VictorJuiz/thesis huggingface dataset:
The question of the beginning and the ending of the so-called history of David's rise: a methodological reflection and its implications

The thesis argues that we can maintain that the so-called History of David’s Rise (HDR) existed independently before the deuteronomistic work, by identifying its beginning in I Samuel 16. 14 and ending in II Samuel 5. 3. Additionally, the thesis proposes that the source was first composed during Hezekiah’s reign with a view to persuading the northerners to embrace Hezekiah’s one Israel policy, and then went through two major redactions – one in the late exilic period and the other in the post-exilic period. These later redactions were prompted not only by the political situations of the time, but also by the literary milieu. In other words, a growing interest in narratives and the emergence of the ‘Jewish novelistic impulse’ in the Neo-Babylonian and Persian period triggered the creation of more extensive narratives about Saul and David.
These historical-critical arguments are preceded in the thesis by a methodological argument that a traditio-historical issue is inevitably related to a literary understanding of the larger whole. The background for this two-foci research is the wild disagreement on the issue, and the confusion around the methodology that has been aggravated by an unnecessary tension between different approaches. The thesis therefore discusses the methodological issues as carefully as possible, so that it might be transparent what actually happens when one does biblical criticism. This gives the thesis the features of a case study, but the thesis also hopes to present a satisfactory and attractive view on a particular traditio-historical issue in its own right. The study hopes to be an experiment of self-reflective biblical criticism that is serious but open. Since the thesis has two different but essentially related theses, the conclusion is established in two stages – methodological and historical. Chapter 1 shows that a literary understanding of the whole is foundational to traditio-historical discussions, and Chapter 2 demonstrates that literary understanding is always open to revision, and so are historical answers, as the latter are inevitably related to the former. Chapter 3 asks what is the most appropriate understanding of the whole HDR at this point, and the answer provides the last two chapters with the foundation by which various evidences can be measured. Chapter 4 revisits the initial question, and provides a provisional answer. And Chapter 5, after discussing the relationship between the materials in the books of Samuel, confirms the conclusion reached in the previous chapter, and elaborates further implications.

Keywords: King Saul
King David
The Books of Samuel
Advisor: Barton, J
Twistor actions for gauge theory and gravity

We first consider four-dimensional gauge theory on twistor space, taking as a case study maximally supersymmetric Yang-Mills theory. Using a twistor action functional, we show that gauge theory scattering amplitudes are naturally computed on twistor space in a manner that is much more efficient than traditional space-time Lagrangian techniques at tree-level and beyond. In particular, by rigorously studying the Feynman rules of a gauge-fixed version of the twistor action, we arrive at the MHV formalism. This provides evidence for the naturality of computing scattering amplitudes in twistor space as well as an alternative proof of the MHV formalism itself.
Next, we study other gauge theory observables in twistor space including gauge invariant local operators and Wilson loops, and discuss how to compute their expectation values with the twistor action. This enables us to provide proofs for the supersymmetric correlation function / Wilson loop correspondence as well as conjectures on mixed Wilson loop - local operator correlators at the level of the loop integrand. Furthermore, the twistorial formulation of such observables is naturally algebro-geometric; this leads to novel recursion relations for computing mixed correlators by performing BCFW-like deformations of the observables in twistor space.
Finally, we apply these twistor actions to gravity. Using the on-shell equivalence between Einstein and conformal gravity in de Sitter space, we argue that the twistor action for conformal gravity should encode the tree-level graviton scattering amplitudes of Einstein's theory. We prove this in terms of generating functionals, and derive the flat space MHV amplitude as well as a recursive version of the MHV amplitude with cosmological constant. We also include some discussion of super-connections and Coulomb branch regularization on twistor space.

Keywords: twistor theory
gauge theory
general relativity
Advisor: Mason, L
Quaternary nanocrystal solar cells

This thesis studies quaternary chalcogenide nanocrystals and their photovoltaic applications. A temperature-dependent phase change between two distinct crystallographic phases of stoichiometric Cu2ZnSnS4 is investigated through the development of a one pot synthesis method. Characterisation of the Cu2ZnSnS4 nanocrystals was performed using absorption spectroscopy, transmission electron microscopy (TEM) and powder X-ray diffraction (XRD). An investigation was conducted into the effects of using hexamethyldisilathiane (a volatile sulphur precursor) in the nucleation of small (<7nm), mono-dispersed and solution-stable quaternary Cu2ZnSnS4 nanocrystals.
A strategy to synthesize high quality thermodynamically stable kesterite Cu2ZnSnS4 nanocrystals is established, which subsequently enabled the systematic study of Cu2ZnSnS4 nanocrystal formation mechanisms, using optical characterization, XRD, TEM and Raman spectroscopy. Further studies employed scanning transmission electron microscopy (STEM) energy dispersive x-ray (EDX) mapping to examine the elemental spatial distributions of Cu2ZnSnS4 nanocrystals, in order to analyse their compositional uniformity. In addition, the stability of nanocrystals synthesised using alternative ligands is investigated using Fourier transform infrared spectroscopy, without solution based ligand substitution protocol is used to replace aliphatic reaction ligands with short, aromatic pyridine ligands in order to further improve Cu2ZnSnS4 colloid stability.
A layer-by-layer spin coating method is developed to fabricate a semiconductor heterojunction, using CdS as an n-type window, which is utilised to investigate the photovoltaic properties of Cu2ZnSnS4 nanocrystals. Finally, three novel passivation techniques are investigated, in order to optimise the optoelectronic properties of the solar cells to the point where a power conversion efficiency (PCE) of 1.00±0.04% is achieved. Although seemingly modest when compared to the performance of leading devices (PCE>12%) this represents one of the highest obtained for a Cu2ZnSnS4 nanocrystal solar cell, fabricated completely under ambient conditions at low temperatures.

Keywords: photovoltaics.
nanocrystal
quaternary
Advisor: Watt, A
Hazel, A
Role of R-loops in pause-dependent transcriptional termination of RNA polymerase II

Transcription termination of RNA polymerase II (Pol II) in mammals requires a functional poly(A) signal and either downstream pause sites or co-transcriptional cleavage (CoTC) sequences together with 3’transcript degradation by the nuclear 5’-3’ exonuclease Xrn2. However the molecular mechanism of pause-dependent transcriptional termination is not yet fully understood. This thesis investigates the molecular role of R-loop structures in pause-dependent transcriptional termination of mammalian genes. The results described in Chapters 3 and 4 indicate that nascent transcripts form RNA/DNA hybrid structures (R-loops) behind elongating Pol II and are especially prevalent over G-rich pause sites positioned downstream of gene poly(A) signals. Senataxin, a helicase protein and the human homologue of the yeast Sen1, acts to resolve these R-loop structures and by so doing allows access of Xrn2 at 3’ cleavage poly(A) sites. This ultimately leads to efficient Pol II termination. In effect R-loops formed over G-rich pause sites, followed by their resolution by senataxin, are required for efficient pause-dependent transcriptional termination. In addition to this, the 3’ end processing factor, Pcf11 is also involved in this process. Experiments presented in the final part of this study reveal a link between R-loops and RNAi-dependent H3K9me2 formation over G-rich termination regions. Overall my results suggest that R-loop structures and the H3K9me2 repressive mark over pause regions are important features of Pol II pause-dependent transcriptional termination of mammalian genes.

Keywords: RNA polymerase II
R-loops
termination
pause
Advisor: Proudfoot, N
Data driven approaches to improve the drug discovery process: a virtual screening quest in drug discovery

Drug discovery has witnessed an increase in the application of in silico methods to complement existing in vitro and in vivo experiments, in an attempt to 'fail fast' and reduce the high attrition rates of clinical phases. Computer algorithms have been successfully employed for many tasks including biological target selection, hit identification, lead optimization, binding affinity determination, ADME and toxicity prediction, side-effect prediction, drug repurposing, and, in general, to direct experimental work.
This thesis describes a multifaceted approach to virtual screening, to computationally identify small-molecule inhibitors against a biological target of interest. Conformer generation is a critical step in all virtual screening methods that make use of atomic 3D data. We therefore analysed the ability of computational tools to reproduce high quality, experimentally resolved conformations of organic small-molecules. We selected the best performing method (RDKit), and developed a protocol that generates a non-redundant conformer ensemble which tends to contain low-energy structures close to those experimentally observed.
We then outline the steps we took to build a multi-million, small-molecule database (including molecule standardization and efficient exact, substructure and similarity searching capabilities), for use in our virtual screening experiments. We generated conformers and descriptors for the molecules in the database. We tagged a subset of the database as `drug-like' and clustered this to provide a reduced, diverse set of molecules for use in more computationally-intensive virtual screening protocols.
We next describe a novel virtual screening method we developed, called Ligity, that makes use of known protein-ligand holo structures as queries to search the small-molecule database for putative actives. Ligity has been validated against targets from the DUD-E dataset, and has shown, on average, better performance than other 3D methods. We also show that performance improved when we fused the results from multiple input structures. This bodes well for Ligity's future use, especially when considering that protein structure databases such as the Protein Data Bank are growing exponentially every year.
Lastly, we describe the fruitful application of structure-based and ligand-based virtual screening methods to Plasmodium falciparum Subtilisin-like Protease 1 (PfSUB1), an important drug target in the human stages of the life-cycle of the malaria parasite. Our ligand-based virtual screening study resulted in the discovery of novel PfSUB1 inhibitors. Further lead optimization of these compounds, to improve binding affinity in the nanomolar range, may promote them as drug candidates.
In this thesis we postulate that the accuracy of computational tools in drug discovery may be enhanced to take advantage of the exponential increase of experimental data and the availability of cheaper computational power such as cloud computing.

Keywords: virtual screening
drug discovery
computational chemistry
Advisor: Deane, CM
Morris, GM
Cavity expansion theory and its application to the analysis of pressuremeters

The successful application of in-situ testing of soils heavily depends on development of methods of interpretation of the tests. The purpose of this thesis is to develop a consistent theoretical basis for the interpretation of pressuremeter tests in cohesive and frictional materials. The research programme is based on cavity expansion theory with additional details provided by a large strain finite element analysis. A unified analytical solution is developed for the expansion and contraction of both cylindrical and spherical cavities in dilatant elastic-plastic soils. For the first time, explicit solutions for the pressure-expansion and pressure-contraction relationships are derived without any restriction being imposed on the magnitude of the deformation. In addition, the finite element method is adopted for solving the cavity expansion problem. This is mainly due to the fact that only in special cases when simple material models and boundary conditions are involved has it been possible to solve the problem analytically. A finite element analysis of the cone-pressuremeter test in sand is described. A series of two-dimensional finite element calculations on both the self-boring pressuremeter test and the cone-pressuremeter test is performed. In modelling the penetration process of cone-pressuremeter tests, the stresses evaluated by the cavity expansion theory are used as the starting condition for the finite element analysis. Emphasis is placed on quantifying the effects of pressuremeter geometry on derived deformation and strength parameters. In the finite element formulation, a special effort is devoted to developing a lower order finite element suitable for analysing axisymmetric elastic-plastic problems which involve incompressibility constraints. The formulation of a new six-noded isoparametric displacement finite element is presented. To account for large strain (rotation) effects, an Eulerian description of deformation is adopted and the Jaumann stress rate is used in the soil constitutive equations. The suitability of the conventional interpretation methods for pressuremeter tests is critically assessed in the light of the finite element results. Based on the numerical results, improved procedures for obtaining in-situ soil parameters from pressuremeter tests in both clay and sand have been proposed.

Keywords: pressuremeter
Advisor: Houlsby, G
Utility-Based Hedging of Stochastic Income

In this dissertation, we study and examine utility-based hedging of the optimal portfolio choice problem in stochastic income. By assuming that the investor has a preference governed by negative exponential utility, we a derive a closed-form solution for the indifference price through the pricing methodology based on utility maximization criteria. We perform asymptotic analysis on this closed form solution to develop the analytic approximation for the indifference price and the optimal hedging strategy as a power series expansion involving the risk aversion and the correlation between the income and a traded asset. This gives a fast computation route to assess these quantities and perform our analysis. We implemented the model to perform simulations for the optimal hedging policy and produce the distributions of the hedging error at terminal time over many sample paths histories. In turn, we analyze the performance of the utility-based hedging strategy together with the strategy which arises from employing the traded asset as a substitute for the stochastic income.
Unifying elements in European Jewish fiction, 1890-1945

This study seeks to identify and describe the characteristic elements of European Jewish fiction during the period 1890-1945. Writings that deal with overtly religious themes or which have Zionist publicistic tendencies have been excluded and emphasis is placed on works with settings that are sim- ilar to those to be found in contemporary European fiction by non-Jewish writers. In order to provide a broad comparison, the study incorporates representative literary material by Jews from both Western and Eastern intellectual traditions, and includes texts in the three major languages of artistic expression in these communities: German, Yiddish, and Hebrew. On the basis of this material, it is argued that, in three respects at least, there is an identifiable unity in secular Jewish writing. Firstly, there is a thematic preoccupation with thwarted idealism, which is elaborated in a complex interaction among such themes as social alienation, ambivalence in interpersonal relationships, political altruism and impotence. Secondly, there is a consistent treatment of the characterisation of women, the devel- opment of their relationships to men, and the role of the family. Finally, there is a special reliance on the literary device of irony, in both its verbal and situational forms. The introductory chapter provides historical background and gives a general outline of the thesis. Subsequent chapters are organised as a sequence of thematic and stylistic comparisons; firstly between represen- tative texts from Eastern and Western Jewish communities and finally between the writings of a Jewish and a non-Jewish author, in an analysis of the use of irony in the works of Siegfried Kracauer and Thomas Mann. The German texts studied are Der Weg ins Freie by Arthur Schnitzler, Junge Frau von 1914 by Arnold Zweig, Kafka's Das Schlofl, Georg and Ginster by Siegfried Kracauer and Die Flucht ohne Ende by Joseph Roth. The Yid- dish writings are Di mishpokhe Karnovski and Khaver Nakhmen by I.J. Singer, Tsvishn emigrantn, Nokh Alemen and Mides-hadin by Dovid Bergelson and Di gas by Yisroel Rabon and the Hebrew texts are Nokhah hayam and Hayey nisu'im by David Vogel.
Studies of the Asian giant honey bee, Apis dorsata fabricius (Apidae) in the submerged Melaleuca forest of Vietnam

This thesis examines the bee, the plant and the human communities in the submerged Melaleuca forests of southern Vietnam. Chapter 1 gives a general introduction to the taxonomy and evolution of the genus Apis (honey bees), the research area and the general objectives of the thesis. Chapter 2 deals with biology of the Asian giant honey bee, Apis dorsata Fabricius and presents new data on the sizes and ratios of the drone and worker cells; the weight of the queen, drone and worker; and the egg production of A. dorsata queens. Chapter 3 demonstrates that properties of nest sites; such as the diameter, slope, length of the nest site, remnants of beeswax from the previous colony, and the size of the open space in front of the nest site, are criteria in the selection of nest sites by A. dorsata colonies. Chapter 4 discusses the floral relations of A. dorsata and other insect visitors in the forest. Three types of partitioning within and among plants and insects in the Melaleuca forest are found. These are the partitioning of visitors by Melaleuca cajuputi and Nypa fruticans flowers, the partitioning of visitation time by the two sympatric honey bee species, A. dorsata and A. florea, and the partitioning of visitation time on Melaleuca and Nypa flowers by either honey bee species. Results of Chapter 5 show that there is temporal partitioning of flower sources among the sympatric Asian honey bee species (A. dorsata, A. cerana and A. florea
); however, there is a competition of flowers between the European bee (A. mellifera) and the Asian bee species. Chapter 6 discusses the important role of A. dorsata rafter beekeeping in forest protection, the conflicts between the beekeepers and new forest holders, and the economic efficiency of A. dorsata rafter beekeeping in comparison with those of A. mellifera and A. cerana beekeeping systems. Finally, Chapter 7 gives general conclusions of the thesis and recommendations for further study.

Advisor: McGavin, G
The role of class 1 KNOX genes in sporophyte evolution

Land plants are characterized by the alternation of two generations: the haploid gametophyte and the diploid sporophyte. As land plants evolved from bryophytes to vascular plants, the sporophyte became the dominant generation in the life cycle. The sporophytes of bryophytes are developmentally simple structures characterized by determinate growth. In contrast, the sporophytes of vascular plants diverged to become highly variable and often complex structures with indeterminate growth.
KNOTTED1-LIKE HOMEOBOX (KNOX) genes encode homeodomain containing transcription factors that are key regulators of sporophyte development. KNOX genes are divided into two subclasses, class 1 and class 2. The critical role of class 1 KNOX genes in the apical growth of all extant land plants studied to date, suggests that modifications to class 1 KNOX gene function may have played an important role in sporophyte evolution. However, the nature of any such modifications is largely unknown. In this study, a number of cross-species complementation experiments were carried out to determine the extent to which class 1 KNOX gene function is conserved between different land plant groups. The role of KNOX genes in hornworts was also investigated because hornworts are believed to be the sister group to vascular plants.
The work presented in this thesis demonstrates that the function of class 1 KNOX genes is conserved between lycophytes and angiosperms. In contrast, the function of class 1 KNOX genes appears to have diversified between bryophytes and vascular plants. Collectively, these results indicate increased complexity of class 1 KNOX gene function during the evolution of land plants.

Keywords: evolution
land plants.
development
KNOX
Advisor: Langdale, JA
Outcome-dependent randomisation schemes for clinical trials with fluctuations in patient characteristics

A clinical trial is considered in which two treatments are to be compared. Treatment allocation schemes are usually designed to assign approximately equal numbers of patients to each treatment. The purpose of this thesis is to investigate the efficiency of estimation and the effect of instability in the response variable for allocation schemes which are aimed at reducing the number of patients who receive the inferior treatment.
The general background to outcome-dependent allocation schemes is described in Chapter 1. A discussion of ethical and practical problems associated with these methods is presented together with brief details of actual trials conducted.
In Chapter 2, the response to treatment is Bernoulli and the trial size is fixed. A simple method for estimating the treatment difference is proposed. Simulation results for a selection of allocation schemes indicate that the effect of instability upon the performance of the schemes can sometimes be substantial.
A decision-theory approach is taken in Chapter 3. The trial is conducted in a number of stages and the interests of both the patients in the trial and those who will be treated after the end of the trial are taken into account. Using results for conditional normal distributions, analytical results are derived for estimation of the treatment difference for both a stable and an unstable normal response variable for three allocation schemes. Some results for estimation are also given for other responses.
The problem of sequential testing is addressed in Chapter 4. With instability in the response variable, it is shown that the error probabilities for the test for a stable response variable can be approximately preserved by using a modified test statistic with appropriately-widened stopping boundaries. In addition, some recent results for estimation following sequential tests are outlined.
Finally, the main conclusions of the thesis are highlighted in Chapter 5.

Advisor: Armitage, P