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The Trifluoromethyltetrafluoro-Λ6-Sulfanyl Group In Organic And Polymer Chemistry, Muqian Deng

Legacy Theses & Dissertations (2009 - 2024)

Fluorine atom was widely applied in the organic chemistry and medicinal chemistry due to its strong electronegativity and lipophilicity. Fluorine atom, trifluoromethyl (CF3) moiety, trifluoromethyl sulfenyl (CF3S) moiety, pentafluoromethylsulfenyl (SF5) moiety have already been applied in the medicinal chemistry. These fluorinated groups brought the good chemical stability, oral stability, low toxicity, and longer half-life compared with the analogs. Fluorine containing compounds can be synthesized via radical reaction, electrophilic fluorinated source as well as nucleophilic sources. Additionally, the fluorinated compounds can also be synthesized via chlorofluoro-oxidation and SN2 reactions. In our lab, we introduced the super fluorine rich moiety (trans-CF3SF4 group) …

Normative Auditory Brainstem Evoked Response Characteristics In Puppies, Lauren E. James

Doctoral Scholarly Projects & Capstones

The brainstem auditory evoked response (BAER) is a potential recorded from the brainstem when an acoustic stimulus is presented (Kramer & Brown, 2019). In humans, the BAER is typically used to evaluate the integrity of the auditory pathway or to assist in estimating hearing sensitivity in newborns and difficult to test populations. The BAER waveforms are evaluated based on components such as the overall morphology, absolute peak latencies, interpeak latencies, and peak amplitudes. When analyzing these characteristics, normative data are utilized to evaluate if the response is considered to represent normal auditory function. The BAER test can be used to …

Foot And Ankle Soft Tissue Sarcomas-Treatment And Oncologic Outcomes: A Systematic Review Of The Literature, Juan Pretell

All Publications

Background: Foot and ankle soft tissue sarcomas (STSs) are rare neoplasms associated with a high risk of local recurrence and metastasis. Although amputation is often performed, its impact on prognosis remains unknown. The aims of our systematic review were identifying risk factors for (1) disease-specific death, (2) local recurrence, (3) metastasis, and assessing (4) whether the type of surgery (amputation or limb-salvage) affected disease-specific survival.

Methods: This systematic review was conducted following PRISMA guidelines. The PubMed, Embase, and Scopus databases were searched. Our study was registered in PROSPERO (ID: 415624). Quality appraisal was done using STROBE guidelines.

Results: A total …

The Evolutionary Responses Of Life-History Strategies To Climatic Variability In Flowering Plants, James Boyko, Eric R. Hagen, Jeremy M. Beaulieu, Thais Vasconcelos

Biological Sciences Faculty Publications and Presentations

• The evolution of annual or perennial strategies in flowering plants likely depends on a broad array of temperature and precipitation variables. Previous documented climate life-history correlations in explicit phylogenetic frameworks have been limited to certain clades and geographic regions.
• To gain insights which generalize to multiple lineages we employ a multi-clade approach analyzing 32 groups of angiosperms across eight climatic variables. We utilize a recently developed method that accounts for the joint evolution of continuous and discrete traits to evaluate two hypotheses: annuals tend to evolve in highly seasonal regions prone to extreme heat and drought; and annuals tend to …

Induced Pluripotent Stem Cells Derived From Patients Carrying Mitochondrial Mutations Exhibit Altered Bioenergetics And Aberrant Differentiation Potential, Fibi Meshrkey, Kelly M. Scheulin, Christopher M. Littlejohn, Joshua Stabach, Bibhuti Saikia, Vedant Thorat, Yimin Huang, Thomas Laframboise, Edward J. Lesnefsky, Raj R. Rao, Franklin D. West, Shilpa Iyer

Biological Sciences Faculty Publications and Presentations

Background

Human mitochondrial DNA mutations are associated with common to rare mitochondrial disorders, which are multisystemic with complex clinical pathologies. The pathologies of these diseases are poorly understood and have no FDA-approved treatments leading to symptom management. Leigh syndrome (LS) is a pediatric mitochondrial disorder that affects the central nervous system during early development and causes death in infancy. Since there are no adequate models for understanding the rapid fatality associated with LS, human-induced pluripotent stem cell (hiPSC) technology has been recognized as a useful approach to generate patient-specific stem cells for disease modeling and understanding the origins of the …

Cux1-Related Neurodevelopmental Disorder: Deep Insights Into Phenotype-Genotype Spectrum And Underlying Pathology, Henry Oppermann, Christina A Gurnett, Et Al.

2020-Current year OA Pubs

Heterozygous, pathogenic CUX1 variants are associated with global developmental delay or intellectual disability. This study delineates the clinical presentation in an extended cohort and investigates the molecular mechanism underlying the disorder in a Cux1

Targeted Proteomic Quantitation Of Nrf2 Signaling And Predictive Biomarkers In Hnscc, Nathan T Wamsley, Emily M Wilkerson, Kyle M Lapak, Robert W Sprung, Petra Erdmann Gilmore, Sophie P Gerndt, Ryan S Jackson, Randal C Paniello, Patrik Pipkorn, Sidharth V Puram, Jason T Rich, Reid R Townsend, José P Zevallos, Paul Zolkind, Dennis Goldfarb, Michael B Major, Et Al.

2020-Current year OA Pubs

The NFE2L2 (NRF2) oncogene and transcription factor drives a gene expression program that promotes cancer progression, metabolic reprogramming, immune evasion, and chemoradiation resistance. Patient stratification by NRF2 activity may guide treatment decisions to improve outcome. Here, we developed a mass spectrometry-based targeted proteomics assay based on internal standard-triggered parallel reaction monitoring to quantify 69 NRF2 pathway components and targets, as well as 21 proteins of broad clinical significance in head and neck squamous cell carcinoma (HNSCC). We improved an existing internal standard-triggered parallel reaction monitoring acquisition algorithm, called SureQuant, to increase throughput, sensitivity, and precision. Testing the optimized platform on …

Background Acoustics In Terrestrial Ecology, Clinton D. Francis, Jennifer N. Phillips, Jesse R. Barber

Biology Faculty Publications and Presentations

The way in which terrestrial organisms use the acoustic realm is fundamentally important and shapes behavior, populations, and communities, but how background acoustics, or noise, influence the patterns and processes in ecology is still relatively understudied. In this review, we summarize how background acoustics have traditionally been studied from the signaling perspective, discuss what is known from a receiver's perspective, and explore what is known about population- and community-level responses to noise. We suggest that there are major gaps linking animal physiology and behavior in noise to fitness; that there is a limited understanding of variation in hearing within and …

Biocrusts Indicators Of Livestock Grazing Effects On Soil Stability In Sagebrush Steppe: A Case Study From A Long-Term Experiment In The Northern Great Basin, Stella M. Copeland, Lea A. Condon, Roger Rosentreter, Jesse E. D. Miller, Maya Kahn-Abrams

Biology Faculty Publications and Presentations

Biocrusts are sensitive to changes in livestock grazing intensity in arid rangelands and may be useful indicators of ecosystem functions, particularly soil properties like soil stability, which may suggest the potential for soil erosion. We compared biocrust community composition and surface soil stability in a big sagebrush (Artemisia tridentata) steppe rangeland in the northwestern Great Basin in several paired sites, with or without long-term cattle grazing exclusion, and similar soils (mostly sandy loams), climate, and vegetation composition. We found that livestock grazing was associated with both lower surface soil stability and cover of several biocrust morphogroups, especially lichens, compared with …

Effect Of Sampling Method On Detection Of The Equine Uterine Microbiome During Estrus, B. A. Heil, M. Van Heule, S. K. Thompson, T. A. Kearns, E. L. Oberhaus, G. King, P. Daels, P. Dini, J. L. Sones

Faculty Publications

Bacterial endometritis is among the most common causes of subfertility in mares. It has a major economic impact on the equine breeding industry. The sensitivity of detecting uterine microbes using culture-based methods, irrespective of the sample collection method, double-guarded endometrial swab, endometrial biopsy, or uterine low-volume lavage (LVL), is low. Therefore, equine bacterial endometritis often goes undiagnosed. Sixteen individual mares were enrolled, and an endometrial sample was obtained using each method from all mares. After trimming, quality control and decontamination, 3824 amplicon sequence variants were detected in the dataset. We found using 16S rRNA sequencing that the equine uterus harbors …

Experimental Studies On The Operation Of Agricultural Crops Mowing Unit With Simultaneous Chopping And Incorporation Of Stubble Into The Soil, Volodymyr Nadykto, Sergey Kiurchev, Tatiana Chorna, Taras Hutsol, Szymon Głowacki, Anatoliy Rud, Alona Shevtsova, Igor Ryabov, Katarzyna Szwedziak

Sociology Faculty Publications

For harvesting crops, one-phase and two-phase methods are most often used. When implementing the second one, mounted and trailed units are used. The latter is becoming less and less used due to the problems with movement stability in the horizontal plane because of the asymmetric layout. A stubble background, which is susceptible to solar and wind influences, is formed as a consequence of application of the mounted harvesting unit, As a result, the field’s soil in the inter-swath space intensively loses moisture. A harvesting unit based on a tractor with rear steerable wheels has been designed to eliminate this shortcoming. …

Utilizing Monobody Technology To Investigate Ras Signaling Mechanisms And Potential Therapeutic Vulnerabilities, Michael Whaby

MUSC Theses and Dissertations

The RAS family of small GTPases, consisting of HRAS, KRAS and NRAS, represent the most frequently mutated oncogenes in human cancers. As such, targeting RAS has remained at the forefront of efforts for cancer therapeutic development. For decades, these efforts were largely unsuccessful. However, recent seminal discoveries led to the development of the first clinically-approved inhibitors of a common oncogenic RAS mutant. While a major milestone, most oncogenic RAS mutants remain without inhibitors. One emerging theme over the past several years has been the notion that RAS multimerization plays a critical role in RAS function and that this process may …

Development And Application Of Sem/Eds In Biological, Biomedical & Nanotechnological Research, Aniruddha Acharya

Faculty Publications - Biological Sciences

This comprehensive review discusses the development of scanning electron microscopy and the application of this technology in different fields such as biology, nanobiotechnology and biomedical science. Besides being a tool for high resolution imaging of surface or topography, the technology is coupled with analytical techniques such as energy dispersive spectroscopy for elemental mapping. Since the commercialization of the technology, it has developed manifold and currently very high-resolution nano scale imaging is possible by this technology. The development of FIB-SEM has allowed three-dimensional imaging of materials while the development of cryostage allows imaging of hydrated biological samples. Though variable pressure or …

Social Sanguinity: Communal Ties And The Pursuit Of Political Power In Saga Age Iceland, Sam Fearnside

History Theses

Prior to the Norwegian annexation, Icelandic society lacked a government with an executive branch. As a result their legal system evolved in a highly privatized fashion in which individuals and their families were expected to self-advocate in order to assert and defend their rights and interests. Icelandic law also privatized the prosecution of criminals and enforcement of legal verdicts. Such a legal system required individual Icelanders to forge and maintain an array of social connections in order to protect themselves from both legal actions brought against them and the violent feuds that resulted due to the system’s short comings.

This …

Novel Castor Oil/Water/Ethanol Pickering Emulsions Stabilized By Magnetic Nanoparticles And Magnetically Controllable Demulsification, Mohammad J. Hasan, Peng Chen, Neithan Dominick, Erick S. Vasquez, Esteban E. Ureña-Benavides

Chemical and Materials Engineering Faculty Publications

A novel castor oil/water/ethanol Pickering emulsion, stabilized by magnetic nanoparticles (NPs), was developed to allow on-demand demulsification by an external magnetic field for the extraction of ethanol from aqueous solution using the castor oil. The emulsion was stabilized by Fe3O4-coated cellulose nanocrystals (CNC@Fe3O4) and lignin-coated Fe3O4 NPs (lignin@Fe3O4). The stability of the emulsions was investigated at various castor oil to ethanol-water ratios (50/50 and 70/30), various NP concentrations, and ethanol concentrations in the aqueous phase. The magnetically controlled demulsification ability of the emulsions was investigated by using a permanent magnet. The results showed that the 70/30 emulsions were more stable …

Cross-Watershed Horizontal Ecological Compensation System : Comparative Examples From China And Germany, Yanyao Yang

SOC 605 Comparative Social Policy Research Project - Student Works

In recent years, horizontal ecological compensation in the Yangtze River basin is a new policy for protecting the ecology. But it still has shortcomings in policy implementation. In contrast, Germany, which reached an ecological compensation agreement with the Czech Republic on the Elbe River as early as the 1990s, is a worthy reference object for China. Therefore, this study systematically reviews the literature on horizontal ecological compensation in China and abroad. It finds that the relevant literature on ecological compensation policies lacks composite research using research methods that combine qualitative and quantitative analysis. So, this study uses social network analysis …

A Haplotype-Resolved Chromosome-Scale Genome For Quercus Rubra L. Provides Insights Into The Genetics Of Adaptive Traits For Red Oak Species, Beant Kapoor, Jerry Jenkins, Jeremy Schmutz, Tatyana Zhebentyayeva, Carsten Kulheim, Mark Coggeshall, Chris Heim, Jesse R. Lasky, Laura Leites, Nurul Islam-Faridi, Jeanne Romero-Severson, Victoria L. Deleo, Sarah M. Lucas, Desanka Lazic, Oliver Gailing, John Carlson, Margaret Staton

Michigan Tech Publications

Northern red oak (Quercus rubra L.) is an ecologically and economically important forest tree native to North America. We present a chromosome-scale genome of Q. rubra generated by the combination of PacBio sequences and chromatin conformation capture (Hi-C) scaffolding. This is the first reference genome from the red oak clade (section Lobatae). The Q. rubra assembly spans 739 Mb with 95.27% of the genome in 12 chromosomes and 33,333 protein-coding genes. Comparisons to the genomes of Quercus lobata and Quercus mongolica revealed high collinearity, with intrachromosomal structural variants present. Orthologous gene family analysis with other tree species revealed that gene …

Convolutional Neural Network-Based Gene Prediction Using Buffalograss As A Model System, Michael Morikone

Complex Biosystems Program: Dissertations and Student Research

The task of gene prediction has been largely stagnant in algorithmic improvements compared to when algorithms were first developed for predicting genes thirty years ago. Rather than iteratively improving the underlying algorithms in gene prediction tools by utilizing better performing models, most current approaches update existing tools through incorporating increasing amounts of extrinsic data to improve gene prediction performance. The traditional method of predicting genes is done using Hidden Markov Models (HMMs). These HMMs are constrained by having strict assumptions made about the independence of genes that do not always hold true. To address this, a Convolutional Neural Network (CNN) …

Continuous Time Recurrent Network For Human Activity Detection, Abdallah Al Zubi

Durham School of Architectural Engineering and Construction: Dissertations, Theses, and Student Research

Human activity detection is crucial to personalize the control of the building environment. For example, understanding certain human activities (e.g., walking, sitting, etc.) for an occupant in a building helps provide the proper thermal comfort control. However, these applications require large-scale neural networks that are challenging to implement and train.

In this thesis, we implemented a continuous-time recurrent neural network implementation (CTRNN) network that can solve real-time human activity detection with a smaller-size network. The CTRNN uses differential equations with a time constant to describe the neuron equations. It was implemented and trained for the first time using TensorFlow. Specifically, …

Cell Surface And Plasma Biomarkers Of Kaposi Sarcoma, Sara R. Privatt

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

Kaposi sarcoma-associated herpesvirus is the etiological agent of several pathologies including Kaposi sarcoma, primary effusion lymphoma, and multicentric Castleman’s disease. Here, we investigated both the tumor microenvironment (TME) in KS lesions as well as plasma from KSHV-infected individuals and how metabolic dysfunction and dysregulated cytokines might have a systemic effect on KS tumorigenesis. Based on previously published KS tumor transcriptomics, one aspect of our investigation involved characterizing cell surface glycoproteins with potential to serve as therapeutic targets against KSHV-infected cells or KS tumors or as biomarkers for disease. Expression patterns of such markers may also suggest the cellular origin of …

Characterization Of Adipocyte Mechanical Properties And Stretch Control Of Mechanosignaling In Adipocytes, Tasneem Bouzid

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

Obesity has reached global epidemic levels in recent decades and is the leading risk factor for type-2 diabetes (T2D). Adipose tissue behaves as a link between obesity and T2D, with dysfunctional extracellular matrix (ECM) remodeling, adipokine secretion and lipid metabolism leading to insulin resistance. The extracellular mechanophysical milieus is understood to regulate adipocyte differentiation and function through activation of mechanosensory machinery and related pathways. Therefore, exploring the adipocytic response to mechanical loading can provide great pathophysiological insight into obesity and T2D.

Adipose tissue is exposed to various compound forces due to weight-bearing and movement, and adipocyte stiffness influences stress distribution …

Attitudes Towards Public Basic Needs Programs: An Analysis Of Question Order Effect, Period And Cohort Changes, And Differences Across Religious Traditions, Jamy Rentschler

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

This dissertation examines public opinions towards public basic needs programs (PBNPs), focusing specifically on differences in attitudes towards spending on assistance to the poor (ATP) and welfare. To do this, I use two different approaches, one focusing on survey methodology and the other looking at social change across time and religious tradition. The first research question addresses potential survey question order effects based upon which question came first, ATP or welfare, and examines how other federal spending priorities may impact opinions towards welfare. I do find question order effects, some of which vary based on the respondent’s race, but the …

Convolutional Neural Network-Based Gene Prediction Using Buffalograss As A Model System, Michael Morikone

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

The task of gene prediction has been largely stagnant in algorithmic improvements compared to when algorithms were first developed for predicting genes thirty years ago. Rather than iteratively improving the underlying algorithms in gene prediction tools by utilizing better performing models, most current approaches update existing tools through incorporating increasing amounts of extrinsic data to improve gene prediction performance. The traditional method of predicting genes is done using Hidden Markov Models (HMMs). These HMMs are constrained by having strict assumptions made about the independence of genes that do not always hold true. To address this, a Convolutional Neural Network (CNN) …

Management Of Atrazine, Glyphosate, And Als-Inhibiting Herbicide-Resistant Palmer Amaranth (Amaranthus Palmeri S. Watson) In Herbicide-Resistant And Food Grade White Field Corn, Ramandeep Kaur

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

A recent survey reported that Palmer amaranth (Amaranthus palmeri S. Watson) is the number one most difficult to control weed in Nebraska. A survey reported that about 6 million acres in Nebraska are infested with at least one glyphosate-resistant weed. Confirmation and widespread occurrence of atrazine, glyphosate, and ALS-inhibitor-resistant Palmer amaranth in Nebraska is one of biggest concerns for corn producers.

Nebraska, the Cornhusker State, is one of the leading corn producing states with the production of corn on about 9 to 10 million acres annually; and it ranks 1st in food grade white corn and 3rd in field …

Game-Theoretic Approaches To Optimal Resource Allocation And Defense Strategies In Herbaceous Plants, Molly R. Creagar

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

Empirical evidence suggests that the attractiveness of a plant to herbivores can be affected by the investment in defense by neighboring plants, as well as investment in defense by the focal plant. Thus, allocation to defense may not only be influenced by the frequency and intensity of herbivory but also by defense strategies employed by other plants in the environment. We incorporate a neighborhood defense effect by applying spatial evolutionary game theory to optimal resource allocation in plants where cooperators are plants investing in defense and defectors are plants that do not. We use a stochastic dynamic programming model, along …

Uv Dynamics Of Different Ring Molecules Studied By Ultrafast Electron Diffraction, Sajib Kumar Saha

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

Understanding natural light-induced phenomena requires a direct viewing of atomic motion during structural evolution, which, in turn, facilitates controlling and manipulating these light-induced processes. Ultrafast Electron Diffraction (UED) is a structure-sensitive technique that can probe electronic and nuclear dynamics at sub-angstrom spatial and femtosecond time scales. UED has become a vital tool for studying photo-induced molecular dynamics and underlying science. Organic ring systems are prevalent in biology, materials, and pharmaceuticals. Their synthesis and transformation are fundamental in synthetic chemistry, influencing various fields. We used UV photons to photo-excite different cyclic molecules and investigated their photo-dynamics using gas phase UED. The …

The Development And Evolution Of The Soil Health Nutrient Tool (Aka Haney Test) After Ten Years Of Implementation In A Commercial Agricultural Laboratory, Lance Michael Gunderson

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

The growing focus on soil health and regenerative agriculture has brought about the need for new integrated approaches for the analysis of soil. Prior, commercial agricultural laboratories relied on methods to measure chemical properties of the soil, such as pH and nutrients. The Soil Health Nutrient Tool (aka Haney Test) developed by Dr. Rick Haney (United States Department of Agriculture, Agricultural Research Service (USDA-ARS), Blackland Research and Extension Station, Temple, Texas) integrates chemical and biological properties to provide a more holistic understanding of soil fertility management. Following adoption by commercial laboratories in 2013, criticisms regarding variability in measurements and lack …

Precipitation And Greenness In Pastoral Lands Of East Turkana, Kenya, Paul Akpejeluh

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

Pastoralism has long supported livelihoods and provided essential ecosystem services in landscapes of East Africa. Vegetation productivity is central to the functioning of pastoral systems but may be affected by changes in climate and landuse. Vegetation monitoring is important for understanding the effects of global change in pastoral lands; however, it can be time and resource intensive. Remote sensing provides opportunities for efficient multi-scale monitoring of vegetation and climatic drivers. In this thesis, I explore the utility of satellite and UAV remote sensing for monitoring vegetation and precipitation trends and relationships in the East of Lake Turkana Region of northern …

Connecting The Nebraska Water Quality Index To The Aquatic Microbial Community Of The North Platte River Basin, Nebraska, Paula R. Guastello

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

The Nebraska Water Quality Index, under development by the Nebraska Department of Environment and Energy, summarizes in a single value eight environmental parameters that have been monitored in Nebraska for nearly 20 years. Water quality parameters including those used in the Nebraska Water Quality Index have been shown in previous studies to impact bacterial growth. As such, this index has the potential to correlate with the freshwater microbial community. Here, I relate the Nebraska Water Quality Index to microbial community composition and structure using 16S rRNA gene amplicon sequence data collected from the North Platte River Basin, Nebraska. This index …

The Role Of Glacier Erosion In Riverine Particulate Organic Carbon Export, Megan Behnke, Jason B. Fellman, Sonia Nagorski, Robert G. Spencer, Eran Hood

Faculty, Staff, and Students

Biospheric particulate organic carbon (POCbio) burial and rock petrogenic particulate organic carbon (POCpetro) oxidation are opposing long-term controls on the global carbon cycle, sequestering and releasing carbon, respectively. Here, we examine how watershed glacierization impacts the POC source by assessing the concentration and isotopic composition (δ13C and Δ14C) of POC exported from four watersheds with 0%–49% glacier coverage across a melt season in Southeast Alaska. We used two mixing models (age-weight percent and dual carbon isotope) to calculate concentrations of POCbio and POCpetro within the bulk POC pool. The fraction POCpetro contribution was highest in the heavily glacierized watershed (age-weight …