Data Science Commons^™

Untapped Potential Of Clinical Text For Opioid Surveillance, Amy L. Olex, Tamas Gal, Majid Afshar, Dmitriy Dligach, Niranjan Karnik, Travis Oakes, Brihat Sharma, Meng Xie, Bridget T. Mcinnes, Julian Solway, Abel Kho, William Cramer, F. Gerard Moeller

Wright Center for Clinical and Translational Research Works

Accurate surveillance is needed to combat the growing opioid epidemic. To investigate the potential volume of missed opioid overdoses, we compare overdose encounters identified by ICD-10-CM codes and an NLP pipeline from two different medical systems. Our results show that the NLP pipeline identified a larger percentage of OOD encounters than ICD-10-CM codes. Thus, incorporating sophisticated NLP techniques into current diagnostic methods has the potential to improve surveillance on the incidence of opioid overdoses.

Deep Patient Representation Of Clinical Notes Via Multi-Task Learning For Mortality Prediction, Yuqi Si, Kirk Roberts

Faculty, Staff and Student Publications

We propose a deep learning-based multi-task learning (MTL) architecture focusing on patient mortality predictions from clinical notes. The MTL framework enables the model to learn a patient representation that generalizes to a variety of clinical prediction tasks. Moreover, we demonstrate how MTL enables small but consistent gains on a single classification task (e.g., in-hospital mortality prediction) simply by incorporating related tasks (e.g., 30-day and 1-year mortality prediction) into the MTL framework. To accomplish this, we utilize a multi-level Convolutional Neural Network (CNN) associated with a MTL loss component. The model is evaluated with 3, 5, and 20 tasks and is …

Population Data Centre Profile - The Western Australian Data Linkage Branch, Steve Hodges, Tom Eitelhuber, Alexandra Merchant, Janine Alan

Research outputs 2014 to 2021

Established in 1995, the Western Australian Data Linkage Branch (DLB) is Australia’s longest running data linkage agency. The Western Australian Data Linkage System (WADLS) employs an enduring linkage model spanning over 60 data collections supported by internally developed and supported software and IT infrastructure. DLB has delivered, and continues to deliver, a range of significant data linkage innovations, many of which have been adopted elsewhere. A current restructure within the Western Australian Department of Health (which we will refer to as the Department of Health) will provide an improved funding model geared toward addressing issues with staff retention, capacity and …

Effects Of A Community Population Health Initiative On Blood Pressure Control In Latinos, James R Langabeer, Timothy D Henry, Carlos Perez Aldana, Larissa Deluna, Nora Silva, Tiffany Champagne-Langabeer

Faculty, Staff and Student Publications

Background Hypertension remains one of the most important, modifiable cardiovascular risk factors. Yet, the largest minority ethnic group (Hispanics/Latinos) often have different health outcomes and behavior, making hypertension management more difficult. We explored the effects of an American Heart Association-sponsored population health intervention aimed at modifying behavior of Latinos living in Texas. Methods and Results We enrolled 8071 patients, and 5714 (65.7%) completed the 90-day program (58.5 years ±11.7; 59% female) from July 2016 to June 2018. Navigators identified patients with risk factors; initial and final blood pressure ( BP ) readings were performed in the physician's office; and interim …

Mapping Opioid Mortality Rates Across Treatment Capacity To Identify Need And Access, Garrett K. Wong, Justin R. Chang, Chase Greco, Yadunandan Pillai, Mohammad A. Shahrezaei, Melissa H. Burton, Rob Lawrence, Alan Dow

Graduate Research Posters

Background: The opioid and heroin overdose epidemic is a public health emergency in the state of Virginia, resulting in the death of more than 1,100 people in 2016. In order to overcome this epidemic, we need to match the places with the greatest need for services related to substance use disorders with the appropriate healthcare workforce.

Aims: As the data about the overdose outbreak and related socioeconomic factors grow in size and complexity, data scientists have attempted to utilize big data techniques to identify communities and risk factors contributing to addiction.

Methods: Using data obtained from the …

Visualizing The Opioid Overdose With A Dynamic Heat Map To Identify And Predict Vulnerable Communities, Justin R. Chang, Garrett K. Wong, Chase Greco, Yadunandan Pillai, Mohammad A. Shahrezaei, Melissa H. Burton, Rob Lawrence, Alan Dow

Graduate Research Posters

Background: Opioid and heroin overdose epidemic is a public health emergency in the state of Virginia. In order to prevent overdose deaths, we need the target expertise in substance use disorders to areas with high rates of overdose. In particular, an area with an acute spike in overdoses might represent an urgent need for intervention.

Aims: The CDC urges the use of near real-time surveillance to effectively identify overdose incidence, and to coordinate community responses in the states affected by the epidemic, including Virginia. However, current opioid overdose datasets for Virginia lack adequate consistency, granularity, and temporality for …

A Frame-Based Nlp System For Cancer-Related Information Extraction, Yuqi Si, Kirk Roberts

Faculty, Staff and Student Publications

We propose a frame-based natural language processing (NLP) method that extracts cancer-related information from clinical narratives. We focus on three frames: cancer diagnosis, cancer therapeutic procedure, and tumor description. We utilize a deep learning-based approach, bidirectional Long Short-term Memory (LSTM) Conditional Random Field (CRF), which uses both character and word embeddings. The system consists of two constituent sequence classifiers: a frame identification (lexical unit) classifier and a frame element classifier. The classifier achieves an F

Degradation Science: Mesoscopic Evolution And Temporal Analytics Of Photovoltaic Energy Materials, Roger H. French, Rudolf Podgornik, Timothy J. Peshek, Laura S. Bruckman, Yifan Xu, Nicholas R. Wheeler, Abdulkerim Gok, Yang Hu, Mohammad A. Hossain, Devin A. Gordon, Pei Zhao, Jiayang Sun, Guo-Qiang Zhang

Faculty Scholarship

Based on recent advances in nanoscience, data science and the availability of massive real-world datastreams, the mesoscopic evolution of mesoscopic energy materials can now be more fully studied. The temporal evolution is vastly complex in time and length scales and is fundamentally challenging to scientific understanding of degradation mechanisms and pathways responsible for energy materials evolution over lifetime. We propose a paradigm shift towards mesoscopic evolution modeling, based on physical and statistical models, that would integrate laboratory studies and real-world massive datastreams into a stress/mechanism/response framework with predictive capabilities. These epidemiological studies encompass the variability in properties that affect performance …

Exploration Of Preterm Birth Rates Using The Public Health Exposome Database And Computational Analysis Methods, Anne D. Kershenbaum, Michael A. Langston, Robert S. Levine, Arnold M. Saxton, Tonny J. Oyana, Barbara J. Kilbourne, Gary L. Rogers, Lisaann S. Gittner, Suzanne H. Baktash, Patricia Matthews-Juarez, Paul D. Juarez

Sociology Faculty Research

Recent advances in informatics technology has made it possible to integrate, manipulate, and analyze variables from a wide range of scientific disciplines allowing for the examination of complex social problems such as health disparities. This study used 589 county-level variables to identify and compare geographical variation of high and low preterm birth rates. Data were collected from a number of publically available sources, bringing together natality outcomes with attributes of the natural, built, social, and policy environments. Singleton early premature county birth rate, in counties with population size over 100,000 persons provided the dependent variable. Graph theoretical techniques were used …

Scalable Combinatorial Tools For Health Disparities Research, Michael A. Langston, Robert S. Levine, Barbara J. Kilbourne, Gary L. Rogers Jr., Anne D. Kershenbaum, Suzanne H. Baktash, Steven S. Coughlin, Arnold M. Saxton, Vincent K. Agboto, Darryl B. Hood, Maureen Y. Litchveld, Tonny J. Oyana, Patricia Matthews-Juarez, Paul D. Juarez

Sociology Faculty Research

Despite staggering investments made in unraveling the human genome, current estimates suggest that as much as 90% of the variance in cancer and chronic diseases can be attributed to factors outside an individual’s genetic endowment, particularly to environmental exposures experienced across his or her life course. New analytical approaches are clearly required as investigators turn to complicated systems theory and ecological, place-based and life-history perspectives in order to understand more clearly the relationships between social determinants, environmental exposures and health disparities. While traditional data analysis techniques remain foundational to health disparities research, they are easily overwhelmed by the ever-increasing size …

The Bivariate Erlang And Its Application In Modeling Recurrence Times Of Kidney Dialysis Data, Norou Diawara, S.H. Sathish Indika, Melva Grant, Edgard M. Maboudou-Tchao

Mathematics & Statistics Faculty Publications

Recent advances in computer modeling allows us to find closer fits to data. Our emphasis is on the interdependence between occurrence at kidney dialysis. The interdependence between kidney dialysis occurrences is modelled by a bivariate exponential that we propose in this article. The application is shown on the McGilchrist and Aisbett kidney data set with the use of the exponential distribution. The proposed bivariate exponential model has exponential marginal densities, correlated via a latent random variables and with finite probability of simultaneous occurrence. Extension of the model to a bivariate Erlang type distribution with same shape parameter is presented.

Comparison Of Clinical Knowledge Management Capabilities Of Commercially-Available And Leading Internally-Developed Electronic Health Records, Dean F Sittig, Adam Wright, Seth Meltzer, Linas Simonaitis, R Scott Evans, W Paul Nichol, Joan S Ash, Blackford Middleton

Faculty, Staff and Student Publications

BACKGROUND: We have carried out an extensive qualitative research program focused on the barriers and facilitators to successful adoption and use of various features of advanced, state-of-the-art electronic health records (EHRs) within large, academic, teaching facilities with long-standing EHR research and development programs. We have recently begun investigating smaller, community hospitals and out-patient clinics that rely on commercially-available EHRs. We sought to assess whether the current generation of commercially-available EHRs are capable of providing the clinical knowledge management features, functions, tools, and techniques required to deliver and maintain the clinical decision support (CDS) interventions required to support the recently defined …

Sequential Incoherence In A Multi-Party Synchronous Computer Mediated Communication For An Introductory Health Informatics Course, Jorge R Herskovic, J Caleb Goodwin, Pamela A Bozzo Silva, Irmgard Willcockson, Amy Franklin

Faculty, Staff and Student Publications

Online courses will play a key role in the high-volume Informatics education required to train the personnel that will be necessary to fulfill the health IT needs of the country. Online courses can cause feelings of isolation in students. A common way to address these feelings is to hold synchronous online "chats" for students. Conventional chats, however, can be confusing and impose a high extrinsic cognitive load on their participants that hinders the learning process. In this paper we present a qualitative analysis that shows the causes of this high cognitive load and our solution through the use of a …

Can Prospective Usability Evaluation Predict Data Errors?, Constance M Johnson, Meredith Nahm, Ryan J Shaw, Ashley Dunham, Kristin Newby, Rowena Dolor, Michelle Smerek, Guilherme Del Fiol, Jiajie Zhang

Faculty, Staff and Student Publications

Increasing amounts of clinical research data are collected by manual data entry into electronic source systems and directly from research subjects. For this manual entered source data, common methods of data cleaning such as post-entry identification and resolution of discrepancies and double data entry are not feasible. However data accuracy rates achieved without these mechanisms may be higher than desired for a particular research use. We evaluated a heuristic usability method for utility as a tool to independently and prospectively identify data collection form questions associated with data errors. The method evaluated had a promising sensitivity of 64% and a …

Clinical Decision Support Capabilities Of Commercially-Available Clinical Information Systems, Adam Wright, Dean F Sittig, Joan S Ash, Sapna Sharma, Justine E Pang, Blackford Middleton

Faculty, Staff and Student Publications

BACKGROUND: The most effective decision support systems are integrated with clinical information systems, such as inpatient and outpatient electronic health records (EHRs) and computerized provider order entry (CPOE) systems. Purpose The goal of this project was to describe and quantify the results of a study of decision support capabilities in Certification Commission for Health Information Technology (CCHIT) certified electronic health record systems.

METHODS: The authors conducted a series of interviews with representatives of nine commercially available clinical information systems, evaluating their capabilities against 42 different clinical decision support features.

RESULTS: Six of the nine reviewed systems offered all the applicable …

Improving Clinical Quality Indicators Through Electronic Health Records: It Takes More Than Just A Reminder, Dean F Sittig, Jonathan M Teich, Jerome A Osheroff, Hardeep Singh

Faculty, Staff and Student Publications

No abstract provided.

Use Of Instructional Video To Prepare Parents For Learning Infant Cardiopulmonary Resuscitation, Timothy S. Brannon, Lisa A. White, Julie N. Kilcrease, Lashawn D. Richard, Jana G. Spillers, Cynthia L. Phelps

Faculty, Staff and Student Publications

Parents of premature infants often receive infant cardiopulmonary resuscitation (CPR) training prior to discharge from the hospital, but one study showed that 27.5% of parents could not demonstrate adequate CPR skills after completing an instructor-led class. We hypothesized that parents who viewed an instructional video on infant CPR before attending the class would perform better on a standardized skills test than parents who attended the class with no preparation. Parents randomized to the intervention (video) group viewed the video within 48 hours of the CPR class. Parents in the control group attended the class with no special preparation. All parents …

Taxonomy Development And Knowledge Representation Of Nurses' Personal Cognitive Artifacts, Sharon Mclane, James P Turley

Faculty, Staff and Student Publications

Nurses prepare knowledge representations, or summaries of patient clinical data, each shift. These knowledge representations serve multiple purposes, including support of working memory, workload organization and prioritization, critical thinking, and reflection. This summary is integral to internal knowledge representations, working memory, and decision-making. Study of this nurse knowledge representation resulted in development of a taxonomy of knowledge representations necessary to nursing practice.This paper describes the methods used to elicit the knowledge representations and structures necessary for the work of clinical nurses, described the development of a taxonomy of this knowledge representation, and discusses translation of this methodology to the cognitive …

Improving Follow-Up Of Abnormal Cancer Screens Using Electronic Health Records: Trust But Verify Test Result Communication, Hardeep Singh, Lindsey Wilson, Laura A Petersen, Mona K Sawhney, Brian Reis, Donna Espadas, Dean F Sittig

Faculty, Staff and Student Publications

BACKGROUND: Early detection of colorectal cancer through timely follow-up of positive Fecal Occult Blood Tests (FOBTs) remains a challenge. In our previous work, we found 40% of positive FOBT results eligible for colonoscopy had no documented response by a treating clinician at two weeks despite procedures for electronic result notification. We determined if technical and/or workflow-related aspects of automated communication in the electronic health record could lead to the lack of response.

METHODS: Using both qualitative and quantitative methods, we evaluated positive FOBT communication in the electronic health record of a large, urban facility between May 2008 and March 2009. …

Ontology Driven Integration Platform For Clinical And Translational Research, Parsa Mirhaji, Min Zhu, Mattew Vagnoni, Elmer V. Bernstam, Jiajie Zhang, Jack W. Smith

Faculty, Staff and Student Publications

Semantic Web technologies offer a promising framework for integration of disparate biomedical data. In this paper we present the semantic information integration platform under development at the Center for Clinical and Translational Sciences (CCTS) at the University of Texas Health Science Center at Houston (UTHSC-H) as part of our Clinical and Translational Science Award (CTSA) program. We utilize the Semantic Web technologies not only for integrating, repurposing and classification of multi-source clinical data, but also to construct a distributed environment for information sharing, and collaboration online. Service Oriented Architecture (SOA) is used to modularize and distribute reusable services in a …

Computerized Provider Order Entry Adoption: Implications For Clinical Workflow, Emily M. Campbell, Kenneth P. Guappone, Dean F. Sittig, Richard H. Dykstra, Joan S. Ash

Faculty, Staff and Student Publications

OBJECTIVE: To identify and describe unintended adverse consequences related to clinical workflow when implementing or using computerized provider order entry (CPOE) systems. METHODS: We analyzed qualitative data from field observations and formal interviews gathered over a three-year period at five hospitals in three organizations. Five multidisciplinary researchers worked together to identify themes related to the impacts of CPOE systems on clinical workflow. RESULTS: CPOE systems can affect clinical work by 1) introducing or exposing human/computer interaction problems, 2) altering the pace, sequencing, and dynamics of clinical activities, 3) providing only partial support for the work activities of all types of …

Sustained Attention In Children With Two Etiologies Of Early Hydrocephalus, Maegan D. Swartwout, Paul T. Cirino, Amy W. Hampson, Jack M. Fletcher, Michael E. Brandt, Maureen Dennis

Faculty, Staff and Student Publications

Several studies have shown that children with spina bifida meningomyelocele (SBM) and hydrocephalus have attention problems on parent ratings and difficulties in stimulus orienting associated with a posterior brain attention system. Less is known about response control and inhibition associated with an anterior brain attention system. Using the Gordon Vigilance Task (Gordon, 1983), we studied error rate, reaction time, and performance over time for sustained attention, a key anterior attention function, in 101 children with SBM, 17 with aqueductal stenosis (AS; another condition involving congenital hydrocephalus), and 40 typically developing controls (NC). In SBM, we investigated the relation between cognitive …

Effect Of Progressive Mandibular Advancement On Pharyngeal Airway Size In Anesthetized Adults, Samuel T Kuna, Lee C Woodson, Daneshvari R Solanki, Oliver Esch, Donald E Frantz, Mali Mathru

Faculty, Staff and Student Publications

BACKGROUND: General anesthesia in adult humans is associated with narrowing or complete closure of the pharyngeal airway. The purpose of this study was to determine the effect of progressive mandibular advancement on pharyngeal airway size in normal adults during intravenous infusion of propofol for anesthesia.

METHODS: Magnetic resonance imaging was performed in nine normal adults during wakefulness and during propofol anesthesia. A commercially available intraoral appliance was used to manually advance the mandible. Images were obtained during wakefulness without the appliance and during anesthesia with the participants wearing the appliance under three conditions: without mandibular advancement, advancement to 50% maximum …

Molecular And Macromolecular Alterations Of Recombinant Adenoviral Vectors Do Not Resolve Changes In Hepatic Drug Metabolism During Infection, Shellie M Callahan, Piyanuch Wonganan, Maria A Croyle

Faculty, Staff and Student Publications

In this report we test the hypothesis that long-term virus-induced alterations in CYP occur from changes initiated by the virus that may not be related to the immune response. Enzyme activity, protein expression and mRNA of CYP3A2, a correlate of human CYP3A4, and CYP2C11, responsive to inflammatory mediators, were assessed 0.25, 1, 4, and 14 days after administration of several different recombinant adenoviruses at a dose of 5.7 x 1012 virus particles (vp)/kg to male Sprague Dawley rats. Wild type adenovirus, containing all viral genes, suppressed CYP3A2 and 2C11 activity by 37% and 39%, respectively within six hours. Levels fell …

Verb Generation In Children With Spina Bifida, Maureen Dennis, Derryn Jewell, Ross Hetherington, Christine Burton, Michael E. Brandt, Susan E. Blaser, Jack M Fletcher

Faculty, Staff and Student Publications

We investigated verb generation in children with spina bifida meningomyelocele (SBM; n = 55) and in typically developing controls (n = 32). Participants completed 6 blocks (40 trials each) of a task requiring them to produce a semantically related verb in response to a target noun and an additional 40 trials on which they were simply required to read target nouns aloud. After controlling for reading response time, groups did not differ significantly in verb generation response time or learning. Children with SBM produced more non-verb errors than controls and tended to repeat their mistakes over blocks. Verb generation performance …

Focal White Matter Changes In Spasmodic Dysphonia: A Combined Diffusion Tensor Imaging And Neuropathological Study, Kristina Simonyan, Fernanda Tovar-Moll, John Ostuni, Mark Hallett, Victor F Kalasinsky, Michael R Lewin-Smith, Elisabeth J Rushing, Alexander O Vortmeyer, Christy L Ludlow

Faculty, Staff and Student Publications

Spasmodic dysphonia is a neurological disorder characterized by involuntary spasms in the laryngeal muscles during speech production. Although the clinical symptoms are well characterized, the pathophysiology of this voice disorder is unknown. We describe here, for the first time to our knowledge, disorder-specific brain abnormalities in these patients as determined by a combined approach of diffusion tensor imaging (DTI) and postmortem histopathology. We used DTI to identify brain changes and to target those brain regions for neuropathological examination. DTI showed right-sided decrease of fractional anisotropy in the genu of the internal capsule and bilateral increase of overall water diffusivity in …

Searching For The Majority: Algorithms Of Voluntary Control, Jin Fan, Kevin G. Guise, Xun Liu, Hongbin Wang

Faculty, Staff and Student Publications

Voluntary control of information processing is crucial to allocate resources and prioritize the processes that are most important under a given situation; the algorithms underlying such control, however, are often not clear. We investigated possible algorithms of control for the performance of the majority function, in which participants searched for and identified one of two alternative categories (left or right pointing arrows) as composing the majority in each stimulus set. We manipulated the amount (set size of 1, 3, and 5) and content (ratio of left and right pointing arrows within a set) of the inputs to test competing hypotheses …

Correlates Of Tobacco Cessation Counseling Among Hispanic Physicians In The Us: A Cross-Sectional Survey Study, Francisco G Soto Mas, Héctor G Balcázar, Julia Valderrama Alberola, Chiehwen Ed Hsu

Faculty, Staff and Student Publications

BACKGROUND: Physician advice is an important motivator for attempting to stop smoking. However, physicians' lack of intervention with smokers has only modestly improved in the last decade. Although the literature includes extensive research in the area of the smoking intervention practices of clinicians, few studies have focused on Hispanic physicians. The purpose of this study was to explore the correlates of tobacco cessation counseling practices among Hispanic physicians in the US. METHODS: Data were collected through a validated survey instrument among a cross-sectional sample of self-reported Hispanic physicians practicing in New Mexico, and who were members of the New Mexico …

Downregulation Of Rap1gap Contributes To Ras Transformation, Oxana Tsygankova, Gregory V. Prendergast, Kanchan Puttaswamy, Yan Wang, Michael D. Feldman, Hongbin Wang, Marcia S. Brose, Judy L. Meinkoth

Faculty, Staff and Student Publications

Although abundant in well-differentiated rat thyroid cells, Rap1GAP expression was extinguished in a subset of human thyroid tumor-derived cell lines. Intriguingly, Rap1GAP was downregulated selectively in tumor cell lines that had acquired a mesenchymal morphology. Restoring Rap1GAP expression to these cells inhibited cell migration and invasion, effects that were correlated with the inhibition of Rap1 and Rac1 activity. The reexpression of Rap1GAP also inhibited DNA synthesis and anchorage-independent proliferation. Conversely, eliminating Rap1GAP expression in rat thyroid cells induced a transient increase in cell number. Strikingly, Rap1GAP expression was abolished by Ras transformation. The downregulation of Rap1GAP by Ras required the …

Quality Of Weight Loss Advice On Internet Forums, Kevin O Hwang, Kiran Farheen, Craig W Johnson, Eric J Thomas, Ann S Barnes, Elmer V Bernstam

Faculty, Staff and Student Publications

BACKGROUND: Adults use the Internet for weight loss information, sometimes by participating in discussion forums. Our purpose was to analyze the quality of advice exchanged on these forums. METHODS: This was a retrospective analysis of messages posted to 18 Internet weight loss forums during 1 month in 2006. Advice was evaluated for congruence with clinical guidelines; potential for causing harm; and subsequent correction when it was contradictory to guidelines (erroneous) or potentially harmful. Message- and forum-specific characteristics were evaluated as predictors of advice quality and self-correction. RESULTS: Of 3368 initial messages, 266 (7.9%) were requests for advice. Of 654 provisions …