Biomedical Informatics Commons^™

Electrochemical Hydrogen Evolution Over Hydrothermally Synthesized Re-Doped Mos2 Flower-Like Microspheres, Juan Aliaga, Pablo Vera, Juan Araya, Luis Ballesteros, Julio Urzúa, Mario Farías, Francisco Paraguay-Delgado, Gabriel Alonso-Núñez, Guillermo González, Eglantina Benavente

Faculty, Staff and Students Publications

In this research, we report a simple hydrothermal synthesis to prepare rhenium (Re)- doped MoS2 flower-like microspheres and the tuning of their structural, electronic, and electrocatalytic properties by modulating the insertion of Re. The obtained compounds were characterized by X-ray diffraction (XRD), scanning electron microscopy (SEM), high-resolution transmission electron microscopy (HRTEM), Raman spectroscopy, and X-ray photoelectron spectroscopy (XPS). Structural, morphological, and chemical analyses confirmed the synthesis of poorly crystalline Re-doped MoS2 flower-like microspheres composed of few stacked layers. They exhibit enhanced hydrogen evolution reaction (HER) performance with low overpotential of 210 mV at current density of 10 mA/cm2, with a …

Single-Nuclei Rna-Seq On Human Retinal Tissue Provides Improved Transcriptome Profiling, Qingnan Liang, Rachayata Dharmat, Leah Owen, Akbar Shakoor, Yumei Li, Sangbae Kim, Albert Vitale, Ivana Kim, Denise Morgan, Shaoheng Liang, Nathaniel Wu, Ken Chen, Margaret M Deangelis, Rui Chen

Faculty, Staff and Students Publications

Single-cell RNA-seq is a powerful tool in decoding the heterogeneity in complex tissues by generating transcriptomic profiles of the individual cell. Here, we report a single-nuclei RNA-seq (snRNA-seq) transcriptomic study on human retinal tissue, which is composed of multiple cell types with distinct functions. Six samples from three healthy donors are profiled and high-quality RNA-seq data is obtained for 5873 single nuclei. All major retinal cell types are observed and marker genes for each cell type are identified. The gene expression of the macular and peripheral retina is compared to each other at cell-type level. Furthermore, our dataset shows an …

Enhancing Clinical Concept Extraction With Contextual Embeddings, Yuqi Si, Jingqi Wang, Hua Xu, Kirk Roberts

Faculty, Staff and Student Publications

OBJECTIVE: Neural network-based representations ("embeddings") have dramatically advanced natural language processing (NLP) tasks, including clinical NLP tasks such as concept extraction. Recently, however, more advanced embedding methods and representations (eg, ELMo, BERT) have further pushed the state of the art in NLP, yet there are no common best practices for how to integrate these representations into clinical tasks. The purpose of this study, then, is to explore the space of possible options in utilizing these new models for clinical concept extraction, including comparing these to traditional word embedding methods (word2vec, GloVe, fastText).

MATERIALS AND METHODS: Both off-the-shelf, open-domain embeddings and …

Microrna-374a, -4680, And -133b Suppress Cell Proliferation Through The Regulation Of Genes Associated With Human Cleft Palate In Cultured Human Palate Cells, Akiko Suzuki, Aimin Li, Mona Gajera, Nada Abdallah, Musi Zhang, Zhongming Zhao, Junichi Iwata

Faculty, Staff and Student Publications

BACKGROUND: Cleft palate (CP) is the second most common congenital birth defect; however, the relationship between CP-associated genes and epigenetic regulation remains largely unknown. In this study, we investigated the contribution of microRNAs (miRNAs) to cell proliferation and regulation of genes involved in CP development.

METHODS: In order to identify all genes for which mutations or association/linkage have been found in individuals with CP, we conducted a systematic literature search, followed by bioinformatics analyses for these genes. We validated the bioinformatics results experimentally by conducting cell proliferation assays and miRNA-gene regulatory analyses in cultured human palatal mesenchymal cells treated with …

Turf For Teams: Considering Both The Team And I In The Work-Centered Design Of Systems, Vickie Nguyen

Dissertations and Theses (Open Access)

Teams are an inherent part of many work domains, especially in the healthcare environment. Yet, most systems are often built with only the individual user in mind. How can we better incorporate the team, as a user, into the design of a system? By better understanding the team, through their user, task, representational, and functional needs, we can create more useful and helpful systems that match their work domain. For this research project, we utilize the TURF framework and expanded it further by also considering teams as a user, thus, creating the TURF for Teams framework. In addition, we chose …

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 …

Melatonin Enhances Sorafenib-Induced Cytotoxicity In Flt3-Itd Acute Myeloid Leukemia Cells By Redox Modification, Tian Tian, Jiajun Li, Yizhuo Li, Yun-Xin Lu, Yan-Lai Tang, Hua Wang, Fufu Zheng, Dingbo Shi, Qian Long, Miao Chen, Guillermo Garcia-Manero, Yumin Hu, Lijun Qin, Wuguo Deng

Faculty, Staff and Student Publications

Acute myeloid leukemia (AML) with an internal tandem duplication in Fms-related tyrosine kinase 3 (FLT3-ITD) is identified as a subgroup with poor outcome and intrinsic resistance to chemotherapy and therefore urgent need for development of novel therapeutic strategies.

Methods: The antitumor effects of melatonin alone or combined with sorafenib were evaluated via flow cytometry and immunoblotting assays in FLT-ITD AML cells. Also, the ex vivo and in vivo models were used to test the synergistic effects of melatonin and sorafenib against leukemia with FLT3/ITD mutation.

Results: Our study shows for the first time that melatonin inhibits proliferation and induces apoptosis …

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 …

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

Regulation Of Hnrnpa1 By Micrornas Controls The Mir-18a–K-Ras Axis In Chemotherapy-Resistant Ovarian Cancer, Cristian Rodriguez-Aguayo, Paloma Del C Monroig, Roxana S Redis, Emine Bayraktar, Maria I Almeida, Cristina Ivan, Enrique Fuentes-Mattei, Mohammed H Rashed, Arturo Chavez-Reyes, Bulent Ozpolat, Rahul Mitra, Anil K Sood, George A Calin, Gabriel Lopez-Berestein

Faculty, Staff and Student Publications

The regulation of microRNA (miRNA) biogenesis, function and degradation involves a range of mechanisms, including interactions with RNA-binding proteins. The potential contribution of regulatory miRNAs to the expression of these RNA interactor proteins that could control other miRNAs expression is still unclear. Here we demonstrate a regulatory circuit involving oncogenic and tumor-suppressor miRNAs and an RNA-binding protein in a chemotherapy-resistant ovarian cancer model. We identified and characterized miR-15a-5p and miR-25-3p as negative regulators of hnRNPA1 expression, which is required for the processing of miR-18a-3p, an inhibitor of the

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 …

What Is Biomedical Informatics?, Elmer V Bernstam, Jack W Smith, Todd R Johnson

Faculty, Staff and Student Publications

Biomedical informatics lacks a clear and theoretically-grounded definition. Many proposed definitions focus on data, information, and knowledge, but do not provide an adequate definition of these terms. Leveraging insights from the philosophy of information, we define informatics as the science of information, where information is data plus meaning. Biomedical informatics is the science of information as applied to or studied in the context of biomedicine. Defining the object of study of informatics as data plus meaning clearly distinguishes the field from related fields, such as computer science, statistics and biomedicine, which have different objects of study. The emphasis on data …

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 …

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 …

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 …

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 …

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 …

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 …

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 …