{"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":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.002802993,0.0006601067,0.0005698451,0.00079681,0.0007728474,0.001381555,0.0005895939,0.0009877068,0.0008488872],"category_scores_gemma":[0.003343895,0.0007049899,0.001853853,0.0008390525,0.0002982031,0.0004816515,0.0009904904,0.001344554,0.0001909389],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0005467161,"about_ca_system_score_gemma":0.0006376587,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.008743462,"about_ca_topic_score_gemma":0.008728506,"domain_scores_codex":[0.9989349,0.0004296883,0.00006789961,0.0003234574,0.0001024957,0.0001414669],"domain_scores_gemma":[0.9983902,0.0004093705,0.0003347923,0.0004069356,0.0001689569,0.0002897457],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"observational","study_design_gemma":"observational","study_design_scores_codex":[0.0005061086,0.00006278176,0.9962613,0.00001709722,0.0007502423,0.00007198664,0.00007428019,0.0001959949,0.0008953917,0.00003022483,0.0001720107,0.0009626827],"study_design_scores_gemma":[0.00003794286,0.0002988408,0.9949954,0.00002323862,0.000558617,0.0002050411,0.0003253658,0.002853387,0.0002982565,0.000108177,0.0002776072,0.00001818409],"study_design_candidate":"observational","study_design_consensus":"observational","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9979357,0.0002456967,0.0006528989,0.0001054284,0.00001566057,0.00002003331,0.0008678557,0.00001041668,0.000146358],"genre_scores_gemma":[0.9983141,0.000126956,0.0007726156,0.00004972098,0.000008711565,0.00001939399,0.0006089888,0.000008130671,0.00009134819],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.008743462,"threshold_uncertainty_score":0.01738513,"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."}}