title: Post-Fire Chronosequence Analysis of Peatland Bog Vegetation Communities Across Hydrogeological Settings

contributor:
Waddington, James Michael
Earth and Environmental Sciences

subject: peatland chronosequence wildfire vegetation margins vulnerable

abstract: Canada’s Boreal Plains peatlands comprise 2.1% of the world’s terrestrial carbon store and are vital water supplies for adjacent upland ecosystems in this sub-humid climate.  Projections indicate that future drought and wildfire events will be more frequent and severe, enhancing moisture deficits and threatening the functional role of peatlands as net carbon sinks. Peatland margins existing at the peatland-upland interface have been identified as deep smouldering hotspots on the landscape, where margin carbon loss accounts for 50 to 90% of total peatland carbon loss, dependent on hydrogeological setting. Previous chronosequence analysis of peatland bog recovery from wildfire disturbance has chronicled a return to carbon sink status within 20 years, but has not included margins nor peatlands located in coarse or heterogeneous-textured hydrogeological settings with varying degrees of groundwater connectivity. This analysis identifies and describes margin vegetation communities and recovery trajectories with time since fire and across hydrogeological settings. No significant differences were identified in margin area over time or margin peat depths across hydrogeological settings. Margin canopy composition consists of mixed coniferous and broadleaf deciduous species, with enhanced litterfall characterizing the dominant early to mid successional ground layer composition. Both peatland bog middle and margin vegetation communities were found to be dominated by feathermoss growth ~60 years following wildfire, which represents an accelerated trajectory from previous chronosequence analyses. Increased peatland and margin fuel loads with time since fire are also demonstrated using aboveground biomass calculations. Restoration practitioners can use this study to identify recovery milestones and altered trajectories, with their associated feedbacks, that perpetuate a broadleaf canopy and limited Sphagnum moss paludification. Fire managers should include confined peatlands in coarse-textured hydrogeological settings with deep smouldering margins in their management considerations and consider intervention (forest treatments) to open the canopy and prevent legacy carbon losses by severe wildfires.

abstract: Thesis

abstract: Master of Science (MSc)


title: On Using Hardware Assertion Checkers for Bit-flip Detection in Post-Silicon Validation

contributor:
Nicolici, Nicola
Electrical and Computer Engineering

abstract:
With the rising demand for integrating more features in a single product, modern designs feature more and more functionality on a single die. The complexity resulted from this growth makes it more difficult to guarantee that all errors are detected and fixed before the product is manufactured. Efforts carried out before the design is manufactured, known as pre-silicon verification, are unable to detect all the errors. Electrical errors, such as those caused by cross-talk or power droops, are particularly difficult to catch during the pre-silicon phase because of the insufficient accuracy of device models, which is often traded-off against simulation time. This challenge is further aggravated by the rising number of voltage domains, especially if subtle errors are excited in unique electrical states. These electrically-induced subtle errors most commonly manifest in the logic domain as bit-flips in flip-flops. Therefore, once the design prototypes are available, the verification tasks continue on them to identify and eliminate errors that have escaped pre-silicon verification phase and have the potential to cause catastrophic problems if they remain undetected. This task is commonly referred to as post-silicon validation and has become an important step in the design flow of system-on-chip devices.
Limited internal node observability is one of the main challenges of post-silicon validation because it causes long error detection latencies. The existing approaches that try to improve this limited observability usually rely on ad-hoc methods which are difficult to maintain when particular changes are requested from one project to another. Hence in this thesis, we propose novel systematic methods which can be used for automatic generation of on-chip blocks that improve internal observability and reduce error detection latency in post-silicon validation.

First we propose an automated methodology that generates and selects hardware assertions for bit-flip detection in post-silicon validation. As part of this methodology, we will introduce two quantitative metrics, the bit-flip coverage estimate and the flip-flop coverage estimate that can be used to assess the quality of the selected assertions. Next, we improve the run-time and the accuracy of our proposed methodology by using emulation platforms that can automatically be integrated into the proposed flow to enable fast, yet accurate assertion selection. Finally in the last contribution, we will propose a novel solution for automatic generation of hardware assertions by leveraging the internal mechanism of Boolean satisfiability solvers, namely learned clauses. In addition, we will formally evaluate the potential of the discovered hardware assertions using an incremental SAT solving approach to assess these hardware assertions for bit-flip detection. We will show that by using this new method, the proportion of errors that can be detected are improved while the area overhead is reduced.

State-of-the-art post-silicon validation practices rely primarily on ad-hoc methods for bit-flip detection and there is a lack of systematic methods that can be applied to generic digital blocks. Consequently, the contributions from this thesis are a step towards introducing assertion-based methods and architectures that facilitate systematic bit-flip detection in post-silicon validation.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)


title: Resolving the Xenarthran Phylogeny Using Nuclear Loci

contributor:
Poinar, Hendrik
Golding, Brian
Biology

subject:
Biology
Ancient DNA
Phylogenetics
Mammalogy

abstract:
Xenarthra form the least diversified major clade of placental mammals, being comprised of 31 described species of sloth, armadillo, and anteater. The past decade has seen a growth in the amount of xenarthran genetic data available, including the recent publication of a phylogenetic framework based on mitochondrial genomes, but more is required to aid in conservation assessments and to elucidate the evolutionary history of this unique order. We aimed to expand upon this by generating a framework based on nuclear genes.

Using molecular baits, we enriched nuclear DNA from all extant and a selection of extinct ancient Xenarthrans for 74 phenotypically relevant genes. We aim to build phylogenetic trees based on each successfully enriched loci. Comparing trees against the previous mitochondrial framework will provide a measure of robustness. By seeing how estimated divergence times and rates vary across nuclear genes, we were able to examine how particular xenarthran phenotypes were selected upon in different points of their evolutionary history. While the sequencing of certain genes and species encountered mixed success rates, we have a solid framework for further study and can confirm that nuclear and mitochondrial information yields very similar evolutionary histories.

abstract: Thesis

abstract: Master of Science (MSc)

abstract: Xenarthrans - sloths, armadillos, and anteaters - have a long and complicated evolutionary history. In recent years a growth of new genetic information has made it easier to answer questions about their relation to each other and to other species. By examining many new gene sequences across all living Xenarthra, plus some extinct species, we aim to bolster our understanding of these relationships and the importance of particular traits.


title: VIRTUAL ERGONOMICS AND GAMING TECHNOLOGY FOR POSTURE ASSESSMENT: FROM AUTOMOTIVE MANUFACTURING TO FIREFIGHTING

contributor:
MacDermid, Joy
Kinesiology

subject:
virtual ergonomics
automotive manufacturing ergonomics
firefighting
injury prevention

abstract:
Virtual ergonomics (VE) tools have had an impressive impact on the automotive, aviation, and defence industries. Despite the progress made in the last four decades, the tool complexity and application potential in other industries continues to invite improvement opportunities. Firefighting is an occupation with a high musculoskeletal injury burden that can benefit from innovative VE tools. This dissertation aims to: 1) improve VE tools for traditional and novel applications, and 2) identify injury risk to firefighters during fire suppression tasks.
This dissertation begins by proposing a set of joint-specific and whole-body posturing guidelines for the manual manipulation of digital human models (DHMs) in the context of automotive manufacturing.  Simulation accuracy improved with the implementation of posturing guidelines. These findings are useful instructions for virtual simulation ergonomists, software developers of posture prediction algorithms, and those charged with determining manufacturing ergonomics protocols.
Descriptive ergonomic analyses of 48 firefighters in full bunker gear performing three common fire suppression tasks were then performed to identify the required ergonomic action needed for these tasks. Next, two VE tools (Jack and 3DSSPP) and Microsoft Kinect® 3D motion capture data were used to conduct an in-depth analysis of the most difficult task, the high-rise pack lift. The analysis included developing a methodology for modeling the external loads due to personal protective equipment. In addition to describing the firefighter injury risk exposure during common fire suppression tasks, the results highlight the strengths, limitations, and areas for further improvement of VE technology.
Overall, VE tool improvements include suggesting guidelines for manual DHM posturing, understanding the strengths and limitations of using 3D motion capture gaming technology for posturing DHMs, and developing strategies to account for external loads due to personal protective equipment. Following these improvements, VE technology shows promise as an ergonomic assessment tool for firefighters.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)

abstract: Virtual ergonomics (VE), which uses digital human models in virtual workstations, allows for efficient and detailed ergonomic assessments of tasks that are otherwise difficult or impossible to perform. However, more research is needed to identify tool improvements for both traditional and new applications. This work proposes, evaluates, and ultimately recommends a set of postural guidelines for the posturing of digital human models to ensure accurate simulation and subsequent assessment of real assembly-line worker movement patterns. Next, firefighter ergonomics, a relatively new application for VE tools, is introduced by first describing the injury risks associated with common fire suppression tasks. The strengths, limitations, and potential of applying VE tools to firefighting ergonomics are then highlighted through an example of simulating the high-rise pack lift task using two VE tools. Overall, the results contribute to the evolving field of VE by challenging current methodologies and highlighting new opportunities for VE tools.


title: Investigating the effects of water level on depth zones for macrophyte distribution and ecological index performance in coastal marshes of Georgian Bay, Lake Huron

contributor:
Chow-Fraser, Patricia
Biology

subject: water level, Georgian Bay, coastal wetland, vegetation, ecological index, slope, monitoring

abstract: Monitoring and maintaining the health of coastal wetlands is a global concern. The greatest threat to coastal wetlands in the Great Lakes Basin are anthropogenic removal and enrichment. The coastal wetlands in Georgian Bay are relatively undisturbed by humans, but face disturbance caused by reduced annual water-level fluctuations. Since these wetlands are critical habitat for many fish, bird, amphibian, and reptile species, many efforts to accurately monitor and maintain their health have been put into place. Recently, these wetlands have been experiencing an abrupt (~1 m) transition to higher water levels, following 14 years of sustained lows, which allowed trees and shrubs to invade the meadow vegetation zone. This sustained water-level pattern has never occurred in this region before, offering the unique opportunity to study wetlands undergoing a transition, where areas of 10+ years of upland plant species growth was inundated and became part of the wetland habitat. This thesis first investigates how this change in water level affects the distribution of meadow, emergent, floating, and submerged vegetation both in physical space and area. The second chapter of this thesis presents long-term water quality, macrophyte, and fish community monitoring using ecological indices. Water quality and macrophyte indices are robust enough to monitor wetlands undergoing a transition; however, issues arise in the calculation of the wetland fish index, as the changes in macrophyte distribution described in Chapter 1 impact the ability to replicate community sampling using fyke nets. The research done throughout this thesis is highly beneficial in adding to the limited knowledge of key factors impacting macrophyte community shifting. This work also identifies water-level scenarios where managers must adjust sampling protocols to succeed in effectively sampling wetland fish communities.

abstract: Thesis

abstract: Master of Science (MSc)

abstract: The coastal wetlands in the Georgian Bay area are primarily threatened by human development and the removal of annual water-level fluctuations. From 1999-2013, the water level decreased and remained low. In 2014, the water level rose about 1 m, causing flooding of grass and trees that had grown in the meadow zone during the 14 years when the water level was low. The first goal of this thesis is to explain how and why all wetland plants are relocating during this period. The second goal is to make sure that common indicators of wetland health (water quality, plants, and fish) can still be used during a time when flooding of grasses and trees was occurring in wetlands. The findings in this thesis contribute to the ability to predict and understand how the plants will shift within a wetland during a time of flooding, as well as informing managers on appropriate sampling protocols.


title: Investigating the relationship between dysglycemia and measures of carotid intima-media thickness in children and youth enrolled in weight management

title: Dysglycemia and carotid intima-media thickness in children and youth with obesity

contributor:
Morrison, Katherine
Medical Sciences

abstract: INTRODUCTION: The prevalence of obesity in Canadian adults is high and is mirrored in the pediatric population. The collective increase of childhood obesity over the last three decades has been associated with a corresponding rise in the deterioration in cardiometabolic health. Abnormally high measures of blood glucose are indicative of impaired glucose metabolism that is related to the development of adverse adult conditions such as type 2 diabetes mellitus (T2DM) and/or cardiovascular disease (CVD). Prediabetes is a transient state of abnormally elevated blood glucose levels that, in adults, has comparable cardiovascular risk to diagnosed diabetes. Previous studies have demonstrated that children with prediabetes can progress to T2DM over a short period of time.  Given that up to 21% of children with obesity have abnormal glucose parameters, it is critical to manage risk at early stages of life in this population in order to prevent adverse adult outcomes. PURPOSE: The purpose of this study was to evaluate if there is a contributing role of prediabetes on vascular structure, assessed via carotid intima-media thickness (cIMT), in children and youth with obesity. Given the high prevalence of adverse health indicators, we aimed to characterize the relationships between these clinical measures and early structural changes associated with atherosclerosis progression. As protocols used to measure cIMT in pediatric studies vary, an additional aim of this project was to assess comparability of cIMT protocols reported in the literature. HYPOTHESIS: It is hypothesized that children with obesity and prediabetes will have greater mean cIMT compared to normal glycemic controls and that mean cIMT will be significantly different across varying cIMT methodologies. METHODS: We recruited 165 participants (ages 5-17y) into this cross-sectional study, a sub-study of the CANadian Pediatric Weight Management Registry (CANPWR). This study assessed cIMT via B-mode ultrasonography in children and youth at time of entry into a weight management program. Clinical measures were obtained via prospective clinical chart review and were evaluated to identify potential relationships between modifiable and non-modifiable cardiovascular health indicators and measures of cIMT, using univariable and multivariable regression analyses. To compare methodologies, we assessed differences of mean cIMT (mm) using an intra-class correlation and a Bland-Altman plot. RESULTS: Fasting plasma glucose was related to mean cIMT (mm) in univariable analyses (p=0.047), but no measure of glycemia was independently correlated to arterial thickness. Segment-specific thickening contributed to significant differences in mean cIMT (mm) between methodologies that included all arterial segments (far and near wall of the common carotid artery, carotid bulb, and internal carotid artery; 12-segment) compared to those limited to the far wall of the common carotid artery (2-segment) (p<0.001). Intra-class correlation between these cIMT methodologies indicated moderate resemblance (ICC: 0.65, 95%CI: 0.55 to 0.73), however, a significant difference between means (mean difference: 0.012mm, 95%CI: -0.016 to -0.009, p<0.001) and a positive proportional bias (r=0.19, 95%CI: 0.06 to 0.31, p=0.003) were present. Furthermore, correlates of mean cIMT were inconsistent between varying methodologies commonly used to assess cIMT in children. CONCLUSIONS: In this study, dysglycemia did not predict on arterial thickness in children and youth with obesity. By comparing determinants and absolute differences between measures of cIMT, this study emphasizes the heterogeneity between the two methodologies and suggests that they should not be used interchangeably.

abstract: Thesis

abstract: Master of Science (MSc)


title: Reinterpretations of the Struggle of the Orders: Re-working Historical Memory

contributor:
Eilers, Claude
Classics

subject:
Classics
Roman History
Roman Historiography
Roman Literature
Struggle of the Orders
Cicero
Livy
Dionysius of Halicarnassus
Piso Frugi

abstract: This is a study of how late Republican and early Imperial authors recast different elements of episodes from the Struggle of the Orders (509-287 BCE) based on the events and circumstances of their own times and their authorial aims. The study is divided into two parts. Part I focuses on portrayals of Sp. Cassius’ third consulship in 486 BCE, when he sought to pass a lex agraria. Part II examines the treatments of Sp. Maelius’ private frumentary distributions, which purportedly occurred in 439 BCE. Both episodes seem to have been treated briefly by earlier sources; the main thread of the stories centred around Cassius’ and Maelius’ desire to acquire regnum, which led to their suppressions and deaths. Over time, the stories evolved and became more detailed. Elements were exaggerated, added, or omitted, which often spoke to what was happening during the time at which a certain author was writing. By means of a comparison of the primary sources I examine the contemporary Roman historical realities contained within our surviving narratives on the patricio-plebeian conflicts of the early period. Late Republican authors frequently recast the patrician-plebeian struggle in the context of the recent political conflicts between optimates and populares, using the political idiom of their own times to describe the Struggle of the Orders. Cassius and Maelius became embedded in the political controversy surrounding the suppression of men (reportedly) seeking kingship by the state that began with the institution of the SCU and continued long into the first century BCE. I analyze the changes that take place in the accounts of Cicero, Livy, and Dionysius of Halicarnassus, our main sources on the episodes involving Cassius and Maelius. Different authors reinterpret, emphasize, and omit various elements of the events of 486 and 439 BCE. A single author might, as is the case with Cicero, reimagine the episodes differently at different times based on his immediate aims. While the ways by which the sources reimagine elements of these episodes has led to harsh criticisms of these authors, especially Livy and Dionysius, I argue that our sources were engaging with the material at their disposal and shaping it in ways that were acceptable to ancient audiences. This historical interpretation helped the Romans to make sense of their own past and derive meaning from it, which, in turn, helped them to engage with and make sense of their present.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)


title: Microfabricated pH, temperature, and free chlorine sensors for integrated drinking water quality monitoring systems

contributor:
Howlader, Matiar M. R.
Deen, M. Jamal
Haddara, Yaser M.
Electrical and Computer Engineering

subject:
Inkjet printing
Sensor
Water quality monitoring
pH sensor
Free chlorine sensor
Temperature sensor

abstract:
The monitoring of pH and free chlorine concentration in drinking water is important for
water safety and public health. However, existing laboratory-based analytical methods are
laborious, inefficient, and costly. This thesis focuses on the development of an easy-to-use,
sensitive, and low-cost drinking water quality monitoring system for pH and free chlorine.
An inkjet printing technology with a two-step thermolysis process in air is developed to
deposit palladium/palladium oxide (Pd/PdO) films as potentiometric pH sensing electrodes.
The redox reaction between PdO and hydronium ions generates the sensor output voltage.
A large PdO percentage in the film provides a high sensitivity of ~60 mV/pH. A defect-free
Pd/PdO film with small roughness contributes to a fast response and a high stability.
When the Pd ink is thermalized in low vacuum, the deposited Pd/PdO film shows a bilayer
structure. The residual oxygen in the low vacuum environment assists the decomposition
of organic ligands for Pd to form a thin and continuous layer beneath submicron Pd
aggregates. The oxidized bilayer film behaves as a temperature sensor with a sensitivity of
0.19% resistance change per °C, which can be used to compensate the sensed pH signals.
Poly(3,4-ethylenedioxythiophene):poly(styrenesulfonate) (PEDOT:PSS) is drawn by hand
to form a free chlorine sensor. Free chlorine oxidises PEDOT:PSS, whose resistivity
increment indicates the free chlorine concentration in the range of 0.5-500 ppm. Also, we
simplified an amperometric free chlorine sensor based on amine-modified pencil leads. The
simplified sensor is calibration-free, potentiostat-free, and easy-to-use.
The pH, temperature, and free chlorine sensors are fabricated on a common substrate and
connected to a field-programmable gate array board for data processing and display. The
sensing system is user-friendly, cheap, and can accurately monitor real water samples.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)

abstract:
Sensitive, easy-to-use, and low-cost pH and free chlorine monitoring systems are important
for drinking water safety and public health. In this thesis, we develop an inkjet printing
technology to deposit palladium/palladium oxide films for potentiometric pH sensors and
resistive temperature sensors. The different electrical and electrochemical properties of the
palladium/palladium oxide films are realized by creating different film morphologies using
different ink thermolysis atmospheres. The developed pH and temperature sensors are
highly sensitive, fast in response, and stable. For free chlorine sensors, a hand drawing
process is used to deposit poly(3,4-ethylenedioxythiophene):poly(styrenesulfonate), which
is an indicator for the free chlorine concentration over a wide range. We also developed a
calibration-free free chlorine sensors based on modified pencil leads. Such a free chlorine
sensor is integrated with the pH and temperature sensors, and an electronic readout system
for accurate on-site drinking water quality monitoring at low cost is demonstrated.


title: A Fixed-scale Pixelated MIMO Visible Light Communication System

contributor:
Hranilovic, Steve
Electrical and Computer Engineering

subject:
pixelated MIMO system
visible light communication

abstract: Visible light communication (VLC) systems take advantage of ubiquitous light-emitting diodes (LED) and leverage existing illumination infrastructure to provide broadband optical communication links. Multiple-input multiple-output (MIMO) VLC systems are among the well studied topics in VLC research. However, most traditional MIMO VLC systems require accurate alignment and have to adjust to different magnifications at various link distances. Consequently, the alignment and calibration modules increase the complexity of the receiver structures. A pixelated MIMO VLC system is introduced in this thesis, which transmits a series of time-varying coded images that can be received and decoded by commercial digital cameras. Using a convex lens placed in front of the transmitter at its focal length, the system exploits the Bokeh effect to obtain fixed-scale images at all link distances. Compared with traditional pixelated MIMO VLC systems, which send information directly in space, this spatial-angular mapping system sends information in different angles instead. In contrast to the complex receiver structures in traditional setups, the proposed system can capture fixed-scale images with a simple receiver requiring no re-focusing as the camera moves. The channel model of the system is measured and modeled and a rateless code is applied to track the truncation of receive images for various link ranges and angular offsets. A proof-of-concept optical communication system is implemented with an LCD display and a high speed CMOS camera. Performance of the system is measured and analysed. The experimental system can achieve a throughput of approximately 10 bit per frame over 90 cm. This fixed-scale pixelated MIMO wireless optical communication system provides a less expensive option for short-range indoor broadcasting optical links and inter-vehicle communications due to its mobility, stability and simpler receiver structure compared to traditional designs in different working conditions.

abstract: Thesis

abstract: Master of Applied Science (MASc)


title: MICROBIAL ELECTROCHEMISTRY APPLICATIONS FOR NUTRIENT RECOVERY AND ORGANIC DETECTION IN WASTEWATER TREATMENT

contributor:
Kim, Younggy
Civil Engineering

subject:
nutrient recovery
microbial electrochemistry
bioanode sensors
struvite
organic detection

abstract:
This thesis presents research work on microbial electrochemistry applications for phosphorus recovery from real wastewater and bioanode sensor development. Phosphorus is a valuable but limited resource which is essential for land fertilizers. Recovering phosphorus using microbial electrolysis cells has been emphasized in wastewater treatment research. Stainless steel mesh (SSM) cathode MECs used in this study showed insufficient phosphorus recovery (68%) because struvite crystals were smaller than the open space between mesh wires (80 µm). Besides, lack of readily biodegradable substrates in the dewatering centrate resulted in limited electric current generation (< 0.2 A/m2) and local pH condition near the cathode. Thus, the following experiments were conducted with stainless steel foil (SSF) cathodes and acetate addition to improve recovery efficiency. Under high electric current density (> 2 A/m2), a thick layer of struvite crystals was formed on the SSF cathode and the phosphorus recovery was increased to 96%. These findings prove that MECs can applied as efficient tools to recover nutrients from real wastewater.
	Bioanode sensors can be used for real-time and in-situ assessment of water quality. However, the sensor performances are often limited by the narrow detection range, long analysis time, and hysteresis. In order to overcome the challenges for practical applications, a new operation method consisting of three sequences (Normal Operation, Reset Step, and Test Step) was proposed and examined using MEC-based bioanode sensors. Reset Step can eliminate hysteresis effects and produce accurate linear correlations between the soluble COD (chemical oxygen demand) and electric current. The total analysis time was found to be 3 min or even less. The increased detection range (from 75 to 130 mg-COD/L) was achieved by applying a high applied voltage during Test Step. The demonstrated results indicate that MECs can be used for accurate estimation of biodegradable organics in natural or engineered water systems.

abstract: Thesis

abstract: Master of Applied Science (MASc)


title: Atomic-resolution Imaging and Spectroscopy of Platinum-alloy Nanoparticles

contributor:
Botton, Gianluigi
Materials Science and Engineering

subject:
fuel cells
nanoparticles
electron microscopy
platinum-alloy
EELS
Electrochemistry
Climate change
renewable energy
hydrogen economy
nanotechnology

abstract: The work presented in this thesis centers on the application of atomic-resolution transmission electron microscopy to study Platinum-alloy nanoparticles. In particular, the thesis focusses on the platinum-iron and platinum-gold systems. Additionally, few other complementary structures based on Pt thin films and nanowires are also characterized. These materials are studied in the context of their catalytic application towards the oxygen reduction reaction in polymer electrolyte membrane fuel cells (PEMFCs). Here we report on the detailed investigation of many structural and compositional aspects of these catalyst nanoparticles including lattice strain, the surface and bulk atomic-structure, the surface/bulk chemical composition, surface segregation, and atomic ordering. In some cases we have even looked beyond the traditional characterization approaches. For instance, instead of observing the particle structures before and after a particular treatment (e.g., heating and degradation tests), we have captured the dynamics of structural evolution over the entire course of such treatments. These investigations were useful in interpreting their catalytic performances, which opened new perspectives towards further optimization of their material structure on the atomic-level.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)


title: Continuous Model Theory and Finite-Representability Between Banach Spaces

contributor:
Hart, Bradd
Mathematics

subject:
logic
continuous model theory

abstract: In this thesis, we consider the problem of capturing finite-representability between Banach spaces using the tools of continuous model theory. We introduce predicates and additional sorts to capture finite-representability and show that these can be used to expand the language of Banach spaces. We then show that the class of infinite-dimensional Banach spaces expanded with this additional structure forms an elementary class K_G , and conclude that the theory T_G of K_G is interpretable in T^{eq} , where T is the theory of infinite-dimensional Banach spaces. Finally, we show that existential equivalence in a reduct of the language implies finite-representability. Relevant background on continuous model theory and Banach space theory is provided.

abstract: Thesis

abstract: Master of Science (MSc)


title: Fluorescence and Diffuse Reflectance Spectroscopy for Margin Analysis in Breast Cancer

contributor: Radiation Sciences (Medical Physics/Radiation Biology)

subject:
Fluorescence
Diffuse reflectance
Optical properties
absorption coeifficient
Breast cancer
reduced scatter coeifficient
intra-operative tool
margin-assessment

abstract: This study investigates the possibility of using a time-resolved Fluorescence and Diffuse Reflectance Spectroscopy (tr-FRS) system to define tumour surgical margins of invasive ducal carcinoma of breast. UV excitation light was used for the fluorescence component and data was collected from the 370-550 nm range. A broadband source was used for diffuse reflectance collection and the emitted response was in the 400-800 nm range. 40 matched pair cases were collected from patients undergoing breast conservation surgeries. Histological analysis was performed on each sample to determine the fat and tumour content within each normal and tumour sample respectively.  Statistical analysis was performed on the optical data to reveal biochemical changes in the endogenous fluorophores collagen, reduced nicotinamide adenine dinucleotide (NADH), and flavin adenine dinucleotide (FAD) as well as changes in absorption and scattering properties attributed to variances in absorber concentrations and cell density respectively. Statistical significant differences in collagen, NADH, and FAD lifetimes, collagen, NADH, FAD and NADH/FAD intensity, diffuse reflectance and reduced scatter coefficient were observed between tumour and normal breast samples. These significant factors were used in Principle Component Analysis model construction and a binary classification scheme using Soft Independent Modeling of Class Analogy (SIMCA) was used as a classification tool to predict unknown breast samples as either normal or tumour with specificity of 60% and sensitivity slightly over 50%.

abstract: Thesis

abstract: Master of Science (MSc)


title: Physical and Biological Properties of Synthetic Polycations in Alginate Capsules

contributor:
Stover, Harald
Chemistry

subject:
Cell Encapsulation
Polycations
Alginate beads
mechanical properties
Polyelectrolyte Complexation
Polymer chemistry
RAFT polymerization
Block copolymers
Thermo-responsive polymers
Micropipette Aspiration
Covalent cross-linking
Micelle morphology

abstract:
The use of cell transplantation to treat enzyme deficiency disorders is limited by
the immune response targeted against foreign tissue or the use of life-long
immunosuppressants. Hiding cells from the immune system in an encapsulation device is
promising. Cells encapsulated within an anionic calcium alginate hydrogel bead are
protected through a semi-permeable membrane formed by polycation, poly-L-lysine
(PLL). A final layer of alginate is added to hide the cationic PLL surface but this has
proved to be difficult creating capsules which are prone to fibrotic overgrowth, blocking
exchange of nutrients, waste and therapeutic enzymes through the capsule. For long term
applications these capsules need to be both biocompatible and mechanically robust.
This thesis aims to address the biocompatibility issue of high cationic surface
charge by synthesizing polycations of reduced charge using N-(3-
aminopropyl)methacrylamide hydrochloride (APM) and N-(2-
hydroxypropyl)methacrylamide (HPM) and study the associated mechanical properties of
the capsules using micropipette aspiration. Micropipette aspiration was applied and
validated for alginate based capsules (gel and liquid core) to quantify stiffness.
Varying ratios of APM were used to control the overall charge of the polycations
formed while HPM was incorporated as a neutral, hydrophilic, nonfouling comonomer.
The molecular weight (MW) was controlled by using reversible addition-fragmentation
chain transfer (RAFT) polymerization. The biocompatibility of these polymers was tested
by cell adhesion and proliferation of 3T3 fibroblasts onto APM/HPM copolymer
functionalized surfaces and by solution toxicity against C2C12 myoblasts. The ability for the APM/HPM copolymers to bind to alginate and form capsules was also assessed, along
with the integrity and stiffness of the capsule membrane with or without additional
covalent cross-linking by reactive polyanion, poly(methacrylic acid-co-2-vinyl-4,4-
dimethylazlactone) (PMV60).
Thermo-responsive block copolymers of N-isopropylacrylamide (NIPAM) and 2-
hydroxyethylacrylamide (HEA) were also synthesized as potential drug delivery
nanoparticles, showing control over micelle morphology with varying NIPAM to HEA
ratios.

abstract: Thesis

abstract: Doctor of Science  (PhD)

abstract:
The treatment of enzyme deficiency disorders by cell transplantation is limited by
the immune attack of foreign tissue in absence of immunosuppressants. Cells protected in
an encapsulation device has shown promise. Poly-L-lysine, a widely used membrane
material in these protective capsules, binds to the anionic gel entrapping living cells
because it is highly cationic. The high cationic charge is difficult to hide causing the
immune system to build tissue around the capsule, preventing the encapsulated cells from
exchanging nutrients and therapeutic enzymes. This thesis aims to replace poly-L-lysine
by synthesizing a series of more biocompatible materials of decreasing cationic charge.
These materials were studied for the ability to support tissue growth and form stable
capsules. The membrane strength was measured using an aspiration method validated for
these types of capsules. Reducing the cationic charge of the materials increased the
biocompatibility of the capsule membrane but also made for weaker membranes.


title: Computing the intersection of regular Hessenberg varieties with Schubert cells

contributor:
Harada, Megumi
Mathematics and Statistics

subject:
mathematics
algebraic geometry
hessenberg variety
algebra

abstract: In his PhD thesis Erik Insko gave the conditions in which the intersection of any Schubert cell with a regular nilpotent Hessenberg variety is smooth. In this thesis we relax the nilpotent condition and aim to extend his method to describe regular Hessenberg varieties without the nilpotent restriction. We conclude that one specific intersection is smooth at the origin.

abstract: Thesis

abstract: Master of Science (MSc)


title: EFFECTS OF DRAG-REDUCING POLYMERS ON TURBULENCE GROWTH AND BURSTING IN NEAR MINIMAL CHANNELS AND EXTENDED DOMAINS

contributor:
Xi, Li
Chemical Engineering

subject:
drag reduction
MDR
laminar-turbulent transition
edge state

abstract:
Two major problems in viscoelastic turbulence, the effects of polymers on the laminar-turbulent transition dynamics and the origin of the maximum drag reduction asymptote, can be both better understood in the regime near the margin of turbulence. In the first part of this thesis, direct numerical simulation trajectories initiated from the edge state are used to follow its unstable manifold into the turbulent basin. In Newtonian flow, the growth of turbulence starts with the intensification of velocity streaks and a sharp rise in the Reynolds shear stress. It is followed by a quick breakdown into high-intensity small-scale fluctuations before entering the core of turbulence. Adding drag-reducing polymers does not affect the initial growth of turbulence but stabilizes the primary streak-vortex structure, which help the flow circumvent the breakdown stage. Throughout the process, polymers act in reaction to the growing turbulence and do not drive the instability. This part not only reveals the transition dynamics into turbulence but also presents a comprehensive view of the bursting stage observed in the near-wall self-sustaining cycle, which starts as the flow leaves hibernating turbulence and is redirected towards the turbulent basin by the unstable manifold of the edge state.
On the other hand, this thesis also discusses the effects of polymer addition on the laminar-turbulent transition in extended domains. Localized turbulent spot can be clearly observed in the large box, and this turbulent region will spread as well as tend to “split” but finally fill up the whole domain before it is separated. Polymers do not affect the flow dynamics until the burst. Similarly, vortex structures rapidly break down into small scales after the first bursting of Reynolds shear stress, but polymer additives depress this process.
The thesis offers a clear and comprehensive overview of the transition into turbulence in the presence of drag-reducing polymers. Future work remains in two major directions. The first is to pinpoint the flow states responsible for the quantitative origin of the universal upper limit of drag reduction observed in experiments. The second is to determine the role, if any, of elasticity-driven instabilities in the transition.

abstract: Thesis

abstract: Master of Applied Science (MASc)

abstract: Turbulence exists everywhere and can be observed in most fluid flows occurring in nature. To reduce the energy consumption, frictional resistance in the turbulence must be considered in fluid transportation. It has been known since the 1940s that a small amount of long-chain polymer additives can dramatically reduce such drag. The mechanism of drag reduction has attracted extensive attention. Two problems of particular interest are the upper limit of drag reduction (termed maximum drag reduction) and the polymer effects on the laminar-turbulent transition. In this thesis, full transient trajectories from marginal turbulent states towards sustained turbulence in both Newtonian and polymeric flows are monitored by direct numerical simulations. It is observed that polymer additives do not affect the initial growth of turbulence but prevent flows from breaking into strong but small-scale fluctuations afterwards. In a more extended domain, turbulence starts as localized spots which spread across the channel. Adding polymers changes the dynamics of turbulence propagation as well. In addition to the aforementioned problems, this study also sheds lights on the so-called bursting events intermittent surges in turbulent activities observed in experiments.


title: A Real-Time Capable Adaptive Optimal Controller for a Commuter Train

contributor:
Sirouspour, Shahin
Electrical and Computer Engineering

subject:
Optimal Control
Commuter Train
Numerical Optimization
Convex
Second Order Cone Program
Multi-Vehicle
Real-Time
Sparse Optimization
Non-Convex Optimization
Energy Optimal
Time Optimal
Closed-Loop
Embedded Systems
Convex Solver
Non-Linear Programming

abstract:
This research formulates and implements a novel closed-loop optimal control system that drives a train between two stations in an optimal time, energy efficient, or mixed objective manner. The optimal controller uses sensor feedback from the train and in real-time computes the most efficient control decision for the train to follow given knowledge of the track profile ahead of the train, speed restrictions and required arrival time windows. The control problem is solved both on an open track and while safely driving no closer than a fixed distance behind another locomotive. In contrast to other research in the field, this thesis achieves a real-time capable and embeddable closed-loop optimization with advanced modeling and numerical solving techniques with a non-linear optimal control problem.
 This controller is first formulated as a non-convex control problem and then converted to an advanced convex second-order cone problem with the intent of using a simple numerical solver, ensuring global optimality, and improving control robustness. Convex and non-convex numerical methods of solving the control problem are investigated and closed-loop performance results with a simulated vehicle are presented under realistic modeling conditions on advanced tracks both on desktop and embedded computer architectures. It is observed that the controller is capable of robust vehicle driving in cases both with and without modeling uncertainty. The benefits of pairing the optimal controller with a parameter estimator are demonstrated for cases where very large mismatches exists between the controller model and the simulated vehicle. Stopping performance is consistently within 25cm of target stations, and the worst case closed-loop optimization time was within 100ms for the computation of a 1000 point control horizon on an i7-6700 machine.

abstract: Thesis

abstract: Master of Applied Science (MASc)

abstract: This research formulates and implements a novel closed-loop optimal control system that drives a train between two stations in an optimal time, energy efficient, or mixed objective manner. It is deployed on a commuter vehicle and directly manages the motoring and braking systems. The optimal controller uses sensor feedback from the train and in real-time computes the most efficient control decision for the train to follow given knowledge of the track profile ahead of the train, speed restrictions and required arrival time windows. The final control implementation is capable of safe, high accuracy and optimal driving all while computing fast enough to reliably deploy on a rail vehicle.


title: THE STRESS OF BEING ON TOP: HIGH-ALTITUDE ADAPTATIONS AND PHENOTYPIC PLASTICITY OF MITOCHONDRIA IN DEER MICE

contributor:
McClelland, Grant
Scott, Graham
Biology

subject:
mitochondria
high altitude
hypoxia
cold
respirometry
muscle metabolism

abstract: Hypoxia is a major stressor at high altitudes that limits tissue oxygen availability. High altitude environments are also extremely cold which increases thermogenic demand. Small mammals living at high altitude face the competing energetic challenge of maintaining thermogenesis in a hypoxic environment that can impair aerobic ATP supply. It has been suggested that hypoxia-induced impairments in ATP synthesis capacity and cold-induced increases in thermogenic demand could be counteracted by an increase in tissue oxidative capacity and/or fuel selection. As the organelle that consumes oxygen to produce ATP, changes in mitochondrial physiology can help offset physiological impairments at high altitudes. We explored this hypothesis in North American deer mice (Peromyscus maniculatus), from populations native to high and low altitude. We compared mitochondrial volume densities, intracellular distribution, respiratory capacities, enzyme activities of the mitochondrial complexes, capillarity, and fibre-type distribution in skeletal and cardiac muscles. To examine potential changes to mitochondrial physiology at high altitudes deer mice (P. maniculatus) were acclimated to: warm (25°C) normoxia; warm hypoxia (simulated altitude of 4300m); cold (5°C) normoxia; and cold + hypoxia. In skeletal muscle, highlanders had higher mitochondrial volume densities than lowlanders, entirely due to an increased abundance of mitochondria in a subsarcolemmal location next to capillaries. Mitochondria from highland mice also had higher mitochondrial respiratory capacities and cytochrome c oxidase activity in control conditions, but these values converged after hypoxia acclimation. Cold acclimation restored pyruvate and fatty acid respiratory capacity to control levels in highland mice, which also showed an increase in mitochondrial uncoupling. Cold increased respiratory capacities in lowland mice. Acclimation to cold+hypoxia did not change mitochondrial physiology beyond cold alone and appeared to counteract the effects of hypoxia on highland mice. In cardiac muscle highland mice had higher respiratory capacities, but after hypoxia acclimation lowland mice significantly increased respiratory capacities. In response to hypoxia, highland mice increased the relative capacity to oxidize carbohydrates compared to fatty acids. Our results suggest that both highland ancestry and plasticity affect mitochondrial physiology, and likely contributes to performance at high altitudes.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)


title: Metabolic and respiratory consequences of wastewater exposure in fish

contributor:
Scott, Graham
Biology

subject:
physiology
aquatic biology
ecotoxicology
Cootes Paradise Marsh
wastewater
metabolism
respiration
fish

abstract: Wastewater effluent is a major source of aquatic pollution, discharging a continuous and complex mix of contaminants into the environment. The physiological impacts of exposure to individual contaminants are well characterized in fish, but less is known about the consequences of complex mixtures that typify wastewater effluent in the environment. This thesis explores the metabolic and respiratory effects of in situ wastewater exposure on bluegill sunfish (Lepomis macrochirus). By assessing multiple levels of biological organization, I provide evidence that wastewater exposure invoked a metabolic cost in bluegill, which was associated with physiological adjustments to enhance oxygen uptake, delivery, and utilization. These findings broaden our understanding of how fish tolerate life in effluent-dominated waters and support the emergence of metabolic and respiratory physiology as biomarkers in ecotoxicology.

abstract: Thesis

abstract: Master of Science (MSc)


title: Dimensionality Reduction with Non-Gaussian Mixtures

contributor:
McNicholas, Paul
Mathematics and Statistics

subject:
clustering
non-Gaussian
latent variables
mixture Models
categorical data
variational method

abstract: Broadly speaking, cluster analysis is the organization of a data set into meaningful groups and mixture model-based clustering is recently receiving a wide interest in statistics. Historically, the Gaussian mixture model has dominated the model-based clustering literature. When model-based clustering is performed on a large number of observed variables, it is well known that Gaussian mixture models can represent an over-parameterized solution. To this end, this thesis focuses on the development of novel non-Gaussian mixture models for high-dimensional continuous and categorical data. We developed a mixture of joint generalized hyperbolic models (JGHM), which exhibits different marginal amounts of tail-weight. Moreover, it takes into account the cluster specific subspace and, therefore, limits the number of parameters to estimate. This is a novel approach, which is applicable to high, and potentially very- high, dimensional spaces and with arbitrary correlation between dimensions. Three different mixture models are developed using forms of the mixture of latent trait models to realize model-based clustering of high-dimensional binary data. A family of mixture of latent trait models with common slope parameters are developed to reduce the number of parameters to be estimated. This approach facilitates a low-dimensional visual representation of the clusters. We further developed the penalized latent trait models to facilitate ultra high dimensional binary data which performs automatic variable selection as well. For all models and families of models developed in this thesis, the algorithms used for model-fitting and parameter estimation are presented. Real and simulated data sets are used to assess the clustering ability of the models.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)


title: THE EFFECT OF MOTIVATION AND ABILITY ON ATTITUDES TOWARDS VIRTUAL COMMUNITIES OF PRACTICE: AN ELABORATION LIKELIHOOD APPROACH

contributor:
Head, Milena
eHealth

subject:
information systems
elaboration likelihood model
technology adoption
ehealth
communities of practice

abstract:
Sharing of information between health care workers improves evidence dissemination and quality of care. One way to share information is through a community of practice (CoP), whereby members interact regularly towards a common goal. Advances in technology allow CoPs to exist virtually, removing the traditional barriers to information sharing.  Virtual CoPs have been shown to be effective, but little is known about why health care workers choose to use them — warranting further investigation.
This exploratory research consisted of 86 participants and took place in partnership with Health Quality Ontario. At the time of data collection, the organization was developing a virtual CoP for those in health care to learn from one another about quality improvement.
The research utilized the elaboration likelihood model (ELM) — a theoretical model of persuasion that posits that one’s motivation and ability determines how information is processed — to guide the study of attitude formation. ELM distinguishes between Central Route information processing, whereby one is highly motivated and able and pays attention to argument quality, and Peripheral Route processing, whereby lower motivation and ability cause one to be persuaded by peripheral messaging cues. The sustainability of resulting attitudes is influenced by the route through which information is processed.
	Higher motivation to use a virtual CoP was found to be more strongly correlated to the central route than peripheral route, as expected. Post-hoc analysis found that argument quality had the greatest overall influence on attitudes towards virtual CoPs, regardless of the user’s experience level with them. Users with more experience were also influenced by peripheral cues.
The chosen theoretical framework provided insight into the determinants of attitude formation, allowing for a better understanding of how to design and position a virtual CoP for those working in health care — a population yet to be studied through ELM.

abstract: Thesis

abstract: Master of Science (MSc)

abstract:
A community of practice (CoP) is a group of people with a shared interest who regularly interact to share knowledge and increase their expertise. Virtual CoPs use information and communications technology to support these knowledge-sharing activities, and have been shown to effectively improve knowledge utilization, but researchers have not examined them from a health care practitioner point of view.
The present research aimed to explore the factors affecting how attitudes towards virtual CoPs are formed. The elaboration likelihood model was used to guide this study and suggests that a person’s motivation and ability determine the route through which they process information and form attitudes, leading to their intention to use the system. By understanding what influences attitudes, we can better understand how to design and position a virtual CoP for health care practitioners.


title: An Exact Assessment of the Two-Stage EPI Sampling Method

contributor:
Viveros-Aguilera, Román
Shannon, Harry
Mathematics and Statistics

subject:
Expanded Program on Immunization
Rapid Survey
EPI
Household Survey
Sector Sampling
Strip Sampling
Google Maps API

abstract:
The Expanded Program on Immunization Sampling Method (known simply as EPI sampling)
is a two-stage sampling procedure originally intended for quick estimation of disease prevalence in large geographical regions. The method was developed in the 1970s and all the subsequent assessments of its performance have been conducted by simulation. In her master's thesis, Reyes (2016) studied in detail the second-stage sampling of the method by developing formulas for the exact calculation of the
household inclusion probabilities when sectors are used to identify the initial household to generate the EPI samples. The inclusion probabilities were used in turn to obtain exact mean, bias, variance and mean square error of any estimator of disease prevalence in the population. Thus, no extensive simulations are required and the results are exact rather than just estimates.

This thesis is an extension of Reyes' (2016) work. The extension is two-fold; (a) employing strips rather than sectors because they narrow the geographic area for field workers and to use strips to select the first household for the EPI sample at the secondary stage, and (b) carrying out an analysis on simulated population and sampling plans, using both stages of the EPI method. Analyzing the simulated populations showed that equal weight estimator that samples primary units with replacement with probability proportional to size (EW1) should be used when the target characteristic is thought to be spread randomly throughout the population, and the Horvitz-Thompson estimator that samples primary units systematically with replacement (HTSYS) should be used when the disease is believed to spread from a central location or through pocketing. Comparing the strip and sector sampling methods at the secondary stage using their effective areas leads to a comparative basis in which the inclusion probabilities are identical for both methods.

abstract: Thesis

abstract: Master of Science (MSc)


title: The online regulation of no-vision walking in typically calibrated and recalibrated perceptual-motor states examined using a continuous pointing task

contributor:
Lyons, James
Kinesiology

subject:
Motor Behaviour
Motor Control
Sensory Recalibration
Virtual Reality
Locomotion
Blind walking
Continuous pointing
Walking
Sensory adaptation

abstract: No-vision walking is supported in the central nervous system (CNS) by a spatial updating process. This process involves the iterative updating of a mental representation of the environment using estimates of distance traveled gleaned from locomotive kinematic activity. An effective means of examining the online regulation of this process is a continuous pointing task, which requires performers to walk along a straight-line forward trajectory while keeping their right arm straight and index finger fixated on a stationary ground-level target beside the walking path. In the current thesis, no-vision continuous pointing was examined in typically calibrated and recalibrated perceptual-motor states. Shoulder and trunk joint angles provided the basis for perceptual measures that reflected spatial updating performance and kinematic measures that reflected its underlying CNS online regulation. In the typically calibrated conditions, no-vision walking demonstrated a slight perceptual underestimation of distance traveled (Study 1). In the recalibrated conditions, no-vision walking demonstrated: a) perceptual underestimation and overestimation following adaptation periods involving walking with low and high visual gains, respectively (Study 2); and b) partial recalibration following exposures to vision and arm gains (Study 3). The latter was suggested as being impacted by task specific changes in CNS multisensory integration resulting from the development of a robust task prior and/or the altering of sensory cue weights. Importantly, this thesis used a novel trajectory parsing procedure to quantify discrete CNS perceptual updating units in the shoulder plane of elevation trajectory. The starts and ends of these updating units were consistently timed to the late left-to-early right foot swing phase of the step-cycle, regardless of perceptual-motor state. This was suggested to reflect perceptual units that were purposely timed, but indirectly mapped, to this kinematic event. The perceptual differences in Studies 1 and 2 were at least partially reflected in these units.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)

abstract: It is well understood that humans can effectively walk without vision to environmental locations up to 15 metres away. However, less is known about how these walking movements are controlled during the course of forward progression. This thesis fills this knowledge gap using a task that requires participants to walk forward along a straight path while keeping their right index finger pointed toward a ground-level target beside the walking path. The patterns of arm movements performed during this task are indicative of the control strategies used by the performer to mentally update their positions in space. One of the key contributions of this work is showing that humans perform this mental updating in a repetitive manner, and that these repetitions are consistently linked to early forward movements of the right leg. This pattern is maintained when walking without vision is performed in a variety of different contexts.


title: Thermal-Electrochemical Modeling and State of Charge Estimation for Lithium Ion Batteries in Real-Time Applications

contributor:
Habibi, Saeid
Mechanical Engineering

subject:
Battery modeling
State of charge
Thermal modeling
State of Health
THERMAL-ELECTROCHEMICAL modeling
REAL-TIME APPLICATIONS
Lithium Ion Batteries
Battery management system
heat generation model

abstract:
In the past decade, automobile manufacturers have gone through the initial adoption phase of electric mobility.
The increasing momentum behind electric vehicles (EV) suggests that electrified storage systems will play an important role in electric mobility going forward. Lithium ion batteries have become one of the most common solutions for energy storage due to their light weight, high specific energy, low self-discharge rate, and non-memory effect. To fully benefit from a lithium-ion energy storage system and avoid its physical limitations, an accurate battery management system (BMS) is required.
One of the key issues for successful BMS implementation is the battery model.
A robust, accurate, and high fidelity battery model is required to mimic the battery dynamic behavior in a harsh environment.
This dissertation introduces a robust and accurate model-based approach for lithium-ion battery management system.

Many strategies for modeling the electrochemical processes in the battery have been proposed in the literature.
The proposed models are often highly complex, requiring long computational time, large memory allocations, and real-time control.
Thus, model-order reduction and minimization of the CPU run-time while maintaining the model accuracy are critical requirements for real-time implementation of lithium-ion electrochemical battery models.
In this dissertation, different modeling techniques are developed. The proposed models reduce the model complexity while maintaining the accuracy.

The thermal management of the lithium ion batteries is another important consideration for a successful BMS.
Operating the battery pack outside the recommended operating conditions could result in unsafe operating conditions with undesirable consequences.
In order to keep the battery within its safe operating range, the temperature of the cell core must be monitored and controlled.
The dissertation implements a real-time electrochemical, thermal model for large prismatic cells used in electric vehicles' energy storage systems.
The presented model accurately predicts the battery's core temperature and terminal voltage.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)


title: Innate Immunity Evasion Through D-Amino Acid Sequestration

title: D-Amino Acid Sequestration as a Mechanism of Innate Immunity Evasion in Salmonella and Uropathogenic Escherichia coli Infections

contributor:
Coombes, Brian
Biochemistry

abstract: The innate immune system functions to limit the spread of bacteria during an infection. This is achieved through a highly complex assault on infiltrating pathogens. One such mechanism is the production of reactive oxygen species. D-amino acid oxidase is an emerging player in the innate immunity as it is capable of producing bactericidal concentrations of reactive oxygen species. Pathogens have evolved an array of strategies to protect themselves against the innate immune system. This work focusses on two bacteria relevant to human health that have evolved two distinct D-amino acid transporters to evade reactive oxygen species produced by D-amino acid oxidase. The Salmonella specific gene, DalS, was found to be co-regulated with the Salmonella Pathogenicity Island-2, a known virulence determinant. DalS is the periplasmic binding domain of a D-alanine ATP Binding Cassette transporter capable of sequestering substrate away from D-amino acid oxidase during Salmonella-neutrophil infections. This work demonstrates a novel host-pathogen interaction that enhances Salmonella survival during an infection. The second transporter, cycA, is conserved across diverse taxa and transports D-alanine and D-serine. This work determined that uropathogenic E. coli uses CycA to sequester D-serine away from DAO during ascending urinary tract infections, and moreover provides another example of how pathogens protect themselves against DAO. Together, these findings contribute to the understanding of the intricate set of virulence strategies of two pathogens that have a significant impact on human health worldwide.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)


title: Intensified Flexible Distillation Process for Multi-Period Operation

contributor:
Adams II, Thomas A.
Chemical Engineering

abstract: Canada’s aspirations towards an energy independent future mean that it can ill-afford to rest while the rest of the world pursues sustainable energy technologies and other efficient means of energy and chemical fuels production. Fortunately, the abundance of biomass—a sustainable energy resource—within Canada’s borders provides a great opportunity for those seeking to help mitigate the threat of fossil fuel induced climate change to intervene; by taking advantage of this abundant resource and using it in new and improved energy and chemicals production pathways. Our current work, therefore, derives from this notion; and in it, our objective is: the development, design, and optimization of a novel separation process for producing high purity—chemical grade—Methanol (MeOH) and Dimethyl Ether (DME) from biomass-derived syngas.Approaches surveyed often focus on designs of entirely new pieces of equipment, but our work is a take on subtly but critically improving one of the oldest and most ubiquitous pieces of process equipment: tray distillation columns. Using a novel approach for solving the optimization problem, an algorithm is furnished and this is implemented in Matlab, while all process simulations are performed in Aspen Plus. The development of a rigorous framework for designing intensified flexible distillation process for high purity DME-MeOH production is one main contribution of this work. Another major finding is that an intensified flexible process design for DME-MeOH separation for multi-period operation has lower total annualized cost compared the conventional processes. Furthermore, the proposed process shows a lower penalty for being flexible whencompared with the status quo. Although further studies on the effects of process dynamic behaviour, including on transitions and other transient characteristics, are needed, the findings so far suggest a potential for substantial life-time cost savings in new process designs for DME-MeOH separations.

abstract: Thesis

abstract: Master of Applied Science (MASc)


title: Tribochemical Interactions between a Polymer Composite and Metals

title: Investigation of Tribochemical Interactions between a PTFE Filled Composite and Common Industrial Metals

contributor:
Thompson, Michael
Chemical Engineering

subject:
Polymer Composite
Tribology
Tribochemical Interactions

abstract: An investigation of the effect of metal counterface composition on the tribological performance and behaviour of a PTFE filled polymer composite using surface analysis techniques.

abstract:
The high specific strength, chemical resistance and processability of polymer composites have made them an attractive alternative to traditional metals and ceramics in many industries. For tribological applications, polymer composites also have the ability to eliminate the need of lubricants and lower maintenance costs. The use of carbon fiber, carbon black and polytetrefluoroethylene (PTFE) are well established in the literature as effective reinforcement agents and solid lubricants respectively but not many studies have explored the tribochemical interactions that occurs during sliding. This study investigates the tribochemical interactions between a polyphenylene ether (PPE) and high impact polystyrene (HIPS) blend based composite and different metal surfaces. Four common metals used in industry were chosen for this study: carbon steel C1018, naval brass 485, Inconel 625 and stainless steel 316.
In order to isolate the effect of tribochemical interactions between the polymer composite and counterface metals, consistent pressure and velocity (PV) settings were used for all tests. Frictional forces and temperature data were recorded during testing and the wear rates were determined by weighing samples before and after testing. The polymer sand metal washer surfaces were then examined under scanning electron microscopy (SEM) and energy dispersive spectroscopy (EDS) for their PTFE surface morphology and transfer film composition, respectively. The surface roughness of both polymer and metal samples were also measured.
It was observed that tribological performance of the polymer composite was affected by the composition of the metal counterface, and each metal had a different tendency to operating in a stable and unstable state. The surface morphology of the PTFE phase and the transfer film composition on the metal washers also differed between each polymer-metal system. SEM micrographs reveal agglomeration of PTFE domains on the polymer surface and each system had a different domain size distribution and PTFE surface coverage.
The polymer-brass system was found to be the most consistent and give the most stable operations with the highest PTFE coverage on the polymer sample’s surface due to brass’ relatively high reactivity. This was explained by tribochemical reaction that occurs at the interface and the reactivity of each metal alloy. Adhesion must be high in order to enable a thicker and more uniform transfer film to adhere, which provides a smooth asperity-free surface for the polymer to slide against, resulting in a stable and low wear operation. A reactive interface allows the introduction of carboxyl groups on both the surfaces and increase electrostatic adhesion between the polymer transfer film and metal surface.  Overall, the reactivity of each metal alloy correlated well with the number of stable tests that each polymer-metal system demonstrated as well as the resulting surface coverage of PTFE.  This was taken as evidence of the tribochemical interactions.

abstract: Thesis

abstract: Master of Applied Science (MASc)

abstract: The field of friction, wear and lubrication, also known as tribology, traditionally focuses on metal and ceramic components that have high maintenance and lubrication costs. In recent years, there has been growing interest in plastic composites as a replacement material for tribological applications. The high strength, light weight, chemical resistance and self-lubricating properties of these plastic composites makes them an attractive substitute for metals and ceramics. Understanding the chemical interaction between plastic and metal during sliding is necessary to exploit their properties and performance for specific applications. In this study, a plastic composite based on a blend of polyphenylene ether (PPE) and high impact polystyrene (HIPS) filled with polytetrafluoroethlyene (PTFE), carbon black and carbon fiber was used to investigate the effects of different metals on tribological performance and behaviour. Four common metals used in industry were chosen for this study: carbon steel C1018, naval brass 485, Inconel 625 and stainless steel 316. The tribology tests conclusively showed that friction and wear results differ between polymer-metals systems, with each system displaying a stable and unstable behaviour. Surface analysis revealed that the surface PTFE morphology of the polymer composite and the transfer film composition on the metal washer also differ between metals. Tribochemical reactions and the reactivity of each metal explained the results and behaviour of each polymer-metal system.


title: Investigating Alternative Testing Techniques for Evaluating the Environmental Stress Cracking Resistance of Polyethylenes in Contact with Ageing Fluids

subject:
polyethylene
slow crack growth
ESC
ESCR
environmental stress cracking
brittle fracture
igepal
biodiesel
polyolefins
HDPE
plastic failure

abstract:
Environmental stress cracking (ESC) is a significant problem that has plagued the plastics industry since its discovery nearly 70 years ago. The accelerated brittle failure brought about when a stressed polymer comes in contact with an aggressive environment can happen suddenly with destructive results. Many classes of polymers are susceptible to this type of slow crack growth; however special emphasis has typically been placed on polyolefins due to their wide range of working environments, market dominance and their seemingly chemical resistance. Much research has been focused on formulating environmentally resistant materials, while the evaluation techniques for gauging environmental stress cracking resistance (ESCR) seem to have been left behind. This research focuses on developing a reliable testing technique for evaluating the ESCR of polyethylene resins.
Passive acoustic monitoring was adapted to an industrially accepted ESCR test in an attempt to hear polymer damage before it was visually apparent. It was discovered that the low energy released during the early stages of damage and excessive background noise masked passive signals, making this method of evaluation impractical. Alternatively, active ultrasonic monitoring through velocity and attenuation measurements was investigated to see if probing techniques could be used to detect structural damage. Active ultrasonic monitoring of static and tensile stressed samples were able to differentiate plasticization after ageing, however no indication of ESCR properties could be inferred.
	A novel forced based monitoring system was developed in response to the acoustic testing techniques. Force monitoring was able to provide useful information regarding the failure cycle of ESC and the acquired profiles could describe a failure onset time. Several ageing environments were also tested with force monitoring and a traditional ESCR test to reveal the stress cracking ability of biodiesel, an important finding.

abstract: Thesis

abstract: Master of Applied Science (MASc)

abstract: Accelerated failure of stressed plastics can occur upon exposure to fluids through a phenomenon known as environmental stress cracking (ESC). The following research outlines the development of a novel testing technique to gauge a material’s environmental stress cracking resistance (ESCR). Adaption of passive acoustics to an existing stress cracking test was unable to provide any indication of ESCR, however the use of active ultrasonics was able to show sample plasticization. A novel forced based measuring technique was found to uniquely map the failure progression of a sample undergoing ESC, providing valuable information for understanding the phenomenon. Additional testing was also completed on various environmental fluids to reveal biodiesel’s ability to provoke ESC, an important observation.


title: Optimizing the large-scale production of Saw1 and the Saw1-Rad1-Rad10 nuclease complex for structural studies

contributor:
Guarné, Alba
Biochemistry and Biomedical Sciences

subject: DNA repair

subject: Recombinant protein expression and purification

subject: Single strand annealing

subject: structure selective nuclease

abstract: Yeast Rad1-Rad10 is a structure specific nuclease that processes branched double-strand break (DSB) repair intermediates; the persistence of which can impede normal DNA metabolism. The single strand annealing (SSA) mechanism of DSB repair acts when homologous repeats flank both sides of the DSB. End resection from the 5′ ends of the break exposes complementary sequences at the flanking repeats, which are annealed to form 3′ non-homologous flap structures. Saw1 recruits Rad1-Rad10 recruits to these 3′ non-homologous flaps, where Rad1-Rad10 incises the DNA and removes the flap. Saw1 has affinity towards branched DNA structures and forms a stable complex with Rad1-Rad10. The mechanism of both structure specific recruitment and nucleolytic activity of the Saw1-Rad1-Rad10 complex is currently unknown. To study this nuclease complex, we need to produce large quantities of pure, stable, and active recombinant protein. Using dynamic light scattering (DLS) and differential scanning fluorimetry (DSF)-based high throughput thermal stability assays, we have developed a method for large-scale production of recombinant Saw1. This optimized method has increased the stability and yield of protein, thereby allowing for future biochemical investigation of Saw1. Similarly, we have optimized the large-scale production of the higher molecular-weight complex (Saw1-Rad1-Rad10) and improved the homogeneity of the recombinant complex. We have also biochemically characterized the minimal branched DNA substrates for both Saw1 and Saw1-Rad1-Rad10. This work allows for biochemical investigation into the molecular mechanism of eukaryotic 3′ non-homologous flap removal during SSA.

abstract: Thesis

abstract: Master of Science (MSc)


title: MODELLING AND DESIGN OF ELECTRIC MACHINES AND ASSOCIATED COMPONENTS FOR MORE ELECTRIC VEHICLES

contributor:
Schofield, Nigel
Electrical and Computer Engineering

subject:
electric machines
electric vehicles
energy storage systems
power-train
machine design

abstract:
Concerns with emissions, CO2 in particular, and energy resource associated with conventional internal combustion engine (ICE) vehicles is motivating a shift towards more electrified power-trains for road transportation, as well as other transportation applications. The modelling, characterization and design of electrified power-trains, including energy storage technologies, traction machine technologies and their associated power electronics, are discussed in this thesis.
Port cranes are a special case of land transportation encompassing many of the power-train objectives found common with road based hybrid electric vehicles; here a port crane system is studied. The power flow for a typical crane loading cycle is analyzed and the value of the energy consumption and saving potential is calculated. Then alternative energy storage applications are considered for hybrid power-train configurations employing diesel engine generators, battery packs, supercapacitors (SCs), and flywheels. A hybrid rubber tyred gantry crane (RTGC) power-train model with power management is developed and the battery-SC hybrid energy storage systems are designed for both short- and long-period operation.
The Induction machine (IM) is a popular technology for traction applications. Although many publications discuss IM design to realize a traction torque-speed characteristic, the IM model is studied to determine the main parameters impacting on the machine performance capability at constant torque and extended speed. Based on the model analysis, an IM design procedure for traction applications is proposed which improves machine performance capability. The machine design parameters are normalized in per unit form and hence the proposed design procedure is applicable across different ratings.
In the specification and definition of vehicle power-trains, it is common (in industry) to quote data at specific operating conditions, for example, full or fixed battery terminal voltage and system temperature. The interactive influence between energy storage devices and the vehicle system is investigated. Using the all-electric Nissan Leaf power-train as a reference example, the Nissan Leaf traction system is evaluated and performance assessed by considering DC-link voltage variation from battery full state of charge (SoC) to zero SoC and temperature variations typical of an automotive application, showing that the system stated performance is reduced as battery SoC decreases. An alternative traction machine design is proposed to satisfy the vehicle target performance requirements over the complete variation of SoC. The vehicle power-train is then modified with the inclusion of a DC/DC converter between the vehicle battery and DC-link to maintain the traction system DC-link voltage near constant. A supercapacitor system is also considered for improved system voltage management. The trade-offs between the actual Nissan Leaf power-train and the redesigned systems are discussed in terms of electronic and machine packaging, and mitigation of faulted operation at high speeds.
Using the Nissan Leaf interior permanent magnet (IPM) machine as the benchmark machine, an example surface permanent magnet (SPM) machine, with same design constraints, is designed and compared with the benchmark IPM machine. The phase voltage distortion of IPM and SPM machines are compared and the mechanisms are revealed. An alternative machine topology with pole shoe rotor is proposed for reduction of machine peak current rating and voltage distortion. The pole shoe topology is common in industrial variable speed drives employing constant torque regimes, but not for traction. Here, the machine with pole shoe rotor is designed to achieve traction performance. The pole shoe concept for vehicle traction is significantly different from existing practice in the electric and hybrid electric automotive industry and thus departure in standard design is a contribution of this thesis.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)


title: Development of the GRADE for patient values and preferences evidence

contributor:
Schünemann, Holger
Health Research Methodology

subject:
patient values and preferences
GRADE
outcome importance
quality of evidence
systematic review
guideline development

abstract:
Background and objectives:
Incorporating patient values and preferences as an essential input for decision-making has its potential merits in respecting the autonomy of patients, improving adherence and clinical outcomes. The Grading of Recommendations Assessment, Development and Evaluation (short GRADE) working group conceptualizes patient values and preferences as “the relative importance patient place on the main outcomes”. The objectives of this thesis include: 1) to provide an overview of a process for systematically incorporating values and preferences in guideline development; 2) to conduct a systematic review on outcome importance studies, using chronic obstructive pulmonary disease (COPD) as an example; 3) to provide guidance on how to assess certainty of evidence describing outcome importance using the GRADE criteria.
Methods:
We performed systematic reviews, asked clinical experts to provide feedback according to their clinical experience, and consulted patient representatives to obtain information about relative importance of outcomes in a new national guideline program. We conducted a systematic review to summarize the COPD related relative importance of outcome studies. We used a multi-pronged approach to develop the guidance for assessing certainty of evidence about relative importance of outcome and values and preferences. We applied the developed GRADE approach to relative importance of outcome systematic review examples and consulted the stakeholders in the GRADE working group for feedback.
Results and conclusion: We provided an empirical strategy to find and incorporate values and preferences in guidelines by performing systematic reviews and eliciting information from guideline panel members and patient representatives. However, we identified the need for researches on how to assess the certainty of this evidence, and best summarize and present the findings. In our comprehensive systematic review project on COPD patient values and preferences we demonstrated the utility of rating evidence in systematic reviews of outcome importance.
We describe the rationale for considering GRADE domains for the evidence about the importance of outcomes. We propose the assessment of the body of evidence starts at “high certainty”, and rate down for serious problems in GRADE domains including risk of bias, indirectness, inconsistency, imprecision and publication bias. Specific to risk of bias domain, we propose a preliminary consideration for risk of bias. The sources of indirectness for relative importance of outcome evidence include indirectness from PICO (population, intervention, comparison, and outcome) elements, and methodological indirectness. As meta-analyses are uncommon when summarizing the evidence about relative importance of outcome, inconsistency and imprecision assessments are challenging. Inconsistency arises from PICO and methodological elements that should be explored. The width of the confidence interval and sample size should inform judgments about imprecision. We also provide suggestions on how to detect publication bias based on empirical information. Finally, we also discuss the applicability of domains to rate up the certainty.
We develop the GRADE approach for rating risk of bias, indirectness, inconsistency, imprecision and other domains when evaluating a body of evidence describing the relative importance of outcomes. Our examples should guide users and provide a basis for discussion and further development of the GRADE system.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)


title: CHARACTERIZING THE EXPRESSION AND FUNCTION OF MESENCEPHALIC ASTROCYTE-DERIVED NEUROTROPHIC FACTOR IN CAENORHABDITIS ELEGANS

contributor:
Gupta, Bhagwati
Neuroscience

subject:
Neurotrophic Factor
C. elegans
MANF
CDNF

abstract: Neurotrophic factors are proteins involved in the maturation, differentiation and survival of neurons.  Due to their neuroprotective properties, they have been regarded as potent candidates for the treatment of neurodegenerative diseases. Recently, a novel family of neurotrophic factors was discovered comprising mesencephalic astrocyte-derived neurotrophic factor (MANF) and cerebral dopamine neurotrophic factor (CDNF). These factors have been shown to protect against the degeneration of nigrostriatal dopaminergic neurons in mammalian models of Parkinson's disease, however their neuroprotective mechanisms of action are not yet understood. Although distinct in vertebrates, MANF and CDNF constitute a single homolog in invertebrates. In the present study, we have characterized the in vivo expression and function of the C. elegans homolog manf-1. We have shown that manf-1 is not essential for neuronal development, however when knocked down, mutants exhibit enhanced age-related dopaminergic neuronal degeneration accompanied by an increase in the endogenous ER stress response. Loss of manf-1 function also results in enhanced alpha-synuclein expression and aggregation, a pathological hallmark of Parkinson’s disease.

abstract: Thesis

abstract: Master of Science (MSc)


title: Towards the Application of Software Architectures in Multi-Agent Systems

contributor:
Maibaum, Thomas
Computer Science

subject: application of software, architectures, multi-agent systems, design paradigm

abstract:
 Software Architecture is a concept that arose during the last two decades as a consequence of the need for a structured design at an early stage. Software Architecture is defined as a pattern of interconnected components satisfying some structural rule. Software architectures are widely used in many types of systems; Multi-Agent Systems should not be an exception. Multi-Agent Systems have emerged as a design paradigm for large and distributed systems. They are composed of autonomous elements that work together in order to pursue a common goal. They are mostly used in Electronic Commerce, Human-Computer
Interfaces, and so on.

 In this research, we investigate the state of the art of Software Architectures in the Multi-Agent Systems field, showing that, generally Multi-Agent Systems do no use the software architecture concept properly and, when they do, they do not
show specific architectures for Multi-Agent Systems. The approach followed is based on the analysis of six case studies, which are implemented applications that have been published in some of the most important conferences in the area. Additionally we show that, based on the initial design of each case and existing architectural patterns, it is possible to impose a software architecture on each case.

 Furthermore, we analyze the way that the term "software architecture" is used in the Multi-Agent Systems literature, showing that, usually, it refers to abstract architectures proposed in standards and frameworks or to an initial design in a system. In addition we clarify related concepts, such as reference architecture, reference models, architectural patterns and design patterns. Finally, we do an exhaustive comparison of the case studies, which aims to highlight commonalities and differences. The objective of this comparison is to analyze if they share a similar architecture that can be reused in more cases and to show how specific properties of Multi-Agent Systems affect in the design of an architecture.

abstract: Thesis

abstract: Master of Science (MSc)


title: Global Routing in VLSI: Algorithms, Theory, and Computation

contributor:
Deza, Antoine
Computing and Software

subject: global routing, VLSI, Algorithms, Theory, Computation, design, optimization

abstract:
 Global routing in VLSI (very large scale integration) design is one of the most challenging discrete optimization problems in computational theory and practice. In this thesis, we present a polynomial time approximation algorithm for the global routing problem based on an integer programming formulation. The algorithm features a theoretical approximation bound, while ensuring all the routing demands are concurrently satisfied.

 We provide both a serial and a parallel implementation, as well as develop several heuristics to improve the quality of the solution and reduce running time. Our computational tests on a well-known benchmark set show that, combined with certain heuristics, our new algorithms perform very well compared with other integer programming approaches.

abstract: Thesis

abstract: Master of Science (MSc)


title: Comparison of Prediction Intervals for the Gumbel Distribution

contributor:
Hoppe, Fred M.
Statistics

subject: prediction interval, Gumbel Distribution, Bayesian Prediction, Ancillary statistic

abstract:
 The problem of obtaining a prediction interval at specified confidence level to contain k future observations from the Gumbel distribution, based on an observed sample from the same distribution, is considered. An existing method due to Hahn, which is originally valid for the normal, is adapted to the Gumbel case. Motivated by the equivalence between Hahn's prediction intervals and Bayesian predictive intervals for the normal, we develop Bayesian predictive intervals for the Gumbel in the case where the scale parameter b is both known and unknown. Furthermore, we perform comparison of Hahn's and Bayesian intervals. We find that the Bayesian is better in the b known case, while Hahn and Bayes perform about the same in the other case when b is unknown. We then consider the maximum of the Hahn's and Bayesian predicted lower limits which is shown to be a better predictor when b is unknown.
All the discussions are based on Monte Carlo simulations. In the end, the results are
applied to Ontario Power Generation data on feeder thicknesses.

abstract: Thesis

abstract: Master of Science (MSc)


title: Verification of Haskell Type Classes

contributor:
Kahl, Wolfram
Computing and Software

subject: verification, Haskell type classes, programming language, QuickCheck, functions

abstract:
 The Haskell programming language uses type classes to deal with overloading. Functions
are overloaded by defining some types to be instances of a class. A meaningful instance should satisfy the invariants of the class.

 In this thesis we present one method to validate the type instances of classes informally, and another one to verify them in a formal way.

 The first method uses QuickCheck, which is an automatic testing tool for
Haskell programs. We introduce how to specify the properties of type classes in QuickCheck by some examples, and I also present testing for Haskell standard types and classes.

 The second method I adopted uses the theorem prover Isabelle/HOL. To facilitate the usage of Isabelle/HOL for Haskell programmers, I define a set of translation rules from Haskell programs to Isabelle/HOL, and design a simple automatic translating tool based on those rules. Logical differences between Haskell and Isabelle/HOL need to be considered in the translation. For example Isabelle/HOL is not suitable to describe the semantics of lazy evaluation and of Haskell functions that are non-terminating. I also prove some type instances to illustrate how the properties are verified in Isabelle/HOL.

abstract: Thesis

abstract: Master of Applied Science (MASc)


title: Lempel-Ziv Factorization Using Less Time and Space

contributor:
Smyth, William F.
Computing and Software

subject: Lempel-Ziv, factorization,string, data structure, algorithm

abstract:
 For 30 years the Lempel-Ziv factorization LZx of a string x = x[1..n] has been a
fundamental data structure of string processing, especially valuable for string compression
and for computing all the repetitions (runs) in x. When the Internet came in, a huge need for Lempel-Ziv factorization was created. Nowadays it has become a basic efficient data transmission format on the Internet.

 Traditionally the standard method for computing LZx was based on O(n)-time processing of the suffix tree STx of x. Ukkonen's algorithm constructs suffix tree online and so permits LZ to be built from subtrees of ST; this gives it an advantage, at least in terms of space, over the fast and compact version of McCreight's STCA [37] due to Kurtz [24]. In 2000 Abouelhoda, Kurtz & Ohlebusch proposed a O(n)-time Lempel-Ziv factorization algorithm based on an "enhanced" suffix array - that is, a
suffix array SAx together with other supporting data structures.

 In this thesis we first examine some previous algorithms for computing Lempel-Ziv factorization. We then analyze the rationale of development and introduce a collection of new algorithms for computing LZ-factorization. By theoretical proof and experimental comparison based on running time and storage usage, we show that our new algorithms appear either in their theoretical behavior or in practice or both to be superior to those previously proposed. In the last chapter the conclusion of our new algorithms are given, and some open problems are pointed out for our future research.

abstract: Thesis

abstract: Master of Science (MSc)


title: DynaComm: The Extension of CommUnity to Support Dynamic Reconfiguration

contributor:
Maibaum, Tom
Computing and Software

subject: Dynacomm, commUnity, dynamic reconfiguration, architecture description languages, interaction pattern

abstract:
 Architecture Description Languages were developed to support the abstract level of software structuring that is the subject matter of software architecture. CommUnity is an ADL built on co-ordination principles and a categorical framework to support the composition of specifications of components to form the system's specification. However, an important problem of CommUnity is the lack of support for specifying the system's architectural changes in both the set of components and the connections between them.

 This thesis presents DynaComm, an extension of CommUnity to support hierarchical design and dynamic reconfiguration of component based systems. Several new language constructs are introduced into DynaComm: subsystems are coarse grained components which are considered as the basic unit for the construction of systems, connectors encapsulate a component interaction pattern that can organize the possibly complicated interactions between the components
of a subsystem. We also propose the idea of interface manager to solve the problem of incorrectly synchronized actions in CommUnity, and the concept of population manager to manage the live instances of components in a subsystem, through which we can model potentially complicated dynamic reconfigurations in a system.

 To use the semantics of CommUnity in defining the semantics of DynaComm, a "normalization" technique is introduced to transform the parameterized (indexed) actions into "normal" actions of CommUnity and reduce the specification of connectors and subsystems to flat CommUnity designs, so that we can derive the system's semantics in a certain state.

 Two illustrative examples, fault-tolerant dynamic client-server and vending machine systems, are also given to show the usage of DynaComm in modeling complicated and dynamic systems.

abstract: Thesis

abstract: Master of Science (MSc)


title: Selection of Video Descriptors: Generating Compact Descriptor Sets for Video Pairwise-Matching

contributor:
CHEN, JUN
Electrical and Computer Engineering

subject:
persistent descriptors
SIFT descriptors
video-content matching

abstract:
This thesis presents several descriptor selection schemes for video content pairwise-matching tasks. Those proposed schemes attempt to leverage two significant properties of videos, temporal correlation and motion information.

Aiming to find an efficient and descriptive representation for a video sequence, the concept of descriptor persistency is defined. Those descriptors that satisfy this definition are called persistent descriptors. In order to exploit descriptor persistency, an encoder is proposed.

The proposed encoder consists of five main components. First, keyframe labelling is introduced to reduce complexity and ensure a reasonable size of persistent sets. After that, persistent descriptor detection is performed on each group of pictures (GOP) separately. The second component is the standard SIFT descriptor extraction. The
third part is to identify persistent descriptors from each GOP, called persistent descriptors extraction. In this stage, three different methods are proposed: The direct method and two approximation approaches. Persistent descriptors selection, which is the fourth stage, is carried out to control the size of the persistent set. For this stage, three selection methods are proposed. All of them attempt to utilize the motion information to select more descriptive descriptors among all the persistent descriptors in the GOP. In order to perform pairwise-matching, in this thesis, a simple but efficient pairwise-matching method is proposed.

Experiments are carried out to evaluate the performance of the proposed schemes. The datasets used for performance evaluation are subsets from the categories that describe in [1]. Two metrics de ned in [2], namely false positive rate (FPR) and true positive rate (TPR), are used for the performance evaluation.

abstract: Thesis

abstract: Master of Applied Science (MASc)