ArticlemedRxiv : the preprint server for health sciences2025
Integrating a host transcriptomic biomarker with a large language model for diagnosis of lower respiratory tract infection.
Hoang Van Phan, Natasha Spottiswoode, Emily C Lydon, Victoria T Chu, Adolfo Cuesta, Alexander D Kazberouk, Natalie L Richmond, Padmini Deosthale, Carolyn S Calfee, Charles R Langelier
Abstract readPreprint
In one paragraphArticle in medRxiv : the preprint server for health sciences, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.
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2 · The registryThe trial behind it
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4 · The recordCorrections and comments
5 · Who and what moneyAuthors and funding
10 authors.
Hoang Van PhanDepartment of Medicine, Division of Infectious Diseases, University of California San Francisco.
Natasha SpottiswoodeDepartment of Medicine, Division of Infectious Diseases, University of California San Francisco.
Emily C LydonDepartment of Medicine, Division of Infectious Diseases, University of California San Francisco.
Victoria T ChuDepartment of Pediatrics, Division of Infectious Diseases and Global Health, University of California San Francisco.
Adolfo CuestaDepartment of Medicine, Division of Infectious Diseases, University of California San Francisco.
Alexander D KazberoukDepartment of Medicine, University of California San Francisco.
Natalie L RichmondDepartment of Medicine, Division of Infectious Diseases, University of California San Francisco.
Padmini DeosthaleDepartment of Medicine, Division of Infectious Diseases, University of California San Francisco.
Carolyn S CalfeeDepartment of Medicine, Division of Pulmonary, Critical Care, Allergy and Sleep Medicine, University of California San Francisco.
Charles R LangelierDepartment of Medicine, Division of Infectious Diseases, University of California San Francisco.
Funding
BIOLOGY OF INFECTIOUS DISEASES TRAINING PROGRAMT32AI007641 · NIAID · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI MATTHEW G DORSEY · 2000 to 2026
$6.9MPrecision Medicine in the Acute Respiratory Distress SyndromeR35HL140026 · NHLBI · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI CALFEE, CAROLYN · 2018 to 2024
$6.8MIntegrated Host-Microbe Metagenomics for Sepsis Pathogen Surveillance, Subphenotyping and Outcome PredictionR01AI185511 · NIAID · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI Charles Langelier · 2024 to 2026
$2.0MMetagenomic surveillance of pathogen and antimicrobial resistance gene transmission in hospitalized neonatesK23AI185326 · NIAID · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI CHU, VICTORIA TIEN-YU · 2024 to 2025
$395kNHLBI NIH HHS R35 HL140026NIAID NIH HHS K23 AI185326NIAID NIH HHS R01 AI185511NIAID NIH HHS T32 AI007641
6 · The paper itselfAbstract
backgroundLower respiratory tract infections (LRTIs) are a leading cause of mortality worldwide and can be difficult to diagnose in critically ill patients, as non-infectious causes of respiratory failure can present with similar clinical features.
methodsWe developed a LRTI diagnostic method combining the pulmonary transcriptomic biomarker
resultsIn the derivation cohort, a combined classifier incorporating
conclusionsIntegrating a host transcriptional biomarker with EMR text analysis using a large language model may offer a promising new approach to improving the diagnosis of LRTIs in critically ill adults.
Identifiers
PMID40236397
PMCPMC11998817
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