VictorJuiz/thesis huggingface dataset:
Nonmodel-based Dynamic Contrast-enhanced Magnetic Resonance Imaging for the Assessment of High versus Low Risk Carotid Atherosclerosis

Background: Parameters of carotid atherosclerosis dynamic contrast-enhanced MRI (DCE-MRI) are associated with stroke risk indices, but studies have only evaluated symptomatic arteries. I hypothesized that DCE-MRI parameters are different between carotid atherosclerotic plaques at high and low risk for precipitating ischemic stroke. Methods: High and low risk carotid plaques undergoing nonmodel-based DCE-MRI (n=18) were compared using two independent schema: 1) clinical standard (high risk defined as ipsilateral stroke/TIA <1 week old or stenosis >70%); 2) MRI standard (high risk defined as presence of intraplaque hemorrhage [IPH]). Results: IPH-positive plaques (n=9) exhibited greater area under the curve, early and late enhancement rate, and peak enhancement than IPH-negative plaques (n=9) (p<0.05 for all). High (n=8) and low (n=7) risk plaques defined by clinical criteria were not differentiated by any DCE-MRI parameters. Conclusions: Nonmodel-based DCE-MRI discriminates high versus low risk carotid plaque based on the presence of IPH, but not by clinical criteria.

Keywords: Dynamic Contrast-Enhanced MRI
Stroke
Atherosclerosis
Carotid Artery
Nonmodel-Based
Semi-Quantitative
Advisor: Mikulis, David J.
Robotic Single Cell Manipulation for Biological and Clinical Applications

Single cell manipulation techniques have important applications in laboratory and clinical procedures such as intracytoplasmic sperm injection (ICSI) and polar body biopsy for preimplantation genetic diagnosis (PGD). Conventionally, manipulation of cells conducted in these procedures have been performed manually, which entails long training hours and stringent skills. Conventional single cell manipulation also has the limitation of low success rates and poor reproducibility due to human fatigue and skill variations across operators. This research focuses on the integration of computer vision microscopy and control algorithms into a system for the automation of the following single cell manipulation techniques: (1) sperm immobilization, (2) cell aspiration into a micropipette, and cell positioning inside a micropipette, and (3) rotational control of cells in three dimensions. These automated techniques eliminate the need for significant human involvement and long training. Through experimental trials on live cells, the automated techniques demonstrated high success rates.

Keywords: robotics
micromanipulation
automation
cellular imaging
computer vision microscopy
visual servo
Advisor: Sun, Yu
Conductive Nanocrystalline Cellulose Polymer Composite Film as a Novel Mediator in Biosensor Applications

Recent biosensors using glucose oxidase enzyme to detect glucose (“blood sugar”) were made with intrinsic conducting polymers such as poly pyrrole (PPY) to mediate the reaction. PPY coated electrodes were difficult to employ via eletropolymerization because PPY is only soluble in solvents potentially damaging to enzymes. Nano crystalline cellulose – poly pyrrole (NCC-PPY) colloid circumvents this by forming natural, enzyme compatible, and hydrophilic films mechanically bound to electrodes using easy-to-disperse colloids. NCC-PPY was studied as mediator to investigate use in biosensor applications. Using NCC-PPY film casted on microfabricated interdigitated electrodes, a glucose biosensor with sensitivity factor of 20 was achieved. NCC-PPY showed enhanced catalysis with no enzyme inactivation and a total current of 2mA. Enhanced sensitivity was attributed to resistance changes of doped PPY, redox mediation, and compatibility of cellulose with enzyme.

Keywords: Glucose Sensor
NCC-PPY
poly pyrrole
nanocrystalline cellulose
biosensor
interdigitated array electrode
Advisor: Yan, Ning
Development of an Upper Limb Robotic Device for Stroke Rehabilitation

Stroke is the major cause of permanent adult disability worldwide. Often stroke affects the motor control of the upper limb, leading to difficulties in performing activities of daily living. Many hours are spent in resource-intensive therapy to regain functionality of the upper limb. In order to decrease the burden to therapists and increase access to rehabilitation, an upper limb rehabilitation robotic device was developed. Observations from therapists and an international survey of stroke therapists were conducted to understand general requirements of an upper limb rehabilitation device. These requirements were the basis of the mechanical design portion of the prototype. The prototype was evaluated with stroke therapists in a focus group. Although more iterations of design, testing and evaluation are needed, this project is a step in developing a lower cost, portable device to increase access to upper limb stroke rehabilitation.

Keywords: Rehabilitation
Robotics
Stroke
Upper limb
User centered design
Advisor: Mihailidis, Alex
A Cell Preparation Stage for Automatic Cell Injection

Cancer study and drug selection research attract more and more researchers, which need a significant laboratory technique, named cell injection. Hundreds of cells are loaded on devices and injected to investigate the behavior of the cells. Traditionally, cell injection is performed manually, which leads to human fatigue, is time-consuming and has a low success rate. Therefore, a system which can replicate the actions of what technicians do, such as to aspirate cells, transfer cells, immobilize cells, and release cells automatically, is needed. This system must be accurate, reliable, and efficient and operate without human intervention. A cell-transfer-cover and a cell-holder have been fabricated and a cell injection system has been set up to investigate the performance of the newly created device. Simulations and experiments have proven that this system would carry out the entire process of cell injection with the result of enhancing the speed of this important activity.

Keywords: bio-mechanical
cell aspiration
cell separation
cell position
cell immobilization
automatic cell injection
flow 3d
cell injection
biomedical
Advisor: Mills, James
The Modulation of Androgen Signaling by Steroid Hormones and Mechanical Tension: A Novel Pathway of Labor Initiation

We investigated the gestational expression of androgen receptor (AR) and defined its regulation and that of its co-repressors, PSF and p54nrb, by steroid hormones and myometrial stretch in vivo in pregnant and non-pregnant rats. Our data demonstrate that, 1) myometrial AR expression decreases prior to term; 2) AR expression is up-regulated by MPA treatment and down-regulated by mechanical stretch; (3) myometrial PSF protein expression is down-regulated by estrogen signaling and by mechanical stretch, and up-regulated by androgen signaling; (4) while myometrial PSF mRNA expression is also down-regulated by stretch, the regulation by estrogen and P4 on PSF mRNA appear to be opposite to the effects on PSF protein. We conclude that the decreased androgen signaling in late pregnancy (as a result of decreased AR and PSF expression mediated by hormonal and mechanical signals) may contribute to the mechanisms leading to labor initiation.

Keywords: Androgen Receptor
Myometrium
PSF
p54nrb
Nuclear Co-repressor
Steroid Hormone Signaling
Mechanical Stretch
Contraction-associated Proteins
Advisor: Lye, Stephen J.
Enrichment of Methanogenic Microcosms on Recalcitrant Lignocellulosic Biomass

To improve biogas production from lignocellulosics, methanogenic microbial enrichments were prepared from moose rumen fluid, beaver droppings, and internal circulation (IC) reactor granules amended with cellulose, pine needles, lignosulphonate, tannic acid, and poplar hydrolysate. Tannic acid delayed methanogenesis compared to cellulose only enrichments, both by reducing initial rates (up to 50% in beaver dropping cultures) and increasing lag times (up to 50 days in moose rumen cultures). Biogas yields from poplar hydrolysate were 56 % by beaver droppings, 51% % by IC granules, and 31 % by moose rumen enrichments. Bacterial community profiles, determined via denaturing gradient gel electrophoresis (DGGE) showed divergent populations between enrichments. Enrichment on pine needles or poplar hydrolysate promoted bioconversion of post extraction wash (PEW), and beaver dropping enrichments fed pine needles equaled the yield (about 23%) from IC granules. Together, the DGGE and PEW results provide evidence of acclimatization to previously recalcitrant feeds.

Keywords: anaerobic digestion
biogas
enrichment
microcosm
environmental
water treatment
waste water
Advisor: Master, Emma
Tran, Honghi
The Nature of Public Law Duty and Citizen Standing in English Law

This thesis explores the often overlooked nature of public law duty and its relationship with the doctrine of standing in English law. Drawing on English and North American legal tradition and thought, it posits that public law obligations should be reconceived of as fiduciary in nature, vesting correlative enforcement rights in citizens to constrain unlawful exercises of public power. This should correspond to the abolition of standing requirements and recognition of the rights of citizens and interest groups to bring administrative and human rights challenges before the courts. This thesis also aims to achieve some synthesis between liberal normativism and communitarianism by recognizing both the individual and the collective interests at stake in public interest litigation.

Keywords: public law
standing
fiduciary
constitutional
duty
rights
Advisor: Roach, Kent
Coding Theorems for Delay Sensitive Communication over Burst-Erasure Channels

In this thesis, we consider error-correction codes for systems which have burst erasure channels, but where the packet delay is constrained. The packet delay itself is the time di erence between the arrival of a source packet at the encoder and the reconstruction of that source packet at the decoder. While such a framework was introduced by Martinian (2004) and his co-authors, several problems remain open. We make three contributions in this thesis. First we develop a rigorous converse proof for the point-to-point case and thus complete the result of Martinian (2004). Our proof technique is also applied to a multicast channel model and new results are obtained. Secondly we study the case when there are multiple parallel links between the encoder and decoder and obtain the capacity in some special cases. Finally we study a setup when there are multiple source streams, each with a di erent delay constraint, and obtain capacity results.

Keywords: Delay
Coding Theory
Information Theory
Streaming Codes
Advisor: Khisti, Ashish
Synthesis and Structural Studies of Oligoproline Macrocycles

Due to inherent rigidity of oligoproline peptides, forcing the C- and N-terminus in proximity for cyclization can be of significant challenge. To address this issue, a cyclization condition involing the help of amphoteric aziridine aldehydes has been developed. This one step cyclization protocol generally proceeds in high yields and goes to completion in relatively short period of time. Despite their cyclic nature, the resulting molecules display spectroscopic characteristics of polyproline II helices. These macrocycles should facilitate systematic studies of various conformational states of polyproline-containing protein regions.

Keywords: Macrocycles
Peptides
Proline
Polyproline
Aziridine aldehyde
ugi reaction
Advisor: Yudin, Andrei
Short and Longer-term Effects of Photodynamic Therapy and Combination Treatments on Healthy and Metastatically-involved Vertebrae

Current treatment for spinal metastasis involves a multimodal approach, including bisphosphonates and radiation therapy. Yet, tumour response varies considerably, thus novel treatments or combination therapies are needed to treat these metastases while preserving stability and integrity of the spinal column. Photodynamic therapy (PDT) has been shown to be successful in destroying vertebral osteolytic tumours and enhancing vertebral structure, particularly in combination with bisphosphonates. This thesis aims to evaluate the longer-term effects of PDT alone and in combination with bisphosphonate or radiation therapy on healthy vertebrae, and the short-term effects of PDT combined with radiation therapy on healthy and metastatically-involved vertebrae. The benefits of PDT on vertebral structure, both at short-term and longer-term time-points, were greatest in combination with previous bisphosphonate therapy. Similar effects, to a lesser magnitude, were seen with PDT in combination with radiation therapy. This work supports future translation of PDT for the treatment of spinal metastases.

Keywords: Photodynamic therapy
Bisphosphonate
Radiation therapy
Spine
Breast cancer metastasis
Bone mechanics
Advisor: Whyne, Cari
Next Generation Nanosatellite Systems: Mechanical Analysis and Test

The Canadian Nanosatellite Advanced Propulsion System is the second generation cold-gas propulsion system. Its purpose is to provide the millinewton thrust required for formation control of nanosatellites, in particular the CanX-4/-5 formation flying mission. Additionally, to inject nanosatellites into orbit, a reliable and robust deployer is needed to bridge the gap between the launch vehicle and space. This bridge is the XPOD, the eXoadaptable PyrOless Deployer. Both of these technologies are designed and developed by the Space Flight Lab. This thesis describes the assembly, integration and preliminary testing of the CanX-4/-5 propulsion system. Emphasis is placed on the phases involved with the assembly and integration while highlighting the problems encountered and lessons learned. In addition, the mechanical analysis of the XPOD as well as its assembly and testing is described in detail.

Keywords: Nanosatellite
Propulsion System
Satellite Deployer
Space Structure
CNAPS
XPOD
Advisor: Zee, Robert E.
Functional Stimulation Induced Change in Cerebral Blood Volume: A Two Photon Fluorescence Microscopy Map of the 3D Microvascular Network Response

The current work investigated the stimulation induced spatial response of the cerebral microvascular network by reconstruction of the 3D microvascular morphology from in vivo two photon fluorescence microscopy (2PFM) volumes using an automated, model based tracking algorithm. In vivo 2PFM imaging of the vasculature in the forelimb representation of the primary somatosensory cortex of alpha-chloralose anesthetized rats was achieved via implantation of a closed cranial window, and intravascular injection of fluorescent dextran. The dilatory and constrictory responses of the cerebral microvascular network to functional stimulation were heterogeneous and depended on resting vascular radius and response latency. Capillaries experienced large relative dilations and constrictions, but the larger vessel absolute volume changes dominated the overall network cerebral blood volume change.

Keywords: cerebral blood volume
cerebral blood flow
functional brain imaging
two photon microscopy
hemodynamics
neurovascular coupling
Advisor: Stefanovic, Bojana
Analysis of Make(Repair)-to-stock Queues with State-dependent Arrival Rates

In this thesis, we study the repair shop scheduling problem(repair-to-stock) and the production/inventory system pricing and production scheduling problem(make-to-stock). For both types of problems, we compare the performance of different scheduling policies. For the make-to-stock type problem, we also study the performance of different pricing strategies. The optimal repair/production scheduling policy of both problems is difficult to characterize, and, therefore, is only formulated as a Markov Decision Process to numerically compute the optimal cost/profit. As an alternative, we propose the dynamic Myopic policy, which is easy to implement. The numerical study we have conducted demonstrates that the performance of Myopic policy is superior compared to the alternative policies and yields costs very close to the optimal for the repair-to-stock type problem. On the other hand, for the make-to-stock type problems, the performance of Myopic policy is not superior compared to the alternative policies when dynamic pricing strategy is implemented.

Keywords: Operations Research
Queueing Theory
Industrial Engineering
Operations Management
Scheduling
Pricing
Advisor: Balcioglu, Baris
Estimating Wind Forecast Errors and Quantifying Its Impact on System Operations Subject to Optimal Dispatch

Wind power is being added to the supply mix of numerous jurisdictions, and an increasing level of uncertainties will be the new reality for many system operators. Accurately estimating these uncertainties and properly analyzing their effects will be very important to the reliable operation of the grid. A method is proposed to use historical wind speed, power, and forecast data to estimate the potential future forecast errors. The method uses the weather conditions and ramp events to improve the accuracy of the estimation. A bilevel programming technique is proposed to quantify the effects of the estimated uncertainties. It improves upon existing methods by modeling the transmission network and the re-dispatch of the generators by operators. The technique is tested with multiple systems to illustrate the feasibility of using this technique to alert system operators to potential problems during operation.

Keywords: power systems
optimal dispatch
wind integration
wind forecast error
Advisor: Tate, Zeb
On the Logarithimic Calculus and Sidorenko's Conjecture

We study a type of calculus for proving inequalities between subgraph densities which is based on Jensen's inequality for the logarithmic function. As a demonstration of the method we verify the conjecture of Erdos-Simonovits and Sidorenko for new families of graphs. In particular we give a short analytic proof for a result by Conlon, Fox and Sudakov. Using this, we prove the forcing conjecture for bipartite graphs in which one vertex is complete to the other side.

Keywords: Combinatorics
Probability
Advisor: Szegedy, Balazs
"Flobject" Analysis: Learning about Static Images from Motion

A critical practical problem in the field of object recognition is an insufficient number of labeled training images, as manually labeling images is a time consuming task. For this reason, unsupervised learning techniques are used to take advantage of unlabeled training images to extract image representations that are useful for classification. However, unsupervised learning is in general difficult. We propose simplifying the unsupervised training problem considerably by taking the advance of motion information. The output of our method is a model that can generate a vector representation from any static image. However, the model is trained using images with additional motion information. To demonstrate the flobject analysis framework, we extend the latent Dirichlet allocation model to account for word-specific flow vectors. We show that the static image representations extracted using our model achieve higher classification rates and better generalization than standard topic models, spatial pyramid matching, and Gist descriptors.

Keywords: Machine Learning
Computer Vision
Object Recognition
Flobjects
Advisor: Frey, Brendan J.
Men1-dependent Increase in RPeD1 Excitability is Required for Long Term Memory Consolidation after Aversive Operant Conditioning in Lymnaea stagnalis.

Long term memory (LTM) formation is a complex process involving signalling cascades, new protein synthesis and gene regulation. Increasing evidence demonstrates a role of intrinsic plasticity in memory formation, but the underlying molecular mechanisms remain relatively unknown. LTM was established using an aversive operant conditioning model in Lymnaea stagnalis. Using intracellular electrophysiology in an isolated preparation, increased gain of firing frequency was observed in the RPeD1 neuron after LTM. This provides the first demonstration of intrinsic plasticity after operant conditioning in RPeD1, a neuron required for the conditioned behaviour and LTM. I also determined the contribution of the transcription factor men1 to plasticity. Using in vivo RNAi silencing, I found that men1 is required for LTM and increasing RPeD1 excitability during consolidation, demonstrating men1-mediated intrinsic plasticity is critical for LTM. I propose a new model of memory formation in which men1-dependent increase of excitability during consolidation is required for LTM.

Keywords: memory
Lymnaea stagnalis
Men1
plasticity
Advisor: Feng, Zhong-Ping
Mechanism of eIF2α Kinase Inhibition by Viral Pseudokinase PK2

Phosphorylation of eukaryotic translation initiation factor 2α (eIF2α) is a conserved eukaryotic mechanism to limit protein synthesis under stress conditions. Baculovirus PK2, which resembles the C-terminal half of a protein kinase domain, inhibits eIF2α family kinases in vivo, thereby increasing viral fitness in the face of host immunological and stress responses. The mechanism by which PK2 modulates eIF2α stress response signaling remains unknown. To address this issue, a combination of biochemical, biophysical and in vivo approaches were employed to probe the mechanism of PK2 inhibition on a prototypical human eIF2α kinase, the RNA-dependent protein kinase (PKR). We discovered that PK2 inhibits PKR catalytic activity by directly binding its kinase domain. This direct interaction requires both the kinase-like C-lobe fold of PK2 and a critical 22 residue N-terminal extension that precedes it. We further show that the PK2 N-terminal extension is required but not sufficient for the ability of PK2 function.

Keywords: eIF2α kinase regulation
Viral pseudokinase PK2
Enzyme catalytic switching
Translation regulation
Advisor: Sicheri, Frank
The Effect of Acute Eccentric Treadmill Running on NF-κB Activation and HSP72 Content in Skeletal Muscle from Late Middle-aged Rats

Eccentric exercise causes skeletal muscle damage, yet the acute cellular responses post-exercise have yet to be fully elucidated. To better understand the post-exercise response, heat shock protein (HSP) 72 content and nuclear factor-κB (NF-κB) activation where examined in Adult (A; 6 month) and Late middle-aged (LMA; 24 month) Fischer 344xBrown Norway rats. Animals were randomly divided into five groups (n=6): non-exercising controls (C), level (L) or eccentric (ECC) (-16°) running at 16m.m-1 and killed immediately post-exercise (0), 48 hours post-exercise (48). Following ECC, vastus intermedius (VI) from A and LMA showed more damage compared to L exercise. Neither age-group had significantly increased VI HSP72 content compared to C. Pooled results founded increased HSP72 content in ECC-48 compared to C (p<0.02). NF-κB activation in the VI was lower in LMA (p<0.001) and unchanged in WG when compared to AC. These findings suggest HSP72 is increased following eccentric exercise in the VI.

Keywords: aging
exercise
muscle
Advisor: Amara, Catherine
Multiple Modality Optical Neural Imaging with VCSELs

I investigate the use of vertical cavity surface emitting lasers (VCSELs) for portable optical neural imaging. In particular, I attempt to use one laser source to produce the different illumination needed for three techniques, imaging flow, oxygenation, and fluorescence. Our group's goal is to combine these techniques using a single source in a simple imaging format, which can be modified for portable use in awake animals. We exploit tuning properties of VCSELs to implement two distinct operation schemes with different illumination characteristics. Single mode operation provides high speckle contrasts, used to map flow speeds in laser speckle contrast imaging (LSCI). Sweep operation provides low noise, allowing us to image small signal changes with intrinsic optical signal imaging (IOSI), which relate to blood oxygenation. Finally, we use our VCSEL devices for on-chip integrated fluorescence sensing. Future work aims to develop a fully portable format, using CMOS detectors and integrated circuit control.

Keywords: Neuroimaging
Lasers
Advisor: Levi, Ofer