Matching Items (49)
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Description
The Southwestern Willow Flycatcher (Empidonax traillii extimus) has been studied for over two decades and listed as endangered for most of that time. Though the flycatcher has been granted protected status since 1995, critical habitat designation for the flycatcher has not shared the same history. Critical habitat designation is essential

The Southwestern Willow Flycatcher (Empidonax traillii extimus) has been studied for over two decades and listed as endangered for most of that time. Though the flycatcher has been granted protected status since 1995, critical habitat designation for the flycatcher has not shared the same history. Critical habitat designation is essential for achieving the long-term goals defined in the flycatcher recovery plan where emphasis is on both the protection of this species and "the habitats supporting these flycatchers [that] must be protected from threats and loss" (U.S. Fish and Wildlife Service 2002). I used a long-term data set of habitat characteristics collected at three study areas along the Lower Colorado River to develop a method for quantifying habitat quality for flycatcher. The data set contained flycatcher nest observations (use) and habitat availability (random location) from 2003-2010 that I statistically analyzed for flycatcher selection preferences. Using both Pearson's Chi-square test and SPSS Principal Component Analysis (PCA) I determined that flycatchers were selecting 30 habitat traits significantly different among an initial list of 127 habitat characteristics. Using PCA, I calculated a weighted value of influence for each significant trait per study area and used those values to develop a habitat classification system to build predictive models for flycatcher habitat quality. I used ArcGIS® Model Builder to develop three habitat suitability models for each of the habitat types occurring in western riparian systems, native, mixed exotic and exotic dominated that are frequented by breeding flycatchers. I designed a fourth model, Topock Marsh, to test model accuracy on habitat quality for flycatchers using reserved accuracy assessment points of previous nest locations. The results of the fourth model accurately predicted a decline in habitat at Topock Marsh that was confirmed by SWCA survey reports released in 2011 and 2012 documenting a significant decline in flycatcher productivity in the Topock Marsh study area.
ContributorsChenevert-Steffler, Ann (Author) / Miller, William (Thesis advisor) / Bateman, Heather (Committee member) / Alford, Eddie (Committee member) / Arizona State University (Publisher)
Created2013
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Description
Modified and artificial water sources can be used as a management tool for game and non-game wildlife species. State, federal, and private agencies allocate significant resources to install and maintain artificial water sources (AWS) annually. Capture mark recapture methods were used to sample small mammal communities in the vicinity of

Modified and artificial water sources can be used as a management tool for game and non-game wildlife species. State, federal, and private agencies allocate significant resources to install and maintain artificial water sources (AWS) annually. Capture mark recapture methods were used to sample small mammal communities in the vicinity of five AWS and five paired control sites (treatments) in the surrounding Sonoran desert from October 2011 to May 2012. I measured plant species richness, density, and percent cover in the spring of 2012. A Multi-response Permutation Procedure was used to identify differences in small mammal community abundance, biomass, and species richness by season and treatment. I used Principle Component Analysis to reduce 11 habitat characteristics to five habitat factors. I related rodent occurrence to habitat characteristics using multiple and logistic regression. A total of 370 individual mammals representing three genera and eight species of rodents were captured across 4800 trap nights. Desert pocket mouse (Chaetodipus penicillatus) was the most common species in both seasons and treatments. Whereas rodent community abundance, biomass, and richness were similar between seasons, community variables of AWS were greater than CS. Rodent diversity was similar between treatments. Desert pocket mouse abundance and biomass were twice as high at AWS when compared to controls. Biomass of white-throated woodrat (Neotoma albigula) was five times greater at AWS. Habitat characteristics were similar between treatments. Neither presence of water nor distance to water explained substantial habitat variation. Occurrence of rodent species was associated with habitat characteristics. Desert rodent communities are adapted for arid environments (i.e. Heteromyids) and are not dependent on "free water". Higher abundances of desert pocket mouse at AWS were most likely related to increased disturbance and debris and not the presence of water. The results of this study and previous studies suggest that more investigation is needed and that short term studies may not be able to detect interactions (if any) between AWS and desert small mammal communities.
ContributorsSwitalski, Aaron (Author) / Bateman, Heather L (Thesis advisor) / Miller, William (Committee member) / Alford, Eddie (Committee member) / Arizona State University (Publisher)
Created2013
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Description
Biological diversity is threatened by increasing anthropogenic modification of natural environments and increasing demands on natural resources. Sonoran desert tortoises (Gopherus morafkai) currently have Candidate status under the Endangered Species Act (ESA) based on health and habitat threats. To ensure this animal persists in the midst of multiple threats requires

Biological diversity is threatened by increasing anthropogenic modification of natural environments and increasing demands on natural resources. Sonoran desert tortoises (Gopherus morafkai) currently have Candidate status under the Endangered Species Act (ESA) based on health and habitat threats. To ensure this animal persists in the midst of multiple threats requires an understanding of the life history and ecology of each population. I looked at one physiological and one behavioral aspect of a population of tortoises at the Sugarloaf Mountain (SL) study site in central Arizona, USA. I used 21 years of capture-recapture records to estimate growth parameters of the entire population. I investigated habitat selection of juvenile tortoises by selecting 117 locations of 11 tortoises that had been tracked by radio-telemetry one to three times weekly for two years, selecting locations from both summer active season and during winter hibernation. I compared 22 microhabitat variables of tortoise locations to random SL locations to determine habitat use and availability. Male tortoises at SL reach a greater asymptotic length than females, and males and females appear to grow at the same rate. Juvenile tortoises at the SL site use steep rocky hillsides with high proportions of sand and annual vegetation, few succulents, and enclosed shelters in summer. They use enclosed shelters on steep slopes for winter hibernation. An understanding of these features can allow managers to quantify Sonoran desert tortoise habitat needs and life history characteristics and to understand the impact of land use policies.
ContributorsBridges, Andrew (Author) / Bateman, Heather L (Thesis advisor) / Miller, William (Committee member) / Ulrich, Jon (Committee member) / Arizona State University (Publisher)
Created2012
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Description
Mathematical modeling of infectious diseases can help public health officials to make decisions related to the mitigation of epidemic outbreaks. However, over or under estimations of the morbidity of any infectious disease can be problematic. Therefore, public health officials can always make use of better models to study the potential

Mathematical modeling of infectious diseases can help public health officials to make decisions related to the mitigation of epidemic outbreaks. However, over or under estimations of the morbidity of any infectious disease can be problematic. Therefore, public health officials can always make use of better models to study the potential implication of their decisions and strategies prior to their implementation. Previous work focuses on the mechanisms underlying the different epidemic waves observed in Mexico during the novel swine origin influenza H1N1 pandemic of 2009 and showed extensions of classical models in epidemiology by adding temporal variations in different parameters that are likely to change during the time course of an epidemic, such as, the influence of media, social distancing, school closures, and how vaccination policies may affect different aspects of the dynamics of an epidemic. This current work further examines the influence of different factors considering the randomness of events by adding stochastic processes to meta-population models. I present three different approaches to compare different stochastic methods by considering discrete and continuous time. For the continuous time stochastic modeling approach I consider the continuous-time Markov chain process using forward Kolmogorov equations, for the discrete time stochastic modeling I consider stochastic differential equations using Wiener's increment and Poisson point increments, and also I consider the discrete-time Markov chain process. These first two stochastic modeling approaches will be presented in a one city and two city epidemic models using, as a base, our deterministic model. The last one will be discussed briefly on a one city SIS and SIR-type model.
ContributorsCruz-Aponte, Maytee (Author) / Wirkus, Stephen A. (Thesis advisor) / Castillo-Chavez, Carlos (Thesis advisor) / Camacho, Erika T. (Committee member) / Kang, Yun (Committee member) / Arizona State University (Publisher)
Created2014
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Description
Grassland habitat restoration activities are occurring within the semi-arid grasslands of the Agua Fria National Monument located 65 km north of Phoenix, AZ. The goal of these restoration activities is to reduce woody species encroachment, remove lignified plant materials and recycle nutrients within the ecosystem thus improving range conditions for

Grassland habitat restoration activities are occurring within the semi-arid grasslands of the Agua Fria National Monument located 65 km north of Phoenix, AZ. The goal of these restoration activities is to reduce woody species encroachment, remove lignified plant materials and recycle nutrients within the ecosystem thus improving range conditions for both wildlife species and livestock. Broadcast burning, juniper thinning and slash pile burns are the principle tools used to accomplish resource objectives. Line cover, belt transect, densities, heights and biomass of vegetation data were collected to determine the response of the vegetative community to habitat restoration activities. Principal Component Analysis (PCA) was used to reduce data analysis to the more influential factors. Regression analysis was conducted for statistically significant response variables. Quadratic regression analysis found low predictive values. In broadcast burn treatment units, all important factors as identified by PCA had low predictive factors but significantly differed (R2 <0.01, p<0.05) between unburned and the years post treatment. Regression analysis found significant, albeit weak, relationships between time since treatment and independent variables. In pile burn treatment units, data reduction by PCA was not possible in a biologically meaningful way due to the high variability within treatment units. This suggests the effect of juniper encroachment on grassland vegetation persists long after junipers have been cut and burned. This study concluded that broadcast burning of the central Arizona grasslands does significantly alter many components of the vegetative community. Fuels treatments generally initially reduced both perennial woody species and grasses in number and height for two year post fire. However, palatable shrubs, in particular shrubby buckwheat, were not significantly different in broadcast burn treatment areas. The vegetative community characteristics of juniper encroached woodlands of central Arizona are unaffected by the removal and burning of junipers aside from the removal of hiding cover for predators for multiple years. It is recommended that habitat restoration activities continue provided the needs of wildlife are considered, especially pronghorn, with the incorporation of state and transition models specific to each of the respective ecological site descriptions and with the consideration of the effects of fire to pronghorn fawning habitat.
ContributorsSitzmann, Paul Roman (Author) / Miller, William (Thesis advisor) / Alford, Eddie (Committee member) / Green, Douglas (Committee member) / Arizona State University (Publisher)
Created2014
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Description
In the field of infectious disease epidemiology, the assessment of model robustness outcomes plays a significant role in the identification, reformulation, and evaluation of preparedness strategies aimed at limiting the impact of catastrophic events (pandemics or the deliberate release of biological agents) or used in the management of disease prevention

In the field of infectious disease epidemiology, the assessment of model robustness outcomes plays a significant role in the identification, reformulation, and evaluation of preparedness strategies aimed at limiting the impact of catastrophic events (pandemics or the deliberate release of biological agents) or used in the management of disease prevention strategies, or employed in the identification and evaluation of control or mitigation measures. The research work in this dissertation focuses on: The comparison and assessment of the role of exponentially distributed waiting times versus the use of generalized non-exponential parametric distributed waiting times of infectious periods on the quantitative and qualitative outcomes generated by Susceptible-Infectious-Removed (SIR) models. Specifically, Gamma distributed infectious periods are considered in the three research projects developed following the applications found in (Bailey 1964, Anderson 1980, Wearing 2005, Feng 2007, Feng 2007, Yan 2008, lloyd 2009, Vergu 2010). i) The first project focuses on the influence of input model parameters, such as the transmission rate, mean and variance of Gamma distributed infectious periods, on disease prevalence, the peak epidemic size and its timing, final epidemic size, epidemic duration and basic reproduction number. Global uncertainty and sensitivity analyses are carried out using a deterministic Susceptible-Infectious-Recovered (SIR) model. The quantitative effect and qualitative relation between input model parameters and outcome variables are established using Latin Hypercube Sampling (LHS) and Partial rank correlation coefficient (PRCC) and Spearman rank correlation coefficient (RCC) sensitivity indices. We learnt that: For relatively low (R0 close to one) to high (mean of R0 equals 15) transmissibility, the variance of the Gamma distribution for the infectious period, input parameter of the deterministic age-of-infection SIR model, is key (statistically significant) on the predictability of the epidemiological variables such as the epidemic duration and the peak size and timing of the prevalence of infectious individuals and therefore, for the predictability these variables, it is preferable to utilize a nonlinear system of Volterra integral equations, rather than a nonlinear system of ordinary differential equations. The predictability of epidemiological variables such as the final epidemic size and the basic reproduction number are unaffected by (or independent of) the variance of the Gamma distribution for the infectious period and therefore for the choice on which type of nonlinear system for the description of the SIR model (VIE's or ODE's) is irrelevant. Although, for practical proposes, with the aim of lowering the complexity and number operations in the numerical methods, a nonlinear system of ordinary differential equations is preferred. The main contribution lies in the development of a model based decision-tool that helps determine when SIR models given in terms of Volterra integral equations are equivalent or better suited than SIR models that only consider exponentially distributed infectious periods. ii) The second project addresses the question of whether or not there is sufficient evidence to conclude that two empirical distributions for a single epidemiological outcome, one generated using a stochastic SIR model under exponentially distributed infectious periods and the other under the non-exponentially distributed infectious period, are statistically dissimilar. The stochastic formulations are modeled via a continuous time Markov chain model. The statistical hypothesis test is conducted using the non-parametric Kolmogorov-Smirnov test. We found evidence that shows that for low to moderate transmissibility, all empirical distribution pairs (generated from exponential and non-exponential distributions) for each of the epidemiological quantities considered are statistically dissimilar. The research in this project helps determine whether the weakening exponential distribution assumption must be considered in the estimation of probability of events defined from the empirical distribution of specific random variables. iii) The third project involves the assessment of the effect of exponentially distributed infectious periods on estimates of input parameter and the associated outcome variable predictions. Quantities unaffected by the use of exponentially distributed infectious period within low transmissibility scenarios include, the prevalence peak time, final epidemic size, epidemic duration and basic reproduction number and for high transmissibility scenarios only the prevalence peak time and final epidemic size. An application designed to determine from incidence data whether there is sufficient statistical evidence to conclude that the infectious period distribution should not be modeled by an exponential distribution is developed. A method for estimating explicitly specified non-exponential parametric probability density functions for the infectious period from epidemiological data is developed. The methodologies presented in this dissertation may be applicable to models where waiting times are used to model transitions between stages, a process that is common in the study of life-history dynamics of many ecological systems.
ContributorsMorales Butler, Emmanuel J (Author) / Castillo-Chavez, Carlos (Thesis advisor) / Aparicio, Juan P (Thesis advisor) / Camacho, Erika T (Committee member) / Kang, Yun (Committee member) / Arizona State University (Publisher)
Created2014
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Description
There has been important progress in understanding ecological dynamics through the development of the theory of ecological stoichiometry. This fast growing theory provides new constraints and mechanisms that can be formulated into mathematical models. Stoichiometric models incorporate the effects of both food quantity and food quality into a single framework

There has been important progress in understanding ecological dynamics through the development of the theory of ecological stoichiometry. This fast growing theory provides new constraints and mechanisms that can be formulated into mathematical models. Stoichiometric models incorporate the effects of both food quantity and food quality into a single framework that produce rich dynamics. While the effects of nutrient deficiency on consumer growth are well understood, recent discoveries in ecological stoichiometry suggest that consumer dynamics are not only affected by insufficient food nutrient content (low phosphorus (P): carbon (C) ratio) but also by excess food nutrient content (high P:C). This phenomenon, known as the stoichiometric knife edge, in which animal growth is reduced not only by food with low P content but also by food with high P content, needs to be incorporated into mathematical models. Here we present Lotka-Volterra type models to investigate the growth response of Daphnia to algae of varying P:C ratios. Using a nonsmooth system of two ordinary differential equations (ODEs), we formulate the first model to incorporate the phenomenon of the stoichiometric knife edge. We then extend this stoichiometric model by mechanistically deriving and tracking free P in the environment. This resulting full knife edge model is a nonsmooth system of three ODEs. Bifurcation analysis and numerical simulations of the full model, that explicitly tracks phosphorus, leads to quantitatively different predictions than previous models that neglect to track free nutrients. The full model shows that the grazer population is sensitive to excess nutrient concentrations as a dynamical free nutrient pool induces extreme grazer population density changes. These modeling efforts provide insight on the effects of excess nutrient content on grazer dynamics and deepen our understanding of the effects of stoichiometry on the mechanisms governing population dynamics and the interactions between trophic levels.
ContributorsPeace, Angela (Author) / Kuang, Yang (Thesis advisor) / Elser, James J (Committee member) / Baer, Steven (Committee member) / Tang, Wenbo (Committee member) / Kang, Yun (Committee member) / Arizona State University (Publisher)
Created2014
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Description
In 1968, phycologist M.R. Droop published his famous discovery on the functional relationship between growth rate and internal nutrient status of algae in chemostat culture. The simple notion that growth is directly dependent on intracellular nutrient concentration is useful for understanding the dynamics in many ecological systems. The cell quota

In 1968, phycologist M.R. Droop published his famous discovery on the functional relationship between growth rate and internal nutrient status of algae in chemostat culture. The simple notion that growth is directly dependent on intracellular nutrient concentration is useful for understanding the dynamics in many ecological systems. The cell quota in particular lends itself to ecological stoichiometry, which is a powerful framework for mathematical ecology. Three models are developed based on the cell quota principal in order to demonstrate its applications beyond chemostat culture.

First, a data-driven model is derived for neutral lipid synthesis in green microalgae with respect to nitrogen limitation. This model synthesizes several established frameworks in phycology and ecological stoichiometry. The model demonstrates how the cell quota is a useful abstraction for understanding the metabolic shift to neutral lipid production that is observed in certain oleaginous species.

Next a producer-grazer model is developed based on the cell quota model and nutrient recycling. The model incorporates a novel feedback loop to account for animal toxicity due to accumulation of nitrogen waste. The model exhibits rich, complex dynamics which leave several open mathematical questions.

Lastly, disease dynamics in vivo are in many ways analogous to those of an ecosystem, giving natural extensions of the cell quota concept to disease modeling. Prostate cancer can be modeled within this framework, with androgen the limiting nutrient and the prostate and cancer cells as competing species. Here the cell quota model provides a useful abstraction for the dependence of cellular proliferation and apoptosis on androgen and the androgen receptor. Androgen ablation therapy is often used for patients in biochemical recurrence or late-stage disease progression and is in general initially effective. However, for many patients the cancer eventually develops resistance months to years after treatment begins. Understanding how and predicting when hormone therapy facilitates evolution of resistant phenotypes has immediate implications for treatment. Cell quota models for prostate cancer can be useful tools for this purpose and motivate applications to other diseases.
ContributorsPacker, Aaron (Author) / Kuang, Yang (Thesis advisor) / Nagy, John (Committee member) / Smith, Hal (Committee member) / Kostelich, Eric (Committee member) / Kang, Yun (Committee member) / Arizona State University (Publisher)
Created2014
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Description
Pre-Exposure Prophylaxis (PrEP) is any medical or public health procedure used before exposure to the disease causing agent, its purpose is to prevent, rather than treat or cure a disease. Most commonly, PrEP refers to an experimental HIV-prevention strategy that would use antiretrovirals to protect HIV-negative people from HIV infection.

Pre-Exposure Prophylaxis (PrEP) is any medical or public health procedure used before exposure to the disease causing agent, its purpose is to prevent, rather than treat or cure a disease. Most commonly, PrEP refers to an experimental HIV-prevention strategy that would use antiretrovirals to protect HIV-negative people from HIV infection. A deterministic mathematical model of HIV transmission is developed to evaluate the public-health impact of oral PrEP interventions, and to compare PrEP effectiveness with respect to different evaluation methods. The effects of demographic, behavioral, and epidemic parameters on the PrEP impact are studied in a multivariate sensitivity analysis. Most of the published models on HIV intervention impact assume that the number of individuals joining the sexually active population per year is constant or proportional to the total population. In the second part of this study, three models are presented and analyzed to study the PrEP intervention, with constant, linear, and logistic recruitment rates. How different demographic assumptions can affect the evaluation of PrEP is studied. When provided with data, often least square fitting or similar approaches can be used to determine a single set of approximated parameter values that make the model fit the data best. However, least square fitting only provides point estimates and does not provide information on how strongly the data supports these particular estimates. Therefore, in the third part of this study, Bayesian parameter estimation is applied on fitting ODE model to the related HIV data. Starting with a set of prior distributions for the parameters as initial guess, Bayes' formula can be applied to obtain a set of posterior distributions for the parameters which makes the model fit the observed data best. Evaluating the posterior distribution often requires the integration of high-dimensional functions, which is usually difficult to calculate numerically. Therefore, the Markov chain Monte Carlo (MCMC) method is used to approximate the posterior distribution.
ContributorsZhao, Yuqin (Author) / Kuang, Yang (Thesis advisor) / Taylor, Jesse (Committee member) / Armbruster, Dieter (Committee member) / Tang, Wenbo (Committee member) / Kang, Yun (Committee member) / Arizona State University (Publisher)
Created2014
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Description
Once considered an abundant species in the eastern United States, local populations of red-shouldered hawks, Buteo lineatus, have declined due to habitat destruction. This destruction has created suitable habitat for red-tailed hawks, Buteo jamaicensis, and therefore increased competition between these two raptor species. Since suitable habitat is the main limiting

Once considered an abundant species in the eastern United States, local populations of red-shouldered hawks, Buteo lineatus, have declined due to habitat destruction. This destruction has created suitable habitat for red-tailed hawks, Buteo jamaicensis, and therefore increased competition between these two raptor species. Since suitable habitat is the main limiting factor for raptors, a computer model was created to simulate the effect of habitat loss in central Maryland and the impact of increased competition between the more aggressive red-tailed hawk. These simulations showed urban growth contributed to over a 30% increase in red-tailed hawk habitat as red-shouldered hawk habitat decreased 62.5-70.1% without competition and 71.8-76.3% with competition. However there was no significant difference seen between the rate of available habitat decline for current and predicted development growth.
ContributorsMurillo, Crystal (Author) / Whysong, Gary (Thesis advisor) / Alford, Eddie (Committee member) / Miller, William (Committee member) / Arizona State University (Publisher)
Created2011