{"id":"W2157219992","doi":"10.1371/journal.ppat.1002106","title":"Detection of Inferred CCR5- and CXCR4-Using HIV-1 Variants and Evolutionary Intermediates Using Ultra-Deep Pyrosequencing","year":2011,"lang":"en","type":"article","venue":"PLoS Pathogens","topic":"HIV Research and Treatment","field":"Immunology and Microbiology","cited_by":60,"is_retracted":false,"has_abstract":true,"ca_institutions":"AIDS Vancouver","funders":"National Institute of Allergy and Infectious Diseases; Rijksinstituut voor Volksgezondheid en Milieu; Canadian Institutes of Health Research; Universiteit van Amsterdam; National Institutes of Health; Stichting Sanquin Bloedvoorziening; Small Business Innovation Research; GlaxoSmithKline","keywords":"Biology; V3 loop; CXCR4; Genetics; Phenotype; Computational biology; Human immunodeficiency virus (HIV); Transition (genetics); Gene; Virology; Peptide sequence; Chemokine; Receptor","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":[0.00009819477,0.0001255759,0.0001959438,0.0001373367,0.000164092,0.000006264989,0.0000497145,0.0001263292,0.00008032397],"category_scores_gemma":[0.0001059856,0.0001120823,0.00003278818,0.00008011428,0.0002509874,0.0001123488,0.00005386381,0.0001247056,0.00002767194],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00005487677,"about_ca_system_score_gemma":0.00004555435,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.000207588,"about_ca_topic_score_gemma":0.00002954032,"domain_scores_codex":[0.9991597,0.0001254547,0.00019386,0.0002220132,0.00003462979,0.0002643294],"domain_scores_gemma":[0.9996158,0.00007205887,0.0000812068,0.000126997,0.00006252131,0.00004134065],"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":[0.00008508223,0.0001156627,0.06067089,0.00003351646,0.0001612623,0.00002346266,0.001477712,0.000001758141,0.9358148,0.00001038835,0.000001023725,0.001604434],"study_design_scores_gemma":[0.001561761,0.000410774,0.2268184,0.0001320108,0.0002091203,0.0004218263,0.0008620126,0.0008094586,0.76825,0.0002789093,0.0000149254,0.0002308163],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9968308,0.001948171,0.0006285759,0.000003617286,0.00008474414,0.0001757536,0.0001404032,0.00002576248,0.0001622082],"genre_scores_gemma":[0.9987808,0.0001169266,0.001004857,0.000006257105,0.00001474331,0.000007224335,0.00003628083,0.00001282305,0.00002013042],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.1675648,"threshold_uncertainty_score":0.4570584,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.04479428727955383,"score_gpt":0.2461303873434034,"score_spread":0.2013361000638496,"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."}}