Physical Sciences and Mathematics Commons^™

Lithofacies And Sequence Architecture Of The Lower Desert Creek Sequence, Middle Pennsylvanian, Aneth, Utah, Chanse James Rinderknecht

Theses and Dissertations

Middle Pennsylvanian (Desmoinesian) strata of the Lower Desert Creek (LDC) sequence within the sub-surface Greater Aneth Field (GAF) reflect a hierarchy of 4th and 5th order carbonate-dominated cycles. The Lower Desert Creek sequence, along the studied transect are composed of eight carbonate facies deposited on an east-facing shelf. There is a lateral transition from open marine algal buildup from the southeast (cores R-19, Q-16, O-16, and J-15) to a more restricted lagoonal environment to the northwest (core K-430 and E-313). The Lower Desert Creek sequence within the GAF contains three main parasequence sets: a basal, relatively deep-water unit (LDC 1), …

Curriculum Decisions And Reasoning Of Middle School Teachers, Anand Mikel Bernard

Theses and Dissertations

For decades curriculum materials have been used as a means to reform the manner in which mathematics is taught. In an attempt to better understand what impact curriculum materials have on the teaching and learning of mathematics, researchers have begun to analyze the process in which teachers transform curriculum materials into instruction. Given that many of these studies have been broad in nature, I sought to study the specific decisions that three teachers made when planning lesson on geometric transformation and their reasoning for those decisions. In this study I found that while the participants in this study ignored the …

Using Advanced Psf Subtraction Techniques On Archival Data Of Herbig Ae/Be Stars To Search For New Candidate Companions, Emily Diane Safsten

Theses and Dissertations

Herbig Ae/Be (HAeBe) stars are intermediate mass (2-10 solar mass) pre-main sequence stars with circumstellar disks. Observing planets within these young disks would greatly aid in understanding planet formation processes and timescales particularly around massive stars. So far, only one planet, HD 100546 b, has been confirmed to orbit a HAeBe star. With over 250 HAeBe stars known, and several observed to have disks with structures thought to be related to planet formation, it seems likely that there are as yet undiscovered planetary companions within the circumstellar disks of some of these young stars. Direct detection of a low-luminosity companion …

Function Of Ric-8a In G Protein E+- Subunit Biogenesis, Barry Willardson

Journal of Undergraduate Research

1. Grant Ludlam. The MEG award helped support Grant’s work from January 2015 through August 2016. During this time Grant has worked on three projects. He investigated the role of Ric8A in the folding of the G protein a subunit and its assembly into the G protein heterotrimeric complex. Unfortunately, his results showed that deletion of Ric8A in the photoreceptor cells of mice did not affect G protein signaling. As a result, he changed his research focus to determining the structure of the BBSome core complex. He assisted a graduate student, Takuma Aoba, in this work. They used a combination of …

Mentoring Undergraduates At The Intersection Of Organic Synthesis And Peptide Science, Steven L. Castle

Journal of Undergraduate Research

Our academic goals were threefold. First, we aimed to synthesize building blocks and begin assembling them to construct the anticancer peptide yaku’amide A (YA, Figure 1). Our purposes in synthesizing YA were to develop new chemical reactions suitable for efficiently preparing its unusual amino acids (shown in red and blue in Figure 1), and synthesize simplified analogues for use in studies designed to reveal its biological target and mode of action. Our second academic goal was derived from the first and involved investigating the ability of bulky dehydroamino acids (i.e., the amino acids of YA shown in blue in Figure …

A Novel Approach To A Big Simulation Problem: Creating Efficient Dry Granular Material Simulations With Accurate Visual Detail And Behavior, Seth Holladay

Journal of Undergraduate Research

We received a MEG grant for researching the simulation of granular materials for computer graphics and animation. Materials such as sand and snow simulation is very expensive but necessary for productions, as well as hard to control the look, so I have been mentoring undergraduate and graduate students researching how to make sand simulations both efficient and art directable.

Alzheimer’S Disease: A New Model Defining The Mechanism Of Iron- Catalyzed Radical Damage To Neurons, Richard Watt, Jonathan Wisco

Journal of Undergraduate Research

The MEG proposal focused on understanding how elevated homocysteine levels cause the inability of cells to control iron levels as a cause for Alzheimer’s disease. Iron is associated with the amyloid plaques and tau tangles that are proposed to cause damage to neurons. Dr. Wisco and I previously submitted an NIH R15 proposal that was viewed positively but was not funded due to a lack of preliminary data. Our goal was to use MEG funding to provide preliminary data supporting the hypothesis. We proposed that Homocysteine was a dangerous trigger for disrupting iron metabolism. Biochemical techniques, immunohistochemistry techniques and MRI …

A Photometric Approach To The Redshift Of Galaxies, John Bohman, Joseph Moody

Journal of Undergraduate Research

It is necessary to study the distribution of matter to better understand the universe. There are many difficulties associated with this task however, one of the most basic being that that the universe is an extremely large space, and it takes a lot of time and effort to observe faint objects. Multi fiber spectrometers have made this task much easier, and over 1.4 million spectroscopic redshifts have been obtained. While this is certainly impressive, much remains to be done. This project attempts to develop a survey method capable of detecting and finding the redshift of relatively close (meaning a redshift …

Weak Synchronization In Excitatory – Inhibitory Neuronal Networks, Joel Eliason, Benjamin Webb

Journal of Undergraduate Research

One ubiquitously observed dynamic phenomenon in the nervous system is that of weak synchronization or clustering, a behavior in which a large group of neurons in a population will all fire synchronously and then fall out of synchronization. When isolated to neurons that only form short-range connections, this behavior is typically referred to as “neuronal avalanches”, and is thought to be particularly important for robustness of information transmission as well as sensitivity to inputs. Given these potential computational benefits, avalanches have been a focus of theoretical biologists for the past 20 years. In particular, my project focused on the conditions, …

Identifying Binary Brown Dwarf Systems Using Model Point Spread Functions, Kyle Matt, Denise Stephens

Journal of Undergraduate Research

The purpose of this project was to improve upon a method for discovering binary brown dwarf systems, and create a program to speed up the implementation of that method. A Brown Dwarf (BD) is a celestial object that is not massive enough to undergo hydrogen fusion in its core, meaning it is too small to be a star, but is also too big to be a planet. BDs can form in low-mass binary pairs. A stellar object located many parsecs away will act as a point source of light for an observer on Earth, therefore the light from such an …

Machine Learning With Scattering Transforms, Jacob Hansen, Gus Hart

Journal of Undergraduate Research

Our goal was to implement scattering transforms as a mathematical representation of materials. The intention of this project was to build intuition on this technique using model data in one and two dimensions. The tools created here will be used as templates in further projects on real materials data. The intuition built during this project is crucial to the machine learning framework for materials design that we hope to build in the near future.

Calculating Music Similarity With Mobile Device Playlists, Jacob O'Bryant, Dennis Ng

Journal of Undergraduate Research

Music recommendation systems, such as Pandora and Spotify, help listeners to discover new music. The similarity of different songs is an important measure used in music recommendation. We have studied manually-created playlists on mobile devices to see if they can be used to accurately calculate song similarity. We collected playlists from 41 research subjects and used a co-occurrence model to calculate similarity between songs in the collection.

Using Frequency Noise Feedback To Satabilize Extended Cavity Diode Lasers For Use In Atomic Physics, Mckinley Pugh, Dallin Durfee

Journal of Undergraduate Research

Diode lasers in particular are useful in atomic physics because they are durable, compact, and relatively inexpensive. Unfortunately diode lasers also have linewidths that are much wider than atomic transitions. One common method to narrow the linewidth of diode lasers is to add a reflection grating outside the laser, creating an extended cavity diode laser (ECDL). While ECDLs are effective at narrowing the linewidth, they also introduce so many variables that affect the wavelength of the laser that small changes in the laser’s environment can cause the laser to mode hop, or jump to an entirely different wavelength.

Characterizing Great Salt Lake Dust Relative Other Regional Dust Sources, Colin Hale, Carling Greg

Journal of Undergraduate Research

Dust storms occur frequently along the Wasatch Front. These dust events may have negative effects on human health and agriculture. To help understand dust events along the Wasatch Front, this study focuses on analyzing dust deposition to better locate dust emission sources. Understanding the source of dust events is important. This is important because Great Salt Lake water levels are dropping exposing lakebed. This newly expose lakebed may result in increased frequency and intensity of dust events. To understand if this lakebed is affecting the Wasatch Front and acting as an emission source.

Identifying Risk Factors For Interstate Crashes Using Spatial Statistics, Kaitlin Gibson, Matthew Heaton

Journal of Undergraduate Research

The goal of systemic highway safety improvement is to identify road characteristics, called risk factors, associated with a higher prevalence of crashes, so that the roads can be modified to avoid these characteristics. However, the statistical analyses these improvement projects are based on generally use methods which are not appropriate for the data. Our project implements novel spatial statistical methodology which is appropriate and state-of-the-art to identify these risk factors.

An Algorithm For Multiple Regression Variable Selection For Biochemical Oxygen Demand, Zach White, Dr. William Christensen

Journal of Undergraduate Research

Biochemical Oxygen Demand (BOD) is used to measure of the amount of oxygen required by aerobic bacteria and other microorganisms to stabilize decomposable organic matter. It is run as a laboratory based biodegradation test and relies upon the presence of a thriving microbial community that may be naturally present in the sample or artificially introduced by addition of a seed, commonly a known volume of sewage effluent of known BOD. A standard BOD test is run in the dark at a temperature of 20 degrees Celsius for 5 days. This is defined as a five-day BOD (BOD5), which is the …

Utilizing The Power Of Graphical Processing For Dna Mapping: A Comparison Of Gnumap And Barracuda, Cole Lyman, Mark Clement

Journal of Undergraduate Research

Recent advances in genome sequencing technologies have resulted in a large increase in the amount of genetic data available. Large Genome Wide Association Studies (GWAS) have the potential to identify the causes of cancer, Alzheimer’s disease, heart failure and many other diseases if the large quantities of data that are becoming available can be analyzed effectively. Next-generation read mapping software, a crucial step in analyzing genetic data, is slow while trying to achieve high mapping accuracy. One approach to speeding up next-generation read mapping focuses on using Graphical Processing Units (GPUs). This project compared the effectiveness of two genome mappers, …

Trace Element Analysis Of Quartz Grains In The Wah Wah Springs Tuff And Granodiorite Intrusion, Joel Barker, Dr. Eric Christiansen

Journal of Undergraduate Research

The Wah Wah Springs tuff and cogenetic granodiorite were part of the creation of the Indian Peak-Caliente Caldera Complex, which lies on the Nevada-Utah border (Skidmore, 2013). The complex formed during the middle Cenozoic (36-18 Ma) during an episode of explosive silicic activity (Best et al., 2013). Rollback of the subducting lithosphere likely caused the silicic activity, evidenced by the migration of magmatism southward (Best et al., 2013). The dehydration of the subducting oceanic lithosphere caused mafic magmas high in water to rise and fractionate in continental crust before eruption (Skidmore, 2013). Over twenty-four different ignimbrites have been found in …

Seeing The World Through New Eyes: Implementing Map-Based Mobile Apps In Field Trips And Research, Mariah Chambers, Ron Harris

Journal of Undergraduate Research

Mobile apps are a resource that can aid in field trip instruction and enhance students’ learning. Because the specific location of the field trip is often an important element in overall understanding, map-based learning materials can be used to integrate information with the place, providing context for the concepts that will be learned on the field trip. The purpose of this project was twofold. One purpose was to provide professors with information and instructions for using map-based mobile apps to prepare students for, and provide resources during, field trips and study abroad experiences. A second purpose was to implement the …

Characterizing The Design Space Of Oscillatory Biological Networks, Leanne Lunsford, Denise Stephens, Eric Hintz

Journal of Undergraduate Research

Characterizing the relevant parameters of a design space in order to satisfy a specific behavior criterion is an important problem throughout all of science and engineering. In this project we proposed to apply model reduction to the case of biological oscillations involving Michaelis-Menten reactions. By removing irrelevant parameters from a fully connected network we were able to reduce a known problem in systems biology to a more general model. Furthermore, significant progress has been made in applying Manifold Boundary Approximation Method (MBAM) to oscillatory models in systems biology.

Active Control Of Cylindrical Shells Using The Weighted Sum Of Spatial Gradients (Wssg) Control Metric, Pegah Aslani

Theses and Dissertations

Cylindrical shells are common structures that are often used in industry, such as pipes, ducts, aircraft fuselages, rockets, submarine pressure hulls, electric motors and generators. In many applications it is desired to attenuate the sound radiated from the vibrating structure. There are both active and passive methods to achieve this purpose. However, at low frequencies passive methods are less effective and often an excessive amount of material is needed to achieve acceptable results. There have been a number of works regarding active control methods for this type of structure. In most cases a considerable number of error sensors and secondary …

Sedimentology And Taphonomy Of The Abydosaurus Mcintoshi Quarry, (Naturita Formation, Early Cretaceous, Latest Albian), Dinosaur National Monument, Utah, Aaron Daniel Holmes

Theses and Dissertations

The holotypic locality of the brachiosaurid titanosauriform sauropod, Abydosaurus mcintoshi, is quarry DNM-16, located in Dinosaur National Monument. The bones are preserved near the base of a heterolithic, trough cross stratified to planar bedded sandstone channel complex. The trough cross to planar bedded sandstones mark times of variable flow with times of high flow velocity based on bones whose upper surfaces were eroded before final burial. The abundance of mud with the dominant medium to fine sand, and poorly confined sandstone channels indicate the bones were transported and buried in medial to distal intermittent flows of a distributive fluvial …

Stability Of Planar Detonations In The Reactive Navier-Stokes Equations, Joshua W. Lytle

Theses and Dissertations

This dissertation focuses on the study of spectral stability in traveling waves, with a special interest in planar detonations in the multidimensional reactive Navier-Stokes equations. The chief tool is the Evans function, combined with STABLAB, a numerical library devoted to calculating the Evans function. Properly constructed, the Evans function is an analytic function in the right half-plane whose zeros correspond in multiplicity and location to the spectrum of the traveling wave. Thus the Evans function can be used to verify stability, or to locate precisely any unstable eigenvalues. We introduce a new method that uses numerical continuation to follow unstable …

The Ogcleaner: Detecting False-Positive Sequence Homology, Masaki Stanley Fujimoto

Theses and Dissertations

Within bioinformatics, phylogenetics is the study of the evolutionary relationships between different species and organisms. The genetic revolution has caused an explosion in the amount of raw genomic information that is available to scientists for study. While there has been an explosion in available data, analysis methods have lagged behind. A key task in phylogenetics is identifying homology clusters. Current methods rely on using heuristics based on pairwise sequence comparison to identify homology clusters. We propose the Orthology Group Cleaner (the OGCleaner) as a method to evaluate cluster level verification of putative homology clusters in order to create higher quality …

Formation Of Rapakivi Feldspars In The Deer Isle Granite Complex, Coastal Maine: In Situ Lead Isotope And Trace Element Analysis, William Desmond Obrien

Theses and Dissertations

Rapakivi and alkali feldspar phenocrysts from the Deer Isle Granite Complex were investigated using in situ trace element and Pb isotope geochemistry to see if magma mixing or isothermal decompression was responsible for their formation. Pb isotope and trace element profiles, along with CL imagery of quartz phenocrysts, indicate compositional changes in the magma chamber occurred during rapakivi and alkali feldspar growth. Repeated episodes of magma mixing/replenishment by relatively isotopically primitive and LREE enriched magmas (along with hybridized variations with the host magma) created localized disequilibration. Alkali feldspar phenocrysts proximal to these zones of thermal perturbation were first resorbed and …

Using Multiview Annotation To Annotate Multiple Images Simultaneously, Timothy C. Price

Theses and Dissertations

In order for a system to learn a model for object recognition, it must have a lot of positive images to learn from. Because of this, datasets of similar objects are built to train the model. These object datasets used for learning models are best when large, diverse and have annotations. But the process of obtaining the images and creating the annotations often times take a long time, and are costly. We use a method that obtains many images of the same objects in different angles very quickly and then reconstructs those images into a 3D model. We then use …

Informing The Use Of Hyper-Parameter Optimization Through Meta-Learning, Samantha Corinne Sanders

Theses and Dissertations

One of the challenges of data mining is finding hyper-parameters for a learning algorithm that will produce the best model for a given dataset. Hyper-parameter optimization automates this process, but it can still take significant time. It has been found that hyperparameter optimization does not always result in induced models with significant improvement over default hyper-parameters, yet no systematic analysis of the role of hyper-parameter optimization in machine learning has been conducted. We propose the use of meta-learning to inform the decision to optimize hyper-parameters based on whether default hyper-parameter performance can be surpassed in a given amount of time. …

Diversity And Efficiency: An Unexpected Result, Joseph Smith Johnson

Theses and Dissertations

Empirical evidence shows that ensembles with adequate levels of pairwise diversity among a set of accurate member algorithms significantly outperform any of the individual algorithms. As a result, several diversity measures have been developed for use in optimizing ensembles. We show that diversity measures that properly combine the diversity space in an additive and multiplicative manner, not only result in ensembles whose accuracy is comparable to the naive ensemble of choosing the most accurate learners, but also results in ensembles that are significantly more efficient than such naive ensembles. In addition to diversity measures found in the literature, we submit …

Robust Object Tracking: A Path-Planning Approach, Bryant Eldon Chandler

Theses and Dissertations

When attempting to follow ground-based moving objects (hereafter referred to as ``waldos'') using an unmanned air vehicle (UAV), occlusion can become a significant problem for computer vision algorithms designed to track the object. When a waldo is occluded, the computer vision algorithm loses the track and the UAV's ability to predict movement degrades. We propose a path-planning and replanning method that moves a UAV to a location that maximizes the important waldos that can be seen while accounting for occlusion, and attempts to maximize the area it can see during travel. The proposed work moves beyond state-of-the-art algorithms designed to …

A Green Form-Based Information Extraction System For Historical Documents, Tae Woo Kim

Theses and Dissertations

Many historical documents are rich in genealogical facts. Extracting these facts by hand is tedious and almost impossible considering the hundreds of thousands of genealogically rich family-history books currently scanned and online. As one approach for helping to make the extraction feasible, we propose GreenFIE—a "Green" Form-based Information-Extraction tool which is "green" in the sense that it improves with use toward the goal of minimizing the cost of human labor while maintaining high extraction accuracy. Given a page in a historical document, the user's task is to fill out given forms with all facts on a page in a document …