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- Genre: Doctoral Dissertation
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
Meditation app usage is associated with decreases in stress, anxiety, and depression symptoms. Many meditation app subscribers, however, quickly abandon or reduce their app usage. This dissertation presents three manuscripts which 1) determined the behavioral, demographic, and socioeconomic factors associated with the abandonment of a meditation app, Calm, during the COVID-19 pandemic, 2) determined which participant characteristics predicted meditation app usage in the first eight weeks after subscribing, and 3) determined if changes in stress, anxiety, and depressive symptoms from baseline to Week 8 predicted meditation app usage from Weeks 8-16. In Manuscript 1, a survey was distributed to Calm subscribers in March 2020 that assessed meditation app behavior and meditation habit strength, and demographic information. Cox proportional hazards regression models were estimated to assess time to app abandonment. In Manuscript 2, new Calm subscribers completed a baseline survey on participants’ demographic and baseline mental health information and app usage data were collected over 8 weeks. In Manuscript 3, new Calm subscribers completed a baseline and Week 8 survey on demographic and mental health information. App usage data were collected over 16 weeks. Regression models were used to assess app usage for Manuscripts 2 and 3. Findings from Manuscript 1 suggest meditating after an existing routine decreased risk of app abandonment for pre-pandemic subscribers and for pandemic subscribers. Additionally, meditating “whenever I can” decreased risk of abandonment among pandemic subscribers. No behavioral factors were significant predictors of app abandonment among the long-term subscribers. Findings from Manuscript 2 suggest men had more days of meditation than women. Mental health diagnosis increased average daily meditation minutes. Intrinsic motivation for meditation increased the likelihood of completing any meditation session, more days with meditation sessions, and more average daily meditation minutes. Findings from Manuscript 3 suggest improvements in stress increased average daily meditation minutes. Improvements in depressive symptoms decreased daily meditation minutes. Evidence from this three-manuscript dissertation suggests meditation cue, time of day, motivation, symptom changes, and demographic and socioeconomic variables may be used to predict meditation app usage.
ContributorsSullivan, Mariah (Author) / Stecher, Chad (Thesis advisor) / Huberty, Jennifer (Committee member) / Buman, Matthew (Committee member) / Larkey, Linda (Committee member) / Chung, Yunro (Committee member) / Arizona State University (Publisher)
Created2022
Description
Young adult collegiate women, particularly students with adverse childhood experiences (ACEs) and who have experienced intimate partner violence (IPV) victimization, report a myriad of adverse mental health and academic difficulties. Practicing yoga has demonstrated promising findings among adults as a healing modality in the aftermath of interpersonal violence victimization and traumatization. Less known are the associations between collegiate women’s yoga participation and their mental health, body connection, and academic well-being examined through a yoga feminist- trauma conceptual framework. Among young adult collegiate women, this study examined (1) associations amongst socio-demographics, mental health service use, IPV types, and yoga participation (2) the strength and direction of associations on measures of ACEs, mental health, body connection, and academic well-being, (3) whether yoga participation predicted students’ mental health, body connection, and academic well-being after controlling for confounding variables, including ACEs and IPV victimization, and (4) whether socio-demographics, mental health service use, ACEs, and IPV types predicted yoga participation. This study was observational, cross-sectional, and gathered self-report quantitative data. Eligible participants were current collegiate women enrolled at an urban, public university in the southwestern United States who were 18 to 24 years of age. The main sub-sample (n = 93) included students who were ever in an intimate relationship and practiced yoga within the past year. IRB approval was obtained. Findings demonstrated that yoga participation was not a significant predictor of students’ mental health, body connection, or academic well-being. Socio-demographics, mental health service use, ACEs, and IPV did not predict yoga participation. However, women with greater ACEs fared worse on measures of mental health (i.e., depression and post-traumatic stress disorder symptoms), and women with experiences of IPV harassment reported greater post-traumatic stress disorder symptoms. Further, employed women reported fewer depression symptoms and were less likely to experience emotional IPV. Lastly, students with greater body connection (more awareness) fared better academically. This research supports prior literature on the adverse mental health outcomes among young adult collegiate women with histories of interpersonal violence. Further examination is warranted into employment and body connection, particularly related to yoga, as protective factors of students' health, safety, and academic well-being.
ContributorsKappas Mazzio, Andrea Alexa (Author) / Messing, Jill T (Thesis advisor) / Mendoza, Natasha (Committee member) / Huberty, Jennifer (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
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
Description
The mutual inhibition between synthetic gene circuits and cell growth produces growth feedback in the host-circuit system. Previous studies have demonstrated that the growth feedback has an marked impact on the molecular dynamics of the host-circuit system. However, the complexity of the growth feedback effect is not fully understood. A theoretical framework was developed to study the dynamics of the coupling between growth feedback and synthetic gene circuits. The study’s results reveal three major points about the impact of growth feedback. First, a nonlinear emergent behavior mediated by growth feedback. The unexpected behavior depends on the dynamic ribosome allocation between gene circuit expression and host cell growth. Second, the emergence and loss of unexpected qualitative states on the host-circuit system generated by ultrasensitive growth feedback. Third, the growth feedback-induced cooperativity behavior in synthetic gene modules competing for resources. In addition, growth feedback attenuated the winner-takes-all rules on resource competition between the two self-activating modules. These results demonstrate that growth feedback plays an important role in the host-circuit system’s molecular dynamics. Characterizing general principles from the effect of growth facilitates the ability to minimize or even harness unexpected gene expression behaviors derived from the effect of growth feedback.
ContributorsMelendez-Alvarez, Juan Ramon (Author) / Tian, Xiaojun (Thesis advisor) / Wang, Xiao (Committee member) / Kuang, Yang (Committee member) / Arizona State University (Publisher)
Created2022