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Hyperseed: An End-To-End Method To Process Hyperspectral Images Of Seeds, Tian Gao, Anil Kumar Nalini Chandran, Puneet Paul, Harkamal Walia, Hongfeng Yu

School of Computing: Faculty Publications

High-throughput, nondestructive, and precise measurement of seeds is critical for the evaluation of seed quality and the improvement of agricultural productions. To this end, we have developed a novel end-to-end platform named HyperSeed to provide hyperspectral information for seeds. As a test case, the hyperspectral images of rice seeds are obtained from a high-performance line-scan image spectrograph covering the spectral range from 600 to 1700 nm. The acquired images are processed via a graphical user interface (GUI)-based open-source software for background removal and seed segmentation. The output is generated in the form of a hyperspectral cube and curve for each …

Hyperseed: An End-To-End Method To Process Hyperspectral Images Of Seeds, Tian Gao, Anil Kumar Nalini Chandran, Puneet Paul, Harkamal Walia, Hongfeng Yu

School of Computing: Faculty Publications

High-throughput, nondestructive, and precise measurement of seeds is critical for the evaluation of seed quality and the improvement of agricultural productions. To this end, we have developed a novel end-to-end platform named HyperSeed to provide hyperspectral information for seeds. As a test case, the hyperspectral images of rice seeds are obtained from a high-performance line-scan image spectrograph covering the spectral range from 600 to 1700 nm. The acquired images are processed via a graphical user interface (GUI)-based open-source software for background removal and seed segmentation. The output is generated in the form of a hyperspectral cube and curve for each …

Microfabricated Platforms To Investigate Cell Mechanical Properties, Amir M. Esfahani, Grayson Minnick, Jordan Rosenbohm, Haiwei Zhai, Xiaowei Jin, Bahareh Tajvidi Safa, Justin Brooks, Ruiguo Yang

Department of Mechanical and Materials Engineering: Faculty Publications

Mechanical stimulation has been imposed on living cells using several approaches. Most early investigations were conducted on groups of cells, utilizing techniques such as substrate deformation and flow-induced shear. To investigate the properties of cells individually, many conventional techniques were utilized, such as AFM, optical traps/optical tweezers, magnetic beads, and micropipette aspiration. In specific mechanical interrogations, microelectro- mechanical systems (MEMS) have been designed to probe single cells in different interrogation modes. To exert loads on the cells, these devices often comprise piezo-electric driven actuators that attach directly to the cell or move a structure on which cells are attached. Uniaxial …

Injectable Decellularized Nucleus Pulposus Tissue Exhibits Neuroinhibitory Properties, Logan M. Piening, David J. Lillyman, Fei San Lee, Alvaro Moreno Lozano, Jeremy R. Miles, Rebecca A. Wachs

Department of Agricultural and Biological Systems Engineering: Faculty Publications

Background: Chronic low back pain (LBP) is a leading cause of disability, but treatments for LBP are limited. Degeneration of the intervertebral disc due to loss of neuroinhibitory sulfated glycosaminoglycans (sGAGs) allows nerves from dorsal root ganglia to grow into the core of the disc. Treatment with a decellularized tissue hydrogel that contains sGAGs may inhibit nerve growth and prevent discassociated LBP.

Methods: A protocol to decellularize porcine nucleus pulposus (NP) was adapted from previous methods. DNA, sGAG, α-gal antigen, and collagen content were analyzed before and after decellularization. The decellularized tissue was then enzymatically modified to be …

Ecological And Morphological Differentiation Among Coi Haplotype Groups In The Plant Parasitic Nematode Species Mesocriconema Xenoplax, Julianne N. Matczyszyn, Timothy Harris, Kirsten S. Powers, Sydney E. Everhart, Thomas O. Powers

Department of Plant Pathology: Faculty Publications

DNA barcoding with the mitochondrial COI gene reveals distinct haplotype subgroups within the monophyletic and parthenogenetic nematode species, Mesocriconema xenoplax. Biological attributes of these haplotype groups (HG) have not been explored. An analysis of M. xenoplax from 40 North American sites representing both native plant communities and agroecosystems was conducted to identify possible subgroup associations with ecological, physiological, or geographic factors. A dataset of 132 M. xenoplax specimens was used to generate sequences of a 712 bp region of the cytochrome oxidase subunit I gene. Maximum-likelihood and Bayesian phylogenies recognized seven COI HG (≥99/0.99 posterior probability/bootstrap value). Species delimitation …

Ecological And Morphological Differentiation Among Coi Haplotype Groups In The Plant Parasitic Nematode Species Mesocriconema Xenoplax, Julianne N. Matczyszyn, Timothy Harris, Kirsten S. Powers, Sydney E. Everhart, Tom Powers

Department of Plant Pathology: Faculty Publications

DNA barcoding with the mitochondrial COI gene reveals distinct haplotype subgroups within the monophyletic and parthenogenetic nematode species, Mesocriconema xenoplax. Biological attributes of these haplotype groups (HG) have not been explored. An analysis of M. xenoplax from 40 North American sites representing both native plant communities and agroecosystems was conducted to identify possible subgroup associations with ecological, physiological, or geographic factors. A dataset of 132 M. xenoplax specimens was used to generate sequences of a 712 bp region of the cytochrome oxidase subunit I gene. Maximum-likelihood and Bayesian phylogenies recognized seven COI HG (≥99/0.99 posterior probability/bootstrap value). Species …

Global Analysis Of Differential Gene Expression Within The Porcine Conceptus Transcriptome As It Transitions Through Spherical, Ovoid, And Tubular Morphologies During The Initiation Of Elongation, Sophie C. Walsh, Jeremy R. Miles, Brittney N. Keel, Lea A. Rempel, Elane C. Wright‐Johnson, Amanda K. Lindholm‐Perry, William T. Oliver, Angela K. Pannier

Department of Agricultural and Biological Systems Engineering: Faculty Publications

This study aimed to identify transcriptome differences between distinct or transitional stage spherical, ovoid, and tubular porcine blastocysts throughout the initiation of elongation. We performed a global transcriptome analysis of differential gene expression using RNA‐Seq with high temporal resolution between spherical, ovoid, and tubular stage blastocysts at specific sequential stages of development from litters containing conceptus populations of distinct or transitional blastocysts. After RNA‐Seq analysis, significant differentially expressed genes (DEGs) and pathways were identified between distinct morphologies or sequential development stages. Overall, 1898 significant DEGs were identified between distinct spherical and ovoid morphologies, with 311 total DEGs between developmental stages …

Aerial Flight Paths For Communication, Alisha Bevins, Brittany Duncan

School of Computing: Faculty Publications

This article presents an understanding of naive users’ perception of the communicative nature of unmanned aerial vehicle (UAV) motions refined through an iterative series of studies. This includes both what people believe the UAV is trying to communicate, and how they expect to respond through physical action or emotional response. Previous work in this area prioritized gestures from participants to the vehicle or augmenting the vehicle with additional communication modalities, rather than communicating without clear definitions of the states attempting to be conveyed. In an attempt to elicit more concrete states and better understand specific motion perception, this work includes …

Evidence Of Western Corn Rootworm (Diabrotica Virgifera Virgifera Leconte) Field-Evolved Resistance To Cry3bb1 + Cry34/ 35ab1 Maize In Nebraska, Jordan D. Reinders, Emily E. Reinders, Emily Robinson, Bryan W. French, Lance J. Meinke

Department of Entomology: Faculty Publications

BACKGROUND: Western corn rootworm (WCR; Diabrotica virgifera virgifera) field-evolved resistance to transgenic maize expressing the Cry3Bb1 protein derived from Bacillus thuringiensis (Bt) has been confirmed across the United States Corn Belt. Although use of pyramided hybrids expressing Cry3Bb1 + Cry34/35Ab1 has increased in recent years to mitigate existing WCR Bt resistance, susceptibility of Nebraska WCR populations to this rootworm–Bt pyramid has not been assessed. Plant-based bioassays were used to characterize the susceptibility of WCR populations to Cry3Bb1 and Cry3Bb1 + Cry34/35Ab1 maize. Populations were collected from areas of northeastern Nebraska with a history of planting Bt maize that expressed …

Irrigation Systems Management, Dean Eisenhauer, Derrel L. Martin, Derek M. Heeren, Glenn J. Hoffman

Department of Agricultural and Biological Systems Engineering: Faculty Publications

Management of irrigation systems should be based on the desired objectives or outcomes consistent with economic, energy, environmental, labor, water, and resource constraints. Goals can vary from maximizing profit, producing a contracted yield, optimizing water resource use, maintaining the quality of produce, or assuring an attractive landscape. Managers cannot achieve these goals without considering the performance of the irrigation system. This chapter discusses the basic characteristics of various irrigation systems, defines terms that quantify performance, describes basic requirements all systems must provide, gives a range of attributes for systems, and discusses how water supply requirements are governed by ET and …

Climate And Agronomy, Not Genetics, Underpin Recent Maize Yield Gains In Favorable Environments, Gonzalo Rizzo, Juan Pablo Monzon, Fatima Amor Tenorio, Réka Howard, Kenneth G. Cassman, Patricio Grassini

Department of Agronomy and Horticulture: Faculty Publications

Quantitative understanding of factors driving yield increases of major food crops is essential for effective prioritization of research and development. Yet previous estimates had limitations in distinguishing among contributing factors such as changing climate and new agronomic and genetic technologies. Here, we distinguished the separate contribution of these factors to yield advance using an extensive database collected from the largest irrigated maize-production domain in the world located in Nebraska (United States) during the 2005-to-2018 period. We found that 48% of the yield gain was associated with a decadal climate trend, 39% with agronomic improvements, and, by difference, only 13% with …

Irrigation Systems Management, Dean E. Eisenhauer, Derrel L. Martin, Derek M. Heeren, Glenn J. Hoffman

Open Educational Resources: Textbooks

Like most textbooks, this book grew out of our desire to have written material that matches the educational needs of both the students and the instructor of a college course, in this case a course entitled Irrigation Systems Management. The book is the culmination of course notes which have been in development and use for nearly 30 years.

The emphasis of this book is on the management of irrigation systems that are used for agricultural crop production. There are two distinct components of the book, starting with the soil-water-plant-atmosphere system and how soil water should be managed to achieve the …

Stink Bug (Hemiptera: Heteroptera: Pentatomidae) Ecology In Nebraska Agroecosystems, Blessing Ademokoya

Department of Entomology: Dissertations, Theses, and Student Research

Stink bugs (Hemiptera: Heteroptera: Pentatomidae) have gained considerable attention in Nebraska in the last decade due to increasing densities of native stink bug and spread of invasive species in the Midwest. Little is known about stink bug dynamics in Nebraska cropping systems. Based on data from a recent field survey, specimens at the University of Nebraska State Museum and the diagnostic lab of the Entomology Department at the University of Nebraska Lincoln, as well as published literature, we present a checklist of 72 species and subspecies of Pentatomidae (55 Pentatominae, 13 Asopinae, 3 Podopinae and 1 Edessinae) that occur in …

Mechanical Overload-Induced Muscle-Derived Extracellular Vesicles Promote Adipose Tissue Lipolysis, Ivan J. Vechetti Jr, Bailey D. Peck, Yuan Wen, R Grace Walton, Taylor R. Valentino, Alexander P. Alimov, Cory M. Dungan, Douglas W. Van Pelt, Ferdinand Von Walden, Bjorn Alkner, Charlotte A. Peterson, John J. Mccarthy

Department of Nutrition and Health Sciences: Faculty Publications

How regular physical activity is able to improve health remains poorly understood. The release of factors from skeletal muscle following exercise has been proposed as a possible mechanism mediating such systemic benefits. We describe a mechanism wherein skeletal muscle, in response to a hypertrophic stimulus induced by mechanical overload (MOV), released extracellular vesicles (EVs) containing muscle-specific miR-1 that were preferentially taken up by epidydimal white adipose tissue (eWAT). In eWAT, miR-1 promoted adrenergic signaling and lipolysis by targeting Tfap2α, a known repressor of Adrβ3 expression. Inhibiting EV release prevented the MOV-induced increase in eWAT miR-1 abundance and expression of …

Novel Approaches For Enhancing Cell Survival And Function In Vivo, Ou Wang

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

FDA has approved several cell-based therapeutics and hundreds of cell therapy clinical trials are ongoing. Cells will be a significant type of medicine after small molecule and protein drugs. However, several obstacles need to be addressed to achieve the widespread use of cellular therapeutics. The first challenge is the low efficacy of cell transplantation due to low retention, survival, integration, and function of cells in vivo. The second challenge is producing a massive number of cells for clinical treatment with cost-effectively and reproducibly technologies.

In this thesis, we proposed and investigated two approaches to address these challenges. To begin …

Computational Solutions To Exosomal Microrna Biomarker Detection In Pancreatic Cancer, Thuy T. An

School of Computing: Dissertations, Theses, and Student Research

Pancreatic cancer is the fourth leading cause of cancer death in the United States and the 5-year survival rate is only 5% to 10%. There are only a few non-specific symptoms associated with the early-stage cancer, therefore most patients are diagnosed in a late stage. Due to the lack of effective treatments and the fact that the early stage has a 39% 5-year survival rate, the biggest hope to control this disease is early detection. Therefore, discovery of effective and reliable non-invasive biomarkers for early detection of pancreatic cancer has been a major topic. Very recently, exosomal microRNAs have become …

The Molecular Basis For Natural Competence In Acinetobacter, Yafan Yu

Department of Food Science and Technology: Dissertations, Theses, and Student Research

Bacteria use Horizontal Gene Transfer (HGT) to acquire genetic material, leading to the development of novel traits, such as the spread and development of antibiotic resistance. Natural competence is one type of HGT accomplished by DNA uptake from the environment and incorporation into the genome. Bacteria from Acinetobacter are wildly distributed in the environment and are naturally competent. This propensity is a key factor to the steady increase in drug resistance in Acinetobacter, which is a cause for concern in human health as Acinetobacter is a major source of nosocomial infections. During natural competence, type IV pili (T4P) and related …

The Application Of Mathematical Optimization And Flavor-Detection Technologies For Modeling Aroma Of Hops, Yutong Liu

Department of Food Science and Technology: Dissertations, Theses, and Student Research

In recent years, proprietary hops (Citra, Simcoe, and Mosaic) become the most sought-after hops among brewers due to their excellent aroma. However, they are restricted to the owners unless other growers purchase the costly licensing agreements. Many public hops are available to the growers without any additional costs, but their aroma is difficult to match to the proprietary hops. Although proprietary and public hop varieties are unique in their aroma profiles, all hops varieties contain similar volatile compounds, merely differ in the quantity of different individual compounds. The main objective of this thesis was to investigate the feasibility of matching …

Development And Characterization Of A Decellularized Neuroinhibitory Scaffold Containing Matrix Bound Nanovesicles, Logan Piening

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

Chronic low back pain (LBP) is a leading cause of disability but treatments for LBP are limited. Degeneration of the intervertebral disc leads to loss of neuroinhibitory sulfated glycosaminoglycans (sGAGs) which allows nerves from dorsal root ganglia (DRG) to grow into the core of the disc, leading to pain. Current treatments for LBP involve drugs that do not target the source of the pain and lack long term efficacy or use invasive surgeries with high complication rates. Treatment with a decellularized tissue scaffold that contains neuroinhibitory components may inhibit nerve growth and prevent disc-associated LBP. Here, a decellularized nucleus pulposus …

Soil Microbial Community Dynamics In Response To Prescribed Extreme Fires Following Juniperus Virginiana Invasion In The Loess Canyons Of Nebraska, Julie A. Fowler

School of Natural Resources: Dissertations, Theses, and Student Research

In Nebraska and other regions of the Great Plains, the conifer Juniperus virginiana (eastern redcedar) is converting grasslands to dense woodlands. This is driven by the interacting drivers of fire suppression, altered grazing regimes, climate change and other anthropogenic factors, impacting the provisioning of ecosystem services. This vegetation state transition modifies water resource regulation and biogeochemical cycles leading to altered edaphic properties including soil microbial community composition. To restore these grasslands and control J. virginiana spread, prescribed extreme burns are implemented as a management tool through local prescribed burn associations. We hypothesized that the alternative state transition to dense J. …

The Centennial Of The Pecking Order: Current State And Future Prospects For The Study Of Dominance Hierarchies, Eli D. Strauss, James P. Curley, Daizaburo Shizuka, Elizabeth A. Hobson

School of Biological Sciences: Faculty Publications

A century ago, foundational work by Thorleif Schjelderup-Ebbe described a ‘pecking order’ in chicken societies, where individuals could be ordered according to their ability to exert their influence over their group-mates. Now known as dominance hierarchies, these structures have been shown to influence a plethora of individual characteristics and outcomes, situating dominance research as a pillar of the study of modern social ecology and evolution. Here, we first review some of the major questions that have been answered about dominance hierarchies in the last 100 years.Next,we introduce the contributions to this theme issue and summarize howthey provide ongoing insight in …

Use Of Attractant And Repellent Semiochemicals To Manage Stable Fly (Stomoxys Calcitrans (L.)) Populations On Pastured Cattle Using A Push–Pull Strategy, Alexander Thomas Lehmann

Department of Entomology: Dissertations, Theses, and Student Research

Stable flies (Diptera: Muscidae) are major economic pests of pastured cattle. Their feeding activity causes billions of dollars of damage to the cattle industry. This project investigated the management of stable flies on pastured cattle using a novel Push-Pull treatment in field trials. The repellent Push treatment, a hydrogenated coconut oil containing approximately 70% of C8, C10, and C12 fatty acids in a starch-pectin water formulation, was applied to the animals weekly. The Pull component was a stable fly trap augmented with an attractant (m-cresol). Permethrin and untreated controls were used as comparisons. Both permethrin and Push-Pull treatments reduced stable …

Constraints To Waterfowl Hunting By Hunters And Anglers In The Central United States, Matthew P. Hinrichs, Matthew P. Gruntorad, Julia A. Nawrocki, Mark P. Vrtiska, Mark A. Pegg, Christopher J. Chizinski

School of Natural Resources: Faculty Publications

Waterfowl hunting participation has been on the decline since the mid‐1980s. We used a web‐based survey to better understand waterfowl hunting constraints (i.e., factors that limit or prohibit participation and enjoyment in leisure activities) among hunters and anglers that hunted or did not hunt waterfowl in the central United States. Forty‐eight constraint items were condensed into 10 constraint factors: Rules and Regulations, Waterfowl Identification, Cost, Waterfowl Hunting Skills, Land Access and Permissions, Interference by Other Hunters, Travel, Social, Waterfowl Populations, and Views of Others. We observed significant effects of both state of residence and activity type (i.e., frequent waterfowl hunters, …

A Physiological Signal Derived From Sun-Induced Chlorophyll Fluorescence Quantifies Crop Physiological Response To Environmental Stresses In The U.S. Corn Belt, Hyungsuk Kimm, Kaiyu Guan, Chongya Jiang, Guofang Miao, Genghong Wu, Andrew Suyker, Elizabeth A. Ainsworth, Carl J. Bernacchi, Christopher M. Montes, Joseph A. Berry, Xi Yang, Christian Frankenberg, Min Chen, Philipp Köhler

School of Natural Resources: Faculty Publications

Sun-induced chlorophyll fluorescence (SIF) measurements have shown unique potential for quantifying plant physiological stress. However, recent investigations found canopy structure and radiation largely control SIF, and physiological relevance of SIF remains yet to be fully understood. This study aims to evaluate whether the SIF-derived physiological signal improves quantification of crop responses to environmental stresses, by analyzing data at three different spatial scales within the U.S. Corn Belt, i.e. experiment plot, field, and regional scales, where ground-based portable, stationary and space-borne hyperspectral sensing systems are used, respectively. We found that, when controlling for variations in incoming radiation and canopy structure, crop …

Towards A More Comprehensive Understanding Of Wild Pig (Sus Scrofa) Impacts On Agricultural Producers: Insights From A Texas Case Study, Keith M. Carlisle, Nicole Didero, Sophie Mckee, Julie Elser, Stephanie A. Shwiff

United States Department of Agriculture Wildlife Services: Staff Publications

This research investigates the impacts of invasive wild pigs (Sus scrofa Linneaus) on agricultural producers in Texas, with the aim of identifying and describing all categories of wild pig impacts and quantifying the extent of producers’ over- or underestimation of their total wild pig-related costs in 2018, as compared to calculations based upon data subsequently provided by the producers about individual wild pig-related costs and losses. Based on interviews with 23 producers in 16 Texas counties, we identified more than 20 discrete categories of negative impacts and negligible positive impacts associated with wild pigs. Among them were categories that have …

Adrenocortical Attunement, Reactivity, And Potential Genetic Correlates Among Parent-Daughter Dyads From Low-Income Families, Jennifer Byrd-Craven, Michael M. Criss, Jessica L. Calvi, Lixian Cui, Amanda Baraldi, Amanda Sheffield Morris

Athletic Performance Research

Examining the multitude of influences on the development of adolescent stress responses, especially among low-income families, is a critical and understudied topic in the field. The current study examined cortisol attunement between adolescent girls and parents (mostly mothers) from predominantly low-income, single parent, ethnic minority families before and after an in-laboratory disagreement discussion task. The sample consisted of 118 adolescents (M_age = 13.79 years, 76.3% ethnic minorities, 23.7% European Americans) and primary caregivers (M_age = 40.62 years; Mdn yearly income = $24,000; 43.2% single parents; 50% living below poverty line). We investigated oxytocin receptor (OXTR rs53576) …

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 …

Lasting Consequences Of Psyllid (Bactericera Cockerelli L.) Infestation On Tomato Defense, Gene Expression, And Growth, Kyle Harrison, Azucena Mendoza-Herrera, Julien Gad Levy, Cecilia Tamborindeguy

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

Background: The tomato psyllid, Bactericera cockerelli Šulc (Hemiptera: Triozidae), is a pest of solanaceous crops such as tomato (Solanum lycopersicum L.) in the U.S. and vectors the disease-causing pathogen ‘Candidatus Liberibacter solanacearum’. Currently, the only effective strategies for controlling the diseases associated with this pathogen involve regular pesticide applications to manage psyllid population density. However, such practices are unsustainable and will eventually lead to widespread pesticide resistance in psyllids. Therefore, new control strategies must be developed to increase host-plant resistance to insect vectors. For example, expression of constitutive and inducible plant defenses can be improved through selection. Currently, it is …

Vaccine Hesitancy - When Emotions Trump Reason, Lawrence C. Scharmann

Department of Teaching, Learning, and Teacher Education: Faculty Publications

Isn’t getting a vaccine a decision of choice or personal liberty? Yes, but only if personal choices don’t create health risks for other citizens. We no longer permit individuals to smoke in public spaces in which second-hand smoke can harm the health of others. In the case of COVID-19, at best, individuals whose choice it is not to be vaccinated slow progress toward herd immunity. At worst, if enough individuals choose not to vaccinate, this pandemic continues unabated, enabling variants of the original virus to emerge – variants that are often of increasing virulence. Fear of ingredients, however, is but …

Index To Volume 89

Nebraska Bird Review

Adams, Marie 52

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