Digital Commons Network^™

Nf2 Loss Malignantly Transforms Human Pancreatic Acinar Cells And Enhances Cell Fitness Under Environmental Stress, Yi Xu, Michael H Nipper, Angel A Dominguez, Chenhui He, Francis E Sharkey, Sajid Khan, Han Xu, Daohong Zhou, Lei Zheng, Yu Luan, Jun Liu, Pei Wang

Faculty, Staff and Student Publications

Pancreatic ductal adenocarcinoma (PDAC) occurs as a complex, multifaceted event driven by the interplay of tumor-permissive genetic mutations, the nature of the cellular origin, and microenvironmental stress. In this study, using primary human pancreatic acinar 3D organoids, we performed a CRISPR-KO screen targeting 199 potential tumor suppressors curated from clinical PDAC samples. Our data revealed significant enrichment of a list of candidate genes, with neurofibromatosis type 2 associated gene (NF2) emerging as the top target. Functional validation confirmed that loss of NF2 promoted the transition of PDAC to an invasive state, potentially through extracellular matrix modulation. NF2 inactivation …

Public Support For Alcohol-Control Policies And Political Ideology In The Us, Joël Fokom Domgue, Robert Yu, Ernest Hawk, Sanjay Shete

Faculty, Staff and Student Publications

This cross-sectional study examines the role of US adults’ political affiliation, perception about alcohol use and cancer, and sociodemographic and behavioral factors in banning outdoor alcohol advertising and adding cancer warnings on alcohol containers.

Efficacy And Safety Of Semaglutide In Adults Without Diabetes Who Are Overweight Or Obese, Rebecca Petty

The PA Department Journal of Medical Science

INTRODUCTION:

Obesity is associated with an increased risk of cardiovascular and metabolic disorders and contributes to the leading cause of death in the US — heart disease. Glucagon-like peptide-1 (GLP-1) receptor agonists (RAs) have recently emerged as a treatment option for obesity. The purpose of this clinical review is to evaluate the efficacy and safety of semaglutide in adults without diabetes who are overweight or obese.

METHODS:

PubMed was searched using a precise search strategy and the key terms “semaglutide,” “weight loss,” and “without diabetes.” Results were filtered and narrowed using specific inclusion and exclusion criteria. Four high-quality studies were …

Peptide Sequencing Via Protein Language Models, Thuong Le Hoai Pham

Computer Science and Engineering Theses - Archive

Protein sequencing is fundamental to understanding biological processes, disease mechanisms, and therapeutic developments. Current protein sequencing techniques, primarily relying on mass spectrometry and Edman degradation, face significant limitations in accurately identifying all amino acids within a protein, hindering comprehensive proteome analysis. Recent advances in click chemistry and bioorthogonal chemistry have enabled the identification of specific amino acids and their positions within a peptide; however, these techniques are still limited by the number of amino acids that can be identified with high accuracy and specificity, resulting in partially known sequences. This thesis presents a novel computational approach that leverages protein language …

Are There Ecological Consequences Of Urban Adaptation? A Test Of Eco-Evolutionary Dynamics In A Terrestrial Isopod (Oniscus Asellus), Aaron Yilmaz, Grace Bellino, Ryan A. Martin

Faculty Scholarship

Urbanization affects many aspects of the environment with the potential to alter both ecological and evolutionary processes. However, while examples of urban evolution are accumulating, tests of urban eco-evolutionary dynamics are rare. We carried out a reciprocal transplantation experiment using the terrestrial isopod Oniscus asellus to test how adaptation to the urban heat island influenced ecological processes. As isopods are important decomposers, we asked if leaf-litter decomposition differed among reciprocal transplant treatments and used a separate laboratory experiment to isolate the effects of temperature on rates of isopod leaf consumption. We found that leaf-litter decomposition was greater in urban habitats, …

South Asians And Renal Disease: Traditional Food Lists For Management Of Chronic Kidney Disease, Ashwini Wagle

Open Educational Resources

The renal food list is a culturally tailored nutrition education tool designed to address the specific dietary needs of the South Asian population. It is an original intellectual work created by Ashwini Wagle, Ed.D., MS, RD, FAND, Chair and Professor, Department of Nutrition, Food Science, and Packaging at San José State University (SJSU).

An earlier version of this tool was published in 2011 with the assistance of graduate student Kalpana Balasubramanian. The development of this renal food list was strengthened by the encouragement and support of the registered dietitian community, whose contributions included verifying the accuracy of the nutritional information …

Examining Drivers Of Brook Trout (Salvelinus Fontinalis) Fecundity And Recruitment In Central Appalachian Headwater Streams, Emilee Esther Briggs

Graduate Theses, Dissertations, and Problem Reports (ETD)

The persistence of fish populations depends on the repeated production and survival of new year classes, also referred to as recruitment. Recruitment is broadly defined as the number of individuals in a fish population or stock that survive to a specific stage. However, the broader recruitment process reflects the cumulative outcome of many earlier life stages, including egg survival, fry emergence, and survival through the recruitment period. As a result, recruitment can vary substantially among years and populations, producing strong or weak year classes that influence population abundance and persistence. Understanding why recruitment varies is therefore central to fisheries ecology …

Meta-Analysis Of Probiotic Yeast Factors And Methodologies, Mones J. Hajizadeh

Biology Theses

In recent years, there has been an expanding interest in ameliorating the gut microbiome through the use of yeast probiotics, in contrast to the general focus on bacterial probiotics. The goal of this paper is to determine trends and variations in the probiotic evaluation of the yeast species Kluyveromyces marxianus, Pichia kudriavzevii, and Saccharomyces cerevisiae var. boulardii across 48 studies, and determine probiotic gene homology amongst the three yeasts. Much of the literature on novel yeast strains employs various approaches to assess probiotic efficacy. In this study, the evolutionary divergence of these three species of interest was also evaluated. Furthermore, …

Mitochondria In Local Control Of Programmed Cell Killing & Resilience, Rashna Sharmin

Biology Dissertations - Archive

Specialized cells are commonplace and defined by different compartments. Organelle transport across cell compartments is critical for cell function, as in morphologically complex neurons. Specialized cells can undergo programmed elimination, an essential facet of normal development. My central thesis question asks how intracellular transport of mitochondria, the cell’s energy producers, regulate fated elimination of complex cells. I explored this using the specialized tail-spike cell (TSC) of the roundworm C. elegans. The TSC dies embryonically through the novel ‘tripartite’ developmental killing program, Compartmentalized Cell Elimination (CCE).  In my study, I defined and characterized events at the CCE initiation compartment of the …

Protecting Wetlands In The State Of Texas: Assessing Gaps In Regulations, Knowledge, And Professional Roles And Responsibilities, Grace A. Moy

Landscape Architecture Masters & Design Theses

Wetlands rank among earth's most productive ecosystems, providing crucial ecological services such as hydrological regulation, water purification, and habitat support (US EPA, 2015). In Texas, however, rapid urbanization, inconsistent policy enforcement, and the absence of statewide protection frameworks of hastened wetland degradation (Brody & Kang, 2011). Without a robust state regulatory framework (Environmental Law Institute [ELI], 2020), these ecosystems face increasing threats from development and hydrological disturbances.

This thesis aims to identify regulatory and knowledge deficiencies that influence Texas’ current wetland protection status and to offer targeted professional recommendations for landscape architecture professionals to address these shortcomings in future public …

The Ecological Consequences Of Horizontal Transmission Of Symbionts, Bibek Singh Parajuli

Biology Dissertations

Most multicellular organisms depend on their microbial symbionts for various functions, such as digestion, nutrient supplementation, pesticide degradation, and defense. While many insects acquire their symbionts vertically from their parents, thousands of species of true bugs (Hemiptera) across different families acquire their microbial symbiont, Caballeronia, from the environment each generation. Acquiring symbionts from the environment (horizontal transmission) has various ecological consequences for the host. In this study, I used the bug-Caballeronia model 1) to understand whether the free-living symbionts benefit from association with multicellular hosts, 2) to evaluate whether host specialization on symbiont strains varies across taxonomic levels, …

Effects Of Fermented Soybean Products On The Human Gut Microbiome, Microbial Metabolism, And Host Physiology, Shannon Moncier

Biology Dissertations

Fermented soybean products (FSPs) contain soybean-derived substrates, fermentation-associated microorganisms, and bioactive compounds that may interact with the human gut microbiome and host physiology. However, despite the growing interest in FSPs, longitudinal human studies specifically evaluating traditional Korean-FSPs (K-FSPs), particularly among United States-based populations, remain limited. The objective of this work was to evaluate the effects of three K-FSPs, including Cheonggukjang, Gochujang, and Doenjang, on host physiological responses, gut microbial community structure, predicted microbial functional potential, and fecal butyrate responses in healthy adults. Three independent dietary intervention cohorts were conducted using FSP formulations produced either by traditional artisan methods (Product A) …

Uncovering The Mechanism Of Reep2-Mediated Emt-Driven Membrane Trafficking In Lung Adenocarcinoma, Kevin Fulp

Theses and Dissertations--Toxicology and Cancer Biology

Membrane trafficking is frequently disrupted during cancer progression, and the underlying mechanisms remain largely unknown. Currently, no effective drugs target dysregulated membrane trafficking for cancer treatment. Recent evidence has demonstrated that epithelial-to-mesenchymal transition (EMT) in lung adenocarcinoma (LUAD) employs a membrane trafficking program to coordinate cancer cell invasion and immunosuppression. To further dissect the pro-tumorigenic membrane trafficking program, we initiated an in vivo CRISPRi screen to assess more than 2,000 membrane trafficking-related genes in a syngeneic mouse LUAD model. We identified REEP2, an endoplasmic reticulum (ER) shaping protein, as a novel regulator of EMT-driven membrane trafficking. High REEP2 expression is …

The Presence Of Predators Moderates Evolutionary Responses Of Trinidadian Killifish To A Novel Parasite, Anne E. Christian

Biology Dissertations

The Healthy Herds Hypothesis suggests the idea that prey populations derive a benefit from their predators: predators reduce the exposure of their prey to infectious disease, both by limiting prey population densities and by eliminating sick individuals. Much research has focused on the balancing effect that predators have on ecosystems. There is a current need for research into whether these effects cause evolutionary shifts in prey populations, where strong predation pressure prevents prey species from evolving physiological tolerance or resistance to infectious agents. Parasites especially often have rapid effects on host evolution, due to exploitative interactions.

I seek to address …

Spatial Temporal Modeling Of Infectious Disease Patterns In Texas, Robert E. Lashbrook

Earth & Environmental Sciences Theses

The Texas Department of State Health Services monitors numerous notifiable conditions statewide, including Campylobacter, Salmonella, Shiga toxin-producing Escherichia coli (STEC), Rabies, and West Nile virus (WNV). Given the substantial health, economic, and public health burden associated with these conditions, improving prediction is an important step toward reducing their overall impact. This study evaluated whether external demographic, social, climate, and environmental data could improve prediction of county-year disease activity across Texas. County level data was analyzed using supervised machine learning models, including linear regression, ridge regression, multilayer perceptron, random forest, XGBoost, as well as K-means clustering to identify broader …

Advancing Lipidomics Through Fluoroalcohol-Induced Multiphase Fractionation And Orthogonal Lc×Lc–Ms Detection, Md Al Amin

Chemistry & Biochemistry Dissertations

Comprehensive characterization of the lipidome remains a significant analytical challenge due to the immense structural diversity, wide dynamic range, and complex physicochemical continuum of lipid species. Conventional extraction methods, such as those by Bligh–Dyer and Folch, and one-dimensional liquid chromatography (1D-LC) often fail to resolve this complexity, leading to chromatographic overlap, severe ion suppression, and limited coverage of low-abundance or highly hydrophobic species. This dissertation addresses these bottlenecks by establishing a separation-driven analytical framework that integrates novel fluoroalcohol-induced multiphase systems (FAiTPS) with orthogonal multidimensional liquid chromatography–mass spectrometry (LC×LC–MS).

The core of this research is the development and physicochemical characterization of …

Influences On Student College-Major Decision And Satisfaction Rate Among Students In The School Of Agriculture, Danielle Shafer

Murray State Theses and Dissertations

The purpose of this study was to determine the factors that influence students to choose agriculture majors and agriculture careers and measure the level of satisfaction with their major based on these influences. There are many factors that influence students to choose a major in college and college-major satisfaction. These influences and satisfaction with major may have an impact on a student’s decision to choose a college career path. Some of the influences mentioned in studies are family, friends, educators, extension programs, clubs, financial, and recruitment efforts. The degree to which each of these influence students may depend on the …

Associations Between Accelerometer-Measured Physical Activity And Sleep Duration And Health Indicators In Children And Adolescents With Attention-Deficit Hyperactivity Disorder: A Systematic Review And Meta-Analysis, Xiao Liang, Hui Qiu, Justin A. Haegele, Xiao Li, Minghui Li, Jiayue Li, Shirley Xin Li

Human Movement Studies & Special Education Faculty Publications

Objective

This systematic review and meta-analysis synthesized available studies to explore relationships between accelerometer-measured physical activity (PA) levels or sleep duration and health-related outcomes in children and adolescents with attention-deficit hyperactivity disorder (ADHD).

Methods

Following the Preferred Reporting Items for Systematic Review and Meta-analyses guidelines, the six databases APA PsychInfo, CINAHL Ultimate, Embase, MEDLINE, SPORTDiscus with Full Text and Web of Science were searched from inception through July 2024. The correlation coefficient (r) was employed to determine the effect size in the meta-analysis. A random-effects model was utilised to estimate the potentially heterogeneously distributed effect sizes with a 95 % …

From Intention To Enactment: Action Planning And Habit Automaticity Distinguish Successful From Unsuccessful Intenders To Engage In Regular Leisure-Time Moderate-To-Vigorous Physical Activity, Yaogang Han, Yubing Wang, Pan Li, Binn Zhang

Human Movement Studies & Special Education Faculty Publications

University students often intend to exercise regularly but fail to translate intention into action. The present study tested which post-intentional processes distinguish successful from unsuccessful intenders in self-reported regular leisure-time moderate-to-vigorous physical activity (MVPA) enactment. Chinese undergraduates from 10 universities completed a three-wave survey administered at roughly two-week intervals. Habit automaticity was assessed at Wave 1, intention together with action planning and coping planning at Wave 2, and self-reported regular-exercise status at Wave 3. Because the dependent variable was assessed using a single stage-based self-report item, the findings should be interpreted as explaining self-reported regular-exercise status rather than objectively measured …

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.

Precision Metagenomics Reveals Microbial Landscape In Acute Upper Respiratory Infections: A Comprehensive Dataset, Sadia Almas, Rob E. Carpenter, Vaibhav K. Tamrakar, Anuradha Singh, Aditya Sharma, Rahul Sharma

Human Resource Development Faculty Publications and Presentations

Objectives The comprehension of the microbial composition in upper respiratory tract infections is pivotal for the progression of diagnostic and treatment methodologies. This article presents a dataset derived from Precision Metagenomic next-generation sequencing using hybridization capture-based targeted sequencing. Nasopharyngeal samples from 24 patients with acute URIs were analyzed using the Illumina®/IDbyDNA Respiratory Pathogen ID/ AMR panel. The dataset contains a wealth of information on the composition of the microbiota, including the relative abundance of known pathogens and their potential clinical significance. Data description This dataset serves as a valuable asset for future research in respiratory medicine, infectious disease epidemiology, antimicrobial …

Testing The Influence Of Increased Predation On The Evolution Of Morphological Coloration Plasticity In Trinidadian Killifish (Anablepsoides Hartii), Alyssa M. Laux

Biology Theses

The ability to camouflage is a widespread trait in both vertebrates and invertebrates that enhances survival in risky environments. The ability of organisms to respond to shifts in environmental conditions and change color is a conspicuous example of camouflage. Such coloration plasticity can occur rapidly (seconds to minutes) versus longer periods of time (days to months). There are numerous examples of physiological coloration plasticity (short-term) and morphological coloration plasticity (long-term). Yet, there are few tests of the conditions that drive the evolution of physiological vs. morphological coloration plasticity. In this study we use Trinidadian killifish (Anablepsoides hartii) as …

Soil Respiration Drivers And Challenges In A Changing Environment, Olivia Rae Haas

Theses, Dissertations and Culminating Projects

This study aims to understand post agricultural forested soils (sandy loam, silt loam, and loam) and the influences that drive carbon sequestration and soil respiration flux. Duke Farms in Hillsborough NJ, has historically been utilized as an agricultural zone for farming a variety of crops. Currently the area is protected with a focus on environmental conservation and restoration of the land. This includes getting a better understanding of the forested portions of the property. Understanding the quality of forested areas is vital as they have the potential to act as a carbon sink which can mitigate the effects of climate …

Effect Of Mid-Range Ultraviolet Light On Avian Embryonic Development, Keelie Hughes

Biology Theses

While it is a known fact that specific environmental conditions must be met to ensure proper embryonic development, the impact of changes in this delicate balance is unclear. Ultraviolet (UV) light has a narrow range of effectiveness in mature tissue, where too little can hinder molecular signaling and too much can cause damage to genetic material. This study exposed in ovo chicken embryos in the preliminary stages of development to mid-range UV radiation to examine developing embryo and tissue morphology using anthropometric methods and comparing proliferative cells among embryos exposed to varying doses of UV light. Additionally, quantitative polymerase chain …

The Complexities Of The Bilingual Advantage, Melisa Sierra

Behavioral Neuroscience Honors Papers

The bilingual advantage hypothesis, which proposes an enhancement of executive functions in bilinguals, remains heavily debated with inconsistent findings across studies. This study investigated working memory performance in bilingual and monolingual young adults using a modified n-back task with an interruption while recording EEG activity. Participants completed 1-back, 2-back, and 3-back conditions across the pre-interruption phase and a post-break 2-back condition. Behavioral measures (accuracy and response times) were analyzed alongside ERP, focusing on P300 and sustained activity components, were analyzed. Results showed a decrease in accuracy as task difficulty increased from 1-back to 3-back, indicating the expected effects of higher …

Triangulating Primary Sources, Professional Judgement, And Llm-Generated Summaries: Educating Nurses In An Ai-First World, Sarah Oerther, Daniel B. Oerther

Civil, Architectural and Environmental Engineering Faculty Research & Creative Works

No abstract provided.

Leveraging Research-Based Knowledge Translation Via Rural Libraries To Improve Maize Postharvest Practices In Uganda, Jackline Estomihi Kiwelu, Patrick Ngulube

Libraries

Background: Rural community libraries are increasingly recognised for providing localised knowledge, yet their potential to support agricultural extension services and improve access to postharvest knowledge in Uganda remains underexplored.
Objectives: This study examined the postharvest information needs of smallholder maize farmers and explored how community libraries can be leveraged to translate and repackage research-based knowledge to meet these needs.
Method: A mixed-methods parallel design was employed. Data were collected from a survey of 312 maize farmers, personal interviews and two focus group discussions (FGDs) with 22 extension workers and four librarians. Desk research was conducted to analyse relevant documents. Quantitative …

Fecal Microbiota Transplantation Modulates Gut Microbiota And Lipid Metabolism To Reduce Diarrhea In Low-Birth-Weight Neonatal Calves, Zhanhe Zhang, Duo You, Donglin Wu, Xintong Li, Yang Jia, David L. Harmon, Ming Xu

Animal and Food Sciences Faculty Publications

This study aimed to elucidate the mechanism by which colonic fecal microbiota transplantation (FMT) improves lipid metabolism in low-birth-weight neonatal calves via modulation of the gut microbial ecosystem. In a completely randomized design, seventy newborn Holstein calves (1 day old, 32.63 ± 3.13 kg BW) were assigned to two groups (35 calves/treatment; 30 females and 5 males per group). A healthy calf was used as a fecal donor. A 10% fecal bacterial suspension was prepared and administered colonically (50 mL, twice daily for 5 days). All calves were fed the same milk replacer and weaned using a step-down protocol at …

Hidden In The Mist: Three New Species Of Salamanders Of The Genus Pseudoeurycea (Amphibia: Plethodontidae) From Oaxaca, Mexico, Eduardo A. Aguilar-Herrera, Salomón Sanabria-Urbán, Dulce L. Flores-Martínez, José David Gómez-Tapia, Misael Seba-Chacha, Leopoldo D. Vázquez-Reyes, Francisco A. Rivera-Ortíz, Patricia Ramírez-Bastida, Bruno Cortés-Ortiz, R. Alejandro Calzada-Arciniega, Etienne U. Avila-Ortega, Dónovan I. Víquez-Vega, Omar Hernández-Ordoñez, Christopher Blair, Víctor H. Jiménez-Arcos

Publications and Research

We describe three new species of lungless salamanders (Plethodontidae) in the genus Pseudoeurycea from Cerro Rabon, located on the eastern slopes of the Sierra Mazateca, Oaxaca, Mexico. This mid-elevation mountain, largely surrounded by warmer lowlands, remains relatively understudied. We present molecular and morphological evidence distinguishing the three new species from their congeners. According to our phylogenetic analysis, one of the new species belongs to the P. leprosa group, while the other two are members of the P. juarezi group. Notably, one of the new species represents the fourth worm salamander known from west of the Isthmus of Tehuantepec, and another …

Trustworthy Multimodal Ai For Medical Imaging: Enhancing Diagnosis, Reasoning, And Human-Agent Interaction In Extended Reality, Jai Prakash Veerla

Computer Science and Engineering Dissertations

The transition from traditional microscopy to digital pathology has digitized diagnostic data, yet clinical workflows remain constrained by two-dimensional screens and passive, opaque analysis tools that fail to capture the spatial complexity of biological systems. While Foundation Models now promise to reason across histology and genomics, a critical disconnect persists between the richness of this data and the limited cognitive bandwidth of clinicians, who currently lack the immersive interfaces and trustworthy agents necessary to utilize it effectively. This dissertation presents a unified framework for "Embodied Agentic AI," establishing a pipeline that augments physician capabilities through immersive visualization, robust security, and …