{"id":"W4415881079","doi":"10.1099/mgen.0.001543","title":"Population structure of Mycobacterium avium subsp. hominissuis provides new insights into genomic evolution","year":2025,"lang":"en","type":"article","venue":"Microbial Genomics","topic":"Mycobacterium research and diagnosis","field":"Medicine","cited_by":0,"is_retracted":false,"has_abstract":true,"ca_institutions":"Public Health Ontario; Manitoba Health; University of Manitoba; Western University","funders":"Canadian Institutes of Health Research; Natural Sciences and Engineering Research Council of Canada; Canada Research Chairs","keywords":"Genetic diversity; Genome; Pathogen; Opportunistic pathogen; Population; Human pathogen; Phylogenetics; Population structure; Gene","routes":{"ca_aff":true,"ca_fund":true,"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":[0.00008308488,0.0002413503,0.0004900821,0.0003862527,0.0001074119,0.00005222846,0.0001945101,0.0002456057,0.0001514115],"category_scores_gemma":[0.000139334,0.0002309842,0.0001548075,0.000359301,0.00007817166,0.0001273148,0.000151215,0.0002356943,0.00002896023],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0006934109,"about_ca_system_score_gemma":0.0008383919,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.003049009,"about_ca_topic_score_gemma":0.0009403339,"domain_scores_codex":[0.9985085,0.00006385596,0.0005253808,0.0004009216,0.0001521511,0.0003491798],"domain_scores_gemma":[0.9989432,0.00005457025,0.0001637973,0.0004568747,0.0001767767,0.0002048279],"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":[0.0006375923,0.00007709796,0.06196237,0.0003783486,0.0000908849,0.000005075009,0.000517361,0.00001855144,0.9290918,0.0003890659,0.004103248,0.002728566],"study_design_scores_gemma":[0.002502747,0.0003090258,0.6268172,0.0002030645,0.0002408453,0.00001840306,0.0001052526,0.0001000597,0.3380524,0.002202443,0.02915043,0.000298164],"study_design_candidate":"bench_or_experimental","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9961868,0.001190363,0.0004327911,0.0005297693,0.0005637781,0.0007795297,0.00005234605,0.00004910341,0.0002155557],"genre_scores_gemma":[0.9947704,0.0002159206,0.003040419,0.0002700192,0.0004635911,0.000005637395,0.0004126758,0.0000314859,0.0007898368],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.5910394,"threshold_uncertainty_score":0.9419262,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.007833479287445896,"score_gpt":0.2530146386981142,"score_spread":0.2451811594106683,"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."}}