VictorJuiz/thesis huggingface dataset:
The Role of Expectations of Science as Promissory Discourses in Shaping Research Policy: A Case Study of the Creation of Genome Canada
Keywords: discourse analysis
expectations of genomics story-lines
Genome Canada
promise of science
research policy
sociology of expectations of science and technology

This thesis examines promise of science discourse and its impacts in shaping research policy. Through a single case study of the origins of Genome Canada, the research was guided by the question: How did expectations of genomics, as promise of genomics discourse, shape the creation of Genome Canada? Background is presented on the long-standing, but largely unacknowledged, relationship between the promise of science and research policy. Theoretical grounding for the study is provided by concepts from the discursive policy analysis and sociology of expectations of science and technology literatures. Promise of genomics discourse, expectations of genomics of story-lines and a conceptualization of knowledge-based discursive power provide the theoretical and analytical basis for an in-depth examination of the ideational effects and material impacts on research policy decisions over three years (1997 – 2000) that sought to position Canada as a leader, internationally, in genomics research. As discourse, the promise of genomics fulfilled an essential role in shaping policy decisions. The promise of genomics discourse and expectations of genomics story-lines functioned in a complex interplay of discursive practices and dynamics among diverse policy actors within a promise of genomics discourse-coalition to produce a range of ideational and material impacts. The promise of genomics discourse produced powerful promise of genomics subject-positions from which policy actors perceived their interests, identities and preferences and gained agency, which led to various material impacts, including the transformation of Canada’s research policy framework. The thesis derives valuable insights about how the diverse policy actors involved in the research policy process perceive and are influenced by the promise of science. With the increasing importance of research policy to a range of broader policy priorities underpinned by expectations that science will resolve societal challenges and contribute to socio-economic benefits, this thesis sheds light on how complex research policy decisions are made; it further contributes to understanding the processes that lead to those decisions that increasingly must reconcile the relationship between science and society.
Turbulent Non-premixed Swirl-Stabilized Flames of Gaseous and Liquid Fuels in a Gas Turbine Model Combustor
Keywords: Gas Turbine Combustion
LII Soot Measurement
SPIV and OH-PLIF
Spray Combustion
Swirl Stabilized Combustion
Turbulent Non-premixed Combustion

Turbulent non-premixed swirl-stabilized flames of gaseous and liquid fuels were investigated experimentally in an optically-accessible gas turbine model combustor. Propane/air and ethylene/air flames were operated at three global fuel-air equivalence ratios. Spray flames of liquid n-heptane fuel were stabilized at six global fuel-air equivalence ratios. The velocity, reaction zone structure and soot measurements were performed using stereoscopic particle image velocimetry, planar laser induced fluorescence of OH radicals and laser induced incandescence, respectively. In all the experimented test flow cases, the time-averaged velocity data show the presence of two large recirculation zones, separated by a zone of high velocity swirled inflow. The inner recirculation zone, which surrounds the combustor axis, shows high turbulence intensities. In gaseous fuel flames, the inner recirculation zone also contained most of the combustion-generated soot concentration of the flow field of gaseous fuel flames. The flow field regions exterior to the inner recirculation zone showed negligible soot values mainly due to the soot oxidation caused by the high intensity turbulence as well as strong OH intensity near the recirculation zone boundary. The time-averaged soot values showed strong sensitivity to changes in the air flow rates. The changes in the air flow rate mostly increased the soot intermittency, while the instantaneous soot concentrations stayed nearly constant. Intensified turbulence as well as shortening of flow time for soot chemistry are speculated to be the reasons for the high sensitivity of soot values to air flow rates. Further, in n-heptane/air flames, the velocity data showed a region of high velocity fuel droplets, positioned in-between two large recirculation zones. The boundary of the inner recirculation zones showed the heat release events, thereby leading to high OH counts. The OH fluorescence profiles showed the major role played by the recirculation zones in fuel droplet evaporation, forming the evaporated fuel-air reactant mixture, and subsequently, igniting the reactant mixture in the presence of hot combustion products and active radicals.
Adaptation and Differentiation in Introduced Plant Species
Keywords: Adaptation
Ambrosia artemisiifolia
Clines
G matrices
Invasive species

Introduced species offer an opportunity to study evolutionary responses in colonizing populations. My dissertation explores local adaptation in two introduced plants, Arabidopsis thaliana and Ambrosia artemisiifolia. North American Arabidopsis populations have a clinal pattern in flowering time, with populations closer to the coast flowering later than those further inland. To test the source of this differentiation, my coauthors and I grew 50 lines from 25 North American populations in a chamber and simulated winter conditions. We found support for the hypothesis that winter precipitation is the selective force driving differentiation among introduced A. thaliana populations. Adaptation can be critical in the ability of a colonizing species to persist and spread. Assessing the adaptive capacity of a population is difficult, and cannot be extrapolated from invasion history or molecular genetic metrics. To estimate the adaptive capacity of A. artemisiifolia populations, I needed to perform controlled crosses. To this end, I developed a system for isolating plants in individual chambers. I then performed crosses for 50 sires with 3 dams each for three native and three invasive populations. This allowed me to isolate estimates of additive genetic variance and generate G matrices for each population. I found that introduced populations did not have a lower ability to respond to selection than native populations. To explore phenotypic divergence in A. artemisiifolia populations, I grew up seeds from 18 introduced and 20 native populations in a common garden. I found parallel clines in flowering time and size. I compared this quantitative differentiation with neutral genetic diversity in 20000+ SNPs. I concluded that the parallel patterns of differentiation seen in native and introduced ragweed are likely the results of local adaptation, and not neutral processes. My thesis integrates multiple approaches and study organisms to investigate the patterns and processes of contemporary adaptation in non-native plants.
Farming for System Change: The Politics of Food Sovereignty and Climate Change in Canada
Keywords: Agroecology
Climate change
Ecological farming
Food sovereignty
Food systems
Political ecology

In this dissertation, I explore the overlap between climate change and food production, focusing on the concept of food sovereignty and the potential for ecological farming to help mitigate greenhouse gas emissions. I unveil how the concepts of food sovereignty and agroecology are (and are not) being taken up by Canadian farmers, farmers’ organizations and others who have a stake in climate change debates. Based on two years of scholar-activist-oriented research, including interviews with farmers and ethnographic engagements on farms and at events focused on agricultural politics and practices, I describe the opportunities and constraints for agroecological approaches to contribute to mitigating climate change, as well as the significant political, geographical and socio-cultural challenges that are generally inhibiting the actualization of food sovereignty in Canada. Focusing on the work of La Vía Campesina’s two member organizations in this country, the National Farmers Union (NFU) and Union Paysanne, I am concerned with the basic problem of how tensions between systemic and pragmatic changes are articulated through agroecology initiatives and food sovereignty advocacy. My essential claim is that a broad counterhegemonic movement will be required in order for there to be a significant shift in climate and food politics in Canada. Food sovereignty and agroecology have the potential to be incorporated into a system change agenda, I argue, but any serious effort to move them forward, and tackle climate change, will require confronting capitalism itself. I do not suggest that this will necessarily require overt anticapitalist campaigns, but rather that farmers and other food sovereignty proponents will do well to grapple with the structural constraints within capitalism, while finding ways to talk about and pursue radical change through ostensibly more prosaic initiatives. As part of the counterhegemonic shift I am pointing to, I also argue that farmers’ organizations will need to prioritize both strategic alliance-building with various groups, as well as political education activities that can help both farmers and non-farmers make progress on these fronts, disrupting apolitical approaches to climate and food issues.
Integrating Electron Paramagnetic Resonance Spectroscopy and Virtual Reality into the Structural Biology Pipeline
Keywords: Biophysics
EPR spectroscopy
Protein crystallography
Protein refolding
Site-directed spin labelling
Structural biology

The advancement of structural biology as a field is limited by the technology involved at the stages of the protein production, structure determination and dissemination to the greater community. This dissertation explores new applications of technologies at each of these three stages. Specifically, new use cases for EPR spectroscopy and VR will be established. Protein production: Refolding membrane proteins from material expressed in Escherichia coli inclusion bodies is an attractive alternative to more complex eukaryotic expression systems. However, detecting refolding on a solid support for the purposes of optimizing protein production is not feasible using standard spectroscopies. Since EPR employs microwave radiation, it can be applied to measure the degree of membrane protein refolding on standard Ni-NTA resins. Refolding workflows from denatured bacteriorhodopsin and bacterioopsin expressed into inclusion bodies are followed, and the refolded fractions are quantitated. Structure determination: DEER spectroscopy is a powerful pulsed EPR technique that measures distance distributions between spin-labelled side chains on proteins. However, the side chains are quite flexible, such that accounting for rotamers is complex and results in a large degree of error when making biological interpretations from distance distributions. To address this problem, the application is shifted away from using standard side chains to a more internally constrained one. Then, a crystallographic rotamer library of the few and discrete rotamers is generated, which can be used for spin-labelled side chain modelling on proteins of interest. Structure dissemination: Communicating intricate 3D biomolecular structures to others using 2D projections often does not deliver a complete picture of the important features of the structure. Options for exploring these structures in immersive environments like virtual reality (VR) exist. However, most of these require costly VR setups and are often limited to single units. How a browser-based molecular visualization tool can give rise to novel applications, such as large-scale VR seminars, is explored in collaboration with Autodesk Life Sciences.
A Theory of Family-Class Immigration and its Policy Implications
Keywords: borders
family
family reunification
migration
rights

In this thesis, I argue for a right to family reunification: a right against one's state to bring in one's foreign family members to reside in the state permanently. Though this conclusion runs against current legal norms, I argue that it flows directly from liberal values and ought to persuade liberal states to recognize this right. My argument is consistent with states' general (though limited) right to exercise their discretion in controlling their borders, foregoing cosmopolitanism. Chapter 2 articulates a functional definition of the family as a group of individuals who share in a relationship of mutual care, responsibility, and sharing of resources and experiences, and defends a right (against one's own state) to family life based on our interests in care and sharing our lives. It also discusses two specific applications of the right to family life: the right to form a family of one's choice and the right to uninterrupted family life. Chapter 3 argues that the right to family life also entails that we have a civil right (against our state) to be reunited with our foreign family members within our state. It also considers and refutes the objection that such a right would be uniquely and unacceptably burdensome. Chapter 4 contextualizes this theoretical defence of the right to family reunification within the broader immigration ethics literature. It examines the debate between open-border and closed-border positions, and reviews immigration theories grounded in communitarianism, individualism, and cosmopolitanism. Most theories do not attend, or attend with limited sensitivity, to the unique considerations at play in family-class immigration. Chapter 5 examines and critiques a number of typical limitations imposed on family reunification: restrictive definitions of family, quotas, the `elsewhere approach.' It also considers a group of limitations that could be permissible so long as they are proportionate. This thesis offers an exhaustive account of the considerations at play in a right to family reunification, building it from its theoretical foundations in the right to family life, assessing its power in the cross-border context, contextualizing it within the broader immigration ethics literature, and discussing its practical implications.
Women Organizations for Peace: Moving Beyond the Rhetoric of the Cyprus Problem
Keywords: Cyprus Problem
divided societies
peace building
transnational feminist theory
women
peace and security
women's organizations

Abstract This research examines enduring women’s organizations working towards women’s rights and a peaceful solution to the Cyprus Problem which has taken precedence over gender equality on the island. This study was based on a 13-year period from 2001 to 2014 examining Hands Across the Divide (HAD), the Gender Advisory Team (GAT), and the Mediterranean Institute of Gender Studies (MIGS) as important groups who have played a key role in women's activism that spans the long-standing partition of Cyprus. This qualitative research-based project applies a transnational feminist lens the following research questions: The central research questions for this study are: 1) How have women’s groups organized for peace? 2) What have been their key issues and organizing strategies? 3) What have been their organizing successes and challenges? I use feminist methods to collect data through participant observation, one-on-one interviews, and focus groups to show how women's organizing within these long-standing groups have played a key role in bicommunal women's activism on the island including the mobilization of the women, peace and security agenda during significant periods in Cypriot history. Each organization is examined through the multi-layered and fragmented ways that the demand for women’s rights has occurred on the island, as well the ways that multigenerational women have sought to make their voices heard in the midst of Cyprus Problem. I conclude with an analysis of how working against ethno-nationalist culture and the need to move beyond the binary of ethnicity and ethnic divisions has resulted in the fight against gendered violence and the marginalization of women’s rights. There is a need to develop a third space in which intersectionality allows women’s groups to engage island-wide with groups fighting other forms of oppression and to create opportunities to work together.
Hardware Specialization for Transaction Processing
Keywords: Database
FPGA
Hardware specialization
OLTP

Hardware specialization has been considered as a promising way to overcome the power wall, ushering in heterogeneous computing paradigm. Meanwhile, several trends, such as cloud computing and advanced reconfigurable computing technology (FPGA), are converging to eliminate the barriers to custom hardware deployment, allowing it to be both technologically and economically feasible. In this thesis, we report a case of hardware specialization for OLTP databases and present a fast and power-efficient transaction processing system, called BionicDB. We first discuss the main challenges of modern software OLTP systems on general-purpose CPUs: frequent memory stalls from indexing and unscalable inter-worker communication. We then design and implement several hardware acceleration techniques to address the problems. Also, we develop a custom processor to deal with heavy control-flow, such as dynamic loops and conditional branches, in transaction logic and tightly integrate it with the acceleration fabric, comprising a hybrid processor-accelerator (software-hardware) architecture. We build BionicDB on FPGA and show that it performs faster or comparable to state-of-the-art software OLTP systems with an order of magnitude higher power-efficiency inherently offered by FPGA.
A Network-based Analysis of Hepatocellular Carcinoma
Keywords: Hepatocellular carcinoma
Network Analysis

Hepatocellular carcinoma (HCC) is a high-fatality cancer with complex pathogenesis, often arising in the setting of various chronic liver diseases when it is too late to offer any curative therapy. This PhD thesis is divided into two parts, the first of which was completed at McGill University under the supervision of Dr. Nahum Sonenberg, and evaluated inhibition of translation downstream of mTOR. This work was performed in the context of much interest in inhibiting the mTOR pathway in HCC, given its identification as a dominant pathway in this cancer. In the first part of this thesis, I evaluated how metformin inhibits HCC growth, by decreasing translation of anti-apoptotic proteins such as Mcl-1 downstream of mTOR. In the second part of this thesis, I sought to better understand the role of the mTOR pathway in relation to other commonly dysregulated pathways in HCC. All publicly available, high-throughput gene expression data in HCC was curated at http://ophid.utoronto.ca/CDIPLiver. Clinical variables such as etiology of liver disease and liver function parameters, important to understanding clinical relevance of gene expression data, were only available in around 50% of studies. Betweenness centrality calculation was performed on genes differentially expressed between HCC and corresponding background liver tissue, and revealed Estrogen Receptor 1 (ESR1) to be most central to the HCC Protein-Protein Interaction (PPI) network. HCC cells transfected with ESR1 and exposed to estradiol had significantly decreased proliferation and viability. Gene expression revealed that ESR1 upregulation significantly affected cellular processes such as histone methylation, transcription, and cell cycle. High expression of ESR1 in HCC tumors was found to be protective. Finally, we curated all publicly available whole exome sequencing, DNA methylation, microRNA, and proteomics data in HCC. Pathway analysis was performed on significantly dysregulated genes, and overlapping pathways identified. The following pathways overlapped among the 5 different datasets: Epidermal Growth Factor (EGFR), B1-integrin and axon guidance proteins, suggesting pathway dependencies in HCC. A systems biology approach to HCC allowed us to elucidate the role of sex-specific differences and importance of specific pathways in HCC biology, providing biological rationale for a more targeted therapeutic approach to HCC.
Investigation of Shear-critical One-way Concrete Slabs Internally Reinforced with GFRP Bars
Keywords: Concrete Slab
GFRP
High Strength Concrete
Reinforced Concrete
Shear

With increasing attractiveness among industry professionals, the application of Glass Fiber Reinforced Polymer (GFRP) bars as internal reinforcement for concrete structures has been rapidly growing for specific conditions such as corrosive or electromagnetic environment. Only limited design guidelines are available primarily due to the fact that the experimental database is also limited. This dissertation presents both experimental data and numerical analysis of GFRP reinforced slabs subjected to one-way shear. The experimental component was conducted on 20 specimens categorized into two groups of small and large slabs with cross-sectional dimensions of 200x1000 mm and 400x1500 mm, and shear-span-to-depth ratios of 6.6 and 3, respectively. The specimens were simply supported, and tested to failure under monotonic four-point loading. To explore the shear behavior, variables included concrete strength, longitudinal reinforcement ratio, longitudinal bar spacing, bar type and surface characteristics, and amount of shear resisting GFRP headed studs. The effect of each variable was investigated and the main findings were reported. In general, it was found that using high strength concrete may not always be of advantageous, and in small slabs particularly resulted lower capacity. Improved performance was observed by increasing the reinforcement ratio, and reducing longitudinal bar spacing. Application of GFRP headed studs, acting as shear reinforcement, also showed promising results in specimens with larger depth and made with normal strength concrete. The results from the current experimental work and those from the previously tested specimens were compared against the predictions using selected design codes including ACI440.1R-15, CAN/CSA S6-14, CAN/CSA S806-12, and previously suggested modifications incorporating 2nd orders of  and θ. A new optimized equation was proposed for mid-depth longitudinal strain, and improvement was observed in the prediction of shear capacities compared with studied design codes and previously suggested methods.