Digital Commons Network^™

Hybridization Between The Rare Gray-Headed Chickadee And The Abundant Boreal Chickadee In The Midst Of Shifting Climate, Matthew R. Armstrong

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

As species respond to changing climate, distributions and abundances may shift and alter species interactions. Hybridization, a relatively widespread phenomenon becoming more common with climate change, can have beneficial and detrimental effects on population growth rates and genetic integrity. Beneficial effects due to the introduction of advantageous alleles and increased genetic diversity may result from hybridization. Species may also accrue fitness costs associated with changing climates if mismatches occur between environmental variables and phenotypes. The gray-headed chickadee, Poecile cinctus lathami, is an extremely rare songbird that has experienced marked declines in recent decades within its restricted distribution in Alaska …

Phylogeny And Disparity Of Ammonoid Family Acanthoceratidae Over Ocean Anoxic Event 2, Lindsey Howard

Department of Earth and Atmospheric Sciences: Dissertations, Theses, and Student Research

The widespread use of genera as proxies for species in paleobiological studies might affect the results of these studies. Although most attention has been given to taxonomic diversity studies, this could also be true of disparity and phylogenetic studies. In particular, the assumption that particular character states truly diagnose all members of a genus might distort results. This study examines the disparity of Acanthoceratid ammonoids at both the generic and species level. 149 species from 42 genera were examined with 52 characters measured. Following the measurements, an inverse modeling simulation was run 100 times to generate a simulated phylogeny with …

Geospatial Distribution Of Rhizocarpon Lichens In The Peri Himal, Matt Lehmann, Daniel Havlat

Nepal: Geoscience in the Himalaya

Lichenometry, a technique used primarily in high latitudes and mountainous regions to date rock surface exposure, relies on estimations of lichen growth rates. Utilizing Rhizocarpon lichen, lichenometry has been extensively applied to date Late Holocene glacial landforms. In this study, we explore Rhizocarpon distribution in the Peri Himal of the Nepal Himalaya to understand the microclimatic and environmental mechanisms that dictate their growth location. We collected 25 data points throughout the western moraine of Ponkar Glacier near Kehcakyu Khola and around Ponkar Lake. Through this data we raised the question, under what conditions do Rhizocarpon lichen grow in high altitude …

Arkansas Corn And Grain Sorghum Research Studies 2023, Jason Kelley, Travis Faske

Arkansas Agricultural Experiment Station Research Series

The 2023 edition of the Arkansas Corn and Grain Sorghum Research Studies Series includes research results on topics pertaining to corn and grain sorghum production, including weed, disease, and insect management; economics; irrigation; agronomics; soil fertility; mycotoxins; cover crop management; and research verification program results. Our objective is to capture and broadly distribute the results of research projects funded by the Arkansas Corn and Grain Sorghum Board. The intended audience includes producers and their advisors, current investigators, and future researchers. The Series serves as a citable archive of research results.

Assessing Rice Phenological Features With Hyperspectral Imaging Insights From Earth Surface Mineral Dust Source Investigation (Emit), Shahryar Fazli, Wenzhao Li, Surendra Maharjan, Hesham El-Askary

Mathematics, Physics, and Computer Science Faculty Articles and Research

In California's Central Valley, water management and crop health, particularly in rice cultivation, are critical. This paper details the application of Earth surface Mineral dust source InvesTigation (EMIT) hyperspectral imaging, specifically employing Spectral Correlation Mapper (SCM) and Spectral Information Divergence (SID), for precise phenological analysis. By aligning EMIT data with Hyperion satellite references, we address spectral and geographical discrepancies. Our methodology includes seasonal sampling of spectral curves to capture the phenological stages of rice. Results show a strong correlation (R ² = 0.86) between August EMIT and Reference dataset, emphasizing EMIT's utility in enhancing agricultural practices and water efficiency in …

Poly(Thioether) Thermosets With Gated Photodegradation, Surabhi Jha

Dissertations

Photodegradable polymer networks are attractive due to the precise spatiotemporal control and large-area applicability of light. Chemical linkages that enable these polymer networks to be photo-responsive, also hinder their applicability in ambient light. Photostable and photodegradable networks have recently been reported to overcome this challenge by combining other stimuli with light for degradation. We report the design of a network that responds to a simultaneous, dual stimulus for photodegradation. We design poly(thioether acetal) networks with benzylidene acetal moieties that are known to undergo β-scission in the presence of free thiols. By blocking these free thiols with a thermally labile protecting …

Efficient Machine Learning On Scientific Data Using Bayesian Optimization, Rui Xin

Theses and Dissertations

Deep Learning is pivotal in advancing data analysis across various scientific fields, from genomics to materials discovery. Despite its widespread use, efficiently learning from limited data and operating under resource constraints remains a significant challenge, often limiting its full potential in environments where data is scarce or resources are restricted. This dissertation explores Active Learning and Automated Machine Learning (AutoML) powered by Bayesian Optimization to enhance the efficiency of machine learning across multiple disciplines. It focuses on algorithm optimization and data management through three interconnected studies. In the first study, we investigate how data management technique - active learning helps …

Multi-Scale Deep Representation Learning In Synthetic Biology, Xiaoyi Liu

Theses and Dissertations

Synthetic biology advances and combines the expertise of engineers and biologists, bridging the gap between engineering and natural life. Synthetic biology has been generally categorized into two broad branches by developing new biological components, networks, and systems to reprogram organisms. The first branch involves using synthetic molecules to mimic natural biological functions. The second branch focuses on assembling natural biological components in novel ways, aiming to produce systems with unique, practical functions. Thus, the de novo engineering of biological modules and synthetic pathways is used in related practical bioengineering applications, such as drug-targeting strategies and microbial product manufacturing. Therefore, synthetic …

Establishment Of Protocols To Measure Near-Ir(Nir) Surface-Enhanced Raman Scattering (Sers) Signals Of Nir Dye, Justin B. Ramsey

Forensic Science Master's Projects

Biomedical imaging techniques are crucial for early disease diagnostics, particularly for life-threatening conditions. However, traditional methods have inherent limitations, such as restricted spatial resolution and potential risks associated with repeated exposure to ionizing radiation. Near-infrared (NIR) surface-enhanced Raman spectroscopy (SERS) presents a promising alternative due to its minimal risks and potential for high-resolution biomedical imaging. A key challenge in NIR-SERS biomedical imaging is the development of biocompatible, nontoxic SERS substrates that can be safely introduced into the human body, targeting specific cells and tissues effectively.

NIR-SERS substrates typically consist of gold nanoparticles (AuNPs) modified with biorecognition elements and reporter molecules, …

The Colorado Wolf Reintroduction Portrayal In News Media, Megan K. Mcarthur, Monica V. Ogra

Student Publications

The Colorado gray wolf (Canis lupus) reintroduction began in December 2023 in the hope of restoring this once native population to the area, and it has received mixed responses from the media. By answering the research question of 'How has the wolf reintroduction in Colorado been framed in news media?', this research poster looks at the portrayal of the reintroduction in news articles from six months before and after the first wolves were released. Media is an influential factor in people's opinions and it is important to be aware of the information being shared and any bias within them.

Synthetic And Mechanistic Studies Of Ruthenium Catalyzed C–N And C–H Bond Activation Reactions, Krishna Prasad Gnyawali

Dissertations (1934 -)

Transition metal catalyzed C–H and C–N functionalization methods have emerged as an innovative tool for designing efficient synthesis of fine chemicals by using readily available starting materials without the formation of wasteful byproducts. One of the paramount challenges in C–H functionalization research field has been to promote regio- and stereoselective C–H bond activation on saturated hydrocarbon substrates. While much progress has been achieved on promoting selective sp2 C–H activation reactions on unsaturated hydrocarbon substrates in the past decades, catalytic sp3 C–H bond and functionalization methods on saturates hydrocarbon substrates remain as the frontier topic of C–H functionalization research. The well-defined …

Precision Deuteration And Hydrofunctionalization Of Aryl Alkynes And Alkenes, Samantha E. Sloane

Dissertations (1934 -)

The similar nature of the hydrogen atom to its isotope, deuterium, allows for the simple exchange of hydrogen atoms for deuterium atoms in drug molecules to alter the absorption, distribution, metabolism, and excretion properties. Installing the deuterium functionality into a specific site in the molecule is essential. Selective hydrofunctionalization reactions of alkynes and alkenes using the highly reactive catalytic Cu–H species have been well developed, and synthetic organic chemistry methods to selectively incorporate one or two deuterium atoms into the benzylic site of organic compounds, a key metabolic position, are elusive. A Cu–H catalytic approach offers selectivity and reactivity to …

Nonlocal Frameworks For Nonlinear Conservation Laws And Advection-Diffusion Processes, Anh Thuong Vo

Dissertations and Doctoral Documents, University of Nebraska-Lincoln, 2023–

Conservation laws are fundamental principles that play an important role in modeling various phenomena in physics, chemistry, and biology. However, their limitations, such as the development of shocks despite smooth initial conditions, are well known. The nonlocal model framework can be used to overcome these challenges. Nonlocal frameworks utilize integral operators that mimic differential operators but also incorporate long-range interactions within a finite horizon. This approach not only allows for non-smooth solutions, but also provides flexibility in modeling different phenomena. This study investigates the convergence of nonlocal divergence operators, defined with a general flux density function, to their classical counterparts. …

Fedgmmat: Federated Generalized Linear Mixed Model Association Tests, Wentao Li, Han Chen, Xiaoqian Jiang, Arif Harmanci

Faculty, Staff and Student Publications

Increasing genetic and phenotypic data size is critical for understanding the genetic determinants of diseases. Evidently, establishing practical means for collaboration and data sharing among institutions is a fundamental methodological barrier for performing high-powered studies. As the sample sizes become more heterogeneous, complex statistical approaches, such as generalized linear mixed effects models, must be used to correct for the confounders that may bias results. On another front, due to the privacy concerns around Protected Health Information (PHI), genetic information is restrictively protected by sharing according to regulations such as Health Insurance Portability and Accountability Act (HIPAA). This limits data sharing …

Identification Of Immune-Associated Biomarkers Of Diabetes Nephropathy Tubulointerstitial Injury Based On Machine Learning: A Bioinformatics Multi-Chip Integrated Analysis, Lin Wang, Jiaming Su, Zhongjie Liu, Shaowei Ding, Yaotan Li, Baoluo Hou, Yuxin Hu, Zhaoxi Dong, Jingyi Tang, Hongfang Liu, Weijing Liu

Faculty, Staff and Student Publications

BACKGROUND: Diabetic nephropathy (DN) is a major microvascular complication of diabetes and has become the leading cause of end-stage renal disease worldwide. A considerable number of DN patients have experienced irreversible end-stage renal disease progression due to the inability to diagnose the disease early. Therefore, reliable biomarkers that are helpful for early diagnosis and treatment are identified. The migration of immune cells to the kidney is considered to be a key step in the progression of DN-related vascular injury. Therefore, finding markers in this process may be more helpful for the early diagnosis and progression prediction of DN.

METHODS: The …

Ghcu, A Molecular Chaperone, Regulates Leaf Curling By Modulating The Distribution Of Kngh1 In Cotton, Yihao Zang, Chenyu Xu, Lishan Yu, Longen Ma, Lisha Xuan, Sunyi Yan, Yayao Zhang, Yiwen Cao, Xiaoran Li, Zhanfeng Si, Jieqiong Deng, Tianzhen Zhang, Yan Hu

Faculty, Staff and Student Publications

Leaf shape is considered to be one of the most significant agronomic traits in crop breeding. However, the molecular basis underlying leaf morphogenesis in cotton is still largely unknown. In this study, through genetic mapping and molecular investigation using a natural cotton mutant cu with leaves curling upward, the causal gene GHCU is successfully identified as the key regulator of leaf flattening. Knockout of GHCU or its homolog in cotton and tobacco using CRISPR results in abnormal leaf shape. It is further discovered that GHCU facilitates the transport of the HD protein KNOTTED1-like (KNGH1) from the adaxial to the abaxial …

Genetic Analysis Of Seven Patients With Inherited Ichthyosis And Nagashima-Type Palmoplantar Keratoderma, Jing Zhang, Yue Yao, Ya Tan, Hua-Ying Hu, Lin-Xi Zeng, Guo-Qiang Zhang

Faculty, Staff and Student Publications

Inherited ichthyosis comprises a series of heterogeneous dermal conditions; it mainly manifests as widespread hyperkeratosis, xerosis and scaling of the skin. At times, overlapping symptoms require differential diagnosis between ichthyosis and several other similar disorders. The present study reports seven patients with confirmed or suspected to be associated with ichthyosis by conducting a thorough clinical and genetic investigation. Genetic testing was conducted using whole-exome sequencing, with Sanger sequencing as the validation method. The MEGA7 program was used to analyze the conservation of amino acid residues affected by the detected missense variants. The enrolled patients exhibited ichthyosis-like but distinct clinical manifestations. …

Missing History Of A Modern Domesticate: Historical Demographics And Genetic Diversity In Farm-Bred Red Fox Populations, Halie M. Rando, Emmarie P. Alexander, Sophie Preckler-Quisquater, Cate B. Quinn, Jeremy T. Stutchman, Jennifer L. Johnson, Estelle R. Bastounes, Beata Horecka, Kristina L. Black, Michael P. Robson, Darya V. Shepeleva, Yury E. Herbeck, Anastasiya V. Kharlamova, Lyudmila N. Trut, Jonathan N. Pauli, Benjamin N. Sacks, Anna V. Kukekova

Computer Science: Faculty Publications

The first record of captive-bred red foxes (Vulpes vulpes) dates to 1896 when a breeding enterprise emerged in the provinces of Atlantic Canada. Because its domestication happened during recent history, the red fox offers a unique opportunity to examine the genetic diversity of an emerging domesticated species in the context of documented historical and economic influences. In particular, the historical record suggests that North American and Eurasian farm-bred populations likely experienced different demographic trajectories. Here, we focus on the likely impacts of founder effects and genetic drift given historical trends in fox farming on North American and Eurasian farms. A …

Beta Lactams Anticancer Effect On Human Breast Cancer, Mcf-7 Cell Line, Ailis A. Abalos

Theses and Dissertations

Cancer is a disease where abnormal cells replicate uncontrollably in that same region and/or other parts of the body. One in eight women are diagnosed with breast cancer, thus making it the second leading cause of cancer-related deaths in the U.S. Chemotherapy, is the utilization of medicinal compounds (drugs) to treat cancer. While most are nonspecific and target both cancer and healthy cells, more emphasis is on developing drugs with specificity (only target tumor cells) and low toxicity. Interestingly, Beta Lactams (β-lactams) have emerged as a class of compounds that are effective in the treatment of various cancers. The benefits …

Modulating Covalency In A Ni-H-Al Subunit: Synthesis And Characterization Of A Series Of Electronically Differentiating Ni-Al Heterometallics, Aleida Guadalupe Gonzalez

Theses and Dissertations

Metal hydrides are moieties that are present in a variety of applications as intermediates in catalysis. Despite the vast utilization of metal hydrides, monometallic metal hydride complexes bear limitations in inert-bond activation and functionalization. A strategy to overcome these limitations and access more challenging reactivity is utilizing metal-metal cooperativity on a single platform to further activate hydride moieties. Although incorporating multiple metal centers on a single ligand scaffold has been realized, access to heterometallic hydride-bearing complexes is a greater synthetic challenge. Given the limitations in accessing such systems, the reactivity and electronic structure of heterometallic hydrides are seldom studied. Recently, …

A Deep Dive Into The Conformations Of Fluorine-Substituted Benzoic Acids And Ethanesulfonic Acid And Spectroscopic Characterizations Of Their Hydrogen-Bonded Complexes, Alitza Gianina Gracia

Theses and Dissertations

Microwave spectroscopy is a technique used to study the molecular structures of a wide range of systems. The first part of the thesis focuses on fluorinated benzoic acids and complexes they form through hydrogen bonding to explore the fluorination effect, while the last part shifts to ethanesulfonic acid and its interaction with water. The study of 3,4,5-triflurorbenzoic acid with formic acid offers insight on the proton tunneling process, which is a process that occurs in many chemical and biological processes. Microwave spectroscopy can help provide dynamic information for the better understanding of this fundamental process. Solvation is another topic that …

Diffuse Reflectance Spectroscopy For Optical Characterizations Of Orthotopic Head And Neck Cancer Models In Vivo, Pranto Soumik Saha, Jing Yan, Caigang Zhu

Markey Cancer Center Faculty Publications

We demonstrated an easy-to-build, portable diffuse reflectance spectroscopy device along with a Monte Carlo inverse model to quantify tissue absorption and scattering-based parameters of orthotopic head and neck cancer models in vivo. Both tissue-mimicking phantom studies and animal studies were conducted to verify the optical spectroscopy system and Monte Carlo inverse model for the accurate extraction of tissue optical properties. For the first time, we reported the tissue absorption and scattering coefficients of mouse normal tongue tissues and tongue tumor tissues. Our in vivo animal studies showed reduced total hemoglobin concentration, lower tissue vascular oxygen saturation, and increased tissue scattering …

A Probabilistic Approach To Estimate The Temporal Order Of Pathway Mutations Accounting For Intra-Tumor Heterogeneity, Menghan Wang, Yanqi Xie, Jinpeng Liu, Austin Li, Li Chen, Arnold Stromberg, Susanne Arnold, Chunming Liu, Chi Wang

Markey Cancer Center Faculty Publications

The development of cancer involves the accumulation of somatic mutations in several essential biological pathways. Delineating the temporal order of pathway mutations during tumori- genesis is crucial for comprehending the biological mechanisms underlying cancer development and identifying potential targets for therapeutic intervention. Several computational and statistical methods have been introduced for estimating the order of somatic mutations based on mutation profile data from a cohort of patients. However, one major issue of current methods is that they do not take into account intra-tumor heterogeneity (ITH), which limits their ability to accurately discern the order of pathway mutations. To address this …

Response To Replication Stress And Maintenance Of Genome Stability By Wrn, The Werner Syndrome Protein, David K. Orren, Amrita Machwe

Markey Cancer Center Faculty Publications

Werner syndrome (WS) is an autosomal recessive disease caused by loss of function of WRN. WS is a segmental progeroid disease and shows early onset or increased frequency of many characteristics of normal aging. WRN possesses helicase, annealing, strand exchange, and exonuclease activities and acts on a variety of DNA substrates, even complex replication and re- combination intermediates. Here, we review the genetics, biochemistry, and probably physiological functions of the WRN protein. Although its precise role is unclear, evidence suggests WRN plays a role in pathways that respond to replication stress and maintain genome stability particularly in telomeric regions.

Enhancing Water Sustainability In North Africa: Literature Review And Synthesis Of Current Knowledge Gaps In Sudan, Osman M. A. Adam, Aaron R. Mittelstet, Derek M. Heeren, Troy E. Gilmore

Department of Agricultural and Biological Systems Engineering: Presentations and White Papers

This study delves into the critical role of groundwater in addressing global water challenges, with a focus on the Nubian Sandstone Aquifer System (NSAS) in North Africa. Groundwater constitutes a source of potable water, irrigation, and industrial use, especially in arid regions where surface water is limited. We analyzed the status of water quantity, withdrawals, recharge, and geological characteristics in the NSAS, specifically in Sudan, Egypt, Libya, and Chad. Though the NSAS is largely an untapped resource, we evaluated various scenarios to determine the quantity of cropland that can be sustainably irrigated. The NSAS is located in an arid region, …

Assessing Soil Properties For Optimized Irrigation Development In Sudan, Northern Africa, Suhib Hamid, Derek M. Heeren, Aaron R. Mittelstet, Saleh Taghvaeian, Randall S. Ritzema

Department of Agricultural and Biological Systems Engineering: Presentations and White Papers

Sustainable irrigation methods maximize agricultural productivity in Northern African countries like Sudan. This project evaluates soil properties to develop optimized irrigation strategies for Sudan's arid and semi-arid climate. Assessing soil characteristics such as texture, infiltration rates, and nutrient content informs the selection of modern irrigation systems. Data from 3,192 locations, collected using GPS and ring infiltrometers for infiltration rates, alongside laboratory analyses for soil properties, were employed. A ranking system determined suitable irrigation systems for specific soil classes, considering factors like slope, wind, crop tolerance, available water capacity (AWC), drainage, germination, capital cost, labor cost, maintenance, and evapotranspiration (ET). The …

Assessing The Gut Content Of Styela Plicata: A Benthic Filter Feeder In The Indian River Lagoon, Honor Lily Triumph Edmands

Theses and Dissertations

The Indian River Lagoon (IRL) has experienced declining water quality due to human activities involving nutrient input, leading to Harmful Algal Blooms (HABs). The Living Docks program affixes oyster mats to dock pilings to promote the settlement and recruitment of benthic filter feeders for water quality improvement. However, questions remain about filtering efficiencies of organisms that make up the mat communities, and whether organisms remove harmful species from the IRL. The pleated sea squirt, Styela plicata, is a common oyster mat resident. The goal of this thesis was to investigate what phytoplankton and bacteria S. plicata consumes, and if …

Sigma Gamma Epsilon Student Research Poster Session, Geological Society Of America Annual Meeting 2022, Denver, Colorado, Usa, Scott R. Beason

The Compass: Earth Science Journal of Sigma Gamma Epsilon

The Society of Sigma Gamma Epsilon sponsors an annual poster session at every Annual Meeting of the Geological Society of America. The 2022 Sigma Gamma Epsilon undergraduate research poster session took place during the 2022 Geological Society of America Annual Meeting in Denver, Colorado, USA, on Monday, October 10, 2022. Ten (10) posters were presented in Exhibit Hall F at the Colorado Convention Center between 2:00 PM and 6:00 PM at the poster session. Titles, authors (italics for the presenting author), affiliations, and abstracts for each poster are listed in this report.

Greenhouse Gas Emissions From Urban Lawn Soil Amended With Biochar And Compost Under Contrasting Redox Conditions, Angel Salinas

Theses and Dissertations

Green fields around the world are being converted to urban land uses to cope with population growth and urbanization. The objective of this study was to investigate how urban lawn soils can contribute to greenhouse gas (GHG) emissions in relation to soil saturation-drainage cycles. We measured carbon dioxide (CO2), methane (CH4), and nitrous oxide (N2O) emissions as well as redox potential (Eh) from garden soils amended with biochar, compost, or biochar + compost under a mesocosm scale. Bermuda turfgrass seed was seeded in each column (5-gallon bucket) and three water saturation conditions (half-saturated, full-saturated, and unsaturated soils) were maintained for …

Generating Bessel Beams With An Elastomeric Replica Of A Weevil Carapace, Paz Victoria T. Ramos, Michie Vianca D. De Vera, Raphael Guerrero

Physics Faculty Publications

We generate a zero-order Bessel beam with a laser beam focused onto an elastomeric replica of a weevil carapace scale. Carapace surface structures are imprinted on an elastomeric cast via soft lithography. The output Bessel beam exhibits the expected properties of non-diffraction over a propagation range of 30 cm. The width of the central spot at a propagation distance of 25 cm is 296:8 μm, corresponding to a replicated weevil scale with a diameter of 64.3 μm acting as an annular slit. Self-healing of the beam after encountering a wire obstruction is also observed.