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1.
Nat Commun ; 12(1): 5757, 2021 10 01.
Article in English | MEDLINE | ID: covidwho-1447304

ABSTRACT

The large amount of biomedical data derived from wearable sensors, electronic health records, and molecular profiling (e.g., genomics data) is rapidly transforming our healthcare systems. The increasing scale and scope of biomedical data not only is generating enormous opportunities for improving health outcomes but also raises new challenges ranging from data acquisition and storage to data analysis and utilization. To meet these challenges, we developed the Personal Health Dashboard (PHD), which utilizes state-of-the-art security and scalability technologies to provide an end-to-end solution for big biomedical data analytics. The PHD platform is an open-source software framework that can be easily configured and deployed to any big data health project to store, organize, and process complex biomedical data sets, support real-time data analysis at both the individual level and the cohort level, and ensure participant privacy at every step. In addition to presenting the system, we illustrate the use of the PHD framework for large-scale applications in emerging multi-omics disease studies, such as collecting and visualization of diverse data types (wearable, clinical, omics) at a personal level, investigation of insulin resistance, and an infrastructure for the detection of presymptomatic COVID-19.


Subject(s)
Data Science/methods , Medical Records Systems, Computerized , Big Data , Computer Security , Data Analysis , Health Information Interoperability , Humans , Information Storage and Retrieval , Software
2.
PLoS One ; 16(9): e0257056, 2021.
Article in English | MEDLINE | ID: covidwho-1438346

ABSTRACT

We present an interpretable machine learning algorithm called 'eARDS' for predicting ARDS in an ICU population comprising COVID-19 patients, up to 12-hours before satisfying the Berlin clinical criteria. The analysis was conducted on data collected from the Intensive care units (ICU) at Emory Healthcare, Atlanta, GA and University of Tennessee Health Science Center, Memphis, TN and the Cerner® Health Facts Deidentified Database, a multi-site COVID-19 EMR database. The participants in the analysis consisted of adults over 18 years of age. Clinical data from 35,804 patients who developed ARDS and controls were used to generate predictive models that identify risk for ARDS onset up to 12-hours before satisfying the Berlin criteria. We identified salient features from the electronic medical record that predicted respiratory failure among this population. The machine learning algorithm which provided the best performance exhibited AUROC of 0.89 (95% CI = 0.88-0.90), sensitivity of 0.77 (95% CI = 0.75-0.78), specificity 0.85 (95% CI = 085-0.86). Validation performance across two separate health systems (comprising 899 COVID-19 patients) exhibited AUROC of 0.82 (0.81-0.83) and 0.89 (0.87, 0.90). Important features for prediction of ARDS included minimum oxygen saturation (SpO2), standard deviation of the systolic blood pressure (SBP), O2 flow, and maximum respiratory rate over an observational window of 16-hours. Analyzing the performance of the model across various cohorts indicates that the model performed best among a younger age group (18-40) (AUROC = 0.93 [0.92-0.94]), compared to an older age group (80+) (AUROC = 0.81 [0.81-0.82]). The model performance was comparable on both male and female groups, but performed significantly better on the severe ARDS group compared to the mild and moderate groups. The eARDS system demonstrated robust performance for predicting COVID19 patients who developed ARDS at least 12-hours before the Berlin clinical criteria, across two independent health systems.


Subject(s)
COVID-19 , Machine Learning , Models, Biological , Respiratory Distress Syndrome , SARS-CoV-2/metabolism , Adolescent , Adult , Aged , Aged, 80 and over , COVID-19/blood , COVID-19/complications , COVID-19/diagnosis , COVID-19/physiopathology , Critical Illness , Female , Humans , Male , Medical Records Systems, Computerized , Middle Aged , Oxygen/blood , Respiratory Distress Syndrome/blood , Respiratory Distress Syndrome/diagnosis , Respiratory Distress Syndrome/etiology , Respiratory Distress Syndrome/physiopathology , Respiratory Rate , Risk Factors
3.
Yearb Med Inform ; 30(1): 69-74, 2021 Aug.
Article in English | MEDLINE | ID: covidwho-1392943

ABSTRACT

OBJECTIVE: To summarize significant research contributions on managing pandemics with health informatics published in 2020. METHODS: An extensive search using PubMed and Scopus was conducted to identify peer-reviewed articles published in 2020 that examined health informatics systems used during the global COVID-19 pandemic. The selection process comprised three steps: 1) 15 candidate best papers were first selected by the two section editors; 2) external reviewers from internationally renowned research teams reviewed each candidate best paper; and 3) the final selection of three best papers was conducted by the editorial committee of the International Medical Informatics Association (IMIA) Yearbook. RESULTS: Selected best papers represent the important and diverse ways that health informatics supported clinical and public health responses to the global COVID-19 pandemic. Selected papers represent four groups of papers: 1) Use of analytics to screen, triage, and manage patients; 2) Use of telehealth and remote monitoring to manage patients and populations; 3) Use of EHR systems and administrative systems to manage internal operations of a hospital or health system; and 4) Use of informatics methods and systems by public health authorities to capture, store, manage, and visualize population-level data and information. CONCLUSION: Health informatics played a critical role in managing patients and populations during the COVID-19 pandemic. Health care and public health organizations both leveraged available information systems and standards to rapidly identify cases, triage infected individuals, and monitor population trends. The selected best papers represent a fraction of the body of knowledge stemming from COVID-19, most of which is focused on pandemic response. Future work will be needed to help the world recover from the pandemic and strengthen the health information infrastructure in preparation for the next pandemic.


Subject(s)
COVID-19 , Medical Informatics , COVID-19/epidemiology , COVID-19/therapy , Humans , Medical Records Systems, Computerized , Public Health Practice , Telemedicine
4.
Am J Health Syst Pharm ; 77(17): 1409-1416, 2020 08 20.
Article in English | MEDLINE | ID: covidwho-1317900

ABSTRACT

PURPOSE: The global coronavirus disease 2019 (COVID-19) pandemic has created unprecedented strains on healthcare systems around the world. Challenges surrounding an overwhelming influx of patients with COVID-19 and changes in care dynamics prompt the need for care models and processes that optimize care in this medically complex patient population. The purpose of this report is to describe our institution's strategy to deploy pharmacy resources and standardize pharmacy processes to optimize the management of patients with COVID-19. METHODS: This retrospective, descriptive report characterizes documented pharmacy interventions in the acute care of patients admitted for COVID-19 during the period April 1 to April 15, 2020. Patient monitoring, interprofessional communication, and intervention documentation by pharmacy staff was facilitated through the development of a COVID-19-specific care bundle integrated into the electronic medical record. RESULTS: A total of 1,572 pharmacist interventions were documented in 197 patients who received a total of 15,818 medication days of therapy during the study period. The average number of interventions per patient was 8. The most common interventions were regimen simplification (15.9%), timing and dosing adjustments (15.4%), and antimicrobial therapy and COVID-19 treatment adjustments (15.2%). Patients who were admitted to an intensive care unit care at any point during their hospital stay accounted for 66.7% of all interventions documented. CONCLUSION: A pharmacy department's response to the COVID-19 pandemic was optimized through standardized processes. Pharmacists intervened to address a wide scope of medication-related issues, likely contributing to improved management of COVID-19 patients. Results of our analysis demonstrate the vital role pharmacists play as members of multidisciplinary teams during times of crisis.


Subject(s)
COVID-19/drug therapy , Medication Therapy Management/organization & administration , Pharmacists/organization & administration , Pharmacy Service, Hospital/organization & administration , Aged , Aged, 80 and over , Anti-Bacterial Agents/administration & dosage , Anti-Bacterial Agents/adverse effects , Anticoagulants/administration & dosage , Anticoagulants/adverse effects , Antiviral Agents/administration & dosage , Antiviral Agents/adverse effects , COVID-19/epidemiology , Critical Care/organization & administration , Drug Therapy, Combination/adverse effects , Drug Therapy, Combination/methods , Electrolytes/administration & dosage , Electrolytes/adverse effects , Female , Hospital Mortality , Humans , Intensive Care Units/organization & administration , Interdisciplinary Communication , Male , Medical Records Systems, Computerized/organization & administration , Middle Aged , Pandemics/prevention & control , Professional Role , Retrospective Studies , Treatment Outcome
5.
J Microbiol Immunol Infect ; 54(1): 85-88, 2021 Feb.
Article in English | MEDLINE | ID: covidwho-1272559

ABSTRACT

As the world witnessed the rapid spread of SARS-CoV-2, the World Health Organization has called for governing bodies worldwide to intensify case findings, contact tracing, monitoring, and quarantine or isolation of contacts with COVID-19. Drive-through (DT) screening is a form of case detection which has recently gain preference globally. Proper implementation of this system can help remediate the outbreak.


Subject(s)
COVID-19/diagnosis , COVID-19/prevention & control , Mass Screening/organization & administration , COVID-19/transmission , Contact Tracing , Disease Outbreaks/prevention & control , Epidemiological Monitoring , Humans , Mass Screening/methods , Medical Records Systems, Computerized , Public Health Surveillance , Quarantine , Research Report , SARS-CoV-2/isolation & purification , World Health Organization
6.
J Am Med Inform Assoc ; 28(7): 1555-1563, 2021 07 14.
Article in English | MEDLINE | ID: covidwho-1132539

ABSTRACT

OBJECTIVE: The study sought to develop an in-depth understanding of how hospitals with a long history of health information technology (HIT) use have responded to the COVID-19 (coronavirus disease 2019) pandemic from an HIT perspective. MATERIALS AND METHODS: We undertook interviews with 44 healthcare professionals with a background in informatics from 6 hospitals internationally. Interviews were informed by a topic guide and were conducted via videoconferencing software. Thematic analysis was employed to develop a coding framework and identify emerging themes. RESULTS: Three themes and 6 subthemes were identified. HITs were employed to manage time and resources during a surge in patient numbers through fast-tracked governance procedures, and the creation of real-time bed capacity tracking within electronic health records. Improving the integration of different hospital systems was identified as important across sites. The use of hard-stop alerts and order sets were perceived as being effective at helping to respond to potential medication shortages and selecting available drug treatments. Utilizing information from multiple data sources to develop alerts facilitated treatment. Finally, the upscaling/optimization of telehealth and remote working capabilities was used to reduce the risk of nosocomial infection within hospitals. DISCUSSION: A number of the HIT-related changes implemented at these sites were perceived to have facilitated more effective patient treatment and management of resources. Informaticians generally felt more valued by hospital management as a result. CONCLUSIONS: Improving integration between data systems, utilizing specialized alerts, and expanding telehealth represent strategies that hospitals should consider when using HIT for delivering hospital care in the context of the COVID-19 pandemic.


Subject(s)
COVID-19/therapy , Hospital Administration , Hospital Information Systems/organization & administration , Medical Informatics , Medical Records Systems, Computerized , Patient Care Management , Attitude of Health Personnel , Electronic Health Records , Humans , Infection Control , Interviews as Topic , Organizational Case Studies , Personnel, Hospital , Telemedicine , United Kingdom , United States
7.
Ann Fam Med ; 19(2): 135-140, 2021.
Article in English | MEDLINE | ID: covidwho-1123691

ABSTRACT

The use of big data containing millions of primary care medical records provides an opportunity for rapid research to help inform patient care and policy decisions during the first and subsequent waves of the coronavirus disease 2019 (COVID-19) pandemic. Routinely collected primary care data have previously been used for national pandemic surveillance, quantifying associations between exposures and outcomes, identifying high risk populations, and examining the effects of interventions at scale, but there is no consensus on how to effectively conduct or report these data for COVID-19 research. A COVID-19 primary care database consortium was established in April 2020 and its researchers have ongoing COVID-19 projects in overlapping data sets with over 40 million primary care records in the United Kingdom that are variously linked to public health, secondary care, and vital status records. This consensus agreement is aimed at facilitating transparency and rigor in methodological approaches, and consistency in defining and reporting cases, exposures, confounders, stratification variables, and outcomes in relation to the pharmacoepidemiology of COVID-19. This will facilitate comparison, validation, and meta-analyses of research during and after the pandemic.


Subject(s)
COVID-19/epidemiology , Consensus , Databases, Factual/standards , Medical Records Systems, Computerized/standards , Primary Health Care/organization & administration , Public Health Surveillance , Big Data , COVID-19/diagnosis , Humans , Pharmacoepidemiology , Public Health , United Kingdom/epidemiology
8.
JMIR Public Health Surveill ; 6(3): e19773, 2020 07 02.
Article in English | MEDLINE | ID: covidwho-791866

ABSTRACT

BACKGROUND: Routinely recorded primary care data have been used for many years by sentinel networks for surveillance. More recently, real world data have been used for a wider range of research projects to support rapid, inexpensive clinical trials. Because the partial national lockdown in the United Kingdom due to the coronavirus disease (COVID-19) pandemic has resulted in decreasing community disease incidence, much larger numbers of general practices are needed to deliver effective COVID-19 surveillance and contribute to in-pandemic clinical trials. OBJECTIVE: The aim of this protocol is to describe the rapid design and development of the Oxford Royal College of General Practitioners Clinical Informatics Digital Hub (ORCHID) and its first two platforms. The Surveillance Platform will provide extended primary care surveillance, while the Trials Platform is a streamlined clinical trials platform that will be integrated into routine primary care practice. METHODS: We will apply the FAIR (Findable, Accessible, Interoperable, and Reusable) metadata principles to a new, integrated digital health hub that will extract routinely collected general practice electronic health data for use in clinical trials and provide enhanced communicable disease surveillance. The hub will be findable through membership in Health Data Research UK and European metadata repositories. Accessibility through an online application system will provide access to study-ready data sets or developed custom data sets. Interoperability will be facilitated by fixed linkage to other key sources such as Hospital Episodes Statistics and the Office of National Statistics using pseudonymized data. All semantic descriptors (ie, ontologies) and code used for analysis will be made available to accelerate analyses. We will also make data available using common data models, starting with the US Food and Drug Administration Sentinel and Observational Medical Outcomes Partnership approaches, to facilitate international studies. The Surveillance Platform will provide access to data for health protection and promotion work as authorized through agreements between Oxford, the Royal College of General Practitioners, and Public Health England. All studies using the Trials Platform will go through appropriate ethical and other regulatory approval processes. RESULTS: The hub will be a bottom-up, professionally led network that will provide benefits for member practices, our health service, and the population served. Data will only be used for SQUIRE (surveillance, quality improvement, research, and education) purposes. We have already received positive responses from practices, and the number of practices in the network has doubled to over 1150 since February 2020. COVID-19 surveillance has resulted in tripling of the number of virology sites to 293 (target 300), which has aided the collection of the largest ever weekly total of surveillance swabs in the United Kingdom as well as over 3000 severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) serology samples. Practices are recruiting to the PRINCIPLE (Platform Randomised trial of INterventions against COVID-19 In older PeopLE) trial, and these participants will be followed up through ORCHID. These initial outputs demonstrate the feasibility of ORCHID to provide an extended national digital health hub. CONCLUSIONS: ORCHID will provide equitable and innovative use of big data through a professionally led national primary care network and the application of FAIR principles. The secure data hub will host routinely collected general practice data linked to other key health care repositories for clinical trials and support enhanced in situ surveillance without always requiring large volume data extracts. ORCHID will support rapid data extraction, analysis, and dissemination with the aim of improving future research and development in general practice to positively impact patient care. INTERNATIONAL REGISTERED REPORT IDENTIFIER (IRRID): DERR1-10.2196/19773.


Subject(s)
Clinical Trials as Topic , Coronavirus Infections/epidemiology , General Practice/organization & administration , Medical Records Systems, Computerized , Pneumonia, Viral/epidemiology , Public Health Surveillance , COVID-19 , Humans , Pandemics , Primary Health Care/organization & administration , Societies, Medical , United Kingdom/epidemiology
9.
J Am Med Inform Assoc ; 27(6): 853-859, 2020 06 01.
Article in English | MEDLINE | ID: covidwho-631869

ABSTRACT

OBJECTIVE: To describe the implementation of technological support important for optimizing clinical management of the COVID-19 pandemic. MATERIALS AND METHODS: Our health system has confirmed prior and current cases of COVID-19. An Incident Command Center was established early in the crisis and helped identify electronic health record (EHR)-based tools to support clinical care. RESULTS: We outline the design and implementation of EHR-based rapid screening processes, laboratory testing, clinical decision support, reporting tools, and patient-facing technology related to COVID-19. DISCUSSION: The EHR is a useful tool to enable rapid deployment of standardized processes. UC San Diego Health built multiple COVID-19-specific tools to support outbreak management, including scripted triaging, electronic check-in, standard ordering and documentation, secure messaging, real-time data analytics, and telemedicine capabilities. Challenges included the need to frequently adjust build to meet rapidly evolving requirements, communication, and adoption, and to coordinate the needs of multiple stakeholders while maintaining high-quality, prepandemic medical care. CONCLUSION: The EHR is an essential tool in supporting the clinical needs of a health system managing the COVID-19 pandemic.


Subject(s)
Betacoronavirus , Coronavirus Infections/epidemiology , Electronic Health Records , Medical Records Systems, Computerized , Pandemics/prevention & control , Pneumonia, Viral/epidemiology , Telemedicine , User-Computer Interface , Academic Medical Centers/organization & administration , COVID-19 , California/epidemiology , Coronavirus Infections/diagnosis , Coronavirus Infections/therapy , Databases, Factual , Decision Support Systems, Clinical , Humans , Medical Informatics , Patient Care Team/organization & administration , Pneumonia, Viral/diagnosis , Pneumonia, Viral/therapy , SARS-CoV-2
10.
J Am Med Inform Assoc ; 27(6): 860-866, 2020 06 01.
Article in English | MEDLINE | ID: covidwho-42077

ABSTRACT

OBJECTIVE: To rapidly deploy a digital patient-facing self-triage and self-scheduling tool in a large academic health system to address the COVID-19 pandemic. MATERIALS AND METHODS: We created a patient portal-based COVID-19 self-triage and self-scheduling tool and made it available to all primary care patients at the University of California, San Francisco Health, a large academic health system. Asymptomatic patients were asked about exposure history and were then provided relevant information. Symptomatic patients were triaged into 1 of 4 categories-emergent, urgent, nonurgent, or self-care-and then connected with the appropriate level of care via direct scheduling or telephone hotline. RESULTS: This self-triage and self-scheduling tool was designed and implemented in under 2 weeks. During the first 16 days of use, it was completed 1129 times by 950 unique patients. Of completed sessions, 315 (28%) were by asymptomatic patients, and 814 (72%) were by symptomatic patients. Symptomatic patient triage dispositions were as follows: 193 emergent (24%), 193 urgent (24%), 99 nonurgent (12%), 329 self-care (40%). Sensitivity for detecting emergency-level care was 87.5% (95% CI 61.7-98.5%). DISCUSSION: This self-triage and self-scheduling tool has been widely used by patients and is being rapidly expanded to other populations and health systems. The tool has recommended emergency-level care with high sensitivity, and decreased triage time for patients with less severe illness. The data suggests it also prevents unnecessary triage messages, phone calls, and in-person visits. CONCLUSION: Patient self-triage tools integrated into electronic health record systems have the potential to greatly improve triage efficiency and prevent unnecessary visits during the COVID-19 pandemic.


Subject(s)
Appointments and Schedules , Betacoronavirus , Coronavirus Infections , Diagnostic Self Evaluation , Medical Records Systems, Computerized , Pandemics , Patient Participation , Patient Portals , Pneumonia, Viral , Triage/methods , Academic Medical Centers , Adult , COVID-19 , Coronavirus Infections/diagnosis , Coronavirus Infections/epidemiology , Humans , Pneumonia, Viral/diagnosis , Pneumonia, Viral/epidemiology , SARS-CoV-2 , San Francisco , Self Care , Telemedicine/organization & administration
11.
JMIR Public Health Surveill ; 6(2): e18606, 2020 04 02.
Article in English | MEDLINE | ID: covidwho-31012

ABSTRACT

BACKGROUND: The Royal College of General Practitioners (RCGP) Research and Surveillance Centre (RSC) and Public Health England (PHE) have successfully worked together on the surveillance of influenza and other infectious diseases for over 50 years, including three previous pandemics. With the emergence of the international outbreak of the coronavirus infection (COVID-19), a UK national approach to containment has been established to test people suspected of exposure to COVID-19. At the same time and separately, the RCGP RSC's surveillance has been extended to monitor the temporal and geographical distribution of COVID-19 infection in the community as well as assess the effectiveness of the containment strategy. OBJECTIVES: The aims of this study are to surveil COVID-19 in both asymptomatic populations and ambulatory cases with respiratory infections, ascertain both the rate and pattern of COVID-19 spread, and assess the effectiveness of the containment policy. METHODS: The RCGP RSC, a network of over 500 general practices in England, extract pseudonymized data weekly. This extended surveillance comprises of five components: (1) Recording in medical records of anyone suspected to have or who has been exposed to COVID-19. Computerized medical records suppliers have within a week of request created new codes to support this. (2) Extension of current virological surveillance and testing people with influenza-like illness or lower respiratory tract infections (LRTI)-with the caveat that people suspected to have or who have been exposed to COVID-19 should be referred to the national containment pathway and not seen in primary care. (3) Serology sample collection across all age groups. This will be an extra blood sample taken from people who are attending their general practice for a scheduled blood test. The 100 general practices currently undertaking annual influenza virology surveillance will be involved in the extended virological and serological surveillance. (4) Collecting convalescent serum samples. (5) Data curation. We have the opportunity to escalate the data extraction to twice weekly if needed. Swabs and sera will be analyzed in PHE reference laboratories. RESULTS: General practice clinical system providers have introduced an emergency new set of clinical codes to support COVID-19 surveillance. Additionally, practices participating in current virology surveillance are now taking samples for COVID-19 surveillance from low-risk patients presenting with LRTIs. Within the first 2 weeks of setup of this surveillance, we have identified 3 cases: 1 through the new coding system, the other 2 through the extended virology sampling. CONCLUSIONS: We have rapidly converted the established national RCGP RSC influenza surveillance system into one that can test the effectiveness of the COVID-19 containment policy. The extended surveillance has already seen the use of new codes with 3 cases reported. Rapid sharing of this protocol should enable scientific critique and shared learning. INTERNATIONAL REGISTERED REPORT IDENTIFIER (IRRID): DERR1-10.2196/18606.


Subject(s)
Coronavirus Infections/epidemiology , Coronavirus , Disease Notification/methods , Medical Records Systems, Computerized , Pandemics/prevention & control , Pneumonia, Viral/epidemiology , Public Health Surveillance/methods , Betacoronavirus , COVID-19 , Disease Outbreaks , England/epidemiology , Female , Humans , Male , Public Health , SARS-CoV-2 , Sentinel Surveillance
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