VictorJuiz/thesis huggingface dataset:
Computational Prediction of PDZ Mediated Protein-protein Interactions
Keywords: protein-protein interactions
interaction prediction
PDZ domains
machine learning

Many protein-protein interactions, especially those involved in eukaryotic signalling, are mediated by PDZ domains through the recognition of hydrophobic C-termini. The availability of experimental PDZ interaction data sets have led to the construction of computational methods to predict PDZ domain-peptide interactions. Such predictors are ideally suited to predict interactions in single organisms or for limited subsets of PDZ domains. As a result, the goal of my thesis has been to build general predictors that can be used to scan the proteomes of multiple organisms for ligands for almost all PDZ domains from select model organisms. A framework consisting of four steps: data collection, feature encoding, predictor training and evaluation was developed and applied for all predictors built in this thesis. The first predictor utilized PDZ domain-peptide sequence information from two interaction data sets obtained from high throughput protein microarray and phage display experiments in mouse and human, respectively. The second predictor used PDZ domain structure and peptide sequence information. I showed that these predictors are complementary to each other, are capable of predicting unseen interactions and can be used for the purposes of proteome scanning in human, worm and fly. As both positive and negative interactions are required for building a successful predictor, a major obstacle I addressed was the generation of artificial negative interactions for training. In particular, I used position weight matrices to generate such negatives for the positive only phage display data and used a semi-supervised learning approach to overcome the problem of over-prediction (i.e. prediction of too many positives). These predictors are available as a community web resource: http://webservice.baderlab.org/domains/POW. Finally, a Bayesian integration method combining information from different biological evidence sources was used to filter the human proteome scanning predictions from both predictors. This resulted in the construction of a comprehensive physiologically relevant high confidence PDZ mediated protein-protein interaction network in human.
Reliable Safety Broadcasting in Vehicular Ad hoc Networks using Network Coding
Keywords: vehicular networks
network coding

We study the application of network coding in periodic safety broadcasting in Vehicular Ad hoc Networks. We design a sub-layer in the application layer of the WAVE architecture. Our design uses rebroadcasting of network coded safety messages, which considerably improves the overall reliability. It also tackles the synchronized collision problem stated in the IEEE 1609.4 standard as well as congestion problem and vehicle-to-vehicle channel loss. We study how massage repetition can be used to optimize the reliability in combination with a simple congestion control algorithm. We analytically evaluate the application of network coding using a sequence of discrete phase-type distributions. Based on this model, a tight safety message loss probability upper bound is derived. Completion delay is defined as the delay that a node receives the messages of its neighbour nodes. We provide asymptotic delay analysis and prove a general and a restricted tighter asymptotic upper bound for the completion delay of random linear network coding. For some safety applications, average vehicle to vehicle reception delay is of interest. An instantly decodable network coding based on heuristics of index coding problem is proposed. Each node at each transmission opportunity tries to XOR some of its received original messages. The decision is made in a greedy manner and based on the side information provided by the feedback matrix. A distributed feedback mechanism is also introduced to piggyback the side information in the safety messages. We also construct a Tanner graph based on the feedback information and use the Belief Propagation algorithm as an efficient heuristic similar to LDPC decoding. Layered BP is shown to be an effective algorithm for our application. Lastly, we present a simple experimental framework to evaluate the performance of repetition based MAC protocols. We conduct an experiment to compare the POC-based MAC protocol with a random repetition-based MAC.
Advances in Tracheal Tissue-Engineering: Evaluation of the Structural Integrity, Immunogenicity and Recellularization of a Decellularized Circumferential Long-segment Trachea for Airway Transplantation
Keywords: Trachea
Tissue-engineering
biological scaffolds

Subglottic stenosis, malignancy and traumatic injury to the trachea require surgical resection. When defects are less than 50% of the tracheal length in adults and 1/3 in children, a circumferential resection and primary anastomosis affords excellent results. For longer lesions, on the other hand, there are no currently acceptable solutions leading to patients requiring permanent tracheostomies or palliative treatment. Tracheal replacement approaches with synthetic prosthesis and scaffolds have all led to inflammation, obstruction, mucous build-up and eventual restenosis. Tissue-engineering approaches using recipients’ own stem cells and biologic scaffolds derived from decellularized donor trachea have shown great promise. They have the potential to abrogate the need for immunosuppressive therapy. Our research focuses on three major limitations in this field including the structural integrity, the immunogenicity and the recellularization of donor tracheae. We compared three decellularization protocols, quantified and qualified the extracellular matrix (ECM) components and performed compliance measurements on large circumferential tracheal scaffolds following cyclical decellularization techniques and illustrated significant differences in ECM composition and resultant structural integrity of decellularized tracheal scaffolds depending on the protocol. In addition, we investigated the immunogenicity of decellularized and recellularized tracheal allografts at a protein level and in vitro and in vivo T cell proliferation. Decellularization is associated with a delay in leukocyte infiltration and recellularization promoted cartilage preservation and the recruitment of regulatory T cells. We described a dramatic increase of TGF-β1 in recellularized scaffolds. Moreover, we designed a dual-chamber bioreactor for recellularization of tracheal allografts. Our method allowed for dynamic perfusion seeding, confirmed adherence of two different cell types and achieved higher cell numbers and homogeneous structures compared to traditional static seeding methods. In summary, we have identified and addressed three major limitations for tissue-engineering of long-segment decellularized tracheal scaffolds relating to structural integrity, immunogenicity and recellularization techniques.
The Role of Diversification in the Pricing of Accruals Quality
Keywords: Accruals Quality
Cost of Capital
Diversification
Ambiguity

A growing number of studies suggest that accounting information risk, primarily idiosyncratic in nature, can be diversified away in the capital market. In this dissertation, I show that accounting information risk, proxied by accruals quality, is priced even if it is entirely idiosyncratic. In particular, building on a model from the ambiguity literature, I demonstrate that (1) in an under-diversified market, idiosyncratic information risk is priced even if it is diversifiable, and (2) in a well-diversified market, idiosyncratic information risk is priced when information is subject to managers' discretion and thus ambiguous. The empirical results corroborate the predictions from the model. Specifically, although an association is observed between (unambiguous if risky) innate accruals quality and cost of capital, the association can be largely mitigated through diversification. However, diversification has little impact on the association between (ambiguous) discretionary accruals quality and cost of capital. Taken together, these findings strengthen our understanding of the fundamental role of accounting information as a basis for capital allocation.
"People Like Me": Racialized Teachers and the Call for Community
Keywords: Equity
Anti-Racism
Racialized Teachers
Inclusive Education
Race
Visible Minority
Diversity
Policy
Multicultural education
Anti-racist education
Racism
Role model
Role-modelling
Marginalized voices
Community
Professional development
Teacher Education
Cultural Studies

The city of Toronto is one of most racially diverse places in the world, with almost half of its population identifying as being a “visible minority” (Statistics Canada, 2010). As a result, the field of education faces the question of how to meet the needs of their transforming student demographics. Numerous researchers and institutional policies have responded to these changes by endorsing the hiring of a teaching staff that is reflective of the racially diversifying student population (Ontario Ministry of Education, 2009; Ryan, Pollock, & Antonelli, 2009; Solomon, & Levine-Rasky, 2003). The assumption, however, that racialized educators will automatically be effective teachers or role models for racialized students homogenizes their social differences and reduces the multiplicity of their identities to the colour of their skin (Martino, & Rezai-Rashti, 2012). What is urgently lacking from these dominant discourses are the voices of racialized individuals, whose inside perspectives and lived experiences can provide valuable insights about the roles of equity and race in education. Using an anti-racist theoretical framework to guide my research methodology, this study examines how racialized teachers understand their classroom practices, school relationships, and institutional policies with respect to race, equity, and the expectations that are cast to them as “visible minority” educators. A document analysis of educational statements that discuss race, equity, and anti-racism reveals that while policy has progressed, the presentation of these issues remains largely superficial and does not provide enough information or transparency to adequately communicate their importance. Nevertheless, the power of these dominant discourses has been vastly significant in shaping the lived experiences and feelings of racialized teachers, 21 of whom were individually interviewed using a qualitative, semi-structured method. The inside perspectives of these teachers demonstrate the complexity of race and its inadvertent impact on their roles as educators; their feelings and reactions illustrate the ongoing gap between policy and practice, the ignorance that is embedded in notions of racial matching between teachers-students, and the persevering call for a professional community where individual differences are viewed as opportunities to learn rather than obstacles that need to be overcome.
Small Spaces for Meaningful Participation in Democratic Life? A Community's Perspectives on tehir particiaptioin in an Early Education and Care program
Keywords: participation
early childhood programs
South Africa

Because the majority of children in many countries are being raised in the dual contexts of home and early childhood settings, early childhood education and care programs are an important site of inquiry not only because of their implications for children’s cognitive, social, and emotional development, but also for their influence on early childhood educators, parents, and the community at large. At the same time that researchers and practitioners were increasingly recognizing the importance of community involvement in early childhood programs, reforms in governance worldwide were giving rise to discourse on small participatory spaces that theorists contend are crucial to the health of a democracy and core to the idea of civil society. This study helps close the gap in the scarcity of research knowledge and educational practice that considers the perspectives of teachers, parents, and other members of a marginalized community in a non-western setting of their participation in an early childhood program. In particular, it sought to understand better whether parental and community participation in an early childhood setting in a South African township has the potential for constructing and strengthening citizenship. This study found generally that participation in this pre-school offered opportunities for meaningful participation in civil society; some participants, however, expressed disappointment and frustration at continuing disparities and inequities.
Radical Musicking: Challenging Dominant Paradigms in Elementary Music Education
Keywords: music education
anti-racism education
elementary music
social justice education
anti-oppression

This project examines the work of four elementary music educators who strive to challenge the dominant paradigm of music education. I employed the methodology of a multiple case study (Merriam, 1998; Yin, 2009) to consider the discourses, practices, and philosophies of these four educators. I observed in each school for an eight-week period for two full days each week, conducting semi-structured interviews at the beginning, middle, and end of each observation process. At each school, I followed an observation protocol, in addition to completing three interviews, and keeping a journal. In this work, I mobilize a tri-faceted lens that combines the theoretical frameworks of anti-colonialism, anti-racism, and anti-racist feminism toward counterhegemonic goals. The teachers' diverse practices include critically engaging with issues of social justice, studying a broad range of musics, introducing multiple musical epistemologies, creating space for students to own the means of cultural production, contextualizing musics, considering differential privilege, and subverting hegemonic practices. In many ways, these four individuals interrupt the traditional Eurocentric focus on Western classical music to explore different possibilities with their students. However, within this work to subvert, there were moments in each classroom where the dominant paradigm was reinscribed. These subversions and reinscriptions are instructive to music education and carry broader implications for the discipline. Ultimately, this thesis argues that a truly radical music education involves shifting from a liberal to a critical paradigm. Many values and strategies traditionally found in liberal education can be reread radically, and doing so puts forward tenets of a radical music education. Within these four classrooms, there were myriad examples of this shift from a liberal to a critical orientation. However, this work also raises questions of positionality and asks explicitly which bodies are able to do radical anti-oppressive work in music education, acknowledging that it is possible to unintentionally reinscribe dominant power relations while working to subvert them.
Interacting Narratives and the Intentional Evolution of Personal Practical Knowledge: Experienced English Teachers' Multiliterate Innovations in the Professional Knowledge Ecosystem
Keywords: Narrative Inquiry
Teacher Development
Multiliteracies Pedagogy

This study is an exploration of the lived experiences of three secondary teachers who have developed innovative approaches to English education in response to the needs of diverse, multi-literate urban students. The research marries multiliteracies pedagogy with narrative inquiry, and explores themes and discourses in the teachers’ narrations of their practices. From the new perspective developed from this pairing emerge two significant findings. First, the study contributes to teacher development by synthesizing concepts of design in multiliteracies pedagogy and personal practical knowledge in narrative inquiry. From this synthesis arises the notion of the intentional design of personal practical knowledge occurring through self-directed professional learning that leads to innovation in teaching. Second, the study develops the concepts of interacting narratives and professional knowledge landscape, offering a method of analyzing the multifaceted interactions of Self and Other narratives in the context of a professional knowledge ecosystem. This method provides a specific framework for contextualizing interacting narratives and provides a new clarity of focus in narrative research texts.
Erosion and Roughness Modeling in Abrasive Jet Micro-machining of Brittle Materials
Keywords: Abrasive jet micro-machining
modeling
Roughness
Erosion

The effect of particle size, velocity, and angle of attack was investigated on the roughness and erosion rate of unmasked channels machined in borosilicate glass using abrasive jet micro-machining (AJM). Single impact experiments were conducted to quantify the damage due to the individual alumina particles. Based on these observations, an analytical model from the literature was modified and used to predict the roughness and erosion rate. A numerical model was then developed to simulate the brittle erosion process leading to the creation of unmasked channels as a function of particle size, velocity, dose, impact angle and target material properties. For the first time, erosion was simulated using models of two damage mechanisms: crater removal due to the formation and growth of lateral cracks, and edge chipping. Accuracy was further enhanced by simulating the actual relationship between particle size, velocity and radial location within the jet using distributions measured with high-speed laser shadowgraphy. The process of post-blasting AJM channels with abrasive particles at a relatively low kinetic energy was also investigated in the present work by measuring the roughness reduction of a reference unmasked channel in borosilicate glass as a function of post-blasting particle size, velocity, dose, and impact angle. The numerical model was modified and used to simulate the post-blasting process leading to the creation of smooth channels as a function of particle size, velocity, dose, impact angle, and target material properties. Finally, the effect of alumina particle kinetic energy and jet impact angle on the roughness and erosion rate of channels machined in borosilicate glass using abrasive slurry jet micro-machining (ASJM) was investigated. The analytical and numerical models derived for AJM, were found to predict reasonably well the roughness and the erosion rate of ASJM channels, despite the large differences in the fluid media, flow patterns, and particle trajectories in AJM and ASJM.
Road Traffic Injury Mortality in India
Keywords: public health
road traffic injury
India
low- and middle-income countries
mortality survey
verbal autopsy
epidemiology
geographic information system
healthcare access
trauma

Introduction: The burden of road traffic injuries (RTI) is worsening globally, particularly in low- and middle-income countries (LMIC) and among the young and economically productive populations. A major barrier to improving road safety in India and other LMIC is that existing RTI data sources are severely limited by poor population coverage and data quality. This dissertation explores the reliability and feasibility of using a novel data source with verbal autopsy (VA) methods for the purposes of RTI surveillance in India. Methods: The reliability of the VA methods was assessed using physician agreement on the specific categories of injury death as the metric. Next, a nationally representative household mortality survey with VA methods was used to directly estimate the age- and gender-specific RTI death rates and to identify context-specific RTI risk factors in India. Finally, a national spatial database was constructed to quantify potential access to trauma care in relation to the spatial distribution of RTI deaths in India. Results: Across a broad array of application settings in India, the level of physician agreement was high indicating that the VA methods were reliable in distinguishing RTI deaths among other specific categories of injury deaths. The estimated 183,600 RTI deaths in 2005 from the mortality survey were over 50% more than the national police statistics. Of these RTI deaths, 65% were males between ages 15-59 years, 68% were pedestrians and other vulnerable road users, and over 55% occurred at the scene of collision, within minutes of collision, and/or involved a head injury. The existing community health centres and district hospitals in the Indian public health system had inadequate trauma care capacity but were suitably located to allow broad spatial access to timely trauma care for the majority of RTI deaths in India, which were most problematic in the northern states of Punjab, Haryana, Himachal Pradesh and in Tamil Nadu. Conclusions: Properly designed VA studies can provide accurate and reliable RTI surveillance data and assist in identifying context-specific road safety interventions.
Touring as Social Practice: Transnational Festivals, Personalized Networks, and New Folk Music Sensibilities
Keywords: Ethnomusicology
Popular Music
Festivals
Transnationalism
Folk Music Revival
Fiddle Music

The aim of this dissertation is to contribute to an understanding of the changing relationship between collectivist ideals and individualism within dispersed, transnational, and heterogeneous cultural spaces. I focus on musicians working in professional folk music, a field that has strong, historic associations with collectivism. This field consists of folk festivals, music camps, and other venues at which musicians from a range of countries, affiliated with broad labels such as ‘Celtic,’ ‘Nordic,’ ‘bluegrass,’ or ‘fiddle music,’ interact. Various collaborative connections emerge from such encounters, creating socio-musical networks that cross boundaries of genre, region, and nation. These interactions create a social space that has received little attention in ethnomusicology. While there is an emerging body of literature devoted to specific folk festivals in the context of globalization, few studies have examined the relationship between the transnational character of this circuit and the changing sensibilities, music, and social networks of particular musicians who make a living on it. To this end, I examine the career trajectories of three interrelated musicians who have worked in folk music: the late Canadian fiddler Oliver Schroer (1956-2008), the Irish flute player Nuala Kennedy, and the Italian organetto player Filippo Gambetta. These musicians are all notable for their taste for transnational collaboration and their reputations as mavericks and boundary-pushers. Through case studies of their projects, relationships, and collaborative networks, I explore transformations in the collectivist folk ideal by focussing on how these musicians are implicated in three phenomena: transnational festivals, new folk music sensibilities, and touring as social practice. This research is based on multi-dimensional, multi-sited fieldwork undertaken in Toronto, Genoa, Edinburgh, and at various festivals in Europe and North America between 2007-2013. I conclude that Schroer, Kennedy, and Gambetta experience transnational folk music space as a field of intersecting transnationalisms that are imaginaries and collectivities of varying size and scope. While festivals in this space increasingly celebrate a transcultural ideal and foster the formation of transnational networks, stable, heterogeneous transnational relationships are proving more difficult to attain. I argue that touring on this circuit generates a desire for community continuity that becomes part of the poetics of new instrumental folk music.