Digital Commons Network^™

Application Of A Correlation Correction Factor In A Microarray Cross-Platform Reproducibility Study, Kellie J. Archer, Catherine I. Dumur, G. Scott Taylor, Michael D. Chaplin, Anthony Guiseppi-Elie, Geraldine Grant, Andrea Ferreira-Gonzalez, Carleton T. Garrett

Biostatistics Publications

Background Recent research examining cross-platform correlation of gene expression intensities has yielded mixed results. In this study, we demonstrate use of a correction factor for estimating cross-platform correlations.

Results In this paper, three technical replicate microarrays were hybridized to each of three platforms. The three platforms were then analyzed to assess both intra- and cross-platform reproducibility. We present various methods for examining intra-platform reproducibility. We also examine cross-platform reproducibility using Pearson's correlation. Additionally, we previously developed a correction factor for Pearson's correlation which is applicable when X and Y are measured with error. Herein we demonstrate that correcting for measurement …

Probing The Outer Mouth Structure Of The Herg Channel With Peptide Toxin Footprinting And Molecular Modeling, Gea-Ny Tseng, Kailas D. Sonawane, Yuliya V. Korolkova, Mei Zhang, Jie Liu, Eugene V. Grishin, H. Robert Guy

Physiology and Biophysics Publications and Presentations

Abstract

Previous studies have shown that the unusually long S5-P linker lining human ether a-go-go related gene’s (hERG’s) outer vestibule is critical for its channel function: point mutations at high-impact positions here can interfere with the inactivation process and, in many cases, also reduce the pore’s K⁺ selectivity. Because no data are available on the equivalent region in the available K channel crystal structures to allow for homology modeling, we used alternative approaches to model its three-dimensional structure. The first part of this article describes mutant cycle analysis used to identify residues on hERG’s outer vestibule that interact …

Telomerase Inhibition And Sensitization Of Breast Tumor Cells, Kennon R. Poynter

Theses and Dissertations

Telomerase, a ribonucleoprotein enzyme minimally composed of an RNA template (hTR) and a catalytically active protein subunit (hTERT), synthesizes telomeric repeats onto chromosome ends and is obligatory for continuous tumor cell proliferation, as well as malignant progression of breast cancer cells. Telomerase is an attractive anticancer therapeutic target because its activity is present in over 90% of human cancers, including more than 95% of breast carcinomas, but undetectable in most somatic cells. Traditions chemo- and radio-therapies lack the ability to effectively control and cure breast cancer, in part because residual cells are or become resistant to DNA damaging modalities.While various …

Addressing Issues In The Detection Of Gene-Environment Interaction Through The Study Of Conduct Disorder, Elizabeth Prom-Wormley

Theses and Dissertations

This work addresses issues in the study of gene-environment interaction (GxE) through research of conduct disorder (CD) among adolescents and extends the recent report of significant GxE and subsequent replication studies. A sub-sample of 1,299 individual participants/649 twin pairs and their parents from the Virginia Twin Study of Adolescent and Behavioral Development was used for whom Monoamine Oxidase A (MAOA) genotype, diagnosis of CD, maternal antisocial personality symptoms, and household neglect were obtained. This dissertation (1) tested for GxE by gender using MAOA and childhood adversity using multiple approaches to CD measurement and model assessment, (2) determined whether other mechanisms …

Art Education In An Age Of Teletechnology: On The Impossibility Of Portraiture, Jan Jagodzinski

Journal of Social Theory in Art Education

Art since the Renaissance has been obsessed with the portrait and defined by it as the form of representation made even more iconic through the invention of photography where the notion of the profile became established as a sign of prosperity, prestige and power (Sekula, 1986). This enlightenment tradition of portraiture is not likely to perish at any given future date; the digitalization of the image continues to make the banal snap-shot proliferate at such an incredible rate identifying the thirst for personal representation in contemporary society. The explosion of celebrity magazines, the spread of the paparazzi, and the easy …

Canadian Multiculturalism Ideology: Mere Tolerance Or Full Acceptance, Laverne M. Lewycky

Ethnic Studies Review

September 11, 2001 will forever be etched in the memory of Canadians who were deeply affected by the events of that day. This cataclysmic occurrence had a pivotal place not only upon the private troubles of those directly related but also upon the public issues and the consequent public policies of all of us who may not have been as directly touched. Such a life-changing experience will impinge upon the politics of our entire nation. The terrorist act was a political statement at one level which must be addressed politically as well It is noteworthy, given this context of the …

Spatial And Temporal Patterns Of Anadromous Fish Passage At Boshers Dam Vertical Slot Fishway On The James River, Richmond, Virginia, Matthew Thomas Fisher

Theses and Dissertations

Boshers dam vertical slot fishway, James River, Virginia, U.S.A., opened in 1999 and restored connectivity to 543.3 km of spawning habitat for anadromous fish. The fishway also allowed local movement of resident species. Video observation from 2001-2005 was used to evaluate environmental predictors of American shad (Alosa sapidissima) and sea lamprey (Petromyzon marinus) passage. The ecological effects of restoring connectivity to upstream habitat for gizzard shad (Dorosoma cepedianum) and blue catfish (Ictalurus furcatus) are also discussed. Regression analysis determined that the best predictor of increased daytime American shad passage is higher water temperatures and discharge and for increased daytime sea …

Role Of Ceramide-1-Phosphate As A Specific And Potent Activator Of Group Iva Cytosolic Phospholipase A2 Alpha, Preeti Subramanian

Theses and Dissertations

Eicosanoids are potent mediators of inflammatory response whose role has been well established in inflammatory disorders. Release of arachidonic acid by group IVA cytosolic phospholipase A2 α (cPLA2α) is the initial rate limiting step for the production of eicosonoids in response to inflammatory mediators. Previous findings from our laboratory have demonstrated that cPLA2α is directly activated by the emerging bioactive sphingolipid, ceramide-1-phosphate (C1P). In this study, we have developed a modified Triton X-100/phosphatidylcholine (PC) mixed micelle assay which was utilized to determine the kinetics and specificity of this lipid-enzyme interaction. Using this assay, the activity of the enzyme increased in …

Evaluating The Psychosocial Effects Of Two Interventions, Tai Chi And Spiritual Growth Groups, In Women With Breast Cancer, Sarah M. Rausch

Theses and Dissertations

One in seven women will develop breast cancer. Most will suffer medically and psychologically from the disease. Complementary and alternative medicine (CAM) interventions such as tai chi and spiritual growth groups have proven to be beneficial for this population, however, many questions remain regarding the mechanisms of action in these techniques. The purpose of this study was to evaluate the psychosocial effects and mechanisms of two 10-week interventions (tai chi and spiritual growth groups) within the context of a larger randomized, controlled NCI-funded study (R01 CA114718, Nancy McCain, PI) in women recently diagnosed with breast cancer. The present study evaluated …

Overbite Correction And Smile Esthetics, Kevin Erick Kelleher

Theses and Dissertations

The purpose of this prospective clinical study was to investigate differences in outcomes from two common treatment modalities used to reduce deep overbite: maxillary incisor intrusion using an intrusion arch and posterior tooth eruption using an anterior bite plate. Pre-treatment, post-overbite correction and post-treatment records were gathered from 32 patients who presented with deep overbite malocclusions to the Virginia Commonwealth University orthodontic clinic. Both groups of patients experienced reductions in overbite and maxillary incisor display as well as maxillary and mandibular incisor proclination and mandibular incisor occlusal movement during treatment. In the intrusion arch group, the center of resistance of …

Novel Sulfated 4-Hydroxycinnamic Acid Oligomers As Potent Anticoagulants, Brian Lawrence Henry

Theses and Dissertations

The occurrence of thrombosis in several pathophysiological conditions creates a huge need for anticoagulation therapy. Thrombin and factor Xa have been prime targets for regulation of clotting through the direct and indirect mechanism of inhibition. This work investigates chemo-enzymatically prepared oligomers of 4-hydroxycinnamic acids (DHPs) as potential anticoagulants. Oligomers were prepared through peroxidase-catalyzed oxidative coupling of 4-hydroxycinnamic acids. The products resulting from this reaction are called CDs, FDs and SDs. Structurally, these sulfated DHPs are unique and do not resemble any of the anticoagulants known in the literature.DHP oligomers were found to increase clotting times at concentrations comparable to heparin. …

Effects Of Cxcl8 Overexpression On Tumor Cell Proliferation And Migration In An Hnscc Cell Model, Emil Paul Christofakis

Theses and Dissertations

Head and neck squamous cell carcinoma is the 6th most common malignancyworldwide. Recently, a link between cancer and inflammation has been found. Mediatingthis relationship are the chemotactic cytokines known as chemokines. CXCL8 (Interleukin-8), a CXC ELR+ Chemokine mainly responsible for neutrophil chemoattraction, has beenimplicated in increased tumor proliferation, migration and angiogenesis. The current studytests the effects of CXCL8 on the tumor proliferation and metastasis. By genetically modifying cells to knockdown or overexpress the CXCL8 gene we tested its biological rolein head and neck cancer progression. Overexpression of CXCL8 in HN4 tumor cells withlow endogenous CXCL8 levels was found to increase …

The Effect Of A Nominal Fee On Treatment Choices For Children Needing Dental Rehabilitation, D'Audra M. Cole

Theses and Dissertations

Objective: The purpose of the study was to determine if a co-payment resulted in a differential preference for general anesthesia (GA) or oral sedation (OS) and, if so, to examine whether age, the number of appointments, perceived risks of treatment, child's awareness during treatment, or insurance type appeared to play a role in this preference.Methods: Using a cross-sectional survey design, questionnaires were distributed to caregivers of patients in the waiting room of the Virginia Commonwealth University Pediatric Dental Clinic. Two different questionnaires were distributed randomly. Both surveys described a scenario with the need for dental treatment under general anesthesia (GA) …

The Quantitative Genetics Of Neurodevelopment: A Magnetic Resonance Imaging Study Of Childhood And Adolescence, James Eric Schmitt

Theses and Dissertations

Understanding the causes of individual differences in brain structure may give clues about the etiology of cognition, personality, and psychopathology, and also may identify endophenotypes for molecular genetic studies on brain development. We performed a comprehensive statistical genetic study of anatomic neuroimaging data from a large pediatric sample (N=600+) of twins and family members from the Child Psychiatry Branch at the NIMH. These analyses included variance decomposition of structural volumetric endophenotypes at several levels of resolution, voxel-level analysis of cortical thickness, assessment of gene by age interaction, several multivariate genetic analyses, and a search for genetically-mediated brain-behavioral relationships. These analyses …

Corticular Photosynthetic Dynamics For A Coastal Evergreen Shrub: Myrica Cerifera, Jaclyn K. Vick

Theses and Dissertations

I quantified seasonal variations in corticular photosynthesis in 1st through 5th order branches of Myrica cerifera L. (Myricaceae) in order to determine whether corticular photosynthesis contributes to whole plant carbon gain by reducing respirational CO2 loss. Maximum % refixation was 110 ± 39 % of CO2 efflux in the dark (Rd) in 1st order branches during winter, minimum was 18 ± 3 % in 5th order branches during summer. Variations in % refixation paralleled changes in photosynthetically active radiation (PAR). As light attenuated with increasing branch order % refixation decreased. Increased PAR in the winter due to a more sparse …

Drift Tube Ion Mobility Measurements For Thermochemistry, Kinetics And Polymerization Of Cluster Ions, Ridha Ben Mohsen Mabrouki

Theses and Dissertations

In this work, the Drift Tube Ion Mobility technique is used to study the hydrophobic hydration and solvation of organic ions and measure the thermochemistry and kinetics of ion-molecule reactions. Furthermore, an exploratory study of the intracluster polymerization of isoprene will be presented and discussed. The ion hydration study is focused on the C3H3+ cation1 and Pyridine▪+ radical cation.2 The chemistry of the cyclic C3H3+ cation1 has received considerable attention and continues to be an active area of research.3-7 The binding energies of the first 5 H2O molecules to c-C3H3+ were determined by equilibrium measurements. The measured binding energies of …

Genetic Variations In Interferon-Induced Genes And Hcv Recurrence After Liver Transplantation, Benjamin Cameron Whitehill

Theses and Dissertations

Hepatitis C Virus (HCV) infection represents a worldwide pandemic and is currently the leading cause of cirrhosis and liver transplantation. After transplantation recurrence is almost universal with 96% of patients testing positive for viral RNA and exhibiting histological evidence of infection within the first year. Type I interferons (IFN) and interferon inducible genes are responsible for the innate antiviral state and single nucleotide polymorphisms (SNPs) within these genes may affect the patients ability to respond post-transplantation. We hypothesize the elucidation of associations between SNPs in Type-I Interferon and Interferon inducible genes and HCV recurrence post-liver transplantation might help to identify …

Amendment (2007)

Amendment, 2004-

Amendment is a VCU student-produced progressive literature and art journal that provides a platform for students to promote equality, tolerance, and social progression through artistic expression.

The Role Of A Family History Of Alcohol Or Drug Abuse On Ptsd Outcomes Following Community Violence Exposure, Kathryn Reid-Quinones

Theses and Dissertations

Research consistently has revealed the damaging consequences of children's repeated exposure to community violence and Posttraumatic Stress Disorder (PTSD) is the most commonly cited internalizing disorder associated with such exposure. However, not all children who are exposed to community violence develop PTSD symptoms; thus, it is important to identify factors that contribute to this deleterious relationship. The purpose of the present study was to examine the relation of community violence exposure (CVE)and PTSD in a sample of urban adolescents. Additionally, the study assessed whether a maternal history of alcohol or drug abuse would exacerbate the association of CVE andPTSD symptoms …

Cannabinoid Modulation Of Chemotaxis Of Macrophages And Macrophage-Like Cells, Erinn Shenee Raborn

Theses and Dissertations

Exogenous and endogenous cannabinoids have been reported to modulate functional activities of macrophages. It is recognized that macrophages express primarily the CB2 cannabinoid receptor, but recent studies indicate that its expression is differential in relation to activation state with maximal levels occurring when cells are in "responsive" and "primed" states. The functional activities of macrophages when in these states of activation are the most susceptible to the action of cannabinoids, at least in terms of a functional linkage to the CB2. To assess the effect of cannabinoid treatment on macrophage chemotaxis and test the hypothesis that cannabinoids inhibit the chemotactic …

Supporting Data-Intensive Wireless Sensor Applications Using Smart Data Fragmentation And Buffer Management, Mbonisi Masilela

Theses and Dissertations

Recent advances in low power device technology have led to the development of smaller powerful sensors geared for use in Wireless Sensor Networks. Some of these sensors are capable of producing large data packets in a single reading. This becomes a challenging problem given the constraints imposed by current MAC and Transport Layer implementations since a single data packet can exceed the MTU of the protocol stack. Little has been done in the way of addressing this issue in Wireless Sensor Networks. This paper proposes a novel solution to this issue. Proposed is a Lightweight Data Transportation Protocol that uses …

An Examination Of The Relationships Among Health Literacy, Social Support, And Patient Activation In Community Residing Older Adults, Brenda L. Harding Hage

Theses and Dissertations

This study examined the relationships among the variables health literacy, social support, and patient activation. The subjects were 90 elderly, community residing adults meeting the inclusion criteria and who volunteered to participate in the study and completed three survey instruments: the Short Form of Functional Health Literacy (Parker, Baker, Williams & Nurss, 1995); the Medical Outcomes Survey (MOS) Social Support Survey Instrument (Sherboume & Stewart, 1991); the Patient Activation Measure (PAM) Short-Form (Hibbard, Mahoney, Stockard, & Tusler, 2005); and a demographic form.

A correlational design was used to test the hypotheses that social support and health literacy are positively related …

Women In Science And Engineering: Politics Of Gender, Ibironke Lawal

VCU Libraries Faculty and Staff Publications

Women are fewer than men in science and engineering, therefore, the assumption is that women generally prefer arts and humanities. But to some analysts, the reason for the low percentage of women in these careers may be due to innate mental and psychological differences between them and men. Others contend that women have the capacity to excel in any profession and that their fewness in science and engineering can be attributed to other factors. They urge educational institutions and employers to develop programs and specific policies that would allow women to strike a better balance between the demands of work …

Supporting Personhood In Dementia: Examining The Impact Of Volition On Function In Everyday Occupations, Christine L. Raber

Theses and Dissertations

Understanding volition and preferences for occupation is a critical underpinning of effective occupational therapy services that promote and preserve identity for persons with moderate dementia. Although it has been posited that this population has significant difficulty expressing volition for daily occupations, little research has examined the role of volition in guiding engagement in occupations. This phenomenological study provides an in-depth description and analysis of volition in eight persons with moderate dementia. Guiding questions related to understanding patterns of past life interests, outward demonstration of volition, volitional continuity. and the relationship of the social environment to volition and engagement in daily …

Camping In The Classroom: Ridiculous Theatre As Serious Drama, John Kenneth Deboer

Theses and Dissertations

My first semester pursuing my MFA in Voice and Speech Pedagogy I vocal-coached an openly gay student playing a straight character who would mask his sexual identity in such a manner that his performance became stiff and uninteresting. Rather than using his personal identity as an asset in the pursuit of a successful performance, his chosen vocal tactics removed any sense of theatricality from his performance. I confronted the student and suggested such extreme vocal suppression diminished the quality of his overall performance. He replied, "So you want me to get the gay out."His use of the phrase, "get the …

Electrospun Blends Of Polydioxanone And Fibrinogen For Urological Applications, Joshua Ford Grant

Theses and Dissertations

The need for tissue and organ replacements cannot be satisfied by autograft and allografts alone. The purpose of this study was to investigate the feasibility of electrospinning a blend of polydioxanone and fibrinogen to produce an engineered tissue scaffold. Fiber diameter and pore size of blends were characterized, as well as mechanical strength. Cell proliferation assays for 1 and 7 day cultures were preformed, and a histological evaluation was performed to determine how favorable the various blends were to cell infiltration and proliferation. Some ratios of blends were identified that contained both acceptable mechanical properties and properties that facilitated cell …

Design Synthesis And Evaluation Of Diterpenones As Potent Chemopreventive Agents For Aflatoxin B1 Induced Carcinogenesis In Human Liver Cells, Miguel Angel Zuniga

Theses and Dissertations

DESIGN, SYNTHESIS, AND EVALUATION OF DITERPENONES AS POTENT CHEMOPREVENTIVE AGENTS FOR AFB1 INDUCED CARCINOGENISIS IN HUMAN LIVER CELLS By Miguel A. Zuniga, Ph.D. A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy at Virginia Commonwealth University. Major Director: Qibing Zhou, Ph.D Assistant Professor Department of Chemistry Terpene quinone methides (TPQMs) have been isolated from a variety of plants and show broad activities against bacteria, fungi, and cancerous cell lines. The biological activity has been attributed to the reactive electrophilic QM moiety, this structural feature has long been recognized as an intermediate in organic …

The Influence Of Parental Monitoring And Peer Deviance On Substance Use Among Middle School Students, Sally Ann Mays

Theses and Dissertations

Substance use is a significant problem among middle school students in the United States. Research indicates that the early use of substances increases the likelihood of negative outcomes including long-term use and abuse. Both parenting and peer variables exert strong influences on children's decisions to use or abstain from substances. As children age, peers begin to exert a stronger influence, but parenting practices can significantly reduce peers' harmful influences. In this study, three waves of data (collected at the end of 6th grade, and the beginning and end of 7th grade) from a large multi-site study were used to examine …

Sodium Hypochlorite's Effect On Nickel-Titanium Rotary Instruments And Its Effect On Resistance To Fracture, Michael Shane Smith

Theses and Dissertations

The purpose of this study was to examine the effect of partial and total immersion in sodium hypochlorite on nickel-titanium rotary files and to determine whether resistance to fracture was influenced by the immersion time. One hundred K3™ and 100 ProFile® rotary files were either partially or totally immersed in 5.25% sodium hypochlorite for zero, one, five, thirty, or sixty minutes. After immersion, files were subjected to cyclic fatigue testing. Time to fracture was recorded and analyzed by a two-way ANOVA. Tukey's honest significant difference was used to identify any differences in immersion times. Within all ProFile groups and partial …

The Ksga Methyltransferase: Characterization Of A Universally Conserved Protein Involved In Robosome Biogenesis, Heather Colleen O'Farrell

Theses and Dissertations

The KsgA enzymes comprise an ancient family of methyltransferases that are intimately involved in ribosome biogenesis. Ribosome biogenesis is a complicated process, involving numerous cleavage, base modification and assembly steps. All ribosomes share the same general architecture, with small and large subunits made up of roughly similar rRNA species and a variety of ribosomal proteins. However, the fundamental assembly process differs significantly between eukaryotes and eubacteria, not only in distribution and mechanism of modifications but also in organization of assembly steps. Despite these differences, members of the KsgA/Dim1 methyltransferase family and their resultant modification of small-subunit rRNA are found throughout …