Digital Commons Network^™

Information Overload In Structured Data, Pinar Yanardag Delul

Open Access Dissertations

Information overload refers to the difficulty of making decisions caused by too much information. In this dissertation, we address information overload problem in two separate structured domains, namely, graphs and text.

Graph kernels have been proposed as an efficient and theoretically sound approach to compute graph similarity. They decompose graphs into certain sub-structures, such as subtrees, or subgraphs. However, existing graph kernels suffer from a few drawbacks. First, the dimension of the feature space associated with the kernel often grows exponentially as the complexity of sub-structures increase. One immediate consequence of this behavior is that small, non-informative, sub-structures occur more …

Immune Modulating Functions By Soypeptide Lunasin In Cancer Immunotherapy, Chun-Yu Tung

Open Access Dissertations

Chemotherapy is currently the mainstay of treatment for most cancer patients. Despite its efficacy in eliminating cancer cells, a high percentage of chemotherapy patients eventually relapse or suffer progression of the disease. Immunosurveillance is capable of recognizing and eliminating continuously arising transformed mutant cells, and thus cancer immunotherapy is one of the emerging therapeutic strategies that harnesses the power of the immune system to eradicate chemotherapy-resistant cancerous cells. However, the adverse side effects of chemotherapy impede the therapeutic effects of immunotherapy. Our previous studies demonstrate that lymphoma patients are refractory to clinical immunotherapy because of chemotherapy-induced immune dysfunction. In addition, …

Investigation Of Climate Variability And Climate Change Impacts On Corn Yield In The Eastern Corn Belt, Usa, Ruoyu Wang

Open Access Dissertations

The increasing demand for both food and biofuels requires more corn production at global scale. However, current corn yield is not able to meet bio-ethanol demand without jeopardizing food security or intensifying and expanding corn cultivation. An alternative solution is to utilize cellulose and hemi-cellulose from perennial grasses to fulfill the increasing demand for biofuel energy. A watershed level scenario analysis is often applied to figure out a sustainable way to strike the balance between food and fuel demands, and maintain environment integrity. However, a solid modeling application requires a clear understanding of crop responses under various climate stresses. This …

Affinity Cryo-Electron Microscopy: Methods Development And Applications, Guimei Yu

Open Access Dissertations

Single particle cryo-electron microscopy (cryo-EM) is an emerging powerful tool for structural studies of macromolecular assemblies. Although less concentrated and smaller amounts of samples are required for single particle cryo-EM compared to X-ray crystallography, it remains challenging to study specimens that are low-abundance, low-yield, or short-lived. The recent development of affinity grid techniques holds great promise to tackle these challenging samples by combining the sample purification and freezing on TEM grids steps in cryo-EM grid preparation into a single step, revolutionize the grid preparation of cryo-EM, and extend single particle cryo-EM to a routine structural biology tool to characterize structures …

Morality, Emotion, And Policy Making: Environmental Decision Making About Recycled Water, Julia Nicole Wester

Open Access Dissertations

Water scarcity and distribution of global water supplies are central to sustainable development, and are likely to be exacerbated by climate change and increasing urbanization. Water reuse has been proposed as a potential solution in some areas, as it is relatively cheaper than, and environmentally preferable to, alternatives such as desalination. In the industrialized world, a psychological aversion to recycled water has been well documented, characterized by reactions of disgust. In several cases, public opposition alone – often driven by messages framed in terms of disgust – has overturned plans to reuse water (i.e., California’s ‘toilet to tap’ campaign and …

The Utility Of Visually Nontraditional Scores In The Collegiate Voice Studio, Jennifer Voigt

Open Access Dissertations

The incorporation of learning science into vocal pedagogy has been a slow process with advancements in biology and physics dominating change in the field. However, recent research into learning styles and the processing of motor skills has revealed areas that could be enhanced within standard vocal teaching procedures. This study addresses the possibility of filling these gaps with the inclusion of visually nontraditional scores as a teaching tool. Specifically, this paper examines the utility of these scores within the collegiate voice studio. Visually nontraditional scores can contribute to a variety of learning needs and facilitate the acquisition of new technical …

The Role Of Gene Co-Option In The Evolution Of Sap-Feeding Insect Endosymbioses (Hemiptera: Sternorrhyncha), Rebecca Pate Duncan

Open Access Dissertations

Symbiosis, the tightly co-evolved partnership between different species, fundamentally influences the evolutionary trajectory of the interacting species. However, with the help of emerging genomic resources, the mechanisms by which symbiotic partners are integrated into a functional organism are only just beginning to be revealed. As a system in which to investigate the mechanisms of host/symbiont integration, sap-feeding insects, which rely on intracellular symbionts for nutrient provisioning, benefit from growing genomic resources and a solid foundation resulting from years of research on the pea aphid, Acyrthosiphon pisum. At the core of the relationship between A. pisum and its endosymbiont Buchnera aphidicola …

Applying World Music Pedagogy Techniques In The Intermediate String Orchestra: A Curriculum For The Study And Performance Of Latin American Folk Music, Sarah Josephine Gongaware

Open Access Dissertations

The purpose of this project was to create an intermediate string orchestra curriculum which develops string techniques through the study and performance of music from Cuba, Brazil, Mexico, Argentina, and Puerto Rico. This year-long curriculum encompasses five, country-specific units which can be interspersed throughout the academic year. Each unit includes musical arrangements which vary in style, genre, or originating region. These arrangements are accompanied by lesson plans which include cultural and historical background information, listening suggestions, learning objectives, learning sequence, and assessment strategies. The musical arrangements seek to develop intonation, left-hand positions, bow distribution, string crossings, bowing styles, and reinforce …

Out Of Time: Queer Temporalities In The Works Of Mina Loy, Djuna Barnes, And Langston Hughes, Lauren Riccelli Zwicky

Open Access Dissertations

Focusing on texts by Mina Loy, Djuna Barnes, and Langston Hughes, this dissertation examines the temporally situated body as a gendered, sexed, and racialized site of contestation through which dominant ontological modalities are challenged and ultimately destabilized. This transgressive politics takes the form of an interrogation of the heteronormative time-table that constructs, regulates, and disciplines subjective ontological progress. Specifically, these texts challenge the notion that legibility is produced through a triad of progressive temporal phases: the adolescent/early adult direction of sexuality towards the heterosexual union, normative marriage and family-based kinship bonds, and finally the transmission of cultural values, norms, and …

An Introduction To Akira Yuyama And His Confections With A Discussion Of Its Pedagogical Effectiveness, Dan Sato

Open Access Dissertations

This thesis introduces Akira Yuyama, a prolific living composer of highest distinction for his contributions to, most notably, repertoire dedicated to performances by young musicians. Confections: A Piano Sweet is arguably his most creative opus and this thesis includes an analysis of the work for its musical content as well as its effectiveness in the pedagogical context. Yuyama’s Confections has been a best-seller for over four decades in Japan and is one of the most popular set of pieces assigned to young piano students. Despite its popularity and uniqueness as programmatic music about food, the composition nor its creator have …

Multi-Scale Modeling And Assessment Of Malaria Risk In Northern South America, Temitope O. Alimi

Open Access Dissertations

With malaria control in Latin America firmly established in most countries and a growing number of these countries in the pre-elimination phase, malaria elimination appears feasible. A review of the literature indicates that malaria elimination in this region will be difficult without locally tailored strategies for vector control, which depend on more research on vector ecology, genetics and behavioral responses to environmental changes, such as those caused by land cover alterations, and human population movements. An essential way to bridge the knowledge gap and improve vector control is through risk mapping. Malaria risk maps based on statistical and knowledge-based modelling …

Synthesis And Optical Properties Of Novel Turn-On, Fluorescent Nuclear Stains With Live Cell Compatability, Demar R. G. Pitter

Open Access Dissertations

Flurorphores are an important class of compounds that are used as tools to better understand the processes that occur in cells. A subset of biologically useful fluorophores are nucleic acid binding probes. The inherent problems of many of the nucleic acid binding probes used on the market today is three-fold; (1) that the probes used produce some amount of autofluoresence from the biological sample due to the excitation wavelength needed for them to emit, (2) that most of the common probes lack cell membrane permeability, thus requiring fixation and pemeablization which limits the ability to observe dynamic processes of the …

Comparative Properties Of Stromal Cells And Their Role In Tissue Regeneration, Santhosh Kumar Sivajothi

Open Access Dissertations

In regenerative medicine, efforts should include utilization of the safest and least invasive methods with the goal of achieving optimal therapeutic outcome. Advancements in stem cell science have triggered the use of cells to cure various disease conditions. However the clinical success of such approaches depends largely on understanding the basic biology of the key players involved- stem cells, stromal cells and their microenvironment. Research shows that stromal cells have key roles in protecting and regulating tissue resident stem cells and maintaining tissue homeostasis. The objective of this dissertation work is to study the role of stromal cells in tissue …

Part 1: Lagrangian Coherent Structures In A Coastal Upwelling Envirnonment; Part 2: Near-Inertial Oscillations In The Northeastern Gulf Of Mexico, Matthew Kenneth Gough

Open Access Dissertations

Part I: Time evolving 2-D observations of near-surface flow with high frequency (HF) radar are well-suited for calculating Lagrangian Coherent Structures (LCSs) which are a valuable tool for observing turbulent flow. By comparing the evolving HF radar-derived LCS fields with satellite sea surface temperature imagery, the evolving structure of upwelling fronts, filaments, retention zones, and eddy-like recirculation are captured in the upwelling environment off the California coast. Part II: The inertial frequency is nearly diurnal at 30°N latitude which transects the northeastern Gulf of Mexico (NeGoM). At this latitude, near-surface inertial oscillations can amplify due to resonance with diurnal wind …

Plasticity And Ontogeny In Dynamic Environments: A Case Study Of Two Neotropical Understory Herbs, Andrea C. Westerband

Open Access Dissertations

For understory plants in tropical forests, light strongly influences rates of growth, survival, and reproduction, i.e., vital rates. To better understand how light availability influences the vital rates of two co-occurring understory herbs, Calathea crotalifera and Heliconia tortuosa, I monitored their growth, survival, and reproduction in forest plots. Plant size influenced the effect of light on vital rates, and increasing light did not always increase vital rates. Both species grew at small sizes but shrank at larger sizes, and larger individuals were more sensitive to changes in light than small individuals. I also found evidence of tradeoffs among vital rates, …

Material Dispersion By Ocean Eddies And Waves, Peng Wang

Open Access Dissertations

Material dispersion in the ocean, such as the dispersion of natural and anthropogenic tracers (e.g. nutrients, dissolved gases, pollutants), is important in understanding processes at a variety of scales, ranging from plankton production to climate variability. Material dispersion is controlled by many dynamic processes; the present research focuses on the 3D material dispersion by ocean eddies and waves (inertial waves and internal gravity waves). Ocean eddies may suffer various hydrodynamic instabilities, such as barotropic instability, inertial instability and 3D instability. In this work, I investigate how instabilities impact the 3D material dispersion by ocean eddies, using analytical methods and numerical …

Reviving The Body, Rina Tzinman

Open Access Dissertations

What are we? According to the two most common answers we are either psychological beings or biological organisms. In my dissertation I develop a novel account, which combines the advantages of these views while avoiding their main pitfalls. I start by arguing against the most developed theory of organism persistence, according to which human organisms persist in virtue of their brainstems persisting. Next, by drawing on the literature on natural properties and biological laws, I argue that biological organisms can persist through death. While organisms don’t necessarily cease to exist when they die, we normally do: according to my New …

Numerical Modeling Of Intervertebral Disc Degeneration And Repair, Qiaoqiao Zhu

Open Access Dissertations

Intervertebral disc (IVD) is the largest avascular structure in the human body and its main function is to support mechanical loading and to provide the flexibility for the spine system. Degenerative disc disease (DDD) is related to low back pain which affects more than 600 million people worldwide. One of the challenges in modeling DDD is that the biological, mechanical, chemical, and electrical events in IVD are coupled at different levels. It is important to develop a numerical model to understand the biophysics and pathophysiology in IVD (a biological system). A multiscale and multi-physics model was developed based on a …

Impacts Of Disrupting Early Motor Behaviors On Spatial And Temporal Patterning Of Synapses In Zebrafish Spinal Cord, Qing Yan

Open Access Dissertations

To generate rhythmic motor behaviors, both single neurons and neural circuits require a balance between excitation and inhibition (E/I balance). Disruption of E/I balance is associated with many neurodevelopmental disorders, such as seizures, autism, startle disease and glycine encephalopathy. E/I balance is maintained at both the cellular and the systems levels, and is influenced by the relative distribution of excitatory and inhibitory synapses. While the spatial and temporal patterns of excitatory and inhibitory synapses strongly associate with E/I balance, it remains unclear how perturbations of E/I balance affect the spatial and temporal patterning of synapses in in vivo neural circuits. …

Role Of Dead-Box Protein Ddx28 In Human Mitochondrial Ribosome Biogenesis, Ya-Ting Tu

Open Access Dissertations

Mammalian mitochondrial ribosomes (mitoribosomes) are macromolecular complexes consisting of nucleus-encoded ribosomal proteins and mitochondrion-encoded rRNAs. They synthesize 13 membrane proteins, all subunits of oxidative phosphorylation system (OXPHOS). The mitoribosome assembly pathway and factors involved are poorly characterized. Here, we have identified a DEAD-box RNA helicase, termed DDX28, as an RNA granule component essential for the biogenesis of the mitoribosome large subunit (mt-LSU). DDX28 interacts with the 16S rRNA and presumably participates in the arrangements of its secondary structures. Silencing of DDX28 in HEK293T cells decreased the steady-state level of both LSU ribosomal proteins and 16S rRNA, which led to a …

Lin28/Let-7 Axis As A Regulator Of Myocardial Ischemic Injury, Shaurya Joshi

Open Access Dissertations

One of the prominent causes of heart failure is atherosclerosis of the coronary arteries. Obstruction of blood flow within the coronary arteries results in inadequate perfusion, or ischemia, of the heart muscle. The let-7 family of microRNAs (miRs) regulates critical cell functions, including survival signaling, metabolic control and glucose utilization, which may be important during myocardial ischemia. MiR-let-7 expression is under tight temporal and spatial control through multiple redundant mechanisms. The mechanisms and functional consequences of miR-let-7 regulation in ischemic myocardium largely remain unknown. Here we show that miR-let-7c, -7a and -7g are downregulated in the adult mouse heart early …

Evolutionary Consequences Of Recent Secondary Contact Between Myzomela Honeyeaters, Jason Michael Sardell

Open Access Dissertations

Secondary contact, the reestablishment of geographic overlap between ranges of closely-related populations that were previously isolated, has important consequences for the evolution of phenotypic biodiversity, as well as for speciation. Yet, opportunities to study evolutionary processes in systems where secondary contact is historically recent are rare, leaving much unknown about this important stage of the speciation process. For my dissertation, I used an integrative approach to conduct the first study of the evolutionary consequences of secondary contact in one such system: the two species of nectivorous Myzomela honeyeaters, M. cardinalis and M. tristrami, which achieved secondary contact on the island …

Plant Interactions Across Common Mycorrhizal Networks, Joanna Weremijewicz

Open Access Dissertations

Arbuscular mycorrhizal fungi associate with roots of the majority of land plants and supply up to 80% and 25% of their P and N requirements, respectively. These fungi do not form mycorrhizas on individual plants in isolation, the way they often have been investigated. Instead, arbuscular mycorrhizas may form when hyphae connected to one root system branch throughout the soil while foraging for mineral nutrients, encounter, and colonize the roots of another plant, thereby forming a common mycorrhizal network (CMN). The importance of CMNs is their potential influence on the distribution of limiting mineral nutrients among plants. Although it is …

Axonal Transport And Life Cycle Of Mitochondria In Parkinson's Disease Model, Hyun Sung

Open Access Dissertations

In neurons, normal distribution and selective removal of mitochondria are essential for preserving compartmentalized cellular function. Parkin, an E3 ubiquitin ligase associated with familial Parkinson’s disease, has been implicated in mitochondrial dynamics and removal. However, it is not clear how Parkin plays a role in mitochondrial turnover in vivo, and whether the mature neurons possess a compartmentalized Parkin-dependent mitochondrial life cycle. Using the live Drosophila nervous system, here, I investigate the involvement of Parkin in mitochondrial dynamics; organelle distribution, morphology and removal. Parkin deficient animals displayed less number of axonal mitochondria without disturbing organelle motility behaviors, morphology and metabolic state. …

Multi-Axial Failure Of High-Performance Fiber During Transverse Impact, Matthew C. Hudspeth

Open Access Dissertations

The effect of projectile nose geometry on ensuing wave development in high-performance yarns is explored during single yarn transverse impact. Special attention has been placed on visualizing the immediate region around the projectile-yarn contact site for 0.30-cal round, 0.30-cal fragment simulation projectiles (FSP), and razor blades using high-speed imaging. Kevlar® KM2, Dyneema®SK76 and AuTx have been impacted at velocities ranging from ∼100 m/s to ∼1200 m/s depending on projectile nose shape, with an emphasis set on determining the critical velocity wherein below said velocity significant development of wave propagation occurs and above said velocity the yarn fails immediately upon impact. …

Analysis Of Scientific Argumentation In Two Physical Chemistry Classrooms Using The Pogil Approach, Alena C. Moon

Open Access Dissertations

The benefits of facilitating argumentation in science education have been well reported (Jimenez-Aleixandre & Erduran, 2007). Engaging in argumentation has shown to model authentic scientific inquiry as well as promote development of content knowledge. However, less emphasis has been placed on facilitating argumentation in upper level undergraduate courses, though it is important for evaluating undergraduate curricula to characterize upper level students’ scientific reasoning. This work considers two implementations of the POGIL physical chemistry curriculum and evaluates the classroom argumentation. The researchers aimed to consider the content of the arguments and dialectical features characteristic of socially constructed arguments (Nielson, 2013). To …

Stenocarpella Maydis: Identification, Management, And Population Diversity, Martha P. Romero Luna

Open Access Dissertations

Diplodia ear rot (DER) has been a persistent corn disease across the Midwest, and in recent years it has become an annual problem. The objectives of this study were to i) develop a molecular assay for the identification of Stenocarpella maydis, causal agent of DER, ii) evaluate the effect of crop rotation and tillage on DER severity, iii) determine the survival period of S. maydis in corn residue at different soil depths in a corn field, and iv) identify genetic diversity among S. maydis isolates collected from the Midwestern and Southern United States. The genus Stenocarpella contains two species, S. …

Development And Evaluation Of A Watershed-Scale Hybrid Hydrologic Model, Younghyun Cho

Open Access Dissertations

A watershed-scale hybrid hydrologic model (Distributed-Clark), which is a lumped conceptual and distributed feature model, was developed to predict spatially distributed short- and long-term rainfall runoff generation and routing using relatively simple methodologies and state-of-the-art spatial data in a GIS environment. In Distributed-Clark, spatially distributed excess rainfall estimated with the SCS curve number method and a GIS-based set of separated unit hydrographs (spatially distributed unit hydrograph) are utilized to calculate a direct runoff flow hydrograph, and time-varied SCS CN values and conditional unit hydrograph approach for different runoff depth-based flow convolution are also used to compute long-term rainfall-runoff flow hydrographs. …

Advances In Solid Phase Microextraction For The Analysis Of Volatile Compounds In Explosives, Tire Treatments, And Entomological Specimens, William D. Kranz

Open Access Dissertations

Solid phase microextraction is a powerful and versatile technique, well-suited to the analysis of numerous samples of forensic interest. The exceptional sensitivity of the SPME platform, combined with its adaptability to traditional GC-MS systems and its ability to extract samples with minimal work-up, make it appropriate to applications in forensic laboratories.

In a series of research projects, solid phase microextraction was employed for the analysis of explosives, commercial tire treatments, and entomological specimens. In the first project, the volatile organic compounds emanating from two brands of pseudo-explosive training aids for use in detector dog imprinting were determined by SPME-GC-MS, and …

Learning From Minimally Labeled Data With Accelerated Convolutional Neural Networks, Aysegul Dundar

Open Access Dissertations

The main objective of an Artificial Vision Algorithm is to design a mapping function that takes an image as an input and correctly classifies it into one of the user-determined categories. There are several important properties to be satisfied by the mapping function for visual understanding. First, the function should produce good representations of the visual world, which will be able to recognize images independently of pose, scale and illumination. Furthermore, the designed artificial vision system has to learn these representations by itself. Recent studies on Convolutional Neural Networks (ConvNets) produced promising advancements in visual understanding. These networks attain significant …