Physical Sciences and Mathematics Commons^™

The Regulation Of Atg9a-Mediated Aggrephagy By An Ulk1-Independent Atg13-Atg101 Complex, Joshua Youngs

Undergraduate Honors Theses

Aggrephagy, a type of autophagy, is an essential cellular process by which protein aggregates are collected and broken down in the lysosome. Protein aggregates are implicated in several diseases including Alzheimer’s disease, diabetes, and cancer. Here, we investigate the ATG13-ATG101 protein complex, a sub-complex of the canonical ULK1 complex whose regulatory role in aggrephagy is not completely understood. We also develop a protein fragment complementation (PFC) assay using the biotin ligase TurboID to study the functions of the ATG13-ATG101 complex with increased specificity. We demonstrate that ATG13 is required for optimal degradation of p62-ubiquitin condensates. We also show that a …

Finding Patterns In The Inertia Of The Distance Squared Matrix Of Unicyclic Graphs, Kellon Sandall, Mark Kempton, Christian Howell

Undergraduate Honors Theses

We analyze the spectrum of the distance squared matrix of a tree and give a relation between the inertia of the distance squared matrix and the structure of the tree. We take the result one step further and consider the addition of exactly one cycle in the tree. We obtain an expression for the inertia of the distance squared matrix of a cycle graph. We obtain a bound on the inertia of the distance squared matrix of an arbitrary unicyclic graph.

Implementing A High-Performance Quantum Computing Emulator, Reece Robertson

Undergraduate Honors Theses

We implement a quantum computing emulator after the manner described by Häner et al. with the goal of temporal and spatial savings. The emulator is compared to the Intel Quantum Simulator to verify speedup and spatial savings over the simulator method. We also implement Shor's algorithm in the emulator and use it to solve a nontrivial factoring problem. This demonstrates that the emulator makes quantum computing more accessible on at least two accounts: it allows users to solve nontrivial problems quickly and it provides those looking to enter quantum computing with an accessible place to start. Finally, we outline future …

Outvoice: Bringing Transparency To Healthcare, Autumn Clark

Undergraduate Honors Theses

Industries are not incentivized to price reasonably and spend responsibly if consumers do not have the ability to shop around within that industry, and shopping around is not possible without pricing transparency (knowing how much a good or service costs before purchasing it). But in the healthcare industry, we typically default to whichever clinic or hospital is closest, with no prior knowledge of what costs we can expect to incur at that particular institution. According to a poll published by Harvard University, nine out of ten Americans feel the healthcare industry is too opaque and greater transparency is needed.

We …

Decision Based Learning Course Design & Implementation For Introductory Statistics, Austin Heath

Undergraduate Honors Theses

Researchers in multiple industries (biomedicine, engineering, etc.) cite the selection of an appropriate statistical test as a common problem. Experts draw on a framework of conceptual and procedural knowledge to navigate when to use statistical methods. Students also struggle determining the correct statistical method to use for a given research question. This is because they lack the opportunity to practice recognizing a host of features in each research question that provide clues for experts as to which method is most appropriate. “Decision Based Learning” (DBL) is a teaching method designed to help teachers and students address this struggle. In this …

Intermountain West Lichen Dna Reference Library, Brian Colgrove

Undergraduate Honors Theses

Accurate estimates of biodiversity can play crucial roles in monitoring ecological health. BYU’s Lichen Air Quality Biomonitoring program (Wright) represents one of the largest biomonitoring programs in the nation. Recently, DNA metabarcoding approaches have shown promise in streamlining lichen biodiversity inventories. However, to date, lichen diversity of western North America is poorly represented in available DNA reference libraries, preventing biologists and land managers from using DNA barcoding to identify unknown specimens. To solve this problem, I have developed a DNA reference library for over 500 species occurring in the Intermountain West region. Using bioinformatic and statistical tools, I created a …

Who Uses Multi-Factor Authentication?, Leah Roberts

Undergraduate Honors Theses

A sample of 47 BYU students were recruited to participate in this study to determine who was using Multi-factor Authentication (MFA) on their online accounts. This study determined that there were many different factors that separated those who used MFA and those who did not. Some of those factors included: time spent on the internet each day, gender, the website itself, and personal privacy behaviors.

A Fret Flow Cytometry-Based Screening Assay For Multiplex Analysis Of Metabolites In T. Brucei, Ronald A. Zegarra

Undergraduate Honors Theses

Kinetoplastid parasites are a significant public health issue in some tropical and subtropical regions of the world. Kinetoplastid parasites all require glycolysis for survival, with host glucose key for ATP production. One such parasite, Trypanosoma brucei, exclusively metabolizes glucose in its bloodstream form. Trypanosomal glycolysis is unique because it displays unconventional structural features. Hence, glucose metabolism has been studied extensively in T. brucei and is a therapeutic target in kinetoplastid parasites.The lack of in vivo analytical techniques for measuring vital glycolytic metabolites in situ has restricted the ability of researchers to test, with high sensitivity and specificity, the essential roles …

Exploration Of Fluorinated Α,Β-Dehydroamino Acids And Their Structure, Austin Lesueur

Undergraduate Honors Theses

This thesis explores the synthesis of fluorinated α,β-dehydroamino acids, specifically a fluorinated dehydrovaline derivative. Previous work has been done on the equivalent dehydrovaline derivative without fluorine present and this work builds toward the fluorinated version with the goal of comparing the two structurally. The synthesis presented here pulls from previous synthetic strategies employed for dehydrovaline while also exploring the synthetic impact of the electronegative fluorine atoms.

Light And Truth: Measuring Unseen Harm In Individuals And Communities, Hannah Pfost

Undergraduate Honors Theses

While the fields of physics and international development may seem disparate, the insights gained from studying each one of them can improve understanding of the other. Here, I demonstrate that concept as applied to computational optics and historical memory. Thus, the purpose of this project is threefold: (1) to computationally model light transport through tissue, and use that model to inform choices about a physical system; (2) to determine the types of historical memory recommended in the final reports of truth commissions; and (3) to give evidence for the usefulness of human-centered design in both areas. To model light transport, …

Telsam-Target Protein Fusions Can Form Diffraction-Quality Crystals Without Direct Inter-Polymer Contacts, Moriah Longhurst

Undergraduate Honors Theses

X-ray diffraction is a robust method for determining the detailed 3D structures of specific proteins. However, this requires the formation of well-ordered protein crystals, a process that is time-consuming, expensive, and only has about a 10-30% success rate. New methods are needed to enable the efficient crystallization of challenging proteins. One such technique is explored here, which utilizes a protein polymer (the sterile alpha motif domain of the human protein translocation Ets leukemia, or TELSAM) as a crystallization chaperone to form a more ordered crystal lattice of target proteins and drive crystallization. This method was successfully used to crystallize, collect …

Realium: Building The Future Of Real Estate On The Blockchain, Demitri Haddad

Undergraduate Honors Theses

This paper discusses the prospective challenges, limitations and opportunities in the real estate sector for blockchain. It outlines the idea of Realium, a financial technology application that aims to assist in the purchase, sale, and legal compliance of real estate assets. For more information see docs.realium.io

Computational Development Of A Miniature Quantum Dot Spectrometer For Use In Space, Joseph Richardson

Undergraduate Honors Theses

Miniature spectrometers are of great interest to NASA as necessary instrumentation is scaled down and optimized for specific space application. Semiconductor nanocrystals called quantum dots (QD) are being used to create a miniature high-resolution filter-based spectrometer, with the goal of use in space within 5 years. Computational imaging techniques— such as automated image analysis and mathematical spectrum reconstruction algorithms—are key to making the QD spectrometer a reality. This thesis will discuss the process of developing these computational methods, along with the improvements that have occurred from previous work.

The Communicative Effects Of Anonymity Online: A Natural Language Analysis Of The Faceless, Caleb Johnson

Undergraduate Honors Theses

An ever-increasing number of Americans have an active social media

presence online. As of March 2020, an estimated 79% of Americans were active

monthly users of some sort. Many of these online platforms allow users to

operate anonymously which could potentially lead to shifts in communicative

behavior. I first discuss my compilation process of the Twitter Anonymity

Dataset (TAD), a human-classified dataset of 100,000 Twitter accounts that are

categorized by their level of identifiability to their real-world agent. Next, I

investigate some of the structural differences between the classification levels

and employ a variety of Natural Language Processing models and …

Building An Ins-1 Cdna Library For A Genome-Wide Crispr-Cas9 Screen, Idongesit Ekpo

Undergraduate Honors Theses

By the year 2040, an estimated 642 million people are expected to have diabetes globally. Diabetes results from an elevation of metabolic stressors, such as glucotoxicity, lipotoxicity, oxidative stress and apoptosis. In type 2 diabetes, these stressful conditions contribute to the malfunction and loss of functional insulin-producing β-cells. Current treatment methods for diabetes include insulin therapy, islet transplant and anti-diabetes medication. These treatments are not curative and ignore other factors that contribute to the pathogenesis of diabetes beyond insulin resistance and islet β-cell failure. Previous research on β-cells has focused on ways to replace functional β-cell mass, trigger β-cell proliferation, …

Using Group Affinity To Predict Community Formation In Social Networks, Joseph Leung

Undergraduate Honors Theses

A well-studied topic in network theory is detecting the communities found in real-world networks. Community detection is a technique to better understand the way in which small dense substructures appear in these networks. Such substructures can often tell important information about groups that form in such systems. A prominent feature of many networks is that they evolve over time, forming and dissolving new edges between different nodes that appear. In this thesis, we consider how we can use the community structure of a network at a certain point in time to predict the state of a network’s communities at some …

An Actuarial Approach To Personal Injury Protection Severity, Jason Colgrove

Undergraduate Honors Theses

Insurance companies examine the risk of financial losses for their policyholders as a way to accurately price insurance policies. Within the automobile insurance sector, the frequency of crashes and the associated liabilities started to increase in late 2013 when it had been on the decline for close to a decade. The purpose of this research focuses on the possible correlated variables that could lead to a better understanding of this change. To embark on this task, we teamed up with the Society of Actuaries, Casualty Actuarial Society, and the American Property Casualty Insurance Association to obtain data regarding frequency, severity, …

Gamma-Ray Burst Afterglow Dynamics In Inhomogeneous Interstellar Media, Jacob Fields

Undergraduate Honors Theses

Gamma-ray bursts (GRBs) are the most luminous electromagnetic phenomena in the universe, but much remains unknown about them. Many models invoked to explain their highly variable light curves are based on complicated dynamics and interactions involving the GRB progenitor but assume simple circumstellar environments. Many long GRBs, however, show late time optical and x-ray flares that may be an indication of a much richer environment. Relativistic hydrodynamics simulations are used to study a family of initial data with a relativistic blast wave encountering a dense circumstellar shell of matter, similar to what an aging star expelling the outer layers of …

Using Logical Specifications For Multi-Objective Reinforcement Learning, Kolby Nottingham

Undergraduate Honors Theses

In the multi-objective reinforcement learning (MORL) paradigm, the relative importance of environment objectives is often unknown prior to training, so agents must learn to specialize their behavior to optimize different combinations of environment objectives that are specified post-training. These are typically linear combinations, so the agent is effectively parameterized by a weight vector that describes how to balance competing environment objectives. However, we show that behaviors can be successfully specified and learned by much more expressive non-linear logical specifications. We test our agent in several environments with various objectives and show that it can generalize to many never-before-seen specifications.

An Analysis Of Opiate Prescription For Chronic Degenerative Disease And Other Pain Syndromes, Catherine Sawyer

Undergraduate Honors Theses

Utilizing the National Ambulatory Medical Care Survey (NAMCS) database, this thesis explores patterns of opiate prescribing during time period from 1993 to 2016, which includes the time period when the opiate crisis was recognized in the United States and efforts begun to combat it. We analyze these patterns particularly as they relate to patients who were prescribed opiates and who were simultaneously suffering from various chronic conditions, and interactions between prescription of opiates and diagnosis of chronic conditions. We examine which demographic groups were most likely to receive opiates, and considered opiate prescription trends among patients with any pain diagnosis …

Machine Learning For Effective Parkinson's Disease Diagnosis, Brennon Brimhall

Undergraduate Honors Theses

Parkinson’s Disease is a degenerative neurological condition that affects approximately 10 million people globally. Because there is currently no cure, there is a strong motivation for research into improved and automated diagnostic procedures. Using Random Forests, a computer can effectively learn to diagnose Parkinson’s disease in a patient with high accuracy (94%), precision (95%), and recall (91%) across the data of over 2800 patients. Using similar techniques, I further determine that the most predictive medical tests relate to tremors observed in patients.

Dynamic Coalescence As A Mathematical Model Of Leadership And Empirical Evidence Of The Value Of Strategic Sacrifice, Jacob D. Valentine

Undergraduate Honors Theses

The topic of leadership belongs to a rich literature that is deep in historical documentation and broad by the many disciplines that have attempted to understand it. However, the contributions of quantitative theorists are scarce, which has resulted in theories of leadership that are primarily qualitative and often subjective. This paper begins building a bridge between the existing scholarship and a more quantitative approach to the study of leadership by rigorously defining leadership as a strategy of interpersonal investment and presenting a mathematical model of this leadership theory. This model provides a theoretical foundation to explain team dynamics, to study …

Emergent Properties Of The Transport Of Sand, Eric Lenhart

Undergraduate Honors Theses

In the interest of drawing conclusions about Aeolian environments based on remote imaging, we investigated how air flow forms self-organizing patterns, such as ripples, across loose particulate surfaces. Specifically, we analyzed various models of sand transport, particularly Nishimori’s model, to note the effects of altering various parameters, including wind direction, saltation length, diffusion, and a saltation proportionality constant. As a measure of the frustration of the emergent patterns, Y-junctions were counted at various values of the parameters. A strong correlation with the saltation proportionality constant and no correlation with the saltation height were found. As an additional use of the …

On The Persecution Of The Salvadoran People, Jacob Newman

Undergraduate Honors Theses

El Salvador is the focal point of an American refugee crisis. This crisis owes its origins to protracted abuse and negligence suffered by the Salvadoran people. They are confronted with violence, apathy, and corruption in their homeland and throughout the international sphere. A complex system of harms has come to a concentrated fruition in the form of governments and gangs, histories and happenstance. The purpose of this thesis is, first, to document the persecution faced by Salvadorans and, second, argue that the conditions in El Salvador put many Salvadorans in need of asylum.

Computational Regiospecific Analysis Of Brain Lipidomic Profiles, Austin Ahlstrom

Undergraduate Honors Theses

Mass spectrometry provides an extensive data set that can prove unwieldy for practical analytical purposes. Applying programming and machine learning methods to automate region analysis in DESI mass spectrometry of mouse brain tissue can help direct and refine such an otherwise unusable data set. The results carry promise of faster, more reliable analysis of this type, and yield interesting insights into molecular characteristics of regions of interest within these brain samples. These results have significant implications in continued investigation of molecular processes in the brain, along with other aspects of mass spectrometry, collective analysis of biological molecules (i.e. omics), and …

Computationally Modeling The Trophic Cascade In Yellowstone National Park, Emily Menden

Undergraduate Honors Theses

Many of the world’s ecosystems are facing species elimination (2). Whether this elimination is intentional or accidental, the consequences need to be understood in order to make better resource management decisions. Computational models can be helpful in making these management decisions. Yellowstone National Park gives ecologists a unique opportunity to study species elimination and reintroduction.

In the 1920s, wolves were extirpated from the Greater Yellowstone Area. The absence of wolves allowed the elk population to increase unbounded by a natural predator. Over the years, Yellowstone management took various measures to control the elk population. In the 1970s, the National Park …

Nonlinear Optical Characterization Of Solids, Alex Farnsworth

Undergraduate Honors Theses

Vibrational Sum Frequency Generation (VSFG) and the similar Second Harmonic Generation (SHG) are both classified as nonlinear optical phenomena, with the hallmark trait being that the input and output frequencies are different. Both of these systems are remarkable tools due to their surface specific nature. Still, there is much that is not known about the response from these systems, especially the nonresonant SFG response. We have worked to better understand SFG signal, specifically the nonresonant temporal profile. We have also collected results that call into question some underlying assumptions about time-based suppression methods when working with single crystal substrates.

As …

User Attitudes About Duo Two-Factor Authentication At Byu, Jonathan Dutson

Undergraduate Honors Theses

Simple password-based authentication provides insufficient protection against increasingly common incidents of online identity theft and data loss. Although two-factor authentication (2FA) provides users with increased protection against attackers, users have mixed feelings about the usability of 2FA. We surveyed the students, faculty, and staff of Brigham Young University (BYU) to measure user sentiment about DUO Security, the 2FA system adopted by BYU in 2017. We find that most users consider DUO to be annoying, and about half of those surveyed expressed a preference for authentication without using a second-factor. About half of all participants reported at least one instance of …

Divisibility Properties Of Coefficients Of Modular Functions Of Genus Zero Levels, Merrill Warnick

Undergraduate Honors Theses

We prove divisibility results for the Fourier coefficients of canonical basis elements for the spaces of weakly holomorphic modular forms of weight 0 and levels 6, 10, 12, 18 with poles only at the cusp at infinity. In addition, we show that these Fourier coefficients satisfy Zagier duality in all weights, and give a general formula for the generating functions of such canonical bases for all genus zero levels. These results originally appeared in a paper of the same title that was accepted by the journal Integers, and was authored by the present author, with Paul Jenkins and Vicki

Examining Multimorbidities Using Association Rule Learning, Kaylee Dudley

Undergraduate Honors Theses

All insurance companies, regardless of the kind of insurance they offer, do their best to predict the future by comparing current to historical information. Any statistically significant correlation, regardless of expectations and hidden factors, can help to actuarially model future behavior. Using deidentified data from over 6 million health insurance policies over one year, we looked for any significant groupings of medical issues. The medical issues are defined based on the commercial “Episode Treatment Groups” (ETGs) classification, and our claims contain 347 different ETGs. We performed different kinds of analysis, including Bayesian posterior cluster analysis, k-means cluster analysis, and association …