VictorJuiz/thesis huggingface dataset:
Molecular genetics of chorea-acanthocytosis

Chorea-acanthocytosis (ChAc) is an autosomal recessive neurological disorder whose characteristic features include hyperkinetic movements and abnormal red blood cell morphology. The disorder shares features with Huntington's disease and McLeod syndrome (MLS), and can sometimes be difficult to distinguish clinically from the latter. In 1997, ChAc was linked to a 6-cM region on chromosome 9q21-22. A novel gene, >em>CHAC
, was identified in the critical region. CHAC (now renamed VPS13A) encodes a large protein called chorein, with a yeast homologue implicated in protein sorting.
In this study, all 73 exons plus flanking intronic sequence in VPS13A were screened for mutations in 83 unrelated ChAc patients. We identified 88 different VPS13A mutations in 72 probands, comprising six deletions of entire exons, 22 nonsense, 36 frameshift, 19 splice-site and five missense mutations. This disorder therefore shows substantial allelic heterogeneity: however, evidence for common inheritance of the EX70_73del mutation in four French Canadian pedigrees indicates a possible founder effect in this population.
Expression of VPS13A appears to be ubiquitous, as determined by tissue-specific analysis of mRNA and chorein distribution. However, chorein expression was markedly reduced or undetectable in lymphoblasts, fibroblasts and erythrocyte membranes from 14 ChAc patients. In contrast, MLS cells showed chorein expression similar to control levels, suggesting that loss of chorein expression is a diagnostic feature of ChAc.
Yeast two-hybrid analysis of six different -600 amino-acid chorein fragments was used to screen a human brain cDNA library for proteins that may interact with chorein. One fragment interacted weakly with constructs derived from transcription factor NF-κB, putative protein phosphatase PP2Cη and TAB2, a protein implicated in the mitogen-activated kinase cascade. Although exogenously expressed chorein and TAB2 did not appear to colocalise, co-immunoprecipitation experiments supported an interaction between the two proteins, suggesting an avenue for future research into chorein function.

Advisor: Monaco, A
Monaco, T
On the construction of invariant tori and integrable Hamiltonians

The main principle of this thesis is to employ the geometric representation of Hamiltonian dynamics: in a broad sense, we study how to construct, in phase space, geometric structures that are related to a dynamical system. More specifically, we study the problem of constructing phase-space tori that are approximate invariant tori of a given Hamiltonian; also, using the constructed tori, we define an integrable Hamiltonian closely approximating the original one. The methods are generally applicable; as examples, we use gravitational potentials that are of interest in stellar dynamics.
First, we construct tori for box and loop orbits in planar, barred potentials, thus demonstrating the applicability of the scheme to potentials that have more than one major orbit family. Also, we show that, in general, the construction scheme needs two types of canonical transformations together: point transformations as well as those expressed by generating functions. To complete the construction scheme, we show how to furnish the tori with consistent coordinate systems, i.e., how to recover the angle variables of a torus labelled by its actions.
Next, the developed methods are employed in creating invariant phase-space tori in nonintegrable potentials supporting minor-orbit families. These tori are used to define an integrable Hamiltonian H0, and a modified form of the standard Hamiltonian perturbation theory is then used to demonstrate that a minor-orbit family can be treated as one made up of orbits trapped by a resonance of H0.
Finally, we generalize the scheme further by constructing tori in time-reversal asymmetric Hamiltonians (by considering the motion in a rotating frame of reference), and study the transition from locally contained stochasticity to global chaos. Using both near-integrable 'laboratory' Hamiltonians and those for which we construct tori, we investigate the transition in the light of the resonance overlap criterion.
Dress pins from Anglo-Saxon England

This thesis examines the development, production and function of dress pins in Anglo- Saxon England. It proposes a dated typology for the mid-5th to the mid-11th century and notes the implications of this for discussions of contact and cultural interaction between England and other parts of Europe.
Chapter 1 defines the parameters of the study, and describes the data that was assembled on Anglo-Saxon pins. An evaluation of the previous work on pins from Northern Europe (Chapter 2) is followed by an investigation in Chapter 3 of the methods and process of typological analysis. After arguing that one of the most important (and neglected) aspects of typological research is 'the process of study' the chapter provides terminological definitions for the components of pins. Chapter 4 examines the problems, principal methods and developments in pin production and discusses how changes in method reflected changes both in fashion and metal working techniques.
Building on this, Chapter 5 defines the groups of pins that have been found on sites of the Anglo-Saxon period, including: (1) definition of the types and sub-types; (2) determination of their date ranges; (3) description of their distribution; and (4) suggestions about the origin of each type. In Chapter 6 the types are put into chronological order, to demonstrate which types existed simultaneously and how pins developed over time. The function of pins is considered in Chapter 7 and several tentative hypotheses are put forward. The final chapter draws a number of conclusions from the study including: (1) Anglo-Saxon pins display a great deal of insularity during all periods, but particularly in the 8th and 9th centuries; (2) while regionalism may have been a feature of 6th century pins, it ceases to be important by the 8th century when many finds from middle Saxon trading sites seem consistently to be the same types, suggesting that in addition to trade between England and the Continent and Scandinavia it is time to evaluate the micro-economic and information exchange networks in Anglo- Saxon England; (3) lastly it notes the problem of dissemination of artefactual analyses and the difficulties to be encountered in using typologies and it puts forward a preliminary proposal for the use of expert systems (computer programs that simulate human performance in specialist task areas) as a tool to distribute this information. An example of a knowledge base that might be used to disseminate the typology presented here, The Anglo-Saxon Pin Identification Assistant, is to be found in Appendix 2, as are several sample identification sessions.
The foreign policy of Anwar Sadat: continuity and change, 1970-1981

This thesis aims to examine both continuity and change in Egyptian foreign policy between 1970 and 1981. The overarching question of this work is: Why and how did President Sadat affect changes in foreign policy? More specifically, the thesis examines the evolution of Egyptian foreign policy in three concentric circles: the Superpowers, the Arab world, and Israel. The broader aim of the thesis is to provide a detailed study of Egyptian foreign policy in this period, which witnessed a multitude of watershed events. The topic is important because Egypt is a leading state in the Arab world, a core actor in the Arab-Israeli conflict, and a strategic ally of the superpowers during the Cold War.
The thesis offers a detailed chronological account of Egyptian foreign policy during the 1970s. It advances a revisionist interpretation of the early Sadat years, arguing that there was much greater continuity with the foreign policy of Gamal Abdel-Nasser than is commonly believed. The account ends in 1981, with the assassination of Anwar Sadat and the succession of Hosni Mubarak. It is argued that Sadat not only managed to reverse Nasser’s radical path in foreign policy, but that he also succeeded in institutionalising his most significant policy changes: peace with Israel and the removal of Egypt from the Arab-Israeli conflict.
The methodology of the thesis is principally empirical and qualitative in nature. The thesis is based on extensive archival research, recently declassified official documents, memoirs of policymakers in English and Arabic, and oral histories in the form of interviews and transcripts of discussions with former Egyptian policymakers.

Keywords: Cold War
International Relations
Arab-Israeli conflict
Middle East
Egypt
Advisor: Shlaim, A
Development of coherent detector technologies for sub-millimetre wave astronomy observations

Superconductor-Insulator-Superconductor (SIS) mixers are now used regularly in sub- millimetre astronomical receivers. They have already achieved sensitivity approaching the quantum limit at frequencies below the superconducting gap of niobium (~680 GHz). Above that, the mixer performance is compromised by losses, unless materials with higher superconducting gap are employed in conjunction with the niobium tunnel junction. In this thesis, we present the development of 700 GHz niobium SIS mixers, employing a unilateral finline taper on a thin Silicon-On-Insulator (SOI) substrate. These mixers are broadband with full on-chip planar circuit integration, and require only a very simple mixer block. They were designed using rigorous 3-D electromagnetic simulator (HFSS), in conjunction with a quantum mixing software package (SuperMix), and have demonstrated good performance with the best noise temperature measured at 143 K. Our mixer devices were fed by multiple flare angle smooth-walled horns, which are easy to fabricated, yet retain the high performance of corrugated horns. The radiation patterns measured from 600–740 GHz have shown good beam circularity, low sidelobe and cross-polarization levels.
In this thesis, we also present SIS mixer designs with balanced and sideband separ- ating capability. These mixers employ back-to-back finline tapers, so that the RF and local oscillator (LO) signals can be injected separately without a beam splitter. We have fabricated and tested the performance of the balanced mixers, and analysed their performance thoroughly. We have also investigated a new method of generating LO signals by beating the tones of two infrared lasers.
Using the current 16-pixel 350 GHz SIS receiver, HARP-B, we have observed the 12CO J=3→2 emission lines from two nearby galaxies. An important result we found is that the 12CO J=3→2 correlates strongly with the 8 μm Polycyclic Aromatic Hydrocarbon emission.

Keywords: superconducting detectors
heterodyne receiver
Superconductor-insulator-superconductor
sub-millimetre astronomy
Advisor: Yassin, G
Becoming a non-immigration country with immigrants: the institutional regime of Japanese immigration policy towards economic migrants

How can one detect and understand change in the face of apparent continuity? This is the question which has been asked by some scholars of institutionalism. One way of answering this is to make analytical room for incremental change as an endogenous source of institutional transformation. Put bluntly, one does not always need spectacular exogenous events, such as wars and revolutions, to explain institutional change.
The present thesis is a qualitative case study of Japan’s immigration policy towards economic migrants since the 1980s. Its aim is to uncover a causal mechanism behind the policy development by drawing on a model of institutional change put forward by James Mahoney, Wolfgang Streeck and Kathleen Thelen. At first, the inquiry may seem ill-founded for Japan is neither an immigration country nor an immigrant-receiving country. Indeed, the country still lacks an immigration policy to speak of, and immigrants continue to be called gaikokujin (foreigners) as opposed to imin (immigrants).
A closer examination of the recent policy development, however, shows that the content and practice of Japanese immigration policy simply belie its self-description. Since 2012 the Japanese government has admitted highly-skilled migrants as potential permanent residents using a points-based system and has incorporated foreigners into the resident register system for Japanese citizens in order to facilitate their integration into Japanese society. The central claim of the present research is that Japanese immigration policy has become increasingly settlement-oriented as an unexpected consequence of earlier policy decisions and that the change has been endogenously effected without dismantling the pre-existing institution of immigration management. In making this claim, I particularly draw attention to the way in which a cumulative effect of minor changes eventually transformed the basic nature of the policy institution.

Keywords: immigration policy
Japan
historical institutionalism
Advisor: David, M
Ian, N
Obesity monitoring in schools

BACKGROUND Population level child measurement is an established international practice. However, there is limited clarity around the protocol and roles of school-based child measurement programmes (CMPs). Furthermore, questions remain about the positive and adverse outcomes associated with CMPs, as well as their longer-term sustainability. This research contributes new information by addressing these key unanswered questions.
METHODS This thesis describes a three-part, mixed methods research project incorporating: a systematic literature review of existing CMPs; an in-depth case study of England’s National Child Measurement Programme; and the development, pilot implementation and evaluation of a CMP in Guernsey. This research was conducted sequentially; individual components informed and guided subsequent work.
RESULTS Routine child measurement is a popular, complex and adaptive practice and offers significant epidemiological value. The principal roles of CMPs are delivery of local prevalence data and assessment of longitudinal trends. However, CMPs are often tasked with additional, diverse and changing roles that do not translate to acknowledged outcomes. Specifically, feedback of individual results represents an unproven programme element. Programme roles can evolve according to political, logistical, or other influences, without consideration of available evidence or wider-reaching implications. There is no evidence of short-term harm from CMPs. Evaluation of the pilot CMP in Guernsey demonstrated that these programmes are perceived to be feasible, acceptable and sustainable.
CONCLUSIONS To maximise the broader utility of CMPs, there should be clarity and consistency around their aims, roles and outcomes. Overall, surveillance reflects the preferred programme type. All CMPs should incorporate a standardised, rigorously applied protocol and routine evaluation. These features are essential to ensure the accuracy and comparability of resultant data, as well as programme credibility. Population level CMPs should not function in isolation; instead, they should be integrated into comprehensive strategies for obesity management. This research has important implications for CMP stakeholders and the wider public health arena.

Keywords: measurement
weight status
monitoring and surveillance
public health
Childhood obesity
Advisor: Foster, C
Paul's use of scripture

The thesis which is argued has two basic elements. First, it is asserted that the methods of using scripture which Paul exhibits in the epistles are largely adaptations of methods found in a wide range of early Jewish sources. Second, it is argued that Paul's method of scriptural interpretation and argumentation is fundamental to the theological development of the discussion in Romans 9-11. In contrast to the types of investigations which focus on specific and in some cases isolated aspects of the use of scripture in the epistles in relation to Jewish literature, a comparative method is employed in this thesis in order to relate the structural, verbal, thematic, and interpretative characteristics of Paul's manner of using biblical quotations to a wide range of Palestinian Jewish sources. With regard to Romans 9-11, the objective is the examination of Paul's method of arriving at a theological statement. Thus, the theological concepts and ideas expressed in chapters 9-11 are viewed in light of the method which Paul has used to construct a response to a troublesome issue in the early church. It is argued that the discourse in these three chapters of Romans has its coherence in the method of scriptural argumentation which Paul has used. Furthermore, it is asserted that the theology reflected in chapters 9-11 is in part the product of scripture's verbal and thematic contribution to the discussion.
Microstructural properties of semiconductor nanostructures

Semiconductor nanostructures have attracted great interest owing to their unique physical properties and potential applications in nanoscale functional devices. The enhancement of the physical properties of semiconductor nanostructures and their performance in devices requires a deeper understanding of their fundamental microstructural properties. Thus this thesis is focused on the experimental and theoretical studies of the microstructural properties of two important semiconductor nanostructures: axial heterostructured silicon nanowires with varying doping and indium nitride colloidal nanoparticles.
In this thesis, axial heterostructured silicon nanowires with varying doping were synthesized on an oxide-removed Si{111} substrate using a vapour-liquid-solid approach. Their fundamental microstructural properties, including the crystalline structure, wire growth direction and morphologies, were studied using various characterization techniques. It is found that a very small fraction of the silicon nanowires crystallize in a hexagonal (wurtzite) phase, which is thermodynamically unstable in bulk silicon under ambient conditions, while a large majority of the synthesized silicon nanowires exhibit the expected diamond cubic crystalline structure. About 75% of the diamond cubic silicon nanowires synthesized grow in a single <111> direction, while the rest contain growth-related kinks, where the nanowire switches to another direction during the growth. The ~109° silicon nanowire kinks are the most commonly observed, and the growth direction before and after such ~109° kink are both <111>. The sidewalls of silicon nanowires do not change abruptly at the ~109° kink, but exhibit an elbow-shaped structure. It is also found that the nanowire sidewalls exhibit periodic nanofaceting, which is strongly doping-dependent. The nanofaceting is found to occur during the enhanced sidewall growth that arises when the diborane dopant gas is introduced. A thermodynamic model predicting the dependence of nanofacet period on the wire diameter is developed.
Another semiconductor nanostructure studied in this thesis is indium nitride colloidal nanoparticles, which were grown using a solution-phase chemical method. The formation of such indium nitride colloidal nanoparticles is confirmed by studying their compositions, crystalline structures and shape using various electron microscopy techniques. The size of the indium nitride colloidal nanoparticles was controlled by varying the time of solution-phase reactions. The most probable size of the colloidal nanoparticles increases and the size distribution broadens with the increase of reaction time. The crystalline structures of the indium nitride colloidal nanoparticles are found to be particle size dependent. The observed dependence of the band gap blueshift of the indium nitride colloidal nanoparticles on the reaction time (hence the particle size) is explained by the quantum-size effect.

Keywords: nanostructures
semiconductors
transmission electron microscopy
Advisor: Cockayne, D
Nellist, P
Pricing Spread Options using Matched Asymptotic Expansions

This document deals with approximating spread options prices using Matched Asymptotic Expansions techniques on the correlation. More precisely, it deals with spreads options on assets that are highly correlated (ρ ∼ 1), which is most commonly observed in Oil Markets (Crude Oil vs. Gasoline for example). We will first start by applying this methodology to exchange options before generalizing our results to spread options. Then we are going to describe an alternative approach of pricing spread options by approximating the bivariate normal distribution. Finally, we will see how we can apply our methodology to the case where we have more than two assets.
The mathematical structure of non-locality and contextuality

Non-locality and contextuality are key features of quantum mechanics that distinguish it from classical physics. We aim to develop a deeper, more structural understanding of these phenomena, underpinned by robust and elegant mathematical theory with a view to providing clarity and new perspectives on conceptual and foundational issues. A general framework for logical non-locality is introduced and used to prove that 'Hardy's paradox' is complete for logical non-locality in all (2,2,l) and (2,k,2) Bell scenarios, a consequence of which is that Bell states are the only entangled two-qubit states that are not logically non-local, and that Hardy non-locality can be witnessed with certainty in a tripartite quantum system. A number of developments of the unified sheaf-theoretic approach to non-locality and contextuality are considered, including the first application of cohomology as a tool for studying the phenomena: we find cohomological witnesses corresponding to many of the classic no-go results, and completely characterise contextuality for large families of Kochen-Specker-like models. A connection with the problem of the existence of perfect matchings in k-uniform hypergraphs is explored, leading to new results on the complexity of deciding contextuality. A refinement of the sheaf-theoretic approach is found that captures partial approximations to locality/non-contextuality and can allow Bell models to be constructed from models of more general kinds which are equivalent in terms of non-locality/contextuality. Progress is made on bringing recent results on the nature of the wavefunction within the scope of the logical and sheaf-theoretic methods. Computational tools are developed for quantifying contextuality and finding generalised Bell inequalities for any measurement scenario which complement the research programme. This also leads to a proof that local ontological models with `negative probabilities' generate the no-signalling polytopes for all Bell scenarios.

Keywords: cohomology
sheaf theory
contextuality
Bell theorem
non-locality
Hardy's paradox
quantum theory
Advisor: Abramsky, S
Coecke, B