Physical Sciences and Mathematics Commons^™

Design And Synthesis Of Beta-Hairpin Peptidomimetics For Modulating Integrin Mediated Cell Adhesion, Abeta Fibrillogenesis And P53-Mdm2 Protein-Protein Interactions, Priyesh Jain

USF Tampa Graduate Theses and Dissertations

Inhibiting therapeutically important protein-protein interactions has been a tremendous challenge for medicinal chemists. The folded 3D structures of peptides and proteins, mainly comprise secondary structural elements i.e α-helices and β-sheet have created an opportunity to design small molecules and peptidomimetic inhibitors of protein-protein interaction (PPI). Hence, information about the formation and stabilization of these secondary structures is vital for designing future drugs. In this dissertation, several cyclic beta-hairpin peptidomimetics that mimic the recognition surface have been designed and synthesized as inhibitors for different targets such as integrin mediated extracellular matrix -cell adhesion in multiple myeloma, p53-MDM2 PPI, amyloid beta fibrillogenesis …

A Framework For Determining The Reliability Of Nanoscale Metallic Oxide Semiconductor (Mos) Devices, Wilkistar Otieno

USF Tampa Graduate Theses and Dissertations

An increase in worldwide investments during the past several decades has pro-pelled scienti c breakthroughs in nanoscience and technology research to new and exciting levels. To ensure that these discoveries lead to commercially viable prod-ucts, it is important to address some of the fundamental engineering and scientific challenges related to nanodevices. Due to the centrality of reliability to product integrity, nanoreliability requires critical analysis and understanding to ensure long-term sustainability of nanodevices and systems. In this study, we construct a relia-bility framework for nanoscale dielectric lms used in Metallic Oxide Semiconductor (MOS) devices. The successful fabrication and incorporation of metallic …

Dna Methylation And Its Association With Prenatal Exposures And Pregnancy Outcomes, Jennifer Straughen

USF Tampa Graduate Theses and Dissertations

Altered DNA methylation may lead to suboptimal fetal programming, increasing the risk of adverse pregnancy outcomes such as small for gestational age (SGA); however, few studies have examined the associations between DNA methylation, prenatal exposures, and fetal outcomes. Cross-sectional data from a larger, ongoing study were used to assess the impact of prenatal smoking on gene specific methylation of umbilical cord blood derived DNA and to investigate the association between gene-specific methylation and risk of SGA. The association between gene-specific DNA methylation and birthweight was also assessed. Maternal and infant covariates were abstracted from medical records, cigarette smoke exposure was …

Evaluation Of Common Inherited Variants In Mitochondrial-Related And Microrna-Related Genes As Novel Risk Factors For Ovarian Cancer, Jennifer Permuth Wey

USF Tampa Graduate Theses and Dissertations

Epithelial ovarian cancer (EOC) is a leading cause of morbidity and mortality among women in the United States, and the etiology is incompletely understood. Common, low penetrant genetic variants such as single nucleotide polymorphisms (SNPs) likely contribute to a significant proportion of EOC. We examined whether SNPs in two understudied yet biologically important types of genes, mitochondrial-related and miRNA-related genes, may contribute to EOC susceptibility using data from a large, homogeneous study population of 1,815 EOC cases and 1,900 controls (frequency-matched on age-group and race/ethnicity) genotyped through stage 1 of an ongoing genome-wide association study. Inter-individual variation in genes involved …

Corrole Synthesis And Catalytic Applications Toward Cobalt(Iii)-Catalyzed Epoxidation, N-H Insertion, And Cyclopropanation, Chung Sik Kim

USF Tampa Graduate Theses and Dissertations

A variety of bromocorroles, useful precusors for Pd-based cross coupling, were sucessfully synthesized in moderate to good yields. Chiral corroles were also synthesized through use of chiral amides in the aforementioned cross coupling reactions. Cobalt complexes bearing π-acceptor (CNtBu) and σ-donor (PPh3) ligands were also prepared in excellent yields. In this dissertation, cobalt (III) corrole complexes were applied to three different reaction areas: epoxidation, N-H insertion, and cyclopropanation. Cobalt(III) corroles were found to be efficient catalysts for epoxidation reactions. The epoxidation reactions can be carried out using ethyl phenyldiazoacetate, an acceptor/donor diazo compound, as a carbenoid precusor.The reaction provided highly …

Aspects Of The Life History Of The Snowy Grouper, Epinephelus Niveatus, In The Gulf Of Mexico, Kelley Kowal

USF Tampa Graduate Theses and Dissertations

Knowledge of many life history parameters are essential to properly assess and manage fish species. Although the snowy grouper, Epinephelus niveatus, is a commercially valuable fish, which is harvested throughout the Gulf of Mexico, little is known about its age, growth, and reproduction from this region. In this study, snowy grouper from the northern and eastern regions of the Gulf of Mexico were examined primarily using commercially-derived samples that were collected between 1984 and 2004. A total of 1,200 snowy grouper with fork lengths between 242 and 1,190 mm were collected. Sectioned saggital otoliths were used to determine the age …

Discovery Of Novel Viruses From Animals, Plants, And Insect Vectors Using Viral Metagenomics, Terry Fei Fan Ng

USF Tampa Graduate Theses and Dissertations

Understanding emerging viruses is critical for disease monitoring and prediction; however, surveys of novel viruses are hindered by the lack of a universal assay for viruses. Viral metagenomics, consisting of viral particle purification and shotgun sequencing, is a powerful technique for discovering viruses in a wide variety of sample types. However, current protocols are not effective on tissue samples (e.g., lungs, livers and tumors), where they are hindered by the high amount of host nucleic acids which limits the percentage of sequences that originate from viruses. In this dissertation, a modified viral metagenomics protocol was developed and utilized to effectively …

Modern Variation In Predation Intensity: Constraints On Assessing Predator-Prey Relationships In Paleoecologic Reconstructions, James Funderburk

USF Tampa Graduate Theses and Dissertations

The complex interaction between predators and their prey is rarely preserved in the fossil record. However, predation of marine mollusks by drilling gastropods leaves a diagnostic hole in the shell of the prey, possibly allowing for quantitative analysis of this ecological interaction. Drilling frequency, as measured in marine mollusks both in the Modern and fossil record, has been heralded as a potential opportunity to quantify these ecological interactions and use these values in the testing of hypotheses.

This study employed the collection, tallying, and analysis of bulk samples derived from shelly deposits on 45 Modern beaches along the contiguous coast …

Design, Synthesis & Biological Activity Of Novel Protein Tyrosine Phosphatase (Ptp) Mimetics, Sridhar Reddy Kaulagari

USF Tampa Graduate Theses and Dissertations

Protein phosphorylation is a post translational modification of proteins in which a serine, a threonine or a tyrosine residue is phosphorylated by an enzyme, kinase. Phosphorylation of proteins is a reversible and very important regulatory mechanism that occurs in both prokaryotes and eukaryotes. Phosphorylation turns many protein enzymes on and off, preventing or causing many diseases such as diabetes, cancer and rheumatoid arthritis. The phosphorylation on tyrosine residues of proteins is essential for transmission of signals for cell growth, proliferation and differentiation. Protein tyrosine phosphatases (PTPs) in concert with protein tyrosine kinases (PTKs) regulate many signal transduction pathways by controlling …

Libs And Lite Emission Based Laser Remote Sensing Of Chemical Species And Enhanced Modeling Of Atmospheric Absorption, Dzianis V. Pliutau

USF Tampa Graduate Theses and Dissertations

Laser-Induced Breakdown spectroscopy (LIBS) and Laser-Induced Thermal Emission (LITE) emission based laser remote sensing were investigated with the application to the remote measurements of trace chemical species. In particular, UVvisible LIBS and Mid-IR LITE systems were developed and measurements of remote targets and chemical surfaces were studied. The propagation through the atmosphere of the multi-wavelength backscattered LIBS and LITE optical spectrum with atmospheric absorption effects on the returned lidar signal was investigated. An enhanced model of the atmospheric effects on emission-based laser-remote sensing was developed and found to be consistent and in agreement with our experimental results.

LITE measurements were …

Linking Soil Loss To Sediment Delivery In Two Estuaries In Puerto Rico, Nekesha Bernadette Williams

USF Tampa Graduate Theses and Dissertations

Enhanced soil loss from the watershed is a major environmental issue. Increased soil loss from a watershed can potentially increase sediment delivery and loading to aquatic ecosystems such as rivers and estuaries. An increase in sediment delivery and loading to freshwater and transitional marine ecosystems can impact water quality and supply specifically by: (1) reducing water clarity, (2) transporting nutrient and pollutant laden sediments and (3) reducing the storage capacity of reservoirs. To address these broader environmental impacts of increased sediment delivery and loading to aquatic ecosystems it is imperative that potential source areas of sediments available for transport are …

Exploring Evaluation In School Districts: School District Evaluators And Their Practice, Susan Hibbard

USF Tampa Graduate Theses and Dissertations

This study explored the evaluation practices of internal evaluators in public school districts in a large southern state. The individuals who conduct evaluations in school districts as internal evaluators were identified and background information was collected. The education and training in evaluation was investigated and the types of evaluations typically conducted by those individuals. Respondents (n = 134) revealed conducting evaluations was a secondary role and part of their main job responsibilities. The types of evaluations carried out and the way in which evaluation was practices were revealed. A descriptive framework of the individuals who conduct evaluations in school districts …

Optical Design Of Beam Shaping Optics For Camera Probe And Led Light Illumination Used For Minimally Invasive Abdominal Surgery, Weiyi He

USF Tampa Graduate Theses and Dissertations

The optical design of a LED illuminator and camera imaging system were studied for potential use in a small medical "robotic type" probe to be used for minimally invasive abdominal surgery. Beam shaping optical reflectors were studied to increase the intensity distribution of the LED beam directed toward a close-by target surface. A CMOS/CCD camera and lens was used to image the targeted area. In addition, extensive optical ray tracing simulations were made to predict the intensity patterns. The experimental measurements and ray tracing simulations were in good agreement, and indicated that 20 degree cone reflectors for the LED sources …

Topics In Random Knots And R-Matrices From Frobenius Algebras, Enver Karadayi

USF Tampa Graduate Theses and Dissertations

In this dissertation, we study two areas of interest in knot theory: Random knots in the unit cube, and the Yang-Baxter solutions constructed from Frobenius algebras.

The study of random knots can be thought of as a model of DNA strings situated in confinement. A random knot with n vertices is a polygonal loop formed by selecting n distinct points in the unit cube, for a positive integer n, and connecting these points by straight line segments successively, such that the last point selected is joined with the first one. We present a step by step description of our algorithm …

The Design And Synthesis Of Functionalized Porphyrins And Their Applications In Group Transfer Reactions, Medicine, And Materials, Kimberly Bliss Fields

USF Tampa Graduate Theses and Dissertations

Porphyrins and their analogs are a class of chemically and biologically important compounds that have found a variety of applications in different fields such as catalysis, medicine, and materials. The physical, chemical, and biological dependence of the peripheral substituents of porphyrins on their properties has prompted great effort towards the synthesis of new porphyrins with different electronic, steric, and conformational environments. To this end, porphyrins have been prepared using a modular approach from bromo- and triflate synthons. These synthons underwent palladium-catalyzed cross-coupling with chiral amines, amides, alcohols, and boronic esters to create products that were tested for biological activity.

Metalloporphyrins …

Synthesis Of Functionalized Resorcin[4]Arene Via Click Chemistry, Ali Husain

USF Tampa Graduate Theses and Dissertations

Click chemistry is a very powerful chemical strategy that overcome carbon-carbon bond with carbon-heteroatom bond by joining small units with heteroatom links (C-X-C) using spring-loaded reactants. The Cu(I)-catalyzed Huisgen 1,3-dipolar cycloaddition is a major example based on the click chemistry philosophy. This method was used for the last 10 years to join different functional groups, carbohydrates, aminoacids, polymers to calix[4]arene and resorcin[4]arene cavitands by a stable 1,2,3-triazole linkages.

Herein I describe our interest in this type of click chemistry reaction in the synthesis of dimeric capsules resorcin[4]arene via four 1,2,3-triazole linkages. Two different resorcin[4]arene derivatives were synthesized in which four …

Design And Combinatorial Synthesis Approach Of Non-Peptidic Trimeric Small Molecules Mimicking I, I + 4(3), I + 7 Positions Of Alpha-Helices, Mingzhou Zhou

USF Tampa Graduate Theses and Dissertations

Protein-protein interactions are key to several biological processes that facilitate signal transduction and many other processes. These interactions are involved in pathways that are critical to many human diseases. Targeting specific protein-protein interactions is a challenging goal because protein-protein interactions are predominately through hydrophobic interactions. Antagonists of the protein-protein interactions need to be perfectly fit into the binding pockets to ensure the activity. The -helical domain of the proteins behaves as the recognition motifs for numerous protein-protein, and protein-nucleic acid interactions. Research has shown that pathways of many diseases contain protein-protein interactions involving -helical domains, e.g. neurological disorders, bacterial infections, …

Applications Of Molecular Dynamics Techniques And Spectroscopic Theories To Aqueous Interfaces, Anthony Green

USF Tampa Graduate Theses and Dissertations

The primary goal of spectroscopy is to obtain molecularly detailed information about the system under study. Sum frequency generation (SFG) vibrational spectroscopy is a nonlinear optical technique that is highly interface specific, and is therefore a powerful tool for understanding interfacial structure and dynamics. SFG is a second order, electronically nonresonant, polarization experiment and is consequently dipole forbidden in isotropic media such as a bulk liquid. Interfaces, however, serve to break the symmetry and produce a signal. Theoretical approximations to vibrational spectra of O-H stretching at aqueous interfaces are constructed using time correlation function (TCF) and instantaneous normal mode (INM) …

Architecture And Compiler Support For Leakage Reduction Using Power Gating In Microprocessors, Soumyaroop Roy

USF Tampa Graduate Theses and Dissertations

Power gating is a technique commonly used for runtime leakage reduction in digital CMOS circuits. In microprocessors, power gating can be implemented by using sleep transistors to selectively deactivate circuit modules when they are idle during program execution. In this dissertation, a framework for power gating arithmetic functional units in embedded microprocessors with architecture and compiler support is proposed. During compile time, program regions are identified where one or more functional units are idle and sleep instructions are inserted into the code so that those units can be put to sleep during program execution. Subsequently, when their need is detected …

Design, Combinatorial Synthesis, And Biological Evaluation Of Novel Α-Helical Mimetics Based On Functionalized Piperazines As Antagonists Of P53/Mdm2 Interactions, Melissa Elizabeth Topper

USF Tampa Graduate Theses and Dissertations

The p53 protein promotes tumor eradication upon activation, making it an attractive target in cancer therapies. A reported 50% of all human cancers display aberrant activation of the MDM2 oncoprotein, which directly promotes tumorgenesis by inactivating the transcriptional activity of wild type p53, and is commonly associated with drug, chemo, and radio therapy resistance. Previously reported crystallographic analysis of the p53/MDM2 complex infers that the p53 protein forms a 2.5 turn amphipathic alpha helix whose hydrophobic face interacts within a deep hydrophobic cleft in the NH2-terminal domain of the globular MDM2. This suggests that the synthesis of small molecular antagonists …

Design Of A New Suturing And Knot Tying Device For Laparoscopic Surgery, Sinan Onal

USF Tampa Graduate Theses and Dissertations

Minimally invasive or laparoscopic surgery has completely changed the focus of surgery becoming an alternative to various types of open surgery. Minimally invasive surgery avoids invasive open surgery as the operation is performed through one or more small incisions in the abdomen and using a small camera called laparoscope. Through these incisions, surgeons insert specialized surgical instruments to perform the operation resulting in less postoperative pain, shorter hospital stay, and faster recovery. However, the main problems during minimally-invasive surgery are the limited space for operating instruments and the reduced visibility and range of motion inside the patient’s body. During minimally-invasive …

The Role Of Rater Motivation In Personnel Selection Validation Studies, Dan Ispas

USF Tampa Graduate Theses and Dissertations

Personnel selection validation studies are routinely conducted in contemporary organizations for selecting and placing employees. Although numerous studies have been conducted with the goal of identifying new predictors, less research was focused on the criterion side. In the current paper, across three studies and five samples, I examined the role played by rater motivation in validation studies. I proposed that rater motivation would impact criterion-related validity of various predictors, the reliability, and the variance of performance ratings. In Study 1, these hypotheses were tested in two samples with varied operationalizations of predictors and of rater motivation. In Study 2, I …

Variable-Density Flow Models Of Saltwater Intrusion In Coastal Landforms In Response To Climate Change Induced Sea Level Rise And A Chapter On Time-Frequency Analysis Of Ground Penetrating Radar Signals, Swagata Guha

USF Tampa Graduate Theses and Dissertations

Populations residing on and near the world’s coasts have become increasingly dependent on coastal groundwater for their supply of freshwater. Under the conditions of predicted climate changes, the expected rise in global sea level can adversely affect the quality and quantity of freshwater resources in coastal areas as a result of saltwater intrusion.

In this study, a suite of two- and three-dimensional variable-density groundwater flow models of major coastal landforms (e.g. deltas, estuaries and small islands) has been constructed to assess the effects of sea level rise (SLR), using different SLR rates of 0.5 m, 1m and 1.5 m over …

Structural Diversity In Crystal Chemistry: Rational Design Strategies Toward The Synthesis Of Functional Metal-Organic Materials, Amy J. Cairns

USF Tampa Graduate Theses and Dissertations

Metal-Organic Materials (MOMs) represent an important class of solid-state crystalline materials. Their countless attractive attributes make them uniquely suited to potentially resolve many present and future utilitarian societal challenges ranging from energy and the environment, all the way to include biology and medicine. Since the birth of coordination chemistry, the self-assembly of organic molecules with metal ions has produced a plethora of simple and complex architectures, many of which possess diverse pore and channel systems in a periodic array. In its infancy however this field was primarily fueled by burgeoning serendipitous discoveries, with no regard to a rational design approach …

Chemical Investigation Of The Antarctic Marine Invertebrates Synoicum Adareanum And Artemisina Plumosa, Jaime Heimbegner Noguez

USF Tampa Graduate Theses and Dissertations

Of the small percentage of organisms chemically investigated over the years as potential sources of natural products, much less is known about those from the marine realm. Despite the lack of attention they have received in comparison to terrestrial organisms, marine life have recently been found to represent a valuable source for novel bioactive compounds. Cold water marine habitats are home to a plethora of organisms that have the ability to produce secondary metabolites that exhibit a great deal of diversity in both their chemical structures and biological activities. The chemical investigation of these unique and relatively unstudied ecosystems is …

Statistical Learning And Behrens-Fisher Distribution Methods For Heteroscedastic Data In Microarray Analysis, Nabin K. Manandhr-Shrestha

USF Tampa Graduate Theses and Dissertations

The aim of the present study is to identify the di®erentially expressed genes be- tween two di®erent conditions and apply it in predicting the class of new samples using the microarray data. Microarray data analysis poses many challenges to the statis- ticians because of its high dimensionality and small sample size, dubbed as "small n large p problem". Microarray data has been extensively studied by many statisticians and geneticists. Generally, it is said to follow a normal distribution with equal vari- ances in two conditions, but it is not true in general. Since the number of replications is very small, …

Metal-Organic Materials: From Design Principles To Practical Applications, Mohamed H. Alkordi

USF Tampa Graduate Theses and Dissertations

The works presented herein outline rational design approaches towards construction of solid state materials with great potentials to answer some of current demanding applications. Specifically, the materials targeted are metal−organic materials with desirable structural features and functional properties. Metal−organic materials are constructed from organic linker molecules and metal ions under relatively mild solvothermal reaction conditions that preserve the structural features of the relatively simple building blocks. Therefore, it is feasible to conceive a retrospective pathway of the reaction and thus deconstruct the desirable structures into simple, chemicallyrelevant, building blocks in an approach known as the molecular building block approach. Due …

Magnetocaloric Effect In Thin Films And Heterostructures, Christopher Bauer

USF Tampa Graduate Theses and Dissertations

The goals of this work are the optimization of the magnetocaloric effect in Gadolinium thin film structures. We approach this issue from two directions, that of process optimization and of interface effects. Past results showed Gd₂O₃ in our Gadolinium thin films, and the presence of such oxide seemed to grow with the temperature at which the film was grown or annealed. Comparison of samples grown without chamber gettering to those that were gettered show differences in their structural and magnetic properties, and we conclude that gettering is an effective step in enhancing the quality of Gd thin …

Serum Antibodies To Human Papillomavirus Type 6, 11, 16 And 18 And Their Role In The Natural History Of Hpv Infection In Men, Beibei Lu

USF Tampa Graduate Theses and Dissertations

Our understanding of humoral immune response to human papillomavirus (HPV) infection has been mainly derived from studies in women. Very little is known about humoral immune response to HPV in men. There is also a growing interest in understanding the burden of HPV exposure in the subgroups of the male population, including men who have sex with women (MSW), men who have sex with men (MSM) and men who have sex with both men and women (MSMW). This dissertation was undertaken to understand and characterize humoral immune response, measured by detectable serum antibody IgG, to HPV 6, 11, 16 and …

Heat Stress Evaluation Of Protective Clothing Ensembles, Amanda Lee Pease

USF Tampa Graduate Theses and Dissertations

Clothing directly affects the level of heat stress exposure. Useful measures to express the thermal characteristics are WBGT (wet bulb globe temperature) clothing adjustment factor (CAF) or apparent total evaporative resistance (R_e,T,_a). The CAF is assigned through laboratory wear trials following a heat stress protocol in which the air temperature and humidity are progressively increased until the participant clearly loses the ability to maintain thermal equilibrium. The critical condition is the point of thermal transition and from these conditions both the CAF and Re,T,a are computed. The first objective of this study is to compare the …