Physical Sciences and Mathematics Commons^™

Streams Guidelines: Standards For Technical Reporting In Environmental And Host-Associated Microbiome Studies, Julia M. Kelliher, Chloe Mirzayi, Sarah R. Bordenstein, Aaron Oliver, Christina A. Kellogg, Eneida L. Hatcher, Maureen Berg, Petr Baldrian, Mashael Aljumaah, Cassandra Maria Luz Miller, Christopher Mungall, Vlastimil Novak, Alexis Palucki, Ethan Smith, Nazifa Tabassum, Gregory Bonito, J. Rodney Brister, Patrick S. Chain, Mingfei Chen, Samuel Degregori, Xuefeng Peng, Et. Al.

Faculty Publications

The interdisciplinary nature of microbiome research, coupled with the generation of complex multi-omics data, makes knowledge sharing challenging. The Strengthening the Organization and Reporting of Microbiome Studies (STORMS) guidelines provide a checklist for the reporting of study information, experimental design and analytical methods within a scientific manuscript on human microbiome research. Here, in this Consensus Statement, we present the standards for technical reporting in environmental and host-associated microbiome studies (STREAMS) guidelines. The guidelines expand on STORMS and include 67 items to support the reporting and review of environmental (for example, terrestrial, aquatic, atmospheric and engineered), synthetic and non-human host-associated microbiome …

Definition Of The 3d Position And Motion Status Of The Moving Heart Based On 2d Projections, Lawrence D. Orijuela

Electronic Theses, Projects, and Dissertations

This thesis presents a novel application of deep learning to the estimation of pulmonary vein coordinates using X-ray image pairs from a FORBILD Thorax phantom derived motion dataset. A Siamese neural network was developed to predict the 3D coordinates of one pulmonary vein at a time, specifically the Right Superior Pulmonary Vein (RSPV), Left Superior Pulmonary Vein (LSPV), Left Inferior Pulmonary Vein (LIPV), or Right Inferior Pulmonary Vein (RIPV), based on two-dimensional projection images.

The input data consisted of over 1.6 million grayscale X-ray image pairs across 1331 virtual patients, each annotated with ground truth 3D coordinates. To manage memory …

East Antarctic Ice Sheet History At The Outback Nunataks Using Geographic Information Systems And Cosmogenic Dating, Jacob P. Baker

Electronic Theses, Projects, and Dissertations

This study investigates the history of ice sheet surface elevation at the Outback Nunataks in East Antarctica using exposure age dating and geomorphic mapping. We identified glacial landforms at Roberts Butte, Miller Butte, and Frontier Mountain, in the Outback Nunatak range, using 2023 Landsat Image Mosaic of Antarctica (LIMA) and 2022 Reference Elevation Model of Antarctica (REMA). We collected bedrock and glacial erratic samples for cosmogenic nuclide analysis from Roberts Butte and Miller Butte during the 2023-24 United States Antarctic Program field season. Analysis of glacial erratics reflect inherited cosmogenic nuclide concentrations, resulting in apparent exposure ages between 359 and …

Robustness Of Network Inference Algorithms Under Network Class Misspecification, Roberto Ceja

Electronic Theses, Projects, and Dissertations

Inferring phylogenies in the presence of hybridization remains a difficult problem. As a result, many current methods for reconstructing phylogenetic networks are restricted to a simple class of networks known as level-1. This restriction arises from theoretical considerations rather than empirical evidence, with real data possibly arising from complex networks. In this work, we evaluate the robustness of two level-1 network inference methods, SNaQ and NANUQ+, through a simulation study, when the input data originates from a more complex network. Specifically, we investigate whether these methods can accurately recover important features of the true species network, such as the circular …

Predictors Of Math Identity In U.S. High School Students, Edwin Flores

Electronic Theses, Projects, and Dissertations

This study explored factors related to high school students’ sense of math identity. Data from the High School Longitudinal Study of 2009 was used which is a nationally representative dataset from the National Center of Education Statistics (NCES). The sample is representative of U.S. high schoolers who began ninth grade in 2009. Multiple regression analysis was performed and factors relating to students’ prior mathematics coursework and attitudes about mathematics were found to predict students’ mathematics identity.

Keywords. Mathematics, identity, high school students

Groundwater Arsenic Contamination In The Oro Grande Wash, Dalila Boice

Electronic Theses, Projects, and Dissertations

This study investigates the distribution of naturally occurring arsenic in groundwater within the Oro Grande Wash in San Bernardino County, California. Depth-discrete groundwater quality data were collected over multiple years using nested and Westbay monitoring wells. Water quality results showed higher levels of arsenic in the deeper aquifers, ranging between 600 feet and 1,000 feet below ground surface. Arsenic levels in these regions reached as high as 66 µg/L. At roughly 800 feet and below, water quality data from the wells reveal that arsenic concentrations exceeded the 10 µg/L maximum contaminant level (MCL) in 87% of cases. These data provide …

Self-Assessment In Calculus I, Bertha Naa Dei Neequaye

All Graduate Theses and Dissertations, Fall 2023 to Present

The purpose of this research investigate how undergraduate students in Calculus I at Utah State University learn and reflect on their level of understanding of Calculus I. In the study, self-assessment practices refer to students reflecting on what they have learned, rating their level of understanding and providing examples that illustrate their level of understanding. The structured and unstructured self-assessment rubrics were the two types of self-assessment rubrics used in the study. The structured self-assessment rubric provides a clear list of objectives of Calculus I topics for students to rate themselves on, while the unstructured self-assessment rubric is an open …

Predicting Major Solar Flares Using Convolutional Neural Networks And Multivariate Magnetic Field Time-Series Data, Arash Azizian Foumani

All Graduate Theses and Dissertations, Fall 2023 to Present

Major solar flares are sudden, intense bursts of X-ray energy from the Sun, capable of severely impacting critical technological infrastructure like satellites, communication networks, and power grids on Earth. Accurate prediction of these high-intensity events is crucial but presents a significant challenge. This is largely due to their infrequent occurrence and the complex, dynamic nature of the Sun's underlying magnetic activity which drives these events. This research focuses on improving the prediction of major solar flares by utilizing detailed historical data that tracks the evolution of magnetic properties within solar active regions over time. This time-based data, however, contains inherent …

Fast Computation Of The Friction Stir Welding Process With Model Order Reduction, Joshua Kay

All Graduate Theses and Dissertations, Fall 2023 to Present

Friction stir welding (FSW) is a manufacturing process used to join materials through intense heat and pressure. To better understand and optimize this FSW process, mathematical models incorporating non-Newtonian Navier-stokes equations for large plastic deformation and heat equation for the heat transfer are used to simulate the FSW process. However, solving these coupled and nonlinear equations with high accuracy requires significant computational power and time. This thesis has applied model order reduction, more precisely the Proper Orthogonal Decomposition (POD) and Discrete Empirical Interpolation Method (DEIM), to efficiently solve the FSW system in low-dimensional space. Slight modifications are made regarding the …

Implications Of The Attenuated Allee Effect On Population Dynamics, Dana Strong

All Graduate Theses and Dissertations, Fall 2023 to Present

The Allee effect is an ecological phenomenon characterized by a per capita growth rate that increases as the population size increases in the context of low population density. The Allee effect can lead to rapid extinction events. Consequently, ecologists can attempt to control the strength of the Allee effect to help increase the population (in the case of endangered species) or decrease the population (in the case of parasites or pests).

This research aimed to study not the strength of the Allee effect, but the intensity of the Allee effect, or how rapidly cooperation between individuals causes the per capita …

Integrating Manager Perspectives Into The Evaluation Of Wetland Revegetation Strategies, Loren F. Taylor

All Graduate Theses and Dissertations, Fall 2023 to Present

Ecological restoration is the process of assisting the recovery of an ecosystem that has been degraded and is dependent on complex and context-specific decisions. The decision-making process influencing restoration is rarely examined alongside ecological processes. There is a need for research that incorporates the social, economic, institutional, and logistical considerations that shape real-world practices, as well as ecological processes. Decisions made by restoration practitioners and land managers (hereon “manager”) are challenged by the lack of information shared regarding the practical constraints (e.g., cost, labor, specialized equipment) they face. Revegetation, particularly in wetlands, poses challenges due to site conditions and degradation …

Machine Learning Applications: Cell Tracking And Nonparametric Estimation Of Non-Smooth Divergences, Mina Mahbub Hossain

All Graduate Theses and Dissertations, Fall 2023 to Present

This thesis brings together two important research directions: how to compare different sets of data more accurately, and how to better understand how brain cancer cells move and change shape.

In the first part, we look at a problem in statistics: measuring how different two data sources are from each other. Traditional methods often make strong assumptions, which may not always hold in real situations. Our approach avoids those assumptions by using an ensemble method, a way of combining many weak estimators into one stronger result. This makes the method more flexible and reliable, especially when dealing with complex or …

The Impact Of Transmission Thresholds Across Multiple Scales On The Spread Of Chronic Wasting Disease In Wisconsin, Jen Mcclure

All Graduate Theses and Dissertations, Fall 2023 to Present

Wildlife diseases can be difficult to control once they are established. This is especially true when they spread through contact with infectious material left in the environment. One such disease is chronic wasting disease (CWD), a fatal illness affecting deer and related species in North America and other regions. CWD is caused by prions, misfolded proteins that can remain infectious for years after shedding by infected hosts.

Recent research shows that CWD infection does not always follow from the gradual accumulation of prions through small contact events. Rather, an individual may need to encounter a certain prion dose all at …

Social Media Mining For Extracting The Experience Of Neurodivergent Individuals On Twitter (X) And Reddit, Kartik Thakkar

All Graduate Theses and Dissertations, Fall 2023 to Present

Neurodiversity refers to the natural neurological variations in the human brain such as autism spectrum disorder (ASD), attention deficit hyperactivity disorder (ADHD), dyslexia, dyspraxia, Tourette syndrome and other neurological disorders. it’s estimated that around 15% to 20% of the world’s population is neurodivergent. This means a significant portion of people experience neurological differences in how they think, learn, and interact with the world.

Social Media has become an important space for neurodivergent individuals to share their experiences, build communities, and seek support. This thesis explores how the online venues like X (Twitter) and Reddit offer themselves as digital spaces where …

Multi-Agent Robotaxi Dispatch Coordination In A Real-World Simulation – Optimizing Rider Assignment, Rebalancing, And Charging Using Battery-Dependent Rewards And Welfare Maximization, Paden Thompson

All Graduate Theses and Dissertations, Fall 2023 to Present

We propose an approach to coordinate a robotaxi fleet for an autonomous ride-hail service. This is a service similar to a traditional ride-hailing service (Uber, Lyft), where customers request a ride and are then picked up in a car and dropped off in a new location; except, driverless vehicles called robotaxis are used to transport the customers.

Our approach teaches helpful coordination strategies to a robotaxi fleet while taking into account the individual battery level of the robotaxis. Each robotaxi acts as an individual agent in our simulation and can choose to pick up a rider, reposition to a new …

An Integrated Lithospheric Geotherm Model From Seismic Data And Plate Ages, Amanda R. Leaman

All Graduate Theses and Dissertations, Fall 2023 to Present

This research aims to develop advanced methods to accurately depict temperature profiles within the lithosphere, the Earth’s rigid outer layer. These temperature profiles extend from Earth’s surface to the asthenosphere, the ductile layer below the lithosphere. Constraining the poorly-known temperature distribution within the upper Earth is important for modeling the deformation of Earth’s crust over varying timescales and is essential for advancing realistic simulations of Earth dynamics. Here, I utilize enhanced global seismic data, coupled with recent advances in our understanding of mineral systems, to create several global lithospheric models in which I estimate temperature profiles from seismically observable features …

Using Luminescence Of Quartz Temper From Archaeological Pottery To Infer Wildfire Intensity In The Southwestern Us, Brooklyn D. Dib

All Graduate Theses and Dissertations, Fall 2023 to Present

The size and frequency of wildfires have increased recently, impacting ecosystems, communities, and human health. This research uses the heat-sensitive luminescence signals of quartz sand temper within archaeological pottery to record past wildfire conditions. Pottery sherds, which are fragments of archaeological pottery, from the forest floor in sites in New Mexico and Arizona were collected from different fire contexts (no fire exposure, historical fires, prescribed burns, and modern wildfires). These forests are primarily Ponderosa Pine with a grassy understory. The interior sand grains of each sherd sample were analyzed using optically stimulated luminescence, which dates when the mineral grains were …

A Software Framework For Translating Onnx Models Onto The Lace-C3a Hardware, Shawn Jones

All Graduate Theses and Dissertations, Fall 2023 to Present

Modern computers are powerful, but they are not always efficient enough for small, low power systems like those used on satellites and scientific instruments. To solve this problem, engineers often turn to FPGAs—reconfigurable computer chips that can be customized to run specific tasks much faster and with far less energy than ordinary processors. However, finding the best possible design for an FPGA program is extremely difficult because there are millions of ways a design could be built, and only a small fraction of them actually perform well.

This thesis presents SNOW, a new framework that helps automate the search for …

Data-Driven Streamflow Forecasting In The Upper Colorado River Basin Using Spatio-Temporal Graph Networks, Akhila Akkala

All Graduate Theses and Dissertations, Fall 2023 to Present

Forecasting river flow is essential for managing water supplies, reducing flood risk, and supporting healthy ecosystems. In the Upper Colorado River Basin, much of the yearly water comes from melting snow. However, many traditional models struggle to capture how snowpack and river flow interact, especially across such a large and complex region.

This study uses a modern machine learning approach called a Spatio-Temporal Graph Neural Network (STGNN) to improve streamflow prediction. The model uses Snow Water Equivalent (SWE)—a measure of how much water is stored in the snowpack—along with river flow data. By treating each river gauge as part of …

Dynamics, Predictability And Impacts Of Multi-Year La Niña Event, Nahid A. Hasan

All Graduate Theses and Dissertations, Fall 2023 to Present

This dissertation investigates the dynamics, predictability, and impacts of multi-year La Niña events. Multi-year La Niña events are referred to as extended periods of unusually cooler tropical Pacific that persist for two or more consecutive winters. These prolonged events can increase the risk of natural hazards such as droughts, floods, and heatwaves in the western US and around the world. Despite their worldwide significance, questions remain about the mechanisms driving their initiation, their predictability, and regional hydroclimate impacts.

The first chapter of the dissertation introduces what scientists currently believe causes them, and how well different types of climate models can …

Process Optimization And Cost Reduction For Cellulose Nanocrystals For Metal Removal From Rendered Fat, Sheikh Abdur Rehman

All Theses

Cellulose nanocrystals (CNCs) coupled with polymers featuring a high density of amine functional groups, such as polyethylenimine (PEI), exhibit significant metal-capturing capabilities. Rendered animal fat has applications in a vast number of industries, with the potential to be used as a feedstock for the biodiesel/renewable diesel industries. Nevertheless, rendered fat samples occasionally contain concentrations of metals/inorganic contaminants above the suitable threshold for use in this application. Thus, a cost-effective solution to remove light metal/inorganic contaminants from rendered fat samples is desirable.

To address this problem, a cellulose nanocrystal coupled with polyethylenimine, i.e., CNC-f-PEI, was developed by previous …

Tradespace Exploration For Multiple Collaborative Vehicles, Mrunal Deshmukh

All Theses

Modern military operations demand systems that adapt to uncertain, rapidly changing missions across diverse terrains. Traditional single-platform vehicle design is insufficient for such complexity. This research introduces a hierarchical tradespace exploration framework for designing and evaluating families of heterogeneous ground vehicles under a System-of-Systems (SoS) architecture. The framework treats vehicle design as a co-optimization problem, where a “parent” vehicle (e.g., a Squad Multipurpose Equipment Transport) coordinates specialized “child” vehicles for reconnaissance, amphibious tasks, terrain traversal, and stealth missions. Unlike conventional approaches that optimize vehicles individually, this study emphasizes collaborative performance, resource sharing, and adaptability at the family level. Central to …

A Leslie System For A Demographic Simulation: From An Actuarial Point Of View, David Kings

Electronic Theses and Dissertations

This thesis develops a discrete stochastic linear systems interpretation of age–stage demographic evolution grounded in Leslie operators and realized in a discrete-event simulation implemented with salabim. The central claim is that one annual cycle of the simulation constitutes a cone-preserving, stochastic affine transformation on a high- dimensional population state vector indexed by age, sex, marital status, household type, employment, and education, and that the composition of yearly operators yields a random matrix product whose top Lyapunov exponent is the stochastic counterpart of the Perron–Frobenius growth rate (Caswell, 2001; Tuljapurkar, 1997)[1, 2]. The actuarial bridge is constructed by mapping simulated survival …

Isolation, Chemical Characterization, And In-Vitro Cytotoxic Evaluation Of Novel Polar Flavonoids From Chromolaena Leivensis, Matthew Tohatsu Tetteh

Electronic Theses and Dissertations

This study focuses on isolation, chemical characterization, and in-vitro cytotoxic evaluation of novel polar flavonoids from chromolaena leivensis. A 95% ethanolic extract of c. leivensis shipped by Prof. Ruben Torrenegra from University of Applied and Environmental Sciences, Bogota, Colombia, was dissolved in 1:1 methanol/chloroform mixture and its purity analyzed by TLC. The sample was eluted with toluene/methanol in an increasing order of polarity on silica gel, resulting in 49 fractions labelled CLA1 to CLA49. Among these fractions, CLA10 (1) and CLA19 (2) obtained yellow and white crystals. They were analyzed by GCMS, IR, and …

Adsorption-Photodegradation Performance Of Silver Titanate For Methylene Blue Removal: Kinetics, Thermodynamics And Isotherm Studies, Nawrin Rahman Shefa, Most. Afroza Khatun, Ahmed Hasnain Jalal, M. Jasim Uddin, Md. Wasikur Rahman

Physics & Astronomy Faculty Publications

Silver titanate (AgTO) was synthesized via an ion-exchange reaction between sodium titanate and silver nitrate. This study investigates the efficiency of AgTO in the combined adsorption-photodegradation process for removing Methylene Blue (MB). The synthesized material was characterized using FTIR, XRD, SEM, and EDX techniques. Batch adsorption experiments were conducted to assess the effects of AgTO dosage (0.1–1.0 g/L), initial MB concentration (5–20 mg/L), pH (3–11), and temperature (313–333 K). The highest MB removal efficiency (90 %) was achieved at 313 K, pH 3, and an initial MB concentration of 5 mg/L. The photocatalytic performance of AgTO was further evaluated under …

Interactions Between Black, Brown, Blue And Green Carbon From Terrestrial To Marine Ecosystems: A Critical Review, Allison White, Richard Kline, Md. Saydur Rahman

School of Earth, Environmental, & Marine Sciences Faculty Publications

Black and brown carbon are byproducts of the incomplete combustion of biomass or fossil fuels. These light-absorbing aerosols influence climate by altering the radiative balance through the absorption and scattering of sunlight, exacerbating global climate change. Their subsequent deposition on terrestrial and marine environments affects surface albedo, snow and ice melt, and biogeochemical processes, leading to further environmental consequences. In contrast, green and blue carbon refer to carbon stored in terrestrial vegetation and marine ecosystems, respectively. These ecosystems play a crucial role in mitigating climate change by sequestering atmospheric carbon; however, they are increasingly threatened by climatic disturbances, anthropogenic activities, …

Revised Draft Final 2022 Unreclaimed Sites Sampling: Ur-22 Site Evaluation Summary Report, Pioneer Technical Services, Inc.

Silver Bow Creek/Butte Area Superfund Site

No abstract provided.

Clark Tailings Consolidated Waste Management Area (Ctcwma) Site Investigation Final Data Summary Report 2019 Surface Water, Groundwater Seep, And Soil Characterization 2021-2023 Surface Water And Groundwater Seep Evaluation 2023 Waterloo Aps Soil And Groundwater Evaluation, Woodard & Curran

Silver Bow Creek/Butte Area Superfund Site

No abstract provided.

Final Quarterly Operations And Maintenance Report Butte Treatment Lagoon System – Second Quarter 2024, Pioneer Technical Services, Inc.

Silver Bow Creek/Butte Area Superfund Site

No abstract provided.

Re: Approval Letter For The Final Butte Priority Soils Operable Unit (Bpsou) Butte Treatment Lagoons (Btl) Groundwater Treatment System Quarterly Operation And Maintenance Report – Quarter 1 2024 (Dated August 14, 2025), Emma Rott

Silver Bow Creek/Butte Area Superfund Site

No abstract provided.