{"id":"W2784010265","doi":"10.1038/s41559-017-0446-6","title":"Salmonella enterica genomes from victims of a major sixteenth-century epidemic in Mexico","year":2018,"lang":"en","type":"article","venue":"Nature Ecology & Evolution","topic":"Salmonella and Campylobacter epidemiology","field":"Agricultural and Biological Sciences","cited_by":307,"is_retracted":false,"has_abstract":false,"ca_institutions":"","funders":"Social Sciences and Humanities Research Council of Canada; Max-Planck-Gesellschaft","keywords":"Salmonella enterica; Outbreak; Salmonella; Ancient DNA; Population; Biology; Serotype; Enteric fever; Virology; Medicine; Environmental health; Typhoid fever; Genetics; Bacteria","routes":{"ca_aff":false,"ca_fund":true,"ca_venue":false,"about_ca":false,"invisible_to_affiliation_only":true},"retraction":null,"screen":null,"direct_labels":[],"prediction":{"model_version":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0004838848,0.0002092181,0.0004949656,0.00005413744,0.0001020097,0.000006043961,0.0003652161,0.0009274497,0.0008540348],"category_scores_gemma":[0.0002753141,0.00009896253,0.0001402418,0.0004475681,0.0002724084,0.00008942901,0.0001261907,0.0004925033,0.0001281167],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0001688193,"about_ca_system_score_gemma":0.00002012299,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00054774,"about_ca_topic_score_gemma":0.003724935,"domain_scores_codex":[0.9978511,0.0004642119,0.0005283167,0.0005371493,0.0001275667,0.0004916434],"domain_scores_gemma":[0.9986687,0.0007175142,0.0002938941,0.0001214947,0.0001099205,0.00008852705],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"observational","study_design_gemma":"observational","study_design_scores_codex":[0.0001631318,0.0001378355,0.8532605,0.000002711736,0.0000312238,0.000003749823,0.00008431252,0.000002734163,0.1412975,0.0002917375,0.001641126,0.003083399],"study_design_scores_gemma":[0.0003037406,0.0004106822,0.9856027,0.00001524712,0.00002319231,0.00000937834,0.0001458444,0.0001761702,0.001202405,0.003609885,0.008335957,0.0001648305],"study_design_candidate":"observational","study_design_consensus":"observational","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9921387,0.004198728,0.00001488759,0.001589747,0.001070288,0.0002470446,0.00007028112,0.00005531044,0.0006149535],"genre_scores_gemma":[0.997718,0.0003490206,0.0002119979,0.0008359512,0.0006689722,0.00002082304,0.0001544719,0.00000208097,0.00003869533],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.1400951,"threshold_uncertainty_score":0.9351082,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.007113761476846868,"score_gpt":0.2308907232125887,"score_spread":0.2237769617357419,"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."}}