VictorJuiz/thesis huggingface dataset:
Accurate Hotspots Detection with Deep Convolutional Neural Network and Generative Adversarial Network Based Data Augmentation

The increasing demand for computational power is pushing the photolithography technology to its physical limit. As one of its crucial technical bottlenecks, the design issue of layout hotspots requires innovative solutions to minimize the necessity of conducting expensive lithography simulation experiments but remain extremely accurate. In addition to the sustained development of conventional hotspots detection, the recent implementation of convolutional neural networks (CNN) has shown high effectiveness in flexible pattern recognitions. However, limited by the industrial data availability, technical issues such as imbalanced learning and rare/new hotspot detection need to be navigated. In this thesis, we introduced a deep learning hotspots detection method with an improved CNN classifier and enhanced the learning effectiveness by augmenting the dataset with the generative adversarial network (GAN) based synthetic pattern generation. Experiment results show competitive performance compared to the existing works, but further development is required to connect with the current industrial processes.

Keywords: Deep Learning
Generative Adversarial Network
Hotspot Detection
Advisor: Behdinan, Kamran
A 10-year Review of Intraoral Salivary Gland Tumor Diagnoses: Diagnostic Challenges and Inter-observer Agreement

Background: Intraoral minor salivary gland tumors (IMSGT) are uncommon and present diagnostic challenges that affect treatment. Objectives: Determine clinical and pathological features of IMSGT associated with diagnostic challenges. Methods: We conducted a retrospective analysis of 248 IMSGT in an outpatient oral pathology service, (2010-2019). Cases were stratified into definitive, favored, or indeterminate diagnoses. We evaluated inter-observer agreement and concordance of biopsy diagnosis with surgical resection diagnosis. Results: There were 191 definitive diagnosis, 38 favored diagnosis, and 19 indeterminate. Younger patient, smaller tumor, and larger biopsy size were significantly associated with definitive diagnosis. Overall inter-observer agreement for 68 representative cases was moderate (Fleiss’ Kappa 0.575). Sixty-five biopsy cases matched with resection specimens showed good concordance (Cramer’s V test 0.76). Conclusion: Diagnostic challenges in IMSGT were infrequent and tended to involve tumors with overlapping histologic patterns. Younger patient age, smaller tumor size and larger biopsy were associated with a definitive diagnosis.

Keywords: intraoral minor salivary gland tumors
minor salivary gland tumors
oral medicine
oral pathology
salivary gland tumors
Advisor: Magalhaes, Marco
IOS: Inter-operator Scheduler for CNN Acceleration

To accelerate CNN inference, existing deep learning frameworks focus on optimizing intra-operator parallelization. However, a single operator can no longer fully utilize the available parallelism given the rapid advances in high-performance hardware, resulting in a large gap between the peak performance and the real performance. This performance gap is more severe under smaller batch sizes. In this work, we extensively study the parallelism between operators and propose Inter-Operator Scheduler (IOS) to automatically schedule multiple operators’ parallel execution through a novel dynamic programming algorithm. IOS consistently outperforms state-of-the-art libraries (e.g., TensorRT) by 1.1 to 1.5x on modern CNN benchmarks.

Keywords: Inference
Inter-Operator
Latency
Neural Network
Optimization
Scheduler
Advisor: Pekhimenko, Gennady
Investigating the Role of p53 in Cellular Stress Responses to Deregulated Anabolic Metabolism

Pharmacology-based cancer risk reduction has emerged as a promising potential complement to existing cancer screening strategies employed in LFS and other CPSs. At a basic, physiological level, cancer prevention effects have been associated most closely with anabolic metabolism and mTORC1. Unfortunately, strategies involving direct inhibition of mTORC1 are clinically undesirable, necessitating further investigation of the molecular mechanisms underlying cancer risk reduction – the correlates of malignancy in LFS. In this work, we provide evidence for a molecular circuitry which may maintain growth homeostasis in the pre-malignant niche. Through pharmacological perturbation of growth rate and cell cycle length, we observed that wild-type p53 and p38 provoke opposite, complementary stress responses to relatively hyperactivated and diminished biosynthesis, respectively. More specifically, p53 inhibits mTORC1 and p38 to curtail further biosynthesis when it is already elevated. The p53 GOF mutant R248Q appears to break this homeostasis, which may contribute to unchecked anabolism and tumour development.

Advisor: Malkin, David
Injection of a Cell Lysate Derived from Wharton’s Jelly Perivascular Mesenchymal Stromal Cells for the Treatment of Inflammation in the Temporomandibular Joint

The objective of this study was to investigate the anti-inflammatory effects of human neonatal mesenchymal stromal cells (MSCs) and their cell lysate (CL) derived from perivascular Wharton’s Jelly (WJ) in a rat model of carrageenan-induced inflammation of the temporomandibular joint (TMJ). Male Wistar rats were injected with carrageenan, 10% CL, 1% CL, 1% gamma-irradiated CL, or MSCs. Rats were sacrificed at 4, 48, and 72-hrs post-injection. Articular tissue and synovial aspirates were analyzed for myeloperoxidase (MPO) and tumor necrosis factor alpha (TNF-alpha) levels, and for leukocyte infiltration. 1% CL and MSC-treated TMJs demonstrated significantly lower concentrations of leukocytes 4-hrs post-Injection compared to controls. No significant differences in the concentrations of MPO and TNF-alpha were found between the treatment groups and controls. Overall, MSCs and the CL derived from perivascular WJ reduced leukocyte infiltration into the synovium, while moderating signs of TMJ inflammation histologically.

Keywords: Anti-Inflammatory
Arthritis
Mesenchymal
Rat-Model
Stem Cell
Temporomandibular Joint
Advisor: Davies, John E.
Effects of Biochar on Green Roofs' Hydrology in a Southern Ontario Climate

Wide implementation of green roofs throughout urban areas has been carried out across the globe and has the potential to reduce and attenuate volume and peak discharge caused by natural precipitation. Research shows that implementing green roofs in urban environments can be a feasible solution to manage stormwater more effectively, alleviating the capacity compromise of conventional combined sewer overflows systems, as well as other ecological and socio-economic benefits. This study evaluated the hydrologic performance from eight extensive green roof testbeds with a substrate depth of 15 cm, two types of soil media (amended with biochar and control), and two types of vegetation (Sedum and native species) at the University of Toronto’s GRITlab 2 (Spadina) between April and August of 2021. This short-term study showed an overall good performance on water retention and peak attenuation, mainly through evapotranspiration (ET) throughout the monitoring period.

Keywords: Biochar
Green roofs
Hydrology
Advisor: Drake, Jennifer JD
Exploring Dentists’ Personal Knowledge in Practice in the Delivery of Mandibular Anesthesia: A Qualitative Study

Background: Local anesthesia, an essential component of dentistry, eliminates the pain associated with invasive surgical treatment. Despite an adequate understanding of theory, students often struggle to consistently achieve mandibular anesthesia in clinic. Objectives: The aim of this study is to explore the personal knowledge and experiences that inform dentists’ delivery of mandibular anesthesia in practice. Methods: Semi-structured interviews were conducted with 12 dentists using the Zoom teleconferencing application and analyzed using thematic analysis. Results: Three themes were developed: 1) Practice makes proficient, 2) Mandibular anesthesia delivery is a dynamic process, not a single injection, and 3) Mandibular anesthesia delivery is patient-tailored and responsive. Conclusion: Mandibular anesthesia delivery is a dynamic process that requires both technical and non-technical competencies. Significance: Collectively, our findings suggest students would benefit from receiving more and diverse clinical instruction and practice, combined with a systematic framework of evaluation for clinical troubleshooting and technique development.

Keywords: Dental education
Dentistry
Local anesthesia
Mandibular anesthesia
Personal knowledge
Tacit knowledge
Advisor: Wong, Michelle MW
Sale, Joanna JS
Examining an Investigative Balance Prosthesis during Balance and Working Memory Tasks in Children and Young Adults with Cochleovestibular Dysfunction

The present study examines balance, working memory, and an investigative balance prosthesis (BalanCI) in children with cochleovestibular dysfunction. Many children with cochleovestibular dysfunction have poor balance. Balance requires cognitive resources and can impact cognitive load. The BalanCI provides auditory balance feedback through the user’s cochlear implants so they can adjust their posture, remaining upright. It was hypothesized that children and young adults with cochleovestibular dysfunction would perform worse than normal on balance perturbations and dual balance-cognition tasks, and performance would be improved with BalanCI use. Children and young adults with cochleovestibular dysfunction responded to balance perturbations and completed auditory and visuospatial dual balance-cognition tasks with and without the BalanCI. Participants with cochleovestibular dysfunction demonstrated poorer balance than normal, but the BalanCI improved stability on some perturbations and alleviated balance deficits associated with the auditory dual balance-cognition task. The BalanCI provides promise as a balance intervention for children with cochleovestibular dysfunction.

Keywords: Balance
Cochlear Implants
Hearing Loss
Vestibular Dysfunction
Working Memory
Advisor: Gordon, Karen A
Characterization of Graft Injury by Respiratory Oscillometry following Lung Transplantation

Long-term survival after lung transplantation is limited by the development of chronic lung allograft dysfunction (CLAD), with acute cellular rejection (ACR) being a significant contributing risk factor. Earlier identification and treatment of ACR are facilitated by routine monitoring with spirometry. Our previous results showed higher sensitivity of oscillometry in detecting graft injury associated with ACR compared to spirometry. As such, we hypothesized that oscillometry is a metric sensitive to ACR- and CLAD-associated injuries. We evaluated association between oscillometry, ongoing graft injury and risk of CLAD development in the post-lung transplant cohort. Our results revealed that the variance in oscillometry was significantly associated with a cumulative rejection index, A-score. The higher intra-subject variance in X5, AX and R5-19 was independently predictive of subsequent CLAD development. We concluded that oscillometry is a sensitive biomarker of ongoing graft injury following lung transplantation and may assist in identifying recipients at increased risk for CLAD.

Keywords: acute rejection
chronic lung allograft disfunction
lung transplantation
oscillometry
pulmonary function testing
Advisor: Chow, Chung-Wai CWC
Nutrient Acquisition Strategies and Performance of Crops in Response to Agroecological Interventions

Despite growing attention on agroecological interventions in crop production, little work explores the effects of multiple strategies to confer both soil and plant health. Here, I utilize a functional-trait approach to evaluate resource acquisition response of soybean and wheat to an organic amendment and to a growth-promoting bacterial seed inoculant. Amendments differentially influenced crops, with only wheat expressing differences in root strategies. There was no detectable influence of inoculation on roots, and interactive effects of amendments and inoculation was minimal. Inoculation and amendments impacted height, leaf chlorophyll content, leaf dry matter content, and stem diameter. Root traits showed trade-offs similar to those described in the root economic spectrum, with crops showing decreases in resource acquiring strategies with ontogeny. Broadly, soil amendments had the strongest impact on crop root response compared to seed inoculants. This study informs crop resource acquisition strategies, and crop response to interventions that emphasize agroecological crop production.

Keywords: agroecology
functional traits
nutrient acquisition
organic systems
root ecology
Advisor: Isaac, Marney
Validation of a Novel Optogenetic Drug Screening Platform for the Discovery of Neuroactive Compounds

Zebrafish provide a powerful system for behavior-based drug discovery aimed at treating disorders of the nervous system. However, current approaches cannot target screening for the identification of drugs that alter specific neuronal cell-types. The incorporation of optogenetics, a technique for the modulation of neural activity using light, with drug screening has the potential to provide targeted screening. Here, we present research aimed at validating this novel screening approach using transgenic zebrafish that express the excitatory optogenetic protein channelrhodopsin-2 in glutamatergic or GABAergic neurons. Using a collection of compounds with known central nervous system targets, we found that optogenetics can enable targeted screening, but in unpredicted ways. We also discovered that optogenetics can amplify the effects of drugs, providing an advantage when screening for new compounds. Our results support further investigation of this drug screening strategy using more compounds with known targets as well as transgenic lines for the optogenetic stimulation of additional cell-types.

Keywords: Drug-screening
Optogenetics
Zebrafish
Advisor: Thiele, Tod
Comparison of Two Administration Methods for Measuring Functional Fitness in Older Adults

Physical activity (PA) enhances quality of life in older adults, yet few older adults participate in regular PA. Exercise prescriptions are valuable to improve PA among older adults, and fitness measures are necessary to develop individualized PA programs. A typical fitness measure is the Senior Fitness Test (SFT) conducted in a supervised setting; however, the acceptability of an unsupervised, self-administered SFT is unknown. The purpose of this study was to assess the acceptability of a home-based self-administered SFT versus a home-based supervised SFT using the Theoretical Framework of Acceptability (TFA). Sixty-five older adults performed select SFT measures in their home on two separate occasions, one supervised and one self-administered. Findings indicated both administration methods was acceptable amongst older adults based on the TFA components. Completing a home-based, self-administered SFT appears to be a viable option for physical fitness testing in older adults.

Advisor: Trinh, Linda
Effect of Ecological Restoration on Plant-Pollinator Networks in Urban Meadows

Implementing restoration and management practices that aim to replicate natural areas within urban green spaces have been demonstrated to promote native species success and combat negative effects of urbanization, such as habitat loss. In my thesis, I set out to determine the impacts of urban green space restoration on wild bee communities to understand how plant richness, surrounding urbanization level, and restoration age support these critically important species. To do this, I evaluate wild bee-plant interaction networks, and wild bee diversity across a multi-year, early-successional meadow restoration project in the City of Toronto in Canada. Bee abundance and richness were positively correlated with restoration year, and bee community evenness was negatively correlated with restoration year. Plant-pollinator networks were specialized, but consisted of several dominant plant species, suggesting that future conservation efforts should focus on supporting the rare and underrepresented bee genera present in this study which may be more susceptible to disturbance.

Keywords: Biodiversity
Conservation
Interaction Network
Pollination
Restoration
Urban green space
Advisor: MacIvor, Scott
Designing a Framework for an Open-source Ventilator Controller Agnostic to Specific Ventilator Designs

The ongoing COVID-19 pandemic has caused a shortage of mechanical ventilators due to the complexity of the devices and lack of proper documentation of open-source designs. The goal is to design an open-source ventilator controller framework agnostic to the mechanical design and able to operate both emergency-use and ICU ventilators. Through understanding the ventilation modes and the existing open-source designs, a list of input and output parameters and a series of flow chart diagrams for each ventilation mode are created. These inform the design of the framework, which is composed of pseudocode for all relevant controller modules and a list of the minimum hardware requirements. The framework is tested by running a ventilation simulation to showcase the output is functional and meets the gap occurring during respiratory illness pandemics. Next steps for the investigation involve publishing the framework under an open-source license and performing testing on a physical ventilator.

Keywords: Controller Design
COVID-19
Mechanical Ventilator
Open-Source Design
Advisor: Behdinan, Kamran
Health Care Organizations Adopting Anchor Institute or Similar Practices: A Scoping Review

Health care organizations and systems have increasingly invested in prevention efforts and addressing upstream social determinants of health. Some of these institutions have worked to develop their role as “anchor institutions”: socially responsible entities that leverage their resources to build community wealth. A scoping review was completed to explore the state of the literature on health care organizations adopting “anchor practices” and more broadly investing in community needs. In total, 81 articles were included in the scoping review, which reflect academic articles and grey literature or reports with an analytical focus on health care organizations and systems adopting an anchor mandate or similar practices. Findings suggest there is a limited evidence base of health care organizations and systems adopting anchor mandates. The results of this research can help to spark health care organizations to think beyond their four walls and create shared value for their organization and the community.

Keywords: anchor institutions
hospitals
scoping review
social determinants
Advisor: Pinto, Andrew
Miller, Fiona
Tracking Cinical Care among Patients with Chronic Low Back Pain: The Utility of Performance-based Measures of Physical Performance and Disability

Objective: The objective was to describe the relationships between four physical performance (PP) tests and the Oswestry Disability Index (ODI) in chronic low back pain (cLBP). Methods: A cross-sectional and longitudinal cohort study of GLA:D® Back participants, with four PP measures (flexibility, endurance, sit-to-stand) pre-, post-program and ODI. Correlations and multiple regression described the relationship between ODI and the four PPs and for additional predictive ability of pre-program PPs. Results: Correlations between ODI and PP tests cross-sectionally were negative (-.2 to -.3), and much weaker (-.01 to -.17) for change. PP tests explained 17-18% of variance in ODI pre- and post. Variance explained in follow-up ODI was R2 = 0.514 using baseline ODI score and increased to 0.569 when adding PPs. Conclusions: While the four PPs had modest relationships with ODI, they added no additional predictive value for disability. PP measures when assessing individuals with cLBP should not be the only outcome utilized.

Keywords: chronic low back pain
disability
physical performance
Advisor: Hogg-Johnson, Sheilah
Formative Feedback on Problem-solving Skills: Intent and Action

Formative feedback is integral for the learning of difficult skills such as problem solving. To understand why less than ideal amounts of feedback are sometimes provided to students, this study elicited undergraduate engineering instructors’ intentions, and then observed their actions regarding formative feedback on midterm exams in courses that purport to teach problem solving. Intentions were collected through a survey that emulated the intentions-focused portion of the Teaching Perspectives Inventory. The questions were reworked to reference Fink’s FIDeLity feedback system. Actions were then measured by analyzing feedback provided on previous midterm exams administered by the same instructors who filled out the survey. Alignment between the instructors’ intentions and actions were analyzed by comparing the survey results and the midterm exam marking. Overall, instructors’ actions are generally aligned with their intentions. However, their intentions tend to favour time saving practices rather than using every known method for providing high-quality formative feedback.

Keywords: Assessment
Formative feedback
Problem solving
Teaching perspectives
Advisor: McCahan, Susan
Automatic Generation and Detection of Motivational Interviewing-style Reflections for Smoking Cessation Therapeutic Conversations using Transformer-based Language Models

If conversational agents can take on a therapeutic role, they may provide a scalable way to help many more people suffering from addictions. Motivational Interviewing (MI) is a validated therapy for behaviour change that has been used to help smokers to quit. A key MI skill is to produce reflections on a patient’s statements about a behaviour. Reflections are simple restatements or complex inferences drawing on conversation history or general experience. This thesis presents a method of generating reflections using GPT-2 and GPT-3 language models. These models produce promising reflections; however, some generated reflections are poor quality. To address this, we train a classifier on samples labeled by an MI expert to act as a filter. Its sensitivity is 90%, and specificity 71%. GPT-2 produces reflections 54% of the time with few-shot priming which GPT-3 improves to 89%. With fine-tuning and filtering, GPT-2 generation hit-rate improves to 81%.

Keywords: automated medicine
chatbot
language model
motivational interviewing
natural language processing
transformer
Advisor: Rose, Jonathan
Identification of Human microRNAs Regulating Skeletal Muscle Regeneration In Patients with Sustained Intensive Care Unit Acquired Weakness

Intensive care unit acquired weakness (ICUAW) is a complication of critical illness characterized by skeletal muscle wasting and impaired contractile function. Dysregulated gene co-expression networks controlling muscle repair/regeneration are present in patients with persistent muscle wasting. MicroRNAs (miRs) regulate gene expression at the post-transcriptional level by affecting the translation/degradation of mRNAs. Thus, we sought to identify miRs regulating the failure of muscle regeneration in patients with sustained ICUAW. We performed an integrated miR/mRNA analysis of quadriceps biopsies from patients with early/sustained ICUAW to identify dysregulated expression of miRs and their gene targets that regulate skeletal muscle myogenesis. We found miRs-490-3p and -744-5p to negatively regulate proliferation and differentiation respectively in human skeletal muscle myoblasts in vitro. We identified genes with significant roles in skeletal muscle repair/regeneration as potential mediators of miR-490-3p’s anti-myogenic activity. In addition, we identified novel miRs-3175 and -4739 as potential regulators of myoblast proliferation/differentiation in vitro.

Keywords: gene network analysis
ICU-acquired weakness
microarray
muscle atrophy
muscle regeneration
muscle weakness
Advisor: Batt, Jane