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Ghosh P, Niesen MJ, Pawlowski C, Bandi H, Yoo U, Lenehan PJ, M. PK, Nadig M, Ross J, Ardhanari S, O’Horo JC, Venkatakrishnan AJ, Rosen CJ, Telenti A, Hurt RT, Soundararajan V. Severe acute infection and chronic pulmonary disease are risk factors for developing post-COVID-19 conditions. medRxiv 2022:2022.11.30.22282831. [PMID: 36523407 PMCID: PMC9753786 DOI: 10.1101/2022.11.30.22282831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Post-COVID-19 conditions, also known as "long COVID", has significantly impacted the lives of many individuals, but the risk factors for this condition are poorly understood. In this study, we performed a retrospective EHR analysis of 89,843 individuals at a multi-state health system in the United States with PCR-confirmed COVID-19, including 1,086 patients diagnosed with long COVID and 1,086 matched controls not diagnosed with long COVID. For these two cohorts, we evaluated a wide range of clinical covariates, including laboratory tests, medication orders, phenotypes recorded in the clinical notes, and outcomes. We found that chronic pulmonary disease (CPD) was significantly more common as a pre-existing condition for the long COVID cohort than the control cohort (odds ratio: 1.9, 95% CI: [1.5, 2.6]). Additionally, long-COVID patients were more likely to have a history of migraine (odds ratio: 2.2, 95% CI: [1.6, 3.1]) and fibromyalgia (odds ratio: 2.3, 95% CI: [1.3, 3.8]). During the acute infection phase, the following lab measurements were abnormal in the long COVID cohort: high triglycerides (meanlongCOVID: 278.5 mg/dL vs. meancontrol: 141.4 mg/dL), low HDL cholesterol levels (meanlongCOVID: 38.4 mg/dL vs. meancontrol: 52.5 mg/dL), and high neutrophil-lymphocyte ratio (meanlongCOVID: 10.7 vs. meancontrol: 7.2). The hospitalization rate during the acute infection phase was also higher in the long COVID cohort compared to the control cohort (ratelongCOVID: 5% vs. ratecontrol: 1%). Overall, this study suggests that the severity of acute infection and a history of CPD, migraine, CFS, or fibromyalgia may be risk factors for long COVID symptoms. Our findings motivate clinical studies to evaluate whether suppressing acute disease severity proactively, especially in patients at high risk, can reduce incidence of long COVID.
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Affiliation(s)
| | | | | | - Hari Bandi
- nference, inc., Cambridge, Massachusetts 02139, USA
| | - Unice Yoo
- nference, inc., Cambridge, Massachusetts 02139, USA
| | | | | | - Mihika Nadig
- nference, inc., Cambridge, Massachusetts 02139, USA
| | - Jason Ross
- nference, inc., 18 3rd St. S.W., Rochester MN 55902, USA
| | | | | | | | - Clifford J. Rosen
- Maine Medical Center, Portland, ME 04102, USA
- NIH RECOVER Initiative, USA
| | | | | | - Venky Soundararajan
- nference Labs, Bengaluru, India
- nference, inc., Cambridge, Massachusetts 02139, USA
- nference, inc., 18 3rd St. S.W., Rochester MN 55902, USA
- nference, inc. 2424 Erwin Road, Durham, NC 27705, USA
- Anumana, inc., Cambridge, Massachusetts 02139, USA
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Murugadoss K, Rajasekharan A, Malin B, Agarwal V, Bade S, Anderson JR, Ross JL, Faubion WA, Halamka JD, Soundararajan V, Ardhanari S. Building a best-in-class automated de-identification tool for electronic health records through ensemble learning. Patterns (N Y) 2021; 2:100255. [PMID: 34179842 PMCID: PMC8212138 DOI: 10.1016/j.patter.2021.100255] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 02/24/2021] [Accepted: 04/07/2021] [Indexed: 10/29/2022]
Abstract
The presence of personally identifiable information (PII) in natural language portions of electronic health records (EHRs) constrains their broad reuse. Despite continuous improvements in automated detection of PII, residual identifiers require manual validation and correction. Here, we describe an automated de-identification system that employs an ensemble architecture, incorporating attention-based deep-learning models and rule-based methods, supported by heuristics for detecting PII in EHR data. Detected identifiers are then transformed into plausible, though fictional, surrogates to further obfuscate any leaked identifier. Our approach outperforms existing tools, with a recall of 0.992 and precision of 0.979 on the i2b2 2014 dataset and a recall of 0.994 and precision of 0.967 on a dataset of 10,000 notes from the Mayo Clinic. The de-identification system presented here enables the generation of de-identified patient data at the scale required for modern machine-learning applications to help accelerate medical discoveries.
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Affiliation(s)
| | | | - Bradley Malin
- Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | | | | | - Jeff R. Anderson
- Mayo Clinic, Rochester, MN 55905, USA
- Mayo Clinic Platform, Rochester, MN 55905, USA
| | | | | | - John D. Halamka
- Mayo Clinic, Rochester, MN 55905, USA
- Mayo Clinic Platform, Rochester, MN 55905, USA
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Altun A, Aydyn G, Bontempi L, Curnis A, Cerini M, D'Aloia A, Lipari A, Pagnoni C, Ashofair N, Vassanelli F, Cas LD, Al Ghamdi S, Dariri K, Al Fagih A, Vodnala D, Ardhanari S, Mangalpally K, Thakur R, Arena F, Metwally D, Barin E, Bontempi L, Curnis A, Cerini M, Vizzardi E, Lipari A, Pagnoni C, Ashofair N, Mutti MG, Vassanelli F, Cas LD. Bradycardia Pacing. Europace 2011. [DOI: 10.1093/europace/euq475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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