VictorJuiz/thesis huggingface dataset:
Modelling Transportation System Impacts of Housing Supply Dynamics

This thesis investigates housing supply dynamics in the City of Toronto and the related transportation impacts in two parts. In the first part, the dynamic temporal interaction of housing starts, public transit ridership, and national/regional socioeconomic factors is investigated using a multichannel singular spectrum analysis (MSSA). Recognizing the importance of a holistic view of the relationship between the interacting variables temporal movements supports research to integrate methods from different analytical domains, or “silos”. The research strategy is to fuse the nonparametric MSSA analysis of the variables series collection with Granger bidirectional/bivariate causality and feedback tests to build a statistically significant causal loop that can empirically explain the oscillatory components in the system. A system view of the temporal interaction of the variables is constructed from the MSSA analysis spectrum decomposition and Granger causality tests. The system’s nonlinear dynamic fingerprint is identified using cause-effect diagrams of the system’s components. Stock components are introduced to absorb the interactions’ lags and to actuate the system’s dynamical behaviour. In the second part of the thesis a traffic impact sketch planning (TISP) model is developed and implemented for estimating the likely travel demand and behaviour generated by Bayside mixed-use development (MXD), a major land development project at Waterfront Toronto. TISP model deploys the operational TASHA-based GTAModel V4.1 travel demand model system for a detailed transportation impacts assessment of the proposed precinct development. To enable the use of an agent-based microsimulation (ABM) model, a population synthesis procedure is developed that converts the architectural design of the development; that is, number and type of dwellings by number of bedrooms and non-residential floorspace into relevant attributes of households, persons, and employment that are likely to occupy the units. Datasets of different geographic areas of Toronto, with some common control variables, are synthesized and cascaded into a disaggregate population of residents and non-residents for Bayside MXD. The diurnal peaking travel times trips estimated by TISP model are compared with the peak period trips shown in the project’s traffic impact study and the Trip Generation Manual peak-hour weekday trip rates of relevant land uses.

Keywords: Causation analysis
Housing supply
Population synthesis
Singular spectrum analysis
System dynamics
Travel demand forecasting
Advisor: Miller, Eric J.
Identification and Characterization of the TGFβ/Hippo Crosstalk through Mathematical Modeling

Transforming Growth Factor-beta (TGFβ) superfamily members control a myriad of cellular activities and are key regulators of most developmental and homeostatic processes. The Hippo pathway is a major regulator of tissue growth and organ size. Hippo and TGFβ pathways are intimately interconnected. Hippo pathway mediators Taz/Yap interact with the TGFβ regulated Smads and when Hippo is activated, the cytoplasmically localized Taz/Yap reduces or prevents Smad nuclear accumulation thereby dampening TGFβ induced transcriptional activity. In the nucleus, Taz/Yap can transcriptionally cooperate with Smads to alter target genes regulation. With the aim of identifying the TGFβ/Hippo crosstalk, I used experimental data and computational modeling of Hippo and TGFβ crosstalk. Quantitative high-content immunofluorescence (IF) microscopy showed that Taz/Yap abrogation reduces nuclear accumulation of Smads and the reduction is not due to degradation of Smad/Taz/Yap proteins or receptors. Immunoblotting experiments revealed that Taz/Yap knock down alters phosphorylation/dephosphorylation of Smads. IF microscopy showed that there is no difference in the export and dephosphorylation rates in cells transfected with siCTL versus siTaz/Yap while TGFβ receptor activity is inhibited. IF microscopy, immunoblotting and statistical analysis showed that Taz/Yap levels in the cytoplasm or nucleus is constant regardless of dose of TGFβ or time of treatment when the Hippo pathway activity is constant. Mathematical modeling predicted that the differential accumulation of Smads at cells transfected with siCTL and siTaz/Yap might be due to both receptor activity alteration and existence of a Taz/Yap regulated retention factor. As a candidate retention factor, Med18 the subunit 18 of the mediator complex was identified. IF experiment results confirmed that knocking down Med18 reduces nuclear accumulation of Smads. Analysis of RNAseq data for cells transfected with siCTL or siTaz/Yap showed that Hippo pathway perturbation yielded differential effects. Mathematical modeling revealed that TGFβ target genes might have constant or time varying mRNA degradation rate. In addition, Taz/Yap could modulate the temporal expression patterns of TGFβ target genes by selectively changing the kinetic parameters of the gene expression model. Analysis of the gene expression patterns of selected genes showed that TGFβ/Hippo pathway crosstalk might be a mechanism to control the sequence of gene activation.

Keywords: Mathematical modelling
Smad nuclear accumulation
TGFβ/Hippo crosstalk
Transforming Growth Factor-beta
Advisor: Attisano, Liliana
Wrana, Jeffrey L
The Influence of Environment, Landscape and Paleogeography on the Evolution and Diversification of Two Neotropical Fish Groups

Different factors drive the origin and maintenance of biodiversity. Although much debate around this topic exists, the importance of the environment in shaping diversity and evolution is undeniable. Changes in environmental properties, from connectivity to physicochemical factors, play fundamental role in diversification. In this thesis, I use two distinct groups of Neotropical fishes as model groups and use different molecular techniques to explore and characterize their molecular diversity. Using traditional and high-throughput sequencing, I have generated thorough phylogenies for the Neotropical freshwater stingrays and the barred knifefish (genus Steatogenys). Combining molecular and environmental data, I explore how geology (paleogeography) and physicochemical factors (water-types) have influenced their evolution across different time scales. Using paleogeographical evidence and fossil data, I generated a continental-level biogeographical hypothesis for the diversification and distribution of the Neotropical freshwater stingrays. I proposed that the evolution of this subfamily is related to changes in the connectivity of bodies of water in the last 20 million years, particularly in paleo mega wetlands in the Amazon region. I then discussed their diversification patterns, identifying an under-estimated diversity for this group and that recent diversification events, mostly related to changes in environment connectivity, are reflected in the incomplete sexual isolation between morphospecies. Using genomic evidence, I identified hybridization between species and proposed a scenario of serial diversification events. For the genus Steatogenys, both mitochondrial and genomic datasets highlighted the under-estimated diversity of this group. Using environmental data and multivariate statistics, I tested for the effects of different water types over diversification and distribution patterns. I proposed that environmental gradients affect population distribution and composition, and that confluence areas act as genomic interchange regions between populations. I found evidence of different species occurring in sympatry, but isolated sexually and with similar patterns of partial gene flow disruption between water bodies with different water types. My thesis combines computational and experimental work investigating the effects of the environment over the diversification of distinct fish groups. Broadly, I highlight the importance of the environment for evolutionary patterns, and that understanding environmental patterns is fundamental in the investigation of diversity and evolution.

Keywords: Amazon
Biogeography
Marine Incursions
Phylogenetics
SNPs
Water Types
Advisor: Lovejoy, Nathan R
Informal Revenue Generation and the State: Evidence from Sierra Leone

How states raise revenue is critical to understanding how they govern. Orthodox analyses of the state, however, have tended to focus only on formal taxation, formal budgets, and formal revenues. I correct his bias by extending the analysis of taxation and the state beyond formal tax systems, capturing the informal dynamics of public finance that affect the majority of citizens in low-income countries. By examining informal revenue generation in the context of formal taxation, I shed light on the how and why of the state and institutional development. This study presents a new approach to understanding formal–informal institutional interactions and offers insight into a set of tangible issues of critical importance to the citizens of modern states. Classic theories of statehood anticipate that the state should always seek to control informal revenue generation. In practice, states often coexist with this informality. Informal taxing actors can reinforce state authority in unexpected ways and the relationship between the state and informal taxing actors is not necessarily zero-sum. State engagement with informal revenue generation is not always driven by a desire to gain a monopoly on taxation and authority. Instead, informal revenue generation may align with or even underpin the state’s governing strategy. Informal revenue generation can also have counterintuitive effects on statebuilding. Though informality is usually seen as detrimental to statebuilding, I show that informal revenue generation can strengthen state institutional capacity. The politics of statebuilding are, at least in part, played out at the local level in conjunction with informal institutions. It is in these local processes where informal revenue generation and informal taxing actors can reinforce modern statehood and statebuilding processes. The state that emerges may not look like a rational, Weberian institutional model. Nevertheless, it may prove more resilient and dynamic than expected.

Keywords: informality
mediated statehood
Sierra Leone
statebuilding
taxation
Advisor: Prichard, Wilson
One-class Collaborative Filtering with Latent Embeddings: Improvements and Interactive Extensions

Systems that recommend personalized lists of items to users are increasingly prevalent in our online experience and critical for the commercial success of online services such as Amazon, Netflix, and Youtube. An important subclass of recommendation is the one-class setting, where only positive feedback is directly observed (e.g., likes, purchases, clicks). While one-class recommendation tasks are challenging due to the lack of explicit negative feedback, collaborative filtering (CF) methods that leverage the collective preferences of a large user population have proved to be effective, especially CF methods that rely on latent embeddings. This thesis aims to extend the state-of-the-art one-class collaborative filtering (OC-CF) with latent embeddings and focuses on three unresolved problems in this research area: (1) existing methods for learning latent embeddings tend to be popularity biased and thus can perform poorly for items in the long tail; (2) in cases where user interests are diverse, existing latent embedding methods tend to be over-confident and fail to model a user’s full preference spectrum; (3) as recommender systems become more interactive, little work has addressed how to co-embed rich (e.g., language-based) user feedback in the same latent space as user preferences. To address (1), we leverage a method known as noise-contrastive estimation (NCE) to learn de-popularized embeddings in both linear and deep learning OC-CF methods. To address (2), we extend methods for Variational Auto-encoders (VAEs) for stochastic embeddings that avoid over-confidence. To address (3), we provide a novel variational extension of neural collaborative filtering that allows co-embedding of language-based feedback to support an interactive recommendation setting. We empirically validate all contributions in comparison to a variety of state-of-the-art OC-CF methods and demonstrate the advantages of our previously outlined contributions. In summary, the thesis makes several significant novel contributions to both improve and extend OC-CF methods based on latent embeddings.

Keywords: Collaborative Filtering
Critiquing-based Conversation
Deep Learning
Machine Learning
Recommender System
Variational Autoencoder
Advisor: Sanner, scott
The Molecular Associations of Host Characteristics in Cancer Genomics

Epidemiological studies have identified myriad differences in cancer burden between people of different sexes, ancestries, and ages. Male individuals are more likely to develop most cancers and die of their disease. While overall cancer incidence is comparable between individuals of African vs. European ancestry, cancer mortality is higher in those of African ancestry. Increasing age is a well-known cancer risk factor, yet there are exceptions such as in pediatric cancers. These are only a few examples of epidemiological differences associated with fundamental characteristics of the cancer host. Since cancer is driven by genomic alterations, it is likely that epidemiological differences can be explained by differences in the cancer genomic landscape. I assessed this by performing a comprehensive pan-cancer analysis of sex-, ancestry-, and age-associated differences in 12,774 tumour genomes across 33 tumour-types using data from The Cancer Genome Atlas and the International Cancer Genome Consortium. I investigated genome-wide and localized phenomena including measures of mutation density and tumour evolution, mutational signatures, and the frequency of single nucleotide variants and copy number aberrations. I used multivariable methods to identify sex-, ancestry-, and age-associations that persisted even after adjusting for confounding factors such as smoking history and tumour stage. Sex-, ancestry-, and age-associations span the spectrum of somatic genomic features across all except three tumour-types studied. While some genomic associations were detected in pan-cancer analysis, many others were tumour-type specific. Finally, I leveraged sex-, ancestry- and age-biased genomic features to identify functional associations. Using transcriptomic data, I found that many sex-, ancestry-, or age -biased mutations were themselves associated with changes in mRNA abundance. Some mRNA abundance changes were also dependent on the context of sex, age, or ancestry. Similarly, I identified biased genomic features that were associated with survival. Some genomic features were only associated with survival in one sex or age group, suggesting host characteristics influence the prognostic potential of genomic features. Ultimately, my findings suggest that tumour genomics are biased to host characteristics, that there are many underlying sources for these genomic differences, and that they can be leveraged to improve biomarker design.

Keywords: Age
Ancestry
Biomarkers
Cancer
Health Disparities
Sex
Advisor: Boutros, Paul C
Organizational Governance in the Public Interest

This thesis examines how the interaction between organizations, institutions, and key stakeholders shapes organizational performance. It includes three studies, each of which examines in detail the relationship between actors engaged in promoting the public interest. The first study investigates how elected state officials shape the performance of government-controlled organizations over time. This study argues that the political incentives of state officials create systematic trends in the behavior and performance of government-controlled organizations, which are particularly common in industries such as power distribution, transportation, and water and sanitation. State officials seeking votes manipulate government-controlled organizations to boost employment just before elections. As a result, these organizations exhibit both higher employment levels and lower financial performance in election years. Data from Brazil’s water sector—an industry managing a crucial societal resource—support these predictions. The second study investigates how the engagement of highly productive workers affects the operational performance of organizations. The research isolates these workers’ direct contributions to organizational performance from their indirect contributions—i.e., the influence on the performance of coworkers in the organization. Exploiting the temporary absences of high-volume physicians, I find that in-hospital patient mortality increases during these absences for two reasons: first, because the physician is absent; and second, because of the impact of the absence on the performance of colleagues. This second pathway—the role of indirect contributions—accounts for about 38 percent of the overall increase in patient mortality. This research shows that highly productive workers have sizeable influence on the performance of organizations, but this influence occurs, to a large extent, through peer effects. The third study investigates how the implementation of strong intellectual property rights for pharmaceuticals in emerging markets influences the strategy of pharmaceutical firms. Prior research suggests that patents shape the behavior of firms by affecting prices. This study argues that patents can shape the market strategy of firms through mechanisms other than price. The results show that patent holders modify their product market strategy despite little changes in drug prices.

Advisor: McGahan, Anita
The Sound of Queer Diaspora: Sonic Enactments of Filipinx Desire, Loss and Belonging

In this dissertation, I foreground Filipinx cultural production in building an aesthetic archive of transpacific aesthetic expression. From this point, I listen for its queer sounds. My research draws on queer theory, performance studies, and Filipinx diaspora studies to suggest that sound offers a methodological framework that can uniquely register modes of collectivity and desire that may otherwise go unrecognized. I also deploy psychoanalytic concepts of mourning and reparation to elaborate a definition of sound that explains its material and metaphorical force as it creates conditions for new relational possibilities. Broadly, I suggest that sound has an affective quality that capaciously allows Filipinx diasporic subjects to create forms of home, desire, and belonging that defy racialized ascriptions born from racism, colonialism, and their gendered dimensions. This dissertation includes four chapters, each offering a critical reading of an aesthetic object. The objects that I have assembled in this dissertation include videos that feature performances by Filipinx children, visual art and music by Filipinx artists, and a film that expresses the queer dynamics of sound. By critically listening for queer sound as it is produced by these aesthetic objects, I hope to contribute a theory of diaspora that may otherwise be rendered unintelligible due to hegemonies of vision, empire, and heterosexuality. Ultimately, this project seeks to expose how sonicity can inhabit the affective force of desire, loss, and belonging in queer, transpacific representation.

Keywords: Aesthetics
Diaspora
Filipinx
Media
Queer
Sound
Advisor: Georgis, Dina
Diaz, Robert
The Durability of Client Regimes: Foreign Sponsorship and Autocracies, 1946-2010

This dissertation investigates the relationship between foreign support and the survival of authoritarian regimes. Conventional wisdom suggests that great power patrons prop up client dictatorships. However, this is generally assumed rather than systematically analyzed. My dissertation provides the first comprehensive assessment of the relationship between foreign sponsorship and authoritarian regime survival with the use of an original dataset of all autocratic client regimes in the postwar period. These results demonstrate that patronage from Western powers - the United States, France, and the United Kingdom - is not associated with client regime survival. Instead, only Soviet sponsorship reduces the risk of regime collapse. I explain this variation by considering the effects of differing strategies of foreign sponsorship on client regime coup vulnerability. Not a single Soviet client regime ever lost power to a military coup. This was the result of Soviet assistance in the implementation of highly penetrative coup prevention strategies that rendered militaries incapable of ousting incumbent regimes. In contrast, a fundamental ambivalence toward their autocratic allies and a focus on building Western-style militaries rendered U.S. and European clients highly vulnerable to coups. Western clients did not receive patron assistance in restructuring their security forces to prevent a coup and were abandoned in the event of a successful coup. I test these arguments using recently declassified archival sources, secondary sources in English and Russian, and a series of statistical analyses using both original and newly available data.

Keywords: authoritarianism
civil-military relations
cold war
great power foreign policy
military coups
Advisor: Way, Lucan A
Development and Evaluation of an Instrument to Measure Discharge Planning Processes in Mental Health Care

Objective: The purpose of this study was to develop and test an instrument to measure and evaluate the quality of discharge planning processes in mental healthcare settings. Methods: Three major study phases were involved in the development of the instrument: 1) conceptualization of discharge planning, 2) item development, structure, and format, and 3) pilot testing of the instrument. Phase I comprised three components: a concept analysis and literature review to identify domains and indicators of discharge planning, focus groups with key informants to validate these findings, and a two-round Delphi study with a multidisciplinary expert panel to determine which indicators were most important for measuring the quality of discharge planning processes. In Phase II, indicators that reached expert consensus in Phase I were formatted into instrument items. In Phase III, the instrument was pilot tested through chart reviews and cognitive interviews. Results: The concept analysis and literature review yielded 73 quality indicators in six domains: Comprehensive Needs Assessment; Collaborative, Patient-Centered Care; Resource Availability Management; Care and Service Coordination; Discharge Planner Role; and Discharge Plan. Following the focus groups, two additional domains were created (i.e., Information Gathering and Synthesis, Patient Capacity Assessment), nine indicators were added, and three indicators were removed. In the first Delphi round, 37 panelists rated the importance of 79 quality indicators. Fifty-four indicators were retained and the Discharge Planner Role domain was removed after this survey round. In the second Delphi round, 36 panelists rated the importance of three new indicators. Two indicators were retained, resulting in a final set of 56 indicators. In Phase II, each indicator was assigned an item response option. In Phase III, the instrument was pilot tested and revisions were made to the instrument items, response scales, and overall format and instructions. These refinements resulted in a 57-item instrument. Conclusions: The instrument developed in this study can be used by healthcare providers to provide insight into practice and knowledge gaps in care, organizational leaders to inform process and structural improvements in mental healthcare settings, and policymakers to design more effective policies and practice guidelines for safer care transitions from hospital to community.

Keywords: discharge planning
instrument development
mental health
nursing research
quality indicators
Advisor: Tourangeau, Ann