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Handling External Events Efficiently In Gillespie's Stochastic Simulation Algorithm, Brad Geltz Oct 2010

Handling External Events Efficiently In Gillespie's Stochastic Simulation Algorithm, Brad Geltz

Theses and Dissertations

Gillespie's Stochastic Simulation Algorithm (SSA) provides an elegant simulation approach for simulating models composed of coupled chemical reactions. Although this approach can be used to describe a wide variety biological, chemical, and ecological systems, often systems have external behaviors that are difficult or impossible to characterize using chemical reactions alone. This work extends the applicability of the SSA by adding mechanisms for the inclusion of external events and external triggers. We define events as changes that occur in the system at a specified time while triggers are defined as changes that occur to the system when a particular condition is …

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Commonwealth Times 2010-10-04 Oct 2010

Commonwealth Times 2010-10-04

Commonwealth Times, 1969-

No abstract provided.

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Commonwealth Times 2010-09-27 Sep 2010

Commonwealth Times 2010-09-27

Commonwealth Times, 1969-

No abstract provided.

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The Regulation Of The Alternative Splicing Of Caspase 9, Rachel Goehe Sep 2010

The Regulation Of The Alternative Splicing Of Caspase 9, Rachel Goehe

Theses and Dissertations

The pro-apoptotic, caspase 9a, and the anti-apoptotic, caspase 9b, are derived from the caspase 9 gene by alternative splicing. This study demonstrates that the alternative splicing of caspase 9 is dysregulated in a large percentage of non-small cell lung cancer (NSCLC) tumors of the adenocarcinoma type. Furthermore, modulation of the levels of splice variants of caspase 9 had dramatic effects on the anchorage-independent growth and tumorigenic capacity of NSCLC cells. Due to these findings, the molecular mechanisms regulating the post-transcriptional processing of caspase 9 were therefore examined and an exonic splicing silencer (ESS) regulating the pre-mRNA processing of caspase 9 …

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Antifolate Modulators Of Amp-Activated Protein Kinase Signaling As Cancer Therapeutics, Scott Rothbart Sep 2010

Antifolate Modulators Of Amp-Activated Protein Kinase Signaling As Cancer Therapeutics, Scott Rothbart

Theses and Dissertations

Since its discovery, it was appreciated that the antifolate pemetrexed had multiple targets within folate metabolism. This laboratory was instrumental in showing that pemetrexed elicited its primary action as a thymidylate synthase inhibitor. Unusual for an antifolate, pemetrexed showed significant clinical activity against malignant pleural mesothelioma and non-small cell lung cancer. Accordingly, the FDA recently issued first-line approvals for pemetrexed in these diseases, leading us to question whether the effects of pemetrexed on other folate-dependent targets could explain this atypical clinical activity of the drug. Studies in this dissertation showed that in addition to thymidylate synthase inhibition, pemetrexed was also …

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B Cell Adam10 Activity Is Increased By Kainate Receptor Activation: Potential Role Of This Pathway In Th2 Immunity And Cancer, Jamie Sturgill Sep 2010

B Cell Adam10 Activity Is Increased By Kainate Receptor Activation: Potential Role Of This Pathway In Th2 Immunity And Cancer, Jamie Sturgill

Theses and Dissertations

CD23 has long been appreciated to be a natural, negative regulator of IgE synthesis. This understanding is due in part to animal models in which CD23 deficient or CD23 transgenic animals display exacerbated or reduced IgE levels respectively. Interestingly, CD23 is susceptible to proteolytic cleavage from the cell surface. When this occurs, CD23 loses its regulatory capability and the solubilized form can lead to pro-inflammatory events through its cytokinergic activity on macrophages. Thus, targeting this specific cleavage would be beneficial to the control of allergic disease by stabilizing CD23 at the cell surface. Inhibitor studies performed by our group as …

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Specificity Determinants Of Arma, A Ribosomal Rna Methyltransferase That Confers Antibiotic Resistance, Tamara Zarubica Sep 2010

Specificity Determinants Of Arma, A Ribosomal Rna Methyltransferase That Confers Antibiotic Resistance, Tamara Zarubica

Theses and Dissertations

Bacterial resistance to 4,6-type aminoglycoside antibiotics, which target the 30S ribosomal subunit, has been traced to the arm/rmt family of rRNA methyltransferases. These plasmid-encoded enzymes transfer a methyl group from S-adenosylmethionine to N7 of the buried G1405 in the aminoglycoside binding site of 16S rRNA in the 30S ribosomal subunit. Neither 16S rRNA alone nor intact 70S ribosome is an efficient substrate for armA methyltransferase. To more fully characterize this family of enzymes, xiii we have investigated the substrate requirements of ArmA. We determined the Mg2+ dependence of ArmA activity and found that the enzyme could recognize both translationally active …

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Commonwealth Times 2010-09-13 Sep 2010

Commonwealth Times 2010-09-13

Commonwealth Times, 1969-

No abstract provided.

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The Predictive Relationship Between Temperament, School Adjustment, And Academic Achievement: A 2-Year Longitudinal Study Of Children At-Risk, Maha Al-Hendawi Sep 2010

The Predictive Relationship Between Temperament, School Adjustment, And Academic Achievement: A 2-Year Longitudinal Study Of Children At-Risk, Maha Al-Hendawi

Theses and Dissertations

Individual differences in temperament can be a risk or a protective factor for a child, especially for children at-risk who possess single or multiple risk factors that may interfere with their educational success and affect their healthy development and their life-long outcomes. This research study examined the concurrent and longitudinal relationships between temperament, school adjustment, and academic achievement in children at-risk. Seventy-seven children, ages five to 11 years, were reassessed two years after an initial study. Their teachers completed the Temperament Assessment Battery for Children (TABC), the Behavior Assessment System for Children (BASC), and reported on the children's academic achievement. …

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Commonwealth Times 2010-09-09 Sep 2010

Commonwealth Times 2010-09-09

Commonwealth Times, 1969-

No abstract provided.

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Commonwealth Times 2010-09-02 Sep 2010

Commonwealth Times 2010-09-02

Commonwealth Times, 1969-

No abstract provided.

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Commonwealth Times 2010-08-30 Aug 2010

Commonwealth Times 2010-08-30

Commonwealth Times, 1969-

No abstract provided.

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The Roads Are Bumpy Ones: A Study Of Body Image Through Abstract Performance, Alexis Goldstein Aug 2010

The Roads Are Bumpy Ones: A Study Of Body Image Through Abstract Performance, Alexis Goldstein

Theses and Dissertations

An overwhelming number of contemporary adolescents struggle with difficult issues. Many of these problems are socially related whereas others can be directly related to the degradation of the family unit. Among the most damaging of issues is distorted body image, which infect youth, often causing them to communicate aggressively, and even landing them in compromising situations. I have sought to challenge my students to redefine themselves through expressive movement and the creation of abstract rhythmic sounds. In teaching these techniques, I have given my former students the means to combat negative thoughts and actions, as well as an excellent tool …

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Informing Social Work Practice Through The Enhancement Of The Biological Perspective: A Course Intervention Model For Human Service Professionals Working With Youth And Problems Of Conduct., Allison Sampson Aug 2010

Informing Social Work Practice Through The Enhancement Of The Biological Perspective: A Course Intervention Model For Human Service Professionals Working With Youth And Problems Of Conduct., Allison Sampson

Theses and Dissertations

The purpose of this study is to evaluate the effectiveness of an intervention model designed to enhance practitioners’ biological lens when using a biopsychosocial-spiritual model of holistic assessment and planning. The specific intervention utilized is a course curriculum developed to broaden human service professionals’ (including clinical social work professionals) understanding of attachment theory, neuroscience and trauma informed methods of practice. The course teaches professionals how to apply this knowledge to clinical assessment and intervention planning with youth who have experienced significant trauma in their lives and exhibit problems of conduct. Using an experimental design, participants from a large private mental …

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Urban Adolescents’ Cognitive Responses To Peer Victimization: Does Psychosocial Adjustment Play A Role?, Amie Bettencourt Aug 2010

Urban Adolescents’ Cognitive Responses To Peer Victimization: Does Psychosocial Adjustment Play A Role?, Amie Bettencourt

Theses and Dissertations

Peer victimization is characterized by acts of physical, relational, and verbal aggression that can contribute to maladjustment. Youths’ responses to peer victimization are guided by social information-processing (SIP) skills that impact their adjustment. Maladjustment can contribute to biases in SIP. Biased processing occurs when youth rely on existing schemas without attending to cues from the immediate social context. These processing deficits contribute to the enactment of problematic responses that may lead to further maladjustment. However, not all youth exhibit SIP deficits. A recent study identified four adjustment clusters based on differences in aggression, anxiety, depression, social acceptance, and victimization within …

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Mechanisms Of Rotator Cuff Disease: Alterations Of Scapular Kinematics On Subacromial Space, Amee Seitz Aug 2010

Mechanisms Of Rotator Cuff Disease: Alterations Of Scapular Kinematics On Subacromial Space, Amee Seitz

Theses and Dissertations

Rotator cuff disease is multi-factored and has been attributed to both intrinsic and extrinsic factors. Extrinsic factors contribute to compression of the rotator cuff tendons. Intrinsic factors that contribute to rotator cuff tendon degradation with tensile/shear overload include alterations in biology, mechanical properties, morphology, and vascularity. Subacromial impingement is related to factors that encroach upon the subacromial space, while internal impingement affects the articular side of the tendons adjacent to glenoid. While the mechanisms of impingement are varied, further research is necessary to improve treatment and patient outcomes. Chapter 2 is a thorough review of literature on the mechanisms of …

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Development And Applications Of The Hint Forcefield In Prediction Of Antibiotic Efflux And Virtual Screening For Antivirals, Aurijit Sarkar Aug 2010

Development And Applications Of The Hint Forcefield In Prediction Of Antibiotic Efflux And Virtual Screening For Antivirals, Aurijit Sarkar

Theses and Dissertations

This work was aimed at developing novel tools that utilize HINT, an empirical forcefield capable of quantitating both hydrophobic and hydrophilic (hydropathic) interactions, for implementation in theoretical biology and drug discovery/design. The role of hydrophobicity in determination of macromolecular structure and formation of complexes in biological molecules is undeniable and has been the subject of research across several decades. Hydrophobicity is introduced, with a review of its history and contemporary theories. This is followed by a description of various methods that quantify this all-pervading phenomenon and their use in protein folding and contemporary drug design projects – including a detailed …

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In Vitro Evaluation Of Mechanical Heart Valve Performance Using A Novel Test Chamber In An Automated Mock Circulatory Loop, Antonio Walker Aug 2010

In Vitro Evaluation Of Mechanical Heart Valve Performance Using A Novel Test Chamber In An Automated Mock Circulatory Loop, Antonio Walker

Theses and Dissertations

Valvular heart disease (VHD) continues to have significant effects on many people’s lives, with numbers expected to grow tremendously over the next few years. Individuals suffering from severe valvular heart disease usually require a heart valve transplant in order to restore the native valve’s vital unidirectional flow regulation. Therefore, artificial heart valve (AHV) research is of very high importance. Previous research studies have provided substantial input in the realm of AHV design relative to durability, thrombotic and hemolytic potential, and overall functionality. However, modifications continue to be warranted due to limitations in the accuracy and time efficiency of the in …

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In Vivo Measurement Of Rat Skeletal Muscle Oxygen Consumption Following Brief Periods Of Ischemia With Reperfusion As Assessed By Phosphorescence Quenching Microscopy, William Nugent Aug 2010

In Vivo Measurement Of Rat Skeletal Muscle Oxygen Consumption Following Brief Periods Of Ischemia With Reperfusion As Assessed By Phosphorescence Quenching Microscopy, William Nugent

Theses and Dissertations

Brief periods of skeletal muscle ischemia (ischemic pre-conditioning) alter cellular metabolism in a way that confers protection over subsequent ischemic episodes. The mechanisms behind this effect have been studied indirectly through assays for the byproducts of ATP synthesis and in vitro studies of cellular signaling cascades and ROS generation. There have been no direct, in vivo assessments of the changes in respiration during reperfusion. We employed phosphorescence quenching microscopy in conjunction with a flow-arrest technique to assess the influences of external, pressure-induced 1- to 10-min focal ischemia on interstitial oxygenation (PISFO2) and the consumption of oxygen (VO2) in spinotrapezius muscles …

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Canopy Disturbance And Reproduction In Cornus Florida L., Daniel Carr Aug 2010

Canopy Disturbance And Reproduction In Cornus Florida L., Daniel Carr

Theses and Dissertations

This study examined aspects of local reproductive variation in the flowering dogwood (Cornus florida L.) coincident with recent differences in primary canopy architecture. The dogwood trees in this study were impacted by a hurricane that created numerous treefall gaps, which created fine scale heterogeneity in the primary canopy. Fine scale disturbances in a forest can result in changes for multiple members of the forest community, including the reproductive responses of the trees and interspecific pollination mutualisms. Previously determined differences in offspring genetic structure suggested that pollen movement among genetically unstructured maternal individuals was significantly impacted between open, or disturbed, canopy …

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Variation In Sound Production Of The Blue Catfish, Ictalurus Furcatus., Zachary Ghahramani Aug 2010

Variation In Sound Production Of The Blue Catfish, Ictalurus Furcatus., Zachary Ghahramani

Theses and Dissertations

The blue catfish, Ictalurus furcatus, is an invasive species introduced to Virginia in 1974 and is the largest catfish in the United States. Like other Ictalurids, they are capable of producing disturbance calls via stridulation of the pectoral spine. These sounds can be made in air and water, and catfish can be preyed upon by both aerial and underwater predators. I characterized these putative distress calls by recording them in air and in the fish’s natural habitat. Sounds exhibited a wide variation in acoustic parameters relative to fish ontogeny: larger fish produced higher amplitude sounds with lower frequency bands. Sweep …

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Effect Of Ph On The Transcriptional Profile Of Porphyromonas Gingivalis W83, Nathan Maietta Aug 2010

Effect Of Ph On The Transcriptional Profile Of Porphyromonas Gingivalis W83, Nathan Maietta

Theses and Dissertations

Porphyromonas gingivalis, a gram-negative, anaerobic bacterium, is widely recognized as a causative agent for periodontal disease. Despite sequencing of the complete genome, no research exists examining gene regulation response in P. gingivalis to shifts in pH. Previous studies have shown that P. gingivalis is capable of surviving in the variety of micro- environmental niches found within the oral cavity, including basic and acidic pH conditions. However, the underlying mechanisms of this survival are not well understood. This study examined P. gingivalis by comparing bacteria shocked at three acidic to neutral pH conditions (5.5, 6.5 and 7.0) to bacteria vii shocked …

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Cannabinoid Receptors In The 3d Reconstructed Mouse Brain: Function And Regulation, Peter Nguyen Aug 2010

Cannabinoid Receptors In The 3d Reconstructed Mouse Brain: Function And Regulation, Peter Nguyen

Theses and Dissertations

CB1 receptors (CB1R) mediate the psychoactive and therapeutic effects of cannabinoids including ∆9-tetrahydrocannabinol (THC), the main psychoactive constituent in marijuana. However, therapeutic use is limited by side effects and tolerance and dependence with chronic administration. Tolerance to cannabinoid-mediated effects is associated with CB1R adaptations, including desensitization (receptor-G-protein uncoupling) and downregulation (receptor degradation). The objectives of this thesis are to investigate the regional-specificity in CB1R function and regulation. Previous studies have investigated CB1Rs in a subset of regions involved in cannabinoid effects, but an inclusive regional comparison of the relative efficacies of different classes of cannabinoids to activate G-proteins has not …

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Environmental Responses Of Two-Component Systems In Streptococcus Sanguinis, Jenishkumar Patel Aug 2010

Environmental Responses Of Two-Component Systems In Streptococcus Sanguinis, Jenishkumar Patel

Theses and Dissertations

The gram-positive bacterium Streptococcus sanguinis is a member of human indigenous oral microbialflora and has long been recognized as a key player in the bacterial colonization of the mouth. S. sanguinis is also the most common viridians streptococcal species implicated in infective endocarditis. Although many studies have focused on two-component systems in closely related Streptococcus species such as S. mutans, S. pneumoniae and S. gordonii; the mechanism of the response regulator in S. sanguinis is still unknown. The ability of S. sanguinis to adapt and thrive in hostile environments suggests this bacterium is capable of sensing and responding to various …

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Volumetric Growth Model Of Human Medulloblastoma In The Nude Mouse Cerebellum, Thomas Gavigan Aug 2010

Volumetric Growth Model Of Human Medulloblastoma In The Nude Mouse Cerebellum, Thomas Gavigan

Theses and Dissertations

Medulloblastoma is the most common brain tumor in children, accounting for 10-20% of primary central nervous system (CNS) neoplasms and approximately 40% of all posterior fossa tumors. It is a highly invasive embryonal neuroepithelial tumor that typically arises in the cerebellar vermis and has a tendency to disseminate throughout the CNS early in its course. The molecular mechanisms of the disease largely remain uncharacterized, as the clinical treatment is still associated with mortality and severe side effects. The development of a clinically relevant in vivo model is important not only to further understand the disease but also to provide a …

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Factors Affecting Gingival Excess, Altered Passive Eruption And Recession In The Mandibular Anterior And Premolar Sites, William Bohlen Aug 2010

Factors Affecting Gingival Excess, Altered Passive Eruption And Recession In The Mandibular Anterior And Premolar Sites, William Bohlen

Theses and Dissertations

Abstract FACTORS AFFECTING GINGIVAL EXCESS, ALTERED PASSIVE ERUPTION AND RECESSION IN THE MANDIBULAR ANTERIOR AND PREMOLAR SITES By William F Bohlen, D.M.D. A thesis submitted in partial fulfillment of the requirements for the degree of Master of Science in Dentistry at Virginia Commonwealth University. Virginia Commonwealth University, 2010 Major Director: Thomas Waldrop, DDS, MS Program director, Department of Periodontics, Virginia Commonwealth University AIM: The aim of this study was to determine the factors affecting gingival excess, altered passive eruption and recession. METHODS: 100 subjects were examined clinically and models of their mandible were fabricated. Demographic, periodontal and cast measurements were …

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Assessing Economic And Hrql Burden Of Food Allergy And Anaphylaxis In The U.S., Dipen Patel Jul 2010

Assessing Economic And Hrql Burden Of Food Allergy And Anaphylaxis In The U.S., Dipen Patel

Theses and Dissertations

Background: Food allergy, an abnormal immunologic response to food protein, has an estimated prevalence of 6% in young children and 3.7% in adults in the U.S. The only proven therapy for food allergy is strict elimination of the offending allergens. As a result, caregivers and patients could experience constant anxiety and stress that affects their quality of life. Additionally, food allergy can lead to significant economic impact on the health care system, since severe reactions often lead to ED visits and hospitalizations. Objectives: The first major objective was to determine the economic burden of Food Allergy and Anaphylaxis (FAA) patients …

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Contribution Of Nuceliec Acids On The Structure Of Recombinant Hepadnavirus Core Antigens, Maimuna Bruce Jul 2010

Contribution Of Nuceliec Acids On The Structure Of Recombinant Hepadnavirus Core Antigens, Maimuna Bruce

Theses and Dissertations

The Hepatitis B core antigen (HBcAg) has been proposed to be an ideal candidate for use as an adjuvant due to its immunogenicity, and tolerance to manipulations such as insertions of epitopes or covalent attachment of ligands. HBcAg is a complex macromolecule containing protein and nucleic acid. We investigated the effect of the removal and reconstitution of nucleic acids upon its structure. It’s been shown that the RNA content of hepadnavirus core antigens can be reduced significantly, but not be completely removed. Following removal of some of the RNA, antigens retain the ability to bind added nucleic acids, in particular, …

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Function And Regulation Of Matrix Metalloproteinase-1 In Glioblastoma Multiforme, Monika Anand Jul 2010

Function And Regulation Of Matrix Metalloproteinase-1 In Glioblastoma Multiforme, Monika Anand

Theses and Dissertations

Glioblastoma Multiforme (GBM) is an aggressive and fatal cancer of the brain. It is characterized with augmented morbidity and elusion to therapies due in part to the incessant infiltration and spread of tumor cells in normal brain. We investigated the function of Matrix metalloproteinase-1, an important enzyme noted to be responsible for invasion in other cancers, in GBM and its regulation by epidermal growth factor receptor (EGFR) signaling. Previous studies from our laboratory demonstrated elevated levels of MMP-1 in GBM. Further studies indicated the involvement of MMP-1 in GBM invasion. The GBM cell lines T98G, U251MG and U87MG were used …

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Characterization And Crystallization Of The Mycobacterium Tuberculosis Trmd, Zohal Hamidi Jul 2010

Characterization And Crystallization Of The Mycobacterium Tuberculosis Trmd, Zohal Hamidi

Theses and Dissertations

One third of the world’s population is affected by Tuberculosis (TB), a disease caused by infection with Mycobacterium tuberculosis (MtB). The emergence of multidrug-resistant MtB makes this disease a major public health concern. New agents are needed to treat TB infections in a manner that circumvents existing pathways of resistance. One strategy is to target the organism at the translational level by inhibiting vital modifications of RNA. One gene responsible for these modifications is the tRNA (guanosine-1)-methyltransferase, trmD, which has been shown to be essential in several bacteria. The eukaryotic and bacterial m1G methyltransferases are structurally dissimilar, making this enzyme …

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