VictorJuiz/thesis huggingface dataset:
Road Traffic Injury Mortality in India

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.

Keywords: public health
road traffic injury
India
low- and middle-income countries
mortality survey
verbal autopsy
epidemiology
geographic information system
healthcare access
trauma
Advisor: Jha, Prabhat
Nathens, Avery B.
Touring as Social Practice: Transnational Festivals, Personalized Networks, and New Folk Music Sensibilities

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.

Keywords: Ethnomusicology
Popular Music
Festivals
Transnationalism
Folk Music Revival
Fiddle Music
Advisor: Kippen, James R.
Dromde Mik en Drom i Nat...

Composed entirely of runes, the 14th century manuscript Codex Runicus is comprised of 101 sheets and contains historical documents such as "Kings until Erik Menved" and "Boundaries between Denmark and Sweden." The end of the codex contains the oldest surviving Nordic music fragment with lyrical text "Drømde mik en drøm i nat um silki ok ærlik pæl" which translates as [I] dreamt me a dream last night of silk and lovely cloth. This melody, alongside three Norwegian folk slåttar written for fiddle, Fjellbekken (The Mountain Stream), Fjøllrosa (The Mountain Rose), and Syrgjefuen (The Bird of Sorrow), is used to generate the pitch material for this composition for string orchestra, english horn and french horn. The piece is contrapuntal in nature. A large portion of the work is formed from essentially five groups or layers of melody that comfortably co-exist towards, as well as away from, each other, their independent natures being most evident in the first half of the piece. Additionally, there are fluctuations within each group itself, for examples, forms of imitation, slippage, change in register, variation in playing technique, and micro-displays of rhythmic independence set against more heterophonic textures (Considerable use of rhythmic embellishment is derived from the ornamental style found in harding fiddle slåttar). Such micro-fluctuations further distinguish the texture-intentional orchestration of each group. Although the use of layered melody forms the framework for the entire composition, there is continual exploration of its possibilities through various parameters such as density vs. transparency, and continuation vs. fragmentation.

Keywords: harding fiddle slattar
string orchestra with english horn and french horn
infinity series
Advisor: Kulesha, Gary
Geo-immersive Surveillance and Canadian Privacy Law

Geo-immersive technologies digitally map public space for the purposes of creating online maps that can be explored by anyone with an Internet connection. This thesis considers the implications of their growth and argues that if deployed on a wide enough scale they would pose a threat to the autonomy of Canadians. I therefore consider legal means of regulating their growth and operation, whilst still seeking to preserve them as an innovative tool. I first consider the possibility of bringing invasion of privacy actions against geo-immersive providers, but my analysis suggests that the jurisprudence relies on a reasonable expectation of privacy approach that makes it virtually impossible for claims to privacy in public to succeed. I conclude that this can be traced to an underlying philosophy that ties privacy rights to an idea of autonomy based on shielding the individual from the collective. I argue instead considering autonomy as relational can inform a dialectical approach to privacy that seeks to protect the ability of the individual to control their exposure in a way that can better account for privacy claims made in public. I suggest that while it is still challenging to craft a private law remedy based on such ideas, Canada’s data protection legislation may be a more suitable vehicle. I criticize the Canadian Privacy Commissioner’s current approach to geo-immersive technologies as inadequate, however, and instead propose an enhanced application of the substantive requirements under Schedule 1 of PIPEDA that is consistent with a relational approach to privacy. I suggest this would serve to adequately curtail the growth of geo-immersive technologies while preserving them as an innovative tool. I conclude that despite criticisms that privacy is an inadequate remedy for the harms of surveillance, in certain commercial contexts the fair information principles can, if implemented robustly, serve to regulate the collection of personal information at source in a fashion that greatly restricts the potential for those harms.

Keywords: law
privacy
google
surveillance
streetview
feminist legal theory
autonomy
PIPEDA
data protection
Canada
mapping
Internet
Advisor: Austin, Lisa M.
Bringing Childhood Health into Focus: Incorporating Survivors into Standard Methods of Investigation

The osteological paradox addresses how well interpretations of past population health generated from human skeletal remains reflect the health of the living population from which they were drawn. Selective mortality and hidden heterogeneity in frailty are particularly relevant when assessing childhood health in the past, as subadults are the most vulnerable group in a population and are therefore less likely to fully represent the health of those who survived. The ability of subadults to represent the health of those who survived is tested here by directly comparing interpretations of childhood stress based on non-survivors (subadults aged 6-20,14 females and 9 males) to those based on retrospective analyses of survivors (adults aged 21-46, 26 females and 27 males). Non-survivors and survivors were directly matched by birth year, using the Coimbra Identified Skeletal Collection; therefore interpretations of childhood stress reflect a shared childhood. Long bone and vertebral canal growth, linear enamel hypoplasia, cribra orbitalia, porotic hyperostosis, scurvy indicators and periosteal bone reactions were assessed for both groups. Overall, long bone growth generates the same interpretation of health for both non-survivors and survivors, and both groups exhibit the same range of stress (mild to severe), but the pattern of stress experienced in childhood differs between the two groups. Female survivors reveal different timing of stress episodes and a higher degree of stress than female non-survivors. Male survivors exhibit less stress than male non-survivors. These different patterns suggest that interpretations based solely on non-survivors would under-represent the stress experienced by female survivors and over-represent the stress experienced by male survivors, further demonstrating the importance of addressing issues of selective mortality. In addition, these different patterns suggest that hidden heterogeneity of frailty may be sex specific where males are more vulnerable to stress and females more able to develop resistance to stress and survive.

Keywords: osteological paradox
sex differentials
child health
skeletal stress indicators
selective mortality
hidden heterogeneity of frailty
Advisor: Rogers, Tracy
Post-transcriptional Gene Regulation in the Vascular Endothelium: Implications of Hypoxia

Cellular messenger RNAs (mRNAs) exist almost exclusively in the context of ribonucleoprotein complexes (RNPs), which are largely responsible for the coordinated regulation of mRNA fate, and in particular, the post-transcriptional regulation of mRNA stability and translation. RNA- binding proteins, antisense RNAs, and microRNAs represent three major classes of post- transcriptional regulatory factors that interact with target mRNAs. Significantly, these interactions are dynamically regulated under both basal and stress conditions, such as hypoxia. Given the prominent contributions of post-transcriptional regulation to overall gene expression, a more comprehensive understanding of the underlying mechanisms is required. In this thesis, we present exciting new evidence for the functional importance of post- transcriptional gene regulation, especially in the vascular endothelium. Firstly, we show that the formation of hnRNP E1-containing RNPs contributes significantly to the remarkable basal stability of endothelial nitric oxide synthase (eNOS) mRNAs in endothelial cells by protecting them from inhibitory post-transcriptional forces. However, hypoxia impairs such RNP formation through hnRNP E1 serine phosphorylation and nuclear localization. Together, these mechanisms contribute significantly to decreased eNOS expression and activity in chronic hypoxia. ii Secondly, we reveal an important functional relationship between the microRNA pathway and the HIF-mediated cellular hypoxic response. Specifically, the down-regulation of Dicer and an important number of Dicer-dependent microRNAs in chronic hypoxia represents an important adaptive mechanism that serves to maintain the cellular hypoxic response through HIF-α- and microRNA-dependent mechanisms, with significant implications for the development of RNAi- based therapies. Finally, we provide evidence that the up-regulation of specific microRNAs in acute hypoxia is a potentially important mechanism that serves to suppress global translation initiation in order to conserve energy and ensure cellular survival. Collectively, the findings presented in this thesis provide important new mechanistic insight into the post-transcriptional regulation of eNOS, as well as the functional integration of the microRNA and the cellular hypoxic response pathways.

Keywords: Post-transcriptional gene regulation
Endothelium
Hypoxia
RNA
microRNA
Dicer
RNA-binding protein
Antisense
Advisor: Marsden, Philip A.
Quantifying Uncertainty in the Efficacy of Vitamin K on Fractures in Postmenopausal Women: Economic Evaluation, Evidence Synthesis and Bayesian Meta-analysis

Vitamin K has a negligible effect on bone mineral density (BMD) and a large but uncertain effect on fractures. The three studies in the thesis explored uncertainty about the effect of vitamin K on fractures using the methods of economic evaluation and Bayesian meta-analysis. In study 1, a Markov probabilistic microsimulation model was developed for a hypothetical cohort of 50-year-old postmenopausal women without osteoporosis. This was a fracture incidence-based model, populated with data from the literature. It was used to examine the cost-effectiveness of two supplementation strategies over a lifetime horizon. We compared vitamin K2 (or vitamin K1) concurrent with vitamin D3 and calcium versus vitamin D3 and calcium alone. Study 2 included a systematic review, and classical and Bayesian univariate meta-analyses to determine the efficacies of the K vitamins on BMD or fractures in current and future trials. Study 3 used Bayesian bivariate random-effects meta-analysis to jointly model the treatment effects on two correlated bone outcomes. We compared the estimates from the univariate and bivariate meta-analyses and explored how these results would change the conclusions of the cost-effectiveness analysis. The strategies including vitamin K were highly cost-effective at willingness-to-pay of $50,000/QALY (quality-adjusted life year); however, the results were most sensitive to changes in the efficacy of vitamin K. The univariate meta-analyses showed large uncertainties in the anti-fracture effects of vitamin K2 in current and future trials. The bivariate 95% credible intervals were considerably narrower than those from the univariate meta-analyses. Using future odds ratios from the bivariate meta-analyses, vitamin K2 cost more than $100,000/QALY while vitamin K1 was cost-saving. Our analyses found substantial uncertainty around the estimates of the vitamin K effect on fractures. We recommend against routine use of vitamin K for fracture prevention. Bayesian bivariate meta-analysis accounts for all available information and should be considered when the treatment effects are measured on two correlated outcomes.

Keywords: vitamin K
cost-effectiveness analysis
evidence synthesis
Bayesian meta-analysis
bivariate random-effects meta-analysis
Advisor: Cheung, Angela M.
TCP Adaptation Framework in Data Centers

Congestion control has been extensively studied for many years. Today, the Transmission Control Protocol (TCP) is used in a wide range of networks (LAN, WAN, data center, campus network, enterprise network, etc.) as the de facto congestion control mechanism. Despite its common usage, TCP operates in these networks with little knowledge of the underlying network or traffic characteristics. As a result, it is doomed to continuously increase or decrease its congestion window size in order to handle changes in the network or traffic conditions. Thus, TCP frequently overshoots or undershoots the ideal rate making it a "Jack of all trades, master of none" congestion control protocol. In light of the emerging popularity of centrally controlled Software-Defined Networks (SDNs), we ask whether we can take advantage of the information available at the central controller to improve TCP. Specifically, in this thesis, we examine the design and implementation of OpenTCP, a dynamic and programmable TCP adaptation framework for SDN-enabled data centers. OpenTCP gathers global information about the status of the network and traffic conditions through the SDN controller, and uses this information to adapt TCP. OpenTCP periodically sends updates to end-hosts which, in turn, update their behaviour using a simple kernel module. In this thesis, we first present two real-world TCP adaptation experiments in depth: (1) using TCP pacing in inter-data center communications with shallow buffers, and (2) using Trickle to rate limit TCP video streaming. We explain the design, implementation, limitation, and benefits of each TCP adaptation to highlight the potential power of having a TCP adaptation framework in today's networks. We then discuss the architectural design of OpenTCP, as well as its implementation and deployment at SciNet, Canada's largest supercomputer center. Furthermore, we study use-cases of OpenTCP using the ns-2 network simulator. We conclude that OpenTCP-based congestion control simplifies the process of adapting TCP to network conditions, leads to improvements in TCP performance, and is practical in real-world settings.

Keywords: TCP
Data Centers
Advisor: Ganjali, Yashar
Novel Regulators of Somatic Cell Reprogramming

Somatic cells can be reprogrammed to induced pluripotent stem (iPS) cells by expression of defined embryonic factors. My thesis is focused on exploring the mechanisms underlying reprogramming using a secondary mouse embryonic fibroblast model that forms iPS cells with high efficiency upon inducible expression of Oct4, Klf4, c-Myc and Sox2. My analyses of the temporal changes in gene expression reveal that reprogramming is a multi-step process characterized by initiation, maturation and stabilization phases. Using functional RNAi screening, I discovered a key role for BMP signaling and the induction of mesenchymal-to-epithelial transition (MET) during the initiation phase. I showed that MET induction was linked to BMP-dependent induction of miR-205 and the miR-200 family of microRNAs. These studies thus defined a multi-step mechanism that incorporates a BMP-miRNA-MET axis during somatic cell reprogramming. Next I focused on the two later phases of reprogramming, maturation and stabilization. I showed the stabilization phase and acquisition of pluripotency is dependent on removal of transgene expression late in the maturation phase. Clonal analysis of reprogramming cells revealed subsets of stabilization competent (SC) versus stabilization incompetent (SI) cells. SC clones robustly entered the pluripotent state upon transgene withdrawal in the late, but not early maturation phase, whereas SI clones failed to reprogram at either stage. Transcriptome profiling by RNA-Seq revealed that SC clones acquire a competency gene expression signature late in the maturation phase. Functional RNAi screening of SC signature genes further identified regulators of transition to the stabilization phase, while screening of the same signature in iPS cells revealed a distinct subset of genes required for maintenance of pluripotency. These studies reveal that the acquisition and subsequent maintenance of pluripotency are controlled by distinct molecular networks and uncover a novel regulatory program that is required for transition to transgene independence.

Keywords: reprogramming
stem cell
Advisor: Wrana, Jeffrey
Encoding Modulates the Interplay between Behavioural Priming and Recognition Processes

Recent research has demonstrated that priming and recognition memory performance are not independent as traditionally thought. Evidence is accumulating suggesting that information recognized in great detail (recollected) also has higher levels of priming (Sheldon &amp; Moscovitch, 2010; Turk-Browne, Yi, &amp; Chun, 2006). The purpose of this dissertation was to delineate the conditions under which recognition processes (estimates of recollection and familiarity) are associated with priming, and how this changes with age. Results from a systematic crossing of level of encoding (deep versus shallow) with type of priming task (conceptual versus perceptual) suggests that the relation between priming and recognition is determined by the nature of the encoding task. Under deep encoding conditions, a greater magnitude of priming&mdash;both perceptual and conceptual&mdash;was related to subsequent recollection but only amongst younger adults. Under shallow encoding conditions, perceptual priming performance was related to subsequent familiarity in both younger and older adults. Taken together, this series of experiments suggests that the processing mode engaged during encoding dictates which processes will be engaged at retrieval (a recollection-based process, or a familiarity-based process; Henke, 2010). These findings also suggest that both recollection and familiarity have rapid and unconscious aspects that are measurable through behavioural priming tasks, aligning with a recently proposed model suggesting recollection is characterized by a two-stage process, an early, relatively automatic and unconscious stage and a later, controlled and conscious stage (Moscovitch, 2008). It is suggested that the rapid, unconscious aspects of recollection may decline across the lifespan, while the rapid, unconscious aspects of familiarity stay intact with age.

Keywords: memory
aging
Advisor: Anderson, Nicole Dianne