{"id":"W3115825159","doi":"10.1093/molbev/msaa323","title":"Genome Reduction Is Associated with Bacterial Pathogenicity across Different Scales of Temporal and Ecological Divergence","year":2020,"lang":"en","type":"article","venue":"Molecular Biology and Evolution","topic":"Streptococcal Infections and Treatments","field":"Medicine","cited_by":111,"is_retracted":false,"has_abstract":true,"ca_institutions":"Université de Montréal","funders":"Biotechnology and Biological Sciences Research Council; Royal Society; University of Cambridge; Wellcome Trust; Newnham College, University of Cambridge; Energy Biosciences Institute","keywords":"Biology; Genome; Pathogenicity island; Pathogenicity; Genome size; Bacterial genome size; Genome evolution; Genetics; Gene; Evolutionary biology; Microbiology","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":[0.00003273612,0.00007843901,0.0001683588,0.00001330126,0.00007672238,0.000003114459,0.00001241297,0.0001177418,0.00002355993],"category_scores_gemma":[0.00003339854,0.00005325757,0.0000301441,0.00006283619,0.0001820485,0.00001687967,0.00003297695,0.00005848529,8.415612e-7],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0000268722,"about_ca_system_score_gemma":0.000008713972,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00002802529,"about_ca_topic_score_gemma":0.000008735662,"domain_scores_codex":[0.999526,0.00005021295,0.0001024724,0.000187017,0.00003225531,0.0001020538],"domain_scores_gemma":[0.9997896,0.000007409199,0.00005418901,0.00004608235,0.00003797065,0.00006477966],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"observational","study_design_gemma":"observational","study_design_scores_codex":[0.0001903575,0.0001037396,0.6392369,0.000007284914,0.00008708668,0.000005647502,0.00005816703,6.840764e-7,0.3600643,0.00005145403,0.000001885415,0.0001925446],"study_design_scores_gemma":[0.0009579867,0.001421715,0.9886807,0.000009283797,0.00007026566,0.00002691972,0.00002967335,0.000063762,0.00850849,0.000169128,0.000009626227,0.00005245022],"study_design_candidate":"observational","study_design_consensus":"observational","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9979433,0.0001740165,0.001356668,0.0002244208,0.00003609074,0.0001852264,0.00005316465,0.00001678297,0.00001032377],"genre_scores_gemma":[0.9997056,0.00003330996,0.00007546574,0.00003420158,0.00002396552,0.0000111609,0.000108565,0.000003026642,0.000004778623],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.3515558,"threshold_uncertainty_score":0.2171781,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01525324592969814,"score_gpt":0.2756614807728488,"score_spread":0.2604082348431507,"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."}}