title: Structural and Functional Aspects of Evolutionarily Conserved Signature Indels in Protein Sequences.

contributor:
Gupta, Radhey S.
Biochemistry and Biomedical Sciences

subject: Genomics;Molecular Signatures;Phylogenetic analysis;Protein evolution;Homology modeling;Protein-protein docking;Molecular dynamics simulations

abstract: Analysis of genome sequences is enabling identification of numerous novel characteristics that provide valuable means for genetic and biochemical studies. Of these characteristics, Conserved Signature Indels (CSIs) in proteins which are specific for a given group of organisms have proven particularly useful for evolutionary and biochemical studies. My research work focused on using comparative genomics techniques to identify a large number of CSIs which are distinctive characteristics of fungi and other important groups of organisms. These CSIs were utilized to understand the evolutionary relationships among different proteins (species), and also regarding their structural features and functional significance. Based on multiple CSIs that I have identified for the PIP4K/PIP5K family of proteins, different isozymes of these proteins and also their subfamilies can now be reliably distinguished in molecular terms. Further, the species distribution of CSIs in the PIP4K/PIP5K proteins and phylogenetic analyses of these protein sequences, my work provides important insights into the evolutionary history of this protein family. The functional significance of one of the CSI in the PIP5K proteins, specific for the Saccharomycetaceae family of fungi, was also investigated. The results from structural analysis and molecular dynamics (MD) simulation studies show that this 8 aa CSI plays an important role in facilitating the binding of fungal PIP5K protein to the membrane surface. In other work, we identified multiple highly-specific CSIs in the phosphoketolase (PK) proteins, which clearly distinguish the bifunctional form of PK found in bifidobacteria from its homologs (monofunctional) found in other organisms. Structural analyses and docking studies with these proteins indicate that the CSIs in bifidobacterial PK, which are located on the subunit interface, play a role in the formation/stabilization of the protein dimer. We have also identified 2 large CSIs in SecA proteins that are uniquely found in thermophilic species from two different phyla of bacteria. Detailed bioinformatics analyses on one of these CSIs show that a number of residues from this CSI, through their interaction with a conserved network of water molecules, play a role in stabilizing the binding of ADP/ATP to the SecA protein at high temperature. My work also involved developing an integrated software pipeline for homology modeling of proteins and analyzing the location of CSIs in protein structures. Overall, my thesis work establishes the usefulness of CSIs in protein sequences as valuable means for genetic, biochemical, structural and evolutionary studies.

abstract: Dissertation

abstract: Doctor of Philosophy (PhD)


title: Does it matter who was where? Learning identity-to-location binding from faces

contributor:
Sun, Hongjin
Psychology

subject:
contextual cueing
implicit learning
location-based learning
identity-to-location binding
repeated-bound
repeated-unbound
single-phase
dual-phase

abstract: People unconsciously learn spatial information about places they encounter frequently, leading them to search through familiar scenes faster than for unfamiliar scenes. We explored this phenomenon—the contextual cueing effect—in scenes containing images of different human faces. Participants searched through a series of scenes for a target among distractors, characterized as a letter T among letter L’s with each letter positioned on top of a face image (Experiment 1) or as a female face among male faces (Experiment 2). Experiment 1 showed that when the binding of identity and location was manipulated during learning, slightly greater (but not statistically significant) contextual cueing effects were found for repeated scenes with constant identity-to-location binding than those repeated scenes with constant spatial configurations but shuffled identity-to-location binding. Experiment 2 showed that if the binding of identity-to-location changed after the learning of a set of identity-to-location binding, small (but not statistically significant) costs of contextual cueing were found. The results suggest that in the contextual cueing paradigm, repeated identity-to-location binding might be learned but the learning of repeated spatial configurations alone account for a major portion of the learning.

abstract: Thesis

abstract: Master of Science (MSc)


title: Development of a Search Engine Tool for Visually Impaired Web Users

contributor:
Dr. Wassyng, Alan
Dr. Lawford, Mark
Dr. Sabri, Kourosh
Dr. Shirani, Shahram
Computing and Software

subject:
Human Computer Interface
Accessibility
Search Engines
Literature Review
Userspace
Usability Evaluation
Web-based interaction

abstract: A detailed walkthrough of the engineering process for the development of an accessible search engine tool. Contributions include a comprehensive literature review, assumptions, requirements, high-level design, implementation, and usability evaluations.

abstract: The internet has become useful in just about anything we do. Unfortunately, as vision degrades so does our ability to perceive the web. The design of Graphical User Interfaces (GUIs) has become overwhelmingly common and is meant to be coupled with a screen and mouse. The interface introduced in this thesis was developed to avoid graphically driven design and create a novel Search Engine interface intended for blind and low vision users. This is achieved by minimizing the total concern of the user (the userspace) to a handful of options and a predetermined structure to the Search Engine Results Page (SERP). This thesis describes the entire development process starting from the literature review and including implementation, evaluation, and future work.

abstract: Thesis

abstract: Master of Applied Science (MASc)


title: Prevalence and predictors of opioid use disorder following prescription of opioids for chronic noncancer pain: A systematic review and meta-analysis of observational studies

contributor:
Busse, Jason W.
Health Research Methodology

subject:
opioid addiction
chronic noncancer pain
opioid use disorder
systematic review
meta-analysis
health research methods
clinical epidemiology
prevalence
predictors

abstract:
Background: Despite the many harms and limited efficacy of opioids in managing chronic noncancer pain (CNCP), they are commonly prescribed for these patients in North America. One of the harms associated with prolonged opioid use is opioid use disorder (OUD); however, the risk of addiction is uncertain. We systematically reviewed observational studies to establish the prevalence of (OUD), and to explore factors associated with OUD in patients with CNCP.

Methods: We searched MEDLINE, EMBASE, CINAHL, Cochrane Library, and PsycINFO from inception to December 2018 to identify studies that explored the prevalence of OUD or risk factors for OUD in patients with CNCP. Two specialists in addiction medicine reviewed each potentially eligible study, blinded to results, to ensure their outcome met DSM-5 criteria for OUD. We pooled estimates of OUD across eligible studies using random-effects models. When possible, we pooled estimates of association with OUD for all independent variables reported by more than one study.

Results: Twenty-two studies reported the prevalence of OUD, and six studies reported the association of 36 factors with OUD in patients with CNCP. The pooled prevalence of OUD was 20% (95% CI: 15% to 25%); however, we found evidence for small study effects (interaction p<0.001). When restricted to larger studies (≥900 patients), the pooled prevalence of OUD was 5.8% (95% CI: 2.8% to 9.5%; moderate certainty evidence). The prevalence of OUD was not associated with level of certainty of OUD criteria, under- or overestimation of instruments compared to DSM-5 criteria, severity of OUD, or risk of bias (interaction p values ranged from 0.34 to 0.92). Moderate certainty evidence demonstrated an association between OUD and male sex (OR 1.50 [95% CI: 1.05 to 2.14]; absolute risk increase (ARI) 2.7% [95% CI: 0.3% more to 5.8% more]), current smokers (OR 1.63; [95% CI: 1.25 to 2.12]; ARI 3.3% [1.3% more to 5.7% more]), and a history of mental health disorders (OR 1.49 [95% CI: 1.17 to 1.89]; ARI 2.6% [95% CI: 0.9% more to 4.6% more]). Low certainty evidence demonstrated an association between OUD and younger age (OR for every 10-year decrement, 1.60 [95% CI: 1.11 to 2.30]; ARI, 3.2% for every 10-year decrement [95% CI: 0.6% more to 6.6% more]). Moderate certainty evidence suggested no association between OUD and a history of alcohol abuse/dependence (OR 1.32 [95% CI: 0.84 to 2.07]; ARI 1.7% [95% CI: 0.9% less to 5.5% more]), and low certainty evidence suggested no association between OUD and a history of drug abuse (OR 1.51 [95% CI: 0.75 to 3.02]; ARI 2.7% [95% CI: 1.4% less to 9.9% more]).

Conclusion: Moderate certainty evidence suggests that 6% of CNCP patients prescribed opioids will develop OUD. Younger men who smoke, with a history of mental health disorders, are at higher risk. Additional research is needed to establish the association between OUD and a history of drug or alcohol abuse.

abstract: Thesis

abstract: Master of Science (MSc)

abstract: Opioids are commonly prescribed for patients with chronic pain that is not due to cancer; however, long-term opioid use inevitably leads to physical dependence and may result in addiction. Prior studies have reported extremely variable rates of opioid use disorder (OUD) following prescription for chronic noncancer pain, ranging from less than 1% to more than 50%, which has led to considerable confusion. My systematic review found moderate certainty evidence that the prevalence of OUD following prescription for chronic pain is 5.8% (95% CI: 2.8% to 9.5%). Patients who were younger, current smokers, males, and had a history of mental health disorders, had a higher risk of developing OUD. These findings will help support shared care decision-making between patients with chronic pain considering opioid therapy and their healthcare providers.


title: FRAMEWORK FOR SUSTAINABILITY METRIC OF THE BUILT ENVIRONMENT

contributor:
Chidiac, Samir
Civil Engineering

subject: Sustainability

subject: Metric

subject: Energy consumption

subject: Building envelope

subject: Building envelope coefficient of performance

subject: Housing

subject: Buildings

subject: Projection to latent structures

subject: Partial least squares

abstract: Sustainability of the built environment is one of the most significant challenges facing the construction industry, and presents significant opportunities to affect change. The absence of quantifiable and holistic sustainability measures for the built environment has hindered their application. As a result, a sustainability performance metric (SPM) framework was conceptually formulated by employing sustainability objectives and function statements a-priori to identify the correlated sustainability indicators that need to be captured equally, with respect to the environment, the economy, and society. Projection to Latent Structures (PLS), a latent variable method, was adopted to mathematically formulate the metric. Detached single-family housing was used to demonstrate the application of SPM. Datasets were generated using Athena Impact Estimator, EnergyPlus, Building Information Modelling (BIM), Socioeconomic Input/Output models, among others. Results revealed that a holistic metric, such as the SPM is necessary to obtain a sustainable design, where qualitative or univariate considerations may result in the contrary. A building envelope coefficient of performance (BECOP) metric based on an idealized system was also developed to measure the energy efficiency of the building envelope.  Results revealed the inefficiencies in the current building envelope construction technologies and the missed opportunities for saving energy. Furthermore, a decision-making tool, which was formulated using the PLS utilities, was shown to be effective and necessary for early stages of the design for energy efficiency.

abstract: Thesis

abstract: Doctor of Science  (PhD)

abstract: Sustainability of the built environment is a significant challenge facing the industry, and presents opportunities to affect changes. The absence of holistic sustainability measures has hindered their application. As a result, a sustainability performance metric (SPM) framework was formulated by employing sustainability objectives and function statements a-priori to identify the indicators that need to be captured. Projection to Latent Structures was adopted to mathematically formulate the metric. A housing prototype was used to demonstrate the application of the SPM utilizing a bespoke dataset. Results revealed that holistic metric, such as the SPM is necessary for achieving sustainable designs. A building envelope coefficient of performance metric was also developed to measure the energy efficiency of the building envelope. Results revealed the inefficiencies in the current building envelope technologies and identified missed opportunities. Furthermore, a decision-making tool was formulated and shown to be effective and necessary for design for energy efficiency.


title: Characterization Strategies for Bone Ultrastructure and Bone-Cell Interfacing Materials

contributor:
Grandfield, Kathryn
Biomedical Engineering

subject: bone, biomaterials, imaging, characterization

abstract: The repair of damaged or diseased bone tissue often requires the use of metallic implants which form an interface with the surrounding bone tissue. Understanding this interface is important for improving the outcomes of implant placement and overall health of patients. Bone is a composite material of organic collagen fibrils and inorganic mineral phases that have structural variations across multiple length scales. This heterogeneous and hierarchical nature poses characterization challenges for (i) understanding bone, (ii) creating biomaterial structures that mimic it, and (iii) approaches for evaluating biomaterials. These challenges formed the basis for the three papers presented in this thesis. In Chapter 3, leporine bone was examined using atom probe tomography (APT) to visualize in vivo mineralized collagen fibrils, their chemical composition, and spatial arrangement in 3D with sub-nanometer accuracy. This provided new insight into the location of biomineral with respect to collagen and demonstrated the power of APT for understanding collagen-mineral arrangement. In Chapter 4, commercially pure titanium was laser ablated to generate periodic surface structures inspired by the periodicity of collagen. Three different periodicities were generated with submicron-scale roughness and a high degree of reproducibility. All the surfaces were non-cytotoxic and encouraged cells to adhere perpendicular to the orientation of the surface structures. In Chapter 5, a simple five-minute room temperature ionic liquid treatment was developed to investigate the same laser-ablated titanium periodic structures with osteoblast-like cells adhered. The development of this technique fulfills an important niche in biological imaging by allowing for simultaneous and repeated visualization of submicron surface features and wet cells. Therefore, the combined impact of this thesis is novel imaging and biomaterials evaluation strategies to (i) improve understanding of bone structure; (ii) leading to bioinspired biomaterials design; and (iii) new methods for simultaneous biological and biomaterials evaluation.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)

abstract: Bone implant devices are required to treat, augment, or replace bone tissue in dental and orthopaedic applications. These, often metallic, implanted devices have success when a structural and functional connection with natural bone tissue is created, a phenomenon known as osseointegration. Good osseointegration is required to ensure stability of the implant without compromising the quality of life of the patient. In order to improve osseointegration of biomaterials, both sides of the interface, i.e. the bone and implant surface, must be better understood. This thesis focuses on exploring methods to improve the evaluation and understanding of both bone structure at the nanoscale and structured metallic implant surfaces for the design of bone-interfacing biomaterials.


title: Sarcopenia in the Canadian Longitudinal Study on Aging: The impact of diagnostic criteria on the agreement between definitions and the association of sarcopenia with falls

title: Sarcopenia - Agreement and association with falls

contributor: Clinical Epidemiology/Clinical Epidemiology & Biostatistics

subject:
sarcopenia
aging
muscle wasting
Canadian Longitudinal Study on Aging
muscle mass
muscle strength

abstract:
Objectives: Sarcopenia is defined using a variety of different muscle variables, muscle mass adjustment techniques and cut offs for each variable. The objectives of this thesis were to assess how operational differences in sarcopenia definitions impact the agreement between definitions and the association between sarcopenia and health outcomes such as falls.
Methods: A list of sarcopenia definitions was developed which captured the combinations of muscle variables, muscle mass adjustment techniques, and cut offs used in the literature based on a systematic review conducted for this thesis. These definitions were applied to participants taking part in the Canadian Longitudinal Study on Aging, a national study of participants aged 45 to 85 years at baseline. The agreement between the definitions and the association of each definition with falls was assessed.
Findings: Both the combination of muscle variables as well as the different muscle mass adjustment techniques generally had limited agreement. Sarcopenia definitions including muscle mass and muscle strength were associated with falls in males, but none of the sarcopenia definitions were associated with falls in females. Area under the curve analyses revealed that even sarcopenia definitions associated with more than two times the odds of falling in males, had a small impact on identifying fallers with values ≤0.56.
Conclusions: The results of this thesis show that the existing range of definitions used to define sarcopenia are not equivalent based on the limited agreement and inconsistent association of sarcopenia with falls. The results also show that sarcopenia may have limitations as clinically useful diagnosis for identifying fallers with area under the curve values for all definitions showing that the identification of fallers based on sarcopenic status was at best, modestly better than chance alone.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)

abstract: Definitions for sarcopenia differ in terms of which muscle variables are included, how muscle mass is adjusted, and which cut offs to use for each variables. This thesis assessed the impact of different methods of operationalizing sarcopenia on the proportion of sarcopenic participants, agreement between definitions, and the strength of the association between sarcopenia and falls. The variables used to operationalize sarcopenia as well as different techniques for adjusting muscle mass resulted in poor agreement between definitions. In males, these factors impacted which definitions were significantly associated with falls, and in females, sarcopenia was not associated with falls for any definition. For all definitions, sarcopenia status poorly discriminated between those that would or would not fall. Together, these results show that different sarcopenia definitions are not equivalent and that a standard definition is required. However, this thesis also shows that more work is required to determine the clinical utility of sarcopenia.


title: Deriving an Induced Pluripotent Stem Cell Model of Acute Myeloid Leukemia to Capture and Isolate Disease Heterogeneity

contributor:
Bhatia, Mick
Biochemistry and Biomedical Sciences

abstract: Leukemia is a cancer of the blood and bone marrow where acute myeloid leukemia (AML) accounts for the most leukemic deaths annually. Only 5-10% of patients over 60 reach complete remission and the median survival for elderly patients is 8.5 months. Elderly patients succumb to the disease due to inability to tolerate conventional chemotherapy regimens. Despite advances in sequencing technologies supporting mutation identification in AML patients, it is still unclear which mutations are disease drivers and specific treatments for almost all patients are not available. This is in part because there are no known targets that distinguishing leukemic cells from their healthy counterparts. Using patient samples to derive new therapies has been challenging due to the technical inability to identify healthy from leukemic cells in a sample. Reprogramming of somatic cells into induced pluripotent stem cells (iPSCs) uniquely enables the separation of healthy and leukemic cells from AML patients through the derivation of AML and healthy isogenic iPSC cell lines.  This holds potential for disease modelling and elucidation of functional driver mutation in AML. Leukemic iPSC lines have not yet been studied comprehensively due to the lack of a robust method to reprogram AML. Deriving iPSCs from leukemia patient samples has proven to be challenging, where all combined studies are limited by capturing a total of four patients spanning only two of fourteen genetic classes. Here, we for the first time interrogate strategies to selectively reprogram AML and healthy cells from patients. Using fluorescently activated cell sorting, we show that AML and healthy reprograming is restricted by the differentiation state. Further, we demonstrate that the use of myeloid markers in deriving AML-iPSCs is disadvantageous as AML clones reside in a variety of compartments. We present, the most successful to date, derivation of mutant and healthy variety of AML-iPSCs from three patients, capturing a wide variety of genetic aberrations. AML-iPSCs demonstrate pluripotency features with the ability to model AML through hematopoietic differentiation. The derived AML-iPSC model has further potential to use gene expression and chromatic availability signatures compared to isogenic controls to identify novel genetic and epigenetic targets in AML.

abstract: Thesis

abstract: Master of Science (MSc)

abstract: Leukemia is the cancer of the blood system, in which leukemic cells divide too quickly and fail to mature into functional blood cells. These cells overcrowd healthy blood cells and prevent their normal function. Acute myeloid leukemia (AML) is a subtype of leukemia where only 5-15% of patients over 60 achieve remission and the median survival for elderly patients is less than a year. Elderly patients succumb to the disease due to their inability to tolerate aggressive and non-selective treatments. The lack of specific treatments is in part, due to a wide variety of genomic mutations in AML leading to variable responses to standardized therapy. In addition, there are no therapies to exclusively eliminate leukemic but not healthy blood cells.  In the laboratory, many cancers are studied by using cell or animal models of the disease. Unfortunately, in the case of AML, these models are flawed as they capture less than half of genomic variations present in patients. When using patient samples directly it is often impossible to discern healthy from leukemic cells making it problematic to derive therapies specific to cancer cells. Reprogramming cancer cells into induced pluripotent stem cells (iPSCs) is a way to capture patient specific genetic mutations and physically separate healthy and mutated cells to be able to study them separately. This model has the potential to dissect variable patient mutations to identify which are root causes of the disease. It has been shown that AML is difficult to reprogram, and here we dissect reprogramming strategies used to the past to for the first time. We then demonstrate the most successful to date capture of three AML patients in an iPSC model and interrogate the model’s ability to capture and recapitulate AML disease.


title: Development of Multi-Model Ensembles for Climate Downscaling in Ontario, Canada

contributor:
Li, Zhong
Civil Engineering

abstract:
Climate change has widespread impacts on the environment, economy, and municipal planning. Thus, generating accurate, high resolution climate predictions could aid in the  assessment of the impacts of climate change on a local scale. Multi-model ensembles have been proven to improve the accuracy of climate prediction, and machine learning techniques are a promising tool for temperature downscaling. The thesis investigates machine learning and statistical methods in the development of multi-model ensembles for climate downscaling.
Firstly, three neural network algorithms are used to develop multi-model ensembles for daily mean temperature downscaling, including Multi-layer Perceptron (MLP), Time-lagged Feed-forward Neural Network (TLFN) and Nonlinear Auto-Regressive Network with exogenous inputs (NARX). The inputs and outputs are the simulated daily mean temperatures obtained from six Regional Climate Models (RCMs) collected from the North American Coordinated Regional Downscaling Experiment (NA-CORDEX) archive and observed daily mean temperatures collected from the Digital Archive of Canadian Climatological Data, respectively. A case study of Big Trout Lake in Ontario, Canada is carried out as a preliminary study to evaluate the performance of the proposed neural network models. The results show that the neural network based ensembles outperformed each of the individual regional climate models and generated predictions with smaller fluctuations.
Secondly, the thesis investigates and compares the applicability and performance of machine learning and statistical methods in developing multi-model ensembles for downscaling long-term daily temperature. The machine learning methods include Long Short-Term Memory (LSTM) networks and Support Vector Machine (SVM) and the statistical methods include arithmetic ensemble mean (EM) and Multiple Linear Regression (MLR). These ensembles share the same input and output variables with the preliminary study. The performance of the proposed machine learning and statistical ensembles are evaluated at twelve meteorological stations across Ontario, Canada. The results show that multi-model ensembles with machine learning or statistical techniques all performed well at downscaling daily temperature, and had similar performance with relatively high accuracy. This is the first attempt to apply advanced machine learning techniques and compare them with statistical methods in developing multi-model ensembles for downscaling in Canadian communities. The results provide a technical basis for applying statistical and machine learning methods to generate long-term high-resolution daily temperature projections. The generated climate projections will also provide useful information to support climate adaptation in Ontario.

abstract: Thesis

abstract: Master of Applied Science (MASc)


title: Corrosion Evaluation of Chromized Steel Utilized in Automotive Exhaust Applications

contributor:
Kish, Joey
Zurob, Hatem
Materials Science and Engineering

subject:
Corrosion
Chromized Steel
Automotive Exhaust System
Stainless Steel

abstract:
Experiments were conducted to determine the suitability of a chromized steel for use in automotive exhaust applications. Due to government regulations leading to higher temperatures and a more corrosive environment within the automotive exhaust system, Cr-lean alloys such as Type 409 no longer suffice. The high cost of increasing alloying elements to reduce the corrosion susceptibility of exhaust components has led to exhaust manufactures moving toward a sacrificially protected aluminized stainless steel (Type 409Al). Yet, costs remain high due to the stainless steel substrate. Arcanum Alloys have designed a process in which an IF steel coil is chromized using a Cr-rich slurry, creating a thin but corrosion resistant layer. This chromized layer drastically increases the corrosion resistance, without affecting the formability of the interstitial-free (IF) steel substrate and remaining cost-effective. The localized corrosion resistance of the chromized IF steel (XHOM) was measured against current generation ferritic stainless steels in a simulated interior (exhaust gas condensate) and exterior (NaCl (aq)) automotive exhaust environment.
Electrochemical polarization measurements along with atmospheric corrosion tests were conducted to characterize and compare the localized corrosion susceptibility of XHOM and benchmark ferritic stainless steels. The specific tests include the following:
I. Potentiodynamic polarization curves in NaCl (aq), measuring the corrosion potential (Ecorr), critical current density (icrit) and breakdown potential (Eb).
II. Double loop electrochemical potentiokinetic reactivation (DLEPR) testing measuring the ratio of the activation critical current density (ia) and the reactivation critical current density (ir).
III. Salt-fog testing (ASTM B117) (external) and exhaust gas condensate exposure testing (internal), measuring the mass loss, pitting density, maximum pit depth and corrosion rate.
Although Type 409 and Type 439 exhibited evidence of sensitization in the mill annealed condition, all materials exhibited a resistance to further sensitization during heat treatment, indicating sensitization will not occur during service.
   The electrochemical polarization curves in the NaCl (aq) resulted in XHOM yielding the highest breakdown potential, yet XHOM also exhibited the highest corrosion rate during the salt fog (ASTM B117) exposure. The latter is due to exposure of the XHOM cut edge where only the plan surface was exposed during the electrochemical polarization measurements. A galvanic couple exists between the chromized coating (cathode) and steel substrate (anode) leading to rapid corrosion of the substrate when exposed. When the cut edge of XHOM is masked, the corrosion rate drops drastically, performing comparably to the highly ferritic stainless steels. During the salt fog (ASTM B117) exposure, pitting of XHOM and Type 409 was caused by cut edge corrosion leading to corrosion product migrating down the panel surfaces and initiating under deposit pitting. A singular pit was observed on the XHOM surface, which led to delamination of the coating surrounding the pit, caused by the galvanic couple at the coating substrate/interface once the substrate was penetrated. The overall corrosion resistance ranking of the materials in the external environment incorporating corrosion rate and pit depth is as follows:  Type 436 ≈ XHOM Masked Edges ≈ Type 439 > Type 409Al > Type 409 > XHOM Edges Exposed. Strain was also found to have an effect on the localized corrosion susceptibility of XHOM in NaCl (aq), unlike Type 409, which exhibited no change. The influence of the drain hole manufacturing method (punching and drilling) on the corrosion susceptibility of XHOM and Type 409 was also measured. The punching method caused a smearing effect of the chromized coating, which served to partially cover and protect the cut edge. The main corrosion mechanism that occurred within the external environment is cut edge corrosion, which led to under deposit pitting.
   Heat treatment of samples prior to testing in the internal exhaust environment led to an intermetallic phase change within the aluminized coating on Type 409Al, drastically reducing the corrosion resistance of the material. An as-received aluminized Type 409 (Type 409Al-A) sample was tested in exhaust condensate exposure conditions to measure the difference in corrosion rate. XHOM with the cut edges exposed exhibited a corrosion rate comparable to Type 409 and heat treated aluminized Type 409, which is promising as XHOM already has an advantage in cost and formability. The overall corrosion resistance ranking of the materials exposed in the internal exhaust environment incorporating corrosion rate and pit depth is as follows: Type 409Al-A > Type 436 > Type 439 > Type 409 ≈ XHOM Edges Exposed ≈Type 409Al-H (heat-treated).

abstract: Thesis

abstract: Master of Applied Science (MASc)


title: Understanding musical emotion: Exploring the interaction between cues, training, and interpretation

contributor:
Schutz, Michael
Psychology

subject: music, emotion, perception, communication, interpretation, training

abstract:
Previous work on conveyed musical emotion has often focused on experimentally composed and manipulated music, or multi-lined music selected to express overt emotions. This highly controlled approach may overlook some aspects of the complex relationship between composers, performers, and listeners in transmitting emotional messages. My PhD research focuses on how listeners perceive emotion in music, specifically, how listeners interpret musical features such as timing, mode and pitch in complex musical stimuli. I also demonstrate how listeners with musical expertise use cues differently to perceive emotion and the effect of performer interpretation on this communication process.
	Throughout this dissertation I use a dimensional approach capturing perceived valence and arousal to assess complex musical stimuli. I adapted a technique used in other domains to music, affording an opportunity to explore nuanced relationships between cues and listener ratings of emotion. In Chapter 1 I show that musically untrained adults mainly use cues of timing and mode when rating emotional valence, mirroring previously reported. Additionally, I show that although pitch information emerges as a significant predictor of listener’s valence ratings, listeners use it less than cues such as timing and mode. Further, I demonstrate that neither mode nor pitch information help listeners rate perceived arousal. Finally, in Chapter 4, I show differences in performer interpretation mediate the strength of individual cues, as well as the distribution of emotional ratings across each album. In Chapter 3, I demonstrate that listeners with musical training use cues differently than untrained listeners, with more reliance on information communicated through mode when making judgements of emotional valence. Altogether these findings corroborate previous evidence suggesting timing and mode cues are of the greatest importance in conveying /perceiving emotion, this process is further mediated by individual differences in both pianist (interpretation) and listener (musical training)—underscoring the complex relationship between composer, performer, and audience.

abstract: Dissertation

abstract: Doctor of Philosophy (PhD)

abstract: Musical performers and composers express emotions through the selection and use of various musical features, or cues. Studies exploring how listeners perceive emotion in music have identified several cues important to this process—often using tightly controlled (and constrained) tone sequences crafted for experimental purposes. More work is needed to examine how listeners decode communicated emotion in unaltered passages created by renowned composers—the kind of music routinely performed and enjoyed by audiences for generations. Here in three sets of experiments I apply a novel stimulus set and analysis to determine the relative importance of three musical features. Additionally, I explore the role of the listener’s level of expertise as well as the importance of performers’ interpretative decisions. My work offers a new way to understand the relationship between musical features and emotional messages, helping to clarify one of music’s most mysterious and powerful capabilities.


title: DEVELOPMENT OF A MULTIPLEXED CONFOCAL FLUORESCENCE LIFETIME IMAGING MICROSCOPE FOR SCREENING APPLICATIONS

contributor:
Fang, Qiyin
Biomedical Engineering

subject:
Fluorescence Microscopy
Confocal Microsopy
Fluorescence Lifetime
Rapid Imaging
Drug Screening

abstract:
Protein-protein interactions are important for biological processes. Therefore, many small molecules target a specific protein or interaction in the cell to have biological consequence.   While we can measure some protein-protein interactions in a test tube, many proteins cannot be purified making it difficult to properly test that a drug is “on target”.   An alternative is to measure these interactions in live cells.  We express the proteins of interest fused to fluorophores allowing the use of fluorescence techniques.  Förster Resonance Energy Transfer (FRET) provides a molecular level ruler to measure the distance, within a few nanometers, between two proteins.  FRET indicates binding.   The gold standard for measuring FRET in live cells is by quantifying changes in fluorescence lifetime using Fluorescence lifetime imaging microscopy (FLIM). The change in fluorescence lifetime is inversely proportional to the ratio of bound to non-bound proteins. Tradition FLIM-FRET microscopy is too slow for screening applications.  Our aim was to develop a highly multiplexed confocal system for rapid FLIM-FRET acquisition.
We present the development of multiple prototypes for confocal multiplexing.  In this work, our final design includes 32×32 multiplexed excitation points which scan the sample using refractive window scanners. We coupled this excitation scheme to a 64×32 time-gated single-photon avalanche photodiode (SPAD) sparse array detector. This multiplexed setup allows the use of the sparse array with high frame rate and sub-nanosecond time-gating to achieve high throughput FLIM acquisition.  Using our multiplexed FLIM prototype we measured Bcl-2 family protein-protein interactions in live cells (310×310 μm FOV) with two-channel confocal FLIM in 1.5 s.  Protein binding affinities were estimated by measuring the changes in FRET as a function of acceptor to donor ratio.  The resulting speed of this system meets requirements for implementation in screening applications.

abstract: Thesis

abstract: Candidate in Philosophy

abstract: Inside a cell, proteins are the “workers” and they interact with each other, doing that work.  Many of these interactions are important for the cell to live.  Pharmaceutical companies may design drugs that can interfere with a specific interaction in order to cause an effect in the cell.  Scientists are interested in measuring these interactions and we can do this by “taking a picture” of the interaction using a specialized microscope.  One of the major issues with these microscopes is that it takes scientists a long time to collect pictures of these interactions.   This means only a few drugs can be tested in a day.  To speed up the drug discovery and testing we want to design faster microscopes that can test hundreds of drugs in a day.  In my thesis I contributed to building a state-of-the-art super fast microscope.  We made progress in steps, and by the third attempt we successfully measured interactions in cells in seconds!  Our new microscope is ~400x faster than current technologies. We hope that this research will be useful to speed up drug discovery in the future.


title: Investigating Behaviour of Elastomeric Bearings Considering Non-Standard Top and Bottom Boundary Rotations

contributor:
Becker, Tracy
Tait, Michael
Civil Engineering

subject:
Experimental
Earthquake
Elastomeric
Bearing
Isolation
Rotation
Natural Rubber
Boundary Rotation

abstract:
Seismic isolation, in which a flexible layer is used to separate a structure from the ground below, is a proven method for reducing earthquake demands that has been recently introduced into the 2015 Canadian building code. Typical installations of seismic isolation use rigid diaphragms to bound the end plates of the isolators, which is easily implemented in new build scenarios but requires extensive excavation and foundation work in retrofit applications. An alternative form of isolation involves placing the isolation plane on top of first floor columns, potentially resulting in flexible boundary conditions. There have been very few experimental programs that mimic these flexible boundary conditions.
	To address conditions that may be found in column-top isolation design schemes, such as flexible framing and lightly axially loaded corner bearings, an experimental program on a quarter-scale column-top isolation system was conducted. The goals of the investigation were to investigate how rotations of both top and bottom bearing end plates impact key design assumptions such as horizontal stiffness, rotational stiffness, and stability, and how these effects change with axial load.
	Experimental findings showed that flexible boundary conditions reduce horizontal stiffness based on the sum of rotation at the ends, regardless of the rotation of one bearing end plate with respect to the other. This decrease is dependent on axial load, with more axial load leading to a higher decrease in horizontal stiffness. The rotational stiffness significantly decreases with bearing shear strain and models that use linear, elastic rotational springs underrepresent rotations at the boundaries. Lastly, traditionally used design limits for stability can be used for bearings of moderate shape factor (S1 = 19.6 used in testing) bounded by flexible framing, but these theoretical limits can overestimate the experimental determined limits by nearly double for bearings of low shape factors (S1 = 7.9 used in testing).

abstract: Thesis

abstract: Master of Applied Science (MASc)

abstract: Seismic isolation, in which a flexible layer is used to separate a structure from the ground below, is a proven method for reducing earthquake demands that has been recently introduced into Canadian building code. Typical installations of seismic isolation use rigid diaphragms to bound the end plates of the isolators, which is more easily implemented in new build scenarios but requires extensive excavation and foundation work in retrofit applications. An alternative form of isolation involves placing the isolation plane on top of first floor columns, potentially resulting in flexible boundary conditions. To address this, an experimental program on a quarter-scale column-top isolation system was conducted to investigate how rotations of both top and bottom bearing end plates impact key design assumptions such as horizontal stiffness, rotational stiffness, and stability. This research can help to expand the number and types of buildings isolation can be applied to, creating more resilient communities.


title: Reinstated but downgraded: Mothers' experiences of post-maternity leave demotion and psychological contract violation

contributor:
Goutor, David
Labour Studies

subject:
mothers
psychological contract
maternity leave
demotion

abstract: While the transition back to work following maternity leave is a stage of a woman’s career that can have significant impact on the rest of her working life, this remains an under-researched topic. The current study examines mothers’ return to work experiences, with a specific focus on the downgrading to their jobs they encounter, perceived as demotions, which no previous study has pursued. Drawing from research investigating mothers’ psychological contracts and their turnover intentions, the current study examines the relationship between demotions, psychological contract violation and employment outcomes. Also of interest was whether psychological contract violation initiated a process of grieving, as mothers struggled to separate from their identities as valued employees. In-depth interviews were conducted with eight mothers. Mothers who perceived their restructured jobs as demotions experienced psychological contract violations in response, and also described emotions consistent with a process of grieving. However, not all mothers who experienced psychological contract breach or violation quit their jobs. Implications for working mothers and for future research are discussed.

abstract: Thesis

abstract: Master of Arts (MA)


title: The Brief Child and Family Intake and Outcomes System for Infants: Psychometric Characteristics

contributor:
Schmidt, Louis
Psychology

subject: infant mental health

abstract: Research has shown that early signs of behaviour problems can be identified in infancy and toddlerhood and, while some of these challenges may resolve over time, often they continue and place children at risk for later mental health problems. To identify infants with early signs of emotional-behavioural problems who may benefit from intervention, psychometrically strong infant mental health measures could be helpful.  Unfortunately, measures for assessing infant mental health often cannot be used to assess children under 12 months old or do not comprehensively address clinically-relevant mental health domains in infants.  The Brief Child and Family Outcome System for Infants (BCFOSI) is a questionnaire for parents of infants 8 to 17 months old with evidence on its reliability and factor structure and promising preliminary evidence on validity (Niccols et al., 2018). Stability and validity of the BCFIOSI were examined in a community sample of 50 infants at 8-, 14-, and 18-months. Total scale scores demonstrated moderate stability over 4, 6, and 10 months, rs =  0.48, 0.31, and 0.39, respectively, ps < 0.05. Criterion validity correlations with other measures of emotional-behavioural functioning (ASQ:SE, BITSEA, CBCL) were significant at 8, 14, and 18 months, rs = 0.36 to 0.61, ps < 0.05.  There were two significant concurrent validity correlations with measures of infant and maternal physiological regulation: 8-month BCFIOSI Total scores and infant vagal withdrawal, r = -0.35, and 8-month BCFIOSI Sleeping and maternal baseline RSA, r = 0.32, ps < 0.05. With regard to maternal behaviour, 8-month BCFIOSI Eating was correlated with observational measures of maternal sensitivity, non-hostility, and structuring, rs = -0.35, -0.44, and -0.28, respectively, ps < 0.05. Measures of parental stress and parenting attitudes also were correlated with 8-month BCFIOSI Total scores, rs = .029 to 0.48, ps < 0.05. Predictive validity was supported by significant longitudinal associations with the CBCL 4 and 10 months later, rs = 0.33 and 0.31, respectively, ps < 0.05. Findings provide additional evidence to support the use of the BCFIOSI with infants at potential risk for later mental health problems who may benefit from intervention.

abstract: Thesis

abstract: Master of Science (MSc)


title: Performance considerations in high-speed TDFA-band silicon photonic micro-ring resonator modulators

contributor:
Knights, Andrew
Engineering Physics

subject:
silicon photonics
mid-infrared
micro-ring resonator modulator
thulium doped fiber amplifier
high-speed

abstract:
The ever-increasing bandwidth requirements to support telecommunications infrastructure
necessitates large-scale fabrication of low-cost and scalable silicon photonic integrated circuits. Wavelength-division multiplexing (WDM) schemes are fundamentally limited in the number of channels supported in long-haul transmission by the erbium doped fiber amplifier (EDFA). To address this, researchers have turned focus toward the thulium doped fiber amplifier (TDFA), which provides 3× more bandwidth. This thesis describes the development of high-speed silicon-on-insulator (SOI) micro-ring resonator (MRR) modulators optimized for wavelengths in the TDFA band. Chapter 2 presents a theoretical performance comparison between MRR modulators designed for optimized use at EDFA and TDFA wavelengths. Chapter 3 presents an experimental study of optical loss mechanisms at extended wavelengths which suggests reduced waveguide scattering and enhanced divacancy defect absorption as well as larger bending and substrate leakage losses when compared with shorter wavelengths. An electronic variable optical attenuator is characterized in Chapter 4 to experimentally verify the predicted 1.7× TDFA-band free-carrier effect enhancement over EDFA-band wavelengths. The
first steady-state operation of an MMR modulator near a central wavelength of 1.97 µm is also demonstrated under the enhanced free-carrier effect. Chapter 5 demonstrates the first high-speed reverse bias operation of an MRR modulator with a measured bandwidth of 12.5 GHz, and an on-chip optical link consisting of a modulator followed by a defectmediated detector with open eye-diagrams up to data rates of 12.5 Gbps. Chapter 6 introduces an electrically-driven post-fabrication defect-assisted resonance trimming technique via local annealing for use in MRR devices. Chapter 7 presents a Monte Carlo simulation of resonance alignment in multi-MRR systems subjected to spatially-correlated wafer variation created through the Virtual Wafer Model process to predict thermal power consumption and power reduction through resonance trimming.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)


title: MULTI-LEVEL RISK MANAGEMENT OF  BUILDING SETTLEMENT INDUCED BY TUNNELLING  IN SOFT CLAY

contributor:
GUO, PEIJUN
Civil Engineering

subject: soft clay

subject: tunnelling-induced settlement

subject: probabilistic risk assessment (PRA)

subject: Rt risk tool

abstract: Tunnelling in urban areas is one of the most challenging engineering activities, as it has relatively high “risk” due to various uncertainties and the intensity of the possible consequences. Numerous studies have been conducted to address the tunnelling risk, by mainly focusing on the “identification” of the causes and how to control or mitigate the risks. However, limited work has been done on how to quantify the risk by considering the multi-level uncertainties encountered in different phases of the project. The primary objective of this work is to develop a multi-scale risk management (RM) framework to address and quantify the risk of ground surface settlement, induced by tunnelling, in soft clay in urbanized areas. The specific focus is placed on quantifying the risk of tunnel-induced settlement for existing buildings, by taking into account multiple uncertainty levels (e.g. uncertainties of parameters, uncertainties of models, etc.). The framework addresses the tunnel-induced settlement risk, both during the construction of the tunnel as well as after its completion, for buildings with shallow and deep foundations. It offers different classes of assessment to quantify the risk, according to the structure’s current condition and the corresponding limit-state function, that is designated to each class. The RM framework is aligned with ISO 31000 risk management act, consisting of “risk identification”, “risk analysis” and “risk evaluation”. Risk identification includes studies on tunnelling technical reports, field observations, etc., in order to identify the causes of short-term and long-term tunnelling-induced settlement. The risk analysis involves a series of fault tree, event tree and consequence tree analyses to estimate the likelihood of the ground subsidence and subsequent events. For risk evaluation, different probabilistic methods (e.g. first-order reliability method, second-order reliability method and Monte Carlo sampling) are utilized to estimate the risk of surface buildings with shallow and deep foundations. The framework has been implemented in an example problem, to demonstrate the procedure and to address the main influential parameters in each class of assessment using the alpha importance measure. Rt risk tool has been utilized to perform reliability calculations and FORM has been used as the primary method due to its valuable balance between computational cost and accuracy. The outcomes of this RM framework are risk registers and colour-coded risk maps including the exceedance probability of a predefined settlement threshold for each building in the affected area. This framework receives technical data and provides risk-based information for higher-level managers and decision-makers to prioritize their actions and allocate their resources in the most effective way.

abstract: Thesis

abstract: Master of Applied Science (MASc)

abstract: The aim of this study is to provide a multi-level risk management (RM) framework to address and quantify the risk of surface building settlement induced by tunnelling in soft clay in urbanized areas. The focused is placed on quantifying the risk of tunnel-induced settlement of existing buildings, by taking into account multiple uncertainty levels. The framework addresses the tunnel-induced settlement risk, both during the construction of the tunnel as well as after its completion, for buildings with shallow and deep foundations. It offers different classes of assessment to quantify the risk, according to the structure’s current condition and with respect to specific limit-state functions designated for each class. The proposed framework was implemented in an example to demonstrate the procedure and outcomes.


title: Climatic Controls on Phenology and Carbon Dynamics in Temperate Deciduous and Coniferous Forests

title: Carbon Dynamics in Temperate Forests

contributor:
Arain, M. Altaf
Geography and Earth Sciences

subject:
Eddy Covariance
Biometeorology
Carbon Exchange
Ecosystem Productivity
Climate Change
Temperate Forests

abstract:
Forests ecosystems cover about 30% of the Earth’s land surface, corresponding to an area of roughly 42 million km2 globally. Forests play an important role in the global carbon cycle by exchanging carbon dioxide (CO2) with the atmosphere. Annually, forests act to effectively sequester large amounts of anthropogenically-emitted CO2 from the atmosphere through photosynthetic processes. Through the unparalleled increase of CO2 emissions over the past century and the subsequent climatic inconsistencies due to global climate change, the carbon sink-capacity of the world’s forests remains uncertain. Furthermore, since increasing temperatures have been shown to extend the vegetative growing season in forests, phenological responses to this change are of particular interest. In an effort to effectively assess the future carbon sequestration potential of forests, a better understanding of the climatic controls on phenology, and its influence on carbon processes, is needed.

The eddy covariance (EC) technique is a stand-level, in-situ, method used widely to assess the net CO2 exchange across the canopy-atmosphere interface. Together with meteorological data, the sequestration of CO2 and the subsequent ecosystem productivity can be quantified over various time scales (half-hours to decades). This dissertation reports results from field observations of EC measured fluxes that were used to study the climatic impacts on forest phenology and the resulting carbon dynamics in southern Ontario, Canada. The study sites, part of the Turkey Point Observatory, consisted of two similarly-aged, temperate, North American forests growing under similar climatic and edaphic conditions: the 80-year old (in 2019) white pine plantation (coniferous evergreen) and 90+ year-old, naturally-regenerated, white oak (deciduous broadleaf) forest. These forests were studied from 2012 to 2017, using the EC technique, digital phenological cameras, and remote-sensing measurements.

At the deciduous broadleaf forest, mid-summer (July and August) meteorological conditions were the key period in determining the annual carbon sink-strength of the site, acting to regulate the interannual variability in carbon uptake. The forest experienced higher net ecosystem productivity (+NEP; carbon sink) when soil temperatures ranged from 15 to 20°C and vapor pressure deficit was 0.7 and 1.2 kPa. From 2012 to 2016, the forest remained a net annual sink, with mean NEP of 206 ± 92 g C m-2 yr-1, similar to that of other North American deciduous forests.

Spring and autumn phenological transition dates were calculated for each year (2012 to 2017) from measured EC data and digital camera greenness indices. The timing of spring and autumn transition dates were impacted by seasonal changes in air temperature and other meteorological variables. Contrary to past studies, an earlier growing season start did not equate to increased annual carbon uptake. In autumn, a later end to the deciduous forest growing season negatively impacted the net carbon uptake of the forest, as ecosystem respiration (RE) outweighed the gains of photosynthesis. The digital camera indices failed to capture the peak dates of photosynthesis, but accurately measured the spring and autumn transition dates, which may be useful in future remote sensing applications.

A comparison of the two forests from 2012 to 2017 found the coniferous forest to have higher but more variable annual NEP (218 ± 109 g C m-2 yr-1) compared to that of the deciduous broadleaf forest (200 ± 83 g C m-2 yr-1). Similarly, the mean annual evapotranspiration (ET) was higher (442 ± 33 mm yr-1) at the coniferous forest compared to that of the broadleaf forest (388 ± 34 mm yr-1). The greatest difference between years resulted from the response to heat and drought. During drought years, deciduous carbon and water fluxes were less sensitive to changes in temperature or water availability compared to the evergreen forest.

Carotenoid sensitive vegetative indices and the red-edge chlorophyll index were shown to effectively capture seasonal changes in photosynthesis phenology within both forests via proximal remote sensing measurements during the 2016 growing season. Satellite vegetative indices were highly correlated to EC photosynthesis, but significant interannual variability resulted from either meteorological inputs or the heterogeneous landscapes of the agriculturally-dominated study area.

This dissertation improved our understanding of the dynamics of carbon exchange within the northeastern North American deciduous forest ecozone, through the examination of climatic variability and its impact on carbon and phenology. This dissertation also contributed to efforts being made to better evaluate the impact of species composition on carbon dynamics in geographically similar forests. Moreover, the use of the digital phenological camera observations and remote sensing techniques to complement and better understand the fluxes observed with the EC method was innovative and may help other researchers in future studies.

abstract: Dissertation

abstract: Doctor of Philosophy (PhD)


title: Language Identification on Short Textual Data

contributor:
Chen, Jun
Electrical and Computer Engineering

subject:
Natural Language Processing
Language identification
Textual data

abstract: Language identification is the task of automatically detecting the languages(s) written in a text or a document given, and is also the very first step of further natural language processing tasks. This task has been well-studied over decades in the past, however, most of the works have focused on long texts rather than the short that is proved to be more challenging due to the insufficiency of syntactic and semantic information. In this work, we present approaches to this problem based on deep learning techniques, traditional methods and their combination. The proposed ensemble model, composed of a learning based method and a dictionary based method, achieves 89.6% accuracy on our new generated gold test set, surpassing Google Translate API by 3.7% and an industry leading tool Langid.py by 26.1%.

abstract: Thesis

abstract: Master of Applied Science (MASc)


title: MY FLAG, MY IDENTITY: FRAGMENTED IDENTITIES IN IRANIAN DIASPORA

contributor:
Satzewich, Victor
Sociology

subject: Diaspora, Iranian diaspora, Identity, Islamophobia, Orientalization

abstract:
A diaspora’s flag is the symbolic representation of that community. The Iranian flag, however, is a contested symbol among the Iranian diasporic community. As this research shows, the Iranian diaspora exhibits its cultural, political, and religious identities through three different Iranian flags. Through qualitative research, entailing months of participant observation and a series of semi-structured interviews, I investigate the underlying reasons for this flag disagreement. Through this research, I argue that an Iranian diaspora’s pre-migration communal history and post-migration environmental factors influence its establishment and maintenance in the host nation.
In this study, I revisit the diaspora literature to argue for the complexity of the concept of diaspora. I demonstrate how a diaspora assists the community in restructuring its lost cultural identity and establishing a social space to belong, in the time of the spatial and cultural dislocation. The Iranian diaspora’s flag selection is a symbolic representation of communal establishment and identity formation for the community. The Iranian flag debate indicates a communal divide; it is also an instrument to set social boundaries to develop a community under the symbolic representation of the ancestral homeland.
Furthermore, this research explores how the Iranian diaspora uses the Iranian flag as a proxy to indicate socio-communal expectations and intersectional social hierarchies that already exist among the Iranian community. When discussing the flag’s symbolic significance, the respondents relate the flag with three recurring themes of religion, gender, and sexuality. The association of the Iranian flag with these three social factors indicates the communal dynamics of the Iranian diaspora. These communal dynamics establish certain norms and values, but they also redefine each flag based on its socio-political history. The attached meaning to each flag consequently causes tension and disagreement among the Iranian community, which is not solely political.

abstract: Dissertation

abstract: Doctor of Philosophy (PhD)

abstract: The Iranian diaspora is a young and growing community that came into existence after the Islamic revolution of 1979. In this diaspora, there are three different flags on display, and each flag represents a socio-political ideology. The symbolic application of the flag facilitates this research in exploring the social interaction among the Iranian diaspora residing in the Greater Toronto Area and York Region. Through the examination of the flag debates, I investigate the significance of community building in the new host nation. I critically analyze the communal divide existing among the Iranian community and the flag debate that is a symbolic representation of Iranian group dynamics. The discussion of the flag for many starts a conversation about community development and socio-communal hierarchy. While the different versions of the Iranian flags bring the diasporic communities together, they also indicate social segregation caused by religious, gender, and sexual hierarchies existing among the Iranian diaspora.


title: Maximizing Energy Recovery in Thermoelectric Generator Waste Heat Recovery Systems for Automotive Applications

contributor:
Cotton, James S.
Emadi, Ali
Mechanical Engineering

abstract:
Thermoelectric generators (TEGs) are solid state devices with the ability to convert heat directly to electrical energy. According to the Seebeck effect, if the junctions of a thermoelectric couple are held at a temperature difference, an electromotive force is induced which translates to power generation when an electrical load is connected. Due to their direct energy conversion, small volume, no use of working fluids, and reliability, thermoelectric generators have been investigated for various waste heat recovery applications. Additionally, TEGs can operate in transient environments without drawbacks such as turbo-lag (experienced by other waste heat recovery technologies), which has made TEGs an exceptional candidate for recovery in dynamic waste heat sources such as the exhaust system of a vehicle.
Greenhouse gas (GHG) emissions generated by the transportation sector account for 29% of global emissions, therefore exploring solutions to mitigate this problem is of most importance. Since light duty vehicles and freight trucks make up 78% of the transportation sector, it is crucial to investigate methods by which the efficiency of vehicles can be increased, thereby reducing losses. Although vehicle electrification will make an impact in reducing emissions, it is expected that over 40% of the future vehicle fleet will continue to use an internal combustion engine (ICE). Approximately 40-60% of the total fuel energy is lost through the exhaust system of an ICE vehicle, therefore, waste heat recovery methods should be investigated, with TEGs having been proven to be a viable technology.
Waste heat recovery (WHR) through the use of TEGs in automotive applications has been investigated since the late 90’s. However, the focus of the research has been on optimizing the TEG module for fixed temperature differences to maximize the power output of the module. This steady-state optimization approach has been applied when investigating the power output from a dynamic waste heat environment such as the vehicle exhaust system. When comparing the performance of TEG WHR systems in vehicles, the current metric is maximum power output. TEG WHR systems both modeled and experimentally tested, have been evaluated for the most part at maximum engine load which is not indicative of real driving scenarios. The few studies which have tested the system during real operating conditions such as a vehicle drive cycle, have experimentally achieved lower power than that produced at steady-state.
To further investigate the cause of this degradation in power during transient operation, this thesis developed a transient TEG WHR system model that considers heat capacity in all components. The model was validated at both steady-state and transient operating conditions. The transient model, coupled with a vehicle model that can predict the exhaust temperatures and mass flow rates for various drive cycles, was used to investigate the total energy produced by the system. By investigating the effect that system size has on power generation, it was found that an optimal system size exists since the additional TEG modules in the system degrade the power performance due to heat transfer through the heat exchanger bases. Therefore, the maximum power point does not coincide with the maximum energy design point. In addition to the development of a TEG WHR system design methodology through the use of the developed models, a maximum power point tracking (MPPT) method was proposed that can achieve a tracking efficiency of 98%, validated through transient experiments. The proposed method can be implemented in current MPPT configurations without the need of additional sensors.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)


title: Application of Frame Selection For Binary Video Classification

abstract:
This thesis presents frame selection based on genetic algorithm and Euclidean distance and its exploitation on binary video classification. The frame selection implementation provides a fast enhancement of classification results.
Parallel frame selection methods are put up in comparison and a series of performance enhancement models are proposed to scrutinize the relationship with frame selection and binary video classification.
Other approaches might also be valid to be exploited in the frame selection baseline in order to improve classification results. We could learn semantic meanings with the assistance of natural language processing, combine audio with pixel-level information to form a fusion model, or directly manage learning methods on video level.

abstract: Thesis

abstract: Master of Applied Science (MASc)


title: The Genetic Predisposition of Paralytic Poliomyelitis Using Genome-Wide Association Studies

contributor:
Loeb, Mark
Health Research Methodology

subject:
Poliomyelitis
Genome-wide association studies (GWAS)
Case-control
Logistic regression

abstract:
Poliomyelitis is a foremost cause of paralysis among preventable diseases among children and adolescents globally. It is caused by persistent infection with poliovirus (PV). The PV infection does not always cause paralysis. A lack of immunization always increases the risk of paralytic polio. Genetic factors also been shown to affect the risk of developing the disease.
The aim of this thesis is to investigate whether there are any genetic associations to paralytic poliomyelitis. This is based on a model for understanding its nature as a complex disease, where many genes are involved in contributing to the disease state. This is a population-based case-control study to identify genetic loci that influence disease risk.
The study examined the association of genetic variation in single nucleotide polymorphisms (SNPs) across the genome with paralytic poliomyelitis susceptibility in the United States and Canadian survivors of poliomyelitis population, using a genome-wide association study (GWAS) approach. No association was observed. Loci that have been previously implicated were not found to affect the susceptibility to poliomyelitis in this study.
The thesis consists of four chapters. Chapter 1 describes the epidemiology, pathogenesis and management of poliomyelitis. Chapter 2 gives an overview of the genomics of infectious diseases in general. Chapter 3 introduces the study population and presents the genome-wide analysis and associations with logistic regression to identify loci explore genes that might be associated with paralytic poliomyelitis and presents results. Chapter 4 discusses the implications of the results and explains future directions.

abstract: Thesis

abstract: Master of Science (MSc)


title: Voices From The Fault Line - Being Muslim in Canada

subject: Migration, integration, marginalization, terrorism, media discourse, stigma, refugees, refugee youth, social problems, Islamophobia, Muslim, acculturation, racism, anti-Black racism, microaggressions, hate crimes,

subject: social marginalization; spiritual marginalization; spiritual homelessness;intentional community; third spaces; marginality facilitator

abstract: Previous literature, although helpful in demonstrating the insidious nature and effects of Islamophobia on Muslims, does not underscore the varying forms and intensities of Islamophobia that a diverse range of Muslims in the West face and the powerful ways in which race and socio-economic class factor into their experiences, coping mechanisms, and stigma responses. This dissertation contributes to the literature on Muslims in The West in three ways: (1) offering a qualitative approach to understanding the ways in which Islamophobia is perpetuated through media discourse and coinciding political legislation, and is experienced differently by a diverse range of Muslims in Canada, (2) adding the concepts of spiritual marginalization, spiritual homelessness, and social status optimization to the analytic vocabulary on integration and articulating their relationship with identity, and (3) making a connection between race and social class and the response to Islamophobia and articulating their relationship with human agency. In chapter one, I provide an in-depth literature review on Islamophobia in the West. In chapter two, I present the results of a discourse analysis study that highlights the structural dimensions of Islamophobia through media representations and framing of incidences involving Muslim vs. non-Muslim perpetrators of violence. In chapter three, I present the results of a study that showcases group level experiences of racism amongst a relatively powerless group of Muslim refugee youth in Hamilton Ontario and St. John’s Newfoundland and Labrador. In chapter four, I provide a contrasting response to stigma by reporting on the experiences and mobilization of a socioeconomically privileged group of first, second and third generation Muslims in Edmonton. Finally, I summarize the conceptual findings of each paper, review and discuss the general theoretical and conceptual contributions of the dissertation to existing literature, and provide suggestions on future directions for studying Islamophobia and Muslim integration in The West.

abstract: Dissertation

abstract: Doctor of Philosophy (PhD)

abstract: This dissertation analyses the varying forms and intensities of Islamophobia that a diverse range of Muslims in Canada face and the powerful ways in which race and socio-economic class factor into their experiences, coping mechanisms, and stigma responses. The thesis explores three themes: 1) how Islamophobia may be structurally maintained and propagated through media discourse and coinciding political legislation, 2) how Islamophobia and anti-Muslim hate is experienced differently by different groups of Muslims in Canada, and (3) how there may be a connection between race and social class in individual responses to Islamophobia. By adding the concepts of spiritual marginalization, spiritual homelessness, and social status optimization to the analytic vocabulary, this work is a unique contribution to existing literature, and to our understanding of the differing lived experiences of being Muslim in the West and the varying ways in which Islamophobia informs the day to day lives of Muslim Canadians.


title: Interactions of NEU1 with ASGR and LDLR

contributor:
Igdoura, Suleiman
Biology

subject: Atherosclerosis, Low-density lipoprotein receptor, Asialoglycoprotein receptor, Sialidase

abstract: Development of atherosclerosis, the hardening of the arteries, is dependent on levels of serum cholesterol, which is regulated by the liver via LDL receptors (LDLR). The expression and internalization of LDL receptors depend on several proteins including PCSK9. In fact, previous studies in our laboratory have shown that NEU1 down regulation leads to LDLR hypersialylation which results in its stabilization via reduced interactions with PCSK9. New evidence suggests that NEU1 which de-sialylates LDLR, may affect the ability of another hepatic receptor, the asialoglycoprotein receptor (ASGR), which is comprised of ASGR1 and ASGR2, to interact with LDLR potentially causing its internalization and therefore reduced ability to take up LDL. We investigated how sialidase plays a role in the interaction of ASGR with LDLR. Knockdown and overexpression experiments suggest that NEU1 allows stabilization of LDLR at the cell membrane via ASGR interactions. Treatment of HepG2 cells with monensin which inhibits recycling from the early endosome, unveiled a new truncated ASGR1 isoform potentially lacking its lectin motif. This may be a novel regulatory step in ASGR biosynthesis that warrants further studies. Lysosomal inhibition with chloroquine resulted in concurrent accumulations of NEU1, LDLR and ASGR1, further suggesting these proteins are biosynthetically connected. Our studies revealed a novel isoform of ASGR1 in membrane fractions of HepG2 cell lysates that can associate with NEU1 and LDLR. The impact of NEU1 and ASGR1 on the function and stability of LDLR might lead to new clues for lowering serum cholesterol and reducing atherosclerosis.

abstract: Thesis

abstract: Master of Science (MSc)


title: Examining The Predictability of Genetic Background Effects in The Drosophila Wing

contributor:
Dworkin, Ian
Biology

subject:
Genetics
Drosophila
Genetic Background Effects
Quantitative Genetics

abstract: Background dependence is a ubiquitous attribute of eukaryotic gene systems that modulates the phenotypic effects of a mutant allele due to segregating genetic variation among different wildtype strains. Despite the wealth of literature demonstrating the presence of genetic background effects, very little is known about how they functionally or mechanistically contribute to the relationship between genetic variation and phenotypic expression. It has been postulated that background dependent effects may be highly specific to the activity of individual alleles or genes. A recent examination of mutant alleles in two interacting genes in the Drosophila wing network demonstrated the magnitude of phenotypic effect of a mutant allele may predict it’s sensitivity to the genetic background. To further understand this, I examined the background dependence of many alleles for genes across the regulatory network of Drosophila wing development in many inbred strains. Our goal was to understand whether effects of the genetic background are an attribute of individual alleles, alleles of the same gene, or genes with similar phenotypes or developmental roles. Our analysis suggests that background dependence is highly positively correlated among alleles of the same gene, especially between alleles with similar magnitudes of phenotypic effect. Similarly, the background dependence of genes within the same regulatory network were also positively correlated. Alleles from different genes, but of the same magnitude of phenotypic effect, generally demonstrated the highest degree of intergenic correlation. However, the background dependence of mutant alleles were generally not well correlated with the wildtype allele. Interestingly, we also found no recovery of any lethal alleles, despite thousands of individuals screened and evident suppression of mutant effects in some strains. We also analyzed the magnitude of intra-line variance in among a subset of our genes. This demonstrated a strong positive relationship between the magnitude of intra-line variation and the severity of phenotypic effects, regardless of the identity of the mutant allele. However, we show no correlation between intra-line variability in the wildtype and the magnitude of perturbation for a given mutant allele. To confirm the quantitative estimates of mean wing size accurately reflected subtle perturbations to wing tissue, we conducted a semi-quantitative analysis and compared it to our quantitative estimates. We demonstrate a high degree of correlation between the quantitative and semi-quantitative approaches, indicating semi-quantitative analysis is a useful way to capture subtle phenotypic effects. In addition, we repeated the quantitative analysis with a subset of the genes and inbred strains from the original data. Importantly, results of the repeated study largely recapitulate our original results.

abstract: Thesis

abstract: Master of Biological Science (MBioSci)


title: The genomic architecture of sex-biased gene expression in Xenopus borealis

contributor:
Evans, Ben
Biology

subject:
transcriptomic
RNAseq
evolution
frog
xenopus borealis
sex chromosome

abstract: Most vertebrates have separate sexes, and sex-specific traits that are regulated by genes with sex-biased expression patterns. In many species with genetic sex determination system, genetic recombination is suppressed in genomic regions linked to the master regulator of sex determination – the gene or set of linked loci that orchestrate sexual differentiation. Natural selection may favour alleles with sex-specific effects - including those with sexually antagonistic (SA) fitness effects (e.g., beneficial to females but harmful to males) – to become fixed in or be translocated to these non-recombining regions of sex chromosomes, because sex-specific or sex-biased modes of inheritance can resolve genomic conflict associated with SA. Sexually antagonism may also be resolve by sex-biased gene expression, and in theory these two mechanism (sex-linkage and sex-biased gene expression) could operate synergistically. However, there are relatively few empirical studies that test whether genes with sex biased expression patterns are indeed more abundant on sex chromosomes – and especially on newly evolved sex chromosomes. We explored this question with an African frog species Xenopus borealis, whose sex chromosome evolved within the last 25 million years (my) and have a large (~50Mbp) region of suppressed recombination, making it a young sex chromosome system compared to many other intensively studied systems, such as the sex chromosomes of mammals. We tested the possibility that a higher proportion of genes with sex-biased expression would be located on the sex-linked region of the sex chromosome of this species. By examining gene expression in adult liver and gonad and also tadpole gonad/mesenephros at two developmental stages, we found that the sex-linked region of these sex chromosome do have a higher proportion of sex biased genes compared to the non-sex-linked region of the same sex chromosomes, compared to (i) a homeologous genomic region in the tetraploid genome of X. borealis, and also (ii) the autosomes of this species. We did not observe the same pattern in a closely related frog species, Xenopus laevis, which has sex chromosome that are not homologous to those of X. borealis and, unlike X. borealis, lacks a large region of suppressed recombination on its sex chromosome. Using Brownian Motion model, we found as well that expression divergence evolution of genes in the sex-linked region of X. borealis is faster compared to its non-sex-linked homeologs (within X. borealis), and also compared to orthologous regions that are also non-sex-linked. One possible explanation for these observations is that natural selection favoured an expansion of recombination suppression (via unknown mechanisms) on chromosome such that polymorphic regulatory regions became linked (or unlinked) to the sex determining locus in such a way to resolve SA. Alternatively, it is possible that these sex-biased expression pattern evolved rapidly after recombination suppression.

abstract: Thesis

abstract: Master of Science (MSc)

abstract: Sexual selection favours the evolution of distinctive traits in each sex in order to optimize the reproductive success of each one. However, because most of the genome is shared between the sexes, sexual selection may result in genomic conflict when mutations are beneficial to one sex but harmful to the other; this conflict is known as sexual antagonism. Genomic conflict associated with alleles with sexually antagonistic (SA) fitness effects can be resolved via the origin of sex-biased expression patterns and this may be catalyzed by genetic linkage to a sex-determining locus on a sex chromosome. Consequently, one might predict there to be an enrichment of genes with sex-biased expression patterns on the sex chromosome as compared to the autosomes. We tested this expectation in an African frog species Xenopus borealis, which has a relatively young sex chromosomes and a large region of recombination suppression on the female-specific W-chromosome. We found enrichment of sex-biased genes on the nonrecombining region of the sex chromosomes of this species in adult liver and gonad tissue and also tadpole mesenephros/gonads at two developmental stages. Additionally, we found that expression divergence of genes in the non-recombining region have a faster rate of evolution as compared to the rate of expression divergence of genes in other genomic regions. One possible explanation for these observations is that natural selection favours an expansion of recombination suppression (via unknown mechanisms) on sex chromosome such that polymorphic regulatory region become linked (or unlinked) to the sex determining locus in such a way as to resolve SA.


title: Comparative Study of Population Analysis Methods With Quasi Atomic-Orbitals

contributor:
Ayers, Paul W.
Chemistry

abstract:
Atom is not an observable of the molecular wavefunction, in quantum chemistry there are myriad ways of defining an atom in a molecule. Partitioning a molecule’s electrons between its atomic constituents (population analysis) remains a challenge.
A popular approach is based on Mulliken’s overlap-based population analysis, which exploits the fact that molecular orbitals can be expressed as linear combinations of user-defined functions: atomic orbitals. In turn, this creates a dependency on the selection of the predetermined atomic orbitals that are used to expand the molecular orbitals. Chemically intuitive atomic orbitals like Minimal Atomic Orbitals (minAO) produces chemically intuitive atomic charges but a non-accurate wave function. Accurate wave functions can be obtained from large atomic basis sets like def2-QZVPd at the cost of chemically unintuitive atomic charges. With this problem in sight, Quasi-Atomic Orbitals (QAO) are constructed from the accurate wave function to resemble the minAO and maximally span the molecular orbital space. The key idea is Mulliken population analysis can be carried out for wave functions with the chemical intuitive power of minAO, without sacrificing the wave function’s accuracy by using QAO. To ensure that overlaps of QAO are divided between different atoms without bias. Zero-Bond Dipole (ZBD) orthogonalization is proposed as a novel way to orthogonalize QAO.
	Common population analysis from literature: Charge Model 5 (CM5), QH, Hu-Lu-Yang (ESP), Mulliken, NPA atomic charges will be compared to QAO (Mulliken with QAO) and ZBD-QAO (Mulliken after ZBD orthogonalization of QAO) and tested for mathematical accuracy and expected chemical trends.

abstract: Thesis

abstract: Master of Science (MSc)


title: The Rab5 GTPase is required for lumen formation in the embryonic Drosophila heart

contributor:
Jacobs, J. Roger
Biology

subject:
tubulogenesis
Drosophila heart formation
endocytosis
Rab GTPases

abstract: Tube formation, or tubulogenesis, is an elaborate form of epithelial morphogenesis that includes processes such as cell migration and cell shape changes. The embryonic Drosophila heart, or dorsal vessel, is an excellent model of tubulogenesis and more specifically the signaling mechanisms required for cell migration and lumen formation. Similar to vertebrate heart formation, Drosophila heart tubulogenesis begins with the collective migration of cardioblasts that meet at the midline and adhere at specialised junctions, enclosing a lumen between them. Roundabout, and its ligand Slit,  are required to restrict cell-to-cell adhesions to the junctional domains of contralateral cardioblasts, as well as maintain the integrity of the lumen. The localisation patterns of Robo, and other luminal cell surface receptors important for lumen formation are significantly modified throughout heart formation. Initial receptor expression is broadly distributed over the cardioblast surface. Receptors are then relocalised to specific cell surface domains by late embryonic development. The mechanisms by which Robo and other cell surface receptors are localised have yet to be determined. Endocytosis is a promising mechanism by which cell surface receptors are targeted and trafficked to cell surface domains. Specifically, vesicular trafficking proteins, such as Rab GTPases, are molecular switches that regulate endocytic events. Here, we investigated the roles of Rab5, Rab11, and Sec6 during heart formation. Of these, only Rab5, a regulator of the early endosome, was required for lumen formation. Particularly, gain of function, loss of function, and overexpression of rab5 resulted in reduced lumen phenotype, characterised by lumen pockets rather than a continuous lumen along the anterior-posterior axis. Perturbed Rab5 function also resulted in the mislocalisation of Robo at the basal domain. Live imaging showed that expression of rab5 dominant negative, constitutively active, and overexpression constructs did not perturb apical membrane motility of migrating cardioblasts in the developing heart.

abstract: Thesis

abstract: Master of Science (MSc)


title: THE CONSISTENCY IN USING HEALTH UTILITIES BETWEEN COST-UTILITY ANALYSES IN ONCOLOGY AND REFERRED ORIGINAL HEALTH UTILITY STUDIES: A REGISTRY-BASED REVIEW

contributor:
Xie, Feng
Health Research Methodology

abstract:
Background: Cancer is a big threat to human health and imposes a heavy financial burden on health care systems worldwide. Cost-utility analyses (CUAs) have been widely used to measure cost-effectiveness of new cancer treatments. In a CUA, health utilities (HUs) are used to calculate quality-adjusted life years (QALYs) and thus play an important role in determining cost-effectiveness results.

Methods: Oncology CUAs that were included in the Cost-Effectiveness Analysis (CEA) Registry of the Center for the Evaluation of Value and Risk in Health (CEVR), published in English through 2016 and reported HUs and QALYs were identified and included in the study. Data were collected from the oncology CUAs and referenced original HU studies. The consistency of HUs were assessed by comparing both health state descriptions and utility values between the oncology CUAs and corresponding original HU studies.

Results: In total, 912 out of 1062 CUAs that investigated cancer diseases from the CEVR CEA Registry and 5583 HUs used in them were included in the analysis. 1353 HUs (24.2%) were measured along with the CUAs (defined as primary data) and 4230 HUs (75.8%) were derived from other sources (defined as secondary data). Out of the 3360 HUs for which the original studies were identified and compared with the CUAs, 1348 (40.1%) had the same health state descriptions and utility values, 633 (18.9%) differed only in value, 390 (11.6%) differed only in description, and 989 (29.4%) differed in both description and value. Among the 2012 HUs had either or both descriptions and utility values different from original HU studies, 377 (18.7%) of them were used without explanation, and 143 (7.1%) were derived from different diseases.

Conclusions: Our study found there were discrepancies in using published health utilities in oncology CUAs. Consistent use of health utilities needs to be improved.

abstract: Thesis

abstract: Master of Science (MSc)


title: Refugee and Forced Migration: The Concept of Resilience A Scoping Review

contributor:
Baumann, Andrea
Global Health

subject:
Resilience
Refugee
Forced migration
Displacement
Scoping review
Global Health

abstract:
Background: Since the 1980s, there has been a growing interest in research to focus on positive mental health instead of narrowing attention toward risk factors and to foster resilience instead of treating trauma. There is substantial empirical evidence that despite being exposed to the same risk; individuals react differently to the same stimuli. The ability of some people to successfully cope and adapt despite adversity is what constitutes resilience. In the context of forced migration, resilience research examines the elements that ameliorate wellbeing and positive adjustment rather than focusing on the pathological consequences of trauma. However, little is known about how the construct of resilience is conceptualized within the field of forced migration research.  This research aims to critically appraise and map the existing literature on resilience in the forced migration population, and to analyze how the concept of resilience is defined, operationalized, and applied in refugee research.
Methods: Arksey and O’Malley scoping review framework was followed to search 5 online databases. Numerical and thematic analysis were both conducted to examine the breadth of the literature and to chart the relevant data.
Results: A total of 20 studies were selected for the scoping review. The findings included a description of the literature regarding geographic distribution, recruited methods, and targeted populations. In addition, the results investigated definitions of resilience, measures used to operationalize resilience, the relationship between resilience and mental health illnesses, internal and external protective factors contributing to fostering resilience processes, and resilience across cultures and languages.
Conclusion: There is an increase in interest to understand the concept of resilience through synthesizing both qualitative and quantitative data. However, longitude and evaluation studies remain the exception. Further research is needed to validate resilience instruments across cultures and languages. The interactions between mental health illnesses and resilience should be better understood in the context of forced migration as well.

abstract: Thesis

abstract: Master of Health Sciences (MSc)


title: An investigation of potential relationships between septic tank microbial communities and system design and performance

contributor:
Schellhorn, Herb
Biology

subject:
Septic tank
Anaerobic digester
Microbial ecology
Second-generation sequencing
16S sequencing
Wastewater treatment

abstract: Septic tanks are utilized by many households across North America for wastewater treatment. Despite the economic and environmental importance of septic tanks, there has been limited innovation in septic tank design and research on the microbial communities responsible for wastewater treatment within these systems. InnerTube systems are septic tanks that employ a novel design to reduce solid accumulation in comparison to conventional septic tanks. For this project, 16S metabarcoding was employed to characterize conventional and InnerTube septic tank microbial communities and evaluate relationships between community composition, system design, and treatment efficacy. Wastewater was sampled along the length of InnerTubes to determine patterns of microbial succession and how they may impact InnerTube function. Wastewater was separated into liquid and solid fractions to identify differentially abundant taxa in each fraction. Populations of methylotrophic methanogens increased with distance from the InnerTube inlet. Solid communities were differentially more abundant in methanogens than liquid communities. Higher rates of solid degradation in InnerTubes may be due to longitudinal stratification of substrates and functionally distinct communities and the activity of methanogenic biomass. Septic tanks throughout Ontario were also surveyed to evaluate the effect of system design (conventional vs. InnerTube) and operational flow (single-pass vs. recirculation) on microbial community composition and to identify taxa correlated with chemical oxygen demand (COD) reduction. Single-pass InnerTube communities were more abundant in Pseudomonas which was attributed increased availability of long-chain fatty acid substrates. Recirculating conventional communities were more abundant in Arcobacter and Desulfomicrobium which was attributed to greater resistance to oxidative stress. Desulfovibrio and Brevundimonas were positively correlated with COD reduction. These putative hydrogen producers may facilitate greater COD reduction by forming syntrophic relationships with hydrogenotrophic methanogens. The findings of this project may be used to develop bioaugmentation inoculum, system designs, or operational strategies to optimize septic tank performance.

abstract: Thesis

abstract: Master of Science (MSc)

abstract: Septic systems (anaerobic digesters) are extensively used for on-site wastewater treatment. We evaluated the use of next-generation DNA sequencing to (1) assess the variability of septic system microbial communities and (2) to investigate relationships between communities and septic system type/performance. Microbial communities within septic systems were determined to be heterogeneous. Analyses also indicated that communities were highly variable between septic systems. Despite this variability, specific system types exhibited distinct microbial profiles. System performance was positively correlated with the abundance of hydrogen-producing bacteria. These results demonstrate the potential of next-generation DNA sequencing as a new tool to augment traditional wastewater analyses.


title: Interplay of Finite Size and Strain on Thermal Conduction

contributor:
Puri, Ishwar
Engineering Physics

subject:
Thermal conduction
Molecular Dynamics
Strain
Thin films
Thermal rectification
Nanowires

abstract:
Since strain changes the interatomic spacing of matter and alters electron and phonon dispersion, an applied strain ϵ can modify the thermal conductivity κ of a material. This thesis shows how the strain induced by heteroepitaxy is a passive mechanism to change κ in a thin film and how the film thickness is key to the functional form of κ(ϵ). Molecular Dynamics simulations of the physical vapor deposition and epitaxial growth of ZnTe thin films provide insights into the role of interfacial strain on the thermal conductivity of a deposited film. ZnTe films grown on a lattice mismatched CdTe substrate exhibit ~6% in-plane biaxial tension and ~7% out-of-plane uniaxial compression. In the T=700 K to 1100 K temperature range, the conductivities of strained ZnTe layers that are 5 unit cells thick decrease by ~ 35%, a result that is relevant to thermoelectric devices since strain can also enhance charge mobility and increase their overall efficiency. The resulting understanding of dκ/dT shows that strain engineering can also be used to create a thermal rectifier in a material that is partly strained and partly relaxed, like at the junction of an axial nanowire heterostructure.
To better isolate the role of strain, the study is extended to free-standing ZnTe films with thicknesses between 116 Å to 1149 Å under the application of both uniform and biaxial strain between -3% to 3% at 300 K. Since the boundaries of the film are diffuse, κ becomes size dependent when the film thickness approaches the order of the mean free path of the phonons. As this thickness is decreased, the magnitude of κ decreases until boundary scattering dominates so that κ(ϵ) depends on v_g (ϵ). This conclusion is important as it can be generalized to other materials and potential functions; it suggests that if a film is thin enough for boundary scattering to dominate, then the behavior of κ(ϵ) can be predicted based on the bulk dispersion curve alone, which should greatly simplify strain-based device design.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)

abstract: Since strain changes the interatomic spacing of matter and alters electron and phonon dispersion, an applied strain ϵ can modify the thermal conductivity κ of a material. This thesis shows how the strain induced by heteroepitaxy is a passive mechanism to change κ in a thin film and how the film thickness is key to the functional form of κ(ϵ). Molecular Dynamics simulations of the physical vapor deposition and epitaxial growth of ZnTe thin films provide insights into the role of interfacial strain on the thermal conductivity of a deposited film. The result is relevant to thermoelectric devices since strain can also enhance charge mobility and increase their overall efficiency. The resulting understanding of dκ/dT shows that strain engineering can also be used to create a thermal rectifier in a material that is partly strained and partly relaxed, like at the junction of an axial nanowire heterostructure.