VictorJuiz/thesis huggingface dataset:
Excitations of Bose-Einstein condensates at finite temperatures

Recent experimental observations of collective excitations of Bose condensed atomic vapours have stimulated interest in the microscopic description of the dynamics of a Bose-Einstein condensate confined in an external potential.
We present a finite temperature field theory for collective excitations of trapped Bose-Einstein condensates and use a finite-temperature linear response formalism, which goes beyond the simple mean-field approximation of the Gross-Pitaevskii equation. The effect of the non-condensed thermal atoms we include using perturbation theory in a quasiparticle basis. This presents a simple scheme to understand the interaction between condensate and non-condensed atoms and enables us to include the effect the condensate has on collision dynamics.
At first we limit our treatment to the case of a spatially homogeneous Bose gas. We include the effect of pair and triplet anomalous averages and thus obtain a gapless theory for the excitations of a weakly interacting system, which we can link to well known results for Landau and Beliaev damping rates. A gapless theory for trapped systems with a static thermal component follows straightforwardly.
We then investigate finite temperature excitations of a condensate in a spherically symmetric harmonic trap. We avoid approximations to the density of states and thus emphasise finite size aspects of the problem. We show that excitations couple strongly to a restricted number of modes, giving rise to resonance structure in their frequency spectra. Where possible we derive energy shifts and lifetimes of excitations. For one particular mode, the breathing mode, the effects of the discreteness of the system are sufficiently pronounced that the simple picture of an energy shift and width fails. Experiments in spherical traps have recently become feasible and should be able to test our detailed quantitative predictions.

Advisor: Burnett, K
A contextual process: Understandings of transitional justice in Rwanda

This thesis examines the practices of international, national, and localised criminal courts in post-genocide Rwanda. It argues that, although the courts are compatible in law, an interpretive cultural analysis shows that they have often competed with one another. The research draws on interviews conducted with judges, lawyers, and a group of witnesses and suspects from the United Nations International Criminal Tribunal for Rwanda (ICTR), the national Rwandan courts, and the gacaca community courts. The courts’ judges and lawyers have interpreted Rwanda’s transitional justice processes very differently. The ICTR has been principally concerned with developing international criminal case law. The national courts purport to have focused on domestic legal reform, while personnel inside gacaca view these local courts as having provided an account of the events and causes of the genocide.
This thesis argues that the different interpretations offered within Rwanda’s post-genocide courts illuminate divergent legal cultures inside the institutions, leading to failures in effective cooperation and evidence gathering. The courts have pursued diverse means to try to establish their legitimate authority. However, among a group of Rwandan citizens, the practices of one court were routinely used as the basis to criticise the actions of the others, raising challenges for the legitimacy of transitional justice in Rwanda. The potential for similar competition between domestic and international justice processes is apparent in the current practice of the International Criminal Court (ICC). However, this competition can be mitigated through more effective communication between different justice systems which respond to the needs of the affected populations, fostering a legal culture of complementarity.

Keywords: Transitional Justice
International Criminal Law
Rwanda
legal culture
Advisor: Lazarus, L
On-the-fly visual category search in web-scale image collections

This thesis tackles the problem of large-scale visual search for categories within large collections of images. Given a textual description of a visual category, such as 'car' or 'person', the objective is to retrieve images containing that category from the corpus quickly and accurately, and without the need for auxiliary meta-data or, crucially and in contrast to previous approaches, expensive pre-training.
The general approach to identifying different visual categories within a dataset is to train classifiers over features extracted from a set of training images. The performance of such classifiers relies heavily on sufficiently discriminative image representations, and many methods have been proposed which involve the aggregating of local appearance features into rich bag-of-words encodings. We begin by conducting a comprehensive evaluation of the latest such encodings, identifying best-of-breed practices for training powerful visual models using these representations. We also contrast these methods with the latest breed of Convolutional Network (ConvNet) based features, thus developing a state-of-the-art architecture for large-scale image classification.
Following this, we explore how a standard classification pipeline can be adapted for use in a real-time setting. One of the major issues, particularly with bag-of-words based methods, is the high dimensionality of the encodings, which causes ranking over large datasets to be prohibitively expensive. We therefore assess different methods for compressing such features, and further propose a novel cascade approach to ranking which both reduces ranking time and improves retrieval performance.
Finally, we explore the problem of training visual models on-the-fly, making use of visual data dynamically collected from the web to train classifiers on demand. On this basis, we develop a novel GPU architecture for on-the-fly visual category search which is capable of retrieving previously unknown categories over unannonated datasets of millions of images in just a few seconds.

Keywords: computer vision
deep learning
object recognition
Advisor: Zisserman, A
Structural studies of the integral membrane component of the twin-arginine transport system, TatC

The twin-arginine protein transport (Tat) system is one of two general protein transport systems in the cytoplasmic membranes of bacteria, and is conserved in the thylakoid membranes of plants. The Tat system transports fully folded proteins of varying sizes across the membrane. This feat is achieved by the use of just three conserved integral membrane proteins, TatA, TatB and TatC. Passenger proteins are designated for transport by the system by the use of an N-terminal extension, termed a signal peptide which contains an invariant twin arginine motif. The TatC component of the transport system is responsible for recognising the signal peptide, as well as binding to TatB and the TatA components. TatC therefore emerges as the functional and organisational ‘core’ of the Tat system. There is a wealth of functional data relating to the TatC protein, but no high resolution structural information on TatC was available to interpret this data. In order to gain an understanding of the Tat system at the molecular level, a structure was required of TatC.
Preliminary expression screening using green fluorescent protein had previously identified the TatC protein from the thermophilic bacterium Aquifex aeolicus as being amenable for structural work. This study purified the A. aeolicus TatC construct in a variety of detergents, used native mass spectrometry and light scattering techniques to assay the sample homogeneity and set up extensive crystallisation trials. Following optimisation of a selenomethionine minimal media growth protocol, crystals grown from selenomethionine-substituted TatC purified in lauryl maltose neopentyl glycol diffracted to 3.5Å resolution, and allowed the structure of TatC to be solved by single wavelength anomalous dispersion.
Analysis of the novel structure of TatC, in combination with an isothermal titration calorimetric binding assay, gave information on how TatC binds to signal peptides. Further structural analysis combined with additional experimental data from collaborators allowed a model to be proposed for how TatC binds to the two additional integral membrane components of the system, TatB and TatA, as part of the transport mechanism. Subsequent work was undertaken in this study to attempt to gain a co-crystal structure of TatC with the signal peptide. Construct and detergent screening was carried out in order to aim towards high resolution structural characterisation of the TatBC complex.

Keywords: twin arginine transport
structural biology
Advisor: Lea, S
Neutron and x-ray scattering studies of strongly correlated electron systems

In this thesis results of x-ray scattering and neutron scattering experiments on several strongly correlated transition metal oxides are presented. The prototypical charge ordered cuprate La1.48Nd0.4Sr0.12CuO4 was investigated using polarised neutron scattering. The results show that several proposed schemes for the magnetic order in this class of materials may be ruled out, however the data are consistent with one-dimensional stripe-like magnetic order. X-ray diffraction was used to show that the charge order is insensitive to an applied magnetic field, but might be affected by the existence of superconductivity. The magnetic excitations were also studied, and at low energies a gap in the magnetic fluctuations was observed and there is tentative evidence that this is related to magnetic anisotropy. The spin state transition in LaCoO3 was investigated using neutron inelastic scattering, and excitations reminiscent of those observed in ferromagnets above their critical temperatures were observed. The debate surrounding the nature of the excited spin state, S=1 or S=2, could not be resolved, however. The nature of the spin excitations in La0.82Sr0.18CoO3 was investigated using polarised neutrons and it was found that at low energies the excitations take the form of spin-waves. At higher energies this mode becomes heavily damped, and several possible damping mechanisms for this are discussed. Finally, the multiferroic material DyMn2O5 was studied using x-ray resonant scattering. A complex, temperature dependent, magnetic structure was found using a Dy resonance, which reflects an underlying order of the Mn ions. The measurements were in agreement with a theory of multiferroics based on acentric spin-density waves.

Keywords: Neutron scattering
x-ray resonant scattering
spin waves
multiferroics
superconductors
Advisor: Boothroyd, A
Exploring school autonomy frontiers in the post-Soviet republics of Central Asia – Kyrgyzstan, Tajikistan and Uzbekistan

This study provides an empirical picture of the ways in which the New Public Management doctrine has been implemented in the context of post-Soviet states in Central Asia. Specifically, the data present evidence on the extent of school autonomy along six dimensions in the three states. The implications of the shift towards education decentralisation have been studied and explained. Based on a mixed method this evidence is drawn from three sources: surveys, interviews, and legislative analysis. With the research limitations in mind, based on the analysis undertaken, it is possible to identify some important messages regarding academic theory and education management practice.
The first message is that neo-institutional theory, particularly historical institutionalism, has been supported by the evidence from the post-Soviet states. Despite quite diverse trajectories of the countries' political, economic and public sectors development over the last two decades, the policies promoted in education appear to be converging in both outputs and outcomes across the region. The three countries demonstrated persistent path-dependency through their inability to overcome institutional inertia, so that operational policy and structure dimensions have not been decentralized, combined with the effect of declining fiscal and bureaucratic capacity at the centre, so that managerial matters have been delegated to a school level. This trend was regional.
The second message is that, the patterns observed in the three post-Soviet states displayed similarities to the patterns observed in education systems of the developed western democracies. Hence, the view that the structure of the post-communist welfare states is problematic, and that the particularities of their transition with budget cuts on top of the communist legacy and a hodge-podge of different approaches do not allow these states to be classified (cf. Orenstein 2008), has not been supported by the evidence. Education institutions in the three post-Soviet countries investigated conformed to a general West European pattern, although for different reasons.

Keywords: New Public Management
school accountability
education decentralization
Advisor: Smith, G
The religion of the landless

In this study, the Babylonian Exile of the Jews is approached from the perspective of a sociological analysis of more recent historical cases of mass deportation and refugee behaviour. After this survey, four behaviour patterns are isolated that function as 'Mechanisms for Survival' for minorities in crisis and under domination in a foreign environment. These 'Mechanisms' include 1) Structural adaptation, 2) The rise of, and conflict between, new leaders. 35 new Folklore patterns, especially 'Hero' stories, and 4) adoption or elaboration of ritual as a means of boundary maintenance and identity preservation.
These four mechanisms are then illustrated from Exilic texts of the Old Testament. The rise of Elders and the changing nature of the Bet Abot is seen as structural adaptation. The conflict of Jeremiah and Hananiah, and the advice of Jeremiah in his 'letter', is seen as the conflict of new leaders in crisis. The 'Diaspora Novella' is compared to Messianic expectation and especially to Suffering Servant to show how folklore can reflect social conditions and serve a function as 'hero stories'. Finally, the latest redactional layers of 'P' reveal concern for purity and separation that expressed itself in social isolationism and boundary maintenance, particularly in the dissolution of marriages with foreign wives. There is also a section on social conflict after the restoration, as a measure of the independent development of exilic social ideology and theology.
The conclusion is that sociological analysis of the Exilic material reveals the exilic-post-exilic community exhibiting features of a minority group under stress, and the creative means by which that group responds by Mechanisms for Survival.
Epigenetic approaches to the study of macrophages in atherosclerosis

Coronary artery disease (CAD) is caused by atherosclerosis, a chronic inflammatory response to modified lipoproteins. A key pathophysiological event is the lipid-induced transformation of macrophages into lipid-laden foam cells and their accumulation in atherosclerotic plaques. Heritable CAD risk is associated with common genetic variants at over 40 genomic loci; the underlying causal mechanisms remain largely unknown and could affect transcriptional regulation in foam cells. Epigenetic and gene expression changes were measured in primary human macrophages before and after exposure to atherogenic, oxidized low-density lipoprotein—with resultant foam cell formation. This unbiased approach involved open chromatin mapping with formaldehyde-assisted isolation of regulatory elements with enhancer and transcription factor mapping using chromatin immuno-precipitation. Foam cell formation was associated with changes in a subset of open chromatin and enhancer sites that were strongly correlated with expression of nearby genes. OxLDL-regulated enhancers were enriched for several transcription factors—including C/EBP-beta— that have no previously documented role in foam cell formation. OxLDL exposure up-regulated C/EBP-beta expression and increased C/EBP-beta binding across the genome, most prominently around genes involved in inflammatory response pathways. Variants at CAD-associated loci were enriched in the subset of oxLDLregulated open chromatin sites. These included rs72664324 in an oxLDL-induced super-enhancer at the PPAP2B locus. OxLDL increased C/EBP-beta binding at rs72664324. C/EBP-beta binding, enhancer activity and oxLDL-induced upregulation of PPAP2B were stronger with the protective A allele of rs72664324. The PPAP2B protein product LPP3 was expressed in foam cells in human atherosclerotic plaques and was upregulated by oxLDL exposure in macrophages, so increasing the degradation of pro-inflammatory mediators. I also found several other CAD risk candidate genes were regulated by oxLDL: Phosphatase and actin regulator 1 (PHACTR1) and macrophage inducible Ca2+ dependent C-type lectin (Mincle). This led us to find a novel expression-quantitative-trait locus for PHACTR1 in macrophages and define new glycolipid ligands for Mincle. Our results demonstrate a genetic mechanism contributing to CAD risk at the PPAP2B locus and highlight the value of integrating gene expression and epigenetic changes to study disease processes involving pathogenic environmental stimuli.

Keywords: atherosclerosis
LPP3
cardiovascular
epigenetics
macrophage
foam cell
PHACTR1
CEBPB
low-density lipoprotein
PLLP3
oxldl
SNP
PPAP2B
genomics
Advisor: O'Callaghan, C
Lunter, G
Essays in dynamic macroeconomics

This thesis is concerned with macroeconomic dynamics under various forms of uncertainty.
Chapter 2 recognizes that the information flow from the interest rate is impeded when the nominal interest rate hits the zero lower bound. This impediment can (a) increase the duration of zero lower bound episodes and (b) bring about more persistent deflationary pressure. Moreover, it can make the exit from the zero lower bound disorderly.
Chapters 3 and 4 are concerned with dynamics of aggregate variables under Knightian Uncertainty. To overcome difficulties with expectations formation under Knightian Uncertainty, the agents follow Interactive Trial and Error Learning (ITEL) (Young, 2009; Pradelski and Young, 2012) to choose investment portfolios. This involves learning by occasionally experimenting with new actions even when the current action proves to be good. Two applications of ITEL are presented. Chapter 3 deals with the growth of aggregate variables.The growth model can match several business cycle features of the US real aggregate wealth data. Chapter 4 considers a portfolio choice problem. The portfolio choice model can match the first two moments of the US real excess return of equity over bonds almost perfectly.
Chapter 5 explores “This Time Is Different Syndrome” of Reinhart and Rogoff (2009) in a setting where the agents are learning under Knightian Uncertainty. The agents are grouped into different generations and their models compete in terms of forecasting power. The predecessor’s model is discarded together with the data set when its forecasting power is worse than the current generation’s model. This loss of relevant data is rooted in focusing only on forecasting well in the short-run. By shifting the weight towards finding the true model of the economy, this problem can be substantially reduced.

Keywords: Macroeconomics
Advisor: Ellison, M
Choice and social segregation in education

The Education Reform Act of 1988 introduced a policy of open enrolment into English secondary education that was designed to enhance the scope for parental choice of schools. In the resulting 'quasi market' for education, state school admissions authorities can no longer deny most expressed parental preferences, and the majority of state educational funding follows pupils to the secondary schools that they attend. Accompanying these policy reforms has been a longstanding concern that the new school attendance patterns resulting from the enhanced choice present within an open enrolment system would further polarize the social compositions of secondary schools in England. This thesis employs recently developed individual-level databases such as the Pupil Level Annual Schools' Census (PLASC), along with GIS mapping software, to investigate the role that choice of non-local schools played in the degree of social segregation in English secondary schools in 2002.
A detailed analysis of the data reveals high rates of non-local school attendance across many areas of England in 2002 as large numbers of pupils from all backgrounds bypassed their local schools in favour of non-local alternatives. Although non-local school choice was exercised by both disadvantaged and more advantaged segments of the schooling population, pupils eligible for free school meals were less likely to attend higher performing non-local schools than their more advantaged counterparts. The disproportionate gains made from non-local school attendance by more advantaged secondary pupils within the marketplace helped to reinforce local school hierarchies already strongly associated with performance and social composition. As the individual level pupil data in PLASC illustrates, the exercise of non-local school choice in 2002 produced school compositions that were more segregated by socio-economic status than they otherwise would be under a system of local school catchments. Thus, rather than helping to diminish the social segregation of secondary pupils resulting from pronounced residential segregation levels, the availability of parental choice instead further stratified most English secondary schools by socio-economic status in 2002.

Advisor: Smith, G
Knowledge and thinking in renaissance Florence: a computer-assisted analysis of the diaries and commonplace books of Giovanni Rucellai and his contemporaries

This thesis investigates cognition and knowledge in a rich selection of late medieval Florentine commonplace books (zibaldoni) and diaries (ricordanze) with a special focus on Giovanni Rucellai’s Zibaldone Quaresimale. In Chapter Two a new methodology, named Mental Model Framework in History (MMFH), is elaborated. By studying mental processes such as categorisation and decision making, MMFH enables us to study cognition in historical documents. The dissertation is based on a computer-assisted analysis described in Chapter Three . This has brought together a number of technologies (Natural Language Processing, Semantic Web, Text Encoding Initiative) and used them according to the interpretative goals of the MMFH. Chapter Four investigates the knowledge-constructing practice of late medieval Florentines, and concludes that commonplace books and diaries were tools of information management and knowledge transmission. The core chapters study four domains of thinking: space, time, agency and perception. Chapter Five analyses social recognition and judgement in Renaissance Florence and reveals how a new ethical thought took shape, one that prepared the transition to capitalism. By applying decision and game theory, Chapter Six examines horizontal friendship, a bond that functioned as an informal but risky social insurance in Florence. Chapter Seven studies how Florentines used superlatives to construct a hierarchy of the world, with Florence on the top. This was the manifestation of a fierce competition within and outside the walls of Florence, competition that strongly influenced the social and physical environment of the city. By studying selection, periodisation and causal reasoning, Chapter Eight pinpoints the gradual secularisation of the conception of time. The thesis concludes that the late medieval revolution in information culture marked by the gradual transition from an overwhelmingly oral culture to an increasingly literate culture produced quantitative and qualitative changes in human thought. This largely contributed to the birth of modern thought, and to the late medieval transformation of the social and physical environment.

Keywords: commonplace book
history of knowledge
digital humanities
cognition
renaissance
Florence
Advisor: Davidson, N