{"id":"W4410850984","doi":"10.1126/science.adt3880","title":"Attenuation of virulence in <i>Yersinia pestis</i> across three plague pandemics","year":2025,"lang":"en","type":"article","venue":"Science","topic":"Yersinia bacterium, plague, ectoparasites research","field":"Biochemistry, Genetics and Molecular Biology","cited_by":17,"is_retracted":false,"has_abstract":true,"ca_institutions":"McMaster University; Canadian Institute for Advanced Research; McMaster University Medical Centre","funders":"Agence Nationale de la Recherche","keywords":"Yersinia pestis; Virulence; Plague (disease); Pandemic; Plasmid; Microbiology; Biology; Virology; Yersiniosis; Rodent; Yersinia pseudotuberculosis; Enterobacteriaceae; Infectious disease (medical specialty); Gene; Coronavirus disease 2019 (COVID-19); Disease; Escherichia coli; Genetics; Medicine; Ecology","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":[0.0008290824,0.00008679037,0.0001100899,0.0001056395,0.0001021532,0.0000281063,0.0005172358,0.00008850117,0.000002876668],"category_scores_gemma":[0.0004398601,0.00008781047,0.0000285515,0.0008413006,0.0006886636,0.00001695088,0.0002479706,0.000112185,0.000006306199],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00004380876,"about_ca_system_score_gemma":0.0004064475,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00008216963,"about_ca_topic_score_gemma":0.0007659644,"domain_scores_codex":[0.9987582,0.00002853079,0.0001962512,0.0003933845,0.0002660639,0.0003575839],"domain_scores_gemma":[0.9993292,0.00003178612,0.0000578266,0.0003612266,0.0001663794,0.00005359383],"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":[0.00003525183,0.00002146518,0.2769613,0.00001240833,0.000001797208,9.528516e-7,0.00005524468,0.00007697073,0.720621,0.00004998201,0.0000445185,0.002119114],"study_design_scores_gemma":[0.0002969505,0.00007353674,0.5286703,0.00004223362,0.000001834356,0.000003643923,0.00006575412,0.0006005301,0.4690322,0.0001137824,0.001009281,0.00008992266],"study_design_candidate":"bench_or_experimental","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9970474,0.0001929591,0.001595748,0.000178786,0.0001280833,0.0001488205,0.00001713251,0.000005455479,0.0006856384],"genre_scores_gemma":[0.9990118,0.00005774977,0.0006019464,0.0001363596,0.00001991278,0.000007862855,0.00001167242,0.000004063417,0.000148693],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.251709,"threshold_uncertainty_score":0.3580807,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01293293687079442,"score_gpt":0.3405463854834723,"score_spread":0.3276134486126779,"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."}}