VictorJuiz/thesis huggingface dataset:
The Bon sman sgrub ritual

The thesis deals with the Tibetan healing mendrub (sman sgrub) ritual as performed by the contemporary exile Bonpo community at the Triten Norbutse Monastery, Kathmandu, Nepal in December 2012. The ritual is described and analysed, particular attention is given to its medical component. The research is based on fieldwork, textual analysis and close work with Tibetan traditional scholars, including a doctor of Tibetan medicine.
The axis of the thesis is the specific "material core of the ritual", the so called medicine (sman) or mendrub medicine (sman sgrub kyi sman), its preparation, the processes it undergoes in the course of the ritual as well as approaches to understanding it and the ritual as a whole: The generated empowered medicine as a miraculous substance represents a universal remedy and the ritual performance pacifies the universe. On the highest spiritual level, both work solely as a symbolic support on one’s path towards enlightenment.
The Tibetan medical system derives from different spheres of knowledge and is tightly tied to religion, philosophy, cosmology and tantric practices. As such it forms a very complex unit all parts of which become materially expressed and "replayed" by the ritual. Within the cosmological framework the medicine, both medical concepts and medicinal substances, as well as the act of healing become 'mandalised'. Similarly, human body and Buddhist philosophical concepts are fitted into the mandalic organizational scheme. Its purpose is to embrace and position every entity in order to make the whole unit, i.e. body, universe etc., balanced.

Keywords: Tibet
Bon
Tibetan religion
Tibetan medicine
sman sgrub / mendrub
ritual
healing
Advisor: Roesler, U
The role of protein arginine methylation in T-lymphocyte activation

T-lymphocytes are an essential cell type of the adaptive immune system. Due to their importance in immune responses and disorders, the molecular mechanisms leading to T-lymphocyte activation have been the subject of extensive research which has translated into important therapeutic developments. Early signalling events involving tyrosine phosphorylation are well characterised. However, later events involving other post-translational modifications are less well understood. Several studies have provided evidence suggesting a role for protein arginine methylation in T-lymphocyte activation. Arginine methylation is an essential post-translational modification in mammals and yet has not been extensively studied. No large scale analysis of arginine methylation sites has been performed.
To gain insight into the role of protein arginine methylation in T-lymphocyte activation, the aims of this work were to: 1. Establish whether levels of arginine methylation are altered during Tlymphocyte activation 2. Use mass spectrometry based proteomics to identify arginine methylated proteins in the T-lymphocyte proteome 3. Further characterise an arginine methylated protein important to Tlymphocyte activation Arginine methylation was found to be induced after long term (>20 hours) stimulation of primary T-lymphocytes. Large increases in the main protein arginine methyltransferase, PRMT1, were also observed. Enrichment and labelling methods were developed to detect arginine methylated peptides from T-lymphocytes by mass spectrometry. This resulted in the identification of 265 unique arginine methylation sites in 141 proteins. 204 of the methylation sites were novel and 103 of the proteins had not previously been described as arginine methylated. Individual arginine methylation sites were characterised before and after activation of T-lymphocytes, with some sites showing significant changes in abundance. Among the novel arginine methylated proteins discovered were Dynamin II, WASp and WIPF1. These proteins are involved in re-organisation of the actin cytoskeleton at the immunological synapse formed between a Tlymphocyte and an antigen presenting cell. The functional consequences of the arginine methylation sites inWASp were characterised. WASp is essential for T-lymphocyte activation and some initial evidence showed that one of the arginine methylation sites is important for WASp activation.

Keywords: T-cell
immunology
mass spectrometry
T-cells
proteomics
WIPF1
protein methylation
PRMT1
heavy methyl SILAC
T-lymphocyte
T-lymphocytes
SILAC
post-translational modifications
arginine methylation
Dynamin
WASp
PTMs
Advisor: Acuto, O
Optically detected cyclotron resonance of GaAs-based semiconductors

Cyclotron resonance has been measured in GaAs and related compounds through the use of a new experimental technique developed for the study of very pure semiconductors called optically detected cyclotron resonance (ODCR).
ODCR differs from other forms of magnetospectroscopy in that the intensity of luminescence excited by a visible laser is monitored rather than the direct absorption of far-infrared radiation. The ODCR technique is initially used on an exceptionally pure sample of GaAs and resolves impurity transitions and central cell effects. An accurate measure of the electron effective mass including band nonparabolicity is made. The ODCR signal represents an interaction between the donor bound electron states and the donor bound exciton states.
Standard cyclotron resonance measurements on high mobility GaAs/Ga1-
xAlxAs heterojunctions are performed with tilted magnetic fields. Resonant coupling between the Landau levels and electric subbands gives rise to a splitting of the cyclotron resonance lineshape which can be used to determine the subband energy spacings. This allows for a direct determination of the shape of the confinement potential which changes dramatically under different illumination conditions.
A dilution refrigerator is modified in order to measure the cyclotron resonance (CR) to 100 mK of the low density, two dimensional electron system in a heterojunction. Anomalies in the CR spectrum are explained in terms of an interacting electron system composed of carriers in the two spin states of the lowest Landau level. Experimental results are presented in terms of a recent theory offered for cyclotron resonance. A series of undoped GaAs quantum wells is studied with ODCR. The conduction band mass was measured for different well widths. An offset is observed in the cyclotron resonance energy which is strongly dependent on the well width.
ODCR is measured on In0.05Ga0.95As/GaAs superlattices using both the Faraday and Voigt magnetic field orientations. Cyclotron resonance in the Voigt geometry reveals a band structure in the growth direction. The impurity transition in the Voigt configuration shifts dramatically, moving from the bulk 1s-2p + to close to the bulk free electron field.

Advisor: Nicholas, R
Applications of quantum mechanical hypervirial theorems

Two applications of the quantum mechanical hypervirial theorem are discussed. This states that for any system having eigenstates A and B of Hamiltonian H, an operator W has the matrix element relation
(A,(HW andminus; WH) B) = (EA andminus; EB) (A, W B)
providing W is such that H is Hermitean between A and W B.
The first application uses the operator W = eitx to derive a further relationship between certain matrix elements. For one dimensional systems in which the potential V(x) involves only positive powers of x, this relationship becomes a differential equation in
f(t) = (A, eitx B)
This differential equation has been solved analytically for the harmonic oscillator and in series for the quartic oscillator which were taken as example systems.
The second application is the off-diagonal hypervirial method, which seeks to require a wave function A to satisfy a number of hypervirial relations. In particular the wave function A is forced to obey as many conditions as it has variable parameters. To accomplish this a computational algorithm was developed which allowed one of these parameters to be non-linear. The results for oscillator test systems are not encouraging. The systems tested were the quartic and sixth power oscillators with a trial basis of harmonic oscillator eigenfunctions. In general the results were not as good as those obtainable by the variational method.
Uncovering the genetic basis of natural variation of leaf form in Cardamine hirsuta

A major goal in biology is to understand the genetic basis of morphological variation at different evolutionary scales, for example between and within species. Here I investigate this issue by using plant leaves as an example. Previously comparative studies between the simple leaf model plant Arabidopsis thaliana and its dissected leaf relative Cardamine hirsuta have shown that inter-specific differences in leaf shape mostly result from variation in local tissue growth and patterning (Vlad et al., 2014; Hay et al., 2006; Barkoulas et al., 2008). Here, I aim to elucidate the genetic basis of natural variation in leaf form within species, by using divergent strains of C. hirsuta. I present evidence that variation in six strains collected from geographically diverse locations results from different rates of progression of an age-dependent leaf development programme in a phenomenon known as heteroblasty. By using Quantitative trait loci (QTL) mapping with a recombinant inbred line (RIL) population derived from a cross between the Oxford and Azores strains, I detected six QTL that influence leaflet production on multiple leaves. A QTL located on the 4th linkage group was validated and selected for further analysis. Characterisation of QTL effect indicated that the QTL influences leaf form by altering the rate of heteroblastic development. Subsequently I fine mapped this QTL to a DNA segment of 48 kb containing the gene SQUAMOSA PROMOTER PROTEIN BINDING LIKE 9 (ChSPL9), a previously characterised regulator of age dependent development. The parental alleles of ChSPL9 show variation in their sequence and were transformed into A. thaliana to evaluate whether they contribute to the QTL effect. Resultant phenotypes mirrored the QTL effect suggesting that ChSPL9 does indeed contribute to this QTL effect. These results indicate that age-dependent leaf shape progression underlies variation in leaflet number within species and more broadly suggest that in the case of plant leaves different processes might underlie morphological variation between and within species.

Keywords: Cardamine hirsuta
natural variation
QTL
Advisor: Tsiantis, M
Self-assembly and anion recognition with binuclear lanthanide complexes

This work describes an investigation into the solution-phase binding of anionic guests by bimacrocyclic lanthanide complexes. It outlines the preparation of different classes of complexes bearing two metallic domains, and the effects of association on both the complex and the guest. Chapter one provides a cursory introduction to the fundamental properties of the lanthanides with a focus on luminescence. A brief literature review is given on the use of emissive lanthanide probes for the sensing of analytes.
Chapter two concerns the preparation and properties of a series of binuclear complexes in which the two centres are linked with a short spacer group, with the aim of selectively sequestering small anions such as the halides in solution. The concept of luminescence titration will be introduced and then used to assess the binding parameters of a selection of guests.
Chapter three describes a related class of ditopic lanthanide complexes in which the two metal centres are separated by a semi-rigid butyne linking group. Luminescence studies are again used to evaluate the binding constants of homologous series of dianions to ascertain how the size, geometry and functionalization of the anionic guest impacts on binding.
Chapter four explores the coordination of phosphate species and assesses the ability to bind biologically significant phosphates of some of the complexes from Chapter 3.
Chapter five details an investigation into the effects on guest-selectivity of further lengthening the linking unit which separates the two macrocyclic binding domains.
Chapter six summarises the work done throughout the thesis and draws some overarching conclusions, as well as highlighting areas for further study.
Chapter seven describes the experimental procedures.

Keywords: luminescence
self-assembly
macrocycle
lanthanide complex
Advisor: Faulkner, S
Mathematical modelling of geophysical melt drainage

Fluid flows involving transport of a liquid phase in close proximity with its solid phase involve continuous transfer of mass and heat, which can influence the nature of the drainage that occurs. We consider mathematical models for two such situations; magma flow in the mantle and water flow beneath glaciers. In part I, we derive a model for porous flow within a partially molten column of mantle undergoing decompression melting. By ignoring composition effects, and by scaling the equations appropriately, approximate analytical solutions can be found for one-dimensional upwelling, which allow the region and extent of melting to be determined. We study the dynamics of open channels of melt flow in the same situation, and find that such channels would have low pressure compared to the surrounding porous flow, and therefore draw in melt from a region of the size of a compaction length. We suggest that such channels could form through the unstable effects of melting caused by heat transfer by the upwelling melt. We emphasise the similarity with channels of meltwater that are known to exist beneath ice. In part II we pose a generalised model for subglacial water flow, which is described as an effective porous medium, the pore space being determined from an evolution equation. This is used to investigate the flow into a channel, which is found to be drawn from a surrounding region whose size, we suggest, determines the spacing between major drainage channels beneath ice sheets. These are compared to the observed spacing of eskers. A critical condition on the discharge necessary to sustain a channel is found, which may provide a criteria to decide where and when channelised drainage occurs. Lastly, a simple drainage model is used to explain seasonal variations in the velocity of a valley glacier.
The use of novel xenografting methods to reveal differential gene expression between breast cancer at primary and metastatic sites 

In developed countries, breast cancer is the commonest malignancy among women. Understanding the mechanisms involved in breast cancer progression and the influence of the microenvironment on cancer cell proliferation, results in better treatments. This study aimed to optimise breast cancer xenograft rates using a novel chamber developed for tissue engineering purposes. The established tumours were subjected to enzyme digestion, creating a single cell suspension, which was then injected into immunocompromised mice at primary, metastatic and intra-cardiac sites. The resulting tumours in the mammary fat pad (MFP) and bone were compared using species-specific reverse-transcription polymerase chain reaction (RT-PCR) and cDNA microarray, to examine the influence of the microenvironment on gene expression.
The achieved xenograft graft rates of 25% were similar to those previously reported. The matrix metalloproteinase family of enzymes (MMPs) degrade extracellular matrix, influencing invasion and migration of malignant cells. RT-PCR results showed that the majority of the MMPs expressed in the cancers were stromal rather than tumour in origin. MT1-MMP, MMP-2 and MMP-11 had significantly higher expression levels in the MFP than in the bone, but MMP-9 was expressed more in the bone than MFP. There was also an up-regulation of stromal production of MT1-MMP and MMP-13 in the MFP in the presence of tumour. This may have significance when considering which MMPs are the most appropriate targets for inhibition during cancer treatment. The most significant of the differentially expressed genes on microarray analysis were trefoil factor 1 (TFF1) and insulin growth-factor binding protein 3 (IGFBP-3), both expressed significantly more in tumours from the MFP than the bone.
The thesis presented demonstrates some of the complexities of tumour-stromal interactions and supports Paget’s seed-soil theory, confirming in several ways the variation in gene expression in breast cancer between primary and metastatic sites.

Keywords: xenograft
gene array
PCR
Microenvironment
Breast
Cancer
matrix-metallo proteinases
Advisor: Thompson, E
'Unregarded age': texts and contexts for elderly characters in English renaissance drama, c.1480-1625

This study seeks to provide historical and literary contexts for elderly characters from English play-texts c.1580 to 1625. Its primary aim, from a literary perspective, is to draw attention to the ways that a better understanding of elderly characterisation can enrich the appreciation of much-studied play-texts, and to indicate some interesting features of more obscure ones. Its secondary aim is to suggest the value, for social historians of old age in early modern England, of play-texts as social evidence.
I have examined most of the published extant play-texts of the period, and have found approximately 150 of these to be relevant (the most important of these are listed in the Appendix). Because of the problems of handling all aspects of such a large amount of material, I have chosen to consider the plays chiefly as texts to be read, with little reference to their performative aspects. However, I analyse the dramas as literary as well as social documents. Specific plays provide illustrations for observations and support for various hypotheses about dramatic representations of the elderly. In some instances, I address plays which have received little critical attention.
The thesis falls into two parts. In the first three chapters, I discuss the socio-historical, cultural and non-dramatic literary contexts for representations of elderly men and women in play-texts. In chapters four through seven, I examine elderly characters in specific role or relationship categories: as sovereigns and magistrates, in sexual and marital relationships, and as parents. In the final chapter, I offer a detailed analysis of The Old Law by Thomas Middleton and William Rowley.

Keywords: early English drama
the elderly
elderly women
ageing
early modern English history
Advisor: Duncan-Jones, K
Jones, E
Partially-drained loading of shallow foundations on sand

Wave loading on offshore structures founded on sand can result in partially drained response of the foundation soil. The characteristics of the rate of loading, the permeability of the soil, and the size of the foundation affect the degree of partial drainage. Partial drainage refers to situations where pore pressures develop in the soil, and the response of the soil is neither fully drained nor undrained. This thesis is concerned with the effects of loading rate, and consequent drainage, on the behaviour of a flat footing that is founded on the surface of a saturated sand base. The results of physical tests performed in the laboratory on a model-sized footing are reported. The footing was founded on oil-saturated fine sand and was subjected to combined loading. The effect of the vertical, horizontal, and rotational displacements are reported. The response of the footing is analysed in the context of existing drained foundation models that are based on work hardening plasticity theory. The rate dependency of the vertical load:deformation behaviour and the combined yield surfaces are described.

Keywords: offshore
foundation
sand
Advisor: Houlsby, G
The evolution of visual representation

Preface
The corpus of artifacts from the Lagas state constitutes what is arguably the single largest cohesive body of elite representational display forms thus far discovered to have come from Early Dynastic (ED) Sumer. Unlike the equally extraordinary finds from ED levels of Ur, which consist primarily of grave goods and small finds (Woolley 1934; Woolley 1956), what is unique about the finds from Lagas is that the majority of them are programmatic artifacts that were intended to be displayed to specific audiences. Specifically, many of them are relief carvings or, to a lesser degree, statues that were carefully composed and executed in order to encode and transmit carefully constructed messages on the part of individual rulers, or the religious establishment. As such, the ED Lagas corpus is a particularly important record of how one particular group of Sumerian rulers viewed themselves and how the wished to be viewed by others.
[continued in text ...

Advisor: Moorey, P
Large-scale layered systems and synthetic biology: model reduction and decomposition

This thesis is concerned with large-scale systems of Ordinary Differential Equations that model Biomolecular Reaction Networks (BRNs) in Systems and Synthetic Biology. It addresses the strategies of model reduction and decomposition used to overcome the challenges posed by the high dimension and stiffness typical of these models. A number of developments of these strategies are identified, and their implementation on various BRN models is demonstrated.
The goal of model reduction is to construct a simplified ODE system to closely approximate a large-scale system. The error estimation problem seeks to quantify the approximation error; this is an example of the trajectory comparison problem. The first part of this thesis applies semi-definite programming (SDP) and dissipativity theory to this problem, producing a single a priori upper bound on the difference between two models in the presence of parameter uncertainty and for a range of initial conditions, for which exhaustive simulation is impractical.
The second part of this thesis is concerned with the BRN decomposition problem of expressing a network as an interconnection of subnetworks. A novel framework, called layered decomposition, is introduced and compared with established modular techniques. Fundamental properties of layered decompositions are investigated, providing basic criteria for choosing an appropriate layered decomposition. Further aspects of the layering framework are considered: we illustrate the relationship between decomposition and scale separation by constructing singularly perturbed BRN models using layered decomposition; and we reveal the inter-layer signal propagation structure by decomposing the steady state response to parametric perturbations.
Finally, we consider the large-scale SDP problem, where large scale SDP techniques fail to certify a system’s dissipativity. We describe the framework of Structured Storage Functions (SSF), defined where systems admit a cascaded decomposition, and demonstrate a significant resulting speed-up of large-scale dissipativity problems, with applications to the trajectory comparison technique discussed above.

Keywords: Timescale Separation
Layering
Biochemical Reaction Networks
Model decomposition
Model reduction
Dissipativity
Storage Functions
Singular Perturbation
Advisor: Papachristodoulou, A