Digital Commons Network^™

Design, Development And Construct Validation Of The Children’S Dietary Inflammatory Index, Samira Khan, Micheal D. Wirth, Andrew Ortaglia, Christian R. Alvarado, Nitin Shivappa, Thomas Hurley, James R. Hébert

Faculty Publications

Objective: To design and validate a literature-derived, population-based Children’s Dietary Inflammatory Index (C-DII)TM. Design: The C-DII was developed based on a review of literature through 2010. Dietary data obtained from children in 16 different countries were used to create a reference database for computing C-DII scores based on consumption of macronutrients, vitamins, minerals, and whole foods. Construct validation was performed using quantile regression to assess the association between C-reactive protein (CRP) concentrations and C-DII scores. Data Sources: All data used for construct validation were obtained from children between six and 14 years of age (n = 3300) who participated in …

Hiv-1 Integrase-Targeted Short Peptides Derived From A Viral Protein R Sequence, Xue Zhi Zhao, Mathieu Métifiot, Evgeny Kiselev, Jacques Kessl, Kasthuraiah Maddali, Christophe Marchand, Mamuka Kvaratskhelia, Yves Pommier, Terrence R. Burke Jr.

Faculty Publications

HIV-1 integrase (IN) inhibitors represent a new class of highly effective anti-AIDS therapeutics. Current FDA-approved IN strand transfer inhibitors (INSTIs) share a common mechanism of action that involves chelation of catalytic divalent metal ions. However, the emergence of IN mutants having reduced sensitivity to these inhibitors underlies efforts to derive agents that antagonize IN function by alternate mechanisms. Integrase along with the 96-residue multifunctional accessory protein, viral protein R (Vpr), are both components of the HIV-1 pre-integration complex (PIC). Coordinated interactions within the PIC are important for viral replication. Herein, we report a 7-mer peptide based on the shortened Vpr …

Predictions Generated From A Simulation Engine For Gene Expression Micro-Arrays For Use In Research Laboratories, Gopinath R. Mavankal, John Blevins, Dominique Edwards, Monnie Mcgee, Andrew Hardin

SMU Data Science Review

In this paper we introduce the technical components, the biology and data science involved in the use of microarray technology in biological and clinical research. We discuss how laborious experimental protocols involved in obtaining this data used in laboratories could benefit from using simulations of the data. We discuss the approach used in the simulation engine from [7]. We use this simulation engine to generate a prediction tool in Power BI, a Microsoft, business intelligence tool for analytics and data visualization [22]. This tool could be used in any laboratory using micro-arrays to improve experimental design by comparing how predicted …

Identification Of Coliphages In The Aviary At Brookgreen Gardens And The Factors That Might Influence Coliphage Population Dynamics In This Cypress Swamp Environment, Olivia Shirley, Lisa Pieterse, Paul E. Richardson

Journal of the South Carolina Academy of Science

It has been understood that the presence of coliphages (bacteriophages specific for E. coli) in water is an indirect measurement of fecal contamination. Bacteriophages have been suggested to hold an important role in regulating the bacterial population. This pilot study analyzes the relationship between the presence of coliphages in the water in the aviary at Brookgreen Gardens and how environmental factors such as temperature, pH, and turbidity affect the presence of these viruses over the time period of three months (June 2017 through August 2017). Coliphages found in volary water sources were speculated to be deposited directly by birds that …

Investigating The Lytic Staphylococcus Aureus Bacteriophage Reservoir Amongst A South Carolina University Population: Discovery, Characterization, And Identification Of A Potential Bacteriophage Treatment For Methicillin-Resistant Staphylococcus Aureus, Lisa Pieterse, Amy Powers, Derek Pride, Lisha Van Onselen, Giovanna E. Leone, Paul E. Richardson

Journal of the South Carolina Academy of Science

Bacteriophages are viruses that only infect bacterial cells and can be used to treat antibiotic resistant bacterial infections. This study focused on the isolation and characterization of bacteriophages lytic to Staphylococcus aureus at Coastal Carolina University (CCU) in Conway, South Carolina, as a means to isolate bacteriophages that can potentially be used to treat methicillin-resistant Staphylococcus aureus (MRSA), an antibiotic-resistant S. aureus variant. From 2014 to 2018, collection of ear and nose samples from 225 randomly selected CCU volunteers was conducted. Filter sterilization, amplification, microbial tests, and PCR analyses were performed in order to identify and characterize bacteriophages. Coliphage populations …

Regulating Mirna Biogenesis By Small Molecules, Hao Yan

Chemistry and Chemical Biology ETDs

MiRNAs are key cellular regulators and their dysregulation is associated with many human diseases. The development of miRNA inhibitors has significant implications for the therapy of diseases associated with aberrant miRNA expression. It also provides chemical tools for studying miRNA function. This dissertation focuses on the development of small-molecule based miRNA inhibitors targeting miRNA biogenesis.

The dissertation consists of four chapters. In Chapter 1, the biogenesis of miRNA was first introduced, followed by the explanation of miRNA function in health and disease. Then the approaches used for regulating miRNA were reviewed. Finally, the difficulties with miRNA regulation were summarized.

One …

Perils Of The Fungal Kingdom: Mycotoxins In Food And Feed, Adrianna Isobel Pribil

LSU Master's Theses

Humans and fungi have a complex relationship, especially in regards to the many fungal secondary metabolites that can be produced. When secondary metabolites are toxic to animals and humans they are defined as mycotoxins. Fungi can grow on crops pre-harvest and post-harvest, and have the potential to produce mycotoxins which occur regularly in animal feed and food for human consumption. In high doses, mycotoxins cause variety of problems that result in economic losses and extreme health issues. However, multiple mycotoxins will co-occur in nature and commonly occur in low doses. Thus chronic low daily doses of multiple mycotoxins overtime may …

Commentary: Plastic Waste Associated With Disease On Coral Reefs, Gorka Bidegain, Ika Paul-Pont

Faculty Publications

No abstract provided.

Interrogation Of Protein Function With Peptidomimetics, Olapeju Bolarinwa

USF Tampa Graduate Theses and Dissertations

Proteins can be described as the “machineries” responsible for almost all tasks in the levels of organizational complexity in multi-cellular organisms namely: the cells, tissues, organs and systems. Any disorder in the function of a protein at any of these levels could result in disease, and a study of protein function is critical to understanding the pathological features of the disease at the molecular level. A quick glance at these abundantly present proteins reveals two striking features: large diversity of biological function, and the variations in structural complexity, which varies from simple random coils, to turns and helices, and on …

Applications Of Big Knowledge Summarization, Ling Zheng

Dissertations

Advanced technologies have resulted in the generation of large amounts of data ("Big Data"). The Big Knowledge derived from Big Data could be beyond humans' ability of comprehension, which will limit the effective and innovative use of Big Knowledge repository. Biomedical ontologies, which play important roles in biomedical information systems, constitute one kind of Big Knowledge repository. Biomedical ontologies typically consist of domain knowledge assertions expressed by the semantic connections between tens of thousands of concepts. Without some high-level visual representation of Big Knowledge in biomedical ontologies, humans cannot grasp the "big picture" of those ontologies. Such Big Knowledge orientation …

Plastics And Microplastics As Vectors For Bacteria And Human Pathogens, Amanda Lee Laverty

OES Theses and Dissertations

Since plastics degrade very slowly, they remain in the environment on much longer timescales than most natural substrates and can thus provide a novel habitat for colonization by bacterial communities. The full spectrum of relationships between plastics and bacteria, however, is little understood. The objective of this study was to examine marine plastic pollution as a substrate for bacteria, with particular focus on Vibrio spp., including the human pathogens, Vibrio cholerae, Vibrio parahaemolyticus, and Vibrio vulnificus.

Colonization experiments were set up in a tributary of the lower Chesapeake Bay to follow Vibrio spp. colonization and …

Characterizing The Activity Of Antimicrobial Peptides Against The Pathogenic Bacterium Clostridium Difficile In An Anaerobic Environment, Adenrele Mojeed Oludiran

Chemistry & Biochemistry Theses & Dissertations

Clostridium difficile is an anaerobic Gram-positive pathogen with high treatment costs and mortality and very high antibiotic tolerance. Antimicrobial host-defense peptides (HDPs) produced naturally by animal immune systems are promising candidates to develop novel therapies for bacterial infection because they cause oxidative stress that damages multiple targets in bacterial cells, so it is difficult for bacteria to evolve resistance to these attacks.

Piscidins, fish-derived HDPs that can also form complexes with copper (Cu) to enhance their activities, are very active against multiple bacterial species in an aerobic environment. We examined their activity against C. difficile and other species in an …

Chemical Investigation Of Bioactive Marine Extracts, Selam Hagos

USF Tampa Graduate Theses and Dissertations

Natural products have been a fundamental source of medicinal scaffolds for decades; with sixty percent of marketed drugs. Many synthetic chemists are focused on synthesizing potent and nontoxic compounds for pharmaceutical targets, however, nature is still proving to be a source of new bioactive compounds. Produced by the host organism for defense, reproduction and communication, secondary metabolites also demonstrate promising bioactivity against human pathogens. Hence, natural product chemists continue their quest for new leads.

As a continuation of these efforts, this thesis attempts to explore fungi and sponges for new chemistry, and ultimately, new drug candidates. Antarctica is largely untapped; …

A Comparative Study On Coastal Zone Changes And Anthropogenic Impacts Between Tampa Bay, Usa, And Xiangshan Harbor, China, During The Last 30 Years, Qiandong Guo

USF Tampa Graduate Theses and Dissertations

Currently, the U.S. and China are the two largest national economic entities in the world. However, it is noticeable that the two countries have considerably different strategies for economic development, environmental protection and land supply in coastal zones. In order to understand the coastline dynamics, land use land cover (LULC) changes and land management policies in the U.S. and China, a case study of the Tampa Bay (TB) watershed, Florida, U.S., and Xiangshan Harbor (XH), Zhejiang Province, China was conducted. The two areas possess similar humid subtropical climate and dense population, but experienced different anthropogenic impacts. TB sat at a …

Full Issue 47(2)

International Journal of Speleology

No abstract provided.

Ripple Effects Of The Belo Monte Dam: A Syndemic Approach To Addressing Health Impacts For The Downstream Community Of Gurupá, Cynthia A. Pace

USF Tampa Graduate Theses and Dissertations

This dissertation examines the public health impacts of a large dam project on a downstream community using the framework of Syndemic Theory. The particular focus is the Belo Monte Dam, located in the Brazilian Amazon, and its impact on the community of Gurupá, Pará. At the present time the Belo Monte Dam, which is nearing completion, stands out in scale as being the world’s third largest dam complex. Gurupá is a community well known (and well-studied) in the social science literature as Amazon Town. The aims of this study are to assess the pre-existing public health of Gurupá, as well …

Channel Capacity Analysis Of Diffusion-Based Molecular Communication Model, Cheng Zhen, Lin Fei, Yanjing Lei, Huiting Zhao

Journal of System Simulation

Abstract: At present, the research on the channel capacity of diffusion-based molecular communication (DBMC) model is very limited. In the slotted point to point communication scenario, considering all the inter-symbol interferences from all the previous time slots, the optimal decisive threshold is provided by using the criterion of minimum average error probability in the detection process for the receiver nanomachine, and the mutual information expression is derived in DBMC model. Thus channel capacity of this model is analyzed. The simulation results show that the different parameters have important influences on the channel capacity. Compared to the existed point to point …

Simulation Of Hot Event Propagation Based On Game Theory And Sirs, Dezhi Wei, Fuji Chen, Lina Lin

Journal of System Simulation

Abstract: The hot events of the internet public opinion spread fast and have great influence. It has become a topic of concern for netizens and governments. The spread of hot spots on the internet is similar to the dynamics of infectious diseases, so a traditional SIRS epidemic model based improved model is proposed, combining the analysis of the game theory. The evolutionary game model of infectious body and immune body is constructed, the equilibrium point of the game is found and the law of the spread of hot spots is obtained. The model is verified by experiment through the …

The Immunity Of The Many: Ethical Considerations Of Vaccinations In Light Of Herd Immunity, Sophia Koval

Dartmouth Undergraduate Journal of Science

No abstract provided.

Visualization And Quantification Of Cancer-Associated Enzymes With Fluorescent Small-Molecule Substrate Probes, Zhenhua Shen

LSU Doctoral Dissertations

Fluorescence imaging can be used both as a tool to diagnose diseases and guide treatment in clinical settings, and as a technique to monitor dynamic events or biological species in basic research. Therefore, there is a great need for the development of a multitude of fluorescent probes that can be incorporated with fluorescence imaging techniques to track and report endogenous enzymes with high specificity and selectivity. In contrast to always-on and targeted always-on fluorescent probes that continually emit light, activity-based substrate probes either emit low numbers of photons or are completely quenched. They can be converted to highly fluorescent reporters …

Evaluating Beach Water Quality And Dengue Fever Risk Factors By Satellite Remote Sensing And Artificial Neural Networks, Abdiel Elias Laureano-Rosario

USF Tampa Graduate Theses and Dissertations

Climatic variations, together with large-scale environmental forces and human development affect the quality of coastal recreational waters, creating potential risks to human health. These environmental forces, including increased temperature and precipitation, often promote specific vector-borne diseases in the Caribbean and Gulf of Mexico. Human activities affect water quality through discharges from urban areas, including nutrient and other pollutants derived from wastewater systems. Both water quality of recreational beaches and vector-borne diseases can be better managed by understanding their relationship with local environmental forces.

I evaluated how changes in vector-borne diseases and poor recreational water quality were related to specific environmental …

Global Stability Of Ebola Virus Disease Model With Contact Tracing And Quarantine, Chinwendu E. Madubueze, Anande R. Kimbir, Terhemen Aboiyar

Applications and Applied Mathematics: An International Journal (AAM)

This study considers a deterministic model of Ebola Virus Disease (EVD) incorporating contact tracing and quarantine as interventions. The model analyze the existence and stability of Disease-Free Equilibrium (DFE) and Endemic Equilibrium (EE) states. The local stability of EE is established using centre manifold theorem. The global stability of the two equilibrium states are obtained by constructing the Lyapunov function. Numerical simulations are carried out to examine the impact of contact tracing and quarantine measures on the transmission dynamics of EVD. The result indicates that EVD could be eliminated faster when contact tracing and quarantine measures are implemented together.

The Prairie Naturalist: The Journal Of The Great Plains Natural Science Society Volume 50 No. 1

The Prairie Naturalist

TABLE OF CONTENTS

1 EDITOR’S NOTE

RESEARCH ARTICLES

3 Spatiotemporal Distribution of Waterfowl Disease Outbreaks in Kansas, USA Thomas A. Becker, Adam A. Ahlers, Shane Hesting, and David A. Haukos

14 Wild Turkey Occupancy in a Prairie Landscape Joshua C. Courlas and R. Scott Lutz

24 Age and Growth of Cottonwood Trees along the Missouri River, North Dakota Jonathan M. Friedman, Fisher R. Ankeny, and Marshall Wolf

NOTES

34 Hoary Bat Impaled on Barbed Wire Fence

37 Lekking Behavior of a Sharp-Tailed Grouse in South-Central Nebraska

BOOK REVIEWS

40 Force of Nature: George Fell, Founder of The Natural Areas Movement. …

Examining Multimorbidities Using Association Rule Learning, Kaylee Dudley

Undergraduate Honors Theses

All insurance companies, regardless of the kind of insurance they offer, do their best to predict the future by comparing current to historical information. Any statistically significant correlation, regardless of expectations and hidden factors, can help to actuarially model future behavior. Using deidentified data from over 6 million health insurance policies over one year, we looked for any significant groupings of medical issues. The medical issues are defined based on the commercial “Episode Treatment Groups” (ETGs) classification, and our claims contain 347 different ETGs. We performed different kinds of analysis, including Bayesian posterior cluster analysis, k-means cluster analysis, and association …

Deconvoluting The Effects Of Surface Chemistry And Nanoscale Topography: Pseudomonas Aeruginosa Biofilm Nucleation On Si-Based Substrates, Jing Zhang, Jingling Huang, Carmen Say, Robert L. Dorit, Kate Queeney

Chemistry: Faculty Publications

Hypothesis

The nucleation of biofilms is known to be affected by both the chemistry and topography of the underlying substrate, particularly when topography includes nanoscale (nm) features. However, determining the role of topography vs. chemistry is complicated by concomitant variation in both as a result of typical surface modification techniques. Analyzing the behavior of biofilm-forming bacteria exposed to surfaces with systematic, independent variation of both topography and surface chemistry should allow differentiation of the two effects.

Experiments

Silicon surfaces with reproducible nanotopography were created by anisotropic etching in deoxygenated water. Surface chemistry was varied independently to create hydrophilic (OH- terminated) …

Spatiotemporal Distribution Of Waterfowl Disease Outbreaks In Kansas, Usa, Thomas A. Becker, Adam A. Ahlers, Shane Hesting, David A. Haukos

The Prairie Naturalist

Causes and impacts of disease outbreaks in wild bird populations are rarely studied beyond documentation of large epizootic events. In Kansas, USA, a central disease surveillance and reporting protocol currently does not exist within the Kansas Department of Wildlife, Parks and Tourism, which has led to a lack of available knowledge of disease occurrences that could be used to predict and manage future outbreaks. We compiled historic records of documented waterbird disease outbreaks in Kansas from 1967–2014 and related the frequency of outbreaks with light geese (Ross’s goose [Anser rossii]; Snow goose [A. caerulescens]) populations from 1970–2014. We found 32 …

Development Of Affinity Monoliths In 3d Printed Microfluidic Devices For Extraction Of Preterm Birth Biomarkers, Ellen Kelsey Parker

Theses and Dissertations

Preterm birth (PTB) is defined as birth before the 37th week of pregnancy and affects 15 million infants per year. Presently, there is no clinical test to determine PTB risk. A 3D printed microfluidic device is being developed as a clinical test for PTB risk via detection of a panel of biomarkers. A significant step is extraction of the PTB biomarkers from blood serum. In this work, I developed 3D printed microfluidic devices in which monoliths can be polymerized. Using the monolith as a solid support to attach antibody, I show that ferritin, one of the PTB biomarkers, can be …

Investigating The Impact Of Seasonal Variations On The Dynamics Of Chikungunya, Md Rafiul Islam

Biology and Medicine Through Mathematics Conference

No abstract provided.

Correlates Of Adherence To Antiretroviral Therapy Among Hiv-Positive Young Men Who Have Sex With Men, Janelle Flores, Douglas Bruce

DePaul Discoveries

Adherence to antiretroviral therapy (ART) is important in HIV management. The objective of this study was to analyze the risk factors for non-adherence to ART in HIV-positive young men who have sex with men (YMSM). Data pertaining to possible risk factors for non-adherence was collected from ATN086-106, a study protocol within the Adolescent Trials Network of HIV/AIDS Interventions (ATN). Variables that were significantly associated with non-adherence to ART in bivariate analyses were entered into multivariate logistic regression models to identify correlates of non-adherence to ART. The results indicate that YMSM who used marijuana and methamphetamine and missed medical appointments were …

Parameter Sensitivity Analysis Of A Infectious Disease Model And Identifying Dominant Transmission Pathways, Md Rafiul Islam

Biology and Medicine Through Mathematics Conference

No abstract provided.