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Articles 1 - 30 of 111
Full-Text Articles in Physical Sciences and Mathematics
Structural Analysis Of Cell Signaling Complexes, Takuma Aoba
Structural Analysis Of Cell Signaling Complexes, Takuma Aoba
Theses and Dissertations
Bardet-Biedl syndrome (BBS) is a rare genetic disease that causes retinal degradation, obesity, kidney dysfunction, polydactyly, and other cilium-related disorders. To date, more than 20 BBS genes, whose mutants cause BBS phenotypes, have been identified, and eight of those (BBS1-2, 4-5, 7-9, and 18) are known to form the BBSome complex. Recent studies have revealed that the BBSome is closely involved in the trafficking of signaling proteins in the primary cilium. Mutations in BBS genes are highly pathogenic because trafficking in the primary cilium is not fully functional when BBS mutations impair assembly of the BBSome. However, the functional links …
Algorithms For Learning The Structure Of Monotone And Nonmonotone Sum-Product Networks, Aaron W. Dennis
Algorithms For Learning The Structure Of Monotone And Nonmonotone Sum-Product Networks, Aaron W. Dennis
Theses and Dissertations
The sum-product network (SPN) is a recently-proposed generative, probabilistic model that is guaranteed to compute any joint or any marginal probability in time linear in the size of the model. An SPN is represented as a directed, acyclic graph (DAG) of sum and product nodes, with univariate probability distributions at the leaves. It is important to learn the structure of this DAG since the set of distributions representable by an SPN is constrained by it. We present the first batch structure learning algorithm for SPNs and show its advantage over learning the parameters of an SPN with fixed architecture. We …
Investigation Of Dynamic Biological Systems Using Direct Injection And Liquid Chromatography Mass Spectrometry, Adam Clayton Swensen
Investigation Of Dynamic Biological Systems Using Direct Injection And Liquid Chromatography Mass Spectrometry, Adam Clayton Swensen
Theses and Dissertations
In biological systems, small changes can have significant impacts. It is, therefore, very important to be able to identify these changes in order to understand what is occurring in the organism. In many cases, this is not an easy task. Mass spectrometry has proven to be a very useful tool in elucidating biological changes even at a very small scale. Several different mass spectrometry based techniques have been developed to discover and investigate complex biological changes. Some of these techniques, such as proteomics, have been through years of development and have advanced to the point that anyone can complete complex …
Redbeds Of The Upper Entrada Sandstone, Central Utah: Facies Analysis And Regional Implications Of Interfingered Sabkha And Fluvial Terminal Splay Sediments, Jeffery Michael Valenza
Redbeds Of The Upper Entrada Sandstone, Central Utah: Facies Analysis And Regional Implications Of Interfingered Sabkha And Fluvial Terminal Splay Sediments, Jeffery Michael Valenza
Theses and Dissertations
First distinguished from other sedimentary successions in 1928, the Entrada Sandstone has been the subject of numerous studies. The western extent of the formation was initially described as laterally continuous "earthy" red beds, and categorized as sub- to supratidal marine-influenced sediments. Recent workers have reexamined the sedimentary facies hosted by the Entrada Sandstone, and findings suggest purely terrestrial depositional environments. Several outcrops of the upper Entrada hosted peculiar sedimentary features, including undulatory and convex-upward, parallel-laminated bedforms, reminiscent of hummocky cross-stratification- unexpected features in a terrestrial environment. The purpose of this study was to collect detailed outcrop measurements of these and …
Facies Analysis And Depositional Environments Of The Saints & Sinners Quarry In The Nugget Sandstone Of Northeastern Utah, Jesse Dean Shumway
Facies Analysis And Depositional Environments Of The Saints & Sinners Quarry In The Nugget Sandstone Of Northeastern Utah, Jesse Dean Shumway
Theses and Dissertations
The Saints & Sinners Quarry preserves the only known vertebrate body fossils in the Nugget Sandstone and the most diverse fauna known from the Nugget-Navajo-Aztec erg system. The fauna includes eight genera and >18,000 bone and bone fragments assignable to >76 individuals, including theropods, sphenosuchians, sphenodontians, drepanosaurs, procolophonids, and a dimorphodontid pterosaur. Cycadeoid fronds are the only plant fossils. There are two depositional environments at the site – dune and interdune, each consisting of two or more faces. The dune facies are (1) Trough Cross-Stratified Sandstone (TCS) representing dry dunes, and (2) Massive and Bioturbated Dunes (MBD) representing bioturbated, damp …
Control Of Matrix Metalloproteinases In A Periodontitis Model: Molecules That Trigger Or Inhibit Mmp Production, Catalina Matias Orozco
Control Of Matrix Metalloproteinases In A Periodontitis Model: Molecules That Trigger Or Inhibit Mmp Production, Catalina Matias Orozco
Theses and Dissertations
In periodontitis, there is a disruption in the homeostasis of the oral microbiome by peridontopathogenic bacteria. However, while bacteria is essential for periodontitis to occur, the severity, pattern and progression of the disease is not solely determined by the microbial burden, and in fact has a lot to do with the overwhelming host inflammatory response. The response can vary even in two individuals with similar periodontopathogenic profiles. The host response leads to extracellular matrix (ECM) destruction, loss of attachment, alveolar bone resorption and eventually, edentulism. The host's reaction is orchestrated by proinflammatory cytokines and chemokines and matrix metalloproteinases (MMPs). MMPs …
Some Spectral Properties Of A Quantum Field Theoretic Hamiltonian, Devin Burnell Mcghie
Some Spectral Properties Of A Quantum Field Theoretic Hamiltonian, Devin Burnell Mcghie
Theses and Dissertations
We derive the ground-state eigenvalues and eigenvectors for a simplified version of the 1-D QED single electron-photon model that Glasgow et al recently developed [2]. This model still allows for meaningful interaction between electrons and photons while keeping only the minimum needed to do so. We investigate the interesting spectral properties of this model. We determine that the eigenvectors are orthogonal as one would expect and normalize them.
Quantum Dot Band Gap Measurements, John Ryan Peterson
Quantum Dot Band Gap Measurements, John Ryan Peterson
Student Works
This presentation was given during the summer of 2016 as part of the BYU REU program funded by the NSF. Here I give a brief explanation of our quantum dot synthesis as well as explain the use of absorption spectroscopy to measure indirect band gap energies of semiconductors. Our experimental setup is shown and recent improvements are explained. We report indirect band gaps of quantum dots containing varying amounts of cobalt oxide and manganese oxide and synthesized in the protein ferritin. The data show that the band gap can be tuned arbitrarily in a certain range by varying the concentrations …
Determining The Index Of Refraction Of Aluminum Fluoride In The Ultra Violet Spectrum, Zoe Hughes
Determining The Index Of Refraction Of Aluminum Fluoride In The Ultra Violet Spectrum, Zoe Hughes
Student Works
A NASA project called Large UV/Optical/Infrared Surveyor (LUVOIR) is looking into ways to coat a mirror for a new space telescope. We contributed to this project by investigating aluminum fluoride (AlF3) as a possible coating for the mirror. We measured the index of refraction of AlF3 in the wavelength range 6 – 49.5 nm by testing three sample mirrors, each made up of a silicon wafer with a coating of AlF3. We took data at the Advanced Light Source (ALS) in Berkeley, California and in the laboratory at Brigham Young University (BYU). There are discrepancies …
Direct Band Gap Measurements, John Ryan Peterson
Direct Band Gap Measurements, John Ryan Peterson
Student Works
This presentation was given during the summer of 2016 as part of the BYU REU program funded by the NSF. Here I give a brief explanation of our quantum dot synthesis and then explain the mechanism of photoluminsecence used to measure indirect band gap energies of semiconductors. Our experimental setup is shown. Direct band gaps of lead sulfide quantum dots synthesized in ferritin are reported. The data show that the band gap can be tuned arbitrarily in a certain range by varying the concentrations of the reactants. We compare stability of quantum dots in ferritin to quantum dots synthesized without …
Quantum Dot Band Gap Investigations, John Ryan Peterson
Quantum Dot Band Gap Investigations, John Ryan Peterson
Student Works
Improving solar panel efficiency has become increasingly important as the world searches for cheap renewable energy. Recent developments in the industry have focused on multi-layer cells, some of which use semiconducting dyes to absorb light in place of crystalline solids. In this paper, I characterize various dyes recently synthesized for use in solar panels. These dyes contain semiconducting nanoparticles enclosed primarily by the protein ferritin to limit particle size. The band gaps were measured using either optical absorption spectroscopy or measuring the photoluminescence spectrum, depending on the type of semiconductor. The results indicate that both manganese oxide and lead sulfide …
A Common Misconception In Multi-Label Learning, Michael Benjamin Brodie
A Common Misconception In Multi-Label Learning, Michael Benjamin Brodie
Theses and Dissertations
The majority of current multi-label classification research focuses on learning dependency structures among output labels. This paper provides a novel theoretical view on the purported assumption that effective multi-label classification models must exploit output dependencies. We submit that the flurry of recent dependency-exploiting, multi-label algorithms may stem from the deficiencies in existing datasets, rather than an inherent need to better model dependencies. We introduce a novel categorization of multi-label metrics, namely, evenly and unevenly weighted label metrics. We explore specific features that predispose datasets to improved classification by methods that model label dependence. Additionally, we provide an empirical analysis of …
Towards Using Certificate-Based Authentication As A Defense Against Evil Twins In 802.11 Networks, Travis S. Hendershot
Towards Using Certificate-Based Authentication As A Defense Against Evil Twins In 802.11 Networks, Travis S. Hendershot
Theses and Dissertations
Wireless clients are vulnerable to exploitation by evil twins due to flaws in the authentication process of 802.11 Wi-Fi networks. Current certificate-based wireless authentication protocols present a potential solution, but are limited in their ability to provide a secure and usable platform for certificate validation. Our work seeks to mitigate these limitations by exploring a client-side strategy for utilizing alternative trust models in wireless network authentication. We compile a taxonomy of various trust models for conducting certificate-based authentication of wireless networks and methodically evaluate each model according to desirable properties of security, usability, and deployability. We then build a platform …
Geochemical Comparison Of Ancient And Modern Eolian Dune Foresets Using Principal Components Analysis, David A. Little
Geochemical Comparison Of Ancient And Modern Eolian Dune Foresets Using Principal Components Analysis, David A. Little
Theses and Dissertations
Geochemistry has been used to determine the provenance and diagenetic history of eolian sandstone deposits. However, the grain size, sorting, cementation, and detrital composition of eolian units can change along dune foreset laminae. The purpose of this study was to test for consistent trends of compositional change along dune foresets. Such trends could increase the quality of geochemical sampling of eolian sandstones and possibly aid in estimating the original height of ancient sand dunes. XRF data was gathered for both major and trace elements from the Pennsylvanian to Permian Weber Sandstone, Early Jurassic Navajo Sandstone, and modern Coral Pink Sand …
Variations In Geochemistry And Mineralogy Of Aeolian Dust Deposition To Mountains In Utah And Nevada, Usa, Dylan Binder Dastrup
Variations In Geochemistry And Mineralogy Of Aeolian Dust Deposition To Mountains In Utah And Nevada, Usa, Dylan Binder Dastrup
Theses and Dissertations
Major and trace metal loading to mountains in the western US depends on dust sources, intensity of storms and their availability for transport during snowmelt and runoff. Previous work has been conducted on dust production, composition, and its affect on solar radiation and timing of snow melt. This study was conducted to 1) examine temporal and spatial variability in dust chemistry; 2) evaluate form and availability of major and trace elements in dust; and 3) identify potential dust sources affecting mountains in Utah and Nevada. Spring and summertime dust was collected across northern Utah over the course of three years …
Verification Of Task Parallel Programs Using Predictive Analysis, Radha Vi Nakade
Verification Of Task Parallel Programs Using Predictive Analysis, Radha Vi Nakade
Theses and Dissertations
Task parallel programming languages provide a way for creating asynchronous tasks that can run concurrently. The advantage of using task parallelism is that the programmer can write code that is independent of the underlying hardware. The runtime determines the number of processor cores that are available and the most efficient way to execute the tasks. When two or more concurrently executing tasks access a shared memory location and if at least one of the accesses is for writing, data race is observed in the program. Data races can introduce non-determinism in the program output making it important to have data …
The State Of Man-In-The-Middle Tls Proxies: Prevalence And User Attitudes, Mark Thomas Oneill
The State Of Man-In-The-Middle Tls Proxies: Prevalence And User Attitudes, Mark Thomas Oneill
Theses and Dissertations
We measure the prevalence and uses of Man-in-the-Middle TLS proxies using a Flash tool deployed with a Google AdWords campaign. We generate 15.2 million certificate tests across two large-scale measurement studies and find that 1 in 250 TLS connections are intercepted by proxies. The majority of these proxies appear to be benevolent, however we identify over 3,600 cases where eight malware products are using this technology nefariously. We also find thousands of instances of negligent, duplicitous, and suspicious behavior, some of which degrade security for users without their knowledge. Distinguishing these types of practices is challenging in practice, indicating a …
Peering Through The Cloud—Investigating The Perceptions And Behaviors Of Cloud Storage Users, Justin Chun Wu
Peering Through The Cloud—Investigating The Perceptions And Behaviors Of Cloud Storage Users, Justin Chun Wu
Theses and Dissertations
We present the results of a survey and interviews focused on user perceptions and behaviors with respect to cloud storage services. In particular, we study behaviors such as which services are used, what types of data are stored, and how collaboration and sharing are performed. We also investigate user attitudes toward cloud storage on topics such as payment, privacy, security, and robustness. We find that users are drawn to cloud storage because it enables robust, ubiquitous access to their files, as well as enabling sharing and collaborative efforts. However, users' preferred medium for file sharing continues to be email, due …
Creating And Automatically Grading Annotated Questions, Alicia Crowder Wood
Creating And Automatically Grading Annotated Questions, Alicia Crowder Wood
Theses and Dissertations
We have created a question type that allows teachers to easily create questions, helps provide an intuitive user experience for students to take questions, and reduces the time it currently takes teachers to grade and provide feedback to students. This question type, or an "annotated" question, will allow teachers to test students' knowledge in a particular subject area by having students "annotate" or mark text and video sources to answer questions. Through user testing we determined that overall the interface and the implemented system decrease the time it would take a teacher to grade annotated quiz questions. However, there are …
Increasing The Computational Efficiency Of Combinatoric Searches, Wiley Spencer Morgan
Increasing The Computational Efficiency Of Combinatoric Searches, Wiley Spencer Morgan
Theses and Dissertations
A new algorithm for the enumeration of derivative superstructures of a crystal is presented. The algorithm will help increase the efficiency of computational material design methods such as cluster expansion by increasing the size and diversity of the types of systems that can be modeled. Modeling potential alloys requires the exploration of all possible configurations of atoms. Additionally, modeling the thermal properties of materials requires knowledge of the possible ways of displacing the atoms. One solution to finding all symmetrically unique configurations and displacements is to generate the complete list of possible configurations and remove those that are symmetrically equivalent. …
Natural And Anthropogenic Sources Of Arsenic And Nitrate In A Semi-Arid Alluvial Basin; Goshen Valley, Utah, Brian John Selck
Natural And Anthropogenic Sources Of Arsenic And Nitrate In A Semi-Arid Alluvial Basin; Goshen Valley, Utah, Brian John Selck
Theses and Dissertations
Arsenic (As) and nitrate (NO3) are common contaminants in groundwater that are introduced through a variety of natural and anthropogenic sources. In this study we investigated the sources and distribution of As and NO3 in Goshen Valley, Utah, USA. Goshen Valley is a semi-arid alluvial basin that is impacted by geothermal waters, agriculture, urban development, and legacy mining. In this study we sampled surface water, springs, and wells to analyze concentrations of major ions, trace elements (As, B, Ba, Ca, Fe, K, Li, Mg, Mn, Mo, Pb, Si, Sr, Zn), and stable isotopes in water (δ18 …
Energy Quantity Estimation In Radiated Acoustic Fields, Eric B. Whiting
Energy Quantity Estimation In Radiated Acoustic Fields, Eric B. Whiting
Theses and Dissertations
Energy quantities, which are calculated from pressure and particle velocity, yield a great deal of information about acoustic fields. Errors in pressure or particle velocity estimation lead to bias errors the estimation of energy quantities. The bias errors arise from different probe configurations and processing methods. Two processing methods are examined: the traditional method and the recently developed Phase and Amplitude Gradient Estimation (PAGE) method. These two methods are compared to investigate how each estimates pressure and particle velocity and the subsequent bias errors in a plane wave, standing wave, and spherical spreading wave field. Analytical expressions are derived for …
Performance Of Phase And Amplitude Gradient Estimator Method For Calculating Energy Quantities In A Plane-Wave Tube Environment, Daxton A. Hawks
Performance Of Phase And Amplitude Gradient Estimator Method For Calculating Energy Quantities In A Plane-Wave Tube Environment, Daxton A. Hawks
Student Works
Acoustic intensity, energy densities, and impedance are useful quantities when considering sound fields. Calculating these energy quantities relies on measurements of acoustic pressure and particle velocity. Pressure and particle velocity can be directly measured, but direct measurements of particle velocity are difficult to make, and are normally inaccurate. A more common and effective way to find particle velocity is to estimate it using pressure measurements from two closely-spaced microphones. The traditional way of estimating particle velocity is severely limited by frequency. The PAGE method, developed at Brigham Young University, extends the frequency bandwidth at which accurate estimations can be made. …
Daxton Hawks Reu Prospectus, Daxton A. Hawks
Daxton Hawks Reu Prospectus, Daxton A. Hawks
Student Works
The purpose of my research is to investigate the ability of the PAGE method to improve the frequency bandwidth of calculations of energy-based quantities from multiple pressure microphones. I will accomplish this by investigating sound waves in both plane-wave and standing-wave environments. I will compare the PAGE method calculations for Ia, Ir, Ep, Ek, and Z to those of traditional and analytical expressions, based on careful ambient condition monitoring. Quantifying the bandwidth extension of the PAGE method for these energy-based quantities will lay a foundation for further application.
Preventing Oxidation Of Aluminum Films With Cadmium Of Zinc Barriers, Spencer B. Perry
Preventing Oxidation Of Aluminum Films With Cadmium Of Zinc Barriers, Spencer B. Perry
Student Works
The planned Large UV/Optical/Near-infrared Telescope (LUVOIR) is expected to launch sometime in the 2030s if NASA surveys recommend LUVOIR over several other projects in early developmental stages [1]. As the project title suggests, the proposed telescope would include large mirrors (between 8 and 16 meters) as part of the orbiting reflector telescope. My research focused on the preparation of aluminum mirrors with zinc or cadmium barrier layers that were designed to prevent oxidation of the aluminum.
From Qualitative To Quantitative: Supporting Robot Understanding In Human-Interactive Path Planning, Daqing Yi
From Qualitative To Quantitative: Supporting Robot Understanding In Human-Interactive Path Planning, Daqing Yi
Theses and Dissertations
Improvements in robot autonomy are changing human-robot interaction from low-level manipulation to high-level task-based collaboration. When a robot can independently and autonomously executes tasks, a human in a human-robot team acts as a collaborator or task supervisor instead of a tele-operator. When applying this to planning paths for a robot's motion, it is very important that the supervisor's qualitative intent is translated into aquantitative model so that the robot can produce a desirable consequence. In robotic path planning, algorithms can transform a human's qualitative requirement into a robot's quantitative model so that the robot behavior satisfies the human's intent. In …
Gas Phase Structure Characterization Using Fourier Transform Ion Cyclotron Resonance Mass Spectrometry, Anupriya Anupriya
Gas Phase Structure Characterization Using Fourier Transform Ion Cyclotron Resonance Mass Spectrometry, Anupriya Anupriya
Theses and Dissertations
This dissertation investigates Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) based techniques to study the impact of molecular structure on conformation and binding energetics. A novel method to determine collison cross sectional areas using FTICR (CRAFTI), initially developed by the Dearden lab, was applied to study the conformations of molecular systems with unique structural attributes in an attempt to explore the molecular range of CRAFTI. The systems chosen for CRAFTI studies include crown-ether alkylammonium complexes and biogenic amino acids. The results were found to be consistent with expected behavior, and strongly correlated with experimental measurements made using ion mobility …
Computational Studies Of Alkane C-H Functionalization By Main-Group Metals, Samantha Jane Gustafson
Computational Studies Of Alkane C-H Functionalization By Main-Group Metals, Samantha Jane Gustafson
Theses and Dissertations
The most efficient homogeneous catalysts for hydroxylation of light alkanes utilize transition metals in superacid solvent and operate by tandem electrophilic C-H activation/metal-alkyl (M-R) functionalization. An emerging alternative strategy to transition metals is the use of high-oxidation state main-group metals (e.g. TlIII, PbIV, IIII) that hydroxylate light alkanes. This dissertation reports density-functional theory calculations that reveal the mechanisms, reactivity, and selectivity of TlIII promoted alkane C-H functionalization in trifluoroacetic acid and TlIII-dialkyl functionalization in water. Calculations reveal that TlIII oxidizes alkanes via a closed-shell C-H activation and M-R functionalization mechanism that is similar to transition-metal C-H functionalization mechanisms. Comparison of …
Usable, Secure Content-Based Encryption On The Web, Scott Ruoti
Usable, Secure Content-Based Encryption On The Web, Scott Ruoti
Theses and Dissertations
Users share private information on the web through a variety of applications, such as email, instant messaging, social media, and document sharing. Unfortunately, recent revelations have shown that not only is users' data at risk from hackers and malicious insiders, but also from government surveillance. This state of affairs motivates the need for users to be able to encrypt their online data.In this dissertation, we explore how to help users encrypt their online data, with a special focus on securing email. First, we explore the design principles that are necessary to create usable, secure email. As part of this exploration, …
Emission From Black Holes And Supernovae In The Early Universe, Brandon Kerry Wiggins
Emission From Black Holes And Supernovae In The Early Universe, Brandon Kerry Wiggins
Theses and Dissertations
To constrain the era when the first galaxies and stars appeared upcoming instruments will rely on the brightest events in the universe: supernovae and brilliant emission from massive black holes. In this dissertation, we investigate the observability of certain types of supernovae of the very first stars (Population III stars) and find that while these events are sufficiently luminous to be observed with deep-sky instruments such as the James Webb Space Telescope (JWST), they may not observe these particular types of events in their lifetimes. We next explore the origins of massive black holes and introduce the direct collapse hypothesis …