VictorJuiz/thesis huggingface dataset:
Power, Performance and Area Consequences of Multi-context Support in Coarse-grained Reconfigurable Arrays

Coarse-Grained Reconfigurable Arrays (CGRAs) are programmable logic devices comprising a two-dimensional array of large, often ALU-like, logic blocks, and datapath-style (multi-bit) programmable interconnect. A feature frequently associated with CGRAs is dynamic reconfigurability, wherein the CGRA supports multiple contexts. The multiple contexts form a set of configuration bitstreams that are loaded into the CGRA simultaneously and cycled through according to a schedule. Multi-context allows the CGRA hardware to be time-multiplexed: the logic blocks and interconnect can perform different functions according to the context selected in each clock cycle. In this thesis, we consider how multi-context may be implemented at the circuit level, and evaluate four circuit implementations from the power, performance, and area (PPA) perspectives. The PPA overhead of the multi-context feature in CGRAs vs. a single-context device is also quantified. We also explore context-switching using a State Transition Controller (STC), which can switch contexts without a fully predefined pattern.

Keywords: cgra
coarse-grained reconfigurable arrays
dynamic reconfiguration
multi-context
time multiplexing
Advisor: Anderson, Jason H
Dual Existence: Performing the Bi-narrative Construction of University of Toronto’s International Students Studying from Home via Zoom

This paper recounts a qualitative research that employed storytelling as a research method to explore how University of Toronto international students who studied from outside Canada due to the Covid-19 travel restrictions construct their experience of space and time; form a community of support despite the divergence in their geographical, social, and cultural backgrounds; and respond with empathy to the one another’s stories. The project involved four participants from diverse nationalities and a range of issues that constitute their narration include language barrier; time difference; dual existence; and how they managed the challenges.

Keywords: Community
Covid-19
Dual existence
International Students
Storytelling
Advisor: Cesare Schotzko, Nikki T.
A Markov Process Approach to Untangling Intention Versus Execution in Tennis

Value functions are used in sports applications to determine the optimal action players should employ. However, most literature implicitly assumes that the player can perform the prescribed action with known and fixed probability of success. The effect of varying this probability or, equivalently, ``execution error'' in implementing an action, has received limited attention. We develop a novel modeling framework based on Markov processes to investigate how execution error impacts a player's value function and strategy in tennis. We power our models with hundreds of millions of simulated tennis shots. We find that optimal strategies become more conservative as execution error grows, and that having perfect execution with the empirical shot selection strategy is roughly equivalent to choosing one or two optimal shots with average execution error. We find that execution error on backhand shots is the costliest, and that optimal shot selection on a serve return is the most valuable.

Keywords: Markov processes
Execution error
OR in sports
Simulation
Tennis
Advisor: Chan, Timothy C.Y.
Ontology Evolution as Ontology Reuse

Throughout the ontology lifecycle, different versions of an ontology are created, and the need for version management has been widely recognized. Although a number of definitions for ontology versioning have been proposed, several questions remain. How are different versions of an ontology related to each other? In what sense are they all versions of the same ontology? In this thesis we present an alternative characterization of ontology evolution as a form of ontology reuse. We propose a formal definition of ontology version with respect to the specification of the intended models of an ontology. We prove that this is equivalent to the formal definition of a reusable ontology. Based on this equivalence, we propose version operators and show how ontology evolution can be formalized through its application. Finally, in a case study of the Semantic Sensor Network Ontology, we leverage different techniques to assist in analyzing the feasibility of the application of the version operator.

Keywords: intended models
ontology design
ontology evolution
ontology versioning
reuse
Advisor: Gruninger, Michael
Inventory Management using Reinforcement Learning

As a significant part of a supply chain, inventory management can involve predicting purchases from customers and controlling order fulfillment. In this thesis, we proposed a Monte Carlo Tree Search (MCTS) algorithm, combined with a local search optimization algorithm for search space reduction and a time series prediction model based on encoder-decoder structure and Bayesian optimization for demand forecasting to tackle an inventory allocation problem from Nestlé Canada, which is a sequential decision problem where we need to minimize the total monthly shortage of supply penalty charged by different companies by suggesting an optimized allocation plan every day with limited inventory on hand and unknown future orders. MCTS is a heuristic search algorithm that has been proved to be powerful in various decision processes, for example board games. In this thesis we introduced a variant of MCTS and showed that MCTS and reinforcement learning can also be effective in inventory management problems.

Keywords: Inventory Management
Monte Carlo Tree Search
Supply Chain Optimization
Advisor: Lee, Chi-Guhn
Reconfigurable Cylindrical Beamformers based on Electromagnetic Surfaces

Communication networks involving data transfers between nodes both in the azimuth and elevation, such as military or search-and-rescue, require an antenna that can beamform and also beam scan. This thesis explores two reconfigurable cylindrical beamformers that can be used in these ad hoc networks. The first design presented is a reconfigurable 1-bit miniaturized frequency selective surface that switches between a reflecting and transmitting mode. The second is a continuously tunable metasurface that achieves both a reflecting and transmitting state along with over 180 deg of phase range in the transmit mode. The first design is fabricated and assembled into a cylindrical configuration. The antenna is shown to be able to both beamform and beam scan in the azimuth plane, between 4.9 GHz and 5.8 GHz.

Keywords: Azimuth
Cylindrical
MEFSS
metasurface
Reconfigurable
Advisor: Hum, Sean V.
The Effects of Cannabidiol (CBD) and Δ9-Tetrahydrocannabinol (THC), Alone and in Combination, in Animal Models of Epilepsy and the Comorbidities of Epilepsy

People with epilepsy often suffer not only from seizures but also from psychiatric comorbidities that accompany the seizures. Recently, cannabidiol (CBD) and combinations of CBD with Δ9-tetrahydrocannabinol (THC) have been proposed for the treatment of epilepsy and the epileptic comorbidities. In the present study, CBD, THC, and combinations of CBD and THC, were evaluated in the mouse maximal electroshock (MES) seizure test, the forced swim test (FST) of antidepressant activity, and the MK-801 model of psychosis. It was found that: 1) CBD and THC were both effective in the MES model, and they were more effective in combination; 2) CBD and THC were ineffective in the FST model, alone or in combination; and 3) CBD and THC were less effective in the MK-801 model but had significant effects in combination. CBD and CBD+THC might be useful in the treatment of epilepsy and possibly psychosis, but not in the treatment of depression.

Keywords: Cannabidiol
Comorbidities
Depression
Epilepsy
Psychosis
Tetrahydrocannabinol
Advisor: Burnham, Willets M
Hardware-accelerated Minimum Probability Flow Training for Boltzmann Machine Problems

Minimum Probability Flow (MPF) learning is a method used to solve parameter estimations such as in machine learning. In this work, we focus on presenting a GPU implementation of the MPF Trainer for Boltzmann machine learning problems. Moreover, to evaluate its performance, we compare it to another GPU accelerated method based on maximum likelihood estimation (MLE), Digital Trainer, for different types of problems. Our experiments are run on NVIDIA TITAN V and show that our GPU implementation of MPF has achieved at least 20x speed-up compared to its CPU version for problems that at least have a network size of 1024 and a data set of 1024 training vectors. Furthermore, we demonstrate that 1. MPF Trainer performs nearly twice as better than Digital Trainer for maximizing the learning capacity of a fully-connected network and 2. in the inverse Ising model problems, Digital Trainer outperforms MPF Trainer by at least an order of magnitude in term of errors in pairwise correlations.

Advisor: Sheikholeslami, Ali
Elucidating the Role of SPEG in Muscle Development and Function

Centronuclear Myopathy is a congenital neuromuscular disorder mostly caused by mutations on Excitation-Contraction Coupling (ECC) genes. One novel gene mutated in these patients is SPEG (Striated Muscle Preferentially Expressed Protein Kinase). Its absence leads to muscle weakness, increased centralized nuclei in myofibers, and dilated cardiomyopathy, with severe cases including early mortality. Evidence suggests SPEG acts through ECC pathway. However, previous research has focused on cardiac muscle and has been limited by neonatal mortality of the mouse model. Therefore, its function throughout embryonic development and in skeletal muscle remains unknown. The work herein presented demonstrates I successfully generated zebrafish speg KO models which I used to study its role in muscle development and function. These mutants effectively replicate the muscle weakness and decreased survival reported in these patients and KO mice. In absence of therapies, my model also allows future high-throughput experiments in aims to find potential therapies for these patients.

Keywords: centronuclear myopathy
disease model
excitation-contraction coupling
muscle
SPEG
zebrafish
Advisor: Dowling, James J
Negative Pressure and its Role in Lung Re-epithelialization

For end-stage lung disease, lung transplantation remains the only treatment. Transplantation, however, is limited due to the lack of organs. While the generation of new lungs via the recellularization of biological scaffolds is an alternative, proper repopulation of the lung remains a challenge. In an attempt to enhance the re-epithelialization of the decellularized lung airways, the inclusion of negative pressure during cell seeding and bioreactor culture phase was investigated. We designed a negative pressure cell seeding method and a physiological wet negative pressure ventilation device that allowed for control over ventilation parameters such as tidal volume and accommodation of physiological respiratory rates. We also designed a biomimetic lung bioreactor system that accommodates vascular perfusion, physiological ventilation and in vivo spatial orientation. These new technologies and methodologies resulted in significantly higher cell surface coverage and number in the decellularized lung scaffolds than the traditional approaches.

Keywords: Bio-engineered lungs
Cell delivery
Lung regeneration
Lung transplantation
Negative pressure ventilation
Tissue engineering
Advisor: Waddell, Tom
Karoubi, Golnaz
Understanding the Disease Pathogenesis of X-linked Myotubular Myopathy

X-linked myotubular myopathy (XLMTM) is a fatal condition caused by mutations in myotubularin 1 (MTM1), which encodes a lipid phosphatase. Despite our increased understanding of XLMTM pathology, how MTM1 functions in skeletal muscle is unknown. To address this, I performed a phenotypic and molecular analysis of Mtm1 knockout mice throughout disease development. These mice exhibit histopathological abnormalities such as central nuclei, muscle hypotrophy, and increased oxidative staining. Alterations in transcriptome (gene expression), epigenome (DNA methylation) and proteome (protein levels of disease markers) are also characteristics of this model. As a secondary aim, I performed AP-MS experiments using a MTM1-6xHis mouse to identify the MTM1 interactome in the context of skeletal muscle. Lastly, as a third aim, I characterized Mtm1 KO C2C12 cell line as a model for XLMTM. This work herein explores the function and interactome of MTM1 in skeletal muscle and expands our current understanding of XLMTM.

Keywords: CNM
MTM1
XLMTM
Advisor: Dowling, James J
Characterizing Striga hermonthica Gibberellin Receptors and Investigating their Crosstalk with Strigolactone Receptors

Gibberellic acids (GAs) are a group of phytohormones known to stimulate germination of land plants. However, a root parasitic plant called Striga hermonthica (Striga) germinates poorly on GA, instead utilizes host root-exuded phytohormones strigolactones (SLs) to initiate germination. It remains unknown why GA signalling is not sufficient to germinate Striga. Here I report the identification and functional analysis of three Striga GA receptors, GA INSENSITIVE DWARF1-Like (GIL), and explored the crosstalk between GA and SL signalling pathways. ShGILs interacted with GA signalling targets, ShDELFAs, and overexpression of ShGIL complemented the germination defect of Atgid1ac loss-of-function mutant, indicating ShGILs may function as GA receptors. In addition, two ShGILs interacted with Striga SL receptors, ShHTLs, and overexpression of ShHTLs increased the GA requirement in GA auxotrophic Arabidopsis (ga1-10) suggesting GA-SL crosstalk and its role in regulating Striga germination. This study provides an insight in understanding GA signalling during Striga seed germination.

Advisor: McCourt, Peter
Lumba, Shelley
Modulation of Spinal Dorsal Horn Long-term Potentiation by Non-ionotropic NMDA Receptor Activity

Pathological pain is characterized by enhanced synaptic strength within nociceptive pathways of the spinal dorsal horn that arises in the absence of any obvious trigger. Unfortunately, current treatment options often fail to provide adequate and lasting pain relief as they do not address the underlying mechanisms of persistent pain. The enhancement of synaptic transmission between nociceptive afferents and dorsal horn neurons (long-term potentiation; LTP) is associated with sensitization. This project aims to investigate the role of non-ionotropic NMDA receptor (NI-NMDAR) signalling in the plasticity of nociceptive neurons and to induce synaptic depotentiation through a combination of electrophysiological recordings and pharmacological interventions. These data indicate that NI-NMDAR activity could reverse dorsal horn LTP with 7CK, a NMDA receptor glycine site antagonist and was dependent on downstream protein phosphatase-1 activity. Overall, this project will provide essential new insights into the mechanisms by which synaptic depotentiation can be exploited to erase pathological pain.

Keywords: Long Term Potentiation
Non-Ionotropic NMDA Receptor
Spinal Cord Dorsal Horn
Advisor: Bonin, Robert P
Implementing Reconfigurable Packet Matchers on Field-programmable Gate Arrays

In networking applications, packets of data can be sorted and filtered using a set of rules. Historically, this matching was done using conventional processors. As network speeds grow faster, the need for specialized circuitry to process these packets increases. Field Programmable Gate Arrays (FPGAs) are a technology that allows a user to create custom circuitry that can be changed to suit the application. Using FPGAs, this work looks to evaluate two approaches to performing packet classification at high-speed line rates of 10 Gbits/s and higher, with a 10% per 10 minute turnover in the ruleset. The first approach utilizes next-gen memory to store a million-entry ruleset; the second approach exploits a real-time partial reconfiguration of FPGAs to reprogram the FPGA circuitry with a variety of matching schemas. The two approaches are then compared to other FPGA-based systems, in terms of performance, rule density, and ease of updates.

Keywords: FPGA
Packet Classification
Advisor: Jacobsen, Hans-Arno
Epigenetics of Schizophrenia and Suicidality

Suicidal behavior is the product of the interaction of many risk factors, such as genetics and environmental factors, and several studies support a strong association between perceived stress and suicidal behaviors. My thesis aimed to understand the DNA methylation age acceleration in individuals with schizophrenia, severe psychosis, and severe current suicide ideation (SI). It also aimed to determine whether DNA methylation could have a mediating effect on the interaction between stress and severe current SI. Bivariate correlation, mediation model 4 on SPSS, Horvath online calculator were used during these analyses. There was no epigenetic age acceleration between schizophrenia and healthy control; likewise, none was found between SI and non-SI groups. Extrinsic epigenetic age acceleration significantly correlated with BPRS disorganization. Furthermore, Horvath Age acceleration showed a significant correlation with the SCL-90 psychotic domain. Furthermore, our data supported the mediating effects of DNA methylation on the interaction between stress and current SI severity.

Keywords: age
DNA
Ideation
Methylation
Suicide
Advisor: De Luca, Vincenzo
Vegetarian Diet, Growth, and Nutrition in Early Childhood

Background: Few studies have evaluated the relationship between vegetarian diet and childhood growth or nutritional status. Methods: A longitudinal cohort study of children aged 6 months to 8 years. Linear mixed effects and generalized estimating equation models were used to determine the association between vegetarian diet and BMI z-score, height-for-age z-score, serum ferritin, 25-hydroxyvitamin D, and serum lipids. Possible effect modification by age and cow’s milk consumption was examined. Results: There was no evidence of an association between vegetarian diet and mean BMI z-score, height-for-age z-score, serum ferritin, 25-hydroxyvitamin D, or serum lipids. Vegetarian diet was associated with higher odds of underweight (OR 1.87, 95%CI: 1.19-2.96; p=0.007). Higher cow’s milk consumption was associated with higher serum lipids among children with vegetarian diet. Conclusion: Children with and without vegetarian diet had similar growth and biochemical measures; however, vegetarian diet was associated with higher odds of underweight.

Keywords: adiposity
early childhood
height
micronutrients
serum lipids
vegetarian diet
Advisor: Maguire, Jonathon L
Impact of Resveratrol, a Uterine Artery Vasodilator, on Placental Oxygen Transport and Fetal Circulatory Physiology: Comparison with Maternal Hyperoxygenation

Increases in fetal oxygen delivery may be achieved by increasing uterine artery (UtA) blood flow with resveratrol (RSV) or by widening the transplacental partial pressure of oxygen (PO2) gradient with maternal hyperoxygenation (MH). Thus, we investigated the impact of chronic RSV on placental oxygen transport and fetal circulatory physiology in a sheep model of normal human pregnancy. We then compared the impact of RSV with an acute episode of MH. RSV resulted in significantly higher UtA blood flow than MH therapy. Despite this increase, there was no change in fetal oxygenation or hemodynamics compared to controls. MH resulted in increased fetal oxygenation compared to baseline and RSV fetuses. MH therapy also increased fetal pulmonary blood flow and reduced flow through the foramen ovale. Thus, our data suggests that in the setting of normal placental perfusion, MH has a greater impact on fetal oxygen delivery than increases in UtA blood flow.

Keywords: Hemodynamics
Magnetic resonance imaging
Maternal Hyperoxygenation
Oxygenation
Placenta
Resveratrol
Advisor: Seed, Mike
Morrison, Janna L
A GPU-Accelerated Population-Based Boltzmann Machine for Solving Combinatorial Optimization Problems

Monte Carlo methods such as Simulated Annealing and Parallel Tempering have been applied to Boltzmann Machines for solving NP-hard combinatorial optimization problems. In practice, their implementations have been limited to small population (only a few CPU cores), not in massively parallel hardware. In this work, we show that Population Annealing algorithm can be applied to Boltzmann Machines and increases their performance in massively parallel hardware. We implement a large-scale GPU-accelerated Population-Based Boltzmann Machine (PBBM) with Population Annealing algorithm for solving all-to-all connected quadratic unconstrained binary optimization problems with up to 20000 binary variables. For 1024-variable problems, PBBM is able to perform parallel energy evaluation and local field calculations on a population size of up to 640 parallel replicas about 500x faster than running replicas serially. Benchmark results on Max-Cut problems show that our implementation outperforms state-of-the-art optimizers and on average is 43x faster and has 2.5x less error.

Keywords: Boltzmann Machine
Combinatorial Optimization
Ising Model
Parallel Tempering
Population Annealing
QUBO
Advisor: Sheikholeslami, Ali
Delivery of Sodium Channel Subunits via Viral Vectors to Ameliorate Seizures in Dravet Syndrome Mice

Dravet Syndrome (DS) is caused primarily by impairment of the voltage-gated sodium channel alpha-1 subunit (Nav1.1) in inhibitory neurons. DS is characterized by febrile seizures, autistic behavior, and sudden unexpected death in epilepsy (SUDEP). Customized adeno-associated virus (AAV) serotype 9 vectors coding for AAV9-Gad1v1-Navβ1 and AAV9-Gad1v2-NaChBac were tested in Scn1a+/- mice, a mouse model of DS, to restore the activity of inhibitory neurons in Scn1a+/- mice. Neonatal injections with AAV9-Gad1v1-Navβ1 resulted in a partial improvement in the mortality of female Scn1a+/- mice and a reduction in the spontaneous seizure frequency in male Scn1a+/- mice, with no effect on the heat-induced seizures. Treatments with AAV9-Gad1v2-NaChBac did not induce inflammation in mouse brain and indicated that Gad1v2 promoter was more selective towards gamma aminobutyric acid (GABA)-ergic inhibitory neurons than the Gad1v1 promoter. The findings of this study demonstrated the capability of AAV as a useful tool in gene therapy for DS.

Keywords: AAV
brain
Dravet Syndrome
epilepsy
Mice
Advisor: Hampson, David R
'The Butcher on the Bus’ is as Familiar to Older Adults as She is to Younger Adults

The “butcher on the bus” is an example of familiarity which arises when we find a person familiar (our butcher) but fail to recollect how we know them due to the unfamiliar context (the bus; Mandler, 1980). To address age-related differences in the butcher on the bus, younger and older adults viewed faces in scene contexts. At test, participants viewed studied faces in studied scenes, studied faces in new scenes, and new faces in new scenes. Participants indicated if they recollected the faces and studied scenes, if the faces were familiar but they could not recollect the studied scene, or if the face and scene were new, and then made source judgments to indicate if the test scene matched the studied scene. Recognition discrimination, estimates of recollection and familiarity (Yonelinas Jacoby, 1995), and source judgements revealed no age-related differences, demonstrating that younger and older adults experience this phenomenon similarly.

Keywords: Aging
Context
Faces
Familiarity
Recollection
Repetition
Advisor: Anderson, Nicole