{"id":"W1481261513","doi":"10.1186/s12977-015-0171-7","title":"In virio SHAPE analysis of tRNALys3 annealing to HIV-1 genomic RNA in wild type and protease-deficient virus","year":2015,"lang":"en","type":"article","venue":"Retrovirology","topic":"HIV Research and Treatment","field":"Immunology and Microbiology","cited_by":29,"is_retracted":false,"has_abstract":true,"ca_institutions":"McGill University; Jewish General Hospital","funders":"Canadian Institutes of Health Research","keywords":"Primer binding site; RNA; Transfer RNA; Reverse transcriptase; Virology; Biology; Transcription (linguistics); Virus; Group-specific antigen; Molecular biology; Chemistry; Gene; Genetics","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":[0.0004782134,0.0001357033,0.0005211132,0.0008358821,0.00002837316,0.000005342501,0.0001443789,0.0001900755,0.0002115406],"category_scores_gemma":[0.000169384,0.0001196841,0.00005414042,0.001014758,0.0001332409,0.00003839056,0.0001174274,0.0002408815,0.0003976542],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0001470181,"about_ca_system_score_gemma":0.000113555,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.001497203,"about_ca_topic_score_gemma":0.001370422,"domain_scores_codex":[0.9985217,0.0003155328,0.0003470392,0.0003454396,0.00004654848,0.0004237271],"domain_scores_gemma":[0.9994563,0.00009136027,0.00007622781,0.0002411332,0.00006000442,0.00007492233],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"observational","study_design_gemma":"observational","study_design_scores_codex":[0.002039957,0.0004065676,0.5971303,0.00001476586,0.0008682842,0.0001460193,0.001887111,0.002009126,0.3920285,0.0001298866,0.0005404939,0.002799017],"study_design_scores_gemma":[0.00708246,0.00377279,0.9590179,0.00002792131,0.0005693761,0.00007649372,0.000561492,0.001606312,0.01718228,0.0001226475,0.009544375,0.0004359733],"study_design_candidate":"observational","study_design_consensus":"observational","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9965864,0.00224215,0.00002350201,0.0004580347,0.00006610638,0.0003081762,0.00007332591,0.000009605467,0.0002326379],"genre_scores_gemma":[0.999318,0.00007870601,0.00008048551,0.000140002,0.00000813736,0.00003048864,0.00009194301,0.000009422037,0.0002428396],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.3748462,"threshold_uncertainty_score":0.5111173,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.02493549808471472,"score_gpt":0.2841785388285815,"score_spread":0.2592430407438668,"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."}}