{"id":"W3040123207","doi":"10.1093/infdis/jiaa358","title":"Predicting <i>Vibrio cholerae</i> Infection and Disease Severity Using Metagenomics in a Prospective Cohort Study","year":2020,"lang":"en","type":"article","venue":"The Journal of Infectious Diseases","topic":"Vibrio bacteria research studies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":38,"is_retracted":false,"has_abstract":true,"ca_institutions":"McGill University; McGill Genome Centre; Université de Montréal","funders":"National Institute of Allergy and Infectious Diseases; National Institutes of Health; Canada Research Chairs","keywords":"Metagenomics; Vibrio cholerae; Biology; Microbiome; Prevotella; Shotgun sequencing; Cholera vaccine; Deep sequencing; Microbiology; DNA sequencing; Gene; Genetics; Genome; 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":[0.0003867773,0.0001438719,0.0002359532,0.00005308848,0.0001667141,0.00005354409,0.00009842762,0.00002767617,0.000003673949],"category_scores_gemma":[0.001087257,0.0001061692,0.00007847687,0.0001627977,0.0001017285,0.00002580429,0.000209593,0.0001827133,4.820039e-7],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00006602819,"about_ca_system_score_gemma":0.0001864373,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0001333655,"about_ca_topic_score_gemma":0.0001035154,"domain_scores_codex":[0.9988706,0.0003033655,0.0002884088,0.0001724028,0.000194835,0.0001703567],"domain_scores_gemma":[0.999217,0.00003631723,0.0002139475,0.000131222,0.0001616839,0.0002398356],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"observational","study_design_gemma":"observational","study_design_scores_codex":[0.0006329253,0.000238002,0.9833565,0.00002855972,0.0003008938,0.00001542612,0.0004423178,0.001040194,0.0138104,7.087508e-7,0.00004047162,0.00009364488],"study_design_scores_gemma":[0.001189069,0.0006454706,0.9964851,0.0000188177,0.0002843726,0.00003477451,0.0002213252,0.0004155434,0.000503503,0.00004535608,0.00004829714,0.0001083554],"study_design_candidate":"observational","study_design_consensus":"observational","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9979973,0.000974124,0.0001893553,0.0001263496,0.00007229477,0.0005816132,0.0000192981,0.000009290611,0.00003038999],"genre_scores_gemma":[0.9988047,0.0006701627,0.00001147005,0.000154326,0.0003261502,0.00001128048,0.000002341099,0.00001637094,0.00000319459],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.0133069,"threshold_uncertainty_score":0.4329454,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01267356366815726,"score_gpt":0.2696178003353241,"score_spread":0.2569442366671668,"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."}}