{"id":"W4319031146","doi":"10.3389/fgene.2023.1043598","title":"Genomic epidemiology of Mycobacterium avium subsp. paratuberculosis isolates from Canadian dairy herds provides evidence for multiple infection events","year":2023,"lang":"en","type":"article","venue":"Frontiers in Genetics","topic":"Mycobacterium research and diagnosis","field":"Medicine","cited_by":14,"is_retracted":false,"has_abstract":true,"ca_institutions":"Agriculture and Agri-Food Canada; Memorial University of Newfoundland","funders":"Agriculture and Agri-Food Canada; Alliance de recherche numérique du Canada; Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement; Atlantic Canada Opportunities Agency; Génome Québec; Compute Canada; Dairy Farmers of Canada","keywords":"Paratuberculosis; Biology; Herd; Multilocus sequence typing; Typing; Genotype; Clade; Molecular epidemiology; Transmission (telecommunications); Mycobacterium; Genetics; Veterinary medicine; Phylogenetics; Gene; Ecology; Bacteria; Medicine","routes":{"ca_aff":true,"ca_fund":true,"ca_venue":false,"about_ca":true,"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":[0.000304978,0.0002502662,0.0002863071,0.001394246,0.00139583,0.0007054819,0.0004087456,0.0003149546,0.000728505],"category_scores_gemma":[0.0007902224,0.0001687113,0.0002131134,0.002318909,0.0004178153,0.00009344111,0.0003563138,0.000300301,0.0001236723],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.005433199,"about_ca_system_score_gemma":0.005626391,"about_ca_topic_candidate":true,"about_ca_topic_consensus":true,"about_ca_topic_score_codex":0.9208866,"about_ca_topic_score_gemma":0.9670885,"domain_scores_codex":[0.9995335,0.00002161296,0.00001714013,0.000101417,0.0001717286,0.0001546266],"domain_scores_gemma":[0.9993494,0.0000495029,0.000112454,0.00002394845,0.000331737,0.0001329235],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"observational","study_design_gemma":"observational","study_design_scores_codex":[0.0002818364,0.00004944545,0.9293527,0.0001044325,0.0000727154,0.0004318642,0.00218821,0.0002803965,0.04928424,0.0001317771,0.0006174517,0.01720499],"study_design_scores_gemma":[0.000002299279,0.00002413021,0.9978879,0.00000856195,0.00001617465,0.000112224,0.0004865873,0.0001324227,0.0004107721,0.000006285882,0.0009091826,0.000003487334],"study_design_candidate":"observational","study_design_consensus":"observational","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9974484,0.0004239666,0.0001415198,0.00004525563,0.000003385732,0.00001681923,0.001103528,0.000005268566,0.0008119316],"genre_scores_gemma":[0.9966829,0.0003364409,0.000669452,0.00005702861,0.000003099411,0.00000998309,0.001680143,0.000003720627,0.0005572835],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.07911336,"threshold_uncertainty_score":0.1591585,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.07028860160805449,"score_gpt":0.3417070283085072,"score_spread":0.2714184267004527,"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."}}