{"id":"W4400387233","doi":"10.1101/2024.07.05.602177","title":"The Enemy Within: how pathogen-free are your commercial specific pathogen-free mice?","year":2024,"lang":"en","type":"preprint","venue":"bioRxiv (Cold Spring Harbor Laboratory)","topic":"Escherichia coli research studies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":0,"is_retracted":false,"has_abstract":true,"ca_institutions":"Institute of Infection and Immunity","funders":"University of Glasgow","keywords":"Virulence; Specific-pathogen-free; Pathogen; Biology; Microbiology; Pathogenicity island; Carriage; Isolation (microbiology); Locus (genetics); Genome; Strain (injury); Virology; Genetics; Gene; Medicine; Virus","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":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.002062926,0.0004459377,0.0004033937,0.0003416785,0.0004147352,0.001942752,0.0005695989,0.001139741,0.005917197],"category_scores_gemma":[0.001614829,0.0001497279,0.0002425895,0.0002313392,0.000842003,0.001660289,0.0006259167,0.001396147,0.002893724],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0002545939,"about_ca_system_score_gemma":0.0004224106,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0004647625,"about_ca_topic_score_gemma":0.0008850541,"domain_scores_codex":[0.9992324,0.0002399053,0.00003912923,0.0001333639,0.0002501844,0.0001050494],"domain_scores_gemma":[0.9983937,0.0001831445,0.0003872451,0.0003824351,0.0002295279,0.0004238701],"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":[0.002031591,0.0008147677,0.01530778,0.0006917502,0.0002141173,0.0008354818,0.0005938363,0.0002602324,0.7597771,0.01168721,0.03889935,0.1688867],"study_design_scores_gemma":[0.0001676703,0.001892266,0.03939247,0.0008759395,0.0003591655,0.003902938,0.001963154,0.0009496915,0.5197887,0.01482038,0.4156807,0.0002069593],"study_design_candidate":"observational","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.7636738,0.03428297,0.05403616,0.0933716,0.006378737,0.0002253955,0.003309097,0.002244944,0.04247726],"genre_scores_gemma":[0.8601758,0.01742602,0.04412158,0.02243818,0.001131174,0.0002509498,0.002519569,0.001036449,0.05090031],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.005917197,"threshold_uncertainty_score":0.019795,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.02056449143534839,"score_gpt":0.2385680930302302,"score_spread":0.2180036015948818,"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."}}