VictorJuiz/thesis huggingface dataset:
The role of polycomb repressive complex 2 in postnatal subventricular zone neural stem/progenitor cell self-renewal and multipotency

The murine subventricular zone (SVZ) in a brain contains a population of stem cells and daily produces tens of thousands of neurons throughout lifetime. However, the mechanisms of SVZ neural stem/progenitor cell (NSPC) maintenance, differentiation and cell-fate specification are still not clear. To understand these parameters via histone methylations with bivalent mechanism, the SVZ NSPCs were first isolated by using a culture technique called neurosphere assay (NSA). It has been a challenge to culture pure cell populations of SVZ subtypes, so the NSA was initially validated. The H3K27me3 mark, which has a dominant role in the bivalent mechanism, has not been studied in postnatal and adult SVZ in vivo, yet their role has been implicated to control the shift of embryonic cortical neurogenesis to gliogenesis. Therefore, we have first investigated whether H3K27me3 marks are present in the postnatal and adult SVZ NSPC population and whether their marks have been changed after stroke or demyelination in central nervous system (CNS) by immunohistrochemistry. With the confirmation of H3K27me3 mark present in SVZ NSPCs, the presence of H3K27me3 catalyzer, called polycomb repressive complex 2 (PRC2) core components (Eed, Ezh2, Suz12) including Jarid2, was investigated and confirmed in postnatal SVZ in vitro by qRT-PCR and Western blot. To understand the role of PRC2 enzymatic activity in postnatal SVZ neurosphere self-renewal and multipotency, Eed was down-regulated by using lentiviral mediated delivery of shRNA. Also, PRC2 dependent or independent function of Jarid2 was examined via knockdown approach. The lack of Eed in the neurospheres resulted the attenuation of self-renewal and oligodendrogenesis, whereas the Jarid2 knockdown neurospheres showed the decreased proliferation with no SVZ NSPC differentiation. Based on these knockdown studies, it suggests Eed and Jarid2 might not share their function in the postnatal SVZ NSPCs to govern postnatal SVZ NSPC self-renewal and multipotency.

Keywords: Subventricular zone
Neural Stem Cells
Epigenetics
Advisor: Szele, F
The third Earl of Shaftesbury (1671-1713)

This thesis seeks to provide a political context for the philosophical work of the third earl of Shaftesbury. A biographical framework is adopted which details Shaftesbury's political interests, both inside and outside parliament. In attempting to trace the links between his political life and his philosophical ideas particular attention is given to Shaftesbury's debt to his tutor, Locke, as well as to the importance of his visits to the Netherlands. Shaftesbury's connections with radical whig politicians at the end of the seventeenth century are also investigated: they are an indication of his interest in practical political issues.
The main argument of the thesis is that Shaftesbury's published work is fully comprehensible only if this political context is taken into account. By concentrating solely on his importance in the history of moral or aesthetic philosophy scholars have effectively removed the political cutting-edge from Shaftesbury's work. It was precisely because Shaftesbury was aware of the political implications of his moral and aesthetic philosophy that he was such a controversial social critic in his own day.
The originality of the thesis lies in the presentation of a more complete biography of Shaftesbury than has previously been attempted. Although the Shaftesbury papers in London are the major source for the thesis, other material has been consulted, including manuscripts in the Netherlands, which gives a fuller picture of the circles in which he moved. Shaftesbury was not an important politician, but his strong political concerns need to be emphasised before his thought can be understood: politics and philosophy were continuous for him.
An ion-binding approach to asymmetric allylation reactions

Ion-binding organocatalysis is an emerging field that has the potential to control the stereochemical outcome of any transformation that goes via charged intermediates. The aim of this project was to explore how this concept could be applied to an asymmetric allylation reaction.
Chapter 2 of this thesis discusses anion-binding catalysis and investigates a chiral cooperative thiourea catalyst that could bind to fluoride to control allylation using an allylsilane. Optimization using a non-chiral thiourea (Schreiner’s catalyst) demonstrated that the reaction proceeded in high yield with TBAT onto an N-benzoylhydrazone. A chiral cooperative thiourea catalyst library was then synthesized but unfortunately, although the allylation using these catalysts proceeded in excellent yield, the product was isolated as the racemate (Scheme 1).
Scheme 1: Anion-binding catalysis gave allylated products in high yields but gave no stereocontrol.
Chapter 3 examines a chiral quaternary ammonium fluoride as an example of chiral cation-directed catalysis. We hypothesized that an allylsilane activated by fluoride would generate an allyl anion species that would associate with the chiral quaternary ammonium cation through electrostatic interactions. Extensive optimization found that the allylation reaction proceeded in good yield in chloroform at reflux with N-benzoylhydrazones. Different fluoride catalysts were prepared using an ion-exchange resin, and cinchonidine-derived catalysts performed the best. This methodology was extended to a phase-transfer catalyzed process, where solid cesium fluoride exchanged with chloride in situ, removing the need to synthesize and isolate ammonium fluoride catalysts (Scheme 2).
Scheme 2: Cation-directed asymmetric allylation.
In Chapter 4 cation-directed asymmetric catalysis was extended to an intramolecular allylation reaction. Substrate synthesis was attempted by cross metathesis but the reaction was capricious and yields were low. Intramolecular allylation with these materials gave promising results (Scheme 3) but a lack of material prevented optimization.
Scheme 3: Intramolecular allylation results.

Keywords: allylation
catalysis
asymmetric synthesis
organocatalysis
Advisor: Smith, M
Plasma vertical position control in the COMPASS–D tokamak

The plasma vertical position system on the COMPASS–D tokamak is studied in this thesis. An analogue P+D controller is used to regulate the plasma vertical position which is open loop unstable. Measurements from inside the vessel are used for the derivative component of the control signal and external measurements for the proportional component.
Two main sources of disturbances are observed on COMPASS–D. One source is 600Hz noise from thyristor power supplies which cause large oscillations at the control amplifier output. Another source is impulse–like disturbances due to ELMs (Edge Localized Modes) and this can occasionally lead to loss of control when the control amplifier saturates.
Models of the plasma open loop dynamics were obtained using the process of system identification. Experimental data is used to fit the coefficients of a mathematical model. The frequency response of the model is strongly dependent on the shape of the plasma. The effect of shielding by the vessel wall on external measurements when compared with internal measurements is also observed. The models were used to predict values of gain margins and phase crossover frequencies which were found to be in good agreement with measured values.
The harsh reactor conditions on the proposed ITER tokamak preclude the use of internal measurements. On COMPASS–D the stability margins of the loop decrease when using only external flux loops. High order controllers were designed to stabilize the system using only external measurements and to reduce the effect of 600Hz noise on the control amplifier voltage. The controllers were tested on COMPASS–D and demonstrated the improved performance of high order controllers over the simple P+D controller.
ELMs cause impulse–like disturbances on the plasma position. The optimal controller minimizing the peak of the impulse response can be calculated analytically for COMPASS–D. A multiobjective controller which combines a small peak impulse response with robust stability and noise attenuation can be obtained using a numerical search.

Keywords: Position Control
Plasma Modelling
Tokamak
System Identification
Advisor: Kouvaritakis, B
Rumination and reward processing in anorexia nervosa

Anorexia nervosa (AN) is an eating disorder characterised by severe emaciation due deliberate restriction of food intake and an intense fear of gaining weight. Theoretical accounts of AN have to date focused predominately on cognitive elements of the disorder, yet resulting treatments have been inadequate and outcome for AN remains poor. Understanding the processes that maintain the disorder is an important step in developing effective strategies to augment existing treatments. With this in mind, the question arises: what processes drive AN?
Novel frameworks for AN suggest that particular information processing configurations or “modes” may underpin many symptoms of AN, such as preoccupation with control of eating, weight and shape. More specifically, it is proposed that a ruminative mode of processing may function as an avoidance strategy in AN, enabling individuals to neglect salient and rewarding stimuli, such as food, and thus uphold restrictive eating practices. Whilst empirical studies have examined processes such as rumination, avoidance and reward in depression, they have seldom been studied in AN. The aim of this thesis is therefore to understand the role of rumination and reward processes in AN.
Chapter 1 reviews the literature on AN, rumination and reward processing. Chapter 2 presents data demonstrating to what extent the content of rumination in AN differs from rumination in depression and the effect that rumination may have on ED symptoms. The study conducted in Chapter 3 examines whether individuals with AN can be switched out of rumination around meal times and what effect this has on AN psychopathology. Chapter 4 presents neuroimaging data which elucidates the brain regions involved in processing rewarding and aversive food stimuli after recovery from AN. The study reported in Chapter 5 teases apart hedonic (liking) versus motivational (wanting) aspects of food reward in AN. The final study (Chapter 6) provides further evidence using neuroimaging that rumination may be an important process in AN which may override appetitive responses to rewarding stimuli, such as food. The studies reported support the notion that rumination and aberrant reward processing may be involved in the maintenance of AN.

Keywords: anorexia nervosa
rumination
reward
eating disorders
Advisor: Park, R
Harmer, C
McCabe, C
The evolution of viral diversity

This thesis focuses on the population dynamics of three antigenically diverse RNA viruses: dengue, influenza and HIV-1. It comprises a set of studies highlighting the roles of structural constraints on critical antigenic determinants, interactions between immune responses to different antigenic types, host lifespan, and the degree of mixing between different host populations in determining the epidemiology and within-host dynamics of these pathogen systems.
Dengue exists in humans as a collection of four antigenically related serotypes. Although infection by one serotype appears to convey life-long protection to homologous infection, it is believed to be a risk factor for severe disease manifestations upon secondary, heterologous infection due to the phenomenon of Antibody-Dependent Enhancement (ADE). It is not clear if third or fourth infections are possible, and if so, how they contribute to dengue epidemiology. In this thesis, I investigate the effect of third and fourth infections on the transmission dynamics of dengue.
By contrast with dengue, human influenza viruses are known to be in rapid antigenic flux, manifesting in the sequential replacement of antigenic types. This pattern of evolution does not appear to be the same in shorter-lived hosts such as swine and birds. In this thesis, I have used a simple multi-locus model to explore the relationship between host lifespan and viral evolution, as well as to elucidate the effects of transmission between hosts of different lifespan in effort to capture the cross-species element of influenza transmission.
My final chapter concerns the within-host evolution of HIV-1. I propose a new model for the pathogenesis of HIV-1 where the transition to AIDS is primarily linked to the gradual loss of the ability to make new antibody responses as the CD4+ population declines.
Together these studies emphasise that it is the changing profile of immune responses – either at the population level or within the host – that is the principal determinant of the dynamics of the pathogen, rather than the mode and tempo of antigenic innovation.

Keywords: virus
antigenic evolution
Advisor: Gupta, S
Pybus, O
Studies in the Syriac versions of St. John Chrysostom's homilies on the New Testament

The thesis conducts systematic studies of the Syriac versions of St. John Chrysostom's Homilies on the New Testamentandmdash;the Homilies on Matthew, the Homilies on John, and the Homilies on the Epistles of St. Paul. The thesis focuses mainly on sixth- and seventh-century British Library manuscripts, but is also concerned with the spread of the material over the course of centuries into different sorts of books. Pre-dating extant Greek witnesses by centuries, the main Syriac manuscripts preserve translations made during the fifth and sixth centuries and constitute unique textual evidence for students of the Greek. By analyzing the methods of translation, it has been possible to place the versions within the framework of the development of Syriac translation technique and to highlight methodological issues for those attempting to relate Syriac versions to their Greek source texts. The translation analysis includes Biblical citations. The analyses have shown that the Homilies on the Epistles were translated last and are the most literal. The Homilies on Matthew and on John were translated earlier, are relatively less literal, and most likely to have Peshitta or even (occasionally) Old Syriac Bible texts rather than direct translations from the Greek.
Several of the Homilies on John are edited and translated, allowing a critique of M.-E. Boismard's interpretation and use of the Syriac version, which is seen to be unsatisfactory in several ways.
Petrogenesis of the phonolitic rocks of the Velay oriental, France

The Velay oriental (Massif Central, France) is a basaltic plateau with abundant viscous phonolite extrusions. The plateau lavas grade from alkali basalt to mugearite, but intermediate compositions are volumetrically scarce. Pyroclastics are absent. The most complete plateau sections are in the south, while in the north intermediate lavas appear only as viscous, phenocryst-rich extrusions.
The plateau lavas were erupted between 11.7Ma and 7.6Ma, the southern phonolites 8.5Ma- 6.5Ma and new data show that the northern phonolites were erupted between 13.3Ma and 10.5Ma. Basement uplift occurred during the plateau-building stage, due to the emplacement of magma chambers. Intermediate lavas are scarce because they remained in the magma chambers due to their density, whereas phonolite was able to rise hydrostatically. The magma chambers were within 5km of the surface.
Phonolites are divided into miaskitic and agpaiitic types on the basis of their chemistry and petrography. They evolved from the basalt by crystal settling in the magma chambers, whereas the aphyric plateau lavas evolved by plating crystals onto their conduit walls as they flowed towards the surface.
Sr-isotopes show that the basalt-phonolite series is uncontaminated, whereas the northern intermediate lavas evolved by assimilation-fractional-crystallisation.
A suite of cumulate nodules was recovered from a pyroclastic unit, which is probably younger than the Velay Miocene lavas. They are related to the northern intermediate lavas, and belong to the "Group II" class of nodules.
Geothermobarometry suggests that both the cumulates and the northern intermediate lavas crystallised at a depth of 15-20km and probably became contaminated due to the smaller temperature difference between the geotherm and granite solidus at that depth.
The vast majority of the Velay lavas are identical to alkalic ocean-island lavas, geochemically unaffected by their passage through the lithosphere, but with their relative proportions at the surface controlled by the density contrast between the basalt and basement granite.

Keywords: basalt
phonolite
Sr-isotope
fractionation
Daly Gap
France
cumulate
K-Ar
Velay oriental
Advisor: Bell, D
Analysing and modelling the impact of habitat fragmentation on species diversity: a macroecological perspective

The destruction and fragmentation of natural habitat is the leading driver of the current extinction crisis. As a result, a research area has emerged focused on studying ecology in islands of natural habitat surrounded by a sea of anthropogenic land uses, so called ‘habitat islands’. However, this research has largely been undertaken on small-medium scales, generally in single systems. Furthermore, many habitat island studies have used previous results and theory derived in the context of oceanic island research. Thus, this thesis aims to examine a variety of macroecological and biogeographical patterns using a large number of purely habitat datasets sourced from both the literature and my own sampling, with the objective of teasing out any general statistical patterns. The various macroecological and biogeographical patterns can be grouped under four broad headings: 1) species–area relationships (SAR), 2) nestedness, 3) species abundance distributions (SADs), and 4) species incidence functions (function of area). Overall, it was found that there were few hard macroecological generalities that hold in all cases across habitat island systems. This is because most habitat island systems are highly disturbed environments, with a variety of confounding variables and undesirable species (e.g. species associated with human land uses) acting to modulate the patterns of interest. Nonetheless, some clear patterns did emerge. In particular, it was found that the power model was by the far the best general SAR model for habitat islands. The slope of the island species–area relationship (ISAR) was related to the matrix type surrounding archipelagos, such that habitat island ISARs were shallower than true island ISARs. Significant compositional and functional nestedness was rare in habitat island datasets, although island area was seemingly responsible for what nestedness was observed. Species abundance distribution models were found to provide useful information for conservation in fragmented landscape, but the presence of undesirable species substantially affected the shape of the SAD. Species incidence function curves were found to vary across space for a given species, but not in any systematic manner. In conclusion, this thesis finds that the application of standard island biogeography theory to habitat islands is too simplistic. It is hoped that the results of this thesis will act as a catalyst for a more macroecological approach to habitat island research, and a starting point for the development of an integrated theory of habitat islands.

Keywords: biogeography
ecology
habitat fragmentation
macroecology
habitat loss
Advisor: Whittaker, R
Balance beyond work life: an empirical study of older people's time use in the UK

This thesis examines how patterns of time use change in later life and how the way in which older people use their time is related to well-being. Arguing that maintaining balance in time use concerns not only people of working age but matters for people of all ages, we propose an alternative theoretical framework of life balance. This consists of two conceptual models: The Life Balance Triangle and Multidimensional Life Balance (MLB). Using UK time use data, the thesis demonstrates the empirical applicability of these two models in enhancing our understanding of older people's daily lives.
The life balance model, which we built by modifying the theoretical categorisation of time use by Ås (1978) and the work-leisure triangle of Gershuny (2003), identifies and presents alteration in time use across the life course as changes in balance between constraints (committed time) and freedom of choice (discretionary time), controlling for time spent on biological/physiological maintenance (regenerative time). We find the balance shifts towards greater discretionary, and less committed, time in later life, with a significant gender gap. Life stage, which reflects social structure and expectations, rather than biological ageing, was found to be the most influential factor for life balance dynamics. Findings suggest that men may find it more difficult to adjust to life beyond work because of abrupt and greater changes in life balance, which may disrupt their daily time structure.
The multidimensional life balance model challenges the assumption of a linear relationship between the level of activity and well-being of older people. Adapting the Alkire-Foster method (Alkire and Foster, 2011), we propose a threshold-based approach that takes the heterogeneity of older people and multidimensionality of daily life into account, and emphasises overall balance in the level of activities across various activity domains. Results show MLB is associated positively with better self-assessed health, suggesting a threshold effect. We also identify the demographic/socio-economic groups more likely to lack MLB, as well as domains in which most people are deficient. The thesis contributes to work-life balance research by moving beyond paid-work centrality, and to ageing research by providing a multidimensional approach to activities and well-being in later life.

Keywords: life course
wellbeing
time use
time use of older people
later life
work-life balance
Advisor: Leeson, GW
Fisher, K
Measurement of the inclusive jet cross section with the ATLAS detector at the Large Hadron Collider

This thesis presents the measurement of the inclusive jet cross section using data collected in 2010 by the ATLAS detector, with a particular focus on the reconstruction and calibration techniques used for jets in this measurement and on the estimate of the systematic uncertainty on their energy scale. The inclusive jet cross section measurement is used as input to fits of parton distribution functions. Although the PDF analysis in this thesis is preliminary and its main purpose is to serve as a proof of principle for future studies, improvements in the knowledge of the gluon density are observed thanks to the inclusion of ATLAS data.

Keywords: jets
parton distribution functions
QCD
JES
inclusive jet cross section
PDF
Advisor: Cooper-Sarkar, A