{"id":"W2268141598","doi":"10.1371/journal.pone.0149017","title":"Genome-Wide Diversity and Phylogeography of Mycobacterium avium subsp. paratuberculosis in Canadian Dairy Cattle","year":2016,"lang":"en","type":"article","venue":"PLoS ONE","topic":"Mycobacterium research and diagnosis","field":"Medicine","cited_by":32,"is_retracted":false,"has_abstract":true,"ca_institutions":"Memorial University of Newfoundland; University of Prince Edward Island; SaskTel (Canada); Université de Montréal; University of Guelph; University of Calgary","funders":"Biotechnology and Biological Sciences Research Council; Alberta Livestock and Meat Agency; Dairy Farmers of Canada","keywords":"Paratuberculosis; Biology; Phylogeography; Genetic diversity; Species richness; Population; Clade; Evolutionary biology; Genetics; Phylogenetics; Ecology; Mycobacterium; Gene; Demography; Bacteria","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":[0.0005092152,0.0002675086,0.0004351178,0.002462013,0.001745134,0.0009868324,0.0006142249,0.0004356314,0.00102278],"category_scores_gemma":[0.001130866,0.0001861821,0.0004606735,0.004079348,0.0006019452,0.0001524786,0.000450672,0.000416395,0.00009897183],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.006860437,"about_ca_system_score_gemma":0.005500544,"about_ca_topic_candidate":true,"about_ca_topic_consensus":true,"about_ca_topic_score_codex":0.927565,"about_ca_topic_score_gemma":0.9552258,"domain_scores_codex":[0.9993868,0.00004254751,0.00001895487,0.0002097848,0.0001283631,0.0002135498],"domain_scores_gemma":[0.9993502,0.0001074826,0.0001180101,0.00004492608,0.0002329431,0.000146356],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"observational","study_design_gemma":"observational","study_design_scores_codex":[0.0002778314,0.00002517406,0.976898,0.00007102462,0.0002407041,0.000132313,0.001439318,0.0009175788,0.007698257,0.0001905367,0.0004737734,0.01163567],"study_design_scores_gemma":[0.000002926966,0.00001092758,0.9985769,0.000009347695,0.00003410494,0.00004468885,0.0003471777,0.0004004937,0.00008014077,0.00001630598,0.0004719127,0.000005245642],"study_design_candidate":"observational","study_design_consensus":"observational","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9972265,0.0004740124,0.0001865526,0.00005535599,0.000002911335,0.00001015214,0.001428455,0.000007094302,0.0006090414],"genre_scores_gemma":[0.9978096,0.000262787,0.000378383,0.00002683189,0.000001945422,0.000006782373,0.001245544,0.000004412449,0.0002638734],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.07243496,"threshold_uncertainty_score":0.145723,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.03188318564953984,"score_gpt":0.2280360260849766,"score_spread":0.1961528404354367,"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."}}