{"id":"W2015213608","doi":"10.1038/ng1470","title":"Comparison of genome degradation in Paratyphi A and Typhi, human-restricted serovars of Salmonella enterica that cause typhoid","year":2004,"lang":"en","type":"article","venue":"Nature Genetics","topic":"Salmonella and Campylobacter epidemiology","field":"Agricultural and Biological Sciences","cited_by":398,"is_retracted":false,"has_abstract":false,"ca_institutions":"University of Calgary","funders":"National Institute of Allergy and Infectious Diseases","keywords":"Biology; Salmonella typhi; Genome; Serotype; Pseudogene; Salmonella enterica; Typhoid fever; Genetics; Gene; Microbiology; Salmonella; Virology; Bacteria; Escherichia coli","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":[],"consensus_categories":[],"category_scores_codex":[0.0001014419,0.0001238477,0.0003176815,0.00003053759,0.00003526838,0.000006529281,0.0001628886,0.0003136515,0.0000182104],"category_scores_gemma":[0.00003297602,0.00005934229,0.00004304153,0.000311069,0.0000824731,0.00002340835,0.00005441336,0.0002229153,0.000001453335],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0000205715,"about_ca_system_score_gemma":0.00000863461,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0001392476,"about_ca_topic_score_gemma":0.0004710969,"domain_scores_codex":[0.9990812,0.00006327814,0.0003275546,0.0002232995,0.0001253562,0.0001793309],"domain_scores_gemma":[0.9995227,0.00009022804,0.0002054114,0.00007430885,0.00005655668,0.00005076803],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"observational","study_design_gemma":"observational","study_design_scores_codex":[0.00004145056,0.0001269542,0.5641286,0.00001167521,0.00001491522,0.000002286226,0.0001878286,0.0002274876,0.4336189,0.00008423315,0.00003233441,0.001523322],"study_design_scores_gemma":[0.0002585706,0.0003032774,0.9796854,0.0000161716,0.00001693899,0.000005144787,0.0001702388,0.00002184635,0.01837329,0.0005691376,0.0004765611,0.0001034795],"study_design_candidate":"observational","study_design_consensus":"observational","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9960002,0.003503931,0.000007413407,0.0001537511,0.00007882115,0.0001499027,0.0000226324,0.00001132834,0.00007203485],"genre_scores_gemma":[0.9989498,0.0004811588,0.0003359454,0.00007789258,0.00005103886,0.000003146507,0.00008879904,0.000001316061,0.00001092076],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.4155567,"threshold_uncertainty_score":0.2419908,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.05338904621001368,"score_gpt":0.3164749920487064,"score_spread":0.2630859458386927,"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."}}