{"id":"W2897710284","doi":"10.1099/mgen.0.000217","title":"Within-host Mycobacterium tuberculosis diversity and its utility for inferences of transmission","year":2018,"lang":"en","type":"article","venue":"Microbial Genomics","topic":"Tuberculosis Research and Epidemiology","field":"Medicine","cited_by":31,"is_retracted":false,"has_abstract":true,"ca_institutions":"BC Centre for Disease Control; University of British Columbia","funders":"National Institute of Allergy and Infectious Diseases; Canadian Institutes of Health Research","keywords":"Mycobacterium tuberculosis; Concordance; Transmission (telecommunications); Biology; Genetic diversity; Outbreak; Phylogenetic tree; Genetics; Tuberculosis; False positive paradox; Single-nucleotide polymorphism; Evolutionary biology; Whole genome sequencing; Genome; Computational biology; Genotype; Virology; Medicine; Computer science; Population; Gene; Artificial intelligence; Environmental health","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":[0.001911337,0.0003075721,0.0004055881,0.001867805,0.0009006904,0.001543304,0.0002806527,0.0003987097,0.0005421532],"category_scores_gemma":[0.004987336,0.000236341,0.0002386297,0.001648371,0.0007240536,0.0004968676,0.0005376813,0.0005290317,0.0001539791],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0009722508,"about_ca_system_score_gemma":0.00079337,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.05201996,"about_ca_topic_score_gemma":0.09729477,"domain_scores_codex":[0.9989406,0.000493026,0.00005114858,0.0002156605,0.0001747874,0.0001246691],"domain_scores_gemma":[0.9981578,0.001006184,0.0003941229,0.0001592926,0.0001617726,0.0001207801],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"observational","study_design_gemma":"observational","study_design_scores_codex":[0.0001357325,0.00002237268,0.9399688,0.0001251577,0.000169684,0.0002501489,0.001475112,0.002514502,0.02282858,0.0007414588,0.0001736372,0.03159481],"study_design_scores_gemma":[0.000004723405,0.00005153034,0.9833244,0.00008402624,0.0000794677,0.0004938228,0.001179263,0.006695033,0.00396518,0.002212652,0.001890848,0.00001891635],"study_design_candidate":"observational","study_design_consensus":"observational","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9879621,0.002145966,0.006380368,0.0001305411,0.000007686066,0.00001851107,0.0005829642,0.00003642184,0.002735546],"genre_scores_gemma":[0.9964041,0.000343401,0.002929551,0.00003439655,0.000005029758,0.000003947936,0.0001698307,0.000004619904,0.0001052317],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.05201996,"threshold_uncertainty_score":0.1034343,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.04422785186587053,"score_gpt":0.3003772448659613,"score_spread":0.2561493930000908,"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."}}