Digital Commons Network^™

Identification Of Orthologous Gene Groups Using Machine Learning, Dillon Burgess

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

Identification of genes that show similarity between different organisms, a.k.a orthologous genes, is an open problem in computational biology. The purpose of this thesis is to create an algorithm to group orthologous genes using machine learning. Following an optimization step to find the best characterization based on training data, we represented sequences of genes or proteins with kmer vectors. These kmer vectors were then clustered into orthologous groups using hierarchical clustering. We optimized the clustering phase with the same training data for the method and parameter selection. Our results indicated that use of protein sequences with k=2 and scaling the …

A New Species Of Celastrina From The Northwestern United States And Southwestern Canada With A Lectotype Designation Of Lycaena Pseudargiolus Var. Nigrescens Fletcher (Lycaenidae: Polyommatinae), Caitlin C. Labar, Jonathan P. Pelham, Norbert G. Kondla

The Taxonomic Report of the International Lepidoptera Survey

A new western azure species, Celastrina asheri, is described from the northwestern United States and southwestern Canada. A lectotype is designated for Lycaena pseudargiolus var. nigrescens Fletcher, 1903 to secure the identity of that name. C. asheri broadly overlaps with the northeastern range of C. echo (W. H. Edwards, 1864) but is usually very distinct from that species. C. lucia (W. Kirby, 1837) is narrowly sympatric with C. asheri in British Columbia, the southwest corner of Alberta and along the Rocky Mountains in Montana. As far as is known, C. asheri uses only red osier dogwood (Cornus sericea …

Educational Design: Does The Design Of A Learning Environment Effect How A Student Learns?, Terrie Larsen

Interior Design Program: Student Creative Activity

New 21^st Century classroom layouts have evolved from the studies of several educational researchers and their findings over the past century. In conjunction with universities across the world, researchers developed progressive outlooks of what the built environment can offer to the newest generation of learners. Their studies have coined several terms such as Active Learning Classrooms (ALC), Student Centered Active Learning Environment for Undergraduate Programs (SCALE-UP) and Technology Enabled Active Learning (TEAL). These classroom models represent higher learning studies for more effective 21^st century learning environments. Some of the models include a specific style of table and number …

Agricultural Intensification Can Help Protect The Amazon Forest And Reduce Global Warming / Protecting The Amazon Forest And Reducing Global Warming Via Agricultural Intensification, Fabio R. Marin, Alencar J. Zanon, Juan P. Monzon, José F. Andrade, Evandro H.F.M. Silva, Gean L. Richter, Luis A.S. Antolin, Bruna S.M.R. Ribeiro, Giovanna G. Ribas, Rafael Battisti, Alexandre B. Heinemann, Patricio Grassini

Department of Agronomy and Horticulture: Faculty Publications

The Amazon basin includes 550 M ha covered with rainforests, with 60% of this area being in Brazil. Conversion of rainforest for soybean production raises concerns about the degree to which Brazil can reconcile production and environmental goals. Here we investigated the degree to which intensification could help Brazil produce more soybean without further encroachment of the Amazon Forest. Our analysis shows that continuation of current trends in soybean yield and area would lead to conversion of additional 5.7 M ha of forests and savannas during the next 15 years, with an associated 2550 Mt of CO2eq released into the …

Climate Change And Management Impacts On Soybean N Fixation, Soil N Mineralization, N2O Emissions, And Seed Yield, Elvis F. Elli, Ignacio A. Ciampitti, Michael J. Castellano, Larry C. Purcell, Seth Naeve, Patricio Grassini, Nicolas C. La Menza, Luiz Moro Rosso, André F. De Borja Reis, Péter Kovács, Sotirios V. Archontoulis

Department of Agronomy and Horticulture: Faculty Publications

Limited knowledge about how nitrogen (N) dynamics are affected by climate change, weather variability, and crop management is a major barrier to improving the productivity and environmental performance of soybean-based cropping systems. To fill this knowledge gap, we created a systems understanding of agroecosystem N dynamics and quantified the impact of controllable (management) and uncontrollable (weather, climate) factors on N fluxes and soybean yields. We performed a simulation experiment across 10 soybean production environments in the United States using the Agricultural Production Systems sIMulator (APSIM) model and future climate projections from five global circulation models. Climate change (2020–2080) increased N …

Creating An Inclusive And Accessible Culture: Supportive Management For People With Disabilities, Sammy Peter, Katie Quirin Manwiller, Kiyomi D. Deards

University of Nebraska-Lincoln Libraries: Presentations

From the perspective of disabled academic librarians, covers the ways academic library managers can be inclusive and support disabled library workers.

Accompanies the article: Sally Lindsay and Kristina Fuentes. 2022. It is time to address ableism in academia: A systematic review of the experiences and impact of ableism among faculty and staff. Disabilities 2(2): 178-203. doi: 10.3390/disabilities2020014

Search For Electroweak Production Of Charginos And Neutralinos In Proton-Proton Collisions At √S = 13 Tev, A. Tumasyan

Department of Physics and Astronomy: Faculty Publications

A direct search for electroweak production of charginos and neutralinos is presented. Events with three or four leptons, with up to two hadronically decaying τ leptons, or two same-sign light leptons are analyzed. The data sample consists of 137 fb⁻¹ of proton-proton collisions with a center of mass energy of 13TeV, recorded with the CMS detector at the LHC. The results are interpreted in terms of several simplified models. These represent a broad range of production and decay scenarios for charginos and neutralinos. A parametric neural network is used to target several of the models with large backgrounds. In …

Characterizing And Predicting Human Visual Perception Of Unmanned Aerial Vehicle Gestures, Paul Fletcher

School of Computing: Dissertations, Theses, and Student Research

Unmanned Aerial Vehicles (UAVs) are being used in public domains and hazardous environments where effective communication strategies are critical. UAV gesture techniques have been shown to communicate meaning to human observers and may be ideal in contexts that require lightweight systems such as unmanned aerial flight, however, this work may be limited to an idealized range of viewer perspectives. As gesture is a visual communication technique it is necessary to consider how the perception of a robot gesture may suffer from obfuscation or self-occlusion from some viewpoints. This thesis presents the results of three online user-studies that examine participants’ ability …

Estimation Of Methane Emissions From Beef Cattle Manure In Nebraska, Noe Hernandez

Department of Civil and Environmental Engineering: Dissertations, Theses, and Student Research

The emission of methane from livestock production contributes to climate change. Cattle manure accounts for one-third of the total methane emission over the lifecycle of beef and dairy production and represents an opportunity to lower the environmental footprint of the beef industry. While models have been developed to estimate methane emissions from manure under certain types of manure storage methods, there is a lack of a user-friendly interface that agricultural or environmental engineers can use to estimate the methane emission from manure for specific regions. Therefore, the goal of this study was to build an interface to estimate methane emissions …

Spatial And Temporal Distribution And Habitat Selection Of Native Yellowstone Cutthroat Trout And Nonnative Utah Chub, Darcy K. Mccarrick, Jeffrey C. Dillon, Brett High, Michael C. Quist

United States Geological Survey: Staff Publications

Henrys Lake, Idaho, is a renowned trophy trout fishery that faces an uncertain future following the establishment of Utah Chub (UTC) Gila atraria. Utah Chub were first documented in the lake in 1993 and have become abundant over the past two decades. Little is known about the ecology of UTC, but they typically have negative effects on salmonids in systems where they have been introduced. We sought to fill knowledge gaps in UTC ecology and provide insight on potential interactions with Yellowstone Cutthroat Trout (YCT) Oncorhynchus clarkii bouvieri. Ninety-four YCT and 95 UTC were radio-tagged in spring 2019 …

Individual Trophic Niche Specialization In American Beaver (Castor Canadensis), Jimmy Taylor, Robert Francis, Scott Rush, Bronson Strickland, Guiming Wang

United States Department of Agriculture Wildlife Services: Staff Publications

The American beaver (Castor canadensis) has been described as a choosy generalist at the species/population scale, yet observational studies have shown little variation in diet among individuals. We compared isotopic values of δ¹³C or δ¹⁵N taken from hair of 32 beaver, representing seven colonies in northern Alabama, USA to determine 1) if colonies of beaver show overlap in isotopic niche width as a result of the similar use of food resources and 2) if individual trophic niche specialization occurs within colonies. Total Trophic Niche Width varied across the wetland with the widest being twice …

Notes On Eastern North American Lepidoptera, Harry Pavulaan, Annette Allor

The Taxonomic Report of the International Lepidoptera Survey

New natural history elements and distribution records of several North American butterflies are reported. While diversity and distribution of butterflies in the eastern United States is commonly believed to be fully known, the findings presented here show that much is yet to be learned of our butterfly fauna.

Includes:

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Celastrina ladon and C. neglecta (Lycaenidae: Polyommatinae) Are Distinct Species Differentiated Primarily by a Diagnostic Wing Scale Structure, Voltinism, and Host Tolerance of Cornus florida.by Harry Pavulaan (International Lepidoptera Survey)

Abstract. With continued confusion of the two species by naturalists, Celastrina neglecta (W. H. Edwards) is here …

Designing Experiments: The Impact Of Peer Review Structure On Organic Chemistry Students' Experimental Designs, Katie Patterson

Department of Chemistry: Dissertations, Theses, and Student Research

To better understand how peer review can be used to support students when designing experiments, the current thesis examined how the structure of the peer review template affects the kinds of feedback students give and the revisions that they make. I utilized a quasi-experimental design to investigate the effects that the peer review template had on the outcome of an experimental design task. A sample of 195 students enrolled in an Organic Chemistry I course participated in the study. The students were divided into two groups, one of which was given a scaffolded peer review template and the other was …

Europium-Doped Cerium Oxide Nanoparticles For Microglial Aβ Clearance And Homeostasis, Jatin Machhi, Pravin Yeapuri, Milica Markovic, Milankumar Patel, Wenhui Yan, Yaman Lu, Jacob D. Cohen, Mahmudul Hasan, Mai Mohamed Abdelmoaty, You Zhou, Huangui Xiong, Xinglong Wang, R. Lee Mosley, Howard E. Gendelman, Bhavesh D. Kevadiya

Nebraska Center for Biotechnology: Faculty and Staff Publications

Alzheimer’s disease (AD) is the most common neurodegenerative disorder. Pathologically, it is characterized by the deposition of amyloid beta (Aβ) plaques and presence of neurofibrillary tangles. These drive microglia neuroinflammation and consequent neurodegeneration. While the means to affect Aβ plaque accumulation was achieved how it affects disease outcomes remains uncertain. Cerium oxide (CeO₂) reduces Aβ plaques, oxidative stress, inflammation, and Alzheimer’s disease (AD) signs and symptoms. Specifically, CeO₂ nanoparticles (CeO₂NPs) induces free radical scavenging and cell protective intracellular signaling. This can ameliorate the pathobiology of an AD-affected brain. In order to investigate, CeO₂NPs …

Retrospective Comparisons Of Competing Demographic Models Give Clarity From “Messy” Management On A Scottish Grouse Moor, Larkin A. Powell, Nicholas J. Aebischer, Sonja C. Ludwig, David Baines

School of Natural Resources: Faculty Publications

Retrospective comparison of predictive models that describe competing hypotheses regarding system function can shed light on regulatory mechanisms within the framework of adaptive resource management. We applied this approach to a 28-year study of red grouse (Lagopus lagopus scotica) in Scotland, with the aims of reducing uncertainty regarding important drivers of grouse population dynamics, and of evaluating the efficacy of using seasonal versus annual model assessments. We developed three sets of models that predicted pre-breeding and post-breeding grouse density, matching the timing of grouse counts on the ground. We updated conditions and management through time in the spirit …

Trout Responses To Stocking Rates And River Discharge Within A Southeastern U.S. Hydropeaking Tailwater, Jonathan J. Spurgeon, Joseph Kaiser, Christy Graham, Steve Lochmann

Nebraska Cooperative Fish and Wildlife Research Unit: Staff Publications

Freshwater fish populations often exist in systems characterized by novel ecological processes resulting from human alteration. Salmonid populations embedded within coldwater sections of warmwater rivers are spatially constrained by habitat availability. Tailwater fish contend with fluctuating river discharges and density-dependent processes associated with fish stocking and exploitation. Salmonid populations sustained through stocking versus natural reproduction may respond differently to changes in hydrologic patterns (e.g., hydropeaking) as well as declines in fish abundance. We assessed differences between stocked (Rainbow Trout Oncorhynchus mykiss) and naturalized (Brown Trout Salmo trutta) trout populations in Greers Ferry tailwater, Arkansas, regarding (1) spatial and …

Two Fingerprinting Sets For Humulus Lupulus Based On Kasp And Microsatellite Markers, Mandie Driskill, Katie Pardee, Kim E. Hummer, Jason D. Zurni, Keenan L. Amundsen, Annette Wiles, Claudia Wiedowi, Josef Patza, John A. Henningi, Nahla V. Bassili

Department of Agronomy and Horticulture: Faculty Publications

Verification of clonal identity of hop (Humulus lupulus L.) cultivars within breeding programs and germplasm collections is vital to conserving genetic resources. Accurate and economic DNA-based tools are needed in dioecious hop to confirm identity and parentage, neither of which can be reliably determined from morphological observations. In this study, we developed two fingerprinting sets for hop: a 9-SSR fingerprinting set containing high-core repeats that can be run in a single PCR reaction and a kompetitive allele specific PCR (KASP) assay of 25 single nucleotide polymorphisms (SNPs). The SSR set contains a sex-linked primer pair, HI-AGA7, that was used …

Undergraduate Students’ Accuracy & Confidence In Detecting Errors In Biological Models Related To Gpa, Mckenna Elliott, Joseph Dauer, Carrie Clark, Mei Grace Behrendt

UNL Student Research Days Posters, Undergraduate

Research Questions 1. Does students’ abilities to Accurately detect errors relate to their GPA? 2. Which concepts affect student ability to Accurately and Confidently detect errors?

GPA was positively related to accuracy but was unrelated to confidence (Fig. 1)

Subject areas affected students’ accuracy and confidence § Students were more accurate on ecology & evolution models (Fig. 2) § Students were more confident in ecology models and less confident in physiology models (Fig. 2)

Variation in student ability and subject area competency can provide teachers with places to focus and improve science understanding.

Similar to the work of Clark et …

“Many People Have No Idea”: A Qualitative Analysis Of Healthcare Barriers Among Yazidi Refugees In The Midwestern United States, Falah Rashoka, Megan S. Kelley, Jeong‑Kyun Choi, Marc A. Garcia, Weiwen Chai, Hazim N. Rashawka

Department of Nutrition and Health Sciences: Faculty Publications

Background: The COVID-19 pandemic has shed new light on inequities in healthcare access faced by immigrant and refugee communities. To address ongoing disparities, there is an urgent need for ecological approaches to better understand the barriers that hinder and resources that facilitate access to healthcare. This study investigates barriers to healthcare system access faced by Yazidi refugees in the Midwestern United States.

Methods: Informed by the Interpretative Phenomenological Approach, three focus group meetings with a community advisory board were conducted between September 2019 and January 2020. The nine-member focus group included social workers, healthcare providers, and members of …

The Chromosome-Level Rambutan Genome Reveals A Significant Role Of Segmental Duplication In The Expansion Of Resistance Genes, Jinfang Zheng1, Lyndel W. Meinhardt, Ricardo Goenaga, Tracie Matsumoto, Dapeng Zhang, Yanbin Yin

Food for Health: Publications

Rambutan (Nephelium lappaceum var. lappaceum), a tropical fruit tree native to southeastern Asia, belongs to the family Sapindaceae. Rambutan is a popular table fruit and is also processed into preserves, juices, wines, and sorbets [1]. At present, only three Sapindaceae genomes are publicly available: Xanthoceras sorbifolium [2], Dimocarpus longan (longan) [3], and Acer yangbiense [4]. During the process of submitting this manuscript, the genome paper for the rambutan cultivar Baoyan7 became available online, but its genome sequence has not yet been released [5].

Observation Of B0 →Ψ(2s)K0SΠ+Π− And B0S→Ψ(2s)K0S Decays, A. Tumasyan

Department of Physics and Astronomy: Faculty Publications

Using a data sample of √ s = 13 TeV proton-proton collisions collected by the CMS experiment at the LHC in 2017 and 2018 with an integrated luminosity of 103 fb⁻¹, the B⁰_s → ψ(2S)K⁰_S and B⁰ → ψ(2S)K⁰_Sπ ⁺ π ⁻ decays are observed with significances exceeding 5 standard deviations. The resulting branching fraction ratios, measured for the first time, correspond to B(B⁰_s → ψ(2S)K⁰_S)/B(B⁰ → ψ(2S)K⁰_S) = (3.33 ± 0.69(stat) ± 0.11 (syst) ± 0.34 ( …

Terrestrial Carbon Isotope Stratigraphy And Mammal Turnover During Post-Petm Hyperthermals In The Bighorn Basin, Wyoming, Usa, Sarah J. Widlansky, Ross Secord, Kathryn E. Snell, Amy E. Chew, William C. Clyde

Department of Earth and Atmospheric Sciences: Faculty Publications

Paleogene hyperthermals, including the Paleocene–Eocene Thermal Maximum (PETM) and several other smaller events, represent global perturbations to Earth’s climate system and are characterized by warmer temperatures, changes in floral and faunal communities, and hydrologic changes. These events are identified in the geologic record globally by negative carbon isotope excursions (CIEs), resulting from the input of isotopically light carbon into Earth’s atmosphere. Much about the causes and effects of hyperthermals remains uncertain, including whether all hyperthermals were caused by the same underlying processes, how biotic effects scale with the magnitude of hyperthermals, and why CIEs are larger in paleosol carbonates relative …

Influence Of Acute Water Ingestion And Prolonged Standing On Raw Bioimpedance And Subsequent Body Fluid And Composition Estimates, Grant M. Tinsley, Matthew T. Stratton, Patrick S. Harty, Abegale D. Williams, Sarah J. White, Christian Rodriguez, Jacob R. Dellinger, Baylor A. Johnson, Robert W. Smith, Eric T. Trexler

Department of Nutrition and Health Sciences: Faculty Publications

This study evaluated the influence of acute water ingestion and maintaining an upright posture on raw bioimpedance and subsequent estimates of body fluids and composition. Twenty healthy adults participated in a randomized crossover study. In both conditions, an overnight food and fluid fast was followed by an initial multi-frequency bioimpedance assessment (InBody 770). Participants then ingested 11 mL/kg of water (water condition) or did not (control condition) during a 5-minute period. Thereafter, bioimpedance assessments were performed every 10 minutes for one hour with participants remaining upright throughout. Linear mixed effects models were used to examine the influence of condition and …

Quantifying Predator Functional Responses Under Field Conditions Reveals Interactive Effects Of Temperature And Interference With Sex And Stage, Kyle E. Coblentz, Amber Squires, Stella Uiterwaal, John Delong

School of Biological Sciences: Faculty Publications

1. Predator functional responses describe predator feeding rates and are central to predator–prey theory. Originally defined as the relationship between predator feeding rates and prey densities, it is now well known that functional responses are shaped by a multitude of factors. However, much of our knowledge about how these factors influence functional responses is based on laboratory studies that are generally logistically constrained to examining only a few factors simultaneously and that have unclear links to the conditions organisms experience in the field.
2. We apply an observational approach for measuring functional responses to understand how sex/stage differences, temperature and predator densities …

Ignoring Species Availability Biases Occupancy Estimates In Single-Scale Occupancy Models, Graziella V. Direnzo, David A. W. Miller, Evan H. C. Grant

United States Geological Survey: Staff Publications

1. Most applications of single-scale occupancy models do not differentiate between availability and detectability, even though species availability is rarely equal to one. Species availability can be estimated using multi-scale occupancy models; however, for the practical application of multi-scale occupancy models, it can be unclear what a robust sampling design looks like and what the statistical properties of the multi-scale and single-scale occupancy models are when availability is less than one.
2. Using simulations, we explore the following common questions asked by ecologists during the design phase of a field study: (Q1) what is a robust sampling design for the multi-scale occupancy …

Auditory Experience Modulates Frontoparietal Theta Activity Serving Fluid Intelligence, Elizabeth Heinrichs-Graham, Elizabeth A. Walker, Brittany K. Taylor, Sophia C. Menting

Department of Psychology: Faculty Publications

Children who are hard of hearing are at risk for developmental language and academic delays compared with children with normal hearing. Some work suggests that high-order cognitive function, including fluid intelligence, may relate to language and academic outcomes in children with hearing loss, but findings in these studies have been mixed and to date, there have been no studies of the wholebrain neural dynamics serving fluid intelligence in the context of hearing loss. To this end, this study sought to identify the impact of hearing loss and subsequent hearing aid use on the neural dynamics serving abstract reasoning in children …

Antibody Dependent Enhancement Of Infectious Bronchitis Virus In Poultry, Zachary Hamilton, Barry Simpson, Donald L. Reynolds

UCARE: Research Products

Avian infectious bronchitis (IB) is a coronavirus infection of chickens that causes respiratory disease and reproductive problems in chickens. Currently, there are vaccines that are effective against IB. However, new variants and strains of avian infectious bronchitis virus (IBV) routinely emerge. A vaccine that is not the same strain as the virus is not completely effective in protecting against other variants because the vaccine will not allow the host antibodies to completely neutralize the strain. This is a problem because it makes IB difficult to control and diagnose.

Antibody-dependent enhancement (ADE) is a phenomenon whereby non-neutralizing antibodies, or low levels …

Als-Associated Kif5a Mutations Abolish Autoinhibition Resulting In A Toxic Gain Of Function, Desiree M. Barron, Adam R. Fenton, Sara Saez-Atienzar, Anthony Giampetruzzi, Aparna Sreeram, Shankaracharya, Pamela J. Keagle, Victoria R. Doocy, Nathan J. Smith, Eric W. Danielson, Megan Andresano, Mary C. Mccormack, Jaqueline Garcia, Valérie Bercier, Ludo Van Den Bosch, Jonathan R. Brent, Claudia Fallini, Brian J. Traynor, Erica L.F. Holzbaur, John E. Landers

Biochemistry -- Faculty Publications

Understandingthepathogenicmechanismsof diseasemutations is critical toadvancingtreatments.ALS-associated mutations in the gene encoding the microtubulemotor KIF5A result in skipping of exon 27 (KIF5ADExon27) and the encoding of a protein with a novel 39 amino acid residue C-terminal sequence. Here, we report that expression of ALS-linked mutant KIF5A results in dysregulated motor activity, cellular mislocalization, altered axonal transport, and decreased neuronal survival. Single-molecule analysis revealed that the altered C terminus of mutant KIF5A results in a constitutively active state. Furthermore,mutant KIF5A possesses altered protein and RNA interactions and its expression results in altered gene expression/splicing. Taken together, our data support the hypothesis that causative …

Variation In Bacterial Community Structure Under Long-Term Fertilization, Tillage, And Cover Cropping In Continuous Cotton Production, Ning Duan, Lidong Li, Xiaolong Liang, Aubrey Fine, Jie Zhuang, Mark Radosevich, Sean M. Schaeffer

Department of Agronomy and Horticulture: Faculty Publications

Agricultural practices alter the structure and functions of soil microbial community. However, few studies have documented the alterations of bacterial communities in soils under long-term conservation management practices for continuous crop production. In this study, we evaluated soil bacterial diversity using 16S rRNA gene sequencing and soil physical and chemical properties within 12 combinations of inorganic N fertilization, cover cropping, and tillage throughout a cotton production cycle. Soil was collected from field plots of the West Tennessee Agriculture Research and Education Center in Jackson, TN, United States. The site has been under continuous cotton production for 38 years. A total …

Considerations For Establishing Silvopastures On Wooded Sites, Brett Chedzoy, Ashley Conway, John Fike, Kate Macfarland

Agroforestry Notes (USDA-NAC)

Like other conservation and production practices, silvopasture management is not the right fit for every site or every land manager. High quality woodlands with high native species diversity are generally not a good starting point for silvopasture establishment. However, silvopasture provides an opportunity for active forest management on other sites that have been neglected or poorly managed with undesirable species composition, invasive species concerns, and other challenges. In some situations, silvopasture management can be used to aid in ecosystem restoration or fuels mitigation. The land manager and others in the silvopasture team should consider natural resource issues highlighted in this …