Digital Commons Network^™

Computational Methods For Enhancing The Quality And Interoperability Of Biomedical Terminologies, Xubing Hao

Dissertations and Theses (Open Access)

Biomedical ontologies or terminologies not only serve as a part of the metadata standards for describing data in the FAIR Data Principles (Findable, Accessible, Interoperable, Reusable), but also play a vital role in downstream applications such as cohort identification from electronic health records (EHR). However, there are two critical barriers that may lead to ambiguity, complexity, and inaccuracies in such ontology-based downstream applications. The first barrier is the quality of the ontology. Despite efforts by ontology curators to ensure ontology accuracy and comprehensiveness, errors and inconsistencies are unavoidable. The second barrier is the semantic heterogeneity since human experts may use …

Advancing Genetic Association Discovery In Brain Mri Using Unsupervised And Self-Supervised Deep Learning: Exploring Learning Dynamics, Region-Specific Features, And Spatially Resolved Representations, Sheikh Muhammad Saiful Islam

Dissertations and Theses (Open Access)

Deep learning has unlocked significant potential for advancing the discovery of genetic associations in imaging genetics, particularly in brain imaging using T1-weighted Magnetic Resonance Imaging (MRI). Traditional methods for this task often relied on hand-crafted or semi-automated feature extraction, followed by genetic association studies utilizing these features. While effective, these approaches are limited by their lack of data-driven exploration and the generation of features with limited informativeness.

Unsupervised deep learning, in particular, has emerged as a powerful alternative, addressing some of these limitations by enabling automated and data-driven feature discovery. Recent research in this domain has primarily focused on adapting …

Accelerating Drug Repurposing And Target Discovery Using Deep Learning, Kohong Lin

Dissertations and Theses (Open Access)

Drug discovery is a long-lasting and expensive process. Computational approaches, particularly deep learning techniques, offer the potential to accelerate this process by integrating diverse perspectives from drug discovery theories and capturing intricate patterns within large, multimodal datasets. This dissertation explores deep learning methodologies to accelerate drug repurposing and genetic target discovery. The first aim focuses on integrating multimodal data, including chemical structures, disease genetics, and systems biology, into comprehensive disease knowledge graphs, followed by applying graph neural networks (GNNs) to prioritize repurposable drug candidates. The second aim is to develop a heterogeneous GNN-based approach capable of modelling distinct semantic relationships …

South Dakota Department Of Health: Office Of Community Engagement Strategic Plan Fiscal Years 2025-2028, Julia E. Platt

Honors Thesis

The goal of a strategic plan is to ensure that resources are used effectively and efforts are focused where they are most required by means of direction and concentration. The South Dakota Department of Health Office of Community Engagement Strategic Plan Fiscal Years 2025-2028 contains objectives and goals aimed at maximizing the use of resource allocations and solutions to best meet the needs of the OCE and its partners. In order to create those goals and objectives, internal and external needs assessments, along with key informant interviews, were conducted and analyzed to pull data into actionable SMART objectives. Alignment with …

A Mechanistic Understanding Of The Effect Of Staphylococcus Aureus Vras Histidine Kinase Single-Point Mutation On Antibiotic Resistance, Liaqat Ali, Salima Karki, Gunavanthi D. Boorgula, Amir Mekakda, Brittnee Cagle-White, Shrijan Bhattarai, Robert Beaudoin, Aryanna Blakeney, Sanjay Singh, Shashikant Srivastava, May H. Abdelaziz

Pharmacy Faculty Publications and Presentations

Bacterial genomic mutations in Staphylococcus aureus have been detected in isolated resistant clinical strains, yet their mechanistic effect on the development of antimicrobial resistance remains unclear. Resistance-associated regulatory systems acquire adaptive mutations under stress conditions that may lead to a gain-of-function effect and contribute to the resistance phenotype. Here, we investigate the effect of a single-point mutation (T331I) in VraS histidine kinase, part of the VraSR two-component system in S. aureus. VraSR senses and responds to environmental stress signals by upregulating gene expression for cell wall synthesis. A combination of enzyme kinetics, microbiological, and transcriptomic analyses revealed the mechanistic effect …

Developing And Validating Brain Tumor Organoid Models To Evaluate Novel Therapeutics In Vitro, Dev P. Patel

Senior Theses

Glioblastoma (GBM), a World Health Organization Grade IV brain tumor, remains one of the most aggressive and treatment-resistant malignancies. It is characterized by rapid proliferation, deep infiltration, and a high level of genotypic and phenotypic heterogeneity. Despite advancements in medical technology and neuro-oncology, GBM remains one of the most treatment-resistant cancers with a median survival rate of only nine months post-diagnosis and less than 5% of patients surviving beyond 5 years of diagnosis. The standard treatment constitutes maximum surgical resection followed by chemotherapy and radiation. These therapeutic strategies are blocked by significant challenges like the blood-brain barrier (BBB), and intratumoral …

Role Of Race And Ethnicity In The Development, Diagnosis, And Treatment Of Gestational Diabetes Mellitus, Gabrielle D. Shupard

Senior Theses

Gestational diabetes mellitus (GDM) is the most common metabolic disorder of pregnancy, and rates of this disease have been steadily increasing over the past ten years. GDM disproportionately impacts racial and ethnic minorities at higher rates than their Caucasian counterparts. In this study, the PRECEDE model framework was employed during a literature review to gain a greater understanding of the complex risk factors contributing to differences in the development, diagnosis, and treatment of GDM among these population subgroups. The second part of this study concentrated on reviewing the extent to which current literature evaluates the role of race and ethnicity …

Investigation Of The Effects Of The Peptidylarginine Deiminase Inhibitor Cl-Amidine On Apoptosis And Gene Expression In Ovarian Cancer, Victoria Walden

Longwood Senior Thesis Proposal

Peptidylarginine deiminases (PADs) are a family of enzymatic proteins responsible for the conversion of arginine and methylarginine residues to citrulline. This conversion is important for several key cellular processes including transcriptional gene regulation. Recently, a link has been established between overexpression of a particular PAD, PAD4, and the accelerated progression of both autoimmune diseases and cancers. Ovarian cancer exhibits heightened levels of PAD4 in affected cells. High levels of PAD4 are associated with the formation of neutrophil extracellular traps (NETs) that promote cancer metastasis, and downregulation of the p53 apoptotic pathway. Thus, it is important to explore inhibitors of PAD4. …

Associations Between B Vitamin Interactions With Polyunsaturated Fatty Acids And Cognitive Function Among Cognitively Healthy Older People As Modified By Amyloid Status And Sex, Chuliang Zhao, Karen A. Abbott, Chinedu Momoh, Geraint Price, Oliver J. K. Robinson, Sujin Kang, Celeste A. De Jager Loots

Brain and Mind Institute

Background/Objectives: Nutrients such as vitamin B12, folate (B9), and polyunsaturated fatty acids (PUFAs) may independently influence cognitive health, but their combined effects and interactions remain unclear. This study aims to investigate the effects of B12, folate, and PUFAs, including their interactions, on cognitive function in cognitively healthy older adults, considering effect modification by sex and amyloid-beta status.

Methods: A cross-sectional analysis was conducted using data from 321 participants aged 60–85 y enrolled in the UK CHARIOT–PRO SubStudy. Dietary intake was assessed using the Scottish Collaborative Group Food Frequency Questionnaire, and cognitive performance was measured via the Repeatable Battery …

From Theory To Practice: A True-Crime Podcast, Lauren V. Peckham

Senior Honors Projects

The Criminal Element is an innovative, victim-centered podcast that bridges the gap between criminological theory and real-world criminal cases. The podcast is designed as an educational resource for undergraduate Criminology and Criminal Justice students, alongside general audience members interested in learning more about criminological theory. Through the lens of true crime, this podcast is an engaging exploration of foundational and advanced theories while avoiding sensationalism and exploitation, a prevalent problem among true crime media. Each episode connects criminological theoretical concepts – such as strain, social learning, and social disorganization – to contemporary and historical cases, providing listeners with accessible and …

The Illusion Of Brain Health Across A Plastic Canvas, Thomas J. Kelly Jr, Lauren Gaspar, Jaime Ross Phd, Guiseppe Coppotelli Phd

Senior Honors Projects

In recent years, there has been increasing concern for the role that plastic waste, and more specifically micro- and nanoplastics, play in our environment and their potential health risks. Microplastics are particles less than 5 mm in size and nanoplastics are considered to be less than 1000 nm in size. Microplastics can either purposely be produced or can sludge off larger pieces of plastic. Microplastics have not only been detected within soil, air, and water, but have also recently been found to accumulate within the human body. The mosaic artwork that is presented in this project, entitled “Our Cerebral Plastic …

Sox18 Unleashed: Exploring The Transcriptomic Landscape – Differential Gene Expression Analysis Via Rna Seq In Overexpressed Sox18, Van Nguyen, Terry Shackleford, Lori Boies

Posters - 2025

Cancer remains a leading cause of death worldwide, and childhood sarcomas such as Rhabdomyosarcoma (RMS) and Ewing Sarcoma (ES) are particularly aggressive with limited targeted treatment options. Despite advancements in cancer therapies, metastatic sarcomas still have a survival rate below 30%, emphasizing the need for new therapeutic targets. SOX18, a transcription factor has played a role in vascular development and endothelial differentiation, functioning as a key driver of angiogenesis. In cancer, increased SOX18 expression has been linked to dysregulated cell migration, invasion, and therapy resistance mechanisms. However, the extent to which SOX18 influences RMS and ES at the transcriptional level …

Maternal Obesity Alters Antigen-Bound Igg Levels In Breast Milk, G. Sophia Noriega, Andrea Paredes, Emma C. Colins, Elizabeth A. Leadbetter

Posters - 2025

• Maternal obesity is an increasingly prevalent condition worldwide that has been associated with adverse outcomes in offspring, including higher propensity to infection and elevated risk of immune-related disorders like asthma and allergies 1 .

• Breast milk contains a wide variety of immunological components that are essential for neonatal immune development. Among these, it contains immunoglobin G (IgG) immune complexes, which are formed by IgG bound to specific antigens2 .

• These immune complexes have been suggested to play a crucial role in antigen-specific immune response in breastfed infants3 , increasing oral tolerance and asthma prevention 4 .

• …

The Impact Of Employer-Provided Drug/Alcohol Education On Marijuana And Alcohol Use In Young Adults., Sonia Cerrillo, Naomi Ramirez

Posters - 2025

According to the American Society of Addiction Medicine, addiction is a treatable, chronic medical disease involving complex interactions among brain circuits, genetics, the environment, and an individual’s life experiences (1). People with addiction use substances or engage in behaviors that become compulsive and often continue despite harmful consequences. The most common addictions in the United States are alcohol and marijuana (2). In the U.S., 59.277 million people twelve and older have used illegal drugs or misused prescription drugs. Out of the 138.522 million Americans who overdrink alcohol, 28.32 million have an alcohol use disorder (3).

Since alcohol and drug abuse …

Spectroscopic And Electrochemical Properties Of Ugi Adducts Of Isatin, Callah Preti, Erick Y. Morales Orrante

Posters - 2025

• β-lactams are essential structural components of many antibiotics and widely studied due to their biological importance and synthetic versatility.

• The Ugi reaction is a multicomponent reaction involving: • Aldehyde, primary amine, carboxylic acid, and isocyanide.

• Rapidly generates α-acetamido carboxamide derivatives (Ugi adducts). • The study focuses on the synthesis and characterization of two oxindole-based β-lactam derivatives:

• 1-Benzyl-N-(tert-butyl)-2-oxo-3-(2-oxoazetidin-1-yl)indoline-3- carboxamide (4a).

• N-(tert-Butyl)-2-oxo-3-(2-oxoazetidin-1-yl)indoline-3- carboxamide (4d).

• Characterization methods included IR Spectroscopy, UV-Visible Spectroscopy, and X-Ray Crystallography.

• Future work will investigate metal complexation to enhance β-lactam stability, alter electronic properties, and improve biological activity

Evaluation Of Angiogenesis In An Ex-Ovo Chick Chorioallantoic Membrane (Cam) Assay To Study The Mmp9 Gene In Pediatric Cancer Cell Lines, Franchesca Tinacba, Kahlie Hernandez, Terry Jo Shackleford

Posters - 2025

Model organisms are widely utilized in cancer research due to their ability to allow researchers to study biological processes that occur within cancer progression. One model organism that is used is the Chorioallantoic Membrane (CAM) assays. Chicken embryos are a sufficient model that are used to study processes such as angiogenesis, tumor growth, and drug effects. What makes these models useful is due to the cost efficiency, accessibility, and the increased speed the blood vessels can grow. Despite the results, it can be difficult to image the results or monitor the CAM assay. That is why Ex-ovo CAM assays have …

Cd36 Deletion Hampers T-Bet B Cell-Differentiation In R848 Immunized Mice And Hfd Models, Andrea Paredes, G. Sophia Noriega, Carlo Vanz, Emma Collins, Elizabeth A. Leadbetter, Benjamin T. Enslow

Posters - 2025

In states of chronic inflammation, a subset of B cells exquisitely responsive to nucleic acid antigen and expressing the proinflammatory transcription factor T-bet have been found to accumulate1. Depending on the context, these T-bet+ B cells can play both protective and pathogenic roles, from enhancing antiviral defenses to contributing to autoreactive antibody production and exacerbating metabolic disease1,2.

• Recently, our laboratory and others have found that T-bet+ B cells extracted from human or murine tissues exhibit unusually high expression of the class B scavenger receptor and fatty acid translocase CD36.

• As CD36 expression in B cells is generally limited …

Acute Physiological Responses To An Infrared Sauna Blanket Towards Home Based Passive Heat Therapy, Arlene Chaidez, Mia Gonzales, Amaryllis Rubalcaba, Meghan Walls, Rene Barbier

Posters - 2025

Repeated passive heat exposure can improve cardiovascular health outcomes. A novel infrared sauna blanket may enable home-based heat therapy, but these devices are yet understudied. By closely monitoring blood pressure, heart rate, core body temperature, and perceptual responses, it could be determined how a participant's body reacts to the infrared treatment. We found elevated cardiovascular activity in response to the sauna blanket, similar to that observed during moderate-intensity exercise. Therefore, the infrared sauna blanket may have potential for inducing long-term cardiovascular adaptations and become an accessible and costeffective way of treating/preventing chronic illness.

Sacred Oath Of Healing - Volume 9

be Still

No abstract provided.

The Essence Of Resilience, Evelyn Echevarria Cruz

be Still

No abstract provided.

Cultivating Compassionate And Inclusive Care For People With Disabilities, Evelyn Echevarria Cruz, Aila Cordero, Maria Fioletova, Amanda Escudero

be Still

The disparity between physicians' preparedness to treat people with disabilities (PWD) and the prevalence of disabilities is a critical healthcare issue. The 2022 Behavioral Risk Factor Surveillance System reported that over 25% of U.S. adults have a disability, yet many healthcare providers feel unprepared. A poll found that only 40.7% of 714 physicians were confident in providing quality care to PWD, while 61% of 600 surveyed PWD indicated that their providers needed more training. Additionally, only 36% of medical schools included disability education in their curricula, often focusing on brief simulations rather than immersive experiences. To effectively address the diverse …

An Oath Fulfilled, Fatima Bawaney

be Still

This poem explores the sacred oath of healing as it relates to a physician-patient relationship.

Cultural And Religious Perspectives On Suicide And Healing, Arielle Friedman

be Still

This essay is built off of a paper I wrote in a college global health course on culture and mental illness. I have always been fascinated by cultural interpretations of illness & believe that as a future physician, it is my responsibility to educate myself and others on the complex interplay between religious ideologies & recognition/management of biological disease in order to provide appropriate patient-centered care.

Nourishing The Body, Nurturing The Soul, Vidhi Raval

be Still

No abstract provided.

A Cellular And Molecular Dissection Of The Breast: Identification Of Pericytes As A Driver Of Tumor Cell Proliferation, Katelyn M. Del Toro

Biomedical Sciences ETDs

Tissues are composed of many different types of cells. Each has a specific function and exists within a unique context—all of which define the landscape of the tissue. The cellular and molecular interactions within a tissue are critical to its form and function. Defining these interactions is an important step in understanding the aberrant nature of diseases like cancer, where tissue homeostasis has been abandoned. This requires reliable models of each cell type. Yet, in many tissues, including the breast, comprehensive methods to identify, purify, and study each tissue cell type have not been defined. This is a critical deficiency …

Larotrectinib Compared With Real-World Non-Tropomyosin Receptor Kinase Inhibitor Therapies In Patients With Tropomyosin Receptor Kinase Fusion Cancer, Marcia S. Brose, C. Benedikt Westphalen, Xiaoyun Pan, Vadim Bernard-Gauthier, Milena Kurtinecz, Helen Guo, Virginie Aris, Neil R. Brett, Abdelali Majdi, Vivek Subbiah, Nathan A. Pennell, Kenneth L. Kehl, Alexander Drilon

Kimmel Cancer Center Faculty Papers

PURPOSE: Neurotrophic tyrosine receptor kinase gene fusions are oncogenic drivers of various solid tumors. Larotrectinib is a highly selective tropomyosin receptor kinase (TRK) inhibitor approved for patients with TRK fusion cancer on the basis of single-arm trials. This study was a matched comparative effectiveness study of larotrectinib in clinical trials versus standard of care (SOC) in the real-world (RW) setting.

METHODS: Adult patients with advanced/metastatic TRK fusion non-small cell lung cancer, colorectal cancer, soft tissue sarcoma, thyroid cancer, or salivary gland carcinoma were included. Deduplicated data from RW patients were from US and ex-US data sources. Patients in the larotrectinib …

Vpac Receptor Positivity In Comparison With Mp-Mri In The Diagnosis Of Prostate Cancer: A Preliminary Study, Nishant Setya, Shridhar Ghagane, Rajendra Nerli, Ashwin Bokare, Mathew Thakur, Leonard Gomella

Kimmel Cancer Center Faculty Papers

Objective: The study aimed to prospectively evaluate the feasibility of diagnosing PCa using voided urine samples and by targeting the genomic VPAC (vasoactive intestinal peptide and pituitary adenylate cyclase-activating peptide) receptors in comparison with multiparametric magnetic resonance imaging (mp-MRI) in male patients (≥40 years of age) with lower urinary tract symptoms and having a serum PSA of >4 but < 15 ng/ml.

Patients and methods: Male patients attending urological services ≥40 years old, with lower urinary tract symptoms and serum PSA levels of >4 but < 15 ng/ml formed the study group. Voided urine samples were collected to target VPAC receptors on malignant cells. All patients underwent mp-MRI. A 12-core transrectal ultrasound-guided prostate biopsy was performed in all, and the results were compared for the diagnosis of PCa.

Results: A total of 61 patients with a median age of 65.33 ± 8.11 years and with a …

Experiences And Attitudes Of Caregivers During Mealtimes In Children With Autism Spectrum Disorder At A Tertiary Facility In Kenya., Lynnette Muthoni Mwangi

Master of Medicine in Paediatrics and Child Health

Introduction: - ASD is a neurodevelopmental disorder characterized by deficits in social interactions and communication along with restrictive and repetitive behaviours affecting 1 in 100 children globally, with a higher prevalence in males. Despite the rising global statistics, there is limited information regarding the prevalence of ASD in Sub-Saharan Africa. Children with ASD often experience feeding challenges, which have been broadly categorized as food selectivity, food refusal, and disruptive mealtime behaviour, which poses challenges for caregivers during mealtime. While medical management of ASD receives considerable attention, less focus has been placed on the impact of ASD on caregivers and …

Spring 2025, Humayun Islam

PMI Newsletter

No abstract provided.

Comparison Of Hand-Wrist And Cvms Methods For Craniofacial Growth Spurt Assessment, Ardita Ajvazi

Master's Theses (2009 -)

Objective: Hand-wrist (HW) radiographs are considered the most accurate method for assessing pubertal growth spurts in orthodontics but have declined in use due to added radiation exposure and the expertise required. Cervical vertebral maturation staging (CVMS) is now commonly used, given the routine availability of lateral cephalograms. However, the validity of CVMS remains uncertain. A recent study reported only 66% inter-observer reliability across time periods (Ingersoll, 2024). This follow-up study aims to evaluate CVMS as a predictor of growth to guide clinical decision-making. Methods: With protocol approval (MU HR-4695), this retrospective study followed a design modeled after a prior study …