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A Coupled Reaction-Diffusion Model Of Promoting And Suppressing Interactions Among Cancer Hallmarks In Endometrial Cancer, Jeddy Bennett

Theses and Dissertations

Spatial transcriptomics enables the scoring of Cancer Hallmarks at a high resolution across a tissue biopsy, yet current analyses of these data remain largely descriptive, treating each spot as a static, independent observation. This thesis develops a coupled system of advection-diffusion-reaction partial differential equations to model the hallmark landscape as the steady-state solution of an underlying spatial process, and casts the recovery of its physical parameters as a PDE-constrained inverse problem. The framework is implemented in FEniCSx on tissue-specific finite element meshes derived from two endometrial cancer biopsies provided by the Huntsman Cancer Institute, with subdomains, boundary interfaces, and an …

65th Annual Rocky Mountain Conference On Magnetic Resonance

Rocky Mountain Conference on Magnetic Resonance

Conference program, abstracts, and information about the 65th annual meeting of the Rocky Mountain Conference on Magnetic Resonance. Held in the Snowbird Resort and Conference Center, Snowbird, Utah, August 2-6, 2026.

Process From Noise: Erosion Threshold Variability And The Morphology Of Gravel-Bed Rivers, Robert Paul Kostynick

Arts & Sciences Graduate Student Theses and Dissertations

Rivers are remarkably consistent as their geometry, width, depth, and slope change systematically downstream in response to differences in fluid discharge and sediment transport throughout a channel. Rivers move both water and sediment through terrains that depend on these downstream geometric adjustments influencing water quality, ecology, infrastructure, channel morphology, and landscape evolution at increasing timescales respectively. Rivers thus influence all aspects of life and define our spatial landscapes that shape boundaries, whether physical, politically, or socially. Nevertheless, a river is dynamic and does not adhere to human-defined boundaries, making it vital that we understand how these features change over time …

Dry After-Ripening Increases Germination Of Critically Imperilled Physaria Thamnophila (Zapata Bladderpod), Christopher A. Gabler, Jerald T. Garrett

School of Earth, Environmental, & Marine Sciences Faculty Publications

Effective endangered plant conservation and recovery require empirical knowledge of seed dormancy release and responses to post-collection handling, yet such information is lacking for many rare taxa. Physaria thamnophila (Zapata bladderpod; Brassicaceae), a critically imperilled (G1) species endemic to southern Texas, USA, is poorly studied, and basic questions regarding seed storage and germination remain unresolved. We evaluated the effects of short-term cool-storage duration (14–180 d), storage temperature (refrigeration vs. freezing), dry after-ripening and maternal plant identity on germination probability and timing in P. thamnophila. Dry after-ripening and increased cool-storage duration consistently increased germination and shortened germination time, whereas storage temperature …

Dynamics Of Microscale Droplets In Respiratory Airways, Md Shamser Ali Javed

Mathematics Theses and Dissertations

We investigate trajectories of microscale evaporating droplets in a stagnation point flow near a wall of a respiratory airway. The configuration is motivated by the problem of advection and deposition of microscale droplets of respiratory fluids in human airways during transmission of infectious diseases such as tuberculosis and COVID-19. Laminar boundary layer equations are solved to describe the air flow while the equations of motion of the droplet include contributions from gravity, aerodynamic drag, and Saffman force. Evaporation is accounted for at both the droplet surface and the wall of the respiratory airway and is shown to delay droplet deposition …

Algebraic And Topological Methods In Computational Neuroscience, Trong-Thuc Trang

Electronic Theses and Dissertations

Neural data is incredibly rich in combinatorial, topological, and geometrical information, reflecting the intricate shape and connectivity of neural firing patterns. To decipher these structures, neuroscience increasingly relies on advanced mathematical tools to analyze neural activity. Here we study (1) neural codes within the poset P_Code of neural codes and (2) the connectivity of neural population activity within the insular cortex when responding to interoceptive information. In (1), we establish combinatorial constructions for all upward covering relations based on what we call “isolated subsets” with supporting theorems and give a slight modification of the existing downward covering relations. We …

Single Fluorogens And Orientation-Localization Microscopy For Quantifying Chemical And Biomolecular Dynamics At The Nanoscale, Yiyang Chen, Yuanxin Qiu, Matthew D. Lew

Electrical & Systems Engineering Publications and Presentations

Many chemical systems look uniform only because ensemble measurements average over their most interesting molecules. Electron-transfer rates vary across electrode surfaces; lipid membranes contain nanodomains with distinct packing and fluidity; peptide aggregates exhibit local polymorphism; and biomolecular condensates contain transient networks of interactions that are blurred in ensemble images. A central challenge in chemical imaging is not simply to see smaller structures, but to measure chemical variables such as polarity, redox potential, and molecular confinement at the single-molecule level. In this Account, we describe how fluorogens, molecules whose brightness, blinking, spectral shifts, orientation, rotational mobility, and motion are directly shaped …

Toroidal Plasmonic Nanodimers For Enhanced Near-Infrared Emission In Heterostructured Inp Quantum Dots, Arda Gülücü, Emre Ozan Polat

Turkish Journal of Physics

Near-infrared (NIR) emitters operating in the 650--900 nm spectral range are highly attractive for imaging and sensing in turbid media. However, cadmium-free InP-based quantum dots (QDs) often exhibit limited brightness owing to nonradiative recombination pathways and inefficient photon outcoupling. In particular, heterostructured InP QDs may possess band alignments that induce partial spatial separation of charge carriers, thereby reducing the electron-hole wavefunction overlap. This characteristic modifies the intrinsic recombination dynamics and increases the sensitivity of their emission to the surrounding photonic environment. Here, we investigate silver toroidal plasmonic nanoantenna dimers (Ag TPNDs) using finite-difference time-domain (FDTD) simulations as a geometry-tunable platform …

Design And Fabrication Of Petri Dish Optimized For High-Frequency Acoustic Microscopy Using 3d Printing, Tuna Pesen, Beyza Ceren Eren, Arda İnanç, Bora Akgün

Turkish Journal of Physics

High-frequency imaging in acoustic microscopy requires the use of Petri dishes with thin and acoustically transparent bottoms to minimize signal attenuation and distortion. Commercially available options suitable for this purpose are often expensive or limited in compatibility with custom setups. Here, we present a cost-effective and easily customizable alternative developed in our laboratory, consisting of a 3D-printed frame combined with commercially available stretch film. The stretch film serves as an ultrathin (8 µm thickness) base that supports efficient high-frequency acoustic transmission, enabling clear and reliable imaging. Beyond acoustic microscopy, the adaptable design is also compatible with other modalities such as …

Changes In Water Quality And Microbiota Over Two Years In Florida Hard Clam (Mercenaria Mercenaria) Hatcheries, Bonnie Getter

Electronic Theses and Dissertations

This thesis characterized the water quality and bacterial communities in nine hard clam hatcheries over two production years through weekly or biweekly water quality and chemistry monitoring, monthly bacterial plating in the second year of production, and select 16S microbiome sampling at select hatcheries to address production bottlenecks and support the reliable production of high-quality seed for Florida’s growing hard clam aquaculture industry. Logistic regression models showed that water source was distinguished by pH, salinity, alkalinity, and nitrite, whereas geographic location was distinguished by temperature, salinity, nitrate, and calcium; temperature, dissolved oxygen, salinity, and alkalinity distinguished seasons. Vibrio bacteria differed …

Crystal Structure Of New Polar Rare Earth Borates Na2.62Ln2.12(Bo3)3 (Ln = Pr, Nd, Sm) Containing Isolated Bo3 Groups, Alevtina A. Maksimova, Mark D. Smith, Hans Conrad Zur Loye

Faculty Publications

Three new rare earth borates, Na2.62Ln2.12(BO3)3 (Ln = Pr, Nd, Sm), were synthesized via a high-temperature solution reaction using a BaCO3–H3BO3–NaF flux and structurally characterized by single-crystal X-ray diffraction analysis. The compounds crystallize in the orthorhombic space group Amm2 with lattice parameters a = 5.0985(10) Å, b = 11.180(2) Å, c = 7.1483(14) Å, and a unit cell volume of 407.48(14) ų (Z = 2) for Na2.62Pr2.12(BO3)3, a = 5.0983(10) Å, b = 11.181(2) Å, c = 7.1491(14) Å, and a unit cell volume of 407.51(14) ų (Z = 2) for Na2.62Nd2.12(BO3)3, and a = 5.08630(10) Å, b …

Single Crystal Growth Of The Orthoborate Nabalu(Bo3)2 And Optical Investigation Of Eu3+ And Tb3+ Doped Nabalu(Bo3)2, Alevtina A. Maksimova, Mark D. Smith, Lakshani W. Masachchi, Hans Conrad Zur Loye

Faculty Publications

Sodium barium lutetium borate NaBaLu(BO₃)₂ crystals were synthesized using a high-temperature solution method. The crystal structure of this layered orthoborate is described and corresponds to that of an extensive orthoborates family, NaBaR(BO₃)₂ (R = Sc, Y, Yb, Tb – Lu). NaBaLu(BO₃)₂ was doped by Eu³⁺ and Tb³⁺ to explore its performance as a host material and to investigate the luminescent properties of the Eu³⁺ and Tb³⁺ doped materials. The emission spectra of the NaBaLu(BO₃)₂:Ln (Ln = Eu, Tb) crystals are presented. The most …

Temperature And Salinity Effects On The Physiology Of Bullfrog Tadpoles (Lithobates Catesbeianus) From A Suburban Temperate Wetland, Angela Brown

Theses, Dissertations and Culminating Projects

One of the most robust amphibians is the American Bullfrog, Lithobates catesbeianus, which is a widespread species that is invasive worldwide, and is broadly tolerant of a range of environmental conditions. Despite this tolerance, survival and performance of adult L. catesbeianus can be negatively affected by increasing temperatures and salinity resulting from anthropogenic impacts, such as climate change and road salts. This study focuses on the effects of acute salinity exposure (mimicking road salt influx into a pond) on L. catesbeianus tadpoles at different larval stages. Increased salinity was predicted to negatively affect two physiological performance measures. Critical maximum temperature …

A Social-Ecological Systems Approach To Integrating Outdoor Recreation And Black Bear Management: A Michigan Case Study, Megan Dorothy Stone

All Graduate Theses and Dissertations, Fall 2023 to Present

Outdoor recreation sits at the intersection of social and ecological systems, representing one of the primary ways in which humans directly interact with their natural environment. As a result, outdoor recreation management must balance providing high-quality outdoor recreation opportunities while simultaneously protecting natural resources in protected areas. Balancing these concurrent management goals has become more challenging in recent years as participation in outdoor recreation increases. This can lead to numerous negative impacts on the environment, such as wildlife disturbance. In this study, I explore the challenges and opportunities for collaboration between managers of outdoor recreation and black bears in the …

Effects Of Bidisperse Gold Nanoparticles On Near-Infrared Surface-Enhanced Raman Spectroscopy (Sers) In Quick-Freezing-Induced Gold Nanoparticle Aggregates (Qfiaas), Elissa M. Dojka

Forensic Science Master's Projects

Gold nanoparticle (AuNP) aggregates formed via rapid freezing in liquid nitrogen exhibit strong near-infrared (NIR) plasmonic coupling. These quick-freezing-induced AuNP aggregates (QFIAAs) form moderately sized, colloidally stable structures that remain suspended for over three months, supporting a variety of analytical applications. Mechanistically, QFIAA formation arises from the confinement of nanoparticles and ions within advancing ice grain boundaries during freeze-concentration. This mechanical crowding promotes extreme physical proximity while simultaneously elevating local ionic strength, which screens electrostatic barriers to drive the assembly of dense, tightly coupled plasmonic networks.

This study investigates the plasmonic and surface-enhanced Raman scattering (SERS) behavior of bidisperse QFIAA …

Land Condition Standards For The Western Australian Nullarbor Pastoral Region, Peter-Jon A. Waddell, Wayne J. Fletcher

Natural resources published reports

This report outlines the quantitative land condition standards that define acceptable pastoral land condition for the Western Australian part of the Nullarbor, to meet the regulatory requirements of the Land Administration Act 1997 and the Soil and Land Conservation Act 1945.

The Department of Primary Industries and Regional Development is developing regional-level pastoral land condition standards for Western Australia as a critical component of the Framework for sustainable pastoral management – revised edition (Fletcher 2022), the purpose of which is to address the Office of the Auditor General’s recommendations to improve the management of pastoral lands in WA …

Cost-Effectiveness Evaluation Of Artificial Intelligence-Assisted Chest Radiograph Interpretation For Tuberculosis Screening In Rural Health Units In The Philippines, Harold Henrison C. Chiu, Bryan Christopher C. Lao, Gloanne C. Adolor

Graduate School of Business Publications

Background: Tuberculosis remains a major public health burden in the Philippines, where diagnostic delays are amplified by limited radiology capacity in rural health units (RHUs) and geographically isolated and disadvantaged areas (GIDAs). Computer-aided diagnosis (CAD) using artificial intelligence (AI)-assisted chest radiograph interpretation may shorten the screening pathway and reduce reliance on scarce specialist readers. However, its economic value for RHUbased tuberculosis screening has not been fully evaluated.
Methods: We developed a decision-tree cost-effectiveness model in Microsoft Excel 365 to compare AI-assisted chest radiograph interpretation with conventional manual radiologist or teleradiology interpretation among a theoretical annual cohort of 1,000 presumptive tuberculosis …

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 …

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 …

Ai-Driven Segmentation And Volumetric Response Modeling Of Liver Regions To Radiotherapy, Aashish Chandra Gupta

Dissertations and Theses (Open Access)

In liver-directed radiotherapy (RT), liver regions receiving higher doses typically undergo atrophy while contralateral/adjacent lower-dose regions may exhibit compensatory hypertrophy through regeneration of healthy tissue. Optimizing the RT plan to promote regional hypertrophy while minimizing the risk of developing atrophy has the potential to enhance post-RT liver function and long-term survivorship. However, current clinical practice largely relies on global liver dose-volume metrics during RT-planning, which may obscure favorable dose-response correlation and limit actionable guidance for clinicians. Therefore, we hypothesized that post-RT regional liver response is governed by a combination of region-specific dose-volume and patient clinical features, and that these responses …

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.

Indigenous Community Research Opportunities, Sharon Hausam, Aaron M. Canter

Faculty Publications

This is a working paper produced as part of National Science Foundation project #2115169, “Transforming Rural-Urban Systems: Trajectories for Sustainability in the Intermountain West,” known as the “Intermountain West Transformation Network” (TN), led by the University of New Mexico with institutional partners at three additional universities in New Mexico, two in Arizona, and one each in Utah, Colorado, and Washington. The TN’s Indigenous and Tribal engagement was supported through a contract with Dr. Sharon Hausam, additional work by Aaron M. Canter, coordination with Dr. Lani Tsinnajinnie, and an Advisory Committee on Indigenous Information Needs primarily comprised of Indigenous representatives in …

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 …

Visualizing The Phase Space Of Two Interacting Spherical Magnets Via Lagrangian Descriptors, Matthew Pontius

All Graduate Theses and Dissertations, Fall 2023 to Present

This thesis studies the motion of one spherical magnet sliding on another fixed spherical magnet. Although the setup is simple, the resulting motion can range from regular and predictable to chaotic as the energy increases. To understand this behavior, mathematical tools are used to visualize how all possible motions are organized in phase space. These methods reveal patterns such as stable regions, repeating motions, and chaotic trajectories. The results show how order and chaos coexist in this system and provide insight into how small changes in the initial conditions can lead to very different outcomes.

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 …

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 …

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 …

Drought And Diet Breadth: Does Insect Specialization Influence Herbivory When Plants Are Under Stress?, Jakob Palmer

All Graduate Theses and Dissertations, Fall 2023 to Present

Climate change will alter precipitation worldwide, causing more frequent and severe drought events worldwide. Drought affects many ecological processes, including plant-herbivore interactions, which are critical to biodiversity and ecosystem health. A variety of plant characteristics can influence herbivory – such as how hairy, nutritious, or toxic a leaf is – and drought has been shown to alter many of these traits. Unique characteristics of herbivore species are also important: herbivores can either feed on a variety of plants (generalists) or a group of closely related plants (specialists). Specialists can cope with traits of the plants they eat, while generalists are …

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 …

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 …