VictorJuiz/thesis huggingface dataset:
An edition of Fulke Greville's A dedication to Sir Philip Sidney (The life of the renowned Sir Philip Sidney)

This thesis sets out, firstly, to establish the relationship "between the known representatives of the textandmdash;the editio princeps of 1652 [1652], Trinity College, Cambridge MSS R.7. 32 and 33 [T], Shrewsbury Public Library MS 295 [S], and a manuscript in the possession of Dr. B.E. Juel-Jensen [J]; and, secondly, to provide, as far as is possible, a readable text of the latest state of revision of the work, and a critical apparatus setting out all the passages from the earlier states of the text that were either altered or omitted during the process of revision. The relationship of the four witnesses of the text, established on the basis of irreversible error and alterations that could only have been authorial, may be represented by the following schema, where X, T, and Z stand for three states of revision:
[Diagram omitted from transcription]
Readings in the present text have been taken from 1652 except where it is thought to be in error. Errors in 1652 have been corrected with readings from T or J and S, depending on where in the transmissional process error was introduced; in a few isolated cases I have emended the text.
The accidental characteristics of none of the representatives of the text have been preserved. Spelling, typography and punctuation have all been brought into line with modern conventions, except insofar as this would involve the introduction of historical inaccuracies.
The critical apparatus has been constructed so as to allow for an approximate reading of the early state of the text represented by J and S. I have included in the introduction a schematic representation of the transformations to which the work was subjected. This schema will help to locate the material of J and S as it may be found in 1652 and T.
In the introduction I have argued that the commonly accepted title of the work should be replaced with that of the Trinity College, Cambridge manuscript: A Dedication to Sir Philip Sidney. This title is not only in accord with Greville's intentions, but it draws attention to the relationship between the work and Greville's other writings.
The introduction also includes brief discussions of the literary traditions of the Dedication, of Greville's sources that have been identified, of the period of composition of the text from before March 1610 till the second half of 1614, and of the prose styles employed by Greville.
In the notes, particular textual problems only mentioned in the introduction have been considered. I have also been able, in the limited time available to me, to collect about two-thirds of the material necessary for an adequate commentary on the text.
Riparian reserves in oil palm plantations: biodiversity, ecological processes and ecosystem services

As the human population expands, agricultural expansion and intensification will exert an increasing pressure on remaining habitats, especially in the tropics. Oil palm is one of the most rapidly expanding crops in these regions, and identifying management strategies that conserve biodiversity and ecosystem services in these landscapes is therefore a priority.
I assess whether riparian forest fragments (riparian reserves) conserve species and the functions they support within oil palm landscapes. Riparian forests are legally required for their beneficial impact on hydrological dynamics and their potential to contribute to the conservation of terrestrial species is poorly documented.
I focussed on two ecologically important indicator groups (ants and dung beetles) and the ecosystem processes that they support.
Whilst protecting primary forest will remain the most important strategy for biodiversity conservation, I found that riparian reserves do support species of ants and dung beetles that would not otherwise persist in oil palm landscapes. However, the extent to which riparian reserves maintained key ecological functions differed between these two taxa. The amount of nutrient distribution carried out by ants in riparian reserves was similar to logged forest areas, and higher than in oil palm. In contrast, dung removal functions did not vary between these land uses.
I also investigated how the vegetation structure and landscape context of riparian reserves affects the dung beetle communities they support. Increasing reserve width and proximity to other forest fragments had a positive impact on the species richness and diversity of dung beetles in riparian reserves.
There was little evidence that riparian reserves enhance the provision of dung removal or pest control services in adjacent areas of oil palm.
The results provide evidence to support the introduction and/or enforcement of legislation to protect riparian forest reserves in order to conserve biodiversity and ecological processes in oil palm landscapes.

Keywords: ants
conservation
Palm oil
dung beetles
riparian zones
Advisor: Lewis, O
Muon-spin relaxation and its application in the study of molecular quantum magnets

This thesis is concerned with the muon-spin relaxation (musr) technique and its application in the study of a number of molecular magnetic systems that may be driven through a quantum phase transition at low temperatures through the application of a magnetic field or hydrostatic pressure.
Musr is a highly sensitive probe of magnetism, but its utility can be severely limited by the lack of knowledge of the muon implantation site and the extent to which the muon perturbs its host. In a system of ionic fluorides, where partial information about the muon site is experimentally available, I demonstrate systematically that these problems can be addressed accurately using electronic-structure calculations. The F--mu--F complex formed by muons in many fluorides can be understood as an exotic molecule-in-a-crystal defect with a zero-point energy larger than that of any naturally-occurring triatomic molecule.
I demonstrate the interesting possibility of controlling the magnetic dimensionality in a molecular magnet using applied pressure. musr and high-field magnetisation experiments under applied pressure on the coordination polymer CuF2(H2O)2(pyrazine) show a transition from a quasi-two-dimensional to a quasi-one-dimensional antiferromagnetic phase. Density-functional theory calculations and calculations of the dipolar anisotropy complement the experiments.
I describe how subtle differences in chemical composition can lead to starkly different structural and magnetic properties. [Cu(pyz)(H2O)(gly)2](ClO4)2 may be considered an antiferromagnetic chain that orders below 50 mK while the related compound [Cu(pyz)(gly)](ClO4) is formed from Cu2+ dimers and remains disordered down to 30 mK in zero field, but displays a field-temperature phase diagram consistent with the Bose-Einstein condensation of triplons. I also describe musr measurements on the strong-leg spin ladder DIMPY and on the molecular nanomagnets Cr8Cd and Cr8Mn which highlight some of the remaining challenges for longitudinal-field musr experiments.

Keywords: Muon-spin relaxation
density-functional theory
molecular magnetism
Advisor: Blundell, SJ
Signal transduction in the barley powdery mildew fungus

Barley powdery mildew disease is caused by the highly specialised phytopathogenic fungus, Blumeria graminis f.sp. hordei. Disease is spread prolifically by the production of asexual conidia. Following contact with the barley leaf surface, a short, primary germ tube (PGT) emerges, followed by elaboration of a second-formed germ tube, the appressorial germ tube (AGT). This second-formed germ tube elongates, swells and hooks to form an appressorium, which allows direct penetration of the barley cuticle and infection of the host.
Infection structure differentiation in B. graminis is a highly regulated and complex process. It demands the coordinated perception of multiple external signals, but little is known about how these signals are integrated and transduced within the fungus. Protein kinase A (PKA) and cAMP signalling are known to play important, but complex, roles during infection structure development. However, signalling via cAMP alone is not sufficient to promote progression through infection structure differentiation.
This study describes the characterization of two B. graminis protein kinase C genes, pkc1 and pkc-like. PKC activity was identified in B. graminis protein extracts. Efforts to find an inhibitor specific for B. graminis PKC were unsuccessful. However, phorbol ester, a PKC agonist, invoked both appressorium formation when applied to spores in vivo and PKC activity in protein extracts. In addition, real-time PCR confirmed the differentially regulated transcript profiles of both pkc1 and pkc-like, revealing a peak in transcript levels just prior to PGT emergence for pkc1, and during PGT differentiation for the pkc-like gene.
Two mitogen-activated protein (MAP) kinases, mpk1 and mpk2, were characterized. MAP kinase activity was detected in conidial protein extracts. The MAP kinase kinase (MEK) inhibitor, PD98059, inhibited B. graminis germling morphogenesis. However, a MAP kinase agonist failed to show any effect on germling differentiation. In addition, real-time PCR confirmed the differentially regulated transcript profiles of both mpk1 and mpk2, and revealed a peak in transcript levels during appressorial germ tube elongation and swelling for both genes.
The "model" phytopathogenic fungus, Magnaporthe grisea, was employed as a "surrogate host" for the functional analysis of the B. graminis MAP kinase gene, mpk1. Firstly, the mpk1 promoter was sequenced and a plasmid construct made comprising the mpk1 gene under the control of the mpk1 promoter. This, and the control construct, that is the M. grisea PMK1 gene under the control of the PMK1 promoter, were transformed into M. grisea Δpmk1. Southern analysis identified transformants for phenotypic studies. These showed that whereas Δpmk1 was complemented by M. grisea PMK1 in the control experiments, B. graminis mpk1 failed to complement Δpmk1. Expression studies showed that there was no expression of mpk1 in an mpk1 transformant.
The effect of relatedness on sexual dynamics. Studies of red junglefowl and fruit flies

In this thesis, I explore four different ways in which relatedness affects sexual interactions in the red junglefowl Gallus gallus ssp., and the fruit fly Drosophila melanogaster. First, I show that in both species, inbreeding depression is sex-specific and modulated by parental age and gametic age. However, the sex that suffers higher inbreeding depression was trait- and species-dependent. Second, I examined patterns of inbreeding avoidance. I found no evidence of inbreeding avoidance in the fruit fly, but in the red junglefowl both males and females avoided mating with relatives, independently from sex-ratio of the social group. Third, I investigated whether relatedness amongst members of one sex affects mate choice in members of the opposite sex. Male fruit flies preferentially courted females unrelated to females with whom they had previously mated, while female flies displayed a weak preference for males related to their previous mates. In the red junglefowl, females exposed to male trios of two males related to each other and one unrelated male, displayed a marked preference for mating with the male unrelated to the other two males, and might also bias postcopulatory sperm utilization in favour of the unrelated male. Fourth, I explored the implications of male relatedness on the intensity of male-male competition. Male red junglefowl were less aggressive towards related competitors, but invested more sperm in females that had previously mated with a related male rather than with an unrelated male. In fruit flies, male relatedness had a strong impact on female life-history and offspring viability, although I found no evidence that these effects were modulated by changes in male-male competition. Collectively, the findings of these studies demonstrate the complex relationship between relatedness and other important biological phenomena as such senescence and sexual conflict.

Keywords: sexual conflict
Coolidge effect
kin selection
senescence
inbreeding
Advisor: Pizzari, T
Wigby, S
Narconovela: four case studies of the representation of drug trafficking in Mexican fiction

In addition to coverage in the national and international media of the ongoing violence in Mexico related to the drug trade, there has been growing interest in fictional representations of the Mexican drug trade, its origins and social context. There is now a considerable body of written narratives that have been christened narconovelas. A small number of academic works has charted the emergence of the narconovela and sought to examine how drug traffickers have been represented and evaluated in fiction. However, very little attention has been paid to the aesthetic qualities of ‘narco-literature’. This study examines four of the most highly-regarded works in detail: Balas de plata (2008), by Élmer Mendoza; Los minutos negros (2006), by Martín Solares; Contrabando (2008), by Víctor Hugo Rascón Banda; and Trabajos del reino (2004), by Yuri Herrera. So embedded is the phenomenon of drug trafficking in northern Mexican culture, so suffused with cliché is its representation in other media, that to write about the topic with originality and ethical nuance is difficult. This thesis accounts for the distinct choices made by the four authors in question to address this difficulty of representation in the structure, style and tone of their novels. The self-awareness exhibited by these works of fiction regarding the challenges of representing their subject matter render them the most sophisticated examples yet created of the so-called narconovela.

Keywords: Mexican Literature
Latin American Literature
Mexico
Narconovela
Drug Trafficking
Advisor: Moran, D
Developing inhibitors of bromodomain-histone interactions

Lysine acetylation is a widespread protein post-translational modification that influences diverse cellular processes. An association between acetylation of histone N-terminal tails and transcriptional activation has been recognised since the 1960s. However, it has only become apparent since 2000 that many of the effects of histone acetylation are mediated by proteins that bind to acetyl-lysine through a specialised acetyl-lysine recognition domain, the bromodomain. Small-molecule inhibitors of bromodomain-histone interactions can greatly assist studies into the functions of bromodomain-containing proteins, and show promise as treatments for several diseases, including cancers. Herein I describe the discovery and development of a novel chemical series of bromodomain-binding ligands containing the 3,5-dimethyisoxazole moiety. This heterocycle acts as an acetyl-lysine bioisostere, mimicking key interactions formed between acetyl-lysine and the bromodomain. Optimised compounds show sub-micromolar affinities for bromodomains of the BET family, a class of transcriptional co-regulators. Crystallographic and structure-activity relationship studies shed light on the structural requirements for potent and selective BET ligands. Furthermore, the compounds show cellular effects consistent with BET bromodomain inhibition: cytotoxicity studies in a range of cell lines, including the NCI-60 human tumour cell line screen, reveal differential activity, with leukaemias showing particular sensitivity. 3,5-Dimethylisoxazole-containing compounds were also shown to downregulate known BET target genes.
Further studies investigated the effect of modifying or replacing the methyl groups of 3,5-dimethylisoxazole on BET bromodomain affinity, which indicated that the 3-methyl group is necessary for affinity. Finally, three novel isoxazole-containing amino acids were synthesised and incorporated into histone peptides as potential bromodomain-binding, non-hydrolysable, acetyl-lysine mimics. These amino acids might be useful in uncovering the function of individual acetylated lysine residues.
The identification of methyl-isoxazoles as acetyl-lysine-mimetic bromodomain ligands represents a significant advance in our understanding of structure-activity relationships for these important proteins. The confirmed cellular activity of these compounds will enable their use in future biological studies.

Keywords: isoxazole
cancer
acetyl-lysine
post-translational modification
histone
bromodomain
Advisor: Conway, S
Brennan, P
The epidemiology of chronic pelvic pain in women

Objectives - This study aimed to estimate for the first time in the UK: (1) the prevalence and incidence of chronic pelvic pain (CPP) in primary care, the duration of symptoms, and patterns of diagnosis and referral; (2) the prevalence of CPP in the community, and its overlap with other types of pelvic pain, irritable bowel syndrome (IBS) and genito-urinary symptoms. Pain severity, use of health care, functioning and well-being, and factors associated with CPP were also investigated.
Methods - (1) Retrospective analysis of the MediPlus UK Primary Care Database, using data for 1991-1995 of 278,509 women aged 12-70. CPP cases were identified on the basis of relevant contacts with practices. Duration of CPP and patterns of diagnosis and referral were investigated in a cohort of 5,051 incident cases followed for 3-4 years from their first contact for pelvic pain. (2) Postal questionnaire survey of 4,000 randomly selected women aged 18-50 in Oxfordshire. Cases were women reporting CPP in the last 3 months, with sub-groups classified according to cumulative pain duration in the last 12 months.
Main results - (1) The annual prevalence of CPP in primary care was 38.3/1,000 (95% CI: 37.5-39.0), comparable to asthma (37/1,000) and back pain (41/1,000). The most common diagnoses given to incident cases were IBS and cystitis, but a quarter received no diagnosis and only 40% had a specialist referral. A third of incident cases had persistent symptoms after 2 years. 2) The community prevalence of CPP in women was 24.0% (95% CI: 22.1-25.8). CPP cases had a high prevalence of dysmenorrhoea (90%), dyspareunia (50%), IBS (39%), and genitourinary symptoms (24%). CPP cases of 'long' duration were much more affected in terms of pain severity, use of health care, and physical impairment than 'short' duration cases. All women with CPP appeared affected in terms of anxiety about their symptoms.
Conclusions - This study provided the first evidence of a high prevalence of CPP in primary care and the community. However, CPP cases varied substantially in the degree to which they were affected by their pain in physical terms. The anxiety in women with CPP about their symptoms emphasises the need for more information about CPP and its possible causes.
The zero-turbulence manifold in fusion plasmas

The transport of heat that results from turbulence is a major factor limiting the temperature gradient, and thus the performance, of fusion devices. We use nonlinear simulations to show that a toroidal equilibrium scale sheared flow can completely suppress the turbulence across a wide range of flow gradient and temperature gradient values. We demonstrate the existence of a bifurcation across this range whereby the plasma may transition from a low flow gradient and temperature gradient state to a higher flow gradient and temperature gradient state. We show further that the maximum temperature gradient that can be reached by such a transition is limited by the existence, at high flow gradient, of subcritical turbulence driven by the parallel velocity gradient (PVG). We use linear simulations and analytic calculations to examine the properties of the transiently growing modes which give rise to this subcritical turbulence, and conclude that there may be a critical value of the ratio of the PVG to the suppressing perpendicular gradient of the velocity (in a tokamak this ratio is equal to q/ε where q is the magnetic safety factor and ε the inverse aspect ra- tio) below which the PVG is unable to drive subcritical turbulence. In light of this, we use nonlinear simulations to calculate, as a function of three parameters (the perpendicular flow shear, q/ε and the temperature gradient), the surface within that parameter space which divides the regions where turbulence can and cannot be sustained: the zero- turbulence manifold. We are unable to conclude that there is in fact a critical value of q/ε below which PVG-driven turbulence is eliminated. Nevertheless, we demonstrate that at low values of q/ε, the maximum critical temperature gradient that can be reached without generating turbulence (and thus, we infer, the maximum temperature gradient that could be reached in the transport bifurcation) is dramatically increased. Thus, we anticipate that a fusion device for which, across a significant portion of the minor radius, the magnetic shear is low, the ratio q/ε is low and the toroidal flow shear is strong, will achieve high levels of energy confinement and thus high performance.

Keywords: turbulence
nuclear fusion
plasma physics
subcritical turbulence
Advisor: Schekochihin, A
Essays in development economics: land rights, ethnicity and birth order

Aside from the introduction and conclusion, this thesis comprises four core chapters: The first chapter investigates the presence of endogenous peer effects in the adoption of formal property rights. Using data from a unique land titling experiment held in an unplanned settlement in Dar es Salaam, Tanzania. I show a strong, positive impact of neighbour adoption on the household’s choice to purchase a land title. I also show that this relationship holds in a separate, identical experiment held a year later in a nearby community, as well as in administrative data for approximately 45,000 land parcels in the same city. I also discuss possible channels, including the possibility of complementarities in the reduction in expropriation risk.
The second chapter examines the relationship between ethnic heterogeneity and the demand for formal land tenure. Using a unique census of two highly fractionalised settle- ments in Dar es Salaam, I show that households located near coethnics are significantly less likely to purchase a limited form of land tenure recently offered by the government. I attempt to address one of the chief concerns, endogenous sorting of households, by con- ditioning on a households choice of neighbors upon arrival in the neighborhood. These results suggest that close-knit ethnic groups may be less likely to accept state-provided goods if they can generate reasonable substitutes.
The third chapter is a short chapter which presents results from a recent policy experi- ment in Tanzania where formal land titles were provided to informal settlers at randomised prices. Land owners were also randomly assigned conditional discounts, which could only be applied if a woman was designated as owner or co-owner of the land in question. Results show that conditionality has no adverse effects on demand for land titles, yet drastically increases the probability a woman is included. We discuss the implications of these results for the expected bargaining power impacts of the intervention.
The final chapter investigates birth order effects on both anthropometric and edu- cation outcomes in a longitudinal survey of children from the Philippines. Birth order effects are present early in life for both outcomes, but attenuate as children approach adulthood. There is also evidence for nonlinear birth order effects, with both firstborn and lastborn children holding an advantage over middleborn children. These results are at odds with prevalent theories of birth order which predict lasting and monotonic differences in outcomes across children.

Keywords: peer effects
birth order
Philippines
Development economic
Tanzania
ethnicity
property rights
Advisor: Dercon, S