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.

Doctoral dissertations from 1948 to present are also available online through Dissertations & Theses @ University of Delaware. Check DELCAT Discovery to locate print or microform copies of dissertations that are not available online.


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    UTILIZING A DYNAMIC WELL-DEFINED 3D CO-CULTURE MODEL FOR INVESTIGATIONS IN ER+ BREAST CANCER DORMANCY
    Moore, DeVonte Lamar
    Prevention of late breast cancer recurrences remains a clinical challenge for physicians. Detection of dormant cancer cells, which are often few in number, is challenging within current diagnostic limitations. Further, current systemic therapies, including neoadjuvant and adjuvant therapies, given to patients before and/or after surgery to eliminate residual cancer cells, are limited by lack of specificity towards these non-proliferating cells. Limited molecular insights into underlying dormancy and reactivation continues to define a gap within our knowledge that remains as to how these breast cancer cells are able to survive through dormancy and reactivation. It has been hypothesized and a few insights have shown that there are key cell-cell and cell-extracellular matrix (ECM) interactions between disseminated ER+ cancer cells and the bone microenvironment that contribute to late recurrence, inducing dormancy in breast cancer cells (BCCs) initially with metastatic outbreak at later times. My thesis aimed to utilize a recently-established, well-defined three-dimensional (3D) ER+ breast cancer dormancy and reactivation co-culture model and innovative molecular tools to understand and target the molecular regulators of ER+ breast cancer dormancy. In collaboration with colleagues, I contributed to studies that identified TNFα and MCP1 as soluble factor regulators of ER+ cancer dormancy induction. Additionally, T47D ER+ breast cancer cells were engineered toward reporting dormancy in real-time using lentivirus with opportunities for single-cell assessment of ER+ breast cancer dormancy in live cells. Continued development of reporter strategies established here will be useful in the assessment of the effects of known small molecule anti-cancer therapeutics. I also was able to isolate and identify extracellular vesicles from this dormancy culture system, which could prove useful in future studies for dormancy induction. These insights and tools provide the framework for more detailed identification and targeting of dormancy and reactivation related biochemical factors and pathways.
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    INVESTIGATION OF A LEGIONELLA PNEUMOPHILA EFFECTOR PROTEIN THAT MANIPULATES HOST AUTOPHAGY
    Evans, Amanda Claire
    Many intracellular bacteria engage with the host cell’s autophagy pathway. The autophagy pathway is designed to isolate and degrade misfolded proteins, damaged organelles, or foreign material. Autophagy can be an obstacle for intracellular bacteria, as it sequesters them into a vacuole before delivering them to the lysosome for degradation (xenophagy). Or it can be a useful tool for the bacteria to acquire nutrients from the host. While some intracellular pathogens actively evade and inhibit the autophagy pathway, others induce it or upregulate it. The facultative intracellular, Gram-negative pathogen Legionella pneumophila is a particularly interesting case-study in the relationship between bacterium intracellular lifecycle and autophagy. L. pneumophila infection can develop into Pontiac Fever, or the more serious Legionnaires’ disease. Upon human inhalation, the bacterium typically infects the alveolar macrophages that inhabit the lung. Within the macrophage, the bacterium can release over 350 effector proteins using a Type 4 Secretion System. These effector proteins have an array of functions within the host, including the development of a nutrient-rich replication vacuole that escapes the phagosomal-degradation pathway designed to dispose of intracellular bacteria. Within this undetectable vacuole, the bacterium will replicate until the host has been effectively colonized. Several of the bacterium’s effector proteins have been characterized as proteins that function to specifically inhibit the autophagy pathway. However, as more effector proteins are being investigated, a number of proteins have been identified that stimulate autophagy. One of those recently identified effector proteins is Lpg2411. Although first identified in 2009, interest in the effector did not peak until 2019, when it was identified in a screen for effectors that bind phosphoinositides, special lipids imbedded in eukaryotic cell membranes. It was discovered that Lpg2411 binds specifically to the phosphoinositide species indicative of the autophagosome membrane, the compartment that transports substrate for the autophagy pathway. Furthermore, an autophagic flux assay indicated that Lpg2411 increases autophagy within the host cell. In this study, Lpg2411 was explored as an L. pneumophila effector protein that upregulates the autophagy pathway. In chapter 2, an anti-Lpg2411 antibody was developed that would allow for the detection of endogenous protein translocated from wildtype L. pneumophila strains. The antibody was determined to be specific to Lpg2411 and highly sensitive to the protein. In chapter 3, the antibody was tested for its ability to detect Lpg2411 ex vivo. The antibody was purified and optimized for use in immunofluorescence. With the newfound antibody, Lpg2411 protein signal was tracked throughout an infection to determine when L. pneumophila expresses the protein. Protein localization was then categorized across a series of infections in order to characterize the subcellular distribution of the protein. In chapter 4, Lpg2411 co-localization and interaction with host proteins was investigated. Lpg2411 co-localized with a variety of host proteins involved in the autophagy pathway. The protein also co-localized with a few unexpected proteins that are involved in separate protein degradation pathways. Lpg2411 interaction was investigated with two of the proteins it localized with. Lpg2411 was determined to associate with HDAC6, a protein fundamental in the formation of the aggresome, a collection of aggregated proteins. Lpg2411 displayed no association with LC3B, an integral membrane protein of the autophagosome, despite showing extensive localization with the protein and others associated with the autophagosome. Together, this suggests that Lpg2411 could be impacting protein degradation in more ways than just targeting the autophagy pathway. Overall, this research has furthered the characterization of Lpg2411 and expanded our understanding on how L. pneumophila may seek to impact the autophagy pathway to serve the bacteria’s needs throughout the course of infection.
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    DEVELOPMENT OF AZA-HECK REACTIONS, THE TOTAL SYNTHESIS OF IMPATIEN A, AND EE MEASUREMENT BY LOW-COST MS
    Korch, Katerina Marie
    Nitrogen-containing compounds, particularly nitrogen heterocycle-containing compounds, are ubiquitous in natural products and pharmaceuticals. For this reason, there is great interest in the development of new methods for the synthesis of these heterocycles as well as interest in the synthesis of nitrogen heterocycle-containing natural products. In this thesis, I will describe the development of an aza-Heck reaction for the synthesis of indolines as well as demonstrate the use of an aza-Heck reaction in the total synthesis of the natural product Impatien A. Additionally, I will describe the use of low-cost mass spectrometers in the enantiomeric excess determination of high throughput samples. In Chapter 1, I will describe the development of a 5-exo aza-Heck reaction of aniline-derived electrophiles for the synthesis of indolines. In addition to demonstrating the first use of aniline electrophiles in the aza-Heck field, this reaction is tolerant of a variety of functionality. This reaction can also deliver highly sterically congested products which pose a significant challenge to other methodologies. In Chapter 2, I will describe the first total synthesis of the spirocyclic natural product Impatien A using an aza-Heck reaction. The key steps in the synthetic sequence include an a-arylation to couple an indanone fragment and a substituted aryl bromide. Following Grignard addition, oxidation, and hydroxamic ether synthesis the key aza-Heck reaction was optimized initially using high throughput experimentation. A phosphite ligand novel to the aza-Heck field was found optimal for the challenging aza-Heck reaction of the tetra-substituted alkene. Impatien A is ultimately delivered in seven linear steps from known compounds. In Chapter 3, I will demonstrate the use of low-cost mass spectrometers in the determination of enantiomeric excesses of high throughput samples. High throughput experimentation presents an analytical challenge in that samples are analyzed with little to no purification and, consequently, the presence of reaction components and byproducts can interfere in accurate data collection. This is especially a challenge in enantiomeric separations which are often non-trivial. Mass spectrometry has been utilized in applications as it allows for the discrimination of compounds selectively by mass but use of low-cost mass spectrometers, which are often the only accessible instrumentation to academic laboratories, has not been rigorously explored. In Chapter 3, I will describe such studies to validate this approach.
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    The Immunostimulatory Roles of Synthetic Bacterial-Derived Peptidoglycan Fragments from Pathogenic and Commensal Bacteria
    Mashayekh, Siavash
    The host-pathogen interactions between the human body and microbial pathogens have been the subject of numerous studies for more than a century. Exploration of different aspects of such interactions has led to the emergence of several models such as ‘Self/Non-self’ and ‘Danger’ models, attempting to describe the underlying principles of these encounters. In recent decades and with the advancement of available chemical tools, we have been able to tackle the molecular details of such interactions. In this regard, the human innate immunity has been shown to play a major role, using different classes of pattern recognition receptors (PRRs) to identify pathogens-associated molecular patterns (PAMPs). One of the main sources of these molecular motifs is the bacterial cell wall. Fragments that are shed from the bacterial cell wall are sensed by different classes of innate immune proteins. The human nucleotide-binding oligomerization domain-like receptors, or NOD-like receptors (NLRs) are among these receptors that recognize small synthetic bacterial fragments such as muramyl dipeptide (MDP) and -D-glutamyl-meso-diaminopimelic acid (iE-DAP) and trigger the immune responses. However, as our understanding of potential receptors for these fragments has evolved, our knowledge of chemical intricacies of the bacterial cell wall construct has also been growing. Despite the commonality of the bacterial peptidoglycan (PG) structure, a host of chemical modifications is observed in different bacterial species suggesting that general PG fragments such as MDP does not necessarily represent the full scope of the PAMPs, and consequently, the corresponding receptors. Currently, researchers are limited to small sets of PG probes to study the cellular responses, despite the large pool of potential fragments. In this thesis, the importance of such chemical diversities in the PG structure is explored. Different synthetic methodologies have been used to expand the scope of the PG probes, while examining the significance of subtle chemical changes in the outcome of their immune recognition. In particular, the synthesis of a diverse set of larger cross-linked PG fragments is followed by testing the ability of these distinct PG fragments to elicit immune responses. The results here show that not only different PG-derived molecules can have a differential effect in activation of immune signaling pathways, some of the subtle chemical changes of the PG structure can alter the immunogenicity of resulting fragments and contribute to the pathogenicity of the microorganism. Moreover, since microbial colonization in the human body comprises other players such as fungi and viruses, this work also focuses on the regulatory effects of PG fragments in cellular settings beyond human cells. Particularly, the role of PG fragments in the virulence of Candida albicans, one of the common fungal species in the human microbiota, is shown here. This work indicates the immunological importance of chemical properties of PG fragments at molecular levels. The results here are essential for improving our knowledge of molecular mechanisms involved in the human innate immunity, which is crucial for a better understanding of the host-pathogen interactions. Furthermore, these results can open new ways for designing new antibiotic and preventive therapeutics, as aberrant responses to the PG fragments are linked to several pathological conditions including inflammatory bowel disease, cardiovascular disease, and cancer.
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    Deep Learning for Financial Services Analytics: Novel Algorithms for Industry Classification, Industry Assignment, and Patent Valuation
    Zhao, Xiaohang
    Over the past years, the Financial Service Industry has witnessed an increasing amount of business solutions driven by Financial Technologies (FinTech). A key ingredient of FinTech is the utilization of diversified data sources that are either impossible or hard to be employed by traditional data analytics pipelines. Two notable data sources are network data and textual data, which have been demonstrated to provide useful information for applications such as credit scoring, fraud detection, asset pricing, etc. Albeit with promising application prospect in the Financial Service Industry, textual data and network data are underutilized by current practice: the representation of a financial document usually reduces to counting the frequencies of unique words in it, while the structure of a patent citation network is often summarized by the number of citations initiated or received by each patent. This thesis takes one step forward towards the direction of proposing a general framework for mining business insights from textual and network data based on deep learning methods. Specifically, it studies three related business problems that are fundamental in the Financial Service Industry. Namely, industry classification, industry assignment, and patent valuation. For each of the three problems, the relevant textual data and network data are identified, and a specialized deep learning model is designed by exploiting the unique structure embedded in the investigated problem. The first problem, Industry classification (IC), refers to the activity of identifying economically related firms. The availability of business descriptions from firms’ financial reports brings a new perspective to IC because industry boundaries are frequently reshaped by disruptive innovations, which is hard to capture dynamically without the capability of automatically digesting a vast volume of financial reports in real time. In this regard, one methodological contribution of the thesis is a novel text representation method which allows the semantic similarity between the business description documents of two firms to be measured more accurately. Armed with firms’ pairwise similarities derived from their business description documents, the most economically related firms of a focal firm can be easily identified by ranking other firms according to their similarities with the focal firm. The superiority of the resulted Industry Classification System is then verified empirically by benchmarking it against several state-of-the-art IC approaches. The second problem, industry assignment (IA), is rooted in traditional expert-driven Industry Classification Systems where groups of experts are responsible for defining the hierarchical structure of industry categories and then assigning firms to the predefined industries. Using the language of machine learning, IA can be formulated as a standard classification problem where firms are instances and an industry hierarchy defined by experts are labels. In terms of the leveraged data, while IC is purely text-based, IA takes one step further by simultaneously consider textual data and a special type of network data: the tree structure of an industry hierarchy. The resulted classification model of IA establishes the second methodological contribution of the thesis. While both IC and IA attempt to answer the question that which firms are related in their economic activities, patent valuation (PV) tackles a different but related problem: which firm is likely to bring disruptive technologies that are highly valued by the market and future innovation activities? Accurate assessment of the value of the patent portfolio hold by a company is critical for pinpointing the industry where creative destruction is about to occur. In comparison to IA, the network data employed by PV is much more complicated. The innovation network is heterogeneous (both patents and firms are nodes of the network; patents are connected via directional citations, while firms are linked by various kinds of economic relationships), dynamic (nascent firms keep entering the market, novel technologies are constantly being invented), and attributed (both patents and firms are annotated with side information such as patent documents and financial ratios). Simultaneously modeling the three properties of innovation network incubates the third methodological contribution of the thesis.
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    NOVEL UBIQUITINATED PCNA PROBES FOR UNDERSTANDING DNA DAMAGE TOLERANCE
    Shen, Siqi
    Chapter 1: Ubiquitin is a 76-amino acid protein and is highly conserved in eukaryotes. Ubiquitination is one of the most complex protein post-translational modification. Ubiquitin is conjugated to the substrate protein through a cascade of enzymatic reactions. Ubiquitination plays an important role in regulating proteasomal degradation, chromatin remodeling, cell cycle, immune response, protein trafficking and DNA damage response. In addition to monoubiquitination, ubiquitin can form polyubiquitin chains through one of its seven lysine residues. For example, the most well-known function of ubiquitin in regulating protein degradation is through the Lys48 polyubiquitination. Both mono- and K63-linked poly-ubiquitinations are formed on a nuclear protein proliferating cell nuclear antigen (PCNA), which serve as signals following the stalling of replication fork during DNA replication. PCNA and its mono- or poly ubiquitination are involved in different DNA damage tolerance pathways (error-prone versus error-free). We are interested in characterizing the reader proteins for mono- or poly-ubiquitinated PCNA in regulating DNA damage tolerance. The Y-family DNA polymerase η (Polη) is one of the critical readers for mono-ubiquitinated PCNA at the stalled replication fork. Polη synthesizes pass damaged DNA nucleotide in eukaryotes through translesion DNA synthesis (TLS). TLS is initiated by monoubiquitination of PCNA, which signals the subsequent recruitment of TLS polymerases. Although individual structures of the Polη catalytic core and PCNA have been solved, a high-resolution structure of the complex of Polη/PCNA or Polη/monoubiquitinated PCNA (Ub-PCNA) still remains elusive, partly due to the disordered Polη C-terminal region and the flexibility of ubiquitin on PCNA. To circumvent these obstacles and obtain structural insights into this important TLS polymerase complex, we developed photo-activatable PCNA and Ub-PCNA probes containing a p-benzoyl-L-phenylalanine (pBpa) crosslinker at selected positions on PCNA. Through photo-crosslinking the probes with full-length Polη, specific crosslinking site(s) were identified following tryptic digestion and tandem mass spectrometry analysis. We discovered direct interactions of the Polη’s catalytic core and C-terminal region with both sides of the PCNA ring. Model building using the crosslinking site information as a restraint revealed multiple conformations of Polη in the polymerase complex. Availability of the photo-activatable PCNA and Ub-PCNA probes will also facilitate investigations into other PCNA-containing complexes important for DNA replication, repair and damage tolerance. Chapter 2: It is important to obtain high-resolution structures of the eukaryotic Y-family DNA polymerases such as Polη in complex with PCNA or Ub-PCNA. We combined photo-crosslinking and chemical ubiquitination to generate photo-activatable Ub-PCNA probe for structural studies of the yeast Polη/Ub-PCNA complex. I generated the (pBpa)Ub and the (pBpa)Ub-PCNA probes for complex formation with Polη. Different chromatography methods including ion exchange, nickel or cobalt affinity, heparin and size exclusion were assessed for purification of the Polη/Ub-PCNA complex. The development of (pBpa)Ub-PCNA probe, generation and purification of Polη/Ub-PCNA complex open the door for obtaining a high resolution structure of the complex through the state-of-the-art cryo-EM methodology. Chapter 3: Maintenance of genome stability 1 (Mgs1) is another important Ub-PCNA reader that preferentially recognizes polyUb-PCNA. Mgs1 is a DNA-dependent AAA(+) ATPase and is conserved from prokaryotes to eukaryotes. Mgs1 is an oligomeric protein with yet unknown number of subunits. Mgs1 has been shown to promote genome stability when the replication fork encounters DNA damage during replication. However, the exact mechanism of Mgs1’s biochemical and cellular functions are unclear. Using our photo-activatable PCNA or Ub-PCNA probes, I unveiled the interaction between Mgs1 and PCNA on both the front and back sides of the PCNA ring. The interaction sites between PCNA and Mgs1 were identified using mass spectrometry. Preliminary electron microscopy study of Mgs1 was attempted. Together the studies provided useful information regarding the structure and function of Mgs1 in DNA damage tolerance.
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    IMPROVING RESISTANCE TO VARROA MITES IN HONEY BEE COLONIES VIA CULTURAL BROOD MIXING
    Menz, John F.
    Honey bee, Apis mellifera, colonies are susceptible to failure due to the novel parasitic mite Varroa destructor. Genetic diversity has been shown to be vital to colony health, productivity, and resistance to mites. Genetic diversity can be augmented within a colony via artificial insemination, which mimics the derived polyandrous state of all members of the genus Apis. Alternatively, brood mixing is a manual method of transferring immature bees between colonies, thereby providing a non-technical method of increasing colony genetic diversity. To evaluate the effectiveness of brood mixing for improvement of colony strength and resistance to Varroa mites via augmented genetic diversity, I conducted two field experiments over two seasons. In the first season (2021), honey bee colonies were established with one of four types of queens from distinct geographic breeding regions in the continental US: Florida, Georgia, and 2 queen types from California. These queens did not have distinct selected resistance traits against Varroa mites and there were only minimal effects of brood mixing and queen source on colony productivity and mite levels. In the second field trial (2022), I investigated the mixing effect between only two types of colonies: those with the highly selected Varroa-sensitive hygienic (VSH) trait and wildtype colonies (WT) that lacked the trait. Mixed colonies were observed to investigate the possibility of trait sharing between colonies via repeated brood mixing and resulted in colonies with intermediate adult bee populations and intermediate mite levels, with WT-control colonies having the highest mite levels and VSH-control colonies having the lowest mite levels. Finally, I conducted a thorough pathogen screen using relative quantification of honey bee viruses, and microsporidian and bacterial parasites using real-time qPCR at 3 time points in the 2021 field trial to assess the risk of pathogen and disease spread between brood mixed colonies. Brood mixing did not affect pathogen prevalence nor relative quantities, however, general increases in Deformed Wing Virus and decreases in Black Queen Cell Virus and Sacbrood Virus were observed over the season.
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    DROUGHTS IN THE MIDST OF CONFLICTS: A MIXED-METHOD ANALYSIS OF WATER INSECURITY & CIVIL WAR DURATION AND OUTCOMES
    Ozturk, Yunus
    This dissertation aims to understand the nexus between water insecurity and civil war duration and outcomes. As many civil wars have occurred in places where people’s livelihoods and agricultural production are sensitive to water availability/scarcity, this dissertation examines whether climate change-induced environmental problems, particularly persistent droughts, lead to prolonged civil wars. Given the interconnectedness of human and state security, as highlighted in the human security literature, this dissertation primarily argues that persistent droughts cause protracted civil wars by undermining both human livelihoods and state capacity in ways that force warring parties to alter their strategic calculations regarding whether to end or continue the war. While a variety of social, political, and economic factors undoubtedly contribute to civil war dynamics, to date, the extant research on civil war duration and outcomes has focused on socio-political and socio-economic factors without considering environmental issues. This study, therefore, examines the contribution of persistent droughts to the prolongation of civil wars and their varying outcomes by changing the balance of power between belligerents. In this regard, this dissertation builds on a mixed-method strategy that combines both quantitative and qualitative analyses to provide internally and externally validated evidence. The results of the quantitative component show that droughts are more likely to shorten the duration of civil wars, primarily through negotiated settlements and, to a lesser extent, through government victories. Moreover, particularly the weight of agricultural production in the economy and the number of active non-state actors contribute to this result. However, no empirical evidence has been found for civil wars that end in rebel victories. Interestingly, the exclusionary and discriminatory state policies against certain social groups do not have any statistically significant impact on the drought-civil war dynamics nexus. The qualitative component, on the other hand, sheds light on how persistent droughts lead to protracted civil wars and concludes that droughts can prolong civil wars by undermining people’s livelihoods and, more importantly, state capacity. Nevertheless, droughts are neither a necessary nor a sufficient condition for protracted civil wars. Civil wars in which warring parties compete for the control of exploitable natural resources are likely to be prolonged regardless of droughts. In such civil wars, droughts are typically used by central governments as tools for counterinsurgency operations by manipulating famine conditions and international emergency aid. Thus, for droughts to prolong civil wars, at least one of the two conditions must be met: Rebel groups are unable to form a united/coordinated front against government forces in the early stages of the war, and/or government forces conducting counterinsurgency operations are unable to obtain external support, be it financial or military.
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    Controlling and predicting siRNA delivery to accelerate the development of clinically relevant nucleic acid therapeutics
    Roh, Esther Heran
    The therapeutic use of short-interfering RNAs (siRNAs) has garnered significant interest as an approach to combat a wide range of intractable diseases, but the clinical translation of nucleic acid-based drugs remains limited because of the inability to formulate and test these treatments for therapeutic potential in an expedient manner. Elucidating structure-relationships between siRNA nanocarriers and gene silencing kinetics can advance clinical application of siRNA therapeutics by guiding the design of more effective nanocarriers and dosing regimens, ultimately reducing the heavy reliance on tedious, experimental testing of current screening methods. In this dissertation, three approaches were explored to gain fundamental insights into interactions between (1) siRNA and delivery materials and (2) delivery materials and biological barriers. In the first approach, a layer-by-layer nanocarrier was formulated by varying cationic block lengths of photo-responsive polymers to modulate siRNA binding efficiency, which enabled the encapsulation of multiple siRNA doses and precise control over the release of each individual dose. In the second approach, a simplified kinetic model was developed by identifying and including only key rate-limiting steps of the RNA interference process, resulting in a model capable of accurately predicting siRNA formulation efficacies both in vitro and in vivo using as few as experimental data from a single time point as an input. In the third approach, a modified kinetic model was developed by identifying a lipid nanoparticle (LNP) characteristic (i.e., measurement of solubility) that showed good correlation to major biological barriers identified using the second approach, and this model was able to predict the effect of changing ionizable lipid structures and the molar ratios of LNP components without experimental testing. Taken together, these approaches have elucidated key structure-function relationships related to siRNA delivery using both polymers and lipid nanocarriers and are expected to guide formulation strategies that can enhance the efficacy of next-generation siRNA delivery technologies.
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    The Roads to Politics: Chinese Private Entrepreneurs and China's Policy-making Processes
    Li, Jing
    This dissertation is a search for a better explanation of Chinese private entrepreneurs’ engagement and influence in China’s policy-making process, aiming to provide a nuanced picture that may aid our understanding of China’s evolving political economy and flourish the existing broader literature of comparative political economy. In particular, it attempts to examine the behavioral pattern of business lobbying and provide structural explanations on the business community’s policy influence. The central question of this study concerns through which pathways Chinese private entrepreneurs engage with policy-makers and conduct policy advocacy, as well as to what extent they exert influence in China’s policy-making process. To this end, this research has followed a historical trail through investigation of how and to what extent Chinese private entrepreneurs are able to vie for influence on China’s policy-making process by working cooperatively with two types of state-business engagement intermediaries in China—business association and think tank. This dissertation adopts a tripartite-embeddedness state-society interaction analytical approach on the premise of existing co-evolutionary analytical framework to trace how Chinese private entrepreneurs engage in China’s policy-making as well as assess business policy influence. It employs a mixed method approach that combines quantitative and qualitative methods to trace a wide spectrum of business lobbying and state-business interactions in China that take place through business associations and think tanks respectively. It informs that China’s policy-making is becoming progressively open and expanded. The shifting advocacy coalitions and policy advocacy patterns in terms of business lobbying might have some implications over state-society relations and the policy-making process in China. It is possible that Chinese private entrepreneurs, having leveraged more formal and official access to China’s policy process, will progressively push forward more institutionalized policy advocacy channels and gain increasing influence over China’s policy process. These changes might recalibrate allocation of resources and networks in Chinese policy and socioeconomic realms and disequilibrate the established distribution of policy-making power among state and societal actors. Although it is still not sure if the bottom-up dynamics in China’s business lobbying and policy-making process prepares the ground for the future surge of China’s political transformation, these changes do add a layer of complexity to China’s policy-making system and might increasingly push forward the broader reconfiguration of the state-society relations in China. Nevertheless, the completion of this dissertation comes at an unsettled time of period under Xi’s governance, during which the CCP-state’s power concentration makes its recent comeback while the collective policy-making leadership begins to wane since 2012. There is now still no sign of how long China will sustain its economic growth while remaining a strong state policy-making power. In current circumstance, while seemingly the policy advocacy channels for business community have been broadened while the chance of social influence in China’s political field increases, I thus far still remain cautious to reach much assertive conclusions on private entrepreneurs’ higher level of influence in China’s policy-making in the short-term.
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    ELUCIDATING BACTERIAL-FUNGAL CROSSTALK THROUGH BACTERIAL PEPTIDOGLYCAN SENSING AND DETECTION IN THE HUMAN COMMENSAL CANDIDA ALBICANS
    Maddison Crump, Geneva
    The human innate immune system is composed of functionally distinct modules that has evolved to provide different forms of protection against invading pathogens. The adaptive immune system provides long lasting pathogen specific immune responses. The innate immune system, though less specific to pathogens, serves as the body’s first line of defense against invading pathogens. The innate immune system is a conserved host response that entails the sensing of pathogen-associated molecular patterns (PAMPS) through germline-encoded pattern recognition receptors (PRRs), which initiate pathway-specific signaling networks, resulting in rapid responses that serve as the hosts’ first line of defense. Such germline encoded PRRs include but are not limited to Toll-like receptors (TLRs), RIG-I-Like (RLRS), NOD-like receptors (NLRs), and DNA receptors. PRRs are an irrefutable asset for the proper maintenance of human health. While they are traditionally known to recognize microbial molecules during infection scenarios, ligands for PRRs are not exclusive to foreign pathogens and are abundantly produced by the resident microbiota during normal colonization. The human microbiota consists of 10-100 trillion symbiotic microbial cells that reside in the body and vastly outnumber human somatic and germ cells. Microorganisms of the microbiota include bacteria, viruses, fungi, and protozoa. Together, these microbes form ecological communities in many anatomical sites. As such, the microbiota affects many vital functions of the human body. One of the most common residents of the human microbiota is the polymorphic fungi Candida albicans (C. albicans). C. albicans is a commensal member of the human microbiota, typically residing in the gut and other mucosal surfaces of the body. In the human host, C. albicans interacts with a plethora of bacterial species and relies on these interactions for homeostasis under normal conditions. In the event of microbiota nice disruption, such as immune incompetence of the host, C. albicans transcends from a commensal state to a virulent state. Specifically, owning to the virulence of C. albicans is the phenotypic switch from budding yeast (blastophore) to filamentous state (hyphae) followed by transcriptional regulation of hyphae specific genes upon introduction of certain environmental signals. Central to transcriptional regulation for virulence associated genes and subsequent pathogenicity, is a spike in the cAMP-PKA cascade. This signaling pathway is upregulated upon binding of the adenyl cyclase Cyr1p to bacterial peptidoglycan. Cyr1p behaves much like a PRR, in its ability to bind and sense ligands that are foreign to the fungi. Particularly, this protein contains an evolutionary conserved leucine rich repeat (LRR) protein domain commonly found in human PRRs such as TLRs, and NOD like receptors. Through its LRR domain, Cyr1p can sense and detect bacterial peptidoglycan (PG). PG, being a major culprit for the transition of C. albicans from commensal to pathogenic, is a focal point of the bacterial-fungal relationship and is at the molecular interface facilitating these cross-kingdom interactions. We sought to understand bacterial-fungal crosstalk by characterizing the Cyr1p LRR domain, investigating the Cyr1p-LRR-PG interactions, and probing the phenotypic plasticity of C. albicans cells in the presence of synthetic PG fragments. In our efforts to characterize the Cyr1p-LRR domain, we have biochemically classified this domain as a peripheral membrane protein and have demonstrated that the extended membrane associated LRR construct retained the ability to interact with previously known bacterial PG fragments such as Muramyl tripeptide (MTP). We have also shown the differential morphological regulation of C. albicans hyphae by various synthetic PG fragments and have correlated these findings to anomalous transcriptional regulation of Hyphae Specific Genes (HSGs). Though maintenance of HSGs at the transcriptional level ensures hyphal growth and elongation, we reasoned that our observed anomalous HSG transcriptional pattern is due to inadequate knowledge of the entire signaling pathways that govern the morphological transition from budding to hyphae and therefore commensalism to pathogenicity. In this dissertation, the characterization of the long-standing difficult nature of the Cyr1p-LRR domain has been explained, as this domain has been shown to be membrane associated. This may also foreshadow how C. albicans can interact with PG fragments that are small, polar, and not readily membrane permeable ligands. Furthermore, the exploration of C. albicans morphological plasticity in the presence of synthetic bacterial PG fragments has indicated that there is specificity in the PG ligands that are able to produce true hyphae in the microbe. These findings, along with anomalous HSG regulation, presage that without proper transcriptional regulation, C. albicans can readily convert between yeast and hyphal forms.
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    Identification and Interrogation of Ubiquitin and Ubiquitin-like Protein Decoders
    Banos, Christine
    Regulation of cellular processes is multifaceted and complex. Regulation can be achieved through post-translational modification (PTM) of a protein to either up or down regulate a cellular pathway. Ubiquitin is a PTM and codes for an array of signaling events in the cell. Because ubiquitin itself can also be a substrate of ubiquitination, a complex network of modifications exists, thus signaling different fates for the substrate proteins, this is known as the ubiquitin code. Ubiquitin is most celebrated for its role in signaling proteosome degradation of the substrate protein, however it is also known to signal autophagy, DNA damage repair, and cell cycle regulation, to name a few. Deubiquitinases, or DUBs, function to remove the ubiquitin modification from the substrate protein and effectively abrogate the signal. DUB dysregulation has been observed in disease such as cancer and neurodegenerative disease leading to aberrant signaling that is detrimental to the cell. This disease-associated dysregulation makes DUBs attractive therapeutic targets for small molecule intervention. Promising DUB inhibitors in preclinical models encourage the development and pursuit of inhibition of other disease-associated DUBs. Ubiquitin-like protein, Interferon Stimulated Gene 15 (ISG15), is structurally similar to diubiquitin and also functions as a PTM. ISG15 is unique in that it additionally functions as a free protein, reportedly acting in a non-covalent manner in anti-viral response by sequestering viral proteins and acting extracellularly as a cytokine-like molecule. Literature surrounding ISG15 has primarily co-opted techniques for studying ubiquitin and has thus focused on ISG15’s PTM activity in its analogous process, ISGylation. Targets of ISGylation have been identified by proteomics as well as characterization of the lone human deISGylase, USP18. Despite this work, a rigorous understanding of ISG15’s non-covalent interactions and functions remains elusive. In this work, the development and utilization of novel protein-based probes was performed to better understand the recognition of branched polyubiquitin chains and to elucidate interactions of ubiquitin-like protein ISG15 in innate immune response in the first and second chapters respectively. The final chapter discusses the development of a cell-based assay in order to advance high-throughput screening in drug discovery efforts to inhibit USP15. In total, this work improves the ability to interrogate critical cellular pathways with novel protein probes, photocrosslinking, and proteomics, while also advancing the physiological relevance and efficiency of drug screening and development efforts using live cell imaging.
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    BONDING OF OVERLAYS TO ULTRA-HIGH PERFORMANCE CONCRETE
    Larfi, Saber
    This thesis studies the bond performance of overlays to ultra-high performance concrete (UHPC) within the context of Delaware Department of Transportation (DelDOT) bridge applications. Polyester polymer concrete (PPC), latex modified concrete (LMC), and modified class D concrete (MCD) are applied as overlays on UHPC components to protect the bridge deck from deicing salts and provide a smooth riding surface. These overlays differ in composition, bonding agents used, mechanical and physical properties. The difference in properties between these materials results in distinct bond performance to the UHPC substrate. It is critical for an overlay to develop good bonding with the substrate to maximize overlay durability and minimize maintenance. UHPC is a cementitious composite material with optimized particle packing, internal steel fiber reinforcement, and a low water-to-cement ratio, resulting in superior mechanical properties. UHPC has high compressive strength (at least 22 ksi) and sustained post-cracking tensile strength (of at least 0.72 ksi). Compared to conventional and high-performance concretes, UHPC is nearly impermeable (owing to its discontinuous pore structure), resulting in considerably improved durability. Transportation agencies are using UHPC in bridges for link slabs, connections between precast components, and entirely UHPC structural members. To ensure adequate bonding of overlays to the UHPC substrate, a minimum pull-off bond strength of 250 psi and 200 psi is recommended for PPC and LMC overlays by AASHTO T-34 and ACI 548.4M-11, respectively. In addition, DelDOT specifies a minimum pull-off bond strength of 250 psi for PPC and MCD overlays; the DelDOT specification does not have an explicit bond strength requirement for LMC. Current literature (Haber et al., 2017) discusses the bond performance of overlays bonded to conventional concrete substrates. However, when it comes to UHPC substrate, the literature is limited to investigating LMC and UHPC as overlay while considering only scarification and hydrodemolition as surface preparation methods. The lack of knowledge regarding the bond performance of other overlays (PPC and MCD) on UHPC as well as the influence of additional surface preparation methods was addressed in this work. The study evaluated the effects of cording depth, overlay age and substrate preparation method, specifically, grinding and sandblasting (GSB), hydrodemolition (HD), surface retarder (SR), and control “non-prepared” (NP) surface on the bond strength. Furthermore, the efficiency of different roughness measurement methods in quantifying the roughness of prepared UHPC was investigated. The three roughness measuring techniques were the ICRI concrete surface profile (ICRI CSP) chips, sand patching, and surface profile gauge. The sensitivity study looking at the effects of coring depth on bond strength concluded that the coring depth of 0.5 in. was the most appropriate for pull-off bond tests on UHPC. Results indicated that surface prepared by GSB performs better than NP substrate surface. However, HD and SR increased surface tortuosity beyond GSB and exposed steel fibers, which further promoted mechanical interlocking across the UHPC-overlay interface. In addition, this study evaluated the effect of each overlay age (7, 14, 28, and 56 days) to show the gain of pull-off bond strength. For MCD overlays, the analysis of the substrate hygric state’s influence (dry versus saturated-surface-dry) on the bond performance showed no distinction due to UHPC being nearly impermeable. Finally, in terms of roughness measuring methods, the surface profile gauge (micrometer) was deemed to be more effective in quantifying the roughness of prepared UHPC surfaces compared to sandpacthing that was only applicable to NP and GSB surfaces. ICRI CSP chips were not used to qualitatively assess the texture of the UHPC substrate because they were created for normal concrete applications which has significantly different microstructure compared to UHPC.
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    ROLE OF TART CHERRY IN THE PREVENTION OF HYPERTENSION AND THE MODULATION OF INFLAMMATORY SIGNALING
    Mansoori, Safiyah
    Hypertension increases the risk for vascular damage, atherosclerosis, and subsequent cardiovascular disease (CVD) related morbidity and mortalities. The development and progression of several chronic conditions, including hypertension, are influenced by inflammation. Chronic low-grade inflammation and hypertension, both prevalent in the aging population, can be modulated by dietary and lifestyle choices. Our laboratory has previously shown that 12 weeks of tart cherry (TC) juice consumption can reduce systolic BP and markers of inflammation and oxidative stress in older adults. There are several bioactive compounds in TC and evidence suggests these compounds in isolation can influence inflammatory signaling pathways that contribute to the pathogenesis of hypertension. To first understand the impact of diet on BP, we conducted a cross-sectional study on 128 adults aged 65–80 years. Multiple linear regressions were conducted to examine the influence of major dietary factors on systolic and diastolic BP. We also wanted to understand the role of TC in reducing BP. To study this, human coronary artery endothelial cells (HCAEC) were exposed to 0-500μg/mL of TC extracts in the presence or absence of Angiotensin-II (Ang-II), which is known to increase BP and inflammation. Western blots were used to examine the effects of TC and/or Ang-II on the protein expression of nitric oxide synthases and inflammatory molecules associated with the NF-κB signaling pathway. Results of the cross-sectional study showed a significant association between intake of added sugar and systolic and diastolic BP in females. Whole fruit consumption was associated with a reduction in diastolic BP in both males and females. The regression model predicted that for every 0.71 cup increase in whole fruit consumption, there would be a 2.8 mmHg reduction in diastolic BP. In the absence of Ang-II, TC exposure did not influence eNOS expression. Expression of iNOS was reduced by TC at all doses in the absence of Ang-II. Levels of p65 were significantly reduced at 62.5 and 125μg/mL compared to the control. Phosphorylated p65 was upregulated at the 62.5 μg/mL dose and ICAM-1 was similar between groups. In the presence of Ang-II, the 62.5 Ang and 125 Ang exposures resulted in a 0.75 fold and 0.71 fold reduction in iNOS respectively. Ang-II did not significantly affect NOS or inflammatory markers compared to the control. This could be due to the metabolism of Ang-II or loss of Ang-II type 1 receptor in cell culture. Our findings support increased fruit consumption for the reduction of BP in older adults. Additionally, TC exposure can reduce the expression of iNOS which is known to contribute to the development of hypertension.
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    EXTRACELLULAR MATRIX (ECM)-BASED BIOMATERIAL STRATEGIES TO CONTROL DELIVERY OF GENE AND SMALL MOLECULE THERAPIES IN WOUND REPAIR
    Hwang, Jeongmin
    Despite the great potential of topically administered therapeutics in wound repair, due to the harsh wound environment, topically administered therapeutics are cleared out from the wound quickly, resulting in the reduced local concentration and their effectiveness of therapeutics. To overcome this limitation, the overall goal of my dissertation work is to improve the efficacy of topically administered therapeutics through the control over the therapeutic delivery kinetics using the interactions between therapeutic carriers and matrices. I specifically leverage the hybridization of collagen mimetic/like peptides (CMP or CLP) with a native collagen through the strand invasion process to tether CMP/CLP modified nanostructure carriers onto collagen-containing matrices. I hypothesize that CMP/CLP modified carrier and collagen tether approach would result in the extended the duration of therapeutic effects and control over the delivery of the cargo in response to cell-mediated collagen degradation. The first/second objectives of this thesis were to control growth factor gene transfer kinetics while regulating cell behaviors via manipulating both the number of CMP-collagen tethers and the ECM composition for the improved wound repair. Disruption in vascularization during wound healing can severely impair healing. Pro-angiogenic growth factor therapies have shown great healing potential; however, controlling growth factor activity and cellular behavior over desired healing time scales remains a critical challenging. I developed gene-activating hyaluronic acid-collagen matrix (GAHCM) comprising DNA/polyethylenimine (PEI) polyplexes retained on hyaluronic acid (HA)-collagen (HCM) hydrogels using CMPs. First, I observed that polyplexes with 50% CMP-modified PEI (50 CP) showed enhanced retention of polyplexes in HCM hydrogels by 2.7-fold as compared to non-CMP modified polyplexes. Moreover, the enhanced the retention of polyplex through CMP modification, as well as HA-CD44 interaction via the incorporation of HA in the collagen hydrogel increased the gene transfection efficiency to fibroblast. Furthermore, when fibroblasts were exposed to pro-angiogenic and pro-healing vascular endothelial growth factor-A (VEGF-A)-GAHCM, the 50 CP matrix facilitated sustained VEGF-A production for up to 7 days, with maximal expression at day 5. This sustained VEGF-A production using VEGF-GAHCM with 50 CP stimulated prolonged pro-healing responses, including the TGF-β1-induced myofibroblast transformation. In addition, application of fibroblasts containing VEGF-GAHCM with 50 CP stimulated the increased growth and persistent migration of endothelial cells (ECs) for at least 7 days, as compared to non-CMP modified GAHCM. Moreover, this resulted in the high CD31 expression on ECs and formation of an interconnected EC network with a significantly higher network volume and a larger diameter network structure. Lastly, application of VEGF-GAHCM with 50 CP in murine splinted excisional wounds facilitated prolonged pro-healing and pro-angiogenic responses resulting in the overall enhanced wound closure via increased myofibroblasts differentiation and blood vessel formation, improved granulation tissue formation, and faster re-epithelialization. Overall, these findings demonstrate the use of ECM-based materials to stimulate efficient gene transfer and regulate cellular phenotype, resulting in improved control of growth factor activity for wound repair. The third objective of this thesis was to design new antibiotic delivery systems that maximize pharmacological effects and minimize side effects. Despite the great promise for antibiotic therapy in wound infections, antibiotic resistance stemming from frequent dosing diminishes drug efficacy and contributes to recurrent infection. To overcome the limitations of current antibiotic therapies, I developed elastin-like peptide and collagen-like peptide (ELP-CLP) nanovesicles tethered to collagen-containing matrices to control vancomycin delivery and provide extended antibacterial effects against methicillin-resistant Staphylococcus aureus (MRSA). I observed that as compared to liposome formulations, ELP-CLP nanovesicles showed enhanced entrapment efficacy of vancomycin by 3-fold and enabled the controlled release of vancomycin at a constant rate with zero-order kinetics. Moreover, ELP-CLP nanovesicles could be retained on both collagen-fibrin (co-gel) matrices and collagen-only matrices, with differential retention and release on/from the two biomaterials resulting in different release profiles of vancomycin. Overall, the biphasic release profiles of vancomycin from ELP-CLP tethered collagen/co-gel more effectively inhibited and delayed the growth of MRSA even after repeated bacterial inoculation as compared to matrices containing free vancomycin. Thus, this newly developed antibiotic delivery system exhibited distinct advantages for controlled vancomycin delivery and prolonged antibacterial activity relevant to the treatment of wound infections. In summary, this dissertation describes CMP modification of nanocarriers enables not only the extended delivery of therapeutics from collagen-containing matrices through CMP and collagen tethers, but also the maximized therapeutic effects in vitro. Thus, this work suggest that CMP-collagen tether approach has significant potential to overcome key challenges in the topically administrated therapeutics for wound healing and regenerative medicine.
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    STEREOSELECTIVE TRANSFORMATIONS OF IMINIUM IONS VIA COPPER CATALYSIS
    Santana, Samantha Olga
    This dissertation focuses on stereoselective transformations of iminium ions, which are mediated via copper(I) catalysts. Chapters 1–3 focus on developing stereoselective alkynylations to yield saturated, substituted N-heterocycles from commercial or easily-synthesized precursors. Chapter 4 describes discovery and examination of a novel kinetic resolution of benzoisoxazolines. Chapter 1 describes an enantioselective alkynylation of unstabilized cyclic iminium ions, formed in situ from cyclic α-methoxyaminals. This method utilizes a copper(I)/PyBOX catalyst to generate chiral copper(I) acetylides, which undergo an addition to the iminium ion to yield enantioenriched, substituted cyclic amines. Broad scope is demonstrated in both alkynyl partners and aminal identity under mild conditions and with high enantioselectivities. This research finds its utility in medicinal chemistry and total synthesis to synthesize saturated heterocycles with highly predictable stereochemical outcomes. Chapter 2 describes a diastereoselective alkynylation of β-bromoiminium ions, which are formed in situ from α,β-methoxy bromoaminals. This method uses a Lewis acid to cleave a C–O bond and form the iminium ion, which is stabilized and stereocontrolled by the bromide moiety. These factors result in a diastereoselective alkynylation using a copper(I) acetylide to yield β-bromo-alkynylated cyclic amines. This method offers broad scope under mild conditions, demonstrating stereoselectiveheterocyclic synthesis and facile derivatization of potentially bioactive compounds. Chapter 3 describes my efforts towards an enantioselective and diastereoselective halogenation-alkynylation of cyclic enecarbamates. I envisioned a dynamic kinetic resolution wherein the enecarbamate could react with a halide source via reversible halogenation. These intermediates could then interconvert between both enantiomers of the halo-iminium ion, where one of the intermediates could be preferentially attacked by a chiral copper(I) acetylide. Alternatively, I hypothesized a pathway in which the halogenation could be achieved via a chiral halogenating reagent, which would provide a single enantiomer of the halo-iminium ion. This reaction could then be followed by a diastereoselective alkynylation to yield enantioenriched halo-alkynylated piperidines. Chapter 4 describes a kinetic resolution of benzoisoxazolines, which employs a chiral copper(I)/PHOX catalyst to differentiate between two enantiomers of starting material. One enantiomer of starting material reacts to form a benzoxazepine while the other enantiomer remains untouched and enantioenriched. This method requires 1.) a stoichiometric amount of terminal alkyne and base and 2.) specific properties for the terminal alkyne for the overall reaction to be successful. Cleavage of the N-O bond may also lead to enantioenriched α-tetrasubstituted amines, allowing for further derivatization and pathways for bioactive synthesis.
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    SURFING THE THIRD WAVE: THE THIRD WAVE FEMINIST MOVEMENT ONLINE
    Craven, Nena Sechler
    This dissertation explores the role of the internet and virtual community organization of the feminist movement of the late 2000s and early 2010s. The third wave of feminism is an internetworked social movement—it exists on and in conjunction with the internet and world wide web. Internetworked social movements can be more accessible to marginalized groups than other forms of social movement, but can also involve unique challenges and disadvantages. This dissertation examines how third wave feminists participated in the feminist blogosphere of the late 2000s/early 2010s, what participants in the feminist blogosphere did to engage with the feminist movement, and how inclusive a space the online feminist blogosphere was. Using original survey data collected in 2010 and 2011, this project analyzes the social characteristics and feminist identity of participants in the feminist blogosphere of that time period, as well as an exploration of challenge incidents in which social boundaries of the space are tested and negotiated.
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    Multi-mode Instabilities Arising in Hypersonic Flow Conditions For Aerospace Applications
    Liang, Tony
    Research in hypersonic aerodynamics is important in understanding the practicality of sustained high-speed flight and the design parameters of such vehicles. Hypersonic boundary layer transition is dominated by the presence of various disturbance (Mack) modes present within the boundary layer which undergo by modal growth and eventually transition the flow to turbulence. Understanding these dynamics of these modes and their interactions within the boundary layer can bridge the knowledge gaps in the fundamental causes of heat transfer, friction drag, lift and other properties which become critically important in hypersonic flight. The aim of this research is to perform a analytical study utilizing computational fluid dynamics (CFD) coupled with boundary layer stability analysis employing linear stability theory (LST) and parabolized stability equations (PSE) to help understand the dynamics of Mack modes and their nonlinear interactions. One question to be studied is the source of energy driving the 1st and 2nd mode instabilities. A characterization of the energetics of the 1st and 2nd modes was performed at various flow conditions to further understand physical mechanisms governing the modal growth pathway to transition, and was shown that the traditional 1st mode definition is incomplete. A design study into a geometry conducive to 1st and 2nd mode interactions was performed and investigated. With such a geometry, the dynamics between a 1st mode dominated boundary layer with an existing 2nd mode was investigated. Finally, with understanding of the thermoacoustic interpretation of the 2nd mode, a impedance boundary condition is applied to a canonical conical geometry in an attempt to analyze its effect on certain unstable waves within the boundary layer. Understanding the dynamics of these modes and their interactions within the boundary layer can bridge fundamental knowledge gaps governing various phenomena in hypersonic flight.
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    EMERGENT SPIN DYNAMICS IN MAGNETIC NANOSTRUCTURES AND MAGNONIC HYBRID SYSTEMS
    Taghipour Kaffash, Mojtaba
    One of the issues regarding current electronic devices is that they are based on electron movements to control and transmit information. As a result, much power is wasted in Joule heating. The field of magnonics is concerned with utilizing magnons, the elementary quanta of spin waves, as energy-efficient alternatives to charge-based electronics. Engineered arrays of 2D or 3D nanomagnetic structures offer interesting opportunities for low-power magnonics. Artificial spin ice, which are 2D or 3D magnonic crystals, in which the band structure can be controlled by external parameters, have attracted increasing attention in recent years. Due to their rich magnetic microstates, they could be used for various magnonic applications including wave-based computing and tunable microwave filters. However, artificial spin ice requires more investigations on lattice design and controlling the magnetization dynamics to make it practical for computing and storage devices. As a part of this thesis project, magnetization dynamics in different types of artificial spin ice (ASI) lattices were studied using two experimental techniques, microwave (MW) absorption, and Brillouin light scattering spectroscopy (BLS) techniques, along with micromagnetic simulation technique (using mumax3). First, an ASI lattice in the form of submicron Ni81Fe19 nanodisk arrays closely packed on a honeycomb lattice was studied. Rich mode spectra related to saturated states at high-frequency/high-field and low-frequency/ low-field dynamics related to vortex creation and annihilation were reported. Controllable spin-wave dynamics and spin-wave channel formation using experimental conditions were shown via micromagnetic simulation. This result was confirmed using the micro-focused BLS technique, which provided the first experimental visualization of magnetization dynamics in ASI. Second, a bicomponent square ASI made of two dissimilar magnetic materials, i.e., Ni81Fe19 and Co90Fe10, was introduced. Unique dynamic spectra related to each sublattice were discovered, and intra- and inter-lattice dynamics originating from different magnetization properties of each material were observed. It was found that the dynamics of the entire lattice are affected by the interaction of the sublattices, and proper choice of materials gives one more degree of freedom to finely tune dynamics in ASI besides other controllable experimental conditions. This result was complemented with a different bicomponent structure defined on a honeycomb lattice. My study demonstrates the capability to achieve an innovative class of 2D magnonic crystals, introducing new concepts in the field of nanomagnonics. Magnons are highly tunable and can be coupled to different types of excitations, such as photons, phonons, etc. A coherent conversion of magnons to photons requires strong coupling between subsystems. This type of strong magnon-photon (MP) coupling can be used for coherent microwave to optical down- and up-conversion, a prerequisite for large-scale quantum information transfer applications. Most works on MP coupling have focused on microwave cavity resonators due to their high-quality factors and bulk yttrium iron garnet (YIG) samples due to their high number of spins. This large size makes them unsuitable for on-chip solutions. Within the framework of this thesis project, direct probing of MP coupling in a planar geometry, a split-ring resonator (SRR), and thin YIG was observed using the BLS technique. It was complemented by the MW absorption technique. Two YIG films with thicknesses of 200 nm and 2.46 μm were investigated, and a strong coupling regime was observed for the thicker sample, while a magnetically induced transparency (MIT) regime was observed for the thinner sample. It was shown that BLS is advantageous in probing the magnonic characteristics of MP coupling, while the MW absorption technique is advantageous in detecting the photonic characteristic. Furthermore, MP coupling detection using the BLS technique demonstrates MW to optical upconversion. The planar geometry studied here provides spatially-resolved observation of MP polaritons and can serve as a foundation for studying magnons strongly coupled to MWs. Lastly, this dissertation discusses the possibility of studying magnetization dynamics in a few arrays of magnetic microstructures with a few spins by introducing mi- microresonators, specifically, R-type microresonators (RTM). RTMs are compatible with nanofabricated devices, and successful detection of the mode spectra for a few arrays of Ni81Fe19 microstructures was demonstrated. This study establishes the groundwork for future investigations into MP coupling based on RTMs in magnetic microstructures.
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    IN SILICO, IN VITRO, AND IN VIVO EVALUATION OF THE TOXICITY PROFILE OF NATURAL PHENOLIC COMPOUNDS AND SYNTHESIZED BISPHENOLS
    Zhang, Xinwen
    Food safety is the priority of the food industry. Natural phenolic compounds are in abundance in plant-based foods, have a wide variety of structures and are known for their potential bioactive benefits; however, the relationship between these biological functionalities and their potential toxicity is not clear. More and more studies have demonstrated potential toxicities of these dietary phenolic components. Bisphenol A (BPA) is an essential building block for many polymeric systems, such as polycarbonates and epoxy resins. Its widespread use in various consumer products and food packaging materials poses significant safety and environmental concerns. Efforts are underway to address the environmental challenges associated with BPA, including regulatory measures and the search for safer alternatives. As society seeks more sustainable, greener and safer alternatives of BPA, it is vital to generate a comprehensive evaluation platform to target its possible toxicity endpoints. The aim of the current project is to investigate the toxicological profile of natural phenolic compounds and synthesized lignin-derivable monomers as BPA alternatives. In the first study, the developmental toxicity, endocrine disruption effect, and mutagenicity of thymol and carvacrol were investigated at low exposure doses. The results indicated that as phenolic isomers, thymol and carvacrol had different toxicity patterns on the three toxicity endpoints. Carvacrol showed higher binding affinities to two estrogen receptors, had weak estrogenic activity (EA) at 10−12 M, and negatively impacted chicken embryonic growth at 50 μg/kg. In the second study, toxicity of four common flavonoids: genistein, apigenin, quercetin, and luteolin were evaluated and compared. In agreement with the in silico molecular docking results, genistein and apigenin showed higher EA from the MCF-7 cell proliferation assay than EA of luteolin and quercetin. Moreover, genistein and luteolin demonstrated high developmental toxicity in the chicken embryonic assay (at 45–477 μg/kg) with a mortality rate of up to 50%. Among the tested flavonoids, quercetin (a flavonol) with a 2-hydroxyl substitution in the phenol ring exhibited lower developmental toxicity and EA. In the third study, we investigated the toxicity of two monolignols: guaiacol (G) and syringol (S), mixtures with varied S/G ratio, and three lignin depolymerization samples from poplar, pine, and miscanthus species. The results revealed that the S/G ratio impacts the mutagenicity and developmental toxicity in chicken embryos caused by lignin monomers. The mutagenicity potential of S/G mixtures and lignin monomers was correlated with the syringol proportion, while the adverse effects observed in the chicken embryonic assay were linked to the guaiacol ratio. In the last three studies (Study 4-6), we focused on exploring the toxicity of bisphenol A (BPA) and lignin-derivable monomers as potential BPA replacements. In the fourth study, genotoxicity of six lignin-derivable bisguaiacols with varying regioisomer contents and degrees of methoxy substitution was investigated. Results showed that most bisguaiacols except m,p’-BGS did neither show signs of mutagenicity in the Ames test nor induce DNA damage in comparison to BPA in the Comet test. The findings suggest that having at least one methoxy ortho to a phenolic hydroxyl group contributed to the lower oxidative DNA damage than BPA. In the fifth study, the EA and developmental toxicity on chicken embryo model of lignin-derivable bisguaiacols/bissyringols were investigated. Bissyringol A (BSA) with four methoxy groups showed undetectable EA and lack of estrogenic response in the chicken fetal liver. A comparable developmental toxicity was observed from the in vivo chicken embryonic assay for lignin-derivable monomers and BPA at environmentally relevant test concentrations. In the sixth study, the in vitro metabolism pattern of three lignin-derivable compounds as well as BPA were explored using ultra-performance liquid chromatography-mass spectrometry. Moreover, we conducted the in vivo toxicokinetic study of BPA via a chicken embryo model. Our results, in agreement with the predicted data, demonstrated that three lignin-derivable compounds had identical in vitro metabolite pathways which are similar to that of BPA. In summary, we found that the two phenolic monoterpenes and four flavonoids tested in the study demonstrated varied level of EA, mutagenicity, and developmental toxicity depending on their structures at a low exposure range. Moreover, the results showed that the methoxy substituents on lignin-derivable bisphenols appear to be a positive factor to reduce genotoxicity and oxidative DNA damage. The number of methoxy groups on lignin-derivable bisguaiacols/bissyringols plays a role on EA level. Additionally, a novel chicken embryo model was developed to target various critical toxicity endpoints, including developmental toxicity, genotoxicity, endocrine disruption, and metabolism, which were closely related to the structure and treatment dose of the natural phenolic compounds and synthesized bisphenols.