VictorJuiz/thesis huggingface dataset:
Robust track based alignment of the ATLAS silicon detectors and assessing patron distribution uncertainties in drell-yan processes

The ATLAS Experiment is one of the four large detectors located at the Large Hadron Collider (LHC) at CERN in Geneva, Switzerland. In summer 2008, ATLAS is expected to start collecting data from proton-proton collisions at 14 TeV centre-of-mass energy. In the centre of the detector, the reconstruction of charged particle tracks is performed by silicon and drift tube based sub-detectors. In order to achieve the ATLAS physics goals the resolutions of the measured track parameters should not be degraded by more than 20% due to misalignment. Thus, the relative positions of the silicon detector elements have to be known to an accuracy of about 10 micrometers in the coordinate with the best measurement precision. This requirement can be achieved by track based alignment algorithms combined with measurements from hardware based alignment techniques. A robust track based alignment method based on track residual and overlap residual optimisation has been developed and implemented into the ATLAS offline software framework. The alignment algorithm has been used to align a test beam setup and also part of the final ATLAS detector using cosmic ray muons. Several simulation studies showed that the algorithm will be able to align the full detector with collision data. In addition to detector misalignments, limitations in the knowledge of the proton structure are going to affect physics discoveries at the LHC. Therefore, parton distribution uncertainties in high-mass Drell-Yan processes have been determined. This study includes the analysis of the forward-backward asymmetry. It has been performed on the level of next-to-leading order in both, Monte Carlo simulation using k-factors and parton distribution functions. This analysis is crucial for new physics searches with the ATLAS detector.

Advisor: Weidberg, T
Optically detected magnetic resonance of radical pairs

Current theories of the effects of static and resonant high frequency magnetic fields on radical pair reaction are presented with a view to establishing how they can form the basis of the high time resolution liquid phase magnetic resonance techniques of MARY and RYDMR. Approximate calculations are performed to reveal RYDMR spectral details for the case of an initial triplet radical pair.
The design of unique apparatus to explore the capabilities of the techniques, and routinely collect quantitative data to test theoretical predictions, is described. This includes the development of an ultra-fast waveform scan-digitizing facility which can attain effective sampling rates of up to 20 GHz.
The apparatus is employed to provide the first demonstration of recombination exciplex fluorescence from pyrene - dicyanobenzene radical-ion pairs. It is also applied in the dimensional characterization of micellar and microemulsion media prior to their use in enhancing MARY and RYDMR signal intensities from solubilized radical pairs.
By means of a laser induced radical fluorescence technique and compartmentalized reaction media, first observations are reported of optically detected RYDMR spectra from neutral radical pairs, the existence of very low field MARY spectral structure and the kinetic effect of a resonant microwave field. The MARY structure is attributed to Heisenberg exchange interaction and shown to be sensitive to microreactor volume.
Structural and functional studies of the hedgehog signalling pathway 

Hedgehog (Hh) morphogens play fundamental roles in development whilst dysregulation of Hh signalling leads to disease. Multiple receptors are involved in the modulation of Hh morphogens at the cell surface. Among these, the interactions of Hh ligands with glycosaminoglycan (GAG) (for example heparan or chondroitin sulphate) chains of proteoglycans in the extracellular matrix play a key role in shaping morphogen gradients and fulfil important functions in signal transduction. Several high resolution crystal structures of Sonic Hh (Shh)-GAG complexes have been determined. The interaction determinants, confirmed by binding studies and mutagenesis reveal a novel Hh site for GAG interactions, which appears to be common to all Hh proteins. This novel site is supported by a wealth of published functional data, and resides in a hot spot region previously found to be crucial for Hh receptor binding. Crystal packing analysis combined with analytical ultracentrifugation on Hh-GAG complexes suggest a potential mechanism for GAG-dependent multimerisation.
A key step in the Hh pathway is the transduction of the Hh signal into the receiving cell. The Hh signal transducer, Smoothened, is a key target drug target in the pathway with several modulators in clinical trials, despite an absence of structural data. Smoothened is required to activate all levels of Hh signalling. Recent evidence points to the conserved N-terminal ectodomain (ECD) in regulating Smo activity, from vertebrates to invertebrates. Despite the central importance of the ECD, its precise function remains elusive. A crystal structure of the ECD at 2.2 Å resolution is reported here. Structural analysis and biophysical experiments are discussed with reference to the potential function of this intriguing domain.

Keywords: Hedgehog signalling
developmental biology
macromolecular crystallography
structural biology
smoothened
protein chemistry
structure
smoothened ectodomain
Advisor: Siebold, C
The sequence stratigraphy of the Lower Jurassic of Western Europe

The Lower Jurassic stratigraphy of seven contrasting areas in western Europe is compared in order to seek evidence for a pan-Western European stratigraphic forcing mechanism. Sequencestratigraphic models are discussed and emphasis is placed upon the differing response of sedimentary systems in "accommodation space-dominated" and "supply-dominated" settings.
Spectral gamma-ray data from clastic successions in the Wessex and Cleveland basins (England) are used to elucidate vertical trends. A proximal-distal model for control of Th/K ratios is advanced. Stage-frequency regressive-transgressive cycles in the two areas are shown to be closely correlative.
Sedimentolgical logs and spectral gamma-ray data are presented for the carbonate ramp into turbidite sequence of Peniche (Portugal) and for a new exposure of the Pliensbachian-Toarcian in southern Germany. Systematic variation in clay mineralogy across Europe is suggested.
Cycles in the Lower Jurassic of the North Viking Graben (Norwegian North Sea) are examined using wireline log correlation and the stratigraphic evolution of the Tethyan Rift in the Western and Southern Alps is reviewed. X-ray diffraction studies of the Pliensbachian-Toarcian interval in the Southern Alps are presented in order to elucidate sediment supply to the pelagic realm.
The cycles observed in the English sections appear to be manifest widely across western Europe in a variety of tectonic and sedimentary settings. Sharp basinward facies shifts (candidate sequence boundaries) do not appear to be synchronous between basins.
87SR/86SR analysis of belemnites from the Portuguese and German sections confirms the regional applicability of the results of Jones (1992) and the utility of this technique in long range correlation. Carbon and oxygen analysis of the same material supplements the data of other workers and a direct relationship is suggested between relative sea level and organic carbon burial in the Early Jurassic.

Advisor: Jenkyns, H
Hesselbo, S
Marriage and the position of women, as presented by some of the early Victorian novelists

The subject of this thesis is the unusual nature, in the presentation of courtship and marriage, of Trollope's depiction of women as compared with that of other novelists of the first part of the Victorian age. To demonstrate Trollope's remarkable objectivity and realism, I consider first the treatment by him and by three other male novelists of the period of the motivations towards marriage of women. In the first chapter I sketch out the concept of marriage that actually prevailed and suggest thereby the importance of its achievement for women; and also give a rough idea of the restrictions imposed on the treatment of the subject by the critical consensus of the times. In the next four chapters I illustrate the artificiality, according with these restrictions, with which Dickens, Thackeray and Kingsley deal with the subject of courtship, and contrast with this the sympathetic understanding towards women that Trollope exhibits. I examine in detail in the sixth chapter critical reactions to the works of these writers, in an attempt to show to what extent the distinctions I have made were noted by the Victorians and by more recent critics. In the second part of the thesis I deal with the treatment of relations in marriage itself. Having first considered the singularly few instances in the novelists discussed earlier of the workings of marriage treated on an independent basis, I examine the approach of George Eliot who, along with Trollope, expands upon the subject at length. Arguing that a dogmatic view of the marital relation vitiates her treatment, in the final chapter I explore the contrast offered by Trollope's realistic presentation of the topic.
Liberal-republicanism and politics in Chile

The subject of this thesis is the historical relation between tradition and modernity in Chile in its transition from the XVIIIth century to Independence and its immediate aftermath.
In order to study this relation, the thesis begins by analysing the effects that Bourbon reformism —the first attempt to modernize the state institutionally— had in Chile. Special emphasis is placed on the attitude of the ruling èlite vis-à-vis these reforms (Part I). Subsequently, the thesis centres its attention on the last thirty years of Spanish dominion and the repercussions brought about by the collapse of monarchy. Why a traditional society chose liberal-republicanism as a new legitimating order is the principal question analysed in Part II. The last section —Part III— is concerned with the immediate effects produced by this political option, in particular the emergence of a new consolidated government order and nationalist state during the 1820s. How liberal-republicanism reinforced a predisposition towards political change in addition to preparing the ground for further changes is also dealt with in this last part. Finally, the thesis contains an analysis of the main historiographical interpretations which have been put forward concerning Independence.
Overall, the dissertation attempts to demonstrate that Chilean Independence is part of a process of long duration of an emancipatory nature, starting in the XVIIIth century, and which entails a gradual change towards modernity. The thesis affirms that a conjunctural change such as Independence, involving basically a political-ideological transformation of the traditional legitimating order, was to be of crucial importance for the later evolution of the country towards a broader form of modernization, even if the latter was not always foreseen or necessarily wanted. The thesis, thus, challenges conventional conservative interpretations which view Independence as a merely epiphenomenal or frustrated revolution, while questioning also voluntarist explanations of a liberal sort which tend to exaggerate the omniscience of the process.
Political parties, irredentism and the Foreign Ministry: Greece and Macedonia, 1878-1910

The Macedonian Question has attracted much attention since the 1990s due to the emergence of the dispute over the name of Macedonia between Greece and the Republic of Macedonia. In Greece there is a prolific literature on this subject, but some basic questions remain unanswered. In particular, the role of the government, and of government institutions – especially the Ministry of Foreign Affairs – have attracted little or no attention: on the contrary, historians have focused on the 'heroes' of the conflict, the fighters themselves, the result being that the Macedonian Question is understood as a military fight of good versus evil. In this D.Phil. thesis, we examine how the government got involved with the Macedonian Question and second, in what ways it was involved, especially given that an official acknowledgement of the government's involvement with the paramilitary operations was diplomatically impossible. We approached these questions by examining the personal archives of Greek politicians and diplomats (most notably of the Dragoumis family) and the Archives of the Ministry of Foreign Affairs, especially the Archives of the Greek Embassies in London, Paris and Constantinople, which have only recently become available. The key finding is that the Greek government, despite its declarations to the opposite effect, was involved heavily with the paramilitary fighting in Macedonia, but also that the official involvement with Macedonia was constrained and influenced by electoral concerns and by the powerful Macedonian lobbies in Athens. Decisions were rarely made in a rational, bureaucratic way, but were more often reached after consultations with journalists, military officers and intellectuals and always bearing domestic political realities in mind. These findings suggest that future research should move away from understanding the 'Macedonian Struggle' solely as a military issue, and put it into the wider context of early twentieth-century Greek political and diplomatic history.

Keywords: Greek politics.
Macedonia
Theotokis
Ottoman Empire
Trikoupis
Advisor: Conway, M
Anastasakis, O
The Muratorian fragment and the development of the canon

The traditional consensus that the New Testament Canon was formed by the end of the second century has been weakened by the results of modern studies. The traditional viewpoint now depends primarily upon the evidence of the Muratorian Fragment. Albert C. Sundberg, Jr., in his argument for a revision of the history of the Christian Canon, has called for the redating of the Muratorian Fragment. Through a careful analysis of the Fragment's traditional dating, and of its place within the history of the Canon, this study will confirm Sundberg's theory.
The second century date of the Fragment is ultimately dependent upon the simple Latin phrase, nuperrime temporibus nostris, within a series of references to The Shepherd of Hermas. Sundberg has attempted to broaden the common interpretation of this phrase, but the commonly held interpretation is dubious in itself because of the known poor transcription and the suspected careless translation of the Fragment, and because the other references to The Shepherd are erroneous and late. No other references within the Fragment support a conclusive second century date.
Within the history of the Christian Canon, the Fragment, if traditionally dated, is a serious anomaly in terms of concept, form, and contents. There is nothing to distinguish the Fragment from the fifteen undisputed Catalogues which appear in the fourth and early fifth century, and nothing to suggest that the Fragment is earlier. Indeed, there are numerous elements within the Fragment that are unparalleled in the West or are exceptional until later. The cumulative evidence is too siqnificant to be dismissed because of one, most likely incorrect, association of Hermas with Pius of Rome.
The Muratorian Fragment redated as a fourth century Eastern document, possibly originating from Palestine or western Syria around 375, is a more reasonable conclusion of the evidence available.
Determinants of medium-term blood pressure variability and the related risks of stroke and dementia

Visit-to-visit variability in blood pressure (BP) increases stroke risk, independent of mean BP. However, its physiological validity, the ideal method of measurement and the mechanisms increasing cardiovascular risk are unclear.
In meta-analyses of individual patient data, I pooled associations between BP variability and risk of stroke, all cardiovascular events and death. I then determined antihypertensive drug-class differences in cardiovascular risk, intra-individual (I-VR) and inter-individual BP variability (M-VR). In 500 Oxford Vascular Study (OXVASC) patients undergoing thrice-daily home (HBPM) and awake ambulatory monitoring (ABPM), associations between mean, maximum or variability in BP (CV-BP) were determined with premorbid BP, hypertensive arteriopathy (creatinine, aortic stiffness, cognitive impairment, stroke versus TIA and leukoaraiosis) and cardiovascular events. In 200 patients, I determined associations with pulsatility or stiffness (pulse wave velocity) in cerebral and aortic vessels.
There was a 21% and 27% increased risk of stroke and myocardial infarction per standard deviation of CV-SBP in 318700 patients, independent of mean SBP. In 244,479 patients, SBP variability was reduced by CCBs and diuretics within (I-VR=0.89, 95% CI=0.82-0.96, p=0.0001) and between individuals (M-VR 0.83, 0.77-0.89, p<0.0001), especially in the first year of treatment, explaining drug class differences in stroke risk (OR=0.76, 0.68-0.87, p<0.0001). In OXVASC, drug class differences on day-to-day SBP variability were greatest immediately after waking.
Residual hypertension after treatment on HBPM but not ABPM (BP>135/85) predicted recurrent cardiovascular events (HR 2.82, 1.44-5.51, p=0.002 vs. 1.48, 0.68-3.23, p=0.33), reflecting stronger associations with premorbid BP and hypertensive arteriopathy, due largely to inaccuracy of ABPM in patients aged >65 years. Furthermore, day-to-day maximum and CV-SBP were associated with premorbid BP, hypertensive arteriopathy and cardiovascular events, with no additional predictive value of mean SBP when analysed with maximum SBP. Maximum SBP was greater in men and CV-SBP in women, whilst age and creatinine determined both. Increased stroke risk may partly be due to the association between BP variability and cerebral pulsatility, which was correlated with leukoaraiosis (p=0.01) and determined by aortic stiffness (p=0.016) and pulsatility (p<0.001).
BP variability is clinically significant and physiologically valid, and is treatable with CCBs and diuretics. After TIA or minor stroke, HBPM best identifies residual hypertension and demonstrates the predictive value of BP variability and maximum BP, but associated arterial changes might explain some of the increased stroke risk.

Keywords: Blood Pressure Variability
Meta-analysis
Dementia
Physiology
Hypertension
Stroke
Advisor: Rothwell, P
Clouds and hazes in Saturn's troposphere and stratosphere

The cloud and haze properties in the troposphere and stratosphere of Saturn are investigated in this thesis by analysing Cassini/VIMS spectra at 0.8-3.5 μm and 4.5-5.1 μm. The aerosol properties are derived from VIMS data by using the retrieval tool NEMESIS developed at the University of Oxford. Near-infared VIMS data between 4.5 and 5.1 μm are mainly sensitive to deeper tropospheric levels down to approximately 5 bar. At such pressure levels, thermochemical models predict the formation of condensed clouds made of ammonia and ammonium hydrosulphide ices, although none of these species has been spectrally detected so far. In addition, phosphine and ammonia are responsible for most of the gaseous absorption at these wavelengths. Therefore, the cloud properties and gas distributions can be retrieved from VIMS near-infared spectra. In this thesis, the analysis of limb-darkening data at 4.5-5.1 μm is performed in order to constrain the aerosol properties in Saturn’s atmosphere. The best-fitting model consists of a scattering cloud between 2 and 3 bar, and a scattering haze layer which can be placed anywhere between 10 and 500 mbar. The composition is still poorly constrained for both the deep cloud and haze layer. The haze physical and optical properties can however be independently retrieved from VIMS near-infrared spectra at shorter wavelengths in the 0.8-3.5 μm spectral range. Saturn’s hazes in the troposphere and stratosphere reflect the sunlight at 0.8-3.5 μm. The properties and vertical structure of tropospheric and stratospheric hazes are then investigated from VIMS reflection spectra in the near-infared. The latitudinal variation of haze properties is compared to a thermal feature known as "the temperature knee", corresponding to a local increase of temperature right below the tropopause. The north-south temperature variations in the troposphere are obtained from the analysis of thermal infrared data measured with the Composite InfraRed Spectromete (CIRS) instrument on board Cassini. Finally, VIMS near-infrared data at 0.8-3.5 and 4.5-5.1 μm are combined in order to obtain a cloud and haze model coherent with both wavelength ranges.

Keywords: retrieval theory
saturn
giant planets
climatology
Advisor: Irwin, P
The role of consumer leverage in financial crises

This thesis demonstrates that consumer leverage can contribute to financial crises such as the subprime mortgage crisis characterised by increased bankruptcy prospects and tightened credit access. A recession may follow even when the leveraged sector is not a production sector and can be triggered by seeming positive events such as a technological innovation and a relaxation of borrowing conditions. The first preliminary chapter updates the Bernanke, Gertler and Gilchrist (1999) approach with financial frictions in the production sector to a two-sector model with consumption and housing. It shows that credit frictions in the capital financing decisions of housing firms are not sufficient to capture the negative consumer experience with falling housing prices and relaxed credit access during the recession. The second chapter brings the model closer to the subprime mortgage crisis by shifting credit constraints to the consumer mortgage market. Increased supply of houses lowers asset prices and reduces the value of the real estate collateral used in the mortgage which in turn worsens the leverage of indebted consumers. A relaxation of borrowing conditions turns credit-constrained households into a potential source of disturbances themselves when market optimism allows them to raise their leverage with little downpayment. Both cases demonstrate that although households are not production agents, their worsening debt levels can trigger a lasting financial downturn. The third chapter develops a chained mortgage contracts model where both homeowner consumers and the financial institutions that securitize their mortgage loan are credit-constrained. Adding credit constraints to the financial sector that provides housing mortgages creates opportunities for risk sharing where banks shift some of the downturn onto indebted consumers in order to hasten their own recovery. This consequence is especially evident in the case of relaxed credit access for banks. Financial institutions repair their debt position relatively fast at the expense of consumers whose borrowing ability is squeezed for a long period despite the fact that they may not be the source of the disturbance. The result mirrors the recent subprime mortgage crisis characterised by a sharp but brief decline for banks and a protracted recovery for mortgaged households.

Keywords: Consumer Leverage
Financial Frictions
Chained Loan Contracts
Financial Institutions Leverage
Subprime Mortgage Crisis
Advisor: Vines, D