{"id":"W2522930703","doi":"10.1038/srep26228","title":"Genome-directed analysis of prophage excision, host defence systems, and central fermentative metabolism in Clostridium pasteurianum","year":2016,"lang":"en","type":"article","venue":"Scientific Reports","topic":"Biochemical and Molecular Research","field":"Biochemistry, Genetics and Molecular Biology","cited_by":21,"is_retracted":false,"has_abstract":true,"ca_institutions":"Centurion Biofuels (Canada); McMaster University; University of Waterloo","funders":"Natural Sciences and Engineering Research Council of Canada; Canada Research Chairs","keywords":"Biology; Organism; CRISPR; Genome; Genetics; Metabolic pathway; Computational biology; Prophage; Gene; Bacteriophage","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":[0.0005474646,0.000128986,0.000261433,0.0002402417,0.00005916853,0.00005511883,0.0001299224,0.00009737993,0.00002812016],"category_scores_gemma":[0.0002242566,0.00008682391,0.00009793968,0.0007735474,0.0003517095,0.000007897122,0.0001812117,0.00005142184,0.000001318372],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00001849062,"about_ca_system_score_gemma":0.0001111496,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00004217837,"about_ca_topic_score_gemma":0.00002203104,"domain_scores_codex":[0.998015,0.0001204595,0.0004330059,0.0007391931,0.000349665,0.0003427173],"domain_scores_gemma":[0.9989326,0.00001282776,0.000188915,0.0005150266,0.0002028538,0.0001477843],"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":[0.00003975948,0.00005567638,0.006306206,0.00001880087,0.0001299748,0.00006882233,0.00005266094,0.000004593012,0.9929141,0.00001024877,0.0001786679,0.0002205207],"study_design_scores_gemma":[0.0002556884,0.00003906728,0.05880251,0.00002390678,0.00008638619,0.00002636185,0.00005876576,0.00002048698,0.9366059,0.00005394468,0.003889072,0.0001378915],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9970545,0.001686986,0.0003339595,0.00004622699,0.0004009732,0.0003166416,0.00003850538,0.000008023539,0.0001141614],"genre_scores_gemma":[0.9984506,0.00007993027,0.000107306,0.000006560879,0.00003007984,0.00002373089,0.0001368907,0.000009110135,0.00115579],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.05630815,"threshold_uncertainty_score":0.3540576,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.0101047787812791,"score_gpt":0.2584367936889377,"score_spread":0.2483320149076586,"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."}}