Digital Commons Network^™

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 …

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 …

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.

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 …

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, …

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, …

Factors Affecting Detection And Quantification Of Schistosoma Haematobium Eggs In Pooled Urine Samples, Abraham Degarege, Bruno Levecke, Christopher R. Bilder, David Brett-Major, Abebe Animut, Yohannes Negash, M. Jana Broadhurst, Tzeyu L. Michaud, Berhanu Erko

Journal Articles: Epidemiology

BACKGROUND: Building on our previous work showing that pooled urine testing can rapidly detect Schistosoma haematobium infections but has limited sensitivity in low-intensity settings or with large pool sizes, this study evaluated how urine volume, pool size, infection intensity, and diagnostic method affect the detection and quantification of S. haematobium eggs in pooled samples.

METHODS: Between July 2022 and April 2023, 2,134 urine samples from school-age children living in three regional states of Ethiopia were individually examined by deploying urine filtration microscopy (UFM). Subsequently, 5, 10, 20 and 40 individual samples were strategically pooled and examined by deploying UFM and …

Creative Works By Reid Sindelar, Reid Sindelar

The Art of Medicine

• holdrege, nebraska

Creative Works By Elizabeth Null, Md, Faap, Facmg, Elizabeth Null

The Art of Medicine

• Rock-a-bye Your Bear

Art Of Medicine - 2026

The Art of Medicine

No abstract provided.

The Impact Of Heavy Resistance Training On Type Ii Muscle Fibers Throughout Female Reproductive Stages, Lily G. Colberg

Scripps Senior Theses

Type II muscle fibers, also known as fast-twitch muscle fibers, are reliant on aerobic glycolysis and are crucial for high-force contractions, mobility, and rapid movements, such as fast reflexes. Heavy resistance training has been found to increase type II muscle fiber concentration in young, middle-aged, and elderly individuals. However, there have been few studies conducted on female-only sample populations. In women, the impact of heavy resistance training on type II muscle fibers is affected by the progressive decline of estrogen that defines the transition throughout the four female reproductive stages: premenopause, perimenopause, late-transition menopause, and postmenopause. Menopausal estrogen depletion causes …

Cross-Neutralization And Antigenic Characterization Of Simian And Equine Group A Rotaviruses, Shalini Soni, Lianne G. Eertink, Ni Shuisong, Alan T. Loynachan, Samantha M. Barnum, Emma Adam, Michael A. Kennedy, Dan Wang, Feng Li

Veterinary Science Faculty Publications

Rotaviral diarrhea in foals is caused by two dominant G3P[12] and G14P[12] genotypes of equine rotavirus A (ERVA). Protection of foals against ERVA infection and disease is achievable by passive antibody transfer through colostrum from mares receiving inactivated monovalent G3P[12] vaccine. Simian rotavirus SA11 G3P[2] is also included in ERVA vaccines to protect foals. Here, we characterized cross-neutralization and protection among three distinctive rotaviruses carrying the same or different G (defined by VP7) or P (defined by VP4) genotype by using a rabbit and equine monospecific antisera panel coupled with structural and computational analyses of viral epitopes. Data from these …

Designing Theranostic Radiopharmaceutical Trials For Uterine Cervix Cancer, Denise Fabian, Molly E. Buffington, Brianna S. Cagle, Steve M. Keefe, Michael K. Schultz, Charles A. Kunos

Radiation Medicine Faculty Publications

Designing and interpreting early phase trials of theranostic radiopharmaceuticals remains challenging because it is difficult to isolate effective levels of activity in enriched patient populations that would be worth following up in later-phase development. This study explores the known challenges and emerging opportunities for clinical research on patients with uterine cervical cancer. We identified eight randomized combination trials for advanced-stage uterine cervix cancer that were activated between 2011 and 2022 and tabulated their results to determine whether combinations were better than individual constituents and which suitable study population is best situated for the study of a new theranostic agent. In …

Broadening The Fetal Alcohol Paradigm: Bdnf Methylation As A Link Between Paternal Alcohol Use And Offspring Neurodevelopmental Deficits, Caitlin E. Muñoz

Scripps Senior Theses

Developmental effects of fetal alcohol exposure are extensively documented as a consequence of maternal gestational alcohol consumption. However, similar consequences of paternal alcohol consumption remain understudied. This proposed pilot study will examine preconception paternal alcohol consumption within its capacity to induce heritable epigenetic modifications in sperm, such that offspring are susceptible to adverse in utero neurodevelopment and neonatal neurobehavioral outcomes. Specifically, it will examine DNA methylation patterns along the brain-derived neurotrophic factor (BDNF) exon IV promoter in paternal spermatozoa. BDNF exon IV is considered a key locus in neurogenesis regulation, synaptic plasticity, and cortical development. It is hypothesized that BDNF …

Corticotropin-Releasing Factor Neurons In The Bed Nucleus Of The Stria Terminalis Modulate Avoidance Behaviors And Feeding, Juan Manuel Romero, Shae-Marie Stafford-Trujillo, Mitzy Mendoza, Pey-Shyuan Chin, Snigdha Srivastava, Mikhail Kochukov, Qingchun Tong, Benjamin Russell Arenkiel

The Brown Foundation: Institute of Molecular Medicine

Introduction: Animals rely on defensive avoidance of exposed or potentially threatening environments as a fundamental survival strategy, often expressing this behavior as thigmotaxis, or a preference for the periphery of an open space. However, researchers still do not understand how neural circuits coordinate avoidance behavior with competing physiological drives such as feeding. In this study, we investigate how corticotropin-releasing factor (CRF)-expressing neurons in the bed nucleus of the stria terminalis (BNST) integrate environmental avoidance and feeding behavior.

Methods: We used adult male and female mice and applied fiber photometry to monitor BNST CRF neuronal activity in vivo. We performed both …

Glial Cytokine Modulation Improves Sleep And Circadian Disruption In Female Saa Knock-In Mice Of Alzheimer’S-Related Pathology, Teresa Macheda, Margaret R. Hawkins, Carrie E. Johnson, Madison G. Lapid, Haleigh R. Whitlock, Savannah M. Shepard, Makayla F. Cox, Kelly N. Roberts, Leke Bytyqi, Heather M. Hash, Omar A. Abou El-Ezz, Mohammed Abou El-Ezz, Katharina Kohler, Sridhar Sunderam, Bruce F. O'Hara, Linda J. Van Eldik, Michael Paul Murphy, Marilyn J. Duncan, Adam D. Bachstetter

Neuroscience Faculty Publications

Introduction: Sleep and circadian disturbances are early Alzheimer's disease (AD) features, yet mechanisms linking amyloid pathology, neuroinflammation, and sex differences remain unclear.

Methods: We longitudinally assessed sleep, circadian rhythms, and cognition in female and male hAPP^SAA knock-in and control mice from 2 to 19 months using piezoelectric monitoring. Aged mice (15 months) received MW151, a glial cytokine inhibitor (2.5 mg/kg, every other day, 6 weeks).

Results: Only females exhibited midlife reductions in light-phase sleep, increased rhythm fragmentation, and reduced rhythm stability, coinciding with selective reversal learning deficits, effects independent of amyloid or cytokine burden. MW151 increased light-phase sleep and …

Evaluation Of The Physical Properties And In Vitro Safety Of Chitosan-Quercus Infectoria Topical Gel, Rani Naga Rakshitha Tillapudi

Theses, Dissertations and Capstones

Due to ongoing inflammation, inadequate blood flow, oxidative stress, and reduced tissue regeneration, chronic diabetic wounds heal slowly, which is a serious health concern. It is important to examine novel strategies that tackle these issues because conventional treatments frequently fail. Therefore, this study examined the physical properties and biocompatibility of a novel topical gel formulated with chitosan and Quercus infectoria gall extract.

Over 28 days, pH, spreadability, texture, homogeneity, color, and drug concentration were assessed. UV-visible spectrophotometry and FTIR analysis were used to establish chemical stability. The MTT assay was used to test its safety in human dermal fibroblast adult …

Mitochondrial Transfer To Granulocytic Myeloid-Derived Suppressor Cells Augments Immunosuppressive Activity, Prabhakar Arumugam, Cortney E. Heim, Rachel W. Fallet, Dhananjay Shinde, Vinai Chittezham Thomas, Rafael J. Argüello, Tammy Kielian

Journal Articles: Pathology and Microbiology

The anti-inflammatory properties of granulocytic myeloid-derived suppressor cells (G-MDSCs) promote Staphylococcus aureus (S. aureus) biofilm persistence. Evidence suggests that G-MDSC activity is shaped not only by S. aureus products but also by intrinsic metabolic programs. This study explores whether G-MDSC activity can be modulated by increasing mitochondrial abundance using a co-culture paradigm with macrophages as a mitochondrial donor. Macrophages transfer mitochondria directly to G-MDSCs via tunneling nanotubes, enhancing G-MDSC respiration, as reflected by increased basal, maximal, and spare respiratory capacity. Augmenting mitochondrial abundance in G-MDSCs enhances T cell-suppressive activity and reduces tumor necrosis factor (TNF) and interleukin 6 (IL-6) production. …

Clinical And Biochemical Effects Of Intra-Articular Autologous Conditioned Serum And Triamcinolone In An Equine Model Of Synovitis, Ana Velloso Alvarez, Anne Wooldridge, Fred Caldwell, Sandra Zetterström, Bruno C. Menarim, Taylor J. Towns, Emily C. Graff, Lindsey Boone

Veterinary Science Faculty Publications

Synovitis is a key contributor to the development of OA, and early modulation of the synovial environment may help limit downstream cartilage damage. This study compared the clinical and biochemical effects of intra-articular triamcinolone acetonide (TA) and autologous conditioned serum (ACS) in an equine model of IL-1β–induced synovitis. Six healthy adult horses were used in a crossover design involving five groups: PBS (negative control), IL-1β (positive control), IL-1β + ACS, IL-1β + TA, and an exploratory ACS-alone group administered post hoc to isolate its effects without IL-1β interference. Both TA and ACS mitigated inflammation through distinct profiles. TA was superior …

Unm Pathology, Pathfinder Winter 2026, Unm Department Of Pathology

Newsletters

No abstract provided.

Childhood Factors That Affect Adult Obesity In Ohio And Mississippi, Rhea Lal, Danielle Wolford

Scholarship in Medicine - All Papers

Over 40% of adults in the United States struggle with obesity. While several social determinants of health have been tied to obesity, only limited research on the effect of childhood education, food environments, and physical activity resources on a state-wide level has been conducted. It is imperative that we identify connections between obesity, associated comorbidities, education, and SDoH as these will inform improvements in national social structures and healthcare systems. States Ohio (OH) and Mississippi (MS) differ in high school completion rates, food access, and exercise opportunities yet both states continue to experience rising adult obesity rates. This study analyzed …

Development And In Vitro Characterization Of 5-Fluorouracil–Loaded Plga Nanoparticles For Controlled Drug Delivery, Kavya Yandapalli

Theses, Dissertations and Capstones

Non-Alcoholic Fatty Liver Disease (NAFLD) is a progressive metabolic disorder characterized by excessive lipid accumulation in hepatocytes and chronic inflammation. Nanoparticle-based drug delivery systems offer a promising strategy to enhance therapeutic efficacy while minimizing systemic toxicity. The objective of this study is to formulate and characterize 5-FU–loaded PLGA nanoparticles and evaluate their in vitro performance. 5-FU–loaded PLGA nanoparticles were prepared using the double emulsion solvent evaporation method. The nanoparticles were characterized by particle size, polydispersity index, zeta potential and SEM. Drug encapsulation efficiency, loading capacity and in vitro drug release studies were conducted. The formulated nanoparticles exhibited sizes within the …

Hepatocyte Peroxisome Biogenesis And Phytol-Induced Metabolic Stress In Liver Disease, William Galloway

Theses, Dissertations and Capstones

Hepatocyte peroxisomes are required for metabolism of phytol-derived branched-chain fatty acids through the ACOX2-SCPx beta-oxidation pathway. This study tests whether hepatocyte-specific deletion of PEX16 (Pex16^Alb-Cre), which eliminates peroxisome biogenesis, sensitizes the liver to phytol-induced injury. The Pex16^Alb-Cre mice and their normal control Pex16^fl/fl mice were fed the Lieber-DeCarli liquid with or without 0.1 percent phytol for eight weeks. Serum alanine aminotransferase (ALT) and liver index were measured. Liver sections were stained with hematoxylin and eosin and Masson’s trichrome. Immunoblot analysis of peroxisomal enzyme expression was also performed. Phytol had no effect in Pex16^fl/fl mice as …

Sexually Dimorphic Effects Of Gpnmb Modulation On Vertebral Bone Mass Regulation And Intravertebral Disc Health, Hakem Altawil, Fayez Safadi

Williams Honors College, Honors Research Projects

Osteoporosis and vertebral degeneration are major contributors to musculoskeletal morbidity, yet the molecular mechanisms regulating vertebral bone and intervertebral disc (IVD) homeostasis remain incompletely understood. GPNMB (osteoactivin) has been identified as a regulator of bone remodeling, though its role in spine health is unclear. This study evaluated the effects of GPNMB deficiency on lumbar vertebral bone microarchitecture and IVD integrity in a sex-dependent context.

Six-month-old male and female wild-type (WT) and GPNMB knockout (KO) mice were analyzed using micro–computed tomography (µCT) of lumbar vertebrae (L4–L6) and histological assessment of the L5–L6 IVD. KO males exhibited increased bone volume fraction, bone …

The Relationship Between Physical Activity, Sleep, And Hallucinations In Adults With Charles Bonnet Syndrome, Jarrod Hollis, Rohit Narayan, Eldre W. Beukes, Rosie Lindsay, Aliyah Bharwani, Umair Mughal, Ikra Yaqoob, Justin A. Haegele, Scott Muriden, Peter M. Allen

Human Movement Studies & Special Education Faculty Publications

Physical activity levels, hallucination experiences, sleep quality, and perceived stress were assessed using a survey administered to 57 adults with a confirmed diagnosis of Charles Bonnet Syndrome (CBS). Physical activity demonstrated a significant negative correlation with hallucination severity (r = –0.335, p = 0.011, two-tailed). A significant negative correlation was also observed between physical activity and perceived stress (r = –0.497, p < 0.001, two-tailed). In contrast, no significant association was identified between hallucination frequency and sleep disruption or insomnia. These findings suggest that engaging in appropriate levels of physical activity may help reduce the severity of hallucinations and mitigate stress among individuals with CBS. The observation that higher levels of physical activity are associated with reduced hallucination burden may help the development of evidence-based management strategies for CBS. Additionally, the finding that physical activity was significantly related to hallucination severity, whereas sleep disruption was not, merits deeper exploration in future research.

Tramadol For Treatment Of Neurogenic Cough: A Retrospective Case Series, Benjamin Joseph Rubinstein, Sheela Saidha, John Todd Sinacori

Department of Otolaryngology (ENT) Faculty Publications

Objectives

Explore the efficacy of tramadol for neurogenic cough and describe the longitudinal treatment experience.

Methods

A retrospective case series of adults with chronic cough who were treated with tramadol for neurogenic cough. A complete response was defined as no pathologic coughing, and a partial response was defined as 50% or greater reduction in severity or frequency.

Results

Sixty-nine patients were included. 38% of patients reported a complete response with an additional 33% reporting a partial response. The most common successful dosing regimen was 50 mg BID. Age, gender, and BMI did not impact treatment response. Patients with a history …

Examining The Physiological Stress-Reducing Effects Of Virtual Nature Exposure And Slow Breathing, Jesse Benefiel

Cal Poly Humboldt theses and projects

In a time of excess stress, it is essential to examine accessible stress-reduction methods. Research has demonstrated that virtual nature exposure and slow breathing can independently reduce stress, but the literature is lacking with regard to their combined effects. The present study aimed to replicate independent effects of breathing and nature on stress and to test for potential effects, including whether their combination would produce an interaction effect. Using a 2 Environment (Natural v. Control) by 2 Breathing (Slow v. Normal) between-subjects design, 63 participants completed a modified color-word Stroop task to induce stress and were then exposed to either …

Dextromethorphan And Trace Level Detections Of Dextrorphan In Post-Race Urine Samples – A Case Report And Analysis, Kimberly Brewer, Justin C. Holmes, Clara Fenger, Abelardo Morales-Briceño, Andreas F. Lehner, George A. Maylin, Robert Holland, Levent Dirikolu, Thomas Tobin

Maxwell H. Gluck Equine Research Center Faculty Publications

Dextrorphan is a Phase I equine metabolite of dextromethorphan, a widely used anti-tussive / cough suppressant medication marketed and available in numerous over-the-counter formulations in the United States. Dextromethorphan is an Association of Racing Commissioners International (ARCI) drug class 4 penalty class B substance and a Horseracing Integrity and Welfare Authority (HIWU) CONTROLLED S7 B substance and is regulated as such in horse racing. In horses, dextromethorphan is metabolized to its Phase I metabolite, dextrorphan, which is next glucuronidated and the resultant dextrorphan-glucuronide conjugate then excreted at remarkably high concentrations in equine urine. Dextrorphan is therefore at times identified in …

Establishment And Histopathological Characterization Of A Kyse-30 Subcutaneous Xenograft Model Of Esophageal Squamous Cell Carcinoma, Pavel A. Solopov, Alayna Enos, Mantas Silkunas, Giedre Silkuniene, Eleni Zivla, Andrei G. Pakhomov, Olga N. Pakhomova

Bioelectrics Publications

Background/Objectives: Esophageal squamous cell carcinoma (ESCC) is an aggressive malignancy with poor prognosis and limited treatment options, highlighting the need for reliable preclinical models for translational research. Although xenograft models are widely used in cancer biology, systematic characterization of subcutaneous ESCC models under defined implantation conditions remains limited. The objective of this study was to systematically compare implantation conditions and define histopathological and growth-related parameters that enable reproducible tumor establishment while maintaining a practical experimental window for therapeutic studies. Methods: We established and characterized a subcutaneous ESCC xenograft model using human ESCC cell line KYSE-30 implanted into immunodeficient J:NU mice. …