Medicine and Health Sciences Commons^™

Incidents Of Snake Fungal Disease Caused By The Fungal Pathogen Ophidiomyces Ophidiicola In Texas, Alan Lizarraga, Lezley Hart, Michele Nolen, Lance R. Williams, Joseph S. Glavy

Pharmacy Faculty Publications and Presentations

The pathogen Ophidiomyces ophidiicola, widely known as the primary cause of snake fungal disease (SFD), has been detected in Texas’s naïve snakes. Our team set out to characterize O. ophidiicola’s spread in eastern Texas. From December 2018 until November 2021, we sampled and screened with ultraviolet (UV) light 176 snakes across eastern Texas and detected 27. O. ophidiicola’s positive snakes using qPCR and one snake in which SFD was confirmed via additional histological examination. Upon finding the ribbon snake with a clear clinical display, we isolated and cultured what we believe to be the first culture from Texas. This cultured …

Feasibility Of And Experience Using A Portable Mri Scanner In The Neonatal Intensive Care Unit., Maura Sien, Amie L. Robinson, Houchun H. Hu, Christopher R. Nitkin, Ara Hall, Marcie G. Files, Nathan S. Artz, John T. Pitts, Sherwin S. Chan

Manuscripts, Articles, Book Chapters and Other Papers

OBJECTIVE: A portable, low-field MRI system is now Food and Drug Administration cleared and has been shown to be safe and useful in adult intensive care unit settings. No neonatal studies have been performed. The objective is to assess our preliminary experience and assess feasibility of using the portable MRI system at the bedside in a neonatal intensive care unit (NICU) at a quaternary children's hospital.

STUDY DESIGN: This was a single-site prospective cohort study in neonates ≥2 kg conducted between October and December 2020. All parents provided informed consent. Neonates underwent portable MRI examination in the NICU with support …

Behavioral Health Grants Overview 2022, Parkview Health

Health Services and Informatics Research

2022 List of Externally and Internally Funded Research for our Behavioral Health Outreach Initiatives.

Our Mission: To strengthen awareness around mental health, support needs in our community, reduce stigma, and encourage people to connect with care.

Conceptualizing Care Partners' Burden, Stress, And Support For Reintegrating Veterans: A Mixed Methods Study., Nicholas A Rattray, Mindy Flanagan, Allison Mann, Leah Danson, Ai-Nghia Do, Diana Natividad, Katrina Spontak, Gala True

Health Services and Informatics Research

BACKGROUND: People who support Veterans as they transition from their military service into civilian life may be at an increased risk of psychological distress. Existing studies focus primarily on paid family caregivers, but few studies include spouses and informal non-family "care partners." We sought to identify key challenges faced by care partners of Veterans with invisible injuries.

METHODS: Semi-structured interviews were conducted with 36 individuals involved in supporting a recently separated US military Veteran enrolled in a 2-year longitudinal study. CPs completed validated measures on perceived stress, caregiving burden, quality of their relationship, life satisfaction, and flourishing. Independent

RESULTS: Care …

Law Enforcement Recruit Health Database, Myles C. Murphy, Simone Radavelli-Bagatini, Garth Allen, Nicolas Hart, Andrea Mosler

Research Datasets

Our study established clear demographic, mental health/physical injury, and physical performance data to be collected in a law enforcement recruit training program for injury surveillance and performance monitoring. Furthermore, we identified several items that were classified as relevant, but unlikely to be reported truthfully. These items which can help inform current practice and assist clinicians to determine the trustfulness of information received by patients when working within law enforcement environments.

Identifying The Serious Clinical Outcomes Of Adverse Reactions To Drugs By A Multi-Task Deep Learning Framework, Haochen Zhao, Peng Ni, Qichang Zhao, Xiao Liang, Di Ai, Shannon Erhardt, Jun Wang, Yaohang Li, Jiianxin Wang

Computer Science Faculty Publications

Adverse Drug Reactions (ADRs) have a direct impact on human health. As continuous pharmacovigilance and drug monitoring prove to be costly and time-consuming, computational methods have emerged as promising alternatives. However, most existing computational methods primarily focus on predicting whether or not the drug is associated with an adverse reaction and do not consider the core issue of drug benefit-risk assessment-whether the treatment outcome is serious when adverse drug reactions occur. To this end, we categorize serious clinical outcomes caused by adverse reactions to drugs into seven distinct classes and present a deep learning framework, so-called GCAP, for predicting the …

Cellbrf: A Feature Selection Method For Single-Cell Clustering Using Cell Balance And Random Forest, Yunpei Xu, Hong-Dong Li, Cui-Xiang Lin, Ruiqing Zheng, Yaohang Li, Jinhui Xu, Jianxin Wang

Computer Science Faculty Publications

Motivation

Single-cell RNA sequencing (scRNA-seq) offers a powerful tool to dissect the complexity of biological tissues through cell sub-population identification in combination with clustering approaches. Feature selection is a critical step for improving the accuracy and interpretability of single-cell clustering. Existing feature selection methods underutilize the discriminatory potential of genes across distinct cell types. We hypothesize that incorporating such information could further boost the performance of single cell clustering. Results

We develop CellBRF, a feature selection method that considers genes’ relevance to cell types for single-cell clustering. The key idea is to identify genes that are most important for discriminating …

Enabling Customization Of Discussion Forums For Blind Users, Mohan Sunkara, Yash Prakash, Hae-Na Lee, Sampath Jayarathna, Vikas Ashok

Computer Science Faculty Publications

Online discussion forums have become an integral component of news, entertainment, information, and video-streaming websites, where people all over the world actively engage in discussions on a wide range of topics including politics, sports, music, business, health, and world affairs. Yet, little is known about their usability for blind users, who aurally interact with the forum conversations using screen reader assistive technology. In an interview study, blind users stated that they often had an arduous and frustrating interaction experience while consuming conversation threads, mainly due to the highly redundant content and the absence of customization options to selectively view portions …

Msdrp: A Deep Learning Model Based On Multisource Data For Predicting Drug Response, Haochen Zhao, Xiaoyu Zhang, Qichang Zhao, Yaohang Li, Jianxin Wang

Computer Science Faculty Publications

Motivation: Cancer heterogeneity drastically affects cancer therapeutic outcomes. Predicting drug response in vitro is expected to help formulate personalized therapy regimens. In recent years, several computational models based on machine learning and deep learning have been proposed to predict drug response in vitro. However, most of these methods capture drug features based on a single drug description (e.g. drug structure), without considering the relationships between drugs and biological entities (e.g. target, diseases, and side effects). Moreover, most of these methods collect features separately for drugs and cell lines but fail to consider the pairwise interactions between drugs and cell …

An Approach To Developing Benchmark Datasets For Protein Secondary Structure Segmentation From Cryo-Em Density Maps, Thu Nguyen, Yongcheng Mu, Jiangwen Sun, Jing He

Computer Science Faculty Publications

More and more deep learning approaches have been proposed to segment secondary structures from cryo-electron density maps at medium resolution range (5--10Å). Although the deep learning approaches show great potential, only a few small experimental data sets have been used to test the approaches. There is limited understanding about potential factors, in data, that affect the performance of segmentation. We propose an approach to generate data sets with desired specifications in three potential factors - the protein sequence identity, structural contents, and data quality. The approach was implemented and has generated a test set and various training sets to study …

Progenitor Cell Isolation From Mouse Epididymal Adipose Tissue And Sequencing Library Construction, Qianglin Liu, Chaoyang Li, Yuxia Li, Leshan Wang, Xujia Zhang, Buhao Deng, Peidong Gao, Mohammad Shiri, Fozi Alkaifi, Junxing Zhao, Jacqueline M. Stephens, Constantine A. Simintiras, Joseph Francis, Jiangwen Sun, Xing Fu

Computer Science Faculty Publications

Here, we present a protocol to isolate progenitor cells from mouse epididymal visceral adipose tissue and construct bulk RNA and assay for transposase-accessible chromatin with sequencing (ATAC-seq) libraries. We describe steps for adipose tissue collection, cell isolation, and cell staining and sorting. We then detail procedures for both ATAC-seq and RNA sequencing library construction. This protocol can also be applied to other tissues and cell types directly or with minor modifications.

For complete details on the use and execution of this protocol, please refer to Liu et al. (2023).¹

*¹ Liu, Q., Li, C., Deng, B., Gao, P., …

A Single-Cell Atlas Of Bovine Skeletal Muscle Reveals Mechanisms Regulating Intramuscular Adipogenesis And Fibrogenesis, Leshan Wang, Peidong Gao, Chaoyag Li, Qianglin Liu, Zeyang Yao, Yuxia Li, Xujia Zhang, Jiangwen Sun, Constantine Simintiras, Matthew Welborn, Kenneth Mcmillin, Stephanie Oprescu, Shihuan Kuang, Xing Fu

Computer Science Faculty Publications

Background: Intramuscular fat (IMF) and intramuscular connective tissue (IMC) are often seen in human myopathies and are central to beef quality. The mechanisms regulating their accumulation remain poorly understood. Here, we explored the possibility of using beef cattle as a novel model for mechanistic studies of intramuscular adipogenesis and fibrogenesis.

Methods: Skeletal muscle single-cell RNAseq was performed on three cattle breeds, including Wagyu (high IMF), Brahman (abundant IMC but scarce IMF), and Wagyu/Brahman cross. Sophisticated bioinformatics analyses, including clustering analysis, gene set enrichment analyses, gene regulatory network construction, RNA velocity, pseudotime analysis, and cell-cell communication analysis, were performed to elucidate …

Comparison Of Physics-Based Deformable Registration Methods For Image-Guided Neurosurgery, Nikos Chrisochoides, Yixun Liu, Fotis Drakopoulos, Andriy Kot, Panos Foteinos, Christos Tsolakis, Emmanuel Billias, Olivier Clatz, Nicholas Ayache, Andrey Fedorov, Alex Golby, Peter Black, Ron Kikinis

Computer Science Faculty Publications

This paper compares three finite element-based methods used in a physics-based non-rigid registration approach and reports on the progress made over the last 15 years. Large brain shifts caused by brain tumor removal affect registration accuracy by creating point and element outliers. A combination of approximation- and geometry-based point and element outlier rejection improves the rigid registration error by 2.5 mm and meets the real-time constraints (4 min). In addition, the paper raises several questions and presents two open problems for the robust estimation and improvement of registration error in the presence of outliers due to sparse, noisy, and incomplete …

Detecting Deceptive Dark-Pattern Web Advertisements For Blind Screen-Reader Users, Satwick Ram Kodandaram, Mohan Sunkara, Sampath Jayarathna, Vikas Ashok

Computer Science Faculty Publications

Advertisements have become commonplace on modern websites. While ads are typically designed for visual consumption, it is unclear how they affect blind users who interact with the ads using a screen reader. Existing research studies on non-visual web interaction predominantly focus on general web browsing; the specific impact of extraneous ad content on blind users' experience remains largely unexplored. To fill this gap, we conducted an interview study with 18 blind participants; we found that blind users are often deceived by ads that contextually blend in with the surrounding web page content. While ad blockers can address this problem via …

Unttangling Irregular Actin Cytoskeleton Architectures In Tomograms Of The Cell With Struwwel Tracer, Salim Sazzed, Peter Scheible, Jing He, Willy Wriggers

Computer Science Faculty Publications

In this work, we established, validated, and optimized a novel computational framework for tracing arbitrarily oriented actin filaments in cryo-electron tomography maps. Our approach was designed for highly complex intracellular architectures in which a long-range cytoskeleton network extends throughout the cell bodies and protrusions. The irregular organization of the actin network, as well as cryo-electron-tomography-specific noise, missing wedge artifacts, and map dimensions call for a specialized implementation that is both robust and efficient. Our proposed solution, Struwwel Tracer, accumulates densities along paths of a specific length in various directions, starting from locally determined seed points. The highest-density paths originating …

Relationships Among Perceptions Of Support, Experiences Of Gatekeeping, And Burnout In Counselor Educators And Supervisors, Alicia Lamar

Dissertations

Counselor educators and supervisors carry out the responsibility of ensuring that counselors in training are competent and fit for practice. Burnout can occur when stressors in the workplace are not addressed. Engagement in the role of gatekeeper and perceptions of support can be factors that impact burnout in counselor educators. The exploration of variables that may relate to counselor educator burnout would benefit the counseling community including counselor educators, counseling students, counseling clients, and the community at large. There has been a paucity of research exploring the relationships among faculty members’ perceptions of support, experiences of gatekeeping, and burnout in …

Hydrogen Deuterium Exchange And Other Mass Spectrometry-Based Approaches For Epitope Mapping, Prashant N Jethva, Michael L Gross

2020-Current year OA Pubs

Antigen-antibody interactions are a fundamental subset of protein-protein interactions responsible for the "survival of the fittest". Determining the interacting interface of the antigen, called an epitope, and that on the antibody, called a paratope, is crucial to antibody development. Because each antigen presents multiple epitopes (unique footprints), sophisticated approaches are required to determine the target region for a given antibody. Although X-ray crystallography, Cryo-EM, and nuclear magnetic resonance can provide atomic details of an epitope, they are often laborious, poor in throughput, and insensitive. Mass spectrometry-based approaches offer rapid turnaround, intermediate structural resolution, and virtually no size limit for the …

Incorporating Public Health Into Transportation Decision Making, Bruce Appleyard, Tim Garrett

Mineta Transportation Institute

Investments in transportation have the potential to significantly affect public health outcomes. Decisions to build highways, transit, or bikeways, for example, influence how residents and visitors move around a metropolitan area. Personal travel habits and proximity to transportation infrastructure play a role in how likely people are to be physically active or be exposed to dangerous traffic and toxic pollution. For this study, the research team reviewed the literature that links transportation infrastructure, the surrounding built environment context, and public health outcomes such as chronic heart and lung diseases, obesity, and death. The team then researched publicly available data that …

A Critical Control Approach To Preventing Fatalities In Construction, Roberta J. Selleck

Theses: Doctorates and Masters

Workplace fatalities continue to occur within the Australian construction industry at an unacceptably high rate. Most fatalities can be attributed to worker exposure to fatal energies while conducting high risk tasks in a dynamic work environment. Construction fatalities are usually single fatality events related to occupational safety hazards which are either not recognised by workers or not consistently controlled through existing safety practices. By comparison other resources industries have lower fatality rates because of their focus on identifying the controls and verification activities needed to address Major Accident Events (MAEs) and Principal Hazards in a manner that prevents fatalities.

The …

A Secure Emr Sharing System With Tamper Resistance And Expressive Access Control, Shengmin Xu, Jianting Ning, Yingjiu Li, Yinghui Zhang, Guowen Xu, Xinyi Huang, Robert H. Deng

Research Collection School Of Computing and Information Systems

To reduce the cost of human and material resources and improve the collaborations among medical systems, research laboratories and insurance companies for healthcare researches and commercial activities, electronic medical records (EMRs) have been proposed to shift from paperwork to friendly shareable electronic records. To take advantage of EMRs efficiently and reduce the cost of local storage, EMRs are usually outsourced to the remote cloud for sharing medical data with authorized users. However, cloud service providers are untrustworthy. In this paper, we propose an efficient, secure, and flexible EMR sharing system by introducing a novel cryptosystem called dual-policy revocable attribute-based encryption …

Adapting An Intervention To Support Young Caregivers Of Cancer Survivors: A Study Protocol, Janet Njelesani, Melinda S. Kavanaugh, Jean Hunleth

2020-Current year OA Pubs

INTRODUCTION: Of the family members providing care, in the United States over 5.4 million are young people (<18 years of age) and they are the caregivers receiving the least support overall. Given the need to support cancer survivors through a family-centered practice approach, this lack of support and intervention for young caregivers represents a substantial gap in cancer care. In this study, we will adapt a young caregivers intervention, YCare, with young caregivers in families affected by cancer in order to advance support for families in cancer settings. YCare is an intervention that improves the support young caregivers provide through a peer-engaged, multidisciplinary model but has previously not been studied in the cancer care setting.

METHODS: Guided by the updated Consolidated Framework for Implementation Research (CFIR) we will engage stakeholders (i.e., young caregivers, cancer survivors, health care providers) using qualitative (i.e., one-on-one semi-structured interviews) and arts-based methods. Stakeholders will be recruited via cancer registries and community partners. Data will be analyzed descriptively using deductive (e.g., CFIR domains) and inductive (e.g., cancer practice settings) approaches.

DISCUSSION: The results will indicate the critical components for adapting the YCare intervention to the cancer practice context including new intervention elements and …

The Association Of Radiation Dose With Overall Survival For Patients Treated With Prostate Stereotactic Body Radiation Therapy, Michael R. Waters, Neal Andruska, Benjamin W. Fischer-Valuck, Temitope Agabalogun, Randall J. Brenneman, Hiram Gay, Jeff M. Michalski, Brian Baumann

2020-Current year OA Pubs

Introduction Stereotactic body radiation therapy (SBRT) for prostate adenocarcinoma (PCa) has demonstrated excellent biochemical recurrence-free survival, with studies showing improved BRFS with higher-dose SBRT. However, current studies have been underpowered to evaluate the relationship of SBRT dose to overall survival (OS). In this retrospective study using the National Cancer Database (NCDB), we hypothesize that, given the low alpha/beta ratio of PCa, a relatively small increase in the dose-per-fraction would be associated with improved survival outcomes for intermediate-risk PCa (IR-PCa) comparing 36.25 Gy/5 fx [biologically equivalent dose (BEDα/β = 1.5 = 211.46 Gy vs. 35 Gy (BED1.5 = 198.33 Gy)]. Materials …

Regulation Of The Volume-Regulated Anion Channel Pore-Forming Subunit Lrrc8a In The Intrahippocampal Kainic Acid Model Of Mesial Temporal Lobe Epilepsy, Manolia R. Ghouli, Carrie R. Jonak, Rajan Sah, Todd A. Fiacco, Devin K. Binder

2020-Current year OA Pubs

Volume-regulated anion channels (VRACs) are a group of ubiquitously expressed outwardly-rectifying anion channels that sense increases in cell volume and act to return cells to baseline volume through an efflux of anions and organic osmolytes, including glutamate. Because cell swelling, increased extracellular glutamate levels, and reduction of the brain extracellular space (ECS) all occur during seizure generation, we set out to determine whether VRACs are dysregulated throughout mesial temporal lobe epilepsy (MTLE), the most common form of adult epilepsy. To accomplish this, we employed the IHKA experimental model of MTLE, and probed for the expression of LRRC8A, the essential pore-forming …

A Randomized Implementation Trial To Increase Adoption Of Evidence-Informed Consent Practices, Erin D Solomon, Jessica Mozersky, Melody Goodman, Meredith V Parsons, Kari A Baldwin, Annie B Friedrich, Jenine K Harris, James M Dubois

2020-Current year OA Pubs

INTRODUCTION: Several evidence-informed consent practices (ECPs) have been shown to improve informed consent in clinical trials but are not routinely used. These include optimizing consent formatting, using plain language, using validated instruments to assess understanding, and involving legally authorized representatives when appropriate. We hypothesized that participants receiving an implementation science toolkit and a social media push would have increased adoption of ECPs and other outcomes.

METHODS: We conducted a 1-year trial with clinical research professionals in the USA (

RESULTS: Participants who engaged more with the toolkit were more likely to have tried to implement an ECP during the trial …

Predictors Of Nonadherence Among Patients With Infectious Complications Of Substance Use Who Are Discharged On Parenteral Antimicrobial Therapy, Shivakumar Narayanan, Patrick R Ching, Edward C Traver, Nivya George, Anthony Amoroso, Shyam Kottilil

2020-Current year OA Pubs

BACKGROUND: The management of invasive infections related to substance use disorder (SUD) needing parenteral antimicrobial therapy is challenging and may have poor treatment outcomes including nonadherence and lack of completion of parenteral antimicrobial therapy.

METHODS: In this retrospective cohort of 201 patients with invasive infections related to SUD, we looked at frequency and determinants of unfavorable outcomes including nonadherence.

RESULTS: Seventy-nine percent of patients with SUD-related infection completed parenteral antibiotic therapy in skilled nursing facilities. A total of 21.5% of patient episodes had documentation of nonadherence. Nonadherence was higher in patients with active injection drug use (IDU) (28.5% versus 15% …

Physiological Plateaus During Childbirth: A Constructivist Grounded Theory And Novel Definition, Marina J. Weckend

Theses: Doctorates and Masters

Background: During childbirth, one of the most common diagnoses of pathology is ‘failure to progress,’ frequently resulting in labour augmentation and intervention cascades. However, ‘failure to progress’ is poorly defined and some evidence suggests that plateauing labour (slowing, stalling and pausing of labour processes) may represent a typical and physiological occurrence during normal childbirth. Therefore, this study aimed to explore what exactly midwives define as ‘physiological plateaus’ and which significance such plateaus may have for the labour trajectory and birth outcome.

Methods: This study followed a constructivist grounded theory approach, assuming a position of ontological critical realism combined with epistemological …

An Examination Of Kinanthropometric And Physical Injury Risk Factors In Elite Australian Football, Callum J. Mccaskie

Theses: Doctorates and Masters

Kinanthropometric assessment is an integral part of understanding an athlete’s physical profile and readiness for competition. This typically includes a variety of different assessments which serve to quantify body shape, proportion, and composition in a bid to understand human physiology. Common assessments include stature, body mass, limb ratios, body circumferences, body mass index, skinfold testing, body composition testing, and musculoskeletal morphological evaluations. Specifically, kinanthropometric evaluations have involved the characterisation of athletes according to sport, sex, competition level and playing position. While this has provided researchers and practitioners with greater insight into athletic phenotypes, more purposeful kinanthropometric assessments which focus on …

An Interpretive Description Study Of The Views And Experience Of Obstetric Fistula Risk Factors Among Women Attending Evangel Vesico Vagina Fistula Centre In Nigeria, Lydia Babatunde-Bulndi

Theses: Doctorates and Masters

An obstetric fistula is a hole between the birth canal and the bladder or rectum, which is caused by prolonged, obstructed labour without intervention. Sufferers of obstetric fistula may experience chronic urinary and/or faecal incontinence. Although obstetric fistula is directly caused by prolonged obstructed labour, factors such as unskilled birth assistance can increase fistula risk indirectly. Harmful traditional practices, such as female genital mutilation, lack of formal education, illiteracy, poverty, limited social role for women, malnutrition, early marriage before the full development of the pelvis, and a lack of emergency obstetric services are some of the additional factors associated with …

Predicting Incident Cardiovascular Disease Among African-American Adults: A Deep Learning Approach To Evaluate Social Determinants Of Health In The Jackson Heart Study, Matthew C. Morris, Hamidreza Moradi, Maryam Aslani, Mario Sims, David Schlundt, Chrystyna D. Kouros, Burel Goodin, Crystal Lim, Kerry Kinney

2020-Current year OA Pubs

The present study sought to leverage machine learning approaches to determine whether social determinants of health improve prediction of incident cardiovascular disease (CVD). Participants in the Jackson Heart study with no history of CVD at baseline were followed over a 10-year period to determine first CVD events (i.e., coronary heart disease, stroke, heart failure). Three modeling algorithms (i.e., Deep Neural Network, Random Survival Forest, Penalized Cox Proportional Hazards) were used to evaluate three feature sets (i.e., demographics and standard/biobehavioral CVD risk factors [FS1], FS1 combined with psychosocial and socioeconomic CVD risk factors [FS2], and FS2 combined with environmental features [FS3]) …

The In Vivo Study Of Cardiac Mechano-Electric And Mechano-Mechanical Coupling During Heart Development In Zebrafish, Jonathan S Baillie, Alex Gendernalik, Deborah M Garrity, David Bark Jr, T Alexander Quinn

2020-Current year OA Pubs

In the adult heart, acute adaptation of electrical and mechanical activity to changes in mechanical load occurs