{"id":"W4408845454","doi":"10.1111/mmi.15355","title":"Multifaceted Evolution of the <scp>PhoPQ</scp> Two‐Component System in <scp><i>Salmonella enterica</i></scp> Enhanced the Expression of Horizontally Acquired Virulence Genes","year":2025,"lang":"en","type":"article","venue":"Molecular Microbiology","topic":"Salmonella and Campylobacter epidemiology","field":"Agricultural and Biological Sciences","cited_by":0,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of Alberta","funders":"Natural Sciences and Engineering Research Council of Canada","keywords":"Virulence; Biology; Regulon; Salmonella enterica; Salmonella; Gene; Pathogenicity island; Niche; Genetics; Gene expression; Microbiology; Bacteria; Ecology","routes":{"ca_aff":true,"ca_fund":true,"ca_venue":false,"about_ca":false,"invisible_to_affiliation_only":false},"retraction":null,"screen":null,"direct_labels":[],"prediction":{"model_version":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0001785697,0.0003105812,0.0001515552,0.0002660801,0.0001407804,0.0002982762,0.0002269059,0.0003052767,0.0003671596],"category_scores_gemma":[0.0001930585,0.0002056236,0.0003147553,0.0001790025,0.000267979,0.0002308919,0.0004645535,0.0006082347,0.0002052459],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.000457965,"about_ca_system_score_gemma":0.0003140135,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.001094057,"about_ca_topic_score_gemma":0.001150054,"domain_scores_codex":[0.9998758,0.00002102684,0.00001148869,0.00002638428,0.00003248053,0.00003276729],"domain_scores_gemma":[0.9998895,0.00001911092,0.00002796315,0.00002381429,0.00001531828,0.00002413848],"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":[0.00002634933,0.00001714927,0.0007443853,0.00001174841,0.000004647315,0.00004661757,0.0000187745,0.0001691769,0.9978296,0.0001389312,0.000009047551,0.0009835318],"study_design_scores_gemma":[0.00002911333,0.0005577012,0.09130094,0.00001482555,0.00005783718,0.001350737,0.0002810453,0.009397419,0.8935884,0.0003410268,0.003042243,0.00003872325],"study_design_candidate":"observational","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9980752,0.00007772364,0.001406406,0.00003860006,0.000003355518,0.000008560864,0.00004909997,0.00002512775,0.000315945],"genre_scores_gemma":[0.9974871,0.00007262977,0.001803458,0.00002442382,0.000001746035,0.00001132404,0.0001460015,0.00001658886,0.0004367035],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.001094057,"threshold_uncertainty_score":0.00332284,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.006236916585725939,"score_gpt":0.2070993549230648,"score_spread":0.2008624383373389,"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."}}