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A Supramolecular Strategy To Assemble Multifunctional Viral Nanoparticles, Limin Chen, Xia Zhao, Yuan Lin, Yubin Huang, Qian Wang

Faculty Publications

Using a one-pot approach driven by the supramolecular interaction between β-cyclodextrin and adamantyl moieties, multifunctional viral nanoparticles can be facilely formulated for biomedical applications.

Biofouling : A Means Of Aquatic Species Transfer, Anne Bouyssou, Josefin Madjidian

NSBWO

Ships carry seawater in their ballast tanks when they are not fully loaded with cargo, in order to maintain adequate trim, draught and stability, adjust list and limit stresses on the hull. It is now well documented that the water pumped into the ship contains aquatic organisms – which can also sink to the sediments at the bottom of tanks – and that these organisms are thereby transferred from the port of origin to the destination. But it is seldom mentioned that aquatic organisms are also found on the outside of ships, attached on their hulls and appendages, as a …

2013 Annual Meeting Program

Journal of the South Carolina Academy of Science

No abstract provided.

Evaluation Of Water Sanitation Options For Poultry Production, Pramir Maharjan

Graduate Theses and Dissertations

An evaluation of poultry farm water supplies was conducted to determine the value and impact of water system sanitation practices in commercial broiler houses on microbial levels. Water line cleaning between flocks using concentrated disinfectant solution before placing chicks reduced biofilms retained in the lines to a safe level. Occasional microbial surges were noticed during different points of flock grow-out period even when daily water sanitation was present indicating water is highly susceptible to microbial contamination. However, the daily water sanitation practice controlled the occasional microbial surges in water from sustaining and kept drinking water to a microbiologically acceptable level. …

Parameter Learning For Latent Network Diffusion, Xiaojian Wu, Akshat Kumar, Daniel Sheldon, Shlomo Zilberstein

Research Collection School Of Computing and Information Systems

Diffusion processes in networks are increasingly used to model dynamic phenomena such as the spread of information, wildlife, or social influence. Our work addresses the problem of learning the underlying parameters that govern such a diffusion process by observing the time at which nodes become active. A key advantage of our approach is that, unlike previous work, it can tolerate missing observations for some nodes in the diffusion process. Having incomplete observations is characteristic of offline networks used to model the spread of wildlife. We develop an EM algorithm to address parameter learning in such settings. Since both the E …

Dynamical Behaviors Of Gonorrhea Strain Competition Model, Marisabel Rodriguez

Theses and Dissertations - UTB/UTPA

In the past decades, Gonorrhea, a sexually transmitted bacterial infection caused by Neisseria gonorrhoeae, has become resistant to a wider range of antibiotics. We apply a phenomenological model that takes into account essential ideas such as the effects of different treatment levels, the transformation and conjugation rates of bacteria, and the response of the immune system. Qualitative analysis provides a more integral view of how model parameters affect the emergence of within-host resistance.

Correlates Of Hiv Acquisition In A Cohort Of Black Men Who Have Sex With Men In The United States: Hiv Prevention Trials Network (Hptn) 061, Beryl A. Koblin, Kenneth H. Mayer, Susan H. Eshleman, Lei Wang, Sharon B. Mannheimer, Carlos Del Rio, Steve Shoptaw, Manya Magnus, Susan Buchbinder, Leo Wilton, Ting-Yuan Liu, Vanessa Cummings, Estelle Piwowar-Manning, Sheldon D. Fields, Sam Griffith, Vanessa Elharrar, Darrell Wheeler

Epidemiology Faculty Publications

Background

Black men who have sex with men (MSM) in the United States (US) are affected by HIV at disproportionate rates compared to MSM of other race/ethnicities. Current HIV incidence estimates in this group are needed to appropriately target prevention efforts.

Methods

From July 2009 to October 2010, Black MSM reporting unprotected anal intercourse with a man in the past six months were enrolled and followed for one year in six US cities for a feasibility study of a multi-component intervention to reduce HIV infection. HIV incidence based on HIV seroconversion was calculated as number of events/100 person-years. Multivariate proportional …

Sample Size Considerations In The Design Of Cluster Randomized Trials Of Combination Hiv Prevention, Rui Wang, Ravi Goyal, Quanhong Lei, M. Essex, Victor Degruttola

Harvard University Biostatistics Working Paper Series

No abstract provided.

Earning Trust And Explaining Complexities As You Communicate Climate Science: The Cause Model, Katherine E. Rowan

July 10, 2013: Best Practices and Communications Strategies for Adapting to Sea Level Rise and Flooding

No abstract provided.

Business And Climate Change: Trends, Issues And Challenges, Badar Alam Iqbal, Munir Hassan, Bhawana Rawat, Shabib Arslan

Business Review

The present century i.e. 21st Century is the century of Business and Climate. These two issues are getting higher attention from both developed countries and developing economies. On the one hand, business has affecting environment and on the other hand environmental products are boosting business and therefore, there is close relationship between business and climate change . Looking into the growing grave concern from different sections over climate change, considerably due to industrial units, businesses had also started to take initiative in this regard. The paper, henceforth, concentrates on what had so far been done, and what more need to …

Collective Diffusion Over Networks: Models And Inference, Akshat Kumar, Daniel Sheldon, Biplav Srivastava

Research Collection School Of Computing and Information Systems

Diffusion processes in networks are increasingly used to model the spread of information and social influence. In several applications in computational sustainability such as the spread of wildlife, infectious diseases and traffic mobility pattern, the observed data often consists of only aggregate information. In this work, we present new models that generalize standard diffusion processes to such collective settings. We also present optimization based techniques that can accurately learn the underlying dynamics of the given contagion process, including the hidden network structure, by only observing the time a node becomes active and the associated aggregate information. Empirically, our technique is …

The Effect Of The Probiotic Pediococcus Acidilactici On The Gut Microbiota Ecology Of Rainbow Trout (Oncorhynchus Mykiss Walbaum) Analysed Using Dgge, Alice Anderson

The Plymouth Student Scientist

The microbiota of the gastrointestinal tract heavily influences the health, growth and survival of fish. Probiotics have proved effective in improving fish productivity in aquaculture. Research suggests that probiotics, supplemented in the feed, may elicit these benefits by altering the ecology of the gastrointestinal microbiota. The probiotic Pediococcus acidilactici has been successfully used for terrestrial animals and humans but its use in aquatic organisms has been less researched. In the present study, rainbow trout Oncorhynchus mykiss (Walbaum) were fed a diet that contained Ped. Acidilactici, or a control diet. Analysis of the posterior digesta bacteria, using a non-culture dependant technique, …

Optimal Control Modeling And Simulation, With Application To Cholera Dynamics, Chairat Modnak

Mathematics & Statistics Theses & Dissertations

The theory of optimal control, a modern extension of the calculus of variations. has found many applications in a wide range of scientific fields, particularly in epidemiology with respect to disease prevention and intervention. In this dissertation. we conduct optimal control modeling, simulation and analysis to cholera dynamics. Cholera is a severe intestinal infectious disease that remains a serious public health threat in developing countries. Transmission of cholera involves complex interactions between the human host, the pathogen, and the environment. The worldwide cholera outbreaks and their increasing severity, frequency and duration in recent years underscore the gap between the complex …

Phylogenetic Linkage Among Hiv-Infected Village Residents In Botswana: Estimation Of Clustering Rates In The Presence Of Missing Data, Nicole Bohme Carnegie, Rui Wang, Vladimir Novitsky, Victor G. Degruttola

Harvard University Biostatistics Working Paper Series

No abstract provided.

Modelling Infertility With Markov Chains, Rebecca Dorff

Theses and Dissertations

Infertility affects approximately 15% of couples. Testing and interventions are costly, in time, money, and emotional energy. This paper will discuss using Markov decision and multi-armed bandit processes to identify a systematic approach of interventions that will lead to the desired baby while minimizing costs.

Informative Retesting For Hierarchical Group Testing, Michael S. Black

Department of Statistics: Dissertations, Theses, and Student Research

Group testing is the process of pooling samples (e.g., blood, chemical compounds) from multiple sources and testing the pooled material for some binary characteristic. It is used in pathogen screening for humans and animals, drug discovery studies, electrical systems testing, and many other applications. Group testing has traditionally been used for two main types of investigations: 1) the identification of positive specimens and 2) the estimation of a characteristic’s prevalence in a population. This dissertation focuses on the identification process. We propose new identification procedures that exploit the heterogeneity among samples in order to reduce the number of tests needed …

When To Start Antiretroviral Therapy: The Need For An Evidence Base During Early Hiv Infection, James D. Lundgren, Abdel G. Babiker, Fred M. Gordin, Alvaro H. Borges, James D. Neaton

Epidemiology Faculty Publications

Background

Strategies for use of antiretroviral therapy (ART) have traditionally focused on providing treatment to persons who stand to benefit immediately from initiating the therapy. There is global consensus that any HIV+ person with CD4 counts less than 350 cells/μl should initiate ART. However, it remains controversial whether ART is indicated in asymptomatic HIV-infected persons with CD4 counts above 350 cells/μl, or whether it is more advisable to defer initiation until the CD4 count has dropped to 350 cells/μl. The question of when the best time is to initiate ART during early HIV infection has always been vigorously debated. The …

Changes On Cran, Kurt Hornik, Achim Zeileis

The R Journal

New CRAN task views

New packages in CRAN task views

New contributed packages

Other changes

Global Dynamics Of A Water-Borne Disease Model With Multiple Transmission Pathways, Prasanta K. Mondal, T. K. Kar

Applications and Applied Mathematics: An International Journal (AAM)

We propose and analyze a water born disease model introducing water-to-person and person-toperson transmission and saturated incidence. The disease-free equilibrium and the existence criterion of endemic equilibrium are investigated. Trans critical bifurcation at the disease-free equilibrium is obtained when the basic reproductive number is one. The local stability of both the equilibria is shown and a Lyapunov functional approach is also applied to explore the global stability of the system around the equilibria. We display the effects of pathogen contaminated water and infection through contact on the system dynamics in the absence of person-to-person contact as well as in the …

Evolutionary Dynamics On Complex Networks, Swami Iyer

Graduate Doctoral Dissertations

Many complex systems such as the Internet can be represented as networks, with vertices denoting the constituent components of the systems and edges denoting the patterns of interactions among the components. In this thesis, we are interested in how the structural properties of a network, such as its average degree, degree distribution, clustering, and homophily affect the processes that take place on it. In the first part of the thesis we focus on evolutionary game theory models for studying the evolution of cooperation in a population of predominantly selfish individuals. In the second part we turn our attention to an …

Unraveling The Activation Mechanism Of The Potato Tuber Adp-Glucose Pyrophosphorylase, Carlos M. Figueroa, Misty L. Kuhn, Christine A. Falaschetti, Ligin Solamen, Kenneth W. Olsen, Miguel Ballicora, Alberto A. Iglesias

Chemistry: Faculty Publications and Other Works

ADP-glucose pyrophosphorylase regulates the synthesis of glycogen in bacteria and of starch in plants. The enzyme from plants is mainly activated by 3-phosphoglycerate and is a heterotetramer comprising two small and two large subunits. Here, we found that two highly conserved residues are critical for triggering the activation of the potato tuber ADP-glucose pyrophosphorylase, as shown by site-directed mutagenesis. Mutations in the small subunit, which bears the catalytic function in this potato tuber form, had a more dramatic effect on disrupting the allosteric activation than those introduced in the large subunit, which is mainly modulatory. Our results strongly agree with …

Targeted Maximum Likelihood Estimation For Dynamic And Static Longitudinal Marginal Structural Working Models, Maya L. Petersen, Joshua Schwab, Susan Gruber, Nello Blaser, Michael Schomaker, Mark J. Van Der Laan

U.C. Berkeley Division of Biostatistics Working Paper Series

This paper describes a targeted maximum likelihood estimator (TMLE) for the parameters of longitudinal static and dynamic marginal structural models. We consider a longitudinal data structure consisting of baseline covariates, time-dependent intervention nodes, intermediate time-dependent covariates, and a possibly time dependent outcome. The intervention nodes at each time point can include a binary treatment as well as a right-censoring indicator. Given a class of dynamic or static interventions, a marginal structural model is used to model the mean of the intervention specific counterfactual outcome as a function of the intervention, time point, and possibly a subset of baseline covariates. Because …

Targeting Udp-Galactopyranose Mutases From Eukaryotic Human Pathogens, Karina Kizjakina, John J. Tanner, Pablo Sobrado

Chemistry Faculty Research & Creative Works

UDP-Galactopyranose mutase (UGM) is a unique flavin-dependent enzyme that catalyzes the conversion of UDPgalactopyranose (UDP-Galp) to UDP-galactofuranose (UDP-Galf). The product of this reaction is the precursor to Galf, a major component of the cell wall and of cell surface glycoproteins and glycolipids in many eukaryotic and prokaryotic human pathogens. The function of UGM is important in the virulence of fungi, parasites, and bacteria. Its role in virulence and its absence in humans suggest that UGM is an ideal drug target. Significant structural and mechanistic information has been accumulated on the prokaryotic UGMs; however, in the past few years the research …

Eradicating Malaria: Improving A Multiple-Timestep Optimization Model Of Malarial Intervention Policy, Taryn M. Ohashi

Scripps Senior Theses

Malaria is a preventable and treatable blood-borne disease whose complications can be fatal. Although many interventions exist in order to reduce the impacts of malaria, the optimal method of distributing these interventions in a geographical area with limited resources must be determined. This thesis refines a model that uses an integer linear program and a compartmental model of epidemiology called an SIR model of ordinary differential equations. The objective of the model is to find an intervention strategy over multiple time steps and multiple geographic regions that minimizes the number of days people spend infected with malaria. In this paper, …

Isolation, Characterization And Synthesis Of Asthma Inducing Fungal Glycolipid And Analytical Method Development For Novel Antimicrobial Peptide Mimics, Vinod Chaudhary

Theses and Dissertations

NKT cells are an important part of human immune system and recognize a specific set of antigens called glycolipids. Only a handful of "natural" NKT cell antigens are known till date. Although NKT cells play a protective role against pathogenic organisms, imbalances in NKT cell functions are implicated in many diseases including asthma. Allergic asthma, a Th2 driven inflammation of airways, is primarily caused by inhalation of environmental allergens. In the last decade, inhaled allergen Aspergillus fumigatus has been under scrutiny for the presence of NKT cell antigens that might trigger asthma. We successfully isolated, characterized and synthesized a "natural" …

A New Class Of Gold Nanoantibotics - Direct Coating Of Ampicillin On Gold Nanoparticles, Dillon S. Pender

Mahurin Honors College Capstone Experience/Thesis Projects

Need for novel, innovative strategies for developing antibiotics is becoming a necessity due to an increasing number of rapidly evolving micro-organismal threats. Antibiotic encapsulated gold nanoparticles (GNPs) are one such strategy showing promise. We report the development of ampicillin encapsulated gold nanoparticles (Amp-GNPs) that possess highly effective, dose dependant antibacterial activity. In this method, ampicillin molecules have been coated on individual GNPs which can then serve as drug carrier devices. Our method for synthesizing Amp-GNPs is an entirely ecofriendly, single step reaction taking place in an aqueous buffer. Following characterization of Amp-GNPs, we find them to be ~15 nm in …

Section Abstracts: Statistics

Virginia Journal of Science

Abstracts of the Statistics Section for the 91st Annual Virginia Journal of Science Meeting, May 2013

Biophysical Characterization Of Optimized Self-Assembling Protein Nanoparticles As A Malaria Vaccine, Sophia Walker

Honors Scholar Theses

Malaria is an infectious disease that affects several million individuals worldwide and is a significant international public health issue. While there is currently a malaria vaccine in phase III clinical trials, recent results demonstrate that it is only about 35% effective in reducing the incidence of the disease. The use of self-assembling protein nanoparticles (SAPNs) that display epitopes of the repeat sequence of the circumsporozoite protein of Plasmodium falciparum, the parasite that causes malaria, has been shown to elicit a strong immune response. This prototype has potential for further improvement by altering the epitope regions of the nanoparticles to …

A Mathematical Model For Antibiotic Resistance In A Hospital Setting With A Varying Population, Edward H. Snyder

Electronic Theses and Dissertations

Antibiotic-resistant bacteria(ARB) is causing increased health risk and cost to society. Mathematical models have been developed to study the transmission of resistant bacteria and the efficacy of preventive measures to slow its spread within a hospital setting. The majority of these models have assumed a constant total hospital population with the admission and discharge rates being equal throughout the duration. But a typical hospital population varies from day to day and season to season. In this thesis, we apply variable admission and discharge daily rates to existing deterministic and stochastic models which examine the transmission of single and dual resistant …

A Cradle To Farm Gate Life Cycle Analysis Of Water Use In U.S. Pork Production, Eric Boles

Graduate Theses and Dissertations

The intent of this study was to analyze water use across a range of regions, scales and practices of the U.S. pork industry. A Life Cycle Assessment of water use within the pork supply chain was performed. Cumulative water use was the environmental impact category used in the LCA to evaluate the impacts of pork production processes throughout the pork supply chain. The functional unit for the analysis was the volume of water required to produce one kilogram of swine (live weight) at the farm gate.

A comprehensive literature review was used to design and propagate algorithms for the National …