VictorJuiz/thesis huggingface dataset:
Fiction and reality in Aristotle's philosophy of geometry

This thesis investigates and attempts to reconstruct Aristotle’s philosophy of geometry. The aim of this work is to tell a plausible story as to how, exactly, Aristotle thought mathematics could work without appealing to Platonic entities. This means investigating, on the one hand, how his account could make sense of mathematical truths and could fit with the mathematical practice of his time, and on the other hand, how it made sense of the application of mathematics to the physical world.
The thesis is divided in two parts. The first part offers a close reading of Metaphysics M.3, and of its two main claims: that geometry is about sensible objects, but not qua sensible, and that geometers are allowed to posit as separate what is in fact not separate. I give a radically anti-Platonist account of geometrical truth, according to which geometry is true in virtue of sensible substances and their properties. However, I claim that Aristotle relies on a moderate form of fictionalism (which only concerns the mode of being of the entities in question) in order to account for geometrical practice.
The second part of the thesis inquires whether Aristotle is justified in assuming that geometry is applicable to sensible reality. I focus in particular on the notion of intelligible matter, and on the role of change in geometry. I find that the applicability of geometry to sensible reality can be granted only by limiting its scope to localised configurations, both in space and in time.

Keywords: geometry
mathematical objects
applicability problem
Aristotle
mathematical truth
Advisor: Coope, U
Peramatzis, M
Nprl3 is a highly conserved regulator of erythropoiesis

The neighbouring genomic positions of Nprl3 and a-globin, which share a topologically associated domain, have been maintained for over 500 million years. Nprl3 contains 4 of the 5 a-globin enhancers in mice, and 3 of 4 in humans. However, the potential functional requirement of this genomic linkage has not been investigated until now.
As part of the Gator-1 complex, the canonical signalling of Nprl3 has been defined in cell lines. Gator-1 provides negative regulation of mTORC1, a critical controller of cellular metabolism. We aimed to confirm this signalling in erythroid cells, and to investigate whether Nprl3 is required during erythropoiesis at steady state. Analysis of Nprl3-/- fetal livers revealed severe impairment of erythroid development. Autophagic flux was significantly dampened in Nprl3-/- erythroblasts, which is a possible driver of the observed block in erythropoiesis.
To discover whether NPRL3 is also required for human erythropoiesis, NPRL3-knockout was induced in primary human CD34+ progenitors using an RNP-editing system. These progenitors demonstrated reduced ability to produce enucleated erythroid cells compared to their negative control counterparts. We also used this model to investigate whether NPRL3 is particularly important in the context of fluctuating nutrients or growth factors. NPRL3-knockout erythroblasts demonstrated defective mTORC1 signalling responses to iron deficiency, amino acid withdrawal and erythropoietin stimulation. This suggested an intriguing role for NPRL3 as an environmental interpreter, which could be particularly important in the highly metabolically active and nutrient-demanding process of erythropoiesis.
We further aimed to characterise the role of Nprl3 in broader haematopoiesis, and to observe whether Nprl3 influences erythroid lineage commitment. In competitive bone marrow - fetal liver chimera experiments, Nprl3-/- fetal liver cells contributed poorly to erythroid lineage reconstitution of irradiated adult bone marrow. An intriguing competitive disadvantage was also observed at the HSC level.
Importantly, Nprl3 expression is known to be elevated in erythroid cells, increasing ~30-fold during erythroid lineage commitment due to a-globin enhancer activity. We sought to discover whether this erythroid-specific increase in Nprl3 expression is required for the functionality outlined above. This was achieved using transgenic mouse models to eliminate all interactions between Nprl3 and the a-globin enhancers, which resulted in impaired erythropoiesis reminiscent of Nprl3-/-.
Overall, in this work we show that Nprl3 is functionally important in erythroid cells, and that this is supported by transcriptional influence of the a-globin enhancers. We hypothesize that the deep evolutionary coupling of a-globin and Nprl3 has enabled the a-globin enhancers to control metabolism, as well as a-globin production, in developing erythroid cells.

Keywords: haematopoiesis
haematopoietic stem cells
red blood cells
erythropoiesis
genomics
cell biology
Advisor: Drakesmith, A
Roy, N
By us alone: army veterans, patriotic values and re-militarization of Russia, 1991-2022

This thesis investigates the aftermath of the Soviet-Afghan war (1979-1989) and two military operations in Chechnya (1994-1996, 1999-2000) and shows that they still have a significant impact on Russian society, influencing it in fundamental ways, from political and social processes down to the socialization of private citizens.
My study contributes to answering two key research questions: in what ways do Russian citizens experience the shifts in social norms, conventions and public discourses brought home by former soldiers? And how exactly did the veterans of these wars become one of the powers supporting the regime? I show how the interests of veterans have been corresponding to, conflicting with, or existing in interplay with, the interests of the state during the last three decades, and how the wars made veterans continue building their self-identity in compliance with the narratives accepted by their comrades-in-arms.
I also examine the social consequences of veterans’ exposure to violence in wartime, which include further violence in later wars, in criminal gangs, and at home. I look at changes in gender norms in post-war society and claim that army service has been crucial for shaping male identity, and a rise in militaristic masculinity became one of the legacies of these wars. The final question that I explore is the role of veterans in the militarization of Russian society through the implementation of the state programmes of “patriotic education”, which also play a significant role in normalizing violence and spreading it throughout Russian society.
The discussion is based on my own semi-structured interviews with war veterans conducted in 2019-2021, and interpreted in terms of narrative analysis. They constitute completely new primary sources which can be used in future research.

Keywords: USSR
war studies
Russia
violence
narrative analysis
war veterans
Chechen war
state propaganda
War in Afghanistan
Advisor: Kelly, C
Zorin, A
Atmospheric circulation on slowly rotating planets in the Solar System, and beyond

Atmospheric circulation on Venus and Titan is characterised by prograde superrotating jets at the equator, and meridional overturning circulations that extend a significant distance towards the poles. Circulation of this type is characteristic of planets that are slowly rotating. By contrast, the atmospheres of the Earth and Mars, which are more rapidly rotating, feature zonal jets in mid-latitudes, and overturning circulation that is confined to the tropics. However, while planetary rotation is likely the main determinant of a given planet’s atmospheric circulation, other factors also have an important influence. This has been illustrated by numerical experiments using models of slowly rotating Earth- like planets, which do not automatically generate Venus or Titan-like circulations.
The aim of this thesis is to improve our understanding of the different circulation regimes that may be obtained on slowly rotating planets. This is achieved by developing a theoretical framework within which the circulation of different slowly rotating planets can be easily compared. Additionally, for the case of Titan, this thesis presents an in- depth investigation of the specific atmospheric phenomena that differentiate it from other slow rotators.
Recently, the array of possible circulation regimes has expanded significantly, due to the discovery of tidally locked planets orbiting stars other than the Sun. If we restrict our attention to temperate planets, then theoretical considerations suggest most will be slowly rotating. Tidally locked planets have a permanent day side and night side, which strongly influences their atmospheric circulation. Consequently, these planets occupy circulation regimes that are different from those exhibited by the slowly rotating planets in the Solar System.
To characterise the atmospheres of slowly rotating tidally locked planets, this thesis proposes a new analysis technique that divides the total circulation into physically meaningful constituent components, in much the same way as the circulation of the Solar System planets is divided into zonal jets and meridional overturning. It is also shown that the proposed decomposition of the circulation can be used to aid the observational characterisation of these planets, by showing how different parts of the decomposed circulation contribute distinct features to a planet’s thermal emission.

Keywords: Solar System planets
exoplanets
atmospheric circulation
Advisor: Read, P
The effects of mTOR inhibition in ischemic stroke

With a global incidence of 9.5 million cases annually and 56 million disability-adjusted life-years, ischemic stroke is the primary cause of adult disability in developed countries. However, the significant successes in stroke trials have been in the field of reperfusion therapies for ischemic stroke, whereas clinical trials focusing on amplifying the brain’s intrinsic neuroprotective pathways have so far been unsuccessful for numerous reasons. One neuroprotective target that has been shown to play an essential role in cell death after stroke is the mammalian target of rapamycin complex 1 (mTORC1), a key regulator of the cells' energy supply, which can be modulated pharmacologically through rapamycin and non-pharmacologically through dietary intervention. The overarching aim of this thesis was to investigate the therapeutic potential of mTOR inhibition in ischemia. I found that post-stroke rapamycin treatment improves cerebral perfusion in the hyperacute phase, decreases lesion volume, and improves functional outcomes at three days in a rat model of focal stroke using magnetic resonance imaging. I then showed that rapamycin application after oxygen-glucose deprivation improves the function of pericytes and endothelial cells in vitro but does not prevent cell death. Finally, I found that fasting following ischemia might be an alternative strategy to improve stroke outcomes by decreasing inflammation, stabilizing the BBB, and reducing stroke volume. Together, these data highlight the potential of therapeutic options beyond reperfusion therapies and suggest that targeting metabolic regulators such as the mTOR pathway using pharmacology or dietary modulation might be effective adjunct therapy options alongside reperfusion for patients suffering from an ischemic stroke.

Keywords: ischemic Stroke
mTOR
rapamycin
fasting
Advisor: Buchan, A
Couch, Y
Ultra-violet photodissociation dynamics of biomolecular building blocks

Velocity-map imaging is a widely used technique for studying the photodissociation dynamics of small systems. The work in this thesis reports on the application of this technique, enhanced by multi-mass imaging capabilities, to the unimolecular photodissociation dynamics of small model molecules for biomolecular building blocks. By employing a universal ionisation source of 118 nm photons, in most cases it is possible to ionise all of the fragments that are produced. This enables measurement of scattering distributions for multiple dissociation products within a single measurement, yielding insight into the detailed multi-channel dissociation dynamics of these systems. The work in this thesis focuses on pump-probe studies of the biologically relevant molecules N,N-dimethylformamide, N-methylformamide and tetrahydrofuran. N,Ndimethylformamide and N-methylformamide provide simple models for the peptide bond found in proteins, whereas tetrahydrofuran is a model for DNA bases. All systems are studied at a photolysis wavelength of 193 nm, and the study of N,Ndimethylformamide is also extended to photolysis wavelengths of 225 and 245 nm. The peptide bond models showed the same bond dissociations regardless of photolysis wavelength used or the number of methyl functional groups attached to the peptide bond. Both peptide bond model systems underwent either peptide bond dissociation or N-methyl bond dissociation. The dissociation of tetrahydrofuran was narrowed down to three main fragmentation pathways involving the cleavage of C-C bonds, each resulting in a fragment with two heavy atoms and the partner fragment having three heavy atoms. All fragments displayed TKER distributions peaking at very low energies, indicating that the majority of the available energy is partitioned into internal excitation. All systems exhibited some involvement of an energetically low-lying mixed state which evolves to possess πσ*/nσ* character at long bond distances, providing a route either for population transfer back to the ground state, or to dissociation. These mixed states are likely to play an important role in the photoprotective mechanisms of many biological chromophores. The gas phase experiments investigated in this thesis provide important dynamical information to help develop a general picture of the dynamics occurring in isolated sub-units of proteins and DNA, an essential piece of the larger puzzle of obtaining a complete mechanistic picture of dynamical processes in these systems. The work in this thesis lays the foundation for studying larger, more complex systems that better represent real-life systems, such as isolated nucleotides and polypeptides.

Keywords: reaction dynamics
photodissociation
biomolecular models
multi-mass imaging
photochemistry
velocity-map imaging
Advisor: Vallance, C
An investigation of the role of mutations in the spliceosome machinery in the myelodysplastic syndromes

The myelodysplastic syndromes (MDS) are common myeloid malignancies. Mutations in splicing factor genes (including SF3B1, SRSF2 and U2AF1) occur in over half of MDS patients and result in aberrant pre-mRNA splicing of many target genes, indicating that aberrant spliceosome function plays a key role in the pathogenesis of MDS. However, the molecular mechanisms through which the splicing factor mutations drive the MDS phenotype are not fully understood. A previous study from our group has shown that the U2AF1S34F mutations induces aberrant splicing of STRAP in cells of the erythroid lineage. We have identified a splicing event of STRAP, identical to the one caused by the U2AF1S34F mutation, in the erythroid precursors of SRSF2 mutant MDS cases. Functional studies demonstrated that knockdown of STRAP leads to inactivation of p38 MAPK and downregulation of CSDE1-bound transcripts, suggesting that underlying mechanism of ineffective erythropoiesis in MDS with low expression of STRAP is caused by SRSF2 mutations. We have also performed an analysis on global splicing alteration using transcriptomic data of splicing factor mutant MDS patients, which revealed that splicing factor mutations (SF3B1 and SRSF2) reshape the mRNA splicing landscape in MDS. This analysis identified that alternative splicing is cell-type dependent and splicing factor mutations alter the pattern of whole mRNA splicing within each bone marrow subpopulation. SRSF2 is the most frequently mutated splicing factor gene with adverse prognosis in MDS. SRSF2 mutations commonly co-occur with mutations of other specific genes, most frequently TET2 and ASXL1. We performed single-cell transcriptomic analysis using the 10X Genomics platform on haematopoietic stem and progenitor cells of MDS patients harbouring SRSF2 mutations and co-mutations of TET2 and/or ASXL1. Cell population composition analysis revealed differences in population abundance across the genotype groups. Differential gene expression analysis unveiled genotype-specific gene expression signatures and dysregulated pathways.

Keywords: MDS
SRSF2
Myelodysplastic syndromes
SF3B1
U2AF1
splicing factor mutation
Advisor: Pellagatti, A
Boultwood, J
Dolatshad, H
Discrete representations of continuous data using deep learning and clustering


The divide between continuous and discrete data is a fundamental one in computer science and mathematics, as well as related areas such as cognitive science. Historically, most of computing has operated in the discrete domain, but connectionism offers an alternative set of techniques for representing data with continuous vectors, an alterative which has come to the fore with the advent of deep learning over the past decade. This thesis explores techniques for converting continuous, high-dimensional data, of the sort processed so successfully by deep learning, to discrete compact representations, of the sort used by traditional computing. Each of the five main chapters introduces a novel technique that contributes towards this goal, but is also able to be read as a stand-alone piece of research. These techniques fall under deep learning and clustering, and, in keeping with representation learning in general, are mostly, though not entirely, in the unsupervised setting. Some chapters focus on deep learning or clustering separately as a means to form discrete representations of continuous data. Others explore how to combine both deep learning and clustering in a single end-to-end learning system. Such a combination itself involves the interface between continuous and discrete, as deep learning operates on the former, and clustering on the latter.
Being able to bridge the gap between the worlds of continuous and discrete also aligns with the original goal of AI to model human intelligence, as an important part of human cognition is the movement between the worlds of continuous and discrete. Our sensory input is largely continuous, but we represent it with a natural language and reasoning apparatus that is largely discrete. A machine that one day thinks and acts as a human will have to learn to do the same.

Keywords: unsupervised learning
artificial intelligence
deep learning
clustering
concept learning
machine learning
Advisor: Lukasiewicz, T
Gal, Y
The role of green ammonia in decarbonised energy systems

Green ammonia is gaining momentum as a globally significant technology for deep decarbonisation. In this thesis, several models are developed across chemical, techno-economic, and energy system modelling disciplines to explore the future role of green ammonia. First, standalone models of production (i.e., power-to-ammonia) and re-electrification (i.e., ammonia-to-power) are developed and compared to competing technologies. Second, these models are integrated into a planning and dispatch energy system model (ESM) of India to 2050. The ESM has several novel additions including the sector coupling of hydrogen and ammonia, multiple years of granular weather data, and learning-curve-based technology cost forecasts. India is chosen as an ideal case study given its globally unmatched demand growth in all three relevant sectors: electricity, green hydrogen, and green ammonia. The projected electricity demands for green hydrogen and ammonia production account for 25% of the total Indian electricity demand in 2050, underscoring the transformational potential that green hydrogen and ammonia sector coupling can have on the Indian energy system.
The results of the state-of-the-art ESM highlight synergistic effects of hydrogen and ammonia sector coupling with the power system. The least-cost system employs seasonal green ammonia production paired with up to 40 million tonnes (i.e., 200 TWh) of ammonia storage, as well as some re-electrification via gas turbines. Sector coupling reduces system curtailment, addresses challenges of long-duration storage, and improves system resilience to interannual weather variations. While India is a crucial case study from a global decarbonisation perspective, the methodology and findings are generally applicable, and it is the aim of this work to motivate and accelerate the wider research community into considering the potential impacts of green ammonia sector coupling on electricity grid design. Finally, this work highlights strategic technology development direction for ammonia producers and gas turbine manufacturers, as well as implications for policymakers.

Keywords: green ammonia
sector coupling
hydrogen
India
power-to-X
Advisor: Bañares-Alcántara, R
Ives, M
Feminine voices of vengeance in Senecan tragedy and its reception

This thesis argues that it is primarily through the revenge of female characters, and that of Medea in particular, that Seneca interrogates the boundary between proportionate and excessive revenge, and explores the problems inherent in like-for-like violence. It further argues that analysing Seneca’s tragedies from the angle of women’s revenge, and then examining some of the reverberations of this theme across the extraordinarily rich reception of Seneca in European drama, and particularly in France, can shed important light on a question that has long proved problematic for students of the tragedies, that is the nature of the relationship between Seneca’s plays and his philosophica. The work contains fourteen chapters structured in three parts. Part I is an analytical survey of all the instances of female revenge across the corpus of eight genuine plays. Part II looks to Seneca’s treatise On Anger (De Ira) for insight into the parameters of revenge in the dramas. The Stoics considered anger, and passion in general, as a product of reason that is not functioning properly. As such, a revenge tragedy depicting an avenger applying rational principles in order to prepare, and then to enact, his or her revenge plan can be analysed in light of the Stoic belief that anger stems from reason. This part of the thesis focuses mainly on Medea and on the Furies, who occupied a prominent role in Stoic philosophical debates relating to the passions. Part III looks to the reception of Seneca in order to illuminate our understanding of the ‘Senecan question’. After giving an account of the reception of Seneca’s tragedies in European drama, I narrow my focus to two French tragedies in particular, the Médée of Jean de La Péruse (1553) and the Médée of Pierre Corneille (1634–5). By citing Médée’s revenge as an illustration of his own controversial stance on the end of tragedy, Corneille gives us an idea of what a Senecan statement in defence of his tragic poetics might have resembled.

Keywords: Seneca
gender
reception
tragedy