VictorJuiz/thesis huggingface dataset:
Generation of Human Synthetic Antibodies against Frizzled-7 Receptor

Antibodies are the fastest growing class of therapeutic agents, capable of targeting diseased phenotypes with high affinity and specificity. Phage display technology was strategically utilized to screen through 10^10 potential binders against Frizzled-7 receptor. Specifically, cell-based selection was performed to capture epitopes in their physiological state, and five unique single-chain antibodies that show differential binding profiles were generated. The antibodies' ability to bind to and detect the target protein was verified using various molecular technics. Importantly, one of the five antibodies is able to recognize an extracellular region outside of the previously targeted cysteine-rich domain, and its ability to pull down the Frizzled-7 was observed by western blotting. As Frizzled-7 is involved in the WNT signalling pathway, which is highly implicated in tumorigenesis, further investigation of the biological role and the therapeutic potential of these antibodies is warranted.

Keywords: Frizzled
High-throughput screening
monoclonal antibodies
phage display
Synthetic antibody
Wnt
Advisor: Moffat, Jason
Sidhu, Sachdev
Layout Optimisation of (In)GaN LEDs for High Brightness Applications

Since the development of the first high-brightness blue light emitting diode (LED), LED technology has gained a significant market share in residential, commercial, and medical applications. A major reason for its growing popularity is the LED's capacity for high luminous efficiency (LE), and consequent low operating cost. This thesis focuses on a comparative study of layout-oriented design considerations in optimising the LE of blue-emitting indium-activated gallium nitride (InGaN) LEDs. Specifically, we propose layout geometries which maximise luminous efficiency by improving device resistance and current uniformity. We study variations on square, interdigitated, and multipixel array geometries across devices with side-lengths ranging from 250um to 1400um. We observe a logarithmic improvement on luminous efficiency when perimeter length to active area ratio is increased across all device sizes. The issue of contact quality is expected to be a limiting factor to the scalability of this trend.

Keywords: gallium nitride
layout geometry
light emitting diode
luminous efficiency
Advisor: Ng, Wai Tung
The Health Economic Implications of Perioperative Delirium in Older Orthopaedic Surgery Patients with Fragility Hip Fractures

Patients who experience fragility hip fractures are at high risk for delirium. However, little is known about changes in health resource utilization associated with this adverse event. The objectives of this work were to quantify the difference in episode of care costs and length of stay from the hospital perspective between patients who do and do not experience perioperative delirium. Patient care data from a single centre were linked with micro-case costing reports. Propensity matching and regression modeling were used to control for potential confounders. Delirium was found to be associated with significant incremental episode of care costs and length of stay. The difference in costs was partly, but not fully, explained by differences in length of stay. Future work should focus on confirming the generalizability of these findings, assessing the impact using broader economic perspectives, and implementing cost-effective interventions to reduce the rate of perioperative delirium in this population.

Advisor: Coyte, Peter C
DNA Methylation of Endothelial Cell-enriched Genes during in Vitro Mouse ES Cell Differentiation and the Role of TET Proteins

Endothelial cell (EC)-enriched genes are regulated by numerous mechanisms, but especially epigenetic mechanisms such as DNA methylation. The current work examines the importance of TET1 and 2 in murine embryonic stem (ES) cells and their relevance to EC-enriched gene expression. The proximal promoters of EC-enriched genes are differentially methylated in expressing versus non-expressing cell types. To examine how this methylation pattern between EC and non-EC is established, we studied ES cells. The DNA methylation pattern was heterogeneous, and partially propagated to daughter cells upon cell division. When in vitro differentiating WT and TET1 and 2 double knockout (DKO) ES cells, the DNA methylation of EC-enriched gene promoters increases at day 4 and day 7 in both cell lines. Despite their hypermenthylation at day 7, EC- enriched gene expression increases in the WT cells but it is blunted in the DKO cells. Suggesting that TET1 and 2 presence in ES cells facilitate the activation of EC-enriched genes later in development.

Keywords: DNA methylation
Endothelial cells
ES cells
TET proteins
Advisor: Marsden, Philip A
The Role of Annexin A4 in Response to Biomechanical and Ischemic Insult

Glaucoma is a progressive neurodegenerative disorder characterized by the loss of retinal ganglion cells (RGCs). Elevation of intraocular pressure (IOP) is commonly observed in glaucoma patients and can exert biomechanical and ischemic insults on the optic nerve head (ONH) resulting in astrocyte reactivity, cytoskeletal dysfunction, and loss of structural support to RGC axons. Proteomic analysis of human ONH astrocytes revealed an increase of Annexin A4 (ANXA4) following application of a pathologically relevant biomechanical stress. The function of ANXA4 is unknown in the retina but members of this family have been implicated in membrane repair processes that involve interactions with cortical actin. In this study, ANXA4 was upregulated during glaucomatous stresses. Mechanical insult increased membrane permeability, and ANXA4 knockdown increased permeability to this insult. Furthermore, ANXA4 interacted with F-actin. These studies highlight the importance of membrane dynamics during biomechanical and ischemic insult and the active role ANXA4 has on membrane stability.

Keywords: actin
ANXA4
calcium
glaucoma
membrane
Advisor: Sivak, Jeremy
Secondary to Post-secondary Mathematics: Factors Perceived by Students as Inhibitors and Enablers to their Success

This study examined the transition from secondary to post-secondary mathematics, through the investigation of first-year and second-year calculus courses. Voluntary participants from a second-year calculus course at an Ontario university were invited to participate in an online survey. The data collected from the survey reflected students' experiences in grade twelve calculus, and university first-year and second-year calculus courses, along with students' perceptions about mathematics. The evidence from the study suggests that the teaching of mathematics at the university level needs to be adapted to students' learning of mathematics at the secondary level. In addition, educators for secondary-level mathematics need to ensure that students are being prepared for university mathematics by building the necessary skills for mathematical proofs and abstract thinking. Students need the opportunity to critically evaluate their own work, and easily see the application of mathematics to their lives.

Keywords: Calculus
Post-secondary
Secondary
Transition
Advisor: McDougall, Doug
Hewitt, Jim
Intraspecific Variation and Phenotypic Plasticity in the Invasive Vine Vincetoxicum rossicum

The human-mediated movement of species across the globe has led to the growing field of invasion biology, which is devoted to understanding more about invasive species and the impact they have on the ecosystems into which they are introduced. One particular invasive species that is extremely abundant and widespread in Southern Ontario is the vine species Vincetoxicum rossicum. V. rossicum is found in a variety of environments including open fields and forest understories, however, little is known about how the traits of this species varies in the different environments. In a field study in the Rouge Urban National Park and a complementary greenhouse study, I found that this invasive species optimizes light capture efficiency by changing its morphological traits. This potentially contributes to its invasion success and provides further insights and its future spread. Additionally, this work can provide insight on other invasive species that exhibit similar invasion strategies

Keywords: Enemy release
Intraspecific trait variation
Morphological traits
Phenotypic plasticity
Southern Ontario
Vincetoxicum rossicum
Advisor: Cadotte, Marc W
Quantification of the Reactivity of Nitrosamine Precursors

N-nitrosodimethylamine (NDMA) is a member of the nitrosamine family of disinfection byproducts recently found in chloraminated drinking water. It is of potential concern because NDMA at ng/L levels can contribute to a high cancer risk. This research quantifies the reactivity of model nitrosamine precursors in terms of their formation potential and formation kinetics, corresponding chlorine residual measurements over time, influence of monochloramine concentration and also assesses the impact from NOM. Research into the formation of nitrosamines from model precursors has shown that high NDMA yields are attributed to the presence of a single carbon atom between the aromatic ring and the DMA structure. Reaction rates were found not to be directly related to the yields but may be associated with the number of carbon atoms. Natural organic matter and its humic acid fraction were shown to influence NDMA formation in terms of reaction rates but not NDMA yields.

Advisor: Andrews, Susan A
Exploring Ontario's Secondary School Reading Achievement Gap: A Longitudinal Examination of Contributing Factors to the Academic - Applied Literacy Divide

Although provincial literacy scores in Ontario have remained relatively consistent over the past few years, provincial averages conceal some concerning trends, where students are performing differently based on placement within applied and academic courses. This study takes a longitudinal look at provincial level data, tracking students from grade three to create a more cohesive understanding of student profiles with reading difficulties. The link between demographic differences, home reading behaviour and achievement differences was explored. Findings suggest student performance on the grade three provincial test can predict subsequent enrollment within applied/academic streams in secondary school. Student trajectories across all three testing years were examined, indicating markedly different experiences between applied students, who were most likely to fail all three tests, and academic students, who were most likely to pass all three tests. These findings suggest the need for more targeted approaches to student reading challenges from as early as grade three.

Keywords: achievement gap
EQAO assessment
longitudinal tracking
reading
secondary school students
student streaming
Advisor: Jang, Eunice E.
Electrolysis of Titanium Oxide to Titanium in Molten Cryolite Salt

Cost-effective production of titanium is becoming a challenge being tackled in the metallurgical and sustainability sector and technological advancements are required to effectively separate the metal from its oxide. The existing methods of Ti production are extremely energy intensive and slow. This proof-of-concept study investigated the feasibility of separating and capturing Ti from TiO2 through electrolysis after it has been dissolved in a cryolite bath at 1050oC. XRD and SEM/EDS results verified that TiO2 is only partially reduced. However, addition of Al assisted in the precipitation of Ti in the form of TiAl and TiAl3. Parameters such as electrolysis time, concentration of TiO2, and electrolysis potential were explored. The experiments that were run for 4h, with TiO2

Keywords: Aluminothermic reduction
Cryolite
Electrodeposition
Electrolysis
Titanium
Titanium oxide
Advisor: Barati, Mansoor
Structure and Conformations of the Bovine ATP Synthase by Single Particle Electron Cryomicroscopy

Adenosine triphosphate (ATP), the energy currency of cellular biology, is synthesized by the mitochondrial ATP synthase in most eukaryotes. Proton translocation in the membrane-bound FO region leads to ATP synthesis in the catalytic F1 region through rotation of a central rotor. The generation of rotation is proposed to occur through a Brownian ratchet mechanism requiring two offset half-channels in the FO region. Here, using single-particle electron cryomicroscopy (cryo-EM), seven distinct conformations within three rotational states of the ATP synthase are presented at sub-nanometre resolution. An average of the FO region of all seven maps provided a detailed view of the proton-translocating a subunit, allowing an atomic model to be built using evolutionary co-variance. The arrangement of subunits in the membrane region suggests two half-channels for proton translocation. These channels, along with an observed oscillation of the c8-ring in the FO region between substates in each rotational state, supports the Brownian ratchet mechanism for the generation of rotor rotation and ATP synthesis.

Keywords: ATP synthase
bovine
electron cryomicroscopy
evolutionary covariance
proton translocation
structure
Advisor: Rubinstein, John L
Genomic Signals of Adaptation in the Allotetraploid Weed Capsella bursa-pastois

Polyploids are often exceptionally evolutionarily successful, and increased adaptive potential may contribute to their prevalence. However, adaptation is not well characterized in polyploids, and the extent that it contributes to polyploid success is currently unclear. Here we investigate the genomic basis of adaptation in one of the world’s most successful weeds. We obtained genotype-by sequencing (GBS) sequences from 261 C. bursa-pastoris accessions and 24 whole genome sequences spanning Eurasia. We identified climate associations and found adaptive signatures consistent with contemporary adaptation in recently colonized Asia, and longer adaptive divergence in the ancestral European range. Signatures of adaptation through selective sweep scans suggest preadapted parental genomes may also contribute to local adaptation in similar habitats. However, native climate did not predict fitness in a common garden. Local environmental adaptation is then likely a subtle factor in C. bursa-pastoris’ success, although the features of its diploid progenitor genomes notably influenced its adaptation.

Keywords: Adaptation
Evolution
Genomic
Polyploidy
Advisor: Stinchcombe, John R
Wright, Stephen I
The Impact of Off-peak Delivery on Urban Freight Movements during the Pan American Games

Large scale sporting events provide distinct challenges to urban freight movement. The 2015 Toronto Pan and Parapan American Games introduces high demand for goods and services as well as delivery restrictions in key sections of Toronto. First-hand accounts from members of London, England’s freight community and relevant literature are presented as a case study on best practices, including off-peak delivery, for freight delivery during such sporting events. A second case study of Nestlé Canada examines the benefits of advanced routing and off-peak delivery in mitigating the impact of the Games, as well as the potential for reducing the fleet size. A heuristic model is used to identify and select off-peak customers and to estimates route travel times. The results show that the Games are expected to increase Nestlé travel times by 6.4%, and that off-peak delivery can be used to reduce the travel time impacts by an average 2.9%.

Keywords: Freight
Off-Peak Delivery
Sporting Events
Vehicle Routing
Advisor: Roorda, Matthew J
Designing for Wide-area Situation Awareness in Future Power Grid Operations

Power grid operation uncertainty and complexity continue to increase with the rise of electricity market deregulation, renewable generation, and interconnectedness between multiple jurisdictions. Human operators need appropriate wide-area visualizations to help them monitor system status to ensure reliable operation of the interconnected power grid. We observed transmission operations at a control centre, conducted critical incident interviews, and led focus group sessions with operators. The results informed a Work Domain Analysis of power grid operations, which in turn informed an Ecological Interface Design concept for wide-area monitoring. I validated design concepts through tabletop discussions and a usability evaluation with operators, earning a mean System Usability Scale score of 77 out of 90. The design concepts aim to support an operator's complete and accurate understanding of the power grid state, which operators increasingly require due to the critical nature of power grid infrastructure and growing sources of system uncertainty.

Keywords: ecological interface design
energy management system
human factors
power grid
user interface
wide-area monitoring
Advisor: Jamieson, Greg A.
Photoemission Spectroscopy Studies of Methylammonium Lead Iodide Perovskite Thin Films and Interfaces

Organometal halide perovskites have recently emerged as promising materials for fundamentally low- cost, high-performance optoelectronics. In this thesis, we utilize thermal co-evaporation of PbI2 and CH3NH3 I to fabricate thin films of CH3NH3PbI3 . We first investigate the effect of stoichiometry on some of its structural, optical and electronic properties. Then, we study the energy level alignment of CH3NH3PbI3 with 6 organic semiconductors, revealing good agreement between the data and the theory of vacuum level alignment. Finally, the interface formed between CH3NH3PbI3 and MoO3 is examined. The findings suggest migration of iodide species into the oxide layer, resulting in deterioration of its chemical and electronic properties. Insertion of an organic interlayer is shown to mitigate these undesirable effects. The results of this work could be of use in device engineering, where knowledge of such interfacial phenomena is of utmost importance in achieving optimized device structures.

Keywords: optoelectronic materials
organic semiconductors
thin films and interfaces
Advisor: Lu, Zheng-Hong
Streaming in Ontario High Schools: Exploring Student Experiences

This practitioner research study adds to the limited research available about high school streaming in Ontario. Unlike most research about streaming, which is quantitative, this study is qualitative and sought student perspectives absent from conversations about structuring students in public education. It explores students' experiences of being separated into pathways for their courses throughout high school, and how these placements affect their academics, relationships, and self-concepts. The project involved semi-structured interviews with nine grade eleven students across the academic, applied, and enriched pathways. The research method captured students' stories and details about how they feel progressing through school with significant labels attached to their names. It revealed problematic social hierarchies present in the school, and vastly different exposures to information about both secondary and post-secondary choices that translate to access to opportunity. The study makes recommendations for changes to the current streaming structure, and for the value of practitioner research.

Keywords: practitioner research
qualitative
secondary school
streaming
student perspectives
tracking
Advisor: Simon, Rob
McCready, Lance T
Design and Development of a Thermophoretic Soot Sampling System for High-pressure Laminar Diffusion Flames

Pollutant formation processes associated with high-pressure combustion pose challenges to optical diagnostics and physical probing of the flames due to various technical problems in comparison to the atmospheric case. One preferred process of studying the size and morphology of soot in atmospheric flames is in situ thermophoretic sampling and transmission electron microscopy. In this work, a multi-probe high-pressure thermophoretic sampling system was developed and used successfully inside a high-pressure combustion chamber. All soot samples were measured at a constant height above the burner exit. Findings show that the mean primary soot particle size decreased about 36% from 2 to 10 atm. In addition, the corresponding soot volume fractions imply that the number of soot nuclei in the soot inception region of the laminar diffusion flames have a strong sensitivity to pressure. The higher amounts of soot are mainly determined by the increasing primary soot particle number densities as pressure increases.

Keywords: Primary soot particle size
Soot formation at high pressures
Soot particle size by TEM
Thermophoretic sampling
Advisor: Gulder, Omer L
The Politics of Claims-making on Cape Town's Urban Peripheries: The Ithemba Farmers' Land Occupation

This paper investigates land occupation on the urban peripheries of Cape Town and the use of de facto land rights to sustain survival strategies and to make broader claims for accessing the state and accessing the city. Using extensive qualitative research in Cape Town with the Ithemba farmers, I investigate the politics of claims-making among a group of ‘squatting farmers’ who have established their access to land owned by the state and explore their insurgent practices and livelihoods. In doing so, I examine the disconnect between policies and lives on the ground indicating desires for equitable and integrated human settlements supporting peoples’ hybrid livelihood strategies and contesting ongoing experiences of social and spatial exclusion post-apartheid.This work is situated within broader discussions of the peripheries as sites of contestation and agency and brings the land question into conversation with contemporary processes of urbanization and unemployment in South Africa.

Keywords: claims
farming
land occupation
peripheries
post-apartheid
Advisor: Kepe, Thembela
Hunter, Mark
Journey into C. albicans Biofilms: Proteomic and functional genomic approaches to uncovering mechanisms of adherence

Candida albicans is an opportunistic fungal human pathogen that naturally forms biofilms, which are a community of yeast and filamentous cells surrounded by an extracellular matrix. C. albicans biofilms form in sequential steps: adhesion, filamentation, maturation and dispersion. To investigate mechanisms of biofilm formation, we conducted a mass spectrometry analysis of biofilm and planktonic proteomes. In parallel, we screened a barcoded tetracycline repressible strain library for reduced adherence. The depletion or deletion of biofilm enriched proteins did not affect biofilm formation. However, the degree of adherence is correlated with biofilm formation. Following up on Arp2/3 complex mutants, we found that its adherence deficiency is a result of Rho1 compensation of reduced Arp2/3 mediated endocytosis.

Keywords: Adherence
Biofilms
Candida
Endocytosis
Advisor: Cowen, Leah E
Integration of Chinese Immigrants Into a Canadian School Environment: A Case Study

My research study focuses on Chinese immigrants who feel marginalized in the Canadian school system due to their lack of proficiency in English. My research question is how do Chinese immigrants who are recent arrivals experience marginalization in an Ontario school in relation to ministry and classroom expectations and teaching strategies. The participants are eight secondary school students who have been in Canada for up to two years and who are at least 18 years of age and are enrolled in courses ranging from grade 9 to 12 at an Ontario private school. The theoretical framework involves social constructivist theory and practices that facilitate second-language acquisition. The study uses a phenomenological approach to data analysis. Interview data and researcher's observations are the main sources of data. The results generally indicate students' dissatisfaction with teaching instruction and suggestions were made about strategies that can be implemented to better suit their needs.

Advisor: Heywood, Daphne