NISO plus 2022 Miles Conrad lecture: The role of a library in a world of unstructured data

Throughout its nearly two hundred year existence, the National Library of Medicine (NLM) (https://www.nlm.nih.gov/) has advanced biomedicine and public health by acquiring, organizing, preserving, and disseminating knowledge essential to health and medicine. NLM has devised many innovations including standard terminologies and messaging formats such as the Journal Article Tag Suite (https://dtd.nlm.nih.gov/) to organize and manage biomedical literature. While scientific communication largely relied on books and journals over the last two hundred years, digital data are quickly forming the substrate of scientific communications. Data come in forms with much less structure than that afforded by publications, and these can vary from observations made during carefully controlled clinical trials to streams of genomic sequences to the counts of footfalls captured by personal devices. Coincidently, an increasingly diverse set of users - from clinicians to laypeople to public health to big pharma to scientists - bring unique perspectives as they draw meaning from new sets of scientific output. How does a modern library meet its mission to acquire, organize, preserve, and disseminate the many outputs of contemporary science? What role do standards play? How does NLM help this diverse set of stakeholders derive meaning from its resources? © 2022 - The authors. Published by IOS Press.

IMI-CDE: an interactive interface for collaborative mapping of study variables to common data elements

The National Institute of Health (NIH) launches the RADx Radical research collaboratives (RADx-rad) to advance new, non-traditional approaches for COVID-19 testing. RADx-rad projects are required to adopt common data elements (CDEs) to collect data to increase data interoperability. To overcome the challenges in finding appropriate CDEs for a wide range of study variables, we create a web application - IMI-CDE to ease the burden of mapping study variables to CDEs from researchers. IMI-CDE can automatically recommend CDE candidates for a study variable based on its name and description. Together with interactive mapping interfaces, IMI-CDE allows researchers to perform variable-CDE mapping with one mouse click. In addition, the IMI-CDE application supports users with multiple roles to work collaboratively on the mapping tasks. We have piloted the IMI-CDE with RADx-rad projects. 22 researchers from 8 different projects have started to use the IMI-CDE system for variable-CDE mappings. The beta-testing evaluators reported the system is intuitive, effective, and easy to use. © 2022 IEEE.

A systemic review of neurological manifestations of COVID-19 infection

Objective: The purpose of the study is to systematically review literature on the neurological manifestations of COVID-19. Our review aims to inform the physicians treating COVID-19 of the neurological manifestations experienced within these patients. Background: While COVID-19 typically presents as a respiratory disease, the neurological manifestations are not uncommon. Neurological reports of COVID-19 patients described headache, dizziness, hypogeusia, hyposmia, acute cerebrovascular disease, myopathy, neuromuscular disorders, encephalitis, ataxia, delirium, and others. There are also reports of Guillaine Barrè syndrome associated with COVID-19. More data is needed to establish the incidence, outcomes and causal mechanisms between COVID-19 and its neurological sequel. Risk factors that may predispose a person with COVID-19 to neurological manifestations also need to be identified. Design/Methods: A PubMed and Scopus search has been conducted identify published papers for systematic review. Case reports, case series, editorials, reviews, case-control and cohort studies were evaluated, and relevant information was ed. Results: We identified 27 article meeting our criteria in the final analysis which included experimental studies, case reports, series of cases, cohort studies, and systematic reviews. Common reported symptoms included hyposmia, headaches, weakness, altered consciousness. Encephalitis, demyelination, neuropathy, and stroke have been associated with COVID-19. The most frequently reported neurological complication was acute ischemic cerebrovascular accident, followed by Guillain-Barré syndrome, with least common being meningitis and/or encephalitis. Presence of preexisting neurological disorders was associated with increased risk of developing neurological signs and/or syndromes with COVID-19. Conclusions: Considering the possibility of neurological involvement in patients with SARSCoV-2 infection can result in earlier diagnosis and treatment. Neurologic manifestations in COVID-19 should alert physicians and medical practitioners to rule in high-risk patients. Using a global network with standardized protocols and common data elements is critical to facilitate further studies to understand COVID-19 neurological manifestations.

A prospective natural history study and biorepository for patients with myasthenia gravis (EXPLORE-MG2)

Objective: To define clinical features, disease course, and collect biospecimens in patients with myasthenia gravis (MG), including understudied subgroups such as seronegative, muscle-specific kinase antibody (MuSK), and LRP4 antibody positive MG. Background: The MG Rare Disease Clinical Research Network (MGNet) was funded by the National Institutes of Health (NIH) to gain better understanding of the clinical course of MG and develop improved approaches to diagnosis and treatment. As part of this initiative a multicenter prospective natural history study and biorepository was developed: Exploring Outcomes and Characteristics of Myasthenia Gravis 2 (EXPLORE-MG2). Design/Methods: EXPLORE-MG2 is a web-based observational registry that incorporates NIH recommended common data elements for MG. Key eligibility criteria include: ≥18 years old;diagnosed with MG within 2-years of study enrollment based on clinical presentation and seropositivity for MG associated autoantibodies, and/or abnormal neurophysiology test or positive edrophonium test. Biospecimen collection focuses on immunosuppressive naïve patients and rare MG subgroups. Participants will be followed for at least 2-years with study visits occurring approximately every 6 months in the context of usual clinical care. The study has been open to enrollment since January 2021 with 6 sites currently activated/participating. Results: A total of 62 patients have been enrolled and 152 biospecimens were collected as of 10/1/2021. The mean age was 57 years (range 20-84);47% were female, 66% were acetylcholine receptor antibody-positive, 16% were MuSK MG, and 18% were seronegative. Enrollment of new participants and follow-up of existing participants are ongoing to reach our current goal of 400 enrolled participants. We will present updated enrollment data and demographics at the meeting. Conclusions: The EXPLORE-MG2 study is active after a COVID-19 pandemic related delay. Samples and clinical data will be available to researchers for current and future investigation. Data from EXPLORE-MG2 will improve clinical trial readiness for future studies and facilitate development of treatment-responsive biomarkers.

Standardizing, harmonizing, and protecting data collection to broaden the impact of COVID-19 research: the rapid acceleration of diagnostics-underserved populations (RADx-UP) initiative.

OBJECTIVE: The Rapid Acceleration of Diagnostics-Underserved Populations (RADx-UP) program is a consortium of community-engaged research projects with the goal of increasing access to Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) tests in underserved populations. To accelerate clinical research, common data elements (CDEs) were selected and refined to standardize data collection and enhance cross-consortium analysis. MATERIALS AND METHODS: The RADx-UP consortium began with more than 700 CDEs from the National Institutes of Health (NIH) CDE Repository, Disaster Research Response (DR2) guidelines, and the PHENotypes and eXposures (PhenX) Toolkit. Following a review of initial CDEs, we made selections and further refinements through an iterative process that included live forums, consultations, and surveys completed by the first 69 RADx-UP projects. RESULTS: Following a multistep CDE development process, we decreased the number of CDEs, modified the question types, and changed the CDE wording. Most research projects were willing to collect and share demographic NIH Tier 1 CDEs, with the top exception reason being a lack of CDE applicability to the project. The NIH RADx-UP Tier 1 CDE with the lowest frequency of collection and sharing was sexual orientation. DISCUSSION: We engaged a wide range of projects and solicited bidirectional input to create CDEs. These RADx-UP CDEs could serve as the foundation for a patient-centered informatics architecture allowing the integration of disease-specific databases to support hypothesis-driven clinical research in underserved populations. CONCLUSION: A community-engaged approach using bidirectional feedback can lead to the better development and implementation of CDEs in underserved populations during public health emergencies.

Who's in the House? Staffing in Long-Term Care Homes Before and During COVID-19 Pandemic.

Critical gaps exist in our knowledge on how best to provide quality person-centered care to long-term care (LTC) home residents which is closely tied to not knowing what the ideal staff is complement in the home. A survey was created on staffing in LTC homes before and during the COVID-19 pandemic to determine how the staff complement changed. Perspectives were garnered from researchers, clinicians, and policy experts in eight countries and the data provides a first approximation of staffing before and during the pandemic. Five broad categories of staff working in LTC homes were as follows: (1) those responsible for personal and support care, (2) nursing care, (3) medical care, (4) rehabilitation and recreational care, and (5) others. There is limited availability of data related to measuring staff complement in the home and those with similar roles had different titles making it difficult to compare between countries. Nevertheless, the survey results highlight that some categories of staff were either absent or deemed non-essential during the pandemic. We require standardized high-quality workforce data to design better decision-making tools for staffing and planning, which are in line with the complex care needs of the residents and prevent precarious work conditions for staff.

Assessing seizure burden in pediatric epilepsy using an electronic medical record-based tool through a common data element approach.

OBJECTIVE: Improvement in epilepsy care requires standardized methods to assess disease severity. We report the results of implementing common data elements (CDEs) to document epilepsy history data in the electronic medical record (EMR) after 12 months of clinical use in outpatient encounters. METHODS: Data regarding seizure frequency were collected during routine clinical encounters using a CDE-based form within our EMR. We extracted CDE data from the EMR and developed measurements for seizure severity and seizure improvement scores. Seizure burden and improvement was evaluated by patient demographic and encounter variables for in-person and telemedicine encounters. RESULTS: We assessed a total of 1696 encounters in 1038 individuals with childhood epilepsies between September 6, 2019 and September 11, 2020 contributed by 32 distinct providers. Childhood absence epilepsy (n = 121), Lennox-Gastaut syndrome (n = 86), and Dravet syndrome (n = 42) were the most common epilepsy syndromes. Overall, 43% (737/1696) of individuals had at least monthly seizures, 17% (296/1696) had a least daily seizures, and 18% (311/1696) were seizure-free for >12 months. Quantification of absolute seizure burden and changes in seizure burden over time differed between epilepsy syndromes, including high and persistent seizure burden in patients with Lennox-Gastaut syndrome. Individuals seen via telemedicine or in-person encounters had comparable seizure frequencies. Individuals identifying as Hispanic/Latino, particularly from postal codes with lower median household incomes, were more likely to have ongoing seizures that worsened over time. SIGNIFICANCE: Standardized documentation of clinical data in childhood epilepsies through CDE can be implemented in routine clinical care at scale and enables assessment of disease burden, including characterization of seizure burden over time. Our data provide insights into heterogeneous patterns of seizure control in common pediatric epilepsy syndromes and will inform future initiatives focusing on patient-centered outcomes in childhood epilepsies, including the impact of telemedicine and health care disparities.

Privacy-protecting, reliable response data discovery using COVID-19 patient observations.

OBJECTIVE: To utilize, in an individual and institutional privacy-preserving manner, electronic health record (EHR) data from 202 hospitals by analyzing answers to COVID-19-related questions and posting these answers online. MATERIALS AND METHODS: We developed a distributed, federated network of 12 health systems that harmonized their EHRs and submitted aggregate answers to consortia questions posted at https://www.covid19questions.org. Our consortium developed processes and implemented distributed algorithms to produce answers to a variety of questions. We were able to generate counts, descriptive statistics, and build a multivariate, iterative regression model without centralizing individual-level data. RESULTS: Our public website contains answers to various clinical questions, a web form for users to ask questions in natural language, and a list of items that are currently pending responses. The results show, for example, that patients who were taking angiotensin-converting enzyme inhibitors and angiotensin II receptor blockers, within the year before admission, had lower unadjusted in-hospital mortality rates. We also showed that, when adjusted for, age, sex, and ethnicity were not significantly associated with mortality. We demonstrated that it is possible to answer questions about COVID-19 using EHR data from systems that have different policies and must follow various regulations, without moving data out of their health systems. DISCUSSION AND CONCLUSIONS: We present an alternative or a complement to centralized COVID-19 registries of EHR data. We can use multivariate distributed logistic regression on observations recorded in the process of care to generate results without transferring individual-level data outside the health systems.

The PhenX Toolkit: Establishing Standard Measures for COVID-19 Research.

The PhenX (consensus measures for Phenotypes and eXposures) Toolkit (https://www.phenxtoolkit.org/) is a publicly available, web-based catalog of recommended, well-established measurement protocols of phenotypes and exposures. The goal of PhenX is to facilitate the use of standard measures, enhance data interoperability, and promote collaborative and translational research. PhenX is driven by the scientific community and historically has depended on working groups of experts to recommend measures for release in the PhenX Toolkit. The urgent need for recommended, standard measures for COVID-19 research triggered the development of a "rapid release" process for releasing new content in the PhenX Toolkit. Initially, PhenX collaborated with the National Institutes of Health (NIH) Office of Behavioral and Social Sciences Research, the National Human Genome Research Institute, and the NIH Disaster Research Response (DR2) program to create a library of COVID-19 measurement protocols. With additional support from NIH, PhenX adapted crowdsourcing techniques to accelerate prioritization and recommendation of protocols for release in the PhenX Toolkit. Prioritized COVID-19-specific protocols were used to anchor and define specialty collections of protocols that were subject to review and approval by the PhenX Steering Committee. In addition to the COVID-19-specific protocols, the specialty collections include existing, well-established PhenX protocols, use of which will further enhance data interoperability and cross-study analysis. The COVID-19 specialty collections are Behaviors and Risks; Ethnicity, Race and Demographics; History, Treatment and Outcomes; Information Resources; Psychosocial and Mental Health; and Socioeconomic. The development and usage of PhenX COVID-19 specialty collections are described in this article. © 2021 The Authors. Basic Protocol: Selecting COVID-19 protocols.

Implementation of regional COVID-19 registry in Hormozgan (RCovidRH), Iran: Rationale and study protocol.

Background: The rapid outbreak of COVID-19 has resulted in a global pandemic in 2020. Information sources such as disease registries through accessing quality, valid, accurate, and timely data empower researchers and health authorities to study and develop appropriate actions. Our study describes the protocol for implementation of regional COVID-19 registry in Hormozgan province (RCovidRH). Methods: We followed approved phases for the development of RCovidRH to cover the population in Hormozgan. Missioned to develop and implement the protocol, the registry's steering committee was made up of 10 members from subject fields of the registry at the core and 5 subgroups. The main purpose of the registry is to provide a comprehensive information profile of demographic, clinical, laboratory, imaging, and treatment data of confirmed and probable COVID-19 patients in Hormozgan. The data is retrospectively and prospectively collected. Case report form (CRF) was mainly based on International Severe Acute Respiratory and Emerging Infection Consortium (ISARIC) CRF. A web-based, 2-language software was also developed to facilitate data collection and storage. Data analysis is to be conducted with collaboration of clinical physicians, data-mining specialists, and epidemiologists after reaching appropriate sample size. Results: We included data related to demographic and identification, onset and admission, signs and symptoms at hospital admission, admission signs and symptoms, comorbidities, pathogen testing, assessment, laboratory, imaging, complications, treatment and medication, and outcomes. We found this registry was limited by incomplete clinical data for small fraction of outpatients, incomplete or inaccurate address by referred people due to fear of social rejection, delay in data entry at the facilities due to workload. Conclusion: This registry via organizing clinical and epidemiological COVID-19 data increases the potentiality of joint studies. Recognition and coordination of a registry is highly important to solve its limitations to collect data. Other universities and provinces can apply our model to develop COVID-19 registries or data sets for this disease.

A Surveillance System for the Maternal and Child Health (MCH) Population During the COVID-19 Pandemic.

Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), the causative agent for coronavirus disease 2019 (COVID-19), and its ensuing mitigation measures have negatively affected the Maternal and Child Health (MCH) population. There is currently no surveillance system established to enhance our understanding of SARS-CoV-2 transmission to guide policy decision making to protect the MCH population in this pandemic. Based on reports of community and household spread of this novel infection, we present an approach to a robust family-centered surveillance system for the MCH population. The surveillance system encapsulates data at the individual and community levels to inform stakeholders, policy makers, health officials and the general public about SARS-CoV-2 transmission dynamics within the MCH population.