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Article ; Online: Identifying signs and symptoms of AL amyloidosis in electronic health records using natural language processing, diagnosis codes, and manually abstracted registry data.

Silvert, Eli / Hester, Laura / Ramudu, Eshwan / Pawlowski, Colin / Kranenburg, Britte / Buadi, Francis / Muchtar, Eli / Khaled, Samer / Tran, Namphuong / Soundararajan, Venky / Khan, Najat / Gertz, Morie / Dispenzieri, Angela

American journal of hematology

2023 Volume 98, Issue 9, Page(s) E255–E258

MeSH term(s)	Humans ; Electronic Health Records ; Natural Language Processing ; Immunoglobulin Light-chain Amyloidosis/diagnosis ; Routinely Collected Health Data ; Algorithms
Language	English
Publishing date	2023-07-04
Publishing country	United States
Document type	Letter ; Research Support, Non-U.S. Gov't
ZDB-ID	196767-8
ISSN	1096-8652 ; 0361-8609
ISSN (online)	1096-8652
ISSN	0361-8609
DOI	10.1002/ajh.27019
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Large Eddy Simulation of Heat Entrainment Under Arctic Sea Ice

Ramudu, Eshwan / Gelderloos, Renske / Yang, Di / Meneveau, Charles / Gnanadesikan, Anand

Journal of geophysical research. 2018 Jan., v. 123, no. 1

2018

Abstract: Arctic sea ice has declined rapidly in recent decades. The faster than projected retreat suggests that free‐running large‐scale climate models may not be accurately representing some key processes. The small‐scale turbulent entrainment of heat from the ... ...

Abstract	Arctic sea ice has declined rapidly in recent decades. The faster than projected retreat suggests that free‐running large‐scale climate models may not be accurately representing some key processes. The small‐scale turbulent entrainment of heat from the mixed layer could be one such process. To better understand this mechanism, we model the Arctic Ocean's Canada Basin, which is characterized by a perennial anomalously warm Pacific Summer Water (PSW) layer residing at the base of the mixed layer and a summertime Near‐Surface Temperature Maximum (NSTM) within the mixed layer trapping heat from solar radiation. We use large eddy simulation (LES) to investigate heat entrainment for different ice‐drift velocities and different initial temperature profiles. The value of LES is that the resolved turbulent fluxes are greater than the subgrid‐scale fluxes for most of our parameter space. The results show that the presence of the NSTM enhances heat entrainment from the mixed layer. Additionally there is no PSW heat entrained under the parameter space considered. We propose a scaling law for the ocean‐to‐ice heat flux which depends on the initial temperature anomaly in the NSTM layer and the ice‐drift velocity. A case study of “The Great Arctic Cyclone of 2012” gives a turbulent heat flux from the mixed layer that is approximately 70% of the total ocean‐to‐ice heat flux estimated from the PIOMAS model often used for short‐term predictions. Present results highlight the need for large‐scale climate models to account for the NSTM layer.
Keywords	basins ; case studies ; climate ; geophysics ; heat transfer ; research ; sea ice ; solar radiation ; summer ; Arctic Ocean ; Arctic region ; Canada
Language	English
Dates of publication	2018-01
Size	p. 287-304.
Publishing place	John Wiley & Sons, Ltd
Document type	Article
Note	JOURNAL ARTICLE
ZDB-ID	161667-5
ISSN	2169-9291 ; 2169-9275 ; 0148-0227 ; 0196-2256
ISSN (online)	2169-9291
ISSN	2169-9275 ; 0148-0227 ; 0196-2256
DOI	10.1002/2017JC013267
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Anemia during SARS-CoV-2 infection is associated with rehospitalization after viral clearance.

Lenehan, Patrick J / Ramudu, Eshwan / Venkatakrishnan, A J / Berner, Gabriela / McMurry, Reid / O'Horo, John C / Badley, Andrew D / Morice, William / Halamka, John / Soundararajan, Venky

iScience

2021 Volume 24, Issue 7, Page(s) 102780

Abstract: Patients with COVID-19 can experience symptoms and complications after viral clearance. It is important to identify clinical features of patients who are likely to experience these prolonged effects. We conducted a retrospective study to compare ... ...

Abstract	Patients with COVID-19 can experience symptoms and complications after viral clearance. It is important to identify clinical features of patients who are likely to experience these prolonged effects. We conducted a retrospective study to compare longitudinal laboratory test measurements (hemoglobin, hematocrit, estimated glomerular filtration rate, serum creatinine, and blood urea nitrogen) in patients rehospitalized after PCR-confirmed SARS-CoV-2 clearance (n = 104) versus patients not rehospitalized after viral clearance (n = 278). Rehospitalized patients had lower median hemoglobin levels in the year prior to COVID-19 diagnosis (Cohen's D = -0.50; p = 1.2 × 10
Language	English
Publishing date	2021-06-24
Publishing country	United States
Document type	Journal Article
ISSN	2589-0042
ISSN (online)	2589-0042
DOI	10.1016/j.isci.2021.102780
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Pre-existing conditions are associated with COVID-19 patients' hospitalization, despite confirmed clearance of SARS-CoV-2 virus.

Pawlowski, Colin / Venkatakrishnan, A J / Ramudu, Eshwan / Kirkup, Christian / Puranik, Arjun / Kayal, Nikhil / Berner, Gabriela / Anand, Akash / Barve, Rakesh / O'Horo, John C / Badley, Andrew D / Soundararajan, Venky

EClinicalMedicine

2021 Volume 34, Page(s) 100793

Abstract: Background: Consecutive negative SARS-CoV-2 PCR test results are being considered to estimate viral clearance in COVID-19 patients. However, there are anecdotal reports of hospitalization from protracted COVID-19 complications despite such confirmed ... ...

Abstract	Background: Consecutive negative SARS-CoV-2 PCR test results are being considered to estimate viral clearance in COVID-19 patients. However, there are anecdotal reports of hospitalization from protracted COVID-19 complications despite such confirmed viral clearance, presenting a clinical conundrum. Methods: We conducted a retrospective analysis of 222 hospitalized COVID-19 patients to compare those that were readmitted post-viral clearance ( Findings: In the year preceding COVID-19 onset, anemia ( Interpretation: Overall, this retrospective study highlights specific pre-existing conditions that are associated with higher hospitalization rates in COVID-19 patients despite viral clearance and motivates follow-up prospective research into the associated risk factors. Funding: This work was supported by Nference, inc.
Language	English
Publishing date	2021-03-23
Publishing country	England
Document type	Journal Article
ISSN	2589-5370
ISSN (online)	2589-5370
DOI	10.1016/j.eclinm.2021.100793
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Higher COVID-19 vaccination rates are linked to decreased county-level COVID-19 incidence across USA

Puranik, Arjun / Venkatakrishnan, AJ / Pawlowski, Colin / Raghunathan, Bharathwaj / Ramudu, Eshwan / Lenehan, Patrick / Agarwal, Vineet / Jayaram, Savita / Choudhary, Mayank / Soundararajan, Venky

medRxiv

Abstract: Real world evidence studies of mass vaccination across health systems have reaffirmed the safety and efficacy of the FDA-authorized mRNA vaccines for COVID-19. However, the impact of vaccination on community transmission remains to be characterized. Here, ...

Abstract	Real world evidence studies of mass vaccination across health systems have reaffirmed the safety and efficacy of the FDA-authorized mRNA vaccines for COVID-19. However, the impact of vaccination on community transmission remains to be characterized. Here, we compare the cumulative county-level vaccination rates with the corresponding COVID-19 incidence rates among 87 million individuals from 580 counties in the United States, including 12 million individuals who have received at least one vaccine dose. We find that cumulative county-level vaccination rate through March 1, 2021 is significantly associated with a concomitant decline in COVID-19 incidence (Spearman correlation ⍴ = -0.22, p-value = 8.3e-8), with stronger negative correlations in the Midwestern counties (⍴ = -0.37, p-value = 1.3e-7) and Southern counties (⍴ = -0.33, p-value = 4.5e-5) studied. Additionally, all examined US regions demonstrate significant negative correlations between cumulative COVID-19 incidence rate prior to the vaccine rollout and the decline in the COVID-19 incidence rate between December 1, 2020 and March 1, 2021, with the US western region being particularly striking (⍴ = -0.66, p-value = 5.3e-37). However, the cumulative vaccination rate and cumulative incidence rate are noted to be statistically independent variables, emphasizing the need to continue the ongoing vaccination roll out at scale. Given confounders such as different coronavirus restrictions and mask mandates, varying population densities, and distinct levels of diagnostic testing and vaccine availabilities across US counties, we are advancing a public health resource to amplify transparency in vaccine efficacy monitoring (https://public.nferx.com/covid-monitor-lab/vaccinationcheck). Application of this resource highlights outliers like Dimmit county (Texas), where infection rates have increased significantly despite higher vaccination rates, ostensibly owing to amplified travel as a vaccination hub; as well as Henry county (Ohio) which encountered shipping delays leading to postponement of the vaccine clinics. This study underscores the importance of tying the ongoing vaccine rollout to a real-time monitor of spatio-temporal vaccine efficacy to help turn the tide of the COVID-19 pandemic.
Keywords	covid19
Language	English
Publishing date	2021-03-08
Publisher	Cold Spring Harbor Laboratory Press
Document type	Article ; Online
DOI	10.1101/2021.03.05.21252946
Database	COVID19

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Article ; Online: Longitudinal lab test analysis confirms pre-existing anemia as a severe risk factor for post-viral clearance hospitalization in COVID-19 patients

Lenehan, Patrick / Ramudu, Eshwan / Venkatakrishnan, AJ / O'Horo, John / Badley, Andrew D / Morice, William G / Soundararajan, Venky

medRxiv

Abstract: As the number of new and recovering cases continues to rise, it is increasingly important to understand the long-term impacts of COVID-19 beyond the time of active SARS-CoV-2 infection. We previously used augmented curation methods to analyze physician ... ...

Abstract	As the number of new and recovering cases continues to rise, it is increasingly important to understand the long-term impacts of COVID-19 beyond the time of active SARS-CoV-2 infection. We previously used augmented curation methods to analyze physician notes from a large EHR system and identified anemia and acute kidney injury as risk factors for admission to the hospital after PCR confirmation of viral clearance in COVID-19 patients. Here, we analyzed longitudinal lab testing data from this same patient cohort to determine whether these measurements corroborate our notes-derived findings. Indeed we found that COVID-19 patients hospitalized after confirmed viral clearance tended to have lower hemoglobin and hematocrit measurements both during their SARS-CoV-2 positive intervals and during the one year prior to COVID-19 diagnosis compared to patients who have not been rehospitalized after viral clearance. Further, outright laboratory-based diagnosis of moderate or severe anemia was strongly enriched in the hospitalized cohort, suggesting that anemia pre-dating or concurrent with SARS-CoV-2 infection may predispose patients to long-term complications of COVID-19. Interventions which may mitigate anemia did not reduce the risk of post clearance hospitalization, although the efficacy of and patient compliance with these interventions could not be established. This study demonstrates the value of integrated large-scale EHR analyses and highlights the need for further research to determine whether the prevention or mitigation of anemia during SARS-CoV-2 infection may reduce the risk of suffering long-term complications of COVID-19.
Keywords	covid19
Language	English
Publishing date	2020-12-04
Publisher	Cold Spring Harbor Laboratory Press
Document type	Article ; Online
DOI	10.1101/2020.12.02.20242958
Database	COVID19

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Article ; Online: Pre-existing conditions are associated with long-COVID patients hospitalization, despite confirmed clearance of SARS-CoV-2 virus

Pawlowski, Colin / Venkatakrishnan, AJ / Ramudu, Eshwan / Kirkup, Christian / Puranik, Arjun / Kayal, Nikhil / Berner, Gabriela / Anand, Akash / Barve, Rakesh / O'Horo, John C / Badley, Andrew D / Soundararajan, Venky

medRxiv

Abstract: The current diagnostic gold-standard for SARS-CoV-2 clearance from infected patients is two consecutive negative PCR test results. However, there are anecdotal reports of hospitalization from protracted COVID complications (long-COVID) despite such ... ...

Abstract	The current diagnostic gold-standard for SARS-CoV-2 clearance from infected patients is two consecutive negative PCR test results. However, there are anecdotal reports of hospitalization from protracted COVID complications (long-COVID) despite such confirmed viral clearance, presenting a clinical conundrum. We conducted a retrospective analysis of 266 COVID patients to compare those that were admitted/re-admitted post-viral clearance (hospitalized post-clearance cohort, n=93) with those that were hospitalized pre-clearance but were not re-admitted post-viral clearance (non-hospitalized post-clearance cohort, n=173). In order to differentiate these two cohorts, we used neural network models for the augmented curation of comorbidities and complications with positive sentiment in the EHR physician notes. In the year preceding COVID onset, acute kidney injury (n=15 (16.1%), p-value: 0.03), anemia (n=20 (21.5%), p-value: 0.02), and cardiac arrhythmia (n=21 (22.6%), p-value: 0.05) were significantly enriched in the physician notes of the hospitalized post-clearance cohort. This study highlights that these specific pre-existing conditions are associated with amplified hospitalization risk in long-COVID patients, despite their successful SARS-CoV-2 viral clearance. Our findings motivate follow-up prospective research into specific risk factors that predispose some patients towards the long-COVID syndrome.
Keywords	covid19
Language	English
Publishing date	2020-10-30
Publisher	Cold Spring Harbor Laboratory Press
Document type	Article ; Online
DOI	10.1101/2020.10.28.20221655
Database	COVID19

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Article ; Online: Real-time analysis of a mass vaccination effort confirms the safety of FDA-authorized mRNA COVID-19 vaccines.

McMurry, Reid / Lenehan, Patrick / Awasthi, Samir / Silvert, Eli / Puranik, Arjun / Pawlowski, Colin / Venkatakrishnan, A J / Anand, Praveen / Agarwal, Vineet / O'Horo, John C / Gores, Gregory J / Williams, Amy W / Badley, Andrew D / Halamka, John / Virk, Abinash / Swift, Melanie D / Carlson, Katie / Doddahonnaiah, Deeksha / Metzger, Anna /

Kayal, Nikhil / Berner, Gabi / Ramudu, Eshwan / Carpenter, Corinne / Wagner, Tyler / Rajasekharan, Ajit / Soundararajan, Venky

Med (New York, N.Y.)

2021 Volume 2, Issue 8, Page(s) 965–978.e5

Abstract: Background: As the coronavirus disease 2019 (COVID-19) vaccination campaign unfolds, it is important to continuously assess the real-world safety of Food and Drug Administration (FDA)-authorized vaccines. Curation of large-scale electronic health ... ...

Abstract	Background: As the coronavirus disease 2019 (COVID-19) vaccination campaign unfolds, it is important to continuously assess the real-world safety of Food and Drug Administration (FDA)-authorized vaccines. Curation of large-scale electronic health records (EHRs) enables near-real-time safety evaluations that were not previously possible. Methods: In this retrospective study, we deployed deep neural networks over a large EHR system to automatically curate the adverse effects mentioned by physicians in over 1.2 million clinical notes between December 1, 2020 and April 20, 2021. We compared notes from 68,266 individuals who received at least one dose of BNT162b2 (n = 51,795) or mRNA-1273 (n = 16,471) to notes from 68,266 unvaccinated individuals who were matched by demographic, geographic, and clinical features. Findings: Individuals vaccinated with BNT162b2 or mRNA-1273 had a higher rate of return to the clinic, but not the emergency department, after both doses compared to unvaccinated controls. The most frequently documented adverse effects within 7 days of each vaccine dose included myalgia, headache, and fatigue, but the rates of EHR documentation for each side effect were remarkably low compared to those derived from active solicitation during clinical trials. Severe events, including anaphylaxis, facial paralysis, and cerebral venous sinus thrombosis, were rare and occurred at similar frequencies in vaccinated and unvaccinated individuals. Conclusions: This analysis of vaccine-related adverse effects from over 1.2 million EHR notes of more than 130,000 individuals reaffirms the safety and tolerability of the FDA-authorized mRNA COVID-19 vaccines in practice. Funding: This study was funded by nference.
MeSH term(s)	BNT162 Vaccine ; COVID-19/prevention & control ; COVID-19 Vaccines/adverse effects ; Drug-Related Side Effects and Adverse Reactions ; Humans ; Mass Vaccination ; RNA, Messenger ; Retrospective Studies ; SARS-CoV-2 ; United States ; United States Food and Drug Administration
Chemical Substances	COVID-19 Vaccines ; RNA, Messenger ; BNT162 Vaccine (N38TVC63NU)
Language	English
Publishing date	2021-07-01
Publishing country	United States
Document type	Journal Article
ISSN	2666-6340
ISSN (online)	2666-6340
DOI	10.1016/j.medj.2021.06.006
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Real-time analysis of a mass vaccination effort via an Artificial Intelligence platform confirms the safety of FDA-authorized COVID-19 vaccines

McMurry, Reid / Lenehan, Patrick J / Awasthi, Samir / Silvert, Eli / Puranik, Arjun / Pawlowski, Colin / Venkatakrishnan, AJ / Anand, Praveen / Agarwal, Vineet / OHoro, John C / Gores, Gregory J / Williams, Amy W / Badley, Andrew D / Halamka, John / Virk, Abinash / Smith, Melanie D / Carlson, Katie / Doddahonnaiah, Deeksha / Metzger, Anna /

Kayal, Nikhil / Berner, Gabi / Ramudu, Eshwan / Carpenter, Corinne / Wagner, Tyler / Rajasekharan, Ajit / Soundararajan, Venky

medRxiv

Abstract: As the COVID-19 vaccination campaign unfolds as one of the most rapid and widespread in history, it is important to continuously assess the real world safety of the FDA-authorized vaccines. Curation from large-scale electronic health records (EHRs) ... ...

Abstract	As the COVID-19 vaccination campaign unfolds as one of the most rapid and widespread in history, it is important to continuously assess the real world safety of the FDA-authorized vaccines. Curation from large-scale electronic health records (EHRs) allows for near real-time safety evaluations that were not previously possible. Here, we advance context- and sentiment-aware deep neural networks over the multi-state Mayo Clinic enterprise (Minnesota, Arizona, Florida, Wisconsin) for automatically curating the adverse effects mentioned by physicians in over 108,000 EHR clinical notes between December 1st 2020 to February 8th 2021. We retrospectively compared the clinical notes of 31,069 individuals who received at least one dose of the Pfizer/BioNTech or Moderna vaccine to those of 31,069 unvaccinated individuals who were propensity matched by demographics, residential location, and history of prior SARS-CoV-2 testing. We find that vaccinated and unvaccinated individuals were seen in the the clinic at similar rates within 21 days of the first or second actual or assigned vaccination dose (first dose Odds Ratio = 1.13, 95% CI: 1.09-1.16; second dose Odds Ratio = 0.89, 95% CI: 0.84-0.93). Further, the incidence rates of all surveyed adverse effects were similar or lower in vaccinated individuals compared to unvaccinated individuals after either vaccine dose. Finally, the most frequently documented adverse effects within 7 days of each vaccine dose were arthralgia (Dose 1: 0.59%; Dose 2: 0.39%), diarrhea (Dose 1: 0.58%; Dose 2: 0.33%), erythema (Dose 1: 0.51%; Dose 2: 0.31%), myalgia (Dose 1: 0.40%; Dose 2: 0.34%), and fever (Dose 1: 0.27%; Dose 2: 0.31%). These remarkably low frequencies of adverse effects recorded in EHRs versus those derived from active solicitation during clinical trials (arthralgia: 24-46%; erythema: 9.5-14.7%; myalgia: 38-62%; fever: 14.2-15.5%) emphasize the rarity of vaccine-associated adverse effects requiring clinical attention. This rapid and timely analysis of vaccine-related adverse effects from contextually rich EHR notes of 62,138 individuals, which was enabled through a large scale Artificial Intelligence (AI)-powered platform, reaffirms the safety and tolerability of the FDA-authorized COVID-19 vaccines in practice.
Keywords	covid19
Language	English
Publishing date	2021-02-23
Publisher	Cold Spring Harbor Laboratory Press
Document type	Article ; Online
DOI	10.1101/2021.02.20.21252134
Database	COVID19

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