VictorJuiz/thesis huggingface dataset:
Evidence of Mobility in the 3-chlorobenzoate Degradative Genes in a Pristine Soil Isolate, Burkholderia phytofirmans OLGA172
Keywords: chlorobenzoate
burkholderia
horizontal gene transfer

The genome of B. phytofirmans OLGA172 has been sequenced by Next Generation sequencing methods. Over 42 kbp of its genome surrounding its 3CBA degradative genes, tfdCIDIEIFI, was assembled and annotated. The most important method used was the synteny method, which implies homology between the genes, and descent from a common ancestor (Guttman, 2008). The conserved gene order between B. phytofirmans PsJN, B. xenovorans LB400, and OLGA172 was used as a confirmation of annotation through BLASTn, enabled closing of the gaps in the sequencing data, and allowed prediction of genes further downstream. Though the whole genome is not yet assembled, a very significant region carrying a concentrated area of mobile genetic elements (MGE) has been found to surround the degradative genes in OLGA172. This thesis details the sequence evidence that, upon examination of closely related strains, OLGA172 and its related strain from pristine soils may be the ancestral chlorobenzoate degraders.
Genetic Variation in Bitter Taste Perception, Food Preference and Dietary Intake
Keywords: Bitter taste
Nutrigenomics
TAS2R50
Taste

The role of variation in the TAS2R50 bitter taste receptor gene is unknown, but may influence taste perception and dietary habits. Individuals (n=1171) aged 20 to 29, from the Toronto Nutrigenomics and Health Study, completed a food preference checklist and a semi-quantitative food frequency questionnaire to assess their preference and intake of potentially bitter foods and beverages. DNA was isolated from blood and genotyped for 3 polymorphisms in the TAS2R50 gene (rs2900554 A>C; rs10772397 A>G; rs1376251 A>G). Taste intensity was examined using taste strips infused with 3µg of naringin. The rs2900554 SNP was associated with naringin taste intensity, grapefruit preference and grapefruit intake in females. Homozygotes for the C allele reported the highest frequency of experiencing a high naringin taste intensity, disliking grapefruit and not consuming grapefruit. The rs10772397 and rs1376251 SNPs were associated with disliking grapefruit. These results suggest that naringin may be a ligand for the T2R50 receptor.
Understanding the geography of Industry Canada's Community Access Program in Toronto
Keywords: Digital Divide
Community Access Program
Geography
GIS

Industry Canada’s Community Access Program (CAP) aims to provide affordable public access to the Internet and the skills that people need to use it effectively. In fact, the CAP is an Industry Canada effort to bridge the digital divide (rural-urban, intra-urban). In the City of Toronto Industry Canada funding is used to support CAP sites managed by two organizations, the Learning Enrichment Foundation and the Toronto District School Board. CAP was implemented through the establishment of community-based public Internet access facilities. The implementation of the CAP in Toronto has resulted in the use of a wide range of organizations and locations including: libraries, schools, community centres, employment and social service agencies, and language development centres. This research asks the question, is the current network of CAP locations adequately geographically organized to meet the demand for service provision? Adequate supply means that the neighbourhood CAP supply is not over-served and under-served. Data from Industry Canada’s CAP database and the Canada census are input to a modeling process that combines multi-attribute decision analysis with a location-allocation model. The results suggest that there is likely a need to reevaluate the geographical structure of the current CAP network, with a view to achieving a more equitable allocation of supply.
The Effect of using Book Clubs to Improve Literacy and Build a Learning Community Among Under-performing Elementary Students
Keywords: Saudi Arabia
Literacy
under-performing students
elementary
reading
writing
learning community
identity
authentic dialogue
academic performance
book clubs

Although literature has extensively documented the stereotypes of developing learning communities in schools through book clubs— especially to improve literacy— little is revealed about varied indicators of improvements, such as student self-identification, authentic dialogues, and transforming small groups into learning communities. In this respect, formal efforts on adopting book clubs to improve literacy in Saudi Arabia are simply absent. This thesis presents research findings that seek to explore the effect of book clubs on improving literacy and building a learning community among seventh-grade, under-performing students in Canada. This thesis is contextualized through a thorough review of related literature and discussion of findings from classroom observations, and students’ interviews. The completion of this thesis indicates positive, causal relationships between using a book club as a learning tool and building a learning community, thus improving literacy. The research concludes with implications for using book clubs in Saudi Arabia.
LINCing Literacies: Literacy Practices among Somali Refugee Women in the LINC Program
Keywords: ESL education
language instruction
Somali refugees
literacy practices
LINC program

This thesis investigated the literacy practices of a group of Somali refugee women participating in Canada’s federally‐funded ESL program LINC (Language Instruction for Newcomers to Canada). Assuming that many Somali women arrive in Canada with limited experience with print literacy, and so encounter novel challenges in their settlement and learning experiences, I interviewed 4 Somali women about their uses and perceptions of the value of literacy in their lives and their experiences of learning to read and write in Canada. A cross‐case analysis revealed how social forces constrain and enable the women’s literacy practices, shaping both how they access and use literacy, as well as the ways in which they understand and value literacy. Implications are outlined for ESL educators, researchers and policy makers.
Shear Resistance of High Strength Concrete I-beams with Large Shear Reinforcement Ratios
Keywords: high strength concrete
shear resistance
heavily shear reinforced
I-beams
anti-symmetric loading

Experiments were performed to examine the shear resistance of heavily reinforced I-beams. Six I-beams with identical cross sections were constructed using high strength self-consolidating concrete, and were tested under monotonic anti-symmetric loading. All specimens had almost the same amount of longitudinal reinforcement, which provided sufficient flexural capacities. There were two variables: shear span and shear reinforcement ratio. Test results showed that ACI code was too conservative in predicting the shear strengths of heavily shear reinforced I-beams, and the shear strength limit for deep beams should be increased to account for the benefit of high strength concrete. However, doubling the amount of stirrups did not improve the ultimate shear resistance much. The three beams that contained around 2.45% stirrups showed over-reinforced shear failures. Longitudinal flange cracking occurred to every specimen due to lack of cross tie reinforcement in the flanges, and it was believed to have reduced the ultimate shear strength.
An In Vitro Investigation of the Spatial Control Involved in Collagen Mineralization
Keywords: In vitro model system
biomineralization
periodontal ligament
hydroxyapatite

An in vitro model system utilizing de-mineralized periodontium tissues was developed for investigating the molecular controls involved in the spatial deposition of minerals on collagenous tissues. Preferential mineral deposition was observed when the de-mineralized tissue sections were incubated in solutions containing a supersaturation of calcium and phosphate ions with respect to hydroxyapatite (HA). Energy dispersive X-Ray (EDX) analysis demonstrated that these minerals are likely to be octacalcium phosphate (OCP) or dicalcium phosphate dihydrate (DCPD); further characterization with a secondary technique is required to draw a more definitive conclusion. The role of collagen fibrils in mineralization was tested by removing all the non-collagenous components from the tissue sections with proteolytic enzymes and exposing them to similar mineralization conditions as the control samples. A substantially less amount of minerals were formed in these samples; this correlates well with the hypothesis in the literature that collagen fibrils alone cannot initiate mineral formation.
Non-invasive Assessment of Pulmonary Wave Reflection Using Phase Contrast Magnetic Resonance Imaging
Keywords: Cardiovascular Imaging
Magnetic Resonance Imaging
Pulmonary Arterial Hypertension

Pulmonary arterial hypertension (PAH) alters pulmonary hemodynamics by changing the vascular wall mechanics. Currently, pulmonary vascular resistance is used clinically to assess the disease. However, the invasive nature of pressure measurements, needed for calculating the resistance, prevents longitudinal monitoring of patients during therapy. This work employs wave reflection as an alternative measure of the downstream stiffness and proposes a new method for wave reflection assessment using only non-invasive phase contrast magnetic resonance (PCMR) flow data. The feasibility of the proposed method was investigated in a numerical model of blood flow in the right pulmonary artery. Furthermore, it was validated experimentally using a flow phantom and compared with an existing invasive technique. Finally, the feasibility of the method was tested in a study of the right pulmonary artery of a volunteer. This approach may provide a non-invasive method to evaluate PAH and its response to therapy.
Why Are You “Active”? -Voices of Young Muslim Women Post-9/11
Keywords: Muslim youth
post 9/11 Canada
Islamophobia
Muslim youth activism
spirituality and education
anti-racism
identity
Islam

Contributing to the literature on the Muslim experience post-9/11, the purpose of this study was to engage with a group that is often talked about, but not with: Muslim youth. Using an integrative anti-racist and anti-colonial approach with an emphasis on a spiritual way of knowing, this study gives voice to young Muslim activists in Toronto who have made the choice to “do something”. The study aims to understand what motivates these young activists, particularly in the context of post-9/11 Islamophobia, with the goal being to challenge stereotypical perceptions of Muslims, while contributing to the body of knowledge that aims to disrupt dominant notions of what “Canadian” identity is. The following analysis helps answer this question, which includes the role of spirituality, the attachment to Canadian identity and the desire to educate. Key challenges and what these youth prescribe for Canada’s future are also discussed.
The Role of Bacteriophage Lambda gpK in Tail Assembly and Host Cell Entry
Keywords: bacteriophage lambda
gpK
NlpC/P60
tail assembly

The bacteriophage lambda tail protein gpK is required for tail assembly. The activity of the protein can be found at the assembling tail tip and is believed to be localized to this structure. GpK is a 27 kDa protein that has sequence identity to two families of proteins: the Mov34 family of peptidases and the NlpC/P60 family of peptidoglycan endopeptidases. Point substitutions and complementation data confirm that gpK possesses each of these domains and that they can function in trans. When the Mov34 domain is inactivated tail assembly is disrupted whereas when the NlpC/P60 domain is inactivated tails assemble but are inactive. Evidence is presented here that the C-terminal domain possesses lytic activity in isolation but not when part of the full-length protein.
The Temporal Trends of Contaminants in Lake Erie Fish Communities
Keywords: Fish contamination
Lake Erie
PCBs
Hg

The Great Lakes has been impaired by elevated concentrations of contaminants, and different regulatory actions are taken to decrease theses concentrations. Recent research of Dr. Azim suggests a decline in mercury levels in the Lake Erie, and an increase in the Hg concentration in the fish communities. This research is a follow up study to examine whether the contaminant levels are indeed increasing. In the first chapter we evaluate the temporal trends of polychlorinated biphenyls (PCBs) in Lake Erie fish over the last 30 years by conducting the Exponential and Dynamic Linear Modeling analysis. DLM analysis in the chapter two detects the PCB and Hg contaminant trends in a broader range. There is a high variability in two contaminants trends. These patterns may be because of factors such as fish physiological parameters, and the impact of invasive species. The results of my research will contribute to the Toxics Reduction Strategy.
Life-cycle Cost Evaluation of Building Envelope Energy Retrofits
Keywords: Building Envelope
Energy efficiency

Improving the energy efficiency of our existing building stock is attainable by upgrading the building envelope through carrying out various retrofit measures. The objective of this thesis is to evaluate the life-cycle cost implications of energy retrofits for existing buildings. Measures examined include improving insulation and air-tightness with overcladding strategies. The life-cycle costs of the upgrades are determined for an existing building and compared with model energy performance. A life-cycle cost evaluation for the building envelope upgrades is provided, together with the payback period and the projected return on investment (ROI) for two energy escalation rate scenarios. A costbenefit matrix for various over-cladding strategies is provided to facilitate the evaluation of each option. Further, this thesis presents a simplified ROI algorithm to enable owners, architects and engineers to evaluate the cost-benefit of their building envelope retrofit options.
Islamic Environmental Stewardship through Aboriginal Spirtual Ecology: How Muslim Students can learn Stewardship through Aborginal Teachings
Keywords: Environmental Education
Islamic Education
Stewardship Education
Islamic Schools
Religious Education
Aboriginal Teachings

This study investigates the challenges and opportunities of using the Aboriginal principles of “Respect,” “Reciprocity,” “Relationship,” and “Responsibility” (known as the “4 R’s”), Seventh Generation Stewardship, and an Aboriginal circle of giving and receiving, to teach Muslim students in one Islamic elementary school setting about environmental stewardship. The research tracked the thoughts and emotional connections of students as they undertook to establish the Aboriginal circle of giving and receiving, with plants they planted for their science unit. Through lessons and practices around the 4 R’s, the majority of students demonstrated an increased emotional attachment to the plants in their respective circles, which was documented in journals. While establishing these practices, the students expressed a heightened awareness of the various ways in which they may enhance the practice of environmental stewardship mandated in traditional Islamic texts.
Positive Affect Promotes Unbiased and Flexible Attention: Towards a Dopaminergic Model of Positivity
Keywords: positive affect
positive psychology
attention
perception
reward learning

A review of extant literature on positive affect suggested that it has two major dimensions: a hedonic dimension related to subjective feelings and reward processing, and a cognitive dimension related to affect-specific changes in perception and cognition. A novel dopaminergic mod el was proposed to provide a unitary account for the effects of positive affect across the two dimensions. The model hypothesized that positive affect is associated with distinct modes of mesocortical and mesolimbic dopa mine transmission, which in turn mediate unbiased, unfiltered and flexible attention. Three separate behavioral tasks on perception, attention, and reward learning were conducted. In line with the hypothesis, positive affect was found to associate with less biased bi-stable perception, faster regain of attention to previously ignored information, and fewer perseverative errors in face of changing reward contingencies.
A Single Phase Grid Connected DC/AC Inverter with Reactive Power Control for Residential PV Application
Keywords: single phase inverter
residential PV
reactive power
grid synchronization

This Master of Applied Science thesis presents a single phase grid connected DC/AC inverter with reactive power (VAR) control for residential photovoltaic (PV) applications. The inverter, utilizing the voltage sourced inverter (VSI) configuration, allows the local residential PV generation to actively supply reactive power to the utility grid. A low complexity grid synchronization method was introduced to generate the parallel and orthogonal components of the grid voltage in a highly computationally efficient manner in order to create a synchronized current reference to the current control loop. In addition, the inverter is able to use a small long life film type capacitor on the DC-link by utilizing a notch filter on the voltage control loop. Simulations were performed on PSCAD/EMTDC platform and a prototype was also developed in the lab to prove the effectiveness of the controllers and the grid synchronization method.
Testing the Limits of Oral Narration: A Case Study on Armenian Genocide Survivors
Keywords: orality
narration
oral history
oral histories
armenian genocide
genocide
walter ong
media theory
communication theory
semiotics
memory
zoryan institute
interview
survivor

This research discusses communication and meaning in the context of orality, using a variety of theoretical perspectives, including memory theory, media and communication theory, and semiotics. Drawing on the work of Walter Ong, it provides new insight about the characteristics and limits of oralnarration by assessing the memes, tropes, and phraseological units in the oral narrations of Armenian Genocide survivors. This research identifies a list of replicable forms of stories and oral devices that are used by the group in question; it then proposes that oral narration of non-fictional topics designed to convey historical or episodic information to others is intuitive, reactive, directed, fuzzy, and sticky. Concerns about the legitimacy and historical value of the narrations under review do not play a role in this research; instead, the focal point is the meaning embedded in the form and structure of the narrations under study.
The Effectiveness of Magnesium Oxide-based Additives in Mitigating Fouling Problems in Kraft Recovery Boilers
Keywords: additives
kraft recovery boilers
fouling problems
pulp and paper

Magnesium oxide-based additives have been used in kraft recovery boilers to minimize deposit accumulation on superheater and generating bank tubes. Due to inconclusive results observed in boilers and claims made for additive effectiveness backed by little scientific evidence, only a few mills still use the additives for fouling control. A systematic study was performed to examine the effect of MgO-based additives on deposit accumulation and removal under controlled laboratory conditions, and to evaluate the additive effect in a kraft recovery boiler. The results show that while the additive coating has no effect on deposition, it could ease deposit removal if a coating greater than 5 µm can be applied on the tube surface effectively. Separate injection of additive and black liquor had insignificant effect on deposition and removal. Results of the field study show that the amount of additive collected on the tube is too small to have an impact.
Protective Effect of Peroxiredoxin 2 on Oxidative Stress Induced β-cell Toxicity in the Pancreatic β-cell Line MIN6
Keywords: Oxidative stress
β-cell
toxicity
Peroxiredoxin 2

Type 1 and type 2 diabetes are characterized by an excessive loss of insulin producing β-cells. β-cells are particularly susceptible to increased oxidative stress induced apoptosis due to low expression of major antioxidants. Peroxiredoxin-2 (PRDX2) belongs to a group of antioxidants with antiapoptotic roles. Preliminary data indicate PRDX2 is expressed in the β-cells. Endogenous PRDX2 in the β-cell line MIN6 is found to decrease under oxidative stress conditions. I hypothesize that PRDX2 has a role in protecting β-cells against oxidative stress induced apoptosis. Overexpression or knockdown strategies were used to examine the role of PRDX2 in insulin-secreting MIN6 cells treated with various stimuli (cytokines, palmitate, streptozotocin) to induce apoptosis. Results showed that PRDX2 overexpression decreased oxidative stress induced apoptosis markers and cell death indicators, whereas knockdown of PRDX2 exaggerated oxidative stress induced toxicity. These findings suggest that PRDX2 plays a protective role in pancreatic β-cells under oxidative stress conditions.
Tat-9c, a Tat-fusion Cysteine-rich Peptide, Attenuates Behaviour Deficits following Traumatic Brain Injury in Rats
Keywords: Traumatic Brain Injury
cysteine

Peroxynitrite, a highly oxidative molecule, plays a role in neuronal cell death following traumatic brain injury (TBI). A peptide comprised of the HIV-1 tat transduction domain fused to nine cysteine residues (Tat-9c) was previously designed to act as an exogenous target for nitrosylation by peroxynitrite. The present study’s aim was to explore the efficacy of Tat-9c in maintaining neurological function following TBI. Rats treated with Tat-9c exhibited significant improvement in performance compared to controls 24 hrs following TBI in the Beam-Walk task but not in the Rota-Rod task. Injured animals, given the drug, show a recovery as indicated by similar performance on the Morris Water Maze task compared to sham controls. These findings suggest Tat-9c may constitute a potential therapy for improving motor and cognitive function following TBI.
Multi-edge Low-density Parity-check Coded Modulation
Keywords: Coded modulation
Coding theory
EXIT
LDPC
Multi-edge-type

A method for designing low-density parity-check (LDPC) codes for bandwidth-efficient high-order coded modulation is proposed. Code structure utilizes the multi-edge-type LDPC code ensemble to achieve an improved match between codeword bit protection ca- pabilities and modulation bit-channel capacities over existing LDPC coded modulation techniques. The multi-dimensional EXIT vector field for the specific multi-edge parame- terization is developed for the analysis and design of code ensembles. A multi-dimensional EXIT decoding convergence condition is derived to enable efficient optimization. Code design results in terms of ensemble thresholds and finite-length Monte-Carlo simulations indicate that the new technique improves on the state-of-the-art performance, with sig- nificantly lower design and implementation complexity.
Parallel Anisotropic Block-based Adaptive Mesh Refinement Finite-volume Scheme
Keywords: adaptive mesh refinement
anisotropic
computational fluid dynamics
Binary Tree
advection diffusion
euler equations
finite-volume

A novel parallel block-based anisotropic adaptive mesh refinement (AMR) technique for multi-block body-fitted grids is proposed and described. Rather than adopting the more usual isotropic approach to mesh refinement, an anisotropic refinement procedure is proposed which allows refinement of grid blocks in each coordinate direction in an independent fashion. This allows for more efficient and accurate treatment of narrow layers and/or discontinuities which occur, for example, in the boundary and mixing layers of viscous flows, and in regions of strong non-linear wave interactions with shocks. The anisotropic AMR technique is implemented within an existing finite-volume framework, which encompasses both explicit and implicit solution methods, and is capable of performing calculations with second- and higher-order spatial accuracy. To clearly demonstrate the feasibility of the proposed technique, it is applied to the unsteady and steady-state solutions of both the advection diffusion equation, as well as the Euler equations, in two space dimensions.