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 Graduate College. The Graduate College 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 to locate print or microform copies of dissertations that are not available online.

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Recent Submissions

Now showing 1 - 20 of 2506
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    Improving resistance to Varroa mites in honey bee colonies via cultural brood mixing
    (University of Delaware, 2024) 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
    (University of Delaware, 2024) 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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    The roads to politics: Chinese private entrepreneurs and China's policy-making processes
    (University of Delaware, 2023) 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
    (University of Delaware, 2022) 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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    Role of tart cherry in the prevention of hypertension and the modulation of inflammatory signaling
    (University of Delaware, 2022) 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
    (University of Delaware, 2022) 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
    (University of Delaware, 2022) Santana, Samantha O.
    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
    (University of Delaware, 2024) 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
    (University of Delaware, 2024) 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
    (University of Delaware, 2024) 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
    (University of Delaware, 2024) 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.
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    Predicted light-regulated mechanisms in freshwater Microbacteriaceae
    (University of Delaware, 2024) Hempel, Priscilla
    Light is an environmental cue and the most abundant source of energy on Earth. Many organisms in surface environments use and rely on light for energy, orientation with respect to time of day, location, and regulation of physiological processes. This includes microbes, which are the most abundant organisms on Earth. Microbes can sense and use light in a wide variety of ways. One way that microbes use light, is as a source of information and multiple light-sensing proteins that regulate physiological processes have been identified. However, the conversion of light to information and the subsequent cellular response(s) has only been characterized in a few species. Moreover, little is known about how bacteria use light as information that then enhances growth. While the use of light as a source of energy in photoautotrophs and photoheterotrophs has been highly characterized, the biological pathways involved in light-enhanced growth of bacteria lacking identifiable photosystems and functional rhodopsins had not been characterized. Sequence analyses, including genomic and transcriptomic, provide a comprehensive approach to the prediction of which metabolic processes are regulated by light. Insight into the bacterial use of light as a source of information to enhance growth expands our knowledge of bacterial sensing and provides insight into bacterial metabolism for future experiments. ☐ Identifying genes and biological functions present in bacterial species with light-enhanced growth, yet lacking identifiable photosystems and functional rhodopsins, is crucial for identifying potential light-capturing systems and predicting which proteins may be involved in the cellular response to light. Chapter 2 presents the genome sequences and annotations of three Actinobacteria species within the Microbacteriaceae family: Aurantimicrobium photophilum strain MWH-Mo1, Aurantimicrobium sp. strain MWH-Uga1, and Microbacterium sp. strain 10M-3C3 as well as the genome comparison of these three species and Rhodoluna lacicola strain MWH-Ta8. Previously, light-enhanced growth was observed in the two Aurantimicrobium species and R. lacicola, while Microbacterium sp. strain 10M-3C3 does not have light enhanced growth. ☐ Chapter 3 presents a pangenome analysis of 27 Microbacteriaceae, including R. lacicola, A. photophilum, Aurantimicrobium sp. strain MWH-Uga1, and Microbacterium sp. strain 10M-3C3. This was done to identify trends in the genetic differences between Microbacteriaceae isolated from different environments. Multiple predicted genes were found to be enriched in marine Microbacteriaceae and a few predicted genes were found to be enriched in terrestrial (freshwater and soil) Microbacteriaceae. These results contribute to our understanding of how Microbacteriaceae are specialized for their environment. Additionally, from the pangenome enrichment analysis, I was able to identify genes that are good candidates for further analysis to understand the light-enhanced growth phenotype in freshwater Microbacteriaceae. ☐ Lastly, the transcriptomes of two Microbacteriaceae with light-enhanced growth, R. lacicola and A. photophilum, are analyzed in Chapter 4. This work shows that although R. lacicola and A. photophilum have the same light-enhanced growth phenotype, which genes are light-regulated and their light-regulated expression patterns differed greatly. These results indicate that different mechanism(s) may be responsible for the increased growth rates in the light. Additionally, it suggests that R. lacicola and A. photophilum may have different signal transduction pathways and/or regulatory proteins that respond to light and darkness. The phylogenetic profiling and expression analyses within this work identified predicted regulatory proteins that are good candidates for future experiments testing the effects of light on physiological and biochemical properties of freshwater Actinobacteria, and identifying the cellular activities that correspond to light-induced transcriptional changes in these organisms.
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    The impact of memory development on adolescent emergent reading: insights from Côte d'Ivoire
    (University of Delaware, 2024) Hannon, Joelle
    Relative to other skills, learning to read requires time and consistent instructional support to master. Reading is a complex skill that relies on multiple cognitive and linguistic abilities including the cognitive ability that underlies all learning, memory. The landscape of memory changes throughout childhood; specifically, procedural learning (which supports sequence and pattern learning) reaches maturity near age 10, while declarative learning (which supports the arbitrary mapping of form and meaning) continues to develop into adulthood. Most reading research takes place in high-income countries where children typically begin learning to read in early childhood, when procedural learning plays a relatively larger role in skill learning. This research, however, does not reflect the experience of many children around the world who learn to read later in childhood or in adolescence when procedural learning is adult-like and the role of declarative learning for skill learning, particularly language related skills, increases. This dissertation presents three studies of procedural and declarative learning's contribution to reading among adolescents in rural Côte d'Ivoire. The first study demonstrates that procedural learning's contribution to emergent reading is through its support of phonological awareness, and this is true for children ages 8-15. The second study evaluated the cultural validity of two measures of declarative learning among children in rural Côte d'Ivoire. This study found that the most reliable measures of declarative learning are those which are based on behaviors children naturally use in their daily life. The final study examined the potential competition between procedural and declarative learning among emergent readers aged 10-16. This study found that declarative learning interferes with the development of early reading skills. Overall, these studies suggest that procedural learning is important for early reading and, among adolescent emergent readers, declarative learning competes with the role of procedural learning.
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    Monolayer functionalization of silicon and metal oxide surfaces with boron- and nitrogen-containing precursors
    (University of Delaware, 2024) Silva-Quinones, Dhamelyz
    As the dimensions of electronic device components shrink, there is a growing need for innovative methods and chemical modification strategies to fabricate nanometer-sized features. The work outlined in this dissertation focuses on two main strategies: the ultra-shallow monolayer doping, and area selective deposition. These strategies necessitate a detailed understanding of the interactions between different precursors and substrates, as well as the development of innovative techniques for governing and manipulating these interactions. ☐ In the following chapters, a novel chemical method for the monolayer functionalization of silicon surfaces with boron- and nitrogen-containing precursors is discussed and proposed as a pathway for ultra-shallow monolayer doping. ☐ Secondly, the monolayer functionalization of metal-oxide surfaces with an organic precursor with unique spectroscopic labels was investigated in order to understand the attachment chemistry of these materials and to develop spectroscopic labels for surface characterization. ☐ And lastly, the use of an organic molecule with unique spectroscopic labels is proposed as an effective resist to block the growth of materials in area selective deposition. ☐ The goals for the research contained in this dissertation are: • 1) Modify the surface of the semiconductor to form direct dopant (B, N)-Si bonds and control the concentration of the dopant. • 2) Explore and control the attachment of the boron-containing precursor that contains unique spectroscopic labels (F, B) with the metal-oxide surfaces. • 3) Modify the chemical reactivity of the surfaces with respect to a metal-organic precursor to inhibit or promote the deposition of TiO2 films. ☐ To achieve these goals, a combination of spectroscopic, microscopic and computational investigations was performed to study the surface chemical modifications processes. X-ray photoelectron spectroscopy (XPS), Fourier-transform infrared spectroscopy (FTIR), time-of-flight secondary ion mass spectrometry (ToF-SIMS) and solid-state nuclear magnetic resonance spectroscopy (ss-NMR) were used to elucidate the chemical environment and to determine the binding modes of the attached compounds on the surfaces. Atomic force microscopy (AFM) was utilized to evaluate the surface morphological changes after the surface chemical modifications. Also density functional theory (DFT) calculations were utilized to supplement the analysis, interpret the results of spectroscopic measurements and to interrogate surface stability of possible surface species.
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    Structural neural networks meet piecewise exponential models on customer acquisition and retention
    (University of Delaware, 2024) Cai, Chuan
    This dissertation examines the dynamics of customer acquisition and retention within the context of higher education with students being recognized as customers. Given the substantial reliance of higher education institutions on tuition fees for operating revenue, student recruitment and retention emerge as pivotal aspects of enrollment management. Furthermore, retention and timely graduation are used to measure institutional reputation and accountability. This study pursues three main objectives: understanding applicant deposit decisions during the admission process, predicting matriculated students' dropout risks, and exploring the impact of student loan debt on timely graduation. ☐ The first segment analyzes the determinants of deposit decisions of out-of-state students admitted to the University of Delaware across three academic years. Utilizing three Bayesian hierarchical piecewise exponential models, we deduce that factors like gender and recruitment events exhibit time-varying effects, while others like financial aid remain stable within an academic year but vary across years. The baseline desire to deposit intensifies as deadlines near, though this trajectory shifts annually. Insights derived inform the Admissions Office's marketing and recruitment tactics. ☐ The second segment introduces a hybrid model, merging a structural neural network with a piecewise exponential model, to predict college attrition. Benchmarking against two alternative models, the hybrid model demonstrates superior or comparable predictive prowess for the University of Delaware across three springs. Categorizing predictors into academic, economic, and socio-demographic facets reveals academic indicators as key discriminants between students who drop out and those retained, especially from freshman to junior years. Emphasis on academic assessments in intervention strategies is thus recommended. ☐ The third segment evaluates the impact of student loan debt on six-year graduation rates by department, over a span of five years. Leveraging five Bayesian hierarchical models, the findings illustrate a pronounced department-wise loan debt effect on first-year students, which attenuates as they advance academically. Tailored financial aid policies, considering academic departments, are posited to amplify the efficient utilization of institutional financial resources. For universities mulling over department-specific financial aid policies, initiation with randomized trials for first-year students is advised. ☐ In summary, this dissertation introduces innovative strategies for strategic enrollment management, encompassing admission, retention, and graduation considerations. Particular attention is given to the dynamic nature of applicant deposit decisions, the development of predictive models for student attrition, and the department-specific effects of student loan debt on graduation rates.
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    The development of new englerin-inspired chemotherapeutic drug candidates and tool compounds & the synthesis of an acyldepsipeptide fluorescent probe
    (University of Delaware, 2024) Hudson, Elijah J.
    Chapter 1 outlines the discovery, biological mechanistic investigations, syntheses, and derivatization of (–)-englerin A, a guaiane sesquiterpene natural product exhibiting potent and selective renal cancer cell growth inhibition first described in 2009. The cellular mechanism by which the compound kills renal cancer cells is the subject of intense and ongoing study. The synthesis of new englerin tool compounds and analogues have been and continue to be used to investigate the mechanism(s) of action against renal cancer cells. The synthesis of analogues have also supported advancement of an englerin-derived compound to therapeutic candidacy. ☐ Chapter 2, the first project herein, describes synthesis and development of a next generation series of analogues addressing the inherent therapeutic liabilities present within the natural product. This series of analogues is informed by a compendium of structure–function data and improved biological activities. The various substituents being incorporated into these analogues address the lethality observed in mice as well as the stability of the compound when administered orally. The goal of this project is to construct an analogue that may proceed through therapeutic candidacy ultimately leading to the development of an anti-cancer treatment. ☐ Chapter 3 describes the efforts towards the synthesis and development of a new series of englerin-inspired proteomic tool compounds to aid in the elucidation of an unambiguous mechanism of action of (–)-englerin A against cancer cells. The tool compounds will integrate covalent modifiers and clickable moieties for the purposes of cellular target identification and other mechanism studies in order to support the development of new drugs toward renal carcinoma based on englerins. Determining the mechanism of action is extremely important in the development of (–)-englerin A as a cancer therapeutic. Although there have been tool compounds developed in the past, the mechanism of action is still largely unknown. There is still a need for further development of tool compounds to probe this biological mechanism of action. ☐ Chapter 4 describes the synthesis of an acyldepsipeptide fragment fluorescent tool compound used by the Karl Schmitz group to investigate the biological mechanism of action of acyldepsipeptide fragments towards tuberculosis. This tool compound was developed in a collaboration with Karl Schmitz and Joseph Fox of the University of Delaware.
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    Private and verifiable computation
    (University of Delaware, 2024) Mouris, Dimitris
    The rise of cloud computing and big data analytics offers significant benefits for individuals and organizations as they enable a plethora of applications in diverse fields such as healthcare, home automation, and many more. These technologies enable individuals and organizations to adjust computational resources effortlessly and take advantage of large amounts of data, leading to improved efficiency and reduced costs. Unfortunately, processing vast amounts of data increases the risk of data theft and misuse as sensitive information is accessible by the cloud provider and vulnerable to attacks from third parties. Zero-knowledge proofs (ZKP), secure multiparty computation (MPC), and homomorphic encryption (HE) are key cryptographic techniques that focus on protecting data confidentiality while enabling valuable computations to be performed on sensitive data. Unfortunately, generic solutions incur significant performance overheads and may not be practical for many real-world use cases; thus, specialized protocols need to be devised. Another challenge with HE and MPC is to provide verifiable guarantees on the integrity of the computation, i.e., that it was performed faithfully. ZKPs offer a solution to this problem, yet combining these technologies requires intricate solutions. ☐ This dissertation focuses on private and verifiable computation. In particular, we start by introducing the Zilch framework for developing transparent ZKPs, i.e., ZKPs that do not need a trusted setup. Zilch consists of a back-end that allows verifying MIPS-like instructions and a front-end that compiles high-level code to our zero-knowledge MIPS back-end. As a result, our framework makes ZKPs more accessible and can facilitate many real-world applications. More specifically, we continue this dissertation by utilizing Zilch to create specialized protocols for proving both functional and security properties of intellectual property (IP) netlists without revealing anything about them. These works focus on thwarting IP piracy in the integrated circuit industry as IP vendors want to convince IP buyers about various properties of their netlists while still maintaining the privacy of their designs. ☐ Finally, we focus on privacy-preserving and verifiable statistics based on inputs from multiple clients. More specifically, we introduce two protocols that offer verifiable guarantees of the correctness of the final result and are secure against participants who do not follow the protocol specification. Both these works assume a set of clients that hold some private inputs and some aggregation servers that wish to compute statistics based on the client inputs privately. The first work is called Masquerade and focuses on aggregations and histograms, while the latter, called PLASMA, focuses on more elaborate statistics such as private heavy-hitters (i.e., finding the most popular client inputs). PLASMA relies on three servers and offers even stronger security guarantees by considering that even one of the servers may be malicious and not follow the protocol specification. These two works showcase real-world applications of private and verifiable computation.
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    Advancing gene-centric approaches for microbial ecology
    (University of Delaware, 2024) Moore, Ryan M.
    Metagenomics is a powerful approach that has enhanced our understanding of microbial communities and the roles microbes play in various environments. A deep examination of single genes, particularly protein-coding genes, can add critical insight to metagenomic datasets by providing functional information and allowing for the prediction of observable traits and the formulation of "genome to phenome" hypotheses. However, gene-centric approaches to metagenomics face unique challenges, and the comparative lack of tools and approaches specifically designed to address these problems makes gene-centric analyses of microbial communities less accessible to many researchers. Though data quality issues arise at all stages of the sample-to-sequence to-discovery pipeline, gene-centric studies are particularly sensitive to issues such as those arising from misannotations of the genes under study, which necessitates time consuming manual curation, or from the compositional nature of metagenomic data, which requires special statistical care. To address some of the barriers to effective gene-centric analysis in metagenomics, this dissertation introduces three tools: PASV, InteinFinder, and Iroki, as well as a novel framework for examining microbial community diversity. PASV (protein amino acid signature validator) automates the manual curation of homology search results to ensure accurate protein annotation. InteinFinder is a pipeline developed to automatically identify and remove inteins, the protein equivalent of introns, from protein sequences commonly used in gene-centric studies. Together, PASV and InteinFinder significantly reduce the amount of time and domain-knowledge traditionally needed to manually curate single gene datasets. Iroki is a userfriendly tool designed to automatically customize phylogenetic and other types of trees with user supplied metadata, facilitating data interpretation. The introduced diversity framework provides a more comprehensive and scalable view of microbial community diversity compared to current approaches, particularly for large metagenomic datasets. Overall, these advancements simplify the gene-centric study of microbial communities and enhance the metagenomic analysis pipeline.
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    Self-interactions and aggregation of therapeutic proteins
    (University of Delaware, 2024) Forder, James K.
    Protein-based therapies are a prominent class of drug products used in the treatment of a broad range of chronic illnesses such as cancers and immune-related disorders, and more recently infectious diseases such as SARS-CoV-2 and RSV. Many of the highest selling drugs globally are protein-based therapeutics, typically monoclonal antibodies (MAbs) or structurally derivative proteins such as Fc-fusion proteins and bispecific antibodies. The development process for therapeutic proteins is particularly uncertain, expensive, and resource-intensive compared to small molecule drugs, so there is sizable interest in the biopharmaceutical industry in methods that can improve predictions of how likely a protein drug candidate is to be successfully developed into a commercial product (also known as “developability”), and in methods that can streamline the development process. ☐ Many of the challenges that are faced during drug development of therapeutic proteins arise from protein-protein self-interactions, which are “weak” intermolecular forces (i.e., weak in comparison with “lock-and-key” specific binding events) between proteins of the same species in solution. The influence of self-interactions on solution nonidealities and problematic behaviors is increased at elevated protein concentrations, which is of particular relevance as the preferred liquid dosage form for many protein-based therapies is at relatively high protein concentration (on the order of 100 mg/mL). Static light scattering (SLS) and dynamic light scattering (DLS) are commonly used to measure net self-interactions in early-stage development to screen for attractive self-interactions that are fundamentally associated with a host of challenging behaviors and properties such as reversible self-association, irreversible aggregation, elevated viscosity, liquid-liquid phase separation, opalescence, and low solubility. Irreversible aggregation is especially problematic because proteins have a common tendency to aggregate and methods to predict changes in aggregation rates or mechanisms between different proteins or as a function of solution conditions are not well-developed. The presence of aggregates can be a liability in a number of manufacturing processes, reduce the efficacy and shelf-life of the product, and elicit a dangerous immunogenic response when administered to a patient. This thesis is focused on the development and assessment of methods to characterize and predict self-interactions and aggregation rates for therapeutic proteins with emphasis on practical applications in streamlining industrial drug development. The experimental datasets are for solution conditions and proteins similar to those in commercial protein-based therapies, fairly diverse in the behaviors they represent, and large compared to many other publicly-available datasets. ☐ Coarse-grained (CG) molecular simulations are applied throughout this thesis to model self-interactions, predict net self-interactions at high-concentration conditions, and probe specific electrostatic interactions between charged residues that were involved in attractive self-interactions. A range of coarse-grained models for therapeutic proteins were evaluated based on the tradeoffs between computational efficiency and accuracy in calculating net self-interactions. A dataset of previously reported experimental values of the second osmotic virial coefficient (B22) from SLS for five MAbs at multiple solution conditions (i.e., different pH and ionic strength conditions) were used as a test case. Lower resolution (e.g., domain-level) models allowed for higher throughput and more intensive simulation algorithms (e.g., simulations with many protein molecules to simulate high concentrations) but were limited in their representation of interactions between specific sites in the protein, such as attractive electrostatic interactions between specific charged amino acids. Higher resolution models were able to capture specific electrostatic attractions, but at great cost to computational efficiency. A hybrid model that combines features from the domain-level and higher resolution models was introduced that can capture specific electrostatic attractions and was tractable for simulations at high-concentrations like those representative of commercial therapeutic protein products. ☐ Net self-interactions via SLS and DLS experiments were measured systematically for four MAbs, two Fc-fusion proteins and the associated fusion partner (FP) protein as a function of solution pH and ionic strength. The measurements for the Fc-fusion proteins and FP protein were confined to low-concentration (e.g., B22 values), while for the four MAbs, the measurements scaled from low to high protein concentration. The solution conditions were chosen to represent fundamental features of commercial drug products within typical bounds of each feature (i.e., pH, ionic strength, and protein concentration). The proteins displayed a broad range of net self-interactions from strong repulsions to strong attractions that were sensitive to the changes in solution conditions that were assessed. ☐ The two Fc-fusion proteins and FP protein displayed reversible self-association at some conditions, which is linked to many industrial development challenges and is also a possible precursor to irreversible aggregation. The reversible self-association appeared to be related to attractive electrostatic self-interactions, so a high-resolution CG model was used to investigate the origins of attractive electrostatic self-interactions for the two Fc-fusion proteins. The results indicated that they were due to cross-domain interactions between the FP and Fc domains, which suggests that reversible self-association was due to those interactions as well. ☐ A previously developed method to combine low-concentration experimental values of B22 with CG molecular simulations to make predictions of high-concentration net self-interactions was improved by the integration of the hybrid CG model. The domain-level and hybrid CG models were directly compared based on how well they predicted high-concentration net self-interactions, using B22 values from SLS for six MAbs (two from prior work) to parameterize the CG models for a given MAb and pH. The predicted net self-interactions were compared against high-concentration SLS measurements. The findings and guidance from the CG model comparison described above with respect to low-concentration net self-interactions were also generally applicable for high-concentration net self-interactions where domain-level CG models were only able to reliably capture net repulsions and weak non-electrostatic attractions, while the hybrid CG model could capture strong electrostatic attractions as well. Inaccurate predictions of high-concentration behavior with the hybrid CG model at certain conditions were improved by methods that represented charge equilibria more precisely. ☐ The four MAbs were also used for studies with the overall goal of understanding and predicting MAb aggregation rates between different MAbs and as a function of solution conditions. Conformational stability of the four MAbs at four different formulations was measured by differential scanning calorimetry, and aggregation rates were measured via isothermal stability studies at four formulations (varying both pH and ionic strength) as a function of protein concentration and incubation temperature. Prediction of aggregation rates for solutions at high protein concentration stored at refrigerated conditions was of particular interest as it was intended to directly represent the protein concentration and storage condition of many commercial products. Studies at higher temperatures, where aggregation rates were generally faster, were judged by how they might relate to aggregation rates at refrigerated conditions and how similar the fundamental factors that mediated aggregation rates were. Overall, studies at elevated temperatures were poor predictors of aggregation rates at refrigerated storage conditions. Interpretable machine learning models were developed to rigorously deconvolute the impacts of fundamental phenomenon on aggregation rates, which included the net self-interactions and conformational stability measurements. At the highest temperatures, conformational stability was the most influential phenomenon, while at lower and refrigerated temperatures, net valence was the most influential, perhaps due to the influence of repulsive electrostatic self-interactions. The ML methods were also used to more thoroughly assess whether results from stability studies at higher incubation temperatures or lower protein concentrations could be useful for predicting aggregation rates. Another goal in developing the ML models was to provide a robust platform for predicting aggregation rates with the vast datasets that are not publicly available but presumably exist in the archives of many pharmaceutical companies. ☐ The studies in this thesis developed computational and statistical methods that were validated by or trained with fairly large, systematic datasets of experimental biophysical characterization, especially with respect to self-interactions. The results demonstrate how to 1) select a CG molecular model for a given application, 2) use CG molecular simulations in close connection with experimental measurements to extract additional knowledge about self-interactions and predict net self-interactions at other conditions (e.g., higher protein concentrations), and 3) understand and predict MAb aggregation rates as a function of protein concentration, incubation temperature, and solution conditions. These findings can be applied to various phases of industrial drug development for MAbs, Fc-fusion proteins, or other therapeutic proteins to improve selection of protein candidates (i.e., candidate selection) and optimization of formulation conditions (i.e., formulation development).
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    Echoes of trauma : ǂb changing perceptions of disaster and the erasure of space in Idaho's backcountry
    (University of Delaware, 2024) Jensen, Jennifer Anne
    This dissertation examines the interaction between Euro-American settlers and miners and the unique environment of central Idaho from 1863 to 1964, highlighting how cultural and social frameworks imported by these settlers led to recurrent disasters. The settlers' adaptation to these disasters, in turn, reshaped their cultural values and land-use practices. Focusing on the cultural impact of recurring small-scale disasters, or ‘chronic traumas,’ this work explores how Euro-Americans' settlement and early industrial activities in central Idaho led to a cycle of disaster and adaptation, including significant shifts in their collective identity and practices. The dissertation contends that vulnerability in relation to disasters is a dynamic, long-term process that reshapes communities beyond any recovery phase. Focusing on central Idaho, the thesis explores how a century of 'chronic traumas' influenced the evolving collective perception of disaster, beginning with a sense of necessary hardship, but later shifting to apathy and resignation. This dissertation also traces the interplay between culture and nature in central Idaho, revealing how their cultural imprints and the natural world's demands co-constructed the historical landscape and perceptions of wilderness. The research outlines how modernity's push on boundaries and the resulting disasters influenced the Euro-Americans' relationship with central Idaho's wilderness, culminating in a changed perception of disaster and use of the land over time.