{"id":"W2096969333","doi":"10.1093/nar/gkv128","title":"Silent mutations at codons 65 and 66 in reverse transcriptase alleviate indel formation and restore fitness in subtype B HIV-1 containing D67N and K70R drug resistance mutations","year":2015,"lang":"en","type":"article","venue":"Nucleic Acids Research","topic":"HIV Research and Treatment","field":"Immunology and Microbiology","cited_by":11,"is_retracted":false,"has_abstract":true,"ca_institutions":"AIDS Vancouver","funders":"National Institute of Allergy and Infectious Diseases; National Health and Medical Research Council; Medical Research Council; National Institutes of Health; Monash University; Burnet Institute","keywords":"Biology; Indel; Nonsynonymous substitution; Reverse transcriptase; Genetics; Silent mutation; Mutation; Resistance mutation; Virology; Synonymous substitution; Drug resistance; Viral evolution; Gene; Genome; Single-nucleotide polymorphism; Codon usage bias; RNA; Genotype; Missense mutation","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":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0001825369,0.0002324697,0.0002607231,0.0002150035,0.0001242782,0.0003111597,0.000199697,0.0002048242,0.0009786754],"category_scores_gemma":[0.0002246339,0.0001374141,0.0001745367,0.00009296739,0.0002216908,0.0001137579,0.0002045884,0.0004412914,0.0003128514],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.000136856,"about_ca_system_score_gemma":0.0001926007,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0004189899,"about_ca_topic_score_gemma":0.0008422213,"domain_scores_codex":[0.999849,0.00003224479,0.00001277855,0.00001946375,0.00004919839,0.00003735193],"domain_scores_gemma":[0.9998657,0.00003363361,0.00003844893,0.00001602043,0.00001237139,0.00003378199],"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":[0.0001135916,0.00006788535,0.0003310322,0.00001979557,0.000006977927,0.00005271942,0.00001851579,0.0001002441,0.99568,0.0001119128,0.00003941354,0.003457914],"study_design_scores_gemma":[0.00004469584,0.0009537358,0.008368884,0.00001683969,0.00003772038,0.0005279156,0.00005179203,0.002448315,0.9853837,0.0001712246,0.001981918,0.00001332159],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9972817,0.0003606883,0.001280555,0.00003502717,0.00001121932,0.00001236287,0.00005451591,0.00005508015,0.0009089054],"genre_scores_gemma":[0.9964843,0.0003220904,0.001874372,0.00008171667,0.000007270904,0.00001112095,0.0001397479,0.00004239195,0.001037091],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.0009786754,"threshold_uncertainty_score":0.003274024,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.06252336997962676,"score_gpt":0.3278688096268917,"score_spread":0.265345439647265,"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."}}