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Description
Rabies disease remains enzootic among raccoons, skunks, foxes and bats in the United States. It is of primary concern for public-health agencies to control spatial spread of rabies in wildlife and its potential spillover infection of domestic animals and humans. Rabies is invariably fatal in wildlife if untreated, with a non-negligible incubation period. Understanding how this latency affects spatial spread of rabies in wildlife is the concern of chapter 2 and 3. Chapter 1 deals with the background of mathematical models for rabies and lists main objectives. In chapter 2, a reaction-diffusion susceptible-exposed-infected (SEI) model and a delayed diffusive susceptible-infected (SI) model are constructed to describe the same epidemic process -- rabies spread in foxes. For the delayed diffusive model a non-local infection term with delay is resulted from modeling the dispersal during incubation stage. Comparison is made regarding minimum traveling wave speeds of the two models, which are verified using numerical experiments. In chapter 3, starting with two Kermack and McKendrick's models where infectivity, death rate and diffusion rate of infected individuals can depend on the age of infection, the asymptotic speed of spread $c^\ast$ for the cumulated force of infection can be analyzed. For the special case of fixed incubation period, the asymptotic speed of spread is governed by the same integral equation for both models. Although explicit solutions for $c^\ast$ are difficult to obtain, assuming that diffusion coefficient of incubating animals is small, $c^\ast$ can be estimated in terms of model parameter values. Chapter 4 considers the implementation of realistic landscape in simulation of rabies spread in skunks and bats in northeast Texas. The Finite Element Method (FEM) is adopted because the irregular shapes of realistic landscape naturally lead to unstructured grids in the spatial domain. This implementation leads to a more accurate description of skunk rabies cases distributions.
ContributorsLiu, Hao (Author) / Kuang, Yang (Thesis advisor) / Jackiewicz, Zdzislaw (Committee member) / Lanchier, Nicolas (Committee member) / Smith, Hal (Committee member) / Thieme, Horst (Committee member) / Arizona State University (Publisher)
Created2013
Description
Bacteriophage (phage) are viruses that infect bacteria. Typical laboratory experiments show that in a chemostat containing phage and susceptible bacteria species, a mutant bacteria species will evolve. This mutant species is usually resistant to the phage infection and less competitive compared to the susceptible bacteria species. In some experiments, both susceptible and resistant bacteria species, as well as phage, can coexist at an equilibrium for hundreds of hours. The current research is inspired by these observations, and the goal is to establish a mathematical model and explore sufficient and necessary conditions for the coexistence. In this dissertation a model with infinite distributed delay terms based on some existing work is established. A rigorous analysis of the well-posedness of this model is provided, and it is proved that the susceptible bacteria persist. To study the persistence of phage species, a "Phage Reproduction Number" (PRN) is defined. The mathematical analysis shows phage persist if PRN > 1 and vanish if PRN < 1. A sufficient condition and a necessary condition for persistence of resistant bacteria are given. The persistence of the phage is essential for the persistence of resistant bacteria. Also, the resistant bacteria persist if its fitness is the same as the susceptible bacteria and if PRN > 1. A special case of the general model leads to a system of ordinary differential equations, for which numerical simulation results are presented.
ContributorsHan, Zhun (Author) / Smith, Hal (Thesis advisor) / Armbruster, Dieter (Committee member) / Kawski, Matthias (Committee member) / Kuang, Yang (Committee member) / Thieme, Horst (Committee member) / Arizona State University (Publisher)
Created2012
Description
In vertebrate outer retina, changes in the membrane potential of horizontal cells affect the calcium influx and glutamate release of cone photoreceptors via a negative feedback. This feedback has a number of important physiological consequences. One is called background-induced flicker enhancement (BIFE) in which the onset of dim background enhances the center flicker response of horizontal cells. The underlying mechanism for the feedback is still unclear but competing hypotheses have been proposed. One is the GABA hypothesis, which states that the feedback is mediated by gamma-aminobutyric acid (GABA), an inhibitory neurotransmitter released from horizontal cells. Another is the ephaptic hypothesis, which contends that the feedback is non-GABAergic and is achieved through the modulation of electrical potential in the intersynaptic cleft between cones and horizontal cells. In this study, a continuum spine model of the cone-horizontal cell synaptic circuitry is formulated. This model, a partial differential equation system, incorporates both the GABA and ephaptic feedback mechanisms. Simulation results, in comparison with experiments, indicate that the ephaptic mechanism is necessary in order for the model to capture the major spatial and temporal dynamics of the BIFE effect. In addition, simulations indicate that the GABA mechanism may play some minor modulation role.
ContributorsChang, Shaojie (Author) / Baer, Steven M. (Thesis advisor) / Gardner, Carl L (Thesis advisor) / Crook, Sharon M (Committee member) / Kuang, Yang (Committee member) / Ringhofer, Christian (Committee member) / Arizona State University (Publisher)
Created2012
Description
During the months from June to November 2012, the city of Bangalore was faced with a serious solid waste management (SWM) crisis. In the wake of the upheaval, the state court declared source segregation to be mandatory. Yet, while the legislation was clear, the pathway towards a course of action for the transition was not clear and hence, Bangalore was stuck in a state of limbo. The objectives for this thesis spiraled organically from this crisis. The first objective was to examine the gaps in Bangalore's transition to a more sustainable SWM system. Six particular gaps were identified, which in essence, were opportunities to re-shape the system. The gaps identified included: conflicting political agendas, the exclusion of some key actors, and lack of adequate attention to cultural aspects, provision of appropriate incentives, protection of livelihoods and promotion of innovation. Opportunities were found in better incentivization of sustainable SWM goals, protecting livelihoods that depend on waste, enhancing innovation and endorsing local, context based SWM solutions. Building on this understanding of gaps, the second objective was to explore an innovative, local, bottom-up waste-management model called the Vellore Zero Waste Model, and assess its applicability to Bangalore. The adaptability of the model depended on several factors such as, willingness of actors to redefine their roles and change functions, ability of the municipality to assure quality and oversight, willingness of citizen to source segregate, and most importantly, the political will and collective action needed to ensure and sustain the transition. The role of communication as a vital component to facilitate productive stakeholder engagement and to promote role change was evident. Therefore, the third objective of the study was to explore how interpersonal competencies and communication strategies could be used as a tool to facilitate stakeholder engagement and encourage collective action. In addressing these objectives, India was compared with Austria because Austria is often cited as having some of the best SWM practices in the world and has high recycling rates to show for its reputation.
ContributorsRengarajan, Nivedita (Author) / Aggarwal, Rimjhim (Thesis advisor) / Chhetri, Nalini (Committee member) / Manuel-Navarrete, David (Committee member) / Arizona State University (Publisher)
Created2013
Description
This dissertation focuses on the endogenous conceptualization of development and sustainability emerging from settled non-native indigenous communities in the transborder region of Baja California, México. The study is comprised of interview data collected from a sample of 19 (n=19) self-identifying non-native indigenous community members and three key informants residing in various municipalities of the state. The purpose of this research is twofold, on the one hand, it aims to highlight the ways global north conceptualizations and praxis of development and sustainability in México have failed to include indigenous communities and fall short of creating feasible or appropriate practices of development and sustainability for marginalized communities. On the other, it focuses on the future perspectives of non-native indigenous communities to understand what development and sustainability look like for marginalized indigenous communities in México. The research finds that non-native indigenous communities’ settled in Baja California align more closely with the notion of Buen Vivir than development, in efforts to implement holistic approaches to progress and the conservation of their ethnic identity, culture and funds of knowledge. Additionally, the data reveals the bordering processes within ethnic and cultural scapes in Baja California’s society incentivizes merging funds of knowledge to achieve community recognition and progress. In essence, the experience and mobilization of settled non-native indigenous communities in Baja California break the perceived dichotomy between rural and urban, traditional and modern. The research also has some auxiliary findings: (1) indicating that in the state of Baja California the proliferation of development and sustainability discourses are polarized and relatively neglected in public discourses, despite its close transborder relationship with the US and growing concerns of development and sustainability in the northern nation. Second, indigenous women have been and continue to be important catalysts in community formation and representation.
ContributorsMora-Castillo, Brenda (Author) / Cruz-Torres, Maria l (Thesis advisor) / Wutich, Amber (Committee member) / Manuel-Navarrete, David (Committee member) / Arizona State University (Publisher)
Created2022
Description
Climate change is one of the most pressing issues affecting the world today. One of the impacts of climate change is on the transmission of mosquito-borne diseases (MBDs), such as West Nile Virus (WNV). Climate is known to influence vector and host demography as well as MBD transmission. This dissertation addresses the questions of how vector and host demography impact WNV dynamics, and how expected and likely climate change scenarios will affect demographic and epidemiological processes of WNV transmission. First, a data fusion method is developed that connects non-autonomous logistic model parameters to mosquito time series data. This method captures the inter-annual and intra-seasonal variation of mosquito populations within a geographical location. Next, a three-population WNV model between mosquito vectors, bird hosts, and human hosts with infection-age structure for the vector and bird host populations is introduced. A sensitivity analysis uncovers which parameters have the most influence on WNV outbreaks. Finally, the WNV model is extended to include the non-autonomous population model and temperature-dependent processes. Model parameterization using historical temperature and human WNV case data from the Greater Toronto Area (GTA) is conducted. Parameter fitting results are then used to analyze possible future WNV dynamics under two climate change scenarios. These results suggest that WNV risk for the GTA will substantially increase as temperature increases from climate change, even under the most conservative assumptions. This demonstrates the importance of ensuring that the warming of the planet is limited as much as possible.
ContributorsMancuso, Marina (Author) / Milner, Fabio A (Thesis advisor) / Kuang, Yang (Committee member) / Kostelich, Eric (Committee member) / Eikenberry, Steffen (Committee member) / Manore, Carrie (Committee member) / Arizona State University (Publisher)
Created2023
Description
Over the past 20 years, the fields of synthetic biology and synthetic biosystems engineering have grown into mature disciplines, leading to significant breakthroughs in cancer research, diagnostics, cell-based medicines, biochemical production, etc. Application of mathematical modelling to biological and biochemical systems have not only given great insight into how these systems function, but also have lent enough predictive power to aid in the forward-engineering of synthetic constructs. However, progress has been impeded by several modes of context-dependence unique to biological and biochemical systems that are not seen in traditional engineering disciplines, resulting in the need for lengthy design-build-test cycles before functional prototypes are generated.In this work, two of these universal modes of context dependence – resource competition and growth feedback –their effects on synthetic gene circuits and potential control mechanisms, are studied and characterized. Results demonstrate that a novel competitive control architecture can be utilized to mitigate the effects of winner-take-all resource competition (a form of context dependence where distinct gene modules influence each other by competing over a shared pool of transcriptional/translational resources) in synthetic gene circuits and restore circuits to their intended function. Application of the fluctuation-dissipation theorem and rigorous stochastic simulations demonstrate that realistic resource constraints present in cells at the transcriptional and translational levels influence noise in gene circuits in a nonmonotonic fashion, either increasing or decreasing noise depending on the transcriptional/translational capacity.
Growth feedback on the other hand links circuit function to cellular growth rate via increased protein dilution rate during exponential growth phase. This in turn can result in the collapse of bistable gene circuits as the accelerated dilution rate forces switches in a high stable state to fall to a low stable state. Mathematical modelling and experimental data demonstrate that application of repressive links can insulate sensitive parts of gene circuits against growth-fluctuations and can in turn increase the robustness of multistable circuits in growth contexts.
The results presented in this work aid in the accumulation of understanding of biological and biochemical context dependence, and corresponding control strategies and design principles engineers can utilize to mitigate these effects.
ContributorsStone, Austin (Author) / Tian, Xiao-jun (Thesis advisor) / Wang, Xiao (Committee member) / Smith, Barbara (Committee member) / Kuang, Yang (Committee member) / Cheng, Albert (Committee member) / Arizona State University (Publisher)
Created2023
Description
The crafting of cultural goods and ethnic arts have been stable means for making a living within many Indigenous communities throughout the world. In order to understand how crafting can be an avenue towards sustainable entrepreneurship, an analysis of the relationships between Indigenous crafting, Indigenous community life, sustainable agency, Indigenous concepts of wellbeing, and sustainable entrepreneurship is needed. Through three-papers focused on an extensive literature review (aggregate to all three papers) and ethnographic field research (semi-structured interviews, verbal surveys, and ethnographic observation) this dissertation examines how the act of Indigenous crafting as carried out by individuals within families and by families within Indigenous communities, link with social relationships, making a living, gender roles, and cultural identity and how these aspects of community life intersect with sustainable forms of agency, Indigenous concepts of wellbeing, and small-scale social entrepreneurial activities in the context of Indigenous crafting in a bid to indigenize the concept of sustainable entrepreneurship. This dissertation proposes a series of conceptual frameworks that depict the discussed linkages between Indigenous crafting, Indigenous community life, sustainable forms of agency, sustainable livelihood, and Indigenous concepts of wellbeing, in the context of sustainable entrepreneurship along with the relevant literature associated with each element in the frameworks. This dissertation draws from a qualitative ethnographic study on Mazahua artisans and their communities in Mexico in an attempt to understand and expand sustainable entrepreneurship from Euro-Western perspectives to Indigenous perspectives in order to better apply SE concepts in the development of an Indigenous fashion goods venture called Vitu™. This Indigenous venture, through the Indigenized sustainable entrepreneurship concept of Adaptive-Transformative Agency, will more deeply address justice, equity, and inclusion for Indigenous peoples and their communities pursuing community development through entrepreneurial activities.
ContributorsTakamura, John Hiroomi (Author) / BurnSilver, Shauna (Thesis advisor) / Manuel-Navarrete, David (Thesis advisor) / Chhetri, Nalini (Committee member) / Arizona State University (Publisher)
Created2022
Description
There is a need in the ecology literature to have a discussion about the fundamental theories from which population dynamics arises. Ad hoc model development is not uncommon in the field often as a result of a need to publish rapidly and frequently. Ecologists and statisticians like Robert J. Steidl and Kenneth P Burnham have called for a more deliberative approach they call "hard thinking". For example, the phenomena of population growth can be captured by almost any sigmoid function. The question of which sigmoid function best explains a data set cannot be answered meaningfully by statistical regression since that can only speak to the validity of the shape. There is a need to revisit enzyme kinetics and ecological stoichiometry to properly justify basal model selection in ecology. This dissertation derives several common population growth models from a generalized equation. The mechanistic validity of these models in different contexts is explored through a kinetic lens. The behavioral kinetic framework is then put to the test by examining a set of biologically plausible growth models against the 1968-1995 elk population count data for northern Yellowstone. Using only this count data, the novel Monod-Holling growth model was able to accurately predict minimum viable population and life expectancy despite both being exogenous to the model and data set. Lastly, the elk/wolf data from Yellowstone was used to compare the validity of the Rosenzweig-MacArthur and Arditi-Ginzburg models. They both were derived from a more general model which included both predator and prey mediated steps. The Arditi-Ginzburg model was able to fit the training data better, but only the Rosenzweig-MacArthur model matched the validation data. Accounting for animal sexual behavior allowed for the creation of the Monod-Holling model which is just as simple as the logistic differential equation but provides greater insights for conservation purposes. Explicitly acknowledging the ethology of wolf predation helps explain the differences in predictive performances by the best fit Rosenzweig-MacArthur and Arditi-Ginzburg models. The behavioral kinetic framework has proven to be a useful tool, and it has the ability to provide even further insights going forward.
ContributorsPringle, Jack Andrew McCracken (Author) / Anderies, John M (Thesis advisor) / Kuang, Yang (Committee member) / Milner, Fabio (Committee member) / Arizona State University (Publisher)
Created2022
Description
Ecology has been an actively studied topic recently, along with the rapid development of human microbiota-based technology. Scientists have made remarkable progress using bioinformatics tools to identify species and analyze composition. However, a thorough understanding of interspecies interactions of microbial ecosystems is still lacking, which has been a significant obstacle in the further development of related technologies. In this work, a genetic circuit design principle with synthetic biology approaches is developed to form two-strain microbial consortia with different inter-strain interactions. The microbial systems are well-defined and inducible. Co-culture experiment results show that our microbial consortia behave consistently with previous ecological knowledge and thus serves as excellent model systems to simulate ecosystems with similar interactions. Colony patterns also emerge when co-culturing multiple species on solid media. With the engineered microbial consortia, image-processing based methods were developed to quantify the shape of co-culture colonies and distinguish microbial consortia with different interactions. Factors that affect the population ratios were identified through induction and variations in the inoculation process. Further time-lapse experiments revealed the basic rules of colony growth, composition variation, patterning, and how spatial factors impact the co-culture colony.
ContributorsChen, Xingwen (Author) / Wang, Xiao (Thesis advisor) / Kuang, Yang (Committee member) / Tian, Xiaojun (Committee member) / Brafman, David (Committee member) / Plaisier, Christopher (Committee member) / Arizona State University (Publisher)
Created2022