Theses, Dissertations, and other Required Graduate Degree Essays

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This collection contains digitized SFU theses except for those theses submitted within the last 12 months. If you cannot find the thesis you are looking for please search Recently Submitted Theses as it may be a recently submitted thesis and thus not yet available in Summit.

The minor pilin TcpB is located at the tip of the toxin co-regulated pilus of Vibrio cholerae and is the receptor for the filamentous phage CTXφ

Date created: 
2017-07-19
Abstract: 

Type IV pili are polymers of the major pilin subunit found on the surfaces of many Gram negative bacteria. They act like grappling hooks, undergoing cycles of polymerization, adhesion, and retraction, to mediate a diverse array of functions, including twitching motility, DNA uptake and adhesion. T4P possess several minor pilins, which are homologous to the major pilin but are produced in much lower quantities. Minor pilins prime Type IV pili assembly and have been proposed to localize to the tip of the pilus, but this has not been shown definitively. The Vibrio cholerae toxin co-regulated pilus (TCP) is a T4P that mediates microcolony formation, which is critical for the development of the gastrointestinal disease cholera. TCP is the primary receptor for the filamentous cholera toxin phage CTXφ, which binds to the pilus via its tip-associated protein, pIII. TCP possess a single minor pilin, TcpB, which initiates pilus assembly as well as retraction. We hypothesized that TcpB is located at the tip of the pilus and forms the binding site for CTXφ pIII. Here I use direct and competition ELISA to show that recombinantly expressed soluble TcpB and pIII interact. I show that CTXφ phage infection of V. cholerae is reduced 90 % in the presence of soluble TcpB or anti-TcpB antibody. Furthermore, gold-labeled anti-TcpB antibody binds to the tip of purified TCP, providing the first direct localization of a minor pilin to the tip of a T4P. Finally, I show that phage uptake is reduced 98 % in a retraction-deficient V. cholerae strain, demonstrating the role of pilus retraction in this process. My results define a two-step mechanism for CTXφ infection of V. cholerae, which involves (i) binding of CTX via its tip-associated pIII protein to its receptor, TcpB, at the tip of the pilus, and (ii) retraction of the pilus, which pulls CTXφ into the bacterial periplasm as if it were an extension of the pilus.

Document type: 
Thesis
File(s): 
Senior supervisor: 
Lisa Craig
Department: 
Science: Department of Molecular Biology and Biochemistry
Thesis type: 
(Thesis) M.Sc.

Event-based control as a cloud service

Date created: 
2017-04-19
Abstract: 

Event-based control has gained significant interest from the research community in recent years because it allows better resource utilization in networked control systems. In this thesis, we propose an architecture for offering event-based control as a service from the cloud, which not only improves resource utilization but also reduces the cost and setup time of large-scale industrial automation systems. Providing event-based control from the cloud, however, poses multiple research challenges. We address two of the main challenges, which are mitigating long and variable network delays and handling controller failures introduced because of moving the controller far away from the plant. We propose novel methods to solve the delay and failure problems and we show that these methods maintain the stability and performance of the control system. We implemented the proposed methods and deployed them on the Amazon cloud. Our results show that our delay mitigation technique can handle large communication delays up to several seconds with practically zero effect on the main performance metrics of the system. Moreover, the proposed fault tolerance approach can transparently handle controller failures even if the controlled system is thousands of miles away from its cloud controllers.

Document type: 
Thesis
File(s): 
Senior supervisor: 
Mohamed Hefeeda
Department: 
Applied Sciences: School of Computing Science
Thesis type: 
(Thesis) M.Sc.

Essays on the economics of linguistic diversity and preference for surprise

Author: 
Date created: 
2017-07-19
Abstract: 

This thesis is composed of three essays, the first two of which are on the economics of linguistic diversity and the last on the evolutionary foundation of the preference for surprise. Chapter 1 is joint work with Leanna Mitchell. We propose a theory that relates linguistic diversity (i.e. the number of languages within a region) to cooperative and competitive incentives in a game theoretic framework. In our model, autonomous groups interact periodically in games that represent either cooperation, competition, or no interaction. Language matters in these interactions because language common to a pair of groups facilitates cooperation; whereas language unique to one group affords that group an advantage in competitions against other groups. The relative frequency of cooperation and conflict in a region provide incentives for each group to modify their own language, and therefore leads to changes in linguistic diversity over time. Hence, a main contribution of our paper is to model strategic incentives as a cause of linguistic divergence. Our model predicts that higher frequency of cooperative interactions relative to competitive ones reduces a region’s linguistic diversity. Chapter 2 reports a laboratory experiment designed to test the theory proposed in the previous chapter. In the experiment, pairs of subjects endowed with a set of words interact repeatedly in a series of underlying games, in which they use the words to signal their intended action. The underlying games are either coordination or zero-sum. As the subjects are allowed to modify their vocabularies by learning words from their counterpart and creating new words, I observe that, over time, the pairs of vocabularies in coordination games tend to converge, while in zero-sum games, the vocabularies experience constant pressure to diverge. This finding is consistent with the theoretical predictions in Chapter 1. Chapter 3 uses a principal-agent model to provide an evolutionary explanation of the preference for surprise, where surprise is measured by the Kullback-Leibler divergence between a decision-maker’s prior and posterior. The principal in the model is interpreted as the blind force of evolution, who tries to maximize the fitness of the agent—generations of human beings—whose objective in turn is to maximize a utility function designed by the principal. In a typical period, the agent first decides how many signals about the state to purchase, and then he chooses an action that, together with the state, determines his fitness. The variance of the signal distribution changes across time, but the agent is predisposed to believe that it is the same as the one in the previous period. I show that if the variance of the signal distribution decreases at a sufficiently fast rate over time, it is evolutionarily optimal for the utility function to include a component that rewards surprises.

Document type: 
Thesis
File(s): 
Senior supervisor: 
Arthur Robson
Department: 
Arts & Social Sciences: Department of Economics
Thesis type: 
(Thesis) Ph.D.

Student actions as a window into goals and motives in the secondary mathematics classroom

Date created: 
2017-06-30
Abstract: 

Students come to the secondary mathematics classroom with a variety of motives. These motives shape the goals a student holds, and the actions that a student performs within the classroom. Ultimately, the approach that a student takes towards learning is a direct consequence of his or her motives. Given the significance of student motive for learning, it is important to understand better the relationship between actions, goals, and motives. The research presented in this thesis aims to do just that. More specifically, it looks closely at student actions in high school mathematics classrooms with the aim of identifying student goals and motives, and further, analysing the relationships between students’ actions and their motives. Using an ethnographic perspective and methods, student actions in three different secondary mathematics classrooms were observed and in situ informal interviews were conducted. Data were first organised and analysed according to actions performed in each activity setting. Then, using classical activity theory, 10 students’ actions and goals in multiple activity settings were analysed to ascertain his or her motives in mathematics class. Finally, the motives and actions of all participants were re-examined from two different perspectives: first, looking at the performed actions of all students holding a given motive in each activity setting; and second, examining the relationships between similar student actions and different motives in one activity setting. This ‘crossover’ approach revealed that similar student actions can be driven by different motives, and that the same motive does not always manifest in similar student action.

Document type: 
Thesis
File(s): 
Senior supervisor: 
Peter Liljedahl
Department: 
Education: Faculty of Education
Thesis type: 
(Thesis) Ph.D.

Archaeology of the Afro-Ecuadorians in La Concepción, Ancestral Territory of the Chota-Mira Valley (Carchi-Ecuador)

Date created: 
2017-06-15
Abstract: 

Historical Archaeology of the African Diaspora in the Americas urges for interdisciplinary, collaborative, and intercultural approaches to shed light on how the material culture reflects conditions of enslavement and racialization, but also process of resistance and historical reparation. This investigation is organized in five articles connected around the topic of the cultural construction of the African Diaspora identities in the Afro-Ecuadorian Ancestral Territory of the Chota-Mira Valley from the perspective of historical, collaborative, de-colonizing archaeology and anthropology. One article involves archaeological and historical analysis of ceramics associated with household contexts of enslaved people in the 18th century Jesuit Andean Hacienda of La Concepcion to reconstruct creativity in production/consumptions of ceramics. Two articles articulate the historical narratives and politics of memory of the Afro-Ecuadorians, mainly from Afro-Ecuadorian Women. The last article focuses on a collaborative approach to reconstruct an 18th century cemetery. Furthermore, this study involves a collaborative project with the African descendant community of La Concepción and CONAMUNE-Carchi (Coordinadora Nacional de Mujeres Negras / National Coordinating Committee of Black Women)

Document type: 
Thesis
File(s): 
Senior supervisor: 
Ross Jamieson
Department: 
Environment: Department of Archaeology
Thesis type: 
(Thesis) Ph.D.

Differences in Prescription Drug use Among 5-year Survivors of Childhood, Adolescent, and Young Adult Cancer and the General Population in British Columbia, Canada

Author: 
Date created: 
2017-07-13
Abstract: 

In this project, we analyze the prescription drug use of childhood, adolescent, and young adult cancer survivors identified by the CAYACS program in BC. Understanding the patterns of prescription use and factors associated with the tendency to be on prescriptions is important to policy and health care planners. Since data on actual prescription usage are not available, we use prescription dispensing data as a proxy. We examine the differences in prescription use between survivors and matched controls selected from the general population, and assess the impact of age and other clinical and sociodemographic factors on prescription use. Specifically, we model subjects' on-/off-prescription status by a first-order Markov transition model, and handle the between-subject heterogeneity using a random effect. Our method captures the differences in prescription drug use between survivors and the general population, as well as differences within the survivor population. Our results show that survivors tend to exhibit a higher probability of going on prescriptions compared to the general population over the course of their lifetime. Further, females appear to have a higher probability of going on prescriptions than males over the course of their lifetime. A simulation study is conducted to assess the performance of the estimators of the model.

Document type: 
Graduating extended essay / Research project
File(s): 
Senior supervisor: 
Rachel Altman
Department: 
Science: Department of Statistics and Actuarial Science
Thesis type: 
(Project) M.Sc.

Direct and indirect interactions between owls, mice and nocturnal seabirds: integrating marine and terrestrial food webs

Author: 
Date created: 
2017-07-31
Abstract: 

Climate variability in semi-arid ecosystems can influence species interactions from the bottom-up, and through these perturbations we can gain insight into both direct and indirect interactions in food webs. In this thesis, I studied the effects of ENSO-driven rainfall pulses and drought on the interactions between a top predator, the Barn Owl (Tyto alba), a mesopredator, an island endemic deer mouse (Peromyscus maniculatus elusus), and a threatened nocturnal seabird, the Scripps’s Murrelet (Synthliboramphus scrippsi). On Santa Barbara Island in the Channel Islands National Park in California, adult breeding murrelets are killed by owls, but their eggs are eaten by mice, which is the main cause of reduced murrelet nest success. First, I assessed how owl predation on murrelets varies with the availability of mice, the primary prey of owls. I found that heavy rainfall years drive the irruptions in the mouse population that precede peaks in owl abundance, which results in high murrelet predation by owls when the mouse population subsequently crashes. Next, I examined evidence for positive indirect effects of owls on murrelets through their influence on mouse foraging behavior. I found that mouse foraging was strongly suppressed as the abundance of owls increased, and survival of murrelet eggs was also positively related to owl abundance. I also examined how both the terrestrial and marine environments influenced overall murrelet nest success over a span of 21 years. I found that the severity of drought was the most important variable determining nest success, which suggests that during severe droughts, mice consume substantially more eggs when there are fewer terrestrial resources and also less risk from predation. Climate-driven indirect interactions with predators therefore influences both survival and nest success of murrelets on this island. Finally, I developed a mathematical model of island community dynamics to assess whether owl management might benefit murrelets given projected changes to rainfall patterns in this region. I found no evidence that managing the owl population would enhance murrelet abundance, demonstrating the importance of considering both direct and indirect effects of predators when evaluating potential conservation strategies.

Document type: 
Thesis
File(s): 
Senior supervisor: 
David Green
Department: 
Science: Biological Sciences Department
Thesis type: 
(Thesis) Ph.D.

Plate Heat Exchangers Using Natural Graphite Sheets

Author: 
Date created: 
2017-07-31
Abstract: 

Graphite heat exchangers (G-HEX) are good alternatives to metallic heat exchangers due to their excellent thermal properties, low cost, light weight, and high resistivity to corrosion. In this study, the potential of fabrication of natural flake graphite-based plate heat exchanger is being investigated. A new layered G-HEX and a graphite plate heat exchanger are fabricated and their thermal and hydraulic performance are compared with an off-the-shelf chevron-type plate heat exchanger using a custom-made experimental setup. An optimization study is then conducted to further improve the graphite plate heat exchanger performance. To understand the potential of utilization of G-HEX in corrosive environments, a corrosion test is then performed on natural flake graphite sheets.

Document type: 
Thesis
File(s): 
Senior supervisor: 
Majid Bahrami
Department: 
Applied Sciences: School of Mechatronic Systems Engineering
Thesis type: 
(Thesis) M.A.Sc.

La comparaison de la lecture humaine avec la lecture machine dans le Système de la Nature de d’Holbach

Author: 
Date created: 
2017-07-07
Abstract: 

In this empirical study, I explored thematic patterns in d’Holbach’s Système de la Nature. The overall purpose of my thesis was to compare the thematic structure of the corpus, in terms of co-occurrence and collocations of the 8 main themes, in human-reading and machine-reading. To achieve this, I used two methods: First, I used a qualitative data analysis software (NVivo 10) to do the comparative analysis of the main themes in consideration of examining the density of the appearance of each theme together. Next, I used RStudio Mallet software package for topic modeling to compare the co-occurrence of these main themes and to discover topics from the corpus. My results revealed that human-reading and machine-reading share only 12.5% of similarity in terms of semantically correlated themes. Additionally, topic models identified some marginalized themes associating with the philosophy of materialism, such as Cerveau, Nation and Vertu.

Document type: 
Thesis
File(s): 
Senior supervisor: 
Jorge Calderon
Department: 
Arts & Social Sciences: Department of French
Thesis type: 
(Thesis) M.A.

Using an activator of hERG (RPR-260245) in a model of acquired and inherited Long QT syndrome type 2

Author: 
Date created: 
2017-07-17
Abstract: 

The human ether-a-go-go related gene (hERG) channel is the molecular correlate of the rapid delayed rectifier current (IKr); its dysfunction causes Long QT syndrome type II (LQT II). RPR-260245 (RPR) is an activator of hERG that increases hERG current by slowing deactivation. Thus, it represents a potential treatment strategy for LQT. However, only few studies have addressed its impact on cardiac physiology. We used electrophysiology techniques in Xenopus Laevis oocytes and optical mapping in induced pluripotent stem cells derived cardiomyocytes (hiPSC-CMs) to test the effects of RPR on hERG and on the cardiac action potential. We show that RPR has little effect on the cardiac AP in WT iPSC-CMs but demonstrate a partial rescue in our model of acquired LQT (aLQT) under dofetilide block and a partial rescue in our model of LQT II. Finally, RPR significantly increases protective hERG current, especially in instances of the R56Q mutation.

Document type: 
Thesis
File(s): 
Senior supervisor: 
Glen Tibbits
Thomas Claydon
Department: 
Science: Department of Biomedical Physiology and Kinesiology
Thesis type: 
(Thesis) M.Sc.