Digital Commons Network^™

Microbiome Variation Across Populations Of Desert Halophyte Zygophyllum Qatarensis, Abdul Latif Khan, Lucas Dantas Lopes, Saqib Bilal, Sajjad Asaf, Kerri M. Crawford, Venkatesh Balan, Ahmed Al-Rawahi, Ahmed Al-Harrasi, Daniel P. Schachtman

Department of Agronomy and Horticulture: Faculty Publications

Microbial symbionts play a significant role in plant health and stress tolerance. However, few studies exist that address rare species of core-microbiome function during abiotic stress. In the current study, we compared the microbiome composition of succulent dwarf shrub halophyte Zygophyllum qatarensis Hadidi across desert populations. The results showed that rhizospheric and endosphere microbiome greatly varied due to soil texture (sandy and gravel). No specific bacterial amplicon sequence variants were observed in the core-microbiome of bulk soil and rhizosphere, however, bacterial genus Alcaligenes and fungal genus Acidea were abundantly distributed across root and shoot endospheres. We also analyzed major nutrients …

Informing Management Of Henrys Lake, Idaho, Using An Integrated Catch-At-Age Model, Joshua L. Mccormick, Jennifer Vincent, Brett High, Darcy K. Mccarrick, Michael C. Quist

United States Geological Survey: Staff Publications

Henrys Lake, Idaho, supports a popular fishery for Yellowstone Cutthroat Trout Oncorhynchus clarkii bouvieri and Yellowstone Cutthroat Trout × Rainbow Trout O. mykiss hybrids. A majority of the adult population of fish in Henrys Lake are of hatchery origin that were stocked as fingerlings. The fishery is closed to angling during the late winter and spring months, but fisheries managers are considering opening the fishery year-round with catch-and-release- only regulations or with a two-fish bag limit during the extended season. However, there is concern that the proposed management actions may negatively affect the current fishery. Therefore, we developed an integrated …

Seabem: An Artificial Intelligence Powered Web Application To Predict Cover Crop Biomass, Aime Christian Tuyishime, Andrea Basche

Honors Program: Senior Projects (Public)

SEABEM, the Stacked Ensemble Algorithms Biomass Estimator Model, is a web application with a stacked ensemble of Machine Learning (ML) algorithms running on the backend to predict cover crop biomass for locations in Sub-Saharan. The SEABEM model was developed using a previously developed database of crop growth and yield that included site characteristics such as latitude, longitude, soil texture (sand, silt, and clay percentages), temperature, and precipitation. The goal of SEABEM is to provide global farmers, mainly small-scale African farmers, the knowledge they need before practicing and benefiting from cover crops while avoiding the expensive and time-consuming operations that come …

A Global Soil Spectral Calibration Library And Estimation Service, Keith D. Sheperd, Rich Ferguson, David Hoover, Fenny Van Egmond, Jonathan Sanderman, Yufeng Ge

Department of Agronomy and Horticulture: Faculty Publications

There is growing global interest in the potential for soil reflectance spectroscopy to fill an urgent need for more data on soil properties for improved decision-making on soil security at local to global scales. This is driven by the capability of soil spectroscopy to estimate a wide range of soil properties from a rapid, inexpensive, and highly reproducible measurement using only light. However, several obstacles are preventing wider adoption of soil spectroscopy. The biggest obstacles are the large variation in the soil analytical methods and operating procedures used in different laboratories, poor reproducibility of analyses within and amongst laboratories and …

Stepping-Stones And Mediators Of Pandemic Expansion: A Context For Humans As Ecological Super-Spreaders, Eric P. Hoberg, Walter A. Boeger, Daniel R. Brooks, Valeria Trivellone, Salvatore J. Agosta

MANTER: Journal of Parasite Biodiversity

Humans represent ecological super-spreaders in the dissemination and introduction of pathogens. These processes, consistent with the dynamics of the Stockholm paradigm, are exemplified in the origin and globalized distributions of SARS-CoV-2 since initial recognition in central Asia during 2019 and 2020. SARS-like viruses are not widespread in mammals but appear widespread in chiropterans. Bats are isolated ecologically from most other assemblages of mammals in terrestrial systems. Humans may be the stepping-stone hosts for broad global dissemination and wider infection (given the opportunity) among diverse assemblages of mammals in which host and viral capacity are compatible. Human globalization mediated insertion in …

Southeast Asia Must Narrow Down The Yield Gap To Continue To Be A Major Rice Bowl, Shen Yuan, Alexander M. Stuart, Alice G. Laborte, Juan I. Rattalino Edreira, Achim Dobermann, Le Vu Ngoc Kien, Lưu Thị Thúy, Kritkamol Paothong, Prachya Traesang, Khin Myo Tint, Su Su San, Marcelino Q. Villafuerte Ii, Emma D. Quicho, Anny Ruth P. Pame, Rathmuny Then, Rica Joy Flor, Neak Thon, Fahmuddin Agus, Nurwulan Agustiani, Nanyan Deng, Tao Li, Patricio Grassini

Department of Agronomy and Horticulture: Faculty Publications

Southeast Asia is a major rice-producing region with a high level of internal consumption and accounting for 40% of global rice exports. Limited land resources, climate change and yield stagnation during recent years have once again raised concerns about the capacity of the region to remain as a large net exporter. Here we use a modelling approach to map rice yield gaps and assess production potential and net exports by 2040. We find that the average yield gap represents 48% of the yield potential estimate for the region, but there are substantial differences among countries. Exploitable yield gaps are relatively …

Using Quantitative Imaging For Personalized Medicine In Pancreatic Cancer: A Review Of Radiomics And Deep Learning Applications, Kiersten Preuss, Nate Thach, Xiaoying Liang, Michael Baine, Justin Chen, Chi Zhang, Huijing Du, Hongfeng Yu, Chi Lin, Michael A. Hollingsworth, Dandan Zheng

School of Biological Sciences: Faculty Publications

As the most lethal major cancer, pancreatic cancer is a global healthcare challenge. Personalized medicine utilizing cutting-edge multi-omics data holds potential for major breakthroughs in tackling this critical problem. Radiomics and deep learning, two trendy quantitative imaging methods that take advantage of data science and modern medical imaging, have shown increasing promise in advancing the precision management of pancreatic cancer via diagnosing of precursor diseases, early detection, accurate diagnosis, and treatment personalization and optimization. Radiomics employs manually-crafted features, while deep learning applies computer-generated automatic features. These two methods aim to mine hidden information in medical images that is missed by …

Recommendations For Discipline-Specific Fairness Evaluation Derived From Applying An Ensemble Of Evaluation Tools, Karsten Peters-Von Gehlen, Heinke Höck, Andrej Fast, Daniel Heydebreck, Andrea Lammert, Hannes Thiemann

Copyright, Fair Use, Scholarly Communication, etc.

From a research data repositories’ perspective, offering research data management services in line with the FAIR principles is becoming increasingly important. However, there exists no globally established and trusted approach to evaluate FAIRness to date. Here, we apply five different available FAIRness evaluation approaches to selected data archived in the World Data Center for Climate (WDCC). Two approaches are purely automatic, two approaches are purely manual and one approach applies a hybrid method (manual and automatic combined).

The results of our evaluation show an overall mean FAIR score of WDCC-archived (meta) data of 0.67 of 1, with a range of …

Spatiotemporal Variability In Swedish Lake Ecosystems, Tarsha Eason, Ahjond Garmestani, David G. Angeler

School of Natural Resources: Faculty Publications

Studying ecosystem dynamics is critical to monitoring and managing linked systems of humans and nature. Due to the growth of tools and techniques for collecting data, information on the condition of these systems is more widely available. While there are a variety of approaches for mining and assessing data, there is a need for methods to detect latent characteristics in ecosystems linked to temporal and spatial patterns of change. Resiliencebased approaches have been effective at not only identifying environmental change but also providing warning in advance of critical transitions in social-ecological systems (SES). In this study, we examine the usefulness …

Ecological And Social Strategies For Managing Fisheries Using The Resist-Accept- Direct (Rad) Framework, Abigail J. Lynch, Frank J. Rahel, Doug Limpinsel, Suresh A. Sethi, Augustin C. Engman, David J. Lawrence, Katherine E. Mills, Wendy Morrison, Jay Jay Peterson, Mark T. Porath

United States Fish and Wildlife Service: Publications

Fisheries management is a complex task made even more challenging by rapid and unprecedented socioecological transformations associated with climate change. The Resist-Accept- Direct (RAD) framework can be a useful tool to support fisheries management in facing the high uncertainty and variability associated with aquatic ecosystem transformations. Here, RAD strategies are presented to address ecological goals for aquatic ecosystems and social goals for fisheries. These strategies are mapped on a controllability matrix which explores the ability to guide a system's behaviour towards a desired state based on ecological responsiveness and societal receptivity to change. Understanding and improving the controllability of aquatic …

Investigation Of Students’ Understanding Of Light Matter Interactions In A Chemistry Context, Archer Harrold

Honors Program: Senior Projects (Public)

Students’ have varying levels of understanding of light matter interactions in chemistry contexts. This study investigated students’ understanding through the use of semi-structured interviews and PhEt simulations of both the single slit and double slit experiments. Coding qualitative analysis and construct maps were used to assign students to specific levels of sophistication. It was found that students’ carry differing levels of understanding of light and light matter interactions where low level learners struggled to connect ideas in their explanations while high level learners had strong connections between their knowledge and explanations.

Editorial: Genomics-Enabled Triticeae Improvement, Xue-Feng Ma, Xianchun Xia, Shuyu Liu, P. Stephen Baenziger, Hakan Özkan

Department of Agronomy and Horticulture: Faculty Publications

No abstract provided.

Western Prairie Fringed Orchid Management, Ecology, And Decline At Mormon Island, Andrew J. Caven

Transactions of the Nebraska Academy of Sciences and Affiliated Societies

The western prairie fringed orchid (Platanthera praeclara Sheviak & M. L. Bowles; WPFO) was first detected in a vegetative state on Mormon Island in 1978 and identification was confirmed following a mass flowering event in 1982. From a high count of ~60 plants the WPFO slowly declined and has not been observed since 2000 despite flowering season surveys conducted in 15 of the last 20 years. We explore the natural history of the WPFO in the contexts of Mormon Island to establish potential causes for its apparent disappearance and evaluate the possibility it persists in some capacity. Our investigation …

Queueing Theory Model Of Pentose Phosphate Pathway, Sylwester M. Kloska, Krzysztof Pałczyński, Tomasz Marciniak, Tomasz Talaśka, Marissa Miller, Beata J. Wysocki, Paul H. Davis, Tadeusz A. Wysocki

Department of Electrical and Computer Engineering: Faculty Publications

Due to its role in maintaining the proper functioning of the cell, the pentose phosphate pathway (PPP) is one of the most important metabolic pathways. It is responsible for regulating the concentration of simple sugars and provides precursors for the synthesis of amino acids and nucleotides. In addition, it plays a critical role in maintaining an adequate level of NADPH, which is necessary for the cell to fight oxidative stress. These reasons prompted the authors to develop a computational model, based on queueing theory, capable of simulating changes in PPP metabolites’ concentrations. The model has been validated with empirical data …

An Evaluation Of Tractors Tested At The Nebraska Tractor Test Lab And The Effect Of Epa Emission Standards Based Upon Average Pto Horsepower And Fuel Efficiency, Dalton Erickson

Honors Program: Senior Projects (Public)

Newly released tractor models are tested to ensure they meet advertising claims. This thesis utilizes tractor test data to analyze performance trends in tractors based upon their power take off (PTO) horsepower and fuel efficiency and it evaluates how the average fuel efficiency of tractors was affected by the introduction of emission standards by the United States Environmental Protection Agencies. In conclusion, tractors have shown continuous improvement and growth in both fuel efficiency and PTO horsepower, and emission standards have had a small, positive effect on tractors’ average fuel efficiency.

Livestock Performance In Response To High Intensity Rotational Grazing System, Austin Kennedy

Honors Program: Senior Projects (Public)

The production of livestock is composed of a variety of factors all effecting the outcome. For grazing livestock, a key factor in production is the grazing management system. Two of the most common grazing management systems are continuous grazing and rotational grazing. There has been evidence found proving benefits of rotational grazing in regard to vegetation productivity, and prevention and restoration of degraded rangeland. However, there is a lack of clear evidence on the relationship between grazing system and production metrics of livestock. Understanding this relationship can provide the necessary information for livestock producers in order to increase their production …

Split Classification Model For Complex Clustered Data, Katherine Gerot

Honors Program: Senior Projects (Public)

Classification in high-dimensional data has generated tremendous interest in a multitude of fields. Data in higher dimensions often tend to reside in non-Euclidean metric space. This prevents Euclidean-based classification methodologies, such as regression, from reliably modeling the data. Many proposed models rely on computationally-complex embedding to convert the data to a more usable format. Others, namely the Support Vector Machine, rely on kernel manipulation to implicitly describe the "feature space" to arrive at a non-linear decision boundary. The proposed methodology in this paper seeks to classify complex data in a relatively computationally-simple and explainable manner.

Source Of Off-Type Frequencies In Winter Wheat Varieties, Michaela Benes

Honors Program: Senior Projects (Public)

The enzyme polyphenol oxidase (PPO) is undesirable in most wheat products due to the discoloration it causes. Purifying wheat varieties through selective breeding is the best way at getting rid of PPO in a variety. The variety NW15443 was planted in both a field in McCook, NE, and in a greenhouse in Lincoln, NE. Individual heads were snapped from the field and the greenhouse seed was harvested in bulk. After completing a PPO test of the seed, it was determined that the percentages of off-type frequencies from the field seed and the greenhouse seed were 11% and 3.6%, respectively. Using …

Creation Of An Influenza A Virus Neuraminidase Consensus Vaccine In An Adenoviral Vector, Leigh Jahnke

Honors Program: Senior Projects (Public)

In the last decade, the estimated annual burden of the flu includes 12,000-52,000 deaths, 140,000-710,000 hospitalizations, and 9 million – 41 million illnesses (Centers for Disease Control and Prevention: Disease burden of the flu). Influenza A virus can mutate and infect a variety of different hosts, which results in frequent antigenic changes and even pandemics. This has led to increased attention on the creation of a universal Influenza A vaccine containing broader immunogenic coverage than current vaccines. Our research involved detailing the steps of the cloning process utilizing a consensus neuraminidase antigen. We utilized the pAdEasy Adenoviral Vector …

Predicting Autism From Infant Characteristics: A Systematic Review, Alysha Y. Henrichs, Cynthia Cress Ph.D.

Honors Program: Senior Projects (Public)

A literature review was conducted of 73 articles to explore 12-month-old characteristics in infants that predicted later diagnosis with autism (ASD). Articles were reviewed if they discussed ASD, infants with siblings diagnosed with autism (high-risk) and/or infants later diagnosed with autism without known family history of ASD (low risk). Articles were not reviewed if the participants were 36 months or older at the start of the study. More factors were identified that discriminate characteristics associated with later ASD diagnosis in infants between 12-24 months compared to characteristics of infants below 12 months. Characteristics of infants under 12 months that were …

Assessment Of Diversity Of Antimicrobial Resistance Phenotypes And Genotypes Of Mannheimia Haemolytica Isolates From Bovine Nasopharyngeal Swabs, Hannah F. Carter, Robert W. Wills, Matthew A. Scott, Alexis C. Thompson, Randall S. Singer, John Dustin Loy, Brandi B. Karisch, William B. Epperson, Amelia R. Woolums

School of Veterinary and Biomedical Sciences: Faculty Publications

The threat of bovine respiratory disease (BRD) for cattle operations is exacerbated by increasing prevalence of antimicrobial resistance (AMR) in Mannheimia haemolytica, a leading cause of BRD. Characterization of AMR in M. haemolytica by culture and susceptibility testing is complicated by uncertainty regarding the number of colonies that must be selected to accurately characterize AMR phenotypes (antibiograms) and genotypes in a culture. The study objective was to assess phenotypic and genotypic diversity of M. haemolytica isolates on nasopharyngeal swabs (NPS) from 28 cattle at risk for BRD or with BRD. NPS were swabbed onto five consecutive blood agar plates; …

Reduction Of Stabilin-2 Contributes To A Protection Against Atherosclerosisstabilin, Yukako Kayashima1*,, Conner A. Clanton, Amanda M. Lewis, Xinghui Sun, Sylvia Hiller, Phillip Huynh, Jennifer Wilder, John Hagaman, Feng Li, Nobuyo Maeda-Smithies, Edward N. Harris

Department of Biochemistry: Faculty Publications

We have previously identified a novel atherosclerosis quantitative trait locus (QTL), Arch atherosclerosis 5 (Aath5), on mouse chromosome 10 by three-way QTL analyses between Apoe^−/− mice on a DBA/2J, 129S6 and C57BL/6J background. The DBA/2J haplotype at the Aath5 locus was associated with smaller plaque size. One of the candidate genes underlying Aath5 was Stabilin-2 (Stab2), which encodes a clearance receptor for hyaluronan (HA) predominantly expressed in liver sinusoidal endothelial cells (LSECs). However, the role of Stab2 in atherosclerosis is unknown. A congenic line of Apoe^−/− mice carrying Aath5 covering the Stab2^DBA allele …

Reduction Of Stabilin-2 Contributes To A Protection Against Atherosclerosis, Yukako Kayashima, Connor A. Clanton, Amanda M. Lewis, Xinghui Sun, Sylvia Hiller, Phillip Huynh, Jennifer Wilder, John Hagaman, Feng Li, Nobuyo Maeda-Smithies, Ed Harris

Department of Biochemistry: Faculty Publications

We have previously identified a novel atherosclerosis quantitative trait locus (QTL), Arch atherosclerosis 5 (Aath5), on mouse chromosome 10 by three-way QTL analyses between Apoe^−/− mice on a DBA/2J, 129S6 and C57BL/6J background. The DBA/2J haplotype at the Aath5 locus was associated with smaller plaque size. One of the candidate genes underlying Aath5 was Stabilin-2 (Stab2), which encodes a clearance receptor for hyaluronan (HA) predominantly expressed in liver sinusoidal endothelial cells (LSECs). However, the role of Stab2 in atherosclerosis is unknown. A congenic line of Apoe^−/− mice carrying Aath5 covering the Stab2 …

Hand Sanitizer Production Distribution Analysis, Regan Monhollon

Honors Program: Senior Projects (Public)

This work is a brief report on the areas reached and the monetary value of the materials produced and distributed by the University of Nebraska-Lincoln Hand Sanitizer Production Project in response to the COVID-19 Pandemic. This project was able to produce approximately 190,000 gallons of hand sanitizer, totaling a minimum commercial value of $15 million and an estimated peak commercial value of $166 million that would be distributed both in and out of the State of Nebraska.

This report contains the calculations used to estimate the worth of the hand sanitizer produced shortly before, during the peak, and near the …

Canopy Spectral Reflectance Detects Oak Wilt At The Landscape Scale Using Phylogenetic Discrimination, Gerard Sapes, Cathleen Lapadat, Anna K. Schweiger, Jennifer Juzwik, Rebecca Montgomery, Hamed Gholizadeh, Philip A. Townsend, John A. Gamon, Jeannine Cavender-Bares

School of Natural Resources: Faculty Publications

The oak wilt disease caused by the invasive fungal pathogen Bretziella fagacearum is one of the greatest threats to oak-dominated forests across the Eastern United States. Accurate detection and monitoring over large areas are necessary for management activities to effectively mitigate and prevent the spread of oak wilt. Canopy spectral reflectance contains both phylogenetic and physiological information across the visible near-infrared (VNIR) and short-wave infrared (SWIR) ranges that can be used to identify diseased red oaks. We develop partial least square discriminant analysis (PLS-DA) models using airborne hyperspectral reflectance to detect diseased canopies and assess the importance of VNIR, SWIR, …

Variants Within Genes Edil3 And Adgrb3 Are Associated With Divergent Fecal Egg Counts In Katahdin Sheep At Weaning, Gabrielle M. Becker, Joan M. Burke, Ronald M. Lewis, James E. Miller, James L.M. Morgan, Benjamin D. Rosen, Curtis P. Van Tassell, David R. Notter, Brenda M. Murdoch

Department of Animal Science: Faculty Publications

Gastrointestinal nematodes (GIN) pose a severe threat to sheep production worldwide. Anthelmintic drug resistance coupled with growing concern regarding potential environmental effects of drug use have demonstrated the necessity of implementing other methods of GIN control. The aim of this study was to test for genetic variants associated with resistance or susceptibility to GIN in Katahdin sheep to improve the current understanding of the genetic mechanisms responsible for host response to GIN. Linear regression and casecontrol genome-wide association studies were conducted with high-density genotype data and cube-root transformed weaning fecal egg counts (tFEC) of 583 Katahdin sheep. The casecontrol GWAS …

Development Of Controller Area Network Bus Programming For Quarter-Scale Tractor Pulling Sled, Brittani Wacker

Honors Program: Senior Projects (Public)

Usage of Controller Area Network (CAN) technology has allowed for advancements in many industries, including agriculture. Most importantly, its application is useful for refining data acquisition methods. With support from the Quarter-scale Tractor Design Team at UNL, this project united a CAN bus with the team’s current tractor pulling sled. The objectives were to install new instrumentation needed for the CAN bus and to program the updated system utilizing CAN data. The program needed to give the pulling sled functionality and the ability to read and log important pulling data. These goals were all accomplished by implementing new sensors, coding …

Determining Pairwise Interactions To Predict Species Interactions In A Complex Community Of Gut Bacteria., Makenzie Maroney

Honors Program: Senior Projects (Public)

The human gastrointestinal (GI) tract houses a diverse and expansive microbial community known as the microbiota. The relationship between the host and the microbiota is considered to be mutualistic, as trillions of bacteria that reside in the hospitable GI tract can assist in essential host functions, including contributing to metabolism and immunity against disease. An important subpopulation of the GI microbiota is the mucin-associated biofilm that is comprised of a dense layer of bacteria that forms on the GI mucin layer. The mucin layer provides an alternative niche to the GI lumen; the glycans of the mucin and the subsequent …

Resource Selection Of Deer Hunters In Georgia's Appalachian Mountains, Jacalyn P. Rosenberger, Andrew R. Little, Adam C. Edge, Cheyenne J. Yates, David A. Osborn, Charlie H. Killmaster, Kristina L. Johannsen, Karl V. Miller, Gino J. D'Angelo

School of Natural Resources: Faculty Publications

White‐tailed deer (Odocoileus virginianus) and hunters on 2 Wildlife Management Areas (WMAs) within the Chattahoochee National Forest of northern Georgia, USA, significantly declined in number from the 1980s to 2018. Managers were interested in understanding how they could manipulate hunter distribution according to deer management goals. To understand the spatial distribution of hunting pressure and factors driving hunter resource selection, we analyzed GPS tracking data from 58 deer hunters over the 2018–2019 and 2019–2020 hunting seasons. We evaluated hunter selection on 3 spatial scales relative to elevation, slope, and distance from roads, trails, wildlife openings, deciduous forest, mixed …

Design Of A Week-Long Introduction To Engineering Summer Camp To Increase Interest And Eagerness Of Stem In Young Children, Beth Cannon

Honors Program: Senior Projects (Public)

For this creative project, a one-week camp curriculum was designed for elementary students (Grades 3-5) to introduce engineering. This work includes a rationale and camp curriculum. The rationale describes the research-based design of the curriculum. It outlines engineering basics and why and how to teach engineering to young students. The curriculum intends to introduce engineering to young children and excite the possibility of a future career. The following engineering disciplines are presented throughout the week of camp: mechanical, environmental, civil, electrical, and chemical. The first day of camp focuses on the basics of engineering. Following that, each day of camp …