{"id":"W3122917998","doi":"10.1038/s41590-020-00836-7","title":"Gut CD4+ T cell phenotypes are a continuum molded by microbes, not by TH archetypes","year":2021,"lang":"en","type":"article","venue":"Nature Immunology","topic":"Immune Cell Function and Interaction","field":"Immunology and Microbiology","cited_by":181,"is_retracted":false,"has_abstract":false,"ca_institutions":"Vector Institute; Canadian Institute for Advanced Research; University of British Columbia","funders":"Boehringer Ingelheim Fonds; National Institute of General Medical Sciences; Harvard Stem Cell Institute; Harvard University; National Institute of Allergy and Infectious Diseases; Division of Intramural Research, National Institute of Allergy and Infectious Diseases; U.S. Department of Health and Human Services","keywords":"Biology; Chromatin; GATA3; Transcriptome; Transcription factor; Cell biology; T cell; T helper cell; Effector; Immunology; Genetics; Gene expression; Gene; Immune system","routes":{"ca_aff":true,"ca_fund":false,"ca_venue":false,"about_ca":false,"invisible_to_affiliation_only":false},"retraction":null,"screen":null,"direct_labels":[],"prediction":{"model_version":"codex-gemma-dda1882f352a","candidate_categories":["metaepi_narrow","research_integrity","insufficient_payload"],"consensus_categories":["research_integrity","insufficient_payload"],"category_scores_codex":[0.0001667371,0.0003922202,0.0005640786,0.0001250537,0.0002868595,0.00004254742,0.0003775393,0.001723647,0.004623549],"category_scores_gemma":[0.0002227403,0.0003751868,0.0002186417,0.0002353097,0.0002706472,0.0001533383,0.0001849851,0.002408637,0.002152264],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0001067408,"about_ca_system_score_gemma":0.0001013846,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00008588067,"about_ca_topic_score_gemma":0.0000511463,"domain_scores_codex":[0.9976502,0.0004988502,0.0004687174,0.0006687279,0.00005582658,0.0006576617],"domain_scores_gemma":[0.9984969,0.0002384556,0.0003152326,0.0005934078,0.0003287484,0.00002721998],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"bench_or_experimental","study_design_scores_codex":[0.0003178411,0.0002426336,0.0001394244,0.00001189,0.0002312977,0.00000692573,0.0001047367,1.589281e-7,0.5976574,0.0001176997,0.400216,0.0009540259],"study_design_scores_gemma":[0.00120636,0.00009310212,0.0006663383,0.00001765358,0.00003872391,0.0001225663,0.0003003998,4.074747e-7,0.5019343,0.00002538359,0.4953862,0.000208532],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.6434832,0.3051427,0.0003182866,0.006555818,0.02269556,0.0005246386,0.0002731168,0.0005091134,0.0204976],"genre_scores_gemma":[0.8134945,0.001283854,0.00007480963,0.003845322,0.00006616449,0.00002879779,0.002022492,0.00005073538,0.1791333],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.3038588,"threshold_uncertainty_score":0.9998928,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.003819736690432212,"score_gpt":0.2069041671001944,"score_spread":0.2030844304097622,"validation_status":"score_only:v0-immature-baseline","note":"Baseline scores from an immature model (maturity gate not passed). Scores rank; they never assert a category."}}