Digital Commons Network^™

Managed Relocation: Reducing The Risk Of Biological Invasion, Edward E. Clark Jr., Dan Simberloff, Mark Schwartz, Brent Stewart, John Peter Thompson

National Invasive Species Council

Key Finding

Any organism that is relocated to a novel ecosystem has the potential to become an invasive species or spread “hitching” invasive species, or both. Managed Relocation is not congruent with Executive Order 13112 to the extent that it might facilitate “economic or environmental harm or harm to human, animal, or plant health.” Consequently, the actions by federal agencies or those entities supported by federal funding to engage in managed relocation need to be addressed in a manner consistent with EO 13751 Section 3(3), which compels Agencies to:

Refrain from authorizing, funding, or implementing actions that are likely to …

Advanced Biotechnology Tools For Invasive Species Management, Invasive Species Advisory Committee

National Invasive Species Council

Increasingly, genetic tools are being used to detect and solve pressing environmental, social, and health-related challenges. It is clear that investments in technology innovation can be game changing, as advances in biotechnology may provide new methods to protect the nation’s resources from the negative impacts of invasive species. The current toolbox of management options is recognizably insufficient to deal with many of the high-impact species that have been introduced. However, “surrendering” to these species is generally not a viable option from ecological, health, economic, socio-cultural, or political perspectives. Cost-efficient solutions to these “grand invasive species challenges” need to be found. …

Failing Food Supply: Permaculture's Potential, John Faltin

Department of Environmental Studies: Undergraduate Student Theses

Conventional agriculture is the currently leading production method to grow crops in the western hemisphere. Long-term sustainability of the system and all the components is secondary to producing high yields each growing season, which leads to issues such as erosion and reduced soil quality. Other agricultural production methods such as permaculture aim to build soil and improve quality every growing season. This experiment intends to look at the potential of permaculture to improve soil quality on small-scales at the end of each growing season. The parameters to gauge success are a larger concentration of macronutrients at the end of the …

The Pul37 Tegument Protein Guides Alphaherpesvirus Retrograde Axonal Transport To Promote Neuroinvasion, Alexsia L. Richards, Patricia J. Sollars, Jared D. Pitts, Austin M. Stults, Ekaterina E. Heldwein, Gary E. Pickard, Gregory A. Smith

School of Veterinary and Biomedical Sciences: Faculty Publications

A hallmark property of the neurotropic alpha-herpesvirinae is the dissemination of infection to sensory and autonomic ganglia of the peripheral nervous system following an initial exposure at mucosal surfaces. The peripheral ganglia serve as the latent virus reservoir and the source of recurrent infections such as cold sores (herpes simplex virus type I) and shingles (varicella zoster virus). However, the means by which these viruses routinely invade the nervous system is not fully understood. We report that an internal virion component, the pUL37 tegument protein, has a surface region that is an essential neuroinvasion effector. Mutation of this region rendered …

Timber Talk, Vol. 55, No. 4, December 2017

Timber Talk: Nebraska Forest Industry Newsletter

Lumber Market Reports: Northern, Southern, Appalachian

Hardwood Lumber Prices: Green, Kiln-Dried, Pallet Lumber, Ties (7x9)

Tribal Walnut Timber Harvesting Expanding in Nebraska, by Anthony Crill, Bureau of Indian Affairs

To Influence Buyers, Tell Stories, by Paul Reilly, Reilly Sales Training

Green Star Energy Group, South Sioux City Celebrates Bioenergy Day

Welcome Kristina Hughes

Nebraska Forest Industry Spotlight: Native Lumber & Sawmill, Litchfield

Wood Businesses Work to Increase Marketing Skills

Trading Post

Summer Habitat Selection Of The Lower Colorado River Valley Population Of Greater Sandhill Cranes, Kammie L. Kruse, Daniel P. Collins, Courtenay M. Conring, Blake A. Grisham, Warren C. Conway, Jeffrey M. Knetter

United States Fish and Wildlife Service: Publications

Identifying habitat selection and use is important to understand in wildlife management because it informs habitat manipulations, conservation efforts, and species distribution. Habitat selection by sandhill cranes (Antigone canadensis) has been studied primarily on overwintering areas and a few summering locations. Summer habitat selection by the Lower Colorado River Valley Population of greater sandhill cranes (A. c. tabida) in the Intermountain West is not widely known, but has been identified as an information need by many wildlife management agencies. We captured and attached satellite platform transmitter terminals to 21 adult sandhill cranes on Cibola and Sonny Bono Salton Sea National …

The Official List Of The Birds Of Nebraska, Mark A. Brogie

Nebraska Bird Review

The last published “Official List” of the NOURC (NOURC 2009) included 454 species. Since then the following species have been added:

Brown-headed Nuthatch (Sitta pusilla) Accidental I-P 2010

Hooded Crane (Grus monacha) Accidental I-P 2011

Crested Caracara (Caracara cheriway) Accidental I-P 2012

Black-chinned Hummingbird (Archilochus alexandri) Casual I-P 2012

Hooded Oriole (Icterus cucullatus) Accidental I-P 2013

Brown Booby (Sula leucogaster) Accidental I-P 2014

Mute Swan (Cygnus olor) Accidental I-P 2014

Anna’s Hummingbird (Calypte anna) Accidental I-P 2016

Pacific Wren (Troglodytes pacificus) Accidental I-P 2017

The Nebraska Bird Review, Volume 85 December 2017 Number 4

Nebraska Bird Review

Fall Field Report, August - November 2017, by W. Ross Silcock … 146-178

The Official List of the Birds of Nebraska, compiled by Mark A. Brogie …179-197

Ogallala Fall Field Days, Sept. 15 - 17, 2017, by Janis Paseka …198-203

Index to Volume 85 …204-218

Subscription and Organization Information … 219

Index To Volume 85

Nebraska Bird Review

Abreu, Shanin 58 ...

through

Ziegelbauer, Amanda 147

(15 pages)

Fall Field Report, August - November 2017, W. Ross Silcock

Nebraska Bird Review

This fall season will be remembered as the fall with the mega-rarities. There were five, one of which, Pacific Wren, is a first Nebraska record. Based on occurrence dates, Hurricane Irma appears to have influenced the appearance of two of the megas, Black Vulture and Magnificent Frigatebird, neither of which provided opportunities for observers to view them, but both well-documented with photographs. There were an extraordinary TWO sightings of Harris’s Hawk, which together with the presence as of this writing (December 19) of one in northeast Kansas and a view of the species map in eBird strongly suggest a single …

Ogallala Fall Field Days, Sept. 15 - 17, 2017, Janis Paseka

Nebraska Bird Review

The 2017 NOU Fall Field Days took place in and around Ogallala on Sept. 15 - 17 with 55 in attendance. The weather on Friday was hot and windy, making finding birds a challenge. Overnight a cold front came through causing birders to shiver on Saturday and Sunday mornings, but the payoff was easier birding and some interesting species. Field trips were led by William Flack, Clem Klaphake, Wayne Mollhoff, Don Paseka, Ross Silcock and T. J. Walker. Locations included Cedar Point Biological Station, Lake Ogallala SRA, various beaches along the shore of Lake McConaughy SRA, Ash Hollow State Historical …

A Swift Guide To Butterflies Of North America, Second Edition., Ann B. Swengel

The Prairie Naturalist

As soon as I got my hands on A Swift Guide to Butterflies of North America, I immediately checked the species account for Aphrodite Fritillary (Speyeria aphrodite). The prairie version of this species can be sufficiently different from the typically illustrated nominate subspecies such that it must be specifically explained as being distinct. This book passed my first test—describing details that were not only essential for identifying this fritillary species but also for realizing how similar its underside can be to our prairie specialty, the stunning Regal Fritillary (S. idalia).

Much of my research on butterflies occurs in grasslands. For …

Avian Diversity, Abundance, And Nest Success Among Managed Prairies And Agricultural Plots In Oklahoma And Texas, Phillip J. Leonard, Douglas R. Wood, Wayne E. Meyer

The Prairie Naturalist

Over the last 50 years, grassland birds experienced rapid declines due to habitat loss and degradation as a result of agricultural practices. Our objective was to document the diversity, abundance, and nest success of bird communities using managed prairie and agricultural plots at the Tishomingo National Wildlife Refuge (NWR) in southern Oklahoma and Hagerman NWR in northern Texas. From April 1 to July 15, 2013–2014, point count surveys, nest searches, nest monitoring, and vegetation sampling were conducted among three habitat treatments: managed prairie, unharvested wheat, and fallow agricultural plots. Species richness values for potential nesting species were higher in managed …

Severe Drought Impacts Female Pheasant Physiology In Southwest Nebraska, Jessica A. Laskowski, Gwen C. Bachman, Joseph J. Fontaine

The Prairie Naturalist

In 2012, Nebraska experienced one of the worst droughts since the 1930s, accompanied by abnormally high temperatures. We studied the impacts of the 2012 summer drought on female ring-necked pheasant (Phasianus colchicus) body condition and baseline and stress-induced corticosterone concentrations (CORT). We hypothesized that drought conditions would reduce pheasant body condition, increase chronic stress resulting in elevated baseline CORT levels, and down-regulate pheasant stress response to acute stressors, resulting in reduced stress-induced CORT concentrations. In southwestern Nebraska, we captured female pheasants in 2012 (pre-drought) and 2013 (post-drought). Pheasants had poorer body condition after the drought. Although female CORT measures were …

Energy Sprawl Solutions, Nicola Koper

The Prairie Naturalist

Energy sprawl affects all the major conservation issues of our age, from habitat loss and fragmentation to anthropogenic noise and climate change. As such, minimizing and solving its associated problems should be a key focus for conservation biologists. Kiesecker and Naugle provide an impressive and compact book that focusses on solving environmental and social problems likely to result from a transition from non- renewable to far less efficient renewable energy sources.

Energy Sprawl Solutions summarizes numerous relevant peer-reviewed academic papers, and outlines management and planning implications of each one, ultimately resolving these into fairly clear prescriptive recommendations for moving forward. …

Unique Nesting Behavior By Trumpeter Swans (Cygnus Buccinator), Heather M. Johnson, Michael Forsberg, Letitia Reichart, Mark P. Vrtiska

The Prairie Naturalist

Nesting behavior by Trumpeter swans (Cygnus buccinator) has been well documented for most populations. Both sexes cooperate in nest construction, which takes 11–35 days to complete (Hansen et al. 1971, Cooper 1979). Nests generally range from 1.5–3.6 meters in diameter and 1.5 meters in height and are typically built on solid structures such as a muskrat (Ondatra zibethicus) house or an island (Hansen et al. 1971, Cooper 1979). However, we discovered an atypical Trumpeter swan nest built of cattail (Typha angustifolia L.) located on Vaughn Lake, in Cherry County, Nebraska on 13 May 2016.

We monitored the atypical nest by …

The Considerations Given To Determining Authorship, Christopher N. Jacques

The Prairie Naturalist

Greetings GPNSS members! Over the past year, I have been asked by prospective authors and colleagues whether The Prairie Naturalist has criteria for authorship. Given that this issue continues to arise, it is comforting to know that I am not the only one who struggles with considerations given to determining authorship. I checked the current submission guidelines and found nothing specific, which in turn motivated me to explore what other journals such as the Journal of Wildlife Management, Proceedings of the National Academy of Sciences, and Ecology recommend to prospective authors (Merrill 2015). Much to my surprise, discussions of authorship …

One More Warbler: A Life With Birds., Laura Erickson

The Prairie Naturalist

Imagine going on a Victor Emanuel Nature Tour, seated in the van next to Victor Emanuel himself. Between birding stops, this man who has seen over 6,000 species as a world-renowned conservationist and innovator in ecotourism regales you with stories. He starts with his “spark bird”: when he was eight years old, he was taken with the beauty of a pair of Northern Cardinals (Cardinalis cardinalis), and was hooked. Whenever people pile back into the van after a birding stop, he starts another story.

That’s how One More Warbler: A Life with Birds reads, as if Emanuel sat down with …

Field Discrimination Of Prairie Deer Mice And White-Footed Mice Using Morphological Characteristics, Jacob L. Berl, Kelton M. Verble, Elizabeth A. Flaherty, Robert K.S. Swihart

The Prairie Naturalist

Field discrimination of prairie deer mice (Peromyscus maniculatus bairdii) and white-footed mice (P. leucopus noveboracensis) can be difficult throughout much of the central United States where they co-occur. We live-trapped prairie deer mice and white-footed mice within forested and row-crop habitats in central Indiana and used multiplex PCR with species-specific primers to positively determine species identification. We collected a suite of commonly measured external morphological traits (body weight and lengths of ear, hindfoot, tail, and body) from each captured animal. Individuals were assigned to species based on analysis of DNA; discriminant function analysis was used to …

R Teaching Column, Matthias Gehrke, Reed Davis, Norman Matloff, Paul Thompson, Tiffany Chen, Emily Watkins, Laurel Beckett

The R Journal

The revisit package, developed as a collaborative tool for scientists, also serves as a tool for teaching statistics, in a manner that can be highly motivating for students. Using either the included case studies or datasets/code provided by the instructor, students can explore several alternate paths of analysis, such as the effects of including/excluding certain variables, employing different types of statistical methodology and so on. The package includes features that help students follow modern statistical standards and avoid various statistical errors, such as “p-hacking” and lack of attention to outlier data.

The R Journal (December 2017) 9(2): Complete Issue, The R Foundation

The R Journal

Editorial, Roger Bivand

Contributed Research Articles

anchoredDistr: A Package for the Bayesian Inversion of Geostatistical Parameters with Multi-type and Multi-scale Data, Heather Savoy, Falk Heße, and Yoram Rubin

dGAselID: An R Package for Selecting a Variable Number of Features in High Dimensional Data, Nicolae Teodor Melita and Stefan Holban

Allele Imputation and Haplotype Determination from Databases Composed of Nuclear Families, Nathan Medina-Rodríguez and Ángelo Santana

Visualization of Regression Models Using visreg, Patrick Breheny and Woodrow Burchett

fourierin: An R package to compute Fourier integrals, Guillermo Basulto-Elias, Alicia Carriquiry, Kris De Brabanter, and Daniel J. Nordman

Discrete Time Markov Chains with …

The Welchadf Package For Robust Hypothesis Testing In Unbalanced Multivariate Mixed Models With Heteroscedastic And Non-Normal Data, Pablo J. Villacorta

The R Journal

A new R package is presented for dealing with non-normality and variance heterogeneity of sample data when conducting hypothesis tests of main effects and interactions in mixed models. The proposal departs from an existing SAS program which implements Johansen’s general formulation of Welch-James’s statistic with approximate degrees of freedom, which makes it suitable for testing any linear hypothesis concerning cell means in univariate and multivariate mixed model designs when the data pose non-normality and non-homogeneous variance. Improved type I error rate control is obtained using bootstrapping for calculating an empirical critical value, whereas robustness against non-normality is achieved through trimmed …

Ctmcd: An R Package For Estimating The Parameters Of A Continuous-Time Markov Chain From Discrete-Time Data, Marius Pfeuffer

The R Journal

This article introduces the R package ctmcd, which provides an implementation of methods for the estimation of the parameters of a continuous-time Markov chain given that data are only available on a discrete-time basis. This data consists of partial observations of the state of the chain, which are made without error at discrete times, an issue also known as the embedding problem for Markovchains. The functions provided comprise matrix logarithm based approximations as described in Israel et al. (2001), as well as Kreinin and Sidelnikova (2001), an expectation-maximization algorithm and a Gibbs sampling approach, both introduced by Bladt and …

Rqgis: Integrating R With Qgis For Statistical Geocomputing, Jannes Muenchow, Patrick Schratz, Alexander Brenning

The R Journal

Integrating R with Geographic Information Systems (GIS) extends R’s statistical capabilities with numerous geoprocessing and data handling tools available in a GIS. QGIS is one of the most popular open-source GIS, and it furthermore integrates other GIS programs such as the System for Automated Geoscientific Analyses (SAGA) GIS and the Geographic Resources Analysis Support System (GRASS) GIS within a single software environment. This and its QGIS Python API makes it a perfect candidate for console-based geoprocessing. By establishing an interface, the R package RQGIS makes it possible to use QGIS as a geoprocessing workhorse from within R. Compared to other …

Afmtoolkit: An R Package For Automated Afm Force-Distance Curves Analysis, Rafael Benítez, Vicente J. Bolós, José-Luis Toca-Herrera

The R Journal

Atomic force microscopy (AFM) is widely used to measure molecular and colloidal inter actions as well as mechanical properties of biomaterials. In this paper the afmToolkit R package is introduced. This package allows the user to automatically batch process AFM force-distance and force-time curves. afmToolkit capabilities range from importing ASCII files and preprocessing the curves (contact point detection, baseline correction...) for finding relevant physical information, such as Young’s modulus, adhesion energies and exponential decay for force relaxation and creep experiments. This package also contains plotting, summary and feature extraction functions. The package also comes with several data sets so the …

Simulating Noisy, Nonparametric, And Multivariate Discrete Patterns, Ruby Sharma, Sajal Kumar, Hua Zhong, Mingzhou Song

The R Journal

Requiring no analytical forms, nonparametric discrete patterns are flexible in representing complex relationships among random variables. This makes them increasingly useful for data-driven applications. However, there appears to be no software tools for simulating nonparametric discrete patterns, which prevents objective evaluation of statistical methods that discover discrete relationships from data. We present a simulator to generate nonparametric discrete functions as contingency tables. User can request strictly many-to-one functional patterns. The simulator can also produce contingency tables representing dependent non-functional and independent relationships. An option is provided to apply random noise to contingency tables. We demonstrate the utility of the simulator …

Rentrez: An R Package For The Ncbi Eutils Api, David J. Winter

The R Journal

The USA National Center for Biotechnology Information (NCBI) is one of the world’s most important sources of biological information. NCBI databases like PubMed and GenBank contain mil lions of records describing bibliographic, genetic, genomic, and medical data. Here I present rentrez, a package which provides an R interface to 50 NCBI databases. The package is well-documented, contains an extensive suite of unit tests and has an active user base. The programmatic interface to the NCBI provided by rentrez allows researchers to query databases and download or import particular records into R sessions for subsequent analysis. The complete nature of …

A Revitalized Educational Conception Of Growth In The 21st Century For Contemporary Education Praxis In Nebraska, Scott Blum

Department of Teaching, Learning, and Teacher Education: Theses and Other Student Research

My dissertation argues for a revitalized conception of growth in the 21^st century and contemporary education. Through reconstruction, re-conceptualizing, and re-emphasis of growth, this revitalization attends to acute challenges in schooling and can impact praxis in education today. This pragmatic and philosophical work places a revitalized conception of growth as the purpose of education and, to the extent that education is life, continual growth as a process for living.

John Dewey provided his conception of growth during the 19^th and 20^th centuries as he valued the natural capacities a human being possesses for experiencing life. He recognized …

Design And Validation Of An Experimental Setup To Study Single Phase Heat Transfer Enhancement Of Femtosecond Laser Processed Metallic Surfaces, Sarah Jane Wallis

Department of Mechanical and Materials Engineering: Dissertations, Theses, and Student Research

In the present work, a single phase flow heat transfer experimental loop was designed with the intention of studying the effects of femtosecond laser surface processing (FLSP) on metallic surfaces with the specific goal of enhancing heat transfer in compact heat exchangers currently in use by NASA. This experimental setup went through two major design iterations which are detailed in this thesis. The first iteration consisted of a counterflow fluid-to-fluid heat exchanger, which measured overall heat transfer coefficients and pressure drops, where the overall heat transfer coefficient is defined in terms of the total thermal resistance to heat transfer between …

Design And Implementation Of A Stand-Alone Tool For Metabolic Simulations, Milad Ghiasi Rad

School of Computing: Dissertations, Theses, and Student Research

In this thesis, we present the design and implementation of a stand-alone tool for metabolic simulations. This system is able to integrate custom-built SBML models along with external user’s input information and produces the estimation of any reactants participating in the chain of the reactions in the provided model, e.g., ATP, Glucose, Insulin, for the given duration using numerical analysis and simulations. This tool offers the food intake arguments in the calculations to consider the personalized metabolic characteristics in the simulations. The tool has also been generalized to take into consideration of temporal genomic information and be flexible for simulation …