{"id":"W3004204695","doi":"10.1099/acmi.mim2019.po0024","title":"Whole genome sequencing reveals genetic diversity in Mycobacterium avium subspecies paratuberculosis population circulating in Irish cattle","year":2020,"lang":"en","type":"article","venue":"Access Microbiology","topic":"Mycobacterium research and diagnosis","field":"Medicine","cited_by":0,"is_retracted":false,"has_abstract":true,"ca_institutions":"","funders":"","keywords":"Biology; Genetics; Genetic diversity; Whole genome sequencing; Genome; Paratuberculosis; Population; Reference genome; DNA sequencing; Irish; Subspecies; Evolutionary biology; Mycobacterium; Zoology; Gene","routes":{"ca_aff":false,"ca_fund":false,"ca_venue":false,"about_ca":true,"invisible_to_affiliation_only":true},"retraction":null,"screen":null,"direct_labels":[],"prediction":{"model_version":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0002116231,0.000195731,0.0005074071,0.000239214,0.00010051,0.0000528548,0.0002812274,0.0002015597,0.0003047773],"category_scores_gemma":[0.0003223619,0.0001978121,0.00008232454,0.0005843648,0.00006664726,0.000253608,0.0006015536,0.0003436707,0.00007815265],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0004055779,"about_ca_system_score_gemma":0.00007849595,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.002836492,"about_ca_topic_score_gemma":0.0005326401,"domain_scores_codex":[0.9981537,0.0002054141,0.0004603034,0.0005227478,0.00009211118,0.0005657643],"domain_scores_gemma":[0.9992533,0.0001258645,0.0001174056,0.0002367385,0.00007912056,0.0001875536],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"observational","study_design_gemma":"observational","study_design_scores_codex":[0.00005884867,0.0000255812,0.5857332,0.000105932,0.00001154731,0.00008802422,0.0004406452,0.00007340554,0.413053,0.000001171714,0.0003521229,0.00005649172],"study_design_scores_gemma":[0.0008625993,0.0001054033,0.9957268,0.0000726147,0.0000257239,0.00004986421,0.0001365668,0.00005119702,0.00246432,0.00002803608,0.0002887235,0.000188213],"study_design_candidate":"observational","study_design_consensus":"observational","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9964176,0.0003709251,0.00001797143,0.002256603,0.00009965387,0.0004924581,0.00009366894,0.00004079869,0.0002103222],"genre_scores_gemma":[0.9970973,0.0001470002,0.0002049195,0.001699743,0.0001795095,0.00002635725,0.0006042493,0.0000196885,0.00002130388],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.4105887,"threshold_uncertainty_score":0.8066545,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.07246852155954134,"score_gpt":0.3134061398492359,"score_spread":0.2409376182896945,"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."}}