VictorJuiz/thesis huggingface dataset:
Ensemble based quantum memory and adiabatic phase gates in electron spins

Quantum computing has been a new and challenging area of research since the concept was put forward in 1980s. A quantum computer is a computer that processes information encoded in systems that exhibit quantum properties and is proved in theory to be more powerful than classical computers. Various approaches to the implementation of the quantum computers have been studied over the decades, each of them having their own advantages and disadvantages in terms of the lifetime of the quantum information, processing time, and scalability of the implementation. Proposals for hybrid quantum processors are interesting because they benefit from the advantages of each comprising system, and thus providing a promising approach to a practical quantum computer.
In this thesis, I demonstrate experimentally the principle of utilizing electron spin ensembles as a quantum memory for hybrid quantum processors. I demonstrate the storage and on-demand retrieval of multiple bits of quantum information into and from a single electron spin ensemble by applying magnetic field gradient pulses. I then study the coupling between an electron spin ensemble and a three-dimensional microwave cavity, in the aim of discussing the condition for the coherent information transfer between the excitations in solid-state matter and photons. As an alternative to the high power pulses in electron paramagnetic resonance (EPR), I study the possibility of controlling the electron spin states via adiabatic processes. I demonstrate the implementation of adiabatic geometric phase gates in electron spins and compare their performances to other phase gates achieved with microwave pulses in both simulation and experiment, verifying the robustness of the adiabatic gates against certain type of noises. Finally I present the simulation method developed for simulating the pulsed EPR experiments in this thesis, using a model more general than some currently-existing simulation packages.

Keywords: spin dynamics
adiabatic passage
electron paramagnetic resonance
quantum memory
Advisor: Briggs, G
Morton, J
Ardavan, A
Targeting the hypoxic tumour phenotype with T-cell immunotherapy

The hypoxic tumour phenotype is a widespread phenomenon in cancers that correlates with malignant behaviour and poor clinical outcomes. The induced expression of hypoxia-regulated genes through post-translational stabilization of hypoxia-inducible factor (HIF), represent a novel class of over expressed tumour antigens that may bear relevance for specific T cell immunity. To assess whether hypoxia inducible proteins can elicit specific T cell responses in vivo, experiments were carried out using complementary models. Initially, specific T cell responses to a hypoxia-regulated antigen |3 galactosidase (pgal) in a mouse melanoma model were investigated. The responses correlated to hypoxia-induced expression of (3gal in vitro, and resulted in anti-tumour effects in vivo. Next, the utility of human carbonic anhydrase 9 (CA9) as a tumour antigen was explored. In particular, renal cell carcinomas (RCC) which constitutively express CA9 as a result of HIF stabilization through loss of von-Hippel Lindau (VHL) tumour suppressor gene, were targeted. Since the HLA-A2 restricted peptide CA9254 . 2 62 was reported to be immunogenic and endogenously presented in human cells, peptide specific T cell responses were induced in vivo using HLA-A2 transgenic mice, and monitored with novel CA9-specific tetramers. Subsequently, CA9 specific T cell responses in HLA-A2 healthy donors and RCC patients were generated in vitro which recognized exogenous but not endogenously presented peptide as a result of low avidity interactions, or failure of correct processing and presentation by antigen presenting cells.
To assess whether anti-angiogenic therapy can be combined with vaccination strategies, the combination of anti-angiogenic and specific T cell immunotherapy was explored using a novel 'metronomic dosing' regime of cytotoxic agent cyclophosphamide. A synergistic anti-tumour effect in a murine melanoma model was demonstrated, while sparing a population of memory T cells that were subsequently capable of re-expansion.
Finally, a novel iron chelator desferri-exochelin was found to induce HIF and downstream targets, suggesting that specific T cell immunotherapy against hypoxiaregulated targets may be enhanced through chemical means. Additionally, desferriexochelin was anti-angiogenic in vitro, and inhibited tumour cell proliferation through HIF independent pathways.

Advisor: Cerundolo, V
Harris, A
In the hall of mirrors: the Arab Nahda, nationalism, and the question of language

The dissertation examines the foundations of modern Arab national thought in nineteenth-century works of Buṭrus al Busta̅ni̅ (1819-1883) and Aḥmad Fa̅ris al Shidya̅q (1804-1887) in which occurred an intersection of language-making practices and a national pedagogic project. It interrogates the centrality of language for Arab identity formation by deconstructing the metaphor "language is the mirror of the nation," an overarching slogan of the nineteenth century, as well as engaging with twentieth-century discussions of the Arab nation and its Nahḍa. The study seeks to challenge the conventional historiography of Arab thought by proposing a re-theorisation of the Arab Nahḍa as an Enlightenment-Modernity construct that constitutes the problematic of the Arab nation.
The study investigates through literature and literary tropes the makings and interstices of the historical Arab Nation: the topography of its making. It covers a series of primary understudied sources: Busta̅ni̅'s enunciative Nafi̅r Su̅riyya pamphlets that he wrote in the wake of the 1860 civil wars of Mount Lebanon and Damascus: his translation of Robinson Crusoe, dictionary, and encyclopaedia. As well as Shidya̅q’s fictional autobiography, linguistic essays and treatise, and travel writings on Europe. The dissertation engages with these works to show how the 'Nahḍa' is a constituted by inherently contradictory and supplementary projects. It forms a moment of fracture in history and temporality – as does the Enlightenment in Europe – from which emerges a seemingly coherent national narrative.

Keywords: liberalism
language and nationalism
Middle East studies
intellectual history
sectarianism
critical theory
Advisor: Rogan, E
A literary commentary on Jerome, Letters 1, 60, 107

This thesis consists of a commentary on Jerome, Letters 1, 60, and 107, literary pieces which readily lend themselves to a study of aspects of Jerome's art by the narratio method, and bear witness to his position as a Christian writer with roots in the Classical tradition. It is thus essentially a literary commentary, though matters of text, language, history, theology, and Scriptural exegesis are also discussed where they are of special interest or where such discussion helps to illuminate particular passages. The commentary on each letter is prefaced by an introduction setting out the background, considering the letter as a whole, and indicating the main themes and other points of importance. A general introduction briefly dicusses the text and the manuscripts, the readership of the letters, prose-rhythm as a feature of Jerome's style, Jerome's work on the Latin Bible and his citations from it, and his familiarity with and use of Classical literature.
Education and class

This thesis aims to compare the relative chances of occupational success of Chinese in Great Britain and the United States. The study uses data from British national Labour Force Surveys (1983 to 1989) and American Census of Population and Housing Public Use Microdata Samples (1980). Using various methods of statistical analysis, mainly logit modelling, the thesis looks at three aspects of the research question. First, analysis is conducted on the relative level of occupational attainment (in access to the service class and avoidance of unemployment) of Chinese immigrants in Britain through comparisons with whites, Indians, Pakistanis, African Asians, West Indians and Irish. Secondly, similar analysis is done for foreign-born and native-born Chinese in the U.S. through comparisons with whites, Blacks, Hispanics, Japanese, Filipinos, Koreans, Indians and Vietnamese. Thirdly, comparisons are made directly on the relative chances of occupational success for being Chinese in Britain versus being Chinese in the U.S.A.. In the thesis, specific attempts are made to bring out the effects of education in determining occupational success for Chinese as well as other ethnic groups in the two countries.
Pricing exotic options using improved strong convergence.

Today, better numerical approximations are required for multi-dimensional SDEs to improve on the poor performance of the standard Monte Carlo integration. With this aim in mind, the material in the thesis is divided into two main categories, stochastic calculus and mathematical finance. In the former, we introduce a new scheme or discrete time approximation based on an idea of Paul Malliavin where, for some conditions, a better strong convergence order is obtained than the standard Milstein scheme without the expensive simulation of the Lévy Area. We demonstrate when the conditions of the 2−Dimensional problem permit this and give an exact solution for the orthogonal transformation (θ Scheme or Orthogonal Milstein Scheme). Our applications are focused on continuous time diffusion models for the volatility and variance with their discrete time approximations (ARV). Two theorems that measure with confidence the order of strong and weak convergence of schemes without an exact solution or expectation of the system are formally proved and tested with numerical examples. In addition, some methods for simulating the double integrals or Lévy Area in the Milstein approximation are introduced. For mathematical finance, we review evidence of non-constant volatility and consider the implications for option pricing using stochastic volatility models. A general stochastic volatility model that represents most of the stochastic volatility models that are outlined in the literature is proposed. This was necessary in order to both study and understand the option price properties. The analytic closed-form solution for a European/Digital option for both the Square Root Model and the 3/2 Model are given. We present the Multilevel Monte Carlo path simulation method which is a powerful tool for pricing exotic options. An improved/updated version of the ML-MC algorithm using multi-schemes and a non-zero starting level is introduced. To link the contents of the thesis, we present a wide variety of pricing exotic option examples where considerable computational savings are demonstrated using the new θ Scheme and the improved Multischeme Multilevel Monte Carlo method (MSL-MC). The computational cost to achieve an accuracy of O(e) is reduced from O(e−3) to O(e−2) for some applications.
Kenneth Waltz and the limits of explanatory theory in international relations

Kenneth Waltz's seminal work Theory of international politics (1979) conceptualizes international relations as a complex system in which the structure of the system and the interacting units (sovereign states) that comprise it are mutually affecting. Nevertheless, Waltz seeks to develop a nomothetic theory in which the structure of the international political system is isolated as an independent variable, state behaviour being the dependent variable. Waltz's explanatory strategy is therefore characterized by a deep tension: he treats structure as an independent variable whilst also arguing that structure and units are mutually affecting. Consequently, his systemic theory only generates partial explanations: it indicates how structure affects behaviour, but not how structure interacts with other variables to produce specific behavioural outcomes.
This thesis draws on Waltz's theoretical writings, on Waltz's applications of his theory to empirical subjects in international relations (superpower relations during the Cold War, Soviet socialization into international society, and NATO's role after the Cold War), and on a wide range of theoretical literature. It explores the implications of the tension in Waltz's approach for explanatory theory in International Relations. It shows that Waltz's theory cannot ground many of his substantive arguments, that realists who attempt to improve Waltz's theory misunderstand the problems Waltz encounters, and that constructivists are unable to offer causal generalizations about complex systems. It concludes that explanatory theory in International Relations is currently poorly equipped to address complex systems in which structure and units are mutually affecting.

Advisor: Roberts, A
Adaptive control of flexible systems

This thesis reports the successful application of the recently introduced Generalised Predictive Control self-tuner to the high-performance positioning of a real flexible single-link robot arm.
The large amount of experimental time available on this high bandwidth system allowed exhaustive testing of the 'tuning-knobs' and 'design-filters' available to the user for tailoring the closed-loop. Based upon these experiments a coherent philosophy for configuring GPC in practice is generated.
Configuration details found to be necessary for satisfactory GPC control of this high-order neutrally stable and non-minimum-phase plant, with its lightly damped resonant modes, are isolated. In particular it is found that band-pass filtering of data is essential for stable offset-free control using finite-order models of the plant. These aspects are considered in detail both theoretically and experimentally.
In this application, as is often the case in practice, some information about the plant dynamics is available beforehand. Novel methods for the inclusion of this prior knowledge are introduced and their beneficial effects on the convergence of the recursive least squares estimation scheme, upon which most self-tuners are based, are demonstrated in simulation and experiment.
A novel high-speed 68010/20 multi-processor computer system is described which allows the implementation of GPC at the required high sample rate (60Hz). The software division of the self-tuning algorithm into concurrently and sequentially executing tasks is discussed in detail.

Advisor: Clarke, D
Regulation of potassium currents in the sino-atrial node

Regulation of potassium channels by cytosolic calcium and other factors was studied in guinea-pig isolated sino-atrial node cells. Rapidly activating IKR and slowly activating IKS were identified on the basis of biophysical factors (range of activating depolarisations, time of activation, rectification) and selective blockers (E4031 to suppress IKR). The protein channels carrying IKR and IKS were localised to the sarcolemmal membrane using specific antibodies in immunohistochemical experiments. Loading cells with a calcium chelator (BAPTA) caused substantial reduction of IKR and IKS. Both currents were also reduced by the CAMK inhibitor KN- 93. It therefore appeared that cytosolic calcium plays a role in regulating IKR and IKS and that this effect was mediated at least in part through CAMK. AC may also be calcium sensitive, and production of cAMP and PKA activity may therefore be calcium dependent. cAMP appeared to regulate pacemaking; basal AC turnover is though to be high, and elevated cAMP appear to augment IKR via PKA activity. Upon cAMP elevation (via AC stimulation or isoprenaline) IKS augmentation was greater than IKR. Agents that interfered with the function of the sarcoplasmic reticulum (ryanodine and cyclopiazonic acid) also reduced IKR and IKS , but to a lesser extent than BAPTA-loading or KN-93, and these observations indicate that calcium from the SR contributed partially to (was not the sole source) the calcium regulating IKR and IKS . The effects of the cytosolic BAPTA and of the other agents listed above were reinvestigated after stimulation of beta-adrenoceptor pathways with isoprenaline, and it was concluded that increased calcium entry and rises in cytosolic calcium play a significant role in mediating the effects of beta-adrenoceptor stimulation on IKR and IKS. Inhibitors with differential specificity for protein kinase subtypes showed a range of inhibitory effects, reflecting complex interactions between the different protein kinases upon IKR and IKS.

Advisor: Terrar, D
Protein-protein recognition in biological systems exhibiting highly-conserved tertiary structure: cytochrome P450

Protein tertiary structure is more conserved than amino acid sequence, leading to a diverse range of functions observed in the same fold. Despite < 20 % overall sequence identity, cytochromes P450 all have the same fold. Bacterial Class I P450s receive electrons from a highly specific, often unidentified, ferredoxin, in which case the hemoprotein is termed “orphaned”.
CYP199A2, a Class I P450, accepts electrons from ferredoxins Pux and HaPux. Five orientation-dependent and one orientation-independent DEER measurements on paramagnetic HaPux and spin-labelled CYP199A2 yielded vector restraints, which were applied to building a model of the CYP199A2:HaPux complex in silico. A different binding mode was observed compared to P450cam:Pdx and P450scc:Adx, both recently elucidated by X-ray crystallography. This protocol was also applied to the CYP101D1:Arx complex. The first three measurements indicate that this heterodimer does not have a similar orientation to CYP199A2:HaPux, P450cam:Pdx, or P450scc:Adx.
P450cam was fused to putidatredoxin reductase (PdR) to explore the kinetic effects with a view to improving electron transfer to orphan P450s. Heme incorporation of this enzyme depends on linker length. In whole cells, the fusion was more active after longer incubations. In vitro kinetics of the fusion exhibited some co-operativity and enhanced kinetics over the unfused system under steady-state conditions.
The putative iron-sulfur biosynthesis ferredoxin PuxB had been engineered by rational mutagenesis to support catalysis by CYP199A2. It was confirmed this arose from improved protein-protein recognition. Engineering of E. coli ferredoxin based on these findings was carried out, resulting in electron-transfer to CYP199A4 from a novel engineered alien ferredoxin.

Keywords: magnetic resonance
cytochrome P450
kinetics
enzyme engineering
structural biology
Advisor: Wong, L
Consequences of birth asphyxia

To investigate the relationship between birth asphyxia and neurological impairment a cohort of 184 infants with a low (≤3) one-minute Apgar score was studied. All were singletons, apparently normally formed, and born at term (≥37 weeks' gestation) in the John Radcliffe Hospital, between January 1984 and September 1985.
The 181 cohort survivors were traced at the age of five years; 159 were assessed by a paediatrician on a battery of neurodevelopmental tests, and information about a further eight was obtained from other sources.
Three infants in the cohort died neonatally with a diagnosis of birth asphyxia, and three had spastic quadriplegia, profound developmental delay and visual impairment. Examination of the perinatal histories of these six children, including their fetal heart rate patterns in labour and acid-base status at delivery, found convincing evidence of birth asphyxia. Only one other child in the cohort exhibited similar signs of birth asphyxia; he was unimpaired at the age of five.
To assess the impact of birth asphyxia on the overall rate of cerebral palsy, all cases of cerebral palsy born to Oxford residents in the study period were identified. Of 30 cases of cerebral palsy, the three identified in the follow-up study were the only ones whose impairment could be attributed to birth asphyxia in a full-term birth. Birth asphyxia therefore accounted for 10% of all cases of cerebral palsy, a fraction that agrees with previous estimates. The frequency of cerebral palsy due to birth asphyxia was estimated as 1 in 3800 full-term livebirths.
A detailed analysis of the test scores of the 159 children assessed by the paediatrician failed to show any association between their acid-base values at delivery and test scores, or between their fetal heart rate patterns in labour and test scores. These results conform with the view that birth asphyxia has an "all or nothing" effect, and that it presents as a cluster of abnormal neonatal signs, including persistent cerebral depression, severe acidaemia, neonatal encephalopathy, and multiorgan dysfunction.

Advisor: Hope, P
Alberman, E
British Catholic identity during the First World War

This thesis looks at ways in which the British Catholic Church confronted the issue of Catholic unity and authority during the First World War. In a period when it was already attempting to articulate its position in relationship to the establishment and in the context of their Catholicity, the First World War offered the British Catholic Church both added difficulties and increased opportunity to express its position. For Catholics, the claim of universality was not only that they were the Church Universal in the sense that they were a supra-national church but that their Church was complete. Catholics argued that the Church was held together as a body united by and under the authority of Christ, the pontiff of Rome and the traditions maintained and accepted by the Church. These factors made it necessary for Catholics not only to make evident the advantage of their practices but to demonstrate that the fullness of the Church in its sacraments, doctrines and structure was neither in internal religious conflict nor fragmented by political or cultural differences; in short, that it was in itself complete. In the context of a world war in which Catholics were fighting one another and an unresolved political situation in Ireland, maintaining this position was both complicated and yet vital to the Catholic understanding of unity, authority and universality. In this thesis are analysed some of the ways in which the British Catholic Church addressed these challenges of self-definition.

Advisor: Garnett, J
From Abraham to the 'Abrahamic religions' : Louis Massignon and the invention of a religious category

As a neologism for Judaism, Christianity, and Islam, the modern construct 'Abrahamic religions' is as ubiquitous as it is contested in the study of the monotheistic religions. Some have argued against the use of the concept on both historical and theological grounds. In particular, the concept is often interpreted as ecumenically motivated in the thought of Louis Massignon. This understanding arises from a parochial interpretation of its origins, in which Massignon's reflections on the subject over time, as well as its varied uses in recent times, have not been fully considered. This thesis calls for a more extensive historical analysis of its genealogy with the aim of discussing its intellectual and cultural backgrounds. In doing so, it seeks to shed light on how the interrelationships between the three religions had been historically examined prior to Massignon, and how the birth of the concept in his thought and its subsequent uses offer a richer understanding of the concept that goes beyond ecumenical significance.
To this end, this thesis unpacks the concept by probing into its antecedents, examining its birth, and reflecting on its future. The first chapter aims to show the historical basis for considering a genus for the three religions, by surveying perspectives on Abraham in historia sacra, and thereafter, discussing works in the nineteenth and early twentieth centuries that explore the connections between the three religions. The second and third chapters introduce Massignon and discuss his Abrahamic thought from both its socio-religious and intellectual perspectives. The main text examined here is his Les trois prières d'Abraham. The fourth chapter traces the different trajectories of the concept after Massignon and highlights its nuanced meanings as derived from these variegated uses. The fifth and concluding chapters explore the ways in which the concept can profit the study of religion.

Keywords: Louis Massignon
comparative religion
Abrahamic religions
Advisor: Stroumsa, G