Digital Commons Network^™

Analysis Of Alternative Gene Splicing Of Natural Killer Cell Exhaustion Markers During Siv Infection, Soledad B. Zayas

Honors Undergraduate Theses

Natural killer cells play a critical role in the innate immune response against Human Immunodeficiency Virus and Simian Immunodeficiency Virus infections. During HIV/SIV infection, NK cells undergo functional impairment characterized by an imbalance between activating and inhibitory surface receptors. The upregulation of inhibitory receptors, TIGIT and TIM-3, has proven to contribute to NK cell exhaustion during different retroviral infections. Although alternative splicing regulates immunity related genes, its role in TIGIT and TIM-3 expression during SIV infection remains poorly understood. This study aimed to characterize alternative splicing patterns of TIGIT and TIM-3 and evaluate transcript variant expression during SIV infection in …

From Needs To Action: Designing Inclusive Writing Workshops For Academics, S. Alison Bolling, Julie Hicks Patrick

2026 Scholarly Teaching Conference: Poster Session Papers

Being productive in academic writing is a critical component of success for graduate students and faculty, yet many scholars report persistent barriers that interfere with successful writing (Kaslow et al., 2025, Sweet et al., 2017). Few faculty and graduate students receive formal training on the art of writing and those who have attended writing programs vary in success (Dankoski et al., 2012). The present study reports results from multiple institutions to inform workshops on writing needs of graduate students, faculty, and postdoctoral scholars.

Data was collected online through a Qualtrics survey distributed by WVU listserv. Participants (N = 26) included …

Research In Progress. Why Physiology Feels Hard: Supporting The Transition To Self-Directed Learning In Post-Secondary Physiology, Jaelyn Zoe Rohrbaugh, Mark Paternostro

2026 Scholarly Teaching Conference: Poster Session Papers

Physiology is widely recognized as one of the most challenging courses for STEM students. Contributing factors include the discipline’s inherent complexity, instructional methods, and student preparedness, with both faculty and students identifying the nature of the discipline as the primary challenge. Many undergraduates enter college having experienced predominantly teacher-directed, pedagogical instruction, whereas success in college-level physiology requires self-directed, andragogical learning strategies. We hypothesize that students’ difficulties arise more from a lack of self-directed learning skills than from content complexity alone. To investigate this, we administered an anonymous survey to 340 students spanning freshman to professional levels, achieving a 93% completion …

Bringing Real Research Into Large-Enrollment Biology Labs, Katrina Klugh Stewart, Mathilda Corbett

2026 Scholarly Teaching Conference: Poster Session Papers

Hundreds of WVU students in a large-enrollment introductory biology laboratory course (BIOL 115L) participated in an authentic research experience through the Prevalence of Antibiotic Resistance in the Environment (PARE) Project. This national crowdsourced research initiative engages students in generating environmental DNA data to identify potential antibiotic resistance hotspots. For the Fall 2025 semester, we designed a multi-week lab module to implement a cost-effective, scalable version of the PARE model suitable for a course serving approximately 900 students annually.

The three-week sequence integrates core scientific practices, including hypothesis generation, field sampling, DNA extraction, PCR amplification of antibiotic resistance genes, gel electrophoresis, …

Illusions Of The Brain, Vaso Manakou

Scientific Kenyon: The Neuroscience Edition

No abstract provided.

The Role Of Small Extracellular Vesicles In Modulating Radiation Resistance In H3k27m-Pediatric Diffuse Midline Glioma, Viral Oza

Theses and Dissertations--Molecular and Cellular Biochemistry

Pediatric diffuse midline gliomas with H3K27M alteration (H3K27M-pDMG) are the leading cause of pediatric brain tumor-associated deaths. All H3K27M-pDMG are initially treated with fractionated radiotherapy, the standard of care, and most children succumb to their disease within two years of diagnosis. There are no universally effective chemotherapies and full resection is impossible due to the diffuse nature of the tumor and sensitive location. There has not been a significant clinical advancement in more than 40 years.

Tumors become completely resistant to radiation within the first six months of treatment. The mechanism of radiation resistance is unknown but is thought to …

Scientific Kenyon: Neuroscience Edition (Full Issue)

Scientific Kenyon: The Neuroscience Edition

No abstract provided.

Get The Fruc(Tose) Out Of My Food, Johanna Huelsman

Scientific Kenyon: The Neuroscience Edition

No abstract provided.

Epigenetic Hangovers: Your Brain On Alcohol, Cindy Chen

Scientific Kenyon: The Neuroscience Edition

No abstract provided.

Losing Yourself To Find Yourself: The Neuroscience Ego Dissolution, Mike D'Eletto

Scientific Kenyon: The Neuroscience Edition

No abstract provided.

What The Body Feels, The Mind Reveals: How Inflammation Shapes Emotions, Jamie Murphy

Scientific Kenyon: The Neuroscience Edition

No abstract provided.

Smile! Your Brain Is On Camera, Natalie Stone

Scientific Kenyon: The Neuroscience Edition

No abstract provided.

When Empathy Goes Quiet, Miko Warshaw

Scientific Kenyon: The Neuroscience Edition

No abstract provided.

A Major Update And Improved Validation Functionality In The Mwtab Python Library And The Metabolomics Workbench File Status Website, P. Travis Thompson, Hunter N. B. Moseley

Markey Cancer Center Faculty Publications

Background: The Metabolomics Workbench (MW) is a public scientific data repository consisting of experimental data and metadata from metabolomics studies collected with mass spectroscopy (MS) and nuclear magnetic resonance (NMR) analyses. Although not as rapidly as in the past, MW has steadily evolved, updating its mwTab and JSON deposition text file formats and its web-based infrastructure. However, the growth of MW has been exponential since its inception in 2013 and continues to be exponential, with the number of datasets hosted on the repository increasing by 50% since April 2024. As part of regular maintenance to keep up with changes to …

The Effect Of Cover Crop Management Strategies On Nutrient Availability In No-Till Corn, Emily C. Marsh

Theses and Dissertations--Plant and Soil Sciences

Cover crops are reported to have long-term soil health improvements, one of which is reducing erosion. However, popular cereal cover crops, such as rye (Secale cereale L.), have the potential to cause a yield penalty in the following corn (Zea mays L.) crop due to a reduction in available nitrogen. Legumes, such as Austrian winter pea (Pisum sativum L. var. arvense), are thought to reduce this yield penalty due to their capacity to fix nitrogen. Sulfur is another nutrient of interest, especially as rates of atmospheric deposition of sulfur have declined, leading to more deficiencies being …

Mineral-Associated Organic Nitrogen Pool Size, Composition, And Accessibility Mediated By Agricultural Management And Soil Geochemical Characteristics, Gabriella M. Griffen, Andrew H. Whitaker, Emma L. Bergh, Marian Carrell, Erik Knatvold, Aniko Konya, A. Stuart Grandy, Andrea Jilling Ph.D., Marco Keiluweit, Rachel Hestrin

Faculty Publications

Mineral-associated organic matter (MAOM) contains a substantial portion of soil nitrogen (N). MAOM-N could serve as an important N source for crops, but its availability and response to agricultural management across different soil types remains largely unknown. We characterized MAOM-N isolated from nine paired soils spanning a range of geochemical characteristics and maintained under two land uses—more intensively managed annual cropping systems or less intensively managed grasslands. On average, we found that MAOM contained approximately two-thirds of total soil N. Across all soil types, more intensive agricultural management resulted in a 50% decline in MAOM-N stocks, as well as a …

Reduced Threat-Related Neural Efficiency: A Possible Biomarker For Pediatric Anxiety Disorders, Julia O. Linke, Reut Naim, Simona P. Haller, Parmis Khosravi, Beck Scheinberg, Meghan E. Byrne, Anita Harrewijn, Ellen Leibenluft, Melissa A. Brotman, Anderson M. Winkler, Daniel Samuel Pine

School of Medicine Publications

Objective: Pediatric anxiety disorders are common and predict adult psychopathology, yet current treatments, such as cognitive-behavioral therapy (CBT), produce lasting remission in less than 50% of affected youths. To support the search for improved, mechanistically grounded interventions, this study evaluated neural efficiency, defined as similarity in functional connectivity between a threat task and rest, as a potential biomarker. The study evaluated neural efficiency in relation to anxiety diagnosis and treatment response.

Methods: The authors compared 103 youths with an anxiety disorder diagnosis (mean age, 12.5 years [SD=2.91], 62% female) to 103 youths with no psychiatric diagnosis (mean age, 13.4 years …

Nanoparticle Carriers Enhance The Prophylactic Antiviral Effects Of Dsrna In Vitro And Ex Vivo, Shayne Oberhoffner, Stephanie Dewitte-Orr, Starla Richardson, Leah Haile, Dominique Daniels, Erin Cooper, Aizah Ijaz, Janet Velasquez Perez, Mathilde Peruzzi, Bertrand Collet, Paul Craig, Kristof Jenik

Theses and Dissertations (Comprehensive)

Aquaculture now outpaces traditional capture fisheries as the world population and demand for sustainable protein sources increases. Wild and farmed species are increasingly susceptible to pathogen spread as global temperatures rise and stocking densities increase. Despite the devastating losses experienced by aquaculture due to viral infections, there remain few effective prophylactic antiviral therapeutics. Long double-stranded (ds)RNA is a uniquely viral molecule produced by nearly all viruses during their replication cycle, and its detection by salmonids like rainbow trout (Oncorhynchus mykiss) and chinook salmon (Oncorhynchus tshawytsha) leads to the establishment of a defensive antiviral state. Previous in vitro studies demonstrated a …

Adapting To Uncertainty: Effects Of Environmental Instability On Zebrafish Behaviour, Britney Sekulovski

Theses and Dissertations (Comprehensive)

This thesis addresses how animals cope with unpredictability by testing how environmental stability changes the behaviour of zebrafish (Danio rerio) in two complementary experiments. In Experiment 1, fish lived for three months in either a Dynamic environment (water temperature, feeding times, habitat complexity, group size, and membership fluctuated) or a Stable environment (all factors constant). Across seven behavioural assays, measuring individual behavioural differences, collective movement, social memory, and information use, Dynamic condition fish were found to be more sensitive to social cues and more likely to conform to recent social information, independent of the quality of the information …

Injury To Insight: Exploring The Influence Of Media On Acl Rehabilitation Experiences Of Female Soccer Players, Chynna Ho-Young Cadogan, Jill Tracey

Theses and Dissertations (Comprehensive)

Participation in soccer inherently carries a risk of injury, with female athletes facing a significantly higher susceptibility to anterior cruciate ligament (ACL) injuries (Campbell et al., 2014; Le et al., 2025; Silvers-Granelli, 2021). The increasing participation in women’s soccer, coupled with the growing demand for its consumption through spectatorship, has contributed to a rise in ACL injuries, and increase in media coverage on this phenomenon (Parsons et al., 2021). Understanding how media narratives surrounding ACL injuries and recovery may influence rehabilitation experiences can educate coaches, mental performance consultants, athletic therapists, and female soccer players to better understand and navigate ACL …

Taylorkan-Vit: Parameter-Efficient Vision Transformers For Medical Image Classification, Kaniz Fatema, Dr. Emad Mohammed, Dr. Sukhjit Singh Sehra

Theses and Dissertations (Comprehensive)

Effective and interpretable classification of medical images remains a critical challenge in computer-aided diagnosis, particularly in data-scarce and resource-constrained clinical settings where traditional deep learning models prove impractical. This study addresses the fundamental barrier to Vision Transformer adoption in medical imaging—massive parameter counts and data requirements—through a systematic two-phase methodology. Phase 1 evaluates three spline-based Kolmogorov–Arnold Network (KAN) variants to identify the optimal nonlinear approximation function for parameter-efficient medical image classification: SBTAYLOR-KAN (B-splines with Taylor series), SBRBF-KAN (B-splines with Radial Basis Functions), and SBWAVELET-KAN (B-splines with Morlet wavelets). Comprehensive experiments across brain MRI, chest X-rays, and tuberculosis datasets—without any image …

Investigating The Immunostimulatory Potential Of Dsrna-Silk Nanoparticle Complexes In Melanoma, Samuel J. Peters

Theses and Dissertations (Comprehensive)

The rate of resistance to immune checkpoint inhibitor treatment in metastatic melanoma is quite high, with an overall rate of 70%. Melanoma achieves these high rates of resistance by suppressing the immune response in the tumour microenvironment (TME), making them immunologically “cold”. The type 1 interferon response could be leveraged to initiate immune responses in melanoma, making their “cold” TMEs “warm” again. Double-stranded ribonucleic acids (dsRNAs) are potent activators of an innate immune response; however, they are susceptible to degradation by nucleases present in the body and need a carrier. Silk nanoparticles (SNPs) are an ideal drug-delivery platform as they …

Analysis Of Alternative Oxidase In Non-Angiosperm Plants, Anissa M. Francis

Theses and Dissertations (Comprehensive)

Alternative oxidase (AOX) is a mitochondrial terminal oxidase that provides an alternative pathway for electron transport, allowing plants to maintain respiratory flexibility under environmental stress conditions. While AOX has been extensively studied in angiosperms (flowering plants), little is known about its distribution and conservation in non-angiosperms. Based on gaps identified in the literature, this thesis investigated the distribution of AOX across non-angiosperm plant lineages. Although AOX is present in many green algae and is therefore considered to be an ancient protein that originated before the existence of non-angiosperm plants, it remains unclear whether the protein is uniformly distributed across these …

Impact Of Cigarette Smoke On Immune And Stromal Cells, Justin Wong

Master's Projects

Cigarette smoke is a plight on human health, being a major contributor to lung diseases. The aryl hydrocarbon receptor (AHR) directs immune regulation and metabolic adaptation in response to environmental toxins. This study investigates transcriptomic changes between wild-type and AHR knockout mouse lung tissue under smoke and air conditions. Single-cell RNA sequencing data were generated by the Butcher Lab and analyzed in Seurat for differential gene expression (DGE) analysis. A two way ANOVA framework was used with DGE analysis to classify genes as smoke induced or suppressed in an AHR dependent or independent manner, and these gene sets were analyzed …

Searching For Cause Of Unexplained Protein Interaction With Multiple Assembly Methods, Gavin Anderson

Master's Projects

Research into colistin adjuvants has identified interactions between a host of proteins and proteins found within certain strains of bacteria. BLAST, a widely adopted local sequence alignment tool, was used to create a database containing the genomes of relevant bacterial strains, which would then be used to query against the previously identified proteins. Many of these strains do not have publicly available assemblies, which makes database construction difficult. CATwalk, a new naïve fragment extender, is first described in this paper and used to extend fragments of interest. BLAST results first identified short fragments with sufficient similarity, which can then be …

Detection And Characterization Of Cancer Using Cfdna Fragmentomic Analysis, Guneet Bhogal

Master's Projects

Cell-free DNA (cfDNA) fragmentomics has emerged as a promising non-invasive approach for detecting and characterizing cancer by analyzing DNA fragmentation patterns. These fragment patterns are unique and can be used to distinguish between tumor and healthy DNA. This paper uses machine learning models to detect cancer by evaluating Shannon entropy of fragment lengths at the first coding exon 1 regions and correlating them to targeted cancer genes. This approach was applied to two datasets consisting of samples with prostate, breast, and lung cancers. Our results indicated that exon 1 fragmentation entropy captures biologically relevant differences in cancer-specific chromatin organization and …

Combining Crispr And Nanoasv To Uncover The Rare Bacterial Communities Of The Human Oral Microbiome, Gilma Ruth Sevilla Alvarez

Master's Projects

Studying the oral microbiome is vital because its health implications are not contained to the mouth. Cariogenic bacteria cause tooth demineralization and oral microbes that translocate to extra-oral organ systems are linked to conditions like Alzheimer’s disease, heart disease, diabetes, and cancer. Some of these pathogens belong to the most abundant phyla in the oral cavity: Bacillota, Pseudomonadota, Bacteroidota, Actinomycetota, Spirochaetota, and Fusobacteriota, which together comprise 94% of the oral microbiome. This project uses CRISPR-Cas9 to deplete sequences from highly abundant phyla and the Eubacteria domain, enriching the remaining 6% of rarer taxa. Paired with NanoASV for single-nucleotide resolution, this …

The Coral Microbiome Under Climate Change: Shifting Symbiotic Interactions, Katherine E. Parker, Kate M. Quigley

Biological Sciences Faculty Publications

Host–microbe symbioses are central to organismal health, yet these complex partnerships are often strongly shaped by the environment. Climate change is increasingly altering environmental conditions, disrupting the balance of host–microbe interactions and pushing them along a continuum from mutualism (both partners benefit) toward parasitism (one partner gains at the other’s expense). Reef-building corals provide a clear example of this vulnerability, as the coral holobiont, an ecological unit comprising diverse photosynthetic algal symbionts (Symbiodiniaceae) and other microbial partners, depends largely on these mutualistic interactions for nutrition, immunity, and stress tolerance. Increasingly, evidence suggests that under heat stress, the algal symbionts retain …

Ovarian Cancer Immunology And Immunotherapy: Editorial Note, Chris D. Platsoucas

Biological Sciences Faculty Publications

[Introduction] As the guest editor of the Special Issue on Ovarian Cancer Immunology Immunotherapy, I would like to include certain brief comments on the current state of the field and to introduce the Special Issue. Ovarian carcinoma and malignant melanoma are the first human tumors where immune responses, primarily restricted to autologous tumor cells, were first demonstrated. T-cell lines and clones developed in recombinant interleukin-2 (rIL-2) from tumor-infiltrating lymphocytes (TIL) from these tumors exhibited cytotoxicity and/or cytokine production, primarily restricted to autologous tumor cells. The T-cell receptor (TCR) and the CD3 differentiation antigen on effector T cells and HLA on …

Microarray Analysis Of Human Abdominal Aortic Aneurysm With Emphasis On Cardiovascular Genes Revealed Differentially Expressed Genes, Song Lu, Li Ping Li, John V. White, Xiaoying Zhang, Ifeyinwa Nwaneshiudu, Adaobi Nwaneshiudu, Nectaria Ntaoula, John Gaughan, Dimitri S. Monos, Wan-Lu Lin, Charalambos C. Solomides, Emilia L. Oleszak, Chris D. Platsoucas

Biological Sciences Faculty Publications

Background/Aim: We examined gene expression profiles in abdominal aortic aneurysm (AAA) lesions vs. normal aortas by cDNA microarray and real-time quantitative reverse-transcriptase polymerase chain reaction (qRT-PCR).

Materials and Methods: Phosphorus (32P)-labeled cDNA from AAA specimens (mean AAA size 6.65 cm) and normal aortas were hybridized with a 588-gene microarray primarily of the cardiovascular system. The results were validated by qRT-PCR.

Results: A total of 35 out of the 588 genes were differentially expressed, with either log2 ratio of AAAs/controls ≥1 (upregulated; 20 genes) or ≤−1 (downregulated; 15 genes) in AAA lesions vs. normal aorta, and 25 of these were significantly …