Digital Commons Network^™

Agent-Based Modeling Of Cellular Dynamics In Adoptive Cell Therapies, Yujia Wang

Dissertations and Theses (Open Access)

Adoptive cell therapies (ACT) have shown promising progress in combating cancer, but clinical responses remain heterogeneous. Key determinants, including the functional states of infused cells, tumor–immune interactions, and dosing strategies, are difficult to resolve experimentally in the dynamic and heterogeneous tumor microenvironment, limiting optimization of ACT products and treatment regimens. To address the gap, we developed ABMACT (Agent-Based Model for Adoptive Cell Therapies), a computational framework that reconstruct key cellular functions, interactions, and molecular signatures to recapitulate cell population dynamics associated with differential treatment responses. ABMACT encodes autonomous “virtual cells” using literature-informed rules calibrated with experimental data, enabling simulation of …

Transcriptional Regulation In The Uterine Luminal Epithelium, Evelyn A. Carrion

Dissertations and Theses (Open Access)

Transcriptional Regulation in the Uterine Luminal Epithelium

Evelyn A. Carrion

Advisor: Richard R. Behringer, PhD

Abstract

The uterus is an organ comprised of multiple tissues that are essential for women’s health and reproduction. The uterus is composed of multiple tissue layers, including the perimetrium, myometrium, and the endometrium. The endometrium is the inner lining of the uterus, and contains the luminal epithelium, glandular epithelium, and stroma. The luminal epithelium is a simple columnar layer of cells that is necessary for embryo implantation. The uterus is derived in part from the embryonic precursor tissue called the Müllerian duct. There are no …

Oxidative Stress Mediated Glutamate Release And Nmda Receptor-Dependent Synaptic Remodeling In Radiation-Induced Cognitive Dysfunction, Thanh Lam

Dissertations and Theses (Open Access)

In children younger than 14 years old, the brain and other parts of the central nervous system are the most common sites for solid tumors. Radiotherapy is an effective treatment for central nervous system (CNS) tumors. However, it often causes a progressive decline in cognitive functions, which is especially devastating for pediatric patients. Although post-mitotic neurons are generally considered resistant to radiation-induced immediate cell death, ionizing radiation causes complex neurochemical and structural changes that damage synaptic integrity. In this study, we examined the molecular cascades following a 10 Gy radiation dose applied to mouse cortical neurons. We found that radiation-induced …

From Geometry To Recognition: A Quantitative Framework For Tcr-Pmhc Structural Analysis In The Age Of Predicted Structures, Kun Hee Kim

Dissertations and Theses (Open Access)

Recognition of antigen by a T cell begins with a single physical event, the engagement of the T cell receptor (TCR) with a peptide-major histocompatibility complex (pMHC), and this interaction is encoded in the geometry with which the receptor docks onto the composite pMHC surface. Whether that docking geometry is biologically organized, and whether the structures now produced at scale by prediction preserve recognition or only reproduce that organization, are the two questions this thesis addresses. Two gaps stand in the way. The first is a gap of measurement, because docking geometry has never been made quantitatively comparable across many …

Alfred Russel Wallace Notes 42: How Accurate Are The Transcriptions Presented At The Alfred Russel Wallace Page Website?, Charles H. Smith

Faculty/Staff Personal Papers

A look is taken at the level of accuracy displayed by the transcriptions of Wallace writings offered at the Alfred Russel Wallace Page website, as determined by a ChatGPT analysis.

A Comparison Of Survival, Growth, And Stress Resilience In Three Different Lineages Of The Pacific Oyster (Crassostrea Gigas) Farmed On The California Central Coast, Victoria F. Hanshaw

Master's Theses

Aquaculture of Pacific oysters on the US West Coast is routinely impacted by seasonal unexplained mortality events. To better understand these large-scale mortality events in oyster aquaculture, shellfish growers and scientists in California have partnered together to conduct comparative, multi-estuary farm trials of discrete Pacific oyster (Crassostrea gigas) lineages. In this thesis we investigate how the more recently imported Midori lineage performs compared to the historically used Miyagi lineage, as well as a Hybrid (Midori x Miyagi) lineage. As part of a 7-month long field study from April-November of 2024 in Morro Bay and Tomales Bay, California, we evaluated …

The Effect Of Specialty Malt On Dry-Hopping, Alexander Kivela

Master's Theses

Dry-Hopping is a modern and ever-increasing method to add hoppy flavors to beer. This is typically seen in pale ales and India Pale Ales (IPA’s). Most research has investigated the effect of dry-hopping only using pale malt, whereas most breweries used specialty malts to create a malty backbone to their beer.

The objectives of this research were to analyze the impact of specialty malts and their concentration on the efficacy of hop flavor and extraction, determined via gas chromatography and sensory analysis. Gas chromatography analysis was modeled after the ASBC Method Beer-48. Sensory analysis was performed via the 15cm line …

Comparative Assessment Of Developmental Fidelity In Hpsc-Derived Neural Crest Cells, Michael H. Zepeda

Electronic Theses, Projects, and Dissertations

Neural crest cells (NCCs) are a transient, multipotent cell population that contributes to craniofacial structures, peripheral neurons, melanocytes, and smooth muscle. Defects in NCC development underlie a broad range of congenital disorders known as neurocristopathies. Human pluripotent stem cell (hPSC)-derived NCCs provide an evaluable model for studying early human development; however, existing differentiation protocols produce variable outcomes, and no standardized method consistently generates high-fidelity NCC populations. To address this challenge, we compared five published hPSC-to-NCC differentiation protocols using the H9 human embryonic stem cell line. We hypothesized that specific protocols more faithfully recapitulate neural crest development through coordinated regulation of …

From Genes To Streams: Mitochondrial Approaches To Population Monitoring Of The Santa Ana Sucker Catostomus Santaanae, Mariana Antonio

Electronic Theses, Projects, and Dissertations

This study was developed to use aquatic environmental DNA (eDNA) as a tool to detect the presence of the Santa Ana sucker (Catostomus santaanae), a federally threatened fish species, across the Santa Ana River in Southern California. Environmental DNA is any genetic material that an organism sheds into the environment. We can get an idea of what aquatic species are present when sampling water at a given site. We sequenced the complete mitochondrial genome (mitogenome) of the Santa Ana sucker and designed custom DNA primers to improve eDNA detection accuracy. These primers were selected based on high genetic …

Testing P300-Based Biometric Authentication Paradigms, Jordan Razzak

Electronic Theses and Dissertations

Bench research suggests that P300 amplitude is greater in response to self-relevant stimuli compared to familiar stimuli. This effect could enable a novel method of biometric authentication based on the self-relevant P300. This dissertation aims to: (1) determine the optimal presentation paradigm for leveraging self-relevance in P300-based biometric authentication, and (2) investigate P300 responses from self-relevant stimuli versus stimuli learned over the course of a week.

Two presentation paradigms were compared – rapid serial visual presentation (RSVP) and matrix presentation (MP). Participant-specific RSVP and MP classifiers were trained by applying stepwise linear discriminant analysis to data collected during presentations of …

Parametric Assessment Of Nicotine Vapor Self-Administration In Rats, Tiffany Alexandra Gonzalez-Gutierrez

Open Access Theses & Dissertations

The increasing prevalence of electronic cigarette (e-cigarette) use among adolescents highlights the need to identify factors that promote nicotine vapor use in populations most susceptible to its long-term consequences. This requires translationally relevant animal models of nicotine vapor self-administration (VSA). Accordingly, the goal of this dissertation was to evaluate 2 key factors hypothesized to influence nicotine VSA in rats, including age and e-liquid vehicle composition. Given recent mandates on studying sex as a biological variable, the present work included both female and male rats. Aim 1 compared VSA behavior during adolescence (adolescent-onset) or adulthood (adult-onset) in groups that received vapor …

Advancing Management Strategies For Two Promising Mason Bee Species (Osmia Ribifloris And Osmia Bruneri) For Berry Pollination, Miranda L. Jones

All Graduate Theses and Dissertations, Fall 2023 to Present

Bee management can broadly refer to human manipulation of one or multiple parts of a bee’s lifecycle. Managing honey bees, commonly referred to as beekeeping, is responsible for providing most pollination for global food crops. However, using more than one bee species for crop pollination can have many benefits. Benefits include better crop pollination and insurance in case one bee species underperforms or its population collapses. Some bees within the genus Osmia are already widely managed for crop pollination because their developmental lifecycle allows bee managers to readily deploy pollinating bees in sync with varying crop blooms, and for certain …

Integrated Soil-Water Processes And Irrigation Management For Agricultural Water Optimization In Semi-Arid Regions, Tejinder Singh

All Graduate Theses and Dissertations, Fall 2023 to Present

Water is one of the most important resources for agriculture in the western United States. In semi-arid regions, farmers depend on irrigation to grow crops, but water supplies are becoming less reliable because of drought, declining snowpack, groundwater depletion, and increasing competition for limited water. Improving agricultural water use is therefore not simply about applying less water. It also requires understanding where water goes after it enters a field, how long it remains available to crops, and how farmers can use that information to make better irrigation decisions. This dissertation follows water through irrigated agricultural systems to better understand how …

Understanding The Impact Of Environmental Change On Shorebird Abundance And Distribution Across The Intermountain West Over The Past 30 Years, Sharon Montecino

All Graduate Theses and Dissertations, Fall 2023 to Present

Shorebirds have declined worldwide over the past century, mainly due to wetland loss and degradation. Wetlands are sites that are temporarily or permanently flooded and provide critical habitat for shorebirds, especially in arid and semi-arid regions such as the Intermountain West. However, climate change and human water use threaten these wetlands, and how these threats may affect shorebirds in this region remains poorly understood. In the early 1990s, shorebird counts at over 160 wetlands across the Intermountain West provided a broad assessment of shorebird populations in the region. These counts remained the only large-scale surveys until 2022, when the Intermountain …

The Effects Of Psychological Stress On Gut Health In Mice Fed Either A Healthy Diet Or The Total Western Diet, David Keenan Thomas Prescott

All Graduate Theses and Dissertations, Fall 2023 to Present

The Total Western Diet (TWD), a rodent diet designed to model the typical American dietary pattern, has been shown to worsen inflammation and colitis severity in mice. Psychological stress has also been associated with increased intestinal inflammation, barrier dysfunction, and alterations to the gut microbiome. The goal of this study was to determine whether combining the TWD with psychological stress would further worsen colitis severity and alter the gut microbiome. To investigate this, mice were fed either a healthy control diet or the TWD and exposed to psychological stress using a social disruption stress model. Colitis was induced using established …

Understanding Agricultural Irrigation Practices Along Utah's Wasatch Front Through Farmer-Reported Data, Garland Ledbetter

All Graduate Theses and Dissertations, Fall 2023 to Present

Water is a growing concern in Utah, especially along the Wasatch Front, where cities, farms, and communities all rely on the same limited water supply. Agriculture uses a large portion of the state’s water, so understanding how farms manage irrigation is important for statewide water planning. Utah currently uses a dataset called Water-Related Land Use (WRLU) to estimate agricultural water use across the state. This dataset provides useful information about irrigated land and crop types. However, it does not capture many of the day-to-day decisions farmers make when managing irrigation.

To better understand irrigation practices, this study surveyed 61 farmers …

Understanding And Predicting Precipitation Characteristics In The United States Through Machine Learning, Numerical Modeling And Measurements, Cody Luther Ratterman

All Graduate Theses and Dissertations, Fall 2023 to Present

Precipitation is one of the most important yet uncertain variables in the climate system. It varies dramatically in terms of timing, accumulation, rate, and phase, depending on location, season, circulation patterns, and atmospheric conditions. Precipitation forecasts, especially snowfall, are essential to supporting drought mitigation and water management in the Intermountain West. Because rainfall and snowfall lead to opposite effects on snowpack, accurately partitioning rain and snow is important to estimate snowpack levels, winter recreation, mountain ecosystems and runoff. The research findings in this dissertation have advanced the understanding and prediction of precipitation and snowpack in the U.S. by addressing the …

The Role Of Individual Specialization In Migration Phenology And How Restored Habits Are Used By Native And Nonnative Fishes, Austin Garner

All Graduate Theses and Dissertations, Fall 2023 to Present

Native fish species around the world have declined due to habitat loss, habitat fragmentation, and the spread of non-native species. Because these problems often happen at the same time and interact, recovery efforts can stall unless they address all of the factors limiting a species' comeback. The June sucker (Chasmistes liorus), native only to Utah Lake, UT, has declined for many of these reasons, though its recovery effort has made significant progress due in large part to a successful hatchery program. Yet, the recovery efforts have not yet been able to establish a self-sustaining population in Utah Lake, …

The Influence Of Habitat And Individual Specialization On Mountain Lion (Puma Concolor) Hunting Strategy In A Multi-Prey System, Hannah B. Klugman

All Graduate Theses and Dissertations, Fall 2023 to Present

There is a growing recognition that animal species considered generalists (having a broad and varied diet), are actually specialists, a collection of individuals with different preferences and strategies known as specializations. The diet of a specialist depends on the variety and quantity of available food options, and their own ability to take what they need. Mountain lions (Puma concolor) are known for their ability and tendency to hunt large prey, such as elk (Cervus canadensis) and mule deer (Odocoileus hemionus), but despite the fact they overlap with other potential large prey, like feral horses …

Integrative Taxonomic Analysis Of Cryptic Species Diversity In The Spiny Witch-Hazel Gall Aphid, Hamamelistes Spinosus (Hemiptera: Aphididae: Hormaphidini) In Eastern North America, Gavin Andrew Powell Munson

All Graduate Theses and Dissertations, Fall 2023 to Present

Taxonomy is the practice of identifying, classifying and categorizing species, providing structure for the vast diversity of life. Aphids are an ecologically important group of soft-bodied insects, but they can be difficult to identify because of their tiny anatomical size, reduced or simplified morphological features, and morphological variation within a single species across different generations. In this study, the taxonomy of the spiny witch-hazel gall aphid, Hamamelistes spinosus, is revised. The complex multi-generational life cycle of the aphids, which alternates between witch-hazel and birch trees, has led to confusion regarding past descriptions. Scientists in the late 1800s who were …

Formulation And Analysis Of Physiochemical And Sensory Properties Of Ready-To-Mix Whey Protein Phospholipid Concentrate Beverage, Chris Jaquin

All Graduate Theses and Dissertations, Fall 2023 to Present

Whey protein phospholipid concentrate (WPPC) is commonly recovered as a coproduct in filtration process whose aim is to obtain whey protein isolate (WPI) from whey protein concentrate (WPC). Whey protein phospholipid concentrate is high in milk fat globule membrane (MFGM), which has been shown in rodent and human studies to have a variety of physiological benefits, including an increase in exercise capacity. Whey protein phospholipid concentrate is currently considered as an underused dairy coproduct, with most of it either being disposed of or used as animal feed. This research consisted of incorporating WPPC in a protein shake–like beverage at a …

Seizure Susceptibility And Morphological Analysis Of A Missense Mutation In Hcfc1a Protein, Jose Manuel Fabela

Open Access Theses & Dissertations

Missense mutations in the HCFC1 gene cause methymalonic acidemia with homocystinuria cblX type (MIM#309541). cblX is an X-linked disorder that is associated with multiple phenotypes such as metabolic defects, failure to thrive, intractable epilepsy, facial dysmorphia, movement disorders, and intellectual disability. The mechanisms underlying these phenotypes are not completely understood. Here we used a zebrafish germline mutant allele (hcfc1aco64/co64) to study seizure susceptibility and adult brain structural malformations. Previous studies have established neural progenitor cell defects and hypoactive mechanistic target of rapamycin (mTOR) in this allele. Given the known role of mTOR in seizure phenotypes, we hypothesized that missense mutation …

An Analysis Of Mating Strategies In Rotifers Inhabiting Temporary Habitats, Ariel Bollinger

Open Access Theses & Dissertations

Reproduction is critical for organisms inhabiting ephemeral aquatic habitats where desiccation risk favors rapid and successful mating. Monogonont rotifers rely on sexual reproduction to produce diapausing eggs that withstand harsh conditions. I investigated how mating behaviors vary among populations of five rotifer species based on the hydroperiod of their habitat: Epiphanes brachionus and E. chihuahuaensis were sampled from habitats with short (SH) and long (LH) hydroperiods; Euchlanis dilatata was collected from a short (SH) and a permanent habitat; and Plationus patulus and Sinantherina socialis were collected from a long (LH) and a permanent (Perm) habitat. I hypothesized that SH populations …

Secondary Biology Teachers’ Understandings Of Growth Mindset, Kathryn Chapman

Dissertations

This case study investigates how high school biology teachers understand and apply growth mindset principles in their daily instruction. Using surveys, semi‑structured interviews, and focus groups, the study examines how biology teachers interpret mindset, how they attempt to enact it, and how curriculum demands shape their efforts. Findings show that teachers’ beliefs about intelligence strongly influence their feedback, expectations, and instructional decisions. Teachers described biology as a subject in which struggle is highly visible, emotionally charged, and often tied to students’ prior knowledge, making mindset work both necessary and challenging. Results also indicate that students’ mindsets are shaped by broader …

The Effect Of Cerebellar Transcranial Direct Current Stimulation On Anxiety, Shivangi Bhardwaj

All-Inclusive List of Electronic Theses and Dissertations

Anxiety is one of the most prevalent mental health disorders in the U.S. Individuals of all ages are affected by anxiety. Therefore, research into anxiety and its potential treatment has constantly been an area of interest. Newer approaches to managing anxiety include non-invasive stimulation techniques, such as Transcranial Direct Current Stimulation (tDCS), because of its accessibility and effectiveness. Past tDCS work typically focused on regions in the frontal lobe. However, tDCS over the cerebellum has not received as much attention compared to the cerebrum, despite recent work demonstrating cerebellar involvement in emotion processing. Thus, a better understanding of how cerebellar …

Trace Element Concentrations In Tissues And Otoliths Of Fishes From Artificial Reefs In The Northern Gulf Of Mexico: The Role Of Size, Age, And Trophic Position, Blaine Savoie

LSU New Orleans Theses and Dissertations

Nearshore artificial reefs and fishes relying on them to forage and refuge can be susceptible to trace element (TE) pollutants from anthropogenic sources. Although some TE are essential, higher concentrations can cause detrimental effects and concern regarding consumption. This study assesses TE accumulation in nearshore reef fishes in the northern Gulf of Mexico, a region influenced by coastal riverine discharge, where fishing has socioeconomic importance. Five fish species from six eco-reefs were collected and analyzed for TE. An inductively coupled plasma mass spectrometer was used to analyze the TE concentrations of muscle, liver, and otoliths. TE concentrations of tissues and …

Extinction Risk Of Coral Reef Fishes In The Philippine Marine Ornamental Trade, Jemelyn Grace Baldisimo Sepulveda

Biological Sciences Theses & Dissertations

Coral reef ecosystems in the Philippines face severe threats from intense fishing and habitat degradation. This dissertation evaluated the extinction risk of fishes in the Philippine Marine Aquarium Trade (MAT) using Productivity Susceptibility Analysis (PSA) and temporal genomics. A global PSA framework was modified by including local susceptibility factors. Of the 103 species evaluated, six were categorized as highly vulnerable and 62 as moderately vulnerable, revealing increased local vulnerability and underscoring the importance of local assessments to guide conservation efforts.

Temporal genomics compared historical (1908–1909 U.S.S. Albatross Expedition) and contemporary populations of the MAT-targeted Sphaeramia nematoptera and Pseudanthias squamipinnis, …

Physiological, Cognitive, Behavioral, And Perceptual Contributors To Falls Risk Across Middle And Older Adulthood, Jacquelyn Moxey

Rehabilitation Sciences Theses & Dissertations

Falls are multifactorial events influenced by physiological, cognitive, behavioral, and perceptual factors. Although falls prevention research has traditionally focused on older adults and objectively measured physical impairments, less is known about how cognitive performance, physical activity, and perceptions of ability collectively contribute to falls risk vulnerability across middle and older adulthood. This dissertation examined these relationships through three complementary studies.

Study 1 examined associations between cognitive screening performance and physiological falls risk in 315 community-dwelling older adults. Lower global cognitive performance was associated with greater physiological falls risk. Performance on items reflecting attention and visuospatial/executive function demonstrated the strongest domain-level …

Long-Term Spatiotemporal Change In Coral Reef Fish Populations And Communities In The Philippines, John Christopher Whalen

Biological Sciences Theses & Dissertations

The Visayas Region of the Philippines is a global epicenter of marine fish biodiversity. Hypotheses attribute this peak of species richness within the Coral Triangle to processes that occur at geological time scales. However, changes in biodiversity may occur on ecological time scales, allowing for the assessment of the potential impact of anthropogenic activities. Recent declines in genetic, species, and ecosystem diversity have been observed in the tropics, including the Philippines. Within the Philippines the Visayas Region is considered the epicenter of species adversity due to anthropogenic stressors such as habitat degradation, overfishing, and harvesting individuals for the aquarium trade. …

Computational And Ai Tools For Understanding Telomere-Associated Cancer Mechanisms, Eleni Adam

Computer Science Theses & Dissertations

Telomeres are the protective caps of the human chromosomes and are critical for genome stability. Dysfunctional telomeres caused by their erosion with age and cell proliferation as well as by defects in their maintenance is a major early event leading to genome changes and cancer. Subtelomeres possess the critical role of regulating adjacent telomeres. Due to their complex repeat structure and high variance from one person to another, these areas have not been analyzed in detail. We present a set of computational and machine learning tools to aid in the understanding of subtelomere structure and its rearrangements in cancer.

Initially, …