{"id":"W2131908402","doi":"10.1128/jb.01691-07","title":"<i>Mycobacterium avium</i>subsp.<i>paratuberculosis</i>and<i>M. avium</i>subsp.<i>avium</i>Are Independently Evolved Pathogenic Clones of a Much Broader Group of<i>M. avium</i>Organisms","year":2008,"lang":"en","type":"article","venue":"Journal of Bacteriology","topic":"Mycobacterium research and diagnosis","field":"Medicine","cited_by":145,"is_retracted":false,"has_abstract":true,"ca_institutions":"McGill University Health Centre","funders":"Rijksinstituut voor Volksgezondheid en Milieu; McGill University; University of Washington","keywords":"Paratuberculosis; Biology; Subspecies; Microbiology; Mycobacterium; Nonsynonymous substitution; Phylogenetic tree; Mycobacterium avium subspecies paratuberculosis; Phylogenetics; Genetics; Bacteria; Gene; Zoology; Genome","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":["metaepi_narrow","insufficient_payload"],"consensus_categories":[],"category_scores_codex":[0.00173266,0.001055751,0.003696331,0.001182654,0.0002787306,0.00006252233,0.0009563307,0.001139525,0.0009481786],"category_scores_gemma":[0.001028488,0.0008914705,0.001263658,0.001032306,0.001239366,0.0008145711,0.0005407503,0.002008998,0.00007181131],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00026287,"about_ca_system_score_gemma":0.0009924632,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0002533929,"about_ca_topic_score_gemma":0.00009434669,"domain_scores_codex":[0.9913191,0.001039039,0.003542186,0.001005788,0.001558233,0.001535711],"domain_scores_gemma":[0.9913473,0.0009139787,0.003057211,0.001246784,0.002067972,0.001366782],"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":[0.002833837,0.001332707,0.3150298,0.0007179855,0.0008255566,0.001165746,0.0009086923,0.000002492929,0.6723942,0.00006923309,0.004220548,0.000499271],"study_design_scores_gemma":[0.01172595,0.007370028,0.8252636,0.001115592,0.001566919,0.01928631,0.0007396539,0.00002096006,0.1222222,0.0003488493,0.009206193,0.001133699],"study_design_candidate":"observational","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.988523,0.006623071,0.0001793558,0.001592285,0.001412529,0.000922545,0.0003254138,0.00006925147,0.000352538],"genre_scores_gemma":[0.9833308,0.01061081,0.003092844,0.001216144,0.001116134,0.00005478032,0.000137457,0.0001786917,0.0002623619],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.5501719,"threshold_uncertainty_score":0.9999651,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.02047047253588395,"score_gpt":0.2599551642033036,"score_spread":0.2394846916674197,"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."}}