Physical Sciences and Mathematics Commons^™

Cnareporter: A Computational Tool For The Generation Of Clinical Reports Of Genomic Alterations, Yuri Kotliarov, Serdar Bozdag, Hangjiong Cheng, Stefan Wuchty, Jean-Claude Zenklusen, Howard A. Fine

Mathematics, Statistics and Computer Science Faculty Research and Publications

Background: Genomic copy number alterations are widely associated with a broad range of human tumors and offer the potential to be used as a diagnostic tool. Especially in the emerging era of personalized medicine medical informatics tools that allow the fast visualization and analysis of genomic alterations of a patient's genomic profile for diagnostic and potential treatment purposes increasingly gain importance. Results: We developed CNAReporter, a software tool that allows users to visualize SNP-specific data obtained from Affymetrix arrays and generate PDF-reports as output. We combined standard algorithms for the analysis of chromosomal alterations, utilizing the widely applied GenePattern framework. …

Resin-Modified Glass-Ionomer Setting Reaction Competition, David W. Berzins, S. Abey, M. C. Costache, Charles A. Wilkie, H. W. Roberts

Chemistry Faculty Research and Publications

Resin-modified glass ionomers (RMGI) set by at least 2 mechanisms dependent upon reactant diffusion prior to gelation. Each reaction’s kinetics and setting mechanism may rely on and/or compete with the other. In this study, we investigated RMGI setting reaction interactions using differential scanning calorimetry (DSC) by varying light-cure initiation times. A RMGI was analyzed with isothermal and dynamic temperature scan DSC with light-curing occurring immediately, or at 5 or 10 minutes after mixing as well as without light-activation. Results show that as time allowed for the acid-base reaction increased, the light-activation polymerization exotherm decreased. Conversely, analysis of DSC data suggests …

Calcium Sparks And Homeostasis In A Minimal Model Of Local And Global Calcium Responses In Quiescent Ventricular Myocytes, Jana M. Hartman, Gregory D. Smith, Eric A. Sobie

Arts & Sciences Articles

"We present a minimal whole cell model that accounts for both local and global aspects of Ca signaling in quiescent ventricular myocytes..."

Modeling The Effects Of Genetic Manipulations Of Calsequestrin On Local Calcium Release And Depletion In Cardiac Myocytes, Ryan P. Carpenter, Gregory D. Smith, Sandor Gyorke

Arts & Sciences Articles

"Cardiac calsequestrin (CASQ2), a Ca buffer localized to the junctional SR (jSR) of cardiac myocytes, is known to bind to the RyR-triadin-junctin complex, participate in the luminal regulation of RyRs, and modulate Ca spark activity..."

Beyond Description: Converting Web Site Usage Statistics Into Concrete Site Improvement Ideas, Julie Arendt, Cassie Wagner

VCU Libraries Faculty and Staff Publications

Web site usage statistics are a widely used tool for Web site development, but libraries are still learning how to use them successfully. This case study summarizes how Morris Library at Southern Illinois University Carbondale implemented Google Analytics on its Web site and used the reports to inform a site redesign. As the main campus library at a research university with about 20,000 undergraduate and graduate students, the library included resources from multiple library departments on a single site. In planning the redesign, Morris Library's Virtual Library Group combined usage reports with information from other sources, such as usability tests …

The Heavily Polluted Atmosphere Of The Daz White Dwarf Galex J193156.8+011745, Stephane Vennes, Adéla Kawka, Péter Németh

Aerospace, Physics, and Space Science Faculty Publications

We report on the discovery of a new heavily polluted white dwarf. The DAZ white dwarf GALEX J193156.8+011745 was identified in a joint Galaxy Evolution Explorer (GALEX)/GSC survey of ultraviolet-excess objects. Optical spectra obtained at ESO New Technology Telescope show strong absorption lines of magnesium and silicon, and a detailed abundance analysis based on Very Large Telescope-Kueyen UVES spectra reveal super-solar abundances of silicon and magnesium and near-solar abundances of oxygen, calcium and iron. The overall abundance pattern bears the signature of on-going accretion on to the white dwarf atmosphere. The infrared spectral energy distribution shows an excess in the …

Chandra Observations Of The Radio Galaxy 3c 445 And The Hot Spot X-Ray Emission Mechanism, Eric S. Perlman, Markos Georganopoulos, Emily M. May, Demosthenes Kazanas

Aerospace, Physics, and Space Science Faculty Publications

We present new Chandra observations of the radio galaxy 3C 445, centered on its southern radio hot spot. Our observations detect X-ray emission displaced upstream and to the west of the radio-optical hot spot. Attempting to reproduce both the observed spectral energy distribution and the displacement excludes all one-zone models. Modeling of the radio-optical hot spot spectrum suggests that the electron distribution has a low-energy cutoff or break approximately at the proton rest mass energy. The X-rays could be due to external Compton scattering of the cosmic microwave background coming from the fast (Lorentz factor Γ ≈ 4) part of …

Model Of Sprite Luminous Trail Caused By Increasing Streamer Current, Ningyu Liu

Aerospace, Physics, and Space Science Faculty Publications

This study investigates a possible physical mechanism responsible for the occurrence of the luminous trail of sprite streamers, which is also known as "afterglow." According to streamer modeling results, when sprite streamers propagate with expansion, acceleration and brightening, the total current flowing through the streamer body also increases. The increasing current results in the rise of the electric field in the streamer channel far behind the streamer head, which leads to effective production of N₂ excited states by electron impact excitation and then the glowing trail.

Acceleration Of Suprathermal Particles By Compressional Plasma Wave Trains In The Solar Wind, Ming Zhang

Aerospace, Physics, and Space Science Faculty Publications

This paper presents a calculation of particle acceleration by an idealized compressional plasma wave train. In this model, suprathermal particles, such as pickup ions, are continuously injected into a wave train consisting of a series of compression or rarefaction regions. The momentum distribution of particles will become broader and broader as they go through the wave train, which is very similar to diffusion in momentum space. The acceleration process is very fast: it does not take too many wave cycles even with a small compression amplitude to reach an asymptotic steady state momentum distribution. In the absence of large-scale adiabatic …

Diffusion Of Relativistic Runaway Electrons And Implications For Lightning Initiation, Joseph R. Dwyer

Aerospace, Physics, and Space Science Faculty Publications

Using detailed Monte Carlo simulations, the diffusion coefficients for relativistic runaway electron avalanches in air are found for the range of electric field strengths applicable to thunderclouds. Diffusion causes runaway electron avalanches to spread perpendicular to and parallel to the avalanche direction, resulting in much smaller peak conductivities than would be inferred otherwise. The idea that runaway electron avalanches seeded by extensive cosmic ray air showers may initiate lightning has gained considerable popularity in recent years. However, using the diffusion coefficients calculated in this paper along with the avalanche multiplication limit from X-ray and positron feedback, it is found that …

First Results On Terrestrial Gamma Ray Flashes From The Fermi Gamma-Ray Burst Monitor, Michael S. Briggs, Joseph R. Dwyer

Aerospace, Physics, and Space Science Faculty Publications

The Gamma-ray Burst Monitor (GBM) on the Fermi Gamma-ray Space Telescope detected 12 intense terrestrial gamma ray flashes (TGFs) during its first year of observation. Typical maximum energies for most of the TGFs are ∼30 MeV, with one TGF having a 38 MeV photon; two of the TGFs are softer and longer than the others. After correcting for instrumental effects, a representative bright TGF is found to have a fluence of ∼0.7 photons cm-2. Pulses are either symmetrical or have faster risetimes than fall times; they are well fit with Gaussian or lognormal functions. The fastest risetime observed was 7 …

Magnetic Cloud Boundary Layer Of 9 November 2004 And Its Associated Space Weather Effects, Pingbing Zuo, Fengsi Wei, Xueshang Feng, Xiaojun Xu, Wenbin Song

Aerospace, Physics, and Space Science Faculty Publications

On 9 November 2004, the WIND spacecraft detected a magnetic cloud boundary layer (MCBL) during the interval from 19:07 UT to 20:30 UT. Within the MCBL, there is intense southward magnetic field and the dynamic pressure is rather high, which makes it much geoeffective. Twenty-three minutes later, the MCBL arrived on the magnetopause. An intense geomagnetic storm main phase was driven by the sustaining strong southward magnetic field within the MCBL. During the passage of the MCBL, a typical magnetospheric substorm was triggered. The substorm onset was synthetically identified by the aurora breakup, magnetic dipolarization, dispersionless particle injection, Pi2 pulsation, …

A Multi-Wavelength Spectral And Polarimetric Study Of The Jet Of 3c 264, Eric S. Perlman

Aerospace, Physics, and Space Science Faculty Publications

We present a comprehensive multi-band spectral and polarimetric study of the jet of 3C 264 (NGC 3862). Included in this study are three Hubble Space Telescope (HST) optical and ultraviolet polarimetry data sets, along with new and archival Very Large Array radio imaging and polarimetry, a re-analysis of numerous HST broadband data sets from the near infrared to the far ultraviolet, and a Chandra ACIS-S observation. We investigate similarities and differences between optical and radio polarimetry, in both degree of polarization and projected magnetic field direction. We also examine the broadband spectral energy distribution of both the nucleus and jet …

Potential Reallocation Mechanisms For The Transfer/And Or Adjustment Of Catch Shares Of Sectors With Application To The Western And South Australian Rock Lobster Fisheries. A Discussion Paper., Chris Reid

Fisheries management papers

To allow for a greater understanding of potential allocation adjustment mechanisms and requirements for their implementation, Western Australia’s Department of Fisheries is exploring potential mechanisms with reference to their application in the Western and South Australian rock lobster fisheries. This work is being conducted as part of the Fisheries Research and Development Corporation (FRDC) project 2007/050 Developing Mechanisms for the Transfer and/or Adjustment of Rock Lobster Shares Between Sectors in Western Australia and South Australia. This report documents the Department of Fisheries’ initial exploration and findings in relation to potential inter-sectoral reallocation mechanisms.

Considerations For The Implementation Of Western Rock Lobster Sectoral Allocations., Integrated Fisheries Allocation Advisory Committee

Fisheries management papers

This paper discusses the Western rock lobster allocation process.

The Minister for Fisheries has determined that the allocation for sectors in the western rock lobster fishery after reserving one tonne for the customary sector shall be 95 per cent commercial and five per cent recreational.

The notional Sustainable Harvest Level (SHL) for rock lobster is expressed as a range, depending on the status of the stock rather than a specific quantitative limit.

Retrieval Of Atmospheric Elemental Carbon Records Using Lake Sediments : Implications In Radiative Forcing, Tanveer Ahmed

Legacy Theses & Dissertations (2009 - 2024)

Elemental or black carbon (EC or BC) aerosols produced during incomplete combustion strongly absorb solar radiation and contribute to global warming, and cause cardiopulmonary disease. Long-term atmospheric EC measurements, [EC]_atm, are needed to validate global climate models to estimate the impact of EC on earth's temperature. Such data is sparse.

First Principles Investigation Of Electronic Structures And Associated Energy And Wave-Function Dependent Properties Of Biological Systems : Deoxyribonucleic Acid (Dna), Oxy-Haemoglobin, Shyam Raj Badu

Legacy Theses & Dissertations (2009 - 2024)

The Hartree-Fock procedure combined with many body perturbation theory has been used to investigate the electronic structures and associated properties of DNA systems and their corresponding muonium (Mu) adducts, as well as oxyhaemoglobin (HbO2).

Recovering Brande : Freewriting And Sustainable (Procedural) Expression, Richard Bower

Legacy Theses & Dissertations (2009 - 2024)

Dorothea Brande is rarely known in rhetoric and composition yet continues to hold popular influence over writers attracted to Cartesian beliefs. The aim of this project is to recover Brande's contributions in order to rethink composition's trajectories. Chiefly, Dorothea Brande's legacy has been in creative writing through Becoming a Writer. In this bestseller, she establishes a program for putting the Cartesian divide to work. "Writing with the unconscious mind in the ascent," as Brande explains about what Ken Macrorie and Peter Elbow later call freewriting, harnesses the bifurcated consciousness of writers and begins a journey of unification.

Toward A Theory-Based Natural Language Capability In Robots And Other Embodied Agents : Evaluating Hausser's Slim Theory And Database Semantics, Robin Kowalchuk Burk

Legacy Theses & Dissertations (2009 - 2024)

Computational natural language understanding and generation have been a goal of artificial intelligence since McCarthy, Minsky, Rochester and Shannon first proposed to spend the summer of 1956 studying this and related problems. Although statistical approaches dominate current natural language applications, two current research trends bring renewed focus on this goal. The nascent field of artificial general intelligence (AGI) seeks to evolve intelligent agents whose multi-subagent architectures are motivated by neuroscience insights into the modular functional structure of the brain and by cognitive science insights into human learning processes. Rapid advances in cognitive robotics also entail multi-agent software architectures that attempt …

Beyond Regular : Pattern Matching With Extended Regular Expressions, Benjamin Robert Carle

Legacy Theses & Dissertations (2009 - 2024)

Regular expression pattern matching or some variant thereof is present

A Spline Kernel Based Smoothing Algorithm : A Comparison Of Methods With A Spatiotemporal Application To Global Climate Fluctuations, Derek Daniel Cyr

Legacy Theses & Dissertations (2009 - 2024)

In statistics, smoothing is a technique that attempts to capture the key patterns or trends in data while leaving out the noise that is obscuring them. Nonparametric techniques are well-suited for smoothing as they do not rely on assumptions that the data arise from a given probability distribution.

Investigation Of The Threshold Voltage Shift Effect Of La2o3 On Tin/Hfo2/La2o3/Sio2/Si Stacks, Ming Di

Legacy Theses & Dissertations (2009 - 2024)

The semiconductor industry continues to scale (shrink) transistor dimensions to both increase the number of transistors per integrated circuit and their speed. One important aspect of scaling is the need to decrease the equivalent oxide thickness of the transistor gate dielectric while minimizing leakage current. Traditional thin layer SiO2 or SiOxNy films have been replaced by higher dielectric constant film stacks Here we study one example, the HfO2/La2O3/SiO2 stack. This dissertation describes an investigation of the use of La2O3 to reduce the threshold voltage of TiN/HfO2/SiO2/Si stacks (high-k/metal gate stacks). A significant aspect of this study is the determination of …

Tropical Cyclogenesis Associated With Extratropical Precursors In The North Atlantic Basin, Thomas J. Galarneau

Legacy Theses & Dissertations (2009 - 2024)

This thesis investigates genesis pathways of tropical cyclones (TCs) over the North Atlantic basin during 2004-2008 with a focus on TCs that form in conjunction with extratropical precursor disturbances. These genesis pathways are nonbaroclinic, low-level baroclinic, trough-induced, transient-trough interaction, weak tropical transition (TT), and strong TT. The transient-trough interaction, trough-induced, weak TT, and strong TT genesis pathways all occur in conjunction with extratropical precursor disturbances. This thesis will assess the physical and dynamical mechanisms relevant to TC genesis among these genesis pathways via composite and case study analyses.

Arsenic Speciation Analysis Of Biological Fluids : A Study Of Liquid Chromatography Coupled To Analytical Atomic Spectrometric Instrumentation, Kanna Ito

Legacy Theses & Dissertations (2009 - 2024)

Arsenic exists as many different chemical forms including inorganic, methylated and dietary species. The toxicity of these species varies: some are highly toxic and can cause adverse health effects in many parts of the body; others are considered relatively non-toxic. Monitoring arsenic exposure is usually accomplished by its direct measurement in biological fluids. Urine is the specimen of choice for assessing arsenic exposure, because of its short biological half-life in blood. There have been very few studies of arsenic species in blood, yet such research can provide valuable information on arsenic distribution and its metabolism in the body.

On Congruence Properties Of P(N, M), James Brandt Kronholm

Legacy Theses & Dissertations (2009 - 2024)

Though congruence properties of p(n) modulo an odd prime L have been well studied since the time of Ramanujan, congruence properties of p(n,m) modulo L were unknown beyond L=3. The purpose of this thesis is to detail the discovery and proofs of several infinite families of congruence properties of p(n,m) modulo every odd prime L. We will also prove a striking congruence relationship of the form p(n,m) congruent to p(n',m) modulo L.

Design And Development Of Highly Active, Nanoengineered, Platinum Based Core-Shell Electrodes For Proton Exchange Membrane Fuel Cells, Seth Louis Knupp

Legacy Theses & Dissertations (2009 - 2024)

Highly active nanoengineered core-shell electrocatalyst have a great potential to be used as fuel cell electrodes. They can alleviate problems related with commercial carbon supported platinum by simultaneously lowering cost while enhancing reaction kinetics and overall performance. More recently, use of nanoengineered core-shell electrode structures have showed their ability to enhance the stability and overall lifetime of the catalyst without sacrificing the electrode's performance. We studied the potential of using highly active core-shell nanoparticles supported on carbon nanomaterials as fuel cell electrodes.

The Energetic And Wave Function Properties Of Atomic, Molecular, And Solid State Systems : H⁻ Ion And The Li, Ne, And P Atoms, Bf3·Nh3 Molecular Complex And Methyl Derivatives, V2+, Cr+, Mn2+, Mn0 Transition Metal Impurities In Silicon, Roger H. Pink

Legacy Theses & Dissertations (2009 - 2024)

The variational Hartree-Fock-Roothaan (HF) method with correlation corrections introduced through Many Body Perturbation Theory (MBPT) and the variational Density Functional Theory (DFT) have been investigated for atomic systems to provide insights into the strengths and weaknesses of each variational approach to solving the multicenter many-electron Hamiltonian. The HF+MBPT method, having been found to be more reliable and physically relevant from the atomic investigations, is used to investigate the electronic structures and associated properties of the BF3*NH3 molecular complex, and through cluster methods, the most likely locations of the transitional metal impurities V2+, Cr+, Mn2+ and Mn0 in Silicon.

Elucidating The Structure Of Protein Aggregates By Raman Spectroscopy, Ludmila A. Popova

Legacy Theses & Dissertations (2009 - 2024)

The structures and properties of amyloid fibrils are of considerable interest due to their associations with numerous neurodegenerative diseases such as Alzheimer's disease, Parkinson's disease and transmissible spongiform encephalopaties (prion diseases). Understanding fibrillogenesis at a molecular level requires detailed structural characterization of amyloid fibrils. However amyloid fibrils are difficult objects to study due to their non-crystalline and insoluble nature. These properties make the application of classical tools of structural biology, such as X-Ray crystallography and solution Nuclear Magnetic Resonance spectroscopy, impractical for structural characterization of protein fibrils.

Quantum Dot Quantum Computation In Iii-V Type Semiconductor, Sanjay K. Prabhakar

Legacy Theses & Dissertations (2009 - 2024)

Among recent proposals for next-generation, non-charge-based logic is the notion that a single electron can be trapped and spin of the electron can be manipulated through the application of gate potentials. In the thesis, there are two major contributions of the manipulation of electron spin. In regard to the first contribution, we present numerical simulations of such a spin in single electron devices for realistic asymmetric potentials in electrostatically confined quantum dot. Using analytical and numerical techniques we show that breaking in-plane rotational symmetry of the confining potential by applied gate voltage leads to a significant effect on the tuning …

Electron Beam Lithography Throughput And Resolution Enhancement With Innovative Blanker Design, Junru Ruan

Legacy Theses & Dissertations (2009 - 2024)

Electron Beam Lithography (EBL) is one of the most important and most widely used methods for nano-fabrication. The primary advantage of electron beam lithography is its high resolution, and its ability to expose nanometer features without a mask. On the other hand, one of the key limitations of electron beam lithography is throughput. Slow blanking speed is one of the major bottlenecks for the system speed. In this dissertation, I will first review the prior literature of high speed blanking. Thorough theoretical and experimental studies are done on the existing designs. Physical models are built and analytical ray tracing is …