Digital Commons Network^™

Enrichment Of Ontologies Using Machine Learning And Summarization, Hao Liu

Dissertations

Biomedical ontologies are structured knowledge systems in biomedicine. They play a major role in enabling precise communications in support of healthcare applications, e.g., Electronic Healthcare Records (EHR) systems. Biomedical ontologies are used in many different contexts to facilitate information and knowledge management. The most widely used clinical ontology is the SNOMED CT. Placing a new concept into its proper position in an ontology is a fundamental task in its lifecycle of curation and enrichment.

A large biomedical ontology, which typically consists of many tens of thousands of concepts and relationships, can be viewed as a complex network with concepts as …

Vampire Bats: Preparing For Range Expansion Into The U.S., Michael J. Bodenchuk, David L. Bergman

United States Department of Agriculture Wildlife Services: Staff Publications

The common vampire bat apparently is expanding its range northwards in Mexico and seems poised to enter the southern United States. Climate models predict suitable habitat in the U.S. in south Texas and parts of southern Arizona. While vampire bats’ northward range expansion is not unexpected, the fact that this species brings a strain of rabies that impacts livestock and people warrants a strategic response. Annual economic damages from bats are estimated between $7M and $9M, largely associated with deaths of livestock from rabies. To prepare for the emerging rabies issue, USDA Wildlife Services programs in Texas and Arizona have …

Get The News Out Loudly And Quickly: Modeling The Influence Of The Media On Limiting Infectious Disease, Anna Mummert, Howard Weiss

Mathematics Faculty Research

During outbreaks of infectious diseases with high morbidity and mortality, individuals closely follow media reports of the outbreak. Many will attempt to minimize contacts with other individuals in order to protect themselves from infection and possibly death. This process is called social distancing. Social distancing strategies include restricting socializing and travel, and using barrier protections. We use modeling to show that for short-term outbreaks, social distancing can have a large influence on reducing outbreak morbidity and mortality. In particular, public health agencies working together with the media can significantly reduce the severity of an outbreak by providing timely accounts of …

Expanding The Potential Prenylome: Prenylation Of Shortened Target Substrates By Ftase And Development Of Fret-Based System For Detecting Potentially “Shunted” Proteins, Sudhat Ashok

Dissertations - ALL

Protein prenylation is a posttranslational modification involving the attachment of a C15 or C20 isoprenoid group to a cysteine residue near the C-terminus of the target substrate by protein farnesyltransferase (FTase) or protein geranylgeranyltransferase type I (GGTase-I), respectively. Both of these protein prenyltransferases recognize a C-terminal "CaaX" sequence in their protein substrates, but recent studies in yeast- and mammalian-based systems have demonstrated FTase can also accept sequences that diverge in length from the canonical four-amino acid motif, such as the recently reported five-amino acid C(x)3X motif. In this work, we further expand the substrate scope of FTase by demonstrating sequence-dependent …

Soil Characteristics Associated With Horse Cases Of Eastern Equine Encephalitis Virus In Florida, Fulya Guzelkucuk

USF Tampa Graduate Theses and Dissertations

Eastern Equine Encephalitis virus (EEEV) is a mosquito-borne virus found in Florida that affects humans and horses. Also, EEEV is an agricultural land management issue in Florida, as it causes mortality in large numbers of horses each year and sometimes humans. This study investigates the characteristics of soils associated with horse cases of EEEV in the State of Florida, focusing on differences in soil characteristics between summer and winter cases. This study analyzed a total of 676 EEEV cases during 2005-2018, including 611 summer cases and 65 winter cases. Soil characteristics that were examined include: soil texture, drainage class, hydrology …

Examining The Intersection Of Environmental Justice, Chronic Disease, And Pandemics; How A Mobile Health App Could Improve Health Outcomes And Inform Policy, Jessica Snow

Master's Projects and Capstones

The purpose of this paper is to analyze the intersection of environmental justice, chronic disease and illness, and pandemics. The inequitable distribution of polluting factories, landfills, and hazardous waste sites have been a long-standing concern in the field of environmental justice. Local zoning codes and land use policies have been tools for segregating people and concentrating pollution in low-income communities and communities of color. Many studies have found that pollution varies among racial and minority groups, and the burden of pollution is not one that is evenly shared. Communities of color and low income communities are disproportionately affected by air …

Analysis Of Risks Transmission And Control In Subway Construction, Qingjun Guo, Hongyu Yan, Bosen Li

Journal of System Simulation

Abstract: The process of the transmission and control of hidden dangers in subway construction is very similar to that of infectious diseases. Based on an engineering example, the characteristics of the complex system in the subway construction site are analyzed, and a simulation method using the propagation dynamics model to describe the interaction and propagation of various elements is proposed. Hazard source and hidden danger data of a section of Qingdao metro line 4 from march to August 2017 are selected as the original state, using by MATLAB R2014a simulation calculation, the densities of different elements are gotten, the process …

Ronald E. Mcnair Scholars Program Profiles And Abstracts 2020, Mcnair Scholars Program

McNair Symposium

This is the complete event program and provides presentation abstracts and biographies of McNair scholars and their mentors.

Protocol For A National Probability Survey Using Home Specimen Collection Methods To Assess Prevalence And Incidence Of Sars-Cov-2 Infection And Antibody Response, Aaron J. Siegler, Patrick S. Sullivan, Travis Sanchez, Ben Lopman, Mansour Fahimi, Charles Sailey, Martin Frankel, Richard Rothenberg, Colleen F. Kelley, Heather Bradley

Publications and Research

Purpose: The U.S. response to the SARS-CoV-2 epidemic has been hampered by early and ongoing delays in testing for infection; without data on where infections were occurring and the magnitude of the epidemic, early public health responses were not data-driven. Understanding the prevalence of SARSCoV- 2 infections and immune response is critical to developing and implementing effective public health responses. Most serological surveys have been limited to localities that opted to conduct them and/or were based on convenience samples. Moreover, results of antibody testing might be subject to high false positive rates in the setting of low prevalence of immune …

Synthesis Of Bacterial Surface Glycans For Conjugate Vaccines, Teron D. Haynie

Theses and Dissertations

Bacteria are coated with repeating units of oligosaccharides that exhibit remarkable diversity. Often, glycan units of three or even two sugars are sufficient to identify a species of bacteria. Such specificity makes bacterial surface glycans attractive vaccine targets. However, efforts to create effective vaccines against carbohydrates have been hampered by poor vaccine design as well as the human immune tendency to respond to glycan antigens with non-specific, T-cell independent mechanisms. As a result, carbohydrate vaccines have historically produced only adequate memory responses in healthy individuals and poor responses in the elderly or immunocompromised. To circumvent these issues, a novel conjugate …

Using Climate To Explain And Predict West Nile Virus Risk In Nebraska, Kelly Helm Smith, Andrew J. Tyre, Jeff Hamik, Michael J. Hayes, Yuzhen Zhou, Li Dai

National Drought Mitigation Center: Faculty Publications

We used monthly precipitation and temperature data to give early warning of years with higher West Nile Virus (WNV) risk in Nebraska. We used generalized additive models with a negative binomial distribution and smoothing curves to identify combinations of extremes and timing that had the most influence, experimenting with all combinations of temperature and drought data, lagged by 12, 18, 24, 30, and 36 months. We fit models on data from 2002 through 2011, used Akaike's Information Criterion (AIC) to select the best‐fitting model, and used 2012 as out‐of‐sample data for prediction, and repeated this process for each successive year, …

Monarch Science Observer, Volume 5, College Of Sciences, Old Dominion University

College of Sciences Newsletter

August-Summer 2020 issue of Monarch Science Observer, ODU College of Sciences Newsletter.

A Novel Correction For The Adjusted Box-Pierce Test — New Risk Factors For Emergency Department Return Visits Within 72 Hours For Children With Respiratory Conditions — General Pediatric Model For Understanding And Predicting Prolonged Length Of Stay, Sidy Danioko

Computational and Data Sciences (PhD) Dissertations

This thesis represents the results of three research projects that underline the breadth and depth of my interests.

Firstly, I devoted some efforts to the well-known Box-Pierce goodness-of-fit tests for time series models which has been an important research topic over the last few decades. All previously proposed tests are focused on changes of the test statistics. Instead, I adopted a different approach that takes the best performing test and modifying the rejection region. Thus, I developed a semiparametric correction of the Adjusted Box-Pierce test that attains the best I error rates for all sample sizes and lags and outperforms …

Likelihood Inference For Flexible Cure Rate Models In The Context Of Infectious Diseases With Multiple Exposures, Zachry Joseph Engel

Mathematics Dissertations - Archive

Cure rate models are mostly used to study data arising from cancer clinical trials. Its use in the context of infectious diseases has not been explored well. In 2007, Tournoud and Ecochard rst proposed a mechanistic formulation of cure rate model in the context of infectious diseases with multiple exposures to infection. However, they assumed a simple Poisson distribution to capture the unobserved number of pathogens at each exposure time. In this thesis, we propose a new exible cure rate model to study infectious diseases with discrete multiple exposures to infection. This new model uses the Conway-Maxwell Poisson (COM-Poisson) distribution …

Mathematical Modeling Of Scavengers And Zebras On The African Savanna With Disease Dynamics, Crystal Dawn Mackey

Mathematics Dissertations - Archive

The purpose of this dissertation is to use mathematical models to see how anthrax in the zebra population in Etosha National Park (ENP) interacts with scavenger populations and disease dynamics. First, we study if scavengers can save zebras from anthrax. Then we introduce a disease in the jackal population to see if anthrax in zebras can help propagate rabies in jackals. Finally, the last two models we develop describe the interaction between competing scavengers: jackals and vultures, with exploitative and interference competition. ENP is home to many different animals such as lions, jackals, hyenas, zebras, elephants, etc. Each year grazing …

Inverse Problems For Polynomial And Rational Matrices, Richard Allen Hollister

Dissertations

Inverse problems have long been studied in mathematics not only because there are many applications in science and engineering, but also because they yield new insight into the beauty of mathematics. Central to the subject of linear algebra is the eigenvalue problem: given a matrix, and its eigenvalues (numerical invariants). Eigenvalue problems play a key role in almost every field of scientific endeavor from calculating the vibrational modes of a molecule to modeling the spread of an infectious disease, and so have been studied extensively since the time of Euler in the 18th century.

If a typical matrix eigenvalue problem …

Traffic Impacts Of The Covid-19 Pandemic: Statewide Analysis Of Social Separation And Activity Restriction, Scott Parr, Brian Wolshon, John Renne, Pamela Murray-Tuite, Karl Kim

Faculty Publications

The COVID-19 pandemic resulted in significant social and economic impacts throughout the world. In addition to the health consequences, the impacts on travel behavior have also been sudden and wide ranging. This study describes the drastic changes in human behavior using the analysis of highway volume data as a representation of personal activity and interaction. Same-day traffic volumes for 2019 and 2020 across Florida were analyzed to identify spatial and temporal changes in behavior resulting from the disease or fear of it and statewide directives to limit person-to-person interaction. Compared to similar days in 2019, overall statewide traffic volume dropped …

Severe Acute Respiratory Syndrome Coronavirus 2 Transmission Potential, Iran, 2020, Kamalich Muniz-Rodriguez, Isaac Fung, Shayesteh R. Ferdosi, Sylvia Ofori, Yiseul Lee, Amna Tariq, Gerardo Chowell

Biostatistics, Epidemiology & Environmental Health Sciences: Faculty Publications

To determine the transmission potential of severe acute respiratory syndrome coronavirus 2 in Iran in 2020, we estimated the reproduction number as 4.4 (95% CI 3.9–4.9) by using a generalized growth model and 3.5 (95% CI 1.3–8.1) by using epidemic doubling time. The reproduction number decreased to 1.55 after social distancing interventions were implemented.

Combating Covid On College Campuses: The Impact Of Structural Changes On Viral Transmissions, Jared Knofczynski, Aria Killebrew Bruehl, Ben Warner, Ryne Shelton

altREU Projects

One of the most significant issues in the COVID-19 pandemic is the reopening of schools while minimizing the transmission of coronavirus. Opportunities for evaluating the effectiveness of policies that might be utilized at such institutions are limited, as the necessary empirical data has not been gathered yet. Agent-based modeling, where various entities within an environment are simulated as agents, offers an opportunity to examine the effectiveness of various policies in a way that drastically minimizes the health and economic risks involved. Agent-based modeling is common within biology, ecology and other fields; and has seen some use within the coronavirus literature. …

Learning Dynamics From Large Biological Data Sets: Machine Learning Meets Systems Biology, William Gilpin, Yitong Huang, Daniel B. Forger

Mathematics Sciences: Faculty Publications

In the past few decades, mathematical models based on dynamical systems theory have provided new insight into diverse biological systems. In this review, we ask whether the recent success of machine learning techniques for large-scale biological data analysis provides a complementary or competing approach to more traditional modeling approaches. Recent applications of machine learning to the problem of learning biological dynamics in diverse systems range from neuroscience to animal behavior. We compare the underlying mechanisms and limitations of traditional dynamical models with those of machine learning models. We highlight the unique role that traditional modeling has played in providing predictive …

Pathogens, Endosymbionts, And Blood-Meal Sources Of Host-Seeking Ticks In The Fast-Changing Maasai Mara Wildlife Ecosystem, Joseph Wang’Ang’A Oundo, Jandouwe Villinger, Maamun Jeneby, George Ong’Amo, Moses Yongo Otiende, Edward Edmond Makhulu, Ali Abdulahi Musa, Daniel Obado Ouso, Lillian Wambua

All Peer-Reviewed Publications

The role of questing ticks in the epidemiology of tick-borne diseases in Kenya’s Maasai Mara National Reserve (MMNR), an ecosystem with intensified human-wildlife-livestock interactions, remains poorly understood. We surveyed the diversity of questing ticks, their blood-meal hosts, and tick-borne pathogens to understand potential effects on human and livestock health. By flagging and hand-picking from vegetation in 25 localities, we collected 1,465 host-seeking ticks, mostly Rhipicephalus and Amblyomma species identified by morphology and molecular analysis. We used PCR with high-resolution melting (HRM) analysis and sequencing to identify Anaplasma, Babesia, Coxiella, Ehrlichia, Rickettsia, and Theileria pathogens and blood-meal remnants in 231 tick …

Beliefs And Perceptions Of Millennials Pertaining To Climate Change And Sustainability, Rae Cade

Theses, Dissertations and Culminating Projects

The purpose of this qualitative multi-case study is to explore the beliefs and perceptions of millennials on the subjects of climate change and sustainability. Some millennials pursuing an undergraduate degree in a non-environmental science field may lack knowledge pertaining to climate change and sustainability. The conceptual framework for this qualitative explanatory multi-case study is grounded in contributions from Henri Lefebvre, Nicholson-Smith (1991), and Simpson (2014) who explore how the notion of space has evolved in recent years, as well as researchers who are quantitatively studying climate change and sustainability. I conducted semistructured focus groups and drafted field notes from two …

An Evaluation Of Bird And Bat Mortality At Wind Turbines In The Northeastern United States, Daniel Y. Choi, Thomas W. Wittig, Bryan M. Kluever

United States Department of Agriculture Wildlife Services: Staff Publications

Wind energy offers substantial environmental benefits, but wind facilities can negatively impact wildlife, including birds and bats. Researchers and managers have made major efforts to chronicle bird and bat mortality associated with wind facilities, but few studies have examined the patterns and underlying mechanisms of spatial patterns of fatalities at wind facilities. Understanding the horizontal fall distance between a carcass and the nearest turbine pole is important in designing effective search protocols and estimating total mortality. We explored patterns in taxonomic composition and fall distance of bird and bat carcasses at wind facilities in the Northeastern United States using publicly …

Estimation Of Wildlife Damage From Federal Crop Insurance Data, Sophie Mckee, Stephanie A. Shwiff, Aaron M. Anderson

United States Department of Agriculture Wildlife Services: Staff Publications

BACKGROUND: Wildlife damage to crops is a persistent and costly problem for many farmers in the USA. Most existing estimates of crop damage have relied on direct assessment methods such as field studies conducted by trained biologists or surveys distributed to farmers. In this paper, we describe a new method of estimating wildlife damage that exploits federal crop insurance data. We focused our study on four crops: corn, soybean, wheat, and cotton, chosen because of their economic importance and their vulnerability to wildlife damage.

RESULTS: We determined crop-raiding hot spots across the USA over the 2015–2019 period and identified the …

Spatial Ecology And Resource Selection Of Bighorn Sheep (Ovis Canadensis) Ewes In A Prairie Badlands Population, Erin Wood

School of Natural Resources: Dissertations, Theses, and Student Research

The basic spatial ecology and habitat relationships of female bighorn sheep in Nebraska are poorly understood. Establishing seasonal patterns of space use and resource selection for this population at the margin of their historical and current range addresses a key knowledge gap and provides important baseline information for ongoing conservation efforts in Nebraska. We deployed GPS radio-collars on 56 adult ewes in western Nebraska to quantify seasonal space use, movements, and resource selection of ewes. To investigate spatial ecology, we quantified movements of ewes and the factors that influence home range size, seasonal use, and spatial stability across seasons. Home …

Pre-Testing Of The Who’S Educational Video: “How To Protect Yourself Against Covid-19”, Hilyatul Fadliyah, Manendra Muhtar, Munih Munih, Sylviasari Risgiantini, Weny Wulandary, Hadi Pratomo

Kesmas

The coronavirus disease 2019 (COVID-19) pandemic, caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was declared a public health emergency in many countries, including Indonesia. The World Health Organization (WHO) released an educational video, entitled "How to Protect Yourself Against COVID-19", which explained how to prevent the spread of COVID-19. This study is a qualitative study that aims to pre-test this video, based on the Information, Education, Communication (IEC) theory, by analyzing teenagers’ perceptions of the video. The design used was a Rapid Assessment Procedure (RAP), and the data were collected by conducting in-depth interviews with participants, through …

Impact Of Lockdown In India: A Case Study Comparing Kanataka With International Model, Stelvin Sebastian, Aby Paul, Jeeva Joseph, Joel Joby, Sanjo Saijan, Jobin Kunjumon Vilapurathu

Kesmas

The COVID-19 was declared a pandemic and a global health emergency by WHO, prompting various countries to implement early and stringent social distancing protocols through lockdown, to flatten the epidemic curve. The objective of the present study was to assess the impacts and effectiveness of the lockdown protocol in Karnataka and Punjab, compared with the implementation of this method in Australia and the UK. This study involved the collection of data from different authorized databases, in two phases. The first phase included the time starting with the first-reported index case through the 14th day after the declaration of lockdown, for …

Review Of Trial Therapies And Treatment For Covid-19: Lessons For Indonesia, Halma Zahro Mukhlida, Hilma Hasro Maulida, Gunanti Khairunnisa, Margaretha Josephine Mantrono, Risky Kusuma Hartono, Rindu Rindu, Eka R W Purnamasari, Rizky Fajar Meirawan

Kesmas

The infectious disease from Coronavirus Disease 2019, or COVID-19, has quickly spread world-wide since 2019. Therapies for managing COVID-19 have yet to be confirmed as medication for the severe sickness that the disease may cause. This study aimed to review the previous research of the efficacy of trial therapy and treatment to the patients in the hospital with COVID-19. Using PRISMA guidelines as a method for conducting a systematic literature review, a total of 67 articles were collected from several online journal databases. Various therapies were found that are effective in the treatment and management of COVID-19. In accordance with …

Chemistry And Biochemistry Authored Faculty Publications: Snapshot Of The Ranking Of Journals In Which They Published Based On Data From Journal Citation Reports (Jcr), Lutishoor Salisbury, Yang Tian, Jeremy Smith

University Libraries Faculty Publications and Presentations

This report presents a snapshot of the research output of the Chemistry and Biochemistry Department at the University of Arkansas for the period 2015-2019. The contents of the report were generated using Web of Science Core Collection databases and the Journal Citation Report only. It highlights the journals in which the researchers published and the ranking of those journals.

Lectures On Mathematical Computing With Python, Jay Gopalakrishnan

PDXOpen: Open Educational Resources

This open resource is a collection of class activities for use in undergraduate courses aimed at teaching mathematical computing, and computational thinking in general, using the python programming language. It was developed for a second-year course (MTH 271) revamped for a new undergraduate program in data science at Portland State University. The activities are designed to guide students' use of python modules effectively for scientific computation, data analysis, and visualization.

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