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Articles 1 - 30 of 93
Full-Text Articles in Physical Sciences and Mathematics
Strategies To Resolve The Three-Dimensional Structure Of The Genome Of Small Single-Stranded Icosahedral Viruses, Eduardo Sanz Garcia
Strategies To Resolve The Three-Dimensional Structure Of The Genome Of Small Single-Stranded Icosahedral Viruses, Eduardo Sanz Garcia
Theses and Dissertations
The aim of this study is the three-dimensional structural characterization of the genome packaging inside viral capsids via cryo-electron microscopy and three-dimensional reconstruction. The genome of some single-stranded viruses can be densely packaged within their capsid shells. Several stretches of the genome are known to adopt stable secondary structures, however, to date, little is known about the three-dimensional organization of the genome inside their capsid shells. Two techniques have been developed to facilitate the structural elucidation of genome packaging: the asymmetric random-model method, and the symmetry-mismatch, random model method. Both techniques were successfully tested with model and experimental data. The …
Sequence Stratigraphy Of The Lower Pennsylvanian (Bashkirian, Morrowan) Round Valley Limestone, Split Mountain Anticline (Dinosaur National Monument) And In The Eastern Uinta Mountains, Utah, Nathan Robert Davis
Theses and Dissertations
The Early Pennsylvanian (Bashkirian/Morrowan) Round Valley Limestone of northeastern Utah was deposited on the Wyoming shelf, a slowly subsiding depositional surface located between the Eagle and Oquirrh basins. The 311-foot-thick Round Valley Limestone displays a distinct cyclicity formed by stacked, meter-scale parasequences, comprised of a limited suite of open- to restricted-marine limestones with minor interbeds of siltstone and shale. Open-marine deposits are characterized by mudstone and heterozoan wackestone-packstone microfacies (MF1-4) and comprise the lower portions of parasequences. Rocks of these microfacies were deposited during maximum high-order transgression of the shelf. As sediment filled the limited accommodation, the shelf became restricted, …
A Reusable Persistence Framework For Replicating Empirical Studies On Data From Open Source Repositories, Scott Bong-Soo Chun
A Reusable Persistence Framework For Replicating Empirical Studies On Data From Open Source Repositories, Scott Bong-Soo Chun
Theses and Dissertations
Empirical research is inexact and error-prone leading researchers to agree that replication of experiments is a necessary step to validating empirical results. Unfortunately, replicating experiments requires substantial investments in manpower and time. These resource requirements can be reduced by incorporating component reuse when building tools for empirical experimentation. Bokeo is an initiative within the Sequoia Lab of the BYU Computer Science Department to develop a platform to assist in the empirical study of software engineering. The i3Persistence Framework is a component of Bokeo which enables researchers to easily build and rapidly deploy tools for empirical experiments by providing an easy-to-use …
Capture And Access Of Multiple Screen Presentations, Kelv H. Cutler
Capture And Access Of Multiple Screen Presentations, Kelv H. Cutler
Theses and Dissertations
Knowledge transferred during meetings is often ephemeral in nature and thus must be captured if it is to be retained. Ideally, a capture solution should be able to 1) accommodate any number of screens without sacrificing image quality and 2) allow dynamic access to a complete media capture while the capture is taking place. Both students and employees can benefit from the information captured during the lectures and meetings for enhanced discussion and afterward for knowledge retention. Current systems do not support multiple screen capture well, and no system supports dynamic access to the active meeting capture during the meeting. …
Chemical Vapor Deposition Of Silanes And Patterning On Silicon, Feng Zhang
Chemical Vapor Deposition Of Silanes And Patterning On Silicon, Feng Zhang
Theses and Dissertations
Self assembled monolayers (SAMs) are widely used for surface modification. Alkylsilane monolayers are one of the most widely deposited and studied SAMs. My work focuses on the preparation, patterning, and application of alkysilane monolayers. 3-aminopropyltriethoxysilane (APTES) is one of the most popular silanes used to make active surfaces for surface modification. To possibly improve the surface physical properties and increase options for processing this material, I prepared and studied a series of amino silane surfaces on silicon/silicon dioxide from APTES and two other related silanes by chemical vapor deposition (CVD). I also explored CVD of 3-mercaptopropyltrimethoxysilane on silicon and quartz. …
Volcanic Stratigraphy And A Kinematic Analysis Of Ne-Trending Faults Of Allens Ranch 7.5' Quadrangle, Utah County, Utah, Adam Paul Mckean
Volcanic Stratigraphy And A Kinematic Analysis Of Ne-Trending Faults Of Allens Ranch 7.5' Quadrangle, Utah County, Utah, Adam Paul Mckean
Theses and Dissertations
The mineral resources of the Tintic Mining District are influenced by three major events in its geologic history; the Mesozoic Sevier Orogeny, Paleogene volcanism and Late Neogene Basin and Range extension. In this paper a detailed analysis of each these geologic events is presented to help us understand the structural host, mineralization and exhumation of the Tintic Mining District ore. A kinematic analysis of the faults was completed to determine the origin of NE-trending faults, Sevier Orogeny or Basin and Range extension, in the northern part of the East Tintic Mountains in Allens Ranch 7.5' quadrangle, near the eastern margin …
Trusted Mobile Overlays, Robert Scott Robertson
Trusted Mobile Overlays, Robert Scott Robertson
Theses and Dissertations
Sensitive information is increasingly moving online and as data moves further from the control of its owner, there are increased opportunities for it to fall into malicious hands. The Web is comprised of three untrusted components where there is a risk of information compromise: networks, service providers, and clients. This thesis presents Trusted Mobile Overlays: a system that leverages trusted mobile devices to protect users from these untrusted components of the Web, while minimizing deployment difficulties. It presents a high-level design of the system as well as a prototype that implements the design.
First Order Analysis Of Nitrate Loading In The Upper Elbe River Basin, Czech Republic, Daniel J. Ritter
First Order Analysis Of Nitrate Loading In The Upper Elbe River Basin, Czech Republic, Daniel J. Ritter
Theses and Dissertations
Nitrate contamination of water is a worldwide issue. Nitrate is especially dangerous for young children, and may result in potentially fatal blue baby syndrome when concentration in drinking water is > 10 mg/L N-NO3. Nitrate in surface water may also lead to eutrophication. Sources of NO3- contamination include nitrate fertilizers, wastewater treatment plants, individual domestic septic systems, runoff from animal feedlots, and natural soil nitrogen. Nitrate contamination in the Elbe River drainage, covering 148,270 km2 in Germany and the Czech Republic, has been a long-term issue. This study examines the upper one-third of the basin, located almost entirely in the Czech …
Gene Network Inference And Expression Prediction Using Recurrent Neural Networks And Evolutionary Algorithms, Heather Y. Chan
Gene Network Inference And Expression Prediction Using Recurrent Neural Networks And Evolutionary Algorithms, Heather Y. Chan
Theses and Dissertations
We demonstrate the success of recurrent neural networks in gene network inference and expression prediction using a hybrid of particle swarm optimization and differential evolution to overcome the classic obstacle of local minima in training recurrent neural networks. We also provide an improved validation framework for the evaluation of genetic network modeling systems that will result in better generalization and long-term prediction capability. Success in the modeling of gene regulation and prediction of gene expression will lead to more rapid discovery and development of therapeutic medicine, earlier diagnosis and treatment of adverse conditions, and vast advancements in life science research.
Asynchronous Database Drivers, Michael Adam Heath
Asynchronous Database Drivers, Michael Adam Heath
Theses and Dissertations
Existing database drivers use blocking socket I/O to exchange data with relational database management systems (RDBMS). To concurrently send multiple requests to a RDBMS with blocking database drivers, a separate thread must be used for each request. This approach has been used successfully for many years. However, we propose that using non-blocking socket I/O is faster and scales better under load. In this paper we introduce the Asynchronous Database Connectivity in Java (ADBCJ) framework. ADBCJ provides a common API for asynchronous RDBMS interaction. Various implementations of the ADBCJ API are used to show how utilizing non-blocking socket I/O is faster …
Drop-In Concurrent Api Replacement For Exploration, Test, And Debug, Everett Allen Morse
Drop-In Concurrent Api Replacement For Exploration, Test, And Debug, Everett Allen Morse
Theses and Dissertations
Complex concurrent APIs are difficult to reason about annually due to the exponential growth in the number of feasible schedules. Testing against reference solutions of these APIs is equally difficult as reference solutions implement an unknown set of allowed behaviors, and programmers have no way to directly control schedules or API internals to expose or reproduce errors. The work in this paper mechanically generates a drop-in replacement for a concurrent API from a formal specification. The specification is a guarded command system with first-order logic that is compiled into a core calculus. The term rewriting system is connected to actual …
Comparison Of H-Alpha And H-Beta Temperature Indices In The Hyades And Coma Star Clusters And Selected H-Beta Standard Stars, Miriam Anne West
Comparison Of H-Alpha And H-Beta Temperature Indices In The Hyades And Coma Star Clusters And Selected H-Beta Standard Stars, Miriam Anne West
Theses and Dissertations
Using the Dominion Astrophysical Observatory's 1.2-m McKellar Telescope, we have obtained spectra on 81 stars from the Hyades Cluster, the Coma Cluster, and selected H-beta standard stars. These spectra cover from 4500 Å to 6900 Å which includes both the H-β and H-α absorption lines. The H-β absorption line has a long history of being used as a temperature index and more recently, calibration of an H-α index has been established for photometric observations. Through spectrophotometric comparison of temperature indices from the H-α and H-β absorption lines we find the expected strong correlation between photometric indices based on the strength …
High Flow Air Sampling For Field Detection Using Gas Chromatography-Mass Spectrometry, Jacolin Ann Murray
High Flow Air Sampling For Field Detection Using Gas Chromatography-Mass Spectrometry, Jacolin Ann Murray
Theses and Dissertations
The ability to rapidly detect and identify hazardous analytes in the field has become increasingly important. One of the most important analytical detection methods in the field is gas chromatography-mass spectrometry (GC-MS). In this work, a hand-portable GC-MS system is described that contains a miniature toroidal ion trap mass analyzer and a low thermal mass GC. The system is self-contained within the dimensions of 47 x 36 x 18 cm and weighs less than 13 kg. Because the instrument has a small footprint, it was used as the detector for an automated near-real-time permeation testing system. In permeation testing, materials …
Work Towards The Isolation And Characterization Of The Muscle Isoform Of Glucose 1,6-Bisphosphatase, Caleb J. Hiller
Work Towards The Isolation And Characterization Of The Muscle Isoform Of Glucose 1,6-Bisphosphatase, Caleb J. Hiller
Theses and Dissertations
Glucose 1,6-bisphosphate is an important small molecule involved in the regulation of glycolysis. Four enzymes synthesize this compound. One enzyme is known to degrade it, glucose 1,6-bisphosphatase. Other groups have produced work that indicates that there are two isoforms of this enzyme, one predominant in the brain and one in the muscle. This thesis contains the work performed in attempts to isolate and characterize the muscle isoform of glucose 1,6-bisphosphatase. While this enzyme was not isolated, much was learned about it and the results from this work may help in the future identification of this enzyme.
Exhumation Mechanisms Of The Greater Himalayan Sequence, Garhwal Region, India, Christopher James Spencer
Exhumation Mechanisms Of The Greater Himalayan Sequence, Garhwal Region, India, Christopher James Spencer
Theses and Dissertations
Geothermobarometric, micro- and macro-structural data indicate that peak metamorphic pressure and temperature of the Greater Himalayan Sequence (GHS) of the Garhwal Region of India increase dramatically across the Main Central Thrust (MCT). Metamorphic pressure and temperature increase from ~5 kbar and ~550 ºC in the Lesser Himalayan Crystalline Sequence (LHCS) in the footwall to ~14 kbar and ~850 ºC at ~3 km above the MCT in the hanging wall (GHS). Pressures decrease slightly upsection to ~8 kbar and temperatures remain nearly constant at ~850 ºC to the structurally overlying South Tibetan Detachment (STD). The LHCS exhibits a high temperature-depth gradient …
Halo Ion Trap Mass Spectrometry: Design, Instrumentation, And Performance, Miao Wang
Halo Ion Trap Mass Spectrometry: Design, Instrumentation, And Performance, Miao Wang
Theses and Dissertations
New ion trap mass spectrometry (ITMS) instrumentation, the toroidal IT and halo IT, were developed to meet the significant growth in on-site analysis applications. The miniature toroidal IT mass analyzer was operated with radio frequency (RF) trapping voltages of 3 kVp-p or less. Despite its reduced dimensions, it has roughly the same ion trapping capacity as conventional 3D quadrupole ITs. Unit-mass resolved spectra for n-butylbenzene, xenon, and naphthalene were obtained. The desired linear mass scale was obtained using conventional mass-selective instability scan combined with resonance ejection. The halo IT was also based on toroidal trapping geometry and microfabrication technology, consisting …
Packing Virtual Machines Onto Servers, David Luke Wilcox
Packing Virtual Machines Onto Servers, David Luke Wilcox
Theses and Dissertations
Data centers consume a significant amount of energy. This problem is aggravated by the fact that most servers and desktops are underutilized when powered on, and still consume a majority of the energy of a fully utilized computer even when idle This problem would be much worse were it not for the growing use of virtual machines. Virtual machines allow system administrators to more fully utilize hardware capabilities by putting more than one virtual system on the same physical server. Many times, virtual machines are placed onto physical servers inefficiently. To address this inefficiency, I developed a new family of …
Assessment Of Acgh Clustering Methodologies, Serena F. Baker
Assessment Of Acgh Clustering Methodologies, Serena F. Baker
Theses and Dissertations
Array comparative genomic hybridization (aCGH) is a technique for identifying duplications and deletions of DNA at specific locations across a genome. Potential objectives of aCGH analysis are the identification of (1) altered regions for a given subject, (2) altered regions across a set of individuals, and (3) clinically relevant clusters of hybridizations. aCGH analysis can be particularly useful when it identifies previously unknown clusters with clinical relevance. This project focuses on the assessment of existing aCGH clustering methodologies. Three methodologies are considered: hierarchical clustering, weighted clustering of called aCGH data, and clustering based on probabilistic recurrent regions of alteration within …
Functionalization Of Diamond And Its Application In High Performance Liquid Chromatography And Solid Phase Extraction, Gaurav Saini
Functionalization Of Diamond And Its Application In High Performance Liquid Chromatography And Solid Phase Extraction, Gaurav Saini
Theses and Dissertations
The primary focus of my work was to chemically functionalize diamond as normal and reversed phases for solid phase extraction (SPE) and high performance liquid chromatography (HPLC). Diamond was functionalized with -NH2 groups via self-limiting adsorption of an amine-containing polymer, polyallylamine (PAAm), onto oxidized diamond particles. The chemical stability of these particles was improved by thermal curing or chemical crosslinking with 1,2,5,6-diepoxycyclooctane. The reversed phase material for SPE was synthesized by reacting amine-functionalized diamond particles with long chain alkyl and a perfluorinated isocyanate. Unlike commercially available silica, functionalized diamond particles were stable under extreme pH conditions (pH 0-14). Functionalized diamond …
Pixel Based Note Taking Through Perceptual Structure Inference, Mitchell Kent Harris
Pixel Based Note Taking Through Perceptual Structure Inference, Mitchell Kent Harris
Theses and Dissertations
Knowledge workers need effective annotation tools to assimilate information. Unfortunately many digital annotators are limited in the range of document that they accept. Those that do accept many different documents do so by converting documents to images, thus losing any awareness about the original content of the document. We introduce a digital note taker that is both universal and content aware. By constructing a hierarchical context tree of document images, the structure of a document is inferred from the image. This hierarchical context tree is shown to be useful by demonstrating how it facilitates selection of document elements, reflowing documents …
Polymeric Monolithic Stationary Phases For Capillary Hydrophobic Interaction Chromatography, Yuanyuan Li
Polymeric Monolithic Stationary Phases For Capillary Hydrophobic Interaction Chromatography, Yuanyuan Li
Theses and Dissertations
Rigid poly[hydroxyethyl acrylate-co-poly(ethylene glycol) diacrylate] (Poly(HEA-co-PEGDA) monoliths were synthesized inside 75-µm i.d. capillaries by one-step UV-initiated copolymerization using methanol and ethyl ether as porogens. The optimized monolithic column was evaluated for hydrophobic interaction chromatography (HIC) of standard proteins. Six proteins were separated within 20 min with high resolution using a 20 min elution gradient, resulting in a peak capacity of 54. The performance of this monolithic column for HIC was comparable or superior to the performance of columns packed with small particles. Monoliths synthesized solely from PEGDA were also found to show excellent performance in HIC …
Detailed Requirements For Robots In Autism Therapy, Alan Atherton, Bonnie Brinton, Mark Colton, Nicole Giullian, Michael A. Goodrich, Daniel Ricks
Detailed Requirements For Robots In Autism Therapy, Alan Atherton, Bonnie Brinton, Mark Colton, Nicole Giullian, Michael A. Goodrich, Daniel Ricks
Faculty Publications
Robot-based autism therapy is a rapidly developing area of research, with a wide variety of robots being developed for use in clinical settings. Specific, detailed requirements for robots and user interfaces are needed to provide guidelines for the creation of robots that more effectively assist therapists in autism therapy. This paper enumerates a set of requirements for a clinical humanoid robot and the associated human interface. The design of two humanoid robots and an intuitive and flexible user interface for use by therapists in the treatment of children with autism are described.
Beyond Robot Fan-Out: Towards Multi-Operator Supervisory Control, Michael A. Goodrich, Yisong Guo, Jonathan M. Whetten
Beyond Robot Fan-Out: Towards Multi-Operator Supervisory Control, Michael A. Goodrich, Yisong Guo, Jonathan M. Whetten
Faculty Publications
This paper explores multi-operator supervisory control (MOSC) of multiple independent robots using two complementary approaches: a human factors experiment and an agent-based simulation. The experiment identifies two task and environment limitations on MOSC: task saturation and task diffusion. It also identifies the correlation between task specialization and performance, and the possible existence of untapped spare capacity that emerges when multiple operators coordinate. The presence of untapped spare capacity is explored using agent-based simulation, resulting in evidence which suggests that operators may be more effective when they operate at less than maximum capacity.
Generalized Acoustic Energy Density And Its Applications, Buye Xu
Generalized Acoustic Energy Density And Its Applications, Buye Xu
Theses and Dissertations
The properties of acoustic kinetic energy density and total energy density of sound fields in lightly damped enclosures have been explored thoroughly in the literature. Their increased spatial uniformity makes them more favorable measurement quantities for various applications than acoustic potential energy density (or squared pressure), which is most often used. In this dissertation, a new acoustic energy quantity, the generalized acoustic energy density (GED), will be introduced. It is defined by introducing weighting factors, α and 1 − α, in the formulation of total acoustic energy density. With the additional degree of freedom, the GED can conform to the …
Application Of Convex Methods To Identification Of Fuzzy Subpopulations, Ryan Lee Eliason
Application Of Convex Methods To Identification Of Fuzzy Subpopulations, Ryan Lee Eliason
Theses and Dissertations
In large observational studies, data are often highly multivariate with many discrete and continuous variables measured on each observational unit. One often derives subpopulations to facilitate analysis. Traditional approaches suggest modeling such subpopulations with a compilation of interaction effects. However, when many interaction effects define each subpopulation, it becomes easier to model membership in a subpopulation rather than numerous interactions. In many cases, subjects are not complete members of a subpopulation but rather partial members of multiple subpopulations. Grade of Membership scores preserve the integrity of this partial membership. By generalizing an analytic chemistry concept related to chromatography-mass spectrometry, we …
Axial Temperature Gradients In Gas Chromatography, Jesse Alberto Contreras
Axial Temperature Gradients In Gas Chromatography, Jesse Alberto Contreras
Theses and Dissertations
The easiest and most effective way to influence the separation process in gas chromatography (GC) is achieved by controlling the temperature of the chromatographic column. In conventional GC, the temperature along the length of the column is constant at any given time, T(t). In my research, I investigated the effects of temperature gradients on GC separations as a function of time and position, T(t,x), along the column. This separation mode is called thermal gradient GC (TGGC). The research reported in this dissertation highlights the fundamental principles of axial temperature gradients and the separation potential of the TGGC technique. These goals …
Unusual-Object Detection In Color Video For Wilderness Search And Rescue, Daniel Richard Thornton
Unusual-Object Detection In Color Video For Wilderness Search And Rescue, Daniel Richard Thornton
Theses and Dissertations
Aircraft-mounted cameras have potential to greatly increase the effectiveness of wilderness search and rescue efforts by collecting photographs or video of the search area. The more data that is collected, the more difficult it becomes to process it by visual inspection alone. This work presents a method for automatically detecting unusual objects in aerial video to assist people in locating signs of missing persons in wilderness areas. The detector presented here makes use of anomaly detection methods originally designed for hyperspectral imagery. Multiple anomaly detection methods are considered, implemented, and evaluated. These anomalies are then aggregated into spatiotemporal objects by …
Integrated Affinity Column Capillary Electrophoresis Microdevices For Biomarker Analysis, Weichun Yang
Integrated Affinity Column Capillary Electrophoresis Microdevices For Biomarker Analysis, Weichun Yang
Theses and Dissertations
In this dissertation, microfluidic systems that integrate antibody-based sample preparation methods with electrophoretic separation are developed to analyze multiple biomarkers in a point-of-care setting. To form an affinity column, both monolith materials and wall-coated channels were explored. I successfully demonstrated that monolith columns can be prepared in microfluidic devices via photopolymerization. The selectivity of monolith columns was improved by immobilizing antibodies on the surface. These affinity columns can selectively enrich target analytes and reduce the signal of contaminant proteins up to 25,000 fold after immunoaffinity extraction. These results clearly demonstrate that microchip affinity monoliths can selectively concentrate and purify target …
Acoustical Analysis Of A Horn-Loaded Compression Drivers Using Numerical Analysis, Daniel Ross Tengelsen
Acoustical Analysis Of A Horn-Loaded Compression Drivers Using Numerical Analysis, Daniel Ross Tengelsen
Theses and Dissertations
Two numerical techniques, the boundary-element method (BEM) and the finite-difference method (FDM), are used for simulating the radiation from horn-loaded compression drivers and from an infinitely-baffled, finite-length pipe. While computations of the horn-loaded compression driver are in steady state, transient analysis of the finite-length pipe is studied as a precursor to transient analysis within the horn-loaded compression driver. BEM numerical simulations show promise for the development of new designs. Numerical simulations serve as a good tool for time and cost-effective prototyping as poor designs are detected before they are built.
Synthesis And Characterization Of An Oligothiophene-Ruthenium Complex And Synthesis And Optical Properties Of Oligothiophene-Ruthenium Complexes Bound To Cdse Nanoparticles, Nathan A. Bair
Theses and Dissertations
Oligothiophenes are of increasing interest in organic based electronic devices in part due to their high electron and hole mobilities. In an organic photovoltaic (OPV) device, the electronic properties of oligothiophenes make them advantageous as charge transfer junctions. To serve as charge transfer junctions, oligothiophenes must be functionalized to bind to the donor and acceptor parts of the device. The donor and acceptor parts are different materials and the synthesis of asymmetric oligothiophenes is of great interest. Previous researchers in our lab synthesized four asymmetric oligothiophenes, two with two thiophene subunits and two with four. Each set of oligothiophenes contained …