{"id":"W4388523918","doi":"10.2196/50733","title":"Genomic, Proteomic, and Phenotypic Biomarkers of COVID-19 Severity: Protocol for a Retrospective Observational Study","year":2023,"lang":"en","type":"article","venue":"JMIR Research Protocols","topic":"SARS-CoV-2 detection and testing","field":"Medicine","cited_by":5,"is_retracted":false,"has_abstract":true,"ca_institutions":"","funders":"National Center for Mental Health; National Institute of Child Health and Human Development; NIHR Maudsley Biomedical Research Centre; Branch Out Neurological Foundation; Instituto de Salud Carlos III; Siemens Healthineers; Gratama Stichting; Universitair Medisch Centrum Groningen; Türkiye Bilimsel ve Teknolojik Araştırma Kurumu; Ministero dell’Istruzione, dell’Università e della Ricerca; National Institutes of Health; GGZ inGeest; University of California, San Francisco; Rivierduinen; Ministero della Salute; Vrije Universiteit Amsterdam; National Alliance for Research on Schizophrenia and Depression; ZonMw; Alberta Children's Hospital Foundation; Klingenstein Third Generation Foundation; Universiteit Leiden; King's College London; Department for the Economy; Amsterdam University Medical Centers; Generalitat de Catalunya; European Regional Development Fund; National Healthcare Group; Bundesministerium für Bildung und Forschung; National Institute for Health and Care Research; Science Foundation Ireland; University of Minnesota; EU Joint Programme – Neurodegenerative Disease Research; National Health and Medical Research Council; Ege Üniversitesi; Public Health Agency; National Institute of Mental Health; Children's Hospital Foundation; Ministerio de Ciencia e Innovación; American Foundation for Suicide Prevention; Universitätsmedizin Göttingen; Medical Research Council; Leids Universitair Medisch Centrum; Department of Health and Social Care; University of Texas MD Anderson Cancer Center; Brain and Behavior Research Foundation","keywords":"Medicine; Cohort study; Retrospective cohort study; Cohort; Observational study; Intensive care medicine; Immunology; Internal medicine","routes":{"ca_aff":false,"ca_fund":true,"ca_venue":true,"about_ca":false,"invisible_to_affiliation_only":true},"retraction":null,"screen":null,"direct_labels":[],"prediction":{"model_version":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.003502105,0.0001867241,0.0003915552,0.0005678029,0.0003768512,0.0000698334,0.0001839518,0.0001206227,0.00006430452],"category_scores_gemma":[0.00349696,0.0001650226,0.00008581788,0.001297027,0.0002766317,0.0001225584,0.00024072,0.0004117018,0.00002585769],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0004064401,"about_ca_system_score_gemma":0.001074684,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00008178213,"about_ca_topic_score_gemma":0.00002329671,"domain_scores_codex":[0.9971835,0.0003461012,0.0004990461,0.0005970962,0.0008464322,0.0005278219],"domain_scores_gemma":[0.9979447,0.0005030264,0.0001744478,0.0004214989,0.000747511,0.0002088595],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"observational","study_design_gemma":"observational","study_design_scores_codex":[0.01112061,0.001733475,0.5508694,0.005060931,0.0002220067,0.00004888088,0.001724211,0.000001180913,0.4165189,0.000248257,0.00928803,0.003164113],"study_design_scores_gemma":[0.03519069,0.01269895,0.721142,0.001313338,0.00001486016,0.0000522913,0.001583519,0.002428256,0.09818088,0.006136741,0.1208129,0.0004455826],"study_design_candidate":"observational","study_design_consensus":"observational","genre_codex":"protocol","genre_gemma":"protocol","genre_scores_codex":[0.1454976,2.030194e-7,0.00006753905,0.000517494,0.000003660853,0.8534111,0.00002636915,0.0001913376,0.0002847359],"genre_scores_gemma":[0.00830265,2.16978e-8,0.001343973,0.0001618708,0.0001258116,0.9897109,0.000006850977,0.00004854532,0.0002993514],"genre_candidate":"protocol","genre_consensus":"protocol","teacher_disagreement_score":0.318338,"threshold_uncertainty_score":0.6729426,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.556494646697397,"score_gpt":0.5866387117050602,"score_spread":0.0301440650076632,"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."}}