VictorJuiz/thesis huggingface dataset:
Proteomic-based Investigation of Cell Surface and Cell Surface-associated Proteins of the Human Heart

Plasma membrane (PM) proteins are at the interface between the cell and the external environment and are therefore the most accessible to therapeutic drugs. I utilized cationic silica beads and mass spectrometry (MS)-based proteomics to enrich for PM proteins of human cardiomyocytes, coronary smooth muscle cells, and coronary endothelial cells. The enrichment of PM proteins was confirmed and 1006 proteins were specifically filtered and enriched into a set of known and novel cardiomyocyte PM-associated proteins of which 42% had PM-associated gene ontology annotations and/or predicted transmembrane helices. Two novel candidates, namely popeye domain-containing protein 2 (POPDC2) and protein kinase C and casein kinase substrate in neurons protein 3 (PACSIN3) were selected and found to have confirmed PM localization. In conclusion, silica bead membrane extraction combined with MS-based proteomics successfully enriched for PM proteins of the human heart of which two novel candidate proteins were shown to have confirmed PM localization.

Keywords: Cardiovascular
Proteomics
Advisor: Gramolini, Anthony
Characterization of ES Cell-derived Cortical Radial Precursor Differentiation

Murine neural precursor cells have been a well studied model for neural cell fate determination and stem cell function both in vivo and in primary culture. However, factors such as cell number, the presence of multiple cell populations and of niche intrinsic factors made it difficult to dissect the mechanisms regulating cortical development. To overcome this issue, we have developed a culture system where mouse embryonic stem cells (ES) are differentiated to cortical radial precursors through retinoic acid treatment of embryoid bodies. One day after plating in neural differentiation conditions, ~70% of cells in the culture are cortical radial precursors (RPs) as indicated by the definitive cortical marker Emx1, and over 8 days in culture, these RPs differentiate to pyramidal glutamatergic neurons of the cortex mimicking in vivo development. Astrocyte differentiation can be observed later as the culture progresses, which again mimics the typical timed genesis of cells in the cortex. The stem cell properties and cell fate of these RPs can be manipulated with growth factors in culture as they are in vivo. In particular, FGF2 promotes proliferation and survival, while ciliary neurotrophic factor (CNTF) induces precocious astrocyte formation. Thus, our ES-derived cortical RP cultures can serve as an alternate and complementary in vitro model to examine neural precursor biology during early development.

Keywords: cortical precursors
neural stem cells
mouse ES cells
corticogenesis
in vitro differentiation
retinoic acid
Advisor: Miller, Freda
Development of a Continuous Density Gradient of Immobilized Probes for Controlling the Stringency of DNA Hybridization

A new format for microfluidic based DNA biosensors is presented in which the biorecognition element (single stranded DNA probes) is immobilized as a continuous density gradient of probes along the length of a microfluidic channel instead of a standard array format commonly used in microarray technologies or DNA based biosensors. The development of continuous density gradients of immobilized probe was achieved by electrokinetically subjecting probes that were terminated with an appropriate functional group for a surface coupling reaction to increasing convective velocity along the length of the microfluidic channel. This gradient format was able to discriminate between a fully complementary target and one containing 3 BPM based on the spatial pattern of hybridization for picomole quantities of DNA targets. Temperature mediated destabilization of DNA hybrids demonstrated that the density of immobilized probes plays an important role in the thermodynamic stability of DNA hybrids. In addition, it was found that efficiency, selectivity and melt temperature of DNA hybrids for surface based hybridization is dependent on the density of the probe molecules.

Keywords: density gradients
selectivity
DNA hybridization
hybridization efficiency
mass transport
Advisor: Krull, Ulrich Jorg
Federal-provincial Relations on Immigration: Striking the Right Balance

This thesis addresses the complex relationship between the federal and provincial governments with regard to the creation and implementation of economic migration policies and programs. As immigration is subject to shared jurisdiction under the Constitution, provinces have begun to take up an important and ever-increasing role in immigration policy and have used it as an effective tool to reach regional economic and demographic objectives. However, devolving responsibilities for economic migration policy to the provinces raises questions about the proper balance between federal and provincial immigration powers. The thesis will address this issue by giving an overview of the current mechanisms in place that govern the division of immigration powers between the two levels of government, the main critiques on it and the theoretical framework that supports the choices made. It then tries to provide the reader with alternative approaches to the division of powers for specific elements of the immigration process.

Keywords: Immigration
Canada
Advisor: Macklin, Audrey
All-optical Wavelength Conversion in Aluminum Gallium Arsenide at Telecommunications Wavelengths

This thesis aims at both developing highly nonlinear Aluminum Gallium Arsenide waveguides(AlGaAs) and demonstrating all-optical wavelength conversion via cross-phase modulation in AlGaAs waveguides at telecommunications wavelengths. This work covers waveguide design, device fabrication, device characterization and system work.

Keywords: Wavelength Conversion
waveguides
Semiconductor
Telecommunications
Advisor: Aitchison, J. Stewart
Qian, Li
The Effect of Teneurin C-terminal Associated Peptide-1 (TCAP-1): Protection Against Hypoxic-stress and Regulation of Brain-derived Neurotrophic Factor (BDNF) in Immortalized Hypothalamic N38 Cells

Teneurin C-terminal associated peptide-1 (TCAP-1) is a recently characterized peptide that may act as one potential neuroprotective agent as it has been shown to regulate several stress-associated behaviours in rodents and possesses a number of protective actions on cells, however the mechanism remains unknown. Brain-derived neurotrophic factor (BDNF) is a neurotrophin recognized for mediating survival, differentiation, and proliferation. TCAP-1 may act, in part, via BDNF to provide neuroprotection via modulation of BDNF expression. The aim of this research was to further investigate the mechanism of TCAP’s neuroprotective actions. I show that TCAP-1 is neuroprotective and a potent enhancer of cell numbers under varying levels of oxygen. I also establish that TCAP-1 is able to influence neuronal behaviour by differentially regulating neurite growth. In addition, I indicate that TCAP-1 is able to regulate BDNF expression in immortalized mouse hypothalamic N38 cells, which suggests that TCAP-1’s neuroprotective mechanism may involve BDNF.

Keywords: Brain-derived neurotrophic factor
BDNF
Teneurin C-terminal associated peptide
TCAP
hypoxia
neuroprotection
teneurin
proliferation
neurite growth
hypothalamus
immortalized cells
hippocampus
Advisor: Lovejoy, David A.
The Need for Post-conflict Investigatory Mechanisms in the R2P Doctrine

In the wake of atrocities arising from internal armed conflicts in the 1990s, the International Commission on Intervention and State Sovereignty introduced the Responsibility to Protect doctrine (“R2P”) as a solution to reconcile the notion of state sovereignty with the need to protect citizens. The lack of available protection for internal armed conflicts and the subsequent evolution of the humanitarian intervention debate facilitated the unanimous acceptance of R2P’s fundamental principles by all UN member states. This paper examines the development of the R2P doctrine and its current status as customary law. By identifying its inadequacies, the paper raises questions of the doctrine’s viability in fulfilling the emerging norm of the collective responsibility to protect. In order to remedy these shortfalls and ensure the doctrine’s effectiveness, the paper argues the need to incorporate post-conflict investigatory mechanisms into the R2P.

Keywords: international humanitarian law
international law
R2P
responsiblity to protect
post-conflict
internal armed conflict
fact-finding
Advisor: Orange, Jennifer
New Approach in Characterizing Accessory Drive Belts for Finite Element Applications

Multi-ribbed serpentine belt is the core of the automotive accessory drive system, which distributes the engine power to other auxiliary systems of the car. Development of a belt life model is of a significant importance to the accessory drive system manufacturers, in order to prevent any premature failures of these belts. However, any numerical analysis on the belt life is heavily dependent on gaining an understanding of stress distribution in the belts under the operational loading conditions. The presented work demonstrates a new systematic approach for determining the hyperelastic material parameters of rubber with specific application in Finite Element Analysis (FEA) of serpentine accessory drive belts. This new approach can be used as a stand-alone tool by manufacturers to determine the stress distribution in the belt under operational conditions; the results of which can be applied to assess the life of accessory drive belts, in a relatively short time.

Keywords: Finite Element Analysis of Accessory Drive Belts
Accessory Drive Belt Characterization
Mechanical Tests on Rubber
Hyperelastic Material Parameterization
Advisor: Zu, Jean W.
Investigating the Role and Nature of Prior Knowledge in Conceptual Change: an fNIRS Study

We used functional Near-Infrared Spectroscopy (fNIRS) and a split ratio paradigm used to investigate the role and nature of prior knowledge in conceptual change in science. Sixteen participants, eight physicists and eight non-physicists were presented with two types of videos, Newtonian (two balls of unequal mass falling at the same rate) and Impetus (two balls of unequal mass, the larger one falling faster), to vary their exposure to plausible and implausible information. Whereas no increased neural activation was found in physicists, non-physicists showed recruitment in the frontopolar areas and DLPFC. Studies implicating these regions in integration and working memory support the notion that prior knowledge held by novices is flexible and context-dependent.

Keywords: functional nearinfrared spectroscopy
conceptual change
Advisor: Dunbar, Kevin
Pho23 Regulates Gene Expression through Histone Methylation and an Mck1-controlled Pathway in Budding Yeast

Eukaryotic organisms utilize post-translational modifications of highly conserved histone proteins to control gene expression programs. Methylation of lysine 4 on histone H3 (H3K4me) in particular, is thought to be associated with actively transcribed DNA. Paradoxically, recent evidence has suggested that H3K4me has a repressive function as well. Pho23, a member of the highly conserved ING family of tumour suppressor proteins, binds H3K4me and is a component of the gene repressive complex, Rpd3L. My genetic analysis suggests that Pho23 controls transcriptional repression via H3K4me and that Pho23 is itself regulated by the sequence-specific DNA-binding protein Ume6. Moreover, this Ume6-regulated function appears to be governed by Ume6 phosphorylation by Mck1, an evolutionarily conserved kinase. Finally, while Ume6/Pho23 are known to function together with the histone deacteylase Rpd3, my findings suggest the existence of an Rpd3-independent function for Pho23.

Keywords: Epigenetics
Mck1
Pho23
Yeast
Advisor: Meneghini, Marc
The Impact of Polypore Fungi on Growth and Physiology of Yellow Birch and Molecular Detection of Fungal Pathogens in Live Trees

Pathogenic fungi, such as polypore fungi that infect live sapwood, decrease quality and value of wood; however their effects on canopy physiology and growth have been little examined. This study examines how Fomes fomentarius, a species of polypore fungus affects canopy physiology in Betula alleghaniensis. A mobile canopy lift enabled the collection of leaf physiology, morphology and chemistry data from canopies of infected, damaged, and control trees. A molecular protocol developed to detect and identify polypore fungi in live trees confirmed that F. fomentarius was the major species present in infected trees. Infected trees exhibited reductions in physiological performance and growth, along with higher leaf carbon and chlorosis. While some characteristics of fungal infection were consistent with a mechanism involving partial xylem occlusion, patterns did not resemble those of a simple drought response. Likely, other factors such as fungal toxins or host defense mechanisms also contribute to these patterns.

Keywords: forest pathology
canopy physiology
mycology
polypore fungi
Advisor: Thomas, Sean C.
Development of a Model to Study the Abscopal Effect: Combining Image-guided Radiation Therapy and Immunotherapy in Cancer Treatment

Distant metastases are a limiting factor in cancer patient survival as they are least accessible to conventional therapies. Effective therapy should treat primary tumours and metastatic disease. Use of image-guided radiation therapy (IGRx) enables high doses of radiation to be delivered for better tumour control while minimizing toxicity to healthy tissues. Systemic effects on distant non-irradiated tissues have been observed following IGRx. This phenomenon, termed the abscopal effect, is hypothesized to be mediated by the immune system. The inflammatory milieu generated following IGRx may activate immune cells to mount specific anti-tumour responses. The work described in this thesis aims to develop a model to study the abscopal effect, and evaluate the potential of combining IGRx and immunotherapy to enhance such distant tumour killing. Results from these studies may have clinical implications, where a combined IGRx and immunotherapy approach may prove useful in eliciting regression of local tumours and distant metastases.

Keywords: Radiation Therapy
Immunotherapy
Abscopal Effect
Advisor: Medin, Jeffrey A.
Jaffray, David A.
Fabrication of Nickel Oxide Thin Films and Application thereof in Organic Electronics

This work investigates fabrication methods of nickel oxide thin films and their use in organic electronics. Two fabrication techniques were studied: UV-ozone oxidation of pure nickel films and reactive RF magnetron sputtering. The former was used to produce Ni/Ni2O3 bi-layer anodes to use as a substitute for the de facto standard ITO anode. OLEDs fabricated using Ni/Ni2O3 bi-layer anodes exhibited comparable device performance to standard ITO devices. UV-ozone oxidation was also used to fabricate Ni2O3 buffer layers for OPVs. Solar cells fabricated using Ni2O3 coated ITO exhibited an enhanced power conversion efficiency of up to 90%. RF magnetron sputtering was used to produce NiOx buffer layers with tunable conductivity and optical transparency for OPVs. Solar cells fabricated using NiOx coated ITO exhibited an enhanced power conversion efficiency of up to 60%. Nickel oxide films have been characterized with various techniques: sheet resistance measurements, optical transmission, XPS, UPS, AFM, and TEM.

Keywords: OLED
OPV
Organic Electronics
Organic Solar Cells
Nickel Oxide
Thin Films
Ozone oxidation
materials science
Advisor: Lu, Zhenghong
Biochemical Investigation of the Bacteriophage Protein HK97 gp74

Bacteriophages are viruses that infect and propagate within bacteria by making use of the host’s biosynthetic machinery. With a global population of 1031, phages pose a significant influence on microbial populations. Studies of bacteriophage proteins can elucidate the influence that bacteriophages play on the evolution of bacteria, as well as, providing the basis for the use of phage proteins as possible therapeutics and bioengineering solutions. This study aims to investigate the structural and functional role of the HK97 phage protein gp74. Sequence alignments indicate that gp74 is related to homing HNH endonucleases. Homing endonucleases are predominantly double-stranded DNases, suggesting that gp74 mediates integration of phage genes into the host genome or may target foreign phage DNA. DNA digestion experiments with gp74 reveals that gp74 mediates non-specific double-stranded cleavage of lambda phage DNA and single strand cleavage of plasmid DNA. Our initial work demonstrates that HK97 gp74 is an HNH endonuclease.

Keywords: Bacteriophage
HK97 gp74
Advisor: Kanelis, Voula
A Wizard-of-Oz Study to Determine the Efficacy of an Automated Prompting System for Children with Autism

This thesis presents a study to develop and explore the use of a computerized system that provided automated prompts to children with ASD during the completion of a self-care activity (handwashing). A Wizard-of-Oz experiment was implemented using an A-B experimental design. During the baseline phase (A) the child’s caregiver was asked to guide the child through handwashing, in the intervention phase (B) the system guided the child. The results showed that the system was not very successful to guide the child. He tended to get distracted very easily presenting off-task behaviour, which resulted in needing assistance from the caregiver. The data obtained showed that during the intervention phase the assistance from the caregiver consisted mostly of verbal instructions versus the hand over hand guidance observed during B phase. From the data analyses and reviewed literature some improvements and redesigns were suggested which could help develop a more automatic prompting system.

Keywords: Autism
Wizard of Oz
Prompting system
Handwashing
Self-care activity
Prompting
ASD
children
Advisor: Mihailidis, Alex
Detection of Prenatal Opiate Exposures in Alternative Matrices

Identification of maternal opioid abuse in pregnancy is often difficult to ascertain in the absence of reliable self report. For this reason, physicians and child protection workers often turn to maternal and neonatal hair analysis for the detection of in utero opioid exposures. Since neonatal opiate hair analysis continues to prove difficult due to the scarcity of the hair sample and low drug concentrations, I developed a sensitive method utilizing headspace solid-phase microextraction (HS-SPME) coupled with gas chromatography-mass spectrometry (GC-MS) for the detection of three principal opiates (morphine, codeine, and 6-monoacetylmorphine) in human hair. Moreover, I characterized an at-risk neonatal population for in utero opiate exposures as well as for other drugs of abuse and alcohol. Equipped with a sensitive and specific method for the detection of opiate exposures and understanding the addiction profiles of pregnant women may lead to better clinical and social management and may benefit an at-risk population.

Keywords: Drug
Opiate
Hair
Prenatal
Advisor: Koren, Gideon
Comparison of Long-term Investments in Single-family Housing with Stocks, and Fixed-income Securities Markets

The historical long-term volatility and return on investment in single-family dwellings was investigated and compared with investments in equity, bonds and T-bill markets. Total return index for equity and fixed-income security indices were obtained from available sources, of course, a proper index for measurement of long-term changes in house prices was unavailable. In an effort to measure the house price changes, a relatively homogeneous pool of houses in the downtown Toronto area was selected and its price tracked over the study period of 44 years. Inflation rate affects the return of investments in everything similarly therefore this was not considered in the calculations. Results of comparing the investment of cash in one's family home versus in other investment vehicles showed that the ratio of investment growth to its volatility for a single-family house exceeded the ratios for other investments by a large margin.

Keywords: Residential real estate investment
long-term investment
Residential real estate derivatives
House price index
Advisor: Paradi, Joseph C.
Role of Flightless I in Cell Migration

A central process in connective tissue homeostasis is cell migration, which involves dynamic interactions between focal adhesions, the actin cytoskeleton and mitochondria, but the role of focal adhesion proteins in cell migration is not wholly defined. We examined focal adhesion-associated proteins from mouse fibroblasts and identified Flightless I (FliI) as a potential focal adhesion protein. We determined that FliI is distributed in the cytosol and co-localizes with actin monomers and mitochondria, but partially with paxillin. Biochemical assays showed that FliI associates with both actin monomers and short oligomers/filaments. Migration assay determined that cells with reduced FliI expression migrated more quickly and that FliI knockdown inhibited activation of β1 integrins. Consistent with these data, cell adhesion assay demonstrated that FliI knockdown cells were less adherent than wildtype cells. Our findings indicate that FliI may regulate cell migration by interacting with the actin monomers and the mitochondria to affect cell adhesion.

Keywords: flightless I
cell migration
actin cytoskeleton
mitochondria
cell adhesions
Advisor: McCulloch, Christopher
A Novel 3D Sensory System for Robotic Urban Search and Rescue Missions

Urban Search and Rescue (USAR) is the emergency response function that deals with the collapse of man-made structures. USAR environments contain concrete rubble, dust and debris, and provide poor lighting conditions. Due to the dangers that USAR rescue workers and their canines face, robots have become of interest in aiding rescue workers in searching. Experiences with robots in USAR missions have shown that a compact 3D sensor for 3D mapping of the environment is beneficial in providing the robot and identified victims’ locations within the structurally unstable environment. This thesis presents the developments of a novel 3D sensory system that provides both 3D and 2D texture information for mapping of cluttered unknown USAR environments. The sensor has been integrated into a robot platform, and experiments conducted to validate its usability in such applications. The experimental results show the potential for using this sensor in USAR robot mission.

Keywords: 3D Structured Light Sensor
Urban Search and Rescue
Advisor: Nejat, Goldie
Canadian Spine Surgery: A Review of Educational Objectives in Fellowship Training and Evaluation of Outcomes in Current Surgical Practice

There have been many advances in surgical residency education and similar interest exists in fellowship education. This study evaluated perceptions among spine surgeons about the specific competencies required for successful spine surgical fellowship training, and then compared these perceptions to clinical practice. Firstly, a questionnaire was administered to spine fellow trainees and academic spine surgeons across Canada in order to identify the cognitive and technical skills required for successful spine fellowship training. Fellowship trainees and supervisors had similar perceptions on the relative importance of specific cognitive and technical competencies. Differences in perceptions were found when comparing surgeons based on background residency specialty training (orthopaedic surgical or neurosurgical). Secondly, using administrative data, a retrospective study assessed volumes, surgeon characteristics, and outcomes for surgery of the degenerative lumbar spine in Ontario between 1995 and 2001. Neurosurgeons were found to perform more decompressions, and more total procedures, than orthopaedic surgeons with similar outcomes.

Keywords: spine surgery
competencies
degenerative lumbar spine
fellowship training
orthopaedic surgery
neurosurgery
Advisor: Yee, Albert