VictorJuiz/thesis huggingface dataset:
Evaluating Efficacy In Vitro and In Vivo of Small Molecules Predicted by Artificial Intelligence to Reduce Alpha-Synuclein Oligomers

Background: Parkinson’s disease (PD) is an incurable neurodegenerative disorder characterized by dopaminergic neuron loss and α-synuclein aggregation. Using artificial intelligence, we previously generated in silico predictions of approved drugs that may inhibit formation of α-synuclein oligomers, which are key mediators of neurodegeneration. Methods: I tested forty compounds highly ranked by the in silico predictions using an in vitro luciferase protein-fragment complementation assay. I then examined the positive hits using an in vivo behavioural assay of α-synuclein-mediated dopaminergic neuron dysfunction in C. elegans. Results: I identified ten compounds which significantly reduced α-synuclein oligomers. Four of these compounds were cytotoxic and thus excluded from further evaluation. I found five of the compounds rescued abnormal motor behaviour. Of these remaining compounds, rifabutin and rapamycin reduced α-synuclein oligomerization in rat primary neuronal cultures. Interpretation: Our combined in silico, in vitro, and in vivo approach discovered compounds that may be repurposed for disease-modifying PD treatments.

Keywords: Behaviour
Drug repurposing
IBM Watson
Neurodegeneration
Parkinson's disease
Synuclein
Advisor: Kalia, Lorraine V
Structural and Functional Analysis of PelH: Insight into the Regulation of Auto-aggregation in Streptococcus intermedius

Regulatory mechanisms governing biosynthesis of biofilm-forming exopolysaccharides are diverse and largely unexplored. Biosynthesis of the Pel polysaccharide by Pseudomonas aeruginosa is post-translationally regulated by the second messenger bis-(3′-5′)-cyclic dimeric guanosine monophosphate (c-di-GMP). While pel operons are found in several Gram-positive genera, the domain architecture of the c-di-GMP receptor PelD is not conserved. pelD encodes a cGMP-specific phosphodiesterases, adenylyl cyclases, and FhlA (GAF) domain and c-di-GMP-binding degenerate GGDEF domain, the latter of which is lost from Streptococcal PelD orthologs, and renamed PelH herein. We show that the C-terminal domain of PelH adopts a GAF fold, and have identified an N-terminal epimerase domain that is likely inactive due to missing catalytic residues. Further, we demonstrate that pelH is essential for aggregation of Streptococcus intermedius. Taken together, PelH is required for Pel biosynthesis in S. intermedius and may regulate Pel using a novel mechanism. Our findings contribute towards understanding Gram-positive Pel-dependent biofilm formation.

Advisor: Howell, Lynne
Investigating the Role of Hfe2 in Maintaining Blood-Brain Barrier Integrity

The Repulsive Guidance molecule a (RGMa) and its receptor, Neogenin, are known to play an important role in central nervous system development through repulsive axonal guidance, neuronal survival and differentiation. Emerging studies show that RGMa is also highly associated with a pathological CNS in several neurodegenerative diseases such as spinal cord injury, stroke and multiple sclerosis (MS). Here, we show that RGMa interacts with brain endothelial Neogenin to disrupt blood-brain barrier (BBB) integrity, and this effect can be prevented by liver-secreted protein, hemojuvelin (Hfe2). We also showed that in Experimental Autoimmune Encephalomyelitis (EAE), disease progression can be mitigated by knocking out endothelial-Neogenin, which indicates that RGMa-Neogenin interaction may be involved in MS pathgenesis. Hfe2 counteracts RGMa-Neognin interaction through interacting with BMP, which we demonstrated with single amino acid substitution mutant of Hfe2. Overall, we demonstrate that Hfe2 helps to maintain BBB integrity and could be a potential therapeutic agent.

Keywords: Blood Brain Barrier
Repulsive Guidance Molecules
Advisor: Monnier, Philippe P
Characterization of the Role of MATR3 in Cryptic Splicing

Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease and the major pathological hallmark of ALS is TDP-43 protein aggregates in the degenerated motor neurons. TDP-43 is an RNA binding protein (RBP) involved in cryptic splicing regulation. Compromised cryptic splicing function of TDP-43 was observed in ALS patients and have been directly linked to defects in axonal regeneration. MATR3 is a recently identified ALS gene which encodes an RBP that interacts with TDP-43. To investigate the possible role of MATR3 in cryptic splicing, we performed RNA-seq experiments and used bioinformatics to examine cryptic splicing events in HeLa cells using MATR3 siRNA. I identified extensive cryptic splicing events upon MATR3 knockdown and confirmed the role of MATR3 in the repression of cryptic exons through rescue experiments. In addition, I found common cryptic splicing events between MATR3 and TDP-43. Together, this work may provide insights into the mechanism underlying ALS.

Keywords: ALS
Cryptic Splicing
MATR3
Advisor: Park, Jeehye
CRISPR/Cas9 Dropout Screen Identifies MEPCE as a Novel Vulnerability in BRCA1-mutated Cancers

The breast cancer susceptibility gene 1 (BRCA1) gene encodes a protein which primarily functions to maintain genomic integrity. Mutations in BRCA1 are associated with increased risk of developing breast (≥70%) and ovarian (≥40%) cancers. Additionally, tumors arising from BRCA1 mutations are typically high grade and recurrent in nature. Thus, there is an urgent need to identify novel optimal therapeutic options for the majority of these patients. Based on the principle of synthetic lethality, which refers to the loss of viability resulting from the disruption of two genes, which, individually, does not cause lethality, we performed a CRISPR-Cas9 dropout screen. Through our screen, we identified Methylphosphate Capping Enzyme (MEPCE) as a potential synthetic lethal interactor of BRCA1. Data collected in this study demonstrates that MEPCE is essential for restraining genomic instability in BRCA1-mutant cancers through attenuating R-loops and transcription-replication conflicts. We propose that MePCE inhibition should be investigated further as a potential therapeutic target for the treatment of BRCA1-associated cancer.

Keywords: BRCA1
breast cancer
MEPCE
synthetic lethal
transcription
Advisor: Hakem, Razqallah
Intranasal Ketamine for Depression in Patients with Cancer Receiving Palliative Care (INKeD-PC): A Feasibility Study

Antidepressants require weeks for onset of action, a lag time that may exceed life expectancy in palliative care. Conversely, ketamine has demonstrated rapid antidepressant effects. Our objective was to determine the feasibility of a clinical trial assessing intranasal ketamine for depression in patients with terminal cancer. Feasibility was determined by conducting an open-label trial over a 12-month period. Participants with terminal cancer with moderate to severe depression received three flexible doses of intranasal ketamine (50-150mg) over a one-week period. Three participants completed the trial. All three demonstrated an antidepressant response, with a mean Montgomery–Åsberg Depression Rating Scale (MADRS) score reduction of 64% by the day 8 primary endpoint with good overall tolerability. Feasibility was found to be poor, as recruitment rates were low; however, retention and antidepressant response rates were high. Expanding to other sites and broadening eligibility criteria would be necessary to achieve adequate recruitment.

Keywords: cancer
clinical trial
ketamine
major depressive disorder
oncology
palliative care
Advisor: McIntyre, Roger S
Li, Madeline
Development of a Rat Model to Characterize the Effects of Ischaemia on the Masseter and Temporalis Muscles

Temporomandibular disorders of the muscles of mastication (mTMD) are associated with muscle ischaemia. The objective of this study was to develop a rat model to characterize the effects of ischaemia on masticatory muscles.The right external carotid arteries of 18 Sprague-Dawley rats were ligated to induce masticatory muscle ischaemia. The animals were euthanized at 10-, 20-, and 35- days post surgery. Right and left masseter and temporalis muscles were evaluated by quantitative sensory testing, histological and gene expression analyses. Data were analyzed using mixed and general linear models. Mechanical detection thresholds increased with time and were greater on the right than the left side after 20-days. Histological changes indicative of fibrosis and degeneration of the right masticatory muscles were evident at all timepoints and complemented by gene expression analyses. This novel model of masticatory muscle ischaemia holds promise for future studies of the role of ischaemia in mTMD.

Advisor: Cioffi, Iacopo
Ging, Siew-Ging
Investigating the Biodegradability of Polyurethane/Gelatin Electrospun Scaffolds for Cardiovascular Tissue Engineering

Polycarbonate-urethanes have been used for tissue engineering and biomedical engineering applications, but an understanding of their degradation and interactions with biopolymers such gelatin remains and area where more knowledge is still needed. In this thesis, a linear polycarbonate polyurethane (PCNU) was blended with the gelatin (PCNU molecular weight ~145,000 g/mol polystyrene equivalent, gelatin bloom strength 225) and electrospun into aligned nanofibrous scaffolds. The scaffolds were subjected to accelerated enzymatic degradation and assessed for degradation rate, molecular weight changes in the PCNU, hydrogen bonding between the PCNU and gelatin, and changes to the crystalline structure of the PCNU. This work showed very unique interactions between the PCNU and gelatin, which were not anticipated and provided for differentiated degradation profiles relative to the native PCNU. The findings suggest a different degradation mechanism for PCNU when blended with gelatin, as compared to PCNU. The degradation products of the scaffolds were tested for cytotoxicity by treating cultured human endothelial cells to the collected supernatants and assessing for viability and proliferation of the cells. The degradation products did not show an adverse effect on the cells.

Keywords: Biodegradation
Cytotoxicity
Electrospinning
Endothelial Cells
Gelatin
Polyurethane
Advisor: Santerre, Paul JP
Investigating dynamic cerebral blood flow response in a randomized controlled trial

Arterial spin labeling (ASL) magnetic resonance imaging (MRI) may be well-suited to evaluate treatment response in psychiatric clinical trials. This thesis reports on a proof-of-concept, double-blind, in-scanner, midazolam-controlled trial, in which 25 adults with refractory bipolar depression were randomized to receive either: 1) inhaled nitrous oxide plus intravenous saline, or 2) intravenous midazolam plus inhaled medical air. Pseudo-continuous ASL MRI monitored changes in cerebral blood flow (CBF) concurrently with treatment interventions. Relative to midazolam, nitrous oxide led to increases in CBF across frontal regions, including the anterior cingulate and ventral prefrontal cortices, and decreases in arterial transit time (ATT) across frontal and parietal regions. Furthermore, baseline CBF within frontal regions-of-interest was associated with greater improvements in depressive symptoms following nitrous oxide treatment. In conclusion, this thesis supports the use of ASL in the evaluation of drug efficacy for individuals suffering from bipolar depression.

Keywords: bipolar disorder
cerebral blood flow
midazolam
nitrous oxide
Advisor: MacIntosh, Bradley J
Evolutionary Search for Authorization Vulnerabilities in Web Applications

Access controls are essential to protect private resources in web applications. However, authorization vulnerabilities resulting from improper access controls are common. Existing detection techniques require manual effort and suffer from false positives as automating authorization vulnerability detection in an app agnostic way is challenging. We present two subproblems- automated discovery of app resources and automated detection. This thesis introduces AuthZee, a tool that automatically generates objects and discovers resources in a web app and automatically detects if those resources are vulnerable to improper authorization, without requiring details about the app code/logic. We present a novel evolutionary crawler and triad testing technique requiring login credentials of three user accounts in the app which allows AuthZee to crawl user account space and perform automated authorization vulnerability detection. AuthZee discovered more resources than existing crawling techniques in 7 open-source web apps and detected 1 vulnerability with 0 false positives for most apps.

Keywords: Access control
Authorization
Crawling
Genetic algorithm
Web vulnerability detection
Advisor: Lie, David DL
Plant-based Dietary Patterns: Cardiometabolic Risk and Nutritional Adequacy

Extensive research on the optimal diet for several health outcomes emphasizes a large, if not entire, proportion of plant foods. Less is understood regarding the effects of a progressive adherence to plant-based dietary patterns and which dietary elements are most protective. While a well-planned plant-based diet can be nutritionally adequate, it is unknown whether Canadians who follow such diets are at a greater risk of nutritional deficiencies. To address these gaps, we conducted a systematic review and meta-analysis of prospective cohorts that demonstrated a plant-based diet had a protective association with cardiometabolic health which was strengthened when higher quality plant foods were emphasized. We additionally assessed nutritional adequacy among Canadians who follow plant-based dietary patterns and found risk for nutritional inadequacy was similar or lower for most key nutrients compared to omnivores. These findings support recommendations for plant-based diets as appropriate high quality diets in Canada.

Keywords: Cardiovascular disease
Diabetes
Dietary pattern
Nutritional adequacy
Plant-based diets
Vegetarian diets
Advisor: Malik, Vasanti
3D Laser Written Mirror-Waveguide Circuits for Silicon Photonic Interconnects

An increase in data usage following demands for faster networks over past decades has prompted data centers to scale up the density of channels and boost the network bandwidth. In this way, a new architecture for assembly and packaging of electro-optical (EO) components is now required to facilitate chip-to-chip and chip-to-network interconnections. This thesis employs femtosecond laser writing combined with 3D structural micro-machining for fabricating glass interposers and a new optical printed circuit board (OPCB) platform. The presented glass interposer provided vertical coupling from a plane of multi-core fiber (MCF) arrays to a two-dimensional (2D) grid of silicon photonics (SiP) grating couplers. The OPCB platform demonstrated a wider scope for all-glass optical routing by providing a high-density optical circuit for MCF-to-MCF linking. The interposer and OPCB optical systems provided tight-turning waveguide bends for 3D interconnectivity by developing total internal reflection (TIR) mirrors and 2D hollow-filament gratings photonic crystals (PhCs).

Advisor: Herman, Peter Robert
Approaching Activism: A Systematic Review of Museum Conservation Education Program Evaluations

The theory of museum activism argues that when faced with social and ecological crises, museums must act. However, pursuing explicitly activist agendas risks the public trust which is essential for museums’ continued operation. Evaluation could help legitimate activist museum work and maintain public trust, but not all approaches to evaluation are appropriate for an activist context. This thesis determines which approaches are being used to evaluate activist museum work, specifically through a systematic review of conservation education program evaluations. The eighty-one reviewed evaluations employed twenty-five approaches to evaluations. The most frequently employed approach was theory-driven evaluation, followed by responsive evaluation. As well, the results suggest a relationship exists between museum genres and which evaluation approach is employed. These findings set a foundation for determining the nature of this relationship and whether the most prevalent evaluation approaches are the most appropriate to use for evaluations of activist museum work.

Keywords: Conservation Education
Museum Studies
Program Evaluation
Systematic Review
Advisor: Mihalache, Irina
McLaughlin, Hooley
Evaluation of the Long-term Cardiac Prognosis of Kawasaki Disease in Canada

To evaluate the long-term risk of hypertension and other major adverse cardiac events (MACE) in individuals with Kawasaki Disease (KD), an inception cohort of 1,169 KD patients diagnosed between 1991-2008 was linked with health administrative data and their risk was compared with 11,690 population comparators. During 21,792 and 218,578 patient years (PY) of follow-up among KD and comparators, respectively, incidence rates of hypertension were 1.38 (95%CI 0.93-1.97) vs 0.62 (95%CI 0.52-0.74)/1000 PY. Multivariable cause-specific hazard models estimated that KD patients had an increased risk for hypertension and MACE. This increased risk for hypertension and MACE was also observed in KD patients with normal coronary arteries relative to comparators. MACE risk was higher in KD patients with coronary aneurysms. For all cardiac outcomes, the increased risk was highest following diagnosis and diminished over follow-up. Despite the relative increase, the low event rates suggest that cardiac prognosis in KD remains favorable.

Keywords: Cardiovascular Disease
Hypertension
Kawasaki Disease
Prognosis
Advisor: Feldman, Brian M.
Widdifield, Jessica
Abundance, Composition, and Factors Impacting the Formation of Microplastic-Associated Biofilm in Freshwaters

Biofilm that colonizes on the surface of microplastics (MPs) may represent a potential health risk. The current study examined factors that influence MP-associated biofilm growth, including polymer type, degree of weathering, and source water quality. Weathered MPs were produced in-lab, and biofilm trials were conducted on-site at drinking water treatment facilities using a passive flow-through system. Biofilm abundance was quantified in terms of adenosine triphosphate (ATP); its composition was assessed via metagenomic sequencing. Biofilm growth was observed on MPs of all polymer types, and most prevalent on polyvinyl chloride (PVC) where ATP levels were 6 to 12 times higher when compared to other polymers. Pathogen-containing species including Salmonella enterica and Escherichia coli were observed on all polymers with relative abundance up to 13.7%; S. enterica was selectively enriched on weathered polymers in specific water matrices. These findings support the need to examine the impact of drinking water treatment to minimize potential health risks. As well they suggest the need for future studies to adopt the use of weathered polymers, as they were observed to increase biofilm growth.

Keywords: Biofilm
Drinking water
Microplastics
Weathering
Advisor: Andrews, Robert C
Acoustic Microfactory for Damage-free and Accurate Microassembly

The state-of-the-art microassembly method uses microgrippers that mechanically grip the objects,potentially causing damage, since force sensors cannot accurately control the gripping force. This work presents an acoustic microfactory which uses various acoustic field distributions to assemble objects without physical contact. A platform capable of producing high resolution acoustic fields and imaging the workspace is developed. This platform enables the study of various field generation algorithms. After characterizing the strengths of existing algorithms and designing new algorithms based on amplitude and phase modulation, the sequence of algorithms needed to assemble objects is defined. For the first time, parts are serially assembled using only acoustic forces and the system achieves an accuracy that improves upon previous non-contact microassembly methods. This thesis work concludes that objects can be manipulated while an interfering subassembly is present in the workspace, provided that appropriate algorithms are used with assembly in mind rather than simply manipulation.

Keywords: Acoustic manipulation
Acoustic traps
Levitation
Microassembly
Micromanipulation
Ultrasonic phased arrays
Advisor: Diller, Eric D
Ultrasound-stimulated Microbubble Induced Fluid Transport in Poroviscohyperelastic Media

Ultrasound stimulated microbubbles have been shown to be capable of inducing deformations of biologically relevant boundaries through both volumetric oscillations and primary radiation forces. In this thesis, it is proposed that microbubble indentation upon saturated poroviscohyperelastic media, resulting from primary radiation forces, plays a role in the transport of fluids into such media. This mechanism is investigated via finite element analysis, where a single load-unload cycle, of a 5μm microbubble to a peak depth of 1μm, is found to cause pore pressure elevation and effective fluid flow velocities of up to 2.7mm/s within the medium. Importantly, fluid exchange between the overlying fluid layer and the poroviscohyperelastic medium occurs in a manner that extends multiple microbubble-contact radii away from the indentation site. These findings offer insight into an unexplored microbubble-mediated fluid transport mechanism, suggesting that the indentation aspect of the microbubble-tissue interaction may play a role in enhancing therapeutic agent delivery.

Keywords: Drug Delivery
Finite Element Method
Fluid Transport
Indentation
Microbubbles
Ultrasound
Advisor: Goertz, David E
Development and Characterization of a Human Model of Arteriovenous Malformations (AVM)-on-a-Chip

Arteriovenous Malformation (AVM) is a vascular disease characterized by arteriovenous shunting that results in dilated and fragile vessels. So far, there are no pharmaceutical treatments available for AVMs. To address this need, we engineered an AVM-on-a-Chip that allows for real-time assessment of barrier function and morphological characteristics. The AVM-on-a-chip is created using a heterogeneous culture of immortalized human umbilical vein endothelial cells (HUVECs) with KRAS-mutant HUVECs, a know mutations associated with AVM formation, and supporting fibroblasts. A fibrin cell suspension is seeded into the platform to naturally form tubular and perfusable vascular networks. Key hallmarks of AVM were captured through areas of vascular dysplasia from KRAS mutant HUVECs, which affected the overall vascular structure. We found a significant increase in vascular permeability due to cell-cell junction breakdown in KRAS-positive vessel segments. Additionally, KRAS positive segments led to increase in vessel width and decreased branch length. Treatment with MEK inhibitor, a previously investigated reagent in AVM therapy, only recovered barrier function but not vascular distension.

Keywords: Ateriovenous Malformation
Microfluidics
Vasculature
Advisor: Vasconcelos, Sara
Mapping of the Novel mRNA Acetylation, ac4C, in the HEK293 Transcriptome

Internal mRNA modifications have been implicated in regulation of RNA function. Advancements in RNA-sequencing technologies have enabled transcriptome-wide mapping of mRNA modifications, expanding our understanding of their influence on mRNA. N4- acetylcytidine (ac4C) was initially discovered in tRNA and rRNA and, more recently, described in mRNA, alongside NAT10 as the acetyltransferase responsible for ac4C deposition across RNA species. As multiple RNA modification sequencing methods arose, contradictory results regarding the presence of ac4C in eukaryotic mRNA were published. I demonstrated ac4C presence in mRNA through dot blot analyses after validating an ac4C antibody. I carried out ac4C-CLIP-seq by using UV light to crosslink the ac4C antibody to mRNAs, found that NAT10 crosslinks next to ac4C sites, and so provided a high-resolution transcriptome-wide map of ac4C. Additionally, I strengthened understanding of the roles of ac4C sites in mRNA by demonstrating differential expression of transcripts containing ac4C in the presence and absence of NAT10.

Keywords: ac4C
mRNA modification
N4-acetylcytidine
NAT10
Advisor: Greenblatt, Jack