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Individual-Level Modelling Of Infectious Disease Data: Epiilm, Vineetha Warriyar, Waleed Almutiry, Rob Deardon

The R Journal

In this article we introduce the R package EpiILM, which provides tools for simulation from, and inference for, discrete-time individual-level models of infectious disease transmission proposed by Deardon et al. (2010). The inference is set in a Bayesian framework and is carried out via Metropolis Hastings Markov chain Monte Carlo (MCMC). For its fast implementation, key functions are coded in Fortran. Both spatial and contact network models are implemented in the package and can be set in either susceptible-infected (SI) or susceptible-infected-removed (SIR) compartmental frameworks. Use of the package is demonstrated through examples involving both simulated and real data.

Preparing To Cocreate: Using Learning Circles To Readyextension Professionals For Meaningful Stakeholderengagement, Bob Bertsch, Jill Heemstra, Doug Golick

Department of Entomology: Faculty Publications

Extension professionals are being asked to address complex public issues. Doing so requires cocreativeapproaches that engage, in a significant way, the people affected by these issues. Successful engagement,however, requires specific skills and a cocreative mind-set. Extension professionals in two states participatedin learning circles to improve their engagement skills. Using a survey and interviews, we studied the impact ofthe learning circle experience on participants. We found that learning circles helped participants practicecolearning, build relationships, and change their mind-sets in ways that could move their work toward morecocreative efforts.

Coronavirus Food Assistance Program For Livestock Producers, Bradley Lubben

Extension Farm and Ranch Management News

United States Congress and the President have approved multiple phases of COVID-19 assistance to date including the $2.3 trillion CARES (Coronavirus Aid, Relief, and Economic Security) Act passed in March that provides financial support for agricultural producers as a small part of the overall relief.

While agricultural producers and agribusinesses are eligible for two programs administered through the Small Business Administration, including the Paycheck Protection Program (PPP) and Economic Injury Disaster Loans (EIDLs), the primary support for agriculture is coming from USDA through the Coronavirus Food Assistance Program (CFAP). The CARES Act provided $9.5 billion directly to the Secretary of …

Genetic Biocontrol For Invasive Species, John L. Teem, Luke Alphey, Sarah Descamps, Matt P. Edgington, Owain Edwards, Neil Gemmell, Tim Harvey-Samuel, Rachel L. Melnick, Kevin P. Oh, Antoinette J. Piaggio, J. Royden Saah, Dan Schill, Paul Thomas, Trevor Smith, Andrew Roberts

United States Department of Agriculture Wildlife Services: Staff Publications

Invasive species are increasingly affecting agriculture, food, fisheries, and forestry resources throughout the world. As a result of global trade, invasive species are often introduced into new environments where they become established and cause harm to human health, agriculture, and the environment. Prevention of new introductions is a high priority for addressing the harm caused by invasive species, but unfortunately efforts to prevent new introductions do not address the economic harm that is presently manifested where invasive species have already become established. Genetic biocontrol can be defined as the release of organisms with genetic methods designed to disrupt the reproduction …

Photographic Validation Of Target Versus Nontarget Take Of Brown Treesnake Baits, Shane R. Siers, Aaron B. Shiels, Cynthia G. Payne, Francinem M. Chlarson, Craig S. Clark, Stephen M. Mosher

United States Department of Agriculture Wildlife Services: Staff Publications

Use of toxic baits or other tools for managing nuisance species must ensure that the species of interest is adequately targeted while exposure to nontarget species is minimized. Nontarget takes of acetaminophen‐laced baits for control of invasive brown treesnakes (Boiga irregularis) on Guam may put those animals at risk of lethal intoxication and render the bait unavailable to the intended target species. We used wildlife cameras to identify species removing toxic and nontoxic baits from brown treesnake bait stations designed to exclude nontarget taxa in 2015 and 2016. Throughout various sites and habitat types, and balanced by season (wet vs. …

Time Allocation To Resources By Three Species Of Rats (Rattus Spp.) In A Radial Arm Maze, Gary Witmer, Nathan P. Snow, Rachael S. Moulton

United States Department of Agriculture Wildlife Services: Staff Publications

Context. Introduced rats (Rattus spp.) can pose a serious threat to native flora and fauna, especially on islands where most species have evolved in the absence of terrestrial predators. Effective detection and eradication methods for introduced rats are essential to the maintenance of insular ecosystem integrity. Thus, it is important to better understand the behaviour of rats when they first arrive in a new setting.

Aims. To determine whether rats would find some novel stimuli to be significantly more attractive than other novel stimuli.

Methods. An eight-arm radial maze was used to study the behaviour of three species of Rattus …

Interactions With Humans Shape Coyote Responses To Hazing, Julie K. Young, Edd Hammill, Stewart W. Breck

United States Department of Agriculture Wildlife Services: Staff Publications

Medium and large carnivores coexist with people in urban areas globally, occasionally resulting in

negative interactions that prompt questions about how to reduce human-wildlife conflict. Hazing,

i.e., scaring wildlife, is frequently promoted as an important non-lethal means for urbanites to reduce

conflict but there is limited scientific evidence for its efficacy. We used a population of captive coyotes (Canis latrans) to simulate urban human-coyote interactions and subsequent effects of hazing on coyote behavior. Past experiences with humans significantly affected the number of times a coyoteapproached a human to necessitate hazing. coyotes that had been hand fed by adults had to …

Hawaii As A Microcosm: Advancing The Science And Practice Of Managing Introduced And Invasive Species, Liba Pejchar, Christopher A. Lepczyk, Jean E. Fantle-Lepczyk, Steven C. Hess, M. Tracy Johnson, Christina R. Leopold, Michael Marchetti, Katherine M. Mcclure, Aaron B. Shiels

United States Department of Agriculture Wildlife Services: Staff Publications

Invasive species are a leading driver of global change, with consequences for biodiversity and society. Because of extraordinary rates of endemism, introduction, and extinction, Hawaii offers a rich platform for exploring the cross-disciplinary challenges of managing invasive species in a dynamic world. We highlight key successes and shortcomings to share lessons learned and inspire innovation and action in and beyond the archipelago. We then discuss thematic challenges and opportunities of broad relevance to invaded ecosystems and human communities. Important research needs and possible actions include eradicating mammals from mainland island sanctuaries, assessing hidden threats from poorly known introduced species, harnessing …

Deciphering Interactions Between White-Tailed Deer And Approaching Vehicle, Morgan Pfeiffer, Raymond B. Iglay, Thomas W. Seamans, Bradley F. Blackwell, Travis L. Devault

United States Department of Agriculture Wildlife Services: Staff Publications

Deer-vehicle collisions are a major transportation hazard, but factors affecting deer escape decision-making in response to vehicle approach remain poorly characterized. We made opportunistic observations of deer response to vehicle approach during daylight hours on a restricted- access facility in Ohio, USA (vehicle speeds were ≤64 km/h). We hypothesized that animal proximity to the road, group size, vehicle approach, and ambient conditions would affect perceived risk by white-tailed deer (Odocoileus virginianus) to vehicle approach, as measured by flight-initiation distance (FID). We constructed a priori models for FID, as well as road-crossing behavior. Deer responses were variable and did not demonstrate …

Evaluating Moose Alces Alces Population Response To Infestation Level Of Winter Ticks Dermacentor Albipictus, Daniel D. Ellingwood, Peter J. Pekins, Henry Jones, Anthony R. Musante

United States Department of Agriculture Wildlife Services: Staff Publications

Many wildlife populations are experiencing a variety of environmental pressures due to the direct and indirect consequences of a changing climate. In the northeast, USA, moose Alces alces are declining in large part because of the increasing parasitism by winter tick Dermacentor albipictus, facilitated by high host density and optimal environmental conditions. To test this hypothesis, and better understand the influence of this interaction on the stability of the regional population, we constructed a population viability model using data collected through comprehensive survival and productivity studies in 2002–2005 and 2014–2018 in northern New Hampshire. Years of heavy tick infestation (epizootics) …

Spillover Of Sars-Cov-2 Into Novel Wild Hosts In North America: A Conceptual Model For Perpetuation Of The Pathogen, Alan B. Franklin, Sarah N. Bevins

United States Department of Agriculture Wildlife Services: Staff Publications

There is evidence that the current outbreak of the novel coronavirus SARS-CoV-2, which causes COVID-19, is of animal origin. As with a number of zoonotic pathogens, there is a risk of spillover into novel hosts. Here, we propose a hypothesized conceptual model that illustrates the mechanism whereby the SARS-CoV-2 could spillover from infected humans to naive wildlife hosts in North America. This proposed model is premised on transmission of SARS-CoV-2 from human feces through municipal wastewater treatment plants into the natural aquatic environment where potential wildlife hosts become infected. We use the existing literature on human coronaviruses, including SARS CoV, …

Stochastic Simulation Of Cellular Metabolism, Emalie J. Clement, Thomas T. Schulze, Ghada A. Soliman, Beata Joanna Wysocki, Paul H. Davis, Tadeusz A. Wysocki

Department of Electrical and Computer Engineering: Faculty Publications

Increased technological methods have enabled the investigation of biology at nanoscale levels. Such systems require the use of computational methods to comprehend the complex interactions that occur. The dynamics of metabolic systems have been traditionally described utilizing differential equations without fully capturing the heterogeneity of biological systems. Stochastic modeling approaches have recently emerged with the capacity to incorporate the statistical properties of such systems. However, the processing of stochastic algorithms is a computationally intensive task with intrinsic limitations. Alternatively, the queueing theory approach, historically used in the evaluation of telecommunication networks, can significantly reduce the computational power required to generate …

Public Perspectives And Media Reporting Of Wolf Reintroduction In Colorado, Rebecca Niemiec, Richard E.W. Berl, Mireille Gonzalez, Tara Teel, Cassiopeia Camara, Matthew Collins, Jonathan Salerno, Kevin Crooks, Courtney Schultz, Stewart Breck, Dana Hoag

United States Department of Agriculture Wildlife Services: Staff Publications

In the state of Colorado, a citizen ballot initiative to reintroduce gray wolves (Canis lupus) is eliciting polarization and conflict among multiple stakeholder and interest groups. Given this complex social landscape, we examined the social context surrounding wolf reintroduction in Colorado as of 2019. We used an online survey of 734 Coloradans representative in terms of age and gender, and we sampled from different regions across the state, to examine public beliefs and attitudes related to wolf reintroduction and various wolf management options. We also conducted a content analysis of media coverage on potential wolf reintroduction in 10 major daily …

Grain Marketing 2020: Survival And Covid-19, Robert Tigner, Jessica J. Groskopf

Extension Farm and Ranch Management News

First paragraph:

Let’s state the obvious: this isn’t a typical year and we all know it. For farmers, it is a survival year. Why? And what might be done to make it through to the other side of the COVID-19 pandemic? This article will discuss how to build a marketing strategy to assure that the farm continues to the next crop year.

Conclusion

This year is shaping up to be a survival year for crop producers. Crop producers need to know at what crop price they will recapture all of the cash they will spend this year. Implementing a marketing …

Has Covid-19 Impacted Price-Weight Relationships And Value Of Gain?, Elliott James Dennis

Extension Farm and Ranch Management News

First paragraph:

In the beginning of COVID-19, much of the attention was focused on managing the redirection of meat product from food service to retail stores. This past month has keenly focused on packing plant closures due to COVID-19 cases among workers and how to manage the supply of fat cattle already ready for slaughter. Fat cattle available for slaughter either cannot get bids or bids are significantly below breakeven prices leaving feedlots with decisions to be made about marketing and placements. The April 2020 Cattle on Feed report (https://usda.library.cornell.edu/concern/publications/m326m174z) revealed March placement decisions. Placements were down about …

Live Cattle Basis Due To Covid-19: Deviations And Convergence, Elliott James Dennis

Extension Farm and Ranch Management News

A Fundamental Review on Basis

Basis is defined as the cash minus futures. Cash market reflects today's supply conditions and price. Futures market reflects upcoming supply and demand conditions. If it is anticipated that there will be a period of increasing supplies, futures prices will decline to reflect that information. Likewise, periods of time with expected decreasing supplies, future prices are expected to increase.

Since cash and futures prices can move simultaneously, basis will fluctuate through time. In periods where basis becomes more positive (i.e. basis is said to be strengthening/narrowing) it implies that cash prices are increasing more relative …

Pre Covid-19 Market Conditions Persist & The Stocker Industry Can Dampen The Damage, Elliott James Dennis

Extension Farm and Ranch Management News

First paragraph:

The effects of COVID-19 on the livestock market are well known and felt. Some effects include depressed futures and cash prices, unusual basis patterns, decreased packer bids and sale barn volume, packing plant closures, consumer hording of meat products, and shifting food service products for retail consumption. All these effects occurred as market participants grappled with everchanging government and industry policy which reduced consumer demand and resulted in bottlenecks and increasing supply gluts upstream. Simultaneously reducing demand and increasing supply always cause prices to plummet, and in the case of COVID-19 very rapidly. Some segments of the market …

Structure, Function And Metabolism Of Hepatic And Adipose Tissue Lipid Droplets: Implications In Alcoholic Liver Disease, Sathish Kumar Natarajan, Karuna Rasineni, Murali Ganesan, Dan Feng, Benita L. Mcvicker, Mark A. Mcniven, Natalia A. Osna, Justin L. Mott, Carol A. Casey, Kusum K. Kharbanda

School of Veterinary and Biomedical Sciences: Faculty Publications

For more than 30 years, lipid droplets (LDs) were considered as an inert bag of lipid for storage of energy-rich fat molecules. Following a paradigm shift almost a decade ago, LDs are presently considered an active subcellular organelle especially designed for assembling, storing and subsequently supplying lipids for generating energy and membrane synthesis (and in the case of hepatocytes for VLDL secretion). LDs also play a central role in many other cellular functions such as viral assembly and protein degradation. Here, we have explored the structural and functional changes that occur in hepatic and adipose tissue LDs following chronic ethanol …

Stunting And Infectious Disease In Ethiopian And Zambian Children, Alyssa Arndt

NUTR/GLST 498b: Global Research Experiences in Nutrition and Health

PURPOSE: To evaluate whether children who are malnourished/stunted are more likely to have experienced infectious disease.

METHODS: 6th and 7th students (n=546) were interviewed about health history and assessed using anthropometry.

RESULTS: Children who are short for their age also have higher rates of stunting. Malaria is the most experienced infectious disease.

CONCLUSIONS: Given that malaria was the most common infectious disease experience listed among middle school children, and that those who have experienced disease are more likely to be stunted, increased malaria prevention methods may improve the long-term health of Ethiopian and Zambian schoolchildren.

Group Testing Identification: Objective Functions, Implementation, And Multiplex Assays, Brianna D. Hitt

Department of Statistics: Dissertations, Theses, and Student Research

Group testing is the process of combining items into groups to test for a binary characteristic. One of its most widely used applications is infectious disease testing. In this context, specimens (e.g., blood, urine) are amalgamated into groups and tested. For groups that test positive, there are many algorithmic retesting procedures available to identify positive individuals. The appeal of group testing is that the overall number of tests needed is significantly less than for individual testing when disease prevalence is small and an appropriate algorithm is chosen. Group testing has a number of applications beyond infectious disease testing, such as …

Talking Trash In The Big Apple: Mitigating Bird Strikes Near The North Shore Marine Transfer Station, Stephan J. Beffre, Brian E. Washburn

United States Department of Agriculture Wildlife Services: Staff Publications

Anthropogenic activities that concentrate wildlife near airports increases the risk of wildlife–aircraft collisions. Placing waste management facilities, natural areas, golf courses, and other landscape features near airports have the potential to attract wildlife hazardous to aviation. We conducted a 3-year study (March 2013–February 2016) to determine if the implementation of a Wildlife Hazard Mitigation Program (WHMP) would influence the bird use of a waste transfer station located near LaGuardia Airport, New York City, New York, USA. We conducted wildlife surveys during 3 phases: (1) no mitigation program and no waste transfer station, (2) active mitigation and no waste transfer station, …

Association Between Sulfur-Metabolizing Bacterial Communities In Stool And Risk Of Distal Colorectal Cancer In Men, Long H. Nguyen, Wenjie Ma, Dong D. Wang, Yin Cao, Himel Mallick, Teklu K. Gerbaba, Jason Lloyd-Price, Galeb Abu-Ali, A. Brantley Hall, Daniel Sikavi, David A. Drew, Raaj S. Mehta, Cesar Arze, Amit D. Joshi, Yan Yan, Tobyn Branck, Casey Dulong, Kerry L. Ivey, Shuji Ogino, Eric B. Rimm, Mingyang Song, Wendy S. Garrett, Jacques Izard, Cutis Huttenhower, Andrew T. Chan

Department of Food Science and Technology: Faculty Publications

Background and aims: Sulfur-metabolizing microbes, which convert dietary sources of sulfur into genotoxic hydrogen sulfide (H₂S), have been associated with development of colorectal cancer (CRC). We identified a dietary pattern associated with sulfur-metabolizing bacteria in stool and then investigated its association with risk of incident CRC using data from a large prospective study of men.

Methods: We collected data from 51,529 men enrolled in the Health Professionals Follow-up Study since 1986 to determine the association between sulfur-metabolizing bacteria in stool and risk of CRC over 26 years of follow-up. First, in a subcohort of 307 healthy men, we …

Integrating The Ecosystem Services Framework To Define Dysbiosis Of The Breastfed Infant Gut: The Role Of B. Infantis And Human Milk Oligosaccharides, Rebbeca M. Duar, Bethany M. Henrick, Giorgio Casaburi, Steven A. Frese

Department of Food Science and Technology: Faculty Publications

Mounting evidence supports a connection between the composition of the infant gut microbiome and long-term health. In fact, aberrant microbiome compositions during key developmental windows in early life are associated with increased disease risk; therefore, making pertinent modifications to the microbiome during infancy offers significant promise to improve human health. There is growing support for integrating the concept of ecosystem services (the provision of benefits from ecosystems to humans) in linking specific microbiome functions to human well-being. This framework is widely applied in conservation efforts of macro-ecosystems and offers a systematic approach to guide restoration actions aimed to recover critical …

Elucidating The Regulon Of A Fur-Like Protein In Mycobacterium Avium Subsp. Paratuberculosis (Map), Fernanda Miyagaki Shoyama, Taveesak Janetanakit, John P. Bannantine, Raul G. Barletta, Srinand Sreevatsan

Nebraska Center for Virology: Faculty Publications

Intracellular iron concentration is tightly regulated to maintain cell viability. Iron plays important roles in electron transport, nucleic acid synthesis, and oxidative stress. A Mycobacterium avium subsp. paratuberculosis (MAP)-specific genomic island carries a putative metal transport operon that includes MAP3773c, which encodes a Fur-like protein. Although well characterized as a global regulator of iron homeostasis in multiple bacteria, the function of Fur (ferric uptake regulator) in MAP is unknown as this organism also carries IdeR (iron dependent regulator), a native iron regulatory protein specific to mycobacteria. Computational analysis using PRODORIC identified 23 different pathways involved in respiration, metabolism, and virulence …

A New Genus And Two New Species Of Unarmed Hymenolepidid Cestodes (Cestoda: Hymenolepididae) From Geomyid Rodents In Mexico And Costa Rica, Scott Lyell Gardner, Altangerel Tsogtsaikhan Dursahinhan, Mariel Campbell, S. Elizabeth Rácz

Scott L. Gardner Publications

Two new cestodes of the family Hymenolepididae are described from two species of rodents of the family Geomyidae collected in Mexico and Costa Rica. One new species of Hymenolepis is described from Cratogeomys planiceps Merriam 1895 from near Toluca, Mexico and another that we allocate to a new genus is described from Heterogeomys heterodus (Peters, 1865) from near Irazú Volcano, Costa Rica. Hymenolepis s. str. includes those Hymenolepididae with an apical organ, with no hooks on suckers or apical organ, and three testes. Hobergia irazuensis n. gen., n. sp. includes a hymenolepidid with an apical organ, unarmed scolex, small …

Before The Pandemic Ends: Making Sure This Never Happens Again, Daniel R. Brooks, Eric P. Hoberg, Walter A. Boeger, Scott Lyell Gardner, Sabrina B. L. Araujo, Katalin Bajer, Sebastian Botero-Cañola, Brian Byrd, Gábor Földvári, Joseph A. Cook, Jonathan L. Dunnum, Altangerel Tsogtsaikhan Dursahinhan, László Zsolt Garamszegi, Dávid Herczeg, Ferenc Jakab, Alicia Juarrero, Gábor Kemenesi, Kornélia Kurucz, Virginia León-Règagnon, Hugo H. Mejía-Madrid, Orsolya Molnár, Richard A. Nisbett, Wolfgang Preiser, Michael Stuart, Eors Szathmary, Valeria Trivellone

Scott L. Gardner Publications

Introduction

On 30 January 2020, the World Health Organization (WHO) declared a Global Health Emergency of international concern attendant to the emergence and spread of SARS-CoV-2, nearly two months after the first reported emergence of human cases in Wuhan, China. In the subsequent two months, global, national and local health personnel and infrastructures have been overwhelmed, leading to suffering and death for infected people, and the threat of socio-economic instability and potential collapse for humanity as a whole. This shows that our current and traditional mode of coping, anchored in responses after the fact, is not capable of dealing with …

Collective Effect Of Landfills And Landscape Composition On Bird–Aircraft Collisions, Morgan Pfeiffer, Bradley F. Blackwell, Travis L. Devault

United States Department of Agriculture Wildlife Services: Staff Publications

Ninety-three percent of all reported bird strikes occur below 1,067 m, which based on the typical approach and departure angles of aircraft is within 8–13 km of an airport. Concomitantly, the Federal Aviation Administration and the International Civil Aviation Organization recommend that any feature that would attract hazardous wildlife to the approach and departure airspace be restricted. Thus, preventing the establishment of wildlife attractants, such as municipal solid waste landfills (MSWLFs) within 8 km or 13 km extents (U.S. and international recommendations, respectively) of airports, has been recommended to mitigate the risk of bird–aircraft collisions (strikes). However, robust evidence linking …

Dgts Production As A Phosphate Starvation Response In The Human Fungal Pathogen Candida Albicans, Caleb J. Wehling

School of Biological Sciences: Dissertations, Theses, and Student Research

Betaine lipids are a class of membrane lipids with betaine head groups. Three betaine lipids are known: diacylglyceryltrimethylhomoserine (DGTS), diacylglycerylhydroxymethylalanine (DGTA), and diacylglycerylcarboxymethylcholine (DGCC). Betaine lipids are most common in algae, although DGTS, the most common betaine lipid, is also found in many bacteria and fungi. Organisms which produce betaine lipids (especially DGTS) often don’t produce phosphatidylcholine (PtdCho), and DGTS structure resembles PtdCho structure without any phosphorous, leading to the hypothesis that betaine lipids may substitute for phospholipids in some organisms. This has been confirmed by discoveries that some organisms are capable of switching their membrane composition from PtdCho to …

Occurrence And Persistence Of Antibiotics Administered To Cattle In A Newly Established Feedlot, Brittany Trejo

Department of Environmental Engineering: Theses and Other Student Research

The common practice of using therapeutic antibiotics in livestock farming is a worldwide phenomenon. Over the last decade, there has been a growing concern of antibiotics entering the environment via animal manure. Similar studies have focused on the occurrence and biological effects of antibiotics in land-applied animal feedlots; however, limited research has been conducted on the occurrence and persistence of antibiotics in animal feedlots. A study was conducted to investigate the occurrence and persistence of four injected antibiotics (ceftiofur enrofloxacin, florfenicol, and tulathromycin) and two continuously fed antibiotics (monensin and tylosin) in feedlot sediment, runoff, and sediment runoff. For antibiotics …

Testing A Key Assumption Of Using Drones As Frightening Devices: Do Birds Perceive Drones As Risky?, Conor C. Egan, Bradley Blackwell, Esteban Fernández-Juricic, Page E. Klug

United States Department of Agriculture Wildlife Services: Staff Publications

Wildlife managers have recently suggested the use of unmanned aircraft systems or drones as nonlethal hazing tools to deter birds from areas of human-wildlife conflict. However, it remains unclear if birds perceive common drone platforms as threatening. Based on field studies assessing behavioral and physiological responses, it is generally assumed that birds perceive less risk from drones than from predators. However, studies controlling for multiple confounding effects have not been conducted. Our goal was to establish the degree to which the perception of risk by birds would vary between common drone platforms relative to a predator model when flown at …