{"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":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0003777518,0.0001894585,0.000405168,0.00002960684,0.00005969623,0.0000389033,0.0002364078,0.0001459382,0.0001789778],"category_scores_gemma":[0.0003683091,0.00006875971,0.00007552871,0.0002121009,0.0002193266,0.0002197305,0.0001433198,0.00009809183,0.0000496651],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00005588297,"about_ca_system_score_gemma":0.00002278117,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0001709698,"about_ca_topic_score_gemma":0.0006503733,"domain_scores_codex":[0.9984646,0.0002458148,0.0003988435,0.000418278,0.0001130934,0.0003593423],"domain_scores_gemma":[0.9980885,0.001459074,0.0001883314,0.0001008087,0.00006269555,0.0001005538],"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":[0.00008036228,0.00002947961,0.1559905,0.00001016975,0.00001692455,0.00003459735,0.0003849252,0.000003045627,0.8406537,0.00004797638,0.0002163778,0.002531898],"study_design_scores_gemma":[0.0004927159,0.0008595313,0.919677,0.0003794551,0.00001747342,0.00004463127,0.002398923,0.000008879214,0.05695167,0.001450503,0.01731782,0.0004014438],"study_design_candidate":"observational","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9942484,0.001393535,0.00001206573,0.003607603,0.0001595074,0.0002227642,0.00004590326,0.0000249003,0.0002852801],"genre_scores_gemma":[0.9955302,0.002828995,0.0001179243,0.0004513375,0.0001352727,0.00001598487,0.00002217577,0.000001970166,0.0008961218],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.7837021,"threshold_uncertainty_score":0.280394,"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."}}