VictorJuiz/thesis huggingface dataset:
Human orthologues of Saccharomyces cerevisiae Trf4/5 non-canonical poly(A) polymerases

RNA waste in the budding yeast nucleus is degraded 3’-5’ via exosome-mediated pathways associated with the non-canonical poly(A) polymerases Trf4 and Trf5. Multiple sequence alignments identify POLS and PAPD5 as the human orthologues of Trf4 and Trf5. This research has investigated the degree of conservation and extent of divergence of POLS and PAPD5 from their orthologues. Mass spectrometric analysis identified interacting protein partners of POLS that are mostly nuclear and are associated with an intricate network of cellular processes, spanning/encompassing RNA metabolism including pre-mRNA splicing, DNA damage responses, chromosome biology, nuclear pore transport and structure. The human orthologue of the Trf4/5-associated helicase Mtr4 was identified as a POLS interactor along with DEAD box RNA helicases and zinc finger proteins. Surprisingly in the light of the identities of these interacting proteins, POLS was found to localize mainly to the cytoplasm with a small proportion visible in the nucleus. Co-immunoprecipitation experiments further indicated POLS interactions with CPSF-73 and BRCA1. Human pre-rRNA transcripts that were polyadenylated within the 3’ETS sequence were identified. Non-A residues incorporated within the A-rich tails of the human 3’ETS rRNA and β-actin mRNA were found to be PCR-induced artefacts. Individual down-regulation of POLS or PAPD5 resulted in a slow growth phenotype. A lethal phenotype was detected following the simultaneous down-regulation of both POLS and PAPD5 (DKD). Low concentrations of the anti cancer drug 5-Fluorouracil (5-FU) increased the accumulation of POLS in the nucleolus and 5-FU concentrations >25 µM caused POLS to move from the cytoplasm to the nucleus. DKD increased the sensitivity of U2-OS cells to 5-FU. I conclude that, although some aspects of the functions of Trf4 and Trf5 have been conserved, in human cells POLS has diverged considerably from its yeast counterparts, opening up many further lines of enquiry.

Keywords: Trf5
PAPD5
RNA turnover
Trf4
polyadenylation
rRNA
POLS
Advisor: Norbury, C
Uncommon knowledge

This dissertation collects four papers on common knowledge and one on introspection principles in epistemic game theory. The first two papers offer a sustained argument against the importance of common knowledge and belief in explaining social behavior. Chapters 3 and 4 study the role of common knowledge of tautologies in standard models in epistemic logic and game theory. The first considers the problem as it relates to Robert Aumann’s Agreement Theorem; the second (joint work with Peter Fritz) studies it in models of awareness. The fifth paper corrects a claimed Agreement Theorem of Geanakoplos (1989), and exploits the corrected theorem to provide epistemic conditions for correlated equilibrium and Nash equilibrium.

Keywords: coordination
common knowledge
bounded rationality
introspection
presupposition
awareness
common ground
Aumann
agreement theorem
Advisor: Arntzenius, F
Williamson, T
Non-contacting shaft seals for gas and steam turbines

Improvements upon current gas turbine sealing technology performance are essential for decreasing specific fuel consumption to meet stringent future efficiency targets. The clearances between rotating and static components of a gas turbine, which need to be sealed, vary over a flight cycle. Hence, a seal which can passively maintain an optimum clearance, whilst preventing contact between itself and the rotor, is extremely desirable.
Various configurations of a Rolls Royce (RR) seal concept, the Large Axial Movement Face Seal (LAMFS), use static pressure forces to locate face seals. Prototypes were tested experimentally at the Osney Thermofluids Laboratory, Oxford. Firstly a proof-of concept rig (simulating a 2-D seal cross-section) manufactured by RR was re-commissioned.
The simplest configuration using parallel seal faces induced an unstable seal housing behaviour. The author used this result, CFD, and analytical methods to improve the design and provide a self-centring ability. A fully annular test rig of this new seal concept was then manufactured to simulate a 3D engine representative seal. The full annulus eliminated leakage paths unavoidable in the simpler rig. A parametric program of experiments was designed to identify geometries and conditions which favoured best-practice design. The new seal design is in the process of being patented by Rolls Royce.
A 'fluidic' seal was also investigated, showing very promising results. A test rig was manufactured so that a row of jets could be directed across a leakage cross-flow. An experimental program identified parameters which could achieve a combined lower leakage mass flow rate compared with the original leakage. Influence of jet spanwise spacing, injection angle, jet to mainstream pressure ratio, mainstream pressure difference and channel height were analysed. It is hoped this thesis can be used as a tool to further improve these seal concepts from the parametric trends which were identified experimentally.

Keywords: Seals
Non-contacting
Secondary Air System
Advisor: Gillepsie, D
The spirit of God and the Christian life

My study centres on Karl Barth’s pneumatology with special attention to its inseparable relationship with his vision of the Christian life. Many critics say that Barth’s emphasis upon the gracious God revealed in Christ improperly undermined both the role of the Spirit and the importance of human agency. In contrast, my research will demonstrate that it is possible to read Barth as offering a robust Spirit theology, which resulted in rich reflection upon the Christian life. More specifically, my thesis will first examine Barth’s pneumatology within the context of his incomplete doctrine of redemption. I will show that his unique understanding of redemption was largely shaped by his exegesis of Paul’s Spirit theology, in which he developed central pneumatological motifs, including the Spirit’s incorporation of humanity into the intra-divine fellowship, mediation in the form of pneumatic prayer, and the shaping of moral agency. I will, then, examine these redemptive works of the Spirit within a more comprehensive context of his theology, coordinating synchronic and diachronic approaches. In particular, I will read ‘through’ and ‘across’ Barth, tracing underpinning pneumatological themes, with special focus on the three modes of the Spirit’s work in the opera ad extra – the mediation of divine and human logic in revelation, the drawing of creation into God’s self-glorification movement through beauty, and the calling of individuals through community into God’s drama of salvation. In short, unlike criticisms that Barth reduced pneumatology to the subjective possibility of revelation, my study will show that his pneumatology is mainly about our prayerful participation in God, the constitution of human agency and a new vision of the Christian life under the direction of the Spirit.

Keywords: Pneumatology
prayer
ethics
redemption
Barth
Advisor: Endean, P
Studies towards and total synthesis of pyrrolidinone containing natural products

Chapters 1 and 2 of this thesis focus on the application manganese(III) and copper(II)-mediated oxidative radical cyclisation of alkenyl amidomalonates to the formation of pyrrolidinone-lactones and their subsequent use in the total syntheses of highly bioactive natural products. A novel concise total synthesis of (-)-salinosporamide A based on the oxidative cyclisation previously developed in the group is presented in chapter 1. The second chapter discusses the work towards the pyrrolidinone core of the oxazolomycin. Each chapter contains its own introduction to set in context the presented results, which discusses the isolation and the biological activity of the two families of natural products. Previous synthetic work toward salinosporamide A and the oxazolomycin family achieved in the group and reported in the literature is also described in the introduction of each chapter.
The third chapter of the thesis succinctly presents the extension of the scope of the manganese(III) and copper(II)-mediated oxidative radical cyclisation reaction. The optimisation, development and scope of the rapid access to fused THF-lactones via the cyclisation of alkenyl oxymalonates is described. Preliminary synthetic manipulations of the resultant bicyclic products to study the application possibilities of the new reaction in future complex molecules syntheses are also presented.
The final conclusion gives a summary of the results obtained and introduces the proposed future work that may arise from these three areas.

Keywords: salinosporamide
oxazolomycin
Advisor: Burton, J
Pierre de L'Estoile and his world in the wars of religion, 1546-1611

Pierre de L'Estoile (1546-1611) kept an extraordinary diary and collection in Paris during the Wars of Religion, recording everything from high-political scandals to low-life criminality during this crucial turning point in early modern history. The first extensive study of L'Estoile in any language, this thesis demonstrates how he negotiated and commemorated the conflicts that divided France as he engaged creatively with the rumours, ephemeral prints, poems, pictures, and books that he assembled in his diary and cabinet. It argues that the story of his life and times is the history of the civil wars in the making. While historians and literary scholars depend on L’Estoile’s diaries as an essential source of information, citing him as a mere passive observer, this thesis instead explores his subjectivity and interprets a wide range of hitherto unseen or neglected manuscript evidence that situates him in the Parisian society of royal office-holders and demonstrates his significance in the republic of letters. It follows a microhistorical approach to L'Estoile and his world in order to challenge established interpretations of his sources as evidence of a widespread mentality of eschatological anxiety in sixteenth-century France, instead focusing on L’Estoile’s personal responses to pieces in his collection. In this way, it critiques a common trend in cultural history to roam freely among ‘collective representations’ and argues for the importance of a precise analysis of social context, materiality, and individual subjectivity in reception studies.

Keywords: Wars of Religion
Life-Writing
Paris
Cultural Reception
Collecting
Record Keeping
Diaries
Pierre de L'Estoile
Microhistory
Advisor: Parrott, D
On social facts

Four concepts are considered in relation to the question: can an illuminating characterization of the social sciences be given in terms of one concept of a relatively natural kind of thing? Weber's concept of 'social action' provides neither a general characterization, nor an important partial account, or so I argue after examining its relation to collectivity concepts, to suicide studies, and to standard desiderata for scientific concepts. I next assess the notion of 'meaningful'action. Peter Winch claims that such action is always 'social' in some sense, because it involves rule-following and rules f presuppose' a social setting. I consider the nature of Winch's Wittgensteinian arguments about rules; two senses in which all action might be 'social' emerge; however, were 'social actions' in either sense the focus of a science, it would not therefore aptly be called a social science, the senses of 'social' here being too weak.
I turn next to what I allege is Durkheim's basic notion of a 'social fact' , roughly, that of a way of acting which 'inheres in' and is 'produced by' a social group. I present a highly articulated reconstruction of this notion: a 'collective practice', Pr, of a social group, G, will "be a 'Durkheimian social phenomenon', according to this revised conception, if and only if either Pr or another collective practice of G provides members of G who conform to Pr with a 'basic' reason for so conforming. A central element in my account of collective practices is a notion of 'group common knowledge' derived from David Lewis.
I finally undertake a detailed critique of David Lewis's account of conventions and of the 'co-ordination problems' Lewis claims underlie conventions; I argue for a kind of account different in form from Lewis's, in which conventions are not, and do not necessarily involve, 'regularities' in behaviour.
The Durkheimian notion is judged the best joartial characterization of a social science considered. Its presupposition of the notion of a social group is, I argue, no flaw. I conclude with a general theory of 'socialness', and hence of social science, based on my judgements about the four concepts considered.
Actions of NAADP and other agents in cardiac myocytes

Modulation of cardiac rate and contraction through calcium-dependent and independent means are of central import to the ability of an organism to adapt to its environment.
Nicotinic acid adenine dinucleotide phosphate (NAADP) is a potent calcium-releasing second messenger across a broad range of tissues and organisms. In cardiac myocytes, NAADP is thought to stimulate calcium release from acidic stores which then bolsters filling and release during CICR. Questions remain: as to the potential need for amplification to generate the size of responses observed and the physiological role of the NAADP pathway.
In contractile myocytes, photorelease of NAADP caused significant increase in calcium transient amplitude and velocity of transient upstroke and decay. Effects were absent during NAADP photorelease in the presence of Ned-19 or CaMKII inhibitors. Cellular calcium transient responses to β-adrenergic stimulation were significantly reduced in the presence of inhibitors of the NAADP pathway.
These data support the hypothesis that NAADP-induced calcium release is relevant during adrenergic stimulation and requires amplification through CaMKII.
Rate modulation at the sino-atrial node can occur through the hyperpolarisation-activated current I(f). Basal cardiac rate is a major determinant in cardiac mortality and compounds which specifically affect rate have clinical utility.
A compound currently used to treat inflammatory conditions was found to have a significant rate-reducing effect in sino-atrial node preparations mediated by inhibition of I(f).
Apelin, an endogenous peptide, has been reported to potently generate improved contractility without development of hypertrophy. Study of its effects in single cells have provided conflicting information, at least in part because of the difficulty in working with the compound.
A method for the consistent observation of apelin-mediated contractile responses is presented, focusing on the timecourse of cell contraction. These observations suggest a role for apelin in both inotropy and lusitropy and will enable further research.

Keywords: electrophysiology
cardiac
funny current
calcium
contractility
apelin
NAADP
Advisor: Terrar, D
Kohl, P
Small steps, large outcome: a historical institutional analysis of Malaysia's political economy

The research attempts to explain the character of Malaysia’s political economy. By adopting a historical institutional analysis it explains that British colonial administration persistently made rational choices within a short-term horizon that encouraged the growth of two autonomous groups – Malays and Chinese - whose political, economic and social organisation, at the point of Malaya’s independence in 1957, had made it inevitable for them to embark on some form of consociational arrangement. British policies engendered two processes; first, a less-than-full incorporation of Chinese as new actors in Malaya’s political economy and second, a less-than-full retrenchment of Malay political dominance by preserving Malay de jure power. In sum, British decision to preserve Malay de jure power while at the same time incorporate Chinese economic and political presence created two communities with mutually exclusive institutions that increasingly competed for access to political and economic resources. The self-reinforcing nature of these exclusive institutions and the flux that came with the demands for Malaya’s independence made it necessary for these two communities to attempt various institutional options that could best reconcile exclusive institutions and negotiate competing political and economic demands. Three institutional options were tried: consociationalism, integration and partition. The research will explain that among the three, the path-dependent nature of Malaya’s political economy had necessitated a particular institutional logic, the consociational logic. Integration failed because attempts to establish common institutions and do away completely with longstanding mutually exclusive ones proved over-ambitious. Partition also did not materialise as it proved politically and financially costly. In sum, the research highlights Malaysia’s consociationalism as a product of small incremental policy steps which proved to be no less transformational in the long run that gives Malaysia’s political economy a quite different character than it had had at the start of British official rule in 1874.

Keywords: Malaysia
political economy
historical institutionalism
Advisor: Soskice, D
Order and righteousness

This thesis is about the life and thought of the scholar Muhammad b. ʻAli al-Shawkānī (d. 1250/1834) and his continuing influence on Yemeni law and society. It is argued here that in order to better understand Shawkānī one must look at the history of the Qāsimī imāmate he served. In the 17th century the imāms lived up to the ideal posited by Hādawī-Zaydī law. They were learned men and able military commanders in their own right and authority was largely based on charisma. In the 18th and 19th century in contrast, the imāms lacked the qualities evident in their predecessors and behaved more like kings. Rule became dynastic and took on patrimonial forms. A further development during the 18th century was the increasing influence of Sunnī Traditionist views among Zaydī-born scholars in northern Yemeni highlands. With the imāms now offering their support to Sunna-oriented scholars, the Hādawīs increasingly become marginalised. These changes were also accompanied by considerable territorial losses by the imāmate and a decline in its revenues generated from the coffee trade.
The alliance between the imāms and the Sunna-oriented scholars became most evident when Shawkānī was appointed chief judge (qāḍī al-quḍāt) of the imāmate. It will be argued that his views on law and reform posited an alternative vision of order and righteousness to that espoused by Hādawīs. His teachings implied that he, in his capacity as mujtahid muṭlaq, was to be the ultimate legal authority to which others must defer. Moreover, his views on the institution of the imāmate refuted the conditions set by Hādawī law and legitimized the rule of the imāms he served. The imām, according to him, need not be a mujtahid and rebellion against him (even if he were unjust) was absolutely forbidden. With the support of the imāms, Shawkānī was able to implement his views. His influence was manifested in his ability to appoint his students to administrative posts throughout the realm. All of this engendered a reaction from the more traditional Zaydī scholars and several clashes, both scholarly and in the form of popular riots, ensued.
After his death Shawkānī's views were carried on by his students who continued to teach his works and the Sunnī ḥadīth collections until modern times. The 20th century Ḥāmīd al-Dīn imāms were interested in publishing Shawkānī's works in order to show the wider Muslim world the convergence between Zaydism and Sunnism. After the 1962 revolution republican intellectuals further focused great attention on Shawkānī in order to undermine the legitimacy of the imīmic regime and for nationalist ends. By making appeal to his views they have tried to mould Yemeni religious identity away from the Zaydī legacy of the past.
The measurement of the production cross section ratio of identified hadrons and the calibration of the magnetic distortion in RICH1 at LHCb

Physics measurements at the LHC rely on the imulation of the proton-proton interaction to estimate detector performance and physics ackgrounds. Therefore, a good understanding of ll the processes involved is crucial to the final precision of any measurement. Monte Carlo event generators try to provide a realistic description of the proton-proton collision by combining the theoretical models describing different stages of the interaction process. Within this framework, the baryon number transport and the hadronisation mechanism are currently described by phenomenological models that need input from experimental data. This thesis investigates these subjects in the unique kinematic region covered by the LHCb detector. The production cross section ratios of identified hadrons (protons, kaons and pions) have been measured as a function of pseudorapidity and transverse momentum both at sqrts=0.9 TeV and sqrts=7 TeV collisions using 320 mub−1 and 1.8 nb−1 of data respectively. The measurements are then compared to the predictions from several tunings of the PYTHIA Monte Carlo generator. In general, current models do not give a satisfactory description of the hadronisation and tend to underestimate the transport of the baryon number into the final state. Critical to this analysis is the particle identification provided by the LHCb Ring Imaging Cherenkov (RICH) system. To ensure high performance, a proper calibration of the RICH photon detectors response is necessary. A system for the calibration of the magnetic distortion induced by the LHCb dipole magnet onto the photon detectors is described. The system currently provides calibration parameters used in the LHCb event reconstruction software and introduces a critical improvement to the overall particle identification performance.

Keywords: LHCb
Baryon Number Transport
MDMS
BNT
RICH
Physics
Hadronisation
Particle Physics
Hadron Ratio
MDCS
Advisor: Harnew, N
War and privatization: a moral theory of private protective agencies, militias, contractors, military firms, and mercenaries

This thesis investigates the moral permissibility of military privatization. My analysis focuses on two distinct concepts: the authorization of war and the supply of war. Entities that authorize war decide that military force will be used and by whom; entities that supply war then execute the various tasks that have been authorized for performance. Part I argues that private actors may not justifiably authorize war. The reason is that, in so doing, they would impose considerable risks on individuals who lack a say in authorization—particularly fellow countrymen who may suffer from retaliatory military action—and we ought not to impose considerable risks on individuals who lack such a say. Public actors have a right, and indeed a duty, to prevent private actors from authorizing military force. Moreover, public actors have a further duty to authorize military force when their constituents are threatened. Part II then seeks to show that public actors who authorize military force may rely upon private contractors to an extent in military supply. Public actors may not rely upon private contractors to exercise command. The reason is that commanders must be able to punish their subordinates in intrusive ways (e.g. imprisonment) to ensure the prosecution of just wars. Such intrusive forms of punishment should only be dispensed by public actors. In addition, public actors may not rely upon private contractors to serve above commanders on the chain of command. Such high-ranking military officers exercise substantial political power over civilian decisions of military authorization and supply; moreover, these officers make weighty decisions in battle that substantially affect the well-being of others. Public actors, however, should be permitted to rely upon private contractors to serve below military commanders on the chain of command in rank-and-file military roles so long as these contractors are properly constrained and regulated.

Keywords: private security companies
legitimate authority
mercenaries
Advisor: Caney, S