Machine Learning-based Analysis of Publications Funded by the National Institutes of Health's Initial COVID-19 Pandemic Response.

Background: The National Institutes of Health (NIH) mobilized more than $4 billion in extramural funding for the COVID-19 pandemic. Assessing the research output from this effort is crucial to understanding how the scientific community leveraged federal funding and responded to this public health crisis. Methods: NIH-funded COVID-19 grants awarded between January 2020 and December 2021 were identified from NIH Research Portfolio Online Reporting Tools Expenditures and Results using the "COVID-19 Response" filter. PubMed identifications of publications under these grants were collected and the NIH iCite tool was used to determine citation counts and focus (eg, clinical, animal). iCite and the NIH's LitCOVID database were used to identify publications directly related to COVID-19. Publication titles and Medical Subject Heading terms were used as inputs to a machine learning-based model built to identify common topics/themes within the publications. Results and Conclusions: We evaluated 2401 grants that resulted in 14 654 publications. The majority of these papers were published in peer-reviewed journals, though 483 were published to preprint servers. In total, 2764 (19%) papers were directly related to COVID-19 and generated 252 029 citations. These papers were mostly clinically focused (62%), followed by cell/molecular (32%), and animal focused (6%). Roughly 60% of preprint publications were cell/molecular-focused, compared with 26% of nonpreprint publications. The machine learning-based model identified the top 3 research topics to be clinical trials and outcomes research (8.5% of papers), coronavirus-related heart and lung damage (7.3%), and COVID-19 transmission/epidemiology (7.2%). This study provides key insights regarding how researchers leveraged federal funding to study the COVID-19 pandemic during its initial phase.

Analysis of National Institutes of Health Funding for the COVID-19 Pandemic.

Background: Evaluating the National Institute's Health's (NIH's) response to the coronavirus disease 2019 (COVID-19) pandemic via grants and clinical trials is crucial to determining the impact they had on aiding US citizens. We determined how the NIH's funding for COVID-19 research was disbursed and used by various institutions across the United States. Methods: We queried NIH RePORTER and isolated COVID-19-related grants from January 2020 to December 2021. We analyzed grant type, geographical location, and awardee institution. Manuscripts published from these grants were quantitatively analyzed. COVID-19 clinical trials were mapped and distances from counties to clinical trial sites were calculated using ArcGis. Results: A total of 2401 COVID-19 NIH grants resulted in 14 654 manuscripts from $4.2 billion and generated more than 150 000 citations. R01s make up 32% of grants (763/2401) and 8% of funding ($329 million). UM1 grants account for the majority of funding (30.8%; $1.3 Billion). Five states received 50.6% of funding: North Carolina, Washington, New York, California, and Massachusetts. Finally, of the 1806 clinical trials across 1266 sites in the United States, the majority were in metropolitan areas in close proximity to areas of high COVID-19 disease burden. Conclusions and Relevance: Evaluating the outcome of the NIH's response to the COVID-19 pandemic is of interest to the general public. The present study finds that the NIH disbursed more than $4 billion in funding to large consortiums and clinical trials to develop diagnostics, therapeutics, and vaccines. Approximately 8% of funding was used for R01 grants. Clinical trial sites were generally located in areas of high COVID-19 burden.

Demographic and Clinical Factors Associated With SARS-CoV-2 Spike 1 Antibody Response Among Vaccinated US Adults: the C4R Study.

This study investigates correlates of anti-S1 antibody response following COVID-19 vaccination in a U.S. population-based meta-cohort of adults participating in longstanding NIH-funded cohort studies. Anti-S1 antibodies were measured from dried blood spots collected between February 2021-August 2022 using Luminex-based microsphere immunoassays. Of 6245 participants, mean age was 73 years (range, 21-100), 58% were female, and 76% were non-Hispanic White. Nearly 52% of participants received the BNT162b2 vaccine and 48% received the mRNA-1273 vaccine. Lower anti-S1 antibody levels are associated with age of 65 years or older, male sex, higher body mass index, smoking, diabetes, COPD and receipt of BNT16b2 vaccine (vs mRNA-1273). Participants with a prior infection, particularly those with a history of hospitalized illness, have higher anti-S1 antibody levels. These results suggest that adults with certain socio-demographic and clinical characteristics may have less robust antibody responses to COVID-19 vaccination and could be prioritized for more frequent re-vaccination.

Pathophysiological Responses to Bloodstream Infection in Critically Ill Transplant Recipients Compared With Non-Transplant Recipients.

BACKGROUND: Identification of bloodstream infection (BSI) in transplant recipients may be difficult due to immunosuppression. Accordingly, we aimed to compare responses to BSI in critically ill transplant and non-transplant recipients and to modify systemic inflammatory response syndrome (SIRS) criteria for transplant recipients. METHODS: We analyzed univariate risks and developed multivariable models of BSI with 27 clinical variables from adult intensive care unit (ICU) patients at the University of Virginia (UVA) and at the University of Pittsburgh (Pitt). We used Bayesian inference to adjust SIRS criteria for transplant recipients. RESULTS: We analyzed 38.7 million hourly measurements from 41 725 patients at UVA, including 1897 transplant recipients with 193 episodes of BSI and 53 608 patients at Pitt, including 1614 transplant recipients with 768 episodes of BSI. The univariate responses to BSI were comparable in transplant and non-transplant recipients. The area under the receiver operating characteristic curve (AUC) was 0.82 (95% confidence interval [CI], .80-.83) for the model using all UVA patient data and 0.80 (95% CI, .76-.83) when using only transplant recipient data. The UVA all-patient model had an AUC of 0.77 (95% CI, .76-.79) in non-transplant recipients and 0.75 (95% CI, .71-.79) in transplant recipients at Pitt. The relative importance of the 27 predictors was similar in transplant and non-transplant models. An upper temperature of 37.5°C in SIRS criteria improved reclassification performance in transplant recipients. CONCLUSIONS: Critically ill transplant and non-transplant recipients had similar responses to BSI. An upper temperature of 37.5°C in SIRS criteria improved BSI screening in transplant recipients.

Early Empiric Antibiotic Use in Patients Hospitalized With COVID-19: A Retrospective Cohort Study.

OBJECTIVE: To investigate temporal trends and outcomes associated with early antibiotic prescribing in patients hospitalized with COVID-19. DESIGN: Retrospective propensity-matched cohort study using the National COVID Cohort Collaborative (N3C) database. SETTING: Sixty-six health systems throughout the United States that were contributing to the N3C database. Centers that had fewer than 500 admissions in their dataset were excluded. PATIENTS: Patients hospitalized with COVID-19 were included. Patients were defined to have early antibiotic use if they received at least 3 calendar days of intravenous antibiotics within the first 5 days of admission. INTERVENTIONS: None. MEASUREMENTS AND MAIN RESULTS: Of 322,867 qualifying first hospitalizations, 43,089 patients received early empiric antibiotics. Antibiotic use declined across all centers in the data collection period, from March 2020 (23%) to June 2022 (9.6%). Average rates of early empiric antibiotic use (EEAU) also varied significantly between centers (deviance explained 7.33% vs 20.0%, p < 0.001). Antibiotic use decreased slightly by day 2 of hospitalization and was significantly reduced by day 5. Mechanical ventilation before day 2 (odds ratio [OR] 3.57; 95% CI, 3.42-3.72), extracorporeal membrane oxygenation before day 2 (OR 2.14; 95% CI, 1.75-2.61), and early vasopressor use (OR 1.85; 95% CI, 1.78-1.93) but not region of residence was associated with EEAU. After propensity matching, EEAU was associated with an increased risk for in-hospital mortality (OR 1.27; 95% CI, 1.23-1.33), prolonged mechanical ventilation (OR 1.65; 95% CI, 1.50-1.82), late broad-spectrum antibiotic exposure (OR 3.24; 95% CI, 2.99-3.52), and late Clostridium difficile infection (OR 1.60; 95% CI, 1.37-1.87). CONCLUSIONS: Although treatment of COVID-19 patients with empiric antibiotics has declined during the pandemic, the frequency of use remains high. There is significant inter-center variation in antibiotic prescribing practices and evidence of potential harm. Our findings are hypothesis-generating and future work should prospectively compare outcomes and adverse events.

How Would You Resuscitate This Patient With Septic Shock? : Grand Rounds Discussion From Beth Israel Deaconess Medical Center.

Sepsis is a potentially life-threatening systemic dysregulatory response to infection, and septic shock occurs when sepsis leads to systemic vasodilation and subsequent tissue hypoperfusion. The Surviving Sepsis Campaign published updated guidelines in 2021 on the management of sepsis and septic shock. Here, in the context of a patient with septic shock, 2 critical care specialists discuss and debate conditional guideline recommendations on using lactate to guide resuscitation, the use of balanced crystalloids versus normal saline, and the use of corticosteroids.

Colistin - That Was Fun, But Now We're Done.

Antimicrobial resistance (AMR) is an increasing global threat with estimates that drug-resistant infections contribute to nearly 5 million deaths worldwide every year.1 In particular, carbapenem-resistant Acinetobacter baumannii (CRAB) is emerging as a challenging pathogen to treat and has been designated by the World Health Organization as a priority pathogen for the development of new antimicrobial agents.2 Studies evaluating the efficacy of therapeutic strategies are vitally important in the fight against drug-resistant A. baumannii and other drug-resistant infections.

COVID-19 in the Critically Ill Patient.

The COVID-19 pandemic has led to significant mortality in the United States with more than 800,000 deaths in 2020 and 2021. The proportion of patients with COVID-19 who develop severe disease varies but is decreasing over time with growing population immunity and improved therapeutic options. Patients who are 65 years and older represent the largest proportion of deaths from COVID-19. Additional risk factors include immunosuppression and chronic medical conditions. Vaccination dramatically reduces the risk of severe COVID-19. Although critical illness from COVID-19 is mostly driven by respiratory disease, critical illness can manifest in several ways and affect several organ systems.

Rapid Telehealth-Centered Response to COVID-19 Outbreaks in Postacute and Long-Term Care Facilities.

Purpose: The vulnerability of postacute and long-term care (PA/LTC) facility residents to COVID-19 has manifested across the world with increasing facility outbreaks associated with high hospitalization and mortality rates. Systematic protocols to guide telehealth-centered interventions in response to COVID-19 outbreaks have yet to be delineated. This article is intended to inform PA/LTC facilities and neighboring health care partners how to collaboratively utilize telehealth-centered strategies to improve outcomes in facility outbreaks. Methods: The University of Virginia rapidly developed a multidisciplinary telehealth-centered COVID-19 facility outbreak strategy in response to a LTC facility outbreak in which 41 (out of 48) facility residents and 7 staff members tested positive. This strategy focused on supporting the facility team remotely using rapidly deployed technologic solutions. Goals included (1) early identification of patients who need their care escalated, (2) monitoring and treating patients deemed safe to remain in the facility, (3) care coordination to facilitate bidirectional transfers between the skilled nursing facility (SNF) and hospital, and (4) daily facility needs assessment related to technology, infection control, and staff well-being. To achieve these goals, a standardized approach centered on daily multidisciplinary virtual rounds and telemedicine consultation was provided. Results: Over a month since the outbreak began, 18 out of 48 (38%) facility residents required hospitalization and 6 (12.5%) died. Eleven facility residents have since returned back to the SNF after recovering from their hospitalization. No staff required hospitalization. Conclusions: Interventions that reduce hospitalizations and mortality are a critical need during the COVID-19 pandemic. The mortality and hospitalization rates seen in this PA/LTC facility outbreak are significantly lower than has been documented in other facility outbreaks. Our multidisciplinary approach centered on telemedicine should be considered as other PA/LTC facilities partner with neighboring health care systems in responding to COVID-19 outbreaks. We have begun replicating these services to additional PA/LTC facilities facing COVID-19 outbreaks.

Pathophysiologic Signatures of Bloodstream Infection in Critically Ill Adults.

OBJECTIVES: Bloodstream infection is associated with high mortality rates in critically ill patients but is difficult to identify clinically. This results in frequent blood culture testing, exposing patients to additional costs as well as the potential harms of unnecessary antibiotics. The purpose of this study was to assess whether the analysis of bedside physiologic monitoring data could accurately describe a pathophysiologic signature of bloodstream infection in patients admitted to the ICU. DESIGN: Development of a statistical model using physiologic data from a retrospective observational cohort. SETTING: University of Virginia Medical Center (Charlottesville, VA), a tertiary-care academic medical center. PATIENTS: Critically ill patients consecutively admitted to either the medical or surgical/trauma ICUs with available physiologic monitoring data between February 2011 and June 2015. INTERVENTIONS: None. MEASUREMENTS AND MAIN RESULTS: We analyzed 9,954 ICU admissions with 144 patient-years of vital sign and electrocardiography waveform data, totaling 1.3 million hourly measurements. There were 15,577 blood culture instances, with 1,184 instances of bloodstream infection (8%). The multivariate pathophysiologic signature of bloodstream infection was characterized by abnormalities in 15 different physiologic features. The cross-validated area under the receiver operating characteristic curve was 0.78 (95% CI, 0.69-0.85). We also identified distinct signatures of Gram-negative and fungal bloodstream infections, but not Gram-positive bloodstream infection. CONCLUSIONS: Signatures of bloodstream infection can be identified in the routine physiologic monitoring data of critically ill adults. This may assist in identifying infected patients, maximizing diagnostic stewardship, and measuring the effect of new therapeutic modalities for sepsis.

Acting Wisely: Eliminating Negative Bias in Medical Education-Part 1: The Fundamentals.

Bias is a ubiquitous problem in human functioning. It has plagued medical decision making, making physicians prone to errors of perception and judgment. Racial, gender, ethnic, and religious negative biases infest physicians' perception and cognition, causing errors of judgment and behavior that are damaging. In Part 1 of this series of 2 papers, the authors address the problem of harmful bias, the science of cognition, and what is known about how bias functions in human perception and information processing. They lay the groundwork for an approach to reducing negative bias through awareness, reflection, and bias mitigation, an approach in which negative biases can be transformed-by education, experience, practice, and relationships-into positive biases toward one another. The authors propose wisdom as a conceptual framework for imagining a different way of educating medical students. They discuss fundamental cognitive, affective, and reflective components of wisdom-based education. They also review the skills of awareness, using debiasing strategies, compassion, fostering positive emotion, and reflection that are inherent to a wisdom-based approach to eliminating the negative effects of bias in medical education. In Part 2, the authors answer a key question: How can medical educators do better? They describe the interpersonal, structural, and cultural elements supportive of a wisdom-based learning environment, a culture of respect and inclusion in medical education.

Acting Wisely: Eliminating Negative Bias in Medical Education-Part 2: How Can We Do Better?

In Part 1 of this 2-article series, the authors reviewed the problem of unmitigated bias in medical education and proposed a wisdom-based framework for a different way of educating medical students. In this article, Part 2, the authors answer a key question: How can medical educators do better? Is a bias-free environment possible? The answer to the latter question likely is "no." In fact, having a zero-bias goal in mind may blind educators and students to the implicit biases that affect physicians' decisions and actions. Biases appear to be a part of how the human brain works. This article explores ways to neutralize their destructive effects by: (1) increasing awareness of personal biases; (2) using mitigation strategies to protect against the undesirable effects of those biases; (3) working to change some negative biases, particularly learned biases; and (4) fostering positive biases toward others. The authors describe the concrete actions-interpersonal, structural, and cultural actions-that can be taken to reduce negative bias and its destructive effects.

Use of sacubitril/valsartan in acute decompensated heart failure: a case report.

Refractory heart failure typically requires costly long-term, continuous intravenous inodilator infusions while patients await mechanical circulatory support or cardiac transplantation. The combined angiotensin receptor blocker-neprilysin inhibitor, sacubitril/valsartan, is a novel therapy that can increase levels of endogenous vasoactive peptides. This therapy has been recommended as an alternative agent in patients with chronic heart failure with reduced ejection fraction and New York Heart Association class II-III symptoms. Here, we report a case of a patient with refractory stage D heart failure with reduced ejection fraction who was successfully weaned off continuous intravenous inodilator support using sacubitril/valsartan after prior failed attempts using standard therapies.

The biology and pathology of vitamin D control in bone.

Vitamin D is a steroid pro-hormone, whose active metabolite binds the vitamin D receptor (VDR) which, in turn, binds to DNA sequences on target genes as a heterodimer with the retinoid-X receptor, resulting in regulation of gene expression. The vitamin D pro-hormone can be synthesized in the skin, in response to ultraviolet radiation; however, dietary sources have become increasingly important as a result of cultural changes over the past few centuries. Based on its initial discovery as an anti-rachitic factor, studies of the role of vitamin D and its receptor have largely focused on the skeleton. Investigations into the pathophysiologic basis and therapeutic responses of skeletal disorders associated with impaired vitamin D action have led to the identification of the molecular pathways involved in hormone activation and regulation of gene expression by the liganded VDR. These studies have also demonstrated that the skeletal actions of the VDR and its ligand are largely redundant if normal mineral ion homeostasis can be maintained by other means. However, investigations in animal models with tissue-specific ablation of the VDR or the enzyme required for hormone activation have demonstrated novel actions in skeletal tissues. The active vitamin D metabolite has been shown to have both paracrine and endocrine actions in other tissues as well.