{"id":"W3005436103","doi":"10.7554/elife.53245","title":"Previously undetected super-spreading of Mycobacterium tuberculosis revealed by deep sequencing","year":2020,"lang":"en","type":"article","venue":"eLife","topic":"Mycobacterium research and diagnosis","field":"Medicine","cited_by":56,"is_retracted":false,"has_abstract":true,"ca_institutions":"McGill University Health Centre; Nunavik Regional Board of Health and Social Services; Public Health Ontario; University of Toronto","funders":"National Institute of Allergy and Infectious Diseases; Canadian Institutes of Health Research; Public Health Agency; National Institutes of Health; Public Health Agency of Canada; McGill University; University of Melbourne; Harvard University","keywords":"Deep sequencing; Biology; Genome; Transmission (telecommunications); Mycobacterium tuberculosis; Computational biology; DNA sequencing; Whole genome sequencing; Genetics; Metagenomics; Outbreak; Genomics; Tuberculosis; Evolutionary biology; Virology; Medicine; Gene; Computer science","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":[0.0002584153,0.0002180297,0.0005595884,0.00008974964,0.00006203197,0.00003137354,0.0001699948,0.0001337208,0.0008959061],"category_scores_gemma":[0.001699251,0.00019635,0.0001736469,0.0004941481,0.00006958694,0.0001524912,0.0001052409,0.0003037068,0.0001397535],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0001626535,"about_ca_system_score_gemma":0.0002083347,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0002084474,"about_ca_topic_score_gemma":0.00001338819,"domain_scores_codex":[0.9978709,0.0001182457,0.0004800622,0.0003982639,0.0006048524,0.0005277033],"domain_scores_gemma":[0.9983334,0.0002136429,0.00009804031,0.0003496193,0.0002592486,0.0007460727],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"bench_or_experimental","study_design_scores_codex":[0.0003361749,0.00007656262,0.1578068,0.0008354601,0.0001671267,0.00005836851,0.00106981,0.000002205521,0.8214707,0.00001405743,0.01675852,0.001404142],"study_design_scores_gemma":[0.003946067,0.002234403,0.1106503,0.0008678659,0.0004262127,0.00007933097,0.0007282796,0.001719931,0.8663548,0.00001330731,0.01234533,0.0006341569],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9933011,0.001107026,0.0002605998,0.002745436,0.00006995043,0.0005518072,0.00005505674,0.0001533757,0.001755645],"genre_scores_gemma":[0.9954673,0.0008500188,0.0009255249,0.002155539,0.0002815693,0.00004700745,0.0001092866,0.00004670569,0.0001170229],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.04715651,"threshold_uncertainty_score":0.9809543,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.02692802935478301,"score_gpt":0.2705848738830794,"score_spread":0.2436568445282964,"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."}}