VictorJuiz/thesis huggingface dataset:
Molecular Phylogenetics of Nav1.4a and Kir2.5 in the Neotropical Electric Knifefish family Hypopomidae (Osteichthys: Gymnotiformes)

Electric fishes possess electric organs that they use to electrolocate and communicate. The rate and frequency of electrical discharges are affected by ion channels. In this study, I sequence two genes that likely play key roles in the generation of electric organ discharges (Nav1.4a and Kir2.5) and test their utility as phylogenetic markers in the family Hypopomidae. In addition, I concatenate these two genes with cyt b and RAG2 to assess species relationships within Hypopomidae using parsimony and Bayesian analyses. Both Nav1.4a and Kir2.5 exhibit sufficient interspecific variation to assess species relationships, and the four genes produce concordant phylogenetic patterns. Ion channel genes are therefore useful markers for electric fish phylogenetics.

Keywords: Electric organ
Gymnotiform
Hypopomidae
Interspecific variation
Kir2.5
Nav1.4a
Advisor: Lovejoy, Nathan R.
Diversity and Ecological Structure of Northern Biting Flies

Contemporary climate change disproportionately impacts northern environments. Understanding these impacts requires knowledge of the ecological structure (e.g. diversity, abundance and distribution) of resident species. Biting flies are among the best-known groups of insects in northern Canada and are excellent sentinels for environmental change. The goals of this thesis are to determine how climate and geographical history affect the ecological structure of black flies and mosquitoes. Assessment of large-scale macroecological patterns revealed contrasts between Arctic and southern assemblages, while highlighting the importance of geographic history in structuring assemblages. Finer-scale sampling and analysis were used to assess the impacts of contemporary climate change on species ranges. A critical threshold temperature for the presence of biting species of black flies was found that approximates minimum requirements for flight and blood-feeding. Finally, mitochondrial DNA markers allowed the assessment of cryptic diversity in a widely distributed assemblage of northern black flies of the genus

Advisor: Currie, Douglas C
The Impact of Ontario's Bariatric Network on Health Services Utilization following Bariatric Surgery

In 2009, the Ontario Bariatric Network (OBN) was created to address the increasing demand for out-of-country bariatric services. This study evaluated the impact of the OBN on postoperative hospital services use among Ontario residents who received bariatric surgery. A retrospective, before-and-after study was conducted. All Ontario residents who underwent funded first-time bariatric surgery were included. Hospital services use within one year following surgery was compared between the 3-year periods before (2007-2009) and after (2010-2012) the OBN. A total of 5,617 and 6,896 patients received bariatric surgery before and after the OBN, respectively. After adjustment, the OBN was associated with fewer postoperative hospital services (RR 0.83, 95%CI 0.78-0.89, P

Keywords: Bariatrics
Ontario
Outsourcing
Program
Surgery
Advisor: Urbach, David
Efficiency Enhancement Techniques in Integrated Tri-mode DC-DC Converters

This thesis presents a tri-mode dc-dc converter that can operate in buck, boost and buck-boost configuration. A power transmission gate is implemented in the converter as the high side driver of the H-bridge output stage. A one-step dead-time correction technique is also implemented based on a previous work of buck converter topology. This tri-mode converter is designed to use the lithium-ion battery as input voltage source (2.7 to 4.2V) and provide an output voltage from 1 to 5V with an output current of up to 0.5A. The switching frequency is fixed at 1.5MHz. This converter combines different efficiency enhancement techniques such as power transmission gate, one-step dead-time correction and segmented power devices on one chip which increases the complexity of integrated circuit implementation. A peak efficiency of 93% is observed in the boost mode. A further improvement of 3.3% in the peak efficiency is achieved with dead-time correction.

Keywords: Buck-boost
DC-DC converters
Efficiency enhancement
SMPS
Tri-mode
Advisor: Ng, Wai Tung
A Dual-engine Fetch/Compute Overlay Processor for FPGAs

High-Level-Synthesis (HLS) tools translate a software description of an application into custom FPGA logic, increasing designer productivity vs. Hardware Description Language (HDL) design flows. Overlays seek to further improve productivity by allowing the designer to target a software-programmable substrate instead of the underlying FPGA, raising abstraction and reducing application compile times. We propose a highly configurable dual-engine, fetch/compute overlay processor which is designed to achieve high throughput per unit area on data-parallel and compute intensive floating-point applications. The fetch component is newly proposed as part of this work. For the compute component, we use an improved version of the TILT overlay processor originally developed by Ovtcharov and Tili. As part of our evaluation, we rigorously compare the performance, area and productivity enabled by our proposed architecture to that of Altera's OpenCL HLS tool.

Keywords: FPGA
HLS
OpenCL
Overlay
Processor
Scheduling
Advisor: Betz, Vaughn
Steffan, Greg
The Synthesis and Reactivity of Highly Electrophilic Phosphonium Cations

Main group Lewis acids are used in a variety of Lewis acid-mediated transformations and as co-catalysts for polymerization reactions. In recent years, group XIII Lewis acids such as BF3, AlCl3, and B(C6F5)3 have been under active investigation for their catalytic applications. Extending this chemistry to group XV elements, our group recently showed that the phosphonium cation, [(C6F5)3PF][B(C6F5)4] displayed significant Lewis acidity. [(C6F5)3PF][B(C6F5)4] was shown to perform catalytic hydrodefluorination of fluoroalkanes; hydrosilylation of alkenes, ketones, imines and nitriles; and transfer hydrogenation of olefins. Similar reactivity was observed for [(SIMes)PFPh2][B(C6F5)4]2, which acquires its Lewis acidity from dicationic charge rather than perfluorinated substituents. Herein, we describe our efforts towards hydrogen activation by [(C6F5)3PF][B(C6F5)4], especially for hydrogenation of imines. Furthermore, the facile synthesis of a library of bis-phosphonium systems and their applications in Lewis acid-mediated catalysis are discussed. The synthesis of a chiral bis-phosphonium which may have applications in asymmetric catalysis is also described.

Keywords: bis-fluorophosphonium cations
chiral bis-phosphonium
electrophilic phosphonium cations
Group XV Lewis acids
hydrogen activation
main group catalysis
Advisor: Stephan, Douglas W.
Exploring Tetracoordinate Silicon Lewis Acids for Frustrated Lewis Pair Chemistry

Although hundreds of papers have been published on frustrated Lewis pair (FLP) chemistry since 2006, only a small number of them have examined the use of silicon as a Lewis acid. Herein, we detail our efforts in employing tetracoordinate silicon Lewis acids (SLAs) in FLP chemistry. The synthesis of SLAs in the forms R4-nSi(OSO2CF3)n (n= 1, 2), R3SiN(SO2CF3)2, and RSi(C6F5)3 is described as well as investigations into their reactivity with a variety of small molecules. Silyl triflates are shown to activate carbon dioxide when paired with a secondary amine base to yield silyl carbamates. Sequestration of CO2 by silyl triflates and triflimides with trialkylphosphines is also described, as well as investigations into CO2 reduction.

Keywords: Carbon Dioxide Activation
Frustrated Lewis Pairs
Inorganic Chemistry
Lewis Acid
Silicon Lewis Acids
Advisor: Stephan, Douglas W
Occupational Stress in Animal Shelter Workers

There is a dearth of research focusing broadly on occupational stressors experienced by animal shelter workers. The present study aimed to classify aspects of shelter work that employees report as stressful and determine whether they fit with current perspectives on generic occupational stress. The sample consisted of 22 female adults employed in a variety of positions at shelters in Canada and the United States. A semi-structured interview used prompts based on current occupational stress literature and allowed for exploration of unprompted topics of workplace stress. Qualitative analysis of the data revealed 17 stressor categories, six of which were identified as shelter specific stressor categories. Evidence of trauma was not observed in the data. This study supports the contention that stressors exist in shelter work beyond euthanasia and that current models of occupational stress may be insufficient for describing the experiences of animal shelter workers.

Keywords: animal-shelter
compassion fatigue
human-animal bond
occupational stress
secondary traumatic stress
Advisor: Schneider, Margaret
Characterization of Thin Film (K,Na)NbO3 for Piezoelectric MEMS Actuators with Applications to Auto-Focus Systems of Hand-Held Devices

A thin film piezoelectric MEMS actuator is designed and simulated to be used as the actuation mechanism of an auto-focus system of a camera phone. The proposed actuator is capable of moving a 4mg micro-lens by 79μm under an applied voltage of 40V. A microfabrication recipe is developed in order to fabricate the actuator using MEMS technology. To reduce negative environmental impacts the lead-free piezoelectric material potassium sodium niobate (known as KNN) is selected due to its relatively high piezoelectric constants. Thin films of KNN are RF sputtered at room temperature and subsequently annealed at high temperature to achieve films with a proper crystal structure. In order to reduce fabrication costs, a highly doped silicon wafer is used as both the structural layer and the bottom electrode, which eliminates the need to deposit a metal film. The films are characterized in terms of crystal structure, stoichiometry, microstructure and electrical properties.

Keywords: Actuator
Lead free
MEMS
Piezoelectric
Thin film
Advisor: Sinclair, Anthony
Ben Mrad, Ridha
The Impact of Secondary Traumatic Stress and Burnout on Mental Health Professionals' Intimate Relationships

Previous research has demonstrated that experiences at work carry over into and affect family life. It has been suggested that the unique nature of the mental health profession holds a particular susceptibility to work-related spillover. Nonetheless, very limited empirical research exists regarding the impact of work stressors in this domain on the interpersonal relationships of those serving it. The study hypothesized that mental heath professionals with higher levels of burnout and secondary traumatic stress would also report disturbances in their personal relationships. Self-care activities and social support were explored as related variables. Results demonstrated significant correlations such that higher levels of burnout and secondary traumatic stress were associated with more destructive relationship conflict behaviours, and lower levels of relationship satisfaction, social intimacy, and perceived social support. Engagement in self-care activities was inversely related to burnout and secondary traumatic stress, and positively associated with social and intimate relationship functioning.

Keywords: Burnout
Mental Health Professionals
Secondary Traumatic Stress
Self-Care
Advisor: Chen, Charles P
Intersections of Cultural Identity in Aboriginal Youth and Employment Outcomes

AbstractMany Aboriginal youth leave their communities to pursue work opportunities in urban areas, but statistics imply there is a pervasive problem Aboriginal youth are facing in terms of securing employment, despite programs and policies which have been designed to increase Aboriginal youth employment rates (Dwyer, 2003; White Maxim, Gyimah, 2003). Previous research examining Aboriginal youth employment has neglected to include the perspectives of Aboriginal youth regarding the barriers they face when seeking employment. Even less research has been dedicated to exploring the role cultural identity plays in an Aboriginal youth's employment experiences. This thesis utilized qualitative methodology to interview and explore the employment narratives of ten urban Aboriginal youth. The results identified four major themes and several meta-themes regarding barriers to successful employment, the role of cultural identity and the hopes for future.

Keywords: Aboriginal youth
Cultural identity
Employment
work identity
Advisor: Stewart, Suzanne L
Targeted Dynamic Analysis for Android Malware

The identification and analysis of Android malware involves either static or dynamic program analysis of the malware binary. While static analysis has good code coverage, it is not as precise due to the lack of run-time information. In contrast, because Android malware is often bundled with applications that have legitimate functionality, dynamic analysis can take a long time to find and analyze the small amount of code implementing the malicious functionality. We propose IntelliDroid, a tool that combines the advantages of both static and dynamic analyses to efficiently analyze suspicious behavior in Android applications. A lightweight static phase identifies possible malicious behavior and gathers information to generate inputs that can dynamically exercise that behavior. IntelliDroid overcomes several key challenges of analyzing Android malware and when evaluated on 30 instances of malicious behavior, IntelliDroid successfully identifies the behavior, extracts path constraints, and executes the malicious code in all but one case.

Keywords: android
constraint solving
dynamic analysis
malware
program analysis
static analysis
Advisor: Lie, David
The Cinema of Leakage: Student Movements in Japan, Subjectivity and the Thinking Cinema of Oshima Nagisa

Japanese cinemas that were produced under the umbrella term of New Wave marked a new regime of images that resonated with the political frustration of the student activists of the 1950s and 1960s. This thesis is a detailed exploration of the relationships between the cinematic form and narrative, and political representations of this time frame, and an appeal to the thinking power of cinema to look at the historical problematics of political and media representations of the Japanese student movements.

Keywords: Cinema
Deleuze
Japanese
New Wave
Oshima Nagisa
Post-structuralist
Advisor: Cazdyn, Eric
The Effects of Bisphosphonates on the Development of Glucocorticoid-induced Osteoporosis in a Mouse Model of Duchenne Muscular Dystrophy

Duchenne Muscular Dystrophy (DMD) is a disease of progressive muscle inflammation and weakness. Glucocorticoids delay muscle damage but lead to loss of bone mineral and increased bone fragility. In this study, C57BL10ScSn-Mdx mice (Mdx), a commonly used animal model for DMD, received continuous glucocorticoid or placebo treatment from 5 to 13 weeks of age. Pamidronate, a bisphosphonate, was given for the first two weeks of glucocorticoid therapy in some mice to ameliorate glucocorticoid-induced bone loss. Mice treated with glucocorticoids lost cortical bone while those treated with both glucocorticoids and bisphosphonates showed improved cortical bone. Trabecular bone mass was not lost with glucocorticoid treatment, and was remarkably increased in the glucocorticoids and bisphosphonate treated Mdx mice. Muscle function was improved by glucocorticoid treatment with or without pamidronate. Thus, early bisphosphonate treatment was demonstrated to ameliorate glucocorticoid-induced cortical bone loss without any negative effects on dystrophic muscles in growing Mdx mice.

Keywords: bisphosphonates
bone biology
glucocorticoids
growth
mouse model
muscular dystrophy
Advisor: Mitchell, Jane A
Grynpas, Marc D
Regulation of BTRC by Gain-of-function TP53 Mutation(s) in Cancer Cells

Mutation or loss of TP53 has been detected in more than 50% of all human tumours. Gain-of-function (GOF) TP53 mutations have been linked to metastasis, altered metabolism, and drug resistance. Cancer patients carrying GOF TP53 mutations in their tumours respond poorly to standard of care treatments and have a worse prognosis. In my Master's thesis, I have focused on understanding the relationship between a frequently observed mutation of TP53 (TP53R248W), and BTRC, an E3 ubiquitin ligase with functions impinging on cell cycle, morphology and metabolism. I observed a correlation between BTRC protein expression and TP53 genotype across a panel cancer cell lines. Additionally, I observed that TP53R248W-mediated regulation of BTRC expression is dependent on a post-transcriptional mechanism, likely involving more than one micro-RNA. In conclusion, I present a model describing the regulation of BTRC by TP53, which may have implications for targeted strategies in cancers harboring GOF TP53 mutations.

Keywords: AKT
BTRC
Cancer
Metabolism
Mir-195
P53
Advisor: Moffat, Jason
Design of Huygens' Metasurfaces for Refraction and Focusing

The systematic design of unit cells for Huygens' metasurfaces is presented here. The Huygens' metasurface implements collocated electromagnetic boundary conditions enforcing the electric and magnetic surface currents of the equivalence principle. This provides the flexibility necessary for efficient interfacial beamforming applications. Furthermore, the boundary condition nature permits achieving this in an electromagnetically thin profile. This concept and its design procedure are verified through application to refraction and Gaussian-beam to Gaussian-beam focusing. The Huygens' metasurfaces presented herein are printed on two bonded boards instead of many stacked, interspaced layers, and can be manufactured using standard PCB fabrication techniques. This simplifies the fabrication, and allows the design to be scaled to higher frequencies. These two bonded boards implement a single, collocated, sub-wavelength array of electric and magnetic dipoles. Furthermore, in contrast to traditional frequency-selective surfaces and transmitarrays, which are on the order of a wavelength thick, these designs are only a tenth of a wavelength thick.

Keywords: Huygens' source
Metasurface
Transmission line
transmitarray
Advisor: Eleftheriades, George V
Xenogeneic Silencer MvaT Differs in its DNA Binding Mechanism from Family Members H-NS and Lsr2

Xenogeneic silencers (H-NS, Lsr2 and MvaT) facilitate bacterial evolution through the cryptic maintenance of horizontally acquired genes, binding and transcriptionally silencing DNA that is more AT-rich than the resident genome. H-NS and Lsr2 employ an AT-hook motif to recognize and bind AT-rich DNA targets. MvaT lacks this motif. Structural data suggested a KGGN motif may act as an analogous AT-hook. In vitro electrophoretic mobility shift assays found that double mutant MvaT K97A/N100A had similar DNA binding affinity and discrimination for target (AT-rich DNA) compared to wild type. Competitive gel shifts also found that while MvaT bound GC-rich and AT-rich DNA with comparable affinities, MvaT greatly prefers AT-rich DNA. We present a model where, within the oligomer, individual binding domains bind tightly to AT-rich DNA and loosely to GC-rich DNA. Together these data suggest that MvaT binds DNA through a novel mechanism dissimilar to xenogeneic silencing family members H-NS and Lsr2.

Advisor: Navarre, William W
The Effects of Folic Acid Supplementation on Natural Killer Cell Activity in an Animal Model

An emerging body of evidence has linked high intake of folic acid, common in the Canadian population due to mandatory folic acid fortification and prevalent supplement use, to certain adverse health effects. High intake and blood levels of folic acid were associated with reduced natural killer cell cytotoxicity in a pilot study of post-menopausal women that has not yet been confirmed. As such, we investigated the effects of folic acid supplementation on natural killer cell activity in a mouse model. Folic acid supplementation, plasma folate, and plasma unmetabolized folic acid were associated with reduced NK cell degranulation in response to stimulation with malignant cells. Our data corroborate the previously observed inverse association between folic acid and natural killer cell cytotoxicity and suggests that reduced natural killer cell mediated tumour immunosurveillance may be an additional mechanism behind the purported tumour promoting effect of folic acid supplementation.

Keywords: Folic acid
Natural killer cells
Advisor: Kim, Young-In J
An Open Source Inertial Sensor Network with Bluetooth Smart

In this thesis, an open source inertial sensor network with Bluetooth Smart connection is presented. The network has multiple sensor nodes connecting to a consumer electronic device with Bluetooth Smart. Each sensor node contains the following components: (a) an inertial sensor measuring acceleration, angular velocity, and magnetic field with good accuracy; (b) a microcontroller with capacity to handle real-time floating number calculations; (c) a Bluetooth Smart module broadcasting the data with low power consumption. The sensor nodes are designed to be small, allowing the users to wear them conveniently. For demonstration, a basic Personal Navigation System is developed using 4 of these sensor nodes and an Android smartphone. The experiments show that the sensor nodes could output accurate results with small noises when at rest or in slow motion. The example Personal Navigation System could measure total distance walked by a pedestrian with less than 10% error.

Keywords: BLE
inertial sensors
personal navigation system
sensor network
Advisor: Johns, David A
Zhu, Jianwen
First Principles Investigation of Nanomaterials for Hydrogen Generation and Hydrogen Storage

Ab initio computational modelling was used to examine nanoscale materials for renewable energy applications. Hydrogen production from water splitting was investigated on three edges of two-dimensional monolayer molybdenum disulfide by studying active sites, reaction pathways, activation energies and rates of reaction. The Mo-edge termination was found to adsorb and spontaneously dissociate water at room temperature conditions. Hydrogen storage through adsorption was studied on metal decorated graphene, defective graphene and metal decorated non-graphene 2-D carbon allotropes. Nickel was found to produce the best hydrogen gravimetric density for metal decorated graphene at 6.12 wt.%, lower than previous studies which neglected van der Waals forces. Defect engineered graphene produced a maximum gravimetric density of 7.02 wt.% while the lithium decorated 2-D carbon allotropes produced a best of 7.12 wt.%.

Keywords: atomistic modelling
density functional theory
hydrogen storage
molybdenum disulfide
water dissociation
Advisor: Singh, Chandra V
Context Awareness via a Smartphone Based Active RFID Proximity Detection System

This thesis explores the possibility of using Active RFID technology and smartphones to build a mobile context-aware system. The development of the system is motivated by the problems such as the information overload and the constant interruptions faced by medical workers today. As a proof-of-concept prototype, the novelty of the system is that 1) contextual information extraction is done through proximity detection 2) proximity detection is achieved using an Active RFID system instead of an Indoor Positioning System 3) the use of smartphones makes it possible to extract richer contextual information including orientation data. A detailed description of the system is presented and a number of tests are carried out to explore the properties of the systems and to determine appropriate technological thresholds and settings. The results from the test suggests that the system is capable for distinguish objects and/or people within one meter from a user from the rest. The system can also detect if the objects and/or the people are faced by the user or not. The usefulness of the proposed mobile context-aware system is demonstrated with respect to two mobile applications designed for medical workers. Design recommendations and system limitations are also presented, and the thesis concludes with suggestions for future research.

Keywords: context-awareness
mobile
proximity
RFID
RSSI
Advisor: Chignell, Mark