VictorJuiz/thesis huggingface dataset:
The Role of Fgfr2 Isoforms and Frem1 in Craniofacial Development

OBJECTIVES: 1) To determine whether the Fgfr2W290R mutant results in the generation of additional isoforms and 2) to characterize the spatial and temporal expression of Frem1 in the developing mid-face of WT mice. METHODS: Polymerase chain reaction using primers specific to different parts of the Fgfr2 gene and gel electrophoresis were performed to compare observed with expected band sizes in WT and mutant tissues. In situ hybridization using Frem1 gene-specific riboprobes was performed on tissue sections of E9.5, E10.5, E11.5 and E13.5 mouse embryos. RESULTS: In the Fgfr2 study, the pattern and sizes of the amplified fragments appear to be identical in all three genotypes. Frem1 was found to be strongly expressed at the epithelial-mesenchymal interface and in the underlying mesenchyme of various structures located in the midline. CONCLUSION: RT-PCR analyses suggest the absence of mutant-specific isoforms in the Fgfr2W290R mutant. The distinct expression of Frem1 especially of structures at the midline suggests an important role for this gene in mediating outgrowth and filling of mesodermal cells in the midface.

Advisor: Gong, Siew-Ging
Sparse Beamforming Design for Network MIMO System with Limited Backhaul

This thesis considers a downlink multicell cooperation model in which the base-stations (BSs) are connected to a central processor via rate-limited backhaul links and each scheduled user is cooperatively served by a potentially overlapped cluster of BSs. Two different problem formulations are considered respectively: optimal tradeoff between the total transmit power and backhaul capacity under fixed user rate constraints, and utility maximization for given per-BS power and backhaul constraints. Motivated by the compressive sensing literature, we propose to approximate the backhaul rate as a function of the weighted $\ell_2$-norm square of the beamformers. This novel idea allows the optimal tradeoff to be converted into a weighted power minimization problem, which then can be solved efficiently using the well-known uplink-downlink duality approach; it also makes the utility maximization problem solvable through a generalized weighted minimum mean square error approach. The effectiveness of the proposed algorithms is justified through numerical simulation results.

Keywords: Beamforming
MIMO
Advisor: Yu, Wei
The Bishan Project: Cultural Production and Place Reconstruction in Rural China

In 2011, curators Ou Ning and Zuo Jing founded the Bishan Project, an effort to address rural-urban inequality in contemporary China through artistic and cultural production, based in Bishan Village of Yi County, Anhui Province. This study will examine how the Bishan Project endeavors to reconstruct rural places in response the decline of rural communities generated by China's marketization and integration with the global economy. Focusing on the material, re-presentational, and symbolic activities that contribute to place construction in Bishan and Yi County, I will reveal how the project attempts to make the rural visible while reconstructing Bishan to symbolize a utopian alternative to the social and spatial realities of China's countryside.

Advisor: Yue, Meng
Calibration of ILIDS and PDPA Droplet Sizing Systems

Laser-based droplet sizing techniques are widely used in industrial prototyping and diagnostics applications. However, their ability to immediately output highly precise droplet size distribution charts, seemingly without any significant user input, belies their vulnerability to bad input parameters, noise, and optical aberrations that can only be identified and resolved by means of careful calibration using monodisperse droplets. The contribution of this paper is threefold: first, we provide a review of well-known and obscure sticking points identified in various publications and how they apply in the context of ILIDS and PDPA calibration procedures; second, we present a novel, cheap and simple droplet generator design of the continuous-stream type, based on the rotary actuator of a computer hard drive; third, we submit a proof-of-concept design of a computer vision algorithm to eliminate the need for camera calibration in combined PIV/ILIDS systems.

Keywords: Calibration
ILIDS
Image processing
Laser optics
PDPA
Spray characterization
Advisor: Ashgriz, Nasser
Automation of a Multiplexed Microbead-based DNA Assay Platform

Microbead-based diagnostic technology has been explored in academia for over 30 years. As the technology matured, it became clear that this was a competitive platform for multiplexed point- of-care diagnostics for a number of different applications spanning from healthcare, border defense, food safety and environmental monitoring. To realize the benefits of this technology to Canada and the rest of the world, it is imperative to develop an automation scheme to enable minimally trained users to be able to leverage this technology in a point-of-care setting where there is no access to a full lab, and often without reliable water or electricity. This thesis aims to leverage the use of microfluidics and magnetism to enable a simple way of automating the microbead platform for this purpose.

Keywords: diagnostics
medical device
microfluidics
nanotechnology
Advisor: Chan, Warren CW
Tin Whisker Growth and Mitigation with a Nanocrysytalline Nickel Coating

Tin Whisker Growth and Mitigation with a Nanocrysytalline Nickel Coating Master of Applied Science, 2015 Szymon Janiuk Materials Science and Engineering, University of Toronto Abstract: Tin whiskers are a problem in the electronics industry since the EU banned the use of lead in Pb-Sn solders as part of the Restriction of Hazardous Substances (RoHS). The biggest concern with Sn whiskers is their ability to short-circuit electronics. High reliability applications such as the aerospace, defense, healthcare, and automotive industries are at most risk. This project explores Sn whisker mitigation and prevention with the use of nanocrystalline nickel coating over Sn surfaces. Sn was plated onto a pure Cu substrate using electroplating. A high temperature and high humidity condition, at 85°C and 85% RH, was effective at growing whiskers. A nNi coating was plated over Sn/Cu coupons. After subjecting the nNi/ Sn/Cu samples through 85°C/85% RH testing conditions, no whiskers were observed penetrating the surface. These results make nNi a viable material to use as a coating to prevent the growth of Sn whiskers in electronic assemblies.

Keywords: Metal coating
Nickel Coating
Tin Whisker mitigation
Tin Whiskers
Advisor: Perovic, Doug D
Adaptive Fault Tolerant Control for Nonlinear Systems with Constraints

In this thesis, fault tolerant control (FTC) design for nonlinear systems with input and output/state constraints are studied. To handle the input constraints, auxiliary systems are integrated with the controller. To deal with output constraints, Barrier Lyapunov Functions (BLFs) are used. When state constraints are in force, command filters are used in conjunction with BLFs. A novel adaptive fault tolerant cooperative tracking control (AFTCTC) scheme is developed for a class of input and output constrained nonlinear multiagent systems. Exponential convergence of the cooperative output tracking error into a small set around zero is guaranteed, while the constraints on the output will not be violated. The results are then extended to the design of a novel adaptive fault tolerant control (AFTC) scheme for a class of input and state constrained multi-input-multi-output (MIMO) nonlinear systems, where the constraints on the system state will not be violated.

Keywords: Adaptive control
Fault tolerant control
Input constraints
Nonlinear systems
State constraints
Advisor: Kwong, Raymond
Analytical Approaches to Investigating Transit Network Resilience

The reliability of public transit networks is of critical importance the world over. As transit demand is forecasted to grow, there exists a need to quantitatively measure the operational resilience of a transit network. Such metrics can be used to transit planners and operators to effectively mitigate the impact of service disruptions on commuters. By representing the public transit network in Toronto, Canada as a directional graph, a series of metrics based in graph theory were employed to analyze resilience. Using simulation allowed one to overcome the inherent limitations in a network science approach and introduced the concepts of `Station Importance' and `Exposure'. These indices are based on the demand-weighted increased in travel cost when service disruptions occur. An analysis on the behavior of trip-makers is conducted via a sentiment analysis using Twitter. The result of the combined efforts discussed above is a framework to capture operational resilience.

Keywords: EMME
Graph Theory
Network
Public Transit
Resilience
Robustness
Advisor: Shalaby, Amer
Co-deposition of Pigment Particles with Nickel through Electrodeposition

This research focuses on the synthesis of a nickel-pigment composite coating in an effort to produce coloured nickel electrodeposits via the codeposition approach. A blue pigment, Copper Phthalocyanine (CuPc) Blue was codeposited to create Ni-CuPc composite coatings. Top surface and cross-sectional Scanning Electron Microscopy (SEM) images confirmed the codeposition of pigment particles within the nickel matrix throughout the entire coating thickness. The top surface of the Ni-CuPc composite coating showed an unexpected metallic copper colour. X-Ray Photoelectron Spectroscopy (XPS) analysis indicates the presence of metallic copper confined to the top surface. It was speculated that this phenomenon is due to the galvanic displacement reaction between copper from the pigment and nickel from the matrix. Upon removing the copper surface layer the colour of the composite remained metallic silver despite the presence of the pigment particles.

Keywords: Codeposition
Copper Phthalocyanine
Nickel Composite
Nickel Electrodeposition
Pigment
Advisor: Erb, Uwe
Structural Analysis of Corneal Nano-nipple Arrays in Nymphalidae Butterflies

This study is concerned with the two-dimensional arrangement of corneal nano-nipples on the eyes of two Nymphalid butterflies. While the nano-nipples are predominantly in close-packed ordered arrangements, there are coordination defects known as 5-7 defects that disrupt the local translational symmetry and generate a number of secondary defects. Most often 5-7 defects align in rows to separate nipple domains with different orientations much like grain boundaries in crystalline materials. Surprisingly, the majority of 5-7 defect rows are special low-sigma; boundaries that occur infrequently in random crystalline materials. Such prevalence of low-sigma; boundaries suggests that they may serve specific purposes. Based on the superlattices associated with the observed low-sigma; boundaries, it is tentatively suggested that they could lead to diffraction effects for infrared light.

Keywords: Antireflection
Biomimicry
Crystallography
CSL
Grain boundaries
Nano-nipples
Advisor: Erb, Uwe
Segmental Irradiation of Healthy Bone

Up to 10% of patients who undergo radiation therapy and surgery for soft tissue sarcoma in the thigh will sustain a pathologic fracture and form non-union. These fractures occur within the irradiated region, on average 5 years post-RTx and often necessitate limb amputation. Three experiments were conducted in order to better understand the pathophysiology behind late-effects of irradiation and surgery on healthy bone. Experiment 1: A model of radiation-induced non-union was created in the rat. It was determined that RTx, and not periosteal removal, was responsible for non-union seen. Experiment 2: OP-1 could not improve healing of irradiated fractures. Experiment 3: Fractional and single dose irradiation alter bone structural properties differently following equivalent doses of irradiation. Overall, equivalent doses of radiation to bone delivered in different (single vs. fractional) dosing schedules do not have equivalent affects. It is recommended that both dosing schedules be considered carefully in future research.

Advisor: Grynpas, Marc
A New Suite of Pathogenesis-induced Gene Expression Markers in Arabidopsis thaliana

Plant immunity comprises of two main branches. In one branch, plants recognize microbial molecules called pathogen-associated molecular patterns (PAMPs); inducing PAMP-triggered immunity (PTI). Successful pathogens suppress PTI using effector proteins. These effectors can be recognized by the plant causing effector-triggered immunity (ETI); causing cell death to prevent further infection. Pathogenesis-Related genes are markers of pathogen infection but do not distinguish between PTI, ETI or susceptibility. Using available transcriptomic data for the interaction between Arabidopsis thaliana and Pseudomonas syringae, I identified 2 genes induced during a susceptible interaction, 1 gene induced by ETI and 4 genes induced by PTI. These genes characterized using protein interaction data from the Proteomics Standards Initiative Common QUery InterfaCe using the BAR's interactive database; the Arabidopsis Interactions Viewer. This analysis produced networks of protein interactions for 6 of these marker genes. Transcriptomic expression analyses demonstrated a correlation of expression between these expression markers and their interactors.

Keywords: Arabidopsis
Gene marker
Interactions database
Interactions network
Pseudomonas psyringae
Advisor: Provart, Nicholas
Desveaux, Darrell
DNA Methylation Machinery Mediates the Bladder's Response to Obstruction

Partial bladder obstruction arises insidiously and compromises quality of life often by perpetuating urinary tract infections, incontinence and kidney failure. Obstruction leads to prolonged over-distension of the bladder, which induces tissue hypoxia and abnormal extracellular matrix (ECM) remodeling that alters bladder smooth muscle cell (BSMC) phenotype. The BSMCs become hypertrophic and proliferative with loss of differentiation and contractility. The persistence of pathology despite de-obstruction in human and animal bladders in vivo, as well as the stable pheno-pathology found in BSMC in vitro, suggests that responses to bladder obstruction are mediated by the microenvironment. We hypothesize that epigenetic mechanisms mediate irreversible BSMC responses to the obstructive environment. In animals, long-term bladder obstruction significantly increased bladder weight and dysregulated gene expressions, neither were completely reversed by de-obstruction. The ECM regulates BSMC phenotype switching in vitro, which is mediated by alterations in the expression as well as the sub-cellular localization of DNA Methyl-Transferase.

Advisor: Bagli, Darius
Optically Transparent Reflectarrays for Satellite Applications

There is a growing need to improve antennas for microsatellite applications in order to achieve higher gain and improved data rates. This project proposes an optically transparent reflectarray antenna with rectangular patch elements fabricated using transparent conductive oxide (TCO). By incorporating a reflectarray into the solar panels of a satellite, the satellite's surface area can be maximized for both solar power collection as well as antenna gain. TCO thin film technology offers a combination of optical transparency at optical frequencies, and electrical conductivity at microwave frequencies. Using TCO materials introduces conductor losses not usually examined in reflectarray design. In order to reduce these losses, the proposed elements are both single-layer and sub-wavelength. Using these elements, a 392 element optically transparent reflectarray prototype operating at 26 GHz is presented that produces a beam at 20 degrees off-broadside.

Advisor: Hum, Sean V.
Signalling Through the PGC-1a Pathway Mediates an Inducible Stress Response in Retinal Astrocytes to Resist Oxidative and Metabolic Insults

Glaucoma is a neurodegenerative disease characterized by the loss of retinal ganglion cells (RGCs) in the eye. Astrocytes are an adjacent cell type that provides metabolic support and antioxidant defense for the RGCs and the loss of these neurosupportive functions contributes to the pathogenesis of glaucoma. Peroxisome proliferator-activated receptor gamma coactivator-1 alpha (PGC-1a) is a transcriptional co-activator that regulates the expression of metabolic and antioxidant genes through interactions with transcription factors. PGC-1a deficiency has recently been implicated in neurodegeneration, but its role in mediating astrocyte functions is not well understood. In this study, PGC-1a activity and its expression were induced in astrocytes following metabolic and oxidative stress. Under these conditions, pharmacological stimulation of PGC-1a improved antioxidant capacity, mitochondria biogenesis, and increase astrocyte viability through regulations of downstream gene expression. Thus, PGC-1a is a key mediator of astrocyte stress responses, which can be targeted to promote their neurosupportive functions.

Keywords: Astrocytes
Glaucoma
Oxidative Stress
PGC-1a
Advisor: Sivak, Jeremy M
The Role of Mental Imagery Ability in Learning Clinical Skills: Development of the Clinical Skills Imagery Ability Questionnaire (CS-IAQ)

The general aim of this thesis was to gain a better understanding of the use of mental imagery in health professions education, as well as the consideration of imagery ability. This was done through a scoping review and the development of a questionnaire to assess the ability to image clinical scenarios. An improvement in skill performance after mental imagery was reported in about half of the experimental research studies. In the development of the questionnaire, three of the resulting clusters of questions were shown to be able to differentiate participants with different levels of experience and all represented the motivational general category. Participants also reported a preference for a first person perspective when imaging, regardless of their level of training. Overall, the results of this thesis project were found to enhance the understanding of mental imagery use by health professionals as well as the effects of imagery ability.

Advisor: Carnahan, Heather
Pictorial Korea: Visualizing the Nation for a Foreign Audience in Cold War Photobooks

In the mid-20th century, a South Korean publication company called the International Publicity League of Korea attempted to change the way that the world perceived their emerging nation-state by producing a series of annual photobooks entitled Pictorial Korea. This thesis examines editions of Pictorial Korea as both constructed visual narratives and material objects to reveal how the IPLK conveyed images of the nation to their intended audience. In order to do so, it traces the company's history, their critique of foreign images of South Korea, their relationship with the world of photography, and the transmission and corroboration of their representations through the materiality of Pictorial Korea. It argues that within the context of the Cold War, the IPLK's works positioned South Korea in relation to the non-communist West and communist North Korea by portraying it as a modern, sovereign nation and the rightful heir to Korean historical tradition.

Keywords: Cold War
International Publicity League of Korea
Photobooks
Photography
Pictorial Korea
South Korea
Advisor: Poole, Janet
Urban-rural Differences in Oral Bisphosphonate Utilization in Ontario Following Formulary Changes and Introduction of New Formulations

Rural populations often have less access to health services and information, potentially resulting in regional variation in drug utilization. We examined urban-rural differences in oral bisphosphonate utilization in Ontario following formulary changes and introduction of new formulations. The Rurality Index of Ontario was used to define urban, nonmajor urban, and rural regions. There were 16,367,752 oral bisphosphonate claims dispensed (77% urban, 18% nonmajor urban, 5% rural) to community-dwelling seniors from 2000/01-2014/03. Trends in dispensing following formulary changes were similar between regions. When examining trends in dispensing of new formulations, urban regions had significantly faster uptake than rural regions, and consistently dispensed a higher proportion of claims. These temporal and regional differences persisted over time. Rural physicians may be less aware of new drugs, indicating a need to improve information dissemination to these areas. Further research examining whether urban-rural differences in dispensing translates into differences in clinical outcomes is warranted.

Keywords: Interrupted time series analysis
Oral bisphosphonates
Osteoporosis treatment
Pharmacoepidemiology
Urban-rural health
Advisor: Cadarette, Suzanne M
Convergence in Shape of Steiner Symmetrized Line Segments

Building on the recent work of Burchard, Bianchi, Gronchi and Volcic, it is shown that for every finite union of line segments, every sequence of Steiner symmetrals will converge in shape. It is also shown via counterexample that the rotation scheme used in the aforementioned paper to establish the square summable case will not work generally.

Advisor: Burchard, Almut
Approach and Avoidance Processing: Investigating a Rostrocaudal Gradient in the Nucleus Accumbens Core

The nucleus accumbens is a site of integration of positively and negatively valenced information. While a rostrocaudal topographical gradient in valence processing has been found in the accumbens shell, a potential gradient has not fully been explored in the core in relation to its role in motivation in response to conditioned cues. In the current study, rats were trained to associate visual cues with appetitive, aversive and neutral outcomes. In a test of motivational bias, the aversive and appetitive cues were superimposed in a maze arm and rats' exploratory bias was measured for this arm vs. a neutral cued arm. Animals receiving GABA receptor agonists in the caudal region displayed a bias in the direction of aversion, whereas those undergoing inactivation of the rostral core displayed an ambivalence similar to controls, with an additional behavioural difference of augmented chewing. This suggests a rostrocaudal differentiation in valence processing in the core.

Keywords: accumbens
approach
avoidance
decision-making
GABA
motivation
Advisor: Ito, Rutsuko
A Comprehensive Study on the Effectiveness of Office-based TDM Policies

The objective of this thesis is to develop an employer-based Transportation Demand Management (TDM) evaluation tool that can be used for evaluating various employer-based TDM policies. The conventional method of evaluating TDM policies has typically been conducting expensive before and after TDM policy implementation surveys. On the contrary, this research used a pre-policy deployment joint Revealed Preference and Stated Preference (RP-SP) survey, where the data were collected to develop a TDM policy sensitive mode choice model, which is packaged into a software system for TDM investment decision support. The evaluation tool (named Off-TET) developed by integrating the mode choice model predicts changes in modal share by integrating all possible effects of single or multiple TDM policies implemented in isolation or combined. While the tool presented in this thesis was developed for the region of Peel, there exist opportunities for the application of this type of analysis across Canada.

Keywords: Experimental Design
Policy Evaluation
Revealed Preference and Stated Preference Survey
TDM Evaluation
TDM:Transportation Demand Management
Advisor: Habib, Khandker Nurul