VictorJuiz/thesis huggingface dataset:
Regulation of CRAC channels and agonist-induced Ca2+ signals

Calcium ions (Ca2+) are extremely important intracellular messengers, activating a plethora of cellular processes. Growing evidence now points to a major role for the local Ca2+ signal in driving specific cellular responses. The simplest and most fundamental local Ca2+ signal is the Ca2+ microdomain, which rapidly forms when Ca2+ permeable ion channels open. In non-excitable cells the dominant Ca2+ entry channels are store-operated Ca2+ channels (SOCCs). The best characterised is the Ca2+ release activated Ca2+ (CRAC) channel. How local Ca2+ entry through CRAC channels impacts on channel function however is unclear. I have investigated the interaction between the Ca2+ binding protein calmodulin and CRAC channel activity and subsequent agonist-induced Ca2+ signals. Furthermore, I have investigated a role for mitofusin 2 (a protein that is known to tether the ER and mitochondria) on these Ca2+ signals.
Using three different calmodulin mutant constructs with alterations to their Ca2+ binding sensitivities, I have shown that calmodulin facilitates CRAC channel dependent Ca2+ entry and maintains agonist-induced cytosolic Ca2+ oscillations in a lobe-specific manner. Calmodulin has four Ca2+ binding sites, two on the N-lobe and two on the C-lobe. I found a dominant negative calmodulin mutant (CAM4M, where all four binding sites had been mutated), or one where the C-lobe could not bind Ca2+ (CAM2C), impaired both Ca2+ influx through CRAC channels and maintenance of cytosolic Ca2+ oscillations. In contrast, a Ca2+-insensitive N-lobe mutant had little effect, (CAM2N). Knockdown of the mitochondrial Ca2+ uniporter regulator (MICU1) or mitochondrial membrane depolarization had similar effects to those seen with CAM4M or CAM2C, suggesting that at least in part, the action of calmodulin was through regulation of mitochondrial Ca2+ dynamics. This was confirmed by directly measuring the mitochondrial matrix Ca2+ concentration in intact RBL-1 cells using the mitochondrial targeted, fluorescent protein, pericam. Both CAM4M and disruption of mitochondrial Ca2+ buffering impaired agonist-induced mitochondrial Ca2+ uptake, suggesting that the modulation of CRAC channels occurred through Ca2+-calmodulin facilitation of mitochondrial Ca2+ uptake. Using a mutant Orai1 (A73E) that cannot bind calmodulin, I have shown that calmodulin tethered to the CRAC channel provides a major source of calmodulin for effective mitochondrial Ca2+ uptake. Physiological relevance of my proposed pathway was provided from experiments where I showed knockdown of MICU1 impaired agonist-induced CRAC channel dependent NFAT-1-driven gene expression. In addition, I establish a crucial role for mitochondrial MFN2 and presumably its ability to properly link the mitochondria and ER in the control of CRAC channels and agonist-induced Ca2+ signals.

Keywords: Store-operated Calcium Channels
Calcium ions
Advisor: Parekh, A
The power of modest multilateralism: the International Centre for Settlement of Investment Disputes (ICSID), 1964-1980

In 1965, amid antagonism between capital-importing and capital-exporting states over investment protection, the World Bank created ICSID. ICSID facilitates the resolution of disputes between foreign investors and states. Since major initiatives to create investment rules have failed within the UN and OECD, ICSID is the only successful attempt to create a multilateral, inter-state organization dedicated to investment. This thesis probes the intellectual, political, and economic forces behind the creation and early development of ICSID.
This study combines archival work, oral histories, and interviews with econometric work. On this basis, it illuminates how ICSID's creators-mainly staff in the World Bank's Legal Department-adapted their ideas to suit the charged political context. When disseminating the idea of ICSID to states, they relied on ambiguity, expertise, and incrementalism. These three characteristics constitute an approach to organization building that I term "modest multilateralism" since the World Bank's President praised ICSID as "a modest proposal." By illustrating how this approach operated in ICSID's case, I generate insights that are applicable to other international organizations.
ICSID's creation differs from the expectations of institutionalist IR theory in important ways. First, there was little state leadership, and ICSID's founding Convention is devoid of substance-it merely outlines a procedure. In this way, it takes the idea of ambiguity to its extreme. Second, ICSID's founders took steps to shield the organization from the politics of investment protection: they asked states to send legal experts, not elected representatives, and avoided deliberative debate. Third, ICSID's design was explicitly evolutionary. ICSID can operate alongside changing substantive rules-multilateral, bilateral, or domestic. Finally, contrary to previous accounts, in this thesis the ICSID Secretariat emerges as a dynamic agent. The Secretariat actively pursued ratifications and advance consents to investor-state arbitration. The creation of ICSID fostered a community of practice, which subsequently redefined international investment law through treaty making and arbitral practice.

Keywords: multilateralism
World Bank
investment arbitration
investor-state arbitration
Advisor: FitzGerald, E
Woods, N
An investigation of scaling parameters governing film-cooling

The thesis describes an investigation into the fundamental scaling parameters which govern the process of film-cooling. This method of cooling has wide applicability in the hot portion of gas turbine engines. Well-designed cooling configurations and accurate prediction of heat transfer loads are essential in this extremely hostile environment. However, a great deal of the design data used has been acquired in constant properties experiments which are unrepresentative of engine conditions. At present, there is no consensus on how best to scale this data to the turbine environment.
In particular, the effect of varying the ratio of coolant-to-freestream density has been studied. Experimentally, this variation has been produced, as in the engine, by varying the the injection-tofreestream temperature ratio. For the three geometries tested (a single and double row of 3O holes and a 30 slot), the effect of this parameter was found to be very significant. The widely used mass flux ratio does not take this dependence into account, so that other scaling parameters need to be determined.
For injection rates where the coolant flow remains close to the surface, good scaling is achieved with the momentum flux ratio. All injection rates for the slot and double row occurred in this largely unseparated, "weak" injection regime. However, for the single row, the injection jets penetrated into the freestream at a critical value of the momentum flux ratio. At higher injection rates, in the "strong" injection regime, fluid mechanic scaling was best with velocity ratio.
A simple model is proposed, based on theoretical and experimental considerations, suggesting scaling parameters which successfully collapse all the data in each regime for different injection rates and distances downstream from injection. Alternative scaling parameters based on pressure and temperature measurements are also found to be highly successful.
The effect on heat transfer of the variation of properties through the injection layer at the wall-to-freestream temperature ratios encountered in gas turbines was also found to be significant. This has been quantified.
Experiments were performed using an Isentropic Light Piston Tunnel, a transient facility which enables conditions representative of those in engines to be attained. The results were interpreted using a superposition model, which is shown to be a valuable and concise method of characterising the effects of injection.

Advisor: Jones, T
The EU's inescapable influence on global regionalism

This thesis examines the EU's influence on regional cooperation in the Association of Southeast Asian Nations (ASEAN), Mercosur in South America and the Southern African Development Community (SADC) by drawing on concepts from diffusion studies. It argues that conventional perspectives have tended to view different cases of regionalism as independent phenomena reflecting particular structural, institutional or ideational conditions, mainly internal to the respective region itself. I propose instead to conceive of regional organisations as asymmetrically interdependent, in that the EU as the most successful regional grouping in the international system influences other regional organisations in important respects; yet in ways that are ill-captured by the conventional depiction of external influence as a form of coercion. The central question addressed in this thesis is thus: Under what conditions and in what ways does the EU affect the trajectory of formal rules in regional cooperation elsewhere? I advance three main arguments. First, I suggest that given the EU's ideational and material power in global regionalism, it is likely to act as a focal point in debates about regional rule change around which actors' expectations converge when being confronted with an exogenous cooperation problem. This renders EU influence difficult to escape. Second, I argue that there are two dynamics by which EU influence affects outcomes in global regionalism - the EU as switchman and as driver. While the former leads policy-makers to choose EU-type rules instead of similarly viable alternatives given a particular cooperation problem, the latter affects the very incentives for regional rule change and thereby acts as an independent driver of regional cooperation. Third, I argue that, in terms of outcomes, EU influence has been highest in SADC, lower in Mercosur and lowest in ASEAN, mainly reflecting different degrees of material and ideational interdependence between the EU and other regions. Yet, policy-makers' widespread reluctance to share national sovereignty has sharply delineated the boundaries of EU influence in all three regions. I test these arguments across three central areas of regional cooperation: market building, institution building and community building.

Keywords: institutional design
regional integration
EU as a model
comparative regionalism
diffusion
Advisor: Nicolaidis, K
Neuroprotection of cone photoreceptors in retinitis pigmentosa

Retinitis pigmentosa (RP) is a genetically and phenotypically heterogeneous condition that affects approximately 1 in 4000 individuals worldwide. The most common presentation of RP is a rod-cone dystrophy, where the degeneration of cone photoreceptors occurs secondary to advanced rod loss, leading to a significant decline in central vision and a corresponding reduction in patient quality of life. The mechanisms underlying secondary cone loss are poorly understood, particularly in disorders where the gene defect is unknown or manifest only in rod photoreceptors. Consequently, the thesis presented herein proceeds on several fronts. First, in the long term a greater understanding of the causes underlying cone loss in RP is likely to be beneficial, and so in chapter one a dominant cone degeneration is characterized using intrinsically fluorescent cone photoreceptors to track the degenerative process. Second, as we develop a greater understanding of the genetic etiology underlying RP it is likely that the number of large genes identified as being causative will increase. As currently there is no efficient way to deliver large genes to photoreceptors, chapter two explores the use of alternate viral vectors that might be used to deliver a large therapeutic transgene. Lastly, whilst our understanding of cone loss in RP remains incomplete, it is necessary to develop a broadly applicable therapy to slow or attenuate further cone loss in RP patients regardless of the underlying cause. In chapters three and four we examine the use of low molecular weight "growth factors‟, such as ciliary neurotrophic factor (CNTF), to preserve cone photoreceptors long-term using a rhodopsin knockout model of RP.

Keywords: gene therapy
growth factor
cone photoreceptor
AAV
Advisor: MacLaren, R
Synthesis and characterisation of large area graphene

The pursuit of high quality, large area graphene has been a major research focus of contemporary materials science research, in the wake of the discovery of the multitude of exceptional properties exhibited by the material. The DPhil project was undertaken with the objective of developing an understanding of the growth of large graphene sheets by chemical vapour deposition (CVD), and also in the subsequent characterisation of their material properties.
By conducting atmospheric pressure CVD growth at high methane flow rates, it was found that few-layered graphene (FLG) could be deposited on a copper catalyst. It is demonstrated that the self-limiting property of a copper catalyst is not universal to all deposition conditions, and shown that FLG grows in a terrace-like configuration.
In depth transmission electron microscopy (TEM) studies were carried out on FLG. By selective image reconstruction from the inverse power spectrum of the TEM images, it was possible to elucidate the inter-grain connectivity of few-layer graphenes. It was determined that there were two possible inter-grain configurations possible; specifically an overlap of graphene layers or a discrete atomic bonding edge. The perturbation of the few-layer structure when subject to an out of plane distortion was found to incur a shift in the conventional AB-Bernal stacking of FLG.
By utilising the aberration corrected TEM (AC-TEM) at Oxford it was possible to resolve atomic detail in CVD synthesised monolayer films, including atomic bond rotations and vacancies. The use of a high current density at low accelerating voltage (80 kV) was demonstrated to allow for the controlled defect creation in graphene sheets. This permitted the creation of monovacancies and iron doped vacancy complexes suitable for further study. The behaviour of these two defect types under electron beam irradiation was subsequently studied.

Keywords: aberration corrected transmission electron microscopy
defects
graphene
chemical vapour deposition
transmission electron microscopy
Advisor: Warner, J
Briggs, A
Scanning optical microscopy of semiconductor devices

This thesis explores the interaction of light and semiconductors using a scanning optical microscope. A key advantage to this approach is its non-destructiveness. This is a critical factor in the assurance of semiconductor device reliability. This research investigates novel ways in which the light beam of a scanning optical microscope may be used to detect defects in semiconductors. Attention is focused on the use of the optical beam induced current technique (OBIC). This method permits the imaging of defects in semiconductor devices which may affect the electrical performance of these devices.
For the first time a theory has been developed which forms the basis of an understanding of how excess minority carriers are distributed in a semiconductor when probed with a with a finely focused light beam. This theory is used to predict the resolution of device defects imaged using OBIC. This work is particularly important in that it may incorporate the exact light probe distribution in the semiconductor material which is calculated in this thesis.
A new method to display low contrast OBIC images has been used to highlight defects in semiconductor devices. In addition an exciting novel method to obtain spatial information on the distribution of defects at the silicon/silicon-dioxide interface in metal oxide semiconductor devices has been found. This method can examine many defects which cause serious problems for device manufacturers including the effect of radiation damage on device performance. Other non-destructive techniques which can complement OBIC imaging are explored including photoluminescence and infrared transmission imaging. Additional research is proposed for the future. This research in conjunction with the research in this thesis would allow a comprehensive and powerful examination approach of both static and dynamic conditions of semiconductor devices.

Advisor: Wilson, T
Silicification in biological systems

This thesis is concerned with the formation and structure of silicified deposits in biology. The major system studied is silicified macrohairs from the lemma of the grass Phalaris canariensis L.. The macrohairs consist of silica and polysaccharides. Chemical and structural studies on the mineral phase utilised electron microscopy (transmission (TEM), scanning (SEM) and ultra high resolution (HRTEM)), energy disoersive X-ray analysis (EDXA), solid state nuclear magnetic resonance ( ᷣ⁹ Si nmr), infrared spectroscopy, birefringence and nitrogen adsorption experiments. Results showed that the silica is chemically 'pure', hydrated, amorphous at a resolution of 1OÅ and a variety of structural morphologies were observed which are related to the maturity of the macrohair. Analytical studies at different times after emergence of the inflorescence utilising EDXA and scanning proton microprob eanalysis (SPM) showed that the inorganic elements Si, K, P, S and Cl are spatially organised within the macrohairs during silicification. It is proposed that the macrohairs are silicified under strict cellular control. The organic matrix in the mature macrohairs was investigated by acid hydrolysis and chromatography. The changing emphasis of polysaccharide synthesis in the macrohairs as mineralisation occurs was followed by in vivo radioactive labelling of inflorescences at different stages using ⁱ⁴C glucose and Harabinose. Analysis o fpolysaccharides synthesised involved acid hydrolysis and enzymic digestions (Amylase and Driselase), followed by paper and thin layer chromatography with scintillation counting of the products. Results showed that at the early stages of mineralisation, arabinoxylans and cellulose are the major polymers synthesised but as the macrohair matures, largely non-cellulosic glucans (as yet unidentified) are synthesised. It is proposed that the change in emphasis of polysaccharide synthesis during wall development is related to the size and ultrastructural arrangements of silica particles observed. The organic matrix was also observed to give additional order to the system, the resulting material being totally impervious. A second system, chosen for comparison, is mineralised teeth from the radula of the common limpet Patella vulgata. The mature teeth contain silica, iron oxide (goethite) and an organic matrix. Investigations on the silicified phase utilising electron microscopy revealed morphological structural variations. Analytical studies involving EDXA and SPM analysis showed that there are complex temporal and spatial variations in the inorganic composition (P, S, Ca, Fe, Si, Cu) in all regions of the teeth. It is proposed that these changes can be correlated with changes in composition of the organic matrix. A comparison is made of the silica from the two systems.

Advisor: Williams, R
A historical and contemporary analysis of the Miki/Kōmoto faction of the Liberal Democratic Party of Japan

A large majority of the members of the Liberal Democratic Party of Japan belong to one or other of its factions, the bodies which dominate the party today. In 1987, when the fieldwork for this study was carried out, there were five factions in number. This thesis examines and analyzes the contemporary structural organization and membership of one of them, the Miki/K5moto faction, after presenting a systematic account of its history. This political grouping was investigated from the inside; as an observer, the writer was able to acquire material through direct interaction with members of the faction in their daily routine. Including the introduction and conclusion, eight chapters make up this thesis. Two of them are devoted to the history of the faction, which is chronicled by taking the career of Miki Takeo, the founder, as the central theme. One chapter is concerned with the organization of the faction, and the roles and functions of the members. The relationships among faction members and their connections with outside individuals and groups are the subjects of scrutiny for the fifth and sixth chapters respectively. Chapter seven, on finance, investigates the methods by which the faction as a group and single members of it raise and distribute money. Some of the conclusions drawn in the thesis are specific to the faction; others relate to the wider phenomenon of factionalism inside the party.
Study of early-stage precipitation in Al-Mg-Si(-Cu) alloys by 3D atom probe

Hardness measurements and Three-Dimensional Atom Probe (3DAP) were used to characterize the early stages of precipitation in three different Al-Mg-Si alloys (Al-0.50 wt%Mg-1.00 wt%Si) with different Cu contents (0.03 wt%, 0.15 wt%, or 0.80 wt% Cu). Heat treatments were chosen to simulate an industrial production line for car body-sheet material and included natural ageing (NA), pre-ageing at 80 °C (PA), paint-bake ageing at 180 °C (PB) and 10 second ageing at 180 °C (spike).
The Cu content and the chosen heat treatments were found to influence the microstructural evolution of the alloy considerably. Based on the determined microstructures and matrix solute concentrations, mechanisms for the effect of NA, PA and Cu additions were proposed.
NA had a deleterious effect on the PB hardening response, which was delayed dramatically after 20 minutes NA or longer. When the NA time was 1 minute, β" precipitates were formed within 30 minutes PB resulting in high hardness of the alloy. The delay with NA time was caused by a decrease in the nucleation rate of elongated precipitates during the subsequent PB. This decrease was thought to be due to a combination of a decrease in the matrix solute concentrations and clusters acting as vacancy sinks.
PA before NA improved the PB response due to the formation of a high density of short elongated precipitates. Small Mg-Si clusters were detected after both NA and PA. Clusters formed during PA were found to be, on average, Mg-richer and larger than those formed during NA. Larger clusters were found to be more stable during PB and, upon PB, to grow into nucleation sites for elongated precipitates. Application of a spike before PA resulted in faster growth of clusters during PA.
Growth of clusters and nucleation of short elongated precipitates during PB was found to be enhanced with increasing Cu content when no PA was given. Cu was found to be present in all precipitates and clusters in the alloy with the highest Cu content. These precipitates were thought to be precursors to the Q' phase.

Keywords: 3D atom probe
diffusion
precipitation
Al-Mg-Si alloys
nucleation
Advisor: Smith, GDW
Cerezo, A