{"id":"W2791126850","doi":"10.1128/jb.00050-18","title":"A Single Amino Acid Change in the Response Regulator PhoP, Acquired during Yersinia pestis Evolution, Affects PhoP Target Gene Transcription and Polymyxin B Susceptibility","year":2018,"lang":"en","type":"article","venue":"Journal of Bacteriology","topic":"Yersinia bacterium, plague, ectoparasites research","field":"Biochemistry, Genetics and Molecular Biology","cited_by":20,"is_retracted":false,"has_abstract":true,"ca_institutions":"McMaster University; Canadian Institute for Advanced Research; Toronto Metropolitan University","funders":"National Institute of Allergy and Infectious Diseases; National Health and Medical Research Council","keywords":"Biology; Yersinia pestis; Virulence; Mutant; Genetics; Gene; Response regulator; Microbiology; Yersinia pseudotuberculosis","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":[0.001410453,0.0002052696,0.0003324502,0.0002235871,0.0001336306,0.00004258802,0.0003104534,0.0002868716,0.00005669361],"category_scores_gemma":[0.0003985112,0.0001650807,0.000111379,0.0001979868,0.0004750054,0.00003979633,0.00008148143,0.0001926235,0.000004580908],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.000140516,"about_ca_system_score_gemma":0.0001396429,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00003317804,"about_ca_topic_score_gemma":0.0001725707,"domain_scores_codex":[0.9974928,0.001118076,0.0004176156,0.0003446051,0.000185243,0.0004416932],"domain_scores_gemma":[0.9989716,0.00007256085,0.0002620096,0.0003574638,0.0002062726,0.0001300789],"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":[0.006414358,0.0001245362,0.04996481,0.00002365799,0.00003738354,0.00004131158,0.0008966175,5.262262e-7,0.9420915,0.000001183603,0.00007714482,0.0003269402],"study_design_scores_gemma":[0.001006904,0.002107648,0.6124876,0.00002237094,0.00001360252,0.00086885,0.00009217357,0.0000131105,0.3825939,0.00001129709,0.0006730794,0.00010948],"study_design_candidate":"bench_or_experimental","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9974277,0.0008811993,0.00009041245,0.0009595715,0.0003036577,0.0002926585,0.0000264828,0.000005675889,0.00001266085],"genre_scores_gemma":[0.9984041,0.00007375341,0.0004890175,0.0001796947,0.0007633048,0.00001094206,0.0000228462,0.00002082186,0.00003555521],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.5625228,"threshold_uncertainty_score":0.6731796,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01792021972514453,"score_gpt":0.2715055761020325,"score_spread":0.2535853563768879,"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."}}