Preparing for the lasting effects of COVID-19 on medical training: The design and pilot study of a low-fidelity virtual reality prototype for Central Venous Catheterization training.

Over the last several decades we have seen a shift from in-person to online training that has been exasperated by the COVID-19 pandemic. Researchers believe that many of these effects will be lasting which makes it even more important that the Human Factors community seek to step back and understand how to best train complex skills in a virtual world. The current paper is focused on understanding the utility of Virtual Reality (VR) in medical education for a hands-on procedural heavy procedure - ultrasound-guided Internal Jugular Central Venous Catheterization. Specifically, the objective of this study is to identify the potential utility of VR in US-IJCVC training through the design of a low-fidelity prototype and user interviews with three subject-matter experts. Results showed that the VR prototype designed is useful and provides a depth of knowledge and educational value which can be used to design innovative VR training approaches.

Multisite learning of high-dimensional heterogeneous data with applications to opioid use disorder study of 15,000 patients across 5 clinical sites.

Integrating data across institutions can improve learning efficiency. To integrate data efficiently while protecting privacy, we propose A one-shot, summary-statistics-based, Distributed Algorithm for fitting Penalized (ADAP) regression models across multiple datasets. ADAP utilizes patient-level data from a lead site and incorporates the first-order (ADAP1) and second-order gradients (ADAP2) of the objective function from collaborating sites to construct a surrogate objective function at the lead site, where model fitting is then completed with proper regularizations applied. We evaluate the performance of the proposed method using both simulation and a real-world application to study risk factors for opioid use disorder (OUD) using 15,000 patient data from the OneFlorida Clinical Research Consortium. Our results show that ADAP performs nearly the same as the pooled estimator but achieves higher estimation accuracy and better variable selection than the local and average estimators. Moreover, ADAP2 successfully handles heterogeneity in covariate distributions.

International comparisons of laboratory values from the 4CE collaborative to predict COVID-19 mortality.

Given the growing number of prediction algorithms developed to predict COVID-19 mortality, we evaluated the transportability of a mortality prediction algorithm using a multi-national network of healthcare systems. We predicted COVID-19 mortality using baseline commonly measured laboratory values and standard demographic and clinical covariates across healthcare systems, countries, and continents. Specifically, we trained a Cox regression model with nine measured laboratory test values, standard demographics at admission, and comorbidity burden pre-admission. These models were compared at site, country, and continent level. Of the 39,969 hospitalized patients with COVID-19 (68.6% male), 5717 (14.3%) died. In the Cox model, age, albumin, AST, creatine, CRP, and white blood cell count are most predictive of mortality. The baseline covariates are more predictive of mortality during the early days of COVID-19 hospitalization. Models trained at healthcare systems with larger cohort size largely retain good transportability performance when porting to different sites. The combination of routine laboratory test values at admission along with basic demographic features can predict mortality in patients hospitalized with COVID-19. Importantly, this potentially deployable model differs from prior work by demonstrating not only consistent performance but also reliable transportability across healthcare systems in the US and Europe, highlighting the generalizability of this model and the overall approach.

The Cosmos Collaborative: A Vendor-Facilitated Electronic Health Record Data Aggregation Platform.

OBJECTIVE: Learning healthcare systems use routinely collected data to generate new evidence that informs future practice. While implementing an electronic health record (EHR) system can facilitate this goal for individual institutions, meaningfully aggregating data from multiple institutions can be more empowering. Cosmos is a cross-institution, single EHR vendor-facilitated data aggregation tool. This work aims to describe the initiative and illustrate its potential utility through several use cases. METHODS: Cosmos is designed to scale rapidly by leveraging preexisting agreements, clinical health information exchange networks, and data standards. Data are stored centrally as a limited dataset, but the customer facing query tool limits results to prevent patient reidentification. RESULTS: In 2 years, Cosmos grew to contain EHR data of more than 60 million patients. We present practical examples illustrating how Cosmos could further efforts in chronic disease surveillance (asthma and obesity), syndromic surveillance (seasonal influenza and the 2019 novel coronavirus), immunization adherence and adverse event reporting (human papilloma virus and measles, mumps, rubella, and varicella vaccination), and health services research (antibiotic usage for upper respiratory infection). DISCUSSION: A low barrier of entry for Cosmos allows for the rapid accumulation of multi-institutional and mostly de-duplicated EHR data to power research and quality improvement queries characteristic of learning healthcare systems. Limitations are being vendor-specific, an "all or none" contribution model, and the lack of control over queries run on an institution's healthcare data. CONCLUSION: Cosmos provides a model for within-vendor data standardization and aggregation and a steppingstone for broader intervendor interoperability.

Multinational characterization of neurological phenotypes in patients hospitalized with COVID-19.

Neurological complications worsen outcomes in COVID-19. To define the prevalence of neurological conditions among hospitalized patients with a positive SARS-CoV-2 reverse transcription polymerase chain reaction test in geographically diverse multinational populations during early pandemic, we used electronic health records (EHR) from 338 participating hospitals across 6 countries and 3 continents (January-September 2020) for a cross-sectional analysis. We assessed the frequency of International Classification of Disease code of neurological conditions by countries, healthcare systems, time before and after admission for COVID-19 and COVID-19 severity. Among 35,177 hospitalized patients with SARS-CoV-2 infection, there was an increase in the proportion with disorders of consciousness (5.8%, 95% confidence interval [CI] 3.7-7.8%, pFDR < 0.001) and unspecified disorders of the brain (8.1%, 5.7-10.5%, pFDR < 0.001) when compared to the pre-admission proportion. During hospitalization, the relative risk of disorders of consciousness (22%, 19-25%), cerebrovascular diseases (24%, 13-35%), nontraumatic intracranial hemorrhage (34%, 20-50%), encephalitis and/or myelitis (37%, 17-60%) and myopathy (72%, 67-77%) were higher for patients with severe COVID-19 when compared to those who never experienced severe COVID-19. Leveraging a multinational network to capture standardized EHR data, we highlighted the increased prevalence of central and peripheral neurological phenotypes in patients hospitalized with COVID-19, particularly among those with severe disease.

Why Is the Electronic Health Record So Challenging for Research and Clinical Care?

BACKGROUND: The electronic health record (EHR) has become increasingly ubiquitous. At the same time, health professionals have been turning to this resource for access to data that is needed for the delivery of health care and for clinical research. There is little doubt that the EHR has made both of these functions easier than earlier days when we relied on paper-based clinical records. Coupled with modern database and data warehouse systems, high-speed networks, and the ability to share clinical data with others are large number of challenges that arguably limit the optimal use of the EHR OBJECTIVES: Our goal was to provide an exhaustive reference for those who use the EHR in clinical and research contexts, but also for health information systems professionals as they design, implement, and maintain EHR systems. METHODS: This study includes a panel of 24 biomedical informatics researchers, information technology professionals, and clinicians, all of whom have extensive experience in design, implementation, and maintenance of EHR systems, or in using the EHR as clinicians or researchers. All members of the panel are affiliated with Penn Medicine at the University of Pennsylvania and have experience with a variety of different EHR platforms and systems and how they have evolved over time. RESULTS: Each of the authors has shared their knowledge and experience in using the EHR in a suite of 20 short essays, each representing a specific challenge and classified according to a functional hierarchy of interlocking facets such as usability and usefulness, data quality, standards, governance, data integration, clinical care, and clinical research. CONCLUSION: We provide here a set of perspectives on the challenges posed by the EHR to clinical and research users.

Ideas for how informaticians can get involved with COVID-19 research

[...]there is a possibility that some of the observed genetic differences may be artifacts of this process. [...]the well-known CCR5-delta32 allele has a variation that protects individuals who have been exposed to the Human Immunodeficiency Virus (HIV);they are protected from developing AIDS (Acquired Immunodeficiency Syndrome) [10]. Because of this, researchers are gearing up to study the genomes of COVID-19 positive patients in comparison to controls (COVID-19-negative patients). Capacity and resource management tools can generate projects based on regional infection counts and current patient admissions to estimate the number of patients that will require hospitalization, intensive care unit beds, medications, and mechanical ventilation. Informaticians can support these efforts by 1) educating patients and care providers about data science resources and electronic health record (EHR) platforms for building point-of-care solutions, 2) joining the open-source community efforts to develop these technologies, and 3) volunteering with the information services divisions within their healthcare organizations to deploy telehealth tools and engage in patient management projects.

What Every Reader Should Know About Studies Using Electronic Health Record Data but May Be Afraid to Ask.

Coincident with the tsunami of COVID-19-related publications, there has been a surge of studies using real-world data, including those obtained from the electronic health record (EHR). Unfortunately, several of these high-profile publications were retracted because of concerns regarding the soundness and quality of the studies and the EHR data they purported to analyze. These retractions highlight that although a small community of EHR informatics experts can readily identify strengths and flaws in EHR-derived studies, many medical editorial teams and otherwise sophisticated medical readers lack the framework to fully critically appraise these studies. In addition, conventional statistical analyses cannot overcome the need for an understanding of the opportunities and limitations of EHR-derived studies. We distill here from the broader informatics literature six key considerations that are crucial for appraising studies utilizing EHR data: data completeness, data collection and handling (eg, transformation), data type (ie, codified, textual), robustness of methods against EHR variability (within and across institutions, countries, and time), transparency of data and analytic code, and the multidisciplinary approach. These considerations will inform researchers, clinicians, and other stakeholders as to the recommended best practices in reviewing manuscripts, grants, and other outputs from EHR-data derived studies, and thereby promote and foster rigor, quality, and reliability of this rapidly growing field.

Validation of an internationally derived patient severity phenotype to support COVID-19 analytics from electronic health record data.

OBJECTIVE: The Consortium for Clinical Characterization of COVID-19 by EHR (4CE) is an international collaboration addressing coronavirus disease 2019 (COVID-19) with federated analyses of electronic health record (EHR) data. We sought to develop and validate a computable phenotype for COVID-19 severity. MATERIALS AND METHODS: Twelve 4CE sites participated. First, we developed an EHR-based severity phenotype consisting of 6 code classes, and we validated it on patient hospitalization data from the 12 4CE clinical sites against the outcomes of intensive care unit (ICU) admission and/or death. We also piloted an alternative machine learning approach and compared selected predictors of severity with the 4CE phenotype at 1 site. RESULTS: The full 4CE severity phenotype had pooled sensitivity of 0.73 and specificity 0.83 for the combined outcome of ICU admission and/or death. The sensitivity of individual code categories for acuity had high variability-up to 0.65 across sites. At one pilot site, the expert-derived phenotype had mean area under the curve of 0.903 (95% confidence interval, 0.886-0.921), compared with an area under the curve of 0.956 (95% confidence interval, 0.952-0.959) for the machine learning approach. Billing codes were poor proxies of ICU admission, with as low as 49% precision and recall compared with chart review. DISCUSSION: We developed a severity phenotype using 6 code classes that proved resilient to coding variability across international institutions. In contrast, machine learning approaches may overfit hospital-specific orders. Manual chart review revealed discrepancies even in the gold-standard outcomes, possibly owing to heterogeneous pandemic conditions. CONCLUSIONS: We developed an EHR-based severity phenotype for COVID-19 in hospitalized patients and validated it at 12 international sites.

Use of electronic health records to support a public health response to the COVID-19 pandemic in the United States: a perspective from 15 academic medical centers.

Our goal is to summarize the collective experience of 15 organizations in dealing with uncoordinated efforts that result in unnecessary delays in understanding, predicting, preparing for, containing, and mitigating the COVID-19 pandemic in the US. Response efforts involve the collection and analysis of data corresponding to healthcare organizations, public health departments, socioeconomic indicators, as well as additional signals collected directly from individuals and communities. We focused on electronic health record (EHR) data, since EHRs can be leveraged and scaled to improve clinical care, research, and to inform public health decision-making. We outline the current challenges in the data ecosystem and the technology infrastructure that are relevant to COVID-19, as witnessed in our 15 institutions. The infrastructure includes registries and clinical data networks to support population-level analyses. We propose a specific set of strategic next steps to increase interoperability, overall organization, and efficiencies.

International electronic health record-derived COVID-19 clinical course profiles: the 4CE consortium.

We leveraged the largely untapped resource of electronic health record data to address critical clinical and epidemiological questions about Coronavirus Disease 2019 (COVID-19). To do this, we formed an international consortium (4CE) of 96 hospitals across five countries (www.covidclinical.net). Contributors utilized the Informatics for Integrating Biology and the Bedside (i2b2) or Observational Medical Outcomes Partnership (OMOP) platforms to map to a common data model. The group focused on temporal changes in key laboratory test values. Harmonized data were analyzed locally and converted to a shared aggregate form for rapid analysis and visualization of regional differences and global commonalities. Data covered 27,584 COVID-19 cases with 187,802 laboratory tests. Case counts and laboratory trajectories were concordant with existing literature. Laboratory tests at the time of diagnosis showed hospital-level differences equivalent to country-level variation across the consortium partners. Despite the limitations of decentralized data generation, we established a framework to capture the trajectory of COVID-19 disease in patients and their response to interventions.

Ideas for how informaticians can get involved with COVID-19 research

The coronavirus disease 2019 (COVID-19) pandemic has had a significant impact on population health and wellbeing. Biomedical informatics is central to COVID-19 research efforts and for the delivery of healthcare for COVID-19 patients. Critical to this effort is the participation of informaticians who typically work on other basic science or clinical problems. The goal of this editorial is to highlight some examples of COVID-19 research areas that could benefit from informatics expertise. Each research idea summarizes the COVID-19 application area, followed by an informatics methodology, approach, or technology that could make a contribution. It is our hope that this piece will motivate and make it easy for some informaticians to adopt COVID-19 research projects.