{"id":"W2086081694","doi":"10.1128/jcm.05880-11","title":"Validation of the MycAssay Pneumocystis Kit for Detection of Pneumocystis jirovecii in Bronchoalveolar Lavage Specimens by Comparison to a Laboratory Standard of Direct Immunofluorescence Microscopy, Real-Time PCR, or Conventional PCR","year":2012,"lang":"en","type":"article","venue":"Journal of Clinical Microbiology","topic":"Pneumocystis jirovecii pneumonia detection and treatment","field":"Medicine","cited_by":53,"is_retracted":false,"has_abstract":true,"ca_institutions":"Hospital for Sick Children; University of Toronto; Public Health Ontario","funders":"Alere","keywords":"Pneumocystis jirovecii; Bronchoalveolar lavage; Pneumocystis pneumonia; Pneumocystis carinii; Pneumocystosis; Biology; Positive predicative value; Virology; Polymerase chain reaction; Gold standard (test); Real-time polymerase chain reaction; Molecular biology; Microbiology; Predictive value; Medicine; Human immunodeficiency virus (HIV); Lung; Internal medicine","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":[0.002450575,0.0002736707,0.001810195,0.0002691747,0.00005980513,0.000007670015,0.0002634886,0.0003512976,0.00009949057],"category_scores_gemma":[0.002230451,0.00018887,0.0005910428,0.0003861039,0.000338428,0.000128866,0.00008677267,0.0004703209,0.000008321511],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0002789517,"about_ca_system_score_gemma":0.0003931616,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00005140031,"about_ca_topic_score_gemma":0.00003207105,"domain_scores_codex":[0.9952087,0.0007309807,0.003135552,0.0002882448,0.0002605149,0.0003759771],"domain_scores_gemma":[0.9942492,0.001750688,0.00263118,0.0003858955,0.0007728899,0.0002101127],"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":[0.009169672,0.001479443,0.03899129,0.0001385495,0.0003262736,0.000004275734,0.0001289117,0.00001699236,0.9473068,0.000008359282,0.0009762117,0.001453199],"study_design_scores_gemma":[0.005357847,0.006595479,0.09813919,0.0005563239,0.000342712,0.0001829575,0.00006201433,0.00001319092,0.8789568,0.00001046634,0.00963455,0.0001484556],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9954717,0.0005160188,0.000518297,0.0005053756,0.001240683,0.0008347753,0.0008408754,0.0000100452,0.00006227745],"genre_scores_gemma":[0.9975223,0.0003360447,0.001610439,0.00008185986,0.0001720991,0.00001529409,0.00002352777,0.00003078529,0.0002076791],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.06835,"threshold_uncertainty_score":0.7701893,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.02789931492563857,"score_gpt":0.3587345960898429,"score_spread":0.3308352811642044,"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."}}