VictorJuiz/thesis huggingface dataset:
The Influence of Coriolis Forces on Flow Structures of Channelized Large-scale Turbidity Currents and their Depositional Patterns

Physical experiments are used to investigate the influence of the Coriolis forces on flow structures in channelized turbidity currents, and their implication for the evolution of straight and sinuous submarine channels. Initial tests were used to determine whether or not saline density currents are a good surrogate for particle-laden currents. Results imply that this assumption is valid when turbidity currents are weakly-depositional and have similar velocity and turbulence structures to saline density currents. Second, the controls of Coriolis forces on flow structures in straight channel sections are compared with two mathematical models: Ekman boundary layer dynamics and the theory of Komar [1969]. Ekman boundary layer dynamics prove to be a more suitable description of flow structures in rotating turbidity currents and should be used to derive flow parameters from submarine channels systems that are subjected to Coriolis forces. The significance of Coriolis forces for submarine channel systems were determined by evaluating the dimensionless Rossby number RoW. The Rossby number is defined as the ratio of the flow velocity, U, of a turbidity current to the channel width, W, and the rotation rate of the Earth represented by the Coriolis parameter, f. Coriolis forces are very significant for channel systems with RoW ≤ O(1). Third, the effect of Coriolis forces on the internal flow structure in sinuous submarine channels is considered. Since previous studies have only considered pressure gradient and centrifugal forces, the Coriolis force provides a crucial contribution to the lateral momentum balance in channel bends. In a curved channel, both the Rossby number RoW and the ratio of the channel curvature radius R to the channel width W, determine whether Coriolis forces affect the internal flow structure. The results demonstrate that Coriolis forces can cause a significant shift of the density interface and the downstream velocity core of channelized turbidity currents. The sediment transport regime in high-latitude channel systems, which have RoW << R/W, is therefore strongly influenced by Coriolis forces. Finally, these findings are incorporated into a conceptual model describing the evolution of submarine channels at different latitudes. For instance, the Northern Hemisphere channels have a distinctly higher right levee system and migrate predominantly to the left side and generally exhibit a low sinuosity. In contrast, low latitude channel systems have RoW >> R/W so that centrifugal forces are more dominant. This results in more sinuous submarine channel systems with varying levee asymmetries in subsequent channel bends. In conclusion, Coriolis forces are negligible around the equator but should be considered in high latitude systems, particularly when RoW ~ O(1) and RoW << R/W.

Keywords: Coriolis force
submarine channels
gravity current
turbulence structure
Boundary layers
Advisor: Wells, Mathew
Gender, the State and a Lifetime of Experience: Understanding Health Inequality among Older Adults in Britain

There is a well-established relationship between socioeconomic position (SEP) and health among older adults, but a short-coming of existing research is its failure to link the SEP-health relationship in later life to the gendered histories of work and family life, or the policy contexts in which these histories unfold. Drawing on the life course perspective and welfare state theory, this research investigates: the dominant patterns of labour market and family experiences over the life course for current cohorts of older adults in Britain; whether health dynamics among older adults vary by gender and life course experiences; and whether SEP and social roles at age 65 mediate these relationships. The data come from a sample of individuals born between 1927 and 1940 participating in the British Household Panel Survey (N=1552). I first examined life course experiences in the labour market and the family from young adulthood to retirement age using a two-stage latent class analysis. Theoretical considerations, along with indices of model fit, suggested that four latent life paths broadly characterized the experiences of the older adults in this sample. Consistent with the social policy context in Britain in the post-World War II years, I found evidence of distinct gender patterns in role configurations at various points across the life course and in the life pathways that link these experiences over time. In the second part of the analysis, I assessed health dynamics using latent growth curve models. Only mental health dynamics were patterned by life course histories, and SEP at age 65 mediated part of this relationship. The life course histories did not have an independent influence on trajectories of chronic health problems or self-assessed health. These findings are considered in the context of our current understanding of health dynamics among older adults, including gender differences and their relationship to SEP.

Keywords: life course
health inequalities
Advisor: McDonough, Peggy
Acadian Accordion Music in South Eastern New Brunswick

Instrumental folk music has flourished in south eastern New Brunswick and the accordion, while a relative newcomer to the region, enjoys great popularity. Over the years, accordion players have filled many roles, from providing wedding music, to entertainment for house parties. However, there has been a lack of scholarly work done on the subject, especially when compared with folksongs, which have been the object of many studies. To date, little has been written on Acadian instrumental music in New Brunswick and there has been nothing written specifically on the accordion. The main focus of this work is a study, transcription, and analysis of accordion pieces collected from players in south eastern New Brunswick between 2007 and 2011. Some time is also spent on detailing the history of the accordion in the region, talking about the players themselves, as well as looking at the role of the instrument and its repertoire in a constantly changing world. The pieces in question were collected over a four year period in various venues, including accordion festivals and players’ places of residence; archival recordings were also consulted. The pieces were transcribed and afterwards analyzed and categorized. Multiple recordings of the same piece were checked for variations, which were found to be an important part of the style of the region. Historical data is often based on personal accounts, which were taken during interviews with players from the region. The accordion remains popular in the region and is adapting to changing circumstances. The annual accordion festivals occurring in Moncton every summer are providing new venues to keep the instrument relevant. This study will help to bring further attention to the instrument, stimulate new research, and perhaps even attract new younger players.

Keywords: accordion
Acadian
New Brunswick
Advisor: Elliott, Robin
The Tradition of Transcription: Handel Aria Arrangements in the Fifth Book of The Ladys Banquet

Eighteenth-century London was a hotbed for instrumental arrangements, and many of these works were derived from the operas of George Frideric Handel (1685-1759). Thirty-one of his operas, in whole or in part, were arranged for recorder or flute, and there were over seventy keyboard transcriptions of the overtures to these operas. While the transcriptions of Handel overtures have been thoroughly examined, opera aria transcriptions have never received an appropriate level of study and analysis. The Ladys Banquet or The Lady’s Entertainment provides an excellent starting point. Not only does it include numerous opera aria arrangements, but its volumes were re-issued several times, suggesting a wide circulation. Its study raises a number of issues, including publication and authorship of Handel transcriptions, gendered music of the eighteenth century and analysis of opera transcriptions. The Ladys Banquet or The Lady’s Entertainment is a collection of six volumes of keyboard music published by John Walsh in the first half of the eighteenth century. The first two books were issued in 1704 and 1706 respectively, and included many undemanding pieces by fashionable composers such as Jeremiah Clarke (c.1674-1707) and Henry Purcell (1659-1695). The Third and Fourth Books followed in circa 1715 and 1716 and contain predominantly dance tunes and popular songs revised for the keyboard. When, in the early 1730s, the Fifth and Sixth Books appeared, the original four volumes were revised, and included wholly different material than the first editions. The publications of John Walsh are notoriously confusing owing to their lack of publication dates, repeated use of title pages, and misleading advertisements. The Ladys Banquet, as a whole, is especially bewildering because of the reissues of the collection and the changing repertoire. My research focuses on the Fifth Book of The Ladys Banquet, first printed around 1734, due to its abundance of opera aria transcriptions and consistency of content within editions. This document compiles relevant background information and offers a lucid guide to The Ladys Banquet. It provides historical context, examination and discussion of the contents of each volume, with specific details about the music in the Fifth Book, as well as analysis of the Handel aria transcriptions.

Keywords: The Ladys Banquet
The Ladies Entertainment
harpsichord transcription
aria arrangement
Handel transcription
Handel arrangement
opera transcription
opera aria transcription
Advisor: Parker, Mary Ann
An Automated Micromanipulation System for 3D Parallel Microassembly

The introduction of microassembly technologies has opened up new venues for the fabrication of sophisticated, three-dimensional Microelectromechanical System (MEMS) devices. This thesis presents the development of a robotic micromanipulation system and its controller algorithms for conventional pick-and-place microassembly processes. This work incorporated the approach of parallel assembly and automation to improve overall productivity and reduce operating costs of the process. A parallel set of three microgrippers was designed and implemented for the grasping and assembly of three microparts simultaneously. The complete microassembly process was automated through a vision-based control approach. Visual images from two vision systems were adopted for precise position evaluation and alignment. Precise alignment between the micropart and microgripper is critical to the microassembly process. Due to the limited field of view of the vision systems, the micropart could displace away from the microscope field of view during the re-orientation process. In this work, a tracking algorithm was developed to constrain the micropart within the camera view. The unwanted translational motions of the micropart were estimated. The algorithm then continuously manipulated and repositioned the micropart for the vision-based assembly. In addition, the limited fields of view of the vision systems are not sufficient to concurrently monitor the assembly operation for all three individual grippers. This work presents a strategy to use visual information from only one gripper set for all the necessary alignment and positioning processes. Through proper system calibration and the alignment algorithms developed, grippers that were not visually monitored could also perform the assembly operations. When using visual images from a single vision camera for 3D positioning, the extra dimension between the 2D image and 3D workspace results in errors in position evaluation. Hence, a novel approach is presented to utilize image reflection of the micropart for online evaluation of the Jacobian matrix. The relative 3D position between the slot and micropart was evaluated with high precision. The developed algorithms were integrated onto the micromanipulation system. Automated parallel microassemblies were conducted successfully.

Keywords: Microassemby
Parallel
Micromanipulation
MEMS
Visual Servoing
Advisor: Mills, James
Cleghorn, William L.
Structural and Functional Analysis of Two Novel Protein Ligases, Dcn1 and IpaH

The ubiquitination pathway regulates virtually all cellular processes such as cell cycle control and immune surveillance in eukaryotes, and is thus highly regulated through a variety of means. For instance, the Cullin-RING ubiquitin E3 ligases are regulated by neddylation through the action of a newly identified protein Dcn1. In chapter two, I describe an X-ray crystal structure of yeast Dcn1, encompassing an N-terminal ubiquitin association (UBA) domain and a C-terminal domain of unique architecture, which I termed the PONY (POtentiating NeddYlation) domain. I describe the identification of the reciprocal, conserved binding surfaces on both Dcn1 and yeast cullin Cdc53. In collaboration with Dr. Matthias Peter’s group (ETH Zurich), we show that Dcn1 is necessary and sufficient for cullin neddylation in a purified recombinant system. Together, our data identify Dcn1 as the long sought-after Nedd8 E3 ligase for cullin neddylation. As a modulator of immune surveillance and inflammatory responses, the ubiquitin system serves as an attractive target for subversion by pathogens. In chapter three, I present a structural and functional analysis of a newly identified bacterial ubiquitin E3 ligase IpaH, present in various pathogenic and commensal bacteria. I demonstrate that the leucine-rich repeat (LRR) substrate recognition domains of different IpaH enzymes auto-inhibit the enzymatic activity of the adjacent catalytic domain by two distinct but conserved structural mechanisms. Auto-inhibition is required for the biological activity of two IpaH enzymes in a yeast model system. Retro-engineering of auto-inhibition into a constitutively active IpaH enzyme from Yersinia demonstrates that most of the infrastructure required to support auto-inhibition is evolutionarily conserved. In brief, my research provides insights into the mechanism of action of two newly identified protein ligases in the ubiquitination pathway, namely the Nedd8 E3 ligase Dcn1 and bacterial ubiquitin E3 ligase IpaH.

Keywords: ubiquitin
ligase
structural biology
neddylation
Advisor: Sicheri, Frank
Search for Dijet Resonances in sqrt(s)=7 TeV Proton-Proton Collisions with the ATLAS Detector at the LHC

A search for new heavy resonances in two-jet final states is described in this thesis. The data were collected by the ATLAS detector proton-proton collisions at sqrt(s) = 7 TeV and correspond to a time-integrated luminosity of 6.1 pb−1. The background-only hypothesis was tested on the observed data using BumpHunter test statistic. Consistency was found between the observed data and the background-only prediction. No resonant features were observed. A Bayesian approach using binned maximum likelihood was used to set upper limits on the product of cross section and detector acceptance for excited-quark (q*) production as a function of q* mass. At 95% credibility level (CL), the q* mass in the interval of 0.50 TeV < mq* < 1.62 TeV is excluded, extending the reach of previous experiments.

Keywords: Dijet
Exotics
Heavy resonances
Test statistics
Excited quark
Bayesian treatment
Advisor: Savard, Pierre
Chorus: Model Kowledge Base for Perfomance Modeling in Datacenters

Due to the imperative need to reduce the management costs, operators multiplex several concurrent applications in large datacenters. However, uncontrolled resource sharing between co-hosted applications often results in performance degradation problems, thus creating violations of service level agreements (SLAs) for service providers. Therefore, in order to meet per-application SLAs, per-application performance modeling for dynamic resource allocation in shared resource environments has recently become promising. We introduce Chorus, an interactive performance modeling framework for building application performance models incrementally and on the fly. It can be used to support complex, multi-tier resource allocation, and/or what-if performance inquiry in modern datacenters, such as Clouds. Chorus consists of (i) a declarative high-level language for providing semantic model guidelines, such as model templates, model functions, or sampling guidelines, from a sysadmin or a performance analyst, as model approximations to be learned or refined experimentally, (ii) a runtime engine for iteratively collecting experimental performance samples, validating and refining performance models. Chorus efficiently builds accurate models online, reuses and adjusts archival models over time, and combines them into an ensemble of models. We perform an experimental evaluation on a multi-tier server platform, using several industry- standard benchmarks. Our results show that Chorus is a flexible modeling framework and knowledge base for validating, extending and reusing existing models while adapting to new situations.

Keywords: performance model
resource provisioning
datacenter
multi-tier system
resource allocation
database
storage server
Advisor: Amza, Cristiana
Roles of Matrix Mechanics in Regulating Aortic Valve Interstitial Cell Pathological Differentiation

Calcific aortic valve disease (CAVD) is associated with increased presence of myofibroblasts, osteoblastic cells and, occasionally, adipocytes and chondrocytes in lesions. The ectopic cell types in diseased valves may be elaborated by an unidentified multipotent progenitor subpopulation within the valve interstitial cells (VICs) that populate the valve interstitium. Notably, lesions form preferentially in the fibrosa layer, the stiffer layer of the valve leaflet. It has been shown that differentiation of VICs to myofibroblasts and osteoblasts is modulated by matrix stiffness. However, the molecular mechanisms involved in mediating stiffness-dependent mechanotransduction remain obscure. The objectives of this thesis were: (1) to determine whether VICs contain a subpopulation of multipotent mesenchymal progenitor cells and to measure the frequencies of the mesenchymal progenitors and osteoprogenitors; (2) to determine the role of β-catenin and matrix stiffness in transforming growth factor-β1 (TGF-β1)-induced myofibroblast differentiation of VICs; and (3) to preliminarily investigate the involvement of four and a half LIM domains protein 2 (FHL2) in CAVD and stiffness-dependent mechanotransduction downstream of RhoA in VICs. Firstly, VICs were found to contain a subpopulation of mesenchymal progenitors that are inducible to osteogenic, myofibroblastic, adipogenic, and chondrogenic lineages. The frequencies of mesenchymal progenitors and osteoprogenitors were significantly higher than other reported sources. Secondly, it was demonstrated that β-catenin is required in TGF-β1-induced, matrix stiffness-regulated myofibroblast differentiation. Notably, TGF-β1 was only able to induce β-catenin nuclear translocation and myofibroblast differentiation on matrices with fibrosa-like stiffness, but not on matrices with ventricularis-like stiffness. Thirdly, FHL2 was found to be upregulated and colocalized with runt-related transcriptional factor 2 (Runx2) in lesions in the fibrosa layer of diseased valves, suggesting its role in osteogenic processes in CAVD. Notably, increasing matrix stiffness increased FHL2 nuclear translocation and RhoA activity in VICs. Preliminary data showed that matrix stiffness regulates FHL2 nuclear translocation via RhoA activity. These results suggest that differentiation of the rich valve progenitor subpopulation, regulated by both mechanical and biochemical cues, may contribute to the preferential occurrence of ectopic cell types in the fibrosa in CAVD. More broadly, these results highlight the critical role of mechanical environment in modulating cellular biochemical signaling.

Keywords: aortic valve
matrix mechanics
mesenchymal progenitors
Advisor: Simmons, Craig Alexander
The Impact of the Splanchnic Bed on the Dietary Requirements of Threonine and Lysine in Humans

The splanchnic bed is a group of organs (liver, intestines, stomach, pancreas and spleen) which are active in the metabolism of amino acids. However, the impact of this group of organs on the dietary requirements of humans has yet to be determined. The focus of this research will be the requirements of two indispensable amino acids, threonine and lysine, and the impact of the splanchnic bed on amino acid kinetics. Threonine is an indispensable amino acid which is critical in the production of mucins in the gut and contributes significantly to collagen, elastin and tooth enamel formation in mammals. The first study was designed to determine the threonine requirement for the parenterally-fed, stable, post-surgical neonate. The mean threonine parenteral requirement, as experimentally derived in human neonates, was 32.8 mg•kg-1•d-1 which was less than the recommended enteral intake of 76 mg•kg-1•d-1 suggesting a splanchnic uptake in humans of 57%. Lysine is an indispensable amino acid used primarily, in the mammalian body, for protein synthesis but it also acts as a precursor for carnitine synthesis. The second study was devised to determine the lysine requirement for the parenterally-fed, stable, post-surgical neonate. The mean lysine parenteral neonatal requirement as experimentally determined in human neonates, was 104.9 mg•kg-1•d-1 which was less than the recommended enteral intake of 119 mg•kg-1•d-1 suggesting a splanchnic uptake in humans of 12%. The third study was intended to increase our knowledge of the metabolism of threonine and lysine by the splanchnic bed. Adult humans were fed isotopic threonine and lysine both enterally and parenterally. We determined that retention of threonine and lysine by the splanchnic bed was 16.7% and 17.1% respectively, which were not significantly different. The conclusion was that, in healthy human adult males, there was no difference in the extraction of threonine and lysine by the splanchnic bed which was different from our findings in parenterally fed piglets and human neonates.

Keywords: Splanchic Bed, Threonine, Lysine, Parenterally Fed Neonates,
Advisor: Pencharz, Paul B.