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Title: A-stable implicit rapid scheme and software solution for electromagnetic wave propagation
Creator: Thavappiragsam, Mathialakan
Date: 2019
Collection: Electronic Theses & Dissertations
Description: "A robust and rapid scheme to solve electromagnetics (EM) is an important requirement in the scientific computing environment in which there are several useful methods used to solve tasks in EM. Our research study is motivated by this need and is targeted to develop a fast A-stable implicit numerical scheme and scalable software solution for EM wave propagation. Our scheme is based on the Method Of Lines Transpose (MOLT) approach which discretizes time first and then solves boundary value...
Show more"A robust and rapid scheme to solve electromagnetics (EM) is an important requirement in the scientific computing environment in which there are several useful methods used to solve tasks in EM. Our research study is motivated by this need and is targeted to develop a fast A-stable implicit numerical scheme and scalable software solution for EM wave propagation. Our scheme is based on the Method Of Lines Transpose (MOLT) approach which discretizes time first and then solves boundary value problems. By applying the free-space Green's function, the solution is derived by decomposing particular and homogeneous solutions. The compact Simpson's quadrature based, O(N) fast convolution, a recursive algorithm, is used to solve the particular solution for N number of grid points. The homogeneous solution is obtained using a particular solution at the boundary points and the applied boundary conditions. The multi-dimensional scheme is developed using the ADI splitting approach and an arbitrary order accuracy in time is achieved by switching the time derivation to a spatial derivation using the Lax-Wendroff approach.The focus of the work in this thesis has been to overcome the limitations in Neumann and outflow boundary conditions to get high-order accuracy by using special treatments that deal with a choice of the interpolation, finite difference stencil, and the initial conditions. In addition, we have extended these ideas to construct perfectly electrically conducting boundary conditions in 2D for the MOLT.In addition to introducing higher-order boundary conditions, an embedded boundary method is employed to deal with complex geometries. As the method is A-stable, it does not suffer from small-time step limitations that are found in explicit finite difference time domain methods when using either embedded boundary or cut cell methods to capture geometry. Further, we are developing an open source code MOLTN (Method Of Lines Transpose, Nth order) which is intended to be a hardware-independent, scalable software tool, using multi-node MPI, multi-core OpenMP, and GPU CUDA implementation. As a test case of the method, we implement and study the A6 magnetron with our embedded boundary method using point sources inside of the domain. The eventual goal is to combine this method with a novel particle method for the simulations of plasma. The particle method would treat particles as point particles that generate fields that are tracked on the mesh. No density or current will be mapped to the mesh. The consistency and performance of the scheme are evaluated for EM wave propagation and scattering using different shaped objects including curved boundaries and the introduction of true point sources that demonstrate how we handle particles. Stable solutions result for a wide range of mesh sizes and potential to leverage novel computing architectures, such as GPU, have been demonstrated."--Pages ii-iii.
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Title: ACHIEVING A LONG-LIVED CHARGE-SEPARATED FE(II) CHROMOPHORE : INSIGHTS INTO THE ROLE OF REORGANIZATION ENERGY ON THE ULTRAFAST PHOTOPHYSICAL PROCESSES OF D6 POLYPYRIDYL COMPLEXES
Creator: Carey, Monica Catherine
Date: 2018
Collection: Electronic Theses & Dissertations
Description: Photoredox catalysis reactions are ubiquitous in nature. These processes require a long-lived charge-separated state that is ideally suited for redox-based chemistry and photovoltaic applications. Many common chromophores used in these systems are ruthenium(II)-based, but the low earth abundance of this metal makes it non-viable for large-scale applications in the long-term. The first row congener of Ru(II) is iron(II), but its decreased ligand field strength relative to the second row...
Show morePhotoredox catalysis reactions are ubiquitous in nature. These processes require a long-lived charge-separated state that is ideally suited for redox-based chemistry and photovoltaic applications. Many common chromophores used in these systems are ruthenium(II)-based, but the low earth abundance of this metal makes it non-viable for large-scale applications in the long-term. The first row congener of Ru(II) is iron(II), but its decreased ligand field strength relative to the second row transition metal causes the metal-to-ligand charge transfer (MLCT) excited state to be depopulated on an ultrafast timescale, deactivating into metal-centered ligand field (LF) excited states that are inefficient for photovoltaic applications. The aim of this work is to understand the fundamental differences in the photophysical processes of Ru(II) and Fe(II) analogues. Three strategies can be envisioned for prolonging the MLCT lifetime in Fe(II) complexes: (1) prohibiting the vibrational modes associated with the MLCT→LF transition with synthetic modifications to the ligand, (2) increasing the ligand field strength to tune the LF and MLCT states such that the potential energy surface diagram for Fe(II) resembles that of Ru(II), or (3) extending conjugation within the ligand away from the metal center, thereby decoupling the MLCT and LF excited states. Any one of these approaches will inherently affect the reorganization energy, or the amount of energy required for the reactants to undergo vibrational and nuclear motions in order to achieve the geometry of the products without any electron transfer or electronic state crossing occurring. Variable-temperature transient absorption (VT-TA) spectroscopy is a methodology that has been developed to initially study the ground state recovery (GSR) processes of some low-spin Fe(II) polypyridyl complexes. Arrhenius parameters for this class of compounds are found experimentally for the first time and from these data, semi-classical Marcus theory analysis is performed, allowing for inner-sphere (i.e., complex-only) reorganization energies to be found for each. The Hab4/λ ratio is determined to be different between bis-tridentate and tris-bidentate species, which is postulated to imply a difference in nuclear coordinate for the relaxation process. The VT-TA methodology is also applied to a bis-tridentate compound for which GSR is both nearly barrierless and nearly at the crossing-point of the 5T2/3T1 as the lowest-energy excited state. The outer-sphere reorganization energy is adjusted through the use of counteranions and solvents in an attempt to tune the barrierless nature of the complex. The identity of the solvent did appear to affect the reorganization energy and the inverted region may have been accessed. The solvation dynamics of the vibrational cooling process in a Ru(II) chromophore were studied as a function of excitation wavelength in a series of alcohol and nitrile solvents. A dual solvation mechanism was observed depending on the amount of excess energy given to the system. Through the use of a sterically-encumbered analogue, the large aryl rotation in the MLCT excited state was determined to be the relevant nuclear coordinate in the vibrational cooling process as it related to the solvation. The Fe(II) analogue of this complex has also been prepared and studied in order to draw direct comparisons of the photophysical processes of these two related systems. These analogues are based on ligands with extended conjugation. In order to study the effects of delocalization on the excited state lifetime, other compounds of this type have been prepared and preliminary measurements of the MLCT lifetimes indicate that increasing delocalization away from the Fe(II) center lengthens the charge-separated lifetime, which is an important first step in achieving long-lived charge transfer states for this class of compounds
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Title: ADVANCING ENGINEERED ENDOSYMBIONTS AS A PLATFORM TECHNOLOGY FOR THERAPEUTIC MACROPHAGE MODULATION
Creator: Madsen, Cody Scott
Date: 2022
Collection: Electronic Theses & Dissertations
Description: This dissertation describes the construction of engineered endosymbionts (EES) as a platform technology for modulating macrophage function for therapeutic applications. Dr. Ashley Makela and I worked closely to advance the EES technology. Dr. Makela focused on the characterization of the EES ability to change macrophage function and I focused on developing the EES technology and working with Dr. Makela on characterization and using the EES in applications (Chapter 2 and 3). In Chapter 2,...
Show moreThis dissertation describes the construction of engineered endosymbionts (EES) as a platform technology for modulating macrophage function for therapeutic applications. Dr. Ashley Makela and I worked closely to advance the EES technology. Dr. Makela focused on the characterization of the EES ability to change macrophage function and I focused on developing the EES technology and working with Dr. Makela on characterization and using the EES in applications (Chapter 2 and 3). In Chapter 2, Bacillus subtilis was developed as a chassis organism for EES that escape phagosome destruction, reside in the cytoplasm of mammalian cells, and secrete proteins that are transported to the nucleus to impact host cell response and function. Two synthetic operons encoding either the mammalian transcription factors (TFs) Stat-1 and Klf6 or Klf4 and Gata-3 were recombined into the genome of B. subtilis expressing listeriolysin O (LLO) from Listeria monocytogenes and expressed from regulated promoters. Controlled expression of the mammalian proteins from B. subtilis LLO in the cytoplasm of J774A.1 macrophage/monocyte cells altered surface marker, cytokine and chemokine expression. Once the EES platform was developed and initially tested in vitro with a macrophage cell line, translating the EES to applications became the next step to understand the capacity of the new technology (Chapter 3). For increased translatability, the effect of the engineered B. subtilis LLO TF strains on murine bone marrow-derived macrophages (BMDMs) function was characterized. The TF strains shifted BMDM production of cytokines, chemokines and metabolic patterns. RNA-seq is still being analyzed to elucidate effects on gene expression. Furthermore, the ability of the B. subtilis LLO TF strains to alter the tumor microenvironment was characterized in a murine 4T1 orthotopic breast cancer model. The B. subtilis LLO strains altered the tumor microenvironment by promoting immune cell invasion, altering the functional metabolism of cells within the tumor, and causing tumor growth stabilization. Additionally, safety of this EES platform was observed as multiple doses at bacterial concentrations 100-fold more than other bacterial therapies were injected without affecting the health of mice. Yet, during the development and characterization of the EES, the sugar (D-mannose) that was used to induce transcription in the EES once inside the host cell was observed to significantly impact macrophage physiology which created additional complexity and was not ideal for in vivo applications. Accordingly, Emily Greeson and I worked on developing a mechanism for non-invasive localized control of gene expression in vivo. Emily Greeson engineered B. subtilis with temperature sensitive repressors (TSRs) and characterized this new genetic switch. I then coated B. subtilis with superparamagnetic iron oxide nanoparticles (SPIONs) which could be stimulated by an alternating magnetic field (AMF) to generate thermal energy. Chapter 4 discusses this new approach, and we investigated the ability of magnetic hyperthermia to regulate TSRs of bacterial transcription. The TSR, TlpA39, was derived from a Gram-negative bacterium, and used here for thermal control of reporter gene expression in Gram-positive B. subtilis. In vitro heating of B. subtilis with TlpA39 controlling bacterial luciferase expression, resulted in a 14.6-fold (12 hour; h) and 1.8-fold (1 h) increase in reporter transcripts with a 9-fold (12 h) and 11.1-fold (1 h) increase in bioluminescence. To develop magnetothermal control, B. subtilis cells were coated with three SPION variations which was confirmed by electron microscopy coupled with energy dispersive X-ray spectroscopy. Furthermore, using long duration AMF, we demonstrated magnetothermal induction of the TSRs in SPION-coated B. subtilis with a maximum of 4.6-fold increases in bioluminescence. Pairing TSRs with magnetothermal energy using SPIONs for localized heating with AMF can lead to improved EES transcriptional control. The research described in this dissertation demonstrates a multi-disciplinary approach towards developing a new modular technology to alter mammalian cell function with the specific focus on macrophages.
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Title: AI ACCELERATED COLLISIONAL CROSS SECTION PREDICTION FOR HIGH THROUGHPUT METABOLITE IDENTIFICATION
Creator: Tanemura, Kiyoto Aramis
Date: 2022
Collection: Electronic Theses & Dissertations
Description: Metabolomics refers to the collective characterization of small organic molecules in a biological sample. While instrumentation and software continues to improve for metabolomics studies, the fraction of annotated signals in untargeted metabolomics experiments remain small. Translating features to metabolite identities present a major bottleneck, confounded by the lack of authentic standards to build comprehensive experimental databases. I illustrate the development of collisional cross...
Show moreMetabolomics refers to the collective characterization of small organic molecules in a biological sample. While instrumentation and software continues to improve for metabolomics studies, the fraction of annotated signals in untargeted metabolomics experiments remain small. Translating features to metabolite identities present a major bottleneck, confounded by the lack of authentic standards to build comprehensive experimental databases. I illustrate the development of collisional cross section (CCS) prediction methods through deduction from theory and induction from available data. The theoretical CCS prediction involves multistep modeling of conformational ensemble followed by simulation of ion mobility. The advanced computational chemistry operations were automated using the AutoGraph conformational clustering protocol and implementation of the workflow in Snakemake. In a complementary approach, I applied a graph convolutional deep Bayesian neural net to predict CCS values and their uncertainty values. The quantified uncertainty was used to guide ab initio prediction of CCS values in an active learning strategy. The developed methodologies lay the foundation to a continuously refining in silico CCS library to aid in metabolite annotation.
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Title: AN INVESTIGATION OF MOTIVATIONAL STRATEGY USE BY FL SWAHILI AND ZULU INSTRUCTORS IN THE UNITED STATES
Creator: AKIDING, MAGDALYNE OGUTI
Date: 2021
Collection: Electronic Theses & Dissertations
Description: Second language (L2) teachers’ practices in the classroom can influence their students’ motivation for learning the L2. However, most of the research in this area has been conducted with students learning English as L2. Guilloteaux and Dörnyei (2008) recommended that more research be conducted on the use of motivational teaching practices in different languages, cultures, and instructional contexts to enrich the literature on this topic. In line with that recommendation, I had three goals...
Show moreSecond language (L2) teachers’ practices in the classroom can influence their students’ motivation for learning the L2. However, most of the research in this area has been conducted with students learning English as L2. Guilloteaux and Dörnyei (2008) recommended that more research be conducted on the use of motivational teaching practices in different languages, cultures, and instructional contexts to enrich the literature on this topic. In line with that recommendation, I had three goals with the current study: first, to investigate which motivational teaching practices are used by four teachers of two African languages in the United States; secondly, to investigate learners’ perceptions of the impacts of those motivational teaching practices on their motivated behaviour; and thirdly, to find out the impact of select factors on teachers’ implementation of those teaching practices. I employed a case study methodology (Duff, 2014) and collected classroom-based data from the four teachers of Swahili and Zulu and their students. Data were collected by means of classroom observations, stimulated recall sessions, and semi-structured interviews. The descriptive qualitative data allowed for the teaching and learning contexts of the participants to be captured in an in-depth manner. Findings revealed that the implementation of motivational teaching practices by the four teachers varied, with some using more motivational strategies than others. While learners’ perceptions about those strategies were mostly positive, results also revealed instances where students did not perceive some practices as motivational despite their teachers thinking that they were. Factors such as the teachers’ cultural backgrounds and training were found to influence the teachers’ motivational strategy use. Additionally, teachers’ preparedness to teach remotely, the challenges of remote teaching, and institutional support were found to affect their implementation of motivational teaching practices. I discuss these results in particular in light of the time of data collection, which was during the COVID-19 pandemic. Overall, the findings revealed that the four teachers implemented motivational teaching practices from all four stages of Dörnyei’s (2001) process-oriented model of L2 motivation, and that the teachers with more communicative orientations to teaching tended to use materials and teaching strategies in the classroom that also further promoted motivation within their students. These findings contribute to the literature on motivational teaching practices and highlight how teachers of African languages may have unique challenges in implementing motivational teaching practices, but that they as a collective work hard to foster motivation in ways that they believe will be most impactful to learners, especially in the virtual teaching environment of the times.
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Title: ANALYSIS OF ERWINIA AMYLOVORA POPULATION DYNAMICS AT FLOWER BLOOM AND FURTHER SYSTEMIC MOVEMENT OF THE PATHOGEN THROUGH HOST TISSUE
Creator: Slack, Suzanne M.
Date: 2021
Collection: Electronic Theses & Dissertations
Description: Population dynamics of Erwinia amylovora have been utilized for many applications over the past 50 years. In this work, populations were tracked over the course of apple bloom under naturally occurring environmental conditions. Flower stigmas inoculated on the 1st day of being open can harbor large (107) populations after 3 or 5 days post inoculation, with 100-fold increases in E. amylovora stigma populations observed in atmospheric conditions with daily average temperatures near 14oC. These...
Show morePopulation dynamics of Erwinia amylovora have been utilized for many applications over the past 50 years. In this work, populations were tracked over the course of apple bloom under naturally occurring environmental conditions. Flower stigmas inoculated on the 1st day of being open can harbor large (107) populations after 3 or 5 days post inoculation, with 100-fold increases in E. amylovora stigma populations observed in atmospheric conditions with daily average temperatures near 14oC. These large 100-fold increases seem to occur at night, indicating that Erwinia amylovora is able to infect flowers in colder field temperatures than previously reported. In tandem, timing of antibiotic application relative to E. amylovora presence on flower stigmas had little impact on population dynamics, with streptomycin and kasugamycin consistently reducing populations while oxytetracycline was more variable. This study also led to the identification that Kasumin is prone to photodegradation. Culturable bacteria, yeast, and fungal populations were assessed over the course of bloom in relation to application of a biological control agent yeast (Aureobasidium pullulans) and a contact sterilant. Though populations fell rapidly directly after application, by 24 hours all populations returned to pre-spray levels. In regards to further systemic spread, a type three secretion system effector was indicted in blocking the abscission of infected flowers. The use of prohexadione calcium (Pro-ca) and acibenzolar-S-methyl (ASM) reduced internal E. amylovora spread in a seemingly synergistic manner on young trees, with rates of 28.3 g Pro-Ca + 28.3 g ASM or 56.6 g Pro-Ca + 28.3 g ASM. The sum of this work gives us a better understanding of E. amylovora population dynamics in field conditions as well as the population response to current treatment options.
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Title: ARID1A MUTANT PATHOGENESIS OF THE ENDOMETRIAL EPITHELIUM
Creator: Reske, Jake Jordan
Date: 2021
Collection: Electronic Theses & Dissertations
Description: Women’s health diseases represent an understudied, widespread medical concern with historically limited treatment options. Diseases of the endometrium, the innermost lining of the uterus, are a highly prevalent public burden. Endometriosis occurs in 1 in 10 women, and endometrial cancer is the most common gynecologic malignancy in the United States. Recent advances have revealed recurrent genetic causes of endometrial diseases, including gene mutations known to play a role in cancer...
Show moreWomen’s health diseases represent an understudied, widespread medical concern with historically limited treatment options. Diseases of the endometrium, the innermost lining of the uterus, are a highly prevalent public burden. Endometriosis occurs in 1 in 10 women, and endometrial cancer is the most common gynecologic malignancy in the United States. Recent advances have revealed recurrent genetic causes of endometrial diseases, including gene mutations known to play a role in cancer development. ARID1A is one such gene that is commonly mutated in endometrial diseases, and it encodes a protein involved in regulating DNA packaging and activity in the cell nucleus within a large complex known as SWI/SNF. The focus of this dissertation is to improve our understanding of how ARID1A mutations promote endometrial diseases at multiple biological levels, with a particular focus on how disrupted chromatin regulation affects physiologically relevant gene expression. In these works, genetic engineering techniques are leveraged in mice and human cell-based models supported by public and clinical data to establish the consequences of ARID1A mutations in the endometrium and how they relate to other common genetic alterations in these diseases. These studies have revealed that ARID1A is a tumor suppressor in the endometrial epithelium, such that ARID1A loss drives cellular invasion into nearby tissue. ARID1A mutations also promote invasive metastasis and squamous metaplasia in the context of aggressive TP53 mutations. At the level of chromatin, ARID1A and SWI/SNF directly regulate endometrial epithelial identity genes through both promoter and distal enhancer chromatin interactions. Mechanistically, ARID1A mutant invasion is driven by cell identity control regions known as super-enhancers that become hyperactivated, which can be reversed pharmacologically. Moreover, ARID1A physically and genomically interacts with other nuclear chromatin regulators to govern gene activation states through variant histone regulation. These works have contributed in multiple aspects toward deciphering how ARID1A mutations promote disease in the endometrium, including pre-clinical support for using epigenetic therapies to treat invasive ARID1A mutant endometrial conditions. Future efforts will aim to further identify and understand molecular and biochemical mechanisms linking ARID1A and SWI/SNF chromatin remodeling activity to regulation of gene expression. Ongoing work seeks to explain roles of ARID1A and SWI/SNF epigenetic regulation in normal physiological processes of the endometrium, such as hormone signaling across the menstrual cycle.
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Title: ASSESSING DISASTER MANAGEMENT EFFECTS ON RECOVERY OUTCOMES IN RURAL POST-DISASTER JAPAN
Creator: Ward, Kayleigh
Date: 2022
Collection: Electronic Theses & Dissertations
Description: As a country frequented by natural disasters, Japan has robust disaster management systems that can be employed quickly to mitigate human, environmental, and economic harm and losses. However, these systems tend to be most effective when handling small-scale localized disasters. In the face of the 2011 Great East Japan Earthquake which decimated the northeastern communities of the Tohoku region, Japan’s disaster management system collapsed, unable to handle such large scale and widespread...
Show moreAs a country frequented by natural disasters, Japan has robust disaster management systems that can be employed quickly to mitigate human, environmental, and economic harm and losses. However, these systems tend to be most effective when handling small-scale localized disasters. In the face of the 2011 Great East Japan Earthquake which decimated the northeastern communities of the Tohoku region, Japan’s disaster management system collapsed, unable to handle such large scale and widespread damage. In the ten years since the disaster many rural communities have contended with a variety of social and economic problems, often left unremedied despite on-going government intervention. In this context, this dissertation will explore the complex problems in Minamisanriku, Miyagi—a rural coastal community decimated by the 2011 Great East Japan Earthquake. By engaging and collaborating with organizations in this community, I assess the connections between disaster management and post-disaster recovery outcomes through various applications of social capital and power. I first investigate how historical legacies of national government policies influenced recovery outcomes in the Tohoku region and how have these processes influenced economic restructuring and social development in Minamisanriku during reconstruction. Next, I consider how governance structures within Miyagi prefecture influenced the social and economic development of Minamisanriku during reconstruction. Lastly, I look to how disaster management affects the ability of residents to handle locally-identified and in turn, how residents utilize their social capital to driver social and economic recovery. I assess several key ideas on the connections between forms and theories of social capital and how they affect long-term disaster recovery outcomes through the disaster management process. The dissertation is situated to improve our understanding of how social capital affects rural communities’ ability to respond to these troubles and to craft context specific solutions to them. It also offers a variety of policy recommendations about how to improve community-centered recovery within disaster management frameworks.
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Title: ASSESSING THE ECOLOGICAL AND ANTHROPOGENIC FACTORS AFFECTING GIRAFFE SURVIVAL IN EAST AFRICA
Creator: Muneza, Arthur Bienvenu
Date: 2021
Collection: Electronic Theses & Dissertations
Description: Giraffe (Giraffa spp.) populations have declined by approximately 35% in the last 30 years, with extinctions documented in seven African countries. This decline has been attributed primarily to ecological and anthropogenic factors. In this dissertation, I assessed the impact that disease and human-interactions with wildlife have had on giraffe populations. In Chapter One, I quantified the severity of a skin disease that manifests as crusty, greyish-brown lesions, and has been recorded in at...
Show moreGiraffe (Giraffa spp.) populations have declined by approximately 35% in the last 30 years, with extinctions documented in seven African countries. This decline has been attributed primarily to ecological and anthropogenic factors. In this dissertation, I assessed the impact that disease and human-interactions with wildlife have had on giraffe populations. In Chapter One, I quantified the severity of a skin disease that manifests as crusty, greyish-brown lesions, and has been recorded in at least seven countries. I positioned my study in Tanzania, which has some of the highest rates of giraffe skin disease (GSD) recorded in Africa. Using photogrammetric analysis of camera trap images and digital photos of known individual giraffes, I classified GSD lesions into categories of none, mild, moderate, and severe. My study demonstrated that camera trap images presented an informative platform for skin disease ecology studies. In Chapter Two, I evaluated giraffe-lion interactions in Ruaha National Park, where more than 85% of the giraffe population has GSD. The aim of my study was to assess whether GSD may negatively influence the likelihood of giraffes surviving lion predation attempts. Occurrence of lion marks of was higher for adults and males in the giraffe population suggesting that these individuals were more likely to survive lion attacks. I also found that giraffes are an important prey species for lions in Ruaha National Park but GSD severity plays a minor role in influencing likelihood of surviving a lion predation attempt. I further explored the ecological implications of disease ecology on predator-prey interactions. In Chapter Three, I documented how giraffe body parts are acquired and their intended use (consumptive, trophy, or medicative), in Tsavo Conservation Area, southern Kenya. I conducted semi-structured surveys among 331 households to assess correlations between nine socioeconomic factors and use of giraffe parts. I found that giraffe parts mostly had consumptive and trophy uses. Giraffe parts were predominantly acquired through one-time suppliers, opportunistic access, and widely-known markets. Three variables, namely gender, occupation, and land ownership were significantly and positively correlated with use of giraffe parts. This study detailed the complex nature of poaching and trade of species of conservation concern in coupled human and natural systems. In Chapter Four, I explored the complex ways in which background conditions in the environment, coupled with previous experience with wildlife risks influences people’s attitudes toward wildlife in Tsavo Conservation Area, southern Kenya. Respondents stated that baboons (Papio cynocephalus), elephants (Loxodonta africana), and lions (Panthera leo) posed the greatest risks to human security and private property. Respondents that experienced previous risks from wildlife in their villages desired those populations to decrease whereas respondents without access to grazing lands for livestock were inclined to see those wildlife populations increase. My study showed that human attitudes toward wildlife in coupled human and natural systems are more complex than previously considered. I conclude my dissertation by providing considerations for future studies and highlighting the importance of tailoring conservation interventions to the critically important local contexts and traditional knowledge.
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Title: ASSURING THE ROBUSTNESS AND RESILIENCY OF LEARNING-ENABLED AUTONOMOUS SYSTEMS
Creator: Langford, Michael Austin
Date: 2022
Collection: Electronic Theses & Dissertations
Description: As Learning-Enabled Systems (LESs) have become more prevalent in safety-critical applications, addressing the assurance of LESs has become increasingly important. Because machine learning models in LESs are not explicitly programmed like traditional software, developers typically have less direct control over the inferences learned by LESs, relying instead on semantically valid and complete patterns to be extracted from the system’s exposure to the environment. As such, the behavior of an LES...
Show moreAs Learning-Enabled Systems (LESs) have become more prevalent in safety-critical applications, addressing the assurance of LESs has become increasingly important. Because machine learning models in LESs are not explicitly programmed like traditional software, developers typically have less direct control over the inferences learned by LESs, relying instead on semantically valid and complete patterns to be extracted from the system’s exposure to the environment. As such, the behavior of an LES is strongly dependent on the quality of its training experience. However, run-time environments are often noisy or not well-defined. Uncertainty in the behavior of an LES can arise when there is inadequate coverage of relevant training/test cases (e.g., corner cases). It is challenging to assure safety-critical LESs will perform as expected when exposed to run-time conditions that have never been experienced during training or validation. This doctoral research contributes automated methods to improve the robustness and resilience of an LES. For this work, a robust LES is less sensitive to noise in the environment, and a resilient LES is able to self-adapt to adverse run-time contexts in order to mitigate system failure. The proposed methods harness diversity-driven evolution-based methods, machine learning, and software assurance cases to train robust LESs, uncover robust system configurations, and foster resiliency through self-adaptation and predictive behavior modeling. This doctoral work demonstrates these capabilities by applying the proposed framework to deep learning and autonomous cyber-physical systems.
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Title: Abstract homomorphisms of algebraic groups : rigidity and group actions
Creator: Ruiter, Joshua
Date: 2022
Collection: Electronic Theses & Dissertations
Description: We investigate two related problems involving abstract homomorphisms between the groups of rational points of algebraic groups. First, we show that under appropriate assumptions, abstract representations of quasi-split special unitary groups associated with quadratic extensions of the field of definition have standard descriptions, i.e. can be factored as a group homomorphism induced by a morphism of algebras, followed by a homomorphism arising from a morphism of algebraic groups. This...
Show moreWe investigate two related problems involving abstract homomorphisms between the groups of rational points of algebraic groups. First, we show that under appropriate assumptions, abstract representations of quasi-split special unitary groups associated with quadratic extensions of the field of definition have standard descriptions, i.e. can be factored as a group homomorphism induced by a morphism of algebras, followed by a homomorphism arising from a morphism of algebraic groups. This establishes a new case of a longstanding conjecture of Borel and Tits. In the second part, we apply existing results on standard descriptions for abstract representations of Chevalley groups to study some rigidity properties of actions of elementary subgroups on algebraic varieties.The thesis is organized as follows. To provide context for the study of abstract homomorphisms, in section 1 we give a historical overview of key developments going back to Cartan's work on homomorphisms of Lie groups. In section 2, we prove our rigidity result for special unitary groups, using a strategy inspired by work of Igor Rapinchuk which depends crucially on the construction of certain algebraic rings associated to abstract representations. In section 3, we apply existing rigidity statements for representations of elementary subgroups of Chevalley groups to study rigidity properties of these groups acting on affine algebraic varieties and projective surfaces. We discuss some open questions and plans for future work in section 4. In the appendices, we collect some relevant background material on algebraic rings, and also provide details on the computations of commutator relations needed for the constructions in section 2.
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Title: Accusing Muslims of terrorism : Islam, secularism, and religious violence in the United States
Creator: Sadequee, Sharmin
Date: 2017
Collection: Electronic Theses & Dissertations
Description: This dissertation describes the ways in which the securitized secular laws of the state act to regulate and control Muslims and the practices of Islam through "terrorism" prosecutions in the United States. In order to eliminate terrorism violence, the security state has created an exception to regular legal norms by establishing a court within a court and a prison within a prison, where normal legal procedures are not followed for those Muslim immigrants and American Muslim citizens accused...
Show moreThis dissertation describes the ways in which the securitized secular laws of the state act to regulate and control Muslims and the practices of Islam through "terrorism" prosecutions in the United States. In order to eliminate terrorism violence, the security state has created an exception to regular legal norms by establishing a court within a court and a prison within a prison, where normal legal procedures are not followed for those Muslim immigrants and American Muslim citizens accused of "terrorism" related offenses. I address the ways in which Muslims have been conditioned and affected by the securitized secular laws that are applied in "terrorism" cases, and I also discuss how human-rights advocacy around the accused challenge and resist these discriminatory practices. Based on 24 months of ethnographic fieldwork; observations of federal terrorism trials; a review of prison writings; and interviews with families of the accused, activists, lawyers, and human-rights advocates, I address the legal practices of securitized laws concerned with preventing "terrorism," their impact both inside and outside of judicial institutions, and the power of these practices on the lived experiences of Muslim Americans. While some authorities claim that preventive "terrorism" prosecutions are necessary to eradicate violence, I suggest that the main concerns of the security state are really about eradicating religious thought and practices that contradict the secular definition of acceptable religion. -- Abstract.
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Title: Achieving reliable distributed systems : through efficient run-time monitoring and predicate detection
Creator: Tekken Valapil, Vidhya
Date: 2020
Collection: Electronic Theses & Dissertations
Description: Runtime monitoring of distributed systems to perform predicate detection is critical as well as a challenging task. It is critical because it ensures the reliability of the system by detecting all possible violations of system requirements. It is challenging because to guarantee lack of violations one has to analyze every possible ordering of system events and this is an expensive task. In this report, wefocus on ordering events in a system run using HLC (Hybrid Logical Clocks) timestamps,...
Show moreRuntime monitoring of distributed systems to perform predicate detection is critical as well as a challenging task. It is critical because it ensures the reliability of the system by detecting all possible violations of system requirements. It is challenging because to guarantee lack of violations one has to analyze every possible ordering of system events and this is an expensive task. In this report, wefocus on ordering events in a system run using HLC (Hybrid Logical Clocks) timestamps, which are O(1) sized timestamps, and present some efficient algorithms to perform predicate detection using HLC. Since, with HLC, the runtime monitor cannot find all possible orderings of systems events, we present a new type of clock called Biased Hybrid Logical Clocks (BHLC), that are capable of finding more possible orderings than HLC. Thus we show that BHLC based predicate detection can find more violations than HLC based predicate detection. Since predicate detection based on both HLC and BHLC do not guarantee detection of all possible violations in a system run, we present an SMT (Satisfiability Modulo Theories) solver based predicate detection approach, that guarantees the detection of all possible violations in a system run. While a runtime monitor that performs predicate detection using SMT solvers is accurate, the time taken by the solver to detect the presence or absence of a violation can be high. To reduce the time taken by the runtime monitor, we propose the use of an efficient two-layered monitoring approach, where the first layer of the monitor is efficient but less accurate and the second layer is accurate but less efficient. Together they reduce the overall time taken to perform predicate detection drastically and also guarantee detection of all possible violations.
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Title: Action-Oriented Studies in Green Criminology and a Harmful Trade in Pet Wildlife in Trinidad and Tobago
Creator: Gibson, Mark Charles
Date: 2022
Collection: Electronic Theses & Dissertations
Description: This dissertation presents five chapters, inclusive of three manuscripts styled as draft publications, to advance the contested paradigm of green criminology—or the study of crimes and harms that involve the natural world, non-human species, and the human communities that depend on them—and to support the emerging professional practice of non-governmental wildlife trade reduction. Two of the presented manuscripts meet the requirements for submission to scientific journals in criminology,...
Show moreThis dissertation presents five chapters, inclusive of three manuscripts styled as draft publications, to advance the contested paradigm of green criminology—or the study of crimes and harms that involve the natural world, non-human species, and the human communities that depend on them—and to support the emerging professional practice of non-governmental wildlife trade reduction. Two of the presented manuscripts meet the requirements for submission to scientific journals in criminology, while another is a long-form text modeled on contemporary non-governmental ‘wildlife trade assessment’ reports. The specific wildlife trade under study is a harmful trade in pet wildlife occurring in Trinidad and Tobago and the wider world. This trade was particularly under-studied prior to this dissertation research project and broader initiative. The dissertation is action-oriented in that it seeks to support the green criminology paradigm's empirical, theoretical, and technical development. The resulting manuscript-style chapters have been designed using a best-practice ‘Open Standards’ planning approach now popular in wildlife trade reduction projects. The underlying research activities were also action-oriented in that they were and continue to be conducted in partnership with local activists and scientists as part of a non-governmental project to reduce the harmful trade in pet wildlife trade in Trinidad and Tobago (see www.nurturenaturett.org). The underlying research included focus group discussions with wild animal keepers (n=75), key informant interviews (n=172) with seven stakeholder groups, more than two years of participant observation of physical sites and social media, a national household survey on animal keeping (n=2004), and a taxonomic legal inventory of wildlife laws in Trinidad and Tobago and its trade partners. The first chapter, “Introduction,” provides essential background information on the dissertation research, encompassing project, and implementing researcher. In this way, the chapter describes the developmental context of this dissertation thesis and the strategies employed to produce the dissertation chapters. The second chapter, “The illegal keeping of pet wildlife in Trinidad and Tobago: Diversity, prevalence, populations, and harms,” is designed for submission to a criminological journal on global crime issues and provides insights into the nature of an illegal wildlife trade in a Caribbean country. The third chapter, “‘We all know it’s inhumane’: The awareness and justification of green crimes and harms among Trinidadian songbird keepers,” is designed for submission to a criminological journal on social deviance and provides insights for the development of Neutralization Theory to reduce green crimes and harms. The fourth chapter, “An assessment of the harmful trade in songbirds in Trinidad and Tobago and the wider world,” is designed as a gray-literature ‘wildlife trade assessment’ to educate and empower activists, donors, and policymakers in Trinidad and Tobago and the wider world. A final chapter, “Conclusion and Reflections,” considers the researcher’s experience in relation to action, green criminology, project-based intervention, and science-based activism. The researcher’s concluding reflections include the identification of several next steps to advance green criminology for the continuing and future reduction of harmful wildlife trades and other green crimes and harms.
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Title: Adaptation to agriculture in a serious crop weed, weedy radish (raphanus raphanistrum)
Creator: Garrison, Ava
Date: 2022
Collection: Electronic Theses & Dissertations
Description: The colonization of novel environments requires organisms to shift their trait means in response to differing abiotic and biotic conditions in order to survive and persist. This response can be done via phenotypic plasticity (a trait shift in response to the environment), adaptation (a trait shift due to genetic change), or both strategies can be used together, with plasticity “buying time” for adaptation to occur. The colonization of novel environments is especially important to the...
Show moreThe colonization of novel environments requires organisms to shift their trait means in response to differing abiotic and biotic conditions in order to survive and persist. This response can be done via phenotypic plasticity (a trait shift in response to the environment), adaptation (a trait shift due to genetic change), or both strategies can be used together, with plasticity “buying time” for adaptation to occur. The colonization of novel environments is especially important to the establishment of agricultural weeds worldwide, which thrive in these extreme environments of intense competition and frequent disturbance. In this dissertation, I address the establishment and evolution of a harmful agricultural weed, weedy radish (Raphanus raphanistrum), as well as its divergence from a wild relative of the same species, the native radish ecotype. I first investigated the hypothesis of phenotypic plasticity “buying time” for adaptation to agricultural fields in weedy radish. Using growth chambers to simulate the ancestral (native) and derived (weedy) environments of weedy radish, I performed a reciprocal transplant with the weedy and native radish ecotypes. I found phenotypic plasticity between environments and genetic divergence between ecotypes to be equally common among traits, suggesting similar importance of plasticity and adaptation in weedy radish establishment. Further, in the majority of traits that were both plastic and differentiated between ecotypes, the direction of change matched, with the weedy environment producing phenotypic shifts in the direction of the weedy ecotype mean. This suggests plasticity in these traits may have enabled the subsequent adaptation and ecotype differentiation, supporting the buying-time hypothesis. Next, I explored the role of the plant hormone Gibberellic Acid (GA) in the evolution of weedy radish. Using exogenous application of GA both in the greenhouse and in weedy and native growth chamber environments, I found evidence that there has been an evolutionary change in the role of GA in trait expression between the two ecotypes. Namely, weedy radish is less responsive to GA application than native radish, suggesting either upregulation in GA production in weeds, or a lower level of GA required to enable gene expression in the weedy ecotype. This change in gene regulation by GA may have been important in the evolution of weedy radish in the agricultural field. Finally, I assessed the likelihood of weedy radish diverging from a native ancestor via adaptive evolution. I found that adaptive evolution was likely in the establishment of weedy radish due to increased fitness of the weedy ecotype compared to the native ecotype in the agricultural field. I also found traits under directional selection in the native ecotype, with the key takeaway that faster flowering is adaptive in the agricultural fields. I finally looked at the ability of weedy radish to evolve advanced flowering in the agricultural field via standing genetic variance by artificially selecting for early flowering in native radish. I found that in only two generations of selection, native populations significantly advanced their flowering time, supporting the notion of weedy radish rapidly adapting to agricultural conditions via standing genetic variation alone. Taken together, these findings work to piece together the evolutionary history of weedy radish, providing insight into its mechanisms of establishment. This work also contributes to our overall understanding of rapid evolution and phenotypic plasticity in the colonization of novel environments, in agricultural weeds and beyond.
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Title: Adaptive and Automated Deep Recommender Systems
Creator: Zhao, Xiangyu
Date: 2021
Collection: Electronic Theses & Dissertations
Description: Recommender systems are intelligent information retrieval applications, and have been leveraged in numerous domains such as e-commerce, movies, music, books, and point-of-interests. They play a crucial role in the users' information-seeking process, and overcome the information overload issue by recommending personalized items (products, services, or information) that best match users' needs and preferences. Driven by the recent advances in machine learning theories and the prevalence of deep...
Show moreRecommender systems are intelligent information retrieval applications, and have been leveraged in numerous domains such as e-commerce, movies, music, books, and point-of-interests. They play a crucial role in the users' information-seeking process, and overcome the information overload issue by recommending personalized items (products, services, or information) that best match users' needs and preferences. Driven by the recent advances in machine learning theories and the prevalence of deep learning techniques, there have been tremendous interests in developing deep learning based recommender systems. They have unprecedentedly advanced effectiveness of mining the non-linear user-item relationships and learning the feature representations from massive datasets, which produce great vitality and improvements in recommendations from both academic and industry communities.Despite above prominence of existing deep recommender systems, their adaptiveness and automation still remain under-explored. Thus, in this dissertation, we study the problem of adaptive and automated deep recommender systems. Specifically, we present our efforts devoted to building adaptive deep recommender systems to continuously update recommendation strategies according to the dynamic nature of user preference, which maximizes the cumulative reward from users in the practical streaming recommendation scenarios. In addition, we propose a group of automated and systematic approaches that design deep recommender system frameworks effectively and efficiently from a data-driven manner. More importantly, we apply our proposed models into a variety of real-world recommendation platforms and have achieved promising enhancements of social and economic benefits.
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Title: Adaptive behavior in sandbox games : how motivation shapes use of affordances in virtual worlds
Creator: Lee, Joomi
Date: 2020
Collection: Electronic Theses & Dissertations
Description: Users of video games actively interact with the game environment, impacting the contents of the environment and altering their subsequent behaviors in meaningful ways. Although motivation is essential to guide behavior, not much work has investigated how motivational processes shape in-game behavior. Therefore, this study incorporates understandings of player motivation with a concept of affordances to build a model of adaptive player behavior in games and virtual environments. The primary...
Show moreUsers of video games actively interact with the game environment, impacting the contents of the environment and altering their subsequent behaviors in meaningful ways. Although motivation is essential to guide behavior, not much work has investigated how motivational processes shape in-game behavior. Therefore, this study incorporates understandings of player motivation with a concept of affordances to build a model of adaptive player behavior in games and virtual environments. The primary prediction was that threats and resources in games will shape initial motivated behaviors to explore and use affordances of the virtual world at variable rates. Using a custom-designed game with varying threats and resources available to players, the approach and avoidance behavior players exhibit in response to motivationally relevant in-game encounters was examined in a laboratory experiment. The moderating role of trait-level motivational reactivity in facilitating and inhibiting motivational responses to the game environment was also examined. A series of repeated measures ANOVAs demonstrated that players' adaptively respond to virtual environment affordances to gain benefits and avoid threats, evidenced by facilitated approach behaviors in the absence of threat as well as facilitated avoidance behaviors under threatening circumstances. Furthermore, individual differences in appetitive and defensive trait motivational reactivity moderated these effects in significant fashion. Overall, these findings clarify the role of game mechanics and affordances of the virtual environment as key shapers of user behavior, and demonstrate that gameplay is made up of discrete adaptive behaviors guided by motivated responses to the game environment.
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Title: Adaptive learning : dilemmas of automated instruction in postsecondary education
Creator: Casarez, Roberto R.
Date: 2019
Collection: Electronic Theses & Dissertations
Description: "American higher education is experiencing a time of extraordinary change where traditional practices that have remained relatively unchanged for decades are being questioned and altered in the face of declining public confidence in higher education . Higher education institutions are turning to technological innovations to address numerous concerns, essentially remaking processes and practices at various levels of higher education such as instruction, learning, and administration. Adaptive...
Show more"American higher education is experiencing a time of extraordinary change where traditional practices that have remained relatively unchanged for decades are being questioned and altered in the face of declining public confidence in higher education . Higher education institutions are turning to technological innovations to address numerous concerns, essentially remaking processes and practices at various levels of higher education such as instruction, learning, and administration. Adaptive learning is one of the latest forms of innovation in teaching and learning, and it is currently receiving a great deal of attention across higher education. This study brings together the historical context, current environment of higher education, and the business market, and presents problems and dilemmas that may well affect the future of adaptive learning with the hope that it aids administrators, faculty, and staff in decision-making about this innovation in postsecondary education."--Page ii.
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Title: Adaptive on-device deep learning systems
Creator: Fang, Biyi
Date: 2019
Collection: Electronic Theses & Dissertations
Description: "Mobile systems such as smartphones, drones, and augmented-reality headsets are revolutionizing our lives. On-device deep learning is regarded as the key enabling technology for realizing their full potential. This is because communication with cloud adds additional latency or cost, or the applications must operate even with intermittent internet connectivity.The key to achieving the full promise of these mobile vision systems is effectively analyzing the streaming video frames. However,...
Show more"Mobile systems such as smartphones, drones, and augmented-reality headsets are revolutionizing our lives. On-device deep learning is regarded as the key enabling technology for realizing their full potential. This is because communication with cloud adds additional latency or cost, or the applications must operate even with intermittent internet connectivity.The key to achieving the full promise of these mobile vision systems is effectively analyzing the streaming video frames. However, processing streaming video frames taken in mobile settings is challenging in two folds. First, the processing usually involves multiple computer vision tasks. This multi-tenant characteristic requires mobile vision systems to concurrently run multiple applications that target different vision tasks. Second, the context in mobile settings can be frequently changed. This requires mobile vision systems to be able to switch applications to execute new vision tasks encountered in the new context.In this article, we fill this critical gap by proposing NestDNN, a framework that enables resource-aware multi-tenant on-device deep learning for continuous mobile vision. NestDNN enables each deep learning model to offer flexible resource-accuracy trade-offs. At runtime,it dynamically selects the optimal resource-accuracy trade-off for each deep learning model to fit the model's resource demand to the system's available runtime resources. In doing so, NestDNN efficiently utilizes the limited resources in mobile vision systems to jointly maximize the performance of all the concurrently running applications.Although NestDNN is able to efficiently utilize the resource by being resource-aware, it essentially treats the content of each input image equally and hence does not realize the full potential of such pipelines. To realize its full potential, we further propose FlexDNN, a novel content-adaptive framework that enables computation-efficient DNN-based on-device video stream analytics based on early exit mechanism. Compared to state-of-the-art earlyexit-based solutions, FlexDNN addresses their key limitations and pushes the state-of-the-artforward through its innovative fine-grained design and automatic approach for generating the optimal network architecture."--Pages ii-iii.
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Title: Addition and removal energies via the in-medium similarity renormalization group method
Creator: Yuan, Fei (Software engineer)
Date: 2018
Collection: Electronic Theses & Dissertations
Description: "The in-medium similarity renormalization group (IM-SRG) is an ab initio many-body method suitable for systems with moderate numbers of particles due to its polynomial scaling in computational cost. The formalism is highly flexible and admits a variety of modifications that extend its utility beyond the original goal of computing ground state energies of closed-shell systems. In this work, we present an extension of IM-SRG through quasidegenerate perturbation theory (QDPT) to compute...
Show more"The in-medium similarity renormalization group (IM-SRG) is an ab initio many-body method suitable for systems with moderate numbers of particles due to its polynomial scaling in computational cost. The formalism is highly flexible and admits a variety of modifications that extend its utility beyond the original goal of computing ground state energies of closed-shell systems. In this work, we present an extension of IM-SRG through quasidegenerate perturbation theory (QDPT) to compute addition and removal energies (single particle energies) near the Fermi level at low computational cost. This expands the range of systems that can be studied from closed-shell ones to nearby systems that differ by one particle. The method is applied to circular quantum dot systems and nuclei, and compared against other methods including equations-of-motion (EOM) IM-SRG and EOM coupled-cluster (CC) theory. The results are in good agreement for most cases. As part of this work, we present an open-source implementation of our flexible and easy-to-use J-scheme framework as well as the HF, IM-SRG, and QDPT codes built upon this framework. We include an overview of the overall structure, the implementation details, and strategies for maintaining high code quality and efficiency. Lastly, we also present a graphical application for manipulation of angular momentum coupling coefficients through a diagrammatic notation for angular momenta (Jucys diagrams). The tool enables rapid derivations of equations involving angular momentum coupling - such as in J-scheme - and significantly reduces the risk of human errors."--Page ii.
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