Digital Commons Network^™

Natural Asset-Based Community Development In The Nebraska Community Foundation Network, Kristen Ohnoutka

Community and Regional Planning Program: Theses

As rural communities explore new ways to stimulate growth and development in their place, one of the biggest challenges they face is reinventing what rural community development is and has been. The conventional way of thinking goes communities must attract new businesses to attract new workers to grow a community’s population. However, population growth and industry attraction are not always equivalent to progress, especially not in rural communities. For decades, rural communities have withstood the boom and bust of industry and economy, whether it be agricultural, industrial, manufacturing, etc. These industries and more have demanded the extraction of rural communities’ …

Complete Modeling Of The Chondrogenic Environment Under Continuous Low-Intensity Ultrasound, Heather Newell

Department of Chemical and Biomolecular Engineering: Dissertations, Theses, and Student Research

Articular cartilage is an avascular tissue that requires therapeutic intervention methods. This work answers the following: determine transducer operation to optimize the bioeffects; calculate the magnitude of pressure exerted on chondrocytes at an injury site; and confirm the theoretical findings by an animal model.

Earlier work has shown that cellular response to US is maximized at the resonance frequency of the cells. Resonance frequencies were calculated for chondrocytes in various layers. The latter configuration closest resembles in vivo conditions and the resonance occurred at 3.8±0.3 ������. The 3D model of US propagation in a rabbit knee was constructed from MRIs …

Index To Volume 89

Nebraska Bird Review

Adams, Marie 52

to

Zonotrichia leucophrys gambelii 168 leucophrys 75, 168-169 oriantha 75, 169

Review Of The Sandhill Crane State: A Naturalist’S Guide To Nebraska By Paul Johnsgard, Ruth Stearns

Nebraska Bird Review

Dr. Paul Austin Johnsgard left us one last gift, in this reference guide to all places natural in Nebraska. Published posthumously, and available for purchase or free via UNL’s Digital Commons, this book arrived at my doorstep like a veritable “seed catalog” of Nebraska’s places of wonder to delight and inspire fair weather adventures just before the long winter set in. He wants us to explore the state as he had done, to be excited by all the out-ofdoors Nebraska has to offer.

Northern Saw-Whet Owl Autumn Migration In Eastern Nebraska: Results From A Three-Year Banding Study, Stephen J. Brenner, Joel G. Jorgensen

Nebraska Bird Review

Prior to 2019, records of NSWOs in Nebraska during fall were limited. There were fewer than five accepted reports in eastern Nebraska since the 1950s (Silcock and Jorgensen, 2021). The Hitchcock banding station along the Missouri River bluffs in nearby western Iowa has captured, banded, and released 20-50 birds during autumn migration for a number of years (J. Toll, personal communication). Furthermore, a single season banding study in central Nebraska during fall 2004 captured 14 NSWOs (Kim 2005), suggesting the species may migrate annually over much of the state in fall, or at least in more years than previously thought. …

Review Of Nest Records Of Nebraska Birds By Wayne J. Mollhoff, W. Ross Silcock

Nebraska Bird Review

This book summarizes a lifetime of investigation of Nebraska’s breeding birds by Wayne Mollhoff. Even though I say the book summarizes a lifetime of investigation, I would not be surprised if Wayne resurfaces in a few years with a follow-up of some sort, intrepid investigator that he is. Over the years Wayne has spent innumerable days in the field climbing trees in full forestry gear, wading and kayaking marshes and rivers, hiking over prairies, and bushwhacking through dense forests (there are still a few in Nebraska). But this isn’t the totality of Wayne’s talents; he is a determined researcher with …

Diproperm: An R Package For The Diproperm Test, Andrew G. Allmon, J.S. Marron, Michael G. Hudgens

The R Journal

High-dimensional low sample size (HDLSS) data sets frequently emerge in many biomedical applications. The direction-projection-permutation (DiProPerm) test is a two-sample hypothesis test for comparing two high-dimensional distributions. The DiProPerm test is exact, i.e., the type I error is guaranteed to be controlled at the nominal level for any sample size, and thus is applicable in the HDLSS setting. This paper discusses the key components of the DiProPerm test, introduces the diproperm R package, and demonstrates the package on a real-world data set

Spnetwork: A Package For Network Kernel Density Estimation, Jeremy Gelb

The R Journal

This paper introduces the new package spNetwork that provides functions to perform Network Kernel Density Estimate analysis (NKDE). This method is an extension of the classical Kernel Density Estimate (KDE), a non parametric approach to estimate the intensity of a spatial process. More specifically, it adapts the KDE for cases when the study area is a network, constraining the location of events (such as accidents on roads, leaks in pipes, fish in rivers, etc.). We present and discuss in this paper the three main versions of NKDE: simple, discontinuous, and continuous that are implemented in spNetwork. We illustrate how to …

Drhotnet: An R Package For Detecting Differential Risk Hotspots On A Linear Network, Álvaro Briz-Redón, Francisco Martínez-Ruiz, Francisco Montes

The R Journal

One of the most common applications of spatial data analysis is detecting zones, at a certain scale, where a point-referenced event under study is especially concentrated. The detection of such zones, which are usually referred to as hotspots, is essential in certain fields such as criminology, epidemiology, or traffic safety. Traditionally, hotspot detection procedures have been developed over areal units of analysis. Although working at this spatial scale can be suitable enough for many research or practical purposes, detecting hotspots at a more accurate level (for instance, at the road segment level) may be more convenient sometimes. Furthermore, it is …

Visual Diagnostics For Constrained Optimisation With Application To Guided Tours, H Sherry Zhang, Dianne Cook, Ursula Laa, Nicolas Langrené, Patricia Menéndez

The R Journal

A guided tour helps to visualise high-dimensional data by showing low-dimensional projections along a projection pursuit optimisation path. Projection pursuit is a generalisation of principal component analysis in the sense that different indexes are used to define the interestingness of the projected data. While much work has been done in developing new indexes in the literature, less has been done on understanding the optimisation. Index functions can be noisy, might have multiple local maxima as well as an optimal maximum, and are constrained to generate orthonormal projection frames, which complicates the optimization. In addition, projection pursuit is primarily used for …

The Nebraska Bird Review, Volume 89 Number 4, December 2021

Nebraska Bird Review

Fall Field Report, August - November 2021 by W. Ross Silcock

Book Review: Nest Records of Nebraska Birds by Wayne J. Mollhoff Reviewed by W. Ross Silcock

Northern Saw-whet Owl Autumn Migration in Eastern Nebraska: Results from a Three-year Banding Study by Stephen J. Brenner and Joel G. Jorgensen

Mute Swan Observation at Gavins Point Dam Area, Cedar/Knox Co., Nebraska by Caleb Strand and Mark A. Brogie

Book Review: The Sandhill Crane State: A Naturalist's Guide to Nebraska by Paul Johnsgard, Reviewed by Ruth Stearns

Index to Volume 89

Subscription and Organization Information

Mute Swan Observation At Gavins Point Dam Area, Cedar/Knox Co., Nebraska, Caleb Strand, Mark A. Brogie

Nebraska Bird Review

The Nebraska Ornithologists’ Union Records Committee (NOURC) considers Mute Swan (Cygnus olor) to be Accidental in Nebraska (NOURC 2017) with only two accepted records. A review of Mute Swan status in the Midwest and Nebraska, how individual records in Nebraska are evaluated to determine wild provenance, and a review of Nebraska reports can be found in “The Mute Swan in Nebraska: History and Current Status” (Brogie et al. 2016).

The following is an account of the third NOURC accepted record for Mute Swan in Nebraska. On 11 June 2021 we observed two sub-adult Mute Swans on Lake Yankton, Cedar County, …

Fall Field Report, August-November 2021, W. Ross Silcock

Nebraska Bird Review

INTRODUCTION Recent years have seen increasing reports of birds lingering quite late, and this fall was no exception. Notable groups exhibiting tardy departures were shorebirds and vireos. Tardy shorebirds were record late Solitary Sandpipers, near-record late Dunlin, and late Long-billed Curlew, Ruddy Turnstone, Least and Semipalmated Sandpipers, Long-billed Dowitcher, and Wilson’s Phalarope. Among the vireos, all regular species were at least tardy; record late was a Red-eyed Vireo, a Warbling Vireo was record late for the Panhandle, and a Blue-headed Vireo was second latest on record. Record late was a Barn Swallow, and a Mountain Bluebird was record late in …

Reproductive Success Of Captive-Reared Allegheny Woodrats (Neotoma Magister) Released Into Genetically Depauperate Populations, Miracle M. Davis, Timothy J. Smyser, Scott A. Johnson, Joseph Duchamp, Jeffery L. Larkin, Robert K. Swihart, Jacqueline M. Doyle

United States Department of Agriculture Wildlife Services: Staff Publications

Habitat fragmentation and degradation have led to a proliferation of small and isolated populations that are vulnerable to genetic erosion. Reduction in habitat and concomitant declines in population connectivity can expediate the collapse of species that exist as natural metapopulations. In recent years, Allegheny woodrats (Neotoma magister) have experienced local extirpations and declines in genetic diversity across their range due to disease-related mortality, reduced food availability, and disruption of connectivity among subpopulations. In response, we developed a captive-breeding program to facilitate genetic management of isolated woodrat populations in Indiana. Between 2010 and 2012, 27 captive-reared individuals were released to four …

Charting A New Frontier Integrating Mathematical Modeling In Complex Biological Systems From Molecules To Ecosystems, Katharine A. White, Kira D. Mcentire, Nicole R. Buan, Lecia Robinson, Elisar Barbar

Department of Biochemistry: Faculty Publications

Advances in quantitative biology data collection and analysis across scales (molecular, cellular, organismal, and ecological) have transformed how we understand, categorize, and predict complex biological systems. This surge of quantitative data creates an opportunity to apply, develop, and evaluate mathematical models of biological systems and explore novel methods of analysis. Simultaneously, thanks to increased computational power, mathematicians, engineers, and physical scientists have developed sophisticated models of biological systems at different scales. Novel modeling schemes can offer deeper understanding of principles in biology, but there is still a disconnect between modeling and experimental biology that limits our ability to fully realize …

The Genome Of The Stable Fly, Stomoxys Calcitrans, Reveals Potential Mechanisms Underlying Reproduction, Host Interactions, And Novel Targets For Pest Control, Pia U. Olafson, Serap Aksoy, Geoffrey M. Attardo, Greta Buckmeier, Xiaoting Chen, Craig J. Coates, Megan Davis, Justin Dykema, Scott J. Emrich, Markus Friedrich, Christopher J. Holmes, Panagiotis Ioannidis, Evan N. Jansen, Emily C. Jennings, Daniel Lawson, Ellen O. Martinson, Gareth L. Maslen, Richard P. Meisel, Terence D. Murphy, Dana Nayduch, David R. Nelson, Kennan J. Oyen, Tyler J. Raszick, José M.C. Ribeiro, Hugh M. Robertson, Andrew J. Rosendale, Timothy B. Sackton, Perot Saelao, Sonja L. Swiger, Sing Hoi Sze, Aaron M. Tarone, David B. Taylor, Wesley C. Warren, Robert M. Waterhouse, Matthew T. Weirauch, John H. Werren, Richard K. Wilson, Evgeny M. Zdobnov, Joshua B. Benoit

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

Background: The stable fly, Stomoxys calcitrans, is a major blood-feeding pest of livestock that has near worldwide distribution, causing an annual cost of over $2 billion for control and product loss in the USA alone. Control of these flies has been limited to increased sanitary management practices and insecticide application for suppressing larval stages. Few genetic and molecular resources are available to help in developing novel methods for controlling stable flies. Results: This study examines stable fly biology by utilizing a combination of high-quality genome sequencing and RNA-Seq analyses targeting multiple developmental stages and tissues. In conjunction, 1600 genes were …

Biodiversity Scale-Dependence And Opposing Multi-Level Correlations Underlie Differences Among Taxonomic, Phylogenetic And Functional Diversity, Nadejda A. Mirochnitchenko, Erica F. Stuber, Joseph J. Fontaine

Nebraska Cooperative Fish and Wildlife Research Unit: Staff Publications

Aim: Biodiversity is a multidimensional property of biological communities that represents different information depending on how it is measured, but how dimensions relate to one another and under what conditions is not well understood. We explore how taxonomic, phylogenetic, and functional diversity can differ in scale-of-effect dependence and habitat-biodiversity relationships, and subsequently how spatial differences among biodiversity dimensions may arise. Location: Nebraska, United States. Taxon: Birds. Methods: Across 2016 and 2017, we conducted 2,641 point counts at 781 sites. We modeled the occupancy of 141 species using Bayesian Bernoulli-Bernoulli hierarchical logistic regressions. We calculated species richness (SR), phylogenetic diversity (PD), …

American Burying Beetle, Plant Richness, And Soil Property Responses To Collapse Of Juniperus Virginiana Woodlands With Fire, Alison K. Ludwig

Department of Agronomy and Horticulture: Dissertations, Theses, and Student Research

Grasslands are declining in the Great Plains due to land use changes, woody plant encroachment, and loss of historic fire cycles. Prescribed burn associations have utilized prescribed fire to collapse invading woodlands and allow the restoration of grasslands. This fire is considered “extreme” because it is capable of changing the structure and function of an ecosystem. Our study site is the Loess Canyons Experimental Landscape, a long-term, ecoregion-scale experiment to apply prescribed fire across the region to restore grasslands. The Nebraska Natural Legacy Project established the Loess Canyons ecoregion as a Biologically-Unique Landscape in 2005 with the state’s wildlife action …

Livestock Grazing Impacts On Crop And Soil Responses For Two Cropping Systems, Alyssa Kuhn

Department of Agronomy and Horticulture: Dissertations, Theses, and Student Research

Diversified crop, forage, and livestock systems are assumed to be more sustainable and economically competitive than traditional cropping systems. Objectives of this study were to determine effects of integrating grazing livestock into corn (Zea mays)-soybean (Glycine max (L.) Merr.) (C-S) and corn-soybean-wheat (Triticum aestivum L.) (C-S-W) cropping systems on plant population, grain yield, soil nutrients and soil carbon dioxide (CO₂) flux following winter grazing corn residue (both systems) and an oat (Avena sativa) cover crop (C-S-W only) planted after wheat. For the 2019 and 2020 production seasons, neither corn nor soybean plant …

The Importance Of Acquisition Learning On Nicotine And Varenicline Drug Substitution In A Drug-Discriminated Goal-Tracking Task, Brady M. Thompson, Scott T. Barrett, Y. Wendy Huynh, David A. Kwan, Jennifer E. Murray, Rick A. Bevins

Department of Psychology: Faculty Publications

Nicotine and varenicline (Chantix®; the leading non-nicotine cessation pharmacotherapy) can come to control appetitive behaviors such as goal-tracking. We tested rats (N = 48) in a drug-discriminated goal-tracking (DGT) task where each rat received daily subcutaneous injections of either nicotine (0.4 mg/kg) or saline (0.9% [w/v]) interspersed across the acquisition phase (Phase 1). On saline days, sucrose was intermittently available. On nicotine days, sucrose was withheld. All rats acquired the discrimination with increased goal-tracking rates on saline days relative to nicotine days. Following acquisition, rats were separated into four groups to assess drug-substitution and discrimination reversal in Phase 2. The …

Characterization Of The Multifunctional Enzyme Proline Utilization A, Yizi Mao

Department of Biochemistry: Dissertations, Theses, and Student Research

Proline is a unique and important amino acid. Proline is a proteogenic amino acid and its metabolism is involved in many critical cellular functions. Therefore, proline metabolism is tightly regulated, and dysfunction of proline metabolism is related to human diseases. The first step of proline oxidization to ∆¹-pyrroline-5-carboxylic acid (P5C) is catalyzed by proline dehydrogenase (PRODH). P5C is then non-enzymatically hydrolyzed to glutamate-γ-semialdehyde (GSA), which can be further oxidized to glutamate by P5C dehydrogenase (P5CDH/GSALDH). In Gram-negative bacteria, the PRODH and P5CDH enzymes are expressed as one polypeptide called proline utilization A (PutA). In some Gram-negative bacteria an …

Intricacies In Agronomic Management: The Role Of Interdisciplinary Education, Adam M. Striegel

Doctor of Plant Health Program: Dissertations and Student Research

As a science, agronomy is built upon the connection of inter-disciplinary fields of study. Management (M) of various discipline considerations (and their subsequent interactions) can be influenced by and have significant effects on genetic by environment (GxE) expression. This has led to the promotion of GxExM systems. However, optimizing GxExM programs requires extensive, interdisciplinary knowledge. To evaluate interdisciplinary training provided in undergraduate education, 11 four-year universities were selected in the United States that offer baccalaureate degree majors in agronomy or crop science. Surveys of undergraduate programs of study were conducted, with all required coursework separated into general degree components (general …

Comparing Machine Learning Techniques With State-Of-The-Art Parametric Prediction Models For Predicting Soybean Traits, Susweta Ray

Department of Statistics: Dissertations, Theses, and Student Research

Soybean is a significant source of protein and oil, and also widely used as animal feed. Thus, developing lines that are superior in terms of yield, protein and oil content is important to feed the ever-growing population. As opposed to the high-cost phenotyping, genotyping is both cost and time efficient for breeders while evaluating new lines in different environments (location-year combinations) can be costly. Several Genomic prediction (GP) methods have been developed to use the marker and environment data effectively to predict the yield or other relevant phenotypic traits of crops. Our study compares a conventional GP method (GBLUP), a …

Economic Estimates Of Wild Hog (Sus Scrofa) Damage And Control Among Young Forest Plantations In Alabama, Micah Fern, Rebecca Barlow, Chris Slootmaker, John Kush, Stephanie Shwiff, Larry Teeter, Jim Armstrong

United States Department of Agriculture Wildlife Services: Staff Publications

Operating as ecological engineers, the increased distribution and abundance of wild hogs (Sus scrofa) has caused considerable socio-economic impacts. The international scope of economic research providing wild hog damage estimates are often confined to agricultural crops, while damage estimates among forest plantations are lacking. In Alabama, private landowners hold the majority of timberland acreage and are less equipped to absorb financial losses from wild hog damage than their industrial counterparts. A survey was conducted to estimate the economic impact of wild hogs, namely costs of damage and control, to privately owned forestlands. The survey was distributed in the …

Distillers' Grains: Past, Present, And Future Economic Analyses, Daniel E. Gertner

Department of Agricultural Economics: Dissertations, Theses, and Student Research

This thesis is comprised of four chapters, each of which discusses or conducts economic research related to the distillers’ grains market. The first three chapters are meant to be standalone papers. Chapter four provides potential paths forward in distillers’ grains research based on the findings of the first three chapters and concludes the thesis.

The first chapter conducts a comprehensive literature review that categorizes and summarizes economic research on distillers’ grains products. This section shows how the physical market has moved beyond the current academic understanding of market products and structure. Existing research finds that traditional distillers’ grains products positively …

Evaluation Of A Novel Approach For Assessing Biological Activity In Agricultural Soils, Karla Melgar

Department of Agricultural and Biological Systems Engineering: Dissertations, Theses, and Student Research

Soil health is a key factor impacting soil resilience and fertility in crop production systems. Favorable soil physical and biological conditions facilitate plant nutrient absorption and nutrient cycling. Demonstrating to farmers the impacts and changes in soil biological activity under different soil management practices has been a challenge due to the limited availability of inexpensive tools for quantifying this component of soil health. The primary goal of this study was to present a simple and readily accessible tool for evaluating soil biological activity to promote the use of organic amendments in crop fields. Research plots were established in two studies …

Deterring Non-Target Birds From Toxic Bait Sites For Wild Pigs, Nathan P. Snow, Joseph M. Halseth, Justin A. Foster, Michael J. Lavelle, Justin W. Fischer, Michael P. Glow, Ingrid A. Messer, Seth M. Cook, Kurt C. Vercauteren

United States Department of Agriculture Wildlife Services: Staff Publications

Toxic baiting of wild pigs (Sus scrofa) is a potential new tool for population control and damage reduction in the US. Field trials testing a prototype toxic bait (HOGGONE 2 containing 5% sodium nitrite [SN]), though, revealed that wild pigs spilled small particles of toxic bait outside of bait stations which subsequently created hazards for non-target species that consumed those particles, primarily passerine birds. To deter non-target birds from consuming particles of spilled bait, we tested four deterrents at mock bait sites (i.e., baited with bird seed) in north-central Colorado, USA during April–May 2020. We found a programable, inflatable deterrent …

Responses Of Turkey Vultures To Unmanned Aircraft Systems Vary By Platform, Morgan B. Pfeiffer, Bradley F. Blackwell, Thomas W. Seamans, Bruce N. Buckingham, Joshua L. Hoblet, Patrice E. Baumhardt

United States Department of Agriculture Wildlife Services: Staff Publications

A challenge that conservation practitioners face is manipulating behavior of nuisance species. The turkey vulture (Cathartes aura) can cause substantial damage to aircraft if struck. The goal of this study was to assess vulture responses to unmanned aircraft systems (UAS) for use as a possible dispersal tool. Our treatments included three platforms (fixed-wing, multirotor, and a predator-like ornithopter [powered by flapping flight]) and two approach types (30 m overhead or targeted towards a vulture) in an operational context. We evaluated perceived risk as probability of reaction, reaction time, flight-initiation distance (FID), vulture remaining index, and latency to return. …

Reintegrating Biology Through The Nexus Of Energy, Information, And Matter, Kim L. Hoke, Sara L. Zimmer, Adam B. Roddy, Mary Jo Ondrechen, Craig E. Williamson, Nicole R. Buan

Department of Biochemistry: Faculty Publications

Information, energy, and matter are fundamental properties of all levels of biological organization, and life emerges from the continuous flux of matter, energy, and information. This perspective piece defines and explains each of the three pillars of this nexus. We propose that a quantitative characterization of the complex interconversions between matter, energy, and information that compose this nexus will help us derive biological insights that connect phenomena across different levels of biological organization. We articulate examples from multiple biological scales that highlight how this nexus approach leads to a more complete understanding of the biological system. Metrics of energy, information, …

Landscape Transformations Produce Favorable Roosting Conditions For Turkey Vultures And Black Vultures, Jacob E. Hill, Kenneth F. Kellner, Bryan M. Kluever, Michael L. Avery, John S. Humphrey, Eric A. Tillman, Travis L. Devault, Jerrold L. Belant

United States Department of Agriculture Wildlife Services: Staff Publications

Recent increases in turkey vulture (Cathartes aura) and black vulture (Coragyps atratus) populations in North America have been attributed in part to their success adapting to human-modified landscapes. However, the capacity for such landscapes to generate favorable roosting conditions for these species has not been thoroughly investigated. We assessed the role of anthropogenic and natural landscape elements on roosting habitat selection of 11 black and 7 turkey vultures in coastal South Carolina, USA using a GPS satellite transmitter dataset derived from previous research. Our dataset spanned 2006–2012 and contained data from 7916 nights of roosting. Landscape …