{"id":"W1538285828","doi":"10.1371/journal.pone.0130902","title":"Identification of Candidate Adherent-Invasive E. coli Signature Transcripts by Genomic/Transcriptomic Analysis","year":2015,"lang":"en","type":"article","venue":"PLoS ONE","topic":"Escherichia coli research studies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":41,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of Toronto; Hospital for Sick Children","funders":"National Institute of Diabetes and Digestive and Kidney Diseases; University of Toronto; New York Genome Center","keywords":"Biology; Gene; Genome; In silico; Escherichia coli; Transcriptome; Genetics; Comparative genomics; Operon; Microbiology; Genomics; Gene expression; Molecular biology","routes":{"ca_aff":true,"ca_fund":true,"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":[0.0002336325,0.0001434492,0.0002977409,0.00008678174,0.00004796829,0.00001992312,0.0002548522,0.000127271,0.00001630453],"category_scores_gemma":[0.0001560173,0.0001435423,0.0001245252,0.0003164264,0.0001082337,0.000006026237,0.00004595608,0.0001128024,0.00000753391],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00003799266,"about_ca_system_score_gemma":0.0001420558,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00009664825,"about_ca_topic_score_gemma":0.0004692028,"domain_scores_codex":[0.99871,0.0001057777,0.0002855012,0.0003286049,0.000332123,0.0002380384],"domain_scores_gemma":[0.9990254,0.00001248348,0.0001202905,0.0003496418,0.0003584845,0.0001337205],"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":[0.0001531197,0.0004762428,0.006167327,0.00007248924,0.002935449,8.558192e-7,0.0002504464,0.00002240955,0.9870673,0.000006734314,0.002822065,0.00002559698],"study_design_scores_gemma":[0.0006576563,0.0002145225,0.003518934,0.00001450092,0.000825298,1.515642e-7,0.0002081468,0.0001728347,0.9937873,0.00002430104,0.0004192633,0.0001570411],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9943304,0.004209689,0.0003625041,0.0001913321,0.00002778732,0.0003361843,0.0003057463,0.00001172846,0.000224612],"genre_scores_gemma":[0.9970815,0.0009477413,0.0001767069,0.00006994185,0.00005615474,0.0000720367,0.0003761188,0.00001923166,0.001200597],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.006720086,"threshold_uncertainty_score":0.5853485,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.03923418288964401,"score_gpt":0.2547050291676583,"score_spread":0.2154708462780143,"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."}}