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An Investigation Into The Antifungal Activities Of N-Thiolated Beta- Lactams Against Selected Candida Species, Marci Culbreath

USF Tampa Graduate Theses and Dissertations

β-lactam antibiotics have long been a reliable course of treatment for bacterial infections. However, with recent increases in resistance and rising populations of immunocompromised patients new β-lactams have been synthesized and tested. The Turos laboratory has recently discovered novel β-lactams that have a mode of action distinct from penicillin and other β-lactam antibiotics as cell lysis is not observed. In the current investigations, these compounds are shown to also have antifungal properties. The rising incidence and prevalence of invasive fungal infections has become an increasing concern. The most common fungal pathogens involved in these infections are species in the genus …

Penalized Splines For Longitudinal Data With An Application In Aids Studies, Hua Liang, Yuanhui Xiao

Journal of Modern Applied Statistical Methods

A penalized spline approximation is proposed in considering nonparametric regression for longitudinal data. Standard linear mixed-effects modeling can be applied for the estimation. It is relatively simple, efficiently computed, and robust to the smooth parameters selection, which are often encountered when local polynomial and smoothing spline techniques are used to analyze longitudinal data set. The method is extended to time-varying coefficient mixed-effects models. The proposed methods are applied to data from an AIDS clinical study. Biological interpretations and clinical implications are discussed. Simulation studies are done to illustrate the proposed methods.

Jmasm23: Cluster Analysis In Epidemiological Data (Matlab), Andrés M. Alonso

Journal of Modern Applied Statistical Methods

Matlab functions for testing the existence of time, space and time-space clusters of disease occurrences are presented. The classical scan test, the Ederer, Myers and Mantel’s test, the Ohno, Aoki and Aoki’s test, and the Knox’s test are considered.

Dynamics Of A Two Serotype Disease With Antibody Dependent Enhancement, Amy Fiorillo

Theses, Dissertations and Culminating Projects

The dengue virus is a serious infectious disease that can be found in many regions of Southeast Asia. There exist four serotypes of the virus. Recovery from one serotype produces a natural immunity from that serotype. However, it also creates complexes with a second infection and will increase viral production. This process is know as antibody dependent enhancement (ADE). As a result, it is very difficult to vaccinate against the disease. An optimal vaccination would have to cover all four serotypes at once. To understand the dynamics of the disease, we will study a mathematical model for two coexisting serotypes …

Variance Estimation And Construction Of Confidence Intervals For Gee Estimator, Shenghai Zhang, Mary E. Thompson

Journal of Modern Applied Statistical Methods

The sandwich estimator, also known as the robust covariance matrix estimator, has achieved increasing use in the statistical literature as well as with the growing popularity of generalized estimating equations (GEE). A modified sandwich variance estimator is proposed, and its consistency and efficiency are studied. It is compared with other variance estimators, such as a model based estimator, the sandwich estimator and a corrected sandwich estimator. Confidence intervals for regression parameters based on these estimators are discussed. Simulation studies using clustered data to compare the performance of variance estimators are reported.

Super Learning: An Application To Prediction Of Hiv-1 Drug Susceptibility, Sandra E. Sinisi, Maya L. Petersen, Mark J. Van Der Laan

U.C. Berkeley Division of Biostatistics Working Paper Series

Many statistical methods exist that can be used to learn a predictor based on observed data. Examples include decision trees, neural networks, support vector regression, least angle regression, Logic Regression, and the Deletion/Substitution/Addition algorithm. The optimal algorithm for prediction will vary depending on the underlying data-generating distribution. In this article, we introduce a "super learner," a prediction algorithm that applies any set of candidate learners and uses cross-validation to select among them. Theory shows that asymptotically the super learner performs essentially as well or better than any of the candidate learners. We briefly present the theory behind the super learner, …

The Two-Sample Problem For Failure Rates Depending On A Continuous Mark: An Application To Vaccine Efficacy, Peter B. Gilbert, Ian W. Mckeague, Yanqing Sun

UW Biostatistics Working Paper Series

The efficacy of an HIV vaccine to prevent infection is likely to depend on the genetic variation of the exposing virus. This paper addresses the problem of using data on the HIV sequences that infect vaccine efficacy trial participants to 1) test for vaccine efficacy more powerfully than procedures that ignore the sequence data; and 2) evaluate the dependence of vaccine efficacy on the divergence of infecting HIV strains from the HIV strain that is contained in the vaccine. Because hundreds of amino acid sites in each HIV genome are sequenced, it is natural to treat the divergence (defined in …

Genome Scanning Methods For Comparing Sequences Between Groups, With Application To Hiv Vaccine Trials, Peter B. Gilbert, Chunyuan Wu, David V. Jobes

UW Biostatistics Working Paper Series

Consider a placebo-controlled preventive HIV vaccine efficacy trial. An HIV amino acid sequence is measured from each volunteer who acquires HIV, and these sequences are aligned together with the reference HIV sequence represented in the vaccine. We develop genome scanning methods to identify HIV positions at which the amino acids in sequences from infected vaccine recipients tend to be more divergent from the corresponding reference amino acid than the amino acids in sequences from infected placebo recipients. We consider five two-sample test statistics, based on Euclidean, Mahalanobis, and Kullback-Leibler divergence measures. Weights are incorporated to reflect biological information contained in …

Is This Safe To Eat?

United States Department of Agriculture Wildlife Services: Staff Publications

The harvest and consumption of wildlife is as old as humankind and often has sustained human exploration into unsettled areas. Wildlife still remain a primary foodbase for many native peoples throughout the world. From shellfish to bear, humans today continue to hunt, fish, and otherwise harvest wildlife for recreation, social and cultural needs, dietary supplementation, subsistence, and other purposes that result in the consumption of game meat (Fig. 5.1).

Over time, experience has taught people what food is safe to eat and how it should be prepared. This is especially true for those who subsist upon wildlife. Fortunately, the meat …

Comparative Analysis Of Biosurveillance Methodologies, David M. Kempisty

Theses and Dissertations

The purpose of this research is to compare two different biosurveillance methodologies: BioWatch and "A Hot Idea". BioWatch is fielded and operating in major US cities today. Air samples are collected on filter paper and analyzed for the presence of harmful biological agents. "A Hot Idea" is an evolving methodology using the human body's immune response to identify the onset of infection from a harmful pathogen. Detecting a temperature increase, using infrared thermographers, in a statistically significant portion of population would allow earlier identification of a biological release, accelerating initiation of response actions. A selected population including policemen, firemen, and …

Kinetic And Spectroscopic Characterization Of The E134a- And E134d-Altered Dape-Encoded N-Succinyl-L,L-Diaminopimelic Acid Desuccinylase From Haemophilus Influenzae, Ryan S. Davis, David L. Bienvenue, Sabina I. Swierczek, Danuta M. Gilner, Lakshman Rajagopal, Brian Bennett, Richard C. Holz

Physics Faculty Research and Publications

Glutamate-134 (E134) is proposed to act as the general acid/base during the hydrolysis reaction catalyzed by the dapE-encoded N-succinyl-l,l-diaminopimelic acid desuccinylase (DapE) from Haemophilus influenzae. To date, no direct evidence has been reported for the role of E134 during catalytic turnover by DapE. In order to elucidate the catalytic role of E134, altered DapE enzymes were prepared in which E134 was substituted with an alanine and an aspartate residue. The Michaelis constant (K _m) does not change upon substitution with aspartate but the rate of the reaction changes drastically in the following order: glutamate (100% …

Vaccines Against Sexually Transmitted Diseases, Lynette B. Corbeil, Carlos M. Campero, Jack C. Rhyan, Robert H. Bondurant

United States Department of Agriculture Wildlife Services: Staff Publications

Human sexually transmitted infections are prevalent throughout the world. Several have been associated with adverse pregnancy outcome and increased susceptibility to HIV infection, in addition to the discomfort of inflammation of the genital tract. Yet vaccines to protect against the infection at the genital mucosa are not available. Hepatitis B is an exception, but this virus becomes systemic and protection may be at the systemic level. Sexually transmitted diseases (STDs) have long been associated with reproductive failure in cattle. These infections cause considerable economic loss, which has been a stimulus to investigation. Consequently, vaccines and mechanisms of immune protection have …

Use Of Infrared Thermography To Detect Signs Of Rabies Infection In Raccoons (Procyon Lotor), Mike R. Dunbar, Kathleen A. Maccarthy B.S.

United States Department of Agriculture Wildlife Services: Staff Publications

Infrared thermography was evaluated as a technique to determine if raccoons (Procyon lotor) experimentally infected with rabies virus could be differentiated from non-infected raccoons. Following a 10-day adjustment period, raccoons (n = 6) were infected with a virulent rabies street strain raccoon variant by injection into the masseter muscle at a dose of 2 x 10⁴ tissue-culture infectious dose (TCID₅₀) in 0.2 ml (n = 4) or 10⁵ TCID₅₀ in 1 ml (n = 2). Five of the six raccoons developed prodromal signs of rabies 17 to 22 days post-inoculation …

Feral Pigs In Queensland - Distribution, Ecology And Impact

Other Publications in Wildlife Management

Domestic pigs (Sus scrofa) were introduced to Australia by early settlers. Subsequent accidental and deliberate releases resulted in the wild (feral) population establishing throughout Australia. Feral pigs damage crops, stock and property, spread weeds and transmit diseases such as Leptospirosis and Foot and Mouth. They also cause environmental damage, digging up large areas of native vegetation and spreading weeds.

Feral pigs are declared Class 2 pests under Land Protection (Pest and Stock Route Management) Act 2002. Declaration requires landholders to control declared pest on the land under their control. A local government may serve a notice …

Prevalence And Serovars Of Salmonella In The Feces Of Free-Ranging White-Tailed Deer (Odocoileus Virginianus) In Nebraska, David G. Renter, David P. Gnad, Jan M. Sargeant, Scott E. Hygnstrom

School of Natural Resources: Faculty Publications

To determine the prevalence and serovars of Salmonella in free-ranging deer, we cultured feces from white-tailed deer (Odocoileus virginianus) harvested by hunters during a regular firearm season in southeastern Nebraska (USA). We recovered Salmonella from 5 (1%; 95% confidence interval: 0.37– 2.20%) of 500 samples and identified four different Salmonella enterica serovars [Litchfield (1), Dessau (1), Infantis (2), and Enteritidis (1)]. Although the prevalence of Salmonella in free-ranging deer appears to be low, the serovars recovered are known to be pathogenic to humans and animals.

On Modeling Hiv Infection Of Cd4+ T Cells, Amy Comerford

Electronic Theses and Dissertations

We examine an early model for the interaction of HIV with CD4+ T cells in vivo and define possible parameters and effects of said parameters on the model. We then examine a newer, more simplified model for the interaction of HIV with CD4+ T cells that also considers four populations: uninfected T cells, latently infected T cells, actively infected T cells, and free virus. The stability of both the disease free steady state and the endemically infected steady state are examined utilizing standard methods and the Routh-Hurwitz criteria. We show that if N, the number of infectious virions produced per …

The H5n1 Avian Influenza Virus: Globalization, Climate Change, And Other Anthropogenic Factors In New Emergent Diseases, Quan Luong

Student Theses 2001-2013

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Differential Expression Of Immune Response Genes In Steller Sea Lions (Eumetopias Jubatus): An Indicator Of Ecosystem Health?, Lizabeth Bowen, Brian Aldridge, Kimberlee Beckmen, Tom Gelatt, Lorrie Rea, Kathy Burek, Ken Pitcher, Jeffrey L. Stott

United States Department of Commerce: Staff Publications

Characterization of the polygenic and polymorphic features of the Steller sea lion major histocompatibility complex (MHC) provides an ideal window for evaluating immunologic vigor of the population and identifying emergence of new genotypes that reflect ecosystem pressures. MHC genotyping can be used to measure the potential immunologic vigor of a population. However, since ecosystem-induced changes to MHC genotype can be slow to emerge, measurement of differential expression of these genes can potentially provide real-time evidence of immunologic perturbations. MHC DRB genes were cloned and sequenced using peripheral blood mononuclear leukocytes derived from 10 Steller sea lions from southeast Alaska, Prince …

Proceedings Of The 118th Annual Meeting Of The Iowa Academy Of Science [Program, 2006], Iowa Academy Of Science

Iowa Academy of Science Documents

Contents:

Iowa Academy of Science Mission --- 1
Schedule --- 2
Business Meeting Agenda --- 3
General Sessions --- 4
Symposia --- 7
2006 IAS Awards --- 8
Senior Poster Session Overview --- 10
Section Meeting Schedules and Oral Presentations --- 12
Field Trips --- 15
Campus Map --- 17
Notes --- 18
Abstracts --- 19
Author Index --- 39

Synthesis Of 2-Oxo-16-(3', 4'-Methylenedioxyphenyl)-Trans-15-Hexadecene, Adelajda Zorba

Honors Theses

This work presents the progress made towards synthesizing 2-oxo-16-(3', 4'methylenedioxyphenyl)-trans-15-hexadecene, an antimycobacterial compound that was originally isolated from the leaves of Piper Sanctum. The hydrocarbon chain of the molecule was synthesized first by opening a 15-pentadecanolactone ring by means of HI, and performing an E2 elimination reaction on the molecule followed by an organolithium reaction with CH3Li. Hexadec-15-en-2-one that was afforded this way was later reacted with 5-bromobenzo[d][1,3]dioxole following the appropriate Heck reaction protocol that allows for the formation of a palladium catalyzed carbon-carbon bond.

The modes of action of 2-oxo-16-(3', 4'-methylenedioxyphenyl)-trans-15hexadecene are comparable to the ones of rifampicin, a …

Computational Sciences: At The Intersection Of Science And Engineering--Case Study For Academic And Research Programs, Menas Kafatos, Peter Becker, Zafer Boybeyi̇

Turkish Journal of Electrical Engineering and Computer Sciences

No abstract provided.

Introduction To N-Adaptive Fuzzy Models To Analyze Public Opinion On Aids, Florentin Smarandache, W.B. Vasantha Kandasamy

Branch Mathematics and Statistics Faculty and Staff Publications

“AIDS is not simply a physical malady, it is also an artifact of social and sexual transgression, violated taboo, fractured identity—political and personal projections. Its key words are primarily the property of the powerful. AIDS: Keywords – is my attempt to identify and contest some of the assumptions underlying our current ‘knowledge’. In this effort I am joined by many AIDS activists including people living with AIDS— Acquired Immuno Deficiency Syndrome. “A syndrome is a pattern of symptoms pointing to a “morbid state” which may or may not be caused by infectious agents; a disease, on the other hand is, …

Mathematical Modeling Of Smallpox Withoptimal Intervention Policy, Niwas Lawot

Electronic Theses and Dissertations

In this work, two differential equation models for smallpox are numerically solved to find the optimal intervention policy. In each model we look for the range of values of the parameters that give rise to the worst case scenarios. Since the scale of an epidemic is determined by the number of people infected, and eventually dead, as a result of infection, we attempt to quantify the scale of the epidemic and recommend the optimum intervention policy. In the first case study, we mimic a densely populated city with comparatively big tourist population, and heavily used mass transportation system. A mathematical …

Information Systems And Health Care Xiii: Examining The Critical Requirements, Design Approaches And Evaluation Methods For A Public Health Emergency Response System, Ann L. Fruhling

Information Systems and Quantitative Analysis Faculty Publications

Research pertaining to emergency response systems has accelerated over the past few years, particularly since 9/11 events, and more recently due to Hurricane Katrina and concern over a potential of an avian flu pandemic. This study examines the requirements that are the most demanding with respect to software and hardware, and the associated design strategies for a public health emergency response system (ERS) for electronic laboratory diagnostics consultation. In addition, this study illustrates ways to evaluate the design decisions.

An important goal of a public health ERS is to improve the communication and notification of life-threatening diseases and harmful agents. …

Algorithms For Haplotype Inference And Block Partitioning, Satya Ravi Vijaya

Electronic Theses and Dissertations

The completion of the human genome project in 2003 paved the way for studies to better understand and catalog variation in the human genome. The International HapMap Project was started in 2002 with the aim of identifying genetic variation in the human genome and studying the distribution of genetic variation across populations of individuals. The information collected by the HapMap project will enable researchers in associating genetic variations with phenotypic variations. Single Nucleotide Polymorphisms (SNPs) are loci in the genome where two individuals differ in a single base. It is estimated that there are approximately ten million SNPs in the …

Computational Sciences: At The Intersection Of Science And Engineering - Case Study For Academic And Research Programs, Menas Kafatos, P. A. Becker, Z. Boybeyi

Mathematics, Physics, and Computer Science Faculty Articles and Research

No abstract provided.

Americans And Climate Change: Closing The Gap Between Science And Action, Daniel R. Abbasi

Yale School of the Environment Publications Series

A Synthesis of Insights and Recommendations from the 2005 Yale F&ES Conference on Climate Change

Epidemiological Models For Mutating Pathogens With Temporary Immunity, Neeta Singh

Electronic Theses and Dissertations

Significant progress has been made in understanding different scenarios for disease transmissions and behavior of epidemics in recent years. A considerable amount of work has been done in modeling the dynamics of diseases by systems of ordinary differential equations. But there are very few mathematical models that deal with the genetic mutations of a pathogen. In-fact, not much has been done to model the dynamics of mutations of pathogen explaining its effort to escape the host's immune defense system after it has infected the host. In this dissertation we develop an SIR model with variable infection age for the transmission …

Experimental Infection Of Fox Squirrels (Sciurus Niger) With West Nile Virus, J. Jeffrey Root, Paul T. Oesterle, Nicole M. Nemeth, Kaci Klenk, Daniel H. Gould, Robert G. Mclean, Larry Clark, Jeffrey S. Hall

United States Department of Agriculture Wildlife Services: Staff Publications

Tree squirrels (Sciurus spp.) have exhibited high seroprevalence rates, suggesting that they are commonly exposed to West Nile virus (WNV). Many characteristics of WNV infections in tree squirrels, such as the durations and levels of viremia, remain unknown. To better understand WNV infections in fox squirrels (S. niger), we subcutaneously inoculated fourteen fox squirrels with WNV. Peak viremias ranged from 10^4.00 plaque-forming units (PFU)/mL of serum on day 2 post-infection (DPI) to 10^4.98 PFU/mL on 3 DPI, although viremias varied between individuals. Oral secretions of some fox squirrels were positive for WNV viral RNA, occasionally …

Multi-Species Patterns Of Avian Cholera Mortality In Nebraska’S Rainwater Basin, Julie A. Blanchong, Michael D. Samuel, Gene Mack

United States Geological Survey: Staff Publications

Nebraska’s Rainwater Basin (RWB) is a key spring migration area for millions of waterfowl and other avian species. Avian cholera has been endemic in the RWB since the 1970s and in some years tens of thousands of waterfowl have died from the disease. We evaluated patterns of avian cholera mortality in waterfowl species using the RWB during the last quarter of the 20th century. Mortality patterns changed between the years before (1976–1988) and coincident with (1989–1999) the dramatic increases in lesser snow goose abundance and mortality. Lesser snow geese (Chen caerulescens caerulescens) have commonly been associated with mortality …