VictorJuiz/thesis huggingface dataset:
Improving Axonal Regeneration: Side-to-side Bridges Coupled with Local Delivery of Glial Cell Line-derived Neurotrophic Factor (GDNF)

Chronic denervation and chronic axotomy present independent barriers for axonal regeneration. Chronic denervation occurs when nerves are no longer connected to their neuronal cell bodies; chronic axotomy occurs when neurons are not connected to their targets for prolonged periods of time. The harmful effects of chronic denervation can be addressed by the side-to-side bridge surgical technique. Additionally, the negative effects of chronic axotomy can be reversed by GDNF delivery to the nerve. The experiments in this thesis were designed to evaluate nerve regeneration in a rat model of chronic injury after treatment with local GDNF delivery, side to-side bridge protection, or both. The GDNF delivery system consisted of poly(lactic-co-glycolic acid) microspheres embedded in fibrin for controlled delivery of GDNF. Overall, the side-to-side bridges technique was effective in protecting against the negative effects of chronic denervation regardless of treatment with or without GDNF. Local delivery of GDNF did not increase axonal regeneration or functional recovery.

Keywords: PNS regeneration
Nerve regeneration
Functional recovery
Growth factors
Nerve injury
Nerve repair
Regenerative medicine
Advisor: Borschel, Gregory
Phenotypic Characterization of Alveolar Macrophages in a Murine Model of Hemorrhagic Shock Induced Acute Respiratory Distress Syndrome

Acute Respiratory Distress Syndrome is a late cause of morbidity and mortality following hemorrhagic shock and resuscitation. Previous work in our laboratory showed that alveolar macrophages were primed for increased responsiveness to lipopolysaccharides, as evidenced by augmented inflammatory cytokine production. Recent studies have shown that macrophages can be polarized into two phenotypes, namely pro-inflammatory M1 and anti-inflammatory M2 macrophages, in response to various environmental cues. The major hypothesis to be tested in this thesis is that HS/R shifts the M1/M2 polarization of alveolar macrophages to favour a pro-inflammatory milieu in the lung. A biphasic shift in the phenotype of alveolar macrophages in response to HS/R characterized by an early reduction of M2 cells followed by a late up-regulation of M1 macrophages was observed. The administration of M2- polarizing PPAR&gamma; agonists prior to HS/R restored the M1/M2 balance of alveolar macrophages and reduced lung injury.

Keywords: Macrophage Phenotype
Hemorrhagic Shock
Advisor: Ori, Rotstein
Examining the Regulation of 3-Deoxy-D-arabino-heptulosonate 7-phosphate Synthase in the Arabidopsis thaliana shikimate Pathway

3-Deoxy-D-arabino-heptulosonate 7-phosphate (DAHP) synthase (DHS) catalyzes the first step of the shikimate pathway - a pathway involved in Tyrosine (Tyr), Tryptophan (Trp) and Phenylalanine (Phe) biosynthesis - by condensation of phosphoenolpyruvate and erythrose-4-phosphate to DAHP. Our lab previously demonstrated that Arabidopsis thaliana shikimate pathway flux is regulated by Tyr and Trp. This project suggests that A. thaliana DHS1 overexpressor lines have increased Trp accumulation with Tyr treatment, and that an A. thaliana DHS2 overexpressor line treated with Tyr has unchanged Trp accumulation, indicating that AtDHS2 is Tyr-sensitive. Confocal microscopy of all 3 AtDHS isoforms fused to yellow fluorescent protein demonstrates chloroplast localization. Bimolecular fluorescence complementation indicates that protein-protein interactions occur in the cytoplasm, and not in the chloroplast, for AtDHS1 and AtDHS2 with the metabolic regulator At14-3-3ω. These findings suggest that protein-protein interactions could regulate accumulation of AtDHS2 in the chloroplast, and are perhaps modulated by Tyr.

Keywords: BiFC
shikimate pathway
tryptophan
tyrosine
confocal
regulation
protein-protein interaction
dahp synthase
14-3-3
phosphorylation
Arabidopsis thaliana
yfp
Advisor: Christendat, Dinesh
An Efficient Wi-Fi RSS Indoor Positioning System and Its Client-server Implementation

The demand of Indoor Location Based Services LBS has increased over the past years as smart phone market expands. As a result, there's a growing interest in developing efficient and reliable indoor positioning systems for mobile devices. Wi-Fi signal strength fingerprint-based approaches attract more and more attention due to the wide deployment of Wi-Fi access points. Indoor positioning problem using Wi-Fi signal fingerprints can be viewed as a machine learning task to be solved mathematically. This thesis proposes an efficient and reliable Wi-Fi real-time indoor positioning system using machine learning algorithms. The proposed positioning system, together with a location server equipped with the same algorithms, are tested and evaluated in several indoor scenarios. Simulation and testing results show that the proposed system is a feasible LBS solution.

Keywords: Wi-Fi RSS
indoor positioning
Advisor: Valaee, Shahrokh
Characterization of the Interactome of the Hippo Tumour Suppressor Pathway using Mass Spectrometry

The Hippo signaling pathway offers an intrinsic mechanism to control organ sizes, and dysfunction of this pathway can often lead to cancer. Great advancement has been made in recent years into understanding this pathway. Despite all this invaluable knowledge, much remains to be explored. Mass spectrometry offers an unbiased approach to characterize the interactome of any protein of interest and is particularly powerful for identifying potential novel regulators of signalling pathways. I therefore set out to characterize the interactome of all the Hippo pathway main components using mass spectrometry, with the goal of uncovering novel regulatory mechanism(s) of the Hippo pathway. In the end, I was able to identify over 250 novel interactors of the Hippo pathway in total. This study demonstrates the utility of mass spectrometry to identify novel regulators of the Hippo pathway and characterization of one such interactor.

Keywords: hippo pathway
mass spectrometry
Advisor: Wrana, Jeffrey
Nonlinear Finite Element Analysis of the Black River Bridge - A Serviceability Study

An attempt was made to predict the service life of the Black River Bridge using non-linear finite element analysis (NLFEA). Numerical modeling was performed using NLFEA software developed by Prof. Evan Bentz. A large number of analytical studies were conducted to assess the strength and behaviour of the bridge under normal truck loading and at failure loads. It was determined that the bridge is shear critical. Location of trucks that would cause maximum deflection and highest crack widths were identified. It is believed that these findings will have a significant impact on physical measurements that can be incorporated into future bridges, helping researchers determine the locations in the bridge that are ideal for instrumentation. Axial compression present in the bridge can significantly affect deflection and crack widths. Incorporating thermal and shrinkage effects into the NLFEA are recommended as topics for further research. Appropriate estimate of thermal and shrinkage strain will aid in better prediction of axial stresses.

Keywords: Finite Element Analysis
Reinforced concrete bridge
Black River Bridge
Serviceability
Axial Compression
Augustus II
Response-2012
Response-2000
Response
Bent-up Bar Modelling
Smooth Rebar
Advisor: Bentz, Evan
Collins, Michael P.
Analysis of Human Appendiceal Peritoneal Carcinomatosis Samples Infected with Oncolytic Viruses

Peritoneal carcinomatosis (PC), the intra-abdominal dissemination of malignancy, is equated with a 5-year survival of 15%, depending on the source. Appendiceal PC is a challenge to treat as cancer cells are embedded in copious amounts of mucin and are difficult to target. Oncolytic viruses (OVs) preferentially replicate and lyse cancer cells and present a targeted, novel strategy for PC. The hypothesis of this study is that appendiceal PC will show variable susceptibility to OVs and that protein expression in these tumours will predict OV replication efficiency. Human appendiceal PC infected ex-vivo with 4 different OVs displayed variable infectivity and replication by fluorescence microscopy and plaque assay. Immunohistochemistry analysis revealed differential expression of IRF3, pERK and TK in tumour compared to normal appendix. No correlation of protein expression with viral replication was observed. Personalizing OV therapy will be critical in the optimization of future care of patients treated with this modality.

Keywords: Peritoneal carcinomatosis
Appendix cancer
Oncolytic virus
Carcinomatosis
Vaccinia virus
Herpes simplex virus
Maraba virus
Farmington virus
Advisor: McCart, Andrea J.
Characterization of Abscisic Acid Deficient 2 (ABA2) and Its Protein Interactors in Arabidopsis thaliana

Abscisic acid (ABA) is a plant hormone involved in many physiological processes in the plant, such as germination, development, and stress responses. One enzyme in the ABA biosynthesis pathway, ABA2, encodes a short-chain dehydrogenase/reductase that functions to convert xanthoxin to abscisic aldehyde. Its unique expression patterns compared with other ABA biosynthetic enzymes during drought stress, makes it an interesting candidate to study. In this study, we report new evidence for nuclear localization of Arabidopsis ABA2, suggesting novel function of ABA2 in the nucleus of cells, in addition to its role in ABA biosynthesis in the cytoplasm. A number of potential interactors of ABA2 were isolated using yeast two-hybrid screens. These potential interactors have diverse functions, which raises the possibilities that ABA2 may serve as important node of cross-talk among many physiological processes in the plant, such as energy metabolism and signal transduction.

Keywords: plant hormone
Arabidopsis thaliana
abscisic acid
ABA2
hormone synthesis
Nicotiana benthamiana
molecular interaction
germination
nuclear localization
Advisor: Nambara, Eiji
A Dimmable LED Driver For Visible Light Communication Based On the LLC Resonant Converter

This work presents a new wireless Visible Light Communication lighting system targeted to future Smart Buildings. A digitally controlled LLC resonant dc-dc converter targeted to white LED luminaires is demonstrated. Visible Light Communication is implemented with minimal incremental cost, by operating the LLC converter in burst mode, without causing any visible disturbance. The converter operates with a regulated average LED current by adjusting the switching frequency, while the burst pulse timing is controlled to minimize the current disturbance and minimize the value of the output capacitor. Variable Pulse Position Modulation is used to modulate the data, while supporting a range of dimming settings. A digital demodulation scheme that supports variable frequency transmission is demonstrated. The 80 W, 400 V to 23 V converter experimental prototype has a peak efficiency of 93.8 %. The bit error rate of the complete system is fully characterized versus distance and angle.

Keywords: Visible Light Communication
LLC Resonant Converter
DC-DC Converter
Burst-Mode
Solid-State Lighting
Advisor: Trescases, Olivier
Impact of Galvanic Corrosion on Lead Release after Partial Lead Service Line Replacement

The EPA Lead and Copper Rule set action limits for lead and copper concentrations in drinking water, but accelerated corrosion of lead in distribution systems due to a galvanic connection to copper. Prior research has demonstrated that the effects of galvanic corrosion can be controlled by water chemistry. This study not only investigated the main effects of alkalinity, natural organic matter (NOM), nitrate, disinfectant and inhibitor to galvanic corrosion, but also the interplay between these factors. A 2-level factorial (2v5-1) design was adopted which resulted in 16 testing conditions. Results of bench-scale experiments using static pipes with lead and copper segments demonstrated that alkalinity, disinfectant, inhibitor and alkalinity-inhibitor interaction had a significant impact on galvanic current. The significant factors affecting total lead release were alkalinity, NOM, disinfectant, alkalinity-inhibitor interaction, NOM-nitrate interaction, NOM-disinfectant interaction, NOM-inhibitor interaction, nitrate-disinfectant interaction and disinfectant-inhibitor interaction.

Keywords: lead release
water treatment
galvanic corrosion
pipe rig test
Advisor: Andrews, Robert C.
Hofmann, Ronald
Application of Ion Concentration Polarization to Water Desalination and Active Control of Analytes in Paper

This thesis focuses on the development of two new applications using ion concentration polarization (ICP): an out-of-plane microfluidic approach for water desalination and a method for concentration and transportation of charged analytes in paper-based biomedical diagnostic device. In the first work, we present an out-of-plane desalination approach using ICP. A depletion boundary separates salt ions and purified water into distinct vertically stacked layers. The out-of-plane design enables multiplexing in three dimensions, providing the functional density required for practical applications. The second work demonstrates an active control mechanism of target analytes in paper using ICP. Both external devices (with all functional units on one side of paper) and integrated paper microfluidic devices (by embedding all functional units in paper) were developed to concentrate and transport charged analyte molecules in the paper. We also demonstrate a new fabrication method of nanofluidic and hydrophobic barriers (nanoporous membrane patterning) in paper microfluidic device.

Keywords: ion concentration polarizaiton
water desalination
paper-based microfluidics
active control mechanism
Advisor: David, Sinton
Numerical Studies of Frictional Sliding Behavior and Influences of Confining Pressure on Accoustic Activities in Compression Tests Using FEM/DEM

The combined finite-discrete element method (FEM/DEM) has been used to simulate processes of brittle fracturing and associated seismicity. With the newly extended FEM/DEM algorithm, two topics involving rock mechanics and geophysics are investigated. In the first topic, a velocity-weakening law is implemented to investigate the initiation of frictional slip, and an innovative method that incorporates surface roughness with varying friction coefficients is introduced to examine the influences of surface roughness. Simulated results revealed detailed responses of stresses to the propagation of the slip front. In the second topic, acoustic activities induced in confined compression tests are simulated and quantitatively studied using the internal monitoring algorithm in FEM/DEM. It is shown that with increasing confinement, AE events are spatially more concentrated and temporally more separated, accompanied by a decreasing b-value. Moreover, interesting correlation between orientations of cracks and the mechanical behavior of the rock was observed.

Keywords: FEM/DEM
slip nucleation
acoustic emission
numerical simulation
compression test
Advisor: Grasselli, Giovanni
Liu, Qinya
Design, Analysis, and Prototyping of A 3&times;PPRS Parallel Kinematic Mechanism for meso-Milling

Parallel Kinematic Mechanisms (PKMs) are well suited for high-accuracy applications such as meso-milling. However, drawbacks such as limited platform tilting angle and high configuration dependency of stiffness often limit their usage. In this Thesis, a new six degree-of-freedom (dof) PKM architecture based on a 3&times;PPRS topology is proposed, in order to address these problems. The new PKM is presented, and its inverse kinematics and Jocobian matrix are derived. The kinematic relations are incorporated into MATLAB to calculate the workspace of the PKM. The stiffness of the new PKM is obtained using Finite Element Analysis (FEA), and configuration dependency of stiffness is investigated. The proposed new mechanism is compared with three similar existing 6-dof PKMs, and it is shown that the new PKM exhibits higher stiffness. Lastly, three meso-Milling Machine Tool prototypes were designed and built. In particular, Prototype III is based on the new mechanism.

Keywords: Parallel Kinematic Mechanism
meso-Milling Machine Tool
Advisor: Benhabib, Beno
Mills, James
Fast Segmentation of Vessels in MR Liver Images using Patient Specific Models

Image-guided therapies have the potential to improve the accuracy of treating liver cancer. In order to register intraoperative with preoperative liver images, joint segmentation and registration methods require fast segmentation of matching vessel centerlines. The algorithm presented in this thesis solves this problem by tracking the centerlines using ridge and cross-section information, and uses knowledge of the patient’s vasculature in the preoperative image to ensure correspondence. The algorithm was tested on three MR images of healthy volunteers and one CT image of a patient with liver cancer. Results show that in the context of join segmentation registration, if the registration error is less than 2.0mm, the average segmentation error is 0.73-1.68mm, with 88-100% of the vessels having an error less than a voxel length. For registration error less than 4.6mm, the average segmentation error is 1.17-2.11mm, with 79-98% of the vessels having an error less than a voxel length.

Keywords: image segmentation
medical imaging
computer vision
image processing
vessel segmentation
Advisor: Drake, James
Huang, Xishi
Unnecessary, Counterproductive, Unconstitutional. An examination of Bill C-54: The Not Criminally Responsible Reform Act

The involvement of individuals with mental illness in the criminal justice system is receiving increased attention. Under the current law, the court or jury makes a special verdict of &ldquo;Not Criminally Responsible on Account of Mental Disorder&rdquo; if the accused did not at the time of the offence appreciate what he or she was doing, or that it was wrong, due to a mental disorder. This paper will outline the current Criminal Code mental disorder regime, before examining how Bill C-54, the Not Criminally Responsible Reform Act, proposes to build on the existing law. By exploring the provisions of Bill C-54 aimed at enhancing public safety, this thesis will discuss whether the reforms are supported by empirical evidence, and will likely achieve its stated objective. This paper will also consider the possibility of constitutional challenge in light of the &lsquo;twin goals&rdquo; statutory framework and Supreme Court jurisprudence.

Keywords: Not Criminally Responsible
Criminal Law
Mental Disorder
Mentally disordered accused
Advisor: Chiao, Vincent
Properdin Binds Pseudomnas aeruginosa and is Required for Neutrophil Extracellular Trap Mediated Activation of Complement Alternative Pathway

Neutrophils play an important, yet poorly understood role, in complement mediated pathologies. Here we identified that neutrophils contain key components from the complement alternative pathway: properdin (CFP), complement component 3 (C3), complement factor B (CFB), and complement factor H (CFH). Activation of neutrophils resulted in secretion of these complement components. When neutrophils are further activated to form neutrophil extracellular traps (NETs), CFP is deposited onto the surfaces of the NETs. In addition, CFP is able to bind to Pseudomonas aeruginosa, an opportunistic bacterium which can activate neutrophils to form NETs. Furthermore, NETs activate complement and increase formation of the terminal complement complex. The activation of complement on NETs can be initiated through multiple pathways, however, activation of the alternative pathway is dependent on CFP. This mechanism, potentially required for effective host defense, may also contribute to complement activation and disease.

Keywords: Complement
Neutrophil
Neutrophil Extracellular Traps
Alternative Pathway
Properdin
Pseudomonas aeruginosa
Advisor: Licht, Christoph
Palaniyar, Nades
Osteogenic Differentiation from Mouse Embryonic Stem Cells and the Role of Calreticulin

Calreticulin, an endoplasmic reticulum (ER)-resident protein, is a calcium buffering chaperone. In this study, with an optimized differentiation protocol from mouse R1 ES cells, we demonstrate a novel role of calreticulin in osteogenic commitment and differentiation. To enhance the efficacy of the method, we manipulated cell density and examined the addition of retinoic acid, dexamethasone and peroxisome proliferator-activated receptor γ. The regimen consisting of seeding 250 cells per embryoid body, with the addition of RA (from day 3 to 5) and Dex (from day 10 to 21) gave the most efficacious output. Using this optimized protocol, we investigated the potential involvement of calreticulin in osteogenesis. Calreticulin knock-out cells displayed impaired osteogenesis compared to wild-type cells. In particular, the nuclear translocation of the runt-domain related transcription factor 2 and Osterix, were impaired in the absence of calreticulin. The stimulatory effect of calreticulin on osteogenesis was mediated by its calcium buffering function.

Keywords: stem cell biology
calreticulin
osteogenesis
Advisor: Opas, Michal
Understanding Glucose-induced Neuronal Activation During Executive 2-back Task Performance In Hypertensive Otherwise Healthy Older Adults: A Functional Magnetic Resonance Imaging Study

The primary objective of this research was to explore the impact of glucose ingestion on 2-back task performance (accuracy, discrimination, and reaction times (RT) to target), its relationship to neural activation, using functional magnetic resonance imaging, and potential modulation by insulin resistance (IR) and low density lipoprotein (LDL) in hypertensive but otherwise healthy older adults. While there was no effect of glucose ingestion on task performance or task-relevant neural activation patterns, this study uniquely observed that IR and LDL associated with all 3 measures of 2-back performance and task-relevant neural activation patterns. The left and right precuneus, left cingulate, and left insula were identified as task-associated regions according to our specific target minus nontarget contrast. Of particular importance was the task activation in the right precuneus as it both showed sensitivity to IR and predicted task RTs to targets, suggesting it plays a modulatory role linking IR to task performance.

Keywords: aging
fMRI
hypertension
glucose
executive function
working memory
insulin resistance
low density lipoprotein
nutritient
memory
Advisor: Greenwood, Carol
Economic Implications of Alternative Sites of Death and Sites of Care in Ontario Palliative Care Recipients

Introduction: This study compared societal costs of care between two settings of palliative care delivery and death (home versus hospital) in an integrated palliative care program in Toronto. Methods: 186 terminal cancer patients participated in the study. Total societal cost of end-of-life care was compared between patients who died in the home and patients who died in the hospital. Total societal cost of end-of-life care was modeled as a function of the number of days the patients spent at home during the palliative trajectory. Results: There was no statistically significant difference in total cost of end-of-life care between home death and hospital death patients (p>0.05). Furthermore, an additional day the patient spent at home led to a significant increase in the total cost of end-of-life care (p<0.05). Conclusion: The results demonstrated that from a societal perspective, providing palliative care under an integrated palliative care program at home may be just as expensive (if not more expensive) as caring for them in the hospital.

Keywords: palliative care
cost
societal
Advisor: Coyte, Peter C.