VictorJuiz/thesis huggingface dataset:
Song and Wind in Canada: The Impact of Arnold Jacobs’s Teaching on Canadian Tuba Pedagogues

The purpose of this study is to investigate the impact of Arnold Jacobs on the pedagogical approaches of prominent tuba teachers in Canada. Nine tuba teachers from different Canadian universities participated in this study. Each participant was interviewed digitally using Skype or FaceTime and asked nine questions designed to understand their personal pedagogical approach and how it relates to Arnold Jacobs. These questions cover important pedagogical ideas including sound concept, breathing, articulation, and embouchure. Arnold Jacobs is considered to be one of the most influential brass pedagogues in history. His method of teaching, referred to as Song and Wind, is a pedagogical concept frequently implemented in contemporary applied tuba teaching. The interview findings of this study demonstrate that the Arnold Jacobs legacy is very present in Canadian tuba pedagogy. The approaches to articulation and sound concept demonstrated by the interview subjects are consistently Jacobs inspired. The approaches to breathing and embouchure, however, are much more varied. Although these elements are not as tightly embedded in the Jacobs pedagogical approach, the results of the study demonstrate that the majority of the interview subjects are fully aware of the ways in which their current approaches have been adapted.

Keywords: Arnold Jacobs
Brass Pedagogy
Canadian Tuba Teachers
Jonathan Rowsell
Song and Wind
Tuba Pedagogy
Advisor: Walter, Cameron
Essays on Technology in Finance and Market Design

I develop information-based theoretical frameworks to (i) explain empirical patterns found in the finance literature, and (ii) provide empirical and policy implications related to recent changes in the technology and the market structure of financial markets. The first chapter explains how the over-the-counter market can coexist with easily acces- sible exchanges, and examines the US Dodd-Frank Act and the EU’s MiFID II. The second chapter explains the recent trend of higher market quality, and reconciles the finding that high frequency traders increase liquidity with the finding that the HFTs reduce institutional traders’ profits. The third chapter analyzes how transparency due to blockchain adoption may affect market quality.

Keywords: Blockchain
Latency
Market quality
Market structure
Over-the-counter market
Transparency
Advisor: Shi, Xianwen
Mondria, Jordi
Parametrizing topological Ramsey spaces

We prove a general theorem indicating that essentially all infinite-dimensional Ramsey-type theorems proven using topological Ramsey space theory can be parametrized by products of infinitely many perfect sets. This theorem has applications in several known spaces, showing that certain ultrafilters are preserved under both side-by-side and iterated Sacks forcing. In particular, the well-known result of 'selective ultrafilters on the natural numbers are preserved under Sacks forcing' is extended to the corresponding ultrafilters on richer structures. We also characterize ultrafilters in topological Ramsey spaces in an abstract setting. The technique of combinatorial forcing is crucial in the proof of the general parametrization theorem, and ultra-Ramsey theory plays an important role in the applications.

Keywords: Combinatorics
Parametrized Ramsey theory
Ramsey theory
Sacks forcing
Topological Ramsey Space
Advisor: Todorcevic, Stevo
Analytical Methods and Devices for Bioenergy and Global Change Science

Human activity is driving global change. Carbon dioxide emissions from fossil fuel combustion results in global effects including increases in temperatures as well as ocean acidification. Further, human-induced global change extends beyond carbon dioxide to pollution including microplastics. It is important to understand the impacts of global change and to optimize ways to mitigate it via technologies like biofuels. This thesis details devices and methods developed with the overall goal to enable experiments to increase this understanding. Specifically, this thesis presents devices and methods to (1) increase experimental throughput, enabling larger, multi-parameter experimental designs; (2) measure endpoints previously impractical to measure; and (3) inform laboratory experiments by improving the methods for obtaining data from environmental samples to set appropriate dosing levels. First, I developed a device which maps microalgae growth as a function of light and nutrients using a hydrogel-based concentration gradient generator to address experimental throughput in the biofuel context. Second, I developed a platform, incorporating a long-range aerogel-based gradient generator, a projector, and well plate compatibility to screen the effect of multiple environmental parameters on biota to further address experimental throughput. The third contribution is a digestible fluorescent coating for plastic particles that is stripped from the plastic upon ingestion by an organism; this can be used to determine if a plastic particle has been ingested in laboratory exposure experiments – providing the ability to measure cumulative plastic ingestion – a new endpoint. The last contribution is a method to bind iron nanoparticles to plastic in environmental samples enabling magnetic recovery, suited to recovering the smallest size fractions of microplastics from environmental samples for analysis– providing the ability to inform laboratory experiments. Overall, the four Chapters that make up the primary contributions of this thesis are technologies that allow experimenters to answer research questions in bioenergy and environmental science more efficiently. The methods and devices described in this thesis make technological progress but have limitations that prescribe caution when applying to new kinds of experiments. Nevertheless, with some adaptation, these technologies could further be applied to help answer several questions inside and outside of environmental science and bioenergy.

Advisor: Sinton, David
Assessing Forest Tree Communities and Assisted Migration Potential in Toronto’s Urban Forest as a Result of Climate Change

Projected climate change in the Toronto, Ontario, Canada area could greatly alter tree composition within the urban forest. Investigating biological change as a result of climate change is complicated due to the variability among climate model outputs and non-climatic influences on local vegetation. This study approaches the issues of composition change in tree species in Toronto through three interdependent studies. The first study is a comparison of Global Climate Models (GCMs) available through the Intergovernmental Panel on Climate Change's Fourth and Fifth Assessment Reports, AR4 and AR5 respectively. Using a performance metric based on how well the GCMs simulate climate relative to observation, GCMs GFDL-CM3, IPSL-CM5A-LR and MPI-ESM-LR were determined to provide the best Canada-wide coverage for annual average temperature and precipitation changes. The second study correlates a series of biologically-relevant climatic variables to tree distributions of 134 North American trees east of the 100th meridian. The geographical absence or presence of a species was correlated to concurrent climate data, creating a species' climate envelope. Using climate projections from an ensemble of the GCMs GFDL-CM3, IPSL-CM5A-LR and MPI-ESM-LR for the year 2050, a suite of statistical regression and machine-learning techniques were used to predict a likelihood of suitability of trees in the Toronto area based on the derived climate envelopes. While the dominant beech-maple communities are largely projected to stay intact, future climate suitability is likely to shift away from conifers and northern hardwoods into more southerly deciduous trees. The third study evaluates using projected tree suitability whether an assisted migration through the translocation of tree species would be effective in the Toronto area. Of particular interest is the increasing climate suitability that likely will be beneficial to Ontario’s Species at Risk trees. However, the conservation of Ontario’s Species at Risk trees cannot be based solely upon projections of climate, a vulnerability assessment conducted in this study indicate that current pest and diseases threats coupled with and the loss of genetic diversity are also cause for concern.

Keywords: Climate Change
Global Climate Models
Species Distribution Modelling
Urban Forestry
Advisor: Gough, William A
Subject-Specificity of SC-FC in the Human Brain

The human brain can be depicted as a connectome, which describes how regions are connected amongst one another. Structural connectivity (SC) describes how physical pathways link areas of the brain, whereby functional connectivity (FC) describes the temporal relationships of neural activity between regions. The present body of work aims to understand individual SC and FC and how they are linked to behaviour, and to compare and combine SC and FC at the individual level. Study 1 describes the limitations of subject-specificity of the SC-FC relationship, and of individual SC and FC variability. Study 2 explores how the existing variability can still be used to explain individual differences in cognition. Study 3 integrates SC and FC in a computational modeling approach in order to understand how biophysics underlying functional dynamics correlate with behaviour in a clinical model. Together, these studies demonstrate how connectomics can be used to understand individual differences in structure, function, their mapping to one another, as well as to cognition.

Advisor: McIntosh, Anthony R
Dispersal, Connectivity, and Population Genetic Structure in the Sea

The spatial distribution of genetic variation across landscapes is influenced by physical features that facilitate or restrict movement and natural selection driven by environmental heterogeneity. Many marine organisms undergo a pelagic larval stage, during which time ocean currents influence dispersal and the degree of gene flow. Furthermore, gradients in temperature, salinity, and other environmental conditions produce spatially varying selection pressures across species ranges. In the first part of my thesis, I offer a novel perspective for marine conservation that emphasizes the importance of considering both connectivity (where connectivity is maintained by dispersal) and the potential for marine populations to adapt to their environment. To do so, I highlight how genomic data can be used to infer population connectivity (i.e. based on neutral genetic variation) and environmental selection (i.e. based on putatively adaptive genetic variation) in the context of marine reserve networks. Next, using a genomic dataset derived from restriction-site associated DNA sequencing (RADseq), I investigated the impact of ocean currents and environmental variables on spatial patterns of neutral and adaptive genetic variation in the commercially harvested giant California sea cucumber (P. californicus) along the northeastern Pacific coast. The results showed evidence for population structure despite the potential for widespread gene flow, and demonstrated that accounting for directionality of ocean currents explained genetic variation better than between-site geographic distances. Strong associations between sea bottom temperature and putatively adaptive loci were identified at a broad spatial scale, as well as moderate evidence that surface salinity and bottom current velocities contribute to regional patterns of adaptive differentiation. In a study using simulations of larval dispersal coupled with demo-genetic simulations, I found that potential dispersal was spatially restricted with shorter pelagic larval duration (PLD), but there was no difference between a model of diffusive (isotropic) larval transport and oceanographic (anisotropic) transport. However, several important caveats were highlighted that should be addressed in future work. Collectively, my thesis integrates genomic, environmental, and oceanographic data to understand the role of seascape features on connectivity and adaptation, with implications for marine conservation plans that aim to connect marine populations and support adaptive responses to environmental change.

Keywords: biophysical modeling
marine invertebrate
seascape genomics
Advisor: Fortin, Marie-Josée
Long-Term Memory Biases Auditory Spatial Attention: Healthy and Impaired “Memory-Guided Attention”

Attention and memory may be impaired in individuals at-risk for Alzheimer’s disease (AD), though standard cognitive assessments typically study the two in parallel. In reality, attention and memory interact to facilitate processing, and thus a more integrative approach is required. Here, I used a novel auditory paradigm to assess how long-term contextual memory facilitates detection of an auditory target in healthy young adults (Study 1 and 2), and whether performance on this task is related to Apolipoprotien E4 (APOE4) genotype, a risk factor for the sporadic AD (Study 3). During an initial familiarization task, participants heard audio-clips some of which included a lateralized target (p = 50%). On each trial, participants indicated whether the target was presented from the left, right or was absent. Following a retention interval, the same audio-clips were presented, but now all included a target. Across three experiments in Study 1, young adults showed memory-based gains in response speed and accuracy associated with informative memory cues. In Study 2, auditory context facilitated speeded target detection 24 hours after learning just as well as 1 hour after learning. Differences between electrophysiological (EEG) responses associated with informative and uninformative audio-clip cues point to memory rather than attention mechanisms. In Study 3, differences in cognitive performance in carriers of APOE4 at a pre-clinical phase were observed. Notably, while memory recall was unaffected by genotype, APOE4 dose impaired memory-guided attention. A relationship between explicit memory and memory-guided attention was only observed in non-carriers, and this relationship was broken in APOE4 heterozygotes and homozygotes, indicating that APOE4 carriers rely less on explicit memory to facilitate attention. Because memory-guided attention declined with age in APOE4 carriers, it may be an early disease-related impairment rather than a life-long impairment.

Keywords: Apolipoprotien E4
Attention
Auditory
Memory
Advisor: Alain, Claude
Annotating Human Interactome to Predict Pathways and Systematically Analyzing Network Rewiring in Cancer across Multiple Tissues

Human protein-protein interaction (PPI) networks are essential in regulating most cellular processes and their disruption can cause complex diseases such as cancer. Currently, hundreds of thousands of binary PPIs comprise human interactome, but they lack annotations about tissue- or disease-specificity. Pathway databases provide more detail about these conditions, but they cover only fraction of the proteome. The main goal of this dissertation was to annotate interactome through integrative computational methods and use these annotations, to predict novel protein-pathway associations (Chapter 2), and perform system-level analysis of interactome in cancer (Chapter 3). Chapter 2 describes integration of 4,968 pathways from twenty curated pathway databases. Analysis of these data highlighted several challenges including low proteome coverage (63%), low overlap across different databases, unavailability of direct information about underlying physical connectivity of pathway members, and high fraction of protein-coding genes without any pathway annotations, i.e., 'pathway orphans'. To address these challenges, I integrated these data with PPIs to predict biologically relevant protein-pathway associations. Cross-validation determined 71% recovery rate of our predictions. Data integration and predictions increase coverage of pathway annotations for proteins to 91% and provide novel annotations for 5,402 pathway orphans. These data are publicly available in pathDIP (http://ophid.utoronto.ca/pathDIP). Chapter 3 describes curation of gene expression data of 3,127 primary cancer and normal samples across sixteen tissues and thirty-five cancer types. I used pairwise gene coexpression and differential coexpression to annotate 276,552 PPIs with tissue- and cancer-specificity. Pan-cancer comparison of annotated PPIs provides novel insights toward dynamics of PPI networks in tissue-cancers. We found that while PPI network hubs are present in most of the tissues and cancers, their interactions are highly tissue-cancer-specific. Comprehensive graph theory-based analysis shows that highly dense network modules (e.g., protein complexes) are frequently maintained in both normal and cancer, but they are wired differently. I demonstrate on two examples of the potential of these annotations in discovering novel cancer genes and drug pathways.

Keywords: biological networks analysis
computational and integrative biology
data integration
high-throuput data analysis
molecular pathways
protein-protein interactions
Advisor: Jurisica, Igor
Development of Prognostic Models for Survival and Quality of Life in Surgically Managed Patients with Metastatic Spinal Cord Compression

Untreated Metastatic Epidural Spinal Cord Compression (MESCC) leads to irreversible neurologic deficits and worsened quality of life (QoL). While all existing Clinical Prognostic Models (CPMs) predict survival, most were derived from retrospective data from small patient samples using unclear methodology and there is no consensus related to their accuracy. Of note, to date, there is no CPM predicting QoL. Accurate CPMs for survival and QoL may assist clinicians and patients in the process of joint therapeutic decision-making and help patients form realistic expectations related to the outcome of surgery. We conducted a survey and a systematic literature review to isolate key preoperative predictors of survival and QoL. In accordance with The Transparent Reporting of a multivariable prediction model for Individual Prognosis Or Diagnosis (TRIPOD) guideline, we identified significant predictors of survival and performed an external validation of eight existing CPMs for survival. Using high-quality prospective data, we integrated evidence from the current literature, expert opinion and statistical findings to create CPMs of survival and QoL in accordance with the TRIPOD guideline. We identified the site of primary tumor, the presence of organ metastasis and the SF-36 physical component score (PCS) to be significant predictors of survival. For all eight CPMs evaluated, discrimination was possibly helpful and calibration was poor. Our CPM of survival includes five predictors (SF-36 PCS, type of primary tumor, presence of organ metastasis, MESCC treated with radiotherapy prior to surgery and male sex) while the CPM of QoL at 3 months after surgery consist of four predictors (KPS, living in NA, SF-36 PCS and SF36 mental component score). Our CPMs demonstrated possibly helpful discrimination and good calibration. In accordance with the TRIPOD guideline, we created and internally validated a CPM of survival and the first CPM of QoL at 3 months after surgery for patients with MESCC. We believe we have achieved the maximum prognostic ability using traditional predictors, methods and outcome measures. Future work will concentrate on further external validation of CPMs of survival and QoL, to examine other predictors of outcome, such as molecular diagnosis and biomarkers, and to employ disease-specific outcome measurement instruments.

Keywords: Clinical Prognostic Model
Metastatic Epidural Spinal Cord Compression
Quality of Life
Surgery
Survival
Advisor: Fehlings, Michael G
Dynamic Mechanism Design without Transfers

This thesis consists of three chapters. In chapter 1, titled "Design of Committee Search," I apply a mechanism design approach to committee search problems, such as hiring by a department or a couple's search for a house. A special class of simple dynamic decisions rules have agents submit in each period one of three votes: veto, approve, or recommend; the current option is adopted whenever no agent vetoes and at least one agent recommends. I show that every implementable payoff can be attained by randomizing among these simple rules. This result dramatically simplifies the design problem. In chapter 2, titled "School Choice with Observable Characteristics," I study a school choice problem where students have observable characteristics that are correlated with their preferences. For example, one such characteristic may be the location of a student's home, which is correlated with preferences if students tend to prefer nearby schools. I consider mechanisms that are envy-free, efficient, and treat students with the same observable characteristics equally. I show that the welfare-maximizing mechanism in this class is a modified probabilistic serial mechanism with capacities. These capacities specify the maximum number of students with given characteristics that can be admitted into each school. In chapter 3, titled "Mechanism Design for Stopping Problems with Two Actions," I analyse a class of dynamic mechanism design problems in which a single agent privately observes a time-varying state, chooses a stopping time, and upon stopping, chooses between two actions. The principal designs transfers that depend only on the time the agent stops and on the alternative the agent chooses. The analysis provides necessary and sufficient conditions for implementability in this environment. In particular, I show that any stopping rule in which the agent stops the first time the state falls outside of an interval in the state space can be implemented if and only if a pair of monotonicity conditions is satisfied.

Keywords: Game Theory
Mechanism Design
Advisor: Peski, Marcin
Stewart, Colin
21st-Century Cello Pedagogy: Examining the Efficacy of Online Cello Lessons

The use of video-conferencing software and online platforms has brought many parts of the world closer together and has enabled audiovisual communication with greater ease than ever before. As with other technological developments, there are both advantages and disadvantages associated with video-conferencing and the rapid transmission of information. This dissertation will focus on the use of video-conferenced teaching in applied cello lessons, and will also examine subscription-based websites, in order to ascertain the efficacy of distance instruction in both synchronous (real time) and asynchronous (pre-recorded) contexts. The thesis begins with a consideration of the history of cello pedagogy over hundreds of years, from early print-based method books to the use of communication and recording technologies in the 20th century. To assess the current state of online cello instruction, the thesis includes interviews with online cello instructors and web creators, as well as a review of the author’s experience in video-conferenced lessons and other online platforms. The conclusion outlines what factors are necessary in order for effective cello instruction to take place via an Internet connection.

Keywords: cello
conference
contemporary
distance
learning
video
Advisor: Elliott, Robin