{"id":"W3154535139","doi":"10.1016/j.xpro.2021.100435","title":"Processing human urine and ureteral stents for 16S rRNA amplicon sequencing","year":2021,"lang":"en","type":"article","venue":"STAR Protocols","topic":"Urinary Tract Infections Management","field":"Medicine","cited_by":5,"is_retracted":false,"has_abstract":true,"ca_institutions":"Western University; Lawson Health Research Institute","funders":"W. Garfield Weston Foundation; Garfield Weston Foundation","keywords":"Amplicon; Amplicon sequencing; 16S ribosomal RNA; Urine; DNA extraction; Microbiome; Stent; Biology; Computational biology; Polymerase chain reaction; Medicine; Bioinformatics; Gene; Genetics; Internal medicine","routes":{"ca_aff":true,"ca_fund":true,"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":[0.0001847367,0.0001394888,0.0002148913,0.00008124551,0.000206356,0.00008525621,0.0000446632,0.00004737444,0.00009116437],"category_scores_gemma":[0.00004653378,0.000132452,0.00005651769,0.0001287654,0.0000354781,0.000166188,0.00007276256,0.0001338571,0.000004989301],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0001548628,"about_ca_system_score_gemma":0.0001106041,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0000154195,"about_ca_topic_score_gemma":0.00001033219,"domain_scores_codex":[0.999004,0.00002599316,0.0002437808,0.0003128798,0.000163641,0.0002496747],"domain_scores_gemma":[0.9993936,0.00001643121,0.00008544128,0.0002526775,0.0001577119,0.00009412593],"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":[0.0019991,0.008283447,0.1935614,0.03360179,0.001171135,0.001590055,0.004302921,0.0000775567,0.6152471,0.008614361,0.005076161,0.1264749],"study_design_scores_gemma":[0.03599621,0.02313756,0.1991007,0.008492168,0.0008632913,0.001736194,0.001868329,0.002809339,0.1844016,0.01015339,0.5294163,0.002024964],"study_design_candidate":"bench_or_experimental","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.8226578,0.00005609198,0.002724953,0.0007734034,0.00005455753,0.1669812,0.00001790953,0.0002392502,0.006494845],"genre_scores_gemma":[0.7674352,0.00000180856,0.01302107,0.0006046572,0.0003277468,0.2130833,0.00007192758,0.00006459134,0.005389682],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.5243402,"threshold_uncertainty_score":0.5401233,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.0826485608709706,"score_gpt":0.3886747898251554,"score_spread":0.3060262289541848,"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."}}