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.

Multiple axon guidance pathways asymmetrically distribute axons in the ventral nerve cord of Caenorhabditis elegans

Author: 
Date created: 
2018-11-22
Abstract: 

Early during development neurons project small filamentous processes, axons and dendrites, that extend and eventually connect with other cells and tissues. These processes can grow over long distances and allow for transmission of information between cells. The proper functioning of our nervous system is dependent on these same processes correctly navigating to specific end targets. This is achieved through guidance cues in the environment which interact with receptors on the extending processes allowing them to be steered in the correct direction. Unfortunately, due to the high complexity of most vertebrate nervous systems our understanding of how axons and dendrites use these cues to navigate is still very limited. The aim of this thesis was to discover novel genes regulating axon guidance to shine additional light on how axons navigate during development. Normally axons of the ventral nerve cord in the nematode Caenorhabditis elegans are invariably sorted asymmetrically. Animals with mutations impacting function in individual axon guidance signaling pathways show no or only very low penetrance of disruption of VNC asymmetry. Here genetic screens successfully isolated four mutants in which asymmetry between major longitudinal axon tracts is disrupted. One of these four mutants include a novel allele of the gene col-99 which encodes a previously uncharacterized transmembrane collagen with vertebrate homologs. Detailed characterization of animals lacking COL-99 revealed widespread axon guidance defects impacting longitudinal and lateral axon navigation of a variety of neurons. Of the remaining three mutants two were found to be alleles of unc-52 and unc-34, both previously characterised for roles in axon guidance, while the final mutation remains unidentified. Disruption of any one signaling pathway does not lead to penetrant VNC asymmetry defects suggesting redundancy between parallel signaling pathways here. To better understand how signaling pathways of multiple guidance cues may converge to control guidance at choice points single mutants were crossed into a nid-1 null mutant background and VNC asymmetry phenotypes examined. Previously nid-1 was found to substantially enhance navigation defects of the VNC pioneering neuron AVG when crossed into mutants showing a low penetrance of AVG navigation defects. Double mutants with nid-1 saw defect penetrance significantly increase in several cases indicating parallel signaling pathways. Combination of mutants into triple and quadruple mutant strains showed that UNC-6, SAX-3, and COL-99 represent members of parallel signaling pathways acting redundantly to guide axons in establishment of asymmetry which in addition depends on basement membranes components, including EPI-1. Thus multiple axon guidance signaling pathways, acting in tandem, ensure correct guidance and segregation of axons at the anterior choice point of the VNC establishing VNC asymmetry.

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

The expression and regulation of lipid transport proteins in the desert locust, Schistocerca gregaria

Author: 
Date created: 
2018-11-19
Abstract: 

Lipids play a central role in insects, both for storage of nutrients and as an energy source during development and dispersal. Due to their low water solubility, special transport mechanisms are required for their efficient mobilization and utilization. In this thesis, I studied intra- and extracellular proteins involved in lipid transport in the desert locust, Schistocerca gregaria. Vitellogenins are very high-density lipoproteins produced by adult females and deposited into the developing eggs. Two different vitellogenins, named VG-A and VG-B, are expressed in locust fat body. Their complete cDNA transcripts of ~5.6 kb each have been sequenced, coding for two proteins of ~200 kDa each. VG-A and VG-B are co-expressed in similar amounts by mature females, commencing 11 days after adult eclosion, and continuing at high levels throughout the entire adult life. The expression of both proteins is dependent on the nuclear transcription factors Met or RXR, and knockdown of each of these proteins almost completely eliminates VG expression. A similar expression profile was observed in adult muscle for the cytosolic fatty acid binding protein FABP, albeit in both sexes. The direct knockdown of the strongly expressed FABP by RNA inference reduced its levels to less than 2% of what is normally found 3 weeks after adult eclosion. In a series of flight experiments, it was demonstrated that in the absence of FABP, insects are incapable of engaging in flight longer than 30 min; at this time, most carbohydrate resources have been depleted, and locusts normally switch to lipids as the sole fuel for muscle energy production. Short-term flight performance of FABP knockdown locusts was identical to control insects, suggesting that the lack of FABP does not interfere with carbohydrate metabolism. Moreover, the mobilization of lipids in the fat body and their transport by the major hemolymph lipoprotein lipophorin was indistinguishable from control animals. In contrast, knockdown of apolipophorin III, which is essential for lipid transport during flight, completely eliminated flight capability, even for short duration flights. Taken together, this thesis highlights the essential role of lipid transport proteins for locust reproduction and dispersal and identifies potential targets for insect control strategies.

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

3D visual-inertial odometry and autonomous mobile robot exploration with learned map prediction

Author: 
Date created: 
2018-12-12
Abstract: 

2D and 3D scene reconstruction are important topics in the field of robotics and computer vision. Mobile robots require a model of the environment to perform navigational tasks, and model acquisition is a useful application in itself . This thesis presents a) A 3D odometry and mapping system producing metric scale map and pose estimates using a minimal sensor-suite b) An autonomous ground robot for 2D mapping of an unknown environment using learned map prediction. The first application proposes a direct visual-inertial odometry method working with a monocular camera. This system builds upon the state-of-the-art in direct vision-only odometry. It demonstrates superior system robustness and camera tracking accuracy compared to the original method. Furthermore, the system is able to produce a 3D map in metric scale, addressing the well known scale ambiguity inherent in monocular SLAM systems.The second application demonstrates an autonomous ground robot capable of exploring unknown indoor environments for reconstructing their 2D maps. This method combines the strengths of traditional information-theoretic approaches towards solving this problem and more recent deep learning techniques. Specifically, it employs a state-of-the-art generative neural network to predict unknown regions of a partially explored map, and uses the prediction to enhance the exploration in an information-theoretic manner. The system is evaluated against traditional methods in simulation using floor plans of real buildings and demonstrates advantage in terms of exploration efficiency. We retain an advantage over end-to-end learned exploration methods in that the robot's behavior is easily explicable in terms of the predicted map.

Document type: 
Thesis
File(s): 
Senior supervisor: 
Ping Tan
Richard Vaughan
Department: 
Applied Sciences: School of Computing Science
Thesis type: 
(Thesis) M.Sc.

How Iceland Writers Retreat markets itself as an international writers event

Author: 
Date created: 
2018-12-10
Abstract: 

The first Iceland Writers Retreat (IWR) was held in 2014. It has since grown to be an annual event that boasts participants from around the globe, who travel to Iceland to learn from internationally renowned faculty, immerse themselves in the literary traditions of Iceland, and explore an unforgettable setting. This report outlines and examines Iceland Writers Retreat marketing efforts, particularly online. Further, it historicizes the beginning and inspirations of IWR, and delineates IWR’s role within both the landscape of international writing events and the liminal space it occupies between the Icelandic tourism industry and cultural sphere. It aims to outline marketing best practices that can be useful not only to other writing retreats and events, but also to any cultural organization that is moving their marketing efforts primarily online. Finally, it attempts to highlight opportunities for IWR to continue to grow their audience—both online and at the event.

Document type: 
Graduating extended essay / Research project
File(s): 
Senior supervisor: 
Leanne Johnson
Department: 
Communication, Art & Technology: Publishing Program
Thesis type: 
(Project) M.Pub.

The role of the editor: The case of Springer

Author: 
Date created: 
2018-12-06
Abstract: 

Springer, as one of the largest commercial academic publishers, merged with Nature in 2015, and now has a new name: Springer Nature. The merger combines strength of two publishers, with strong book publishing plus strong journal publishing in one publisher. However, the merger does not affect the working modes of the editors at Springer or Nature. Different from the in-house editors at Nature who are handing peer-reviewing process of every article, what are the responsibilities of the editors at Springer? What skills should the editors at Springer have? How can one be a qualified editor at Springer? Facing the new trends in publishing, including big data, open access policies, information exposure, competitive markets, among others, what challenges are awaiting these editors? In particular, in the fast-growing Chinese market, with its enormous output of scientific documents, how can editors based in China work to address this challenge? This report describes the role of editors at Springer regarding the Chinese market, from skills to experiences and from opportunities to challenges.

Document type: 
Graduating extended essay / Research project
File(s): 
Senior supervisor: 
John Maxwell
Department: 
Communication, Art & Technology: Publishing Program
Thesis type: 
(Project) M.Pub.

Applying self-attention neural networks for sentiment analysis classification and time-series regression tasks

Date created: 
2018-11-26
Abstract: 

Many machine learning tasks are structured as sequence modeling problems, predominantly dealing with text and data with a time dimension. It is thus very important to have a model that is good at capturing both short range and long range dependencies across sequence steps. Many approaches have been used over the past few decades, with various neural network architectures becoming the standard in recent years. The main neural network architecture types that have been applied are recurrent neural networks (RNNs) and convolutional neural neworks (CNNs). In this work, we explore a new type of neural network architecture, self-attention networks (SANs), by testing on sequence modeling tasks of sentiment analysis classification and time-series regression. First we perform a detailed comparison between simple SANs, RNNs, and CNNs on six sentiment analysis datasets, where we demonstrate SANs achieving higher classification accuracy while having other better model characteristics over RNNs such as faster training and inference times, lower number of trainable parameters, and consuming less memory during training. Next we propose a more complex self-attention based architecture called ESSAN and use it to achieve state-of-the-art (SOTA) results on the Stanford Sentiment Treebank fine-grained sentiment analysis dataset. Finally, we apply our ESSAN architectures for the regression task of multivariate time-series prediction. Our preliminary results show that ESSAN once again achieves SOTA results, beating previous SOTA RNN with attention architectures.

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

Testing the ability of in-vitro depletion rates to assess the biotransformation rate and bioconcentration factor of hydrophobic chemicals in rainbow trout (Oncorhynchus mykiss)

Date created: 
2018-12-03
Abstract: 

The objective of this study was to test the ability of in-vitro biotransformation rates to predict in-vivo biotransformation rates and BCFs to ultimately improve chemical bioaccumulation assessment. In-vitro biotransformation rates of hydrophobic chemicals pyrene, methoxychlor, cyclohexyl salicylate, and 2,6 dimethyldecane were determined using a rainbow trout liver S9 preparation and then input into two in-vitro-in-vivo extrapolation (IVIVE) models to estimate in-vivo biotransformation rates (kMET) and modelled BCFs. Comparisons of in-vitro derived kMET values using both IVIVE models were in reasonable agreement when compared to in-vivo derived kMET values for pyrene and methoxychlor. Estimated BCFs from this study for pyrene, methoxychlor, and cyclohexyl salicylate were also in good agreement with estimated BCFs from previous studies using in-vitro biotransformation rates as inputs to IVIVE models, but were significantly higher compared to empirical BCFs. This indicates the potential usefulness of in-vitro biotransformation assays and IVIVE models for estimating kMET and BCFs, however kMET values from IVIVE models and BCF estimates should only be considered a conservative estimate at this time due to the uncertainty (i.e. extrahepatic metabolism) associated with these models and the further work required to fine-tune these models.

Document type: 
Graduating extended essay / Research project
File(s): 
Senior supervisor: 
Frank Gobas
Department: 
Science: Biological Sciences Department
Thesis type: 
(Project) M.E.T.

Evaluating harvest strategies that account for fish population structure: an integrative review of key uncertainties and future research needs

Author: 
Date created: 
2018-12-20
Abstract: 

Fisheries management decisions are guided by the outcomes from stock assessment models, which typically assume that fish stocks represent single homogenous populations. However, species normally exhibit complex spatial structure. Using outputs from spatially aggregated stock assessment models to inform harvest strategies in spatially structured fisheries could lead to management failure and erosion of biocomplexity. This paper summarizes how spatial population structure has been addressed in the fisheries literature and explores options for developing harvest strategies that address fish population spatial structure. I also highlight common pitfalls and data needs associated with spatial modeling and harvest strategies. Continued investment in spatial and finer-scale data collection and associated spatial analysis are necessary to develop effective spatial harvest strategies. I conclude that developing spatial modelling and harvest strategies for fishery species is an important step to address the complex nature of marine population structure.

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

Application of the Blue Mussel (Mytilus edulis) as an indicator of microplastic pollution within the Salish Sea

Date created: 
2018-11-27
Abstract: 

Plastic polymers less than 5 mm in diameter, called microplastics (MPs), are an emerging contaminant of concern impacting marine organisms globally. The blue mussel (Mytilus edulis) is a prominent bioindicator used to quantify the accumulation of lipophilic contaminants to assess the health of marine environments. For this reason, blue mussels were utilized to establish baseline MP abundances in British Columbia (BC) and assess the practicality of using mussels as indicators of MP pollution. Mussels (n = ~15, 000) were placed in cages at 11 locations within the Strait of Georgia and southern BC waters in the winter of 2017. Mussels were sampled on Day 0, Day 30 and Day 60 post deployment and MP abundances quantified. For all sites combined, a total of 336 suspected microplastics (SMPs) were identified in 171 mussels, resulting in an average of 1.96 (0.13 SE) SMPs per mussel. After correcting for contamination and standardizing for weight, mean SMP abundances averaged 0.43 (0.06 SE) CSMP/GWW (gram wet weight). 91% of the SMPs enumerated were microfibers. A two-factor complete randomized design analysis of variance revealed that mean CSMP/GWW differed significantly over the 60-day period between the 11 sites (p = 0.0003), however, only mussels at the T60 – Powell River site had significantly more CSMPs/GWW. Furthering this, Fourier Transform Infrared Spectroscopy identified a total of 11 of 66 SMP particles (17%) as plastic. A complimentary exposure experiment was conducted in the spring of 2018 to assess particle fate post mussel filtration. Using a combination of polymer types and sizes, mussels were exposed to three environmentally relevant concentrations of MPs. Pseudofaeces, faeces and whole mussels were examined for MPs 24-hours post exposure. While whole mussels had significantly more MPs than pseudofaeces and faeces (p<0.01; mean proportions ranged from 46-68%, 2-4%, 3-8%, respectively) our results confirmed that MPs were both rejected prior to, and eliminated post digestion, suggesting that blue mussels might be a poor indicator of MP pollution. If plastic loads continue to increase as theorized, however, it is probable that the ability of blue mussels to reject and eliminate MPs efficiently will be impacted.

Document type: 
Thesis
File(s): 
Senior supervisor: 
Leah Bendell
Department: 
Science: Biological Sciences Department
Thesis type: 
(Thesis) M.Sc.

Improving reliability of large-scale multimedia services

Author: 
Date created: 
2018-11-20
Abstract: 

Online multimedia communication services such as Skype and Google Hangouts, are used by millions of users every day. They have Service Level Agreements (SLAs) covering various aspects like reliability, response times, and up-times. They provide acceptable quality on average, but users occasionally suffer from reduced audio quality, dropped video streams, and failed sessions. The cost of SLA violation is low customer satisfaction, fines, and even loss of business. Service providers monitor the performance of their services, and take corrective measures when failures are encountered. Current techniques for managing failures and anomalies are reactive, do not adapt to dynamic changes, and require massive amounts of data to create, train, and test the predictors. In addition, the accuracy of these methods is highly compromised by changes in the service environment and working conditions. Furthermore, multimedia services are composed of complex software components typically implemented as web services. Efficient coordination of web services is challenging and expensive, due to their stateless nature and their constant change. We propose a new approach to creating dynamic failure predictors for multimedia services in real-time and keeping their accuracy high during run-time changes. We use synthetic transactions to generate current data about the service. The data is used in its ephemeral state to create, train, test, and maintain accurate failure predictors. Next, we propose a proactive light-weight approach for estimating the capacity of different components of the multimedia system, and using the estimates in allocating resources to multimedia sessions in {\em real time}. Last, we propose a simple and effective optimization to current web service transaction management protocols.We have implemented all the proposed methods for failure prediction, capacity estimation, and web services coordination in a large-scale, commercial, multimedia system that processes millions of sessions every day. Our empirical results show significant performance gains across several metrics, including quality of the multimedia sessions, number of failed sessions, accuracy of failure prediction, and false positive rates of the anomaly detectors.

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