Physical Sciences and Mathematics Commons^™

Quantitative Surface-Enhanced Raman Spectroscopy For Antiretroviral Drug Monitoring: Novel Quality Index And Distributional Approaches In Aqueous And Plasma Matrices, Marguerite Rose Butler

Chemistry & Biochemistry Theses & Dissertations

Surface-enhanced Raman spectroscopy (SERS) offers high sensitivity for molecular detection but is limited for quantitative applications by spatial heterogeneity in signal enhancement on dried colloidal substrates. This Dissertation addresses these limitations through the development and evaluation of novel quantitative methods applied to the antiretroviral drugs tenofovir and emtricitabine.

A quality index (Qi) metric was developed to rank individual SERS spectra within each well based on analyte peak prominence relative to local baseline. SERS spectra were acquired from evaporated silver colloid deposits on aluminum well plates using a custom raster-scanning Raman system. Calibration curves were constructed using the top-ranked spectra (Top-Qi …

Variability In Nutrient And Enterococcus Concentrations In Tidal Floodwater Across Watersheds With Different Land Uses, Alyssa Bucci

OES Theses and Dissertations

Tidal flooding is an increasingly pressing hazard in coastal Virginia due to sea level rise and land subsidence. The Hampton Roads region of Virginia has the second-highest rate of relative sea level rise in the United States and experiences frequent tidal flooding, but the water quality impacts of this flooding on the Chesapeake Bay are not being accounted for. High concentrations of dissolved nutrients and Enterococcus bacteria (a fecal indicator) have been observed in tidal floodwater of the Lafayette River, a tributary of the James River and the lower Chesapeake Bay. This study investigates variability in dissolved nutrient and Enterococcus …

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, …

A Large And Robust Legless Lizard (Squamata, Anguinae) From The Gray Fossil Site Of Eastern Tennessee, Justice D. Lamer

Electronic Theses and Dissertations

The early Pliocene Gray Fossil Site in Tennessee preserved an abundance of microfossils, including numerous anguid lizard specimens. This includes the following elements: dentaries, a pterygoid fragment, a jugal, frontals, parietal fragments, dorsal and caudal vertebrae, and many osteoderms. Because these specimens had not been placed taxonomically beyond the subfamily level, comparative anatomy of similar elements from extant anguids and some quantitative data were used to provide more refined identifications. Using these methods, it was determined that a new, robust type of Ophisaurus is represented at the Gray Fossil Site. Important novel features include relatively robust dentaries, fewer but broader …

Viability Assessment Of Bovine Embryos: A Public Dataset And Deep Learning Baselines, Erfan Khayyati

All Graduate Theses and Dissertations, Fall 2023 to Present

Improving the success rates of cattle breeding is essential for sustainable agriculture, global food security, and high-quality livestock production. Currently, determining whether a lab-grown bovine embryo is healthy enough for a successful pregnancy requires highly trained experts to manually evaluate days of continuous time-lapse video footage. This process is not only incredibly time-consuming but also highly subjective; human reviewers often suffer from visual fatigue when tracking subtle, microscopic cellular changes over a seven-day period, leading to significant disagreement among even top experts on an embryo’s true potential. Furthermore, assessing bovine embryos is notoriously difficult due to their dark, lipid-dense cellular …

Integrating Hydrology And Human Water Footprints: A Case Study Of The Great Salt Lake Basin, Rachel Lynne Seeley

All Graduate Theses and Dissertations, Fall 2023 to Present

Global demand for water is outrunning supply, and how we account for water is part of the problem. Many water management frameworks are based solely on how much physical water moves through rivers, aquifers, and other water bodies, missing the water that is embedded in food and other products a region produces and exports. This study developed a new, generalizable water accounting framework that incorporates this “hidden water,” known as virtual water, into water management and applied the framework in the Great Salt Lake Basin.

The Great Salt Lake is shrinking, and an often-overlooked driver of the lake’s decline is …

Spatial Prediction Under Uncertainty: Methodological And Computational Advances In Bayesian Maximum Entropy, Kinspride K. Duah

All Graduate Theses and Dissertations, Fall 2023 to Present

Environmental decisions such as infrastructure design, water management, and snow load estimation depend on spatial data that are often incomplete or uncertain. In many cases, measurements are not exact values but ranges, reflecting limitations in data collection methods. Traditional mapping techniques typically simplify these uncertain measurements, which can lead to less accurate predictions. This dissertation introduces improved statistical tools for making spatial predictions when data are uncertain or partially known. By utilizing a framework called Bayesian Maximum Entropy (BME), this research demonstrates how exact measurements and range-based data can be combined in a mathematically consistent way. The work demonstrates that …

Unifying And Expanding Global And Local Variable Importance Methods For Explainable Machine Learning, Kelvyn K. Bladen

All Graduate Theses and Dissertations, Fall 2023 to Present

Machine learning methods are powerful analytical tools used across all scientific disciplines and many other fields of investigation for prediction and inference from diverse data sources. Despite their broad applicability, machine learning methods are often highly complex and difficult to interpret. Developing a greater understanding of which variables most influence a response is essential for increasing the interpretability of these models and supporting informed decision-making. This research focuses on improving how we evaluate the importance of these variables.

One common approach is to shuffle the values of a variable and see how much the model accuracy gets worse. Another approach …

Learning Latent Structure In High-Dimensional Data Via Geometry And Graphs, Haozhe Chen

All Graduate Theses and Dissertations, Fall 2023 to Present

Modern datasets often contain many measured variables for each observation, such as gene-expression levels, brain activity signals, or features in tabular data. These data are also often noisy, meaning that useful patterns are mixed with measurement error or irrelevant variation. Although such datasets can appear complex, they are frequently represented by simpler hidden structures, such as trajectories, clusters, or relationships between observations. This dissertation develops methods for uncovering these hidden structures by learning geometric and graph-based representations directly from data. The first part introduces Functional Information Geometry, which represents local patterns in high-dimensional data using functional features and constructs a …

Pesticide Dissipation In Agroecosystems – Exploring Pesticide Fate And Transport Mechanisms To Protect Alternative Pollinators, Calvin Luu

All Graduate Theses and Dissertations, Fall 2023 to Present

Honey bees are the most well-known pollinators, but there exists thousands of other bee species that contribute to pollination; one such group of bees are the solitary bees. True to their namesake, solitary bees do not live in hives like honey bees. Some solitary bees, like alfalfa leafcutting bees (ALCB) and blue orchard bees, can pollinate crops more efficiently than honey bees. However, since they live solitary lives, pesticide exposure is much more harmful to their overall population. If one honey bee dies from pesticide exposure, the hive can still survive, and the queen bee will continue producing offspring. If …

Hidden Symmetries And Higher Dimensional Rotating Black Holes, Luis Fernando Temoche Hurtado

All Graduate Theses and Dissertations, Fall 2023 to Present

A standard approach to probing the dynamics of a physical system is to expose it to an external perturbation—such as an incident wave—and analyze its response after the interaction. Mathematically, this procedure is formulated in terms of differential equations governing the evolution of the perturbation.

In the context of black hole physics, an analogous strategy can be employed by studying the response of the event horizon to external perturbations. The differential equations describing these interactions are often invariant under nontrivial transformations, revealing hidden symmetries that help explain distinctive features of higher-dimensional black holes.

By exploiting these hidden symmetries in the …

Method Validation Of The Cdc Bottle Bioassay And A Historical Record Of Polycyclic Aromatic Hydrocarbons In Glacier National Park, Evah F. Peard

All Graduate Theses and Dissertations, Fall 2023 to Present

Certain contaminants can persist in the environment for long periods of time, build up within living tissues, travel far from their origin, and harm both ecosystems and organisms. This thesis focuses on two types of contaminants: insecticides and polycyclic aromatic hydrocarbons (PAHs). Insecticides are manufactured to control pests while PAHs are found in oil and gas products and can be produced by industry, vehicle engines, and wildfires. Understanding how harmful these contaminants are and where they end up in the environment is critical for protecting environmental health.

First, I evaluated a widely used test developed by the Centers for Disease …

Applications Of Machine Learning To Gas Plume Analysis In Longwave Infrared Hyperspectral Images, Scout C. Jarman

All Graduate Theses and Dissertations, Fall 2023 to Present

Each pixel from a hyperspectral camera measures the intensity of light over a continuous range of wavelengths, which is in contrast to traditional color cameras, which just measure the intensity of red, green, and blue wavelengths of light. Longwave infrared hyperspectral images can be used to detect gases from a distance by measuring how different materials emit and absorb heat. This makes them useful for applications such as monitoring industrial emissions or locating hazardous gas leaks. In practice, however, gas signatures in these hyperspectral images are often weak and easily obscured by variations in the background scene, making reliable identification …

Assessing Ecological Integrity Of Streams Across The Western U.S., Jennifer L. Courtwright

All Graduate Theses and Dissertations, Fall 2023 to Present

Large-scale assessments of stream health (ecological integrity) are required by policies such as the U.S. Clean Water Act and provide critical information needed to properly manage public lands. Our ability to quantify the ecological condition of streams in the western U.S. and identify the causes of degraded conditions has previously been impeded by a lack of standardized large-scale datasets, high natural temporal and spatial variability of ecological attributes, and poor-quality land use data. I compiled large-scale monitoring datasets and built models to predict the values of ecological attributes (metrics) at a given site in the absence of human impacts. In …

The Role Of Heterogeneity In Earthquake Rupture Dynamics: Insights From Friction Experiments On A 1-Meter Laboratory Fault, Alejandro Aguilar

All Graduate Theses and Dissertations, Fall 2023 to Present

Tectonic faults are made of many kinds of rocks and minerals, creating natural weak and strong zones along faults where earthquakes occur. These differences can affect how faults move, including whether slip occurs slowly and quietly or suddenly and destructively during an earthquake. However, it is not fully understood how these variations influence when earthquakes start, how fast they spread, and whether they stop or grow into large ruptures. This research studies how different fault materials interact during earthquake slip. Using a large laboratory machine that simulates fault movement under realistic conditions, we recreate earthquake processes and closely measure how …

Investigation Of Yy Production Methods For Invasive Channel Catfish Ictalurus Punctatus Population Management, Andrew M. Wisniewski

All Graduate Theses and Dissertations, Fall 2023 to Present

Aquatic invasive species are one of the leading causes of native fish declines in the Southwestern United States. Channel Catfish Ictalurus punctatus were introduced into the Colorado River Basin, including the San Juan River, New Mexico, Colorado, and Utah for fishery enhancement during the 20th century. This introduction has contributed to the decline of native species and despite intensive mechanical removal efforts, the Channel Catfish population has persisted in the San Juan River. The Trojan Sex Chromosome approach is a promising eradication strategy that proposes the production and release of Trojan sex chromosome carriers (YY) to skew a targeted population’s …

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 …

Counterfactual Explanations For Time Series Classification: From Localized Perturbations To Realistic Generation, Peiyu Li

All Graduate Theses and Dissertations, Fall 2023 to Present

Machine learning models are often used to classify signals collected over time, such as heart rhythms, movement recordings, industrial sensor measurements, and scientific observations. These models can be accurate, but they are often difficult to understand. Users may need to know not only what a model predicted, but also what would have needed to change for the model to reach a different decision.

This dissertation studies counterfactual explanations for time series data. A counterfactual explanation answers a “what-if” question. For example, if a model classifies a signal as one activity instead of another, the explanation shows how the signal would …

Mapler: An R Package For Estimating The Impact Of Climate Change On Maple Syrup Production, Matthew T. White

All Graduate Theses and Dissertations, Fall 2023 to Present

Successful maple sap tapping depends on the freeze/thaw cycle (i.e., temperatures fluctuating above/below freezing) during the winter and spring. Climate change threatens to alter the timing and duration of the tapping season. This necessitates research into how maple sap tapping will be impacted by climate change in order to help maple syrup producers prepare for the future. We define a sap day as a day where the freeze/thaw cycle occurred. Using information climate scientists use to predict future temperatures, we calculate how many sap days could occur each year. We develop software to analyze these sap day calculations to determine …

Causal Discovery In Photospheric Magnetic Field Time Series For Interpretable Solar Flare Prediction, Nathan W. Nelson

All Graduate Theses and Dissertations, Fall 2023 to Present

Solar flares are capable of damaging many valuable resources, including satellites, power grids, and even human lives. Being able to predict solar flares can allow for proactive measures to be taken that can prevent that damage. Many new deep learning methods for predicting solar flares have shown promise in this task, but the decisions they make are harder to explain to humans. This makes understanding why these models make mistakes difficult, which in turn makes fixing and maintaining them more challenging. We test a recent deep learning method that helps discover relationships between different measurements of the Sun as they …

A Data-Driven Nutrient Density Scoring Framework For Beef Using Principal Component Analysis, Teja Vuppala

All Graduate Theses and Dissertations, Fall 2023 to Present

Beef is one of the most nutrient-rich foods in the human diet, providing high-quality protein, iron, omega-3 fatty acids, B vitamins, and a wide range of other compounds important to health. However, current nutrition scoring systems used on food labels were designed to compare different foods to one another — for example, beef versus broccoli — and do not work well for judging the nutritional quality of different beef samples relative to each other. A grass-fed steak and a conventionally-finished steak can carry nearly identical Nutrition Facts panels while differing substantially in their content of omega-3 fatty acids, vitamins, and …

Glioma Segmentation In Mri Using A 3d Hybrid U-Net With Adaptive Self-Attention And Multi-Modal Fusion, Evan P. Savaria

Computer Science Theses & Dissertations

Accurate glioma segmentation from multi-modal Magnetic Resonance Imaging (MRI) is essential for diagnosis, treatment planning, surgical guidance, radiation targeting, and longitudinal monitoring. MRI modalities such as T1, T1Gd, T2, and FLAIR provide complementary information for identifying clinically important tumor sub-regions, including enhancing tumor (ET), tumor core (TC), and whole tumor (WT). However, many existing segmentation methods do not fully preserve modality-specific information, process all modalities and slices uniformly, and often rely on a single shared fusion strategy for all sub-regions. These limitations can reduce segmentation accuracy, increase computational cost, and limit clinical interpretability.

This dissertation addresses these challenges through three …

The Role Of Phenotypic Plasticity And Bet-Hedging In Coping With Unpredictable Temperature Fluctuations In The Marine Annelid Ophryotrocha Labronica, Gabrielle Dawn Newton

Biological Sciences Theses & Dissertations

Coastal ecosystems are increasingly exposed to unpredictable temperature fluctuations, potentially favoring strategies that buffer populations against environmental uncertainty. This study examines how phenotypic plasticity and diversified bet-hedging contribute to variation in life-history traits under differing thermal predictability in the marine annelid Ophryotrocha labronica. After three generations at 24 °C, broods were reared for three generations under four thermal regimes: constant 24 °C (C24), constant 27 °C (C27), predictable fluctuations (Fp), and unpredictable fluctuations (Fu). Survival was assessed before and after acclimation to evaluate selective pressure among regimes. Age at maturity, fecundity, and growth rate were used to quantify plasticity (trait …

Modeling And Generating Crash Avoidance Behaviors In Safety-Critical Vehicle–Pedestrian Interactions Using Deep Reinforcement Learning, Qingwen Pu

Civil & Environmental Engineering Theses & Dissertations

Traffic crashes between vehicles and pedestrians arise from complex, split-second interactions in which both parties make rapid evasive decisions. Four fundamental gaps persist in existing research. Surrogate safety measures assume linear trajectories, failing to capture the curved movements of turning vehicles and crossing pedestrians at intersections. Single-agent modeling treats one party as a fixed obstacle, ignoring the joint decision-making that governs near-miss outcomes. The effect of vehicle type on pedestrian avoidance behavior—whether pedestrians respond differently to automated vehicles (AVs) than to human-driven vehicles (HDVs)—remains poorly understood. Finally, automated driving system development is hampered by a severe scarcity of large-scale, behaviorally …

Developing Solvent Tolerant Microbial Membranes: Lipid Extraction And Laurdan Fluorescence Approaches For Biofuel Optimization, Gladstone Anku

Electronic Theses and Dissertations

The high demand for sustainable energy has increased interest in advanced biofuels, though production is limited by solvent toxicity to microbial hosts. This study investigated the role of lipid composition in modulating membrane fluidity and solvent tolerance using Bacillus subtilis as a model organism. Five strains were cultured, and membrane lipids were extracted and analyzed using thin-layer chromatography and gas chromatography–mass spectrometry; however, inconsistent results limited compositional characterization. To address this problem, reconstituted vesicles composed of phosphatidylglycerol (PG) and phosphatidylethanolamine (PE) were used as model membranes. Membrane fluidity was assessed using Laurdan fluorescence spectroscopy by measuring generalized polarization (GP) values …

Predicting Student Belonging In Computing Education: A Multimodal Machine Learning Approach Using Eeg And Survey Data, Hannah Moshtaghi

Master's Theses

Measuring students’ sense of belonging, characterized by feelings of acceptance, inclusion, and encouragement from teachers, remains a significant challenge in computing education. Prior research has associated this multidimensional construct with positive academic outcomes and has identified instructors’ growth- and fixed-mindset messaging as a potential influence. However, belonging is a complex and deeply personal experience that is difficult to capture through direct observation alone. Current measurement methods rely on self-report surveys, which may not capture every aspect of an experience that can also involve emotional and cognitive responses.

This thesis investigates whether combining EEG data recorded during a belonging questionnaire with …

Synthesis And Characterization Of Carbon Quantum Dots And Gold Nanoparticles For Norovirus Biosensing Applications In Water Systems, Breanne Evans

Master's Theses

Rapid, reliable detection of viral pathogens remains a significant challenge across water-treatment and environmental monitoring systems, including drinking-water, wastewater, water reuse, and environmental surveillance applications. Waterborne viral contamination can pose substantial public-health risks, making early detection essential for protecting water quality and responding quickly to treatment failures or contamination events. Direct potable reuse (DPR) is one particularly demanding example because it requires continuous verification of treatment performance and the broader need for rapid virus monitoring extends across many water-treatment and environmental surveillance applications. Norovirus is a priority target because of its widespread occurrence in wastewater, environmental persistence, and exceptionally low …

Comparing 3-Connectedness And Roundness In Matroid Theory, Blanca Delia Larios

Electronic Theses, Projects, and Dissertations

A matroid is a discrete mathematical object that abstracts and connects the various notions of independence found throughout mathematics. Such notions of independence include linear independence, algebraic independence, as well as notions of independence that arise in graph theory. There are many broad classes of matroids. Important examples include binary matroids, graphic matroids, regular matroids, uniform matroids, and various levels of connected matroids. Some of the most important problems in matroid theory involve characterizing classes of matroids so that such characterizations can be used to prove results concerning these matroid classes. This thesis is a study of two important classes …

The Relativity Of Education: Student Perspectives On Artificial Intelligence In Community College, Ashley Greta Magana

Electronic Theses, Projects, and Dissertations

This hermeneutic phenomenological study examined how diverse community college students experience and make meaning of the integration of generative artificial intelligence (AI) into their educational contexts. Although AI is quickly transforming higher education through automated grading, personalized learning systems, and new models of assessment, the discourse surrounding its implementation remains dominated by administrators, faculty, and institutional stakeholders, while the perspectives of students, specifically community college students who are often historically underrepresented and economically marginalized, are systematically excluded. Most existing research is quantitative and centered on universities, leaving a critical gap in qualitative understanding of the most diverse population in higher …

Painting A Scene: 3d Painterly Rendering From Curves To Rebelle, William M. Luttrell

All Theses

Stylized 3D rendering has seen much development and success over the past few years. From Spider-Man: Across the Spider-Verse to The Bad Guys, many studios have developed tools to incorporate stylistic elements from graphic novels, comic books, watercolor paintings, and more into their productions. This stylization process incorporates the pacing, visual style, and themes from the source medium into the animated work, allowing a much greater freedom of expression for artists and directors.

Inspired by these films as well as the needs of the short film Kate Shelley and the Bridge of Darkness currently in production, This paper presents …