VictorJuiz/thesis huggingface dataset:
Linear optics quantum computing with single photons from an atom-cavity system

One of today’s challenges to realise computing based on quantum mechanics is to reliably and scalably encode information in quantum systems. Here, we present a photon source to on-demand deliver photonic quantum bits of information based on a strongly coupled atom-cavity system. The source operates intermittently for periods of up to 100 μs, with a single-photon repetition rate of 1 MHz, and an intra-cavity production efficiency of up to 85%. Our ability to arbitrarily control the photons’ wavepackets and phase profiles, together with long coherence times of 500 ns, allows to store time-bin encoded quantum information within a single photon. To do so, the spatio-temporal envelope of a single photon is sub-divided in d time bins which allows for the delivery of arbitrary qu-d-its. This is done with a fidelity of > 95% for qubits, and 94% for qutrits verified using a newly developed time-resolved quantum-homodyne measurement technique.

Additionally, we combine two separate fields of quantum physics by using our deterministic single-photon source to seed linear optics quantum computing (LOQC) circuits. As a step towards quantum networking, it is shown that this photon source can be combined with quantum gates, namely a chip-integrated beam splitter, a controlled-NOT (CNOT) gate as well as a CNOT4 gate. We use this CNOT4 gate to entangle photons deterministically emitted from our source and observe non-classical correlations between events separated by periods exceeding the travel time across the chip by three orders of magnitude. Additionally, we use time-bin encoded qubits to systematically study the de- and re-phasing of quantum states as well as the the effects of time-varying internal phases in photonic quantum circuits.

Keywords: single photons
cavity QED
linear optics quantum computing
quantum information
atomic physics
Advisor: Kuhn, A
Interpersonal influence and network effects on voting behavior: experimental evidence from Mozambique

During the 2009 Mozambican elections a randomized controlled trial implemented a voter education campaign. My thesis analyses the peer effects triggered by that campaign. The first essay looks at peer effects within the household. The second essay (co-authored with Marcel Fafchamps and Pedro Vicente) focuses on peer effects at the village level. The campaign targeted heads of household or their spouse (i.e., the primary target). In the first essay (Chapter 2) I test the effect of the campaign on other household members. I interpret this effect as evidence of interpersonal influence exerted by the primary target over other household members. The main finding of this analysis is that the transmission of voter education campaign’s effects tends to occur through sharing of opinions and social pressure, instead of information sharing. In this essay I also explore the determinants of interpersonal influence within the household. I test whether the effect of the campaign on other household members (i.e., secondary targets) varies with age, gender and education. I find a stronger effect on younger secondary targets, consistent with the idea that they are more susceptible to social pressure. The second essay (Chapter 3) examines whether the campaign’s effect is transmitted within the village through social networks (kinship and chatting) and geographical proximity. We test whether the impact of the campaign on targeted and untargeted individuals depends on proximity to other targeted individuals in the village. Our main finding is that the campaign increases voter participation on average, but much less so among individuals who are socially or geographically closer to other targeted individuals. This result is interpreted as evidence of free-riding on voting as a civic duty.

Advisor: Fafchamps, M
Alkire, S
Unconscious Christianity: a neglected element in Dietrich Bonhoeffer's late theology

In this thesis I argue that unconscious Christianity (unbewußtes Christentum), referred to by Dietrich Bonhoeffer in several of his later writings, is a significant idea in his late theology. There has as yet been no in-depth study of this theological concept as it appears in Bonhoeffer's work, and I therefore aim with this thesis to begin a new conversation in Bonhoeffer studies on this important topic. Bonhoeffer does not offer a definition of unconscious Christianity, but by analysing the ways in which he uses the term in his writing, I offer a constructed definition of unconscious Christianity as used by Bonhoeffer. The first three chapters of the thesis build towards this definition with a close analysis of each relevant text. By examining unconscious Christianity alongside other theological ideas in Bonhoeffer's prison writing, I show how an awareness and understanding of unconscious Christianity adds depth to readings of Bonhoeffer's late work. This thesis also clarifies the differences between unconscious Christianity and religionless Christianity, and shows how unconscious Christianity fits alongside the other, more widely-studied, concepts present in the later writings, such as the world come of age. This work demonstrates that there is movement within Bonhoeffer's thoughts on unconscious Christianity and points to Bonhoeffer's readiness to allow his personal circumstances to inform his theology. It also shows how unconscious Christianity represents a shift within Bonhoeffer's theology. This thesis also makes the subsidiary point that Bonhoeffer's prison fiction should be considered as theological writing. Through it Bonhoeffer addresses not only unconscious Christianity as discussed in this thesis, but many other issues that reoccur in his theological prison letters. I conclude by showing how an understanding of unconscious Christianity is beneficial not only for Bonhoeffer studies, but for contemporary theology more widely.

Keywords: Dietrich Bonhoeffer
Advisor: Zachhuber, J
Kirkpatrick, M
Mechanisms underlying the endogenous neuroprotection of hamartin in ischaemic stroke

Introduction: Hamartin has been shown to mediate the endogenous resistance of Cornu Ammonis 3 (CA3) neurons to ischaemia. Proposed mechanisms concern the inhibition of mammalian target of rapamycin (mTOR) which could promote productive autophagy and prevent endoplasmic reticulum (ER) stress. A small molecule targeted at these pathways could protect neurons and buy valuable time for recanalization therapy for stroke.
Methods: In vivo, the modified four vessel occlusion model of global cerebral ischaemia was used in male Wistar rats. A temporal and spatial profile for hamartin and mTOR proteins and their downstream mechanisms of autophagy and ER stress was characterised using Western blotting. In vitro, small molecules were assessed in E18 neuronal cultures exposed to oxygen and glucose deprivation (OGD) in an attempt to replicate hamartin’s protective effect.
Results: Time course experiments revealed that global ischaemia selectively induced hamartin expression in the membrane fraction of the hippocampal CA3 region, peaking at 12 hours of reperfusion. Autophagy-associated proteins were differentially expressed in CA1 and CA3 after global ischaemia. Decreased levels of ER stress proteins were observed in CA3 neurons while increased ER stress was found in CA1 neurons after global ischaemia. In vitro, hamartin’s neuroprotective effect appeared to be due to the induction of productive autophagy. The mTOR inhibitor rapamycin did not replicate hamartin’s protective effect. Induction of autophagy with metformin and attenuation of the ER stress response with salubrinal also failed to afford neuroprotection. A novel mTORC1/2 inhibitor, AZD2014, currently in clinical trials for cancer, caused increased neurotoxicity following OGD which was associated with increased ER stress.
Conclusions: The selective dynamic response of hamartin is involved in the endogenous resistance of CA3 neurons to global ischaemia. The temporal association between increased hamartin expression, induction of productive autophagy and decreased ER stress levels in CA3 neurons may contribute to the mechanism of hamartin’s endogenous protective effect. None of the pharmacological agents that targeted downstream mechanisms of hamartin replicated these neuroprotective effects. Further research is needed to fully understand the neuroprotection elicited by hamartin and discover a small molecule that can mimic these effects.

Advisor: Papadakis, M
The spleen in sickle cell anaemia during early childhood

In a study of the natural history of homozygous sickle cell (SS) disease 154 of 160 Jamaican children in whom SS genotype had been diagnosed by cord blood haemoglobin electrophoresis were followed to age 1 to 5 years. Seventeen girls and five boys died. Severe bacterial infections and acute splenic sequestration (ASS) were the principal causes of death. The incidence of each of these complications of SS disease was studied in relation to the natural history of splenomegaly and of splenic reticuloendothelial function.
Splenomegaly was assessed by physical examination at each clinic visit. 37% SS children had had palpable spleens by age 6 months, 66% by age 12 months, 79% by age 24 months and 85% by age 36 months.
Splenic reticuloendothelial function was assessed by estimating the percentage of pitted blood cells (pit count) using differential interference contrast microscopy. Pit counts in 139 control children with normal haeomoglobin genotype AA were always below 9%. Pit counts performed serially in 130 of the SS children (in 46 from birth) rose with age, and were greater than 9% in 23 SS children at age 1 year, 42% at age 2 years and 52% at age 3 years. Radioactive colloid spleen scans showed no splenic uptake of colloid in 11 SS children with palpable spleens and pit counts greater than 9%, confirming impairment of their splenic reticuloendothelial activity.
Abstract continued in thesis
Investigations into the structure, function and pharmacology of TREK K2P potassium channels

TREK channels are polymodal potassium channels which act as integrators of diverse chemical and physical stimuli to dynamically control the cellular membrane potential. How the channels sense different stimuli, and how this is transduced to channel gating is not fully understood. Here I report the results of electrophysiological investigations into the structure-function relationship and pharmacology of TREK channels. Firstly, the mechanism of action of plant derived alkylamides at TREK-1 was found to be complex and assay-context dependent. Subsequent studies of TREK-2, guided by recent X-ray crystal structures, provide novel insights into the mechanisms of gating in mechano-, temperature-, arachidonic acid- and pH-modulation. Studying the effect of these different gating stimuli, and the effects of different gating mutations on the potency of state-dependent inhibitors reveals the existence of multiple, distinct open conformations. The results of these studies are consolidated into a structural model for polymodal gating in TREK channels.

Keywords: ion channels
pharmacology
TREK-2
mechano-sensitivity
TREK-1
polymodal gating
patch clamp electrophysiology
TRAAK
K2P
norfluoxetine
Advisor: Tucker, S
Ashcroft, F
Functional analysis of the fat mass and obesity associated (Fto) gene and protein

Genome wide association studies have shown that common variants in the human fat mass and obesity-associated (FTO) gene predispose to obesity and increased fat mass. Mice globally lacking Fto are lean, while mice globally overexpressing Fto have increased body weight due to increased fat mass. FTO protein was shown to localise to the nucleus and demethylate ssDNA and ssRNA. However, the mechanisms by which FTO mediates its effects on body phenotype remain unknown.
In this thesis, I found that native FTO can be detected in both the nucleus and the cytoplasm during interphase, and that nuclear FTO was exported through the nuclear membrane during early prophase of the mitotic cell division. I developed co-immunoprecipitation (Co-IP) protocol to pull-down native FTO and identified a large number of new candidate binding partners (CBPs). Computational analysis predicted a role for FTO, and many CBPs, in RNA post-transcriptional modification and processing. I confirmed that the E3 ubiquitin-protein ligase TRIM21 interacts with FTO in multiple mouse tissues and binds FTO through its SPRY domain. Importantly, TRIM21 ubiquitinated FTO which did not lead to its degradation. FTO partially co-localised with TRIM21 and the decapping enzyme DCP2 in mRNA processing bodies (p-bodies). Overexpression of TRIM21 led to the accumulation of FTO outside the nucleus, but was reversed when both proteins were overexpressed. Additionally, I created a muscle specific Fto knock-out mouse model and found that lack of FTO in muscle did not result in the body composition phenotype reported in global Fto knock-out mice.
Taken together, FTO can function in both the cytoplasm and the nucleus, where it interacts with TRIM21 which ubiquitinates FTO and potentiates its cytoplasmic localisation. Moreover, function of FTO in muscle does not mediate the obesity phenotype in mice.

Keywords: FTO
nuclear transport
mouse models
protein-protein interactions
gene knock-out
cellular localisation
Advisor: Ashcroft, F
Cox, R
Computational design of biomimetic nanopores: a molecular dynamics study

Molecular dynamics simulations are used to study the function of hydrophobic gates within models of biomimetic nanopores and in ligand-gated ion channels. A computational approach to building and simulating model β-barrel nanopores has been established to explore the effects of changing the shape and polarity of amino acids lining the pore lumen. Changing the position of such residues resulted in different water conductive states. In 14 β-strand pores, a computationally transplanted hydrophobic barrier to water and ions has been demonstrated and characterised in detail using free energy calculations. Electrowetting of such a hydrophobic gate within a model β-barrel nanopore is demonstrated in simulation, using two different methods to apply a transmembrane electric eld. An increase in the transmembrane voltage results in breakdown of the hydrophobic barrier, resulting in the ow of water and ions. The effect (electrowetting) is shown to be reversed upon the removal of the transmembrane voltage. An investigation into the possible hydrophobic gate of the 5-HT3 receptor channel via free energy calculations and simulations con firmed that the crystal structure is in a closed conformation with respect to the ow of ions. This demonstrates that simulations and free energy calculations may be used to functionally annotate crystal structures of ion channels.

Advisor: Sansom, M
Wallace, J
Bayley, H
Unravelling the molecular and cellular mechanisms of fetal B cell lymphopoiesis to help understand childhood leukaemia

Childhood Leukaemia accounts for nearly one in three of all childhood cancers, with approximately 400 cases diagnosed in the UK every year. Initial genetic lesions in paediatric and infant B cell leukaemias occur in utero in fetal haematopoietic progenitors. Despite the importance of understanding fetal B cell lymphopoiesis in relation to the aetiology of leukaemia, fetal B cell development remains poorly characterised. We hypothesised that by understanding and characterising murine fetal B cell lymphopoiesis, we would gain insights into the development of childhood leukaemias. In chapter III of this thesis I show that the first immune restricted cells with B cell potential in the mouse emerge in the E9.5 vascular plexus of the yolk sac. Subsequently, in chapter IV, I use a Mb1-cre fate mapping approach to show that progenitors which are entirely restricted to the B cell lineage can be detected as early as E12.5 in the fetal liver (FL), prior to the cell surface expression of CD19. In chapter V, I investigate B cell progenitors in the E14.5 FL, applying an advanced B cell staging originally developed for the adult bone marrow, modified to include the key lymphoid cytokine receptors IL-7Rα, KIT and FLT3. I identify and functionally and molecularly characterise a rare CD19+ B cell progenitor that expresses FLT3 and peaks in frequency in late gestation embryos. I further show that FLT3+ CD19+ adult Pro B cells demonstrate an increased engraftment when transplanted into recipient mice compared to CD19+FLT3- Pro B cells. Finally in chapter VI, I apply our new understanding of fetal B cell lymphopoiesis to characterise B cell progenitors in a mouse that expresses the TEL-AML1 translocation, an oncogene associated with 25% of paediatric B cell leukaemias. We find that the novel FLT3+ CD19+ ProB cell progenitor identified here is expanded in the fetal liver of E14.5 TEL-AML1 embryos, giving a new developmental insight into the functional impact of this oncogene.

Advisor: Jacobsen, S
Boiers, C
Vanguard capitalism: party, state, and market in the EPRDF's Ethiopia

Since the fall of the Derg regime in 1991, Ethiopia has undergone a remarkable economic transformation. Shunning liberal policy advice yet avoiding the pathologies of patrimonialism, its experience is increasingly presented as an example for others to follow. However, there has been surprisingly little research, and even less consensus, on what actually constitutes this 'Ethiopian model.'
The present thesis provides an answer to this question by focusing on the role of the EPRDF – the former insurgency movement which has governed Ethiopia since 1991 – and the fundamental reconstruction of state and market it has overseen. It argues that the resulting political economy is best characterised as a form of 'vanguard capitalism,' which combines the centralising political logic of a Leninist movement party with the expansive logic of capitalist markets. At its base lies the monopolisation of state-society relations by the EPRDF which, in turn, allows for the creation, centralisation and strategic use of economic rents by its administration. The two processes of illiberal state- and market-building are complementary, and their outcomes mutually reinforcing: a state that seeks to derive legitimacy from 'developmental' interventions in the economy, and an economy that advances a particular vision of the Ethiopian state.
To bear out this argument, the thesis traces the evolving relationship between party, state, and market through four distinct periods in the EPRDF's Ethiopia. While the administrative and economic institutions built during the wartime years were all subsumed into the movement's thrust toward military victory, structural adjustment during the 1990s led to a gradual differentiation between party, state, and market. The propagation of an Ethiopian 'developmental state' in the early 2000s implied a re-centralisation of economic rents, yet without a corresponding degree of control over society the party was left vulnerable. After the electoral near-defeat of 2005 the EPRDF thus reclaimed its ‘vanguard’ role, again fusing party, state, and market into a campaign for economic transformation that it presents as a logical extension of the original struggle for liberation.
The thesis draws on over one hundred stakeholder interviews conducted during ten months of field research in Addis Ababa, Mekelle, and among the Ethiopian diaspora, as well as on extensive archival research.

Advisor: de Oliveira, R
Essays in the economics of higher education

This DPhil thesis consists of three related but independent chapters discussing the question of admission and access to higher education. Chapter 1 explores the extent to which the underrepresentation of students from certain population groups at highly selective universities, can be explained by poor information and high non-monetary application costs, and how the universities' admission policies may affect outcomes. This chapter takes a positive approach and proposes a theoretical model to explore the implications of implementing alternative admission policies. Motivated by the results that arise from this exploration, Chapter 2 proceeds with a normative approach, proposing a general framework to study the optimal selection policy from a pool of applicants, taking into account that the pool of applicants is endogenous. This, it is argued, allows a characterisation of the optimal form of discrimination in university admissions. Chapter 3 studies the relationship between tuition fees and academic selectivity, by developing a different, although somewhat related model of monopolistic competition, where universities compete for students by simultaneously selecting prices and admission standards.

Advisor: Jewitt, I
Royal coinage in Hellenistic Bactria: A die study of coins from Euthydemus I to Antimachus I

The history of Hellenistic Bactria (northern Afghanistan, and areas of Tajikistan and Uzbekistan) is particularly obscure and its reconstruction contentious. Unlike other Hellenistic kingdoms very little evidence survives from literary sources and inscriptions; the best primary source is the large quantity of coins issued under the Graeco-Bactrian kings who ruled the area from the third century to the mid first century BC. With limited details of the find spots of the coins and only a few published hoards, their use has often been limited to a superficial analysis of their iconography.
This thesis presents the results of a die study, an approach to studying the coins that can give many insights into the way they were produced. The coins of six kings (Euthydemus I, Demetrius I, Euthydemus II, Pantaleon, Agathocles, and Antimachus I) are included. Different mints and rhythms of production can be identified, and the overall size of the coinages estimated. Using a thorough understanding of their production this thesis proposes a new, soundly-based, history of the Graeco-Bactrian kingdom under these kings.

Advisor: Smith, B
Bhandare, S
Ideology and war in Bosnia and Herzegovina, 1992-95

This thesis relies on evidence from the International Criminal Tribunal for the former Yugoslavia to argue that systematic ethnic violence occurred during the 1992-95 war in Bosnia and Herzegovina because of the implementation of extreme ideological visions promoted by top political leaders. The first section demonstrates how Serb and Croat nationalist politicians in Serbia, Croatia, and Bosnia determined to create expanded monoethnic states as Yugoslavia collapsed in 1991-92. The second section illustrates how institutions dominated by Serbian President Slobodan Miloševi&cacute; and the Croatian government led by Franjo Tuđman sponsored the military campaigns conducted by Bosnian Serb and Croat forces, which attempted to realise the visions imagined in 1991-92. The final section reveals how in 1994-95, leaders from Croatia and Serbia shifted their short term strategies towards Bosnia for pragmatic reasons, and while the Croatian leadership succeeded in forcing Bosnian Croat nationalists to abate their separatist campaign, Miloševi&cacute;'s efforts to pacify the Bosnian Serb leadership failed and Radovan Karad&zcaron;i&cacute;'s regime continued to pursue its state-building programme until its defeat in summer 1995. Although both Miloševi&cacute; and Tuđman yielded their pre-war ambitions in the face of battlefield outcomes and international pressure, this thesis argues that both leaders regarded the peace agreements they signed as temporary compromises on their long-term ambitions. The words of top political decision-makers reveal the ideas and reasoning that inspired programmes to homogenise multi-ethnic Bosnia and divide it between Serbia and Croatia.

Advisor: Evans, R
Thomspon, M