Digital Commons Network^™

Detecting Differentially Co-Expressed Gene Modules Via The Edge-Count Test, Anne Gratius Lin

Graduate Theses and Dissertations

Background

Gene expression profiling by microarray has been used to uncover molecular variations in many different diseases. Complementary to conventional differential expression analysis, differential co-expression analysis can identify gene markers from the systematic and granular level. There are three aspects for differential co-expression network analysis, including the network global topological comparison, differential co-expression cluster identification, and differential co-expressed genes and gene pair identification. To date, most of the methods available still rely on Pearson’s correlation coefficient despite its nonlinear insensitivity.

Results

Here we present an approach that is robust to nonlinearity by using the edge-count test for differential co-expression analysis. …

Natural Variation In Yeast Stress Signaling Reveals Multiple Paths To Similar Phenotypes, Amanda N. Scholes

Graduate Theses and Dissertations

Natural environments are dynamic, and organisms must sense and respond to changing conditions. One common way organisms deal with stressful environments is through gene expression changes, allowing for stress acclimation and resistance. Variation in stress sensing and signaling can potentially play a large role in how individuals with different genetic backgrounds are more or less resilient to stress. However, the mechanisms underlying how gene expression variation affects organismal fitness is often obscure.

To understand connections between gene expression variation and stress defense phenotypes, we have been exploiting natural variation in Saccharomyces cerevisiae stress responses using a unique phenotype called acquired …

Genetic Relationships Using Mitochondrial Versus Nuclear Markers: Is The Catfish Rag1 Gene Suitable For Species Differentiation In The Family Pangasiidae?, Huong Thanh Hoang

Graduate Theses and Dissertations

The Mekong River located in Southeast Asia is a global “hotspot” for aquatic biodiversity. It includes an extensive variety of fish species second only to the Amazon River in South America. Recent studies have revealed the impacts of anthropogenic and climate factors on this river system. Such impacts can result in the formation of barriers, which divide a species population and impede gene flow between separated sub-populations. Barriers influence evolutionary trajectories resulting in the generation of geographic variants or subspecies from an ancestral population. Catfish (Teleostei: Siluriformes) are a key species of the Mekong River ecosystem and are an essential …

Analyzing Multigene Stacking And Genome Editing Strategies In Rice, Bhuvan Pathak

Graduate Theses and Dissertations

Crop improvement through biotechnology is an integrated effort, incorporating multiple approaches like integration of genes, editing of native genes, and removal of selection marker genes. Before streamlining the protocols, the efficiency and feasibility of the individual approach and their components must be tested. This study evaluated following approaches: 1) stacking an array of genes into a single locus by site-specific integration via Cre-lox recombination in rice, 2) determining the efficiency of I-SceI and the CCR5-ZFN in the targeted excisions of gene fragments in rice and Arabidopsis, and 3) determining the efficiency of CRISPR/Cas9 in generating targeted mutations for genome editing …

Global Acetylation Dynamics In The Heat Shock Response Of Saccharomyces Cerevisiae, Rebecca E. Hardman

Graduate Theses and Dissertations

All organisms face a constant barrage of environmental stresses. Single-cell organisms such as Saccharomyces cerevisiae, or common Baker’s yeast, must rely solely on cellular responses in order to survive. This response must occur in a rapid and highly coordinated manner to quickly inhibit all unnecessary processes and shuttle all available resources to those necessary for survival. One method that cells utilize for rapid protein regulation is the use of post-translational modifications. Enzymes within the cell add or remove a variety of chemical modifications, thus altering the local chemical environment of a protein. This creates a conformational change in the protein …

Genetic Resistance To The Downy Mildew Pathogen And Mapping The Rpf Resistance Loci In Spinach, Gehendra Bhattarai

Graduate Theses and Dissertations

Spinach (Spinacia oleracea) is an important cool-season leafy vegetable crop in the United States (US). Downy mildew, caused by the obligate oomycete Peronospora effusa, is the most economically important disease of spinach. A total of 17 races of P. effusa have been reported on spinach, and many of these races (>10) have emerged in the last three decades. The new races of the pathogen are continually overcoming the genetic resistances used in the newly released cultivars.

A detached leaf inoculation assay was evaluated, standardized, and validated as a new method to differentiate resistant and susceptible spinach genotypes. Disease response …

Theoretical Investigations Of The Electronic, Magnetic, And Thermoelectric Properties Of Transition-Metal Based Compounds, Haleoot Edaan Raad

Graduate Theses and Dissertations

The electronic, magnetic, and thermoelectric properties of transition-metal based compounds were investigated by using the density functional theory and Boltzmann transport formalism. It was found that the Co-based Heusler compounds and InSe monochalcogenide are among the materials that may be used for future thermoelectric devices. Furthermore, the investigation showed that the quaternary Heusler compounds, such as, CoFeYGe, where Y is Ti or Cr, are half-metallic ferromagnetic materials with full electron spin polarization. The lattice thermal conductivity (κL) was found to decrease for these alloys as the temperature increases. The present investigation indicated that the phonon optical modes have a major …

Recovered Images: Medieval Echoes In C. S. Lewis’S Space Trilogy, Nathan Earl Houston Fayard

Graduate Theses and Dissertations

C. S. Lewis has begun to garner more scholarly attention in the last few decades, but his first novels, his science fiction or Space trilogy, continue to be largely ignored by academia. Yet, these three novels are deserving of more serious study, as they are pioneering works of literary science fiction, and even more surprisingly, of literary medievalism. Though long derided as mere reactionary attacks on Modernism and science, when properly understood, these strange and wonderful tales actually reveal the complexity and nuance of Lewis’s response to his times. In them, the Inkling author creates a unique combination of the …

Tax Indemnification And The Association Between Unrecognized Tax Benefit Reserves And Future Tax Cash Outflows, Patrick Lee Hopkins

Graduate Theses and Dissertations

Tax indemnification transfers from a firm to an outside party the risk of potential cash settlements associated with uncertain tax positions taken in prior years. The current accounting treatment of tax indemnification under Accounting Standards Codification (ASC) 805 and the required disclosures for uncertain tax positions under ASC 740 provide little or no information regarding this risk transfer in the financial statements or notes. I examine merger and acquisition (M&A) contracts from 2008 through 2013 and find that tax indemnification is commonly present in M&A transactions. I then provide evidence that the association between current uncertain tax benefit reserves and …

Sentiment Analysis, Quantification, And Shift Detection, Kevin Labille

Graduate Theses and Dissertations

This dissertation focuses on event detection within streams of Tweets based on sentiment quantification. Sentiment quantification extends sentiment analysis, the analysis of the sentiment of individual documents, to analyze the sentiment of an aggregated collection of documents. Although the former has been widely researched, the latter has drawn less attention but offers greater potential to enhance current business intelligence systems. Indeed, knowing the proportion of positive and negative Tweets is much more valuable than knowing which individual Tweets are positive or negative. We also extend our sentiment quantification research to analyze the evolution of sentiment over time to automatically detect …

The Effects Of Foot And Udder Scoring On Cow And Calf Performance, Clayton Lee Mcguire

Graduate Theses and Dissertations

Foot soundness and udder conformation are essential for longevity in beef cattle. The objective of this study was to investigate the effects of foot angle (FA), claw set (CS), teat size (TS) and udder suspension (US) scores on cowherd performance. Data were analyzed for 1,685 observations on Angus-based cows over a four-year period. At weaning FA, CS, TS, and US were evaluated. Scores are based on nine-point scales. A score of one indicates straight pasterns, divergent toes, enlarged bottle shaped teats, and absence of a median suspensory ligament; nine indicates weak pasterns, curled toes, small symmetrical teats, and a tight …

Coccidiosis Vaccination And Nutrient Utilization In Broiler Chickens, Alyson Elaine Gautier

Graduate Theses and Dissertations

Four experiments were conducted to evaluate the interrelationships among coccidiosis vaccination and nutrient utilization in floor-reared broiler chickens. Experiment 1 longitudinally compared the effects of coccidiosis vaccination and a chemical coccidiostat on broiler performance, nutrient digestibility, and intestinal morphology. Coccidiosis vaccination had no significant impact on morphology, overall body weight gain and feed intake of vaccinated birds, although vaccination impaired overall FCR. Vaccination elicited a transient reduction in digestibility of energy and nutrients, particularly for lipids, but vaccinated birds were able to recover from these reductions by 20 d. Experiment 2 assessed the impact of vaccination in digestibility of different …

The Anonymous Web In Adichie’S Americanah, Michelle Jude Gibeault

Graduate Theses and Dissertations

Adichie’s Americanah is a novel that elevates anonymous blogging into black cultural performance. The novel follows a young Nigerian, Ifemelu, who arrives in the United States on a student visa and depicts her stressful confrontation with racism in post-slavery America. Through beginning a blog, Ifemelu voices her experiences as a black woman and immigrant in ways that renew the concerns of James Baldwin, an author whom she studies closely. Like Baldwin, her style blends humor and techniques of persuasion that trace to traditional oral folklore. Ifemelu’s success rests partly on Adichie’s construction of her as a character of good ethos, …

Observations Of A Multi-Component Intervention For Elementary Students With Emotional Behavioral Disorder After Self-Efficacy Coaching, Anna Kristen Bensinger

Graduate Theses and Dissertations

Students with Emotional and Behavioral Disorders (EBD) experience more negative student outcomes compared to other special education disability categories, specifically, higher dropout rates, less access to higher education and incarceration. Mathematically, 73% of students with EBD achieve below the 50th percentile on standardized tests (Wagner, Kutash, Duchnowski, Epstein, & Sumi, 2005). This study focused on the exploration of a multi-component mathematics and behavior intervention targeting student self-efficacy for productive learning behaviors in the general education mathematics classroom setting for elementary students with EBD. Participants for this study were students from two 4th grade classrooms, who have been identified with co-occurring …

Special Relationships: Anglo-American Latin America Policy And The Redefining Of National Security, 1969-1982, Benjamin Jared Pack

Graduate Theses and Dissertations

From 1969–82, the United States and Great Britain redefined national security in a distinctive way, separating the notion of national security from its traditional foundations in realist thought. The way the two powers come to define national security was the result of more than a century of historical interaction with Latin America and their own historical experience with ideology, imperialism, and colonialism. As such, the way the United States and Great Britain perceived their respective special relationships influenced the way they chose to intervene in matters of national security, particularly in Latin America’s Southern Cone countries of Chile and Argentina. …

Investigating Growth Performance And Intestinal Barrier Integrity In Heat-Stressed Modern Broilers And Their Ancestor Jungle Fowl, Travis Tabler

Graduate Theses and Dissertations

Heat stress (HS) has a negative effect on poultry production sustainability due to its adverse consequence on bird welfare, health, growth, and mortality. Although modern broilers have greater gut mass and higher energy use efficiency than unselected birds, they are more vulnerable to HS that induces “leaky gut syndrome,” or increased intestinal permeability. The aim of the current study was to determine the effect of HS on growth performance and gut barrier integrity in three modern broiler lines and their ancestor the Jungle Fowl. Four chicken populations including Giant Jungle Fowl (JF), Athens Canadian Random Bred (ACRB), 1995 Arkansas Random …

Design And Optimization Of A High Power Density Silicon Carbide Traction Inverter, Tyler Adamson

Graduate Theses and Dissertations

This project was initiated with the goal of demonstrating a 3-phase silicon carbide based 150-kW 25 kW/L DC-AC power conversion unit capable of operation with coolant temperatures up to 90°C. The project goals were met and exceeded by first analyzing the established inverter topologies to find which one would yield the highest power density while still meeting electrical performance needs in the 150-kW range. Following topology selection, the smallest silicon carbide power module that met the electrical requirements of the system was found through experimental testing and simulation. After a power module selection was finalized, a DC link capacitor bank …

Development Of A Comsol Microdialysis Model, Towards Creation Of Microdialysis On A Chip With Improved Geometries And Recovery, Patrick Pysz

Graduate Theses and Dissertations

Microdialysis (µD) sampling is a diffusion-limited sampling method that has been widely used in different biomedical fields for greater than 35 years. Device calibration for in vivo studies is difficult for current non-steady state analytes of interest correlated with both inflammatory response and microbial signaling molecules (QS); which exist in low ng/mL to pg/mL with molecular weights over a wide range of 170 Da to 70 kDa. The primary performance metric, relative recovery (RR), relating the collected sample to the extracellular space concentration varies from 10% to 60% per analyte even under controlled bench-top conditions. Innovations in microdialysis device design …

Development Of A Multimode Instrument For Remote Measurements Of Unsaturated Soil Properties, Sean Elliott Salazar

Graduate Theses and Dissertations

The hydromechanical behavior of soil is governed by parameters that include the moisture content, soil matric potential, texture, and the mineralogical composition of the soil. Remote characterization of these and other key properties of the soil offers advantages over conventional in situ or laboratory-based measurements: information may be acquired rapidly over large, or inaccessible areas; samples do not need to be collected; and the measurements are non-destructive. A field-deployable, ground-based remote sensor, designated the Soil Observation Laser Absorption Spectrometer (SOLAS), was developed to infer parameters of bare soils and other natural surfaces over intermediate (100 m) and long (1,000 m) …

Toolpath Planning Methodology For Multi-Gantry Fused Filament Fabrication 3d Printing, Hieu Trung Bui

Graduate Theses and Dissertations

Additive manufacturing (AM) has revolutionized the way industries manufacture and prototype products. Fused filament fabrication (FFF) is one of the most popular processes in AM as it is inexpensive, requires low maintenance, and has high material utilization. However, the biggest drawback that prevents FFF printing from being widely implemented in large-scale production is the cycle time. The most practical approach is to allow multiple collaborating printheads to work simultaneously on different parts of the same object. However, little research has been introduced to support the aforementioned approach. Hence a new toolpath planning methodology is proposed in this paper. The objectives …

The Archaeology Of Mississippian Vulnerability And Resilience In The New Madrid Seismic Zone, Michelle Megan Rathgaber

Graduate Theses and Dissertations

This work examines the vulnerability and resilience of Mississippian people in the Central Mississippi Valley to the large-scale New Madrid seismic zone earthquakes of the late15th to early 16th century. This is done using the theory of eventful archaeology/anthropology to look at cultural materials both before and after an event (such as an earthquake and sand blows) to look for evidence of changes to the schema and resources on which a society relies. If changes are present, the event can be labeled as such, if there are no changes, it means that the society affected did not see the event …

Spatio-Temporal Analysis Of Tree Ring Chronology And Precipitation, Ruizhe Yin

Graduate Theses and Dissertations

Tree ring chronology data is known to reflect regional climate due to the strong impact of rainfall and temperature. Therefore, tree ring data can be used to reconstruct historical climate in order to understand how climate changed in the past and make prediction about the future behavior of the climate. For simplicity, this research only considers the influence of precipitation on tree ring growth within the New England area. A total of 94 measurement sites are used to record tree ring width over 881 years and corresponding precipitation data are given at some locations for 121 years. We developed a …

Blackting: The Inseparable Act Of Being Black And Acting: For The Magical Negro, Austin Dean Ashford

Graduate Theses and Dissertations

I am honored to present my Thesis for my M.F.A. in Theatre, in the form of a multidimensional project, drawing inspiration from the structure of Moby Dick by Herman Melville. As an undergraduate, the structure of Moby Dick intrigued me as it defies the form we call “a novel.” The book includes traditional prose, an entire play, verses of poetry, and even an essay. The structure of Moby Dick further influenced my love for Speech and Debate, especially around the event of Program Oral Interpretation (POI). POI places multiple genres of literature in conversation with each other and centers them …

The Effect Of Prescribed Burning On Wood-Decay Fungi In The Forests Of Northwest Arkansas, Nawaf Ibrahim Alshammari

Graduate Theses and Dissertations

Prescribed burning is defined as the process of the planned application of fire to a predetermined area under specific environmental conditions in order to achieve a desired outcome such as land management. This project used both morphological and molecular methods to identify and characterize the wood-decay fungi associated with the forests of northwest Arkansas—Pea Ridge National Military Park, Devil’s Den State Park, and the Buffalo National River—through frequent visits made between February 2018 and February 2019. In addition, in order to assess the effects of prescribed burning, incubation chambers were used to compare the growth of fungi from both unburned …

Investigation Of Microbiota In Health And Disease Of Poultry, Bishnu Adhikari

Graduate Theses and Dissertations

The microbiotas play vital roles in health and diseases of both humans and animals. 16S rRNA genes sequence analysis is one of the most popular and commonly used methods in the analysis of microbiotas associated with hosts. In this dissertation, the microbiotas of chickens (broilers, breeders, and layers) and turkeys were evaluated by 16S rRNA gene sequencing. Characterization of the culturable subpopulations of Lactobacillus in the chicken gut can serve as a valuable resource for probiotic development. In Chapter 2, Lactobacillus subpopulations recovered on MRS from chicken gut were defined comprehensively for the first time using 16S rRNA gene profiling, …

The Paleozoic Sedimentary Rocks Of The Ouachita Mountains And Their Genetic Relationship To The Mississippi Valley-Type Mineralization In The Southern Ozark Region: Insights From Radiogenic Pb Isotopes And Trace Elements Studies, Christophe Wakamya Simbo

Graduate Theses and Dissertations

Cluster of Pb and/or Zn deposits of the well-known Tri-State and Northern Arkansas Mississippi Valley Type (MVT) districts located north of the Arkoma basin and the Ouachita fold-thrust belt in north America are genetically connected to the Pennsylvanian-Permian Ouachita orogeny which triggered a South-North topographic gradient flow of basinal brines, leaching metal rich sediments en route. The objective of the research is twofold. First, to ascertain whether the organic-rich shales and sandstones from the study area provided metals during the mineralization event, which was coeval with the Ouachita orogeny. Second, to assess the depositional environment of the potential source rocks, …

A Study Of Protein And Peptide-Directed Nanoparticle Synthesis For Catalytic Materials, Abdollah Mosleh

Graduate Theses and Dissertations

Nanoparticles have received much attentions due to their unique properties that makes them suitable candidates for a broad range of applications. As the size of particles decreases, their surface area-to-volume ratio would increase which is the main cause of much attention. In addition to the size, their morphologies and compositions may also play important roles for defining unique properties. Nanoparticle synthesis include both bottom-up and top-down strategies. To control the process of inorganic nanoparticles synthesis one could follow the bottom-up approach to have atom-level control over their compositions, morphologies, phases, and sizes which is the subject of this work. Due …

The Disk Structure Of Late Type Galaxies: Determining The Black Hole Mass Function Of Low Surface Brightness Galaxies Through Logarithmic Spiral Arm Pitch Angle Measurement, Michael S. Fusco

Graduate Theses and Dissertations

This dissertation pertains to the geometric structure of late type (spiral) galaxies, specifically on the relation between the logarithmic spiral pitch angle of the galactic spiral arms with other properties of the galaxy, such as central Supermassive Black Hole (SMBH) mass. Our work continues a study of the Black Hole Mass Function (BHMF) in local galaxies by recording the pitch angles of spiral galaxies with lower surface brightness than were previously included. We also conduct a case study on the structure of an interestingly shaped galaxy, UGC 4599. Previous studies on the topic of spiral arm pitch angles have measured …

Mothers Of Intention: Women In The Ku Klux Klan And Massive Resistance, 1954-1968, Michele R. Johnson

Graduate Theses and Dissertations

This dissertation examines women in the Massive Resistance movement and the Ku Klux Klan of the classic Civil Rights period, 1954-1968. Specifically, it illustrates the way in which these women used their assigned gender roles as women, and specifically as mothers, to further white supremacist goals. White women have been an integral part of white supremacy in the United States from the beginning, yet are rarely portrayed as such. White supremacist movements are most often viewed through a male lens and gender in white supremacy is most often focused on how white men perform gender within the movements. While that …

The Effects Of Hand Holding On Cancer Patients Level Of Anxiety: A Single-Case Study, West Loveland

Graduate Theses and Dissertations

The purpose of this dissertation was to explore how the anxiety levels of non-Hodgkin’s lymphoma patients receiving chemotherapy are affected while holding hands with a secure attachment. This study utilized three experimental single-case designs: participant one measured under a B-design, participant two measured under a B-A design, and participant three measured under an A-B design. Each participant’s anxiety was assessed during six chemotherapy treatments and one meeting with their primary oncologist to discuss the prognosis of their cancerous disease. Results visually indicate a greater effect on anxiety reduction during treatment when the intervention is utilized compared to only having a …