John H. Holmes

John H. Holmes
University of Pennsylvania | UP

PhD

About

152
Publications
12,733
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5,456
Citations

Publications

Publications (152)
Article
Full-text available
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 acr...
Article
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Objective To assess changes in international mortality rates and laboratory recovery rates during hospitalisation for patients hospitalised with SARS-CoV-2 between the first wave (1 March to 30 June 2020) and the second wave (1 July 2020 to 31 January 2021) of the COVID-19 pandemic. Design, setting and participants This is a retrospective cohort s...
Article
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The risk profiles of post-acute sequelae of COVID-19 (PASC) have not been well characterized in multi-national settings with appropriate controls. We leveraged electronic health record (EHR) data from 277 international hospitals representing 414,602 patients with COVID-19, 2.3 million control patients without COVID-19 in the inpatient and outpatien...
Preprint
Background In electronic health records, patterns of missing laboratory test results could capture patients’ course of disease as well as reflect clinician’s concerns or worries for possible conditions. These patterns are often understudied and overlooked. This study aims to characterize the patterns of missingness among laboratory data collected a...
Article
Background: Admissions are generally classified as COVID-19 hospitalizations if the patient has a positive SARS-CoV-2 polymerase chain reaction (PCR) test. However, because 35% of SARS-CoV-2 infections are asymptomatic, patients admitted for unrelated indications with an incidentally positive test could be misclassified as a COVID-19 hospitalizati...
Preprint
BACKGROUND Admissions are generally classified as COVID-19 hospitalizations if the patient has a positive SARS-CoV-2 polymerase chain reaction (PCR) test. However, because 35% of SARS-CoV-2 infections are asymptomatic, patients admitted for unrelated indications with an incidentally positive test could be misclassified as a COVID-19 hospitalization...
Preprint
Admissions are generally classified as COVID-19 hospitalizations if the patient has a positive SARS-CoV-2 polymerase chain reaction (PCR) test. However, because 35% of SARS-CoV-2 infections are asymptomatic, patients admitted for unrelated indications with an incidentally positive test could be misclassified as a COVID-19 hospitalization. EHR-based...
Preprint
Objective For multi-center heterogeneous Real-World Data (RWD) with time-to-event outcomes and high-dimensional features, we propose the SurvMaximin algorithm to estimate Cox model feature coefficients for a target population by borrowing summary information from a set of health care centers without sharing patient-level information. Materials and...
Article
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Human immunodeficiency virus (HIV) infection and in utero exposure increase the risk of neurocognitive deficits, but comprehensive neurocognitive screening is unavailable in settings with high HIV prevalence (e.g., Sub-Saharan Africa). The Penn Computerized Neurocognitive Battery (PennCNB) was culturally adapted and translated for use among childre...
Preprint
UNSTRUCTURED Authorship Correction: International Changes in COVID-19 Clinical Trajectories Across 315 Hospitals and 6 Countries: Retrospective Cohort Study In “International Changes in COVID-19 Clinical Trajectories Across 315 Hospitals and 6 Countries: Retrospective Cohort Study” (J Med Internet Res 2021 Oct 11;23(10):e31400. doi: 10.2196/31400),...
Article
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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 participat...
Article
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Most patients with hepatitis C virus (HCV) infection perceive some degree of disease-related stigma. Misunderstandings about diseases may contribute to disease-related stigma. The objective of this study was to evaluate patient-level knowledge about HCV infection transmission and natural history and its association with HCV-related stigma among HCV...
Article
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Background For some SARS-CoV-2 survivors, recovery from the acute phase of the infection has been grueling with lingering effects. Many of the symptoms characterized as the post-acute sequelae of COVID-19 (PASC) could have multiple causes or are similarly seen in non-COVID patients. Accurate identification of PASC phenotypes will be important to gu...
Article
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 w...
Preprint
BACKGROUND Many countries have experienced two predominant waves of COVID-19-related hospitalizations. Comparing the clinical trajectories of patients hospitalized in separate waves of the pandemic enables further understanding of the evolving epidemiology, pathophysiology, and healthcare dynamics of the COVID-19 pandemic. OBJECTIVE In this retros...
Article
Background: Many countries have experienced two predominant waves of COVID-19-related hospitalizations. Comparing the clinical trajectories of patients hospitalized in separate waves of the pandemic enables further understanding of the evolving epidemiology, pathophysiology, and healthcare dynamics of the COVID-19 pandemic. Objective: In this re...
Article
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Unstructured: 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 th...
Article
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Background Stigma is an important and understudied barrier to hepatitis C virus (HCV) infection treatment and elimination. Education to dispel disease-based myths and misinformation has been identified as a key intervention point to reduce disease-related stigma; however, the association between knowledge about HCV infection and perceptions of stig...
Preprint
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Objectives To perform an international comparison of the trajectory of laboratory values among hospitalized patients with COVID-19 who develop severe disease and identify optimal timing of laboratory value collection to predict severity across hospitals and regions. Design Retrospective cohort study. Setting The Consortium for Clinical Characteri...
Article
Background The allergic march refers to the natural history of allergic conditions during infancy and childhood. However, population-level disease incidence patterns do not necessarily reflect the development of allergic disease in individuals. A better understanding of the factors that predispose to different allergic trajectories is needed. Obje...
Article
Stigma around hepatitis C virus (HCV) infection is an important and understudied barrier to HCV treatment and elimination. The determinants of HCV‐related stigma, including the impacts of stage of HCV treatment (i.e., spontaneously‐cleared; diagnosed, untreated; previously treated, not cured; currently being treated; treated, cured) and coinfection...
Article
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Introduction Little literature addresses the burden of injury in Botswana, including trauma from motor-vehicle crashes (MVCs). In response, the University of Botswana and the Botswana Ministry of Health and Wellness are collaborating with the University of Pennsylvania to enhance injury and trauma research capacity in Botswana. Here we describe thi...
Article
Importance Incoming text messages and calls on nurses’ mobile telephones may interrupt medication administration, but whether such interruptions are associated with errors has not been established. Objective To assess whether a temporal association exists between mobile telephone interruptions and subsequent errors by pediatric intensive care unit...
Article
There is a lack of evidence on how to identify high-risk patients admitted to home healthcare. This study aimed (1) to identify which disease characteristics, medications, patient needs, social support characteristics, and other factors are associated with patient priority for the first home health nursing visit; and (2) to construct and validate a...
Article
Objectives: Although hospital clinicians strive to effectively refer patients who require post-acute care (PAC), their discharge planning processes often vary greatly, and typically are not evidence-based. Design: Quasi-experimental study employing pre-/postdesign. Aimed at improving patient-centered discharge processes, we examined the effects...
Article
Objective: Build and validate a clinical decision support (CDS) algorithm for discharge decisions regarding referral for post-acute care (PAC) and to what site of care. Materials and Methods: Case studies derived from EHR data were judged by 171 interdisciplinary experts and prediction models were generated. Results: A two-step algorithm emerged wi...
Article
Importance: Bedside monitor alarms alert nurses to life-threatening physiologic changes among patients, but the response times of nurses are slow. Objective: To identify factors associated with physiologic monitor alarm response time. Design, setting, and participants: This prospective cohort study used 551 hours of video-recorded care adminis...
Conference Paper
As biomedical knowledge continues to explode, medical students and doctors need to assimilate a lot of information for learning and clinical practice. The use of mobile devices provides an opportunity to improve access to information, enhance communication and collaboration and deliver self-paced learning opportunities. However, implementation of m...
Article
Background: The clinical value of teledermatology in the primary care setting remains relatively unknown. Objective: We sought to determine the impact of teledermatology on outpatient diagnosis, management, and access to dermatologic care in a resource-poor primary care setting. Methods: We performed a prospective study of store-and-forward te...
Article
Background: Rapid response systems (RRSs) aim to identify and rescue hospitalized patients whose condition is deteriorating before respiratory or cardiac arrest occurs. Previous studies of RRS implementation have shown variable effectiveness, which may be attributable in part to barriers preventing staff from activating the system. Objective: To...
Article
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To review the published, peer-reviewed literature on clinical research data warehouse governance in distributed research networks (DRNs). Medline, PubMed, EMBASE, CINAHL, and INSPEC were searched for relevant documents published through July 31, 2013 using a systematic approach. Only documents relating to DRNs in the USA were included. Documents we...
Article
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Given the extensive data stored in healthcare data warehouses, data warehouse governance policies are needed to ensure data integrity and privacy. This review examines the current state of the data warehouse governance literature as it applies to healthcare data warehouses, identifies knowledge gaps, provides recommendations, and suggests approache...
Article
The US government has allocated $30 billion dollars to implement Electronic Health Records (EHRs) in hospitals and provider practices through a policy called Meaningful Use. Small, rural hospitals, particularly those designated as Critical Access Hospitals (CAHs), comprising nearly a quarter of US hospitals, had not implemented EHRs before. Little...
Article
Tuberculosis remains a leading cause of morbidity and mortality worldwide. In 2011, there were 8.7 million new cases and 1.4 million deaths from the disease, with >95% of these deaths taking place in low- and middle-income countries [1]. Contact tracing prevents the spread of tuberculosis by identifying and screening a case's contacts and referring...
Article
Administrators play a major role in choosing and managing the use of the electronic health record (EHR). The documentation policies and EHR changes enacted or approved by administrators affect the ability to use clinical data for research. This article illustrates the challenges that can be avoided through awareness of the consequences of customiza...
Article
BACKGROUND Early warning scores (EWSs) assign points to clinical observations and generate scores to help clinicians identify deteriorating patients. Despite marginal predictive accuracy in retrospective datasets and a paucity of studies prospectively evaluating their clinical effectiveness, pediatric EWSs are commonly used.OBJECTIVE To identify me...
Article
BACKGROUND Medical emergency teams have been shown to reduce mortality in children's hospitals, but there are many potential barriers to their activation. Surveillance tools using electronic health record data help identify children at risk of deterioration. Existing early warning scores primarily include vital signs, but may benefit from the incor...
Article
Purpose: While patients often use the internet as a medium to search for and exchange health-related information, little is known about the extent to which patients use social media to discuss side effects related to medications. We aim to understand the frequency and content of side effects and associated adherence behaviors discussed by breast c...
Article
Background: Idiopathic pulmonary fibrosis (IPF) can lead to the development of pulmonary hypertension, which is associated with an increased risk of death. In pulmonary arterial hypertension, survival is directly related to the capacity of the right ventricle to adapt to elevated pulmonary vascular load. The relative importance of right ventricula...
Article
Objectives: To review technical and methodological challenges for big data research in biomedicine and health. Methods: We discuss sources of big datasets, survey infrastruc-tures for big data storage and big data processing, and describe the main challenges that arise when analyzing big data. Results: The life and biomedical sciences are massively...
Conference Paper
Contact tracing plays a critical role in preventing the spread of tuberculosis in countries with a high prevalence of HIV. Botswana, with an HIV prevalence of 17.1% (2nd highest in the world) and tuberculosis notification rate of >500 cases per 100,000 (4th highest), serves as a case in point. In Botswana, the Tuberculosis Contact Tracing Team ma...
Article
Identification of the characteristics that put hospitalized children at high risk of deterioration may help to target patients whose physiologic status should be intensively monitored for signs of deterioration, and reduce unnecessary monitoring in patients at very low risk. Previous studies have evaluated vital sign-based early warning scores to d...
Article
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The AMIA Public Health Informatics 2011 Conference brought together members of the public health and health informatics communities to revisit the national agenda developed at the AMIA Spring Congress in 2001, assess the progress that has been made in the past decade, and develop recommendations to further guide the field. Participants met in five...
Article
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Medical message boards are online resources where users with a particular condition exchange information, some of which they might not otherwise share with medical providers. Many of these boards contain a large number of posts and contain patient opinions and experiences that would be potentially useful to clinicians and researchers. We present an...
Article
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There are millions of public posts to medical message boards by users seeking support and information on a wide range of medical conditions. It has been shown that these posts can be used to gain a greater understanding of patients' experiences and concerns. As investigators continue to explore large corpora of medical discussion board data for res...
Article
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As the incidence of H1N1 increases, the lay public may turn to the Internet for information about natural supplements for prevention and treatment. Our objective was to identify and characterize websites that provide information about herbal and natural supplements with information about H1N1 and to examine trends in the public's behavior in search...
Article
The purpose of the study was to discover which patient and support system characteristics and interventions documented by home health clinicians were associated with improvement in urinary and bowel incontinence contrasting logistic regression and data mining approaches. Seventeen hundred ninety-three patients in this study experienced 2072 episode...
Article
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Information seeking and scanning refers to active pursuit of information and passive exposure, respectively. Cancer is the leading cause of mortality for Asian Americans, yet little is known about their cancer information seeking/scanning behaviors (SSB). We aimed to evaluate cancer SSB among older limited English proficient (LEP) Vietnamese immigr...
Article
Comparative effectiveness research, medical product safety evaluation, and quality measurement will require the ability to use electronic health data held by multiple organizations. There is no consensus about whether to create regional or national combined (eg, "all payer") databases for these purposes, or distributed data networks that leave most...
Article
Introduction: The overall objective of this project is to design a scalable distributed research network (DRN) that supports secure data analyses for research on the comparative effectiveness and safety of therapeutics. The plan for achieving this objective includes designing an information system architecture, implementation of a prototype of the...
Article
Full-text available
Researchers, policy makers and others commonly use electronic data routinely collected during the delivery of, or payment for, medical care to study the "real world" effectiveness, comparative effectiveness, safety, and costs of medical interventions. However, even very large individual healthcare data resources are often not big enough to adequate...
Conference Paper
Background: Current guidelines specify that practitioners should discuss prostate cancer screening, (PCS) with patients. Using a computerized patient-centered intervention to increase awareness of PCS could encourage more men to initiate a discussion with their physician regarding prostate cancer screening. Objective/purpose: To test the usabilit...
Conference Paper
Background: Current guidelines recommend that men should discuss prostate cancer screening (PCS) with their provider. Patient race often affects the frequency and quality of these discussions. Objectives: To assess a new computerized interactive intervention that is tailored on race and designed to teach patients how to start and engage in a disc...
Article
A distributed health data network is a system that allows secure remote analysis of separate data sets, each comprising a different medical organization's or health plan's records. Distributed health data networks are currently being planned that could cover millions of people, permitting studies of comparative clinical effectiveness, best practice...
Article
To improve insight into fatal child cervical spine injuries (CSI) caused by motor vehicle collisions. Two large national mortality datasets were linked at the level of the individual decedent to analyse and compare anatomical injuries and vehicle crash characteristics for fatally injured child occupants. Cervical spine injury was identified among 1...
Article
The Program Requirements for Fellowship Education identify the knowledge and skills that physicians must master through the course of a training program to be certified in the subspecialty of clinical informatics. They also specify accreditation requirements for clinical informatics training programs. The AMIA Board of Directors approved this docum...
Article
The Core Content for Clinical Informatics defines the boundaries of the discipline and informs the Program Requirements for Fellowship Education in Clinical Informatics. The Core Content includes four major categories: fundamentals, clinical decision making and care process improvement, health information systems, and leadership and management of c...
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Each year, more than 13 million post acute referral decisions are made for Medicare recipients, yet there are no national, empirically derived decision support tools to assist in making these important decisions. The aim of this study was to elicit expert knowledge about factors important to referral decision making and identify the characteristics...
Article
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b Background: Each year, more than 13 million post acute re-ferral decisions are made for Medicare recipients, yet there are no national, empirically derived decision support tools to assist in making these important decisions. b Objectives: The aim of this study was to elicit expert knowl-edge about factors important to referral decision making an...
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Delayed allograft function (DGF) is a common adverse event in postrenal transplantation. The etiology of DGF is thought to include both nonimmunologic (donor age, cold ischemia time, and recipient race) and immunologic factors. We examined the association of DGF with amino acid mismatches at 66 variable sites of the HLA-A molecule in a prospective...
Conference Paper
This session provides the learner with knowledge regarding key issues in informatics: standards and information security, privacy, and confidentiality, change management and project management.
Conference Paper
Use cases serve as an important tool for requirements gathering and testing in system development projects. Use case development requires examination of the system vision statement, interaction with stakeholders, determining critical success factors, and the development of achievable goals.
Conference Paper
Informatics is becoming an important component of the practice of pubic health, but is relatively unfamiliar to most public health practitioners. This session provides the learner with definitions of informatics concepts and principles.
Conference Paper
The Unified Process within systems development provides the foundation for an information architecture that supports the use of information systems within public health. This presentation highlights key concepts within the Unified Process.
Conference Paper
Writing the system vision statement is done at the earliest phase of the systems development project. A focus will be made on project feasibility and determination of a business case.
Conference Paper
The faculty will summarize the information presented and provide give and take dialogue through open discussion with the attendees. A post evaluation will be distributed and collected.
Conference Paper
Information and information technology often outpace the public health practitioners' ability to stay current with developments at all levels of public health. This session provides the learner with an opportunity to discuss current trends in informatics development.
Article
Numerous factors play a part in health disparities. Although health disparities are manifested at the level of the individual, other contexts should be considered when investigating the associations of disparities with clinical outcomes. These contexts include families, neighborhoods, social organizations, and healthcare facilities. This paper repo...
Article
We sought to determine whether intimate partner violence (IPV) risk factors differed depending upon the presence of children in the home, and to estimate the annual prevalence of IPV first in the general population and then in homes with and without children. We analyzed data from a cross-sectional random sample of 6,836 women in southeastern Penns...
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Little is known about the impact of extrinsic factors on pressure ulcer risk. The objective of this study was to determine whether risk of pressure ulcers early in the hospital stay is associated with extrinsic factors such as longer emergency department (ED) stays, night or weekend admission, potentially immobilizing procedures and medications, an...
Article
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Anticipating post-acute needs and making referrals for follow-up care are crucial for quality discharge planning. Several studies reveal serious gaps in quality for these common and important processes. Compare experts' and hospital clinicians' discharge referral decisions for the same elderly patients, and examine 12-week outcomes for patients who...