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Articles 1 - 30 of 71
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 …
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 …
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.
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 …
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 …
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 …
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 …
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 …
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 …
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. …
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 …
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 …
Theoretical And Experimental Investigation Of A Quadspectral Nonlinearity Indicator, Kyle Glen Miller
Theoretical And Experimental Investigation Of A Quadspectral Nonlinearity Indicator, Kyle Glen Miller
Theses and Dissertations
Understanding the impact of jet noise and other high-amplitude sound sources can be improved by quantifying the nonlinearity in a signal with a single-microphone measurement. An ensemble-averaged, frequency-domain version of the generalized Burgers equation has been used to derive a quantitative expression for the change in spectral levels (in decibels) over distance due to geometric spreading, thermoviscous absorption, and nonlinearity, respectively. The nonlinearity indicator, called νN , is based on the quadspectral Morfey-Howell indicator, which has been used in the past to characterize nonlinearity in noise waveforms. Unlike the Morfey-Howell indicator, the νN indicator has direct physical significance, giving a …
Computational Studies On Mechanisms And Reactivity Of Mercury And Cobalt Organometallic Reactions, Jack Terrell Fuller
Computational Studies On Mechanisms And Reactivity Of Mercury And Cobalt Organometallic Reactions, Jack Terrell Fuller
Theses and Dissertations
Density Functional Theory (DFT) is a powerful tool for treating large organometallic structures efficiently and accurately. DFT calculations on the Hg-catalyzed oxidation of methane to methyl bisulfate in sulfuric acid suggest the lowest energy pathway involves a closed-shell electrophilic C–H activation mechanism coupled with metal alkyl reductive functionalization and oxidation by SO3. Comparison to Tl, Zn, and Cd suggests that Hg is unique in its ability to catalyze this set of reaction steps. Comparison to K2S2O8 highlights the selectivity of this C–H activation reaction as opposed to radical conditions. In contrast, DFT calculations indicate that CoIII(TFA)3 oxidizes methane through a …
Studies Toward Yaku'amide A And Synthesis And Applications Of Bulky Α,Β-Dehydroamino Acids, Jintao Jiang
Studies Toward Yaku'amide A And Synthesis And Applications Of Bulky Α,Β-Dehydroamino Acids, Jintao Jiang
Theses and Dissertations
Yaku'amide A shows a unique inhibitory profile against a series of 39 human cancer cell lines (JFCR39). In our efforts to synthesize yaku'amide A, we have optimized our regioselective base-free aminohydroxylation method with a series of nitrogen sources, developed a chiral reagent-mediated aminohydroxylation strategy and chemoselective deprotections of the resulting aminohydroxylation product, and explored a stereospecific E2 dehydration and O-N acyl transfer sequence. In addition, we have prepared the right-hand tetrapeptide and the NTA subunit. For our bulky α,β-dehydroamino acids project, we have developed strategies to incorporate α,β-dehydroamino acids such as ΔVal and ΔEnv into small synthetic peptides via Solid …
The Quest To Secure Email: A Usability Analysis Of Key Management Alternatives, Jeffrey Thomas Andersen
The Quest To Secure Email: A Usability Analysis Of Key Management Alternatives, Jeffrey Thomas Andersen
Theses and Dissertations
The current state of email security is lacking, and the need for end-to-end encryption of email is clear. Recent research has begun to make progress towards usable, secure email for the masses (i.e., novice users without IT support). In this paper, we evaluate the usability implications of three different key management approaches: PGP, IBE, and passwords. Our work is the first formal A/B evaluation of the usability of different key management schemes, and the largest formal evaluation of secure email ever performed. Our results reveal interesting inherent usability trade-offs for each approach to secure email. Furthermore, our research results in …
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 …
Synthesis And Biological Evaluation Of Small Molecule Inhibitors Of Bmpr1b, Paulo Andre Machicao Tello
Synthesis And Biological Evaluation Of Small Molecule Inhibitors Of Bmpr1b, Paulo Andre Machicao Tello
Theses and Dissertations
Methods for preparing an array of potential small molecule inhibitors of Bone Morphogenetic Protein Receptor 1b (BMPR1b) are described. Target molecules were prepared from two general classes: (1) N9-aryl-N6-ureidoadenines, and (2) dicarbamyl iodoacetamides. Recent data from the Peterson lab indicated that both classes might bind to BMPR1b and thus inhibit this key receptor. Docking studies performed using Sureflex Dock suggested the N9-aryl-N6-ureidoadenines would bind to the active site of BMPR1b. In addition antiproliferative activities of dicarbamyl iodoacetamides previously synthesized in the Peterson lab pointed to this moiety as an attractive target for structure activity relationship (SAR) development. Compounds were prepared …
Steady State Configurations Of Cells Connected By Cadherin Sites, Jared Adam Mcbride
Steady State Configurations Of Cells Connected By Cadherin Sites, Jared Adam Mcbride
Theses and Dissertations
Many cells employ cadherin complexes (c-sites) on the cell membrane to attach to neighboring cells, as well as integrin complexes (i-sites) to attach to a substrate in order to accomplish cell migration. This paper analyzes a model for the motion of a group of cells connected by c-sites. We begin with two cells connected by a single c-site and analyze the resultant motion of the system. We find that the system is irrotational. We present a result for reducing the number of c-sites in a system with c-sites between pairs of cells. This greatly simplifies the general system, and provides …
Modeling Of Acoustic Resonators And Resonator Systems For Use In Passive Noise Control, Matthew Franklin Calton
Modeling Of Acoustic Resonators And Resonator Systems For Use In Passive Noise Control, Matthew Franklin Calton
Theses and Dissertations
Acoustic resonators, such as the Helmholtz and quarter-wave resonator, can be used to attenuate unwanted noise in an enclosed space. Classical formulations can be used to approximate resonator performance for a given resonator configuration, but may lack sufficient accuracy for some applications. This research aims to improve the analytical characterization of resonators to provide better correlation to experimental results. Using higher-order approximations and proper end corrections, more accuracy can be obtained in calculating the impedance and resonance frequency of a single resonator, which will then carry over into the overall configuration of the model. The impedance of a system of …