Physical Sciences and Mathematics Commons^™

Comparison Of Threshold Selection Methods For Microarray Gene Co-Expression Matrices, Bhavesh R. Borate, Elissa J. Chesler, Michael A. Langston, Arnold M. Saxton, Brynn H. Voy

Faculty Publications and Other Works -- EECS

Abstract

Background

Network and clustering analyses of microarray co-expression correlation data often require application of a threshold to discard small correlations, thus reducing computational demands and decreasing the number of uninformative correlations. This study investigated threshold selection in the context of combinatorial network analysis of transcriptome data.

Findings

Six conceptually diverse methods - based on number of maximal cliques, correlation of control spots with expressed genes, top 1% of correlations, spectral graph clustering, Bonferroni correction of p-values, and statistical power - were used to estimate a correlation threshold for three time-series microarray datasets. The validity of thresholds was tested by …

Open Heavy Flavor Measurement At Forward Angles For Cu+Cu Collisions At Center Of Mass Nn Collision Energy 200 Gev, Irakli Garishvili

Doctoral Dissertations

The main purpose of Relativistic Heavy Ion Collider (RHIC) program is to study the Quark-Gluon Plasma (QGP), a deconfined state of matter believed to be created in ultra-relativistic heavy ion collisions. Heavy quarks, expected to be produced during the earlier stages of heavy ion collisions, serve as an important probe of the QGP.‎

‎The following dissertation presents measurements of single muons resulting from the semileptonic decay of heavy flavor quarks in the rapidity range of $1.4 < \vert\eta\vert < 1.9$ for Cu+Cu nuclei collisions at $\sqrt{s_{NN}}=200$ GeV measured by the PHENIX experiment. Single muon spectra were measured for three different centrality classes (0 - 20 \% , 20 - 40 \%, 40 - 94 \%) within the $p_{T}$ range of 1.0 - 4.0 GeV/c.‎

‎To calculate single muon spectra, a full background estimate was statistically subtracted from inclusive spectra of muon candidate tracks reconstructed in the PHENIX muon …

Beta-Decay, Beta-Delayed Neutron Emission And Isomer Studies Around 78Ni, Mustafa Moiz Rajabali

Doctoral Dissertations

A study of nuclei with few nucleons outside the closed shell provides benchmarks for the nuclear shell model especially in this modern era of physics where exotic doubly magic nuclei can be tested. The subject of this thesis is to experimentally investigate the properties of nuclei near ⁷⁸Ni and to confront them with the predictions of modern large scale shell model calculations. In this regard, an experiment was performed at the National Superconducting Cyclotron Laboratory (NSCL) to measure excited states in ^71-73Ni populated via the beta-decay of ^71-73Co. Data collected from this experiment lead to partial level …

Controlled Self-Organization And Tunable Collective Phenomena In Surface-Based Nanostructures, Eun Ju Moon

Doctoral Dissertations

Nanostructure systems possessing certain desirable features can arise from the self-organization of fundamental building blocks. In this thesis we explore two types of controlled self-assembly mechanisms in hetero-epitaxy: (a) classical assembly of atom vacancies into quasi one-dimensional line structures and (b) quantum-driven assembly of atoms into atomically-smooth two-dimensional thin films. In the classical assembly phenomenon, adatom vacancies, created via elastic strain-relaxation in compressively strained atom chains on a silicon substrate, self-organize into meandering vacancy lines. The average spacing between these line defects can be varied by adjusting the chemical potential μ of the adsorbed atoms. We implemented a lattice model …

Biological Simulations And Biologically Inspired Adaptive Systems, Edgar Alfredo Duenez-Guzman

Doctoral Dissertations

Many of the most challenging problems in modern science lie at the interface of several fields. To study these problems, there is a pressing need for trans-disciplinary research incorporating computational and mathematical models. This dissertation presents a selection of new computational and mathematical techniques applied to biological simulations and problem solving: (i) The dynamics of alliance formation in primates are studied using a continuous time individual-based model. It is observed that increasing the cognitive abilities of individuals stabilizes alliances in a phase transition-like manner. Moreover, with strong cultural transmission an egalitarian regime is established in a few generations. (ii) A …

Physical Adsorption Of Ethylene On Mgo(100): Effects Of Substrate Ionicity And Symmetry On Wetting, Andi Barbour

Doctoral Dissertations

The wetting behavior of ethylene adsorbed on MgO(100) was investigated from 83{ 135 K using high resolution volumetric adsorption isotherms. Layering transitions for ethylene on MgO(100) are observed below the bulk triple point at 79.2 K and 98.4 K, respectively. From these isotherms, thermodynamic quantities associated with physical adsorption are determined. It was found that the average area occupied by ethylene on MgO(100) is around 22.6 squared angstroms per molecule. Using the two dimensional isothermal compressibility, the location of two potential phase transitions are identified at 108.6 K and 116.5 K for the first and second layer, respectively. The potential …

Sequence-Based Specification Of Embedded Systems, Jason Martin Carter

Doctoral Dissertations

Software has become integral to the control mechanism of modern devices. From transportation and medicine to entertainment and recreation, embedded systems integrate fundamentally with time and the physical world to impact our lives; therefore, product dependability and safety are of paramount importance.

Model-based design has evolved as an effective way to prototype systems and to analyze system function through simulation. This process mitigates the problems and risks associated with embedding software into consumer and industrial products. However, the most difficult tasks remain: Getting the requirements right and reducing them to precise specifications for development, and providing compelling evidence that the …

Studies Of Tungsten Alkyl Alkylidyne Compounds And Iron Porphyrin Derivatives, Brenda Ann Dougan

Doctoral Dissertations

This dissertation focuses on two research projects. The first project examines the reactions of tungsten(VI) alkyl alkylidyne and bis-alkylidene complexes with phosphines and water and the studies of thermodynamics and kinetics of the reactions. These studies have been conducted in part to determine the mechanistic pathway in the formation of novel tungsten(VI) species. The second portion of this dissertation focuses on the spin density and structures of biomimetic Fe(III) porphyrin derivatives using neutron and X-ray diffraction techniques. The spin density and magnetic properties of an Fe(III) porphyrin derivative has been determined by polarized neutron diffraction.

In the first portion of …

The Design And Synthesis Of Biotinylated Tylophorine Analogues For Use As Affinity Probes In The Elucidation Of The Cellular Targets Of Dcb-3503, Samson Francis

Doctoral Dissertations

The tylophorine analogue, DCB-3503 (1-62b, NSC-716802), has been found to exhibit broad spectrum activity in vitro in the National Cancer Institute’s (NCI) panel of 60 human-derived cell lines. Recent studies involving HepG2, a human hepatocellular carcinoma cell line, and two pancreatic ductal carcinoma cell lines (PANC-1 and HPAC), have suggested that DCB-3503 (1-62b) exerts its unique growth inhibition properties by modulating nuclear factor kappa B activity as well as through the inhibition of nuclear protein synthesis. However, the physiologically relevant protein binding partner(s) of DCB-3503 (1-62b) have not been identified. Herein, the design and …

Synthesis And Characterization Of Branched Polyelectrolytes: Star-Branched Napss, Daniel W. Holley

Doctoral Dissertations

In this thesis, we examined the effect of branching on the solution characteristics of polyelectrolytes using a set of star-branched NaPSS. The polystyrene precursors to these polyelectrolytes were synthesized using anionic polymerization allowing for the production of three distinct groups of star-branched polystyrenes with varying functionality and arm length.

Following sulfonation, several methods commonly employed in the literature for evaluation of sulfonation degree we established that sulfonation was quantitative. TGA was also demonstrated to reveal important characteristics of the sample.

We used aqueous SEC coupled with a multiple angle light scattering detector to determine several molecular characteristics of the star-branched …

Design And Synthesis Of Novel Tylophorine Analogs And Their Biological Activity, Julio Gutierrez

Doctoral Dissertations

Alkaloids containing the nitrogen atom in the bridgehead position of two rings, such as indolizidine, pyrrolizidine, and quinolizidine alkaloids, have a wide and varied distribution in nature. Some of these alkaloids demonstrate a broad range of pharmacological activities and have generated substantial synthetic interest. This thesis covers the total synthesis of novel tylophorine analogs called DCB 3503, DCB 3506, DCB 3507, DCB 3508, DCB 3509, and a derivative with a biotinylated chain attached to DCB 3506 for use as a biological probe. This thesis discusses the biological activity of these compounds as well.

Deciphering Climate From The Characterization Of Ring Width, Carbon, And Oxygen Isotopes In Latewood Tree-Ring Cellulose, Big Thicket National Preserve, Texas, Usa, Daniel Bruce Lewis

Doctoral Dissertations

Trees are excellent archives of paleoclimatic information. They can preserve records of past temperature, precipitation, drought, and extreme weather events. The focus of this dissertation is to use tree ring width, carbon isotopes, oxygen isotopes from multiple trees to characterize climate variability and the tree-ring tropical cyclone record. Living longleaf pine trees (Pinus palustris Mill.) were sampled from the Turkey Creek and Big Sandy Creek Units at Big Thicket National Preserve, Texas. Annual tree rings were measured and assigned yearly calendar dates. The latewood portion of each annual ring was shaved with a scalpel, and alpha-cellulose was extracted for …

Development And Implementation Of A New Technique To Study (P,Α) Reactions Relevant To Nucleosynthesis In Binary Systems, Brian Hossain Moazen

Doctoral Dissertations

The accurate determination of the strengths and energies of resonances in (p,alpha) reactions is important for understanding the influence of reaction cycles to element synthesis in many astrophysical environments. Thus far, (p,alpha) studies in inverse kinematics have employed solid polypropylene targets. These are not always advantageous, especially when the energy loss of the incoming beam in the solid target is significantly larger than the resonance width. At the Holifield Radioactive Ion Beam Facility, a new technique has been developed for measuring the strengths and energies of (p,alpha) reactions. In this technique, a large differentially-pumped scattering chamber is filled with hydrogen …

Wide-Range Characterization Of Current Conduction In Superconductors-Tuning Their Properties By Nanoscale Modification Of Materials, Özgür Polat

Doctoral Dissertations

Significant progress has been made in the development of YBa₂Cu₃O_7-x (YBCO)-based coated conductors (CCs) since the discovery of YBCO in 1987. Nowadays, high temperature superconductor (HTS) materials are advancing toward wide application areas in medical physics, industry, and science. The successful applications of these materials require clear understanding of the mechanisms controlling the current carrying capacity. It has been demonstrated the maximum current that a HTS can support is strongly affected by the vortex dynamics within the HTS materials. In this dissertation, we employed a combination of methods: conventional transport, magnetometry in a swept magnetic …

Static And Dynamic Scheduling For Effective Use Of Multicore Systems, Fengguang Song

Doctoral Dissertations

Multicore systems have increasingly gained importance in high performance computers. Compared to the traditional microarchitectures, multicore architectures have a simpler design, higher performance-to-area ratio, and improved power efficiency. Although the multicore architecture has various advantages, traditional parallel programming techniques do not apply to the new architecture efficiently. This dissertation addresses how to determine optimized thread schedules to improve data reuse on shared-memory multicore systems and how to seek a scalable solution to designing parallel software on both shared-memory and distributed-memory multicore systems.

We propose an analytical cache model to predict the number of cache misses on the time-sharing L2 cache …

Computational Exploration Of The Interaction Of Molecular Hydrogen With An Anionic Hydrogen Atom, Patrick Karl Moehlen

Doctoral Dissertations

The focus of this dissertation is to facilitate the computation of the infrared absorption line shape of solid para-hydrogen with an anionic hydrogen atom dopant. For this, we compute the complete potential energy surface for the interaction of H¯ with H². The coupled cluster with singles, doubles, and perturbative treatment of triple excitations method was used with augmented correlationconsistent polarized valence triple-zeta atom-centered basis sets and a set of bonding functions.

The focus then turns to describing the rovibrational Hamiltonian of the system with the coupledchannel method. We find bound and quasi-bound stationary states of the system for …

Development Of A Novel Lysophosphatidic Acid Activity Probe To Identify And Characterize New Protein Targets, Leah M. Cuthriell

Masters Theses

Lipids are categorized according to their biological function. Phospholipids, glycolipids, and cholesterol are bulk membrane lipids that offer structure and support to the cells and organelle membranes. Signaling lipids include diacylglycerol, phosphatidic acid, and lysophosphatidic acid (LPA). These are low abundance lipids that are active in various pathways. LPA acts through GPCR receptors to activate G or beta mediated stimulation of phospholipase C leading to phosphatidylinositol-(4,5)-bisphosphate hydrolysis, G_i mediated inhibition of adenyl cyclase, and G_i mediated stimulation of the mitogenic Ras- MAP kinase. To further elucidate the biological activity of LPA and potentially identify new LPA binding receptors, …

An Exploration Of Monophonic Instrument Classification Using Multi-Threaded Artificial Neural Networks, Marc Joseph Rubin

Masters Theses

The use of computers for automated music analysis could benefit several aspects of academia and industry, from psychological and music research, to intelligent music selection and music copyright investigation. In the following thesis, one of the first steps of automated musical analysis, i.e., monophonic instrument recognition, was explored. A multi-threaded artificial neural network was implemented and used as the classifier in order to utilize multi-core technology and allow for faster training. The parallelized batch-mode backpropagation algorithm used provided linear speedup, an improvement to the current literature. For the classification experiments, eleven different sets of instruments were used, starting with perceptively …

Phosphorus Transport From A Field Receiving Long-Term Liquid Dairy Manure Application In A Karst Landscape, Dustin Cody Graham

Masters Theses

Agricultural runoff is a leading non-point source contributor to water quality impairment in the United States and is associated with eutrophication of surface waters. Phosphorus (P) is often the most limiting nutrient for eutrophication in freshwaters. The objectives of this study were to characterize the P forms in surface runoff from an agricultural field that has received long-term applications of liquid dairy manure and to determine the forms of soil P that occur within a sinkhole feature located within the application field. Three 21-m x 6 m bermed plots were established to collect storm water runoff from a portion of …

An Investigation Into The Activities Of 1,2,3 & 1,2,4 Triazoles In Biological And Catalytic Systems, David John Schneider

Masters Theses

Selective epigenetic control of the cellular machinery is a grail of drug development. The balance between HAT’s and HDAC’s activities is one way the cell controls what, and at when during the cellular lifecycle a gene is expressed. Having the ability to lock chromatin down to the histone is a powerful tool for the treatment of disease states like cancer. Presented here is a preliminary exploration of the synthesis, and basic testing of novel compounds that use a triazole motif as a zinc binding group in an attempt to gain further selectivity in inhibition over HDAC’s.

Interest in the development …

Polarimetry Studies For The Npdgamma Experiment At The Sns, Mostafa Jon Dadras

Masters Theses

The NPDGamma collaboration aims to measure a parity{violating directional gamma-ray asymmetry from the capture of polarized cold neutrons on protons. The asymmetry, predicted to be on the order of 50 ppb, is a result of the weak interaction between mesons and nucleons during the neutron capture reaction. The experiment is designed to make a statistics limited measurement of the asymmetry at the level of about 20%. The experiment will be carried out at the Fundamental neutron Physics Beamline (FnPB) at the Spallation Neutron Source (SNS). The neutron beam is polarized by a super{mirror polarizer. A 9.5 G magnetic field guides …

Design And Synthesis Of Fret-Based Boronic Acid Receptors To Detect Carbohydrate Clustering And Development Of Diacylglycerol-Based Lipid Probesto Investigate Lipid-Protein Binding Interactions, Manpreet Kaur Cheema

Masters Theses

Carbohydrate–protein interactions play vital roles in various biochemical processes such as signal transduction and cell surface recognition events. The clustering of carbohydrates into dense domains such as lipid rafts regulates recognition by multivalent receptors (i.e. lectins). These regions are known to play important roles in biological processes such as cellular transduction and trafficking. In order to characterize the clustering of glycans on cell surfaces, detection of domains with high carbohydrate density is of great interest. In this thesis, we present the work based on a modular strategy to design and synthesize boronic acid-based carbohydrate receptors, which are termed as boronolectins …

A Statistical Analysis Of Key Factors Influencing The Location Of Biomass-Using Facilities, Xu Liu

Masters Theses

Bioenergy and biofuels are emerging industries in the U.S. economy that will require statistical and economical analyses of woody biomass resources, supply chains, and other key factors that influence the siting of industrial facilities. This thesis develops models using logistic regression to improve the understanding of the key factors that influence the locations of existing wood-using bioenergy and biofuels plants, and other wood-using plants. The scope of the study is 13 Southeastern states.¹ Logistic regression models are developed at the state and regional levels. The resolution of the study is the ZIP Code tabulation area (ZCTA). There are 9,416 …

Accelerated Ctis Using The Cell Processor, Thaddeus James Thompson

Masters Theses

The Computed Tomography Imaging Spectrometer (CTIS) is a device capable of simultaneously acquiring imagery from multiple bands of the electromagnetic spectrum. Due to the method of data collection from this system, a processing intensive reconstruction phase is required to resolve the image output. This paper evaluates a parallelized implementation of the Vose-Horton CTIS reconstruction algorithm using the Cell processor. In addition to demonstrating the feasibility of a mixed precision implementation, it is shown that use of the parallel processing capabilities of the Cell may provide a significant reduction in reconstruction time.

The Impact Of Iron Deprivation On The Metabolism Of Escherichia Coli As Measured By Targeted Hplc-Ms/Ms Based Metabolomics, Jamie Rhea Light

Masters Theses

Iron is a necessity for all living organisms, and bacteria typically need an internal concentration of iron in the micromolar range.¹ This becomes quite problematic, especially in pathogenic bacteria, because the concentration of free ions within the human body is only 10^-24 Molar due to iron binding proteins, like transferrin.¹ In order to circumvent this problem, bacteria produce small iron chelating molecules called siderophores.¹ The bacteria utilized for this study, a K-12 derivative of Escherichia coli, produce only one siderophore, enterobactin. Not only is the transcription of genes associated with iron acquisition initiated in response …

Cross Sections Fall 2009, Department Of Physics And Astronomy

Cross Sections

No abstract provided.

Bridging The Gap Between Systems Biology And Medicine, Gilles Clermont, Charles Auffray, Yves Moreau, David M. Rocke, Daniel Dalevi, Devdatt Dubhashi, Dana R. Marshall, Peter Raasch, Frank Dehne, Paolo Provero, Jesper Tegner, Bruce J. Aronow, Michael A. Langston, Mikael Benson

Faculty Publications and Other Works -- EECS

Abstract

Systems biology has matured considerably as a discipline over the last decade, yet some of the key challenges separating current research efforts in systems biology and clinically useful results are only now becoming apparent. As these gaps are better defined, the new discipline of systems medicine is emerging as a translational extension of systems biology. How is systems medicine defined? What are relevant ontologies for systems medicine? What are the key theoretic and methodologic challenges facing computational disease modeling? How are inaccurate and incomplete data, and uncertain biologic knowledge best synthesized in useful computational models? Does network analysis provide …

Experimental Studies Of Exotic Negative Ions, Shaun Gerald Ard

Doctoral Dissertations

Although negative ions have been studied extensively for quite some time, their study continues to offer insight into developing and refining quantum chemical modeling techniques. Negative ion states remain difficult to treat ab initio due to the significant electron-electron correlation, thus putting a premium on experimental results to guide the way. Experimental techniques such as Electrospray Ionization (ESI) and Rydberg Electron Transfer (RET) have made study of some exotic negative ions in the gas phase possible for the first time. Multiply Charged Anions (MCAs) of several families of molecules were studied using Collision Induced Dissociation (CID) and Infrared Multi Photon …

Single Walled Carbon Nanotube Networks As Transparent Conductors, Matthew Patrick Garrett

Doctoral Dissertations

A variety of technological applications depend on transparent conducting films, and carbon nanotubes have the properties required to serve in that role. Single-walled carbon nanotube networks have been studied as transparent conductors in order to understand and optimize their electrical and optical properties. Nanotube films are complex networks of semiconducting and metallic nanotubes, bundled and branched in multifarious directions, with different strength connections between bundles. Chemical modification of nanotubes and inclusion of non-nanotube material can further alter network properties. Separating the contributions of all aspects of the network is a necessary but daunting task in order to optimize nanotube films. …

Enhancing User Queries In Scientific Visualization With Distribution Information, Christopher Johnson

Doctoral Dissertations

Scientific visualization is concerned with the graphical portrayal of data. Using symbols, color, and natural perceptual cues, humans gain insight into collections of raw numbers that may not be as efficiently processed in non-graphical formats. For simple data, visualization may require only a simple mapping between numeric values and a color scale. But modern scientific, economic, and social data is far from simple. Multiple variables, duration of time, fine resolutions, and wide sampling have yielded data sets of unprecedented complexity. The mapping between such data and its visual appearance is difficult to define. The works described here attempt to make …