Matching Items (87)
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
A P-value based method is proposed for statistical monitoring of various types of profiles in phase II. The performance of the proposed method is evaluated by the average run length criterion under various shifts in the intercept, slope and error standard deviation of the model. In our proposed approach, P-values are computed at each level within a sample. If at least one of the P-values is less than a pre-specified significance level, the chart signals out-of-control. The primary advantage of our approach is that only one control chart is required to monitor several parameters simultaneously: the intercept, slope(s), and the error standard deviation. A comprehensive comparison of the proposed method and the existing KMW-Shewhart method for monitoring linear profiles is conducted. In addition, the effect that the number of observations within a sample has on the performance of the proposed method is investigated. The proposed method was also compared to the T^2 method discussed in Kang and Albin (2000) for multivariate, polynomial, and nonlinear profiles. A simulation study shows that overall the proposed P-value method performs satisfactorily for different profile types.
ContributorsAdibi, Azadeh (Author) / Montgomery, Douglas C. (Thesis advisor) / Borror, Connie (Thesis advisor) / Li, Jing (Committee member) / Zhang, Muhong (Committee member) / Arizona State University (Publisher)
Created2013
Description
In a healthcare setting, the Sterile Processing Department (SPD) provides ancillary services to the Operating Room (OR), Emergency Room, Labor & Delivery, and off-site clinics. SPD's function is to reprocess reusable surgical instruments and return them to their home departments. The management of surgical instruments and medical devices can impact patient safety and hospital revenue. Any time instrumentation or devices are not available or are not fit for use, patient safety and revenue can be negatively impacted. One step of the instrument reprocessing cycle is sterilization. Steam sterilization is the sterilization method used for the majority of surgical instruments and is preferred to immediate use steam sterilization (IUSS) because terminally sterilized items can be stored until needed. IUSS Items must be used promptly and cannot be stored for later use. IUSS is intended for emergency situations and not as regular course of action. Unfortunately, IUSS is used to compensate for inadequate inventory levels, scheduling conflicts, and miscommunications. If IUSS is viewed as an adverse event, then monitoring IUSS incidences can help healthcare organizations meet patient safety goals and financial goals along with aiding in process improvement efforts. This work recommends statistical process control methods to IUSS incidents and illustrates the use of control charts for IUSS occurrences through a case study and analysis of the control charts for data from a health care provider. Furthermore, this work considers the application of data mining methods to IUSS occurrences and presents a representative example of data mining to the IUSS occurrences. This extends the application of statistical process control and data mining in healthcare applications.
ContributorsWeart, Gail (Author) / Runger, George C. (Thesis advisor) / Li, Jing (Committee member) / Shunk, Dan (Committee member) / Arizona State University (Publisher)
Created2014
Description
In a 2004 paper, John Nagy raised the possibility of the existence of a hypertumor \emph{i.e.}, a focus of aggressively reproducing parenchyma cells that invade part or all of a tumor. His model used a system of nonlinear ordinary differential equations to find a suitable set of conditions for which these hypertumors exist. Here that model is expanded by transforming it into a system of nonlinear partial differential equations with diffusion, advection, and a free boundary condition to represent a radially symmetric tumor growth. Two strains of parenchymal cells are incorporated; one forming almost the entirety of the tumor while the much more aggressive strain
appears in a smaller region inside of the tumor. Simulations show that if the aggressive strain focuses its efforts on proliferating and does not contribute to angiogenesis signaling when in a hypoxic state, a hypertumor will form. More importantly, this resultant aggressive tumor is paradoxically prone to extinction and hypothesize is the cause of necrosis in many vascularized tumors.
appears in a smaller region inside of the tumor. Simulations show that if the aggressive strain focuses its efforts on proliferating and does not contribute to angiogenesis signaling when in a hypoxic state, a hypertumor will form. More importantly, this resultant aggressive tumor is paradoxically prone to extinction and hypothesize is the cause of necrosis in many vascularized tumors.
ContributorsAlvarez, Roberto L (Author) / Milner, Fabio A (Thesis advisor) / Nagy, John D. (Committee member) / Kuang, Yang (Committee member) / Thieme, Horst (Committee member) / Mahalov, Alex (Committee member) / Smith, Hal (Committee member) / Arizona State University (Publisher)
Created2014
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 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
Description
The phycologist, M. R. Droop, studied vitamin B12 limitation in the flagellate Monochrysis lutheri and concluded that its specific growth rate depended on the concentration of the vitamin within the cell; i.e. the cell quota of the vitamin B12. The Droop model provides a mathematical expression to link growth rate to the intracellular concentration of a limiting nutrient. Although the Droop model has been an important modeling tool in ecology, it has only recently been applied to study cancer biology. Cancer cells live in an ecological setting, interacting and competing with normal and other cancerous cells for nutrients and space, and evolving and adapting to their environment. Here, the Droop equation is used to model three cancers.
First, prostate cancer is modeled, where androgen is considered the limiting nutrient since most tumors depend on androgen for proliferation and survival. The model's accuracy for predicting the biomarker for patients on intermittent androgen deprivation therapy is tested by comparing the simulation results to clinical data as well as to an existing simpler model. The results suggest that a simpler model may be more beneficial for a predictive use, although further research is needed in this field prior to implementing mathematical models as a predictive method in a clinical setting.
Next, two chronic myeloid leukemia models are compared that consider Imatinib treatment, a drug that inhibits the constitutively active tyrosine kinase BCR-ABL. Both models describe the competition of leukemic and normal cells, however the first model also describes intracellular dynamics by considering BCR-ABL as the limiting nutrient. Using clinical data, the differences in estimated parameters between the models and the capacity for each model to predict drug resistance are analyzed.
Last, a simple model is presented that considers ovarian tumor growth and tumor induced angiogenesis, subject to on and off anti-angiogenesis treatment. In this environment, the cell quota represents the intracellular concentration of necessary nutrients provided through blood supply. Mathematical analysis of the model is presented and model simulation results are compared to pre-clinical data. This simple model is able to fit both on- and off-treatment data using the same biologically relevant parameters.
First, prostate cancer is modeled, where androgen is considered the limiting nutrient since most tumors depend on androgen for proliferation and survival. The model's accuracy for predicting the biomarker for patients on intermittent androgen deprivation therapy is tested by comparing the simulation results to clinical data as well as to an existing simpler model. The results suggest that a simpler model may be more beneficial for a predictive use, although further research is needed in this field prior to implementing mathematical models as a predictive method in a clinical setting.
Next, two chronic myeloid leukemia models are compared that consider Imatinib treatment, a drug that inhibits the constitutively active tyrosine kinase BCR-ABL. Both models describe the competition of leukemic and normal cells, however the first model also describes intracellular dynamics by considering BCR-ABL as the limiting nutrient. Using clinical data, the differences in estimated parameters between the models and the capacity for each model to predict drug resistance are analyzed.
Last, a simple model is presented that considers ovarian tumor growth and tumor induced angiogenesis, subject to on and off anti-angiogenesis treatment. In this environment, the cell quota represents the intracellular concentration of necessary nutrients provided through blood supply. Mathematical analysis of the model is presented and model simulation results are compared to pre-clinical data. This simple model is able to fit both on- and off-treatment data using the same biologically relevant parameters.
ContributorsEverett, Rebecca Anne (Author) / Kuang, Yang (Thesis advisor) / Nagy, John (Committee member) / Milner, Fabio (Committee member) / Crook, Sharon (Committee member) / Jackiewicz, Zdzislaw (Committee member) / Arizona State University (Publisher)
Created2015
Description
Network traffic analysis by means of Quality of Service (QoS) is a popular research and development area among researchers for a long time. It is becoming even more relevant recently due to ever increasing use of the Internet and other public and private communication networks. Fast and precise QoS analysis is a vital task in mission-critical communication networks (MCCNs), where providing a certain level of QoS is essential for national security, safety or economic vitality. In this thesis, the details of all aspects of a comprehensive computational framework for QoS analysis in MCCNs are provided. There are three main QoS analysis tasks in MCCNs; QoS measurement, QoS visualization and QoS prediction. Definitions of these tasks are provided and for each of those, complete solutions are suggested either by referring to an existing work or providing novel methods.
A scalable and accurate passive one-way QoS measurement algorithm is proposed. It is shown that accurate QoS measurements are possible using network flow data.
Requirements of a good QoS visualization platform are listed. Implementations of the capabilities of a complete visualization platform are presented.
Steps of QoS prediction task in MCCNs are defined. The details of feature selection, class balancing through sampling and assessing classification algorithms for this task are outlined. Moreover, a novel tree based logistic regression method for knowledge discovery is introduced. Developed prediction framework is capable of making very accurate packet level QoS predictions and giving valuable insights to network administrators.
A scalable and accurate passive one-way QoS measurement algorithm is proposed. It is shown that accurate QoS measurements are possible using network flow data.
Requirements of a good QoS visualization platform are listed. Implementations of the capabilities of a complete visualization platform are presented.
Steps of QoS prediction task in MCCNs are defined. The details of feature selection, class balancing through sampling and assessing classification algorithms for this task are outlined. Moreover, a novel tree based logistic regression method for knowledge discovery is introduced. Developed prediction framework is capable of making very accurate packet level QoS predictions and giving valuable insights to network administrators.
ContributorsSenturk, Muhammet Burhan (Author) / Li, Jing (Thesis advisor) / Baydogan, Mustafa G (Committee member) / Wu, Teresa (Committee member) / Arizona State University (Publisher)
Created2014
Description
Data imbalance and data noise often coexist in real world datasets. Data imbalance affects the learning classifier by degrading the recognition power of the classifier on the minority class, while data noise affects the learning classifier by providing inaccurate information and thus misleads the classifier. Because of these differences, data imbalance and data noise have been treated separately in the data mining field. Yet, such approach ignores the mutual effects and as a result may lead to new problems. A desirable solution is to tackle these two issues jointly. Noting the complementary nature of generative and discriminative models, this research proposes a unified model fusion based framework to handle the imbalanced classification with noisy dataset.
The phase I study focuses on the imbalanced classification problem. A generative classifier, Gaussian Mixture Model (GMM) is studied which can learn the distribution of the imbalance data to improve the discrimination power on imbalanced classes. By fusing this knowledge into cost SVM (cSVM), a CSG method is proposed. Experimental results show the effectiveness of CSG in dealing with imbalanced classification problems.
The phase II study expands the research scope to include the noisy dataset into the imbalanced classification problem. A model fusion based framework, K Nearest Gaussian (KNG) is proposed. KNG employs a generative modeling method, GMM, to model the training data as Gaussian mixtures and form adjustable confidence regions which are less sensitive to data imbalance and noise. Motivated by the K-nearest neighbor algorithm, the neighboring Gaussians are used to classify the testing instances. Experimental results show KNG method greatly outperforms traditional classification methods in dealing with imbalanced classification problems with noisy dataset.
The phase III study addresses the issues of feature selection and parameter tuning of KNG algorithm. To further improve the performance of KNG algorithm, a Particle Swarm Optimization based method (PSO-KNG) is proposed. PSO-KNG formulates model parameters and data features into the same particle vector and thus can search the best feature and parameter combination jointly. The experimental results show that PSO can greatly improve the performance of KNG with better accuracy and much lower computational cost.
The phase I study focuses on the imbalanced classification problem. A generative classifier, Gaussian Mixture Model (GMM) is studied which can learn the distribution of the imbalance data to improve the discrimination power on imbalanced classes. By fusing this knowledge into cost SVM (cSVM), a CSG method is proposed. Experimental results show the effectiveness of CSG in dealing with imbalanced classification problems.
The phase II study expands the research scope to include the noisy dataset into the imbalanced classification problem. A model fusion based framework, K Nearest Gaussian (KNG) is proposed. KNG employs a generative modeling method, GMM, to model the training data as Gaussian mixtures and form adjustable confidence regions which are less sensitive to data imbalance and noise. Motivated by the K-nearest neighbor algorithm, the neighboring Gaussians are used to classify the testing instances. Experimental results show KNG method greatly outperforms traditional classification methods in dealing with imbalanced classification problems with noisy dataset.
The phase III study addresses the issues of feature selection and parameter tuning of KNG algorithm. To further improve the performance of KNG algorithm, a Particle Swarm Optimization based method (PSO-KNG) is proposed. PSO-KNG formulates model parameters and data features into the same particle vector and thus can search the best feature and parameter combination jointly. The experimental results show that PSO can greatly improve the performance of KNG with better accuracy and much lower computational cost.
ContributorsHe, Miao (Author) / Wu, Teresa (Thesis advisor) / Li, Jing (Committee member) / Silva, Alvin (Committee member) / Borror, Connie (Committee member) / Arizona State University (Publisher)
Created2014
Description
Sparse learning is a powerful tool to generate models of high-dimensional data with high interpretability, and it has many important applications in areas such as bioinformatics, medical image processing, and computer vision. Recently, the a priori structural information has been shown to be powerful for improving the performance of sparse learning models. A graph is a fundamental way to represent structural information of features. This dissertation focuses on graph-based sparse learning. The first part of this dissertation aims to integrate a graph into sparse learning to improve the performance. Specifically, the problem of feature grouping and selection over a given undirected graph is considered. Three models are proposed along with efficient solvers to achieve simultaneous feature grouping and selection, enhancing estimation accuracy. One major challenge is that it is still computationally challenging to solve large scale graph-based sparse learning problems. An efficient, scalable, and parallel algorithm for one widely used graph-based sparse learning approach, called anisotropic total variation regularization is therefore proposed, by explicitly exploring the structure of a graph. The second part of this dissertation focuses on uncovering the graph structure from the data. Two issues in graphical modeling are considered. One is the joint estimation of multiple graphical models using a fused lasso penalty and the other is the estimation of hierarchical graphical models. The key technical contribution is to establish the necessary and sufficient condition for the graphs to be decomposable. Based on this key property, a simple screening rule is presented, which reduces the size of the optimization problem, dramatically reducing the computational cost.
ContributorsYang, Sen (Author) / Ye, Jieping (Thesis advisor) / Wonka, Peter (Thesis advisor) / Wang, Yalin (Committee member) / Li, Jing (Committee member) / Arizona State University (Publisher)
Created2014
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 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.
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