Data Science Commons^™

Information In Biological Systems And The Fluctuation Theorem, Yaşar Demirel

Department of Chemical and Biomolecular Engineering: Faculty Publications

Some critical trends in information theory, its role in living systems and utilization in fluctuation theory are discussed. The mutual information of thermodynamic coupling is incorporated into the generalized fluctuation theorem by using information theory and nonequilibrium thermodynamics. Thermodynamically coupled dissipative structures in living systems are capable of degrading more energy, and processing complex information through developmental and environmental constraints. The generalized fluctuation theorem can quantify the hysteresis observed in the amount of the irreversible work in nonequilibrium regimes in the presence of information and thermodynamic coupling.

Rigidity Analysis Of Protein Biological Assemblies And Periodic Crystal Structures, Filip Jagodzinski, Pamela Clark, Jessica Grant, Tiffany Liu, Samantha Monastra, Ileana Streinu

All Faculty Scholarship for the College of the Sciences

Background

We initiate in silico rigidity-theoretical studies of biological assemblies and small crystals for protein structures. The goal is to determine if, and how, the interactions among neighboring cells and subchains affect the flexibility of a molecule in its crystallized state. We use experimental X-ray crystallography data from the Protein Data Bank (PDB). The analysis relies on an effcient graph-based algorithm. Computational experiments were performed using new protein rigidity analysis tools available in the new release of our KINARI-Web server http://kinari.cs.umass.edu.

Results

We provide two types of results: on biological assemblies and on crystals. We found that when only isolated …

Growth Of Tropical Dasyatid Rays Estimated Using A Multi-Analytical Approach, Owen R. O'Shea, Matias Braccini, Rory Mcauley, Conrad W. Speed, Mark G. Meekan

Fisheries Research Articles

We studied the age and growth of four sympatric stingrays: reticulate whipray, Himanutra uarnak (n=19); blue mask, Neotrygon kuhlii (n=34); cowtail, Pastinachus atrus (n=32) and blue-spotted fantail, Taeniura lymma (n=40) rays at Ningaloo Reef, a fringing coral reef on the north-western coast of western Australia. Age estimates derived from band counts within sectioned vertebrae ranged between 1 and 27 years (H. uarnak, 1 - 25 yrs.; N. kuhlii, 1.5 - 13 yrs.; P. atrus, 1 - 27 yrs. and T. lymma, 1 -11 yrs.). Due to limitations of sample sizes, we combined several analytical methods …

A Conservation And Rigidity Based Method For Detecting Critical Protein Residues, Bahar Akbal-Delibas, Filip Jagodzinski, Nurit Haspel

All Faculty Scholarship for the College of the Sciences

Background

Certain amino acids in proteins play a critical role in determining their structural stability and function. Examples include flexible regions such as hinges which allow domain motion, and highly conserved residues on functional interfaces which allow interactions with other proteins. Detecting these regions can aid in the analysis and simulation of protein rigidity and conformational changes, and helps characterizing protein binding and docking. We present an analysis of critical residues in proteins using a combination of two complementary techniques. One method performs in-silico mutations and analyzes the protein's rigidity to infer the role of a point substitution to Glycine …

Gulf-Wide Decreases In The Size Of Large Coastal Sharks Documented By Generations Of Fishermen, Sean P. Powers, F. Joel Frodrie, Steven B. Scyphers, J. Marcus Drymon, Robert L. Shipp, Gregory W. Stunz

University Faculty and Staff Publications

Large sharks are top predators in most coastal and marine ecosystems throughout the world, and evidence of their reduced prominence in marine ecosystems has been a serious concern for fisheries and ecosystem management. Unfortunately, quantitative data to document the extent, timing, and consequences of changes in shark populations are scarce, thwarting examination of long-term (decadal, century) trends, and reconstructions based on incomplete data sets have been the subject of debate. Absence of quantitative descriptors of past ecological conditions is a generic problem facing many fields of science but is particularly troublesome for fisheries scientists who must develop specific targets for …

Multiscale Analysis Of Factors That Affect The Distribution Of Sharks Throughout The Northern Gulf Of Mexico, J. Marcus Drymon, Laure Carassou, Sean P. Powers, Mark Grace, John Dindo, Brian Dzwonkowski

University Faculty and Staff Publications

Identification of the spatial scale at which marine communities are organized is critical to proper management, yet this is particularly difficult to determine for highly migratory species like sharks. We used shark catch data collected during 2006–09 from fishery- independent bottom-longline surveys, as well as biotic and abiotic explanatory data to identify the factors that affect the distribution of coastal sharks at 2 spatial scales in the northern Gulf of Mexico. Centered principal component analyses (PCAs) were used to visualize the patterns that characterize shark distributions at small (Alabama and Mississippi coast) and large (northern Gulf of Mexico) spatial scales. …

Reconstructability Analysis Of Genetic Loci Associated With Alzheimer Disease, Martin Zwick, Shawn K. Westaway, Stephen Shervais, Patricia L. Kramer

Complex Systems Faculty Publications and Presentations

Reconstructability Analysis (RA) is an information- and graph-theory-based method which has been successfully used in previous genomic studies. Here we apply it to genetic (14 SNPs) and non-genetic (Education, Age, Gender) data on Alzheimer disease in a well-characterized Case/Control sample of 424 individuals. We confirm the importance of APOE as a predictor of the disease, and identify one non-genetic factor, Education, and two SNPs, one in BINI and the other in SORCS1, as likely disease predictors. SORCS1 appears to be a common risk factor for people with or without APOE. We also identify a possible interaction effect between Education and …

Age Composition And Distribution Of Red Drum (Sciaenops Ocellatus) In Offshore Waters Of The North Central Gulf Of Mexico: An Evaluation Of A Stock Under A Federal Harvest Moratorium, Sean P. Powers, Crystal Hightower, J. Marcus Drymon, Matthew W. Johnson

University Faculty and Staff Publications

Because of a lack of fishery- dependent data, assessment of the recovery of fish stocks that undergo the most aggressive form of management, namely harvest moratoriums, remains a challenge. Large schools of red drum (Sclaenops ocellatus) were common along the northern Gulf of Mexico until the late 1980s when increased fishing effort quickly depleted the stock. After 24 years of harvest moratorium on red drum in federal waters, the stock is in need of reassessment; however, fishery dependent data are not available in federal waters and fishery-independent data are limited. We document the distribution, age composition, growth, and condition of …

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 …

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 …

A Day In The Life Of Pubmed: Analysis Of A Typical Day's Query Log, Jorge R Herskovic, Len Y Tanaka, William Hersh, Elmer V Bernstam

Faculty, Staff and Student Publications

OBJECTIVE: To characterize PubMed usage over a typical day and compare it to previous studies of user behavior on Web search engines. DESIGN: We performed a lexical and semantic analysis of 2,689,166 queries issued on PubMed over 24 consecutive hours on a typical day. MEASUREMENTS: We measured the number of queries, number of distinct users, queries per user, terms per query, common terms, Boolean operator use, common phrases, result set size, MeSH categories, used semantic measurements to group queries into sessions, and studied the addition and removal of terms from consecutive queries to gauge search strategies. RESULTS: The size of …

Imaging Of Pulmonary Embolism And T-Pa Therapy Effects Using Mdct And Liposomal Iohexol Blood Pool Agent: Preliminary Results In A Rabbit Model, Stephen J Burke, Ananth Annapragada, Eric A Hoffman, Emmanuel Chen, Ketan B Ghaghada, Jered Sieren, Edwin J R Van Beek

Faculty, Staff and Student Publications

RATIONALE AND OBJECTIVES: Polyethylene glycol-coated liposomal blood pool contrast agents maintain contrast enhancement over several hours. This study aimed to evaluate (long-term) imaging of pulmonary arteries, comparing conventional iodinated contrast with a liposomal blood pool contrast agent. Also, visualization of the (real-time) therapeutic effects of tissue plasminogen activator (t-PA) on pulmonary embolism (PE) was attempted. MATERIALS AND METHODS: Six rabbits (weight approximately 4 kg) had autologous blood clots injected through the superior vena cava. Imaging was performed using conventional contrast (iohexol, 350 mg I/ml; GE HealthCare, Princeton, NJ) at a dose of 1400 mg I per animal, and after wash-out, …

A Spatial-Temporal Approach To Surveillance Of Prostate Cancer Disparities In Population Subgroups, Chiehwen E. Hsu, Francisco Soto Mas, Jerry A. Miller, Ella T. Nkhoma

Faculty, Staff and Student Publications

BACKGROUND: Prostate cancer mortality disparities exist among racial/ethnic groups in the United States, yet few studies have explored the spatiotemporal trend of the disease burden. To better understand mortality disparities by geographic regions over time, the present study analyzed the geographic variations of prostate cancer mortality by three Texas racial/ethnic groups over a 22-year period.

METHODS: The Spatial Scan Statistic developed by Kulldorff et al was used. Excess mortality was detected using scan windows of 50% and 90% of the study period and a spatial cluster size of 50% of the population at risk. Time trend was analyzed to examine …