Physical Sciences and Mathematics Commons^™

Sigtree: An Automated Meta-Analytic Approach To Find Significant Branches In A Phylogenetic Tree, Todd R. Jones

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

An experiment was performed on two groups of mice, the first group receiving a refined wheat diet, and the second group receiving a whole wheat diet. The levels of abundance of hundreds of bacteria in the guts of the mice were measured. Of interest was whether the levels of these bacteria were different depending on type of diet. In addition, it was desired to examine differences by diet in all of the families of bacteria. These family relationships are represented in a tree, and it was determined helpful to color the branches of this tree based on the differences of …

The Chemical Evolution Of Oceanic And Continental Lithosphere: Case Studies In The Us Cordillera, Marlon Mauricio Jean

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Among the terrestrial planets, only Earth has volcanism and plutonism that is related to plate tectonics. At the bottom of the oceans, mid-ocean ridges form where tectonic plates drift apart. More visible, and explosively dangerous, is volcanism related to the subduction of oceanic plates back into the Earth’s mantle. Less clear is the origin of the third major type of volcanism, the so-called intra-plate volcanism, which is thought to represent thermally driven upwellings from the lower mantle. This dissertation investigates two of these unique volcano-tectonic settings which occur in the western United States.

Subduction zones are regions of intense earthquake …

A Mechanistic Study Of Catalytic Promiscuity In Protein Phosphatase 1, Yuan Chu

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

"Catalytic promiscuous" enzymes, which possess additional activities besides their "native" activity, albeit with a lower efficiency than the main reaction, have become a new frontier for biochemistry and have received considerable attention. Catalytic promiscuity has been suggested to contribute to enzyme evolution through the mechanism of gene duplication followed by specialization of one of the two copies for the new function. Mimicking this evolutionary shortcut could also provide a more efficient route to changing the function of proteins by directed evolution.

The promiscuous phosphatase PP1 is a member of the phosphoprotein phosphatase (PPP) gene family, which is critical for the …

Robust Computational Tools For Multiple Testing With Genetic Association Studies, William L. Welbourn Jr.

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

The mapping of the human genome and the completion of the Human HapMap project over the past decade have significantly altered how research is conducted with respect to the genetic epidemiology of human disease. Study designs and analytic approaches have evolved rapidly from investigations involving relatively few targeted candidate genes to hypothesis-free genome-wide association studies, where thousands – and now even millions – of single molecular mutations are simultaneously analyzed to identify regions of the genome that may influence disease. As laboratory techniques continue to improve and costs decrease, the volume of genetic data will inexorably rise, and robust tools …

Planning, Acting, And Learning In Incomplete Domains, Christopher H. Weber

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

The engineering of complete planning domain descriptions is often very costly because of human error or lack of domain knowledge. Learning complete domain descriptions is also very challenging because many features are irrelevant to achieving the goals and data may be scarce. Given incomplete knowledge of their actions, agents can ignore the incompleteness, plan around it, ask questions of a domain expert, or learn through trial and error.

Our agent Goalie learns about the preconditions and effects of its incompletely-specified actions by monitoring the environment state. In conjunction with the plan failure explanations generated by its planner DeFault, Goalie diagnoses …

The Kinetics And Mechanisms Of Some Fundamental Organic Reactions Of Nitro Compounds, Zhao Li

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

In chemistry, kinetics is the study of the rates of chemical reactions. A reaction mechanism describes in detail exactly what takes place at each stage of an overall chemical reaction from reactants to products. The work outlined in this dissertation was carried out in order to find out the true mechanisms of some fundamental organic reactions of nitro compounds by means of a series of novel kinetic techniques and analysis methods.

The target reactions include (1) the proton transfer reactions of nitroalkanes and (2) the aromatic nucleophilic reactions of trinitroarenes, both of which are undeniably among the most elementary and …

Instances Of Conflict And Cooperation: An Exploration Into The Role Of Competition Between Usda-Wildlife Services And Wildlife Control Operators, Gary J. Bezzant Jr.

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

In early 1994 the United States Department of Agriculture’s Animal Damage Control agency implemented a directive providing guidance to help avoid competition between themselves and private businesses, known as Wildlife Control Operators (WCOs) engaging in similar work. Nearly two decades later some WCOs still complain about having to compete with the Animal Damage Control agency, now named Wildlife Services. Other businesses report enjoying a cooperative relationship with the agency.

I analyzed four policies that regulate competition between Wildlife Services and WCOs and found that there is a good amount of guidance given to Wildlife Services in regards to their competitive …

Sustainable Ski Resorts In The State Of Utah: Working Toward The Future, Andrew Call

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

The Utah State University Extension branch funded a research project designed to meet an identified need and create a baseline in knowledge of the implementation of environmentally sustainable practices among Utah ski resorts. Because of the potential impacts of climate change and unsustainable practices that negatively impact both the biophysical and human/cultural aspects of these environments, the ski resort industry is facing an uncertain future both environmentally and economically. However, very little is known about this issue, or how to address it. Collecting baseline information on the subject of environmental sustainability amongst Utah area ski resorts is crucial to ensure …

1. Improving The Yield Of Biodiesel From Microalgae And Other Lipids. 2. Studies Of The Wax Ester Biosynthetic Pathway And Potential Biotechnological Application, Bradley D. Wahlen

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

The production of biofuels and oleochemicals from renewable sources offers an opportunity to reduce our dependence on fossil fuels. The work contained in this dissertation has focused on developing and improving methods for the production of biodiesel from non-traditional feedstocks and understanding biosynthetic pathways that result in the production of oleochemicals and fuels.

Pure vegetable oil can account for 70-80% of the total cost of biodiesel production. Many low-cost oils contain high amounts of free fatty acids, which are unsuitable for base-catalyzed transesterification. Herein an approach is described that efficiently accomplishes the simultaneous esterification and transesterification of both free fatty …

The Survival And Growth Of Adult Bonneville Cutthroat Trout (Oncorhynchus Clarkii Utah) In Response To Different Movement Patterns In A Tributary Of The Logan River, Utah, Jared W. Randall

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

In the past many inland trout species were believed to be sedentary, only occupying small stream segments (20 meters) during their life span. Recently it has been found that cutthroat trout do move and many populations do contain both mobile and non-mobile strategies. Most organisms move to attain greater growth rates, but movement also leads to higher detection by predators. Both mobile and non-mobile strategies have been observed in Spawn creek, a tributary of the Logan River in Northern Utah. My research evaluated the movement patterns, survival, and growth of adult Bonneville cutthroat trout Oncorhynchus clarkii Utah. My objectives …

Test Case Generation Using Combinatorial Based Coverage For Rich Web Applications, Chad Maughan

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Web applications are increasingly moving business and processing logic from the server to the browser. Traditional, multiple-page request/response applications are quickly being replaced by single-page applications where complex application logic is downloaded on the initial page load and data is then subsequently fetched asynchronously via the browser's native XMLHttpRequest (XHR) object.

These new generation web applications are called Rich Web Applications (RWA). Frameworks such as the Google Web Toolkit (GWT), and JavaScript model-view-controller (MVC) frameworks such as Backbone.js are facilitating this move. With this migration, testing frameworks need to follow the logic by moving analysis and test generation from the …

Combinatorial-Based Prioritization For User-Session-Based Test Suites, Schuyler Manchester

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Software defects caused by inadequate software testing can cost billions of dollars. Further, web application defects can be costly due to the fact that most web applications handle constant user interaction. However, software testing is often under time and budget constraints. By improving the time efficiency of software testing, many of the costs associated with defects can be saved.

Current methods for web application testing can take too long to generate test suites. In addition, studies have shown that user-session-based test suites often find faults missed by other testing techniques. This project addresses this problem by utilizing existing user sessions …

Java Api-Aware Code Generation Engine: A Prototype, Chandra Sekhar Vijyapurpu

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Software reuse enhances a programmer's productivity and reduces programming errors. Improving software reuse through libraries and frameworks is a vast problem area. This thesis offers an approach to solve two sub-problems within the problem area - to identify the right library components, and to offer code snippets that use the components correctly. The Java API-Aware Code Generation Engine, or JAGE for short, is a prototype system that demonstrates the feasibility of generating semantically valid code snippets consisting of method calls to classes in the J2SDK library.

Developers often search for sample code snippets that describe how to use the …

The Mechanisms Of Hydride Exchange, Organic Combination And Displacement Reactions, Weifang Hao

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

The primary aim of this dissertation was to seek the answer to the question: “Is the single transition-state model appropriate for the fundamental reactions in organic chemistry?” The goal was accomplished by performing enormous kinetic data collection and detailed mechanistic analysis on several typical fundamental organic chemical reactions. Three new methodologies for differentiating between a simple one-step and complex multi-step mechanism were developed and extensively confirmed during the application in the kinetic studies of all of the reaction discussed in this dissertation. The three methods consist of (1) half-life dependence of kapp, (2) sequential linear pseudo-first-order correlation, and (3) revised …

Rock Properties And Structure Within The San Andreas Fault Observatory At Depth (Safod) Borehold, Northwest Of Parkfield, California: In Situ Observations Of Rock Deformation Processes And Fluid-Rock Interactions Of The San Andreas Fault Zone At ~ 3 Km Depth, Kelly Keighley Bradbury

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

The San Andreas Fault Observatory at Depth (SAFOD) is a scientific drilling experiment situated along the central creeping segment of the San Andreas Fault, near Parkfield, California, and north of a segment of the fault that has experienced large historical earthquakes. Drilling into active fault zones allows scientist’s to examine in situ rock samples and to record real-time data.

The main goal of this study is to characterize the geologic setting and rock properties of the San Andreas fault at ~ 3 km depth in the SAFOD borehole. In this region, the fault deforms nearly continuously through aseismic creep and …

Geothermal Alteration Of Basaltic Core From The Snake River Plain, Idaho, Christopher Joseph Sant

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

The Snake River Plain is located in the southern part of the state of Idaho. The eastern plain, which this study focuses on, is a trail of volcanics from the Yellowstone
hotspot. Three exploratory geothermal wells were drilled on the Snake River Plain. This project studies basaltic core from the first well at Kimama, north of Burley, Idaho. The objectives of this project are to establish zones of geothermal alteration and analyze the potential for geothermal power production near the center of the Snake River Plain. Thirty samples from 1,912 m of core were sampled and analyzed. Mineral data, temperature …

Planning In Incomplete Domains, Jared William Robertson

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Automated planning in computer science consists of finding a sequence of actions leading from an initial state to a goal state. People who have expert knowledge of the specific problem domain work with experts in automated planning to define the domain states and actions. This knowledge engineering required to create complete and correct domain descriptions for planning problems is often very costly and difficult. Our goal with incomplete planning is to allow people to program domains without the need for planning experts.

Throughout the process of instruction of intelligent systems, teachers can often leave out whole procedures and aspects of …

A 2d Finite Element/1d Fourier Solution To The Fokker-Planck Equation, Joseph Andrew Spencer

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Plasma, the fourth state of matter, is a gas in which a significant portion of the atoms are ionized. It is estimated that more than 99% of the material in the visible universe is in the plasma state. The process that stars, including our sun, combine atomic nuclei and produce large amounts of energy is called thermonuclear fusion. It is anticipated future energy demands will be met by large terrestrial devices harnessing the energy of nuclear fusion. A gas hot enough to produce the number of atomic collisions needed for fusion is necessarily in the plasma state. Therefore, plasmas are …

Integrating Remote Sensing And Ecosystem Models For Terrestrial Vegetation Analysis: Phenology, Biomass, And Stand Age, Gong Zhang

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Terrestrial vegetation plays an important role in global carbon cycling and climate change by assimilating carbon into biomass during the growing season and releasing it due to natural or anthropogenic disturbances. Remote sensing and ecosystem models can help us extend our studies of vegetation phenology, aboveground biomass, and disturbances from field sites to regional or global scales. Nonetheless, remote sensing-derived variables may differ in fundamental and important ways from ground measurements. With the growth of remote sensing as a key tool in geoscience research, comparisons to ground data and intercomparisons among satellite products are needed. Here I conduct three separate …

Water Infrastructure Challenges In Urbanizing Environments: A Case Study Of The 2009 Logan Canal Landslide, Kathryn Davis Henderson

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

In July, 2009 in Logan, Utah, a wet, steep hillside failed, leveling a home below and destroying an irrigation canal that ran along the hill. Three people were killed. The event and the resulting policy changes present an opportunity to uncover how frames, or social constructions, play into the policy development cycle. This case also uncovers the nuances involved when old infrastructure takes on new social meanings. Planners and policymakers that pay attention to frames and social dimensions may be able to minimize conflict.

The landslide received immediate media attention and spurred state legislation on canal safety. The event had …

Homogenization Of Large-Scale Movement Models In Ecology With Application To The Spread Of Chronic Wasting Disease In Mule Deer, Martha J. Garlick

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Chronic wasting disease (CWD) is a transmissible spongiform encephalopathy (TSE) that affects deer, elk, and moose. TSEs are prion diseases which include mad cow disease and scrapie in sheep and goats. The disease agent is a misshapen protein called a prion, which causes lesions in the brain, and to date, there is no cure. CWD is a slow-developing, fatal disease, which is rare in the free-ranging mule deer population of Utah. Infected deer shed prions into the environment through saliva, feces, and decaying carcasses. These prions remain infective in soils for many years and healthy deer may contract CWD by …

Factors Influencing The Distribution Of Brown Trout (Salmo Trutta) In A Mountain Stream: Implications For Brown Trout Invasion Success, Christy Meredith

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Brown trout (Salmo trutta), one of the world’s most successful introduced species in river and lake systems, negatively impacts native species through predation, competition, and systemwide effects. Thus, there is a need to understand factors controlling the distribution of brown trout, in order to prioritize and develop conservation and management strategies. Within the context of invasion success, I investigated how the physical characteristics of the Logan River influence the distribution of brown trout, as well as the potential for brown trout predation on a native fish, the mottled sculpin (Cottus bairdi).

In chapter 1, I evaluated …

The Influence Of Geology And Other Environmental Factors On Stream Water Chemistry And Benthic Invertebrate Assemblages, John R. Olson

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Determining if a stream has been degraded by human activities requires knowing what that stream’s natural water quality and freshwater species composition would likely be without any alteration. However stream natural conditions vary greatly from stream to stream, making predicting natural conditions difficult. To determine natural stream conditions, I developed models to predict natural stream water chemistry at individual streams across the western USA. Specifically, the models predict a stream’s electrical conductivity (a measure of the amount of solids dissolved in water), acid neutralization capacity, and concentrations of calcium, magnesium, sulfate, total phosphorus, and total nitrogen. These models predict chemistry …

Production Of Biodiesel From Oleaginous Organisms Using Underutilized Wastewaters, Valerie Godfrey

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

As part of the BioEnergy Team at Utah State Univeristy, my research objectives have been centered around the common theme of innovating new methods and
technology for producing biological compounds and, by means of chemical conversion and/or extraction, isolating new forms of biodiesel available for transportation fuel.
Within the broad scope of this project, I focused on the replacement of freshwater in cultivating such biological systems with wastewaters. If accomplished and correctly
applied, such research would reduce the environmental impact of biodiesel production by reducing the demand for freshwater. It also would reduce production costs by reducing the amount of …

Environmental Assessment Of Streams: Linking Land Use, Instream Stressors, And Biological Indices To Infer Likely Causes Of Ecological Impairment, Jacob J. Vander Laan

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

To protect and restore stream biota, managers need to be able to both detect biological degradation and infer likely causes of impairment. Managers commonly develop indices based on stream biota to assess the biological condition of streams. However, the performance of these indices dictates the ability to detect degradation, and although index performance varies widely, the sources of this variation are often unclear. In addition, bioassessments do not identify causes of impairment. My thesis research had two general goals: 1) develop indices to measure biological condition in Nevada streams and 2) quantify relationships between land uses, stressors, and biological condition …

Peer-To-Peer Simulation Of Massive Virtual Environments, James Dean Mathias

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Massively multiplayer games make up a large and growing segment of the computer game industry. One of the best known examples of these games is World of Warcraft, developed and published by Activision Blizzard. World of Warcraft boasts a subscriber base of over eleven million active subscribers, earning an estimated $1 billion dollars in 2010.

Some of the core issues for companies that publish these games are the cost of the computers, Internet bandwidth usage, and supporting technical staff. These costs easily reach hundreds of thousands of dollars each month, and in the case of World of Warcraft, millions of …

A Localized Geometric-Distortion Resilient Digital Watermarking Scheme Using Two Kinds Of Complementary Feature Points, Jiyuan Wang

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

More and more digital images are being distributed over the Internet to an evergrowing number of people for sharing, studying, or other purposes. However, most of those digital products are exposed without any protection, and such information can be easily transferred, copied, and tampered without authorization simply by using readily available digital multimedia editing software. Digital watermarking techniques have been developed as a tool to discriminate whether the original content of digital media is tampered or not. A digital watermark is embedded on digital images as an invisible message and is used to demonstrate the proof by the owner.

In …

Adaptive Re-Segmentation Strategies For Accurate Bright Field Cell Tracking, Nare Hayrapetyan

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Cell migration is central for many fundamental biological processes and development of multi-cellular organisms. The failure of cells to migrate or migration of cells to inappropriate locations during embryo development can result in life threatening consequences such as brain malfunctions. In adults, cell migration plays an important role in wound healing and immune responses. Failure in these processes can have dramatic medical implications and can lead to vascular diseases and tumor formation. Therefore, studying cell migration is critical to helping prevent and cure diseases.

Cell migration is usually studied by observing cells photographed through a microscope at regular time intervals. …

Rationalizing Structure, Stability, And Chemical Bonding Of Pure And Doped Clusters Isolated And Solvated Multiply Charged Anions, And Solid State Materials, Alina P. Sergeeva

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Chemistry is the study of materials and the changes that materials undergo. One can tune the properties of the known materials and design the novel materials with desired properties knowing what is responsible for the chemical reactivity, structure, and stability of those materials. The unified chemical bonding theory could address all these questions, but we do not have one available yet. The most accepted general theory of chemical bonding was proposed by Lewis in 1916, though Lewis’s theory fails to explain the bonding in materials with delocalized electron density such as sub-nano and nanoclusters, as well as aromatic organic and …

A Novel And Effective Short Track Speed Skating Tracking System, Yuxuan Wang

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Short track speed skating lends itself to intense competitions with a strong visual impact. Thus, the sport has become increasingly popular. In fact, in 1992, short track speed skating became an official Winter Olympic sport with four events, and four more events were added in 2002. Because of the sport’s growing popularity, there is a high demand from both coaches and TV broadcasters for a means of automatically gathering competition data such as trajectories, velocities, and 2D reconstruction animation. We call this vision-based sports video analysis.

In competitive short track speed skating, multiple skaters skate together on an ice track …