Digital Commons Network^™

Functional Analysis Reveals G/U Pairs Critical For Replication And Trafficking Of An Infectious Non-Coding Viroid Rna, Jian Wu, Cuiji Zhou, James Li, Chun Li, Xiaorong Tao, Neocles B. Leontis, Craig L. Zirbel, David M. Bisaro, Biao Ding

Mathematics and Statistics Faculty Publications

While G/U pairs are present in many RNAs, the lack of molecular studies to characterize the roles of multiple G/U pairs within a single RNA limits our understanding of their biological significance. From known RNA 3D structures, we observed that the probability a G/U will form a Watson-Crick (WC) base pair depends on sequence context. We analyzed 17 G/U pairs in the 359-nucleotide genome of Potato spindle tuber viroid (PSTVd), a circular non-coding RNA that replicates and spreads systemically in host plants. Most putative G/U base pairs were experimentally supported by selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE). Deep …

Economic Estimates Of Invasive Wild Pig Damage To Crops In 12 Us States, Sophie Mckee, Aaron Anderson, Keith Carlisle, Stephanie A. Shwiff

United States Department of Agriculture Wildlife Services: Staff Publications

We report the results of a survey on invasive wild pig (Sus scrofa L.) damage and control in 12 US states (Alabama, Arkansas, California, Florida, Georgia, Louisiana, Mississippi, Missouri, North Carolina, Oklahoma, South Carolina, and Texas). The crops chosen for this study represent the “second-tier” in terms of economic importance after the six crops that were the subject of Anderson et al. (2016). The survey was distributed by the USDA National Agricultural Statistical Service (NASS) in the summer of 2019 to a sample of producers in each of the states (except California) of the following six crops: hay, pecans (Carya …

Rabies Management Implications Based On Raccoon Population Density Indexes, Dennis Slate, Brandi D. Saidy, Ashlee Simmons, Kathleen M. Nelson, Amy Davis, Timothy P. Algeo, Stacey A. Elmore, Richard B. Chipman

United States Department of Agriculture Wildlife Services: Staff Publications

An estimate or index of target species density is important in determining oral rabies vaccination (ORV) bait densities to control and eliminate specific rabies variants. From 1997–2011, we indexed raccoon (Procyon lotor) densities 253 times based on cumulative captures on 163 sites from Maine to Alabama, USA, near ORV zones created to prevent raccoon rabies from spreading to new areas. We conducted indexing under a common cage trapping protocol near the time of annual ORV to aid in bait density decisions. Unique raccoons (n = 8,415) accounted for 68.0% of captures (n = 12,367). We recaptured raccoons 2,669 times. We …

Individual And Population Fitness Consequences Associated With Large Carnivore Use Of Residential Development, Heather Johnson, David L. Lewis, Stewart W. Breck

United States Department of Agriculture Wildlife Services: Staff Publications

Large carnivores are negotiating increasingly developed landscapes, but little is known about how such behavioral plasticity influences their demographic rates and population trends. Some investigators have suggested that the ability of carnivores to behaviorally adapt to human development will enable their persistence, and yet, others have suggested that such landscapes are likely to serve as population sinks or ecological traps. To understand how plasticity in black bear (Ursus americanus) use of residential development influences their population dynamics, we conducted a 6-yr study near Durango, Colorado, USA. Using space-use data on individual bears, we examined the influence of use of residential …

Migratory Flyways May Affect Population Structure In Double‐Crested Cormorants, Steven J.A. Kimble, Brian S. Dorr, Katie C. Hanson-Dorr, Olin E. Rhodes Jr., Travis L. Devault

United States Department of Agriculture Wildlife Services: Staff Publications

Double‐crested cormorants (Phalacrocorax auritus) recovered from a demographic bottleneck so well that they are now considered a nuisance species at breeding and wintering grounds across the United States and Canada. Management of this species could be improved by refining genetic population boundaries and assigning individuals to their natal population. Further, recent radio‐telemetry data suggest the existence of Interior and Atlantic migratory flyways, which could reduce gene flow and result in substantial genetic isolation. In this study, we used 1,784 individuals collected across the eastern United States, a large panel of microsatellite markers developed for this species, and individuals banded as …

Effects Of Deepwater Horizon Oil On Feather Structure And Thermoregulation In Gulls: Does Rehabilitation Work?, Katherine Horak, Nicole L. Barrett, Jeremy W. Ellis, Emma M. Campbell, Nicholas G. Dannemiller, Susan A. Shriner

United States Department of Agriculture Wildlife Services: Staff Publications

Impacts of large-scale oil spills on avian species are far-reaching.While media attention often focuses on lethal impacts, sub-lethal effects and the impacts of rehabilitation receive less attention. The objective of our study was to characterize effects of moderate external oiling and subsequent rehabilitation on feather structure and thermoregulation in gulls. We captured 30 wild ring-billed gulls (Larus delawarensis) and randomly assigned each individual to an experimental group: 1) controls, 2) rehabilitated birds (externally oiled, rehabilitated by washing), or 3) oiled birds (externally oiled, not rehabilitated). We externally oiled birds with weathered MC252 Deepwater Horizon oil (water for controls) …

Rainfall, Precipitation, And Drought Patterns Associated With Wintertime Transmission Of Eastern Equine Encephalitis Virus (Eeev) In Florida, Bestami Cevher

USF Tampa Graduate Theses and Dissertations

Eastern Equine encephalitis virus (EEEV) is a highly pathogenic alphavirus that causes disease in humans and horses. EEEV cases are common in the eastern North America, especially in horses in the State of Florida. EEEV cases are most common in Florida during May to August but also occur year-round, unlike most other locations. According to the Florida Department of Health, 65 EEEV horse cases were documented in the winter months between 2005 and 2018. This study investigates the meteorological activities that affect the wintertime transmission of the EEEV virus to horses. In this, we examined meteorological data up to a …

Optimal Bait Density For Delivery Of Acute Toxicants To Vertebrate Pests, Kim M. Pepin, Nathan P. Snow, Kurt C. Vercauteren

United States Department of Agriculture Wildlife Services: Staff Publications

Oral baiting is a fundamental method for delivering toxicants to pest species. Planning baiting strategies is challenging because bait-consumption rates depend on dynamic processes including space use and demographics of the target species. To determine cost-effective strategies for optimizing baiting, we developed a spatially explicit model of population dynamics using field-based measures of wild-pig (Sus scrofa) space use, bait consumption, and mortality probabilities. The most cost-effective baiting strategy depended strongly on the population reduction objective and initial density. A wide range of baiting strategies were cost-effective when the objective was 80% population reduction. In contrast, only a narrow range of …

Brodifacoum Residues In Fish Three Years After An Island-Wide Rat Eradication Attempt In The Tropical Pacific, Shane R. Siers, Aaron B. Shiels, Steven F. Volker, Kristen Rex, William C. Pitt

United States Department of Agriculture Wildlife Services: Staff Publications

Invasive rats are known to threaten natural resources and human health and safety. Island-wide rat eradication attempts have been increasing in number and scale during the past several decades, as has the frequency of eradication success. The most common method to remove all rats from an island is to broadcast anticoagulant rodenticide bait into every rat’s home range on the island. Broadcast of toxicants can put humans and other nontarget species in marine and terrestrial environments at risk of exposure. The persistence of anticoagulant residues is somewhat unknown, particularly in marine environments. Three years after ~ 18,000 kg of 25 …

Estimation Of Conditional Power For Cluster-Randomized Trials With Interval-Censored Endpoints, Kaitlyn Cook, Rui Wang

Harvard University Biostatistics Working Paper Series

Cluster-randomized trials (CRTs) of infectious disease preventions often yield correlated, interval-censored data: dependencies may exist between observations from the same cluster, and event occurrence may be assessed only at intermittent clinic visits. This data structure must be accounted for when conducting interim monitoring and futility assessment for CRTs. In this article, we propose a flexible framework for conditional power estimation when outcomes are correlated and interval-censored. Under the assumption that the survival times follow a shared frailty model, we first characterize the correspondence between the marginal and cluster-conditional survival functions, and then use this relationship to semiparametrically estimate the cluster-specific …

Predicting Livestock Depredation Risk By African Lions (Panthera Leo) In A Multi-Use Area Of Northern Tanzania, K. Beattie, E. R. Olson, B. Kissui, A. Kirschbaum, C. Kiffner

United States National Park Service: Publications

Human-wildlife conflicts, especially those involving large carnivores, are of global conservation and livelihood concern and require effective and locally-adapted prevention measures. Risk of lion attack on livestock (i.e. depredation) may vary seasonally and may be associated with variation in wild prey abundance or landscape characteristics. To test these competing hypotheses, we used a resource selection approach, and determined whether prey catchability (indicated by geo-spatial variables), or prey availability (indicated by modeled abundance recorded via camera traps) explained spatial and seasonal variation in livestock depredation risk by African lions on Manyara Ranch Conservancy, a multi-use area in northern Tanzania. Seasonal variation …

Local Adaptation Constrains Drought Tolerance In A Tropical Foundation Tree, Kasey E. Barton, Casey Jones, Kyle F. Edwards, Aaron B. Shiels, Tiffany Knight

United States Department of Agriculture Wildlife Services: Staff Publications

1. Plant species with broad climatic ranges might be more vulnerable to climate change than previously appreciated due to intraspecific variation in climatic stress tolerance. In tropical forests, drought is increasingly frequent and severe, causing widespread declines and altering community dynamics. Yet, little is known about whether foundation tropical trees vary in drought tolerance throughout their distributions, and how intraspecific variation in drought tolerance might contribute to their vulnerability to climate changE.
2. We tested for local adaptation in seedling emergence and establishment with a full-factorial reciprocal transplant experiment including 27 populations and 109,350 seeds along a 3,500 mm precipitation gradient for …

Peregrine Falcon Survival Rates Derived From A Long-Term Study At A Migratory And Overwintering Area In Coastal Washington, D.E. Varland, L.A. Powell, J.B. Buchanan, T.L. Fleming, C. Vanier

School of Natural Resources: Faculty Publications

No abstract provided.

Genetic And Evolutionary Considerations Of The Chronic Wasting Disease – Human Species Barrier, Robert M. Zink

School of Natural Resources: Faculty Publications

Transmissible spongiform encephalopathies can jump species barriers. In relatively few cases is the possible route of transmission thought to be known, mostly involving humans, cattle and sheep. It is thought that sheep might be the cause of Bovine Spongiform Encephalopathy (BSE) and Chronic Wasting Disease (CWD) in cervids, and that humans might have gotten prion disease (e.g., vCJD) from eating meat from BSE+ cows. A looming societal question is whether humans will acquire a prion disease from ingesting prions from CWD+ deer. On an evolutionary tree of the PRNP gene in mammals, deer, sheep and cow are relatively closely related, …

Randomization-Based Confidence Intervals For Cluster Randomized Trials, Dustin J. Rabideau, Rui Wang

Harvard University Biostatistics Working Paper Series

In a cluster randomized trial (CRT), groups of people are randomly assigned to different interventions. Existing parametric and semiparametric methods for CRTs rely on distributional assumptions or a large number of clusters to maintain nominal confidence interval (CI) coverage. Randomization-based inference is an alternative approach that is distribution-free and does not require a large number of clusters to be valid. Although it is well-known that a CI can be obtained by inverting a randomization test, this requires randomization testing a non-zero null hypothesis, which is challenging with non-continuous and survival outcomes. In this paper, we propose a general method for …

Power Calculation For Cross-Sectional Stepped-Wedge Cluster Randomized Trials With Binary Outcomes, Linda J. Harrison, Rui Wang

Harvard University Biostatistics Working Paper Series

Power calculation for stepped-wedge cluster randomized trials (SW-CRTs) presents unique challenges, beyond those of standard cluster randomized trials (CRTs), due to the need to consider temporal within cluster correlations and background period effects. To date, power calculation methods specific to SW-CRTs have primarily been developed under a linear model. When the outcome is binary, the use of a linear model corresponds to assessing a prevalence difference; yet trial analysis often employs a non-linear link function. We assess power for cross-sectional SW-CRTs under a logistic model fitted by generalized estimating equations. Firstly, under an exchangeable correlation structure, we show the power …

A Game-Theoretic Model Of Monkeypox To Assess Vaccination Strategies, Sri Vibhaav Bankuru, Samuel Kossol, William Hou, Parsa Mahmoudi, Jan Rychtář, Dewey Taylor

Mathematics and Applied Mathematics Publications

Monkeypox (MPX) is a zoonotic disease similar to smallpox. Its fatality rate is about 11% and it is endemic to the Central and West African countries. In this paper, we analyze a compartmental model of MPX dynamics. Our goal is to see whether MPX can be controlled and eradicated by voluntary vaccinations. We show that there are three equilibria—disease free, fully endemic and previously neglected semi-endemic (with disease existing only among humans). The existence of semi-endemic equilibrium has severe implications should the MPX virus mutate to increased viral fitness in humans. We find that MPX is controllable and can be …

Markov Chain Epidemic Models And Parameter Estimation, Oluwatobiloba Ige

Theses, Dissertations and Capstones

Over the years, various parts of the world have experienced disease outbreaks. Mathematical models are used to describe these outbreaks. We study the transmission of disease in simple cases of disease outbreaks by using compartmental models with Markov chains. First, we explore the formulation of compartmental SIS (Susceptible-Infectious-Susceptible) and SIR (Susceptible-Infectious-Recovered) disease models. These models are the basic building blocks of other compartmental disease models. Second, we build SIS and SIR disease models using both discrete and continuous time Markov chains. In discrete time models, transmission occurs at fixed time steps, and in continuous time models, transmission may occur at …

A Review Of The Current Testing Methods For Sars-Cov-2 In The Us, Joshua Korn-Heilner

Seton Hall Biochemistry II Annals of Student Reviews

On March 11th 2020, the WHO classified the Covid-19 out-break as a pandemic1. As of May 10th 2020, according the WHO Situation Report-111, there are 3,917,366 confirmed cases of Covid-19 with 274,361 deaths globally2. The estimated basic reproduction number for Covid-19 is 2.2, meaning on average a person with the disease will infect 2 other people3. As of the date this paper was written, there are no conclusive methods of treatment, nor a vaccine for Covid-194. It is because of this that, arguably, the most effective policy to preventing deaths, harm, and extending isolation policies, is with mass tracking of …

Potential Drugs And Therapies To Treat Covid-19 And Other Related Coronaviruses, Emily Borland

Seton Hall Biochemistry II Annals of Student Reviews

The novel coronavirus that has recently emerged in Wuhan, China with probable bat origin is part of the betacoronavirus family which is similar to previously seen zoonotic based out breaks in the early 2000’s with SARS as well as in 2012 with MERS1. COVID-19 is the disease obtained from being infected by the novel SARS-CoV-2 virus, which enters through ACE2 (angiotensin-converting enzyme 2) cell receptors which is similar to SARS-CoV and MERS-CoV uses the DDP4 (dipeptidyl peptidase 4) cell receptor1. SARS-CoV-2 shares approximately 80% of its genomic identity with SARS-CoV2. Currently, there is a lot research being conducted to understand …

Tufts Analytics Without Borders 2020 Conference Conference Summary Report, Tufts University

Analytics Without Borders

This conference provided a single venue for interdisciplinary research, collaboration, and communication on applied data analytics in the fields of business, public health, nutrition, and the environment. We advanced a shared agenda to harness the power of data sciences to discuss the complexities of health and nutrition problems through the lens of data sciences. The conference showcased numerous opportunities for students including hands-on workshops on topics related to data sciences, panel discussions on topics ranging from business to health, and both oral and poster presentations for sharing research.

Development Towards An Ethylene Sensing Artificial Metalloenzyme, Mitchell Lee Ellinwood

Electronic Theses and Dissertations

Ethylene (ethene) is the essential ripening hormone for climacteric plants, and consequently its detection and quantification is of considerable interest to the horticulture industry. Its detection however is a non-trivial pursuit, traditionally requiring expensive and inaccessible instrumentation that fail to provide in vivo information about ethylene. A ruthenium based fluorescent probe for the selective detection of ethylene has recently been developed, and it was envisioned that this probe could be made biocompatible by encasing it within a protein scaffold making it an artificial metalloenzyme. To this end biotinylated N-heterocyclic carbenes (NHCs) were synthesized, which can be appended onto the ruthenium …

Influence Of Conformational Restriction On The Antibacterial Activity And Ribosomal Selectivity Of Aminoglycoside Antibiotics, Michael Gabriel Pirrone

Wayne State University Dissertations

The ever-increasing threat posed by multidrug-resistant infectious bacteria necessitates

the development of novel antibiotics. Aminoglycoside antibiotics are growing in interest due to

their broad spectrum of activity, lack of known drug related allergies, low manufacturing cost,

and their well-studied mechanism of action. The simplification of rational drug design due to the

well-studied mechanism of action is the key to overcoming the issues presented by these drugs,

namely ototoxicity and nephrotoxicity.

A study of the effect of the conformation of the aminoglycoside ring I side chain is

described wherein it was discovered that an increase in a particular conformation augments the …

Critical Analysis Of The Value Of Drought Information And Impacts On Land Management And Public Health, Tingting Liu, Kelly Helm Smith, Richard Krop, Tonya Haigh, Mark Svoboda

National Drought Mitigation Center: Faculty Publications

This paper reviews previous efforts to assign monetary value to climatic or meteorological information, such as public information on drought, climate, early warning systems, and weather forecast information. Methods and tools that have been explored to examine the benefits of climatic and meteorological information include the avoided cost, contingent valuation, choice experiments, benefit transfer, and descriptive approaches using surveys. The second part of this paper discusses specific considerations related to valuing drought information for public health and the Bureau of Land Management. We found a multitude of connections between drought and the land management and health sectors in the literature. …

Using Climate To Explain And Predict West Nile Virus Risk In Nebraska, Kelly Smith, Andrew Tyre, Jeff Hamik, Michael 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, …

Geographic Distribution Of Chronic Wasting Disease Resistant Alleles In Nebraska, With Comments On The Evolution Of Resistance, H. Vazquez-Miranda, R. M. Zink

School of Natural Resources: Faculty Publications

No abstract provided.

Exploring The Scope And Limitations Of The Oxidative Deamination Of N-Acetyl Neuraminic Acid, Mohammed Bakr Hawsawi

Wayne State University Dissertations

Sialic acids are molecules of importance in the fields of carbohydrate chemistry and glycoscience, and their diversity make them even more attractive to scientific research. Modifications of sialic acid derivatives may lead to several biological and chemical features that can be utilized for medicinal purposes. The modern drug therapy is dependent on the chemical discoveries of potent and effective molecules. N-Acetyl neuraminic acid is the parent and most common molecule in sialic acid family that received considerable attention in glycochemical research. This dissertation explores the scope as well as the limitations of the Zbiral oxidative deamination of N-acetyl neuraminic acid …

Algebraic And Combinatorial Approaches For Counting Cycles Arising In Population Biology, Brian Chau

Honors Undergraduate Theses

Within population biology, models are often analyzed for the net reproduction number or other generalized target reproduction numbers, which describe the growth or decline of the population based on specific mechanisms. This is useful in determining the strength and efficiency of control measures for inhibiting or enhancing population growth. The literature contains many algebraic and combinatorial approaches for deriving the net reproduction number and generalized target reproduction numbers from digraphs and associated matrices. Finding, categorizing, and counting the permutations of disjoint cycles, or cycles unions is a requirement of the Cycle Union approach by Lewis et al. (2019). These cycles …

Nutrition And Health Status Of Hemodialysis Patients In Dhaka, Bangladesh, Tanjina Rahman

Wayne State University Dissertations

Methods to identify patients at risk for End stage renal disease (ESRD) are a high priority in Bangladesh, where kidney transplants/dialysis options are limited and costly. Every year, 35,000 to 40,000 people reach ESRD in Bangladesh, but currently available facilities can hardly accommodate only 9000 to 10,000 new patients with twice weekly dialysis and the remaining 66% have no access to any kind of renal replacement therapy (RRT) in the form of dialysis or transplantation. Nutrition is an important factor in maintaining good health of hemodialysis patients. However, data on nutritional status of Bangladeshi dialysis patients is limited and is …

Quantitative Analysis Of A Stochastic Seitr Epidemic Model With Multiple Stages Of Infection And Treatment, Olusegun M. Otunuga, Mobolaji O. Ogunsolu

Mathematics Faculty Research

We present a mathematical analysis of the transmission of certain diseases using a stochastic susceptible-exposed-infectious-treated-recovered (SEITR) model with multiple stages of infection and treatment and explore the effects of treatments and external fluctuations in the transmission, treatment and recovery rates. We assume external fluctuations are caused by variability in the number of contacts between infected and susceptible individuals. It is shown that the expected number of secondary infections produced (in the absence of noise) reduces as treatment is introduced into the population. By defining R_T,n and ℛ_T,n as the basic deterministic and stochastic reproduction …