VictorJuiz/thesis huggingface dataset:
The Role of Neck Muscles Afferentation in Planning and Online Control of Goal-directed Movement

Head position signal is crucial for preparing reaching movements because it contributes to specifying the position of body and target in space and relative to each other. However, it is unclear whether sensory information pertaining head position is used to control the movement after movement onset. In this study, nineteen participants performed discrete reaches towards a virtual target while neck vibration was randomly applied before and/or during the movement or not at all. The main dependent variable was the directional bias of the reaching finger. Neck vibration induced early leftward or late rightward trajectory biases. It appears that participants interpreted the sensed head shift as a target or an eye-in-head motion, which can be explained by individual differences in the use of reference frames. Nevertheless, body-centered and head-centered frames of reference appear to be important for the early and late stages of a goal-directed movement, respectively.

Keywords: upper limb reaching
neck proprioception
muscle vibration
movement control
frames of reference
Advisor: Tremblay, Luc
Cyberspace: The Gated Public Sphere

Cyberspace, as a notional environment, is a reality that comes into existence only through the proprietary technologies, platforms, and infrastructures of private industry. This has given “Internet companies”, as the non-substitutable pathways to the virtual world, a truly unique and tremendously powerful role in exercising their discretion in regulating citizens’ behavior online. Consequently, citizen’s fundamental rights and liberties in the virtual world, such as freedom of speech, thought, assembly and association, access to information and dissemination, are at the mercy of a handful profit seeking enterprises. With the ever-increasing role of the Internet in our social life, it seems that the time is ripe for revisiting some of the foundational questions in cyberspace in order to preserve the cornerstones of our liberal societies in the information era.

Advisor: Austin, Lisa M.
Work Zone Throughput Models for Southern Ontario

Highway lane closures cause reductions in the traffic throughput which lead to premature queuing. To minimize user delays, contractors are required to keep highway lanes open during the peak traffic hours and work at nights. However, these limitations can reduce the quality of the work and extend project duration. Finding a right balance between the times that the lanes can be closed and the times they should be kept open can increase the efficiency of the contractors’ work. Over 100 hours of throughput data were collected in two phases from 2007 to 2010 from Southern Ontario highways. Using regression analysis, a generic and a highway specific model were developed predicting the mean throughput in approximately 50% of cases within one hundred vehicles per hour per lane of the actual mean. Also the Simplified Work Zone User Delay Analysis model, developed in Phase 1, was refined to investigate the resulting queues.

Keywords: Highway Work Zones, Lane Throughput, User Delay
Advisor: McCabe, Brenda
OpenCL Framework for a CPU, GPU, and FPGA Platform

With the availability of multi-core processors, high capacity FPGAs, and GPUs, a heterogeneous platform with tremendous raw computing capacity can be constructed consisting of any number of these computing elements. However, one of the major challenges for constructing such a platform is the lack of a standardized framework under which an application’s computational task and data can be easily and effectively managed amongst the computing elements. In this thesis work such a framework is developed based on OpenCL (Open Computing Language). An OpenCL API and run time framework, called O4F, was implemented to incorporate FPGAs in a platform with CPUs and GPUs under the OpenCL framework. O4F help explore the possibility of using OpenCL as the framework to incorporate FPGAs with CPUs and GPUs. This thesis details the findings of this first-generation implementation and provides recommendations for future work.

Keywords: FPGA
Heterogeneous Computing
OpenCL
Reconfigurable Computing
Advisor: Chow, Paul
Fabrication of MEMS Based Air Quality Sensors

This thesis deals with the fabrication of MEMS air quality sensors for automotive applications. The goal of this project is to design, fabricate and test an integrated sensor that measures three important air quality components inside the automotive cabin, which are temperature, relative humidity and carbon monoxide (CO) concentration. The sensors are fabricated on silicon substrate covered with thermal oxide and LPCVD nitride. Various deposition and etching techniques were utilized to fabricate these sensors including E-beam evaporation, thermal oxide growth, PECVD, LPCVD, RIE, KOH and HF etching. The temperature and humidity sensor use nickel as the sensitive material while the CO sensor was designed to use SnO2 although it was not fabricated to completion. A chamber was created where the temperature and humidity are controlled and the sensors were tested. Curves of sensor resistance vs. temperature and sensor resistance vs. humidity were created and the two sensor’s sensitivity was calculated.

Keywords: Microfabrications, MEMS, Sensors, Automotive
Advisor: Cleghorn, William L.
Mills, James
Constitutional Approaches to Resource Control in Oil Producing Federations

This thesis considers models of approach adopted by oil producing federations in the way their constitutions regulate the control of such resources, particularly in the assignment of ownership and legislative competence to federal and sub-national authorities. I argue that any federal democratic constitution adopted in any oil rich country after 1973 is more likely to provide for an approach in favour of greater federal involvement through a central control model that vests ownership of such oil resources in the federal authority coupled with the legislative competence to regulate such resources. This is because (a.) oil is now a more lucrative commodity, (b.) the means and technology used to exploit it are now safer, more advanced and more available (c.) and because in today’s global economy, federal and national governments face more challenges and responsibilities, thus requiring access to more resources and greater flexibility to address these challenges.

Advisor: Choudhry, Sujit
Economies of Speed? Bike Couriers, Pace, and Economic Development in the Global City

In this thesis, I propose that bike courier delivery is not merely a convenient service for clients but an important function in the operation of successful economies. By allowing the regions to function at higher speeds, same-day courier networks seem to play an active role in generating positive economic outcomes. The availability of courier networks is found to be as uneven as economic vitality itself. Cities like New York and Toronto have large, dense courier networks, capable of delivering items within an hour while smaller cites, do not support same-day courier service at all. They do this, in part, by allowing for couriers to cope with the precariousness of their work, and in part by providing supportive sub-cultures. These findings point to the role of service workers, and wider eco-systems in fostering regional advantage.

Keywords: Economic Geography
Economic Development
Cycling Culture
Urban Metabolism
Global Cities
Skill Based Technological Change
Advisor: Deborah, Leslie
Synthesis of Caseinolytic Protease Agonists Towards the Synthesis of the Natural Acyldepsipeptides

Caseinolytic protease (ClpP) is a cylindrical protease forming the core of protein degradation machinery in eubacteria. ClpP is tightly regulated and is non-functional without a member of the Clp-ATPases. A new class of antibiotics, termed ADEPs, bind to ClpP and allow for activation without the Clp-ATPases; leading to cell death. A more efficient synthetic route to the ADEPs utilizing solid-phase peptide synthesis was investigated. A linear peptide was synthesized, however attempts to close the depsipeptidic macrocycle via macrolactonization failed. Further attempts of assembling a branched depsipeptide for ring closure via a macrolactamization resulted in products that were not stable to cleavage conditions. A group of molecules termed Activators of Self-Compartmentalizing Proteases (ACP) were identified through a screen for activity towards ClpP. Compound ACP1 was synthesized along with twelve analogs and their activity towards ClpP evaluated. The project resulted in a compound with a higher activity than its natural product counterpart.

Keywords: Chemistry
Medicinal chemistry
ClpP
depsipeptide
antibiotic
caseinolytic protease
ACP
Activators of Self-Compartmentalizing Proteases
Advisor: Batey, Robert A.
New Synthetic Strategies, Spectral and Molecular Recognition Studies on Verdazyl-Derived [n]-Paracyclophanes

Verdazyl radicals are a unique class of stable radicals that have found uses as reporter molecules in biological systems, substrates for molecular-based magnets and mediators in living radical polymerizations. Over the past few years, our laboratory has pioneered the use of verdazyl radicals as substrates in 1,3-dipolar cycloaddition reactions to provide unique small molecule five-membered ring systems containing structural features commonly found in therapeutic agents. As an extension to this work we became interested in seeing whether this chemistry could be applied to the synthesis of macrocyclic scaffolds, in particular cyclophanes. Cyclophanes have been attractive synthetic targets for organic chemists because of their unique structural properties, conformational behaviours and molecular recognition capabilities. Presented in this thesis is the successful demonstration of the extension of the verdazyl chemistry to novel [n]-paracyclophanes. The structural features and conformational biases of these molecules as evidenced by 1H-NMR and X-ray crystallography are highlighted along with molecular recognition studies.

Keywords: Verdazyl
Cyclophane
Advisor: Georges, Michael
Leaf Area Index, Carbon Cycling Dynamics and Ecosystem Resilience in Mountain Pine Beetle Affected Areas of British Columbia from 1999 to 2008

The affect on leaf area index (LAI) and net ecosystem production (NEP) of the mountain pine beetle (Dendroctonus ponderosae) (MPB) outbreak in British Columbia affecting lodgepole pine (Pinus contorta var. latifolia) forests was examined from 1999 to 2008. The process-based carbon (C) cycle model – Boreal Ecosystem Productivity Simulator (BEPS) with remotely sensed LAI inputs was used to produce annual NEP maps, which were validated using field measurements. The annual NEP ranged from 2.43 to -8.03 MtC between 1999 and 2008, with sink to source conversion in 2000. The inter-annual variability for both LAI and NEP displayed initial decreases followed by a steadily increasing trend from 2006 to 2008 with NEP returning to near C neutrality in 2008 (-1.84 MtC). The resistance of LAI and NEP to MPB attack was attributed to ecosystem resilience in the form of secondary overstory growth and increased production of non-attacked host trees.

Keywords: Insect disturbance
Boreal Ecosystem Productivity Simulator
Biophysical parameter mapping
Spatially explicit, process-oriented ecosystem modelling
TRAC
LAI-2000
Advisor: Chen, Jing Ming
Regulation of Cell Polarity by Septin 7

Septins are a group of filament forming proteins that act as scaffolds and diffusion barriers that regulate various cellular functions, such as cytokinesis. Recently, evidence was obtained in our laboratory that septins may also regulate mammalian cell polarity through their interaction with Par3, an important metazoan polarity regulator. In this thesis I sought to examine whether septins regulated the polarization of migrating cells through their interaction with Par3 as well as how this interaction occurred. I demonstrated that the C terminus of Sept7 was capable of binding to Par3 in vitro. Sept7 was also able to colocalize with Par3, but an interaction between the two proteins could not be detected by immunoprecipitation. Migration assays used to examine the significance of Sept7 in polarization showed a small decrease in polarization after Sept7 depletion. This suggests that septins may play a non-essential role in regulating the polarization of migrating cells.

Keywords: septins
cell polarity
Advisor: Trimble, William S.
System-level Structural Reliability of Bridges

The purpose of this thesis is to demonstrate that two-girder or two-web structural systems can be employed to design efficient bridges with an adequate level of redundancy. The issue of redundancy in two-girder bridges is a constraint for the bridge designers in North America who want to take advantage of efficiency in this type of structural system. Therefore, behavior of two-girder or two-web structural systems after failure of one main load-carrying component is evaluated to validate their safety. A procedure is developed to perform system-level reliability analysis of bridges. This procedure is applied to two bridge concepts, a twin steel girder with composite deck slab and a concrete double-T girder with unbonded external tendons. The results show that twin steel girder bridges can be designed to fulfill the requirements of a redundant structure and the double-T girder with external unbonded tendons can be employed to develop a robust structural system.

Keywords: Bridge engineering
Robustness
Reliability analysis
Redundancy
Two-girder and two-web bridges
Advisor: Gauvreau, Douglas Paul
Iroquois Homeobox 3 is an Essential Transcription Factor in the Maintenance of Proper Electrical Propagation and Development of the Ventricular Conduction System

The specialized myocytes of the ventricular conduction system (VCS) coordinate ventricular contraction and are critical for efficient pumping by the heart. Impaired VCS conduction is characteristic of inherited forms of cardiac conduction disorders. Here we show that the Iroquois homeobox 3 (Irx3) transcription factor is preferentially expressed in the developing and mature VCS. Loss of Irx3 in mice results in slowed VCS conduction and prolonged QRS duration with right bundle branch block, caused by reduction (42%) in VCS-specific connexin 40 (Cx40) expression and VCS fiber hypoplasia, absent in littermate controls. Therefore, we show that the role of Irx3 in the heart is two-fold, whereby Irx3 (1) indirectly regulates Cx40 gene expression, by repressing a repressor of Cx40 transcript, and (2) controls VCS maturation, possibly in an Nkx2-5-dependent manner. To our knowledge, this is the first report of a role for Irx3 in regulating the development and function of the VCS.

Keywords: ventricular conduction system
transcription factor
development
gap junction
Advisor: Backx, Peter
SLIT/ROBO Signaling in Monocyte Chemotaxis and Function: A Role in Vascular Inflammation

Vascular inflammation and associated leukocyte influx is a hallmark in the pathogenesis of atherosclerosis. In both animal models and human subjects, inhibiting monocyte recruitment is beneficial in preventing atherosclerosis and its clinical manifestations. The trafficking signals that recruit cells to areas of inflammation are provided by small secreted proteins called chemokines. Chemokines play a major role in the pathogenesis of inflammation, and redundancy among the chemokine signaling pathways means that blocking one pathway could result in another assuming its function. Therefore, we aim to block a cell’s response to a range of chemokine-induced directional migration signals. Slit2 treatment inhibits monocyte migration in vitro using transwell migration assays, and in vivo, using a murine peritonitis model of inflammatory cell influx. This inhibition is shown to be dose- and time- dependent. Furthermore, Slit2 inhibits monocyte adhesion to activated endothelial cell monolayers. These data may suggest a therapeutic role for Slit2 in atherosclerosis.

Keywords: slit2
monocyte
Advisor: Robinson, Lisa
White Matter Damage and Inflammation in Rat Models of Ischemic and Hemorrhagic Stroke

Cerebral ischemia and intracerebral hemorrhage (ICH) are both characterized by a prolonged inflammatory response and secondary injury phase, yet the spatial/temporal relationships between inflammation and white matter (WM) damage were largely unknown. Thus, I quantified the development of WM damage and inflammation over 7 days after ischemia, and 14 days after ICH. Following ischemia, myelin and axons were progressively damaged, and myelin damage coincided with neutrophil infiltration. Activated microglia/macrophages increased dramatically in the lesion core and edge, and selectively infiltrated damaged WM tracts while surrounding undamaged ones. To investigate the involvement of neutrophils in WM damage and inflammation after ICH, rats were rendered neutropenic before performing ICH. Neutrophil depletion reduced peri-hematomal axonal damage, BBB breakdown, and MMP-9 production at early times, and lessened microglia/macrophage and astrocyte responses at later times. Activated microglia/macrophages infiltrated peri-hematomal WM tracts, correlating with myelin fragmentation and axonal loss, and this was reduced with neutrophil depletion.

Keywords: Stroke
Inflammation
White matter
Advisor: Schlichter, Lyanne C.
Folate Absorption across the Colon: Caplet Study

The purpose of this study was to determine the absorption of [13C]5-formyltetrahydrofolic acid across the human colon with an intact microflora. Bioavailability was determined after administration of a pH-dependent acrylic co-polymer coated barium sulphate caplet containing 855 nmol and measuring the plasma appearance of [13C5]5-methyltetrahydrofolic acid compared to an intravenous injection of the same compound (214 nmol). Blood samples serially collected after both test doses were analyzed by microbiological assay and tandem mass spectrometry to determine total folates and ratio of labeled to unlabeled folates, respectively. Caplet disintegration in the colon was quantitatively assessed by fluoroscopic imaging for six of nine subjects. The plasma [13C5]5-methyltetrahydrofolic acid appearance rate was 4 + 0.9 nmol/h (intravenous) and 0.35 + 0.02 nmol/h (caplet). Mean apparent absorption across the colon was 35%. These findings suggest that physiological doses of natural folate are absorbed across the human colon in the presence of an undisturbed microbiota.

Keywords: folate
caplet
colon
Advisor: O'Connor, Deborah Louise
Phospho-proteomic Analysis of Neuroblastoma Tumor Initiating Cell Signaling Pathways: Identification of Src Family and B Cell Receptor Signaling as Novel Drug Targets

Neuroblastoma (NB) is the most common extra-cranial solid tumor in children. Recently discovered neuroblastoma tumor-initiating cells (NB-TICs) have many properties of cancer stem cells and form tumors with as few as 10 cells. To elucidate the signaling pathways driving NB- TIC survival and proliferation, we surveyed the phospho-tyrosine containing subset of the NB- TIC proteome. Over 300 phosphorylated proteins were identified, including 21 tyrosine kinases of which several belong to the Src kinase family. Using bioinformatics tools, several hematopoietic signaling pathways were identified, including the B cell receptor (BCR) pathway. Further proteomic approaches substantiated molecular hematopoietic features in NB-TICs. Inhibitors of BCR proximal kinases SYK and SFKs were cytotoxic to NB-TICs. Clinically utilized inhibitors of SFKs induce apoptosis in NB-TICs. Targeting hematopoietic survival pathways in NB-TICs from the bone marrow, which have thus far not been predicted to play a role in this neural malignancy, may provide new drug therapies for NB.

Keywords: Neuroblastoma
Phospho-proteomics
Advisor: Kaplan, David
Moran, Michael
Detection of the BCR-ABL Leukemia Gene Fusion using Chip-based Electrochemical Assay

Ability to diagnose cancer before it progresses into advanced stages is highly desirable for the best treatment outcome. A sensitive test to analyze complex samples for specific cancer biomarkers would provide with important prognostic information and help to select the best treatment regimen. A highly robust, ultra sensitive and cost-effective electronic chip platform was used to detect nucleic acid biomarkers in heterogeneous biological samples without any amplification or purification. Chronic myelogenous leukemia (CML) was chosen as a model disease due to its hallmark genetic abnormality. This disease state therefore has an ideal market to test the detection of the fusion transcripts in complex samples, such as blood. It was shown that the CML-related fusion can be detected from unpurified cell lysates and as low as 10 cells were needed for detection. Finally, patient samples were analyzed using the assay and the fusion transcripts were accurately identified in all of them.

Keywords: biosensor
CML
diagnostics
Advisor: Kelley, Shana O.
Transition to Seizure in the CA3 Hippocampal Network: Predominant Preictal GABAergic Potentials, followed by Predominant Ictal Glutamatergic Potentials

The mechanisms underlying the transition to seizure are still unresolved. Proposed mechanisms include excitatory GABAergic drive, loss of interneuron-mediated inhibition, and glutamatergic input potentiation. The objective of this thesis was to investigate the relative contributions of synchronized glutamatergic and GABAergic inputs and their functional roles during ictogenesis in the epileptic neonatal (postnatal days 6-12) mouse hippocampus, induced with 0.25mM Mg2+/5mM K+ perfusion. Simultaneous field and whole-cell patch-clamp recordings were obtained from CA3 stratum-oriens interneurons and pyramidal cells. The antagonists for GABAA and glutamate receptors abolished the preictal and ictal discharges, respectively, suggesting that the preictal state is mediated by the coherent discharges of GABAergic inhibitory interneurons, whereas the recurrent excitatory inputs are required for ictogenesis. Synaptic charge transfers underlying the synchronized discharges showed a dynamic change in the balance between the inputs: GABAergic currents markedly diminished by ictal onset whereas glutamatergic currents dominated at ictal onset and throughout the ictus.

Keywords: epilepsy
hippocampus
GABA
glutamate
Advisor: Carlen, Peter Louis
New Generation of Programmable Neuroprostheses - Switched Mode Power Supply Functional Electrical Stimulator

Functional electrical stimulation (FES) devices have direct applications in the realm of rehabilitation engineering, physiotherapy, occupational therapy and medicine for research, diagnostic and therapeutic purposes. This thesis presents a novel electrical stimulator for use in a FES system. The stimulator produces regulated current pulses using two switched mode power supplies (SMPS) in series. The first power stage - a flyback converter - steps up the supply voltage using primary side digital control. The second power stage is a buck converter with output current hysteretic control. An output switched capacitor circuit shapes the current pulses. All pulse variables are programmable and various pulses can be formed for virtually any FES application. Compared to previous FES devices, the pulses generated here are sharper, have faster rise time and the amplitude and temporal characteristics are more tightly regulated. A single channel prototype system is implemented and experimental results are shown.

Keywords: Functional Electrical Stimulator
Switched Mode Power Supply
Neuroprostheses
Functional Electrical Stimulation
FES
Neuroprosthesis
Switch-mode power supply
SMPS
Advisor: Prodic, Aleksandar
Popovic, Milos R.