{"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":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0007077692,0.0002085326,0.0005936389,0.0005211424,0.00007405013,0.000008268394,0.0001732905,0.0002739308,0.00003410803],"category_scores_gemma":[0.003038608,0.0002084054,0.0001642913,0.0004540983,0.0000972187,0.00008907212,0.0000700318,0.0002027918,0.00002783589],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0003884191,"about_ca_system_score_gemma":0.0005356175,"about_ca_topic_candidate":true,"about_ca_topic_consensus":true,"about_ca_topic_score_codex":0.05878581,"about_ca_topic_score_gemma":0.03722804,"domain_scores_codex":[0.9978768,0.0002123529,0.0005792694,0.0004524145,0.0001378473,0.0007413457],"domain_scores_gemma":[0.9979022,0.0009555625,0.0001374017,0.0004308165,0.0001616112,0.0004124405],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"observational","study_design_gemma":"observational","study_design_scores_codex":[0.000323509,0.00004848543,0.9682107,0.0002607055,0.0001128166,0.000006631905,0.000196456,0.0001625744,0.006842854,0.000001403318,0.02097406,0.002859807],"study_design_scores_gemma":[0.0009367745,0.0004035706,0.9781099,0.0002636279,0.00009683801,0.000002089614,0.00008067157,0.01135529,0.004011295,0.0005710056,0.003994087,0.0001748824],"study_design_candidate":"observational","study_design_consensus":"observational","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9909512,0.004316057,0.0008513496,0.001013684,0.001308754,0.001184111,0.0003151907,0.00004201375,0.00001765071],"genre_scores_gemma":[0.9799373,0.008166471,0.01051948,0.0002083403,0.0002824799,0.0003038866,0.0004237515,0.00004252487,0.0001157305],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.02155777,"threshold_uncertainty_score":0.9803401,"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."}}