VictorJuiz/thesis huggingface dataset:
Deep Neural Network Model Inversion Attack via Auxiliary Generative Adversarial Network

In recent years, predictive deep neural networks have enabled remarkable progress in pattern recognition tasks and are being used in many domains. Given this widespread use, it is important that these models do not reveal information about sensitive training data that they have been trained on. In this work, we consider a malicious ML user that attempts to recover the training dataset of a supervised neural network by having access to an "auxiliary" training dataset that only shares high-level information with the original dataset. Specifically, we propose "Auxiliary GANs" which is an algorithm based on generative adversarial networks (GAN) to recover the original training data by combining the leaked information from the predictive model with the shared information of the auxiliary dataset. We evaluate the performance of our algorithm on several datasets and show that it outperforms the previous works both in terms of accuracy and the FID score.

Keywords: Adversarial Machine Learning
Deep Neural Networks
Generative Adversarial Network
Machine Learning
Model Inversion
Advisor: Khisti, Ashish
Change in Patterns of Anatomical and Enzymatic Expression and Allocation during the Evolution of C4 Photosynthesis in the genus Flaveria

The evolution of C4 photosynthesis is marked by changes in anatomical and enzymatic patterns. The allocation of chloroplast, mitochondria, and the enzyme glycine decarboxylase (GDC) to photosynthetic tissues was investigated in 19 populations within the Flaveria genus. Results show a progressive increase in chloroplast and mitochondrial investment in bundle sheath (BS) cells and tissue in comparison to mesophyll (M) cells and tissue which emphasizes the BS accommodating an increase in photosynthetic metabolic activity for C2, C4-like and C4 plants. GDC localization to the BS increases in PK and C2- species, indicating a role of this enzyme in the upregulation of a rudimentary C2 cycle. Notably, populations of F. linearis from the Yucatan Peninsula were observed to have larger and more prominent BS chloroplasts than other F. linearis populations. This indicates Yucatan-localized populations can more effectively trap photorespired CO2, which could explain the lower CO2 compensation points observed in these plants.

Keywords: C4 photosynthesis
Flaveria
Advisor: Sage, Rowan F
Effect of Curing Agents on the Cure Behaviour and Thermal and Mechanical Properties of a Novel Vanillin-based Bio-epoxy Resin

In recent decades, there has been extensive research on bio-based polymers due to growing environmental and economic concerns regarding the inevitable depletion of petrochemical resources. In this work, the effect of functionality and molecular structure of the cure agent on cure kinetics and performance of a novel vanillin-based phosphorus-containing epoxy resin (VPE) was investigated. The three aliphatic amines used as the curing agents: ethylenediamine (EDA), diethylenetriamine (DETA), and triethylenetetramine (TETA), varied in the number of active hydrogens from 4 to 6. It was found that the type of amine used had a determining effect on both cure kinetics and the characteristics of the cured resins. Notably, minimal autocatalytic effect was observed in VPE-DETA system, while only a weak autocatalytic effect was observed in VPE-EDA and VPE-TETA systems. These cured VPE samples exhibited excellent thermal stability and tensile properties consistent with those of similar vanillin-based epoxy-amine systems reported in the literature. Among the three VPE-amine systems, VPE-DETA showed the best overall performance.

Keywords: cure kinetics
epoxy
Advisor: Yan, Ning NY
Effect of At-home Bodyweight Interval Exercise Before or After Breakfast on Postprandial Glycemic Control, Post-exercise Fat Oxidation and Perceptions of Appetite in Females

Our study investigated the effect of at-home bodyweight interval exercise (BWI), performed before or after breakfast, on postprandial glycemia, post-exercise fat oxidation and appetite control. In a randomized order, 12 female participants completed two virtual trials in the mid-follicular phase of the menstrual cycle involving BWI before (EX-FED) or after (FED-EX) a standardized breakfast. Heart rate and rating of perceived exertion (RPE) were measured during exercise, capillary blood samples were obtained postprandial, and fat oxidation and appetite perceptions were measured post-exercise. Exercise-induced heart rate and RPE were similar between conditions. Postprandial glycemia following breakfast was reduced in FED-EX relative to EX-FED, with a lower glucose mean (p=0.03), peak (p=0.01) and area under the curve (AUC) (p=0.004). Post-exercise fat oxidation was similar between conditions. Appetite was lower in FED-EX, as reflected by a greater negative AUC (p=0.029). Performing BWI after, rather than before, breakfast is superior for lowering postprandial glycemia and appetite in females.

Keywords: Appetite
Carbohydrate
Exercise Physiology
Glycemic Control
HIIT
Lipid
Advisor: Gillen, Jenna B
Evaluation of the Prescription Patterns of Antibiotics among Oral and Maxillofacial Surgeons in Canada

Background: The rise in bacterial resistance is attributed to the inappropriate or unnecessary use of antibiotics. Objectives: The aim of this study was to evaluate the current knowledge and antibiotic prescription patterns among Canadian oral and maxillofacial surgeons. Methods: A web-based survey featuring 17 clinical scenarios was distributed to active oral and maxillofacial surgeons in Canada. The sample group was asked questions about their management these clinical scenarios. Descriptive and multivariate logistic regression analyses were performed (P ≤ .05). Results: More than half of the prescriptions were generated in clinical scenarios where there is little evidence to support their use. Most prescriptions followed the correct antibiotic regimen. Clinicians with a limited scope of practice had a significantly higher overprescribing index rate than those with a more extensive scope of practice. Conclusion: Improving the available evidence and ensuring that all practitioners have up-to-date, evidence-based guidelines could help minimize unnecessary antibiotic use.

Keywords: Antibiotic Prophylaxis
Evidence-Based Practice
Oral and Maxillofacial Surgeons
Over prescribing
Advisor: Azarpazhooh, Amir
Assessing the Impact of Gamification Rewards on Enjoyment and Cognitive Performance

BrainTagger (intro.braintagger.com) games target more convenient and enjoyable cognitive assessment. Four different rewarding feedback conditions were implemented in order to improve the motivation of BrainTagger users who use the games for repeated cognitive assessments over time. Two longitudinal studies involving over 400 participants evaluated the impact of these reward conditions on participant enjoyment and cognitive performance. Leaderboard was the most enjoyable condition. Although the Within-subject Comparison condition was also enjoyable, it provided more reliable measures of executive functions over time. The Emphasis on Accuracy and Emphasis on RT conditions were less enjoyable, but participants in the latter condition exhibited faster RT. The results are discussed in terms of the strengths and weaknesses of the different reward conditions and the prospects for developing cognitive assessment games, with improved rewarding feedback, that will constitute valid and enjoyable methods of cognitive assessment over extended periods of time.

Advisor: Chignell, Mark
Spin-orbital Coupling and Geometric Phase Effects in the Vicinity of a Conical Seam

Non-adiabatic dynamics are ubiquitous in chemical systems, many of which have significant spin-orbital coupling. In locations where electronic states are degenerate, conical intersections often occur and from which the geometric phase arises. Here, we investigate how the geometric phase in doublet spin systems affects dynamics, by comparing these geometric phase effects with those formed previously in the case of zero spin and absence of spin-orbit coupling. To address this, we analyze the crude-adiabatic Hamiltonian modeled with parameters of the collision reaction OH + H2 → H + H2O. To reduce complexity, symmetric considerations were taken into account as an σh horizontal plane is present in the system. This symmetry operator was projected on the general 4x4 crude-adiabatic Hamiltonian, reducing our problem to a decoupled2x2 Hamiltonian. It was found that spin-orbital coupling suppresses diabatic population trans- fer from its integer-spin counterpart. Further studies are needed to understand the mechanisms surrounding this reason.

Keywords: Chemical Physics
Non-Adiabatic Dynamics
Advisor: Izmaylov, Artur A.F.I
Feasibility, Acceptability, and Outcomes of an 8-week Online Multidimensional Cancer Rehabilitation and Exercise Intervention: Mixed Methods Pilot Study

Facility-based cancer rehabilitation programs exist, yet patients are often unable to attend due to distance, cost, and other obligations. A mixed methods pilot study was conducted to assess the feasibility, acceptability, and impact of CaRE@Home: an 8-week online multidimensional cancer rehabilitation and exercise program. Outcomes were captured by attendance and adherence metrics and through qualitative interviews. Preliminary estimates of the effects of CaRE@Home on patient-reported and clinical outcomes were calculated with a sample of n=35 cancer survivors. Recruitment (64%), retention (83%), and adherence (80%) rates, along with qualitative findings, support the feasibility of the intervention. Acceptability was also high. Disability (WHODAS 2.0) scores significantly decreased from baseline (T1) to post-intervention (T2) and three-months post-intervention (T3) (p = 0.03 and p = 0.008). The CaRE@Home program is a feasible and acceptable program that may help cancer survivors decrease disability. A phase III controlled trial is required to confirm these findings.

Keywords: Cancer
Digital
Exercise
Rehabilitation
Advisor: Jones, Jennifer M
A Robotic MRI-guided High-intensity Focused Ultrasound Neonatal Neurosurgery Platform: Non-invasive Treatment of Intraventricular Hemorrhage

Intraventricular Hemorrhage (IVH) is one of the most serious neurovascular complications associated with premature birth, which results in clotting of blood within the cerebral ventricles and blockage of cerebrospinal fluid (CSF). The current standard of care is an invasive surgery to insert a shunt to remove CSF since there are no direct treatments for these blood clots. Magnetic resonance-guided high-intensity focused ultrasound (MRgHIFU) has been shown as a non-invasive treatment to lyse these blood clots. This thesis evaluates a robotic MRgHIFU neurosurgical platform optimized for neonatal patients. The platform’s targeting ability was quantified and its efficacy at treating blood clots was assessed in brain-mimicking phantoms inside a clinical MRI. Results demonstrated the platform’s high targeting ability and clot lysis efficacy when targeting through simulated brain matter. These results served as an initial verification of the MRgHIFU platform and showed promise towards its final application in a neonatal brain.

Advisor: Drake, James M
Visibly Transparent, RF Transmitting, and Low-emissive Metamaterials: Theoretical and Experimental Study

We propose a set of RF and visibly transparent composite metasurfaces comprising newly developed transparent conductive coatings. Detailed experimental and theoretical analysis of the RF and visible transparency of the proposed meta-glass is presented. The proposed nature-inspired symmetrical honeycomb-shaped meta-glass designs, alter the electromagnetic properties of the glass substrate in the RF spectrum. We show that by using multilayer metallo-dielectric coatings, RF transparency of the meta-glasses can be enhanced while preserving visible transparency. Herein, we demonstrate high transparency meta-glass with up to 92% (i.e., 87% enhancement when compared to low-emissivity glass) and 86% peak RF and optical transmission at ~30 GHz and ~550 nm, respectively. Moreover, the meta-glass possesses high IR control (i.e., >60%). The meta-glass design presented here is amenable to a variety of 5G applications including automobile radar systems. This study paves the way for the design of new visibly transparent metamaterials and artificial dielectrics.

Keywords: Low-emissvity
Metamaterials
Metasurfaces
Transparency
Advisor: Kherani, Nazir P.
Eleftheriades, George V.
Nickel-catalyzed Cross-coupling Reactions to Access a-Aryl Nitriles

a-Aryl nitriles are medicinally and biologically relevant compounds that also provide a synthetic handle for further chemical diversification. This thesis focuses on the development of Ni-catalyzed cross-coupling to access a-aryl nitriles. The first methodology described is a Ni-catalyzed reductive decarboxylative cross-coupling of NHPI esters and aryl iodides. The reaction development and the scope of the reaction will be presented. The second methodology is a Ni-catalyzed decyanation and arylation of disubstituted malononitrile derivatives. In this Chapter, the key focus is on the development of a benzonitrile ligand for Ni catalysis. The reaction development, ligand design and optimization, and preliminary scope of the reaction will be discussed.

Keywords: Cyanation
Ligand Design
NHPI Esters
Nickel Catalysis
Reductive Cross-Coupling
Advisor: Rousseaux, Sophie A.L.
Considering the Solvent Effects on the Crystallization of Boron Subphthalocyanines and New Pathways to Controlled Chlorination

The goal of this thesis was to synthesize and optimize pathways towards chlorinated boron subpthahlocyanines (BsubPcs) and boron subnaphthalocyanines (BsubNcs). We start by synthesizing hexachloro BsubPcs with chlorine or aromatic axial ligands and examined the solvent effects on the solid-state arrangement to give perspective on the effects solvents may have in solution-processed organic photovoltaics (OPVs). Then, we examine alternative synthetic routes to the synthesis of chloro dodecachloro boron subphthalocyanines (Cl-Cl12BsubPc) to achieve the final product in appropriate yields. In the final section, we look at potential routes to synthesize 1,4-dichloro-2,3-dicyanonaphthalene for the production of chloro hexachloro boron subnaphthalocyanine (Cl-Cl6BsubNc), in our goal to achieve efficient, fullerene-free OPVs.

Advisor: Bender, Timothy P
An Evaluation of Potential Sex and Socioeconomic Disparities in Inpatient Stroke Rehabilitation Outcomes

There are limited data examining associations of sex and socioeconomic status with inpatient stroke rehabilitation outcomes. This thesis examined (i) sex differences in discharge FIM, length of stay, and proportion discharged home and (ii) associations between material deprivation and discharge to long-term care and length of stay after inpatient stroke rehabilitation using a retrospective, population-based cohort. Although females (versus males) had a lower discharge FIM, this was not significant in the adjusted analysis. Females had similar lengths of stay to males, but a smaller proportion discharged home. Accounting for baseline differences, females (versus males) had slightly shorter lengths of stay and a higher odds of discharge home. There was no association between material deprivation and direct discharge to long-term care. Individuals living in the most (versus least) deprived areas had a longer length of stay. In summary, there were minimal differences in inpatient rehabilitation outcomes by sex or socioeconomic status.

Advisor: Jaglal, Susan B
Bell, Chaim M
Role of Basal Ganglia in Cognitive Function of Parkinson's Disease Patients

Parkinson’s disease (PD) can be associated with significant cognitive impairments that may lead to dementia. A research priority is to identify biomarkers of cognitive decline in this population, but efforts are hampered by a lack of understanding of the role of globus pallidus in cognitive processing. We studied single units, beta oscillatory LFP activity as well as event related potentials from the globus pallidus internus (GPi) of 16 PD patients, while they performed an auditory oddball task. Of 62 neurons studied, the majority (51 or 82%) responded selectively to the deviant tones. Beta oscillatory activity showed an overall desynchronization during attended tones. P300s were recorded in GPi selective to the attended tone and averages of trials showing a difference in beta oscillatory activity between deviant and standard also had a significant difference in ERP amplitude. These findings may explain the deficits in the cognitive function following DBS procedures.

Keywords: attention
basal ganglia
cognition
deep brain stimulation
intraoperative recordings
movement disorders
Advisor: Hutchison, William D
Investigating the Role of VMA21 in Relation to Autophagy and Myopathy with Excessive Autophagy (MEA)

Autophagy is a highly conserved process and is essential in degrading proteins. Dysregulation of this pathway leads to distinct diseases including autophagic vacuolar myopathies (AVM). Myopathy with excessive autophagy (MEA) is a type of AVM that is genetically heterogeneous and shows progressive muscle weakness characterized by vacuolated myofibers. In MEA patients, cells have aberrant autophagy, vacuolization or abnormal lysosomal proteolysis. Presently, mutations in the X-linked gene VMA21 are the only known causes of MEA. I generated the first in vivo model for vma21 associated MEA using CRISPR/Cas9 editing. The vma21 knockout zebrafish showed lack of pigmentation, decrease in size and a slow progressive lack of motor movement. Additionally, drug treated Bafilomycin fish were generated. Both models recapitulated similar human phenotypes, and are excellent models for future dissection into vma21 function and MEA disease mechanism, as well as high-throughput chemical screen to identify therapeutic targets.

Advisor: Dowling, James
Flow Characterization of Jammed Microgels in Straight and Bifurcating Microfluidic Channels in Bioprinting Devices

Jammed microgels have important implications in bioprinting applications. Characterizing flow of jammed microgels within confined channel is important to understand the flow behavior under different conditions and identify potential sources affecting uniform deposition. Using microfluidic-based channels and PIV approach, the velocity profile in the straight and single-level bifurcation channels are measured under different conditions. Velocity profile of jammed microgels in straight channel is impacted by wall roughness and the viscosity of the continuous phase solution, and in bifurcating branches, it is asymmetrical with a velocity gradient near the inner wall. Near bifurcation junction, the velocity profile shows a peak-valley-peak pattern which implies the presence of a stagnation zone. In addition, the volume fraction of microgels is studied to determine its consistency. From these experiments, the potential sources for non-uniform distribution through bifurcating channels can be identified, thus establishing the groundwork in developing a design rule for bifurcating distribution systems.

Advisor: Guenther, Axel
Development of Chemically Heterogenous Polymeric Carriers for Delivery of Peptides

Atherosclerosis is a disease in which lipids build up in artery walls leading to reduced blood flow. Treatment options available focus on the immediate restoration of the blood flow but, these are often followed by restenosis. The work in this thesis was a collaborative effort between the Santerre Lab and the Bendeck Lab. The Bendeck Lab is developing N-cadherin mimetic peptides capable of halting smooth muscle migration to address restenosis. D-PHI PU (degradable polar hydrophobic ionic polyurethane), developed in the Santerre Lab, is a material with immunomodulatory and anti-inflammatory characteristics. Here, the biocompatibility and the efficacy of the D-PHI PU nanoparticles as a delivery vehicle for the N-cadherin peptides was characterized. A polymer coating was also identified to deliver the peptide-loaded nanoparticles from balloon catheter substrates. The principal motivation was to develop a new polymeric carrier to contribute to a better method of treatment for blood vessels affected by atherosclerosis.

Advisor: Santerre, Paul
Bendeck, Michelle P
Selective Control-flow Reduction for Hardware Synthesis

Control flow in a program can be represented in a directed graph, called the control flow graph (CFG). Nodes represent straight-line segments of code, basic blocks, and directed edges between nodes correspond to transfers of control. In this thesis, we present a methodology to selectively reduce control flow by collapsing basic blocks, providing increased instruction-level parallelism, and enabling the generation of pipelined circuits. Our work is motivated by the synthesis of hardware from software programs. Costing for potential collapses is determined by measuring the consequences on the speed performance of the generated hardware. We evaluate our framework within a high-level synthesis tool that allows a C-language software program to be automatically synthesized into a hardware circuit, using the CHStone benchmark suite, targeting an Intel Cyclone V FPGA. For individual benchmarks this yielded cycle latency reductions up to 20.7% and wall-clock time reductions up to 22.6%.

Keywords: Compiler Optimization
Hardware Synthesis
High Level Synthesis
Advisor: Anderson, Jason Dr.
Characterization and Biological Evaluation of HDAC6 Selective Inhibitors

Multiple studies implicating the dysregulated activity of Histone Deacetylases (HDACs) in several human pathologies have prompted tremendous interest into this family of enzymes as druggable epigenetic targets. Current clinical approaches using non-selective HDAC inhibitors (HDACi) have been associated with several toxicities and undesirable side effects. Thus, recent drug discovery has focused on the design of highly selective HDACi as a novel therapeutic strategy. Herein, we investigate the biological evaluation of novel HDAC6-selective inhibitors. These small molecules have demonstrated in vitro selectivity for HDAC6 inhibition, several fold greater than current clinical standards, ACY-241 and ACY-1215. This inhibition is recapitulated in cellulo, with nM-µM efficacy in hematological cancer cells (e.g. MV4-11, MM.1S) coupled to limited cytotoxicity against healthy cells (e.g. NHF, HUVEC). Additional mechanistic studies into the activity of these HDAC inhibitors revealed possible secondary mechanisms, such as cleavage of caspase 3, PARP-1, and the generation of reactive oxygen species, which collectively lead towards apoptosis.

Keywords: HDAC6
Leukemia
Advisor: Gunning, Patrick T
Effects of Probiotic Lactobacilli Administration during Pregnancy on the Bone of CD-1 Mouse Dams at Weaning

Alterations in bone structure occur during low-estrogen stages of life (lactation, menopause). Selected probiotic lactobacilli prevent bone loss in ovariectomized mice. However, whether probiotic lactobacilli have similar effects during lactation remains to be elucidated. This study assessed the effect of the probiotic Lacidofil® strains (Lactobacillus rhamnosus R0011 and Lactobacillus helveticus R0052) on the bone microarchitecture of dams at weaning. Female CD-1 mice received sterile or probiotic-supplemented water. Treatment started pre-mating until weaning, when tibia, lumbar vertebra, and mandible were collected for ex-vivo structure analysis. Probiotic administration did not modify trabecular and cortical bone outcomes. A positive association was found between the fecal Lacidofil® strains concentration and bone volume fraction in the lumbar vertebra. The administration of probiotics did not impact bone microarchitecture. However, observed positive correlations suggest that probiotics may be beneficial at higher doses or under dysbiotic conditions.

Keywords: Bone
Lactation
Mouse
Pregnancy
Probiotic
Advisor: Comelli, Elena M