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.

Survivorship and life history strategies in relation to migration distance in western and semipalmated sandpipers in Perú

Date created: 
2020-03-31
Abstract: 

This thesis explored the relationships between life history, migration distance, survivorship components of fitness, and molt strategies of Western and Semipalmated Sandpipers in one of the most austral non-breeding sites for both species, at Paracas, Perú. I asked how migration distance relates to pre-migratory preparation, survivorship and migratory decisions for different age classes and ecological circumstances between species and within populations. I focused particularly on how timing of first breeding relates to survivorship and thus future overall fitness. I found that adults from both species prepare for northward migration, but no juvenile Western Sandpipers did so, confirming a non-migratory over-summering ‘slow’ life history strategy for more southerly non-breeding populations. Juvenile Semipalmated Sandpipers showed bimodality in migration strategy. Most showed no migratory preparation, but ~30% fattened, molted into breeding plumage, and performed partial post-juvenal wing molt (PPW) during the pre-migratory period. The frequency of PPW is positively related to culmen length (as a proxy for eastern breeding birds with a shorter migration distance). To decompose survivorship between migrant and oversummering (resident) Semipalmated Sandpipers, I used a multi-state model with 5 years of data and found survivorship 8 percentage point higher for oversummering juveniles and 21 percentage points higher for oversummering adults compared to same aged migrant birds, as expected as compensation for the loss of a breeding opportunity. I estimated annual survivorship with an open robust multi state model using 7 years of mark-resighting data from several thousand shorebirds marked at Paracas. As predicted by some migration theories, both species had higher annual survival estimates than those obtained previously at non-breeding sites further north. Western Sandpiper juveniles also had substantially higher annual survival estimates than adults, in line with the predicted survivorship benefits needed to offset their delayed reproduction. I found that the size of the survival advantage in juvenile Semipalmated Sandpipers is migration distance dependent. Western, but not Semipalmated Sandpipers showed a negative relationship in survival with the ENSO warm phase, probably due to the former’s closer association with the Pacific migratory flyway. Finally, I corroborated that the size of the survival advantage is distance dependent. My results provide novel information on non-breeding shorebird survivorship and perspective on the interrelationships that drive avian life history strategies. I confirm that Paracas is also a site with high demographic value.

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

Weighted l1 minimization techniques for compressed sensing and their applications

Author: 
Date created: 
2020-04-17
Abstract: 

Compressed sensing (CS) provides effective techniques for the recovery of a sparse vector from a small number of measurements by finding a solution to an underdetermined linear system. In recent years, CS has attracted substantial attention in applied mathematics, computer science and electrical engineering, and it has the potential to improve many applications, such as medical imaging and function approximation. One standard technique for solving the CS problem is l1 minimization; however, the performance of l1 minimization might be limited for many practical applications. Hence, in the past few years, there are many investigations into how to modify the l1 minimization approach so that better performance can be achieved. One such approach is weighted l1 minimization. In this thesis, we extend the weighted l1 minimization technique, traditionally used to solve the standard CS problem, to other applications. First, we develop a variance-based joint sparse (VBJS) algorithm based on weighted l1 minimization to solve the multiple measurement vector (MMV) problem. Unlike the standard l2,1 minimization method for this problem, the VBJS method is easily parallelizable. Moreover, we observe through various numerical experiments that the VBJS method often uses fewer measurements to reach the same accuracy as the l2,1 minimization method. Second, we apply weighted l1 minimization to the high-dimensional function approximation problem, focusing on the case of gradient-augmented measurements. The high-dimensional function approximation problem has many applications, including uncertainty quantification (UQ), where it arises in the task of approximating a quantity of interest (QoI) of a parametric differential equation (DE). For a fixed amount of computational cost, we see in various examples that, with additional gradient information, better approximation results are often achieved compared to non-gradient augmented sampling. Theoretically, we prove that, with the same sample complexity as the case of function samples only, the gradient-augmented problem gives a better error bound in a stronger Sobolev norm as opposed to an L2 norm. Finally, we use the adjoint sensitivity analysis method to compute the gradient information. As we show, this method computes the gradient samples of the QoI of a parametric DE with around the same computational cost as computing the samples of the QoI itself. We apply this approach to several parametric DE problems, and numerically demonstrate the benefits of incorporating gradient information into the approximation procedure.

Document type: 
Thesis
File(s): 
Senior supervisor: 
Ben Adcock
Department: 
Science: Department of Mathematics
Thesis type: 
(Thesis) Ph.D.

A bivariate longitudinal model for psychometric data

Author: 
Date created: 
2020-04-30
Abstract: 

Psychometric test data are useful for predicting a variety of important life outcomes and personality characteristics. The Cognitive Reflection Test (CRT) is a short, well-validated rationality test, designed to assess subjects' ability to override intuitively appealing but incorrect responses to a series of math- and logic-based questions. The CRT is predictive of many other cognitive abilities and tendencies, such as verbal intelligence, numeracy, and religiosity. Cognitive psychologists and psychometricians are concerned with whether subjects improve their scores on the test with repeated exposure, as this may threaten the test's predictive validity. This project uses the first publicly available longitudinal dataset derived from subjects who took the CRT multiple times over a predefined period. The dataset includes a multitude of predictors, including number of previous exposures to the test (our variable of primary interest). Also included are two response variables measured with each test exposure: CRT score and time taken to complete the CRT. These responses serve as a proxy for underlying latent variables, "rationality" and "reflectiveness", respectively. We propose methods to describe the relationship between the responses and selected predictors. Specifically, we employ a bivariate longitudinal model to account for the presumed dependence between our two responses. Our model also allows for subpopulations ("clusters") of individuals whose responses exhibit similar patterns. We estimate the parameters of our one- and two-cluster models via adaptive Gaussian quadrature. We also develop an Expectation-Maximization algorithm for estimating models with greater numbers of clusters. We use our fitted models to address a range of subject-specific questions in a formal way (building on earlier work relying on ad hoc methods). In particular, we find that test exposure has a greater estimated effect on test scores than previously reported and we find evidence of at least two subpopulations. Additionally, our work has generated numerous avenues for future investigation.

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.

The motivations and operational realities of mixed model developments in the Province of B.C.

Date created: 
2020-04-09
Abstract: 

This thesis analyzes four housing developments in the Province of B.C. that involve mixed rental rates, uses and, in some instances, tenures (oftentimes referred to as mixed model developments in this document) to understand the political, economic and social motivations that lead to this form of housing development and their operational benefits and challenges. The main theme—through interviews, analysis of each project’s publicly available planning documentation and the project’s economic model—are that while these developments may have been desired from a social perspective, there are also large economic and political motivations driving them forward. It is often suggested that mixed income development attempts to counteract the negative effects associated with highly concentrated inner-city poverty, however, the true social outcomes of mixed income development on lower income individuals is unclear. What is generally accepted is that mixed income development is an economically and politically feasible urban redevelopment strategy. This study finds that while economics and politics were motivating factors of these projects, community building was also an important aspect of the four case studies; however, it wasn’t indicated by interviewees as being because of mixes of income levels within the developments. It was because there was a belief that building community with your neighbors was important to social well being. Furthermore, operationally, adequate amenity space and appropriate commercial space with facilitated programming to all tenants was noted by interviewees as being important to community building and social mixing in these developments. In most instances, when there was limited amenity/commercial space and limited facilitated programming, social mixing wasn’t occurring according to the housing providers interviewed.

Document type: 
Graduating extended essay / Research project
File(s): 
Senior supervisor: 
Peter V. Hall
Department: 
Arts & Social Sciences: Urban Studies Program
Thesis type: 
(Project) M.Urb.

Morphological and functional characterization of host proteins during infections by actin-hijacking bacterial pathogens

Author: 
Date created: 
2020-04-14
Abstract: 

Cells, much like mammals, possess an internal skeleton. This cellular skeleton (called the cytoskeleton) provides structure to cells, enables their movement within the environment and promotes the internalization of extracellular cargo (endocytosis). Many pathogens have devised strategies to hijack the cytoskeleton and other crucial sub-cellular processes for their disease processes. The bacterium Listeria monocytogenes (L. monocytogenes) utilizes the clathrin endocytic machinery to invade cells, and later, the actin polymerization machinery to generate actin-rich comet/rocket tails to move within and amongst host cells. Salmonella enterica serovar Typhimurium (S. Typhimurium) and Shigella flexneri (S. flexneri) generate actin-rich membrane ruffles at the cell surface to enter cells. Once inside, S. Typhimurium occupies a long-lived vacuole, whereas S. flexneri generates comet/rocket tails. Enteropathogenic Escherichia coli (EPEC) on the other hand remain extracellular and co-opt clathrin and actin to form motile pedestals directly beneath the site of bacterial adherence. In this thesis, I explored the involvement of several host actin- and/or endocytic-associated proteins during bacterial infections and simultaneously used these infections to gain insight into novel roles of the proteins studied. In chapter 2, I discovered that L. monocytogenes co-opts the actin-associated protein palladin during its entry and intracellular motility. Importantly, I revealed that palladin can functionally replace the Arp2/3 complex during bacterial actin-based motility. In chapter 3, I uncovered that the internalization strategy used by L. monocytogenes to transfer between host cells exploits caveolin-mediated endocytosis. In chapter 4, I investigated the host enzyme cyclophilin A (CypA) and found that it is crucial for maintaining the structural integrity of L. monocytogenes membrane protrusions generated during bacterial dissemination events. In chapter 5, I determined that CypA restricts S. Typhimurium invasion but is dispensable for EPEC pedestal formation. Finally, in chapters 6 and 7, I examined the receptor of CypA, CD147, and found that this membrane protein, like CypA, is crucial for the proper formation and function of L. monocytogenes membrane protrusions. In conclusion, my research has 2 major implications: 1) I have uncovered new insight into the mechanisms behind how actin-hijacking pathogens cause disease and 2) I have demonstrated novel cellular functions for host actin-associated proteins.

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

Under Fire: Improving Wildfire Prevention in BC’s Wildland-Urban Interface

Author: 
Date created: 
2020-03-11
Abstract: 

The province of BC has experienced a rapid increase in wildfires, causing forest ecosystems to lose resiliency and requiring human intervention to restore affected landscapes. One area that is particularly prone to the destructive effects of wildfires in BC is the wildland-urban interface (WUI), which is the transition zone between wildland and human development. In the WUI, many communities are exposed to excessive wildfire risks and are underprepared for the threat of increasing wildfires. To understand the approach to wildfire prevention taken in WUI communities in BC, this paper uses a survey research methodology that collects opinions and perspectives on the barriers to taking preventative action. Following this, three policy options are identified that address the improvement of wildfire prevention and mitigation initiatives at the community level. Policy options are then analyzed using a set of evaluation criteria that propose a policy package as the recommended course of action.

Document type: 
Graduating extended essay / Research project
File(s): 
Senior supervisor: 
Doug McArthur
Department: 
Arts & Social Sciences: School of Public Policy
Thesis type: 
(Project) M.P.P.

C. briggsae genome annotation and comparative analysis with C. elegans using RNA-Seq data

Author: 
Date created: 
2020-04-06
Abstract: 

Complete genome annotations are essential for comparative genomics. Currently, the C. briggsae genome annotation is incomplete that limits its utility as a comparative platform for C. elegans. Using RNA-Seq data, we have generated a more complete C. briggsae genome annotation. We identified 20,660 novel introns, 35,635 novel exons, and 5,654 novel protein-coding transcripts, and generated improved databases consisting of 123,974 introns, 150,690 exons, and 28,129 protein-coding transcripts, respectively. The improved C. briggsae annotation together with comparative analyses revealed 132 novel ortholog relationships (between C. briggsae and C. elegans) and 2 novel C. elegans protein-coding genes. This has shown that despite limited data available for C. briggsae, the improved annotation has enhanced the utility of C. briggsae as a comparative platform for C. elegans. As more RNA-Seq data becomes available, this method can be used to further refine not only C. briggsae annotation but also C. elegans annotation.

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

Statistical analysis of data from opioid use disorder study

Author: 
Date created: 
2020-04-24
Abstract: 

This project presents statistical analyses of data from a population based opioid use disorder research program. The primary interest is in estimating the association of a range of demographic, clinical and provider-related characteristics on retention in treatment for opioid use disorders. This focus was motivated by the province’s efforts to respond to the opioid overdose crisis, and the methodological challenges inherent in analyzing the recurrent nature of opioid use disorder and the treatment episodes. We start with executing a network analysis to clarify the influence of provider-related characteristics, including individual-, case-mix and prescriber network-related characteristics on treatment retention. We observe that the network characteristics have a statistically significant impact on OAT retention. Then we use a Cox proportional hazards model with a gamma frailty, while also considering how the ending of the previous episode will impact the future ones to start our investigation into the importance of the episode endings. Moreover, we consider three different analyses under multiple scenarios to reach our final goal of analyzing the multi-type events. The OAT episode counts of the study subjects throughout the follow-ups are analyzed using Poisson regression models. Logistic regression analyses of the records of the OAT episode types are conducted with mixed effects. Lastly, we analyze the OAT episode duration times marginally via an estimating function approach. The robust variance estimator is identified for the estimator of the model parameters. In addition, we conduct a simulation study to verify the findings of the data analysis. The outcomes of the analyses indicate that the OAT episode counts and duration times are significantly associated with a few covariates, such as gender and birth era, and the relationships are varying according to the OAT episode types.

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

Quantifying Blue Carbon for the largest salt marsh in southern British Columbia

Author: 
Date created: 
2019-03-12
Abstract: 

Salt marshes are highly valuable ecosystems that have recently been recognized for the climate change mitigation potential of their soil carbon sequestration. This ‘blue carbon’ is sequestered annually and can be stored for more than a century, but their storage potential has not been well studied on the Pacific coast of North America. This study collected sediment cores from high and low marsh zones in the western portion of Boundary Bay, Delta, British Columbia (BC), to assess carbon storage and carbon accumulation rates (CARs). Carbon stocks in the high marsh were significantly higher compared to low marsh, averaging 84.2 ± 30.9 Mg C/ha and 39.3 ± 24.2 Mg C/ha, respectively. CARs ranged from 19.5 to 454 g C/m2yr, with an average of 137 ± 162 g C/m2yr and a median of 70.1 g C/m2yr. Our CARs indicate that the marsh exhibits substantial variability. Both carbon stocks and accumulation rates were at least 45% lower than global estimates but were similar to other studies on the Pacific coast of North America. By controlling for marsh environment and dating method, we provide a new 210Pb estimate of CAR of 88 ± 20 g C/m2yr for the Pacific coast of North America. Our low carbon stock and accumulation rates in comparison to global estimates are likely due to the shallow depth of the marsh and the dominant type of vegetation. Despite historical modifications and disturbances to the marsh, our study suggests that the western portion of Boundary Bay marsh has been growing in areal extent since at least 1930. Current legislation in the province of BC does not adequately protect salt marshes. This study provides the first quantification of carbon stocks and CARs, which is an important step towards leveraging the co-benefit of salt marshes for improved management, restoration, and preservation for these ecologically and culturally important ecosystems. This study outlines subsequent steps and research needed for Boundary Bay marsh, or other salt marshes in BC, to be included in a voluntary carbon market in British Columbia.

Document type: 
Graduating extended essay / Research project
File(s): 
Senior supervisor: 
Karen Kohfeld
Department: 
Environment: School of Resource and Environmental Management
Thesis type: 
(Project) M.R.M. (Planning)

Magnetic composite polymer membrane actuators with applications to microfluidic devices

Author: 
Date created: 
2020-04-08
Abstract: 

This thesis demonstrates new materials and microfabrication techniques for integrating membrane-type magnetic composite polymer (M-CP) actuators into microfluidic devices and systems. A membrane actuator with a powerful stroke volume that displaces 7.4 µL of water under a 110mT external magnetic field is developed and demonstrated in a hybrid M-CP/thermoplastic microfluidic device and in an all-PDMS microfluidic device. To achieve injection mouldable M-CP devices, a new M-CP is developed that consists of an injection mouldable off-thiol-ene-epxoy (OSTE+) polymer resin that is embedded with 25 weight-% rare earth magnet particles to be permanently magnetized. To support the rapid prototyping of PDMS and OSTE+ polymer microfluidic devices, a new type of micromould is developed that uses laser ablation of tape to deliver low cost, ultra-rapid moulds. These developments facilitate future commercial mass production through integration with thermoplastic polymers favored by the microfluidics industry in a scalable, “design-to-manufacture” scheme.

Document type: 
Thesis
File(s): 
Senior supervisor: 
Bonnie Gray
Department: 
Applied Sciences: School of Engineering Science
Thesis type: 
(Thesis) M.A.Sc.