{"id":"W2744747386","doi":"10.1097/mib.0000000000001208","title":"Integrated Analysis of Biopsies from Inflammatory Bowel Disease Patients Identifies SAA1 as a Link Between Mucosal Microbes with TH17 and TH22 Cells","year":2017,"lang":"en","type":"article","venue":"Inflammatory Bowel Diseases","topic":"Gut microbiota and health","field":"Biochemistry, Genetics and Molecular Biology","cited_by":40,"is_retracted":false,"has_abstract":true,"ca_institutions":"","funders":"National Institute of Dental and Craniofacial Research; National Institute of Diabetes and Digestive and Kidney Diseases; National Institute of Allergy and Infectious Diseases; National Cancer Institute; National Institutes of Health; York University; Doris Duke Charitable Foundation; U.S. Department of Veterans Affairs","keywords":"Inflammatory bowel disease; Transcriptome; Immunology; Crohn's disease; Disease; Biology; Medicine; Pathology; Gene expression; Gene; Genetics","routes":{"ca_aff":false,"ca_fund":true,"ca_venue":false,"about_ca":false,"invisible_to_affiliation_only":true},"retraction":null,"screen":null,"direct_labels":[],"prediction":{"model_version":"codex-gemma-dda1882f352a","candidate_categories":["metaepi_narrow"],"consensus_categories":[],"category_scores_codex":[0.000104588,0.0004172109,0.0004759723,0.0002296012,0.0004433548,0.0002223661,0.0005347204,0.0001951346,0.00004439318],"category_scores_gemma":[0.00018741,0.0003543058,0.0002580493,0.00008782761,0.0007263306,0.00005166963,0.000352666,0.0001377088,0.00001536291],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00002597621,"about_ca_system_score_gemma":0.0003785582,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0003238518,"about_ca_topic_score_gemma":0.0005193308,"domain_scores_codex":[0.9980178,0.000118695,0.0005397773,0.0006800932,0.0002513615,0.0003922888],"domain_scores_gemma":[0.9974241,0.00004664329,0.0005782561,0.001127831,0.0003604001,0.0004627763],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"observational","study_design_gemma":"observational","study_design_scores_codex":[0.0005789339,0.00013707,0.9213925,0.0002083255,0.001293546,0.00003420255,0.0001683594,0.00002173683,0.07497117,0.000009276278,0.0007909122,0.0003939639],"study_design_scores_gemma":[0.001421886,0.0001089429,0.9741868,0.0001349259,0.001644279,3.706566e-7,0.0001580885,0.00002767432,0.02054358,0.00005745133,0.001294183,0.0004218595],"study_design_candidate":"observational","study_design_consensus":"observational","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9948485,0.001230021,0.00001684167,0.0001322086,0.0001266206,0.0003748554,0.003184586,0.00003537173,0.0000509222],"genre_scores_gemma":[0.9969558,0.0004527179,0.00007114714,0.0001323412,0.0002238323,0.00002972428,0.001922481,0.0000461415,0.0001658887],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.0544276,"threshold_uncertainty_score":0.9998909,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.00648686759741523,"score_gpt":0.2362822075539998,"score_spread":0.2297953399565845,"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."}}