diff --git a/paper-releases/pbisc-diffusion/updates/20261013T115045Z-figure-strengthening-154/diffusion/dataset/server_1/model8/presentations/2026-09-30--paper-summary--r00/data/strengthening_20261013/rare_literature/result.json b/paper-releases/pbisc-diffusion/updates/20261013T115045Z-figure-strengthening-154/diffusion/dataset/server_1/model8/presentations/2026-09-30--paper-summary--r00/data/strengthening_20261013/rare_literature/result.json new file mode 100644 index 0000000000000000000000000000000000000000..ade8af317eddc0696cf1ca7e72a628ccee55333f --- /dev/null +++ b/paper-releases/pbisc-diffusion/updates/20261013T115045Z-figure-strengthening-154/diffusion/dataset/server_1/model8/presentations/2026-09-30--paper-summary--r00/data/strengthening_20261013/rare_literature/result.json @@ -0,0 +1,537 @@ +{ + "schema": "pbisc.strengthening.rare-literature.v1", + "slides": [ + { + "kind": "content", + "key": "rare_literature_published_population_targets", + "role": "f5_original_paper_observed_gate", + "title": "Figure 5 targets begin with the source paper", + "section_label": "Fig. 5 \u00b7 Source-defined populations", + "layout": "full", + "keywords": [], + "figures": [ + "figures/strengthening_20261013/rare_literature/published_population_targets.png" + ], + "palette": "biological", + "footnote": "Ye: Fig. 5 proliferating pediatric monocytes. Imperial: Fig. 5 wave-2 steroid-associated monocytes; fine labels/timing still needed.", + "footnote_full": "Original-cohort retrospective analysis. No new generation, label inference or embedding fit. Literature targets are not automatically rare; rarity and identity require observed evidence. Ye: Fig. 5 proliferating pediatric monocytes. Imperial: Fig. 5 wave-2 steroid-associated monocytes; fine labels/timing still needed. [{\"cohort\": \"ye2026_sepsis\", \"citation\": \"Ye et al., Nature Immunology 2026\", \"doi\": \"10.1038/s41590-025-02345-x\", \"url\": \"https://www.nature.com/articles/s41590-025-02345-x\", \"figure\": \"Fig. 5a\\u2013f; validation Fig. 7f / Extended Data Fig. 9e\", \"population\": \"Mono_c06-CD14-MKI67\", \"kind\": \"Reported discrete proliferating monocyte subset; rarity must be measured locally\", \"setting\": \"Pediatric pulmonary sepsis (paper: within 48 h of onset); pediatric HC/ICU, abdominal sepsis and adults remain controls.\", \"markers\": [\"CD14\", \"MKI67\", \"STMN1\", \"MPO\", \"ELANE\"], \"negative_markers\": [], \"interpretation\": \"MKI67/STMN1/MPO/ELANE jointly support the published proliferative program in a CD14 monocyte context. PCLAF is not required by this original Fig. 5 definition.\", \"gate\": \"No fine-cluster labels found in 133 audited canonical obs schemas or the paired table. Marker co-detection is not a Mono_c06 cluster assignment.\", \"pdf\": \"/home/sj_server_1/PBISC/paper-release-20260928/reference-papers/paired-cohorts/Single-cell multi-omic landscape reveals anatomical-specific immune features in adult and pediatric sepsis.pdf\", \"all_paired_samples\": 85, \"identity_passed_samples\": 82, \"identity_passed_donors\": 82, \"legacy_cache_genes\": 73, \"legacy_cache_path\": \"/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/rare_states_paired_20261008/work/ye2026_sepsis/draw0/lora5.npz\", \"observed_path\": \"/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/ye2026_sepsis/cells_obs.parquet\", \"observed_author_labels\": {\"\": 610713}, \"observed_full_panel_path\": \"/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/ye2026_sepsis/cells_panel6k.npz\", \"wave_counts\": {}, \"sex_by_group\": {}, \"available_cache_markers\": [\"MKI67\", \"MPO\", \"ELANE\"], \"missing_cache_markers\": [\"CD14\", \"STMN1\"]}, {\"cohort\": \"imperial_eskd\", \"citation\": \"Stephenson et al., Cell Genomics 2025\", \"doi\": \"10.1016/j.xgen.2025.100918\", \"url\": \"https://pmc.ncbi.nlm.nih.gov/articles/PMC12366655/\", \"figure\": \"Fig. 5A\\u2013G (especially 5C\\u2013E)\", \"population\": \"Dexamethasone-related monocytes\", \"kind\": \"Reported treatment-associated discrete subset; not automatically rare\", \"setting\": \"Wave 2 COVID-positive patients receiving glucocorticoids; align each blood visit to treatment start.\", \"markers\": [\"CD163\", \"ADAMTS2\", \"SLC1A3\", \"SESN1\", \"FPR1\", \"MTSS1\", \"MFGE8\", \"MRC1\"], \"negative_markers\": [\"JUN\", \"CXCL8\", \"HLA-DRA\", \"HLA-DRB5\"], \"interpretation\": \"The paper contrasts an anti-inflammatory/phagocytic program with lower inflammatory and antigen-presentation expression. Fig. 3 HLA-II suppression is a program, not a rare-cell identity.\", \"gate\": \"Paired metadata include wave 2, but the available author labels collapse these cells into broad monocytes. Treatment dates and fine labels must be joined before frequency recovery.\", \"pdf\": \"/home/sj_server_1/PBISC/paper-release-20260928/reference-papers/paired-cohorts/Stephenson2025_CellGenom_temporal_multiomics_COVID19_ESKD.pdf\", \"all_paired_samples\": 172, \"identity_passed_samples\": 158, \"identity_passed_donors\": 58, \"legacy_cache_genes\": 73, \"legacy_cache_path\": \"/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/rare_states_paired_20261008/work/imperial_eskd/draw0/lora5.npz\", \"observed_path\": \"/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/imperial_eskd/cells_obs.parquet\", \"observed_author_labels\": {\"T CD4 Helper\": 85235, \"NK\": 77242, \"T CD8 CTL\": 70657, \"CD14mono\": 53967, \"T CD4 Naive\": 49943, \"B_naive\": 33633, \"CD16mono\": 29056, \"T CD8 CM\": 19962, \"T CD8 Naive\": 18113, \"T CD4 CTL\": 17209, \"B_switched_mem\": 9223, \"T reg\": 9176, \"NK CD56 bright\": 8610, \"Int.mono\": 7136, \"DC2\": 5972, \"NKT\": 4647, \"DC3\": 4318, \"T g/d\": 3911, \"pDC\": 3034, \"B_non-switched_mem\": 2815, \"RBC\": 2604, \"Platelet\": 2576, \"B_ASC_IgA\": 2538, \"B_CD11c\": 2108, \"MAIT\": 1984, \"T CD8 EM\": 1860, \"B_ASC_dividing\": 1785, \"B_ASC_IgG\": 1182, \"HSPC\": 1004, \"DC1\": 754, \"B_ASC_IgM\": 499, \"T CD4 cycling\": 447, \"T CD8 EMRA\": 400, \"ASDC\": 231, \"ILC\": 147, \"B_ASC_other\": 36}, \"observed_full_panel_path\": \"/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/imperial_eskd/cells_panel6k.npz\", \"wave_counts\": {\"w2\": 83, \"w1\": 75, \"w1|w2\": 14}, \"sex_by_group\": {}, \"available_cache_markers\": [\"CD163\", \"HLA-DRA\"], \"missing_cache_markers\": [\"ADAMTS2\", \"SLC1A3\", \"SESN1\", \"FPR1\", \"MTSS1\", \"MFGE8\", \"MRC1\", \"JUN\", \"CXCL8\", \"HLA-DRB5\"]}]", + "notes": "Original-cohort retrospective analysis. No new generation, label inference or embedding fit. Literature targets are not automatically rare; rarity and identity require observed evidence. Ye: Fig. 5 proliferating pediatric monocytes. Imperial: Fig. 5 wave-2 steroid-associated monocytes; fine labels/timing still needed. [{\"cohort\": \"ye2026_sepsis\", \"citation\": \"Ye et al., Nature Immunology 2026\", \"doi\": \"10.1038/s41590-025-02345-x\", \"url\": \"https://www.nature.com/articles/s41590-025-02345-x\", \"figure\": \"Fig. 5a\\u2013f; validation Fig. 7f / Extended Data Fig. 9e\", \"population\": \"Mono_c06-CD14-MKI67\", \"kind\": \"Reported discrete proliferating monocyte subset; rarity must be measured locally\", \"setting\": \"Pediatric pulmonary sepsis (paper: within 48 h of onset); pediatric HC/ICU, abdominal sepsis and adults remain controls.\", \"markers\": [\"CD14\", \"MKI67\", \"STMN1\", \"MPO\", \"ELANE\"], \"negative_markers\": [], \"interpretation\": \"MKI67/STMN1/MPO/ELANE jointly support the published proliferative program in a CD14 monocyte context. PCLAF is not required by this original Fig. 5 definition.\", \"gate\": \"No fine-cluster labels found in 133 audited canonical obs schemas or the paired table. 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MKI67/STMN1 mean: pulmonary 2.33%, abdominal 4.10%; pulmonary specificity is not reproduced.", + "footnote_full": "Original-cohort retrospective analysis. No new generation, label inference or embedding fit. Literature targets are not automatically rare; rarity and identity require observed evidence. Native-depth diagnostic, not Mono_c06 identity. MKI67/STMN1 mean: pulmonary 2.33%, abdominal 4.10%; pulmonary specificity is not reproduced. {\"n_cells\": 610713, \"input_genes\": 6000, \"retained_genes\": 5, \"csr_entries_streamed\": 255556515, \"max_entries_per_block\": 1000000, \"no_full_sparse_or_dense_matrix_loaded\": true, \"identity_passed_samples\": 82, \"analyzed_samples\": 82, \"analyzed_monocytes\": 111269, \"all_five_genes_measured_in_all_source_samples\": true, \"labels_npz_rows_exact\": true, \"author_fine_labels_present\": false, \"source_sha256\": \"c814b53d04ffdbe8e257f1fb35df80e7945479db95a924774522b9a967745280\", \"limitations\": [\"Native depth; marker dropout and depth differ between donors.\", \"Parent uses the frozen AIFI label; published Mono_c06 fine labels are absent.\", \"Co-detection patterns are diagnostics, not author-cluster calls.\", \"This is reuse of the original cohort, not independent replication.\"], \"no_new_inference\": true, \"no_embedding_fit\": true, \"observed_pattern_comparison\": {\"pattern\": \"MKI67+STMN1\", \"pediatric_pulmonary_mean_percent\": 2.331039105701644, \"pediatric_abdominal_mean_percent\": 4.103247268955951, \"pulmonary_specificity_reproduced\": false}, \"author_label_inventory\": \"/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/data/strengthening_20261013/rare_literature/ye_author_label_inventory.json\"}", + "notes": "Original-cohort retrospective analysis. No new generation, label inference or embedding fit. Literature targets are not automatically rare; rarity and identity require observed evidence. Native-depth diagnostic, not Mono_c06 identity. MKI67/STMN1 mean: pulmonary 2.33%, abdominal 4.10%; pulmonary specificity is not reproduced. {\"n_cells\": 610713, \"input_genes\": 6000, \"retained_genes\": 5, \"csr_entries_streamed\": 255556515, \"max_entries_per_block\": 1000000, \"no_full_sparse_or_dense_matrix_loaded\": true, \"identity_passed_samples\": 82, \"analyzed_samples\": 82, \"analyzed_monocytes\": 111269, \"all_five_genes_measured_in_all_source_samples\": true, \"labels_npz_rows_exact\": true, \"author_fine_labels_present\": false, \"source_sha256\": \"c814b53d04ffdbe8e257f1fb35df80e7945479db95a924774522b9a967745280\", \"limitations\": [\"Native depth; marker dropout and depth differ between donors.\", \"Parent uses the frozen AIFI label; published Mono_c06 fine labels are absent.\", \"Co-detection patterns are diagnostics, not author-cluster calls.\", \"This is reuse of the original cohort, not independent replication.\"], \"no_new_inference\": true, \"no_embedding_fit\": true, \"observed_pattern_comparison\": {\"pattern\": \"MKI67+STMN1\", \"pediatric_pulmonary_mean_percent\": 2.331039105701644, \"pediatric_abdominal_mean_percent\": 4.103247268955951, \"pulmonary_specificity_reproduced\": false}, \"author_label_inventory\": \"/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/data/strengthening_20261013/rare_literature/ye_author_label_inventory.json\"}", + "sources": "https://www.nature.com/articles/s41590-025-02345-x; https://pmc.ncbi.nlm.nih.gov/articles/PMC12366655/; https://pmc.ncbi.nlm.nih.gov/articles/PMC9271053/; https://pmc.ncbi.nlm.nih.gov/articles/PMC12049347/" + }, + { + "kind": "content", + "key": "rare_literature_published_program_boundaries", + "role": "f5_original_paper_observed_gate", + "title": "A transcriptional program is not automatically a rare population", + "section_label": "Fig. 5 \u00b7 Source-defined populations", + "layout": "full", + "keywords": [], + "figures": [ + "figures/strengthening_20261013/rare_literature/published_program_boundaries.png" + ], + "palette": "biological", + "footnote": "Giroux: pre-seroconversion RNA/regulon states and sex imbalance. Ji: common-cell-type DE/TCR changes; no paper-defined rare identity established.", + "footnote_full": "Original-cohort retrospective analysis. No new generation, label inference or embedding fit. Literature targets are not automatically rare; rarity and identity require observed evidence. Giroux: pre-seroconversion RNA/regulon states and sex imbalance. Ji: common-cell-type DE/TCR changes; no paper-defined rare identity established. [{\"cohort\": \"giroux2022\", \"citation\": \"Giroux et al., Scientific Reports 2022\", \"doi\": \"10.1038/s41598-022-15668-8\", \"url\": \"https://pmc.ncbi.nlm.nih.gov/articles/PMC9271053/\", \"figure\": \"Fig. 5A\\u2013F; Supplementary Tables S8/S9\", \"population\": \"IgG-negative CD14 monocyte clusters 2/4 (mild) and 7 (moderate)\", \"kind\": \"Transcriptomic/regulon states with epigenetic corroboration; rarity not established\", \"setting\": \"Before IgG seroconversion, mild versus moderate outpatients; local severe label must be checked against the paper\\u2019s moderate definition.\", \"markers\": [\"CD14\", \"IRF7\", \"IRF1\", \"STAT1\", \"CEBPB\", \"KLF3\", \"CCR2\"], \"negative_markers\": [], \"interpretation\": \"IRF7/IRF1/STAT1 versus CEBPB/KLF3 are regulatory-program findings, not an exact RNA-only positivity gate. scRNA clusters connect to scATAC states.\", \"gate\": \"No author fine labels locally; IRF1/KLF3 are outside the saved 6k panel. Align serostatus, longitudinal donors and marked sex imbalance; no exact rare-cluster claim.\", \"xml\": \"/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/data/strengthening_20261013/rare_literature/Giroux2022_PMC9271053.xml\", \"all_paired_samples\": 26, \"identity_passed_samples\": 24, \"identity_passed_donors\": 9, \"legacy_cache_genes\": 73, \"legacy_cache_path\": \"/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/rare_states_paired_20261008/work/giroux2022/draw0/lora5.npz\", \"observed_path\": \"/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/giroux2022/cells_obs.parquet\", \"observed_author_labels\": {\"\": 276615}, \"observed_full_panel_path\": \"/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/giroux2022/cells_panel6k.npz\", \"wave_counts\": {}, \"sex_by_group\": {\"FEMALE\": {\"mild\": 0, \"severe\": 11}, \"MALE\": {\"mild\": 13, \"severe\": 2}}, \"available_cache_markers\": [], \"missing_cache_markers\": [\"CD14\", \"IRF7\", \"IRF1\", \"STAT1\", \"CEBPB\", \"KLF3\", \"CCR2\"]}, {\"cohort\": \"ji2025_chili\", \"citation\": \"Ji et al., Cancer Immunology, Immunotherapy 2025\", \"doi\": \"10.1007/s00262-025-04033-z\", \"url\": \"https://pmc.ncbi.nlm.nih.gov/articles/PMC12049347/\", \"figure\": \"Fig. 2 (TCR clonality); Fig. 4A/B and Table 2 (cell-type DE/programs)\", \"population\": \"CD8 TEM, CD8 naive, CD4 TCM and CD16 monocyte programs\", \"kind\": \"Common cell-type expression changes; no specific rare subset established in the original paper\", \"setting\": \"Liver-injury timepoint TOL versus pretreatment BC / control AC; FU1 is follow-up and must not be silently pooled with TOL.\", \"markers\": [], \"negative_markers\": [], \"interpretation\": \"Original HuBMAP-type labels survive locally. DEG counts and pathways can be reproduced as Figure 4 evidence; TCR clonality cannot be recovered from generated 6k expression alone.\", \"gate\": \"Do not substitute a generic cycling/plasmablast rule for the paper\\u2019s main finding. Select a genuinely paper-defined rare target only if supplementary evidence supports one.\", \"pdf\": \"/home/sj_server_1/PBISC/paper-release-20260928/reference-papers/paired-cohorts/Ji2025_CancerImmunolImmunother_checkpoint_inhibitor_liver_injury.pdf\", \"all_paired_samples\": 40, \"identity_passed_samples\": 33, \"identity_passed_donors\": 20, \"legacy_cache_genes\": 72, \"legacy_cache_path\": \"/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/rare_states_paired_20261008/work/ji2025_chili/draw0/lora5.npz\", \"observed_path\": \"/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/ji2025_chili/cells_obs.parquet\", \"observed_author_labels\": {\"CD4 TCM\": 48811, \"CD14 Mono\": 38304, \"NK\": 19796, \"CD8 TEM\": 15575, \"CD16 Mono\": 6512, \"B naive\": 4822, \"CD8 Naive\": 2736, \"CD4 Naive\": 2559, \"B intermediate\": 2372, \"Platelet\": 2165, \"Treg\": 2001, \"cDC2\": 1259, \"CD8 TCM\": 1134, \"NK_CD56bright\": 1010, \"B memory\": 878, \"Plasmablast\": 852, \"MAIT\": 801, \"HSPC\": 724, \"CD4 TEM\": 600, \"pDC\": 582, \"NK Proliferating\": 358, \"dnT\": 314, \"Eryth\": 230, \"CD4 CTL\": 80, \"ILC\": 68, \"cDC1\": 55, \"ASDC\": 50, \"CD8 Proliferating\": 28, \"gdT\": 14, \"CD4 Proliferating\": 8}, \"observed_full_panel_path\": \"/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/ji2025_chili/cells_panel6k.npz\", \"wave_counts\": {}, \"sex_by_group\": {}, \"available_cache_markers\": [], \"missing_cache_markers\": []}]", + "notes": "Original-cohort retrospective analysis. No new generation, label inference or embedding fit. Literature targets are not automatically rare; rarity and identity require observed evidence. Giroux: pre-seroconversion RNA/regulon states and sex imbalance. Ji: common-cell-type DE/TCR changes; no paper-defined rare identity established. 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Align serostatus, longitudinal donors and marked sex imbalance; no exact rare-cluster claim.",,26,24,9,73,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/rare_states_paired_20261008/work/giroux2022/draw0/lora5.npz,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/giroux2022/cells_obs.parquet,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/giroux2022/cells_panel6k.npz,,CD14; IRF7; IRF1; STAT1; CEBPB; KLF3; CCR2,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/data/strengthening_20261013/rare_literature/Giroux2022_PMC9271053.xml +ji2025_chili,"Ji et al., Cancer Immunology, Immunotherapy 2025",10.1007/s00262-025-04033-z,https://pmc.ncbi.nlm.nih.gov/articles/PMC12049347/,Fig. 2 (TCR clonality); Fig. 4A/B and Table 2 (cell-type DE/programs),"CD8 TEM, CD8 naive, CD4 TCM and CD16 monocyte programs",Common cell-type expression changes; no specific rare subset established in the original paper,Liver-injury timepoint TOL versus pretreatment BC / control AC; FU1 is follow-up and must not be silently pooled with TOL.,,,Original HuBMAP-type labels survive locally. 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PCLAF is not required by this original Fig. 5 definition.", + "gate": "No fine-cluster labels found in 133 audited canonical obs schemas or the paired table. Marker co-detection is not a Mono_c06 cluster assignment.", + "pdf": "/home/sj_server_1/PBISC/paper-release-20260928/reference-papers/paired-cohorts/Single-cell multi-omic landscape reveals anatomical-specific immune features in adult and pediatric sepsis.pdf", + "all_paired_samples": 85, + "identity_passed_samples": 82, + "identity_passed_donors": 82, + "legacy_cache_genes": 73, + "legacy_cache_path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/rare_states_paired_20261008/work/ye2026_sepsis/draw0/lora5.npz", + "observed_path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/ye2026_sepsis/cells_obs.parquet", + "observed_author_labels": { + "": 610713 + }, + "observed_full_panel_path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/ye2026_sepsis/cells_panel6k.npz", + "wave_counts": {}, + "sex_by_group": {}, + "available_cache_markers": [ + "MKI67", + "MPO", + "ELANE" + ], + "missing_cache_markers": [ + "CD14", + "STMN1" + ] + }, + { + "cohort": "imperial_eskd", + "citation": "Stephenson et al., Cell Genomics 2025", + "doi": "10.1016/j.xgen.2025.100918", + "url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC12366655/", + "figure": "Fig. 5A\u2013G (especially 5C\u2013E)", + "population": "Dexamethasone-related monocytes", + "kind": "Reported treatment-associated discrete subset; not automatically rare", + "setting": "Wave 2 COVID-positive patients receiving glucocorticoids; align each blood visit to treatment start.", + "markers": [ + "CD163", + "ADAMTS2", + "SLC1A3", + "SESN1", + "FPR1", + "MTSS1", + "MFGE8", + "MRC1" + ], + "negative_markers": [ + "JUN", + "CXCL8", + "HLA-DRA", + "HLA-DRB5" + ], + "interpretation": "The paper contrasts an anti-inflammatory/phagocytic program with lower inflammatory and antigen-presentation expression. 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