Physical Sciences and Mathematics Commons^™

Evaluation Of The Community Multiscale Air Quality Model For Simulating Winter Ozone Formation In The Uinta Basin, Rebecca Matichuk, Gail Tonnesen, Deborah Luecken, Rob Gillam, Sergey L. Napelenok, Kirk R. Baker, Donna Schwede, Ben Murphy, Detlev Helmig, Seth N. Lyman, Shawn Roselle

Bingham Research Center

The Weather Research and Forecasting (WRF) and Community Multiscale Air Quality (CMAQ) models were used to simulate a 10 day high-ozone episode observed during the 2013 Uinta Basin Winter Ozone Study (UBWOS). The baseline model had a large negative bias when compared to ozone (O₃) and volatile organic compound (VOC) measurements across the basin. Contrary to other wintertime Uinta Basin studies, predicted nitrogen oxides (NO_x) were typically low compared to measurements. Increases to oil and gas VOC emissions resulted in O₃ predictions closer to observations, and nighttime O₃ improved when reducing the deposition velocity …

Expression Of Wnt-Signaling Pathway Genes And Their Associations With Mirnas In Colorectal Cancer, Martha L. Slattery, Lila E. Mullany, Lori C. Sakoda, Wade S. Samowitz, Roger K. Wolff, John R. Stevens, Jennifer S. Herrick

Mathematics and Statistics Faculty Publications

The Wnt-signaling pathway functions in regulating cell growth and thus is involved in the carcinogenic process of several cancers, including colorectal cancer. We tested the hypothesis that multiple genes in this signaling pathway are dysregulated and that miRNAs are associated with these dysregulated genes. We used data from 217 colorectal cancer (CRC) cases to evaluate differences in Wnt-signaling pathway gene expression between paired CRC and normal mucosa and identify miRNAs that are associated with these genes. Gene expression data from RNA-Seq and miRNA expression data from Agilent Human miRNA Microarray V19.0 were analyzed. We focused on genes most strongly associated …

Mitigating Projected Impacts Of Climate Change And Building Resiliency Through Permaculture: A Community ‘Bee Inspired Gardens’ Movement In The Desert Southwest, Usa, Roslynn Brain, Jeffrey Adams, Jeremy Lynch

Environment and Society Faculty Publications

Permaculture, an integrative design process creating resilient and productive landscapes and communities, can serve as a useful mitigation tool for projected climate change impacts. In the United States, the desert southwest town of Moab, Utah, has employed permaculture design in a community initiative called ‘Bee Inspired Gardens.’ This initiative has harnessed social capital to create resilient landscapes demonstrating pollinator health, water conservation, and perennial food and forage systems. Bee Inspired Gardens have been designed at a University, middle school, charter school, Bureau of Land Management property, hotel, public park, environmental education non-profit, and more. Community members are now harvesting fruit …

Effect Of An 860-M Thick, Cold, Freshwater Aquifer On Geothermal Potential Along The Axis Of The Eastern Snake River Plain, Idaho, Thomas E. Lachmar, Thomas G. Freeman, Christopher J. Sant, Jeffrey R. Walker, Joseph F. Batir, John W. Shervais, James P. Evans, Dennis L. Nielson, David D. Blackwell

Geosciences Faculty Publications

A 1912-m exploration corehole was drilled along the axis of the eastern Snake River Plain, Idaho. Two temperature logs run on the corehole display an obvious inflection point at about 960 m. Such behavior is indicative of downward fluid flow in the wellbore. The geothermal gradient above 935 m is 4.5 °C/km, while the gradient is 72–75 °C/km from 980 to 1440 m. Projecting the higher gradients upward to where they intersect the lower gradient on the temperature logs places the bottom of the cold, freshwater Snake River Plain aquifer, which suppresses the geothermal gradient at this location, at least …

Seasonal Resource Selection And Habitat Treatment Use By A Fringe Population Of Greater Sage-Grouse, Rhett Boswell

All Graduate Plan B and other Reports, Spring 1920 to Spring 2023

Movement and habitat selection by Greater Sage-grouse (Centrocercus uropasianus) is of great interest to wildlife managers tasked with applying conservation measures for this iconic western species. Current technology has created small and lightweight GPS (Global Positioning Systems) transmitters that can be attached to sage-grouse. Using GIS software and statistical programs such as Program R, land managers can analyze GPS location data to assess how sage-grouse are geospatially interacting with their habitats. Within the Panguitch Sage-Grouse Management Area (SGMA) thousands of acres of land have been restored or manipulated to enhance sage-grouse habitat; this usually involves removal of pinyon pine …

An Investigation Of The Alkali Metals In The Fcc Structure Using An Embedded-Atom-Method (Eam) Model, Marcus Jackman

Physics Capstone Projects

Embedded-atom-method models have been used in the calculation and prediction of many vibrational and thermal properties of materials. In 2012 Wilson and Riffe constructed a model that predicts dispersion relations and frequency-moment Debye temperatures of the alkali metals with a greater degree of accuracy than previous models. The Wilson-Riffe model was implemented using MATLAB code. Here that model is extended to model alkali metals in the close-packed fcc structure. Code development is discussed, and results are presented for dispersion relations, density of states, Debye temperatures and free energy. The vibrational free energy combined with a suitable constant representing the electronic …

Usarray Imaging Of Continental Crust In The Conterminous United States, Xiaofei Ma, Anthony R. Lowry

Geosciences Faculty Publications

The thickness and bulk composition of continental crust provide important constraints on the evolution and dynamics of continents. Crustal mineralogy and thickness both may influence gravity anomalies, topographic elevation, and lithospheric strength, but prior to the inception of EarthScope’s USArray, seismic measurements of crustal thickness and properties useful for inferring lithology are sparse. Here we improve upon a previously published methodology for joint inversion of Bouguer gravity anomalies and seismic receiver functions by using parameter space stacking of cross correlations of modeled synthetic and observed receiver functions instead of standard H-κ amplitude stacking. The new method is applied to estimation …

The Value Of Native Plants And Local Production In An Era Of Global Agriculture, Oren Shelef, Peter J. Weisberg, Frederick D. Provenza

Wildland Resources Faculty Publications

For addressing potential food shortages, a fundamental tradeoff exists between investing more resources to increasing productivity of existing crops, as opposed to increasing crop diversity by incorporating more species. We explore ways to use local plants as food resources and the potential to promote food diversity and agricultural resilience. We discuss how use of local plants and the practice of local agriculture can contribute to ongoing adaptability in times of global change. Most food crops are now produced, transported, and consumed long distances from their homelands of origin. At the same time, research and practices are directed primarily at improving …

Ion Parallel Closures, Jeong-Young Ji, Hankyu Q. Lee, Eric D. Held

All Physics Faculty Publications

Ion parallel closures are obtained for arbitrary atomic weights and charge numbers. For arbitrary collisionality, the heat flow and viscosity are expressed as kernel-weighted integrals of the temperature and flow-velocity gradients. Simple, fitted kernel functions are obtained from the 1600 parallel moment solution and the asymptotic behavior in the collisionless limit. The fitted kernel parameters are tabulated for various temperature ratios of ions to electrons. The closures can be used conveniently without solving the kinetic equation or higher order moment equations in closing ion fluid equations.

3d Photogrammetry Quantifies Growth And External Erosion Of Individual Coral Colonies And Skeletons, Renata Ferrari, Will F. Figueira, Morgan S. Pratchett, Tatiana Boube, Arne Adam, Tania Kobelkowsky-Vidrio, Steve S. Doo, Trisha Brooke Atwood, Maria Byrne

Watershed Sciences Faculty Publications

Growth and contraction of ecosystem engineers, such as trees, influence ecosystem structure and function. On coral reefs, methods to measure small changes in the structure of microhabitats, driven by growth of coral colonies and contraction of skeletons, are extremely limited. We used 3D reconstructions to quantify changes in the external structure of coral colonies of tabular Acropora spp., the dominant habitat-forming corals in shallow exposed reefs across the Pacific. The volume and surface area of live colonies increased by 21% and 22%, respectively, in 12 months, corresponding to a mean annual linear extension of 5.62 cm yr⁻¹ (±1.81 SE). …

Optimizing Bioengineered Vascular Systems: A Genetic Algorithm Approach, Sima Mehri Kochaki

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Efficiency of current cell cultures producing biological products is limited due to accumulation of the product and waste on the cells. A previous work aims at assisting bioengineers in solving this problem by introducing a new set of cells which possess the ability to connect to one another and thus form a network. Once created, the network of cells can help the initial cellules by removing their waste and product as well as nourishing them. Our project explores a technique to be able to create the best network of such cells; hence maximizing the amount of metabolic product in the …

Mechanistic Studies Of The Iron And Molybdenum Nitrogenases, Derek Harris

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

As a basic building block in many biological molecules the element nitrogen (N) is essential for life. Dinitrogen (N2) is abundant in Earth’s atmosphere, but this form is biologically unavailable. To be biologically available N2 must undergo an energy demanding reduction reaction to the fixed form, ammonia (NH3). The industrial Haber-Bosch process, which accounts for approximately 50% of the worlds fixed nitrogen, uses energy from fossil fuels to achieve high pressures and temperatures to facilitate the reaction. The energy used by Haber-Bosch accounts for approximately 2% of the world’s annual supply. The remainder of fixed nitrogen is produced biologically by …

Non-Methane Hydrocarbon Source Apportionment And Btex Risk Assessment Of Winter 2015 In Roosevelt, Utah, Jerimiah Lamb

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Non-Methane Hydrocarbons (NMHC) monitored in Roosevelt Utah including Benzene, Toluene, Ethylbenzene and Xylene (collectively known as BTEX) are associated with deleterious effects including cancer. This study was designed to assess the origin and effect of the toxicants and addressed two points: 1) Source identification using the USEPA’s Positive Matrix Factorization (PMF) and NOAA’s Hybrid Single Particle Lagrangian Integrated Trajectory (HYSPLIT) model and 2) A human health risk assessment based on ambient concentrations of BTEX collected at the Roosevelt site. Model fit indicated that the primary contributor to total NMHCs was local oil and gas operations and was supported by previous …

Rancher Perceptions Of Ecosystem Services From Rangelands Of The Intermountain West, Elisabeth C. York

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Rangelands within the Great Basin are responsible for the provision of multiple resources that humans depend on for a variety of reasons. Ranchers in this region are dependent on public lands to remain economically viable in their cattle operations. As a majority of land in this region is publically owned, there are varying interests at play in what should and could be the focus of management. Ranchers are charged with implementing strategies aimed at conserving these landscapes and their motivations for what to manage may significantly influence resource provision from Intermountain West ecosystem.

In this study, I sought to understand …

Novel Statistical Models For Quantitative Shape-Gene Association Selection, Xiaotian Dai

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Other research reported that genetic mechanism plays a major role in the development process of biological shapes. The primary goal of this dissertation is to develop novel statistical models to investigate the quantitative relationships between biological shapes and genetic variants. However, these problems can be extremely challenging to traditional statistical models for a number of reasons: 1) the biological phenotypes cannot be effectively represented by single-valued traits, while traditional regression only handles one dependent variable; 2) in real-life genetic data, the number of candidate genes to be investigated is extremely large, and the signal-to-noise ratio of candidate genes is expected …

Longitudinal Thermal And Solute Dynamics In Regulated Rivers, Muhammad Rezaul Haider

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Dam releases increase river stage and can reverse groundwater movement into and out of the river. As the flood, thermal, and solute waves travel downstream in a regulated river, the size of the waves is anticipated to be affected both by river processes and exchanges with near river groundwater. This study established a modeling framework to quantify the influences of the groundwater exchanges on the temperatures and solute concentration dynamics along regulated rivers. The wave properties, volume of exchanges, conservative solute mass exchanges, and heat energy exchanges were calculated as a function of time and distance downstream. Results show that …

Exploring And Describing The Spatial And Temporal Dynamics Of Medusahead In The Channeled Scablands Of Eastern Washington Using Remote Sensing Techniques, Timothy M. Bateman

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Medusahead is a harmful weed that is invading public lands in the West. The invasion is a serious concern to the public because it can reduce forage for livestock and wildlife, increase fire frequency, alter important ecosystem cycles (like water), reduce recreational activities, and produce landscapes that are aesthetically unpleasing. Invasions can drive up costs that generally require taxpayer’s dollars. Medusahead seedlings typically spread to new areas by attaching itself to passing objects (e.g. vehicles, animals, clothing) where it can quickly begin to affect plants communities. To be effective, management plans need to be sustainable, informed, and considerate to invasion …

Real Simple Lie Algebras: Cartan Subalgebras, Cayley Transforms, And Classification, Hannah M. Lewis

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

The differential geometry software package in Maple has the necessary tools and commands to automate the classification process for complex simple Lie algebras. The purpose of this thesis is to write the programs to complete the classification for real simple Lie algebras. This classification is difficult because the Cartan subalgebras are not all conjugate as they are in the complex case. For the process of the real classification, one must first identify a maximally noncompact Cartan subalgebra. The process of the Cayley transform is used to find this specific Cartan subalgebra. This Cartan subalgebra is used to find the simple …

Exact Approaches For Bias Detection And Avoidance With Small, Sparse, Or Correlated Categorical Data, Sarah E. Schwartz

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Every day, traditional statistical methodology are used world wide to study a variety of topics and provides insight regarding countless subjects. Each technique is based on a distinct set of assumptions to ensure valid results. Additionally, many statistical approaches rely on large sample behavior and may collapse or degenerate in the presence of small, spare, or correlated data. This dissertation details several advancements to detect these conditions, avoid their consequences, and analyze data in a different way to yield trustworthy results.

One of the most commonly used modeling techniques for outcomes with only two possible categorical values (eg. live/die, pass/fail, …

Geological Characterization Of Precambrian Nonconformities: Implications For Injection-Induced Seismicity In The Midcontinent United States, Laura Cuccio

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

The midcontinent United States, a region which typically does not experience many earthquakes, has experienced a significant increase in the number of earthquakes over the last decade. This increase in earthquake activity has been linked to wastewater injection, a process in which large volumes of wastewater from oil and gas extraction are injected into deep (2-3 km), high-permeability sedimentary rocks, near low-permeability Precambrian (>540-million-year-old) crystalline ‘basement’ rocks. The contact between these two rock types is referred to as the Precambrian nonconformity. Injection-induced earthquakes occur on or near basement-hosted faults due to an increase in pore fluid pressures, which implies …

Optimizing Barrier Removal To Restore Connectivity In Utah’S Weber Basin, Maggi Kraft

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

River barriers, such as dams, culverts and diversions are important for water conveyance, but disrupt river ecosystems and hydrologic processes. River barrier removal is increasingly used to restore and improve river habitat and connectivity. Most past barrier removal projects prioritized individual barriers using score-and-rank techniques, neglecting the spatial structure and cumulative change from multiple barrier removals. Similarly, most water demand models satisfy human water uses or, only prioritize aquatic habitat, failing to include both human and environmental water use benefits. In this study, a dual objective optimization model identified in-stream barriers that impede quality-weighted aquatic habitat connectivity for Bonneville cutthroat …

Extracting And Visualizing Data From Mobile And Static Eye Trackers In R And Matlab, Chunyang Li

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Eye tracking is the process of measuring where people are looking at with an eye tracker device. Eye tracking has been used in many scientific fields, such as education, usability research, sports, psychology, and marketing. Eye tracking data are often obtained from a static eye tracker or are manually extracted from a mobile eye tracker. Visualization usually plays an important role in the analysis of eye tracking data. So far, there existed no software package that contains a whole collection of eye tracking data processing and visualization tools. In this dissertation, we review the eye tracking technology, the eye tracking …

Twentieth Century Channel Change Of The Green River In Canyonlands National Park, Utah, Alexander E. Walker

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Since the early 20^th century, river channels of the Colorado River basin have narrowed, decreasing available riparian and aquatic habitat. Changes are considered to be the result of three major factors: wide-spread water development, increasing hydroclimate variability and the invasion of non-native tamarisk (Tamarix spp.), altering flow regime and sediment supply. Different studies have reached different conclusions about the relative roles of flow regime, sediment supply and tamarisk in causing narrowing.

I investigated channel change in the lower Green River within Canyonlands National Park to describe channel changes in the 20^th century and understand the roles …

The Investigation Of Gravity Waves In The Mesosphere / Lower Thermosphere And Their Effect On Sporadic Sodium Layer, Xuguang Cai

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Gravity waves in the atmosphere are the waves with gravity and buoyancy force as the restoring forces. Gravity waves will significantly impact the Mesosphere Lower / Thermosphere (MLT), and the breaking of gravity waves is the key factor to cause the cool summer and warm winter in the Mesopause region. Therefore, it is important for us to investigate gravity waves. In this dissertation, we mainly use USU Na lidar data to explore gravity waves in the MLT. The exploration is made up of two projects. One is the investigation of gravity wave breaking and the associated dynamic instability by USU …

Application Of Machine Learning And Statistical Learning Methods For Prediction In A Large-Scale Vegetation Map, Carla M. Brookey

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Original analyses of a large vegetation cover dataset from Roosevelt National Forest in northern Colorado were carried out by Blackard (1998) and Blackard and Dean (1998; 2000). They compared the classification accuracies of linear and quadratic discriminant analysis (LDA and QDA) with artificial neural networks (ANN) and obtained an overall classification accuracy of 70.58% for a tuned ANN compared to 58.38% for LDA and 52.76% for QDA.

Because there has been tremendous development of machine learning classification methods over the last 35 years in both computer science and statistics, as well as substantial improvements in the speed of computer hardware, …

Usarray Imaging Of North American Continental Crust, Xiaofei Ma

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

The layered structure and bulk composition of continental crust contains important clues about its history of mountain-building, about its magmatic evolution, and about dynamical processes that continue to happen now. Geophysical and geological features such as gravity anomalies, surface topography, lithospheric strength and the deformation that drives the earthquake cycle are all directly related to deep crustal chemistry and the movement of materials through the crust that alter that chemistry.

The North American continental crust records billions of years of history of tectonic and dynamical changes. The western U.S. is currently experiencing a diverse array of dynamical processes including modification …

Approaches, Techniques, And Tools For Identifying Important Code Changes To Help Code Reviewers, Maneesh M. Mohanavilasam

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Software development is a collaborative process where many developers come together and work on a project. To make things easy and manageable, software is developed on a version control system. A version control system is a centralized system which stores code and adds code from all other developers as an increment to the code base in the repository. Since multiple people work on the same code repository together, it is important to make sure that their contributions do not conflict with each other. It is important to maintain the quality and integrity of the repository. This is where the code …

Extensions And Improvements To Random Forests For Classification, Anna Quach

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

The motivation of my dissertation is to improve two weaknesses of Random Forests. One, the failure to detect genetic interactions between two single nucleotide polymorphisms (SNPs) in higher dimensions when the interacting SNPs both have weak main effects and two, the difficulty of interpretation in comparison to parametric methods such as logistic regression, linear discriminant analysis, and linear regression.

We focus on detecting pairwise SNP interactions in genome case-control studies. We determine the best parameter settings to optimize the detection of SNP interactions and improve the efficiency of Random Forests and present an efficient filtering method. The filtering method is …

Stream Temperature Monitoring And Modeling To Inform Restoration: A Study Of Thermal Variability In The Western Us, Jessica R. Wood

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Water temperature is an important variable for aquatic ecosystems. Salmonid population numbers and distribution are heavily influenced by stream temperature, and there is growing concern about the health of salmonid populations with anticipated climate change. Managers are looking to efficiently evaluate options to maintain stream temperatures needed by salmonids. This study evaluated and compared stream temperature restoration alternatives in two streams with warm temperatures using stream temperature monitoring and modeling.

The first study identified pockets of cold water that are important to native fish species in Nevada’s Walker River. Comparison of monitoring results with existing basin-scale model outputs identified two …

Foundations Of Translational Ecology, Carolyn Af Enquist, Stephen T. Jackson, Gregg M. Garfin, Frank W. Davis, Leah R. Gerber, Jeremy A. Littell, Jennifer L. Tank, Adam J. Terando, Tamara U. Wall, Benjamin Halpern, J. Kevin Hiers, Toni Kyn Morelli, Elizabeth Mcnie, Nathan L. Stephenson, Matthew A. Williamson, Connie A. Woodhouse, Laurie Yung, Mark W. Brunson, Kimberly R. Hall, Lauren M. Hallett, Dawn M. Lawson, Max A. Mortiz, Koren Nydick, Amber Pairis, Andrea J. Ray, Claudia Regan, Hugh D. Safford, Mark W. Schwartz, M. Rebecca Shaw

Environment and Society Faculty Publications

Ecologists who specialize in translational ecology (TE) seek to link ecological knowledge to decision making by integrating ecological science with the full complement of social dimensions that underlie today's complex environmental issues. TE is motivated by a search for outcomes that directly serve the needs of natural resource managers and decision makers. This objective distinguishes it from both basic and applied ecological research and, as a practice, it deliberately extends research beyond theory or opportunistic applications. TE is uniquely positioned to address complex issues through interdisciplinary team approaches and integrated scientist–practitioner partnerships. The creativity and context-specific knowledge of resource managers, …