Physical Sciences and Mathematics Commons^™

Time Dependent Kernel Density Estimation: A New Parameter Estimation Algorithm, Applications In Time Series Classification And Clustering, Xing Wang

USF Tampa Graduate Theses and Dissertations

The Time Dependent Kernel Density Estimation (TDKDE) developed by Harvey & Oryshchenko (2012) is a kernel density estimation adjusted by the Exponentially Weighted Moving Average (EWMA) weighting scheme. The Maximum Likelihood Estimation (MLE) procedure for estimating the parameters proposed by Harvey & Oryshchenko (2012) is easy to apply but has two inherent problems. In this study, we evaluate the performances of the probability density estimation in terms of the uniformity of Probability Integral Transforms (PITs) on various kernel functions combined with different preset numbers. Furthermore, we develop a new estimation algorithm which can be conducted using Artificial Neural Networks to …

The Infinity(X)-Equation In Grushin-Type Spaces, Thomas Bieske

Mathematics and Statistics Faculty Publications

We employ Grushin jets which are adapted to the geometry of Grushin-type spaces to obtain the existence-uniqueness of viscosity solutions to the infinity(x)-Laplace equation in Grushin-type spaces. Due to the differences between Euclidean jets and Grushin jets, the Euclidean method of proof is not valid in this environment.

Gamma Aapeptides As Host Defense Peptide Mimics, Yaqiong Li

USF Tampa Graduate Theses and Dissertations

There has been increasing concern regarding the emergence of multi-drug resistant pathogens. The resistance develops when pathogens, especially bacteria, are frequently exposed to conventional antibiotics, as they are heavily used in both human and livestock. This is due to the high target specificity of conventional antibiotics, which places pathogens in high selective pressures and eventually results in drug resistant by mutations. To address this issue, global actions and cooperation are needed. At the same time, new technologies and strategies need to be developed. Host defense peptides (HDPs) are widely found in the innate immune system. They show both direct antimicrobial …

Search For An Artificially Buried Karst Cave Entrance Using Ground Penetrating Radar: A Successful Case Of Locating The S-19 Cave In The Mt. Kanin Massif (Nw Slovenia), Andrej Gosar, Teja Čeru

International Journal of Speleology

The S-19 Cave was with its explored depth of 177 m one of the most important caves of the Mt. Kanin massif, but after its discovery in 1974, a huge snow avalanche protection dyke was constructed across the cave entrance. To excavate the buried cave, the accurate location of the cave had to be determined first. Since the entrance coordinates were incorrect and no markers were available, application of geophysical techniques was necessary to do this. A Ground Penetrating Radar (GPR) with special 50 MHz rough terrain antennas was selected as the single suitable geophysical method for the given conditions …

Age Re-Assessment Of The Cave Bear Assemblage From Urşilor Cave, North-Western Romania, Marius V. Robu

International Journal of Speleology

The most common methods used for assessing the relative age of a cave bear bone assemblage are the P⁴/₄ index (morphodynamic index of the cave bear fourth premolar), the K-index and the Index of Plumpness (both used for cave bear’s 2^nd metatarsal). Preliminary work on this (Robu et al., 2011), for Urşilor Cave (NW Romania), has indicated one of the youngest European cave bear populations. As the number of extracted fossil bones from the palaeontological excavation increased recently, a re-assessment of the of the age of the cave bear assemblage is necessary. 206 cave bear fourth …

Molecular Mechanism Of Protein Kinase Recognition And Sorting By The Hsp90 Kinome-Specific Cochaperone Cdc37, Dimitra Keramisanou, Adam Aboalroub, Ziming Zhang, Wenjun Liu, Devon Marshall, Andrea Diviney, Randy W. Larsen, Ralf Landgraf, Ioannis Gelis

Chemistry Faculty Publications

Despite the essential functions of Hsp90, little is known about the mechanism that controls substrate entry into its chaperone cycle. We show that the role of Cdc37 cochaperone reaches beyond that of an adaptor protein and find that it participates in the selective recruitment of only client kinases. Cdc37 recognizes kinase specificity determinants in both clients and nonclients and acts as a general kinase scanning factor. Kinase sorting within the client-to-nonclient continuum relies on the ability of Cdc37 to challenge the conformational stability of clients by locally unfolding them. This metastable conformational state has high affinity for Cdc37 and forms …

Agonist-Mediated Activation Of Sting Induces Apoptosis In Malignant B Cells, Chih-Hang Anthony Tang, Joseph A. Zundell, Sujeewa Ranatunga, Cindy Lin, Yulia Nefedova, Juan R. Del Valle, Chih-Chi Andrew Hu

Chemistry Faculty Publications

Endoplasmic reticulum (ER) stress responses through the IRE-1/XBP-1 pathway are required for the function of STING (TMEM173), an ER-resident transmembrane protein critical for cytoplasmic DNA sensing, IFN production, and cancer control. Here we show that the IRE-1/XBP-1 pathway functions downstream of STING and that STING agonists selectively trigger mitochondria-mediated apoptosis in normal and malignant B cells. Upon stimulation, STING was degraded less efficiently in B cells, implying that prolonged activation of STING can lead to apoptosis. Transient activation of the IRE-1/XBP-1 pathway partially protected agonist-stimulated malignant B cells from undergoing apoptosis. In Eμ-TCL1 mice with chronic lymphocytic leukemia, injection of …

Morphodynamics Of Egmont Key At The Mouth Of Tampa Bay: West-Central Florida, Zachary James Tyler

USF Tampa Graduate Theses and Dissertations

Egmont Key, located at the mouth of Tampa Bay, is part of a dynamic system with many interrelated natural and anthropogenic factors influencing its morphodynamics. This study started in August 2012. During the 3-year period until August 2015, 28 beach profile transects were established and surveyed 10 times. Seventeen historical aerial images from 1942 to 2013 were geo-rectified and analyzed. Three hundred and fourteen sediment samples were procured from the navigation channel dredge area and the beach nourishment area and analyzed for grain size. A numerical wave model was established to simulate the nearshore wave field. The overall goals of …

Renewable Energy Investment Planning And Policy Design, Alireza Ghalebani

USF Tampa Graduate Theses and Dissertations

In this dissertation, we leverage predictive and prescriptive analytics to develop decision support systems to promote the use of renewable energy in society. Since electricity from renewable energy sources is still relatively expensive, there are variety of financial incentive programs available in different regions. Our research focuses on financial incentive programs and tackles two main problem: 1) how to optimally design and control hybrid renewable energy systems for residential and commercial buildings given the capacity based and performance based incentives, and 2) how to develop a model-based system for policy makers for designing optimal financial incentive programs to promote investment …

Chiral Boro-Phosphates In Asymmetric Catalysis: 1,4-Reduction Of Enones And Reductive Aldol, Susana Sorina Lopez

USF Tampa Graduate Theses and Dissertations

The biological activity of the pharmaceutical drugs often depends on how it fits with a receptor making stereochemistry a key component. Selective reactions can limit or avoid the mixture of enantiomers obtained. One such reaction is the selective reduction of a carbon-carbon double bond in the presence of a carbonyl. Although efficient, current asymmetric synthesis methods have limitations such as harsh reaction conditions, the high costs of chiral catalysts and the toxicity of the metal-based catalysts. Catalysts derived from small organic molecules have become an attractive alternative which have been explored more rigorously in recent years. Using a BINOL-derived boro-phosphate …

The Role Of Social Ties In Dynamic Networks, Xiang Zuo

USF Tampa Graduate Theses and Dissertations

Social networks are everywhere, from face-to-face activities to online social networks such as Flickr, YouTube and Facebook. In social networks, ties (relationships) are connections between people. The change of social relationships over time consequently leads to the evolution of the social network structure. At the same time, ties serve as carriers to transfer pieces of information from one person to another.

Studying social ties is critical to understanding the fundamental processes behind the network. Although many studies on social networks have been carried out over the last many decades, most of the work either used small in-lab datasets, or focused …

Design Exploration And Application Of Reversible Circuits In Emerging Technologies, Saurabh Kotiyal

USF Tampa Graduate Theses and Dissertations

The reversible logic has promising applications in emerging computing paradigms, such as quantum computing, quantum dot cellular automata, optical computing, etc. In reversible logic gates, there is a unique one-to-one mapping between the inputs and outputs. To generate a useful gate function, the reversible gates require some constant ancillary inputs called ancilla inputs. Also to maintain the reversibility of the circuits some additional unused outputs are required that are referred to as the garbage outputs. The number of ancilla inputs, the number of garbage outputs and quantum cost plays an important role in the evaluation of reversible circuits. Thus minimizing …

The Use Of Synthetic Mixture Based Libraries To Identify Hit Compounds For Eskape Pathogens, Leishmaniasis, And Inhibitors Of Palmitoylation, Marcello Giulianotti

USF Tampa Graduate Theses and Dissertations

The goal of this work is to demonstrate the utility of using systematically formatted mixture based libraries as part of the drug discovery processes. While there are a number of different valid approaches for identifying hit and tool compounds, systematically formatted mixture based libraries, such as those described in this study, offer the ability to develop a significant amount of structure activity relationship data from the testing of very few samples. In support of this claim a review of recent developments in the area of systematically formatted mixture based libraries as well as three case studies are presented. The three …

Co(Ii)-Based Metalloradical Catalysis For Asymmetric Radical Cyclopropanation, Qigan Cheng

USF Tampa Graduate Theses and Dissertations

Metal-catalyzed cyclopropanation of olefins with diazo reagents is one of the most general and efficient method to prepare cyclopropanes. The resulting cyclopropyl units are found as a basic structural element in a wide range of naturally occurring compounds and biologically active compounds, and can serve as versatile synthetic intermediates in the synthesis of multifunctionalized cycloalkanes and acyclic compounds. Since Co(II) complexes of D₂-symmetric chiral amidoporphyrins [Co(D₂-Por*)] were first introduced in 2004, Co(II)-metalloradical catalysis (MRC) have emerged as a new platform for asymmetric cyclopropanation. These metalloradical catalysts have been shown to be highly effective for asymmetric intermolecular …

Evaluation Of Pulmonary Function Among Workers Engaged In The Manufacture Of Hydraulic Fracking Ceramic Proppant, Humairat H. Rahman

USF Tampa Graduate Theses and Dissertations

Workers involved in hydraulic fracking processes are exposed to various types of chemicals and dusts in their workplaces, such as proppants, which hold open the fissures created in the fracking process. Recently, ceramic proppants have been developed that may be less hazardous to workers than traditional proppants. Pulmonary function testing of workers producing ceramic proppant was used to assess the potential inhalation hazards of ceramic proppant. Male workers (n = 100) from a producer of ceramic proppant were evaluated with pulmonary function test data collected and evaluated using The American Thoracic Society (ATS) acceptability criteria. A comparison group was selected …

Human Health Risk Characterization Of Petroleum Coke Calcining Facility Emissions, Davinderjit Singh

USF Tampa Graduate Theses and Dissertations

Calcined coke is a high quality carbon material produced by calcining green petroleum coke. Calcining is the process of heating green petroleum coke in a kiln to remove excess moisture, extract all remaining hydrocarbons, and modify the crystalline structure of the coke into a denser, electrically conductive product. The final product, calcined coke, is primarily used to make carbon anodes for the aluminum industry and recarburizing agent for industries such as the steel industry. If not appropriately controlled, the calcining process could lead to excess production of particulate emissions from either handling or storing of raw coke, or from the …

A Statistical Analysis Of Hurricanes In The Atlantic Basin And Sinkholes In Florida, Joy Marie D'Andrea

USF Tampa Graduate Theses and Dissertations

Beaches can provide a natural barrier between the ocean and inland communities, ecosystems, and resources. These environments can move and change in response to winds, waves, and currents. When a hurricane occurs, these changes can be rather large and possibly catastrophic. The high waves and storm surge act together to erode beaches and inundate low-lying lands, putting inland communities at risk. There are thousands of buoys in the Atlantic Basin that record and update data to help predict climate conditions in the state of Florida. The data that was compiled and used into a larger data set came from two …

Costumbres, Creencias, Y “Lo Normal”: A Biocultural Study On Changing Prenatal Dietary Practices In A Rural Tourism Community In Costa Rica, Allison Rachel Cantor

USF Tampa Graduate Theses and Dissertations

This study explores the relationship between tourism, the nutrition transition, and prenatal dietary practices in the Monteverde Zone, Costa Rica. This rural tourism community, located in the central highlands of Costa Rica, has seen rapid growth and development since the tourism boom in the early 1990s, leading to changes in the local food system and increased food insecurity. This investigation added to this work by identifying the ways that prenatal dietary practices have shifted over time in the context of increased tourism and the concomitant nutrition transition, and by describing the relationship between food insecurity and nutritional status among pregnant …

A Quantified Model Of Security Policies, With An Application For Injection-Attack Prevention, Donald James Ray

USF Tampa Graduate Theses and Dissertations

This dissertation generalizes traditional models of security policies, from specifications of whether programs are secure, to specifications of how secure programs are. This is a generalization from qualitative, black-and-white policies to quantitative, gray policies. Included are generalizations from traditional definitions of safety and liveness policies to definitions of gray-safety and gray-liveness policies. These generalizations preserve key properties of safety and liveness, including that the intersection of safety and liveness is a unique allow-all policy and that every policy can be written as the conjunction of a single safety and a single liveness policy. It is argued that the generalization provides …

Subsidence Along The Atlantic Coast Of North America: Insights From Gps And Late Holocene Relative Sea Level Data, Makan A. Karegar, Timothy H. Dixon, Simon E. Engelhart

School of Geosciences Faculty and Staff Publications

The Atlantic Coast of North America is increasingly affected by flooding associated with tropical and extratropical storms, exacerbated by the combined effects of accelerated sea‐level rise and land subsidence. The region includes the collapsing forebulge of the Laurentide Ice Sheet. High‐quality records of late Holocene relative sea‐level (RSL) rise are now available, allowing separation of long‐term glacial isostatic adjustment‐induced displacement from modern vertical displacement measured by GPS. We compare geological records of late Holocene RSL to present‐day vertical rates from GPS. For many coastal areas there is no significant difference between these independent data. Exceptions occur in areas of recent …

Hercules And Diana Hypogene Caves (Herculane Spa, Romania): Dissimilar Chemical Evolutions Documented By Their Present-Day Thermal Water Discharges, Horia Mitrofan, Constantin Marin, Ioan Povară, Bogdan P. Onac

School of Geosciences Faculty and Staff Publications

Hercules Cave and Diana Cave are two small caves situated some 600 m apart, for which a hypogene origin has been previously suggested. Thermal water discharges (up to about 54°C) are hosted by each cave, and were recently made the object of an eight-month chemical monitoring operation. By plotting the concentrations of several chemical species (Na, K, Ca, Sr, Mg, SiO2, Br) against the concentration of the conservative anion Cl, it was found that both caves discharged a binary water mixture, which was derived from the same saline (and hot) parent-fluid and the same fresh (and cold) parent-fluid. This fact …

Removal Of Six Estrogenic Endocrine-Disrupting Compounds (Edcs) From Municipal Wastewater Using Aluminum Electrocoagulation, Monica M. Cook, Erin M. Symonds, Bert Gerber, Armando Hoare, Edward S. Van Vleet, Mya Breitbart

Marine Science Faculty Publications

Conventional wastewater treatment plant (WWTP) processes are primarily designed to reduce the amount of organic matter, pathogens, and nutrients from the incoming influent. However, these processes are not as effective in reducing the concentrations of micropollutants, including endocrine-disrupting compounds (EDCs), which notoriously evade traditional wastewater treatment technologies and are found even in tertiary-treated effluent. For WWTPs practicing deep-well injection or surface-water discharge, EDCs in the treated effluent are discharged into groundwater or the aquatic environment where humans and wildlife may potentially suffer the effects of chemical exposure. In the current laboratory-scale study, we tested a bench-top electrocoagulation (EC) unit utilizing …

Quandle Coloring And Cocycle Invariants Of Composite Knots And Abelian Extensions, W Edwin Clark, Masahico Saito, Leandro Vendramin

Mathematics and Statistics Faculty Publications

Quandle colorings and cocycle invariants are studied for composite knots, and applied to chirality and abelian extensions. The square and granny knots, for example, can be distinguished by quandle colorings, so that a trefoil and its mirror can be distinguished by quandle coloring of composite knots. We investigate this and related phenomena. Quandle cocycle invariants are studied in relation to quandle coloring of the connected sum, and formulas are given for computing the cocycle invariant from the number of colorings of composite knots. Relations to corresponding abelian extensions of quandles are studied, and extensions are examined for the table of …

Polyglutamine Aggregates Impair Lipid Membrane Integrity And Enhance Lipid Membrane Rigidity, Chian Sing Ho, Nawal K. Khadka, Fengyu She, Jianfeng Cai, Jianjun Pan

Physics Faculty Publications

Lipid membranes are suggested as the primary target of amyloid aggregates. We study aggregates formed by a polyglutamine (polyQ) peptide, and their disruptive effect on lipid membranes. Using solution atomic force microscopy (AFM), we observe polyQ oligomers coexisting with short fibrils, which have a twisted morphology that likely corresponds to two intertwined oligomer strings. Fourier transform infrared spectroscopy reveals that the content of β-sheet enriched aggregates increases with incubation time. Using fluorescence microscopy, we find that exposure to polyQ aggregates results in deflated morphology of giant unilamellar vesicles. PolyQ aggregates induced membrane disruption is further substantiated by time-dependent calcein leakage …

Pastoralists' Perception On The Trend Of Various Climatic, Social And Environmental Variables In Baringo County, Kenya, Geoffrey L. Lelenguyah, Samuel K. Kabochi, John C. Biwot

Journal of Ecological Anthropology

As global temperatures increase, more intense rainfall and more frequent droughts will have devastating effects on pastoral livelihoods. The aim of this study was to investigate pastoralists' perceptions on the impacts of climate variability on their livelihoods from 1971 to 2010. This study utilized household structured questionnaires. Statistical tests included t-test and Chi-square test (χ²). Statistically significant differences between the responses in strata 1 and 2 on the perceived trend of rainfall and floods towards the future were noted. This study recommends the strengthening of local institutions to be able to deal with impacts of climate variability and …

Mechanistic Binding Insights For 1-Deoxy-D-Xylulose-5-Phosphatesynthase, The Enzyme Catalyzing The First Reaction Of Isoprenoid Biosynthesis In The Malaria-Causing Protists, Plasmodium Falciparum And Plasmodium Vivax, Matthew R. Battistini, Christopher Shoji, Sumit Handa, Leonid Breydo, David J. Merkler

Chemistry Faculty Publications

We have successfully truncated and recombinantly-expressed 1-deoxy-D-xylulose-5-phosphate synthase (DXS) from both Plasmodium vivax and Plasmodium falciparum. We elucidated the order of substrate binding for both of these ThDP-dependent enzymes using steady-state kinetic analyses, dead-end inhibition, and intrinsic tryptophan fluorescence titrations. Both enzymes adhere to a random sequential mechanism with respect to binding of both substrates: pyruvate and D-glyceraldehyde-3-phosphate. These findings are in contrast to other ThDP-dependent enzymes, which exhibit classical ordered and/or ping-pong kinetic mechanisms. A better understanding of the kinetic mechanism for these two Plasmodial enzymes could aid in the development of novel DXS-specific inhibitors that might prove useful …

The Household Water Management System In The Village Of Falifah, Gambia: A Case Study In Sustainable Local Development, Baboucar Jobe

USF Tampa Graduate Theses and Dissertations

Access to safe and clean water is a problem in many countries in the world, especially sub-Saharan Africa. The urgency of the was recognized by the United Nations through its 2008 Millennium Development Goals, which were recently replaced by the new Sustainable Development Goals. Lack or poor access to clean water not only creates conflicts and rifts among the people, but also makes them more susceptible to a wide assortment of water borne diseases.

The purpose of this dissertation is to complete a pilot study of ways of thinking and actions of a small group of people from Falifah, a …

Structure-Interaction Effects In Novel Nanostructured Materials, Nam B. Le

USF Tampa Graduate Theses and Dissertations

Recent advances in experimental and computational methods have opened up new directions in graphene fundamental studies. In addition to understanding the basic properties of this material and its quasi-one dimensional structures, significant efforts are devoted to describing their long ranged dispersive interactions. Other two-dimensional materials, such as silicene, germanene, and transition metal dichalcogenides, are also being investigated aiming at finding complementary to graphene systems with other "wonder" properties. The focus of this work is to utilize first principles simulations methods to build our basic knowledge of structure-interaction relations in two-dimensional materials and design their properties. In particular, mechanical folding and …

A New Volcanic Event Recurrence Rate Model And Code For Estimating Uncertainty In Recurrence Rate And Volume Flux Through Time With Selected Examples, James Adams Wilson

USF Tampa Graduate Theses and Dissertations

Recurrence rate is often used to describe volcanic activity. There are numerous documented ex- amples of non-constant recurrence rate (e.g. Dohrenwend et al., 1984; Condit and Connor, 1996; Cronin et al., 2001; Bebbington and Cronin, 2011; Bevilacqua, 2015), but current techniques for calculating recurrence rate are unable to fully account for temporal changes in recurrence rate. A local–window recurrence rate model, which allows for non-constant recurrence rate, is used to calculate recurrence rate from an age model consisting of estimated ages of volcanic eruption from a Monte Carlo simulation. The Monte Carlo age assignment algorithm utilizes paleomagnetic and stratigraphic information …

Increasing 18f-Fdg Pet/Ct Capabilities In Radiotherapy For Lung And Esophageal Cancer Via Image Feature Analysis, Jasmine Alexandria Oliver

USF Tampa Graduate Theses and Dissertations

Positron Emission Tomography (PET) is an imaging modality that has become increasingly beneficial in Radiotherapy by improving treatment planning (1). PET reveals tumor volumes that are not well visualized on computed tomography CT or MRI, recognizes metastatic disease, and assesses radiotherapy treatment (1). It also reveals areas of the tumor that are more radiosensitive allowing for dose painting - a non-homogenous dose treatment across the tumor (1). However, PET is not without limitations. The quantitative unit of PET images, the Standardized Uptake Value (SUV), is affected by many factors such as reconstruction algorithm, patient weight, and tracer uptake time (2). …