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{"title": "Systematic immunotherapy target discovery using genome-scale in vivo CRISPR screens in CD8 T cells", "year": 2019, "venue_abbr": "Cell", "venue_name": "Cell", "authors": [], "abstract": null, "doi": "10.1016/j.cell.2019.07.044", "arxiv_id": null, "pmid": "31442407", "openalex_id": null, "s2_id": "10c584f5c9c3ad5f233bc96b0e47f376e5901a75", "cited_by": 268, "type": null, "is_oa": true, "pdf_urls": ["http://www.cell.com/article/S009286741930844X/pdf"], "github": [], "sources": ["semanticscholar"], "landing": null, "s2_venue": "Cell"}
{"title": "γδ T Cells Support Pancreatic Oncogenesis by Restraining αβ T Cell Activation.", "year": 2020, "venue_abbr": "Cell", "venue_name": "Cell", "authors": [], "abstract": null, "doi": "10.1016/j.cell.2020.10.041", "arxiv_id": null, "pmid": "33186522", "openalex_id": null, "s2_id": "11084230b2cd100ce9cae035015aa2393d319a4c", "cited_by": 25, "type": null, "is_oa": true, "pdf_urls": ["https://www.cell.com/article/S0092867420314483/pdf"], "github": [], "sources": ["semanticscholar"], "landing": null, "s2_venue": "Cell"}
{"title": "The PP2A-Integrator-CDK9 axis fine-tunes transcription and can be targeted therapeutically in cancer", "year": 2021, "venue_abbr": "Cell", "venue_name": "Cell", "authors": [], "abstract": null, "doi": "10.1016/j.cell.2021.04.022", "arxiv_id": null, "pmid": "34004147", "openalex_id": null, "s2_id": "1119fc42c6b4ccbcaec16042d21de7558ad29b37", "cited_by": 176, "type": null, "is_oa": true, "pdf_urls": ["http://www.cell.com/article/S009286742100502X/pdf"], "github": [], "sources": ["semanticscholar"], "landing": null, "s2_venue": "Cell"}
{"title": "Listening to Voices that Matter.", "year": 2020, "venue_abbr": "Cell", "venue_name": "Cell", "authors": [], "abstract": null, "doi": "10.1016/j.cell.2020.10.014", "arxiv_id": null, "pmid": "33125877", "openalex_id": null, "s2_id": "111cdefa40f470b8ad818ebcea40c48d33b4687d", "cited_by": 1, "type": null, "is_oa": true, "pdf_urls": ["https://www.cell.com/article/S0092867420313209/pdf"], "github": [], "sources": ["semanticscholar"], "landing": null, "s2_venue": "Cell"}
{"title": "SnapShot: Clinical proteomics.", "year": 2021, "venue_abbr": "Cell", "venue_name": "Cell", "authors": [], "abstract": null, "doi": "10.1016/j.cell.2021.08.015", "arxiv_id": null, "pmid": "34478659", "openalex_id": null, "s2_id": "1123d877d78f53bbe67bc81ad34833a0fecaf0a2", "cited_by": 32, "type": null, "is_oa": true, "pdf_urls": ["https://doi.org/10.1016/j.cell.2021.08.015"], "github": [], "sources": ["semanticscholar"], "landing": null, "s2_venue": "Cell"}
{"title": "Splicing-Correcting Therapy for SMA.", "year": 2017, "venue_abbr": "Cell", "venue_name": "Cell", "authors": [], "abstract": null, "doi": "10.1016/j.cell.2017.06.028", "arxiv_id": null, "pmid": "28666123", "openalex_id": null, "s2_id": "112d6eee20b5cf578ebc495debaeda599c2ff048", "cited_by": 42, "type": null, "is_oa": true, "pdf_urls": ["https://doi.org/10.1016/j.cell.2017.06.028"], "github": [], "sources": ["semanticscholar"], "landing": null, "s2_venue": "Cell"}
{"title": "Untangling the Web of Lymphoma Somatic Mutations.", "year": 2017, "venue_abbr": "Cell", "venue_name": "Cell", "authors": [], "abstract": null, "doi": "10.1016/j.cell.2017.09.031", "arxiv_id": null, "pmid": "28985559", "openalex_id": null, "s2_id": "113353b33df29842f727b1d570e0f07c80bc231d", "cited_by": 2, "type": null, "is_oa": true, "pdf_urls": ["http://www.cell.com/article/S009286741731125X/pdf"], "github": [], "sources": ["semanticscholar"], "landing": null, "s2_venue": "Cell"}
{"title": "Pathogenic mechanisms of somatic mutation and genome mosaicism in aging", "year": 2020, "venue_abbr": "Cell", "venue_name": "Cell", "authors": [], "abstract": null, "doi": "10.1016/j.cell.2020.06.024", "arxiv_id": null, "pmid": "32649873", "openalex_id": null, "s2_id": "1163c19e31dd429d4eb40eac1b7c13a4421b3085", "cited_by": 204, "type": null, "is_oa": true, "pdf_urls": ["https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7354350"], "github": [], "sources": ["semanticscholar"], "landing": null, "s2_venue": "Cell"}
{"title": "Structural basis of γ-secretase inhibition and modulation by small molecule drugs.", "year": 2020, "venue_abbr": "Cell", "venue_name": "Cell", "authors": [], "abstract": null, "doi": "10.1016/j.cell.2020.11.049", "arxiv_id": null, "pmid": "33373587", "openalex_id": null, "s2_id": "116420aaaf256daad319e55c1b176db7948bf105", "cited_by": 142, "type": null, "is_oa": true, "pdf_urls": ["http://www.cell.com/article/S0092867420316214/pdf"], "github": [], "sources": ["semanticscholar"], "landing": null, "s2_venue": "Cell"}
{"title": "Deep Mutational Scanning of SARS-CoV-2 Receptor Binding Domain Reveals Constraints on Folding and ACE2 Binding", "year": 2020, "venue_abbr": "Cell", "venue_name": "Cell", "authors": [], "abstract": null, "doi": "10.1016/j.cell.2020.08.012", "arxiv_id": null, "pmid": "32841599", "openalex_id": null, "s2_id": "1168aa8b36226ff31f4cd248f25191ba588228f8", "cited_by": 988, "type": null, "is_oa": true, "pdf_urls": ["https://doi.org/10.1016/j.cell.2020.08.012"], "github": [], "sources": ["semanticscholar"], "landing": null, "s2_venue": "Cell"}
{"title": "How Hard It Is Seeing What Is in Front of Your Eyes.", "year": 2018, "venue_abbr": "Cell", "venue_name": "Cell", "authors": [], "abstract": null, "doi": "10.1016/j.cell.2018.06.027", "arxiv_id": null, "pmid": "29958112", "openalex_id": null, "s2_id": "116f087abf08183c42616029e02bfd597f5978c3", "cited_by": 5, "type": null, "is_oa": false, "pdf_urls": [], "github": [], "sources": ["semanticscholar"], "landing": null, "s2_venue": "Cell"}
{"title": "A multiplexed single-cell CRISPR screening platform enables systematic dissection of the unfolded protein response", "year": 2016, "venue_abbr": "Cell", "venue_name": "Cell", "authors": [], "abstract": null, "doi": "10.1016/j.cell.2016.11.048", "arxiv_id": null, "pmid": "27984733", "openalex_id": null, "s2_id": "119a59578a114c6274fc863d4a3212b0357b365d", "cited_by": 1128, "type": null, "is_oa": true, "pdf_urls": ["https://dspace.mit.edu/bitstream/1721.1/116762/1/nihms832990.pdf"], "github": [], "sources": ["semanticscholar"], "landing": null, "s2_venue": "Cell"}
{"title": "Humans with inherited T cell CD28 deficiency are susceptible to skin papillomaviruses but are otherwise healthy", "year": 2021, "venue_abbr": "Cell", "venue_name": "Cell", "authors": [], "abstract": null, "doi": "10.1016/j.cell.2021.06.004", "arxiv_id": null, "pmid": "34214472", "openalex_id": null, "s2_id": "11ad4c0c07018db7dddbae41b9f93165114073aa", "cited_by": 78, "type": null, "is_oa": true, "pdf_urls": ["http://www.cell.com/article/S0092867421007054/pdf"], "github": [], "sources": ["semanticscholar"], "landing": null, "s2_venue": "Cell"}
{"title": "A New Drug Target for Type 2 Diabetes.", "year": 2017, "venue_abbr": "Cell", "venue_name": "Cell", "authors": [], "abstract": null, "doi": "10.1016/j.cell.2017.06.024", "arxiv_id": null, "pmid": "28666114", "openalex_id": null, "s2_id": "11c0495b87de9838a1183e71c345dd57937f55b4", "cited_by": 25, "type": null, "is_oa": true, "pdf_urls": ["https://www.cell.com/article/S0092867417307080/pdf"], "github": [], "sources": ["semanticscholar"], "landing": null, "s2_venue": "Cell"}
{"title": "Structure and Conformational Dynamics of the Human Spliceosomal Bact Complex.", "year": 2018, "venue_abbr": "Cell", "venue_name": "Cell", "authors": [], "abstract": null, "doi": "10.1016/j.cell.2018.01.010", "arxiv_id": null, "pmid": "29361316", "openalex_id": null, "s2_id": "11c627925bf33a1f58e793f62c45de6310fcb895", "cited_by": 179, "type": null, "is_oa": true, "pdf_urls": ["https://doi.org/10.1016/j.cell.2018.01.010"], "github": [], "sources": ["semanticscholar"], "landing": null, "s2_venue": "Cell"}
{"title": "Self-Maintaining Gut Macrophages Are Essential for Intestinal Homeostasis.", "year": 2018, "venue_abbr": "Cell", "venue_name": "Cell", "authors": [], "abstract": null, "doi": "10.1016/j.cell.2018.07.048", "arxiv_id": null, "pmid": "30173915", "openalex_id": null, "s2_id": "120f82f9c85b85c32b46a5905e38e3dff8400481", "cited_by": 506, "type": null, "is_oa": true, "pdf_urls": ["http://www.cell.com/article/S0092867418309760/pdf"], "github": [], "sources": ["semanticscholar"], "landing": null, "s2_venue": "Cell"}
{"title": "Glucose Metabolism Linked to Antiviral Responses.", "year": 2019, "venue_abbr": "Cell", "venue_name": "Cell", "authors": [], "abstract": null, "doi": "10.1016/j.cell.2019.05.057", "arxiv_id": null, "pmid": "31251910", "openalex_id": null, "s2_id": "122aedf0a842a68e6184119fefe418b112079191", "cited_by": 9, "type": null, "is_oa": true, "pdf_urls": ["https://www.cell.com/article/S0092867419306282/pdf"], "github": [], "sources": ["semanticscholar"], "landing": null, "s2_venue": "Cell"}
{"title": "Insights into Nucleosome Organization in Mouse Embryonic Stem Cells through Chemical Mapping", "year": 2016, "venue_abbr": "Cell", "venue_name": "Cell", "authors": [], "abstract": null, "doi": "10.1016/j.cell.2016.10.049", "arxiv_id": null, "pmid": "27889238", "openalex_id": null, "s2_id": "122d7040e5beb976455f6101ccdc17fe09585dd2", "cited_by": 190, "type": null, "is_oa": true, "pdf_urls": ["https://www.cell.com/article/S0092867416315100/pdf"], "github": [], "sources": ["semanticscholar"], "landing": null, "s2_venue": "Cell"}
{"title": "An expanded view of complex traits: from polygenic to omnigenic", "year": 2017, "venue_abbr": "Cell", "venue_name": "Cell", "authors": [], "abstract": null, "doi": "10.1016/j.cell.2017.05.038", "arxiv_id": null, "pmid": "28622505", "openalex_id": null, "s2_id": "1239b88111a5f1c20622d58406fb15bf02c31947", "cited_by": 2715, "type": null, "is_oa": true, "pdf_urls": ["http://www.cell.com/article/S0092867417306293/pdf"], "github": [], "sources": ["semanticscholar"], "landing": null, "s2_venue": "Cell"}
{"title": "The Spanish 1918 Flu and the COVID-19 Disease: The Art of Remembering and Foreshadowing Pandemics", "year": 2020, "venue_abbr": "Cell", "venue_name": "Cell", "authors": [], "abstract": null, "doi": "10.1016/j.cell.2020.09.030", "arxiv_id": null, "pmid": "33064981", "openalex_id": null, "s2_id": "12526ecdc4aafe92d624b6d042e9f9ea9228af7f", "cited_by": 12, "type": null, "is_oa": true, "pdf_urls": ["http://www.cell.com/article/S0092867420312277/pdf"], "github": [], "sources": ["semanticscholar"], "landing": null, "s2_venue": "Cell"}
{"title": "The gut microbiota mediates the anti-seizure effects of the ketogenic diet", "year": 2018, "venue_abbr": "Cell", "venue_name": "Cell", "authors": [], "abstract": null, "doi": "10.1016/j.cell.2018.04.027", "arxiv_id": null, "pmid": "29804833", "openalex_id": null, "s2_id": "12560dfded09ec4852d934647ae082a0ab281b9f", "cited_by": 944, "type": null, "is_oa": true, "pdf_urls": ["http://www.cell.com/article/S0092867418305208/pdf"], "github": [], "sources": ["semanticscholar"], "landing": null, "s2_venue": "Cell"}
{"title": "Marine DNA viral macro- and micro-diversity from pole to pole", "year": 2019, "venue_abbr": "Cell", "venue_name": "Cell", "authors": [], "abstract": null, "doi": "10.1016/j.cell.2019.03.040", "arxiv_id": null, "pmid": "31031001", "openalex_id": null, "s2_id": "1264f6a75b064e7e914446f2ec364a2722a5748d", "cited_by": 716, "type": null, "is_oa": true, "pdf_urls": ["http://www.cell.com/article/S0092867419303411/pdf"], "github": [], "sources": ["semanticscholar"], "landing": null, "s2_venue": "Cell"}
{"title": "The continuing search for the origins of SARS-CoV-2", "year": 2021, "venue_abbr": "Cell", "venue_name": "Cell", "authors": [], "abstract": null, "doi": "10.1016/j.cell.2021.07.035", "arxiv_id": null, "pmid": "34416143", "openalex_id": null, "s2_id": "127bf996470d7523073972e3d589b2ec5011d55e", "cited_by": 4, "type": null, "is_oa": true, "pdf_urls": ["https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8375251"], "github": [], "sources": ["semanticscholar"], "landing": null, "s2_venue": "Cell"}
{"title": "An Excitatory Circuit in the Perioculomotor Midbrain for Non-REM Sleep Control.", "year": 2019, "venue_abbr": "Cell", "venue_name": "Cell", "authors": [], "abstract": null, "doi": "10.1016/j.cell.2019.03.041", "arxiv_id": null, "pmid": "31031008", "openalex_id": null, "s2_id": "1294c138cf640486ebf512fa4303054d5b693f75", "cited_by": 68, "type": null, "is_oa": true, "pdf_urls": ["http://www.cell.com/article/S0092867419303423/pdf"], "github": [], "sources": ["semanticscholar"], "landing": null, "s2_venue": "Cell"}
{"title": "Optimal decoding of cellular identities in a genetic network", "year": 2016, "venue_abbr": "Cell", "venue_name": "Cell", "authors": ["Mariela D. Petkova", "Ga\\v{s}per Tka\\v{c}ik", "William Bialek", "Eric F.\n  Wieschaus", "and Thomas Gregor"], "abstract": "  Gene expression levels carry information about signals that have functional\nsignificance for the organism. Using the gap gene network in the fruit fly\nembryo as an example, we show how this information can be decoded, building a\ndictionary that translates expression levels into a map of implied positions.\nThe optimal decoder makes use of graded variations in absolute expression\nlevel, resulting in positional estimates that are precise to ~1% of the\nembryo's length. We test this optimal decoder by analyzing gap gene expression\nin embryos lacking some of the primary maternal inputs to the network. The\nresulting maps are distorted, and these distortions predict, with no free\nparameters, the positions of expression stripes for the pair-rule genes in the\nmutant embryos.\n", "doi": "10.1016/j.cell.2019.01.007", "arxiv_id": "1612.08084", "pmid": "30712870", "openalex_id": null, "s2_id": "12b0884b24fe9c63a2258a4938c6c94dd4ca4010", "cited_by": 167, "type": "journal", "is_oa": true, "pdf_urls": ["http://www.cell.com/article/S0092867419300406/pdf", "https://arxiv.org/pdf/1612.08084"], "github": [], "sources": ["semanticscholar", "open-arxiv"], "landing": null, "s2_venue": "Cell", "journal_ref": "Cell 176, 844 (2019)", "categories": "q-bio.MN physics.bio-ph"}
{"title": "Pervasive, coordinated protein level changes driven by transcript isoform switching during meiosis", "year": 2018, "venue_abbr": "Cell", "venue_name": "Cell", "authors": [], "abstract": null, "doi": "10.1016/j.cell.2018.01.035", "arxiv_id": null, "pmid": "29474919", "openalex_id": null, "s2_id": "12ba0f4b512068585a57946402eadb6dc38ed5d8", "cited_by": 146, "type": null, "is_oa": true, "pdf_urls": ["https://europepmc.org/articles/pmc5826577?pdf=render"], "github": [], "sources": ["semanticscholar"], "landing": null, "s2_venue": "Cell"}
{"title": "Deconstruction of corticospinal circuits for goal-directed motor skills", "year": 2017, "venue_abbr": "Cell", "venue_name": "Cell", "authors": [], "abstract": null, "doi": "10.1016/j.cell.2017.08.014", "arxiv_id": null, "pmid": "28942925", "openalex_id": null, "s2_id": "12bb5a5a7c30f2faa1d0ccf2a7dc95820691ce9a", "cited_by": 183, "type": null, "is_oa": true, "pdf_urls": ["https://doi.org/10.1016/j.cell.2017.08.014"], "github": [], "sources": ["semanticscholar"], "landing": null, "s2_venue": "Cell"}
{"title": "On a Quest for Principles, Big Data in Hand.", "year": 2016, "venue_abbr": "Cell", "venue_name": "Cell", "authors": [], "abstract": null, "doi": "10.1016/j.cell.2016.05.014", "arxiv_id": null, "pmid": "27203104", "openalex_id": null, "s2_id": "12c905e3383675b8fd46ad76d6e36d248c0d6266", "cited_by": 1, "type": null, "is_oa": true, "pdf_urls": ["https://www.cell.com/article/S0092867416305621/pdf"], "github": [], "sources": ["semanticscholar"], "landing": null, "s2_venue": "Cell"}
{"title": "Sugar Turns Bacteria Sweet: A Peace Offering in the Gut.", "year": 2018, "venue_abbr": "Cell", "venue_name": "Cell", "authors": [], "abstract": null, "doi": "10.1016/j.cell.2018.08.053", "arxiv_id": null, "pmid": "30241612", "openalex_id": null, "s2_id": "12cc973e114087518b732657140572dcb58a6774", "cited_by": 1, "type": null, "is_oa": true, "pdf_urls": ["https://doi.org/10.1016/j.cell.2018.08.053"], "github": [], "sources": ["semanticscholar"], "landing": null, "s2_venue": "Cell"}
{"title": "PDGFRA Antibody for Soft Tissue Sarcoma.", "year": 2017, "venue_abbr": "Cell", "venue_name": "Cell", "authors": [], "abstract": null, "doi": "10.1016/j.cell.2017.01.028", "arxiv_id": null, "pmid": "28187274", "openalex_id": null, "s2_id": "12cf06d1aacb32be3c2844375f9cac248c14c3e9", "cited_by": 10, "type": null, "is_oa": true, "pdf_urls": ["https://doi.org/10.1016/j.cell.2017.01.028"], "github": [], "sources": ["semanticscholar"], "landing": null, "s2_venue": "Cell"}
{"title": "A Viral Movement Protein Prevents Spread of the Gene Silencing Signal in Nicotiana benthamiana.", "year": 2016, "venue_abbr": "Cell", "venue_name": "Cell", "authors": [], "abstract": null, "doi": "10.1016/j.cell.2016.07.015", "arxiv_id": null, "pmid": "27471969", "openalex_id": null, "s2_id": "12d41c3ff2ff8806a37a8c9063397127143597ad", "cited_by": 7, "type": null, "is_oa": true, "pdf_urls": ["https://www.cell.com/article/S0092867416309229/pdf"], "github": [], "sources": ["semanticscholar"], "landing": null, "s2_venue": "Cell"}
{"title": "The Ties That Bind: Mapping the Dynamic Enhancer-Promoter Interactome", "year": 2016, "venue_abbr": "Cell", "venue_name": "Cell", "authors": [], "abstract": null, "doi": "10.1016/j.cell.2016.10.054", "arxiv_id": null, "pmid": "27863237", "openalex_id": null, "s2_id": "12d96277c2d2b42cce1b45d3e496c0bd7baae801", "cited_by": 27, "type": null, "is_oa": true, "pdf_urls": ["http://www.cell.com/article/S0092867416315197/pdf"], "github": [], "sources": ["semanticscholar"], "landing": null, "s2_venue": "Cell"}
{"title": "Representational geometry of perceptual decisions in the monkey parietal cortex", "year": 2021, "venue_abbr": "Cell", "venue_name": "Cell", "authors": [], "abstract": null, "doi": "10.1016/j.cell.2021.05.022", "arxiv_id": null, "pmid": "34171308", "openalex_id": null, "s2_id": "12e90517a608f82005daa074881ed392c2624b6c", "cited_by": 107, "type": null, "is_oa": true, "pdf_urls": ["http://www.cell.com/article/S0092867421006528/pdf"], "github": [], "sources": ["semanticscholar"], "landing": null, "s2_venue": "Cell"}
{"title": "Tissue Determinants of Human NK Cell Development, Function, and Residence", "year": 2020, "venue_abbr": "Cell", "venue_name": "Cell", "authors": [], "abstract": null, "doi": "10.1016/j.cell.2020.01.022", "arxiv_id": null, "pmid": "32059780", "openalex_id": null, "s2_id": "12f9d3d172ec761fc61f704b2244ff558582fadf", "cited_by": 369, "type": null, "is_oa": true, "pdf_urls": ["http://www.cell.com/article/S0092867420301033/pdf"], "github": [], "sources": ["semanticscholar"], "landing": null, "s2_venue": "Cell"}
{"title": "Profound Tissue Specificity in Proliferation Control Underlies Cancer Drivers and Aneuploidy Patterns", "year": 2018, "venue_abbr": "Cell", "venue_name": "Cell", "authors": [], "abstract": null, "doi": "10.1016/j.cell.2018.02.037", "arxiv_id": null, "pmid": "29576454", "openalex_id": null, "s2_id": "132a6d3f2f776bc82c290f96a1f5cb813ac568a2", "cited_by": 202, "type": null, "is_oa": true, "pdf_urls": ["https://europepmc.org/articles/pmc6643283?pdf=render"], "github": [], "sources": ["semanticscholar"], "landing": null, "s2_venue": "Cell"}
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{"title": "The Walrus and the Carpenter: Complex Regulation of Tumor Immunity in Colorectal Cancer.", "year": 2018, "venue_abbr": "Cell", "venue_name": "Cell", "authors": [], "abstract": null, "doi": "10.1016/j.cell.2018.06.009", "arxiv_id": null, "pmid": "29958104", "openalex_id": null, "s2_id": "e25562ba8b11defdc659c959d20141a34523064d", "cited_by": 8, "type": null, "is_oa": true, "pdf_urls": ["http://www.cell.com/article/S0092867418307347/pdf"], "github": [], "sources": ["semanticscholar"], "landing": null, "s2_venue": "Cell"}
{"title": "Boosting Immunity by Targeting Post-translational Prenylation of Small GTPases.", "year": 2018, "venue_abbr": "Cell", "venue_name": "Cell", "authors": [], "abstract": null, "doi": "10.1016/j.cell.2018.10.032", "arxiv_id": null, "pmid": "30388448", "openalex_id": null, "s2_id": "e26e132500560ec4b2919bc28de98c0a948c87e4", "cited_by": 7, "type": null, "is_oa": true, "pdf_urls": ["https://www.cell.com/article/S0092867418313850/pdf"], "github": [], "sources": ["semanticscholar"], "landing": null, "s2_venue": "Cell"}
{"title": "Induction of HIV Neutralizing Antibody Lineages in Mice with Diverse Precursor Repertoires", "year": 2016, "venue_abbr": "Cell", "venue_name": "Cell", "authors": [], "abstract": null, "doi": "10.1016/j.cell.2016.07.029", "arxiv_id": null, "pmid": "27610571", "openalex_id": null, "s2_id": "e2a50ac93fededec57a1e27a7e1cdd702f649cb8", "cited_by": 234, "type": null, "is_oa": true, "pdf_urls": ["http://www.cell.com/article/S0092867416309758/pdf"], "github": [], "sources": ["semanticscholar"], "landing": null, "s2_venue": "Cell"}
{"title": "Viral generated inter-organelle contacts redirect lipid flux for genome replication", "year": 2019, "venue_abbr": "Cell", "venue_name": "Cell", "authors": [], "abstract": null, "doi": "10.1016/j.cell.2019.05.030", "arxiv_id": null, "pmid": "31204099", "openalex_id": null, "s2_id": "e2b2930f92279287d33132fe2ee408538d51e153", "cited_by": 143, "type": null, "is_oa": true, "pdf_urls": ["https://www.cell.com/article/S0092867419305586/pdf"], "github": [], "sources": ["semanticscholar"], "landing": null, "s2_venue": "Cell"}
{"title": "Human gut mycobiota tune immunity via CARD9-dependent induction of anti-fungal IgG antibodies", "year": 2021, "venue_abbr": "Cell", "venue_name": "Cell", "authors": [], "abstract": null, "doi": "10.1016/j.cell.2021.01.016", "arxiv_id": null, "pmid": "33548172", "openalex_id": null, "s2_id": "e2b636fb6c7bc52504ef715a7c0835c5ba5de9b0", "cited_by": 180, "type": null, "is_oa": true, "pdf_urls": ["https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7936855"], "github": [], "sources": ["semanticscholar"], "landing": null, "s2_venue": "Cell"}
{"title": "Genomic Insights into Zika Virus Emergence and Spread.", "year": 2018, "venue_abbr": "Cell", "venue_name": "Cell", "authors": [], "abstract": null, "doi": "10.1016/j.cell.2018.02.027", "arxiv_id": null, "pmid": "29522736", "openalex_id": null, "s2_id": "e2bf19b024f0b0f1a7207037d9002450413873a3", "cited_by": 64, "type": null, "is_oa": true, "pdf_urls": ["http://www.cell.com/article/S0092867418301715/pdf"], "github": [], "sources": ["semanticscholar"], "landing": null, "s2_venue": "Cell"}
{"title": "Recording of elapsed time and temporal information about biological events using Cas9.", "year": 2021, "venue_abbr": "Cell", "venue_name": "Cell", "authors": [], "abstract": null, "doi": "10.1016/j.cell.2021.01.014", "arxiv_id": null, "pmid": "33539780", "openalex_id": null, "s2_id": "e2c125501c13182ca2aae3e71383d95e0c8b10e7", "cited_by": 35, "type": null, "is_oa": true, "pdf_urls": ["https://ir.ymlib.yonsei.ac.kr/handle/22282913/182173"], "github": [], "sources": ["semanticscholar"], "landing": null, "s2_venue": "Cell"}
{"title": "Proteomic analysis of unbounded cellular compartments: synaptic clefts", "year": 2016, "venue_abbr": "Cell", "venue_name": "Cell", "authors": [], "abstract": null, "doi": "10.1016/j.cell.2016.07.041", "arxiv_id": null, "pmid": "27565350", "openalex_id": null, "s2_id": "e2cbe4446a527d61848f4e13960b7be19824bfc9", "cited_by": 364, "type": null, "is_oa": true, "pdf_urls": ["http://www.cell.com/article/S0092867416309916/pdf"], "github": [], "sources": ["semanticscholar"], "landing": null, "s2_venue": "Cell"}
{"title": "Influenza infection in humans induces broadly cross-reactive and protective neuraminidase-reactive antibodies", "year": 2018, "venue_abbr": "Cell", "venue_name": "Cell", "authors": [], "abstract": null, "doi": "10.1016/j.cell.2018.03.030", "arxiv_id": null, "pmid": "29625056", "openalex_id": null, "s2_id": "e2d10e120f53c840aed90d1e161f2ac39ae0320b", "cited_by": 384, "type": null, "is_oa": true, "pdf_urls": ["http://www.cell.com/article/S0092867418303106/pdf"], "github": [], "sources": ["semanticscholar"], "landing": null, "s2_venue": "Cell"}
{"title": "The genetic basis of metabolic disease", "year": 2019, "venue_abbr": "Cell", "venue_name": "Cell", "authors": [], "abstract": null, "doi": "10.1016/j.cell.2019.02.024", "arxiv_id": null, "pmid": "30901536", "openalex_id": null, "s2_id": "e334055b1e4d216a3fe04ff80a16f5688d06a6fd", "cited_by": 100, "type": null, "is_oa": true, "pdf_urls": ["http://www.cell.com/article/S0092867419302065/pdf"], "github": [], "sources": ["semanticscholar"], "landing": null, "s2_venue": "Cell"}
{"title": "Characterizing genetic intra-tumor heterogeneity across 2,658 human cancer genomes", "year": 2020, "venue_abbr": "Cell", "venue_name": "Cell", "authors": [], "abstract": null, "doi": "10.2139/ssrn.3582701", "arxiv_id": null, "pmid": "33831375", "openalex_id": null, "s2_id": "e38375abdd535539fee546781ab5efd42e18be5b", "cited_by": 455, "type": null, "is_oa": true, "pdf_urls": ["https://doi.org/10.2139/ssrn.3582701"], "github": [], "sources": ["semanticscholar"], "landing": null, "s2_venue": "Cell"}
{"title": "A lymphocyte-glia connection sets the pace for smoldering inflammation.", "year": 2021, "venue_abbr": "Cell", "venue_name": "Cell", "authors": [], "abstract": null, "doi": "10.1016/j.cell.2021.10.018", "arxiv_id": null, "pmid": "34767775", "openalex_id": null, "s2_id": "e801cc104b1d50d2b19ffcc070f12236ef4b1ef3", "cited_by": 4, "type": null, "is_oa": true, "pdf_urls": ["https://doi.org/10.1016/j.cell.2021.10.018"], "github": [], "sources": ["semanticscholar"], "landing": null, "s2_venue": "Cell"}
{"title": "Targeted degradation of CTCF decouples local insulation of chromosome domains from genomic compartmentalization", "year": 2017, "venue_abbr": "Cell", "venue_name": "Cell", "authors": [], "abstract": null, "doi": "10.1016/j.cell.2017.05.004", "arxiv_id": null, "pmid": "28525758", "openalex_id": null, "s2_id": "e8afa0f77d39684b99c6679f6d08fd74cf1d90f5", "cited_by": 1550, "type": null, "is_oa": true, "pdf_urls": ["https://dspace.mit.edu/bitstreams/ed8f6491-dea5-46ac-9110-780db5c7f0d9/download"], "github": [], "sources": ["semanticscholar"], "landing": null, "s2_venue": "Cell"}
{"title": "Potent Neutralizing Antibodies against SARS-CoV-2 Identified by High-Throughput Single-Cell Sequencing of Convalescent Patients’ B Cells", "year": 2020, "venue_abbr": "Cell", "venue_name": "Cell", "authors": [], "abstract": null, "doi": "10.1016/j.cell.2020.05.025", "arxiv_id": null, "pmid": "32425270", "openalex_id": null, "s2_id": "e8ff6223d6308149a06f372e4a5bebe8667526fd", "cited_by": 1166, "type": null, "is_oa": true, "pdf_urls": ["https://doi.org/10.1016/j.cell.2020.05.025"], "github": [], "sources": ["semanticscholar"], "landing": null, "s2_venue": "Cell"}
{"title": "Distinctive Activation Mechanism for Angiotensin Receptor Revealed by a Synthetic Nanobody", "year": 2019, "venue_abbr": "Cell", "venue_name": "Cell", "authors": [], "abstract": null, "doi": "10.1016/j.cell.2018.12.006", "arxiv_id": null, "pmid": "30639100", "openalex_id": null, "s2_id": "eb09d206b36bced125ffe5592d55925a31f10ed4", "cited_by": 169, "type": null, "is_oa": true, "pdf_urls": ["http://www.cell.com/article/S0092867418315897/pdf"], "github": [], "sources": ["semanticscholar"], "landing": null, "s2_venue": "Cell"}
{"title": "FXR regulates intestinal cancer stem cell proliferation", "year": 2019, "venue_abbr": "Cell", "venue_name": "Cell", "authors": [], "abstract": null, "doi": "10.1016/j.cell.2019.01.036", "arxiv_id": null, "pmid": "30794774", "openalex_id": null, "s2_id": "eba5f78f59e7086d9082b7cd2c4bbaae42a03b18", "cited_by": 416, "type": null, "is_oa": true, "pdf_urls": ["https://www.ncbi.nlm.nih.gov/pmc/articles/6701863"], "github": [], "sources": ["semanticscholar"], "landing": null, "s2_venue": "Cell"}
{"title": "Isolation and visualization of a structural trigger that uncouples TCR signaling from pMHC binding", "year": 2018, "venue_abbr": "Cell", "venue_name": "Cell", "authors": [], "abstract": null, "doi": "10.1016/j.cell.2018.06.017", "arxiv_id": null, "pmid": "30053426", "openalex_id": null, "s2_id": "ec01c8107421c1282ca71a08ad2a0669f79d6a92", "cited_by": 269, "type": null, "is_oa": true, "pdf_urls": ["https://www.cell.com/article/S0092867418307852/pdf"], "github": [], "sources": ["semanticscholar"], "landing": null, "s2_venue": "Cell"}
{"title": "Budding Epithelial Morphogenesis Driven by Cell-Matrix versus Cell-Cell Adhesion", "year": 2021, "venue_abbr": "Cell", "venue_name": "Cell", "authors": [], "abstract": null, "doi": "10.1016/j.cell.2021.05.015", "arxiv_id": null, "pmid": "34133940", "openalex_id": null, "s2_id": "ec96cd7343655bd49cec77f3b77b0b9171bc6ae7", "cited_by": 106, "type": null, "is_oa": true, "pdf_urls": ["http://www.cell.com/article/S0092867421006322/pdf"], "github": [], "sources": ["semanticscholar"], "landing": null, "s2_venue": "Cell"}
{"title": "The ground state and evolution of promoter region directionality", "year": 2017, "venue_abbr": "Cell", "venue_name": "Cell", "authors": [], "abstract": null, "doi": "10.1016/j.cell.2017.07.006", "arxiv_id": null, "pmid": "28803729", "openalex_id": null, "s2_id": "ecfe14c0a19bb02ef195d58b8b52c84b7ae179f3", "cited_by": 77, "type": null, "is_oa": true, "pdf_urls": ["http://www.cell.com/article/S0092867417308139/pdf"], "github": [], "sources": ["semanticscholar"], "landing": null, "s2_venue": "Cell"}
{"title": "Optical Mapping of cAMP Signaling at the Nanometer Scale.", "year": 2021, "venue_abbr": "Cell", "venue_name": "Cell", "authors": [], "abstract": null, "doi": "10.1016/j.cell.2021.04.043", "arxiv_id": null, "pmid": "33989549", "openalex_id": null, "s2_id": "ed0a341f8f1ddcab1d7a4a9acaac65a6f2e63784", "cited_by": 9, "type": null, "is_oa": true, "pdf_urls": ["https://doi.org/10.1016/j.cell.2021.04.043"], "github": [], "sources": ["semanticscholar"], "landing": null, "s2_venue": "Cell"}
{"title": "Insight into the Neuron's Insight.", "year": 2019, "venue_abbr": "Cell", "venue_name": "Cell", "authors": [], "abstract": null, "doi": "10.1016/j.cell.2019.04.019", "arxiv_id": null, "pmid": "31051103", "openalex_id": null, "s2_id": "ed1a012537b8d6b3930ca450d4b445c1caf2b921", "cited_by": 0, "type": null, "is_oa": true, "pdf_urls": ["http://www.cell.com/article/S0092867419304064/pdf"], "github": [], "sources": ["semanticscholar"], "landing": null, "s2_venue": "Cell"}
{"title": "A single-embryo, single-cell time-resolved model for mouse gastrulation", "year": 2021, "venue_abbr": "Cell", "venue_name": "Cell", "authors": [], "abstract": null, "doi": "10.1016/j.cell.2021.04.004", "arxiv_id": null, "pmid": "33932341", "openalex_id": null, "s2_id": "edbb1c3fd7a5944fc48fb104b5d89c0e02cb9fd8", "cited_by": 171, "type": null, "is_oa": true, "pdf_urls": ["https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8162424"], "github": [], "sources": ["semanticscholar"], "landing": null, "s2_venue": "Cell"}
{"title": "TOP1 inhibition therapy protects against SARS-CoV-2-induced lethal inflammation", "year": 2021, "venue_abbr": "Cell", "venue_name": "Cell", "authors": [], "abstract": null, "doi": "10.1016/j.cell.2021.03.051", "arxiv_id": null, "pmid": "33836156", "openalex_id": null, "s2_id": "ee75d93f44642647800b9f31cd987be07f13b870", "cited_by": 111, "type": null, "is_oa": true, "pdf_urls": ["http://www.cell.com/article/S0092867421003822/pdf"], "github": [], "sources": ["semanticscholar"], "landing": null, "s2_venue": "Cell"}
{"title": "Retraction Notice to: Cytohesins Are Cytoplasmic ErbB Receptor Activators", "year": 2016, "venue_abbr": "Cell", "venue_name": "Cell", "authors": [], "abstract": null, "doi": "10.1016/j.cell.2016.05.013", "arxiv_id": null, "pmid": "27203114", "openalex_id": null, "s2_id": "f0781d4564a5789d73c328047b4ffdf478fa571c", "cited_by": 1, "type": null, "is_oa": true, "pdf_urls": ["http://www.cell.com/article/S009286741630561X/pdf"], "github": [], "sources": ["semanticscholar"], "landing": null, "s2_venue": "Cell"}
{"title": "Repopulating Microglia Promote Brain Repair in an IL-6-Dependent Manner.", "year": 2020, "venue_abbr": "Cell", "venue_name": "Cell", "authors": [], "abstract": null, "doi": "10.1016/j.cell.2020.02.013", "arxiv_id": null, "pmid": "32142677", "openalex_id": null, "s2_id": "f0ebf6364246f62cc6b0016bad743f4d71eecc4a", "cited_by": 467, "type": null, "is_oa": true, "pdf_urls": ["http://www.cell.com/article/S0092867420301574/pdf"], "github": [], "sources": ["semanticscholar"], "landing": null, "s2_venue": "Cell"}
{"title": "Sunlight Brightens Learning and Memory.", "year": 2018, "venue_abbr": "Cell", "venue_name": "Cell", "authors": [], "abstract": null, "doi": "10.1016/j.cell.2018.05.044", "arxiv_id": null, "pmid": "29906444", "openalex_id": null, "s2_id": "f15e4219ef20b05891ebadfabab91d8263b4873c", "cited_by": 9, "type": null, "is_oa": true, "pdf_urls": ["https://doi.org/10.1016/j.cell.2018.05.044"], "github": [], "sources": ["semanticscholar"], "landing": null, "s2_venue": "Cell"}
{"title": "The mTORC1 pathway stimulates glutamine metabolism and cell proliferation by repressing SIRT4.", "year": 2021, "venue_abbr": "Cell", "venue_name": "Cell", "authors": [], "abstract": null, "doi": "10.1016/j.cell.2021.03.059", "arxiv_id": null, "pmid": "33861966", "openalex_id": null, "s2_id": "f4f9d057033bf6eb507b93cad753335b6ac20606", "cited_by": 28, "type": null, "is_oa": true, "pdf_urls": ["http://www.cell.com/article/S0092867421004323/pdf"], "github": [], "sources": ["semanticscholar"], "landing": null, "s2_venue": "Cell"}
{"title": "Enter Sofosbuvir: The Path to Curing HCV.", "year": 2016, "venue_abbr": "Cell", "venue_name": "Cell", "authors": [], "abstract": null, "doi": "10.1016/j.cell.2016.08.044", "arxiv_id": null, "pmid": "27634323", "openalex_id": null, "s2_id": "f5d54f49bb15e697c10ed8d62d79f07377d39bc5", "cited_by": 11, "type": null, "is_oa": true, "pdf_urls": ["http://www.cell.com/article/S0092867416311412/pdf"], "github": [], "sources": ["semanticscholar"], "landing": null, "s2_venue": "Cell"}
{"title": "Harvesting Benefits from Cannabinoids.", "year": 2016, "venue_abbr": "Cell", "venue_name": "Cell", "authors": [], "abstract": null, "doi": "10.1016/j.cell.2016.12.001", "arxiv_id": null, "pmid": "27984713", "openalex_id": null, "s2_id": "f7d14412aec96abbd802ac6be00cfad892947b26", "cited_by": 1, "type": null, "is_oa": true, "pdf_urls": ["https://www.cell.com/article/S0092867416316750/pdf"], "github": [], "sources": ["semanticscholar"], "landing": null, "s2_venue": "Cell"}
{"title": "Extracellular matrix remodeling regulates glucose metabolism through TXNIP destabilization", "year": 2018, "venue_abbr": "Cell", "venue_name": "Cell", "authors": [], "abstract": null, "doi": "10.1016/j.cell.2018.08.017", "arxiv_id": null, "pmid": "30197082", "openalex_id": null, "s2_id": "f9101c65742d4b4da0422d9d3518eec87a626e9b", "cited_by": 222, "type": null, "is_oa": true, "pdf_urls": ["https://www.cell.com/article/S009286741831033X/pdf"], "github": [], "sources": ["semanticscholar"], "landing": null, "s2_venue": "Cell"}
{"title": "Phytochromes: Where to Start?", "year": 2017, "venue_abbr": "Cell", "venue_name": "Cell", "authors": [], "abstract": null, "doi": "10.1016/j.cell.2017.11.020", "arxiv_id": null, "pmid": "29195071", "openalex_id": null, "s2_id": "f99360c8f0fc3fc67765d82a9f17ac816ca60d4e", "cited_by": 8, "type": null, "is_oa": true, "pdf_urls": ["https://www.cell.com/article/S0092867417313673/pdf"], "github": [], "sources": ["semanticscholar"], "landing": null, "s2_venue": "Cell"}
{"title": "Lipid-associated macrophages control metabolic homeostasis in a Trem2-dependent manner", "year": 2019, "venue_abbr": "Cell", "venue_name": "Cell", "authors": [], "abstract": null, "doi": "10.1016/j.cell.2019.05.054", "arxiv_id": null, "pmid": "31257031", "openalex_id": null, "s2_id": "fcac220b41c234093ce72bf55f75da21ddb37434", "cited_by": 1177, "type": null, "is_oa": true, "pdf_urls": ["https://www.cell.com/article/S0092867419306257/pdf"], "github": [], "sources": ["semanticscholar"], "landing": null, "s2_venue": "Cell"}
{"title": "An Amazing Turn of Events.", "year": 2017, "venue_abbr": "Cell", "venue_name": "Cell", "authors": [], "abstract": null, "doi": "10.1016/j.cell.2017.08.021", "arxiv_id": null, "pmid": "28888325", "openalex_id": null, "s2_id": "fd623f9894f6a647ab699faa60a407dd29f94347", "cited_by": 11, "type": null, "is_oa": true, "pdf_urls": ["https://doi.org/10.1016/j.cell.2017.08.021"], "github": [], "sources": ["semanticscholar"], "landing": null, "s2_venue": "Cell"}
{"title": "Initiation of Antiviral B Cell Immunity Relies on Innate Signals from Spatially Positioned NKT Cells", "year": 2017, "venue_abbr": "Cell", "venue_name": "Cell", "authors": [], "abstract": null, "doi": "10.1016/j.cell.2017.11.036", "arxiv_id": null, "pmid": "29249358", "openalex_id": null, "s2_id": "febe5fb3a790df6abf468de177937adf7b6aacf8", "cited_by": 157, "type": null, "is_oa": true, "pdf_urls": ["http://www.cell.com/article/S0092867417313879/pdf"], "github": [], "sources": ["semanticscholar"], "landing": null, "s2_venue": "Cell"}
{"title": "Molecular-level tuning of cellular autonomy controls the collective\n  behaviors of cell populations", "year": 2016, "venue_abbr": "Cell", "venue_name": "Cell", "authors": ["Th\\'eo Maire", "Hyun Youk"], "abstract": "  A rigorous understanding of how multicellular behaviors arise from the\nactions of single cells requires quantitative frameworks that bridge the gap\nbetween genetic circuits, the arrangement of cells in space, and\npopulation-level behaviors. Here, we provide such a framework for a ubiquitous\nclass of multicellular systems - namely, \"secrete-and-sense cells\" that\ncommunicate by secreting and sensing a signaling molecule. By using formal,\nmathematical arguments and introducing the concept of a phenotype diagram, we\nshow how these cells tune their degrees of autonomous and collective behavior\nto realize distinct single-cell and population-level phenotypes; these\nphenomena have biological analogs, such as quorum sensing or paracrine\nsignaling. We also define the \"entropy of population,\" a measurement of the\nnumber of arrangements that a population of cells can assume, and demonstrate\nhow a decrease in the entropy of population accompanies the formation of\nordered spatial patterns. Our conceptual framework ties together diverse\nsystems, including tissues and microbes, with common principles.\n", "doi": "10.1016/j.cels.2015.10.012", "arxiv_id": "1602.05558", "pdf_urls": ["https://arxiv.org/pdf/1602.05558"], "github": [], "is_oa": true, "sources": ["open-arxiv"], "type": "journal", "journal_ref": "Cell Systems 1:349-360 (November 2015)", "categories": "q-bio.MN nlin.CG nlin.PS physics.bio-ph q-bio.CB"}
{"title": "Autocrine signaling and quorum sensing: Extreme ends of a common\n  spectrum", "year": 2016, "venue_abbr": "Cell", "venue_name": "Cell", "authors": ["Berkalp A. Do\\u{g}aner", "Lawrence K. Q. Yan", "Hyun Youk"], "abstract": "  \"Secrete-and-sense cells\" can communicate by secreting a signaling molecule\nwhile also producing a receptor that detects the molecule. The cell can\npotentially \"talk\" to itself (\"self-communication\") or talk to neighboring\ncells with the same receptor (\"neighbor-communication\"). The predominant forms\nof secrete-and-sense cells are self-communicating \"autocrine cells\" that are\nlargely found in animals, and neighbor-communicating \"quorum sensing cells\"\nthat are mostly associated with bacteria. While assumed to function independent\nof one another, recent studies have discovered quorum sensing organs and\nautocrine signaling microbes. Moreover, similar types of genetic circuits\ncontrol many autocrine and quorum sensing cells. We outline these recent\nfindings and explain how autocrine and quorum sensing are two sides of a\nmany-sided \"dice\" created by the versatile secrete-and-sense cell.\n", "doi": "10.1016/j.tcb.2015.11.002", "arxiv_id": "1602.06859", "pdf_urls": ["https://arxiv.org/pdf/1602.06859"], "github": [], "is_oa": true, "sources": ["open-arxiv"], "type": "journal", "journal_ref": "Trends in Cell Biology 26(4):262-271 (2016)", "categories": "q-bio.CB"}
{"title": "What Mathematical Logic Says about the Foundations of Mathematics", "year": 2016, "venue_abbr": "Cell", "venue_name": "Cell", "authors": ["Claudio Bernardi"], "abstract": "  My purpose is to examine some concepts of mathematical logic, which have been\nstudied by Carlo Cellucci. Today the aim of classical mathematical logic is not\nto guarantee the certainty of mathematics, but I will argue that logic can help\nus to explain mathematical activity; the point is to discuss what and in which\nsense logic can \"explain\". For example, let's consider the basic concept of an\naxiomatic system: an axiomatic system can be very useful to organize, to\npresent, and to clarify mathematical knowledge. And, more importantly, logic is\na science with its own results: so, axiomatic systems are interesting also\nbecause we know several revealing theorems about them. Similarly, I will\ndiscuss other topics such as mathematical definitions, and some relationships\nbetween mathematical logic and computer science. I will also consider these\nsubjects from an educational point of view: can logical concepts be useful in\nteaching and learning elementary mathematics?\n", "doi": null, "arxiv_id": "1602.07551", "pdf_urls": ["https://arxiv.org/pdf/1602.07551"], "github": [], "is_oa": true, "sources": ["open-arxiv"], "type": "journal", "journal_ref": "in \"From a heuristic point of view. Essays in honor of Carlo\n  Cellucci\" (edited by E. Ippoliti and C. Cozzo), Cambridge Scholars\n  Publishing, Newcastle upon Tyne, UK, 2014, pag. 41-53", "categories": "math.HO"}
{"title": "The Garden of Eden Theorem for Cellular Automata on Group Sets", "year": 2016, "venue_abbr": "Cell", "venue_name": "Cell", "authors": ["Simon Wacker"], "abstract": "  We prove the Garden of Eden theorem for cellular automata with finite set of\nstates and finite neighbourhood on right amenable left homogeneous spaces with\nfinite stabilisers. It states that the global transition function of such an\nautomaton is surjective if and only if it is pre-injective. Pre-Injectivity\nmeans that two global configurations that differ at most on a finite subset and\nhave the same image under the global transition function must be identical.\n", "doi": "10.1007/978-3-319-44365-2_7", "arxiv_id": "1603.07272", "pdf_urls": ["https://arxiv.org/pdf/1603.07272"], "github": [], "is_oa": true, "sources": ["open-arxiv"], "type": "journal", "journal_ref": "12th International Conference on Cellular Automata for Research\n  and Industry, ACRI 2016, Fez, Morocco, September 5-8, 2016. Proceedings\n  (2016) 66-78", "categories": "math.GR cs.FL"}
{"title": "The group of reversible Turing machines", "year": 2016, "venue_abbr": "Cell", "venue_name": "Cell", "authors": ["Sebasti\\'an Barbieri", "Jarkko Kari", "Ville Salo"], "abstract": "  We consider Turing machines as actions over configurations in\n$\\Sigma^{\\mathbb{Z}^d}$ which only change them locally around a marked position\nthat can move and carry a particular state. In this setting we study the monoid\nof Turing machines and the group of reversible Turing machines. We also study\ntwo natural subgroups, namely the group of finite-state automata, which\ngeneralizes the topological full groups studied in the theory of\norbit-equivalence, and the group of oblivious Turing machines whose movement is\nindependent of tape contents, which generalizes lamplighter groups and has\nconnections to the study of universal reversible logical gates. Our main\nresults are that the group of Turing machines in one dimension is neither\namenable nor residually finite, but is locally embeddable in finite groups, and\nthat the torsion problem is decidable for finite-state automata in dimension\none, but not in dimension two.\n", "doi": "10.1007/978-3-319-39300-1_5", "arxiv_id": "1603.08715", "pdf_urls": ["https://arxiv.org/pdf/1603.08715"], "github": [], "is_oa": true, "sources": ["open-arxiv"], "type": "journal", "journal_ref": "AUTOMATA 2016: Cellular Automata and Discrete Complex Systems pp\n  49-62", "categories": "math.GR math.DS"}
{"title": "Contact inhibition of locomotion and mechanical cross-talk between\n  cell-cell and cell-substrate adhesion determines the pattern of junctional\n  tension in epithelial cell aggregates", "year": 2016, "venue_abbr": "Cell", "venue_name": "Cell", "authors": ["Luke Coburn", "Hender Lopez", "Adrian Noppe", "Benjamin J. Caldwell", "Elliott\n  Moussa", "Chloe Yap", "Rashmi Priya", "Vladimir Lobaskin", "Anthony P. Roberts", "Alpha\n  S. Yap", "Zoltan Neufeld", "Guillermo A. Gomez"], "abstract": "  We generated a computational approach to analyze the biomechanics of\nepithelial cell aggregates, either island or stripes or entire monolayers, that\ncombines both vertex and contact-inhibition-of-locomotion models to include\nboth cell-cell and cell-substrate adhesion. Examination of the distribution of\ncell protrusions (adhesion to the substrate) in the model predicted high order\nprofiles of cell organization that agree with those previously seen\nexperimentally. Cells acquired an asymmetric distribution of basal protrusions,\ntraction forces and apical aspect ratios that decreased when moving from the\nedge to the island center. Our in silico analysis also showed that tension on\ncell-cell junctions and apical stress is not homogeneous across the island.\nInstead, these parameters are higher at the island center and scales up with\nisland size, which we confirmed experimentally using laser ablation assays and\nimmunofluorescence. Without formally being a 3-dimensional model, our approach\nhas the minimal elements necessary to reproduce the distribution of cellular\nforces and mechanical crosstalk as well as distribution of principal stress in\ncells within epithelial cell aggregates. By making experimental testable\npredictions, our approach would benefit the mechanical analysis of epithelial\ntissues, especially when local changes in cell-cell and/or cell-substrate\nadhesion drive collective cell behavior.\n", "doi": "10.1091/mbc.e16-04-0226", "arxiv_id": "1604.03733", "pdf_urls": ["https://arxiv.org/pdf/1604.03733"], "github": [], "is_oa": true, "sources": ["open-arxiv"], "type": "journal", "journal_ref": "Molecular Biology of the Cell 27(22), 3436-3448, 2016", "categories": "physics.bio-ph q-bio.CB q-bio.TO"}
{"title": "Nonequilibrium physics aspects of probabilistic cellular automata", "year": 2016, "venue_abbr": "Cell", "venue_name": "Cell", "authors": ["Christian Maes"], "abstract": "  Probabilistic cellular automata (PCA) are used to model a variety of discrete\nspatially extended systems undergoing parallel-updating. We propose an\nembedding of a number of classical nonequilibrium concepts in the PCA-world. We\nstart from time-symmetric PCA, satisfying detailed balance, and we give their\nKubo formula for linear response. Close-to-detailed balance we investigate the\nform of the McLennan distribution and the minimum entropy production principle.\nMore generally, when time-symmetry is broken in the stationary process, there\nis a fluctuation symmetry for a corresponding entropy flux. For linear response\naround nonequilibria we also give the appropriate formula which is now not only\nentropic in nature.\n", "doi": null, "arxiv_id": "1605.02876", "pdf_urls": ["https://arxiv.org/pdf/1605.02876"], "github": [], "is_oa": true, "sources": ["open-arxiv"], "type": "journal", "journal_ref": "Probabilistic Cellular Automata - Theory, Applications and Future\n  Perspectives, Chapter 9, 109--116, Springer, 2017", "categories": "cond-mat.stat-mech"}
{"title": "Group Methodologies and Simulations for the Development of Transversal\n  Skills: A Pilot Study on Health Sciences Higher Education", "year": 2016, "venue_abbr": "Cell", "venue_name": "Cell", "authors": ["Laura San Martin Galindo", "Juan Jose Cabrera-Martinez", "Camilo\n  Abalos-Labruzzi and Jose Gomez-Galan"], "abstract": "  One of the methodologies based on group dynamics is Role Playing (RP). This\nmethod consists on the simulation of a real situation, allowing its study and\nunderstanding. Knowledge and technical skills are not the only prerequisites\nfor proper practice in health sciences. RP has been used as Communication\nSkills Training (CST) amongst health professionals. In the teaching of\nodontology and stomatology, object of our research, dental assistance brings up\nsituations where the professional must develop transversal skills, which\nimprove the interaction with the patient and the dental treatment itself. The\naim of this study is to evaluate the efficacy of the proposed RP methodology\nthrough the students' opinion. The study sample is made out of dental students\n(n=80), all of them on the 4th year at the College of Dentistry (University of\nSeville, Spain). The students who took part in the activity considered the\nincorporation of RP in the syllabus as relevant, though further study should be\nconsidered in order to analyze the efficacy of this teaching methodology in\ndepth.\n", "doi": "10.18562/ijee.2015.0008", "arxiv_id": "1605.06658", "pdf_urls": ["https://arxiv.org/pdf/1605.06658"], "github": [], "is_oa": true, "sources": ["open-arxiv"], "type": "journal", "journal_ref": "International Journal of Educational Excellence, 2015, Vol. 1, No.\n  1, 93-109 ISSN 2373-5929", "categories": "cs.CY"}
{"title": "Information and Communications Technologies (ICT) and Pre-Service\n  Education Professionals: A Case Study of Motivation and Knowledge", "year": 2016, "venue_abbr": "Cell", "venue_name": "Cell", "authors": ["Maria Isabel Ponce-Escudero and Jose Gomez-Galan"], "abstract": "  The importance of knowing ICT training and motivation -so relevant in today's\nsociety- which currently offers the first year college students, mostly in\ndegrees in Education, focuses the object of interest in this study. The\nfollowing targets have been proposed: [1] knowing what basic skills regarding\ninitial instrumental knowledge presents the prospective teacher (aptitudes) and\n[2] knowing their motivation for the educational use of ICT in the classroom\n(attitudes). For this purpose a non-experimental descriptive quantitative\nmethodology has been used, with a sample of subjects (N=282) of the Autonomous\nRegion of Extremadura (Spain). The results show that new degree college\nstudents possess a basic knowledge of ICT alongside a highly positive\nmotivation towards the use of these. However, it is worrying that they only\nshow an instrumental and technical knowledge of computing and telematic tools\nimplied in social environments, but not pedagogical ones. Also they are\nunfamiliar with the true power of social, economic, political, ethical,\ninfluence as well as the effects and problems that their misuse can generate in\ntheir future students (addictions, manipulation, consumerism, etc.). Dimensions\ntherefore for which they are urged to be trained at University for a proper\nperformance as future professionals in education.\n", "doi": "10.18562/ijee.2015.0014", "arxiv_id": "1605.06659", "pdf_urls": ["https://arxiv.org/pdf/1605.06659"], "github": [], "is_oa": true, "sources": ["open-arxiv"], "type": "journal", "journal_ref": "International Journal of Educational Excellence, 2016, Vol. 2, No.\n  1, 63-79, ISSN 2373-5929", "categories": "cs.CY"}
{"title": "Dynamic electrical behavior of halide perovskite based solar cells", "year": 2016, "venue_abbr": "Cell", "venue_name": "Cell", "authors": ["George Alexandru Nemnes", "Cristina Besleaga", "Andrei Gabriel Tomulescu", "Ioana Pintilie", "Lucian Pintilie", "Kristinn Torfason", "Andrei Manolescu"], "abstract": "  A dynamic electrical model is introduced to investigate the hysteretic\neffects in the I-V characteristics of perovskite based solar cells. By making a\nsimple ansatz for the polarization relaxation, our model is able to reproduce\nqualitatively and quantitatively detailed features of measured I-V\ncharacteristics. Pre-poling effects are discussed, pointing out the differences\nbetween initially over- and under-polarized samples. In particular, the\npresence of the current over-shoot observed in the reverse characteristics is\ncorrelated with the solar cell pre-conditioning. Furthermore, the dynamic\nhysteresis is analyzed with respect to changing the bias scan rate, the\nobtained results being consistent with experimentally reported data: the\nhysteresis amplitude is maximum at intermediate scan rates, while at very slow\nand very fast ones it becomes negligible. The effects induced by different\nrelaxation time scales are assessed. The proposed dynamic electrical model\noffers a comprehensive view of the solar cell operation, being a practical tool\nfor future calibration of tentative microscopic descriptions.\n", "doi": "10.1016/j.solmat.2016.09.012", "arxiv_id": "1606.00335", "pdf_urls": ["https://arxiv.org/pdf/1606.00335"], "github": [], "is_oa": true, "sources": ["open-arxiv"], "type": "journal", "journal_ref": "Solar Energy Materials & Solar Cells 159, 197 (2017)", "categories": "cond-mat.mtrl-sci"}
{"title": "Engineering design optimisation using tabu search", "year": 2016, "venue_abbr": "Cell", "venue_name": "Cell", "authors": ["Andy M. Connor", "P. John Clarkson", "Shahrokh Shahpar and Paul Leonard"], "abstract": "  This paper describes an optimisation methodology that has been specifically\ndeveloped for engineering design problems. The methodology is based on a Tabu\nsearch (TS) algorithm that has been shown to find high quality solutions with a\nrelatively low number of objective function evaluations. Whilst the methodology\nwas originally intended for a small range of design problems it has since been\nsuccessfully applied to problems from different domains with no alteration to\nthe underlying method. This paper describes the method and its application to\nthree different problems. The first is from the field of structural design, the\nsecond relates to the design of electromagnetic pole shapes and the third\ninvolves the design of turbomachinery blades.\n", "doi": null, "arxiv_id": "1606.05924", "pdf_urls": ["https://arxiv.org/pdf/1606.05924"], "github": [], "is_oa": true, "sources": ["open-arxiv"], "type": "journal", "journal_ref": "Proceedings of Design for Excellence: Engineering Design\n  Conference (EDC 2000), 371-378 (2000)", "categories": "math.OC"}
{"title": "Unifying notions of generalized weights for universal security on\n  wire-tap networks", "year": 2016, "venue_abbr": "Cell", "venue_name": "Cell", "authors": ["Umberto Mart\\'inez-Pe\\~nas and Ryutaroh Matsumoto"], "abstract": "  Universal security over a network with linear network coding has been\nintensively studied. However, previous linear codes used for this purpose were\nlinear over a larger field than that used on the network. In this work, we\nintroduce new parameters (relative dimension/rank support profile and relative\ngeneralized matrix weights) for linear codes that are linear over the field\nused in the network, measuring the universal security performance of these\ncodes. The proposed new parameters enable us to use optimally universal secure\nlinear codes on noiseless networks for all possible parameters, as opposed to\nprevious works, and also enable us to add universal security to the recently\nproposed list-decodable rank-metric codes by Guruswami et al. We give several\nproperties of the new parameters: monotonicity, Singleton-type lower and upper\nbounds, a duality theorem, and definitions and characterizations of\nequivalences of linear codes. Finally, we show that our parameters strictly\nextend relative dimension/length profile and relative generalized Hamming\nweights, respectively, and relative dimension/intersection profile and relative\ngeneralized rank weights, respectively. Moreover, we show that generalized\nmatrix weights are larger than Delsarte generalized weights.\n", "doi": "10.1109/allerton.2016.7852315", "arxiv_id": "1607.01263", "pdf_urls": ["https://arxiv.org/pdf/1607.01263"], "github": [], "is_oa": true, "sources": ["open-arxiv"], "type": "journal", "journal_ref": "Proc. 2016 54th Annual Allerton Conference on Communication,\n  Control, and Computing, pp.800-807, Monticello, Illinois, USA, September\n  27-30, 2016", "categories": "cs.IT math.IT"}
{"title": "Machine Learning with Memristors via Thermodynamic RAM", "year": 2016, "venue_abbr": "Cell", "venue_name": "Cell", "authors": ["Timothy W. Molter and M. Alexander Nugent"], "abstract": "  Thermodynamic RAM (kT-RAM) is a neuromemristive co-processor design based on\nthe theory of AHaH Computing and implemented via CMOS and memristors. The\nco-processor is a 2-D array of differential memristor pairs (synapses) that can\nbe selectively coupled together (neurons) via the digital bit addressing of the\nunderlying CMOS RAM circuitry. The chip is designed to plug into existing\ndigital computers and be interacted with via a simple instruction set.\nAnti-Hebbian and Hebbian (AHaH) computing forms the theoretical framework from\nwhich a nature-inspired type of computing architecture is built where, unlike\nvon Neumann architectures, memory and processor are physically combined for\nsynaptic operations. Through exploitation of AHaH attractor states,\nmemristor-based circuits converge to attractor basins that represents machine\nlearning solutions such as unsupervised feature learning, supervised\nclassification and anomaly detection. Because kT-RAM eliminates the need to\nshuttle bits back and forth between memory and processor and can operate at\nvery low voltage levels, it can significantly surpass CPU, GPU, and FPGA\nperformance for synaptic integration and learning operations. Here, we present\na memristor technology developed for use in kT-RAM, in particular\nbi-directional incremental adaptation of conductance via short low-voltage 1.0\nV, 1.0 microsecond pulses.\n", "doi": null, "arxiv_id": "1608.04105", "pdf_urls": ["https://arxiv.org/pdf/1608.04105"], "github": [], "is_oa": true, "sources": ["open-arxiv"], "type": "journal", "journal_ref": "CNNA 2016, 15th International Workshop on Cellular Nanoscale\n  Networks and their Applications, Dresden, Germany, 2016, pp. 1-2", "categories": "cs.ET cs.NE"}
{"title": "The Generalized Metastable Switch Memristor Model", "year": 2016, "venue_abbr": "Cell", "venue_name": "Cell", "authors": ["Timothy W. Molter and M. Alexander Nugent"], "abstract": "  Memristor device modeling is currently a heavily researched topic and is\nbecoming ever more important as memristor devices make their way into CMOS\ncircuit designs, necessitating accurate and efficient memristor circuit\nsimulations. In this paper, the Generalized Metastable Switch (MSS) memristor\nmodel is presented. The Generalized MSS model consists of a voltage-dependent\nstochastic component and a voltage-dependent exponential diode current\ncomponent and is designed to be easy to implement, computationally efficient,\nand amenable to modeling a wide range of different memristor devices.\n", "doi": null, "arxiv_id": "1608.04659", "pdf_urls": ["https://arxiv.org/pdf/1608.04659"], "github": [], "is_oa": true, "sources": ["open-arxiv"], "type": "journal", "journal_ref": "CNNA 2016, 15th International Workshop on Cellular Nanoscale\n  Networks and their Applications, Dresden, Germany, 2016, pp. 1-2", "categories": "cs.ET"}
{"title": "Visualizing septins in early Drosophila embryos", "year": 2016, "venue_abbr": "Cell", "venue_name": "Cell", "authors": ["Manos Mavrakis (MOSAIC)"], "abstract": "  Functional studies in Drosophila have been key for establishing a role for\nthe septin family of proteins in animal cell division and thus extending for\nthe first time observations from the budding yeast to animal cells. Visualizing\nthe distribution of specific septins in different Drosophila tissues and, in\nparticular, in the Drosophila embryo, together with biochemical and mutant\nphenotype data, has contributed important advances to our understanding of\nanimal septin biology, suggesting roles in processes other than in cytokinesis.\nSeptin localization using immunofluorescence assays has been possible due to\nthe generation of antibodies against different Drosophila septins. The recent\navailability of lines expressing fluorescent protein fusions of specific\nseptins further promises to facilitate studies on septin dynamics. Here, we\nprovide protocols for preparing early Drosophila embryos to visualize septins\nusing immunofluorescence assays and live fluorescence microscopy. The genetic\ntractability of the Drosophila embryo together with its amenability to\nhigh-resolution fluorescence microscopy promises to provide novel insights into\nanimal septin structure and function.\n", "doi": "10.1016/bs.mcb.2016.03.026", "arxiv_id": "1609.03829", "pdf_urls": ["https://arxiv.org/pdf/1609.03829"], "github": [], "is_oa": true, "sources": ["open-arxiv"], "type": "journal", "journal_ref": "Methods in Cell Biology, Elsevier, 2016, Septins, 136, pp.183", "categories": "q-bio.SC q-bio.CB"}
{"title": "Purification of recombinant human and Drosophila septin hexamers for\n  TIRF assays of actin-septin filament assembly", "year": 2016, "venue_abbr": "Cell", "venue_name": "Cell", "authors": ["Manos Mavrakis (MOSAIC)", "Tsai Feng-Ching (FOM Institute AMOLF)", "Gijsje\n  H. Koenderink (FOM Institute AMOLF)"], "abstract": "  Septins are guanine nucleotide-binding proteins that are conserved from fungi\nto humans. Septins assemble into heterooligomeric complexes and higher-order\nstructures with key roles in various cellular functions including cell\nmigration and division. The mechanisms by which septins assemble and interact\nwith other cytoskeletal elements like actin remain elusive. A powerful approach\nto address this question is by cell-free reconstitution of pu- rified\ncytoskeletal proteins combined with fluorescence microscopy. Here, we describe\nprocedures for the purification of recombinant Drosophila and human septin\nhexamers from Escherichia coli and reconstitution of actin-septin coassembly.\nThese procedures can be used to compare assembly of Drosophila and human\nseptins and their coassembly with the actin cytoskeleton by total internal\nreflection fluorescence microscopy.\n", "doi": "10.1016/bs.mcb.2016.03.020", "arxiv_id": "1609.03845", "pdf_urls": ["https://arxiv.org/pdf/1609.03845"], "github": [], "is_oa": true, "sources": ["open-arxiv"], "type": "journal", "journal_ref": "Methods in Cell Biology, Elsevier, 2016, Septins, 136, pp.199", "categories": "q-bio.SC q-bio.CB"}
{"title": "Drawing a Waddington landscape to capture dynamic epigenetics", "year": 2016, "venue_abbr": "Cell", "venue_name": "Cell", "authors": ["Floriane Nicol-Benoit", "Pascale le Goff and Denis Michel"], "abstract": "  Epigenetics is most often reduced to chromatin marking in the current\nliterature, whereas this notion was initially defined in a more general\ncontext. This restricted view ignores that epigenetic memories are in fact more\nrobustly ensured in living systems by steady state mechanisms with permanent\nmolecule renewal. This misconception is likely to result from misleading\nintuitions and insufficient dialogues between traditional and quantitative\nbiologists. To demystify dynamic epigenetics, its most famous image, a\nWaddington landscape and its attractors, are explicitly drawn. The simple\nexample provided is sufficient to highlight the main requirements and\ncharacteristics of dynamic gene networks, underlying cellular differentiation,\nde-differentiation and trans-differentiation.\n", "doi": "10.1111/boc.201300029", "arxiv_id": "1609.08331", "pdf_urls": ["https://arxiv.org/pdf/1609.08331"], "github": [], "is_oa": true, "sources": ["open-arxiv"], "type": "journal", "journal_ref": "Biol. Cell. 105, 576-584 (2013)", "categories": "q-bio.MN"}
{"title": "X-Rule's Precursor is also Logically Universal", "year": 2016, "venue_abbr": "Cell", "venue_name": "Cell", "authors": ["Jos\\'e Manuel G\\'omez Soto", "Andrew Wuensche"], "abstract": "  We re-examine the isotropic Precursor-Rule (of the anisotropic X-Rule) and\nshow that it is also logically universal. The Precursor-Rule was selected from\na sample of biased cellular automata rules classified by input-entropy. These\nbiases followed most \"Life-Like\" constraints --- in particular isotropy, but\nnot simple birth/survival logic. The Precursor-Rule was chosen for its\nspontaneously emergent mobile and stable patterns, gliders and\neaters/reflectors, but glider-guns, originally absent, have recently been\ndiscovered, as well as other complex structures from the Game-of-Life lexicon.\nWe demonstrate these newly discovered structures, and build the logical gates\nrequired for universality in the logical sense.\n", "doi": null, "arxiv_id": "1611.08829", "pdf_urls": ["https://arxiv.org/pdf/1611.08829"], "github": [], "is_oa": true, "sources": ["open-arxiv"], "type": "journal", "journal_ref": "Journal of CELLULAR AUTOMATA (JCA), Vol.12, NO.o.6 (2017)", "categories": "nlin.CG"}
{"title": "Automatic time-series phenotyping using massive feature extraction", "year": 2016, "venue_abbr": "Cell", "venue_name": "Cell", "authors": ["Ben D Fulcher and Nick S Jones"], "abstract": "  Across a far-reaching diversity of scientific and industrial applications, a\ngeneral key problem involves relating the structure of time-series data to a\nmeaningful outcome, such as detecting anomalous events from sensor recordings,\nor diagnosing patients from physiological time-series measurements like heart\nrate or brain activity. Currently, researchers must devote considerable effort\nmanually devising, or searching for, properties of their time series that are\nsuitable for the particular analysis problem at hand. Addressing this\nnon-systematic and time-consuming procedure, here we introduce a new tool,\nhctsa, that selects interpretable and useful properties of time series\nautomatically, by comparing implementations over 7700 time-series features\ndrawn from diverse scientific literatures. Using two exemplar biological\napplications, we show how hctsa allows researchers to leverage decades of\ntime-series research to quantify and understand informative structure in their\ntime-series data.\n", "doi": "10.1016/j.cels.2017.10.001", "arxiv_id": "1612.05296", "pdf_urls": ["https://arxiv.org/pdf/1612.05296"], "github": [], "is_oa": true, "sources": ["open-arxiv"], "type": "journal", "journal_ref": "Cell Systems 5 (2017) 527", "categories": "cs.LG physics.data-an q-bio.QM"}
{"title": "Recursive constructions and their maximum likelihood decoding", "year": 2017, "venue_abbr": "Cell", "venue_name": "Cell", "authors": ["Ilya Dumer and Kirill Shabunov"], "abstract": "  We consider recursive decoding techniques for RM codes, their subcodes, and\nnewly designed codes. For moderate lengths up to 512, we obtain near-optimum\ndecoding with feasible complexity.\n", "doi": null, "arxiv_id": "1703.05302", "pdf_urls": ["https://arxiv.org/pdf/1703.05302"], "github": [], "is_oa": true, "sources": ["open-arxiv"], "type": "journal", "journal_ref": "Proc. 38th Allerton Conf. Communication, Control, and Computing,\n  Monticello, IL, USA, 2000, pp. 71-80", "categories": "cs.IT math.IT"}
{"title": "Recursive decoding of Reed-Muller codes", "year": 2017, "venue_abbr": "Cell", "venue_name": "Cell", "authors": ["Ilya Dumer"], "abstract": "  New soft- and hard decision decoding algorithms are presented for general\nReed-Muller codes $\\left\\{\\genfrac{}{}{0pt}{}{m}{r}\\right\\} $ of length $2^{m}$\nand distance $2^{m-r}$. We use Plotkin $(u,u+v)$ construction and decompose\ncode $\\left\\{\\genfrac{}{}{0pt}{}{m}{r}\\right\\} $ onto subblocks\n$u\\in\\left\\{\\genfrac{}{}{0pt}{}{m-1}{r}\\right\\} $ and\n$v\\in\\left\\{\\genfrac{}{}{0pt}{}{m-1}{r-1}\\right\\} .$ In decoding, we first try\nto find a subblock $v$ from the better protected code and then proceed with the\nblock $u$. The likelihoods of the received symbols are recalculated in a way\nsimilar to belief propagation. Thus, decoding is relegated to the two\nconstituent codes. We repeat this recursion and execute decoding only at the\nend nodes $\\left\\{\\genfrac{}{}{0pt}{}{j}{1}\\right\\} $ and\n$\\left\\{\\genfrac{}{}{0pt}{}{j}{j-1}\\right\\} $. The overall complexity has low\norder of $n\\log n.$ It is shown that this decoding substantially outperforms\nother algorithms of polynomial complexity known for RM codes. In particular,\nfor medium and high code rates, the algorithm corrects most error patterns of\nweight $d\\ln d/2.$\n", "doi": null, "arxiv_id": "1703.05303", "pdf_urls": ["https://arxiv.org/pdf/1703.05303"], "github": [], "is_oa": true, "sources": ["open-arxiv"], "type": "journal", "journal_ref": "Proc. 37th Allerton Conf. on Commun., Control, and Computing,\n  Monticello, IL, USA, 1999, pp. 61-69", "categories": "cs.IT math.IT"}
{"title": "Shape analysis on homogeneous spaces: a generalised SRVT framework", "year": 2017, "venue_abbr": "Cell", "venue_name": "Cell", "authors": ["Elena Celledoni", "S{\\o}lve Eidnes and Alexander Schmeding"], "abstract": "  Shape analysis is ubiquitous in problems of pattern and object recognition\nand has developed considerably in the last decade. The use of shapes is natural\nin applications where one wants to compare curves independently of their\nparametrisation. One computationally efficient approach to shape analysis is\nbased on the Square Root Velocity Transform (SRVT). In this paper we propose a\ngeneralised SRVT framework for shapes on homogeneous manifolds. The method\nopens up for a variety of possibilities based on different choices of Lie group\naction and giving rise to different Riemannian metrics.\n", "doi": "10.1007/978-3-030-01593-0_7", "arxiv_id": "1704.01471", "pdf_urls": ["https://arxiv.org/pdf/1704.01471"], "github": [], "is_oa": true, "sources": ["open-arxiv"], "type": "journal", "journal_ref": "E. Celledoni et al. (eds.), Computation and Combinatorics in\n  Dynamics, Stochastics and Control, Abelsymposium 2016, Abel Symposia 13", "categories": "math.DG math.NA"}
{"title": "Muscle-Cell-Based \"Living Diodes\"", "year": 2017, "venue_abbr": "Cell", "venue_name": "Cell", "authors": ["Uryan Isik Can", "Neerajha Nagarajan", "Dervis Can Vural", "Pinar Zorlutuna"], "abstract": "  A new type of diode that is made entirely of electrically excitable muscle\ncells and nonexcitable fibroblast cells is designed, fabricated, and\ncharacterized. These two cell types in a rectangular pattern allow the signal\ninitiated on the excitable side to pass to the nonexcitable side, and not in\nthe opposite direction.\n", "doi": null, "arxiv_id": "1706.00383", "pdf_urls": ["https://arxiv.org/pdf/1706.00383"], "github": [], "is_oa": true, "sources": ["open-arxiv"], "type": "journal", "journal_ref": "Can UI, Nagarajan N, Vural DC, Zorlutuna P. Muscle-Cell-Based\n  \"Living Diodes\". Advanced Biosystems. 2017 Jan 1", "categories": "q-bio.TO physics.bio-ph"}
{"title": "Streaming Bayesian inference: theoretical limits and mini-batch\n  approximate message-passing", "year": 2017, "venue_abbr": "Cell", "venue_name": "Cell", "authors": ["Andre Manoel", "Florent Krzakala", "Eric W. Tramel", "Lenka Zdeborov\\'a"], "abstract": "  In statistical learning for real-world large-scale data problems, one must\noften resort to \"streaming\" algorithms which operate sequentially on small\nbatches of data. In this work, we present an analysis of the\ninformation-theoretic limits of mini-batch inference in the context of\ngeneralized linear models and low-rank matrix factorization. In a controlled\nBayes-optimal setting, we characterize the optimal performance and phase\ntransitions as a function of mini-batch size. We base part of our results on a\ndetailed analysis of a mini-batch version of the approximate message-passing\nalgorithm (Mini-AMP), which we introduce. Additionally, we show that this\ntheoretical optimality carries over into real-data problems by illustrating\nthat Mini-AMP is competitive with standard streaming algorithms for clustering.\n", "doi": "10.1109/allerton.2017.8262853", "arxiv_id": "1706.00705", "pdf_urls": ["https://arxiv.org/pdf/1706.00705"], "github": [], "is_oa": true, "sources": ["open-arxiv"], "type": "journal", "journal_ref": "2017 55th Annual Allerton Conference on Communication, Control,\n  and Computing (Allerton), Monticello, IL, USA, 2017, pp. 1048-1055", "categories": "stat.ML cond-mat.stat-mech cs.IT math.IT"}
{"title": "Investigation and modeling of photocurrent collection process in\n  multiple quantum well solar cells", "year": 2017, "venue_abbr": "Cell", "venue_name": "Cell", "authors": ["Kasidit Toprasertpong", "Tomoyuki Inoue", "Yoshiaki Nakano", "Masakazu\n  Sugiyama"], "abstract": "  Solar cells employing quantum wells can enhance the light absorption but\nsuffer from the difficulty in photogenerated carrier extraction. Here, we\nanalyzed the spectral response and the photocarrier collection mechanism of\np-i-n multiple quantum well (MQW) solar cells using the effective-mobility\nmodel. Both the simulation and experiment results imply that the spatial\nprofiles of electron and hole densities in MQWs play an important role in the\ncarrier collection process. By considering the recombination increment under\nillumination, our findings suggest that the concept of the majority/minority\ncarriers is important even in the intrinsic region: photogenerated electrons\nand holes only experience significant recombination when passing through the\nhole-rich and electron-rich regions, respectively. This can accurately explain\nthe photocurrent behavior in cells with high background doping, background\nillumination, and different MQW positions. Based on the experimental findings,\nwe derived analytical formulae for carrier collection efficiency, which\ndirectly show the impact of each cell parameter and can be used for the\nsystematic cell design.\n", "doi": "10.1016/j.solmat.2017.08.036", "arxiv_id": "1706.03088", "pdf_urls": ["https://arxiv.org/pdf/1706.03088"], "github": [], "is_oa": true, "sources": ["open-arxiv"], "type": "journal", "journal_ref": "Solar Energy Materials and Solar Cells 174 (2018) 146-156", "categories": "physics.app-ph"}
{"title": "Roles of Diffusion Dynamics and Molecular Concentration Gradients in\n  Cellular Differentiation and Three-Dimensional Tissue Development", "year": 2017, "venue_abbr": "Cell", "venue_name": "Cell", "authors": ["Richard J. McMurtrey"], "abstract": "  Recent advancements in the ability to construct three-dimensional (3D)\ntissues and organoids from stem cells and biomaterials have not only opened\nabundant new research avenues in disease modeling and regenerative medicine but\nalso have ignited investigation into important aspects of molecular diffusion\nin 3D cellular architectures. This paper describes fundamental mechanics of\ndiffusion with equations for modeling these dynamic processes under a variety\nof scenarios in 3D cellular tissue constructs. The effects of these diffusion\nprocesses and resultant concentration gradients are described in the context of\nthe major molecular signaling pathways in stem cells that both mediate and are\ninfluenced by gas and nutrient concentrations, including how diffusion\nphenomena can affect stem cell state, cell differentiation, and metabolic\nstates of the cell. The application of these diffusion models and pathways is\nof vital importance for future studies of developmental processes, disease\nmodeling, and tissue regeneration.\n", "doi": "10.1089/scd.2017.0066", "arxiv_id": "1707.08543", "pdf_urls": ["https://arxiv.org/pdf/1707.08543"], "github": [], "is_oa": true, "sources": ["open-arxiv"], "type": "journal", "journal_ref": "Stem Cells and Development. 2017", "categories": "q-bio.TO"}
{"title": "Technological guidelines for the design of tandem III-V nanowire on Si\n  solar cells from opto-electrical simulations", "year": 2017, "venue_abbr": "Cell", "venue_name": "Cell", "authors": ["Vladimir Maryasin", "Davide Bucci", "Quentin Rafhay", "Federico Panicco", "J\\'er\\^ome Michallon", "Anne Kaminski-Cachopo"], "abstract": "  Effect of geometrical and structural parameters on the efficiency of the\ntandem solar cell based on the III-V nanowire array on silicon is studied by\nthe means of coupled opto-electrical simulations. A close to realistic\nstructure, consisting of AlGaAs core-shell nanowire array, connected through a\ntunnel diode to a Si subcell is modelled, revealing the impact of top contact\nlayer, growth mask and tunnel junction. Optical simulation of the tandem\nstructure under current matching condition determine optimal geometrical\nparameters of the nanowire array. They are then used in the extensive\nelectrical optimization of the radial junction in the nanowire subcell. Device\nsimulations show the necessity of high doping of the junction in order to avoid\nfull shell depletion. The influence of bulk and surface recombination on the\nperformance of the top subcell is studied, exposing the importance of the good\nsurface passivation near the depleted region of the radial p - n junction.\nFinally, simulations of the fully optimized tandem structure show that a\npromising efficiency of 27.6% with the short-circuit current density of 17.1\nmA/cm^2 can be achieved with reasonable bulk and surface carrier lifetime.\n", "doi": "10.1016/j.solmat.2017.07.041", "arxiv_id": "1708.00406", "pdf_urls": ["https://arxiv.org/pdf/1708.00406"], "github": [], "is_oa": true, "sources": ["open-arxiv"], "type": "journal", "journal_ref": "Solar Energy Materials and Solar Cells 172, (2017), pp. 314-323", "categories": "cond-mat.mtrl-sci physics.app-ph physics.optics"}
{"title": "Quantifying homologous proteins and proteoforms", "year": 2017, "venue_abbr": "Cell", "venue_name": "Cell", "authors": ["Dmitry Malioutov", "Tianchi Chen", "Jacob Jaffe", "Edoardo Airoldi", "Steven\n  Carr", "Bogdan Budnik and Nikolai Slavov"], "abstract": "  Many proteoforms - arising from alternative splicing, post-translational\nmodifications (PTMs), or paralogous genes - have distinct biological functions,\nsuch as histone PTM proteoforms. However, their quantification by existing\nbottom-up mass-spectrometry (MS) methods is undermined by peptide-specific\nbiases. To avoid these biases, we developed and implemented a first-principles\nmodel (HIquant) for quantifying proteoform stoichiometries. We characterized\nwhen MS data allow inferring proteoform stoichiometries by HIquant, derived an\nalgorithm for optimal inference, and demonstrated experimentally high accuracy\nin quantifying fractional PTM occupancy without using external standards, even\nin the challenging case of the histone modification code.\n  HIquant server is implemented at:\nhttps://web.northeastern.edu/slavov/2014_HIquant/\n", "doi": "10.1074/mcp.tir118.000947", "arxiv_id": "1708.01772", "pdf_urls": ["https://arxiv.org/pdf/1708.01772"], "github": [], "is_oa": true, "sources": ["open-arxiv"], "type": "journal", "journal_ref": "Molecular & Cellular Proteomics, 2018", "categories": "q-bio.QM q-bio.GN stat.AP stat.ME stat.ML"}
{"title": "Salt-n-pepper noise filtering using Cellular Automata", "year": 2017, "venue_abbr": "Cell", "venue_name": "Cell", "authors": ["Dimitrios Tourtounis", "Nikolaos Mitianoudis", "Georgios Ch. Sirakoulis"], "abstract": "  Cellular Automata (CA) have been considered one of the most pronounced\nparallel computational tools in the recent era of nature and bio-inspired\ncomputing. Taking advantage of their local connectivity, the simplicity of\ntheir design and their inherent parallelism, CA can be effectively applied to\nmany image processing tasks. In this paper, a CA approach for efficient\nsalt-n-pepper noise filtering in grayscale images is presented. Using a 2D\nMoore neighborhood, the classified \"noisy\" cells are corrected by averaging the\nnon-noisy neighboring cells. While keeping the computational burden really low,\nthe proposed approach succeeds in removing high-noise levels from various\nimages and yields promising qualitative and quantitative results, compared to\nstate-of-the-art techniques.\n", "doi": null, "arxiv_id": "1708.05019", "pdf_urls": ["https://arxiv.org/pdf/1708.05019"], "github": [], "is_oa": true, "sources": ["open-arxiv"], "type": "journal", "journal_ref": "Journal of Cellular Automata, Vol. 13, No. 1-2, pp. 81-101, 2018", "categories": "cs.CV"}
{"title": "Exploring Gender Differences in Graduation Proficiency in Mathematics\n  Education Using a Markov Chain Model: Implications for Economic Growth in\n  Nigeria", "year": 2017, "venue_abbr": "Cell", "venue_name": "Cell", "authors": ["Clement Iji", "Joshua Abah"], "abstract": "  This study employs an ex-post facto research design to explore the\nfluctuations of gender difference in academic achievement among graduating\nstudents of mathematics education. Graduation statistics for a total of 1106\ngraduating students of mathematics education (923 males and 183 females) from a\nUniversity in North Central Nigeria were used to design a discrete-time Markov\nchain model for the movement of the difference (d) in graduating proficiency\nfrom one range of values (states) to the other. Additional goodness of fit test\n($\\chi$ 2 = 1.731, p = 0.99924) and t-test (t = 0.4055, p = 0.6852) unveiled\nthat d has stayed much the same over the 12 graduation cycles used in the\nstudy, and that whatever factors determine the difference in academic\nachievement between male and female graduating students of mathematics\neducation on a graduation cycle basis have remained much the same over the\nyears. Further analysis of the model predicted the closure of the observed\ngender gap in the next 15 graduation cycles (p 15). The results of this study\nhas specifically highlighted the fact that female graduates of mathematics\neducation are as proficient as their male counterparts in driving value added\nservices in and beyond the education sub-sector of the Nigerian economy. Based\non the findings of this study, it was recommended that future work may consider\nan in-depth investigation of the sensitivity of parameters that may have\ninfluenced specific probabilities given in the model.\n", "doi": "10.18562/ijee.028", "arxiv_id": "1708.09288", "pdf_urls": ["https://arxiv.org/pdf/1708.09288"], "github": [], "is_oa": true, "sources": ["open-arxiv"], "type": "journal", "journal_ref": "International Journal of Educational Excellence International\n  Journal of Educational Excellence, 2017, 3 (2), pp.75 - 86", "categories": "math.HO"}
{"title": "Organic and perovskite solar cells for space applications", "year": 2017, "venue_abbr": "Cell", "venue_name": "Cell", "authors": ["Ilaria Cardinaletti", "Tim Vangerven", "Steven Nagels", "Rob Cornelissen", "Dieter Schreurs", "Jaroslav Hruby", "Jelle Vodnik", "Dries Devisscher", "Jurgen\n  Kesters", "Jan DHaen", "Alexis Franquet", "Valentina Spampinato", "Thierry Conard", "Wouter Maes", "Wim Deferme", "and Jean V. Manca"], "abstract": "  For almost sixty years, solar energy for space applications has relied on\ninorganic photovoltaics, evolving from solar cells made of single crystalline\nsilicon to triple junctions based on germanium and III-V alloys. The class of\norganic-based photovoltaics, which ranges from all-organic to hybrid\nperovskites, has the potential of becoming a disruptive technology in space\napplications, thanks to the unique combination of appealing intrinsic\nproperties (e.g. record high specific power, tunable absorption window) and\nprocessing possibilities. Here, we report on the launch of the stratospheric\nmission OSCAR, which demonstrated for the first time organic-based solar cell\noperation in extra-terrestrial conditions. This successful maiden flight for\norganic-based photovoltaics opens a new paradigm for solar electricity in\nspace, from satellites to orbital and planetary space stations.\n", "doi": "10.1016/j.solmat.2018.03.024", "arxiv_id": "1709.01787", "pdf_urls": ["https://arxiv.org/pdf/1709.01787"], "github": [], "is_oa": true, "sources": ["open-arxiv"], "type": "journal", "journal_ref": "Solar Energy Materials & Solar Cells 182, 121-127 (2018)", "categories": "physics.app-ph"}
{"title": "Joint Coordination-Channel Coding for Strong Coordination over Noisy\n  Channels Based on Polar Codes", "year": 2017, "venue_abbr": "Cell", "venue_name": "Cell", "authors": ["Sarah A. Obead", "J\\\"org Kliewer and Badri N. Vellambi"], "abstract": "  We construct a joint coordination-channel polar coding scheme for strong\ncoordination of actions between two agents $\\mathsf X$ and $\\mathsf Y$, which\ncommunicate over a discrete memoryless channel (DMC) such that the joint\ndistribution of actions follows a prescribed probability distribution. We show\nthat polar codes are able to achieve our previously established inner bound to\nthe strong noisy coordination capacity region and thus provide a constructive\nalternative to a random coding proof. Our polar coding scheme also offers a\nconstructive solution to a channel simulation problem where a DMC and shared\nrandomness are together employed to simulate another DMC. In particular, our\nproposed solution is able to utilize the randomness of the DMC to reduce the\namount of local randomness required to generate the sequence of actions at\nagent $\\mathsf Y$. By leveraging our earlier random coding results for this\nproblem, we conclude that the proposed joint coordination-channel coding scheme\nstrictly outperforms a separate scheme in terms of achievable communication\nrate for the same amount of injected randomness into both systems.\n", "doi": "10.1109/allerton.2017.8262789", "arxiv_id": "1710.03210", "pdf_urls": ["https://arxiv.org/pdf/1710.03210"], "github": [], "is_oa": true, "sources": ["open-arxiv"], "type": "journal", "journal_ref": "55th Annual Allerton Conference on Communication, Control, and\n  Computing (Allerton), Monticello, IL, USA, Oct 2017, pp. 580-587", "categories": "cs.IT math.IT"}
{"title": "Dispersion of Boron Nitride Powders in Aqueous Suspensions with\n  Cellulose", "year": 2017, "venue_abbr": "Cell", "venue_name": "Cell", "authors": ["Florian Bouville", "Sylvain Deville"], "abstract": "  The dispersion of nitride and carbide ceramic particles in water is\ndifficult, due to the absence of hydroxyl groups on their surface. Boron\nnitride is not an exception and despite its numerous applications, no effective\ndispersant has been identified so far. We demonstrate here the dispersion\nproperties of two cellulose derivatives for hexagonal boron nitride powders,\nhydroxyl ethyl cellulose and methyl cellulose. The effect of particle sizes and\ncellulose concentration was investigated. The adsorption of cellulose onto the\nsurface of the BN particles was confirmed by isotherm adsorption. Zeta\npotential measurements shows a charge screening effect of the cellulose The\nsuspensions obtained were highly loaded and stable versus pH, and thus could\nlead to homogeneous codispersion of BN particles and sintering additives.\n", "doi": "10.1111/jace.12653", "arxiv_id": "1710.04239", "pdf_urls": ["https://arxiv.org/pdf/1710.04239"], "github": [], "is_oa": true, "sources": ["open-arxiv"], "type": "journal", "journal_ref": "Bouville, F., & Deville, S. (2014). Dispersion of boron nitride\n  powders in aqueous suspensions with cellulose. Journal of the American\n  Ceramic Society, 97(2), 394-398", "categories": "cond-mat.mtrl-sci"}
{"title": "Details Matter: noise and model structure set the relationship between\n  cell size and cell cycle timing", "year": 2017, "venue_abbr": "Cell", "venue_name": "Cell", "authors": ["Felix Barber", "Po-Yi Ho", "Andrew W. Murray", "Ariel Amir"], "abstract": "  Organisms across all domains of life regulate the size of their cells.\nHowever, the means by which this is done is poorly understood. We study two\nabstracted \"molecular\" models for size regulation: inhibitor dilution and\ninitiator accumulation. We apply the models to two settings: bacteria like\nEscherichia coli, that grow fully before they set a division plane and divide\ninto two equally sized cells, and cells that form a bud early in the cell\ndivision cycle, confine new growth to that bud, and divide at the connection\nbetween that bud and the mother cell, like the budding yeast Saccharomyces\ncerevisiae. In budding cells, delaying cell division until buds reach the same\nsize as their mother leads to very weak size control, with average cell size\nand standard deviation of cell size increasing over time and saturating up to\n100-fold higher than those values for cells that divide when the bud is still\nsubstantially smaller than its mother. In budding yeast, both inhibitor\ndilution or initiator accumulation models are consistent with the observation\nthat the daughters of diploid cells add a constant volume before they divide.\nThis adder behavior has also been observed in bacteria. We find that in\nbacteria an inhibitor dilution model produces adder correlations that are not\nrobust to noise in the timing of DNA replication initiation or in the timing\nfrom initiation of DNA replication to cell division (the C + D period). In\ncontrast, in bacteria an initiator accumulation model yields robust adder\ncorrelations in the regime where noise in the timing of DNA replication\ninitiation is much greater than noise in the C + D period, as reported\npreviously [1]. In bacteria, division into two equally sized cells does not\nbroaden the size distribution.\n", "doi": "10.3389/fcell.2017.00092", "arxiv_id": "1710.06486", "pdf_urls": ["https://arxiv.org/pdf/1710.06486"], "github": [], "is_oa": true, "sources": ["open-arxiv"], "type": "journal", "journal_ref": "Frontiers in Cell and Developmental Biology, 2017, vol. 5, pp. 92", "categories": "q-bio.MN q-bio.CB"}
{"title": "Particle-based membrane model for mesoscopic simulation of cellular\n  dynamics", "year": 2017, "venue_abbr": "Cell", "venue_name": "Cell", "authors": ["Mohsen Sadeghi", "Thomas R. Weikl", "Frank No\\'e"], "abstract": "  We present a simple and computationally efficient coarse-grained and\nsolvent-free model for simulating lipid bilayer membranes. In order to be used\nin concert with particle-based reaction-diffusion simulations, the model is\npurely based on interacting and reacting particles, each representing a coarse\npatch of a lipid monolayer. Particle interactions include nearest-neighbor\nbond-stretching and angle-bending, and are parameterized so as to reproduce the\nlocal membrane mechanics given by the Helfrich energy density over a range of\nrelevant curvatures. In-plane fluidity is implemented with Monte Carlo\nbond-flipping moves. The physical accuracy of the model is verified by five\ntests: (i) Power spectrum analysis of equilibrium thermal undulations is used\nto verify that the particle-based representation correctly captures the\ndynamics predicted by the continuum model of fluid membranes. (ii) It is\nverified that the input bending stiffness, against which the potential\nparameters are optimized, is accurately recovered. (iii) Isothermal area\ncompressibility modulus of the membrane is calculated and is shown to be\ntunable to reproduce available values for different lipid bilayers, independent\nof the bending rigidity. (iv) Simulation of two-dimensional shear flow under a\ngravity force is employed to measure the effective in-plane viscosity of the\nmembrane model, and show the possibility of modeling membranes with specified\nviscosities. (v) Interaction of the bilayer membrane with a spherical\nnanoparticle is modeled as a test case for large membrane deformations and\nbudding involved in cellular processes such as endocytosis...\n", "doi": "10.1063/1.5009107", "arxiv_id": "1710.06907", "pdf_urls": ["https://arxiv.org/pdf/1710.06907"], "github": [], "is_oa": true, "sources": ["open-arxiv"], "type": "journal", "journal_ref": "M. Sadeghi, T. R. Weikl, and F. No\\'e, \"Particle-based membrane\n  model for mesoscopic simulation of cellular dynamics'', The Journal of\n  Chemical Physics 148(4), 044901 (2018)", "categories": "physics.bio-ph physics.chem-ph physics.comp-ph"}
{"title": "Evolution of Social Power for Opinion Dynamics Networks", "year": 2017, "venue_abbr": "Cell", "venue_name": "Cell", "authors": ["Susana Rey", "Patricio Reyes (ITMATI)", "Alonso Silva (LINCS)"], "abstract": "  This article studies the evolution of opinions and interpersonal influence\nstructures in a group of agents as they discuss a sequence of issues, each of\nwhich follows an opinion dynamics model. In this work, we propose a general\nopinion dynamics model and an evolution of interpersonal influence structures\nbased on the model of reflected appraisals proposed by Friedkin. Our\ncontributions can be summarized as follows: (i) we introduce a model of opinion\ndynamics and evolution of interpersonal influence structures between issues\nviewed as a best response cost minimization to the neighbor's actions, (ii) we\nshow that DeGroot's and Friedkin-Johnsen's models of opinion dynamics and their\nevolution of interpersonal influence structures are particular cases of our\nproposed model, and (iii) we prove the existence of an equilibrium. This work\nis a step towards providing a solid formulation of the evolution of opinions\nand interpersonal influence structures over a sequence of issues.\n", "doi": null, "arxiv_id": "1711.06441", "pdf_urls": ["https://arxiv.org/pdf/1711.06441"], "github": [], "is_oa": true, "sources": ["open-arxiv"], "type": "journal", "journal_ref": "55th Annual Allerton Conference on Communication, Control, and\n  Computing, Oct 2017, Monticello, Illinois, United States", "categories": "cs.SI cs.GT"}
{"title": "Integrative biological simulation praxis: Considerations from physics,\n  philosophy, and data/model curation practices", "year": 2017, "venue_abbr": "Cell", "venue_name": "Cell", "authors": ["Gopal P. Sarma and Victor Faundez"], "abstract": "  Integrative biological simulations have a varied and controversial history in\nthe biological sciences. From computational models of organelles, cells, and\nsimple organisms, to physiological models of tissues, organ systems, and\necosystems, a diverse array of biological systems have been the target of\nlarge-scale computational modeling efforts. Nonetheless, these research agendas\nhave yet to prove decisively their value among the broader community of\ntheoretical and experimental biologists. In this commentary, we examine a range\nof philosophical and practical issues relevant to understanding the potential\nof integrative simulations. We discuss the role of theory and modeling in\ndifferent areas of physics and suggest that certain sub-disciplines of physics\nprovide useful cultural analogies for imagining the future role of simulations\nin biological research. We examine philosophical issues related to modeling\nwhich consistently arise in discussions about integrative simulations and\nsuggest a pragmatic viewpoint that balances a belief in philosophy with the\nrecognition of the relative infancy of our state of philosophical\nunderstanding. Finally, we discuss community workflow and publication practices\nto allow research to be readily discoverable and amenable to incorporation into\nsimulations. We argue that there are aligned incentives in widespread adoption\nof practices which will both advance the needs of integrative simulation\nefforts as well as other contemporary trends in the biological sciences,\nranging from open science and data sharing to improving reproducibility.\n", "doi": "10.1080/21592799.2017.1392400", "arxiv_id": "1712.01417", "pdf_urls": ["https://arxiv.org/pdf/1712.01417"], "github": [], "is_oa": true, "sources": ["open-arxiv"], "type": "journal", "journal_ref": "Cellular Logistics, Volume 7, No. 4 e1392400 (2017)", "categories": "q-bio.QM"}
{"title": "Physical epistatic landscape of antibody binding affinity", "year": 2017, "venue_abbr": "Cell", "venue_name": "Cell", "authors": ["Rhys M. Adams", "Justin B. Kinney", "Aleksandra M. Walczak", "Thierry Mora"], "abstract": "  Affinity maturation produces antibodies that bind antigens with high\nspecificity by accumulating mutations in the antibody sequence. Mapping out the\nantibody-antigen affinity landscape can give us insight into the accessible\npaths during this rapid evolutionary process. By developing a carefully\ncontrolled null model for noninteracting mutations, we characterized epistasis\nin affinity measurements of a large library of antibody variants obtained by\nTite-Seq, a recently introduced Deep Mutational Scan method yielding physical\nvalues of the binding constant. We show that representing affinity as the\nbinding free energy minimizes epistasis. Yet, we find that epistatically\ninteracting sites contribute substantially to binding. In addition to negative\nepistasis, we report a large amount of beneficial epistasis, enlarging the\nspace of high-affinity antibodies as well as their mutational accessibility.\nThese properties suggest that the degeneracy of antibody sequences that can\nbind a given antigen is enhanced by epistasis - an important property for\nvaccine design.\n", "doi": "10.1016/j.cels.2018.12.004", "arxiv_id": "1712.04000", "pdf_urls": ["https://arxiv.org/pdf/1712.04000"], "github": ["https://github.com/rhys-m-adams/epistasis_4_4_20"], "is_oa": true, "sources": ["open-arxiv"], "type": "journal", "journal_ref": "Cell Systems 8 86-93 (2019)", "categories": "q-bio.PE q-bio.BM"}
{"title": "Self-organization and chaos in the metabolism of a cell", "year": 2018, "venue_abbr": "Cell", "venue_name": "Cell", "authors": ["V. I. Grytsay", "I. V. Musatenko"], "abstract": "  Aim. To study the dynamics of auto-oscillations arising at the level of\nenzyme-substrate interaction in a cell and to find the conditions for the\nself-organization and the formation of chaos in the metabolic process. Methods.\nA mathematical model of the metabolic process of steroids transformation in\nArthrobacter globiformis. The mathematical apparatus of nonlinear dynamics.\nResults. The bifurcations resulting in the appearance of strange attractors in\nthe metabolic process are determined. The projections of the phase portraits of\nattractors are constructed for some chosen modes. The total spectra of\nLyapunov's indices are calculated. The structural stability of the attractors\nobtained is studied. By the general scenario of formation of regular and\nstrange attractors, the structural-functional connections in the metabolic\nprocess in the cell are found. Their physical nature is investigated.\nConclusions. The presented model explains the mechanism of formation of\nauto-oscillations observed in the A. globiformis cells and demonstrates a\npossibility of the mathematical modeling of metabolic processes for the\nphysical explanation of the self-organization of a cell and its vital activity.\n", "doi": "10.7124/bc.0008b9", "arxiv_id": "1801.07711", "pdf_urls": ["https://arxiv.org/pdf/1801.07711"], "github": [], "is_oa": true, "sources": ["open-arxiv"], "type": "journal", "journal_ref": "Biopolymers and cell.-2014.-Vol.30,No 5.-pp. 403-409", "categories": "nlin.AO q-bio.CB"}
{"title": "Professional Practice in Higher Education: A Case Study in Faculty\n  Training and Development in Brazil", "year": 2018, "venue_abbr": "Cell", "venue_name": "Cell", "authors": ["Edileuza de Freitas Miranda de Mendonca", "Jose Gomez-Galan"], "abstract": "  One of the most important debates is currently focusing on specifying the\ntraining that university teachers must receive for their professional practice.\nImproving it in higher education is extremely important not only for the\nscientific production generated by university but also for the adequacy of the\ntraining that future graduates will be offered; professionals facing an\nincreasingly demanding labour market with new needs. University teachers\ntraining, thus, should be a priority in academic policies due to their\ninfluence and the role played in the evolution of society, as well as being the\nbasis of the quality of Higher Education. This research, a case study in the\nState of Goias (Brazil), is focused on a sample of practicing university\nteachers from different fields of knowledge, and has as main objective to know\nthe characteristics of the training received for their professional practice,\nboth in the field of scientific education and their educational role and\nability to transfer knowledge. The methodology used has been mixed, not\nexperimental and descriptive, with the help of instruments for data collection\nand analysis of quantitative and qualitative nature (questionnaires,\ninterviews, monitoring, checklists, documentary analysis, etc.). The results\nconfirmed the initial hypothesis, which stated that university teachers current\ntraining is primarily scientific and technical, and has gaps in the teacher\ntraining required today for a more effective work in the classroom. In this\narea teachers often use teaching methodologies supported by previous\nexperiences with traditional features. Finally, to optimize this situation,\ndifferent strategies for university teachers training are proposed seeking to\nimprove both their reflection and teaching practice.\n", "doi": "10.18562/ijee.018", "arxiv_id": "1802.06853", "pdf_urls": ["https://arxiv.org/pdf/1802.06853"], "github": [], "is_oa": true, "sources": ["open-arxiv"], "type": "journal", "journal_ref": "International Journal of Educational Excellence, 2016, Vol. 2, No.\n  2, 51-64 ISSN 2373-5929", "categories": "physics.ed-ph"}
{"title": "Thermodynamics of Restricted Boltzmann Machines and related learning\n  dynamics", "year": 2018, "venue_abbr": "Cell", "venue_name": "Cell", "authors": ["Aur\\'elien Decelle", "Giancarlo Fissore", "Cyril Furtlehner"], "abstract": "  We investigate the thermodynamic properties of a Restricted Boltzmann Machine\n(RBM), a simple energy-based generative model used in the context of\nunsupervised learning. Assuming the information content of this model to be\nmainly reflected by the spectral properties of its weight matrix $W$, we try to\nmake a realistic analysis by averaging over an appropriate statistical ensemble\nof RBMs.\n  First, a phase diagram is derived. Otherwise similar to that of the\nSherrington- Kirkpatrick (SK) model with ferromagnetic couplings, the RBM's\nphase diagram presents a ferromagnetic phase which may or may not be of\ncompositional type depending on the kurtosis of the distribution of the\ncomponents of the singular vectors of $W$.\n  Subsequently, the learning dynamics of the RBM is studied in the\nthermodynamic limit. A \"typical\" learning trajectory is shown to solve an\neffective dynamical equation, based on the aforementioned ensemble average and\nexplicitly involving order parameters obtained from the thermodynamic analysis.\nIn particular, this let us show how the evolution of the dominant singular\nvalues of $W$, and thus of the unstable modes, is driven by the input data. At\nthe beginning of the training, in which the RBM is found to operate in the\nlinear regime, the unstable modes reflect the dominant covariance modes of the\ndata. In the non-linear regime, instead, the selected modes interact and\neventually impose a matching of the order parameters to their empirical\ncounterparts estimated from the data.\n  Finally, we illustrate our considerations by performing experiments on both\nartificial and real data, showing in particular how the RBM operates in the\nferromagnetic compositional phase.\n", "doi": "10.1007/s10955-018-2105-y", "arxiv_id": "1803.01960", "pdf_urls": ["https://arxiv.org/pdf/1803.01960"], "github": [], "is_oa": true, "sources": ["open-arxiv"], "type": "journal", "journal_ref": "Decelle, A., Fissore, G. & Furtlehner, C. J Stat Phys (2018)", "categories": "cond-mat.dis-nn cond-mat.stat-mech cs.LG"}
{"title": "Logical Gates via Gliders Collisions", "year": 2018, "venue_abbr": "Cell", "venue_name": "Cell", "authors": ["Genaro J. Martinez", "Andrew Adamatzky", "Kenichi Morita"], "abstract": "  An elementary cellular automaton with memory is a chain of finite state\nmachines (cells) updating their state simultaneously and by the same rule. Each\ncell updates its current state depending on current states of its immediate\nneighbours and a certain number of its own past states. Some cell-state\ntransition rules support gliders, compact patterns of non-quiescent states\ntranslating along the chain. We present designs of logical gates, including\nreversible Fredkin gate and controlled NOT gate, implemented via collisions\nbetween gliders.\n", "doi": null, "arxiv_id": "1803.05496", "pdf_urls": ["https://arxiv.org/pdf/1803.05496"], "github": [], "is_oa": true, "sources": ["open-arxiv"], "type": "journal", "journal_ref": "Journal of Cellular Automata, 13(4), 325--346, 2018", "categories": "nlin.CG cs.ET"}
{"title": "Titanium diboride ceramics for solar thermal absorbers", "year": 2018, "venue_abbr": "Cell", "venue_name": "Cell", "authors": ["E. Sani", "M. Meucci", "L. Mercatelli", "A. Balbo", "C. Musa", "R. Licheri", "R.\n  Orr\\`u", "G. Cao"], "abstract": "  Titanium diboride (TiB2) is a low-density refractory material belonging to\nthe family of ultra-high temperature ceramics (UHTCs). This paper reports on\nthe production and microstructural and optical characterization of nearly fully\ndense TiB2, with particular interest to its potential utilization as novel\nthermal solar absorber. Monolithic bulk samples are produced starting from\nelemental reactants by a two-step method consisting of the Self-propagating\nHigh-temperature Synthesis (SHS) followed by the Spark Plasma Sintering (SPS)\nof the resulting powders. The surface of obtained samples has-been\ncharacterized from the microstructural and topological points of view. The\nhemispherical reflectance spectrum has been measured from 0.3 to 15 um\nwavelength, to evaluate the potential of this material as solar absorber for\nfuture concentrating solar plants.\n", "doi": "10.1016/j.solmat.2017.05.038", "arxiv_id": "1803.06526", "pdf_urls": ["https://arxiv.org/pdf/1803.06526"], "github": [], "is_oa": true, "sources": ["open-arxiv"], "type": "journal", "journal_ref": "Solar Energy Materials and Solar Cells, Volume 169 (2017) Pages\n  313-319", "categories": "physics.app-ph cond-mat.mtrl-sci"}
{"title": "Refractive index measurements of single, spherical cells using digital\n  holographic microscopy", "year": 2018, "venue_abbr": "Cell", "venue_name": "Cell", "authors": ["Mirjam Sch\\\"urmann and Jana Scholze and Paul M\\\"uller and Chii J. Chan\n  and Andrew E. Ekpenyong and Kevin J. Chalut and Jochen Guck"], "abstract": "  In this chapter, we introduce digital holographic microscopy (DHM) as a\nmarker-free method to determine the refractive index of single, spherical cells\nin suspension. The refractive index is a conclusive measure in a biological\ncontext. Cell conditions, such as differentiation or infection, are known to\nyield significant changes in the refractive index. Furthermore, the refractive\nindex of biological tissue determines the way it interacts with light. Besides\nthe biological relevance of this interaction in the retina, a lot of methods\nused in biology, including microscopy, rely on light-tissue or light-cell\ninteractions. Hence, determining the refractive index of cells using DHM is\nvaluable in many biological applications. This chapter covers the main topics\nwhich are important for the implementation of DHM: setup, sample preparation\nand analysis. First, the optical setup is described in detail including notes\nand suggestions for the implementation. Following that, a protocol for the\nsample and measurement preparation is explained. In the analysis section, an\nalgorithm for the determination of the quantitative phase map is described.\nSubsequently, all intermediate steps for the calculation of the refractive\nindex of suspended cells are presented, exploiting their spherical shape. In\nthe last section, a discussion of possible extensions to the setup, further\nmeasurement configurations and additional analysis methods are given.\nThroughout this chapter, we describe a simple, robust, and thus easily\nreproducible implementation of DHM. The different possibilities for extensions\nshow the diverse fields of application for this technique.\n", "doi": "10.1016/bs.mcb.2014.10.016", "arxiv_id": "1804.01721", "pdf_urls": ["https://arxiv.org/pdf/1804.01721"], "github": [], "is_oa": true, "sources": ["open-arxiv"], "type": "journal", "journal_ref": "Methods in Cell Biology, Volume 125, Chapter 9, Pages 143-159\n  (2015)", "categories": "q-bio.QM physics.bio-ph physics.optics"}
{"title": "Classification of large DNA methylation datasets for identifying cancer\n  drivers", "year": 2018, "venue_abbr": "Cell", "venue_name": "Cell", "authors": ["Fabrizio Celli", "Fabio Cumbo", "and Emanuel Weitschek"], "abstract": "  DNA methylation is a well-studied genetic modification crucial to regulate\nthe functioning of the genome. Its alterations play an important role in\ntumorigenesis and tumor-suppression. Thus, studying DNA methylation data may\nhelp biomarker discovery in cancer. Since public data on DNA methylation become\nabundant, and considering the high number of methylated sites (features)\npresent in the genome, it is important to have a method for efficiently\nprocessing such large datasets. Relying on big data technologies, we propose\nBIGBIOCL an algorithm that can apply supervised classification methods to\ndatasets with hundreds of thousands of features. It is designed for the\nextraction of alternative and equivalent classification models through\niterative deletion of selected features. We run experiments on DNA methylation\ndatasets extracted from The Cancer Genome Atlas, focusing on three tumor types:\nbreast, kidney, and thyroid carcinomas. We perform classifications extracting\nseveral methylated sites and their associated genes with accurate performance.\nResults suggest that BIGBIOCL can perform hundreds of classification iterations\non hundreds of thousands of features in few hours. Moreover, we compare the\nperformance of our method with other state-of-the-art classifiers and with a\nwide-spread DNA methylation analysis method based on network analysis. Finally,\nwe are able to efficiently compute multiple alternative classification models\nand extract, from DNA-methylation large datasets, a set of candidate genes to\nbe further investigated to determine their active role in cancer. BIGBIOCL,\nresults of experiments, and a guide to carry on new experiments are freely\navailable on GitHub.\n", "doi": "10.1016/j.bdr.2018.02.005", "arxiv_id": "1804.04839", "pdf_urls": ["https://arxiv.org/pdf/1804.04839"], "github": ["https://github.com/fcproj/BIGBIOCL"], "is_oa": true, "sources": ["open-arxiv"], "type": "journal", "journal_ref": "F. Celli, F. Cumbo, E. Weitschek: Classification of Large DNA\n  Methylation Datasets for Identifying Cancer Drivers. Big Data Research,\n  10.1016/j.bdr.2018.02.005, 2018", "categories": "q-bio.GN cs.CE"}
{"title": "Measuring and modeling interventions in aging", "year": 2018, "venue_abbr": "Cell", "venue_name": "Cell", "authors": ["Nicholas Stroustrup"], "abstract": "  At the physiological level, aging is neither rigid nor unchangeable. Instead,\nthe molecular and mechanisms driving aging are sufficiently plastic that a\nvariety of diverse interventions--dietary, pharmaceutical, and genetic--have\nbeen developed to radically manipulate aging. These interventions, shown to\nincrease the health and lifespan of laboratory animals, are now being explored\nfor therapeutic applications in humans.\n  This clinical potential makes it especially important to understand how,\nquantitatively, aging is altered by lifespan-extending interventions. Do\ninterventions delay the onset of aging? Slow it down? Ameliorate only its\nsymptoms? Perhaps some interventions will alter only a subset of aging\nmechanisms, leading to complex and unintuitive systemic outcomes. Statistical\nand analytic models provide a crucial framework in which to interpret the\nphysiological responses to interventions in aging.\n  This review covers a range of quantitative models of lifespan data and places\nthem in the context of recent experimental work. The careful application of\nthese models can help experimentalists move beyond merely identifying\nstatistically significant differences in lifespan, to instead use lifespan data\nas a versatile means for probing the underlying physiological dynamics of\naging.\n", "doi": "10.1016/j.ceb.2018.07.004", "arxiv_id": "1805.06681", "pdf_urls": ["https://arxiv.org/pdf/1805.06681"], "github": [], "is_oa": true, "sources": ["open-arxiv"], "type": "journal", "journal_ref": "Current Opinion in Cell Biology Volume 55, December 2018, Pages\n  129-138", "categories": "q-bio.QM"}
{"title": "Ridge Regression Estimated Linear Probability Model Predictions of\n  O-glycosylation in Proteins with Structural and Sequence Data", "year": 2018, "venue_abbr": "Cell", "venue_name": "Cell", "authors": ["Rajaram Gana and Sona Vasudevan"], "abstract": "  The likelihood of O-GlcNAc glycosylation in human proteins is predicted using\nthe ridge regression estimated linear probability model (LPM). To achieve this,\nsequences from three similar post-translational modifications (PTMs) of\nproteins occurring at, or very near, the S or T site are analyzed:\nN-glycosylation, O-mucin type (O-GalNAc) glycosylation, and phosphorylation.\nResults found include: 1) The consensus composite sequon for O-glycosylation\ndoes NOT have W on either side of the glycosylation site. 2) The same holds for\nthe consensus sequon for phosphorylation. 3) For LPM estimation, N-glycosylated\nsequences are found to be good approximations to non-O-glycosylatable\nsequences. 4) The selective positioning of an amino acid along the sequence,\ndifferentiates the PTMs of proteins. 5) Some N-glycosylated sequences are also\nphosphorylated at the S or T site. 6) ASA values for N-glycosylated sequences\nare stochastically larger than those for O-GlcNAc glycosylated sequences. 7)\nStructural attributes (beta turn II, II', helix, beta bridges, beta hairpin,\nand the phi angle) are significant LPM predictors of O-GlcNAc glycosylation.\nThe LPM with sequence and structural data as explanatory variables yields a\nKolmogorov-Smirnov (KS) statistic value of 99%. 8) With only sequence data, the\nKS statistic erodes to 80%, underscoring the germaneness of structural\ninformation, which is sparse on O-glycosylated sequences. With 50% as the\ncutoff probability for predicting O-GlcNAc glycosylation, this LPM mispredicts\n21% of out-of-sample O-GlcNAc glycosylated sequences as not being glycosylated.\nThe 95% confidence interval around this mispredictions rate is 16% to 26%\n", "doi": "10.1186/s12860-019-0200-9", "arxiv_id": "1805.09884", "pdf_urls": ["https://arxiv.org/pdf/1805.09884"], "github": [], "is_oa": true, "sources": ["open-arxiv"], "type": "journal", "journal_ref": "BMC Molecular and Cell Biology 2019", "categories": "q-bio.QM"}
{"title": "Light-trapping enhanced thin-film III-V quantum dot solar cells\n  fabricated by epitaxial lift-off", "year": 2018, "venue_abbr": "Cell", "venue_name": "Cell", "authors": ["F Cappelluti", "D Kim", "M van Eerden", "AP C\\'edola", "T Aho", "G Bissels", "F\n  Elsehrawy", "J Wu", "H Liu", "P Mulder", "G Bauhuis", "J Schermer", "T Niemi", "M Guina"], "abstract": "  We report thin-film InAs/GaAs quantum dot (QD) solar cells with $n-i-p{+}$\ndeep junction structure and planar back reflector fabricated by epitaxial\nlift-off (ELO) of full 3-inch wafers. External quantum efficiency measurements\ndemonstrate twofold enhancement of the QD photocurrent in the ELO QD cell\ncompared to the wafer-based QD cell. In the GaAs wavelength range, the ELO QD\ncell perfectly preserves the current collection efficiency of the baseline\nsingle-junction ELO cell. We demonstrate by full-wave optical simulations that\nintegrating a micro-patterned diffraction grating in the ELO cell rearside\nprovides more than tenfold enhancement of the near-infrared light harvesting by\nQDs. Experimental results are thoroughly discussed with the help of\nphysics-based simulations to single out the impact of QD dynamics and defects\non the cell photovoltaic behavior. It is demonstrated that non radiative\nrecombination in the QD stack is the bottleneck for the open circuit voltage\n($V_{oc}$) of the reported devices. More important, our theoretical\ncalculations demonstrate that the $V_{oc}$ offest of 0.3 V from the QD ground\nstate identified by \\emph{Tanabe et al., 2012}, from a collection of\nexperimental data of high quality III-V QD solar cells is a reliable - albeit\nconservative - metric to gauge the attainable $V_{oc}$ and to quantify the\nscope for improvement by reducing non radiative recombination. Provided that\nmaterial quality issues are solved, we demonstrate - by transport and rigorous\nelectromagnetic simulations - that light-trapping enhanced thin-film cells with\ntwenty InAs/GaAs QD layers reach efficiency higher than 28\\% under\nunconcentrated light, ambient temperature. If photon recycling can be fully\nexploited, 30\\% efficiency is deemed to be feasible.\n", "doi": "10.1016/j.solmat.2017.12.014", "arxiv_id": "1805.10275", "pdf_urls": ["https://arxiv.org/pdf/1805.10275"], "github": [], "is_oa": true, "sources": ["open-arxiv"], "type": "journal", "journal_ref": "Solar Energy Materials and Solar Cells, Volume 181, July 2018,\n  Pages 83-92", "categories": "physics.app-ph"}
{"title": "Cell Dynamic Simulations of Diblock Copolymer/Colloid Systems", "year": 2018, "venue_abbr": "Cell", "venue_name": "Cell", "authors": ["Javier Diaz", "Marco Pinna", "Andrei Zvelindovsky", "Adelchi Asta", "Ignacio\n  Pagonabarraga"], "abstract": "  The presence of nanoparticles in a diblock copolymer leads to changes in the\nmorphology and properties of the matrix and can produce highly organized hybrid\nmaterials. The resulting material properties depend not only on the polymer\ncomposition but also on the size, shape, and surface properties of the\ncolloids. The dynamics of this kind of systems using a hybrid mesoscopic\napproach has been studied in this work. A continuum description for the polymer\nis used, while colloids are individually resolved. The method allows for a\nvariable preference of the colloids, which can have different sizes, to the\ndifferent components the block copolymer is made of. The impact that the\nnanoparticle preference for either, both, or none of the blocks has on the\ncollective properties of nanoparticle-block copolymer composites can be\nanalyzed. Several experimental results are reproduced covering colloid-induced\nphase transition, particles' placement within the matrix, and the role of\nincompatibilities between colloids and monomers.\n", "doi": "10.1002/mats.201600050", "arxiv_id": "1805.11573", "pdf_urls": ["https://arxiv.org/pdf/1805.11573"], "github": [], "is_oa": true, "sources": ["open-arxiv"], "type": "journal", "journal_ref": "Diaz, J., Pinna, M., Zvelindovsky, A.V., Asta, A. and\n  Pagonabarraga, I., 2017. Cell dynamic simulations of diblock\n  copolymer/colloid systems. Macromolecular Theory and Simulations, 26(1)", "categories": "cond-mat.soft"}
{"title": "Pulsing dynamics in randomly wired glider cellular automata", "year": 2018, "venue_abbr": "Cell", "venue_name": "Cell", "authors": ["Andrew Wuensche", "Edward Coxon"], "abstract": "  Sustained rhythmic oscillations, pulsing dynamics, emerge spontaneously when\nthe local connection scheme is randomised in 3-value cellular automata that\nfeature\"glider\" dynamics. Time-plots of pulsing measures maintain a distinct\nwaveform for each glider rule, and scatter plots of entropy/density and the\ndensity return-map show unique signatures, which have the characteristics of\nchaotic strange attractors. We present case studies, possible mechanisms, and\nimplications for oscillatory networks in biology.\n", "doi": null, "arxiv_id": "1806.06416", "pdf_urls": ["https://arxiv.org/pdf/1806.06416"], "github": [], "is_oa": true, "sources": ["open-arxiv"], "type": "journal", "journal_ref": "Journal of CELLULAR AUTOMATA (JCA) ,Vol.14, No.1-2,95-128, 2019", "categories": "nlin.CG q-bio.TO"}
{"title": "Sesame: a 2-dimensional solar cell modeling tool", "year": 2018, "venue_abbr": "Cell", "venue_name": "Cell", "authors": ["Benoit Gaury", "Yubo Sun", "Peter Bermel", "and Paul M. Haney"], "abstract": "  This work introduces a new software package `Sesame' for the numerical\ncomputation of classical semiconductor equations. It supports 1 and\n2-dimensional systems and provides tools to easily implement extended defects\nsuch as grain boundaries or sample surfaces. Sesame has been designed to\nfacilitate fast exploration of the system parameter space and to visualize\nlocal charge transport properties. Sesame is distributed as a Python package or\nas a standalone GUI application, and is available at\nhttps://pages.nist.gov/sesame/ .\n", "doi": "10.1016/j.solmat.2019.03.037", "arxiv_id": "1806.06919", "pdf_urls": ["https://arxiv.org/pdf/1806.06919"], "github": [], "is_oa": true, "sources": ["open-arxiv"], "type": "journal", "journal_ref": "Solar Energy Materials and Solar Cells Volume 198 (2019) 53-62", "categories": "physics.app-ph cond-mat.mes-hall"}
{"title": "On Convergence of Heuristics Based on Douglas-Rachford Splitting and\n  ADMM to Minimize Convex Functions over Nonconvex Sets", "year": 2018, "venue_abbr": "Cell", "venue_name": "Cell", "authors": ["Shuvomoy Das Gupta"], "abstract": "  Recently, heuristics based on the Douglas-Rachford splitting algorithm and\nthe alternating direction method of multipliers (ADMM) have found empirical\nsuccess in minimizing convex functions over nonconvex sets, but not much has\nbeen done to improve the theoretical understanding of them. In this paper, we\ninvestigate convergence of these heuristics. First, we characterize optimal\nsolutions of minimization problems involving convex cost functions over\nnonconvex constraint sets. We show that these optimal solutions are related to\nthe fixed point set of the underlying nonconvex Douglas-Rachford operator.\nNext, we establish sufficient conditions under which the Douglas-Rachford\nsplitting heuristic either converges to a point or its cluster points form a\nnonempty compact connected set. In the case where the heuristic converges to a\npoint, we establish sufficient conditions for that point to be an optimal\nsolution. Then, we discuss how the ADMM heuristic can be constructed from the\nDouglas-Rachford splitting algorithm. We show that, unlike in the convex case,\nthe algorithms in our nonconvex setup are not equivalent to each other and have\na rather involved relationship between them. Finally, we comment on convergence\nof the ADMM heuristic and compare it with the Douglas-Rachford splitting\nheuristic.\n", "doi": "10.1109/allerton.2018.8636076", "arxiv_id": "1807.02878", "pdf_urls": ["https://arxiv.org/pdf/1807.02878"], "github": [], "is_oa": true, "sources": ["open-arxiv"], "type": "journal", "journal_ref": "2018 56th Annual Allerton Conference on Communication, Control,\n  and Computing (Allerton), Monticello, IL, USA, 2018, pp. 56-63", "categories": "math.OC"}
{"title": "Regional Control of Probabilistic Cellular Automata", "year": 2018, "venue_abbr": "Cell", "venue_name": "Cell", "authors": ["Franco Bagnoli", "Sara Dridi", "Samira El Yacoubi", "Raul Rechtman"], "abstract": "  Probabilistic Cellular Automata are extended stochastic systems, widely used\nfor modelling phenomena in many disciplines. The possibility of controlling\ntheir behaviour is therefore an important topic. We shall present here an\napproach to the problem of controlling such systems by acting only on the\nboundary of a target region.\n", "doi": "10.1007/978-3-319-99813-8_22", "arxiv_id": "1807.05067", "pdf_urls": ["https://arxiv.org/pdf/1807.05067"], "github": [], "is_oa": true, "sources": ["open-arxiv"], "type": "journal", "journal_ref": "Cellular Automata LNCS vol 11115, 243-254 (2028)", "categories": "nlin.CG"}
{"title": "Profiling of FSHR Negative Allosteric Modulators on LH/CGR Reveals\n  Biased Antagonism with Implications in Steroidogenesis", "year": 2018, "venue_abbr": "Cell", "venue_name": "Cell", "authors": ["Mohammed Akli Ayoub", "Romain Yvinec", "Gwenha\\\"el J\\'egot", "James A. Dias", "Sonia-Maria Poli", "Anne Poupon", "Pascale Cr\\'epieux", "Eric Reiter"], "abstract": "  Biased signaling has recently emerged as an interesting mean to modulate the\nfunction of many G protein-coupled receptors (GPCRs). Previous studies reported\ntwo negative allosteric modulators (NAMs) of follicle-stimulating hormone\nreceptor (FSHR), ADX68692 and ADX68693, with differential effects on\nFSHR-mediated steroidogenesis and ovulation. In this study, we attempted to\npharmacologically profile these NAMs on the closely related\nluteinizing/chorionic gonadotropin hormone receptor (LH/CGR) with regards to\nits canonical Gs/cAMP pathway as well as \\beta-arrestin recruitment in HEK293\ncells. The NAMs effects on progesterone and testosterone production were also\nassessed in murine Leydig tumor cell line (mLTC-1). We found that both NAMs\nstrongly antagonized LH/CGR signaling in both HEK293 and mLTC-1 cells. ADX68693\nappeared more potent than ADX68692 to inhibit hCG-induced cAMP and\n\\beta-arrestin 2 in HEK293 and mLTC-1 cells whereas no significant difference\nin their efficacy on hCG-promoted \\beta-arrestin 2 recruitment. Interestingly,\ndifferential antagonism of the two NAMs on hCG-promoted steroidogenesis in\nmLTC-1 cells was observed with significant inhibition of testosterone but not\nprogesterone production. These observations suggest biased effects of the two\nNAMs on LH/CGR-dependent pathways controlling steroidogenesis, which appeared\nto be different to that previously shown on FSHR. This also illustrates the\ncomplexity of signaling pathways controlling FSHR- and LH/CGR-mediated\nsteroidogenesis, suggesting differential implication of cAMP and\n\\beta-arrestins. Together, our data demonstrate that ADX68692 and ADX68693 are\nNAMs at the LH/CGR in addition to FSHR. These pharmacological characteristics\nare important to consider for potential contraceptive and therapeutic\napplications based on such compounds.\n", "doi": "10.1016/j.mce.2016.07.013", "arxiv_id": "1808.00310", "pdf_urls": ["https://arxiv.org/pdf/1808.00310"], "github": [], "is_oa": true, "sources": ["open-arxiv"], "type": "journal", "journal_ref": "Molecular and Cellular Endocrinology, 436:10--22 (2016)", "categories": "q-bio.MN q-bio.TO"}
{"title": "Follicle-stimulating hormone receptor: Advances and remaining challenges", "year": 2018, "venue_abbr": "Cell", "venue_name": "Cell", "authors": ["Francesco De Pascali", "Aur\\'elie Tr\\'efier", "Flavie Landomiel", "V\\'eronique Bozon", "Gilles Bruneau", "Romain Yvinec", "Anne Poupon", "Pascale\n  Cr\\'epieux", "Eric Reiter"], "abstract": "  Follicle-stimulating hormone (FSH) is produced in the pituitary and is\nessential for reproduction. It specifically binds to a membrane receptor (FSHR)\nexpressed in somatic cells of the gonads. The FSH/FSHR system presents many\npeculiarities compared to classical G protein-coupled receptors (GPCRs). FSH is\na large naturally heterogeneous heterodimeric glycoprotein. The FSHR is\ncharacterized by a very large NH2-terminal extracellular domain, which binds\nthe FSH and participates to the activation/inactivation switch of the receptor.\nOnce activated, the FSHR couples to G{\\alpha}s and, in some instances, to other\nG{\\alpha} subunits. G protein-coupled receptor kinases and \\beta-arrestins are\nalso recruited to the FSHR and account for its desensitization, the control of\nits trafficking and its intracellular signalling. Of note, the FSHR\ninternalization and recycling are very fast and involve very early endosomes\ninstead of early endosomes. All the transduction mechanisms triggered upon FSH\nstimulation lead to the activation of a complex signalling network that\ncontrols gene expression by acting at multiple levels. The integration of these\nmechanisms leads to context-adapted responses from the target gonadal cells,\nbut also indirectly affects the fate of germ cells. Depending of the\nphysiological/developmental stage, FSH elicits proliferation, differentiation\nor apoptosis in order to maintain the homeostasis of the reproductive system.\nPharmacological tools targeting FSHR recently came to the fore and open\npromising prospects both for basic research and therapeutic applications. This\npaper provides an updated review of the most salient aspects and peculiarities\nof FSHR biology and pharmacology.\n", "doi": "10.1016/bs.ircmb.2018.02.001", "arxiv_id": "1808.01965", "pdf_urls": ["https://arxiv.org/pdf/1808.01965"], "github": [], "is_oa": true, "sources": ["open-arxiv"], "type": "journal", "journal_ref": "In: Arun K. Shukla (ed.), dir., G Protein-Coupled Receptors:\n  Emerging Paradigms in Activation, Signaling and Regulation Part A (p. 1-58).\n  International Review of Cell and Molecular Biology, 338 (1\\`ere ed.). USA :\n  Elsevier. 171 p. (2018)", "categories": "q-bio.MN"}
{"title": "A hierarchical cellular automaton model of distributed traffic signal\n  control", "year": 2018, "venue_abbr": "Cell", "venue_name": "Cell", "authors": ["Bart{\\l}omiej P{\\l}aczek"], "abstract": "  This paper introduces a hierarchical cellular automaton (HCA)model for\nsimulation of distributed self-organizing control of traffic signals at\nintersections in road network. The proposed HCA consists of three hierarchy\nlevels that describe the movement of particular vehicles, occupancy of traffic\nlanes, and signal phases at intersections. Update rule of the HCA was designed\nto control traffic signals and minimize delays of vehicles in the road network.\nThe introduced update rule takes into account states of cells from different\nhierarchy levels of the HCA that represent neighboring traffic lanes and\nintersections. Simulation experiments were conducted for a wide range of\ntraffic conditions - from free flow to saturated traffic in two scenarios:\nanhattan-like grid road network, and arterial road. Results of the simulations\nshow that the proposed HCA-based traffic control strategy achieves better\neffectiveness in comparison with the state-of-the-art back pressure algorithm.\n", "doi": null, "arxiv_id": "1809.10892", "pdf_urls": ["https://arxiv.org/pdf/1809.10892"], "github": [], "is_oa": true, "sources": ["open-arxiv"], "type": "journal", "journal_ref": "Bart{\\l}omiej P{\\l}aczek, A hierarchical cellular automaton model\n  of distributed traffic signal control. Cellular Automata and Discrete Complex\n  Systems, 2018, pp. 1-12", "categories": "cs.SY nlin.CG"}
{"title": "Analysis of evolutionary origins of genomic loci harboring 59,732 candidate human-specific regulatory sequences identifies genetic divergence patterns during evolution of Great Apes", "year": 2018, "venue_abbr": "Cell", "venue_name": "Cell", "authors": ["Gennadi Glinsky"], "abstract": "Our view of the universe of genomic regions harboring various types of candidate human-specific regulatory sequences (HSRS) has been markedly expanded in recent years. To infer the evolutionary origins of loci harboring HSRS, analyses of conservations patterns of 59,732 loci in Modern Humans, Chimpanzee, Bonobo, Gorilla, Orangutan, Gibbon, and Rhesus genomes have been performed. Two major evolutionary pathways have been identified comprising thousands of sequences that were either inherited from extinct common ancestors (ECAs) or created de novo in humans after human/chimpanzee split. Thousands of HSRS appear inherited from ECAs yet bypassed genomes of our closest evolutionary relatives, presumably due to the incomplete lineage sorting and/or species-specific loss or regulatory DNA. The bypassing pattern is prominent for HSRS associated with development and functions of human brain. Common genomic loci that may contributed to speciation during evolution of Great Apes comprise 248 insertions sites of African Great Ape-specific retrovirus PtERV1 (45.9%; p = 1.03E-44) intersecting regions harboring 442 HSRS, which are enriched for HSRS associated with human-specific (HS) changes of gene expression in cerebral organoids. Among non-human primates (NHP), most significant fractions of candidate HSRS associated with HS expression changes in both excitatory neurons (347 loci; 67%) and radial glia (683 loci; 72%) are highly conserved in Gorilla genome. Modern Humans acquired unique combinations of regulatory sequences highly conserved in distinct species of six NHP separated by 30 million years of evolution. Concurrently, this unique mosaic of regulatory sequences inherited from ECAs was supplemented with 12,486 created de novo HSRS. These observations support the model of complex continuous speciation process during evolution of Great Apes that is not likely to occur as an instantaneous event.", "doi": "10.1089/dna.2019.4988", "arxiv_id": "1810.01062", "pdf_urls": ["https://arxiv.org/pdf/1810.01062"], "github": [], "is_oa": true, "sources": ["open-arxiv"], "type": "journal", "journal_ref": "DNA and Cell Biology 39: 126-143 (2020)", "categories": "q-bio.GN"}
{"title": "Capacity of Private Linear Computation for Coded Databases", "year": 2018, "venue_abbr": "Cell", "venue_name": "Cell", "authors": ["Sarah A. Obead", "Hsuan-Yin Lin", "Eirik Rosnes and J\\\"org Kliewer"], "abstract": "  We consider the problem of private linear computation (PLC) in a distributed\nstorage system. In PLC, a user wishes to compute a linear combination of $f$\nmessages stored in noncolluding databases while revealing no information about\nthe coefficients of the desired linear combination to the databases. In\nextension of our previous work we employ linear codes to encode the information\non the databases. We show that the PLC capacity, which is the ratio of the\ndesired linear function size and the total amount of downloaded information,\nmatches the maximum distance separable (MDS) coded capacity of private\ninformation retrieval for a large class of linear codes that includes MDS\ncodes. In particular, the proposed converse is valid for any number of messages\nand linear combinations, and the capacity expression depends on the rank of the\ncoefficient matrix obtained from all linear combinations.\n", "doi": "10.1109/allerton.2018.8636039", "arxiv_id": "1810.04230", "pdf_urls": ["https://arxiv.org/pdf/1810.04230"], "github": [], "is_oa": true, "sources": ["open-arxiv"], "type": "journal", "journal_ref": "56th Annual Allerton Conference on Communication, Control, and\n  Computing (Allerton), Monticello, IL, USA , Oct. 2018, pp. 813-820", "categories": "cs.IT math.IT"}
{"title": "Mapping excellence in national research systems: the case of Italy", "year": 2018, "venue_abbr": "Cell", "venue_name": "Cell", "authors": ["Giovanni Abramo", "Ciriaco Andrea D'Angelo", "Flavia Di Costa"], "abstract": "  The study of the concept of \"scientific excellence\" and the methods for its\nmeasurement and evaluation is taking on increasing importance in the\ndevelopment of research policies in many nations. However, scientific\nexcellence results as difficult to define in both conceptual and operational\nterms, because of its multi-dimensional and highly complex character. The\nliterature on the theme is limited to few studies of an almost pioneering\ncharacter. This work intends to contribute to the state of the art by exploring\na bibliometric methodology which is effective, simple and inexpensive, and\nwhich further identifies \"excellent\" centers of research by beginning from\nexcellence of the individual researchers affiliated with such centers. The\nstudy concentrates on the specific case of public research organizations in\nItaly, analyzing 109 scientific categories of research in the so called \"hard\"\nsciences and identifying 157 centers of excellence operating in 60 of these\ncategories. The findings from this first application of the methodology should\nbe considered exploratory and indicative. With a longer period of observation\nand the addition of further measurements, making the methodology more robust,\nit can be extended and adapted to a variety of national and supranational\ncontexts, aiding with policy decisions at various levels.\n", "doi": "10.1177/0193841x08322871", "arxiv_id": "1812.07840", "pdf_urls": ["https://arxiv.org/pdf/1812.07840"], "github": [], "is_oa": true, "sources": ["open-arxiv"], "type": "journal", "journal_ref": "Abramo, G., D'Angelo, C.A., Di Costa, F. (2009). Mapping\n  excellence in national research systems: the case of Italy. Evaluation\n  Review, 33(2), 159-188", "categories": "cs.DL"}
{"title": "Bounding the minimal number of generators of groups and monoids of\n  cellular automata", "year": 2019, "venue_abbr": "Cell", "venue_name": "Cell", "authors": ["Alonso Castillo-Ramirez and Miguel Sanchez-Alvarez"], "abstract": "  For a group $G$ and a finite set $A$, denote by $\\text{CA}(G;A)$ the monoid\nof all cellular automata over $A^G$ and by $\\text{ICA}(G;A)$ its group of\nunits. We study the minimal cardinality of a generating set, known as the rank,\nof $\\text{ICA}(G;A)$. In the first part, when $G$ is a finite group, we give\nupper bounds for the rank in terms of the number of conjugacy classes of\nsubgroups of $G$. The case when $G$ is a finite cyclic group has been studied\nbefore, so here we focus on the cases when $G$ is a finite dihedral group or a\nfinite Dedekind group. In the second part, we find a basic lower bound for the\nrank of $\\text{ICA}(G;A)$ when $G$ is a finite group, and we apply this to show\nthat, for any infinite abelian group $H$, the monoid $\\text{CA}(H;A)$ is not\nfinitely generated. The same is true for various kinds of infinite groups, so\nwe ask if there exists an infinite group $H$ such that $\\text{CA}(H;A)$ is\nfinitely generated.\n", "doi": null, "arxiv_id": "1901.02808", "pdf_urls": ["https://arxiv.org/pdf/1901.02808"], "github": [], "is_oa": true, "sources": ["open-arxiv"], "type": "journal", "journal_ref": "in Cellular Automata and Discrete Complex Systems, Proceedings of\n  AUTOMATA 2019, Guadalajara, Mexico, June, 2019", "categories": "math.GR cs.FL"}
{"title": "Tracking yeast pheromone receptor Ste2 endocytosis using\n  fluorogen-activating protein tagging", "year": 2019, "venue_abbr": "Cell", "venue_name": "Cell", "authors": ["Anita Emmerstorfer-Augustin", "Christoph M. Augustin", "Shadi Shams", "Jeremy Thorner"], "abstract": "  To observe internalization of the yeast pheromone receptor Ste2 by\nfluorescence microscopy in live cells in real time, we visualized only those\nmolecules present at the cell surface at the time of agonist engagement (rather\nthan the total cellular pool) by tagging this receptor at its N-terminus with\nan exocellular fluorogen-activating protein (FAP). A FAP is a single-chain\nantibody engineered to bind tightly a nonfluorescent, cell-impermeable dye\n(fluorogen), thereby generating a fluorescent complex. The utility of FAP\ntagging to study trafficking of integral membrane proteins in yeast, which\npossesses a cell wall, had not been examined previously. A diverse set of\nsignal peptides and propeptide sequences were explored to maximize expression.\nMaintenance of the optimal FAP-Ste2 chimera intact required deletion of two,\nparalogous, glycosylphosphatidylinositol (GPI)-anchored extracellular aspartyl\nproteases (Yps1 and Mkc7). FAP-Ste2 exhibited a much brighter and distinct\nplasma membrane signal than Ste2-GFP or Ste2-mCherry yet behaved quite\nsimilarly. Using FAP-Ste2, new information was obtained about the mechanism of\nits internalization, including novel insights about the roles of the\ncargo-selective endocytic adaptors Ldb19/Art1, Rod1/Art4, and Rog3/Art7.\n", "doi": "10.1091/mbc.e18-07-0424", "arxiv_id": "1901.06956", "pdf_urls": ["https://arxiv.org/pdf/1901.06956"], "github": [], "is_oa": true, "sources": ["open-arxiv"], "type": "journal", "journal_ref": "Mol Biol Cell. 2018 Nov 1; 29(22): 2720-2736", "categories": "q-bio.CB"}
{"title": "Generic properties in some classes of automaton groups", "year": 2019, "venue_abbr": "Cell", "venue_name": "Cell", "authors": ["Thibault Godin (IECL", "IMAG)"], "abstract": "  We prove, for various important classes of Mealy automata, that almost all\ngenerated groups have an element of infinite order. In certain cases, it also\nimplies other results such as exponential growth.\n", "doi": null, "arxiv_id": "1903.11315", "pdf_urls": ["https://arxiv.org/pdf/1903.11315"], "github": [], "is_oa": true, "sources": ["open-arxiv"], "type": "journal", "journal_ref": "25th International Workshop on Cellular Automata and Discrete\n  Complex Systems AUTOMATA 2019, Jun 2019, Guadalajara, Mexico", "categories": "cs.FL cs.DM math.GR"}
{"title": "Extending planning knowledge using ontologies for goal opportunities", "year": 2019, "venue_abbr": "Cell", "venue_name": "Cell", "authors": ["Mohannad Babli", "Eva Onaindia", "Eliseo Marzal"], "abstract": "  Approaches to goal-directed behaviour including online planning and\nopportunistic planning tackle a change in the environment by generating\nalternative goals to avoid failures or seize opportunities. However, current\napproaches only address unanticipated changes related to objects or object\ntypes already defined in the planning task that is being solved. This article\ndescribes a domain-independent approach that advances the state of the art by\nextending the knowledge of a planning task with relevant objects of new types.\nThe approach draws upon the use of ontologies, semantic measures, and ontology\nalignment to accommodate newly acquired data that trigger the formulation of\ngoal opportunities inducing a better-valued plan.\n", "doi": null, "arxiv_id": "1904.03606", "pdf_urls": ["https://arxiv.org/pdf/1904.03606"], "github": [], "is_oa": true, "sources": ["open-arxiv"], "type": "journal", "journal_ref": "31st IBIMA Conference (2018), INNOVATION MANAGEMENT AND EDUCATION\n  EXCELLENCE THROUGH VISION 2020, VOLS IV-VI (3199-3208)", "categories": "cs.AI"}
{"title": "A context-aware knowledge acquisition for planning applications using\n  ontologies", "year": 2019, "venue_abbr": "Cell", "venue_name": "Cell", "authors": ["Mohannad Babli and Eva Onaindia"], "abstract": "  Automated planning technology has developed significantly. Designing a\nplanning model that allows an automated agent to be capable of reacting\nintelligently to unexpected events in a real execution environment yet remains\na challenge. This article describes a domain-independent approach to allow the\nagent to be context-aware of its execution environment and the task it\nperforms, acquire new information that is guaranteed to be related and more\nimportantly manageable, and integrate such information into its model through\nthe use of ontologies and semantic operations to autonomously formulate new\nobjectives, resulting in a more human-like behaviour for handling unexpected\nevents in the context of opportunities.\n", "doi": null, "arxiv_id": "1904.09845", "pdf_urls": ["https://arxiv.org/pdf/1904.09845"], "github": [], "is_oa": true, "sources": ["open-arxiv"], "type": "journal", "journal_ref": "33rd International Business Information Management (IBIMA),\n  INNOVATION MANAGEMENT AND EDUCATION EXCELLENCE THROUGH VISION 2020 (pp.\n  3199-3208)", "categories": "cs.AI"}
{"title": "Novel heterojunction bipolar transistor architectures for the practical\n  implementation of high-efficiency three-terminal solar cells", "year": 2019, "venue_abbr": "Cell", "venue_name": "Cell", "authors": ["Pablo G. Linares", "Elisa Antol\\'in and Antonio Mart\\'i"], "abstract": "  Practical device architectures are proposed here for the implementation of\nthree-terminal heterojunction bipolar transistor solar cells (3T-HBTSCs). These\nphotovoltaic devices, which have a potential efficiency similar to that of\nmultijunction cells, exhibit reduced spectral sensitivity compared with\nmonolithically and series-connected tandem solar cells. In addition, the\nsimplified n-p-n (or p-n-p) structure does not require the use of tunnel\njunctions. In this framework, four architectures are proposed and discussed in\nthis paper: 1) one in which the top cell is based on silicon and the bottom\ncell is based on a heterojunction between silicon and III-V nanomaterials; 2)\none in which the top cell is made of amorphous silicon and the bottom cell is\nmade of an amorphous silicon-silicon heterojunction; 3) one based on the use of\nIII-V semiconductors aimed at space applications; and 4) one in which the top\ncell is based on a perovskite material and the bottom cell is made of a\nperovskite-silicon heterostructure.\n", "doi": "10.1016/j.solmat.2019.01.027", "arxiv_id": "1904.12305", "pdf_urls": ["https://arxiv.org/pdf/1904.12305"], "github": [], "is_oa": true, "sources": ["open-arxiv"], "type": "journal", "journal_ref": "Solar Energy Materials and Solar Cells, Volume 194, 1 June 2019,\n  Pages 54-61", "categories": "physics.app-ph cond-mat.mtrl-sci"}
{"title": "Coarse Graining of Partitioned Cellular Automata", "year": 2019, "venue_abbr": "Cell", "venue_name": "Cell", "authors": ["Pedro C. S. Costa", "Fernando de Melo"], "abstract": "  Partitioned cellular automata are known to be an useful tool to simulate\nlinear and nonlinear problems in physics, specially because they allow for a\nstraightforward way to define conserved quantities and reversible dynamics.\nHere we show how to construct a local coarse graining description of\npartitioned cellular automata. By making use of this tool we investigate the\neffective dynamics in this model of computation. All examples explored are in\nthe scenario of lattice gases, so that the information lost after the coarse\ngraining is related to the number of particles. It becomes apparent how\ndifficult it is to remain with a deterministic dynamics after coarse graining.\nSeveral examples are shown where an effective stochastic dynamics is obtained\nafter a deterministic dynamics is coarse grained. These results suggest why\nrandom processes are so common in nature.\n", "doi": null, "arxiv_id": "1905.10391", "pdf_urls": ["https://arxiv.org/pdf/1905.10391"], "github": [], "is_oa": true, "sources": ["open-arxiv"], "type": "journal", "journal_ref": "Journal of Cellular Automata 2020", "categories": "nlin.CG"}
{"title": "Astrophysical aspects of general relativistic mass twin stars", "year": 2019, "venue_abbr": "Cell", "venue_name": "Cell", "authors": ["David Blaschke", "David Edwin Alvarez-Castillo", "Alexander Ayriyan", "Hovik\n  Grigorian", "Noshad Khosravi Lagarni", "Fridolin Weber"], "abstract": "  In this chapter we will introduce an effective equation of state (EoS) model\nbased on polytropes that serves to study the so called \"mass twins\" scenario,\nwhere two compact stars have approximately the same mass but (significant for\nobservation) quite different radii. Stellar mass twin configurations are\nobtained if a strong first-order phase transition occurs in the interior of a\ncompact star. In the mass-radius diagram of compact stars, this will lead to a\nthird branch of gravitationally stable stars with features that are very\ndistinctive from those of white dwarfs and neutron stars. We discuss rotating\nhybrid star sequences in the slow rotation approximation and in full general\nrelativity and draw conclusions for an upper limit on the maximum mass of\nnonrotating compact stars that has recently be deduced from the observation of\nthe merger event GW170817.\n", "doi": "10.1142/9789813277342_0007", "arxiv_id": "1906.02522", "pdf_urls": ["https://arxiv.org/pdf/1906.02522"], "github": [], "is_oa": true, "sources": ["open-arxiv"], "type": "journal", "journal_ref": "in: \"Topics on Strong Gravity\" C. A. Zen Vasconcellos (Ed.), World\n  Scientific (2020), pp. 207-256", "categories": "astro-ph.HE nucl-th"}
{"title": "Distributed Approximation of Functions over Fast Fading Channels with\n  Applications to Distributed Learning and the Max-Consensus Problem", "year": 2019, "venue_abbr": "Cell", "venue_name": "Cell", "authors": ["Igor Bjelakovic", "Matthias Frey", "Slawomir Stanczak"], "abstract": "  In this work, we consider the problem of distributed approximation of\nfunctions over multiple-access channels with additive noise. In contrast to\nprevious works, we take fast fading into account and give explicit probability\nbounds for the approximation error allowing us to derive bounds on the number\nof channel uses that are needed to approximate a function up to a given\napproximation accuracy. Neither the fading nor the noise process is limited to\nGaussian distributions. Instead, we consider sub-gaussian random variables\nwhich include Gaussian as well as many other distributions of practical\nrelevance. The results are motivated by and have immediate applications to a)\ncomputing predictors in models for distributed machine learning and b) the\nmax-consensus problem in ultra-dense networks.\n", "doi": "10.1109/allerton.2019.8919875", "arxiv_id": "1907.03777", "pdf_urls": ["https://arxiv.org/pdf/1907.03777"], "github": [], "is_oa": true, "sources": ["open-arxiv"], "type": "journal", "journal_ref": "2019 57th Annual Allerton Conference on Communication, Control,\n  and Computing (Allerton), Monticello, IL, USA, September 24-27, 2019, pp.\n  1146-1153", "categories": "cs.IT eess.SP math.IT"}
{"title": "Effect of the organic cation on the optical properties of Lead Iodine\n  perovskites", "year": 2019, "venue_abbr": "Cell", "venue_name": "Cell", "authors": ["C\\'esar Tablero"], "abstract": "  The effect of 14 organic cations on the optical properties of the lead iodine\nperovskite is analyzed. The electronic and optical properties are obtained\nusing first principles. The absorption coefficients are split into inter-atomic\nspecies components in order to quantify all of the contributions. For energies\nclose to the bandgaps, the main contribution is from the Pb-Pb intra-species\ntransitions. For higher energy this contribution is still important in addition\nto I-I and Pb-I contributions, and to the 3 and 4 species term. Almost all\nabsorption properties are qualitatively similar. Furthermore, this absorption\ncoefficient splitting also allows the optical characteristics that the\nsubstitution of Pb by another element should satisfy to be identified in order\nto reduce the toxicity because of Pb while maintaining a high absorption\ncapacity.\n", "doi": "10.1016/j.solmat.2019.110022", "arxiv_id": "1907.12832", "pdf_urls": ["https://arxiv.org/pdf/1907.12832"], "github": [], "is_oa": true, "sources": ["open-arxiv"], "type": "journal", "journal_ref": "Solar Energy Materials and Solar Cells, Volume 200, 2019, 110022", "categories": "physics.app-ph cond-mat.mtrl-sci"}
{"title": "Analysis of hydrogen distribution and migration in fired passivating\n  contacts (FPC)", "year": 2019, "venue_abbr": "Cell", "venue_name": "Cell", "authors": ["Mario Lehmann", "Nathalie Valle", "J\\\"org Horzel", "Alisa Pshenova", "Philippe\n  Wyss", "Max D\\\"obeli", "Matthieu Despeisse", "Santhana Eswara", "Tom Wirtz", "Quentin\n  Jeangros", "A\\\"icha Hessler-Wyser", "Franz-Josef Haug", "Andrea Ingenito", "Christophe Ballif"], "abstract": "  In this work, the hydrogenation mechanism of fired passivating contacts (FPC)\nbased on c-Si/SiO$_{x}$/nc-SiC$_{x}$(p) stacks was investigated, by correlating\nthe passivation and local re-distribution of hydrogen. Secondary ion mass\nspectroscopy (SIMS) depth profiling was used to assess the hydrogen\n(/deuterium) content. The SIMS profiles show that hydrogen almost completely\neffuses out of the SiC$_{x}$(p) during firing, but can be re-introduced by\nhydrogenation via forming gas anneal (FGA) or by release from a hydrogen\ncontaining layer such as SiN$_{x}$:H. A pile-up of H at the c-Si/SiO$_{x}$\ninterface was observed and identified as a key element in the FPC's passivation\nmechanism. Moreover, the samples hydrogenated with SiN$_{x}$:H exhibited higher\nH content compared to those treated by FGA, resulting in higher iV$_{OC}$\nvalues. Further investigations revealed that the doping of the SiC$_{x}$ layer\ndoes not affect the amount of interfacial defects passivated by the\nhydrogenation process presented in this work. Eventually, an effect of the\noxide's nature on passivation quality is evidenced. iV$_{OC}$ values of up to\n706 mV and 720 mV were reached with FPC test structures using chemical and\nUV-O$_{3}$ tunneling oxides, respectively, and up to 739 mV using a reference\npassivation sample featuring a ~25 nm thick thermal oxide.\n", "doi": "10.1016/j.solmat.2019.110018", "arxiv_id": "1907.13069", "pdf_urls": ["https://arxiv.org/pdf/1907.13069"], "github": [], "is_oa": true, "sources": ["open-arxiv"], "type": "journal", "journal_ref": "Sol. Energy Mater. Sol. Cells. 200 (2019) 110018", "categories": "physics.app-ph"}
{"title": "Efficient indoor p-i-n hybrid perovskite solar cells using low\n  temperature solution processed NiO as hole extraction layers", "year": 2019, "venue_abbr": "Cell", "venue_name": "Cell", "authors": ["Lethy Krishnan Jagadamma", "Oskar Blaszczyk", "Muhammad T. Sajjad", "Arvydas\n  Ruseckas", "Ifor D. W. Samuel"], "abstract": "  Hybrid perovskites have received tremendous attention due to their\nexceptional photovoltaic and optoelectronic properties. Among the two widely\nused perovskite solar cell device architectures of n-ip and p-i-n, the latter\nis interesting in terms of its simplicity of fabrication and lower energy\ninput. However this structure mostly uses PEDOT:PSS as a hole transporting\nlayer which can accelerate the perovskite solar cell degradation. Hence the\ndevelopment of stable, inorganic hole extraction layers (HEL), without\ncompromising the simplicity of device fabrication is crucial in this\nfast-growing photovoltaic field. Here we demonstrate a low temperature (~100\noC) solution - processed and ultrathin (~ 6 nm) NiO nanoparticle thin films as\nan efficient HEL for CH3NH3PbI3 based perovskite solar cells. We measure a\npower conversion efficiency (PCE) of 13.3 % on rigid glass substrates and 8.5 %\non flexible substrates. A comparison with PEDOT:PSS based MAPbI3 solar cells\n(PCE ~ 7.9 %) shows that NiO based solar cells have higher short circuit\ncurrent density and improved open circuit voltage (1.03V). Apart from the\nphotovoltaic performance under 1 Sun, the efficient hole extraction property of\nNiO is demonstrated for indoor lighting as well with a PCE of 23.0 % for NiO\nbased CH3NH3PbI2.9Cl0.1 p-i-n solar cells under compact fluorescent lighting.\nCompared to the perovskite solar cells fabricated on PEDOT:PSS HEL, better\nshelf-life stability is observed for perovskite solar cells fabricated on NiO\nHEL. Detailed microstructural and photophysical investigations imply uniform\nmorphology, lower recombination losses, and improved charge transfer properties\nfor CH3NH3PbI3 grown on NiO HEL.\n", "doi": "10.1016/j.solmat.2019.110071", "arxiv_id": "1909.03838", "pdf_urls": ["https://arxiv.org/pdf/1909.03838"], "github": [], "is_oa": true, "sources": ["open-arxiv"], "type": "journal", "journal_ref": "Solar Energy Materials and Solar Cells, 201, 110071, 2019", "categories": "physics.app-ph"}
{"title": "Computational model combined with in vitro experiments to analyse\n  mechanotransduction during mesenchymal stem cell adhesion", "year": 2019, "venue_abbr": "Cell", "venue_name": "Cell", "authors": ["Jean-Louis Milan (ISM)", "Sandrine Lavenus (IMN)", "Paul Pilet (LIOAD)", "Guy Louarn (IMN)", "Sylvie Wendling (ISM)", "Dominique Heymann", "Pierre Layrolle", "Patrick Chabrand (ISM)"], "abstract": "  The shape that stem cells reach at the end of adhesion process influences\ntheir differentiation. Rearrangement of cytoskeleton and modification of\nintracellular tension may activate mechanotransduction pathways controlling\ncell commitment. In the present study, the mechanical signals involved in cell\nadhesion were computed in in vitro stem cells of different shapes using a\nsingle cell model, the so-called Cytoskeleton Divided Medium (CDM) model. In\nthe CDM model, the filamentous cytoskeleton and nucleoskeleton networks were\nrepresented as a mechanical system of multiple tensile and compressive\ninteractions between the nodes of a divided medium. The results showed that\nintracellular tonus, focal adhesion forces as well as nuclear deformation\nincreased with cell spreading. The cell model was also implemented to simulate\nthe adhesion process of a cell that spreads on protein-coated substrate by\nemitting filopodia and creating new distant focal adhesion points. As a result,\nthe cell model predicted cytoskeleton reorganisation and reinforcement during\ncell spreading. The present model quantitatively computed the evolution of\ncertain elements of mechanotransduction and may be a powerful tool for\nunderstanding cell mechanobiology and designing biomaterials with specific\nsurface properties to control cell adhesion and differentiation.\n", "doi": "10.22203/ecm.v025a07", "arxiv_id": "1909.05573", "pdf_urls": ["https://arxiv.org/pdf/1909.05573"], "github": [], "is_oa": true, "sources": ["open-arxiv"], "type": "journal", "journal_ref": "European Cells and Materials, 2013, 25, pp.97-113", "categories": "q-bio.CB physics.bio-ph q-bio.SC"}
{"title": "Graded composition Cd$_x$Zn$_{1-x}$Te films grown by Isothermal Close\n  Space Sublimation technique", "year": 2019, "venue_abbr": "Cell", "venue_name": "Cell", "authors": ["O. de Melo", "A. Dom\\'inguez", "K. Guti\\'errez Z-B", "G. Contreras-Puente", "S. Gallardo-Hern\\'andez", "A. Escobosa", "J. C. Gonz\\'alez", "R. Paniago", "J. Ferraz\n  Dias", "M. Behar"], "abstract": "  Graded composition CdxZn1-xTe films were prepared by growing several\nalternate layers of CdTe and ZnTe by the Isothermal Close Space Sublimation\ntechnique. The thickness of both kinds of layers was modified along the\nstructure to produce an increase of the average concentration of CdTe towards\nthe surface of the films. Due to Zn/Cd inter-diffusion during the growth\nprocess the sequence of layers was converted into a relatively smooth graded\ncomposition film. According to X- ray diffraction characterization the layers\ngrew coherently with the (100) oriented GaAs substrates although they showed a\nrelatively high mosaicity. Theta-2theta plots show very wide diffraction peaks\nas expected from variable composition samples. The band gap grading effect in\nlight absorption was also verified through transmission measurements, using\ntransparent substrates. Graded composition profiles of the thin films were\nconfirmed by x-ray photoelectron and secondary ion mass spectroscopies.\nMoreover, quantitative Cd, Zn and Te profiles were obtained by the analysis of\nRutherford backscattering spectra of the samples. This analysis showed a CdTe\nmolar fraction profile ranging from approximately x = 0.8 at the surface of the\nsample and x = 0.35 at the interface with the substrate. The possibility of\ngrowing graded composition layers using a simple and cost-effective procedure\nwas demonstrated. This could be interesting in technological applications like\nCdxZn1-xTe layers of variable composition in CdS/CdTe solar cells\n", "doi": "10.1016/j.solmat.2015.02.025", "arxiv_id": "1909.08196", "pdf_urls": ["https://arxiv.org/pdf/1909.08196"], "github": [], "is_oa": true, "sources": ["open-arxiv"], "type": "journal", "journal_ref": "Solar Energy Materials & Solar Cells 138 (2015) 17 21", "categories": "cond-mat.mtrl-sci"}
{"title": "The Variant-Rule, Another Logically Universal Rule", "year": 2019, "venue_abbr": "Cell", "venue_name": "Cell", "authors": ["Jos\\'e Manuel G\\'omez Soto", "Andrew Wuensche"], "abstract": "  The Variant-rule derives from the Precursor-rule by interchanging two classes\nof its 28 isotropic mappings. Although this small mutation conserves most\nglider types and stable blocks, glider-gun engines are changed, as are most\nlarge scale pattern behaviors, illustrating both the robustness and fragility\nof evolution. We demonstrate these newly discovered structures and dynamics,\nand utilising two different glider types, build the logical gates required for\nuniversality in the logical sence.\n", "doi": null, "arxiv_id": "1909.08224", "pdf_urls": ["https://arxiv.org/pdf/1909.08224"], "github": [], "is_oa": true, "sources": ["open-arxiv"], "type": "journal", "journal_ref": "Journal of Cellular Automata, Vol. 15, pp. 147-173, 2020", "categories": "nlin.CG"}
{"title": "Nonexistence of minimal-time solutions for some variations of the firing\n  squad synchronization problem having simple geometric configurations", "year": 2019, "venue_abbr": "Cell", "venue_name": "Cell", "authors": ["Kojiro Kobayashi"], "abstract": "  We prove nonexistence of minimal-time solutions for three variations of the\nfiring squad synchronization problem (FSSP, for short). Configurations of these\nvariations are paths in the two-dimensional grid space having simple geometric\nshapes. In the first variation a configuration is an L-shaped path such that\nthe ratio of the length of horizontal line to that of the vertical line is\nfixed. The general may be at any position. In the second and the third\nvariations a configuration is a rectangular wall such that the ratio of the\nlength of the two horizontal walls to that of the two vertical walls is fixed.\nThe general is at the left down corner in the second variation and may be at\nany position in the third variation. We use the idea used in the proof of\nYamashita et al's recent similar result for variations of FSSP with\nsub-generals.\n", "doi": null, "arxiv_id": "1909.10125", "pdf_urls": ["https://arxiv.org/pdf/1909.10125"], "github": [], "is_oa": true, "sources": ["open-arxiv"], "type": "journal", "journal_ref": "Journal of Cellular Automata, vol.14, pp.351-396, 2019", "categories": "cs.FL"}
{"title": "Contour models of cellular adhesion", "year": 2019, "venue_abbr": "Cell", "venue_name": "Cell", "authors": ["Luca Giomi"], "abstract": "  The development of traction-force microscopy, in the past two decades, has\ncreated the unprecedented opportunity of performing direct mechanical\nmeasurements on living cells as they adhere or crawl on uniform or\nmicro-patterned substrates. Simultaneously, this has created the demand for a\ntheoretical framework able to decipher the experimental observations, shed\nlight on the complex biomechanical processes that govern the interaction\nbetween the cell and the extracellular matrix and offer testable predictions.\nContour models of cellular adhesion, represent one of the simplest and yet most\ninsightful approach in this problem. Rooted in the paradigm of active matter,\nthese models allow to explicitly determine the shape of the cell edge and\ncalculate the traction forces experienced by the substrate, starting from the\ninternal and peripheral contractile stresses as well as the passive restoring\nforces and bending moments arising within the actin cortex and the plasma\nmembrane. In this chapter I provide a general overview of contour models of\ncellular adhesion and review the specific cases of cells equipped with\nisotropic and anisotropic actin cytoskeleton as well as the role of bending\nelasticity.\n", "doi": "10.1007/978-3-030-17593-1_2", "arxiv_id": "1910.11173", "pdf_urls": ["https://arxiv.org/pdf/1910.11173"], "github": [], "is_oa": true, "sources": ["open-arxiv"], "type": "journal", "journal_ref": "Book chapter from \"Cell migrations: causes and functions\", C. A.\n  M. La Porta and S. Zapperi (eds), Advances in Experimental Medicine and\n  Biology, vol 1146. Springer, Cham (2019)", "categories": "physics.bio-ph cond-mat.soft q-bio.CB"}
{"title": "If your P value looks too good to be true, it probably is: Communicating\n  reproducibility and variability in cell biology", "year": 2019, "venue_abbr": "Cell", "venue_name": "Cell", "authors": ["Samuel J. Lord", "Katrina B. Velle", "R. Dyche Mullins", "Lillian K.\n  Fritz-Laylin"], "abstract": "  The cell biology literature is littered with erroneously tiny P values, often\nthe result of evaluating individual cells as independent samples. Because\nreaders use P values and error bars to infer whether a reported difference\nwould likely recur if the experiment were repeated, the sample size N used for\nstatistical tests should actually be the number of times an experiment is\nperformed, not the number of cells (or subcellular structures) analyzed across\nall experiments. P values calculated using the number of cells do not reflect\nthe reproducibility of the result and are thus highly misleading. To help\nauthors avoid this mistake, we provide examples and practical tutorials for\ncreating figures that communicate both the cell-level variability and the\nexperimental reproducibility.\n", "doi": "10.1083/jcb.202001064", "arxiv_id": "1911.03509", "pdf_urls": ["https://arxiv.org/pdf/1911.03509"], "github": ["https://github.com/duzzio/Superplots_R_script"], "is_oa": true, "sources": ["open-arxiv"], "type": "journal", "journal_ref": "J. Cell. Biol. 219 (2020) e202001064", "categories": "q-bio.OT"}
{"title": "Active interfacial dynamic transport of fluid in fibrous connective\n  tissues and a hypothesis of interstitial fluid circulatory system", "year": 2019, "venue_abbr": "Cell", "venue_name": "Cell", "authors": ["Li Hongyi", "Yin Yajun", "Yang Chongqing", "Chen Min", "Wang Fang", "Ma Chao", "Li\n  Hua", "Kong Yiya", "Ji Fusui", "Hu Jun"], "abstract": "  Fluid in interstitial spaces accounts for ~20% of an adult body weight. Does\nit circulate around the body like vascular circulations besides a diffusive and\nshort-ranged transport? This bold conjecture has been debated for decades. As a\nconventional physiological concept, interstitial space was the space between\ncells and a micron-sized space. Fluid in interstitial spaces is thought to be\nentrapped within interstitial matrix. However, our serial data have further\ndefined an interfacial transport zone on a solid fiber of interstitial matrix.\nWithin this fine space that is probably nanosized, fluid can transport along a\nfiber under a driving power. Since 2006, our imaging data from volunteers and\ncadavers have revealed a long-distance extravascular pathway for interstitial\nfluid flow, comprising four types of anatomic distributions at least. The\nframework of each extravascular pathway contains the longitudinally assembled\nand oriented fibers, working as a fibrous guiderail for fluid flow.\nInterestingly, our data showed that the movement of fluid in a fibrous pathway\nis in response to a dynamic driving source and named as dynamotaxis. By\nanalysis of some representative studies and our experimental results, a\nhypothesis of interstitial fluid circulatory system is proposed.\n", "doi": "10.1111/cpr.12760", "arxiv_id": "1911.04835", "pdf_urls": ["https://arxiv.org/pdf/1911.04835"], "github": [], "is_oa": true, "sources": ["open-arxiv"], "type": "journal", "journal_ref": "Cell Proliferation. 2020;00:e12760", "categories": "q-bio.TO"}
{"title": "Strongly enhanced upconversion in trivalent erbium ions by tailored gold\n  nanostructures: toward high-efficient silicon-based photovoltaics", "year": 2019, "venue_abbr": "Cell", "venue_name": "Cell", "authors": ["Jeppe Christiansen", "Joakim Vester-Petersen", "S{\\o}ren Roesgaard", "S{\\o}ren H. M{\\o}ller", "Rasmus E. Christiansen", "Ole Sigmund", "S{\\o}ren P.\n  Madsen", "Peter Balling", "and Brian Julsgaard"], "abstract": "  Upconversion of sub-band-gap photons constitutes a promising way for\nimproving the efficiency of silicon-based solar cells beyond the\nShockley-Queisser limit. 1500 to 980 nm upconversion by trivalent erbium ions\nis well-suited for this purpose, but the small absorption cross section hinders\nreal-world applications. We employ tailored gold nanostructures to vastly\nimprove the upconversion efficiency in erbium-doped TiO$_2$ thin films. The\nnanostructures are found using topology optimization and parameter optimization\nand fabricated by electron beam lithography. In qualitative agreement with a\ntheoretical model, the samples show substantial electric-field enhancements\ninside the upconverting films for excitation at 1500 nm for both s- and\np-polarization under a wide range of incidence angles and excitation\nintensities. An unprecedented upconversion enhancement of 913(51) is observed\nat an excitation intensity of 1.7 Wcm$^{-2}$. We derive a semi-empirical\nexpression for the photonically enhanced upconversion efficiency, valid for all\nexcitation intensities. This allows us to determine the upconversion properties\nneeded to achieve significant improvements in real-world solar-cell devices\nthrough photonic-enhanced upconversion.\n", "doi": "10.1016/j.solmat.2020.110406", "arxiv_id": "1911.07242", "pdf_urls": ["https://arxiv.org/pdf/1911.07242"], "github": [], "is_oa": true, "sources": ["open-arxiv"], "type": "journal", "journal_ref": "Solar Energy Materials and Solar Cells 208 (2020) 110406", "categories": "physics.app-ph cond-mat.mtrl-sci"}
{"title": "The double dealing of cyclin D1", "year": 2020, "venue_abbr": "Cell", "venue_name": "Cell", "authors": ["Guergana Tchakarska (GPMCND)", "Brigitte Sola (GPMCND)"], "abstract": "  The cell cycle is tightly regulated by cyclins and their catalytic moieties,\nthe cyclin-dependent kinases (CDKs). Cyclin D1, in association with CDK4/6,\nacts as a mitogenic sensor and integrates extracellular mitogenic signals and\ncell cycle progression. When deregulated (overexpressed, accumulated,\ninappropriately located), cyclin D1 becomes an oncogene and is recognized as a\ndriver of solid tumors and hemopathies. Recent studies on the oncogenic roles\nof cyclin D1 reported non-canonical functions dependent on the partners of\ncyclin D1 and its location within tumor cells or tissues. Support for these new\nfunctions was provided by various mouse models of oncogenesis. Finally,\nproteomic and transcriptomic data identified complex cyclin D1 networks. This\nreview focuses on these aspects of cyclin D1 pathophysiology, which may be\ncrucial for targeted therapy.\n", "doi": "10.1080/15384101.2019.1706903", "arxiv_id": "2001.00837", "pdf_urls": ["https://arxiv.org/pdf/2001.00837"], "github": [], "is_oa": true, "sources": ["open-arxiv"], "type": "journal", "journal_ref": "Cell Cycle, Taylor & Francis, 2010, pp.1-16", "categories": "q-bio.SC q-bio.CB"}
{"title": "On the anti-cancer effect of cold atmospheric plasma and the possible\n  role of catalase-dependent apoptotic pathways", "year": 2020, "venue_abbr": "Cell", "venue_name": "Cell", "authors": ["Charlotta Bengtson and Annemie Bogaerts"], "abstract": "  Cold atmospheric plasma (CAP) is a promising new agent for (selective) cancer\ntreatment, but the underlying cause of the anti-cancer effect of CAP is not\nwell understood yet. Among different theories and observations, one theory in\nparticular has been postulated in great detail and consists of a very complex\nnetwork of reactions that are claimed to account for the anti-cancer effect of\nCAP. Here, the key concept is a reactivation of two specific apoptotic cell\nsignaling pathways through catalase inactivation caused by CAP. Thus, it is\npostulated that the anti-cancer effect of CAP is due to its ability to\ninactivate catalase, either directly or indirectly. A theoretical investigation\nof the proposed theory, especially the role of catalase inactivation, can\ncontribute to the understanding of the underlying cause of the anti-cancer\neffect of CAP. In the present study, we develop a mathematical model to analyze\nthe proposed catalase-dependent anti-cancer effect of CAP. Our results show\nthat a catalase-dependent reactivation of the two apoptotic pathways of\ninterest is unlikely to contribute to the observed anti-cancer effect of CAP.\nThus, we believe that other theories of the underlying cause should be\nconsidered and evaluated to gain knowledge about the principles of CAP-induced\ncancer cell death.\n", "doi": "10.3390/cells9102330", "arxiv_id": "2001.09936", "pdf_urls": ["https://arxiv.org/pdf/2001.09936"], "github": [], "is_oa": true, "sources": ["open-arxiv"], "type": "journal", "journal_ref": "Cells 2020, 9, 2330", "categories": "q-bio.MN"}
{"title": "$q$-VFCA: $q$-state Vector-valued Fuzzy Cellular Automata", "year": 2020, "venue_abbr": "Cell", "venue_name": "Cell", "authors": ["Yuki Nishida", "Sennosuke Watanabe", "Akiko Fukuda and Yoshihide Watanabe"], "abstract": "  Elementary fuzzy Cellular Automata (CA) are known as continuous counterpart\nof elementary CA, which are 2-state CA, via the polynomial representation of\nlocal rules. In this paper, we first develop a new fuzzification methodology\nfor $q$-state CA. It is based on the vector representation of $q$-state CA,\nthat is, the $q$-states are assigned to the standard basis vectors of the\n$q$-dimensional real space and the local rule can be expressed by a tuple of\n$q$ polynomials. Then, the $q$-state vector-valued fuzzy CA are defined by\nexpanding the set of the states to the convex hull of the standard basis\nvectors in the $q$-dimensional real space. The vector representation of states\nenables us to enumerate the number-conserving rules of 3-state vector-valued\nfuzzy CA in a systematic way.\n", "doi": null, "arxiv_id": "2002.02653", "pdf_urls": ["https://arxiv.org/pdf/2002.02653"], "github": [], "is_oa": true, "sources": ["open-arxiv"], "type": "journal", "journal_ref": "Journal of Cellular Automata, 15: 207-222, 2020", "categories": "nlin.CG math.DS"}
{"title": "Evaluating the Quality of Local Structure Approximation Using Elementary\n  Rule 14", "year": 2020, "venue_abbr": "Cell", "venue_name": "Cell", "authors": ["Henryk Fuk\\'s and Francis Kwaku Combert"], "abstract": "  Cellular automata (CA) can be viewed as maps in the space of probability\nmeasures. Such maps are normally infinitely-dimensional, and in order to\nfacilitate investigations of their properties, especially in the context of\napplications, finite-dimensional approximations have been proposed. The most\ncommonly used one is known as the local structure theory, developed by H.\nGutowitz et al. in 1987. In spite of the popularity of this approximation in CA\nresearch, examples of rigorous evaluations of its accuracy are lacking. In an\nattempt to fill this gap, we construct a local structure approximation for rule\n14, and study its dynamics in a rigorous fashion, without relying on numerical\nexperiments. We then compare the outcome with known exact results.\n", "doi": "10.1007/978-3-319-92675-9", "arxiv_id": "2002.08920", "pdf_urls": ["https://arxiv.org/pdf/2002.08920"], "github": [], "is_oa": true, "sources": ["open-arxiv"], "type": "journal", "journal_ref": "J. M. Baetens and M. Kutrib (eds.), Cellular Automata and Discrete\n  Complex Systems - 24th IFIP WG 1.5 International Workshop, AUTOMATA 2018,\n  Ghent, Belgium, June 20-22, 2018, LNCS vol. 10875 pp. 43--56. Springer, 2018", "categories": "nlin.CG"}
{"title": "Explicit solution of the Cauchy problem for cellular automaton rule 172", "year": 2020, "venue_abbr": "Cell", "venue_name": "Cell", "authors": ["Henryk Fuk\\'s"], "abstract": "  Cellular automata (CA) are fully discrete alternatives to partial\ndifferential equations (PDE). For PDEs, one often considers the Cauchy problem,\nor initial value problem: find the solution of the PDE satisfying a given\ninitial condition. For many PDEs of the first order in time, it is possible to\nfind explicit formulae for the solution at the time $t>0$ if the solution is\nknown at $t=0$. Can something similar be achieved for CA? We demonstrate that\nthis is indeed possible in some cases, using elementary CA rule 172 as an\nexample. We derive an explicit expression for the state of a given cell after\n$n$ iteration of the rule 172, assuming that states of all cells are known at\n$n=0$. We then show that this expression (\"solution of the CA\") can be used to\nobtain an expected value of a given cell after $n$ iterations, provided that\nthe initial condition is drawn from a Bernoulli distribution. This can be done\nfor both finite and infinite lattices, thus providing an interesting test case\nfor investigating finite size effects in CA.\n", "doi": null, "arxiv_id": "2002.09362", "pdf_urls": ["https://arxiv.org/pdf/2002.09362"], "github": [], "is_oa": true, "sources": ["open-arxiv"], "type": "journal", "journal_ref": "J. of Cellular Automata, 12(6):423--444, 2017", "categories": "nlin.CG"}
{"title": "Impact of chronic fetal hypoxia and inflammation on cardiac pacemaker\n  cell development", "year": 2020, "venue_abbr": "Cell", "venue_name": "Cell", "authors": ["Martin G. Frasch", "Dino A. Giussani"], "abstract": "  Chronic fetal hypoxia and infection are examples of adverse conditions during\ncomplicated pregnancy, which impact cardiac myogenesis and increase the\nlifetime risk of heart disease. However, the effects that chronic hypoxic or\ninflammatory environments exert on cardiac pacemaker cells are poorly\nunderstood. Here, we review the current evidence and novel avenues of\nbench-to-bed research in this field of perinatal cardiogenesis as well as its\ntranslational significance for early detection of future risk for\ncardiovascular disease.\n", "doi": "10.3390/cells9030733", "arxiv_id": "2002.10430", "pdf_urls": ["https://arxiv.org/pdf/2002.10430"], "github": [], "is_oa": true, "sources": ["open-arxiv"], "type": "journal", "journal_ref": "Cells 9(3), 733, 2020", "categories": "q-bio.CB q-bio.SC q-bio.TO"}
{"title": "Radiation hardness and post irradiation regeneration behavior of GaInAsP\n  solar cells", "year": 2020, "venue_abbr": "Cell", "venue_name": "Cell", "authors": ["R. Lang", "J. Sch\\\"on", "J. Lef\\`evre", "B. Boizot", "F. Dimroth and D.\n  Lackner"], "abstract": "  Recent developments have renewed the demand for solar cells with increased\ntolerance to radiation damage. To investigate the specific irradiation damage\nof 1 MeV electron irradiation in GaInAsP lattice matched to InP for varying In\nand P contents, a simulation based analysis is employed: by fitting the quantum\nefficiency and open-circuit voltage simultaneously before and after\nirradiation, the induced changes in lifetime are detected. Furthermore, the\nreduction of irradiation damage during regeneration under typical satellite\noperating conditions for GEO missions (60{\\deg}C and AM0 illumination) is\ninvestigated. A clear decrease of the radiation damage is observed after post\nirradiation regeneration. This regeneration effect is stronger for increasing\nInP-fraction. It is demonstrated that the irradiation induced defect\nrecombination coefficient for irradiation with 1 MeV electrons after\nregeneration for 216 hours can be described with a linear function of\nInP-fraction between 1*10$^{-5}$ cm$^2$/s for GaAs and 7*10$^{-7}$ cm$^2$/s for\nInP. The results show that GaInAsP is a promising material for radiation hard\nspace solar cells.\n", "doi": "10.1016/j.solmat.2020.110551", "arxiv_id": "2004.00308", "pdf_urls": ["https://arxiv.org/pdf/2004.00308"], "github": [], "is_oa": true, "sources": ["open-arxiv"], "type": "journal", "journal_ref": "Solar Energy Materials & Solar Cells 211 (2020) 110551", "categories": "physics.app-ph cond-mat.mtrl-sci"}
{"title": "Reaction Cycles of Halogen Species in the Immune Defense: Implications\n  for Human Health and Diseases and the Pathology and Treatment of COVID-19", "year": 2020, "venue_abbr": "Cell", "venue_name": "Cell", "authors": ["Qing-Bin Lu"], "abstract": "  There is no vaccine or specific antiviral treatment for COVID-19. One current\nfocus is drug repurposing research, but those drugs have limited therapeutic\nefficacies and known adverse effects. The pathology of COVID-19 is essentially\nunknown. It is therefore challenging to discover a successful treatment to be\napproved for clinical use. This paper addresses several key biological\nprocesses of reactive oxygen, halogen and nitrogen species (ROS, RHS and RNS)\nthat play crucial physiological roles in organisms from plants to humans. These\ninclude why superoxide dismutases, the enzymes to catalyze the formation of\nH2O2, are required for protecting ROS-induced injury in cell metabolism, why\nthe amount of ROS/RNS produced by ionizing radiation at clinically relevant\ndoses is ~1000 fold lower than the endogenous ROS/RNS level routinely produced\nin the cell and why a low level of endogenous RHS plays a crucial role in\nphagocytosis for immune defense. Herein we propose a plausible amplification\nmechanism in immune defense: ozone-depleting-like halogen cyclic reactions\nenhancing RHS effects are responsible for all the mentioned physiological\nfunctions, which are activated by H2O2 and deactivated by NO signaling\nmolecule. Our results show that the reaction cycles can be repeated thousands\nof times and amplify the RHS pathogen-killing (defense) effects by 100,000 fold\nin phagocytosis, resembling the cyclic ozone-depleting reactions in the\nstratosphere. It is unraveled that H2O2 is a required protective signaling\nmolecule (angel) in the defense system for human health and its dysfunction can\ncause many diseases or conditions such as autoimmune disorders, aging and\ncancer. We also identify a class of potent drugs for effective treatment of\ninvading pathogens such as HIV and SARS-CoV-2 (COVID-19), cancer and other\ndiseases, and provide a molecular mechanism of action of the drugs or\ncandidates.\n", "doi": "10.3390/cells9061461", "arxiv_id": "2004.02631", "pdf_urls": ["https://arxiv.org/pdf/2004.02631"], "github": [], "is_oa": true, "sources": ["open-arxiv"], "type": "journal", "journal_ref": "Cells 2020, 9(6), 1461", "categories": "q-bio.CB q-bio.BM q-bio.SC"}
{"title": "Electron and proton irradiation effect on the minority carrier lifetime\n  in SiC passivated p-doped Ge wafers for space photovoltaics", "year": 2020, "venue_abbr": "Cell", "venue_name": "Cell", "authors": ["C. Weiss", "S. Park", "J. Lef\\`evre", "B. Boizot", "C. Mohr", "O. Cavani", "S.\n  Picard", "R. Kurstjens", "T. Niewelt", "S. Janz"], "abstract": "  We report on the effect of electron and proton irradiation on effective\nminority carrier lifetimes (${\\tau}_{eff}$) in p-type Ge wafers. Minority\ncarrier lifetimes are assessed using the microwave-detected photoconductance\ndecay (${\\mu}$W-PCD) method. We examine the dependence of ${\\tau}_{eff}$ on the\np-type doping level and on electron and proton radiation fluences at 1 MeV. The\nmeasured ${\\tau}_{eff}$ before and after irradiation are used to estimate the\nminority carriers diffusion lengths, which is an important parameter for solar\ncell operation. We observe ${\\tau}_{eff}$ ranging from 50 to 230 ${\\mu}$s for\nGe doping levels between 1E17 and 1E16 at.cm$^{-3}$, corresponding to diffusion\nlengths of 500-1400 ${\\mu}$m. A separation of ${\\tau}_{eff}$ in Ge bulk\nlifetime and surface recombination velocity is conducted by irradiating Ge\nlifetime samples of different thicknesses. The possible radiation-induced\ndefects are discussed on the basis of literature.\n", "doi": "10.1016/j.solmat.2020.110430", "arxiv_id": "2005.07366", "pdf_urls": ["https://arxiv.org/pdf/2005.07366"], "github": [], "is_oa": true, "sources": ["open-arxiv"], "type": "journal", "journal_ref": "Solar Energy Materials and Solar Cells, vol. 209, p. 110430, 2020", "categories": "physics.app-ph cond-mat.mtrl-sci"}
{"title": "Selection of optimal wavelengths for optical soiling modelling and\n  detection in photovoltaic modules", "year": 2020, "venue_abbr": "Cell", "venue_name": "Cell", "authors": ["Leonardo Micheli", "Eduardo F. Fernandez", "Matthew Muller", "Greg P.\n  Smestad", "Florencia Almonacid"], "abstract": "  Soiling impacts the photovoltaic (PV) module performance by reducing the\namount of light reaching the photovoltaic cells and by changing their external\nspectral response. Currently, the soiling monitoring market is moving toward\noptical sensors that measure transmittance or reflectance, rather than directly\nmeasuring the impact of soiling on the performance of photovoltaic modules.\nThese sensors, which use a single optical measurement, are not able to correct\nthe soiling losses that depend on the solar irradiance spectra and on the\nspectral response of the monitored PV material. This work investigates methods\nthat can improve the optical detection of soiling by extracting the full\nsoiling spectrum profiles using only two or three monochromatic measurements.\nSpectral transmittance data, measured with a spectrophotometer and collected\nduring a 46-week experimental soiling study carried out in Ja\\'en, Spain, was\nanalysed in this work. The use of a spectral profile for the hemispherical\ntransmittance of soiled PV glass is found to significantly improve the soiling\ndetection, returning the lowest errors independently of the PV materials and\nirradiance conditions. In addition, this work shows that it is also possible to\nselect the measurement wavelengths to minimize the soiling loss detection error\ndepending on the monitored PV semiconductor material (silicon, CdTe, a-Si, CIGS\nand a representative perovskite). The approaches discussed in this work are\nalso found to be more robust to potential measurement errors compared to single\nwavelength measurement techniques.\n", "doi": "10.1016/j.solmat.2020.110539", "arxiv_id": "2005.13020", "pdf_urls": ["https://arxiv.org/pdf/2005.13020"], "github": [], "is_oa": true, "sources": ["open-arxiv"], "type": "journal", "journal_ref": "Solar Energy Materials and Solar Cells 212 (2020), 110539", "categories": "physics.app-ph physics.optics"}
{"title": "Modeling adult skeletal stem cell response to laser-machined\n  topographies through deep learning", "year": 2020, "venue_abbr": "Cell", "venue_name": "Cell", "authors": ["Benita S. Mackay", "Matthew Praeger", "James A. Grant-Jacob", "Janos\n  Kanczler", "Robert W. Eason", "Richard O.C. Oreffo and Ben Mills"], "abstract": "  The response of adult human bone marrow stromal stem cells to surface\ntopographies generated through femtosecond laser machining can be predicted by\na deep neural network. The network is capable of predicting cell response to a\nstatistically significant level, including positioning predictions with a\nprobability P < 0.001, and therefore can be used as a model to determine the\nminimum line separation required for cell alignment, with implications for\ntissue structure development and tissue engineering. The application of a deep\nneural network, as a model, reduces the amount of experimental cell culture\nrequired to develop an enhanced understanding of cell behavior to topographical\ncues and, critically, provides rapid prediction of the effects of novel surface\nstructures on tissue fabrication and cell signaling.\n", "doi": "10.1016/j.tice.2020.101442", "arxiv_id": "2006.00248", "pdf_urls": ["https://arxiv.org/pdf/2006.00248"], "github": [], "is_oa": true, "sources": ["open-arxiv"], "type": "journal", "journal_ref": "Tissue and Cell: Volume 67, December 2020, 101442", "categories": "eess.IV cs.LG"}
{"title": "Theory of random nanoparticle layers in photovoltaic devices applied to\n  self-aggregated metal samples", "year": 2020, "venue_abbr": "Cell", "venue_name": "Cell", "authors": ["Christin David", "James P. Connolly", "Christian Chaverri Ramos", "F. Javier\n  Garc\\'ia de Abajo", "Guillermo S\\'anchez Plaza"], "abstract": "  Random Al and Ag nanoparticle distributions are studied on varying\nsubstrates, where we exploit the nanosphere self-aggregation method (NSA) for\nfabrication. Relying on the measured particle size distributions of these\nsamples, we develop a theoretical model that can be applied to arbitrary random\nnanostructure layers as is demonstrated for several distinct NSA samples. As a\nproof of concept, the optical properties of the exact same particles\ndistributions, made from the quasi random modeling input with electron beam\nlithography (EBL), are investigated from both theory and experiment. Our\nnumerical procedure is based on rigorous solutions of Maxwell's equations and\nyields optical spectra of fully interacting randomly positioned nanoparticle\narrays. These results constitute a new methodology for improving the optical\nperformance of layers of nanoparticles with direct application to enhanced\nphotovoltaics.\n", "doi": "10.1016/j.solmat.2012.11.004", "arxiv_id": "2006.15959", "pdf_urls": ["https://arxiv.org/pdf/2006.15959"], "github": [], "is_oa": true, "sources": ["open-arxiv"], "type": "journal", "journal_ref": "Solar Energy Materials & Solar Cells 109 294-299 (2013)", "categories": "physics.optics cond-mat.mes-hall"}
{"title": "Impact of the III-V/Ge nucleation routine on the performance of high\n  efficiency multijunction solar cells", "year": 2020, "venue_abbr": "Cell", "venue_name": "Cell", "authors": ["Laura Barrutia", "Ivan Garc\\'ia", "Enrique Barrigon", "Mario Ochoa", "Carlos\n  Algora and Ignacio Rey-Stolle"], "abstract": "  This paper addresses the influence of III-V nucleation routines on Ge\nsubstrates for the growth of high efficiency multijunction solar cells. Three\nexemplary nucleation routines with differences in thickness and temperature\nwere evaluated. The resulting open circuit voltage of triple-junction solar\ncells with these designs is significantly affected (up to 50 mV for the best\noptimization routine), whereas minimal differences in short circuit current are\nobserved. Electroluminescence measurements show that both the Ge bottom cell\nand the Ga(In)As middle cell present a VOC gain of 25 mV each. This result\nindicates that the first stages of the growth not only affect the Ge subcell\nitself but also to subsequent subcells. This study highlights the impact of the\nnucleation routine design in the performance of high efficiency multijunction\nsolar cell based on Ge substrates.\n", "doi": "10.1016/j.solmat.2019.110355", "arxiv_id": "2007.00951", "pdf_urls": ["https://arxiv.org/pdf/2007.00951"], "github": [], "is_oa": true, "sources": ["open-arxiv"], "type": "journal", "journal_ref": "Solar Energy Materials and Solar Cells 207 (2020) 110355", "categories": "physics.app-ph"}
{"title": "Nonlinear conductance, rectification and mechanosensitive channel\n  formation of lipid membranes", "year": 2020, "venue_abbr": "Cell", "venue_name": "Cell", "authors": ["Karis A. Zecchi and Thomas Heimburg"], "abstract": "  There is mounting evidence that lipid bilayers display conductive properties.\nHowever, when interpreting the electrical response of biological membranes to\nvoltage changes, they are commonly considered as inert insulators. However,\nlipid bilayers under voltage-clamp conditions do not only display current\ntraces with discrete conduction-steps indistinguishable from those attributed\nto the presence of protein channels. In current-voltage (I-V) plots they may\nalso display outward rectification, i.e., voltage-gating. Surprisingly, this\nhas even been observed in chemically symmetric lipid bilayers. Here, we\ninvestigate this phenomenon using a theoretical framework that models the\nelectrostrictive effect of voltage on lipid membranes in the presence of a\nspontaneous polarization, which can be recognized by a voltage offset in\nelectrical measurements. It can arise from an asymmetry of the membrane, for\nexample from a nonzero spontaneous curvature of the membrane. This curvature\ncan be caused by voltage via the flexoelectric effect, or by hydrostatic\npressure differences across the membrane. Here, we describe I-V relations for\nlipid membranes formed at the tip of patch pipettes situated close to an\naqueous surface. We measured at different depths relative to air/water surface,\nresulting in different pressure gradients across the membrane. Both linear and\nnonlinear I-V profiles were observed. Nonlinear conduction consistently takes\nthe form of outward rectified currents. We explain the conductance properties\nby two mechanisms: One leak current with constant conductance without pores,\nand a second process that is due to voltage-gated pore opening correlating with\nthe appearance of channel-like conduction steps. In some instances, these\nnonlinear I-V relations display a voltage regime in which dI/dV is negative.\nThis has also been previously observed in the presence of sodium channels. ...\n", "doi": "10.3389/fcell.2020.592520", "arxiv_id": "2008.03200", "pdf_urls": ["https://arxiv.org/pdf/2008.03200"], "github": [], "is_oa": true, "sources": ["open-arxiv"], "type": "journal", "journal_ref": "Front. Cell Dev. Biol. 8 (2021), 592520", "categories": "physics.bio-ph"}
{"title": "Tetracycline as an inhibitor to the coronavirus SARS-CoV-2", "year": 2020, "venue_abbr": "Cell", "venue_name": "Cell", "authors": ["Tom Y. Zhao and Neelesh A. Patankar"], "abstract": "  The coronavirus SARS-CoV-2 remains an extant threat against public health on\na global scale. Cell infection begins when the spike protein of SARS-CoV-2\nbinds with the cell receptor, angiotensin-converting enzyme 2 (ACE2). Here, we\naddress the role of Tetracycline as an inhibitor for the receptor-binding\ndomain (RBD) of the spike protein. Targeted molecular investigation show that\nTetracycline binds more favorably to the RBD (-9.40 kcal/mol) compared to\nChloroquine (-6.31 kcal/mol) or Doxycycline (-8.08 kcal/mol) and inhibits\nattachment to ACE2 to a greater degree (binding efficiency of 2.98\n$\\frac{\\text{kcal}}{\\text{mol}\\cdot \\text{nm}^2}$ for Tetracycline-RBD, 5.59\n$\\frac{\\text{kcal}}{\\text{mol}\\cdot \\text{nm}^2}$ for Chloroquine-RBD, 5.16\n$\\frac{\\text{kcal}}{\\text{mol}\\cdot \\text{nm}^2}$ for Doxycycline-RBD).\nStronger Tetracycline inhibition is verified with nonequilibrium PMF\ncalculations, for which the Tetracycline-RBD complex exhibits the lowest free\nenergy profile along the dissociation pathway from ACE2. Tetracycline appears\nto target viral residues that are usually involved in significant hydrogen\nbonding with ACE2; this inhibition of cellular infection complements the\nanti-inflammatory and cytokine suppressing capability of Tetracycline, and may\nfurther reduce the duration of ICU stays and mechanical ventilation induced by\nthe coronavirus SARS-CoV-2.\n", "doi": "10.1002/jcb.29909", "arxiv_id": "2008.06034", "pdf_urls": ["https://arxiv.org/pdf/2008.06034"], "github": [], "is_oa": true, "sources": ["open-arxiv"], "type": "journal", "journal_ref": "J Cell Biochem (2021) 1-8", "categories": "q-bio.BM q-bio.QM"}
{"title": "Benchmarking database performance for genomic data", "year": 2020, "venue_abbr": "Cell", "venue_name": "Cell", "authors": ["Matloob Khushi"], "abstract": "  Genomic regions represent features such as gene annotations, transcription\nfactor binding sites and epigenetic modifications. Performing various genomic\noperations such as identifying overlapping/non-overlapping regions or nearest\ngene annotations are common research needs. The data can be saved in a database\nsystem for easy management, however, there is no comprehensive database\nbuilt-in algorithm at present to identify overlapping regions. Therefore I have\ndeveloped a region-mapping (RegMap) SQL-based algorithm to perform genomic\noperations and have benchmarked the performance of different databases.\nBenchmarking identified that PostgreSQL extracts overlapping regions much\nfaster than MySQL. Insertion and data uploads in PostgreSQL were also better,\nalthough general searching capability of both databases was almost equivalent.\nIn addition, using the algorithm pair-wise, overlaps of >1000 datasets of\ntranscription factor binding sites and histone marks, collected from previous\npublications, were reported and it was found that HNF4G significantly\nco-locates with cohesin subunit STAG1 (SA1).\n", "doi": "10.1002/jcb.25049", "arxiv_id": "2008.06835", "pdf_urls": ["https://arxiv.org/pdf/2008.06835"], "github": [], "is_oa": true, "sources": ["open-arxiv"], "type": "journal", "journal_ref": "J Cell Biochem. 2015 Jun;116(6):877-83", "categories": "cs.DB"}
{"title": "Isotropic Cellular Automata: the DDLab iso-rule paradigm", "year": 2020, "venue_abbr": "Cell", "venue_name": "Cell", "authors": ["Andrew Wuensche", "Jos\\'e Manuel G\\'omez Soto"], "abstract": "  To respect physics and nature, cellular automata (CA) models of\nself-organisation, emergence, computation and logical universality should be\nisotropic, having equivalent dynamics in all directions. We present a novel\nparadigm, the iso-rule, a concise expression for isotropic CA by the output\ntable for each isotropic neighborhood group, allowing an efficient method of\nnavigating and exploring iso-rule-space. We describe new functions and tools in\nDDLab to generate iso-groups and iso-rules, for multi-value as well as binary,\nin one, two and three dimensions. These methods include filing, filtering,\nmutating, analysing dynamics by input-frequency and entropy, identifying the\ncritical iso-groups for glider-gun/eater dynamics, and automatically\nclassifying iso-rule-space. We illustrate these ideas and methods for two\ndimensional CA on square and hexagonal lattices.\n", "doi": null, "arxiv_id": "2008.11279", "pdf_urls": ["https://arxiv.org/pdf/2008.11279"], "github": [], "is_oa": true, "sources": ["open-arxiv"], "type": "journal", "journal_ref": "Journal of CELLULAR AUTOMATA (JCA) ,Vol.15, No.5-6,439-470, 2021", "categories": "nlin.CG"}
{"title": "Polymer Modelling Predicts Chromosome Reorganisation in Senescence", "year": 2020, "venue_abbr": "Cell", "venue_name": "Cell", "authors": ["Michael Chiang", "Davide Michieletto", "Chris A. Brackley", "Nattaphon\n  Rattanavirotkul", "Hisham Mohammed", "Davide Marenduzzo", "Tamir Chandra"], "abstract": "  Lamina-associated domains (LADs) cover a large part of the human genome and\nare thought to play a major role in shaping the nuclear architectural\nlandscape. Here, we perform polymer simulations, microscopy and mass\nspectrometry to dissect the roles played by heterochromatin- and\nlamina-mediated interactions in nuclear organisation. Our model explains the\nconventional organisation of heterochromatin and euchromatin in growing cells\nand the pathological organisation found in oncogene-induced senescence and\nprogeria. We show that the experimentally observed changes in the locality of\ncontacts in senescent and progeroid cells can be explained as arising due to\nphase transitions in the system. Within our simulations LADs are highly\nstochastic, as in experiments. Our model suggests that, once established, the\nsenescent phenotype should be metastable even if lamina-mediated interactions\nwere reinstated. Overall, our simulations uncover a generic physical mechanism\nthat can regulate heterochromatin segregation and LAD formation in a wide range\nof mammalian nuclei.\n", "doi": null, "arxiv_id": "2010.09688", "pdf_urls": ["https://arxiv.org/pdf/2010.09688"], "github": [], "is_oa": true, "sources": ["open-arxiv"], "type": "journal", "journal_ref": "Cell Reports 28, 3212 (2019)", "categories": "physics.bio-ph cond-mat.soft q-bio.SC"}
{"title": "Interpretable and synergistic deep learning for visual explanation and\n  statistical estimations of segmentation of disease features from medical\n  images", "year": 2020, "venue_abbr": "Cell", "venue_name": "Cell", "authors": ["Sambuddha Ghosal and Pratik Shah"], "abstract": "  Deep learning (DL) models for disease classification or segmentation from\nmedical images are increasingly trained using transfer learning (TL) from\nunrelated natural world images. However, shortcomings and utility of TL for\nspecialized tasks in the medical imaging domain remain unknown and are based on\nassumptions that increasing training data will improve performance. We report\ndetailed comparisons, rigorous statistical analysis and comparisons of widely\nused DL architecture for binary segmentation after TL with ImageNet\ninitialization (TII-models) with supervised learning with only medical\nimages(LMI-models) of macroscopic optical skin cancer, microscopic prostate\ncore biopsy and Computed Tomography (CT) DICOM images. Through visual\ninspection of TII and LMI model outputs and their Grad-CAM counterparts, our\nresults identify several counter intuitive scenarios where automated\nsegmentation of one tumor by both models or the use of individual segmentation\noutput masks in various combinations from individual models leads to 10%\nincrease in performance. We also report sophisticated ensemble DL strategies\nfor achieving clinical grade medical image segmentation and model explanations\nunder low data regimes. For example; estimating performance, explanations and\nreplicability of LMI and TII models described by us can be used for situations\nin which sparsity promotes better learning. A free GitHub repository of TII and\nLMI models, code and more than 10,000 medical images and their Grad-CAM output\nfrom this study can be used as starting points for advanced computational\nmedicine and DL research for biomedical discovery and applications.\n", "doi": "10.1016/j.crmeth.2021.100107", "arxiv_id": "2011.05791", "pdf_urls": ["https://arxiv.org/pdf/2011.05791"], "github": [], "is_oa": true, "sources": ["open-arxiv"], "type": "journal", "journal_ref": "Published in Cell Reports Methods 1, 100107, 2021. \"A\n  deep-learning toolkit for visualization and interpretation of segmented\n  medical images\"", "categories": "stat.ML cs.LG"}
{"title": "Comprehensive Energy Balance Analysis of Photon-Enhanced Thermionic\n  Power Generation Considering Concentrated Solar Absorption Distribution", "year": 2020, "venue_abbr": "Cell", "venue_name": "Cell", "authors": ["A. N. M. Taufiq Elahi", "Mohammad Ghashami", "Devon Jensen", "Keunhan Park"], "abstract": "  The present article reports a comprehensive energy balance analysis of a\nphoton-enhanced thermionic emission (PETE) device when it is used for\nconcentrated solar power (CSP) generation. To this end, we consider a realistic\nPETE device composed of a boron-doped silicon emitter on glass and a\nphosphorus-doped diamond collector on tungsten separated by the inter-electrode\nvacuum gap. Depth-dependent spectral solar absorption and its photovoltaic and\nphotothermal energy conversion processes are rigorously calculated to predict\nthe PETE power output and energy conversion efficiency. Our calculation\npredicts that when optimized, the power output of the considered PETE device\ncan reach 1.6 W/cm$^2$ with the energy conversion efficiency of $\\sim$18 \\% for\n100$\\times$ solar concentration, which is substantially lower than those\npredicted in previous works under ideal conditions. In addition, the\nphoton-enhancement ratio is lower than 10 and decreases with the increasing\nsolar concentration due to the photothermal heating of the emitter, suggesting\nthat PETE may be an adequate energy conversion process for low-to-medium CSP\nbelow $\\sim$100$\\times$ concentration. These observations signify the\nimportance of a rigorous energy balance analysis based on spectral and spatial\nsolar absorption distribution for the accurate prediction of PETE power\ngeneration.\n", "doi": "10.1016/j.solmat.2021.111067", "arxiv_id": "2011.12909", "pdf_urls": ["https://arxiv.org/pdf/2011.12909"], "github": [], "is_oa": true, "sources": ["open-arxiv"], "type": "journal", "journal_ref": "Sol. Energy Mater. Sol. Cells 226 (2021) 111067", "categories": "physics.app-ph"}
{"title": "Magnetic Resonance Elastography and Portal Hypertension: Influence of\n  the Portal Venous Flow on the Liver Stiffness", "year": 2020, "venue_abbr": "Cell", "venue_name": "Cell", "authors": ["Simon Chatelin (ICube)", "Raoul Pop (IHU Strasbourg)", "C\\'eline Giraudeau\n  (IHU Strasbourg)", "Khalid Ambarki", "Ning Jin", "Fran\\c{c}ois Severac (ICube", "HUS)", "Elodie Breton (ICube)", "Jonathan Vappou (ICube)"], "abstract": "  The invasive measurement of the hepatic venous pressure gradient is still\nconsidered as the reference method to assess the severity of portal\nhypertension. Even though previous studies have shown that the liver stiffness\nmeasured by elastography could predict portal hypertension in patients with\nchronic liver disease, the mechanisms behind remain today poorly understood.\nThe main reason is that the liver stiffness is not specific to portal\nhypertension and is also influenced by concomitant pathologies, such as\ncirrhosis. Portal hypertension is also source of a vascular incidence, with a\nsubstantial diversion of portal venous blood to the systemic circulation,\nbypassing the liver. This study focuses on this vascular effect of portal\nhypertension. We propose to generate and control the portal venous flow (to\nisolate the modifications in the portal venous flow as single effect of portal\nhypertension) in an anesthetized pig and then to quantify its implications on\nliver stiffness by an original combination of MRE and 4D-Flow Magnetic\nResonance Imaging (MRI). A catheter balloon is progressively inflated in the\nportal vein and the peak flow, peak velocity magnitude and liver stiffness are\nquantified in a 1.5T MRI scanner (AREA, Siemens Healthcare, Erlangen, Germany).\nA strong correlation is observed between the portal peak velocity magnitude,\nthe portal peak flow or the liver stiffness and the portal vein intraluminal\nobstruction. Moreover, the comparison of mechanical and flow parameters\nhighlights a correlation with the possibility of identifying linear\nrelationships. These results give preliminary indications about how liver\nstiffness can be affected by portal venous flow and, by extension, by\nhypertension.\n", "doi": null, "arxiv_id": "2012.03552", "pdf_urls": ["https://arxiv.org/pdf/2012.03552"], "github": [], "is_oa": true, "sources": ["open-arxiv"], "type": "journal", "journal_ref": "Stem Cells and Regenerative Medicine -- the 9th International\n  Europe-China Symposium, Strasbourg 2-4 Oct 2019, In press", "categories": "physics.med-ph"}
{"title": "Diffusion processes in germanium and silicon films grown on Si$_3$N$_4$\n  substrates", "year": 2020, "venue_abbr": "Cell", "venue_name": "Cell", "authors": ["Larisa V. Arapkina", "Kirill V. Chizh", "Dmitry B. Stavrovskii", "Vladimir\n  P. Dubkov", "Elizabeth P. Lazareva", "and Vladimir A. Yuryev"], "abstract": "  In this article, the results of investigation of processes occurring during\nthe molecular-beam deposition of germanium layers on Si$_3$N$_4$ dielectric\nsubstrates within a wide range of the Ge film growth temperatures (30 to\n600{\\deg}C) are presented. The intensity of the IR absorption bands related to\nthe vibrations of the N$-$H and Si$-$N bonds are established to decrease with\nthe increase of the Ge deposition temperature. It appears that this phenomenon\ncannot be explained only as a thermally activated process. Simultaneously, the\npeak corresponding to the Ge$-$N vibration bonds emerges in the X-ray\nphotoelectron spectra. We suppose that the deposition of germanium layers on\nSi3N4 dielectric substrates containing hydrogen atoms causes the diffusion of\nhydrogen atoms from the dielectric layer into the growing film. The\nexperimental results may be interpreted in terms of a model, according to which\nthe migration of hydrogen atoms from the Si$_3$N$_4$ layer into the growing\ngermanium film is due to the difference in chemical potentials of hydrogen\natoms in the dielectric layer and the germanium film. This process initiates\nthe diffusion of germanium atoms in the opposite direction, into the\nSi$_3$N$_4$ layer, where they connect to free bonds of nitrogen atoms arising\ndue to the escape of hydrogen atoms. The analogous processes occur during the\ndeposition of silicon layers on Si$_3$N$_4$ substrates.\n", "doi": "10.1016/j.solmat.2021.111231", "arxiv_id": "2012.10358", "pdf_urls": ["https://arxiv.org/pdf/2012.10358"], "github": [], "is_oa": true, "sources": ["open-arxiv"], "type": "journal", "journal_ref": "Sol. Energy Mater. Sol. Cells 230 (2021) 111231", "categories": "cond-mat.mtrl-sci cond-mat.mes-hall"}
{"title": "Adsorption of a fabric conditioner on cellulose nanocrystals:\n  Synergistic effects of surfactant vesicles and polysaccharides on softness\n  properties", "year": 2020, "venue_abbr": "Cell", "venue_name": "Cell", "authors": ["Evdokia K. Oikonomou", "Grazia M.L. Messina", "Laurent Heux", "Giovanni\n  Marletta and Jean-Fran\\c{c}ois Berret"], "abstract": "  Concentrated fabric conditioners are water-based formulations containing 10\nwt. % of cationic surfactants that are deposited on textile fibers during the\nrinse cycle in a washing machine to make them smoother and softer to touch. In\ntopical formulations, the concentration of cationic surfactants is reduced by\nhalf, this reduction being compensated by the addition of environment-friendly\npolysaccharides. Using atomic force microscopy (AFM), quartz crystal\nmicrobalance with dissipation (QCM-D) and ellipsometry, the deposition of\nformulations with or without polysaccharides on model cellulose substrates is\nstudied. We found that 180 nm long cellulose nanocrystals (CNCs) deposited by\nspin-coating on amorphous silicon dioxide or on quartz crystal sensors provide\na good model of cellulose surfaces. QCM-D results reveal strong electrostatic\ninteractions of the surfactant vesicles and polysaccharides with the CNC layer.\nIn the presence of polysaccharides, the adsorbed quantities are less (by 60%)\nthan the sum of the respective amounts of each component, the structure of the\ninterface being however more homogenous and rigid. This outcome suggests that\nsurface techniques coupled with CNC coated substrates are promising for\nstudying interactions of current formulations with cellulose surfaces.\n", "doi": "10.1007/s10570-020-03672-y", "arxiv_id": "2012.14887", "pdf_urls": ["https://arxiv.org/pdf/2012.14887"], "github": [], "is_oa": true, "sources": ["open-arxiv"], "type": "journal", "journal_ref": "Cellulose 28 (4) 2551-2566 (2021)", "categories": "cond-mat.soft"}
{"title": "The Internet of Things in Ports: Six Key Security and Governance\n  Challenges for the UK (Policy Brief)", "year": 2021, "venue_abbr": "Cell", "venue_name": "Cell", "authors": ["Feja Lesniewska", "Uchenna D Ani", "Jeremy M Watson", "Madeline Carr"], "abstract": "  In January 2019, the UK Government published its Maritime 2050 on Navigating\nthe Future strategy. In the strategy, the government highlighted the importance\nof digitalization (with well-designed regulatory support) to achieve its goal\nof ensuring that the UK plays a global leadership role in the maritime sector.\nPorts, the gateways for 95% of UK trade movements, were identified as key sites\nfor investment in technological innovation. The government identified the\npotential of the Internet of Things (IoT), in conjunction with other\ninformation-sharing technologies, such as shared data platforms, and Artificial\nIntelligence applications (AI), to synchronize processes within the port\necosystem leading to improved efficiency, safety, and environmental benefits,\nincluding improved air quality and lower greenhouse gas emissions.\n", "doi": null, "arxiv_id": "2101.08812", "pdf_urls": ["https://arxiv.org/pdf/2101.08812"], "github": [], "is_oa": true, "sources": ["open-arxiv"], "type": "journal", "journal_ref": "The Internet of Things in Ports: Six Key Security and Governance\n  Challenges for the UK (A Policy Brief). London: PETRAS National Centre of\n  Excellence for IoT System Cybersecurity (2019)", "categories": "cs.CY"}
{"title": "Spectral nature of soiling and its impact on multi-junction based\n  concentrator systems", "year": 2021, "venue_abbr": "Cell", "venue_name": "Cell", "authors": ["Eduardo F. Fernandez", "Daniel Chemisana", "Leonardo Micheli and Florencia\n  Almonacid"], "abstract": "  Soiling, which consists of dust, dirt and particles accumulated on the\nsurface of conventional or concentrator photovoltaic modules, absorbs,\nscatters, and reflects part of the incoming sunlight. Therefore, it reduces the\namount of energy converted by the semiconductor solar cells. This work focuses\non the effect of soiling on the spectral performance of multi-junction (MJ)\ncells, widely used in concentrator photovoltaic (CPV) applications. Novel\nindexes, useful to quantify the spectral impact of soiling are introduced, and\ntheir meanings are discussed. The results of a one-year experimental\ninvestigation conducted in Spain are presented and are used to discuss how\nsoiling impacts each of the subcells of a MJ cell, as well as the cell\ncurrent-matching. Results show that soiling affects the current balance among\nthe junctions, i.e. the transmittance losses have found to be around 4% higher\nin the top than in the middle subcell. The spectral nature of soiling has\ndemonstrated to increase the annual spectral losses of around 2%. Ideal\nconditions for the mitigation of soiling are also discussed and found to be in\nblue-rich environments, where the higher light intensity at the shorter\nwavelengths can limit the impact of soiling on the overall production of the\nCPV system.\n", "doi": "10.1016/j.solmat.2019.110118", "arxiv_id": "2103.01873", "pdf_urls": ["https://arxiv.org/pdf/2103.01873"], "github": [], "is_oa": true, "sources": ["open-arxiv"], "type": "journal", "journal_ref": "Solar Energy Materials and Solar Cells (2019)", "categories": "eess.SY cs.SY"}
{"title": "Thinned GaInP/GaInAs/Ge solar cells grown with reduced cracking on Ge|Si\n  virtual substrates", "year": 2021, "venue_abbr": "Cell", "venue_name": "Cell", "authors": ["Ivan Garc\\'ia", "Laura Barrutia", "Shabnam Dadgostar", "Manuel Hinojosa", "Andrew Johnson and Ignacio Rey-Stolle"], "abstract": "  Reducing the formation of cracks during growth of GaInP/GaInAs/Ge 3-junction\nsolar cells on Ge|Si virtual substrates has been attempted by thinning the\nstructure, namely the Ge bottom cell and the GaInAs middle cell. The\ntheoretical analysis performed using realistic device parameters indicates that\nthe GaInAs middle cell can be drastically thinned to 1000 nm while increasing\nits In content to 8% with an efficiency loss in the 3-junction cell below 3%.\nThe experimental results show that the formation of macroscopic cracks is\nprevented in thinned GaInAs/Ge 2-junction and GaInP/GaInAs/Ge 3-junction cells.\nThese prototype crack-free multijunction cells demonstrate the concept and were\nused to rule out any possible component integration issue. The performance\nmetrics are limited by the high threading dislocation density over 2e7cm-2 in\nthe virtual substrates used, but an almost current matched, crack-free, thinned\n3-junction solar cell is demonstrated, and the pathway towards solar cells with\nhigher voltages identified.\n", "doi": "10.1016/j.solmat.2021.111034", "arxiv_id": "2104.03288", "pdf_urls": ["https://arxiv.org/pdf/2104.03288"], "github": [], "is_oa": true, "sources": ["open-arxiv"], "type": "journal", "journal_ref": "Solar Energy Materials and Solar Cells, vol. 225, p. 111034, Jun.\n  2021", "categories": "cond-mat.mtrl-sci physics.app-ph"}
{"title": "Capacity Self-Planning in Small Cell Multi-Tenant 5G Networks", "year": 2021, "venue_abbr": "Cell", "venue_name": "Cell", "authors": ["Pablo Mu\\~noz", "Oriol Sallent", "Jordi P\\'erez-Romero"], "abstract": "  Multi-tenancy allows diverse agents sharing the infrastructure in the 5 th\ngeneration of mobile networks. Such a feature calls for more automated and\nfaster planning procedures in order to adapt the network capacity to the\nvarying traffic demand. To achieve these goals, Small Cells offer network\nproviders more flexible, scalable, and cost-effective solutions compared to\nmacrocell deployments. This paper proposes a novel framework for cell planning\nin multi-tenant Small Cell networks. In this framework, the tenant's contracted\ncapacity is translated to a set of detailed planning specifications over time\nand space domains in order to efficiently update the network infrastructure and\nconfiguration. Based on this, an algorithm is proposed that considers different\nactions such as adding/removing channels and adding or relocating small cells.\nThe proposed approach is evaluated considering the deployment of a new tenant,\nwhere different sets of planning specifications are tested.\n", "doi": "10.23919/inm.2017.7987449", "arxiv_id": "2104.14833", "pdf_urls": ["https://arxiv.org/pdf/2104.14833"], "github": [], "is_oa": true, "sources": ["open-arxiv"], "type": "journal", "journal_ref": "P. Munoz, O. Sallent, J. Perez-Romero, \"Capacity Self-Planning in\n  Small Cell Multi-Tenant 5G Networks\", 2nd IFIP/IEEE International Workshop on\n  Management of 5G Networks (5GMan 2017), pp. 1109-1114, Lisbon, 2017", "categories": "cs.NI"}
{"title": "Self-Dimensioning and Planning of Small Cell Capacity in Multitenant 5G\n  Networks", "year": 2021, "venue_abbr": "Cell", "venue_name": "Cell", "authors": ["Pablo Mu\\~noz", "Oriol Sallent", "Jordi P\\'erez-Romero"], "abstract": "  An important concept in the fifth generation of mobile networks is\nmultitenancy, which allows diverse operators sharing the same wireless\ninfrastructure. To support this feature in conjunction with the challenging\nperformance requirements of future networks, more automated and faster planning\nof the required radio capacity is needed. Likewise, installing small cells is\nan effective resource to provide greater performance and capacity to both\nindoor and outdoor places. This paper proposes a new framework for automated\ncell planning in multitenant small cell networks. In particular, taking\nadvantage of the available network data, a set of detailed planning\nspecifications over time and space domains are generated in order to meet the\ncontracted capacity by each tenant. Then, the network infrastructure and\nconfiguration are updated according to an algorithm that considers different\nactions such as adding/removing channels and adding or relocating small cells.\nThe simulation results show the effectiveness of various methods to derive the\nplanning specifications depending on the correlation between the tenant's and\nnetwork's traffic demands.\n", "doi": "10.1109/tvt.2018.2793418", "arxiv_id": "2105.00001", "pdf_urls": ["https://arxiv.org/pdf/2105.00001"], "github": [], "is_oa": true, "sources": ["open-arxiv"], "type": "journal", "journal_ref": "P. Munoz, O. Sallent, J. Perez-Romero, \"Self-Dimensioning and\n  Planning of Small Cell Capacity in Multi-Tenant 5G Networks\", IEEE\n  Transactions on Vehicular Technology, 67-5, pp. 4552-4564, 2018", "categories": "cs.NI"}
{"title": "Effect of Cd diffusion on the electrical properties of the Cu(In,Ga)Se2\n  thin-film solar cell", "year": 2021, "venue_abbr": "Cell", "venue_name": "Cell", "authors": ["Anna Koprek", "Pawel Zabierowski", "Marek Pawlowski", "Luv Sharma", "Christoph\n  Freysoldt", "Baptiste Gault", "Roland Wuerz", "Oana Cojocaru-Miredin"], "abstract": "  Cu(In,Ga)Se2 (CIGSe)-based solar cells are promising candidates for efficient\nsunlight harvesting. However, their complex composition and microstructure can\nchange under operation conditions, for instance heating from sun light\nillumination can lead to a degradation in performance. Here, we investigate the\nthermally-induced degradation processes in a set of CIGSe-based solar cells\nthat were annealed at temperatures between 150C and 300C. Using correlative\natom probe tomography (APT)/transmission electron microscope (TEM), we found\nthat the buffer-absorber interface is not sharp but consists of an interfacial\nzone (2 - 6.5 nm wide) where a gradient of constituent elements belonging to\nthe CdS buffer and CIGSe absorber appears. An enhanced short-range Cd\nin-diffusion inside the CIGSe was observed whenever a low Ga/(Ga+In) ratio\noccurred at the interface. This might indicate the presence of Ga vacancies as\na channeling defect for Cd in-diffusion inside the CIGSe layer leading to a\nburied pn-homojunction. We evidence that a considerable amount of Cd is found\ninside the CIGSe layer at annealing temperatures higher than 150C. Further\ninvestigations of the elemental redistribution inside the CIGSe layer combined\nwith C-V measurements support the formation of CdCu donor like defects deep\ninside the p-type CIGSe which lead to a strong compensation of the CIGSe layer\nand hence to strong deterioration of cell efficiency at annealing temperatures\nhigher than 200C. Hence, understanding the degradation processes in\nCu(In,Ga)Se2 (CIGSe)-based solar cells opens new opportunities for further\nimprovement of the long-term device performance.\n", "doi": "10.1016/j.solmat.2021.110989get", "arxiv_id": "2105.13676", "pdf_urls": ["https://arxiv.org/pdf/2105.13676"], "github": [], "is_oa": true, "sources": ["open-arxiv"], "type": "journal", "journal_ref": "Solar Energy Materials and Solar Cells Volume 224, 1 June 2021,\n  110989 Solar Energy Materials and Solar Cells, volume 224, 110989", "categories": "physics.app-ph cond-mat.mtrl-sci"}
{"title": "Enrichment of gut microbiome strains for cultivation-free genome\n  sequencing using droplet microfluidics", "year": 2021, "venue_abbr": "Cell", "venue_name": "Cell", "authors": ["Anna Pryszlak", "Tobias Wenzel", "Kiley West Seitz", "Falk Hildebrand", "Ece\n  Kartal", "Marco Raffaele Cosenza", "Vladimir Benes", "Peer Bork", "Christoph Merten"], "abstract": "  We report a droplet microfluidic method to target and sort individual cells\ndirectly from complex microbiome samples, and to prepare these cells for bulk\nwhole genome sequencing without cultivation. We characterize this approach by\nrecovering bacteria spiked into human stool samples at a ratio as low as 1:250\nand by successfully enriching endogenous Bacteroides vulgatus to the level\nrequired for de-novo assembly of high-quality genomes. While microbiome strains\nare increasingly demanded for biomedical applications, the vast majority of\nspecies and strains are uncultivated and without reference genomes. We address\nthis shortcoming by encapsulating complex microbiome samples directly into\nmicrofluidic droplets and amplify a target-specific genomic fragment using a\ncustom molecular TaqMan probe. We separate those positive droplets by droplet\nsorting, selectively enriching single target strain cells. Finally, we present\na protocol to purify the genomic DNA while specifically removing amplicons and\ncell debris for high-quality genome sequencing.\n", "doi": "10.1016/j.crmeth.2021.100137", "arxiv_id": "2106.01455", "pdf_urls": ["https://arxiv.org/pdf/2106.01455"], "github": [], "is_oa": true, "sources": ["open-arxiv"], "type": "journal", "journal_ref": "Cell Reports Methods 12/2021", "categories": "q-bio.GN physics.bio-ph q-bio.QM"}
{"title": "Comprehensive analysis of optimized near-field tandem thermophotovoltaic\n  system", "year": 2021, "venue_abbr": "Cell", "venue_name": "Cell", "authors": ["Jaeman Song", "Minwoo Choi", "Mikyung Lim", "Jungchul Lee", "Bong Jae Lee"], "abstract": "  It is well known that performance of a thermophotovoltaic (TPV) device can be\nenhanced if the vacuum gap between the thermal emitter and the TPV cell becomes\nnanoscale due to the photon tunneling of evanescent waves. Having multiple\nbandgaps, multi-junction TPV cells have received attention as an alternative\nway to improve its performance by selectively absorbing the spectral radiation\nin each subcell. In this work, we comprehensively analyze the optimized\nnear-field tandem TPV system consisting of the thin-ITO-covered tungsten\nemitter (at 1500 K) and GaInAsSb/InAs monolithic interconnected tandem TPV cell\n(at 300 K). We develop a simulation model by coupling the near-field radiation\nsolved by fluctuational electrodynamics and the diffusion-recombination-based\ncharge transport equations. The optimal configuration of the near-field tandem\nTPV system obtained by the genetic algorithm achieves the electrical power\noutput of 8.41 W/cm$^2$ and the conversion efficiency of 35.6\\% at the vacuum\ngap of 100 nm. We show that two resonance modes (i.e., surface plasmon\npolaritons supported by the ITO-vacuum interface and the confined waveguide\nmode in the tandem TPV cell) greatly contribute to the enhanced performance of\nthe optimized system. We also show that the near-field tandem TPV system is\nsuperior to the single-cell-based near-field TPV system in both power output\nand conversion efficiency through loss analysis. Interestingly, the\noptimization performed with the objective function of the conversion efficiency\nleads to the current matching condition for the tandem TPV system regardless of\nthe vacuum gap distances.\n", "doi": "10.1016/j.solmat.2021.111522", "arxiv_id": "2106.09465", "pdf_urls": ["https://arxiv.org/pdf/2106.09465"], "github": [], "is_oa": true, "sources": ["open-arxiv"], "type": "journal", "journal_ref": "Sol. Energy Mater. Sol. Cells 236, 111522, 2022", "categories": "physics.app-ph physics.optics"}
{"title": "Cell types and ontologies of the Human Cell Atlas", "year": 2021, "venue_abbr": "Cell", "venue_name": "Cell", "authors": ["David Osumi-Sutherland", "Chuan Xu", "Maria Keays", "Peter V. Kharchenko", "Aviv Regev", "Ed Lein", "Sarah A. Teichmann"], "abstract": "  Massive single-cell profiling efforts have accelerated our discovery of the\ncellular composition of the human body, while at the same time raising the need\nto formalise this new knowledge. Here, we review current cell ontology efforts\nto harmonise and integrate different sources of annotations of cell types and\nstates. We illustrate with examples how a unified ontology can consolidate and\nadvance our understanding of cell types across scientific communities and\nbiological domains.\n", "doi": "10.1038/s41556-021-00787-7", "arxiv_id": "2106.14443", "pdf_urls": ["https://arxiv.org/pdf/2106.14443"], "github": [], "is_oa": true, "sources": ["open-arxiv"], "type": "journal", "journal_ref": "Nat Cell Biol 23, 1129-1135 (2021)", "categories": "q-bio.CB"}
{"title": "Reduction of Trapping and Recombination in Upgraded Metallurgical Grade\n  Silicon: Impact of Phosphorous Diffusion Gettering", "year": 2021, "venue_abbr": "Cell", "venue_name": "Cell", "authors": ["N. Dasilva-Villanueva", "S. Catal\\'an-G\\'omez", "D. Fuertes Marr\\'on", "J.J.\n  Torres", "M. Garc\\'ia-Corpas and C. del Ca\\~nizo"], "abstract": "  Upgraded metallurgical grade (UMG) silicon (Si) has raised interest as an\nalternative material for solar cells due to its low cost, low environmental\nimpact and low CAPEX. Maximum cell efficiencies at the level of those obtained\nfrom high purity poly-Si have been reported. However, a higher defect density\nand the compensated doping character result in UMG-based cell efficiencies\nvarying over wider ranges in frequency distribution charts. In this report we\ncharacterize mc-Si UMG samples with different defect densities, comparing them\nwith mono-Si UMG and commercial high-performance mc-Si samples, analysing the\nimpact of carrier trapping by means of photoconductance (PC) decay\nmeasurements, and its evolution after applying a phosphorous diffusion\ngettering (PDG) process. When analyzing the decay time constant of the PC\nmeasurements, slow (66.8+-14.3 ms) and fast (16.1+-3.5 ms) traps are found in\nmc-Si samples, while no evidence of trapping is found in mono-UMG samples. Slow\ntraps are effectively removed after the PDG process, while fast traps do\nremain. The influence of dislocations clusters and the possible role of oxygen,\nas revealed by Fourier-transform infrared spectroscopy (FTIR) is discussed.\nFinally, the improvement in minority carrier lifetime due to the PDG treatment\nis reported for each sample type, reaching values up to 140 us in mc-Si samples\nwith no slow traps neither interstitial oxygen FTIR-peaks\n", "doi": "10.1016/j.solmat.2021.111410", "arxiv_id": "2106.15926", "pdf_urls": ["https://arxiv.org/pdf/2106.15926"], "github": [], "is_oa": true, "sources": ["open-arxiv"], "type": "journal", "journal_ref": "Solar Energy Materials and Solar Cells, Volume 234, January 2022,\n  111410", "categories": "physics.app-ph cond-mat.mtrl-sci"}
{"title": "Codabench: Flexible, Easy-to-Use and Reproducible Benchmarking Platform", "year": 2021, "venue_abbr": "Cell", "venue_name": "Cell", "authors": ["Zhen Xu", "Sergio Escalera", "Isabelle Guyon", "Adrien Pav\\~ao", "Magali\n  Richard", "Wei-Wei Tu", "Quanming Yao", "Huan Zhao"], "abstract": "  Obtaining standardized crowdsourced benchmark of computational methods is a\nmajor issue in data science communities. Dedicated frameworks enabling fair\nbenchmarking in a unified environment are yet to be developed. Here we\nintroduce Codabench, an open-source, community-driven platform for benchmarking\nalgorithms or software agents versus datasets or tasks. A public instance of\nCodabench (https://www.codabench.org/) is open to everyone, free of charge, and\nallows benchmark organizers to compare fairly submissions, under the same\nsetting (software, hardware, data, algorithms), with custom protocols and data\nformats. Codabench has unique features facilitating the organization of\nbenchmarks flexibly, easily and reproducibly, such as the possibility of\nre-using templates of benchmarks, and supplying compute resources on-demand.\nCodabench has been used internally and externally on various applications,\nreceiving more than 130 users and 2500 submissions. As illustrative use cases,\nwe introduce 4 diverse benchmarks covering Graph Machine Learning, Cancer\nHeterogeneity, Clinical Diagnosis and Reinforcement Learning.\n", "doi": "10.1016/j.patter.2022.100543", "arxiv_id": "2110.05802", "pdf_urls": ["https://arxiv.org/pdf/2110.05802"], "github": ["https://github.com/codalab/codabench", "https://github.com/codalab/competitions-v2"], "is_oa": true, "sources": ["open-arxiv"], "type": "journal", "journal_ref": "Patterns Cell Press 2022", "categories": "cs.LG cs.DC"}
{"title": "Semiconductor-Dielectric-Metal Solar Absorbers with High Spectral\n  Selectivity", "year": 2021, "venue_abbr": "Cell", "venue_name": "Cell", "authors": ["Eric J. Tervo and Myles A. Steiner"], "abstract": "  An ideal solar thermal absorber has a sharp transition between high and low\nabsorptance at the wavelength where the blackbody emissive power begins to\nexceed the solar irradiance. However, most real selective absorbers have a\nfairly broad transition, leading to both solar absorption and thermal emission\nlosses. Here, we model, fabricate, and characterize a highly selective\nsemiconductor-dielectric-metal (Ga0.46In0.54As - MgF2 - Ag) solar absorber with\nan extremely sharp transition from high to low absorptance. The thin\nsemiconductor serves as a selective filter, absorbing photons with wavelengths\nshorter than the bandgap and transmitting those with longer wavelengths. The\nhighly reflective dielectric-metal rear mirror allows the structure to have\nvery low emittance for longer wavelengths. These characteristics provide the\nabsorber with a measured solar absorptance >91% below the bandgap wavelength\nand infrared emittance <5% at 100 C above the bandgap wavelength. This\ntransition wavelength can be tuned by modifying the semiconductor composition,\nand modeling indicates that the absorber's optical properties should be stable\nat high temperatures, making the structure a good candidate for unconcentrated\nto highly concentrated solar thermal energy conversion.\n", "doi": "10.1016/j.solmat.2022.111735", "arxiv_id": "2112.09134", "pdf_urls": ["https://arxiv.org/pdf/2112.09134"], "github": [], "is_oa": true, "sources": ["open-arxiv"], "type": "journal", "journal_ref": "Solar Energy Materials and Solar Cells vol. 240, p. 111735, 2022", "categories": "physics.optics physics.app-ph"}
{"title": "Low-intensity pulsed ultrasound promotes mesenchymal stem cell\n  transplantation-based articular cartilage regeneration via inhibiting the TNF\n  signaling pathway", "year": 2021, "venue_abbr": "Cell", "venue_name": "Cell", "authors": ["Yiming Chen", "Huiyi Yang", "Zhaojie Wang", "Rongrong Zhu", "Liming Cheng", "Qian Cheng"], "abstract": "  Background: Mesenchymal stem cell (MSC) transplantation therapy is highly\ninvestigated for the regenerative repair of cartilage defects. Low-intensity\npulsed ultrasound (LIPUS) has the potential to promote chondrogenic\ndifferentiation of MSCs. However, its underlying mechanism remains unclear.\nHere, we investigated the promoting effects and mechanisms underlying LIPUS\nstimulation on the chondrogenic differentiation of human umbilical cord\nmesenchymal stem cells (hUC-MSCs) and further evaluated its regenerative\napplication value in articular cartilage defects in rats.\n  Methods: LIPUS was applied to stimulate cultured hUC-MSCs and C28/I2 cells in\nvitro. Immunofluorescence staining, qPCR analysis, and transcriptome sequencing\nwere used to detect mature cartilage-related markers of gene and protein\nexpression for a comprehensive evaluation of differentiation. Injured articular\ncartilage rat models were established for further hUC-MSC transplantation and\nLIPUS stimulation in vivo. Histopathology and H&E staining were used to\nevaluate the repair effects of the injured articular cartilage with LIPUS\nstimulation.\n  Results: The results showed that LIPUS stimulation with specific parameters\neffectively promoted the expression of mature cartilage-related genes and\nproteins, inhibited TNF-{\\alpha} gene expression in hUC-MSCs, and exhibited\nanti-inflammation in C28/I2 cells. In addition, the articular cartilage defects\nof rats were significantly repaired after hUC-MSC transplantation and LIPUS\nstimulation.\n  Conclusions: Taken together, LIPUS stimulation could realize articular\ncartilage regeneration based on hUC-MSC transplantation due to the inhibition\nof the TNF signaling pathway, which is of clinical value for the relief of\nosteoarthritis.\n", "doi": "10.1186/s13287-023-03296-6", "arxiv_id": "2112.13774", "pdf_urls": ["https://arxiv.org/pdf/2112.13774"], "github": [], "is_oa": true, "sources": ["open-arxiv"], "type": "journal", "journal_ref": "Stem Cell Res Ther 14, 93 (2023)", "categories": "physics.med-ph"}