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An Evolutionary Vaccination Game In The Modified Activity Driven Network By Considering The Closeness, Dun Han, Mei Sun

Publications and Research

In this paper, we explore an evolutionary vaccination game in the modified activity driven network by considering the closeness. We set a closeness parameter p which is used to describe the way of connection between two individuals. The simulation results show that the closeness p may have an active role in weakening both the spreading of epidemic and the vaccination. Besides, when vaccination is not allowed, the final recovered density increases with the value of the ratio of the infection rate to the recovery rate λ/μ. However, when vaccination is allowed the final density of recovered individual first increases and …

Antimalarial Drug Discovery Using Triazoles To Overcome Chloroquine Resistance, Elias Sibhatu Tesfaselassie

Dissertations and Theses

Malaria is considered as one of the most prevalent and debilitating diseases affecting humans. Plasmodium falciparum is the most virulent form of the parasite which developed resistance to several antimalarial drugs. Chloroquine is one of the most successful antimalarials developed that is safe, effective, and cheap. However, its use has been limited due to the emergence of drug resistance. Click chemistry, particularly, the copper(I)-catalyzed reaction between azides and alkynes has shown to have a cutting-edge advantage in medicinal chemistry by its reliability, selectivity and biocompatibility.

Triazole-based antimalarials were synthesized via copper(I)-catalyzed alkyne-azide cycloaddition reaction by modifying the aliphatic chains terminal …

Dead/Live Microbial Culture Technique, Michael Veri

USF Tampa Graduate Theses and Dissertations

New methodology has been utilized to provoke or increase targeted metabolic pathways in microbes. The low hanging fruit of natural products has been discovered over the last 50 years. To continue finding new metabolites to be used as possible drug candidates, methodology development such as those proposed herein are necessary. This methodology uses extracts from known pathogenic bacteria to elicit production of latent biosynthetic pathways from environmental bacterial isolates that may be active against the original pathogenic strains. A new compound, MAV-1 (1) of the diketopiperazine family (Figure 1) was isolated and identified utilizing these techniques. The structure of MAV-1 …

A Pairwise Likelihood Augmented Estimator For The Cox Model Under Left-Truncation, Fan Wu, Sehee Kim, Jing Qin, Rajiv Saran, Yi Li

The University of Michigan Department of Biostatistics Working Paper Series

Survival data collected from prevalent cohorts are subject to left-truncation and the analysis is challenging. Conditional approaches for left-truncated data under the Cox model are inefficient as they typically ignore the information in the marginal likelihood of the truncation times. Length-biased sampling methods can improve the estimation efficiency but only when the stationarity assumption of the disease incidence holds, i.e., the truncation distribution is uniform; otherwise they may generate biased estimates. In this paper, we propose a semi-parametric method for the Cox model under general left-truncation, where the truncation distribution is unspecified. Our approach is to make inference based on …

On Partial Identification Of The Pure Direct Effect, Caleb Miles, Phyllis Kanki, Seema Meloni, Eric Tchetgen Tchetgen

Harvard University Biostatistics Working Paper Series

No abstract provided.

Mining Biological Networks Towards Protein Complex Detection And Gene-Disease Association, Eileen Marie Hanna

Dissertations

Large amounts of biological data are continuously generated nowadays, thanks to the advancements of high-throughput experimental techniques. Mining valuable knowledge from such data still motivates the design of suitable computational methods, to complement the experimental work which is often bound by considerable time and cost requirements. Protein complexes or groups of interacting proteins, are key players in most cellular events. The identification of complexes not only allows to better understand normal biological processes but also to uncover Disease-triggering malfunctions. Ultimately, findings in this research branch can highly enhance the design of effective medical treatments. The aim of this research is …

Event And Strategy Analytics, Jin Song Dong, Jun Sun, Yang Liu, Yuan-Fang Li, Jing Sun, Ling Shi

Research Collection School Of Computing and Information Systems

Model checking has been pervasive and successful in finding bugs in hardware and software systems, including real-time and probabilistic systems. Applying model checking to decision making is relative new and has an excellent potential to be compliment to data analytics and other Artificial Intelligent (AI) or Operational Research (OR) based decision making techniques. Our last 8 years research has focused on the development of PAT (Process Analysis Toolkit) [18] which supports modelling languages that combine the expressiveness of event, state, time and probability based modeling techniques to which model checking can be directly applied. The next direction for PAT is …

Design, Synthesis And Evaluation Of Bivalent Inhibitors Of Trehalose-6-Phosphate Phosphatase, Chunliang Liu

Chemistry and Chemical Biology ETDs

The D-glucose disaccharide α, α-D-trehalose is synthesized by a variety of bacteria, fungi, plants and invertebrates to support cell survival by functioning as a fuel, a metabolic regulator or a protectant against environmental stress. Five different trehalose biosynthetic pathways are known to exist, one of which, the OtsA/OtsB pathway is common among pathogenic bacteria and fungi and is also found in parasitic nematodes. Previously reported otsA and otsB gene knockout (or knockdown) experiments have shown that both pathway enzymes are essential for M. tuberculosis cell growth and host colonization. RNAi gene silencing carried out in the nematode model system Caenohabditis …

Per-Contact Infectivity Of Hcv Associated With Injection Exposures In A Prospective Cohort Of Young Injection Drug Users In San Francisco, Ca (Ufo Study), Yuridia Leyva

Mathematics & Statistics ETDs

Sharing needles and ancillary injection drug equipment places injection drug users (IDU) at risk for Hepatitis C Virus (HCV), a highly infectious blood-borne virus. A limited number of studies have analyzed the per-contact infectivity of HCV associated with the use of previously-used needles, but per-contact infectivity of ancillary injecting equipment has not been previously investigated. Our goal is to estimate the per-contact infectivity of HCV associated with (1) injecting with another person's previously-used needle, classified as receptive needle sharing (RNS), and (2) using another person's previously-used ancillary injecting equipment, such as cookers to melt drugs and cottons to strain impurities …

Sociodemographic Factors To Dengue Hemmorrhagic Fever Case In Indonesia, Desy Nuryunarsih

Kesmas

Demam berdarah dengue (DBD) adalah penyebab utama rawat inap dan kematian pada anak-anak. Indonesia adalah salah satu negara yang oleh WHO dikategorikan hyperendemicity dengan empat serotipe virus tersebar di daerah perkotaan. Faktor sosiodemografi dianggap sebagai faktor pendukung terjadinya DBD di Indonesia. Studi ini menggunakan data sekunder yang diunduh dari Basis Data Kesehatan Provinsi tahun 2010 Kementerian Kesehatan Republik Indonesia untuk menentukan korelasi antara ketiga faktor sosiodemografi dengan insiden DBD. Penelitian ini menggunakan metode kuantitatif deskripsi korelasi. Hasil penelitian menunjukkan bahwa dua faktor sosiodemografi terpilih memiliki korelasi linier dengan insiden DBD. Analisa regresi multivariat menunjukkan kecilnya korelasi antara insiden DBD dengan …

Synthesis And Structure−Activity Relationships Of Tambjamines And B‑Ring Functionalized Prodiginines As Potent Antimalarials, Papireddy Kancharla, Jane Xu Kelly, Kevin A. Reynolds

Chemistry Faculty Publications and Presentations

Synthesis and antimalarial activity of 94 novel bipyrrole tambjamines (TAs) and a library of B-ring functionalized tripyrrole prodiginines (PGs) against a panel of Plasmodium falciparum strains are described. The activity and structure–activity relationships demonstrate that the ring-C of PGs can be replaced by an alkylamine, providing for TAs with retained/enhanced potency. Furthermore, ring-B of PGs/TAs can be substituted with short alkyl substitutions at either 4-position (replacement of OMe) or 3- and 4-positions without impacting potency. Eight representative TAs and two PGs have been evaluated for antimalarial activity against multidrug-resistant P. yoelii in mice in the dose range of 5–100 mg/kg …

Inhibition Of The Dape-Encoded N-Succinyl- ʟ, ʟ-Diaminopimelic Acid Desuccinylase From Neisseria Meningitidis By ʟ-Captopril, Anna Starus, Boguslaw Nocek, Brian Bennett, James A. Larrabee, Daniel L. Shaw, Wisath Sae-Lee, Marie T. Russo, Danuta M. Gillner, Magdalena Makowska-Grzyska, Andzrej Joachimiak, Richard C. Holz

Physics Faculty Research and Publications

Binding of the competitive inhibitor ʟ-captopril to the dapE-encoded N-succinyl-ʟ, ʟ-diaminopimelic acid desuccinylase from Neisseria meningitidis (NmDapE) was examined by kinetic, spectroscopic, and crystallographic methods. ʟ-Captopril, an angiotensin-converting enzyme (ACE) inhibitor, was previously shown to be a potent inhibitor of the DapE from Haemophilus influenzae (HiDapE) with an IC₅₀ of 3.3 μM and a measured K_i of 1.8 μM and displayed a dose-responsive antibiotic activity toward Escherichia coli. ʟ-Captopril is also a competitive inhibitor of NmDapE with a K_i of 2.8 μM. To examine the nature of the interaction …

A Survey Of Mathematical Models Of Dengue Fever, James P. Braselton, Iurii Bakach

Mathematical Sciences: Faculty Publications

In this paper, we compare and contrast five models of dengue fever, a serious illness that affects tropical and subtropical areas around the world. We evaluate each model using different scenarios and identify the strengths and weakness of each of the models. The goal of our analysis is to indicate the strengths and weaknesses of current mathematical models of dengue fever that should assist future researchers in forming models that accurately measure the variables they are studying that affect the spread and progression of the disease.

A Framework For Inferring Unobserved Multistrain Epidemic Subpopulations Using Synchronization Dynamics, Eric Forgoston, Leah B. Shaw, Ira B. Schwartz

Department of Applied Mathematics and Statistics Faculty Scholarship and Creative Works

A new method is proposed to infer unobserved epidemic subpopulations by exploiting the synchronization properties of multistrain epidemic models. A model for dengue fever is driven by simulated data from secondary infective populations. Primary infective populations in the driven system synchronize to the correct values from the driver system. Most hospital cases of dengue are secondary infections, so this method provides a way to deduce unobserved primary infection levels. We derive center manifold equations that relate the driven system to the driver system and thus motivate the use of synchronization to predict unobserved primary infectives. Synchronization stability between primary and …

Sexual Networks And Hiv Risk Among Black Men Who Have Sex With Men In 6 U.S. Cities, Hong-Van Tieu, Ting-Yuan Liu, Sophia Hussen, Matthew Connor, Lei Wang, Gregory Phillips Ii, + 11 More

Epidemiology Faculty Publications

Background

Sexual networks may place U.S. Black men who have sex with men (MSM) at increased HIV risk.

Methods

Self-reported egocentric sexual network data from the prior six months were collected from 1,349 community-recruited Black MSM in HPTN 061, a multi-component HIV prevention intervention feasibility study. Sexual network composition, size, and density (extent to which members are having sex with one another) were compared by self-reported HIV serostatus and age of the men. GEE models assessed network and other factors associated with having a Black sex partner, having a partner with at least two age category difference (age difference between …

Acceleration Of Agent-Based Pandemicmodeling On Multiple Gpus, Barzan Shekh

Masters Theses

Epidemiology computation models are crucial for the assessment and control of public health crises. Agent-based simulations of pandemic inuenza are useful for forecasting the infectious disease spreading in order to help public health policy makers during emergencies. In such emergencies decisions are required for public health preparedness in cycles of less than a day, and the agent-based model should be adaptable and tractable for quick and simple calibration with low computational overhead.

GPU accelerated computing involves the use of a graphics processing unit (GPU) in combination with the CPU to perform heterogeneous computing by o_oading a compute-expensive portion of the …

Computational Modeling Of Rna-Small Molecule And Rna-Protein Interactions, Lu Chen

Dissertations and Theses (Open Access)

The past decade has witnessed an era of RNA biology; despite the considerable discoveries nowadays, challenges still remain when one aims to screen RNA-interacting small molecule or RNA-interacting protein. These challenges imply an immediate need for cost-efficient while predictive computational tools capable of generating insightful hypotheses to discover novel RNA-interacting small molecule or RNA-interacting protein. Thus, we implemented novel computational models in this dissertation to predict RNA-ligand interactions (Chapter 1) and RNA-protein interactions (Chapter 2).

Targeting RNA has not garnered comparable interest as protein, and is restricted by lack of computational tools for structure-based drug design. To test the potential …

Effects Of Allosteric Mutations On Dihydrofolate Reductase, Marian Okondo

Theses, Dissertations and Culminating Projects

Dihydrofolate reductase (DHFR) is an essential enzyme necessary in the synthesis of DNA precursors. DHFR acquires resistance to numerous known anti-folates and this has led to the continuous need to discover novel and selective DHFR inhibitors. Allosteric mutations on Bacillus stearothermophilus (Bs.) DHFR were previously found to alter inhibitor binding and specificity. In this work, we investigate how these mutations affect the conformational motions of DHFR associated with inhibitor binding. Two distal allosteric mutations, isoleucine at position 86 to alanine (I86A) and tyrosine at position 127 to alanine (Y127A) were separately introduced to C73A/S131C, a previously modified wild type DHFR …

Geospatial Resolution Of Human And Bacterial Diversity With City-Scale Metagenomics, Ebrahim Afshinnekoo, Cem Meydan, Shanin Chowdhury, Dyala Jaroudi, Collin Boyer, Nick Bernstein, Julia M. Maritz, Darryl Reeves, Jorge Gandara, Sagar Chhangawala, Sofia Ahsanuddin, Amber Simmons, Timothy Nessel, Bharathi Sundaresh, Elizabeth Pereira, Ellen Jorgensen, Sergios-Orestis Kolokotronis, Nell Kirchberger, Isaac Garcia, David Gandara, Sean Dhanraj, Tanzina Nawrin, Yogesh Saletore, Noah Alexander, Priyanka Vijay, Elizabeth M. Hénaff, Paul Zumbo, Michael Walsh, Gregory D. O'Mullan, Scott Tighe, Joel T. Dudley, Anya Dunaif, Sean Ennis, Eoghan O'Halloran, Tiago R. Magalhaes, Braden Boone, Angela L. Jones, Theodore R. Muth, Katie Schneider Paolantonio, Elizabeth Alter, Eric E. Schadt, Jeanne Garbarino, Robert J. Prill, Jane M. Carlton, Shawn Levy, Christopher E. Mason

Publications and Research

The panoply of microorganisms and other species present in our environment influence human health and disease, especially in cities, but have not been profiled with metagenomics at a city-wide scale. We sequenced DNA from surfaces across the entire New York City (NYC) subway system, the Gowanus Canal, and public parks. Nearly half of the DNA (48%) does not match any known organism; identified organisms spanned 1,688 bacterial, viral, archaeal, and eukaryotic taxa, which were enriched for harmless genera associated with skin (e.g., Acinetobacter). Predicted ancestry of human DNA left on subway surfaces can recapitulate U.S. Census demographic data, and bacterial …

Steps Towards Deciphering The Post-Polyketide Synthase Tailoring Steps In The Phoslactomycin Biosynthesis Pathway, Patience Marimo

Dissertations and Theses

Phoslactomycins (PLMs) are a group of natural products belonging to a polyketides class. These polyketides are synthesized by sequential reaction catalyzed by a collection of enzymes activities called polyketide synthases. A polyketide is a large class of diverse compounds that are characterized by more than two carbonyl groups connected by single intervening carbon atoms. In other words, a polyketide is a polymer whose monomer is a ketide. The PLMs are also known as phosphazomycins or phospholines. These compounds were isolated based on antifungal and antitumor activities. This array of promising biological activities has stimulated research into the field of PLMs …

The 24th Annual Research Conference Abstract Booklet, University Of Gondar, Ethiopia

University of Gondar Research Conferences

The 25th Annual Staff-Student Research Conference of the University of Gondar will be held on June 19 and 20, 2015 at the Science Amba Auditorium. This year's conference is special in that the year marks the Silver Jubilee of the Annual Staff and Student Research Conference. Drawing on the experiences we have accumulated for the past 25 years, we vow to strive to realize the development and transformation of the country through research and community services.

Staff, postgraduate and senior undergraduate students of the University, invited guests, and speakers will participate in the conference. The annual conference of the University …

A Stage-Structured Two Species Competition Mathematical Model Under The Effect Of Disease, Manju Agarwal, Vinay Verma

Applications and Applied Mathematics: An International Journal (AAM)

In this paper we study the dynamics of two competing species model; one of this competing species is stage structured and the disease spreads only in the other competing specie. In order to keep the model simple, we present it under the strong assumption that the disease can not cross the species barrier. Dynamical behaviors such as positivity, boundedness, stability, bifurcation and persistence of the model are studied analytically using the theory of differential equations. Computer simulations are carried out to substantiate the analytical findings. It is noted that c the loss rate of the population, T the maturation time …

Peptides: A Package For Data Mining Of Antimicrobial Peptides, Daniel Osorio, Paola Rondón-Villarreal, Rodrigo Torres

The R Journal

Antimicrobial peptides (AMP) are a promising source of antibiotics with a broad spectrum activity against bacteria and low incidence of developing resistance. The mechanism by which an AMPexecutes its function depends on a set of computable physicochemical properties from the amino acid sequence. The Peptides package was designed to allow the quick and easy computation of ten structural characteristics own of the antimicrobial peptides, with the aim of generating data to increase the accuracy in classification and design of new amino acid sequences. Moreover, the options to read and plot XVG output files from GROMACS molecular dynamics package are included.

Controllability Of An Eco-Epidemiological System With Disease Transmission Delay: A Theoretical Study, Samadyuti Haldar, Kunal Chakraborty, T. K. Kar

Applications and Applied Mathematics: An International Journal (AAM)

This paper deals with the qualitative analysis of a disease transmission delay induced prey preda-tor system in which disease spreads among the predator species only. The growth of the preda-tors’ susceptible and infected subpopulations is assumed as modified Leslie–Gower type. Suffi-cient conditions for the persistence, permanence, existence and stability of equilibrium points are obtained. Global asymptotic stability of the system is investigated around the coexisting equilib-rium using a geometric approach. The existence of Hopf bifurcation phenomenon is also exam-ined with respect to some important parameters of the system. The criterion for disease a trans-mission delay the induced Hopf bifurcation phenomenon …

Spatial Heterogeneity, Host Movement And Mosquito-Borne Disease Transmission, Miguel A. Acevedo, Olivia Prosper, Kenneth Lopiano, Nick Ruktanonchai, T. Trevor Caughlin, Maia Martcheva, Craig W. Osenberg, David L. Smith

Dartmouth Scholarship

Mosquito-borne diseases are a global health priority disproportionately affecting low-income populations in tropical and sub-tropical countries. These pathogens live in mosquitoes and hosts that interact in spatially heterogeneous environments where hosts move between regions of varying transmission intensity. Although there is increasing interest in the implications of spatial processes for mosquito-borne disease dynamics, most of our understanding derives from models that assume spatially homogeneous transmission. Spatial variation in contact rates can influence transmission and the risk of epidemics, yet the interaction between spatial heterogeneity and movement of hosts remains relatively unexplored. Here we explore, analytically and through numerical simulations, how …

The Biological Consequences Of Kaolin Geophagia, Deloris Alexander, Desire Richardson, Lakisha Odom, Kara Cromwell, Dejuana Grant, Micoya Myers, Eddy Cadet, Hamid Mahama, Vijaya Rangari, Ralphenia Pace, Ramble Ankumah, Kokoasse Kpomblekou-A, Curtis Fluker

Professional Agricultural Workers Journal

Abstract

Kaolin geophagia is associated with the relief of gastrointestinal distress, but it may also cause adverse health effects on the body. This study was designed to: assess kaolin composition; test if 129SvEv mice would consume kaolin and determine the consequences of consumption; and assess rotational stress modulation of consumption. Thirteen kaolin samples were purchased from Alabama and Georgia stores. Chemical and physical properties were characterized for each sample using a Munsell chart, pH meter, Energy Dispersive Spectroscopy, Transmission Electron Microscopy, Visible Near-InfraRed Spectra, and Inductively Coupled Plasma-Optical Emission Spectrometry. Kaolin was then given to mice as food supplements and …

Bounded Rationality Alters The Dynamics Of Paediatric Immunization Acceptance, Tamer Oraby, Chris T. Bauch

School of Mathematical & Statistical Sciences Faculty Publications

Interactions between disease dynamics and vaccinating behavior have been explored in many coupled behavior-disease models. Cognitive effects such as risk perception, framing, and subjective probabilities of adverse events can be important determinants of the vaccinating behaviour, and represent departures from the pure “rational” decision model that are often described as “bounded rationality”. However, the impact of such cognitive effects in the context of paediatric infectious disease vaccines has received relatively little attention. Here, we develop a disease-behavior model that accounts for bounded rationality through prospect theory. We analyze the model and compare its predictions to a reduced model that lacks …

West Nile Virus And Ferruginous Hawks (Buteo Regalis) In The Northern Great Plains, Shubham Datta, Jonathan A. Jenks, David E. Knudsen, Kent C. Jensen, Will M. Inselman, Christopher C. Swanson, Troy W. Grovenburg

The Prairie Naturalist

Emerging infectious diseases (EID) present significant threats to the conservation of global biodiversity (Daszak et al. 2000). Evaluating impacts (spatial, temporal and demographic) of EIDs on sensitive and declining wildlife populations is challenging because quantitative information is usually dependent on estimates rather than counts (Wobeser 2007) and mortality rates are seldom quantified with conventional monitoring (Naugle et al. 2005).

West Nile virus (WNv), a mosquito-borne Flavivirus (family Flaviviridae; Komar 2001), was discovered in northwest Uganda in 1937 (Smithburn et al. 1940). First encountered in the western hemisphere in New York in 1999 (Nash et al. 2001), WNv has become enzootic …

The R Journal (June 2015) 7(1): Complete Issue, The R Foundation

The R Journal

Editorial, Bettina Grün

Contributed Research Articles

Peptides: A Package for Data Mining of Antimicrobial Peptides, Daniel Osorio, Paola Rondón-Villarreal, and Rodrigo Torres

fanplot: An R Package for Visualising Sequential Distributions, Guy J. Abel

sparkTable: Generating Graphical Tables for Websites and Documents with R, Alexander Kowarik, Bernhard Meindl, and Matthias Templ

rdrobust: An R Package for Robust Nonparametric Inference in Regression-Discontinuity Designs, Sebastian Calonico, Matias D. Cattaneo, and Rocío Titiunik

Frames2: A Package for Estimation in Dual Frame Surveys, Antonio Arcos, David Molina, Maria Giovanna Ranalli, and María del Mar Rueda

The Complex Multivariate Gaussian Distribution, Robin K. S. Hankin

sae: …

Designing Novel Abstraction Networks For Ontology Summarization And Quality Assurance, Christopher Ochs

Dissertations

Biomedical ontologies are complex knowledge representation systems. Biomedical ontologies support interdisciplinary research, interoperability of medical systems, and Electronic Healthcare Record (EHR) encoding. Ontologies represent knowledge using concepts (entities) linked by relationships. Ontologies may contain hundreds of thousands of concepts and millions of relationships. For users, the size and complexity of ontologies make it difficult to comprehend “the big picture” of an ontology's content. For ontology editors, size and complexity make it difficult to uncover errors and inconsistencies. Errors in an ontology will ultimately affect applications that utilize the ontology.

In prior studies abstraction networks (AbNs) were developed to provide a …