VictorJuiz/thesis huggingface dataset:
Super-Resolution Fluorescence Microscopy Studies of Protein Association and Higher-Order Structure
Keywords: Hyperspectral imaging
Membrane contact sites
Protein interaction and association
Super-Resolution Microscopy
Supramolecular protein structure

The spatial organization and interaction of proteins within cells fuels a myriad of biological processes. Protein modification, transport, signaling, polymerization and membrane remodeling are just a few examples. In cellular pathways, such as the endocytic membrane transport pathway, the recruitment of specific proteins and protein complexes to the membrane are hallmarks of the maturation and progression of the process. Interaction of membrane proteins from different organelles is of great importance as well. Recent discoveries have suggested that organelles may communicate with each other and exchange lipids and metabolites through the association of tethering proteins. Their proliferation may also be directly dependent on inter-organelle cooperativity such as the interaction of the endoplasmic reticulum with mitochondria and peroxisomes. Protein polymerization allows the creation of large macromolecular foundations that are mediators of diffusion and compartmentalization. The organizational motifs by which these assemblies are built are of interest for structure-function relationships. The interaction and association of protein complexes as described above takes place at the nanoscale, below the optical diffraction limit. Although the colocalization of proteins can be visualized via traditional forms of fluorescence microscopy, many biological questions require a finer level of resolution. Super-resolution fluorescence microscopy has revolutionized optical imaging by harnessing advances in hardware, software and the modulation of light. Variations in illumination and emission can be used to break the diffraction limit and observe a new level of detail in the cell. This thesis focuses on two of these techniques, Structured Illumination Microscopy and Single-Molecule Localization Microscopy, and their application to questions of nanoscale protein interactions in the endomembrane system, peroxisomal division and the supramolecular arrangement of septin proteins. The work concludes with a novel technological extension of Single-Molecule Localization Microscopy.
Mutagenic Gene Trapping to Study Novel Genes in Zebrafish Cardiovascular Development
Keywords: Cardiovascular
Genetics
Gene trapping
Heart
Lymphatic
Zebrafish

Cardiovascular development is a finely tuned process involving multiple conserved signaling pathways. Perturbation of this process can lead to congenital malformations. Despite the considerable progress, the entire suite of genes and regulatory pathways involved in cardiovascular development are unknown. In this study, we utilized to a Tol2-based gene trap system, a transposition-based forward genetics tool, to mutate and functionally characterize genes involved in cardiovascular development in zebrafish (Danio rerio). Zebrafish exhibit the anatomical and physiological complexity of a closed circulatory system, with arteries, veins and lymphatic vessels. Of the 51 generated mutant fish lines, we expounded on a mutant line, in which the Tol2 transgene was incorporated into the platelet-derived growth factor receptor alpha (pdgfra) gene, resulting in truncation and fusion of the native transcript to monomeric red fluorescent protein (mRFP). PDGFRα is a highly conserved tyrosine kinase receptor essential for development and organogenesis. Disruption of PDGFRα function in murine models is embryonic lethal due to severe cardiovascular defects, thus, necessitating the use of alternative models to explore its precise function in cardiovascular development. Our results demonstrate that zebrafish pdgfra mutants develop cardiac defects as a result of abnormal endocardial and myocardial precursor migration to the midline during the process of cardiac fusion, an essential step for cardiac assembly and development. Moreover, we show that the Pdgfra-mRFP fusion protein is initially expressed in venous-derived endothelial cells, including lymphangioblasts, followed by progressive specification into lymphatic endothelial cell fate. Investigation of blood and lymphatic vessels in pdgfra mutants revealed significant defects in venous and lymphatic vessel development. Together, the results acquired from this project reveal a hitherto unknown expression of Pdgfra in developing lymphatic vessels and uncovers a functional role for Pdgfra signaling in regulating cardiac fusion and lympho-venous sprouting events. Broadly speaking, the content of this research will advance our knowledge in fundamental processes of cardiac and lymphatic development, with potential diagnostic and therapeutic utility.
Game Changers: Everyday Gamemakers and the Development of the Video Game Industry
Keywords: Creative Workers
Cultural Industry
Digital Games
Digital Game Workers
Scenes
Video Game Industry

This dissertation examines the emergence of everyday gamemakers and their roles in transforming the cultural norms and practices of the global video game industry. Everyday gamemakers are digital game creators who share multiple professional and leisure-based gamemaking identities, including developers, “indies,” modders, user-generated content creators, and writers of interactive fiction. Since the Apple App Store opened in 2008, game engines and digital venues have developed and enabled widespread production and distribution of digital games. Game engines such as Unity3D, GameMaker Studio, and Construct 2, which simplify the process of making a digital game using “drag-and-drop” tools and editors, have enabled a range of gamemakers with no programming or artistic experience and training to create digital games. The simultaneous release of digital platforms such as Google Play, Steam, and itch.io, has also streamlined the process of distributing digital games into new and traditional communities of players. These developments have emerged because the video game industry perceives everyday gamemakers to be innovators in diversifying and producing products, creating jobs, and increasing profits. However, I argue that the inclusion of the everyday gamemaker has simultaneously enabled local and grassroots norms and practices to transform the production process of digital game creation in the global video game industry. To demonstrate how these gamemakers are changing norms and practices across the industry, I focus on gamemakers’ work and leisure identities as creators of digital games; the cultural activities of the scenes in which they participate; the game engines and tools of production they use to make their games; the working conditions in which they build their games; and the distribution platforms on which they release their games. I argue that gamemakers wear many labour hats within their craft of gamemaking, which not only diversifies the work and leisure contexts of digital game production, but also enables the mixing and transformation of cultural norms and practices within the mainstream industry and the places of leisure more broadly.
Tissue Engineering Architectural Cues for in vitro Models of Respiratory Epithelium
Keywords: Alveolar
Architecture
Epithelium
Fabrication
Topography
Trachea

Diseases affecting the respiratory system are one of the major leading causes of death worldwide. Epithelial dysfunction is associated with many lung diseases and therefore tools for primary cell culture are important for generating models of human lung epithelium. Respiratory epithelium is comprised of many diverse cell types that inhabit structurally distinct regions in the lung and airways. In vitro approaches to generate or repair epithelium are inadequate as they do not incorporate the specific architecture that lung and airway tissues exhibit in vivo, resulting in disorganized and dysfunctional epithelial cells. We hypothesized micropatterned biophysical cues, in the form of stiffness and topography, will induce alignment of airway epithelial cells along a defined tissue axis. We also hypothesized that culture of distal lung epithelial cells in biomimetic architecture will extend the maintenance of viability and phenotype. We employed three scaffolding approaches with microengineered biophysical cues to control epithelial behaviour. In the first two approaches, we applied micropatterning techniques to create hydrogel systems that were compatible with air-liquid interface (ALI) culture of airway epithelium. Although our stiffness-patterning platform did not support primary culture, we found that primary epithelial cells can be cultured on collagen vitrigel membranes and groove topography induces morphological alignment for up to 14 days of ALI culture. In the third approach, we generated a poly-dimethylsiloxane culture substrate with alveolar-mimetic curvature for culture of lung epithelial cells. Specifically, primary mouse cells grown in cavity culture conditions remain viable (96 ± 4% vs. 2 ± 1% on flat controls) and maintained expression of phenotypic markers (surfactant protein C, aquaporin-5) over one week. These findings demonstrate the profound influence of biophysical cues on epithelial behaviours including spreading, polarization and phenotype. Our rationally-designed biomaterial substrates are able to mimic numerous aspects of the extracellular matrix and direct the behaviour of adult primary cells derived from mammalian trachea and lung epithelial progenitors. Biomaterial scaffolds with defined architectural cues advance the capabilities of lung and airway epithelial models to instruct tissue function and provide platforms for understanding mechanisms of lung disease and repair.
Israeli Jazz Musicians in the International Scene: A Case Study of Musical Transculturation in Contemporary Jazz Performance and Composition
Keywords: composition
Israel
jazz
Jewish
performance

This dissertation is a case study of transculturation in jazz composition and performance through the examination of the practices of Israeli jazz musicians who began to operate on the international jazz scene starting in the 1990s. An impressive number of Israeli jazz performers have received widespread exposure and acclaim over the last twenty years. Artists such as Omer Avital (bass), Anat Cohen (woodwinds), Avishai Cohen (bass) among many others have successfully established themselves on a global scale, creating music that melds various aspects of “American” jazz with an array of Israeli, Jewish and Middle-Eastern influences and those from numerous other non-Western musical traditions. While each musician is developing his or her own approach to musical transculturation, common threads connect them all. Unraveling these entangled sounds and related discourses lies at the center of my study. While this is the first comprehensive study of the contributions of Israeli musicians in the international jazz scene, it is also intended to engage with the “global” phenomenon of transcultural jazz practice more broadly. By considering the performers discussed in the study as multi-local musicians, I offer an alternative to both American exceptionalist views of jazz, for instance, jazz as America’s gift to the world, and to “jazz nationalism”, a scholarly outlook that emphasizes the localization of “jazz” in (non-American) nation-states, and that continues to hold sway around the world, especially in Europe. In so doing, I also aim to invite explorations of the multi-local music making practices of jazz musicians worldwide. Thus, this project simultaneously provides insight into the nature and role of transcultural music making in contemporary jazz practice while enhancing knowledge of modern Israeli society and culture.
Resistance Along the Rails: Confronting Deindustrialization and Urban Renewal as a Neoliberal Socio-Ecological Fix through Social Movement Alliance-Forming in Toronto, Canada
Keywords: community benefits agreement
green economy
labor-community coalition
participatory community-based research
social movement coalitions
urban restructuring

This dissertation analyzes post-Fordist social movement coalitions between labour, community and environmental groups that responded to, but also helped constitute, processes of deindustrialization and so-called urban renewal in Toronto, Canada between 2004-2015. I theorize this urban restructuring not only as a spatio-temporal fix but as a more encompassing “socio-ecological fix” that better accounts for the socio-ecological constraints and opportunities placed on the production of urban space for and by capital, labour and a wider range of social (movement) actors. The emergence, development, efficacy and impacts of two labour-community coalitions in Toronto are analyzed by integrating macro-scale theories of coalitions (i.e., eco-Marxist and Gramscian approaches) with social movement theory and ethnographic approaches. The Mount Dennis Weston Network (2007-2012) sought to create “green jobs” on a brownfield site before scaling-up into the Toronto Community Benefits Network (TCBN). The TCBN (2013-2015) aimed to win Ontario's first “community benefits agreement” (CBA) as a tool for leveraging rapid transit infrastructure investments to achieve other social and environmental policy objectives (e.g., employment equity, social procurement, environmental design, etc.). I appraise these coalitions as efforts to demand a right to the city—i.e., more democratic and egalitarian production of urban space (including the regulation of the urban metabolism)—and in terms of social movement alliance-forming that I define as a two-way shift in scale: an institutional broadening (or organizational scaling-up) and an ideological deepening (i.e. praxis). These social movement processes require more extensive on-the-ground organizing within neighbourhoods and unions without which coalitions risk becoming coopted and confined to negotiating minor concessions and trade-offs that deepen socio-ecological tensions and contradictions. In this way, discourses around “green jobs,” “sustainable cities,” and “community benefits” have been used by the state and corporations to organize consent for neoliberal urban governance (i.e., increased privatization and deregulation of the transit and energy sectors, and transit-led gentrification).
Optimizing Geotechnical Data Collection Campaigns in Open Pit Mines
Keywords: confidence level
data variability
geotechnical model
open pit design
quantitative guidelines
slope stability

Open pit slope design requires sufficient geotechnical data to establish a representative geotechnical model for slope stability analyses. Geotechnical data uncertainty can result in a poor performance of the pit slopes with potential adverse consequences (loss of life, increased costs, operational delays, etc.). It is generally accepted that different confidence levels in the collected geotechnical data are targeted per project stage, with an increased confidence level from the early stage to the more mature stages of a mine. The absence of quantitative guidelines is an important issue due to the risk associated with data uncertainty that can be quite high. This thesis proposes a methodology to quantify the confidence level in the employed geotechnical data for open pit slope design. It furthermore provides quantitative guidelines for the minimum number of boreholes, laboratory tests and joint orientation data required to reach targeted levels of confidence in the collected geotechnical data. Three South African mine sites were selected to construct comprehensive case studies. The analyses of the collected geotechnical data allowed to quantify the impact of collecting additional data in the slope design process for different project stages in the life of a mine. The minimum number of boreholes to minimize the variation of the interpreted geological model from the real rock mass was evaluated by progressively increasing the number of boreholes simulated in 3D geological models. Statistical analyses, using the small-sampling theory, were performed to determine the minimum number of specimens required to reach targeted levels of confidence in the normally distributed laboratory testing results. A new methodology was developed to accommodate for lognormally distributed data. Structural data were analysed using discrete fracture networks (DFN) by simulating sampling boreholes in the models. The minimum number of joint orientation data required to reach targeted levels of confidence was evaluated by progressively increasing the simulated drilling density. The principal contribution of this thesis is an innovative methodology for planning geotechnical data collection campaigns to insure to reach targeted levels of confidence in the collected data. These quantitative measures can eventually replace subjective measures in subsequent risk analyses.
The Impact of Spoken Semantic Threat on Cognitive and Linguistic Processing Involved in Spoken Language Following a Traumatic Brain Injury (TBI)
Keywords: cognition
emotion processing
language
semantic threat
speech processing
traumatic brain injury

A traumatic brain injury (TBI) significantly impacts many functions, with changes in emotional and social behaviours being among the most debilitating consequences. Accruing literature attests to emotion processing deficits in this population, with a particular impairment in processing negative emotions (including semantic threat) across visual and auditory modalities (Bornhofen McDonald, 2008; Croker McDonald, 2005; Maki-Marttunen et al., 2015). Impairments in processing negative emotions may lead to problems in interpersonal interactions, which could significantly impact the quality of life for individuals with TBI (Dijkers, 2004; Henry, Phillips, Crawford, Theodorous Summers, 2006). Despite the growing prevalence of emotion processing deficits in the TBI population, there is still a paucity of research investigating the extent and nature of these deficits. Importantly, no study to date has directly examined the impact of spoken semantic threat, particularly in the context of how it may hinder cognitive and linguistic processes used in spoken language as part of everyday conversation. Thus, a novel paradigm known as the Linguistic Acoustic ThreaT Effect (LATTE) was employed in three experimental studies to examine this impact in more detail. Results from Study 1 showed that individuals with TBI were impacted by spoken semantic threat to a greater extent than healthy matched controls. Results from Study 2 showed that the threat effect has a physiological basis in terms of increased autonomic arousal and varies in the extent of the impact based on the content of threat presented. Lastly, the results of Study 3 demonstrated that semantic threat seems to have a critical period during which it exerts its impact, and is most observable during the stages of speech processing following the immediate presentation of the verbal threat, as tested in our sequence of tasks. Taken together, our results reveal important information on the impact of semantic threat on cognitive and linguistic processes used in spoken language after TBI. Our findings could have potential implications for the training of rehabilitation clinicians and researchers regarding emotion expression when communicating with individuals with TBI.
Signal Normalization Strategies Towards Robust Carbon-13 Imaging for Clinical Translation
Keywords: cancer
carbon-13
lactate
magnetic resonance imaging
metabolism

Prostate cancer is a heterogeneous disease. Some patients present with rapid progression, while many others never exhibit clinical symptoms. Difficulties in assessing risk of disease progression with currently available medical imaging modalities lead to treatment of both groups. However, inappropriate treatment of an indolent disease can have potential side effects with little benefit to the patient. Hyperpolarized ¹³C magnetic resonance imaging is presented as a modality that can detect increased lactate production associated with transformation to metastatic disease. An increased ¹³C lactate signal may be a valuable early indication of disease progression for patients under active surveillance. There is currently no consensus on how to interpret the observed lactate signal. In this dissertation, three signal normalization techniques are presented to prospectively account for the experimental factors of spin polarization, substrate delivery, and off-resonance. Dynamic nuclear polarization confers a temporary signal enhancement resulting from a non-equilibrium spin polarization. The polarization decreases with time due to longitudinal relaxation. For pyruvate, a spectral feature known as asymmetry can be correlated with the spin polarization. Calibration data were acquired as an empirical relationship between asymmetry and spin polarization. By prospectively accounting for the spin polarization, the normalized signal better reflects the metabolic activity in the tissue. Low ¹³C lactate signal could be attributed to slow metabolic activity or poor substrate delivery. Normalization of ¹³C lactate by the signal intensity of a co-polarized perfusion agent is proposed as an approach to account for substrate delivery. Spectrally-selective signal excitation schemes can greatly simplify signal encoding requirements, but the frequency sensitivity can also lead to incomplete excitation and imaging artifacts if the prescribed excitation frequency does not match the resonance frequency of the signal of interest. A modified pulse sequence with wider spectral passbands and multi-echo acquisition is proposed as a prospective flip angle normalization strategy. The dissertation concludes with a presentation of the current state of clinical translation of hyperpolarized ¹³C imaging technology in Toronto. The first ¹³C image of the human heart is shown along with preliminary data from the prostate cancer clinical trial.