{"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":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.002257994,0.001672807,0.001834111,0.003728642,0.001522986,0.001614464,0.00129848,0.0021264,0.01905199],"category_scores_gemma":[0.004383652,0.001204008,0.001990012,0.002164497,0.0008429423,0.0006026932,0.002086605,0.001817256,0.02234928],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0002713439,"about_ca_system_score_gemma":0.001895095,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.001429113,"about_ca_topic_score_gemma":0.0030173,"domain_scores_codex":[0.9964278,0.000458362,0.0004802145,0.001017801,0.001232204,0.000383515],"domain_scores_gemma":[0.9984643,0.000240294,0.000104915,0.0003154322,0.0007615244,0.000113593],"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":[0.001214413,0.0005112255,0.007592453,0.002994047,0.0001618809,0.001704499,0.0009506296,0.0009841574,0.8300485,0.001495207,0.02732076,0.1250222],"study_design_scores_gemma":[0.0002235129,0.001761478,0.03030256,0.002022098,0.0002846632,0.002345772,0.0007940349,0.003348105,0.5260686,0.004503059,0.4280422,0.0003039833],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"methods","genre_gemma":"methods","genre_scores_codex":[0.1049791,0.01437163,0.6998423,0.002257818,0.004444303,0.02705975,0.09393399,0.01550497,0.03760612],"genre_scores_gemma":[0.1045592,0.01469634,0.6874685,0.0042924,0.001108803,0.02774995,0.1250515,0.004009697,0.03106358],"genre_candidate":"methods","genre_consensus":"methods","teacher_disagreement_score":0.01905199,"threshold_uncertainty_score":0.06373531,"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."}}