{"id":"W4402412060","doi":"10.1128/iai.00314-24","title":"Pathogenic diversification of the gut commensal <i>Providencia alcalifaciens</i> via acquisition of a second type III secretion system","year":2024,"lang":"en","type":"article","venue":"Infection and Immunity","topic":"Vibrio bacteria research studies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":10,"is_retracted":false,"has_abstract":true,"ca_institutions":"BC Children's Hospital; University of British Columbia","funders":"National Institute of General Medical Sciences; Genentech; National Institutes of Health; National Institute of Allergy and Infectious Diseases; Washington State University","keywords":"Biology; Microbiology; Shigella flexneri; Type three secretion system; Shigella; Virulence; Secretion; Salmonella enterica; Vacuole; Effector; Cell biology; Salmonella; Gene; Genetics; Bacteria; Escherichia coli; Cytoplasm","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":[0.0002531937,0.00005884733,0.00007767479,0.00003342003,0.0001107372,0.000013816,0.00005062437,0.00006263262,0.00001491659],"category_scores_gemma":[0.00003554002,0.00004541622,0.00005183698,0.0001318448,0.0001008851,0.000009169829,0.0001250033,0.00007068123,0.00000188418],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0000243944,"about_ca_system_score_gemma":0.00003410702,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0002058718,"about_ca_topic_score_gemma":0.00004886251,"domain_scores_codex":[0.9994735,0.0001489479,0.0001331509,0.00009945356,0.00007726112,0.00006773405],"domain_scores_gemma":[0.9995915,0.00001438606,0.00006086632,0.0001717962,0.0001446719,0.00001682315],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"bench_or_experimental","study_design_scores_codex":[0.00004945302,0.00001717706,0.00332724,0.00018649,0.0000464031,1.110902e-7,0.0001298521,0.000001379321,0.995095,0.0000617905,0.000188232,0.0008968929],"study_design_scores_gemma":[0.0004352633,0.0005233321,0.3385524,0.0001446595,0.00006095599,0.00003235048,0.0003225439,0.0005963945,0.6548806,0.00005028117,0.004279295,0.0001219034],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9982589,0.0004393616,0.000588964,0.00004180118,0.0002350268,0.0001461876,0.00003987054,0.00001122046,0.0002386086],"genre_scores_gemma":[0.9996231,0.0001874312,0.000009736387,0.0000176056,0.00003139353,0.000005621445,0.00006032333,0.000004319931,0.00006044955],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.3402144,"threshold_uncertainty_score":0.185202,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01249721622184401,"score_gpt":0.2549570524290519,"score_spread":0.2424598362072078,"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."}}