{"id":"W4200341764","doi":"10.1101/2021.12.16.473094","title":"Genomic characteristics of recently recognized <i>Vibrio cholerae</i> El Tor lineages associated with cholera in Bangladesh, 1991-2017","year":2021,"lang":"en","type":"preprint","venue":"bioRxiv (Cold Spring Harbor Laboratory)","topic":"Vibrio bacteria research studies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":2,"is_retracted":false,"has_abstract":true,"ca_institutions":"","funders":"Foreign, Commonwealth and Development Office; Global Affairs Canada; Japan Agency for Medical Research and Development; International Centre for Diarrhoeal Disease Research, Bangladesh; Foreign and Commonwealth Office; Styrelsen för Internationellt Utvecklingssamarbete","keywords":"Vibrio cholerae; Biology; Genetics; Genome; Cholera; El Tor; Lineage (genetic); Single-nucleotide polymorphism; Comparative genomics; Gene; Genomics; Virology; Genotype","routes":{"ca_aff":false,"ca_fund":true,"ca_venue":false,"about_ca":false,"invisible_to_affiliation_only":true},"retraction":null,"screen":null,"direct_labels":[],"prediction":{"model_version":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0001274939,0.0002036517,0.0002062592,0.001208015,0.000357781,0.0004577399,0.0001923968,0.0002011228,0.002134473],"category_scores_gemma":[0.0004022854,0.0001620537,0.0002234409,0.001592943,0.0002609043,0.0001281576,0.0003728905,0.0002221491,0.0004903404],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0005030658,"about_ca_system_score_gemma":0.0002465359,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.01912815,"about_ca_topic_score_gemma":0.03078407,"domain_scores_codex":[0.999816,0.00001309124,0.00001766352,0.00006354816,0.00002708041,0.00006268662],"domain_scores_gemma":[0.9995945,0.00003804082,0.0001576894,0.00001978088,0.00008577064,0.0001042512],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"observational","study_design_gemma":"observational","study_design_scores_codex":[0.0003606657,0.00001760041,0.9688325,0.00004807819,0.00003773988,0.0003030902,0.0006289075,0.00008378734,0.02564408,0.00006435499,0.0004249338,0.003554307],"study_design_scores_gemma":[0.000002200206,0.00001700516,0.9989126,0.000004717589,0.00000561521,0.0001151813,0.0004092077,0.00002136802,0.000185152,0.000006906102,0.0003177208,0.000002436417],"study_design_candidate":"observational","study_design_consensus":"observational","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9966682,0.0001225497,0.00004636555,0.00001991105,0.000002583196,0.000006225778,0.002533666,0.000003555232,0.00059706],"genre_scores_gemma":[0.9953091,0.0001348024,0.00006647407,0.0000165533,0.000002825206,0.00001002202,0.003991157,0.000004586361,0.0004645075],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.01912815,"threshold_uncertainty_score":0.0380336,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01461455049406452,"score_gpt":0.2381660415186802,"score_spread":0.2235514910246157,"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."}}