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Theses and Dissertations

2010

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Articles 1 - 30 of 216

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 Dec 2010

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 …

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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 Dec 2010

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, …

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A Reusable Persistence Framework For Replicating Empirical Studies On Data From Open Source Repositories, Scott Bong-Soo Chun Dec 2010

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 …

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Capture And Access Of Multiple Screen Presentations, Kelv H. Cutler Dec 2010

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. …

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Fitting A Distribution To Catastrophic Event, Ebenezer Osei Dec 2010

Fitting A Distribution To Catastrophic Event, Ebenezer Osei

Theses and Dissertations

Statistics is a branch of mathematics which is heavily employed in the area of Actuarial Mathematics. This thesis first reviews the importance of statistical distributions in the analysis of insurance problems and the applications of Statistics in the area of risk and insurance. The Normal, Log-normal, Pareto, Gamma, standard Beta, Frechet, Gumbel, Weibull, Poisson, binomial, and negative binomial distributions are looked at and the importance of these distributions in general insurance is also emphasized. A careful review of literature is to provide practitioners in the general insurance industry with statistical tools which are of immediate application in the industry. These …

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Chemical Vapor Deposition Of Silanes And Patterning On Silicon, Feng Zhang Dec 2010

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. …

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Volcanic Stratigraphy And A Kinematic Analysis Of Ne-Trending Faults Of Allens Ranch 7.5' Quadrangle, Utah County, Utah, Adam Paul Mckean Dec 2010

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 …

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Trusted Mobile Overlays, Robert Scott Robertson Dec 2010

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.

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Tunable Optical Delay In Doppler-Broadened Cesium Vapor, Monte D. Anderson Dec 2010

Tunable Optical Delay In Doppler-Broadened Cesium Vapor, Monte D. Anderson

Theses and Dissertations

Variable-delay tunable optical delay line or optical buffers are critical for the development of all-optical networks components as well as interferometry and analytic instruments. Recent research on slow light may hold the key for the development of the first practical tunable optical delay device. In this research the linear dispersion delay effects in an alkali vapor. The hyperfine relaxation observations present insight into the complex bleach wave dynamics during a high-intensity pulsed pump in DPAL systems.

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First Order Analysis Of Nitrate Loading In The Upper Elbe River Basin, Czech Republic, Daniel J. Ritter Dec 2010

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 …

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Factors Influencing Macroinvertebrate Diversity And Community Composition In Riverine Freshwater Rock Pools, Chtaura Jackson Dec 2010

Factors Influencing Macroinvertebrate Diversity And Community Composition In Riverine Freshwater Rock Pools, Chtaura Jackson

Theses and Dissertations

I examined a system of 378-riverine rock pools situated along the James River in Richmond, Virginia, to uncover the factors influencing their macroinvertebrate diversity and community composition. I characterized (total = 60) the physical characteristics, water quality, hydrology, and community assemblages in July 2009 for a subset of pools. I examined whether selected environmental factors (pH, nearest neighbor distance, depth, surface area and inundation height) were related to macroinvertebrate diversity and community composition. Species richness and total abundance of all taxa increased with pool pH and surface area. Ordination indicates that nearest neighbor distance (NND) and pH varied significantly among …

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Gene Network Inference And Expression Prediction Using Recurrent Neural Networks And Evolutionary Algorithms, Heather Y. Chan Dec 2010

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.

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Scattering Matrix Elements For The Nonadiabatic Collision B (2PJₐ) + H2 (1Σ+G, Ν, Ј) ↔ B (2PJ’ₐ) + H2 (1Σ+G, Ν’, J’)., Luke A. Barger Dec 2010

Scattering Matrix Elements For The Nonadiabatic Collision B (2PJₐ) + H2 (1Σ+G, Ν, Ј) ↔ B (2PJ’ₐ) + H2 (1Σ+G, Ν’, J’)., Luke A. Barger

Theses and Dissertations

Scattering matrix elements are calculated for the nonadiabatic inelastic collision B (2Pjₐ) + H2 (1Σ+g, ν, ј) ↔ B (2Pj’ₐ) + H2 (1Σ+g, ν’, j’). This calculation utilizes the effective potential energy surfaces for this collision generated by Garvin along with a correction to the asymptotic H2 potential. Wavepackets are propagated on these surfaces using a split-operator propagator. This propagation yields correlation functions between reactant and product Møller states which are used to calculate the scattering …

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Asynchronous Database Drivers, Michael Adam Heath Dec 2010

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 …

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Drop-In Concurrent Api Replacement For Exploration, Test, And Debug, Everett Allen Morse Dec 2010

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 …

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Tracking Floral Visitation Using Dna Barcodes, Ivan Ray Shoemaker Dec 2010

Tracking Floral Visitation Using Dna Barcodes, Ivan Ray Shoemaker

Theses and Dissertations

Floral visitation resulting in interspecific pollen transfer (IPT) from non-native or invasive plant species can affect the reproductive fitness of native plant species through pollen allelopathy, stigma clogging, stylar clogging, and ovule (seed) discounting. The prevalence of IPT and the importance of pollinators in mediating its impacts, however, remain poorly understood. Although most traditional methods for examining visitor movement are insufficient for determining rates of potential IPT, one promising alternative is the use of DNA barcoding. Because floral visitors eat, collect or unknowingly obtain pollen, nectar and other floral tissues, plant DNA should be recoverable from their bodies, permitting molecular …

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Characterization Of Watersheds On Fort Benning Military Reservation: Comparison Of Field Data To Watershed Parameters, Melinda Rosetta Stahl Dec 2010

Characterization Of Watersheds On Fort Benning Military Reservation: Comparison Of Field Data To Watershed Parameters, Melinda Rosetta Stahl

Theses and Dissertations

Sixteen watersheds located on Fort Benning Military Installation in Georgia were analyzed using both physically collected data and computer modeling data. Physical data collected included total suspended solids (TSS) and grain size analysis using the Wolman Pebble Count method. Computer modeling analyzed the watersheds using ArcGIS 9.3 for comparison to physical data. Land use, slope, and soil data were used in a modified revised universal soil loss equation (RUSLE) to create a soil erodibility index map. Wolman Pebble Count data showed that in half of the watersheds, 84% of the sampled grains were less than half a millimeter in size. …

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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 Dec 2010

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 …

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High Flow Air Sampling For Field Detection Using Gas Chromatography-Mass Spectrometry, Jacolin Ann Murray Dec 2010

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 …

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Phytoremediation Of Copper Contaminated Waste Water Using Lemna Minor, Mark Apelt Nov 2010

Phytoremediation Of Copper Contaminated Waste Water Using Lemna Minor, Mark Apelt

Theses and Dissertations

The use of natural remediation methods to remove contaminants from waste water is becoming more popular. Plants have been used for several decades, yet their use for municipal waste water contaminated by heavy metals is limited to a few studies which focus on the Mercury and Chromium (Bennicelli, et.al, 2004). This study specifically attempted to determine the viability for using Lemna minor to remediate municipally generated wastewater contaminated with copper. The study used 100 ml samples of wastewater, artificially spiked with 8 mg/L of copper sulfate and seeded with approximately 100 Lemna minor fronds. Each treatment was repeated 15 times …

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Inferential Methods For High-Throughput Methylation Data, Maria Capparuccini Nov 2010

Inferential Methods For High-Throughput Methylation Data, Maria Capparuccini

Theses and Dissertations

The role of abnormal DNA methylation in the progression of disease is a growing area of research that relies upon the establishment of sound statistical methods. The common method for declaring there is differential methylation between two groups at a given CpG site, as summarized by the difference between proportions methylated db=b1-b2, has been through use of a Filtered Two Sample t-test, using the recommended filter of 0.17 (Bibikova et al., 2006b). In this dissertation, we performed a re-analysis of the data used in recommending the threshold by fitting a mixed-effects ANOVA model. It was determined that the 0.17 filter …

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Work Towards The Isolation And Characterization Of The Muscle Isoform Of Glucose 1,6-Bisphosphatase, Caleb J. Hiller Nov 2010

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.

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Exhumation Mechanisms Of The Greater Himalayan Sequence, Garhwal Region, India, Christopher James Spencer Nov 2010

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 …

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Power And Sample Size For Three-Level Cluster Designs, Tina Cunningham Nov 2010

Power And Sample Size For Three-Level Cluster Designs, Tina Cunningham

Theses and Dissertations

Over the past few decades, Cluster Randomized Trials (CRT) have become a design of choice in many research areas. One of the most critical issues in planning a CRT is to ensure that the study design is sensitive enough to capture the intervention effect. The assessment of power and sample size in such studies is often faced with many challenges due to several methodological difficulties. While studies on power and sample size for cluster designs with one and two levels are abundant, the evaluation of required sample size for three-level designs has been generally overlooked. First, the nesting effect introduces …

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Halo Ion Trap Mass Spectrometry: Design, Instrumentation, And Performance, Miao Wang Nov 2010

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 …

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Technologies Of Mobile Communication, Monika Margilaj Nov 2010

Technologies Of Mobile Communication, Monika Margilaj

Theses and Dissertations

Long-Term Evolution (LTE) is a new technology recently specified by 3GPP-Third Generation Partnership Project on the way towards fourth-generation mobile. This thesis presents the main technical features of this technology as well as its performances in terms of peak bit rate and average cell throughput, among others. LTE entails a big technological improvement as compared with the previous 3G standards. 1 However, this thesis also demonstrates that LTE performances do not fulfill the technical requirements established by ITU-R to classify one radio access technology as a member of the IMT-Advanced family of standards. Thus, this thesis describes the procedure followed …

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Allocating Homeland Security Screening Resources Using Knapsack Problem Models, Rebecca Dreiding Oct 2010

Allocating Homeland Security Screening Resources Using Knapsack Problem Models, Rebecca Dreiding

Theses and Dissertations

Since the events of September 11, 2001, the federal government is focused on homeland security and the fight against terrorism. This thesis addresses the idea of terrorist groups smuggling nuclear weapons through the borders of the United States. Security screening decisions are analyzed within maritime and aviation domains using discrete optimization models, specifically knapsack problems. The focus of the maritime chapters involves a risk-based approach for prescreening intelligence classifications for primary and secondary screening decisions given limited budget and resources. Results reveal that screening decisions are dependent on prescreening classification and the efficacy of the screening technologies. The screening decisions …

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Stereotype Logit Models For High Dimensional Data, Andre Williams Oct 2010

Stereotype Logit Models For High Dimensional Data, Andre Williams

Theses and Dissertations

Gene expression studies are of growing importance in the field of medicine. In fact, subtypes within the same disease have been shown to have differing gene expression profiles (Golub et al., 1999). Often, researchers are interested in differentiating a disease by a categorical classification indicative of disease progression. For example, it may be of interest to identify genes that are associated with progression and to accurately predict the state of progression using gene expression data. One challenge when modeling microarray gene expression data is that there are more genes (variables) than there are observations. In addition, the genes usually demonstrate …

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Packing Virtual Machines Onto Servers, David Luke Wilcox Oct 2010

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 …

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Assessment Of Acgh Clustering Methodologies, Serena F. Baker Oct 2010

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 …

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