VictorJuiz/thesis huggingface dataset:
Ḥisba and Maṣlaḥa as political thought: Fadlallah and Khomeini compared

This dissertation explores how ethical and political concepts inform and bolster theories of sovereignty in modern Islamic political thought. Commanding right and forbidding wrong, as an ethical-social concept, and maṣlaḥa, as a political concept, are intimately connected in Muslim formulations of state and good governance in the modern period. In other words, when mobilised together, the two constitute a comprehensive claim to sovereignty; where commanding right and forbidding wrong addresses social ethics related to sound public and private conduct, maṣlaḥa is used for legal decisions and national interest. Placing Ayatullah Muḥammad Ḥusayn Faḍlallah (d. 2010) in conversation with Ayatullah Rūḥallah Mūsavī Khumaynī (d. 1989) demonstrates most clearly the spectrum of debate on these concepts as they relate to sovereignty in Shi‘i political thought. On the one hand, Fadlallah developed his ideas on sovereignty primarily within the precarious political environment during and after Lebanon’s Civil War, when a strong centralised state was absent, and in which he promoted a politically integrous and ethically just community. Khomeini, on the other hand, wrote from within a centralised and secular monarchy, and subsequently from exile, to promote an Islamic state with juridical rule. This work examines how both scholars linked commanding right and forbidding wrong with maṣlaḥa to themes of law, the public-private spheres, gender, and state. Doing so, I demonstrate how and why these two concepts are appealing for contemporary Islamic politics and in which ways they are effective weapons for politics and sovereign claims.

Keywords: sovereignty
Ayatollah Khomeini
Iranian Revolution
Ayatollah Fadlallah
hisba
maslaha
Advisor: Devji, F
Herzig, E
Transcriptional regulation at the angiogenic sprout

Angiogenesis, the formation of new blood vessels from existing ones, depends on very precise spatio-temporal gene expression patterns in different sub-types of endothelial cells. These patterns are controlled by pro-angiogenic stimuli but the transcriptional mechanism by which these stimuli induce specific gene expression in endothelial cells is not well understood. In this thesis I identify and characterize a novel sprouting-specific enhancer upstream of the angiogenesis-specific H2.0-like homeobox protein (HLX/hlx) gene. This conserved enhancer, termed HLX-3/hlx-3, is able to direct gene expression specifically and selectively to angiogenic endothelial cells in both transgenic zebrafish and mice during physiological and pathological angiogenesis. Analysis of the transcription factor binding sites within the HLX-3/hlx-3 enhancer reveals a requirement for myocyte enhancer factor-2 (MEF2) family members for enhancer activity. Endothelial-specific Mef2A/C knockout results in reduced sprouting in the mouse retina, confirming an important role for MEF2 factors in the regulation of both Hlx and sprouting angiogenesis more generally. Further, I use the hlx-3:GFP transgenic zebrafish line to generate a genome-wide map of accessible chromatin regions from isolated sprouting cells, and compare them to arterial and venous endothelial cells. My results demonstrate that accessible chromatin is not sufficient to reliably predict enhancer activity patterns, and that within the endothelial-lineage, regulatory elements are constitutively open irrespective of the sub-endothelial cell type. Interestingly, despite these observations, binding motifs for MEF2C and angiogenic-associated transcription factors are enriched in sprouting endothelial cells. These results provide novel insights into the transcriptional regulatory landscape of endothelial cells and confirm the importance of MEF2 factors during angiogenesis.

Keywords: Sprouting angiogenesis
ATAC-seq
Endothelial cells
HLX regulation
Zebrafish
MEF2 transcription factors
Advisor: De Val, S
Goding, C
The impact of iron technology on the economy of the Aegean and Cyprus from 1200-850 BCE

The thesis investigates the development of ironworking industries in the Aegean and Cyprus during the Early Iron Age, covering the crucial years from the twelfth to the ninth centuries BCE. It advocates for a move away from pan-Mediterranean models that rely on a centre of ‘innovation’ from which the technology radiated to new regions via itinerant craftsmen. It argues instead for the development of models based on region-specific cultural and economic factors that influenced iron production and use. This comparative method reveals that the iron industries of the Aegean and Cyprus developed along separate trajectories.
This thesis shows that iron objects were locally produced in the Mycenaean sphere during the Late Bronze Age. The Aegean did not depend on itinerant craftsmen from Cyprus to stimulate ironworking, but it was instead a local tradition that continued through the end of the palatial period in the Peloponnese. Iron spread throughout the Aegean in the ensuing century, with each region adapting objects to iron according to how it was valued. In the Peloponnese, iron was suitable for practical implements immediately, while Attica, Crete, Euboea, and the islands emphasised a high value ornamental purpose in mortuary display. By the 10th century, the standardisation of burial rituals during the Protogeometric integrated iron into general use across the Aegean. It became a widely produced, moderately valued metal for daily use implements like tools, as well as a regular part of mortuary display.
In Cyprus, ironworking sprang up rapidly across the island, and without a Bronze Age tradition. It began as part of a package that included the arrival of Urnfield-type goods from the Aegean, iron being the more appropriate than bronze for items such as knives, daggers, fibulae, obeloi. Iron was applied in two spheres immediately, to tools of practical use and to high value mortuary display items. Local production due to the lack of ore sources in favour for a copper-smelting by-product method remains debatable, but Cypriot smiths were capable of mass-producing a series of knives. The iron industry did not disrupt but developed alongside the Early Iron Age investments made in the copper industry.

Keywords: iron
Early Iron Age
metalworking
bronzeworking
apprenticeship
forge
iron working
Greece
Late Bronze Age
iron knives
metals
ironworking
smith
Cyprus
ingot
metallurgy
apprentice
metal trade
billet
blacksmith
smelting
Advisor: Lemos, I
Studying partially ordered systems using stochastic differential equations

This thesis looks at two different problems in the field of partially ordered systems - modelling biopolymers on multiple scales as well as modelling two-dimensional nematic liquid crystal wells - and seeks to gain insight using stochastic differential equations, through mathematical analysis and numerical simulations.
In the field of biopolymers, we generalize existing models for a coarse-grained polymer to multiple resolutions, which allows for faster computations while maintaining a high level of detail in regions of interest. This is done for two bead spring models; the Rouse model, which does not account for hydrodynamic interactions, as well as the bead-spring model with hydrodynamic interactions. For both models mathematical analysis is done to find expressions for global statistics to derive scaling laws for the models. This is implemented by generalizing existing algorithms using a multi-resolution approach which utilizes multiple spatial and temporal scales. These simulations show that the scaling laws for multiple resolutions match expected analytic results through simulations. For the Rouse model, a model for the binding of a protein to DNA is introduced, along with a mechanism for changing resolutions along the filament on-the-fly. Within reasonable error, the results for the chain in multiple resolutions matches the chain modelled entirely in high-resolution.
The work on nematic liquid crystals is concerned with a stochastic dynamics model of nematic liquid crystals contained within a square well, looking at their behaviour under Brownian motion using the Gay-Berne potential. In particular, we are interested in the parameter regimes which are responsible for different types of steady states to form in the system and whether steady states suggested by continuum modelling are stable.

Keywords: Stochastic Differential Equation
Brownian Motion
Advisor: Erban, R
Electronic transport in magnetic materials at diﬀerent dimensionalities

The miniaturisation of devices has become of paramount importance in modern technology in the last century. Since then, the lower bound of the nanotech world has been pushed down until the molecular and atomic scale. At these dimensions, classic and quantum processes coexist both for magnetic and electric phenomena. This is creating a physical limit for modern silicon-based technologies based on classic transport. Molecular spintronics is one of the most promising approaches to overcome these limits. This field relies on the exploitation of single-molecules magnets, the smallest possible molecular magnets that can be created. Not only it allows for the ultimate electrical miniaturisation to the molecular scale, but it also has the potential to unlock the power of quantum computation. However, the electric transport properties and the magnetic interaction with the environment at this scale require more investigation.
The present work focuses on the charge transport in molecular magnetic materials through different dimensionalities. We begin the journey by analysing microscopic crystals of nitronyl-nitroxide radicals, getting an insight on their conduction channels through space-charge-limited currents. We then scale down one dimension, and analyse thin-film devices based on rare-earth single-molecule magnets, to verify their behaviour when deposited on surfaces. Finally, we embed graphene nanoribbons and rare-earth single-molecule magnets in graphene break junctions, unravelling their magnetic properties as single-molecule transistor.

Advisor: Bogani, L
Transcriptional and epigenetic mechanisms of promiscuous gene expression by thymic epithelial cells

The thymus is the primary lymphoid organ responsible for the generation and selection of a T-cell repertoire that is able to respond to foreign antigens whilst remaining tolerant to self. For the purposes of T-cell central tolerance induction thymic epithelial cells (TEC) express almost all protein coding genes in a process termed promiscuous gene expression (PGE), which is partly under the control of the Autoimmune Regulator (AIRE). Many aspects of the molecular mechanisms underlying PGE in TEC remain unclear. It has not yet been conclusively established whether PGE within single mTEC is a stochastic or coordinated process. The mechanisms that target AIRE to tissue-restricted genes (TRGs) are also incompletely defined, with previous studies suggesting that interaction partners of AIRE may localise AIRE to repressive epigenetic marks associated with TRGs in TEC. The first part of this study examines the transcriptional patterns associated with PGE in single mTEC. Analysis of the transcriptomes of 6,894 single mTEC revealed 50 robustly defined co-expression groups supporting the hypothesis that PGE in individual mTEC is a highly ordered process. The second part of this study addresses the role of a putative AIRE interaction partner, Chromodomain-helicase-DNA-binding protein 4 (CHD4), in TEC biology. Using a variety of cellular and molecular tools, CHD4 was demonstrated to play important roles in TEC development, architectural organisation and function. In particular, CHD4 was found to cooperate functionally with AIRE to induce the promiscuous expression of AIRE-induced TRGs found in particularly repressive chromatin contexts and was consequently required for proper T-cell central tolerance induction.

Keywords: Thymic epithelial cells
Promiscuous gene expression
Thymus
Central tolerance
Immunology
Advisor: Hollander, G
Aerosol effects on microphysical processes and deep convective clouds

Aerosol–cloud interactions are an essential feature of the Earth’s climate system. How- ever, aerosol effects on deep convection are highly uncertain. Different conceptual models for the effects of aerosols on deep convective clouds have been proposed, and assessments based on both models and observations show a wide range of results. This thesis aims at unravelling the cloud microphysical pathways involved in these interactions using a hier- archy of different model simulations and novel analysis tools. A detailed pathway ana- lysis based on microphysical process rates for individually tracked clouds is developed and applied to idealised supercell simulations with three different microphysics schemes in a cloud-resolving model (CRM). This reveals both consistent responses between the schemes, e.g. a suppression of warm rain formation and elevated freezing, and signific- ant differences between the schemes due to the definition of hydrometeor classes and microphysical processes. The cloud tracking framework tobac is developed to provide a consistent way to perform analyses resolving the time evolution of individual clouds in a wide range of datasets. Its application is demonstrated for both CRM simulation results and geostationary satellite data. The cloud tracking and the pathway analysis are combined to investigate deep convective clouds in a large case study simulation and their aerosol response for two different CRMs. Separating the tracked clouds into different categories and compositing along a relative time axis allows for a detailed assessment of the cloud microphysics that resolves the time evolution of the clouds. Despite some similar aerosol responses like a suppression of warm-rain formation and surface precipit- ation, the analyses highlight significant differences in the cloud types and cloud evolution simulated by the two models, especially regarding the mixed- and ice-phase processes. The detailed investigation of the microphysical evolution of individually tracked clouds reveals important pathways for aerosol effects on deep convective clouds and substantial uncertainties that arise from the representation of microphysical processes in numerical models.

Keywords: Microphysics
Aerosols
Atmospheric physics
Deep convection
Numerical weather prediction
Climate modelling
Weather modelling
Aerosol–cloud interactions
Deep convective clouds
Convection
Microphysical processes
Tracking
Python
Cloud tracking
Clouds
Convective clouds
Numercial modelling
Cloud physics
Cloud ice
Thunderstorms
Mixed-phase clouds
Aerosol indirect effect
Cloud microphysics
Advisor: Stier, P
Planning for pleasure: Plato on hedonist prudentialism

Plato has a sustained interest in pleasure, and he represents Socrates in dialogue with hedonists repeatedly. Usually this is to critique them, and frequently it involves arguing not just that they seek the wrong life, but that they will fail to get the life of pleasure they do seek. Two pressing questions arise: what exactly does Plato take to be the fatal flaw in the hedonists’ plans? And, given that flaw, why does he return to the subject of hedonist prudentialism recurrently?
In ‘Planning for Pleasure: Plato on Hedonist Prudentialism’, I confront these interpretive questions by analysing Plato’s views on hedonist prudentialism (Chapter One), by looking at specific passages representing confrontations with hedonist views in Protagoras 356b-357e (Chapter Two), Gorgias 492e-493d (Chapter Three), Republic IX 583c-585a (Chapter Four), and Philebus 20b-23a (Chapter Five), and by arguing for an alternative understanding of Plato’s attitude to how we relate to pleasure (Conclusion).
Against existing characterisations of this development which understand it as increasingly pessimistic about pleasure, I argue instead that Plato develops an increasingly fine-grained conception of pleasure, becoming suspicious of only some types as he goes along, while becoming more enthusiastic about others. His focus shifts to putting ourselves in the right position to accurately judge pleasures and what will please us – a position which, he is increasingly aware, is difficult to occupy.
My thesis makes a clear contribution to this debate in providing an alternative to the more sceptical view. I encourage the re-evaluation of familiar texts, and raise new questions and avenues of inquiry. I contribute to current debates about Plato’s understanding of the nature and role of pleasure in the good life, and highlight implications relevant to modern discussions of pleasure and prudentialism, in order to show how Plato’s views remain philosophically relevant.

Advisor: Nielsen, KM
Origen and prophecy

This thesis is an attempt to understand prophecy in the thought of Origen of Alexandria.
There is no speculative theological work of Origen (or, indeed, of any other Church writer of his period) on prophecy as a theological category in its own right. Yet prophecy lies at the heart of Christian understandings of the world, as a topic which intersects with all of the most complex questions of theological philosophy – free will, foreknowledge, eschatology, soteriology, cosmology. To understand the thought of Origen, who is frequently characterised as the first systematic theologian, we must have some understanding of his concept of prophecy.
The overall argument of the thesis is that Origen was the first Christian writer to attempt to unite disparate notions of prophecy – as future-telling, ethical instruction, and mystical revelation – in order to counter the challenges to Christianity put forward both by breakaway Christian movements and by Jewish and pagan critics. To do so I propose a new framework for understanding how Origen thought about prophecy. I argue that Origen understood prophecy as tripartite in the same way in which he understood scripture as tripartite: that is, as a layered phenomenon of ‘somatic’ or bodily readings, ‘psychic’ or moral readings, and ‘pneumatic’ or spiritual readings. In demonstrating this tripartite structure, I make the case that prophecy and exegesis are, in Origen’s thought, mirror-images of one another, reflected in the mirror of Christ.

Keywords: Origen
prophecy
exegesis
free will
allegory
prediction
Advisor: Edwards, M
Zeta functions and modularity of Calabi-Yau manifolds

We study the Dwork operator U(λ) on a four dimensional subspace of the Dwork cohomology in the large structure limit of a one parameter family of quintic threefolds. The Dwork cohomology becomes singular in this limit, but we recover it by introducing formal logarithmic states which remain well defined at λ = 0. In a suitable basis, U(0) is known to have a single nonzero off-diagonal component at the large structure point, whose value is a rational multiple of ζp(3). We compute the value of this off-diagonal component via a direct computation in our "logarithmic Dwork cohomology" at λ =0$, and obtain an expansion for U(λ) around λ=0.
This expansion provides an efficient means to compute a quartic factor R(T) of the local zeta function, not just for the quintic but for a large number of one parameter families of Calabi-Yau manifolds. We exploit the miraculous fact that U(λ) becomes a rational function mod p4 to avoid evaluating the series for U(λ) directly. This is vital to the performance of the computation for large primes.
The behaviour of the zeta function at singular values of the parameter is particularly interesting. The Weil conjectures ensure rationality, but say nothing about the form of the zeta function when the variety is singular. What generally happens is that one or more eigenvalues of U(λ) go to zero and the degree of R(T) falls. Typically a quadratic factor occurs in R(T) with which a modular form can be associated. For a number of one parameter families, we evaluate R(T) at the singular points, for 7 ≤ p ≤ 97, and seek to identify the associated modular form. We reproduce various known results with higher certainty by checking up to p=97. We identify modular forms in many new cases, including Hilbert modular forms of parallel weight 4 at irrational conifold singularities.

Advisor: Candelas, P
Keeping Britannia afloat: the challenges of maintaining a proportionate grand strategy

Why do states fail to adjust to changes in the relative distribution of power? Some overreact against perceived threats and find themselves overstretched; they may have committed an excessive amount of limited resources to tackle the threat, become party to a burdensome number of entangling alliances, or simply taken on too many adversaries. In contrast, others underreach and pursue overly conservative goals that are not commensurate with their security interests. Their forces might be too few or ill-prepared for the threat they face, or they may lack a sufficient number of allies. This thesis therefore seeks to explain the poor quality of states’ grand strategies and why they often end up doing too much or too little. Unfortunately, the literature on grand strategy is not up to the task. Using a neoclassical realist framework, I argue that we must look inside the “black box” of the state if we are to understand how policymakers perceive and respond to changes in the international environment. The thesis employs a range of qualitative methods, including archival research and process tracing, in order to highlight the importance of unit-level intervening variables, such as individual biases and domestic veto players, on the process of grand strategy. I look at three past cases of British grand strategy: the Second World War, the withdrawal from East of Suez, and the 2003 Iraq War. I argue that the imminence and proximity of external threats shapes who makes decisions and how effectively they do so. A proportionate grand strategy is more likely when the state faces an existential challenge. In contrast, decision-makers in benign security environments are more likely to become distracted and focus on parochial interests. The thesis concludes with policy recommendations and a call to action for greater engagement with strategic studies in the United Kingdom.

Advisor: Johnson, D
Johnson, R
Determinism, moralism, and rationalism

This thesis examines several historical ideas that were prevalent in British intellectual life between the 1920s and 1960s. It regards the philosophy of history not as a theorisation of history, but as an intellectual activity participated in not only by philosophers and theorists, but also historians and literary critics as public intellectuals. Therefore, this thesis is neither a disciplinary study of the ‘philosophy of history’, nor a philosophical treatise that either makes a case for, or repudiates, a Hegelian, metaphysical conception of history. Rather, it is a work of intellectual history that not only seeks to explore how conceptualising the historical process was related to the political, religious, and philosophical contexts during this period, but also attempts to argue that these conceptions of history informed and underpinned many intellectuals’ political views and religious attitudes. Specifically, it tries to investigate several important debates in British intellectual culture over different, and sometimes antagonistic, presuppositions of the meaning and driving force of history. It illustrates the ways in which the relationships between morality and rationality in history were discussed, and argues that disagreements about the nature of history often arose from irreconcilable moral, philosophical and religious standpoints. It also shows that making projections about the future either by drawing historical parallels or by discovering irreversible historical tendencies in the past tended to be accepted by people living in an age that lacks certainty, but it became unacceptable to many when its determinist and teleological implications were underlined.

Advisor: Young, B