VictorJuiz/thesis huggingface dataset:
Novel Formulations of Antioxidant and Anti-inflammatory Drugs to Ameliorate Ischemic Damage Measured In Vitro
Keywords: Neuroinflammation
Ischemia

The two of major pathways that cause ischemic damage are oxidative stress and inflammation. To decreasing oxidative stress and inflammation, new anti-oxidant and anti-inflammatory agents are tested in ischemic models. In order to study ALRX828C anti-inflammatory properties, an in vivo six-day old air pouch model of inflammation was used to evaluate the anti-inflammatory potential of ALRX828C. Also, the dose response of ALRX828C for TNFα (IC50 = 30 μM) and IL-17 (IC50 = 1.3 μM) were determined by using human peripheral blood mononuclear cell cultures stimulated with ionomycin and PMA. To examine ALRX828C anti-inflammatory effect in neuroinflammation, a neurodegenerative model was used to evaluate its potential. I also showed that reducing oxidative stress with a potent antioxidant, Idebenone in nano-emulsion form, can effectively reduce tissue damage during ischemia in organotypic slice culture subjected to oxygen-glucose depravation (OGD). In conclusion, reducing oxidative stress and inflammation after stroke can reduce ischemic damage substantially.
Aerostructural Optimization of Non-planar Lifting Surfaces
Keywords: Aero-structural Desgin
Multidisciplinary Optimization
Numerical Optimization
Non-planar Lifting Surfaces

Non-planar lifting surfaces offer potentially significant gains in aerodynamic efficiency by lowering induced drag. Non-aerodynamic considerations, such as structures can impact the overall efficiency. Here, a panel method and equivalent beam finite element model are used to explore non-planar configurations taking into account the coupling between aerodynamics and structures. A single discipline aerodynamic optimization and a multidisciplinary aerostructural optimization are investigated. Due to the complexity of the design space and the presence of multiple local minima, an augmented Lagrangian particle swarm optimizer is used. The aerodynamic optimum solution found for rectangular lifting surfaces is a box wing, while allowing for sweep and taper yields a joined wing. Adding parasitic drag in the aerodynamic model reduces the size of the non--planar elements. The aerostructural optimal solution found is a winglet configuration when the span is constrained and a wing rake when there is no such constraint.
Stereoscopic PIV In Steady Flow Through a Bileaflet Mechanical Heart Valve
Keywords: stereoscopic particle image velocimetry
bileaflet mechanical heart valve flow
PIV image dewarping

The tendency of aortic bileaflet mechanical heart valves (BiMHVs) to promote thrombosis has been well documented in the literature. The relationship of thrombosis to valve fluid dynamics has prompted numerous studies of aortic BiMHV flow. In this study, steady flow was investigated downstream of a model Carbomedics No. 25 BiMHV in an axisymmetric aortic sinus using stereoscopic particle image velocimetry (SPIV). The Reynolds number based on inlet diameter was 7600, and the measurement plane was perpendicular to the leaflet axes at the centerline of the aortic sinus. The typical formation of three jets was observed: the upper and lower lateral orifice jets, and the central jet. Flow separation from the valve ring was seen, and large scale vortices were identified in both the upper and lower sinus regions. An asymmetry in the reverse flow was found, and possible causes were discussed. All three jets were seen to decay similarly to free rectangular jets, with zero decay initially, followed by a 'linear' decay rate in which Umax^2~X. The central jet was also seen to be self similar in the linear decay region. Analysis of the out-of-plane velocity yielded two alternate explanations of streamwise vortex (i.e. Wx) structure, with either a four-cell or an eight-cell streamwise vortex structure being present in the mean velocity field. Organization of large scale three dimensional flow structures was thus apparent. Calculation of in-plane Reynolds stresses showed that values were highest in the outer shear layers of the lateral orifice jets. Elevated Reynolds shear stress values were also found in the leaflet wake regions, and the shear layers of the central jet.
Functional Outcomes in the Aged with Hip Fractures: A Systematic Review of Randomized Clinical Trials
Keywords: hip fracture
measurement

Hip fracture trials have used a wide range of patient-reported outcomes (PRO) suggesting a lack of consensus among clinicians on what are considered the most relevant functional outcomes. We conducted a systematic review to identify the outcomes used in hip fracture randomized controlled trials (RCTs). We hypothesized that there had been an increase in numbers of PROs over time and the health status measure, SF-36, would be used the most. A database search and screening yielded 86 original trials. The mean Detsky score (and standard error) for quality was: 75.8% ± 1.76%. There was a trend in the increase of functional outcome; however, the SF-36 was used only in (10 out of 86) 11.6% trials. Both the ADL-Katz Index and HHS have lower respondent burden than the SF36 which may contribute to their frequent use in hip RCTs. There is a lack of applicable measures suitable for patients with dementia.
The Closed Circle of Empathy: Mirror Neuron System Activation and Anterior EEG Asymmetries in Response to Outgroup Members
Keywords: Empathy
Prejudice
Mirror Neurons
Prefrontal Alpha Asymmetry

Empathy varies with similarity and familiarity of the other. Since outgroups are seen as dissimilar to the self, empathy might be restricted to the ingroup. We looked at two neural correlates of empathy: mirror neuron system activation as indicated by electroencephalographic mu suppression and prefrontal alpha asymmetry. Non black participants watched videos of ingroup and outgroup members acting and expressing emotions, and then acted and experienced emotions themselves. Due to methodological problems, mirror neuron system activation was not obtained. However, anterior asymmetries indicated avoidance motivation during the experience of sadness and the mere observation of sad ingroup members while participants did not show anterior asymmetry when observing the black outgroup. These findings suggest that empathy is bounded to a closed circle of similar others.
On Large-scale Peer-to-peer Streaming Systems
Keywords: Computer Networks
Peer-to-Peer Networks
Peer-to-Peer Streaming Systems

Peer-to-peer (P2P) streaming has recently received much research attention, with successful commercial systems showing its viability in the Internet. Despite the remarkable popularity in real-world systems, the fundamental properties and limitations are not yet well understood from a theoretical perspective, as there exists a significant gap between the fundamental limits and the performance achieved in practice. In this thesis, we seek to provide an in-depth analytical understanding of fundamental properties and limitations of P2P streaming systems, with a particular spotlight on the performance gap. We first identify the major problem in existing streaming protocols and show that this problem accounts for most of the gap separating the actual and optimal performances of the streaming systems. We then propose a remedy based on network coding to address this problem and show that the gap to the fundamental limits can be significantly reduced.
Phonetic Discrimination in the First and Second Half-year of Life: An Investigation of Monolingual and Bilingual Infants using Event-Related Functional Near-infrared Spectroscopy (fNIRS)
Keywords: Infant
Brain
Language
Bilingual
fNIRS
Phonetic
Discrimination

How do infants learn the sounds of their native language? Do they need to use general-auditory or language-specific mechanisms to make sense of the distributional nature of their phonetic input? To answer this question, this study investigated the neural correlates of phonetic discrimination in monolingual and bilingual infants (2-6 and 10-14 months) and adults using a new lens afforded by functional Near-Infrared Spectroscopy (fNIRS) neuroimaging. All participants heard syllables phonetically contrastive in their native English and Hindi (non-native) in an oddball paradigm while being imaged with fNIRS. Age comparisons of infant brain activation in multiple sites revealed that left Broca‟s area showed a developmental decline in response to native-language experience only. Bilateral STG showed robust recruitment at both ages in response to both stimulus languages. These findings were robust across monolinguals and bilinguals. Together, the results suggest that all infants use neural tissue predisposed for linguistic-phonetic processing in early life.
The Isolation and Identification of the Definitive Adult Neural Stem Cell Following Ablation of the Neurogenic GFAP Expressing Subependymal Cell
Keywords: Adult neural stem cells
Neuroscience
Neural stem cells

Neural stem cells (NSCs) in the adult forebrain are thought to comprise a subpopulation of cells that express glial fibrillary acidic protein (GFAP), termed B cells. These GFAP+ cells generate proliferating neuroblasts that migrate from the lateral ventricle subependyma along the rostral migratory stream to become olfactory bulb interneurons. Based on this lineage, we set out to create a NSC deficient mouse through targeted ablation of dividing GFAP+ cells in vivo. We successfully depleted the GFAP+ cells as seen using an in vitro colony forming assay in multiple kill paradigms, however we were unable to permanently eliminate the multipotent, self-renewing colony forming cells. Instead, the targeted ablation of GFAP+ cells revealed an upstream, GFAP- cell that was induced to proliferate in the presence of leukemia inhibitory factor (LIF). These findings support the hypothesis that a population of GFAP-, LIF responsive cells are the definitive adult NSC upstream of GFAP+ cells.
Development of Monolithically Integrated Photonic Devices Through Simulation and Characterization
Keywords: Monolithical Integration
Photonics

Simulations were carried out to determine the optical properties of 2 different layer structures which have been used in quantum well intermixed devices. The supported modes, effective refractive indices and optimal device dimensions prior to intermixing were reported. 1.5 micrometer ridge waveguides with 600 micrometer bend radii are shown to be suitable for minimizing loss. A first approximation to the intermixed structures were also simulated. An Asymmetric Mach-Zehnder Interferometer (AMZI) fabricated using a sputtered SiO2 Quantum Well Intermixing (QWI) process was also characterized. A 100 GHz channel spacing with an extinction ratio up to 16 dB was observed. Tuning of the device was achieved using current injection. A 0.45 nm tuning range was achieved at 15 mA of injected current. The design of a monolithically integrated all optical binary half-adder is also presented, with physical dimensions based on the results of the previous simulations.
DNA Palindrome Revision in Mammalian Cells
Keywords: DNA Repair
Palindrome

A DNA palindrome is a sequence of DNA followed by an exact inverted copy of itself. Palindromes are associated with gross chromosomal instability in mammalian cells. This may be related to their ability to extrude a double-stranded cruciform structure. In mammalian cells, palindromes have been shown to undergo centre-directed rearrangements resulting in a central region of asymmetry. This process occurs via a mechanism termed 'centre break palindrome revision'. In this thesis, I have investigated palindrome revision in mammalian cells using two existing assays. In the first, performed by transfection of an extrachromosomal palindromic dimer, I have shown that joining of palindrome-mediated double-strand breaks does not depend solely on NHEJ and instead relies heavily on an alternate end-joining pathway. Using the second assay, the Line78 mouse model which contains a 15.4kb transgenic palindrome, I have shown that small modifications near the centre of the palindrome prevent these centre-directed rearrangements possibly by inhibiting cruciform formation.
Intrinsic Artefacts of Circular Cone-beam Computed Tomography
Keywords: cone-beam
computed tomography
artefacts
artifacts
Defrise
circular
Fourier

Circular source and detector trajectories in cone-beam computed tomography (CT) are known to collect insufficient data for accurate object reconstruction. One model predicts that the lacking information corresponds to a shift-variant cone of missing spatial frequency components in the local Fourier domain. These predictions were experimentally verified by imaging small, localized objects and observing their Fourier transforms. Measurements indicated that the internal angle of the ‘missing cone’ varies as the angle of locally intersecting x rays with respect to the horizontal plane, as expected. Object recovery was also found to depend greatly on the distribution of the object’s frequency spectrum relative to the missing cone, as predicted. Findings agreed with more anatomically relevant phantoms, which showed preferential intensity discrepancies at gradients oriented within or near the missing cone. Methods for artefact correction are in general limited to approximation unless a priori information is incorporated.
Mitochondrial Remodeling During Hyperosmotic Stress
Keywords: Hyperosmotic stress
mitochondria

Hyperosmotic stress represents a major threat to cellular integrity and may lead to cell death via apoptosis. Accordingly, each cell reacts to hyperosmolarity with a set of functional and structural compensatory responses. Recently it has been shown that the mitochondria remodel during hyperosmotic stress. Although changes in mitochondrial dynamics could be crucial for both adaptation and apoptosis, hyperosmolarity-induced mitochondrial remodeling has not been characterized. We found that hyperosmotic stress translocates dynamin like protein 1 (DLP-1) to the mitochondria and induces DLP-1 mediated, F-actin-modulated, Rac-dependent fragmentation of these organelles in LLC-PK1 cells. Downregulation of DLP-1 mitigates the activation of the osmotic response element and increases the susceptibility of tubular cells to hyperosmotically-induced apoptosis, suggesting that DLP-1 (or mitochondrial fragmentation) may have a protective role during osmotic stress. The hyperosmolarity-triggered remodeling of the mitochondrion represents a hitherto unrecognized response to osmotic shock, which may have significant impact on adaptation and apoptosis.
Measurement and Modeling of Polybrominated Diphenyl Ethers (PBDEs) and Polychlorinated Biphenyls (PCBs) in the Indoor Environment
Keywords: PBDEs
PCBs
Indoor Environment
Modeling
Measurement

The indoor environment is a potentially dominant source of exposure for polybrominated diphenyl ethers (PBDEs) and polychlorinated biphenyls (PCBs). This thesis describes a study on levels, sources, emissions, and fate of PBDEs and PCBs indoors. PBDEs and PCBs air levels in 20 indoor environments in Toronto were sampled and measured. The geometric means of PBDE (Σ10BDE) and PCB (Σ35PCB) concentrations were 0.072 and 7.2 ng m-3 respectively. Statistical analysis on chemical profiles distinguished the chemical sources in the 20 environments. A multimedia indoor environmental model was applied on two test rooms. Estimated PBDE and PCB emission rates were 5.4-550 ng h-1 and 280-5870 ng h-1 respectively. Particle movement dominates within-room transport processes, and dust removal and air advection are the main chemical loss processes. Temperature, particle concentration and deposition velocity, and air exchange rate are the most influential parameters, which can alter source or sink behaviors of household products for the chemicals.
Application of Bayesian Inference Techniques for Calibrating Eutrophication Models
Keywords: Bayesian Calibration
Eutrophication
Aquatic Biogeochemical Models
Markov Chain Monte Carlo
Hierarchical Bayes
Uncertainty Analysis
Water Quality Standards
Environmental Management

This research aims to integrate mathematical water quality models with Bayesian inference techniques for obtaining effective model calibration and rigorous assessment of the uncertainty underlying model predictions. The first part of my work combines a Bayesian calibration framework with a complex biogeochemical model to reproduce oligo-, meso- and eutrophic lake conditions. The model accurately describes the observed patterns and also provides realistic estimates of predictive uncertainty for water quality variables. The Bayesian estimations are also used for appraising the exceedance frequency and confidence of compliance of different water quality criteria. The second part introduces a Bayesian hierarchical framework (BHF) for calibrating eutrophication models at multiple systems (or sites of the same system). The models calibrated under the BHF provided accurate system representations for all the scenarios examined. The BHF allows overcoming problems of insufficient local data by “borrowing strength” from well-studied sites. Both frameworks can facilitate environmental management decisions.
Pretreatment of Pulp Mill Wastewater Treatment Residues to Improve Their Anaerobic Digestion
Keywords: anaerobic digestion
sludge
wastewater treatment
pretreatment
pulp mill
waste activated sludge

Anaerobic digestion of excess biological wastewater treatment sludge (WAS) from pulp mills has the potential to reduce disposal costs and to generate energy through biogas production. The organic matter in WAS is highly structured, which normally hinders biogas production. This study investigated three methods of pretreating WAS from two different pulp mills before anaerobic digestion to improve biogas yield and production rate. The three pretreatment methods tested were: i) thermal pretreatment at 170oC, ii) caustic pretreatment at 140oC and pH 12, and iii) sonication at 20 kHz and 1 W/mL. Thermal pretreatment proved to be the most effective, increasing biogas yield by 280% and 50% and increasing production rates 300-fold and 10-fold for the two samples, respectively. Caustic pretreatment showed similar results, but resulted in the formation of soluble non-biodegradable compounds. Sonication was the least effective pretreatment and did not substantially increase biogas yield, but increased biogas production rate.
Design and Evaluation of a Disulphide-crosslinked Hyaluronan Hydrogel for Regeneration of the Intervertebral Disc
Keywords: hyaluronan hydrogel
elastin-like polypeptide
nucleus pulposus
regeneration
mechanical response
coacervation
0541

A cysteine-containing elastin-like polypeptide (ELP2cys) was successfully synthesized and purified, and was shown to behave in a similar fashion to other well-characterized ELPs. Incorporating the ELP2cys as a crosslinking agent into a solution of sulphated hyaluronan (CMHA-S) not only decreased the gelation time of the solution but also increased the crosslinking density of the resultant hydrogel, in turn increasing both the resiliency and stiffness of the construct. Preliminary in vitro work involved culture of human disc cells, followed by their encapsulation within the hydrogel. Unfortunately the results were inconclusive, although it appeared as though the addition of ELP2cys to the matrix did not negatively affect the viability of the cells, as compared to hydrogels with CMHA-S only. This study showed that ELP2cys is a valuable addition to the family of recombinant elastin-like polypeptides, and shows promise as a crosslinking agent in the formation of hyaluronan hydrogels.
The Influence of Elliptical Nozzle Holes on Mixing and Combustion in Direct Injection Natural Gas Engines
Keywords: natural gas
alternative fuel
mechanical engineering
internal combustion engines

Experiments were conducted to compare mixing and combustion of natural gas jets from round and elliptical nozzle holes in an optically accessible combustion bomb. A flame ionization detector was used to measure the concentration fields of the two jet types. Pressure data, combustion imaging, and hydrocarbon measurements of exhaust gas were used to compare the ignition delay, heat release, and combustion efficiency of the two nozzles. Concentration measurements indicated that the elliptical nozzle produced jets with smaller rich core regions and lower peak concentrations at all conditions. Firing tests indicated that the two nozzles produced equivalent ignition delays. Peak heat release rates were higher for the round nozzle, while the elliptical nozzle produced smoother transitions from premixed to diffusion burning. Combustion efficiency was slightly higher for the round nozzle. Results indicate that elliptical nozzles could potentially lower NOx and particulate emissions, but further experiments are required to test this hypothesis.
Application of Singular Spectrum-based Change-point Analysis to EMG Event Detection
Keywords: EMG signal processing
change-point detection
singular spectrum analysis-based detection

Electromyogram (EMG) is an established tool to study operation of neuromuscular systems. In analysing EMG signals, accurate detection of the movement-related events in the signal is frequently necessary. I explored the application of change-point detection algorithm proposed by Moskvina et. al., 2003 to EMG event detection, and evaluated the technique’s performance comparing it to two common threshold-based event detection methods and to the visual estimates of the EMG events performed by trained practitioners in the field. The algorithm was implemented in MATLAB and applied to EMG segments recorded from wrist and trunk muscles. The quality and frequency of successful detection were assessed for all methods, using the average visual estimate as the baseline, against which techniques were evaluated. The application showed that the change-point detection can successfully locate multiple changes in the EMG signal, but the maximum value of the detection statistic did not always identify the muscle activation onset.
Improvement of Passivity of Fe - xCr Alloys (x < 10%) by Cycling Through the Reactivation Potential
Keywords: Fe - Cr
Low-Cr alloys
Potential cycling

Classically 13% Cr is required for stable passivity of steel in acidic and neutral solutions. Some authors (Mansfeld, Fujimoto) have published potential cycling procedures that generate thick Cr-rich films. Fujimoto cycles right to the transpassivity potential and back in H2SO4 solution. Our idea is to work close to the reactivation potential where the passive film (Fe2O3) is reductively dissolved to Fe2+. While using an equimolar acetate buffer (pH 4.7), we have obtained new insights into the reactivation process. It is under a kind of thermodynamic control, in that the film cannot be reduced, and the metal cannot be dissolved, faster than would exceed the equilibrium concentration of Fe2+ at the electrode surface. Reductive dissolution leads to gel-like Cr-rich film, but Fe dissolution occurs through it, if formed in a single step. However alternating formation and reductive dissolution of a Fe-rich film assist the formation of a more robust Cr-rich film