{"id":"W4380302915","doi":"10.1101/2023.06.08.23291055","title":"Genomic insights into the 2022–2023 <i>Vibrio cholerae</i> outbreak in Malawi","year":2023,"lang":"en","type":"preprint","venue":"medRxiv","topic":"Vibrio bacteria research studies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":6,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of British Columbia","funders":"Universiteit van die Vrystaat; Yale University; National Institute for Health and Care Research; Government of the United Kingdom; Bill and Melinda Gates Foundation","keywords":"Outbreak; Vibrio cholerae; Prophage; Serotype; Cholera; El Tor; Biology; Pandemic; Genotype; Phylogenetic tree; Population; Virology; Microbiology; Geography; Veterinary medicine; Coronavirus disease 2019 (COVID-19); Environmental health; Bacteria; Genetics; Medicine; Gene; Bacteriophage; Escherichia coli; Infectious disease (medical specialty)","routes":{"ca_aff":true,"ca_fund":false,"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":[0.0001516282,0.0001945809,0.0001176296,0.0003895307,0.0004598208,0.0007132242,0.0001019109,0.0003350321,0.001686227],"category_scores_gemma":[0.0003232947,0.0001201424,0.0002079914,0.000931347,0.00022672,0.0001784177,0.0004223567,0.0004752249,0.0003691125],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0005088024,"about_ca_system_score_gemma":0.0004934302,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.01432948,"about_ca_topic_score_gemma":0.01156604,"domain_scores_codex":[0.9999219,0.000009687041,0.000003281222,0.00002286822,0.00001004293,0.00003211153],"domain_scores_gemma":[0.999894,0.00002089521,0.00003859804,0.000008503433,0.00001793766,0.00002012031],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"observational","study_design_scores_codex":[0.000665574,0.0001350042,0.4540499,0.0004105828,0.0001258875,0.002737215,0.006129325,0.002380615,0.4962245,0.002208431,0.002863939,0.03206903],"study_design_scores_gemma":[0.000005170556,0.00004610726,0.9734099,0.0000428093,0.00002600525,0.0006541739,0.001751987,0.001032101,0.0118496,0.000272405,0.01090204,0.000007694413],"study_design_candidate":"observational","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.994404,0.0003844811,0.0007852418,0.000245686,0.000008039831,0.00001179838,0.002873174,0.00002480002,0.001262708],"genre_scores_gemma":[0.9919403,0.0004965058,0.001270592,0.0001670064,0.000013505,0.0000110498,0.005120517,0.00001660141,0.0009640008],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.01432948,"threshold_uncertainty_score":0.02849215,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.02558080996845807,"score_gpt":0.2881068948782686,"score_spread":0.2625260849098106,"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."}}