VictorJuiz/thesis huggingface dataset:
An investigation of the stability of viscous channel flow

This thesis focuses on the use of systems theory to study the stability of viscous channel flow. In the first part of the thesis, the flow is modelled as a feedback connection between a linear dynamical subsystem and a memoryless nonlinear subsystem. After discretisation, the system is approximated by a finite-dimensional model and its global stability is analysed using the passivity theorems, which are extended from finite-dimensional Euclidean spaces to finite-dimensional Hilbert spaces. The passivity analysis leads to the Reynolds number below which the flow is globally stable and the flow can be unstable above this number because of possible energy amplification. The thesis then addresses inaccuracy of the numerical methods that are typically used in the literature to calculate the energy amplification in the flow. It is identified that the inaccuracy is caused by the presence of spurious eigenvalues with negative real parts of large magnitude and numerical integration errors. A remedy to this problem is given in the thesis.
In the second part of the thesis, the effects of riblets on the linear stability and the energy amplification in channel flow are investigated numerically. Riblets are small protrusions aligned with the direction of the flow and it is known that the use of riblets on an aerodynamic body can result in significant reduction in drag, although the mechanism of drag reduction by riblets is not yet clear. Three types of riblets (sinusoidal, triangular and semi-circular ones) are considered and in order to use spectral methods to discretise the governing equations, the complex geometry associated with the riblets is transformed to a standard domain by a change of coordinates. The differential equations also have to be transformed into the new coordinate system and the presence of riblets poses a serious difficulty in representing the fluid flow by a state space model. To circumvent this difficulty, a novel formulation of the Navier-Stokes equations is derived.

Advisor: Duncan, S
Cato the censor and the creation of a paternal paradigm

This thesis analyses the relationship between Marcus Porcius Cato Censorius and his eldest son, Marcus Porcius Cato Licinianus, considering its importance for Cato's public image and political career, investigating its place within some of the central cultural debates of the 2nd century BC, and looking at the impact which this relationship had upon received impressions of Cato the Censor as presented by later Latin authors. This is done primarily through the examination of the written works which Cato addressed to Licinianus, the extant fragments of which are presented here, with a translation and commentary, in the first modern edition to treat these texts as a unified project. The subsequent sections of this thesis set the works which Cato addressed to his son within the context of the general cultural debate and individual political competition which engaged Rome's ruling elite during this period; Cato's adoption of a paternal persona within these works is related to the character's popular appeal in the military sphere and on the comic stage; and the didactic pose and agricultural instruction featured in these texts is used to illuminate some of the challenges posed to Cato's successful performance of his duties as censor. A final section considers the reappropriation of Cato's relationship with his son as found in the De officiis of Cicero, the Institutio oratoria of Quintilian, and the anonymous Disticha Catonis. This thesis suggests that the Censor's relationship with his son, and the works which he addressed to the young man, played a more significant part in Cato's public image and political career than has hitherto been acknowledged. These texts illuminate some of the finer points of Cato's clever political strategy and they offer fresh insight into the popular culture and elite competition of the period in which he lived. The relative importance of this relationship within Cato's public life helps to explain the popularity of later images of the Censor as a paternal and educational figure and offers us a better understanding of modern conceptions of Cato.

Keywords: Political Competition
Roman Comedy
Latin Didactic
Classical Reception
Roman Oratory
Roman Republic
Advisor: Leigh, M
Blood glucose and diabetes mellitus as risk factors for cardiovascular disease in the China Kadoorie Biobank of 0.5 million people

Background: In China, the incidence of diabetes is rising, but little is known about its impact on cardiovascular diseases (CVD). Moreover, substantial uncertainty remains, both in China and elsewhere, about the relevance to CVD of blood glucose levels below the glycaemic threshold for diabetes. This thesis assessed these associations in Chinese adults.
Methods: In 2004-08, the China Kadoorie Biobank recruited 0.5 million adults aged 30-79 years from 10 diverse regions, recording 25 488 deaths by 1st January 2014. Logistic and Cox regression yielded adjusted odds (ORs) and hazard ratios (HRs), respectively, relating self-reported diabetes and, among people without self-reported diabetes, random plasma glucose (RPG) levels to prevalent and incident CVD.
Results: At baseline, 5.9% of participants had self-reported (3.2%) or screen-detected (2.8%) diabetes. Self-reported diabetes was associated with approximately 2-fold increased odds of prevalent ischaemic heart disease (IHD) (n=14 771, OR 2.16, 95% CI 2.05-2.28) and stroke/transient ischaemic attack (n=8430, 1.88, 1.75-2.02). There were also significant excess risks of CVD mortality (n=6916, HR 2.07, 95% CI 1.90-2.26) and incident IHD (n=3465, 2.44, 2.18-2.73), ischaemic stroke (n=19 778, 1.68, 1.60-1.77) and intra-cerebral haemorrhage (ICH) (n=4423, 1.24, 1.07-1.44). These risks increased with longer diabetes duration and number of other presenting risk factors. Screen-detected diabetes was also associated with significant, though more modest, excess incident CVD risks. Among participants without self-reported diabetes, there was a positive log-linear association of RPG with prevalent and incident CVDs. In prospective analyses the association continued down to baseline RPG of &Tilde;4.0 mmol/L. After adjusting for regression dilution bias, each 1 mmol/L higher usual RPG was associated with &Tilde;10% increased risks of incident ischaemic CVDs and CVD mortality, and &Tilde;5% increased risks of incident ICH. In &Tilde;89 000 genotyped individuals, a RPG-related genetic risk score was associated significantly with RPG. It showed no significant association with ischaemic CVD risks, but power to detect such an association was low.
Conclusions: Among adult Chinese, diabetes is associated with significantly increased risks of major CVDs. In individuals without diabetes, there is a positive log-linear association between RPG and CVDs, with no evidence of a threshold.

Advisor: Chen, Z
Bennett, D
Realising intersectionality in discrimination law

The central aim of the thesis is to understand why intersectionality remains at the fringes of mainstream discrimination law and to provide an alternative vision to the dominant conception of single-axis discrimination. This aim is pursued by translating intersectionality theory into the conceptual and doctrinal precincts of comparative discrimination law of South Africa, Canada and the United Kingdom.
The thesis is divided into three parts. Part One posits the framework of 'intersectional integrity' as forming the backbone of the category of intersectional discrimination. Its normative core insists on mapping the intersections between identities as creating unique and shared patterns of group disadvantage by considering people’s identities as a whole. It is this bipartite framework against which the doctrine is considered.
Part Two deals with the doctrinal limitations which impede a successful claim of intersectional discrimination. The comparative analysis fine-combs through the judicial interpretation to understand how it fares against the framework of intersectional integrity. The judicial strategies emerging from the doctrinal analysis are consolidated in the form of a graded spectrum which captures the proximity of each response from the category of intersectional discrimination. Beyond this conceptual reimagination, it also considers how other tools in discrimination law need to be recalibrated to accommodate an intersectional claim. These include the conception of equality and discrimination, the criteria for selection of analogous grounds, the understanding of indirect discrimination, the relationship between impact and justification analysis, apportioning the burden of proof and determining the standard of scrutiny.
Part Three consolidates the normative insights emerging from the thesis. A restatement of the theoretical and doctrinal recalibrations helps imagine how a lawyer would walk through the labyrinth of discrimination law for realising a claim of intersectional discrimination.

Keywords: Equality
Intersectionality
Discrimination
Advisor: Fredman, S
Identification and initial characterisation of protein methylation sites in Saccharomyces cerevisiae

The field of protein arginine methylation has seen a surge in the number of known methylation sites in higher eukaryotes over recent years, but our understanding of the functions of these modifications is lagging behind. A better knowledge of arginine methylation in a model organism like Saccharomyces cerevisiae that is relatively amenable to experimental manipulation may inform on arginine methylation also in higher eukaryotes.
The proteome-wide identification of methylation sites in S. cerevisiae, based on liquid chromatography tandem mass spectrometry in combination with several enrichment and fractionation strategies and on the use of heavy methyl SILAC is presented here. The majority of sites identified are in good agreement with previous reports of arginine methylation, i.e. occur in glycine-arginine-rich regions, locate to proteins involved in RNA-processing and overlap with known sites. Additionally, the data obtained suggest a bias for localisation of arginine methylation in unstructured protein regions and asparagine-rich contexts. It is further shown that the use of heavy methyl SILAC is useful for confident site identification.
To overcome challenges in the global approach, the detection of methylation sites on overexpressed candidate proteins was also employed. This strategy yielded methylation sites on more than half of the 38 successfully purified proteins, but also brought to light challenges in the localisation of sites.
Subsequently, it was investigated which methyltransferases are responsible for methylating mapped sites on two of these proteins. These experiments strongly indicate that Lsm4 is neither exclusively methylated by Hmt1 nor Hsl7, while Hmt1 appears to be the sole methyltransferase responsible for methylating Scd6. It was further shown that the methylation of the glycine-arginine-rich region of Scd6 is reduced upon prolonged sodium azide stress which may have potential implications in stress-induced translational repression. Overall, these results both inform on methods for the assignment of arginine methylation and improve its biological characterisation.

Advisor: Schofield, C
Kessler, B
Pears, C
The emergence of multiple status systems in adolescent communities

How do informal groups emerge in adolescent communities? What distinguishes a group from just a set of students? Who will end up together in a group and who will be left out? Why are there more groups in some classrooms and fewer in others? What determines whether these groups overlap in their members or they are completely segregated, perhaps antagonistic?
While a huge body of research in sociology and social psychology focuses on these questions, an integrated approach that is able to answer all of them is yet to be developed. Without realizing that these five issues are interrelated, we cannot hope to understand how groups influence individuals and how they shape our communities.
This thesis proposes an integrative theory of informal group formation in communities. Based on the tradition of Social Network Analysis, it develops a framework in which interpersonal relations and reputations are formed through a process called informal status production. Groups emerge from this micro-process by the alignment of positive relations and agreement in peer-perceptions between actors.
The main micro-mechanisms predicted by the theory are tested on a unique longitudinal network dataset from school classrooms. To this end, a new empirical procedure was developed, by which a few aggregated networks can be constructed from tens of relational items. This allows the analysis of rich network data with several relational dimensions.
The empirical studies of multiplex network dynamics confirm that there are strong interdependencies between friendships and perceptions. Students who agree about their peers tend to become friends, but more so when they hold a minority opinion in the class. This contributes to group formation. Friends also influence each other's perceptions, but we manage to show that the presence of groups around them interferes with this process by moderating the influence of individual peers.

Keywords: status hierarchies
Stochastic Actor-oriented Model (SIENA)
multiplex networks
group formation
adolescent communities
network evolution
Advisor: Snijders, T
Monden, C
Identification and characterisation of myofibroblast markers in human colon and colorectal cancer microenvironment

Myofibroblasts (MFs) are one of the most significant stromal cell types in epithelia such as in the gut. They play an important role in regulating the normal colorectal stem cell niche and facilitating tumour initiation, growth and progression through inter-cell signalling. Abundant presence of MFs is often associated with poor prognosis in cancers. The aim of this project is to identify new myofibroblast markers to distinguish them from others cells in the stroma, and also to establish patterns of myofibroblast gene regulation.
First, we identify the membrane protein that home-raised IgG1 antibody PR2D3 recognises on myofibroblasts, by using immunoprecipitation and mass spectrometry based amino acid sequencing, as the AOC3 membrane primary amine oxidase, with additional reactivity to myosin heavy chain 11 (Chapter 3). The AOC3 expression in myofibroblasts in vivo and in vitro is validated by extensive expression profiling analyses. Our results demonstrate that AOC3 is expressed by myofibroblasts and that it functions as an SSAO enzyme (Chapter 4). Furthermore, we successfully separated primary myofibroblasts from fresh tissues by FACS sorting using AOC3 as a myofibroblast-specific surface marker (Chapter 5). Analysis of whole genome microarray mRNA expression profiles between myofibroblasts and fibroblasts revealed 4 candidate genes that were the most significantly differentially expressed in the two cell types; NKX2.3 and LRRC17 are highly expressed in myofibroblasts, while SHOX2 and TBX5 are highly expressed in fibroblasts (Chapter 6). NKX2.3 is essential for TGFβ-induced myofibroblast contraction and migration ability. Knockdown of NKX2.3 using siRNA caused a decrease of myofibroblast-related gene (ACTA2, MYH11 and AOC3) expression and an increased expression of fibroblast gene, SHOX2 in myofibroblasts. This suggests that NKX2.3 is a key mediator for maintaining myofibroblast characteristics and functions. Our work presented here shows that myofibroblasts and fibroblasts have significantly different expression profiles for a few key genes and that they differ in their response to TGFβ.
In conclusion, the results clearly show that TGFβ activated fibroblasts and myofibroblasts, as defined by the expression of AOC3 and NKX2.3, are distinctly different cell types.

Keywords: AOC3
myofibroblasts
cancer microenvironment
NKX2-3
Studies of the MuSK system using molecular dynamics simulations

Formation and maintenance of neuromuscular junctions, as well as signalling from the nerve to the muscle, depends on the concerted action of a number of membrane proteins. Muscle-Specific Kinase (MuSK) and Downstream-of-Kinase 7 (Dok7) are key players in these processes. MuSK acts as the central component in the complexes responsible for nervemuscle communication. Dok7 then regulates full activation of MuSK. Despite available structural data for these proteins, the structure of the overall Dok7/MuSK complex in a cell membrane remains elusive. In this thesis, a multi scale molecular simulation approach (combining coarsegrained and atomistic simulations) was used to study the formation of the Dok7/MuSK/membrane complex. Three major insights into this process were obtained. Firstly, dimerisation of the transmembrane helix of MuSK is mediated by a small-x-x-x-small amino acid motif, and it is not affected significantly by the addition of anionic lipids or unstructured extensions on each end of the helices. Secondly, Dok7 interacts with PIP-containing bilayers via a positive patch on its pleckstrin-homology (PH) domain. Thirdly, it is shown that MuSK's behaviour in a complex model membrane is potentially influenced by the presence of Dok7. Taken together, these results allow formulation of a defined model of the structure and mechanism of MuSK in a model membrane.

Advisor: Sansom, M
Uniform multicommodity flows in random networks

Given a network &Nscr;, and a collection &Vscr; of unordered pairs of vertices in &Nscr;, a corresponding uniform multicommodity flow F of volume φ consists of simultaneous flows of volume φ of unique commodities between each pair of vertices in &Vscr;. The maximum uniform flow volume is the maximum value of φ such that there is a uniform multicommodity flow of volume φ in &Nscr;, within the capacity constraints.
This thesis considers networks with random edge-capacities. Multicommodity flows are of interest in operational research and combinatorial optimisation and sampling. They have been studied extensively from a "worst-case" perspective, but the "typical" behaviour of multicommodity flow problems is much less well understood. In order to address this, a model is considered in which the underlying graph is fixed and the edge capacities are random. Aldous, McDiarmid and Scott studied the case in which the underlying graph is complete, the edge capacities are independent, each distributed like a given random variable C, and &Vscr; is the collection of all unordered pairs of vertices.
Another very natural example is the d-dimensional (hyper)cube Qd, with independent random edge capacities, where the probability of an edge having zero capacity is less than 1/2. Two models are studied. In the first, flows are routed between all antipodal (opposite) pairs of vertices, and in the second, flows are routed between all vertex pairs. In both cases, as d tends to infinity, asymptotic values for the maximum uniform flow volumes are determined.
A detailed characterisation is given next for the size and distribution of components in a random subgraph of the hypercube where the probability of an edge being present is a constant less than 1/2. It is shown that, whp, other than the main component, the number of vertices in any component is bounded by a constant and that the number of components of a given size or configuration is asymptotically normal. Multicommodity flows in the largest component of such a network are then analysed.
Two further random structures are considered. Firstly, a network formed by giving each edge of a random cubic graph a capacity of 1 is considered. In this case the capacities are not random but the structure of the underlying graph is. This case is of interest as it is a tractable example of a graph with the 'small world' property that the diameter increases like log n. Secondly the argument of Aldous, McDiarmid and Scott is generalised to give results for directed and undirected complete multipartite graphs. Lastly multicommodity flows in a directed hypercube are considered.

Keywords: Random Graph
Multicommodity flow
Component structure
Percolation
Hypercube
Network
Advisor: Scott, A
McDiarmid, C
Gary Snyder's green Dharma

Twentieth-century environmentalist discourse often laid the blame for environmental degradation on Western civilization, and presented the religious traditions of the East as offering an ecocentric antidote to Western dualism and anthropocentrism. Gary Snyder has looked to Chinese and Japanese Buddhism to inform his environmentalist poetry and prose. While Snyder often writes in terms of a dualism of East and West, he synthesizes traditional forms of Buddhism with various Western traditions, and his green Buddhism ultimately undermines more simplistic oppositions of East and West.
The first chapter reads Snyder's writing of the mid-1950s alongside several of his West Coast contemporaries—Kenneth Rexroth, Allen Ginsberg, Michael McClure, Philip Whalen and Jack Kerouac—showing that these writes evoked the natural world together with Buddhist themes before the advent of the modern environmental movement in order to mount a critique of Cold War American culture. Snyder's early interest in Buddhism was motivated largely by translations of Chinese poetry and Chapter Two examines his own translations of the Tang Dynasty poet Hanshan. In Snyder's translations and contemporaneous original poetry, Buddhist poetics mingle with American conceptions of wilderness. Chapter Three shows how Snyder's Buddhism was influenced by Anglophone writers such as D.T. Suzuki and Alan Watts, and argues that from the late 1960s Snyder aimed to Americanize Buddhism as ideas of localism became more central to his environmentalism. Chapter Four examines Snyder’s synthesis of Hua-yen Buddhism and Western scientific ecology in the 1970s and 1980s. Chapter Five examines 'The Hokkaido Book,' an unfinished prose work on environmental attitudes in the Far East in which Snyder considers the relationship between the civilized and the primitive. Chapter Six examines the influence of Chinese landscape painting and Japanese N&omacr; drama, two forms steeped in Buddhist ideas, on the poems of Mountains and Rivers Without End.

Advisor: Bate, J