VictorJuiz/thesis huggingface dataset:
Modal Shift Forecasting Models for Transit Service Planning

This research aims at developing a better understanding of commuters preferences and mode switching behaviour towards local transit for work trips. The proposed methodological approach incorporates three main stages. The first introduces a conceptual framework for modal shift maximized transit route design model that extends the use of demand models beyond forecasting transit ridership to the operational extent of transit route design. The second deals with designing and implementing a socio-psychometric COmmuting Survey for MOde Shift (COSMOS). Finally, the third stage focuses on developing econometric choice models of mode switching behaviour towards public transit. Advanced mode shift models are developed using state-of-the-art methodology of combining Revealed Preference (RP) and Stated Preference (SP) information. The results enriched our understanding of mode switching behaviour and revealed some interesting findings. Some socio-psychological variables have shown to have strong influence on mode shift and improved the models in terms of fitness and statistical significance. In an indication of the superiority of the car among other travel options, strong car use habit formation was realized for car drivers, making it hard to persuade them to switch to public transit. Further, unlike conventional choice models, the developed mode shift models showed that travel cost and in-vehicle travel time are of lower importance compared to other transit Level of Service (LOS) attributes such as waiting time, service reliability, number of transfers, transit technology, and crowding level. The results also showed that passengers are more likely to shift to rail-based modes (e.g. LRT and subway) than rubber-tyred modes (e.g. BRT). On the other hand, the availability of park-and-ride facilities as well as both schedule and real-time information provision did not appear to be significant for mode switching to public transit for work trips. This research provides evidence that mode shift is a complex process which involves socio-psychological variables beside common socio-demographic and modal attributes. The developed mode switching models present a new methodologically sound tool for evaluating the impacts of alternative transit service designs on travel behaviour. Such tool is more desirable for transit service planning than the traditional ones and can aid in precisely estimating transit ridership.

Keywords: COSMOS
Mode Choice
Mode Switching
Stated Preference
Survey Design
Transit Service Planning
Advisor: Shalaby, Amer Saïd
Habib, Khandker Nurul
Computational Prediction of PDZ Mediated Protein-protein Interactions

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.

Keywords: protein-protein interactions
interaction prediction
PDZ domains
machine learning
Advisor: Bader, Gary D.
Reliable Safety Broadcasting in Vehicular Ad hoc Networks using 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.

Keywords: vehicular networks
network coding
Advisor: Valaee, Shahrokh
Advances in Tracheal Tissue-Engineering: Evaluation of the Structural Integrity, Immunogenicity and Recellularization of a Decellularized Circumferential Long-segment Trachea for Airway Transplantation

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.

Keywords: Trachea
Tissue-engineering
biological scaffolds
Advisor: Waddell, Thomas K.
The Role of Diversification in the Pricing of Accruals Quality

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.

Keywords: Accruals Quality
Cost of Capital
Diversification
Ambiguity
Advisor: Callen, Jeffrey
Richardson, Gordon
"People Like Me": Racialized Teachers and the Call for Community

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.

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
Advisor: Gérin-Lajoie, Diane
Small Spaces for Meaningful Participation in Democratic Life? A Community's Perspectives on tehir particiaptioin in an Early Education and Care program

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.

Keywords: participation
early childhood programs
South Africa
Advisor: Mundy, Karen
Radical Musicking: Challenging Dominant Paradigms in Elementary Music Education

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.

Keywords: music education
anti-racism education
elementary music
social justice education
anti-oppression
Advisor: Magnusson, Jamie Lynn
Interacting Narratives and the Intentional Evolution of Personal Practical Knowledge: Experienced English Teachers' Multiliterate Innovations in the Professional Knowledge Ecosystem

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.

Keywords: Narrative Inquiry
Teacher Development
Multiliteracies Pedagogy
Advisor: Beattie, Mary
Berkeley's Bodies

George Berkeley (1685-1753) defends immaterialism, the view that there is no such thing as matter. In place of matter, what exists are only minds and ideas. Berkeley also styles himself a defender of common sense. From early on many of Berkeley's readers doubted that these two commitments could be reconciled. I consider Berkeley's joint commitment to immaterialism and common sense in respect of two philosophical theses. (1) Berkeley argues against a version of scepticism that bodies are single collections, constituted by many ideas placed in certain relations, and veridically sensed by finite minds. I identify these collections as Berkeley's enigmatic archetypes. (2) Berkeley argues that finite minds are able to act causally upon their own bodies by nothing more than an act of will. Both of these theses are defended in the context of immaterialism, and Berkeley persuasively presents them as elements of common sense. I reconstruct Berkeley's arguments for these theses, and suggest that he succeeds in reconciling immaterialism and common sense in these areas. My account draws on previous research, but I introduce a single mechanism to understand both theses. I call this mechanism overlap. On Berkeley's view, finite minds represent bodies by constructing representing-collections that are intended to resemble body-collections. However, these representing-collections overlap with body-collections, meaning that they share members which are numerically the same. My account of (1) depends on the fact that sensed ideas are in the overlapping area, and therefore represent the body-collection exactly as it is. My account of (2) depends on supposing that the causal powers of finite minds are exercised on ideas in the area of overlap, and thus they act on ideas that are accessible to them but are also constituent parts of bodies.

Advisor: Ainslie, Donald
Erosion and Roughness Modeling in Abrasive Jet Micro-machining of Brittle Materials

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.

Keywords: Abrasive jet micro-machining
modeling
Roughness
Erosion
Advisor: Spelt, Jan K.