VictorJuiz/thesis huggingface dataset:
Dromde Mik en Drom i Nat...
Keywords: harding fiddle slattar
string orchestra with english horn and french horn
infinity series

Composed entirely of runes, the 14th century manuscript Codex Runicus is comprised of 101 sheets and contains historical documents such as "Kings until Erik Menved" and "Boundaries between Denmark and Sweden."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.
Geo-immersive Surveillance and Canadian Privacy Law
Keywords: law
privacy
google
surveillance
streetview
feminist legal theory
autonomy
PIPEDA
data protection
Canada
mapping
Internet

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.
Bringing Childhood Health into Focus: Incorporating Survivors into Standard Methods of Investigation
Keywords: osteological paradox
sex differentials
child health
skeletal stress indicators
selective mortality
hidden heterogeneity of frailty

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.
Post-transcriptional Gene Regulation in the Vascular Endothelium: Implications of Hypoxia
Keywords: Post-transcriptional gene regulation
Endothelium
Hypoxia
RNA
microRNA
Dicer
RNA-binding protein
Antisense

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.
Quantifying Uncertainty in the Efficacy of Vitamin K on Fractures in Postmenopausal Women: Economic Evaluation, Evidence Synthesis and Bayesian Meta-analysis
Keywords: vitamin K
cost-effectiveness analysis
evidence synthesis
Bayesian meta-analysis
bivariate random-effects 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.
TCP Adaptation Framework in Data Centers
Keywords: TCP
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.
Novel Regulators of Somatic Cell Reprogramming
Keywords: reprogramming
stem cell

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.
Encoding Modulates the Interplay between Behavioural Priming and Recognition Processes
Keywords: memory
aging

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.
Form and Function: Seeing, Knowing, and Reasoning with Diagrams in the Practice of Science
Keywords: Visual
Diagram
Reasoning
Visualization
Physics
Feynman
Chemistry
Kekule
Crum-Brown
Van 't Hoff
models
representation

In virtue of what do scientific diagrams acquire their epistemic legitimacy? Which factors serve to validate schematic visual representations, rendering them useful and accepted components of scientific practice? This thesis addresses the epistemic legitimacy of scientific diagrams by investigating a variety of diagrams whose referents are “invisible”, that is, whose targets either cannot be seen, lack physical form, or have no material analogue. In focusing on such images, we shall gain insight into the factors that shape the forms that practicing scientists give to their diagrams and shed light on contemporary issues in the philosophy of scientific models and representations. In this work, common factors underscoring the epistemic legitimacy of scientific diagrams are identified through three in-depth historical case studies. First, we consider several diagrammatic approaches to visualizing chemical structure that emerged around the 1860s, especially the competing approaches of August Kekulé and Alexander Crum Brown, and investigate the factors that led to the enduring success of Crum Brown’s visual representations and the corresponding abandonment of Kekulé’s. Second, we examine a spectrum of stereochemical diagrams and material models produced from the 1870s to the early 20th century, particularly those produced by J. H. van ‘t Hoff, and consider the factors that determined the forms given to representations of three-dimensional structures of chemical compounds. Third, we explore the diagrammatic approaches taken by physicist Richard Feynman in his mid-20th century lectures on quantum electrodynamics, paying close attention to his diagrams’ stylistic commonalities and dissimilarities as well as their ability to mediate between various aspects of the practice of physics. Finally, this thesis concludes by considering several common factors regarding the epistemic legitimacy of scientific diagrams that can be identified in these case studies, including the importance of a bijective relationship between scientists’ understanding of their diagrams and of their diagrams’ referents, the utility of diagrams for productively reasoning about their referents, and ability of certain diagrams to reduce scientists’ cognitive burden, especially through visual similarities. These factors serve to unite divergent approaches to the philosophy of scientific models and representation and reorient contemporary debates concerning representation towards an integrated historical-philosophical methodology.
Numerical Geodynamic Experiments of Continental Collision: Past and Present
Keywords: Geodynamics

Research explores deep continental lithosphere (i.e., the continental lower crust and mantle lithosphere) deformation during continental collision. I found that depending on the composition/rheology of the crust and the amount of radiogenic heat production in the crust, three dominant modes of mantle lithosphere deformation evolve under Neoarchean-like conditions: (1) a pure-shear thickening style; (2) an imbrication style; (3) and a "flat-subduction" style. The imbrication and the flat-subduction styles result in the emplacement of "plate-like" mantle lithosphere at depths between 200 km and 325 km. The imbrication style behavior shifts to the "flat-subduction" style behavior after a crustal inversion event. I investigated mature Phanerozoic-style collision and found that it is sensitive to mantle lithosphere density, mantle lithosphere yield stress, lower-crustal strength and to the presence of phase change-related density changes in the lower crust. The early stages of collision are accommodated by subduction of lower crust and mantle lithosphere along a discrete shear zone beneath the overriding plate. Next, the subducting lower crust and mantle lithosphere retreat from the collision zone, permitting the sub-lithospheric mantle to upwell and intrude the overriding plate. Next, the lower crust and mantle lithosphere of the overriding plate delaminate from the overlying crust. This process produces plateau-like uplift. These modeling results are interpreted in the context of available geological and geophysical observables for the Himalayan-Tibetan orogen. I quantitatively investigated the effects that sediment deposition may have on continental lithosphere deformation during collision. In the absence of sedimentation, the early stages of collision are accommodated by subduction of lower crust and mantle lithosphere beneath the overriding plate. Next, the subducting lower crust and mantle lithosphere retreat from the collision zone. This permits the sub-lithospheric mantle to upwell and come into contact with the thickened upper crust. When sedimentation is imposed subduction-like consumption of the subducting plate remains stable. Using numerical geodynamic models, I studied the influence of the pressure-dependence of viscosity on tectonic deformation during collision. At low activation volumes, high convergence rates, and low to moderate initial Moho temperatures the subduction style of mantle lithosphere deformation is dominant. At low activation volumes, high convergence rates, and high initial Moho temperatures distributed pure-shear style deformation occurs. At low activation volumes, low convergence rate, and moderate to high initial Moho temperatures the mantle lithosphere prefers a convective removal style of deformation. Increasing the activation volume of mantle material in either of these three cases changes the style of mantle lithosphere deformation because its viscosity increases non-linearly.