{"id":"W4387931240","doi":"10.1128/jcm.00260-23","title":"Whole genome sequencing-based identification of human tuberculosis caused by animal-lineage <i>Mycobacterium orygis</i>","year":2023,"lang":"en","type":"article","venue":"Journal of Clinical Microbiology","topic":"Tuberculosis Research and Epidemiology","field":"Medicine","cited_by":14,"is_retracted":false,"has_abstract":true,"ca_institutions":"Provincial Laboratory of Public Health; BC Centre for Disease Control; University of Manitoba; Public Health Agency of Canada","funders":"Public Health Agency; Public Health Agency of Canada","keywords":"Biology; Genetics; Phylogenetic tree; Single-nucleotide polymorphism; Mycobacterium tuberculosis complex; Genome; Whole genome sequencing; Mycobacterium tuberculosis; Reference genome; Tuberculosis; SNP; Identification (biology); Genotype; Gene; 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":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0002236973,0.0002148046,0.0002463921,0.0006156619,0.0002905251,0.0003480965,0.0001539373,0.0002982242,0.0005544128],"category_scores_gemma":[0.0003594869,0.0000871279,0.0002836207,0.0007426122,0.0001681042,0.00005472323,0.000151575,0.0001682995,0.0001729567],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0003886021,"about_ca_system_score_gemma":0.0006413807,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.05632774,"about_ca_topic_score_gemma":0.07297496,"domain_scores_codex":[0.999793,0.00002520429,0.00001582016,0.00007006415,0.00006013933,0.00003574444],"domain_scores_gemma":[0.9998209,0.00002843533,0.00004476433,0.00001580381,0.00006559855,0.0000245881],"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":[0.00111998,0.000118362,0.4352862,0.0002814255,0.0003089639,0.001096531,0.0005819112,0.001367623,0.529174,0.0001533187,0.001455635,0.02905616],"study_design_scores_gemma":[0.0000265947,0.0002028809,0.9535382,0.00003769861,0.0002042844,0.001154935,0.0005514233,0.003058121,0.03542171,0.00005466786,0.005738758,0.00001081883],"study_design_candidate":"observational","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9918785,0.0004933889,0.00175366,0.00005630351,0.000009535594,0.00005069208,0.005033973,0.00003398739,0.0006899789],"genre_scores_gemma":[0.9872974,0.0003002755,0.00533947,0.0001015501,0.000006664717,0.00001804876,0.006338991,0.00001519242,0.0005823284],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.05632774,"threshold_uncertainty_score":0.1119998,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.07479047558059934,"score_gpt":0.4075234583538718,"score_spread":0.3327329827732725,"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."}}