VictorJuiz/thesis huggingface dataset:
Amplifying On-Chip Memory Storage Capacity via Compression for Neural Network Workloads

Deep Neural Networks (DNNs) have been proven to be state-of-the-art for many applications. DNNs are an excellent target for hardware acceleration for several reasons: they are essentially a large collection of independent multiply-accumulate operations, they require large amounts of data to be transferred, and they are deployed in an ever increasing set of applications. Hence, hardware acceleration for DNNs has been a highly active area in research and development where new designs and techniques are proposed to achieve faster and more energy-efficient DNN execution on hardware. The need to investigate such hardware acceleration techniques requires tools that allow us to experiment with such methods and to estimate their potential performance and energy benets. Accordingly, this thesis targets two main contributions: 1) DNNsim, a DNN hardware accelerators simulator to evaluate new designs, and 2) Boveda, an on-chip memory compression technique designed for Deep Learning accelerator memory hierarchies.

Keywords: Deep Learning
Hardware Accelerators
Machine Learning
Memory Compression
On-chip compression
Advisor: Moshovos, Andreas
The Impact of Photodynamic and Radiation Therapies in the Metastatic Spine

There is an increasing number of treatment options for spinal metastasis including stereotactic body radiotherapy (SBRT), and emerging modalities such as photodynamic therapy (PDT). Quantifying the impact of treatments on bone quality is critical to improve fracture risk prediction and multimodal treatment planning, towards optimizing quality of life for patients with spinal metastases. Treatment efficacy for these local minimally invasive therapies requires personalized treatment planning. This is standard of care for SBRT. In the context of PDT however, treatment planning protocols are needed to optimize the number, power and interstitial locations of the fiber-based diffusers. Critical to safety in this process is knowledge of the photodynamic threshold of the spinal cord. As such, this work accomplishes two objectives: 1) derives the PDT spinal cord threshold value for a preclinical model of spinal bone metastasis, and 2) characterizes changes in healthy and metastatically involved vertebral bone secondary to SBRT and PDT.

Keywords: bone
metastasis
osteolytic
PDT
radiation
spine
Advisor: Whyne, Cari M
Exploring NADPH Levels during ER Stress using Novel HomoFRET Sensors

In beta-cells, insulin misfolding occurs at rates as high as 20%. Misfolded insulin aggregates lead to endoplasmic reticulum (ER) stress and the unfolded protein response (UPR). The adaptive UPR works to refold insulin, but if unsuccessful leads to programmed cell death. Proper insulin refolding requires reducing equivalents, which the ER lacks, thus external support in the form of NADPH is needed. This thesis investigates the role of NADPH in supporting insulin refolding in the ER. A novel homoFRET reporter, Apollo-IRE1, was developed to monitor the progression of ER stress. Apollo-IRE1 functionality was validated with chemical ER stressors. Additionally, our lab’s reporter, Apollo-NADP+, was used to track organelle NADPH levels during ER stress. Mitochondrial NADPH, not cytoplasmic NADPH, was found to be consumed during ER stress. The consumption of mitochondrial NADPH during ER stress demonstrates a potential supportive role of NADPH in the beta-cells protein refolding process.

Keywords: Deep Learning
ER Stress
Fluorescence Anisotropy
Microscopy
Type 2 Diabetes
Advisor: Rocheleau, Jonathan V
Morphology and Mechanical Properties of In-situ Fibrillated Polyethylene Based Composites

Spunbond fibrillation, an industrial scaled technology, is utilized in a wide range of applications such as medical products, textiles, and others. Here, an in-situ fibrillated method was proposed to fabricate the fiber-in-fiber polymer composite using spunbond technology. In the study, we investigated four researches: Chapter 2 explored the influence of morphology of PBT domains on the crystallization, rheological, and mechanical properties of PBT/HDPE composites; Chapter 3 investigated the effectiveness of the coupling agent on the surface compatibility between PBT and PE interfaces and its mechanical behaviour; Chapter 4 discussed the impacts of the UV curing time and the second phase content on the morphology, and mechanical behaviours of the EPDM/PE composites; and Chapter 5 studied the morphology of the E-beam cured EPDM/PE (and mPE/PE) composites. The in-situ fibrillar strengthened/ toughened composites are promising for applications such as automotive, astronomy, medical services, and consumer goods, and so on.

Keywords: in-situ fibrillation
photocrosslinking
polyethylene
polymer composites
polymer processing
spunbond
Advisor: Park, Chul B.
Lee, Patrick C.
Readout Transimpedance Amplifiers Monolithically Integrated with Quantum Dot Structures in a Production 22-nm FDSOI CMOS Technology

This thesis investigates the design of spin qubit readout systems in a production 22-nm FDSOI CMOS technology for monolithically integrated quantum processors operated at temperatures above 4 K. At 300 K, the readout amplifier was measured to have a transimpedance gain of 108 dBΩ with 8 GHz of bandwidth, S22 output matching

Keywords: FDSOI CMOS
Quantum Computing
Quantum Dot
Qubit Readout
Spin Qubits
Transimpedance Amplifier
Advisor: Voinigescu, Sorin P
Space–time Codes from Sum-rank Codes

Just as rank-metric or Gabidulin codes may be used to construct rate–diversity tradeoff optimal space–time codes, a recently introduced generalization for the sum-rank metric—linearized Reed–Solomon codes—accomplishes the same in the case of multiple fading blocks. In this thesis, we provide the first explicit construction of minimal delay rate–diversity optimal multiblock space–time codes as an application of linearized Reed–Solomon codes. We further provide sequential decoders for these codes and, more generally, space–time codes constructed from finite field codes. These decoders then enable a study of the performance of the constructed codes in simulation whereby we demonstrate that they can outperform full diversity alternatives at low SNRs as well as utilize significantly smaller constellations.

Keywords: Rank-Metric Codes
Space–Time Codes
Sum-Rank Codes
Wireless Communication
Advisor: Kschischang, Frank R
Polarized Light for Stromal Morphology Assessment and Optical Biomarker Discovery in Breast Cancer

Breast cancer remains a leading cause of oncologic mortality amongst women and a challenging public health issue. The collagen within, and surrounding, breast tumours has been shown to hold prognostic information and offers a potential method of patient risk stratification. This thesis uses polarized light microscopy to examine the collagenous stromal content and morphology in human breast cancer samples. It develops upon a novel form of cross-polarized light microscopy and introduces an accompanying signal and image processing pipeline. This methodological combination is applied to two projects in the context of breast cancer: 1) the development of a computational signature that can distinguish prognostically informative collagen organization patterns and 2) the correlation of collagen abundance and alignment with a popular genomic risk panel, OncotypeDX. The work presented herein can serve as a first step towards alternative methods of collagen assessment and future prognostic testing in breast and other cancers.

Advisor: Vitkin, Alex
Are Fatty Acid Amide Hydrolase Levels Elevated in Social Anxiety Disorder? Preliminary Findings of a PET Study using [C-11]CURB

Background: Upregulation of the major catabolic enzyme for anandamide, fatty acid amide hydrolase (FAAH), has been implicated in animal models of anxiety disorders, however no in-vivo human data exist. We tested the hypothesis that FAAH levels would be elevated in social anxiety disorder (SAD). Methods: FAAH levels were measured with the positron emission tomography probe [C-11]CURB in 12 participants with SAD and 34 healthy controls. The Liebowitz Social Anxiety Scale was used to evaluate SAD symptom severity. Results: [C-11]CURB binding was marginally elevated in whole brain in SAD; effects were significant in the dorsal striatum (p=0.006) and hippocampus (p=0.04). [C-11]CURB binding was positively associated with SAD symptom severity. Conclusion: Our preliminary findings suggest that FAAH levels might be elevated in SAD, particularly in individuals with more severe symptoms. Replication of these findings in a larger sample is warranted and has implication for treatment strategies targeting FAAH.

Keywords: endocannabinoid
fatty acid amide hydrolase
neuroscience
PET imaging
social anxiety
Advisor: Kloiber, Stefan
Boileau, Isabelle
Clinical and Neuroimaging Correlates of Cardiorespiratory Fitness in Adolescents with Bipolar Disorder

Cardiovascular disease (CVD) is more prevalent, and occurs prematurely, in individuals with bipolar disorder (BD) vs. the general population. Cardiorespiratory (i.e. aerobic) fitness (CRF) is a key modifiable CVD risk factor and is also associated with brain structure and function. There is an important gap in the literature on this topic in relation to BD, particularly in adolescents. 54 adolescents with BD and 53 healthy controls (HC) completed semi-structured interviews, self-report questionnaires, and 20 minutes of cardiorespiratory exercise. Power/weight (watts/kilogram) within 60-80% of estimated maximum heart rate (HR) on a bicycle ergometer served as a proxy for CRF. Structural magnetic resonance imaging analysis was done using FreeSurfer. CRF was reduced among adolescents with BD, particularly females, related in part to depression symptoms and inactivity. CRF is differentially associated with brain structure in frontal, parietal and occipital regions in adolescents with BD. Studies engaging CRF as a treatment target are warranted.

Keywords: Adolescents
Bipolar Disorder
Cardiorespiratory Fitness
Depression
Neuroimaging
Physical Activity
Advisor: Goldstein, Benjamin I
Analysis and Evaluation of a Minimally-invasive Cavopulmonary Assist Device

A cavopulmonary assist device is a medical device intended to improve blood flow to the heart to bridge patients with failing Fontan circulations to heart transplants. This work redesigns a previously-designed cavopulmonary assist device to design constraints of a cross-sectional area of less than 166 mm2, pressure gains within 2-6 mmHg, and wall shear rates (WSRs) less than 5000 s-1. Hemodynamics and misalignment-induced effects were investigated across one idealized and three patient-specific Fontan geometries over a range of conditions, showing that target pressure gains are achieved, endothelial damage is limited, and WSR and recirculation increase with misalignment. A cannula prototype was fabricated for evaluation in a custom mock circulatory loop. This previously-constructed loop was re-tuned to better model failing Fontan conditions with a new cannula test section manufactured to match adult anatomy. Flow and pressures in the loop show good agreement with failing Fontan conditions, particularly for large flow rates.

Keywords: Cavopulmonary Assist
Congenital Heart Defects
Fontan
Advisor: Amon, Cristina
Efficient Simulation of Driven Finite Periodic Structures using the Finite-difference Time-domain Method

Infinitely-periodic geometries are efficiently modelled in the finite-difference time-domain (FDTD) method using periodic boundary conditions (PBCs). Several PBC implementations operate by maintaining a constant wave vector component in the periodic directions. This work presents the underlying mathematical background for all these methods and demonstrates their usage. However, infinitely-periodic structures modelled by PBCs are unrealizable physically. Therefore, an efficient FDTD technique for determining electromagnetic fields interacting with finite-sized periodic structures is proposed. The technique combines periodic boundary conditions—modelling fields away from the edges of the structure—with independent simulations of fields near the edges of the structure. It is shown that this algorithm efficiently determines the size of a periodic structure necessary for fields to converge to the infinitely-periodic case. Numerical validations of the technique illustrate the savings concomitant with the algorithm.

Keywords: Edge effects
FDTD
Finite periodic structures
Advisor: Sarris, Costas D
Identifying Novel Targets in Chemo-resistant Cell Populations in Glioblastoma Multiforme

Glioblastoma multiforme is an aggressive brain tumour characterized by poor prognosis, with overall patient survival rates averaging less than 15 months. Current treatment methods display immediate control of the disease, however treatment-resistant cell populations persevere, and disease recurrence is inevitable. As a result, all patients eventually succumb to the effects of their disease. Therefore, there is a need for therapeutic approaches that are capable of targeting the treatment-resistant cell populations in glioblastoma in order to provide patients their most meaningful period of remission. In this study, we propose that FDA-approved agents capable of crossing the blood-brain barrier can be repurposed for use in glioblastoma. In particular, the lipid-lowering agent lomitapide shows promising therapeutic potential in glioblastoma due to its ability to alter exogenous cholesterol levels, which Villa et al. have shown GBM cells rely on for survival.

Keywords: Cancer
Chemotherapy
Cholesterol
Drug Discovery
Drug Repurposing
Glioblastoma
Advisor: Das, Sunit
Angle of Arrival Estimation as an Ising Energy Minimization Problem

A popular approach to realizing decimetre-level localization involves estimating the angle between a target and one or more anchors. In the context of wireless communication, this work implements compressive sensing to first discretize the angular domain and then optimize a suitable objective function. This thesis presents the problem using an L0-norm function that is then formulated as an Ising energy minimization problem; although NP-hard, the optimization is efficiently solved using the Digital Annealer (DA) machine. This work leverages the computational efficiency of the DA to further develop the Ising formulation by devising a unique iterative search procedure. The performance of this approach is studied extensively and compared to other state-of-the-art works. Test results show that the proposed method outperforms other approaches.

Keywords: Angle of Arrival
Compressive Sensing
Localization
Advisor: Valaee, Shahrokh
Archival Imperialism: An Analysis of Racial Hierarchy in the Six Day War Files

Using a theoretical framework of critical race theory, settler colonialism, and symbolic annihilation, this research investigates how records creators and archivists of the Six Day War Files Collection have constructed their own narrative of the War, thereby legitimizing a racial hierarchy between Palestinians and Israelis and sustaining Israeli imperialism. Chapter One problematizes why there is little written about Palestine from the archival perspective, despite the abundance of scholarship on the colonial power of the archive. Chapter Two analyzes the content of the Collection, investigating how records creators used symbolic annihilation to construct Palestinians as a racialized Other. Chapter Three analyzes the context of the Collection, investigating how archival practices have sustained the colonizer’s representation of the colonized and furthered racial inequality. This thesis offers a novel perspective to the current archival scholarship regarding Palestine, revealing how symbolic annihilation in the archive extends, and is an extension of, systemic annihilation.

Keywords: Archives
Colonialism
Israel
Palestine
Recordkeeping
War
Advisor: Duff, Wendy
Cowen, T.L.
Genome-wide Investigation of Rare Genetic Variation in Epilepsy and Autism Spectrum Disorder

Epilepsy and autism spectrum disorder (ASD) are a clinically heterogeneous group of neurological disorders. Despite their known genetic basis, many cases of epilepsy and ASD remain unresolved without a molecular diagnosis. In this thesis, I describe the use of whole-genome sequencing (WGS) to conduct a genome-wide investigation of rare genetic variation in two cohorts. In a cohort of unexplained epilepsies, I identified clinically relevant rare variants in 9/28 (32.1%) participants, for whom prior genetic tests were inconclusive. In a cohort of 20 participants with a duplication of the 7q11.23 region (Dup7), I found that in the presence of the same pathogenic Dup7 variant, rare and low frequency genetic variants act additively to contribute to components of the overall Dup7-ASD phenotype. Overall, my findings demonstrate that the use of WGS enables molecular diagnosis, points to the role of multiple contributing variants in the genetic background, and yields insights into epilepsy-ASD genetics.

Keywords: 7q11.23 duplication
Autism Spectrum Disorder
Epilepsy
Genetics
Whole genome sequencing
Advisor: Yuen, Ryan K.C.
Synthesis of a Reversible Crosslinked Hydrogel

Detachment of fragile cell types cultured on two-dimensional (2D) surfaces detrimentally affects cell viability. Accutase treatment of neurons growing in 2D damaged fragile neuronal connections, resulting in cell death and host tissue damage in vivo. Avoiding cell detachment altogether by developing an in vitro culture system may better maintain cell viability; therefore, we present the synthesis of a reversible crosslinked three-dimensional (3D) hydrogel which would provide stability for culture/differentiation when crosslinked and injectability for transplantation following crosslink degradation. A blend of hyaluronan (HA) and methylcellulose (MC), HAMC, was chemically crosslinked with an enzyme-degradable peptide sequence using oxime click-chemistry. Specifically, HA and MC were modified with ketone and aldehyde groups, respectively, and a TEV protease-degradable peptide crosslinker was synthesized and modified with oxyamine groups. The gel components were characterized, and gels were formed that demonstrated good stability, improved injectability upon crosslink degradation, and cytocompatibility with iPSC-derived neural progenitor cells.

Keywords: degradable
dynamic
hyaluronan
hydrogel
methylcellulose
TEV protease
Advisor: Shoichet, Molly S
Unintended Consequences in a Children’s Public Dental Care Program

Objectives: To explore pediatric dentists’ self-reported changes in their practice of dentistry in response to implementation of the children’s public dental care program Healthy Smiles Ontario (HSO). Methods: A qualitive study based on one-on-one, semi-structured interviews with pediatric dentists in Ontario. Results: Eighteen pediatric dentists (mean age 50 years, 56% female) whose primary practices were located in 13 cities and towns across Ontario were interviewed. Pediatric dentists report weighing their frustrations with HSO against their own personal beliefs resulting in various coping mechanisms. Some pediatric dentists cope by limiting/excluding HSO patients to varying degrees, including not participating in HSO altogether. Some pediatric dentists reported feelings of burnout due to the economic stresses associated with HSO. Conclusions: The exclusion of HSO patients resulting in barriers to care and the potential for provider burnout constitutes the unintended consequences of HSO.

Advisor: Quiñonez, Carlos
Electrophysiological Substrates of Cognition in the Basal Ganglia and Basal Forebrain

Cognitive and non-motor behavioral functions have recently been described to heavily engage basal ganglia (BG) and subcortical circuitry and nuclei. Functionality at the neural level may be examined by analyzing single unit spiking activity and/or the aggregate activity of a population of neurons in various frequency bands known as local field potentials. This thesis addresses the role of the subthalamic nucleus (STN) in a cognitive 2-item choice decision-making task; and the role of the nucleus basalis of Meynert (nbM) in an auditory oddball attention task. Utilizing intraoperative electrophysiological recordings and behavioral testing in patients undergoing deep brain stimulation surgery, we expand upon the current understanding of the physiological function of the STN, subcortical beta, and the nbM in cognitive functions. The research presented here carries clinical implications for progressing DBS technologies as well as bettering our understanding of cognitive/non-motor deficits in patients with basal ganglia dysfunction.

Keywords: decision making
neurophysiology
single units
Advisor: Hutchison, William D
A Streaming Accelerator for Heterogeneous Multicore-FPGA Processing of Graph Analytics Applications

This work explores the acceleration of graph processing on a heterogeneous platform that tightly integrates an FPGA with a multicore processor to share system memory. The key research challenge addressed is that of designing an accelerator that exclusively accesses graph data in system memory, enabling the concurrent use of both the accelerator and software. Specifically, the work proposes a streaming accelerator design for the scatter phase of iterative scatter-gather graph processing. The streaming design is implemented and evaluated on the second-generation Intel Heterogeneous Architecture Research Platform (HARPv2). Evaluation of three key graph processing kernels using a combination of synthetic and real-world graphs shows that this design achieves highperformance, up to 1100 MTEPS. Further, the accelerator has high FPGA–to–Memory bandwidth utilization, over 90%. The streaming accelerator also features fine-grain granularity sharing with the CPU that enables integration with efficient load-balancing schemes, such as work-stealing.

Keywords: accelerator
analytics
fpga
graph
heterogeneous
streaming
Advisor: Abdelrahman, Tarek S
Circadian Oscillations of the Mouse and Human Epigenome

Circadian rhythmicity in biological processes is an evolutionary adaptation in response to Earth’s rotation. Epigenetics refers to chemical modifications of histones and DNA, for the regulation of the genome. Although previous evidence suggested the involvement of DNA modification in the circadian machinery, direct confirmation has been elusive. This thesis presents evidence for oscillating modified cytosines with circadian periodicity in both mouse and human genomes. Furthermore, oscillating modified cytosines (osc-modCs) are associated with cytosines that change their modification status with age. Linking circadian patterns with linearly changing epigenomes over years provides new insights into the mechanisms of aging. Finally, we investigated plausible roles of osc-modCs in malignant, psychiatric, and metabolic diseases. Intriguingly, osc-modCs significantly overlapped with the cytosines exhibiting differential modification in these diseases. In summary, my findings indicate that fine tuning of evolutionary advantageous adaptations such as circadian rhythmicity may contribute to the decline in the fitness of the organism.

Keywords: Aging
Circadian rhthmicity
Complex diseases
DNA modification
Epigenetics
Advisor: Petronis, Art
Ontario Pharmacy Smoking Cessation Program: A Descriptive Analysis, 2011-2016

The Ontario Pharmacy Smoking Cessation Program was introduced in September 2011 and reimburses pharmacies for providing counseling services to residents eligible for Ontario Drug Benefits. Using healthcare administrative data through to November 2016, we described patient (demographic, healthcare) and program (enrolment, follow-up services, smoking cessation medication and success) characteristics. Analyses were completed overall and by age (≥65 [seniors] versus

Keywords: administrative claims data
Pharmacy
smoking cessation
Advisor: Cadarette, Suzanne M