Digital Commons Network^™

Simulating Detection-Censored Movement Records For Home Range Analysis Planning, Lyndsie S. Wszola, Victoria L. Simonsen, Lucía Corral, Christopher J. Chizinski, Joseph J. Fontaine

Nebraska Cooperative Fish and Wildlife Research Unit: Staff Publications

Home range estimation is an important analytical method in applied spatial ecology, yet best practices for addressing the effects of spatial variation in detection probability on home range estimates remain elusive. We introduce the R package “DiagnoseHR,” simulation tools for assessing how variation in detection probability arising from landscape, animal behavior, and methodological processes affects home range inference. We demonstrate the utility of simulation methods for home range analysis planning by comparing bias arising from three home range estimation methods under multiple detection scenarios. We simulated correlated random walks in three landscapes that varied in detection probability and constructed home …

Efficacy Of A T Cell-Biased Adenovirus Vector As A Zika Virus Vaccine, Brianna L. Bullard, Brigette N. Corder, Matthew J. Gorman, Michael S. Diamond, Eric A. Weaver

Nebraska Center for Virology: Faculty Publications

Zika virus (ZIKV) is a major public health concern due to the risk of congenital Zika syndrome in developing fetuses and Guillain-Barre syndrome in adults. Currently, there are no approved vaccines available to protect against infection. Adenoviruses are safe and highly immunogenic vaccine vectors capable of inducing lasting humoral and cellular immune responses. Here, we developed two Adenovirus (Ad) vectored Zika virus vaccines by inserting a ZIKV prM-E gene expression cassette into human Ad types 4 (Ad4-prM-E) and 5 (Ad5-prM-E). Immune correlates indicate that Ad5-prM-E vaccination induces both an anti-ZIKV antibody and T-cell responses whereas Ad4-prM-E vaccination only induces a …

Seasonality Of Nitrogen Balances In A Mediterranean Climate Watershed, Oregon, Us, Jiajia Lin, Jana E. Compton, Scott G. Leibowitz, George Mueller-Warrant, William Matthews, Stephen H. Schoenholtz, Daniel M. Evans, Rob A. Coulombe

United States Environmental Protection Agency: Publications

We constructed a seasonal nitrogen (N) budget for the year 2008 in the Calapooia River Watershed (CRW), an agriculturally dominated tributary of the Willamette River (Oregon, U.S.) under Mediterranean climate. Synthetic fertilizer application to agricultural land (dominated by grass seed crops) was the source of 90% of total N input to the CRW. Over 70% of the stream N export occurred during the wet winter, the primary time of fertilization and precipitation, and the lowest export occurred in the dry summer. Averaging across all 58 tributary subwatersheds, 19% of annual N inputs were exported by streams, and 41% by crop …

Six Key Components Of A Farm Or Ranch Business Plan, Jay Parsons

Cornhusker Economics

Developing a good farm or ranch business plan can have many benefits. In an earlier Cornhusker Economics article, I outlined six good reasons to develop a business plan (Parsons 2015). It helps to get your business organized and moving in the right direction. It lets your lender know you have a plan to succeed, which opens up your access to capital. It also helps you organize your thoughts, clarifying the goals and objectives you wish to achieve. In summary, putting together a written business plan increases the likelihood of your business achieving success (Scarborough 2011).

The Beetle Chronicler, Chris Dunker, Kayla Wolf, Brett Ratcliffe

University of Nebraska State Museum: Entomology Papers

Longtime UNL entomologist names beetles for dragons

Gymnetis rhaegali, Gymnetis drogoni, Gymnetis viserioni, Ambyoproctus boondocksius, Cyclocephala nadanotherwon, Strategus longichomperus

University of Nebraska entomology professor Brett Ratcliffe, who also curates the Nebraska State Museum's beetle collection, shows elephant beetles, a member of the scarab beetle family, in his office in Nebraska Hall.

Unlike their namesakes, three species of scarab beetles newly described by University of Nebraska-Lincoln entomologist Brett Ratcliffe do not breathe fire. Or, at least, entomologists and field researchers haven't observed them doing so.

Nor do the scarabs have the thick, reptilian scales and leathery wings like the trio of …

Recycling Just Got More Expensive. Can It Be Done Better?, Zachery Homolka

Op-Eds from ENSC230 Energy and the Environment: Economics and Policies

There was a time in history that America led the world in recycling. In World War Two, Americans were asked to recycle tin, steel, paper, and rubber for the war effort. The University of Southern Carolina states that children were so eager to participate, they went door to door collecting recyclable scraps to turn in to be made into tanks, planes, and ammunition. Yet, in 2017 the National Geographic estimated about 91% of plastic produced globally has not been recycled and instead is landfilled or littered into the environment. America is no longer leading the recycling charge, the World Economic …

Repeats Of Unusual Size In Plant Mitochondrial Genomes: Identification, Incidence And Evolution, Emily L. Wynn, Alan C. Christensen

School of Biological Sciences: Faculty Publications

Plant mitochondrial genomes have excessive size relative to coding capacity, a low mutation rate in genes and a high rearrangement rate. They also have abundant non-tandem repeats often including pairs of large repeats which cause isomerization of the genome by recombination, and numerous repeats of up to several hundred base pairs that recombine only when the genome is stressed by DNA damaging agents or mutations in DNA repair pathway genes. Early work on mitochondrial genomes led to the suggestion that repeats in the size range from several hundred to a few thousand base pair are underrepresented. The repeats themselves are …

Riverbank Filtration Impacts On Post Disinfection Water Quality In Small Systems—A Case Study From Auburn And Nebraska City, Nebraska, Matteo D'Alessio, Bruce Dvorak, Chittaranjan Ray

Daugherty Water for Food Global Institute: Faculty Publications

Small water systems can experience a fluctuating quality of water in the distribution system after disinfection. As chlorine is the most common disinfectant for small systems, the occurrence of disinfection byproducts (DBPs) represents a common problem for these systems. Riverbank filtration (RBF) can be a valuable solution for small communities located on riverbanks. The objectives of this study were to evaluate (i) the improvements in water quality at two selected RBF systems, and (ii) the potential lower concentrations of DBPs, in particular, trihalomethanes (THMs), in small systems that use RBF. Two small communities in Nebraska, Auburn and Nebraska City, using …

Methanogens: Pushing The Boundaries Of Biology, Nicole R. Buan

Department of Biochemistry: Faculty Publications

Methanogens are anaerobic archaea that grow by producing methane gas. These microbes and their exotic metabolism have inspired decades of microbial physiology research that continues to push the boundary of what we know about how microbes conserve energy to grow. The study of methanogens has helped to elucidate the thermodynamic and bioenergetics basis of life, contributed our understanding of evolution and biodiversity, and has garnered an appreciation for the societal utility of studying trophic interactions between environmental microbes, as methanogens are important in microbial conversion of biogenic carbon into methane, a high-energy fuel. This review discusses the theoretical basis for …

Methanogens: Pushing The Boundaries Of Biology, Nicole R. Buan

Department of Biochemistry: Faculty Publications

Methanogens are anaerobic archaea that grow by producing methane gas. These microbes and their exotic metabolism have inspired decades of microbial physiology research that continues to push the boundary of what we know about how microbes conserve energy to grow. The study of methanogens has helped to elucidate the thermodynamic and bioenergetics basis of life, contributed our understanding of evolution and biodiversity, and has garnered an appreciation for the societal utility of studying trophic interactions between environmental microbes, as methanogens are important in microbial conversion of biogenic carbon into methane, a high-energy fuel. This review discusses the theoretical basis for …

Comparing Strategies For Selection Of Low-Density Snps For Imputation-Mediated Genomic Prediction In U.S. Holsteins, Jun He, Jiaqi Xu, Xiao-Lin Wu, Stewart Bauck, Jungjae Lee, Gota Morota, Stephen D. Kachman, Matthew L. Spangler

Department of Animal Science: Faculty Publications

SNP chips are commonly used for genotyping animals in genomic selection but strategies for selecting low-density (LD) SNPs for imputation-mediated genomic selection have not been addressed adequately. The main purpose of the present study was to compare the performance of eight LD (6K) SNP panels, each selected by a different strategy exploiting a combination of three major factors: evenly-spaced SNPs, increased minor allele frequencies, and SNP-trait associations either for single traits independently or for all the three traits jointly. The imputation accuracies from 6K to 80K SNP genotypes were between 96.2 and 98.2%. Genomic prediction accuracies obtained using imputed 80K …

Assessing The Feasibility Of Soil Infiltration Trenches For Highway Runoff Control On The Island Of Oahu, Hawaii, Martina Sobotkova, Jaromir Dusek, Ghasem Alavi, Laxman Sharma, Chittaranjan Ray

Daugherty Water for Food Global Institute: Faculty Publications

The coastal waters of Hawaii are extremely important for recreation as well as for the health of the marine environment. Non-point source pollution from storm runoff poses a great threat to surface water quality in Hawaii. The State of Hawaii Department of Transportation (HDOT) includes infiltration trenches as a best management practice (BMP) option to reduce pollution caused by stormwater runoff. HDOT guidelines state that the implementation of BMPs is needed to reduce sediment and pollutant loads to streams and the ocean. In this study, the suitability of soils adjacent to highways on Oahu for the siting of infiltration trenches …

Design And Methodology Of A Cluster-Randomized Trial In Early Care And Education Centers To Meet Physical Activity Guidelines: Sustainability Via Active Garden Education (Sage), Rebecca E. Lee, Elizabeth Lorenzo, Jacob Szeszulski, Anel Arriola, Meg Bruening, Paul A. Estabrooks, Jennie Hill, Flavio F. Marsiglia, Teresia O'Connor, Kim Sellers Pollins, Gabriel Q. Shaibi, Erica Soltero, Michael Todd

United States Department of Agriculture-Agricultural Research Service / University of Nebraska-Lincoln: Faculty Publications

Strategies are needed to help early care and education centers (ECEC) comply with policies to meet daily physical activity and fruit and vegetable guidelines for young children. This manuscript describes the design and methodology of Sustainability via Active Garden Education (SAGE), a 12-session cluster-randomized controlled crossover design trial using community-based participatory research (CBPR) to test a garden-based ECEC physical activity and fruit and vegetables promotion intervention for young children aged 3–5 years in 20 sites. The SAGE curriculum uses the plant lifecycle as a metaphor for human development. Children learn how to plant, water, weed, harvest, and do simple food …

Fire, Grazing And Climate Shape Plant–Grasshopper Interactions In A Tallgrass Prairie, Ellen A.R. Welti, Fan Qiu, Hannah M. Tetreault, Mark Ungerer, Anthony Joern

United States Department of Agriculture-Agricultural Research Service / University of Nebraska-Lincoln: Faculty Publications

1. Species interactions are integral to ecological community function, and the structure of species interactions has repercussions for the consequences of species extinctions. Few studies have examined the role of environmental factors in controlling species interaction networks across time.

2. We examined variation in plant–grasshopper network structural properties in response to three major grassland drivers: periodic fire, ungulate grazing and climate.

3. We sequenced a plant barcoding gene from extracted grasshopper gut contents to characterize diets of 26 grasshopper species. Resulting grasshopper species’ diets were combined with long‐term plant and grasshopper surveys to assemble plant–grasshopper networks across 13–19 years for …

The Effects Of Sample Storage Conditions On The Microbial Community Composition In Hydraulic Fracturing Produced Water, Daniel Lipus, Amit Vikram, Richard Hammack, Kyle Bibby, Djuna Gulliver

Roman L. Hruska U.S. Meat Animal Research Center: Reports

The petroleum industry has an increasing interest in understanding the microbial communities driving biofouling and biocorrosion in reservoirs, wells, and infrastructure. However, sampling of the relevant produced fluids from subsurface environments for microbiological analyses is often challenged by high liquid pressures, workplace regulations, operator liability concerns, and remote sampling locations. These challenges result in infrequent sampling opportunities and the need to store and preserve the collected samples for several days or weeks. Maintaining a representative microbial community structure from produced fluid samples throughout storage and handling is essential for accurate results of downstream microbial analyses. Currently, no sample handling or …

International Commission On Trichinellosis: Recommendations For Genotyping Trichinella Muscle Stage Larvae, Edoardo Pozio, Dante Zarlenga

United States Department of Agriculture-Agricultural Research Service / University of Nebraska-Lincoln: Faculty Publications

Being able to identify the species or genotype of Trichinella is of paramount importance not only for epidemiological studies but to better ascertain the source of outbreaks that still occur worldwide. This has become more critical in recent years given the increase in imported meat products and the relationship that wild animals play in the domestic and sylvatic transmission cycles. In contrast to a time when the genus Trichinella was considered monospecific, research in recent years has revealed that the genus consists of 9 species and at least 3 additional genotypes which have yet to be named. Except for a …

Dynamical Electron Vortices In Attosecond Double Photoionization Of H2, Jean Marcel Ngoko Djiokap, A. V. Meremianin, N. L. Manakov, L. B. Madsen, S. X. Hu, Anthony F. Starace

Anthony F. Starace Publications

We study electron momentum vortices in single-photon double ionization of H2 by time-delayed, counterrotating, elliptically polarized attosecond pulses propagating along kˆ either parallel or perpendicular to the molecular axis R. For kˆ | R, kinematical vortices occur similar to those found for He. For kˆ ⊥ R, we find dynamical vortex structures originating from an ellipticity-dependent interplay of ¹∑⁺_u and ¹∏⁺_u continuum amplitudes. We propose a complete experiment to determine the magnitudes and relative phase of these amplitudes by varying pulse ellipticities and time delays.

Why The Endangered Species Act Shouldn’T Be Endangered, Ryan Kendall

Op-Eds from ENSC230 Energy and the Environment: Economics and Policies

The Trump Administration has announced that they intend to rework the endangered species act. Unsurprisingly, they plan to rework in ways that have the potential to undermine its effectiveness.

One would think that reworking the act would potentially increase its effectiveness, given the nearly fifty years that we have had to advance our knowledge since it was passed. Unfortunately, the opposite may very well be true.

The new changes to the act would allow for the decision of whether or not to list an animal to be made not just by scientific data, but also by determining the economic impact …

Simulating The Impacts Of Irrigation Levels On Soybean Production In Texas High Plains To Manage Diminishing Groundwater Levels, Vaishali Sharda, Prasanna H. Gowda, Gary Marek, Isaya Kisekka, Chittaranjan Ray, Pradip Adhikari

Nebraska Water Center: Faculty Publications

There is an increasing need to strategize and plan irrigation systems under varied climatic conditions to support efficient irrigation practices while maintaining and improving the sustainability of groundwater systems. This study was undertaken to simulate the growth and production of soybean [Glycine max (L.)] under different irrigation scenarios. The objectives of this study were to calibrate and validate the CROPGRO-Soybean model under Texas High Plains’ (THP) climatic conditions and to apply the calibrated model to simulate the impacts of different irrigation levels and triggers on soybean production. The methodology involved combining short-term experimental data with long-term historical weather data (1951–2012), …

Gmaim: An Analytical Pipeline For Microrna Splicing Profiling Using Generative Model, Kan Liu

School of Computing: Dissertations, Theses, and Student Research

MicroRNAs (miRNAs) are a class of short (~22 nt) single strand RNA molecules predominantly found in eukaryotes. Being involved in many major biological processes, miRNAs can regulate gene expression by targeting mRNAs to facilitate their degradation or translational inhibition. The imprecise splicing of miRNA splicing which introduces severe variability in terms of sequences of miRNA products and their corresponding downstream gene expression regulation. For example, to study biogenesis of miRNAs, usually, biologists can deplete a gene in the miRNA biogenesis pathway and study the change of miRNA sequences, which can cause impression of miRNAs. Although high-throughput sequencing technologies such as …

Recoupling Fire And Grazing Reduces Wildland Fuel Loads On Rangelands, Heath D. Starns, Samuel D. Fuhlendore, R. Dwayne Elmore, Dirac L. Twidwell Jr, Eric T. Thacker, Torre J. Hovick, Barney Luttbeg

Department of Agronomy and Horticulture: Faculty Publications

Fire suppression and exclusion, the historically dominant paradigm of fire management, has resulted in major modifications of fire-dependent ecosystems worldwide. These changes are partially credited with a recent increase in wildfire number and extent, as well as more extreme fire behavior. Fire and herbivory historically interacted, and research has shown that the interaction creates a unique mosaic of vegetation heterogeneity that each disturbance alone does not create. Because fire and grazing have largely been decoupled in modern times, the degree to which the interaction affects fuels and fire regimes has not yet been quantified. We evaluated effects of fire-only and …

The Transcriptomes Of The Cattle Parasitic Nematode Ostertagia Ostartagi, Sahar Abubucker, Dante S. Zarlenga, John Martin, Yong Yin, Zhengyuan Wang, James P. Mccarter, Louis Gasbarree, Richard K. Wilson, Makedonka Mitreva

United States Department of Agriculture-Agricultural Research Service / University of Nebraska-Lincoln: Faculty Publications

Ostertagia ostertagi is a gastrointestinal parasitic nematode that affects cattle and leads to a loss of production. In this study, we present the first large-scale genomic survey of O. ostertagi by the analysis of expressed transcripts from three stages of the parasite: third- stage larvae, fourth-stage larvae and adult worms. Using an in silico approach, 2284 genes were identified from over 7000 expressed sequence tags and abundant transcripts were analyzed and characterized by their functional profile. Of the 2284 genes, 66% had similarity to other known or predicted genes while the rest were novel and potentially represent genes specific to …

Implications Of Spatially Variable Costs And Habitat Conversion Risk In Landscape-Scale Conservation Planning, Max Post Van Der Burg, Neil Chartier, Ryan Drum

United States Geological Survey, Northern Prairie Wildlife Research Center: Publications

‘‘Strategic habitat conservation’’ refers to a process used by the U.S. Fish and Wildlife Service to develop cost-efficient strategies for conserving wildlife populations and their habitats. Strategic habitat conservation focuses on resolving uncertainties surrounding habitat conservation to meet specific wildlife population objectives (i.e., targets) and developing tools to guide where conservation actions should be focused on the landscape. Although there are examples of using optimization models to highlight where conservation should be delivered, such methods often do not explicitly account for spatial variation in the costs of conservation actions. Furthermore, many planning approaches assume that habitat protection is a preferred …

The R Journal (December 2018) 10(2): Complete Issue, The R Foundation

The R Journal

Editorial, John Verzani

Contributed Research Articles

stplanr: A Package for Transport Planning, Robin Lovelace and Richard Ellison

The utiml Package: Multi-label Classification in R, Adriano Rivolli and Andre C. P. L. F. de Carvalho

rcss: R Package for Optimal Convex Stochastic Switching, Juri Hinz and Jeremy Yee

nsROC: An R package for Non-Standard ROC Curve Analysis, Sonia Pérez-Fernández, Pablo Martínez-Camblor, Peter Filzmoser, and Norberto Corral

addhaz: Contribution of Chronic Diseases to the Disability Burden Using R, Renata Tiene de Carvalho Yokota, Caspar WN Looman, Wilma Johanna Nusselder, Herman Van Oyen, and Geert Molenberghs

Snowboot: Bootstrap Methods for Network Inference, Yuzhou …

Designing A Protected Area To Safeguard Imperiled Species From Urbanization, Stephanie S. Romanach, Brad Stith, Fred A. Johnson

United States Geological Survey: Staff Publications

Reserve design is a process that can address ecological, social, and political factors to identify parcels of land needed to sustain wildlife populations and other natural resources. Acquisition of parcels for a large terrestrial reserve is difficult because it typically occurs over a long timeframe and thus invokes consideration of future conditions such as climate and urbanization changes. In central Florida, the U.S. government has authorized a new protected area, the Everglades Headwaters National Wildlife Refuge. The new refuge will host important threatened and endangered species and habitats, and will be located to allow for species adaptation from climate change …

Sandhill Crane Activity In The Central Platte River Valley In Late May And Early June, Jenna M. Malzahn, Andrew J. Caven, Marin Dettweiler, Joshua D. Wiese

Nebraska Bird Review

In this report we discuss observations of Sandhill Cranes remaining in the Central Platte River Valley until early June 2018 and discuss potential explanations for this extended stay into the breeding season.

We detected two pairs of adult Sandhill Cranes in two different locations on 15 May 2018 (Table 1). We then detected three injured adult Sandhill Cranes in a third location on 16 May 2018 (Table 1). Two of the three Sandhill Cranes each had a missing leg and the third crane’s leg was broken above the tibiotarsal joint; however, all were still capable of foraging and flight. Later, …

Fall Field Report, August - November 2018, W. Ross Silcock

Nebraska Bird Review

As far as birds go, this was a relatively quiet season, but, as usual, there was much of interest to chew on. Most important in any report are range changes, major changes in expected numbers or early and late dates, all of which relate directly to the status, positive or negative, of a given species.

Waterfowl in general were only average in numbers; new high counts are rare these days compared with numbers 20 or so years ago. Two winter finches, Common Redpoll and Red Crossbill, that normally arrive in late fall, were virtually unreported. Notable range expansions are under …

Review: Canids Of The World: Wolves, Wild Dogs, Foxes, Jackals, Coyotes, And Their Relatives. José R. Castelló., Jonathan (Jon) Way

The Prairie Naturalist

Canids of the World is one of those reads where just when you think that something cannot be beat, this book comes out. What I mean by that is that I have read many works on wolves and other canids, most recently Nate Blakeslee’s American Wolf (Way 2017), and I have enjoyed and been enthralled with many of them. But Canids of the World may take the cake for being the most impressive book available on canids. For a modest price of just under $30.00, you can own a book that has over 600 amazing high-resolution glossy photographs of every …

Review: Behavior Of The Golden Eagle: An Illustrated Ethogram. David H. Ellis (Illustrated By N. John Schmitt)., Jeremy E. Guinn

The Prairie Naturalist

Author David H. Ellis and illustrator N. John Schmitt deliver precisely what is promised in Behavior of the Golden Eagle: An Illustrated Ethogram. This “little volume,” as the author coins it, represents a single source for defining, identifying, and describing behaviors of the Golden Eagle (Aquila chrysaetos). With the inclusion of Schmitt’s exceptional drawings, the book is a piece of art, as well as the most useful manual describing Golden Eagle behaviors. Nearly four decades earlier, Ellis (1979) authored the very first Golden Eagle ethogram—the set of repeated standard behaviors for a species called action patterns—and in his new book, …

Snowboot: Bootstrap Methods For Network Inference, Yuzhou Chen, Yulia R. Gel, Vyacheslav Lyubchich, Kusha Nezafati

The R Journal

Complex networks are used to describe a broad range of disparate social systems and natural phenomena, from power grids to customer segmentation to human brain connectome. Challenges of parametric model specification and validation inspire a search for more data-driven and flexible nonparametric approaches for inference of complex networks. In this paper we discuss methodology and R implementation of two bootstrap procedures on random networks, that is, patchwork bootstrap of Thompson et al. (2016) and Gel et al. (2017) and vertex bootstrap of Snijders and Borgatti (1999). To our knowledge, the new R package snowboot is the first implementation of the …