Digital Commons Network^™

Protein Identification Using Bayesian Stochastic Search, Christina Nicole Lewis

Theses and Dissertations

Current methods for protein identification in tandem mass spectrometry (MS/MS) involve database searches or de novo peptide sequencing, with database searches being the standard method. With database searches, issues arise when the species is not in the database. Shortcomings of de novo peptide sequencing and database searches include chemical noise, overly complex fragments, and incomplete b and y ion sequences. Here we present a Bayesian approach to identifying peptides. Our model uses prior information about the average relative abundances of bond cleavages and the prior probability of any particular amino acid sequence. The proposed likelihood function is composed of two …

Benthic Boundary Layer Processes: Bedform Evolution And Bottom Turbulence, Timothy Robert Nelson

Theses and Dissertations

Bedform roughness, caused by ripples on the seabed, plays an important role in controlling sediment dynamics in the nearshore region. In this dissertation, the temporal and spatial evolution of ripples from two field sites located in the South Atlantic Bight, offshore Long Bay, SC and Georgia are used to relate wave-induced ripple geometry (wavelength and orientation) to near bed directional wave velocities. 2-D spectral analysis techniques were developed to automate detection of ripple wavelength, direction, and irregularity. This analysis showed that magnitude, direction, and duration of wave forcing controls ripple geometry and irregularity. During highly energetic events, ripple geometry changes …

An Investigation Into The Influence Of Dietary Saturated Fat And Quercetin Supplementation On Adiposity, Macrophage Behavior, Inflammation, And Non-Alcoholic Fatty-Liver Disease, Reilly Enos

Theses and Dissertations

The overall objective of this dissertation was to examine the degree to which manipulation of the saturated fat content of a high-fat diet influenced obesity-related outcomes as well as to see if the naturally-occurring flavonoid, quercetin, could attenuate the resulting obesity and related metabolic and inflammatory side effects. Specifically, these studies examined 1) the influential role of saturated fat on macrophage function, inflammation, and other obesity-related comorbidities, including non-alcoholic fatty-liver disease, and 2) the potential benefits of quercetin supplementation. Overall, results from these studies suggest that adiposity, macrophage behavior, inflammation, insulin resistance, and non-alcoholic fatty-liver disease progression can be greatly …

The Effects Of Rainfall-Runoff On Particulate Organic Carbon Cycling In Salt Marshes, Si Chen

Theses and Dissertations

Low tide rainfall-runoff processes have been proposed as a kind of coastal ocean "hot moment" capable of transporting disproportionately large amounts of material from the salt marsh surface to the water column. However, the resulting organic matter cycling has not been well characterized and the cumulative effects of recurring short-term low tide rainfall events are not known, especially in the context of outwelling. The purpose of this Ph.D. research is to quantitatively evaluate the effects of low tide rainfall on particulate organic carbon (POC) cycling in a South Carolina salt marsh.

This dissertation is comprised of four parts. First, a …

Characterization Of The Role Of Fro6 In Metal Homeostasis In Arabidopsis Thaliana, Margo Ellen Maynes

Theses and Dissertations

Iron deficiency is the most common human nutritional disorder in the world today, affecting approximately 2 billon people worldwide, almost a third of the world's population. For most of the world's population, plant foods serve as the major source of dietary iron. One approach that may contribute towards the solution of iron deficiency is the development of crop plants that contain higher levels of bioavailable iron. This project focuses on FRO6, a ferric chelate reductase in Arabidopsis thaliana that is thought to reduce apoplastic iron for transport across the plasma membrane in leaf cells. We hypothesize therefore that FRO6 controls …

Environmental Pre-Conditioning Of Bacterial Populations And Communities To Extreme Acidity, Gabriel Joseph Swenson

Theses and Dissertations

The ability of opportunistic enteric pathogens to cause disease is effected by their ability to survive the variable and lethal acidity of the mammalian host gastrointestinal milieu. In many of these pathogens, survival is conferred by an acid stress response (ASR). ASR is elicited when bacterial cells are pre-conditioned in sub-lethal acidity (pH 4-6) which induces rapid biochemical and physiological modifications and facilitates survival when extreme acidity (pH 1-3) is encountered. In Vibrio cholerae, the causative agent of the diarrheal disease Cholera, ASR was initially investigated in an effort to determine how this ubiquitous aquatic bacterium is capable of causing …

The Role Of Reactive Oxygen Species In Cell Death Induced By Thymidylate Synthase Inhibitors, Ufuk Ozer

Theses and Dissertations

Thymidylate synthase (TS) catalyzes the reductive transfer of a methyl group from N5,N10-methylenetetrahydrofolate (CH₂-THF) to dUMP, forming dTMP and dihydrofolate (DHF). It is generally accepted that inhibition of the enzyme leads to a deficiency of dTMP, followed by genome damage and programmed cell death. As such, TS has long been viewed as an important target of anti-neoplastic agents, such as 5-fluorouracil (5-FU) and raltitrexed (RTX), which lead to inhibition of the enzyme. Oxidative stress is well-recognized as having a central role in cellular response to a number of DNA damaging agents, and may be a proximate cause of …

The Role Of Host-Tumor Interactions In Liver Metastasis Of Colorectal Cancer, Yu Zhang

Theses and Dissertations

Colon cancer is the third most frequent cancer and the second leading cause of cancer deaths in the United States. Liver metastasis is the major cause of death in colon cancer. Successful metastases depend on productive collaborations between tumor cells and host-derived cells in the tumor microenvironment, target organ environments, and cells in the hematopoietic compartment.

To identify the host-tumor interactions promoting liver metastasis and their molecular and cellular mediators, an orthotopic mouse model of liver metastasis of colon cancer was established that recapitulates all stages of tumor growth and metastasis. A highly metastatic mouse carcinoma cell line CT26-FL3 was …

Quantifying Regional-Scale Water Storage Using Models And Observations: Application For Drought Assessment In South Carolina, Mirza Md Mozaddid Billah

Theses and Dissertations

Hydrologic models are widely used to determine the occurrence and severity of droughts, and to aid in the decision making process for reducing drought impacts. These models apply approaches including water and energy balance equations to determine water availability at field to continental scales. One challenge in implementing hydrologic models at larger scales (regional to continental) is the lack of data with sufficient spatial and temporal resolution to represent actual conditions within the modeling domain. If such data is available, the challenge remains how best to find, access, and process the data so that it can be used within hydrologic …

Gelation Characteristics And Osteogenic Differentiation Of Stromal Cells In Inert Hydrolytically Degradable Micellar Polyethylene Glycol Hydrogels, Danial Barati

Theses and Dissertations

The use of polyethylene glycol (PEG) hydrogels in tissue engineering is limited by their persistence in the site of regeneration. In an attempt to produce degradable PEG-based hydrogels while preserving the unique properties of PEG, linear (LPELA) and star (SPELA) poly(ethylene glycol-co-lactide) acrylate, star (SPEDA) poly(ethylene glycol-co-dioxanone), star (SPEGA) poly(ethylene glycol-co-glycolide) acrylate as the least hydrophobic and (SPECA) poly(ethylene glycol-co-caprolactone) as the most hydrophobic macromonomers with short hydrophobic segments were synthesized. The hydrogels were characterized with respect to gelation time, modulus, water content, sol fraction, degradation, and osteogenic differentiation of encapsulated marrow stromal cells (MSCs). Chain extension of PEG with …

Development And Figures Of Merit Of Microextraction And Ultra-Performance Liquid Chromatography For Forensic Characterization Of Dye Profiles On Trace Acrylic, Nylon, Polyester, And Cotton Textile Fibers, Scott James Hoy

Theses and Dissertations

Methodology for the microextraction of basic dyes on acrylic, acid dyes on nylon, disperse dyes on polyester, and reactive dyes, direct dyes, and indigo on cotton textile fibers is reported. Although these processes are destructive to the fiber evidence, the ability to analyze dye extracts from sub-millimeter fiber lengths of single fibers, coupled with detection limits in the hundred picogram range by ultra-performance liquid chromatography (UPLC) with both diode array detection (DAD) and tandem mass spectrometry (MS-MS) makes routine forensic characterization feasible.

Microextraction, followed by UPLC, can often distinguish similar fibers containing different, but similar, dyes with the combination of …

Dislocation Reduction In Silicon Doped High Aluminum Content Algan Layers For Deep Uv Optoelectronic Devices, Hung-Chi Chen

Theses and Dissertations

III-Nitride based deep ultraviolet (UV) light emitting diodes (LEDs) are prospective candidates to replace the conventional bulky, expensive and environmentally harmful mercury lamp as new UV light sources, used in the applications of water and air purification, germicidal and biomedical instrumentation systems, etc. Due to the lack of native substrates and poor carrier injection, AlGaN-based deep UV LED is suffering from low optical power and low overall efficiency, which prevents the availability of low cost, high efficiency deep UV LED on the market.

This dissertation is focused on improving the efficiency of deep UV LEDs, by improving the base template …

Investigating The Predictive Validity Of A Domain-Specific Versus Global Measure Of Life Satisfaction In The Context Of School, Rachel Long

Theses and Dissertations

This study compared the utility of a global versus a domain-specific measure of life satisfaction in predicting behavioral and achievement outcome variables among a sample of adolescents in the context of school. The sample included 694 middle school students (7th and 8th grade) from a suburban school district located in the Southeastern United States who completed self-report measures of life satisfaction, engagement, behavior, and grades. Actual grade point average (GPA) and standardized MAP test scores were reported by the school. Based on previous research and the guiding principal, specificity matching, this study hypothesized that a measure of school satisfaction would …

Silylation-Based Kinetic Resolution Of Α-Hydroxy Carbonyl Compounds And Synthesis Of Chiral Isothiourea Catalysts, Yan Zhang

Theses and Dissertations

The thesis describes the silylation-based kinetic resolution for α-hydroxy carbonyl compounds catalyzed by isothiourea catalyst as well as our effort to make novel chiral isothiourea catalyst.

In Chapter 1, general background will be introduced, including chirality, general methods to obtain enantiopure compounds and kinetic resolution. In Chapter 2, the mechanism of the chiral recognition was discussed and a novel isothiourea catalyst was design to investigate the mechanism. The synthesis of the new catalyst was also described in this chapter.

In Chapter 3, the silylation-based kinetic resolution for α-hydroxy carbonyl compounds will be discussed. Since silylation-based kinetic resolution have already been …

Going Hard, Going Easy, Going Home: Death And Dying In 20th Century African American Literature, Chayah Amayala Stoneberg-Cooper

Theses and Dissertations

This dissertation answers the question: How can art represent the essential human experience of death, particularly when the creative context is one of extreme violence? And, what can be learned about the risks and rewards of the living's relationship with the dead by way of these artistic representations? Further, how do these aesthetic renderings of death construct the ethics of life for survivors? In the case of African America, discussion of, and responses to, these questions have been primarily explored in novelist and creative writing. This dissertation examines these novelistic treatments of death-tropes, or thanatropes in eight novels written by …

An Essay On Musical Narrative Theory And Its Role In Interpretation, With Analyses Of Works For Saxophone By Alfred Desenclos And John Harbison, Ian Macdonald Jeffress

Theses and Dissertations

In recent years the field of semiotics has increasingly been applied to musicology, with particular attention paid to the area of narrative theory. This study will provide an introduction to the essential concepts of semiotics and narrative theory, the development of a methodology of narrative analysis with examples from the saxophone repertoire, and the application of that analytical approach to Alfred Desenclos' Prélude, Cadence, et Finale and John Harbison's San Antonio. The goal of this study will be the demonstration of narrative theory's applicability to a variety of styles pertinent to the concert saxophone repertoire. It is hoped that this …

Plant Virus Based Materials For Cell Alignment And Differentiation, Elizabeth Balizan

Theses and Dissertations

This research focused on developing and using plant virus based scaffolds to understand substrate control over cell alignment and differentiation. The first part of this work centered on development of virus based patterns that were then used to align and elongate aortic smooth muscle cells (SMCs). Virus patterns were generated in capillary tubes via a simple drying method. Three experimental parameters were used to control pattern formation: (1) protein concentration, (2) salt concentration, and (3) hydrophobicity of the pre-deposition surface. By controlling these parameters several aspects of the final virus patterns were controlled. First, virus orientation was controlled. Patterns were …

A Silylation Based Kinetic Resolution Of Secondary Alcohols And The Synthesis And Structural Characterization Of Pyridyl-Oxazolidine Compounds, Cody Ian Sheppard

Theses and Dissertations

Described herein is the first enantioselective silylation based kinetic resolution of monofunctional secondary alcohols to achieve useful levels of enantioselectivity. Using commercially available reagents, the reaction conditions were optimized and found to successfully resolve several secondary alcohols with high enantioselectivity. It was discovered that the nucleophilic isothiourea compound (-)-tetramisole, with Ph3SiCl as the silyl source, gave superior results to other nucleophilic catalysts and was capable of performing the kinetic resolution in as little as 45 minutes using mild reaction conditions. The structural and electronic characteristics of successful and less successful substrates are also discussed.

Chapter three discusses mechanistic investigations and …

The Role Of The Trickster Figure And Four Afro-Caribbean Meta-Tropes In The Realization Of Agency By Three Slave Protagonists, David Sebastian Cross

Theses and Dissertations

In this dissertation, I aim to demonstrate that the figure of the trickster is a key trope for the achievement of agency by the narrators of the three slave narratives Autobiografia de un esclavo, "Routes in North Africa by Abu Bekr es siddik" [sic], and Biografia de un cimarron. I also intend to show how both the realization of the trickster's role and the achievement of agency to which such a role is oriented are dependent on the use of the four Afro-Caribbean meta-tropes ndoki, nkisi, nganga, and simbi. To demonstrate this, I plan to analyze these four meta-tropes; their …

Identifying Values And Benefits Of Congaree National Park, Maka Bitsadze

Theses and Dissertations

Protected areas are important tools for the conservation of biological diversity. They also support a wide range of ecosystem services and provide economic, cultural and social values and benefits. Many values and benefits of protected areas are poorly understood and greatly under-valued by decision-makers, the business sector, and the general public. Accordingly, identification and assessment of values and benefits of protected areas has been increasingly promoted during recent years.

This research investigates values and benefits of Congaree National Park and provides guidance for the further economic valuation of identified values and benefits. While the ecological significance of Congaree National Park …

Adhd And Positive Smoking Expectancies The Role Of Peer Influence As A Moderating Factor, Lauren Dattilo

Theses and Dissertations

Research has demonstrated considerable links between symptoms of ADHD and negative outcomes such as increased risk for cigarette use, which, despite an overall decline, remains a serious public health concern. Cigarette use is often associated with positive expectancies, or ideas about the effects of smoking. While some work on ADHD symptoms has focused on alcohol expectancies, no work has investigated how they might be related to smoking expectancies Other factors, such as susceptibility to peer influence, also remain shallowly explored. The present study is the first to examine interrelations among ADHD symptoms, smoking expectancies, and susceptibility to peer influence. It …

Investigations Of The Non-Covalent Ch-Π Interactions Using Molecular Torsional Balances, Chen Zhao

Theses and Dissertations

Several bicycle N-arylimide based molecular balances were designed to study aliphatic CH-pi interactions and aromatic CH-pi interactions (edge-to-face arene-arene interactions). In each case, the geometries of the interactions were characterized in the solid-state via X-ray analysis, and the strengths of interactions were characterized in solution by their folded/unfolded ratios, as measured by integration of their 1H NMR spectra.

The balances are very sensitive to variations in the strengths of weak non-covalent interactions. Several different aspects of the CH-pi interactions were studied, such as sterics, conformational entropy, cooperativity, deuterium isotope effect, substitution effects, and solvent effects. It showed that due to …

Iii-V Nitride Micro- And Nano-Scale Cantilevers For Multimodal Sensing Applications, Ehtesham Bin Quddus

Theses and Dissertations

Recent research trends in chemical and biological sensing have been geared toward developing molecular sensor devices that are fast, label free, miniaturized and portable. The performance of these devices can be dramatically improved by utilizing multimodal detection techniques, new materials and micro-/nanofabrication technologies. This is especially true for micro-/nanoscale cantilever sensors, which undergo changes in mechanical or electrical properties upon the specific binding of molecules. To develop the sensor devices with the above attributes, we utilized III-V nitride materials: InN nanowires for realizing nanoscale cantilevers and AlGaN/GaN heterostuctures with or without embedded HFETs, for developing microcantilevers. There are mainly two …

Wireless Pressure Sensor System For Medical Applications, Xuehe Wang

Theses and Dissertations

Telemedicine in the modern era is a rapidly developing industry. In a telemedicine system, sensor is the key elements and play important role in any telemedicine applications, especially implantable sensors. Unlike traditional in vitro sensors, there are some special requirements for them like battery-less, compact, and bio-friendly. Therefore, many researchers in institutes as well as in industry are continually developing implantable sensor and sensor system to fulfill the requirements of medical applications.Nine in one thousand people in the United States are born with congenital heart defects and sixty percent die before one year old. As a result, it will be …

Multi-Culturalism & Alzheimer’S Disease: Patient-Centered Design As A New Care Model For Multi-Cultural Patients With Alzheimer’S Disease, Sang Ryu

Theses and Dissertations

The multi-cultural demographics of those who are diagnosed with Alzheimer’s disease should be closely examined. From a designer’s standpoint, its cultural traits can foster positive behaviors that lead to better quality of life for patients and caregivers. A patient-centered approach in design was explored in order to shape community-based care that empowers (1) individuality in care services, (2) interpersonal connection in caregiver–patient activities, and (3) a communal culture of being valued via humanitarian approaches.

Using Coaching As A Professional Development Modality To Train Teachers In The Use Of Evidence-Based Practices For Students With Autism Spectrum Disorders., Samantha Hollins

Theses and Dissertations

Professional development for teachers currently working in the classroom is an important focus of educational programs and school systems. Continuous professional development is especially important for special education teachers to maintain current information related to strategies and supports that are effective in educating students with disabilities. The increase in identification of students with autism has forced many teachers to quickly adapt to working with a population of students they have limited experience in teaching through preservice education and previous classroom experience. Coaching is a popular method for professional development delivery to special education teachers currently working in the classroom. This …

The Impact Of Imprecision In Hcv Viral Load Test Results On Clinicians’ Therapeutic Management Decisions And On The Economic Value Of The Test, Roberta M. Madej

Theses and Dissertations

Clinical laboratory test results are integral to patient management. Important aspects of laboratory tests’ contributions are the use of the test information and the role they have in facilitating efficient and effective use of healthcare resources. Methods of measuring those contributions were examined using quantitative HCV RNA test results (HCV VL) in therapeutic management decisions as a model. Test precision is important in those decisions; therefore, the clinical use was evaluated by studying the impact that knowledge of inherent assay imprecision had on clinicians’ decisions. A survey describing a simulated patient at a decision point for HCV triple-combination therapy management …

The Ticking Of The “Biological Clock”: Worry About Future Fertility In Nulliparous Women, Karen E. Kersting

Theses and Dissertations

Abstract

Title: The Ticking of the “Biological Clock”: Worry about Future Fertility in Nulliparous Women

By: Karen Kersting, M.A., M.S.

A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy at Virginia Commonwealth University.

Virginia Commonwealth University, 2013.

Major Director: Kathleen M. Ingram, J.D., Ph.D.

Associate Professor of Psychology

Department of Psychology

Modern women are waiting until later in their lives to have children than women of previous generations, a trend influenced by a number of factors including financial stability, dating norms, and career goals and responsibilities. As women age, their fertility may decline …

Analysis Of Polyethylene Glycol In The Α-Hemolysin Nanopore, David M. Dancho

Theses and Dissertations

Nanopores have been shown to be a useful analytical tool for single molecule detection. They have been used to study the composition of DNA and other molecules of interest. These pores are usually α-hemolysin which is a toxin from Staphylococcus aureus or more recently nanoscale synthetic solid state pores. Now we are beginning to look at other molecules or proteins by sending them into the nanopores and measuring a characteristic partial current blockade. In this thesis we look at polyethylene glycol (PEG) as it enters and blocks current through a single alpha hemolysin pore. We report the effects of ionic …

Early Adolescent Nicotine Exposure Has Long-Lasting Effects On Cocaine-Induced Behaviors In Mice, Mai Alajaji

Theses and Dissertations

Nicotine is one of the most commonly used drugs among adolescent populations. Given the fact that adolescence is a unique developmental stage, during which nicotine has long-term effects on future drug-taking behavior, it is essential to understand how early exposure to nicotine during adolescence may affect the abuse liability of other drugs. We hypothesize that repeated exposure to low doses of nicotine in adolescence induce age-specific enhancement of the rewarding effects of several drugs of abuse in the conditioned place preference (CPP) test. Furthermore, we predict that these changes in behavioral responses are mediated by nicotine-induced brain region-specific increases in …