VictorJuiz/thesis huggingface dataset:
Applying Stable Carbon Isotopic Analysis at the Natural Abundance Level to Determine the Origin of Docosahexaenoic Acid in the Brain of the Fat-1 Mouse
Keywords: Brain
compound specific isotope analysis
docosahexaenoic acid
Fat-1 mouse
isotope ratio mass spectrometry

Current methods applied to study the origin and metabolism of brain fatty acids involve the administration of synthesized fatty acid tracers. The high cost of these tracers makes it infeasible to conduct chronic studies through this approach, limiting study durations to acute time points that may not reflect the chronic, steady-state, metabolism of fatty acids. Here, we provide the proof-of-concept of a cost-efficient alternative method: natural abundance compound specific isotope analysis by isotope ratio mass spectrometry. Through the application of this method, we differentiated between tissue docosahexaenoic acid (DHA) originating directly from diet or DHA biochemically synthesized in a complex transgenic model: the fat-1 mouse. We further determined pre-formed dietary DHA to be the main source of brain DHA in fat-1 mice fed a diet rich in n-6 and/or n-3 PUFA. Future studies could utilize this approach to answer complex question pertaining to brain fatty acids origin and metabolism.
The Neurostructural Phenotypes of CACNA1C rs1006737 in Adolescents with Bipolar Disorder and Healthy Controls of Caucasian Race
Keywords: Adolescent
Bipolar Disorder
brain structure
CACNA1C
Neuroimaging
rs1006737

Background: CACNA1C rs1006737 has been implicated in structural brain differences in adults with bipolar disorder (BD) and/or healthy controls (HCs). No prior study has examined associations between rs1006737 and brain structure in adolescents. Methods: Seventy-one adolescents (14-20 years; 38BD, 33HC) underwent 3-Tesla Magnetic Resonance Imaging (MRI). ROI and whole-brain vertex-wise analyses examined cortical and subcortical volume, surface area (SA), and/or thickness. General linear models included main effects of diagnosis and rs1006737, and an interaction term, controlling for age, sex, and total intracranial volume. Results: Vertex-wise analysis found significant diagnosis-by-rs1006737 interactions for prefrontal and occipital brain structure Main effects of rs1006737 were found on anterior cingulate cortex SA from ROI analysis, and occipital SA from vertex-wise analysis. Conclusion: The current study identified neurostructural intermediate phenotypes relevant to the impact of CACNA1C rs1006737 on adolescent BD. Further investigation is warranted into the relevance of rs1006737 associations with BD-specific elevations in regional SA.
Genotyping and Phenotypic Analysis of Streptococcus mutans Isolates From Children With and Without Dental Caries
Keywords: Acidurance
Caries
Early Childhood Caries
Persistence
S mutans
Streptococcus mutans

Within dental plaque, Streptococcus mutans produces acids from fermentable carbohydrates, decreasing the biofilm pH, causing enamel demineralization. S. mutans produces persisters, dormant variants of cells that survive lethal antibiotic concentrations without developing antibiotic resistance. Persisters have been associated with infection chronicity. We hypothesized that phenotypic heterogeneity of S. mutans is directly associated with cariogenicity. S. mutans were isolated from plaque collected from caries-free (CF) children and children with Severe Early Childhood Caries (S-ECC). For each identified genotype, an acid tolerance analysis was performed and persisters were quantified. In S-ECC patients with >1 strain, the dominant strain exhibited higher cell survival following exposure to pH 3.2, whereas in CF patients, survival was similar. S. mutans isolates from S-ECC patients produced ~15x more persisters than isolates from CF patients. S. mutans exhibits phenotypic diversity. The ability of S. mutans to produce high levels of persisters may be a hallmark of cariogenicity.
The Sooting Propensities of Ethanol, Ethylene, Propylene, and Butylene at Elevated Pressures
Keywords: combustion
flame
pressure
soot

Laminar co-flow diffusion flames of ethanol-doped methane flames with 10% of carbon from ethanol up to 6 bar and nitrogen-diluted alkene flames of ethylene and propylene up to 8 bar and 1-butylene up to 2.5 bar were investigated. Line-of-sight spectral emission measurements were inverted with an Abel-type algorithm to obtain radially resolved soot volume fraction and temperature measurements. Ethanol-doped methane flames displayed consistently higher soot yields than neat methane flames, but only a slightly higher pressure dependence. Comparing the nitrogen-diluted alkene flames, 1-butylene produced the most soot, followed by propylene and ethylene. Propylene and 1-butylene displayed similar sooting propensity pressure dependencies, but ethylene was found to have a significantly stronger pressure dependence. This was attributed to the greater concentration of aromatics in the pyrolysis products of propylene and 1-butylene as aromatics have been found to have a weaker sooting propensity pressure dependence.
Adversarial Attacks on Face Detectors using Neural Net based Constrained Optimization
Keywords: Adversarial Attacks
Computer Vision
Face Detection
Faster R-CNN
Machine Learning
Neural Networks

Adversarial attacks involve adding, small, often imperceptible, perturbations to inputs with the goal of getting a machine learning model to misclassifying them. While many different adversarial attack strategies have been proposed on image classification models, object detection pipelines have been much harder to break. In this thesis, we propose a novel strategy to craft adversarial examples by solving a constrained optimization problem using an adversarial generator network. Our approach is fast and scalable, requiring only a forward pass through our trained generator network to craft an adversarial sample. Unlike in many attack strategies we show that the same trained generator is capable of attacking new images without explicitly optimizing on them. We evaluate our attack on a trained Faster R-CNN face detector on the cropped 300-W face dataset where we manage to reduce the number of detected faces to 0.5% of all originally detected faces.
Quantification of Mutans Streptococci and Persister Cells in Orthodontic Patients: A Pilot Investigation
Keywords: Biofilm
Dental Caries
Dental Plaque
Mutans Streptococci
Orthodontics
Persisters

Orthodontic patients have higher risk for dental caries. Within plaque biofilm, mutans streptococci (MS) are present together with persister cells (PC), a microbial subset that confers disease chronicity and relapse potential. PC levels are elevated by environmental stresses, e.g., orthodontic treatment. Our purpose was to quantify, for the first time, MS and PC in orthodontic patients. Plaque samples were collected in 17 patients at 0, 1 and 6 months after fixed appliance bonding. Percentage of MS and PC were determined by microbiological assays. Overall, treatment did not affect %MS and %PC (P>0.05). However, %PC response to treatment appeared to be dependent on baseline %MS values. Patients with low %MS at baseline had an increase in %PC during treatment, while %PC decreased in those with high baseline %MS. Orthodontic treatment may provide a way for MS to persist in individual orthodontic patients with specific subtypes and contribute to higher caries incidence.
The Role of Synaptic Inhibition in the Primary Motor Cortex of an ALS Mouse Model
Keywords: Amyotrophic Lateral Sclerosis
Chemogenetics
Electrophysiology
Primary Motor Cortex
Riluzole
Synaptic Inhibition

Amyotrophic Lateral Sclerosis (ALS) is a fatal disease resulting from the degeneration of motor neurons in the cortex and spinal cord. ALS is the most common neurodegenerative disorder of the motor system and involves progressive muscle weakness and atrophy. Cortical hyperexcitability is a hallmark feature of ALS, and recent studies report reductions in synaptic inhibition in the primary motor cortex (M1) presymptomatically. Rescuing interneuron-mediated inhibition is a promising strategy for reducing hyperexcitability and slowing the onset of ALS. This study aimed to determine whether chemogenetic or pharmacological tools could decrease pyramidal neuron hyperexcitability in Layer 5 of the M1 (L5-M1) in the SOD1G93A ALS mouse model. The principle novel findings of my work are: (i) increasing GABAergic interneuron-mediated inhibition onto L5-M1 pyramidal neurons rescues hyperexcitability of M1 pyramidal neurons and (ii) riluzole reduces hyperexcitability and affects intrinsic membrane properties of M1 pyramidal neurons.
The Role of ATP and P2X Purinoceptor 7 in the Development of Cerebral Tau
Keywords: ATP
Neurodegeneration
P2X7R
Tau
Tauopathy

ATP release and signalling via the P2X7 receptor have been implicated in numerous pathological processes including neurodegeneration and may play a role in the development of tauopathies. We injected ATP analogue bzATP intraventricularly into C57BL/6 mice, pre-treated with either intraperitoneal P2X7R antagonist Brilliant Blue G (BBG) or vehicle. Behavioural outcomes, levels of phosphorylated tau, and immunohistochemical changes in astrocytes and microglia were assessed at 2 weeks and 3 months after treatment. We observed increased immobile time in the tail suspension test and poor performance on rotarod for bzATP-treated mice at 3 months post-treatment, which were diminished by BBG pre-treatment. Western blot revealed increased levels of phosphorylated tau in bzATP-treated mice compared to controls. Astrocytic marker GFAP showed increased periventricular staining at both 2 weeks and 3 months for bzATP-treated mice but microglial marker IBA1 showed no changes. In summary, ATP-P2X7R-mediated mechanisms lead to development of behavioural deficits and increased phosphorylated tau.
Survival of Class III Amalgam and Composite Restorations in Primary Cuspid Teeth
Keywords: Amalgam
Caries
Composite
Dentistry
Restorations
Survival

OBJECTIVE: The aim of this retrospective cohort study was to determine the survival of class III amalgam and composite restorations in primary canines. METHODS: A chart review was done on patients seen at the University of Toronto’s pediatric dental clinic between 1999 and 2017. RESULTS: The median survival time of amalgam and composite was approximately 4.5 years and 3.8 years respectively. There was no significant difference between the clinical survival of amalgam and composite (log-rank test: p=0.09, Wilcoxon: p=0.31). Amalgam was significantly less likely to fail due to recurrent caries versus composite (p
Cultivating an American Worldview: A Comparative Analysis of Perspectives of the Middle East, Arabs, and Muslims in US Public High School “World History” Curricula
Keywords: Islamic History
Middle Eastern History
Middle East Studies
Secondary Education
Social Studies
United States

The institution of public education in democratic societies has been used as an effective tool for regulating national identity. In the last four decades, “World History” courses have become a fundamental part of mainstream American social studies. These courses offer a standardized narrative regarding the histories of non-Western regions. This study explores high school social studies curricula in Texas, New York, California,Virginia, and North Dakota focusing on how the frameworks address Islamic, Middle Eastern, and North African history. The analysis addresses the state frameworks’ ability to effectively present Islamic and Arab history within proper context and critiques various problematic paradigms rooted in modernization theory and orientalism. In critiquing the content of these frameworks and contextualizing policy in American public education, this paper intends to scrutinize the challenges of teaching the Middle East in the United States public high schools.
Enhancing FPGA Architecture for Efficient Deep Learning Inference
Keywords: Convolutional Neural Networks
Deep Learning
FPGA Architecture
Hardware Acceleration

Deep Learning (DL) has become best-in-class for numerous applications but at a high computational cost that necessitates high-performance energy-efficient acceleration. FPGAs offer an appealing DL inference acceleration platform due to their flexibility and energy-efficiency. This thesis explores FPGA architectural changes to enhance the efficiency of a class of DL models, convolutional neural networks (CNNs), on FPGAs. We first build three state-of-the-art CNN computing architectures (CAs) as benchmarks representative of the DL domain and quantify the FPGA vs. ASIC efficiency gaps for these CAs to highlight the bottlenecks of current FPGA architectures. Then, we enhance the flexibility of digital signal processing (DSP) blocks on current FPGAs for low-precision DL. Our DSP block increases the performance of 8-bit and 4-bit CNN inference by 1.3x and 1.6x respectively with minimal block area overhead. Finally, we present a preliminary evaluation of logic block architectural changes, leaving their detailed evaluation for future work.
Identification of E3 Ubiquitin Ligase, UBR5, as a Potential Interactor of TTC7A and PI4KIIIα
Keywords: FAM126A
PI4KIIIα
PI4P
TTC7A
UBR5
VEO-IBD

Mutations in Tetratricopeptide Repeat Domain 7A (TTC7A) results in severe intestinal and immune disease phenotypes, one of them being Very Early Onset Inflammatory Bowel Disease (VEO-IBD). TTC7A is part of an evolutionarily conserved pathway and acts as a scaffolding protein recruiting Phosphatidylinositol 4-kinase Type III Alpha (PI4KIIIα) to the plasma membrane (PM). This conserved pathway helps PI4KIIIA phosphorylate phosphatidylinositol (PI) to PI 4-phosphate (PI4P) at the PM. The PIPs downstream of PI4P have been implicated in maintaining cell polarity and survival. Previously, mass spectrometry was performed to identify potential TTC7A binding partners. Ubiquitin protein ligase E3 component N-recognin 5 (UBR5) was identified as one of the top TTC7A binding proteins. Results show co-immunoprecipitation of UBR5 with TTC7A along with mutants (E71K, Q526X, A832T) identified at The Hospital for Sick Children. Results also suggest that UBR5 may be part of the PI4KIIIA-FAM126A-TTC7A complex (and therefore implicate UBR5 in PM PI4P synthesis).
Development of a Low-Cost Diagnostic Tool to Assess the Sufficiency of Food Drying Processes in Developing Countries
Keywords: Co-operatives
Developing countries
Dried food
Moisture content
Moisture measurement
Small-scale operations

Food drying reduces moisture content supporting microbial growth that contributes to food spoilage in developing countries. However, there is a lack of efficient low-cost tools to assess the sufficiency of food drying in small-scale operations in developing countries. Thus, a model was developed using a thermal imaging process to determine the moisture content of dried Royal Gala apples based on their cooling rate. Fitted regression curves showing absolute temperature versus cooling time were plotted for different wet basis moisture contents. The regression curve obtained for a safe range of moisture (9-11%) produced an equation with a higher constant and exponent than the curve for a potentially unsafe range (15-17%), showing the potential of this method. Further analysis is needed to evaluate the applicability of this method in other types of dried foods and conditions, as well as to explore the possibility to use the developed model in a mobile application.
Exploring the Role of Somatostatin in the Pathogenesis of Alzheimer’s disease
Keywords: Alzheimer's disease
Amyloid-β
Neurodegeneration
Neuroscience
P-type ATPase
Somatostatin

The amyloid-β (Aβ) peptide is understood to be a critical factor in the pathogenesis of Alzheimer’s disease (AD), with soluble Aβ oligomers (oAβ) observed to be particularly toxic to neurons. For this reason, we undertook an in-depth search for oAβ binders in human brain, taking advantage of advanced mass spectrometry workflows. This analysis revealed the peptide somatostatin (SST) to be the most selective binder to oAβ in affinity capture experiments. Furthermore, SST was observed to interfere with Aβ aggregation kinetics and promote the formation of distinct 50-60 kDa Aβ assemblies. In a follow-up investigation of the SST interactome, it was revealed that SST predominantly binds to several members of the family of P-type ATPases, particularly the Na+/K+-ATPase. Subsequent validation experiments confirmed this interaction and identified a tryptophan residue within SST as critical for binding. These findings bring to light potentially new mechanisms for SST action in normal physiology and AD.
On Establishing PPG Biometrics for Human Recognition: Feasibility and Variability
Keywords: Authentication
Biometric Recognition
BioSec.Lab PPG database
Machine Learning
Pattern Recognition
Photoplethysmograph (PPG)

This thesis presents a new biometric modality called Photoplethysmograph (PPG) for biometric authentication. PPG records the blood volume change from any part of the body with a combination of a light emitting diode and a photo diode. Therefore, it is the easiest to acquire amongst all medical biometric traits. Although PPG is a time-dependent physiological signal and alters with physical and psychological stress, most of the prior art has neglected these factors. This work presents the ‘BioSec.Lab PPG Database’ and establishes the PPG as biometrics through a comprehensive analysis on its distinctiveness and robustness under exercise, emotions, time-lapse, and noisy conditions. Performances under all variations mentioned above are assessed using various methodologies. Encouraging Equal Error Rates (EER) between 0.00%-36.09% were achieved with relaxed states and under different variations from the three databases.
Evaluation of a Novel Recombinant Human Bone Morphogenetic Protein-2 Bioimplant for Alveolar Ridge Augmentation in Dogs
Keywords: Bioimplants
BMP
Bone grafting
rhBMP

Autografts (ABG) are the gold standard for alveolar ridge augmentation (ARA), but involve second-site surgical morbidity. The novel BMP bioimplant URIST™ has been designed to be an effective alternative to autografts. The efficacy of URIST™ with 0.5(D1) or 1(D2) mg BMP/unit was compared to ABG or Bio-Oss®. A split mouth design was employed in Beagle dogs. Caliper and Cone Beam CT analyses were utilized to compare dimensional changes in the alveolus. After 12 weeks, dental implant were placed and bone cores analyzed by histology. Dogs that did not have dental implant placement were analyzed for the effect of prolonged healing time on dimensional bony changes. URIST™ had comparable dimensional changes in ARA to the gold standard autograft, with some statistically significant increases in width. All grafted sites had successful primary stability of dental implant placement. Histology showed no clear differences in the character of new trabecular bone deposited among grafted sites.
Towards Clinical Translation of the Porphysome: Establishment of Endometrial Cancer Applications and Investigation of Metabolic Differences in Pyrolipid Isomers
Keywords: Endometrial Cancer
Fluorescence Imaging
Lymphadenectomy
Metastasis
Molecular Imaging
Nanoparticle

Treatment of endometrial cancer consists of surgery ± adjuvant therapy depending on lymph node involvement determined by lymphadenectomy. Targeting lymphadenectomy to patients with known metastases would provide diagnostic and therapeutic benefits while reducing morbidity. Porphysomes are self-assembling nanoparticles made from a multifunctional porphyrin-lipid monomer (pyrolipid) which accumulate preferentially in malignant tissue. Pyrolipid is created through an acylation reaction during which isomerization can occur. A VX2 model of endometrial cancer with retroperitoneal metastases was used to investigate the accuracy of pre-operative 64Cu-Porphysome-enabled PET imaging of lymph nodes and the sensitivity / specificity of in-vivo porphyrin-fluorescence image-guided lymphadenectomy. Pharmacokinetic, biodistribution and biodegradation studies were used to determine differences in Sn1 and Sn2 isomeric Porphysomes. This study demonstrated that Porphysomes are a highly sensitive imaging tool to diagnose primary tumour, metastatic lymph nodes and intra-abdominal metastases and that Sn2 pyrolipid is the optimal isomer for clinical translation due to the preferential biodegradation profile.
The Financial Production of Bankruptcy: Denaturalizing Fiscal Crisis in the City of Detroit
Keywords: Financialization
Municipal bankruptcy
Urban decline
Urban governance

Accounts of urban crisis in the United States focus largely on issues of deindustrialization, depopulation, property abandonment, and racial conflict. In the aftermath of the 2008 financial crisis, however, another issue has come to light: the role of financial shocks and volatile debt arrangements in shaping urban outcomes. Through a case study of the City of Detroit’s 2013 bankruptcy, this thesis questions the seeming inevitability of fiscal crises in declining cities. Instead, it analyzes the ways in which fiscal crises can be understood as products of risky financial relationships and debt structures. Drawing on archival data, policy analysis, and quantitative financial data, the thesis focuses on the City of Detroit’s use of one risk-laden financial instrument—the interest rate swap—and follows this instrument through the city’s fiscal crisis. In so doing, I map out how this volatile financial instrument shaped both the economic and political dynamics of Detroit’s bankruptcy.
The Effect of Bone Marrow-Derived Progenitor Cell Therapy to Improve Fracture Healing in a Diabetic Rat Critical Size Defect Model
Keywords: Cell Therapy
Diabetes
EPC
Regenerative Medicine

Our study aimed to explore the efficacy of locally implanted endothelial progenitor cells (EPCs) from healthy and diabetic animals on bone defect healing in healthy and diabetic recipients. EPCs seeded on gelatin scaffolds were implanted in surgically created 5mm femoral defects to create six randomized treatment groups. The animals underwent biweekly radiographic assessment until the 10-week endpoint. Post-mortem specimens were analyzed by micro-computed tomography and biomechanics. Most cell-treated healthy animals achieved union by 8 weeks. EPC-treated diabetic animals achieved higher radiographic scores than the diabetic controls. Healthy animals that received diabetic cells demonstrated greater bone volume, fractional bone volume, bone mineral density and biomechanical stiffness to diabetic animals that received diabetic cells but did not significantly differ from healthy animals that received healthy cells. Thus, EPC therapy promotes fracture healing in diabetic animals irrespective of the cell source, though diabetes may decrease their healing capacities compared to treatment-matched healthy animals.
Effects of Anxiety and Daytime Clenching on Orthodontic Pain Perception
Keywords: anxiety
orthodontic pain
wake-time clenching

Objectives: This study assessed the relationship between anxiety and oral parafunctional behaviours in individuals with and without orofacial pain; and whether the relationship between anxiety and orthodontic tooth pain is dependent upon wake-time tooth clenching. Methods: The State-Trait Anxiety Inventory (STAI), Oral Behaviour Checklist (OBC) and TMD-Pain Screener were completed by 255 students with (n=47, 24.8±4.2 years) and without (n=208; 26.0±4.8 years) TMD pain. STAI score distribution was examined and 45 volunteers (26.0±3.4 years) with low-, intermediate-, and high-anxiety were recruited and submitted to experimental orthodontic-tooth-movement. Results: A significant effect of the interaction group*trait anxiety on OBC scores was found (p=0.028). A significant effect of the interaction clenching*study group*day on tooth-pain was found (p