{"id":"W2507521757","doi":"10.1128/mbio.00527-16","title":"What’s in a Name? Species-Wide Whole-Genome Sequencing Resolves Invasive and Noninvasive Lineages of Salmonella enterica Serotype Paratyphi B","year":2016,"lang":"en","type":"article","venue":"mBio","topic":"Salmonella and Campylobacter epidemiology","field":"Agricultural and Biological Sciences","cited_by":40,"is_retracted":false,"has_abstract":true,"ca_institutions":"Public Health Agency of Canada","funders":"Wellcome; Medical Research Council; Agence Nationale de la Recherche; Biotechnology and Biological Sciences Research Council; Cardiff University; Wellcome Trust","keywords":"Serotype; Salmonella enterica; Salmonella; Biology; Context (archaeology); Virology; Population; Microbiology; Genomics; Disease; Genome; Genetics; Medicine; Gene; Bacteria","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":[0.003145466,0.0006184402,0.0007427156,0.001102004,0.001357358,0.005061511,0.0009239435,0.003324487,0.003880519],"category_scores_gemma":[0.009360814,0.0003478402,0.000690607,0.001168872,0.00215942,0.005155251,0.001294951,0.003150647,0.001930499],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0007832496,"about_ca_system_score_gemma":0.001343873,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.001478601,"about_ca_topic_score_gemma":0.003084874,"domain_scores_codex":[0.9985663,0.000275186,0.0001053775,0.0004838041,0.0003307887,0.0002385118],"domain_scores_gemma":[0.9941701,0.001474739,0.0009552622,0.000604337,0.00143853,0.001357099],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"design_other","study_design_gemma":"observational","study_design_scores_codex":[0.001432083,0.0003959751,0.1616344,0.003449979,0.00106317,0.001888601,0.003265127,0.002069337,0.1950374,0.01475911,0.1871568,0.4278481],"study_design_scores_gemma":[0.000137852,0.000932348,0.2307871,0.00371981,0.0008701216,0.005198303,0.01644368,0.005002443,0.0301663,0.03805495,0.668183,0.0005040644],"study_design_candidate":"observational","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.4056647,0.1693107,0.04756204,0.2985932,0.04234614,0.0001936398,0.008586351,0.002058594,0.02568465],"genre_scores_gemma":[0.6588253,0.06868243,0.05227115,0.1792513,0.02122026,0.0001975756,0.006757055,0.001187661,0.0116072],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.005061511,"threshold_uncertainty_score":0.01663506,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.03863298440930966,"score_gpt":0.2323028703718559,"score_spread":0.1936698859625463,"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."}}