title: Nanostructured Manganese Oxide and Composite Electrodes for Electrochemical Supercapacitors

contributor:
Zhitomirsky, I.
Materials Science and Engineering

subject: nanostructured, manganese oxide, composite electrodes, electrochemical, supercapacitors, carbon nanotubes

abstract:
 Electrochemical supercapacitors (ES) are urgently needed as components in many
advanced power systems. The development of advanced ES is expected to enable radical
innovation in the area of hybrid vehicles and electronic devices. Nanostructured manganese oxides in amorphous or various crystalline forms have been found to be promising electrode materials for ES. The use of composite electrodes of manganese oxide with carbon nanotubes is being proposed to improve the overall electrochemical performance of the ES.

 Electrodeposition methods have been developed for the fabrication of manganese oxide films with/without carbon nanotubes for applications in ES. Electrolytic deposition of manganese oxides was found to be possible using Mn2+ and Mn7+ species, co-deposition of multi wall carbon nanotubes (MWNT) and manganese oxide using cathodic electrosynthesis was successfully achieved.

 Novel chemical process has been developed for the synthesis of nano-size manganese oxide particles. Electrophoretic deposition of the nano-size manganese oxide particles was able to be performed in both aqueous and non-aqueous solutions. Electrophoretic co-deposition of the nano-size manganese oxide particles with carbon nanotubes was successfully achieved.

 The mechanisms and kinetics of all the deposition methods are discussed. Charge storage properties of the films prepared by different deposition methods are investigated and compared.

abstract: Thesis

abstract: Master of Applied Science (MASc)


title: The Role of the Unfolded Protein Response and Alternatively Activated Macrophages in Pulmonary Fibrosis.

title: THE UNFOLDED PROTEIN RESPONSE, ALTERNATIVELY ACTIVATED MACROPHAGES, AND IPF

contributor:
Ask, Kjetil
Medical Sciences

subject:
Idiopathic Pulmonary Fibrosis
M2 macrophages
Alternatively Activated Macrophages
Interstitial Lung Disease
Nintedanib
Fibroblasts
Myofibroblasts
Unfolded Protein Response
IRE1
XBP1
ER stress

abstract:
Fibroproliferative disorders are the leading cause of morbidity and mortality
worldwide, with one specific group of fibroproliferative disorders being interstitial lung
diseases (ILD). Idiopathic pulmonary fibrosis is the most common ILD; however its
pathogenesis is not entirely understood. What is known is that there is repetitive cellular
injury preceding the fibrotic remodeling in the lungs that contributes to the irreversible
deposition of extracellular matrix (ECM) proteins. Myofibroblasts that accumulate at the
site of injury are thought to be the key drivers of ECM deposition and are often associated
in the disease. Although it is poorly understood how these immune cells differentiate in
the lung, one hypothesis suggests the role of alternatively activated profibrotic
macrophages in this process. The data presented in this thesis suggest that there are a presence of UPR and macrophage proteins in the lungs of IPF patients and the UPR may be necessary in the polarization of alternatively activated macrophages.

abstract: Thesis

abstract: Master of Science (MSc)


title: Flexible Crystalline Silicon Solar Cell

contributor:
Kitai, A.H.
Engineering Physics

subject: Silicon solar cell, Laser beam induced current

abstract:
A new type of flexible silicon solar cell has been fabricated by interconnecting solar cell die on a flexible substrate. The fabrication process is described in this thesis. The solar cell die were diced using two methods. One method was to dice a solar cell completely through. The other method was to dice a solar cell from its back partially and then cleave through. To study the effects of different dicing methods on the performance of solar cell die, storage delay time measurement was employed to determine the lifetime of excess electrons in the p region of the two types of solar cell die. A laser beam induced current (LBIC) scanning technique was employed to study the electrical performance of the two types of solar cell die. The carrier diffusion lengths of two types of solar cell die were also determined by traveling light spot diffusion length measurement.

The theoretical response of a solar cell was compared to experimental results at various incident light angles. OpticLab software was used to model the incident light angle and lens spacing dependence of solar cell performance.

abstract: Thesis

abstract: Master of Applied Science (MASc)


title: The Role of Nucleotide Excision Repair Genes in the Repair of Methylene Blue Plus Visible Light-Induced DNA and Cellular Damage in Chinese Hamster Ovary Cells

contributor:
Rainbow, A.J.
Biology

subject: Nucleotide excision, Hydroxyguanine, Chinese Hamster Ovary

abstract: Base excision repair (BER) is a DNA repair mechanism that involves the removal of single damaged bases from DNA and their excision as free bases. Another DNA repair mechanism known as nucleotide excision repair (NER) involves the removal of bulky lesions from DNA. Previous published reports have suggested a role for certain NER proteins in BER. Methylene blue (MB) is a type II photosensitizer, which upon excitation by visible light (VL) produces singlet oxygen that reacts with DNA to form 8hydroxyguanine (8-oxoG) lesions. The BER mechanism has been shown to preferentially remove 8-oxoG lesions from DNA. In the current work, the role of NER proteins in the BER of [MB+VL]-induced DNA damage was examined using a reporter gene assay. AdMCMVlacZ and AdHCMVlacZ are non-replicating adenoviruses that express the bacterial  β-galactosidase ( β-gal) reporter gene under the control of the murine or human cytomegalovirus immediate early promoter, respectively. Host cell reactivation (HCR) of  β-gal activity for a [MB+VL]-treated AdMCMVlacZ was examined in two repair-proficient normal Chinese hamster ovary (CHO) cell lines, NER-deficient mutants from rodent complementation groups (RCGs) 1 through 6, and the HER-deficient cell line EM9. Results show a decreased HCR capacity of [MB+VL]-induced DNA damage in the UV61 (RCG-6; CSB) cell line when compared to the repair-proficient normal AA8. This suggests an involvement of CSB in BER of [MB+VL]-induced damage. In contrast, the XRCCl-deficient EM9 showed an increased HCR capacity when compared to the parental AA8. This suggests a beneficial role for an XRCCl deficiency or for the specific gain-of-function gene mutation in the XRCCl gene for the repair of [MB+VL]induced damage. Similarly, the ERCCl-deficient UV20 (RCG-1) showed an increased HCR capacity when compared to the parental AA8. In contrast, another ERCCJdeficient cell line, 30PV, and the ERCCJ knock-out cell line, CH0-7-27, showed no significant increase in  β-gal activity when compared to the parental CHO-Kl. The ability to induce BER of [MB+VL]-induced DNA damage was also examined. HCR of  β-gal activity for [MB+VL]-treated AdHCMVlacZ or AdMCMVlacZ was examined in several CHO cell lines that were either untreated or treated with low levels of UVC or MB plus VL. Pre-treatment of NER-deficient UV61 and repair-proficient AA8 cells with UVC resulted in an enhanced HCR for [MB+VL]-treated AdHCMVlacZ, although the results were only significant for UV61. Similarly, an enhanced HCR of [MB+VL]-treated AdMCMVlacZ was observed in AA8 cells, suggesting that the repair of the [MB+VL]treated reporter gene is inducible by UVC. A significant enhancement in HCR of [MB+VL]-treated AdMCMV lacZ was not observed in AA8 cells following pre-treatment with MB, VL, or both, indicating that the detection of any induction in the repair of DNA damage from MB plus VL could not be made with the conditions of the HCR assay employed. As investigations into the effects of MB plus VL on whole cells have been limited, clonogenic survival of BER-and NER-deficient CHO cell lines was also observed following treatment with MB alone or MB plus VL. Results showed that the sensitivities of the NER-deficient CHO cell lines from RCGs 2, 4 and 5 and the BERdeficient EM9 cell line to MB alone were within the range obtained for the two repairproficient CHO normal cell lines, AA8 and K 1. In contrast, the UV20 cell line was more sensitive to MB alone compared to the normal cell lines. Additionally, both UV24 (RCG-3; XPB) and UV61 showed a decreased sensitivity toMB alone when compared to the normal AA8 cell line. The sensitivity of cells to MB plus VL was greater in the UV24, UV135 (RCG-5; XPG) and the XRCCl-deficient EM9 cell lines compared to that of the range obtained for the two repair-proficient normal cell lines, AA8 and Kl. Taken together with the results from the HCR assays, these results suggest that [MB+VL]induced DNA damage to cells and its repair do not play a major role in the survival of cells following treatment with MB plus VL. It appears likely that damage to cellular components other than DNA, such as protein, lipid and biological membranes, play a more important role in cell killing by MB plus VL.

abstract: Thesis

abstract: Master of Science (MSc)


title: Using a Structuring Approach to Assess the Mechanical Properties of Cellulose Nanocrystal-Based Thin Films

title: Mechanical Properties Of Cellulose Nanocrystal Thin Films

contributor:
Moran-Mirabal, Jose M.
Cranston, Emily D.
Chemistry and Chemical Biology

subject: cellulose nanocrystals; layer-by-layer; solvent-casting; polystyrene; thin film structuring; biaxial wrinkling; mechanical properties; elastic modulus; humidity-independent

abstract: The goal of this work was to quantify the mechanical properties of cellulose nanocrystal (CNC)-based thin films using a polystyrene (PS) structuring approach. This structuring approach was used to biaxially wrinkle CNC-polymer and all-CNC films, in order to assess how changes in the film fabrication process affected the elastic modulus of these films. All films were prepared on pre-stressed PS substrates and structured by heating them above the glass transition temperature of PS, which caused the substrates to shrink and the films to wrinkle biaxially. CNC-polymer films were prepared using the layer-by-layer approach, where three parameters were modified to obtain films of varying compositions: 1) type of polymer (xyloglucan, XG, or polyethyleneimine, PEI), 2) polymer concentration (0.1 wt% or 1 wt%), and 3) film thickness (i.e., number of deposited bilayers). After these films were structured, their elastic moduli were calculated to be 70 ± 2 GPa for CNC-XG0.1, 72 ± 2 GPa for CNC-PEI0.1, and 32.2 ± 0.8 GPa for CNC-PEI1.0 films, indicating that the mechanical properties of CNC-polymer films changed with film composition. This structuring method was also found to provide a humidity-independent measurement of the modulus due to the irreversible nature of the wrinkling. Next, to prepare all-CNC films, CNC suspensions were evaporated under conditions designed to control the film thickness (using 0.005 wt% – 8 wt% CNC suspensions) and CNC nanoparticle orientation (chiral nematic, isotropic, or uniaxial). Suspensions were dried slowly under vacuum, quickly by heating, or by spin-coating to form films with chiral nematic, isotropic, or uniaxial (radial) CNC orientations, respectively. Following structuring, these wrinkled films showed unique morphologies that changed with nanoparticle orientation, suggesting that their mechanical properties are dependent on the CNC orientation within the films. The work presented in this thesis implies that the mechanical properties of films fabricated from hygroscopic bio-based nanomaterials can be assessed in a humidity-independent way by using the structuring method presented. Quantifying the mechanical properties of these films is critical to assess the potential applications of CNCs, where CNC-based materials may be used in developing paper-based electronics, extracellular matrix mimics, and plant cell wall mimics.

abstract: Thesis

abstract: Master of Science (MSc)


title: Pure Zinc and Zinc/Ceramic Composite Coatings by Electrodeposition

contributor:
McDermid, Joseph R.
Zhitomirsky, Igor
Materials Science and Engineering

subject: pure zinc, ceramic, composite, coatings, electrodeposition, x-ray diffraction, orientation, grains

abstract:
 Pure zinc and zinc/yttria stabilized zirconia (YSZ) composite coatings for combined wear
and corrosion protection of ferrous substrates were prepared by electrodeposition using acidic zinc sulphate solutions containing YSZ and gelatin. The morphology of the electrodeposit was studied by Field Emission Scanning Electron Microscopy (FESEM) with energy dispersive spectroscopy (EDS). X-ray diffraction was employed to determine the texture of the zinc deposits. In the electrodeposition of pure zinc coatings, the influence of electrodeposition parameters, including current density, deposition time and solution pH was studied. It was found that the deposition rate was controlled by the current density and that an increase in deposition time resulted in the formation of deposit microstructures with coarse, columnar grains. The deposits prepared from solutions with lower pH were composed of uniform, fine grains and exhibited a basal plane preferred orientation.

 The effects of gelatin on zinc electrodeposition were investigated. It was found that the addition of gelatin profoundly modified the microstructure and crystallographic orientation of the zinc deposit. As the gelatin concentration increased, the mean grain size of zinc deposit was reduced and the basal plane preferred orientation was inhibited. The modification of the microstructure and orientation by gelatin increased microhardness of the zinc coating. However, the corrosion protection property which was assessed by potentiodynamic polarization test was not significantly changed.

 In the study on composite coatings, the incorporation of ceramic particles in the zinc deposit was characterized as a function of the deposition solution composition. The effect of ceramic particles on the hardness of the composite coatings was assessed by
microhardness. The corrosion potential of the composite coating was determined by potentiodynamic polarization tests. The results showed that decrease in solution pH and addition of gelatin promoted the co-deposition of ceramic particles with zinc. The mechanical and corrosion properties of conventional zinc coatings were improved by the incorporation of ceramic particles.

abstract: Thesis

abstract: Master of Applied Science (MASc)


title: The Emergence of the RNA World on the Early Earth

contributor:
Pudritz, Ralph
Physics and Astronomy

subject:
origins of life
astrobiology
planetary science
meteoritics
RNA world
habitability
biosignatures
early Earth

abstract: Life on Earth likely began as an RNA world, where cell-free or compartmentalized ribonucleic acid (RNA) molecules dominated as the replicating and evolving lifeforms prior to the emergence of DNA- and protein-based life. The focus of this thesis is on when and how this RNA world emerged. We use astrophysical and geophysical studies to constrain when the Earth was habitable, and biosignature studies to constrain when the Earth was inhabited. From this we obtain a time interval for the emergence of life. Considering all these constraints, we find that the Earth was habitable as early as 4.5 Ga, or as late as 3.9 Ga, depending on whether the early influx of asteroids inhibited life from emerging. The time that the Earth was inhabited is more precisely constrained to 3.7 Ga. This suggests life emerged within 800 Myr, and possibly in < 200 Myr. Between 4.5–3.7 Ga, the continental crust was slowly rising up from the global ocean, providing dry land on which warm little ponds could form. We develop the theory for the emergence of RNA polymers in these pond environments, whose wet-dry cycles promote polymerization. RNA is comprised of chains of nucleotides, and the latter is made up of ribose, phosphate, and a characteristic nucleobase. We numerically model the survival and evolution of nucleobases in warm little ponds from meteorite and interplanetary dust sources. The wet-dry cycles of our ponds are controlled by precipitation, evaporation, and seepage. The nucleobase sinks include photodissociation, seepage, and hydrolysis. Nucleobase and nucleotide seepage is efficient, therefore nucleotides and RNA molecules must have emerged rapidly (< a few years) in order to avoid falling through pores at the base of the pond. We find that meteorites, not interplanetary dust particles, are the dominant source of nucleobases used for RNA synthesis. Finally, under these conditions, we find that first RNA polymers likely emerged before 4.17 Ga.

abstract: Thesis

abstract: Master of Science (MSc)


title: Development of an Elastin-Like Polypeptide Carrier for an Influenza Virus Antiviral Peptide

contributor:
Mahony, James
Medical Sciences

subject:
Influenza
Antiviral
Peptide
Elastin-like Polypeptide

abstract:
Background: Despite the availability of a yearly vaccine and antivirals, the incidence of influenza infections remains high. The genome of the influenza virus can mutate rapidly, therefore novel influenza strains that may be resistant to the current vaccine or antivirals frequently enter the population. Because of the long production time necessary to produce a vaccine, new antivirals must be created to combat early stages of influenza outbreaks. The most effective antivirals will target a highly conserved and essential stage of virus replication. The influenza RNA-dependent RNA polymerase is a heterotrimeric complex composed of three subunits: PA, PB1, and PB2. The three components of the polymerase interact through well-defined domains and are essential for viral replication. Previously, influenza replication has been inhibited using a small synthetic peptide that mimics the interaction domain between PA and PB1 and inhibits the formation of the heterotrimeric complex.
Problem and Hypothesis: Although the peptide could inhibit influenza replication, synthetic peptides are costly to produce and are not a viable option for large-scale production. This problem can often be overcome by attaching the peptide to a highly soluble carrier protein. We hypothesize that influenza replication can be inhibited by attaching a peptide, that mimics the binding domain between the PA and PB1 subunits, to a human elastin-like polypeptide (ELP) carrier protein.
Methods and Results: The peptide and a nuclear localization sequence was genetically linked to a maltose binding protein (MBP) or ELP carrier protein. The MBP construct was purified by affinity chromatography using FPLC. A high yield of the ELP construct was obtained using inverse transition cycling, a method unique to ELPs because of their temperature-dependent solubility. The ELP construct was designed to be soluble at physiological temperature to limit cellular toxicity due to protein aggregation. The cytotoxicity of the ELP construct was assessed by monitoring the growth of A549 cells, a human lung epithelial cell line. The ELP construct did not have any adverse effects on A549 cell growth. Both constructs could localize to cell nuclei using their respective nuclear localization sequences and could also interact with the PA subunit, demonstrating their potential to inhibit influenza replication. Despite this, only the MBP construct was able to inhibit the replication of influenza. The MBP construct could inhibit the replication of both the H1N1 and H3N2 subtypes of influenza, indicating the recombinant protein had cross-strain activity.
Conclusion: Linking a small peptide to carrier protein can result in high protein yields, however a carrier protein must be chosen that will maintain the peptides’ therapeutic activity. In this study, a small anti-influenza peptide inhibited influenza replication when attached to an MBP carrier protein, however was not able to inhibit influenza replication when attached to an ELP carrier protein. Although the peptide was ineffective when attached to this particular ELP carrier protein, different ELP proteins of various lengths and compositions may still be effective carrier proteins for an antiviral peptide.

abstract: Thesis

abstract: Master of Science (MSc)

abstract: The influenza virus causes seasonal outbreaks each year and can have life-threatening symptoms in the young and elderly. In addition, it can rapidly mutate through antigenic drift; therefore, a new vaccine is required each year. Pandemic influenza strains can enter the population when the virus undergoes genetic reassortment by antigenic shift. However, it can take a significant amount of time to formulate a vaccine against pandemic influenzas, which means antiviral drugs are often used as the first line of defense. New antivirals to treat influenza must be developed because resistance to the current influenza antivirals has steadily increased. In this work, we developed an antiviral peptide to disrupt a critical interaction in the influenza RNA-dependent RNA polymerase and inhibit virus replication. This peptide was previously conjugated to an E. coli MBP carrier protein, which would likely not be compatible in vivo. This thesis focused on attaching the antiviral peptide to an elastin-like polypeptide protein, which mimics human tropoelastin, and should be non-immunogenic in humans.


title: Defining public health systems: A critical interpretive synthesis of how public health systems are defined and classified.

contributor: Clinical Epidemiology/Clinical Epidemiology & Biostatistics

subject:
public health
health care
public health systems
healthcare systems
health systems
critical interpretive synthesis

abstract:
Background:
With recent emphasis on creating a stronger, more patient-centred, health system in Ontario, there remains no clear definition of a “public health” system, hindering the ability to integrate preventive public health and health care practices. This study aims to describe public health systems and initiate a research agenda for this field.

Methods:
A critical interpretive synthesis of the literature was conducted using six electronic databases. In addition, data extraction, coding and analysis followed a best-fit framework analysis method. Initial codes were based on two current leading health systems and policy classification schemes: health systems arrangements (based on governance, financial and delivery arrangements) and the 3I+E framework for health policy formulation (institutions, interests, ideas and external factors). New codes were developed as guided by the data. A constant comparative method was used to develop concepts and to further link these into themes. Additional documents were identified to fill conceptual gaps.

Results:
5,933 unique documents were identified and 338 documents met the inclusion criteria. 81 documents were purposively sampled for full-text review and 58 of these were included in this study. Nine documents were found to help fill conceptual gaps. Generally, public health systems can be defined using traditional healthcare systems and policy frameworks. There was also a strong emphasis on identifying and standardizing the roles and functions of public health.
Partnerships (community and multi-sectoral) are common features within and between components of public health systems. A public health system framework and a model of a population health system were conceptualized.

Discussion:
Understanding public health systems can help strengthen these systems and further integrate preventive public health and primary care services. Systems are influenced by organizational and contextual factors that need to be explored to improve population health. A research agenda is proposed to move this field forward.

abstract: Thesis

abstract: Master of Public Health (MPH)


title: The Effect of High-Intensity Interval Training on Skeletal Muscle Oxidative Capacity in Middle-Aged Sedentary Adults

contributor:
Gibala, Martin
Kinesiology

subject: Skeletal muscle, Middle-aged sedentary adults, needle biopsy samples

abstract: There is growing appreciation of the potential for high intensity interval training (HIT) to rapidly stimulate metabolic adaptations that resemble traditional endurance training, despite a low total exercise volume. However, much of the work has been conducted on young active individuals and the results may not be applicable to older, less active populations. In addition, many studies have employed "all out", variable-load exercise interventions (e.g., repeated Wingate Tests) that may not be safe, practical or well tolerated by certain individuals. We determined the effect of a short program of low-volume, submaximal, constant-load HIT on skeletal muscle oxidative capacity and insulin sensitivity in sedentary middle-aged individuals who may be at higher risk for inactivity-related chronic diseases. Sedentary but otherwise healthy men (n=3) and women (n=4) with a mean (±SE) age, body mass index and peak oxygen uptake (VO_2peak) of 45±2 yr, 27±2 kg-m^2 and 30±1 ml·kg^-1·min^-1 were recruited. Subjects performed 6 training sessions over 2 wk, each consisting of 10 x 1 min cycling at 60% of peak power elicited during a ramp VO_2peak test (<90% of heart rate reserve) with 1 min recovery between intervals. Needle biopsy samples (v. lateralis) were obtained before training and <72 h after the final training session. Muscle oxidative capacity, as reflected by the maximal activity and protein content of citrate synthase, increased by ~20% after training, which is similar to changes previously reported after 2 wk of Wingate-based HIT in young active subjects. Insulin sensitivity, based on fasting glucose and insulin, improved by ~35% after training. These data support the notion that low-volume HIT may be a practical, time- efficient strategy to induce metabolic adaptations that reduce the risk for inactivity-related disorders in previously sedentary adults.

abstract: Thesis

abstract: Master of Science (MSc)


title: A Performance Predictive Model for Emergency Medicine Residents

contributor:
Samavi, Reza
eHealth

subject: Machine Learning, Learning Analytics, SVM, kNN, Neural Network, Medical Education, Emergency Residency Training

abstract: Competency-based medical education (CBME) is a paradigm of assessing resident performance through well-defined tasks, objectives and milestones. A large number of data points are generated during a five-year period as a resident accomplishes the assigned tasks. However, no tool support exists to process this data for early identification of a resident-at-risk failing to achieve future milestones. In this thesis, the implementation of CBME at McMaster's Royal College Emergency Medicine residency program was studied and the development of a machine learning algorithm (MLA) to identify patterns in resident performance was reported. The adaptivity of multiple MLAs to build a tool support for monitoring residents' progress and flagging those who are in most need of assistance in the context of emergency medicine education was evaluated.

abstract: Thesis

abstract: Master of Science (MSc)


title: Influence of Sample Preparation Methods and Interlocking on Sand Behaviour: An Experimental Investigation

contributor:
Guo, P. J.
Civil Engineering

subject: interlocking on sand behaviour, Bishop-type triaxial testing method,Moist tamping, water pluviation

abstract:
This thesis investigates the effects of sample preparation methods, which has
substantial influence on the internal structure or fabric of the sample, and interparticle
locking on the behaviour of sand through experimental study. Extensive laboratory tests
were conducted on two sands (namely, Ottawa sand and crushed limestone) with distinct
particle shape and surface texture, using a Bishop-type triaxial testing system.

A total of eight sample preparation methods were used to fabricate specimens
with different initial fabric, with specimens being fabricated using water pluviation,
moist tamping, and moist rodding. The experimental data reveal that sample preparation
methods have significant effect on both deformation characteristics and shear strength of
sand, in addition to the density and the effective confining pressure applied to the
specimens. More specifically, water pluviation and moist tamping tend to yield
specimens of high anisotropy and large dilation, which in turn results in higher friction
angle in conventional triaxial compression. The effect of sample preparation methods
was also observed from undrained tests on saturated sand.

Laboratory tests on crushed limestone consisting of angular particles
demonstrate that strong interparticle locking may develop owing to particle angularity.
The shear resistance of sand with angular particles has contributions from interparticle
friction, dilatation and interparticle locking. Moreover, interparticle locking, which
largely exists at the peak shear resistance of sand but vanishes with dilation at large
deformation, exists under both low and high stress levels investigated in this study. A conceptual model was proposed to take into account the energy consumption associated
with breaking interparticle locking during deformation when estimating the dilatancy
and strength of granular soils.

The behaviour of sand along proportional strain paths was also investigated, with
the focus being placed on strain softening and material instability in the context of Hill's
second order work. Depending on the strain path or the deformation history, a dilatant
sand displaying hardening and stable behaviour under isochronic (undrained) conditions,
which is often used as a reference in soil mechanics, may succumb to unstable flow type
behaviour along dilative strain paths. More specifically, when the imposed rate of dilation
exceeds the inherent rate of dilation of the material, a dense sand specimen will have flow
failure similar to that of a saturated loose specimen subjected to undrained compression.
On the other hand, a loose sand may not have a flow failure when it is forced to have
contractive volume change along imposed strain paths.

abstract: Thesis

abstract: Master of Science (MSc)


title: Functional Relationship Between Gut Microbiota and Anxiety

title: The Functional Relationship Between The Gut Microbiota And Generalized Anxiety Disorder in The Murine Model

contributor: Medical Sciences (Division of Physiology/Pharmacology)

subject: microbiota anxiety

abstract:
Depression and anxiety are etiologically heterogeneous disorders and their pathophysiology remains largely unknown. Gut microbiota has been shown to modulate brain function, behavior, and immune responses, and it has also been proposed to play a role in the pathophysiology of depression and anxiety. Our study aimed to investigate whether microbiota from patients with Generalized Anxiety Disorder (GAD) can induce anxiety and depressive-like behaviour in germ-free mice and whether this is accompanied by changes in immune markers and brain activity.

Germ-free NIH Swiss mice (n=27) were colonized with microbiota from either a GAD patient (n=13) with severe anxiety and comorbid depression or an age and sex-matched healthy control (HC) (n=14). Six mice from each group were treated with infliximab for three weeks (5mg/kg/week) starting at week 1 post-colonization. Microbiota profiles were assessed via 16S rRNA based Illumina. Three weeks post-colonization, all mice underwent six standard psychometric tests, including the open field, digging, marble-burying, and tail-suspension test. Cecal -defensin-3 and serum kynurenine/tryptophan were measured via ELISA. BDNF expression was assessed by immunofluorescence, and gene expression by using Nanostring gene assay.

Fecal -defensin levels were higher in GAD patients than in healthy controls. Similarly, -defensin levels were higher in GAD-colonized mice than in HC-colonized mice. GAD and HC-colonized mice had a unique and distinct microbiota, similar to that of their respective human donors. GAD-colonized mice exhibited anxiety and depressive-like behavior compared to HC- colonized mice, as assessed by the open field, digging, marble burying and tail suspension tests. BDNF expression was decreased in the hippocampus but increased in the amygdala of GAD-colonized mice. GAD-colonized mice also had a greater kynurenine/tryptophan ratio than HC-colonized mice. GAD and HC infliximab-treated mice showed no differences in behavior, central BDNF expression or kynurenine/tryptophan levels.

Our results suggest that GAD microbiota has the ability to induce anxiety and depressive-like behavior and alter brain BDNF expression in a murine host. These changes are accompanied by the activation of the innate immune system and seem to be TNF- dependent.

abstract: Thesis

abstract: Master of Science (MSc)


title: Assessing the functional asymmetry of the Bacillus subtilis MutL homodimer

contributor:
Guarné, Alba
Biochemistry and Biomedical Sciences

subject:
MutL
mismatch repair
homodimer
DNA
endonuclease activity

abstract: DNA mismatch repair corrects base-base mismatches and small insertion/deletion loops generated during normal DNA replication. If left unrepaired, these errors become permanent mutations and can lead to increased susceptibility to cancer. In most prokaryotes and all eukaryotes, the mismatch repair protein MutL is a sequence-unspecific endonuclease that plays an essential role in the strand discrimination step of this pathway. Prokaryotic MutL forms homodimers with two endonuclease sites, whereas eukaryotic MutL homologs form heterodimers with a single active site. To elucidate the mechanistic differences between prokaryotic and eukaryotic MutL, we tested whether both endonuclease sites are necessary for prokaryotic MutL nicking activity. MutL interaction with the processivity clamp is required to stimulate endonuclease activity. Therefore, we also tested whether both subunits of the MutL dimer needed to interact with the processivity clamp. To this end, we engineered a system to independently manipulate each protomer of the homodimer. We demonstrated that prokaryotic MutL is regulated by the processivity clamp to act in a similar manner to eukaryotic MutL with only one functional site contributing to the endonuclease activity. We also devised a strategy to stabilize the transient interactions between MutL, the β-clamp, and DNA through disulfide bridge crosslinking and heterobifunctional crosslinking. Stabilizing transient protein-protein and protein-DNA interactions will help optimize future structural studies in obtaining the ternary complex for mechanistic insights to the MutL endonuclease activity and regulation imposed by the β-clamp.

abstract: Thesis

abstract: Master of Science (MSc)


title: Effect of Small Cerium Additions on Microstructure and Mechanical Properties of Al-Mg-Fe Alloy

contributor:
Wilkinson, David
Malakhov, Dmitri
Materials Science and Engineering

subject: Cerium, Alloy fabrication, Al-Mg-Fe Alloy

abstract:
The application aluminum sheet alloy for light vehicle development was limited
by the high cost of alloy fabrication. The impurity iron, which is easily picked up during
fabrication, deteriorates its formability. The sheet alloy produced by continuous casting
techniques was showing lower in-service performance than the one produced with
traditional high-cost direct-chill casting technique. Therefore, enhancing the general
formability of the aluminum alloy became .the aim of many researchers and engineers in
past decades.

This project was launched to detect a possible modification effect of rare-earth
(RE) element on a Al-Mg-Fe alloy, which is a simplified AA5754 alloy. Cerium was
chosen as the RE element to test with. The influence of this rare-earth element on the
alloy grain microstructure, phase morphology, and corresponding mechanical behavior
was investigated.

It was found that cerium had a modification effect on the phase morphology to
some extent. Its addition provided a great grain refinement in as-cast alloys. However,
after thermo-mechanical processing, this effect would be eliminated by the small broken
particles and recrystallized fine grains. It was found that the mechanical performance of the cerium-containing AA5754 was neither enhanced nor deteriorated. The AA5754 alloy
remained non-heat-treatable after the addition of cerium.

abstract: Thesis

abstract: Master of Applied Science (MASc)


title: INFLUENCE OF TITANIUM INTERLAYER THICKNESS ON THE ADHESION OF TiCN THIN FILMS DEPOSITED ON STAINLESS STEEL

contributor:
Mascher, Peter
Engineering Physics

subject:
TiCN
Titanium Carbo-Nitride
Interlayer
Adhesion
Deposition
Cathodic Arc PVD

abstract: Hard coatings deposited by physical vapour deposition (PVD) are commonly used to improve the scratch resistance and hardness of objects made of softer materials such as steel, and they can also be used as decorative coatings since they exhibit a wide range of different colours. In this research, stainless steel tableware utensils were coated with multilayer Ti/TiCN thin films to give the tableware a wear-resistant decorative finish. A cathodic arc PVD system was used to deposit the coatings since it has the potential to produce very dense coatings with excellent adhesion and wear-resistance properties in relatively short deposition times. Several system parameters were varied between deposition cycles to create a large set of samples which included: changing the amount of flatware present inside of the chamber during deposition, changing the size of the flatware used, changing the mounting location of the flatware inside of the chamber, and changing the depletion level of the titanium cathode targets used to deposit titanium. It was found that changing these variables had an effect on the deposition rate of the coating and thus had an effect on the thickness of the titanium interlayer, which was found to be an important factor in achieving good adhesion of the TiCN layer. The optimal titanium interlayer thickness was found to be in the range of approximately 120 to 230 nm.

abstract: Thesis

abstract: Master of Applied Science (MASc)


title: Re-Imagining Child Welfare With Service Users: What Children's Social Workers Need to be Taught in School

contributor:
Dumbrill, Gary
Social Work

subject: thesis, child welfare, service users, social work education, McMaster, Canada

abstract:
As social workers we understand that service users are the most impacted
stakeholders involved in service delivery models at various agencies. When it comes to the field of child welfare, there are added barriers and complications that impact a
worker’s ability to develop relationships with service users. What do child welfare
service users consider to be “good” social work practice, and what do they expect from their workers? This thesis will focus on the voices of those who have been most
impacted by the system: those who are or have been in the care of a child welfare
system. At McMaster University, a program is being initiated in partnership between the School of Social Work and various local Children’s Aid Societies in Hamilton and the surrounding areas, which will explore how child welfare service users can be
incorporated into the education of social work students who plan to work in the field of child welfare. This thesis will explore what individuals who are or have been youth in the care of an Ontario Children’s Aid Society want to teach the students of this program before they become child welfare social workers. This expert feedback will then be incorporated into the curriculum of McMaster’s program, entitled: “Preparing for Critical Practice in Child Welfare” (PCPCW), which will be carried into practice by the students who graduate from the program to become child welfare social workers.

abstract: Thesis

abstract: Master of Social Work (MSW)


title: A Study on Polymer-induced Flocculation in Industrial Wastewater Treatment Via a High-throughput Method

contributor:
Latulippe, David
Chemical Engineering

abstract:
The main purpose of specialized industrial wastewater treatment facilities is to
treat incoming wastewater loads from various industries which do not have the
capability of treating their wastewater on site. Accordingly, specialized industrial
wastewater treatment facilities face a challenge in quickly identifying optimal treatment
options for the varying incoming wastewater loads they receive. With the new discharge
limits set by the federal Wastewater System Effluent Regulations (WSER) and a
compliance deadline by 2020, it became crucial for such facilities to optimize their
processes and ensure having a method to determine optimal treatment options and
conditions to meet the new discharge limits. One such limit is the Chemical Oxygen
Demand (COD), which is representative of the amount of organic matter present in a
solution.
Polymer flocculation is a common mechanism used for solid-liquid separation in
industrial wastewater treatment. While many previous research studies have been
previously conducted on polymer flocculation and industrial wastewater treatment, there
seems to be a lack in studies that focus on running experiments in a rapid high-
throughput manner and using samples that vary in composition and come from different
generators/sources.
In this work, a high-throughput method was implemented to investigate several
aspects in the polymer flocculation area on various wastewater samples obtained from
a specialized industrial wastewater treatment facility. Using this method, the optimum
polymer flocculant type, dosage and concentration were successfully identified for
several wastewater samples. In addition to that, scale-up experiments were done in the
v
facility on various wastewater tanks to compare the performance of undiluted and
diluted polymer flocculant. Diluted polymer flocculant was proven to successfully treat
wastewater tanks to a level safe enough for discharge and just as good as undiluted
polymer flocculant while using less “neat” polymer flocculant volumes. Moreover,
possible cost savings and a better treated water quality were also achieved by
implementing multi-staged polymer flocculation concept for industrial wastewater on a
small scale.
This work also focused on testing the FBRM as an in-line method for particle size
distribution measurements in industrial wastewater. However, even after an optimization
attempt, it did not work well on the samples tested. Another in-line method that was also
tested was UV spectroscopy. This method was proven to successfully work as a
method to determine optimum polymer flocculant dose and could be a promising in-line
tool.
Finally, bentonite was used as a flocculation aid along with polymer flocculants
and design of experiments (DOE) methods were implemented to almost successfully
reduce the COD, which as mentioned is an important water quality parameter, in
automotive industrial wastewater samples with initial average COD of 77,000 ppm to the
safe discharge limit (i.e. 600 ppm)

abstract: Thesis

abstract: Master of Applied Science (MASc)


title: Targeting the antagonism of AHR by MSI2 as a novel anti-leukemic strategy in human acute myeloid leukemia

contributor:
Hope, Kristin
Biochemistry and Biomedical Sciences

subject:
AML
Acute myeloid leukemia
MSI2
Musashi-2
AHR
Aryl hydrocarbon receptor
FICZ
Antagonism

abstract:
Acute myeloid leukemia (AML) is an aggressive malignancy of the hematopoietic system, characterized by the accumulation of abnormally differentiated blast cells that is driven by leukemic stem cells (LSCs). In murine AML, Musashi-2 (MSI2), an RNA-binding protein and positive regulator of stemness, has been implicated in the propagation of disease. While its enhanced expression correlated with poor disease outcome for human AML patients, no study has yet examined its actual functional role in human leukemia.
In normal human hematopoietic stem cells (HSCs), we have recently reported the inhibitory effects of MSI2 on the pro-differentiative aryl hydrocarbon receptor (AHR) signaling pathway as a mechanism for promoting self-renewal in HSCs. We hypothesized that elevated MSI2 is critical for maintenance of human AML and promotes unrestrained self-renewal of LSCs in part through constitutive repression of AHR signaling. Our work aimed to unravel the relationship between MSI2 and AHR in the human leukemic context and to determine if activation of AHR signaling can promote differentiation.
Results confirmed that MSI2 is preferentially expressed in primary patient LSCs and is negatively correlated with the expression of AHR gene targets. Upon lentiviral knockdown of MSI2 in-vitro and in-vivo, leukemic growth was compromised and increased AHR signaling was observed. Circumventing the inhibitory role of MSI2 in AML, activation of AHR with a potent agonist impaired leukemic progenitor activity and proliferation. In-vivo studies employing reconstitution of immunodeficient mice with primary AML samples showed impairment of AML engraftment for a significant proportion of tested samples upon treatment with an AHR agonist.
Overall, our findings from this project indicated that MSI2 is required for human AML propagation and that a decrease in MSI2 inhibitory effects on AHR signaling or direct activation of the AHR signaling pathway via a potent agonist can promote AML cell differentiation and loss.

abstract: Thesis

abstract: Master of Science (MSc)

abstract: The human blood system is sustained by a population of blood stem cells that are tightly regulated in their production of stem and differentiated cells. The Musashi-2 (MSI2) protein is a key regulator of blood stem cell identity through its inhibition of the aryl hydrocarbon receptor (AHR) signaling pathway. When there is dysregulation of blood cell homeostasis, blood malignancies such as acute myeloid leukemia (AML) may arise. In this work, the relationship between MSI2 and the AHR signaling pathway was explored within a myeloid leukemic context. It was shown that MSI2 imposes inhibitory effects on AHR to promote disease progression and that its reduction could help alleviate disease burden. Additionally, it was found that activation of the AHR signaling pathway could overcome the MSI2 differentiation block to create a therapeutic effect. Overall, the results of this project shed light on novel therapeutic strategies and targets for the treatment of AML.


title: Removal of Pharmaceutical Carbamazepine Using Pulsed Corona Discharge Generated in Water

contributor:
Dickson, Sarah
Civil Engineering

subject: Water Treatment- Pharmaceutical- Corona discharge- Carbamazepine

abstract:
Increasing concentrations of pharmaceutical compounds and their metabolites in aquatic environment threatens both aquatic species and human health. Many pharmaceuticals are persistent in the environment and resistant to conventional water treatment; hence, alternate treatment techniques are required to remove these compounds from water. Aqueous phase electrical discharge has been demonstrated to successfully remove a range of pharmaceutical compounds from water. This technique is characterized by the simultaneous generation of highly reactive species and physical effects within the aqueous solution to be treated.
The present study investigates and optimizes the efficacy of pulsed corona discharges generated in water for the treatment of carbamazepine (CBZ) in a relatively clean water matrix by varying the solution pH, solution conductivity, gas type injected, and gas flow rate injected.
A point-to-plane reactor configuration was employed to produce plasma channel- streamers. In this geometry, the electrical discharges were produced directly within the aqueous phase to be treated by charging a 1nF pulse forming capacitor using a high voltage (25 KV) DC power supply through 10 MΩ resistor to generate discharges within the water at a 30 HZ pulse repetition rate.
Solution pH, solution conductivity, gas type, and gas flow rate were optimized to maximize the removal efficacy of CBZ removal by pulsed corona at the laboratory scale. The CBZ degradation rate (concentration decrease over time) was monitored using LC/MS/MS, with overall degradation ranging from 14-94% depending on the experimental conditions. The results demonstrate that higher CBZ removal efficiency is achieved under lower pH and conductivity conditions. Moreover, enhanced degradation efficiency is obtained when gas, and particularly oxygen, is bubbled through the high voltage hollow electrode, especially at higher flow rates.

abstract: Thesis

abstract: Master of Applied Science (MASc)

abstract: Pharmaceuticals are being released into the environment at an increasing rate due to population growth and a rising dependence on these compounds. Pharmaceuticals are resistant to many common water treatment methods; however, electrical discharge generated within the water to be treated (pulsed corona discharge) is an emerging water treatment technology that has been shown to successfully treat many pharmaceuticals. In the present work, pulsed corona discharge has been used to treat carbamazepine present in a relatively clean water matrix. Removal was maximized by optimizing the solution pH, solution conductivity, type of gas bubbled through the electrode, and gas flow rate. The best removal was achieved in solutions with lower pH and conductivities where oxygen was bubbled through the electrode at a relatively high rate.


title: Subspace Clustering with the Multivariate-t Distribution

contributor:
McNicholas, Paul D.
Franczak, Brian C.
Statistics

subject:
Model-Based Clustering
High-Dimensional

abstract: Clustering procedures suitable for the analysis of very high-dimensional data are needed for many modern data sets. One model-based clustering approach called high-dimensional data clustering (HDDC) uses a family of Gaussian mixture models to model the sub-populations of the observed data, i.e., to perform cluster analysis. The HDDC approach is based on the idea that high-dimensional data usually exists in lower-dimensional subspaces; as such, the dimension of each subspace, called the intrinsic dimension, can be estimated for each sub-population of the observed data. As a result, each of these Gaussian mixture models can be fitted using only a fraction of the total number of model parameters. This family of models has gained attention due to its superior classification performance compared to other families of mixture models; however, it still suffers from the usual limitations of Gaussian mixture model-based approaches. Herein, a robust analogue of the HDDC approach is proposed. This approach, which extends the HDDC procedure to include the mulitvariate-t distribution, encompasses 28 models that rectify one of the major shortcomings of the HDDC procedure. Our tHDDC procedure is fitted to both simulated and real data sets and is compared to the HDDC procedure using an image reconstruction problem that arose from satellite imagery of Mars' surface.

abstract: Thesis

abstract: Master of Science (MSc)


title: Assessing differential microRNA expression in endometriotic implants

subject: endometriosis miRNA reproduction endometrium

abstract:
Endometriosis is an estrogen-dependent disease that is characterized by the growth of endometrial tissue outside of the uterine cavity. The most common endometriotic lesions are ovarian endometrioma, peritoneal lesions, and deeply-infiltrating endometriosis. Ten percent of women in reproductive age are affected, a gross underestimate due to the delay in diagnosis and non-specific symptoms. The etiology of endometriosis is not well understood, making diagnosis difficult, and treatments suboptimal. Currently, laparoscopic surgery is the gold standard for diagnosis, however this method is invasive, costly, and physicians are often reluctant to send their patients to surgery without certainty of disease. It is therefore a research priority to identify a minimally-invasive biomarker for endometriosis.
	Over the years, the search for a biomarker has shifted from a single circulating biomarker, to a panel of circulating biomarkers, and finally to the advent of newer technologies. The studies of proteomics, genomics, phenomics, and metabolomics have shown some promise thus far. MicroRNAs, a discovery of genomics, are short, non-coding RNA strands that regulate mRNA expression by silencing or degrading the transcript. The dysregulation of miRNAs have been shown to contribute to the pathology of many gynecological conditions, and have shown to be dysregulated in endometriosis. To date however, results have been underwhelming due to differences in methodologies and failure to consider endometriosis as a heterogeneous disease. Three miRNAs were studied based on their prevalence in the literature (miR-9, -21, and -424), and three others (miR-10a, -10b, and -204) were measured based on their association with BDNF. In the current study, miR-204 expression was significantly lower (p=0.0016) in the eutopic endometrium of women with endometriosis compared to controls. Relative expression of miR-21, miR-424, and miR-10b differed significantly (p<0.05) across lesion types in women with exclusively endometriomas, peritoneal or deep-infiltrating lesions. Corresponding BDNF expression in the lesion types were inversely correlated to miRNA expression suggesting these miRNA regulate BDNF and are implicated in endometriosis pathology. Due to the findings that miRNAs are differentially expressed between endometriotic lesions, this study also suggests that, different lesion types are biochemically distinct.

abstract: Thesis

abstract: Master of Health Sciences (MSc)


title: A Novel Amendment Delivery System for Groundwater Impacted by Vinyl Chloride

contributor:
Dickson, S.E.
Civil Engineering

subject: novel amendment, delivery system, groundwater, vinyl chloride, solvents, design

abstract:
 Although successful in laboratory studies, field applications of in situ remediation of chlorinated solvents in groundwater have met with limited success. This is most often attributed to the inability to deliver the amendment evenly throughout the target zone, especially in low permeability and heterogeneous materials. The goal of this research was to employ a prototype of a novel delivery system to evenly deliver amendment across the depth and breadth of the subsurface in a cost-effective method. The research was conducted at 42 Voyager Court, Toronto, ON where concentrations of vinyl chloride in groundwater were in excess of Ontario Ministry of the Environment guidelines (O.Reg.153/04). The subsurface consisted of sandy and clayey silt fill underlain by sandy silt till.

 The delivery system comprised 29, 1/4" diameter, delivery points with small perforations along the length, installed in a fence perpendicular to groundwater flow, approximately 0.5 m upgradient of the area of concern. The delivery system used low flow rates (approximately 13 to 23% of total
groundwater flow) and discrete delivery holes to deliver a potassium permanganate solution (approximately 40 g/L) amended with sodium bromide (approximately 0.8 g/L) across the depth of the subsurface. Fourteen multi-level monitoring wells, each with five sampling ports were installed to monitor the effectiveness.

 After six months of delivery, sample results indicated that oxidant demand hindered the ability of potassium permanganate to reach and degrade the vinyl chloride. However, elevated bromide concentrations were detected at all downgradient sampling ports within a 1.5 m distance. Thus, the delivery system was successful at delivering the amendment across the depth and breadth of the
target area and achieving even delivery.

 Problems, typically leaks, were encountered with the delivery system design. Additional engineering would be required to improve the header system prior to commercializing this process. This would be a beneficial endeavor, as results of this work indicate that this passive delivery fence technique meets a real need in the remediation industry, which is the even distribution of amendment to target zones in the saturated subsurface, including zones of low permeability.

abstract: Thesis

abstract: Master of Applied Science (MASc)


title: Defect Engineering for Silicon Photonic Applications

contributor:
Knights, Andrew
Engineering Physics

subject: defect, engineering, silicon, photonic, applications, epitaxial regrowth, polycrystalline, annealing

abstract:
 The work described in this thesis is devoted to the application of defect engineering in the development of silicon photonic devices. The thesis is divided into simulation and experimental portions, each focusing on a different form of defect engineered silicon: ion implantation induced amorphous silicon and solid-phase epitaxial regrowth suppressed polycrystalline silicon.

 The simulations are directed at silicon rib waveguide Raman laser applications. It is shown that a uniform, divacancy defect concentration will not enhance Raman gain. The excess optical loss and free carrier lifetime of rib waveguides with remote
amorphous silicon volumes were simulated. Net gain was demonstrated depending on the geometry of the structure. For a waveguide structure with rib width, rib height and slab height of W = 1.5, H = 1.5 and h = 0.8 μm respectively, the optimal separation between the edge of the rib and the amorphous region is ~2.0 μm. Surface recombination velocity modification was shown to be an effective means to reduce free carrier lifetime.

 Experimental work was devoted to the characterization of a novel form of polycrystalline silicon created by amorphizing the entire silicon overlayer of a silicon-on-insulator wafer. Solid-phase epitaxial regrowth of the amorphous silicon is suppressed upon annealing due to the lack of a crystal seed and results in polycrystalline silicon. This material was characterized with ellipsometry, positron annihilation spectroscopy and x-ray diffraction. The material properties are shown to be heavily dependent on the annealing conditions. Ellipsometry showed that the refractive index at 1550 nm is comparable to crystalline silicon. Positron annihilation spectroscopy showed that the polycrystalline material exhibits a high concentration of vacancy-type defects while vertically regrown crystalline silicon does not. X-ray diffraction showed that the polycrystalline silicon is non-textured, strained in tension and is characterized by grain sizes less than 300 nm.

 Defect etching and optical measurements using a waveguide geometry were performed in order to characterize the lateral regrowth and the optical loss of the polycrystalline material. Lateral regrowth in the [011] direction was 1.53 and 0.96 μm
for 10 minute anneals at 750 and 900 °C respectively, and at least 2.5 μm at 650 °C.
Waveguide optical loss measurements with adjacent polycrystalline regions separated from the rib by at least 5.5 μm showed no separation dependence. The intrinsic optical loss of the polycrystalline material was estimated to be 1.05 and 1.57 dB/cm for TM and TE polarizations after a 900 °C anneal. Vertically regrown c-Si was shown to exhibit less than 3.0 dB/cm optical loss after annealing at 550 °C .

abstract: Thesis

abstract: Master of Applied Science (MASc)


title: Torque Ripple Minimization in Switched Reluctance Machines

contributor:
Emadi, Ali
Electrical and Computer Engineering

subject:
switched reluctance machines
torque ripple

abstract:
Due to its cheap production costs, simple construction, and robustness, switched reluctance machines are viable candidates for traction motor drive applications in the electrification of transportation. However, high torque ripple and acoustic noise limit the performance of switched reluctance motors (SRM). This thesis considers control methods to reduce the electromagnetic torque ripple in SRM, while also analyzing the impact of these control methods on other aspect of machine performance, such as copper losses and radial force production.
Traditionally, SRM is controlled using rectangular current profiles which are excited using discrete pulsations. Timing of these pulsations is quantified with conduction angles, and the performance of the machine at a given operating point can be optimized by carefully choosing these conduction angles. This thesis starts the analysis on controls of SRM using the conduction angle parameters to determine a baseline of torque ripple performance for comparison against advanced control techniques developed afterwards.
Recently, current profiling techniques have been developed, and have been shown to have high performance for torque ripple reduction. In this thesis, one such technique is proposed in the form of an optimization problem where the solution of this problem yields an optimized current profile that both minimizes torque ripple while reducing copper losses. The proposed current profiling technique ensures good current tracking, which allow for optimal control performance over a wide speed range.
Finally, this thesis shows the torque more generally as one component of the nodal forces in SRM. The other component of the nodal forces is the radial forces, which contributes to the noise, vibrations, and harshness of the machine. In this thesis, modeling of the radial forces has been conducted, and effects of the proposed current profiling technique on radial forces have been shown to comprehensively illustrate the performance of the current profiling technique.

abstract: Thesis

abstract: Master of Applied Science (MASc)


title: Damage Detection in Composite Structures Using a Dielectric Signature Variation Approach

contributor:
El-Dakhakhni, Wael
Civil Engineering

subject: damage detection, composite structures, dielectric, signature, variation approach, delamination, fibre rupture

abstract:
Composite materials, constructed from a combination of fibre and resin, have rapidly
emerged as a high performance alternative to conventional materials for new constructions as well as strengthening and repair of existing structures. However, the use of such materials may be accompanied by various types of damages and failure modes, including delamination, debonding, fibre rupture, and matrix cracking. This thesis presents a new nondestructive evaluation (NDE) technique for damage detection in composite structures. The concept, based on detecting local dielectric permittivity variations, was employed to design capacitance sensors with high sensitivity to detect such damages. An analytical and 2D finite element models were used to assess the influence of the sensor geometrical parameters on the output signals and to optimize the sensor design. Concrete and wood specimens wrapped with glass-fibre composites containing pre-induced defects with different types and sizes were constructed and inspected. The sensors were also used to detect the delaminations and water intrusion defects in pultruded composite members. The principles behind the sensor operation were also applied to detect other damages in other structures; the capacitance sensors were
designed and used to locate ungrouted cells in a concrete masonry wall. The proposed sensors, coupled with a commercially available portable capacitance meter, facilitate employing this technique in the field for rapid inspection of composite structures without the need for sophisticated data analyses that are usually required by other more expensive and time consuming NDE techniques.

abstract: Thesis

abstract: Master of Applied Science (MASc)


title: How does reading internet and texting abbreviations affect processing?

contributor:
Stroinska, Magda
Service, Elisabet
Cognitive Science of Language

subject: linguistics, cognitive science, textisms, internet language

abstract:
The use of shortcuts and abbreviations in everyday communications, both
online and through texts, has become increasingly popular over the past decade.
Shortcuts like ’lol’ for ’laugh out loud’ aim to provide emotional nuance and
context that would otherwise be lost in standard written communication. However,
studies have shown that there is a processing cost associated with using these
shortcuts (Perea, Acha, & Carreiras, 2009; Ganushchak, Krott, Frisson, & Meyer,
2013). Other studies have found that texting shortcuts are lexically independent
units: they are represented and stored in the brain independently of their full,
standard form (Ganushchak, Krott, & Meyer, 2010; 2012; Tat & Azuma, 2015).
The current study examines the effect of newer, more diverse shortcuts on
processing and Working Memory (WM) capacity through two experiments. It
was hypothesised that reading shortcuts would lead to an increased processing cost
and poorer recall. Furthermore, it was hypothesised that this processing cost and
poorer recall would depend on the type of shortcut. Phrasal shortcuts (e.g. ’brb’
for ’be right back’) would be more difficult to read and would lead to poorer recall
compared to contractions and clippings (e.g. ‘txt’ for ‘text’). In Experiment 1, the
processing cost of reading shortcuts was explored through a self-paced reading
task, with results supporting our hypotheses. In Experiment 2, participants read
sentences which contained memory words to be remembered for recall at the end
of a trial, with the number of correct items recalled used as a gauge of working memory capacity and processing efficiency (Service & Maury, 2014; Daneman
& Carpenter, 1980). Results were mixed, with no clear effect of the presence of
a shortcut or shortcut type modulating recall. Implications of these results are
discussed with regard to reading and the direction of language evolution.

abstract: Thesis

abstract: Master of Science (MSc)

abstract: The use of shortcuts and abbreviations in everyday communications, both online and through texts, has become increasingly popular over the past decade. Shortcuts like 'lol' for 'laugh out loud'  aim to provide emotional nuance and context that would otherwise be lost in standard written communication. These shortcuts are more difficult to read than standard English, however (Perea, Acha, & Carreiras, 2009; Ganushchak, Krott, Frisson, & Meyer, 2013). The current study examines the effect of newer, more diverse shortcuts on reading and memory recall through two experiments. We hypothesise that sentences with shortcuts are more difficult to read than sentences without shortcuts, and will result in poorer recall. Results of this study are mixed; Experiment 1 indicates shortcuts to be more difficult to read, whereas Experiment 2 shows a limited effect of shortcuts on recall. This has implications on how the perception of shortcuts in everyday use may be changing.


title: Towards Fabrication of Flexible Solar Cells Using PN-Junction GaAs Nanowires

contributor:
LaPierre, R. R.
Engineering Physics

subject: flexible, solar cells, fabrication, PN-junction, GaAs nanowires, epitaxy

abstract: In the current research, use of p-n junction GaAs nanowires (NWs) grown by gas source molecular beam epitaxy on GaAs (111) B substrates for the fabrication of flexible solar cells are reported. The solar cells were fabricated by embedding the NWs in a polymer matrix (SU8 2), followed by ohmic contact formation to the tops of the NWs as well as the rear side of the substrate. I-V characteristic curves were obtained by illuminating the solar cells using a solar simulator, indicating a photovoltaic effect. NWs were also detached from the substrate by different methods and successfully transferred onto a flexible substrate for potential use as solar cells. Scanning electron microscopy was used throughout the research for characterization and optimization of the fabrication processes including NW embedment, removal from the substrate, and contact formation.

abstract: Thesis

abstract: Master of Applied Science (MASc)


title: A Wireless Sensor for Fault Detection and Diagnosis of Internal Combustion Engines

contributor:
Habibi, Saeid
Mechanical Engineering

subject:
Artificial Neural Networks
Fault Detection
Fault Diagnosis
Internal Combustion Engine
Smooth Variable Structure Filter
Accelerometer
Electronic Design
Vibration Analysis
Wireless Sensor
Automotive
Extended Kalman Filter
Levenberg-Marquardt

abstract:
A number of non-invasive fault detection and diagnosis (FDD) techniques have been researched and have proven to have worked well in classifying faults in internal combustion engines (ICE) and other mechanical and electrical systems. These techniques are an integral step to creating more robust and accurate methods of determining where or how a fault has or will occur in such systems. These FDD techniques have the potential to not only save time avoiding a tear-down of a costly machine, but could potentially add another layer of safety in detecting and diagnosing a fault much earlier than was possible before.
Looking at the previous research methods and the systems they used to acquire this data, it is a natural progression to try and make a system which is able to encapsulate all of these ideologies into one inexpensive module capable of integrating itself into the advanced set of FDD. This thesis follows along with the development of a new wireless sensor that is developed specifically for the use in FDD for ICE and other mechanical systems. A new set of software and firmware is created for the system to be able to be incorporated into previously designed algorithms.
After creating and manufacturing the sensor it is put to the test by incorporating it into several Artificial Neural Networks (ANN) and comparing the results to previous experiments done with previous research equipment. Using vibration data acquired from a running engine to train a neural network, the wireless sensor was able to perform equally as well as its expensive counter parts. It proved to have the ability to achieve 100% accuracy in classifying specific engine faults. The performance of three ANN training algorithms, Levenberg-Marquardt (LM), extended Kalman Filter (EKF), and Smooth Variable Structure filter (SVSF), were tested and compared. Adding to the feasibility of a standalone system the wireless sensor was tested in a live environment as a method of instant ICE fault detection.

abstract: Thesis

abstract: Master of Applied Science (MASc)


title: TRANSRACIAL ADOPTION IN THE UNITED STATES OF AMERICA

contributor:
Gedge, Elisabeth
Sciaraffa, Stefan
Philosophy

abstract: Thesis

abstract:
In this thesis, I will explore the issue of transracial adoption in the United States of America, wherein Caucasian American parents domestically adopt African American children that are not biologically or genetically related to them. In 1972, the National Association of Black Social Workers (NABSW) released an influential position paper, which articulated a strong objection to the practise of transracial adoption. Their position paper has informed and inspired strong objections from other opponents.
	The NABSW and other opponents of transracial adoption argue that there are certain goods that African American children need, goods that are essential to their healthy development within the United States of America, given its historical, political, and social climate. African American parents and the African American family–adoptive or otherwise––have traditionally been responsible for providing these goods to African American children. Furthermore, the aforesaid opponents of transracial adoption believe that White parents cannot provide these goods to their adoptive Black children, they cannot serve the traditional role of African American parents and the African American family, and thus should not be allowed to adopt African American children.
	In the first chapter of my thesis, I develop a typology of these goods, wherein I philosophically explicate and define exactly what these goods are and why they are important for African American children. In chapter two, I explore the issue of whether African American children need African American parents to provide these goods for them, or whether White parents and families can sufficiently serve the traditional role of Black parents and provide these goods to their adoptive Black children. Finally, in chapter three, I explore the moral responsibilities that Caucasian American parents who adopt African American children have in order to provide for the aforementioned goods, and meet the unique needs of their children.

abstract: Thesis

abstract: Master of Arts (MA)


title: Pharmaceutical care for pulmonary tuberculosis treatment in Thailand

contributor:
Xie, Feng
Health Research Methodology

subject:
Pharmaceutical care
Tuberculosis
Adherence

abstract:
Objectives
Three objectives were to compare: 1) treatment success; 2) healthcare resource uses; and 3) out-of-pocket (OOP) expenditures, indirect costs, and health-related quality of life (HRQoL) associated with pharmaceutical care, home visit, and modified DOT in three referral hospitals in Songkhla province, Thailand.

Methods
Project 1&2 were retrospective cohort study collecting data from 1,398 pulmonary TB patients who started treatment between October 2010 and September 2013. Project 3 was a prospective study collecting data from 104 pulmonary TB patients who started treatment between January and May 2014. The propensity score matching and generalized linear models (GLMs) were used to compare the outcomes associated with three supervision approaches by adjusting for baseline characteristics.

Results
Project1: The differences in treatment success rate were not statistically significant when comparing pharmaceutical care with either home visit (success rate: 92.76% versus 94.74%) or modified DOT (success rate 93.37% for both).

Project2: The mean direct healthcare costs to public payer were $519.96 (95% confidence interval (CI): $437.31 to $625.58) for pharmaceutical care, $1,020.39 (CI:$911.13 to $1,154.11) for home visit, and $887.79 (CI:$824.28 to $955.91) for modified DOT.

Project3: Mean OOP expenditures were $907.56 (CI:$603.80 to $1,269.41), $148.47 (CI:$109.49 to $194.89), and $95.35 (CI:$69.11 to $129.63), while the indirect costs were $1,925.68 (CI:$922.06 to $3,284.94), $2,393.66 (CI:$1,435.01 to $3,501.98), and $833.33 (CI:$453.87 to $1,263.45), for those receiving pharmaceutical care, home visit, and SAT, respectively. Mean health utility scores at the baseline and the end of treatment were 0.679 and 0.830, 0.713 and 0.905, and 0.708 and 0.913 for the patients receiving pharmaceutical care, home visit, and SAT, respectively.

Conclusion
Pharmaceutical care is clinically and economically effective compared with the other strategies studied. A large-scale prospective study is warranted to strengthen evidence to support policy making in TB management in Thailand.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)


title: INCREMENTAL COMPUTATION OF TAYLOR SERIES AND SYSTEM JACOBIAN IN DAE SOLVING USING AUTOMATIC DIFFERENTIATION

contributor:
Nedialkov, Nedialko
Computational Engineering and Science

subject:
Automatic Differentiation
Differential-Algebraic Equations
Common Subexpression Elimination
Taylor Series

abstract:
We propose two efficient automatic differentiation (AD) schemes to compute incrementally Taylor series and System Jacobian for solving differential-algebraic equations (DAEs) by Taylor series. Our schemes are based on topological ordering of a DAE's computational graph and then partitioning the topologically sorted nodes using structural information obtained from the DAE. Solving a DAE by Taylor series is carried out in stages. From one stage to another, partitions of the computational graph are incrementally activated so that we can reuse Taylor coefficients and gradients computed in previous stages. As a result, the computational complexity of evaluating a System Jacobian is independent of the number of stages.

We also develop a common subexpression elimination (CSE) method to build a compact computational graph through operator overloading. The CSE method is of linear time complexity, which makes it suitable as a preprocessing step for general operator overloaded computing. By applying CSE, all successive overloaded computation can save time and memory.

Furthermore, the computational graph of a DAE reveals its internal sparsity structure. Based on it, we devise an algorithm to propagate gradients in the forward mode of AD using compressed vectors. This algorithm can save both time and memory when computing the System Jacobian for sparse DAEs. We have integrated our approaches into the \daets solver. Computational results show multiple-fold speedups against two popular AD tools, \FAD~and ADOL-C, when solving various sparse and dense DAEs.

abstract: Thesis

abstract: Master of Science (MSc)


title: Development and calibration of “calcite rafts” as a proxy for Holocene aquifer conditions in anchialine settings, Quintana Roo, Yucatán Peninsula, Mexico

contributor:
Reinhardt, Eduard G.
Geography and Earth Sciences

subject:
Coastal Karst Aquifers
Salinity
Hurricanes
Yucatán
Halocline
Calcite Rafts
Precipitation
Hoyo Negro
Paleohydrological Reconstructions
Potable Water

abstract:
Coastal karst aquifers are important water resources, often providing the only source of freshwater to coastal communities for agriculture, industrial usage and human consumption.  In order to implement management strategies and preventative measures for future perseveration of this resource, it is imperative to understand how coastal groundwater conditions are controlled by the interaction of freshwater/seawater on local and regional scales, but also over recent and past time periods.  However, there is a limited resource of published hydrological data on recent aquifer conditions.  In the Yucatán Peninsula and other anchialine environments, this lack of information inhibits the understanding of the spatial and temporal interaction of the meteoric and marine water masses.  Documenting how the aquifer is responding to forcing mechanisms such as large precipitation events, seasonal cycles and short-term sea level rise (e.g. storm surge) will assist in understanding modern aquifer condition but also the interpretation of paleo-records.
Utilization of water level and salinity sensors in strategic positions in the aquifer demonstrate that meteoric water mass salinity varies over wet and dry seasons with the movement of the halocline, but also on a short-term basis though large rainfall events.  Salinity in the meteoric water mass is influenced by mixing with the marine water mass during intense precipitation events associated with Hurricane Ingrid (2013), Tropical Storm Hanna (2014) and a series of unnamed events in 2015.  During wet periods, induced flow from increase precipitation causes turbulent mixing with the marine water mass, increasing salinity in the upper meteoric lens.  On the contrary, during dry periods, mixing is reduced, therefore making the meteoric lens less saline.
This contemporary understanding of meteoric/marine water mass dynamics can be applied to developing and calibrating the geochemical record of calcite rafts, calcite precipitation at the air-water interface of cave pools, as a hydrological proxy for aquifer conditions.  Our monitoring of calcite raft formation, deposition and geochemistry shows that raft accumulations (e.g., raft piles/cones) can offer a good paleoenvironmental archive of changing hydrological conditions.  Based on a 2-year observational record, results indicate that calcite raft precipitation/formation occurs continuously but with only minor biases with intense rainfall events altering supersaturation conditions in the surface waters.  Testing the use of calcite rafts in sediment cores from Hoyo Negro show that geochemical analyses (87Sr/86Sr, δ18O, δ13C, Sr/Ca and Cl/Ca) show that meteoric water mass salinity varied during the Holocene (~ 8.5 Ka – present) likely due to changing rainfall and or cave passage geomorphology, which is coherent with other independent climate records.  Prior to this study, calcite rafts have never been considered a paleo-hydrological archive for aquifer conditions, however, the consistency and cross-validation with independent records demonstrates great potential for future paleohydrological reconstructions.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)


title: Accurate Calculations of Nonlinear Optical Properties Using Finite                                                                                Field Methods

contributor:
Ayers, Paul W.
Chemistry

subject:
nonlinear optical properties
finite field
density functional theory
polarizability
hyperpolarizability
error reduction
Richardson extrapolation
Rational functions

abstract:
Molecular nonlinear optical (NLO) properties are extensively studied using both theory and experiment because of their use in myriad applications. Experimental measurements of the most interesting molecules’ NLO properties are difficult, so experimental data for molecules with desirable NLO properties is scarce. Theoretical tools don’t suffer from the same limitations and can provide significant insights into the physico-chemical phenomena underlying the nonlinear responses, can help in interpreting response behaviour of molecules, and can guide design the materials with desirable response properties. Here, I present my work on developing methods for accurately calculating the NLO properties of molecules using the finite field (FF) approach.
The first chapter provides a background for the finite field and electronic structure methods used in this dissertation. Chapter two is a thorough investigation of the finite field method. The limitations of the method are highlighted and the optimal conditions for overcoming its drawbacks and obtaining meaningful and accurate results are described. Chapter three presents the first systematic study of the dependence of optimal field strengths on molecular descriptors. The first protocol for predicting the optimal field for the second hyperpolarizability is presented and successfully tested, and the dependence of the optimal field strength for the first hyperpolarizability on the molecular structure is investigated. Chapter four is an assessment of various DFT functionals in calculating the second hyperpolarizabilities of organic molecules and oligomers. This study shows the limitations of conventional DFT methods and the importance of electron correlation to response properties. In chapter five we present a new method of calculating NLO properties using a rational function model that is shown to be more robust and have lower computational cost than the traditional Taylor expansion. Finally, chapter six includes a summary of the thesis and an overview of future work.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)


title: HUMANITARIAN POLICY-MAKER PERSPECTIVES ON PALLIATIVE CARE

contributor:
Schwartz, Lisa
Global Health

subject:
Palliative Care
Global Health
Humanitarian
Healthcare
Interpretive Description

abstract:
Background: In the face of overwhelming need and increasingly scarce resources, the humanitarian charge of “saving lives and alleviating suffering” is often reduced to simply saving lives. In 2014, World Health Assembly Resolution 67.19 called for the strengthening of palliative care as a key component of comprehensive care. However, even when palliative care is the only available option (ie. 2014-2015 Ebola Crisis), there is little evidence showing it is available in the field. More research is needed to understand this dissonance between policy and practice, and to ensure that humanitarians are providing ethical and contextually appropriate care.
Methodology: Twelve individual, in-depth, semi-structured interviews were conducted in English and French with humanitarian healthcare policy makers from North America, Europe, and the Middle East, average 10+ years of experience representing various international organizations. Interviews were transcribed and coded using NVivo11 and an interpretive description framework.
Findings: Participant comments suggested the existence of an institutionalized rescue culture, characterized by the fear of failure, equating of death with failure of the humanitarian healthcare professional, and a resultant systemic devaluation of palliative- type care in disaster contexts. The indoctrination of this culture may begin as early as medical school, and manifests clearly in the lack of consistent nomenclature and awareness of palliative care, treatment of palliative-triaged individuals, and resources allocated to palliative care in humanitarian contexts. Palliative care provision is a moral obligation as a final bastion of the human right to dignity and to health.
Discussion & Conclusion: In order for palliative care to be integrated into the humanitarian mandate, a significant cultural shift must first take place. The findings of this thesis and the larger Humanitarian Health Ethics study will provide key guidance for the adoption and adaptation of policies that help humanitarians maintain the dignity of individuals in their most vulnerable moments.

abstract: Thesis

abstract: Master of Science (MSc)


title: Characteristics and Behavior of Plasma Cut-Welded H-Shaped Steel Columns

contributor:
Sivakumaran, K. S.
Civil Engineering

subject: Cut-welded H-shaped steel columns, plasma cutting, welding process

abstract:
Welded built-up structural steel members are widely used as columns, beams, and
beam-columns in various buildings, bridges, industrial complexes, etc. Modern cutting
techniques are used in the fabrication of such members. Besides traditional saw cutting and
oxy-flame cutting, the modern cutting techniques include plasma cutting, laser cutting, water- jet
cutting, etc. The different cutting techniques induce different degrees of Heat Affected
Zones (HAZ), which subsequently creates different degrees of geometrical and mechanical
imperfections (residual stresses). Therefore, it could be expected that the true behavior of
structural steel columns manufactured by such cutting techniques be different.

The main objective of this investigation was to study the characteristics and behavior of
plasma cut-welded H-shaped steel columns at different slenderness ratios. However, this
investigation also considered similar flame cut-welded H-shaped steel columns for comparison
purposes. The H-shaped column sections were fabricated from plates having specified yield
strength of 350MPa. First, the initial plate was cut into plate strips and then the plate strips
(flanges and web) were welded together to form the H-shaped section in this investigation. The
strength of these columns were established under uni-axial compressive loading with pinned
end condition, allowing for minor axis rotation. Moreover, the structural imperfections such as
residual stresses and geometrical imperfections were established. The residual stresses
distributions were established at various stages of fabrication processes using the "method of
section" technique. That is, the residual stresses in initial plate, plate strips (cutting effects), and
column sections (cutting and welding effects) were established. Similarly, the geometrical
imperfections were established at various stages of fabrication processes in this investigation.The temperature profiles were measured during the cutting and welding processes. As part of
the scientific documentation, the mechanical characteristic of virgin steel plates were obtained
by standard coupon tensile test.

Based on the experimental results on column strength, the general behavior of plasma
cut columns and flame cut columns were similar. However, it was found that the plasma cut-welded
steel columns seemed to carry higher loads than that of flame cut-welded columns for
higher slenderness ratios( λ≥1). For lower slenderness ratios (0.5<λ<1), it was found that the
flame cut-welded columns had higher strength than plasma cut-welded columns in this
investigation. The residual stress distribution of both plasma cut column section and flame cut
column section had the same general distribution. However, in general, the flame cut columns
had high intensity of tensile residual stresses at their flange tips than the plasma cut columns.
Moreover, the out-of-plane imperfections of column sections were within the code limitations.
However, it was found that the flame cut-welded H-shaped steel columns seemed to have
higher out-of-plane imperfections than the similar plasma cut-welded H-shaped steel columns
in this investigation.

abstract: Thesis

abstract: Master of Applied Science (MASc)


title: Tunable Second Harmonic Generation Devices with an Integrated Micro-Heater

contributor:
Xu, Chang-Qing
Engineering Physics

subject: tunable, second harmonic, generation, devices, integrated, micro-heater, fabrication

abstract:
Single-pass frequency conversion by a nonlinear optical crystal is an attractive method to generate coherent radiation in various spectral domains from ultraviolet to mid-infrared. Wavelength converters based on quasi-phase matched (QPM) periodically poled lithium niobate (PPLN) have proved to be important wavelength conversion devices for many useful applications. This thesis develops a novel integration design for temperature controlling and temperature wavelength tuning of a QPM-PPLN waveguide wavelength converter. A Cr/Pt/Au thin film alloy layer is deposited on a PPLN device with a polymer buffer layer to work as a
micro-heater and a temperature sensor at the same time. The temperature of the device can be tailored by applying current to the micro-heater layer, which changes the effective period of the QPM grating and thus the QPM wavelength through the thermal optical effect (TOE). The device's temperature can be monitored by measuring the resistance change of the alloy layer. Micro-heater design and mode profile simulation are involved in the thesis. The entire device fabrication process is introduced. Both electrical and optical features of the device are characterized and discussed. In contrast to the conventional temperature tuning method based on a bulky oven, the proposed design has some excellent characteristics such as compact package size and low power consumption.

abstract: Thesis

abstract: Master of Applied Science (MASc)


title: Phase-Field Simulations of Rapid Solidification in Binary Alloys

contributor:
Provatas, Nikolas
Materials Science

subject: phase-field simulation, Rapid solidification, Binary alloys, solute trapping, four-fold dendritic

abstract:
Rapid solidification is a well established method to produce novel materials with improved
mechanical or electrical properties. The sharp-interface kinetics of rapid solidification
for a binary alloy is summarized. A Phase Field model mapping to this sharp interface
model is summarized and solved by a new adaptive mesh refinement algorithm.
Simulation results are consistent with experiments: The solidification velocity increases
in power-law like fashion at low undercooling and approximately linearly at high undercooling;
The solid/liquid interface undergoes a transition from four-fold dendritic to circular
crystal structures; Solute trapping emerges and the solute partitioning approaches
unity as the solidification velocity increases. Our Phase Field simulations are the first self -consistent
predictions of velocity selection and morphological selection at both low and
high undercoolings and also the first independent check of the solute trapping model in two
dimensions.

abstract: Thesis

abstract: Master of Applied Science (MASc)


title: CHARACTERIZING PROTEIN ARGININE METHYLTRANSFERASE EXPRESSION AND ACTIVITY DURING MYOGENESIS

title: CHARACTERIZING PRMT BIOLOGY DURING MYOGENESIS

contributor:
Ljubicic, Vladimir
Kinesiology

subject:
Protein arginine methyltransferase
skeletal muscle
myogenesis
PGC-1α
mitochondria

abstract: Despite the emerging importance of protein arginine methyltransferases (PRMTs) in regulating skeletal muscle plasticity, the biology of these enzymes during muscle development remains poorly understood. Therefore, our purpose was to investigate PRMT1, -4, and -5 expression and function in skeletal muscle cells during the phenotypic remodeling elicited by myogenesis. C2C12 muscle cell maturation, assessed during the myoblast stage, and during days 1, 3, 5, and 7 of differentiation, was employed as an in vitro model of myogenesis. We observed PRMT-specific patterns of expression and activity during myogenesis. PRMT4 and -5 gene expression was unchanged, while PRMT1 mRNA and protein content were significantly induced. Cellular monomethylarginines and symmetric dimethylarginines, indicative of global and type II PRMT activities, respectively, remained steady during development, while type I PRMT activity indicator asymmetric dimethylarginines increased through myogenesis. Histone 4 arginine 3 (H4R3) and H3R17 contents were elevated coincident with the myonuclear accumulation of PRMT1 and -4. Collectively, this suggests that PRMTs are methyl donors throughout myogenesis and demonstrate specificity for their protein targets. Cells were then treated with TC-E 5003 (TC-E), a selective inhibitor of PRMT1 in order to specifically examine the enzymes role during myogenic differentiation. TC-E treated cells exhibited decrements in muscle differentiation, which were consistent with attenuated mitochondrial biogenesis and respiratory function. In summary, this study increases our understanding of PRMT1, -4, and -5 biology during the plasticity of skeletal muscle development. Our results provide evidence for a role of PRMT1, via a mitochondrially-mediated mechanism, in driving the muscle differentiation program.

abstract: Thesis

abstract: Master of Science (MSc)

abstract: Protein arginine methyltransferases (PRMTs) are responsible for many important functions in skeletal muscle. However, significant knowledge gaps exist with respect to PRMT expression and activity during conditions of muscle remodeling. Therefore, the purpose of this Thesis was to investigate PRMT biology throughout skeletal muscle development. Mouse muscle cells were employed to examine characteristics of PRMT1, -4, and -5 at numerous timepoints during myogenesis. PRMTs exhibited distinct patterns of gene expression and activity during muscle maturation. A PRMT1 inhibitor (TC-E) was utilized to investigate the role of this enzyme during myogenesis. Muscle differentiation was impaired in TC-E-treated cells, which coincided with reduced mitochondrial biogenesis and respiratory function. Altogether, these results suggest a PRMT-specific pattern of expression and activity during myogenesis. Furthermore, PRMT1 plays a crucial role in skeletal muscle differentiation via a mitochondrially-mediated mechanism. Our study provides a more comprehensive view on the role of PRMTs in governing skeletal muscle plasticity.


title: Seeing is Deceiving: The Effects of Stimulus Adaptation on Perceptual Error in the Ebbinghaus Illusion

contributor:
Lyons, James
Kinesiology

subject: stimulus adaptation, perceptual error, Ebbinghaus illusion, seeing, deceiving

abstract: Page 193 is included twice. Numbered the same, but are different pages.

abstract:
Although visual illusions have been used extensively to explore the mechanisms subserving perception and action, controversy exists regarding the extent to which illusions may differentially affect the perceptual and motor systems. In part, this is because it is often difficult to accurately assess the perceptual influence of illusory stimuli since participants are usually asked only to report binary size decisions (bigger or smaller) of an illusory stimulus relative to a control figure. Questions of relative size or the direction of misperception remain
unanswered. In this thesis, 10 experiments, comprising eight separate studies, were conducted to address these issues. In Experiment 1, a software tool was developed that allowed participants to size-match a target to a Control figure (Experiment 1a), as well as both the Large (Experiment 1b) and Small Annuli (Experiment 1c) Ebbinghaus Illusion stimuli. These experiments provided an accurate percentage of misperception score when each of the three conditions was presented in isolation. Results from Experiment 2, however, suggest that
when each of the three conditions are presented in a random and repeated stimulus array, a degree of perceptual adaptation occurs in which illusory effects are biased in the direction of the large annuli stimulus. Experiments 3-8 provided evidence to suggest that the degree of motor involvement (Experiment 3), number of illusory stimuli present (Experiments 4 and 5), direction of attention (Experiment 6) and visual field laterality (Experiments 7 and 8) have minimal influence on the adaptation effects observed in Experiment 2.

abstract: Thesis

abstract: Master of Science (MSc)