VictorJuiz/thesis huggingface dataset:
Communism in context: The Indonesian Communist Party in West Java, 1949-66

This study of the Indonesian Communist Party (Partai Komunis Indonesia, PKI) addresses Indonesian communism as a phenomenon at the intersection of global and local contexts, one shaped by both top-down and bottom-up forces. It argues that the PKI’s experience amid Indonesia’s ecological, social and ethnic diversity provides an important case study in ‘plural communism’ and a ‘de-centred Cold War’. Between 1949 and 1965 the PKI’s membership grew from a few thousand to over three million, before the Party was violently destroyed in the mid-1960s. Although there is a growing body of literature on anti-communist violence of 1965-6, much less has been written about the PKI prior to the purge. The few existing studies of the Party during those years concentrate on developments at a national level and tend to have a top-down emphasis. This dissertation focuses on events in one province to explore how transnational, national and local histories interacted. It combines oral history, contemporary publications, and newly accessible Party archives to recreate Party life in unprecedented depth. The dissertation acknowledges that the PKI’s trajectory was shaped by its national leadership, which engaged in an ongoing dialogue with comrades abroad. However, it argues that it is also essential to understand how the Party navigated cleavages within Indonesian society and unleashed activist energies at the grassroots. The dissertation shows that the PKI became increasingly bureaucratic and hierarchical over time, but argues that it maintained a hybrid nature, as both an organisation and movement that was deeply intertwined with the groundswell of popular mobilisation that characterised Indonesia’s long revolution. The PKI’s destruction, in the mid 1960s, occurred at the intersection of rising Cold War tensions and the emergence of a counter-revolution driven by an evolving anti-communist coalition, a counter-revolution which entailed a dramatic realignment of the socio-political order.

Advisor: Fogg, K
Brain health in ageing and Parkinson's disease

Age-related decline in brain health appears to be inevitable to some extent. In some people, ageing is also associated with additional burden of neurodegenerative diseases, such as Parkinson’s disease (PD). However, distinguishing between normal and pathological ageing trajectories is complicated, as neither are well characterised. This thesis quantifies effects of normal and pathological ageing on mood, motivation, and brain structure, with a focus on PD. In the first part of the thesis, I estimate general effects of healthy ageing on mood and brain structure. I address whether mood generally improves or whether age-related changes to the brain increase risk for mood disorders. I calculate trajectories of grey matter atrophy, and present norm values for one of the most vulnerable brain areas in ageing, the hippocampus. In the second part of the thesis, I investigate how PD affects mood, motivation, and brain structure differently from healthy ageing. Debilitating mood symptoms like apathy and depression are often reported in PD, but it is unclear whether they might be secondary to the disability that patients live with, or a direct result of PD-related pathology. This is tested formally by analysing prevalence of these symptoms and taking into account levels of disability, as well as by investigating effects of serotonergic modulation on affective processing and decision-making. Finally, I evaluate whether these potential differences in PD can be linked to brain structure. The results demonstrate that normal ageing is on average more likely to be associated with improvements in mood. In contrast, PD was linked to higher rates of neuropsychiatric symptoms, even when accounting for levels of disability. This supports the hypothesis that neuropsychiatric symptoms in PD are primarily the result of PD-related brain pathology, rather than due to secondary effects. Serotonergic modulation during behavioural testing further revealed a role for serotonin in apathy that may depend on levels of baseline intrinsic motivation. Finally, while healthy ageing is associated with strong declines in volume in almost all areas of the brain, no robust specific effects of PD on brain structure were found. Together, this work contributes to the search for MRI-based biomarkers of neurodegeneration, as well as the understanding of mood disorders in Parkinson’s disease.

Advisor: MacKay, C
Husain, M
Time-series analysis of B[e] supergiant stars

B[e] supergiant stars (B[e]SGs) are a rare and unusual class of massive evolved stars which are poorly understood. I demonstrate how studying \sgBeshorthand s by analysing time-series observations reveals key information about this stellar class which may help to build a common picture and determine the origin of their phenomena. I utilise spectroscopic data from the Global Jet Watch, which is able to observe astronomical objects with sustained high time-resolution, and describe my contributions to the data reduction pipeline. I access and analyse high-resolution FEROS spectra, and photometry from the ASAS, ASAS-SN, OMC, and TESS surveys.
I take an in-depth case study of the B[e]SG binary GG Carinae, which has been widely studied but poorly understood. I demonstrate that previous determinations of the binary's orbital solution were incorrect and accurately measure it for the first time, finding that the binary is significantly eccentric (e=0.50+/-0.03) and that the system is brightest at periastron. I discovered a pulsation mode in the system from photometric and spectroscopic variability, and analysed it in depth for the first time. The variability has a period of 1.583156+/-0.0002 days and displays amplitude modulation over the binary's orbital period, such that the amplitude of the detected variability is largest just after periastron. The variability is most likely due to an l=2 f-mode pulsation in the primary which is modulated by the time-varying tidal potential in the eccentric orbit. I study the two atomic circumbinary rings of GG Carinae and find evidence of subtle variability of the line centres and the blue-peak to red-peak ratios of the emission lines arising from the inner circumbinary ring over the FEROS observations. I show these variations may be caused due to the binary exciting the circumbinary rings to higher eccentricities over the observation timescales.
A preliminary study utilising TESS and ASAS-SN data of the Galactic B[e]SG sample reveals signatures of binarity in a further three specimens. This increases the ratio of confirmed or suspected binaries in the Galactic B[e]SG population from 4/9 to 7/9, indicating that binarity may be key in understanding the phenomenon. Pulsations similar to those seen in GG Carinae are also detected in at least two further objects for the first time, demonstrating that pulsations may also be a commonality of the class.

Keywords: astrophysics
B[e] supergiant
binary star
GG Carinae
stellar physics
Advisor: Blundell, K
Multiplicative relations among special points of modular and Shimura curves

We consider a number of Diophantine problems for (mixed) Shimura varieties. Specifically, we look at the multiplicative relations satisfied by special points of modular and Shimura curves. These problems are closely related to the André--Oort and Zilber--Pink conjectures, and we will resolve some special cases of these conjectures.
Let Y
be a modular or Shimura curve. Let V⊂Y×Gm
be an algebraic correspondence defined over
¯
Q
. For each n≥1
, we prove that all multiplicative dependencies among n
V
-images of special points of Y
belong to one of finitely many components of Vn
of a particular special kind.
We then strengthen this result in the case that Y
is the modular curve Y(1)=SL2(Z)∖H
and V
is the graph of a (suitably generic) rational function. In this case, we prove that, for each n≥1
, there are only finitely many n
-tuples of distinct V
-images of special points which are multiplicatively dependent and minimal for this property. The key ingredient in this strengthening is a functional multiplicative independence statement for modular functions, which we prove.
Finally, we give a complete classification of the triples of singular moduli which have rational product. We show that all such triples are trivial'' in a suitable sense. This establishes a completely explicit André--Oort statement for the family of cubic surfaces defined (in C3
) by an equation x1x2x3=α∈Q
.

Keywords: André--Oort conjecture
unlikely intersections
modular functions
O-minimality
Zilber--Pink conjecture
Advisor: Pila, J
Viral haemorrhagic fevers in pregnancy with a focus on lassa fever

The viral haemorrhagic fevers (VHFs) are thought to be major causes of morbidity and mortality in pregnant women. However, there remains a paucity of evidence in pregnancy, due in part to the exclusion of pregnant women from clinical trials. The recent occurrence of large VHF outbreaks, coupled with the increased vulnerability of Sub-Saharan Africa to VHF epidemics, particularly in areas reporting high poverty and high maternal mortality increases the importance of improving our understanding of VHFs in pregnancy.
The thesis sets out to generate evidence to inform disease control and clinical trial design and implementation by investigating the epidemiology of the VHFs in pregnancy and exploring issues around trial implementation. It consists of three results chapters. Chapter 2 is an epidemiological evidence synthesis of the priority VHFs in pregnancy. It identifies research gaps and facilitates selection of one of the VHFs for in-depth study. Chapter 3 sets the stage for the next two results chapters. Chapter 4 investigates three gaps in the epidemiology of Lassa fever in pregnancy. Specifically, prevalence, incidence, and risk factors for Lassa fever, and begins work on the kinetics of Lassa antibodies in pregnancy by presenting evidence regarding transplacental transfer of Lassa antibodies. Chapter 5 explores issues around trial implementation by generating qualitative evidence specific to participation, recruitment, and retention of pregnant women in Lassa fever clinical trials.
The thesis presents new data on the epidemiology of the VHFs in pregnancy, particularly Lassa fever, which facilitates estimation of disease burden and, as such inform policy for disease control and drug and vaccine development. It describes trial design and implementation issues that arise with respect to the inclusion of pregnant women in clinical trials and suggests relevant actors and subject areas for effective trial implementation.

Keywords: pregnancy
clinical trial participation
vaccine trials
lassa fever
seroconversion
transplacental transfer
seroprevalence
viral haemorrhagic fever
Advisor: Horby, P
Ariana, P
Understanding Valanginian continental climate using δ18O from sphaerosiderites as a proxy for precipitation

Terrestrial and marine carbon isotopes record a significant perturbation of the global carbon cycle during the Valanginian: the Valanginian positive Carbon Isotope Event (CIE). The CIE was associated with warm, invariant, low-latitude sea surface temperatures, increased humidity, and ocean fertilization. Although marine changes are well documented, terrestrial temperatures and hydrological response during the CIE are not yet fully understood. The non-marine Wealden Supergroup of Southern England (Berriasian–Hauterivian) provides an ideal record for reconstructing low-latitude continental palaeoclimate during the CIE. These strata contain abundant sphaerosiderites, spherical iron carbonate concretions (FeCO3), which formed mainly in wetland environments and are thought to record meteoric δ18Ogroundwater reflective of regional hydrology. Wealden δ18Osiderite varies between –3.5‰ and 0.6‰ VPDB, Δ47 temperatures are 33–39° C, and reconstructed groundwater values are isotopically heavy (–3.7‰ to 2.6‰ VSMOW). Compositional and morphological heterogeneity of the sphaerosiderites, comparison to experimental siderite syntheses, isotope transects of individual spheres, high Δ47 temperatures, and comparisons to climate models suggest that the sphaerosiderites are a seasonally, summer-biased palaeohydrological record.
The δ18Osiderite values from sphaerosiderite horizons alternate between isotopically heavy and light values, interpreted as drier (less precipitation/higher evaporation) and wetter (higher precipitation/less evaporation) conditions, respectively. Correlation to marine records using carbon isotope stratigraphy suggests synchronous relatively arid periods at the onset of the CIE, and just proceeding the peak of the CIE. A peak in humidity observed in the Tethyan realm during the peak of the CIE cannot be assessed conclusively in the Weald basin, due to poor siderite and organic matter preservation in the Wadhurst Clay. A facies-specific δ13Corg shift and these poorly-preserved sphaerosiderites suggest a significant palaeoenvironmental change during deposition of the Wadhurst Clay, which needs further assessment. The geochemical records from the Weald Basin indicate that low-latitude terrestrial temperatures continued to be warm during the Valanginian CIE, supporting evidence from sea surface temperature reconstructions, and that there was periodic enhancement of the hydrological cycle during the Valanginian.

Keywords: Valanginian
Wealden
sphaerosiderite
cretaceous
Advisor: Robinson, S
Tosca, N
Pudeur, place, and print: modesty, agency, and collaboration in sixteenth-century French women’s writing

This thesis considers responses to modesty in the works of four sixteenth-century French women writers who work with and reclaim modesty in different ways. I focus on Marguerite de Navarre, the Dames des Roches, and Gabrielle de Coignard who span the sixteenth century and operate in different locations: Nérac, Poitiers, and Toulouse. Firstly, I examine how far their works reflect discourses of modesty in circulation, and whether these responses are shaped by the locations, physical and thematic, in which they live. Occasionally tracking (im)pudeur and cognate terms, this exploration mainly offers textual commentaries on these key terms: virginity, chastity, desire, sex, the female body, nudity, shame, and silence. I document how the importance of modesty changes over time and the shifts or movement between locations in the production and circulation of texts, from salon-type structures to printed works. The process becomes more complex when considering common associations between print and sexual deviance which compromised a woman’s modesty. A second aspect of this thesis explores a creative response to this nexus, which I term ‘collaborative modesty’: networks of male and female collaborators that influence the composition, publication, and reception of women writers’ texts. Alongside the intervention of male figures, a striking mother-daughter relationship emerges; daughters play a vital role in how their mothers are received in print, contemporarily and retrospectively. This thesis reconsiders understandings of early modern French women writers as ‘submissive’ or ‘subversive’, by focusing on the agency that they achieve within the confines of society. Secondly, it offers a new concept of collaboration which dispels the myth of ‘male genius’ that for too long defined understandings of authorship. Literary collaboration is translocational and transactional; it does not simply consist of poets and writers. ‘Modest’ figures such as daughters, printers, and editors, all play an important role in literary creation.

Keywords: women's writing
early modern France
print
Marguerite de Navarre
literary collaboration
women and agency
pudeur
collaborative modesty
Dames des Roches
Gabrielle de Coignard
modesty
Advisor: Williams, W
The doctrine of the mean in Aristotle’s ethics

In this thesis I build on the scholarship on Aristotle’s doctrine of the mean that has proposed an interpretation closely connected to ideas of harmony and especially Aristotle’s notion of the καλόν. The central question of this paper is whether Aristotle’s application of the idea of harmony to ethics presents, as for example Hursthouse has argued, a fruitless spillover of a vacuous principle or rather a substantial ethical position. As a first step, I will argue that Aristotle envisages the doctrine of the mean to be at its core concerned with the intensity of a person’s affective response. Having established this central connection of the doctrine with the emotions, I will situate the emotions in the wider terrain of Aristotle’s ethics in particular with respect to moral formation and motivation. Having followed the argument for a reading of the mean as tied to ideas of harmony, as epitomised in Aristotle’s notion of the καλόν, I contrast two fundamentally different readings of the harmony Aristotle envisages. McDowell seems to suggest that such a harmony stems from a silencing of contrary reasons due to the distinct perception of the virtuous person, while Hartmann, who seems largely overlooked in the anglophone debate, understands the mean as the expression of a fundamental tension at the heart of ethics. In light of the textual material in the Nicomachean Ethics, I argue against McDowell’s silencing account as an interpretation of Aristotle and building on Hartmann argue that the doctrine of the mean may be read as a position of substantial insight in terms of ethics and moral psychology. In particular, I argue, the doctrine of the mean may be read as capturing the remarkable dual demands the virtuous person has to integrate on the level of personality. The contrast between McDowell and Hartmann, furthermore, elucidates what I read as Aristotle’s attempt to accommodate for two distinct senses of human excellence – one as essentially responsive, the other informed by and reflecting a correct understanding of values.

Keywords: Doctrine of the mean
Hartmann
McDowell
Silencing account
Aristotle
Advisor: Crisp, R
Mathematical modelling and computational simulation studies of flagellate motility

In this thesis, we explore different topics in the broad field of microscale swimming, focussing on microswimmers that propel themselves via slender appendages known as flagella. There is a wealth of biological examples, including helically driven bacteria, such as E. coli, and the well known and well studied human spermatozoon. Commensurate with this variety of examples from which microswimmer study draws inspiration and motivation, potential applications of developed understanding of this microscale world are also broad, spanning industry and medicine, particularly with the recent advent of synthetic microswimmers. Driven by open questions in both biology and the theory of swimming at low Reynolds number, we investigate the behaviours of two flagellated organisms, one canonical and one lesser studied, in a range of computationally simulated microenvironments, from confined to multiswimmer settings. We form approximate dynamical systems for each of these model scenarios, averaging over the relatively short period of the flagellar beat, enabling thorough analysis of the dynamics via the resulting phase planes. Fundamental to these studies is knowledge of the motion of the flagellum, which we seek out from experimental data for the swimmer Leishmania mexicana, though we later relax this assumption of kinematic knowledge and move to consider the so-called elastohydrodynamic problem, in which fluid dynamics and elasticity can reshape the flagellar beat. We look towards realising systematic improvements to the accuracy of modern elastohydrodynamic techniques and, further, significantly broaden the scope of recent efficient methodologies to address the three-dimensional motion of slender elastic bodies in viscous fluid.

Advisor: Gaffney, E
Design of modulatory peptides against chemokines

Chemotactic cytokines or chemokines are small signalling proteins responsible for the recruitment of leukocytes to sites of inflammation. Although, chemokines are critical to orchestrate effective immune response, many have been associated to several inflammatory disorders. Despite being recognised as therapeutic target, no efficient treatments targeting the chemokine network for inflammatory diseases are available to date. This is attributed with the complexity of the many and varied chemokine interactions with themselves, their receptors and glycosaminoglycans on extracellular matrix. Thus, the pharmaceutical industry dogma of “one molecule, one target” is rendered ineffective against this network. Evasins are small tick saliva proteins that can bind and neutralise several chemokines, therefore allowing the tick to feed on their host for days without sparking an immune response. The potential of Evasins as effective anti-inflammatory agents was proven in many pre-clinical disease models. The interest in Evasins led to the discovery of a novel Evasin, P672, that can bind a wide range of CC chemokines. This work describes the discovery of peptides inspired by the chemokine binding site of P672. These peptides were shown to neutralise several chemokines and exhibited in vivo anti-inflammatory activity. A novel generation of P672-inspired peptides were designed and exhibited multiple chemokine-binding properties with increased human plasma resistance. Finally, P672/chemokine interfaces were mapped using peptide display techniques informing on P672 binding sites and its mode of action to neutralise chemokines. This work demonstrates the exciting potential of utilising Evasin/chemokine interaction studies with informed mode of action as starting points for anti-inflammatory peptide development.

Keywords: inflammation
chemokine
CCL8
evasin
peptide
tick
Advisor: Kawamura, A
Bhattacharya, S
Generation and analysis of attack graphs on computer networks

The complexity of computer network attacks requires a sophisticated understanding of network security. Attackers combine seemingly inconsequential vulnerabilities into damaging attacks. Attack graphs compactly represent the possible ways exploits can be combined in the network by attackers. Armed with an accurate, up-to-date and sufficiently-detailed attack graph model, network defenders could straightforwardly select the most critical vulnerabilities and weaknesses in their network, allowing them to perform the necessary actions to optimally mitigate the threat.
But attack graphs suffer from a number of problems that stand in the way. They rely heavily on data sources that were not intended to be used for this purpose, and have not been demonstrated to be reliable enough. Graphical models frequently suffer from complexity problems, and attack graphs are no exception. Once an attack graph is constructed, it requires analysis methods that are hard to verify, making any conclusions hard to justify.
In this thesis, I address each of these problems through a variety of theoretical methods. I begin by establishing a clear definition of attack graph, based on template-matching methods. This is used to provide a set of comparisons by which attack graph analysis techniques can be verified theoretically, demonstrating that some common analysis methods perform unreasonable assessments. From this basis, I examine the assumptions that underlie attack graph models, and propose two novel assumptions, the single-precondition assumption and the partitioned-preconditioned assumption. I also provide a motivating smart home example, together with a dataset of vulnerabilities.
I provide two independent contributions towards the generation and analysis of attack graphs; the first is a method to construct attack graphs without vulnerability data, making them easier to construct and allowing them to model zero-day vulnerabilities. The second is a method to parametrise attack graphs, enabling analysis to incorporate characteristics of the attacker and decisions of the defender, so that analysis can be performed across the full spectrum of possible attackers and defender decisions. Finally, these techniques are combined and presented with a collection of possible analysis methods, and applied to the smart home use case through a software implementation.

Keywords: attack graphs
cybersecurity
network security
Advisor: Goldsmith, M
Happa, J