{"id":"W3005366639","doi":"10.1093/ecco-jcc/jjaa021","title":"A Pilot Integrative Analysis of Colonic Gene Expression, Gut Microbiota, and Immune Infiltration in Primary Sclerosing Cholangitis-Inflammatory Bowel Disease: Association of Disease With Bile Acid Pathways","year":2020,"lang":"en","type":"article","venue":"Journal of Crohn s and Colitis","topic":"Liver Diseases and Immunity","field":"Medicine","cited_by":141,"is_retracted":false,"has_abstract":true,"ca_institutions":"Toronto General Hospital; University of Toronto","funders":"Medical Research Council; Surgical Reconstruction and Microbiology Research Centre; University of Birmingham; Department of Health and Social Care; National Institute for Health and Care Research; UK Research and Innovation; Birmingham Biomedical Research Centre; University Hospitals Birmingham NHS Foundation Trust; Cancer Research UK; Wellcome Trust","keywords":"Inflammatory bowel disease; Primary sclerosing cholangitis; Transcriptome; Immune system; Medicine; Ulcerative colitis; Colitis; Gene expression profiling; Microbiome; Immunology; Internal medicine; Gene expression; Biology; Disease; Gene; Bioinformatics; Genetics","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":[],"consensus_categories":[],"category_scores_codex":[0.0001976683,0.0001151591,0.0004716856,0.0001899809,0.00005161254,0.00002920783,0.00005302497,0.00003228774,0.00002795342],"category_scores_gemma":[0.0001438172,0.00008722887,0.0001270439,0.0002953511,0.00008254666,0.0002702514,0.00003652832,0.000169891,1.029357e-7],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0001191091,"about_ca_system_score_gemma":0.0003816586,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00005114489,"about_ca_topic_score_gemma":0.00001377507,"domain_scores_codex":[0.9988761,0.0001144595,0.0005251915,0.0001156167,0.0002508956,0.0001177609],"domain_scores_gemma":[0.9985375,0.00006752031,0.0006804562,0.0001024117,0.0003532999,0.000258773],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"observational","study_design_gemma":"observational","study_design_scores_codex":[0.01502994,0.0004099162,0.6909087,0.000504079,0.000734682,0.00009340265,0.001796426,0.00003618986,0.2898542,0.00002955829,0.0001317418,0.0004711262],"study_design_scores_gemma":[0.002159829,0.0007592868,0.9871529,0.0008335353,0.001284807,0.00000422723,0.0003994265,0.0001455557,0.00714129,0.00002154055,0.00001475008,0.00008289756],"study_design_candidate":"observational","study_design_consensus":"observational","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9947051,0.00441217,0.00007565458,0.0003123475,0.00002081109,0.0002065331,0.0002380245,0.000003797057,0.00002553148],"genre_scores_gemma":[0.9983684,0.001188134,0.0001894846,0.0001340223,0.00004003969,0.000004560976,0.00005451797,0.000008725193,0.00001206429],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.2962441,"threshold_uncertainty_score":0.355709,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01055033549359998,"score_gpt":0.2190358864812079,"score_spread":0.2084855509876079,"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."}}