VictorJuiz/thesis huggingface dataset:
Low-cost Hardware Profiling of Run-time and Energy in FPGA Soft Processors

Field Programmable Gate Arrays (FPGAs) are a reconfigurable hardware platform which enable the acceleration of software code through the use of custom-hardware circuits. Complex systems combining processors with programmable logic require partitioning to decide which code segments to accelerate. This thesis provides tools to help determine which software code sections would most benefit from hardware acceleration. A low-overhead profiling architecture, called LEAP, is proposed to attain real-time profiles of an FPGA-based processor. LEAP is designed to be extensible for a variety of profiling tasks, three of which are investigated and implemented to identify candidate software for acceleration. 1) Cycle profiling determines the most time-consuming functions to maximize speedup. 2) Cache stall profiling detects memory-intensive code; large memory overheads reduce the benefits of acceleration. 3) Energy consumption profiling detects energy-inefficient code through the use of an instruction-level power database to minimize the system's energy consumption.

Keywords: Profiling
FPGAs
hardware/software co-design
hardware/software partitioning
soft processors
Advisor: Anderson, Jason
Brown, Stephen
Extraction of Proliferation and Death Rates in Cytokine-stimulated Erythroid Progenitors Using Cell-division Tracking and Mathematical Modeling

Controlling fates of stem and progenitor cells is one of the central goals of regenerative medicine. However, conventional cell enumeration methods are unable to distinguish between the effects of cell death, proliferation, and differentiation through molecular interventions on the output of specific cell types. We have devised a strategy to simultaneously obtain proliferation and death rates in cultures of highly purified erythroid progenitors. The approach is based on combining cell-surface marker analysis, cell-division tracking and 7-amino-actinomycin-D staining to monitor cell death. A compartment model of cell proliferation was developed to evaluate cell generation-specific length of cell-division, rates of entry into division, and cell death, from the experimental cell-division tracking data obtained following stimulation with erythropoietin (EPO) and Stem cell factor (SCF). The results indicated that EPO and SCF, either as single factor or in combination, differentially affect the rates of differentiation, length of cell-division and rates of death.

Keywords: erythroid
mathematical modeling
stem cells
cell division
differentiation
CFSE
CFDA-SE
red blood cell
Advisor: Julie, Audet
Validation of an Internet-based Approach to Cognitive Screening in Multiple Sclerosis

Cognitive impairment affects approximately half of multiple sclerosis (MS) patients. The Multiple Sclerosis Neuropsychological Questionnaire (MSNQ) has previously demonstrated validity for detecting cognitive impairment in MS, and is quick and easy to complete. The objective was to validate an internet version of the MSNQ. The following were completed at home over the internet for 82 MS patients: (a) patient self-report version of the MSNQ (P-MSNQ), (b) informant version of the MSNQ (I-MSNQ), and (c) Centre for Epidemiological Studies Depression Scale (CES-D). Thereafter, patients completed in-office neuropsychological testing using the Brief Repeatable Battery of Neuropsychological Tests (BRB-N). Both the P-MSNQ and I-MSNQ were highly correlated with depression. The best-cut off score on the I-MSNQ was a 26, which gave a sensitivity of 72% and 60% for detecting cognitive impairment on the BRB-N. Given the modest sensitivity and specificity values, the MSNQ is not recommended for neuropsychological screening purposes over the internet.

Keywords: multiple sclerosis
cognition
neuropsychology
internet
Advisor: Feinstein, Anthony
New-generation Fully Programmable Controller for Functional Electrical Stimulation Applications

Functional electrical stimulation (FES) systems have been developed to help restore various neuromuscular functions in individuals with neurological disorders leading to paralysis. Most of the current FES systems are designed for specific neuroprosthesis applications (i.e., walking, grasping, bladder voiding, coughing, etc.) and when one intends to use them in other custom made applications they are very limited due to a lack of functionality and flexibility in hardware and programmability. This prevents effective and efficient development of customized neuroprostheses. Research and development efforts at the Rehabilitation Engineering Laboratory at the University of Toronto were being carried out with an objective to produce a new, fully programmable and portable FES system. This thesis presents a novel proof-of-concept prototype controller for use in the new FES system. The controller subsystem manages and controls the overall FES system including the real-time decoding and execution of stimulation, data acquisition, external systems interfaces and user interface.

Keywords: Functional Electrical Stimulation
Neuroprostheses
Controller
Advisor: Popovic, Milos R.
Effect of Potassium and Magnesium Doping on Sintering and Properties of Calcium Polyphosphate

Porous constructs of calcium polyphosphate (CPP) are under investigation as a substrate for tissue engineering of cartilage for repair of osteochondral defects. Previous studies have shown that CPP has the required features to satisfy these requirements. However, its degradation rate is lower than desired. This study investigated the effect of doping with MgCO3, MgCl2, K2CO3 or KCl at a molar ratio of M/Ca = 0.02 on sintering and in vitro degradation behavior of CPP. Doping with magnesium or potassium improved the tensile and compressive strengths of CPP at similar porosities. After 15 days of aging in phosphate buffer saline, the rate of tensile strength loss was faster for the doped CPP groups than undoped CPP. The chemical degradation rate of Mg-doped CPP groups was the fastest among CPP groups. The chemical degradation rate of K-doped CPP groups was slower than undoped CPP.

Keywords: calcium polyphosphate
CPP
doping
magnesium
potassium
degradation
Advisor: Grynpas, Marc D.
Coyle, Thomas W.
The Appeal of Israel: Whiteness, Anti-Semitism, and the Roots of Diaspora Zionism in Canada

This thesis explores the appeal of Israel and Zionism for Ashkenazi Jews in Canada. The origins of Diaspora Zionism are examined using a genealogical methodology and analyzed through a bricolage of theoretical lenses including post-structuralism, psychoanalysis, and critical race theory. The active maintenance of Zionist hegemony in Canada is also explored through a discourse analysis of several Jewish-Zionist educational programs. The discursive practices of the Jewish National Fund and Taglit Birthright Israel are analyzed in light of some of the factors that have historically attracted Jews to Israel and Zionism. The desire to inhabit an alternative Jewish subject position in line with normative European ideals of whiteness is identified as a significant component of this attraction. It is nevertheless suggested that the appeal of Israel and Zionism is by no means immutable and that Jewish opposition to Zionism is likely to only increase in the coming years.

Keywords: Jewish
Diaspora
Israel
Zionism
Whiteness
Race
Advisor: Nestel, Sheryl
A Role for a Novel β-catenin Binding Protein in Epithelial-mesenchymal Transitions and Breast Cancer Progression

Epithelial-mesenchymal transition (EMT) has a critical role in tumor progression and has been correlated with the basal-like subtype of human breast cancers. Here I report a novel β-catenin binding protein, which I have shown to be expressed in invasive breast cancer and hypothesized to have a role in breast tumor progression. In normal breast tissue, expression is restricted to the myoepithelium while in breast cancer the expression pattern is similar to smooth muscle actin and vimentin. I have demonstrated that silencing of this protein in breast tumor cells reduces migration by over 50 percent. Furthermore, I have identified this β-catenin binding protein as a target of the Snail EMT network and have demonstrated this protein to be a marker of basal-like carcinomas. These results define a role for this novel protein in EMT, as a marker for the basal subtype, and a promising therapeutic target for metastasis inhibition.

Keywords: EMT
basal phenotype breast cancer
Advisor: Rozakis-Adcock, Maria
The Role of Mindin, a Member of the Mindin-F-spondin Family, in Immune Responses and Cardiac Remodeling Post Myocardial Infarction

Mindin (Spondin 2) is a highly conserved extracellular matrix protein of the Mindin-F-spondin family and a regulator of host innate immunity. Despite its expression in the heart, its role in cardiac stress response is unknown. The objective of this study was to determine the role of mindin following myocardial infarction (MI). C57/BL6 wild-type (mindin+/+) or mindin knockout (mindin-/-) mice were randomized to permanent left anterior descending (LAD) coronary artery ligation or sham operation. Mindin expression level increased maximally on day 7 post MI, but returned to baseline by day 28. Mindin-/- mice showed reduced mortality, rupture rate, cardiac MMP-9/-2 activities, NF-kB activation, cytokines and macrophage recruitment. We concluded that mindin is a significant contributor to mortality and acute adverse remodeling post MI, partly through its unique attributes of innate immune regulator and inhibitor of angiogenesis. Mindin may function as a potential biomarker or therapeutic target post MI.

Keywords: Myocardial infarction
cardiac remodeling
Advisor: Liu, Peter
Segregation versus Self-determination: A Black and White Debate on Canada's First Africentric School

The racialized realities faced by Black students provide an impetus to examine the controversy over Canada's first Africentric Alternative School, approved on January 29, 2008 by the Toronto District School Board. Newspaper articles, editorials and letters to the editor, as well as speeches by delegations and trustees, provide a rich snapshot of the arguments put forth in the heated political debate. Through the lens of equity and critical race theory, the diverse and divergent stances taken by both proponents and opponents of the school are analysed and understood. A conceptual framework of hidden and public transcripts (Scott, 1990) is used to distinguish arguments that reflect on the lived experiences of Black students from those that reiterate the dominant discourses of liberal democratic societies. The findings emerge as three opposing sets of themes that reveal a transcript reflective of the ongoing salience of racism within ostensibly liberal claims to racial equality.

Keywords: Africentric
Afrocentric
Black-focused
Black school
Toronto District School Board
critical race theory
liberal democratic discourses
hidden transcripts
lived experiences
race
racism
education
Advisor: Eichler, Margrit
The Role of Cell Adhesion Genes in the Pathogenesis of Medulloblastoma

Medulloblastoma is the most common pediatric brain tumour, yet many of the underlying genetic and epigenetic factors have yet to be discovered. After a genome wide screen of a large cohort of primary medulloblastomas, we discovered that many of the genes within the cell adhesion family are affected by either copy number loss and/or decreased expression unexplained by copy number change. This led us to believe that both genetic and epigenetic factors were affecting this gene family. Through methylation-specific PCR, RT-PCR and high-throughput methylation status analysis, we have concluded that promoter CpG methylation plays a role in the expression of the PCDH10 protein in both medulloblastoma cell lines and primary tumours. Through functional validation with a stable cell line re-expressing PCDH10, I show that cell cycle and proliferation remain unchanged but migration is decreased in cells with PCDH10 re-expression. This suggests that PCDH10 has characteristics of a tumour suppressor in medulloblastoma.

Keywords: medulloblastoma
PCDH10
Advisor: Taylor, Michael
Muscle-macrophage & Macrophage-macrophage Interactions in Diabetogenic Environment

Diabetes and obesity are associated with inflammation and activation of the immune system with infiltration of adipose tissue by macrophages. This is mainly studied in adipose tissue, with limited information to clarify immune-skeletal muscle interactions in these conditions. We show that exposure of L6 rat skeletal muscle cells to saturated fatty acid palmitate results in insulin resistance, activation of inflammatory pathways, upregulation of pro-inflammatory cytokine and chemokine gene expression and secretion. We identified monocyte chemoattractant protein-1 [MCP-1] as the main factor responsible for macrophage attraction, as blocking it reduced macrophage migration to muscle cells. When macrophages are exposed to palmitate, a similar response ensues with production of macrophage chemoattractants and activation of inflammatory pathways and gene expression profiles, and secretion of multiple cytokines. Our work identifies MCP-1 chemokine produced in response to palmitate treatment by both muscle cells and macrophages and provides a potential link in immune-metabolic crosstalk in diabetogenic environment.

Keywords: Obesity
Inflammation
Diabetes
Macrophage
Muscle
Advisor: Klip, Amira
The Response of Annulus Fibrosus Cells to Fibronectin- Coated Nanofibrous Polyurethrane-Carbonate Anionic Dihydroxyoligomer Scaffolds

Tissue engineering of the annulus fibrosus (AF) is challenging due to its complex lamellar structure. Polyurethane scaffolds have shown promise in AF tissue engineering. The current study examines whether matrix protein coatings (collagen type I, fibronectin, or vitronectin) would enhance cell attachment and promote cell and collagen orientation that more closely mimics native AF. The results demonstrate that the greatest cell attachment occurred with fibronectin (Fn)-coated scaffolds. Cells on Fn-coated scaffolds were also aligned parallel to scaffold fibers, a process that involved α5β1 integrin, determined by integrin-specific blocking antibodies. The inhibition of this integrin reduced AF cell spreading and alignment and the changes in cell shape were regulated by the actin cytoskeleton, demonstrated using cytochalasin D inhibitor. Cells on Fn-coated scaffolds formed fibrillar Fn, synthesized significantly more collagen, and showed alignment of type I collagen that more closely mimics native AF therefore facilitating the development of the tissue in vitro.

Keywords: annulus fibrosus
tissue engineering
nanofibrous scaffolds
polyurethane
Advisor: Kandel, Rita A.
Santerre, J. Paul
Role of DNedd4 Splice Isoforms in Neuromuscular Synaptogenesis in Drosophila Melanogaster

Drosophila Nedd4 (DNedd4), an E3 ubiquitin ligase, is known to be involved in neuromuscular (NM) synaptogenesis during embryogenesis. To further elucidate its mechanism and function in this process, two major splice isoforms, dNedd4 short (dNedd4S) and dNedd4 long (dNedd4L), were studied. My work shows that while dNedd4S positively regulates NM synaptogenesis, dNedd4L plays a negative role in this process. Unique regions in dNedd4L, including the N-terminal 66 amino acid-long sequence (but not the putative dAkt phosphorylation site) and the middle 159 amino acid-long sequence, as well as the catalytic site, are required for its negative function. I proposed one possible mechanism of dNedd4L acting as a negative regulator of dNedd4S. Results from my studies of the putative effect of dNedd4L on the catalytic activity of dNedd4S in vitro, as well as on the function of dNedd4S towards Comm in Drosophila S2 cells, did not support this mechanism.

Keywords: E3 ubiquitin ligase
neuromuscular synaptogenesis
Nedd4
Advisor: Rotin, Daniela
Optimization of an Affinity Purification-mass Spectrometry Pipeline and Characterization of the Rub1p and Smt3p Interactomes

The ubiquitin-like proteins (Ubls) are small polypeptides that function as post-translational modifications. Modification of a protein with a Ubl can alter its localization, activity and/or half-life. SUMO and Rub1p/Nedd8 are two Ubls that play important roles in a number of critical cellular processes, yet their specific cellular functions remain poorly understood. To better understand these important Ubls, we developed a robust affinity purification-mass spectrometry (AP-MS) technique to generate protein-protein interaction maps for the Ubl systems. Each bait was systematically expressed as a C-terminal HA-tagged fusion protein in S. cerevisiae. A standardized method in which affinity purification via the HA epitope, followed by mild washing and mass spectrometric analysis, was performed and the data generated were used to build interaction maps. Affinity purification of the Rub1p E3 ligase Dcn1p identified a novel interaction with the AAA ATPase Cdc48p. This interaction was further studied to determine its biological significance.

Keywords: Ubiquitin-like Proteins
Affinity Purification-Mass Spectrometry
Dcn1p
Cdc48p
Advisor: Raught, Brian
Depression, Psychological Distress and Breast and Cervical Cancer Screening: A Population-based Study in Ontario Women

Purpose: The objective of this study was to investigate both depression and psychological distress as determinants of breast and cervical cancer screening. Methods: Ontario female respondents to the Canadian Community Health Survey version 1.2 (2002) were assessed for both Major Depressive Disorder (World Mental Health-Composite International Diagnostic Interview for depression) and psychological distress (Kessler 6-item Distress Scale (K6)>/= 8). Respondents eligible for screening (N=4042 for cervical cancer; N=1403 for breast cancer) were linked to Ontario administrative health service data to prospectively ascertain screening outcomes. Results: Women with K6 >/= 8 had reduced breast cancer screening compliance in adjusted analyses (AOR 0.63, 95% CI 0.40-0.97). The association between K6 >/= 8 and cervical cancer screening approached significance in women over age 40 (AOR=0.65, 95%CI 0.41-1.04). Conclusion: Decreased likelihood of screening in women with clinically significant psychological distress suggests that attention to adequacy of preventive services is a potential target for intervention.

Keywords: Depression
Psychological Distress
breast cancer screening
cervical cancer screening
Advisor: Goering, Paula N.
Oxygen Transport Measured by Isotope Tracing through Solid Oxides

The following thesis demonstrates two isotope tracing experiments that measure oxygen transport through electrochemically polarized solid oxides. Cathode-symmetric ‘button’ cells with yttria stabilized zirconia(YSZ) electrolytes and either strontium doped lanthanum manganate(LSM) or composite LSM/YSZ cathodes were studied. The first experiment measured the residence time distributions(RTD) of 34O2. The measured RTDs were compared at different temperatures(700-800°C) and applied potentials(-2 to -8V). Comparisons with simulated RTDs revealed that oxygen transport was laterally heterogeneous. Delamination of the counter electrode is likely the source of the heterogeneity. The second experiment measured a wave of 18O by exposing an interior cross section and applying ToF-SIMS analysis. A depth profile was produced that spans the cathode and electrolyte interface. The depth profile was compared with a variety of limiting oxygen activation scenarios predicted by a simple 1-D model. Comparisons demonstrated that oxygen activation is likely not restricted to the cathode and electrolyte interface.

Keywords: Isotope tracing
Solid oxides
Secondary Ion Mass Spectroscopy
SIMS
Residence Time Distributions
RTD
Advisor: Mims, Charles A.
Teaching Mathematics for Social Justice and its Effects on Affluent Students

There is a crisis in mathematics education (National Research Council, 1989). This crisis has caused stakeholders to question the purpose of mathematics education. Teaching mathematics for social justice is a pedagogy that uses mathematics as a tool to expose students to issues concerning power, resource inequities, and disparate opportunities between different social groups to illicit social and political action (Gutstein, 2006). This study uses action research to explore the effects of incorporating social justice issues in mathematics with affluent, middle school students. Findings indicate that integrating social justice issues into mathematics affected some students’ cognitive and affective domains and in some cases led to empowerment and action. The study also found that students’ perception of responsibility, their age and personal connections along with the amount of teacher direction may have affected students’ development of social agency. These findings help to inform teachers’ practices and contribute to literature on critical mathematics.

Keywords: social justice
mathematics
social agency
Advisor: Esmonde, Indigo
History From the Heart: Difficult Pasts and Possible Futures in the Heterogeneous Doukhobor Community in Canada

This thesis shares the results of oral history interviews with members of the heterogeneous Doukhobor community in Canada. The stories and memories of fifteen different voices highlight the influence of intersecting demographic variables (age, gender, ideological affiliation, and geographic location) on the experience of Doukhobor life in Canada during times of sensationalized conflict. The interviews are framed and analyzed through broader questions of history and cultural sustainability. What considerations influence the representation of difficult Doukhobor pasts in Canada? In the contemporary context of unification and reconciliation, how does one speak of conflict? This thesis shows that discussions of the past surface considerable contradiction in the collective memory of the Doukhobor community; the results outline various individual and community strategies that are used to manage the past in favour of the present. Ultimately, this thesis locates memory as a social and cultural anchor that must support a history for the future.

Keywords: oral history
Doukhobor
Dukhobor
heterogeneous
cultural community
Canada
temporality
cultural sustainability
difficult past
depredation
conflict
reconciliation
memory
representation
strategy
Verigin
Sons of Freedom
Christian Community of Universal Brotherhood
contradiction
pacifism
colonial state
ethics
Advisor: Restoule, Jean-Paul
Stories of Wisdom: A Qualitative Analysis of Autobiographical Narratives of Relatively Wise and Unwise Individuals

The scientific study of wisdom is a contentious field. There is little agreement among dominant research programs concerning how to conceptualize and measure the elusive phenomenon of wisdom. The current study argues for a narrative analysis of this concept given that autobiographical stories offer a contextually rich vista into real-life manifestations of wisdom. Presented here is a qualitative investigation of autobiographical wisdom narratives from 8 individuals distributed across parameters of age, gender, and degree of wisdom. Results point to the possibility that relatively wise persons define wisdom more elaborately, participate in more sophisticated autobiographical reasoning processes, and engage with master narratives in a more evaluative and critical manner than relatively unwise individuals. These features did not appear to differ across levels of age and gender. This study validates a narrative approach to the science of wisdom, and suggests that stories may be central to advancing our understanding of this concept.

Keywords: wisdom
narrative
autobiographical reasoning
master narrative engagement
stories
coherence
Advisor: Ferrari, Michel