Digital Commons Network^™

Novel Inducers Of Gliotoxin Production In Aspergillus Fumigatus, Taylor J. Schoberle

Dissertations and Theses (Open Access)

Secondary metabolites are produced by numerous organisms and can either be benign to humans or harmful. Genes involved in the synthesis and transport of these secondary metabolites are frequently found in gene clusters, which are often located in subtelomeric regions of the chromosome. These clusters are often coordinately regulated, being almost exclusively dependent on transcription factors that are located within the clusters themselves. Secondary metabolites are also regulated by a variety of factors, including nutritional factors, environmental factors and developmental processes. Gliotoxin, which is produced by a variety of Aspergillus species, Trichoderma species, and Penicillium species, exhibits immunosuppressive properties and …

Development And Implementation Of A Dynamic Heterogeneous Proton Equivalent Anthropomorphic Thorax Phantom For The Assessment Of Scanned Proton Beam Therapy, James L. Neihart

Dissertations and Theses (Open Access)

DEVELOPMENT AND IMPLEMENTATION OF A DYNAMIC HETEROGENEOUS PROTON EQUIVALENT ANTHROPOMORPHIC THORAX PHANTOM FOR THE ASSESSMENT OF SCANNED PROTON BEAM THERAPY

by

James Leroy Neihart, B.S.

APPROVED:

______________________________
David Followill, Ph.D.

______________________________
Peter Balter, Ph.D.

______________________________
Narayan Sahoo, Ph.D.

______________________________
Kenneth Hess, Ph.D.

______________________________
Paige Summers, M.S.

APPROVED:

____________________________

Dean, The University of Texas

Graduate School of Biomedical Sciences at Houston

DEVELOPMENT AND IMPLEMENTATION OF A DYNAMIC HETEROGENEOUS PROTON EQUIVALENT ANTHROPOMORPHIC THORAX PHANTOM FOR THE ASSESSMENT OF SCANNED PROTON BEAM THERAPY

A

THESIS

Presented to the Faculty of
The University of Texas
Health Science Center at Houston
and
The University of …

Use Of Echogenic Immunoliposomes For Delivery Of Both Drug And Stem Cells For Inhibition Of Atheroma Progression, Ali K. Naji

Dissertations and Theses (Open Access)

Use of Echogenic Immunoliposomes for Delivery of both Drug and Stem Cells for Inhibition of Atheroma Progression

By Ali K. Naji B.S. Advisor: Dr. Melvin E. Klegerman PhD

Background and significance: Echogenic liposomes can be used as drug and cell delivery vehicles that reduce atheroma progression. Vascular endothelial growth factor (VEGF) is a signal protein that induces vasculogenesis and angiogenesis. VEGF functionally induces migration and proliferation of endothelial cells and increases intracellular vascular permeability. VEGF activates angiogenic transduction factors through VEGF tyrosine kinase domains in high-affinity receptors of endothelial cells. Bevacizumab is a humanized monoclonal antibody specific for VEGF-A which …

Rna-Sequencing Applications: Gene Expression Quantification And Methylator Phenotype Identification, Guoshuai Cai

Dissertations and Theses (Open Access)

My dissertation focuses on two aspects of RNA sequencing technology. The first is the methodology for modeling the overdispersion inherent in RNA-seq data for differential expression analysis. This aspect is addressed in three sections. The second aspect is the application of RNA-seq data to identify the CpG island methylator phenotype (CIMP) by integrating datasets of mRNA expression level and DNA methylation status.

Section 1: The cost of DNA sequencing has reduced dramatically in the past decade. Consequently, genomic research increasingly depends on sequencing technology. However it remains elusive how the sequencing capacity influences the accuracy of mRNA expression measurement. We …

Characterization Of Jak, Stat, And Src Interactions In Head And Neck Squamous Cell Carcinoma, Reshma Jaseja, Reshma Jaseja

Dissertations and Theses (Open Access)

Recurrence of Head and Neck Squamous Cell Carcinoma (HNSCC) is common; thus, it is essential to improve the effectiveness and reduce toxicity of current treatments. Proteins in the Src/Jak/STAT pathway represent potential therapeutic targets, as this pathway is hyperactive in HNSCC and it has roles in cell migration, metastasis, proliferation, survival, and angiogenesis. During short-term Src inhibition, Janus kinase (Jak) 2, and signal transducer and activator of transcription (STAT) 3 and STAT5 are dephosphorylated and inactivated. Following sustained Src inhibition, STAT5 remains inactive, but Jak2 and STAT3 are reactivated following their early inhibition. To further characterize the mechanism of this …

A Novel Cardiac Function Of Sumo2/3 And Senp5 Dependent Pathway And Its Physiological Impact On Congestive Cardiomyopathy, Eun Young Kim

Dissertations and Theses (Open Access)

A Novel cardiac function of SUMO2/3 and SENP5 dependent pathway and its physiologic impact on congestive cardiomyopathy

Publication No.___________

Eun Young Kim, M.S.

Supervisory professor: Robert J. Schwartz, Ph.D.

SUMOylation regulates diverse cellular processes including transcription, cell cycle, protein stability, and apoptosis. Although SUMO1 has been extensively studied so far, relevance of SUMO2/3 is unclear, especially in heart. Here we show that failing heart induces SUMO2/3 conjugation. Increased SUMO2/3-dependent modification leads to congestive heart disease such as cardiac hypertrophy by promoting cardiac cell death. Calpain2 and Calpastatin as a novel SUMO2 targets have been known to be involved in mitochondrial-independent …

Evaluation Of Presage® Dosimeters For Brachytherapy Sources And The 3d Dosimetry And Characterization Of The New Agx100 125i Seed Model, Olivia Huang

Dissertations and Theses (Open Access)

With continuous new improvements in brachytherapy source designs and techniques, method of 3D dosimetry for treatment dose verifications would better ensure accurate patient radiotherapy treatment. This study was aimed to first evaluate the 3D dose distributions of the low-dose rate (LDR) Amersham 6711 Oncoseed^TM using PRESAGE^® dosimeters to establish PRESAGE^® as a suitable brachytherapy dosimeter. The new AgX100 ¹²⁵I seed model (Theragenics Corporation) was then characterized using PRESAGE^® following the TG-43 protocol.

PRESAGE^® dosimeters are solid, polyurethane-based, 3D dosimeters doped with radiochromic leuco dyes that produce a linear optical density response to radiation dose. …

A Genomic Approach To Identify The Notch Pathway As A Putative Tumor Suppressor In Endometrial Cancer, Rajshi Gandhi

Dissertations and Theses (Open Access)

Endometrial cancer is the most common gynecological malignancy and the fourth most frequently diagnosed cancer among women. The molecular changes that distinguish normal endometrium from endometrial carcinoma are not thoroughly understood. Identification of these changes could potentially aid in identifying at-risk women who are especially prone to develop endometrial cancer, such as obese women and women with Lynch Syndrome.

A microarray analysis was performed using normal endometrium from thin and obese women and cancerous endometrium from obese women. We validated the differential expression of ten genes whose expression was significantly up-regulated or down-regulated using qRT-PCR. All of the genes had …

Induction Of Synthetic Lethality In Mutant Kras Cells For Non-Small Cell Lung Cancers Chemoprevention And Therapy, Shaoyi Huang

Dissertations and Theses (Open Access)

Lung cancer is the leading cause of cancer death in both men and women in the United States and worldwide. Despite improvement in treatment strategies, the 5-year survival rate of lung cancer patients remains low. Thus, effective chemoprevention and treatment approaches are sorely needed. Mutations and activation of KRAS occur frequently in tobacco users and the early stage of development of non-small cell lung cancers (NSCLC). So they are thought to be the primary driver for lung carcinogenesis. My work showed that KRAS mutations and activations modulated the expression of TNF-related apoptosis-inducing ligand (TRAIL) receptors by up-regulating death receptors and …

The Role Of K63-Linked Ubiquitination Cycles In Akt Kinase Activation, Wei-Lei Yang

Dissertations and Theses (Open Access)

Akt (also known as protein kinase B) serves a central regulator in PI3K/Akt signaling pathways to regulate numerous physiological functions including cell proliferation, survival and metabolism. Akt activation requires the binding of Akt to phospholipid PIP3 on the plasma membrane and subsequent phosphorylation of Akt by its kinases. Growth factor-mediated membrane recruitment of Akt is a crucial step for Akt activation. However, the mechanism of Akt membrane translocation is unclear. Protein ubiquitination is a significant posttranslational modification that controls many biological functions such as protein trafficking and signaling activation. Therefore, we hypothesize that ubiquitination may be involved in Akt signaling …

Development And Characterization Of An In Vitro Four-Species Anaerobic Dental Biofilm Model, Fernando Andrade

Dissertations and Theses (Open Access)

Dental caries is the most common chronic disease worldwide. It is characterized by the demineralization of tooth enamel caused by acid produced by cariogenic dental bacteria growing on tooth surfaces, termed bacterial biofilms. Cariogenesis is a complex biological process that is influence by multiple factors and is not attributed to a sole causative agent. Instead, caries is associated with multispecies microbial biofilm communities composed of some bacterial species that directly influence the development of a caries lesion and other species that are seemingly benign but must contribute to the community in an uncharacterized way. Clinical analysis of dental caries and …

Altering Attention In Adjudication, Chris Guthrie, Jeffrey J. Rachlinski, Andrew J. Wistrich

Vanderbilt Law School Faculty Publications

Judges decide complex cases in rapid succession but are limited by cognitive constraints. Consequently judges cannot allocate equal attention to every aspect of a case. Case outcomes might thus depend on which aspects of a case are particularly salient to the judge. Put simply, a judge focusing on one aspect of a case might reach a different outcome than a judge focusing on another. In this Article, we report the results of a series of studies exploring various ways in which directing judicial attention can shape judicial outcomes. In the first study, we show that judges impose shorter sentences when …

Seeking Genomic Knowledge: The Case For Clinical Restraint, Ellen Wright Clayton, Wylie Burke, Susan Brown Trinidad

Vanderbilt Law School Faculty Publications

Genome sequencing technology provides new and promising tests for clinical practice, including whole genome sequencing, which measures an individual's complete DNA sequence, and whole exome sequencing, which measures the DNA for all genes coding for proteins. These technologies make it possible to test for multiple genes in a single test, which increases the efficiency of genetic testing. However, they can also produce large amounts of information that cannot be interpreted or is of limited clinical utility. This additional information could be distracting for patients and clinicians, and contribute to unnecessary healthcare costs. The potential for genomic sequencing to improve care …

Fabrication And Characterization Of Radio-Frequency Sensors For Liquid Material Detection, Yuxi He

All Theses

This thesis presents a series of studies on fabrication and characterization of radio-frequency (RF) sensors. In the light of Electromagnetics and Transmission Line Theory, we designed multiple RF sensors with different detection capability emphasis and used them to detect various materials, especially liquid samples and materials in solutions such as dielectric thin films, confined liquids, red blood cells, and malarial pigments (hemozoin). Most sensors were fabricated under clean room environment following the standard process protocols. Proper process developments were also made to achieve special structures and functionalities of our novel sensors. Scanning Electron Microscopy (SEM) and Atomic Force Microscopy (AFM) …

Statistical Regression Methods For Gpgpu Design Space Exploration, Nimisha Raut

All Theses

General Purpose Graphics Processing Units (GPGPUs) have leveraged the performance and power efficiency of today's heterogeneous systems to usher in a new era of innovation in high-performance scientific computing. These systems can offer significantly high performance for massively parallel applications; however, their resources may be wasted due to inefficient tuning strategies. Previous application tuning studies pre-dominantly employ low-level, architecture specific tuning which can make the performance modeling task difficult and less generic. In this research, we explore the GPGPU design space featuring the memory hierarchy for application tuning using regression-based performance prediction framework and rank the design space based on …

Continuum Robotic Surface: Forward Kinematic Analysis And Implementation, Jessica Merino

All Theses

This thesis presents a new class of biologically inspired robots: continuum robotic surfaces. This work is fueled by the question: can the interaction between robot and environment be advanced with “programmable surfaces in space?” The novelty of continuum robotic surfaces lies in their ability to be actively controlled and reconfigured in what we believe is the current “missing dimension” in robot movements — two–dimensional space. We believe that such surfaces will lend themselves to more complex applications. However, to effectively deploy such surfaces for these complex applications, kinematic models will be necessary to plan and control desired configurations. The forward …

Problems In The Study And Use Of Ac Dielectrophoresis And Their Consequences: A Study Based On Comsol Multiphysics Modeling, Vandana Devi Pandian Babu

All Theses

Dielectrophoresis (or DEP) is an important phenomenon which is induced when a dielectric particle is placed in a non-uniform electric field. The force generated by DEP has been exploited for various micro and nano fluidics applications like positioning, sorting and separation of particles involved in medical diagnostics, drug discovery, cell therapeutics, biosensors, microfluidics, nanoassembly, particle filtration etc. The integration of DEP systems into the microfluidics enables inexpensive, fast, highly sensitive, highly selective, label-free detection and also the analysis of target bioparticles.

This work aims to provide a complete compilation of the factors affecting the DEP force. It elucidates the underlying …

The Extraction Of Acetic Acid From Thermotoga Neapolitana Fermentation Spent Medium Using Fresh/Recovered Aliquat 336 And Produce Cma, Yifan Du

All Theses

To offer an alternative pathway to produce calcium magnesium acetate (CMA) as an environmental friendly deicer to relieve the pressure on fossil fuels demand, a liquid-liquid extraction process was studied. This process includes using Aliquat 336 (tri-n-octylmethylammonium chloride) diluted in kerosene as an organic extractant to extract acetic acid from Thermotoga neapolitana fermentation spent medium, which contained 34 g/L of acetic acid and 10 g/L of NaCl.
The extraction efficiency of Aliquat 336 was studied under several different extraction conditions. The initial pH of the spent medium was adjusted to a pH range of 2.25 to 5.75 with a 0.5 …

Women In Engineering: Identity Communication In Social Media, Dongni Wang

All Theses

This thesis examines women engineers' experience in social media with a focus on identity communication. Framing as a case study, this study attempts to explore women engineers' online presence and how they utilize social media in their daily activities. Using the concept of intersectionality, this study addresses the differences of social media usage among women engineers in terms of the use of social media by professional organizations of women engineers and the use of individual women engineers. Thematic analysis was conducted to analyze the public available data from a Facebook page maintain by a well-known women engineers' professional organization. Online …

Hydrogen Production By Thermotoga Lettingae Using Spent Fermentation Media Containing Acetic Acid, Archana Ganesh

All Theses

Biological production of hydrogen (H₂) gas from fermentation of agricultural feedstock is one method to produce clean and sustainable source of energy. During fermentation of glucose to H₂, acetic acid and carbon dioxide (CO₂) by Thermotoga neapolitana, only 33% of the energy contained in glucose is converted to hydrogen. The aim of this study was to use a second thermotogale, Thermotoga lettingaeto ferment sugars and acetic acid in spent media to produce H₂. Hydrogen production by this bacterium in fresh and spent media was studied by quantifying the amount of …

Development Of Map/Reduce Based Microarray Analysis Tools, Guangyu Yang

All Theses

High density oligonucleotide array (microarray) from the Affymetrix GeneChip¨ system has been widely used for the measurements of gene expressions. Currently, public data repositories, such as Gene Expression Omnibus (GEO) of the National Center for Biotechnology Information (NCBI), have accumulated very large amount of microarray data. For example, there are 84389 human and 9654 Arabidopsis microarray experiments in GEO database. Efficiently integrative analysis large amount of microarray data will provide more knowledge about the biological systems. Traditional microarray analysis tools all implemented sequential algorithms and can only be run on single processor. They are not able to handle very large …

Modeling Benefits Of Implementing Low Impact Development Practices Within Forecasted Growth Scenarios Of The Reedy River Watershed, Stephen Taylor

All Theses

For this research, a previously developed comprehensive watershed water quality model for the Reedy River as developed for South Carolina Department of Health and Environmental Control (SCDHEC) and the US Environmental Protection Agency (EPA) as a total maximum daily load (TMDL) assessment tool was used to assess the benefits of using low impact development (LID) designs in future growth of Greenville County, within the Reedy River watershed. The original intent of this model was to provide SCDHEC with a defensible model that could be used to prepare nutrient TMDLs for an area located at Boyd Millpond and the Reedy River …

Biofabrication Of Scaffolds For Intervertebral Disc (Ivd) Tissue Regeneration, Benjamin Whatley

All Dissertations

The ultimate goal of tissue regeneration is to replace damaged or diseased tissue with a cell-based or biomaterial-based tissue that accurately mimics the functionality, biology, mechanics, and cellular and extracellular matrix (ECM) composition of the native tissue. Specifically, the ability to control the architecture of tissue engineered constructs plays a vital role in all of these issues as scaffold architecture has an affect on function, biomechanics, and cellular behavior. Many tissue engineered scaffolds focus on the ability to mimic natural tissue by simulating the ECM due to the fact that in each distinct tissue, the ECM serves as a structural …

Ecology And Management Of Stink Bugs (Hemiptera: Pentatomidae) In Southeastern Farmscapes, Grant Pilkay

All Dissertations

A three-year study (2009-2011) was conducted to examine the spatial and temporal dynamics of stink bugs in three commercial farmscapes in South Carolina and Georgia. Crops included wheat, Triticum aestivum (L.), corn, Zea mays (L.), soybean, Glycine max (L.), cotton, Gossypium hirsutum (L.), and peanuts, Arachis hypogaea (L.). Farmscapes were sampled weekly using whole-plant examinations for corn, with all other crops sampled using sweep nets. The predominant pest species of phytophagous stink bugs were the brown stink bug, Euschistus servus (Say), the green stink bug, Chinavia hilaris (Say), and the southern green stink bug, Nezara viridula (L.). Chi-square tests indicated …

A Localized Controlled Delivery System Utilizing A Block Copolymer To Improve The Current Paradigm Of Chemotherapy, Jason Olbrich

All Dissertations

The goal of the field of Bioengineering has always been to bring about a better standard of care for patients. As a field encompassing a broad array of researchers and talents, such improvements often are brought about through the integration of different fields. This work advances the integration of controlled delivery and chemotherapy. The use of cytotoxic chemotherapy has become and will continue to be a powerful tool for the treatment of solid malignancies. Conventional dose scheduling of cytotoxic agents and newer biological response modifiers are investigated under a clinical paradigm initially designed to identify a drug dose that elicits …

Comparing Mechanical Mastication, Herbicide Application, And Prescribed Fire Within An Established Longleaf Pine (Pinus Palustris Mill.) Ecosystem, Brett Moule

All Dissertations

Longleaf pine (Pinus palustris Mill.) forests once dominated the landscape throughout the Southeast and much of its success could be attributed to ecological disturbances such as fire. However, the use of fire as a management tool may be at risk due to a growing human population, negative impacts resulting from smoke production, and the imposition of restrictive federal and state laws, policies, and standards. This study was designed to determine whether alternative silviculture treatments such as herbicide or mechanical mastication can be used as surrogates to prescribed fire. We applied three commonly used silviculture treatments (prescribed burning, mechanical mastication, …

Effects Of Varying Spring Hollow Tine Aerification Size And Timing On Bentgrass Greens, Lewis Hubbard Jr

All Dissertations

The desire to maintain optimal turfgrass and surface properties often leads turfgrass managers to minimize impact from cultural practices like hollow tine aerification (HTA). Comprehensive research is essential to developing aerification programs which allow optimal use of turfgrass surfaces without sacrificing overall turf health.
A two-year field experiment was conducted on a 14-year-old U.S. Golf Association (USGA)-specified Crenshaw creeping bentgrass [Agrostis stolonifera L. var palustris (Huds.)] research putting green in Clemson, SC, to evaluate the effects of varying spring HTA size and timing on turfgrass, surface, organic matter (OM), and soil properties.
Spring HTA treatments included 1.2-cm i.d. tines spaced …

Gap Junctions: Regulators Of Cellular Immunity And Parasite Manipulation In The Remarkable Tripartite Relationship Involving Insects And Genome-Integrated Polydnaviruses, Daniel Hasegawa

All Dissertations

Communication means everything. From vocalization to the firing of a neuron, coordination through the exchange of signals is essential to the survival of all living things. At the cellular level, communication is accomplished through the use of gap junction channels. Gap junctions are found in virtually all multicellular animals, where they play critical roles in developmental, physiological, metabolic, and even structural processes. From the maintenance of heart rhythms in humans, to the coordination of tissue regeneration in flatworms, and to the processing of visual stimuli in flies, the roles for gap junctions are diverse. However, how this diversity is accomplished …

Feeling For Failure: Haptic Force Perception Of Soft Tissue Constraints In A Simulated Minimally Invasive Surgery Task, Lindsay Long

All Dissertations

In minimally invasive surgery (MIS), the ability to accurately interpret haptic information and apply appropriate force magnitudes onto soft tissue is critical for minimizing bodily trauma. Force perception in MIS is a dynamic process in which the surgeon's administration of force onto tissue results in useful perceptual information which guides further haptic interaction and it is hypothesized that the compliant nature of soft tissue during force application provides biomechanical information denoting tissue failure. Specifically, the perceptual relationship between applied force and material deformation rate specifies the distance remaining until structural capacity will fail, or indicates Distance-to-Break (DTB). Two experiments explored …

Influences Of Riparian Land-Uses On Habitat Use And Interspecific Competition Of Stream-Dwelling Salamanders: Evidence From Blue Ridge & Piedmont, Thilina Surasinghe

All Dissertations

Human-induced disturbances can result in persistent influences on ecosystems, including habitat loss and biogeographical changes. Global amphibian decline, a consequence of habitat degradation, is among prime conservation concerns. To better understand causes of the amphibian crisis, investigations a multiple levels of biological organization - behavior, communities, and landscapes - is imperative. I investigated the responses of stream-associated Plethdontid salamanders of the Blue Ridge and Piedmont of the Southeastern US to historical and current land uses in the riparian zone and watershed to determine, (1) change in the community structure and mechanisms driving the change and uses operating at different spatial-temporal …