Digital Commons Network^™

Stem Exploration Club, Erin Case, Caitlyn Scott

Honors Program: Expanded Learning Clubs

No abstract provided.

A Segmentation-Guided Deep Learning Framework For Leaf Counting, Xijian Fan, Rui Zhou, Tardi Tjahjadi, Sruti Das Choudhury, Qiaolin Ye

Department of Agricultural and Biological Systems Engineering: Faculty Publications

Deep learning-based methods have recently provided a means to rapidly and effectively extract various plant traits due to their powerful ability to depict a plant image across a variety of species and growth conditions. In this study, we focus on dealing with two fundamental tasks in plant phenotyping, i.e., plant segmentation and leaf counting, and propose a two-steam deep learning framework for segmenting plants and counting leaves with various size and shape from two-dimensional plant images. In the first stream, a multi-scale segmentation model using spatial pyramid is developed to extract leaves with different size and shape, where the fine-grained …

Guard-Cell-Targeted Overexpression Of Arabidopsis Hexokinase 1 Can Improve Water Use Efficiency In Field-Grown Tobacco Plants, Liana G. Acevedo-Siaca, Katarzyna Glowacka, Steven M. Driever, Coralie E. Salesse-Smith, Nitsan Lugassi, David Granot, Stephen P. Long, Johannes Kromdijk

Department of Biochemistry: Faculty Publications

Water deficit currently acts as one of the largest limiting factors for agricultural productivity worldwide. Additionally, limitation by water scarcity is projected to continue in the future with the further onset of effects of global climate change. As a result, it is critical to develop or breed for crops that have increased water use efficiency and that are more capable of coping with water scarce conditions. However, increased intrinsic water use efficiency (iWUE) typically brings a trade-off with CO₂ assimilation as all gas exchange is mediated by stomata, through which CO₂ enters the leaf while water vapor exits. …

Towards A Cybersecurity Testbed For Agricultural Vehicles And Environments, Mark Freyhof, George Grispos, Santosh Pitla, Cody Stolle

Department of Agricultural and Biological Systems Engineering: Faculty Publications

In today’s modern farm, an increasing number of agricultural systems and vehicles are connected to the Internet. While the benefits of networked agricultural machinery are attractive, this technological shift is also creating an environment that is conducive to cyberattacks. While previous research has focused on general cybersecurity concerns in the farming and agricultural industries, minimal research has focused on techniques for identifying security vulnerabilities within actual agricultural systems that could be exploited by cybercriminals. Hence, this paper presents STAVE – a Security Testbed for Agricultural Vehicles and Environments – as a potential solution to assist with the identification of cybersecurity …

Mutant Microorganisms And Methods Of Making And Using, Raghuveer Singh, Derrick White, Paul Blum

School of Biological Sciences: Faculty Publications

This disclosure describes methods that allow for the uncoupling of microbial growth from product formation, which allows for maximal use of raw material and optimal end product formation.

Large-Scale Analyses Of Heat Shock Transcription Factors And Database Construction Based On Whole-Genome Genes In Horticultural And Representative Plants, Tong Yu, Yun Bai, Zhuo Liu, Zhiyuan Wang, Qihang Yang, Tong Wu, Shuyan Feng, Yu Zhang, Shaoqin Shen, Qiang Li, Liqiang Gu, Xiaoming Song

Department of Food Science and Technology: Faculty Publications

Heat shock transcription factor (Hsf) plays a critical role in regulating heat resistance. Here, 2950 Hsf family genes were identified from 111 horticultural and representative plants. More Hsf genes were detected in higher plants than in lower plants. Based on all Hsf genes, we constructed a phylogenetic tree, which indicated that Hsf genes of each branch evolved independently after species differentiation. Furthermore, we uncovered the evolutionary trajectories of Hsf genes by motif analysis. There were only six motifs (M1–M6) in lower plants, and then four novel motifs (M7–M10) appeared in higher plants. However, the motifs of some Hsf …

Comparing Artificial-Intelligence Techniques With State-Of-The-Art Parametric Prediction Models For Predicting Soybean Traits, Susweta Ray, Diego Jarquin, Reka Howard

Department of Statistics: Faculty Publications

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

Digital Hydrography Underestimates Stream Length And Leads To Underestimates Of Trout Population Size, Daniel C. Dauwalter, Tim Gatewood, Zachary J. Jackson, Jean Barney, Zachary S. Beard

United States Fish and Wildlife Service: Publications

Stream length is measured for many fisheries management applications. Characteristics of populations and habitats measured at field sites are commonly generalized to unsampled areas using estimates of stream length or stream network length. There are many ways to measure stream length, but map-based stream length measurements are commonly used in fisheries applications even though they are known to be biased. We evaluated how length of headwater streams in Arizona may be underestimated by the National Hydrography Dataset and how that bias influences streamwide abundance estimates for adult Apache Trout Oncorhynchus apache. As expected, stream lengths measured using National Hydrography …

Nutrient Restoration Of A Large, Impounded, Ultra-Oligotrophic Western River To Recover Declining Native Fishes, Ryan S. Hardy, Tyler J. Ross, Kevin N. Mcdonnell, Michael C. Quist, Charlie Holderman, Bryan S. Stevens

United States Geological Survey: Staff Publications

Declines in many fish populations in large, western rivers have been primarily attributed to the anthropogenic reduction of nutrient inputs and subsequent impacts to the food web. The largest known river fertilization program was implemented starting in 2005 on the Kootenai River in northern Idaho to restore resident fisheries. Annual electrofishing surveys were conducted at multiple sites in Idaho and Montana before and during nutrient addition to evaluate assemblage and population-level responses. Although few responses in fish assemblage structure were observed, the addition of liquid ammonium polyphosphate fertilizer (3 μg/L) to the Kootenai River increased fish abundance and biomass over …

Sprouting Systems, Abaigeal Aydt, Cassidy Smith

Honors Program: Expanded Learning Clubs

After taking a class at UNL about environmental awareness, two honors students paired up to start a hydroponics club at a local Lincoln school. In reaching out to the LPS director of sustainability, they were paired up with Prescott Elementary School. Over the course of a semester, they developed a club that got a hydroponic grow tower functioning for the school and taught students about nutrition and sustainability. This club is only in its beginning stages, but the impacts that it is making around the school can already be seen.

Molecular-Level Control Over Ionic Conduction And Ionic Current Direction By Designing Macrocycle-Based Ionomers, Shyambo Chatterjee, Ehsan Zamani, Seefat Farzin, Iman Evazzade, Oghenetega Allen Obewhere, Tyler James Johnson, Vitaly Alexandrov, Shudipto Konika Dishari

Department of Chemical and Biomolecular Engineering: Faculty Publications

Poor ionic conductivity of the catalyst-binding, submicrometer- thick ionomer layers in energy conversion and storage devices is a huge challenge. However, ionomers are rarely designed keeping in mind the specific issues associated with nanoconfinement. Here, we designed nature-inspired ionomers (calix-2) having hollow, macrocyclic, calix[4]arene-based repeat units with precise, sub-nanometer diameter. In ≤100 nm-thick films, the in-plane proton conductivity of calix-2 was up to 8 times higher than the current benchmark ionomer Nafion at 85% relative humidity (RH), while it was 1−2 orders of magnitude higher than Nafion at 20−25% RH. Confocal laser scanning microscopy and other synthetic techniques allowed us …

Development Of A Data-Assimilation System To Forecast Agricultural Systems: A Case Study Of Constraining Soil Water And Soil Nitrogen Dynamics In The Apsim Model, Marissa S. Kivi, Bethany Blakely, Michael Masters, Carl J. Bernacchi, Fernando E. Miguez, Hamze Dokoohaki

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

As we face today's large-scale agricultural issues, the need for robust methods of agricultural forecasting has never been clearer. Yet, the accuracy and precision of our forecasts remains limited by current tools and methods. To overcome the limitations of process-based models and observed data, we iteratively designed and tested a generalizable and robust data-assimilation system that systematically constrains state variables in the APSIM model to improve forecast accuracy and precision. Our final novel system utilizes the Ensemble Kalman Filter to constrain model states and update model parameters at observed time steps and incorporates an algorithm that improves system performance through …

Reinventing Educational Spaces, Angel Coleman

Masters in Architecture Program: Theses

Problems always existed in our educational system, but many issues intensified in the pandemic. One of the biggest is the mental impact on the children, with those in high school tripling in numbers. The spaces these students spend their time has a great impact on their mental well-being. Our schools need to create places for the students to make communities and feel a sense of ownership. Giving students a place to belong and making them proud of their work helps build their self-esteem, relieving some mental health issues.

My thesis is redesigning these environments to create classrooms, schools and a …

Seasonal Variation And Tracking Of Climate Niche Of A Migratory Bird, Javier Gutiérrez Illán, Guiming Wang, D. Tommy King, Fred L. Cunningham

United States Department of Agriculture Wildlife Services: Staff Publications

Migratory birds inhabit different areas during breeding and non-breeding seasons. Depending on the time of the year, they may utilize different resources available in seasonal habitats, but also are subjected to changing climate regimes during their annual life cycle. Migratory birds may adopt ecological niche tracking to cope with different environmental conditions between breeding and non-breeding grounds. The American White Pelican (Pelecanus erythrorhynchos, hereafter ‘AWPE’) is a short-distance migrant between the Gulf of Mexico coastal regions (nonbreeding grounds) and the Northern Great Plains (breeding grounds) of Canada and the US. The American White Pelican is a piscivore, feeding …

Age And Water-Quality Characteristics Of Groundwater Discharge To The South Loup River, Nebraska, 2019, Christopher M. Hobza, John E. Solder

United States Geological Survey: Water Reports and Publications

Streams in the Loup River Basin are sensitive to groundwater withdrawals because of the close hydrologic connection between groundwater and surface water. The U.S. Geological Survey, in cooperation with the Upper Loup and Lower Loup Natural Resources Districts, and the Nebraska Environmental Trust, studied the age and water-quality characteristics of groundwater near the South Loup River to assess the possible effects of a multiyear drought on streamflow.

Groundwater sampled in wells screened in Quaternary-age deposits displayed a wide range of mean ages (27 to 2,100 years), fraction modern, and susceptibility index values. Groundwater with higher concentrations of chloride and higher …

The Impact Of Interactions Among Native Grassland Species: A Study Of Interactions Between Two Invasive Species (Bromus Tectorum And Setaria Faberi) And Two Native Species (Helianthus Annuus And Rudbeckia Hirta), Nash Leef

Department of Environmental Studies: Undergraduate Student Theses

Allelopathy is a description of an interaction between two plant species, usually negative, that impacts their growth or germination. There has been ample data published regarding the impact of allelopathic species in agricultural settings, but little attention has been given to the potential interactions between invasive and native species. Two culprits that have employed allelopathy to great effect in agricultural settings are cheatgrass (Bromus tectorum) and giant foxtail (Setaria faberi). This study posits that allelopathic interactions, similar to those found in agriculture, are occurring between native and invasive species on the Great Plains.

A set of greenhouse trials was established …

Resource Amount And Discontinuity Influence Flight And Reproduction In Hippodamia Convergens (Coleoptera: Coccinellidae), Hannah E. Stowe, J. P. Michaud, Tania N. Kim

Department of Entomology: Faculty Publications

Industrial-scale agriculture creates a mosaic of large monocultures in the landscape, where seasonal cropping cycles generate discontinuous resource availability for insect predators both spatially and temporally. In this environment, selection will favor predator movement and reproductive behaviors that optimize the location and effective utilization of resource (prey) pulses that are both patchy and ephemeral in nature. Using a model system to study predator movement and reproduction, we tested how discontinuous periods of food resource access that mimic fluctuating resource populations (aphids) would influence flight behavior and reproduction of a highly mobile predator, Hippodamia convergens (convergent lady beetle), and possibly modify …

Individual Beef Cattle Identification Using Muzzle Images And Deep Learning Techniques, Guoming Li, Galen E. Erickson, Yijie Xiong

Department of Animal Science: Faculty Publications

The ability to identify individual animals has gained great interest in beef feedlots to allow for animal tracking and all applications for precision management of individuals. This study assessed the feasibility and performance of a total of 59 deep learning models in identifying individual cattle with muzzle images. The best identification accuracy was 98.7%, and the fastest processing speed was 28.3 ms/image. A dataset containing 268 US feedlot cattle and 4923 muzzle images was published along with this article. This study demonstrates the great potential of using deep learning techniques to identify individual cattle using muzzle images and to support …

Great Northern Beans (Phaseolus Vulgaris L.) Lower Cholesterol In Hamsters Fed A High-Saturated-Fat Diet, An T. Nguyen, Sami A. Althwab, Haowen Qiu, Richard Zbasnik, Carlos A. Urrea, Timothy P. Carr, Vicki Schlegel

Department of Food Science and Technology: Faculty Publications

Background: Dietary interventions for high cholesterol, a primary risk factor for cardiovascular disease, are generally considered before prescribing drugs.

Objective: This study investigated the effects of whole Great Northern beans (wGNBs) and their hull (hGNB) incorporated into a high-saturated-fat (HSF) diet on cholesterol markers and hepatic/small intestinal genes involved in cholesterol regulation.

Methods: Each of the 4 groups of 11 male golden Syrian hamsters at 9 wk old were fed a normal-fat [NF; 5% (wt:wt) of soybean oil], HSF [5% (wt:wt) of soybean oil + 10% (wt:wt) of coconut oil], HSF+5% (wt:wt) wGNB, or HSF+0.5% (wt:wt) hGNB diet for 4 …

Why Plasmodium Vivax And Plasmodium Falciparum Are So Different? A Tale Of Two Clades And Their Species Diversities, Ananias A. Escalante, Axl S. Cepeda, M. Andreína Pacheco

Harold W. Manter Laboratory of Parasitology: Library Materials

The global malaria burden sometimes obscures that the genus Plasmodium comprises diverse clades with lineages that independently gave origin to the extant human parasites. Indeed, the differences between the human malaria parasites were highlighted in the classical taxonomy by dividing them into two subgenera, the subgenus Plasmodium, which included all the human parasites but Plasmodium falciparum that was placed in its separate subgenus, Laverania. Here, the evolution of Plasmodium in primates will be discussed in terms of their species diversity and some of their distinct phenotypes, putative molecular adaptations, and host–parasite biocenosis. Thus, in addition to a current …

Restoration Of A Lake Ontario-Connected Fen Through Invasive Typha Removal, Andie Graham, Bradley Mudrzynski, Eli Polzer, Douglas A. Wilcox

United States Fish and Wildlife Service: Publications

Lake-level regulation that began in 1960 eliminated large fluctuations of Lake Ontario water levels, altering coastal wetland plant communities. More than a half century later, the altered hydroperiod supports dense, monotypic stands of invasive cattail (Typha angustifolia and Typha × glauca), which have diminished overall plant community diversity. As a result, Lake Ontario coastal wetlands are less capable of providing many of their traditional ecological functions. One such wetland is Buttonwood Fen, a floating, lake-connected peatland on Lake Ontario’s southern shore near Rochester, NY. We implemented cattailcontrol measures from 2016 to 2018 with the goal of decreasing live …

A Comprehensive Bison Management And Research Plan For The Crane Trust, Joshua D. Wiese

Other Publications in Wildlife Management

The Great Plains were once a vast grassland ecosystem, but, due to agricultural and human development, are one of the most endangered ecosystems in North America. What remains is generally fragmented, threatened by invasive species, and lacks the natural ecosystem processes that shaped these grasslands such as periodic wildfire and bison grazing. Since 1978, the Platte River Whooping Crane Maintenance Trust, Inc. (dba “Crane Trust”) has worked to maintain the function of grassland and riparian habitats to benefit endangered Whooping Cranes, Sandhill Cranes, and other migratory bird species. They protect ~8,100 acres, including the largest contiguous portion of lowland tallgrass …

Checking The Checkered Taxonomy Of Plötz's Checkered Skippers (Hesperiidae: Pyrgini), Jing Zhang, Qing Cong, John M. Burns, Nick V. Grishin

The Taxonomic Report of the International Lepidoptera Survey

We present an analysis of the names proposed by Carl Plötz in 1884 for the New World species in the genus Pyrgus Hübner, [1819] facilitated by the genomic sequencing of extant primary type specimens comparatively with a larger sample of more recently collected specimens of these species and their relatives. The changes to nomenclature suggested here are only caused by the identity of primary type specimens as revealed by their phenotypes or though genomic sequencing. All neotypes are designated to stabilize nomenclature in agreement with the current usage of these names, which in unison agrees best with the information available …

Genomic Dna Sequencing Reveals Two New North American Species Of Staphylus (Hesperiidae: Pyrginae: Carcharodini), Jing Zhang

The Taxonomic Report of the International Lepidoptera Survey

Two new skipper butterfly (Hesperiidae) species are described from the United States: Staphylus floridus Grishin, sp. n. (type locality in Florida, Volusia County) and Staphylus ecos Grishin, sp. n. (type locality in Texas, Brewster County). They are cryptic and hence escaped recognition. They differ from their sister species by the relative size and morphology of genitalia and by genotype—including and beyond the COI barcode—thus, suggesting genetic isolation that argues for their species-level status. A lectotype is designated for Helias ascalaphus Staudinger, 1876. Staphylus opites (Godman & Salvin, 1896), stat. rest. is a species-level taxon and not a synonym of Staphylus …

First Record Of Ancognatha Erythrodera (Blanchard, 1846) (Coleoptera: Scarabaeidae: Dynastinae: Cyclocephalini) In The Altiplano Of Chile, José Mondaca, Sergio Rothmann

Insecta Mundi

The presence of Ancognatha erythrodera (Blanchard, 1846) (Coleoptera: Scarabaeidae) is confirmed for the first time in Chile based on male and female specimens collected in the extreme north of the country. This is the second species of Ancognatha Erichson, 1847 recorded in Chile. Morphological characters, illustrations of male genitalia, male and female habitus photographs of this species, and additional records in Argentina and Bolivia are provided. A map with the collection sites and montane habitats photograph in Chile are included.

The Dynastinae (Coleoptera: Scarabaeidae) that occur in Chile were comprehensively revised by Ratcliffe et al. (2021), who recorded nine species …

Comparative Analyses Of De Novo Transcriptome Assembly Pipelines For Diploid Wheat, Natasha Pavlovikj

School of Computing: Dissertations, Theses, and Student Research

Gene expression and transcriptome analysis are currently one of the main focuses of research for a great number of scientists. However, the assembly of raw sequence data to obtain a draft transcriptome of an organism is a complex multi-stage process usually composed of pre-processing, assembling, and post-processing. Each of these stages includes multiple steps such as data cleaning, error correction and assembly validation. Different combinations of steps, as well as different computational methods for the same step, generate transcriptome assemblies with different accuracy. Thus, using a combination that generates more accurate assemblies is crucial for any novel biological discoveries. Implementing …

Rheological Behavior Of Dspc-, Dbpc-, And Dppc-Oxygen Microbubbles And Their Effectiveness In Improving Survival In A Rat Model Of Lipopolysaccharide-Induced Acute Respiratory Distress Syndrome, Riaz Ur Rehman Mohammed

Department of Mechanical and Materials Engineering: Dissertations, Theses, and Student Research

Acute respiratory distress syndrome (ARDS) causes 75,000 deaths in the U.S., annually. It is characterized by hypoxemia and damage to the lung alveoli. ARDS Management strategies involve extracorporeal membrane oxygenation (ECMO) and mechanical ventilation, but none of these methods improve the mortality rates. Oxygen microbubbles (OMBs) consist of a lipid shell with an oxygen core and have potential to augment oxygenation to manage ARDS. Previous studies demonstrated significant improvements in systemic oxygenation and mortality upon administering OMBs.

We replicated an ARDS rat model by intratracheal administration of lipopolysaccharide at a 24 mg/kg dose. After inducing the disease in rats, the …

The Effects Of Human Activity On Reintroduced Bighorn Sheep (Ovis Canadensis) Populations, Justine Cherovsky

Department of Environmental Studies: Undergraduate Student Theses

Since the decimation of North America’s bighorn sheep (Ovis canadensis) populations due to human impacts, translocations have been the primary conservation strategy to repopulate the native habitat. Following the extirpation of the species in Nebraska, bighorns were reintroduced with the hope to establish a stable population, but nearly four decades of management has resulted in large-scale die-offs and unstable herds. Ongoing human impacts have created similar results across the country as reintroductions struggle to establish independent bighorn herds. A systematic literature review was conducted to analyze current human related effects, evaluate the effectiveness of management practices, and compare these findings …

How Can Stakeholders In Food Sovereignty Achieve More Political Power?, Micah Dierks

Department of Environmental Studies: Undergraduate Student Theses

Food sovereignty (FSv) is a peasant-driven, transnational movement that emerged in response to land-grabbing and the consolidation of power in food production. It advocates for the rights of people to define their own food practices and systems. To provide targeted feedback for movement reflexivity, 21 ecological conflicts referencing food sovereignty were sampled from the Global Atlas of Environmental Justice (the EJAtlas). Involved groups of actors and their forms of mobilization were correlated with interpretations of success from the EJAtlas. I recommend that stakeholders in food sovereignty pursue the acquisition of greater political power through improving messaging, leveraging or disrupting existing …

The Accessibility And Sustainability Of Local Foods: A Snapshot From The Food Hubs Of Lincoln, Nebraska, Tess Foxall

Department of Environmental Studies: Undergraduate Student Theses

The current state of agriculture in the United States utilizes industrial practices that pose a myriad of risks to both human and environmental health. By focusing on smaller farms and local food systems that utilize more sustainable agriculture practices, communities can benefit in terms of economic, environmental, and social health. Food hubs can play a key role in local food systems to connect local producers with consumers and increase access to local food. The goal of the research was to analyze the accessibility and sustainability of local food from food hubs in Lincoln, Nebraska to find the key barriers to …