{"id":"W2131071075","doi":"10.1056/nejmoa1003176","title":"Whole-Genome Sequencing and Social-Network Analysis of a Tuberculosis Outbreak","year":2011,"lang":"en","type":"article","venue":"New England Journal of Medicine","topic":"Tuberculosis Research and Epidemiology","field":"Medicine","cited_by":748,"is_retracted":false,"has_abstract":true,"ca_institutions":"Fraser Health; Public Health Agency of Canada; Health Canada; Simon Fraser University; Canada's Michael Smith Genome Sciences Centre; BC Centre for Disease Control; University of British Columbia","funders":"Canadian Institutes of Health Research","keywords":"Outbreak; Genotyping; Genome; Whole genome sequencing; Tuberculosis; Mycobacterium tuberculosis; Contact tracing; Biology; Transmission (telecommunications); Genetics; Genotype; Evolutionary biology; Virology; Medicine; Disease; Infectious disease (medical specialty); Gene; Pathology","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":[0.002635545,0.0001625886,0.001400452,0.0006788108,0.00006027186,0.000003036845,0.0001234844,0.0001192843,0.0004078303],"category_scores_gemma":[0.000755798,0.0001025932,0.0002284949,0.0007150622,0.0002660633,0.00007479919,0.00004130596,0.0004457811,0.000002208606],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00007592644,"about_ca_system_score_gemma":0.000174369,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0007812076,"about_ca_topic_score_gemma":0.0001503845,"domain_scores_codex":[0.9978657,0.0002530702,0.0009074882,0.0001654298,0.0004478537,0.0003604594],"domain_scores_gemma":[0.9982333,0.0003691096,0.0004499699,0.0001707607,0.0003304081,0.0004464178],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"observational","study_design_gemma":"observational","study_design_scores_codex":[0.005469212,0.0002493741,0.7404968,0.000397393,0.02010252,0.001070801,0.0300226,0.0002267866,0.07473794,0.001174554,0.0179741,0.108078],"study_design_scores_gemma":[0.0242879,0.00379119,0.9347752,0.0003548686,0.00933715,0.001357557,0.00143879,0.0004344367,0.0001677465,0.001584731,0.02227439,0.0001960587],"study_design_candidate":"observational","study_design_consensus":"observational","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9771878,0.004336101,0.0007723048,0.01463213,0.0001468488,0.0001222661,0.000009281373,0.00001010141,0.0027832],"genre_scores_gemma":[0.9938579,0.001108672,0.001365782,0.001303052,0.002173578,9.16902e-7,0.00001879564,0.00001446585,0.0001568726],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.1942784,"threshold_uncertainty_score":0.4465456,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.05737237002724913,"score_gpt":0.3184656879593674,"score_spread":0.2610933179321182,"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."}}