{"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":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0002136527,0.0001338433,0.00037022,0.0004376734,0.0001097238,0.000008759448,0.0001149213,0.0001028714,0.0004230778],"category_scores_gemma":[0.000301295,0.0001039722,0.00006273764,0.0003069491,0.0001512947,0.0001104587,0.0002088404,0.0001200076,0.00003849668],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0001302649,"about_ca_system_score_gemma":0.0001525058,"about_ca_topic_candidate":true,"about_ca_topic_consensus":true,"about_ca_topic_score_codex":0.1055543,"about_ca_topic_score_gemma":0.08468225,"domain_scores_codex":[0.9986291,0.00005318917,0.0001946854,0.0002766423,0.0003138405,0.0005325603],"domain_scores_gemma":[0.9986218,0.0001788159,0.00004458227,0.0003124081,0.0001375321,0.0007048469],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"observational","study_design_gemma":"observational","study_design_scores_codex":[0.0001094807,0.0004628729,0.9394891,0.0002125439,0.0001573996,0.00003714234,0.0002398496,1.566385e-8,0.05901931,0.000008654693,0.0001503125,0.0001132962],"study_design_scores_gemma":[0.001020075,0.000229457,0.978022,0.0002514367,0.0001156638,0.000001923028,0.00002892979,0.000001044708,0.01993235,0.00003571933,0.0002422036,0.0001191397],"study_design_candidate":"observational","study_design_consensus":"observational","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9955523,0.0004330503,7.428184e-7,0.002328,0.00002170459,0.0003435175,0.0001877477,0.00001635012,0.001116585],"genre_scores_gemma":[0.9979402,0.001441879,0.00009924554,0.0002433002,0.00005741423,0.00002544801,0.00002847825,0.0000138472,0.0001501931],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.03908696,"threshold_uncertainty_score":0.9320199,"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."}}