{"id":"W4409567315","doi":"10.1002/jmv.70353","title":"Enrichment of G‐to‐U Substitution in SARS‐CoV‐2 Functional Regions and Its Compensation via Concurrent Mutations","year":2025,"lang":"en","type":"article","venue":"Journal of Medical Virology","topic":"RNA regulation and disease","field":"Biochemistry, Genetics and Molecular Biology","cited_by":0,"is_retracted":false,"has_abstract":true,"ca_institutions":"Queen's University","funders":"Ralph W. and Grace M. Showalter Research Trust Fund; School of Medicine, Indiana University; Walther Cancer Foundation","keywords":"Nonsynonymous substitution; APOBEC; Biology; Mutation; Genetics; RNA; Nucleotide; Molecular biology; Genome; 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":[],"consensus_categories":[],"category_scores_codex":[0.0002909471,0.00005065329,0.0001223121,0.000143739,0.0000235164,0.000002857847,0.00006537155,0.0001138083,0.00002904681],"category_scores_gemma":[0.0003440249,0.00004462454,0.00004110748,0.0000961784,0.0000786856,0.000004020377,0.00003319854,0.00008741461,0.000001380041],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00001680379,"about_ca_system_score_gemma":0.0001950896,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.000003345221,"about_ca_topic_score_gemma":0.00002590913,"domain_scores_codex":[0.9992254,0.00008711793,0.0003323566,0.00008695642,0.0001968887,0.00007122537],"domain_scores_gemma":[0.9995983,0.00003352717,0.0001219854,0.00004965656,0.0001120914,0.00008446511],"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":[0.0007984569,0.0007210739,0.02817847,0.00006428098,0.0001498511,0.00002886966,0.0001079392,0.001769312,0.8992665,0.05276953,0.00668842,0.009457255],"study_design_scores_gemma":[0.006320161,0.0008375815,0.9178433,0.0001323233,0.0001062246,0.0001739935,0.00009135233,0.005785964,0.03476441,0.002664299,0.03111043,0.0001699584],"study_design_candidate":"observational","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9457573,0.0007576442,0.04607768,0.006966792,0.000293412,0.00007283906,0.000002485552,0.000001103702,0.00007079817],"genre_scores_gemma":[0.9987487,0.0001435908,0.00006069294,0.0009305094,0.00006517023,0.000003236185,0.00001915395,0.000001770709,0.00002719477],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.8896648,"threshold_uncertainty_score":0.1819736,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.0196378307924885,"score_gpt":0.3148704838029958,"score_spread":0.2952326530105073,"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."}}