{"id":"W2559271309","doi":"10.1007/978-1-4939-6691-2_5","title":"DNA-, RNA-, and Protein-Based Stable-Isotope Probing for High-Throughput Biomarker Analysis of Active Microorganisms","year":2016,"lang":"en","type":"article","venue":"Methods in molecular biology","topic":"Microbial Community Ecology and Physiology","field":"Environmental Science","cited_by":28,"is_retracted":false,"has_abstract":false,"ca_institutions":"University of Waterloo","funders":"Natural Environment Research Council; Sight Research UK","keywords":"Stable-isotope probing; Biology; Computational biology; Amplicon; DNA sequencing; Genome; Amplicon sequencing; Microorganism; Gene; 16S ribosomal RNA; Genetics; Bacteria; Polymerase chain reaction","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":[],"consensus_categories":[],"category_scores_codex":[0.001130012,0.0001632115,0.0004772924,0.0001747153,0.00007873302,0.000003533084,0.0002798426,0.0002536737,0.0007784811],"category_scores_gemma":[0.0003122263,0.0001215371,0.00009218499,0.0004932813,0.0006293008,0.00003863372,0.0002630444,0.000105919,0.000003469915],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00008231208,"about_ca_system_score_gemma":0.00002298154,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0003651726,"about_ca_topic_score_gemma":0.0004708516,"domain_scores_codex":[0.997164,0.001780481,0.0003021183,0.0004030521,0.00003070432,0.0003196057],"domain_scores_gemma":[0.9987442,0.0006567806,0.0001777111,0.000361782,0.00002053723,0.00003895692],"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":[0.0001669087,0.00007471565,0.002028926,0.00001064186,0.0001897443,0.000001267766,0.00009897429,0.00005307642,0.9824557,0.0008295356,0.0000127085,0.01407781],"study_design_scores_gemma":[0.0007571914,0.0002602445,0.01044923,0.000011051,0.0001267851,7.322946e-7,0.00001709099,0.0001369733,0.9741148,0.01297419,0.0009790931,0.0001726301],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.5115305,0.00002001532,0.4876806,0.0002174681,0.00003053681,0.00038918,0.00003846687,0.000007324292,0.00008585036],"genre_scores_gemma":[0.5758484,0.000004736605,0.4237053,0.0002504922,0.000003184711,0.00009161088,0.00003182639,0.00001231622,0.00005218727],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.06431788,"threshold_uncertainty_score":0.8523821,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01932883471571928,"score_gpt":0.3335172428464167,"score_spread":0.3141884081306974,"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."}}