Doctoral Dissertations (Winter 2014 to Present)
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New submissions to the University of Delaware Doctoral Dissertations collection are added as they are released by the Office of Graduate & Professional Education. The Office of Graduate & Professional Education deposits all dissertations from a given semester after the official graduation date.
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Item The effect of gait retraining on external loading and associated bony loading in runners(University of Delaware, 2011) Fellin, Rebecca ElizabethIn the United States alone, approximately 16.4 million people participate in running activities. Unfortunately, up to 79% of these runners are injured each year. One more serious type of injury runners sustain is a tibial stress fracture, which is an injury that requires 6-8 weeks of rest. These injuries also have an alarmingly high 36% re-injury rate. Excessive vertical loading, such as load rates and tibial shock, has been linked to an increased risk of tibial stress fractures. Many runners exhibit excessive vertical loading bilaterally. Furthermore, torsional loading, quantified by the free moment, has been also implicated in tibial stress fracture development. Although both of these risk factors involve external loading, stress fractures occur due to loading at the bony level. Gait retraining to decrease vertical loading has been effective at decreasing these loads on the trained limb that received feedback. However, the impact of gait retraining on other risk factors such as free moment, contralateral limb loading, and the bony loading along the entire region where stress fractures are most common is unknown. Therefore, this dissertation consisted of three aims to examine changes following gait retraining with respect to each of these areas. ☐ The purpose of Aim 1 was to identify if runners who have high vertical and torsional loads can decrease those torsional loads through gait retraining to decrease vertical loading. We hypothesized that runners would decrease those loads following gait retraining. We further hypothesized that the decrease in torsional loading would be less than the decrease in vertical loading as the subjects were not receiving feedback on torsional loads. We collected data on twenty runners both pre and post gait retraining during overground running at 3.7 m/s. The gait retraining protocol consisted of eight sessions of real-time visual feedback during treadmill running at a self-selected speed. This feedback was from an accelerometer attached to the anterior-medial aspect of the subject's tibia on their limb with higher loads. The results revealed that runners with high peak adduction free moments reduce this peak following gait retraining. The decrease in free moment was moderately correlated to the decrease in vertical loading. Furthermore, the subjects decreased their free moment to a lesser degree than their vertical loading. ☐ The purpose of Aim 2 was to identify if reductions in vertical loading on the trained limb transfer to the contralateral, untrained limb. We hypothesized that runners would decrease vertical load rates and tibial shock on their trained and untrained, contralateral limb following gait retraining. We collected data on ten runners both pre and post gait retraining during treadmill running at 3.35 m/s and a self-selected speed. The gait retraining protocol consisted of eight sessions of real-time visual feedback during treadmill running at a self-selected speed. This feedback was from an accelerometer attached to the anterior-medial aspect of the subject's tibia on their limb with higher loads. Runners significantly decreased vertical load rates and tibial shock following gait retraining on both limbs and both running speeds. ☐ The purpose of Aim 3 was to identify if runners with high vertical loading decrease tibial strain rates from the midshaft to distal third following gait retraining. We hypothesized that runners would decrease tibial strain rates following gait retraining. Furthermore, we hypothesized that these tibial strain rate decreases would be proportional to the subject's external, vertical loading decreases. We collected data on five runners both pre and post gait retraining during overground running at 3.7 m/s. The gait retraining protocol consisted of eight sessions of real-time visual feedback during treadmill running at a self-selected speed. This feedback was from an accelerometer attached to the anterior-medial aspect of the subject's tibia on their limb with higher loads. The results were mixed as only 4/5 subjects demonstrated decreased tibial strain rates following gait retraining. These external loading decreases were similar in magnitude to the strain rate decreases for 2/5 subjects. Additional subjects should be studied to further validate these findings.Item Investigation of chemical ubiquitination of PCNA and mechanism, inhibition of USP1/UAF1 & the molecular recognition of RNA by the pseudouridine synthase RluA(University of Delaware, 2011) Chen, JunjunChapter 1: Pseudouridine synthases (Ψ synthases) catalyze the isomerization of uridine to pseudouridine (Ψ) and are present in all domains of life. The Ψ synthases fall into six families based on sequence similarity, and crystal structure of members of each family show that they share the same core fold and have one universally conserved aspartic acid residue in motif II. The cocrystal structures of the E. coli Ψ synthase RluA bound to an RNA oligomer corresponding to the anticodon stem-loop (ASL) of E. coli tRNAPhe has been determined. This structure is only the second of a Ψ synthase bound to an RNA substrate. In the RluA•RNA cocrystal, the RNA has undergone significant conformational changes from its unbound form. The isomerized uridine U32, is everted in the active site of RluA. This conformation is stabilized by the reverse-Hoogsteen base pair formed by U33 and A36 and the hydrogen bond formed between A36 and Pro 36 on RluA. To test the importance of particular interactions in the RluA•RNA cocrystal structure, kinetic studies were undertaken. RNA containing 5-fluorouridine, F5U, has been used as a mechanistic probe to distinguish the two proposed Ψ synthases’ mechanisms. RluA forms heat-sensitive and apparently covalent adduct with [F5U]RNA. Upon heating, hydrated F5U products are also formed by the collapse of the adduct of RluA. Thus, the reactivity between RluA and two altered [F5U]ASLs (A36C and U33C) was investigated. ☐ Chapter 2 to Chapter 4: The non-proteolytic function of ubiquitination has attracted increasing attention in recent years, including protein trafficking, immune response, transcription regulation and DNA damage response. Monoubiquitination of proliferating cell nuclear antigen (PCNA) plays an important role in eukaryotic translesion synthesis (TLS), a mechanism utilized by cells to synthesize past DNA lesion. One obstacle in studying eukaryotic TLS resides in the difficulty of preparing sufficient amount of ubiquitinated PCNA for in-depth biochemical and biophysical investigation. In Chapter 2, we developed a chemical approach that combines the power of intein chemistry and the facile disulfide exchange chemistry for efficient protein ubiquitination and SUMOylation. The chemically ubiquitinated PCNA is functionally equivalent to the native ubiquitinated PCNA in effecting polymerase switch between the replicative and the specialized DNA polymerases. We also demonstrated the strict requirement of PCNA ubiquitination for polymerase switch. Moreover, we probed the effect of the site of ubiquitination by preparing chemically ubiquitinated PCNAs that differ only in the position of modification. Our study revealed a surprising degree of flexibility of ubiquitin modification. ☐ Deubiquitinating enzymes (DUBs) cleave the ubiquitin moiety from mono- and poly-ubiquitinated proteins. Close to 100 DUBs have been identified in the human proteome. Abnormal cellular expression of DUBs or the loss of function due to mutation in certain DUB genes have been linked to various human diseases, including cancer and neurodegenerative diseases. Ubiquitin-specific proteases (USPs) constitute the largest DUB family. There is growing evidence suggesting that the activity of DUBs, in particular USPs, is stringently regulated through their interaction with many other protein partners. A recent global proteomic analysis of human DUBs identified 774 interacting proteins for the 75 DUBs studied. Remarkably, 34 human USPs were found to be associated with WD40-repeat proteins that adopt a β-propeller structure comprising up to eight blades. Given its widespread occurrence, the interaction between WD40-repeat proteins and USPs likely represents a fundamentally important way of regulating USP activity. Based on the reported kinetic data for USP1/UAF1 complex and USP1 alone, we hypothesize that the interaction between UAF1 and USP1 may reorganize the catalytic triad into a more productive conformation. To probe the active site conformation, in Chapter 3, cysteine-reactive small organic molecules (H2O2 or iodoacetamide) were used to determine the reactivity of the catalytic sulfhydryl group in USP1/UAF1 complex or USP1 alone. ☐ DUBs are promising targets for pharmacological intervention. The advantage of inhibiting DUB lies in the specificity of therapeutic intervention that can lead to better efficacy and eliminate nonspecific side effects seen in proteasome inhibitors. In Chapter 4, we identified small-molecule inhibitors against the USP1/UAF1 complex through high throughput screening. Two highly selective inhibitors, pimozide and GW7647, inhibit USP1/UAF1 noncompetitively with a Ki of 0.50 and 0.75 μM, respectively. We demonstrated that both compounds are reversible inhibitors that bind the USP1/UAF1 complex at a site different from the active site. Because USP1/UAF1 is involved in DNA damage response through deubiquitinating PCNA and FANCD2 in translesion synthesis and Fanconi anemia pathways, we tested USP1/UAF1 inhibitors as a sensitizer of cancer cells to DNA damaging agent, cisplatin. Our results indicated that the USP1/UAF1 inhibitors act synergistically with cisplatin in inhibiting the proliferation of cancer cells.Item Not so obscure a challenge: battered female migrants and public policies in the United States and Greece(University of Delaware, 2011) Wasileski, GabrielaImmigration is becoming an increasingly important policy concern both in the U.S. and Greece, and also in many other nations. Importantly, there is an ever-growing number of women who migrate, many of whom are undocumented. Violence against immigrant women is nearly impossible to estimate. However, immigrant women who are abused face multiple barriers to seeking legal protection from the abuse as a result of their migration status. In many cases, immigrant women are unaware of the protection afforded to noncitizens, or the legal protection is limited so they may fear deportation from being exposed as noncitizens or fear the loss of custody of their children. Those immigrants who entered the country through a family reunion program are awarded derivative immigration status, so they can join their spouses in the United States. Consequently, a battered immigrant's ability to obtain or maintain lawful immigration status may depend on her relationship to her United States citizen or lawful permanent resident spouse and his willingness to file an immigrant relative petition on her behalf. ☐ Despite the increase in female migration, there is a paucity of research on gender issues within regularization and family programs. This study sheds light on how the migration status of battered immigrant women affects their options for seeking a remedy from interpersonal violence. Moreover, this research highlights how migration policies in Greece and the United States interfere with social and legal protection of undocumented immigrant battered women.Item Reading matter: animals, vegetables, and media in Renaissance England(University of Delaware, 2012) Calhoun, JoshuaReading Matter explores the poetic interplay of words and matter in sixteenth- and seventeenth- century English texts. Made of recycled clothes, slaughtered animals, and felled trees, books in Renaissance England were filled with visible traces of ecological matter. Reading Matter demonstrates that the flora and fauna from which a text was made were legible, significant elements of its poetic form. Attending to the ecologies of writing and reading in sixteenth- and seventeenth-century England, this dissertation seeks to first recover and then to read those organic elements of Renaissance texts that both inflect meaning and indicate much about the intertwined acts of poesis and textual production in Renaissance England. I consider how plant fibers in the pages of printed and written texts were legible to Renaissance readers, how animals became illegible or invisible in paper even as their boiled down body parts allowed readers to make themselves legible in the margins of their printed books, how blots on a page make legible that which one might wish to obliterate, and how trees might be read, misread, and ventriloquized on the stage of the wooden Globe theater. ☐ More broadly, by studying the negotiations between poetics and ecology in Renaissance texts and by drawing on critical approaches such as material culture studies, book history, and historical formalism, Reading Matter seeks to outline a scholarly reading strategy that attends to the natural history of books, to both the function and the form of the organic matter used to mediate human ideas. Though focused on Renaissance texts, the project offers a methodology by which others might interrogate the textual ecologies of millennia-old Eastern palm leaf books, eighteenth-century Japanese texts, post-colonial Caribbean texts, or the latest iPad.Item A life less valuable? Adjudication and sentencing outcomes for perpetrators of child homicide.(University of Delaware, 2013) Poteyeva, MargaritaKilling a child almost universally galvanizes great outrage among the public. Despite this condemnation, little is known about how and if this abhorrence of killing a child translates into criminal justice practices. The purpose of this dissertation is to advance our understanding about the imposition of the law in cases of child homicide using a mixed-method design. The two general research objectives of the current study are: (1) to explore whether there are any differentials in the application of the law (e.g. decisions to prosecute, probability of conviction for offenders, and sentences received) for those who kill children compared to those who kill older victims; (2) to gain insight into the moral gradation of child homicide by exploring whether certain types of child homicide or certain perpetrators of the crime are treated more harshly than others. ☐ Quantitative analysis of a nationally representative data collected from prosecutors' offices in 33 large urban counties revealed that while killing a child did not have any effect on the probability of conviction, those who killed children received significantly shorter sentences than those who killed older victims. Being a mother-offender exuded a significant influence over the sentencing decision of the courts. ☐ Thematic and qualitative content analyses of data from the State of Maryland showed that the majority of death eligible cases with child victims either originated in a romantic conflict or involved a sexual assault on the child. No definitive conclusions could be drawn about the criteria that state attorneys in Maryland considered in determining whether or not to seek capital punishment in a particular child homicide case. In fact, there were several instances where legally similar crimes and offenders received different treatment. No female defendant in the Maryland sample was tried capitally, including the two women who were mothers to their victims. Contrasting these cases with female child homicide perpetrators who were sentenced to the death penalty in other states, however, suggests that prosecutors need to overcome a number of challenges to successfully portray female defendants as death-worthy.Item Integrating perspectives on social vulnerability to disasters and emergency management in Puerto Rico(University of Delaware, 2013) Santos-Hernández, Jenniffer MarieAs economic losses associated to disasters continue on the rise, the study of disasters continues to show that the causes of these events are fundamentally social. In a macrocosm, this dissertation explores how the practice of emergency management may impact, address, or fail to address social vulnerability to disasters at the community level. This research explored how the emergency management organization evolved, how it functions, and how their services are delivered. In addition, it presents a case study of the 2009 explosion at a fuel storage facility in Cataño, Puerto Rico. This case study moves beyond inventories of indicators of social vulnerability to explore the interaction between the emergency management organization and community units during crisis and non-crisis times. Max Weber's ideal type of bureaucracy was used as a conceptual tool to guide the analysis and to explore management changes. The findings provide insights that could assist practitioners and researchers working in the areas of development, emergency management, bureaucratic change, decision-making, and policy making.Item Improving the spatial, angular, and temporal resolution in light field imaging(University of Delaware, 2013) Yu, ZhanA light field captures a dense set of rays as scene descriptions in place of geometry. Recent advances on computational imaging have enabled novel and efficient light field acquisition devices. For example, the new Lytro and Raytrix cameras are able to capture light fields in a single shot. However, the effective spatial resolution is reduced by the number of microlenses. For example, in Lytro, the resulting image at a desired focal plane has a resolution of 1080x1080, which is too low for photographic uses or in computer vision tasks. The acquired light field also has a low angular resolution, usually less than 10x10 for each spatial sample. This results in aliasing artifacts when synthesizing dynamic Depth-of-Field (DoF). Finally, the data size of each captured light field can easily reach 20 MB, prohibiting live streaming and processing at interactive frame rates. ☐ In this dissertation, I develop a new class of image processing algorithms and camera designs that can significantly improve the spatial, angular, and temporal resolution in light field imaging. ☐ Spatial Resolution: We develop a simple but effective technique by maneuvering the demosaicing process. We first show that traditional solutions that demosaic each individual microlense image and then blend them for DoF synthesis is suboptimal. We instead propose to demosaic the synthesized view at the rendering stage by first mapping the rays onto the refocusing plane and then conduct resampling. Our approach can significantly improve the spatial resolution while reducing the aliasing artifacts. ☐ Angular Resolution: We introduce a light field triangulation scheme to improve the angular resolution. Our triangulation technique aims to fill in the ray space with continuous and non-overlapping simplices anchored at sampled points (rays). Such a triangulation provides a piecewise-linear interpolant useful for angular super-resolution. We develop a novel triangulation algorithm that uses the depths and structures of 3D lines as constraints for producing high quality triangulations. For robust depth estimation, we further present two light field stereo matching algorithms that greatly outperform the state-of-the-art. ☐ Spatial-Angular Resolution: We further present a unified framework to simultaneously enhance the spatial and angular resolutions by stitching multiple light fields. We first estimate the warping function between two light fields and then stitch them by finding an optimal cut through the overlapping region. We further accelerate the graph-cut algorithm via a coarse-to-fine scheme. We demonstrate various stitching applications to improve the field-of-view as well as translational and rotational parallaxes of the light fields. ☐ Temporal Resolution: Finally, we construct a hybrid-resolution stereo camera system for acquiring and rendering dynamic light fields. Our system couples a high-res/low-res camera pair to replace the bulky camera array system. From the input stereo pair, we recover a low-resolution disparity map and upsample it via fast cross bilateral filters. We subsequently use the recovered high-resolution disparity map and its corresponding video frame to synthesize a light field using GPU-based disparity warping. Our system can produce racking and tracking focus effects at a resolution of 640x480 at 15 fps.Item First-principles-based kinetic modeling of the zeolite-catalyzed conversion of furans to aromatics(University of Delaware, 2014) Nikbin, NimaThe development of strategies to convert renewable feedstocks into fuels and chemicals and displace petroleum is motivated from economic, environmental and political reasons and is arguably one of the world's foremost scientific energy challenges. The nascent shale gas revolution may, at best, postpone the transition to renewables. Shale gas, however, does not provide aromatics to the extent that naphtha does and thus the development of renewables-based strategies for aromatics is more crucial than ever. A promising, sustainable route to synthesize aromatics from biomass-derived furans has recently been proposed following the discovery that DMF and ethylene can be selectively converted to p-xylene by dehydration of the Diels-Alder product over zeolites that contain Brønsted sites. The objective of this thesis is to reveal the underlying mechanism and provide insights into catalyst design principles. In order to achieve this, we combine electronic structure calculations and microkinetic modeling to describe how the two reactions - Diels-Alder cycloaddition and dehydration - work in tandem and to investigate the side reactions that affect selectivity. Specifically, we study the Brønsted acid-catalyzed dehydration of the cycloadduct and the ring opening hydrolysis reaction of DMF. We show that Brønsted acids are quite effective at catalyzing dehydration and hydrolysis. We pay particular attention to the ability of zeolites with extra-framework Lewis acid centers to heterogeneously catalyze the Diels-Alder cycloaddition. We elucidate the factors that determine Lewis acid activity and propose reactivity descriptors that encapsulate the underlying physics. In order to accomplish this study, we vary the active Lewis acid site environment from an isolated active site center to an active site cluster model and an embedded active site cluster model to determine the balance between accuracy and computational cost and guide future computational studies about a suitable way of modeling the active site. Even though Lewis acids are known to catalyze Diels-Alder cycloaddition by closing the gap between the frontier molecular orbitals of the addends, our calculations show that alkali-exchanged zeolites Y do not generally exhibit notable Lewis acid activity. Charge screening of the Lewis acid centers, due to significant charge transfer from the framework oxygen atoms to the alkali cations, diminishes their catalytic ability. As a result, the reaction is shown to follow bi-directional instead of normal electron flow and homogeneous catalyzed chemistry is equally effective. We propose that effective heterogeneous catalysis of Diels-Alder cycloaddition should involve zeolite frameworks whereby the Lewis acid centers are less embedded and thus less screened from electron density transfer from the framework. Microkinetic modeling of the conversion of DMF and ethylene over the zeolite HY revealed that HY can only catalyze the dehydration of the Diels-Alder product and that the cycloaddition itself proceeds uncatalyzed, outside the zeolite, i.e., homogeneously. The overall process follows two distinct kinetic regimes as a function of catalyst concentration. At low catalyst loadings, the rate of p-xylene production increases linearly with the concentration of active sites and the rate-limiting step is the Brønsted-catalyzed dehydration. At high catalyst loadings, the reaction rate is maximal and independent of the available Brønsted sites. In this regime, the rate is controlled by the uncatalyzed cycloaddition, despite the fact that the cycloaddition activation energy is higher than that of the catalyzed dehydration.Item Sparse signal processing for machine learning and computer vision(University of Delaware, 2014) Zhou, YinSignal sparse representation solves inverse problems to find succinct expressions of data samples as a linear combination of a few atoms in the dictionary or codebook. This model has proven effective in image restoration, denoising, inpainting, compression, pattern classification and automatic unsupervised feature learning. Many classical sparse coding algorithms have exorbitant computational complexity in solving the sparse solution, which hinders their applicability in real-world large-scale machine learning and computer vision problems. In this dissertation, we will first present a family of locality-constrained dictionary learning algorithms, which can be seen as a special case of sparse coding. Compared to classical sparse coding, locality-constrained coding has closed-form solution and is much more computationally efficient. In addition, the locality-preserving property enables the newly proposed algorithms to better exploit the geometric structures of data manifold. Experimental results demonstrate that our algorithms are capable of achieving superior classification performance with substantially higher efficiency, compared to sparse-coding based dictionary algorithms. Sparse coding is an effective building block of learning visual features. A good feature representation is critical for machine learning algorithms to achieve satisfactory results. In recent years, unsupervised feature learning has received increasing research interest in various computer vision and pattern recognition problems. Unlike humanengineered feature extractors that typically require domain knowledge and a large amount of labeled data, unsupervised learning algorithms are generic and designed to automatically discover the intrinsic patterns from the abundant unlabeled data that are usually readily available (from Internet) and require no laborious human labeling. In this dissertation, we will explore the capability of feature learning algorithms in automated biomedical image analysis. Specifically, we will present two unsupervised feature learning models for histopathology image classification. We will also introduce a novel convolutional regression model for nuclei segmentation. Experiments on biomedical image classification and segmentation benchmarks demonstrate that the proposed feature learning systems can achieve very competitive results compared to dedicated systems incorporating biological prior knowledge. Finally, we propose a sparse coding based framework for classifying complicated human gestures represented as multi-variate time series (MTS). Specifically, we will present a novel feature extraction strategy, which can overcome the problem of inconsistent lengths among MTS data and is robust to the large variability within human gestures. Moreover, we will introduce a generic approach to kernelize sparse representation, which leads to enhanced classification performance. Extensive experiments verify the effectiveness of the proposed framework.Item Exploring natural supersymmetry at the LHC(University of Delaware, 2014) Nasir, FarihaThis dissertation demonstrates how a variety of supersymmetric grand unified theories can resolve the little hierarchy problem in the minimal supersymmetric standard model and also explain the observed deviation in the anomalous magnetic moment of the muon. The origin of the little hierarchy problem lies in the sensitive manner in which the Z boson mass depends on parameters that can be much larger than its mass. Large values of these parameters imply that a large fine tuning is required to obtain the correct Z boson mass. With large fine tuning supersymmetry appears unnatural which is why models that attempt to resolve this problem are referred to as natural SUSY models. We show that a possible way to exhibit natural supersymmetry is to assume non-universal gauginos in a class of supersymmetric grand unified models. We further show that considering non-universal gauginos in a class of supersymmetric models can help explain the apparent anomaly in the magnetic moment of the muon.Item Dioxygen activation by low valent cobalt complexes supported by ferrocenyl-substituted, redox active hydrotris(pyrazolyl)borate ligands(University of Delaware, 2014) Sirianni, Eric R.The successful synthesis and structural characterization of a new family of second and third generation ferrocenyl-substituted tris(pyrazolyl)borate ligands was achieved. These ligands employ ferrocenyl (Fc) moieties for increased C-H bond strengths as well as maintaining the steric demands necessary to remain "tetrahedral enforcers". The thallium(I) salts of the TP Fc* (1 ) and TpFc,Me* (2 ) ligands were isolated as N-confused asymmetric isomers. However, Tp Fc,iPr Tl (3 ) was isolated as the symmetric ligand as a dimer with an apparent Tl - Tl interaction. Cyclic voltammetry of 1, 2 , and 3 revealed single, reversible, three electron redox processes which suggests a lack of electronic communication between the ferrocenyl moieties when bound to a hydrotris(pyrazolyl)borate ligand. Conversely, TpCF3,Fc Tl (4 ) displays an irreversible redox process that is accompanied by decomposition during the oxidation wave of the CV. Thallium salts 1 and 2 undergo borotropic rearrangements to form the symmetric TpFc Tl (7 ) and Tp Fc,Me Tl (8 ), respectively. These ligands react with CoX 2 (X: Cl, I) to form their symmetric TpCoX complexes. Salt metathesis of 3 with CoI2 led to the isolation of TpFc,iPr CoI (13 ) as the only observable product. However, the reaction of 3 with CoCl2 yielded an N-confused Tp Fc,iPr* CoCl (14 ) complex. The electronic characterization of TpFc, (R: H, Me, i -Pr) has been sought through the synthesis of their corresponding copper(I) carbonyl complexes. Although the reaction of 7 and 8 with CuI under CO yields the symmetric TpFc Cu(CO) (16 ) and Tp Fc,Me Cu(CO) (17 ), respectively, the reaction of 3 with CuI under CO yielded the singly N-confused TpFc,iPr* Cu(CO) (19 ) and doubly N-confused TpFc,iPr** Cu(CO) (18 ) complexes. The TpFc,Me ligand has been employed in cobalt oxygen chemistry and has displayed its ability to resist C-H bond activation on the ligand. TpFc,Me Co(η3 -C3 H 5 ) (22 ) reacted with O2 to form an apparent TpFc,Me CoOOC3 H5 intermediate which underwent O - O bond homolysis to form TpFc,Me CoOH (21 ). 22 reacted with CO to form TpFc,Me Co(CO) (23 ). 23 reacts with O2 to form the side-on superoxo complex, TpFc,Me Co(O2 ), which has been structurally characterized by X-ray diffraction. Furthermore, the terminal imido complex, TpFc,Me CoNAd (25 ), displayed greater thermal stability than its analogous alkyl-substituted TptBu,Me CoNR complexes.Item Essays on computational applications in land and environmental economics(University of Delaware, 2014) Fooks, Jacob R.This dissertation presents three papers. The first considers a new approach to measuring and estimating willingness-to-pay for the class of nonmarket amenities with spatially explicit components. The second examines the significance, and a possible solution for poorly observed benefits in a conservation planning setting. The third reports on experiments in mechanisms for funding the development of coastal infrastructure, a spatially explicit public good, given complex inundation dynamics.Item The effects of high-speed, low-force recumbent cycling: an intervention in older a dults [sic] and Parkinson's disease(University of Delaware, 2014) Bellumori, MariaDecreased mobility substantially reduces independence and quality of life while contributing to increased rates of disability and health care costs. Exercise is a proven strategy to improve these qualities. Exercise is known to benefit every physiological system with the strongest literature support for cardiovascular health and strength gains. However, less is known about the potential to enhance mobility with exercises that target rapidly adapting central nervous system (CNS) factors. While the current exercise recommendations from federal agencies (CDC, NIH, and DHHS) are prudent, they neglect the potential benefits of high speed exercises that target the CNS correlates of muscular quickness. Results of this research are expected to inform improvements in exercise recommendations for older adults and people with movement disorders. Additionally, results are expected to fill a gap in the literature related to neural adaptations to high speed training in older adults and people with Parkinson's disease (PD). The purpose of Aim 1 was to determine whether there exist age-related differences in the speed and control of rapid isometric force pulses in different muscles in young and older adults. It was hypothesized that older adults would have lesser rate of force development-scaling factors (RFD-SF) and more variability in the performance of rapid force production. The purpose of Aim 2 was to determine the effects of a six week exercise intervention that uses high-speed, low-resistance stationary recumbent cycling in older adults. Participants completed pre- and post-exercise tests as well as 4 week follow-up to determine retention of changes. It was hypothesized that there would be improvements in the following measures: 1) Time to peak force and the RFD-SF during isometric knee extension; 2) Standardized measures of walking function; 3) Perceived function and quality of life. It was also hypothesized that improvements in the previous measures would be retained four weeks after training. To elucidate the neuromuscular mechanisms that occur with improved speed in older adults, it was hypothesized that this would be most strongly related to the rate of rise in the surface electromyogram (RER). We also aimed to determine if training the legs affects CNS mechanisms that transfer to the following in older adults: 1) Increased time to peak force and RFD-SF during isometric elbow extension; 2) Improved RER in elbow extensors; 3) Improved hand dexterity. It was also hypothesized that improvements in the previous measures would be retained four weeks after training. The purpose of Aim 3 was to develop an improved method to selectively quantify paired motor unit discharge behavior underlying tremor. The method was then tested before and after three different treatments. It was hypothesized that interspike interval serial correlation with cluster analysis would allow us to quantify paired motor unit discharge behavior from isometric contractions in which motor unit discharge behavior is not solely bimodal.Item Towards an equitable cap-and-trade scheme in South Korea: based on input-output analysis of the distributional implications of carbon pricing mechanisms(University of Delaware, 2014) Kim, HanaWhile the efficiency of cap-and-trade programs has attracted the attention of several countries, equity implications of the programs require equal attention. The programs impact income distribution as the cost of mitigation is passed on to consumers in the form of increased prices. A great deal of literature shows that the incidence of these programs is regressive in developed countries, indicating that this program will exacerbate the distributional equity without appropriate countermeasures. Facing the impending implementation of cap-and trade schemes in South Korea in 2015, a handful of experts have studied the equity implications of the scheme. The literature often provides a partial analysis on equity implications of the scheme focusing only on regional distribution or on distribution between different income groups. However, this dissertation evaluates the comprehensive equity implications of a carbon pricing policy as well as the impacts on other dimensions. Input-output analysis (IOA) is employed to assess the comprehensive impacts of a carbon pricing policy in South Korea. Beyond a typical IOA, hybrid IO tables are developed to estimate energy consumption and CO 2 emissions by sector and to analyze the impacts of the implementation on different sectors. In addition, this study makes it possible to assess equity implications by introducing a transition matrix to link Household Survey Data with the IO table. The analysis of three different carbon-pricing scenarios reveals that a comprehensive participation scenario (S1) impacts economy less adversely than the partial participation case (S2). The S1 more adversely impacts the distribution without revenue recycling. Coal consumption is reduced more in the S2 and the reduction in non-energy use such as naphtha is larger in the S1. Of course, a higher carbon price (S3) can reduce more emissions and energy consumption, but can more adversely affect economy and distributional equity. Regardless of scenarios, the analysis shows that the households with lower capacity, such as those with low-income or with elderly heads, are likely to be more adversely affected. However, these groups can be beneficiaries if the program is in practice together with revenue recycling through lump-sum transfer. In addition, there is not great difference between the burdens on rural and urban households. In conclusion, there is no best-case scenario for every dimension. Since the policy impacts economy, energy, environment and equity--important pillars of sustainable development--we need to consider the comprehensive impacts of the policy. In addition, we need to explore a more effective method to recycle the revenue to alleviate the inequity.Item Examining the physiology of harmful microalgae during algicidal control and diel vertical migration(University of Delaware, 2014) Tilney, Charles L.The frequency of harmful algal blooms (HABs) has increased, and so too has the societal and environmental costs associated with them. Anthropogenic eutrophication has played some part in this, but is not always implicated, as HABs and their drivers are diverse. Continued investigation into HAB biology and ecology may help to identify the underlying factors controlling algal blooms in general, and factors implicated in their recent increase in particular. Investigation of the various methods for the prevention, control, and mitigation of HABs is also warranted, to identify 'solutions' to reduce or eliminate some or all of the costs imposed by HABs. In this dissertation, both basic and applied work was conducted, initially on the control of dinoflagellates with a sterile bacterially-derived algicidal filtrate that is strongly specific toward dinoflagellates, and then on the diel vertical migration (DVM) of two potentially harmful species of microalgae. Initial investigations of the algicidal filtrate (termed IRI-160AA) assessed the effects in cultured dinoflagellates, and identified that electron transport through the photosynthetic apparatus at photosystem II (PSII) was broadly inhibited in algicide treated dinoflagellates. Moreover, IRI-160AA induced dose-dependent effects on both cell viability and PSII efficiency, and although dinoflagellate responses were highly species specific, one apparent generalization was that thecae reduced overall susceptibility. Next, the algicidal filtrate was tested on field collected water samples containing dinoflagellates. These dinoflagellates were less susceptible than uni-algal cultures because they were not in the most susceptible phase of growth, which corroborated the idea of Pokrzywinski et al. (2012) that identifying the growth stage of dinoflagellate blooms in the field would be crucial to achieving high levels of bioactivity with the algicide. Using a combination of polymerase chain reaction denaturing gradient gel electrophoresis (PCR-DGGE) and quantitative real-time PCR, I determined what changes occurred in the eukaryotic and prokaryotic microbial communities after applications of IRI-160AA. A common theme among these applications was the rise of bactivorous protists, most notably Paraphysomonas spp., which likely arose as a response to bacterial growth from dissolved organic matter (DOM) within the filtrate and released from dying dinoflagellates. This result highlighted how the microbial loop might transfer dinoflagellate carbon back to higher trophic levels in large-scale applications, and perhaps in HAB control more generally. The results suggest that IRI-160AA could be a potent and species-specific method to control harmful dinoflagellates in nature, but future work is required to identify methods to appropriately and cost-effectively scale- up algicide production, as well as to isolate the active compounds and determine the molecular targets and mode of action. Finally, a detailed comparison of the diel vertical migrations (DVM) of two sympatric harmful algal species (Karlodinium veneficum and Chattonella subsalsa ) was conducted in laboratory columns under various sampling regimes and lighting conditions. Both species exhibited markedly different DVM patterns, which were consistent with different photoprotective mechanisms, and carbon assimilation rates. DVM was found to be under the control of a circadian clock in C. subsalsa but not K. veneficum. This work provides a useful comparison between two potentially harmful species from the Delaware Inland Bays, and improves our understanding of the niches that these algae are adapted to. Collectively, this dissertation has raised many interesting questions for future research addressing the control of harmful algae with biologically derived compounds, and laid important foundations for deeper investigations into the role of diel vertical migration in two cosmopolitan harmful algae.Item Energy transfer in nanostructured materials(University of Delaware, 2014) Haughn, ChelseaEnergy transport and loss are critical to the performance of optoelectronic devices such as photovoltaics and terahertz imaging devices. Nanostructured materials provide many opportunities to tailor transport and loss parameters for specific device applications. However, it has been very difficult to correlate specific nanoscale structural parameters with changes in these performance metrics. I report the development of new ways of using time-resolved photoluminescence (TRPL) to probe charge and energy transport and loss dynamics. These techniques are applied to several types of nanostructured materials, including bulk semiconductors with defects, self-assembled quantum dots and colloidal quantum dots. First, GaAs/InP double heterostructures grown via metal organic chemical vapor deposition (MOCVD) were characterized with TRPL. TRPL is typically used to extract minority carrier lifetimes, but we discovered that the measured lifetime depended critically on the intensity of the exciting laser. We developed a Shockley-Read-Hall model to extract trap state densities from intensity-dependent TRPL measurements. Second, we characterized energy and charge transfer between InAs quantum dots and ErAs nanoinclusions within III-V heterostructures. Using intensity- and temperature-dependent TRPL, we confirmed tunneling as the dominant mechanism of charge transport and characterized the electronic structure of the ErAs nanoparticles. Finally, we characterized energy transport in colloidal quantum dot cascade structures. These cascade structures utilize Forster Resonance Energy Transfer and trap state recycling to funnel excitons from donor layers to acceptor layers and suggest a promising method for avoiding losses associated with surface trap states. Collectively, the analysis of these disparate material types advances our understanding of energy dynamics in nanostructured materials and improves our ability to design the next generation of photovoltaic and optoelectronic materials and devices.Item Modulation of paracrine interactions between prostate cancer cells and bone marrow stromal cells by transforming growth factor-beta signaling during colonization of bone(University of Delaware, 2014) Kurtoglu, SenemProstate cancer (PCa) is the most prevalent cancer and the second leading cause of cancer related death for men in the United States. Death is primarily due to bone metastasis with more than 80% of men who die of PCa having bone involvement at autopsy. The complex bone microenvironment may initially resist the newly resident PCa cells but PCa cells acquire adaptive changes that allow them to survive and grow in the "hostile" new microenvironment as they co-evolve in their genotypic and phenotypic characters with bone cells. We have previously shown that soluble factors released from immortalized human bone marrow stromal cells (BMSC) induce apoptosis of PCa cells, and the surviving cells undergo neuroendocrine differentiation (NED), characterized by morphological changes consistent with a neuroendocrine phenotype. The presence of neuroendocrine tumor cells in PCa is associated with aggressiveness, resistance to hormonal therapy, and poor prognosis. Using the LNCaP progression model of increasingly metastatic and castrate-resistant prostate cancer (CRPC) cell lines, I examined the influence of BMSC factors on PCa survival, using the HS-5 and HS-27a BMSC lines, which were characterized previously for their ability to support different stages of hematopoiesis. Neuroendocrine markers were elevated in PCa cells surviving HS-5 BMSC conditioned medium (CM) treatment, while differentiation markers such as androgen receptor (AR) and prostate-specific antigen (PSA) were decreased. PCa cells that undergo NED using HS-5 BMSC CM or serum withdrawal had elevated phosphorylated-Smad2 levels. Furthermore, NED of PCa cells prevented HS-5 BMSC-induced apoptosis. Cell death induced by BMSC CM was analyzed using live/dead analysis while the effect on cell growth was examined in soft agarose colony formation assays in the presence and absence of intact TGF-Beta signaling. Using immunoblotting and luciferase reporter assays, I measured levels and activity of phosphorylated-Smad2 in PCa cells surviving treatment with HS-5 BMSC CM. Treatment of PCa cells with the ALK-4, 5, and 7 kinase inhibitor, SB-431542, resulted in a significant reduction in HS-5-mediated cell death. Correspondingly, pre-treatment of HS-5 BMSC with TGF-Beta1 yielded a CM that elicited a marked reduction in PCa cell death. The ancillary TGF-Beta receptor endoglin levels were also decreased upon TGF-Beta1 stimulation of HS-5 cells suggesting the importance of endoglin in mediating BMSC-induced PCa cell death. Small interfering RNA-mediated knockdown of endoglin in HS-5 cells verified that the effect on PCa cell death was a direct result of the attenuation of endoglin. Futhermore, the loss of the cytoplasmic domain of endoglin in HS-5 cells attenuated BMSC-induced PCa cell death indicating the importance of the cytoplasmic domain in maintaining endoglin function and expression of the factor(s) responsible for PCa cell death. Collectively, my findings indicate that 1) TGF-Beta signaling in PCa cells is induced during stimulation of NED, 2) TGF-Beta family cytokines secreted from HS-5 BMSC mediate PCa cell death, 3) TGF-Beta signaling in HS-5 BMSC alters paracrine signaling to promote PCa survival, 4) Endoglin is required for HS-5 BMSC-induced PCa cell death, 5) The cytoplasmic domain of endoglin is required for the expression of the factor(s) responsible for PCa cell death.Item Thermochemical conversion of biomass: models and modeling approaches(University of Delaware, 2014) Moreno, Brian MatthewFuels produced from lignocellulosic biomass are a promising renewable energy source that will aid in the transition from petroleum-derived liquid transportation fuels while utilizing the existing processing and distribution infrastructures. Lignocellulosic biomass is composed of lignin, cellulose, and hemicellulose, in fractions that vary by plant species. Pyrolysis of these biopolymers results in a biomass pyrolysis oil (BPO) containing aromatics, hydrocarbons, and various oxygenated species. The high oxygen content of BPO must be decreased before use in conventional internal combustion engines. Deoxygenation of BPO results in a mixture of hydrocarbons with properties similar to those of petroleum-derived fuels, which can be co-processed in traditional refineries. The compositional variability of both the petroleum and biomass fractions motivates the need for molecular-level kinetic models to track these novel species and reaction pathways during the production of biofuel-petroleum blends. Molecular-level modeling of the thermochemical conversion of biomass requires the prediction of reaction networks that identify each chemical pathway from the biomass feedstock to the desired fuel products. The Klein research group has developed a software package that is capable of rapidly generating complete reaction networks and associated kinetic models. First, the Interactive Network Generator (INGen) produces a reaction network from the molecular reactants. Next, the Kinetic Modeling Editor (KME) automatically writes the corresponding rate equations and material balances for each species. The resulting molecular-level kinetic model is solved numerically to provide model predictions of the product composition at varying process conditions. In this dissertation, the capabilities of these software tools are expanded to incorporate various biomass chemistries. The biomass-to-fuels models described in this dissertation provide insight into competing kinetic pathways for the production of renewable liquid fuels from lignocellulosic materials. Predictions are made for product composition at varying feedstock composition and processing conditions; experimental data provides validation. Comparison of the activation energy barriers for competing deoxygenation routes will direct catalyst research to modulate between pathways and provide the highest quality products at the mildest process conditions. The ability to rapidly generate and solve molecular-level kinetic models will enable real-time optimization of fuel production and increase the viability of biofuels in the renewable energy market.Item From the ground up: conceptualizing the space of Los Angeles commercial aeromobility(University of Delaware, 2014) Edlins, GeoffreyDespite the capacity of air travel to radically transform life on the ground, aerial space is seldom considered a site whose constitutive practices, technologies, and physical forces have indeed reconfigured social, political, economic, and spatial relations--both within and between terrestrial city-regions. This dissertation integrates aeromobility and atmospheric space within a relational mode of urban analysis. It analyzes the processually-unfolding atmospheres of Los Angeles city-regional air passenger traffic. To do this, it first considers the spatial development of the Los Angeles city-regional airport system as a functional assemblage within nested, overlapping, and aerial-enabled relationships among city-regional infrastructures and institutions. It traces the production of urban forms and processes most directly related with the commercial airline activity centered on LAX and neighboring airports, which relationally configure the Los Angeles city-region, both within and throughout global air traffic networks. This analysis finds, among other things, that LAX has undergone a shift towards transpacific linkages. Future growth in these markets suggests the airport must accommodate larger aircraft and more intensive passenger flows. The project then describes how one protracted struggle over the reuse by Orange County of a decommissioned military air base can help us understand more fully that aerial spatial production is informed not only by political or economic interests, including demands for more a more even distribution of intensifying LAX air traffic throughout LA city-regional facilities, either operational or dormant. The project finds that, despite these regional demands, aerial spatial production becomes constrained and enabled to certain degrees by the materiality of air and air travel, including the topographical context of existing airport sites, the configuration and condition of runways, prevailing wind or weather patterns, the presence of aerial flows involving nearby airports, and the physical laws governing flight itself. Within this discussion, the dissertation considers some of the major institutional practices and arrangements that have assembled the Los Angeles city-regional airport system as a site of intersection between networked infrastructures and a territorial palimpsest. The analysis suggests that forms of political resistance to airport expansion and construction--which often appeal to improving how airport neighbors dwell-on-the-earth --can become strengthened by integrating appeals to improving how passengers and pilots dwell-in-the-air. The research contributes to an understanding of urban space and governance, particularly of how aerial-related institutions and actors constitute the city both as territorially-bounded node and relationally-articulated network.Item Particles and particle-verb constructions in English and other Germanic languages(University of Delaware, 2014) Larsen, DarrellThis dissertation examines the lexical semantics of particles and the syntax of particles and particle-verb constructions. I argue against the notion that there are distinct types of particles (e.g. resultative versus idiomatic versus aspectual), claiming instead that they are semantic predicates consisting of an often metaphorical spatial meaning and, with a few exceptions, an unpronounced Ground argument. As a result, particle verbs are argued to be semantically compositional. The syntactic behavior of particle verbs is primarily explained through the adoption of the following major claims: (i) particles are optionally projecting syntactic heads whose topmost projection merges with a verbal head to form either a complex head or a resultative-like structure; (ii) nonprojecting particles (which combine with verbs to form complex heads) remain in situ, the verb raising out of the complex via phonological head movement; and (iii) objects raise to receive Case by LF, but they may do so overtly or covertly. These claims are shown to account for the behavior of the particle-verb construction when interacting with a wide range of other phenomena. The adoption of a further claim--(iv) ECM subjects of small-clauses preferably or obligatorily (depending on the speaker) raise out of the small clause overtly, whereas ECM subjects of IPs need not--is then shown to be able to explain the pattern of grammaticality and acceptability judgments encountered in the so-called 'complex' particle-verb constructions. Finally, the ability of particle verbs to undergo various word-formation processes is considered within the context of these theoretical assumptions.