Browsing by Subject "Reproducibility of Results"
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Item Computer-facilitated review of electronic medical records reliably identifies emergency department interventions in older adults(Society for Academic Emergency Medicine, 2013-06) Biese, Kevin J.; Forbach, Cory R.; Medlin, Richard P.; Platts- Mills, Timothy F.; Scholer, Matthew J.; McCall, Brenda; Shofer, Frances S.; LaMantia, Michael; Hobgood, Cherri; Kizer, J. S.; Busby-Whitehead, Jan; Cairns, Charles B.; Emergency Medicine, School of MedicineOBJECTIVES: An estimated 14% to 25% of all scientific studies in peer-reviewed emergency medicine (EM) journals are medical records reviews. The majority of the chart reviews in these studies are performed manually, a process that is both time-consuming and error-prone. Computer-based text search engines have the potential to enhance chart reviews of electronic emergency department (ED) medical records. The authors compared the efficiency and accuracy of a computer-facilitated medical record review of ED clinical records of geriatric patients with a traditional manual review of the same data and describe the process by which this computer-facilitated review was completed. METHODS: Clinical data from consecutive ED patients age 65 years or older were collected retrospectively by manual and computer-facilitated medical record review. The frequency of three significant ED interventions in older adults was determined using each method. Performance characteristics of each search method, including sensitivity and positive predictive value, were determined, and the overall sensitivities of the two search methods were compared using McNemar's test. RESULTS: For 665 patient visits, there were 49 (7.4%) Foley catheters placed, 36 (5.4%) sedative medications administered, and 15 (2.3%) patients who received positive pressure ventilation. The computer-facilitated review identified more of the targeted procedures (99 of 100, 99%), compared to manual review (74 of 100 procedures, 74%; p < 0.0001). CONCLUSIONS: A practical, non-resource-intensive, computer-facilitated free-text medical record review was completed and was more efficient and accurate than manually reviewing ED records.Item Foundations for Studying Clinical Workflow: Development of a Composite Inter-Observer Reliability Assessment for Workflow Time Studies(American Medical Informatics Association, 2019) Lopetegui, Marcelo; Yen, Po-Yin; Embi, Peter; Payne, Philip; Medicine, School of MedicineThe ability to understand and measure the complexity of clinical workflow provides hospital managers and researchers with the necessary knowledge to assess some of the most critical issues in healthcare. Given the protagonist role of workflow time studies on influencing decision makers, major efforts are being conducted to address existing methodological inconsistencies of the technique. Among major concerns, the lack of a standardized methodology to ensure the reliability of human observers stands as a priority. In this paper, we highlight the limitations of the current Inter-Observer Reliability Assessments, and propose a novel composite score to systematically conduct them. The composite score is composed of a) the overall agreement based on Kappa that evaluates the naming agreement on virtually created one-seconds tasks, providing a global assessment of the agreement over time, b) a naming agreement based on Kappa, requiring an observation pairing approach based on time-overlap, c) a duration agreement based on the concordance correlation coefficient, that provides means to evaluate the correlation concerning tasks duration, d) a timing agreement, based on descriptive statistics of the gaps between timestamps of same-task classes, and e) a sequence agreement based on the Needleman-Wunsch sequence alignment algorithm. We hereby provide a first step towards standardized reliability reporting in workflow time studies. This new composite IORA protocol is intended to empower workflow researchers with a standardized and comprehensive method for validating observers' reliability and, in turn, the validity of their data and results.Item Functional variants in the LRRK2 gene confer shared effects on risk for Crohn's disease and Parkinson's disease(American Association for the Advancement of Science, 2018-01-10) Hui, Ken Y.; Fernandez-Hernandez, Heriberto; Hu, Jianzhong; Schaffner, Adam; Pankratz, Nathan; Hsu, Nai-Yun; Chuang, Ling-Shiang; Carmi, Shai; Villaverde, Nicole; Li, Xianting; Rivas, Manual; Levine, Adam P.; Bao, Xiuliang; Labrias, Philippe R.; Haritunians, Talin; Ruane, Darren; Gettler, Kyle; Chen, Ernie; Li, Dalin; Schiff, Elena R.; Pontikos, Nikolas; Barzilai, Nir; Brant, Steven R.; Bressman, Susan; Cheifetz, Adam S.; Clark, Lorraine N.; Daly, Mark J.; Desnick, Robert J.; Duerr, Richard H.; Katz, Seymour; Lencz, Todd; Myers, Richard H.; Ostrer, Harry; Ozelius, Laurie; Payami, Haydeh; Peter, Yakov; Rioux, John D.; Segal, Anthony W.; Scott, William K.; Silverberg, Mark S.; Vance, Jeffery M.; Ubarretxena-Belandia, Iban; Foroud, Tatiana; Atzmon, Gil; Pe’er, Itsik; Ioannou, Yiannis; McGovern, Dermot P.B.; Yue, Zhenyu; Schadt, Eric E.; Cho, Judy H.; Peter, Inga; Medical and Molecular Genetics, School of MedicineCrohn's disease (CD), a form of inflammatory bowel disease, has a higher prevalence in Ashkenazi Jewish than in non-Jewish European populations. To define the role of nonsynonymous mutations, we performed exome sequencing of Ashkenazi Jewish patients with CD, followed by array-based genotyping and association analysis in 2066 CD cases and 3633 healthy controls. We detected association signals in the LRRK2 gene that conferred risk for CD (N2081D variant, P = 9.5 × 10-10) or protection from CD (N551K variant, tagging R1398H-associated haplotype, P = 3.3 × 10-8). These variants affected CD age of onset, disease location, LRRK2 activity, and autophagy. Bayesian network analysis of CD patient intestinal tissue further implicated LRRK2 in CD pathogenesis. Analysis of the extended LRRK2 locus in 24,570 CD cases, patients with Parkinson's disease (PD), and healthy controls revealed extensive pleiotropy, with shared genetic effects between CD and PD in both Ashkenazi Jewish and non-Jewish cohorts. The LRRK2 N2081D CD risk allele is located in the same kinase domain as G2019S, a mutation that is the major genetic cause of familial and sporadic PD. Like the G2019S mutation, the N2081D variant was associated with increased kinase activity, whereas neither N551K nor R1398H variants on the protective haplotype altered kinase activity. We also confirmed that R1398H, but not N551K, increased guanosine triphosphate binding and hydrolyzing enzyme (GTPase) activity, thereby deactivating LRRK2. The presence of shared LRRK2 alleles in CD and PD provides refined insight into disease mechanisms and may have major implications for the treatment of these two seemingly unrelated diseases.Item Identifying Associations Between Brain Imaging Phenotypes and Genetic Factors via A Novel Structured SCCA Approach(Springer, 2017-06) Du, Lei; Zhang, Tuo; Liu, Kefei; Yan, Jingwen; Yao, Xiaohui; Risacher, Shannon L.; Saykin, Andrew J.; Han, Junwei; Guo, Lei; Shen, Li; Alzheimer's Disease Neuroimaging Initiative; Radiology and Imaging Sciences, School of MedicineBrain imaging genetics attracts more and more attention since it can reveal associations between genetic factors and the structures or functions of human brain. Sparse canonical correlation analysis (SCCA) is a powerful bi-multivariate association identification technique in imaging genetics. There have been many SCCA methods which could capture different types of structured imaging genetic relationships. These methods either use the group lasso to recover the group structure, or employ the graph/network guided fused lasso to find out the network structure. However, the group lasso methods have limitation in generalization because of the incomplete or unavailable prior knowledge in real world. The graph/network guided methods are sensitive to the sign of the sample correlation which may be incorrectly estimated. We introduce a new SCCA model using a novel graph guided pairwise group lasso penalty, and propose an efficient optimization algorithm. The proposed method has a strong upper bound for the grouping effect for both positively and negatively correlated variables. We show that our method performs better than or equally to two state-of-the-art SCCA methods on both synthetic and real neuroimaging genetics data. In particular, our method identifies stronger canonical correlations and captures better canonical loading profiles, showing its promise for revealing biologically meaningful imaging genetic associations.Item Measuring dispositional cancer worry in China and Belgium: a cross-cultural validation(Taylor & Francis, 2014) Bernat, Jennifer Kim; Jensen, Jakob D.; IU School of NursingDispositional cancer worry (DCW) is the uncontrollable tendency to dwell on cancer independent of relevant stimuli (e.g., diagnosis of the disease). Past research has suggested that DCW has two underlying dimensions: severity and frequency. Available measures of DCW severity and frequency were translated and validated in two countries: China and Belgium. Participants (N = 623) completed translated scales, as well as measures of general dispositional worry, cancer fear, and perceived risk. In both locations, DCW measures were reliable (Cronbach's alphas ranged from .78 - .93) and demonstrated strong convergent, divergent, and concurrent validity. Severity and frequency factors loaded as expected in exploratory factor analysis. Future research should pursue longitudinal tests of DCW's predictive validity and explore DCW in theoretical models predicting the relationship between worry and cancer prevention and early detection behaviors.Item Measuring research mistrust in adolescents and adults: Validity and reliability of an adapted version of the Group-Based Medical Mistrust Scale(PLOS, 2021-01-22) Knopf, Amelia S.; Krombach, Peter; Katz, Amy J.; Baker, Rebecca; Zimet, Gregory; School of NursingMistrust of health care providers among persons of color is a significant barrier to engaging them in research studies. Underrepresentation of persons of color is particularly problematic when the health problem under study disproportionately affects minoritized communities. The purpose of this study was to test the validity and reliability of an abbreviated and adapted version of the Group Based Medical Mistrust Scale. The GBMMS is a 12-item scale with three subscales that assess suspicion, experiences of discrimination, and lack of support in the health care setting. To adapt for use in the research setting, we shortened the scale to six items, and replaced "health care workers" and "health care" with "medical researchers" and "medical research," respectively. Using panelists from a market research firm, we recruited and enrolled a racially and ethnically diverse sample of American adults (N = 365) and adolescents aged 14-17 (N = 250). We administered the adapted scale in a web-based survey. We used Cronbach's alpha to evaluate measure internal reliability of the scale and external factor analysis to evaluate the relationships between the revised scale items. Five of the six items loaded onto a single factor, with (α = 0.917) for adolescents and (α = 0.912) for adults. Mean scores for each item ranged from 2.5-2.9, and the mean summary score (range 6-25) was 13.3 for adults and 13.1 for adolescents. Among adults, Black respondents had significantly higher mean summary scores compared to whites and those in other racia/ethnic groups (p<0.001). There was a trend toward significance for Black adolescents as compared to white respondents and those in other racial/ethnic groups (p = 0.09). This five-item modified version of the GBMMS is reliable and valid for measuring research mistrust with American adults and adolescents of diverse racial and ethnic identities.Item The Minimal Clinically Important Difference for the Mayo-Portland Adaptability Inventory(Wolters Kluwer, 2017-07) Malec, James F.; Kean, Jacob; Monahan, Patrick O.; Physical Medicine and Rehabilitation, School of MedicineOBJECTIVES: To determine the Minimal Clinically Important Difference (MCID) and Robust Clinically Important Difference (RCID) of the Mayo-Portland Adaptability Inventory-4 (MPAI-4) as measures of response to intervention. METHODS: Retrospective analysis of existing data. Both distribution- and anchor-based methods were used to triangulate on the MCID and to identify a moderate, that is, more robust, level of change (RCID) for the MPAI-4. These were further evaluated with respect to clinical provider ratings. PARTICIPANTS: Data for individuals with acquired brain injury in rehabilitation programs throughout the United States in the OutcomeInfo Database (n = 3087) with 2 MPAI-4 ratings. MAIN MEASURES: MPAI-4, Supervision Rating Scale, Clinician Rating of Global Clinical Improvement. RESULTS: Initial analyses suggested 5 T-score points (5T) as the MCID and 9T as the RCID. Eighty-one percent to 87% of clinical raters considered a 5T change and 99% considered a 9T change to indicate meaningful improvement. CONCLUSIONS: 5T represents the MCID for the MPAI-4 and 9T, the RCID. Both values are notably less than the Reliable Change Index (RCI). While the RCI indicates change with a high level of statistical confidence, it may be insensitive to change that is considered meaningful by providers and participants as indicated by the MCID.Item Twenty-Four-Hour Urine Phosphorus as a Biomarker of Dietary Phosphorus Intake and Absorption in CKD: A Secondary Analysis from a Controlled Diet Balance Study(American Society of Nephrology, 2018-07-06) Stremke, Elizabeth R.; McCabe, Linda D.; McCabe, George P.; Martin, Berdine R.; Moe, Sharon M.; Weaver, Connie M.; Peacock, Munro; Hill Gallant, Kathleen M.; Department of Medicine, IU School of MedicineBACKGROUND AND OBJECTIVES: Twenty-four-hour urine phosphorus is commonly used as a surrogate measure for phosphorus intake and absorption in research studies, but its reliability and accuracy are unproven in health or CKD. This secondary analysis sought to determine the reliability and accuracy of 24-hour urine phosphorus as a biomarker of phosphorus intake and absorption in moderate CKD. DESIGN, SETTING, PARTICIPANTS, & MEASUREMENTS: Eight patients with stage 3-4 CKD participated in 2-week balance studies with tightly controlled phosphorus and calcium intakes. Thirteen 24-hour urine collections per patient were analyzed for variability and reliability of 24-hour urine phosphorus and phosphorus-to-creatinine ratio. The accuracy of 24-hour urine phosphorus to predict phosphorus intake was determined using a published equation. The relationships of 24-hour urine phosphorus with phosphorus intake, net absorption, and retention were determined. RESULTS: There was wide day-to-day variation in 24-hour urine phosphorus within and among subjects (coefficient of variation of 30% and 37%, respectively). Two 24-hour urine measures were needed to achieve ≥75% reliability. Estimating dietary phosphorus intake from a single 24-hour urine resulted in underestimation up to 98% in some patients and overestimation up to 79% in others. Twenty-four-hour urine phosphorus negatively correlated with whole-body retention but was not related to net absorption. CONCLUSIONS: From a sample of eight patients with moderate CKD on a tightly controlled dietary intake, 24-hour urine phosphorus was highly variable and did not relate to dietary phosphorus intake or absorption, rather it inversely related to phosphorus retention.