Medicine and Health Sciences Commons^™

Identifying Relevant Covariates In Rna-Seq Analysis By Pseudo-Variable Augmentation, Yet Nguyen, Dan Nettleton

Mathematics & Statistics Faculty Publications

RNA-sequencing (RNA-seq) technology allows for the identification of differentially expressed genes, which are genes whose mean transcript abundance levels vary across conditions. In practice, RNA-seq datasets often include covariates that are of primary interest in addition to a set of covariates that are subject to selection. Some of these covariates may be relevant to gene expression levels, while others may be irrelevant. Ignoring relevant covariates or attempting to adjust for the effect of irrelevant covariates can compromise the identification of differentially expressed genes. To address this issue, we propose a variable selection method that uses pseudo-variables to control the expected …

Utilizing Machine Learning Techniques For Computer-Aided Covid-19 Screening Based On Clinical Data, Honglun Xu, Andrews T. Anum, Michael Pokojovy, Sreenath Chalil Madathil, Yuxin Wen, Md Fashiar Rahman, Tzu-Liang (Bill) Tseng, Scott Moen, Eric Walser

Mathematics & Statistics Faculty Publications

The COVID-19 pandemic has highlighted the importance of rapid clinical decision-making to facilitate the efficient usage of healthcare resources. Over the past decade, machine learning (ML) has caused a tectonic shift in healthcare, empowering data-driven prediction and decision-making. Recent research demonstrates how ML was used to respond to the COVID-19 pandemic. This paper puts forth new computer-aided COVID-19 disease screening techniques using six classes of ML algorithms (including penalized logistic regression, random forest, artificial neural networks, and support vector machines) and evaluates their performance when applied to a real-world clinical dataset containing patients’ demographic information and vital indices (such as …

Investigation Of Genx Exposure To Pathways Associated With Colorectal Cancer Risk, Emily J. Ferguson

Theses and Dissertations--Toxicology and Cancer Biology

Per- and polyfluoroalkyl substances (PFAS) are persistent environmental contaminants widely detected in drinking water and food sources, resulting in chronic human exposure. Among these compounds, hexafluoropropylene oxide dimer acid (HFPO-DA), commonly known as GenX, has been introduced as a short-chain replacement for legacy PFAS such as perfluorooctanesulfonic acid (PFOS) and perfluorooctanoic acid (PFOA). Although GenX is believed to be a safer alternative, emerging research suggests it can still affect human health.

Colorectal cancer (CRC) is the third most commonly diagnosed cancer and the second leading cause of cancer-related death in the United States, highlighting the need to better understand environmental …

Strong Foundations: Supporting Mental Well-Being In School-Age Youth, Skylar Simpson

Occupational Therapy | OTD Capstone Projects

School-age youth in the United States increasingly face stressors that disrupt their overall mental well-being, highlighting a need for accessible preventative interventions. To address this gap, this doctoral capstone project developed a program titled Strong Foundations: Supporting Mental Well-Being in School-Age Youth, an evidence- and occupation-based program consisting of various interventions designed to enhance the well-being of youth attending a San Francisco Recreation and Park (SFRPD) community-based summer camp. Through embedding occupational therapy-based programming into an environment that currently lacks dedicated mental well-being promotion methods, the Strong Foundations aims to foster mental well-being among school-age youth through occupational engagement that …

Access Resource Guide For Bay Area Cultural Arts Organizations Developed In Collaboration With People With Intellectual And Developmental Disabilities, Clarissa Junio

Occupational Therapy | OTD Capstone Projects

Background: Hidden access barriers persist within cultural arts organizations. As a result, people with IDD continue to experience reduced levels of community participation, limiting the associated benefits to health, well-being, and quality of life. Organizational-level occupational therapy (OT) consultation can address barriers and expand organizational capacity to meet the needs of people with IDD.

Purpose: The project aimed to strengthen organizational capacity of Bay Area cultural arts organizations and expand existing accessibility resources by co-developing a resource guide centered on lived experience to maximize community social participation for people with IDD. The guide was disseminated to cultural arts …

The Role Of Occupational Therapy In Developing Aquatic Programs For Children Diagnosed With Autism, Giavanna Stavros

Occupational Therapy | OTD Capstone Projects

There is a need for inclusion in therapeutic aquatic programming for children diagnosed with autism (ASD), as their increased participation in aquatic interventions and activities promotes safety and well-being for this population. Pediatric occupational therapists (OTs) are vital to fill this gap in skill, as pediatric OTs consistently work with children diagnosed with ASD (Jaicks, 2024), and core principles of the occupational therapy (OT) profession include enhancing one’s safety and well-being (American Occupational Therapy Association (AOTA), 2025). Children diagnosed with ASD must have the opportunity to engage in swimming and aquatic therapy, as this population is at a higher risk …

Sensory Modulation For Adults With Developmental Disabilities: An Occupational Therapy Approach For Adult Day Programs, Aveen Dulai

Occupational Therapy | OTD Capstone Projects

This occupational therapy (OT) doctoral capstone project focused on the development and implementation of a proactive sensory modulation program with the use of Assistive Technology (AT) for adults with Developmental Disabilities (DD) at an adult day program. Adults with DD have diverse needs such as - motor, communication, behavioral, cognitive, and sensory processing challenges. These varying abilities often require AT and environmental adaptations to afford meaningful participation in occupations.  Providing customized and accessible programing for adults with DD arediversity, equity, inclusion, justice and accessibility (DEIJA) issues (Kripke, 2018). Often, adult day programs are limited in OT services, including accessible sensory …

Strengthening Communication And Collaboration Between The Student Support Triad (Teachers, Caregivers, And Health Professionals) In Schools, Jasmine E. Henley

Occupational Therapy | OTD Capstone Projects

Teachers, caregivers, and health professionals, who are key stakeholders that form a student support triad, each face a range of challenges and barriers that impact their ability to communicate and collaborate with one another, therefore impacting the student and their ability to access and participate in meaningful occupations. Though these challenges and barriers for each stakeholder are well-documented individually, there is limited evidence on solutions to strengthen communication across the triad and solutions that center the student and their engagement in meaningful occupations. This project aims to bridge this gap, despite the greater systemic barriers, by developing remedial solutions that …

Sensory Friendly Summers: Designing Inclusive Camp Experiences For Children With Sensory Processing Challenges, Isandla Blanc

Occupational Therapy | OTD Capstone Projects

Children with sensory processing challenges may experience barriers to participation in everyday activities. While summer camps offer opportunities for social development, play, and growth, staff may have limited training and resources to support children with different sensory needs. This can create challenges to participation and inclusion within traditional summer camp environments. The purpose of this capstone project was to develop, implement, and evaluate a staff training program aimed at increasing staff understanding of sensory processing and providing practical strategies to support campers with sensory processing challenges.

A project-level needs assessment was conducted through informal staff conversations, observations of daily camp …

Occupational Therapy’S Role In Promoting An Accessible Playground Environment For Parents With Physical Disabilities, Molly M. Busby

Occupational Therapy | OTD Capstone Projects

Limited implementation of the Americans with Disabilities Act (ADA) accessibility standards and concepts of universal design in the playground environment restrict parents with physical disabilities' engagement in the co-occupation of visiting the playground with their children. The outdoor playground environment promotes the child’s physical, social, emotional, and cognitive development and has positive benefits on the mental health of the parent. Local community park organizations have the power to make accessibility changes to playgrounds in the community but often they lack the knowledge to do so. The purpose of this capstone project is to facilitate increased inclusivity and physically accessible playground …

A Digital Resource To Support Occupational Therapy Fieldwork Students And New Graduates In Applying Occupation-Based Practice In Inpatient Adult Settings, Alyssa Vessel

Occupational Therapy | OTD Capstone Projects

Occupation-based practice is a core concept within the occupational therapy profession. However, Level II fieldwork students and new graduate occupational therapists may struggle to translate their knowledge of occupation-based practice into clinical practice. This doctoral capstone project aimed to support the implementation of occupation-based practice in adult inpatient settings by developing a website with educational and practical resources. Stakeholder needs and existing evidence on barriers and supports to occupation-based practice informed project development. A questionnaire was distributed to Level II fieldwork students, while discussions with new graduate occupational therapists provided an informal needs assessment. Findings guided the development of website …

Pbms And Exploitation Of America's Prescription Drug System, Ayaan Nihal Unni

A with Honors Projects

This project aims to tackle the issue of America's disproportionately expensive  prescription drug system by tracking the issue to its powerful intermediaries: PBMs. I then analyze procedures both the government and the people can undertake in order to overcome this faulty system.

Wearable Biosensors For Continuous Monitoring Of Chronic Kidney Disease: Materials, Biofluids, And Digital Health Integration, Anupamaa Sivasubramanian, Shankara Narayanan, Gymama Slaughter

Center for Bioelectronics Publications

Chronic kidney disease (CKD) is a progressive and irreversible disorder affecting over 850 million individuals globally and is associated with significant morbidity, mortality, and healthcare burden. Conventional diagnostic approaches rely on intermittent laboratory measurements, including serum creatinine, estimated glomerular filtration rate (eGFR), and urinary albumin, which provide limited temporal resolution and fail to capture dynamic physiological changes. Recent advances in wearable biosensing technologies offer new opportunities for continuous, non-invasive monitoring of biochemical and physiological markers relevant to renal function. This review provides a comprehensive analysis of wearable biosensors for CKD monitoring, focusing on sensing mechanisms (electrochemical, optical, and field-effect transistor), …

Gender, And Socioeconomic Status In School-Based Speech-Language Pathology Decision-Making For Adolescents With Traumatic Brain Injury: A Critically Appraised Topic, Geneva Renee Toledo

Selected Full-Text Master Theses 2021-

Purpose: Adolescents are at greater risk for traumatic brain injury (TBI), and TBI-related symptoms may contribute to disciplinary actions that increase their risk of entering the school-toconfinement pipeline. Given the disproportionate representation of racially marginalized male adolescents within this pipeline, this critically appraised topic (CAT) examined how race, gender, and socioeconomic status may influence school-based speech-language pathology (SLP) services and clinical decision-making following TBI. Method: A structured search of five electronic databases was conducted to identify studies examining speech-language pathologists’ (SLPs’) clinical decision-making and management of adolescents with TBI in relation to race, gender, and socioeconomic status. Relevant studies were …

Covid-19 Pandemic-Induced Social Isolation: A Hermeneutic Phenomenological Exploration Of Age And Time, Renee Reedy

Dissertations and Theses

Lockdown measures during the COVID-19 pandemic fundamentally altered social functioning, creating an urgent need to understand the lived experience of isolation across life stages. This qualitative hermeneutic phenomenological study explored how age and time shaped social isolation during the pandemic. Sixteen participants from three-generation households—adolescents (n=5), adults (n=6), and older adults (n=5)—were interviewed approximately five years post-isolation. Recruitment occurred through ResearchMatch, and interviews were conducted between February and March 2025. Participants represented diverse racial, ethnic, and geographic backgrounds, with isolation periods ranging from 27 to 426 consecutive days (¯x = 165 ± 124 days). Data analysis followed Gadamer’s hermeneutic circle …

The Role Of Bacteriophage In The Rgg1-Mediated Virulence Control Of Streptococcus Pyogenes, Yuan Tian

Dissertations and Theses

In Streptococcus pyogenes, bacteriophages and other horizontally transmissible elements (HTEs) comprise approximately 10% of the genome, and each clinical isolate carries a unique combination of these elements, contributing to genetic diversity, virulence, antibiotic resistance, and immune evasion. Previously, our laboratory identified binding sites of the transcriptional regulator Rgg1 in the clinical isolate NZ131 and demonstrated that Rgg1 influences genome-wide gene expression, including bacteriophage genes. In the clinical isolate SF370, the prophage SpyCIM1, positioned in the chromosome between the mutL and mutS genes, controls DNA mismatch repair through excision and reintegration into the chromosome. In the integrated form, the prophage displaces …

Asthma, Hailey Gaines

A with Honors Projects

Basic facts about asthma including signs and symptoms, tests, causes, preventative measures, and treatments.

Crispr-Cas9: Transforming Biomedical Technology Through Gene Editing, Zaina Issa

A with Honors Projects

The research paper describe the gene editing technique CRISPR-Cas9 and the implications of its use in different fields, including medicine and agriculture.

A Mixed Methods Study On Mexican American Satisfaction And Perception Of Clinical Trials, Grace Manzo

Dissertations and Theses

In the United States, the Food and Drug Administration sets expectations on the collection and reporting of race and ethnicity data. Ethnic data for Mexican Americans is often reported as “Hispanic or Latino.” Mexican Americans make up a significant percentage of “Hispanic or Latinos,” however, they remain significantly underrepresented in clinical trials. Grounded in Expectation-Disconfirmation Theory (EDT) and Social Cognitive Theory (SCT), this mixed-methods study investigates the relationship between satisfaction and perception of Mexican Americans who have participated in an ophthalmology clinical trial. This research aimed to understand the relationships among satisfaction with the clinical trial process, patient-reported outcomes, and …

Effects Of Hurricane Weather Events On Perceived Stress, Academic Motivation, And Resilience In College Students From Louisiana, Courtney Renee Harrington

Dissertations and Theses

In the fall semester of 2020, five hurricanes were projected to make landfall along the coast of Louisiana. The following fall semester of 2021, Hurricane Ida, a major category 4 storm landed and wreaked havoc among Louisiana’s coastal universities. The purpose of this study was to assess the effects of hurricane events on students’ perceived stress, academic performance, and resilience. It was hypothesized that students affected by the landfall of a hurricane would have increased stress, decreased academic motivation, and decreased resilience compared to normative college students. A cross-sectional survey was administered at two southern Louisiana universities as well as …

Inhibition Of Fatty Acid Synthase Enhances Therapeutic Efficacy And Delays Acquired Resistance To Braf-Targeted Therapy In Colorectal Cancer, Mariah E. Geisen, Elisane W. Tessmann, Courtney O. Kelson, Daheng He, Chi Wang, Abu Saleh Mosa Faisal, Ellen J. Beswick, Yasmine Baca, Stephanie Rock, Jill M. Kolesar, Yekaterina Y. Zaytseva

Toxicology and Cancer Biology Faculty Publications

The presence of BRAF ^V600E mutations is associated with poor prognosis in colorectal cancer (CRC). Although the FDA-approved combination of encorafenib and cetuximab provides clinical benefit in this population, only 22% of patients respond and most eventually develop resistance. This study investigated the mechanisms of resistance to PLX8394, a second-generation BRAF inhibitor. Using primary and established BRAF ^V600E CRC cells, we show that the development of resistance to PLX8394 results in cross-resistance of cells to encorafenib. Moreover, the acquired resistance is associated with increased proliferation, invasion, and upregulation of lipid metabolism, including increased expression of fatty acid synthase (FASN), a …

Long Acting Beta2-Adrenergic Receptor Agonists Reverse Diabetic Nephropathy And Liver Steatosis In Murine Models Of Diabetes And Are Associated With Protection In Retrospective Human Studies, Brennan Winkler

MUSC Theses and Dissertations

Diabetes Mellitus (DM) affects 13.9% of men and 14.3% of women worldwide, a total of approximately 828 million people. Patients with diabetes are at risk of several complications including diabetic nephropathy (DN) and metabolic-associated steatohepatitis (MASH). These diseases eventually lead to end stage kidney disease (ESKD) and liver failure requiring dialysis and organ transplantation. In addition, diabetes exacerbates disease severity of autosomal dominant polycystic kidney disease (ADPKD), the most common potentially lethal genetic disease to affect humans with a prevalence of 1 in 500-1000. Therefore, a therapeutic approach that can attenuate organ damage and restore function in patients with DM, …

A Scenario Analysis Of The Impact Of H.R.1 2025 Medicaid Coverage Loss And Payment Reductions On U.S. Hospital Operating Margins, Tangee Pruitt

MUSC Theses and Dissertations

The “Big Beautiful Bill” is expected to affect the financial health of U.S. hospitals. We performed a scenario analysis using five case studies combined with national data on payer mix information to illustrate potential impact in 2027. The scenarios explored the following question: What is the expected healthcare access and economic impact of H.R.1 under three sets of assumptions: 1) loss of Medicaid coverage for 10% or more of an institution’s current patients who will then become uninsured; 2) decrease in Medicaid payments by 10% or more; 3) loss of Medicaid coverage and decrease in Medicaid payments simultaneously. We defined …

Twenty-First Century Data Systems: Evolving Cancer Registries To A Learning Health System, Peter P. Yu, W. Scott Campbell, Eric B. Durbin, Lawrence N. Shulman, Jeremy L. Warner

Markey Cancer Center Faculty Publications

Introduction: Oncology is a data-rich environment reflecting the increasing incidence of cancer in the US aging population, transformation of cancer into a chronic disease due to advances in treatment, and the emergence of new data categories such as genomics. Concomitantly, healthcare systems are challenged to meet regulatory and voluntary reporting of cancer data to support government, quality certification, research and strategic partnership needs.

Materials and Methods: The National Academies of Science, Engineering, and Medicine organized a workshop entitled “Enabling 21st-century applications for cancer surveillance through enhanced registries and beyond” with representation from NCI Comprehensive Cancer Centers, oncology and medical informatics …

Clopidogrel Versus Aspirin Monotherapy Following Dual Antiplatelet Therapy After Percutaneous Coronary Intervention: An Updated Meta- Analysis Of 162,829 Patients, Mohammed A. Elbahloul, Ahmed Mansour, Amr Galal, Walaa M. Moawad, Manar Khaled, Ahmed Wahdan Kasem, Eman E. Labeeb, Islam Y. Elgendy

Gill Heart & Vascular Institute Faculty Publications

Background: Dual antiplatelet therapy (DAPT) following percutaneous coronary intervention (PCI) remains a cornerstone for preventing ischemic events; however, the optimal long-term single antiplatelet therapy after completion of DAPT remains unclear. We aimed to compare clopidogrel and aspirin monotherapy after completion of the standard duration of DAPT.

Methods: A systematic search was conducted on PubMed, Scopus, Cochrane Library, and Web of Science from inception to April 2025. We included randomized clinical trials and observational studies that compared aspirin versus clopidogrel monotherapy after completion of standard-duration DAPT. The primary and co-primary outcomes were major adverse cardiovascular events (MACE) and major bleeding, respectively. …

Linking Curiosity To Career: A Master Adaptive Approach To Resident Elective In Family Medicine Training, Shayna Blikshteyn, Drew Keister Md, Karla J Felix Phd, Susan S. Mathieu Md, Lynn M. Wilson Do

Department of Family Medicine

No abstract provided.

Colchicine Among Patients With Acute Coronary Syndrome: A Meta‑Analysis Of Randomized Trials, Mohamed Hamed, Sheref A. Mohamed, Mohamed Abdelazeem, Eric Lieberman, Abdelrahman Ali, Dharam J. Kumbhani, Anthony Bavry, Hani Jneid, Islam Y. Elgendy, Ayman Elbadawi

Gill Heart & Vascular Institute Faculty Publications

Introduction: Prior trials evaluating the benefit of colchicine in patients with acute coronary syndrome (ACS) have yielded mixed results. Hence, we conducted a meta-analysis of randomized controlled trials (RCTs) to evaluate the role of colchicine after ACS.

Methods: We performed an electronic search of MEDLINE, Embase, and Cochrane databases through November 2024 for studies comparing colchicine with placebo after ACS. Our study’s primary outcome was major adverse cardiac events (MACE).

Results: Our final analysis included five RCTs with 12,979 patients with a mean follow-up of 26.6 months. The weighted mean age was 59.8 years. Colchicine was associated with a modest …

2026 Nebraska Beef Cattle Report

Nebraska Beef Cattle Reports

The 2026 Nebraska Beef Cattle Report brings together applied research, emerging technologies, and management insights that directly address the evolving challenges and opportunities facing today’s beef industry. This year’s collection includes 36 articles that span the full beef production system, from cow/calf and forage management to feedlot nutrition, animal health, behavior, meat quality, and sustainability, providing science-based guidance grounded in real-world production contexts.

Cow/Calf Nutrition, Reproduction, and Management

This section highlights management strategies that influence reproductive success and long-term herd performance. Articles focus on late-gestation heifer nutrition and practical applications of artificial insemination to support efficient, productive cow/calf systems.

Forage, …

A Case Of Primary Gastric Diffuse Large B-Cell Non-Hodgkin Lymphoma With Tumor Lysis Syndrome And The Warburg Effect, Sarah Barnhardt, Brooke Escoe, Mary Carter

South Atlantic Division GME Research Day 2025

No abstract provided.

West Nile Virus Transmission Suitability Modeling For Culex Pipiens Via Temperature And Humidity, Hunter Jones, David Brett-Major, Joseph R. Fauver, Yeongjin Gwon, Jesse E. Bell

Journal Articles: Epidemiology

West Nile Virus (WNV) is the leading cause of mosquito-borne disease in the United States, yet predicting its transmission remains a significant challenge for public health officials. Many studies use correlative statistical models to predict disease cases using temperature and humidity, but accessible mechanistic approaches that simulate mosquito behavior traits can capture more of the transmission process. This study adapts an existing R-language package, the Mosquito-borne Viral Suitability Estimator (MVSE), which was created to model Aedes aegypti mosquito transmission of dengue, and tunes it to Culex pipiens transmission of WNV. Equations for mortality, biting rate, and incubation period were updated, …