{"id":"W3195620685","doi":"10.1128/msystems.00889-21","title":"A Combination of Metagenomic and Cultivation Approaches Reveals Hypermutator Phenotypes within Vibrio cholerae-Infected Patients","year":2021,"lang":"en","type":"article","venue":"mSystems","topic":"Vibrio bacteria research studies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":16,"is_retracted":false,"has_abstract":true,"ca_institutions":"McGill Genome Centre; Université de Montréal; McGill University","funders":"National Institute of Allergy and Infectious Diseases; Canadian Institutes of Health Research; Fogarty International Center; National Institutes of Health; Government of Canada","keywords":"Vibrio cholerae; Biology; Metagenomics; Nonsynonymous substitution; Cholera; Genome; Genetics; Whole genome sequencing; Asymptomatic carrier; DNA sequencing; Microbiology; Gene; Virology; Asymptomatic; Medicine; Bacteria","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":[0.0001860773,0.0001049053,0.0001978621,0.000035553,0.00005858376,0.00002937196,0.00005606598,0.00007580651,0.000002813232],"category_scores_gemma":[0.000281993,0.00009558789,0.00003688536,0.00009633388,0.00005297044,0.000006868418,0.0001036129,0.00004341501,0.000002226926],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00002015952,"about_ca_system_score_gemma":0.00004561094,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00002502139,"about_ca_topic_score_gemma":0.00001631817,"domain_scores_codex":[0.999094,0.0001568802,0.0002432069,0.0002487822,0.0001353593,0.0001217442],"domain_scores_gemma":[0.999411,0.0000145985,0.0001402505,0.0001808915,0.0002138828,0.00003935708],"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":[0.00003502568,0.00009018685,0.04858967,0.0001519577,0.0001255479,5.771179e-7,0.000266402,0.000009207384,0.9502192,0.0001221554,0.00009065802,0.0002994175],"study_design_scores_gemma":[0.001459582,0.0002145151,0.2597817,0.00006104734,0.00003205406,0.00000490528,0.0002536896,0.0001646805,0.7368213,0.00002969179,0.001003448,0.000173423],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9985684,0.0005447637,0.0001133012,0.00004007358,0.00009670799,0.0002722548,0.00003282515,0.00000796004,0.0003237814],"genre_scores_gemma":[0.9990504,0.00003681688,0.0002359339,0.00001528039,0.00005423628,0.00003057065,0.0003020203,0.000014093,0.0002606763],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.2133979,"threshold_uncertainty_score":0.3897961,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.02401376363803187,"score_gpt":0.241802595847384,"score_spread":0.2177888322093521,"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."}}