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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 …

News From The Bioconductor Project, Bioconductor Core Team

The R Journal

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor 3.14 was released on 27 October, 2021. It is compatible with R 4.1.0 and consists of 2083 software packages, 408 experiment data packages, 904 up-to-date annotation packages, and 29 workflows.

Volume Approximation And Sampling For Convex Polytopes In R, Apostolos Chalkis, Vissarion Fisikopoulos

The R Journal

Sampling from high-dimensional distributions and volume approximation of convex bodies are fundamental operations that appear in optimization, finance, engineering, artificial intelligence, and machine learning. In this paper, we present volesti, an R package that provides efficient, scalable algorithms for volume estimation, uniform, and Gaussian sampling from convex polytopes. volesti scales to hundreds of dimensions, handles efficiently three different types of polyhedra and provides non existing sampling routines to R. We demonstrate the power of volesti by solving several challenging problems using the R language

Volesti: Volume Approximation And Sampling For Convex Polytopes In R, Apostolos Chalkis, Vissarion Fisikopoulos

The R Journal

Sampling from high-dimensional distributions and volume approximation of convex bodies are fundamental operations that appear in optimization, finance, engineering, artificial intelligence, and machine learning. In this paper, we present volesti, an R package that provides efficient, scalable algorithms for volume estimation, uniform, and Gaussian sampling from convex polytopes. volesti scales to hundreds of dimensions, handles efficiently three different types of polyhedra and provides non existing sampling routines to R. We demonstrate the power of volesti by solving several challenging problems using the R language.

G2f As A Novel Tool To Find And Fill Gaps In Metabolic Networks, Daniel Osorio, Kelly Botero, Andrés Pinzón Velasco, Nicolás Mendoza-Mejía, Felipe Rojas-Rodríguez, George Barreto, Janneth González

The R Journal

During the building of a genome-scale metabolic model, there are several dead-end metabolites and substrates which cannot be imported, produced, nor used by any reaction incorporated in the network. The presence of these dead-end metabolites can block out the net flux of the objective function when it is evaluated through Flux Balance Analysis (FBA), and when it is not blocked, bias in the biological conclusions increase. In this aspect, the refinement to restore the connectivity of the network can be carried out manually or using computational algorithms. The g2f package was designed as a tool to find the gaps from …

The R Quest: From Users To Developers, Simon Urbanek

The R Journal

R is not a programming language, and this produces the inherent dichotomy between analytics and software engineering. With the emergence of data science, the opportunity exists to bridge this gap, especially through teaching practices.

Software Engineering And R Programming: A Call For Research, Melina Vidoni

The R Journal

Although R programming has been a part of research since its origins in the 1990s, few studies address scientific software development from a Software Engineering (SE) perspective. The past few years have seen unparalleled growth in the R community, and it is time to push the boundaries of SE research and R programming forwards. This paper discusses relevant studies that close this gap Additionally, it proposes a set of good practices derived from those findings aiming to act as a call-to-arms for both the R and RSE (Research SE) community to explore specific, interdisciplinary paths of research

Bcmixed: A Package For Median Inference On Longitudinal Data With The Box–Cox Transformation, Kazushi Maruo, Ryota Ishii, Yusuke Yamaguchi, Masahiko Gosho

The R Journal

This article illustrates the use of the bcmixed package and focuses on the two main functions: bcmarg and bcmmrm. The bcmarg function provides inference results for a marginal model of a mixed effect model using the Box–Cox transformation. The bcmmrm function provides model median inferences based on the mixed effect models for repeated measures analysis using the Box–Cox transformation for longitudinal randomized clinical trials. Using the bcmmrm function, analysis results with high power and high interpretability for treatment effects can be obtained for longitudinal randomized clinical trials with skewed outcomes. Further, the bcmixed package provides summarizing and visualization tools, which …

Survidm: An R Package For Inference And Prediction In An Illness-Death Model, Gustavo Soutinho, Marta Sestelo, Luís Meira-Machado

The R Journal

Multi-state models are a useful way of describing a process in which an individual moves through a number of finite states in continuous time. The illness-death model plays a central role in the theory and practice of these models, describing the dynamics of healthy subjects who may move to an intermediate "diseased" state before entering into a terminal absorbing state. In these models, one important goal is the modeling of transition rates which is usually done by studying the relationship between covariates and disease evolution. However, biomedical researchers are also interested in reporting other interpretable results in a simple and …

Analysis Of Corneal Data In R With The Rpaci Package, Darío Ramos-López, Ana D. Maldonado

The R Journal

In ophthalmology, the early detection of keratoconus is still a crucial problem. Placido disk corneal topographers are essential in clinical practice, and many indices for diagnosing corneal irregularities exist. The main goal of this work is to present the R package rPACI, providing several functions to handle and analyze corneal data. This package implements primary indices of corneal irregularity (based on geometrical properties) and compound indices built from the primary ones, either using a generalized linear model or as a Bayesian classifier using a hybrid Bayesian network and performing approximate inference. rPACI aims to make the analysis of corneal …

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 …

Genetic Mapping And Qtl Analysis For Peanut Smut Resistance, Francisco J. De Blas, Cecilia I. Bruno, Renee Arias, Carolina Ballén-Taborda, Eva Mamani, Claudio Oddino, Melina Rosso, Beatriz P. Costero, Marina Bressano, Juan H. Soave, Sara J. Soave, Mario I. Buteler, J. Guillermo Seijo, Alicia Massa

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

Background: Peanut smut is a disease caused by the fungus Thecaphora frezii Carranza & Lindquist to which most commercial cultivars in South America are highly susceptible. It is responsible for severely decreased yield and no effective chemical treatment is available to date. However, smut resistance has been identified in wild Arachis species and further transferred to peanut elite cultivars. To identify the genome regions conferring smut resistance within a tetraploid genetic background, this study evaluated a RIL population {susceptible Arachis hypogaea subsp. hypogaea (JS17304-7-B) × resistant synthetic amphidiploid (JS1806) [A. correntina (K 11905) × A. cardenasii (KSSc 36015)] × A. …

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 …

Genome Annotation Using Average Mutual Information, Garin P. Newcomb

Department of Electrical and Computer Engineering: Dissertations, Theses, and Student Research

Advancements in high-throughput DNA sequencing technologies and ambitious goals for their use are resulting in the generation of a deluge of unannotated sequenced genomes. This makes computational tools that can aid in annotation increasingly valuable.

Here, we provide a detailed exploration of the utility as well as the limitations of average mutual information (AMI) in several steps of genome annotation. For a genomic sequence, AMI is a measure of the information a base contains about the base separated by a fixed lag. A profile is constructed by calculating AMI at multiple lags. In addition to traditional AMI, we employ two …

Comparative Analysis Of Kmer Counting And Estimation Tools, Ankitha Vejandla

School of Computing: Dissertations, Theses, and Student Research

The rapid development of next-generation sequencing (NGS) technologies for determining the sequence of DNA has revolutionized genome research in recent years. De novo assemblers are the most commonly used tools to perform genome assembly. Most of the assemblers use de Bruijn graphs that break the sequenced reads into smaller sequences (sub-strings), called kmers, where k denotes the length of the sub-strings. The kmer counting and analysis of kmer frequency distribution are important in genome assembly. The main goal of this research is to provide a detailed analysis of the performance of different kmer counting and estimation tools that are currently …

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), …

Formation Of B Horizons In Engineered Putting Green Soils, Glen R. Obear

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

Engineered turfgrass putting green soils are designed to drain quickly, while maintaining adequate water- and nutrient-holding capacity to sustain plant growth. These soils are designed to meet specific performance characteristics when they are constructed, but the process of soil formation changes these characteristics over time. Chapter 1 of this dissertation is a literature review of soil formation in engineered putting green soils. Pedogenesis of putting greens is such that A horizons form as organic matter accumulates near the surface, and B horizons form as particles and solutes are translocated to textural or pH boundaries in soil profiles. In the engineered …

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 …

An Intersectionality Framework On The Role Of Student-Teacher Relationships On Student Social Outcomes, Kenji Madison

College of Education and Human Sciences: Dissertations, Theses, and Student Research

This research aimed to build on the great wealth of knowledge on student-teacher relationships, social competence, and peer outcomes while utilizing a different approach integrating race and gender. The view of intersectionality may influence those who join in reading this research to consider race coupled with student gender as a strong influence affecting the formation of a relationship as instrumental as the student-teacher relationship.

In a sample of 10,886 (8489 White, 2397 Black) students from third to fifth grade, the research completed three aims: characterizing the relationship between teacher rated closeness and conflict and students’ social outcomes in fourth and …

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 …

The Impact Of Beneficial Organisms In Corn Agroecosystems, Callie Rosalind Braley

Doctor of Plant Health Program: Dissertations and Student Research

Corn is one of the world’s, and Nebraska’s, most important crops. Millions of acres are planted to corn each year in the Cornhusker State. However, each year there are a plethora of arthropod, weed, and microorganism pests that rob farmers of reaching their maximum yield potential. There are many options available to manage these pests in corn agroecosystems, but one option is often underutilized: beneficial organisms. For each pest, there are a variety of natural enemies that can assist in mitigating the damage caused by pests.

Many beneficial organisms exist, and they can be grouped by the type of pest …

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 …

Examination Of Cajeput Oil (Melaleuca Cajuputi) Phytochemicals As Tools To Manage The Yellow Fever Mosquito (Aedes Aegypti L.), Ellis Johnson

Department of Entomology: Dissertations, Theses, and Student Research

The yellow fever mosquito, Aedes aegypti L., is among the most important insects as it pertains to public health. It vectors several health-endangering pathogens, including yellow fever, dengue fever, chikungunya, and Zika viruses. Insecticides are among the most effective tools used to manage mosquito populations however, their efficacy to manage mosquito populations is being threatened by insecticide resistance. This ongoing threat warrants new chemical strategies to reduce or incapacitate a mosquito population capable of pathogen transmission. Plant essential oils are candidates for identifying novel management tools for disease-vectoring arthropods. Commercially, essential oils have been used for pharmaceuticals, flavoring, fragrances, cosmetics, …