VictorJuiz/thesis huggingface dataset:
Biophysical Drivers of Tree Crop Performance in Shade Agroforestry Systems: The Case of Coffee in Costa Rica

Agroforestry production methods present one option for addressing growing concerns about the long term sustainability of intensive coffee production techniques. A study was designed to compare the effects of fertilization and shading from two leguminous species, Erythrina poeppigiana and Chloroleucon eurycyclum, on coffee grown at a Costa Rican research site. Coffee below biannually pruned, conventionally fertilized Erythrina exhibited the highest photosynthetic performance under both low and high light levels as well as greater biomass and higher N concentration. Soil P did not affect coffee performance, although shade trees on sites with higher soil P fixed more N compared to trees grown on low P sites, most of which were not found to be fixing. Results suggest shade mechanisms are the most important drivers of coffee adaptation in coffee agroforestry systems, though proper soil nutrient management and legume species pairing also appear to augment coffee response to microclimate conditions.

Keywords: Agroecology
Resource management
Agroforestry
Coffee
Tropical agriculture
Soil management
Shade management
Advisor: Isaac, Marney E.
Construction and Characterization of Microbial Fuel Cells Using a Defined Co-culture of G. sulfurreducens and E. coli

An air cathode, membrane-less microbial fuel cell (MFC) containing a co-culture of Geobacter sulfurreducens and Escherichia coli was constructed and compared to pure culture MFCs of both organisms. The E. coli containing MFCs were unsparged and relied on E. coli for oxygen removal. The pure G. sulfurreducens MFC had a power output of 128 mW/m2, compared to 63 mW/m2 for the co-culture at an early stage and 56 mW/m2 for the late stage co-culture. The limiting current density is 404 mA/m2 for the pure G. sulfurreducens culture, 184 mA/m2 for the early co-culture, and 282 mA/m2 for the late co-culture, despite an increase in internal resistance between the early and late co-culture cells. Analysis of metabolites has shown that succinate production is likely to have negatively affected current production by G. sulfurreducens, and the removal of succinate is responsible for the increased current density in the late co-culture cell.

Keywords: Microbial fuel cell
geobacter sulfurreducens
E. coli
Advisor: Mahadevan, Radhakrishnan
Identifying and Phenotyping an ENU Derived Mouse Model of MYH9 Related Disease

A dominant ENU screen produced mouse line 7238 with large platelets. Sequence capture and Next Generation sequencing identified a mutation in Myh9 at Q1443L [1]. Mice were tested for aspects of MYH9-Related Disease (MYH9RD), a rare human condition caused by mutations within MYH9; macrothrombocytopenia and neutrophil inclusions are found in almost all cases, while deafness, cataracts and renal disease have variable penetrance and severity. Myh9Q1443L/+ and Myh9Q1443L/Q1443L animals have neutrophil inclusions [1] and increased cataracts at 2, 6 and 12 months; Myh9Q1443L/Q1443L animals at 12 months have changes in kidney output [2]. Immunofluoresence showed changes in protein expression in glomeruli at two months. This is the first ENU mouse model identified by a sequence capture mechanism, and the first mouse line to produce a point mutation within the Myh9 gene [1,2]. This mouse models MYH9RD, and is an invaluable tool to understand the role of this protein, and to determine mechanisms underlying this disease.

Keywords: ENU
MYH9-RD
Next Generation Sequencing
Advisor: Stanford, William L.
Effectiveness of Prequalification Practices in Public Procurement

Due to legally restrictive nature of public work, contracts are often awarded solely based on the price of the bid. This has often resulted in contracts being awarded to less qualified contractors. Between the practices developed to deal with this issue, prequalification has proven to be one of the most effective practices in dealing with this problem. As it was investigated in this research, practice of prequalification is widespread amongst the public owners in the region. However, an in-depth look at the practices has revealed that these owners are not currently using this process to its fullest potential and integration of some of the best practices suggested in this paper has the potential to make this process more effective. This research also contains a specially fabricated model which encumbers all of the suggested practices and aims at creating a simple, practical and transparent model for the public owners in the Southern Ontario region.

Keywords: Construction Management
Prequalification
Advisor: McCabe, Brenda
Design of a Catalytic Combustor for Pure Methanol and HTPEM Fuel Cell Anode Waste Gas

Transportation sector CO2 emissions contribute to global warming. Methanol generated from clean energy sources has been proposed as a transportation fuel as an alternative to gasoline or diesel to reduce emissions. Catalytic methanol-steam reformers can be combined with high temperature polymer electrolyte membrane (HTPEM) fuel cell systems to create compact electrical power modules which run on liquid methanol. These modules combine the efficiency of a fuel cell system with the convenience of using a traditional, liquid hydrocarbon fuel. Catalytic methanol-steam reformers require a heat source as the methanol-steam reforming process is endothermic. The heat source for this system will initially be from the catalytic combustion of either pure methanol, during startup, or from HTPEM fuel cell anode waste gas during system operation. Efficient use of catalyst requires effective premixing of the fuel and air. This study will investigate parameters affecting premixing and their effect on temperature distributions and emissions.

Keywords: Catalytic Combustion
Methanol
HTPEM
Anode Waste Gas
Advisor: Thomson, Murray J.
The Characterization of Staphylococcal Phage Tails as an Alternative to Chemical Antibiotics

The emergence of multidrug resistant Staphylococcus aureus strains has increased the difficulty of treating these infections. Bacteriophages can eliminate bacterial infections and some bacteriophage tails are lethal to their bacterial hosts. Interestingly, strains of Pseudomonas produce specialized phage tail-like molecules, called pyocins, which are lethal to bacterial strains. The central goal of my project was to explore the use of phages lacking DNA (ghosts) and genetically engineered phage tail variants as anti-staphylococcal disinfectants or therapeutic agents. I tested a variety of methods to generate staphylococcal phage ghosts and tails. For one of these, engineered tails derived from staphylococcal phage 77, I tested its ability to effectively kill S. aureus by measuring their effect on cell growth and survival, their ability to bind staphylococcal cells and induction of potassium efflux. These genetically created tails bound staphylococcal cells, but no effect on growth or survival was observed from tails or ghosts.

Advisor: Navarre, William
A Platform for High-throughput Mechanobiological Stimulation of Engineered Microtissues

While tissue-engineering approaches of heart valves have made great strides towards creating functional tissues in vitro, the instruments used, named bioreactors, cannot efficiently integrate multiple stimuli to accurately emulate the physiological microenvironment. To address this, we conceptually designed and built a bioreactor system that applied a range of mechanical tension conditions, modulated matrix stiffness, and introduced biochemical signals in a combinatorial and high-throughput manner. Proof-of-concept experiments on PAVIC-seeded hydrogels were performed to assess the independent and combined effects of tensile strain, matrix stiffness and TGF-β1 on myofibroblast differentiation by measuring α-SMA expression, a marker that indicates a disease-associated phenotype. We found that matrix stiffness and TGF-β1 significantly increased α-SMA levels (p < 0.001), while the effect of mechanical strain was only significant on soft gels (~12 kPa) without TGF-β1. This study therefore demonstrated independent and integrated effects of multiple stimuli in regulating key cellular events in the aortic valve.

Keywords: bioreactor
high-throughput
mechanobiology
microtissues
Advisor: Simmons, Craig Alexander
Sun, Yu
Determinants of Adaptation and their Interactions in Experimental Populations of Saccharomyces cerevisiae

The goal of my M.Sc. thesis research was to investigate the link between divergent adaptation and reproductive isolation in speciation, the process by which one species becomes two over time. Previous studies followed the evolution of 12 replicate experimental populations of the yeast Saccharomyces cerevisiae in either of two non-optimal environments, high-salt or low-glucose, over 500 generations. In this research, I re-sequenced the whole genomes of six diploid strains of these populations, three from high salt and three from low glucose. Among the replicates, there was remarkable degree of parallelism in the underlying determinants of adaptation including multiple mutations in PMA1, encoding the main proton exporter, in high-salt and in several genes in the ras signalling pathway in both environments. A variety of positive and negative epistatic interactions were found among mutations from within and among populations, emphasizing the importance of epistasis in adaptation and potentially in speciation.

Keywords: adaptation
evolution
yeast
cerevisiae
speciation
Advisor: Anderson, James
Finding Meaning in Place: The Perspectives of People with Severe Mental Illness Living Long Term in a Psychiatric Hospital

This study explored the perspectives on place of eight people with severe mental illness living, for one year or longer, in an urban psychiatric hospital. The research questions were: how do people with severe mental illness view the psychiatric hospital as place?; and how do they make meaning of the experience of living in hospital. The research employed a phenomenological approach, as described by Giorgi (1985). Using purposive sampling, one time, semi-structured, individual interviews were conducted. The audio recorded interviews were transcribed and thematically coded using Giorgi’s (2005) method. The meanings of the participants’ experiences are captured by the meta-theme: this is not a home; it’s a hospital. Four additional major themes emerged; and each of the major themes also had sub-themes The findings of this study challenged commonly held assumptions on how people living long term in a psychiatric hospital view the hospital as place and on institutionalization.

Keywords: place
severe mental illness
Advisor: Kirsh, Bonnie
Polatajko, Helene J.
Chemical Genetic Interactions for Antibiotics in Escherichia coli

The discovery of penicillin ushered in the era of the mass use of antibiotics in clinical settings. Today the development of antibiotic resistance and lack of discoveries of new antibiotics have created a serious public health concern. Recently, new experimental tools, such as bacterial genome-wide deletion collections, have provided exciting new possibilities for studying biological networks in bacteria that could potentially also be exploited for antibiotic research. In this study, I used the Keio knockout collection of Escherichia coli (E.coli) strains, along with an in-house collection of hypomorphic alleles of essential genes, to study the effects of chemical perturbations by twenty-two antibiotics and four other chemicals on the biological pathways of E.coli. These experiments uncovered a set of mutants hypersensitive to drugs of different classes, information which could potentially be exploited for future antibiotic research. The results also shed light on how different classes of antibiotics behave with respect to their target pathways and the various functional modules with which they are associated.

Keywords: Escherichia coli
chemical genetics
Advisor: Greenblatt, Jack F.
Understanding the Mechanism of Aberrant FLVCR1 Splicing and Disrupted erythropoiesis in Diamond-Blackfan Anemia

Diamond Blackfan Anemia (DBA) is a congenital disorder characterized by a specific reduction in erythroid progenitor cells. Approximately 55% of patients have heterozygous mutations in ribosomal protein with 25% of these mutations in RPS19. However, it is unclear how a defect in ribosomal proteins specifically disrupts erythroid development. FLVCR1, a heme exporter, has been implicated as a potential DBA factor. FLVCR1 is essential for erythropoiesis as its disruption leads to apoptosis and disrupted erythroid differentiation. Though no FLVCR1 mutations have been found in DBA patients, our lab has shown that it is aberrantly spliced in DBA erythroid cells. Using RPS19 reduced K562 erythroid cells, I found that disruption of RPS19 leads to aberrant FLVCR1 splicing, disrupted erythropoiesis and reduced Tra2-β, ASF2 and SRp30c protein expression. This was specific to DBA as I did not find these features in a cell culture model of Shwachmann Diamond Syndrome, another ribosomal disorder.

Keywords: Diamond-Blackfan Anemia
FLVCR1 aberrant splicing
RPS19
Erythropoiesis
SR proteins
Tra2Beta
Advisor: Tailor, Chetankumar
Towards International Islamic Human Rights: A Comparative Study of Islamic Law, Shari’ah, with Universal Human Rights as Defined in the International Bill of Human Rights

Islamic law, also known as Shari’ah law, is one of the most complex and multifaceted, yet easily misunderstood areas of law. It is complex because its subjects, but not limited to, human rights, politics, religion, economics, and criminal. Islamic law is also misunderstood because it is greatly understudied and grossly over-generalized. This regretfully has lead to a situation where Islamic law is often characterized as an inhumane and discriminatory set of laws which have no respect for human rights. The questions that remain to be answered are whether or not there is a human rights discourse in Islamic law, and is Islamic law compatible with the Universal Declaration of Human Rights and its two subsequent International Covenants? The aim of this paper is to ascertain whether or not Shari’ah law, as it has been reflected in the Islamic human rights documents discussed, is compatible with universal human rights standards.

Keywords: International Islamic Human Rights
Advisor: Emon, Anver
Mindfulness beyond the Third Wave: The Role of Mindfulness outside the Cognitive-behavioural Tradition

Mindfulness has been defined in cognitive-behavioural terms in the mental health literature despite its broader application by many practitioners. Mindfulness is a complex and often ambiguous concept that has historically been understood and applied in myriad ways depending on the context; thus its application to psychotherapy outside the cognitive-behavioural tradition is not necessarily straightforward, and has not been addressed. This study addressed this gap in the literature through interviews with 9 experienced psychotherapists who integrate mindfulness with non-cognitive-behavioural psychotherapeutic modalities or eclectic psychotherapy. Interviews addressed how participants a) define mindfulness, b) apply it to psychotherapy, and c) the aims of that integration. Data were analyzed via the grounded theory approach. The results depicted mindfulness and its potential applications as broader than its presentation in the mental health literature, and emphasized the role of contexts in shaping conceptualization and application. A broad, context-based model of mindfulness/psychotherapy integration is proposed.

Keywords: mindfulness
psychotherapy
Buddhism
psychotherapeutic modality
psychology
qualitative research
therapist
Advisor: Moodley, Roy
Composition Skills of Children with ADHD: An Intervention Study to Improve Communicative Clarity

The aim of the current study was to assess whether providing visual feedback on the written compositions of children with ADHD was an effective method to improve communicative clarity. Participants were twenty children, aged 7 to 9 years with ADHD. Children composed instructions on how to build a figure so that a confederate could reproduce the image based only on the child’s instructions. Participants in the experimental group received feedback on their compositions in the form of the reconstructed figure and were able to then compare the figures side by side on-screen and edit their instructions. Participants who received visual feedback outperformed participants in the no feedback group on the clarity of compositions at post-test, and at a six-week delayed post-test, and were able to apply their learning to transfer tasks. This research makes valuable contributions to understanding the factors that contribute to successful early writing for children with ADHD.

Keywords: ADHD
Communication
Advisor: Peskin, Joan
An Examination of Trauma-mediated Pathways from Childhood Maltreatment to Alcohol and Marijuana Use and the Perpetration of Dating Violence in Adolescence

Despite high rates of alcohol and marijuana use and dating violence among individuals between the ages of 15 and 24, limited research has examined a link between substance use and dating violence within adolescent samples. Moreover, although both problem drinking and dating violence perpetration have been linked to a history of childhood maltreatment (CM), few studies have examined the potential mechanisms of a relationship between these variables. The current study tested the predictive role of CM in adolescent alcohol and cannabis use and dating violence perpetration in a sample of youth with CM histories; in particular, we were interested in predicting the temporal co-occurrence of these behaviours. It was hypothesized that trauma symptomatology would play a mediating role in this relationship. Results demonstrated that only witnessing emotional domestic violence predicted the co-occurrence of substance use and dating violence; in general, trauma symptomatology was not found to be a significant mediator.

Keywords: Childhood Maltreatment
Substance Use
Dating Violence
Posttraumatic Stress
Advisor: Goldstein, Abby
Relationship between Participation in the Webinar and Students’ Behaviours and Engagement in Online Learning

A graduate level Flex Mode course “Introduction to Computers in Education” using online learning concept, which includes the discourse environment and the webinars, was investigated in the current study. Twenty one students enrolled in the course in fall 2010. Since the design of this course is new and in its experimental stage, this study explored how webinar participation predicts students’ behaviours and engagement in online learning, and the experiences and perspectives of students who take this course. Data retrieved from the course database show that webinar participation correlated significantly with the engagement construct (about reading and writing online). Results from the questionnaire suggest that students were satisfied with both the webinar and online discussion components of the course. Interview findings indicate that students credit the webinar with helping them feel more connected to their classmates. Implications for the design of online learning program will be discussed.

Keywords: Online learning
Behaviours
Engagement
Webinar
Advisor: Woodruff, Earl
Bodied Curriculum: A Rhizomean Landscape of Possibility

Undergoing a self-study using the method of currere (Pinar, 1976), I examine my own learning as holistic, embodied, and relational in the context of my mother’s garden. Specifically, I explore my mother’s garden as a site of relational learning that intersects with various classrooms that feature in my educational experiences. The garden and the classroom intersect with/in one curricular landscape, where self and other engage in an embodied process fostering connections and knowledges about each other and place. In bringing forth my narrative through currere, I engage in reflective and reflexive praxis through journal writing, poetry, meditation, and photographic collage. Using these forms of expression, I reflect upon my experiential learning process, analyze issues and concepts related to the body-in-movement, as well as focus on community connections and ecology-based learning as pedagogical praxis.

Keywords: community
currere
ecology
elementary education
embodiment
ethics
experiential learning
garden
holistic
lived experience
narrative inquiry
relationality
Advisor: Springgay, Stephanie
The Results and Implications of Fundraising in Elementary Public Schools: Interviews with Ontario Principals

A growing pressure to fundraise at the school level in Ontario is a direct result of funding cuts by the Ministry of Education. The purpose of this study is to examine and analyze the kinds of different fundraising strategies principals use in select elementary public schools in a southern Ontario large city and to determine the positive and negative results of fundraising. Principals of eight elementary schools were interviewed from high and low fundraising schools. Five included school observation tours. The findings show a positive correlation between student achievement and fundraised amounts and utilization, but that the benefits of fundraising only apply to a small number of students. The findings also show that an equal educational opportunity is not being provided to all students, and that moral, civic and democratic values are being eroded. This study highlights the need for Ontario’s Ministry of Education to fully fund public education.

Keywords: fundraising strategies
elementary schools
principals
equity
neoliberalism
commercialism
students
exclusions
dignity
Ministry of Education
fundraising results
fundraising disparities
achievement
democracy
curriculum
funding
public schools
funding cuts
Advisor: Norris, Trevor
An Examination of the Role of Parental Influences on Girl’s Development of Embodiment

Adolescence is marked with significant changes in how girls feel and act within their bodies, and is considered a special risk period for body image disruptions. Cross sectional quantitative research within this area suggests that parents represent an important contextual and developmental contributor to body image. The present study aimed to address gaps in previous research by investigating parental influences, including both protective and risk factors, on girls’ embodied experiences through utilizing a prospective qualitative design with a diverse sample of twelve girls, ages 9-18, interviewed annually over four years. Results revealed the presence of both protective and risk factors related to embodiment experiences within the parental relationships, including aspects of relational qualities, self-care, evaluative gaze and social location. Results are discussed in relation to Bronfenbrenner’s Ecological Systems Theory and to previous research. The implications for future research are also discussed.

Keywords: sociocultural factors
parental role
body image
embodiment
protective factors
risk factors
adolescent development
social location
Advisor: Piran, Niva
Canadian Youth Abroad: Rethinking Issues of Power and Privilege

Since the 1960s, over 65,000 young Canadians have participated in volunteer abroad programs (Tiessen, 2008). Lately, the media and academia have questioned and criticized the benefits of volunteerism as development. This study highlights how issues of power and privilege extend beyond the individual, and reaches into institutional structures. The research design uses Institutional Ethnography (IE) as a method of inquiry, and maps out the social relations between the experiences of seven former youth volunteers and field staff, and their organizations. The aim is to explore how to improve individual and organizational pedagogy in the field of international volunteering, so that equity becomes a commitment by everyone in the development of sustainable and just communities.

Keywords: Youth
International Development
Volunteerism
Equity
Advisor: Ng, Roxana