VictorJuiz/thesis huggingface dataset:
On Pin-to-wire Routing in FPGAs

While FPGA interconnect networks were originally designed to connect logic block output pins to input pins, FPGA users and architects sometimes become motivated to create connections between pins and specific wires in the interconnect. These pin-to-wire connections are motivated by both a desire to employ routing-by-abutment, in modular, pre-laid out systems, and to make direct use of resources in the fabric itself. The goal of this work is to measure the difficulty of forming such pin-to-wire connections. We show that compared to a flat placement of the complete system, the routed wirelength and critical path delay increase by 6% and 15% respectively, and the router effort increases 3.5 times. We show that while pin-to-wire connections impose increased stress on the router, they can be used under some circumstances. We also measure the impact of increasing routing architecture flexibility on these results, and propose a low-cost enhancement to improve pin-to-wire routing.

Keywords: FPGA CAD
Pin-to-Wire
Routing
FPGA Routing Architecture
Advisor: Jonathan, Rose
Characterizing Changes in the Transcriptional Networks underlying Pluripotency in Mouse Embryonic Stem Cells upon the Induction of Differentiation

Mouse embryonic stem cells (mESCs) are pluripotent cells capable of differentiating into all three germ layers present in the adult mouse. In this thesis, I have investigated the transcriptional changes that mESCs undergo as they are induced to differentiate towards the mesoderm lineage by 2i/LIF withdrawal and dimethyl sulfoxide (DMSO) treatment. 5 days of differentiation causes significant drops in expression of Sox2 and Oct4 primary transcript, while expression of Nanog and Kit significantly drops after only 1 day. It was determined that DMSO has no effect on the short-term changes in Nanog and Kit expression induced by 2i/LIF withdrawal. An expanded look at pluripotency-associated genes shows significant up-regulation of Oct4 and down-regulation of Klf4 and Stat3 following only 6 hours of 2i/LIF withdrawal. This data indicates that while some aspects of the transcriptional networks underlying pluripotency respond quickly to mesodermal differentiation cues, others remain unchanged for up to 5 days.

Keywords: Gene Expression
Pluripotency
Mouse Embryonic Stem Cells
Nanog
Advisor: Mitchell, Jennifer
Development of an Optical Brain-computer Interface Using Dynamic Topographical Pattern Classification

Near-infrared spectroscopy (NIRS) in an imaging technique that has gained much attention in brain-computer interfaces (BCIs). Previous NIRS-BCI studies have primarily employed temporal features, derived from the time course of hemodynamic activity, despite potential value contained in the spatial attributes of a response. In an initial offline study, we investigated the value of using joint spatial-temporal pattern classification with dynamic NIR topograms to differentiate intentional cortical activation from rest. With the inclusion of spatiotemporal features, we demonstrated a significant increase in achievable classification accuracies from those obtained using temporal features alone (p < 10-4). In a second study, we evaluated the feasibility of implementing joint spatial-temporal pattern classification in an online system. We developed an online system-paced NIRS-BCI, and were able to differentiate two cortical states with high accuracy (77.4±10.5%). Collectively, these findings demonstrate the value of including spatiotemporal features in the classification of functional NIRS data for BCI applications.

Keywords: Near-infrared spectroscopy
Brain-computer interface
Near-infrared topography
Prefrontal cortex
Spatiotemporal features
User feedback
Advisor: Chau, Tom
The Role of Pumilio 2 in Axonal Outgrowth

Pumilio 2 (PUM2) is a member of the Puf family of mRNA binding proteins and translational regulators which are involved in various processes including embryonic patterning and memory formation. Nevertheless, its functions in the outgrowth of neuronal axons have not been studied. This study shows endogenous expression of PUM2 in neurites of dorsal root ganglia (DRG) neurons and transport of PUM2 along retinal ganglion cell (RGC) axons and their growth cones. Overexpression of PUM2 in DRG neurons resulted in shorter axons when compared to control neurons. Expression of either dominant negative mutation (dnPUM2) or PUM2W349G displayed a reduction in axonal length. PUM2 downregulation with microRNA (miRNA) also caused a reduction in neurite length compared to control neurons. Finally, PUM2 silencing did not alter eye size at E4, which allows investigation of axonal outgrowth in RGC in vivo. These results suggest a novel role for PUM2 in axonal outgrowth.

Keywords: Pumilio 2
Axonal outgrowth
Translational regulation
Advisor: Monnier, Philippe
Generation of Transient Quantum Coherence Using Partially Coherent Radiation

We investigate quantum coherences between excited states induced on quantum systems upon excitation by partially coherent radiation sources. Attempts at rejuvenating coherences using noisy sources are also explored. This work is most relevant to studies of photo-excitation of light harvesting systems under natural conditions as well as to quantum optical experiments using partially coherent lasers. The transient coherent response of a model V system upon irradiation by various models of incoherent light is explored and it was found that it was possible to induce transient excited state coherences upon excitation. These excited state coherences eventually become a small fraction of population and the system reaches a mixed state. Lastly, we critique an existing literature model of excitation by noisy laser and we show that the coherence observed in that scenario is artificial. We propose an alternative using a physical model of noisy excitation.

Keywords: incoherent light
quantum coherence
Advisor: Brumer, Paul
Factors Affecting Distribution of Borate to Protect Building Envelope Components from Biodegradation

Borate can be a potential candidate to protect building envelope components from biodegradation as it has low toxicity and can penetrate wood without pressure treatment, even in the refractory species commonly used in construction industries as structural components. In this research, wood moisture content, grain direction, formulation and species that affect the diffusion of borate in refractory species were investigated. Two highly concentrated formulations were applied and a novel approach (borate bandage) was used to keep the preservative on the surface and enhance the diffusion by reducing surface drying. From ANOVA test for different diffusion periods and depths of penetration, it was found that grain directions and moisture content are significant factors. A mould test was performed, the diffusion co-efficients were calculated and some recommendations were made about the quantity required to protect a specific volume of wood considering the distance moved by diffusion and volume treated in different directions.

Keywords: borate
wood preservative
Advisor: Cooper, Paul
Extracting FMRI Brain Patterns Significantly Related to Behavior via Individual Preprocessing Pipeline Optimization

Background: Functional magnetic resonance imaging (fMRI) can require extensive preprocessing to minimize noise and maximize signal. There is evidence suggesting that fixed-subject preprocessing pipelines, the current standard in fMRI preprocessing, are suboptimal compared to individual-subject pipelines. Aim: We sought to test if individual-subject preprocessing pipeline optimization, compared to fixed, resulted in stronger and more reliable brain-patterns in episodic recognition. Methodology: 27 young healthy controls were scanned via fMRI while performing forced-choice episodic recognition. Several sets of fMRI preprocessing pipelines were tested and optimized in a fixed and individual-subject manner, using methods outlined by Churchill et al. (2011). Results: Individual-subject pipeline optimization, compared to fixed, significantly increased reproducibility, significantly increased the detection of positively and negatively activated voxels, and resulted in a brain-pattern with significant correlation to a task behavioral measure. Conclusions: Individual-subject pipeline optimization, compared to fixed, led to stronger and more reliable brain-patterns that are significantly correlated with behavior.

Keywords: Magnetic resonance imaging
Functional magnetic resonance imaging
Memory
Cognition
Brain mapping
Reproducibility
Multivariate analysis
Statistical models
Advisor: Strother, Stephen
Analysis of Somatic Copy Number Gains in Pancreatic Ductal Adenocarcinoma Implicates ECT2 as a Candidate Therapeutic Target

This study presents an integrated analysis of pancreatic ductal adenocarcinomas (PDACs) for identification of putative cancer driver genes in somatic copy number gains (SCNGs). SCNG data on 60 PDAC genomes was extracted to identify 756 genes, mapping to 20 genomic loci that are recurrently gained. Through copy number and gene expression analysis on a panel of 29 human pancreatic cancer cell lines, this gene catalogue was refined to 34 PDAC high-confidence candidate genes. The performance of these genes was assessed in pooled shRNA screens and only ECT2 showed significant essentiality to cell viability in specific PDAC cell lines with genomic gains at the 3q26.3 locus that harbor this gene. Targeted shRNA-mediated interference of ECT2, as well as pharmacological inhibition, are supportive of the pooled shRNA screen findings. These results favor ECT2 as a candidate target gene for further evaluation in the subset of PDACs presenting with 3q26 somatic copy number gains.

Keywords: Pancreatic Cancer
Copy Number Gains
Advisor: Hudson, Thomas J.
Motion Control of Rigid Bodies in SE(3)

This thesis investigates the control of motion for a general class of vehicles that rotate and translate in three-space, and are propelled by a thrust vector which has fixed direction in body frame. The thesis addresses the problems of path following and position control. For path following, a feedback linearization controller is presented that makes the vehicle follow an arbitrary closed curve while simultaneously allowing the designer to specify the velocity profile of the vehicle on the path and its heading. For position control, a two-stage approach is presented that decouples position control from attitude control, allowing for a modular design and yielding almost global asymptotic stability of any desired hovering equilibrium. The effectiveness of the proposed method is verified both in simulation and experimentally by means of a hardware-in-the-loop setup emulating a co-axial helicopter.

Keywords: path following
position control
control system
motion control
Advisor: Maggiore, Manfredi
Dynamic Imaging of the Fetal Heart Using Metric Optimized Gating

Advances in fetal cardiovascular MRI have been limited by the absence of a reliable cardiac gating signal. Recently, metric optimized gating (MOG) has been proposed as a solution to this limitation. In this thesis, I have developed and validated MOG for cine imaging of the fetal heart. ECG gated cine MR data of the adult heart were acquired from a healthy volunteer to compare MOG reconstructions to conventional ECG reconstructions. The image quality of ECG and MOG reconstructions was compared as was the difference between MOG and ECG trigger times. Fetal images were also acquired, their quality evaluated by experienced radiologists, and the theoretical error in the MOG trigger times calculated. Excellent agreement between ECG and MOG reconstructions was observed. Using MOG, the world’s first gated MR images of the human fetal heart were obtained. Small moving structures were visualized during radial contraction, thus capturing normal fetal cardiac wall motion.

Keywords: MRI
Fetal
Advisor: Macgowan, Christopher K.
The Effectiveness of Checklists versus Bar-codes towards Detecting Medication Planning and Execution Errors

The primary objective of this research was to evaluate the effectiveness of a checklist, compared to a smart pump and bar-code verification system, at detecting different categories of errors in intravenous medication administration. To address this objective, a medication administration safety checklist was first developed in an iterative user-centered design process. The resulting checklist design was then used in a high-fidelity simulation experiment comparing the effectiveness of interventions towards two classifications of error: execution and planning errors. Results showed the checklist provided no additional benefit for error detection over the control condition of current nursing practice. Relative to the checklist group, the smart pump and bar-coding intervention demonstrated increased effectiveness at detecting planning errors. Results of this work will this work will help guide the selection, implementation and design of appropriate interventions for error mitigation in medication administration.

Keywords: checklists
smart pumps
patient safety
medication errors
medication administration
Advisor: Cafazzo, Joseph
Trbovich, Patricia
Investigating Memory for Spatial and Temporal Relations with Eye Movement Monitoring

By using eye movement monitoring (EMM) techniques, investigators have been able to examine the processes that support relational memory as they occur online. However, EMM studies have only focused on memory for spatial relations, producing a lack of EMM evidence for temporal relations. Thus, in the present study, participants performed a recognition memory task with stimuli that varied in their spatial and temporal relations. They were presented with a sequence of objects in a unique spatial configuration, and were instructed to either detect changes in the spatial or temporal relations between study and test presentations. The results provide novel EMM evidence for an interaction between spatial and temporal memory, and the obligatory effects of relational memory processes on eye movement behaviours. Moreover, the current study was also able to test predictions from the temporal context model (Howard & Kahana, 2002), and found evidence for a temporal contiguity effect.

Keywords: eye-tracking
relational memory
aging
Advisor: Ryan, Jennifer D.
A Langendorff-perfused Mouse Heart Model for Delayed Remote Limb Ischemic Preconditioning Studies

Remote ischemic preconditioning (rIPC) through transient limb ischemia induces potent cardioprotection against ischemia reperfusion (IR) injury. I examined the delayed phase of protection that appears 24 hours after the initial rIPC stimulus. The primary objective of this study was to establish a mode of sedation and control treatment for delayed rIPC experiments. I used an ex-vivo, Langendorff isolated-mouse heart preparation of IR injury to examine the delayed effects of an intra-peritoneal (IP) injection, sodium-pentobarbital (SP), halothane and nitrous oxide (N2O) anesthesia on post-ischemic cardiac function. Each anesthetic method improved left-ventricular function after IR injury. SP and halothane anesthesia also reduced LV infarct size. Delayed cardioprotection after IP injections was associated with an increase in phosphorylated-Akt levels. The present study shows that IP injections and inhalational anesthesia invoke cardioprotection and, therefore, indicates that these modes of sedation should not be used as control treatments for studies examining the delayed rIPC phenotype.

Keywords: Ischemia Reperfusion
Myocardial Infarction
Cardiology
Preconditioning
Advisor: Caldarone, Christopher
Requirement(s) for the Replication of Lucerne Transient Streak Virus Satellite RNA

The satellite RNA of Lucerne Transient Streak Virus (LTSV) is a 322-nucleotide, single-stranded circular RNA that has a rod-like structure very similar to that of viroids. As it does not encode any translation products and cannot replicate independently of a helper virus, the satellite RNA is proposed to rely on viral-encoded proteins for the replication and/or cell-to-cell movement that facilitate its systemic infection in a host. To investigate the requirements for replication of the LTSV satellite RNA, transgenic plant systems were generated to express the viral RNA-dependent RNA polymerase and predicted viral transport protein independently as well as in combination. Results of infectivity assays of these transgenic lines demonstrated for the first time that the viral-encoded RNA-dependent RNA polymerase is necessary and sufficient for the replication of LTSV satellite RNA, and that no additional viral proteins are required for its cell-to-cell or systemic transport.

Keywords: Lucerne Transient Streak Virus
Satellite RNA
Viral RNA-dependent RNA polymerase
Viroid
Advisor: AbouHaidar, Mounir
Thermodynamic and Spectroscopic Studies on the Molecular Interaction of Doxorubicin (DOX) with Negatively Charged Polymeric Nanoparticles

The aim of this study was to investigate the molecular interactions of the anti-cancer drug Doxorubicin (DOX) with poly(methacrylic acid) grafted starch nanoparticles (PMAA-g-St). In order to fully understand the DOX/PMAA-g-St system, we conducted in-depth studies on DOX dimer dissociation and DOX/PMAA-g-St binding interactions using various techniques such as isothermal titration calorimetry (ITC), dynamic light scattering (DLS), and fluorescence and absorption spectroscopy. Based on our experimental results, we developed a quantitative thermodynamic model with relevant parameters such as dissociation constant, Kd, as well as enthalpy of binding, ΔH, in order to explain DOX/PMAA-g-St interactions. In addition, we also studied the effect of environmental factors such as pH and NaCl on DOX self-association and DOX/PMAA-g-St complex formation. In conclusion, the combination of results obtained from various techniques as well as the multispecies equilibrium model, enables us to interpret quantitatively the data of drug loading onto and release from polymeric nanoparticles.

Keywords: Doxorubicin
Isothermal Titration Calorimetry
Dynamic Light Scattering
Drug/Polymer Interactions
Electrostatic Interactions
Specific binding
Mechanism of binding
effect of sodium chloride
effect of pH
Advisor: Heiko, Heerklotz
Shirley, Wu
Dental Treatment Needs in the Canadian Population

Objective: To determine the dental treatment needs of Canadians and how they are distributed. Methods: A secondary analysis of data from the Canadian Health Measures Survey was undertaken. Weights were applied to make the data nationally representative. Bivariate and multivariate regressions were used to identify predictors of need. Sensitivity, specificity, positive and negative predictive values were calculated to compare self-reported and clinically determined needs. Results: Of the 34.2% who required dental treatment, most needed restorative (20.4%) and preventive (13.7%) care. The strongest predictors of need were having poor oral health, reporting a self-perceived need for treatment and visiting the dentist infrequently. A discrepancy was found between clinical and self-reported needs. Conclusions: Roughly 12 million Canadians have unmet dental needs. A number of factors are predictive of having unmet dental conditions. Program and policymakers now have information by which to assess if their programs match the dental needs of Canadians.

Keywords: Dental care needs
Health policy
Socio-demographic/economic factors
Advisor: Quiñonez, Carlos
The Supreme Court of Canada's Multifactorial Approach to Deference in Judicial Review

The Supreme Court of Canada has attempted several times to reform the way it approaches the issue of curial deference in judicial review. Each attempt however, has been in vain. This paper argues that the cause of this failure of each reform of the deference test proposed by the Supreme Court is not necessarily one of content, but instead one of structure. Each of the reforms retained a ‘multifactorial approach’ to the deference test, involving the weighing of several factors leading to a prescribed level of deference. Through critical analysis of the approach, and the postulation of an alternative, this paper argues that the multifactorial approach is what thwarts the Court’s intentions, and that it needs to abandon it should it wish to achieve clarity and coherence within judicial review.

Keywords: law
administrative law
Advisor: Dyzenhaus, David
A High-order Finite-volume Scheme for Large-Eddy Simulation of Premixed Flames on Multi-block Cartesian Mesh

Large-eddy simulation (LES) is emerging as a promising computational tool for reacting flows. High-order schemes for LES are desirable to achieve improved solution accuracy with reduced computational cost. In this study, a parallel, block-based, three-dimensional high-order central essentially non-oscillatory (CENO) finite-volume scheme for LES of premixed turbulent combustion is developed for Cartesian mesh. This LES formulation makes use of the flame surface density (FSD) for subfilter-scale reaction rate modelling. An algebraic model is used to approximate the FSD. A detailed explanation of the governing equations for LES and the mathematical framework for CENO schemes are presented. The CENO reconstruction is validated and is also applied to three-dimensional Euler equations prior to its application to the equations governing LES of reacting flows.

Keywords: CFD
Aerospace
Finite-Volume
High-Order
Large-Eddy Simulation
LES
Computational Fluid Dynamics
Premixed Flames
Advisor: Groth, Clinton P. T.
Cortical Morphology in Children with Alcohol-related Neurodevelopmental Disorder

Individuals exposed to alcohol in utero have reduced cortical grey matter volumes. However, the underlying determinants of these reductions have not been investigated exclusively in alcohol-related neurodevelopmental disorder (ARND). Using magnetic resonance imaging scans from 121 participants (57 ARND and 64 controls) aged 8 to 16 years, cortical morphology was analyzed. Results revealed the ARND group had reduced cortical grey matter volumes, but did not differ from controls in cortical thickness. Rather, the cortical abnormalities reflected reductions in global surface area, local surface area reductions in the right occipital-temporal area and right superior temporal gyrus, as well as reduced gyrification. A significant interaction between sex and group was observed, with females showing greater reductions than males in cortical volume and surface area. Results suggest that ARND is characterized by global reductions in cortical surface area and gyrification and females are more vulnerable than males to the teratogenic effects of alcohol.

Keywords: Alcohol-related Neurodevelopmental Disorder
Structural MRI
Cortical Thickness
Surface Area
Gyrification
Advisor: Rovet, Joanne
Investigations into Tyrosine-mediated Hyperphosphorylation and Aggregation of Tau Protein via Ferrocene Bioconjugates

Tau, a microtubule associated protein, has been implicated in the formation of neurofibrillary tangles, a hallmark of Alzheimer’s disease.1 Resulting from the hyperphosphorylation of tyrosine, serine and threonine residues, protein kinases play an intricate role in the pathway of NFT formation.2 While a number of serine/ threonine kinases such as Glycogen Synthase Kinase 3 beta, have been implicated in the hyperphosphorylation of tau, and it is now believed that tyrosine phosphorylation plays a role. It appears that the degree to which tau is phosphorylated, and region in which phosphorylation occurs play a critical role in aggregate formation. Here we present the use of Ferrocene bioconjugates to monitor tyrosine-mediated hyperphosphorylation and aggregation. Electrochemistry, electron microscopy, surface plasmon resonance, Time of Flight Secondary Ion Mass Spectrometry and X-Ray Photoelectron Spectroscopy were used to gain insight into the role of tyrosine phosphorylation on hyperphosphorylation.

Keywords: Tau
Electrochemistry
Ferrocene
Hyperphosphorylation
Advisor: Kraatz, Heinz-Bernhard