VictorJuiz/thesis huggingface dataset:
Characterising the cell biology of leukemic stem cells in acute myeloid leukemia.

Acute Myeloid leukemia (AML) is an aggressive haematological malignancy that mainly affects the elderly. Relapse is common and is thought to be due to the presence of chemotherapy resistant leukemic stem cells (LSC). Within the CD34+ disease (>5% of the blast cells expressing CD34) , two subtypes have been identified; an LMPP/GMPlike expanded type and a MPP/CMP-like expanded type, the former is the most common, accounting for around 80% of CD34+ AML. Both the GMP-like and LMPPlike expanded populations show LSC activity. To improve our understanding of the disease and gain better insight in to how to develop treatments, the molecular basis of the disease needs to be investigated. I investigated miRNAs in the GMP/LMPP-like expanded AML. miRNAs are small non-coding RNAs involved in the regulation of mRNA. In recent years miRNAs have been shown to be implicated in many different diseases. To investigate the role miRNAs play in AML, miRNA expression was profiled in leukemic and normal bone marrow. Bioinformatic analysis was then used to examine the different miRNA expression profiles between normal and leukemic marrow. Our study showed that miRNAs are dysregulated in AML. miRNAs from the miR-17-92 and its paralogous cluster miR-106b-92 were amongst the miRNAs to be found down regulated in AML As had been seen previously at an mRNA level, on an miRNA level the LSC populations more closely resembled more mature progenitor populations than HSC and MPP populations, however the LSC populations did display an aberrant stem cell-like miRNA signature.

Keywords: leukemic stem cells
microRNAs
acute myeloid leukemia
Advisor: Vyas, P
The role of the planar cell polarity pathway in branching morphogenesis

The development of organs such as the lung and kidney occurs by branching morphogenesis. Changes in the cytoskeletal architecture, cell-cell adhesion and cell polarity are necessary for the formation of new branches. Interactions and reciprocal signalling between epithelial and mesenchymal cells mediate these organised cell movements that give rise to a complex system of tubes suitable for the transport of gas or fluids. Mutations that disrupt formation of either the correct number, or shape of epithelial branches, affect lung function. This, in turn, can lead to congenital abnormalities such as cystadenomatoid malformations, pulmonary hypertension or lung hypoplasia. Defects in lung architecture are also associated with adult lung disease, particularly in cases of idiopathic lung ﬁbrosis. Identifying the signaling pathways that drive epithelial tube formation will likely shed light on both congenital and adult lung disease. This study shows that mutations in the planar cell polarity (PCP) genes: Celsr1; Vangl2 and Scribble, lead to disrupted lung development and defects in lung architecture. Examination of Vangl2 mutant kidneys reveals similar impairment of branching morphogenesis. Detailed histological and immunocytochemical analysis reveals that lungs from Celsr1Crsh/Crsh, Vangl2Lp/Lp and ScribbleCrc/Crc mice are small and misshapen with fewer branches, and by late gestation exhibit thickened interstitial mesenchyme and defective saccular formation. Moreover, epithelial integrity is disrupted, cytoskeletal remodeling perturbed and mutant endoderm does not branch normally in response to the chemoattractant FGF10. In ex-vivo culture, inhibition of Rho kinase, an important downstream effector of the PCP signaling pathway, can mimic the branching defects observed in these three mouse mutants. Furthermore, all three proteins are present in restricted spatial domains within lung epithelium. ScribbleCrc/Crc lungs, the most severely affected line, exhibit additional defects in components of the tight and adherens junctions; this in turn affects lumen diameter. These findings show that components of the PCP pathway: Celsr1; Vangl2 and Scribble are required for normal foetal lung development, thereby revealing a novel signalling pathway critical for this process. Examination of postnatal mice was not possible as homozygous mutations result in embryonic lethality. However, an assessment of Vangl2Lp/+ mice reveals that loss of a single copy of Vangl2 is enough to cause defects in embryonic lung development that persist into adult life, affecting lung function. Similarly, Vangl2Lp/+ mice show a small but significant reduction in kidney glomeruli.

Keywords: Planar Cell Polarity
Lung Development
Branching Morphogenesis
Advisor: Dean, C
Privilege and policy

The development of educational policies in colonial Ceylon has hitherto been examined from the perspective of either the government or missionary agencies. The role of the indigenous elite in this process has not received the attention it deserves, but merely treated as a peripheral theme. This thesis attempts to redress the imbalance by focusing on the interaction between elite initiatives and the growth of cultural nationalism as key factors in the formulation of educational policy. The many dimensions of the elite's concern with educational policy are explored. The nature of their involvement and their contribution over time are the central themes of the present study. Newspapers, contemporary journals, various school magazines, the writings of the elite themselves and transcripts of debates in the Legislative and State Councils provide an insight into the public and private opinion of the English educated Ceylonese. Chapter one sketches the social background of colonial Ceylon. It describes the plural composition of the population and highlights the importance of language and religion as components of plurality. It also identifies the economic and educational opportunities through which elite status could be acquired. The form and content of education are similarly discussed. Chapter two describes the formulation of government policy and the early contributions of the indigenous leaders. Particular attention is paid to two issues - language and the administration of schools - which emerged as problems crucial to Ceylon's educational structure under colonial rule. Chapter three traces the organizational and individual responses of the upper strata in local society to education as shaped by growing cultural nationalism. The issues of language and religion now assumed a greater degree of political significance. New techniques of opposition, including the establishment of schools and cultural associations on Buddhist, Hindu and Muslim denominational lines, are analyzed in this chapter. In chapter four the repercussions of universal franchise in the educational field are assessed. The increasing political and social aspirations of the masses became the catalyst for action on the part of the leaders, as did the ethnic and caste antagonisms that had surfaced as potentially powerful factors. In chapter five, further political developments that induced the leadership to take a bold step forward - the construction of a free and egalitarian system of education - are examined. How elite competition emerged as a determinant of policy implementation is also discussed. This thesis concludes that while knowledge of English remained the sine qua non for the acquisition and preservation of status, the response of the privileged social group to educational problems in the face of increasing political challenges was to ensure that the availability to the masses of an education, albeit a vernacular education remained secure.
Investigations of suction caissons in dense sand

Offshore structures are used in a variety of applications ranging from the traditional oil and gas extraction facilities to emerging renewable energy concepts. These structures must be secured to the seabed in an efficient and cost effective manner. A novel approach is to use shallow inverted buckets as foundations, installed by suction, in place of the more usual piles. These foundations lead to cost savings through reduction in materials and in time required for installation. It is necessary to determine how these foundations perform under typical offshore loading conditions so that design calculations may be developed. This thesis presents experimental data from a comprehensive series of investigations aimed at determining the important mechanisms to consider in the design of these shallow foundations for dense sand. Initially the long term loading behaviour (e.g. wind and current) was investigated by conducting three degree of freedom loading {V:M/2R:H} tests on a foundation embedded in dry sand. The results were interpreted through existing work-hardening plasticity theories. The analysis of the data has suggested a number of improved modelling features. Cyclic and transient tests, representing wave loading, were carried out on a foundation embedded in an oil saturated sand. The novel feature of the cyclic loading was that a 'pseudo-random' load history (based on the 'NewWave' theory) was used to represent realistic loading paths. Of particular interest was the tensile load capacity of the foundation. The results observed suggested that for tensile loading serviceability requirements rather than capacity may govern design. Under combined-load cyclic conditions the results indicated that conventional plasticity theory would not provide a sufficient description of response. A new theory, termed 'continuous hyperplasticity' was used, reproducing the results with impressive accuracy. Surprisingly, under the conditions investigated, loading rate was found to have a negligible effect on response.

Keywords: sand
offshore
foundation
Advisor: Houlsby, G
'Changing times': war and social transformation in Mid-Western Nepal

This thesis is an ethnographic account of social change, triggered by the civil war in Nepal (1996-2006). Based on an ethnographic fieldwork in the village of Thabang, the war-time capital of the Maoist base area, this thesis explores the transformative impact of the conflict on people’s everyday lives and on the constitution of key hierarchies structuring Nepali society. Rather than focusing on violence and fear – the commonly researched themes in warzones – the thesis examines people’s everyday social and embodied practices during the war and its aftermath, arguing that these remain central to our understanding of war-time social processes and the ways in which they shape the contours of post-conflict society. By focusing on mundane practices – such as meat-eating and alcohol-drinking, raising livestock and worshipping gods – the thesis demonstrates how change at the micro-level is illustrative of a profound transformation in the social structures constituting Nepali society.
Theoretically, the thesis seeks to understand how the situation of war re-orders society: in this case, how people in the Maoist base area interiorized formerly transgressive norms and practices, and how these practices were normalized in the post-conflict environment. The research revealed that much of the change triggered by the conflict came as a result of the ‘exceptional’ times of war and the necessity to follow ‘rules that apply in times of crisis’. Thus, in adopting transgressive practices during the conflict, people were responding to the expediency of war-time rather than following Maoist war-time policies or ‘propaganda’. Furthermore, while adopting hitherto unimaginable practices and making them into habitual action, people transformed the rigid social structures, without necessarily intending to do so. The thesis puts particular stress on the centrality of unintended consequences in social change, the power of embodied practice in making change real, and the ways in which agency and structure are mutually constitutive.

Keywords: embodiment and embodied change
war-time social processes
Maoism
Maoist base area
everyday life during war
Nepal
Bourdieu
agency in conflict
practice theory
post-conflict reconstruction
anthropology of war and conflict
conflict zone
generation and conflict
People's War
revolution
civilians and guerillas
social change
guerilla enclave
youth
civil war
peasants
habitus
post-conflict societies
Advisor: Jo, B
David, G
Authority, states and persons: in the search for optimal reconciliation

The problem of legitimate authority is widely regarded as fundamental to moral and political philosophy. This thesis aims to explain what the problem precisely is, and to offer a practical method for solving it. The starting point is a claim about the phenomenology of the person as an inherently authoritative agent: we are persons, as distinct from mere ‘things’, by virtue of the authority we possess over ourselves. This claim explains, I argue, why there is a problem of legitimate authority – why the exercise of state authority stands in need of justification – and what the problem precisely is: given the inherent tension between the authority of the state on the one hand, and the self-governing authority of persons on the other, the problem of legitimate authority is essentially that of creating the conditions for optimal reconciliation between them.
The bulk of the thesis is devoted to a search for a solution to this problem. The ideal solution lies in developing a concept which I call the Authorization Principle. In its most basic form, the principle states that the exercise of state authority is legitimate only when it is exercised to enforce arrangements that all citizens authorize the state to enforce. The conclusion of the thesis is that the principle should be formulated as follows: The exercise of state authority is legitimate insofar as it is exercised within the provisions of a constitutional arrangement constructed through a process that gives equal weight to all the epistemically undefeated concerns in the society regarding the conditions necessary for persons to exercise personal authority.
The solution proposed in the thesis for the problem of legitimate authority has three important implications. The first is that it is entirely within the capacity of ordinary democratic societies to solve the problem. The second is that there is no single legitimate way to govern a society. Standards for the legitimate use of state authority are in some way indexed to culture, ability and resources as well as to other aspects of a society’s unique circumstances. The third is that a society cannot settle the problem of legitimate authority once and for all. The state’s arrangement will require revision every so often in order to maintain the legitimacy of state authority.

Keywords: authority
respect
legitimacy
Liberalism
Advisor: Swift, A
Aspects of organosulphur chemistry

Section I of this thesis is concerned with the rearrangement of allylic sulphinate esters to sulphones. Isomerisation of cyclohex-2-enyl toluene-p-sulphinate (1) and several related substituted sulphinates was investigated particularly in ionising solvents such as formamide. The substituted systems, 1-[2H]-cyclohex-2-enyl toluene-p- sulphinate and 3-methylcyclohex-2-enyl toluene-p-sulphinate (2), gave sulphones with the label scrambled between C-1 and C-3. Rearrangement of the conformationally biased esters, cis- and trans-5-t-butylcyclohex-2-enyl toluene-p-sulphinate, was not stereospecific. Sulphinate (1), both diastereoisomers of which reacted at the same rate, rearranged more slowly than did sulphinate (2). Rearrangement of sulphinate (1) in the presence of sodium benzenesulphinate lead to formation of some of the phenyl sulphone. A dissociative mechanism involving ion-pairs is proposed for the rearrangement of the above allylic sulphinates in ionising media.
The [1,3] sulphonyl group migration of some allylic sulphones is discussed in Section II. 3-Methyl-3-(p-tolylsulphonyl)- 1-butene rearranged on heating in acetic acidwater (3:2 v/v) containing toluene-p-sulphinic acid or its sodium salt, and in this case slow rearrangement did occur in the absence of such additives. Substituted 3-(p-tolyl-sulphonyl)cyclohexenes rearranged in hot aqueous acetic acid containing sodium toluene-p-sulphonate, but were stable in the absence of added sulphinate. Under these conditions, epimerisation of cis- and trans-5-t-butyl-3-(p-tolylsulphonyl)- cyclohexene occurred at the same rate as deuterium was scrambled between C-1 and C-3 starting with 5-t-butyl-3-[2H]- 3-(p-tolylsulphonyl)cyclohexene. Benzenesulphinate was incorporated in a crossover experiment with 3-(p-tolyl-sulphonyl)cyclohexene. A chain addition - elimination mechanism involving either radicals or radical anions (an SRN1 process) is suggested for the [1,3] rearrangement of the allylic sulphones under the above conditions.
Attempts to develop a stereospecific 5-membered ring annulation procedure involving allylic sulphones are described in Section III. As a model system, 1-(p-tolylsulphonyl)-1-vinylcyclopropane, prepared from 3-(p-tolylsulphonyl)propene, rearranged on flow pyrolysis to 1-(p-tolylsulphonyl)- cyclopentene.

Advisor: Whitham, G
Advancing human pose and gesture recognition

This thesis presents new methods in two closely related areas of computer vision: human pose estimation, and gesture recognition in videos.
In human pose estimation, we show that random forests can be used to estimate human pose in monocular videos. To this end, we propose a co-segmentation algorithm for segmenting humans out of videos, and an evaluator that predicts whether the estimated poses are correct or not. We further extend this pose estimator to new domains (with a transfer learning approach), and enhance its predictions by predicting the joint positions sequentially (rather than independently) in an image, and using temporal information in the videos (rather than predicting the poses from a single frame). Finally, we go beyond random forests, and show that convolutional neural networks can be used to estimate human pose even more accurately and efficiently. We propose two new convolutional neural network architectures, and show how optical flow can be employed in convolutional nets to further improve the predictions.
In gesture recognition, we explore the idea of using weak supervision to learn gestures. We show that we can learn sign language automatically from signed TV broadcasts with subtitles by letting algorithms 'watch' the TV broadcasts and 'match' the signs with the subtitles. We further show that if even a small amount of strong supervision is available (as there is for sign language, in the form of sign language video dictionaries), this strong supervision can be combined with weak supervision to learn even better models.

Keywords: machine learning
deep learning
gesture recognition
computer vision
human pose estimation
Advisor: Zisserman, A
Factors affecting breeding in captive Carnivora

Captive carnivores pose a challenge for conservationists and institutions alike, presenting many problems that range from diseases to poor welfare and unsuccessful breeding. Available databases of captive populations are rich sources of information that can help determine which factors can affect breeding success and the real potential of these populations in conservation programmes. Some species, such as tigers Panthera tigris, seem to preserve in captivity the same reproductive parameters seen in wild animals, making captive individuals extremely useful in the research of reproductive biology, that can be applied in evolutionary and physiological studies of the order Carnivora. Specific reproductive characteristics, mainly connected with the altriciality of the young, can make some species more prone to lose young in captivity than others, and these factors must be taken into consideration when developing ex situ conservation programmes. Infant mortality in captivity seems to be primarily caused by inadequate maternal behaviour, which can be connected to biological factors as well as to individual characteristics such as origin and rearing methods. Maternal infanticide, either passive or active, is also affected by biological and ecological characteristics of the species, and there may be an effect of the origin of the females, i.e. if they were wildcaught or captive-born. Housing conditions and individual history affect infant mortality, with females that suffered transfer between institutions exhibiting lower breeding success. Also, institutions with thriving research programmes presented higher infant mortality overall, independently of their latitude or management system, which can indicate an effect of human interference. Further research, both in the wild and in captivity, is needed to fully understand the factors affecting breeding success of captive carnivores.

Advisor: Dawkins, M
Macdonald, D
Simpson, S
MacDonald, D
A Mixed PDE/Monte Carlo approach as an efficient way to price under high-dimensional systems


We propose to price derivatives modelled by multi-dimensional systems of stochastic differential equations using a mixed PDE/Monte Carlo approach. We derive a stochastic PDE where some of the coefficients are conditional on stochastic ancillary factors. The stochastic PDE is solved with either analytical or finite difference methods, where we simulate all the ancillary processes using Monte Carlo. The multilevel technique has also been introduced to further reduce the variance. The combined method showed over 80% cost reduction for the same accuracy, in pricing a barrier option in an FX market with stochastic interest rate and volatility (which is usually expensive to work with) , when compared to the pure Monte Carlo simulation.
Silicon surfaces

The fundamental atomic and electronic behaviour of clean silicon surfaces has been studied within a simple tight-binding picture of bonding in solids. Of the various contributions to the surface binding energy, the lowering in the promotion energy (i.e. rehybridization) which accompanies localized Jahn-Teller distortions has been identified as a major electronic driving force underlying the stability of silicon surfaces.
The structure of Si(113) has been experimentally determined by the technique of scanning tunnelling microscopy (STM). Despite its high index, the Si(113) surface is found to be highly stable. STM images of both empty and filled states provide strong evidence for a particular structural model with a 3x2 unit cell. The STM results are explained in terms of a general rehybridization principle, suggested by the earlier theoretical study, which accounts for the low surface energy as well as the observed spatial distribution of empty and filled states. In addition, the STM images reveal a high density of domain boundaries which introduce energy states that pin the Fermi level and explain earlier reports of a 3x1 reconstruction for this surface.
Voltage-dependent STM image simulations for the Si(113)3x2 surface have been carried out using a simple tight-binding description of surface electronic structure. Quantitative agreement with experiment is obtained confirming the qualitative rehybridization arguments used previously. The local barrier for tunnelling electrons is shown to have an important effect on the interpretation of STM images.
The high stability of clean Si(l 13) is shown by STM to be disrupted by adsorption of submonolayer amounts of atomic hydrogen which saturates dangling bonds. Mass transport of silicon occurs and structural models are proposed for the resultant mixed 2x2 and 2x3 surface.

Advisor: Sutton, A
Pethica, J