{"id":"W4386317459","doi":"10.1371/journal.pbio.3002253","title":"The microbiota conditions a gut milieu that selects for wild-type Salmonella Typhimurium virulence","year":2023,"lang":"en","type":"article","venue":"PLoS Biology","topic":"Gut microbiota and health","field":"Biochemistry, Genetics and Molecular Biology","cited_by":19,"is_retracted":false,"has_abstract":true,"ca_institutions":"","funders":"Botnar Research Centre for Child Health, University of Basel; Gebert Rüf Stiftung; Boehringer Ingelheim Fonds; Geschwister Boehringer Ingelheim Stiftung für Geisteswissenschaften; Cree Board of Health and Social Services of James Bay; Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung; National Science Foundation","keywords":"Virulence; Biology; Microbiology; Pathogen; Mutant; Colonisation resistance; Pathogenicity island; Gut flora; Salmonella; Colonization; Phenotype; Bacteria; Genetics; Gene; Immunology","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":[0.0001920229,0.0001722748,0.0001722726,0.00005178702,0.0004222936,0.00002061215,0.0003210461,0.0002699775,0.0000163107],"category_scores_gemma":[0.0001517168,0.0001303495,0.00009274557,0.0001966233,0.0002163869,0.000002160004,0.0001264814,0.0001142528,0.0001905744],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00001576625,"about_ca_system_score_gemma":0.0001503321,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00001696135,"about_ca_topic_score_gemma":0.0001065415,"domain_scores_codex":[0.9986957,0.00009036581,0.0001888869,0.0004287197,0.00003586212,0.0005605198],"domain_scores_gemma":[0.9991972,0.0001138537,0.000083012,0.0003932096,0.000134299,0.00007835722],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"not_applicable","study_design_scores_codex":[0.00008143426,0.00003529493,0.001381804,0.0000260085,0.00007106592,7.425547e-7,0.0000296698,0.000002856392,0.9433877,0.0003109696,0.05455548,0.0001169684],"study_design_scores_gemma":[0.0009056003,0.0009879352,0.01169924,0.00002697505,0.00006157684,0.00003706419,0.0001285609,0.0001242684,0.3862186,0.001104374,0.5982674,0.0004383825],"study_design_candidate":"bench_or_experimental","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9946758,0.00146181,0.00005253709,0.002135215,0.0005625049,0.0005578861,0.0002684833,0.00006053636,0.000225267],"genre_scores_gemma":[0.9922163,0.002009311,0.0002034038,0.001193445,0.0002988078,0.00008468011,0.00136863,0.00003297473,0.002592441],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.5571691,"threshold_uncertainty_score":0.5315496,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.02959105459257533,"score_gpt":0.3036266434234058,"score_spread":0.2740355888308305,"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."}}