_year": 2023, "q_cid": "259037517", "pos_cid": 60285653, "source": "eval_collection"}
{"query_id": "scaleup_25330458_49266726", "query": "How to understand what patients first notice in information about positive, neutral, and negative doctor–patient relationships", "pos": ["Effects of social and affective content on exogenous attention as revealed by event-related potentials. ABSTRACT The social content of affective stimuli has been proposed as having an influence on cognitive processing and behaviour. This research was aimed, therefore, at studying whether automatic exogenous attention demanded by affective pictures was related to their social value. We hypothesised that affective social pictures would capture attention to a greater extent than non-social affective stimuli. For this purpose, we recorded event-related potentials in a sample of 24 participants engaged in a digit categorisation task. Distracters were affective pictures varying in social content, in addition to affective valence and arousal, which appeared in the background during the task. Our data revealed that pictures depicting high social content captured greater automatic attention than other pictures, as reflected by the greater amplitude and shorter latency of anterior P2, and anterior and posterior N2 components of the ERPs. In addition, social content also provoked greater allocation of processing resources as manifested by P3 amplitude, likely related to the high arousal they elicited. These results extend data from previous research by showing the relevance of the social value of the affective stimuli on automatic attentional processing."], "field": "Health Professions", "q_year": 2022, "q_cid": "253304586", "pos_cid": 49266726, "source": "eval_collection"}
{"query_id": "scaleup_25333611_15142082", "query": "How to determine whether self-paid training helps people handle technology-related threats to job quality or makes switching off harder when those threats remain on their minds", "pos": ["Non‐Work Time Activities Predicting Teachers’ Work‐Related Fatigue and Engagement: An Effort‐Recovery Approach. Objective Drawing on the effort‐recovery model of work stress, this study examined the effects of school teachers’ sleep quality and time spent in various non‐work time activities on work‐related stress and motivational outcomes. We proposed that sleep quality and different types of non‐work time activities would have differential effects on levels of work‐related fatigue and engagement. Method Nine hundred and sixty Australian school teachers (mean age 46-years, 707 females, 237 males) completed a cross‐sectional online survey measuring sleep quality, time spent in non‐work time activities, and work‐related fatigue and engagement. Results Teachers spent relatively higher amounts of time on work‐related activities outside of formal work hours, and lower amounts of time on health‐promoting activities such as exercise. Multiple regression analyses indicated that sleep quality was related to reduced fatigue and increased engagement, while time spent socialising outside of work was related to reduced fatigue. Time spent on work‐related tasks outside of working hours was related to both increased fatigue and engagement. Other activities, including passive activity, exercise, and hobbies, were not significantly related to either outcome. Conclusions We discuss the implications of our findings in relation to theories and research in work stress, particularly in the context of where priorities should be placed for self‐care interventions to facilitate teachers’ day‐to‐day recovery from work demands."], "field": "Health Professions", "q_year": 2022, "q_cid": "253336115", "pos_cid": 151420821, "source": "eval_collection"}
{"query_id": "scaleup_25143548_16646795", "query": "How to determine whether inertial sensor and camera-based gait joint-angle measurements differ systematically for each joint motion or show variable disagreement, and whether they are interchangeable", "pos": ["Understanding Bland Altman analysis. In a contemporary clinical laboratory it is very common to have to assess the agreement between two quantitative methods of measurement. The correct statistical approach to assess this degree of agreement is not obvious. Correlation and regression studies are frequently proposed. However, correlation studies the relationship between one variable and another, not the differences, and it is not recommended as a method for assessing the comparability between methods. In 1983 Altman and Bland (B&A) proposed an alternative analysis, based on the quantification of the agreement between two quantitative measurements by studying the mean difference and constructing limits of agreement. The B&A plot analysis is a simple way to evaluate a bias between the mean differences, and to estimate an agreement interval, within which 95% of the differences of the second method, compared to the first one, fall. Data can be analyzed both as unit differences plot and as percentage differences plot. The B&A plot method only defines the intervals of agreements, it does not say whether those limits are acceptable or not. Acceptable limits must be defined a priori, based on clinical necessity, biological considerations or other goals. The aim of this article is to provide guidance on the use and interpretation of Bland Altman analysis in method comparison studies."], "field": "Health Professions", "q_year": 2022, "q_cid": "251435480", "pos_cid": 16646795, "source": "eval_collection"}
{"query_id": "scaleup_27033420_25373319", "query": "How to understand how interacting work-environment conditions affect care aides’ use of best practices in long-term care homes when several conditions may be required together and different combinations may lead to the same outcome", "pos": ["Facility-level program components leading to population impact: a coincidence analysis of obesity treatment options within the Veterans Health Administration.. Obesity is a well-established risk factor for increased morbidity and mortality. Comprehensive lifestyle interventions, pharmacotherapy, and bariatric surgery are three effective treatment approaches for obesity. The Veterans Health Administration (VHA) offers all three domains but in different configurations across medical facilities. Study aim was to explore the relationship between configurations of three types of obesity treatments, context, and population impact across VHA using coincidence analysis. This was a cross-sectional analysis of survey data describing weight management treatment components linked with administrative data to compute population impact for each facility. Coincidence analysis was used to identify combinations of treatment components that led to higher population impact. Facilities with higher impact were in the top two quintiles for (1) reach to eligible patients and (2) weight outcomes. Sixty-nine facilities were included in the analyses. The final model explained 88% (29/33) of the higher-impact facilities with 91% consistency (29/32) and was comprised of five distinct pathways. Each of the five pathways depended on facility complexity-level plus factors from one or more of the three domains of weight management: comprehensive lifestyle interventions, pharmacotherapy, and/or bariatric surgery. Three pathways include components from multiple treatment domains. Combinations of conditions formed \"recipes\" that lead to higher population impact. Our coincidence analyses highlighted both the importance of local context and how combinations of specific conditions consistently and uniquely distinguished higher impact facilities from lower impact facilities for weight management."], "field": "Health Professions", "q_year": 2024, "q_cid": "270334208", "pos_cid": 253733195, "source": "eval_collection"}
{"query_id": "scaleup_28165210_24971479", "query": "How to determine whether body-mass loss during military training indicates sustained physiological changes under energy deficits of varying severity and duration", "pos": ["Moderate Weight Loss is associated with Reductions in LH Pulse Frequency and Increases in 24-hour Cortisol with no change in Perceived Stress in Young Ovulatory Women.. OBJECTIVE Determine the potential role of cortisol as an indicator of both metabolic and psychosocial stress and its relation to LH pulse dynamics during a three-month diet and exercise intervention causing moderate weight loss. METHODS Secondary analysis of a randomized, controlled trial that demonstrated the causal role of low energy availability in the disruption of the menstrual cycle. Twenty-one women aged (18-24 yrs), BMI (21.7± 1.9 kg·m-2), completed a baseline menstrual cycle and three intervention menstrual cycles of a controlled diet and supervised exercise program. Twenty-four-hour LH pulse dynamics (q10 min) and diurnal patterns of cortisol (q60 min) as well as Perceived Stress Scale scores were determined in the early follicular phase prior to the intervention and in the post intervention cycle. Pre to post comparisons were determined with paired t-tests, and Pearson bivariate correlations assessed associations. RESULTS Subjects lost weight (-2.8±1.97 kg) and LH pulse frequency declined pre=0.79±0.23 pulses·hr-1 to post=0.60±0.29 pulses·hr-1 (p=0.014). Weight loss was associated with an increase in cortisol AUC R=-0.473, (p=0.03) and the decline in LH pulse frequency R= 0.523; (p=0.026). Increases in cortisol AUC were associated with declines in LH pulse frequency R=-0.472; (p=0.048). The morning cortisol rise AUC increased from pre=2140±878 µg·dL-1 · day to post=2556±1067 µg·dL-1 · day (p=0.034). Changes in PSS were not associated with changes in LH or cortisol. CONCLUSION The initial perturbation of LH pulsatility with moderate diet and exercise is associated with metabolically driven increases in cortisol AUC with no influence of psychological stress."], "field": "Health Professions", "q_year": 2025, "q_cid": "281652102", "pos_cid": 249714791, "source": "eval_collection"}
{"query_id": "scaleup_23820225_17585970", "query": "How to sustain engagement and adherence to recommended health behaviors among adolescents with obesity before clinic-based weight management begins", "pos": ["Supportive Accountability: A Model for Providing Human Support to Enhance Adherence to eHealth Interventions. The effectiveness of and adherence to eHealth interventions is enhanced by human support. However, human support has largely not been manualized and has usually not been guided by clear models. The objective of this paper is to develop a clear theoretical model, based on relevant empirical literature, that can guide research into human support components of eHealth interventions. A review of the literature revealed little relevant information from clinical sciences. Applicable literature was drawn primarily from organizational psychology, motivation theory, and computer-mediated communication (CMC) research. We have developed a model, referred to as “Supportive Accountability.” We argue that human support increases adherence through accountability to a coach who is seen as trustworthy, benevolent, and having expertise. Accountability should involve clear, process-oriented expectations that the patient is involved in determining. Reciprocity in the relationship, through which the patient derives clear benefits, should be explicit. The effect of accountability may be moderated by patient motivation. The more intrinsically motivated patients are, the less support they likely require. The process of support is also mediated by the communications medium (eg, telephone, instant messaging, email). Different communications media each have their own potential benefits and disadvantages. We discuss the specific components of accountability, motivation, and CMC medium in detail. The proposed model is a first step toward understanding how human support enhances adherence to eHealth interventions. Each component of the proposed model is a testable hypothesis. As we develop viable human support models, these should be manualized to facilitate dissemination."], "field": "Health Professions", "q_year": 2020, "q_cid": "238202255", "pos_cid": 17585970, "source": "eval_collection"}
{"query_id": "scaleup_28165210_22114480", "query": "How to clarify relationships among chronic military training, psychological wellbeing, and musculoskeletal health to support early prevention of injury, underperformance, and psychological harm", "pos": ["Allostatic Load and Its Impact on Health: A Systematic Review. Introduction: Allostatic load refers to the cumulative burden of chronic stress and life events. It involves the interaction of different physiological systems at varying degrees of activity. When environmental challenges exceed the individual ability to cope, then allostatic overload ensues. Allostatic load is identified by the use of biomarkers and clinical criteria. Objective: To summarize the current knowledge on allostatic load and overload and its clinical implications based on a systematic review of the literature. Methods: PubMed, PsycINFO, Web of Science, and the Cochrane Library were searched from inception to December 2019. A manual search of the literature was also performed, and reference lists of the retrieved articles were examined.We considered only studies in which allostatic load or overload were adequately described and assessed in either clinical or non-clinical adult populations. Results: A total of 267 original investigations were included. They encompassed general population studies, as well as clinical studies on consequences of allostatic load/overload on both physical and mental health across a variety of settings. Conclusions: The findings indicate that allostatic load and overload are associated with poorer health outcomes. Assessment of allostatic load provides support to the understanding of psychosocial determinants of health and lifestyle medicine. An integrated approach that includes both biological markers and clinimetric criteria is recommended."], "field": "Health Professions", "q_year": 2025, "q_cid": "281652102", "pos_cid": 221144801, "source": "eval_collection"}
{"query_id": "scaleup_25806462_21107287", "query": "How to identify the words children prefer when discussing their weight", "pos": ["Youth perspectives on weight-related words used by healthcare professionals. A qualitative study.. BACKGROUND Although healthcare professionals often consider body weight a sensitive and difficult topic to discuss with children, a contextualized and comprehensive understanding of youth perspectives on weight-related words used in healthcare has yet to be established. This qualitative study aims to explore perspectives of Dutch children on the terminology healthcare professionals use when discussing weight. METHODS Fourteen interviews and one focus group discussion were held with children (age 8-16) who were in care because of their weight. A toolkit with customizable interview techniques was used in order to facilitate reflection and tailor the interview to each respondent. A narrative content analysis was conducted. RESULTS Respondents attached both clear and subtle differences in meanings to (certain) weight-related words. Their perspectives were not unanimous for any single word. Moreover, at times, respondents framed certain words in positive or negative ways, or used a word they disliked to describe themselves. This illustrates that meanings of weight-related words are not fixed, but context and situation specific. CONCLUSION This study revealed that meanings children assign to weight-related words are shaped by their experiences in the broader social context, especially at school, as well as with (previous) healthcare professionals. It pointed towards the importance of bedside manner, acquaintanceship, and support. Healthcare professionals treating children because of their body weight are advised to invest in a good patient-caregiver relationship, pay attention to children's previous (negative) social weight-related experiences, and reflect critically on their own preconceptions about body weight and the impact these preconceptions might have on their patient-caregiver relationships."], "field": "Health Professions", "q_year": 2023, "q_cid": "258064620", "pos_cid": 211072874, "source": "eval_collection"}
{"query_id": "scaleup_28399273_11983098", "query": "How to determine whether visual attention differs across age, education, and household groups and identify which groups differ, without assuming a particular data distribution and while limiting false positives across multiple comparisons", "pos": ["Methodology and Application of the Kruskal-Wallis Test. This paper describes the methodology and application of the very popular nonparametric test which is a rank based test named as Kruskal-Wallis. This test is useful as a general nonparametric test for comparing more than two independent samples. It can be used to test whether such samples come from the same distribution. This test is powerful alternative to the one-way analysis of variance. Nonparametric ANOVA has no assumption of normality of random error but the independence of random error is required. If the Kruskal-Wallis statistic is significant, the nonparametric multiple comparison tests are useful methods for further analysis. The statistical analysis of the application data in this paper was performed with software MATLAB."], "field": "Health Professions", "q_year": 2025, "q_cid": "283992738", "pos_cid": 119830984, "source": "eval_collection"}
{"query_id": "scaleup_27802427_54549167", "query": "How to define meaningful categories for values with boundaries that do not obscure similarities among values or differences between groups", "pos": ["RESEARCH ON GEOGRAPHICAL ENVIRONMENT UNIT DIVISION BASED ON THE METHOD OF NATURAL BREAKS (JENKS). Abstract. Zoning which is to divide the study area into different zones according to their geographical differences at the global, national or regional level, includes natural division, economic division, geographical zoning of departments, comprehensive zoning and so on. Zoning is of important practical significance, for example, knowing regional differences and characteristics, regional research and regional development planning, understanding the favorable and unfavorable conditions of the regional development etc. Geographical environment is arising from the geographical position linkages. Geographical environment unit division is also a type of zoning. The geographical environment indicators are deeply studied and summed up in the article, including the background, the associated and the potential. The background indicators are divided into four categories, such as the socio-economic, the political and military, the strategic resources and the ecological environment, which can be divided into more sub-indexes. While the sub-indexes can be integrated to comprehensive index system by weighted stacking method. The Jenks natural breaks classification method, also called the Jenks optimization method, is a data classification method designed to determine the best arrangement of values into different classes. This is done by seeking to minimize each class’s average deviation from the class mean, while maximizing each class’s deviation from the means of the other groups. In this paper, the experiment of Chinese surrounding geographical environment unit division has been done based on the natural breaks (jenks) method, the geographical environment index system and the weighted stacking method, taking South Asia as an example. The result indicates that natural breaks (jenks) method is of good adaptability and high accuracy on the geographical environment unit division. The geographical environment research was originated in the geopolitics and flourished in the geo-economics. The main representatives of the geopolitics are German geographer Friedrich Ratzel, British geographer Mackinder and American geographical politician Nicholas John Spykman etc. The main representative of the geo-economics is American geographical economist Edward Luttwak. China has the most neighboring countries in the world, and its geographical environment is extremely complex. With the continuous development of globalization, China's relations with neighboring countries have become more complex and more closely. So it is very meaningful to have depth research on geographical environment unit division of China."], "field": "Health Professions", "q_year": 2025, "q_cid": "278024271", "pos_cid": 54549167, "source": "eval_collection"}
{"query_id": "scaleup_25285032_55891432", "query": "How to understand Generation Y medical doctors’ experiences of a group Positive Psychology 2.0 burnout intervention in a South African public hospital, including perceived benefits and needed amendments within their cultural context", "pos": ["Husserlian Descriptive Phenomenology: A review of intentionality, reduction and the natural attitude. Background and aim: Descriptive phenomenology is widely used in social science research as a method to explore and describe the lived experience of individuals. It is a philosophy and a scientific method and has undertaken many variations as it has moved from the original European movement to include the American movement. The aim of this paper is to describe descriptive phenomenology in the tradition of Edmund Husserl. Integrative literature discussing the nature of descriptive phenomenology was used within this paper to elucidate the core fundamental principles of Husserlian descriptive phenomenology. Methods: This is a methodology paper that provides both an overview of the historical context and the development of descriptive phenomenology in the tradition of Husserl. Results and discussion: Descriptive phenomenology is explained from its historical underpinnings. The principles of the natural attitude, intentionality and the phenomenological reduction are described and using practical examples illustrate how each of these principles is applied within a research context. Conclusions: Understanding the key philosophical foundations of Husserlian descriptive phenomenology as a research method can be daunting to the uninitiated. This paper adds to the discussion around descriptive phenomenology and will assist and inform readers in understanding its key features as a research method."], "field": "Health Professions", "q_year": 2022, "q_cid": "252850328", "pos_cid": 55891432, "source": "eval_collection"}
{"query_id": "scaleup_28194600_18493647", "query": "How to sustain healthcare access for socio-economically vulnerable people facing systemic barriers in a fragmented healthcare system when informal social networks alone are insufficient", "pos": ["The provision of NHS health checks in a community setting: an ethnographic account. BackgroundThe UK National Health Service Health Checks programme aims to reduce avoidable cardiovascular deaths, disability and health inequalities in England. However, due to the reported lower uptake of screening in specific black and minority ethnic communities who are recognised as being more at risk of cardiovascular disease, there are concerns that NHS Health Checks may increase inequalities in health. This study aimed to examine the feasibility and acceptability of community outreach NHS Health Checks targeted at the Afro-Caribbean community.MethodsThis paper reports findings from an ethnographic study including direct observation of four outreach events in four different community venues in inner-city Bristol, England and follow up semi-structured interviews with attendees (n = 16) and staff (n = 4). Interviews and field notes were transcribed, anonymized and analysed thematically using a process of constant comparison.ResultsAnalysis revealed the value of community assets (community engagement workers, churches, and community centres) to publicise the event and engage community members. People were motivated to attend for preventative reasons, often prompted by familial experience of cardiovascular disease. Attendees valued outreach NHS Health Checks, reinforcing or prompting some to make healthy lifestyle changes. The NHS Health Check provided an opportunity for attendees to raise other health concerns with health staff and to discuss their test results with peers. For some participants, the communication of test results, risk and lifestyle information was confusing and unwelcome. The findings additionally highlight the need to ensure community venues are fit for purpose in terms of assuring confidentiality.ConclusionsOutreach events provide evidence of how local health partnerships (family practice staff and health trainers) and community assets, including informal networks, can enhance the delivery of outreach NHS Health Checks and in promoting the health of targeted communities. To deliver NHS Health Checks effectively, the location and timing of events needs to be carefully considered and staff need to be provided with the appropriate training to ensure patients are supported and enabled to make lifestyle changes."], "field": "Health Professions", "q_year": 2025, "q_cid": "281946002", "pos_cid": 18493647, "source": "eval_collection"}
{"query_id": "scaleup_28194600_23322167", "query": "How to study changes in healthcare access barriers over a sufficiently long observation period while maintaining participant engagement and data relevance", "pos": ["Longitudinal qualitative research in medical education: Time to conceptualise time. Longitudinal qualitative research is an approach to research that entails generating qualitative data with the same participants over extended periods of time to understand their lived experiences as those experiences unfold. Knowing about dynamic lived experiences in medical education, that is, learning journeys with stops and starts, detours, transitions and reversals, enriches understanding of events and accomplishments along the way. The purpose of this paper is to create access points to longitudinal qualitative research in support of increasing its use in medical education."], "field": "Health Professions", "q_year": 2025, "q_cid": "281946002", "pos_cid": 233221671, "source": "eval_collection"}
{"query_id": "scaleup_8419776_11037018", "query": "How to independently establish whether relationship counts, connection patterns, and rankings of central elements are robust rather than dependent on a single approach?", "pos": ["Reverse engineering and analysis of large genome-scale gene networks. Reverse engineering the whole-genome networks of complex multicellular organisms continues to remain a challenge. While simpler models easily scale to large number of genes and gene expression datasets, more accurate models are compute intensive limiting their scale of applicability. To enable fast and accurate reconstruction of large networks, we developed Tool for Inferring Network of Genes (TINGe), a parallel mutual information (MI)-based program. The novel features of our approach include: (i) B-spline-based formulation for linear-time computation of MI, (ii) a novel algorithm for direct permutation testing and (iii) development of parallel algorithms to reduce run-time and facilitate construction of large networks. We assess the quality of our method by comparison with ARACNe (Algorithm for the Reconstruction of Accurate Cellular Networks) and GeneNet and demonstrate its unique capability by reverse engineering the whole-genome network of Arabidopsis thaliana from 3137 Affymetrix ATH1 GeneChips in just 9 min on a 1024-core cluster. We further report on the development of a new software Gene Network Analyzer (GeNA) for extracting context-specific subnetworks from a given set of seed genes. Using TINGe and GeNA, we performed analysis of 241 Arabidopsis AraCyc 8.0 pathways, and the results are made available through the web."], "field": "Immunology and Microbiology", "q_year": 2014, "q_cid": "8419776", "pos_cid": 11037018, "source": "eval20x26"}
{"query_id": "scaleup_20117835_7686073", "query": "How to identify the sources of background hydroxylamine oxidation in the absence of ceruloplasmin to avoid misleading free radical detection and quantification", "pos": ["Amyloid β Peptides Do Not Form Peptide-derived Free Radicals Spontaneously, but Can Enhance Metal-catalyzed Oxidation of Hydroxylamines to Nitroxides*. Amyloid β (Aβ) peptides play an important role in the pathogenesis of Alzheimer’s disease. Free radical generation by Aβ peptides was suggested to be a key mechanism of their neurotoxicity. Reports that neurotoxic free radicals derived from Aβ-(1–40) and Aβ-(25–35) peptides react with the spin trapN-tert-butyl-α-phenylnitrone (PBN) to form a PBN/⋅Aβ peptide radical adduct with a specific triplet ESR signal assert that the peptide itself was the source of free radicals. We now report that three Aβ peptides, Aβ-(1–40), Aβ-(25–35), and Aβ-(40–1), do not yield radical adducts with PBN from the Oklahoma Medical Research Foundation (OMRF). In contrast to OMRF PBN, incubation of Sigma PBN in phosphate buffer without Aβ peptides produced a three-line ESR spectrum. It was shown that this nitroxide is di-tert-butylnitroxide and is formed in the Sigma PBN solution as a result of transition metal-catalyzed auto-oxidation of the respective hydroxylamine present as an impurity in the Sigma PBN. Under some conditions, incubation of PBN from Sigma with Aβ-(1–40) or Aβ-(25–35) can stimulate the formation of di-tert-butylnitroxide. It was shown that Aβ peptides enhanced oxidation of cyclic hydroxylamine 1-hydroxy-4-oxo-2,2,6,6-tetramethylpiperidine (TEMPONE-H), which was strongly inhibited by the treatment of phosphate buffer with Chelex-100. It was shown that ferric and cupric ions are effective oxidants of TEMPONE-H. The data obtained allow us to conclude that under some conditions toxic Aβ peptides Aβ-(1–40) and Aβ-(25–35) enhance metal-catalyzed oxidation of hydroxylamine derivatives, but do not spontaneously form peptide-derived free radicals."], "field": "Immunology and Microbiology", "q_year": 2012, "q_cid": "20117835", "pos_cid": 7686073, "source": "eval20x26"}
{"query_id": "scaleup_3530255_3909981", "query": "How to clarify the relationship between activating c-type lectin receptor expression and capacities for phagocytosis, reactive oxygen species production, and inflammatory cytokine release among monocyte subsets in pathogen responses", "pos": ["Dectin-1 Mediates the Biological Effects of β-Glucans. The ability of fungal-derived β-glucan particles to induce leukocyte activation and the production of inflammatory mediators, such as tumor necrosis factor (TNF)-α, is a well characterized phenomenon. Although efforts have been made to understand how these carbohydrate polymers exert their immunomodulatory effects, the receptors involved in generating these responses are unknown. Here we show that Dectin-1 mediates the production of TNF-α in response to zymosan and live fungal pathogens, an activity that occurs at the cell surface and requires the cytoplasmic tail and immunoreceptor tyrosine activation motif of Dectin-1 as well as Toll-like receptor (TLR)-2 and Myd88. This is the first demonstration that the inflammatory response to pathogens requires recognition by a specific receptor in addition to the TLRs. Furthermore, these studies implicate Dectin-1 in the production of TNF-α in response to fungi, a critical step required for the successful control of these pathogens."], "field": "Immunology and Microbiology", "q_year": 2016, "q_cid": "3530255", "pos_cid": 3909981, "source": "eval20x26"}
{"query_id": "scaleup_20864649_11608684", "query": "How to distinguish subgroups with similar profiles in heterogeneous datasets at an appropriate granularity for each dataset despite differences in coverage and heterogeneity", "pos": ["Data-driven phenotypic dissection of AML reveals progenitor-like cells that correlate with prognosis. SUMMARY Acute myeloid leukemia (AML) manifests as phenotypically and functionally diverse cells, often within the same patient. Intratumor phenotypic and functional heterogeneity have been linked primarily by physical sorting experiments, which assume that functionally distinct subpopulations can be prospectively isolated by surface phenotypes. This assumption has proven problematic and we therefore developed a data-driven approach. Using mass cytometry, we profiled surface and intracellular signaling proteins simultaneously in millions of healthy and leukemic cells. We developed PhenoGraph, which algorithmically defines phenotypes in high-dimensional single-cell data. PhenoGraph revealed that the surface phenotypes of leukemic blasts do not necessarily reflect their intracellular state. Using hematopoietic progenitors, we defined a signaling-based measure of cellular phenotype, which led to isolation of a gene expression signature that was predictive of survival in independent cohorts. This study presents new methods for large-scale analysis of single-cell heterogeneity and demonstrates their utility, yielding insights into AML pathophysiology."], "field": "Immunology and Microbiology", "q_year": 2019, "q_cid": "208646490", "pos_cid": 11608684, "source": "eval20x26"}
{"query_id": "scaleup_4969434_6003119", "query": "How to explain the origin and establishment of recombinant SIVagm strains across distinct African green monkey species under species-specific virus–host co-evolution", "pos": ["Discordance Between Spatial Distributions of Y-Chromosomal and Mitochondrial Haplotypes in African Green Monkeys (Chlorocebus spp.): A Result of Introgressive Hybridization or Cryptic Diversity?. Introgressive hybridization may cause substantial discordances among phylogenies based on different genetic markers. Such discordances have been found in diverse mammal species including primates. A recent study of mitochondrial DNA (mtDNA) revealed several poly- and paraphyletic relationships in African green monkeys (Chlorocebus), suggesting contemporary and/or ancient introgressive hybridization among almost all parapatric species of the genus. However, mtDNA analyses alone do not allow us to draw conclusions concerning introgression events. In this study we analyzed two Y chromosomal (Y-chr) markers for 30 African green monkey samples and compared the resulting genetic relationships to those based on published mtDNA data. In line with the results for mtDNA, we found no Y-chr evidence of hypothesized hybridization among Chlorocebus sabaeus and C. tantalus in the northern part of the contact zone in West Africa, and we found two distinct and distantly related Y-chr haplotypes within the range of C. tantalus, suggesting possible cryptic genetic diversity rather than ancient introgressive hybridization in this species. In contrast, Y-chr data revealed monophyletic relationships within Chlorocebus pygerythrus from East Africa, suggesting that mtDNA paraphylies found in this species are most likely to be the result of ancient introgressive hybridization and subsequent cytonuclear extinction of an earlier taxon. Our results accentuate the importance of analyzing sex chromosomal data in addition to mtDNA to obtain more information on the potential outcomes of hybridization with respect to genetic and species diversity. Analysis of more diverse nuclear marker sets is needed to obtain a more complete picture of the African green monkey evolution."], "field": "Immunology and Microbiology", "q_year": 2014, "q_cid": "4969434", "pos_cid": 6003119, "source": "eval20x26"}
{"query_id": "scaleup_3466486_11744469", "query": "How to establish that rabies virus sequence sampling dates contain a genuine temporal signal rather than a chance association for reliable estimation of evolutionary rates and spread timescales", "pos": ["Using Time-Structured Data to Estimate Evolutionary Rates of Double-Stranded DNA Viruses. Double-stranded (ds) DNA viruses are often described as evolving through long-term codivergent associations with their hosts, a pattern that is expected to be associated with low rates of nucleotide substitution. However, the hypothesis of codivergence between dsDNA viruses and their hosts has rarely been rigorously tested, even though the vast majority of nucleotide substitution rate estimates for dsDNA viruses are based upon this assumption. It is therefore important to estimate the evolutionary rates of dsDNA viruses independent of the assumption of host-virus codivergence. Here, we explore the use of temporally structured sequence data within a Bayesian framework to estimate the evolutionary rates for seven human dsDNA viruses, including variola virus (VARV) (the causative agent of smallpox) and herpes simplex virus-1. Our analyses reveal that although the VARV genome is likely to evolve at a rate of approximately 1 × 10−5 substitutions/site/year and hence approaching that of many RNA viruses, the evolutionary rates of many other dsDNA viruses remain problematic to estimate. Synthetic data sets were constructed to inform our interpretation of the substitution rates estimated for these dsDNA viruses and the analysis of these demonstrated that given a sequence data set of appropriate length and sampling depth, it is possible to use time-structured analyses to estimate the substitution rates of many dsDNA viruses independently from the assumption of host-virus codivergence. Finally, the discovery that some dsDNA viruses may evolve at rates approaching those of RNA viruses has important implications for our understanding of the long-term evolutionary history and emergence potential of this major group of viruses."], "field": "Immunology and Microbiology", "q_year": 2017, "q_cid": "3466486", "pos_cid": 11744469, "source": "eval20x26"}
{"query_id": "scaleup_20559793_16022587", "query": "How to counteract p17 toxicity in HIV-1-associated neurocognitive disorder", "pos": ["The Efficacy of Tetracyclines in Peripheral and Intracerebral Prion Infection. We have previously shown that tetracyclines interact with and reverse the protease resistance of pathological prion protein extracted from scrapie-infected animals and patients with all forms of Creutzfeldt-Jakob disease, lowering the prion titre and prolonging survival of cerebrally infected animals. To investigate the effectiveness of these drugs as anti-prion agents Syrian hamsters were inoculated intramuscularly or subcutaneously with 263K scrapie strain at a 10−4 dilution. Tetracyclines were injected intramuscularly or intraperitoneally at the dose of 10 mg/kg. A single intramuscular dose of doxycycline one hour after infection in the same site of inoculation prolonged median survival by 64%. Intraperitoneal doses of tetracyclines every two days for 40 or 44 days increased survival time by 25% (doxycycline), 32% (tetracycline); and 81% (minocycline) after intramuscular infection, and 35% (doxycycline) after subcutaneous infection. To extend the therapeutic potential of tetracyclines, we investigated the efficacy of direct infusion of tetracyclines in advanced infection. Since intracerebroventricular infusion of tetracycline solutions can cause overt acute toxicity in animals, we entrapped the drugs in liposomes. Animals were inoculated intracerebrally with a 10−4 dilution of the 263K scrapie strain. A single intracerebroventricular infusion of 25 µg/ 20 µl of doxycycline or minocycline entrapped in liposomes was administered 60 days after inoculation, when 50% of animals showed initial symptoms of the disease. Median survival increased of 8.1% with doxycycline and 10% with minocycline. These data suggest that tetracyclines might have therapeutic potential for humans."], "field": "Immunology and Microbiology", "q_year": 2017, "q_cid": "205597931", "pos_cid": 16022587, "source": "eval20x26"}
{"query_id": "scaleup_43282480_11594230", "query": "How to determine whether NLRP12 is required across dendritic cell subsets to support CD4+ T cell responses", "pos": ["Characterization of NLRP12 during the Development of Allergic Airway Disease in Mice. Among the 22 members of the nucleotide binding-domain, leucine rich repeat-containing (NLR) family, less than half have been functionally characterized. Of those that have been well studied, most form caspase-1 activating inflammasomes. NLRP12 is a unique NLR that has been shown to attenuate inflammatory pathways in biochemical assays and mediate the lymph node homing of activated skin dendritic cells in contact hypersensitivity responses. Since the mechanism between these two important observations remains elusive, we further evaluated the contribution of NLRP12 to organ specific adaptive immune responses by focusing on the lung, which, like skin, is exposed to both exogenous and endogenous inflammatory agents. In models of allergic airway inflammation induced by either acute ovalbumin (OVA) exposure or chronic house dust mite (HDM) antigen exposure, Nlrp12−/− mice displayed subtle differences in eosinophil and monocyte infiltration into the airways. However, the overall development of allergic airway disease and airway function was not significantly altered by NLRP12 deficiency. Together, the combined data suggest that NLRP12 does not play a vital role in regulating Th2 driven airway inflammation using common model systems that are physiologically relevant to human disease. Thus, the allergic airway inflammation models described here should be appropriate for subsequent studies that seek to decipher the contribution of NLRP12 in mediating the host response to agents associated with asthma exacerbation."], "field": "Immunology and Microbiology", "q_year": 2013, "q_cid": "43282480", "pos_cid": 11594230, "source": "eval20x26"}
{"query_id": "scaleup_19741814_33635135", "query": "How to determine whether IL-6 and IL-27 share a basis for impairing human regulatory T cell suppressive function", "pos": ["Interleukin-27 Induces a STAT1/3- and NF-κB-dependent Proinflammatory Cytokine Profile in Human Monocytes*. IL-27 is a heterodimeric cytokine bridging innate and adaptive immunity by playing a role in the activation of naive T cells and in development of Th1 cells. Additionally, recent evidence supports a role for IL-27 in the activation of monocytic cells. Both pro-inflammatory and anti-inflammatory activities have been attributed to IL-27; however, the role played by IL-27 in the activation of human monocytic cells in terms of cytokine production has not been well described. Our results show that IL-27 is a strong inducer of proinflammatory cytokine and chemokine expression, including enhancement of IL-6, IP-10, MIP-1α, MIP-1β, and TNF-α expression in human primary monocytes. Furthermore, we observed that IL-27-induced cytokine and chemokine production was mediated by STAT1, STAT3, and NF-κB activation. Understanding how IL-27 exerts its effects on monocytic cells will identify important molecular mechanisms in the regulation of immune responses, particularly in the modulation of monocyte activation."], "field": "Immunology and Microbiology", "q_year": 2019, "q_cid": "197418146", "pos_cid": 33635135, "source": "eval20x26"}
{"query_id": "scaleup_4876493_24184132", "query": "How to explain age-related impairment in cellular secretion and conflicting findings on responses to stimulation", "pos": ["Effect of aging on murine macrophages. Diminished response to IFN-gamma for enhanced oxidative metabolism.. The ability of macrophages to secrete reactive oxygen intermediates, as well as reactive nitrogen intermediates, correlates closely with their capacity to perform two critical effector functions: intracellular killing of microorganisms and lysis of tumor cells. In this study, age-associated changes in the ability of caseinate-elicited peritoneal macrophages to release hydrogen peroxide were determined. Macrophages from aged BALB/c mice produced 50% less hydrogen peroxide than those from young mice in response to PMA or opsonized zymosan. In contrast, the production of macrophage-activating cytokines including IFN-gamma was not diminished in splenocyte supernatants from the aged group. Furthermore, no difference was detected in surface expression of IFN-gamma receptor in old and young mice. Macrophage responses to IFN-gamma, however, declined with aging. In vitro, IFN-gamma-induced release of hydrogen peroxide and nitric oxide was 50% lower in old mice than in young mice. IFN-gamma-induced tyrosine phosphorylation of MAPK, an early activation event, was undetectable in macrophages from the aged mice. These data demonstrate that diminished responses of macrophages to activating signals are one aspect of the impaired immune response in aged mice."], "field": "Immunology and Microbiology", "q_year": 2018, "q_cid": "4876493", "pos_cid": 24184132, "source": "eval20x26"}
{"query_id": "scaleup_2717761_12424151", "query": "How to determine the effect of intracellular signalling abnormalities in CD56brightCD16dim/− NK cells on IFN-γ production and inflammatory immune dysfunction in CFS/ME", "pos": ["p38 MAP-kinases pathway regulation, function and role in human diseases.. Mammalian p38 mitogen-activated protein kinases (MAPKs) are activated by a wide range of cellular stresses as well as in response to inflammatory cytokines. There are four members of the p38MAPK family (p38alpha, p38beta, p38gamma and p38delta) which are about 60% identical in their amino acid sequence but differ in their expression patterns, substrate specificities and sensitivities to chemical inhibitors such as SB203580. A large body of evidences indicates that p38MAPK activity is critical for normal immune and inflammatory response. The p38MAPK pathway is a key regulator of pro-inflammatory cytokines biosynthesis at the transcriptional and translational levels, which makes different components of this pathway potential targets for the treatment of autoimmune and inflammatory diseases. However, recent studies have shed light on the broad effect of p38MAPK activation in the control of many other aspects of the physiology of the cell, such as control of cell cycle or cytoskeleton remodelling. Here we focus on these emergent roles of p38MAPKs and their implication in different pathologies."], "field": "Immunology and Microbiology", "q_year": 2016, "q_cid": "2717761", "pos_cid": 12424151, "source": "eval20x26"}
{"query_id": "scaleup_20864649_2374637", "query": "How to determine whether mouse tumor-infiltrating t helper type 1 cells share a statistically meaningful overall pattern of gene activity with their counterparts in human colon tumors, beyond similarities in individual genes", "pos": ["From the Cover: Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles. Although genomewide RNA expression analysis has become a routine tool in biomedical research, extracting biological insight from such information remains a major challenge. Here, we describe a powerful analytical method called Gene Set Enrichment Analysis (GSEA) for interpreting gene expression data. The method derives its power by focusing on gene sets, that is, groups of genes that share common biological function, chromosomal location, or regulation. We demonstrate how GSEA yields insights into several cancer-related data sets, including leukemia and lung cancer. Notably, where single-gene analysis finds little similarity between two independent studies of patient survival in lung cancer, GSEA reveals many biological pathways in common. The GSEA method is embodied in a freely available software package, together with an initial database of 1,325 biologically defined gene sets."], "field": "Immunology and Microbiology", "q_year": 2019, "q_cid": "208646490", "pos_cid": 2374637, "source": "eval20x26"}
{"query_id": "scaleup_24697192_17826093", "query": "How to determine whether circulating cytokines causally affect the risk of critical COVID-19 or critical COVID-19 causally affects circulating cytokine levels", "pos": ["Mendelian Randomization Analysis With Multiple Genetic Variants Using Summarized Data. Genome‐wide association studies, which typically report regression coefficients summarizing the associations of many genetic variants with various traits, are potentially a powerful source of data for Mendelian randomization investigations. We demonstrate how such coefficients from multiple variants can be combined in a Mendelian randomization analysis to estimate the causal effect of a risk factor on an outcome. The bias and efficiency of estimates based on summarized data are compared to those based on individual‐level data in simulation studies. We investigate the impact of gene–gene interactions, linkage disequilibrium, and ‘weak instruments’ on these estimates. Both an inverse‐variance weighted average of variant‐specific associations and a likelihood‐based approach for summarized data give similar estimates and precision to the two‐stage least squares method for individual‐level data, even when there are gene–gene interactions. However, these summarized data methods overstate precision when variants are in linkage disequilibrium. If the P‐value in a linear regression of the risk factor for each variant is less than 1×10−5 , then weak instrument bias will be small. We use these methods to estimate the causal association of low‐density lipoprotein cholesterol (LDL‐C) on coronary artery disease using published data on five genetic variants. A 30% reduction in LDL‐C is estimated to reduce coronary artery disease risk by 67% (95% CI: 54% to 76%). We conclude that Mendelian randomization investigations using summarized data from uncorrelated variants are similarly efficient to those using individual‐level data, although the necessary assumptions cannot be so fully assessed."], "field": "Immunology and Microbiology", "q_year": 2022, "q_cid": "246971920", "pos_cid": 17826093, "source": "eval_collection"}
{"query_id": "scaleup_21104585_18324011", "query": "How to identify statistically meaningful gene-expression differences between neonatal and adult macaque immune cells after HIV Env immunization, both collectively and within individual immune-cell types", "pos": ["Data exploration, quality control and testing in single-cell qPCR-based gene expression experiments. Motivation: Cell populations are never truly homogeneous; individual cells exist in biochemical states that define functional differences between them. New technology based on microfluidic arrays combined with multiplexed quantitative polymerase chain reactions now enables high-throughput single-cell gene expression measurement, allowing assessment of cellular heterogeneity. However, few analytic tools have been developed specifically for the statistical and analytical challenges of single-cell quantitative polymerase chain reactions data. Results: We present a statistical framework for the exploration, quality control and analysis of single-cell gene expression data from microfluidic arrays. We assess accuracy and within-sample heterogeneity of single-cell expression and develop quality control criteria to filter unreliable cell measurements. We propose a statistical model accounting for the fact that genes at the single-cell level can be on (and a continuous expression measure is recorded) or dichotomously off (and the recorded expression is zero). Based on this model, we derive a combined likelihood ratio test for differential expression that incorporates both the discrete and continuous components. Using an experiment that examines treatment-specific changes in expression, we show that this combined test is more powerful than either the continuous or dichotomous component in isolation, or a t-test on the zero-inflated data. Although developed for measurements from a specific platform (Fluidigm), these tools are generalizable to other multi-parametric measures over large numbers of events. Availability: All results presented here were obtained using the SingleCellAssay R package available on GitHub (http://github.com/RGLab/SingleCellAssay). Contact: rgottard@fhcrc.org Supplementary information: Supplementary data are available at Bioinformatics online."], "field": "Immunology and Microbiology", "q_year": 2020, "q_cid": "211045852", "pos_cid": 18324011, "source": "eval_collection"}
{"query_id": "scaleup_21575705_16429880", "query": "How to determine whether evolutionary changes in seahorses and pipefishes are associated with male pregnancy", "pos": ["A comprehensive analysis of teleost MHC class I sequences. BackgroundMHC class I (MHCI) molecules are the key presenters of peptides generated through the intracellular pathway to CD8-positive T-cells. In fish, MHCI genes were first identified in the early 1990′s, but we still know little about their functional relevance. The expansion and presumed sub-functionalization of cod MHCI and access to many published fish genome sequences provide us with the incentive to undertake a comprehensive study of deduced teleost fish MHCI molecules.ResultsWe expand the known MHCI lineages in teleosts to five with identification of a new lineage defined as P. The two lineages U and Z, which both include presumed peptide binding classical/typical molecules besides more derived molecules, are present in all teleosts analyzed. The U lineage displays two modes of evolution, most pronouncedly observed in classical-type alpha 1 domains; cod and stickleback have expanded on one of at least eight ancient alpha 1 domain lineages as opposed to many other teleosts that preserved a number of these ancient lineages. The Z lineage comes in a typical format present in all analyzed ray-finned fish species as well as lungfish. The typical Z format displays an unprecedented conservation of almost all 37 residues predicted to make up the peptide binding groove. However, also co-existing atypical Z sub-lineage molecules, which lost the presumed peptide binding motif, are found in some fish like carps and cavefish. The remaining three lineages, L, S and P, are not predicted to bind peptides and are lost in some species.ConclusionsMuch like tetrapods, teleosts have polymorphic classical peptide binding MHCI molecules, a number of classical-similar non-classical MHCI molecules, and some members of more diverged MHCI lineages. Different from tetrapods, however, is that in some teleosts the classical MHCI polymorphism incorporates multiple ancient MHCI domain lineages. Also different from tetrapods is that teleosts have typical Z molecules, in which the residues that presumably form the peptide binding groove have been almost completely conserved for over 400 million years. The reasons for the uniquely teleost evolution modes of peptide binding MHCI molecules remain an enigma."], "field": "Immunology and Microbiology", "q_year": 2020, "q_cid": "215757052", "pos_cid": 16429880, "source": "eval_collection"}
{"query_id": "scaleup_23438547_45236457", "query": "How to achieve vaccine protection against HPV, HSV-2, and Chlamydia trachomatis", "pos": ["Flagellin as an Adjuvant: Cellular Mechanisms and Potential. Flagellin is a potent activator of a broad range of cell types involved in innate and adaptive immunity. An increasing number of studies have demonstrated the effectiveness of flagellin as an adjuvant, as well as its ability to promote cytokine production by a range of innate cell types, trigger a generalized recruitment of T and B lymphocytes to secondary lymphoid sites, and activate TLR5+CD11c+ cells and T lymphocytes in a manner that is distinct from cognate Ag recognition. The plasticity of flagellin has allowed for the generation of a range of flagellin–Ag fusion proteins that have proven to be effective vaccines in animal models. This review summarizes the state of our current understanding of the adjuvant effect of flagellin and addresses important areas of current and future research interest."], "field": "Immunology and Microbiology", "q_year": 2020, "q_cid": "234385476", "pos_cid": 45236457, "source": "eval_collection"}
{"query_id": "scaleup_27034297_85494256", "query": "How to understand the peptide’s anticancer activity and the relationship between altered enzyme activity and apoptosis in cancer cells", "pos": ["The Specific Inhibition of SOD1 Selectively Promotes Apoptosis of Cancer Cells via Regulation of the ROS Signaling Network. Multiple signaling pathways including ERK, PI3K-Akt, and NF-κB, which are essential for onset and development of cancer, can be activated by intracellularly sustained high levels of H2O2 provided by elevated activity and expression of copper/zinc superoxide dismutase (SOD1) that catalyzes the dismutation of O2 •− into H2O2. Here, tests performed by the utilization of our designed specific SOD1 inhibitor LD100 on cancer and normal cells reveal that the signaling pathways and their crosstalk to support cancer cell growth are repressed, but the signaling pathways to promote cancer cell cycle arrest and apoptosis are stimulated by specific SOD1 inhibition-mediated ROS changes. These regulated pathways constitute an ROS signaling network that determines the fate of cancer cells. This ROS signaling network is also regulated in SOD1 knockdown cells. These findings might facilitate disclosure of action mechanisms by copper-chelating anticancer agents and design of SOD1-targeting and ROS signaling pathway-interfering anticancer small molecules."], "field": "Immunology and Microbiology", "q_year": 2024, "q_cid": "270342970", "pos_cid": 85494256, "source": "eval_collection"}
{"query_id": "scaleup_25149794_553179", "query": "How to achieve organoids that reproduce gastrointestinal fluid flow, shear forces, peristalsis, and automated nutrient supply and waste removal for studying nematode development and host interactions", "pos": ["Development of a primary human Small Intestine-on-a-Chip using biopsy-derived organoids. Here we describe a method for fabricating a primary human Small Intestine-on-a-Chip (Intestine Chip) containing epithelial cells isolated from healthy regions of intestinal biopsies. The primary epithelial cells are expanded as 3D organoids, dissociated, and cultured on a porous membrane within a microfluidic device with human intestinal microvascular endothelium cultured in a parallel microchannel under flow and cyclic deformation. In the Intestine Chip, the epithelium forms villi-like projections lined by polarized epithelial cells that undergo multi-lineage differentiation similar to that of intestinal organoids, however, these cells expose their apical surfaces to an open lumen and interface with endothelium. Transcriptomic analysis also indicates that the Intestine Chip more closely mimics whole human duodenum in vivo when compared to the duodenal organoids used to create the chips. Because fluids flowing through the lumen of the Intestine Chip can be collected continuously, sequential analysis of fluid samples can be used to quantify nutrient digestion, mucus secretion and establishment of intestinal barrier function over a period of multiple days in vitro. The Intestine Chip therefore may be useful as a research tool for applications where normal intestinal function is crucial, including studies of metabolism, nutrition, infection, and drug pharmacokinetics, as well as personalized medicine."], "field": "Immunology and Microbiology", "q_year": 2022, "q_cid": "251497942", "pos_cid": 553179, "source": "eval_collection"}
{"query_id": "scaleup_27872981_24727494", "query": "How to improve antimicrobial agent stability, therapeutic efficacy, and spectrum of activity while achieving sufficient drug concentrations at the site of action and minimizing adverse effects", "pos": ["Synergistic Effects Between Metal Nanoparticles and Commercial Antimicrobial Agents: A Review. Nanotechnology has expanded into a broad range of clinical applications. In particular, metal nanoparticles (MNPs) display unique antimicrobial properties, a fundamental function of novel medical devices. The combination of MNPs with commercial antimicrobial drugs (e.g., antibiotics, antifungals, and antivirals) may offer several opportunities to overcome some disadvantages of their individual use and enhance effectiveness. MNP conjugates display multiple advantages. As drug delivery systems, the conjugates can extend the circulation of the drugs in the body, facilitate intercellular targeting, improve drug stabilization, and possess superior delivery. Concomitantly, they reduce the required drug dose, minimize toxicity, and broaden the antimicrobial spectrum. In this work, the common strategies to combine MNPs with clinically used antimicrobial agents are underscored. Furthermore, a comprehensive survey about synergistic antimicrobial effects, the mechanism of action, and cytotoxicity is depicted."], "field": "Immunology and Microbiology", "q_year": 2025, "q_cid": "278729814", "pos_cid": 247274941, "source": "eval_collection"}
{"query_id": "scaleup_26948397_24437715", "query": "How to understand the genetic basis of genome plasticity and the potential for horizontal spread of antimicrobial resistance genes in A. pleuropneumoniae", "pos": ["Genomic analysis of antibiotic-resistant Enterococcus spp. reveals novel enterococci strains and the spread of plasmid-borne Tet(M), Tet(L) and Erm(B) genes from chicken litter to agricultural soil in South Africa.. Manure from food animals exposed to antibiotics is often used as soil fertiliser, potentially releasing antibiotic-resistant bacteria (ARB) with diverse antibiotic-resistance genes (ARGs) into the soil. To determine the impact of chicken litter application on the soil resistome, Enterococcus spp. isolated from chicken litter and soil samples collected before and after the soil amendment were characterised, using whole-genome sequencing and bioinformatics tools. Nineteen Enterococcus spp. isolates from the three sources were sequenced on Illumina Miseq platform to ascertain the isolates' resistome, mobilome, virulome, clonality, and phylogenomic relationships. Multilocus sequence typing (MLST) analysis revealed eight novel sequence types (STs) (ST1700, ST1752, ST1753, ST1754, ST1755, ST1756, ST1004, and ST1006). The isolates harboured multiple resistance genes including those conferring resistance to inter alia macrolides-lincosamide-streptogramin (erm(B), lnu(B), lnu(G), lsaA, lsaE, eat(A), msr(C)), tetracycline (tet(M), tet(L), tet(S)), aminoglycosides (aac(6')-Ii, aac(6')-Iih, ant(6)-Ia, aph(3')-III, ant(9)-Ia), fluoroquinolones (efmA, and emeA), vancomycin (VanC {VanC-2, VanXY, VanXYC-3, VanXYC-4, VanRC}), and chloramphenicol (cat). The litter-amended soil harboured new ARB (particularly E. faecium) and ARGs (ant(6)-Ia, aac(6')-Ii, aph(3')-III), lnu(G), msr(C), and eat(A), efmA) that were not previously detected in the soil. The identified ARGs were associated with diverse mobile genetic elements (MGEs) such as insertion sequences (IS6, ISL3, IS256, IS30), transposons (Tn3 and Tn916) and plasmids (repUS43, repUS1, rep9b, and rep 22). Twenty-eight virulence genes encoding adherence/biofilm formation (ebpA, ebpB, ebpC), antiphagocytosis (elrA) and bacterial sex pheromones (Ccf10, cOB1, cad, and camE), were detected in the genomes of the isolates. Phylogenomic analysis revealed a close relationship between a few isolates from litter-amended soil and the chicken litter isolates. The differences in the ARG and ARB profiles in the soil before and after the litter amendment and their association with diverse MGEs indicate the mobilisation and transmission of ARGs and ARB from the litter to the soil."], "field": "Immunology and Microbiology", "q_year": 2024, "q_cid": "269483977", "pos_cid": 244377157, "source": "eval_collection"}
{"query_id": "scaleup_28160185_25032978", "query": "How to efficiently deliver Cecropin A to mucosal sites despite its poor stability, solubility, and bioavailability while protecting it from enzymatic degradation", "pos": ["Oral Immunization With a M Cell-Targeting Recombinant L. Lactis Vaccine LL-plSAM-FVpE Stimulate Protective Immunity Against H. Pylori in Mice. There are many virulence factors of H. pylori that contribute in diverse ways to gastric disease. Therefore, designing multivalent epitope vaccines against many key virulence factors virulence factors of H. pylori is a promising strategy to control H. pylori infection. In previous studies, we constructed a multivalent epitope vaccine FVpE against four key virulence factors of H. pylori (Urease, CagA, VacA, and NAP), and oral immunization with the FVpE vaccine plus a polysaccharide adjuvant (PA) containing lycium barbarum polysaccharide and chitosan could provide protection against H. pylori infection in the Mongolian gerbil model. Oral vaccines have many advantages over injected vaccines, such as improved safety and compliance, and easier manufacturing and administration. However, the harsh gastrointestinal (GI) environment, such as gastric acid and proteolytic enzymes, limits the development of oral vaccines to some extent. Oral vaccines need a gastrointestinal delivery system with high safety, low price and promoting vaccine antigen to stimulate immune response in the gastrointestinal mucosa. Lactic acid bacteria are gastrointestinal probiotics that have unique advantages as a delivery system for oral vaccines. In this study, a M cell-targeting surface display system for L. lactis named plSAM was designed to help vaccine antigens to stimulate effective immune responses in the gastrointestinal tract, and a M cell-targeting recombinant L. lactis vaccine LL-plSAM-FVpE was constructed by using the surface display system plSAM. recombinant L. lactis vaccine LL-plSAM-FVpE could secretively express the SAM-FVpE protein and display it on the bacterial surface. Moreover, experimental results confirmed that LL-plSAM-FVpE had an enhanced M cell-targeting property. In addition, LL-plSAM-FVpE had excellent M cell-targeting property to promote the phagocytosis and transport of the antigen SAM-FVpE by gastrointestinal M cells. More importantly, oral immunization of LL-plSAM-FVpE or SAM-FVpE plus PA can stimulate IgG and sIgA antibodies and CD4+ T cell immune responses against four virulence factors of H. pylori (Urease, CagA, VacA, and NAP), thus providing protective immunity against H. pylori infection in mice. The M cell-targeting recombinant L. lactis vaccine against various key H. pylori virulence factors could be a promising vaccine candidate for controlling H. pylori infection."], "field": "Immunology and Microbiology", "q_year": 2025, "q_cid": "281601851", "pos_cid": 250329783, "source": "eval_collection"}
{"query_id": "scaleup_27929316_26390819", "query": "How to determine the requirements for effective targeting of poorly responsive tumors when effectiveness depends on multiple processes and external factors", "pos": ["The cancer-immunity cycle: Indication, genotype, and immunotype.. The cancer-immunity cycle provides a framework to understand the series of events that generate anti-cancer immune responses. It emphasizes the iterative nature of the response where the killing of tumor cells by T cells initiates subsequent rounds of antigen presentation and T cell stimulation, maintaining active immunity and adapting it to tumor evolution. Any step of the cycle can become rate-limiting, rendering the immune system unable to control tumor growth. Here, we update the cancer-immunity cycle based on the remarkable progress of the past decade. Understanding the mechanism of checkpoint inhibition has evolved, as has our view of dendritic cells in sustaining anti-tumor immunity. We additionally account for the role of the tumor microenvironment in facilitating, not just suppressing, the anti-cancer response, and discuss the importance of considering a tumor's immunological phenotype, the \"immunotype\". While these new insights add some complexity to the cycle, they also provide new targets for research and therapeutic intervention."], "field": "Immunology and Microbiology", "q_year": 2025, "q_cid": "279293163", "pos_cid": 263908199, "source": "eval_collection"}
{"query_id": "scaleup_22929087_4535551", "query": "How to determine when extracellular self-DNA becomes harmful, particularly when neutrophil extracellular traps are not completely removed", "pos": ["Systemic activation of NLRP3 inflammasome in patients with severe primary Sjögren's syndrome fueled by inflammagenic DNA accumulations.. Sjögren's syndrome (SS) patients manifest high cell-free DNA (cf-DNA) levels in serum, associated with impaired DNaseI activity. Undegraded DNA may accumulate in tissues and act as an inflammasome-activating signal. Herein, we investigated the occurrence of aberrant DNA build-up in various biologic compartments of SS patients and its correlation with the activity of NLRP3 and AIM2 inflammasomes. For this purpose, we evaluated sera, PBMC, circulating monocytes and salivary glands (SG) from different SS patient subgroups and controls. We found that SS patients at high risk for lymphoma and those with established lymphoma display high serum cf-DNA levels, substantial extranuclear DNA accumulations in PBMC and SG tissues, a unique NLRP3 inflammasome gene signature in PBMC, and significantly increased serum IL-18 and ASC levels. In these patients, the circulating monocytes manifested NLRP3 inflammasome activation and increased response to NLRP3 stimuli, whereas SG-infiltrating macrophages exhibited signs of NLRP3 activation and pyroptosis. Cell-free nucleic acids isolated from patients' sera competently primed the activation of both NLRP3 and AIM2 inflammasomes in healthy monocytes. SS patients also manifested diminished DNaseI activity in serum and DNaseII expression in PBMC, which inversely correlated with indices of inflammasome activation. DNaseII gene-silencing in healthy monocytes led to cytoplasmic DNA deposition and activation of inflammasome-related genes and of caspase1. Our data reveal the occurrence of systemic NLRP3 inflammasome activation in severe SS, which is associated with widespread extranuclear accumulations of inflammagenic DNA and impaired DNA degradation. These findings can provide novel biomarkers and new therapeutic targets for the management of SS patients with adverse outcomes."], "field": "Immunology and Microbiology", "q_year": 2020, "q_cid": "229290877", "pos_cid": 4535551, "source": "eval_collection"}
{"query_id": "scaleup_25997384_21610781", "query": "How to determine the effect of IL-21 on B cells after B cell receptor stimulation", "pos": ["STAT3 Protein Interacts with Class O Forkhead Transcription Factors in the Cytoplasm and Regulates Nuclear/Cytoplasmic Localization of FoxO1 and FoxO3a Proteins in CD4+ T Cells*. Background: Molecular signals that control how long activated lymphocytes remain activated are unknown. Results: Unphosphorylated STAT3 interacts with and sequesters pFoxO1/pFoxO3a in cytoplasm whereas pSTAT3 terminates TCR activation by inducing nuclear localization of FoxO1/FoxO3a and p27Kip1 expression. Conclusion: STAT3/FoxO are gatekeepers that determine whether T cells remain quiescent or proliferate. Significance: STAT3 is convergence point for mechanisms that regulate cellular quiescence and lymphocyte activation. An important feature of the adaptive immune response is its remarkable capacity to regulate the duration of inflammatory responses, and effector T cells have been shown to limit excessive immune responses by producing anti-inflammatory cytokines such as IL-10 and IL-27. However, how anti-inflammatory cytokines mediate their suppressive activities is not well understood. In this study, we show that STAT3 contributes to mechanisms that control the duration of T cell proliferation by regulating the subcellular location of FoxO1 and FoxO3a, two Class O Forkhead transcription factors that mediate lymphocyte quiescence and inhibit T cell activation. We show that active FoxO1 and FoxO3a reside exclusively in the nucleus of naïve T cells whereas inactive pFoxO1 and pFoxO3a were most abundant in activated T cells and sequestered in their cytoplasm in association with unphosphorylated STAT3 (U-STAT3) and 14-3-3. We further show that FoxO1/FoxO3a rapidly relocalized into the nucleus in response to pSTAT3 activation by IL-6 or IL-10, and the accumulation of FoxO1/FoxO3a in their nuclei coincided with increased expression of p27Kip1 and p21WAF1. STAT3 inhibitors completely abrogated cytokine-induced translocation of FoxO1/FoxO3a into the nucleus. In naïve or resting STAT3-deficient T cells, expression of pFoxO1/pFoxO3a was predominantly in the cytoplasm and correlated with defects in p27Kip1 and p21WAF1 expression, suggesting requirement of STAT3 for importation or retention of FoxO in the nucleus and attenuation of lymphocyte proliferation. Taken together, these results suggest that U-STAT3 collaborates with 14-3-3 to sequester pFoxO1/pFoxO3a in cytoplasm and thus prolong T cell activation, whereas pSTAT3 activation by anti-inflammatory cytokines would curtail the duration of TCR activation and re-establish lymphocyte quiescence by inducing nuclear localization of FoxO1/FoxO3a and FoxO-mediated expression of growth-inhibitory proteins."], "field": "Immunology and Microbiology", "q_year": 2023, "q_cid": "259973846", "pos_cid": 21610781, "source": "eval_collection"}
{"query_id": "scaleup_22929087_8860368", "query": "How to determine whether extracellular dna affects cell growth differently depending on its self or non-self origin, concentration, and phylogenetic relatedness to the exposed organism", "pos": ["Inhibitory effects of extracellular self-DNA: a general biological process?. Self-inhibition of growth has been observed in different organisms, but an underlying common mechanism has not been proposed so far. Recently, extracellular DNA (exDNA) has been reported as species-specific growth inhibitor in plants and proposed as an explanation of negative plant-soil feedback. In this work the effect of exDNA was tested on different species to assess the occurrence of such inhibition in organisms other than plants. Bioassays were performed on six species of different taxonomic groups, including bacteria, fungi, algae, plants, protozoa and insects. Treatments consisted in the addition to the growth substrate of conspecific and heterologous DNA at different concentration levels. Results showed that treatments with conspecific DNA always produced a concentration dependent growth inhibition, which instead was not observed in the case of heterologous DNA. Reported evidence suggests the generality of the observed phenomenon which opens new perspectives in the context of self-inhibition processes. Moreover, the existence of a general species-specific biological effect of exDNA raises interesting questions on its possible involvement in self-recognition mechanisms. Further investigation at molecular level will be required to unravel the specific functioning of the observed inhibitory effects."], "field": "Immunology and Microbiology", "q_year": 2020, "q_cid": "229290877", "pos_cid": 8860368, "source": "eval_collection"}
{"query_id": "scaleup_21104585_13613348", "query": "How to clearly visualize multiple b cell populations so they can be distinguished and analyzed", "pos": ["Algorithmic tools for mining high-dimensional cytometry data. The advent of mass cytometry has led to an unprecedented increase in the number of analytes measured in individual cells, thereby increasing the complexity and information content of cytometric data. Although this technology is ideally suited to the detailed examination of the immune system, the applicability of the different methods for analyzing such complex data is less clear. Conventional data analysis by manual gating of cells in biaxial dot plots is often subjective, time consuming, and neglectful of much of the information contained in a highly dimensional cytometric dataset. Algorithmic data mining has the promise to eliminate these concerns, and several such tools have been applied recently to mass cytometry data. We review computational data mining tools that have been used to analyze mass cytometry data, outline their differences, and comment on their strengths and limitations. This review will help immunologists to identify suitable algorithmic tools for their particular projects."], "field": "Immunology and Microbiology", "q_year": 2020, "q_cid": "211045852", "pos_cid": 13613348, "source": "eval_collection"}
{"query_id": "scaleup_23331278_53238450", "query": "How to understand miRNA regulation of STAT3-dependent Th17 cell differentiation and the contribution of Th17 dysregulation to inflammatory autoimmune diseases", "pos": ["Exosomes Released from Tumor-Associated Macrophages Transfer miRNAs That Induce a Treg/Th17 Cell Imbalance in Epithelial Ovarian Cancer. The Treg/Th17 ratio is altered in epithelial ovarian cancer. Exosomal miRNAs from tumor-associated macrophages contribute to this T-cell imbalance, which promotes an immune suppressive tumor microenvironment and favors progression and metastasis of epithelial ovarian cancer cells. The immune microenvironment is crucial for epithelial ovarian cancer (EOC) progression and consists of tumor-associated macrophages (TAM) and T lymphocytes, such as regulatory T cells (Treg) and T helper 17 (Th17) cells. In this study, the Treg/Th17 ratio was significantly higher in EOC in situ and in metastatic peritoneal tissues than in benign ovarian tumors and benign peritoneum. The Treg/Th17 ratio was associated with histologic grade and was an independent prognostic factor for overall survival of EOC patients. On the basis of microarray analysis of exosomes derived from TAMs, we identified miRNAs enriched in the exosomes, including miR-29a-3p and miR-21-5p. When the two miRNA mimics were transfected into CD4+ T cells, they directly suppressed STAT3 and regulated Treg/Th17 cells, inducing an imbalance, and they had a synergistic effect on STAT3 inhibition. Taken together, these results indicate that exosomes mediate the interaction between TAMs and T cells, generating an immune-suppressive microenvironment that facilitates EOC progression and metastasis. These findings suggest that targeting these exosomes or their associated miRNAs might pave the way for the development of novel treatments for EOC."], "field": "Immunology and Microbiology", "q_year": 2021, "q_cid": "233312781", "pos_cid": 53238450, "source": "eval_collection"}
{"query_id": "scaleup_27872981_26874072", "query": "How to achieve stable peptide attachment and selective target-cell interactions in peptide–nanoparticle systems to improve therapeutic efficacy and limit systemic toxicity across varying peptide properties, nanoparticle materials, and biomedical applications", "pos": ["Peptide‐conjugated Nanoparticle Platforms for Targeted Delivery, Imaging, and Biosensing Applications. Peptides have become an indispensable tool in engineering of multifunctional nanostructure platforms for biomedical applications such as targeted drug and gene delivery, imaging and biosensing. They can be covalently incorporated into a variety of nanoparticles (NPs) including polymers, metallic nanoparticles, and others. Using different bioconjugation techniques, multifunctional peptide‐modified NPs can be formulated to produce therapeutical and diagnostic platforms offering high specificity, lower toxicity, biocompatibility, and stimuli responsive behavior. Targeting peptides can direct the nanoparticles into specific tissues for targeted drug and gene delivery and imaging applications due to their specificity towards certain receptors. Furthermore, due to their stimuli‐responsive features, they can offer controlled release of therapeutics into desired sites of disease. In addition, peptide‐based biosensors and imaging agents can provide non‐invasive detection and monitoring of diseases including cancer, infectious diseases, and neurological disorders. In this review, we covered the design and formulation of recent peptide‐based NP platforms, as well as their utilization in in vitro and in vivo applications such as targeted drug and gene delivery, targeting, sensing, and imaging applications. In the end, we provided the future outlook to design new peptide conjugated nanomaterials for biomedical applications."], "field": "Immunology and Microbiology", "q_year": 2025, "q_cid": "278729814", "pos_cid": 268740727, "source": "eval_collection"}
{"query_id": "scaleup_27157079_20666426", "query": "How to determine whether counterparts of two conserved virulence-associated proteins are essential for growth in related organisms during asexual stages", "pos": ["Uncovering the essential genome of the human malaria parasite Plasmodium falciparum by saturation mutagenesis. Saturating malaria mutagenesis Malaria is caused by eukaryotic Plasmodium spp. parasites that classically infect red blood cells. These are difficult organisms to investigate genetically because of their AT-rich genomes. Zhang et al. have exploited this peculiarity by using piggyBac transposon insertion sites to achieve saturation-level mutagenesis for identifying and ranking essential genes and drug targets (see the Perspective by White and Rathod). Genes that are current candidates for drug targets were identified as essential, in contrast to many vaccine target genes. Notably, the proteasome degradation pathway was confirmed as a target for developing therapeutic interventions because of the several essential genes involved and the link to the mechanism of action of the current frontline drug, artemisinin. Science, this issue p. eaap7847; see also p. 490 Mutagenesis of a human malaria parasite reveals a core set of genes essential for asexual growth in red blood cells in vitro. INTRODUCTION Malaria remains a devastating global parasitic disease, with the majority of malaria deaths caused by the highly virulent Plasmodium falciparum. The extreme AT-bias of the P. falciparum genome has hampered genetic studies through targeted approaches such as homologous recombination or CRISPR-Cas9, and only a few hundred P. falciparum mutants have been experimentally generated in the past decades. In this study, we have used high-throughput piggyBac transposon insertional mutagenesis and quantitative insertion site sequencing (QIseq) to reach saturation-level mutagenesis of this parasite. RATIONALE Our study exploits the AT-richness of the P. falciparum genome, which provides numerous piggyBac transposon insertion targets within both gene coding and noncoding flanking sequences, to generate more than 38,000 P. falciparum mutants. At this level of mutagenesis, we could distinguish essential genes as nonmutable and dispensable genes as mutable. Subsequently, we identified 2680 genes essential for in vitro asexual blood-stage growth. RESULTS We calculated mutagenesis index scores (MISs) and mutagenesis fitness scores (MFSs) in order to functionally define the relative fitness cost of disruption for 5399 genes. A competitive growth phenotype screen confirmed that MIS and MFS were predictive of the fitness cost for in vitro asexual growth. Genes predicted to be essential included genes implicated in drug resistance—such as the “K13” Kelch propeller, mdr, and dhfr-ts—as well as targets considered to be high value for drugs development, such as pkg and cdpk5. The screen revealed essential genes that are specific to human Plasmodium parasites but absent from rodent-infective species, such as lipid metabolic genes that may be crucial to transmission commitment in human infections. MIS and MFS profiling provides a clear ranking of the relative essentiality of gene ontology (GO) functions in P. falciparum. GO pathways associated with translation, RNA metabolism, and cell cycle control are more essential, whereas genes associated with protein phosphorylation, virulence factors, and transcription are more likely to be dispensable. Last, we confirm that the proteasome-degradation pathway is a high-value druggable target on the basis of its high ratio of essential to dispensable genes, and by functionally confirming its link to the mode of action of artemisinin, the current front-line antimalarial. CONCLUSION Saturation-scale mutagenesis allows prioritization of intervention targets in the genome of the most important cause of malaria. The identification of more than 2680 essential genes, including ~1000 Plasmodium-conserved essential genes, will be valuable for antimalarial therapeutic research. Saturation-scale mutagenesis of P. falciparum reveals genes essential and dispensable for asexual blood-stage development. (Top) A high-resolution map of a ~50-kb region of chromosome 13 depicts an essential gene cluster, including K13, that lacks insertions in the coding DNA sequence (CDS) but is flanked by dispensable genes with multiple CDS-disrupting insertions. (Left) The MIS rates the potential mutability of P. falciparum genes based on the number of recovered CDS insertions relative to the potential number that could be recovered through large-scale mutagenesis. (Right) The MFS rates the relative fitness of P. falciparum genes based on QIseq scores of transposon insertion sites in each gene. Severe malaria is caused by the apicomplexan parasite Plasmodium falciparum. Despite decades of research, the distinct biology of these parasites has made it challenging to establish high-throughput genetic approaches to identify and prioritize therapeutic targets. Using transposon mutagenesis of P. falciparum in an approach that exploited its AT-rich genome, we generated more than 38,000 mutants, saturating the genome and defining mutability and fitness costs for over 87% of genes. Of 5399 genes, our study defined 2680 genes as essential for optimal growth of asexual blood stages in vitro. These essential genes are associated with drug resistance, represent leading vaccine candidates, and include approximately 1000 Plasmodium-conserved genes of unknown function. We validated this approach by testing proteasome pathways for individual mutants associated with artemisinin sensitivity."], "field": "Immunology and Microbiology", "q_year": 2024, "q_cid": "271570799", "pos_cid": 206664261, "source": "eval_collection"}
{"query_id": "scaleup_21575705_7091278", "query": "How to determine how species maintain protection despite major pathway alterations and the loss or high divergence of associated genes", "pos": ["A CD74-DEPENDENT MHC CLASS I ENDOLYSOSOMAL CROSS-PRESENTATION PATHWAY. Immune responses are initiated and primed by dendritic cells (DCs) that cross-present exogenous antigen. The chaperone CD74 (invariant chain) is thought to promote DC priming exclusively in the context of major histocompatibility complex (MHC) class II. However, we demonstrate here a CD74-dependent MHC class I cross-presentation pathway in DCs that had a major role in the generation of MHC class I–restricted, cytolytic T lymphocyte (CTL) responses to viral protein– and cell-associated antigens. CD74 associated with MHC class I in the endoplasmic reticulum of DCs and mediated the trafficking of MHC class I to endolysosomal compartments for loading with exogenous peptides. We conclude that CD74 has a previously undiscovered physiological function in endolysosomal DC cross-presentation for priming MHC class I–mediated CTL responses."], "field": "Immunology and Microbiology", "q_year": 2020, "q_cid": "215757052", "pos_cid": 7091278, "source": "eval_collection"}
{"query_id": "scaleup_26086064_3722387", "query": "How to clarify a parasite’s effects on virus-induced IRF7 nuclear translocation in plasmacytoid dendritic cells and antiviral interferon responses", "pos": ["Toxoplasma gondii inactivates human plasmacytoid dendritic cells by functional mimicry of IL-10. Plasmacytoid dendritic cells (pDCs) are the major producers of IFN-α, an antiviral cytokine involved in immunomodulation and control of HIV type 1 replication, whereas Toxoplasma gondii is a life-threatening opportunistic infection in AIDS patients. During infection with HIV type 1, human pDCs decrease in circulation and remaining pDC produce lower amounts of IFN-α in response to viral stimulation. In this study, we investigated the impact of coinfection with T. gondii on the innate virus-directed responses of human pDCs. Using intracellular flow cytometry and fluorescence microscopy, we determined that T. gondii invaded but did not induce IFN-α or TNF-α in human pDC. However, T. gondii inhibited IFN-α and TNF-α produced in response to HSV and HIV, thus functionally inactivating pDC. IFN-α production was inhibited only in cells infected by T. gondii, which inhibited neither uptake of GFP-HSV nor localization of TLR9 in CD71+ endosomes, directing us to investigate downstream events. Using imaging flow cytometry, we found that both T. gondii and IL-10 inhibited virus-induced nuclear translocation, but not phosphorylation, of IFN response factor 7. Blockade of IFN response factor 7 nuclear translocation and inhibition of the IFN-α response was partially reversed by a deficiency in the T. gondii–derived ROP16 kinase, known to directly phosphorylate STAT3, a critical mediator of IL-10’s anti-inflammatory effects. Taken together, our results indicate that T. gondii suppresses pDC activation by mimicking IL-10’s regulatory effects through an ROP16 kinase-dependent mechanism. Our findings further imply a convergent mechanism of inhibition of TLR signaling by T. gondii and IL-10 and suggest potential negative consequences of HIV/T. gondii coinfection."], "field": "Immunology and Microbiology", "q_year": 2023, "q_cid": "260860649", "pos_cid": 3722387, "source": "eval_collection"}
{"query_id": "scaleup_27159908_1204574", "query": "How to establish the clinical feasibility of targeting the interferon response in acute myocardial infarction, with human tolerability as a requirement", "pos": ["Sifalimumab, an anti-interferon-α monoclonal antibody, in moderate to severe systemic lupus erythematosus: a randomised, double-blind, placebo-controlled study. Objectives The efficacy and safety of sifalimumab were assessed in a phase IIb, randomised, double-blind, placebo-controlled study (NCT01283139) of adults with moderate to severe active systemic lupus erythematosus (SLE). Methods 431 patients were randomised and received monthly intravenous sifalimumab (200 mg, 600 mg or 1200 mg) or placebo in addition to standard-of-care medications. Patients were stratified by disease activity, interferon gene-signature test (high vs low based on the expression of four genes) and geographical region. The primary efficacy end point was the percentage of patients achieving an SLE responder index response at week 52. Results Compared with placebo, a greater percentage of patients who received sifalimumab (all dosages) met the primary end point (placebo: 45.4%; 200 mg: 58.3%; 600 mg: 56.5%; 1200 mg 59.8%). Other improvements were seen in Cutaneous Lupus Erythematosus Disease Area and Severity Index score (200 mg and 1200 mg monthly), Physician's Global Assessment (600 mg and 1200 mg monthly), British Isles Lupus Assessment Group-based Composite Lupus Assessment (1200 mg monthly), 4-point reductions in the SLE Disease Activity Index−2000 score and reductions in counts of swollen joints and tender joints. Serious adverse events occurred in 17.6% of patients on placebo and 18.3% of patients on sifalimumab. Herpes zoster infections were more frequent with sifalimumab treatment. Conclusions Sifalimumab is a promising treatment for adults with SLE. Improvement was consistent across various clinical end points, including global and organ-specific measures of disease activity. Trial registration number NCT01283139; Results."], "field": "Immunology and Microbiology", "q_year": 2024, "q_cid": "271599088", "pos_cid": 1204574, "source": "eval_collection"}
{"query_id": "scaleup_24648609_85494128", "query": "How to identify interactions consistent with transcriptomic data from cells infected with different VSV strains when the intracellular targets of wild-type and mutant M proteins are unknown", "pos": ["Bio-ModelChecker: Using Bounded Constraint Satisfaction to Seamlessly Integrate Observed Behavior With Prior Knowledge of Biological Networks. The in silico study and reverse engineering of regulatory networks has gained in recognition as an insightful tool for the qualitative study of biological mechanisms that underlie a broad range of complex illness. In the creation of reliable network models, the integration of prior mechanistic knowledge with experimentally observed behavior is hampered by the disparate nature and widespread sparsity of such measurements. The former challenges conventional regression-based parameter fitting while the latter leads to large sets of highly variable network models that are equally compliant with the data. In this paper, we propose a bounded Constraint Satisfaction (CS) based model checking framework for parameter set identification that readily accommodates partial records and the exponential complexity of this problem. We introduce specific criteria to describe the biological plausibility of competing multi-valued regulatory networks that satisfy all the constraints and formulate model identification as a multi-objective optimization problem. Optimization is directed at maximizing structural parsimony of the regulatory network by mitigating excessive control action selectivity while also favoring increased state transition efficiency and robustness of the network's dynamic response. The framework's scalability, computational time and validity is demonstrated on several well-established and well-studied biological networks."], "field": "Immunology and Microbiology", "q_year": 2022, "q_cid": "246486090", "pos_cid": 85494128, "source": "eval_collection"}
{"query_id": "scaleup_27034297_22048131", "query": "How to determine whether peptide-induced stress causes skin cell death or protective responses that limit cell killing, and why different skin cell types differ in resistance to this stress", "pos": ["Oxidative Stress in Cancer. Contingent upon concentration, reactive oxygen species (ROS) influence cancer evolution in apparently contradictory ways, either initiating/stimulating tumorigenesis and supporting transformation/proliferation of cancer cells or causing cell death. To accommodate high ROS levels, tumor cells modify sulfur-based metabolism, NADPH generation, and the activity of antioxidant transcription factors. During initiation, genetic changes enable cell survival under high ROS levels by activating antioxidant transcription factors or increasing NADPH via the pentose phosphate pathway (PPP). During progression and metastasis, tumor cells adapt to oxidative stress by increasing NADPH in various ways, including activation of AMPK, the PPP, and reductive glutamine and folate metabolism."], "field": "Immunology and Microbiology", "q_year": 2024, "q_cid": "270342970", "pos_cid": 220481312, "source": "eval_collection"}
{"query_id": "scaleup_23331278_20475413", "query": "How to clarify the regulation of Th17 cell differentiation and IL-17A expression", "pos": ["AhR Activation by TCDD (2,3,7,8-Tetrachlorodibenzo-p-dioxin) Attenuates Pertussis Toxin-Induced Inflammatory Responses by Differential Regulation of Tregs and Th17 Cells Through Specific Targeting by microRNA. The Aryl Hydrocarbon Receptor (AhR) is a transcription factor that, when activated by ligand-binding, has been shown to regulate the immune response. Pertussis Toxin (PTX) is a virulence factor found in Bordetella pertussis, a human respiratory pathogen that causes whooping cough. PTX promotes colonization and disease promotion by triggering a heightened inflammatory response. The role of AhR in the regulation of PTX-mediated inflammation has not previously been studied. In the current study, we investigate if AhR activation by 2,3,7,8-Tetrachlorodibenzo-p-dioxin (TCDD), a well characterized ligand, can attenuate PTX-mediated systemic inflammation. To that end, C57BL/6 mice were injected intraperitoneally (IP) with PTX twice and treated with TCDD or vehicle (VEH). The PTX+VEH group showed elevated levels of pro-inflammatory cytokines (IL-17A, IL-6, and IFNγ) in serum and increased proportions of CD4+ Th1 and Th17 cells in their spleens. In contrast, the PTX+TCDD group showed significantly lower levels of these inflammatory cytokines and decreased proportions of Th1 and Th17 cells, but increased proportions of Th2 and FoxP3+Tregs when compared to the PTX+VEH group. PTX+TCDD treated mice also showed elevated levels of IL-10, and TFG-b, potent anti-inflammatory cytokines. MicroRNAs (miRs) analysis of CD4+ T cells from the spleens of the PTX+TCDD treated mice revealed significant alterations in their expression and several of these miRs targeted cytokines and signaling molecules involved in inflammation. Specifically, the PTX+TCDD group had a significantly enhanced expression of miR-3082-5p that targeted IL-17, and a decreased expression of miR-1224-5p, which targeted FoxP3. Transfection studies with these miR mimics and inhibitors confirmed the specificity of the target genes. The current study suggests that AhR activation by TCDD suppresses PTX-induced inflammation through miR regulation that triggers reciprocal polarization of Tregs and Th17 cells and also suggests that AhR activation may serve as a treatment modality to suppress heightened inflammation induced during B. pertussis infection."], "field": "Immunology and Microbiology", "q_year": 2021, "q_cid": "233312781", "pos_cid": 204754134, "source": "eval_collection"}
{"query_id": "scaleup_27159908_21269007", "query": "How to identify what disrupts the balance between inflammatory and reparative macrophage states with distinct energy requirements", "pos": ["Obesity, Hypertension, and Cardiac Dysfunction: Novel Roles of Immunometabolism in Macrophage Activation and Inflammation. Obesity and hypertension, which often coexist, are major risk factors for heart failure and are characterized by chronic, low-grade inflammation, which promotes adverse cardiac remodeling. While macrophages play a key role in cardiac remodeling, dysregulation of macrophage polarization between the proinflammatory M1 and anti-inflammatory M2 phenotypes promotes excessive inflammation and cardiac injury. Metabolic shifting between glycolysis and mitochondrial oxidative phosphorylation has been implicated in macrophage polarization. M1 macrophages primarily rely on glycolysis, whereas M2 macrophages rely on the tricarboxylic acid cycle and oxidative phosphorylation; thus, factors that affect macrophage metabolism may disrupt M1/M2 homeostasis and exacerbate inflammation. The mechanisms by which obesity and hypertension may synergistically induce macrophage metabolic dysfunction, particularly during cardiac remodeling, are not fully understood. We propose that obesity and hypertension induce M1 macrophage polarization via mechanisms that directly target macrophage metabolism, including changes in circulating glucose and fatty acid substrates, lipotoxicity, and tissue hypoxia. We discuss canonical and novel proinflammatory roles of macrophages during obesity-hypertension–induced cardiac injury, including diastolic dysfunction and impaired calcium handling. Finally, we discuss the current status of potential therapies to target macrophage metabolism during heart failure, including antidiabetic therapies, anti-inflammatory therapies, and novel immunometabolic agents."], "field": "Immunology and Microbiology", "q_year": 2024, "q_cid": "271599088", "pos_cid": 212690075, "source": "eval_collection"}
{"query_id": "scaleup_24380161_51653698", "query": "How to achieve sensitive detection of atherosclerosis-related disease before vascular events occur, when chronic arterial inflammation is already present", "pos": ["Autoantibodies as Potential Biomarkers in Breast Cancer. Breast cancer is a major cause of mortality in women; however, technologies for early stage screening and diagnosis (e.g., mammography and other imaging technologies) are not optimal for the accurate detection of cancer. This creates demand for a more effective diagnostic means to replace or be complementary to existing technologies for early discovery of breast cancer. Cancer neoantigens could reflect tumorigenesis, but they are hardly detectable at the early stage. Autoantibodies, however, are biologically amplified and hence may be measurable early on, making them promising biomarkers to discriminate breast cancer from healthy tissue accurately. In this review, we summarized the recent findings of breast cancer specific antigens and autoantibodies, which may be useful in early detection, disease stratification, and monitoring of treatment responses of breast cancer."], "field": "Immunology and Microbiology", "q_year": 2021, "q_cid": "243801611", "pos_cid": 51653698, "source": "eval_collection"}
{"query_id": "scaleup_27979659_25822930", "query": "How to determine whether STING export from the ER is necessary for downstream TBK1 and IRF3 activation", "pos": ["SARS-CoV-2 spike host cell surface exposure promoted by a COPI sorting inhibitor. Via an insufficient coat protein complex I (COPI) retrieval signal, the majority of SARS-CoV-2 spike (S) is resident in host early secretory organelles and a tiny amount is leaked out in cell surface. Only surface-exposed S can be recognized by B cell receptor (BCR) or anti-S therapeutic monoclonal antibodies (mAbs) that is the trigger step for B cell activation after S mRNA vaccination or infected cell clearance by S mAbs. Now, a drug strategy to promote S host surface exposure is absent. Here, we first combined structural and biochemical analysis to characterize S COPI sorting signals. A potent S COPI sorting inhibitor was then invented, evidently capable of promoting S surface exposure and facilitating infected cell clearance by S antibody-dependent cellular cytotoxicity (ADCC). Importantly, with the inhibitor as a probe, we revealed Omicron BA.1 S is less cell surface exposed than prototypes because of a constellation of S folding mutations, possibly corresponding to its ER chaperone association. Our findings not only suggest COPI is a druggable target against COVID-19, but also highlight SARS-CoV-2 evolution mechanism driven by S folding and trafficking mutations."], "field": "Immunology and Microbiology", "q_year": 2025, "q_cid": "279796596", "pos_cid": 258229304, "source": "eval_collection"}
{"query_id": "scaleup_28059838_26841503", "query": "How to assess the structural stability of a selected peptide–target complex over time and compare it with that of a standard antifungal drug", "pos": ["Synthesis, spectroscopic analysis, and computational-based investigations on ‘azo-coumarin-Co(II)-galangin’ hybrids exhibit multipotential activities. Abstract The present study synthesized a series of cobalt (II) metal ion frame hybrid candidates (6a–6f) bearing phyto-flavonol galangin with substituted aryl diazenyl coumarins, and further structural confirmation was validated by various spectral techniques, including NMR, ATR-FTIR, UV-vis, HPLC, XRD, etc. Therapeutic potency was investigated via PASS (prediction of activity spectra for substances), molecular docking, molecular dynamics simulation, prediction of toxicity, pharmacokinetics, and drug-likeness scores, along with the highest occupied molecular orbital (HOMO), the lowest unoccupied molecular orbital (LUMO), with their energy gaps (ΔEH–L) to locate the most potential therapeutic candidates. The PASS prediction (Pa > Pi score) showed that proposed metal complexes have kinase inhibitors, antioxidative, and antischistosomal activities with potential molecular docking scores (> −7 kcal/mol) against selected targeted enzymes. Further, the MD-simulation (RMSD, RMSF, Rg, and H-bonds) of the most potential docking complex, ‘HER2-6d’, showed a minimum deviation similar to the standard drug (lapatinib) at 100 ns, indicating that 6d could be a potential noncovalent anticancer inhibitor. In addition, metal complexes possess a non-toxic and ideal drug-ability profiles, and positive electron space in an excited state increases the binding affinity towards target enzymes. Among all six ligands, 6c and 6d were the two most multipotent therapeutic agents from the above analyses. In summary, this could be a feasible approach towards the utilization of phytochemicals in mainstream therapeutic applications, where bioinformatics tools help to select a lead drug candidate at an early stage and guide for higher experimental success by proceeding with potential candidates."], "field": "Immunology and Microbiology", "q_year": 2025, "q_cid": "280598389", "pos_cid": 268415033, "source": "eval_collection"}
{"query_id": "scaleup_27114088_20494277", "query": "How to distinguish macrophage-related subtypes of atherosclerosis and establish the stability and reliability of the sample groupings", "pos": ["ConsensusClusterPlus: a class discovery tool with confidence assessments and item tracking. Summary: Unsupervised class discovery is a highly useful technique in cancer research, where intrinsic groups sharing biological characteristics may exist but are unknown. The consensus clustering (CC) method provides quantitative and visual stability evidence for estimating the number of unsupervised classes in a dataset. ConsensusClusterPlus implements the CC method in R and extends it with new functionality and visualizations including item tracking, item-consensus and cluster-consensus plots. These new features provide users with detailed information that enable more specific decisions in unsupervised class discovery. Availability: ConsensusClusterPlus is open source software, written in R, under GPL-2, and available through the Bioconductor project (http://www.bioconductor.org/). Contact: mwilkers@med.unc.edu Supplementary Information: Supplementary data are available at Bioinformatics online."], "field": "Immunology and Microbiology", "q_year": 2024, "q_cid": "271140888", "pos_cid": 20494277, "source": "eval_collection"}
{"query_id": "scaleup_27929316_26168008", "query": "How to strengthen STING-associated antitumor immune responses in SETD2-deficient clear cell renal cell carcinoma to achieve tumor-cell killing and suppress tumor growth", "pos": ["SETD2 Deficiency Confers Sensitivity to Dual Inhibition of DNA Methylation and PARP in Kidney Cancer. SETD2 deficiency alters the epigenetic landscape by causing depletion of H3K36me3 and plays an important role in diverse forms of cancer, most notably in aggressive and metastatic clear cell renal cell carcinomas (ccRCC). Development of an effective treatment scheme targeting SETD2-compromised cancer is urgently needed. Considering that SETD2 is involved in DNA methylation and DNA repair, a combination treatment approach using DNA hypomethylating agents (HMA) and PARP inhibitors (PARPi) could have strong anti-tumor activity in SETD2-deficient kidney cancer. We tested the effects of the DNA HMA 5-aza-2’-dexoxydytidine (DAC), the PARPi talazoparib (BMN-673), and both in combination in human ccRCC models with or without SETD2 deficiency. The combination treatment of DAC and BMN-673 synergistically increased cytotoxicity in vitro in SETD2-deficient ccRCC cell lines but not in SETD2-proficient cell lines. DAC and BMN-673 led to apoptotic induction, increased DNA damage, insufficient DNA damage repair, and increased genomic instability. Furthermore, the combination treatment elevated immune responses, upregulated STING, and enhanced viral mimicry by activating transposable elements. Finally, the combination effectively suppressed the growth of SETD2-deficient ccRCC in in vivo mouse models. Together, these findings indicate that combining HMA and PARPi is a promising potential therapeutic strategy for treating SETD2-compromised ccRCC."], "field": "Immunology and Microbiology", "q_year": 2025, "q_cid": "279293163", "pos_cid": 261680082, "source": "eval_collection"}
{"query_id": "scaleup_25149794_3496911", "query": "How to sustain epithelial cultures for gastrointestinal nematode–host interaction studies while precisely controlling exposure of apical and basal surfaces to pathogens, signalling molecules and other cells", "pos": ["Polarised epithelial monolayers of the gastric mucosa reveal insights into mucosal homeostasis and defence against infection. Objective Helicobacter pylori causes life-long colonisation of the gastric mucosa, leading to chronic inflammation with increased risk of gastric cancer. Research on the pathogenesis of this infection would strongly benefit from an authentic human in vitro model. Design Antrum-derived gastric glands from surgery specimens served to establish polarised epithelial monolayers via a transient air–liquid interface culture stage to study cross-talk with H. pylori and the adjacent stroma. Results The resulting ‘mucosoid cultures’, so named because they recapitulate key characteristics of the gastric mucosa, represent normal stem cell-driven cultures that can be passaged for months. These highly polarised columnar epithelial layers encompass the various gastric antral cell types and secrete mucus at the apical surface. By default, they differentiate towards a foveolar, MUC5AC-producing phenotype, whereas Wnt signalling stimulates proliferation of MUC6-producing cells and preserves stemness—reminiscent of the gland base. Stromal cells from the lamina propria secrete Wnt inhibitors, antagonising stem-cell niche signalling and inducing differentiation. On infection with H. pylori, a strong inflammatory response is induced preferentially in the undifferentiated basal cell phenotype. Infection of cultures for several weeks produces foci of viable bacteria and a persistent inflammatory condition, while the secreted mucus establishes a barrier that only few bacteria manage to overcome. Conclusion Gastric mucosoid cultures faithfully reproduce the features of normal human gastric epithelium, enabling new approaches for investigating the interaction of H. pylori with the epithelial surface and the cross-talk with the basolateral stromal compartment. Our observations provide striking insights in the regulatory circuits of inflammation and defence."], "field": "Immunology and Microbiology", "q_year": 2022, "q_cid": "251497942", "pos_cid": 3496911, "source": "eval_collection"}
{"query_id": "scaleup_25149794_23902682", "query": "How to make the apical epithelial surface accessible for studying gastrointestinal nematode interactions while preserving the organoid’s three-dimensional structure", "pos": ["Controlling the polarity of human gastrointestinal organoids to investigate epithelial biology and infectious diseases. Human epithelial organoids—3D spheroids derived from adult tissue stem cells—enable investigation of epithelial physiology and disease and host interactions with microorganisms, viruses and bioactive molecules. One challenge in using organoids is the difficulty in accessing the apical, or luminal, surface of the epithelium, which is enclosed within the organoid interior. This protocol describes a method we previously developed to control human and mouse organoid polarity in suspension culture such that the apical surface faces outward to the medium (apical-out organoids). Our protocol establishes apical-out polarity rapidly (24–48 h), preserves epithelial integrity, maintains secretory and absorptive functions and allows regulation of differentiation. Here, we provide a detailed description of the organoid polarity reversal method, compatible characterization assays and an example of an application of the technology—specifically the impact of host–microbe interactions on epithelial function. Control of organoid polarity expands the possibilities of organoid use in gastrointestinal and respiratory health and disease research. The polarity of gastrointestinal organoids is reversed to study epithelial biology and host–microbe interactions. Access to the apical surface of the epithelium is increased while preserving epithelial integrity and secretory and absorptive functions."], "field": "Immunology and Microbiology", "q_year": 2022, "q_cid": "251497942", "pos_cid": 239026829, "source": "eval_collection"}
{"query_id": "scaleup_27766375_25472831", "query": "How to identify the cellular source of the rapid rise in circulating Metrnl during sepsis", "pos": ["Endothelial METRNL determines circulating METRNL level and maintains endothelial function against atherosclerosis. METRNL is a recently identified secreted protein with emerging functions. This study is to find major cellular source of circulating METRNL and to determine METRNL novel function. Here, we show METRNL is abundant in human and mouse vascular endothelium and released by endothelial cells using endoplasmic reticulum-Golgi apparatus pathway. By creating endothelial cell-specific Metrnl knockout mice, combined with bone marrow transplantation to produce bone marrow-specific deletion of Metrnl, we demonstrate that most of circulating METRNL (approximately 75%) originates from the endothelial cells. Both endothelial and circulating METRNL decrease in atherosclerosis mice and patients. By generating endothelial cell-specific Metrnl knockout in apolipoprotein E-deficient mice, combined with bone marrow-specific deletion of Metrnl in apolipoprotein E-deficient mice, we further demonstrate that endothelial METRNL deficiency accelerates atherosclerosis. Mechanically, endothelial METRNL deficiency causes vascular endothelial dysfunction including vasodilation impairment via reducing eNOS phosphorylation at Ser1177 and inflammation activation via enhancing NFκB pathway, which promotes the susceptibility of atherosclerosis. Exogenous METRNL rescues METRNL deficiency induced endothelial dysfunction. These findings reveal that METRNL is a new endothelial substance not only determining the circulating METRNL level but also regulating endothelial function for vascular health and disease. METRNL is a therapeutic target against endothelial dysfunction and atherosclerosis."], "field": "Immunology and Microbiology", "q_year": 2025, "q_cid": "277663759", "pos_cid": 254728313, "source": "eval_collection"}
{"query_id": "scaleup_27766375_49612506", "query": "How to explain the rapid secretion of meteorin-like protein and its early rise in blood during sepsis", "pos": ["A comprehensive review of signal peptides: Structure, roles, and applications.. Signal peptides (SP) are short peptides located in the N-terminal of proteins, carrying information for protein secretion. They are ubiquitous to all prokaryotes and eukaryotes. SPs have been of special interest in several scientific and industrial fields, including recombinant protein production, disease diagnosis, immunization, and laboratory techniques. Recently, the role of SPs in recombinant protein production has gained too much attention. Herein, several studies have been reviewed to elucidate the precise structure and function of SPs, particularly the optimized ones for recombinant protein production. However, some features of SPs still have remained obscure. In this review, some approaches concerning elucidation and optimization of SPs are discussed, and pragmatic conclusions and suggestions for future studies are also proposed. Moreover, a summary of secretory pathways, evolutionary changes, functions, applications, and different types of SPs is mentioned. At last, current limitations and prospects are discussed."], "field": "Immunology and Microbiology", "q_year": 2025, "q_cid": "277663759", "pos_cid": 49612506, "source": "eval_collection"}
{"query_id": "scaleup_22025251_8418333", "query": "How to determine whether zebrafish are a suitable alternative to mice for studying early human vascular disease and associated inflammatory responses", "pos": ["Apoc2 loss-of-function zebrafish mutant as a genetic model of hyperlipidemia. ABSTRACT Apolipoprotein C-II (APOC2) is an obligatory activator of lipoprotein lipase. Human patients with APOC2 deficiency display severe hypertriglyceridemia while consuming a normal diet, often manifesting xanthomas, lipemia retinalis and pancreatitis. Hypertriglyceridemia is also an important risk factor for development of cardiovascular disease. Animal models to study hypertriglyceridemia are limited, with no Apoc2-knockout mouse reported. To develop a genetic model of hypertriglyceridemia, we generated an apoc2 mutant zebrafish characterized by the loss of Apoc2 function. apoc2 mutants show decreased plasma lipase activity and display chylomicronemia and severe hypertriglyceridemia, which closely resemble the phenotype observed in human patients with APOC2 deficiency. The hypertriglyceridemia in apoc2 mutants is rescued by injection of plasma from wild-type zebrafish or by injection of a human APOC2 mimetic peptide. Consistent with a previous report of a transient apoc2 knockdown, apoc2 mutant larvae have a minor delay in yolk consumption and angiogenesis. Furthermore, apoc2 mutants fed a normal diet accumulate lipid and lipid-laden macrophages in the vasculature, which resemble early events in the development of human atherosclerotic lesions. In addition, apoc2 mutant embryos show ectopic overgrowth of pancreas. Taken together, our data suggest that the apoc2 mutant zebrafish is a robust and versatile animal model to study hypertriglyceridemia and the mechanisms involved in the pathogenesis of associated human diseases. Highlighted Article: Apoc2 loss-of-function zebrafish display severe hypertriglyceridemia, which is characteristic of human patients with defective lipoprotein lipase activity."], "field": "Immunology and Microbiology", "q_year": 2020, "q_cid": "220252513", "pos_cid": 8418333, "source": "eval_collection"}
{"query_id": "scaleup_24712262_20106242", "query": "How to improve human immunodeficiency virus control in people receiving antiretroviral therapy", "pos": ["Acyl-CoA-Binding Protein Is a Lipogenic Factor that Triggers Food Intake and Obesity.. Autophagy facilitates the adaptation to nutritional stress. Here, we show that short-term starvation of cultured cells or mice caused the autophagy-dependent cellular release of acyl-CoA-binding protein (ACBP, also known as diazepam-binding inhibitor, DBI) and consequent ACBP-mediated feedback inhibition of autophagy. Importantly, ACBP levels were elevated in obese patients and reduced in anorexia nervosa. In mice, systemic injection of ACBP protein inhibited autophagy, induced lipogenesis, reduced glycemia, and stimulated appetite as well as weight gain. We designed three approaches to neutralize ACBP, namely, inducible whole-body knockout, systemic administration of neutralizing antibodies, and induction of antiACBP autoantibodies in mice. ACBP neutralization enhanced autophagy, stimulated fatty acid oxidation, inhibited appetite, reduced weight gain in the context of a high-fat diet or leptin deficiency, and accelerated weight loss in response to dietary changes. In conclusion, neutralization of ACBP might constitute a strategy for treating obesity and its co-morbidities."], "field": "Immunology and Microbiology", "q_year": 2022, "q_cid": "247122629", "pos_cid": 201062424, "source": "eval_collection"}
{"query_id": "scaleup_23547071_7072049", "query": "How to clarify why higher ligand concentrations may not produce stronger ALX/FPR2 signaling", "pos": ["FPR2/ALX receptor expression and internalization are critical for lipoxin A4 and annexin-derived peptide-stimulated phagocytosis. Lipoxins (LXs) are endogenously produced eicosanoids with well‐described anti‐inflammatory and proresolution activities, stimulating nonphlogistic phagocytosis of apoptotic cells by macrophages. LXA4 and the glucocorticoid‐derived annexin A1 peptide (Ac2–26) bind to a common G‐proteincoupled receptor, termed FPR2/ALX. However, direct evidence of the involvement of FPR2/ALX in the anti‐inflammatory and proresolution activity of LXA4 is still to be investigated. Here we describe FPR2/ALX trafficking in response to LXA4 and Ac2–26 stimulation. We have transfected cells with HA‐tagged FPR2/ALX and studied receptor trafficking in unstimulated, LXA4 (1–10 nM)‐ and Ac2–26 (30 µM)‐treated cells using multiple approaches that include immunofluorescent confocal microscopy, immunogold labeling of cryosections, and ELISA and investigated receptor trafficking in agonist‐stimulated phagocytosis. We conclude that PKC‐dependent internalization of FPR2/ALX is required for phagocytosis. Using bone marrow‐derived macrophages (BMDMs) from mice in which the FPR2/ALX ortholog Fpr2 had been deleted, we observed the nonredundant function for this receptor in LXA4 and Ac2–26 stimulated phagocytosis of apoptotic neutrophils. LXA4 stimulated phagocytosis 1.7‐fold above basal (P< 0.001) by BMDMs from wild‐type mice, whereas no effect was found on BMDMs from Fpr2‐/‐ mice. Similarly, Ac2–26 stimulates phagocytosis by BMDMs from wild‐type mice 1.5‐fold above basal (P<0.05). However, Ac2–26 failed to stimulate phagocytosis by BMDMs isolated from Fpr2‐/‐ mice relative to vehicle. These data reveal novel and complex mechanisms of the FPR2/ALX receptor trafficking and functionality in the resolution of inflammation.—Maderna, P., Cottell, D. C., Toivonen, T., Dufton, N., Dalli, J., Perretti, M., Godson, C. FPR2/ALX receptor expression and internalization are critical for lipoxin A4 and annexinderived peptide‐stimulated phagocytosis. FASEB J. 24, 4240–4249 (2010). www.fasebj.org"], "field": "Immunology and Microbiology", "q_year": 2021, "q_cid": "235470718", "pos_cid": 7072049, "source": "eval_collection"}
{"query_id": "scaleup_27159908_22626961", "query": "How to clarify the role of eosinophils in regulating inflammation, macrophage polarization, and inflammatory-cell recruitment during myocardial injury and repair in ischemic heart disease", "pos": ["Eosinophils Protect Mice from Angiotensin-II Perfusion-Induced Abdominal Aortic Aneurysm. Supplemental Digital Content is available in the text. Rationale: Blood eosinophil count and ECP (eosinophil cationic protein) associate with human cardiovascular diseases. Yet, whether eosinophils play a role in cardiovascular disease remains untested. The current study detected eosinophil accumulation in human and murine abdominal aortic aneurysm (AAA) lesions, suggesting eosinophil participation in this aortic disease. Objective: To test whether and how eosinophils affect AAA growth. Methods and Results: Population-based randomized clinically controlled screening trials revealed higher blood eosinophil count in 579 male patients with AAA than in 5063 non-AAA control (0.236±0.182 versus 0.211±0.154, 109/L, P<0.001). Univariate (odds ratio, 1.381, P<0.001) and multivariate (odds ratio, 1.237, P=0.031) logistic regression analyses indicated that increased blood eosinophil count in patients with AAA served as an independent risk factor of human AAA. Immunostaining and immunoblot analyses detected eosinophil accumulation and eosinophil cationic protein expression in human and murine AAA lesions. Results showed that eosinophil deficiency exacerbated AAA growth with increased lesion inflammatory cell contents, matrix-degrading protease activity, angiogenesis, cell proliferation and apoptosis, and smooth muscle cell loss using angiotensin-II perfusion–induced AAA in Apoe−/− and eosinophil-deficient Apoe−/−ΔdblGATA mice. Eosinophil deficiency increased lesion chemokine expression, muted lesion expression of IL (interleukin) 4 and eosinophil-associated-ribonuclease-1 (mEar1 [mouse EOS-associated-ribonuclease-1], human ECP homolog), and slanted M1 macrophage polarization. In cultured macrophages and monocytes, eosinophil-derived IL4 and mEar1 polarized M2 macrophages, suppressed CD11b+Ly6Chi monocytes, and increased CD11b+Ly6Clo monocytes. mEar1 treatment or adoptive transfer of eosinophil from wild-type and Il13−/− mice, but not eosinophil from Il4−/− mice, blocked AAA growth in Apoe−/−ΔdblGATA mice. Immunofluorescent staining and immunoblot analyses demonstrated a role for eosinophil IL4 and mEar1 in blocking NF-κB (nuclear factor-κB) activation in macrophages, smooth muscle cells, and endothelial cells. Conclusions: Eosinophils play a protective role in AAA by releasing IL4 and cationic proteins such as mEar1 to regulate macrophage and monocyte polarization and to block NF-κB activation in aortic inflammatory and vascular cells."], "field": "Immunology and Microbiology", "q_year": 2024, "q_cid": "271599088", "pos_cid": 226269618, "source": "eval_collection"}
{"query_id": "scaleup_27159908_25821641", "query": "How to effectively treat myocardial tissue fibrosis after myocardial infarction in ischemic heart disease", "pos": ["Desmoplastic stroma restricts T cell extravasation and mediates immune exclusion and immunosuppression in solid tumors. The desmoplastic stroma in solid tumors presents a formidable challenge to immunotherapies that rely on endogenous or adoptively transferred T cells, however, the mechanisms are poorly understood. To define mechanisms involved, we treat established desmoplastic pancreatic tumors with CAR T cells directed to fibroblast activation protein (FAP), an enzyme highly overexpressed on a subset of cancer-associated fibroblasts (CAFs). Depletion of FAP+CAFs results in loss of the structural integrity of desmoplastic matrix. This renders these highly treatment-resistant cancers susceptible to subsequent treatment with a tumor antigen (mesothelin)-targeted CAR and to anti-PD1 antibody therapy. Mechanisms include overcoming stroma-dependent restriction of T cell extravasation and/or perivascular invasion, reversing immune exclusion, relieving T cell suppression, and altering the immune landscape by reducing myeloid cell accumulation and increasing endogenous CD8+ T cell and NK cell infiltration. These data provide strong rationale for combining tumor stroma-and malignant cell-targeted therapies to be tested in clinical trials."], "field": "Immunology and Microbiology", "q_year": 2024, "q_cid": "271599088", "pos_cid": 258216411, "source": "eval_collection"}
{"query_id": "scaleup_10378181_10124680", "query": "How to establish the local symmetry of europium sites in doped zirconia and their association with oxygen vacancies despite overlapping spectral contributions", "pos": ["Interpretation of europium(III) spectra. Abstract The trivalent europium ion (Eu 3+ ) is well known for its strong luminescence in the red spectral region, but this ion is also interesting from a theoretical point of view. Due to the even number of electrons in the 4f shell (4f 6 configuration), the crystal-field perturbation by the crystalline host matrix lifts partly or completely the degeneracies of the 2 S +1 L J levels. The Eu 3+ ion has the great advantage over other lanthanide ions with an even number of 4f electrons that the starting levels of the transitions in both the absorption and the luminescence spectrum are non-degenerate ( J = 0). Moreover, the interpretation of the spectra is facilitated by the small total angular momentum J of the end levels in the transitions. The number of lines observed for the 5 D 0 → 7 F J transitions in the luminescence spectrum or the 5 D J ← 7 F 0 transitions in the absorption spectrum allows determining the site symmetry of the Eu 3+ ion. This review describes the spectroscopic properties of the trivalent europium ion, with emphasis on the energy level structure, the intensities of the f–f transitions (including the Judd–Ofelt theory), the decay times of the excited states and the use of the Eu 3+ ion as a spectroscopic probe for site symmetry determination. It is illustrated how the maximum amount of information can be extracted from optical absorption and luminescence spectra of europium(III) compounds, and how pitfalls in the interpretation of these spectra can be avoided."], "field": "Materials Science", "q_year": 2018, "q_cid": "103781814", "pos_cid": 101246807, "source": "eval20x26"}
{"query_id": "scaleup_15537325_11460089", "query": "How to determine which Gd-LC6-SH–albumin binding reactions can occur before unbound-agent clearance in vivo to interpret Gd-LC6-SH as a tumor redox marker", "pos": ["Albumin Thiolate Anion Is an Intermediate in the Formation of Albumin-S–S-Homocysteine*. An elevated concentration of plasma total homocysteine is an independent risk factor for cardiovascular disease. Greater than 80% of circulating homocysteine is covalently bound to plasma protein by disulfide bonds. It is known that albumin combines with cysteine in circulation to form albumin-Cys34-S–S-Cys. Studies are now presented to show that the formation of albumin-bound homocysteine proceeds through the generation of an albumin thiolate anion. Incubation of human plasma withl-35S-homocysteine results in the association of >90% of the protein-bound 35S-homocysteine with albumin as shown by nonreduced SDS-polyacrylamide gel electrophoresis. Treatment of the complex with β-mercaptoethanol results in near quantitative release of the boundl-35S-homocysteine, demonstrating that the binding of homocysteine to albumin is through a disulfide bond. Furthermore, using an in vitro model system to study the mechanisms of this disulfide bond formation, we show that homocysteine binds to albumin in two steps. In the first step homocysteine rapidly displaces cysteine from albumin-Cys34-S–S-Cys, forming albumin-Cys34 thiolate anion and homocysteine-cysteine mixed disulfide. In the second step, albumin thiolate anion attacks homocysteine-cysteine mixed disulfide to yield primarily albumin-Cys34-S–S-Hcy and to a much lesser extent albumin-Cys34-S–S-Cys. The results clearly suggest that when reduced homocysteine enters circulation, it attacks albumin-Cys34-S–S-Cys to form albumin-Cys34thiolate anion, which in turn, reacts with homocysteine-cysteine mixed disulfide or homocystine to form albumin-bound homocysteine."], "field": "Materials Science", "q_year": 2016, "q_cid": "15537325", "pos_cid": 11460089, "source": "eval20x26"}
{"query_id": "scaleup_4334780_27943742", "query": "How to understand bacterial survival after exposure to pegylated silver-coated carbon nanotubes", "pos": ["Alkyl hydroperoxide reductase subunit C (AhpC) protects bacterial and human cells against reactive nitrogen intermediates.. In Salmonella typhimurium, ahpC encodes subunit C of alkyl hydroperoxide reductase, an enzyme that reduces organic peroxides. Here, we asked if ahpC could protect cells from reactive nitrogen intermediates (RNI). Salmonella disrupted in ahpC became hypersusceptible to RNI. ahpC from either Mycobacterium tuberculosis or S. typhimurium fully complemented the defect. Unlike protection against cumene hydroperoxide, protection afforded by ahpC against RNI was independent of the reducing flavoprotein, AhpF. Mycobacterial ahpC protected human cells from necrosis and apoptosis caused by RNI delivered exogenously or produced endogenously by transfected nitric oxide synthase. Resistance to RNI appears to be a physiologic function of ahpC. ahpC is the most widely distributed gene known that protects cells directly from RNI, and provides an enzymatic defense against an element of antitubercular immunity."], "field": "Materials Science", "q_year": 2018, "q_cid": "4334780", "pos_cid": 27943742, "source": "eval20x26"}
{"query_id": "scaleup_3323202_11942186", "query": "How to explain rapid, efficient electronic energy transfer to the lattice in photoexcited MoSe₂ and the role of the excited carrier population", "pos": ["Two bounds on the maximum phonon-mediated superconducting transition temperature. Two simple bounds on the $T_c$ of conventional, phonon-mediated superconductors are derived within the framework of Eliashberg theory in the strong coupling regime. The first bound is set by the total electron-phonon coupling available within a material given the hypothetical ability to arbitrarily dope the material. This bound is studied by deriving a generalization of the McMillan-Hopfield parameter, $\\widetilde{\\eta}(E)$, which measures the strength of electron-phonon coupling including anisotropy effects and rigid-band doping of the Fermi level to $E$. The second bound is set by the softening of phonons to instability due to strong electron-phonon coupling with electrons at the Fermi level. We apply these bounds to some covalent superconductors including MgB$_2$, where $T_c$ reaches the first bound, and boron-doped diamond, which is far from its bounds."], "field": "Materials Science", "q_year": 2017, "q_cid": "3323202", "pos_cid": 119421865, "source": "eval20x26"}
{"query_id": "scaleup_45163004_44922342", "query": "How to explain differences in catalytic activity, methane breakdown, and hydrogen removal between gold- and molybdenum-modified nickel anodes and unmodified nickel anodes", "pos": ["A theoretical study of CH4 dissociation on pure and gold‐alloyed Ni(111) surfaces. We present a density functional theory study of the first step of CH4 adsorption on the Ni(111) surface, dissociation into adsorbed CH3 and H. The rupture of the C–H bond occurs preferentially on top of a Ni atom, with a dissociation barrier of about 100 kJ/mol (including zero point corrections). The transition state involves considerable internal excitation of the molecule. The active C–H bond is both stretched to 1.6 A and tilted relative to the methyl group. A normal mode analysis shows that the reaction coordinate is mainly a C–H stretch, while the orientation of the C–H bond relative to the surface is responsible for the highest real mode. Alloying the surface with gold also affects the reactivity of the Ni atoms on adjacent surface sites. The dissociation barrier is increased by 16 and 38 kJ/mol for a Ni atom with one or two gold neighbors, respectively. We attribute these changes to a shift in the local density of d states at the nickel atoms in the neighborhood of gold."], "field": "Materials Science", "q_year": 2017, "q_cid": "45163004", "pos_cid": 44922342, "source": "eval20x26"}
{"query_id": "scaleup_22186466_43767221", "query": "How to characterize a confined system’s response when interactions are attractive, pairing is energetically favored, and transfers occur individually and in pairs", "pos": ["Density-operator approaches to transport through interacting quantum dots: Simplifications in fourth-order perturbation theory. Various theoretical methods address transport effects in quantum dots beyond single-electron tunneling while accounting for the strong interactions in such systems. In this paper we report a detailed comparison between three prominent approaches to quantum transport: the fourth-order Bloch-Redfield quantum master equation (BR), the real-time diagrammatic technique (RT), and the scattering rate approach based on the T-matrix (TM). Central to the BR and RT is the generalized master equation for the reduced density matrix. We demonstrate the exact equivalence of these two techniques. By accounting for coherences (nondiagonal elements of the density matrix) between nonsecular states, we show how contributions to the transport kernels can be grouped in a physically meaningful way. This not only significantly reduces the numerical cost of evaluating the kernels but also yields expressions similar to those obtained in the TM approach, allowing for a detailed comparison. However, in the TM approach an ad hoc regularization procedure is required to cure spurious divergences in the expressions for the transition rates in the stationary (zero-frequency) limit. We show that these problems derive from incomplete cancellation of reducible contributions and do not occur in the BR and RT techniques, resulting in well-behaved expressions in the latter two cases. Additionally, we show that a standard regularization procedure of the TM rates employed in the literature does not correctly reproduce the BR and RT expressions. All the results apply to general quantum dot models and we present explicit rules for the simplified calculation of the zero-frequency kernels. Although we focus on fourth-order perturbation theory only, the results and implications generalize to higher orders. We illustrate our findings for the single impurity Anderson model with finite Coulomb interaction in a magnetic field."], "field": "Materials Science", "q_year": 2017, "q_cid": "22186466", "pos_cid": 43767221, "source": "eval20x26"}
{"query_id": "scaleup_11919281_44943573", "query": "How to characterize the gate-dependent current–voltage response of GaTe along two perpendicular crystal directions", "pos": ["Density-functional method for nonequilibrium electron transport. We describe an ab initio method for calculating the electronic structure, electronic transport, and forces acting on the atoms, for atomic scale systems connected to semi-infinite electrodes and with an applied voltage bias. Our method is based on the density-functional theory (DFT) as implemented in the well tested SIESTA approach (which uses nonlocal norm-conserving pseudopotentials to describe the effect of the core electrons, and linear combination of finite-range numerical atomic orbitals to describe the valence states). We fully deal with the atomistic structure of the whole system, treating both the contact and the electrodes on the same footing. The effect of the finite bias (including self-consistency and the solution of the electrostatic problem) is taken into account using nonequilibrium Green's functions. We relate the nonequilibrium Green's function expressions to the more transparent scheme involving the scattering states. As an illustration, the method is applied to three systems where we are able to compare our results to earlier ab initio DFT calculations or experiments, and we point out differences between this method and existing schemes. The systems considered are: (i) single atom carbon wires connected to aluminum electrodes with extended or finite cross section, (ii) single atom gold wires, and finally (iii) large carbon nanotube systems with point defects."], "field": "Materials Science", "q_year": 2019, "q_cid": "119192816", "pos_cid": 44943573, "source": "eval20x26"}
{"query_id": "scaleup_15537325_29140163", "query": "How to noninvasively assess tumor vascular maturation and function over time and distinguish responses to pro-oxidant therapy in drug-sensitive and drug-resistant tumors", "pos": ["Vascular profile characterization of liver tumors by magnetic resonance imaging using hemodynamic response imaging in mice.. Recently, we have demonstrated the feasibility of using hemodynamic response imaging (HRI), a functional magnetic resonance imaging (MRI) method combined with hypercapnia and hyperoxia, for monitoring vascular changes during liver pathologies without the need of contrast material. In this study, we evaluated HRI ability to assess changes in liver tumor vasculature during tumor establishment, progression, and antiangiogenic therapy. Colorectal adenocarcinoma cells were injected intrasplenically to model colorectal liver metastasis (CRLM) and the Mdr2 knockout mice were used to model primary hepatic tumors. Hepatic perfusion parameters were evaluated using the HRI protocol and were compared with contrast-enhanced (CE) MRI. The hypovascularity and the increased arterial blood supply in well-defined CRLM were demonstrated by HRI. In CRLM-bearing mice, the entire liver perfusion was attenuated as the HRI maps were significantly reduced by 35%. This study demonstrates that the HRI method showed enhanced sensitivity for small CRLM (1-2 mm) detection compared with CE-MRI (82% versus 38%, respectively). In addition, HRI could demonstrate the vasculature alteration during CRLM progression (arborized vessels), which was further confirmed by histology. Moreover, HRI revealed the vascular changes induced by rapamycin treatment. Finally, HRI facilitates primary hepatic tumor characterization with good correlation to the pathologic differentiation. The HRI method is highly sensitive to subtle hemodynamic changes induced by CRLM and, hence, can function as an imaging tool for understanding the hemodynamic changes occurring during CRLM establishment, progression, and antiangiogenic treatment. In addition, this method facilitated the differentiation between different types of hepatic lesions based on their vascular profile noninvasively."], "field": "Materials Science", "q_year": 2016, "q_cid": "15537325", "pos_cid": 29140163, "source": "eval20x26"}
{"query_id": "scaleup_19902293_13794438", "query": "How to compare the tumor-regression efficacy of different drug treatments in renal cell carcinoma xenografts while limiting animal experiment costs", "pos": ["Evaluation of alternative in vivo drug screening methodology: a single mouse analysis. Traditional approaches to evaluating antitumor agents using human tumor xenograft models have generally used cohorts of 8–10 mice against a limited panel of tumor models. An alternative approach is to use fewer animals per tumor line, allowing a greater number of models that capture greater molecular/genetic heterogeneity of the cancer type. We retrospectively analyzed 67 agents evaluated by the Pediatric Preclinical Testing Program (PPTP) to determine whether a single mouse, chosen randomly from each group of a study, predicted the median response for groups of mice using 83 xenograft models. The individual tumor response from a randomly chosen mouse was compared to the group median response using established response criteria. A total of 2134 comparisons were made. The single tumor response accurately predicted the group median response in 1604 comparisons (75.16%). The mean tumor response correct prediction rate for 1,000 single mouse random samples was 78.09%. Models had a range for correct prediction (60%–87.5%). Allowing for mis-prediction of ± one response category, the overall mean correct single mouse prediction rate was 95.28%, and predicted overall objective response rates for group data in 66 of 67 drug studies. For molecularly targeted agents occasional exceptional responder models were identified and the activity of that agent confirmed in additional models with the same genotype. Assuming that large treatment effects are targeted, this alternate experimental design has similar predictive value as traditional approaches, allowing for far greater numbers of models to be used that more fully encompass the heterogeneity of disease types."], "field": "Materials Science", "q_year": 2019, "q_cid": "199022931", "pos_cid": 13794438, "source": "eval20x26"}
{"query_id": "scaleup_20835501_93417464", "query": "How to synthesize relatively unstable bimetallic nanocrystals", "pos": ["Synthesis of inorganic solids using microwaves. Use of microwaves in the synthesis of materials is gaining importance. Microwave-assisted synthesis is generally much faster, cleaner, and more economical than the conventional methods. A variety of materials such as carbides, nitrides, complex oxides, silicides, zeolites, apatite, etc. have been synthesized using microwaves. Many of these are of industrial and technological importance. An understanding of the microwave interaction with materials has been based on concepts of dielectric heating and of the resonance absorption due to rotational excitation. This review presents a summary of recent reports of microwave synthesis of inorganic materials. Various observations regarding microwave interaction with materials are also briefly discussed."], "field": "Materials Science", "q_year": 2019, "q_cid": "208355011", "pos_cid": 93417464, "source": "eval20x26"}
{"query_id": "scaleup_2784018_25880956", "query": "How to establish the peptide–paclitaxel conjugate’s resistance to degradation in serum", "pos": ["Synthetic Peptides in the Form of Dendrimers Become Resistant to Protease Activity*. In previous papers, we observed that dendrimers of peptide mimotopes of the nicotinic receptor ligand site are strong antidotes against the lethality of the nicotinic receptor ligand α-bungarotoxin. Although their in vitro activity is identical to that of dendrimers, the corresponding monomeric peptide mimotopes are not effective in vivo. Because the higher in vivo efficiency of dendrimers could not in this case be related to polyvalent interaction, the stability to blood protease activity of monomeric versus tetrabranched dendrimeric mimotope peptides was compared here by incubating three different mimotopes with human plasma and serum. Unmodified peptides and cleaved sequences were followed by high pressure liquid chromatography and mass spectrometry. Tetrabranched peptides were shown to be much more stable in plasma and also in serum. To assess the notable stability of multimeric peptides, different bioactive neuropeptides, including enkephalins, neurotensin and nociceptin, were synthesized in monomeric and tetrabranched forms and incubated with human plasma and serum and with rat brain membrane extracts. All the tetrabranched neuropeptides fully retained biological activity and generally showed much greater stability to blood and brain protease activity. Some tetrabranched peptides were also resistant to trypsin and chymotrypsin. Our findings provide new insights into the possible therapeutic use of bioactive peptides."], "field": "Materials Science", "q_year": 2015, "q_cid": "2784018", "pos_cid": 25880956, "source": "eval20x26"}
{"query_id": "scaleup_25328135_18535713", "query": "How to clarify the roles of catechol groups and backbone amino groups in gelation of catechol-grafted chitosan alone", "pos": ["Reaction Pathways in Catechol/Primary Amine Mixtures: A Window on Crosslinking Chemistry. Catechol chemistry is used as a crosslinking tool abundantly in both natural organisms (e.g. mussels, sandcastle worms) and synthetic systems to achieve the desired mechanical properties. Despite this abundance and success, the crosslinking chemistry is still poorly understood. In this study, to simplify the system, yet to capture the essential chemistry, model compounds 4-methyl catechol and propylamine are used. The reaction of 4-methyl catechol (2 mM) with propylamine (6 mM) is carried out in the presence of NaIO4 (2 mM) in 10 mM Na2CO3 aqueous solution. A variety of spectroscopic/spectrometric and chromatographic methods such as 1H NMR, LC-MS, and UV-VIS are used to track the reaction and identify the products/intermediates. It is found that the crosslinking chemistry of a catechol and an amine is both fast and complicated. Within five minutes, more than 60 products are formed. These products encompass 19 different masses ranging from molecular weight of 179 to 704. By combining time-dependent data, it is inferred that the dominant reaction pathways: the majority is formed via aryloxyl-phenol coupling and Michael-type addition, whereas a small fraction of products is formed via Schiff base reactions."], "field": "Materials Science", "q_year": 2022, "q_cid": "253281355", "pos_cid": 18535713, "source": "eval_collection"}
{"query_id": "scaleup_23900415_4493646", "query": "How to achieve strong connections between substrates with stable mechanical hysteresis for force and energy transmission without abrupt failure", "pos": ["Tough Adhesives for Diverse Wet Surfaces. Sticky even when wet Tissue adhesives are used as an alternative to stitches or staples and can be less damaging to the healthy tissues. But they can suffer from low biocompatibility and poor matching of the mechanical properties with the tissues. Li et al. combined an adhesive surface with a flexible matrix to develop an adhesive that has the right level of stick but moves with the surrounding tissues. The adhesive is effective in the presence of blood and thus might work during wound repair. Science, this issue p. 378 Tough adhesives stick to wet surfaces and show compatibility with blood exposure and dynamic movements. Adhesion to wet and dynamic surfaces, including biological tissues, is important in many fields but has proven to be extremely challenging. Existing adhesives are cytotoxic, adhere weakly to tissues, or cannot be used in wet environments. We report a bioinspired design for adhesives consisting of two layers: an adhesive surface and a dissipative matrix. The former adheres to the substrate by electrostatic interactions, covalent bonds, and physical interpenetration. The latter amplifies energy dissipation through hysteresis. The two layers synergistically lead to higher adhesion energies on wet surfaces as compared with those of existing adhesives. Adhesion occurs within minutes, independent of blood exposure and compatible with in vivo dynamic movements. This family of adhesives may be useful in many areas of application, including tissue adhesives, wound dressings, and tissue repair."], "field": "Materials Science", "q_year": 2021, "q_cid": "239004153", "pos_cid": 4493646, "source": "eval_collection"}
{"query_id": "scaleup_27510019_73668724", "query": "How to clarify the link between uv irradiation and damage to microbial cell membranes", "pos": ["Photocatalysis: Oxidative Processes in Water Treatment. The efficiency of various homogeneous and heterogeneous systems photocatalytic processes destructive oxidation of organic compounds of different classes is considered. It is shown that photocatalytic methods can significantly increase the speed and depth (up to complete mineralization) of decomposition processes of toxicants. The use of photocatalysis (PC) in the creation of low-power water treatment technologies is a promising direction in addressing environmental problems of the hydrosphere."], "field": "Materials Science", "q_year": 2024, "q_cid": "275100197", "pos_cid": 73668724, "source": "eval_collection"}
{"query_id": "scaleup_25831759_43049418", "query": "How to assess β-cyclodextrin’s suitability as a cryoprotectant for PEG-b-PCL micelles given aggregation and disrupted morphology", "pos": ["Polycaprolactone/Amino-β-Cyclodextrin Inclusion Complex Prepared by an Electrospinning Technique. Electrospun scaffolds of neat poly-ε-caprolactone (PCL), poly-ε-caprolactone/β-cyclodextrin inclusion complex (PCL/β-CD) and poly-ε-caprolactone amino derivative inclusion complex (PCL/β-CD-NH2) were prepared by the electrospinning technique. The obtained mats were analyzed by a theoretical model using the Hartree–Fock method with an STO-3G basis set, and characterized by X-ray diffraction (XRD), field emission scanning electron microscopy (FESEM), Fourier transform infrared spectroscopy-attenuated total reflectance (FTIR-ATR), differential scanning calorimetry (DSC), confocal-Raman spectroscopy, proton nuclear magnetic resonance (1HNMR) and contact angle measure (CA). Different mixtures of solvents, such as dimethylformamide (DMF)-tetrahydrofuran (THF), dichlormethane (DCM)-dimethyl sulfoxide (DMSO) and 2,2,2-Trifluoroethanol (TFE), were tested in the fiber preparation. The results indicate that electrospun nanofibers have a pseudorotaxane structure and when it was prepared using a 2,2,2-Trifluoroethanol (TFE) as solvent, the nanofibers were electrospun well and, with the other solvents, fibers present defects such as molten fibers and bead-like defects into the fiber structure. This work provides insights into the design of PCL/β-CD-NH2 based scaffolds that could have applications in the biomedical field."], "field": "Materials Science", "q_year": 2023, "q_cid": "258317592", "pos_cid": 43049418, "source": "eval_collection"}
{"query_id": "scaleup_25605699_52881341", "query": "How to assess whether curcumin-containing wound-dressing composites exhibit curcumin’s documented activity", "pos": ["Antioxidant activity of different species and varieties of turmeric (Curcuma spp): Isolation of active compounds.. There are >80 species of turmeric (Curcuma spp.) and some species have multiple varieties, for example, Curcuma longa (C. longa) has 70 varieties. They could be different in their chemical properties and biological activities. Therefore, we compared antioxidant activity, total phenolic and flavonoid content of different species and varieties of turmeric namely C. longa [variety: Ryudai gold (RD) and Okinawa ukon], C. xanthorrhiza, C. aromatica, C. amada, and C. zedoaria. The antioxidant activity was determined using the 1,1-diphenyl-2-picrylhydrazyl (DPPH) free radical scavenging activity, oxygen radical absorbance capacity (ORAC), reducing power and 2-deoxyribose (2-DR) oxidation assay. Our results suggested that RD contained significantly higher concentrations of total phenolic (157.4 mg gallic acid equivalent/g extract) and flavonoids (1089.5 mg rutin equivalent/g extract). RD also showed significantly higher DPPH radical-scavenging activity (IC50: 26.4 μg/mL), ORAC (14,090 μmol Trolox equivalent/g extract), reducing power absorbance (0.33) and hydroxyl radical scavenging activity (IC50: 7.4 μg/mL). Therefore, RD was chosen for the isolation of antioxidant compounds using silica gel column, Toyopearl HW-40F column, and high-performance liquid chromatography. Structural identification of the compounds was conducted using 1H NMR, 13C NMR, and liquid chromatography-tandem mass spectrometry. The purified antioxidant compounds were bisabolone-9-one (1), 4-methyllene-5-hydroxybisabola-2,10-diene-9-one (2), turmeronol B (3), 5-hydroxy-1,7-bis(4-hydroxy-3-methoxyphenyl)-1-hepten-3-one (4), 3-hydroxy-1,7-bis(4-hydroxyphenyl)-6-hepten-1,5-dione (5), cyclobisdemethoxycurcumin (6), bisdemethoxycurcumin (7), demethoxycurcumin (8) and curcumin (9). The IC50 for DPPH radical-scavenging activity were 474, 621, 234, 29, 39, 257, 198, 47 and 18 μM and hydroxyl radical-scavenging activity were 25.1, 24.4, 20.2, 2.1, 5.1, 17.2, 7.2, 3.3 and 1.5 μM for compound 1, 2, 3, 4, 5, 6, 7, 8 and 9, respectively. Our findings suggested that the RD variety of C. longa, developed by the University of the Ryukyus, Okinawa, Japan, is a promising source of natural antioxidants."], "field": "Materials Science", "q_year": 2023, "q_cid": "256056993", "pos_cid": 52881341, "source": "eval_collection"}
{"query_id": "scaleup_23542344_21893040", "query": "How to strengthen bonding at an interface with insufficient surface roughness and weak adhesion", "pos": ["Nondestructive growing nano-ZnO on aramid fibers to improve UV resistance and enhance interfacial strength in composites. Abstract It is a great challenge in various applications to improve the resistances of aramid fibers (AFs) to harsh environments and enhance the interfacial bonding strength in composites along with maintaining the excellent mechanical properties. Herein, a simple nondestructive method was developed to prepare modified AF with zinc oxide (ZnO) micro-nano structures. Assisted by the adhesion and secondary functionalization of poly L-3,4-dihydroxyphenylalanine (PDOPA), ZnO nanoparticles (NPs) were successfully “seeded” onto the AF surface, and subsequently ZnO nanowires (NWs) were grown on the seed layer. As a result, the surface modification did not cause the significant changes of the tensile strength, and the surface roughness and UV resistance of the modified fibers were significantly improved. After 168 h of UV exposure, the retention of the tensile strength for the modified fiber was as high as 97.2%. Comparing with the pristine AF-reinforced composite, the interfacial shear strengths of AF-PDOPA-ZnO NP/epoxy resin and AF-PDOPA-ZnO NW/epoxy resin composites increased by 31.8% and 37.8%, respectively. Therefore, this effectively nondestructive modification method to grow ZnO nanostructures on a polymer substrate exhibits an extensive application prospect for organic fibers and their composites."], "field": "Materials Science", "q_year": 2021, "q_cid": "235423445", "pos_cid": 218930402, "source": "eval_collection"}
{"query_id": "scaleup_25021820_21172491", "query": "How to balance prediction accuracy and biomarker panel size for nanomaterial toxicity in multi-omics data", "pos": ["Feature set optimization in biomarker discovery from genome-scale data. MOTIVATION Omics technologies have the potential to facilitate the discovery of new biomarkers. However, only few omics-derived biomarkers have been successfully translated into clinical applications to date. Feature selection is a crucial step in this process that identifies small sets of features with high predictive power. Models consisting of a limited number of features are not only more robust in analytical terms, but also ensure cost-effectiveness and clinical translatability of new biomarker panels. Here we introduce GARBO, a novel multi-island adaptive genetic algorithm to simultaneously optimize accuracy and set size in omics-driven biomarker discovery problems. RESULTS Compared to existing methods, GARBO enables the identification of biomarker sets that best optimize the trade-off between classification accuracy and number of biomarkers. We tested GARBO and six alternative selection methods with two high relevant topics in precision medicine: cancer patient stratification and drug sensitivity prediction. We found multivariate biomarker models from different omics data types such as mRNA, miRNA, copy number variation, mutation and DNA methylation. The top performing models were evaluated by using two different strategies: the Pareto-based selection, and the weighted sum between accuracy and set size (w = 0.5). Pareto-based preferences shows the ability of the proposed algorithm to search minimal subsets of relevant features that can be used to model accurate Random Forest-based classification systems. Moreover, GARBO systematically identified, on larger omics data types, such as gene expression and DNA methylation, biomarker panels exhibiting higher classification accuracy or employing a number of features much lower than those discovered with other methods. These results were confirmed on independent data sets. AVAILABILITY github.com/Greco-Lab/GARBO. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online."], "field": "Materials Science", "q_year": 2022, "q_cid": "250218202", "pos_cid": 211724914, "source": "eval_collection"}
{"query_id": "scaleup_25023651_17959047", "query": "How to quantitatively characterize time-dependent sirolimus release from activated carbon of different particle sizes for controlled drug delivery in biological media", "pos": ["Determination and Estimation of Pharmacokinetic Profile of Caffeine in Form of Extract of Green Tea Leaves and its Analogy with Synthetic Form. The aim of the study was to formulate and investigate the pharmacokinetic parameters for the tablets of herbal extract of caffeine with comparison to synthetic formulation. The tablets of the aqueous herbal extract of leaves of Camellia sinensis and synthetic caffeine were formulated by wet granulation technique. The HPLC and HPTLC were applied as analytical tools for estimation of caffeine. The batches of formulation (B1 to B7) were subjected for various pre and post-formulation studies. The pharmacokinetic of the batch B5 was assessed in rabbits, and the results were compared to synthetic batch B7. With the suitable pre and post-formulation results, the B5 showed in vitro release of 90.54% of caffeine at the end of 60 min. The release followed first order kinetics and the plot of Higuchi and Peppas confirms anomalous diffusion as the basic mechanism behind the release. B5 revealed non-significant mean Cmax, t1/2, and AUC of 1.88 μg/ml, 5.52 h and 9.67 μg.h/ml respectively compared to B7. The study highlights; no significant difference in the pharmacological effect of caffeine when administered in the form of extract. The administration of herbal extract can further provide the other health benefits lacked by synthetic caffeine."], "field": "Materials Science", "q_year": 2022, "q_cid": "250236512", "pos_cid": 17959047, "source": "eval_collection"}
{"query_id": "scaleup_23954722_22172195", "query": "How to obtain hydroxyethylcellulose hydrogels with open, interconnected super-macropores while maintaining mechanical stability, elasticity, and substantial water uptake", "pos": ["Cryostructuring of Polymeric Systems. 55. Retrospective View on the More than 40 Years of Studies Performed in the A.N.Nesmeyanov Institute of Organoelement Compounds with Respect of the Cryostructuring Processes in Polymeric Systems. The processes of cryostructuring in polymeric systems, the techniques of the preparation of diverse cryogels and cryostructurates, the physico-chemical mechanisms of their formation, and the applied potential of these advanced polymer materials are all of high scientific and practical interest in many countries. This review article describes and discusses the results of more than 40 years of studies in this field performed by the researchers from the A.N.Nesmeyanov Institute of Organoelement Compounds, Russian Academy of Sciences—one of the key centers, where such investigations are carried out. The review includes brief historical information, the description of the main effects and trends characteristic of the cryostructuring processes, the data on the morphological specifics inherent in the polymeric cryogels and cryostructurates, and examples of their implementation for solving certain applied tasks."], "field": "Materials Science", "q_year": 2021, "q_cid": "239547221", "pos_cid": 221721958, "source": "eval_collection"}
{"query_id": "scaleup_27599212_38596899", "query": "How to determine whether cubic calcium silicate perovskite exhibits anomalous elastic softening near the tetragonal–cubic phase boundary", "pos": ["Strain relaxation mechanisms of elastic softening and twin wall freezing associated with structural phase transitions in (Ca,Sr)TiO3 perovskites. Resonant ultrasound spectroscopy has been used to measure the bulk modulus (K), shear modulus (G) and acoustic dissipation of polycrystalline perovskite samples across the CaTiO3–SrTiO3 solid solution in the temperature range ∼10–1350 K. A remarkable pattern of up to ∼25% softening of G as a function of both temperature and composition is due to coupling of shear strain with order parameters for the Pm 4/mcm, I4/mcm ↔ Pnma and I4/mcm ↔ Pbcm transitions. Anomalies in K associated with the phase transitions are small, consistent with only weak coupling of octahedral tilting order parameter(s) with volume strain. A change from tricritical character for the Pm 4/mcm transition towards second order character at Sr-rich compositions appears to be due to changing properties of the soft optic mode rather than to changes in magnitude of strain/order parameter coupling coefficients. Precursor softening of G ahead of the Pm 4/mcm transition, due to fluctuations or clustering, occurs over a temperature interval of up to ∼200 K, and also changes character at the most Sr-rich compositions. The tetragonal structure with Sr-rich compositions is characterized by additional softening with falling temperature which is most likely related to the proximity of a ferroelectric instability. The I4/mcm ↔ Pnma transition is accompanied by stiffening, which is attributed to the effects of strong coupling between order parameters for M-point and R-point tilting. The pattern of attenuation at RUS frequencies in the tetragonal phase can be understood in terms of the mobility of twin walls which become pinned below ∼500 K, and the loss mechanism most likely involves local bowing of the walls by lateral motion of ledges rather than the advance and retraction of needle tips. Twin wall mobility is suppressed in the orthorhombic structure."], "field": "Materials Science", "q_year": 2025, "q_cid": "275992122", "pos_cid": 38596899, "source": "eval_collection"}
{"query_id": "scaleup_24652094_93231776", "query": "How to verify the stability and effectiveness of biomarker monitoring in biological media", "pos": ["The dissolution and biological effects of silver nanoparticles in biological media.. Silver ions and silver nanoparticles have a well-known biological effect that typically occurs in biological or environmental media of complex composition. Silver nanoparticles release silver ions if oxidizing species like molecular oxygen or hydrogen peroxide are present. The presence of glucose as a model for reducing sugars has only a small effect on the dissolution rate. In the presence of chloride ions, precipitation of silver chloride nanoparticles occurs. At physiological salt concentrations, no precipitation of silver phosphate occurs as the precipitation of silver chloride always occurs first. If the surface of a silver nanoparticle is passivated by cysteine, the dissolution is quantitatively inhibited. Upon immersion of silver nanoparticles in pure water for 8 months, leading to about 50% dissolution, no change in the surface was observed by transmission electron microscopy. A model for the dissolution was derived from immersion and dissolution experiments in different media and from high-resolution transmission electron microscopy. A literature survey on the available data on the dissolution of silver nanoparticles showed that only qualitative trends can be identified as the nature of the nanoparticles and of the immersion medium are practically never comparable. The dissolution effects were confirmed by cell culture experiments (human mesenchymal stem cells and neutrophil granulocytes) where silver nanoparticles that were stored under argon had a clearly lower cytotoxicity than those stored under air. They also led to a less formation of reactive oxygen species (ROS). This underscores that silver ions are the toxic species."], "field": "Materials Science", "q_year": 2022, "q_cid": "246520940", "pos_cid": 93231776, "source": "eval_collection"}
{"query_id": "scaleup_26769349_86121932", "query": "How to identify optimal conditions for curcumin nanoparticles while accounting for the effects of multiple variables on particle diameter and encapsulation efficiency", "pos": ["Optimisation of pumpkin mass transfer kinetic during osmotic dehydration using artificial neural network and response surface methodology modelling. In this study, the response surface methodology (RSM) was used to optimise osmo-dehydration of pumpkin cubes. Effect of different parameters including osmotic solution temperature in the range of 5 to 50 °C, the immersion time from 0 to 180 min and the concentration of osmotic solution (from 5% salt + 50% sucrose w/v to 15% salt + 50% sucrose w/v) on water loss (WL), solid gain (SG), weight reduction and final moisture content were investigated by central composite design. The optimum condition for osmotic dehydration was found to be at a temperature of 5 °C, an immersion time of 180 min and an osmotic solution concentration of 15% salt + 50% sucrose w/v. At this optimum condition WL, SG, weight reduction and moisture content were found to be 70.7 g/100 g initial sample, 10.2 g/100 g initial sample, 59.06 g/100 g initial sample and 0.64 g water/g dry matter, respectively. The comparison of the obtained results by artificial neural network and RSM modelling showed that the artificial neural approach has a ..."], "field": "Materials Science", "q_year": 2024, "q_cid": "267693497", "pos_cid": 86121932, "source": "eval_collection"}
{"query_id": "scaleup_26457347_12580861", "query": "How to identify jute retting conditions that meet textile requirements across multiple fiber-quality characteristics simultaneously", "pos": ["Application of multi response optimization with grey relational analysis and fuzzy logic method. Multi-response optimization is an optimization process by considering multiple responses simultaneously. The purpose of this research is to get the optimum point on multi-response optimization process using grey relational analysis and fuzzy logic method. The optimum point is determined from the Fuzzy-GRG (Grey Relational Grade) variable which is the conversion of the Signal to Noise Ratio of the responses involved. The case study used in this research are case optimization of electrical process parameters in electrical disharge machining. It was found that the combination of treatments resulting to optimum MRR and SR was a 70 V gap voltage factor, peak current 9 A and duty factor 0.8."], "field": "Materials Science", "q_year": 2023, "q_cid": "264573472", "pos_cid": 125808619, "source": "eval_collection"}
{"query_id": "scaleup_22630719_40705796", "query": "How to improve absorption of insulin-loaded nanocarriers across the intestinal epithelium into the bloodstream while preserving the biological activity of encapsulated insulin", "pos": ["Zonula occludin toxin, a microtubule binding protein.. AIM:To investigate the interaction of Zot with microtubule.METHODS:Zot affinity column was applied to purify Zot-binding protein(s) from crude intestinal cell lysates. After incubation at room temperature, the column was washed and the proteins bound to the Zot affinity column were eluted by step gradient with NaCl (0.3molcenter dotL(-1) -0.5molcenter dotL(-1)). The fractions were subjected to 6.0%-15.0% (w/v) gradient SDS-PAGE and then transferred to PVDF membrane for N-terminal sequencing.Purified Zot and tau protein were blotted by using anti-Zot or anti tau antibodies. Finally, purified Zot was tested in an in vitro tubulin binding assay.RESULTS:Fractions from Zot affinity column yielded two protein bands with a M(r) of 60kU and 45kU respectively. The Nterminal sequence of the 60kU band resulted identical to beta-tubulin. Zot also crossreacts with antitau antibodies. In the in vitro tubulin binding assay, Zot coprecipitate with Mt, further suggesting that Zot possesses tubulin-binding properties.CONCLUSION:Taken together, these results suggest that Zot regulates the permeability of intestinal tight junctions by binding to intracellular Mt, with the subsequent activation of the intracellular signaling leading to the permeabilization of intercellular tight junctions."], "field": "Materials Science", "q_year": 2020, "q_cid": "226307194", "pos_cid": 40705796, "source": "eval_collection"}
{"query_id": "scaleup_25023651_26176557", "query": "How to characterize concentration-dependent sirolimus binding across particle sizes in phosphate-buffered saline and blood plasma for controlled delivery", "pos": ["Guidelines for the use and interpretation of adsorption isotherm models: A review.. Adsorption process is considered as one of the most used separation and purification processes, in which adsorption occurs by the formation of the physical or chemical bonds between a porous solid medium and a mixture of liquid or gas multi-component fluid. By taking into consideration the equilibrium data and the adsorption properties of both the adsorbent and the adsorbate, adsorption isotherm models can describe the interaction mechanisms between the adsorbent and the adsorbate at constant temperature. Therefore, understanding modelling of the equilibrium data is a very essential way of predicting the adsorption mechanisms of various adsorption systems. Furthermore, adsorption isotherms in batch experiments can be used for the determination of the solid-water distribution coefficient (Kid). This review paper discusses the guidelines of using mono/multi-parametric isotherm models with different applications. The aim of this paper is to establish criteria for choosing the optimum isotherm model through a critical review of different adsorption models and the use of various mathematically error functions such as linear regression analysis, nonlinear regression analysis, and error functions for adsorption data optimization. In this paper, 15 mono-parametric adsorption isotherm models having one, two, three, four and five parameters were investigated. In addition, 10 multi-parameter isotherm models were reviewed as well as addressing their applications."], "field": "Materials Science", "q_year": 2022, "q_cid": "250236512", "pos_cid": 261765577, "source": "eval_collection"}
{"query_id": "scaleup_26430314_16458402", "query": "How to achieve strong infrared absorption and high sensitivity over a wide range of incident angles", "pos": ["Self-rolling and light-trapping in flexible quantum well–embedded nanomembranes for wide-angle infrared photodetectors. Flexible semiconductor nanomembranes bend into microscale scroll architectures for wide-angle infrared photodetection. Three-dimensional (3D) design and manufacturing enable flexible nanomembranes to deliver unique properties and applications in flexible electronics, photovoltaics, and photonics. We demonstrate that a quantum well (QW)–embedded nanomembrane in a rolled-up geometry facilitates a 3D QW infrared photodetector (QWIP) device with enhanced responsivity and detectivity. Circular geometry of nanomembrane rolls provides the light coupling route; thus, there are no external light coupling structures, which are normally necessary for QWIPs. This 3D QWIP device under tube-based light-trapping mode presents broadband enhancement of coupling efficiency and omnidirectional detection under a wide incident angle (±70°), offering a unique solution to high-performance focal plane array. The winding number of these rolled-up QWIPs provides well-tunable blackbody photocurrents and responsivity. 3D self-assembly of functional nanomembranes offers a new path for high conversion efficiency between light and electricity in photodetectors, solar cells, and light-emitting diodes."], "field": "Materials Science", "q_year": 2023, "q_cid": "264303147", "pos_cid": 16458402, "source": "eval_collection"}
{"query_id": "scaleup_25021820_21473384", "query": "How to distinguish molecular changes that indicate early mechanisms of harm from responses that merely reflect toxicity", "pos": ["Next-Generation Sequencing Reveals Differential Responses to Acute versus Long-Term Exposures to Graphene Oxide in Human Lung Cells.. Numerous studies have addressed the biological impact of graphene-based materials including graphene oxide (GO), yet few have focused on long-term effects. Here, RNA sequencing is utilized to unearth responses of human lung cells to GO. To this end, the BEAS-2B cell line derived from normal human bronchial epithelium is subjected to repeated, low-dose exposures of GO (1 or 5 µg mL-1 ) for 28 days or to the equivalent, cumulative amount of GO for 48 h. Then, samples are analyzed by using the NovaSeq 6000 sequencing system followed by pathway analysis and gene ontology enrichment analysis of the differentially expressed genes. Significant differences are seen between the low-dose, long-term exposures and the high-dose, short-term exposures. Hence, exposure to GO for 48 h results in mitochondrial dysfunction. In contrast, exposure to GO for 28 days is characterized by engagement of apoptosis pathways with downregulation of genes belonging to the inhibitor of apoptosis protein (IAP) family. Validation experiments confirm that long-term exposure to GO affects the apoptosis threshold in lung cells, accompanied by a loss of IAPs. These studies reveal the sensitivity of RNA-sequencing approaches and show that acute exposure to GO is not a good predictor of the long-term effects of GO."], "field": "Materials Science", "q_year": 2022, "q_cid": "250218202", "pos_cid": 214733848, "source": "eval_collection"}
{"query_id": "scaleup_28188460_26776818", "query": "How to extend cation emission to red-to-near-infrared wavelengths while maintaining high emission efficiency despite intrinsic instability and strong non-radiative decay at smaller energy gaps", "pos": ["Unveiling Three Interconvertible Redox States of Boraphenalene.. Neutral 1-boraphenalene displays the isoelectronic structure of the phenalenyl carbocation and is expected to behave as an attractive organoboron multi-redox system. However, the isolation of new redox states have remained elusive even though the preparation of neutral boron(III)-containing phenalene compounds have been extensively studied. Herein, we have adopted an N-heterocyclic carbene ligand stabilization approach to achieve the first isolation of the stable and ambipolar 1-boraphenalenyl radical 1•. The 1-boraphenalenyl cation 1+ and anion 1- have also been electrochemically observed and chemically isolated, representing new redox forms of boraphenalene for the study of non-Kekulé polynuclear benzenoid molecules. Experimental and theoretical investigations suggest that the interconvertible three-redox-state species undergo reversible electronic structure modifications, which primarily take place on the polycyclic framework of the molecules, exhibiting atypical behavior compared to known donor-stabilized organoboron compounds. Initial reactivity studies, aromaticity evaluations, and photophysical studies show redox-state-dependent trends. While 1+ is luminescent in both the solution and solid states, 1• exhibits boron-centered reactivity and 1- undergoes substitution chemistry on the boraphenalenyl skeleton and serves as a single-electron transfer reductant."], "field": "Materials Science", "q_year": 2025, "q_cid": "281884605", "pos_cid": 267768181, "source": "eval_collection"}
{"query_id": "scaleup_28254369_27378659", "query": "How to limit fresh produce spoilage and extend shelf life in packaging suitable for food-contact applications", "pos": ["Phytochemical Profiling and Therapeutic Potential of Thyme (Thymus spp.): A Medicinal Herb. ABSTRACT Thymol is a phenol monoterpene that is naturally derived from cymene and is an isomer of carvacrol. It constitutes a significant portion (10%–64%) of the essential oils found in thyme (Thymus vulgaris L., Lamiaceae), a medicinal plant renowned for its therapeutic properties. Wild thyme is native to the Mediterranean region and has been used in cooking and medicine for a long time. In contemporary contexts, both thymol and thyme offer diverse functional applications in the pharmaceutical, food, and cosmetic industries. Thymol has attracted scientific interest for its potential therapeutic applications in pharmaceuticals and nutraceuticals. Studies have explored its efficacy in treating respiratory, nervous, and cardiovascular disorders, highlighting its promising role in diverse therapeutic interventions. Additionally, this compound demonstrates antimicrobial, antioxidant, anticarcinogenic, anti‐inflammatory, and antispasmodic properties. It also shows potential as a growth enhancer and has immunomodulatory properties as well. Other discussed aspects include thymol toxicity, bioavailability, metabolism, and distribution in animals and humans. This review summarizes the most significant data regarding the beneficial effects of thyme bioactive compounds and their applications as a food preservative while taking into account the thyme plant extract and its essential oil."], "field": "Materials Science", "q_year": 2025, "q_cid": "282543697", "pos_cid": 273786593, "source": "eval_collection"}
{"query_id": "scaleup_23645642_20944474", "query": "How to determine what controls impact response when competing models can reasonably reproduce the observed trajectories", "pos": ["Power-Law Scaling of Early-Stage Forces during Granular Impact.. We experimentally and computationally study the early-stage forces during intruder impacts with granular beds in the regime where the impact velocity approaches the granular force propagation speed. Experiments use 2D assemblies of photoelastic disks of varying stiffness, and complimentary discrete-element simulations are performed in 2D and 3D. The peak force during the initial stages of impact and the time at which it occurs depend only on the impact speed, the intruder diameter, the stiffness of the grains, and the mass density of the grains according to power-law scaling forms that are not consistent with Poncelet models, granular shock theory, or added-mass models. The insensitivity of our results to many system details suggests that they may also apply to impacts into similar materials like foams and emulsions."], "field": "Materials Science", "q_year": 2020, "q_cid": "236456428", "pos_cid": 209444746, "source": "eval_collection"}
{"query_id": "scaleup_26942593_40929353", "query": "How to explain the weld fusion boundary’s susceptibility to preferential flow-accelerated corrosion cracking in multipass welding", "pos": ["The Effect of Ultrafast Heating in Cold-Rolled Low Carbon Steel: Recrystallization and Texture Evolution. The microstructure and texture evolution of cold-rolled low carbon steel after ultrafast heating and quenching is investigated. Experiments were carried out at heating rates of 150 °C/s and 1500 °C/s. The recrystallization of ferrite is studied by scanning electron microscopy and electron backscattered diffraction techniques. The texture evolution of cold rolled steel during ultrafast heating was studied, making it possible to estimate the precise effect of heating rate on the orientations of newly formed grains. The experimental results showed that the recrystallization of ferrite was not completed before the full transformation of austenite. The noticeable increase in the fraction of recrystallized grains of diameter less than 1 µm, when the heating rate is increased from 150 °C/s to 1500 °C/s suggests that the increase of the heating rate enhances the nucleation of ferrite. The crystallographic orientations in recrystallized ferrite are strongly influenced by the heating rates. The effect of heating rate in the releasing of stored energy, carbon diffusion and spheroidization of cementite might explain some differences in textures observed in recrystallized ferrite."], "field": "Materials Science", "q_year": 2024, "q_cid": "269425935", "pos_cid": 40929353, "source": "eval_collection"}
{"query_id": "scaleup_23881942_32530222", "query": "How to understand the relationship between drug-release kinetics and thermodynamic parameters—enthalpy, entropy, and Gibbs free energy", "pos": ["Understanding Drug Release Data through Thermodynamic Analysis. Understanding the factors that can modify the drug release profile of a drug from a Drug-Delivery-System (DDS) is a mandatory step to determine the effectiveness of new therapies. The aim of this study was to assess the Amphotericin-B (AmB) kinetic release profiles from polymeric systems with different compositions and geometries and to correlate these profiles with the thermodynamic parameters through mathematical modeling. Film casting and electrospinning techniques were used to compare behavior of films and fibers, respectively. Release profiles from the DDSs were performed, and the mathematical modeling of the data was carried out. Activation energy, enthalpy, entropy and Gibbs free energy of the drug release process were determined. AmB release profiles showed that the relationship to overcome the enthalpic barrier was PVA-fiber > PVA-film > PLA-fiber > PLA-film. Drug release kinetics from the fibers and the films were better fitted on the Peppas–Sahlin and Higuchi models, respectively. The thermodynamic parameters corroborate these findings, revealing that the AmB release from the evaluated systems was an endothermic and non-spontaneous process. Thermodynamic parameters can be used to explain the drug kinetic release profiles. Such an approach is of utmost importance for DDS containing insoluble compounds, such as AmB, which is associated with an erratic bioavailability."], "field": "Materials Science", "q_year": 2021, "q_cid": "238819424", "pos_cid": 32530222, "source": "eval_collection"}
{"query_id": "scaleup_27839463_6352419", "query": "How to rapidly predict grain growth evolution while accounting for spatial microstructural patterns and long-term temporal dependencies under computational cost constraints", "pos": ["Convolutional LSTM Network: A Machine Learning Approach for Precipitation Nowcasting. The goal of precipitation nowcasting is to predict the future rainfall intensity in a local region over a relatively short period of time. Very few previous studies have examined this crucial and challenging weather forecasting problem from the machine learning perspective. In this paper, we formulate precipitation nowcasting as a spatiotemporal sequence forecasting problem in which both the input and the prediction target are spatiotemporal sequences. By extending the fully connected LSTM (FC-LSTM) to have convolutional structures in both the input-to-state and state-to-state transitions, we propose the convolutional LSTM (ConvLSTM) and use it to build an end-to-end trainable model for the precipitation nowcasting problem. Experiments show that our ConvLSTM network captures spatiotemporal correlations better and consistently outperforms FC-LSTM and the state-of-the-art operational ROVER algorithm for precipitation nowcasting."], "field": "Materials Science", "q_year": 2025, "q_cid": "278394634", "pos_cid": 6352419, "source": "eval_collection"}
{"query_id": "scaleup_23881942_73607345", "query": "How to achieve biocompatible, controlled release of anticancer drugs for triple-negative breast cancer treatment and characterize the release kinetics and thermodynamics", "pos": ["Formulation of water-in-oil-in-water (W/O/W) emulsions containing trans -resveratrol. Resveratrol is a high-value bioactive polyphenolic compound with vast applications in functional foods; as such, effective and scalable delivery strategies for this compound are worthy of study. In this research, W/O/W emulsions were successfully prepared using polyglycerol polyricinoleate (PGPR) as a lipophilic emulsifier and Tween 80 as a hydrophilic emulsifier with the goal of developing biocompatible carriers to improve the bioavailability of resveratrol. The effects of the type of emulsifier, the concentration of emulsifier, the ratio of the oil phase to the internal water phase, and homogeneous pressure on the physical properties of the W/O/W emulsions (such as microstructure, droplet size, distribution, zeta potential, viscosity and encapsulation efficiency) were investigated. The optimum processing conditions for preparing W/O/W emulsions are as follows: the ratio of the oil phase to the internal water phase is 80 : 20, the concentrations of lipophilic and hydrophilic emulsifiers are 10 wt% and 5 wt%, and the homogeneous pressures in the first and second steps are 30 MPa and 10 MPa. The optimal preparation process of the W/O/W emulsions was used to encapsulate resveratrol. The results showed that at up to 0.040 wt% in the internal water phase (ethanol), resveratrol could be successfully encapsulated in W/O/W emulsions with an encapsulation efficiency of 99.97 ± 0.001%. Moreover, resveratrol was successfully encapsulated in the internal water phase and oil phase together; thus, it was not necessary to increase the amount of carrier materials. This study provides a novel encapsulation formulation to increase the delivery efficacy of resveratrol."], "field": "Materials Science", "q_year": 2021, "q_cid": "238819424", "pos_cid": 73607345, "source": "eval_collection"}
{"query_id": "scaleup_24565023_19098240", "query": "How to accurately and computationally efficiently analyze thermal transport across GaN–BAs heterostructures at multiple scales to understand interfacial heat transfer and predictively design efficient heat dissipation in high-power microelectronic devices", "pos": ["Deep Potential Molecular Dynamics: a scalable model with the accuracy of quantum mechanics. We introduce a scheme for molecular simulations, the deep potential molecular dynamics (DPMD) method, based on a many-body potential and interatomic forces generated by a carefully crafted deep neural network trained with ab initio data. The neural network model preserves all the natural symmetries in the problem. It is first-principles based in the sense that there are no ad hoc components aside from the network model. We show that the proposed scheme provides an efficient and accurate protocol in a variety of systems, including bulk materials and molecules. In all these cases, DPMD gives results that are essentially indistinguishable from the original data, at a cost that scales linearly with system size."], "field": "Materials Science", "q_year": 2022, "q_cid": "245650232", "pos_cid": 19098240, "source": "eval_collection"}
{"query_id": "scaleup_26920732_30732984", "query": "How to understand the energy differences in gold between free-standing goldene and its parent layered material", "pos": ["Surface core-level shifts of clean and oxygen-covered Ru(0001). We have performed high resolution x-ray photoemission spectroscopy experiments on the Ru~0001! surface, both clean and covered with well-defined amounts of oxygen up to 1 monolayer coverage. For the clean surface we detected two distinct components in the Ru 3d5/2 core-level spectra, for which a definite assignment was made using the high resolution angle-scan photoelectron diffraction approach. For the p(232), p(231), ( 232)-3O, and ( 131)-O oxygen structures we found Ru 3d5/2 core-level peaks that are shifted to higher binding energies by up to 1 eV. Very good agreement with density functional theory calculations of these surface core-level shifts ~SCLS’s ! is reported. The overriding parameter for the resulting Ru SCLS’s turns out to be the number of directly coordinated O atoms. Since the calculations permit the separation of initial and final state effects, our results give valuable information for the understanding of bonding and screening at the surface that is not accessible in measurements of the core-level energies alone."], "field": "Materials Science", "q_year": 2024, "q_cid": "269207325", "pos_cid": 30732984, "source": "eval_collection"}
{"query_id": "scaleup_27379745_23847483", "query": "How to achieve sufficient hardness in flexible ultrathin glasses to resist deformation while retaining flexibility", "pos": ["Fracture, fatigue, and friction of polymers in which entanglements greatly outnumber cross-links. Description Longer and stronger; stiff but not brittle Hydrogels are highly water-swollen, cross-linked polymers. Although they can be highly deformed, they tend to be weak, and methods to strengthen or toughen them tend to reduce stretchability. Two papers now report strategies to create tough but deformable hydrogels (see the Perspective by Bosnjak and Silberstein). Wang et al. introduced a toughening mechanism by storing releasable extra chain length in the stiff part of a double-network hydrogel. A high applied force triggered the opening of cycling strands that were only activated at high chain extension. Kim et al. synthesized acrylamide gels in which dense entanglements could be achieved by using unusually low amounts of water, cross-linker, and initiator during the synthesis. This approach improves the mechanical strength in solid form while also improving the wear resistance once swollen as a hydrogel. —MSL Gels and elastomers with sparse cross-links and dense entanglements have improved mechanical properties without embrittlement. In gels and elastomers, the role of entanglements on deformation has been studied, but their effects on fracture, fatigue, and friction are less well understood. In this study, we synthesized polymers in which entanglements greatly outnumber cross-links. The dense entanglements enable transmission of tension in a polymer chain along its length and to many other chains. The sparse cross-links prevent the polymer chains from disentangling. These polymers have high toughness, strength, and fatigue resistance. After submersion in water, the polymers swell to equilibrium, and the resulting hydrogels have low hysteresis, low friction, and high wear resistance."], "field": "Materials Science", "q_year": 2024, "q_cid": "273797451", "pos_cid": 238474832, "source": "eval_collection"}
{"query_id": "scaleup_27839463_56177943", "query": "How to predict grain growth while preserving grain boundary topology, structural integrity, accurate boundary contours, and grain morphology", "pos": ["Boundary loss for highly unbalanced segmentation. Widely used loss functions for CNN segmentation, e.g., Dice or cross-entropy, are based on integrals over the segmentation regions. Unfortunately, for highly unbalanced segmentations, such regional summations have values that differ by several orders of magnitude across classes, which affects training performance and stability. We propose a boundary loss, which takes the form of a distance metric on the space of contours, not regions. This can mitigate the difficulties of highly unbalanced problems because it uses integrals over the interface between regions instead of unbalanced integrals over the regions. Furthermore, a boundary loss complements regional information. Inspired by graph-based optimization techniques for computing active-contour flows, we express a non-symmetric L2 distance on the space of contours as a regional integral, which avoids completely local differential computations involving contour points. This yields a boundary loss expressed with the regional softmax probability outputs of the network, which can be easily combined with standard regional losses and implemented with any existing deep network architecture for N-D segmentation. We report comprehensive evaluations and comparisons on different unbalanced problems, showing that our boundary loss can yield significant increases in performances while improving training stability. Our code is publicly available1."], "field": "Materials Science", "q_year": 2025, "q_cid": "278394634", "pos_cid": 56177943, "source": "eval_collection"}
{"query_id": "scaleup_25072608_10266611", "query": "How to characterize light-induced absorption changes in cellulose fibres in situ and determine the energy distribution of electron traps as a potential measure of crystalline defect density", "pos": ["Identification and characterization of titania photocatalyst powders using their energy-resolved distribution of electron traps as a fingerprint. Abstract Here we report identification of powders of titania, one of the most important metal oxides, with their energy-resolved distribution of electron traps (ERDT), as a fingerprint, measured by reversed double-beam photoacoustic spectroscopy (RDB-PAS). The ERDT patterns combined with conduction-band bottom (CBB) position data measured by ordinary PAS for various titania powders and other metal-oxide powders were different depending on the kind of sample. The degree of coincidence (ζ) of ERDT/CBB patterns was evaluated for a given pair of samples as a product of each degree of coincidence for ERDT-pattern matching, total density of electron traps and CBB position. Titania samples collected from close positions in a container exhibited high values of ζ, while samples with different code names showed low values of ζ, except for pairs of samples prepared in the same way but coded differently. It was shown that the higher was the values of ζ, the higher was the degree of coincidence for photocatalytic activity of titania samples. ERDT/CBB-pattern arrays arranged in the order of photocatalytic activities in three reaction systems suggested preferable patterns for each photocatalytic reaction."], "field": "Materials Science", "q_year": 2022, "q_cid": "250726080", "pos_cid": 102666110, "source": "eval_collection"}
{"query_id": "scaleup_24839191_7365802", "query": "How to achieve efficient, robust structural optimization when force and stress gradients contain stochastic noise", "pos": ["ADADELTA: An Adaptive Learning Rate Method. We present a novel per-dimension learning rate method for gradient descent called ADADELTA. The method dynamically adapts over time using only first order information and has minimal computational overhead beyond vanilla stochastic gradient descent. The method requires no manual tuning of a learning rate and appears robust to noisy gradient information, different model architecture choices, various data modalities and selection of hyperparameters. We show promising results compared to other methods on the MNIST digit classification task using a single machine and on a large scale voice dataset in a distributed cluster environment."], "field": "Materials Science", "q_year": 2022, "q_cid": "248391910", "pos_cid": 7365802, "source": "eval_collection"}
{"query_id": "scaleup_28188460_22113309", "query": "How to distinguish whether light emission in an aggregate originates from a single monomer or two interacting monomers", "pos": ["Excimer Intermediates en Route to Long-Lived Charge-Transfer States in Single-Stranded Adenine DNA as Revealed by Nonadiabatic Dynamics. The ultrafast time evolution of a single-stranded adenine DNA is studied using a hybrid multiscale quantum mechanics/molecular mechanics (QM/MM) scheme coupled to nonadiabatic surface hopping dynamics. As a model, we use (dA)20 where a stacked adenine tetramer is treated quantum chemically. The dynamical simulations combined with on-the-fly quantitative wave function analysis evidence the nature of the long-lived electronically excited states formed upon absorption of UV light. After a rapid decrease of the initially excited excitons, relaxation to monomer-like states and excimers occurs within 100 fs. The former monomeric states then relax into additional excimer states en route to forming stabilized charge-transfer states on a longer timescale of hundreds of femtoseconds. The different electronic-state characters is reflected on the spatial separation between the adenines: excimers and charge-transfer states show a much smaller spatial separation than the monomer-like states and the initially formed excitons."], "field": "Materials Science", "q_year": 2025, "q_cid": "281884605", "pos_cid": 221133095, "source": "eval_collection"}
{"query_id": "scaleup_28188460_24386196", "query": "How to achieve efficient solid-state deep-red-to-near-infrared emission", "pos": ["Exciton Delocalization Counteracts the Energy Gap: A New Pathway toward NIR-Emissive Dyes. Exciton coupling between the transition dipole moments of ordered dyes in supramolecular assemblies, so-called J/H-aggregates, leads to shifted electronic transitions. This can lower the excited state energy, allowing for emission well into the near-infrared regime. However, as we show here, it is not only the excited state energy modifications that J-aggregates can provide. A bay-alkylated quaterrylene was synthesized, which was found to form J-aggregates in 1,1,2,2-tetrachloroethane. A combination of superradiance and a decreased nonradiative relaxation rate made the J-aggregate four times more emissive than the monomeric counterpart. A reduced nonradiative relaxation rate is a nonintuitive consequence following the 180 nm (3300 cm–1) red-shift of the J-aggregate in comparison to the monomeric absorption. However, the energy gap law, which is commonly invoked to rationalize increased nonradiative relaxation rates with increasing emission wavelength, also contains a reorganization energy term. The reorganization energy is highly suppressed in J-aggregates due to exciton delocalization, and the framework of the energy gap law could therefore reproduce our experimental observations. J-Aggregates can thus circumvent the common belief that lowering the excited state energies results in large nonradiative relaxation rates and are thus a pathway toward highly emissive organic dyes in the NIR regime."], "field": "Materials Science", "q_year": 2025, "q_cid": "281884605", "pos_cid": 243861963, "source": "eval_collection"}
{"query_id": "scaleup_24654390_4932551", "query": "How to reversibly select either mirror-image product from the same starting material at a metal center with no inherent handedness", "pos": ["Asymmetric Ion-Pairing Catalysis. Charged intermediates and reagents are ubiquitous in organic transformations. The interaction of these ionic species with chiral neutral, anionic, or cationic small molecules has emerged as a powerful strategy for catalytic, enantioselective synthesis. This review describes developments in the burgeoning field of asymmetric ion-pairing catalysis with an emphasis on the insights that have been gleaned into the structural and mechanistic features that contribute to high asymmetric induction."], "field": "Materials Science", "q_year": 2022, "q_cid": "246543903", "pos_cid": 4932551, "source": "eval_collection"}
{"query_id": "scaleup_22178662_14624499", "query": "How to explain the effect of layered filler particles on PVA chain mobility, particularly at polymer–filler interfaces", "pos": ["Facile fabrication of tough photocrosslinked polyvinyl alcohol hydrogels with cellulose nanofibrils reinforcement. Abstract A high-strength polyvinyl alcohol (PVA) hydrogel was prepared via a facile photocrosslinked polymerization with cellulose nanofibrils (CNF) reinforcement. The mechanism of CNF reinforcement was studied systematically. The hydroxyl groups in the surface of CNF generate hydrogen bonds with the pendant hydroxyl of PVA chains, which promotes the interaction of already chemical crosslinked PVA chains and increases the crystallinity of the resultant PVA-MA/CNF hydrogel. By optimizing the CNF incorporation content to the PVA-MA/CNF hydrogel, a compressive fracture stress of 490 kPa was obtained, which is higher than that of previously reported nanocellulose reinforced PVA hydrogels. And more importantly, this gel exhibits excellent cyclic compressive performance. This work provides a novel method to improve the mechanical strength of PVA hydrogel which is beneficial for its application in tissue engineering field."], "field": "Materials Science", "q_year": 2020, "q_cid": "221786628", "pos_cid": 146244997, "source": "eval_collection"}
{"query_id": "scaleup_23519920_17075193", "query": "How to predict damage in already-defected zirconia under simultaneous low- and high-energy irradiation", "pos": ["Synergy of elastic and inelastic energy loss on ion track formation in SrTiO3. While the interaction of energetic ions with solids is well known to result in inelastic energy loss to electrons and elastic energy loss to atomic nuclei in the solid, the coupled effects of these energy losses on defect production, nanostructure evolution and phase transformations in ionic and covalently bonded materials are complex and not well understood due to dependencies on electron-electron scattering processes, electron-phonon coupling, localized electronic excitations, diffusivity of charged defects and solid-state radiolysis. Here we show that a colossal synergy occurs between inelastic energy loss and pre-existing atomic defects created by elastic energy loss in single crystal strontium titanate (SrTiO3), resulting in the formation of nanometer-sized amorphous tracks, but only in the narrow region with pre-existing defects. These defects locally decrease the electronic and atomic thermal conductivities and increase electron-phonon coupling, which locally increase the intensity of the thermal spike for each ion. This work identifies a major gap in understanding on the role of defects in electronic energy dissipation and electron-phonon coupling; it also provides insights for creating novel interfaces and nanostructures to functionalize thin film structures, including tunable electronic, ionic, magnetic and optical properties."], "field": "Materials Science", "q_year": 2021, "q_cid": "235199208", "pos_cid": 17075193, "source": "train_step3"}
{"query_id": "scaleup_26001451_17007616", "query": "How to clarify chitosan’s role in plants’ ability to withstand adverse conditions", "pos": ["Nitric oxide, stomatal closure, and abiotic stress.. Various data indicate that nitric oxide (NO) is an endogenous signal in plants that mediates responses to several stimuli. Experimental evidence in support of such signalling roles for NO has been obtained via the application of NO, usually in the form of NO donors, via the measurement of endogenous NO, and through the manipulation of endogenous NO content by chemical and genetic means. Stomatal closure, initiated by abscisic acid (ABA), is effected through a complex symphony of intracellular signalling in which NO appears to be one component. Exogenous NO induces stomatal closure, ABA triggers NO generation, removal of NO by scavengers inhibits stomatal closure in response to ABA, and ABA-induced stomatal closure is reduced in mutants that are impaired in NO generation. The data indicate that ABA-induced guard cell NO generation requires both nitric oxide synthase-like activity and, in Arabidopsis, the NIA1 isoform of nitrate reductase (NR). NO stimulates mitogen-activated protein kinase (MAPK) activity and cGMP production. Both these NO-stimulated events are required for ABA-induced stomatal closure. ABA also stimulates the generation of H2O2 in guard cells, and pharmacological and genetic data demonstrate that NO accumulation in these cells is dependent on such production. Recent data have extended this model to maize mesophyll cells where the induction of antioxidant defences by water stress and ABA required the generation of H2O2 and NO and the activation of a MAPK. Published data suggest that drought and salinity induce NO generation which activates cellular processes that afford some protection against the oxidative stress associated with these conditions. Exogenous NO can also protect cells against oxidative stress. Thus, the data suggest an emerging model of stress responses in which ABA has several ameliorative functions. These include the rapid induction of stomatal closure to reduce transpirational water loss and the activation of antioxidant defences to combat oxidative stress. These are two processes that both involve NO as a key signalling intermediate."], "field": "Materials Science", "q_year": 2023, "q_cid": "260014519", "pos_cid": 17007616, "source": "train_step3"}
{"query_id": "scaleup_27525462_23719903", "query": "How to obtain sufficient twelve-carbon precursor for nylon 12 monomer production from glucose without relying on plant-derived fatty acids", "pos": ["Genome-scale target identification in Escherichia coli for high-titer production of free fatty acids. To construct a superior microbial cell factory for chemical synthesis, a major challenge is to fully exploit cellular potential by identifying and engineering beneficial gene targets in sophisticated metabolic networks. Here, we take advantage of CRISPR interference (CRISPRi) and omics analyses to systematically identify beneficial genes that can be engineered to promote free fatty acids (FFAs) production in Escherichia coli. CRISPRi-mediated genetic perturbation enables the identification of 30 beneficial genes from 108 targets related to FFA metabolism. Then, omics analyses of the FFAs-overproducing strains and a control strain enable the identification of another 26 beneficial genes that are seemingly irrelevant to FFA metabolism. Combinatorial perturbation of four beneficial genes involving cellular stress responses results in a recombinant strain ihfAL−-aidB+-ryfAM−-gadAH−, producing 30.0 g L−1 FFAs in fed-batch fermentation, the maximum titer in E. coli reported to date. Our findings are of help in rewiring cellular metabolism and interwoven intracellular processes to facilitate high-titer production of biochemicals. Identification of gene targets is one of the major challenges to construct superior microbial cell factory for chemical synthesis. Here, the authors employ CRISPRi and omics analyses for genome-scale target genes identification for high-titer production of free fatty acids in E. coli."], "field": "Materials Science", "q_year": 2025, "q_cid": "275254621", "pos_cid": 237199036, "source": "train_step3"}
{"query_id": "scaleup_26316607_23232416", "query": "How to define a coral specimen’s outer boundary in three dimensions, treating its skeleton and internal pores and cavities as one whole distinct from its surroundings, excluding disconnected regions", "pos": ["Automated Segmentation of Fractured Distal Radii by 3D Geodesic Active Contouring of in vivo HR-pQCT Images. Radius fractures are among the most common fracture types; however, there is limited consensus on the standard of care. A better understanding of the fracture healing process could help to shape future treatment protocols and thus improve functional outcomes of patients. High-resolution peripheral quantitative computed tomography (HR-pQCT) allows monitoring and evaluation of the radius on the micro-structural level, which is crucial to our understanding of fracture healing. However, current radius fracture studies using HR-pQCT are limited by the lack of automated contouring routines, hence only including small number of patients due to the prohibitively time-consuming task of manually contouring HR-pQCT images. In the present study, a new method to automatically contour images of distal radius fractures based on 3D morphological geodesic active contours (3D-GAC) is presented. Contours of 60 HR-pQCT images of fractured and conservatively treated radii spanning the healing process up to one year post-fracture are compared to the current gold standard, hand-drawn 2D contours, to assess the accuracy of the algorithm. Furthermore, robustness was established by applying the algorithm to HR-pQCT images of intact radii of 73 patients and comparing the resulting morphometric indices to the gold standard patient evaluation including a threshold- and dilation-based contouring approach. Reproducibility was evaluated using repeat scans of intact radii of 19 patients. The new 3D-GAC approach offers contours within inter-operator variability for images of fractured distal radii (mean Dice score of 0.992 ± 0.004 versus median operator Dice score of 0.993 ± 0.006). The generated contours for images of intact radii yielded morphometric indices within the in vivo reproducibility limits compared to the current gold standard. Additionally, the 3D-GAC approach shows an improved robustness against failure (n = 4) when dealing with cortical interruptions, fracture fragments, etc. compared with the automatic, default manufacturer pipeline (n = 40). Using the 3D-GAC approach assures consistent results, while reducing the need for time-consuming hand-contouring."], "field": "Materials Science", "q_year": 2021, "q_cid": "263166074", "pos_cid": 232324166, "source": "train_step3"}
{"query_id": "scaleup_23238453_53568764", "query": "How to obtain a cellulose-derived polyol suitable as a raw material for manufacturing highly filled polyurethane composites", "pos": ["Chitin and waste shrimp shells liquefaction and liquefied products/polyvinyl alcohol blend membranes.. Ball-milled chitin was liquefied with an optimal yield of 92% under sulfuric acid in diethylene glycol (DEG) at 160 °C for 120 min. The resulting liquid mixture was roughly separated into two portions: the real products of the reaction (liquefied ball-milled chitin, LBMC) and the remaining unreacted DEG. LBMC was further mingled with polyvinyl alcohol (PVA) to prepare LBMC/PVA blend membranes. To promote the direct utilization of shellfishery waste, raw shrimp shells were used to replace chitin for the liquefaction and membrane preparation operations. Liquefied ball-milled shrimp shells (LBMS) and the corresponding LBMS/PVA blend membranes were obtained. After adding LBMC or LBMS, the mechanical, thermal, water content and antibacterial performance of blend membranes were significantly improved compared to pure PVA membrane. Surprisingly, all the measured properties of LBMC/PVA and LBMS/PVA blend membranes were comparable, and even some properties of the latter were slightly superior than those of the former."], "field": "Materials Science", "q_year": 2021, "q_cid": "232384533", "pos_cid": 53568764, "source": "train_step3"}
{"query_id": "scaleup_13739156_13292337", "query": "How to determine how often observational drug-safety studies report statistically significant findings when the drug does not cause the outcome", "pos": ["Negative Controls: A Tool for Detecting Confounding and Bias in Observational Studies. Noncausal associations between exposures and outcomes are a threat to validity of causal inference in observational studies. Many techniques have been developed for study design and analysis to identify and eliminate such errors. Such problems are not expected to compromise experimental studies, where careful standardization of conditions (for laboratory work) and randomization (for population studies) should, if applied properly, eliminate most such noncausal associations. We argue, however, that a routine precaution taken in the design of biologic laboratory experiments—the use of “negative controls”—is designed to detect both suspected and unsuspected sources of spurious causal inference. In epidemiology, analogous negative controls help to identify and resolve confounding as well as other sources of error, including recall bias or analytic flaws. We distinguish 2 types of negative controls (exposure controls and outcome controls), describe examples of each type from the epidemiologic literature, and identify the conditions for the use of such negative controls to detect confounding. We conclude that negative controls should be more commonly employed in observational studies, and that additional work is needed to specify the conditions under which negative controls will be sensitive detectors of other sources of error in observational studies."], "field": "Mathematics", "q_year": 2013, "q_cid": "13739156", "pos_cid": 13292337, "source": "eval20x26"}
{"query_id": "scaleup_21684499_12283183", "query": "How to characterize algebraic systems and their completely positive maps in Hilbert modules over a commutative operator algebra, clarifying their categorical structures and how morphisms relate to complete positivity in each fibre", "pos": ["Categories of quantum and classical channels. We introduce a construction that turns a category of pure state spaces and operators into a category of observable algebras and superoperators. For example, it turns the category of finite-dimensional Hilbert spaces into the category of finite-dimensional C*-algebras and completely positive maps. In particular, the new category contains both quantum and classical channels, providing elegant abstract notions of preparation and measurement. We also consider nonstandard models that can be used to investigate which notions from algebraic quantum information theory are operationally justifiable."], "field": "Mathematics", "q_year": 2017, "q_cid": "216844995", "pos_cid": 122831837, "source": "eval20x26"}
{"query_id": "scaleup_5323186_8263323", "query": "How to stabilize a local environment to limit growth when mass increases unpredictably rather than continuously", "pos": ["The Potential Role of Systemic Buffers in Reducing Intratumoral Extracellular pH and Acid-Mediated Invasion. A number of studies have shown that the extracellular pH (pHe) in cancers is typically lower than that in normal tissue and that an acidic pHe promotes invasive tumor growth in primary and metastatic cancers. Here, we investigate the hypothesis that increased systemic concentrations of pH buffers reduce intratumoral and peritumoral acidosis and, as a result, inhibit malignant growth. Computer simulations are used to quantify the ability of systemic pH buffers to increase the acidic pHe of tumors in vivo and investigate the chemical specifications of an optimal buffer for such purpose. We show that increased serum concentrations of the sodium bicarbonate (NaHCO3) can be achieved by ingesting amounts that have been used in published clinical trials. Furthermore, we find that consequent reduction of tumor acid concentrations significantly reduces tumor growth and invasion without altering the pH of blood or normal tissues. The simulations also show that the critical parameter governing buffer effectiveness is its pKa. This indicates that NaHCO3, with a pKa of 6.1, is not an ideal intratumoral buffer and that greater intratumoral pHe changes could be obtained using a buffer with a pKa of ~7. The simulations support the hypothesis that systemic pH buffers can be used to increase the tumor pHe and inhibit tumor invasion."], "field": "Mathematics", "q_year": 2014, "q_cid": "5323186", "pos_cid": 8263323, "source": "eval20x26"}
{"query_id": "scaleup_13668993_4330122", "query": "How to adequately describe human movement distances with long tails", "pos": ["The scaling laws of human travel. The dynamic spatial redistribution of individuals is a key driving force of various spatiotemporal phenomena on geographical scales. It can synchronize populations of interacting species, stabilize them, and diversify gene pools. Human travel, for example, is responsible for the geographical spread of human infectious disease. In the light of increasing international trade, intensified human mobility and the imminent threat of an influenza A epidemic, the knowledge of dynamical and statistical properties of human travel is of fundamental importance. Despite its crucial role, a quantitative assessment of these properties on geographical scales remains elusive, and the assumption that humans disperse diffusively still prevails in models. Here we report on a solid and quantitative assessment of human travelling statistics by analysing the circulation of bank notes in the United States. Using a comprehensive data set of over a million individual displacements, we find that dispersal is anomalous in two ways. First, the distribution of travelling distances decays as a power law, indicating that trajectories of bank notes are reminiscent of scale-free random walks known as Lévy flights. Second, the probability of remaining in a small, spatially confined region for a time T is dominated by algebraically long tails that attenuate the superdiffusive spread. We show that human travelling behaviour can be described mathematically on many spatiotemporal scales by a two-parameter continuous-time random walk model to a surprising accuracy, and conclude that human travel on geographical scales is an ambivalent and effectively superdiffusive process."], "field": "Mathematics", "q_year": 2017, "q_cid": "13668993", "pos_cid": 4330122, "source": "eval20x26"}
{"query_id": "scaleup_20943595_12373349", "query": "How to predict tumor-specific responses to targeted drugs to guide colorectal cancer patient stratification", "pos": ["Dynamic simulation of regulatory networks using SQUAD. BackgroundThe ambition of most molecular biologists is the understanding of the intricate network of molecular interactions that control biological systems. As scientists uncover the components and the connectivity of these networks, it becomes possible to study their dynamical behavior as a whole and discover what is the specific role of each of their components. Since the behavior of a network is by no means intuitive, it becomes necessary to use computational models to understand its behavior and to be able to make predictions about it. Unfortunately, most current computational models describe small networks due to the scarcity of kinetic data available. To overcome this problem, we previously published a methodology to convert a signaling network into a dynamical system, even in the total absence of kinetic information. In this paper we present a software implementation of such methodology.ResultsWe developed SQUAD, a software for the dynamic simulation of signaling networks using the standardized qualitative dynamical systems approach. SQUAD converts the network into a discrete dynamical system, and it uses a binary decision diagram algorithm to identify all the steady states of the system. Then, the software creates a continuous dynamical system and localizes its steady states which are located near the steady states of the discrete system. The software permits to make simulations on the continuous system, allowing for the modification of several parameters. Importantly, SQUAD includes a framework for perturbing networks in a manner similar to what is performed in experimental laboratory protocols, for example by activating receptors or knocking out molecular components. Using this software we have been able to successfully reproduce the behavior of the regulatory network implicated in T-helper cell differentiation.ConclusionThe simulation of regulatory networks aims at predicting the behavior of a whole system when subject to stimuli, such as drugs, or determine the role of specific components within the network. The predictions can then be used to interpret and/or drive laboratory experiments. SQUAD provides a user-friendly graphical interface, accessible to both computational and experimental biologists for the fast qualitative simulation of large regulatory networks for which kinetic data is not necessarily available."], "field": "Mathematics", "q_year": 2019, "q_cid": "209435952", "pos_cid": 12373349, "source": "eval20x26"}
{"query_id": "scaleup_52270903_13745179", "query": "How to make heterogeneous, time-stamped electronic health record information across multiple clinical domains suitable for atherosclerotic cardiovascular disease risk assessment", "pos": ["Design and implementation of a standardized framework to generate and evaluate patient-level prediction models using observational healthcare data. Abstract Objective To develop a conceptual prediction model framework containing standardized steps and describe the corresponding open-source software developed to consistently implement the framework across computational environments and observational healthcare databases to enable model sharing and reproducibility. Methods Based on existing best practices we propose a 5 step standardized framework for: (1) transparently defining the problem; (2) selecting suitable datasets; (3) constructing variables from the observational data; (4) learning the predictive model; and (5) validating the model performance. We implemented this framework as open-source software utilizing the Observational Medical Outcomes Partnership Common Data Model to enable convenient sharing of models and reproduction of model evaluation across multiple observational datasets. The software implementation contains default covariates and classifiers but the framework enables customization and extension. Results As a proof-of-concept, demonstrating the transparency and ease of model dissemination using the software, we developed prediction models for 21 different outcomes within a target population of people suffering from depression across 4 observational databases. All 84 models are available in an accessible online repository to be implemented by anyone with access to an observational database in the Common Data Model format. Conclusions The proof-of-concept study illustrates the framework’s ability to develop reproducible models that can be readily shared and offers the potential to perform extensive external validation of models, and improve their likelihood of clinical uptake. In future work the framework will be applied to perform an “all-by-all” prediction analysis to assess the observational data prediction domain across numerous target populations, outcomes and time, and risk settings."], "field": "Mathematics", "q_year": 2018, "q_cid": "52270903", "pos_cid": 13745179, "source": "eval20x26"}
{"query_id": "scaleup_73570537_88518595", "query": "How to determine which isotropic covariance function families and parameter ranges are positive semidefinite for a chosen distance metric on graphs with continuous edges, including graphs with cycles", "pos": ["Strictly and non-strictly positive definite functions on spheres. Isotropic positive definite functions on spheres play important roles in spatial statistics, where they occur as the correlation functions of homogeneous random fields and star-shaped random particles. In approximation theory, strictly positive definite functions serve as radial basis functions for interpolating scattered data on spherical domains. We review characterizations of positive definite functions on spheres in terms of Gegenbauer expansions and apply them to dimension walks, where monotonicity properties of the Gegenbauer coefficients guarantee positive definiteness in higher dimensions. Subject to a natural support condition, isotropic positive definite functions on the Euclidean space $\\mathbb{R}^3$, such as Askey's and Wendland's functions, allow for the direct substitution of the Euclidean distance by the great circle distance on a one-, two- or three-dimensional sphere, as opposed to the traditional approach, where the distances are transformed into each other. Completely monotone functions are positive definite on spheres of any dimension and provide rich parametric classes of such functions, including members of the powered exponential, Mat\\'{e}rn, generalized Cauchy and Dagum families. The sine power family permits a continuous parameterization of the roughness of the sample paths of a Gaussian process. A collection of research problems provides challenges for future work in mathematical analysis, probability theory and spatial statistics."], "field": "Mathematics", "q_year": 2017, "q_cid": "73570537", "pos_cid": 88518595, "source": "eval20x26"}
{"query_id": "scaleup_23620900_53554576", "query": "How to maintain societies’ core functions and minimise COVID-19 impacts across interconnected health, social, economic, environmental and governance systems", "pos": ["Resilience ( Republished ). Resilience thinking in relation to the environment has emerged as a lens of inquiry that serves a platform for interdisciplinary dialogue and collaboration. Resilience is about cultivating the capacity to sustain development in the face of expected and surprising change and diverse pathways of development and potential thresholds between them. The evolution of resilience thinking is coupled to socialecological systems and a truly intertwined human-environment planet. Resilience as persistence, adaptability, and transformability of complex adaptive social-ecological systems is the focus, clarifying the dynamic and forward-looking nature of the concept. Resilience thinking emphasizes that social-ecological systems, from the individual, to community, to society as a whole, are embedded in the biosphere. The biosphere connection is an essential observation if sustainability is to be taken seriously. In the continuous advancement of resilience thinking there are efforts aimed at capturing resilience of social-ecological systems and finding ways for people and institutions to govern social-ecological dynamics for improved human well-being, at the local, across levels and scales, to the global. Consequently, in resilience thinking, development issues for human well-being, for people and planet, are framed in a context of understanding and governing complex social-ecological dynamics for sustainability as part of a dynamic biosphere. This invited article is a republication of Folke, C. 2016. “Resilience” of the Oxford Research Encyclopedia of Environmental Science (http://dx.doi.org/10.1093/acrefore/9780199389414.013.8)"], "field": "Mathematics", "q_year": 2021, "q_cid": "236209005", "pos_cid": 53554576, "source": "eval_collection"}
{"query_id": "scaleup_25950161_14094707", "query": "How to isolate the effect of varying the spatial arrangement of contacts on disease-induced herd immunity while keeping each individual’s number of contacts unchanged", "pos": ["Configuring Random Graph Models with Fixed Degree Sequences. Random graph null models have found widespread application in diverse research communities analyzing network datasets, including social, information, and economic networks, as well as food webs, protein-protein interactions, and neuronal networks. The most popular family of random graph null models, called configuration models, are defined as uniform distributions over a space of graphs with a fixed degree sequence. Commonly, properties of an empirical network are compared to properties of an ensemble of graphs from a configuration model in order to quantify whether empirical network properties are meaningful or whether they are instead a common consequence of the particular degree sequence. In this work we study the subtle but important decisions underlying the specification of a configuration model, and investigate the role these choices play in graph sampling procedures and a suite of applications. We place particular emphasis on the importance of specifying the appropriate graph labeling (stub-labeled or vertex-labeled) under which to consider a null model, a choice that closely connects the study of random graphs to the study of random contingency tables. We show that the choice of graph labeling is inconsequential for studies of simple graphs, but can have a significant impact on analyses of multigraphs or graphs with self-loops. The importance of these choices is demonstrated through a series of three vignettes, analyzing network datasets under many different configuration models and observing substantial differences in study conclusions under different models. We argue that in each case, only one of the possible configuration models is appropriate. While our work focuses on undirected static networks, it aims to guide the study of directed networks, dynamic networks, and all other network contexts that are suitably studied through the lens of random graph null models."], "field": "Mathematics", "q_year": 2023, "q_cid": "259501610", "pos_cid": 14094707, "source": "eval_collection"}
{"query_id": "scaleup_27628779_25792192", "query": "How to obtain accurate meteorological states at arbitrary resolutions from low-resolution grids while accounting for satellite information and remaining consistent with coarse meteorological fields and local weather-station observations", "pos": ["Generative Diffusion Prior for Unified Image Restoration and Enhancement. Existing image restoration methods mostly leverage the posterior distribution of natural images. However, they often assume known degradation and also require supervised training, which restricts their adaptation to complex real applications. In this work, we propose the Generative Diffusion Prior (GDP) to effectively model the posterior distributions in an unsupervised sampling manner. GDP utilizes a pre-train denoising diffusion generative model (DDPM) for solving linear inverse, non-linear, or blind problems. Specifically, GDP systematically explores a protocol of conditional guidance, which is verified more practical than the commonly used guidance way. Furthermore, GDP is strength at optimizing the parameters of degradation model during the denoising process, achieving blind image restoration. Besides, we devise hierarchical guidance and patch-based methods, enabling the GDP to generate images of arbitrary resolutions. Experimentally, we demonstrate GDP's versatility on several image datasets for linear problems, such as super-resolution, deblurring, inpainting, and colorization, as well as non-linear and blind issues, such as low-light enhancement and HDR image recovery. GDP outperforms the current leading unsupervised methods on the diverse benchmarks in reconstruction quality and perceptual quality. Moreover, GDP also generalizes well for natural images or synthesized images with arbitrary sizes from various tasks out of the distribution of the ImageNet training set. The project page is available at https://generativediffusionprior.github.io/"], "field": "Mathematics", "q_year": 2025, "q_cid": "276287798", "pos_cid": 257921922, "source": "eval_collection"}
{"query_id": "scaleup_25151196_23751832", "query": "How to determine whether SARS-CoV-2 replication varies with time of day", "pos": ["The circadian clock component BMAL1 regulates SARS-CoV-2 entry and replication in lung epithelial cells. Summary The coronavirus disease 2019 pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) coronavirus, is a global health issue with unprecedented challenges for public health. SARS-CoV-2 primarily infects cells of the respiratory tract via spike glycoprotein binding to angiotensin-converting enzyme (ACE2). Circadian rhythms coordinate an organism's response to its environment and can regulate host susceptibility to virus infection. We demonstrate that silencing the circadian regulator Bmal1 or treating lung epithelial cells with the REV-ERB agonist SR9009 reduces ACE2 expression and inhibits SARS-CoV-2 entry and replication. Importantly, treating infected cells with SR9009 limits SARS-CoV-2 replication and secretion of infectious particles, showing that post-entry steps in the viral life cycle are influenced by the circadian system. Transcriptome analysis revealed that Bmal1 silencing induced interferon-stimulated gene transcripts in Calu-3 lung epithelial cells, providing a mechanism for the circadian pathway to limit SARS-CoV-2 infection. Our study highlights alternative approaches to understand and improve therapeutic targeting of SARS-CoV-2."], "field": "Mathematics", "q_year": 2022, "q_cid": "251511964", "pos_cid": 237518322, "source": "eval_collection"}
{"query_id": "scaleup_25512516_21608090", "query": "How to represent real-world spreading dynamics while accounting for the disproportionate influence of certain individuals", "pos": ["Mathematical modeling of COVID-19 transmission dynamics with a case study of Wuhan. We propose a compartmental mathematical model for the spread of the COVID-19 disease with special focus on the transmissibility of super-spreaders individuals. We compute the basic reproduction number threshold, we study the local stability of the disease free equilibrium in terms of the basic reproduction number, and we investigate the sensitivity of the model with respect to the variation of each one of its parameters. Numerical simulations show the suitability of the proposed COVID-19 model for the outbreak that occurred in Wuhan, China."], "field": "Mathematics", "q_year": 2022, "q_cid": "255125164", "pos_cid": 216080909, "source": "eval_collection"}
{"query_id": "scaleup_27277039_10193995", "query": "How to determine whether centered Gaussian inputs give the sharp inverse Brascamp–Lieb bound for degenerate data restricted to even, log-concave admissible functions", "pos": ["The Brascamp–Lieb Inequalities: Finiteness, Structure and Extremals. Abstract.We consider the Brascamp–Lieb inequalities concerning multilinear integrals of products of functions in several dimensions. We give a complete treatment of the issues of finiteness of the constant, and of the existence and uniqueness of centred gaussian extremals. For arbitrary extremals we completely address the issue of existence, and partly address the issue of uniqueness. We also analyse the inequalities from a structural perspective. Our main tool is a monotonicity formula for positive solutions to heat equations in linear and multilinear settings, which was first used in this type of setting by Carlen, Lieb, and Loss [CLL]. In that paper, the heat flow method was used to obtain the rank-one case of Lieb’s fundamental theorem concerning exhaustion by gaussians; we extend the technique to the higher-rank case, giving two new proofs of the general-rank case of Lieb’s theorem."], "field": "Mathematics", "q_year": 2024, "q_cid": "272770397", "pos_cid": 10193995, "source": "eval_collection"}
{"query_id": "scaleup_26620981_25019930", "query": "How to efficiently solve fractional problems with specified final values while obtaining highly accurate solutions to the required problems with specified initial values", "pos": ["A general framework for solving differential equations. Recently, the efficient numerical solution of Hamiltonian problems has been tackled by defining the class of energy-conserving Runge-Kutta methods named Hamiltonian Boundary Value Methods (HBVMs). Their derivation relies on the expansion of the vector field along a suitable orthonormal basis. Interestingly, this approach can be extended to cope with more general differential problems. In this paper we sketch this fact, by considering some relevant examples."], "field": "Mathematics", "q_year": 2023, "q_cid": "266209816", "pos_cid": 250199306, "source": "eval_collection"}
{"query_id": "scaleup_23620900_54897382", "query": "How to sustain economic activity and recover from pandemic-induced supply and demand shocks across countries and sectors with differing fiscal space and access to borrowing?", "pos": ["Economic resilience: definition and measurement. The welfare impact of a disaster does not only depend on the physical characteristics of the event or its direct impacts in terms of lost lives and assets. Welfare impacts also depend on the ability of the economy to cope, recover, and reconstruct and therefore to minimize aggregate consumption losses. This ability can be referred to as the macroeconomic resilience to natural disasters. Macroeconomic resilience has two components: instantaneous resilience, which is the ability to limit the magnitude of immediate production losses for a given amount of asset losses, and dynamic resilience, which is the ability to reconstruct and recover. Welfare impacts also depend on micro-economic resilience, which depends on the distribution of losses; on households' vulnerability, such as their pre-disaster income and ability to smooth shocks over time with savings, borrowing, and insurance, and on the social protection system, or the mechanisms for sharing risks across the population. The (economic) welfare disaster risk in a country can be reduced by reducing the exposure or vulnerability of people and assets (reducing asset losses), increasing macroeconomic resilience (reducing aggregate consumption losses for a given level of asset losses), or increasing microeconomic resilience (reducing welfare losses for a given level of aggregate consumption losses). The paper proposes rules of thumb to estimate macroeconomic and microeconomic resilience based on the relevant parameters in the economy. It also provides a toolbox of policies to increase macro- or micro-economic resilience and a list of indicators that can be used to build a resilience indicator."], "field": "Mathematics", "q_year": 2021, "q_cid": "236209005", "pos_cid": 54897382, "source": "eval_collection"}
{"query_id": "scaleup_28141070_22563461", "query": "How to assess numerical conditioning and identify support sets for stable polynomial interpolation from measurements over diffuse compact domains", "pos": ["On a generalization of the Lebesgue's constant. Abstract In this work we generalize the definition of the Lebesgue's constant to the case of field interpolation by high-order Whitney's forms on simplices. We underline the important theoretical concepts at play."], "field": "Mathematics", "q_year": 2025, "q_cid": "281410705", "pos_cid": 225634614, "source": "eval_collection"}
{"query_id": "scaleup_27688525_25339779", "query": "How to explore complex surfaces within limited time and computational cost while achieving good coverage and spending more time in regions believed to contain more information", "pos": ["Safety-Critical Ergodic Exploration in Cluttered Environments via Control Barrier Functions. In this paper, we address the problem of safe trajectory planning for autonomous search and exploration in constrained, cluttered environments. Guaranteeing safe (collision-free) trajectories is a challenging problem that has garnered significant due to its importance in the successful utilization of robots in search and exploration tasks. This work contributes a method that generates guaranteed safety-critical search trajectories in a cluttered environment. Our approach integrates safety-critical constraints using discrete control barrier functions (DCBFs) with ergodic trajectory optimization to enable safe exploration. Ergodic trajectory optimization plans continuous exploratory trajectories that guarantee complete coverage of a space. We demonstrate through simulated and experimental results on a drone that our approach is able to generate trajectories that enable safe and effective exploration. Furthermore, we show the efficacy of our approach for safe exploration using real-world single- and multi- drone platforms."], "field": "Mathematics", "q_year": 2025, "q_cid": "276885250", "pos_cid": 253397797, "source": "eval_collection"}
{"query_id": "scaleup_23874824_19819487", "query": "How to understand changes in distinct dimensions of human mobility during the Covid-19 pandemic", "pos": ["Towards a comprehensive set of GPS-based indicators reflecting the multidimensional nature of daily mobility for applications in health and aging research. BackgroundGPS tracking is increasingly used in health and aging research to objectively and unobtrusively assess individuals’ daily-life mobility. However, mobility is a complex concept and its thorough description based on GPS-derived mobility indicators remains challenging.MethodsWith the aim of reflecting the breadth of aspects incorporated in daily mobility, we propose a conceptual framework to classify GPS-derived mobility indicators based on their characteristic and analytical properties for application in health and aging research. In order to demonstrate how the classification framework can be applied, existing mobility indicators as used in existing studies are classified according to the proposed framework. Then, we propose and compute a set of selected mobility indicators based on real-life GPS data of 95 older adults that reflects diverse aspects of individuals’ daily mobility. To explore latent dimensions that underlie the mobility indicators, we conduct a factor analysis.ResultsThe proposed framework enables a conceptual classification of mobility indicators based on the characteristic and analytical aspects they reflect. Characteristic aspects inform about the content of the mobility indicator and comprise categories related to space, time, movement scope, and attribute. Analytical aspects inform how a mobility indicator is aggregated with respect to temporal scale and statistical property. The proposed categories complement existing studies that often underrepresent mobility indicators involving timing, temporal distributions, and stop-move segmentations of movements. The factor analysis uncovers the following six dimensions required to obtain a comprehensive view of an older adult’s daily mobility: extent of life space, quantity of out-of-home activities, time spent in active transport modes, stability of life space, elongation of life space, and timing of mobility.ConclusionThis research advocates incorporating GPS-based mobility indicators that reflect the multi-dimensional nature of individuals’ daily mobility in future health- and aging-related research. This will foster a better understanding of what aspects of mobility are key to healthy aging."], "field": "Mathematics", "q_year": 2021, "q_cid": "238748246", "pos_cid": 198194877, "source": "eval_collection"}
{"query_id": "scaleup_23216251_21438153", "query": "How to understand potentially nonlinear relationships between climatic factors, health security preparedness, and COVID-19 spread", "pos": ["Climate factors and the East Asian summer monsoon may drive large outbreaks of dengue in China.. OBJECTIVE To investigate the relationship between climate variables, East Asian summer monsoon (EASM) and large outbreaks of dengue in China. METHODS We constructed ecological niche models (ENMs) to analyse the influence of climate factors on dengue occurrence and predict dengue outbreak areas in China. Furthermore, we formulated a generalised additive model (GAM) to quantify the impact of the EASM on dengue occurrence in mainland China from 1980 to 2016. RESULTS Mean Temperature of Coldest Quarter had a 62.6% contribution to dengue outbreaks. Southern China including Guangdong, Guangxi, Fujian and Yunnan provinces are more vulnerable to dengue emergence and resurgence. In addition, we found population density had a 68.7% contribution to dengue widely distribution in China using ENMs. Statistical analysis indicated a dome-shaped association between EASM and dengue outbreak using GAM, with the greatest impact in the South-East of China. Besides, there was a positive nonlinear association between monthly average temperature and dengue occurrence. CONCLUSION We demonstrated the influence of climate factors and East Asian summer monsoon on dengue outbreaks, providing a framework for future studies on the association between climate change and vector-borne diseases."], "field": "Mathematics", "q_year": 2021, "q_cid": "232162519", "pos_cid": 214381537, "source": "eval_collection"}
{"query_id": "scaleup_23620900_15834409", "query": "How to enable individuals and households to meet basic needs and recover economically amid pandemic-related income loss and depleted savings, especially where safety nets are absent and precarious workers depend on heavily affected sectors", "pos": ["Household coping behavior and its contribution to resilience to global macroeconomic shocks in Vanuatu and Solomon Islands. This paper examines the resilience of households in Vanuatu and Solomon Islands—two small island developing states in Melanesia renowned for their vulnerabilities—to the adverse effects of global macroeconomic shocks. The focus is on the spike in international food and fuel prices in 2008 and the subsequent shock to global demand, known as the Global Economic Crisis (GEC). Using a unique retrospective cross‐section survey, the results show that experience of these shocks was widespread across urban and rural areas. Households with more education, access to income‐generating activities—particularly in the informal sector—and greater wealth were best placed to withstand a deterioration in their well‐being, measured as a fall in self‐reported disposable income. Households also employed a variety of coping strategies in response to the shocks. Local food gardens and informal insurance are seen as key safety nets in times of stress, yet neither provided full insurance from the shocks. Some households, particularly in urban areas, employed harmful coping strategies, such as reducing spending on health, education, and food. While potentially effective in withstanding a temporary fall in disposable income, these responses are likely to weaken overall resilience and leave households vulnerable to future shocks."], "field": "Mathematics", "q_year": 2021, "q_cid": "236209005", "pos_cid": 158344094, "source": "eval_collection"}
{"query_id": "scaleup_25803166_2981342", "query": "How to determine whether drug-sensitive, multidrug-resistant, and isolated tuberculosis populations all approach zero over time regardless of their initial levels", "pos": ["An extension of LaSalle's invariance principle for switched systems. In this paper we address invariance principles for a certain class of switched nonlinear systems. We provide an extension of LaSalle's invariance principle for these systems and state asymptotic stability criteria. We also present some related results on the compactness of the trajectories of these switched systems."], "field": "Mathematics", "q_year": 2023, "q_cid": "258031666", "pos_cid": 2981342, "source": "eval_collection"}
{"query_id": "scaleup_21969233_1592811", "query": "How to distinguish very sparse disease-related signals from unrelated features in high-dimensional gene-expression data and reliably assess how well candidate gene subsets predict patient survival outcomes", "pos": ["A weakly informative default prior distribution for logistic and other regression models. We propose a new prior distribution for classical (nonhierarchical) logistic regression models, constructed by first scaling all nonbinary variables to have mean 0 and standard deviation 0.5, and then placing independent Student-t prior distributions on the coefficients. As a default choice, we recommend the Cauchy distribution with center 0 and scale 2.5, which in the simplest setting is a longer-tailed version of the distribution attained by assuming one-half additional success and one-half additional failure in a logistic regression. Cross-validation on a corpus of datasets shows the Cauchy class of prior distributions to outperform existing implementations of Gaussian and Laplace priors. We recommend this prior distribution as a default choice for routine applied use. It has the advantage of always giving answers, even when there is complete separation in logistic regression (a common problem, even when the sample size is large and the number of predictors is small), and also automatically applying more shrinkage to higher-order interactions. This can be useful in routine data analysis as well as in automated procedures such as chained equations for missing-data imputation. We implement a procedure to fit generalized linear models in R with the Student-t prior distribution by incorporating an approximate EM algorithm into the usual iteratively weighted least squares. We illustrate with several applications, including a series of logistic regressions predicting voting preferences, a small bioassay experiment, and an imputation model for a public health data set."], "field": "Mathematics", "q_year": 2020, "q_cid": "219692331", "pos_cid": 1592811, "source": "eval_collection"}
{"query_id": "scaleup_26706830_504588", "query": "How to establish local convergence for low-tubal-rank tensor recovery from a small number of potentially corrupted linear measurements under noise", "pos": ["Statistical guarantees for the EM algorithm: From population to sample-based analysis. We develop a general framework for proving rigorous guarantees on the performance of the EM algorithm and a variant known as gradient EM. Our analysis is divided into two parts: a treatment of these algorithms at the population level (in the limit of infinite data), followed by results that apply to updates based on a finite set of samples. First, we characterize the domain of attraction of any global maximizer of the population likelihood. This characterization is based on a novel view of the EM updates as a perturbed form of likelihood ascent, or in parallel, of the gradient EM updates as a perturbed form of standard gradient ascent. Leveraging this characterization, we then provide non-asymptotic guarantees on the EM and gradient EM algorithms when applied to a finite set of samples. We develop consequences of our general theory for three canonical examples of incomplete-data problems: mixture of Gaussians, mixture of regressions, and linear regression with covariates missing completely at random. In each case, our theory guarantees that with a suitable initialization, a relatively small number of EM (or gradient EM) steps will yield (with high probability) an estimate that is within statistical error of the MLE. We provide simulations to confirm this theoretically predicted behavior."], "field": "Mathematics", "q_year": 2024, "q_cid": "267068304", "pos_cid": 504588, "source": "eval_collection"}
{"query_id": "scaleup_21846880_21106500", "query": "How to identify potential COVID-19 infection risk zones early in megacities for targeted prevention and control, with forecasts that reflect socioeconomic influences on spread and reliably distinguish at-risk areas", "pos": ["Modeling the lumpy skin disease risk probability in central Zagros Mountains of Iran.. BACKGROUND New Lumpy Skin Disease (LSD) outbreaks are currently circulating in Chaharmahal and Bakhtiari province, (western Iran, in central Zagros Mountains). OBJECTIVES The aim of this study was to model the risk probability of LSD in this area. METHOD Data were collected from veterinary organizations between 2012 and 2016. During this period, 290 outbreaks were registered. The herds were grazing and zero grazing. The average size of herds was 2958. We analyzed the potential for an outbreak of LSD in this area basing on the grid maps with the resolution of 1 km. In this study, 22 environmental variables (19 bioclimatic and 3 topography variables) were used to explore the environmental influences on LSD outbreak by maximum entropy ecological niche modeling (MaxEnt). RESULTS The results showed that mainly the central, northern, northeast and southern parts of Charmahal and Bakhtiari were the most very high risk areas for LSD. The MaxEnt model performed, with an area under the receiver operating characteristic curve (AUC) of 0.977 and 0.972 for training and test data, respectively. It showed high accuracy for predicting the prevalence of LSD (AUC close to 1). The precipitation of coldest season, isothermality and mean temperature of wettest season made the greatest contribution to the model (68.1%). Evaluating the importance of environmental variables, which were derived from the jackknife test, stated the precipitation of the wettest period and the coldest season and isothermality as the bioclimatic variables in explaining LSD prevalence compared to the other variables. CONCLUSION The MaxEnt model could be applied to predict the LSD risk probability of occurrence in central Zagros Mountains of Iran based on the current prevalence data of the disease. Also, the model confirmed that coexistence of weather conditions including defined humidity and temperature is necessary for the disease occurrence."], "field": "Mathematics", "q_year": 2020, "q_cid": "218468806", "pos_cid": 211065006, "source": "eval_collection"}
{"query_id": "scaleup_27607924_26508058", "query": "How to perform inference for fuzzy-data regression and obtain numerical solutions for the associated calculations", "pos": ["Tractable skew-normal approximations via matching. Many approximate Bayesian inference methods assume a particular parametric form for approximating the posterior distribution. A Gaussian distribution provides a convenient density for such approaches; examples include the Laplace, penalized quasi-likelihood, Gaussian variational, and expectation propagation methods. Unfortunately, these all ignore potential posterior skewness. The recent work of Durante et al. [Skewed Bernstein-von Mises theorem and skew-modal approximations; 2023. ArXiv preprint arXiv:2301.03038.] addresses this using skew-modal (SM) approximations, and is theoretically justified by a skewed Bernstein-von Mises theorem. However, the SM approximation can be impractical to work with in terms of tractability and storage costs, and uses only local posterior information. We introduce a variety of matching-based approximation schemes using the standard skew-normal distribution to resolve these issues. Experiments were conducted to compare the performance of this skew-normal matching method (both as a standalone approximation and as a post-hoc skewness adjustment) with the SM and existing Gaussian approximations. We show that for small and moderate dimensions, skew-normal matching can be much more accurate than these other approaches. For post-hoc skewness adjustments, this comes at very little cost in additional computational time."], "field": "Mathematics", "q_year": 2025, "q_cid": "276079240", "pos_cid": 265080588, "source": "eval_collection"}
{"query_id": "scaleup_25931474_24565178", "query": "How to establish sufficient evidence of tacrolimus effectiveness and safety to support label expansion for a lung-related indication", "pos": ["Lung Transplant Outcomes in Adults in the United States: Retrospective Cohort Study Using Real-world Evidence from the SRTR. Background. The Scientific Registry of Transplant Recipients was retrospectively analyzed to provide real-world evidence of the efficacy and safety of tacrolimus-based immunosuppressive regimens in adult lung transplant recipients in the United States. Methods. Adult recipients (N = 25 355; ≥18 y) of a primary deceased-donor lung transplant between January 1, 1999, and December 31, 2017, were followed for 3 y posttransplant based on immunosuppressive regimen at discharge: immediate-release tacrolimus (TAC) + mycophenolate mofetil (MMF), TAC + azathioprine (AZA), cyclosporine (CsA) + MMF, or CsA + AZA. The primary outcome was the composite endpoint of graft failure or death (all-cause) at 1 y posttransplant (calculated via a modified Kaplan–Meier method). Results. Discharge immunosuppressive regimens in lung transplant recipients changed over time, with a substantial increase in the use of TAC + MMF. TAC + MMF was the most common immunosuppressive regimen (received by 61.0% of individuals at discharge). The cumulative incidence of graft failure or death at 1 y posttransplant in adult lung transplant patients receiving TAC + MMF was 8.6% (95% confidence interval 8.1-9.1). Risk of graft failure or death was significantly higher in adults receiving CsA + MMF or CsA + AZA compared with TAC + MMF, with no significant difference seen between TAC + MMF and TAC + AZA. TAC + MMF had the highest continued use at 1 y posttransplant (72.0% versus 35.4%–51.5% for the other regimens). There was no increase in the rate of infection or malignancy in the TAC + MMF group. Conclusions. Real-world evidence from the most comprehensive database of transplant recipients in the United States supports the use of TAC in combination with MMF or AZA as maintenance immunosuppression in adult lung transplant recipients."], "field": "Mathematics", "q_year": 2023, "q_cid": "259314746", "pos_cid": 245651786, "source": "eval_collection"}
{"query_id": "scaleup_22724912_21284403", "query": "How to improve the accuracy of COVID-19 outbreak forecasts in Wuhan", "pos": ["ComDA: A common software for nonlinear and Non-Gaussian Land Data Assimilation. Abstract Common software for land data assimilation is urgently needed to implement a wide variety of assimilation applications; however, a fast, easy-to-use, and multidisciplinary application-oriented assimilation platform has not been achieved. Therefore, we developed Common software for Nonlinear and non-Gaussian Land Data Assimilation (ComDA). ComDA integrates multiple algorithms (including diverse Kalman and particle filters), models and observation operators (e.g., common land model (CoLM), Advanced Integral Equation Model (AIEM)), and provides general interfaces for additional operators. Using mixed-language programming and parallel computing technologies (Open Multi-Processing (OpenMP), Message Passing Interface (MPI) and Compute Unified Device Architecture (CUDA)), ComDA can assimilate various land surface variables and remote sensing observations. High-performance computing and synthetic tests and real-world tests indicate that ComDA achieves the standard of common land data assimilation software with parallel computation, multiple operators, and assimilation algorithms and is compatible with many models. ComDA can be applied for multidisciplinary data assimilation."], "field": "Mathematics", "q_year": 2020, "q_cid": "227249125", "pos_cid": 212844035, "source": "eval_collection"}
{"query_id": "scaleup_26455598_1444386", "query": "How to select allocation policies that perform well over time in utility, robustness, and fairness when their effects on future societal bias are uncertain", "pos": ["Robust Bayesian Reinforcement Learning through Tight Lower Bounds. In the Bayesian approach to sequential decision making, exact calculation of the (subjective) utility is intractable. This extends to most special cases of interest, such as reinforcement learning problems. While utility bounds are known to exist for this problem, so far none of them were particularly tight. In this paper, we show how to efficiently calculate a lower bound, which corresponds to the utility of a near-optimal memoryless policy for the decision problem, which is generally different from both the Bayes-optimal policy and the policy which is optimal for the expected MDP under the current belief. We then show how these can be applied to obtain robust exploration policies in a Bayesian reinforcement learning setting."], "field": "Mathematics", "q_year": 2023, "q_cid": "264555988", "pos_cid": 1444386, "source": "eval_collection"}
{"query_id": "scaleup_27044047_5665033", "query": "How to simplify sharing patterns without losing the ability to represent global dependencies across different combinations of dimensions", "pos": ["Understanding the Effective Receptive Field in Deep Convolutional Neural Networks. We study characteristics of receptive fields of units in deep convolutional networks. The receptive field size is a crucial issue in many visual tasks, as the output must respond to large enough areas in the image to capture information about large objects. We introduce the notion of an effective receptive field size, and show that it both has a Gaussian distribution and only occupies a fraction of the full theoretical receptive field size. We analyze the effective receptive field in several architecture designs, and the effect of sub-sampling, skip connections, dropout and nonlinear activations on it. This leads to suggestions for ways to address its tendency to be too small."], "field": "Mathematics", "q_year": 2024, "q_cid": "270440479", "pos_cid": 5665033, "source": "eval_collection"}
{"query_id": "scaleup_22040886_15367286", "query": "How to estimate the future course and ultimate total of cumulative confirmed COVID-19 cases in Puerto Rico from cases observed so far", "pos": ["Classical Mathematical Models for Description and Prediction of Experimental Tumor Growth. Despite internal complexity, tumor growth kinetics follow relatively simple laws that can be expressed as mathematical models. To explore this further, quantitative analysis of the most classical of these were performed. The models were assessed against data from two in vivo experimental systems: an ectopic syngeneic tumor (Lewis lung carcinoma) and an orthotopically xenografted human breast carcinoma. The goals were threefold: 1) to determine a statistical model for description of the measurement error, 2) to establish the descriptive power of each model, using several goodness-of-fit metrics and a study of parametric identifiability, and 3) to assess the models' ability to forecast future tumor growth. The models included in the study comprised the exponential, exponential-linear, power law, Gompertz, logistic, generalized logistic, von Bertalanffy and a model with dynamic carrying capacity. For the breast data, the dynamics were best captured by the Gompertz and exponential-linear models. The latter also exhibited the highest predictive power, with excellent prediction scores (≥80%) extending out as far as 12 days in the future. For the lung data, the Gompertz and power law models provided the most parsimonious and parametrically identifiable description. However, not one of the models was able to achieve a substantial prediction rate (≥70%) beyond the next day data point. In this context, adjunction of a priori information on the parameter distribution led to considerable improvement. For instance, forecast success rates went from 14.9% to 62.7% when using the power law model to predict the full future tumor growth curves, using just three data points. These results not only have important implications for biological theories of tumor growth and the use of mathematical modeling in preclinical anti-cancer drug investigations, but also may assist in defining how mathematical models could serve as potential prognostic tools in the clinic."], "field": "Mathematics", "q_year": 2020, "q_cid": "220408861", "pos_cid": 15367286, "source": "eval_collection"}
{"query_id": "scaleup_23620900_22490338", "query": "How to control pandemic transmission while preserving civil liberties, the rule of law, functioning institutions, and democratic safeguards", "pos": ["The Impact of the COVID-19 Pandemic in Central and Eastern Europe. The COVID-19 pandemic represents a new and unparalleled stress-test for the already disrupted liberal-representative, democracies The challenges cluster around three democratic disfigurations: technocracy, populism, and plebiscitarianism-each have the potential to contribute to democratic decay Still, they can also trigger pushback against illiberalism mobilizing citizens in defense of democracy, toward democratic resilience This article looks at how the COVID-19 pandemic affects democratic decay and democratic resilience in Central and Eastern Europe (CEE) It finds varied responses to the COVID-19 crisis by the CEE populist leaders and identifies two patterns: the rise of autocracy and democratic resilience First, in Hungary and Poland, the populist leaders instrumentalized the state of emergency to increase executive aggrandizement Second, in the Czech Republic and Slovakia, democracy proved resilient The COVID-19 pandemic alone is not fostering the rise of authoritarianism However, it does accentuate existing democratic disfigurations"], "field": "Mathematics", "q_year": 2021, "q_cid": "236209005", "pos_cid": 224903386, "source": "eval_collection"}
{"query_id": "scaleup_26825180_897967", "query": "How to consistently assess the quality of fragmented oncology data for reliable estimation of real-world time to treatment discontinuation", "pos": ["A Harmonized Data Quality Assessment Terminology and Framework for the Secondary Use of Electronic Health Record Data. Objective: Harmonized data quality (DQ) assessment terms, methods, and reporting practices can establish a common understanding of the strengths and limitations of electronic health record (EHR) data for operational analytics, quality improvement, and research. Existing published DQ terms were harmonized to a comprehensive unified terminology with definitions and examples and organized into a conceptual framework to support a common approach to defining whether EHR data is ‘fit’ for specific uses. Materials and Methods: DQ publications, informatics and analytics experts, managers of established DQ programs, and operational manuals from several mature EHR-based research networks were reviewed to identify potential DQ terms and categories. Two face-to-face stakeholder meetings were used to vet an initial set of DQ terms and definitions that were grouped into an overall conceptual framework. Feedback received from data producers and users was used to construct a draft set of harmonized DQ terms and categories. Multiple rounds of iterative refinement resulted in a set of terms and organizing framework consisting of DQ categories, subcategories, terms, definitions, and examples. The harmonized terminology and logical framework’s inclusiveness was evaluated against ten published DQ terminologies. Results: Existing DQ terms were harmonized and organized into a framework by defining three DQ categories: (1) Conformance (2) Completeness and (3) Plausibility and two DQ assessment contexts: (1) Verification and (2) Validation. Conformance and Plausibility categories were further divided into subcategories. Each category and subcategory was defined with respect to whether the data may be verified with organizational data, or validated against an accepted gold standard, depending on proposed context and uses. The coverage of the harmonized DQ terminology was validated by successfully aligning to multiple published DQ terminologies. Discussion: Existing DQ concepts, community input, and expert review informed the development of a distinct set of terms, organized into categories and subcategories. The resulting DQ terms successfully encompassed a wide range of disparate DQ terminologies. Operational definitions were developed to provide guidance for implementing DQ assessment procedures. The resulting structure is an inclusive DQ framework for standardizing DQ assessment and reporting. While our analysis focused on the DQ issues often found in EHR data, the new terminology may be applicable to a wide range of electronic health data such as administrative, research, and patient-reported data. Conclusion: A consistent, common DQ terminology, organized into a logical framework, is an initial step in enabling data owners and users, patients, and policy makers to evaluate and communicate data quality findings in a well-defined manner with a shared vocabulary. Future work will leverage the framework and terminology to develop reusable data quality assessment and reporting methods."], "field": "Mathematics", "q_year": 2024, "q_cid": "268251804", "pos_cid": 897967, "source": "eval_collection"}
{"query_id": "scaleup_26455598_23157338", "query": "How to ensure fairness across an entire sequence of allocation decisions when current allocations can change societal bias and affect future opportunities", "pos": ["Towards Long-term Fairness in Recommendation. As Recommender Systems (RS) influence more and more people in their daily life, the issue of fairness in recommendation is becoming more and more important. Most of the prior approaches to fairness-aware recommendation have been situated in a static or one-shot setting, where the protected groups of items are fixed, and the model provides a one-time fairness solution based on fairness-constrained optimization. This fails to consider the dynamic nature of the recommender systems, where attributes such as item popularity may change over time due to the recommendation policy and user engagement. For example, products that were once popular may become no longer popular, and vice versa. As a result, the system that aims to maintain long-term fairness on the item exposure in different popularity groups must accommodate this change in a timely fashion. Novel to this work, we explore the problem of long-term fairness in recommendation and accomplish the problem through dynamic fairness learning. We focus on the fairness of exposure of items in different groups, while the division of the groups is based on item popularity, which dynamically changes over time in the recommendation process. We tackle this problem by proposing a fairness-constrained reinforcement learning algorithm for recommendation, which models the recommendation problem as a Constrained Markov Decision Process (CMDP), so that the model can dynamically adjust its recommendation policy to make sure the fairness requirement is always satisfied when the environment changes. Experiments on several real-world datasets verify our framework's superiority in terms of recommendation performance, short-term fairness, and long-term fairness."], "field": "Mathematics", "q_year": 2023, "q_cid": "264555988", "pos_cid": 231573387, "source": "eval_collection"}
{"query_id": "scaleup_25541537_23736373", "query": "How to obtain theoretically justified, less informative priors for singular-value scale parameters in Bayesian interaction models while ensuring proper posterior distributions and stable parameter estimation without corrections to prior degrees of freedom?", "pos": ["Shrinkage in the Bayesian analysis of the GGE model: A case study with simulation. The genotype main effects plus the genotype × environment interaction effects model has been widely used to analyze multi-environmental trials data, especially using a graphical biplot considering the first two principal components of the singular value decomposition of the interaction matrix. Many authors have noted the advantages of applying Bayesian inference in these classes of models to replace the frequentist approach. This results in parsimonious models, and eliminates parameters that would be present in a traditional analysis of bilinear components (frequentist form). This work aims to extend shrinkage methods to estimators of those parameters that composes the multiplicative part of the model, using the maximum entropy principle for prior justification. A Bayesian version (non-shrinkage prior, using conjugacy and large variance) was also used for comparison. The simulated data set had 20 genotypes evaluated across seven environments, in a complete randomized block design with three replications. Cross-validation procedures were conducted to assess the predictive ability of the model and information criteria were used for model selection. A better predictive capacity was found for the model with a shrinkage effect, especially for unorthogonal scenarios in which more genotypes were removed at random. In these cases, however, the best fitted models, as measured by information criteria, were the conjugate flat prior. In addition, the flexibility of the Bayesian method was found, in general, to attribute inference to the parameters of the models which related to the biplot representation. Maximum entropy prior was the more parsimonious, and estimates singular values with a greater contribution to the sum of squares of the genotype + genotype × environmental interaction. Hence, this method enabled the best discrimination of parameters responsible for the existing patterns and the best discarding of the noise than the model assuming non-informative priors for multiplicative parameters."], "field": "Mathematics", "q_year": 2023, "q_cid": "255415372", "pos_cid": 237363733, "source": "eval_collection"}
{"query_id": "scaleup_25195417_5661488", "query": "How to determine disease severity from non-linked, aggregate surveillance data when delays between case ascertainment, hospital admission, and death are uncertain and vary with age and variant", "pos": ["Measuring and testing dependence by correlation of distances. Distance correlation is a new measure of dependence between random vectors. Distance covariance and distance correlation are analogous to product-moment covariance and correlation, but unlike the classical definition of correlation, distance correlation is zero only if the random vectors are independent. The empirical distance dependence measures are based on certain Euclidean distances between sample elements rather than sample moments, yet have a compact representation analogous to the classical covariance and correlation. Asymptotic properties and applications in testing independence are discussed. Implementation of the test and Monte Carlo results are also presented."], "field": "Mathematics", "q_year": 2022, "q_cid": "251954174", "pos_cid": 5661488, "source": "eval_collection"}
{"query_id": "scaleup_27044047_3819852", "query": "How to make neural networks for multi-user multiple-input-multiple-output communication respect permutation symmetries across multiple tensor dimensions while keeping parameter counts manageable", "pos": ["Deep Models of Interactions Across Sets. We use deep learning to model interactions across two or more sets of objects, such as user-movie ratings, protein-drug bindings, or ternary user-item-tag interactions. The canonical representation of such interactions is a matrix (or a higher-dimensional tensor) with an exchangeability property: the encoding's meaning is not changed by permuting rows or columns. We argue that models should hence be Permutation Equivariant (PE): constrained to make the same predictions across such permutations. We present a parameter-sharing scheme and prove that it could not be made any more expressive without violating PE. This scheme yields three benefits. First, we demonstrate state-of-the-art performance on multiple matrix completion benchmarks. Second, our models require a number of parameters independent of the numbers of objects, and thus scale well to large datasets. Third, models can be queried about new objects that were not available at training time, but for which interactions have since been observed. In experiments, our models achieved surprisingly good generalization performance on this matrix extrapolation task, both within domains (e.g., new users and new movies drawn from the same distribution used for training) and even across domains (e.g., predicting music ratings after training on movies)."], "field": "Mathematics", "q_year": 2024, "q_cid": "270440479", "pos_cid": 3819852, "source": "eval_collection"}
{"query_id": "scaleup_23902446_88523267", "query": "How to make covariance-matrix computations efficient for missing-value prediction in massive datasets while preserving prediction accuracy", "pos": ["Likelihood approximation with hierarchical matrices for large spatial datasets. We use available measurements to estimate the unknown parameters (variance, smoothness parameter, and covariance length) of a covariance function by maximizing the joint Gaussian log-likelihood function. To overcome cubic complexity in the linear algebra, we approximate the discretized covariance function in the hierarchical (H-) matrix format. The H-matrix format has a log-linear computational cost and storage $O(kn \\log n)$, where the rank $k$ is a small integer and $n$ is the number of locations. The H-matrix technique allows us to work with general covariance matrices in an efficient way, since H-matrices can approximate inhomogeneous covariance functions, with a fairly general mesh that is not necessarily axes-parallel, and neither the covariance matrix itself nor its inverse have to be sparse. We demonstrate our method with Monte Carlo simulations and an application to soil moisture data. The C, C++ codes and data are freely available."], "field": "Mathematics", "q_year": 2021, "q_cid": "239024468", "pos_cid": 88523267, "source": "eval_collection"}
{"query_id": "scaleup_21758796_26467366", "query": "How to assess the relationship between meteorological factors and mumps incidence among children, accounting for potentially nonlinear associations and delayed effects", "pos": ["Distributed Lag Linear and Non-Linear Models in R: The Package dlnm. Distributed lag non-linear models (DLNMs) represent a modeling framework to flexibly describe associations showing potentially non-linear and delayed effects in time series data. This methodology rests on the definition of a crossbasis, a bi-dimensional functional space expressed by the combination of two sets of basis functions, which specify the relationships in the dimensions of predictor and lags, respectively. This framework is implemented in the R package dlnm, which provides functions to perform the broad range of models within the DLNM family and then to help interpret the results, with an emphasis on graphical representation. This paper offers an overview of the capabilities of the package, describing the conceptual and practical steps to specify and interpret DLNMs with an example of application to real data."], "field": "Mathematics", "q_year": 2020, "q_cid": "217587965", "pos_cid": 264673660, "source": "eval_collection"}
{"query_id": "scaleup_23902446_73643684", "query": "How to predict missing data in massive medical datasets with low computational cost and numerical stability", "pos": ["Multi-level restricted maximum likelihood covariance estimation and kriging for large non-gridded spatial datasets. We develop a multi-level restricted Gaussian maximum likelihood method for estimating the covariance function parameters and computing the best unbiased predictor. Our approach produces a new set of multi-level contrasts where the deterministic parameters of the model are filtered out thus enabling the estimation of the covariance parameters to be decoupled from the deterministic component. Moreover, the multi-level covariance matrix of the contrasts exhibit fast decay that is dependent on the smoothness of the covariance function. Due to the fast decay of the multi-level covariance matrix coefficients only a small set is computed with a level dependent criterion. We demonstrate our approach on problems of up to 512,000 observations with a Matern covariance function and highly irregular placements of the observations. In addition, these problems are numerically unstable and hard to solve with traditional methods."], "field": "Mathematics", "q_year": 2021, "q_cid": "239024468", "pos_cid": 73643684, "source": "eval_collection"}
{"query_id": "scaleup_25512516_23741811", "query": "How to determine how memory affects interacting groups’ ability to withstand and recover from brief and periodic disturbances", "pos": ["Quantifying the impact of ecological memory on the dynamics of interacting communities. Ecological memory refers to the influence of past events on the response of an ecosystem to exogenous or endogenous changes. Memory has been widely recognized as a key contributor to the dynamics of ecosystems and other complex systems, yet quantitative community models often ignore memory and its implications. Recent modeling studies have shown how interactions between community members can lead to the emergence of resilience and multistability under environmental perturbations. We demonstrate how memory can be introduced in such models using the framework of fractional calculus. We study how the outcomes of a well-characterized interaction model are affected by gradual increases in ecological memory under varying initial conditions, perturbations, and stochasticity. Our results highlight the implications of memory on several key aspects of community dynamics. In general, memory introduces inertia into the dynamics. This favors species coexistence under perturbation, enhances system resistance to state shifts, mitigates hysteresis, and can affect system resilience both ways depending on the time scale considered. Memory also promotes long transient dynamics, such as long-standing oscillations and delayed regime shifts, and contributes to the emergence and persistence of alternative stable states. Our study highlights the fundamental role of memory on ecological communities, and provides quantitative tools to introduce it in ecological models and analyse its impact under varying conditions. Author summary An ecosystem is said to exhibit ecological memory when its future states do not only depend on its current state but also on its initial state and trajectory. Memory may arise through various mechanisms as organisms adapt to their environment, modify it, and accumulate biotic and abiotic material. It may also emerge from phenotypic heterogeneity at the population level. Despite its commonness in nature, ecological memory and its potential influence on ecosystem dynamics have been so far overlooked in many applied contexts. Here, we use modeling to investigate how memory can influence the dynamics, composition, and stability landscape of ecological communities. We incorporate long-term memory effects into a multi-species model recently introduced to investigate alternative stable states in microbial communities. We assess the impact of memory on key aspects of model behavior and validate our findings using a model parameterized by empirical data from the human gut microbiota. Our approach for modeling memory and studying its implications has the potential to improve our understanding of microbial community dynamics and ultimately our ability to predict, manipulate, and experimentally design microbial ecosystems. It could also be applied more broadly in the study of systems composed of interacting components."], "field": "Mathematics", "q_year": 2022, "q_cid": "255125164", "pos_cid": 237418115, "source": "eval_collection"}
{"query_id": "scaleup_25931474_23480812", "query": "How to address clinical pharmacology questions when available real-world data are insufficient and combining sources is not feasible", "pos": ["Improving Collection of Real-World Data: The Experience of the Joven & Fuerte Prospective Cohort for Mexican Young Women With Breast Cancer.. The prospective collection of clinical data can generate detailed information on heterogeneous populations. This article reviews the strengths and limitations of the collection of real-world data and provides insight into the feasibility of routine collection of high-quality evidence even in a resource-constrained setting. The acquisition of high-quality data to assess the clinical and psychosocial needs of young Mexican patients with breast cancer has been enhanced through the use of preplanned, standardized data definitions and instrumentation to provide internally and externally comparable results, optimization of data collection with web-based surveys, engagement of participants to minimize missing data, and routine review for data consistency. A similar approach by other research groups could improve the quality of real-world data and accomplish enhanced inference of information."], "field": "Mathematics", "q_year": 2023, "q_cid": "259314746", "pos_cid": 234808124, "source": "eval_collection"}
{"query_id": "scaleup_21972127_18395085", "query": "How to establish error guarantees for probability-distribution inputs that do not form a vector space and determine whether optimal convergence rates for function-valued inputs remain attainable", "pos": ["Methodology and convergence rates for functional linear regression. In functional linear regression, the slope \"parameter\" is a function. Therefore, in a nonparametric context, it is determined by an infinite number of unknowns. Its estimation involves solving an ill-posed problem and has points of contact with a range of methodologies, including statistical smoothing and deconvolution. The standard approach to estimating the slope function is based explicitly on functional principal components analysis and, consequently, on spectral decomposition in terms of eigenvalues and eigen-functions. We discuss this approach in detail and show that in certain circumstances, optimal convergence rates are achieved by the PCA technique. An alternative approach based on quadratic regularisation is suggested and shown to have advantages from some points of view."], "field": "Mathematics", "q_year": 2020, "q_cid": "219721275", "pos_cid": 18395085, "source": "train_step3"}
{"query_id": "scaleup_26119274_7726508", "query": "How to obtain unbiased system parameter estimates and distinguish corrupted observations from good data in outlier-contaminated data without prior knowledge of the outliers?", "pos": ["Iteratively reweighted least squares minimization for sparse recovery. Under certain conditions (known as the restricted isometry property, or RIP) on the m × N matrix Φ (where m < N), vectors x ∈ ℝN that are sparse (i.e., have most of their entries equal to 0) can be recovered exactly from y := Φx even though Φ−1(y) is typically an (N − m)—dimensional hyperplane; in addition, x is then equal to the element in Φ−1(y) of minimal 𝓁1‐norm. This minimal element can be identified via linear programming algorithms. We study an alternative method of determining x, as the limit of an iteratively reweighted least squares (IRLS) algorithm. The main step of this IRLS finds, for a given weight vector w, the element in Φ−1(y) with smallest 𝓁2(w)‐norm. If x(n) is the solution at iteration step n, then the new weight w(n) is defined by w i(n) := [|x i(n) |2 + ε n2 ]−1/2, i = 1, …, N, for a decreasing sequence of adaptively defined εn; this updated weight is then used to obtain x(n + 1) and the process is repeated. We prove that when Φ satisfies the RIP conditions, the sequence x(n) converges for all y, regardless of whether Φ−1(y) contains a sparse vector. If there is a sparse vector in Φ−1(y), then the limit is this sparse vector, and when x(n) is sufficiently close to the limit, the remaining steps of the algorithm converge exponentially fast (linear convergence in the terminology of numerical optimization). The same algorithm with the “heavier” weight w i(n) = [|x i(n) |2 + ε n2 ]−1+τ/2, i = 1, …, N, where 0 < τ < 1, can recover sparse solutions as well; more importantly, we show its local convergence is superlinear and approaches a quadratic rate for τ approaching 0. © 2009 Wiley Periodicals, Inc."], "field": "Mathematics", "q_year": 2023, "q_cid": "261192746", "pos_cid": 7726508, "source": "train_step3"}
{"query_id": "scaleup_27743532_14364048", "query": "How to explain gender differences in household contact patterns in urban and rural settings in sub-Saharan Africa", "pos": ["‘Women Can Do What Men Can Do’: The Causes and Consequences of Growing Flexibility in Gender Divisions of Labour in Kitwe, Zambia. Economic insecurity has catalysed growing flexibility in gender divisions of labour in Kitwe, Zambia. People's resulting exposure to, as well as collective reflection about, a critical mass of women performing work that was previously presumed to be beyond their capabilities, and valorised because of its association with masculinity, appears to erode gender stereotypes relating to competence and status. It is this weakening of gender beliefs, rather than women's increased access to resources per se, that appears to have directly undermined gender-status inequalities. This article's portrayal of growing gender egalitarianism contrasts with (though does not dispute the empirical claims of) earlier accounts of economic crisis in Zambia, which emphasised women's increased burdens. Some domains, such as unpaid care work, continue to be marked by persistent inequalities; however, drawing on ethnographic research (comprising life history narratives, group interviews and observation), it is argued that this is not necessarily an indicator of women's low status generally."], "field": "Mathematics", "q_year": 2025, "q_cid": "277435324", "pos_cid": 143640489, "source": "train_step3"}
{"query_id": "scaleup_27187444_24850609", "query": "How to obtain all required equation terms for simultaneous changes in three or four particles, accounting for three-particle interactions in both combined spin–orbital and spin-separated forms", "pos": ["Automatic derivation of many-body theories based on general Fermi vacua.. This paper describes Wick&d, an implementation of the algebra of second-quantized operators normal ordered with respect to general correlated references and the corresponding Wick theorem [D. Mukherjee, Chem. Phys. Lett. 274, 561 (1997) and W. Kutzelnigg and D. Mukherjee, J. Chem. Phys. 107, 432 (1997)]. Wick&d employs a compact representation of operators and a backtracking algorithm to efficiently evaluate Wick contractions. Since Wick&d can handle both fully and partially contracted terms, it can be applied to both projective and Fock-space many-body formalisms. To demonstrate the usefulness of Wick&d, we use it to evaluate the single-reference coupled cluster equations up to octuple excitations and report an automated derivation and implementation of the second-order driven similarity renormalization group multireference perturbation theory."], "field": "Mathematics", "q_year": 2024, "q_cid": "271874446", "pos_cid": 248506099, "source": "train_step3"}
{"query_id": "scaleup_27206059_14513473", "query": "How to understand students’ creative thought processes during non-routine mathematical problem-solving", "pos": ["The Use of Think-aloud Methods in Qualitative Research An Introduction to Think-aloud Methods. Think-aloud is a research method in which participants speak aloud any words in their mind as they complete a task. A review of the literature has shown that think-aloud research methods have a sound theoretical basis and provide a valid source of data about participant thinking, especially during language based activities. However, a researcher needs to design a process which takes into account a number of concerns, by selecting a suitable task, a role for the researcher, a source of triangulation, and, most importantly, an appropriate method of interpretation. This paper argues that think-aloud research can be effectively interpreted through a qualitative lens. A qualitative approach also has implications for the choice of participant(s) and the treatment of the data. Participants should be treated as quasi-researchers, and their efforts rewarded with reciprocity."], "field": "Mathematics", "q_year": 2024, "q_cid": "272060597", "pos_cid": 145134734, "source": "train_step3"}
{"query_id": "scaleup_23223417_21016448", "query": "How to calibrate epidemic models to observed data without assuming they faithfully represent actual epidemic dynamics", "pos": ["Considering discrepancy when calibrating a mechanistic electrophysiology model. Uncertainty quantification (UQ) is a vital step in using mathematical models and simulations to take decisions. The field of cardiac simulation has begun to explore and adopt UQ methods to characterize uncertainty in model inputs and how that propagates through to outputs or predictions; examples of this can be seen in the papers of this issue. In this review and perspective piece, we draw attention to an important and under-addressed source of uncertainty in our predictions—that of uncertainty in the model structure or the equations themselves. The difference between imperfect models and reality is termed model discrepancy, and we are often uncertain as to the size and consequences of this discrepancy. Here, we provide two examples of the consequences of discrepancy when calibrating models at the ion channel and action potential scales. Furthermore, we attempt to account for this discrepancy when calibrating and validating an ion channel model using different methods, based on modelling the discrepancy using Gaussian processes and autoregressive-moving-average models, then highlight the advantages and shortcomings of each approach. Finally, suggestions and lines of enquiry for future work are provided. This article is part of the theme issue ‘Uncertainty quantification in cardiac and cardiovascular modelling and simulation’."], "field": "Mathematics", "q_year": 2021, "q_cid": "232234173", "pos_cid": 210164483, "source": "train_step3"}
{"query_id": "scaleup_24513101_19020079", "query": "How to determine whether bounded potential slopes force uniform geometric regularity for uniformly scaling, one-dimension-lower measures when coefficient continuity weakens from power-law control to summable average variation", "pos": ["On the uniform rectifiability of AD-regular measures with bounded Riesz transform operator: the case of codimension 1. We prove that if μ is a d-dimensional Ahlfors-David regular measure in $${\\mathbb{R}^{d+1}}$$Rd+1 , then the boundedness of the d-dimensional Riesz transform in L2(μ) implies that the non-BAUP David–Semmes cells form a Carleson family. Combined with earlier results of David and Semmes, this yields the uniform rectifiability of μ."], "field": "Mathematics", "q_year": 2021, "q_cid": "245131017", "pos_cid": 19020079, "source": "train_step3"}
{"query_id": "scaleup_22101836_22171675", "query": "How to determine whether number judgments are independent of apparent area when apparent area differs from mathematical area", "pos": ["Judgments of spatial extent are fundamentally illusory: 'Additive-area' provides the best explanation.. How do we represent extent in our spatial world? Recent work has shown that even the simplest spatial judgments - estimates of 2D area - present challenges to our visual system. Indeed, area judgments are best accounted for by 'additive area' (the sum of objects' dimensions) rather than 'true area' (i.e., a pixel count). But is 'additive area' itself the right explanation - or might other models better explain the results? Here, we offer two direct and novel demonstrations that 'additive area' explains area judgments. First, using stimuli that are simultaneously equated for number and all other confounding dimensions, we show that area judgments are nevertheless explained by 'additive area'. Next, we show how 'scaling' models of area fail to explain even basic illusions of area. By contrasting squares with diamonds (i.e., the same squares, but rotated), we show a robust tendency to perceive the diamonds as having more area - an effect that no other model of area perception would predict. These results not only confirm the fundamental role of 'additive area' in judgments of spatial extent, but they highlight the importance of accounting for this dimension in studies of other features (e.g., density, number) in visual perception."], "field": "Mathematics", "q_year": 2020, "q_cid": "221018361", "pos_cid": 221716759, "source": "train_step3"}
{"query_id": "scaleup_27828136_21998151", "query": "How to reliably assess and improve survival model calibration without underestimating calibration error or substantially reducing predictive accuracy", "pos": ["Calibration of Neural Networks using Splines. Calibrating neural networks is of utmost importance when employing them in safety-critical applications where the downstream decision making depends on the predicted probabilities. Measuring calibration error amounts to comparing two empirical distributions. In this work, we introduce a binning-free calibration measure inspired by the classical Kolmogorov-Smirnov (KS) statistical test in which the main idea is to compare the respective cumulative probability distributions. From this, by approximating the empirical cumulative distribution using a differentiable function via splines, we obtain a recalibration function, which maps the network outputs to actual (calibrated) class assignment probabilities. The spine-fitting is performed using a held-out calibration set and the obtained recalibration function is evaluated on an unseen test set. We tested our method against existing calibration approaches on various image classification datasets and our spline-based recalibration approach consistently outperforms existing methods on KS error as well as other commonly used calibration measures."], "field": "Mathematics", "q_year": 2025, "q_cid": "278281365", "pos_cid": 219981518, "source": "train_step3"}
{"query_id": "scaleup_13052737_15124064", "query": "How to suppress harmful liver inflammation and allow liver regeneration", "pos": ["Macrophage Polarization in Inflammatory Diseases. Diversity and plasticity are two hallmarks of macrophages. M1 macrophages (classically activated macrophages) are pro-inflammatory and have a central role in host defense against infection, while M2 macrophages (alternatively activated macrophages) are associated with responses to anti-inflammatory reactions and tissue remodeling, and they represent two terminals of the full spectrum of macrophage activation. Transformation of different phenotypes of macrophages regulates the initiation, development, and cessation of inflammatory diseases. Here we reviewed the characters and functions of macrophage polarization in infection, atherosclerosis, obesity, tumor, asthma, and sepsis, and proposed that targeting macrophage polarization and skewing their phenotype to adapt to the microenvironment might hold great promise for the treatment of inflammatory diseases."], "field": "Medicine", "q_year": 2017, "q_cid": "13052737", "pos_cid": 15124064, "source": "eval20x26"}
{"query_id": "scaleup_1305031_1212143", "query": "How to determine how a region that is unstructured in isolation interacts with its target to prevent another molecule from binding", "pos": ["SOCS3 binds specific receptor–JAK complexes to control cytokine signaling by direct kinase inhibition. The inhibitory protein SOCS3 plays a key part in the immune and hematopoietic systems by regulating signaling induced by specific cytokines. SOCS3 functions by inhibiting the catalytic activity of Janus kinases (JAKs) that initiate signaling within the cell. We determined the crystal structure of a ternary complex between mouse SOCS3, JAK2 (kinase domain) and a fragment of the interleukin-6 receptor β-chain. The structure shows that SOCS3 binds JAK2 and receptor simultaneously, using two opposing surfaces. While the phosphotyrosine-binding groove on the SOCS3 SH2 domain is occupied by receptor, JAK2 binds in a phosphoindependent manner to a noncanonical surface. The kinase-inhibitory region of SOCS3 occludes the substrate-binding groove on JAK2, and biochemical studies show that it blocks substrate association. These studies reveal that SOCS3 targets specific JAK–cytokine receptor pairs and explains the mechanism and specificity of SOCS action."], "field": "Medicine", "q_year": 2017, "q_cid": "1305031", "pos_cid": 1212143, "source": "eval20x26"}
{"query_id": "scaleup_3765127_12953725", "query": "How to resolve the uncertain identity of human endometrial epithelial and stromal side population cells", "pos": ["Profiling of differentially expressed genes in human stem cells by cDNA microarray.. Stem cells are unique cell populations with the ability to undergo both self-renewal and differentiation, although a wide variety of adult stem cells as well as embryonic stem cells have been identified and stem cell plasticity has recently been reported. To identify genes implicated in the control of the stem cell state as well as the characteristics of each stem cell line, we analyzed the expression profiles of genes in human embryonic, hematopoietic (CD34+ and CD133+), and mesenchymal stem cells using cDNA microarrays, and identified genes that were differentially expressed in specific stem cell populations. In particular we were able to identify potential hESC signature-like genes that encode transcription factors (TFAP2C and MYCN), an RNA binding protein (IMP-3), and a functionally uncharacterized protein (MAGEA4). The overlapping sets of 22 up-regulated and 141 down-regulated genes identified in this study of three human stem cell types may also provide insight into the developmental mechanisms common to all human stem cells. Furthermore, our comprehensive analyses of gene expression profiles in various adult stem cells may help to identify the genetic pathways involved in self-renewal as well as in multi-lineage specific differentiation."], "field": "Medicine", "q_year": 2010, "q_cid": "3765127", "pos_cid": 12953725, "source": "eval20x26"}
{"query_id": "scaleup_3470674_31845893", "query": "How to determine how differences in STAT5 expression or activation, including recurrent mutations, affect cellular sensitivity to STAT5 inhibition", "pos": ["Activating mutations of STAT5B and STAT3 in lymphomas derived from γδ-T or NK cells. Lymphomas arising from NK or γδ-T cells are very aggressive diseases and little is known regarding their pathogenesis. Here we report frequent activating mutations of STAT3 and STAT5B in NK/T-cell lymphomas (n=51), γδ-T-cell lymphomas (n=43) and their cell lines (n=9) through next generation and/or Sanger sequencing. STAT5B N642H is particularly frequent in all forms of γδ-T-cell lymphomas. STAT3 and STAT5B mutations are associated with increased phosphorylated protein and a growth advantage to transduced cell lines or normal NK cells. Growth-promoting activity of the mutants can be partially inhibited by a JAK1/2 inhibitor. Molecular modelling and surface plasmon resonance measurements of the N642H mutant indicate a marked increase in binding affinity of the phosphotyrosine-Y699 with the mutant histidine. This is associated with the prolonged persistence of the mutant phosphoSTAT5B and marked increase of binding to target sites. Our findings suggest that JAK-STAT pathway inhibition may represent a therapeutic strategy. NK-cell and γδ-T cell lymphoma share clinic-pathological features; however the driving mutations are largely unknown. Here the authors, using a combination of RNA-Seq analysis, targeted re-sequencing and functional analysis, identify frequent activating mutations in STAT3 and STAT5Bthat may be driver mutations in these diseases."], "field": "Medicine", "q_year": 2018, "q_cid": "3470674", "pos_cid": 31845893, "source": "eval20x26"}
{"query_id": "scaleup_20822924_4545918", "query": "How to reliably determine the number of protein molecules represented in filtered data when protein amounts are very small", "pos": ["The efficacy and further functional advantages of random-base molecular barcodes for absolute and digital quantification of nucleic acid molecules. Accurate quantification of biomolecules in system-wide measurements is in high demand, especially for systems with limited sample amounts such as single cells. Because of this, digital quantification of nucleic acid molecules using molecular barcodes has been developed, making, e.g., transcriptome analysis highly reproducible and quantitative. This counting scheme was shown to work using sequence-restricted barcodes, and non-sequence-restricted (random-base) barcodes that may provide a much higher dynamic range at significantly lower cost have been widely used. However, the efficacy of random-base barcodes is significantly affected by base changes due to amplification and/or sequencing errors and has not been investigated experimentally or quantitatively. Here, we show experimentally that random-base barcodes enable absolute and digital quantification of DNA molecules with high dynamic range (from one to more than 104, potentially up to 1015 molecules) conditional on our barcode design and variety, a certain range of sequencing depths, and computational analyses. Moreover, we quantitatively show further functional advantages of the molecular barcodes: the molecular barcodes enable one to find contaminants and misidentifications of target sequences. Our scheme here may be generally used to confirm that the digital quantification works in each platform."], "field": "Medicine", "q_year": 2019, "q_cid": "208229241", "pos_cid": 4545918, "source": "eval20x26"}
{"query_id": "scaleup_11994599_7256297", "query": "How to determine whether one factor directly controls another’s production and which associated elements support that control", "pos": ["Mastermind mediates chromatin-specific transcription and turnover of the Notch enhancer complex.. Signaling through the Notch pathway activates the proteolytic release of the Notch intracellular domain (ICD), a dedicated transcriptional coactivator of CSL enhancer-binding proteins. Here we show that chromatin-dependent transactivation by the recombinant Notch ICD-CBF1 enhancer complex in vitro requires an additional coactivator, Mastermind (MAM). MAM provides two activation domains necessary for Notch signaling in mammalian cells and in Xenopus embryos. We show that the central MAM activation domain (TAD1) recruits CBP/p300 to promote nucleosome acetylation at Notch enhancers and activate transcription in vitro. We also find that MAM expression induces phosphorylation and relocalization of endogenous CBP/p300 proteins to nuclear foci in vivo. Moreover, we show that coexpression with MAM and CBF1 strongly enhances phosphorylation and proteolytic turnover of the Notch ICD in vivo. Enhanced phosphorylation of the ICD and p300 requires a glutamine-rich region of MAM (TAD2) that is essential for Notch transcription in vivo. Thus MAM may function as a timer to couple transcription activation with disassembly of the Notch enhancer complex on chromatin."], "field": "Medicine", "q_year": 2017, "q_cid": "11994599", "pos_cid": 7256297, "source": "eval20x26"}
{"query_id": "scaleup_13689796_15701711", "query": "How to understand the origins of solitary fibrous tumors and develop effective treatments for advanced disease resistant to chemotherapy", "pos": ["Aldehyde Dehydrogenase 1, a Potential Marker for Cancer Stem Cells in Human Sarcoma. Tumors contain a small population of cancer stem cells (CSC) proposed to be responsible for tumor maintenance and relapse. Aldehyde dehydrogenase 1 (ALDH1) activity has been used as a functional stem cell marker to isolate CSCs in different cancer types. This study used the Aldefluor® assay and fluorescence-activated cell sorting (FACS) analysis to isolate ALDH1high cells from five human sarcoma cell lines and one primary chordoma cell line. ALDH1high cells range from 0.3% (MUG-Chor1) to 4.1% (SW-1353) of gated cells. Immunohistochemical staining, analysis of the clone formation efficiency, and xCELLigence microelectronic sensor technology revealed that ALDH1high cells from all sarcoma cell lines have an increased proliferation rate compared to ALDH1low cells. By investigating of important regulators of stem cell biology, real-time RT-PCR data showed an increased expression of c-Myc, β-catenin, and SOX-2 in the ALDH1high population and a significant higher level of ABCG2. Statistical analysis of data demonstrated that ALDH1high cells of SW-982 and SW-1353 showed higher resistance to commonly used chemotherapeutic agents like doxorubicin, epirubicin, and cisplatin than ALDH1low cells. This study demonstrates that in different sarcoma cell lines, high ALDH1 activity can be used to identify a subpopulation of cells characterized by a significantly higher proliferation rate, increased colony forming, increased expression of ABC transporter genes and stemness markers compared to control cells. In addition, enhanced drug resistance was demonstrated."], "field": "Medicine", "q_year": 2013, "q_cid": "13689796", "pos_cid": 15701711, "source": "eval20x26"}
{"query_id": "scaleup_11994599_4460649", "query": "How to determine rapamycin’s effects on quiescent neural stem-like cells in angiomyolipomas when lack of proliferation alone cannot distinguish different states of quiescence", "pos": ["mTORC1 controls the adaptive transition of quiescent stem cells from G0 to GAlert. A unique property of many adult stem cells is their ability to exist in a non-cycling, quiescent state. Although quiescence serves an essential role in preserving stem cell function until the stem cell is needed in tissue homeostasis or repair, defects in quiescence can lead to an impairment in tissue function. The extent to which stem cells can regulate quiescence is unknown. Here we show that the stem cell quiescent state is composed of two distinct functional phases, G0 and an ‘alert’ phase we term GAlert. Stem cells actively and reversibly transition between these phases in response to injury-induced systemic signals. Using genetic mouse models specific to muscle stem cells (or satellite cells), we show that mTORC1 activity is necessary and sufficient for the transition of satellite cells from G0 into GAlert and that signalling through the HGF receptor cMet is also necessary. We also identify G0-to-GAlert transitions in several populations of quiescent stem cells. Quiescent stem cells that transition into GAlert possess enhanced tissue regenerative function. We propose that the transition of quiescent stem cells into GAlert functions as an ‘alerting’ mechanism, an adaptive response that positions stem cells to respond rapidly under conditions of injury and stress, priming them for cell cycle entry."], "field": "Medicine", "q_year": 2017, "q_cid": "11994599", "pos_cid": 4460649, "source": "eval20x26"}
{"query_id": "scaleup_1305031_25519190", "query": "How to clarify the negative feedback limiting IRS1- and IRS2-mediated insulin signaling and their tyrosine phosphorylation-dependent binding interactions", "pos": ["Altered Glucose Homeostasis in Mice with Liver-specific Deletion of Src Homology Phosphatase 2*. The Src homology 2 domain-containing protein-tyrosine phosphatase Shp2 has been implicated in a variety of growth factor signaling pathways, but its role in insulin signaling has remained unresolved. In vitro studies suggest that Shp2 is both a negative and positive regulator of insulin signaling, although its physiological function in a number of peripheral insulin-responsive tissues remains unknown. To address the metabolic role of Shp2 in the liver, we generated mice with either chronic or acute hepatic Shp2 deletion using tissue-specific Cre-LoxP and adenoviral Cre approaches, respectively. We then analyzed insulin sensitivity, glucose tolerance, and insulin signaling in liver-specific Shp2-deficient and control mice. Mice with chronic Shp2 deletion exhibited improved insulin sensitivity and increased glucose tolerance compared with controls. Acute Shp2 deletion yielded comparable results, indicating that the observed metabolic effects are directly caused by the lack of Shp2 in the liver. These findings correlated with, and were most likely caused by, direct dephosphorylation of insulin receptor substrate (IRS)1/2 in the liver, accompanied by increased PI3K/Akt signaling. In contrast, insulin-induced ERK activation was dramatically attenuated, yet there was no effect on the putative ERK site on IRS1 (Ser612) or on S6 kinase 1 activity. These studies show that Shp2 is a negative regulator of hepatic insulin action, and its deletion enhances the activation of PI3K/Akt pathway downstream of the insulin receptor."], "field": "Medicine", "q_year": 2017, "q_cid": "1305031", "pos_cid": 25519190, "source": "eval20x26"}
{"query_id": "scaleup_24809915_75885524", "query": "How to distinguish activity of muscles beside the breastbone from nearby chest muscle contributions in surface recordings during breathing under load", "pos": ["Electromyographic study on the sternocleidomastoid and pectoralis major muscles during respiratory activity in humans. Introduction: This study aimed to evaluate the simultaneous and maximum activities ofthe sternocleidomastoid (SCM) and pectoralis major (PM) muscles, to determine how the two types of breathing patterns (normal and forced) can affect these activities , and to verify which of these muscles could be used to establish an evaluation protocol for patients undergoing mechanical ventilation. Methods: Eleven healthy men, aged 18 to 25 years, participated in this study. The individuals remained in supine position using a respiratory belt to monitor both inspiratory and expiratory phase during shifts in the rib cage, performing three repetitions for the normal and forced respiratory movements, while keeping the breathing rhythm with a standard metronome. Electromyographic signals were captured using bipolar surface electrodes placed on the lower third of the SCM muscle and on the lower PM muscle fibers. Electromyographic signals were analyzed and the root mean square (RMS) values were calculated for a complete respiratory cycle. The EMG values were analyzed using the Bonferroni test for multiple comparisons. The homogeneity of variances was verified using the logarithmic transformation (LOG). The level of statistical significance was set at 5% (SPSS 19.0). Results: The values showed that there are signiicant differences between the EMG values of the SCM muscle during normal and forced respiration and the EMG values of the ECM and PM muscles during forced respiration. Conclusion: These results showed that the SCM muscle can be an indicator for the development of parameters to be used in the analysis of patients with respiratory failure."], "field": "Medicine", "q_year": 2022, "q_cid": "248099156", "pos_cid": 75885524, "source": "eval_collection"}
{"query_id": "scaleup_26125599_18709752", "query": "How to identify brain-enriched proteins detectable in cerebrospinal fluid as candidate biomarkers of long-term progression in multiple sclerosis", "pos": ["Identification of brain-enriched proteins in the cerebrospinal fluid proteome by LC-MS/MS profiling and mining of the Human Protein Atlas. Cerebrospinal fluid (CSF) is a proximal fluid which communicates closely with brain tissue, contains numerous brain-derived proteins and thus represents a promising fluid for discovery of biomarkers of central nervous system (CNS) diseases. The main purpose of this study was to generate an extensive CSF proteome and define brain-related proteins identified in CSF, suitable for development of diagnostic assays. Six non-pathological CSF samples from three female and three male individuals were selected for CSF analysis. Samples were first subjected to strong cation exchange chromatography, followed by LC-MS/MS analysis. Secreted and membrane-bound proteins enriched in the brain tissues were retrieved from the Human Protein Atlas. In total, 2615 proteins were identified in the CSF. The number of proteins identified per individual sample ranged from 1109 to 1421, with inter-individual variability between six samples of 21 %. Based on the Human Protein Atlas, 78 brain-specific proteins found in CSF samples were proposed as a signature of brain-enriched proteins in CSF. A combination of Human Protein Atlas database and experimental search of proteins in specific body fluid can be applied as an initial step in search for disease biomarkers specific for a particular tissue. This signature may be of significant interest for development of novel diagnostics of CNS diseases and identification of drug targets."], "field": "Medicine", "q_year": 2023, "q_cid": "261255999", "pos_cid": 18709752, "source": "eval_collection"}
{"query_id": "scaleup_26001626_25250995", "query": "How to quantitatively distinguish joint-motion patterns in rats with spinal cord injury to assess movement disturbances and the quality of therapeutic interventions", "pos": ["The Automatization of the Gait Analysis by the Vicon Video System: A Pilot Study. The quality of modern measuring instruments has a strong influence on the speed of diagnosing diseases of the human musculoskeletal system. The research is focused on automatization of the method of gait analysis. The study involved six healthy subjects. The subjects walk straight. Each subject made several gait types: casual walking and imitation of a non-standard gait, including shuffling, lameness, clubfoot, walking from the heel, rolling from heel to toe, walking with hands in pockets, and catwalk. Each type of gait was recorded three times. For video fixation, the Vicon Nexus system was used. A total of 27 reflective markers were placed on the special anatomical regions. The goniometry methods were used. The walk data were divided by steps and by step phases. Kinematic parameters for estimation were formulated and calculated. An approach for data clusterization is presented. For this purpose, angle data were interpolated and the interpolation coefficients were used for clustering the data. The data were processed and four cluster groups were found. Typical angulograms for cluster groups were presented. For each group, average angles were calculated. A statistically significant difference was found between received cluster groups."], "field": "Medicine", "q_year": 2023, "q_cid": "260016268", "pos_cid": 252509959, "source": "eval_collection"}
{"query_id": "scaleup_24797536_9495669", "query": "How to improve overall survival in patients already receiving treatment", "pos": ["A phase I/II trial of hydroxychloroquine in conjunction with radiation therapy and concurrent and adjuvant temozolomide in patients with newly diagnosed glioblastoma multiforme. Preclinical studies indicate autophagy inhibition with hydroxychloroquine (HCQ) can augment the efficacy of DNA-damaging therapy. The primary objective of this trial was to determine the maximum tolerated dose (MTD) and efficacy of HCQ in combination with radiation therapy (RT) and temozolomide (TMZ) for newly diagnosed glioblastoma (GB). A 3 + 3 phase I trial design followed by a noncomparative phase II study was conducted in GB patients after initial resection. Patients received HCQ (200 to 800 mg oral daily) with RT and concurrent and adjuvant TMZ. Quantitative electron microscopy and immunoblotting were used to assess changes in autophagic vacuoles (AVs) in peripheral blood mononuclear cells (PBMC). Population pharmacokinetic (PK) modeling enabled PK-pharmacodynamic correlations. Sixteen phase I subjects were evaluable for dose-limiting toxicities. At 800 mg HCQ/d, 3/3 subjects experienced Grade 3 and 4 neutropenia and thrombocytopenia, 1 with sepsis. HCQ 600 mg/d was found to be the MTD in this combination. The phase II cohort (n = 76) had a median survival of 15.6 mos with survival rates at 12, 18, and 24 mo of 70%, 36%, and 25%. PK analysis indicated dose-proportional exposure for HCQ. Significant therapy-associated increases in AV and LC3-II were observed in PBMC and correlated with higher HCQ exposure. These data establish that autophagy inhibition is achievable with HCQ, but dose-limiting toxicity prevented escalation to higher doses of HCQ. At HCQ 600 mg/d, autophagy inhibition was not consistently achieved in patients treated with this regimen, and no significant improvement in overall survival was observed. Therefore, a definitive test of the role of autophagy inhibition in the adjuvant setting for glioma patients awaits the development of lower-toxicity compounds that can achieve more consistent inhibition of autophagy than HCQ."], "field": "Medicine", "q_year": 2022, "q_cid": "247975361", "pos_cid": 9495669, "source": "eval_collection"}
{"query_id": "scaleup_27754902_22135733", "query": "How to determine whether a drug’s effects depend specifically on a particular modification rather than other actions of the drug", "pos": ["Lysine-222 succinylation reduces lysosomal degradation of lactate dehydrogenase a and is increased in gastric cancer. Background Lysine succinylation is an emerging posttranslational modification that has garnered increased attention recently, but its role in gastric cancer (GC) remains underexplored. Methods Proteomic quantification of lysine succinylation was performed in human GC tissues and adjacent normal tissues by mass spectrometry. The mRNA and protein levels of lactate dehydrogenase A (LDHA) in GC and adjacent normal tissues were analyzed by qRT-PCR and western blot, respectively. The expression of K222-succinylated LDHA was measured in GC tissue microarray by the K222 succinylation-specific antibody. The interaction between LDHA and sequestosome 1 (SQSTM1) was measured by co-immunoprecipitation (co-IP) and proximity ligation assay (PLA). The binding of carnitine palmitoyltransferase 1A (CPT1A) to LDHA was determined by co-IP. The effect of K222-succinylated LDHA on tumor growth and metastasis was evaluated by in vitro and in vivo experiments. Results Altogether, 503 lysine succinylation sites in 303 proteins were identified. Lactate dehydrogenase A (LDHA), the key enzyme in Warburg effect, was found highly succinylated at K222 in GC. Intriguingly, this modification did not affect LDHA ubiquitination, but reduced the binding of ubiquitinated LDHA to SQSTM1, thereby decreasing its lysosomal degradation. We demonstrated that CPT1A functions as a lysine succinyltransferase that interacts with and succinylates LDHA. Moreover, high K222-succinylation of LDHA was associated with poor prognosis in patients with GC. Finally, overexpression of a succinylation-mimic mutant of LDHA promoted cell proliferation, invasion, and migration. Conclusions Our data revealed a novel lysosomal pathway of LDHA degradation, which is mediated by the binding of K63-ubiquitinated LDHA to SQSTM1. Strikingly, CPT1A succinylates LDHA on K222, which thereby reduces the binding and inhibits the degradation of LDHA, as well as promotes GC invasion and proliferation. This study thus uncovers a new role of lysine succinylation and the mechanism underlying LDHA upregulation in GC."], "field": "Medicine", "q_year": 2025, "q_cid": "277549023", "pos_cid": 221357334, "source": "eval_collection"}
{"query_id": "scaleup_24794801_23238712", "query": "How to assess the overall frequency of myocarditis in athletes recovering from COVID-19", "pos": ["The PRISMA 2020 statement: an updated guideline for reporting systematic reviews. The Preferred Reporting Items for Systematic reviews and Meta-Analyses (PRISMA) statement, published in 2009, was designed to help systematic reviewers transparently report why the review was done, what the authors did, and what they found. Over the past decade, advances in systematic review methodology and terminology have necessitated an update to the guideline. The PRISMA 2020 statement replaces the 2009 statement and includes new reporting guidance that reflects advances in methods to identify, select, appraise, and synthesise studies. The structure and presentation of the items have been modified to facilitate implementation. In this article, we present the PRISMA 2020 27-item checklist, an expanded checklist that details reporting recommendations for each item, the PRISMA 2020 abstract checklist, and the revised flow diagrams for original and updated reviews."], "field": "Medicine", "q_year": 2022, "q_cid": "247948015", "pos_cid": 232387120, "source": "eval_collection"}
{"query_id": "scaleup_28152115_49386945", "query": "How to identify shared injury and illness prevention priorities at key points in an athlete’s season", "pos": ["The impact of sport related stressors on immunity and illness risk in team-sport athletes.. OBJECTIVES Elite team-sport athletes are frequently exposed to stressors that have the potential to depress immunity and increase infection risk. Therefore, the purpose of this review is to describe how team-sport stressors impact upon immune responses, along with exploring whether alterations in these markers have the potential to predict upper respiratory tract illness symptoms. DESIGN Narrative review. METHODS Salivary secretory immunoglobulin A (SIgA) and T-cell markers have been shown to predict infection risk in individual endurance athletes. Papers discussing the impact of team-sport stressors on SIgA and T-cells were discussed in the review, studies discussing other aspects of immunity were excluded. Journal articles were sourced from PubMed, Web of science and Scopus. Key search terms included team-sport athletes, stressors, immunity, T-cells, cytokines, SIgA and upper respiratory illness. RESULTS Most team-sport stressors appear to increase risk for illness. An association between reduced SIgA and increased illness incidence has been demonstrated. Intensive training and competition periods have been shown to reduce SIgA, however, it is less clear how additional stressors including extreme environmental conditions, travel, psychological stress, sleep disturbance and poor nutrition affect immune responses. CONCLUSIONS Monitoring SIgA may provide an assessment of a team-sport athletes risk status for developing upper respiratory tract symptoms, however there is currently not enough evidence to suggest SIgA alone can predict illness. Team-sport stressors challenge immunity and it is possible that the combination of stressors could have a compounding effect on immunodepression and infection risk. Given that illness can disrupt training and performance, further research is required to better elucidate how stressors individually and collectively influence immunity and illness."], "field": "Medicine", "q_year": 2025, "q_cid": "281521155", "pos_cid": 49386945, "source": "eval_collection"}
{"query_id": "scaleup_28264635_25032978", "query": "How to improve oral vaccination against E. multilocularis to activate mucosal immune responses and prevent and control infection", "pos": ["Oral Immunization With a M Cell-Targeting Recombinant L. Lactis Vaccine LL-plSAM-FVpE Stimulate Protective Immunity Against H. Pylori in Mice. There are many virulence factors of H. pylori that contribute in diverse ways to gastric disease. Therefore, designing multivalent epitope vaccines against many key virulence factors virulence factors of H. pylori is a promising strategy to control H. pylori infection. In previous studies, we constructed a multivalent epitope vaccine FVpE against four key virulence factors of H. pylori (Urease, CagA, VacA, and NAP), and oral immunization with the FVpE vaccine plus a polysaccharide adjuvant (PA) containing lycium barbarum polysaccharide and chitosan could provide protection against H. pylori infection in the Mongolian gerbil model. Oral vaccines have many advantages over injected vaccines, such as improved safety and compliance, and easier manufacturing and administration. However, the harsh gastrointestinal (GI) environment, such as gastric acid and proteolytic enzymes, limits the development of oral vaccines to some extent. Oral vaccines need a gastrointestinal delivery system with high safety, low price and promoting vaccine antigen to stimulate immune response in the gastrointestinal mucosa. Lactic acid bacteria are gastrointestinal probiotics that have unique advantages as a delivery system for oral vaccines. In this study, a M cell-targeting surface display system for L. lactis named plSAM was designed to help vaccine antigens to stimulate effective immune responses in the gastrointestinal tract, and a M cell-targeting recombinant L. lactis vaccine LL-plSAM-FVpE was constructed by using the surface display system plSAM. recombinant L. lactis vaccine LL-plSAM-FVpE could secretively express the SAM-FVpE protein and display it on the bacterial surface. Moreover, experimental results confirmed that LL-plSAM-FVpE had an enhanced M cell-targeting property. In addition, LL-plSAM-FVpE had excellent M cell-targeting property to promote the phagocytosis and transport of the antigen SAM-FVpE by gastrointestinal M cells. More importantly, oral immunization of LL-plSAM-FVpE or SAM-FVpE plus PA can stimulate IgG and sIgA antibodies and CD4+ T cell immune responses against four virulence factors of H. pylori (Urease, CagA, VacA, and NAP), thus providing protective immunity against H. pylori infection in mice. The M cell-targeting recombinant L. lactis vaccine against various key H. pylori virulence factors could be a promising vaccine candidate for controlling H. pylori infection."], "field": "Medicine", "q_year": 2025, "q_cid": "282646359", "pos_cid": 250329783, "source": "eval_collection"}
{"query_id": "scaleup_23222389_3447774", "query": "how to suppress cytochrome c oxidase activity and limit injury-associated mitochondrial membrane hyperpolarization and excessive reactive oxygen species generation", "pos": ["Inhibitory modulation of cytochrome c oxidase activity with specific near-infrared light wavelengths attenuates brain ischemia/reperfusion injury. The interaction of light with biological tissue has been successfully utilized for multiple therapeutic purposes. Previous studies have suggested that near infrared light (NIR) enhances the activity of mitochondria by increasing cytochrome c oxidase (COX) activity, which we confirmed for 810 nm NIR. In contrast, scanning the NIR spectrum between 700 nm and 1000 nm revealed two NIR wavelengths (750 nm and 950 nm) that reduced the activity of isolated COX. COX-inhibitory wavelengths reduced mitochondrial respiration, reduced the mitochondrial membrane potential (ΔΨm), attenuated mitochondrial superoxide production, and attenuated neuronal death following oxygen glucose deprivation, whereas NIR that activates COX provided no benefit. We evaluated COX-inhibitory NIR as a potential therapy for cerebral reperfusion injury using a rat model of global brain ischemia. Untreated animals demonstrated an 86% loss of neurons in the CA1 hippocampus post-reperfusion whereas inhibitory NIR groups were robustly protected, with neuronal loss ranging from 11% to 35%. Moreover, neurologic function, assessed by radial arm maze performance, was preserved at control levels in rats treated with a combination of both COX-inhibitory NIR wavelengths. Taken together, our data suggest that COX-inhibitory NIR may be a viable non-pharmacologic and noninvasive therapy for the treatment of cerebral reperfusion injury."], "field": "Medicine", "q_year": 2021, "q_cid": "232223895", "pos_cid": 3447774, "source": "eval_collection"}
{"query_id": "scaleup_28310620_25619212", "query": "How to understand the breadth of autoantibody targets in acute rheumatic fever, why these responses differ between patients, and how autoreactivity relates to the disease’s diverse clinical manifestations", "pos": ["Human antibody profiling technologies for autoimmune disease. Autoimmune diseases are caused by the break-down in self-tolerance mechanisms and can result in the generation of autoantibodies specific to human antigens. Human autoantigen profiling technologies such as solid surface arrays and display technologies are powerful high-throughput technologies utilised to discover and map novel autoantigens associated with disease. This review compares human autoantigen profiling technologies including the application of these approaches in chronic and post-infectious autoimmune disease. Each technology has advantages and limitations that should be considered when designing new projects to profile autoantibodies. Recent studies that have utilised these technologies across a range of diseases have highlighted marked heterogeneity in autoantibody specificity between individuals as a frequent feature. This individual heterogeneity suggests that epitope spreading maybe an important mechanism in the pathogenesis of autoimmune disease in general and likely contributes to inflammatory tissue damage and symptoms. Studies focused on identifying autoantibody biomarkers for diagnosis should use targeted data analysis to identify the rarer public epitopes and antigens, common between individuals. Thus, utilisation of human autoantigen profiling technology, combined with different analysis approaches, can illuminate both pathogenesis and biomarker discovery."], "field": "Medicine", "q_year": 2025, "q_cid": "283106206", "pos_cid": 256192127, "source": "eval_collection"}
{"query_id": "scaleup_26986284_24785425", "query": "How to clarify the cellular context of disulfidptosis-related gene expression and its relationship to immune regulation in non-alcoholic fatty liver disease single-cell data, including liver cell types and functional differences among mononuclear phagocyte subsets", "pos": ["Single-cell RNA sequencing reveals intrahepatic and peripheral immune characteristics related to disease phases in HBV-infected patients. Objective A comprehensive immune landscape for HBV infection is pivotal to achieve HBV cure. Design We performed single-cell RNA sequencing of 2 43 000 cells from 46 paired liver and blood samples of 23 individuals, including six immune tolerant, 5 immune active (IA), 3 acute recovery (AR), 3 chronic resolved and 6 HBV-free healthy controls (HCs). Flow cytometry and histological assays were applied in a second HBV cohort for validation. Results Both IA and AR were characterised by high levels of intrahepatic exhausted CD8+ T (Tex) cells. In IA, Tex cells were mainly derived from liver-resident GZMK+ effector memory T cells and self-expansion. By contrast, peripheral CX3CR1+ effector T cells and GZMK+ effector memory T cells were the main source of Tex cells in AR. In IA but not AR, significant cell–cell interactions were observed between Tex cells and regulatory CD4+ T cells, as well as between Tex and FCGR3A+ macrophages. Such interactions were potentially mediated through human leukocyte antigen class I molecules together with their receptors CANX and LILRBs, respectively, contributing to the dysfunction of antiviral immune responses. By contrast, CX3CR1+GNLY+ central memory CD8+ T cells were concurrently expanded in both liver and blood of AR, providing a potential surrogate marker for viral resolution. In clinic, intrahepatic Tex cells were positively correlated with serum alanine aminotransferase levels and histological grading scores. Conclusion Our study dissects the coordinated immune responses for different HBV infection phases and provides a rich resource for fully understanding immunopathogenesis and developing effective therapeutic strategies."], "field": "Medicine", "q_year": 2024, "q_cid": "269862849", "pos_cid": 247854251, "source": "eval_collection"}
{"query_id": "scaleup_25107228_49671200", "query": "How to explain kinase regulation of TFEB-dependent Trop-2 expression and kinase inhibitor-associated suppression of Trop-2 in breast cancer cells", "pos": ["A TFEB nuclear export signal integrates amino acid supply and glucose availability. How cells coordinate the response to fluctuating carbon and nitrogen availability required to maintain effective homeostasis is a key issue. Amino acid limitation that inactivates mTORC1 promotes de-phosphorylation and nuclear translocation of Transcription Factor EB (TFEB), a key transcriptional regulator of lysosome biogenesis and autophagy that is deregulated in cancer and neurodegeneration. Beyond its cytoplasmic sequestration, how TFEB phosphorylation regulates its nuclear-cytoplasmic shuttling, and whether TFEB can coordinate amino acid supply with glucose availability is poorly understood. Here we show that TFEB phosphorylation on S142 primes for GSK3β phosphorylation on S138, and that phosphorylation of both sites but not either alone activates a previously unrecognized nuclear export signal (NES). Importantly, GSK3β is inactivated by AKT in response to mTORC2 signaling triggered by glucose limitation. Remarkably therefore, the TFEB NES integrates carbon (glucose) and nitrogen (amino acid) availability by controlling TFEB flux through a nuclear import-export cycle. On amino acid deprivation TFEB translocates from the cytoplasm to the nucleus. Here the authors identify a nuclear export signal in TFEB that requires dual phosphorylation at the S142 ERK/mTORC1 and S138 GSK3β sites, and further show glucose limitation drives nuclear accumulation of TFEB and inhibits GSK3β via an mTORC2-AKT dependent mechanism."], "field": "Medicine", "q_year": 2022, "q_cid": "251072282", "pos_cid": 49671200, "source": "eval_collection"}
{"query_id": "scaleup_27832156_25214357", "query": "How to reliably determine whether iron status affects the likelihood of subarachnoid hemorrhage", "pos": ["Genetic Causal Association between Iron Status and Osteoarthritis: A Two-Sample Mendelian Randomization. Objective: Observational studies have shown the association between iron status and osteoarthritis (OA). However, due to difficulties of determining sequential temporality, their causal association is still elusive. Based on the summary data of genome-wide association studies (GWASs) of a large-scale population, this study explored the genetic causal association between iron status and OA. Methods: First, we took a series of quality control steps to select eligible instrumental SNPs which were strongly associated with exposure. The genetic causal association between iron status and OA was analyzed using the two-sample Mendelian randomization (MR). Inverse-variance weighted (IVW), MR-Egger, weighted median, simple mode, and weighted mode methods were used for analysis. The results were mainly based on IVW (random effects), followed by sensitivity analysis. IVW and MR-Egger were used for heterogeneity testing. MR-Egger was also used for pleiotropy testing. Leave-one-SNP-out analysis was used to identify single nucleotide polymorphisms (SNPs) with potential impact. Maximum likelihood, penalized weighted median, and IVW (fixed effects) were performed to further validate the reliability of results. Results: IVW results showed that transferrin saturation had a positive causal association with knee osteoarthritis (KOA), hip osteoarthritis (HOA) and KOA or HOA (p < 0.05, OR > 1), and there was a negative causal association between transferrin and HOA and KOA or HOA (p < 0.05, OR < 1). The results of heterogeneity test showed that our IVW analysis results were basically free of heterogeneity (p > 0.05). The results of the pleiotropy test showed that there was no pleiotropy in our IVW analysis (p > 0.05). The analysis results of maximum likelihood, penalized weighted median and IVW (fixed effects) were consistent with our IVW results. No genetic causal association was found between serum iron and ferritin and OA. Conclusions: This study provides evidence of the causal association between iron status and OA, which provides novel insights to the genetic research of OA."], "field": "Medicine", "q_year": 2025, "q_cid": "278321560", "pos_cid": 252143574, "source": "eval_collection"}
{"query_id": "scaleup_27643519_58564774", "query": "How to confine sebaceous hyperplasia treatment to very small dermal targets while avoiding incomplete treatment and recurrence", "pos": ["High‐frequency (20‐MHz) high‐intensity focused ultrasound (HIFU) system for dermal intervention: Preclinical evaluation in skin equivalents. High‐intensity focused ultrasound (HIFU) for non‐invasive treatment of a range of internal pathologies including cancers of major organs and cerebral pathologies is in exponential growth. Systems, however, operate at relatively low frequencies, in the range of 200‐2000 kHz as required for deep axial penetration of the body. HIFU utilizing frequencies in excess of 15 MHz has so far not been explored, but presents an opportunity to extend the HIFU modality to target specific dermal lesions and small animal research."], "field": "Medicine", "q_year": 2025, "q_cid": "276435192", "pos_cid": 58564774, "source": "eval_collection"}
{"query_id": "scaleup_28074502_16721133", "query": "How to identify and prevent high-glucose-induced metabolic changes that initiate diabetic embryopathy during early embryogenesis", "pos": ["Activation of the unfolded protein response in high glucose treated endothelial cells is mediated by methylglyoxal. Metabolic dysfunction of endothelial cells in hyperglycemia contributes to the development of vascular complications of diabetes where increased reactive glycating agent, methylglyoxal (MG), is involved. We assessed if increased MG glycation induced proteotoxic stress, identifying related metabolic drivers and protein targets. Human aortal endothelial cells (HAECs) were incubated in high glucose concentration (20 mM versus 5 mM control) in vitro for 3–6 days. Flux of glucose metabolism, MG formation and glycation and changes in cytosolic protein abundances, MG modification and proteotoxic responses were assessed. Similar studies were performed with human microvascular endothelial HMEC-1 cells where similar outcomes were observed. HAECs exposed to high glucose concentration showed increased cellular concentration of MG (2.27 ± 0.21 versus 1.28 ± 0.03 pmol/106 cells, P < 0.01) and formation of MG-modified proteins (24.0 ± 3.7 versus 14.1 ± 3.2 pmol/106 cells/day; P < 0.001). In proteomics analysis, high glucose concentration increased proteins of the heat shock response – indicating activation of the unfolded protein response (UPR) with downstream inflammatory and pro-thrombotic responses. Proteins susceptible to MG modification were enriched in protein folding, protein synthesis, serine/threonine kinase signalling, glycolysis and gluconeogenesis. MG was increased in high glucose by increased flux of MG formation linked to increased glucose metabolism mediated by proteolytic stabilisation and increase of hexokinase-2 (HK-2); later potentiated by proteolytic down regulation of glyoxalase 1 (Glo1) - the major enzyme of MG metabolism. Silencing of Glo1, selectively increasing MG, activated the UPR similarly. Silencing of HK-2 prevented increased glucose metabolism and MG formation. trans-Resveratrol and hesperetin combination (tRES-HESP) corrected increased MG and glucose metabolism by increasing expression of Glo1 and decreasing expression of HK-2. Increased MG glycation activates the UPR in endothelial cells and thereby may contribute to endothelial cell dysfunction in diabetic vascular disease where tRES-HESP may provide effective therapy."], "field": "Medicine", "q_year": 2025, "q_cid": "280745029", "pos_cid": 167211335, "source": "eval_collection"}
{"query_id": "scaleup_28404582_7081101", "query": "How to understand biological changes across COVID-19 disease phases as patients deteriorate or recover", "pos": ["Pathway-GPS and SIGORA: identifying relevant pathways based on the over-representation of their gene-pair signatures. Motivation. Predominant pathway analysis approaches treat pathways as collections of individual genes and consider all pathway members as equally informative. As a result, at times spurious and misleading pathways are inappropriately identified as statistically significant, solely due to components that they share with the more relevant pathways. Results. We introduce the concept of Pathway Gene-Pair Signatures (Pathway-GPS) as pairs of genes that, as a combination, are specific to a single pathway. We devised and implemented a novel approach to pathway analysis, Signature Over-representation Analysis (SIGORA), which focuses on the statistically significant enrichment of Pathway-GPS in a user-specified gene list of interest. In a comparative evaluation of several published datasets, SIGORA outperformed traditional methods by delivering biologically more plausible and relevant results. Availability. An efficient implementation of SIGORA, as an R package with precompiled GPS data for several human and mouse pathway repositories is available for download from http://sigora.googlecode.com/svn/."], "field": "Medicine", "q_year": 2025, "q_cid": "284045826", "pos_cid": 7081101, "source": "eval_collection"}
{"query_id": "scaleup_24809915_19037492", "query": "How to reliably track respiratory muscle signal amplitudes in surface electromyographic and mechanomyographic recordings despite cardiac artifacts for noninvasive assessment of neural respiratory drive", "pos": ["Improvement in Neural Respiratory Drive Estimation From Diaphragm Electromyographic Signals Using Fixed Sample Entropy. Diaphragm electromyography is a valuable technique for the recording of electrical activity of the diaphragm. The analysis of diaphragm electromyographic (EMGdi) signal amplitude is an alternative approach for the quantification of the neural respiratory drive (NRD). The EMGdi signal is, however, corrupted by electrocardiographic (ECG) activity, and this presence of cardiac activity can make the EMGdi interpretation more difficult. Traditionally, the EMGdi amplitude has been estimated using the average rectified value (ARV) and the root mean square (RMS). In this study, surface EMGdi signals were analyzed using the fixed sample entropy (fSampEn) algorithm, and compared to the traditional ARV and RMS methods. The fSampEn is calculated using a tolerance value fixed and independent of the standard deviation of the analysis window. Thus, this method quantifies the amplitude of the complex components of stochastic signals (such as EMGdi), and being less affected by changes in amplitude due to less complex components (such as ECG). The proposed method was tested in synthetic and recorded EMGdi signals. fSampEn was less sensitive to the effect of cardiac activity on EMGdi signals with different levels of NRD than ARV and RMS amplitude parameters. The mean and standard deviation of the Pearson's correlation values between inspiratory mouth pressure (an indirect measure of the respiratory muscle activity) and fSampEn, ARV, and RMS parameters, estimated in the recorded EMGdi signal at tidal volume (without inspiratory load), were 0.38 ± 0.12, 0.27 ± 0.11, and 0.11 ± 0.13, respectively. Whereas at 33 cmH2O (maximum inspiratory load) were 0.83 ± 0.02, 0.76 ± 0.07, and 0.61 ± 0.19, respectively. Our findings suggest that the proposed method may improve the evaluation of NRD."], "field": "Medicine", "q_year": 2022, "q_cid": "248099156", "pos_cid": 19037492, "source": "eval_collection"}
{"query_id": "scaleup_23238244_6781044", "query": "How to determine whether hippocampal inflammation, oxidative stress, and changes in a diet-sensitive inflammatory marker in young animals return to normal after fructose withdrawal", "pos": ["High Fat Diet and Inflammation – Modulation of Haptoglobin Level in Rat Brain. Obesity and dietary fats are well known risk factors for the pathogenesis of neurodegenerative diseases. The analysis of specific markers, whose brain level can be affected by diet, might contribute to unveil the intersection between inflammation/obesity and neurodegeneration. Haptoglobin (Hpt) is an acute phase protein, which acts as antioxidant by binding free haemoglobin (Hb), thus neutralizing its pro-oxidative action. We previously demonstrated that Hpt plays critical functions in brain, modulating cholesterol trafficking in neuroblastoma cell lines, beta-amyloid (Aβ) uptake by astrocyte, and limiting Aβ toxicity on these cells. A major aim of this study was to evaluate whether a long term (12 or 24 weeks) high-fat diet (HFD) influences Hpt and Hb expression in rat hippocampus. We also assessed the development of obesity-induced inflammation by measuring hippocampal level of TNF-alpha, and the extent of protein oxidation by titrating nitro-tyrosine (N-Tyr). Hpt concentration was lower (p < 0.001) in hippocampus of HFD rats than in control animals, both in the 12 and in the 24 weeks fed groups. HFD was also associated in hippocampus with the increase of Hb level (p < 0.01), inflammation and protein oxidative modification, as evidenced by the increase in the concentration of TNF-alpha and nitro-tyrosine. In fact, TNF-alpha concentration was higher in rats receiving HFD for 12 (p < 0.01) or 24 weeks (p < 0.001) compared to those receiving the control diet. N-Tyr concentration was more elevated in hippocampus of HFD than in control rats in both 12 weeks (p = 0.04) and 24 weeks groups (p = 0.01), and a positive correlation between Hb and N-Tyr concentration was found in each group. Finally, we found that the treatment of the human glioblastoma-astrocytoma cell line U-87 MG with cholesterol and fatty acids, such as palmitic and linoleic acid, significantly impairs (p < 0.001) Hpt secretion in the extracellular compartment. We hypothesize that the HFD-dependent decrease of Hpt in hippocampus, as associated with Hb increase, might enhance the oxidative stress induced by free Hb. Altogether our data, identifying Hpt as a molecule modulated in the brain by dietary fats, may represent one of the first steps in the comprehension of the molecular mechanisms underlying the diet-related effects in the nervous system."], "field": "Medicine", "q_year": 2021, "q_cid": "232382444", "pos_cid": 6781044, "source": "eval_collection"}
{"query_id": "scaleup_24750870_15153602", "query": "How to characterize mutations in coexisting SARS-CoV-2 populations within the same sample, distinguish those populations, and assess their relative abundance?", "pos": ["Haplotype-based variant detection from short-read sequencing. The direct detection of haplotypes from short-read DNA sequencing data requires changes to existing small-variant detection methods. Here, we develop a Bayesian statistical framework which is capable of modeling multiallelic loci in sets of individuals with non-uniform copy number. We then describe our implementation of this framework in a haplotype-based variant detector, FreeBayes."], "field": "Medicine", "q_year": 2022, "q_cid": "247508708", "pos_cid": 15153602, "source": "eval_collection"}
{"query_id": "scaleup_27845351_20659388", "query": "How to accurately distinguish intrahepatic cholangiocarcinoma from hepatocellular carcinoma and colorectal liver metastases on computed tomography images", "pos": ["Rethinking the Inception Architecture for Computer Vision. Convolutional networks are at the core of most state of-the-art computer vision solutions for a wide variety of tasks. Since 2014 very deep convolutional networks started to become mainstream, yielding substantial gains in various benchmarks. Although increased model size and computational cost tend to translate to immediate quality gains for most tasks (as long as enough labeled data is provided for training), computational efficiency and low parameter count are still enabling factors for various use cases such as mobile vision and big-data scenarios. Here we are exploring ways to scale up networks in ways that aim at utilizing the added computation as efficiently as possible by suitably factorized convolutions and aggressive regularization. We benchmark our methods on the ILSVRC 2012 classification challenge validation set demonstrate substantial gains over the state of the art: 21:2% top-1 and 5:6% top-5 error for single frame evaluation using a network with a computational cost of 5 billion multiply-adds per inference and with using less than 25 million parameters. With an ensemble of 4 models and multi-crop evaluation, we report 3:5% top-5 error and 17:3% top-1 error on the validation set and 3:6% top-5 error on the official test set."], "field": "Medicine", "q_year": 2025, "q_cid": "278453511", "pos_cid": 206593880, "source": "eval_collection"}
{"query_id": "scaleup_26873869_24652989", "query": "How to determine whether suppressing a specific activity alters the release of a measured substance, with changes attributable to the strength of that suppression rather than other effects", "pos": ["A Selective and Orally Bioavailable Quinoline-6-carbonitrile-based Inhibitor of CDK8/19 Mediator Kinase with Tumor-enriched Pharmacokinetics. The Senexins are potent and selective quinazoline inhibitors of CDK8/19 Mediator kinases. To improve their potency and metabolic stability, quinoline-based derivatives were designed through a structure-guided strategy based on the simulated drug-target docking model of Senexin A and B. A library of quinoline-Senexin derivatives was synthesized to explore the structure-activity relationship. An optimized compound 20a (Senexin C) exhibits potent CDK8/19 inhibitory activity with a high selectivity. Senexin C is more metabolically stable and provides a more sustained inhibition of CDK8/19-dependent cellular gene expression when compared with the prototype inhibitor Senexin B. In vivo pharmacokinetic (PK) and pharmacodynamic (PD) evaluation using a novel tumor-based PD assay showed good oral bioavailability of Senexin C with a strong tumor-enrichment PK profile and tumor-PD marker responses. Senexin C inhibits MV4-11 leukemia growth in a systemic in vivo model with good tolerability."], "field": "Medicine", "q_year": 2024, "q_cid": "268738691", "pos_cid": 246529892, "source": "eval_collection"}
{"query_id": "scaleup_26537918_23062806", "query": "How to remove virus-containing ultrafine particles from indoor air to reduce respiratory virus transmission risk", "pos": ["Coagulation and capture of fine particles in the coupling system of corona discharge and embedded turbulence. Abstract Fine particles with the size below 1 μm are difficult to be captured with the traditional dust removal devices because of their poor charge capacity and filterability. Using the agglomeration pretreatment can realize the fine particles growth, then facilitating the capture process. In this study, a novel system with the combination of corona discharge and embedded turbulence was put forward. The results showed that the device can agglomerate the smaller particles into bigger ones, and the maximum decrease of number concentration for small particles can reach 40% in the bipolar corona discharge condition. The median diameters of fine particles can be improved by 47% maximumly in the condition of arrangement of turbulence bars and loopholes with a lower flow velocity. The simulated calculation and pilot scale test were conducted and the results were consistent with experimental conclusions."], "field": "Medicine", "q_year": 2023, "q_cid": "265379180", "pos_cid": 230628065, "source": "eval_collection"}
{"query_id": "scaleup_23165156_14716313", "query": "How to consistently interpret responses across five dimensions for female childhood cancer survivors and healthy controls and assess how reported conditions relate to participants’ self-assessments", "pos": ["Swedish experience-based value sets for EQ-5D health states. AbstractPurposeTo estimate Swedish experience-based value sets for EQ-5D health states using general population health survey data.MethodsApproximately 45,000 individuals valued their current health status by means of time trade off (TTO) and visual analogue scale (VAS) methods and answered the EQ-5D questionnaire, making it possible to model the association between the experience-based TTO and VAS values and the EQ-5D dimensions and severity levels. The association between TTO and VAS values and the different severity levels of respondents’ answers on a self-rated health (SRH) question was assessed.ResultsAlmost all dimensions (except usual activity) and severity levels had less impact on TTO valuations compared with the UK study based on hypothetical values. Anxiety/depression had the greatest impact on both TTO and VAS values. TTO and VAS values were consistently related to SRH. The inclusion of age, sex, education and socioeconomic group affected the main effect coefficients and the explanatory power modestly.ConclusionsA value set for EQ-5D health states based on Swedish valuations has been lacking. Several authors have recently advocated the normative standpoint of using experience-based values. Guidelines of economic evaluation for reimbursement decisions in Sweden recommend the use of experience-based values for QALY calculations. Our results that anxiety/depression had the greatest impact on both TTO and VAS values underline the importance of mental health for individuals’ overall HRQoL. Using population surveys is in line with recent thinking on valuing health states and could reduce some of the focusing effects potentially appearing in hypothetical valuation studies."], "field": "Medicine", "q_year": 2021, "q_cid": "231651564", "pos_cid": 14716313, "source": "eval_collection"}
{"query_id": "scaleup_25861996_44861858", "query": "How to determine whether interactions between chemokines and other inflammatory mediators affect tissue regeneration after muscle injury or bone fracture and identify which chemokine receptors are required for these effects", "pos": ["High mobility group box 1 orchestrates tissue regeneration via CXCR4. Inflammation and tissue regeneration follow tissue damage, but little is known about how these processes are coordinated. High Mobility Group Box 1 (HMGB1) is a nuclear protein that, when released on injury, triggers inflammation. We previously showed that HMGB1 with reduced cysteines is a chemoattractant, whereas a disulfide bond makes it a proinflammatory cytokine. Here we report that fully reduced HMGB1 orchestrates muscle and liver regeneration via CXCR4, whereas disulfide HMGB1 and its receptors TLR4/MD-2 and RAGE (receptor for advanced glycation end products) are not involved. Injection of HMGB1 accelerates tissue repair by acting on resident muscle stem cells, hepatocytes, and infiltrating cells. The nonoxidizable HMGB1 mutant 3S, in which serines replace cysteines, promotes muscle and liver regeneration more efficiently than the wild-type protein and without exacerbating inflammation by selectively interacting with CXCR4. Overall, our results show that the reduced form of HMGB1 coordinates tissue regeneration and suggest that 3S may be used to safely accelerate healing after injury in diverse clinical contexts."], "field": "Medicine", "q_year": 2023, "q_cid": "258619969", "pos_cid": 44861858, "source": "eval_collection"}
{"query_id": "scaleup_26873869_4469743", "query": "How to clarify how Mediator kinases balance gene expression needed for cancer cell proliferation, CRPC adaptation to androgen deprivation, and continued castration-resistant growth", "pos": ["Mediator Kinase Inhibition Further Activates Super-Enhancer Associated Genes in AML. Super-enhancers (SEs), which are composed of large clusters of enhancers densely loaded with the Mediator complex, transcription factors and chromatin regulators, drive high expression of genes implicated in cell identity and disease, such as lineage-controlling transcription factors and oncogenes. BRD4 and CDK7 are positive regulators of SE-mediated transcription. By contrast, negative regulators of SE-associated genes have not been well described. Here we show that the Mediator-associated kinases cyclin-dependent kinase 8 (CDK8) and CDK19 restrain increased activation of key SE-associated genes in acute myeloid leukaemia (AML) cells. We report that the natural product cortistatin A (CA) selectively inhibits Mediator kinases, has anti-leukaemic activity in vitro and in vivo, and disproportionately induces upregulation of SE-associated genes in CA-sensitive AML cell lines but not in CA-insensitive cell lines. In AML cells, CA upregulated SE-associated genes with tumour suppressor and lineage-controlling functions, including the transcription factors CEBPA, IRF8, IRF1 and ETV6 (refs 6, 7, 8). The BRD4 inhibitor I-BET151 downregulated these SE-associated genes, yet also has anti-leukaemic activity. Individually increasing or decreasing the expression of these transcription factors suppressed AML cell growth, providing evidence that leukaemia cells are sensitive to the dosage of SE-associated genes. Our results demonstrate that Mediator kinases can negatively regulate SE-associated gene expression in specific cell types, and can be pharmacologically targeted as a therapeutic approach to AML."], "field": "Medicine", "q_year": 2024, "q_cid": "268738691", "pos_cid": 4469743, "source": "eval_collection"}
{"query_id": "scaleup_24797536_40517879", "query": "How to explain the potential antineoplastic activity of hydroxychloroquine", "pos": ["Targeting Autophagy in Cancer. Autophagy is a mechanism by which cellular material is delivered to lysosomes for degradation, leading to the basal turnover of cell components and providing energy and macromolecular precursors. Autophagy has opposing, context-dependent roles in cancer, and interventions to both stimulate and inhibit autophagy have been proposed as cancer therapies. This has led to the therapeutic targeting of autophagy in cancer to be sometimes viewed as controversial. In this Review, we suggest a way forwards for the effective targeting of autophagy by understanding the context-dependent roles of autophagy and by capitalizing on modern approaches to clinical trial design."], "field": "Medicine", "q_year": 2022, "q_cid": "247975361", "pos_cid": 40517879, "source": "eval_collection"}
{"query_id": "scaleup_26873869_10218090", "query": "How to distinguish direct tumor-cell effects from other antitumor effects of Mediator kinase inhibition in castration-resistant prostate cancer", "pos": ["CDK8-Mediated STAT1-S727 Phosphorylation Restrains NK Cell Cytotoxicity and Tumor Surveillance. Summary The transcription factor STAT1 is important in natural killer (NK) cells, which provide immediate defense against tumor and virally infected cells. We show that mutation of a single phosphorylation site (Stat1-S727A) enhances NK cell cytotoxicity against a range of tumor cells, accompanied by increased expression of perforin and granzyme B. Stat1-S727A mice display significantly delayed disease onset in NK cell-surveilled tumor models including melanoma, leukemia, and metastasizing breast cancer. Constitutive phosphorylation of S727 depends on cyclin-dependent kinase 8 (CDK8). Inhibition of CDK8-mediated STAT1-S727 phosphorylation may thus represent a therapeutic strategy for stimulating NK cell-mediated tumor surveillance."], "field": "Medicine", "q_year": 2024, "q_cid": "268738691", "pos_cid": 10218090, "source": "eval_collection"}
{"query_id": "scaleup_28181210_23248643", "query": "How to accurately and non-invasively assess heterogeneous expression of both human B7-H3 isoforms", "pos": ["The expression of B7-H3 isoforms in newly diagnosed glioblastoma and recurrence and their functional role. Short survival of glioblastoma (GBM) patients is due to systematic tumor recurrence. Our laboratory identified a GBM cell subpopulation able to leave the tumor mass (TM) and invade the subventricular zone (SVZ-GBM cells). SVZ-GBM cells escape treatment and appear to contribute to GBM recurrence. This study aims to identify proteins specifically expressed by SVZ-GBM cells and to define their role(s) in GBM aggressiveness and recurrence. The proteome was compared between GBM cells located in the initial TM and SVZ-GBM cells using mass spectrometry. Among differentially expressed proteins, we confirmed B7-H3 by western blot (WB) and quantitative RT-PCR. B7-H3 expression was compared by immunohistochemistry and WB (including expression of its isoforms) between human GBM ( N = 14) and non-cancerous brain tissue ( N = 8), as well as newly diagnosed GBM and patient-matched recurrences ( N = 11). Finally, the expression of B7-H3 was modulated with short hairpin RNA and/or over-expression vectors to determine its functional role in GBM using in vitro assays and a xenograft mouse model of GBM. B7-H3 was a marker for SVZ-GBM cells. It was also increased in human GBM pericytes, myeloid cells and neoplastic cells. B7-H3 inhibition in GBM cells reduced their tumorigenicity. Out of the two B7-H3 isoforms, only 2IgB7-H3 was detected in non-cancerous brain tissue, whereas 4IgB7-H3 was specific for GBM. 2IgB7-H3 expression was higher in GBM recurrences and increased resistance to temozolomide-mediated apoptosis. To conclude, 4IgB7-H3 is an interesting candidate for GBM targeted therapies, while 2IgB7-H3 could be involved in recurrence through resistance to chemotherapy."], "field": "Medicine", "q_year": 2025, "q_cid": "281812104", "pos_cid": 232486439, "source": "eval_collection"}
{"query_id": "scaleup_21087076_11555516", "query": "How to assess the relevance of hispidulin doses to human intake and compare them with flavonoid doses tested in humans when no clinical studies of hispidulin have been reported", "pos": ["A simple practice guide for dose conversion between animals and human. Understanding the concept of extrapolation of dose between species is important for pharmaceutical researchers when initiating new animal or human experiments. Interspecies allometric scaling for dose conversion from animal to human studies is one of the most controversial areas in clinical pharmacology. Allometric approach considers the differences in body surface area, which is associated with animal weight while extrapolating the doses of therapeutic agents among the species. This review provides basic information about translation of doses between species and estimation of starting dose for clinical trials using allometric scaling. The method of calculation of injection volume for parenteral formulation based on human equivalent dose is also briefed."], "field": "Medicine", "q_year": 2020, "q_cid": "210870766", "pos_cid": 11555516, "source": "eval_collection"}
{"query_id": "scaleup_28404582_10196486", "query": "How to identify activated or suppressed biological functions in individual blood samples and distinguish disease stages despite changes in immune, cellular, and metabolic function over time and variation associated with disease severity", "pos": ["GSVA: gene set variation analysis for microarray and RNA-Seq data. Gene set enrichment (GSE) analysis is a popular framework for condensing information from gene expression profiles into a pathway or signature summary. The strengths of this approach over single gene analysis include noise and dimension reduction, as well as greater biological interpretability. As molecular profiling experiments move beyond simple case-control studies, robust and flexible GSE methodologies are needed that can model pathway activity within highly heterogeneous data sets. To address this challenge, we introduce Gene Set Variation Analysis (GSVA), a GSE method that estimates variation of pathway activity over a sample population in an unsupervised manner. We demonstrate the robustness of GSVA in a comparison with current state of the art sample-wise enrichment methods. Further, we provide examples of its utility in differential pathway activity and survival analysis. Lastly, we show how GSVA works analogously with data from both microarray and RNA-seq experiments. GSVA provides increased power to detect subtle pathway activity changes over a sample population in comparison to corresponding methods. While GSE methods are generally regarded as end points of a bioinformatic analysis, GSVA constitutes a starting point to build pathway-centric models of biology. Moreover, GSVA contributes to the current need of GSE methods for RNA-seq data. GSVA is an open source software package for R which forms part of the Bioconductor project and can be downloaded at http://www.bioconductor.org."], "field": "Medicine", "q_year": 2025, "q_cid": "284045826", "pos_cid": 10196486, "source": "eval_collection"}
{"query_id": "scaleup_23621197_29325074", "query": "How to reliably determine protein abundance differences among metastasizing primary melanomas, non-metastasizing primary melanomas, and normal tissue to distinguish metastatic potential and identify prognostic biomarkers", "pos": ["Quantitative Proteomics: Comparison of the Macular Bruch Membrane/Choroid Complex from Age-related Macular Degeneration and Normal Eyes. A quantitative proteomics analysis of the macular Bruch membrane/choroid complex was pursued for insights into the molecular mechanisms of age-related macular degeneration (AMD). Protein in trephine samples from the macular region of 10 early/mid-stage dry AMD, six advanced dry AMD, eight wet AMD, and 25 normal control post-mortem eyes was analyzed by LC MS/MS iTRAQ (isobaric tags for relative and absolute quantitation) technology. A total of 901 proteins was quantified, including 556 proteins from ≥3 AMD samples. Most proteins differed little in amount between AMD and control samples and therefore reflect the proteome of normal macular tissues of average age 81. A total of 56 proteins were found to be elevated and 43 were found to be reduced in AMD tissues relative to controls. Analysis by category of disease progression revealed up to 16 proteins elevated or decreased in each category. About 60% of the elevated proteins are involved in immune response and host defense, including many complement proteins and damage-associated molecular pattern proteins such as α-defensins 1–3, protein S100s, crystallins, histones, and galectin-3. Four retinoid processing proteins were elevated only in early/mid-stage AMD, supporting a role for retinoids in AMD initiation. Proteins uniquely decreased in early/mid-stage AMD implicate hematologic malfunctions and weakened extracellular matrix integrity and cellular interactions. Galectin-3, a receptor for advanced glycation end products, was the most significantly elevated protein in advanced dry AMD, supporting a role for advanced glycation end products in dry AMD progression. The results endorse inflammatory processes in both early and advanced AMD pathology, implicate different pathways of progression to advanced dry and wet AMD, and provide a new database for hypothesis-driven and discovery-based studies of AMD."], "field": "Medicine", "q_year": 2021, "q_cid": "236211979", "pos_cid": 29325074, "source": "eval_collection"}
{"query_id": "scaleup_28310620_3797894", "query": "How to distinguish ARF samples from uncomplicated Strep A pharyngitis and healthy controls despite autoantibody profiles spanning thousands of proteins and varying markedly between patients", "pos": ["mixOmics: An R package for ‘omics feature selection and multiple data integration. The advent of high throughput technologies has led to a wealth of publicly available ‘omics data coming from different sources, such as transcriptomics, proteomics, metabolomics. Combining such large-scale biological data sets can lead to the discovery of important biological insights, provided that relevant information can be extracted in a holistic manner. Current statistical approaches have been focusing on identifying small subsets of molecules (a ‘molecular signature’) to explain or predict biological conditions, but mainly for a single type of ‘omics. In addition, commonly used methods are univariate and consider each biological feature independently. We introduce mixOmics, an R package dedicated to the multivariate analysis of biological data sets with a specific focus on data exploration, dimension reduction and visualisation. By adopting a system biology approach, the toolkit provides a wide range of methods that statistically integrate several data sets at once to probe relationships between heterogeneous ‘omics data sets. Our recent methods extend Projection to Latent Structure (PLS) models for discriminant analysis, for data integration across multiple ‘omics data or across independent studies, and for the identification of molecular signatures. We illustrate our latest mixOmics integrative frameworks for the multivariate analyses of ‘omics data available from the package."], "field": "Medicine", "q_year": 2025, "q_cid": "283106206", "pos_cid": 3797894, "source": "eval_collection"}
{"query_id": "scaleup_25258436_20528472", "query": "How to preserve melittin’s ability to disrupt cell membranes and induce tumor-cell necrosis or apoptosis when loaded into a carrier for cancer treatment", "pos": ["Activatable Protein Nanoparticles for Targeted Delivery of Therapeutic Peptides. Clinical translation of therapeutic peptides, particularly those that require penetration of the cell membrane or are cytolytic, is a major challenge. A novel approach based on a complementary mechanism, which has been widely used for guided synthesis of DNA or RNA nanoparticles, for de novo design of activatable protein nanoparticles (APNPs) for targeted delivery of therapeutic peptides is described. APNPs are formed through self‐assembly of three independent polypeptides based on pairwise coiled‐coil dimerization. They are capable of long circulation in the blood and can be engineered to target diseases. Peptides to be delivered are incorporated into APNPs and released into the disease microenvironment by locally enriched proteases. It is demonstrated that APNPs mediate efficient delivery of NR2B9c, a neuroprotective peptide that functions after cell penetration, and melittin, a cytolytic peptide that perturbs the lipid bilayer, for effective treatment of stroke and cancer, respectively. Due to their robust properties, simple design, and economic costs, APNPs have great potential to serve as a versatile platform for controlled delivery of therapeutic peptides."], "field": "Medicine", "q_year": 2022, "q_cid": "252584364", "pos_cid": 205284723, "source": "eval_collection"}
{"query_id": "scaleup_27998458_6722414", "query": "How to clarify an intervention’s effects reported in other contexts but understudied in the target context, and its potential to improve another intervention’s effectiveness", "pos": ["Cisplatin-Induced Antitumor Immunomodulation: A Review of Preclinical and Clinical Evidence. Contrary to the long held belief that chemotherapy is immunosuppressive, emerging evidence indicates that the anticancer activity of cisplatin is not limited to its ability to inhibit mitosis, but that cisplatin also has important immunomodulatory effects. We therefore methodically examined the relevant preclinical literature and identified four main mechanisms of cisplatin-induced antitumor immunomodulation: (i) MHC class I expression upregulation; (ii) recruitment and proliferation of effector cells; (iii) upregulation of the lytic activity of cytotoxic effectors; and (iv) downregulation of the immunosuppressive microenvironment. Cisplatin-based combination chemotherapy's antitumor immunomodulatory effects are also beginning to be harnessed in the clinic; we therefore additionally reviewed the applicable clinical literature and discussed how monitoring various components of the immune system (and their responses to cisplatin) can add new levels of sophistication to disease monitoring and prognostication. In summation, this growing body of literature on cisplatin-induced antitumor immunomodulation ultimately highlights the therapeutic potential of synergistic strategies that combine traditional chemotherapy with immunotherapy. Clin Cancer Res; 20(21); 5384–91. ©2014 AACR."], "field": "Medicine", "q_year": 2025, "q_cid": "279984580", "pos_cid": 6722414, "source": "eval_collection"}
{"query_id": "scaleup_25590290_3192315", "query": "How to achieve relief of osteoarthritis-related knee pain without permanent harm or surrounding tissue damage, with evidence of efficacy, durability, and complications", "pos": ["Wallerian Degeneration and Recovery of Motor Nerves after Multiple Focused Cold Therapies. Introduction: A device has been developed to apply freezing temperatures to temporarily impede nerve conduction, resulting in inhibition of voluntary skeletal muscle contraction. This device was designed as an alternative to the neurotoxins usually used to treat movement disorders. Methods: We evaluated the effects of single and 3 repeat treatments with a cryoprobe device (−55°C) on a sciatic nerve rat model. Long‐term effects of repeated treatment were evaluated through assessments of physiological function and histological analysis. Results: There was consistent weakening of physiological function after each treatment, with recovery of normal function by 8 weeks posttreatment. Histological findings showed axonal degeneration with no disruption to the epineurial or perineurial structures. Progressive axonal regeneration was followed by normal recovery by 24 weeks post‐treatment. Conclusions: Low‐temperature treatment of motor nerves did not result in permanent or long‐term changes to nerve function or structure. Muscle Nerve 51: 268–275, 2015"], "field": "Medicine", "q_year": 2023, "q_cid": "255902903", "pos_cid": 3192315, "source": "eval_collection"}
{"query_id": "scaleup_27737902_22509896", "query": "How to clarify the types and frequency of symptomatic toxicities associated with non–immune-checkpoint monoclonal antibodies across cancer indications despite limited patient accounts of symptoms", "pos": ["Isatuximab for the treatment of relapsed/refractory multiple myeloma. ABSTRACT Introduction Although new drug classes have significantly extended survival of patients with multiple myeloma, they continue to experience multiple relapses and/or become refractory to treatment. Therefore, novel therapies and treatment combinations with different mechanisms of action are needed to improve the outcomes of patients with relapsed/refractory multiple myeloma. Areas covered Here, the authors review the published data regarding the development and clinical investigation of isatuximab, a CD38 monoclonal antibody, for treatment of patients with relapsed/refractory multiple myeloma. The mechanisms of action, clinical efficacy, and safety of isatuximab treatment are summarized. Expert opinion Isatuximab is approved in combination with pomalidomide/dexamethasone for the treatment of adults with relapsed/refractory multiple myeloma who have received at least two prior therapies, including lenalidomide and a proteasome inhibitor. Isatuximab displays a manageable safety profile, with infusion reactions being the most common adverse events. Isatuximab is currently being further evaluated in combination with other backbone regimens in relapsed/refractory and newly diagnosed multiple myeloma."], "field": "Medicine", "q_year": 2025, "q_cid": "277379025", "pos_cid": 225098964, "source": "eval_collection"}
{"query_id": "scaleup_24797536_999374", "query": "How to overcome treatment resistance and improve drug sensitivity in poorly responsive cells", "pos": ["Wnt/Ca2+/NFAT signaling maintains survival of Ph+ leukemia cells upon inhibition of Bcr-Abl. Summary Although Bcr-Abl kinase inhibitors have proven effective in the treatment of chronic myeloid leukemia (CML), they generally fail to completely eradicate Bcr-Abl+ leukemia cells. To identify genes whose inhibition sensitizes Bcr-Abl+ leukemias to killing by Bcr-Abl inhibitors, we performed an RNAi-based synthetic lethal screen with imatinib in CML cells. This screen identified numerous components of a Wnt/Ca2+/NFAT signaling pathway. Antagonism of this pathway led to impaired NFAT activity, decreased cytokine production and enhanced sensitivity to Bcr-Abl inhibition. Furthermore, NFAT inhibition with cyclosporin A facilitated leukemia cell elimination by the Bcr-Abl inhibitor dasatinib and markedly improved survival in a mouse model of Bcr-Abl+ acute lymphoblastic leukemia (ALL). Targeting this pathway in combination with Bcr-Abl inhibition could improve treatment of Bcr-Abl+ leukemias."], "field": "Medicine", "q_year": 2022, "q_cid": "247975361", "pos_cid": 999374, "source": "eval_collection"}
{"query_id": "scaleup_25282281_53711886", "query": "How to determine whether training can achieve concentrations sufficient to stimulate growth and which intensities or protocols are required", "pos": ["Lactate Promotes Myoblast Differentiation and Myotube Hypertrophy via a Pathway Involving MyoD In Vitro and Enhances Muscle Regeneration In Vivo. Lactate is a metabolic substrate mainly produced in muscles, especially during exercise. Recently, it was reported that lactate affects myoblast differentiation; however, the obtained results are inconsistent and the in vivo effect of lactate remains unclear. Our study thus aimed to evaluate the effects of lactate on myogenic differentiation and its underlying mechanism. The differentiation of C2C12 murine myogenic cells was accelerated in the presence of lactate and, consequently, myotube hypertrophy was achieved. Gene expression analysis of myogenic regulatory factors showed significantly increased myogenic determination protein (MyoD) gene expression in lactate-treated cells compared with that in untreated ones. Moreover, lactate enhanced gene and protein expression of myosin heavy chain (MHC). In particular, lactate increased gene expression of specific MHC isotypes, MHCIIb and IId/x, in a dose-dependent manner. Using a reporter assay, we showed that lactate increased promoter activity of the MHCIIb gene and that a MyoD binding site in the promoter region was necessary for the lactate-induced increase in activity. Finally, peritoneal injection of lactate in mice resulted in enhanced regeneration and fiber hypertrophy in glycerol-induced regenerating muscles. In conclusion, physiologically high lactate concentrations modulated muscle differentiation by regulating MyoD-associated networks, thereby enhancing MHC expression and myotube hypertrophy in vitro and, potentially, in vivo."], "field": "Medicine", "q_year": 2022, "q_cid": "252822810", "pos_cid": 53711886, "source": "eval_collection"}
{"query_id": "scaleup_26986284_22724466", "query": "How to determine differences in disulfidptosis-related gene expression within specific cell subpopulations between patients with non-alcoholic fatty liver disease and controls", "pos": ["muscat detects subpopulation-specific state transitions from multi-sample multi-condition single-cell transcriptomics data. Single-cell RNA sequencing (scRNA-seq) has become an empowering technology to profile the transcriptomes of individual cells on a large scale. Early analyses of differential expression have aimed at identifying differences between subpopulations to identify subpopulation markers. More generally, such methods compare expression levels across sets of cells, thus leading to cross-condition analyses. Given the emergence of replicated multi-condition scRNA-seq datasets, an area of increasing focus is making sample-level inferences, termed here as differential state analysis; however, it is not clear which statistical framework best handles this situation. Here, we surveyed methods to perform cross-condition differential state analyses, including cell-level mixed models and methods based on aggregated pseudobulk data. To evaluate method performance, we developed a flexible simulation that mimics multi-sample scRNA-seq data. We analyzed scRNA-seq data from mouse cortex cells to uncover subpopulation-specific responses to lipopolysaccharide treatment, and provide robust tools for multi-condition analysis within the muscat R package. Single-cell transcriptomics enhanced our ability to profile heterogeneous cell populations. It is not known which statistical frameworks are performant to detect subpopulation-level responses. Here, the authors developed a simulation framework to evaluate various methods across a range of scenarios."], "field": "Medicine", "q_year": 2024, "q_cid": "269862849", "pos_cid": 227244666, "source": "eval_collection"}
{"query_id": "scaleup_24797536_2788123", "query": "How to determine whether conventional antirheumatic drugs enhance temozolomide’s cytotoxic activity against melanoma cells", "pos": ["Measurements of tumor cell autophagy predict invasiveness, resistance to chemotherapy, and survival in melanoma. Purpose: Autophagy consists of lysosome-dependent degradation of cytoplasmic contents sequestered by autophagic vesicles (AV). The role of autophagy in determining tumor aggressiveness and response to therapy in melanoma was investigated in this study. Experimental Design: Autophagy was measured in tumor biopsies obtained from metastatic melanoma patients enrolled on a phase II trial of temozolomide and sorafenib and correlated to clinical outcome. These results were compared with autophagy measurements in aggressive and indolent melanoma cells grown in two- and three-dimensional (3D) culture and as xenograft tumors. The effects of autophagy inhibition with either hydroxychloroquine or inducible shRNA (short hairpin RNA) against the autophagy gene ATG5 were assessed in three-dimensional spheroids. Results: Patients whose tumors had a high autophagic index were less likely to respond to treatment and had a shorter survival compared with those with a low autophagic index. Differences in autophagy were less evident in aggressive and indolent melanoma cells grown in monolayer culture. In contrast, autophagy was increased in aggressive compared with indolent melanoma xenograft tumors. This difference was recapitulated when aggressive and indolent melanoma cells were grown as spheroids. Autophagy inhibition with either hydroxychloroquine or inducible shRNA against ATG5 resulted in cell death in aggressive melanoma spheroids, and significantly augmented temozolomide-induced cell death. Conclusions: Autophagy is a potential prognostic factor and therapeutic target in melanoma. Three dimensional culture mimics the tumor microenvironment better than monolayer culture and is an appropriate model for studying therapeutic combinations involving autophagy modulators. Autophagy inhibition should be tested clinically in patients with melanoma. Clin Cancer Res; 17(10); 3478–89. ©2011 AACR."], "field": "Medicine", "q_year": 2022, "q_cid": "247975361", "pos_cid": 2788123, "source": "eval_collection"}
{"query_id": "scaleup_27998458_470557", "query": "How to explain patient-to-patient differences in responses to the same chemotherapeutic agent in triple-negative breast cancer despite limited investigation and small treatment groups", "pos": ["Inflammatory cytokine production in tumor cells upon chemotherapy drug exposure or upon selection for drug resistance. Tumor Necrosis Factor alpha (TNF-α) has been shown to be released by tumor cells in response to docetaxel, and lipopolysaccharides (LPS), the latter through activation of toll-like receptor 4 (TLR4). However, it is unclear whether the former involves TLR4 receptor activation through direct binding of the drug to TLR4 at the cell surface. The current study was intended to better understand drug-induced TNF-α production in tumor cells, whether from short-term drug exposure or in cells selected for drug resistance. ELISAs were employed to measure cytokine release from breast and ovarian tumor cells in response to several structurally distinct chemotherapy agents and/or TLR4 agonists or antagonists. Drug uptake and drug sensitivity studies were also performed. We observed that several drugs induced TNF-αrelease from multiple tumor cell lines. Docetaxel-induced cytokine production was distinct from that of LPS in both MyD88-positive (MCF-7) and MyD88-deficient (A2780) cells. The acquisition of docetaxel resistance was accompanied by increased constitutive production of TNF-αand CXCL1, which waned at higher levels of resistance. In docetaxel-resistant MCF-7 and A2780 cell lines, the production of TNF-α could not be significantly augmented by docetaxel without the inhibition of P-gp, a transporter protein that promotes drug efflux from tumor cells. Pretreatment of tumor cells with LPS sensitized MyD88-positive cells (but not MyD88-deficient) to docetaxel cytotoxicity in both drug-naive and drug-resistant cells. Our findings suggest that taxane-induced inflammatory cytokine production from tumor cells depends on the duration of exposure, requires cellular drug-accumulation, and is distinct from the LPS response seen in breast tumor cells. Also, stimulation of the LPS-induced pathway may be an attractive target for treatment of drug-resistant disease."], "field": "Medicine", "q_year": 2025, "q_cid": "279984580", "pos_cid": 470557, "source": "eval_collection"}
{"query_id": "scaleup_9887907_23959790", "query": "How to clarify the relationship between GLP-1, satiety, and sensitivity to food reward", "pos": ["Glucagon-like peptide 1 receptor activation regulates cocaine actions and dopamine homeostasis in the lateral septum by decreasing arachidonic acid levels. Agonism of the glucagon-like peptide 1 (GLP-1) receptor (GLP-1R) has been effective at treating aspects of addictive behavior for a number of abused substances, including cocaine. However, the molecular mechanisms and brain circuits underlying the therapeutic effects of GLP-1R signaling on cocaine actions remain elusive. Recent evidence has revealed that endogenous signaling at the GLP-1R within the forebrain lateral septum (LS) acts to reduce cocaine-induced locomotion and cocaine conditioned place preference, both considered dopamine (DA)-associated behaviors. DA terminals project from the ventral tegmental area to the LS and express the DA transporter (DAT). Cocaine acts by altering DA bioavailability by targeting the DAT. Therefore, GLP-1R signaling might exert effects on DAT to account for its regulation of cocaine-induced behaviors. We show that the GLP-1R is highly expressed within the LS. GLP-1, in LS slices, significantly enhances DAT surface expression and DAT function. Exenatide (Ex-4), a long-lasting synthetic analog of GLP-1 abolished cocaine-induced elevation of DA. Interestingly, acute administration of Ex-4 reduces septal expression of the retrograde messenger 2-arachidonylglycerol (2-AG), as well as a product of its presynaptic degradation, arachidonic acid (AA). Notably, AA reduces septal DAT function pointing to AA as a novel regulator of central DA homeostasis. We further show that AA oxidation product γ-ketoaldehyde (γ-KA) forms adducts with the DAT and reduces DAT plasma membrane expression and function. These results support a mechanism in which postsynaptic septal GLP-1R activation regulates 2-AG levels to alter presynaptic DA homeostasis and cocaine actions through AA."], "field": "Neuroscience", "q_year": 2017, "q_cid": "9887907", "pos_cid": 23959790, "source": "eval20x26"}
{"query_id": "scaleup_53106789_4494981", "query": "How to predict cognitive performance while accounting for regional influences on brain-wide information flow and brain-state transitions and individual differences in neural coding and circuit function", "pos": ["Communicability in complex networks.. We propose a new measure of the communicability of a complex network, which is a broad generalization of the concept of the shortest path. According to the new measure, most of the real-world networks display the largest communicability between the most connected (popular) nodes of the network (assortative communicability). There are also several networks with the disassortative communicability, where the most \"popular\" nodes communicate very poorly to each other. Using this information we classify a diverse set of real-world complex systems into a small number of universality classes based on their structure-dynamic correlation. In addition, the new communicability measure is able to distinguish finer structures of networks, such as communities into which a network is divided. A community is unambiguously defined here as a set of nodes displaying larger communicability among them than to the rest of the nodes in the network."], "field": "Neuroscience", "q_year": 2018, "q_cid": "53106789", "pos_cid": 4494981, "source": "eval20x26"}
{"query_id": "scaleup_7626094_17274955", "query": "How to distinguish genuine presynaptic inputs to intended projection neurons from false-positive labeling", "pos": ["Axonal transport of adeno-associated viral vectors is serotype-dependent. We have previously shown that adeno-associated virus type 2 (AAV2) undergoes anterograde axonal transport in rat and non-human primate brain. We screened other AAV serotypes for axonal transport and found that AAV6 is transported almost exclusively in a retrograde direction and, in the same way as AAV2, it is also neuron-specific in rat brain. Our findings show that axonal transport of AAV is serotype dependent and this has implications for gene therapy of neurological diseases such as Huntington's disease."], "field": "Neuroscience", "q_year": 2015, "q_cid": "7626094", "pos_cid": 17274955, "source": "eval20x26"}
{"query_id": "scaleup_3655593_17076077", "query": "How to determine whether binding to the human dopamine transporter and amphetamine-induced dopamine efflux specifically depend on phosphatidylinositol bisphosphate availability rather than unrelated effects", "pos": ["Probing the Regulation of M (Kv7) Potassium Channels in Intact Neurons with Membrane-Targeted Peptides. M-type (Kv7) potassium channels are closed by Gq/11 G-protein-coupled receptors. Several membrane- or channel-associated molecules have been suggested to contribute to this effect, including depletion of phosphatidylinositol-4,5-bisphosphate (PIP2) and activation of Ca2+/calmodulin and protein kinase C. To facilitate further study of these pathways in intact neurons, we have devised novel membrane-targeted probes that can be applied from the outside of the neuron, by attaching a palmitoyl group to site-directed peptides (“palpeptides”) (cf. Covic et al., 2002a,b). A palpeptide incorporating the 10-residue C terminus of Gαq/11 reduced Gq/11-mediated M-current inhibition in sympathetic neurons by the muscarinic acetylcholine receptor (mAChR) agonist oxotremorine-M but not Go-mediated inhibition of the N-type Ca2+ current by norepinephrine. Instead, the latter was inhibited by the corresponding Go palpeptide. A PIP2 palpeptide, based on the putative PIP2 binding domain of the Kv7.2 channel, inhibited M current (IC50 = ∼1.5 μm) and enhanced inhibition by oxotremorine-M. Inhibition could not be attributed to activation of mAChRs, calcium influx, or block of M channels but was antagonized by intracellular diC8-PIP2 (dioctanoyl-phosphatidylinositol-4,5-bisphosphate), suggesting that it disrupted PIP2–M channel gating. A fluorescently tagged PIP2 palpeptide was highly targeted to the plasma membrane but did not accumulate in the cytoplasm. We suggest that these palpeptides are anchored in the plasma membrane via the palmitoyl group, such that the peptide moiety can interact with target molecules on the inner face of the membrane. The G-protein-replicating palpeptides were sequence specific and probably compete with the receptor for the cognate G-protein. The PIP2 palpeptide was not sequence specific so probably interacts electrostatically with anionic PIP2 head groups."], "field": "Neuroscience", "q_year": 2014, "q_cid": "3655593", "pos_cid": 17076077, "source": "eval20x26"}
{"query_id": "scaleup_10266113_3951486", "query": "How to identify which executive-control demands link anterior cingulate and supplementary motor cortex activation to dual-task performance requiring maintenance and coordination of distinct task rules and selection of appropriate motor responses", "pos": ["Role of the human anterior cingulate cortex in the control of oculomotor, manual, and speech responses: a positron emission tomography study.. 1. Two experiments were aimed at investigating the functional organization of the human anterior cingulate cortex (ACC) in relation to higher-order motor control. 2. The 15O-labeled H2O bolus method was used to measure relative changes of regional cerebral blood flow (rCBF) in 18 healthy human subjects as they performed oculomotor, manual, or speech tasks. 3. Task-specific rCBF changes were obtained in distinct subregions of the ACC, depending on the output system employed. The oculomotor and the manual task-related foci were found in the rostral and caudal regions of the ACC, respectively, whereas the speech foci were localized within two cingulate subregions, the intermediate dorsal and the rostral ACC. 4. In the manual tasks, two groups of activation foci could be distinguished, one just behind and the other just in front of the vertical plane traversing the anterior commissure. 5. The above pattern of rCBF changes was observed only if there was concomitant activation within the lateral prefrontal cortex (except for the posterior group of foci obtained in the manual tasks). 6. The localization of output-specific rCBF changes within the human ACC is consistent with the known somatotopic organization of the cingulate cortex in the monkey. 7. It is tentatively proposed that the ACC participates in motor control by facilitating the execution of the appropriate responses and/or suppressing the execution of the inappropriate ones. Such a modulatory effect would be of particular importance when behavior has to be modified in new and challenging situations."], "field": "Neuroscience", "q_year": 2015, "q_cid": "10266113", "pos_cid": 3951486, "source": "eval20x26"}
{"query_id": "scaleup_12823522_23586454", "query": "How to clarify the relationship between disrupted ryanodine receptor-dependent calcium signaling in aged neurons and age-related impairments in hippocampal synaptic plasticity and memory", "pos": ["Crosstalk Between Calcium and Redox Signaling: From Molecular Mechanisms to Health Implications. Studies done many years ago established unequivocally the key role of calcium as a universal second messenger. In contrast, the second messenger roles of reactive oxygen and nitrogen species have emerged only recently. Therefore, their contributions to physiological cell signaling pathways have not yet become universally accepted, and many biological researchers still regard them only as cellular noxious agents. Furthermore, it is becoming increasingly apparent that there are significant interactions between calcium and redox species, and that these interactions modify a variety of proteins that participate in signaling transduction pathways and in other fundamental cellular functions that determine cell life or death. This review article addresses first the central aspects of calcium and redox signaling pathways in animal cells, and continues with the molecular mechanisms that underlie crosstalk between calcium and redox signals under a number of physiological or pathological conditions. To conclude, the review focuses on conditions that, by promoting cellular oxidative stress, lead to the generation of abnormal calcium signals, and how this calcium imbalance may cause a variety of human diseases including, in particular, degenerative diseases of the central nervous system and cardiac pathologies."], "field": "Neuroscience", "q_year": 2017, "q_cid": "12823522", "pos_cid": 23586454, "source": "eval20x26"}
{"query_id": "scaleup_1670367_12130282", "query": "How to determine whether unsaturated fatty acids can suppress hypothalamic inflammation and insulin resistance", "pos": ["GPR120 is an Omega-3 Fatty Acid Receptor Mediating Potent Anti-Inflammatory and Insulin Sensitizing Effects. SUMMARY Omega-3 fatty acids (ω-3 FAs), DHA and EPA, exert anti-inflammatory effects, but the mechanisms are poorly understood. Here we show that the G protein-coupled receptor 120 (GPR120) functions as an ω-3 FA receptor/sensor. Stimulation of GPR120 with ω-3 FAs or a chemical agonist causes broad anti-inflammatory effects in monocytic RAW 264.7 cells and in primary intraperitoneal macrophages. All of these effects are abrogated by GPR120 knockdown. Since chronic macrophage-mediated tissue inflammation is a key mechanism for insulin resistance in obesity, we fed obese WT and GPR120 knockout mice a high fat diet with or without ω-3 FA supplementation. The ω-3 FA treatment inhibited inflammation and enhanced systemic insulin sensitivity in WT mice, but was without effect in GPR120 knockout mice. In conclusion, GPR120 is a functional ω-3 FA receptor/sensor and mediates potent insulin sensitizing and anti-diabetic effects in vivo by repressing macrophage-induced tissue inflammation."], "field": "Neuroscience", "q_year": 2012, "q_cid": "1670367", "pos_cid": 12130282, "source": "eval20x26"}
{"query_id": "scaleup_10235348_37398988", "query": "How to clarify the roles of pro-inflammatory cytokines, PMP22 duplication, and increased PMP22 protein expression in CMT1A pathogenesis given the multiple, context-dependent functions of these cytokines", "pos": ["Cytokines and chemokines: At the crossroads of cell signalling and inflammatory disease.. Inflammation occurs as a result of exposure of tissues and organs to harmful stimuli such as microbial pathogens, irritants, or toxic cellular components. The primary physical manifestations of inflammation are redness, swelling, heat, pain, and loss of function to the affected area. These processes involve the major cells of the immune system, including monocytes, macrophages, neutrophils, basophils, dendritic cells, mast cells, T-cells, and B-cells. However, examination of a range of inflammatory lesions demonstrates the presence of specific leukocytes in any given lesion. That is, the inflammatory process is regulated in such a way as to ensure that the appropriate leukocytes are recruited. These events are in turn controlled by a host of extracellular molecular regulators, including members of the cytokine and chemokine families that mediate both immune cell recruitment and complex intracellular signalling control mechanisms that characterise inflammation. This review will focus on the role of the main cytokines, chemokines, and their receptors in the pathophysiology of auto-inflammatory disorders, pro-inflammatory disorders, and neurological disorders involving inflammation."], "field": "Neuroscience", "q_year": 2019, "q_cid": "102353481", "pos_cid": 37398988, "source": "eval20x26"}
{"query_id": "scaleup_10235348_20619361", "query": "How to determine whether elevated cytokine expression in CMT1A is sufficient to attract monocytes", "pos": ["Monocyte Chemoattractant Protein 1 (MCP-1): An Overview. Chemokines constitute a family of chemoattractant cytokines and are subdivided into four families on the basis of the number and spacing of the conserved cysteine residues in the N-terminus of the protein. Chemokines play a major role in selectively recruiting monocytes, neutrophils, and lymphocytes, as well as in inducing chemotaxis through the activation of G-protein-coupled receptors. Monocyte chemoattractant protein-1 (MCP-1/CCL2) is one of the key chemokines that regulate migration and infiltration of monocytes/macrophages. Both CCL2 and its receptor CCR2 have been demonstrated to be induced and involved in various diseases. Migration of monocytes from the blood stream across the vascular endothelium is required for routine immunological surveillance of tissues, as well as in response to inflammation. This review will discuss these biological processes and the structure and function of CCL2."], "field": "Neuroscience", "q_year": 2019, "q_cid": "102353481", "pos_cid": 206193619, "source": "eval20x26"}
{"query_id": "scaleup_3885204_6868055", "query": "How to reliably assess experimental effects on reaction times despite differences across participants and items and among participants’ responses to repeated conditions", "pos": ["Random effects structure for confirmatory hypothesis testing: Keep it maximal. Linear mixed-effects models (LMEMs) have become increasingly prominent in psycholinguistics and related areas. However, many researchers do not seem to appreciate how random effects structures affect the generalizability of an analysis. Here, we argue that researchers using LMEMs for confirmatory hypothesis testing should minimally adhere to the standards that have been in place for many decades. Through theoretical arguments and Monte Carlo simulation, we show that LMEMs generalize best when they include the maximal random effects structure justified by the design. The generalization performance of LMEMs including data-driven random effects structures strongly depends upon modeling criteria and sample size, yielding reasonable results on moderately-sized samples when conservative criteria are used, but with little or no power advantage over maximal models. Finally, random-intercepts-only LMEMs used on within-subjects and/or within-items data from populations where subjects and/or items vary in their sensitivity to experimental manipulations always generalize worse than separate F1 and F2 tests, and in many cases, even worse than F1 alone. Maximal LMEMs should be the ‘gold standard’ for confirmatory hypothesis testing in psycholinguistics and beyond."], "field": "Neuroscience", "q_year": 2018, "q_cid": "3885204", "pos_cid": 6868055, "source": "eval20x26"}
{"query_id": "scaleup_17148170_9297578", "query": "How to relate limited information-processing capacity to the formation of abstractions and decision-making hierarchies in perception-action systems while accounting for the tension between utility maximization and resource demands", "pos": ["Information-Theoretic Bounded Rationality. Bounded rationality, that is, decision-making and planning under resource limitations, is widely regarded as an important open problem in artificial intelligence, reinforcement learning, computational neuroscience and economics. This paper offers a consolidated presentation of a theory of bounded rationality based on information-theoretic ideas. We provide a conceptual justification for using the free energy functional as the objective function for characterizing bounded-rational decisions. This functional possesses three crucial properties: it controls the size of the solution space; it has Monte Carlo planners that are exact, yet bypass the need for exhaustive search; and it captures model uncertainty arising from lack of evidence or from interacting with other agents having unknown intentions. We discuss the single-step decision-making case, and show how to extend it to sequential decisions using equivalence transformations. This extension yields a very general class of decision problems that encompass classical decision rules (e.g. EXPECTIMAX and MINIMAX) as limit cases, as well as trust- and risk-sensitive planning."], "field": "Neuroscience", "q_year": 2015, "q_cid": "17148170", "pos_cid": 9297578, "source": "eval20x26"}
{"query_id": "scaleup_9887907_38283632", "query": "How to understand how hunger-related hypothalamic signals influence dopamine reward sensitivity and motivation for palatable foods, and how highly rewarding foods disrupt hunger–satiety balance and promote excessive consumption", "pos": ["The hypocretin–orexin system regulates cocaine self-administration via actions on the mesolimbic dopamine system. Recent evidence suggests that the hypocretin–orexin system participates in the regulation of reinforcement processes. The current studies examined the extent to which hypocretin neurotransmission regulates behavioral and neurochemical responses to cocaine, and behavioral responses to food reinforcement. These studies used a combination of fixed ratio, discrete trials, progressive ratio and threshold self‐administration procedures to assess whether the hypocretin 1 receptor antagonist, SB‐334867, reduces cocaine self‐administration in rats. Progressive ratio sucrose self‐administration procedures were also used to assess the extent to which SB‐334867 reduces responding to a natural reinforcer in food‐restricted and food‐sated rats. Additionally, these studies used microdialysis and in vivo voltammetry in rats to examine whether SB‐334867 attenuates the effects of cocaine on dopamine signaling within the nucleus accumbens core. Furthermore, in vitro voltammetry was used to examine whether hypocretin knockout mice display attenuated dopamine responses to cocaine. Results indicate that when SB‐334867 was administered peripherally or within the ventral tegmental area, it reduced the motivation to self‐administer cocaine and attenuated cocaine‐induced enhancement of dopamine signaling. SB‐334867 also reduced the motivation to self‐administer sucrose in food‐sated but not food‐restricted rats. Finally, hypocretin knockout mice displayed altered baseline dopamine signaling and reduced dopamine responses to cocaine. Combined, these studies suggest that hypocretin neurotransmission participates in reinforcement processes, likely through modulation of the mesolimbic dopamine system. Additionally, the current observations suggest that the hypocretin system may provide a target for pharmacotherapies to treat cocaine addiction."], "field": "Neuroscience", "q_year": 2017, "q_cid": "9887907", "pos_cid": 38283632, "source": "eval20x26"}
{"query_id": "scaleup_1613715_1895384", "query": "How to understand the coordination of Schwann cell growth arrest with terminal differentiation and myelination", "pos": ["microRNA-34a inhibits glioblastoma growth by targeting multiple oncogenes. microRNA-34a (miR-34a) is a transcriptional target of p53 that is down-regulated in some cancer cell lines. We studied the expression, targets and functional effects of miR-34a in brain tumor cells and human gliomas. Transfection of miR-34a down-regulated c-Met in human glioma and medulloblastoma cells and Notch-1, Notch-2 and CDK6 protein expressions in glioma cells. miR-34a expression inhibited c-Met reporter activities in glioma and medulloblastoma cells and Notch-1 and Notch-2 3′UTR reporter activities in glioma cells and stem cells. Analysis of human specimens showed that miR-34a expression is down-regulated in glioblastoma tissues as compared to normal brain and in mutant p53 gliomas as compared to wild-type p53 gliomas. miR-34a levels in human gliomas inversely correlated to c-Met levels measured in the same tumors. Transient transfection of miR-34a into glioma and medulloblastoma cell lines strongly inhibited cell proliferation, cell cycle progression, cell survival and cell invasion, but transfection of miR-34a into human astrocytes did not affect cell survival and cell cycle status. Forced expression of c-Met or Notch1/Notch2 transcripts lacking the 3′UTR sequences partially reversed the effects of miR-34a on cell cycle arrest and cell death in glioma cells and stem cells, respectively. Also, transient expression of miR-34a in glioblastoma cells strongly inhibited in vivo glioma xenograft growth. Together, these findings represent the first comprehensive analysis of the role of miR-34a in gliomas. They show that miR-34a suppresses brain tumor growth by targeting c-Met and Notch. The results also suggest that miR-34a could serve as a potential therapeutic agent for brain tumors."], "field": "Neuroscience", "q_year": 2010, "q_cid": "1613715", "pos_cid": 1895384, "source": "eval20x26"}
{"query_id": "scaleup_73515132_11708565", "query": "How to rigorously evaluate exercise and training effects with a limited number of available participants", "pos": ["CLINICAL RESEARCH FOR RARE DISEASE: OPPORTUNITIES, CHALLENGES, AND SOLUTIONS. Over 7000 rare diseases, each <200,000 US residents, affect nearly 30 million people in the United States. Furthermore, for the 10% of people with a rare disease and for their families, these disorders no longer seem rare. Molecular genetics have characterized the cause of many rare diseases and provide unprecedented opportunities for identifying patients, determining phenotypes, and devising treatments to prevent, stabilize, or improve each disease. Rare disease research poses challenges to investigators requiring specific approaches to: (1) the design of clinical studies; (2) the funding of research programs; (3) the discovery, testing, and approval of new treatments, and (4) the training of clinical scientists. Rigorous, statistically-valid, natural history-controlled, cross-over, and n-of-1 trials can establish efficacy and support regulatory approval of new treatments for rare diseases. The U.S. Orphan Drug Act of the U.S. FDA has stimulated industry investment in clinical trials to develop treatments for rare diseases. For trainees interested in finding a treatment for a rare disease, a commitment to longitudinal care of patients provides a base for the characterization of phenotype and natural history, a stimulus for innovation, a target population for research and helps fund training and research. The scientific methodology, financial resources, and logistics of clinical research for rare diseases have changed dramatically in the past two decades resulting in increased understanding of the pathophysiology of these disorders and direct benefit to patients."], "field": "Neuroscience", "q_year": 2019, "q_cid": "73515132", "pos_cid": 11708565, "source": "eval20x26"}
{"query_id": "scaleup_23530179_59159299", "query": "How to quantify how predictability, including initial uncertainty and prediction error, affects the rate at which heightened responses to novelty diminish with repeated exposure", "pos": ["Modeling Emotions Associated With Novelty at Variable Uncertainty Levels: A Bayesian Approach. Acceptance of novelty depends on the receiver's emotional state. This paper proposes a novel mathematical model for predicting emotions elicited by the novelty of an event under different conditions. It models two emotion dimensions, arousal and valence, and considers different uncertainty levels. A state transition from before experiencing an event to afterwards is assumed, and a Bayesian model estimates a posterior distribution as being proportional to the product of a prior distribution and a likelihood function. Our model uses Kullback-Leibler divergence of the posterior from the prior, which we termed information gain, to represent arousal levels because it corresponds to surprise, a high-arousal emotion, upon experiencing a novel event. Based on Berlyne's hedonic function, we formalized valence as a summation of reward and aversion systems that are modeled as sigmoid functions of information gain. We derived information gain as a function of prediction errors (i.e., differences between the mean of the posterior and the peak likelihood), uncertainty (i.e., variance of the prior that is proportional to prior entropy), and noise (i.e., variance of the likelihood function). This functional model predicted an interaction effect of prediction errors and uncertainty on information gain, which we termed the arousal crossover effect. This effect means that the greater the uncertainty, the greater the information gain for a small prediction error. However, for large prediction errors, greater uncertainty means a smaller information gain. To verify this effect, we conducted an experiment with participants who watched short videos in which different percussion instruments were played. We varied uncertainty levels by using familiar and unfamiliar instruments, and we varied prediction error magnitudes by including congruent or incongruent percussive sounds in the videos. Event-related potential P300 amplitudes and subjective reports of surprise in response to the percussive sounds were used as measures of arousal levels, and the findings supported the hypothesized arousal crossover effect. The concordance between our model's predictions and our experimental results suggests that Bayesian information gain can be decomposed into uncertainty and prediction errors and is a valid measure of emotional arousal. Our model's predictions of arousal may help identify positively accepted novelty."], "field": "Neuroscience", "q_year": 2021, "q_cid": "235301796", "pos_cid": 59159299, "source": "eval_collection"}
{"query_id": "scaleup_27916151_26488916", "query": "How to determine whether associations between therapeutic alliance and interpersonal neural synchrony reflect genuine relationships rather than inflated participant self-reports shaped by awareness of study aims", "pos": ["The Good-Subject Effect: Investigating Participant Demand Characteristics. Although researchers are often concerned with the presence of participant demand, few have directly examined effects of demand on participant behavior. Before beginning the present study, a confederate informed participants (N = 100) of the study's purported hypothesis. Participants then performed a laboratory task designed to evaluate the extent to which they would respond in ways that may confirm or disconfirm the hypothesis of the study. The authors found that participants tended to respond in ways that confirmed the hypothesis, yet this tendency depended on attitudes toward the experiment or experimenter and other individual differences. In addition, results suggested that suspicion probes may be ineffective in measuring participants' previous knowledge and suspicion. Findings indicate the need for more research and consideration of demand in the design of studies and analysis of data."], "field": "Neuroscience", "q_year": 2025, "q_cid": "279161514", "pos_cid": 26488916, "source": "eval_collection"}
{"query_id": "scaleup_26086801_16581640", "query": "How to distinguish the output circuits of genetically defined VTA neuronal subtypes despite the VTA’s cellular heterogeneity", "pos": ["A CRE-DEPENDENT, ANTEROGRADE TRANS-SYNAPTIC VIRAL TRACER FOR MAPPING OUTPUT PATHWAYS OF GENETICALLY MARKED NEURONS. SUMMARY Neurotropic viruses that conditionally infect or replicate in molecularly defined neuronal subpopulations, and then spread trans-synaptically, are powerful tools for mapping neural pathways. Genetically targetable retrograde trans-synaptic tracer viruses are available to map the inputs to specific neuronal subpopulations, but an analogous tool for mapping synaptic outputs is not yet available. Here we describe a Cre recombinase-dependent, anterograde trans-neuronal tracer, based on the H129 strain of herpes simplex virus (HSV). Application of this virus to transgenic or knock-in mice expressing Cre in peripheral neurons of the olfactory epithelium or the retina reveals widespread, polysynaptic labeling of higher-order neurons in the olfactory and visual systems, respectively. Polysynaptic pathways were also labeled from cerebellar Purkinje cells. In each system, the pattern of labeling was consistent with classical circuit-tracing studies, restricted to neurons and anterograde-specific. These data provide proof-of-principle for a conditional, non-diluting anterograde trans-synaptic tracer for mapping synaptic outputs from genetically marked neuronal subpopulations."], "field": "Neuroscience", "q_year": 2023, "q_cid": "260868016", "pos_cid": 16581640, "source": "eval_collection"}
{"query_id": "scaleup_22051897_15413966", "query": "How to estimate interaction coefficients across varying penalty strengths while allowing some coefficients to remain unpenalised", "pos": ["PATHWISE COORDINATE OPTIMIZATION. We consider “one-at-a-time” coordinate-wise descent algorithms for a class of convex optimization problems. An algorithm of this kind has been proposed for the L1-penalized regression (lasso) in the literature, but it seems to have been largely ignored. Indeed, it seems that coordinate-wise algorithms are not often used in convex optimization. We show that this algorithm is very competitive with the well-known LARS (or homotopy) procedure in large lasso problems, and that it can be applied to related methods such as the garotte and elastic net. It turns out that coordinate-wise descent does not work in the “fused lasso,” however, so we derive a generalized algorithm that yields the solution in much less time that a standard convex optimizer. Finally, we generalize the procedure to the two-dimensional fused lasso, and demonstrate its performance on some image smoothing problems. 1. Introduction. In this paper we consider statistical models that lead to convex optimization problems with inequality constraints. Typically, the optimization for these problems is carried out using a standard quadratic programming algorithm. The purpose of this paper is to explore “one-at-a-time” coordinate-wise descent algorithms for these problems. The equivalent of a coordinate descent algorithm has been proposed for the L1-penalized regression (lasso) in the literature, but it is not commonly used. Moreover, coordinate-wise algorithms seem too simple, and they are not often used in convex optimization, perhaps because they only work in specialized problems. We ourselves never appreciated the value of coordinate descent methods for convex statistical problems before working on this paper. In this paper we show that coordinate descent is very competitive with the wellknown LARS (or homotopy) procedure in large lasso problems, can deliver a path of solutions efficiently, and can be applied to many other convex statistical problems such as the garotte and elastic net. We then go on to explore a nonseparable problem in which coordinate-wise descent does not work—the “fused lasso.” We derive a generalized algorithm that yields the solution in much less time that a standard convex optimizer. Finally, we generalize the procedure to"], "field": "Neuroscience", "q_year": 2020, "q_cid": "220518974", "pos_cid": 15413966, "source": "eval_collection"}
{"query_id": "scaleup_26086801_19826041", "query": "How to determine how excitation of distinct neuronal populations in the VTA affects activity across the brain", "pos": ["Chemogenetic silencing of neurons in the mouse anterior cingulate area modulates neuronal activity and functional connectivity. The anterior cingulate area (ACA) is an integral part of the prefrontal cortex in mice and has been implicated in several cognitive functions. Previous anatomical and functional imaging studies demonstrated that the ACA is highly interconnected with numerous brain regions acting as a hub region in functional networks. However, the importance of the ACA in regulating functional network activity and connectivity remains to be elucidated. Recently developed neuromodulatory techniques, such as Designer Receptors Exclusively Activated by Designer Drugs (DREADDs) allow for precise control of neuronal activity. In this study, we used an inhibitory kappa-opioid receptor DREADDs (KORD) to temporally inhibit neuronal firing in the right ACA of mice and assessed functional network activity and connectivity using non-invasive functional MRI. We demonstrated that KORD-induced inhibition of the right ACA induced blood oxygenation-level dependent (BOLD) signal decreases and increases in connected brain regions throughout of hemispheres. Furthermore, these modulations in neuronal activity were associated with decreased intra- and interhemispheric functional connectivity. These results demonstrate that the combination of the DREADD technology and non-invasive functional imaging methods is a valuable tool for unraveling the underlying mechanisms of network function and dysfunction."], "field": "Neuroscience", "q_year": 2023, "q_cid": "260868016", "pos_cid": 198260418, "source": "eval_collection"}
{"query_id": "scaleup_24434905_52812607", "query": "How to clarify the involvement of necroptosis in depression and its relationship to inflammation and associated pathological changes", "pos": ["APOPTOSIS AND NECROPTOSIS IN THE LIVER: A MATTER OF LIFE AND DEATH. Cell death represents a basic biological paradigm that governs outcomes and long-term sequelae in almost every hepatic disease condition. Acute liver failure is characterized by massive loss of parenchymal cells but is usually followed by restitution ad integrum. By contrast, cell death in chronic liver diseases often occurs at a lesser extent but leads to long-term alterations in organ architecture and function, contributing to chronic hepatocyte turnover, the recruitment of immune cells and activation of hepatic stellate cells. These chronic cell death responses contribute to the development of liver fibrosis, cirrhosis and cancer. It has become evident that, besides apoptosis, necroptosis is a highly relevant form of programmed cell death in the liver. Differential activation of specific forms of programmed cell death might not only affect outcomes in liver diseases but also offer novel opportunities for therapeutic intervention. Here, we summarize the underlying molecular mechanisms and open questions about disease-specific activation and roles of programmed cell death forms, their contribution to response signatures and their detection. We focus on the role of apoptosis and necroptosis in acute liver injury, nonalcoholic fatty liver disease (NAFLD), nonalcoholic steatohepatitis (NASH) and liver cancer, and possible translations into clinical applications.Cell death is a fundamental driver of liver disease progression. Here, the authors summarize the specific roles of apoptosis and necroptosis in different liver disease aetiologies, including nonalcoholic fatty liver disease, nonalcoholic steatohepatitis and liver cancer.Key pointsCell death is a fundamental driver of liver disease progression to liver fibrosis, cirrhosis and hepatocellular carcinoma.Depending on the underlying disease entity, distinct forms of programmed cell death and cell death response pathways can be activated in the liver.Necroptosis is a new form of programmed cell death that is activated by the necrosome, which consists of the kinases receptor-interacting serine/threonine-protein kinase 1 (RIPK1) and RIPK3 and the pseudokinase mixed lineage kinase domain-like protein (MLKL).Despite necroptosis being challenging to detect in vivo, there is accumulating evidence that this cell death form is a pathogenically relevant driver in several liver diseases that were associated with apoptosis.Necroptosis seems to be particularly important in nonalcoholic fatty liver disease, nonalcoholic steatohepatitis and liver cancer but does not contribute to acetaminophen toxicity or ischaemia–reperfusion injury.A better functional characterization of necroptosis in liver disease models might lead to novel therapeutic strategies that target necroptosis to prevent the progression and decompensation of chronic liver disease."], "field": "Neuroscience", "q_year": 2021, "q_cid": "244349056", "pos_cid": 52812607, "source": "eval_collection"}
{"query_id": "scaleup_27328841_23419986", "query": "How to understand the hierarchical organization of macroscale brain morphology, its relationship to cortical function and cognitive decline in Alzheimer’s disease, and how disease-related changes differ from normal aging and other neurodegenerative conditions", "pos": ["Cortical patterning of morphometric similarity gradient reveals diverged hierarchical organization in sensory-motor cortices.. The topological organization of the cerebral cortex provides hierarchical axes, namely gradients, which reveal systematic variations of brain structure and function. However, the hierarchical organization of macroscopic brain morphology and how it constrains cortical function along the organizing axes remains unclear. We map the gradient of cortical morphometric similarity (MS) connectome, combining multiple features conceptualized as a \"fingerprint\" of an individual's brain. The principal MS gradient is anchored by motor and sensory cortices at two extreme ends, which are reliable and reproducible. Notably, divergences between motor and sensory hierarchies are consistent with the laminar histological thickness gradient but contrary to the canonical functional connectivity (FC) gradient. Moreover, the MS dissociates with FC gradients in the higher-order association cortices. The MS gradient recapitulates fundamental properties of cortical organization, from gene expression and cyto- and myeloarchitecture to evolutionary expansion. Collectively, our findings provide a heuristic hierarchical organization of cortical morphological neuromarkers."], "field": "Neuroscience", "q_year": 2024, "q_cid": "273288410", "pos_cid": 234199860, "source": "eval_collection"}
{"query_id": "scaleup_24601969_931503", "query": "How to clarify the emergence and timing of coordinated autonomic regulation during fetal development", "pos": ["Development of fetal movement--fetal heart rate coupling from 20 weeks through term.. This study documents the development of fetal heart rate (FHR) change in response to fetal movement (FM) in healthy fetuses from 20 weeks' gestational age through term. Thirty-one fetuses received 50 min of Doppler-based monitoring at 20, 24, 28, 32, 36 and 38-39 weeks. FHR and FM were continuously digitized. A coupling index was computed as the percentage of FMs associated with increases in FHR of 5 beats/min or more within -5 or +15 s of movement onset. The latency between FM onset and FHR change was also computed, as were the amplitude and duration of all movements. FM and FHR became more integrated with advancing gestation. Coupling increased and the latency between FM and FHR changes decreased. Maternal age, blood pressure and fetal sex did not affect FM-FHR coupling, but fetuses of women who reported greater stress in their daily lives and had faster heart rates displayed reduced coupling. These data suggest that the development of FM-FHR coupling reflects the development of the central nervous system during gestation, and that development may be affected by maternal factors."], "field": "Neuroscience", "q_year": 2022, "q_cid": "246019692", "pos_cid": 931503, "source": "eval_collection"}
{"query_id": "scaleup_25563780_4968316", "query": "How to identify additional contributors to Alzheimer’s disease, Parkinson’s disease and major depression given their shared links with platelet characteristics and studies that may include the same participants", "pos": ["Multi-trait analysis of genome-wide association summary statistics using MTAG. We introduce multi-trait analysis of GWAS (MTAG), a method for joint analysis of summary statistics from genome-wide association studies (GWAS) of different traits, possibly from overlapping samples. We apply MTAG to summary statistics for depressive symptoms (Neff = 354,862), neuroticism (N = 168,105), and subjective well-being (N = 388,538). As compared to the 32, 9, and 13 genome-wide significant loci identified in the single-trait GWAS (most of which are themselves novel), MTAG increases the number of associated loci to 64, 37, and 49, respectively. Moreover, association statistics from MTAG yield more informative bioinformatics analyses and increase the variance explained by polygenic scores by approximately 25%, matching theoretical expectations. MTAG is a new method for joint analysis of summary statistics from genome-wide association studies of different traits. Applying MTAG to summary statistics for depressive symptoms, neuroticism and subjective well-being increased discovery of associated loci as compared to single-trait analyses."], "field": "Neuroscience", "q_year": 2023, "q_cid": "255637803", "pos_cid": 4968316, "source": "eval_collection"}
{"query_id": "scaleup_25915043_14019986", "query": "How to compare hippocampal subfield volumes across diagnostic groups without overall cranial size obscuring disorder-related differences", "pos": ["Statistical adjustments for brain size in volumetric neuroimaging studies: Some practical implications in methods. Volumetric magnetic resonance imaging (MRI) brain data provide a valuable tool for detecting structural differences associated with various neurological and psychiatric disorders. Analysis of such data, however, is not always straightforward, and complications can arise when trying to determine which brain structures are “smaller” or “larger” in light of the high degree of individual variability across the population. Several statistical methods for adjusting for individual differences in overall cranial or brain size have been used in the literature, but critical differences exist between them. Using agreement among those methods as an indication of stronger support of a hypothesis is dangerous given that each requires a different set of assumptions be met. Here we examine the theoretical underpinnings of three of these adjustment methods (proportion, residual, and analysis of covariance) and apply them to a volumetric MRI data set. These three methods used for adjusting for brain size are specific cases of a generalized approach which we propose as a recommended modeling strategy. We assess the level of agreement among methods and provide graphical tools to assist researchers in determining how they differ in the types of relationships they can unmask, and provide a useful method by which researchers may tease out important relationships in volumetric MRI data. We conclude with the recommended procedure involving the use of graphical analyses to help uncover potential relationships the ROI volumes may have with head size and give a generalized modeling strategy by which researchers can make such adjustments that include as special cases the three commonly employed methods mentioned above."], "field": "Neuroscience", "q_year": 2023, "q_cid": "259150432", "pos_cid": 14019986, "source": "eval_collection"}
{"query_id": "scaleup_27002521_34124292", "query": "How to clarify the link between glymphatic dysfunction and psychiatric disorders given shared pathophysiological features but a lack of clear evidence", "pos": ["PSYCHIATRIC DISORDERS AND SLEEP. SYNOPSIS Psychiatric disorders and sleep are related in important ways. In contrast to the longstanding view of this relationship which viewed sleep problems as symptoms of psychiatric disorders, there is growing experimental evidence that the relationship between psychiatric disorders and sleep is complex and includes bi-directional causation. In this article we provide the evidence that supports this point of view, reviewing the data on the sleep disturbances seen in patients with psychiatric disorders but also reviewing the data on the impact of sleep disturbances on psychiatric conditions. Although much has been learned about the psychiatric disorders-sleep relationship, additional research is needed to better understand these relationships. This work promises to improve our ability to understand both of these phenomena and to allow us to better treat the many patients with sleep disorders and with psychiatric disorders."], "field": "Neuroscience", "q_year": 2024, "q_cid": "270025218", "pos_cid": 34124292, "source": "eval_collection"}
{"query_id": "scaleup_12781397_19561036", "query": "How to synthesize evidence on the association between social class and spontaneous face memory while accounting for differences across only three studies", "pos": ["Integrative Data Analysis: The Simultaneous Analysis of Multiple Data Sets. Both quantitative and methodological techniques exist that foster the development and maintenance of a cumulative knowledge base within the psychological sciences. Most noteworthy of these techniques is meta-analysis which allows for the synthesis of summary statistics drawn from multiple studies when the original data are not available. However, when the original data can be obtained from multiple studies, many advantages stem from the statistical analysis of the pooled data. The authors define integrative data analysis (IDA) as the analysis of multiple data sets that have been pooled into one. Although variants of IDA have been incorporated into other scientific disciplines, the use of these techniques are much less evident in psychology. In this paper the authors present an overview of IDA as it may be applied within the psychological sciences; a discussion of the relative advantages and disadvantages of IDA; a description of analytic strategies for analyzing pooled individual data; and offer recommendations for the use of IDA in practice."], "field": "Neuroscience", "q_year": 2022, "q_cid": "127813972", "pos_cid": 19561036, "source": "eval_collection"}
{"query_id": "scaleup_24601969_22200353", "query": "How to determine whether and when early self-regulation is linked to fetal sleep–wake states and motor behavior during gestation", "pos": ["Fetal Heart Rate Variability Is Affected by Fetal Movements: A Systematic Review. Introduction: Fetal heart rate variability (FHRV) evaluates the fetal neurological state, which is poorly assessed by conventional prenatal surveillance including cardiotocography (CTG). Accurate FHRV on a beat-to-beat basis, assessed by time domain and spectral domain analyses, has shown promising results in the scope of fetal surveillance. However, accepted standards for these techniques are lacking, and the influence of fetal breathing movements and gross movements may be especially challenging. Thus, current standards for equivalent assessments in adults prescribe rest and controlled respiration. The aim of this review is to clarify the importance of fetal movements on FHRV. Methods: A systematic review in accordance with the PRISMA guidelines based on publications in the EMBASE, the MEDLINE, and the Cochrane Library databases was performed. Studies describing the impact of fetal movements on time domain, spectral domain and entropy analyses in healthy human fetuses were reviewed. Only studies based on fetal electrocardiography or fetal magnetocardiography were included. PROSPERO registration number: CRD42018068806. Results: In total, 14 observational studies were included. Fetal movement detection, signal processing, length, and selection of appropriate time series varied across studies. Despite these divergences, all studies showed an increase in overall FHRV in the moving fetus compared to the resting fetus. Especially short-term, vagal mediated indexes showed an increase during fetal breathing movements including an increase in Root Mean Square of the Successive Differences (RMSSD) and High Frequency power (HF) and a decrease in Low Frequency power/High Frequency power (LF/HF). These findings were present even in analyses restricted to one specific fetal behavioral state defined by Nijhuis. On the other hand, fetal body movements seemed to increase parameters supposed to represent the sympathetic response [LF and Standard Deviation of RR-intervals from normal sinus beats (SDNN)] proportionally more than parameters representing the parasympathetic response (RMSSD, HF). Results regarding entropy analyses were inconclusive. Conclusion: Time domain analyses as well as spectral domain analyses are affected by fetal movements. Fetal movements and especially breathing movements should be considered in these analyses of FHRV."], "field": "Neuroscience", "q_year": 2022, "q_cid": "246019692", "pos_cid": 222003537, "source": "eval_collection"}
{"query_id": "scaleup_24798495_10662074", "query": "How to distinguish the unique relationships of age and language aptitude with task-related activity during novel word learning without attributing their shared associations to either factor alone", "pos": ["Regression-based estimation of ERP waveforms: I. The rERP framework. ERP averaging is an extraordinarily successful method, but can only be applied to a limited range of experimental designs. We introduce the regression-based rERP framework, which extends ERP averaging to handle arbitrary combinations of categorical and continuous covariates, partial confounding, non-linear effects, and overlapping responses to distinct events, all within a single unified system. rERPs enable a richer variety of paradigms (including high-N naturalistic designs) while preserving the advantages of traditional ERPs. This article provides an accessible introduction to what rERPs are, why they are useful, how they are computed, and when we should expect them to be effective, particularly in cases of partial confounding. A companion article discusses how non-linear effects and overlap correction can be handled within this framework, as well as practical considerations around baselining, filtering, statistical testing, and artifact rejection. Free software implementing these techniques is available."], "field": "Neuroscience", "q_year": 2022, "q_cid": "247984956", "pos_cid": 10662074, "source": "eval_collection"}
{"query_id": "scaleup_26131633_22947896", "query": "How to overcome vanishing gradients and combine information within individual electroencephalography epochs and across adjacent epochs while accounting for their location-dependent importance", "pos": ["Residual Fusion Network Based Attention for Aspect Level Sentiment Analysis. Aspect level sentiment analysis is a more fine-grain task compared to document level and sentence level. The aim of the task is to identify the sentiment polarity expressed to the given aspect in the text. In this paper, we propose a residual aspect fusion network with attention for the aspect level sentiment classification. In this network, bidirectional GRU is used to collect semantic information of both sentence words and aspect words, and then attention mechanism is applied to construct aspect vectors for each word in the sentence. In the residual fusion module, the model fuses the aspect information and sentence information together by residual connection structure, in which position weight is applied to utilize the position information of aspect words. At the end of the model, Transformer encode layer is used to extract global feature and fully connected layers are used as the classifier. We train and test the network on SemEval2014 task 4 (Restaurant and Laptop) and Twitter datasets, and the experiments demonstrate that our model performs better than previous methods."], "field": "Neuroscience", "q_year": 2023, "q_cid": "261316332", "pos_cid": 229478963, "source": "eval_collection"}
{"query_id": "scaleup_27611336_11953529", "query": "How to determine the appropriate number of eeg microstate classes for each eye condition and preprocessing level when segmentation quality has multiple evaluation criteria", "pos": ["NbClust: An R Package for Determining the Relevant Number of Clusters in a Data Set. Clustering is the partitioning of a set of objects into groups (clusters) so that objects within a group are more similar to each others than objects in different groups. Most of the clustering algorithms depend on some assumptions in order to define the subgroups present in a data set. As a consequence, the resulting clustering scheme requires some sort of evaluation as regards its validity. The evaluation procedure has to tackle difficult problems such as the quality of clusters, the degree with which a clustering scheme fits a specific data set and the optimal number of clusters in a partitioning. In the literature, a wide variety of indices have been proposed to find the optimal number of clusters in a partitioning of a data set during the clustering process. However, for most of indices proposed in the literature, programs are unavailable to test these indices and compare them. The R package NbClust has been developed for that purpose. It provides 30 indices which determine the number of clusters in a data set and it offers also the best clustering scheme from different results to the user. In addition, it provides a function to perform k-means and hierarchical clustering with different distance measures and aggregation methods. Any combination of validation indices and clustering methods can be requested in a single function call. This enables the user to simultaneously evaluate several clustering schemes while varying the number of clusters, to help determining the most appropriate number of clusters for the data set of interest."], "field": "Neuroscience", "q_year": 2025, "q_cid": "276113368", "pos_cid": 119535291, "source": "eval_collection"}
{"query_id": "scaleup_24872643_51600332", "query": "How to understand hemin’s cellular specificity and how it initiates damage to myelinated axons", "pos": ["Continuous Uptake or Saturation-Investigation of Concentration and Surface-Packing-Specific Hemin Interaction with Lipid Membranes.. Drug design and targeted delivery in cells serve as a flourishing area not only for scientific inquiry, owing to numerous clinical applications, but also for understanding cell interaction with exogenous materials. The membrane localization of heme and its analog hemin, one of the most biologically relevant planar organic molecule, is very important to understand the molecular mechanism of intercalation and adsorption of this cytotoxic molecule after its dissociation from proteins such as hemoglobin. Herein, we investigate the differential behavior of hemin on the soft membrane surfaces of phospholipids by synchrotron-based X-ray scattering techniques, Langmuir monolayer measurements, and molecular dynamics simulation. A continuous hemin uptake from the subphase and intercalation into and/or adsorption on to the membrane surface have been witnessed in a strong membrane surface packing-specific manner. Competitive interactions between hemin-membrane and hemin-hemin are proposed to be responsible for the critical hemin concentration. Up to the limit, a continuous hemin uptake is possible and beyond that the hemin-hemin interaction dominates, effectively reducing the hemin intercalation into the membrane. This structural model of the hemin-uptake process can be generalized to understand the localization and transport across membranes and also for the development and design of new drugs."], "field": "Neuroscience", "q_year": 2022, "q_cid": "248726433", "pos_cid": 51600332, "source": "eval_collection"}
{"query_id": "scaleup_27916151_22717469", "query": "How to determine whether the relationship with therapeutic outcomes generalizes across clinical encounters despite differences in social tasks and patient–therapist relationships", "pos": ["Human attachments shape interbrain synchrony toward efficient performance of social goals. The human brain has undergone massive expansion across primate evolution through life amidst multi-layered social attachments; within families, among friends, and between clan members and this enabled humans to coordinate their brains with those of others toward the execution of complex social goals. We examined how human attachments facilitate efficient, resource-sensitive performance of social goals by balancing neural and behavioral synchrony. Using hyperscanning EEG, we collected neural data from male-female pairs in three groups (N=158, 79 pairs); long-term couples, best friends, and unfamiliar group members, during two ecologically-valid naturalistic tasks; motor coordination and empathy giving. Across groups and tasks, neural synchrony was supported by behavior coordination and orchestrated multiple neural rhythms. In the goal-directed motor task, interbrain synchrony implicated beta and gamma rhythms localized to sensorimotor areas. Couples showed the highest neural synchrony combined with greatest behavioral synchrony and such brain-behavior linkage resulted in speedy performance, conserving energy in the long run. The socially-oriented empathy task triggered neural synchrony in widely-distributed sensorimotor and bilateral temporal regions, integrated alpha, beta, and gamma rhythms, and implicated brain-behavior complementarity; couples displayed the highest behavioral synchrony combined with lowest neural synchrony toward greatest felt support while strangers exhibited the opposite pattern. Findings suggest that human attachments provide a familiar backdrop of temporal regularities, required for the brain's allostatic function, and interbrain and behavioral synchrony are sculpted by familiarity and closeness toward resource-sensitive performance of survival-related social goals, toiled by two."], "field": "Neuroscience", "q_year": 2025, "q_cid": "279161514", "pos_cid": 227174697, "source": "eval_collection"}
{"query_id": "scaleup_25990505_16906441", "query": "How to determine the importance of pyruvate carboxylase activity for human astrocyte survival", "pos": ["Inhibitors of Pyruvate Carboxylase. This review aims to discuss the varied types of inhibitors of biotin-dependent carboxylases, with an emphasis on the inhibitors of pyruvate carboxylase. Some of these inhibitors are physiologically relevant, in that they provide ways of regulating the cellular activities of the enzymes e.g. aspartate and prohibitin inhibition of pyruvate carboxylase. Most of the inhibitors that will be discussed have been used to probe various aspects of the structure and function of these enzymes. They target particular parts of the structure e.g. avidin – biotin, FTP – ATP binding site, oxamate – pyruvate binding site, phosphonoacetate – binding site of the putative carboxyphosphate intermediate."], "field": "Neuroscience", "q_year": 2023, "q_cid": "259905055", "pos_cid": 16906441, "source": "eval_collection"}
{"query_id": "scaleup_25674793_58005005", "query": "How to determine the role of a specific group of cells in appetite and growth without damaging other cells", "pos": ["Live imaging of leukocyte recruitment in a zebrafish model of chemical liver injury. Studying early immune responses to organ damage in situ requires animal models amenable to intravital imaging. Here, we used transparent zebrafish larvae, a powerful animal model for innate immunity, to measure leukocyte recruitment to damaged livers. Bath application of metronidazole (Mtz) to fish expressing nitroreductase (NTR) under a liver-specific promoter damaged the organ within 24 hours causing oxidative stress, distorted liver morphology, accumulation of TUNEL-positive cells, and transcriptional upregulation of apoptotic and antioxidant genes. Inflammatory gene transcription in damaged hepatocytes was attenuated. In line with predominant apoptosis, macrophages were massively recruited into Mtz/NTR-damaged livers. By contrast, neutrophil infiltration was more variable and delayed, consistent with less abundant necrosis and an attenuated inflammatory capacity of damaged hepatocytes."], "field": "Neuroscience", "q_year": 2023, "q_cid": "256747933", "pos_cid": 58005005, "source": "eval_collection"}
{"query_id": "scaleup_23741828_23157987", "query": "How to distinguish the effects of localized seizures during sleep on dreaming and dream recall from epilepsy-related memory difficulties while awake", "pos": ["The Oscillatory Basis of Working Memory Function and Dysfunction in Epilepsy. Working memory (WM) deficits are pervasive co-morbidities of epilepsy. Although the pathophysiological mechanisms underpinning these impairments remain elusive, it is thought that WM depends on oscillatory interactions within and between nodes of large-scale functional networks. These include the hippocampus and default mode network as well as the prefrontal cortex and frontoparietal central executive network. Here, we review the functional roles of neural oscillations in subserving WM and the putative mechanisms by which epilepsy disrupts normative activity, leading to aberrant oscillatory signatures. We highlight the particular role of interictal epileptic activity, including interictal epileptiform discharges and high frequency oscillations (HFOs) in WM deficits. We also discuss the translational opportunities presented by greater understanding of the oscillatory basis of WM function and dysfunction in epilepsy, including potential targets for neuromodulation."], "field": "Neuroscience", "q_year": 2021, "q_cid": "237418289", "pos_cid": 231579873, "source": "eval_collection"}
{"query_id": "scaleup_27002904_22886720", "query": "How to effectively find the best solution", "pos": ["Chaos based optics inspired optimization algorithms as global solution search approach. Abstract Metaheuristic optimization algorithms are efficiently used in many large-scale complex problems. Recently, a physics-based metaheuristic search and optimization method entitled Optics Inspired Optimization (OIO) has been proposed. OIO treats the search field of the interested problem to be optimized as a wavy mirror in which the concave mirror is represented as a valley and the convex mirror is represented as a peak. Each candidate solution represents an artificial light point. OIO is a very new metaheuristic method and different approaches should be integrated to obtain a faster convergence with high accuracy by balancing the exploitation and exploration. This paper is the first work on performance improvement of this method by preventing the falling into local optimum solutions and slow convergence speed. In this article, different ergodic chaotic systems are used for the first time to generate chaotic values instead of random values in OIO processes in order to enhance the global convergence speed and prevent stuck on local solutions of classical OIO algorithm. For this purpose, three new enhanced OIO methods are proposed. Furthermore, a new application area for chaos is proposed. The chaotic OIO algorithms proposed in this study are tested in unconstrained benchmark problems and constrained real-world engineering problems. Promising results are obtained from the detailed simulations."], "field": "Neuroscience", "q_year": 2024, "q_cid": "270029040", "pos_cid": 228867204, "source": "eval_collection"}
{"query_id": "scaleup_28293860_12297612", "query": "How to assess whether changes in kynurenine levels impair glomerular filtration in vivo", "pos": ["A novel transgenic zebrafish model for blood-brain and blood-retinal barrier development. BackgroundDevelopment and maintenance of the blood-brain and blood-retinal barrier is critical for the homeostasis of brain and retinal tissue. Despite decades of research our knowledge of the formation and maintenance of the blood-brain (BBB) and blood-retinal (BRB) barrier is very limited. We have established an in vivo model to study the development and maintenance of these barriers by generating a transgenic zebrafish line that expresses a vitamin D-binding protein fused with enhanced green fluorescent protein (DBP-EGFP) in blood plasma, as an endogenous tracer.ResultsThe temporal establishment of the BBB and BRB was examined using this transgenic line and the results were compared with that obtained by injection of fluorescent dyes into the sinus venosus of embryos at various stages of development. We also examined the expression of claudin-5, a component of tight junctions during the first 4 days of development. We observed that the BBB of zebrafish starts to develop by 3 dpf, with expression of claudin-5 in the central arteries preceding it at 2 dpf. The hyaloid vasculature in the zebrafish retina develops a barrier function at 3 dpf, which endows the zebrafish with unique advantages for studying the BRB.ConclusionZebrafish embryos develop BBB and BRB function simultaneously by 3 dpf, which is regulated by tight junction proteins. The Tg(l-fabp:DBP-EGFP) zebrafish will have great advantages in studying development and maintenance of the blood-neural barrier, which is a new application for the widely used vertebrate model."], "field": "Neuroscience", "q_year": 2025, "q_cid": "282938608", "pos_cid": 12297612, "source": "eval_collection"}
{"query_id": "scaleup_27343339_54526174", "query": "How to reliably detect selective publication of findings about differences in average outcomes relative to their variability, despite small samples of repeatedly measured participants or substantial differences across studies, without falsely identifying bias", "pos": ["Testing for funnel plot asymmetry of standardized mean differences. Publication bias and other forms of outcome reporting bias are critical threats to the validity of findings from research syntheses. A variety of methods have been proposed for detecting selective outcome reporting in a collection of effect size estimates, including several methods based on assessment of asymmetry of funnel plots, such as the Egger's regression test, the rank correlation test, and the Trim‐and‐Fill test. Previous research has demonstated that the Egger's regression test is miscalibrated when applied to log‐odds ratio effect size estimates, because of artifactual correlation between the effect size estimate and its standard error. This study examines similar problems that occur in meta‐analyses of the standardized mean difference, a ubiquitous effect size measure in educational and psychological research. In a simulation study of standardized mean difference effect sizes, we assess the Type I error rates of conventional tests of funnel plot asymmetry, as well as the likelihood ratio test from a three‐parameter selection model. Results demonstrate that the conventional tests have inflated Type I error due to the correlation between the effect size estimate and its standard error, while tests based on either a simple modification to the conventional standard error formula or a variance‐stabilizing transformation both maintain close‐to‐nominal Type I error."], "field": "Neuroscience", "q_year": 2024, "q_cid": "273433397", "pos_cid": 54526174, "source": "eval_collection"}
{"query_id": "scaleup_23387133_19576496", "query": "How to determine when antibiotic-induced taste and smell disorders occur, whether their risk decreases during treatment, and when patients need careful monitoring", "pos": ["Analyses of Respiratory Depression Associated with Opioids in Cancer Patients Based on the Japanese Adverse Drug Event Report Database.. Opioid-induced respiratory depression is a potentially life-threatening adverse drug event. The purpose of this study was to evaluate the incidence of respiratory depression using the Japanese Adverse Drug Event Report (JADER) Database to obtain data to promote proper use of opioids. The JADER database from April 2004 to March 2017 was obtained from the Pharmaceuticals and Medical Devices Agency. We calculated the reporting odds ratios (RORs) of suspected opioids (morphine, fentanyl, oxycodone, tapentadol, methadone, tramadol, pentazocine, buprenorphine, and codeine phosphate hydrate), analyzed the daily dose at first appearance and the time-to-onset profile, and assessed the hazard type using the Weibull shape parameter. ROR analysis detected adverse event signals for all opioids. Morphine showed a large ROR value with statistical significance in elderly (≥70 years old) patients. The median daily doses of oral morphine and oxycodone for inducing respiratory depression were comparably low (30 mg/d as oral morphine equivalent dose), while that of transdermal fentanyl was 120 mg/d (oral morphine equivalent dose). On time-to-onset analysis using the Weibull distribution, those opioids were classified as the early failure type. The median time-to-onset of oral morphine, oral oxycodone and transdermal fentanyl was 5.5, 11 and 12.5 d, respectively, and almost 50% of cases were reported within 30 d. Taken together, our results suggest that it is important to monitor patients carefully for at least the first one week to one month, even if opioids are administered at a relatively low dose, especially in elderly patients administered morphine."], "field": "Neuroscience", "q_year": 2021, "q_cid": "233871338", "pos_cid": 195764965, "source": "eval_collection"}
{"query_id": "scaleup_27182223_18600099", "query": "How to predict three-year rates of lateral ventricular enlargement in early-stage Huntington’s disease and identify patients with similar expected progression for clinical trial stratification despite a high-dimensional feature space", "pos": ["An Introduction to Recursive Partitioning: Rationale, Application and Characteristics of Classification and Regression Trees, Bagging and Random Forests. Recursive partitioning methods have become popular and widely used tools for non-parametric regression and classification in many scientific fields. Especially random forests, that can deal with large numbers of predictor variables even in the presence of complex interactions, have been applied successfully in genetics, clinical medicine and bioinformatics within the past few years. High dimensional problems are common not only in genetics, but also in some areas of psychological research, where only few subjects can be measured due to time or cost constraints, yet a large amount of data is generated for each subject. Random forests have been shown to achieve a high prediction accuracy in such applications, and provide descriptive variable importance measures reflecting the impact of each variable in both main effects and interactions. The aim of this work is to introduce the principles of the standard recursive partitioning methods as well as recent methodological improvements, to illustrate their usage for low and high dimensional data exploration, but also to point out limitations of the methods and potential pitfalls in their practical application. Application of the methods is illustrated using freely available implementations in the R system for statistical computing."], "field": "Neuroscience", "q_year": 2024, "q_cid": "271822237", "pos_cid": 18600099, "source": "eval_collection"}
{"query_id": "scaleup_25784929_27884972", "query": "How to determine the effectiveness and long-term safety of chemically synthesized compounds intended to prevent ischemic-stroke-related damage", "pos": ["Free radicals, antioxidants and functional foods: Impact on human health. In recent years, there has been a great deal of attention toward the field of free radical chemistry. Free radicals reactive oxygen species and reactive nitrogen species are generated by our body by various endogenous systems, exposure to different physiochemical conditions or pathological states. A balance between free radicals and antioxidants is necessary for proper physiological function. If free radicals overwhelm the body's ability to regulate them, a condition known as oxidative stress ensues. Free radicals thus adversely alter lipids, proteins, and DNA and trigger a number of human diseases. Hence application of external source of antioxidants can assist in coping this oxidative stress. Synthetic antioxidants such as butylated hydroxytoluene and butylated hydroxyanisole have recently been reported to be dangerous for human health. Thus, the search for effective, nontoxic natural compounds with antioxidative activity has been intensified in recent years. The present review provides a brief overview on oxidative stress mediated cellular damages and role of dietary antioxidants as functional foods in the management of human diseases."], "field": "Neuroscience", "q_year": 2023, "q_cid": "257849292", "pos_cid": 27884972, "source": "eval_collection"}
{"query_id": "scaleup_27182223_21889700", "query": "How to determine which input features matter most for classification outcomes and how they influence those outcomes individually and together", "pos": ["A Unified Approach to Interpreting Model Predictions. Understanding why a model makes a certain prediction can be as crucial as the prediction's accuracy in many applications. However, the highest accuracy for large modern datasets is often achieved by complex models that even experts struggle to interpret, such as ensemble or deep learning models, creating a tension between accuracy and interpretability. In response, various methods have recently been proposed to help users interpret the predictions of complex models, but it is often unclear how these methods are related and when one method is preferable over another. To address this problem, we present a unified framework for interpreting predictions, SHAP (SHapley Additive exPlanations). SHAP assigns each feature an importance value for a particular prediction. Its novel components include: (1) the identification of a new class of additive feature importance measures, and (2) theoretical results showing there is a unique solution in this class with a set of desirable properties. The new class unifies six existing methods, notable because several recent methods in the class lack the proposed desirable properties. Based on insights from this unification, we present new methods that show improved computational performance and/or better consistency with human intuition than previous approaches."], "field": "Neuroscience", "q_year": 2024, "q_cid": "271822237", "pos_cid": 21889700, "source": "eval_collection"}
{"query_id": "scaleup_27328841_23568220", "query": "How to robustly characterize brain-network topography and morphological relationships among brain regions in aging and neurodegenerative disease and connect spatial patterns of brain abnormalities to the distinct biological mechanisms underlying Alzheimer’s disease and other conditions", "pos": ["Regional radiomics similarity networks (R2SNs) in the human brain: Reproducibility, small-world properties and a biological basis. Abstract A structural covariance network (SCN) has been used successfully in structural magnetic resonance imaging (sMRI) studies. However, most SCNs have been constructed by a unitary marker that is insensitive for discriminating different disease phases. The aim of this study was to devise a novel regional radiomics similarity network (R2SN) that could provide more comprehensive information in morphological network analysis. R2SNs were constructed by computing the Pearson correlations between the radiomics features extracted from any pair of regions for each subject (AAL atlas). We further assessed the small-world property of R2SNs, and we evaluated the reproducibility in different datasets and through test-retest analysis. The relationships between the R2SNs and general intelligence/interregional coexpression of genes were also explored. R2SNs could be replicated in different datasets, regardless of the use of different feature subsets. R2SNs showed high reproducibility in the test-retest analysis (intraclass correlation coefficient > 0.7). In addition, the small-word property (σ > 2) and the high correlation between gene expression (R = 0.29, p < 0.001) and general intelligence were determined for R2SNs. Furthermore, the results have also been repeated in the Brainnetome atlas. R2SNs provide a novel, reliable, and biologically plausible method to understand human morphological covariance based on sMRI."], "field": "Neuroscience", "q_year": 2024, "q_cid": "273288410", "pos_cid": 235682206, "source": "eval_collection"}
{"query_id": "scaleup_23180833_8249689", "query": "How to explain how tasks represented in sensory coordinates guide commands in motor coordinates", "pos": ["Bayesian Action&Perception: Representing the World in the Brain. Theories of perception seek to explain how sensory data are processed to identify previously experienced objects, but they usually do not consider the decisions and effort that goes into acquiring the sensory data. Identification of objects according to their tactile properties requires active exploratory movements. The sensory data thereby obtained depend on the details of those movements, which human subjects change rapidly and seemingly capriciously. Bayesian Exploration is an algorithm that uses prior experience to decide which next exploratory movement should provide the most useful data to disambiguate the most likely possibilities. In previous studies, a simple robot equipped with a biomimetic tactile sensor and operated according to Bayesian Exploration performed in a manner similar to and actually better than humans on a texture identification task. Expanding on this, “Bayesian Action&Perception” refers to the construction and querying of an associative memory of previously experienced entities containing both sensory data and the motor programs that elicited them. We hypothesize that this memory can be queried (i) to identify useful next exploratory movements during identification of an unknown entity (“action for perception”) or (ii) to characterize whether an unknown entity is fit for purpose (“perception for action”) or (iii) to recall what actions might be feasible for a known entity (Gibsonian affordance). The biomimetic design of this mechatronic system may provide insights into the neuronal basis of biological action and perception."], "field": "Neuroscience", "q_year": 2021, "q_cid": "231808334", "pos_cid": 8249689, "source": "eval_collection"}
{"query_id": "scaleup_28004888_5236928", "query": "How to understand how peripheral inflammation triggers counteracting sympathetic responses", "pos": ["Sensory afferent and hypoxia-mediated activation of nucleus tractus solitarius neurons that project to the rostral ventrolateral medulla. The nucleus tractus solitarius (nTS) of the brainstem receives sensory afferent inputs, processes that information, and sends projections to a variety of brain regions responsible for influencing autonomic and respiratory output. The nTS sends direct projections to the rostral ventrolateral medulla (RVLM), an area important for cardiorespiratory reflexes and homeostasis. Since the net reflex effect of nTS processing ultimately depends on the properties of output neurons, we determined the characteristics of these RVLM-projecting nTS neurons using electrophysiological and immunohistochemical techniques. RVLM-projecting nTS neurons were identified by retrograde tracers. Patch clamp analysis in the horizontal brainstem nTS slice demonstrated that RVLM-projecting nTS cells exhibit constant latency solitary tract evoked EPSCs, suggesting they receive strong monosynaptic contacts from visceral afferents. Three distinct patterns of action potential firing, associated with different underlying potassium currents, were observed in RVLM-projecting cells. Following activation of the chemoreflex in conscious animals by three hours of acute hypoxia, 11.2 ± 1.9% of the RVLM-projecting nTS neurons were activated, as indicated by positive Fos-immunoreactivity. Very few RVLM-projecting nTS cells were catecholaminergic. Taken together, these data suggest that RVLM projecting nTS neurons receive strong monosynaptic inputs from sensory afferents and a subpopulation participates in the chemoreflex pathway."], "field": "Neuroscience", "q_year": 2025, "q_cid": "280048881", "pos_cid": 5236928, "source": "eval_collection"}
{"query_id": "scaleup_12781397_21655641", "query": "How to explain social-class differences in spontaneous social attunement and determine whether they extend to face memory", "pos": ["Social Class Predicts Emotion Perception and Perspective-Taking Performance in Adults. “Theory of Mind” (ToM; people’s ability to infer and use information about others’ mental states) varies across cultures. In four studies (N = 881), including two preregistered replications, we show that social class predicts performance on ToM tasks. In Studies 1A and 1B, we provide new evidence for a relationship between social class and emotion perception: Higher-class individuals performed more poorly than their lower-class counterparts on the Reading the Mind in the Eyes Test, which has participants infer the emotional states of targets from images of their eyes. In Studies 2A and 2B, we provide the first evidence that social class predicts visual perspective taking: Higher-class individuals made more errors than lower-class individuals in the Director Task, which requires participants to assume the visual perspective of another person. Potential mechanisms linking social class to performance in different ToM domains, as well as implications for deficiency-centered perspectives on low social class, are discussed."], "field": "Neuroscience", "q_year": 2022, "q_cid": "127813972", "pos_cid": 216556415, "source": "eval_collection"}
{"query_id": "scaleup_28098344_16869086", "query": "How to explain imaginative engagement in immersive art across artforms, including how artworks elicit fantasy and challenge the distinction between imagination and reality", "pos": ["Superior pattern processing is the essence of the evolved human brain. Humans have long pondered the nature of their mind/brain and, particularly why its capacities for reasoning, communication and abstract thought are far superior to other species, including closely related anthropoids. This article considers superior pattern processing (SPP) as the fundamental basis of most, if not all, unique features of the human brain including intelligence, language, imagination, invention, and the belief in imaginary entities such as ghosts and gods. SPP involves the electrochemical, neuronal network-based, encoding, integration, and transfer to other individuals of perceived or mentally-fabricated patterns. During human evolution, pattern processing capabilities became increasingly sophisticated as the result of expansion of the cerebral cortex, particularly the prefrontal cortex and regions involved in processing of images. Specific patterns, real or imagined, are reinforced by emotional experiences, indoctrination and even psychedelic drugs. Impaired or dysregulated SPP is fundamental to cognitive and psychiatric disorders. A broader understanding of SPP mechanisms, and their roles in normal and abnormal function of the human brain, may enable the development of interventions that reduce irrational decisions and destructive behaviors."], "field": "Neuroscience", "q_year": 2025, "q_cid": "280983443", "pos_cid": 16869086, "source": "eval_collection"}
{"query_id": "scaleup_25565240_23207651", "query": "How to characterize skill-related temporal variability in thousands of grip-force measurements across multiple sensors, hands, and task sessions to distinguish novice from expert manual robot control performance", "pos": ["Human Symmetry Uncertainty Detected by a Self-Organizing Neural Network Map. Symmetry in biological and physical systems is a product of self-organization driven by evolutionary processes, or mechanical systems under constraints. Symmetry-based feature extraction or representation by neural networks may unravel the most informative contents in large image databases. Despite significant achievements of artificial intelligence in recognition and classification of regular patterns, the problem of uncertainty remains a major challenge in ambiguous data. In this study, we present an artificial neural network that detects symmetry uncertainty states in human observers. To this end, we exploit a neural network metric in the output of a biologically inspired Self-Organizing Map Quantization Error (SOM-QE). Shape pairs with perfect geometry mirror symmetry but a non-homogenous appearance, caused by local variations in hue, saturation, or lightness within and/or across the shapes in a given pair produce, as shown here, a longer choice response time (RT) for “yes” responses relative to symmetry. These data are consistently mirrored by the variations in the SOM-QE from unsupervised neural network analysis of the same stimulus images. The neural network metric is thus capable of detecting and scaling human symmetry uncertainty in response to patterns. Such capacity is tightly linked to the metric’s proven selectivity to local contrast and color variations in large and highly complex image data."], "field": "Neuroscience", "q_year": 2023, "q_cid": "255652406", "pos_cid": 232076513, "source": "eval_collection"}
{"query_id": "scaleup_28314670_16489114", "query": "How to establish clear purpose and research questions for a scoping review while maintaining guidance, rigor, and transparency across subsequent research stages", "pos": ["Scoping studies: advancing the methodology. BackgroundScoping studies are an increasingly popular approach to reviewing health research evidence. In 2005, Arksey and O'Malley published the first methodological framework for conducting scoping studies. While this framework provides an excellent foundation for scoping study methodology, further clarifying and enhancing this framework will help support the consistency with which authors undertake and report scoping studies and may encourage researchers and clinicians to engage in this process.DiscussionWe build upon our experiences conducting three scoping studies using the Arksey and O'Malley methodology to propose recommendations that clarify and enhance each stage of the framework. Recommendations include: clarifying and linking the purpose and research question (stage one); balancing feasibility with breadth and comprehensiveness of the scoping process (stage two); using an iterative team approach to selecting studies (stage three) and extracting data (stage four); incorporating a numerical summary and qualitative thematic analysis, reporting results, and considering the implications of study findings to policy, practice, or research (stage five); and incorporating consultation with stakeholders as a required knowledge translation component of scoping study methodology (stage six). Lastly, we propose additional considerations for scoping study methodology in order to support the advancement, application and relevance of scoping studies in health research.SummarySpecific recommendations to clarify and enhance this methodology are outlined for each stage of the Arksey and O'Malley framework. Continued debate and development about scoping study methodology will help to maximize the usefulness and rigor of scoping study findings within healthcare research and practice."], "field": "Neuroscience", "q_year": 2025, "q_cid": "283146707", "pos_cid": 16489114, "source": "eval_collection"}
{"query_id": "scaleup_28004888_58656706", "query": "How to understand peripheral inflammation’s disruption of brain function and cognition and the breakdown of neural regulation that normally restrains inflammation", "pos": ["Chronic hyperammonemia induces peripheral inflammation that leads to cognitive impairment in rats: reversal by anti-tnfa treatment.. BACKGROUND & AIMS Chronic hyperammonemia induces neuroinflammation which mediates cognitive impairment. How hyperammonemia induces neuroinflammation remains unclear. We propose the hypothesis that chronic hyperammonemia would induce peripheral inflammation that would induce neuroinflammation and cognitive impairment, which would be prevented by reducing peripheral inflammation. The aims of this work were to assess whether: 1) chronic hyperammonemia induces peripheral inflammation; 2) peripheral inflammation contributes to hyperammonemia-induced neuroinflammation, altered neurotransmission and impaired spatial learning; 3) hyperammonemia-induced inflammation and neurpoinflammation are reversible following hyperammonemia elimination; 4) reducing peripheral inflammation with anti-TNFa reduces neuroinflammation and improves neurotransmission and cognitive impairment in hyperammonemic rats. METHODS Chronic hyperammonemia was induced by feeding rats an ammonia-containing diet. Peripheral inflammation was analyzed by measuring prostaglandin E2 (PGE2), TNFa, IL-6 and IL-10. We tested whether chronic anti-TNFa treatment improves peripheral inflammation, neuroinflammation, membrane expression of glutamate receptors in hippocampus and spatial learning. RESULTS Hyperammonemic rats show a rapid and reversible induction of peripheral inflammation, with increased pro-inflammatory PGE2, TNFa and IL-6, followed at around 10 days by reduced anti-inflammatory IL-10. Peripheral anti-TNFa treatment prevents peripheral inflammation induction and the increase in IL-1b and TNFa and microglia activation in hippocampus of the rats, which remain hyperammonemic. This is associated with prevention of the altered membrane expression of glutamate receptors and of the impairment of spatial memory assessed in the radial and Morris water mazes. CONCLUSIONS This report unveils a new mechanism by which chronic hyperammonemia induces neurological alterations: induction of peripheral inflammation. This supports that reducing peripheral inflammation by safe procedures would improve cognitive function in patients with minimal hepatic encephalopathy. LAY SUMMARY This article unveils a new mechanism by which chronic hyperammonemia induces cognitive impairment in rats: chronic hyperammonemia per se induces peripheral inflammation, which mediates many of its effects on brain, including induction of neuroinflammation, which alters neurotransmission, leading to cognitive impairment. It is also shown that reducing peripheral inflammation by treating rats with anti-TNFa, which does not cross the blood-brain barrier, prevents hyperammonemia-induced neuroinflammation, alterations in neurotransmission and cognitive impairment. This new view may have an important impact on the understanding of the mechanisms involved in minimal hepatic encephalopathy in cirrhotic patients and may allow developing new therapeutic approaches."], "field": "Neuroscience", "q_year": 2025, "q_cid": "280048881", "pos_cid": 58656706, "source": "eval_collection"}
{"query_id": "scaleup_20473915_41258858", "query": "How to limit acrylamide formation and reduce rapid starch digestibility in baked starchy foods?", "pos": ["Inhibition of α-Amylase and α-Glucosidase Activity by Tea and Grape Seed Extracts and their Constituent Catechins. We evaluated the inhibitory effects of plant-based extracts (grape seed, green tea, and white tea) on α-amylase and α-glucosidase activity, glucosidases required for starch digestion. The abundant flavan-3-ol monomers (catechins) in these extracts were also tested for their inhibitory potential and evaluated against the pharmacological glucosidase inhibitor, acarbose. To evaluate relative potency of these extracts and catechins, the concentrations required for 50 and 90% inhibition of enzyme activity were determined. Maximum enzyme inhibition was used to assess an inhibitor’s relative efficacy. Results showed that grape seed extract strongly inhibited both α-amylase and α-glucosidase activity, with equal and much higher potency, respectively, than acarbose. While tea extracts and individual catechin 3-gallates were less effective inhibitors of α-amylase, they were potent inhibitors of α-glucosidase. Our data show that plant extracts containing catechin 3-gallates are potent inhibitors of α-glucosidase, and suggest that procyanidins found in grape seed extract strongly inhibit α-amylase activity."], "field": "Nursing", "q_year": 2019, "q_cid": "204739159", "pos_cid": 41258858, "source": "eval20x26"}
{"query_id": "scaleup_35595464_3103103", "query": "How to identify the signal that triggers increased copper accumulation at sites of M. tuberculosis infection", "pos": ["Upregulated Copper Transporters in Hypoxia-Induced Pulmonary Hypertension. Pulmonary vascular remodeling and increased arterial wall stiffness are two major causes for the elevated pulmonary vascular resistance and pulmonary arterial pressure in patients and animals with pulmonary hypertension. Cellular copper (Cu) plays an important role in angiogenesis and extracellular matrix remodeling; increased Cu in vascular smooth muscle cells has been demonstrated to be associated with atherosclerosis and hypertension in animal experiments. In this study, we show that the Cu-uptake transporter 1, CTR1, and the Cu-efflux pump, ATP7A, were both upregulated in the lung tissues and pulmonary arteries of mice with hypoxia-induced pulmonary hypertension. Hypoxia also significantly increased expression and activity of lysyl oxidase (LOX), a Cu-dependent enzyme that causes crosslinks of collagen and elastin in the extracellular matrix. In vitro experiments show that exposure to hypoxia or treatment with cobalt (CoCl2) also increased protein expression of CTR1, ATP7A, and LOX in pulmonary arterial smooth muscle cells (PASMC). In PASMC exposed to hypoxia or treated with CoCl2, we also confirmed that the Cu transport is increased using 64Cu uptake assays. Furthermore, hypoxia increased both cell migration and proliferation in a Cu-dependent manner. Downregulation of hypoxia-inducible factor 1α (HIF-1α) with siRNA significantly attenuated hypoxia-mediated upregulation of CTR1 mRNA. In summary, the data from this study indicate that increased Cu transportation due to upregulated CTR1 and ATP7A in pulmonary arteries and PASMC contributes to the development of hypoxia-induced pulmonary hypertension. The increased Cu uptake and elevated ATP7A also facilitate the increase in LOX activity and thus the increase in crosslink of extracellular matrix, and eventually leading to the increase in pulmonary arterial stiffness."], "field": "Nursing", "q_year": 2015, "q_cid": "35595464", "pos_cid": 3103103, "source": "eval20x26"}
{"query_id": "scaleup_2965729_8698458", "query": "How to determine whether calmodulin bound to iron-free lactoferrin occupies a single state or a range of different states", "pos": ["Recognition pliability is coupled to structural heterogeneity: a calmodulin intrinsically disordered binding region complex.. Protein interactions within regulatory networks should adapt in a spatiotemporal-dependent dynamic environment, in order to process and respond to diverse and versatile cellular signals. However, the principles governing recognition pliability in protein complexes are not well understood. We have investigated a region of the intrinsically disordered protein myelin basic protein (MBP(145-165)) that interacts with calmodulin, but that also promiscuously binds other biomolecules (membranes, modifying enzymes). To characterize this interaction, we implemented an NMR spectroscopic approach that calculates, for each conformation of the complex, the maximum occurrence based on recorded pseudocontact shifts and residual dipolar couplings. We found that the MBP(145-165)-calmodulin interaction is characterized by structural heterogeneity. Quantitative comparative analysis indicated that distinct conformational landscapes of structural heterogeneity are sampled for different calmodulin-target complexes. Such structural heterogeneity in protein complexes could potentially explain the way that transient and promiscuous protein interactions are optimized and tuned in complex regulatory networks."], "field": "Nursing", "q_year": 2012, "q_cid": "2965729", "pos_cid": 8698458, "source": "eval20x26"}
{"query_id": "scaleup_15983412_21622277", "query": "How to determine whether higher selenium intake benefits insulin function or worsens insulin resistance", "pos": ["Reactive oxygen species enhance insulin sensitivity. SUMMARY Chronic reactive oxygen species (ROS) production by mitochondria may contribute to the development of insulin resistance, a primary feature of type 2 diabetes. In recent years it has become apparent that ROS generation in response to physiological stimuli such as insulin may also facilitate signaling by reversibly oxidizing and inhibiting protein tyrosine phosphatases (PTPs). Here we report that mice lacking one of the key enzymes involved in the elimination of physiological ROS, glutathione peroxidase 1 (Gpx1), were protected from high fat diet-induced insulin resistance. The increased insulin sensitivity in Gpx1−/− mice was attributed to insulin-induced phosphatidylinositol-3-kinase/Akt signaling and glucose uptake in muscle and could be reversed by the anti-oxidant N-acetylcysteine. Increased insulin signaling correlated with enhanced oxidation of the PTP family member PTEN, which terminates signals generated by phosphatidylinositol-3-kinase. These studies provide causal evidence for the enhancement of insulin signaling by ROS in vivo."], "field": "Nursing", "q_year": 2017, "q_cid": "15983412", "pos_cid": 21622277, "source": "eval20x26"}
{"query_id": "scaleup_3790872_37321809", "query": "How to identify reliable indicators for early prediction of cisplatin resistance despite inconsistent detection of cisplatin-induced damage", "pos": ["Relationships between cisplatin-induced adducts and DNA strand-breaks, mutation and recombination in vivo in somatic cells of Drosophila melanogaster, under different conditions of nucleotide excision repair.. Cisplatin is a chemotherapeutic drug widely used in the treatment of several tumours, but this chemotherapy presents problems in terms of side-effects and patient resistance. The detection and determination of cisplatin-induced adducts and the relationship with the physiological or clinical effects of this drug under different repair conditions could be a good measure to assess patient's response to such chemotherapy. A new methodological approach to detect and quantify cisplatin adducts by use of high-performance liquid chromatography with inductively coupled plasma mass-spectrometric detection (HPLC-ICP-MS) and isotope-dilution analysis (IDA), is evaluated for its application in vivo, under different repair conditions. This analysis is combined with the use of the Comet assay, which detects DNA strand-breaks, and the w/w(+) SMART assay, which monitors induction of somatic mutation and recombination in Drosophila melanogaster in vivo under different conditions of nucleotide-excision repair. Results show that (i) cisplatin induces in Drosophila several adducts not detected in mammals. The two most abundant cisplatin-induced adducts, identified by electrospray-mass spectrometry as G monoadduct and G-G intrastrand cross-links, were quantified individually; (ii) cisplatin induces higher levels of G monoadducts and G-G cross-links in NER-proficient than in NER-deficient cells; (iii) the level of adducts correlates with their biological consequences, both in terms of DNA strand-breaks (tail-moment values), and of somatic mutation and recombination (frequency of mosaic eyes and clones in 10(4) cells), when the repair status is considered. This work demonstrates the validity and potential of the adduct detection and quantification methodology in vivo, and its use to correlate adducts with their genetic consequences."], "field": "Nursing", "q_year": 2017, "q_cid": "3790872", "pos_cid": 37321809, "source": "eval20x26"}
{"query_id": "scaleup_20183547_19798624", "query": "How to establish strong clinical evidence on whether omega-3 fatty acids provide reliable psychiatric benefits despite variation in trial populations, supplements, and outcomes and methodological shortcomings", "pos": ["The Levels of Evidence and their role in Evidence-Based Medicine. As the name suggests, evidence-based medicine (EBM), is about finding evidence and using that evidence to make clinical decisions. A cornerstone of EBM is the hierarchical system of classifying evidence. This hierarchy is known as the levels of evidence. Physicians are encouraged to find the highest level of evidence to answer clinical questions. Several papers published in Plastic Surgery journals concerning EBM topics have touched on this subject.1–6 Specifically, previous papers have discussed the lack of higher level evidence in PRS and need to improve the evidence published in the journal. Before that can be accomplished, it is important to understand the history behind the levels and how they should be interpreted. This paper will focus on the origin of levels of evidence, their relevance to the EBM movement and the implications for the field of plastic surgery as well as the everyday practice of plastic surgery."], "field": "Nursing", "q_year": 2019, "q_cid": "201835474", "pos_cid": 19798624, "source": "eval20x26"}
{"query_id": "scaleup_7594921_33813689", "query": "How to explain changes in lactoferrin binding to S. pneumoniae and P. aeruginosa over lactation", "pos": ["Identification of an active disaccharide unit of a glycoconjugate receptor for pneumococci attaching to human pharyngeal epithelial cells. Glycoconjugates containing the disaccharide unit GlcNAc beta 1 leads to 3Gal beta were suggested as receptors for pneumococci adhering to human pharyngeal epithelial cells. The receptor activity was detected both by inhibition of adhesion by an excess of free oligosaccharide and by induction or increase of adhesion after coating of target cells with glycolipid. Studies with free natural and synthetic oligosaccharides identified the disaccharide GlcNAc beta 1 leads to 3Gal beta as one critical binding site. The specificity of recognition was shown inter alia by the lack of inhibitory activity of GlcNAc beta 1 leads to 4Gal beta, which differs only in the linkage of the two sugars. Specific interference with pneumococcal adhesion by administration of soluble receptor sugar may improve our understanding of the role of adhesion in vivo."], "field": "Nursing", "q_year": 2017, "q_cid": "7594921", "pos_cid": 33813689, "source": "eval20x26"}
{"query_id": "scaleup_5683120_19680915", "query": "How to identify the causes of variation in rice grain mineral concentrations across diverse rice types while avoiding false associations due to group differences", "pos": ["Genome-wide association mapping reveals a rich genetic architecture of complex traits in Oryza sativa. Asian rice, Oryza sativa is a cultivated, inbreeding species that feeds over half of the world's population. Understanding the genetic basis of diverse physiological, developmental, and morphological traits provides the basis for improving yield, quality and sustainability of rice. Here we show the results of a genome-wide association study based on genotyping 44,100 SNP variants across 413 diverse accessions of O. sativa collected from 82 countries that were systematically phenotyped for 34 traits. Using cross-population-based mapping strategies, we identified dozens of common variants influencing numerous complex traits. Significant heterogeneity was observed in the genetic architecture associated with subpopulation structure and response to environment. This work establishes an open-source translational research platform for genome-wide association studies in rice that directly links molecular variation in genes and metabolic pathways with the germplasm resources needed to accelerate varietal development and crop improvement."], "field": "Nursing", "q_year": 2014, "q_cid": "5683120", "pos_cid": 19680915, "source": "eval20x26"}
{"query_id": "scaleup_51905790_5622325", "query": "How to assess the food-resource potential of raw and extruded Prosopis laevigata seed flour", "pos": ["Chilean Prosopis Mesocarp Flour: Phenolic Profiling and Antioxidant Activity. In South America, the mesocarp flour of Prosopis species plays a prominent role as a food resource in arid areas. The aim of this work was the characterization of the phenolic antioxidants occurring in the pod mesocarp flour of Chilean Prosopis. Samples were collected in the Copiapo, Huasco and Elqui valleys from the north of Chile. The samples of P. chilensis flour exhibited a total phenolic content ranging between 0.82–2.57 g gallic acid equivalents/100 g fresh flour weight. The highest antioxidant activity, measured by the DPPH assay, was observed for samples from the Huasco valley. HPLC-MS/MS analysis allowed the tentative identification of eight anthocyanins and 13 phenolic compounds including flavonol glycosides, C-glycosyl flavones and ellagic acid derivatives. The antioxidant activity and the phenolic composition in the flour suggest that this ancient South American resource may have potential as a functional food."], "field": "Nursing", "q_year": 2018, "q_cid": "51905790", "pos_cid": 5622325, "source": "eval20x26"}
{"query_id": "scaleup_51905790_85034460", "query": "How to determine whether extrusion cooking generates heat-induced compounds in mesquite seed flour that can affect radical scavenging capacity and measured total phenolic content", "pos": ["Correspondence analysis of antioxidant activity and UV–Vis absorbance of Maillard reaction products as related to reactants. In this study, the antioxidant activity (including ABTS radical scavenging activity and reducing power) and UV-Vis spectra of Maillard reaction products (MRPs) prepared from four sugars (glucose/fructose/ xylose/ribose) and twenty amino acids were studied. The effects of reactants on the antioxidant activity and UV-Vis absorbance of MRPs were investigated using correspondence analysis, which revealed that MRPs from fructose-amino acid models showed the similar UV-Vis absorbance and antioxidant activity with MRPs from glucose-amino acid models, MRPs from ribose-amino acid models showed the similar UV-Vis absorbance and antioxidant activity with MRPs from xylose-amino acid models, while there was significant difference between MRPs from hexose (glucose and fructose)-amino acid models and MRPs from pentose (ribose and xylose)-amino acid models, especially for methionine and valine. The correlation analysis demonstrated that ABTS radical scavenging activity showed the highest linearity (r = 0.831) with UV absorbance at 280 nm while reducing power showed the highest linearity (r = 0.689) with UV absorbance at 355 nm, indicating that different antioxidant properties of MRPs might derive from different compounds. Besides, as compared with cysteine, tyrosine and tryptophan showed a certain ABTS radical scavenging activity in spite of little reducing power. (C) 2011 Elsevier Ltd. All rights reserved."], "field": "Nursing", "q_year": 2018, "q_cid": "51905790", "pos_cid": 85034460, "source": "eval20x26"}
{"query_id": "scaleup_24757171_26117491", "query": "How to explain the anti-inflammatory activity of gold compounds", "pos": ["Cysteine-179 of IκB kinase β plays a critical role in enzyme activation by promoting phosphorylation of activation loop serines. IκB kinase β (IKKβ) subunit of IKK complex is essential for the activation of NF-κB in response to various proinflammatory signals. Cys-179 in the activation loop of IKKβ is known to be the target site for IKK inhibitors such as cyclopentenone prostaglandins, arsenite, and antirheumatic gold compounds. Here we show that a mutant IKKβ in which Cys-179 is substituted with alanine had decreased activity when it was expressed in HEK-293 cells, and TNF stimulation did not restore the activity. Phosphorylation of activation loop serines (Ser-177 and Ser-181) which is required for IKKβ activation was reduced in the IKKβ (C179A) mutant. The activity of IKKβ (C179A) was partially recovered when its phosphorylation was enforced by coexpression with mitogen-activated protein kinase kinase kinases (MAPKKK) such as NF-κB inducing kinase (NIK) and MAPK/extracellular signal-regulated kinase kinase kinase 1(MEKK1) or when the serine residues were replaced with phospho-mimetic glutamate. The IKKβ (C179A) mutant was normal in dimer formation, while its activity abnormally responded to the change in the concentration of substrate ATP in reaction mixture. Our results suggest that Cys-179 of IKKβ plays a critical role in enzyme activation by promoting phosphorylation of activation-loop serines and interaction with ATP."], "field": "Nursing", "q_year": 2022, "q_cid": "247571712", "pos_cid": 26117491, "source": "eval_collection"}
{"query_id": "scaleup_23793570_22530336", "query": "How to clarify the relationship between metallothioneins and megalin in premalignant and malignant oral lesions and its relevance to malignant behavior", "pos": ["Neuronal megalin mediates synaptic plasticity—a novel mechanism underlying intellectual disabilities in megalin gene pathologies. Abstract Donnai-Barrow syndrome, a genetic disorder associated to LRP2 (low-density lipoprotein receptor 2/megalin) mutations, is characterized by unexplained neurological symptoms and intellectual deficits. Megalin is a multifunctional endocytic clearance cell-surface receptor, mostly described in epithelial cells. This receptor is also expressed in the CNS, mainly in neurons, being involved in neurite outgrowth and neuroprotective mechanisms. Yet, the mechanisms involved in the regulation of megalin in the CNS are poorly understood. Using transthyretin knockout mice, a megalin ligand, we found that transthyretin positively regulates neuronal megalin levels in different CNS areas, particularly in the hippocampus. Transthyretin is even able to rescue megalin downregulation in transthyretin knockout hippocampal neuronal cultures, in a positive feedback mechanism via megalin. Importantly, transthyretin activates a regulated intracellular proteolysis mechanism of neuronal megalin, producing an intracellular domain, which is translocated to the nucleus, unveiling megalin C-terminal as a potential transcription factor, able to regulate gene expression. We unveil that neuronal megalin reduction affects physiological neuronal activity, leading to decreased neurite number, length and branching, and increasing neuronal susceptibility to a toxic insult. Finally, we unravel a new unexpected role of megalin in synaptic plasticity, by promoting the formation and maturation of dendritic spines, and contributing for the establishment of active synapses, both in in vitro and in vivo hippocampal neurons. Moreover, these structural and synaptic roles of megalin impact on learning and memory mechanisms, since megalin heterozygous mice show hippocampal-related memory and learning deficits in several behaviour tests. Altogether, we unveil a complete novel role of megalin in the physiological neuronal activity, mainly in synaptic plasticity with impact in learning and memory. Importantly, we contribute to disclose the molecular mechanisms underlying the cognitive and intellectual disabilities related to megalin gene pathologies."], "field": "Nursing", "q_year": 2021, "q_cid": "237935707", "pos_cid": 225303362, "source": "eval_collection"}
{"query_id": "scaleup_23166562_13775124", "query": "How to limit children’s exposure to fecally contaminated soil in domestic environments without exacerbating flooding or the spread of fecal pathogens", "pos": ["Housing, health and happiness. Despite the importance of housing for people's well-being, there has been little work done to assess the causal impact of housing and housing improvement programs on health and welfare. In this paper the authors help fill this gap by investigating the impact of a large-scale effort by the Mexican government to replace dirt floors with cement floors on child health and adult happiness. They find that replacing dirt floors with cement floors significantly reduces parasitic infestations in young children, reduces diarrhea, reduces anemia, and improves cognitive development. Finally, they also find that this program leave adults substantially better off, as measured by satisfaction with their housing and quality of life and by their significantly lower rates of depression and perceived stress."], "field": "Nursing", "q_year": 2021, "q_cid": "231665620", "pos_cid": 13775124, "source": "eval_collection"}
{"query_id": "scaleup_24736391_21318754", "query": "How to determine what influences the lasting retention of a taste experience", "pos": ["Glutamatergic basolateral amygdala to anterior insular cortex circuitry maintains rewarding contextual memory. Findings have shown that anterior insular cortex (aIC) lesions disrupt the maintenance of drug addiction, while imaging studies suggest that connections between amygdala and aIC participate in drug-seeking. However, the role of the BLA → aIC pathway in rewarding contextual memory has not been assessed. Using a cre-recombinase under the tyrosine hydroxylase (TH+) promoter mouse model to induce a real-time conditioned place preference (rtCPP), we show that photoactivation of TH+ neurons induced electrophysiological responses in VTA neurons, dopamine release and neuronal modulation in the aIC. Conversely, memory retrieval induced a strong release of glutamate, dopamine, and norepinephrine in the aIC. Only intra-aIC blockade of the glutamatergic N-methyl-D-aspartate receptor accelerated rtCPP extinction. Finally, photoinhibition of glutamatergic BLA → aIC pathway produced disinhibition of local circuits in the aIC, accelerating rtCPP extinction and impairing reinstatement. Thus, activity of the glutamatergic projection from the BLA to the aIC is critical for maintenance of rewarding contextual memory. Gil-Lievana et al. show that the basolateral amygdala → anterior insular cortex (BLA → aIC) pathway is involved in the maintenance of rewarding contextual memory. They use pharmacological, behavioral and electrophysiological approaches to demonstrate that this is due to the glutamatergic projection from the BLA to the aIC."], "field": "Nursing", "q_year": 2022, "q_cid": "247363910", "pos_cid": 213187541, "source": "eval_collection"}
{"query_id": "scaleup_27358711_89621327", "query": "How to clarify the relationship between nurse managers’ leadership, nurses’ work embeddedness, and innovative behaviors amid complex boundary-work dynamics", "pos": ["Boundary Spanning Leadership: Promising Practices for Public Health. The complexities of solving challenges to improve population health necessitate that public health practitioners work with partners from multiple sectors. As public health leaders increase their involvement in multisectoral collaboration toward the goal of building healthy communities, they often encounter a range of obstacles and barriers. Typically, working with other groups and organizations presents challenges resulting from different assumptions and guiding principles and a lack of understanding of the expertise and regulatory or other barriers of the partner. Although multisectoral collaborations are common in public health practice, many fail to reach their full potential. In this column, we outline a promising practice—boundary spanning leadership (BSL)—that offers a research-based and field-tested conceptual framework along with practical tools that have recently been enthusiastically adopted by a few public health agencies."], "field": "Nursing", "q_year": 2024, "q_cid": "273587116", "pos_cid": 89621327, "source": "eval_collection"}
{"query_id": "scaleup_26877122_23162283", "query": "How to clarify the effects of acetylsalicylic acid on micronutrient absorption and patients’ micronutritional status", "pos": ["Common Pitfalls in the Management of Patients with Micronutrient Deficiency: Keep in Mind the Stomach. Micronutrient deficiencies are relatively common, in particular iron and cobalamin deficiency, and may potentially lead to life-threatening clinical consequences when not promptly recognized and treated, especially in elderly patients. The stomach plays an important role in the homeostasis of some important hematopoietic micronutrients like iron and cobalamin, and probably in others equally important such as ascorbic acid, calcium, and magnesium. A key role is played by the corpus oxyntic mucosa composed of parietal cells whose main function is gastric acid secretion and intrinsic factor production. Gastric acid secretion is necessary for the digestion and absorption of cobalamin and the absorption of iron, calcium, and probably magnesium, and is also essential for the absorption, secretion, and activation of ascorbic acid. Several pathological conditions such as Helicobacter pylori-related gastritis, corpus atrophic gastritis, as well as antisecretory drugs, and gastric surgery may interfere with the normal functioning of gastric oxyntic mucosa and micronutrients homeostasis. Investigation of the stomach by gastroscopy plus biopsies should always be considered in the management of patients with micronutrient deficiencies. The current review focuses on the physiological and pathophysiological aspects of gastric acid secretion and the role of the stomach in iron, cobalamin, calcium, and magnesium deficiency and ascorbate homeostasis."], "field": "Nursing", "q_year": 2024, "q_cid": "268771227", "pos_cid": 231622839, "source": "eval_collection"}
{"query_id": "scaleup_23564312_97227755", "query": "How to assess the effects of moisture content and water absorption capacity on banana starch flowability for cosmetic powder preparations", "pos": ["Influence of water activity on the compressibility and mechanical properties of cocoa products. Abstract The work described in this paper investigated influence of content (cocoa, crystal and sugar powders, milk powder and maltodextrin) and water activity (at three levels of 0, 0.34 and 0.65) on compressibility and mechanical properties of cocoa products. The flow characteristics of powders were determined according to the Jenike test. Compression test was done by ZWICK 1445 at the compressive stress of 5.34 kPa. Ingredients of cocoa powder beverages are characterized by very diverse particle size distribution and bulk density which in turn has an influence on relative humidity of powders. An increase of water activity in powders causes an increase in cohesion for all powders. Particle size has an influence on the values of cohesive forces and compressibility ratio. The increase of water activity in powders causes the increase of flow index. The increase of normal consolidating stress for cocoa causes the increase of flow index. Crystal sugar has the greatest values of flow index at all the levels of water activity."], "field": "Nursing", "q_year": 2021, "q_cid": "235643127", "pos_cid": 97227755, "source": "eval_collection"}
{"query_id": "scaleup_25671244_37191757", "query": "How to determine bovine lactoferrin’s potential effects on oral squamous cell carcinoma invasion", "pos": ["Low density lipoprotein receptor-related protein and gp330 bind similar ligands, including plasminogen activator-inhibitor complexes and lactoferrin, an inhibitor of chylomicron remnant clearance.. The low density lipoprotein receptor-related protein/alpha 2-macroglobulin receptor (LRP) and gp330, two members of the low density lipoprotein receptor gene family, share a multitude of cysteine-rich repeats. LRP has been shown to act as an endocytosis-mediating receptor for several ligands, including protease-antiprotease complexes and plasma lipoproteins. The former include alpha 2-macroglobulin-protease complexes and plasminogen activator inhibitor-activator complexes. The latter include chylomicron remnant-like particles designated beta-very low density lipoproteins (beta-VLDL) complexed with apoprotein E or lipoprotein lipase. The binding specificity of gp330 is unknown. In the current studies we show that gp330 from rat kidney membranes binds several of these ligands on nitrocellulose blots. We also show that both LRP and gp330 bind an additional ligand, bovine lactoferrin, which is known to inhibit the hepatic clearance of chylomicron remnants. Lactoferrin blocked the LRP-dependent stimulation of cholesteryl ester synthesis in cultured human fibroblasts elicited by apoprotein E-beta-VLDL or lipoprotein lipase-beta-VLDL complexes. Cross-competition experiments in fibroblasts showed that the multiple ligands recognize at least three distinct, but partially overlapping sites on the LRP molecule. Binding of all ligands to LRP and gp330 was inhibited by the 39-kDa protein, which co-purifies with the two receptors, suggesting that the 39-kDa protein is a universal regulator of ligand binding to both receptors. The correlation of the inhibitory effects of lactoferrin in vivo and in vitro support the notion that LRP functions as a chylomicron remnant receptor in liver. LRP and gp330 share a multiplicity of binding sites, and both may function as endocytosis-mediating receptors for a large number of ligands in different organs."], "field": "Nursing", "q_year": 2023, "q_cid": "256712449", "pos_cid": 37191757, "source": "eval_collection"}
{"query_id": "scaleup_27944381_20698120", "query": "How to clarify vitamin K’s potential role in preventing type 2 diabetes", "pos": ["Mechanisms of inflammatory responses and development of insulin resistance: how are they interlinked?. BackgroundInsulin resistance (IR) is one of the major hallmark for pathogenesis and etiology of type 2 diabetes mellitus (T2DM). IR is directly interlinked with various inflammatory responses which play crucial role in the development of IR. Inflammatory responses play a crucial role in the pathogenesis and development of IR which is one of the main causative factor for the etiology of T2DM.MethodsA comprehensive online English literature was searched using various electronic search databases. Different search terms for pathogenesis of IR, role of various inflammatory responses were used and an advanced search was conducted by combining all the search fields in abstracts, keywords, and titles.ResultsWe summarized the data from the searched articles and found that inflammatory responses activate the production of various pro-inflammatory mediators notably cytokines, chemokines and adipocytokines through the involvement of various transcriptional mediated molecular pathways, oxidative and metabolic stress. Overnutrition is one of the major causative factor that contributes to induce the state of low-grade inflammation due to which accumulation of elevated levels of glucose and/or lipids in blood stream occur that leads to the activation of various transcriptional mediated molecular and metabolic pathways. This results in the induction of various pro-inflammatory mediators that are decisively involved to provoke the pathogenesis of tissue-specific IR by interfering with insulin signaling pathways. Once IR is developed, it increases oxidative stress in β-cells of pancreatic islets and peripheral tissues which impairs insulin secretion, and insulin sensitivity in β-cells of pancreatic islets and peripheral tissues, respectively. Moreover, we also summarized the data regarding various treatment strategies of inflammatory responses-induced IR.ConclusionsIn this article, we have briefly described that how pro-inflammatory mediators, oxidative stress, transcriptional mediated molecular and metabolic pathways are involved in the pathogenesis of tissues-specific IR. Moreover, based on recent investigations, we have also described that to counterfeit these inflammatory responses is one of the best treatment strategy to prevent the pathogenesis of IR through ameliorating the incidences of inflammatory responses."], "field": "Nursing", "q_year": 2025, "q_cid": "279443810", "pos_cid": 206981207, "source": "eval_collection"}
{"query_id": "scaleup_27330473_26480300", "query": "How to reduce psoriasis severity while maintaining compatibility with biological tissues and avoiding unwanted immune reactions", "pos": ["Spanlastics: a novel elastic drug delivery system with potential applications via multifarious routes of administration. Abstract Drug delivery systems (DDS) based on nanocarriers are designed to transport therapeutic agents to specific areas of the body where they are required to exhibit pharmacodynamic effect. These agents rely on an appropriate carrier to protect them from rapid degradation or clearance and enhance their concentration in target tissues. Spanlastics, an elastic, deformable surfactant-based nanovesicles have the potential to be used as a drug delivery vehicle for wide array of drug molecules. Spanlastics are formed by the self-association of non-ionic surfactants and edge activators in an aqueous phase and have gained attention as promising drug carriers due to their biodegradable, biocompatible, and non-immunogenic structure. In recent years, numerous scientific journals have published research articles exploring the potential of spanlastics to serve as a DDS for various types of drugs as they offer targeted delivery and regulated release of the drugs. Following brief introduction to spanlastics, their structure and methods of preparation, this review focuses on the delivery of various drugs using spanlastics as a carrier via various routes viz. topical, transdermal, ototopical, ocular, oral and nasal. Work carried out by various researchers by employing spanlastics as a carrier for enhancing therapeutic activity of different moieties has been discussed in detail. Graphical Abstract"], "field": "Nursing", "q_year": 2024, "q_cid": "273304739", "pos_cid": 264803008, "source": "eval_collection"}
{"query_id": "scaleup_27330473_67750276", "query": "How to limit inflammation and tissue damage in psoriasis", "pos": ["Rutin and ascorbic acid cooperation in antioxidant and antiapoptotic effect on human skin keratinocytes and fibroblasts exposed to UVA and UVB radiation. The combination of ascorbic acid and rutin is frequently used in oral preparations. However, despite numerous protective effects of each component individually, their combined effect on ultraviolet (UV)-irradiated skin cells has never been evaluated. The aim of this study was to evaluate the combined effect of ascorbic acid and rutin on human keratinocytes and fibroblasts exposed to UVA and UVB radiation. Skin keratinocytes and fibroblasts exposed to UVA and UVB radiation were treated with ascorbic acid or/and rutin. The total antioxidant properties of both components, as well as their effect on cellular pro- and antioxidant status, lipid and protein oxidation, transmembrane transport, and pro-inflammatory and pro/antiapoptotic protein expression were measured. The combination of ascorbic acid and rutin had higher antioxidant properties compared to the activity of the single compound alone, and showed a stronger effect against UV-induced reactive oxygen species generation. The ascorbic acid and rutin combination also showed increased antioxidant enzyme activity (catalase, superoxide dismutase, thioredoxin reductase), which was impaired following UV irradiation. Moreover, ascorbic acid additional stimulated UV-induced bilitranslocase activity responsible for rutin transport, and therefore favored rutin effect on Nrf2 pathway, simultaneously differentiating the reaction of keratinocytes and fibroblasts. In keratinocytes, Nrf2 is strongly activated, while in fibroblasts decreased Nrf2 activity was observed. Used mixture, also significantly silenced UV-induced expression of pro-inflammatory factor NFκB and pro-apoptotic proteins such as caspases 3, 8, and 9. These results showed that ascorbic acid and rutin are complementary in their antioxidant actions, transport and signaling functions. Their combined antioxidant, antiinflammatory and antiapoptotic actions suggest rutin and ascorbic acid are a potentially cytoprotective team against UV-induced skin damage."], "field": "Nursing", "q_year": 2024, "q_cid": "273304739", "pos_cid": 67750276, "source": "eval_collection"}
{"query_id": "scaleup_22895744_26713871", "query": "How to trace the evolution of professional obstetric nursing across more than a century of textbooks while accounting for historical context and ensuring consistent judgments from a single researcher", "pos": ["Qualitative Content Analysis in Practice. Introduction: What Is Qualitative Content Analysis? What Is Qualitative about Qualitative Content Analysis? Will Qualitative Content Analysis Work for Me? Decision Aids The Coding Frame Building a Coding Frame Strategies for Building a Data-Driven Coding Frame Segmentation and Units of Coding Trying It Out: The Pilot Phase What to Keep in Mind: Evaluating Your Coding Frame The Main Analysis Phase How to Present Your Results Using Software in Doing Qualitative Content Analysis"], "field": "Nursing", "q_year": 2020, "q_cid": "228957440", "pos_cid": 267138710, "source": "eval_collection"}
{"query_id": "scaleup_26722002_21229051", "query": "How to improve bread’s nutritional profile while maintaining yeast fermentation, gas production, required loaf volume, and crumb porosity", "pos": ["Curcumin Inhibits Growth of Saccharomyces cerevisiae through Iron Chelation. ABSTRACT Curcumin, a polyphenol derived from turmeric, is an ancient therapeutic used in India for centuries to treat a wide array of ailments. Interest in curcumin has increased recently, with ongoing clinical trials exploring curcumin as an anticancer therapy and as a protectant against neurodegenerative diseases. In vitro, curcumin chelates metal ions. However, although diverse physiological effects have been documented for this compound, curcumin's mechanism of action on mammalian cells remains unclear. This study uses yeast as a model eukaryotic system to dissect the biological activity of curcumin. We found that yeast mutants lacking genes required for iron and copper homeostasis are hypersensitive to curcumin and that iron supplementation rescues this sensitivity. Curcumin penetrates yeast cells, concentrates in the endoplasmic reticulum (ER) membranes, and reduces the intracellular iron pool. Curcumin-treated, iron-starved cultures are enriched in unbudded cells, suggesting that the G1 phase of the cell cycle is lengthened. A delay in cell cycle progression could, in part, explain the antitumorigenic properties associated with curcumin. We also demonstrate that curcumin causes a growth lag in cultured human cells that is remediated by the addition of exogenous iron. These findings suggest that curcumin-induced iron starvation is conserved from yeast to humans and underlies curcumin's medicinal properties."], "field": "Nursing", "q_year": 2024, "q_cid": "267220026", "pos_cid": 21229051, "source": "eval_collection"}
{"query_id": "scaleup_24906622_2683403", "query": "How to clarify the relationship between development trends and changes in household drinking-water sources in Ghana over the study period", "pos": ["Repeated Measures Correlation. Repeated measures correlation (rmcorr) is a statistical technique for determining the common within-individual association for paired measures assessed on two or more occasions for multiple individuals. Simple regression/correlation is often applied to non-independent observations or aggregated data; this may produce biased, specious results due to violation of independence and/or differing patterns between-participants versus within-participants. Unlike simple regression/correlation, rmcorr does not violate the assumption of independence of observations. Also, rmcorr tends to have much greater statistical power because neither averaging nor aggregation is necessary for an intra-individual research question. Rmcorr estimates the common regression slope, the association shared among individuals. To make rmcorr accessible, we provide background information for its assumptions and equations, visualization, power, and tradeoffs with rmcorr compared to multilevel modeling. We introduce the R package (rmcorr) and demonstrate its use for inferential statistics and visualization with two example datasets. The examples are used to illustrate research questions at different levels of analysis, intra-individual, and inter-individual. Rmcorr is well-suited for research questions regarding the common linear association in paired repeated measures data. All results are fully reproducible."], "field": "Nursing", "q_year": 2022, "q_cid": "249066227", "pos_cid": 2683403, "source": "eval_collection"}
{"query_id": "scaleup_23166562_15705181", "query": "How to determine which human and domestic animal fecal sources require control to protect children in densely populated compounds where unsafe human feces disposal and domestic animals are common", "pos": ["Giardia duodenalis genetic assemblages and hosts. Techniques for sub-classifying morphologically identical Giardia duodenalis trophozoites have included comparisons of the electrophoretic mobility of enzymes and of chromosomes, and sequencing of genes encoding β-giardin, triose phosphate isomerase, the small subunit of ribosomal RNA and glutamate dehydrogenase. To date, G. duodenalis organisms have been sub-classified into eight genetic assemblages (designated A–H). Genotyping of G. duodenalis organisms isolated from various hosts has shown that assemblages A and B infect the largest range of host species, and appear to be the main (or possibly only) G. duodenalis assemblages that undeniably infect human subjects. In at least some cases of assemblage A or B infection in wild mammals, there is suggestive evidence that the infection had resulted from environmental contamination by G. duodenalis cysts of human origin."], "field": "Nursing", "q_year": 2021, "q_cid": "231665620", "pos_cid": 15705181, "source": "eval_collection"}
{"query_id": "scaleup_27663516_52096232", "query": "How to distinguish genetically distinct Enterococcus strains from duplicate isolates to avoid redundancy in subsequent characterization", "pos": ["Evaluation of BOX-PCR and ERIC-PCR as Molecular Typing Tools for Pathogenic Leptospira. In the last decades, leptospirosis had gained public health concern due to morbidity and mortality rates caused by pathogenic Leptospira. The need for rapid and robust molecular typing methods to differentiate this zoonotic pathogen is of utmost importance. Various studies had been conducted to determine the genetic relatedness of Leptospira isolates using molecular typing methods. In this study, 29 pathogenic Leptospira isolates from rat, soil, and water samples in Sarawak, Malaysia, were characterized using BOX-PCR and ERIC-PCR. The effectiveness of these two methods with regard to the ease of interpretation, reproducibility, typeability, and discriminatory power was also being evaluated. Using BOX-PCR, six clusters and 3 single isolates were defined at a genetic distance percentage of 11.2%. ERIC-PCR clustered the isolates into 6 clusters and 2 single isolates at a genetic distance percentage of 6.8%. Both BOX-PCR and ERIC-PCR produced comparable results though the discriminatory index for ERIC-PCR (0.826) was higher than that for BOX-PCR (0.809). From the constructed dendrogram, it could be summarized that the isolates in this study were highly heterogeneous and genetically diverse. The findings from this study indicated that there is no genetic relatedness among the pathogenic Leptospira isolates in relation to the locality, source, and identity, with some exceptions. Out of the 29 pathogenic Leptospira isolates studied, BOX-PCR and ERIC-PCR successfully discriminated 4 isolates (2 isolates each) into the same cluster in relation to sample sources, as well as 2 isolates into the same cluster in association with the sample locality. Future studies shall incorporate the use of other molecular typing methods to make a more thorough comparison on the genetic relatedness of pathogenic Leptospira."], "field": "Nursing", "q_year": 2025, "q_cid": "276635164", "pos_cid": 52096232, "source": "eval_collection"}
{"query_id": "scaleup_27641806_6233191", "query": "How to understand the effects of household flooring on residents in rural Kenyan communities", "pos": ["Developing empirically supported theories of change for housing investment and health. The assumption that improving housing conditions can lead to improved health may seem a self-evident hypothesis. Yet evidence from intervention studies suggests small or unclear health improvements, indicating that further thought is required to refine this hypothesis. Articulation of a theory can help avoid a black box approach to research and practice and has been advocated as especially valuable for those evaluating complex social interventions like housing. This paper presents a preliminary theory of housing improvement and health based on a systematic review conducted by the authors. Following extraction of health outcomes, data on all socio-economic impacts were extracted by two independent reviewers from both qualitative and quantitative studies. Health and socio-economic outcome data from the better quality studies (n = 23/34) were mapped onto a one page logic models by two independent reviewers and a final model reflecting reviewer agreement was prepared. Where there was supporting evidence of links between outcomes these were indicated in the model. Two models of specific improvements (warmth & energy efficiency; and housing led renewal), and a final overall model were prepared. The models provide a visual map of the best available evidence on the health and socio-economic impacts of housing improvement. The use of a logic model design helps to elucidate the possible pathways between housing improvement and health and as such might be described as an empirically based theory. Changes in housing factors were linked to changes in socio-economic determinants of health. This points to the potential for longer term health impacts which could not be detected within the lifespan of the evaluations. The developed theories are limited by the available data and need to be tested and refined. However, in addition to providing one page summaries for evidence users, the theory may usefully inform future research on housing and health."], "field": "Nursing", "q_year": 2025, "q_cid": "276418061", "pos_cid": 6233191, "source": "eval_collection"}
{"query_id": "scaleup_26754688_24422896", "query": "How to establish the maximum reliability of the Persian scale’s subscales for accurately evaluating novice nurses’ perceptions of care in acute situations", "pos": ["Thanks coefficient alpha, we'll take it from here.. Empirical studies in psychology commonly report Cronbach's alpha as a measure of internal consistency reliability despite the fact that many methodological studies have shown that Cronbach's alpha is riddled with problems stemming from unrealistic assumptions. In many circumstances, violating these assumptions yields estimates of reliability that are too small, making measures look less reliable than they actually are. Although methodological critiques of Cronbach's alpha are being cited with increasing frequency in empirical studies, in this tutorial we discuss how the trend is not necessarily improving methodology used in the literature. That is, many studies continue to use Cronbach's alpha without regard for its assumptions or merely cite methodological articles advising against its use to rationalize unfavorable Cronbach's alpha estimates. This tutorial first provides evidence that recommendations against Cronbach's alpha have not appreciably changed how empirical studies report reliability. Then, we summarize the drawbacks of Cronbach's alpha conceptually without relying on mathematical or simulation-based arguments so that these arguments are accessible to a broad audience. We continue by discussing several alternative measures that make less rigid assumptions which provide justifiably higher estimates of reliability compared to Cronbach's alpha. We conclude with empirical examples to illustrate advantages of alternative measures of reliability including omega total, Revelle's omega total, the greatest lower bound, and Coefficient H. A detailed software appendix is also provided to help researchers implement alternative methods. (PsycINFO Database Record"], "field": "Nursing", "q_year": 2024, "q_cid": "267546887", "pos_cid": 24422896, "source": "eval_collection"}
{"query_id": "scaleup_25549985_23302749", "query": "How to achieve high short-chain fatty acid levels in pistachio milk and determine whether it induces cytotoxicity and apoptosis in human colon carcinoma cells", "pos": ["Quality characteristics of yogurts fermented with short-chain fatty acid-producing probiotics and their effects on mucin production and probiotic adhesion onto human colon epithelial cells.. Probiotics can ferment nondigestible carbohydrates and produce short-chain fatty acids (SCFA; acetate, propionate, and butyrate) in the human colon. In this study, the levels of SCFA were determined in the following yogurts fermented with different combinations of probiotics: (1) cocultures of Streptococcus thermophilus and Lactobacillus bulgaricus (control, C); (2) S. thermophilus, L. bulgaricus, and Bifidobacterium bifidum (C-Bb); (3) S. thermophilus, L. bulgaricus, and Lactobacillus acidophilus (C-La); and (4) S. thermophilus, L. bulgaricus, and Lactobacillus gasseri (C-Lg). Results showed that the acetate levels were significantly higher in C-Bb, C-La, and C-Lg yogurts than in C yogurt. Fermentation and physicochemical characteristics of all yogurts were identical. Treatment of mucus-secreting colon epithelial cells (HT29-MTX) with C-Bb, C-La, and C-Lg yogurt supernatants resulted in an increase in the expression of MUC2 and CDX2 and the production of mucin proteins. The adhesion of probiotics onto HT29-MTX cells increased following treatment with C-Bb, C-La, and C-Lg yogurt supernatants. Our data suggest that a yogurt diet rich in acetate improves the protective function of the intestinal epithelium."], "field": "Nursing", "q_year": 2023, "q_cid": "255499858", "pos_cid": 233027493, "source": "eval_collection"}
{"query_id": "scaleup_21541088_21211618", "query": "How to establish useful, adequate, clear, feasible, and future-oriented evaluation criteria for assessing minimum requirements in an initial accreditation cycle", "pos": ["How to execute Context, Input, Process, and Product evaluation model in medical health education. Improvements to education are necessary in order to keep up with the education requirements of today. The Context, Input, Process, and Product (CIPP) evaluation model was created for the decision-making towards education improvement, so this model is appropriate in this regard. However, application of this model in the actual context of medical health education is considered difficult in the education environment. Thus, in this study, literature survey of previous studies was investigated to examine the execution procedure of how the CIPP model can be actually applied. For the execution procedure utilizing the CIPP model, the criteria and indicators were determined from analysis results and material was collected after setting the material collection method. Afterwards, the collected material was analyzed for each CIPP element, and finally, the relationship of each CIPP element was analyzed for the final improvement decision-making. In this study, these steps were followed and the methods employed in previous studies were organized. Particularly, the process of determining the criteria and indicators was important and required a significant effort. Literature survey was carried out to analyze the most widely used criteria through content analysis and obtained a total of 12 criteria. Additional emphasis is necessary in the importance of the criteria selection for the actual application of the CIPP model. Also, a diverse range of information can be obtained through qualitative as well as quantitative methods. Above all, since the CIPP evaluation model execution result becomes the basis for the execution of further improved evaluations, the first attempt of performing without hesitation is essential."], "field": "Nursing", "q_year": 2020, "q_cid": "215410889", "pos_cid": 212116187, "source": "eval_collection"}
{"query_id": "scaleup_22097843_21276577", "query": "How to predict the bulk density of instant whole milk powder with agglomerated particles that vary in shape and size across brands and particle size fractions", "pos": ["Effects of morphology on the dispersibility of instant whole milk powder. Abstract The functionality and performance of instant whole milk powder (IWMP) can be related to its physical and chemical properties; i.e. particle size, morphology and fat distribution. Dispersibility, a measure of rehydration, has become one of the most important quality characteristics of IWMP. Many milk powder properties may affect the dispersibility. Based on literature and our own experience, particle size and morphology may be the two most important factors. This work investigated the quantitative relationship between particle size, morphology and dispersibility. Samples of different brands of IWMPs were fractionated using sieving and then remixed. The powder dispersibility was then measured, and the particle morphology characteristics obtained using light microscopy combined with image processing. Principal component analysis (PCA), partial least squares (PLS) and artificial neural network (ANN) methods were used to process the data. It was found that IWMP produced by different plants have different shape factors (circularity, convexity, and area) and the trends of the dispersibility versus the changes in the shape factors (circularity, convexity and area) for different particle size groups are different. Then, by the use of the size fractions and shape factors, prediction models for dispersibility were developed. A further experiment addressed the validity of the ANN model."], "field": "Nursing", "q_year": 2020, "q_cid": "220978438", "pos_cid": 212765770, "source": "eval_collection"}
{"query_id": "scaleup_27425871_1038422", "query": "How to clarify the effects of eicosapentaenoic acid on cardiovascular health given the potentially opposing effects of polyunsaturated fatty acid derivatives", "pos": ["Omega-3 Fatty Acids and Inflammation: Novel Interactions Reveal a New Step in Neutrophil Recruitment. While investigating new mechanisms by which the dietary omega-3 fatty acids regulate inflammation, the authors have identified a new step in the regulation of neutrophil migration across vascular endothelial cells."], "field": "Nursing", "q_year": 2024, "q_cid": "274258715", "pos_cid": 1038422, "source": "eval_collection"}
{"query_id": "scaleup_26541051_93152211", "query": "How to improve ancient-grain dough functionality and baked-product quality compared with conventional bread wheat", "pos": ["Changes in secondary structure of gluten proteins due to emulsifiers. Abstract Changes in the secondary structure of gluten proteins due to emulsifiers were analyzed by Raman Spectroscopy. The protein folding induced by 0.25% SSL (Sodium Stearoyl Lactylate) (GS0.25, Gluten + 0.25% SSL) included an increase in α-helix conformation and a decrease in β-sheet, turns and random coil. The same behavior, although in a less degree, was observed for 0.5% gluten–DATEM (Diacetyl Tartaric Acid Esters of Monoglycerides) system. The low burial of Tryptophan residues to a more hydrophobic environment and the low percentage area of the C–H stretching band for GS0.25 (Gluten + 0.25% SSL), could be related to the increased in α-helix conformation. This behavior was also confirmed by changes in stretching vibrational modes of disulfide bridges (S–S) and the low exposure of Tyrosine residues. High levels of SSL (0.5% and 1.0%) and DATEM (1.0%) led to more disordered protein structures, with different gluten networks. SSL (1.0%) formed a more disordered and opened gluten matrix than DATEM, the last one being laminar and homogeneous."], "field": "Nursing", "q_year": 2023, "q_cid": "265410510", "pos_cid": 93152211, "source": "eval_collection"}
{"query_id": "scaleup_27515953_55512796", "query": "How to reliably determine how environmental exposures relate to enteropathogen infection when observations are interrelated and other factors are linked to both exposure and infection", "pos": ["The R Package geepack for Generalized Estimating Equations. This paper describes the core features of the R package geepack, which implements the generalized estimating equations (GEE) approach for fitting marginal generalized linear models to clustered data. Clustered data arise in many applications such as longitudinal data and repeated measures. The GEE approach focuses on models for the mean of the correlated observations within clusters without fully specifying the joint distribution of the observations. It has been widely used in statistical practice. This paper illustrates the application of the GEE approach with geepack through an example of clustered binary data."], "field": "Nursing", "q_year": 2024, "q_cid": "275159534", "pos_cid": 55512796, "source": "eval_collection"}
{"query_id": "scaleup_25013812_11220349", "query": "How to determine whether post-program empowerment differences reflect the program’s effects without pre-program empowerment data", "pos": ["Running Randomized Evaluations: A Practical Guide. This book provides a comprehensive yet accessible guide to running randomized impact evaluations of social programs. Drawing on the experience of researchers at the Abdul Latif Jameel Poverty Action Lab, which has run hundreds of such evaluations in dozens of countries throughout the world, it offers practical insights on how to use this powerful technique, especially in resource-poor environments. This step-by-step guide explains why and when randomized evaluations are useful, in what situations they should be used, and how to prioritize different evaluation opportunities. It shows how to design and analyze studies that answer important questions while respecting the constraints of those working on and benefiting from the program being evaluated. The book gives concrete tips on issues such as improving the quality of a study despite tight budget constraints, and demonstrates how the results of randomized impact evaluations can inform policy. With its self-contained modules, this one-of-a-kind guide is easy to navigate. It also includes invaluable references and a checklist of the common pitfalls to avoid. Rachel Glennerster is executive director of the Abdul Latif Jameel Poverty Action Lab (J-PAL) at the Massachusetts Institute of Technology. Kudzai Takavarasha holds degrees in chemical engineering and economics from the Massachusetts Institute of Technology, and was a policy manager at J-PAL from 2004 to 2012."], "field": "Nursing", "q_year": 2022, "q_cid": "250138129", "pos_cid": 112203491, "source": "eval_collection"}
{"query_id": "scaleup_24906622_20021201", "query": "How to ensure equitable access to safe, affordable, reliable drinking water in Ghana’s diverse and expanding sachet water markets while protecting water as a basic human right and addressing environmental concerns?", "pos": ["The diversity of water markets: Prospects and perils for the SDG agenda. Water markets are used in a wide variety of contexts to (a) increase access to water, and (b) increase water use efficiency by reallocating water to uses with a higher economic value. The global prevalence of water markets may help or hinder achievement of Sustainable Development Goal 6, making it essential to understand their role in water management. However, an overarching understanding of what water markets are and how they work across different regulatory and geographic contexts is surprisingly elusive. The literature separates water markets based on their formality and the nature of the goods and services being sold (typically either domestic water or agricultural), but growing water scarcity and increasing urban water demands means that agricultural and urban water use can no longer be considered separately. This review brings together two disparate strands of literature on water markets: (a) markets as a tool for re‐allocation between agricultural uses (including both water rights and irrigation services), and (b) urban water markets to expand access to safe water supplies. Based on a review of 148 studies of water markets, this article explores the similarities and differences between urban and agricultural markets across the spectrum of regulatory formality to identify key findings in water market operation and outcomes, including critiques of market function. Bringing together the work on urban and agricultural water markets highlights important lessons on the role water markets can play in achieving SDG 6."], "field": "Nursing", "q_year": 2022, "q_cid": "249066227", "pos_cid": 200212011, "source": "eval_collection"}
{"query_id": "scaleup_26467087_23847648", "query": "How to determine selenium’s effects on brain cortical structure independently of obesity, smoking, or hypertension", "pos": ["Kidney damage causally affects the brain cortical structure: A Mendelian randomization study. Background Alterations in the brain cortical structures of patients with chronic kidney disease (CKD) have been reported; however, the cause has not been determined yet. Herein, we used Mendelian randomization (MR) to reveal the causal effect of kidney damage on brain cortical structure. Methods Genome-wide association studies summary data of estimated glomerular filtration rate (eGFR) in 480,698 participants from the CKDGen Consortium were used to identify genetically predicted eGFR. Data from 567,460 individuals from the CKDGen Consortium were used to assess genetically determined CKD; 302,687 participants from the UK Biobank were used to evaluate genetically predicted albuminuria. Further, data from 51,665 patients from the ENIGMA Consortium were used to assess the relationship between genetic predisposition and reduced eGFR, CKD, and progressive albuminuria with alterations in cortical thickness (TH) or surficial area (SA) of the brain. Magnetic resonance imaging was used to measure the SA and TH globally and in 34 functional regions. Inverse-variance weighted was used as the primary estimate whereas MR Pleiotropy RESidual Sum and Outlier, MR-Egger and weighted median were used to detect heterogeneity and pleiotropy. Findings At the global level, albuminuria decreased TH (β = −0.07 mm, 95% CI: −0.12 mm to −0.02 mm, P = 0.004); at the functional level, albuminuria reduced TH of pars opercularis gyrus without global weighted (β = −0.11 mm, 95% CI: −0.16 mm to −0.07 mm, P = 3.74×10−6). No pleiotropy was detected. Interpretation Kidney damage causally influences the cortex structure which suggests the existence of a kidney-brain axis. Funding This study was supported by the Science and Technology Planning Project of Guangdong Province (Grant No. 2020A1515111119 and 2017B020227007), the National Key Research and Development Program of China (Grant No. 2018YFA0902803), the National Natural Science Foundation of China (Grant No. 81825016, 81961128027, 81772719, 81772728), the Key Areas Research and Development Program of Guangdong (Grant No. 2018B010109006), Guangdong Special Support Program (2017TX04R246), Grant KLB09001 from the Key Laboratory of Malignant Tumor Gene Regulation and Target Therapy of Guangdong Higher Education Institutes, and Grants from the Guangdong Science and Technology Department (2020B1212060018)."], "field": "Nursing", "q_year": 2023, "q_cid": "264670879", "pos_cid": 238476482, "source": "eval_collection"}
{"query_id": "scaleup_27663516_23791787", "query": "How to determine whether enterocin genes in strains from an underexplored traditional food matrix correspond to effective bacterial inhibition and potential as natural food preservatives", "pos": ["Characterization of Enterococcus durans EDD2, a strain from beehives with inhibitory activity against Paenibacillus larvae. In this research, we report the isolation of Enterococcus durans EDD2, which showed strong inhibitory activity against Paenibacillus larvae, the causative agent of the American foulbrood disease (AFB). The strain was found in freshly collected pollen granules from four beehives in Dushantzi village (Pirdop region, Bulgaria), and was determined by polyphase approach including molecular, biochemical, and physiological tests. Whole-genome sequencing by the Illumina HiSeq NGS platform with 2 x 150 bases paired-end reads revealed the presence of two contigs containing genetic determinants for Enterocin L50A/L50B and Enterocin P -like bacteriocins, the first ones being carried out by the chromosome, while the second one being present on a putative plasmid. E. durans EDD2 was also subjected to genetic and microbiological tests for several pathogenicity factors, and none was found. These results, combined with the fact that the strain was present in four, but not all of the 15 beehives in the apiary, suggest that it is not a result from some human or animal fecal or other types of contamination in the adjacent fields, but rather it is maintained within the bees microbiomes and was transferred to the pollen granules by the insects' saliva. It was proven that E. durans EDD2 possesses a strong probiotic inhibitory activity against P. larvae due to the production of bacteriocins."], "field": "Nursing", "q_year": 2025, "q_cid": "276635164", "pos_cid": 237917878, "source": "eval_collection"}
{"query_id": "scaleup_25343941_769687", "query": "How to retain enough iodine in biofortified crops to meet dietary needs despite iodine loss from plants", "pos": ["Purification and Characterization of a Novel Methyltransferase Responsible for Biosynthesis of Halomethanes and Methanethiol in Brassica oleracea(*). A novel S-adenosyl- L-methionine:halide/bisulfide methyltransferase (EC 2.1.1.-) was purified approximately 1000-fold to apparent homogeneity from leaves of Brassica oleracea. The enzyme catalyzed the S-adenosyl- L-methionine-dependent methylation of the halides iodide, bromide, and chloride to monohalomethanes and of bisulfide to methanethiol. The dual function of the enzyme was demonstrated through co-purification of the halide- and bisulfide-methylating activities in the same ratio and by studies of competition between the alternative substrates iodide and bisulfide. The purification procedure included gel filtration, anion exchange chromatography, and affinity chromatography on adenosine-agarose. Elution of the protein from a chromatofocusing column indicated a pI value of 4.8. The pH optimum of halide methylation (5.5-7.0) was different from that of bisulfide methylation (7.0-8.0). The molecular mass values for the native and denatured protein were 29.5 and 28 kDa, respectively, suggesting that the active enzyme is a monomer. The enzyme had the highest specificity constant for iodide and the next highest for bisulfide. Substrate interaction kinetics and product inhibition patterns were consistent with an Ordered Bi Bi mechanism."], "field": "Nursing", "q_year": 2022, "q_cid": "253439412", "pos_cid": 769687, "source": "eval_collection"}
{"query_id": "scaleup_26754688_1837377", "query": "How to determine whether the Persian PCAS scale is suitable for assessing novice nurses’ perceptions of care in acute situations over time", "pos": ["A Guideline of Selecting and Reporting Intraclass Correlation Coefficients for Reliability Research.. OBJECTIVE Intraclass correlation coefficient (ICC) is a widely used reliability index in test-retest, intrarater, and interrater reliability analyses. This article introduces the basic concept of ICC in the content of reliability analysis. DISCUSSION FOR RESEARCHERS There are 10 forms of ICCs. Because each form involves distinct assumptions in their calculation and will lead to different interpretations, researchers should explicitly specify the ICC form they used in their calculation. A thorough review of the research design is needed in selecting the appropriate form of ICC to evaluate reliability. The best practice of reporting ICC should include software information, \"model,\" \"type,\" and \"definition\" selections. DISCUSSION FOR READERS When coming across an article that includes ICC, readers should first check whether information about the ICC form has been reported and if an appropriate ICC form was used. Based on the 95% confident interval of the ICC estimate, values less than 0.5, between 0.5 and 0.75, between 0.75 and 0.9, and greater than 0.90 are indicative of poor, moderate, good, and excellent reliability, respectively. CONCLUSION This article provides a practical guideline for clinical researchers to choose the correct form of ICC and suggests the best practice of reporting ICC parameters in scientific publications. This article also gives readers an appreciation for what to look for when coming across ICC while reading an article."], "field": "Nursing", "q_year": 2024, "q_cid": "267546887", "pos_cid": 1837377, "source": "eval_collection"}
{"query_id": "scaleup_28373612_3453979", "query": "How to understand childhood stunting and household food insecurity across kebeles while accounting for differences between communities and similarities within communities", "pos": ["Measures of clustering and heterogeneity in multilevel Poisson regression analyses of rates/count data. Multilevel data occur frequently in many research areas like health services research and epidemiology. A suitable way to analyze such data is through the use of multilevel regression models. These models incorporate cluster‐specific random effects that allow one to partition the total variation in the outcome into between‐cluster variation and between‐individual variation. The magnitude of the effect of clustering provides a measure of the general contextual effect. When outcomes are binary or time‐to‐event in nature, the general contextual effect can be quantified by measures of heterogeneity like the median odds ratio or the median hazard ratio, respectively, which can be calculated from a multilevel regression model. Outcomes that are integer counts denoting the number of times that an event occurred are common in epidemiological and medical research. The median (incidence) rate ratio in multilevel Poisson regression for counts that corresponds to the median odds ratio or median hazard ratio for binary or time‐to‐event outcomes respectively is relatively unknown and is rarely used. The median rate ratio is the median relative change in the rate of the occurrence of the event when comparing identical subjects from 2 randomly selected different clusters that are ordered by rate. We also describe how the variance partition coefficient, which denotes the proportion of the variation in the outcome that is attributable to between‐cluster differences, can be computed with count outcomes. We illustrate the application and interpretation of these measures in a case study analyzing the rate of hospital readmission in patients discharged from hospital with a diagnosis of heart failure."], "field": "Nursing", "q_year": 2025, "q_cid": "283736125", "pos_cid": 3453979, "source": "eval_collection"}
{"query_id": "scaleup_22060674_52090887", "query": "How to clarify the potential link between mercury exposure and metabolic syndrome, particularly disturbances in lipid metabolism", "pos": ["Chronic effects of mercury on Bufo gargarizans larvae: Thyroid disruption, liver damage, oxidative stress and lipid metabolism disorder.. Mercury is severely detrimental to organisms and is ubiquitous in both terrestrial and aquatic ecosystems. In the present study, we examined the effects of chronic mercury (Hg) exposure on metamorphosis, body size, thyroid microstructures, liver microstructural and ultrastructural features, and transcript levels of genes associated with lipid metabolism, oxidative stress and thyroid hormones signaling pathways of Chinese toad (Bufo gargarizans) tadpoles. Tadpoles were exposed to mercury concentrations at 0, 6, 12, 18, 24 and 30 µg/L from Gosner stage 26-42 of metamorphic climax. The present results showed that high dose mercury (24 and 30 µg/L) decelerated metamorphosis rate and inhibited body size of B. gargarizans larvae. Histological examinations have clearly exhibited that high mercury concentrations caused thyroid gland and liver damages. Moreover, degeneration and disintegration of hepatocytes, mitochondrial vacuolation, and endoplasmic reticulum breakdown were visible in the ultrastructure of liver after high dose mercury treatment. Furthermore, the larvae exposed to high dose mercury demonstrated a significant decrease in type II iodothyronine deiodinase (Dio2) and thyroid hormone receptor α and β (TRα and TRβ) mRNA levels. Transcript level of superoxide dismutase (SOD) and heat shock protein (HSP) were significantly up regulated in larvae exposed to high dose mercury, while transcript level of phospholipid hydroperoxide glutathione peroxidase (PHGPx) was significantly down regulated. Moreover, exposure to high dose mercury significantly down regulated mRNA expression of carnitine palmitoyltransferase (CPT), sterol carrier protein (SCP), acyl-CoA oxidase (ACOX) and peroxisome proliferator-activated receptor α (PPAPα), but significantly up regulated mRNA expression of fatty acid elongase (FAE), fatty acid synthetase (FAS) and Acetyl CoA Carboxylase (ACC). Therefore, we conclude that high dose mercury induced thyroid function disruption, liver oxidative stress and lipid metabolism disorder by damaging thyroid and liver cell structures and altering the expression levels of relevant genes."], "field": "Nursing", "q_year": 2020, "q_cid": "220606740", "pos_cid": 52090887, "source": "eval_collection"}
{"query_id": "scaleup_26467087_23351807", "query": "How to assess the robustness of causal estimates linking selenium levels to brain cortical structure against horizontal pleiotropy and disproportionate influence from individual genetic variants", "pos": ["Assessing the Causal Role of Selenium in Amyotrophic Lateral Sclerosis: A Mendelian Randomization Study. Objectives: The relation between selenium overexposure and increased risk of amyotrophic lateral sclerosis (ALS) has been subject to considerable interest. Epidemiologic studies have reported suggestive associations between selenium and ALS, although the causal inference between selenium and ALS remains to be established. Methods: We conducted a two-sample Mendelian randomization (MR) analysis to analyze the causal role of selenium on ALS risk. Variants associated with selenium levels were obtained from the GWAS meta-analysis of circulating selenium levels (n = 5,477) and toenail selenium levels (n = 4,162) in the European population. Outcome data were from the largest ALS GWAS dataset with 20,806 ALS cases and 59,804 controls in the European population. Inverse variance weighted (IVW) method was used as the main analysis, with an array of sensitivity analyses performed to detect potential violations of MR assumptions. Results: Inverse variance weighted (IVW) analysis indicated no evidence of a causal role for selenium levels in ALS development (odds ratio (OR) = 1.02, 95% confidence interval (CI) = 0.96–1.08). Similar results were observed for the sensitivity analyses (OR = 1.00, 95% CI = 0.95–1.07 for weighted median; OR = 1.07, 95% CI = 0.87–1.32 for MR-Egger), with no pleiotropy detected. Conclusions: Although selenium was found associated with ALS according to earlier epidemiologic studies, current evidence based on the population of European ancestry does not support the causal effect of selenium on ALS risk."], "field": "Nursing", "q_year": 2023, "q_cid": "264670879", "pos_cid": 233518072, "source": "eval_collection"}
{"query_id": "scaleup_23213178_22171186", "query": "How to assess whether infant formula composition affects maturation when size alone may not adequately predict function", "pos": ["Microstructural Integrity of the Hippocampus During Childhood: Relations With Age and Source Memory. The hippocampus is a brain structure known to be important for memory. However, studies examining relations between hippocampal volume and memory across development yield mixed results. This may be due in part to the fact that volume is a coarser measure of hippocampal composition. Studies have begun to examine measures of diffusion, which capture characteristics of the microstructure of the hippocampus, and thus may provide additional information about the integrity of the underlying neural circuits. The present study applied this approach to a developmental period characterized by dramatic changes in both hippocampal microstructure and memory behavior – early childhood. Specifically, measures of hippocampal microstructural integrity were related to age and source memory performance in 93 children aged 4–8 years. Results revealed significant negative associations between hippocampal mean diffusivity and both age and memory, even after controlling for differences in hippocampal volume. These results suggest that hippocampal diffusion may provide additional, independent information about hippocampal integrity compared to volume, particularly during early childhood when important developmental changes have been proposed."], "field": "Nursing", "q_year": 2021, "q_cid": "232131788", "pos_cid": 221711861, "source": "eval_collection"}
{"query_id": "scaleup_28002966_23903360", "query": "How to assess whether unmeasured confounders could change the statistical significance of the estimated effect of community-led total sanitation on open defecation", "pos": ["Effect of disclosure of HIV status on patient representation and adherence to clinic visits in eastern Uganda: A propensity-score matched analysis. Background Disclosure of human immunodeficiency virus (HIV) status improves adherence to antiretroviral therapy (ART) and increases the chance of virological suppression and retention in care. However, information on the effect of disclosure of HIV status on adherence to clinic visits and patient representation is limited. We evaluated the effects of disclosure of HIV status on adherence to clinic visits and patient representation among people living with HIV in eastern Uganda. Methods In this quasi-randomized study, we performed a propensity-score-matched analysis on observational data collected between October 2018 and September 2019 from a large ART clinic in eastern Uganda. We matched participants with disclosed HIV status to those with undisclosed HIV status based on similar propensity scores in a 1:1 ratio using the nearest neighbor caliper matching technique. The primary outcomes were patient representation (the tendency for patients to have other people pick-up their medications) and adherence to clinic visits. We fitted a logistic regression to estimate the effects of disclosure of HIV status, reported using the odds ratio (OR) and 95% confidence interval (CI). Results Of 957 participants, 500 were matched. In propensity-score matched analysis, disclosure of HIV status significantly impacts adherence to clinic visits (OR = 1.63; 95% CI, 1.13–2.36) and reduced patient representation (OR = O.49; 95% CI, 0.32–0.76). Sensitivity analysis showed robustness to unmeasured confounders (Gamma value = 2.2, p = 0.04). Conclusions Disclosure of HIV status is associated with increased adherence to clinic visits and lower representation to collect medicines at the clinic. Disclosure of HIV status should be encouraged to enhance continuity of care among people living with HIV."], "field": "Nursing", "q_year": 2025, "q_cid": "280029665", "pos_cid": 239033606, "source": "eval_collection"}
{"query_id": "scaleup_27330473_33340574", "query": "How to clarify the relationship between serum antioxidant defenses and high-density lipoprotein susceptibility to oxidation in psoriasis progression and associated complications", "pos": ["HUMAN PARAOXONASE-1 (PON1): GENE STRUCTURE AND EXPRESSION, PROMISCUOUS ACTIVITIES AND MULTIPLE PHYSIOLOGICAL ROLES. Human PON1 is a HDL-associated lipolactonase capable of preventing LDL and cell membrane oxidation and is therefore considered to be atheroprotective. PON1 contributes to the antioxidative function of HDL and reductions in HDL-PON1 activity, prevalent in a wide variety of diseases with an inflammatory component, is believed to lead to dysfunctional HDL which can promote inflammation and atherosclerosis. However, PON1 is multifunctional and may contribute to other HDL functions such as in innate immunity, preventing infection by quorum sensing gram negative bacteria by destroying acyl lactone mediators of quorum sensing, and putative new roles in cancer development and the promotion of healthy ageing. In this review we explore the physiological roles of PON1 in disease development, as well as PON1 gene and protein structure, promiscuous activities and the roles of SNPs and ethnicity in determining PON1 activity."], "field": "Nursing", "q_year": 2024, "q_cid": "273304739", "pos_cid": 33340574, "source": "eval_collection"}
{"query_id": "scaleup_27694844_23237684", "query": "How to achieve reliable fine-scale prediction when relationships between variables vary spatially and may be nonlinear, while limiting parameter-estimation bias and overfitting", "pos": ["Geographically weighted machine learning model for untangling spatial heterogeneity of type 2 diabetes mellitus (T2D) prevalence in the USA. Type 2 diabetes mellitus (T2D) prevalence in the United States varies substantially across spatial and temporal scales, attributable to variations of socioeconomic and lifestyle risk factors. Understanding these variations in risk factors contributions to T2D would be of great benefit to intervention and treatment approaches to reduce or prevent T2D. Geographically-weighted random forest (GW-RF), a tree-based non-parametric machine learning model, may help explore and visualize the relationships between T2D and risk factors at the county-level. GW-RF outputs are compared to global (RF and OLS) and local (GW-OLS) models between the years of 2013–2017 using low education, poverty, obesity, physical inactivity, access to exercise, and food environment as inputs. Our results indicate that a non-parametric GW-RF model shows a high potential for explaining spatial heterogeneity of, and predicting, T2D prevalence over traditional local and global models when inputting six major risk factors. Some of these predictions, however, are marginal. These findings of spatial heterogeneity using GW-RF demonstrate the need to consider local factors in prevention approaches. Spatial analysis of T2D and associated risk factor prevalence offers useful information for targeting the geographic area for prevention and disease interventions."], "field": "Nursing", "q_year": 2025, "q_cid": "276948448", "pos_cid": 232376841, "source": "eval_collection"}
{"query_id": "scaleup_24716869_23831766", "query": "How to assess cognition in pigs with simpler, less labour-intensive tests", "pos": ["The touchscreen operant platform for testing learning and memory in rats and mice. An increasingly popular method of assessing cognitive functions in rodents is the automated touchscreen platform, on which a number of different cognitive tests can be run in a manner very similar to touchscreen methods currently used to test human subjects. This methodology is low stress (using appetitive rather than aversive reinforcement), has high translational potential and lends itself to a high degree of standardization and throughput. Applications include the study of cognition in rodent models of psychiatric and neurodegenerative diseases (e.g., Alzheimer's disease, schizophrenia, Huntington's disease, frontotemporal dementia), as well as the characterization of the role of select brain regions, neurotransmitter systems and genes in rodents. This protocol describes how to perform four touchscreen assays of learning and memory: visual discrimination, object-location paired-associates learning, visuomotor conditional learning and autoshaping. It is accompanied by two further protocols (also published in this issue) that use the touchscreen platform to assess executive function, working memory and pattern separation."], "field": "Nursing", "q_year": 2022, "q_cid": "247168690", "pos_cid": 23831766, "source": "eval_collection"}
{"query_id": "scaleup_23213178_4902106", "query": "How to interpret indicators of brain maturation when developmental patterns differ between cortical and deep grey matter", "pos": ["Delineation of early brain development from fetuses to infants with diffusion MRI and beyond. &NA; Dynamic macrostructural and microstructural changes take place from the mid‐fetal stage to 2 years after birth. Delineating structural changes of the brain during early development provides new insights into the complicated processes of both typical development and the pathological mechanisms underlying various psychiatric and neurological disorders including autism, attention deficit hyperactivity disorder and schizophrenia. Decades of histological studies have identified strong spatial and functional maturation gradients in human brain gray and white matter. The recent improvements in magnetic resonance imaging (MRI) techniques, especially diffusion MRI (dMRI), relaxometry imaging, and magnetization transfer imaging (MTI) have provided unprecedented opportunities to non‐invasively quantify and map the early developmental changes at whole brain and regional levels. Here, we review the recent advances in understanding early brain structural development during the second half of gestation and the first two postnatal years using modern MR techniques. Specifically, we review studies that delineate the emergence and microstructural maturation of white matter tracts, as well as dynamic mapping of inhomogeneous cortical microstructural organization unique to fetuses and infants. These imaging studies converge into maturational curves of MRI measurements that are distinctive across different white matter tracts and cortical regions. Furthermore, contemporary models offering biophysical interpretations of the dMRI‐derived measurements are illustrated to infer the underlying microstructural changes. Collectively, this review summarizes findings that contribute to charting spatiotemporally heterogeneous gray and white matter structural development, offering MRI‐based biomarkers of typical brain development and setting the stage for understanding aberrant brain development in neurodevelopmental disorders. HighlightsDramatic microstructural changes take place in developing fetal and infant brain.Diffusion and other MRI modalities effectively quantify these developmental changes.Emergence of different white matter tracts were delineated with dMRI tractography.Cerebral cortical microstructural changes were quantified with dMRI metrics.4D spatiotemporal patterns of brain structural development were delineated."], "field": "Nursing", "q_year": 2021, "q_cid": "232131788", "pos_cid": 4902106, "source": "eval_collection"}
{"query_id": "scaleup_27673782_3348787", "query": "How to obtain a sufficiently comprehensive set of studies on fish oil processing and omega-3 bioavailability for a review", "pos": ["Guidelines for snowballing in systematic literature studies and a replication in software engineering. Background: Systematic literature studies have become common in software engineering, and hence it is important to understand how to conduct them efficiently and reliably. Objective: This paper presents guidelines for conducting literature reviews using a snowballing approach, and they are illustrated and evaluated by replicating a published systematic literature review. Method: The guidelines are based on the experience from conducting several systematic literature reviews and experimenting with different approaches. Results: The guidelines for using snowballing as a way to search for relevant literature was successfully applied to a systematic literature review. Conclusions: It is concluded that using snowballing, as a first search strategy, may very well be a good alternative to the use of database searches."], "field": "Nursing", "q_year": 2025, "q_cid": "276737822", "pos_cid": 3348787, "source": "eval_collection"}
{"query_id": "scaleup_1828230_6051572", "query": "How to explain Icariin’s protection against endothelial dysfunction and atherosclerosis", "pos": ["Epigenetic regulation of NKG2D ligands is involved in exacerbated atherosclerosis development in Sirt6 heterozygous mice. Sirt6 is a member of the class III histone deacetylase family which is associated with aging and longevity. Sirt6 deficient mice show an aging-like phenotype, while male transgenic mice of Sirt6 show increased longevity. Sirt6 acts as a tumor suppressor and deficiency of Sirt6 leads to cardiac hypertrophy and heart failure. Whether Sirt6 is involved in atherosclerosis development, the major cause of cardiovascular diseases, is unknown. We found that the expression of Sirt6 is lower in human atherosclerotic plaques than that in controls. When Sirt6+/−ApoE−/− and ApoE−/− mice are fed with high fat diet for 16 weeks, Sirt6+/−ApoE−/− mice show increased plaque fromation and exhibit feature of plaque instability. Furthermore, Sirt6 downregulation increases expression of NKG2D ligands, which leads to increased cytokine expression. Blocking NKG2D ligand almost completely blocks this effect. Mechanistically, Sirt6 binds to promoters of NKG2D ligand genes and regulates the H3K9 and H3K56 acetylation levels."], "field": "Pharmacology, Toxicology and Pharmaceutics", "q_year": 2017, "q_cid": "1828230", "pos_cid": 6051572, "source": "eval20x26"}
{"query_id": "scaleup_32111297_2827302", "query": "How to identify new 1,4-naphthoquinone compounds with enhanced cytotoxic activity for potential anticancer agent development", "pos": ["Aspartate-modified doxorubicin on its N-terminal increases drug accumulation in LAT1-overexpressing tumors. L‐type amino acid transporter 1 (LAT1), overexpressed on the membrane of various tumor cells, is a potential target for tumor‐targeting therapy. This study aimed to develop a LAT1‐mediated chemotherapeutic agent. We screened doxorubicin modified by seven different large neutral amino acids. The aspartate‐modified doxorubicin (Asp‐DOX) showed the highest affinity (Km = 41.423 μmol/L) to LAT1. Aspartate was attached to the N‐terminal of DOX by the amide bond with a free carboxyl and a free amino group on the α‐carbon atom of the Asp residue. The product Asp‐DOX was characterized by HPLC/MS. In vitro, Asp‐DOX exerted stronger inhibition on the cancer cells overexpressing LAT1 and the uptake of Asp‐DOX was approximately 3.5‐fold higher than that of DOX in HepG2 cells. Pharmacokinetic data also showed that Asp‐DOX was expressed over a longer circulation time (t1/2 = 49.14 min) in the blood compared to DOX alone (t1/2 = 15.12 min). In HepG2 and HCT116 tumor‐bearing mice, Asp‐DOX achieved 3.1‐fold and 6.4‐fold accumulation of drugs in tumor tissue, respectively, than those of the unmodified DOX. More importantly, treatment of tumor‐bearing mice with Asp‐DOX showed a significantly stronger inhibition of tumor growth than mice treated with free DOX in HepG2 tumor models. Furthermore, after Asp modification, Asp‐DOX avoided MDR mediated by P‐glycoprotein. These results suggested that the Asp‐DOX modified drug may provide a new treatment strategy for tumors that overexpress LAT1 and MDR1."], "field": "Pharmacology, Toxicology and Pharmaceutics", "q_year": 2015, "q_cid": "32111297", "pos_cid": 2827302, "source": "eval20x26"}
{"query_id": "scaleup_12738112_24810765", "query": "How to determine whether coadministration of lobeglitazone meaningfully alters warfarin exposure or anticoagulant effects given warfarin’s narrow therapeutic index", "pos": ["The revised EMA guideline for the investigation of bioequivalence for immediate release oral formulations with systemic action.. On August 1, 2010, a revised guidance regarding bioequivalence (BE) assessment for the approval of innovator (bridging studies, variations, line extensions) and generic medicinal products in the EU came into effect (EMA Guideline on the Investigation of Bioequivalence, CPMP/EWP/QWP/1401/98 Rev. 1/Corr**, London, 20 January 2010). This guideline specifies the requirements for BE assessment for immediate release oral dosage forms with systemic action. Compared to the previous BE guideline of the EMA, clearer guidance is now given on several topics including BE assessment of highly variable drugs/drug products (HVDs/HVDPs), the use of metabolite data, acceptance criteria for narrow therapeutic index drugs (NTIDs), BCS-based biowaivers, and dose strength to be used in case of application for marketing authorization of several strengths. However, the health authorities of the various EU member states do not necessarily apply the same rules as far as substitution and switchability between medicinal products are concerned. Moreover, differences still exist between the BE guidelines of the major health authorities (FDA, EMA, NIHC, ...) on topics such as HVDs/HVDPs, NTIDs and BCS-based biowaivers. Global harmonization should be the next logical step to guarantee accessibility to safe and efficacious drug products for patients in all parts of the world."], "field": "Pharmacology, Toxicology and Pharmaceutics", "q_year": 2015, "q_cid": "12738112", "pos_cid": 24810765, "source": "eval20x26"}
{"query_id": "scaleup_44699416_17181695", "query": "How to predict differences in gastric residence and gastrointestinal transit times among lipid-based formulations with the same volume and caloric content", "pos": ["Fat Emulsion Intragastric Stability and Droplet Size Modulate Gastrointestinal Responses and Subsequent Food Intake in Young Adults. Background: Intragastric creaming and droplet size of fat emulsions may affect intragastric behavior and gastrointestinal and satiety responses. Objectives: We tested the hypotheses that gastrointestinal physiologic responses and satiety will be increased by an increase in intragastric stability and by a decrease in fat droplet size of a fat emulsion. Methods: This was a double-blind, randomized crossover study in 11 healthy persons [8 men and 3 women, aged 24 ± 1 y; body mass index (in kg/m2): 24.4 ± 0.9] who consumed meals containing 300-g 20% oil and water emulsion (2220 kJ) with 1) larger, 6-μm mean droplet size (Coarse treatment) expected to cream in the stomach; 2) larger, 6-μm mean droplet size with 0.5% locust bean gum (LBG; Coarse+LBG treatment) to prevent creaming; or 3) smaller, 0.4-μm mean droplet size with LBG (Fine+LBG treatment). The participants were imaged hourly by using MRI and food intake was assessed by using a meal that participants consumed ad libitum. Results: The Coarse+LBG treatment (preventing creaming in the stomach) slowed gastric emptying, resulting in 12% higher gastric volume over time (P < 0.001), increased small bowel water content (SBWC) by 11% (P < 0.01), slowed appearance of the 13C label in the breath by 17% (P < 0.01), and reduced food intake by 9% (P < 0.05) compared with the Coarse treatment. The Fine+LBG treatment (smaller droplet size) slowed gastric emptying, resulting in 18% higher gastric volume (P < 0.001), increased SBWC content by 15% (P < 0.01), and significantly reduced food intake by 11% (P < 0.05, equivalent to an average of 411 kJ less energy consumed) compared with the Coarse+LBG treatment. These high-fat meals stimulated substantial increases in SBWC, which increased to a peak at 4 h at 568 mL (range: 150–854 mL; P < 0.01) for the Fine+LBG treatment. Conclusion: Manipulating intragastric stability and fat emulsion droplet size can influence human gastrointestinal physiology and food intake."], "field": "Pharmacology, Toxicology and Pharmaceutics", "q_year": 2016, "q_cid": "44699416", "pos_cid": 17181695, "source": "eval20x26"}
{"query_id": "scaleup_44699416_102665", "query": "How to quantitatively describe the kinetics of successive triglyceride, diglyceride, and monoglyceride digestion", "pos": ["Action of phospholipase A at interfaces.. Abstract The heterogeneous catalysis of pancreatic phospholipase A (EC 3.1.1.4) is studied by kinetics on monomolecular layers of short chain phospholipids. Under certain conditions long induction times are observed experimentally which can be related with a slow reversible penetration of the enzyme into the monolayer. The influence of surface pressure, pH, sodium chloride, and Ca2+ ions on this penetration step is reported. Based on a proposed two-dimensional Michaelis model, steady state and presteady state equations are derived and together with computer analysis show a good fit with the experimental results. A quantitative comparison between enzyme kinetics obtained by monolayer and bulk techniques is attempted using a common definition of the \"quality\" of the lipid-water interface. Possible implications of the concept of a penetration site on the enzyme are discussed."], "field": "Pharmacology, Toxicology and Pharmaceutics", "q_year": 2016, "q_cid": "44699416", "pos_cid": 102665, "source": "eval20x26"}
{"query_id": "scaleup_9881500_30823503", "query": "How to clarify the effect of Phyllanthus extracts on melanoma cell death", "pos": ["p53 Induces Apoptosis by Caspase Activation through Mitochondrial Cytochrome c Release*. The p53 tumor suppressor gene is critically involved in cell cycle regulation, DNA repair, and programmed cell death. Several lines of evidence suggest that p53 death signals lead to caspase activation; however, the mechanism of caspase activation by p53 still is unclear. Expressing wild type p53 by means of an adenoviral expression vector, we were able to induce apoptotic cell death, as characterized by morphological changes, phosphatidylserine externalization, and internucleosomal DNA fragmentation, in p53null Saos-2 cells. This cell death was accompanied by caspase activation as well as by cleavage of caspase substrates and was preceded by mitochondrial cytochrome c release. The addition of the broad-spectrum caspase inhibitor benzyloxycarbonyl-Val-Ala-Asp-fluoromethyl ketone (zVAD-fmk) directly after transduction almost completely prevented p53-induced apoptotic cell death but did not inhibit mitochondrial cytochrome crelease. In contrast, N-acetylcysteine, even at high concentrations, could not prevent induction of programmed cell death by p53 expression. Cytosolic extracts from Saos-2 cells transduced with p53, but not from Saos-2 cells transduced with the empty adenoviral vector, contained a cytochrome c-releasing activityin vitro, which was still active in the presence of zVAD-fmk. When Bax was immunodepleted from the cytosolic extracts of p53-expressing cells before incubation with isolated mitochondria, thein vitro cytochrome c release was abolished. Thus, we could demonstrate in cells and in vitro that p53 activates the apoptotic machinery through induction of the release of cytochrome c from the mitochondrial intermembrane space. Furthermore, we provide in vitro evidence for the requirement of cytosolic Bax for this cytochromec-releasing activity of p53 in Saos-2 cells."], "field": "Pharmacology, Toxicology and Pharmaceutics", "q_year": 2014, "q_cid": "9881500", "pos_cid": 30823503, "source": "eval20x26"}
{"query_id": "scaleup_4848120_5890517", "query": "How to determine whether 3-FMC causes loss of HT22 neuronal cells rather than cellular stress alone", "pos": ["Apoptosis and Beyond: Cytometry in Studies of Programmed Cell Death. A cell undergoing apoptosis demonstrates multitude of characteristic morphological and biochemical features, which vary depending on the inducer of apoptosis, cell type and the “time window” at which the process of apoptosis is observed. Because the gross majority of apoptotic hallmarks can be revealed by flow and image cytometry, the cytometric methods become a technology of choice in diverse studies of cellular demise. Variety of cytometric methods designed to identify apoptotic cells, detect particular events of apoptosis and probe mechanisms associated with this mode of cell death have been developed during the past two decades. In the present review, we outline commonly used methods that are based on the assessment of mitochondrial transmembrane potential, activation of caspases, DNA fragmentation, and plasma membrane alterations. We also present novel developments in the field such as the use of cyanine SYTO and TO-PRO family of probes. Strategies of selecting the optimal multiparameter approaches, as well as potential difficulties in the experimental procedures, are thoroughly summarized."], "field": "Pharmacology, Toxicology and Pharmaceutics", "q_year": 2018, "q_cid": "4848120", "pos_cid": 5890517, "source": "eval20x26"}
{"query_id": "scaleup_15903783_7503984", "query": "How to repeatedly assess the viability of the same skin tissue at different time points without damaging it", "pos": ["Comparison of four different colorimetric and fluorometric cytotoxicity assays in a zebrafish liver cell line. BackgroundA broad spectrum of cytotoxicity assays is currently used in the fields of (eco)toxicology and pharmacology. To choose an appropriate assay, different parameters like test compounds, detection mechanism, specificity, and sensitivity have to be considered. Furthermore, tissue or cell line can influence test performance. For zebrafish (Danio rerio), as emerging model organism, cell lines are now increasingly used, but few studies examined cytotoxicity in these cell systems. Therefore, we compared four cytotoxicity assays in the zebrafish liver cell line, ZFL, to test four differently acting model compounds. The tests comprised two colorimetric assays (MTT assay using 3-[4,5-dimethylthiazol-2-yl]-2,5-diphenyl tetrazolium bromide, and the LDH assay detecting lactate dehydrogenase activity) and two fluorometric assays (alamarBlue® using resazurin, and CFDA-AM based on 5-carboxyfluorescein diacetate acetoxymethyl ester). Model compounds were the pharmaceutical Tamoxifen, its metabolite 4-Hydroxy-Tamoxifen, the fungicide Flusilazole and the polycyclic aromatic hydrocarbon Benzo[a]pyrene.ResultsAll four assays performed well in the ZFL cells and led to reproducible dose-response curves for all test compounds. Effective concentrations causing 10% or 50% loss of cell viability (EC10 and EC50 values) varied by a maximum factor of 7.0 for the EC10 values and a maximum factor of 1.8 for the EC50 values. The EC values were not statistically different between the four assays, which is due to the assessed unspecific effects of the compounds. However, most often, the MTT assay and LDH assay showed the highest and lowest EC values, respectively. Nevertheless, the LDH assay showed the highest intra- and inter-assay variabilities and the lowest signal-to-noise ratios. In contrast to MTT, the other three assays have the advantage of being non-destructive, easy to handle, and less time consuming. Furthermore, AB and CFDA-AM can be combined on the same set of cells without damaging the cells, allowing later on their use for the investigation of other endpoints.ConclusionWe recommend the alamarBlue and CFDA-AM assays for cytotoxicity assessment in ZFL cells, which can be applied either singly or combined."], "field": "Pharmacology, Toxicology and Pharmaceutics", "q_year": 2019, "q_cid": "159037837", "pos_cid": 7503984, "source": "eval20x26"}
{"query_id": "scaleup_28067046_7211473", "query": "How to characterise mitragynine’s susceptibility to degradation under different environmental conditions", "pos": ["Stress degradation studies and development of a validated stability-indicating-assay-method for determination of diacerein in presence of degradation products. Background: To understand the degradation behavior of diacerein and to develop a simple, rapid, sensitive, and validated RP-HPLC method for the determination of diacerein, in the presence of its degradation products. Materials and Methods: An accurate, sensitive, precise, rapid, and isocratic reversed-phase high-performance liquid chromatography (RP-HPLC) method, equipped with a photo-diode array (PDA) detector for analysis of diacerein in the bulk drug has been developed and validated. The best separation was achieved on a 250 mm × 4.6 mm i.d., 5-μm particle, RP C18 column with 50 : 50 (v/v) of water (pH adjusted to 2.9 with orthophosphoric acid) : acetonitrile as the mobile phase, at a flow rate of 1.0 ml/minute. The detection wavelength was set at 257 nm. Results: The response was a linear function of concentration over the range of 0.50 – 20 μg/ml (r = 0.999) and the limits of detection and quantitation were 0.1 μg/ml and 0.50 μg/ml, respectively. The method was validated in accordance with the International Conference on Harmonization (ICH) guidelines. The drug was subjected to oxidative, hydrolytic, photolytic, and thermal stress. The drug decomposed under alkaline hydrolytic stress conditions and also on thermal degradation and photolysis. It was stable on acid hydrolysis and oxidation. The degradation products produced as a result of this stress did not interfere with the detection of diacerein, and the assay could thus be regarded as stability-indicating. Conclusion: The method was suitable for application in the analysis of formulations of diacerein in quality-control laboratories, because it was simple and rapid, with good accuracy and precision."], "field": "Pharmacology, Toxicology and Pharmaceutics", "q_year": 2025, "q_cid": "280670463", "pos_cid": 7211473, "source": "eval_collection"}
{"query_id": "scaleup_22628494_11547925", "query": "How to characterize drug clearance from viable skin in vivo, distinguish slow skin disposition from systemic elimination in plasma concentrations after patch removal, and predict local drug concentrations after topical application", "pos": ["Flip-flop pharmacokinetics – delivering a reversal of disposition: challenges and opportunities during drug development. Flip-flop pharmacokinetics is a phenomenon often encountered with extravascularly administered drugs. Occurrence of flip-flop spans preclinical to human studies. The purpose of this article is to analyze both the pharmacokinetic interpretation errors and opportunities underlying the presence of flip-flop pharmacokinetics during drug development. Flip-flop occurs when the rate of absorption is slower than the rate of elimination. If it is not recognized, it can create difficulties in the acquisition and interpretation of pharmacokinetic parameters. When flip-flop is expected or discovered, a longer duration of sampling may be necessary in order to avoid overestimation of fraction of dose absorbed. Common culprits of flip-flop disposition are modified dosage formulations; however, formulation characteristics such as the drug chemical entities themselves or the incorporated excipients can also cause the phenomenon. Yet another contributing factor is the physiological makeup of the extravascular site of administration. In this article, these causes of flip-flop pharmacokinetics are discussed with incorporation of relevant examples and the implications for drug development outlined."], "field": "Pharmacology, Toxicology and Pharmaceutics", "q_year": 2020, "q_cid": "226284944", "pos_cid": 11547925, "source": "eval_collection"}
{"query_id": "scaleup_23948510_21088304", "query": "How to clarify the relationship between compound structure and enhancement of calcitriol-induced differentiation of acute myeloid leukemia cells", "pos": ["Curcumin induces stabilization of Nrf2 protein through Keap1 cysteine modification.. The present study was aimed to investigate the effects of curcumin, a representative chemopreventive phytochemical with pronounced antioxidant and anti-inflammatory properties, on activation of Nrf2 and its target protein heme oxygenase-1 (HO-1) in mouse skin in vivo and in cultured murine epidermal cells. Treatment of mouse epidermal JB-6 cells with curcumin resulted in the induction of HO-1 expression, and this was abrogated in cells transiently transfected with Nrf2 siRNA. While curcumin treatment increased protein expression of Nrf2, it failed to did not alter the steady-state level of the Nrf2 mRNA transcript. Treatment of cells with curcumin stabilized Nrf2 by inhibiting ubiquitination and subsequent 26S proteasomal degradation of this transcription factor. Tetrahydrocurcumin, a non-electrophilic analogue of curcumin that lacks the α,β-unsaturated carbonyl group, failed to induce HO-1 expression as well as Nrf2 nuclear translocation of Nrf2 and its binding to the antioxidant/electrophile response elements. Cells transfected with a mutant Keap1 protein in which cysteine 151 is replaced by serine exhibited marked reduction in curcumin-induced Nrf2 transactivation. Mass spectrometric analysis revealed that curcumin binds to Keap1 Cys151, supporting that this amino acid is a critical target for curcumin modification of Keap1, which facilitates the liberation of Nrf2. Thus, it is likely that the α,β-unsaturated carbonyl moiety of curcumin is critical essential for its binding to Keap1 and stabilization of Nrf2 by hampering ubiquitination and proteasomal degradation."], "field": "Pharmacology, Toxicology and Pharmaceutics", "q_year": 2021, "q_cid": "239485100", "pos_cid": 210883042, "source": "eval_collection"}
{"query_id": "scaleup_27335365_25755561", "query": "How to noninvasively characterize metabolic differences between oily sensitive skin and healthy skin to enable objective assessment of the condition and its associated barrier impairment", "pos": ["Does mask wearing affect skin health? An untargeted skin metabolomics study.. Wearing masks is used as an effective way to prevent the spread of viruses. However, the effect of wearing masks on skin health requires further assessment. In this study, a non-invasive D-squame sampling method coupled with an untargeted metabolomics analysis by liquid chromatography high-resolution mass spectrometry was developed to identify the changes in the skin metabolome caused by wearing masks. D-squame method was found to have advantages over the commonly used sterile gauze method, especially for the lipids and lipid-like molecules. A total of 356 skin metabolites were putatively identified from the stratum corneum of 10 volunteers, and 17 differential metabolites were significantly downregulated after wearing surgical masks or N95 respirators. The downregulation of metabolites such as phosphatidylethanolamine and sphingomyelin might be related to hypoxia or increased skin moisture caused by wearing masks. Changes in skin metabolomics indicated a potential risk of skin barrier disruption and skin inflammation. Intermittent removal of the masks can effectively alleviate changes in the skin metabolome."], "field": "Pharmacology, Toxicology and Pharmaceutics", "q_year": 2024, "q_cid": "273353650", "pos_cid": 257555613, "source": "eval_collection"}
{"query_id": "scaleup_26916365_88907111", "query": "How to determine whether changes in gut bacterial populations indicate a healthier intestinal environment relevant to colorectal cancer prevention", "pos": ["Colon microbiota fermentation of dietary prebiotics towards short-chain fatty acids and their roles as anti-inflammatory and antitumour agents: A review. Abstract Some plant polysaccharides cannot be digested by humans, arriving intact to the colon, where they are fermented by a distinct group of anaerobic beneficial bacterial species ( Lactobacillus, Bifidobacterium, Roseburia, Faecalibacterium, Anaerostipes, Coprococcus , etc.). As a result of this fermentation, in the case of some of these compounds, diverse short-chain fatty acids (SCFA) are produced in situ in the colon lumen, mainly acetate, propionate, and butyrate. Acetate and propionate possess principally energetic effects for eukaryotic cells. Butyrate is the preferred energy source for normal colonocytes, contributing to their normal homeostasis, and it is a strong antitumour compound for tumour colonocytes, downregulating cell multiplication pathways and promoting pro-apoptotic routes. These polysaccharides that increase beneficial colon bacteria populations in the colon are called prebiotics. This review will describe their different dietary sources and structures, as well as the metabolic pathways leading to SCFA and the antitumour and anti-inflammatory effect of these SCFA."], "field": "Pharmacology, Toxicology and Pharmaceutics", "q_year": 2024, "q_cid": "269163652", "pos_cid": 88907111, "source": "eval_collection"}
{"query_id": "scaleup_25185396_9548113", "query": "How to enable drug-carrying nanoparticles to enter cells", "pos": ["Targeting receptor-mediated transport for delivery of biologics across the blood-brain barrier. Biologics are an emerging class of medicines with substantial promise to treat neurological disorders such as Alzheimer’s disease, stroke and multiple sclerosis. However, the blood-brain barrier (BBB) presents a formidable obstacle that appreciably limits brain uptake and hence, therapeutic potential, of biologics following intravenous administration. One promising strategy for overcoming the BBB to deliver biologics is the targeting of endogenous receptor-mediated transport (RMT) systems that employ vesicular trafficking to transport ligands across the BBB endothelium. If a biologic is modified with an appropriate targeting ligand, it can gain improved access to the brain via RMT. Various RMT targeting strategies have been developed over the past 20 years, and this review will explore exciting recent advances, with a particular emphasis on those studies showing brain targeting in vivo."], "field": "Pharmacology, Toxicology and Pharmaceutics", "q_year": 2022, "q_cid": "251853967", "pos_cid": 9548113, "source": "eval_collection"}
{"query_id": "scaleup_24399025_22725948", "query": "How to achieve effective anti-inflammatory treatment without worsening bone loss, increasing fracture risk, or causing other organ damage", "pos": ["Ginsenoside Rg1 promotes lymphatic drainage and improves chronic inflammatory arthritis. Objective: The lymphatic system plays an important role in joint diseases. This study aimed to evaluate the effects of ginsenoside Rg1 on lymphatic drainage and accumulation of inflammatory products in the joints. Methods: Two-month-old transgenic mice that overexpress tumor necrosis factor alpha (TNF-α; TNF-Tg) were used as the animal models. Ginsenoside Rg1 was administered for 12 weeks and the lymphatic drainage in the mice was evaluated using near infrared-indocyanine green (NIR-ICG) lymphatic imaging system. The clinical symptoms of arthritis were evaluated weekly. The ankle and knee joints were harvested for hematoxylin-eosin (HE), alcian blue/orange G (ABOG), and tartrate-resistant acid phosphatase (TRAP) staining, and the foot dorsal skin was used for whole-mount immuno-staining. Simultaneously, the serum levels of IL-6 and TNF-α were detected using enzyme-linked immunosorbent assay (ELISA). Results: Ginsenoside Rg1 significantly improved the lymphatic drainage function, reduced synovial inflammation and bone erosion, decreased serum IL-6 and TNF-α concentration, and increased smooth muscle coverage on the collecting lymphatic vessels in the foot skin of the TNF-Tg mice. Furthermore, ginsenoside Rg1 treatment for 12 weeks did not cause any damage to the liver and kidney tissues. Conclusion: Ginsenoside Rg1 improves lymphatic drainage and joint inflammation in TNF-Tg mice. Therefore, ginsenoside Rg1 has the potential to be a candidate drug for the treatment of inflammatory arthritis."], "field": "Pharmacology, Toxicology and Pharmaceutics", "q_year": 2021, "q_cid": "243990252", "pos_cid": 227259485, "source": "eval_collection"}
{"query_id": "scaleup_27430000_7428628", "query": "How to identify the most suitable ligand to inhibit BlaR1 and prevent β-lactamase production", "pos": ["Thermodynamics of Ligand-Protein Interactions: Implications for Molecular Design. Biologically relevant macromolecules, such as proteins, do not operate as static, isolated entities. On the contrary, they are involved in numerous interactions with other species, such as proteins, nucleic acid, membranes, small molecule ligands, and also, critically, solvent molecules. These interactions often display a remarkable degree of specificity and high affinity. Fundamentally, the biological processes rely on molecular organisation and recognition events. Binding between two interacting partners has both enthalpic (H) and entropic (-TS) components, which means the recognition event is associated with changes of both the structure and dynamics of each counterpart. Like any other spontaneous process, binding occurs only when it is associated with a negative Gibbs' free energy of binding ( G  ), which may have differing thermodynamic signatures, varying from enthalpyto entropy-driven. Thus, the understanding of the forces driving the recognition and interaction require a detailed description of the binding thermodynamics, and a correlation of the thermodynamic parameters with the structures of interacting partners. Such an understanding of the nature of the recognition phenomena is of a great importance for medicinal chemistry and material research, since it enables truly rational structure-based molecular design. This chapter is organised in the following way. The first part of it introduces general principles which govern macromolecular associations under equilibrium conditions: the free energy of binding and its enthalpic and entropic components, the contributions from both interacting partners, interaction energy of the association, and specific types of interactions – such as hydrogen bonding or van der Waals interactions, ligand and protein flexibility, and ultimately solvent effects (e.g. solute-solvent interactions, solvent reorganisation). The second part is dedicated to methods applied to assess particular contributions, experimental as well as computational. Specifically, there will be a focus on isothermal titrational calorimetry (ITC), solution nuclear magnetic resonance (NMR), and a discussion of computational approaches to the estimation of enthalpic and entropic contributions to the binding free energy. I will discuss the applicability of these methods, the approximations behind them, and their limitations. In the third part of this chapter, I will provide the reader several examples of ligand-protein interactions and focus on the forces driving the associations, which can be very different from case to case. Finally, I will address several practical aspects of assessing the thermodynamic parameters in molecular design, the"], "field": "Pharmacology, Toxicology and Pharmaceutics", "q_year": 2024, "q_cid": "274300006", "pos_cid": 7428628, "source": "eval_collection"}
{"query_id": "scaleup_28036347_3540120", "query": "How to determine whether effects on IBS are attributable to proteins rather than other factors", "pos": ["Mendelian randomization: genetic anchors for causal inference in epidemiological studies. Observational epidemiological studies are prone to confounding, reverse causation and various biases and have generated findings that have proved to be unreliable indicators of the causal effects of modifiable exposures on disease outcomes. Mendelian randomization (MR) is a method that utilizes genetic variants that are robustly associated with such modifiable exposures to generate more reliable evidence regarding which interventions should produce health benefits. The approach is being widely applied, and various ways to strengthen inference given the known potential limitations of MR are now available. Developments of MR, including two-sample MR, bidirectional MR, network MR, two-step MR, factorial MR and multiphenotype MR, are outlined in this review. The integration of genetic information into population-based epidemiological studies presents translational opportunities, which capitalize on the investment in genomic discovery research."], "field": "Pharmacology, Toxicology and Pharmaceutics", "q_year": 2025, "q_cid": "280363470", "pos_cid": 3540120, "source": "eval_collection"}
{"query_id": "scaleup_26429713_21889511", "query": "How to explain sex-related differences in susceptibility to an elevated international normalized ratio during warfarin therapy and the balance between bleeding and thrombosis risk", "pos": ["Estrogen and Thrombosis: a Bench to Bedside Review. Estrogen, in the clinical setting is used primarily for contraception and hormone replacement therapy. It has been well established that estrogen increases the risk of both arterial and venous thrombosis. While estrogen is known to induce a prothrombotic milieu through various effects on the hemostatic pathways, the exact molecular mechanism leading to those effects is not known. The most common clinical presentation of estrogen-related thrombosis is venous thromboembolism (VTE) of the deep veins of the legs or pulmonary vessels, usually within the first few months of use. Estrogen has also been associated with increased risk of “unusual site” thromboses, as well as arterial thrombosis. Women at high-risk of thrombosis need careful evaluation and counseling for contraception, pregnancy, menopausal hormonal therapy and other estrogen-related conditions or treatments in order to lower the risk of thromboses. We review the most recent evidence on management of high-estrogen states in women at high-risk of thrombosis, as well as emerging data on unique populations such as transgender women. More studies are needed to better understand the pathophysiology of hormone-related thrombosis, as well as more comprehensive techniques to stratify risks for thrombosis so as to enable tailoring of recommendations for each individual."], "field": "Pharmacology, Toxicology and Pharmaceutics", "q_year": 2023, "q_cid": "264297133", "pos_cid": 218895113, "source": "eval_collection"}
{"query_id": "scaleup_25985796_23208615", "query": "How to determine the duration and rate of antifungal activity and explain rapid fungal killing", "pos": ["Development of Microemulsion Containing Alpinia galanga Oil and Its Major Compounds: Enhancement of Antimicrobial Activities. The aim of the present study was to develop a microemulsion (ME) containing Alpinia galanga oil (AGO), 1,8-cineole (C), or methyl eugenol (M) as an active pharmaceutical ingredient (API) for enhancing their antimicrobial activities. Agar diffusion, broth microdilution, and killing kinetics were used for antimicrobial evaluations. The ME composed of 30% API, 33.4% Tween 80, 16.6% ethanol, and 20% water appeared as translucent systems with droplet size and polydispersity index of 101.1 ± 1.3 nm and 0.3 ± 0.1, 80.9 ± 1.1 nm and 0.4 ± 0.1, and 96.6 ± 2.0 nm and 0.2 ± 0.1 for ME-AGO, ME-C, and ME-M, respectively. These ME formulations showed minimum bacterial concentrations of 3.91–31.25 µg/mL and 50% fungal inhibition concentrations of 1.83 ± 0.27–0.46 ± 0.13 µg/mL, 2–4 times stronger, and faster kinetic killing rate than their respective API alone. Keeping the ME formulations at 4 °C, 25 °C, and 40 °C for 12 weeks did not affect their activities against fungi and Gram-negative bacteria, but the high temperature of 40 °C decreased their activities against Gram-positive bacteria. It is concluded that ME is a promising delivery system for AGO and its major compounds to enhance their water miscibility and antimicrobial activities."], "field": "Pharmacology, Toxicology and Pharmaceutics", "q_year": 2023, "q_cid": "259857962", "pos_cid": 232086155, "source": "eval_collection"}
{"query_id": "scaleup_28220652_22111322", "query": "How to achieve efficient, scalable synthesis of structurally diverse natural and unnatural benzylisoquinoline alkaloids", "pos": ["Divergent Synthesis of Complex Diterpenes via a Hybrid Oxidative Approach. Trio of enzymes power divergent synthesis Diterpene natural products are built from a 20-carbon building block, with a huge range of possible structures and modifications. Chemical synthesis of specific molecules, some of which have valuable biological activities, is tricky because of the need for selective oxidations and rearrangements when starting from widely available scaffolds. Zhang et al. characterized selectivities for three oxidative enzymes that each attack different positions on a common scaffold. They then seamlessly combined chemical transformations with the enzymatic oxidations to produce nine distinct compounds across three families of diterpenes. These results highlight the potential of hybrid organic-biocatalytic synthetic schemes for divergent synthesis. Science, this issue p. 799 Synthesis of nine complex diterpenes is achieved through combined chemical and enzymatic C–H oxidation methods. Polycyclic diterpenes exhibit many important biological activities, but de novo synthetic access to these molecules is highly challenging because of their structural complexity. Semisynthetic access has also been limited by the lack of chemical tools for scaffold modifications. We report a chemoenzymatic platform to access highly oxidized diterpenes by a hybrid oxidative approach that strategically combines chemical and enzymatic oxidation methods. This approach allows for selective oxidations of previously inaccessible sites on the parent carbocycles and enables abiotic skeletal rearrangements to additional underlying architectures. We synthesized a total of nine complex natural products with rich oxygenation patterns and skeletal diversity in 10 steps or less from ent-steviol."], "field": "Pharmacology, Toxicology and Pharmaceutics", "q_year": 2025, "q_cid": "282206529", "pos_cid": 221113229, "source": "eval_collection"}
{"query_id": "scaleup_28111708_36493197", "query": "How to ensure successive coating layers attach reliably to drug-loaded liposomes and to one another to form a stable multilayer coating", "pos": ["Layer-by-layer assembly of graphene oxide on thermosensitive liposomes for photo-chemotherapy.. Stimuli responsive polyelectrolyte nanoparticles have been developed for chemo-photothermal destruction of breast cancer cells. This novel system, called layer by layer Lipo-graph (LBL Lipo-graph), is composed of alternate layers of graphene oxide (GO) and graphene oxide conjugated poly (l-lysine) (GO-PLL) deposited on cationic liposomes encapsulating doxorubicin. Various concentrations of GO and GO-PLL were examined and the optimal LBL Lipo-graph was found to have a particle size of 267.9 ± 13 nm, zeta potential of +43.9 ± 6.9 mV and encapsulation efficiency of 86.4 ± 4.7%. The morphology of LBL Lipo-graph was examined by cryogenic-transmission electron microscopy (Cryo-TEM), atomic force microcopy (AFM) and scanning electron microscopy (SEM). The buildup of LBL Lipo-graph was confirmed via ultraviolet-visible (UV-Vis) spectrophotometry, thermogravimetric analysis (TGA) and differential scanning calorimetry (DSC) analysis. Infra-red (IR) response suggests that four layers are sufficient to induce a gel-to-liquid phase transition in response to near infra-red (NIR) laser irradiation. Light-matter interaction of LBL Lipo-graph was studied by calculating the absorption cross section in the frequency domain by utilizing Fourier analysis. Drug release assay indicates that the LBL Lipo-graph releases much faster in an acidic environment than a liposome control. A cytotoxicity assay was conducted to prove the efficacy of LBL Lipo-graph to destroy MD-MB-231 cells in response to NIR laser emission. Also, image stream flow cytometry and two photon microcopy provide supportive data for the potential application of LBL Lipo-graph for photothermal therapy. Study results suggest the novel dual-sensitive nanoparticles allow intracellular doxorubin delivery and respond to either acidic environments or NIR excitation. STATEMENT OF SIGNIFICANCE Stimuli sensitive hybrid nanoparticles have been synthesized using a layer-by-layer technique and demonstrated for dual chemo-photothermal destruction of breast cancer cells. The hybrid nanoparticles are composed of alternating layers of graphene oxide and graphene oxide conjugated poly-l-lysine coating the surface of a thermosensitive cationic liposome containing doxorubicin as a core. Data suggests that the hybrid nanoparticles may offer many advantages for chemo-photothermal therapy. Advantages include a decrease of the initial burst release which may result in the reduction in systemic toxicity, increase in pH responsivity around the tumor environment and improved NIR light absorption."], "field": "Pharmacology, Toxicology and Pharmaceutics", "q_year": 2025, "q_cid": "281117080", "pos_cid": 36493197, "source": "eval_collection"}
{"query_id": "scaleup_27765666_24000013", "query": "How to increase activity against tumor cells while limiting toxicity to normal cells", "pos": ["Antitumor and toxicity study of mitochondria-targeted triptolide derivatives using triphenylphosphine (TPP+) as a carrier.. Based on the higher mitochondrial membrane potential (Δψm) of tumor cells than normal cells, a mitochondria-targeting strategy using delocalized lipophilic cations as carriers is a promising way to improve the antitumor effect of small molecules and to reduce toxicity. Triptolide (TP) has a strong antitumor effect but is limited in the clinic due to high systemic toxicity. Mitochondria-targeted TP derivatives were designed and synthesized using triphenylphosphine cations as carriers. The optimal derivative not only maintained the antitumor activity of TP but also showed a tumor cell selectivity trend. Moreover, the optimal derivative increased the release of lactate dehydrogenase and the production of ROS, decreased Δψm, and arrested HepG2 cells in G0/G1 phase. In a zebrafish HepG2 xenograft tumor model, the inhibitory effect of the optimal derivative was comparable to that of TP, while it had no obvious toxic effect on multiple indicators in zebrafish at the test concentrations. This work provided some evidence to support the mitochondria-targeting strategy."], "field": "Pharmacology, Toxicology and Pharmaceutics", "q_year": 2025, "q_cid": "277656669", "pos_cid": 240000130, "source": "eval_collection"}
{"query_id": "scaleup_28291857_25723953", "query": "How to identify which metabolites in ginger-derived exosome-like nanoparticles may act on which lung cancer-related biological targets", "pos": ["Network pharmacology, a promising approach to reveal the pharmacology mechanism of Chinese medicine formula.. ETHNOPHARMACOLOGICAL RELEVANCE Network pharmacology is a new discipline based on systems biology theory, biological system network analysis, and multi-target drug molecule design specific signal node selection. The mechanism of action of TCM formula has the characteristics of multiple targets and levels. The mechanism is similar to the integrity, systematization and comprehensiveness of network pharmacology, so network pharmacology is suitable for the study of the pharmacological mechanism of Chinese medicine compounds. AIM OF THE STUDY The paper summarizes the present application status and existing problems of network pharmacology in the field of Chinese medicine formula, and formulates the research ideas, up-to-date key technology and application method and strategy of network pharmacology. Its purpose is to provide guidance and reference for using network pharmacology to reveal the modern scientific connotation of Chinese medicine. MATERIALS AND METHODS Literatures in this review were searched in PubMed, China National Knowledge Infrastructure (CNKI), Web of Science, ScienceDirect and Google Scholar using the keywords \"traditional Chinese medicine\", \"Chinese herb medicine\" and \"network pharmacology\". The literature cited in this review dates from 2002 to 2022. RESULTS Using network pharmacology methods to predict the basis and mechanism of pharmacodynamic substances of traditional Chinese medicines has become a trend. CONCLUSION Network pharmacology is a promising approach to reveal the pharmacology mechanism of Chinese medicine formula."], "field": "Pharmacology, Toxicology and Pharmaceutics", "q_year": 2025, "q_cid": "282918570", "pos_cid": 257239539, "source": "eval_collection"}
{"query_id": "scaleup_24862551_14624758", "query": "How to clarify AKAP12’s role in liver injury and determine whether it regulates PI3K/AKT activity in this setting", "pos": ["Loss of the ssecks/gravin/akap12 Gene Results in Prostatic Hyperplasia. SSeCKS/Gravin/AKAP12 (SSeCKS) is a kinase scaffolding protein that encodes metastasis-suppressor activitythrough the suppression of Src-mediated oncogenic signaling and vascular endothelial growth factor expression. SSeCKS expression is down-regulated in Src- and Ras-transformed fibroblasts, in human cancer cell lines and in several types of human cancer, including prostate. Normal human and mouse prostates express abundant SSeCKS in secretory epithelial cells and, to a lesser extent, in the surrounding mesenchyme. Here, we show that the loss of SSeCKS results in prostatic hyperplasia in the anterior and ventral lobes as well as increased levels of apoptosis throughout the prostate. Dysplastic foci were observed less frequently but were associated with the loss of E-cadherin staining and the loss of high molecular weight cytokeratin-positive basal epithelial cells. SSeCKS-null prostate tissues expressed significantly higher relative levels of AKTpoS473 compared with wild-type controls, suggesting that SSeCKS attenuates phosphatidylinositol-3-OH kinase signaling. The data suggest that SSeCKS-null mice have increased susceptibility for oncogenic transformation in the prostate."], "field": "Pharmacology, Toxicology and Pharmaceutics", "q_year": 2022, "q_cid": "248625515", "pos_cid": 14624758, "source": "eval_collection"}
{"query_id": "scaleup_25271814_11013801", "query": "How to enable isobavachalcone biosynthesis in tobacco", "pos": ["A One Pot, One Step, Precision Cloning Method with High Throughput Capability. Current cloning technologies based on site-specific recombination are efficient, simple to use, and flexible, but have the drawback of leaving recombination site sequences in the final construct, adding an extra 8 to 13 amino acids to the expressed protein. We have devised a simple and rapid subcloning strategy to transfer any DNA fragment of interest from an entry clone into an expression vector, without this shortcoming. The strategy is based on the use of type IIs restriction enzymes, which cut outside of their recognition sequence. With proper design of the cleavage sites, two fragments cut by type IIs restriction enzymes can be ligated into a product lacking the original restriction site. Based on this property, a cloning strategy called ‘Golden Gate’ cloning was devised that allows to obtain in one tube and one step close to one hundred percent correct recombinant plasmids after just a 5 minute restriction-ligation. This method is therefore as efficient as currently used recombination-based cloning technologies but yields recombinant plasmids that do not contain unwanted sequences in the final construct, thus providing precision for this fundamental process of genetic manipulation."], "field": "Pharmacology, Toxicology and Pharmaceutics", "q_year": 2022, "q_cid": "252718145", "pos_cid": 11013801, "source": "eval_collection"}
{"query_id": "scaleup_27100980_22115849", "query": "How to predict individual clinical outcomes among Egyptian patients", "pos": ["Association of the Trough, Peak/Trough Ratio of Imatinib, Pyridine–N-Oxide Imatinib and ABCG2 SNPs 34 G>A and SLCO1B3 334 T>G With Imatinib Response in Egyptian Chronic Myeloid Leukemia Patients. Imatinib mesylate (IM) is highly efficacious in the treatment of chronic myeloid leukemia (CML). Therapeutic drug monitoring and pharmacogenetic screening are affirmed for better management of IM therapy. The goal of this study was to gain a greater mechanistic understanding of the factors controlling variability in IM level and its relation to the response. One hundred and two patients with CML at chronic phase were recruited in this study. Blood samples were withdrawn at least 30 days after drug administration, and trough and peak concentrations of imatinib, N-des-methyl imatinib, and pyridine-N-oxide imatinib were determined by HPLC/MS/MS. Genetic polymorphism of the genes ABCG2 SNPs 34 G>A and 421C >A; ABCB1 SNPs 2677 G>A/T, 1236 C>T, 3435 C>T; SLCO1B3 SNPs 334 T>G and CYP3A5 were studied using PCR-RFLP technique. Our study presented significant higher trough IM (1,281 ± 578 ng/ml), lower Peak/Trough ratio, clearance (Cl), and elimination rate constant, ke, among patients who achieved favorable responses (N = 64) than those for patients who suffered unfavorable response (N = 37). The P/T ratio was the only significant independent factor affecting response, as the P/T ratio increased by one, the risk of unfavorable response increased by more than double as compared to favorable response with 95% CI (1.28–3.92, P = 00.005). Moreover, like the results of IM, the trough concentration of Pyridine-N-oxide imatinib was significantly higher (P = 0.01) and its P/T ratio was significantly lower (P = 0.008) in patients achieved favorable response than those without. The wild GG genotype of the ABCG2.34 G>A gene was associated with favorable response (P = 0.01), lower Cl, Ke and high plasma IM trough level than both (AA+GA) genotypes. ABCG2.421C >A (CC) genotype had a significantly higher plasma peak of IM, N-des-methyl imatinib and higher Css. The GG and TG alleles of the SLCO1B3.334 T>G gene were significantly correlated to favorable response, while the wild allele TT was linked to unfavorable response (P = 0.03). In conclusion, the trough and P/ T ratio for both IM and Pyridine-N-oxide imatinib, in addition to Polymorphism of ABCG2 SNPs 34 G>A and SLCO1B3.334 T>G gene, is a good predictor for response of IM in CML Egyptian patients."], "field": "Pharmacology, Toxicology and Pharmaceutics", "q_year": 2024, "q_cid": "271009805", "pos_cid": 221158491, "source": "eval_collection"}
{"query_id": "scaleup_27751583_40533883", "query": "How to protect spatial memory and cognitive and motor functions from toxic damage", "pos": ["Pistachio supplementation attenuates motor and cognition impairments induced by cisplatin or vincristine in rats. Background: A large number of natural products and dietary components have been evaluated as potential chemoprotective agents. In the present investigation we report the effects of treatment with the dietary antioxidant, pistachio, on cisplatin- or vincristine-induced neurotoxicity in male Wistar rats. Materials and Methods: Dietary pistachio (10%) was assessed for its neuroprotective effects through the alteration in performance of hippocampus- and cerebellum-related behaviors following chronic cisplatin (5 mg/kg) or vincristine (0.2 mg/kg) treatment in male rats. We also evaluated the effects of cisplatin, vincristine, and pistachio administration on nociception. Six behavioral tasks were used: open field, rotarod, grasping, Morris water maze (MWM), hot plate, and motor nerve conductive velocity (MNCV). Results: We showed that the exposure of adolescent rats to cisplatin or vincristine resulted in a significant decrease in explorative behaviors and memory retention. Pistachio consumption somewhat improved memory and motor abilities in cisplatin- or vincristine-treated rats, while pistachio alone did not show any significant changes in these abilities compared to saline. Cisplatin and vincristine increased the latency of response to nociception, and pistachio did not reverse this effect. Conclusion: We conclude that pistachio in the diet following anticancer drugs such as cisplatin and vincristine might have a protective effect against anticancer drug-induced disruptions in motor and cognitive function. However, further studies are needed to elucidate the exact mechanisms of this protective effect of pistachio."], "field": "Pharmacology, Toxicology and Pharmaceutics", "q_year": 2025, "q_cid": "277515834", "pos_cid": 40533883, "source": "eval_collection"}
{"query_id": "scaleup_23621144_20989453", "query": "How to continuously track drug-induced cellular damage over time and relate the timing of toxic effects to drug bioavailability", "pos": ["An evaluation of the impact of clinical bacterial isolates on epithelial cell monolayer integrity by the electric Cell-Substrate Impedance Sensing (ECIS) method.. Virulence is the relative capacity of a pathogenic microorganism to cause damage in susceptible host cells such as those found in airway passages and the gut. In this study, the effect of clinical bacterial isolates on the monolayer integrity of cultured human alveolar basal epithelial cells (A549) was evaluated using the Electric Cell-Substrate Impedance Sensing (ECIS) system. ECIS is a morphological biosensor which records electrical properties of cell-covered microelectrodes in an AC circuit including impedance (ohm), resistance (ohm), and capacitance (μFarad). In the current study, fluctuations in the electrical properties of cell-covered microelectrodes reflect dynamic changes in cell morphology resulting from disrupted cell monolayers following exposure to bacteria. Using the ECIS system, real-time changes of cell morphology and disruption of monolayer integrity of cell-cultures in vitro were revealed for A549 cells infected with either Pseudomonas aeruginosa, ESBL Escherichia coli, Staphylococcus aureus (MRSA), or Enterococcus (VRE). We determined empirically that the optimal signal response was obtained for resistance (ohm) measurements at 4000 hertz. Following infection of A549 cells, the data revealed that Pseudomonas aeruginosa resulted in little change in microelectrode resistance (ohm @4 kHz) as compared to pathogen-free controls within the first 12 h. In contrast, E. coli, MRSA, and VRE caused significant changes in electrode resistance (ohm @4 kHz) values in the infected cells compared to controls over the first 5 h. Resistance (ohm @4 kHz) changes were also observed in cell monolayers infected with different bacterial concentrations for all isolates over 24 h. The highest concentration of bacteria caused the measured resistance (ohm @4 kHz) to drop faster than its' immediate lower concentration, suggesting a dose-dependent effect. Compared to live bacteria, cells exposed to heat-killed bacteria did not show significant changes in resistance (ohm @4 kHz) over 48 h post-exposure. Functionally, cytokine responses were different between cells treated with live and heat-killed bacteria. Of note, live bacteria induced IFNγ, IL-13, and IL-1β production in A549 cells, whereas heat-killed bacteria induced IL-8 production suggesting a differential interaction with cells that could reveal the underlying causes of resistance (ohm @4 kHz) changes. Our findings indicate that ECIS provides a means to quantify, automate, and measure bacterial virulence, which may have broader implications governing the course of treatment compared to traditional methods alone."], "field": "Pharmacology, Toxicology and Pharmaceutics", "q_year": 2021, "q_cid": "236211445", "pos_cid": 209894536, "source": "eval_collection"}
{"query_id": "scaleup_26905787_23218962", "query": "How to protect RAW264.7 cells from BDE-47-induced damage, cell death, and impaired immune function", "pos": ["Activation of Nrf2 signaling pathway by natural and synthetic chalcones: a therapeutic road map for oxidative stress. ABSTRACT Introduction: Nuclear factor erythroid 2-related factor 2 (Nrf2) signaling pathway plays a key role in diverse gene expressions responsible for protection against oxidative stress and xenobiotics. Chalcones with a common chemical scaffold of 1,3-diaryl-2- propen-1-one, are abundantly present in nature with a wide variety of pharmacological properties. This review will discuss the interactions of natural and synthetic chalcones with Nrf2 signaling. Areas covered: Chalcones are reportedly found to activate Nrf2 signaling pathway, expression of Nrf2-regulated antioxidant genes, induce cytoprotective proteins and upregulate multidrug resistance-associated proteins. Chalcones being soft electrophiles are less prone to hostile off-target effects and unlikely to induce carcinogenicity and mutagenicity. Furthermore, their low toxicity, structural diversity, feasibility in structural reorganization and the presence of α,β-unsaturated carbonyl group which makes them suitable drug candidates targeting Nrf2-dependent diseases. Expert opinion: Nrf2-Keap1 signaling pathway plays a central role in redox signaling. However, available therapeutic agents for Nrf2 activation have limited practical applications due to their associated risks, relatively low efficacy and bioavailability. The designing and fabrication of new chemical entities with chalcone scaffold-based Michael acceptor mechanism should be aimed as potential therapeutic Nrf2 activators to target oxidative stress and inflammation-mediated diseases such as atherosclerosis, Parkinson’s disease and many more."], "field": "Pharmacology, Toxicology and Pharmaceutics", "q_year": 2024, "q_cid": "269057870", "pos_cid": 232189627, "source": "eval_collection"}
{"query_id": "scaleup_24886864_11953494", "query": "How to improve peptide drug cellular uptake, permeability, and bioavailability while achieving sustained, controlled release", "pos": ["The roles of short and long chain fatty acids on physicochemical properties and improved cancer targeting of albumin-based fattigation-platform nanoparticles containing doxorubicin.. The aim of this study was to investigate the impact of different chain length fatty acids on physicochemical properties and cancer targeting of fattigation-platform nanoparticles (NPs). Two different types of fatty acids (short chain, 2-hydroxybutyric acid, C4; long chain, oleic acid, C18:1) were successfully conjugated to human serum albumin (HSA) via simple 1-ethyl-3-(3-dimethylaminopropyl) carbodiimide hydrochloride (EDC) coupling reaction. These conjugates readily formed HSA-C4 and HSA-C18:1 NPs which showed good stability in serum and desirable biocompatibility with normal cell line (HEK293T). Doxorubicin hydrochloride (DOX) was efficiently loaded into NPs by incubation process via electrostatic interaction. The structure, morphology, and texture of DOX-loaded NPs were characterized by Transmission electron microscopy (TEM) equipped with Energy-dispersive X-ray spectroscopy (EDS). The initial burst release of DOX-loaded NPs was controlled by the presence and chain length of fatty acids. In vitro cytotoxicity studies with three cancer cell lines (A549, HT-29, and PANC-1) suggested that fattigation-platform NPs have distinctive cytotoxic effects compared to Doxil®. Confocal microscopy and flow cytometry exhibited that the cellular uptake of DOX-loaded NPs was varied by the different chain lengths of fatty acids. It was evident that the chain length of fatty acids in the fattigation-platform NPs could play a vital role in varying physicochemical properties and cancer cell targeting of NPs."], "field": "Pharmacology, Toxicology and Pharmaceutics", "q_year": 2022, "q_cid": "248868646", "pos_cid": 119534944, "source": "eval_collection"}
{"query_id": "scaleup_22931532_41169302", "query": "How to clarify piplartine’s effects on cancer cell growth", "pos": ["Cytotoxic 3,4,5-trimethoxychalcones as mitotic arresters and cell migration inhibitors. Based on classical colchicine site ligands and a computational model of the colchicine binding site on beta tubulin, two classes of chalcone derivatives were designed, synthesized and evaluated for inhibition of tubulin assembly and toxicity in human cancer cell lines. Docking studies suggested that the chalcone scaffold could fit the colchicine site on tubulin in an orientation similar to that of the natural product. In particular, a 3,4,5-trimethoxyphenyl ring adjacent to the carbonyl group appeared to benefit the ligand-tubulin interaction, occupying the same subcavity as the corresponding moiety in colchicine. Consistent with modeling predictions, several 3,4,5-trimethoxychalcones showed improved cytotoxicity to murine acute lymphoblastic leukemia cells compared with a previously described parent compound, and inhibited tubulin assembly in vitro as potently as colchicine. The most potent chalcones inhibited the growth of human leukemia cell lines at nanomolar concentrations, caused microtubule destabilization and mitotic arrest in human cervical cancer cells, and inhibited human breast cancer cell migration in scratch wound and Boyden chamber assays."], "field": "Pharmacology, Toxicology and Pharmaceutics", "q_year": 2020, "q_cid": "229315329", "pos_cid": 41169302, "source": "eval_collection"}
{"query_id": "scaleup_25009692_21104883", "query": "How to clarify Chinese herbal constituents’ effects on JAK-related inflammatory signaling and assess their potential overlap with Western JAK inhibitors and complementary role in COVID-19 treatment", "pos": ["Cinnamaldehyde Inhibits Inflammation of Human Synoviocyte Cells Through Regulation of Jak/Stat Pathway and Ameliorates Collagen-Induced Arthritis in Rats. Cinnamaldehyde (Cin), a bioactive cinnamon essential oil from traditional Chinese medicine herb Cinnamomum cassia, has been reported to have multipharmacological activities including anti-inflammation. However, its role and molecular mechanism of anti-inflammatory activity in musculoskeletal tissues remains unclear. Here, we first investigated the effects and molecular mechanisms of Cin in human synoviocyte cells. Then in vivo therapeutic effect of Cin on collagen-induced arthritis (CIA) also studied. Cell Counting Kit ‎CCK-8 assay was performed to evaluate the cell cytotoxicity. Proinflammatory cytokine expression was evaluated using quantitative polymerase chain reaction and ELISA. Protein expression was measured by western blotting. The in vivo effect of Cin (75 mg/kg per day) was evaluated in rats with CIA by gavage administration. Disease progression was assessed by clinical scoring, radiographic, and histologic examinations. Cin significantly inhibited interleukin (IL)-1β–induced IL-6, IL-8, and tumor necrosis factor-α release from human synoviocyte cells. The molecular analysis revealed that Cin impaired IL-6–induced activation of Janus kinase 2 (JAK2), signal transducer and activator of transcription 1 (STAT1), and STAT3 signaling pathway by inhibiting the phosphorylation of JAK2, STAT1, and STAT3, without affecting NF-κB pathway. Cin reduced collagen-induced swollen paw volume of arthritic rats. The anti-inflammation effects of Cin were associated with decreased severity of arthritis, joint swelling, and reduced bone erosion and destruction. Furthermore, serum IL-6 level was decreased when Cin administered therapeutically to CIA rats. Cin suppresses IL-1β–induced inflammation in synoviocytes through the JAK/STAT pathway and alleviated collagen-induced arthritis in rats. These data indicated that Cin might be a potential traditional Chinese medicine–derived, disease-modifying, antirheumatic herbal drug. SIGNIFICANCE STATEMENT In this study, we found that cinnamaldehyde (Cin) suppressed proinflammatory cytokines secretion in rheumatology arthritis synoviocyte cells by Janus kinase/signal transducer and activator of transcription pathway. The in vivo results showed that Cin ameliorated collagen-induced arthritis in rats. These findings indicate that Cin is a potential traditional Chinese medicine–derived, disease-modifying, antirheumatic herbal drug."], "field": "Pharmacology, Toxicology and Pharmaceutics", "q_year": 2022, "q_cid": "250096922", "pos_cid": 211048832, "source": "eval_collection"}
{"query_id": "scaleup_23171322_16916572", "query": "How to explain dopaminergic neuron damage associated with neuroinflammation in Parkinson’s disease", "pos": ["The inflammasomes.. Inflammasomes are molecular platforms activated upon cellular infection or stress that trigger the maturation of proinflammatory cytokines such as interleukin-1beta to engage innate immune defenses. Strong associations between dysregulated inflammasome activity and human heritable and acquired inflammatory diseases highlight the importance this pathway in tailoring immune responses. Here, we comprehensively review mechanisms directing normal inflammasome function and its dysregulation in disease. Agonists and activation mechanisms of the NLRP1, NLRP3, IPAF, and AIM2 inflammasomes are discussed. Regulatory mechanisms that potentiate or limit inflammasome activation are examined, as well as emerging links between the inflammasome and pyroptosis and autophagy."], "field": "Pharmacology, Toxicology and Pharmaceutics", "q_year": 2021, "q_cid": "231713227", "pos_cid": 16916572, "source": "eval_collection"}
{"query_id": "scaleup_22622084_14978327", "query": "How to identify broccoli constituents that could account for COVID-19 symptom relief within minutes", "pos": ["Naringenin stimulates cholecystokinin secretion in STC-1 cells. BACKGROUND/OBJECTIVES Cholecystokinin (CCK), a hormone or neuropeptide, is secreted in response to intraluminal nutrients by enteroendocrine I-cells of the intestine and has important physiological actions related to appetite regulation and satiety. The stimulation on CCK secretion from the intestine is of potential relevance for body weight management. Naringenin (4',5,7-trihydroxyflavanone) and its glycoside naringin (naringenin 7-rhamnoglucoside) have been reported to have many biological functions. In the current study, we investigated the question of whether naringenin and naringin could stimulate CCK secretion and then examined the mechanisms involved in CCK release. MATERIALS/METHODS STC-1 cells were used as a model of enteroendocrine cells. CCK release and changes in intracellular Ca2+ ([Ca2+]i) were measured after incubation of cells with naringenin and naringin for 1 h. RESULTS Naringenin caused significant (P < 0.05) stimulation of CCK secretion, but naringin did not. In addition, regarding the secretory mechanisms, naringenin-induced CCK secretion involved increases in [Ca2+]i, influx of extracellular Ca2+, at least in part, and activation of TRP channels, including TRPA1. CONCLUSION Findings of this study suggest that naringenin could have a role in appetite regulation and satiety."], "field": "Pharmacology, Toxicology and Pharmaceutics", "q_year": 2020, "q_cid": "226220842", "pos_cid": 14978327, "source": "eval_collection"}
{"query_id": "scaleup_22670078_15015235", "query": "How to identify the ways midazolam binds to CYP3A4 relevant to hydroxylation at C1′ and C4 and reliably estimate their relative prevalence", "pos": ["Gaussian Accelerated Molecular Dynamics: Unconstrained Enhanced Sampling and Free Energy Calculation. A Gaussian accelerated molecular dynamics (GaMD) approach for simultaneous enhanced sampling and free energy calculation of biomolecules is presented. By constructing a boost potential that follows Gaussian distribution, accurate reweighting of the GaMD simulations is achieved using cumulant expansion to the second order. Here, GaMD is demonstrated on three biomolecular model systems: alanine dipeptide, chignolin folding, and ligand binding to the T4-lysozyme. Without the need to set predefined reaction coordinates, GaMD enables unconstrained enhanced sampling of these biomolecules. Furthermore, the free energy profiles obtained from reweighting of the GaMD simulations allow us to identify distinct low-energy states of the biomolecules and characterize the protein-folding and ligand-binding pathways quantitatively."], "field": "Pharmacology, Toxicology and Pharmaceutics", "q_year": 2021, "q_cid": "226700780", "pos_cid": 15015235, "source": "eval_collection"}
{"query_id": "scaleup_27129237_26891428", "query": "How to deliver poorly water-soluble drugs in aqueous environments and control their release to sustain drug availability", "pos": ["Polymeric Micelles and Alternative Nanonized Delivery Vehicles for Poorly Soluble Drugs. Poorly soluble drugs often encounter low bioavailability and erratic absorption patterns in the clinical setting. Due to the rising number of compounds having solubility issues, finding ways to enhance the solubility of drugs is one of the major challenges in the pharmaceutical industry today. Polymeric micelles, which form upon self-assembly of amphiphilic macromolecules, can act as solubilizing agents for delivery of poorly soluble drugs. This manuscript examines the fundamentals of polymeric micelles through reviews of representative literature and demonstrates possible applications through recent examples of clinical trial developments. In particular, the potential of polymeric micelles for delivery of poorly water-soluble drugs, especially in the areas of oral delivery and in cancer therapy, is discussed. Key considerations in utilizing polymeric micelles’ advantages and overcoming potential disadvantages have been highlighted. Lastly, other possible strategies related to particle size reduction for enhancing solubilization of poorly water-soluble drugs are introduced."], "field": "Pharmacology, Toxicology and Pharmaceutics", "q_year": 2024, "q_cid": "271292374", "pos_cid": 26891428, "source": "eval_collection"}
{"query_id": "scaleup_24745870_19088936", "query": "How to more completely classify and identify the chemical constituents of P. pellucida, particularly compounds not previously reported in the Peperomia genus", "pos": ["MolNetEnhancer: Enhanced Molecular Networks by Integrating Metabolome Mining and Annotation Tools. Metabolomics has started to embrace computational approaches for chemical interpretation of large data sets. Yet, metabolite annotation remains a key challenge. Recently, molecular networking and MS2LDA emerged as molecular mining tools that find molecular families and substructures in mass spectrometry fragmentation data. Moreover, in silico annotation tools obtain and rank candidate molecules for fragmentation spectra. Ideally, all structural information obtained and inferred from these computational tools could be combined to increase the resulting chemical insight one can obtain from a data set. However, integration is currently hampered as each tool has its own output format and efficient matching of data across these tools is lacking. Here, we introduce MolNetEnhancer, a workflow that combines the outputs from molecular networking, MS2LDA, in silico annotation tools (such as Network Annotation Propagation or DEREPLICATOR) and the automated chemical classification through ClassyFire to provide a more comprehensive chemical overview of metabolomics data whilst at the same time illuminating structural details for each fragmentation spectrum. We present examples from four plant and bacterial case studies and show how MolNetEnhancer enables the chemical annotation, visualization, and discovery of the subtle substructural diversity within molecular families. We conclude that MolNetEnhancer is a useful tool that greatly assists the metabolomics researcher in deciphering the metabolome through combination of multiple independent in silico pipelines."], "field": "Pharmacology, Toxicology and Pharmaceutics", "q_year": 2022, "q_cid": "247458709", "pos_cid": 190889369, "source": "eval_collection"}
{"query_id": "scaleup_25009692_22696458", "query": "How to assess molecular interactions and potential complementary effects of Chinese herbal and Western medicines for COVID-19 while ensuring reliable links between drug ingredients and target proteins", "pos": ["Identifying the Chinese Herbal Medicine Network and Core Formula for Allergic Rhinitis on a Real-World Database. Materials and Methods Patients with a primary diagnosis of AR (ICD-9-CM code: 477.9) in 2010 were included, and the National Health Insurance Research Database in Taiwan was used as the data source. Association rule mining and social network analysis were used to establish and explore the CHM network. Possible molecular pathways of the CHM network were summarized and compared with commonly used western medicine (WM) by conducting overrepresentation analysis in the Reactome pathway database. The potential proteins acted by CHMs were obtained from the CHM ingredient-protein databases, including STITCH, TCMSP, TCMID, and TCM@Taiwan. Results There were 89,148 AR subjects found in 2010, and a total of 33,507 patients ever used CHM. On an average, 5.6 types of CHMs were utilized per prescription. Xin-Yi-Qing-Fei-Tang was used most frequently (25.5% of 222,279 prescriptions), while Xiao-Qing-Long-Tang with Xin-Yi-San was the most commonly prescribed CHM-CHM combination. Up to six distinctive clusters could be found among the CHM network, and core CHMs could be found for AR, such as Xiao-Qing-Long-Tang and Xin-Yi-Qing-Fei-Tang. A total of 140 molecular pathways were covered by the CHM network (2,432 ingredients from 31 kinds of CHMs), while 39 WMs covered 55 pathways. Among pathways responding to the immune system, WM mainly acted on cytokine signaling-related pathways, while CHM mostly acted on neutrophil/macrophage-related innate pathways and dendritic cell-related adaptive immunity pathways. Conclusion Our study demonstrated and analyzed the CHM network for AR. Core CHM for AR and possible molecular pathways were presented as well, and this information is crucial for researchers to select candidates for CHM-related studies."], "field": "Pharmacology, Toxicology and Pharmaceutics", "q_year": 2022, "q_cid": "250096922", "pos_cid": 226964585, "source": "eval_collection"}
{"query_id": "scaleup_25154316_20816998", "query": "How to maintain stable, nonaggregated lipid-based drug carrier formulations despite particle lamellarity-related stability challenges", "pos": ["Development of Injectable PEGylated Liposome Encapsulating Disulfiram for Colorectal Cancer Treatment. Disulfiram (DS), an anti-alcoholism medicine, shows strong anti-cancer activity in the laboratory, but the application in clinics for anti-cancer therapy has been limited by its prompt metabolism. Conventional liposomes have shown limited ability to protect DS. Therefore, the aim of this study is to develop PEGylated liposomes of DS for enhanced bio-stability and prolonged circulation. PEGylated liposomes were prepared using ethanol-based proliposome methods. Various ratios of phospholipids, namely: hydrogenated soya phosphatidylcholine (HSPC) or dipalmitoyl phosphatidylcholine (DPPC) and N-(Carbonyl-methoxypolyethylenglycol-2000)-1,2-distearoyl-sn-glycero-3-phosphoethanolamine (DSPE-PEG2000) with cholesterol were used. DS was dissolved in the alcoholic solution in different lipid mol% ratios. The size of the resulting multilamellar liposomes was reduced by high-pressure homogenization. Liposomal formulations were characterized by size analysis, zeta potential, drug loading efficiency and stability in horse serum. Small unilamellar vesicles (SUVs; nanoliposomes) were generated with a size of approximately 80 to 120 nm with a polydispersity index (PDI) in the range of 0.1 to 0.3. Zeta potential values of all vesicles were negative, and the negative surface charge intensity tended to increase by PEGylation. PEGylated liposomes had a smaller size (80–90 nm) and a significantly lower PDI. All liposomes showed similar loading efficiencies regardless of lipid type (HSPC or DPPC) or PEGylations. PEGylated liposomes provided the highest drug biostability amongst all formulations in horse serum. PEGylated DPPC liposomes had t1/2 =77.3 ± 9.6 min compared to 9.7 ± 2.3 min for free DS. In vitro cytotoxicity on wild type and resistant colorectal cancer cell lines was evaluated by MTT assay. All liposomal formulations of DS were cytotoxic to both the wild type and resistant colorectal cancer cell lines and were able to reverse chemoresistance at low nanomolar concentrations. In conclusion, PEGylated liposomes have a greater potential to be used as an anticancer carrier for disulfiram."], "field": "Pharmacology, Toxicology and Pharmaceutics", "q_year": 2022, "q_cid": "251543166", "pos_cid": 208169987, "source": "eval_collection"}
{"query_id": "scaleup_25185396_52978552", "query": "How to achieve sufficient electrostatic interaction between nanoparticles and cell membranes for drug delivery to the brain", "pos": ["A Novel Botulinum Toxin TAT-EGFP-HCS Fusion Protein Capable of Specific Delivery Through the Blood-brain Barrier to the Central Nervous System.. OBJECTIVE Botulinum toxin has many applications in the treatment of central diseases, as biological macromolecules, it is difficult to pass through the blood-brain barrier which greatly limits their application. In this paper, we verified whether the botulinum toxin heavy chain HCS has a specific neural guidance function. METHODS We have constructed a fusion protein with botulinum toxin heavy chain and a membrane penetrating peptide TAT (TAT-EGFP-HCS). Recombinant plasmid of botulinum toxin light chain (LC) and TAT were also constructed. The biological activity of HCS, LC, TAT-EGFP-HCS and TAT-EGFP-LC were measured by its ability to cleave protein SNAP-25. The intracellular expression efficiency was evaluated by detecting the fluorescence intensity of EGFP in the cells by fluorescence microscopy and FACS. In addition, we also determined the effect of the above plasmid expression on the apoptosis of PC12 cells. Finally, the tissue specificity of TAT-EGFP-HCS in vivo experiments was also examined. RESULTS In the present study, we have constructed a fusion protein with botulinum toxin heavy chain and a membrane penetrating peptide TAT which can lead the entire molecule through the blood-brain barrier and reach the central nervous system. Moreover, we also examined the biological activities of this recombinant biological macromolecule and its physiological effects on nerve cells in vitro and in vivo. CONCLUSION TAT-EGFP-HSC expressed in vitro has neural guidance function and can carry large proteins across the cell membrane without influencing the biological activity."], "field": "Pharmacology, Toxicology and Pharmaceutics", "q_year": 2022, "q_cid": "251853967", "pos_cid": 52978552, "source": "eval_collection"}
{"query_id": "scaleup_25649237_10466134", "query": "How to efficiently extract target compounds from plant particles of different sizes", "pos": ["Effect of particle size and co-extractant in Momordica charantia extract yield and diffusion coefficient using supercritical CO2. Supercritical carbon dioxide (SC-CO2) is a fluid with high diffusivity and low viscosity which can penetrate deep into the solid particle efficiently compared to liquid or gas. SC-CO2 commonly used as a green solvent in the modern extraction of bioactive compound from plants. Sometimes, a co-solvent was added in the system to increase solvent polarity or mix a co-extractant with dried sample to improve solute’s transport properties. Hence, the aim of this study was to determine Momordica charantia extract yield with different mean particle size as well as diffusion coefficient, De in the extraction process with and without co-extractant. Different mean particle sizes used were 0.2, 0.3, 0.5 and 0.7 mm at constant operating condition (20 MPa, 65 oC and 4 mL/min). A ratio 1:3 of pure ethanol was used in the extraction process with co-extractant. Based on the results, mean particle size of 0.3 mm gave the highest extract yield, 3.32% and 1.34% with and without co-extractant respectively. Whereas, the value of De at 0.3 mm mean particle size, with and without co-extractant are 8.820 x 10-12 and 7.920 x 10-12 m2/s respectively. Therefore, 0.3 mm is the best mean particle size to produce highest Momordica charantia extract yield and De value in SC-CO2 extraction with co-extractant."], "field": "Pharmacology, Toxicology and Pharmaceutics", "q_year": 2023, "q_cid": "256492375", "pos_cid": 104661341, "source": "eval_collection"}
{"query_id": "scaleup_28220652_24698290", "query": "How to ensure sufficient supply of a costly cofactor required for heterologous activity in E. coli", "pos": ["Improved methylation in E. coli via an efficient methyl supply system driven by betaine.. Methylation reactions are involved in the biosynthesis of various natural molecules, in which S-adenosyl-L-methionine (SAM) acts as the principal biological methyl donor. The limited availability of SAM often affects the biosynthesis of methylated metabolites in cells, especially when heterologous SAM-mediated methyltransferases are employed. To solve this problem, a methyl supply system driven by betaine was developed in this study to enhance SAM availability in cells. A reconstructed methionine cycle was designed in E. coli using betaine as the methyl source by introducing betaine-homocysteine methyltransferase. Ferulic acid served as a model product was used to test the efficiency of methyl supply system. ATP is a co-factor for SAM biosynthesis and a pathway for ATP regeneration from adenosine was introduced to maintain the stability of the adenylate pool. After testing two different S-adenosyl-L-homocysteine (SAH) hydrolysis pathways, the optimized SAHase pathway was adopted for converting SAH back to homocysteine (Hcy). Thus, a methyl supply system was developed which increased SAM availability and therefore improved the titer and productivity of ferulic acid by 12.6-fold and 15.9-fold, respectively. The system was also applied successfully for other methyltransferase-catalyzed reactions. This work provides an efficient methyl supply system for enhanced production of methylated chemicals using betaine as the methyl source."], "field": "Pharmacology, Toxicology and Pharmaceutics", "q_year": 2025, "q_cid": "282206529", "pos_cid": 246982901, "source": "eval_collection"}
{"query_id": "scaleup_21859668_14290600", "query": "How to determine the strength and nature of protopine’s CYP2D6 inhibition and assess the safety of protopine-containing herbal remedies taken with prescription drugs", "pos": ["In vitro metabolic interactions between black cohosh (Cimicifuga racemosa) and tamoxifen via inhibition of cytochromes P450 2D6 and 3A4. Women who experience hot flashes as a side effect of tamoxifen (TAM) therapy often try botanical remedies such as black cohosh to alleviate these symptoms. Since pharmacological activity of TAM is dependent on the metabolic conversion into active metabolites by the action of cytochromes P450 2D6 (CYP2D6) and 3A4, the objective of this study was to evaluate whether black cohosh extracts can inhibit formation of active TAM metabolites and possibly reduce its clinical efficacy. At 50 μg/mL, a 75% ethanolic extract of black cohosh inhibited formation of 4-hydroxy- TAM by 66.3%, N-desmethyl TAM by 74.6% and α-hydroxy TAM by 80.3%. In addition, using midazolam and dextromethorphan as probe substrates, this extract inhibited CYP3A4 and CYP2D6 with IC50 values of 16.5 and 50.1 μg/mL, respectively. Eight triterpene glycosides were identified as competitive CYP3A4 inhibitors with IC50 values ranging from 2.3–5.1 µM, while the alkaloids protopine and allocryptopine were identified as competitive CYP2D6 inhibitors with Ki values of 78 and 122 nM, respectively. The results of this study suggests that co-administration of black cohosh with TAM might interfere with the clinical efficacy of this drug. However, additional clinical studies are needed to determine the clinical significance of these in vitro results."], "field": "Pharmacology, Toxicology and Pharmaceutics", "q_year": 2020, "q_cid": "218596680", "pos_cid": 14290600, "source": "eval_collection"}
{"query_id": "scaleup_28311862_23694804", "query": "How to obtain small, single-layer structures with uniform morphology from heterogeneous preparations", "pos": ["The Elucidation of the Molecular Mechanism of the Extrusion Process. Extrusion is a popular method for producing homogenous population of unilamellar liposomes. The technique relies on forcing a lipid suspension through cylindrical pores in a polycarbonate membrane. The quantification of the extrusion and/or recalibration processes make possible the acquisition of experimental data, which can be correlated with the mechanical properties of the lipid bilayer. In this work, the force needed for the extrusion process was correlated with the mechanical properties of a lipid bilayer derived from other experiments. Measurements were performed using a home-made dedicated device capable of maintaining a stable volumetric flux of a liposome suspension through well-defined pores and to continuously measure the extrusion force. Based on the obtained results, the correlation between the lipid bilayer bending rigidity and extrusion force was derived. Specifically, it was found that the bending rigidity of liposomes formed from well-defined lipid mixtures agrees with data obtained by others using flicker-noise spectroscopy or micromanipulation. The other issue addressed in the presented studies was the identification of molecular mechanisms leading to the formation of unilamellar vesicles in the extrusion process. Finally, it was demonstrated that during the extrusion, lipids are not exchanged between vesicles, i.e., vesicles can divide but no membrane fusion or lipid exchange between bilayers was detected."], "field": "Pharmacology, Toxicology and Pharmaceutics", "q_year": 2025, "q_cid": "283118622", "pos_cid": 236948042, "source": "eval_collection"}
{"query_id": "scaleup_23171322_72332922", "query": "How to limit inflammatory damage and protect neurons from protein-induced injury", "pos": ["Novel compound VB‐037 inhibits A&bgr; aggregation and promotes neurite outgrowth through enhancement of HSP27 and reduction of P38 and JNK‐mediated inflammation in cell models for Alzheimer's disease. ABSTRACT The pathogenesis of Alzheimer's disease (AD) is involved in the aggregation of misfolded amyloid &bgr; (A&bgr;), which upregulates the activity of acetylcholinesterase (AChE), increases the production of reactive oxygen species (ROS), enhances neuroinflammation, and eventually leads to neuronal death. Therefore, compounds targeting these mechanisms may be candidates for multitarget drugs in AD treatment. We found that two quinoline derivatives, VB‐030 and VB‐037, markedly reduced A&bgr; aggregation and ROS levels in the thioflavin T biochemical assay and Tet‐On A&bgr;‐green fluorescent protein (GFP) 293 AD cell model. These compounds further improved neurite outgrowth, reduced AChE activity and upregulated the molecular chaperone heat shock protein family B [small] member 1 (HSP27), whereas knockdown of HSP27 counteracted the compounds' neuroprotective effects on the Tet‐On A&bgr;‐GFP SH‐SY5Y AD neuronal model. Furthermore, VB‐037 attenuated lipopolysaccharide (LPS)/interferon (IFN)‐&ggr;‐induced activation of BV‐2 microglial cells. In addition, VB‐037 demonstrated its potential to diminish LPS/IFN‐&ggr;‐induced upregulation of caspase 1 activity, expression of interleukin (IL)‐1&bgr;, and active phosphorylation of mitogen‐activated protein kinase 14 (P38), mitogen‐activated protein kinase 8 (JNK), and Jun proto‐oncogene, AP‐1 transcription factor subunit (JUN) signalings, as well as improve cell viability in the Tet‐On A&bgr;‐GFP SH‐SY5Y AD neuronal model. Our findings strongly indicate the potential of VB‐037 for modifying AD progression by targeting multiple mechanisms, thereby offering a new drug development avenue for AD treatment. HIGHLIGHTSNovel compound VB‐037 directly reduced A&bgr; aggregation.VB‐037 reduced ROS and AChE activity in A&bgr;‐GFP cells.VB‐037 up‐regulated chaperone HSP27 in A&bgr;‐GFP neurons.VB‐037 reduced neuroinflammation by down‐regulating P38 and JNK signaling.VB‐037 has great potential as a novel multi‐target drug for Alzheimer's disease."], "field": "Pharmacology, Toxicology and Pharmaceutics", "q_year": 2021, "q_cid": "231713227", "pos_cid": 72332922, "source": "eval_collection"}
{"query_id": "scaleup_23615556_18943620", "query": "How to determine whether Heracleum candicans protects hepatocytes against free-radical damage associated with carbon tetrachloride-induced liver injury", "pos": ["Plasma Malondialdehyde (MDA): An Indication of Liver Damage in Women with Pre-Eclamsia. Background One of the features associated with pre-eclampsia is elevated liver transaminases. The reason this happens has not been fully described. However, the hepatocytes are not known to be spared by free radical injury. This study was conducted to examine the relationship between product of free radical injury (malondialdehyde) and transaminases in pre-eclamptic women. Patients and Methods A total of 98 and 115 pre-eclamptic and apparently normal pregnant women were selected from the booking clinic of Ladoke Akintola University of Technology Teaching Hospital, Osogbo. Non-pregnant women were selected from volunteered members of staff. Malondialdehyde (MDA), aspartate transaminase (AST) and alanine transaminase (ALT) analyses were determined on collected venous blood sample. Statistical analyses of variables were done using SPSS 17 taking level of significance to be p<0.05. Results Subjects with plasma AST between 10 and 20U/L had mean plasma MDA of 0.92µmol/l whereas those with plasma levels greater than 41U/L had mean plasma MDA of 4.72µmol/l. Similarly, Subjects with plasma ALT between 10 and 20U/L had mean plasma MDA of 0.86µmol/l, and subjects with plasma ALT greater than 51 U/L had mean plasma MDA of 4.71µmol/l. Positive correlation was observed between AST and ALT(r=0.79; p=0.047), between AST and MDA(r=0.690; p=0.061) as well as between ALT and MDA(r=0.571; p=0.049). Conclusion The elevated liver enzymes seen in women with pre-eclampsia may be due to free radical injury to the liver. Pre-eclamptic women without free radical injury did not have elevated transaminases"], "field": "Pharmacology, Toxicology and Pharmaceutics", "q_year": 2021, "q_cid": "236155567", "pos_cid": 18943620, "source": "eval_collection"}
{"query_id": "scaleup_26924752_13804746", "query": "How to determine which covariates in high-dimensional patient data are most relevant to drug-induced liver injury risk and how many to retain for prediction", "pos": ["High-dimensional propensity score adjustment in studies of treatment effects using health care claims data. Background: Adjusting for large numbers of covariates ascertained from patients’ health care claims data may improve control of confounding, as these variables may collectively be proxies for unobserved factors. Here, we develop and test an algorithm that empirically identifies candidate covariates, prioritizes covariates, and integrates them into a propensity-score-based confounder adjustment model. Methods: We developed a multistep algorithm to implement high-dimensional proxy adjustment in claims data. Steps include (1) identifying data dimensions, eg, diagnoses, procedures, and medications; (2) empirically identifying candidate covariates; (3) assessing recurrence of codes; (4) prioritizing covariates; (5) selecting covariates for adjustment; (6) estimating the exposure propensity score; and (7) estimating an outcome model. This algorithm was tested in Medicare claims data, including a study on the effect of Cox-2 inhibitors on reduced gastric toxicity compared with nonselective nonsteroidal anti-inflammatory drugs (NSAIDs). Results: In a population of 49,653 new users of Cox-2 inhibitors or nonselective NSAIDs, a crude relative risk (RR) for upper GI toxicity (RR = 1.09 [95% confidence interval = 0.91–1.30]) was initially observed. Adjusting for 15 predefined covariates resulted in a possible gastroprotective effect (0.94 [0.78–1.12]). A gastroprotective effect became stronger when adjusting for an additional 500 algorithm-derived covariates (0.88 [0.73–1.06]). Results of a study on the effect of statin on reduced mortality were similar. Using the algorithm adjustment confirmed a null finding between influenza vaccination and hip fracture (1.02 [0.85–1.21]). Conclusions: In typical pharmacoepidemiologic studies, the proposed high-dimensional propensity score resulted in improved effect estimates compared with adjustment limited to predefined covariates, when benchmarked against results expected from randomized trials."], "field": "Pharmacology, Toxicology and Pharmaceutics", "q_year": 2024, "q_cid": "269247520", "pos_cid": 13804746, "source": "eval_collection"}
{"query_id": "scaleup_25831512_22241220", "query": "How to clarify the molecular basis of disrupting interactions at a shared phenylalanine–glycine binding pocket", "pos": ["Structural and mechanistic bases for a potent HIV-1 capsid inhibitor. Attacking HIV by stabilizing its capsid Current HIV treatments require drugs that must be taken daily, and care would be improved with an effective drug that is long-acting. GS-6207 (Lenacapavir) is a drug developed by Gilead Sciences that shows potential for a 6-month dosing interval and is in phase 2/3 clinical trials. Bester et al. describe structural and biophysical studies that provide a basis for the potent antiviral activity of GS-6207. The HIV capsid is cone shaped, and GS-6207 binds two neighboring capsid subunits and stabilizes the curved capsid. GS-6207 also interferes with capsid binding of cofactors that play a role in viral infection. This insight into GS-6207 activity provides a platform for the rational development of improved long-acting therapies. Science, this issue p. 360 The potent HIV-1 inhibitor GS-6207 binds and stabilizes curved capsid assemblies. The potent HIV-1 capsid inhibitor GS-6207 is an investigational principal component of long-acting antiretroviral therapy. We found that GS-6207 inhibits HIV-1 by stabilizing and thereby preventing functional disassembly of the capsid shell in infected cells. X-ray crystallography, cryo–electron microscopy, and hydrogen-deuterium exchange experiments revealed that GS-6207 tightly binds two adjoining capsid subunits and promotes distal intra- and inter-hexamer interactions that stabilize the curved capsid lattice. In addition, GS-6207 interferes with capsid binding to the cellular HIV-1 cofactors Nup153 and CPSF6 that mediate viral nuclear import and direct integration into gene-rich regions of chromatin. These findings elucidate structural insights into the multimodal, potent antiviral activity of GS-6207 and provide a means for rationally developing second-generation therapies."], "field": "Pharmacology, Toxicology and Pharmaceutics", "q_year": 2023, "q_cid": "258315126", "pos_cid": 222412205, "source": "eval_collection"}
{"query_id": "scaleup_26930547_26092418", "query": "How to determine the relative importance of the forces governing berberine–baicalin association in aqueous solution", "pos": ["Simple, Efficient, and Universal Energy Decomposition Analysis Method Based on Dispersion-Corrected Density Functional Theory.. Energy decomposition analysis (EDA) is an important class of methods to explore the nature of interaction between fragments in a chemical system. It can decompose the interaction energy into different physical components to understand the factors that play key roles in the interaction. This work proposes an EDA strategy based on dispersion-corrected density functional theory (DFT), called sobEDA. This method is fairly easy to implement and very universal. It can be used to study weak interactions, chemical bond interactions, open-shell systems, and interactions between multiple fragments. The total time consumption of sobEDA is only about twice that of conventional DFT single-point calculation for the entire system. This work also proposes a variant of the sobEDA method named sobEDAw, which is designed specifically for decomposing weak interaction energies. Through a proper combination of DFT correlation energy and dispersion correction term, sobEDAw gives a ratio between dispersion energy and electrostatic energy that is highly consistent with the symmetry-adapted perturbation theory, which is quite popular and robust in studying weak interactions but expensive. We present a shell script sobEDA.sh to implement the methods proposed in this work based on the very popular Gaussian quantum chemistry program and Multiwfn wavefunction analysis code. Via the script, theoretical chemists can use the sobEDA and sobEDAw methods very conveniently in their study. Through a series of examples, the rationality of the new methods and their implementation are verified, and their great practical values in the study of various chemical systems are demonstrated."], "field": "Pharmacology, Toxicology and Pharmaceutics", "q_year": 2024, "q_cid": "269305471", "pos_cid": 260924186, "source": "eval_collection"}
{"query_id": "scaleup_27845912_23209168", "query": "How to treat chronic kidney disease-associated pruritus while addressing oxidative stress and inflammation", "pos": ["κ-opioid receptor agonist U50488H attenuates postoperative cognitive dysfunction of cardiopulmonary bypass rats through the PI3K/AKT/Nrf2/HO-1 pathway. Postoperative cognitive dysfunction (POCD) is a common complication following cardiopulmonary bypass (CPB). U50488H, a κ-opioid receptor (KOR) agonist, can specifically activate KORs on hippocampal nerve cells, resulting in neuroprotective effects. The present study established a CPB rat model, observed the protective effect of U50488H on CPB-induced POCD and brain damage and explored the regulatory mechanism of the PI3K/AKT/nuclear factor erythroid 2-related factor 2 (Nrf2)/heme oxygenase (HO)-1 pathway. Sprague-Dawley rats were divided into the following groups: Sham operation (Sham group), CPB (CPB group), KOR agonist (U50488H) + CPB (U50488H group), CPB + U50488H + HO-1 antagonist (ZnPP-IX; ZnPP group) and CPB + U50488H + PI3K antagonist (LY294002; LY294002 group), with 10 rats in each group. Neurological scores and the Morris water maze test were used to evaluate cognitive function; hematoxylin and eosin and terminal deoxynucleotidyl transferase dUTP nick end labeling assays were performed to observe hippocampal neuron damage in rats. Immunofluorescence was used to detect reactive oxygen species, glial fibrillary acidic protein and Nrf2 expression in the hippocampus. Enzyme-linked immunosorbent assays were used to detect inflammatory and oxidative stress factors. Western blotting was used to examine the expression of PI3K/AKT/Nrf2/HO-1-related proteins. It was demonstrated that U50488H significantly reduced the neural function score of rats with POCD induced by CPB, relieved cognitive dysfunction, reduced hippocampal neuron damage, inhibited the rate of apoptosis, repaired oxidative stress injury and protected against brain damage caused by CPB. In addition, U50488H could promote Nrf2 entry into the nucleus and upregulate HO-1 and thioredoxin 1 (Trx1) expression. In CPB rats treated with PI3K inhibitors, less Nrf2 was detected in the nucleus and HO-1 and Trx-1 expression levels were reduced in the nucleus. Therefore, U50488H, a KOR agonist, can activate Nrf2/HO-1 via the PI3K/AKT pathway to improve cognitive function and reduce brain damage in CPB rats."], "field": "Pharmacology, Toxicology and Pharmaceutics", "q_year": 2025, "q_cid": "278459122", "pos_cid": 232091685, "source": "eval_collection"}
{"query_id": "scaleup_4783402_41892728", "query": "How to resolve ultrafast photocurrent dynamics in high-frequency circuit junctions with picosecond or better time resolution and distinguish the immediate optical response from slower thermal-relaxation and contact contributions", "pos": ["Ultrafast electronic readout of diamond nitrogen-vacancy centres coupled to graphene.. Non-radiative transfer processes are often regarded as loss channels for an optical emitter because they are inherently difficult to access experimentally. Recently, it has been shown that emitters, such as fluorophores and nitrogen-vacancy centres in diamond, can exhibit a strong non-radiative energy transfer to graphene. So far, the energy of the transferred electronic excitations has been considered to be lost within the electron bath of the graphene. Here we demonstrate that the transferred excitations can be read out by detecting corresponding currents with a picosecond time resolution. We detect electronically the spin of nitrogen-vacancy centres in diamond and control the non-radiative transfer to graphene by electron spin resonance. Our results open the avenue for incorporating nitrogen-vacancy centres into ultrafast electronic circuits and for harvesting non-radiative transfer processes electronically."], "field": "Physics and Astronomy", "q_year": 2016, "q_cid": "4783402", "pos_cid": 41892728, "source": "eval20x26"}
{"query_id": "scaleup_51688635_11855134", "query": "How to calculate radiative corrections beyond one loop to the false-vacuum decay rate in four-dimensional scalar field theory", "pos": ["Three-loop Correction to the Instanton Density. II. The Sine-Gordon potential. In this second paper on quantum fluctuations near the classical instanton configurations, see [1], we focus on another well studied quantum-mechanical problem, the one-dimensional Sine-Gordon potential (the Mathieu potential). Using only the tools from quantum field theory, the Feynman diagrams in the instanton background, we calculate the tunneling amplitude (the instanton density) to the three-loop order. The result confirms (to seven significant figures) the one recently recalculated by G. V. Dunne and M. ¨ Unsal, Phys. Rev. D 89, 105009 (2014) from the resurgence perspective. As in the double well potential case, we found that the largest contribution is given by the diagrams originating from the Jacobian. We again observe that in the three-loop case individual Feynman diagrams contain irrational contributions, while their sum does not."], "field": "Physics and Astronomy", "q_year": 2018, "q_cid": "51688635", "pos_cid": 118551346, "source": "eval20x26"}
{"query_id": "scaleup_71145349_7719957", "query": "How to compute temporal walk-counting centrality that accounts for link availability and non-zero travel times to distinguish traversable walks under network timing constraints", "pos": ["Connectivity and inference problems for temporal networks. Many network problems are based on fundamental relationships involving time. Consider, for example, the problems of modeling the flow of information through a distributed network, studying the spread of a disease through a population, or analyzing the reachability properties of an airline timetable. In such settings, a natural model is that of a graph in which each edge is annotated with a time label specifying the time at which its endpoints \"communicated.\" We will call such a graph a temporal network. To model the notion that information in such a network \"flows\" only on paths whose labels respect the ordering of time, we call a path time-respecting if the time labels on its edges are non-decreasing. The central motivation for our work is the following question: how do the basic combinatorial and algorithmic properties of graphs change when we impose this additional temporal condition? The notion of a path is intrinsic to many of the most fundamental algorithmic problems on graphs; spanning trees, connectivity, flows, and cuts are some examples. When we focus on time-respecting paths in place of arbitrary paths, many of these problems acquire a character that is different from the traditional setting, but very rich in its own right. We provide results on two types of problems for temporal networks. First, we consider connectivity problems, in which we seek disjoint time-respecting paths between pairs of nodes. The natural analogue of Menger's Theorem for node-disjoint paths fails in general for time-respecting paths; we give a non-trivial characterization of those graphs for which the theorem does hold in terms of an excluded subdivision theorem, and provide a polynomial-time algorithm for connectivity on this class of graphs. (The problem on general graphs is NP-complete.) We then define and study the class of inference problems, in which we seek to reconstruct a partially specified time labeling of a network in a manner consistent with an observed history of information flow."], "field": "Physics and Astronomy", "q_year": 2019, "q_cid": "71145349", "pos_cid": 7719957, "source": "eval20x26"}
{"query_id": "scaleup_20253951_11953698", "query": "How to determine the energy-scale dependence of an inflationary potential and its parameters when perturbative treatment is insufficient and the evolution of its scale-dependent, field-independent term is not uniquely determined", "pos": ["Exact evolution equation for the effective potential. Abstract We derive a new exact evolution equation for the scale dependence of an effective action. The corresponding equation for the effective potential permits a useful truncation. This allows one to deal with the infrared problems of theories with massless modes in less than four dimensions which are relevant for the high temperature phase transition in particle physics or the computation of critical exponents in statistical mechanics."], "field": "Physics and Astronomy", "q_year": 2019, "q_cid": "202539517", "pos_cid": 119536989, "source": "eval20x26"}
{"query_id": "scaleup_13652864_14113765", "query": "How to determine how a tweet’s grammar affects its likelihood of being retweeted independently of the popularity of its author and topic", "pos": ["Part-of-Speech Tagging for Twitter: Annotation, Features, and Experiments. We address the problem of part-of-speech tagging for English data from the popular micro-blogging service Twitter. We develop a tagset, annotate data, develop features, and report tagging results nearing 90% accuracy. The data and tools have been made available to the research community with the goal of enabling richer text analysis of Twitter and related social media data sets."], "field": "Physics and Astronomy", "q_year": 2014, "q_cid": "13652864", "pos_cid": 14113765, "source": "eval20x26"}
{"query_id": "scaleup_20938690_8251885", "query": "How to solve the stated equation for the function required in the calculation while keeping computational effort manageable", "pos": ["Time-dependent density functional theory scheme for efficient calculations of dynamic (hyper)polarizabilities.. The authors present an efficient perturbative method to obtain both static and dynamic polarizabilities and hyperpolarizabilities of complex electronic systems. This approach is based on the solution of a frequency-dependent Sternheimer equation, within the formalism of time-dependent density functional theory, and allows the calculation of the response both in resonance and out of resonance. Furthermore, the excellent scaling with the number of atoms opens the way to the investigation of response properties of very large molecular systems. To demonstrate the capabilities of this method, they implemented it in a real-space (basis-set-free) code and applied it to benchmark molecules, namely, CO, H2O, and para-nitroaniline. Their results are in agreement with experimental and previous theoretical studies and fully validate their approach."], "field": "Physics and Astronomy", "q_year": 2019, "q_cid": "209386906", "pos_cid": 8251885, "source": "eval20x26"}
{"query_id": "scaleup_6853980_18560644", "query": "How to identify the intrinsic properties of processes that produce growing interfaces from their data when existing classifications leave differences in their behavior unresolved", "pos": ["Description of stochastic and chaotic series using visibility graphs.. Nonlinear time series analysis is an active field of research that studies the structure of complex signals in order to derive information of the process that generated those series, for understanding, modeling and forecasting purposes. In the last years, some methods mapping time series to network representations have been proposed. The purpose is to investigate on the properties of the series through graph theoretical tools recently developed in the core of the celebrated complex network theory. Among some other methods, the so-called visibility algorithm has received much attention, since it has been shown that series correlations are captured by the algorithm and translated in the associated graph, opening the possibility of building fruitful connections between time series analysis, nonlinear dynamics, and graph theory. Here we use the horizontal visibility algorithm to characterize and distinguish between correlated stochastic, uncorrelated and chaotic processes. We show that in every case the series maps into a graph with exponential degree distribution P(k)∼exp(-λk), where the value of λ characterizes the specific process. The frontier between chaotic and correlated stochastic processes, λ=ln(3/2) , can be calculated exactly, and some other analytical developments confirm the results provided by extensive numerical simulations and (short) experimental time series."], "field": "Physics and Astronomy", "q_year": 2014, "q_cid": "6853980", "pos_cid": 18560644, "source": "eval20x26"}
{"query_id": "scaleup_52080806_11811350", "query": "How to clarify the nature of physical entities and their interactions in a reality without space or time, consistent with quantum theory and with a flow of time coexisting with relativity’s four-dimensional block universe", "pos": ["Quantum Theory and Conceptuality: Matter, Stories, Semantics and Space-Time. We elaborate the new interpretation of quantum theory that we recently proposed, according to which quantum particles are considered conceptual entities mediating between pieces of ordinary matter which are considered to act as memory structures for them. Our aim is to identify what is the equivalent for the human cognitive realm of what physical space-time is for the realm of quantum particles and ordinary matter. For this purpose, we identify the notion of 'story' as the equivalent within the human cognitive realm of what ordinary matter is in the physical quantum realm, and analyze the role played by the logical connectives of disjunction and conjunction with respect to the notion of locality. Similarly to what we have done in earlier investigations on this new quantum interpretation, we use the specific cognitive environment of the World-Wide Web to elucidate the comparisons we make between the human cognitive realm and the physical quantum realm."], "field": "Physics and Astronomy", "q_year": 2015, "q_cid": "52080806", "pos_cid": 118113502, "source": "eval20x26"}
{"query_id": "scaleup_17745392_12930544", "query": "How to relate interacting electron transport dynamics to probabilities of transferring different numbers of electrons while preserving coherence and characterizing current fluctuations and higher cumulants relevant to interaction-induced phase coherence", "pos": ["Spontaneous relaxation of a charge qubit under electrical measurement.. In this work we first derive a generalized conditional master equation for quantum measurement by a mesoscopic detector, then study the readout characteristics of qubit measurement where a number of remarkable new features are found. The work would, in particular, highlight the qubit spontaneous relaxation effect induced by the measurement itself rather than an external thermal bath."], "field": "Physics and Astronomy", "q_year": 2015, "q_cid": "17745392", "pos_cid": 12930544, "source": "eval20x26"}
{"query_id": "scaleup_24402691_37267268", "query": "How to make fiducial placement for image-guided radiotherapy of upper gastrointestinal cancers accessible with routine gastroenterology skills and equipment", "pos": ["Glueing of fundal varices.. Gastric variceal bleeding is an uncommon, serious complication of portal hypertension. The significant morbidity and mortality resulting from bleeding from gastric varices presents a challenge for gastroenterologists. The management of this complication has not been standardized. Although transjugular intrahepatic portosystemic shunt (TIPS) is used in many centres to treat gastric varices, endoscopic treatment with the tissue glue cyanoacrylate (N-butyl-2-cyanoacrylate) has been used successfully in many countries for 20 years and is considered, by many clinicians, to be the optimal initial treatment for bleeding gastric varices (1). Despite the widespread use of cyanoacrylate, there are still controversies in the literature regarding its use. The present article deals with the indications, technique, preparation, catheter use, long-term results and cost-effectiveness of the procedure. Close attention to these recommendations can result in successful and safe usage of the tissue glue. The endoscopy unit planning to perform gastric variceal glueing should have a detailed nursing protocol established before performing this procedure."], "field": "Physics and Astronomy", "q_year": 2021, "q_cid": "244026910", "pos_cid": 37267268, "source": "eval_collection"}
{"query_id": "scaleup_25275646_59460139", "query": "How to characterize excitations in nonlinear soliton crystals when standard linear-system descriptions are not directly applicable", "pos": ["Topological Zak phase in strongly coupled LC circuits. We show the emergence of topological Bogoliubov bosonic excitations in the relatively strong coupling limit of an LC (inductance-capacitance) one-dimensional quantum circuit. This dimerized chain model reveals a ${\\cal Z}_2$ local symmetry as a result of the counter-rotating wave (pairing) terms. The topology is protected by the sub-lattice symmetry, represented by an anti-unitary transformation. We present a methos to measure the winding of the topological Zak phase across the Brillouin zone by a reflection measurement of (microwave) light. Our method probes bulk quantities and can be implemented even in small systems. We study the robustness of edge modes towards disorder."], "field": "Physics and Astronomy", "q_year": 2022, "q_cid": "252756462", "pos_cid": 59460139, "source": "eval_collection"}
{"query_id": "scaleup_27056061_24777933", "query": "How to computationally study emergent electronic phases in strongly correlated systems with large moiré unit cells while preserving superlattice periodicity and fermionic antisymmetry", "pos": ["Ab initio calculation of real solids via neural network ansatz. Neural networks have been applied to tackle many-body electron correlations for small molecules and physical models in recent years. Here we propose an architecture that extends molecular neural networks with the inclusion of periodic boundary conditions to enable ab initio calculation of real solids. The accuracy of our approach is demonstrated in four different types of systems, namely the one-dimensional periodic hydrogen chain, the two-dimensional graphene, the three-dimensional lithium hydride crystal, and the homogeneous electron gas, where the obtained results, e.g. total energies, dissociation curves, and cohesive energies, reach a competitive level with many traditional ab initio methods. Moreover, electron densities of typical systems are also calculated to provide physical intuition of various solids. Our method of extending a molecular neural network to periodic systems can be easily integrated into other neural network structures, highlighting a promising future of ab initio solution of more complex solid systems using neural network ansatz, and more generally endorsing the application of machine learning in materials simulation and condensed matter physics."], "field": "Physics and Astronomy", "q_year": 2024, "q_cid": "270560616", "pos_cid": 247779339, "source": "eval_collection"}
{"query_id": "scaleup_21084343_16920799", "query": "How to balance potentially conflicting objectives in community detection without preset weights while satisfying each objective as well as possible", "pos": ["Multi-Criteria Optimization for Fleet Size with Environmental Aspects. Abstract This research concerns multi-criteria vehicle routing problems. Mathematical models are formulated with mixed-integer programming. We consider maximization of capacity of truck vs. minimization of utilization of fuel, carbon emission and production of noise. The problems deal with green logistics for routes crossing the Western Pyrenees in Navarre, Basque Country and La Rioja, Spain. We consider heterogeneous fleet of trucks. Different types of trucks have not only different capacities, but also require different amounts of fuel for operations. Consequently, the amount of carbon emission and noise vary as well. Companies planning delivery routes must consider the trade-off between the financial and environmental aspects of transportation. Efficiency of delivery routes is impacted by truck size and the possibility of dividing long delivery routes into smaller ones. The results of computational experiments modeled after real data from a Spanish food distribution company are reported. Computational results based on formulated optimization models show some balance between fleet size, truck types, utilization of fuel, carbon emission and production of noise. As a result, the company could consider a mixture of trucks sizes and divided routes for smaller trucks. Analyses of obtained results could help logistics managers lead the initiative in environmental conservation by saving fuel and consequently minimizing pollution."], "field": "Physics and Astronomy", "q_year": 2020, "q_cid": "210843431", "pos_cid": 169207991, "source": "eval_collection"}
{"query_id": "scaleup_26313159_21071890", "query": "How to achieve delocalized driving profiles compatible with measurements that assume localization, given their special preparation and nontrivial driving-field fine-tuning requirements", "pos": ["Bulk detection of time-dependent topological transitions in quenched chiral models. The topology of one-dimensional chiral systems is captured by the winding number of the Hamiltonian eigenstates. Here we show that this invariant can be read-out by measuring the mean chiral displacement of a single-particle wavefunction that is connected to a fully localized one via a unitary and translational-invariant map. Remarkably, this implies that the mean chiral displacement can detect the winding number even when the underlying Hamiltonian is quenched between different topological phases. We confirm experimentally these results in a quantum walk of structured light."], "field": "Physics and Astronomy", "q_year": 2023, "q_cid": "263131598", "pos_cid": 210718907, "source": "eval_collection"}
{"query_id": "scaleup_27664747_11118105", "query": "How to preserve distinctive features for reconstruction as repeated processing makes them increasingly similar", "pos": ["Deeper Insights into Graph Convolutional Networks for Semi-Supervised Learning. Many interesting problems in machine learning are being revisited with new deep learning tools. For graph-based semi-supervised learning, a recent important development is graph convolutional networks (GCNs), which nicely integrate local vertex features and graph topology in the convolutional layers. Although the GCN model compares favorably with other state-of-the-art methods, its mechanisms are not clear and it still requires considerable amount of labeled data for validation and model selection. In this paper, we develop deeper insights into the GCN model and address its fundamental limits. First, we show that the graph convolution of the GCN model is actually a special form of Laplacian smoothing, which is the key reason why GCNs work, but it also brings potential concerns of over-smoothing with many convolutional layers. Second, to overcome the limits of the GCN model with shallow architectures, we propose both co-training and self-training approaches to train GCNs. Our approaches significantly improve GCNs in learning with very few labels, and exempt them from requiring additional labels for validation. Extensive experiments on benchmarks have verified our theory and proposals."], "field": "Physics and Astronomy", "q_year": 2025, "q_cid": "276647473", "pos_cid": 11118105, "source": "eval_collection"}
{"query_id": "scaleup_23203739_27800887", "query": "How to establish a clinically justified limit on low-dose lung exposure in esophageal cancer radiotherapy to reduce radiation pneumonitis risk", "pos": ["Predictors of Radiation Pneumonitis in Patients Receiving Intensity-Modulated Radiation Therapy for Hodgkin and Non-Hodgkin Lymphoma. Purpose Few studies to date have evaluated factors associated with the development of radiation pneumonitis (RP) in patients with Hodgkin lymphoma (HL) and non-Hodgkin lymphoma (NHL), especially in patients treated with contemporary radiation techniques. These patients represent a unique group owing to the often large radiation target volumes within the mediastinum and to the potential to receive several lines of chemotherapy that add to pulmonary toxicity for relapsed or refractory disease. Our objective was to determine the incidence and clinical and dosimetric risk factors associated with RP in lymphoma patients treated with intensity modulated radiation therapy (IMRT) at a single institution. Methods We retrospectively reviewed clinical charts and radiation records of 150 consecutive patients who received mediastinal IMRT for HL and NHL from 2009 through 2013. Clinical and dosimetric predictors associated with RP per the Radiation Therapy Oncology Group (RTOG) acute toxicity criteria were identified in univariate analysis using the Pearson χ2 test and logistic multivariate regression. Results Mediastinal radiation was administered as consolidation therapy in 110 patients with newly diagnosed HL or NHL and in 40 patients with relapsed or refractory disease. The overall incidence of RP (RTOG grade 1–3) was 14% in the entire cohort. Risk of RP was increased for patients who received radiation for relapsed or refractory disease (25%) versus those who received consolidation (10%, P=0.019). Several dosimetric parameters predicted RP, including mean lung dose (MLD) >13.5 Gy, V20 >30%, V15 >35%, V10 >40% and V5>55%. The likelihood ratio (LR) χ2 value was highest for V5< 55% (LR χ2=19.37). Conclusions In using IMRT to treat mediastinal lymphoma, all dosimetric parameters predicted RP, although small doses to large volumes of lung had the greatest influence. Patients with relapsed or refractory lymphoma who received salvage chemotherapy and hematopoietic stem cell transplantation were at higher risk for symptomatic RP."], "field": "Physics and Astronomy", "q_year": 2021, "q_cid": "232037396", "pos_cid": 27800887, "source": "eval_collection"}
{"query_id": "scaleup_27664747_26391091", "query": "How to simultaneously reconstruct albedo and depth in non-line-of-sight imaging while balancing both objectives and limiting computational and storage demands for dense three-dimensional grid data", "pos": ["Occlusion relationship reasoning with a feature separation and interaction network. Occlusion relationship reasoning aims to locate where an object occludes others and estimate the depth order of these objects in three-dimensional (3D) space from a two-dimensional (2D) image. The former sub-task demands both the accurate location and the semantic indication of the objects, while the latter sub-task needs the depth order among the objects. Although several insightful studies have been proposed, a key characteristic of occlusion relationship reasoning, i.e., the specialty and complementarity between occlusion boundary detection and occlusion orientation estimation, is rarely discussed. To verify this claim, in this paper, we integrate these properties into a unified end-to-end trainable network, namely the feature separation and interaction network (FSINet). It contains a shared encoder-decoder structure to learn the complementary property between the two sub-tasks, and two separated paths to learn specialized properties of the two sub-tasks. Concretely, the occlusion boundary path contains an image-level cue extractor to capture rich location information of the boundary, a detail-perceived semantic feature extractor, and a contextual correlation extractor to acquire refined semantic features of objects. In addition, a dual-flow cross detector has been customized to alleviate false-positive and false-negative boundaries. For the occlusion orientation estimation path, a scene context learner has been designed to capture the depth order cue around the boundary. In addition, two stripe convolutions are built to judge the depth order between objects. The shared decoder supplies the feature interaction, which plays a key role in exploiting the complementarity of the two paths. Extensive experimental results on the PIOD and BSDS ownership datasets reveal the superior performance of FSINet over state-of-the-art alternatives. Additionally, abundant ablation studies are offered to demonstrate the effectiveness of our design."], "field": "Physics and Astronomy", "q_year": 2025, "q_cid": "276647473", "pos_cid": 263910914, "source": "eval_collection"}
{"query_id": "scaleup_27282745_20631559", "query": "How to make the earliest physical conditions testable with sufficiently strong observable signals in a physically realizable scenario", "pos": ["Primordial Black Holes from Sound Speed Resonance during Inflation.. We report on a novel phenomenon of the resonance effect of primordial density perturbations arisen from a sound speed parameter with an oscillatory behavior, which can generically lead to the formation of primordial black holes in the early Universe. For a general inflaton field, it can seed primordial density fluctuations, and their propagation is governed by a parameter of sound speed square. Once, if this parameter achieves an oscillatory feature for a while during inflation, a significant nonperturbative resonance effect on the inflaton field fluctuations takes place around a critical length scale, which results in significant peaks in the primordial power spectrum. By virtue of this robust mechanism, primordial black holes with specific mass function can be produced with a sufficient abundance for dark matter in sizable parameter ranges."], "field": "Physics and Astronomy", "q_year": 2024, "q_cid": "272827450", "pos_cid": 206315596, "source": "eval_collection"}
{"query_id": "scaleup_25882298_10639772", "query": "How to realize magnetic-field effects and nontrivial band topology for propagating optical pulses with controllable band flatness for exploring fractional quantum Hall physics", "pos": ["Coupled atomic wires in a synthetic magnetic field. We propose and study systems of coupled atomic wires in a perpendicular synthetic magnetic field as a platform to realize exotic phases of quantum matter. This includes (fractional) quantum Hall states in arrays of many wires inspired by the pioneering work [C. L. Kane et al., Phys. Rev. Lett. 88, 036401 (2002)], as well as Meissner phases and vortex phases in double wires. With one continuous and one discrete spatial dimension, the proposed setup naturally complements recently realized discrete counterparts, i.e., the Harper-Hofstadter model and the two-leg flux ladder, respectively. We present both an in-depth theoretical study and a detailed experimental proposal to make the unique properties of the semicontinuous Harper-Hofstadter model accessible with cold-atom experiments. For the minimal setup of a double wire, we explore how a subwavelength spacing of the wires can be implemented. This construction increases the relevant energy scales by at least an order of magnitude compared to ordinary optical lattices, thus rendering subtle many-body phenomena such as Lifshitz transitions in Fermi gases observable in an experimentally realistic parameter regime. For arrays of many wires, we discuss the emergence of Chern bands with readily tunable flatness of the dispersion and show how fractional quantum Hall states can be stabilized in such systems. Using for the creation of optical potentials Laguerre-Gauss beams that carry orbital angular momentum, we detail how the coupled atomic wire setups can be realized in nonplanar geometries such as cylinders, disks, and tori."], "field": "Physics and Astronomy", "q_year": 2023, "q_cid": "258822989", "pos_cid": 106397723, "source": "eval_collection"}
{"query_id": "scaleup_22083118_55391471", "query": "How to determine the lower edge of the dark matter exclusion-limit contour when an unknown background complicates attributing observed events to dark matter", "pos": ["Finding an Upper Limit in the Presence of Unknown Background. Experimenters report an upper limit if the signal they are trying to detect is non-existent or below their experiment's sensitivity. Such experiments may be contaminated with a background too poorly understood to subtract. If the background is distributed differently in some parameter from the expected signal, it is possible to take advantage of this difference to get a stronger limit than would be possible if the difference in distribution were ignored. We discuss the ``Maximum Gap'' method, which finds the best gap between events for setting an upper limit, and generalize to ``Optimum Interval'' methods, which use intervals with especially few events. These methods, which apply to the case of relatively small backgrounds, do not use binning, are relatively insensitive to cuts on the range of the parameter, are parameter independent (i.e., do not change when a one-one change of variables is made), and provide true, though possibly conservative, classical one-sided confidence intervals."], "field": "Physics and Astronomy", "q_year": 2020, "q_cid": "220831184", "pos_cid": 55391471, "source": "eval_collection"}
{"query_id": "scaleup_28380343_88518170", "query": "How to ensure a state-estimation objective targets the intended summary of the conditional state distribution, such as a specified quantile or mode, rather than a different point estimate", "pos": ["Making and Evaluating Point Forecasts. Typically, point forecasting methods are compared and assessed by means of an error measure or scoring function, with the absolute error and the squared error being key examples. The individual scores are averaged over forecast cases, to result in a summary measure of the predictive performance, such as the mean absolute error or the mean squared error. I demonstrate that this common practice can lead to grossly misguided inferences, unless the scoring function and the forecasting task are carefully matched. Effective point forecasting requires that the scoring function be specified ex ante, or that the forecaster receives a directive in the form of a statistical functional, such as the mean or a quantile of the predictive distribution. If the scoring function is specified ex ante, the forecaster can issue the optimal point forecast, namely, the Bayes rule. If the forecaster receives a directive in the form of a functional, it is critical that the scoring function be consistent for it, in the sense that the expected score is minimized when following the directive. A functional is elicitable if there exists a scoring function that is strictly consistent for it. Expectations, ratios of expectations and quantiles are elicitable. For example, a scoring function is consistent for the mean functional if and only if it is a Bregman function. It is consistent for a quantile if and only if it is generalized piecewise linear. Similar characterizations apply to ratios of expectations and to expectiles. Weighted scoring functions are consistent for functionals that adapt to the weighting in peculiar ways. Not all functionals are elicitable; for instance, conditional value-at-risk is not, despite its popularity in quantitative finance."], "field": "Physics and Astronomy", "q_year": 2025, "q_cid": "283803439", "pos_cid": 88518170, "source": "eval_collection"}
{"query_id": "scaleup_24680976_12030345", "query": "How to quantify how heavy water and ordinary water divide between vapor and ice across martian temperatures", "pos": ["Laboratory measurements of HDO/H2O isotopic fractionation during ice deposition in simulated cirrus clouds. Significance The preferential deposition of heavy water (HDO or H218O) as ice is a fundamental tracer in the geosciences, used for understanding paleoclimate and water cycling, but the basic physical chemistry is not well measured. We describe here measurements of the preferential fractionation of HDO vs. H2O at the cold temperatures relevant to cirrus clouds on Earth and snow on Mars. We also provide a quantitative demonstration of kinetic isotope effects in nonequilibrium conditions, and show how targeted dynamic experiments can be used to understand processes at ice surfaces. The stable isotopologues of water have been used in atmospheric and climate studies for over 50 years, because their strong temperature-dependent preferential condensation makes them useful diagnostics of the hydrological cycle. However, the degree of preferential condensation between vapor and ice has never been directly measured at temperatures below 233 K (−40 °C), conditions necessary to form cirrus clouds in the Earth’s atmosphere, routinely observed in polar regions, and typical for the near-surface atmospheric layers of Mars. Models generally assume an extrapolation from the warmer experiments of Merlivat and Nief [Merlivat L, Nief G (1967) Tellus 19:122–127]. Nonequilibrium kinetic effects that should alter preferential partitioning have also not been well characterized experimentally. We present here direct measurements of HDO/H2O equilibrium fractionation between vapor and ice (αeq) at cirrus-relevant temperatures, using in situ spectroscopic measurements of the evolving isotopic composition of water vapor during cirrus formation experiments in a cloud chamber. We rule out the recent proposed upward modification of αeq, and find values slightly lower than Merlivat and Nief. These experiments also allow us to make a quantitative validation of the kinetic modification expected to occur in supersaturated conditions in the ice–vapor system. In a subset of diffusion-limited experiments, we show that kinetic isotope effects are indeed consistent with published models, including allowing for small surface effects. These results are fundamental for inferring processes on Earth and other planets from water isotopic measurements. They also demonstrate the utility of dynamic in situ experiments for studying fractionation in geochemical systems."], "field": "Physics and Astronomy", "q_year": 2022, "q_cid": "246809765", "pos_cid": 12030345, "source": "train_step3"}
{"query_id": "scaleup_26657344_15165788", "query": "How to determine whether post-selected quantum sensing offers cost-sensitive practical advantages over the Hermitian case when average information is unchanged", "pos": ["Technical advantages for weak value amplification: When less is more. The technical merits of weak value amplification techniques are analyzed. We consider models of several different types of technical noise in an optical context and show that weak value amplification techniques (which only use a small fraction of the photons) compare favorably with standard techniques (which uses all of them). Using the Fisher information metric, we demonstrate that weak value techniques can put all of the Fisher information about the detected parameter into a small portion of the events and show how this fact alone gives technical advantages. We go on to consider a time correlated noise model, and find that a Fisher information analysis indicates that while the standard method can have much larger information about the detected parameter than the postselected technique. However, the estimator needed to gather the information is technically difficult to implement, showing that the inefficient (but practical) signal-to-noise estimation of the parameter is usually superior. We also describe other technical advantages unique to imaginary weak value amplification techniques, focusing on beam deflection measurements. In this case, we discuss combined noise types (such as detector transverse jitter, angular beam jitter before the interferometer and turbulence) for which the interferometric weak value technique gives higher Fisher information over conventional methods. We go on to calculate the Fisher information of the recently proposed photon recycling scheme for beam deflection measurements, and show it further boosts the Fisher information by the inverse postselection probability relative to the standard measurement case."], "field": "Physics and Astronomy", "q_year": 2023, "q_cid": "266573442", "pos_cid": 15165788, "source": "train_step3"}
{"query_id": "scaleup_26549889_16034699", "query": "How to improve the reliability and temporal consistency of noisy pseudo labels generated for unlabeled event streams for detector training", "pos": ["Simple online and realtime tracking. This paper explores a pragmatic approach to multiple object tracking where the main focus is to associate objects efficiently for online and realtime applications. To this end, detection quality is identified as a key factor influencing tracking performance, where changing the detector can improve tracking by up to 18.9%. Despite only using a rudimentary combination of familiar techniques such as the Kalman Filter and Hungarian algorithm for the tracking components, this approach achieves an accuracy comparable to state-of-the-art online trackers. Furthermore, due to the simplicity of our tracking method, the tracker updates at a rate of 260 Hz which is over 20x faster than other state-of-the-art trackers."], "field": "Physics and Astronomy", "q_year": 2023, "q_cid": "265498891", "pos_cid": 16034699, "source": "train_step3"}
{"query_id": "scaleup_26657344_2217936", "query": "How to minimize average search cost while accounting for search-operation costs, result-reading costs, success probability, and repeated attempts", "pos": ["Generalized quantum search with parallelism. We generalize Grover's unstructured quantum search algorithm to enable it to work with arbitrary starting superpositions and arbitrary unitary operators. We show that the generalized quantum search algorithm, when cast in a special orthonormal basis, can be understood as performing an exact rotation of a starting superposition into a target superposition. We derive a formula for the success probability of the generalized quantum search algorithm after n rounds of amplitude amplification. We then use this formula to determine the optimal strategy for a punctuated quantum search algorithm, i.e., one in which the amplitude amplified state is observed before the point of maximum success probability. On average, the optimal strategy is about 12% better than the naive use of Grover's algorithm. The speedup obtained is not dramatic but it illustrates that a hybrid use of quantum computing and classical computing techniques can yield a performance that is better than either alone. In addition, we show that a punctuated quantum algorithm that takes the same average computation time as Grover's standard algorithm only requires half the coherence time. We then extend the analysis to the case of a society of k quantum searches acting in parallel. We derive an analytic formula that connects the degree of parallelism with the expected computation time for k-parallel quantum search. The resulting parallel speedup scales as $O(\\sqrt{k}),$ while the minimum number of agents needed to ensure success, k, decreases as the inverse of the square of the achievable coherence time. This result has practical significance for the design of rudimentary quantum computers that are likely to have a limited coherence time."], "field": "Physics and Astronomy", "q_year": 2023, "q_cid": "266573442", "pos_cid": 2217936, "source": "train_step3"}
{"query_id": "scaleup_26964356_25095343", "query": "How to introduce cavities and diverse structural features for binding or enzymatic functions into de novo TIM barrels while preserving the barrel framework and without predetermining the new elements’ secondary structures", "pos": ["Scaffolding protein functional sites using deep learning. The binding and catalytic functions of proteins are generally mediated by a small number of functional residues held in place by the overall protein structure. Here, we describe deep learning approaches for scaffolding such functional sites without needing to prespecify the fold or secondary structure of the scaffold. The first approach, “constrained hallucination,” optimizes sequences such that their predicted structures contain the desired functional site. The second approach, “inpainting,” starts from the functional site and fills in additional sequence and structure to create a viable protein scaffold in a single forward pass through a specifically trained RoseTTAFold network. We use these two methods to design candidate immunogens, receptor traps, metalloproteins, enzymes, and protein-binding proteins and validate the designs using a combination of in silico and experimental tests. Description Designing around function Protein design has had success in finding sequences that fold into a desired conformation, but designing functional proteins remains challenging. Wang et al. describe two deep-learning methods to design proteins that contain prespecified functional sites. In the first, they found sequences predicted to fold into stable structures that contain the functional site. In the second, they retrained a structure prediction network to recover the sequence and full structure of a protein given only the functional site. The authors demonstrate their methods by designing proteins containing a variety of functional motifs. —VV Deep-learning methods enable the scaffolding of desired functional residues within a well-folded designed protein."], "field": "Physics and Astronomy", "q_year": 2024, "q_cid": "269643560", "pos_cid": 250953434, "source": "train_step3"}
{"query_id": "scaleup_27405538_19582577", "query": "How to determine whether a target description of part of a many-body system is compatible with a state of the whole system despite exponentially growing consistency constraints and limits on description size and sequential operations on near-term hardware", "pos": ["An adaptive variational algorithm for exact molecular simulations on a quantum computer. Quantum simulation of chemical systems is one of the most promising near-term applications of quantum computers. The variational quantum eigensolver, a leading algorithm for molecular simulations on quantum hardware, has a serious limitation in that it typically relies on a pre-selected wavefunction ansatz that results in approximate wavefunctions and energies. Here we present an arbitrarily accurate variational algorithm that, instead of fixing an ansatz upfront, grows it systematically one operator at a time in a way dictated by the molecule being simulated. This generates an ansatz with a small number of parameters, leading to shallow-depth circuits. We present numerical simulations, including for a prototypical strongly correlated molecule, which show that our algorithm performs much better than a unitary coupled cluster approach, in terms of both circuit depth and chemical accuracy. Our results highlight the potential of our adaptive algorithm for exact simulations with present-day and near-term quantum hardware. Quantum algorithms for simulating chemical systems are limited because of the a priori assumption about the form of the target wavefunction. Here the authors present a new variational hybrid quantum-classical algorithm which allows the system being simulated to determine its own optimal state."], "field": "Physics and Astronomy", "q_year": 2024, "q_cid": "274055389", "pos_cid": 195825773, "source": "train_step3"}
{"query_id": "scaleup_24638800_26960442", "query": "How to predict an irradiated solid’s dynamics while accurately accounting for energy absorbed during interaction with x rays so its simulated response reflects the deposited energy", "pos": ["Theory for the ultrafast ablation of graphite films.. The physical mechanisms for damage formation in graphite films induced by femtosecond laser pulses are analyzed using a microscopic electronic theory. We describe the nonequilibrium dynamics of electrons and lattice by performing molecular dynamics simulations on time-dependent potential energy surfaces. We show that graphite has the unique property of exhibiting two distinct laser-induced structural instabilities. For high absorbed energies ( >3.3 eV/atom) we find nonequilibrium melting followed by fast evaporation. For low intensities above the damage threshold ( >2.0 eV/atom) ablation occurs via removal of intact graphite sheets."], "field": "Physics and Astronomy", "q_year": 2022, "q_cid": "246388009", "pos_cid": 26960442, "source": "train_step3"}
{"query_id": "scaleup_22190673_16218127", "query": "How to determine the atomic structure of oxide interfaces without prior structural knowledge", "pos": ["Rapid Structure Determination of Molecular Solids Using Chemical Shifts Directed by Unambiguous Prior Constraints. NMR-based crystallography approaches involving the combination of crystal structure prediction methods, ab initio calculated chemical shifts and solid-state NMR experiments are powerful methods for crystal structure determination of microcrystalline powders. However, currently structural information obtained from solid-state NMR is usually included only after a set of candidate crystal structures has already been independently generated, starting from a set of single-molecule conformations. Here, we show with the case of ampicillin that this can lead to failure of structure determination. We propose a crystal structure determination method that includes experimental constraints during conformer selection. In order to overcome the problem that experimental measurements on the crystalline samples are not obviously translatable to restrict the single-molecule conformational space, we propose constraints based on the analysis of absent cross-peaks in solid-state NMR correlation experiments. We show that these absences provide unambiguous structural constraints on both the crystal structure and the gas-phase conformations, and therefore can be used for unambiguous selection. The approach is parametrized on the crystal structure determination of flutamide, flufenamic acid, and cocaine, where we reduce the computational cost by around 50%. Most importantly, the method is then shown to correctly determine the crystal structure of ampicillin, which would have failed using current methods because it adopts a high-energy conformer in its crystal structure. The average positional RMSE on the NMR powder structure is ⟨rav⟩ = 0.176 Å, which corresponds to an average equivalent displacement parameter Ueq = 0.0103 Å2."], "field": "Physics and Astronomy", "q_year": 2020, "q_cid": "221906732", "pos_cid": 162181273, "source": "train_step3"}
{"query_id": "scaleup_27174522_25802475", "query": "How to accurately predict penetration into an open-ended rectangular structure for any incoming pattern", "pos": ["Comprehensive Multimode Reflection Analysis of a Dielectric-Loaded Rectangular Waveguide Terminated by Semi-Infinite Dielectric Media. This article presents a comprehensive multimode reflection analysis of a dielectric-loaded rectangular waveguide terminated by semiinfinite dielectric media. A Fourier-based analysis approach is extended for different incident modes of the waveguide to calculate the amplitude coefficients of the reflected modes when the flange or the waveguide walls have different finite conductivities. We calculate the complex propagation constant using the method of perturbation of the boundary conditions. The modal scattering parameters are defined based on the voltage wave normalized amplitudes to be valid for both propagating and evanescent fields. The inclusion of coupled and noncoupled modes in the solution is evaluated in terms of calculation time and the accuracy of the results. An algorithm is presented to calculate the reflection coefficient of variations in terms of the coupled modes included in the solution. It is shown that these variations are dependent on the operating frequency and dielectric properties used in the geometry. Our results are compared with 3-D full-wave simulations, and an excellent agreement is achieved over a wide frequency range by using the primary coupled modes in the solution. The modal aperture admittance is calculated for different modes to show the coupled modes’ effect on the results. Also, the proposed algorithm is modified to find the effective coupled modes much faster. These modes are used to obtain accurate results for different dielectric-loaded structures."], "field": "Physics and Astronomy", "q_year": 2024, "q_cid": "271745221", "pos_cid": 258024755, "source": "train_step3"}
{"query_id": "scaleup_24705838_4438685", "query": "How to externally control the center-of-mass momentum of two-dimensional excitons to access higher-momentum states and probe and tune momentum-dependent intravalley spin-flip scattering", "pos": ["Subluminal group velocity and dispersion of Laguerre Gauss beams in free space. That the speed of light in free space c is constant has been a pillar of modern physics since the derivation of Maxwell and in Einstein’s postulate in special relativity. This has been a basic assumption in light’s various applications. However, a physical beam of light has a finite extent such that even in free space it is by nature dispersive. The field confinement changes its wavevector, hence, altering the light’s group velocity vg. Here, we report the subluminal vg and consequently the dispersion in free space of Laguerre-Gauss (LG) beam, a beam known to carry orbital angular momentum. The vg of LG beam, calculated in the paraxial regime, is observed to be inversely proportional to the beam’s divergence θ0, the orbital order ℓ and the radial order p. LG beams of higher orders travel relatively slower than that of lower orders. As a consequence, LG beams of different orders separate in the temporal domain along propagation. This is an added effect to the dispersion due to field confinement. Our results are useful for treating information embedded in LG beams from astronomical sources and/or data transmission in free space."], "field": "Physics and Astronomy", "q_year": 2022, "q_cid": "247058387", "pos_cid": 4438685, "source": "train_step3"}
{"query_id": "scaleup_25325280_23385195", "query": "How to determine whether lightning current can be attenuated", "pos": ["Mechanism for truncating power-frequency continuation and reburning by means of a super-strong arc-extinguishing gas. The process of arc suppression with a super-strong arc-extinguishing gas (AEG) includes arc truncation and reburning suppression. In this paper, the plasma mechanics, the mechanics of the super-strong AEG, and the arc-reburning suppression by the AEG are all modeled. Combined with test data, the characteristics of arc truncation, pressure characteristics, and time characteristics of the AEG are analyzed, and the law of medium recovery and reignition suppression of arc fracture under the action of the super-strong AEG are discussed. The test results show that with a super-strong AEG, the arc-extinguishing threshold and time are 40 kA and less than 0.5 ms, respectively."], "field": "Physics and Astronomy", "q_year": 2022, "q_cid": "253252806", "pos_cid": 233851950, "source": "train_step3"}
{"query_id": "scaleup_27833899_51693566", "query": "How to maintain sufficient spatial overlap between an emitter and an environmental photon state for triggered emission while keeping the environmental excitation localized near the emitter despite photon propagation", "pos": ["Artificial flat band systems: from lattice models to experiments. Abstract Certain lattice wave systems in translationally invariant settings have one or more spectral bands that are strictly flat or independent of momentum in the tight binding approximation, arising from either internal symmetries or fine-tuned coupling. These flat bands display remarkable strongly interacting phases of matter. Originally considered as a theoretical convenience useful for obtaining exact analytical solutions of ferromagnetism, flat bands have now been observed in a variety of settings, ranging from electronic systems to ultracold atomic gases and photonic devices. Here we review the design and implementation of flat bands and chart future directions of this exciting field. Graphical Abstract"], "field": "Physics and Astronomy", "q_year": 2025, "q_cid": "278338996", "pos_cid": 51693566, "source": "train_step3"}
{"query_id": "scaleup_24777892_18980837", "query": "How to update a parameterized representation of a many-component system to follow a specified evolution while remaining within a restricted family of allowed states", "pos": ["Weak binding between two aromatic rings: feeling the van der Waals attraction by quantum Monte Carlo methods.. We report a systematic study of the weak chemical bond between two benzene molecules. We first show that it is possible to obtain a very good description of the C(2) dimer and the benzene molecule by using pseudopotentials for the chemically inert 1s electrons and a resonating valence bond wave function as a variational ansatz, expanded on a relatively small Gaussian basis set. We employ an improved version of the stochastic reconfiguration technique to optimize the many-body wave function, which is the starting point for highly accurate simulations based on the lattice regularized diffusion Monte Carlo method. This projection technique provides a rigorous variational upper bound for the total energy, even in the presence of pseudopotentials, and substantially improves the accuracy of the trial wave function, which already yields a large fraction of the dynamical and nondynamical electron correlation. We show that the energy dispersion of two benzene molecules in the parallel displaced geometry is significantly deeper than the face-to-face configuration. However, contrary to previous studies based on post-Hartree-Fock methods, the binding energy remains weak ( approximately 2 kcal/mol) also in this geometry, and its value is in agreement with the most accurate and recent experimental findings [H. Krause et al., Chem. Phys. Lett. 184, 411 (1991)]."], "field": "Physics and Astronomy", "q_year": 2022, "q_cid": "247778928", "pos_cid": 18980837, "source": "train_step3"}
{"query_id": "scaleup_27833899_27803963", "query": "How to determine whether correlated pairs of light particles can travel where individual light particles are trapped", "pos": ["Interaction induced delocalization for two particles in a periodic potential. We consider two interacting particles evolving in a one-dimensional periodic structure embedded in a magnetic field. We show that the strong localization induced by the magnetic field for particular values of the flux per unit cell is destroyed as soon as the particles interact. We study the spectral and dynamical aspects of this transition."], "field": "Physics and Astronomy", "q_year": 2025, "q_cid": "278338996", "pos_cid": 27803963, "source": "train_step3"}
{"query_id": "scaleup_26741253_11856866", "query": "How to determine whether direction-dependent localization considered in chiral symmetry classes can also occur in eigenstates of non-Hermitian operators in fundamental symmetry classes", "pos": ["Non-hermitian random matrix theory: Method of hermitian reduction. Abstract We consider random non-hermitian matrices in the large- N limit. The power of analytic function theory cannot be brought to bear directly to analyze non-hermitian random matrices, in contrast to hermitian random matrices. To overcome this difficulty, we show that associated to each ensemble of non-hermitian matrices there is an auxiliary ensemble of random hermitian matrices which can be analyzed by the usual methods. We then extract the Green function and the density of eigenvalues of the non-hermitian ensemble from those of the auxiliary ensemble. We apply this “method of hermitization” to several examples, and discuss a number of related issues."], "field": "Physics and Astronomy", "q_year": 2024, "q_cid": "267412538", "pos_cid": 118568660, "source": "train_step3"}
{"query_id": "scaleup_25892966_5254408", "query": "How to describe a slowly evolving field that accounts for a much faster field’s influence without requiring the faster field’s full time-dependent dynamics", "pos": ["Adiabatic elimination in a lambda system. This paper deals with different ways to extract the effective two-dimensional lower level dynamics of a lambda system excited by off-resonant laser beams. We present a commonly used procedure for elimination of the upper level, and we show that it may lead to ambiguous results. To overcome this problem and better understand the applicability conditions of this scheme, we review two rigorous methods which allow us both to derive an unambiguous effective two-level Hamiltonian of the system and to quantify the accuracy of the approximation achieved: the first relies on the exact solution of the Schrödinger equation, while the second resorts to the Green's function formalism and the Feshbach projection operator technique."], "field": "Physics and Astronomy", "q_year": 2023, "q_cid": "258929660", "pos_cid": 5254408, "source": "train_step3"}
{"query_id": "scaleup_26221720_24833043", "query": "How to determine when motion governed by average interactions and confined to only some available states remains stable or becomes unstable under perturbations that disrupt its original constraints", "pos": ["Notes on Hamiltonian Dynamical Systems. Starting with the basics of Hamiltonian dynamics and canonical transformations, this text follows the historical development of the theory culminating in recent results: the Kolmogorov–Arnold–Moser theorem, Nekhoroshev's theorem and superexponential stability. Its analytic approach allows students to learn about perturbation methods leading to advanced results. Key topics covered include Liouville's theorem, the proof of Poincaré's non-integrability theorem and the nonlinear dynamics in the neighbourhood of equilibria. The theorem of Kolmogorov on persistence of invariant tori and the theory of exponential stability of Nekhoroshev are proved via constructive algorithms based on the Lie series method. A final chapter is devoted to the discovery of chaos by Poincaré and its relations with integrability, also including recent results on superexponential stability. Written in an accessible, self-contained way with few prerequisites, this book can serve as an introductory text for senior undergraduate and graduate students."], "field": "Physics and Astronomy", "q_year": 2023, "q_cid": "262217201", "pos_cid": 248330439, "source": "train_step3"}
{"query_id": "scaleup_27863571_43569614", "query": "How to determine how nonlinearity affects the stability and localization of non-Hermitian skin states and whether localization–delocalization transitions and mobility edges can arise without disorder", "pos": ["Localization Transitions in Non-Hermitian Quantum Mechanics.. We study the localization transitions which arise in both one and two dimensions when quantum mechanical particles described by a random Schr\\\"odinger equation are subjected to a constant imaginary vector potential. A path-integral formulation relates the transition to flux lines depinned from columnar defects by a transverse magnetic field in superconductors. The theory predicts that, close to the depinning transition, the transverse Meissner effect is accompanied by stretched exponential relaxation of the field into the bulk and a diverging penetration depth."], "field": "Physics and Astronomy", "q_year": 2025, "q_cid": "278635712", "pos_cid": 43569614, "source": "train_step3"}
{"query_id": "scaleup_28141072_55930958", "query": "How to coordinate paired events from continuous-wave probabilistic sources that lack a synchronous generation clock", "pos": ["Entangling independent photons by time measurement. Entanglement is at the heart of quantum physics, both for its conceptual foundations and for applications in quantum communication. Remarkably, entanglement can be ‘swapped’: if we prepare two independent entangled pairs A1–A2 and B1–B2, a joint measurement on A1 and B1 (called a ‘Bell-state measurement’, BSM) has the effect of projecting A2 and B2 onto an entangled state, although these two particles have never interacted nor share any common past1,2. Entanglement swapping with photon pairs has already been experimentally demonstrated3,4,5,6 using pulsed sources—where the challenge was to achieve sufficiently sharp synchronization of the photons in the BSM—but never with continuous-wave sources, as originally proposed2. Here, we present an experiment where the coherence time of the photons exceeds the temporal resolution of the detectors. Hence, photon timing can be obtained by the detection times, and pulsed sources can be replaced by continuous-wave sources, which do not require any synchronization6,7. This allows for the first time the use of completely autonomous sources, an important step towards real-world quantum networks with truly independent and distant nodes."], "field": "Physics and Astronomy", "q_year": 2025, "q_cid": "281410724", "pos_cid": 55930958, "source": "train_step3"}
{"query_id": "scaleup_25315944_22940443", "query": "How to resolve the microscopic energy-transfer pathways between the two rings of the LH2 complex, including quantum nuclear effects in its twenty-four interacting pigments coupled to many molecular vibrations", "pos": ["Small Matrix Path Integral with Extended Memory.. The small matrix decomposition of the path integral (SMatPI) for a discrete system coupled to a harmonic bath expresses the reduced density matrix in terms of matrices whose size is given by the number of states comprising the system, circumventing the large storage requirements of iterative tensor-based algorithms. The present work extends the SMatPI methodology to account for residual memory that exceeds the entanglement length without an increase in computational effort."], "field": "Physics and Astronomy", "q_year": 2022, "q_cid": "253159441", "pos_cid": 229404438, "source": "train_step3"}
{"query_id": "scaleup_21480233_11900265", "query": "How to describe mechanically equilibrated granular media with stress fields that satisfy local force balance when the relevant matrix need not be symmetric", "pos": ["Gapless bosonic excitation without symmetry breaking: An algebraic spin liquid with soft gravitons. A quantum ground state of matter is realized in a bosonic model on a three-dimensional fcc lattice with emergent low energy excitations. The phase obtained is a stable gapless boson liquid phase, with algebraic boson density correlations. The stability of this phase is protected against the instanton effect and superfluidity by self-duality and large gauge symmetries on both sides of the duality. The gapless collective excitations of this phase closely resemble the graviton, although they have a soft $\\ensuremath{\\omega}\\ensuremath{\\sim}{k}^{2}$ dispersion relation. There are three branches of gapless excitations in this phase, one of which is gapless scalar trace mode, the other two have the same polarization and gauge symmetries as the gravitons. The dynamics of this phase is described by a set of Maxwell's equations. The defects carrying gauge charges can drive the system into the superfluid order when the defects are condensed; also the topological defects are coupled to the dual gauge field in the same manner as the charge defects couple to the original gauge field, after the condensation of the topological defects, the system is driven into the Mott insulator phase. In the two-dimensional case, the gapless soft graviton as well as the algebraic liquid phase are destroyed by the vertex operators in the dual theory, and the stripe order is most likely to take place close to the two-dimensional quantum critical point at which the vertex operators are tuned to zero."], "field": "Physics and Astronomy", "q_year": 2020, "q_cid": "214802334", "pos_cid": 119002657, "source": "train_step3"}
{"query_id": "scaleup_23559323_11918403", "query": "How to describe boundary relationships in an expanding space for quantities of any mass while preserving the expected behavior when the space becomes flat", "pos": ["Proof of the formula of Cachazo, He and Yuan for Yang-Mills tree amplitudes in arbitrary dimension. A bstractA proof is given of the formula, recently proposed by Cachazo, He and Yuan (CHY) for gluon tree amplitudes in pure Yang-Mills theory in arbitrary dimension. The approach is to first establish the corresponding result for massless ϕ3 theory using the BCFW recurrence relation and then to extend this to the gauge theory case. Additionally, it is shown that the scattering equations introduced by CHY can be generalized to massive particles, enabling the description of tree amplitudes for massive ϕ3 theory."], "field": "Physics and Astronomy", "q_year": 2021, "q_cid": "235593235", "pos_cid": 119184038, "source": "train_step3"}
{"query_id": "scaleup_26515019_24759540", "query": "How to establish relationships among system-level variables in large systems with interdependent component failures", "pos": ["Emergence and Breaking of Duality Symmetry in Generalized Fundamental Thermodynamic Relations.. Thermodynamics as limiting behaviors of statistics is generalized to arbitrary systems with probability a priori where the thermodynamic infinite-size limit is replaced by a multiple-measurement limit. A duality symmetry between Massieu's and Gibbs's entropy arises in the limit of infinitely repeated observations, yielding the Gibbs equation and Hill-Gibbs-Duhem equation (HGDE) as a dual pair. If a system has a thermodynamic limit satisfying Callen's postulate, entropy being an Eulerian function, the symmetry is lost: the HGDE reduces to the Gibbs-Duhem equation. This theory provides a de-mechanized foundation for classical and nanothermodynamics and offers a framework for distilling emergence from large data, free from underlying details."], "field": "Physics and Astronomy", "q_year": 2023, "q_cid": "265150194", "pos_cid": 247595402, "source": "train_step3"}
{"query_id": "scaleup_26549889_20920261", "query": "How to learn from noisy labels generated for unlabeled event data without destabilizing learning", "pos": ["Learning From Noisy Anchors for One-Stage Object Detection. State-of-the-art object detectors rely on regressing and classifying an extensive list of possible anchors, which are divided into positive and negative samples based on their intersection-over-union (IoU) with corresponding ground-truth objects. Such a harsh split conditioned on IoU results in binary labels that are potentially noisy and challenging for training. In this paper, we propose to mitigate noise incurred by imperfect label assignment such that the contributions of anchors are dynamically determined by a carefully constructed cleanliness score associated with each anchor. Exploring outputs from both regression and classification branches, the cleanliness scores, estimated without incurring any additional computational overhead, are used not only as soft labels to supervise the training of the classification branch but also sample re-weighting factors for improved localization and classification accuracy. We conduct extensive experiments on COCO, and demonstrate, among other things, the proposed approach steadily improves RetinaNet by ~2% with various backbones."], "field": "Physics and Astronomy", "q_year": 2023, "q_cid": "265498891", "pos_cid": 209202611, "source": "train_step3"}
{"query_id": "scaleup_26043144_53729285", "query": "How to enable soft robotic materials to autonomously capture cargo and avoid obstacles without step-by-step external control", "pos": ["Dielectrophoresis: From Molecular to Micrometer-Scale Analytes.. The complexity of biological analytes demands powerful analysis techniques in order to reveal cellular processes and pathways on the molecular level.1 Thus, ever refining analytical tools or combinations of various analysis techniques are required to reveal such complexities. Dielectrophoresis (DEP) refers to an analytical technique in which a polarizable particle experiences an attractive or repulsive force when placed in a non-uniform electric field. Realized in microenvironments, DEP phenomena have allowed innovative analytical applications due to the strong dependency on the size of the analyte in conjunction with its dielectric properties and are especially suitable for manipulating µm-sized, cellular bioanalytes. However, the demonstration of DEP for smaller sub-cellular entities or non-biological, sub-µm sized particles has been more difficult, as the required DEP forces impose design challenges.2 In addition, the structural complexity of sub-cellular bioanalytes, and the huge variety of microbes such as bacteria and viruses as well as innovative nanoparticles imposes the need of refined theoretical models as well as suitable DEP platforms for these analytes. Here, we specifically focus on recent DEP studies and applications for analyte dimensions below the size of a typical mammalian cells and include DEP studies related to microbes, sub-cellular entities such as organelles and exosomes but also to biomolecules such as nucleic acids and proteins. We also include non-biological analytes that fall under this size range and review related DEP applications in the past 10 years."], "field": "Physics and Astronomy", "q_year": 2023, "q_cid": "260431446", "pos_cid": 53729285, "source": "train_step3"}
{"query_id": "scaleup_27874211_20419973", "query": "How to selectively target a specific configuration in an interacting multi-particle system with microscopic scales, large configuration spaces, and non-conservative, non-reciprocal interactions", "pos": ["Noncontact Dynamic Oscillations of Acoustically Levitated Particles by Parametric Excitation. The phenomenon of $a\\phantom{\\rule{0}{0ex}}c\\phantom{\\rule{0}{0ex}}o\\phantom{\\rule{0}{0ex}}u\\phantom{\\rule{0}{0ex}}s\\phantom{\\rule{0}{0ex}}t\\phantom{\\rule{0}{0ex}}i\\phantom{\\rule{0}{0ex}}c$ $l\\phantom{\\rule{0}{0ex}}e\\phantom{\\rule{0}{0ex}}v\\phantom{\\rule{0}{0ex}}i\\phantom{\\rule{0}{0ex}}t\\phantom{\\rule{0}{0ex}}a\\phantom{\\rule{0}{0ex}}t\\phantom{\\rule{0}{0ex}}i\\phantom{\\rule{0}{0ex}}o\\phantom{\\rule{0}{0ex}}n$ has lately found application in noncontact particle manipulation in research laboratories, but is not mature enough for commercial use, as the dynamics of a levitated particle are not understood well enough. The authors derive a refined model for these particle dynamics, and use it with parametric excitation in real time to control the oscillations of one specific particle in a levitated group. This insight brings acoustic-levitator design a step closer to commercial reality."], "field": "Physics and Astronomy", "q_year": 2025, "q_cid": "278742115", "pos_cid": 204199736, "source": "train_step3"}
{"query_id": "scaleup_23900219_1371968", "query": "How to accurately estimate small tissue displacements in the male pelvis at successive times relative to a reference for an individualized intrafractional motion model", "pos": ["Determining Optical Flow. Optical flow cannot be computed locally, since only one independent measurement is available from the image sequence at a point, while the flow velocity has two components. A second constraint is needed. A method for finding the optical flow pattern is presented which assumes that the apparent velocity of the brightness pattern varies smoothly almost everywhere in the image. An iterative implementation is shown which successfully computes the optical flow for a number of synthetic image sequences. The algorithm is robust in that it can handle image sequences that are quantized rather coarsely in space and time. It is also insensitive to quantization of brightness levels and additive noise. Examples are included where the assumption of smoothness is violated at singular points or along lines in the image."], "field": "Physics and Astronomy", "q_year": 2021, "q_cid": "239002195", "pos_cid": 1371968, "source": "train_step3"}
{"query_id": "scaleup_27442323_23342318", "query": "How to efficiently optimize tunable parameters of physically implemented large quantum systems without extracting experimental gradients when their nonlinear dynamics cannot be efficiently simulated", "pos": ["Deep physical neural networks trained with backpropagation. Deep-learning models have become pervasive tools in science and engineering. However, their energy requirements now increasingly limit their scalability1. Deep-learning accelerators2–9 aim to perform deep learning energy-efficiently, usually targeting the inference phase and often by exploiting physical substrates beyond conventional electronics. Approaches so far10–22 have been unable to apply the backpropagation algorithm to train unconventional novel hardware in situ. The advantages of backpropagation have made it the de facto training method for large-scale neural networks, so this deficiency constitutes a major impediment. Here we introduce a hybrid in situ–in silico algorithm, called physics-aware training, that applies backpropagation to train controllable physical systems. Just as deep learning realizes computations with deep neural networks made from layers of mathematical functions, our approach allows us to train deep physical neural networks made from layers of controllable physical systems, even when the physical layers lack any mathematical isomorphism to conventional artificial neural network layers. To demonstrate the universality of our approach, we train diverse physical neural networks based on optics, mechanics and electronics to experimentally perform audio and image classification tasks. Physics-aware training combines the scalability of backpropagation with the automatic mitigation of imperfections and noise achievable with in situ algorithms. Physical neural networks have the potential to perform machine learning faster and more energy-efficiently than conventional electronic processors and, more broadly, can endow physical systems with automatically designed physical functionalities, for example, for robotics23–26, materials27–29 and smart sensors30–32. A hybrid algorithm that applies backpropagation is used to train layers of controllable physical systems to carry out calculations like deep neural networks, but accounting for real-world noise and imperfections."], "field": "Physics and Astronomy", "q_year": 2024, "q_cid": "274423233", "pos_cid": 233423180, "source": "train_step3"}
{"query_id": "scaleup_26043144_26392735", "query": "How to predict whether a hydrogel’s response requires light or occurs spontaneously under different acidity conditions", "pos": ["Characterization of the Thermal and Photoinduced Reactions of Photochromic Spiropyrans in Aqueous Solution. Six water-soluble spiropyran derivatives have been characterized with respect to the thermal and photoinduced reactions over a broad pH-interval. A comprehensive kinetic model was formulated including the spiro- and the merocyanine isomers, the respective protonated forms, and the hydrolysis products. The experimental studies on the hydrolysis reaction mechanism were supplemented by calculations using quantum mechanical (QM) models employing density functional theory. The results show that (1) the substitution pattern dramatically influences the pKa-values of the protonated forms as well as the rates of the thermal isomerization reactions, (2) water is the nucleophile in the hydrolysis reaction around neutral pH, (3) the phenolate oxygen of the merocyanine form plays a key role in the hydrolysis reaction. Hence, the nonprotonated merocyanine isomer is susceptible to hydrolysis, whereas the corresponding protonated form is stable toward hydrolytic degradation."], "field": "Physics and Astronomy", "q_year": 2023, "q_cid": "260431446", "pos_cid": 263927353, "source": "train_step3"}
{"query_id": "scaleup_24342267_17122673", "query": "How to determine the extent of agreement about mentees’ and mentors’ experiences", "pos": ["A Qualitative Framework for Collecting and Analyzing Data in Focus Group Research. Despite the abundance of published material on conducting focus groups, scant specific information exists on how to analyze focus group data in social science research. Thus, the authors provide a new qualitative framework for collecting and analyzing focus group data. First, they identify types of data that can be collected during focus groups. Second, they identify the qualitative data analysis techniques best suited for analyzing these data. Third, they introduce what they term as a micro-interlocutor analysis, wherein meticulous information about which participant responds to each question, the order in which each participant responds, response characteristics, the nonverbal communication used, and the like is collected, analyzed, and interpreted. They conceptualize how conversation analysis offers great potential for analyzing focus group data. They believe that their framework goes far beyond analyzing only the verbal communication of focus group participants, thereby increasing the rigor of focus group analyses in social science research."], "field": "Psychology", "q_year": 2016, "q_cid": "24342267", "pos_cid": 17122673, "source": "eval20x26"}
{"query_id": "scaleup_20590616_13239946", "query": "How to determine whether cognitive-control network connectivity differences in OCD reflect vulnerability to psychiatric symptoms or factors associated with remaining unaffected", "pos": ["The frontoparietal control system: A central role in mental health. Recent findings suggest the existence of a frontoparietal control system consisting of flexible hubs that regulate distributed systems (e.g., visual, limbic, motor) according to current task goals. A growing number of studies are reporting alterations of this control system across a striking range of mental diseases. We suggest this may reflect a critical role for the control system in promoting and maintaining mental health. Specifically, we propose that this system implements feedback control to regulate symptoms as they arise (e.g., excessive anxiety reduced via regulation of amygdala), such that an intact control system is protective against a variety of mental illnesses. Consistent with this possibility, recent results indicate that several major mental illnesses involve altered brain-wide connectivity of the control system, likely altering its ability to regulate symptoms. These results suggest that this “immune system of the mind” may be an especially important target for future basic and clinical research."], "field": "Psychology", "q_year": 2019, "q_cid": "205906162", "pos_cid": 13239946, "source": "eval20x26"}
{"query_id": "scaleup_25755792_17019178", "query": "How to reliably and validly assess the incidence of distress among professional rugby players", "pos": ["Validation Study of a Distress Screener. Objectives A 3-item screening instrument called the Distress Screener was developed for early identification of distress among employees on sick leave. The Distress Screener consists of three items obtained from the distress subscale of the four-dimensional symptom questionnaire (4DSQ). This study assessed an optimal cut-off point and validated the Distress Screener by relating it to the 4DSQ and to medical diagnoses. Methods 171 sick-listed employees filled in the Distress Screener and the 4DSQ (containing four subscales: distress, depression, anxiety and somatisation) and medical diagnoses were obtained from occupational physicians (OPs). The optimal cut-off point was assessed by computing sensitivity and specificity values. Validity was assessed by relating the Distress Screener score to the scores on 4DSQ subscales. In addition scores were compared to mental health medical diagnoses and the degree of similarity between two repeated measurements was obtained. Results Using the 4DSQ distress score >10 as reference standard, the optimal cut-off point of the Distress Screener was ≥4. Regarding validity, a high correlation (0.82) existed between the Distress Screener and the 4DSQ distress subscale and it was significantly different from the correlations with the other 4DSQ subscales. Also a high correlation existed for the test–retest reliability (0.83). Furthermore, a high score on the Distress Screener seemed to be related to the medical diagnosis ‘Stress-related complaints’. All low scores seemed to be related to the medical diagnosis ‘Other complaints’. Sensitivity (0.85) and specificity (0.78) values, and positive and negative predictive values of the screener were comparable to those of the 4DSQ distress subscale. Conclusions The Distress Screener is a valid instrument for use by the OP during consulting time as a quick scan for early identification of distress in employees on sick leave. The cut-off point ≥4 is useful for early identification of distress in employees on sick leave."], "field": "Psychology", "q_year": 2018, "q_cid": "25755792", "pos_cid": 17019178, "source": "eval20x26"}
{"query_id": "scaleup_3808249_6312833", "query": "How to reliably assess the role of specific brain regions in judging weight from observed actions despite individual variability in neural responses", "pos": ["Attenuation of N2 amplitude of laser-evoked potentials by theta burst stimulation of primary somatosensory cortex. Theta burst stimulation (TBS) is a special repetitive transcranial magnetic stimulation (rTMS) paradigm, where bursts of low-intensity stimuli are applied in the theta frequency. The aim of this study was to investigate the effect of neuronavigated TBS over primary somatosensory cortex (SI) on laser-evoked potentials (LEPs) and acute pain perception induced with Tm : YAG laser stimulation. The amplitude changes of the N1, N2, and P2 components of LEPs and related subjective pain rating scores of 12 healthy subjects were analyzed prior to and following continuous TBS (cTBS), intermittent TBS (iTBS), intermediate TBS (imTBS), and sham stimulation. Our results demonstrate that all active TBS paradigms significantly diminished the amplitude of the N2 component, when the hand contralateral to the site of TBS was laser-stimulated. Sham stimulation condition had no significant effect. The subjective pain perception also decreased during the experimental sessions, but did not differ significantly from the sham stimulation condition. The main finding of our study is that TBS over SI diminished the amplitude of the N2 component evoked from the contralateral side without any significant analgesic effects. Furthermore, imTBS produced responses similar to those observed by other forms of TBS induced excitability changes in the SI."], "field": "Psychology", "q_year": 2017, "q_cid": "3808249", "pos_cid": 6312833, "source": "eval20x26"}
{"query_id": "scaleup_19576425_16468104", "query": "How to judge the significance of small associations when weak short-term effects may not reflect their long-term importance", "pos": ["Evaluating Effect Size in Psychological Research: Sense and Nonsense. Effect sizes are underappreciated and often misinterpreted—the most common mistakes being to describe them in ways that are uninformative (e.g., using arbitrary standards) or misleading (e.g., squaring effect-size rs). We propose that effect sizes can be usefully evaluated by comparing them with well-understood benchmarks or by considering them in terms of concrete consequences. In that light, we conclude that when reliably estimated (a critical consideration), an effect-size r of .05 indicates an effect that is very small for the explanation of single events but potentially consequential in the not-very-long run, an effect-size r of .10 indicates an effect that is still small at the level of single events but potentially more ultimately consequential, an effect-size r of .20 indicates a medium effect that is of some explanatory and practical use even in the short run and therefore even more important, and an effect-size r of .30 indicates a large effect that is potentially powerful in both the short and the long run. A very large effect size (r = .40 or greater) in the context of psychological research is likely to be a gross overestimate that will rarely be found in a large sample or in a replication. Our goal is to help advance the treatment of effect sizes so that rather than being numbers that are ignored, reported without interpretation, or interpreted superficially or incorrectly, they become aspects of research reports that can better inform the application and theoretical development of psychological research."], "field": "Psychology", "q_year": 2019, "q_cid": "195764256", "pos_cid": 164681045, "source": "eval20x26"}
{"query_id": "scaleup_25475369_16307985", "query": "How to identify which anterior cingulate cortex subregions and emotion-related functions are relevant to long-term cognitive behavior therapy outcomes in social anxiety disorder", "pos": ["Emotional processing in anterior cingulate and medial prefrontal cortex. Negative emotional stimuli activate a broad network, including the medial prefrontal (mPFC) and anterior cingulate (ACC) cortices. An early influential view dichotomized these regions into dorsal-caudal “cognitive” and ventral-rostral “affective” subdivisions. In this review, we examine a wealth of recent research on negative emotions in animals and humans, using the example of fear/anxiety, and conclude that, contrary to the traditional dichotomy, both subdivisions make key contributions to emotional processing. Specifically, dorsal-caudal regions of the ACC/mPFC are involved in appraisal and expression of negative emotion, while ventral-rostral portions of the ACC/mPFC have a regulatory role with respect to limbic regions involved in generating emotional responses. Moreover, this new framework is broadly consistent with emerging data on other negative and positive emotions."], "field": "Psychology", "q_year": 2015, "q_cid": "25475369", "pos_cid": 16307985, "source": "eval20x26"}
{"query_id": "scaleup_8323219_14271280", "query": "How to understand military spouses’ collective experiences and concerns beyond the adverse impacts of deployment", "pos": ["A Pragmatic View of Thematic Analysis. Ethnographic interviews have become a commonly used qualitat ive methodology for collecting data (Aronson, 1992). Once the information is gathered, res earchers are faced with the decision on how to analyze the data. There are many ways to anal yze informants' talk about their experiences (Mahrer, 1988; Spradley, 1979; Taylor & Bogdan, 1984), a nd thematic analysis is one such way. Although thematic analysis has been described (Benner, 1985; Leininger, 1985; Taylor & Board, 1984), there is insufficient literature that outlines the pragmatic process of thematic analysis. This article attempts to outline the procedure for perform ing a thematic analysis. Creative Commons License This work is licensed under a Creative Commons Attribution-Noncommercial-Share Alike 4.0 License. This article is available in The Qualitative Report: http://nsuworks.nova.edu/tqr/vol2/iss1/3 A Pragmatic View of Thematic Analysis by Jodi Aronson The Qualitative Report, Volume 2, Number 1, Spring, 1994 Ethnographic interviews have become a commonly used qualitative methodology for collecting data (Aronson, 1992). Once the information is gathered, researchers are faced with the decision on how to analyze the data. There are many ways to analyze informants' talk about their experiences (Mahrer, 1988; Spradley, 1979; Taylor & Bogdan, 1984), and thematic analysis is one such way. Although thematic analysis has been described (Benner, 1985; Leininger, 1985; Taylor & Board, 1984), there is insufficient literature that outlines the pragmatic process of thematic analysis. This article attempts to outline the procedure for performing a thematic analysis. Performing a Thematic Analysis The ethnographic interview is a commonly used interviewing process employed by researchclinicians (Kuehl & Newfield, 1991; Kuehl, Newfield & Joanning, 1990; Newfield, Joanning, Kuehl, & Quinn, 1990; Newfield, Kuehl, Joanning & Quinn, 1991; William, 1992). From the conversations that take place in a therapy session or those that are encouraged for the sake of researching a process, ideas emerge that can be better understood under the control of a thematic analysis. Thematic analysis focuses on identifiable themes and patterns of living and/or behavior. The first step is to collect the data. Audiotapes should be collected to study the talk of a session or of an enthnographic interview (Spradley, 1979). From the transcribed conversations, patterns of experiences can be listed. This can come from direct quotes or paraphrasing common ideas. The following is an example. A family was interviewed to get a better understanding of their experience with a juvenile justice system. The entire interview was transcribed. The first pattern of experience listed, was the process of the juvenile being arrested, and the different explanations from the various family members. The second pattern of experience listed was the attitude that each family member had toward the process (Aronson, 1992). The next step to a thematic analysis is to identify all data that relate to the already classified patterns. To continue the above example, the identified patterns are then expounded on. All of the talk that fits under the specific pattern is identified and placed with the corresponding pattern. For example, each family member somehow named their \"attitude\" while they were speaking. The father stated that he is \"anti-statist,\" the mother said that she is \"protective,\" and the son stated that \"felt bad for what he had done\" (Aronson, 1992). The next step to a thematic analysis is to combine and catalogue related patterns into sub-themes. Themes are defined as units derived from patterns such as \"conversation topics, vocabulary, recurring activities, meanings, feelings, or folk sayings and proverbs\" (Taylor & Bogdan, 1989, p.131). Themes are identified by \"bringing together components or fragments of ideas or experiences, which often are meaningless when viewed alone\" (Leininger, 1985, p. 60). Themes that emerge from the informants' stories are pieced together to form a comprehensive picture of their collective experience. The \"coherence of ideas rests with the analyst who has rigorously studied how different ideas or components fit together in a meaningful way when linked together\" (Leininger, 1985, p. 60). Constas (1992) reiterates this point and states that the \"interpretative approach should be considered as a distinct point of origination\" (p. 258). When gathering sub-themes to obtain a comprehensive view of the information, it is easy to see a pattern emerging. When patterns emerge it is best to obtain feedback from the informants about them. This can be done as the interview is taking place or by asking the informants to give feedback from the transcribed conversations. In the former, the interviewer uses the informants' feedback to establish the next questions in the interview. In the latter, the interviewer transcribes the interview or the session, and asks the informants to provide feedback that is then incorporated in the theme analysis. The next step is to build a valid argument for choosing the themes. This is done by reading the related literature. By referring back to the literature, the interviewer gains information that allows him or herself to make inferences from the interview or therapy session. Once the themes have been collected and the literature has been studied, the researcher is ready to formulate theme statements to develop a story line. When the literature is interwoven with the findings, the story that the interviewer constructs is one that stands with merit. A developed story line helps the reader to comprehend the process, understanding, and motivation of the interviewer. References Aronson, J. (1992). The interface of family therapy and a juvenile arbitration and mediation program. Unpublished doctoral dissertation, Nova Southeastern University, Fort Lauderdale, FL. Benner, P. (1985). Quality of life: A phenomenological perspective on explanation, prediction, and understanding in nursing science. Advances in Nursing Science, 8(1), 1-14. Constas, M. A. (1992). Qualitative analysis as a public event: The documentation of category development procedures. American Educational Research Journal, 29(2), 253-266. Kuehl, B. P., & Newfield, N. A. (1991). Family listeners among the Nacirema: Their curative ceremonies and how the natives view them. Family Therapy Case Studies, 6(1), 55-66. Kuehl, B. P., Newfield, N. A., & Joanning, H. (1990). Toward a client-based description of family therapy. Journal of Family Psychology, 3(3), 310-321. Leininger, M. M. (1985). Ethnography and ethnonursing: Models and modes of qualitative data analysis. In M. M. Leininger (Ed.), Qualitative research methods in nursing (pp. 33-72). Orlando, FL: Grune & Stratton. Mahrer, A. R. (1988). Discovery-oriented psychotherapy research. American Psychologist, 43(9), 694-702. Newfield, N. A., Kuehl, B. P., Joanning, H., & Quinn, W. H. (1990). A mini-ethnography of the family therapy of adolescent drug abuse: The ambiguous experience. Alcoholism Treatment Quarterly, 7(2), 57-80. Newfield, N. A., Kuehl, B. P., Joanning, H., & Quinn, W. H. (1991). We can tell you about psychos and shrinks: An ethnography of the family therapy of adolescent substance abuse. In T. C. Todd & M. D. Selekman (Eds.), Family therapy approaches with adolescent substance abusers (pp. 277-310). Boston: Allyn & Bacon. Spradley, J. (1979). The ethnographic interview. New York: Holt, Rinehart and Winston. Taylor, S. J., & Bogdan, R. (1984). Introduction to qualitative research methods: The search for meanings. New York: John Wiley & Sons. William, J. L. (1992). Don't discuss it: Reconciling illness, dying, and death in a medical school anatomy laboratory. Family Systems Medicine, 10(1), 65-78. Jodi Aronson, Ph.D., LMFT is the Clinical Director of MCC Behavioral Care, 3313 West Commercial Boulevard, Suite 112, Fort Lauderdale, FL 33309."], "field": "Psychology", "q_year": 2014, "q_cid": "8323219", "pos_cid": 142712805, "source": "eval20x26"}
{"query_id": "scaleup_23886274_70680856", "query": "How to reduce dropout and improve treatment outcomes for bulimia nervosa while preserving accessibility and affordability", "pos": ["The impact of guidance on Internet-based mental health interventions — A systematic review. Abstract Introduction The aim of this study was to systematically review the impact of guidance on the efficacy of Internet-based interventions. Methods Included were RCTs with a comparison of (1) guided vs. unguided interventions, (2) different doses of guidance, (3) different qualification levels of e-coaches, and (4) synchronous vs. asynchronous communication mode. Outcomes were symptom severity, completer rates and number of completed intervention modules. A systematic search of MEDLINE, CENTRAL and PsycINFO, PsycARTICLES and Psyndex (search date 4th June 2013) was conducted, as well as a hand search of trial-registers and the reference lists of included articles. Methodological quality was rated using the Cochrane Risk of Bias tool. Relevant study characteristics and outcome data were extracted. Random-effects analyses were conducted if appropriate. Results 5328 articles were retrieved of which 14 fulfilled inclusion criteria. Guided interventions were significantly superior to unguided interventions ((symptom severity: standardized mean difference (SMD) = − .27 [95% CI: − .45; − .10]), n = 8; completed modules: SMD = .52 [.37; .67], n = 7; completer rate: OR = 2.76 [1.68; 4.53], n = 6). The four trials that examined different levels of e-coach qualification showed no significant differences on either of the outcome measures. Only one trial each examined the remaining two research questions, without significant effects on either of the outcome measures. Conclusions Guidance is a beneficial feature of Internet-based interventions, although its effect is smaller than reported before when compared to unguided interventions. The qualification of the e-coaches seems of minor importance. However, methodological limitations need to be considered when interpreting these findings. Overall, the number of studies was small and mainly limited to depression and social phobia restricting the generalizability of the findings."], "field": "Psychology", "q_year": 2021, "q_cid": "238862741", "pos_cid": 70680856, "source": "eval_collection"}
{"query_id": "scaleup_28389704_27485980", "query": "How to scale the coding of collaborative problem-solving discourse while preserving reliability and human control over coding decisions", "pos": ["Human-in-the-loop or AI-in-the-loop? Automate or Collaborate?. Human-in-the-loop (HIL) systems have emerged as a promising approach for combining the strengths of data-driven machine learning models with the contextual understanding of human experts. However, a deeper look into several of these systems reveals that calling them HIL would be a misnomer, as they are quite the opposite, namely AI-in-the-loop (AI2L) systems: the human is in control of the system, while the AI is there to support the human. We argue that existing evaluation methods often overemphasize the machine (learning) component's performance, neglecting the human expert's critical role. Consequently, we propose an AI2L perspective, which recognizes that the human expert is an active participant in the system, significantly influencing its overall performance. By adopting an AI2L approach, we can develop more comprehensive systems that faithfully model the intricate interplay between the human and machine components, leading to more effective and robust AI systems."], "field": "Psychology", "q_year": 2025, "q_cid": "283897045", "pos_cid": 274859808, "source": "eval_collection"}
{"query_id": "scaleup_27117689_25448842", "query": "How to process and integrate unexpected experiences that lack a suitable interpretive framework or conflict with a person’s worldview, and adequately describe changes in metaphysical beliefs and their relevance to outcomes", "pos": ["The roles and impacts of worldviews in the context of meditation-related challenges. Previous research has shown that worldviews can serve as a coping response to periods of difficulty or struggle, and worldviews can also change on account of difficulty. This paper investigates the impacts worldviews have on the nature and trajectory of meditation-related challenges, as well as how worldviews change or are impacted by such challenges. The context of meditation-related challenges provided by data from the Varieties of Contemplative Experience research project offers a unique insight into the dynamics between worldviews and meditation. Buddhist meditation practitioners and meditation experts interviewed for the study report how, for some, worldviews can serve as a risk factor impacting the onset and trajectory of meditation-related challenges, while, for others, worldviews (e.g., being given a worldview, applying a worldview, or changing a worldview) were reported as a remedy for mitigating challenging experiences and/or their associated distress. Buddhist meditation practitioners and teachers in the contemporary West are also situated in a cultural context in which religious and scientific worldviews and explanatory frameworks are dually available. Furthermore, the context of “Buddhist modernism” has also promoted a unique configuration in which the theory and practice of Buddhism is presented as being closely compatible with science. We identify and discuss the various impacts that religious and scientific worldviews have on meditation practitioners and meditation teachers who navigate periods of challenge associated with the practice."], "field": "Psychology", "q_year": 2024, "q_cid": "271176897", "pos_cid": 254488423, "source": "eval_collection"}
{"query_id": "scaleup_25679993_21415695", "query": "How to understand adolescents’ vulnerability associated with a lack of meaning in life", "pos": ["Cognitive failure susceptibility and personality: Self-directedness predicts everyday cognitive failure. Abstract Susceptibility to everyday cognitive failure is often assessed in clinical and vocational settings to estimate the effectiveness of interventions or to predict performance and performance decline in stressful situations. Comparatively little is known about the relationship between cognitive failure susceptibility as quantified by the Cognitive Failure Questionnaire (CFQ) and personality factors. We examined the relationships between the CFQ and the seven personality dimensions as assessed by the Temperament and Character Inventory (TCI). Through regression analyses with out-of-sample prediction in two samples, we explained around 18% of the variance in cognitive failure from personality scores. We established the character trait self-directedness as the main inversely related predictor of everyday cognitive failure. High cognitive failure thus seems to reflect low levels of self-confidence, self-acceptance, and responsibility for one's own actions which are the key aspects of self-directedness. This result provides evidence for the previously stated ‘complaint’ hypothesis that cognitive failure results from a poor self-image rather than a vulnerability to stress."], "field": "Psychology", "q_year": 2023, "q_cid": "256799931", "pos_cid": 214156950, "source": "eval_collection"}
{"query_id": "scaleup_26998662_96461829", "query": "How to distinguish explicit from implicit interactions in digital habit-formation interventions and clarify the roles of user intention, attention, and awareness when systems can sense the environment without deliberate user input", "pos": ["Explicating \"Implicit Interaction\": An Examination of the Concept and Challenges for Research. The term implicit interaction is often used to denote interactions that differ from traditional purposeful and attention demanding ways of interacting with computers. However, there is a lack of agreement about the term's precise meaning. This paper develops implicit interaction further as an analytic concept and identifies the methodological challenges related to HCI's particular design orientation. We first review meanings of implicit as unintentional, attentional background, unawareness, unconsciousness and implicature, and compare them in regards to the entity they qualify, the design motivation they emphasize and their constructive validity for what makes good interaction. We then demonstrate how the methodological challenges can be addressed with greater precision by using an updated, intentionality-based definition that specifies an input-effect relationship as the entity of implicit. We conclude by identifying a number of new considerations for design and evaluation, and by reflecting on the concepts of user and system agency in HCI."], "field": "Psychology", "q_year": 2024, "q_cid": "269986621", "pos_cid": 96461829, "source": "eval_collection"}
{"query_id": "scaleup_23365021_4785471", "query": "How to strengthen participants’ capacity to act and sustain action beyond deliberation while addressing root causes rather than symptoms", "pos": ["Habitual behaviors or patterns of practice? Explaining and changing repetitive climate‐relevant actions. Understanding human behavior lies at the heart of responses to climate change. Many environmentally relevant behavior patterns are frequent, stable, and persistent. There is an increasing focus on understanding these patterns less in terms of deliberative processes and more in terms of habits and routines embedded in everyday life. Examinations of the ‘habitual’ nature of environmentally consequential activities have been approached from two theoretically distinct perspectives. From a social psychological perspective, ‘habit’ is studied as an intra‐individual psychological construct that sustains ingrained behavior patterns in stable settings and obstructs adoption of more environmentally friendly alternatives. Sociologists from the social practice tradition, in contrast, have sought to highlight the ways in which resource‐intensive ‘habitual practices’ become established and maintained in society through a commingling of material, procedural, and socio‐discursive elements. We reflect critically upon key theoretical differences underpinning these two approaches to repetitive behaviors and review empirical work from both traditions that speaks to the relevance of ‘habitual behavior patterns’ central to addressing climate change. Finally, we examine how changes in habits are theorized and operationalized within both social psychological and social practice approaches, and practical implications for promoting environmentally sustainable societies. WIREs Clim Change 2015, 6:113–128. doi: 10.1002/wcc.327"], "field": "Psychology", "q_year": 2021, "q_cid": "233650216", "pos_cid": 4785471, "source": "eval_collection"}
{"query_id": "scaleup_24473003_11174435", "query": "How to identify distinct combinations of goals that individuals pursue simultaneously in sport and exercise", "pos": ["Introduction: The Person-oriented approach: Roots and roads to the future. This first issue of Journal for Person-Oriented Research is a special issue devoted to the presentation of person-oriented approaches taken by leading researchers in the area. A prototypic person-oriented approach has three characteristics: (1) A pattern focus, (2) A focus on the individual, and (3) A process focus. The approach includes a theoretical framework, based on the holistic-interactionistic research paradigm, and it usually implies using methods for studying individual development, particularly subject-specific methods, and methods for studying patterns of information as undivided “wholes”. Four papers in this special issue are theory-oriented, dealing with historical roots of the approach, implications of a person-oriented theory for the methodology applied in empirical research, and discussing conceptual issues, including definitions of terms and communalities and differences of a person-oriented approach to standard approaches. The next three articles concern the use of various forms of a multi-level approach that points to promising ways for further development of the person-oriented approach. In the penultimate article, a statistical package for person-oriented analysis (ROPstat) is introduced. In the last article, a dynamic systems approach is presented for studying adaptive equilibrium regulation that separates forces working at a short and a long timescale."], "field": "Psychology", "q_year": 2021, "q_cid": "244730039", "pos_cid": 111744357, "source": "eval_collection"}
{"query_id": "scaleup_22896424_37227262", "query": "How to classify perceived family resilience, characterize resilience within each category, and clarify differences across categories rather than describe only an overall resilience score for all respondents", "pos": ["Everyday Discrimination and Mood and Substance Use Disorders: A Latent Profile Analysis with African Americans and Caribbean Blacks. Perceived discrimination is a major source of health-related stress. The purpose of this study was to model the heterogeneity of everyday-discrimination experiences among African American and Caribbean Blacks and to identify differences in the prevalence of mood and substance use outcomes, including generalized anxiety disorder, major depressive disorder, alcohol-use disorder, and illicit drug-use disorder among the identified subgroups. The study uses data from the National Survey of American Life obtained from a sample of African American and Caribbean Black respondents (N = 4,462) between 18 and 65 years. We used latent profile analysis and multinomial regression analyses to identify and validate latent subgroups and test hypotheses, yielding 4 classes of perceived everyday discrimination: Low Discrimination, Disrespect and Condescension, General Discrimination, and Chronic Discrimination. Findings show significant differences exist between the Low Discrimination and General Discrimination classes for major depressive disorder, alcohol-use disorder, and illicit drug-use disorder. Moreover, we find significant differences exist between the Low Discrimination and Chronic Discrimination classes for the four disorders examined. Compared with the Chronic Discrimination class, members of the other classes were significantly less likely to meet criteria for generalized anxiety disorder, major depressive disorder, alcohol-use disorder, and illicit drug-use disorder. Findings suggest elevated levels of discrimination increase risk for mood and substance-use disorders. Importantly, results suggest the prevalence of mood and substance-use disorders is a function of the type and frequency of discrimination that individuals experience."], "field": "Psychology", "q_year": 2020, "q_cid": "228964241", "pos_cid": 37227262, "source": "eval_collection"}
{"query_id": "scaleup_26963076_25281761", "query": "How to determine which patients will respond to online cognitive behavioral therapy, which demographic and clinical factors influence treatment success, and who may need additional support", "pos": ["Predicting the Outcomes of Internet-Based Cognitive Behavioral Therapy for Tinnitus: Applications of Artificial Neural Network and Support Vector Machine.. PURPOSE Internet-based cognitive behavioral therapy (ICBT) has been found to be effective for tinnitus management, although there is limited understanding about who will benefit the most from ICBT. Traditional statistical models have largely failed to identify the nonlinear associations and hence find strong predictors of success with ICBT. This study aimed at examining the use of an artificial neural network (ANN) and support vector machine (SVM) to identify variables associated with treatment success in ICBT for tinnitus. METHOD The study involved a secondary analysis of data from 228 individuals who had completed ICBT in previous intervention studies. A 13-point reduction in Tinnitus Functional Index (TFI) was defined as a successful outcome. There were 33 predictor variables, including demographic, tinnitus, hearing-related and treatment-related variables, and clinical factors (anxiety, depression, insomnia, hyperacusis, hearing disability, cognitive function, and life satisfaction). Predictive models using ANN and SVM were developed and evaluated for classification accuracy. SHapley Additive exPlanations (SHAP) analysis was used to identify the relative predictor variable importance using the best predictive model for a successful treatment outcome. RESULTS The best predictive model was achieved with the ANN with an average area under the receiver operating characteristic value of 0.73 ± 0.03. The SHAP analysis revealed that having a higher education level and a greater baseline tinnitus severity were the most critical factors that influence treatment outcome positively. CONCLUSIONS Predictive models such as ANN and SVM help predict ICBT treatment outcomes and identify predictors of outcome. However, further work is needed to examine predictors that were not considered in this study as well as to improve the predictive power of these models. SUPPLEMENTAL MATERIAL https://doi.org/10.23641/asha.21266487."], "field": "Psychology", "q_year": 2024, "q_cid": "269630765", "pos_cid": 252817615, "source": "eval_collection"}
{"query_id": "scaleup_27057666_6311495", "query": "How to capture the complex interrelationships between occupational stress and job satisfaction without including unnecessary connections", "pos": ["Extended Bayesian Information Criteria for Gaussian Graphical Models. Gaussian graphical models with sparsity in the inverse covariance matrix are of significant interest in many modern applications. For the problem of recovering the graphical structure, information criteria provide useful optimization objectives for algorithms searching through sets of graphs or for selection of tuning parameters of other methods such as the graphical lasso, which is a likelihood penalization technique. In this paper we establish the consistency of an extended Bayesian information criterion for Gaussian graphical models in a scenario where both the number of variables p and the sample size n grow. Compared to earlier work on the regression case, our treatment allows for growth in the number of non-zero parameters in the true model, which is necessary in order to cover connected graphs. We demonstrate the performance of this criterion on simulated data when used in conjunction with the graphical lasso, and verify that the criterion indeed performs better than either cross-validation or the ordinary Bayesian information criterion when p and the number of non-zero parameters q both scale with n."], "field": "Psychology", "q_year": 2024, "q_cid": "270576662", "pos_cid": 6311495, "source": "eval_collection"}
{"query_id": "scaleup_25636821_23237116", "query": "How to understand participants’ experiences of mental healthcare in the carceral state, including changing life circumstances and previously mentioned events and topics requiring further exploration", "pos": ["Probing the processes: longitudinal qualitative research on social determinants of HIV. Longitudinal qualitative research can provide rich understanding of the life circumstances of vulnerable groups who experience health inequities, of whether, how and why these circumstances change, and of how these circumstances and processes of change impact health. But, this rich understanding is not automatic and requires systematic and thoughtful approaches to data collection and analysis. The purpose of this paper is to describe two longitudinal qualitative studies embedded in mixed-methods studies of social determinants of HIV in the United States and the Dominican Republic. We compare these two studies to critically reflect on specific techniques that facilitate longitudinal and iterative data collection, management, and analysis, in particular the use of participant-specific matrices and analytic summaries across the distinct phases of the research. We conclude that combining cross-sectional and longitudinal analysis that engages with both themes and processes of change can contribute to improved contextualization and understanding of social determinants of HIV."], "field": "Psychology", "q_year": 2022, "q_cid": "256368218", "pos_cid": 232371169, "source": "eval_collection"}
{"query_id": "scaleup_24428023_23691758", "query": "How to assess flexibility in reinforcement learning across development while distinguishing current-environment adaptation from environment-order effects when environments differ in the effort required to make good choices", "pos": ["Asymmetrical adaptations to increases and decreases in environmental volatility. Humans adapt their learning strategies to changing environments by estimating the volatility of the reinforcement conditions. Here, we examine how volatility affects learning and the underlying functional brain organizations using a probabilistic reward reversal learning task. We found that the order of conditions was critically important; participants adjusted learning rate going from volatile to stable, but not from stable to volatile, environments. Subjective volatility of the environment was encoded in the striatal reward system and its dynamic connections with the prefrontal control system. Flexibility, which captures the dynamic changes of network modularity in the brain, was higher in the environmental transition from volatile to stable than from stable to volatile. These findings suggest that behavioral adaptations and dynamic brain organizations in transitions between stable and volatile environments are asymmetric, providing critical insights into the way that people learn under uncertainty."], "field": "Psychology", "q_year": 2021, "q_cid": "244280235", "pos_cid": 236917588, "source": "eval_collection"}
{"query_id": "scaleup_23873079_21863070", "query": "How to improve healthcare quality for individuals in ICE detention who primarily speak a non-English language", "pos": ["Implications of Language Barriers for Healthcare: A Systematic Review. Objectives Language barriers pose challenges in terms of achieving high levels of satisfaction among medical professionals and patients, providing high- quality healthcare and maintaining patient safety. To address these challenges, many larger healthcare institutions offer interpreter services to improve healthcare access, patient satisfaction, and communication. However, these services increase the cost and duration of treatment. The purpose of this review is to investigate the impact of language barriers on healthcare and to suggest solutions to address the challenges. Methods We identified published studies on the implications of language barriers in healthcare using two databases: PubMed and Medline. We included 14 studies that met the selection criteria. These studies were conducted in various countries, both developed and developing, though most came from the US. The 14 studies included 300 918 total participants, with participation in each study ranging from 21 to 22 353 people. Results We found that language barriers in healthcare lead to miscommunication between the medical professional and patient, reducing both parties’ satisfaction and decreasing the quality of healthcare delivery and patient safety. In addition, the review found that interpreter services contribute indirectly to increased cost and the length of treatment visits. One study reported the implementation of online translation tools such as Google Translate and MediBabble in hospitals, which increased the satisfaction of both medical providers and patients (to 92%) and improved the quality of healthcare delivery and patient safety. Language barriers are responsible for reducing the satisfaction of medical providers and patients, as well as the quality of healthcare delivery and patient safety. Many healthcare institutions use interpreter services that increase the cost and length of treatment visits. Conclusions The results of our review suggest that implementing online translation tools such as Google Translate and MediBabble may improve the quality of healthcare and the level of satisfaction among both medical providers and patients."], "field": "Psychology", "q_year": 2021, "q_cid": "238730796", "pos_cid": 218630703, "source": "eval_collection"}
{"query_id": "scaleup_24473003_24040044", "query": "How to establish whether identified goal profiles differ meaningfully in self-determined motivation, sport and exercise activity levels and categories, and gender", "pos": ["Latent Class Analysis With Distal Outcomes: A Flexible Model-Based Approach. Although prediction of class membership from observed variables in latent class analysis is well understood, predicting an observed distal outcome from latent class membership is more complicated. A flexible model-based approach is proposed to empirically derive and summarize the class-dependent density functions of distal outcomes with categorical, continuous, or count distributions. A Monte Carlo simulation study is conducted to compare the performance of the new technique to 2 commonly used classify-analyze techniques: maximum-probability assignment and multiple pseudoclass draws. Simulation results show that the model-based approach produces substantially less biased estimates of the effect compared to either classify-analyze technique, particularly when the association between the latent class variable and the distal outcome is strong. In addition, we show that only the model-based approach is consistent. The approach is demonstrated empirically: latent classes of adolescent depression are used to predict smoking, grades, and delinquency. SAS syntax for implementing this approach using PROC LCA and a corresponding macro are provided."], "field": "Psychology", "q_year": 2021, "q_cid": "244730039", "pos_cid": 24040044, "source": "eval_collection"}
{"query_id": "scaleup_24538992_16764156", "query": "How to determine whether anorexia nervosa and smoking causally influence one another rather than merely occur together", "pos": ["Commentary: Two-sample Mendelian randomization: opportunities and challenges. In this volume of the IJE, Gao and colleagues explore the causal effect of adiposity on several cancers using two-sample Mendelian randomization (MR), and find some evidence that greater adult body mass index (BMI) causally reduces the risk of breast cancer while increasing ovarian, lung and colorectal cancer.1 The authors conclude that the study provides ‘…additional understanding of the complex relationship between adiposity and cancer risks’. Beyond the study findings themselves, this paper is interesting in its use of publicly available genome-wide association study (GWAS) summary data in a two-sample MR approach. Whereas MR has been increasingly used over the past decade since it was first proposed in the IJE,2 two-sample MR is a relatively recent extension.3 With the increasing availability of complete summary results from GWAS consortia that are easily accessible on the internet, the use of two-sample MR is likely to increase considerably over the next decade.4 By complete summary data I mean results for all genetic loci with a trait or disease outcome, and not just those reaching a pre-specified P-value threshold as shown in journal publications. It is this extensive availability of results that allows Gao et al. to relate genetic variants used as instrumental variables for adiposity traits to the cancer outcomes that they are interested in; the published GWAS for the cancer outcomes would not have reported on the adiposity variants unless they reached a pre-specified GWAS significance value."], "field": "Psychology", "q_year": 2021, "q_cid": "245389925", "pos_cid": 16764156, "source": "eval_collection"}
{"query_id": "scaleup_26683684_22016566", "query": "How to identify patterns relevant to minority stress and mental and sexual health in Arab sexual minority men’s experiences where sexual, ethnic/racial, and immigrant identities intersect within a sociocultural context", "pos": ["What can “thematic analysis” offer health and wellbeing researchers?. The field of health and wellbeing scholarship has a strong tradition of qualitative research*and rightly so. Qualitative research offers rich and compelling insights into the real worlds, experiences, and perspectives of patients and health care professionals in ways that are completely different to, but also sometimes complimentary to, the knowledge we can obtain through quantitative methods. (Published: 16 October 2014) Citation: Int J Qualitative Stud Health Well-being 2014, 9 : 26152 - http://dx.doi.org/10.3402/qhw.v9.26152"], "field": "Psychology", "q_year": 2024, "q_cid": "266836848", "pos_cid": 22016566, "source": "eval_collection"}
{"query_id": "scaleup_21889382_30717555", "query": "How to determine whether each proposed factor meets the requirements for inclusion in a study of the effect of longer shifts on staff sickness absence", "pos": ["Regression Discontinuity Designs Using Covariates. Abstract We study regression discontinuity designs when covariates are included in the estimation. We examine local polynomial estimators that include discrete or continuous covariates in an additive separable way, but without imposing any parametric restrictions on the underlying population regression functions. We recommend a covariate-adjustment approach that retains consistency under intuitive conditions and characterize the potential for estimation and inference improvements. We also present new covariate-adjusted mean-squared error expansions and robust bias-corrected inference procedures, with heteroskedasticity-consistent and cluster-robust standard errors. We provide an empirical illustration and an extensive simulation study. All methods are implemented in R and Stata software packages."], "field": "Psychology", "q_year": 2020, "q_cid": "218893828", "pos_cid": 30717555, "source": "eval_collection"}
{"query_id": "scaleup_27045452_25933050", "query": "How to understand why youth continue, begin, or stop volunteering during disruptions such as the COVID-19 pandemic", "pos": ["Service-Learning as Entry Into or Enhancement of University Volunteering? Student Characteristics at an Elective Service-Learning Institution. Abstract:Service-learning is a pedagogical practice that enhances university coursework through volunteering. Current challenges for the field are understanding the benefits of service-learning in relation to volunteering and with regard to pre-service student characteristics. Although students are the focus of service-learning research and practice, understanding how institutions structure service-learning is needed to appreciate its benefits. A model of institutional structuring of service-learning (offered or not, elective or mandatory) is presented. The model is used to inform a study of the academic, psychological, and prosocial characteristics among 266 undergraduate students enrolled in an elective service-learning course at a single large Canadian public university. The study revealed four groups of students: (a) service-learners with prior volunteer engagements, (b) volunteers, (c) non-volunteers, and (d) service-learners with no prior volunteer engagements. The paper is the first to identify and examine service-learners with no prior volunteer engagements and to situate these students in the context of other service-learners, volunteers, and non-volunteers. Although service-learners with prior volunteer engagement resembled volunteers, service-learners with no other volunteer engagement differed from all other groups. The findings are discussed with regard to the benefits of service-learning and volunteering in a variety of institutions."], "field": "Psychology", "q_year": 2024, "q_cid": "270454524", "pos_cid": 259330501, "source": "eval_collection"}
{"query_id": "scaleup_26431629_6409574", "query": "How to explain the selective association of social interaction rewards with otherwise neutral stimuli in romantic attraction and clarify dopamine’s role in that association", "pos": ["Dopaminergic reward system: a short integrative review. Memory is an essential element to adaptive behavior since it allows consolidation of past experience guiding the subject to consider them in future experiences. Among the endogenous molecules that participate in the consolidation of memory, including the drug-seeking reward, considered as a form of learning, is dopamine. This neurotransmitter modulates the activity of specific brain nucleus such as nuclei accumbens, putamen, ventral tegmental area (VTA), among others and synchronizes the activity of these nuclei to establish the neurobiological mechanism to set the hedonic element of learning. We review the experimental evidence that highlights the activity of different brain nuclei modulating the mechanisms whereby dopamine biases memory towards events that are of motivational significance."], "field": "Psychology", "q_year": 2023, "q_cid": "264316292", "pos_cid": 6409574, "source": "eval_collection"}
{"query_id": "scaleup_28310482_444498", "query": "How to assess the strength of associations between habitual avoidance, internalizing symptoms, and compulsive behaviors when ceiling effects in habit testing restrict response variability", "pos": ["Measurement of Individual Differences. An examination of test manuals and published research indicates that widely used memory tests (e.g., Verbal Paired Associates and Word List tests of the Wechsler Memory Scale, Rey Auditory Verbal Learning Test, and California Verbal Learning Test) are afflicted by severe ceiling effects. In the present study, the true extent of memory ability in healthy young adults was tested by giving 208 college undergraduates verbal paired-associate and verbal learning tests of various lengths; the findings demonstrate that healthy adults can remember much more than is suggested by the normative data for the memory tests just mentioned. The findings highlight the adverse effects of low ceilings in memory assessment and underscore the severe consequences of ceiling effects on score distributions, means, standard deviations, and all variability-dependent indices, such as reliability, validity, and correlations with other tests. The article discusses the optimal test lengths for verbal paired-associate and verbal list-learning tests, shows how to identify ceiling-afflicted data in published research, and explains how proper attention to this phenomenon can improve future research and clinical practice."], "field": "Psychology", "q_year": 2025, "q_cid": "283104820", "pos_cid": 444498, "source": "eval_collection"}
{"query_id": "scaleup_24654606_45198969", "query": "How to determine whether the BR-ACS questionnaire has comparable factor structure and item characteristics across genders and measures motivation for active commuting to school equivalently", "pos": ["Testing measurement invariance across groups: applications in cross-cultural research.. Researchers often compare groups of individuals on psychological variables. When comparing groups an assumption is made that the instrument measures the same psychological construct in all groups. If this assumption holds, the comparisons are valid and differences/similarities between groups can be meaningfully interpreted. If this assumption does not hold, comparisons and interpretations are not fully meaningful. The establishment of measurement invariance is a prerequisite for meaningful comparisons across groups. This paper first reviews the importance of equivalence in psychological research, and then the main theoretical and methodological issues regarding measurement invariance within the framework of confirmatory factor analysis. A step-by-step empirical example of measurement invariance testing is provided along with syntax examples for fitting such models in LISREL"], "field": "Psychology", "q_year": 2022, "q_cid": "246546067", "pos_cid": 45198969, "source": "eval_collection"}
{"query_id": "scaleup_25332455_73544834", "query": "How to protect animal welfare and conservation while avoiding commodification and exploitative photo opportunities in paid zoo animal–visitor encounters and preserving visitor income for animal care and conservation", "pos": ["Towards a Decommodified Wildlife Tourism: Why Market Environmentalism Is Not Enough for Conservation. Wildlife tourism is frequently touted as a solution to the problems of increased poaching, habitat destruction, and species extinction. When wildlife is able to pay for its right to survive through attracting tourists, there is an incentive to conserve wildlife populations and the habitats that support them. However, numerous reports in recent years have drawn attention to the potential negative impacts of wildlife tourism attractions. This paper examines whether market environmentalism diminishes the potential of wildlife tourism to contribute to conservation and the welfare of individual animals. Market environmentalism commodifies the animals involved in wildlife tourism attractions and fuels an anthropocentric worldview where animals are resources to be used by humans for entertainment or economic gain, potentially presenting a threat to long-term conservation. Instead, we call for a decommodified experience of wildlife tourism based on more than just economic value."], "field": "Psychology", "q_year": 2022, "q_cid": "253324558", "pos_cid": 73544834, "source": "eval_collection"}
{"query_id": "scaleup_28027980_18981283", "query": "How to explain changes in participants resulting from interactions within a caregiver group", "pos": ["Identifying change processes in group-based health behaviour-change interventions: development of the mechanisms of action in group-based interventions (MAGI) framework. ABSTRACT Group-based interventions are widely used to promote health-related behaviour change. While processes operating in groups have been extensively described, it remains unclear how behaviour change is generated in group-based health-related behaviour-change interventions. Understanding how such interventions facilitate change is important to guide intervention design and process evaluations. We employed a mixed-methods approach to identify, map and define change processes operating in group-based behaviour-change interventions. We reviewed multidisciplinary literature on group dynamics, taxonomies of change technique categories, and measures of group processes. Using weight-loss groups as an exemplar, we also reviewed qualitative studies of participants’ experiences and coded transcripts of 38 group sessions from three weight-loss interventions. Finally, we consulted group participants, facilitators and researchers about our developing synthesis of findings. The resulting ‘Mechanisms of Action in Group-based Interventions’ (MAGI) framework comprises six overarching categories: (1) group intervention design features, (2) facilitation techniques, (3) group dynamic and development processes, (4) inter-personal change processes, (5) selective intra-personal change processes operating in groups, and (6) contextual influences. The framework provides theoretical explanations of how change occurs in group-based behaviour-change interventions and can be applied to optimise their design and delivery, and to guide evaluation, facilitator training and further research."], "field": "Psychology", "q_year": 2025, "q_cid": "280279802", "pos_cid": 189812831, "source": "eval_collection"}
{"query_id": "scaleup_27095444_15632607", "query": "How to improve sales robots’ ability to encourage customers to engage with products and make purchases", "pos": ["Possession, feelings of ownership and the endowment effect. Research in judgment and decision making generally ignores the distinction between factual and subjective feelings of ownership, tacitly assuming that the two correspond closely. The present research suggests that this assumption might be usefully reexamined. In two experiments on the endowment effect we examine the role of subjective ownership by independently manipulating factual ownership (i.e., what participants were told about ownership) and physical possession of an object. This allowed us to disentangle the effects of these two factors, which are typically confounded. We found a significant effect of possession, but not of factual ownership, on monetary valuation of the object. Moreover, this effect was mediated by participants’ feelings of ownership, which were enhanced by the physical possession of the object. Thus, the endowment effect did not rely on factual ownership per se but was the result of subjective feelings of ownership induced by possession of the object. It is these feelings of ownership that appeared to lead individuals to include the object into their endowment and to shift their reference point accordingly. Potential implications and directions for future research are discussed."], "field": "Psychology", "q_year": 2024, "q_cid": "270954448", "pos_cid": 15632607, "source": "eval_collection"}
{"query_id": "scaleup_21153502_27129758", "query": "How to determine whether education can mitigate cognitive and motor impairments associated with probable rapid eye movement sleep behavior disorder in community-dwelling older adults", "pos": ["Efficiency, capacity, compensation, maintenance, plasticity: emerging concepts in cognitive reserve. Cognitive reserve (CR) is a concept meant to account for the frequent discrepancy between an individual’s measured level of brain pathology and her expected cognitive performance. It is particularly important within the context of aging and dementia, but has wider applicability to all forms of brain damage. As such, it has intimate links to related compensatory and neuroprotective concepts, as well as to the related notion of brain reserve. In this article, we introduce the concept of cognitive reserve and explicate its potential cognitive neural implementation. We conclude that cognitive reserve is compatible and complementary with many related concepts, but that each much draw sharper conceptual boundaries in order to truly explain preserved cognitive function in the face of aging or brain damage."], "field": "Psychology", "q_year": 2020, "q_cid": "211535022", "pos_cid": 27129758, "source": "eval_collection"}
{"query_id": "scaleup_28310482_20111943", "query": "How to distinguish outcome-insensitive habits from goal-directed responses to aversive outcomes in persistent threat avoidance", "pos": ["Enhanced Avoidance Habits in Relation to History of Early-Life Stress. The effect of stress on the balance between goal-directed behavior and stimulus–response habits has been demonstrated in a number of studies, but the extent to which stressful events that occur during development affect the balance between these systems later in life is less clear. Here, we examined whether individuals with a history of early-life stress (ELS) show a bias toward avoidance habits on an instrumental learning task as adults. Participants (N = 189 in Experiment 1 and N = 112 in Experiment 2) were undergraduate students at the University of California, Los Angeles. In Experiment 1, we hypothesized that a history of ELS and a longer training phase would be associated with greater avoidance habits. Participants learned to make button-press responses to visual stimuli in order to avoid aversive auditory outcomes. Following a training phase involving extensive practice of the responses, participants were tested for habitual responding using outcome devaluation. After completing the instrumental learning task, participants provided retrospective reports of stressful events they experienced during their first 16 years of life. We did not observe evidence for an effect of the length of training, but we did observe an effect of ELS, with greater stress predicting greater odds of performing the avoidance habit. In Experiment 2, we sought to replicate the effect of ELS observed in Experiment 1, and we also tested whether the presence of distraction during training would increase avoidance habit performance. We replicated the effect of ELS but we did not observe evidence of an effect of distraction. Taken together, these data lend support to the hypothesis that stress occurring during development can have lasting effects on the balance between goal-directed behavior and stimulus–response habits in humans. Enhancement of avoidance habits may help explain the higher levels of negative health outcomes such as heart and liver disease that have been observed in individuals with a history of ELS. Some of the negative health behaviors that contribute to these negative health outcomes, e.g., overeating and substance use, may be performed initially to avoid feelings of distress and then transition to being performed habitually."], "field": "Psychology", "q_year": 2025, "q_cid": "283104820", "pos_cid": 201119437, "source": "eval_collection"}
{"query_id": "scaleup_27783416_22554897", "query": "How to establish a rigorous, impartial, and comprehensive picture of mindfulness research in business contexts and its development, and identify underexplored topics and future research priorities", "pos": ["CSR reporting: a review of research and agenda for future research. Purpose - This paper aims to provide a systematic review of the published literature on corporate social responsibility reporting (CSRR). Furthermore, it assesses the main limitations reported in previous CSRR studies and offers recommendations for best practice and future research. Design/methodology/approach - A review protocol was developed to search nine major databases over a decade (2005–2017) using specific keywords. As a result, 221 articles were identified that deal explicitly with CSRR in both developed and developing countries, and a descriptive analysis was undertaken. Findings - Findings of the review show that scholarly work on CSRR across the globe have increased exponentially. However, there still remain quite a few countries and industries that have been underrepresented in CSRR literature. Moreover, methodological- and sampling-related limitations have been noted by a number of scholars in the area. Based on these results, the review provides directions for future research. Originality/value - The review provides a categorised bibliography of CSRR research on developed and developing countries from 2005 to 2017, covering a range of journals and countries. The review provides state of the art of the CSRR research and highlights the major loopholes in the current literature. This is a valuable study for academics pursuing research on CSRR as it provides a comprehensive and critical discussion on academic research in the field."], "field": "Psychology", "q_year": 2025, "q_cid": "277834169", "pos_cid": 225548975, "source": "eval_collection"}
{"query_id": "scaleup_22076876_19898136", "query": "How to determine which previously associated factors uniquely matter for well-being or productivity among professionals abruptly forced to work from home during COVID-19 restrictions", "pos": ["Soft Theory: A Pragmatic Alternative to Conduct Quantitative Empirical Studies. Practitioners and scholars often face new software engineering phenomena which lack sufficient theoretical grounding. When studying such nascent and emerging topics, it is important to establish an initial and rudimentary understanding, leaving a more precise understanding of underpinning mechanisms till later. Controlled experiments, for example, might lead to insights into the specific mechanisms underpinning a certain practice, such as distributed development, pair programming, and test-driven development. However, at an initial stage of research, such highly controlled studies may not be feasible. In other domains, it may not be clear what the key constructs are, so that effective measurement cannot be done. Instead, researchers might opt for pragmatic alternative research approaches that do not require experimental control or active intervention in a study's setting. In this paper we advocate the use of soft theory (based on soft modeling techniques) for quantitative studies in software engineering research. We discuss the use of soft theory and position it within an existing taxonomy of quantitative data analysis techniques. Soft modeling and soft theory affords us a pragmatic approach to developing inferential and predictive research models, rather than aiming to develop a causal understanding. Soft theory approaches are grounded in robust quantitative data analysis techniques. We argue that these techniques can be effectively used in industry settings which are not amenable to highly controlled studies."], "field": "Psychology", "q_year": 2020, "q_cid": "220768766", "pos_cid": 198981361, "source": "eval_collection"}
{"query_id": "scaleup_25185037_16266885", "query": "How to determine whether the mental health impacts of nearby firearm homicide exposure differ between youth at lower and higher risk of that exposure, which disproportionately affects disadvantaged and marginalized youth", "pos": ["Estimating Heterogeneous Treatment Effects with Observational Data. Individuals differ not only in their background characteristics but also in how they respond to a particular treatment, intervention, or stimulation. In particular, treatment effects may vary systematically by the propensity for treatment. In this paper, we discuss a practical approach to studying heterogeneous treatment effects as a function of the treatment propensity, under the same assumption commonly underlying regression analysis: ignorability. We describe one parametric method and two nonparametric methods for estimating interactions between treatment and the propensity for treatment. For the first method, we begin by estimating propensity scores for the probability of treatment given a set of observed covariates for each unit and construct balanced propensity score strata; we then estimate propensity score stratum-specific average treatment effects and evaluate a trend across them. For the second method, we match control units to treated units based on the propensity score and transform the data into treatment-control comparisons at the most elementary level at which such comparisons can be constructed; we then estimate treatment effects as a function of the propensity score by fitting a nonparametric model as a smoothing device. For the third method, we first estimate nonparametric regressions of the outcome variable as a function of the propensity score separately for treated units and for control units and then take the difference between the two nonparametric regressions. We illustrate the application of these methods with an empirical example of the effects of college attendance on women’s fertility."], "field": "Psychology", "q_year": 2022, "q_cid": "251850378", "pos_cid": 16266885, "source": "eval_collection"}
{"query_id": "scaleup_27746002_14308899", "query": "How to identify the key aspects of managers’ and employees’ experiences of the transition to activity-based workplaces relevant to health promotion", "pos": ["The qualitative content analysis process.. AIM This paper is a description of inductive and deductive content analysis. BACKGROUND Content analysis is a method that may be used with either qualitative or quantitative data and in an inductive or deductive way. Qualitative content analysis is commonly used in nursing studies but little has been published on the analysis process and many research books generally only provide a short description of this method. DISCUSSION When using content analysis, the aim was to build a model to describe the phenomenon in a conceptual form. Both inductive and deductive analysis processes are represented as three main phases: preparation, organizing and reporting. The preparation phase is similar in both approaches. The concepts are derived from the data in inductive content analysis. Deductive content analysis is used when the structure of analysis is operationalized on the basis of previous knowledge. CONCLUSION Inductive content analysis is used in cases where there are no previous studies dealing with the phenomenon or when it is fragmented. A deductive approach is useful if the general aim was to test a previous theory in a different situation or to compare categories at different time periods."], "field": "Psychology", "q_year": 2025, "q_cid": "277460026", "pos_cid": 14308899, "source": "eval_collection"}
{"query_id": "scaleup_28027980_23677859", "query": "How to determine whether a caregiver support programme developed for low- and middle-income countries meets the needs of ethnically and linguistically diverse, economically deprived UK communities", "pos": ["Adapting interventions to new contexts—the ADAPT guidance. Implementing interventions with a previous evidence base in new contexts might be more efficient than developing new interventions for each context. Although some interventions transfer well, effectiveness and implementation often depend on the context. Achieving a good fit between intervention and context then requires careful and systematic adaptation. This paper presents new evidence and consensus informed guidance for adapting and transferring interventions to new contexts."], "field": "Psychology", "q_year": 2025, "q_cid": "280279802", "pos_cid": 236778591, "source": "eval_collection"}
{"query_id": "scaleup_24538992_3822103", "query": "How to assess the reliability of the estimated relationship between anorexia nervosa and smoking given weak inputs and measurement error", "pos": ["Assessing the suitability of summary data for two-sample Mendelian randomization analyses using MR-Egger regression: the role of the I2 statistic. Background MR-Egger regression has recently been proposed as a method for Mendelian randomization (MR) analyses incorporating summary data estimates of causal effect from multiple individual variants, which is robust to invalid instruments. It can be used to test for directional pleiotropy and provides an estimate of the causal effect adjusted for its presence. MR-Egger regression provides a useful additional sensitivity analysis to the standard inverse variance weighted (IVW) approach that assumes all variants are valid instruments. Both methods use weights that consider the single nucleotide polymorphism (SNP)-exposure associations to be known, rather than estimated. We call this the `NO Measurement Error’ (NOME) assumption. Causal effect estimates from the IVW approach exhibit weak instrument bias whenever the genetic variants utilized violate the NOME assumption, which can be reliably measured using the F-statistic. The effect of NOME violation on MR-Egger regression has yet to be studied. Methods An adaptation of the I2 statistic from the field of meta-analysis is proposed to quantify the strength of NOME violation for MR-Egger. It lies between 0 and 1, and indicates the expected relative bias (or dilution) of the MR-Egger causal estimate in the two-sample MR context. We call it IGX2. The method of simulation extrapolation is also explored to counteract the dilution. Their joint utility is evaluated using simulated data and applied to a real MR example. Results In simulated two-sample MR analyses we show that, when a causal effect exists, the MR-Egger estimate of causal effect is biased towards the null when NOME is violated, and the stronger the violation (as indicated by lower values of IGX2), the stronger the dilution. When additionally all genetic variants are valid instruments, the type I error rate of the MR-Egger test for pleiotropy is inflated and the causal effect underestimated. Simulation extrapolation is shown to substantially mitigate these adverse effects. We demonstrate our proposed approach for a two-sample summary data MR analysis to estimate the causal effect of low-density lipoprotein on heart disease risk. A high value of IGX2 close to 1 indicates that dilution does not materially affect the standard MR-Egger analyses for these data. Conclusions Care must be taken to assess the NOME assumption via the IGX2 statistic before implementing standard MR-Egger regression in the two-sample summary data context. If IGX2 is sufficiently low (less than 90%), inferences from the method should be interpreted with caution and adjustment methods considered."], "field": "Psychology", "q_year": 2021, "q_cid": "245389925", "pos_cid": 3822103, "source": "eval_collection"}
{"query_id": "scaleup_24443420_15201553", "query": "How to address Covid-19-related suffering and trauma while supporting constructive expression of distressing feelings, hope, solidarity, empathy, and togetherness", "pos": ["Visual methodologies for research with refugee youth. Abstract In the current moment of social, political, economic and environmental disquiet, unprecedented numbers of children have been forced to leave their homes and settle in new communities. As schools worldwide receive increasing numbers of refugee youth, there is a pressing need for thoughtful educational research that inquires into the unique individual needs and experiences of displaced learners. Given that students’ journeys are shaped by movements across physical, cultural and linguistic spaces, we suggest that related scholarship might benefit from Third Space theory. Within this theoretical framework, neither language nor culture is static. Rather, both are continuously shaped through interactions – including those that are non-verbal. For students who may be learning in an unfamiliar language, visual methodologies offer a means and venue for communication. To explore how refugee youth might benefit from Third Space theory and visual methodologies, we first review scholarship that examines how children and schools negotiate educational space. We then describe a series of methodologies that scholars might consider when conducting research with refugee youth, including photovoice, fotonovela, digital storytelling and quilting. Significantly, pairing a Third Space theoretical framework with visual and participatory methodologies may address issues of language, power, vulnerability and ethics."], "field": "Psychology", "q_year": 2021, "q_cid": "244434204", "pos_cid": 152015534, "source": "eval_collection"}
{"query_id": "scaleup_28317938_31493918", "query": "How to assess lifetime and recent psychological, physical, and sexual violence against transgender women across different perpetrator types", "pos": ["Validity of the WHO VAW study instrument for estimating gender-based violence against women.. OBJECTIVE To validate the instrument of the World Health Organization Violence Against Women (WHO VAW) study on psychological, physical and sexual violence against women perpetrated by intimate partners. METHODS This was a cross-sectional study conducted in several countries between 2000 and 2003, including Brazil. Representative random samples of women aged 15-49 years with intimate partners were selected, living in the city of São Paulo (n = 940) and in the Zona da Mata, Pernambuco (n = 1,188), southeastern and northeastern regions, respectively. Exploratory factor analysis on questions relating to violence was performed (four psychological, six physical and three sexual questions), with varimax rotation and creation of three factors. Cronbach's alpha was calculated to analyze the internal consistency. To validate through extreme groups, mean scores (0 to 13 points) for violence were tested in relation to the following outcomes: self-rated health, daily activities, presence of discomfort or pain, suicidal ideation or attempts, heavy alcohol consumption and presence of common mental disorders. RESULTS Three factors were defined, with similar accumulated variance (0.6092 in São Paulo and 0.6350 in the Zona da Mata). For São Paulo, the first factor was determined by physical violence, the second by sexual violence and the third by psychological violence. For the Zona da Mata, the first factor was formed by psychological violence, the second by physical violence and the third by sexual violence. Cronbach's alpha coefficients were 0.88 in São Paulo and 0.89 in the Zona da Mata. The mean scores for violence were significantly higher for less favorable outcomes, with the exception of suicide attempts in São Paulo. CONCLUSIONS The instrument was shown to be adequate for estimating gender-based violence against women perpetrated by intimate partners and can be used in studies on this subject. It has high internal consistency and a capacity to discriminate between different forms of violence (psychological, physical and sexual) perpetrated in different social contexts. The instrument also characterizes the female victim and her relationship with the aggressor, thereby facilitating gender analysis."], "field": "Psychology", "q_year": 2025, "q_cid": "283179382", "pos_cid": 31493918, "source": "eval_collection"}
{"query_id": "scaleup_28267876_21241594", "query": "How to accurately assess the abilities of Cantonese-speaking people in Hong Kong without confounding effects from poorer performance with other-race than own-race individuals", "pos": ["The Own-Race Bias for Face Recognition in a Multiracial Society. The own-race bias (ORB) is a reliable phenomenon across cultural and racial groups where unfamiliar faces from other races are usually remembered more poorly than own-race faces (Meissner and Brigham, 2001). By adopting a yes–no recognition paradigm, we found that ORB was pronounced across race groups (Malaysian–Malay, Malaysian–Chinese, Malaysian–Indian, and Western–Caucasian) when faces were presented with only internal features (Experiment 1), implying that growing up in a profoundly multiracial society does not necessarily eliminate ORB. Using a procedure identical to Experiment 1, we observed a significantly greater increment in recognition performance for other-race faces than for own-race faces when the external features (e.g. facial contour and hairline) were presented along with the internal features (Experiment 2)—this abolished ORB. Contrary to assumptions based on the contact hypothesis, participants’ self-reported amount of interracial contact on a social contact questionnaire did not significantly predict the magnitude of ORB. Overall, our findings suggest that the level of exposure to other-race faces accounts for only a small part of ORB. In addition, the present results also support the notion that different neural mechanisms may be involved in processing own- and other-race faces, with internal features of own-race faces being processed more effectively, whereas external features dominate representations of other-race faces."], "field": "Psychology", "q_year": 2025, "q_cid": "282678765", "pos_cid": 212415943, "source": "eval_collection"}
{"query_id": "scaleup_23621361_20629212", "query": "How to clarify the relationship between escape room design and students’ learning, motivation, and social behaviour, and how these outcomes relate to students’ experiences", "pos": ["Combining qualitative and quantitative research within mixed method research designs: A methodological review. Objectives It has been argued that mixed methods research can be useful in nursing and health science because of the complexity of the phenomena studied. However, the integration of qualitative and quantitative approaches continues to be one of much debate and there is a need for a rigorous framework for designing and interpreting mixed methods research. This paper explores the analytical approaches (i.e. parallel, concurrent or sequential) used in mixed methods studies within healthcare and exemplifies the use of triangulation as a methodological metaphor for drawing inferences from qualitative and quantitative findings originating from such analyses. Design This review of the literature used systematic principles in searching CINAHL, Medline and PsycINFO for healthcare research studies which employed a mixed methods approach and were published in the English language between January 1999 and September 2009. Results In total, 168 studies were included in the results. Most studies originated in the United States of America (USA), the United Kingdom (UK) and Canada. The analytic approach most widely used was parallel data analysis. A number of studies used sequential data analysis; far fewer studies employed concurrent data analysis. Very few of these studies clearly articulated the purpose for using a mixed methods design. The use of the methodological metaphor of triangulation on convergent, complementary, and divergent results from mixed methods studies is exemplified and an example of developing theory from such data is provided. Conclusion A trend for conducting parallel data analysis on quantitative and qualitative data in mixed methods healthcare research has been identified in the studies included in this review. Using triangulation as a methodological metaphor can facilitate the integration of qualitative and quantitative findings, help researchers to clarify their theoretical propositions and the basis of their results. This can offer a better understanding of the links between theory and empirical findings, challenge theoretical assumptions and develop new theory."], "field": "Psychology", "q_year": 2021, "q_cid": "236213610", "pos_cid": 20629212, "source": "eval_collection"}
{"query_id": "scaleup_24428023_472686", "query": "How to determine how the balance between learning from better- and worse-than-expected outcomes changes from childhood to adulthood across environments with different reward patterns", "pos": ["Neural and Psychological Maturation of Decision-making in Adolescence and Young Adulthood. We examined the maturation of decision-making from early adolescence to mid-adulthood using fMRI of a variant of the Iowa gambling task. We have previously shown that performance in this task relies on sensitivity to accumulating negative outcomes in ventromedial PFC and dorsolateral PFC. Here, we further formalize outcome evaluation (as driven by prediction errors [PE], using a reinforcement learning model) and examine its development. Task performance improved significantly during adolescence, stabilizing in adulthood. Performance relied on greater impact of negative compared with positive PEs, the relative impact of which matured from adolescence into adulthood. Adolescents also showed increased exploratory behavior, expressed as a propensity to shift responding between options independently of outcome quality, whereas adults showed no systematic shifting patterns. The correlation between PE representation and improved performance strengthened with age for activation in ventral and dorsal PFC, ventral striatum, and temporal and parietal cortices. There was a medial-lateral distinction in the prefrontal substrates of effective PE utilization between adults and adolescents: Increased utilization of negative PEs, a hallmark of successful performance in the task, was associated with increased activation in ventromedial PFC in adults, but decreased activation in ventrolateral PFC and striatum in adolescents. These results suggest that adults and adolescents engage qualitatively distinct neural and psychological processes during decision-making, the development of which is not exclusively dependent on reward-processing maturation."], "field": "Psychology", "q_year": 2021, "q_cid": "244280235", "pos_cid": 472686, "source": "eval_collection"}
{"query_id": "scaleup_23794884_16558889", "query": "How to estimate the effect of body mass index on work hours in longitudinal data when the effect may vary across body mass index levels", "pos": ["Dynamic panels with threshold effect and endogeneity. This paper addresses an important issue of modeling nonlinear asymmetric dynamics and unobserved individual heterogeneity in the threshold panel data framework, simultaneously. As a general approach, we develop the first-differenced GMM estimator, which allows both threshold variable and regressors to be endogenous. When the threshold variable becomes strictly exogenous, we propose a more efficient two-step least squares estimator. We provide asymptotic theory and develop the testing procedure for threshold effects and the threshold variable exogeneity. Monte Carlo studies provide a support for theoretical predictions. We present an empirical application investigating an asymmetric sensitivity of investment to cash flows."], "field": "Psychology", "q_year": 2021, "q_cid": "237948848", "pos_cid": 16558889, "source": "eval_collection"}
{"query_id": "scaleup_26997282_56517517", "query": "How to predict patients’ risk of developing depressive symptoms when self-reported feelings are interrelated, only small datasets are available, and larger biomarker research datasets are difficult to obtain", "pos": ["Graph Neural Networks: A Review of Methods and Applications. Lots of learning tasks require dealing with graph data which contains rich relation information among elements. Modeling physics system, learning molecular fingerprints, predicting protein interface, and classifying diseases require a model to learn from graph inputs. In other domains such as learning from non-structural data like texts and images, reasoning on extracted structures, like the dependency tree of sentences and the scene graph of images, is an important research topic which also needs graph reasoning models. Graph neural networks (GNNs) are connectionist models that capture the dependence of graphs via message passing between the nodes of graphs. Unlike standard neural networks, graph neural networks retain a state that can represent information from its neighborhood with arbitrary depth. Although the primitive GNNs have been found difficult to train for a fixed point, recent advances in network architectures, optimization techniques, and parallel computation have enabled successful learning with them. In recent years, systems based on variants of graph neural networks such as graph convolutional network (GCN), graph attention network (GAT), gated graph neural network (GGNN) have demonstrated ground-breaking performance on many tasks mentioned above. In this survey, we provide a detailed review over existing graph neural network models, systematically categorize the applications, and propose four open problems for future research."], "field": "Psychology", "q_year": 2024, "q_cid": "269972823", "pos_cid": 56517517, "source": "eval_collection"}
{"query_id": "scaleup_26431629_37404831", "query": "How to determine whether the psychological features and progression of early romantic love, including preoccupation relative to early parental love, support an evolutionary origin in mother–infant bonding rather than an independently evolved emotion system", "pos": ["Preoccupations and behaviors associated with romantic and parental love. Perspectives on the origin of obsessive-compulsive disorder.. This article first examines the hypothesis that the early phases of romantic love and early parental love share phenomenologically an overlapping set of mental states and behaviors. Second, the authors consider what is known of the neurobiologic substrates of these behaviors. Third, the authors evaluate the hypothesis that these highly conserved behavioral and neural systems and the genetic messages that guide their development are intimately involved in the pathogenesis of OCD."], "field": "Psychology", "q_year": 2023, "q_cid": "264316292", "pos_cid": 37404831, "source": "eval_collection"}
{"query_id": "scaleup_25165889_29572510", "query": "How to draw conclusions about observational learning in physical education from limited study evidence that reflect its reliability rather than the number of studies", "pos": ["Best evidence synthesis: an intelligent alternative to meta-analysis.. Research review has long been one of the most important scholarly activities in all branches of science. While there is sometimes a single study so well-designed, well carried out, and difficult to replicate that its findings are accepted as conclusive, more often there are many studies on a given topic, no one of which clearly supersedes the others. These studies may be done by different investigators using different methods or different populations. They may arrive at different conclusions. When this is the case, there is a need for reviewers to carefully consider the evidence and to put forth conclusions or hypotheses about where the weight of the evidence lies."], "field": "Psychology", "q_year": 2022, "q_cid": "251658893", "pos_cid": 29572510, "source": "eval_collection"}
{"query_id": "scaleup_25312578_15500694", "query": "How to clarify the relationship between kindergarten teachers’ motivation and their intention to stay in their current roles in ethnic minority areas of China", "pos": ["The impact of management on the engagement and well-being of high emotional labour employees. Australia, like many other countries, suffers high turnover of nurses and police officers. Contributions to effectively manage the turnover challenge have been called for, and there are few Australian studies of nursing/policing turnover intentions. The purpose of this study was to examine the impact of supervisor–subordinate relationships and perceived organisational support (POS) upon engagement, well-being, organisational commitment and turnover intentions. Second, we examined the similarities and differences between nursing and policing work contexts. The retention of nurses/police has been investigated from traditional management perspectives; however, we used a different theoretical approach – social exchange theory – and evaluated its utility as a framework. Findings are from Australian data collected during 2010–2011 from 510 nurses and 193 police officers, using a survey-based, self-report strategy. Partial least squares path modelling was used to analyse these data. Results indicated that for both samples, engagement predicts well-being and then, well-being predicts affective commitment and intentions to leave. MANOVA results suggested that nurses had significantly higher levels of satisfaction with their supervisor–subordinate relationships, POS, engagement, well-being and affective commitment than police officers. Only the intention to leave was similar for both groups. Given that turnover can be influenced by supervisors/management, this study provides new knowledge about targeted retention strategies."], "field": "Psychology", "q_year": 2022, "q_cid": "253125782", "pos_cid": 155006941, "source": "eval_collection"}
{"query_id": "scaleup_26047485_21452972", "query": "How to understand the relationship between pandemic-related changes in physical activity, sedentary behavior, and children’s mental well-being in the context of COVID-19 restrictions, concerns, and daily experiences", "pos": ["How to Construct a Mixed Methods Research Design. This article provides researchers with knowledge of how to design a high quality mixed methods research study. To design a mixed study, researchers must understand and carefully consider each of the dimensions of mixed methods design, and always keep an eye on the issue of validity. We explain the seven major design dimensions: purpose, theoretical drive, timing (simultaneity and dependency), point of integration, typological versus interactive design approaches, planned versus emergent design, and design complexity. There also are multiple secondary dimensions that need to be considered during the design process. We explain ten secondary dimensions of design to be considered for each research study. We also provide two case studies showing how the mixed designs were constructed."], "field": "Psychology", "q_year": 2021, "q_cid": "260474857", "pos_cid": 21452972, "source": "eval_collection"}
{"query_id": "scaleup_54064700_4836709", "query": "How to estimate the effect of educational class on first childbirth without distortion from focusing only on people who enter first marriage", "pos": ["Endogenous Selection Bias: The Problem of Conditioning on a Collider Variable. Endogenous selection bias is a central problem for causal inference. Recognizing the problem, however, can be difficult in practice. This article introduces a purely graphical way of characterizing endogenous selection bias and of understanding its consequences (Hernán et al. 2004). We use causal graphs (direct acyclic graphs, or DAGs) to highlight that endogenous selection bias stems from conditioning (e.g., controlling, stratifying, or selecting) on a so-called collider variable, i.e., a variable that is itself caused by two other variables, one that is (or is associated with) the treatment and another that is (or is associated with) the outcome. Endogenous selection bias can result from direct conditioning on the outcome variable, a post-outcome variable, a post-treatment variable, and even a pre-treatment variable. We highlight the difference between endogenous selection bias, common-cause confounding, and overcontrol bias and discuss numerous examples from social stratification, cultural sociology, social network analysis, political sociology, social demography, and the sociology of education."], "field": "Social Sciences", "q_year": 2018, "q_cid": "54064700", "pos_cid": 4836709, "source": "eval20x26"}
{"query_id": "scaleup_19175177_22042723", "query": "How to understand whose interests shape home-care marketization and why its implementation remains contested", "pos": ["What can feminist theory offer policy implementation challenges?. Implementation has long been a vexed issue in the mainstream public policy literature. The literature has remained more concerned with the design of policy and evidence of its impact than on the process by which it plays out. While implementation is often portrayed as a simple process of adopting best practice, experiences indicate that it is a far more complex process involving a range of actors translating policy into practice under varying conditions. Substantial changes to public service environments over the past few decades, both incremental and disruptive, have compounded this complexity. Commentators argue that it is time to look beyond current 'best practice' for new conceptual tools to tackle implementation challenges, particularly relating to those that take place around the many boundaries of public services (Dickinson and Sullivan, 2014a). In this paper we consider how post-structural feminist perspectives, with scope to actively challenge orthodoxies and embrace diversity and competing views, might further contemporary policy implementation research and practice."], "field": "Social Sciences", "q_year": 2019, "q_cid": "191751779", "pos_cid": 220427237, "source": "eval20x26"}
{"query_id": "scaleup_28370645_27262674", "query": "How to develop actionable ideas for nitrous oxide harm reduction messaging that reflects young people’s lived experience and is relevant and engaging to them", "pos": ["Co-creation in healthcare and research to improve service delivery for young people with chronic pain. Introduction The process of co-creation can enable more effective, agile and integrated healthcare solutions achieving outcomes that effectively translate to healthcare delivery. Collaborative knowledge generation is particularly important in fields such as pediatric chronic pain where there is a complex interplay between biological, social, environmental, emotional, familial and school factors. The co-creation initiative described here was designed to amplify the voices of youth with chronic pain and their families and a variety of key stakeholders and generate novel approaches to the management of chronic pediatric pain in the setting of the South Australian Pediatric Chronic Pain Service. Methods Stakeholders who were identified as influential in this ecosystem were allocated to 6 groups. A skilled facilitator co-prepared and delivered the workshop, engaging participants in three structured activities. Firstly, the challenges to service delivery were outlined, followed by the groups discussing what is currently working. The second activity involved lateral thinking without restrictions on time, resources or system to generate solutions to the key challenges presented. Finally, stakeholders were asked to agree on a generated solution from Activity 2 and build a case for actionable implementation of this solution. Data were summarised by the workshop facilitator and reflexive thematic analysis was used for coding and generating themes. Results From Activity 1, six themes collectively demonstrated that stakeholders valued many of the existing strengths of the service delivery, but some areas such as pain education was undervalued. Activity 2 generated solutions from high-level ideas to more day-to- day management strategies. Each of six groups generated unique solutions to an identified challenge for Activity 3. Discussion Engaging a wide variety of stakeholders in collaborative knowledge generation successfully provided the South Australian Pediatric Chronic Pain Service with a variety of novel, scalable solution across the healthcare continuum. Equally important is that this initiative helped to raise awareness about the complex issues faced in pediatric chronic pain care and helped to establish new partnerships that have led to enhanced service delivery."], "field": "Social Sciences", "q_year": 2025, "q_cid": "283706455", "pos_cid": 272626743, "source": "eval_collection"}
{"query_id": "scaleup_27169844_13683547", "query": "How to prevent overreliance on risk prediction scores and preserve independent human judgment, responsibility, and meaningful control over consequential decisions", "pos": ["The accuracy, fairness, and limits of predicting recidivism. Should we trust computers to make life-altering decisions in the criminal justice system? Algorithms for predicting recidivism are commonly used to assess a criminal defendant’s likelihood of committing a crime. These predictions are used in pretrial, parole, and sentencing decisions. Proponents of these systems argue that big data and advanced machine learning make these analyses more accurate and less biased than humans. We show, however, that the widely used commercial risk assessment software COMPAS is no more accurate or fair than predictions made by people with little or no criminal justice expertise. In addition, despite COMPAS’s collection of 137 features, the same accuracy can be achieved with a simple linear classifier with only two features."], "field": "Social Sciences", "q_year": 2024, "q_cid": "271698448", "pos_cid": 13683547, "source": "eval_collection"}
{"query_id": "scaleup_24696895_14991148", "query": "How to understand people’s vulnerability to particular false claims and political provocations in relation to their alignment or conflict with shared beliefs", "pos": ["Audiences in an Age of Datafication: Critical Questions for Media Research. This article critically examines how fears of audience gullibility, ignorance, and exploitation impede media studies’ response to the pressing challenges posed by the growing power of social media platforms and their innovative datafication practices. I revisit the history of audience research to show how empirical findings contested the pejorative conception of the audience problematically yet persistently imagined by theorists of media power during the twentieth century. As media studies joins other disciplines in responding to the growing datafication of society, I propose that the circuit of culture model can help theorize media (including platform and algorithmic) power by opening up the hermeneutic and action space between production and consumption. In this way, critical scholarship might more effectively analyze such metaprocesses as mediatization and datafication precisely by recognizing rather than erasing audiences’ relation to both the everyday lifeworld and the public world of citizen action, regulatory intervention, and the wider society."], "field": "Social Sciences", "q_year": 2022, "q_cid": "246968957", "pos_cid": 149911489, "source": "eval_collection"}
{"query_id": "scaleup_27844375_55800088", "query": "How to increase participation of diverse, geographically distributed populations in knowledge creation and improve the local relevance of research findings and educational resources", "pos": ["Building public health capacity through online global learning. Rising disease burden and health inequalities remain global concerns, highlighting the need for health systems strengthening with a sufficient and appropriately trained workforce. The current models for developing such a workforce are inadequate and newer approaches are needed. In this paper we describe a model for public health capacity building through online Global Learning, defined as “innovative, integrated, global opportunities for capacity building through online learning and shared experiences between and within Low- to Middle-Income Countries and High-Income Countries, in a continuous process that helps health care workers learn as they progress through their careers”. We demonstrate how two programmes, Peoples-uni and NextGenU.org , have implemented this model using a mix of low-cost and free online learning courses, a global community of volunteer tutors, mentors and peers, and appropriate high quality competence-based content."], "field": "Social Sciences", "q_year": 2025, "q_cid": "278443758", "pos_cid": 55800088, "source": "eval_collection"}
{"query_id": "scaleup_25569127_23700886", "query": "How to establish whether parental experience can shape offspring preparedness for conditions they have not yet encountered", "pos": ["Phenotypic plasticity in plant defense across life stages: Inducibility, transgenerational induction, and transgenerational priming in wild radish. Significance Herbivore attack on plants is known to elicit defensive responses. Such environmentally induced responses can also be expressed by the offspring of attacked plants via DNA methylation—an epigenetic response—but little is known about if and how epigenetic induction varies with plant ontogeny (e.g., seedlings, reproductive plants). Here, we report that herbivory by caterpillars induced changes in the plant epigenome and chemical and physical defenses within and across generations in wild radish. We show that herbivore offense in a plant’s generation affects its progeny’s deployment of defenses throughout its life cycle and that herbivory operates as an important and nuanced driver of phenotypic diversity in plant populations. As they develop, many plants deploy shifts in antiherbivore defense allocation due to changing costs and benefits of their defensive traits. Plant defenses are known to be primed or directly induced by herbivore damage within generations and across generations by long-lasting epigenetic mechanisms. However, little is known about the differences between life stages of epigenetically inducible defensive traits across generations. To help fill this knowledge gap, we conducted a multigenerational experiment to determine whether defense induction in wild radish plants was reflected in chromatin modifications (DNA methylation); we then examined differences between seedlings and reproductive plants in current and transgenerational plasticity in chemical (glucosinolates) and physical (trichomes) defenses in this species. Herbivory triggered genome methylation both in targeted plants and their offspring. Within one generation, both defenses were highly inducible at the seedling stage, but only chemical defenses were inducible in reproductive plants. Across generations, herbivory experienced by mother plants caused strong direct induction of physical defenses in their progeny, with effects lasting from seedling to reproductive stages. For chemical defenses, however, this transgenerational induction was evident only in adults. Transgenerational priming was observed in physical and chemical defenses, particularly in adult plants. Our results show that transgenerational plasticity in plant defenses in response to herbivore offense differs for physical and chemical defense and changes across plant life stages."], "field": "Social Sciences", "q_year": 2023, "q_cid": "255691276", "pos_cid": 237008863, "source": "eval_collection"}
{"query_id": "scaleup_27056834_24521210", "query": "How to determine whether press reports critical of “queue-jumping” accusations also reject treating asylum seekers as illegitimate arrivals", "pos": ["The master’s tools: Media repurposing of exclusionary metaphors to challenge racist constructions of migrants. Metaphors are powerful mechanisms by which to rally exclusionary nationalist sentiment without necessarily appearing racist. However, sometimes those metaphors are challenged, inverting exclusionary functions. In this paper, we track how metaphors in the Australian press over the last 165 years which have generally constructed migration as a threat to the integrity of the nation, are repurposed to counter the claims embedded within them. For example, while invasion, swamping and flooding are generally recruited to negative ends, the same tropes are used to argue that fears of invasion are unjustified, that numbers of migrants are too small to swamp the nation and that the so-called floods of foreigners are overstated. However, this does not necessarily result in a decrease in metaphor use, nor challenge the fundamental implications of the metaphors. We explore how the repurposing occurs, and why it may not be an effective tool for anti-racist action."], "field": "Social Sciences", "q_year": 2024, "q_cid": "270568341", "pos_cid": 245212106, "source": "eval_collection"}
{"query_id": "scaleup_26984661_21099867", "query": "How to understand the link between mobile phone dependence and impaired physical and cognitive functioning in athletes", "pos": ["Sleep and Athletic Performance: Impacts on Physical Performance, Mental Performance, Injury Risk and Recovery, and Mental Health. Research has characterized the sleep of elite athletes and attempted to identify factors associated with athletic performance, cognition, health, and mental well-being. Sleep is a fundamental component of performance optimization among elite athletes, yet only recently embraced by sport organizations as an important part of training and recovery. Sleep plays a crucial role in physical and cognitive performance and is an important factor in reducing risk of injury. This article aims to highlight the prevalence of poor sleep, describe its impacts, and address the issue of sport culture surrounding healthy sleep."], "field": "Social Sciences", "q_year": 2024, "q_cid": "269846613", "pos_cid": 210998679, "source": "eval_collection"}
{"query_id": "scaleup_25715669_20693845", "query": "How to assess ease of walking and access to nearby facilities while distinguishing walkable connections from others and ensuring consistent representation of closely spaced connection points", "pos": ["OSMnx: New methods for acquiring, constructing, analyzing, and visualizing complex street networks. Urban scholars have studied street networks in various ways, but there are data availability and consistency limitations to the current urban planning/street network analysis literature. To address these challenges, this article presents OSMnx, a new tool to make the collection of data and creation and analysis of street networks simple, consistent, automatable and sound from the perspectives of graph theory, transportation, and urban design. OSMnx contributes five significant capabilities for researchers and practitioners: first, the automated downloading of political boundaries and building footprints; second, the tailored and automated downloading and constructing of street network data from OpenStreetMap; third, the algorithmic correction of network topology; fourth, the ability to save street networks to disk as shapefiles, GraphML, or SVG files; and fifth, the ability to analyze street networks, including calculating routes, projecting and visualizing networks, and calculating metric and topological measures. These measures include those common in urban design and transportation studies, as well as advanced measures of the structure and topology of the network. Finally, this article presents a simple case study using OSMnx to construct and analyze street networks in Portland, Oregon."], "field": "Social Sciences", "q_year": 2023, "q_cid": "257156695", "pos_cid": 206938450, "source": "eval_collection"}
{"query_id": "scaleup_25569127_4411321", "query": "How to explain the evolutionary origins of ancient organisms’ capacity to anticipate recurring environmental conditions rather than merely react to them", "pos": ["Peroxiredoxins are conserved markers of circadian rhythms. Cellular life emerged ∼3.7 billion years ago. With scant exception, terrestrial organisms have evolved under predictable daily cycles owing to the Earth’s rotation. The advantage conferred on organisms that anticipate such environmental cycles has driven the evolution of endogenous circadian rhythms that tune internal physiology to external conditions. The molecular phylogeny of mechanisms driving these rhythms has been difficult to dissect because identified clock genes and proteins are not conserved across the domains of life: Bacteria, Archaea and Eukaryota. Here we show that oxidation–reduction cycles of peroxiredoxin proteins constitute a universal marker for circadian rhythms in all domains of life, by characterizing their oscillations in a variety of model organisms. Furthermore, we explore the interconnectivity between these metabolic cycles and transcription–translation feedback loops of the clockwork in each system. Our results suggest an intimate co-evolution of cellular timekeeping with redox homeostatic mechanisms after the Great Oxidation Event ∼2.5 billion years ago."], "field": "Social Sciences", "q_year": 2023, "q_cid": "255691276", "pos_cid": 4411321, "source": "eval_collection"}
{"query_id": "scaleup_26913934_22706035", "query": "How to help learners develop an integrated understanding of what they read", "pos": ["Impact of the KWL reading strategy on mathematical problem-solving achievement of primary school 4th graders. Abstract In this study, it was aimed to investigate possible impact of using the KWL reading strategy in teaching the topic of “fractions and operations with fractions” to the 4th graders on students’ problem-solving achievement. A quasi-experimental design with pretest-posttest control group (CG) was employed in the study. The study group consisted of 35 4th graders studying at a primary school in Bartın, Turkey. In the research, an experimental group (EG) and a control group (CG) were used. There were 18 students in the experimental group (EG) and 17 students in the control group (CG). The test of equivalency (TE), Problem-Solving Achievement Test (PSAT) to gauge effect of instruction with the KWL strategy and reading texts were employed as data collection tools. The Wilcoxon Signed Rank Test and Mann Whitney U Test were employed in the research. It was found as a result of the research that the KWL strategy fostered the students’ problem-solving achievement. However, there were no significant differences between the EG and CG in terms of the scores received in the step of implementing the plan."], "field": "Social Sciences", "q_year": 2024, "q_cid": "269139345", "pos_cid": 227060353, "source": "eval_collection"}
{"query_id": "scaleup_27339345_21300841", "query": "How to understand autistic students’ and students with adhd’s overlooked perspectives on access, inclusion, and systemic barriers within intersecting higher education systems designed for the majority", "pos": ["Understanding Persistence Using a Phenomenological Variant of Ecological Systems Theory. Objective: Despite significant enrollment in community colleges, persistence and graduation rates are quite low. This study aims to better understand how students’ person–environment relationships and self-organization together contribute to the persistence decisions of community college students. Using Spencer et al.’s phenomenological variant on ecological systems theory (PVEST) framework, we aim to clarify the psychological functioning behind students’ persistence that is impacted by diverse systems, including the community college itself, family, and the broader community. Method: This study utilized qualitative interviews with 66 participants across two community colleges. Findings: We find that when participants’ experiences were analyzed through a PVEST frame, a majority of students described having phenomenological experiences around their student/learner identities. The feedback from these experiences prompted participants to negatively or positively reorganize their self-perceptions in regard to how they saw themselves as students and learners; this reorganization led to behaviors that influenced persistence plans. When participants’ microsystems (e.g., family, work, college) intersected, patterns emerged regarding how participants processed environmental feedback that resulted in a cyclical feedback loop, suggesting a more dynamic relationship with environments than previously presented. Contributions: Using PVEST as a framework allows for a more in-depth examination of the interface between students’ psychological foundations, processing of environmental feedback, and the resulting reorganization of self in regard to how role identities (e.g., student) provide greater insight into students’ persistence decisions. This study offers PVEST as an important framework for rethinking previous models of researching and supporting community college student persistence."], "field": "Social Sciences", "q_year": 2024, "q_cid": "273393456", "pos_cid": 213008419, "source": "eval_collection"}
{"query_id": "scaleup_26615560_15926866", "query": "How to explain the continued political force of failed-state categories in contemporary justifications for military intervention despite the crisis of the failed-states agenda", "pos": ["Justifying military intervention: Yemen as a failed state. Abstract The Saudi-led military intervention into Yemen began on 26 March 2015, and it has largely been supported by the international community despite resulting in the world’s largest current humanitarian disaster. The paper explores the emergence of the failed state concept, particularly as it has impacted the norm of sovereignty. It shows how being defined as a failed state can undermine the norm of sovereignty. This article argues that Saudi Arabia has utilised the failed state concept to legitimise its military intervention into Yemen by framing the intervention as necessary to establish a strong executive power and protect the Yemeni people."], "field": "Social Sciences", "q_year": 2023, "q_cid": "266155604", "pos_cid": 159268668, "source": "eval_collection"}
{"query_id": "scaleup_28069007_28660472", "query": "How to distinguish changes in perceived procedural justice within individuals over time from differences between individuals and assess how conspiracy beliefs relate to initial perceptions and subsequent trajectories", "pos": ["Twelve Frequently Asked Questions About Growth Curve Modeling. Longitudinal data analysis has long played a significant role in empirical research within the developmental sciences. The past decade has given rise to a host of new and exciting analytic methods for studying between-person differences in within-person change. These methods are broadly organized under the term growth curve models. The historical lines of development leading to current growth models span multiple disciplines within both the social and statistical sciences, and this in turn makes it challenging for developmental researchers to gain a broader understanding of the current state of this literature. To help address this challenge, the authors pose 12 questions that frequently arise in growth curve modeling, particularly in applications within developmental psychology. They provide concise and nontechnical responses to each question and make specific recommendations for further readings."], "field": "Social Sciences", "q_year": 2025, "q_cid": "280690074", "pos_cid": 28660472, "source": "eval_collection"}
{"query_id": "scaleup_26984661_14412683", "query": "How to clarify why athletes develop problematic mobile phone use in stressful situations, given its potential implications for their mental health and athletic performance", "pos": ["Foundation for a General Strain Theory of Crime and Delinquency. This paper presents a general strain theory of crime and delinquency that is capable of overcoming the criticisms of previous strain theories. In the first section, strain theory is distinguished from social control and differential association/social learning theory. In the second section, the three major types of strain are described: (1) strain as the actual or anticipated failure to achieve positively valued goals, (2) strain as the actual or anticipated removal of positively valued stimuli, and (3) strain as the actual or anticipated presentation of negatively valued stimuli. In the third section, guidelines for the measurement of strain are presented. And in the fourth section, the major adaptations to strain are described, and thcwe factors influencing the choice of delinquent versus nondelinquent adaptations are discussed. After dominating deviance research in the 196Os, strain theory came under heavy attack in the 1970s (Bernard, 1984; Cole, 1975), with several prominent researchers suggesting that the theory be abandoned (Hirschi, 1969; Kornhauser, 1978). Strain theory has survived those attacks, but its influence is much diminished (see Agnew, 1985a; Bernard, 1984; Farnworth and Leiber, 1989). In particular, variables derived from strain theory now play a very limited role in explanations of crime/delinquency. Several recent causal models of delinquency, in fact, either entirely exchde strain variables or assign them a small role (e.g., Elliott et al., 1985; Johnson, 1979; Massey and Krohn, 1986; Thornberry, 1987; Tonry et al., 1991). Causal models of crime/delinquency are dominated, instead, by variables derived from differential association/social learning theory and social control theory. This paper argues that strain theory has a central role to play in explanations of crime/delinquency, but that the theory has to be substantially revised to play this role. Most empirical studies of strain theory continue to rely on the strain models developed by Merton (1938), A. Cohen (1955), and Cloward and Ohlin (1960). In recent years, however, a wealth of research in several fields has questioned certain of the assumptions underlying those theories and pointed to new directions for the development of strain theory. Most notable in this area is the research on stress in medical sociology and psychology, on equity/justice in social psychology, and on aggression in psychology-particularly recent versions of frustration-aggression and social"], "field": "Social Sciences", "q_year": 2024, "q_cid": "269846613", "pos_cid": 144126837, "source": "eval_collection"}
{"query_id": "scaleup_24879218_15029332", "query": "How to help students with limited technical skills manage the technical demands of online learning and examinations", "pos": ["Walking the tightrope with an e-portfolio: imbalance between support and autonomy hampers self-directed learning. ABSTRACT Teacher coaching is essential to support self-directed learning, but requires a lot of time and energy. This mixed-methods study investigated the effects of using an e-portfolio with a self-coaching protocol and limited teacher coaching on the development of self-directed learning skills and motivation. With regard to self-directed learning, students’ overestimation of performance on learning tasks grew over time, while their ability to formulate points for improvement did not change significantly. With regard to motivation, students’ controlled (i.e. largely extrinsic) motivation increased while their autonomous (i.e. largely intrinsic) motivation decreased. Thematic analysis of interviews demonstrated students needed more support and feedback from their teacher. The use of suboptimal cues for performance assessment and an imperfect balance between autonomy and support hampered self-directed learning and motivation. We recommend providing just-in-time feedback about performance on learning tasks and giving students some autonomy over the choice of learning tasks, to enhance reflection and motivation."], "field": "Social Sciences", "q_year": 2022, "q_cid": "248792184", "pos_cid": 150293321, "source": "eval_collection"}
{"query_id": "scaleup_28370645_22497942", "query": "How to identify which groups of young nitrous oxide users and non-users need targeted advice and what guidance is relevant to their social settings and peer dynamics", "pos": ["The ‘social worlds’ concept: a useful tool for public health-oriented studies of drinking cultures. Abstract Intervening in heavy drinking cultures within groups below the level of the population has been under-utilized as a means of reducing alcohol-associated harms. We argue that the concept of ‘social worlds’ is useful for the identification and investigation of heavy drinking cultures in collectivities at this level. The concept may also support investigations into other practices with health implications, such as other substance use or gambling. Social worlds are understood to be loosely bounded groups that change over time and any individual may be affiliated with many. Membership of a social world entails shared commitments, practices and norms generated and reiterated through interaction with other members, albeit not necessarily with all members participating together or at once. Social worlds of heavy alcohol consumption are also framed by the settings where people drink, products consumed and technologies used in doing so. As a tool to support public health efforts, we suggest that these social worlds should entail collective drinking, include sufficient members and involve a magnitude of harm to warrant public health investment and be accessible for research and intervention. Researchers can usefully consider how wider forces, including discourses about alcohol and the gendering of drinking practices, are enacted within particular social worlds. Although they may be explored through empirical research, social worlds of heavy drinking are analytic devices rather than perfect reflections of an objective reality. To see them as such allows us to define them strategically, looking for opportunities to modify cultures associated with harms."], "field": "Social Sciences", "q_year": 2025, "q_cid": "283706455", "pos_cid": 224979420, "source": "eval_collection"}
{"query_id": "scaleup_25487641_14441902", "query": "How to verify that human nucleotide sequence reagents reported in gene research papers match their claimed identities", "pos": ["Basic local alignment search tool.. A new approach to rapid sequence comparison, basic local alignment search tool (BLAST), directly approximates alignments that optimize a measure of local similarity, the maximal segment pair (MSP) score. Recent mathematical results on the stochastic properties of MSP scores allow an analysis of the performance of this method as well as the statistical significance of alignments it generates. The basic algorithm is simple and robust; it can be implemented in a number of ways and applied in a variety of contexts including straightforward DNA and protein sequence database searches, motif searches, gene identification searches, and in the analysis of multiple regions of similarity in long DNA sequences. In addition to its flexibility and tractability to mathematical analysis, BLAST is an order of magnitude faster than existing sequence comparison tools of comparable sensitivity."], "field": "Social Sciences", "q_year": 2022, "q_cid": "254876415", "pos_cid": 14441902, "source": "eval_collection"}
{"query_id": "scaleup_23710152_52821568", "query": "How to explain older adults’ use of e-health amid privacy concerns and limited information about these services’ benefits", "pos": ["Using the UTAUT2 Model to Determine Factors Affecting Adoption of Mobile Banking Services: A Qualitative Approach. The main purpose of this study is to investigate the determinants that affect the adoption of mobile banking services in Jordan. The current study extends the Unified Theory of Acceptance and Use of Technolgy2 (UTAUT2) by adding two important factors, mass media and trust utilizing by seven respondents based on qualitative approach, this study shows that the adoption of mobile banking is positively and significantly influenced by the mass media, trust, effort expectancy, performance expectancy, facilitating conditions, and social influence. In contrast, hedonic motivation seems to be insignificantly related to adoption of mobile banking services. There are numerous variables affect the of adoption mobile banking. While most previous studies address the relationship between these factors and the attitudes toward mobile banking services by using the quantitative approaches, this study adopts qualitative approach (focus group method) to provide further insight into the main factors which affect adoption of mobile banking. Furthermore, the current study extends the original UTAUT2 by testing the impact of two new variables. This is considered the important contribution in the paper."], "field": "Social Sciences", "q_year": 2021, "q_cid": "237101522", "pos_cid": 52821568, "source": "eval_collection"}
{"query_id": "scaleup_28053414_21641094", "query": "How to address poor mutual understanding among nurses from different cultural backgrounds", "pos": ["Team innovation through collaboration: how visionary leadership spurs innovation via team cohesion. ABSTRACT Post-bureaucratic, collaborative organizational arrangements possess great potential for innovation, but alignment of the dissimilar goals, values and interests of participants is required. We propose and empirically test how visionary leadership can increase innovation in multidisciplinary teams, by fostering internal team cohesion and external team boundary management. We rely on longitudinal, multi-source data concerning social welfare professionals and their team leaders across 95 teams. Our results show that visionary leadership is positively related to improved team cohesion and team boundary management over time. The positive relationship between visionary leadership and team innovation is mediated by team cohesion, but not team boundary management."], "field": "Social Sciences", "q_year": 2025, "q_cid": "280534143", "pos_cid": 216410949, "source": "eval_collection"}
{"query_id": "scaleup_24966403_15066216", "query": "How to determine what access to qualitative data from earlier studies can offer beyond those studies’ established interpretations", "pos": ["Arguing, Obeying and Defying. Stanley Milgram's obedience experiments are among the most influential and controversial scientific studies ever conducted. The experiments are commonly understood to have shown how easily people can be led into harming another person, simply as a result of following orders. Recently, however, Milgram's studies have been subjected to a sustained critique and re-evaluation. This book draws on the vast stock of audio recordings from Milgram's experiments to reveal how these experiments can be understood as occasions for argumentation and rhetoric, rather than showing how passive subjects can be led into simply doing as they are told. In doing so, it reconsiders what we understand by 'obedience' and extends how social psychologists have understood rhetoric itself."], "field": "Social Sciences", "q_year": 2022, "q_cid": "249664032", "pos_cid": 150662163, "source": "eval_collection"}
{"query_id": "scaleup_27592060_16636952", "query": "How to reliably assess treatment effects in observational surveys when comparison groups have little in common and some observations have disproportionate influence", "pos": ["Comment: Performance of Double-Robust Estimators When “Inverse Probability” Weights Are Highly Variable. Comment on ``Performance of Double-Robust Estimators When ``Inverse Probability'' Weights Are Highly Variable'' [arXiv:0804.2958]"], "field": "Social Sciences", "q_year": 2025, "q_cid": "275920604", "pos_cid": 16636952, "source": "eval_collection"}
{"query_id": "scaleup_27754587_16954911", "query": "How to define all necessary sections and their required coverage for AI Act technical documentation when combined legal and software engineering expertise is scarce", "pos": ["Demonstrating Rigor Using Thematic Analysis: A Hybrid Approach of Inductive and Deductive Coding and Theme Development. In this article, the authors describe how they used a hybrid process of inductive and deductive thematic analysis to interpret raw data in a doctoral study on the role of performance feedback in the self-assessment of nursing practice. The methodological approach integrated data-driven codes with theory-driven ones based on the tenets of social phenomenology. The authors present a detailed exemplar of the staged process of data coding and identification of themes. This process demonstrates how analysis of the raw data from interview transcripts and organizational documents progressed toward the identification of overarching themes that captured the phenomenon of performance feedback as described by participants in the study."], "field": "Social Sciences", "q_year": 2025, "q_cid": "277545875", "pos_cid": 16954911, "source": "eval_collection"}
{"query_id": "scaleup_26075434_20134330", "query": "How to help parents with uneven digital and algorithm literacies recognize how their own digital practices affect their children’s digital lives and better support them", "pos": ["Your Data Is My Data: A Framework for Addressing Interdependent Privacy Infringements. Everyone holds personal information about others. Each person’s privacy thus critically depends on the interplay of multiple actors. In an age of technology integration, this interdependence of data protection is becoming a major threat to privacy. Yet current regulation focuses on the sharing of information between two parties rather than multiactor situations. This study highlights how current policy inadequacies, illustrated by the European Union General Data Protection Regulation, can be overcome by means of a deeper understanding of the phenomenon. Specifically, the authors introduce a new phenomenological framework to explain interdependent infringements. This framework builds on parallels between property and privacy and suggests that interdependent peer protection necessitates three hierarchical steps, “the 3Rs”: realize, recognize, and respect. In response to observed failures at these steps, the authors identify four classes of intervention that constitute a toolbox addressing what can be done by marketers, regulators, and privacy organizations. While the first three classes of interventions address issues arising from the corresponding 3Rs, the authors specifically advocate for a fourth class of interventions that proposes radical alternatives that shift the responsibilities for privacy protection away from consumers."], "field": "Social Sciences", "q_year": 2023, "q_cid": "260754344", "pos_cid": 201343307, "source": "eval_collection"}
{"query_id": "scaleup_26759051_22885144", "query": "How to increase engagement with green alternatives and generate creative options that support green projects", "pos": ["Influence of the Green Leadership Toward Environmental Policies Support. This paper aimed to study the role of green leadership toward environmental policies support in university. Furthermore, this study investigated the influence of green leadership toward environmental policies support and discussed the mediation effect of Green Self efficacy, Green Mindfulness, organization identity and environmental responsibility. The number of Population sample in this research was taken from 1,456 lecturers and staff of Universitas Negeri Semarang, Indonesia. Total sample in this research is 312 respondents. Structural Equation Models (SEM) was used in this research to develop the model of green leadership role toward environmental policies support of Lecturer and Staff in the University. This study found that green leadership had significant influences toward environmental policies support, environmental responsibility, green mindfulness and green self-efficacy but had insignificant influence toward organizational identity. Path analysis showed strong mediation effect of environmental responsibility and green mindfulness, but had a weak mediation from organizational identity and green self-efficacy. Finally, this study concluded that the role of green leadership in influencing environmental responsibility and green mindfulness was required to be enhanced in order to increase the support of environmental policies at the university. Further study needs to be carried out to determine the effect of green leadership on green performance and green behavior in organizations."], "field": "Social Sciences", "q_year": 2024, "q_cid": "267590514", "pos_cid": 228851445, "source": "eval_collection"}
{"query_id": "scaleup_27062912_26218769", "query": "How to capture geographical variation in the relationship between urban compactness and carbon emissions from energy consumption", "pos": ["Spatially varying relationships of soil Se concentration and rice Se concentration in Guangxi, China: A geographically weighted regression approach.. In recent years, the biogeochemical behavior and environmental impact of Selenium (Se) on soil-plant systems have received widespread attention, and traditional statistical methods reveal generally positive correlations between rice Se and soil Se. However, that initial positive relationship may have been obscured by local external factors. Using local scale data from the geochemical evaluation of land quality project, this work employed geographically weighted regression (GWR) to examine the spatial variation of rice Se (as the dependent variable) and soil Se (as the independent variable) in Guangxi. Strong and weak correlation coefficients occur between rice Se and soil Se, thereby indicating that their relationships are spatially varying. Guangxi is characterized by significantly positive correlations in most areas, with weak correlations mostly found in the south-western and central-eastern regions. Areas with weak correlation can be divided into two patterns: high soil Se with low rice Se and high rice Se with low soil Se. The unique patterns are correlated with distinct natural factors, particularly the abundance of Fe-rich soils in the carbonate area; by contrast, sandstone areas in central Guangxi may have been affected by anthropogenic activities. To reveal the spatially varying relationships at the local scale, we employed GWR, an effective tool that allowed us to identify the association between environmental variables and influencing factors and explore spatially varying relationships between them. This study breaks through the existing understanding that soil Se is completely positively correlated with rice Se for the first time, and concludes that their correlation is spatially variable, providing an effective approach for the study of complex relationships."], "field": "Social Sciences", "q_year": 2024, "q_cid": "270629128", "pos_cid": 262187697, "source": "eval_collection"}
{"query_id": "scaleup_28144571_53557829", "query": "How to understand what connection with distant peers on TikTok means to young people amid shared pandemic experiences, mutual understanding, and debates focused on the platform’s addictive appeal and risks", "pos": ["Rethinking responsibility and care for a postcolonial world. Both responsibility and care have much to offer in thinking through the relationalities that make up a postcolonial world. Although contemporary political systems often posit responsibility and care within the context of individuated and autonomous selves, geographers have done much to relocate responsibility and care within narratives of interdependency – spatially and temporally. They have argued that both terms offer a route for thinking about ethical geographical relations between myriad places. In this article we take this project further, by looking at how the nature and shape of these relationships might be construed in a postcolonial world. We suggest that, through a more critical engagement with postcolonial thinking, any exploration of existing practices of responsibility and care will not only reveal the enormous potential of imagining these geographies as forms of existing and evolving relationalities, but will also lead us to interrogate the deployments of these terms in the context of past and present inequalities. We show that routing care and responsibility through postcolonial geographies moves us towards a more pragmatic responsiveness, one that involves a ‘care-full’ recognition of postcolonial interaction."], "field": "Social Sciences", "q_year": 2025, "q_cid": "281445714", "pos_cid": 53557829, "source": "eval_collection"}
{"query_id": "scaleup_25487641_24320085", "query": "How to deter low-quality or fraudulent paper-mill manuscripts at scale in human gene research publishing despite paper mills adapting to avoid scrutiny", "pos": ["The past, present and future of Registered Reports. Registered Reports are a form of empirical publication in which study proposals are peer reviewed and pre-accepted before research is undertaken. By deciding which articles are published based on the question, theory and methods, Registered Reports offer a remedy for a range of reporting and publication biases. Here, we reflect on the history, progress and future prospects of the Registered Reports initiative and offer practical guidance for authors, reviewers and editors. We review early evidence that Registered Reports are working as intended, while at the same time acknowledging that they are not a universal solution for irreproducibility. We also consider how the policies and practices surrounding Registered Reports are changing, or must change in the future, to address limitations and adapt to new challenges. We conclude that Registered Reports are promoting reproducibility, transparency and self-correction across disciplines and may help reshape how society evaluates research and researchers. Registered Reports were introduced a decade ago as a means for improving the rigour and credibility of confirmatory research. Chambers and Tzavella overview the format’s past, its current status and future developments."], "field": "Social Sciences", "q_year": 2022, "q_cid": "254876415", "pos_cid": 243200855, "source": "eval_collection"}
{"query_id": "scaleup_23989097_14919704", "query": "How to clarify the implicit beliefs shaping teachers’ expectations and classroom decisions about technology in teaching argumentative commentary on multimodal texts", "pos": ["Por qué es necesario repensar la competencia docente para el mundo digital. This article analyses the most impacting institutional models of digital teaching competence, and critically addresses three characteristics common to all of them, understood as deficiencies in their approach. Firstly, they do not explicitly start from a model of teaching action, and implicitly reduce the teaching function to the classroom performance, avoiding aspects such as social and political commitment, or the role of the school in community development. Secondly, they are based on a taxonomic vision of the concept of competence, ignoring the complexity of the different contexts in which competence is carried on and developed, as well as its role in the construction of teacher identity, something that socio-material and holistic approaches do include. Thirdly, they are based on an instrumentalist vision of technology as a neutral tool in values and, on the contrary, on a deterministic conception of the relationship between technology and society. Finally, we present a model that we have called \"Integral Teaching Competence for the digital world\", specifically designed for basic education, which is the subject of a more ambitious research."], "field": "Social Sciences", "q_year": 2021, "q_cid": "239890977", "pos_cid": 149197046, "source": "eval_collection"}
{"query_id": "scaleup_26330969_23575530", "query": "How to determine whether an adjustment is needed when several checks are performed, given that multiple checks do not automatically require one", "pos": ["When to adjust alpha during multiple testing: a consideration of disjunction, conjunction, and individual testing. Scientists often adjust their significance threshold (alpha level) during null hypothesis significance testing in order to take into account multiple testing and multiple comparisons. This alpha adjustment has become particularly relevant in the context of the replication crisis in science. The present article considers the conditions in which this alpha adjustment is appropriate and the conditions in which it is inappropriate. A distinction is drawn between three types of multiple testing: disjunction testing, conjunction testing, and individual testing. It is argued that alpha adjustment is only appropriate in the case of disjunction testing, in which at least one test result must be significant in order to reject the associated joint null hypothesis. Alpha adjustment is inappropriate in the case of conjunction testing, in which all relevant results must be significant in order to reject the joint null hypothesis. Alpha adjustment is also inappropriate in the case of individual testing, in which each individual result must be significant in order to reject each associated individual null hypothesis. The conditions under which each of these three types of multiple testing is warranted are examined. It is concluded that researchers should not automatically (mindlessly) assume that alpha adjustment is necessary during multiple testing. Illustrations are provided in relation to joint studywise hypotheses and joint multiway ANOVAwise hypotheses."], "field": "Social Sciences", "q_year": 2023, "q_cid": "263309692", "pos_cid": 235755301, "source": "eval_collection"}
{"query_id": "scaleup_23767074_14577638", "query": "How to explain the persistence of cultural restraints on crime in the Torres Strait when many community rules are unspoken", "pos": ["A Torres Strait Islander Perspective on the Concept of Indigenous Knowledge. The concept of Indigenous knowledge itself has life; it is ‘living’ knowledge. This Indigenous knowledge or ‘living’ knowledge is not written, but rather transmitted orally by the gatekeepers and holders of knowledge, especially from our Elders ‘Athe’ (grandfather), ’Aka’ (grandmother), our parents ‘Baba’ (father), and ‘Ama’ (mother), as well as our (uncles) ‘Awahdeh’ and our (aunties) ‘Ama’. These holders of knowledge play a major part in our individual lives as they mould or shape our minds, values, ethics, morals and opinions about society today and its influences on us as individuals. The Elders also influence where we place ourselves in our community and in the wider community. This transmission of Indigenous knowledge is ‘passed on’ through traditional language, traditional lores, understandings of totems, kinship ties, performance of dances, songs, stories, myths, legends, rituals, ceremonies and activities or events which influence our lives daily."], "field": "Social Sciences", "q_year": 2021, "q_cid": "237670743", "pos_cid": 145776382, "source": "eval_collection"}
{"query_id": "scaleup_27056834_24207644", "query": "How to clarify the racial meanings of negative metaphors portraying asylum seekers as illegal threats to sovereignty and their connection to anxieties about the legitimacy of settler rule", "pos": ["The Chinese Invasion: Settler Colonialism and the Metaphoric Construction of Race. ABSTRACT The arrival of Chinese immigrants during the Australian goldrushes of the 1850s precipitated a vehement backlash, culminating in legislation to restrict their immigration. Contemporary Australian press discourse focused on Chinese racial difference, with immigrants metaphorically constructed as invaders, influxes and hordes of barbarians. This article argues that Chinese immigrants were racialised through pre-existing metaphoric language of deviance and threat, while the metaphors became simultaneously codified as signifiers of racial difference. It further argues that this characterisation resulted from settler-colonial anxieties about legitimacy, which intensified due to Chinese immigration. The consequent racialisation of Chinese immigrants functioned as a means to displace both the violence of settler-colonial invasion and lower-class white deviance, facilitating the construction of the egalitarian white Australian subject."], "field": "Social Sciences", "q_year": 2024, "q_cid": "270568341", "pos_cid": 242076448, "source": "eval_collection"}
{"query_id": "scaleup_23231269_20307157", "query": "How to assess social contract theory’s assumptions about human nature given uncertainty over whether moral behaviour in small-scale societies reflects stable individual dispositions or depends on social context", "pos": ["Hadza Hunter-Gatherers Disagree on Perceptions of Moral Character. To the extent that moral character is grounded in stable and observable truths, there should exist agreement between people in their judgments of others’ character. In Western populations, this agreement is found. We examine whether this is universal in Hadza hunter-gatherers of Tanzania. Ninety-four judges ranked their campmates on global character and relevant character traits for a total of 802 observations. Judges disagreed on rankings of global character, generosity, and honesty but agreed more on hard work and hunting ability. Individual rankings on specific traits predicted character evaluations. There was agreement between judges on the extent to which generosity and hard work related to character. These findings suggest that Hadza have shared beliefs about what traits constitute character but disagree on which of their campmates exhibit these traits. We discuss these findings in light of other research suggesting that stable moral dispositions may not be universal."], "field": "Social Sciences", "q_year": 2021, "q_cid": "232312691", "pos_cid": 203071579, "source": "eval_collection"}
{"query_id": "scaleup_26075434_23902073", "query": "How to explain parents’ understandings of algorithms in their children’s lives and their responses to platforms when technical knowledge alone is insufficient", "pos": ["Algorithmic Folk Theories and Identity: How TikTok Users Co-Produce Knowledge of Identity and Engage in Algorithmic Resistance. Algorithms in online platforms interact with users' identities in different ways. However, little is known about how users understand the interplay between identity and algorithmic processes on these platforms, and if and how such understandings shape their behavior on these platforms in return. Through semi-structured interviews with 15 US-based TikTok users, we detail users' algorithmic folk theories of the For You Page algorithm in relation to two inter-connected identity types: person and social identity. Participants identified potential harms that can accompany algorithms' tailoring content to their person identities. Further, they believed the algorithm actively suppresses content related to marginalized social identities based on race and ethnicity, body size and physical appearance, ability status, class status, LGBTQ identity, and political and social justice group affiliation. We propose a new algorithmic folk theory of social feeds-The Identity Strainer Theory-to describe when users believe an algorithm filters out and suppresses certain social identities. In developing this theory, we introduce the concept of algorithmic privilege as held by users positioned to benefit from algorithms on the basis of their identities. We further propose the concept of algorithmic representational harm to refer to the harm users experience when they lack algorithmic privilege and are subjected to algorithmic symbolic annihilation. Additionally, we describe how participants changed their behaviors to shape their algorithmic identities to align with how they understood themselves, as well as to resist the suppression of marginalized social identities and lack of algorithmic privilege via individual actions, collective actions, and altering their performances. We theorize our findings to detail the ways the platform's algorithm and its users co-produce knowledge of identity on the platform. We argue the relationship between users' algorithmic folk theories and identity are consequential for social media platforms, as it impacts users' experiences, behaviors, sense of belonging, and perceived ability to be seen, heard, and feel valued by others as mediated through algorithmic systems."], "field": "Social Sciences", "q_year": 2023, "q_cid": "260754344", "pos_cid": 239020738, "source": "eval_collection"}
{"query_id": "scaleup_27177778_21086323", "query": "How to reliably assess the impact, quality, relevance, and effectiveness of science outreach initiatives and their alignment with societal values and needs despite a research–practice gap", "pos": ["Evidence-Based Science Communication. Effective science communication can empower research and innovation systems to address global challenges and put public interests at the heart of how knowledge is produced, shared, and applied. For science communication to play this mediating role effectively, we propose a more integrated and “evidence-based” approach. This commentary identifies key issues facing the science communication field. It suggests a series of prescriptions, inspired by the impact of “evidence-based medicine” over the past decades. In practice, evidence-based science communication should combine professional expertise and skills with the best available evidence from systematic research. Steps required to achieve this outcome include more quality assurance in science communication research, significant changes in teaching and training, and improved interfaces between science communication research and practice."], "field": "Social Sciences", "q_year": 2024, "q_cid": "271777787", "pos_cid": 210863231, "source": "eval_collection"}
{"query_id": "scaleup_23961937_92904", "query": "How to explain paramedics’ perceptions of chaplains’ role and value and the organisational factors influencing that role", "pos": ["Using the framework method for the analysis of qualitative data in multi-disciplinary health research. BackgroundThe Framework Method is becoming an increasingly popular approach to the management and analysis of qualitative data in health research. However, there is confusion about its potential application and limitations.DiscussionThe article discusses when it is appropriate to adopt the Framework Method and explains the procedure for using it in multi-disciplinary health research teams, or those that involve clinicians, patients and lay people. The stages of the method are illustrated using examples from a published study.SummaryUsed effectively, with the leadership of an experienced qualitative researcher, the Framework Method is a systematic and flexible approach to analysing qualitative data and is appropriate for use in research teams even where not all members have previous experience of conducting qualitative research."], "field": "Social Sciences", "q_year": 2021, "q_cid": "239619371", "pos_cid": 92904, "source": "eval_collection"}
{"query_id": "scaleup_28390589_25865401", "query": "How to reduce barriers to early detection for sexual assault survivors who may avoid examinations because of distress and re-traumatisation", "pos": ["Effect of HPV self-collection kits on cervical cancer screening uptake among under-screened women from low-income US backgrounds (MBMT-3): a phase 3, open-label, randomised controlled trial. Summary Background Most cervical cancer in the USA occurs in under-screened women. The My Body, My Test-3 (MBMT-3) trial sought to assess the efficacy of mailed human papillomavirus (HPV) self-collection kits with appointment-scheduling assistance to increase uptake of cervical cancer screening among under-screened women from low-income backgrounds compared with scheduling assistance alone. Methods MBMT-3 is a phase 3, open-label, two-arm, randomised controlled trial. Participants were recruited from 22 counties in North Carolina state, USA, and we partnered with 21 clinics across these counties. Participants were eligible for inclusion if they were aged 25–64 years, had an intact cervix, were uninsured or enrolled in Medicaid or Medicare, had an income of 250% or less of the US Federal Poverty Level, were living within the catchment area of a trial-associated clinic, and were overdue for screening (ie, Papanicolaou test ≥4 years ago or high-risk HPV test ≥6 years ago). Participants were randomly assigned (2:1) to receive a mailed HPV self-collection kit and assistance for scheduling a free screening appointment (intervention group) or to receive scheduling assistance alone (control group). Randomisation was conducted by county using permuted blocks of nine patients and assignment to group was not masked. Participants in the intervention group were mailed HPV self-collection kits to collect a cervical-vaginal sample and return it by mail for testing. Samples were tested with the Aptima HPV assay (Hologic, San Diego, CA, USA), and participants were informed of high-risk HPV results by telephone call. Trial staff made up to three telephone call attempts to provide scheduling assistance for in-clinic screening for all participants. The primary outcome was cervical cancer screening uptake (ie, attending an in-clinic screening appointment or testing negative for high-risk HPV with a returned self-collected sample) within 6 months of enrolment in the intention-to-treat population. This trial is registered with ClinicalTrials.gov, NCT02651883, and has been completed. Findings Recruitment occurred between April 11, 2016, and Dec 16, 2019. 4256 women contacted the trial to participate, of whom 899 (21%) were eligible for inclusion and 697 (78%) returned consent forms. Of those who consented, 461 (66%) women were randomly assigned to the intervention group and 236 (34%) women were randomly assigned to the control group. We excluded 32 ineligible women post-randomisation, leaving 665 for primary analysis. Screening uptake was higher in the intervention group (317 [72%] of 438) than control group (85 [37%] of 227; risk ratio 1·93, 95% CI 1·62–2·31). Among intervention participants, 341 (78%) of 438 returned a self-collection kit. Three participants reported hurt or injury when using the self-collection kit; no participants withdrew due to adverse effects. Interpretation Among under-screened women from low-income backgrounds, mailed HPV self-collection kits with scheduling assistance led to greater uptake of cervical cancer screening than scheduling assistance alone. At-home HPV self-collection testing has the potential to increase screening uptake among under-screened women. Funding National Cancer Institute."], "field": "Social Sciences", "q_year": 2025, "q_cid": "283905893", "pos_cid": 258654013, "source": "eval_collection"}
{"query_id": "scaleup_25772267_53010548", "query": "How to understand the motivational value of internationalized learning experiences that complement traditional coursework for future primary education teachers", "pos": ["Collaborative Online International Learning to Prepare Students for Multicultural Work Environments.. BACKGROUND Collaborative Online International Learning (COIL) is a pedagogical approach using digital technology to provide experiential international learning without travel abroad. Through web-based, cross-country intellectual exchange, COIL helps prepare nursing students for increasingly diverse and multicultural health care work environments globally. PROBLEM Opportunities to engage in multicultural learning experiences have traditionally relied on intensive study abroad trips, which can be prohibitive for students with limited fiscal resources or who are place-bound. APPROACH A COIL experience for undergraduate nursing students at universities in the United States and the Philippines was designed to fulfill academic degree program goals related to professional communication, collaborative practice, and respect for diversity. CONCLUSION After completing the COIL experience, students expressed valuing shared learning with peers in another country and reported gains in intercultural competence. Our efforts indicated that COIL-style endeavors provide meaningful, rewarding opportunities to engage with others across borders, while enhancing students' skills to relate positively to an increasingly diverse world."], "field": "Social Sciences", "q_year": 2023, "q_cid": "257722677", "pos_cid": 53010548, "source": "eval_collection"}
{"query_id": "scaleup_27754587_26652139", "query": "How to assess whether complex technical documentation meets AI Act requirements and identify missing information despite limited combined legal and technical expertise", "pos": ["An Empirical Study on Compliance with Ranking Transparency in the Software Documentation of EU Online Platforms. Compliance with the European Union’s Platform-to-Business (P2B) Regulation helps fostering a fair, ethical and secure online environment. However, it is challenging for online platforms, and assessing their compliance can be difficult for public authorities. This is partly due to the lack of automated tools for assessing the information (e.g., software documentation) platforms provide concerning ranking transparency. Our study tackles this issue in two ways. First, we empirically evaluate the compliance of six major platforms (Amazon, Bing, Booking, Google, Tripadvisor, and Yahoo), revealing substantial differences in their documentation. Second, we introduce and test automated compliance assessment tools based on ChatGPT and information retrieval technology. These tools are evaluated against human judgments, showing promising results as reliable proxies for compliance assessments. Our findings could help enhance regulatory compliance and align with the United Nations Sustainable Development Goal 10.3, which seeks to reduce inequality, including business disparities, on these platforms.Data and materials: https://doi.org/10.5281/zenodo.10478546.CCS CONCEPTS•Software and its engineering → Documentation;•Information systems →Data analytics;•Appliedcomputing → Law;•Computing methodologies → Natural language processing.LAY ABSTRACTIn the digital world, software powers online platforms such as marketplaces and search engines. For instance, software determines the display order of products on Amazon or hotels on Booking.com. Understanding these systems is vital for businesses, yet the explanations can be complex. The European Union mandates online platforms to reveal the main parameters of their ranking algorithms, aiming for fairness and reducing inequalities. However, ensuring these platforms comply is difficult due to the lack of a standard evaluation method. Our study examined explanations from Google, Yahoo, Bing, Amazon, Booking, and Tripadvisor. We gathered insights from three legal experts and over a hundred people to gauge the clarity of these explanations, finding significant variations in clarity across platforms. Reviewing these explanations manually is cumbersome. To streamline this, we developed automated tools and compared their effectiveness against human assessments. Our discussion revolves around how these tools can enhance transparency on online platforms."], "field": "Social Sciences", "q_year": 2025, "q_cid": "277545875", "pos_cid": 266521390, "source": "eval_collection"}
{"query_id": "scaleup_26931616_22938772", "query": "How to interpret the novel’s gendered and religio-political meanings concerning women’s marginalisation, violence, and denial of autonomy while accounting for its distinct voices, differing perceptions of reality, and social world beyond the text", "pos": ["The translingual subjects: Shaping identities and deconstructing rainbowism in One Foreigner’s Ordeal. The end of the apartheid era in South Africa inaugurated an increased mobility and accessibility to previously prohibited spaces. Although African migrant populations are still highly regulated in South Africa, their presence has also profoundly transformed the country’s present-day sociolinguistic and cultural landscape. The textual construction of the literary text in this study draws attention to the post-structuralist perspective which argues that languages are not closed entities but rather open systems utilised for expressive purposes in specific social contexts. Most significantly, recent sociolinguistic studies show that languages are no longer regarded as discrete systems in communication because they form expansive linguistic repertoires in contact spaces. Such an understanding of multilingual use facilitates communication across cultural, linguistic and national borders, thereby subverting exclusionary normative practices. The present article draws from translingual perspectives to examine communicative practices in literary discourse. A close textual analysis is adopted to identify how translingual practices make languaging a contested terrain meant to project multi-voiced and multi-perspectival discourses with transformative capacities in the context of the ‘rainbow nation’ metanarrative."], "field": "Social Sciences", "q_year": 2024, "q_cid": "269316164", "pos_cid": 229387721, "source": "eval_collection"}
{"query_id": "scaleup_25487641_19521774", "query": "How to identify and understand hidden sources of inauthentic gene research that resemble research support services", "pos": ["Strong by concealment? How secrecy, trust, and social embeddedness facilitate corporate crime. This article examines how corporate crime is organised through studying the longevity of illegal business cartels. Previous studies demonstrate cartels can remain undetected for years or decades. Similar to criminal networks, cartel participants need to communicate in order to collaborate effectively, but operate covertly at the same time. The case study analysis of fourteen Dutch cartel cases in this study demonstrates two main findings. First, cartel participants communicate frequently and elaborately, and the need for trust and communication impedes concealment. Second, the longevity of cartels cannot be explained by isolation from but by embeddedness in their social environment. The context of legitimacy and a facilitating environment are significant factors. Criminal collaboration is studied extensively in literature on organised crime, however gained little attention in the literature on corporate crime. Hereby, this study contributes to an understanding of how corporate criminal conduct is organised, by applying relevant theory on criminal networks gleaned from the literature on organised crime."], "field": "Social Sciences", "q_year": 2022, "q_cid": "254876415", "pos_cid": 195217744, "source": "eval_collection"}
{"query_id": "scaleup_24696895_20737416", "query": "How to explain people’s interpretations of racially tinged Covid-19 disinformation when their existing narratives alone are insufficient", "pos": ["Reliance on Facebook for news and its influence on political engagement. This paper examines the link between reliance on Facebook for news, political knowledge, and political engagement in the Philippines. We tested five hypotheses using data gathered from an online survey of 978 Filipinos conducted from February 1 to March 31, 2016. Findings support the hypothesis that those who rely less on social media as a news source exhibit higher levels of perceived knowledge about politics than those who rely more on it for news. Controlling for traditional news use, following political officials or institutions on social media is associated with higher levels of political interest and engagement, those with more politically active friends on Facebook have higher levels of exposure to political content online, and there is a positive correlation between Facebook being a source of information about politics and discussing politics more often with others. However, the hypothesis that those with more friends on their network who are politically active, will have greater political knowledge and more political engagement than those who have few politically active friends on their Facebook network is not supported."], "field": "Social Sciences", "q_year": 2022, "q_cid": "246968957", "pos_cid": 207374160, "source": "eval_collection"}
{"query_id": "scaleup_24906484_34720979", "query": "How to clarify the relationship between hospital employees’ concern for others and their willingness to vaccinate", "pos": ["Global Evidence on Economic Preferences*. This paper studies the global variation in economic preferences. For this purpose, we present the Global Preference Survey (GPS), an experimentally validated survey dataset of time preference, risk preference, positive and negative reciprocity, altruism, and trust from 80,000 individuals in 76 countries. The data reveal substantial heterogeneity in preferences across countries, but even larger within-country heterogeneity. Across individuals, preferences vary with age, gender, and cognitive ability, yet these relationships appear partly country specific. At the country level, the data reveal correlations between preferences and bio-geographic and cultural variables such as agricultural suitability, language structure, and religion. Variation in preferences is also correlated with economic outcomes and behaviors. Within countries and subnational regions, preferences are linked to individual savings decisions, labor market choices, and prosocial behaviors. Across countries, preferences vary with aggregate outcomes ranging from per capita income, to entrepreneurial activities, to the frequency of armed conflicts."], "field": "Social Sciences", "q_year": 2022, "q_cid": "249064845", "pos_cid": 34720979, "source": "eval_collection"}
{"query_id": "scaleup_26647809_25346021", "query": "How to clarify how TikTok citizen journalists’ understandings of personalized news distribution shape their reporting choices and expectations about whom their news will reach", "pos": ["The Algorithmic Crystal: Conceptualizing the Self through Algorithmic Personalization on TikTok. This research examines how TikTok users conceptualize and engage with personalized algorithms on the TikTok platform. Using qualitative methods, we analyzed 24 interviews with TikTok users to explore how algorithmic personalization processes inform people's understanding of their identities as well as shape their orientation to others. Building on insights from our qualitative data and previous scholarship on algorithms and identity, we propose a novel conceptual model to understand how people think about and interact with personalized algorithmic systems. Drawing on the metaphor of crystals and their properties, the algorithmic crystal framework is an analytic frame that captures user understandings of how personalized algorithms (1) interact with user identity by reflecting user self-concepts that are both multifaceted and dynamic and (2) shape perspectives on others encountered through the algorithm, by orienting users to recognize parts of themselves refracted in other users and to experience ephemeral, diffracted connections with groups of similar others. We describe how the algorithmic crystal framework can extend theory and inform new lines of research around the implications of algorithms in self-concept development and social life."], "field": "Social Sciences", "q_year": 2023, "q_cid": "266478094", "pos_cid": 253460219, "source": "eval_collection"}
{"query_id": "scaleup_25487641_21121823", "query": "How to recognize untrustworthy paper mill articles with manipulated or duplicated figures and unconvincing supporting evidence despite limited awareness of paper mills and expectations that research fraud is rare", "pos": ["No raw data, no science: another possible source of the reproducibility crisis. A reproducibility crisis is a situation where many scientific studies cannot be reproduced. Inappropriate practices of science, such as HARKing, p-hacking, and selective reporting of positive results, have been suggested as causes of irreproducibility. In this editorial, I propose that a lack of raw data or data fabrication is another possible cause of irreproducibility. As an Editor-in-Chief of Molecular Brain, I have handled 180 manuscripts since early 2017 and have made 41 editorial decisions categorized as “Revise before review,” requesting that the authors provide raw data. Surprisingly, among those 41 manuscripts, 21 were withdrawn without providing raw data, indicating that requiring raw data drove away more than half of the manuscripts. I rejected 19 out of the remaining 20 manuscripts because of insufficient raw data. Thus, more than 97% of the 41 manuscripts did not present the raw data supporting their results when requested by an editor, suggesting a possibility that the raw data did not exist from the beginning, at least in some portions of these cases. Considering that any scientific study should be based on raw data, and that data storage space should no longer be a challenge, journals, in principle, should try to have their authors publicize raw data in a public database or journal site upon the publication of the paper to increase reproducibility of the published results and to increase public trust in science."], "field": "Social Sciences", "q_year": 2022, "q_cid": "254876415", "pos_cid": 211218234, "source": "eval_collection"}
{"query_id": "scaleup_24703957_14872107", "query": "How to understand tradition-based calling beyond a deeply felt sense of calling, accounting for workers’ tradition-specific meanings, moral justifications for work choices, and relationship to an external caller", "pos": ["Employing Interpretivism in Social Work Research. Interpretivism is a research paradigm that is associated with qualitative research. A tradition of Interpretivism can be linked to the ethnographies of non-western peoples in the 19th century and continues to be a popular way to explain human behaviour and social phenomenon today. The interpretivist view invites the researcher to investigate meaning behind the understanding of human behaviour, interactions and society. This involves the researcher attempting to develop an in-depth subjective understanding of people's lives. The difference between the natural sciences and social sciences is that the natural sciences requires the researcher to observe and interpret natural processes but the social sciences requires the researcher to observe a phenomenon and understand the interpretations that individuals have already made. Social work research aims to explain human behavior and social phenomenon and not to focus on isolating and objectively measuring variables or on developing generalizations. Social work research requires a focus on gaining an empathic understanding of an individual's feelings and the meaning that they give to everyday life with the goal to gaining greater understanding of the individual's behavior. For this reason, interpretive research is well suited to social work research. In this introductory paper, the authors present the validity of interpretive research and the value of using it in social work research."], "field": "Social Sciences", "q_year": 2022, "q_cid": "247039576", "pos_cid": 148721076, "source": "eval_collection"}
{"query_id": "scaleup_27273081_14968416", "query": "How to explain why and how creative-sector relationships form and capture their diverse, sometimes intangible value beyond numerical data alone", "pos": ["Social Network Analysis: An Example of Fusion Between Quantitative and Qualitative Methods. A quantitative approach to social network analysis involves the application of mathematical and statistical techniques and graphical presentation of results. Nonetheless—as with all sciences—subjectivity is an integral aspect of network analysis, manifested in the selection of measures to describe connection patterns and actors’ positions (e.g., choosing a centrality indicator), in the visualization of social structure in graphs, and in translating numbers into words (telling the story). Here, we use network research as an example to illustrate how quantitative and qualitative approaches, techniques, and data are mixed along a continuum of fusion between quantitative and qualitative realms."], "field": "Social Sciences", "q_year": 2024, "q_cid": "272730813", "pos_cid": 149684160, "source": "eval_collection"}
{"query_id": "scaleup_24747302_22528884", "query": "How to determine whether secondary school teachers with different combinations of beliefs about teacher and student roles differ in their knowledge related to video-based learning", "pos": ["Exploring the relationship between Chinese pre-service teachers’ epistemic beliefs and their perceptions of technological pedagogical content knowledge (TPACK). ABSTRACT This study aimed to investigate the differences between pre-service teachers’ (PSTs) perceived TPACK given the different clusters of their epistemic beliefs collected via a questionnaire. The responses gathered from 807 Chinese PSTs were utilised to elicit such a relationship. All of the participants responded to the Pre-service Teachers’ Epistemic Belief (PTEB) survey and the Technology, Pedagogy and Content Knowledge (TPACK) survey. The results of the cluster analysis revealed that the PSTs were characterised into three clusters according to their responses to the PTEB, labelled as the Positivist, Partial Constructivist and Constructivist clusters. The ANOVA revealed that the pre-service teachers in both the Positivist and Partial Constructivist clusters had stronger perceptions of their TPACK than did the Constructivist PSTs. The results imply that more nuanced approaches are needed to develop PSTs’ TPACK with reference to their epistemic profiles. In addition, it seems that the epistemic nature of creating TPACK may need to be discussed explicitly to foster PSTs’ epistemic developments."], "field": "Social Sciences", "q_year": 2022, "q_cid": "247473021", "pos_cid": 225288843, "source": "eval_collection"}
{"query_id": "scaleup_26174149_23347627", "query": "How to determine whether travel demand has returned to its previous daily pattern amid near-normal traffic volumes and changes in remote work, given that highway capacity investments are based on peak-hour travel", "pos": ["The potential stickiness of pandemic-induced behavior changes in the United States. Human behavior is notoriously difficult to change, but a disruption of the magnitude of the COVID-19 pandemic has the potential to bring about long-term behavioral changes. During the pandemic, people have been forced to experience new ways of interacting, working, learning, shopping, traveling, and eating meals. A critical question going forward is how these experiences have actually changed preferences and habits in ways that might persist after the pandemic ends. Many observers have suggested theories about what the future will bring, but concrete evidence has been lacking. We present evidence on how much US adults expect their own postpandemic choices to differ from their prepandemic lifestyles in the areas of telecommuting, restaurant patronage, air travel, online shopping, transit use, car commuting, uptake of walking and biking, and home location. The analysis is based on a nationally representative survey dataset collected between July and October 2020. Key findings include that the “new normal” will feature a doubling of telecommuting, reduced air travel, and improved quality of life for some."], "field": "Social Sciences", "q_year": 2023, "q_cid": "261741490", "pos_cid": 233476277, "source": "eval_collection"}
{"query_id": "scaleup_19589345_45211287", "query": "How to identify available databases with adequate publication coverage for a comprehensive review of factors linked to abdominal pain in horses", "pos": ["Searching the veterinary literature: a comparison of the coverage of veterinary journals by nine bibliographic databases.. A thorough search of the literature to find the best evidence is central to the practice of evidence-based veterinary medicine. This requires knowing which databases to search to maximize journal coverage. The aim of the present study was to compare the coverage of active veterinary journals by nine bibliographic databases to inform future systematic reviews and other evidence-based searches. Coverage was assessed using lists of included journals produced by the database providers. For 121 active veterinary journals in the \"Basic List of Veterinary Medical Serials, Third Edition,\" the percentage coverage was the highest for Scopus (98.3%) and CAB Abstracts (97.5%). For an extensive list of 1,139 journals with significant veterinary content compiled from a variety of sources, coverage was much greater in CAB Abstracts (90.2%) than in any other database, the next highest coverage being in Scopus (58.3%). The maximum coverage of the extensive journal list that could be obtained in a search without including CAB Abstracts was 69.8%. It was concluded that to maximize journal coverage and avoid missing potentially relevant evidence, CAB Abstracts should be included in any veterinary literature search."], "field": "Veterinary", "q_year": 2019, "q_cid": "195893452", "pos_cid": 45211287, "source": "eval20x26"}
{"query_id": "scaleup_16066105_30245244", "query": "How to identify compounds that bind strongly to the binding site of the putative B. melitensis target protein and could serve as inhibitors for treating brucellosis", "pos": ["AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization and multithreading. AutoDock Vina, a new program for molecular docking and virtual screening, is presented. AutoDock Vina achieves an approximately two orders of magnitude speed‐up compared with the molecular docking software previously developed in our lab (AutoDock 4), while also significantly improving the accuracy of the binding mode predictions, judging by our tests on the training set used in AutoDock 4 development. Further speed‐up is achieved from parallelism, by using multithreading on multicore machines. AutoDock Vina automatically calculates the grid maps and clusters the results in a way transparent to the user. © 2009 Wiley Periodicals, Inc. J Comput Chem 2010"], "field": "Veterinary", "q_year": 2015, "q_cid": "16066105", "pos_cid": 30245244, "source": "eval20x26"}
{"query_id": "scaleup_11625833_658229", "query": "How to safely address ivermectin-related harm in lions when species-specific safety guidance is lacking and serious adverse reactions are a concern", "pos": ["Intravenous lipid emulsion in clinical toxicology. Intravenous lipid emulsion is an established, effective treatment for local anesthetic-induced cardiovascular collapse. The predominant theory for its mechanism of action is that by creating an expanded, intravascular lipid phase, equilibria are established that drive the offending drug from target tissues into the newly formed 'lipid sink'. Based on this hypothesis, lipid emulsion has been considered a candidate for generic reversal of toxicity caused by overdose of any lipophilic drug. Recent case reports of successful resuscitation suggest the efficacy of lipid emulsion infusion for treating non-local anesthetic overdoses across a wide spectrum of drugs: beta blockers, calcium channel blockers, parasiticides, herbicides and several varieties of psychotropic agents. Lipid emulsion therapy is gaining acceptance in emergency rooms and other critical care settings as a possible treatment for lipophilic drug toxicity. While protocols exist for administration of lipid emulsion in the setting of local anesthetic toxicity, no optimal regimen has been established for treatment of acute non-local anesthetic poisonings. Future studies will shape the evolving recommendations for lipid emulsion in the setting of non-local anesthetic drug overdose."], "field": "Veterinary", "q_year": 2015, "q_cid": "11625833", "pos_cid": 658229, "source": "eval20x26"}
{"query_id": "scaleup_20171128_3478889", "query": "How to reliably determine when laying hens die during on-farm killing and assess the welfare impact of different killing methods", "pos": ["A novel non‐invasive method for evaluating electroencephalograms on laying hens. Abstract The use of electroencephalograms (EEG) to study the avian brain relative to behavior was conducted as early as the 1960's. EEG readings, combined with visual cues, provide the ability to elucidate and correlate behaviors to neurological and physiological changes in a chicken. The use of EEG recordings in animal models require access to the brain to implant electrodes. Having the ability to observe EEG activity on sensible birds without surgical implantation could broaden the research in this area and give further insight related to the hen's state of awareness. The development, construction, and implementation of a minimally invasive EEG electrode placement method is described. After implementation, test animals were exposed to extreme environmental stressors as part of a concurrent depopulation methods study and EEG placement withstood the condition changes and corresponding animal physical activity. Sixteen white commercial laying hens had three monopolar 32‐gauge needle electrodes inserted subcutaneously and secured to their head and body. Electrodes were attached to a pre‐amplifier which transferred EEG signals to a laptop based recording system. Once the electrodes were in place, the hens were placed in individual treatment/observation chamber then various environmental stressors were applied. Verification that the observed brainwave activity was neural and not muscular was done using a photic stimulation validation test. Behavior observations were recorded to correlate sensible and insensible brainwave activity. The validation test and behavior observations demonstrated the method was successful in measuring EEG in sensible laying hens. The use of a non‐surgical method for recording EEG will broaden research capabilities and enhance the understanding of a hen's response its environment, eliminate the need for invasive surgical procedures, and minimizes the confounding components of anesthesia, brain surgery, and recovery. With further refinements, the method could open new avenues in avian behavioral and physiological research."], "field": "Veterinary", "q_year": 2019, "q_cid": "201711282", "pos_cid": 3478889, "source": "eval20x26"}
{"query_id": "scaleup_19589345_12719181", "query": "How to clarify what is known about equine colic risk factors and which areas warrant more detailed evaluation given a large and diverse evidence base", "pos": ["Scoping studies: towards a methodological framework. This paper focuses on scoping studies, an approach to reviewing the literature which to date has received little attention in the research methods literature. We distinguish between different types of scoping studies and indicate where these stand in relation to full systematic reviews. We outline a framework for conducting a scoping study based on our recent experiences of reviewing the literature on services for carers for people with mental health problems. Where appropriate, our approach to scoping the field is contrasted with the procedures followed in systematic reviews. We emphasize how including a consultation exercise in this sort of study may enhance the results, making them more useful to policy makers, practitioners and service users. Finally, we consider the advantages and limitations of the approach and suggest that a wider debate is called for about the role of the scoping study in relation to other types of literature reviews."], "field": "Veterinary", "q_year": 2019, "q_cid": "195893452", "pos_cid": 12719181, "source": "eval20x26"}
{"query_id": "scaleup_14699036_24803735", "query": "How to clarify the relationship between gut-derived hormones and excessive hormone secretion in horses given the limitations of intravenous testing", "pos": ["GIP biology and fat metabolism.. The gastrointestinal hormone, gastric inhibitory polypeptide (GIP), is synthesized and released from the duodenum and proximal jejunum postprandially. Its release depends upon several factors including meal content and pre-existing health status (ie. obesity, diabetes, age, etc.). It was initially discovered and named for its gastric acid inhibitory properties. However, its more physiologically relevant role appears to be as an insulinotropic agent with a stimulatory effect on insulin release and synthesis. Accordingly, it was later renamed glucose-dependent insulinotropic polypeptide because its action on insulin release depends upon an increase in circulating levels of glucose. GIP is considered to be one of the principle incretin factors of the enteroinsular axis. The GIP receptor is a G-protein-coupled receptor belonging to the family of secretin/VIP receptors. GIP receptor mRNA is widely distributed in peripheral organs, including the pancreas, gut, adipose tissue, heart, adrenal cortex, and brain, suggesting it may have other functions in addition to the ones mentioned above. An overactive enteroinsular axis has been suggested to play a role in the pathogenesis of diabetes and obesity. In addition to stimulating insulin release, GIP has been shown to amplify the effect of insulin on target tissues. In adipose tissue, GIP has been reported to (1) stimulate fatty acid synthesis, (2) enhance insulin-stimulated incorporation of fatty acids into triglycerides, (3) increase insulin receptor affinity, and (4) increase sensitivity of insulin-stimulated glucose transport. In addition, although controversial, lipolytic properties of GIP have been proposed. The mechanism of action of GIP-induced effects on adipocytes is unknown, and it is unclear whether these effects of GIP on adipocytes are direct or indirect. However, there is now evidence that GIP receptors are expressed on adipocytes and that these receptors respond to GIP stimulation. Given the location of its release and the timing of its release, GIP is an ideal anabolic agent and expanding our understanding of its physiology will be needed to determine its exact role in the etiology of diabetes mellitus and obesity."], "field": "Veterinary", "q_year": 2016, "q_cid": "14699036", "pos_cid": 24803735, "source": "eval20x26"}
{"query_id": "scaleup_64309205_83812805", "query": "How to improve health and immunity in pre-weaned dairy calves highly susceptible to digestive diseases", "pos": ["Dietary rice bran supplementation prevents Salmonella colonization differentially across varieties and by priming intestinal immunity. The global burden of enteric dysfunction and diarrhoeal disease remains a formidable problem that requires novel interventions. This study investigated the immune-modulatory capacity of bran across rice varieties with phytochemical differences. 129SvEvTac mice were fed a 10% rice bran or control diet followed by infection with Salmonella enterica. Faecal shedding titres were quantified and flow cytometry was used to investigate intestinal immunity. The largest protection against Salmonella colonization was observed with IAC600 variety. Reduced faecal shedding correlated with increased levels of boron, soluble fibre, vitamin E isomers, and fatty acids. IAC600 and Red Wells rice bran modulated small intestinal neutrophils, macrophages, interdigitating dendritic cells, CD8+, γδ, and regulatory T cells, as well as CD8+ and γδ T cells in the mesenteric lymph nodes. Rice bran is a promising functional food and merits evaluation for the prevention of Salmonella colonization and regulation of intestinal immunity in people."], "field": "Veterinary", "q_year": 2019, "q_cid": "64309205", "pos_cid": 83812805, "source": "eval20x26"}
{"query_id": "scaleup_18883879_41172612", "query": "How to quantify each remaining support’s share of total weight-bearing load after removal of a rear support", "pos": ["Modifications of a force plate system for equine gait analysis.. A force plate system for measurement of the vertical component of the force applied by a horse's limb on ground contact was modified. The modifications included use of steel supporting posts for improved durability and an additional strain gauge on each arm of the Wheatstone bridge for increased sensitivity and temperature compensation. Data from clinically normal horses are provided to indicate the performance obtained with these modifications of the force plate system."], "field": "Veterinary", "q_year": 2016, "q_cid": "18883879", "pos_cid": 41172612, "source": "eval20x26"}
{"query_id": "scaleup_26465240_1180991", "query": "How to evaluate genetic susceptibility to claw disorders when claw health is recorded in ordered severity categories", "pos": ["Sire evaluation for ordered categorical data with a threshold model. A method of evaluation of ordered categorical responses is presented. The probability of response in a given category follows a normal integral with an argument dependent on fixed thresholds and random variables sampled from a conceptual distribution with known first and second moments, a priori. The prior distribution and the likelihood function are combined to yield the posterior density from which inferences are made. The mode of the posterior distribution is taken as an estimator of location. Finding this mode entails solving a non-linear system ; estimation equations are presented. Relationships of the procedure to \"generalized linear models\" and \"normal scores are discussed. A numerical example involving sire evaluation for calving ease is used to illustrate the method."], "field": "Veterinary", "q_year": 2015, "q_cid": "26465240", "pos_cid": 1180991, "source": "eval20x26"}
{"query_id": "scaleup_28104257_45995237", "query": "How to determine when early immune responses favor Brucella clearance versus persistent infection", "pos": ["Antagonistic crosstalk between type I and II interferons and increased host susceptibility to bacterial infections. Type I and II interferons (IFNs αβ and γ) have opposing effects on immune resistance to certain pathogenic bacteria. While IFNγ generally plays a protective role, IFNαβ exacerbates Listeria monocytogenes and Mycobacterium tuberculosis infections. Our findings provided evidence that this increased susceptibility reflects a novel antagonistic cross talk between IFNαβ and IFNγ. Macrophages infected with L. monocytogenes strains that induce IFNαβ production responded poorly to IFNγ, as measured by reduced phosphorylation of STAT1 and reduced IFNγ-dependent gene expression. The impaired responsiveness to IFNγ correlated with reduced expression of its receptor, IFNGR, by both infected and bystander macrophages. Down regulation of IFNGR was dependent on responsiveness to IFNγ and mimicked by recombinant IFNβ. Mice lacking responsiveness to IFNαβ (IFNAR1-/-) retained high IFNGR expression, developed higher expression of MHC-II on macrophages and DCs, and were more resistant to systemic L. monocytogenes infection - but only in the presence of IFNγ. Thus, the ability of IFNαβ to down regulate IFNGR provides an explanation for its ability to reduce responsiveness to IFNγ and to increase host susceptibility to bacterial infection. It remains to be determined whether and how such antagonistic interferon crosstalk benefits the host."], "field": "Veterinary", "q_year": 2025, "q_cid": "281042572", "pos_cid": 45995237, "source": "eval_collection"}
{"query_id": "scaleup_26092080_19581359", "query": "How to assess the physiological effects of kidney nerve disruption despite uncertain completeness and effectiveness and methodological and technical flaws in earlier human trials", "pos": ["Renal Denervation: Is It Ready for Prime Time?. Purpose of ReviewInterventional cardiology and in particular the field of renal denervation is subject to constant change. This review provides an up to date overview of renal denervation trials and an outlook on what to expect in the future.Recent FindingsAfter the sham-controlled SYMPLICITY HTN-3 trial dampened the euphoria following early renal denervation trials, the recently published results of the sham-controlled SPYRAL HTN and RADIANCE HTN trials provided proof-of-principle for the blood pressure-lowering efficacy of renal denervation. However, these studies underline the major issue of patients’ non-adherence to antihypertensive medication as well as the need for reliable patient- and procedure-related predictors of response.SummaryThe second generation of sham-controlled renal denervation trials provided proof of principle for the blood pressure-lowering efficacy of RDN. However, larger trials have to assess long-term safety and efficacy."], "field": "Veterinary", "q_year": 2023, "q_cid": "260920802", "pos_cid": 195813596, "source": "eval_collection"}
{"query_id": "scaleup_26509311_22088560", "query": "How to reliably confirm germ-free conditions in mouse colonies", "pos": ["Steam Sterilization Chemical Indicators Are Not Adequate for Monitoring Real Steam Sterilization Cycles. Chemical indicators are commonly used in hospitals to monitor steam sterilization conditions, indicating that medical devices are safe to be used. The results are stored for future evidence in the event of an infection incident root cause analysis. This type of indicator is also becoming an option for cycle monitoring in pharmaceutical steam sterilizers, improving cycle control. Chemical indicators are commonly used in hospitals to monitor steam sterilization conditions, indicating that medical devices are safe to be used. The results are stored for future evidence in the event of an infection incident root cause analysis. This type of indicator is also becoming an option for cycle monitoring in pharmaceutical steam sterilizers, improving cycle control. They are constructed and tested according to published standards, but contradictory results between chemical indicators and cycle printouts have a critical impact on process control. We found that Type 6 chemical indicators used in steam sterilizer cycles did not perform according to their intended use, showing an “approved” result in a “failed” cycle (a false positive). This study demonstrated that Type 6 chemical indicator specifications are not adequate for monitoring steam sterilizers. A change in standards is therefore needed."], "field": "Veterinary", "q_year": 2023, "q_cid": "265093116", "pos_cid": 220885608, "source": "eval_collection"}
{"query_id": "scaleup_24808828_21371255", "query": "How to determine how full versus partial maternal contact affects calf development and explain potential differences", "pos": ["Microbial transmission in animal social networks and the social microbiome. Host-associated microbiomes play an increasingly appreciated role in animal metabolism, immunity and health. The microbes in turn depend on their host for resources and can be transmitted across the host’s social network. In this Perspective, we describe how animal social interactions and networks may provide channels for microbial transmission. We propose the ‘social microbiome’ as the microbial metacommunity of an animal social group. We then consider the various social and environmental forces that are likely to influence the social microbiome at multiple scales, including at the individual level, within social groups, between groups, within populations and species, and finally between species. Through our comprehensive discussion of the ways in which sociobiological and ecological factors may affect microbial transmission, we outline new research directions for the field. This Perspective discusses the microbial metacommunity of animal social groups, and the social and environmental forces that shape it at different levels, from individuals to species."], "field": "Veterinary", "q_year": 2022, "q_cid": "248088284", "pos_cid": 213712554, "source": "eval_collection"}
{"query_id": "scaleup_27193177_26746232", "query": "How to obtain standardized diagnostic reagents for reliable, specific detection of antibodies against Brucella when natural antigen isolation and standardization are difficult", "pos": ["Fluorescence-Polarization-Based Assaying of Lysozyme with Chitooligosaccharide Tracers. Lysozyme is a well-known enzyme found in many biological fluids which plays an important role in the antibacterial protection of humans and animals. Lysozyme assays are used for the diagnosis of a number of diseases and utilized in immunohistochemistry, genetic and cellular engineering studies. The assaying methods are divided into two categories measuring either the concentration of lysozyme as a protein or its activity as an enzyme. While the first category of methods traditionally uses an enzyme-linked immunosorbent assay (ELISA), the methods for the determination of the enzymatic activity of lysozyme use either live bacteria, which is rather inconvenient, or natural peptidoglycans of high heterogeneity and variability, which leads to the low reproducibility of the assay results. In this work, we propose the use of a chemically synthesized substrate of a strictly defined structure to measure in a single experiment both the concentration of lysozyme as a protein and its enzymatic activity by means of the fluorescence polarization (FP) method. Chito-oligosaccharides of different chain lengths were fluorescently labeled and tested leading to the selection of the pentasaccharide as the optimal size tracer and the further optimization of the assay conditions for the accurate (detection limit 0.3 μM) and rapid (<30 min) determination of human lysozyme. The proposed protocol was applied to assay human lysozyme in tear samples and resulted in good correlation with the reference assay. The use of synthetic fluorescently labeled tracer, in contrast to natural peptidoglycan, in FP analysis allows for the development of a reproducible method for the determination of lysozyme activity."], "field": "Veterinary", "q_year": 2024, "q_cid": "271931773", "pos_cid": 267462321, "source": "eval_collection"}
{"query_id": "scaleup_23549521_14190444", "query": "How to accurately count steps in equine accelerometer recordings during stall confinement", "pos": ["Accelerometer-Based Step Regularity Is Lower in Older Adults with Bilateral Knee Osteoarthritis. Purpose: To compare the regularity and symmetry of gait between a cohort of older adults with bilateral knee osteoarthritis (OA) and an age and sex-matched control group of older adults with healthy knees. Methods: Fifteen (8 females) older adults with knee OA (64.7 ± 6.7 years) and fifteen (8 females) pain-free controls (66.1 ± 10.0 years) completed a 9-min. walk at a self-selected, comfortable speed while wearing a single waist-mounted tri-axial accelerometer. The following gait parameters were compared between the two groups according to sex: mean step time, mean stride time, stride and step regularity (defined as the consistency of the stride-to-stride or step-to-step pattern) and the symmetry of gait (defined as the difference between step and stride regularity) as determined by an unbiased autocorrelation procedure that analyzed the pattern of acceleration in the vertical, mediolateral and anteroposterior directions. Results: Older adults with knee OA displayed significantly less step regularity in the vertical (p < 0.05) and anteroposterior (p < 0.05) directions than controls. Females with knee OA were also found to have significantly less mediolateral step regularity than female controls (p < 0.05), whereas no difference was found between males. Conclusion: The results showed that the regularity of the step pattern in individuals with bilateral knee OA was less consistent compared to similarly-aged older adults with healthy knees. The findings suggest that future studies should investigate the relationship between step regularity, sex and movement direction as well as the application of these methods to the clinical assessment of knee OA."], "field": "Veterinary", "q_year": 2021, "q_cid": "235495210", "pos_cid": 14190444, "source": "eval_collection"}
{"query_id": "scaleup_25287797_9482743", "query": "How to protect piglets’ respiratory health during farrowing and lactation while managing purchased replacement gilts and limiting additional costs", "pos": ["Survey on Mycoplasma hyopneumoniae gilt acclimation practices in Europe. Gilts are considered to play a key role in Mycoplasma hyopneumoniae (M. hyopneumoniae) transmission and control. An effective gilt acclimation program should ideally reduce M. hyopneumoniae shedding at first farrowing, decreasing pre-weaning colonization prevalence and potential respiratory problems in fatteners. However, information on gilt acclimation practices is scarce in Europe. The aim of this study was to identify current acclimation strategies for M. hyopneumoniae in Europe using a questionnaire designed to assess 15 questions focused on gilt replacement status, acclimation strategies and methods used to ascertain its effect. A total of 321 questionnaires (representing 321 farms) were voluntarily completed by 108 veterinarians (from 18 European countries). From these farms, 280 out of 321 (87.2%) were aware of the health status of gilts on arrival. From these 280 farms, 161 (57.5%) introduced M. hyopneumoniae positive replacements. In addition, 249 out of 321 (77.6%) farms applied an acclimation process using different strategies, being M. hyopneumoniae vaccination (145 out of 249, 58.2%) and the combination of vaccine and exposure to sows selected for slaughter (53 out of 249, 21.3%) the most commonly used. Notwithstanding, only 53 out of 224 (23.6%) farms, knowing the M. hyopneumoniae initial status and performing acclimation strategies against it, verified the effect of the acclimation by ELISA (22 out of 53, 41.5%), PCR (4 out of 53, 7.5%) or both (27 out of 53, 50.9%). This study showed that three fourths of the farms represented in this European survey have M. hyopneumoniae acclimation strategies for gilts, and one fifth of them verify to some extent the effect of the process. Taking into account that the assessment of acclimation efficacy could help in optimizing replacement gilt introduction into the breeding herd, it seems these practices for M. hyopneumoniae are still poorly developed in Europe."], "field": "Veterinary", "q_year": 2022, "q_cid": "252877974", "pos_cid": 9482743, "source": "eval_collection"}
{"query_id": "scaleup_23523253_15442815", "query": "How to understand the relationships between multiple attitudes towards antibiotic use and resistance, behaviours, and structural characteristics together rather than in isolation", "pos": ["Attitudes to Agricultural Policy and Farming Futures in the Context of the 2003 CAP Reform: a Comparison of Farmers in Selected Established and New Member States. Farmers’ attitudes, to agricultural production, diversification and policy support, and behavioural intentions in five Member States of the EU (France, Lithuania, Slovakia, Sweden, England) are analysed comparatively. Groups of farmers with similarly held attitudes are identified using cluster analysis to investigate whether differences in attitudes are defined predominately according to national, east–west, size or other criteria. The results highlight that the vast majority of farmers in the enlarged EU retain a productivist mindset, wish to maintain an agricultural focus and strongly reject notions of policy liberalisation. However, while the overwhelming majority advocate protection they are more receptive to greater flexibility in terms of the instruments through which policy support may be delivered. Overall, the strongest opposition to policy liberalisation comes from farmers in the New Member States of the EU."], "field": "Veterinary", "q_year": 2021, "q_cid": "235232531", "pos_cid": 154428158, "source": "eval_collection"}
{"query_id": "scaleup_22478348_56321659", "query": "How to determine whether glycomacropeptide can improve gut bacterial balance in inflammatory bowel disease, for which current treatments remain insufficient", "pos": ["Modulation of mice fecal microbiota by administration of casein glycomacropeptide. Casein glycomacropeptide (GMP) is known to promote the in vitro growth of Bifidobacteria and Lactobacilli . In this paper, we used conven- tional culture techniques and fluorescent in situ hybridization (FISH) techniques to investigate the effect of casein GMP on mice fecal microbiota. The population structure of the intestinal microbiota, including Lactobacillus , Bifidobacteria , Enterococcus , coliforms and Enterobacteriaceae , was tested and compared. After consecutive administration of casein GMP for 15 days, numbers of Lactobacillus and Bifidobacteria increased significantly (P<0.01), numbers of Enterobacteriaceae and Coliforms decreased significantly (P<0.05) while no significant changes were observed for Enterococcus. The detection limits of FISH technique were significantly lower (P<0.01) than the traditional culture method. These results suggested that consumption of casein GMP had a prebiotic effect on male BALB/c mice. Casein GMP helped establish a healthier intestinal microbiota. Additionally, FISH was proved to be a rapid and relatively low-cost detection method that can be used to further our understanding of human intestinal microbiota."], "field": "Veterinary", "q_year": 2020, "q_cid": "224783481", "pos_cid": 56321659, "source": "eval_collection"}
{"query_id": "scaleup_21086880_26392891", "query": "How to establish clear, consistent distinctions among animal emotional processes, clarify their relationships to cognition and subjective feeling, and understand the neural basis of different emotional experiences", "pos": ["Affective neuroscience of the emotional BrainMind: evolutionary perspectives and implications for understanding depression. Cross-species affective neuroscience studies confirm that primary-process emotional feelings are organized within primitive subcortical regions of the brain that are anatomically, neurochemically, and functionally homologous in all mammals that have been studied. Emotional feelings (affects) are intrinsic values that inform animals how they are faring in the quest to survive. The various positive affects indicate that animals are returning to “comfort zones” that support survival, and negative affects reflect “discomfort zones” that indicate that animals are in situations that may impair survival. They are ancestral tools for living - evolutionary memories of such importance that they were coded into the genome in rough form (as primary brain processes), which are refined by basic learning mechanisms (secondary processes) as well as by higher-order cognitions/thoughts (tertiary processes). To understand why depression feels horrible, we must fathom the affective infrastructure of the mammalian brain. Advances in our understanding of the nature of primary-process emotional affects can promote the development of better preclinical models of psychiatric disorders and thereby also allow clinicians new and useful ways to understand the foundational aspects of their clients' problems. These networks are of clear importance for understanding psychiatric disorders and advancing psychiatric practice."], "field": "Veterinary", "q_year": 2020, "q_cid": "210868801", "pos_cid": 263928913, "source": "eval_collection"}
{"query_id": "scaleup_22478348_22331940", "query": "How to reduce intestinal permeability in athletes during peak training", "pos": ["Oral Supplementation with Bovine Colostrum Decreases Intestinal Permeability and Stool Concentrations of Zonulin in Athletes. Increased intestinal permeability has been implicated in various pathologies, has various causes, and can develop during vigorous athletic training. Colostrum bovinum is a natural supplement with a wide range of supposed positive health effects, including reduction of intestine permeability. We assessed influence of colostrum supplementation on intestinal permeability related parameters in a group of 16 athletes during peak training for competition. This double-blind placebo-controlled study compared supplementation for 20 days with 500 mg of colostrum bovinum or placebo (whey). Gut permeability status was assayed by differential absorption of lactulose and mannitol (L/M test) and stool zonulin concentration. Baseline L/M tests found that six of the participants (75%) in the colostrum group had increased intestinal permeability. After supplementation, the test values were within the normal range and were significantly lower than at baseline. The colostrum group Δ values produced by comparing the post-intervention and baseline results were also significantly lower than the placebo group Δ values. The differences in stool zonulin concentration were smaller than those in the L/M test, but were significant when the Δ values due to intervention were compared between the colostrum group and the placebo group. Colostrum bovinum supplementation was safe and effective in decreasing of intestinal permeability in this series of athletes at increased risk of its elevation."], "field": "Veterinary", "q_year": 2020, "q_cid": "224783481", "pos_cid": 22331940, "source": "eval_collection"}
{"query_id": "scaleup_21086880_20283202", "query": "How to reliably assess positive emotional states in animal social relationships", "pos": ["Strongly bonded family members in common marmosets show synchronized fluctuations in oxytocin. Oxytocin is a key regulator of social bonding and is positively linked to affiliation and prosocial behavior in several mammal species. In chimpanzees, this link is dyad-specific as affiliative interactions only elicit high oxytocin release if they involve strongly bonded individuals. These studies involved isolated dyads and sampling events. Little is known about the role of oxytocin in affiliation and social bonding, and about potential long-term patterns of bonding-related and dyad-specific oxytocin effects within highly affiliative and cooperative social groups. Our aim was to investigate whether bonding-related oxytocin signatures linked to dyadic affiliation are present in family groups of cooperatively breeding marmoset monkeys (Callithrix jacchus) that show high levels of cohesion and cooperation. In 30 dyads from four family groups and one pair, we measured urinary baseline oxytocin over six weeks and analyzed the link to bond strength (mean dyadic affiliation). Strongly bonded dyads showed synchronized longitudinal fluctuations of oxytocin, indicating that dyad-specific oxytocin effects can also be traced in the group context and in an interdependent species. We discuss these results in light of the potential function of differentiated relationships between marmoset dyads other than the breeding pair, and the role of oxytocin as a mediator for social bonding."], "field": "Veterinary", "q_year": 2020, "q_cid": "210868801", "pos_cid": 20283202, "source": "eval_collection"}
{"query_id": "scaleup_26994897_5378988", "query": "How to quantify the timing, magnitude, duration and repeatability of circadian body temperature changes in breeding sows across seasons and oestrus states while accounting for environmental conditions", "pos": ["Cosinor-based rhythmometry. A brief overview is provided of cosinor-based techniques for the analysis of time series in chronobiology. Conceived as a regression problem, the method is applicable to non-equidistant data, a major advantage. Another dividend is the feasibility of deriving confidence intervals for parameters of rhythmic components of known periods, readily drawn from the least squares procedure, stressing the importance of prior (external) information. Originally developed for the analysis of short and sparse data series, the extended cosinor has been further developed for the analysis of long time series, focusing both on rhythm detection and parameter estimation. Attention is given to the assumptions underlying the use of the cosinor and ways to determine whether they are satisfied. In particular, ways of dealing with non-stationary data are presented. Examples illustrate the use of the different cosinor-based methods, extending their application from the study of circadian rhythms to the mapping of broad time structures (chronomes)."], "field": "Veterinary", "q_year": 2024, "q_cid": "269948975", "pos_cid": 5378988, "source": "eval_collection"}
{"query_id": "scaleup_24931880_41660", "query": "How to determine whether candidate Lawsonia intracellularis type 3 secretion effectors perturb conserved cellular processes in a eukaryotic environment", "pos": ["Yeast as a Heterologous Model System to Uncover Type III Effector Function. Type III effectors (T3E) are key virulence proteins that are injected by bacterial pathogens inside the cells of their host to subvert cellular processes and contribute to disease. The budding yeast Saccharomyces cerevisiae represents an important heterologous system for the functional characterisation of T3E proteins in a eukaryotic environment. Importantly, yeast contains eukaryotic processes with low redundancy and are devoid of immunity mechanisms that counteract T3Es and mask their function. Expression in yeast of effectors from both plant and animal pathogens that perturb conserved cellular processes often resulted in robust phenotypes that were exploited to elucidate effector functions, biochemical properties, and host targets. The genetic tractability of yeast and its amenability for high-throughput functional studies contributed to the success of this system that, in recent years, has been used to study over 100 effectors. Here, we provide a critical view on this body of work and describe advantages and limitations inherent to the use of yeast in T3E research. “Favourite” targets of T3Es in yeast are cytoskeleton components and small GTPases of the Rho family. We describe how mitogen-activated protein kinase (MAPK) signalling, vesicle trafficking, membrane structures, and programmed cell death are also often altered by T3Es in yeast and how this reflects their function in the natural host. We describe how effector structure–function studies and analysis of candidate targeted processes or pathways can be carried out in yeast. We critically analyse technologies that have been used in yeast to assign biochemical functions to T3Es, including transcriptomics and proteomics, as well as suppressor, gain-of-function, or synthetic lethality screens. We also describe how yeast can be used to select for molecules that block T3E function in search of new antibacterial drugs with medical applications. Finally, we provide our opinion on the limitations of S. cerevisiae as a model system and its most promising future applications."], "field": "Veterinary", "q_year": 2022, "q_cid": "249318803", "pos_cid": 41660, "source": "eval_collection"}
{"query_id": "scaleup_27614450_80174904", "query": "How to quantify the amount of bovine colostrum retained in capsules and their holding capacity across different ingredient ratios", "pos": ["Nanoliposome Encapsulation with Donkey Milk Bioactive Proteins and Its Possible Application in Dermatology and Cosmetics. Summary Nanoliposomes represent natural or synthetic nanoparticles made of phospholipids, which may spontaneously aggregate in an aqueous medium. Their use in dermatology and for cosmetic purposes may offer facilitated delivery in skin via enhanced opening of the tight junctions between the epithelial cell monolayers. As far as their use in dermatology is concerned, both transdermal and local application may offer successful release profile. Donkey milk may have special therapeutic properties when used in cosmetology for skin treatment. The aim of our study was to establish encapsulation efficacy of nanoliposome loaded with skimmed donkey milk and to explore the efficiency of encapsulation of different skimmed donkey milk concentrations in nanoliposomes. In our experimental study, it was documented that 1%, 2% and 5% solutions of skimmed donkey milk were almost equally effectively encapsulated, more than 80% in 1% solution of nanoliposomes, while 10% solution of skimmed donkey milk was encapsulated more efficiently, with 88.9% in 1% of nanoliposome solution. Encapsulation can lead to greater efficiency by enabling the use of lower administration doses and preventing the corresponding side effects, which may be the result of higher doses. Skimmed donkey milk is a suitable encapsulation solution."], "field": "Veterinary", "q_year": 2025, "q_cid": "276144504", "pos_cid": 80174904, "source": "eval_collection"}
{"query_id": "scaleup_25939415_22178940", "query": "How to determine whether a dog’s acute illness after anthelmintic administration was associated with the medication or a pre-existing condition when elevated enzyme activity before administration had an uncertain cause", "pos": ["Hyperlipasemia in critically ill dogs with and without acute pancreatitis: Prevalence, underlying diseases, predictors, and outcome. Abstract Background Hyperlipasemia is frequent in critically ill people without evidence of acute pancreatitis (AP), and has been associated with increased morbidity and mortality. Objective To evaluate the prevalence of hyperlipasemia at admission and development of hyperlipasemia during hospitalization in critically ill dogs, explore factors associated with hyperlipasemia, and evaluate association with outcome. Animals Critically ill, client owned dogs (n = 1360), presented on emergency and admitted to the intensive care unit, that had 1,2‐o‐dilauryl‐rac‐glycero‐3‐glutaric acid‐(6′‐methylresorufin) ester (DGGR) lipase activity measured within 24 hours of admission. Methods Retrospective cross‐sectional study of clinical and laboratory records. Results The DGGR lipase activity was increased >3× the upper reference limit at admission in 216/1360 (16%) dogs, of which 70/216 (32%) had a clinical diagnosis of AP. Other primary conditions associated with hyperlipasemia were renal, endocrine, and immune‐mediated diseases, and upper airway obstruction. Predictors of hyperlipasemia at admission were prior glucocorticoid administration, vomiting and abdominal pain, increased age, plasma bilirubin and creatinine concentrations, and decreased hematocrit. Of dogs with repeat measurements, 78/345 (23%) had significantly increased lipase during hospitalization, of which 13/78 (17%) had a clinical diagnosis of AP. Other primary conditions associated with in‐hospital hyperlipasemia were renal and immune‐mediated disorders. Predictors of developing hyperlipasemia during hospitalization were hemodialysis events, increased plasma bilirubin and creatinine concentrations, and decreased hematocrit. Hyperlipasemia both at admission and during hospitalization was associated with longer hospitalization and higher mortality. Conclusions and Clinical Importance Significant DGGR‐hyperlipasemia is frequent in critically ill dogs and associated with a variety of nonpancreatic conditions and negative outcome."], "field": "Veterinary", "q_year": 2023, "q_cid": "259394152", "pos_cid": 221789402, "source": "eval_collection"}
{"query_id": "scaleup_22478348_58568525", "query": "How to prevent late-onset infection in preterm infants with clinically demonstrated effectiveness", "pos": ["Enteral lactoferrin supplementation for very preterm infants: a randomised placebo-controlled trial. Summary Background Infections acquired in hospital are an important cause of morbidity and mortality in very preterm infants. Several small trials have suggested that supplementing the enteral diet of very preterm infants with lactoferrin, an antimicrobial protein processed from cow's milk, prevents infections and associated complications. The aim of this large randomised controlled trial was to collect data to enhance the validity and applicability of the evidence from previous trials to inform practice. Methods In this randomised placebo-controlled trial, we recruited very preterm infants born before 32 weeks' gestation in 37 UK hospitals and younger than 72 h at randomisation. Exclusion criteria were presence of a severe congenital anomaly, anticipated enteral fasting for longer than 14 days, or no realistic prospect of survival. Eligible infants were randomly assigned (1:1) to receive either enteral bovine lactoferrin (150 mg/kg per day; maximum 300 mg/day; lactoferrin group) or sucrose (same dose; control group) once daily until 34 weeks' postmenstrual age. Web-based randomisation minimised for recruitment site, gestation (completed weeks), sex, and single versus multifetal pregnancy. Parents, caregivers, and outcome assessors were unaware of group assignment. The primary outcome was microbiologically confirmed or clinically suspected late-onset infection (occurring >72 h after birth), which was assessed in all participants for whom primary outcome data was available by calculating the relative risk ratio with 95% CI between the two groups. The trial is registered with the International Standard Randomised Controlled Trial Number 88261002. Findings We recruited 2203 participants between May 7, 2014, and Sept 28, 2017, of whom 1099 were assigned to the lactoferrin group and 1104 to the control group. Four infants had consent withdrawn or unconfirmed, leaving 1098 infants in the lactoferrin group and 1101 in the sucrose group. Primary outcome data for 2182 infants (1093 [99·5%] of 1098 in the lactoferrin group and 1089 [99·0] of 1101 in the control group) were available for inclusion in the modified intention-to-treat analyses. 316 (29%) of 1093 infants in the intervention group acquired a late-onset infection versus 334 (31%) of 1089 in the control group. The risk ratio adjusted for minimisation factors was 0·95 (95% CI 0·86–1·04; p=0·233). During the trial there were 16 serious adverse events for infants in the lactoferrin group and 10 for infants in the control group. Two events in the lactoferrin group (one case of blood in stool and one death after intestinal perforation) were assessed as being possibly related to the trial intervention. Interpretation Enteral supplementation with bovine lactoferrin does not reduce the risk of late-onset infection in very preterm infants. These data do not support its routine use to prevent late-onset infection and associated morbidity or mortality in very preterm infants. Funding UK National Institute for Health Research Health Technology Assessment programme (10/57/49)."], "field": "Veterinary", "q_year": 2020, "q_cid": "224783481", "pos_cid": 58568525, "source": "eval_collection"}
{"query_id": "scaleup_27614450_25902345", "query": "How to extend the shelf life of bovine colostrum proteins in cosmetic applications exposed to heat, moisture, and oxygen", "pos": ["Strategies for overcoming protein and peptide instability in biodegradable drug delivery systems. The global pharmaceutical market has recently shifted its focus from small molecule drugs to peptide, protein, and nucleic acid drugs, which now comprise a majority of the top-selling pharmaceutical products on the market. Although these biologics often offer improved drug specificity, new mechanisms of action, and/or enhanced efficacy, they also present new challenges, including an increased potential for degradation and a need for frequent administration via more invasive administration routes, which can limit patient access, patient adherence, and ultimately the clinical impact of these drugs. Controlled-release systems have the potential to mitigate these challenges by offering superior control over in vivo drug levels, localizing these drugs to tissues of interest (e.g., tumors), and reducing administration frequency. Unfortunately, adapting controlled-release devices to release biologics has proven difficult due to the poor stability of biologics. In this review, we summarize the current state of controlled-release peptides and proteins, discuss existing techniques used to stabilize these drugs through encapsulation, storage, and in vivo release, and provide perspective on the most promising opportunities for the clinical translation of controlled-release peptides and proteins."], "field": "Veterinary", "q_year": 2025, "q_cid": "276144504", "pos_cid": 259023454, "source": "eval_collection"}
{"query_id": "scaleup_21086880_1565490", "query": "How to determine whether animals’ resource preferences reflect positive or negative affective states at first encounter despite the close links between preference, learning, and memory", "pos": ["A Translational Rodent Assay of Affective Biases in Depression and Antidepressant Therapy. The subjective measures used to study mood disorders in humans cannot be replicated in animals; however, the increasing application of objective neuropsychological methods provides opportunities to develop translational animal tasks. Here we describe a novel behavioral approach, which has enabled us to investigate similar affective biases in rodents. In our affective bias test (ABT), rats encounter two independent positive experiences—the association between food reward and specific digging substrate—during discrimination learning sessions. These are performed on separate days under either neutral conditions or during a pharmacological or affective state manipulation. Affective bias is then quantified using a preference test where both previously rewarded substrates are presented together and the rat’s choices recorded. The absolute value of the experience is kept consistent and all other factors are counterbalanced so that any bias at recall can be attributed to treatment. Replicating previous findings from studies in healthy volunteers, we observe significant positive affective biases following acute treatment with typical (fluoxetine, citalopram, reboxetine, venlafaxine, clomipramine) and atypical antidepressants (agomelatine, mirtazapine), and significant negative affective biases following treatment with drugs associated with inducing negative affective states in humans (FG7142, rimonabant, 13-cis retinoic acid). We also observed that acute psychosocial stress and environmental enrichment induce significant negative and positive affective biases, respectively, and provide evidence that these affective biases involve memory consolidation. The positive and negative affective biases induced in our test also mirror the antidepressant and pro-depressant effects of these drugs in patients suggesting our test has both translational and predictive validity. Our results suggest that cognitive affective biases could contribute to drug- or stress-induced mood changes in people and support the hypothesis that a cognitive neuropsychological mechanism contributes to antidepressant drug efficacy."], "field": "Veterinary", "q_year": 2020, "q_cid": "210868801", "pos_cid": 1565490, "source": "eval_collection"}
{"query_id": "scaleup_26808455_22215551", "query": "How to reduce parasite transmission in soil and dung when existing drugs are increasingly ineffective", "pos": ["Fungi–Nematode Interactions: Diversity, Ecology, and Biocontrol Prospects in Agriculture. Fungi and nematodes are among the most abundant organisms in soil habitats. They provide essential ecosystem services and play crucial roles for maintaining the stability of food-webs and for facilitating nutrient cycling. As two of the very abundant groups of organisms, fungi and nematodes interact with each other in multiple ways. Here in this review, we provide a broad framework of interactions between fungi and nematodes with an emphasis on those that impact crops and agriculture ecosystems. We describe the diversity and evolution of fungi that closely interact with nematodes, including food fungi for nematodes as well as fungi that feed on nematodes. Among the nematophagous fungi, those that produce specialized nematode-trapping devices are especially interesting, and a great deal is known about their diversity, evolution, and molecular mechanisms of interactions with nematodes. Some of the fungi and nematodes are significant pathogens and pests to crops. We summarize the ecological and molecular mechanisms identified so far that impact, either directly or indirectly, the interactions among phytopathogenic fungi, phytopathogenic nematodes, and crop plants. The potential applications of our understanding to controlling phytophagous nematodes and soilborne fungal pathogens in agricultural fields are discussed."], "field": "Veterinary", "q_year": 2024, "q_cid": "268084550", "pos_cid": 222155517, "source": "eval_collection"}
{"query_id": "scaleup_27614450_24892646", "query": "How to resist microbial growth in cosmetic formulations with available water to maintain preservation and shelf life", "pos": ["Skin Barrier Enhancing Alternative Preservation Strategy of O/W Emulsions by Water Activity Reduction with Natural Multifunctional Ingredients. Water activity (aw) as an important parameter for self-preservation can help to control microbial growth in cosmetic formulations. However, high amounts of water-binding substances are required to lower the aw enough to affect microbial growth. Since consequences for the skin barrier have been poorly studied so far, we investigated the effect of aw-lowering agents on both the antimicrobial properties of o/w emulsions and skin physiological parameters. A combination of selected natural humectants (Sodium lactate, Propanediol, Erythritol, Betaine and Sodium PCA) with a total concentration of 28 wt% in an o/w emulsion was able to reduce its aw from 0.980 ± 0.003 to 0.865 ± 0.005. The challenge test results of the aw-lowered emulsion showed a convincing microbial count reduction in potentially pathogenic microorganisms. The addition of as little as 0.5% of the antimicrobial multifunctionals Glyceryl Caprylate and Magnolia Officinalis Bark Extract further enhanced the antimicrobial effect, resulting in adequate antimicrobial protection. Moreover, twice-daily application of the aw-lowered emulsion for a period of four weeks led to a skin barrier-enhancing effect: TEWL significantly decreased, and SC hydration significantly increased. Thus, we present an opportunity to replace conventional preservatives with a natural alternative preservation strategy that has been shown to offer benefits for the skin."], "field": "Veterinary", "q_year": 2025, "q_cid": "276144504", "pos_cid": 248926462, "source": "eval_collection"}
{"query_id": "scaleup_23523253_4785471", "query": "how to change farmers’ traditional antibiotic-use habits that are tied to familiar contextual cues and persist despite new good-practice recommendations", "pos": ["Habitual behaviors or patterns of practice? Explaining and changing repetitive climate‐relevant actions. Understanding human behavior lies at the heart of responses to climate change. Many environmentally relevant behavior patterns are frequent, stable, and persistent. There is an increasing focus on understanding these patterns less in terms of deliberative processes and more in terms of habits and routines embedded in everyday life. Examinations of the ‘habitual’ nature of environmentally consequential activities have been approached from two theoretically distinct perspectives. From a social psychological perspective, ‘habit’ is studied as an intra‐individual psychological construct that sustains ingrained behavior patterns in stable settings and obstructs adoption of more environmentally friendly alternatives. Sociologists from the social practice tradition, in contrast, have sought to highlight the ways in which resource‐intensive ‘habitual practices’ become established and maintained in society through a commingling of material, procedural, and socio‐discursive elements. We reflect critically upon key theoretical differences underpinning these two approaches to repetitive behaviors and review empirical work from both traditions that speaks to the relevance of ‘habitual behavior patterns’ central to addressing climate change. Finally, we examine how changes in habits are theorized and operationalized within both social psychological and social practice approaches, and practical implications for promoting environmentally sustainable societies. WIREs Clim Change 2015, 6:113–128. doi: 10.1002/wcc.327"], "field": "Veterinary", "q_year": 2021, "q_cid": "235232531", "pos_cid": 4785471, "source": "eval_collection"}
{"query_id": "scaleup_27737944_22188292", "query": "How to identify the cell types or tissues associated with differentially expressed genes linked to drug resistance", "pos": ["A single-cell RNAseq atlas of Schistosoma mansoni identifies a key regulator of blood feeding. Schistosome biology illuminated Schistosomiasis is caused by a parasitic flatworm about which little is known. Therefore, options to combat human disease caused by schistosome infection are limited. To aid in our quest to develop treatments, two studies undertook molecular investigations of the parasite Schistosoma mansoni. By generating a single-cell atlas, Wendt et al. identified the developmental trajectory of the flatworm, including the blood-feeding gut required for its survival in the host. From these data, they found a gene required for gut development that, when knocked out through RNA interference, confers reduced pathology in infected mice. Wang et al. performed a large-scale RNA interference survey of S. mansoni and identified an essential pair of protein kinases that can be targeted by approved pharmacological intervention (see the Perspective by Anderson and Duraisingh). These molecular investigations add to our understanding of the schistosome parasite and provide biological information that may help to combat this neglected tropical disease. Science, this issue p. 1644, p. 1649; see also p. 1562 A single-cell atlas of a parasitic flatworm elucidates schistosome biology, including their feeding and reproduction. Schistosomiasis is a neglected tropical disease that infects 240 million people. With no vaccines and only one drug available, new therapeutic targets are needed. The causative agents, schistosomes, are intravascular flatworm parasites that feed on blood and lay eggs, resulting in pathology. The function of the parasite’s various tissues in successful parasitism are poorly understood, hindering identification of therapeutic targets. Using single-cell RNA sequencing (RNA-seq), we characterize 43,642 cells from the adult schistosome and identify 68 distinct cell populations, including specialized stem cells that maintain the parasite’s blood-digesting gut. These stem cells express the gene hnf4, which is required for gut maintenance, blood feeding, and pathology in vivo. Together, these data provide molecular insights into the organ systems of this important pathogen and identify potential therapeutic targets."], "field": "Veterinary", "q_year": 2025, "q_cid": "277379448", "pos_cid": 221882921, "source": "eval_collection"}
{"query_id": "scaleup_23947489_14443450", "query": "How to detect and address disease before it becomes clinically apparent to prevent progression and reduce high mortality and population-level burden", "pos": ["Cryptococcal Antigen Screening in Patients Initiating ART in South Africa: A Prospective Cohort Study. Treating cryptococcal antigen (CrAg)-positive, antiretroviral therapy naiive patients with preemptive fluconazole resulted in markedly fewer cases of cryptococcal meningitis compared with unscreened historic cohorts. However, the same CrAg-positive patients experienced excess mortality not directly attributable to cryptococcal disease."], "field": "Veterinary", "q_year": 2021, "q_cid": "239474894", "pos_cid": 14443450, "source": "eval_collection"}
{"query_id": "scaleup_26808455_13217866", "query": "How to understand the influence of ecological conditions and other dung organisms on fungal suppression of parasites", "pos": ["Bacteria can mobilize nematode-trapping fungi to kill nematodes. In their natural habitat, bacteria are consumed by bacterivorous nematodes; however, they are not simply passive preys. Here we report a defensive mechanism used by certain bacteria to mobilize nematode-trapping fungi to kill nematodes. These bacteria release urea, which triggers a lifestyle switch in the fungus Arthrobotrys oligospora from saprophytic to nematode–predatory form; this predacious form is characterized by formation of specialized cellular structures or ‘traps’. The bacteria significantly promote the elimination of nematodes by A. oligospora. Disruption of genes involved in urea transport and metabolism in A. oligospora abolishes the urea-induced trap formation. Furthermore, the urea metabolite ammonia functions as a signal molecule in the fungus to initiate the lifestyle switch to form trap structures. Our findings highlight the importance of multiple predator–prey interactions in prey defense mechanisms. Certain soil fungi form specialized cellular structures or 'traps' to feed on nematodes, which in turn eat bacteria. Here, the authors show that urea released from bacteria induces trap formation in the fungi and this promotes nematode elimination."], "field": "Veterinary", "q_year": 2024, "q_cid": "268084550", "pos_cid": 13217866, "source": "eval_collection"}
{"query_id": "scaleup_25065246_76666990", "query": "How to consistently assess vaccine-induced immunity and protection against brucellosis in mouse models despite variability in host characteristics, vaccine properties, administration conditions, and challenge conditions", "pos": ["Factors That Influence the Immune Response to Vaccination. There is substantial variation between individuals in the immune response to vaccination. In this review, we provide an overview of the plethora of studies that have investigated factors that influence humoral and cellular vaccine responses in humans. SUMMARY There is substantial variation between individuals in the immune response to vaccination. In this review, we provide an overview of the plethora of studies that have investigated factors that influence humoral and cellular vaccine responses in humans. These include intrinsic host factors (such as age, sex, genetics, and comorbidities), perinatal factors (such as gestational age, birth weight, feeding method, and maternal factors), and extrinsic factors (such as preexisting immunity, microbiota, infections, and antibiotics). Further, environmental factors (such as geographic location, season, family size, and toxins), behavioral factors (such as smoking, alcohol consumption, exercise, and sleep), and nutritional factors (such as body mass index, micronutrients, and enteropathy) also influence how individuals respond to vaccines. Moreover, vaccine factors (such as vaccine type, product, adjuvant, and dose) and administration factors (schedule, site, route, time of vaccination, and coadministered vaccines and other drugs) are also important. An understanding of all these factors and their impacts in the design of vaccine studies and decisions on vaccination schedules offers ways to improve vaccine immunogenicity and efficacy."], "field": "Veterinary", "q_year": 2022, "q_cid": "250652467", "pos_cid": 76666990, "source": "eval_collection"}
{"query_id": "scaleup_23474375_21240246", "query": "How to improve YAK308’s anti-parasitic potency as a nematocidal candidate", "pos": ["Novel class of benzimidazole-thiazole hybrids: The privileged scaffolds of potent anti-inflammatory activity with dual inhibition of cyclooxygenase and 15-lipoxygenase enzymes.. The present study includes design and synthesis of new molecular hybrids of 2-methylthiobenzimidazole linked to various anti-inflammatory pharmacophores through 2-aminothiazole linker, to investigate the effect of such molecular variation on cyclooxygenase (COX) and 15-lipoxygenase (15-LOX) enzymes inhibition as well as in vivo anti-inflammatory activity. The chemical structures of new hybrids were confirmed using different spectroscopic tools and elemental analyses. Benzimidazole-thiazole hybrids linked to acetyl moiety 13, phenyl thiosemicarbazone 14, 1,3-thiazolines 15a-c and 4-thiazolidinone 16 exhibited significant COX-2 inhibition (IC50 = 0.045-0.075 µM) with significant COX-2 selectivity indices (SI = 142-294). All hybrids revealed potent 15-LOX inhibitory activity (IC50 = 1.67-6.56 µM). Benzimidazole-thiazole hybrid 15b was the most potent dual COX-2 (IC50 = 0.045 µM, SI = 294) inhibitor approximate to celecoxib (COX-2; IC50 = 0.045 µM, SI = 327), with double inhibitory activity versus 15-LOX enzyme (IC50 = 1.67 µM) relative to quercetin (IC50 = 3.34 µM). Three hybrids (14, 15b &16) were selected for in vivo screening using carrageenan-induced paw edema method. Benzimidazole-thiazole hybrid linked to 4-thiazolidinone 16 showed the maximum edema inhibition at both 3 h and 4 h intervals as well (~119% and 102% relative to indomethacin, respectively). The gastric ulcerogenic effect of benzimidazole-thiazole hybrid 16 was estimated compared with indomethacin showing superior gastrointestinal safety profile. In bases of molecular modeling; all new active hybrids were subjected to docking simulation into active sites of COX-2 and 15-LOX enzymes to study the binding mode of these novel potent dual COX-2/15-LOX inhibitors."], "field": "Veterinary", "q_year": 2021, "q_cid": "234743750", "pos_cid": 212402469, "source": "eval_collection"}
{"query_id": "scaleup_28031878_25876721", "query": "How to elicit both antibody and t-cell responses to BtaE", "pos": ["Detoxified synthetic bacterial membrane vesicles as a vaccine platform against bacteria and SARS-CoV-2. The development of vaccines based on outer membrane vesicles (OMV) that naturally bud off from bacteria is an evolving field in infectious diseases. However, the inherent inflammatory nature of OMV limits their use as human vaccines. This study employed an engineered vesicle technology to develop synthetic bacterial vesicles (SyBV) that activate the immune system without the severe immunotoxicity of OMV. SyBV were generated from bacterial membranes through treatment with detergent and ionic stress. SyBV induced less inflammatory responses in macrophages and in mice compared to natural OMV. Immunization with SyBV or OMV induced comparable antigen-specific adaptive immunity. Specifically, immunization with Pseudomonas aeruginosa -derived SyBV protected mice against bacterial challenge, and this was accompanied by significant reduction in lung cell infiltration and inflammatory cytokines. Further, immunization with Escherichia coli -derived SyBV protected mice against E. coli sepsis, comparable to OMV-immunized group. The protective activity of SyBV was driven by the stimulation of B-cell and T-cell immunity. Also, SyBV were engineered to display the SARS-CoV-2 S1 protein on their surface, and these vesicles induced specific S1 protein antibody and T-cell responses. Collectively, these results demonstrate that SyBV may be a safe and efficient vaccine platform for the prevention of bacterial and viral infections."], "field": "Veterinary", "q_year": 2025, "q_cid": "280318786", "pos_cid": 258767215, "source": "eval_collection"}
{"query_id": "scaleup_27417776_27505127", "query": "How to explain the link between unemployment and non-prescription tramadol use among youth in urban informal settlements", "pos": ["Associations between exposure to stressful life events and alcohol use disorder in a longitudinal birth cohort studied to age 30.. BACKGROUND To examine associations between measures of stressful life events exposure and alcohol abuse/dependence (AAD) from ages 18 to 30 using data from a longitudinal birth cohort (n=987 to 1011). METHODS Outcome measures included DSM-IV (American Psychiatric Association, 1994) AAD symptoms and AAD, at ages 20-21, 24-25, and 29-30 years. Exposure to a range of stressful life events was measured during the periods 18-21, 21-25, and 25-30 years using items adapted from the social readjustment rating scale (Holmes and Rahe, 1967). Data were analysed using Generalised Estimating Equation models, adjusted for non-observed sources of confounding using conditional fixed effects regression. Further analyses examined: gender×life events exposure interactions, structural equation modelling of possible reciprocal causal pathways linking stressful life events and AAD symptoms, and an alternative conceptualization of the stressful life events measure. RESULTS After adjustment, those with the highest exposure to stressful life events had rates of AAD symptoms that were 2.24 (p<.0001) times higher, and odds of AAD that were 2.24 times higher(p<.01), than those at the lowest level of exposure. Associations between life events exposure and AAD symptoms were stronger for females than for males (p<.05), with results consistent using a count measure of stressful life events. Structural equation modelling showed that the best-fitting model was one in which life events influenced AAD symptoms. CONCLUSIONS The results suggest that there were persistent linkages between stressful life events and AAD, providing support for a stress-reduction model of alcohol consumption."], "field": "Veterinary", "q_year": 2024, "q_cid": "274177766", "pos_cid": 27505127, "source": "eval_collection"}
{"query_id": "scaleup_28104257_23340169", "query": "How to understand the roles of host immune cell interactions in Brucella persistence, immune evasion, and the establishment and maintenance of chronic infection", "pos": ["Microphysiological Systems for Studying Cellular Crosstalk During the Neutrophil Response to Infection. Neutrophils are the primary responders to infection, rapidly migrating to sites of inflammation and clearing pathogens through a variety of antimicrobial functions. This response is controlled by a complex network of signals produced by vascular cells, tissue resident cells, other immune cells, and the pathogen itself. Despite significant efforts to understand how these signals are integrated into the neutrophil response, we still do not have a complete picture of the mechanisms regulating this process. This is in part due to the inherent disadvantages of the most-used experimental systems: in vitro systems lack the complexity of the tissue microenvironment and animal models do not accurately capture the human immune response. Advanced microfluidic devices incorporating relevant tissue architectures, cell-cell interactions, and live pathogen sources have been developed to overcome these challenges. In this review, we will discuss the in vitro models currently being used to study the neutrophil response to infection, specifically in the context of cell-cell interactions, and provide an overview of their findings. We will also provide recommendations for the future direction of the field and what important aspects of the infectious microenvironment are missing from the current models."], "field": "Veterinary", "q_year": 2025, "q_cid": "281042572", "pos_cid": 233401692, "source": "eval_collection"}
{"query_id": "scaleup_22731292_20835632", "query": "How to identify a small set of management factors most strongly and consistently associated with colostrum bacterial contamination to prioritize practical on-farm recommendations", "pos": ["Use of bootstrapped, regularised regression to identify factors associated with lamb-derived revenue on commercial sheep farms.. The profitability of UK sheep farms is variable with many farms making a net loss. For economic sustainability, farms have to be profitable, therefore it is important to maximise income whilst controlling costs. The most important source of income in sheep flocks is from lamb production but there is little information on factors that explain variability between farms in revenue from lamb sales. The aim of this research was to identify farm, farmer and management factors likely to have the largest, most reliable associations with lamb-derived revenue. From a population of 830 sheep farms, 408 farmers completed an online questionnaire comprising over 300 variables. Total lamb-derived revenue was calculated for each farm using abattoir information including carcass classification. The median flock size was 560 ewes, median land size 265 acres, median revenue per acre from lambs sold was £197 (IQR = 120-296) and median revenue per ewe £95 (IQR = 72-123). A robust analytic approach using regularised (elastic net) regression with bootstrapping was implemented to account for multicollinearity in the data and to reduce the likelihood of model over-fitting. To provide model inference and allow ranking of variables in terms of relevance, covariate stability and coefficient distributions were evaluated. Factors with high stability and relatively large positive associations with revenue per acre were (median effect size (£); 95 % bootstrap probability interval); an increased stocking rate of 0.2 ewe/acre (13; 6-17), fertilizer being used on most of the grazing land (18; 0.1-37), the use of rotational grazing (13; 0.3-34), decreased proportion of ewes with prolapses (4; 0.3-9), separation of lame sheep from the rest of the flock (16; 0.9-37), selecting ewes for culling based on prolapses (20; 0.2-55) and infertility (20; 2-46), conducting body condition scoring of ewes at lambing (28; 3-58), early lactation (21; 1-54) or weaning (25; 2-70), increased farmer education (20; 2-54) and farmers with a positive business attitude (15; 0.2-38). Additional factors with a high stability and relatively large associations with increased revenue per ewe were; never trimming diseased feet of lame ewes (9; 0.8-22) and making use of farm records (5; 0.3-12). This is the first study in animal health epidemiology to use bootstrapped regularised regression to evaluate a wide dataset to provide a ranking of the importance of explanatory covariates. We conclude that the relatively small set of variables identified, with a potentially large influence on lamb-derived revenue, should be considered prime candidates for future intervention studies."], "field": "Veterinary", "q_year": 2020, "q_cid": "227312921", "pos_cid": 208356322, "source": "eval_collection"}
{"query_id": "scaleup_27317135_931721", "query": "How to determine a sample size sufficient to detect an odds ratio of 5 with adequate statistical power while accounting for variation across interfaces and study sites", "pos": ["Power analysis for generalized linear mixed models in ecology and evolution. ‘Will my study answer my research question?’ is the most fundamental question a researcher can ask when designing a study, yet when phrased in statistical terms – ‘What is the power of my study?’ or ‘How precise will my parameter estimate be?’ – few researchers in ecology and evolution (EE) try to answer it, despite the detrimental consequences of performing under‐ or over‐powered research. We suggest that this reluctance is due in large part to the unsuitability of simple methods of power analysis (broadly defined as any attempt to quantify prospectively the ‘informativeness’ of a study) for the complex models commonly used in EE research. With the aim of encouraging the use of power analysis, we present simulation from generalized linear mixed models (GLMMs) as a flexible and accessible approach to power analysis that can account for random effects, overdispersion and diverse response distributions. We illustrate the benefits of simulation‐based power analysis in two research scenarios: estimating the precision of a survey to estimate tick burdens on grouse chicks and estimating the power of a trial to compare the efficacy of insecticide‐treated nets in malaria mosquito control. We provide a freely available R function, sim.glmm, for simulating from GLMMs. Analysis of simulated data revealed that the effects of accounting for realistic levels of random effects and overdispersion on power and precision estimates were substantial, with correspondingly severe implications for study design in the form of up to fivefold increases in sampling effort. We also show the utility of simulations for identifying scenarios where GLMM‐fitting methods can perform poorly. These results illustrate the inadequacy of standard analytical power analysis methods and the flexibility of simulation‐based power analysis for GLMMs. The wider use of these methods should contribute to improving the quality of study design in EE."], "field": "Veterinary", "q_year": 2024, "q_cid": "273171359", "pos_cid": 931721, "source": "eval_collection"}
{"query_id": "scaleup_24663592_22053066", "query": "How to reliably identify intracranial hemorrhage in large cats", "pos": ["Susceptibility weighted imaging at 1.5 Tesla magnetic resonance imaging in dogs: Comparison with T2*-weighted gradient echo sequence and its clinical indications.. Susceptibility weighted imaging (SWI) is a high resolution, fully velocity-compensated, three-dimensional gradient echo (GE) MRI technique. In humans, SWI has been reported to be more sensitive than T2*-weighted GE sequences in the identification of both intracranial hemorrhage and intra-vascular deoxyhemoglobin. However, published clinical studies comparing SWI to T2*-weighted GE sequences in dogs are currently lacking. The aim of this retrospective, observational study was to compare SWI and T2*-weighted GE sequences in a group of dogs with intracranial disease. Medical records were searched for dogs that underwent a brain MRI examination that included T2*-weighted GE and SWI sequences. The presence and appearance of non-vascular and vascular signal voids observed on T2*-weighted GE and SWI were compared. Thirty-two dogs were included with the following diagnoses: presumed and confirmed intracranial neoplasia (27), cerebrovascular accidents (3), and trauma (2). Hemorrhagic lesions were significantly more conspicuous on SWI than T2*-weighted GE sequences (P < .0001). Venous structures were well defined in all SWI sequences, and poorly defined in all dogs on T2*-weighted GE. Susceptibility weighted imaging enabled identification of vascular abnormalities in 30 of 32 (93.8%) dogs, including: neovascularization in 19 of 32 (59.4%) dogs, displacement of perilesional veins in five of 32 (15.6%) dogs, and apparent dilation of perilesional veins in 10 of 32 (31.3%) dogs. Presence of neovascularization was significantly associated with T1-weighted post-contrast enhancement (P = .0184). Hemorrhagic lesions and venous structures were more conspicuous on SWI compared to T2*-weighted GE sequences. Authors recommend adding SWI to standard brain protocols in dogs for detecting hemorrhage and identifying venous abnormalities for lesion characterization."], "field": "Veterinary", "q_year": 2022, "q_cid": "246635923", "pos_cid": 220530665, "source": "eval_collection"}
{"query_id": "scaleup_27737944_6024051", "query": "How to determine whether triclabendazole resistance in geographically separated F. hepatica has a common origin when exchange between regions is limited", "pos": ["Parallel Adaptation: One or Many Waves of Advance of an Advantageous Allele?. Models for detecting the effect of adaptation on population genomic diversity are often predicated on a single newly arisen mutation sweeping rapidly to fixation. However, a population can also adapt to a new environment by multiple mutations of similar phenotypic effect that arise in parallel, at the same locus or different loci. These mutations can each quickly reach intermediate frequency, preventing any single one from rapidly sweeping to fixation globally, leading to a “soft” sweep in the population. Here we study various models of parallel mutation in a continuous, geographically spread population adapting to a global selection pressure. The slow geographic spread of a selected allele due to limited dispersal can allow other selected alleles to arise and start to spread elsewhere in the species range. When these different selected alleles meet, their spread can slow dramatically and so initially form a geographic patchwork, a random tessellation, which could be mistaken for a signal of local adaptation. This spatial tessellation will dissipate over time due to mixing by migration, leaving a set of partial sweeps within the global population. We show that the spatial tessellation initially formed by mutational types is closely connected to Poisson process models of crystallization, which we extend. We find that the probability of parallel mutation and the spatial scale on which parallel mutation occurs are captured by a single compound parameter, a characteristic length, which reflects the expected distance a spreading allele travels before it encounters a different spreading allele. This characteristic length depends on the mutation rate, the dispersal parameter, the effective local density of individuals, and to a much lesser extent the strength of selection. While our knowledge of these parameters is poor, we argue that even in widely dispersing species, such parallel geographic sweeps may be surprisingly common. Thus, we predict that as more data become available, many more examples of intraspecies parallel adaptation will be uncovered."], "field": "Veterinary", "q_year": 2025, "q_cid": "277379448", "pos_cid": 6024051, "source": "eval_collection"}
{"query_id": "scaleup_26808455_4851284", "query": "How to determine how earthworm activity alters fungal communities in dung and affects parasite transmission and biological parasite control", "pos": ["Comparison of the effectiveness of composting and vermicomposting for the biological stabilization of cattle manure.. Cattle manure is produced in large quantities in industrial breeding facilities and the storage and/or spreading of this waste on land may cause contamination of the atmosphere, soil and water. The aim of the present study was to evaluate the effectiveness of the active phases of composting, vermicomposting, and also a combination of composting and vermicomposting for reducing the polluting potential and for stabilizing cattle manure in the short-term. For this, the degree of decomposition as well as the microbial activity and microbial composition of the resulting products after the active phase of composting and vermicomposting were analysed. None of the treatments significantly reduced the dissolved organic carbon and dissolved organic nitrogen contents relative to the control, and therefore more time may be required for stabilization. Nevertheless, the lowest values of microbial biomass and activity corresponded to the earthworm-worked substrates, in which fungal growth was also promoted; the combined treatment (composting + vermicomposting) was the most effective in terms of stabilizing the cattle manure. Moreover, earthworms promoted the retention of nitrogen and gradual release of P, as well as a reduction in electrical conductivity, thereby producing improved substrates for agricultural use."], "field": "Veterinary", "q_year": 2024, "q_cid": "268084550", "pos_cid": 4851284, "source": "eval_collection"}
{"query_id": "scaleup_24882809_22029648", "query": "How to restore normal alignment and stability and achieve successful union in the presence of Brucella infection and structural slippage", "pos": ["High-Grade Spondylolisthesis in Adults: Current Concepts in Evaluation and Management. ABSTRACT Background: Information regarding the treatment of high-grade spondylolisthesis (HGS) in adults has been previously described; however, previous descriptions of the evaluation and surgical management of HGS do not represent more recent and now established approaches. The purpose of the current review is to discuss current concepts in the evaluation and management of patients with HGS. Methods: Literature review. Results: HGS is diagnosed in up to 11.3% of adults with spondylolisthesis and typically presents as nonspecific lower back pain. Regarding evaluation, a thorough history and physical examination should be performed, which may help predict the presence of HGS. Diagnostic imaging, and specifically the use of spino-pelvic parameters, are now commonly implicated in guiding treatment course and prognosis. When surgical intervention is indicated, surgical approaches include in situ fusion variations, reduction and partial reduction with fusion, and vertebrectomy. Although the majority of studies suggest improvements with these approaches, the literature is limited by a low level of evidence with regards to the superiority of one technique when compared with others. Conclusions: HGS is a unique cause of low back pain in adults that carries considerable morbidity, but rarely presents with neurologic symptoms. Although the definitions, classifications, and methods of diagnosis of this spinal deformity have been established and accepted, the ideal surgical management of this deformity remains highly debated. Fusion in situ techniques are often technically easier to perform and provide lower risk of neurologic complications, whereas reduction and fusion techniques offer greater restoration of global spino-pelvic balance. Preoperative spino-pelvic parameters may have utility in assisting in procedural selection; however, future, higher-quality and longer-term studies are warranted to determine the optimal surgical intervention among the widely available techniques currently used, and to better define the indications for these interventions."], "field": "Veterinary", "q_year": 2022, "q_cid": "248828097", "pos_cid": 220296482, "source": "eval_collection"}
{"query_id": "scaleup_23538291_20183707", "query": "How to assess the risk of codeine abuse becoming a gateway to drug addiction", "pos": ["The Mechanisms Involved in Morphine Addiction: An Overview. Opioid use disorder is classified as a chronic recurrent disease of the central nervous system (CNS) which leads to personality disorders, co-morbidities and premature death. It develops as a result of long-term administration of various abused substances, along with morphine. The pharmacological action of morphine is associated with its stimulation of opioid receptors. Opioid receptors are a group of G protein-coupled receptors and activation of these receptors by ligands induces significant molecular changes inside the cell, such as an inhibition of adenylate cyclase activity, activation of potassium channels and reductions of calcium conductance. Recent data indicate that other signalling pathways also may be involved in morphine activity. Among these are phospholipase C, mitogen-activated kinases (MAP kinases) or β-arrestin. The present review focuses on major mechanisms which currently are considered as essential in morphine activity and dependence and may be important for further studies."], "field": "Veterinary", "q_year": 2021, "q_cid": "235382918", "pos_cid": 201837077, "source": "eval_collection"}
{"query_id": "scaleup_27678126_23615810", "query": "How to determine whether an animal’s willingness to obtain different rewards remains stable across repeated trials as hunger or desire for social contact decreases", "pos": ["Reward-specific satiety affects subjective value signals in orbitofrontal cortex during multicomponent economic choice. Significance Ongoing consumption reduces the subjective value of rewards to different degrees depending on their individual properties, a phenomenon referred to as sensory-specific satiety. Such value change should be manifested in economic choices, and neuronal signals for subjective economic reward value should be sensitive to reward-specific satiety. We tested monkeys during the choice between two options that each contained two different rewards (“bundles”); the two rewards were prone to different degrees of satiety. Ongoing reward consumption affected choices in a way that indicated satiety-induced reward-specific change of subjective economic value. Neuronal responses in the monkey orbitofrontal cortex (OFC) followed the differential reduction of subjective economic value. These results satisfy a crucial requirement for subjective reward value coding in OFC neurons. Sensitivity to satiety constitutes a basic requirement for neuronal coding of subjective reward value. Satiety from natural ongoing consumption affects reward functions in learning and approach behavior. More specifically, satiety reduces the subjective economic value of individual rewards during choice between options that typically contain multiple reward components. The unconfounded assessment of economic reward value requires tests at choice indifference between two options, which is difficult to achieve with sated rewards. By conceptualizing choices between options with multiple reward components (“bundles”), Revealed Preference Theory may offer a solution. Despite satiety, choices against an unaltered reference bundle may remain indifferent when the reduced value of a sated bundle reward is compensated by larger amounts of an unsated reward of the same bundle, and then the value loss of the sated reward is indicated by the amount of the added unsated reward. Here, we show psychophysically titrated choice indifference in monkeys between bundles of differently sated rewards. Neuronal chosen value signals in the orbitofrontal cortex (OFC) followed closely the subjective value change within recording periods of individual neurons. A neuronal classifier distinguishing the bundles and predicting choice substantiated the subjective value change. The choice between conventional single rewards confirmed the neuronal changes seen with two-reward bundles. Thus, reward-specific satiety reduces subjective reward value signals in OFC. With satiety being an important factor of subjective reward value, these results extend the notion of subjective economic reward value coding in OFC neurons."], "field": "Veterinary", "q_year": 2025, "q_cid": "276781269", "pos_cid": 236158108, "source": "eval_collection"}
{"query_id": "scaleup_27729954_26315895", "query": "How to identify ear-directed behavioral warning signs of subsequent ear damage and associated welfare risks when ear biting does not cause immediate damage and ear damage has multiple causes", "pos": ["Porcine ear necrosis: characterization of lesions and associated pathogens. Porcine ear necrosis (PEN) is characterized by ulcerative lesions of the ear auricle. To investigate that problem, three farms with PEN in nursery pigs were included, and the study aim was to characterize PEN and the potential role of pathogens and mycotoxins. Within each farm, one batch of weaned piglets was included and the prevalence and severity of PEN were monitored for 6–7 weeks. Within each batch, 30 PEN-affected/non-affected animals were randomly selected. Blood samples were taken from these animals, to assess the systemic presence of pathogens and mycotoxins, as well as punch biopsies from the ear auricle for histopathological examination. From 10 animals, scrapings and swabs from the lesions were subjected to nanopore metagenomic sequencing and bacteriological cultivation, respectively. In all three farms, lesions appeared within 3–4 weeks post-weaning. The prevalence at the end of the nursery was 33%, 24%, and 46% for farms A, B, and C, respectively. Most affected pigs had mild to moderate lesions. Blood samples revealed low to very low levels of pathogens and mycotoxins. Different bacteria such as Staphylococcus , Streptococcus , Fusobacterium , Mycoplasma , and Clostridium species were identified by sequencing in the scrapings. The first two pathogens were also most often identified in bacterial cultures. Mycoplasma hyopharyngis was only found in PEN-affected pigs. Histopathological changes were primarily observed in the outer layer of the epidermis. The results suggest that PEN lesions develop by damage to the outer part of the skin e.g. by ear suckling or biting, followed by multiplication of opportunistic pathogens."], "field": "Veterinary", "q_year": 2025, "q_cid": "277299541", "pos_cid": 263158959, "source": "eval_collection"}
{"query_id": "scaleup_28104257_13572724", "query": "How to effectively control Brucella infection and prevent chronic infection", "pos": ["Immunosuppressive networks and checkpoints controlling antitumor immunity and their blockade in the development of cancer immunotherapeutics and vaccines. Vaccines that promote protective adaptive immune responses have been successfully developed against a range of infectious diseases, and these are normally administered prior to exposure with the relevant virus or bacteria. Adaptive immunity also plays a critical role in the control of tumors. Immunotherapeutics and vaccines that promote effector T cell responses have the potential to eliminate tumors when used in a therapeutic setting. However, the induction of protective antitumor immunity is compromised by innate immunosuppressive mechanisms and regulatory cells that often dominate the tumor microenvironment. Recent studies have shown that blocking these suppressor cells and immune checkpoints to allow induction of antitumor immunity is a successful immunotherapeutic modality for the treatment of cancer. Furthermore, stimulation of innate and consequently adaptive immune responses with concomitant inhibition of immune suppression, especially that mediated by regulatory T (Treg) cells, is emerging as a promising approach to enhance the efficacy of therapeutic vaccines against cancer. This review describes the immunosuppressive mechanisms controlling antitumor immunity and the novel strategies being employed to design effective immunotherapeutics against tumors based on inhibition of suppressor cells or blockade of immune checkpoints to allow induction of more potent effector T cell responses. This review also discusses the potential of using a combination of adjuvants with inhibition of immune checkpoint or suppressor cells for therapeutic vaccines and the translation of pre-clinical studies to the next-generation vaccines against cancer in humans."], "field": "Veterinary", "q_year": 2025, "q_cid": "281042572", "pos_cid": 13572724, "source": "eval_collection"}
{"query_id": "scaleup_22478348_49644905", "query": "How to limit inflammatory immune-cell reactivity to toll-like receptor ligands and associated cytokine secretion in inflammatory bowel disease", "pos": ["Bovine Lactoferrin Modulates Dendritic Cell Differentiation and Function. Lactoferrin is an abundant glycoprotein in bovine milk that has immunomodulatory effects on human cells. Bovine lactoferrin (LF) binds lipopolysaccharides (LPS) with high affinity and is postulated to act via TLR4-dependent and -independent mechanisms. It has been shown that LF modulates differentiation of human monocytes into tolerogenic dendritic cells. However, in a previous study, we showed that LPS also mediates differentiation into tolerogenic dendritic cells (DC). Since LF binds LPS with high affinity, it remains to be investigated whether LF or LPS is mediating these effects. We, therefore, further investigated the LPS-independent effect of LF on differentiation of human monocytes into dendritic cells (DC). Human monocytes were isolated by magnetic cell sorting from freshly isolated PBMCs and cultured for six days in the presence of IL-4 and GM-CSF with or without LF or proteinase K treated LF to generate DC. These immature DC were stimulated for 48 h with LPS or Poly I:C + R848. Cell surface marker expression and cytokine production were measured by flow cytometry. DC differentiated in the presence of LF produced higher IL-6 and IL-8 levels during differentiation and showed a lower expression of CD1a and HLA-DR. These LFDCs showed to be hyporesponsive towards TLR ligands as shown by their semi-mature phenotype and reduced cytokine production. The effect of LF was abrogated by proteinase K treatment, showing that the functional effects of LF were not mediated by LPS contamination. Thus, LF alters DC differentiation and dampens responsiveness towards TLR ligands. This study indicates that LF can play a role in immune homeostasis in the human GI tract."], "field": "Veterinary", "q_year": 2020, "q_cid": "224783481", "pos_cid": 49644905, "source": "eval_collection"}