ANALYSES OF PREVENTIVE CARE MEASURES WITH INCOMPLETE HISTORICAL DATA IN ELECTRONIC MEDICAL RECORDS: AN EXAMPLE FROM COLORECTAL CANCER SCREENING.
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ABSTRACT:
SUBMITTER: Zheng Y
PROVIDER: S-EPMC8442666 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:electronic Medical Records & Genomics (eMERGE)
| PRJNA158491 | ENA
Project description:BackgroundImprovements in the quality of health care services are often measured using data present in medical records. Electronic Medical Records (EMRs) contain potentially valuable new sources of health data. However, data quality in EMRs may not be optimal and should be assessed. Data reliability (are the same data elements being measured over time?) is a prerequisite for data validity (are the data accurate?). Our objective was to measure the reliability of data for preventive services in primary care EMRs during the transition to EMR.MethodsOur data sources were randomly selected eligible patients' medical records and data obtained from provincial administrative datasets. Eighteen community-based family physicians in Toronto, Ontario that implemented EMRs starting in 2006 participated in this study. We measured the proportion of patients eligible for a service (Pap smear, screening mammogram or influenza vaccination) that received the service. We compared the change in rates of selected preventive services calculated from the medical record audits with the change in administrative datasets.ResultsIn the first year of EMR use (2006) services decreased by 8.7% more (95% CI -11.0%- - 6.4%, p < 0.0001) when measured through medical record audits as compared with administrative datasets. Services increased by 2.4% more (95% CI 0%-4.9%, p = 0.05) in the medical record audits during the second year of EMR use (2007).ConclusionThere were differences between the change measured through medical record audits and administrative datasets. Problems could include difficulties with organizing new data entry processes as well as continued use of both paper and EMRs. Data extracted from EMRs had limited reliability during the initial phase of EMR implementation. Unreliable data interferes with the ability to measure and improve health care quality.
| S-EPMC3442990 | biostudies-literature
Project description:ObjectiveAmbiguous definitions of quality measures in natural language impede their automated computability and also the reproducibility, validity, timeliness, traceability, comparability, and interpretability of computed results. Therefore, quality measures should be formalized before their release. We have previously developed and successfully applied a method for clinical indicator formalization (CLIF). The objective of our present study is to test whether CLIF is generalizable--that is, applicable to a large set of heterogeneous measures of different types and from various domains.Materials and methodsWe formalized the entire set of 159 Dutch quality measures for general practice, which contains structure, process, and outcome measures and covers seven domains. We relied on a web-based tool to facilitate the application of our method. Subsequently, we computed the measures on the basis of a large database of real patient data.ResultsOur CLIF method enabled us to fully formalize 100% of the measures. Owing to missing functionality, the accompanying tool could support full formalization of only 86% of the quality measures into Structured Query Language (SQL) queries. The remaining 14% of the measures required manual application of our CLIF method by directly translating the respective criteria into SQL. The results obtained by computing the measures show a strong correlation with results computed independently by two other parties.ConclusionsThe CLIF method covers all quality measures after having been extended by an additional step. Our web tool requires further refinement for CLIF to be applied completely automatically. We therefore conclude that CLIF is sufficiently generalizable to be able to formalize the entire set of Dutch quality measures for general practice.
| S-EPMC3932459 | biostudies-literature
Project description:PurposeThe purpose of the study is to evaluate whether primary care electronic medical records (EMRs) from patients with severe asthma can be used to identify allergic bronchopulmonary aspergillosis (ABPA) cases.MethodsThis cross-sectional feasibility study was conducted in adults with active and severe asthma registered with the Clinical Practice Research Datalink. A set of keywords flagged terms potentially indicative of ABPA in free-text comments of patients' EMRs to produce a grid on the basis of keywords' hit or miss. The grid was examined for occurrence and concurrence of keywords to discern patterns of concurrence potentially indicative of an underlying diagnosis of ABPA.ResultsThe analyses included 3 653 169 free-text items from 21 054 patients. In total, 52 patients (0.25%) had at least one mention of 'ABPA' in their medical record; 67% of these patients also had a mention of 'aspergillus/aspergillosis', 54% of 'bronchiectasis', 42% of 'itraconazole' and 62% of 'IgE'. The term 'aspergillus/aspergillosis' occurred with a proportion of 1.84% (N = 387); 9% of these patients also had a mention of 'ABPA', and the remaining 91% were potential additional cases of ABPA. From the observed concurrence of keywords, we were able to devise a potential algorithm to identify cases with varying degrees of specificity.ConclusionsThis study suggests that analysis of free text within asthmatic patients' EMRs may be used to identify potential cases of ABPA. This could be an efficient approach to identify rare conditions and to quantify their potential burden. © 2017 The Authors. Pharmacoepidemiology & Drug Safety Published by John Wiley & Sons Ltd.
| S-EPMC5573984 | biostudies-literature
Project description:BackgroundOutliers and class imbalance in medical data could affect the accuracy of machine learning models. For physicians who want to apply predictive models, how to use the data at hand to build a model and what model to choose are very thorny problems. Therefore, it is necessary to consider outliers, imbalanced data, model selection, and parameter tuning when modeling.MethodsThis study used a joint modeling strategy consisting of: outlier detection and removal, data balancing, model fitting and prediction, performance evaluation. We collected medical record data for all ICH patients with admissions in 2017-2019 from Sichuan Province. Clinical and radiological variables were used to construct models to predict mortality outcomes 90 days after discharge. We used stacking ensemble learning to combine logistic regression (LR), random forest (RF), artificial neural network (ANN), support vector machine (SVM), and k-nearest neighbors (KNN) models. Accuracy, sensitivity, specificity, AUC, precision, and F1 score were used to evaluate model performance. Finally, we compared all 84 combinations of the joint modeling strategy, including training set with and without cross-validated committees filter (CVCF), five resampling techniques (random under-sampling (RUS), random over-sampling (ROS), adaptive synthetic sampling (ADASYN), Borderline synthetic minority oversampling technique (Borderline SMOTE), synthetic minority oversampling technique and edited nearest neighbor (SMOTEENN)) and no resampling, seven models (LR, RF, ANN, SVM, KNN, Stacking, AdaBoost).ResultsAmong 4207 patients with ICH, 2909 (69.15%) survived 90 days after discharge, and 1298 (30.85%) died within 90 days after discharge. The performance of all models improved with removing outliers by CVCF except sensitivity. For data balancing processing, the performance of training set without resampling was better than that of training set with resampling in terms of accuracy, specificity, and precision. And the AUC of ROS was the best. For seven models, the average accuracy, specificity, AUC, and precision of RF were the highest. Stacking performed best in F1 score. Among all 84 combinations of joint modeling strategy, eight combinations performed best in terms of accuracy (0.816). For sensitivity, the best performance was SMOTEENN + Stacking (0.662). For specificity, the best performance was CVCF + KNN (0.987). Stacking and AdaBoost had the best performances in AUC (0.756) and F1 score (0.602), respectively. For precision, the best performance was CVCF + SVM (0.938).ConclusionThis study proposed a joint modeling strategy including outlier detection and removal, data balancing, model fitting and prediction, performance evaluation, in order to provide a reference for physicians and researchers who want to build their own models. This study illustrated the importance of outlier detection and removal for machine learning and showed that ensemble learning might be a good modeling strategy. Due to the low imbalanced ratio (IR, the ratio of majority class and minority class) in this study, we did not find any improvement in models with resampling in terms of accuracy, specificity, and precision, while ROS performed best on AUC.
| S-EPMC9594939 | biostudies-literature
Project description:Post-market medical device surveillance is a challenge facing manufacturers, regulatory agencies, and health care providers. Electronic health records are valuable sources of real-world evidence for assessing device safety and tracking device-related patient outcomes over time. However, distilling this evidence remains challenging, as information is fractured across clinical notes and structured records. Modern machine learning methods for machine reading promise to unlock increasingly complex information from text, but face barriers due to their reliance on large and expensive hand-labeled training sets. To address these challenges, we developed and validated state-of-the-art deep learning methods that identify patient outcomes from clinical notes without requiring hand-labeled training data. Using hip replacements-one of the most common implantable devices-as a test case, our methods accurately extracted implant details and reports of complications and pain from electronic health records with up to 96.3% precision, 98.5% recall, and 97.4% F1, improved classification performance by 12.8-53.9% over rule-based methods, and detected over six times as many complication events compared to using structured data alone. Using these additional events to assess complication-free survivorship of different implant systems, we found significant variation between implants, including for risk of revision surgery, which could not be detected using coded data alone. Patients with revision surgeries had more hip pain mentions in the post-hip replacement, pre-revision period compared to patients with no evidence of revision surgery (mean hip pain mentions 4.97 vs. 3.23; t?=?5.14; p?<?0.001). Some implant models were associated with higher or lower rates of hip pain mentions. Our methods complement existing surveillance mechanisms by requiring orders of magnitude less hand-labeled training data, offering a scalable solution for national medical device surveillance using electronic health records.
| S-EPMC6761113 | biostudies-literature
Project description:Background:The significant risk of adverse events following medical procedures supports a clinical epidemiological approach based on the analyses of collections of electronic medical records. Data analytical tools might help clinical epidemiologists develop more appropriate case-crossover designs for monitoring patient safety. Objective:To develop and assess the methodological quality of an interactive tool for use by clinical epidemiologists to systematically design case-crossover analyses of large electronic medical records databases. Material and Methods:We developed IT-CARES, an analytical tool implementing case-crossover design, to explore the association between exposures and outcomes. The exposures and outcomes are defined by clinical epidemiologists via lists of codes entered via a user interface screen. We tested IT-CARES on data from the French national inpatient stay database, which documents diagnoses and medical procedures for 170 million inpatient stays between 2007 and 2013. We compared the results of our analysis with reference data from the literature on thromboembolic risk after delivery and bleeding risk after total hip replacement. Results:IT-CARES provides a user interface with 3 columns: (i) the outcome criteria in the left-hand column, (ii) the exposure criteria in the right-hand column, and (iii) the estimated risk (odds ratios, presented in both graphical and tabular formats) in the middle column. The estimated odds ratios were consistent with the reference literature data. Discussion:IT-CARES may enhance patient safety by facilitating clinical epidemiological studies of adverse events following medical procedures. The tool's usability must be evaluated and improved in further research.
| S-EPMC5391728 | biostudies-literature
Project description:MotivationUnderrepresentation of racial groups represents an important challenge and major gap in phenomics research. Most of the current human phenomics research is based primarily on European populations; hence it is an important challenge to expand it to consider other population groups. One approach is to utilize data from EMR databases that contain patient data from diverse demographics and ancestries. The implications of this racial underrepresentation of data can be profound regarding effects on the healthcare delivery and actionability. To the best of our knowledge, our work is the first attempt to perform comparative, population-scale analyses of disease networks across three different populations, namely Caucasian (EA), African American (AA) and Hispanic/Latino (HL).ResultsWe compared susceptibility profiles and temporal connectivity patterns for 1988 diseases and 37 282 disease pairs represented in a clinical population of 1 025 573 patients. Accordingly, we revealed appreciable differences in disease susceptibility, temporal patterns, network structure and underlying disease connections between EA, AA and HL populations. We found 2158 significantly comorbid diseases for the EA cohort, 3265 for AA and 672 for HL. We further outlined key disease pair associations unique to each population as well as categorical enrichments of these pairs. Finally, we identified 51?key 'hub' diseases that are the focal points in the race-centric networks and of particular clinical importance. Incorporating race-specific disease comorbidity patterns will produce a more accurate and complete picture of the disease landscape overall and could support more precise understanding of disease relationships and patient management towards improved clinical outcomes.Contactsrong.chen@mssm.edu or joel.dudley@mssm.eduSupplementary informationSupplementary data are available at Bioinformatics online.
| S-EPMC4908366 | biostudies-literature
Project description:As the deployment of electronic medical records (EMR) expands, so is the availability of long-term datasets that could serve to enhance public health surveillance. We hypothesized that EMR-based surveillance systems that incorporate seasonality and other long-term trends would discover outbreaks of acute respiratory infections (ARI) sooner than systems that only consider the recent past.We simulated surveillance systems aimed at discovering modeled influenza outbreaks injected into backgrounds of patients with ARI. Backgrounds of daily case counts were either synthesized or obtained by applying one of three previously validated ARI case-detection algorithms to authentic EMR entries. From the time of outbreak injection, detection statistics were applied daily on paired background+injection and background-only time series. The relationship between the detection delay (the time from injection to the first alarm uniquely found in the background+injection data) and the false-alarm rate (FAR) was determined by systematically varying the statistical alarm threshold. We compared this relationship for outbreak detection methods that utilized either 7 days (early aberrancy reporting system (EARS)) or 2-4 years of past data (seasonal autoregressive integrated moving average (SARIMA) time series modeling).In otherwise identical surveillance systems, SARIMA detected epidemics sooner than EARS at any FAR below 10%. The algorithms used to detect single ARI cases impacted both the feasibility and marginal benefits of SARIMA modeling. Under plausible real-world conditions, SARIMA could reduce detection delay by 5-16 days. It also was more sensitive at detecting the summer wave of the 2009 influenza pandemic.Time series modeling of long-term historical EMR data can reduce the time it takes to discover epidemics of ARI. Realistic surveillance simulations may prove invaluable to optimize system design and tuning.
| S-EPMC5791979 | biostudies-literature
Project description:OBJECTIVE:The traditional fee-for-service approach to healthcare can lead to the management of a patient's conditions in a siloed manner, inducing various negative consequences. It has been recognized that a bundled approach to healthcare - one that manages a collection of health conditions together - may enable greater efficacy and cost savings. However, it is not always evident which sets of conditions should be managed in a bundled manner. In this study, we investigate if a data-driven approach can automatically learn potential bundles. METHODS:We designed a framework to infer health condition collections (HCCs) based on the similarity of their clinical workflows, according to electronic medical record (EMR) utilization. We evaluated the framework with data from over 16,500 inpatient stays from Northwestern Memorial Hospital in Chicago, Illinois. The plausibility of the inferred HCCs for bundled care was assessed through an online survey of a panel of five experts, whose responses were analyzed via an analysis of variance (ANOVA) at a 95% confidence level. We further assessed the face validity of the HCCs using evidence in the published literature. RESULTS:The framework inferred four HCCs, indicative of (1) fetal abnormalities, (2) late pregnancies, (3) prostate problems, and (4) chronic diseases, with congestive heart failure featuring prominently. Each HCC was substantiated with evidence in the literature and was deemed plausible for bundled care by the experts at a statistically significant level. CONCLUSIONS:The findings suggest that an automated EMR data-driven framework conducted can provide a basis for discovering bundled care opportunities. Still, translating such findings into actual care management will require further refinement, implementation, and evaluation.
| S-EPMC5771885 | biostudies-literature