{"id":"W4213178920","doi":"10.3390/microorganisms10020441","title":"Clinical Metagenomics Is Increasingly Accurate and Affordable to Detect Enteric Bacterial Pathogens in Stool","year":2022,"lang":"en","type":"article","venue":"Microorganisms","topic":"Probiotics and Fermented Foods","field":"Agricultural and Biological Sciences","cited_by":23,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of Saskatchewan; Saskatchewan Disease Control Laboratory; Manitoba Health; University of Manitoba; Public Health Agency of Canada","funders":"","keywords":"Metagenomics; Subtyping; Multiplex; Biology; Shigella; Salmonella; Campylobacter; Microbiome; Microbiological culture; Pathogen; Multiplex polymerase chain reaction; Gold standard (test); Microbiology; Polymerase chain reaction; Computational biology; Medicine; Bioinformatics; Genetics; Bacteria; Gene","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":["insufficient_payload"],"consensus_categories":[],"category_scores_codex":[0.0005270548,0.0001315776,0.0002191922,0.00002062854,0.0002382636,0.00008706907,0.0002502587,0.00005871673,0.000993324],"category_scores_gemma":[0.00002355081,0.00006565059,0.0000614383,0.0002938642,0.00002813336,0.00004726683,0.0005258972,0.0001746232,0.00002518953],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00005459629,"about_ca_system_score_gemma":0.00001362755,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0001211577,"about_ca_topic_score_gemma":0.0001759777,"domain_scores_codex":[0.9988057,0.0001519064,0.0003068347,0.0003536406,0.00009187133,0.0002900415],"domain_scores_gemma":[0.9996778,0.00005777324,0.00007038777,0.00006548193,0.00001525864,0.0001133053],"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":[0.000092818,0.00006902384,0.002856605,0.000001691748,0.00001098226,0.00001082858,0.0001365261,0.000001710363,0.9753811,0.000009687697,0.0002289684,0.02120008],"study_design_scores_gemma":[0.001940247,0.004759038,0.4711621,0.00002234628,0.00008195573,0.0001666294,0.001563043,0.00009699783,0.1740549,0.000870314,0.344044,0.001238417],"study_design_candidate":"bench_or_experimental","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9984274,0.00008929841,0.00001150593,0.0005959974,0.0002495145,0.0002504521,0.0002786266,0.00002482044,0.00007239822],"genre_scores_gemma":[0.9972929,0.00004721715,0.001061909,0.001301231,0.0001014024,0.00001267524,0.00004577542,0.000002531787,0.0001343316],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.8013262,"threshold_uncertainty_score":0.9999199,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.02256993602124431,"score_gpt":0.2415921977907503,"score_spread":0.219022261769506,"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."}}