{"id":"W2998923716","doi":"10.1016/j.tube.2020.101899","title":"Comparative genomics shows differences in the electron transport and carbon metabolic pathways of Mycobacterium africanum relative to Mycobacterium tuberculosis and suggests an adaptation to low oxygen tension","year":2020,"lang":"en","type":"article","venue":"Tuberculosis","topic":"Tuberculosis Research and Epidemiology","field":"Medicine","cited_by":27,"is_retracted":false,"has_abstract":true,"ca_institutions":"Global Institute for Water Security","funders":"European Research Council; Medical Research Council; European and Developing Countries Clinical Trials Partnership; Research Councils UK","keywords":"Mycobacterium tuberculosis; Biology; Tuberculosis; Genetics; In silico; Lineage (genetic); Comparative genomics; Adaptation (eye); Gene; Mutation; Phenotype; Mycobacterium; Genomics; Genome; Bacteria","routes":{"ca_aff":true,"ca_fund":false,"ca_venue":false,"about_ca":false,"invisible_to_affiliation_only":false},"retraction":null,"screen":null,"direct_labels":[],"prediction":{"model_version":"codex-gemma-dda1882f352a","candidate_categories":["metaepi_narrow"],"consensus_categories":[],"category_scores_codex":[0.0006134021,0.0004054974,0.00126741,0.0002927764,0.00009337839,0.00002637138,0.0002019443,0.0001900239,0.00001833402],"category_scores_gemma":[0.0002917479,0.0002912194,0.0001098102,0.0007673535,0.0001569386,0.0002159732,0.00008741772,0.000470168,0.000006439407],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00008811003,"about_ca_system_score_gemma":0.0001095902,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00171214,"about_ca_topic_score_gemma":0.001436515,"domain_scores_codex":[0.9968087,0.000645685,0.00069196,0.0007908922,0.0004220899,0.0006406872],"domain_scores_gemma":[0.9982455,0.0003828683,0.0001249946,0.0003670202,0.0002034481,0.000676137],"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":[0.002531047,0.0003880106,0.2236527,0.000290045,0.000412838,0.00003599128,0.09816064,0.000101412,0.6720952,0.0003350226,0.0001434299,0.001853676],"study_design_scores_gemma":[0.0008310259,0.002571813,0.9775285,0.00009574809,0.0002971121,0.00002931788,0.004486155,0.004432081,0.009015777,0.00008094481,0.000304851,0.0003266737],"study_design_candidate":"observational","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9831294,0.0007528777,0.00007230975,0.01411944,0.00003845086,0.001494795,0.0001182899,0.00003847564,0.0002359396],"genre_scores_gemma":[0.994756,0.001061561,0.000706278,0.003039929,0.0001318554,0.0001647439,0.00009971162,0.00003294407,0.000006949286],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.7538759,"threshold_uncertainty_score":0.999954,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.04761099517448883,"score_gpt":0.2871745089628769,"score_spread":0.2395635137883881,"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."}}