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.

Candidate protein interactors of sexually dimorphic on the Y chromosome (SdY) in Atlantic salmon

Author: 
Date created: 
2017-01-20
Abstract: 

Atlantic salmon depend on genetic cues to determine whether an individual is male or female. A novel sex-determining gene, sexually dimorphic on the Y chromosome (sdY), is found exclusively in all salmonids. Unlike other sex-determining genes, sdY lacks a DNA-binding domain. Instead, it is a divergent, truncated form of interferon regulatory factor 9. As a recently discovered gene, little is known about sdY; how it is involved in sex-determination and what proteins interact with it. Identification of protein interactors was done through a variety of techniques including yeast two-hybridization, co-immunoprecipitation and histidine-tagged pull down assays. These assays identified several proteins: SdY itself, 40S ribosomal protein S16 and SA, isocitrate dehydrogenase, heat shock protein HSP 90-beta, and ras GTPase-activating-like protein IQGAP1, as well as creatine kinase, GDP-mannose-4,6-dehydratase, sodium/potassium-transporting ATPase subunit alpha-1, AP-1 complex subunit beta-1, and hydroxysteroid dehydrogenase (17-beta) 4. The yeast two-hybrid assay also identified 3’ UTR of annexin A7-like and transmembrane protein 91-like, most likely false positives. This broad range of candidates has led me to believe that SdY is involved either in the biosynthesis of testosterone or in the testosterone signalling pathway.

Document type: 
Thesis
Senior supervisor: 
William Davidson
Department: 
Science: Department of Molecular Biology and Biochemistry
Thesis type: 
(Thesis) M.Sc.

Development of a Point-Of-Care Lensless Birefringent Molecule Detection System

Date created: 
2017-03-10
Abstract: 

This thesis is a proof-of-concept exploration of an optical birefringent Point-Of-Care (POC) detection device. Birefringent detection can be useful for monitoring glucose and cholesterol, as well as diagnoses of diseases such as malaria, Ebola, bacterial infection and AIDS. Many diseases cause optical birefringent materials to precipitate in blood. These precipitates can be used as a biomarker to diagnose the disease. In this thesis, we will focus on the development of a device for detection of a birefringent phantom, called Tetrabutylammonium (TA), suspend in deionized water. We will show a method for, a low cost, Point-Of-Care, and easy to use birefringent detection platform. This thesis builds on the concepts of flow cytometry for detection of depolarized light and uses these concepts for the development of a miniaturized optical birefringent detection setup, utilizing a lensless design, for a sample flowing through a microchannel. A microfluidic channel with a serpentine shape was developed in order to increase the volume of sample present within the detection area, while also decreasing the total volume used per measurement by reducing the cross sectional area of the channel. To demonstrate the concept of birefringent detection, a bulk optic setup was developed which used two detection channels. The two detection channels were a 2 dimensional (2D) Charged Coupled Device (CCD) and a 1 dimensional (1D) Avalanche Photodiode (APD). Using the bulk optic setup, we compared 2D imaging with 1D sensing and compared the ability of the two detectors to identify detection events. We identify detection events at a concentration of 1 µg/mL of TA using both 1D sensing and 2D imaging in the bulk optic setup, before using a 1D APD detector for the miniaturized optical setup. In the miniaturized optical setup, we detected events at the same concentration limit.

Document type: 
Thesis
File(s): 
Senior supervisor: 
Marinko V Sarunic
Ash Parameswaran
Department: 
Applied Sciences: School of Engineering Science
Thesis type: 
(Thesis) M.A.Sc.

Implementation of machine learning on an innovative processor for IoT

Date created: 
2016-12-19
Abstract: 

The “Internet of Things” (IoT) is a very rapidly increasing market segment for electronics, and it holds the promise to be one of the most significant drivers for innovation in the semiconductor industry in the near future. “IoT” is providing new and different specifications to the design of embedded systems, and such specifications are likely to change the constraints that drive embedded systems design. In particular, “IoT” is introducing a wave of innovation on the design of embedded microprocessors that are the heart and soul of such systems. This report took place in the context of larger investigation on innovative embedded processor architectures for “IoT”. The work started from an existing processor design, developed in Simon Fraser University in form of a Hardware Description Language (HDL) open source library. Such processor design advantages on the RISC-V instruction set distributed since 2011 by the University of California at Berkley. This work focused on analyzing a reference algorithmic application of relevance for the “IoT” (Linear Discriminant Analysis, a well-known Machine Learning tool for data classification), that is currently being utilized in two different research projects in Simon Fraser University. This report contributed to the larger project by: 1) Porting a C version of the LDA algorithm developed for ARM cores on the newly proposed processor architecture. 2) Evaluating the performance of the LDA algorithm on the proposed architecture in terms of available data sample rates and required energy consumption. 3) Profiling the LDA algorithm on the proposed processor in order to determine the critical operation kernels that mostly affect the performance. 4) Defining the hardware configuration for the proposed processor that leads to the most efficient implementation of LDA.

Document type: 
Graduating extended essay / Research project
File(s): 
Senior supervisor: 
Lakshman One
Department: 
Applied Sciences: School of Engineering Science
Thesis type: 
(Project) M.Eng.

Joining Learning and Making: A Practitioner’s Retrospective Auto/biographical Account of How Inquiry Can Contribute to Social Justice Efforts in a Community

Author: 
Date created: 
2017-01-25
Abstract: 

An opportunity arose in the author’s work as an animator in a community group to design a socially innovative project to address homelessness in her city. Her retrospective auto/biographical account of the design and implementation process demonstrates how qualitative inquiry can contribute to the efforts of community-based practitioners committed to advancing social justice in their communities. Two inquiry frameworks were used. The first, mindful inquiry, is guided by phenomenology, hermeneutics, critical social theory, and the Eastern knowledge tradition of Buddhism. The second, ALMOLIN (alternative models of local social innovation), explores the dynamics of social exclusion and social innovation. Its ethical social-justice position provides alternative criteria to determine whether a social innovation responds to human deprivation; empowers disenfranchised citizens by building capabilities; and changes social and power relations, transforming exclusionary mechanisms into inclusionary strategies. Drawing on these intersecting frameworks, and thinking through and with relationships and lived experiences in her practice setting, a bold vision emerged of what the author here calls the Whole Community Project. Practical actions of coordination and collaboration with multiple stakeholders brought into being places and spaces in the community that provided material pathways to formal education, employment, affordable housing, and home ownership for citizens who had been left behind due to homelessness, addiction, mental health issues, and unemployment. In joining inquiry with making, this unique project design demonstrated that such citizens can recover, achieve employment that provides a sustainable livelihood, and own their own homes in less than two years. The project met the goals of improving the lives of citizens in the author’s practice. The inquiry also informed the design of inclusive interactive civic spaces to promote broader inclusive participatory inquiry: what had been perceived as individual troubles (e.g., homelessness, addiction) could now be transformed into community issues for public deliberation towards more socially just public policy.

Document type: 
Thesis
File(s): 
Senior supervisor: 
Suzanne Smythe
Department: 
Education: Faculty of Education
Thesis type: 
(Thesis) Ed.D.

Applications of Individual Evolutionary Learning

Date created: 
2017-01-30
Abstract: 

This research investigates three applications of the Individual Evolutionary Learning (IEL) model. Chapter 2 utilizes a horse-race approach to investigate the overall performance of 4 learning algorithms in games with congestion. The games utilized are Market Entry games and Choice of Route games. I show that a version of the IEL has the best fit of the experimental data relative when the experimental subjects have full information. Chapter 3 (joint work the Jasmina Arifovic and John Duffy) applies the IEL to games with correlated equilibrium suggested by an external third party. The IEL nearly perfectly matches the behavior of experimental subjects playing the Battle of the Sexes game, but requires an adjustment to the initial conditions to match the behavior of experimental subjects in the Chicken game. Chapter 4 extends the Individual Evolutionary Learning with Other-Regarding Preferences (IELORP*) model to force the algorithm to match the discrete nature of the experimental choices and introduce beliefs via adaptive expectations. The algorithm continues to match the stylized facts associated with the standard LPGG, but does not appear to extend to games where beliefs are elicited using monetary incentives.

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

Competition and efficiency: application to tax haven, profit shifting and platform competition

Date created: 
2017-01-18
Abstract: 

The first chapter considers the tax information exchange agreement as a way to draw Pareto improvement between off-shore tax havens and non-haven countries. Individuals who reside in a non-haven country choose the volume of tax evasion to maximize the expected payoff which depends on the tax rate and the probability of being detected. A tax haven might be reluctant to sign a TIEA since establishing a TIEA increases the probability of detection thus decreasing the volume of individuals' tax evasion ceteris paribus. However, we find that establishing a TIEA makes the non-haven country increase the tax rate so that both tax evasion and welfare increase. This is because non-haven country government catches tax criminals with greater probability so it can handle greater volume of tax evasion under higher tax rate. Because not only the non-haven country's welfare but also the capital inflow into the tax haven are increased, tax havens would sign TIEAs with non-haven countries voluntarily in anticipation of greater future payoff. The second chapter, I, jointly with Dr. Mongrain and Dr. Ypersele, develop a continuous fiscal competition model in which two countries compete over multinational firms (MNF) by varying the tax rates and the tightness of profit shifting control. Being loose on profit shifting decreases the tax base of one country but at the same time it brings two benefits. First, the country attracts more MNFs for given tax rate. Second, loose control of one country allows the other country to set high tax rate by alleviating the pressure of tax competition. Since the tax rates of the two countries are strategic complements, both countries can achieve efficiency gain by not actively controlling international profit shifting. We also show that relaxing the profit shifting regulations can reduce the equilibrium tax gap between high tax region and low tax region. This is because the high tax region's tax choice is generally more sensitive to the profit shifting control. As all the downward forces on the tax rate choices, which are resulted by the location effect and per-firm profit shifting effect, are positively related to the equilibrium tax gap, choosing the lax profit shifting control may close the tax gap and lead to the higher tax revenue even for the high tax region. The third paper studies the competition in the platform markets where companies improve the quality standard to attract the consumers. In some platform markets, e.g. video game industry, improving the quality standard decreases the number of software developed due to the greater pressure of development cost. Such disadvantage of the quality upgrade in one platform is spread to its competitors because all the platforms share a certain portion of video game software through `porting.' Because of the negative externality created by porting, the platforms tend to increase the quality standard by extra amount. Our model shows that the quality competition in the competitive market is excessive because the platforms fail to internalize the inter-platform externality.

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

Optical characterization of doped zinc oxide nanowires

Date created: 
2017-01-24
Abstract: 

ZnO is a promising semiconductor material with a direct band gap energy of 3.3 eV which makes it a good candidate for UV and visible range light emitting devices. Metalorganic chemical vapour epitaxy (MOVPE) provides the possibility of industrial scale growth of ZnO, with very fine control of impurity dopants. Despite the vast recent literature on ZnO, there are very few studies of systematic intentional doping. ZnO nanowires (NWs) can be grown easily on various substrates with high crystalline quality and low defect densities and tend to exhibit reduced substrate induced strain. This enables us to perform careful spectroscopic analysis of impurity related optical transitions and identify the physical nature of various dopant species. A detailed study of low temperature photoluminescence (PL) transitions in doped ZnO NWs, thin films, and bulk crystals grown by MOVPE and chemical vapour transport (CVT) methods is presented. The standard group III donors were first investigated. Donor bound exciton (D0X) transitions previously assigned to Ga, Al, and In were confirmed in intentionally doped samples. Group IV dopants such as carbon, and tin are interesting since they can act in principle as double donors or double acceptors. We report four new shallow D0X transitions (Z-lines), at 3360.8 (Z1), 3361.2 (Z2), 3361.7 (Z3) and 3361.9 (Z4) meV, which can be greatly enhanced by co-doping with carbon tetrachloride and hydrogen. These shallow donors appear to be due to carbon impurities complexed with other unknown defects in four distinct configurations. Carbon-doped samples also exhibit two distinct acceptors with binding energies of 133 ± 5 and 181 ± 5 meV. Doping concentration and temperature dependent PL studies of unintentionally doped and Sn-doped ZnO single crystals confirmed emission from the I10 D0X transition which was recently proven to contain Sn on a Zn site. Sb-doped ZnO NWs were grown in an attempt to produce p-type material as reported by some groups. Our PL studies including Magneto PL, have shown that rather than p-doped material, the addition of small amounts of Sb-dopant resulted in a new PL transition at 3364.3 meV, which turns out to be the shallowest D0X transition so far observed in ZnO.

Document type: 
Thesis
File(s): 
Senior supervisor: 
Simon Watkins
Department: 
Science: Department of Physics
Thesis type: 
(Thesis) Ph.D.

Undergraduate students' understanding of transformations of sinusoidal functionss

Date created: 
2017-01-23
Abstract: 

Trigonometry is one of the fundamental topics taught in high school and university curricula. However, it is considered as one of the most challenging subjects for teaching and learning. Contributing to research on learning trigonometry, this dissertation sheds light on aspects of undergraduate students’ understanding of transformations of sinusoidal functions. Six undergraduate students participated in the study. Two types of tasks – (A) Identifying sinusoidal functions and (B) Assigning coordinates – were presented to participants in a clinical interview.To analyze the collected data, three theoretical frameworks, Mason’s theory of shifts of attention, Presmeg’s visual imagery and Carlson, Jacobs, Coe, Larsen, and Hsu covariational reasoning were used in this dissertation. Mason’s theory provided opportunity to study the critical role of attention and awareness in learning and understanding mathematics, and in particular the concept of transformation of sinusoidal functions. Presmeg’s classification of visual imagery was applied for investigating students’ visual mental constructs since the participants applied their imagery on different occasions when they completed the interview tasks. Lastly, participants’ solution approaches were evaluated using covariational reasoning, focusing on Carlson’s et al. description of mental actions associated with developmental levels. The results of this research show that undergraduate students participating in this study experienced difficulty in identifying a phase shift/ horizontal transformation of the sinusoidal functions. They, in fact, determined “BC” as phase shift instead of “C” when they relied on the representation of sinusoids as f(x)= A sin/cos((B(x+C))+D. Some participants were also unable to complete tasks in which coefficient of x was a fraction. I conclude this dissertation with some pedagogical suggestions in terms of learning and teaching transformations of sinusoidal functions.

Document type: 
Thesis
File(s): 
Senior supervisor: 
Rina Zazkis
none
Department: 
Education: Faculty of Education
Thesis type: 
(Thesis) Ph.D.

Mountain militarism and urban modernity: Balkanism, identity and the discourse of urban-rural cleavages during the Bosnian War

Author: 
Date created: 
2017-01-11
Abstract: 

Recent years have witnessed a growth in research addressing the ways in which policymakers, academics and the media characterized the Bosnian war of the 1990s using a variety of problematic discursive frames. However, there has been relatively little scholarship exploring how the conflict was often portrayed as a battle between innocent urban centres and an antagonistic countryside. This thesis uses a discourse analysis of Western and Bosnian textual material to argue that perceptions of the Bosnian war have been characterized by a discourse that attributes the violence to cleavages between urban Bosnians and their rural counterparts. Moreover, this thesis engages with post-colonial theory to demonstrate that this discourse of urban-rural cleavages, in which Western and Bosnian urban self-identity was constructed in opposition to the supposed atavism of the Bosnian countryside, is an advancement of Bakic-Hayden’s concept of “nesting Orientalisms.” The results of this thesis problematize a common representation of the conflict, expand the concept of nesting Orientalism and help us to understand why urban participation in the ideologies and violence of the Bosnian conflict has often gone unexamined.

Document type: 
Thesis
File(s): 
Senior supervisor: 
Jeffrey Checkel
Department: 
Arts and Social Sciences: School for International Studies
Thesis type: 
(Thesis) M.A.

Generalized methods for application specific hardware specialization

Author: 
Date created: 
2016-11-21
Abstract: 

Since the invention of the microprocessor in 1971, the computational capacity of the microprocessor has scaled over 1000x with Moore and Dennard scaling. Dennard scaling ended with a rapid increase in leakage power 30 years after it was proposed. This ushered in the era of multiprocessing where additional transistors afforded by Moore's scaling were put to use. The breakdown of Moore's law indicates the start of a new era for computer architects. With the scaling of computational capacity no longer guaranteed every generation, application specific hardware specialization is an attractive alternative to sustain scaling trends. Hardware specialization broadly refers to the identification and optimization of recurrent patterns, dynamic and static, in software via integrated circuitry. This dissertation describes a two-pronged approach to architectural specialization.First, a top down approach uses program analysis to determine code regions amenable for specialization. We have implemented a prototype compiler tool-chain to automatically identify, analyze, extract and grow code segments which are amenable to specialization in a methodical manner. Second, a bottom up approach evaluated particular hardware enhancements to enable the efficient data movement of specialized regions. We have devised and evaluated coherence protocols and flexible caching mechanisms to reduce the overhead of data movement within specialized regions. The former workload centric approach analyses programs at the path granularity. We enumerate static and dynamic program characteristics accurately with low overhead. Our observations show that analysis of amenability for specialization along the path granularity yield different conclusions than prior work. We show that analyses at coarser granularities tend to smear program characteristics critical to specialization. We analyse the potential for performance and energy improvement via specialization at the path granularity. We develop mechanisms to extract and merge amenable paths into segments called Braids. Braids are constructed from the observation that oft-executed program paths have the same start and end point. This allows for increased offload opportunity while retaining the same interface as path granularity specialization. To address the challenges of data movement, the latter micro-architecture first approach, proposes a specialized coherence protocol tailored for accelerators and an adaptive granularity caching mechanism. The hybrid coherence protocol localizes data movement to a specialized accelerator-only tile reducing energy consumption and improving performance. Modern workloads have varied program characteristics where fixed granularity caching often introduces waste in the cache hierarchy. Frequently cache blocks are evicted before all words in the fetched line are touched by the processor. We propose a variable granularity caching mechanism which reduces energy consumption while improving performance via better utilization of the available storage space.

Document type: 
Thesis
File(s): 
Senior supervisor: 
Arrvindh Shriraman
Department: 
Applied Sciences: School of Computing Science
Thesis type: 
(Thesis) Ph.D.