VictorJuiz/thesis huggingface dataset:
Higgs bundles for N=1 gauge theories

We consider two constructions of 4d N = 1 gauge theories in M-theory. The first is purely geometric and involves compactifying M-theory on singular manifolds of G2-holonomy. The geometries studied are ALE-fibered over a compact base M3. This fibration admits a description in terms of a Higgs bundle with three-dimensional base M3 which arises as the BPS equations of M-theory reduced adiabatically along the ALE fibers. The gauge theory sector of these compactifications originates from M2-branes wrapped on vanishing cycles of the ALE fibration with interactions set by Euclidean M2-branes wrapped on associative submanifolds traced out by the vanishing cycles. The first part of this thesis develops the physics of these models and introduces a colored supersymmetric quantum mechanics organizing and quantifying non-perturbative effects due to M2-brane instantons. In this framework we study the local models of twisted connected sum G2-manifolds and describe their possible chiral deformations.
The second construction considered in this thesis utilizes M5-branes wrapped on Rie- mann surfaces embedded in local Calabi-Yau threefolds. We focus on the subset of such configurations derived from 4d N = 2 theories of class S breaking to N = 1. Their BPS equations construct Higgs bundles differing from the standard class S Higgs bundle by an additional Higgs field. The associated N = 1 curve collects the spectral data of both Higgs fields and different curves describe distinct vacua of the same gauge theory. The second part of this thesis studies the construction of such Higgs bundles and derives the confinement properties of each vacuum from the associated N = 1 curve. This allows for the study of confinement in non-Lagrangian N = 1 theories which is illustrated by constructing an infinite class of non-Lagrangian N = 1 theories that contain confining vacua.

Keywords: G2-manifold
M-theory
Higgs Bundle
class S
supersymmetric quantum mechanics
Advisor: Schafer-Nameki, S
Translational investigation of circadian rhythm modulating drugs on metabolic disorder

The metabolic syndrome represents a cluster of metabolic anomalies (including hyperglycaemia, obesity, hypercholesterolemia), that affects 25% of the world’s population and is recognised as a major risk factor for development of diabetes and cardiovascular diseases. Several key enzymes identified in this disorder are directly under circadian regulation and evidence from both pre-clinical research and epidemiological studies strongly implicate disturbed circadian rhythms in metabolic disorders. Further, the recent demonstration that pharmacological enhancement of the clock ameliorate symptoms of metabolic syndrome suggests this could indeed be a novel therapeutic paradigm. In light of this, our study aimed to investigate the effects of three novel circadian modulators using a range of in-vitro models for metabolic syndrome and translate these findings to an in-vivo model of obesity.
Following a medium-throughput screen of ~5000 molecules using reporter cell-lines that track clock gene expression, 3 novel circadian modulators; Linopirdine, Diclazuril and Zaprinast were identified. Phenotypic characterization of these molecules in adipocytes demonstrated a lack of correlation between pharmacological amplitude enhancement of the adipocyte clock and metabolic phenotypes, despite displaying positive metabolic outcomes in in-vitro model system, thereby highlighting the significance of drug targets in metabolic outcomes. Using in-silico mining, followed by transcription-factor screening and siRNA knockdown, we identified a novel mechanism mediating Linopirdine’s chrono-modulatory effect. We provide the first direct evidence of MEIS1 being a regulator of circadian clock expression and demonstrate Linopirdine as a novel modulator of MEIS1 and HIF. Furthermore, in a diet-induced obesity mouse model, Linopirdine mimicked HIF and MEIS1 activation in-vivo, emphasising the significance of the drug target in predicting in-vivo outcomes. Finally, using Zaprinast as a pharmacological tool, we provided new insight on the role of cGMP in regulating peripheral circadian clocks. Thus, this DPhil thesis provides original insight into the use of chrono-modulators in the treatment of metabolic syndrome and introduces novel targets for circadian modulation.

Keywords: amplitude enhancers
MEIS1
Metabolic syndrome
circadian modulating drugs
circadian biology
HFD
metabolic phenotyping
metabolic screens
Metabolic disorder
Advisor: Vasudevan, S
On the locality of indistinguishable quantum systems

This thesis investigates local realism in quantum indistinguishable particle systems, focusing on bosonic, fermionic, and 2D non-abelian anyonic systems. The local realism of quantum indistinguishable particle systems is asserted. It proves annihilation operators represent the local ontic states in these systems. It closes the literature gap on obtaining Deutsch-Hayden descriptors in indistinguishable particle systems. The prima facie paradox of action at a distance using fermionic annihilation operators as descriptors is resolved. The work provides examples of using and interpreting the annihilation operators as local ontic states. It contains the novel construction and characterisation of the annihilation operators for 2 D non-abelian anyonic systems. The explicit form of Fibonacci anyon annihilation operators is provided, and their usefulness is shown in expressing the anyonic Hubbard model Hamiltonian algebraically. By studying the indistinguishable particle systems’ local realistic structure, the thesis showcases the relevance of the choice of subsystem lattice and exotic possible compositions of subsystems.

Keywords: fermions
anyons
local realism
ontic states
Advisor: Vedral, V
The somatic mutational landscape of the normal fallopian tube epithelium

There is currently no screening test available for ovarian cancer. This is largely due to the lack of understanding of mechanisms of tumour initiation. Using single cell sequencing, we have recently demonstrated the individual subtypes of the fallopian tube epithelial cells, and how these are recapitulated in high grade serous ovarian cancer (HGSOC) subtypes, providing compelling evidence that the fallopian tube epithelium (FTE) harbours the elusive cell of origin of HGSOC [1]. Using these insights, it was now a priority to explore the somatic mutational landscape of the normal FTE.
Investigating mutational processes in normal tissue is central to our under- standing of the cancers that originate in these tissues. Recent studies have shed light on the clonal dynamics of various tissue types in the human body, informing our understanding of how somatic mutations contribute to tissue homeostasis, ageing, cancer, and other diseases. In this study, I performed ultra-deep targeted sequencing of a collection of over 350 laser capture microdissected samples from the normal FTE of six patients (4 patients without cancer; 2 patients with concurrent HGSOC and macroscopically normal fallopian tubes). A machine learning approach was developed to enable accurate and comprehensive discovery of subclonal variants from small numbers of cells using a low-cost, high-throughput sequencing workflow.
This study has revealed that somatic mutations are ubiquitous in the normal fallopian tube, with considerable intra- and inter-patient heterogeneity. Muta- tional processes that underpin positive selection and clonal expansion of fallopian tube epithelial cells were explored in order to gain an understanding of the transformation of healthy cells into cancer cells. The highest burden of somatic mutations was found in FAT1, the NOTCH genes, and CSMD3, which are all known to play a role in the pathogenesis of both benign diseases and cancer. The majority of mutations were shown to be missense mutations with likely damaging impacts on protein function. TP53 mutations, which are pathognomonic for HGSOC [2], were found to be uncommon in the histologically normal FTE, suggesting that these may not confer large clonal advantages in the normal FTE, but as key drivers of HGSOC development likely occur later in the pathogenesis.
This is the first insight into the somatic mutational landscape of healthy human fallopian tubes and provides novel insights into fallopian tube biology and the clonal dynamics of fallopian tube epithelium. These results lay a foundation for subsequent exploration of the interface between health and disease and will be an important stepping-stone towards establishing screening tools for early detection of HGSOC.

Keywords: Fallopian tubes
Genomics
Ovarian cancer
Somatic mutations
Early detection
Advisor: Ahmed, A
Corporations and justice: a theory of corporate justice responsibility

Political theorists have developed theories of responsibility for injustice, but rarely identify the corporation as a responsibility-bearer. Management scholars, on the other hand, widely acknowledge that corporations bear extra-commercial responsibilities but rarely include responsibility for justice, casting corporate social responsibility as discretionary duties of benevolence, mostly in service of corporate interests. These two literatures expose a gap in corporations’ responsibility for injustice.
This thesis addresses this responsibility gap by bringing these two literatures into conversation. It argues that the responsibility gap derives in part from the gap, found in both literatures, in the conception of corporate injustice, which in turn derives from a misconception of corporate behaviour.
The thesis argues that corporations are mistakenly conceived as atomistic actors when, in reality, they operate in networks consisting of complex webs of corporate interactions. Upon setting right this misconception, the thesis identifies an overlooked mode of injustice, that of networked injustice that corporations routinely commit by their participation in corporate networks. With this conception of networked injustice, the thesis develops a non-discretionary account of corporate responsibility for injustice, termed corporate justice responsibility.
The thesis contributes to political theory by bringing the corporation firmly into the set of responsibility-bearers for injustice while also identifying networks as mediators of injustice. While networked injustice is developed in the context of corporate behaviour, the concept is applicable to any agents engaged in networked action. The thesis contributes to management and political theory by presenting corporations as fundamentally networked actors, and developing an account of non-discretionary, extra-commercial responsibility borne by corporations, grounded in their contributions to networked injustice.
By these theoretical contributions, the thesis, and the theory of corporate justice responsibility, contribute to closing the gap in accounting for corporations’ justice responsibilities.

Keywords: corporate justice debt
harmonisation of corporate behaviours
justice
corporation
just-profit
structural injustice
responsibility
networked injustice
Advisor: Elford, G
Stemplowska, Z
Choreographing tragedy into the twenty-first century

What makes a tragedy? In the fifth century BCE this question found an answer through the conjoined forms of song and dance. Since the mid-twentieth century, and the work of the Tanztheater Wuppertal Pina Bausch, tragedy has been variously articulated as form coming apart at the seams. This thesis approaches tragedy through the work of five major choreographers and a director who each, in some way, turn back to Bausch. After exploring the Tanztheater Wuppertal’s techniques for choreographing tragedy in chapter one, I dedicate a chapter each to Dimitris Papaioannou, Akram Khan, Trajal Harrell, Ivo van Hove with Wim Vandekeybus, and Gisèle Vienne.
Bringing together work in Queer and Trans* studies, Performance studies, Classics, Dance, and Classical Reception studies I work towards an understanding of the ways in which these choreographers articulate tragedy through embodiment and relation. I consider how tragedy transforms into the twenty-first century, how it shapes what it might mean to live and die with(out) one another. This includes tragic acts of mythic construction, attempts to describe a sense of the world as it collapses, colonial claims to ownership over the earth, and decolonial moves to enact new ways of being human.
By developing an expanded sense of both choreography and the tragic one of my main contributions is a re-theorisation of tragedy that brings together two major pre-existing schools, to understand tragedy not as an event, but as a process. Under these conditions, and the shifting conditions of the world around us, I argue that the choreography of tragedy has and might continue to allow us to think about, name, and embody ourselves outside of the ongoing catastrophes we face.

Keywords: classics
decoloniality
relation
tragedy
COVID-19
performance
climate crisis
queer theory
postcolonial
chosen family
the end of the world
choreography
classical reception
Advisor: Budelmann, F
Macintosh, F
Isotope fractionation during volatile loss from planets and asteroids

Volatile element depletion trends of the terrestrial mantle and extra-terrestrial bodies relative to CI carbonaceous chondrites indicate that evaporative loss from silicate melts had a considerable effect on the trace element budget and isotopic composition of these bodies. This large scale volatile loss occurred during the early stages of planetary evolution where bodies were partially or wholly molten due to the heat generated by impactors and the decay of short-lived radionuclides. The 50% condensation temperature is often used to describe volatility in planetary sciences, but the restriction to solar nebula conditions hinders its applicability beyond the first ~3 Myr of the solar system.
This study assessed evaporative loss of Li, P, V, Cu, Zn, Ga, Ge, As, Rb, Ag, Cd, In, Sn, Sb, Cs, Tl and Pb from silicate melts. Evaporation experiments were performed in a one atmosphere gas mixing furnace at 1300 – 1400°C and fO2 between air and the iron-wüstite oxygen buffer reaction in three different melt compositions. Evaporative loss was quantified using the volatility factor which showed that evaporative loss for all elements increased with decreasing fO2 and that trace element volatility decreased in more felsic melts. Volatility factors showed reasonable correlations with CI carbonaceous chondrite normalized bulk silicate Earth abundances and experimentally determined 1% evaporation temperatures, but poor correlations with the equilibrium partial pressures and the 50% condensation temperature. The modified Hertz-Knudsen-Langmuir equation (HKL) was used to infer the apparent equilibrium constant, enthalpy and entropy of the evaporation reactions with mixed results.
The Zn isotopic composition showed that evaporative loss of Zn from silicate melts was a diffusion-limited process with a Zn depleted boundary layer in the silicate melt. Liquid – vapour fractionation factors (α(66/64)) closer to unity than expected further confirmed that evaporation was diffusion-limited. The experimental α(66/64) were used to model isotope fractionation on various solar system bodies and terrestrial materials assuming a closed-batch system. These showed that α(66/64) were able to reproduce the Zn isotopic fractionation observed in lunar basalts. For the other (extra-)terrestrial environments the observed fractionation was not reproduced using experimental α(66/64).

Keywords: evaporation
isotope geochemistry
planetary sciences
experimental petrology
zinc
volatility
Advisor: Barling, J
Wood, B
Knowledge in terms of Logos in Plato's Theaetetus

This thesis concerns the definition “Knowledge is True Belief Accompanied by Logos”, as discussed in Plato’s Theaetetus (201c-210d). I aim to show that the discussion between Socrates and Theaetetus progresses coherently and that the aporetic ending of the dialogue should be read as a genuine impasse; neither Plato nor his character Socrates favours an interpretation of logos that may render the definition successful.
First, I argue that neither a propositional nor an objectual reading for knowledge in Socrates’ Dream (201d-202c) should be dismissed before we reach 206d-e.
Second, I argue in favour of the soundness of the argument at 202d-206c and suggest that this passage constitutes an amendment to Socrates’ Dream, not a refutation.
Third, I examine the first meaning for logos (“making one's thought plain by means of speech”, 206d-e) and argue that its rejection serves as a clarification that logoi of concern must in some way be special and that the content of the true belief is different from the content of the logos, although both concern the same object.
Fourth, I examine the second meaning for logos (“being able, when one is asked what anything is, to provide the questioner with an answer in terms of its elements”, 206e-208b). I argue that this is not a simple revisiting of Socrates’ Dream, but the amended and mereologically upgraded version Socrates argued for at 202d-206c.
Fifth, I examine the third meaning for logos (“being able to state some mark by which the thing one is asked for differs from everything else”, 208c-210b). I argue that no such mark can offer the precisification required to meet the strict demands Socrates has set for knowledge. Furthermore, I highlight the issue of the accompaniment of logos and bolster the view that the final argument refutes the definition, regardless of what meaning we attribute to logos.

Keywords: knowledge
ancient philosophy
Theaetetus
Logos
Plato
epistemology
Advisor: Peramatzis, M
Castagnoli, L
On the complexity of queries with intersection joins

This thesis studies the complexity of join processing on interval data. It defines a class of queries, called Conjunctive Queries with Intersections Joins (IJQs). An IJQ is a query in which the variables range both over scalars and intervals with real-valued endpoints. The joins are expressed through intersection predicates; an intersection predicate over a multi-set that consists of both scalars and intervals is a true assertion, if the elements in the multi-set intersect; otherwise, it is false. The class of IJQs includes queries that are often asked in practice.
This thesis introduces techniques for obtaining reductions from the problem of evaluating IJQs to the problem of evaluating Conjunctive Queries with Equality Joins (CQs). The key idea is the rewriting of an intersection predicate over a set of intervals into an equivalent predicate with equality conditions. This rewriting is achieved by building a segment tree where the nodes hierarchically encode intervals using bit-strings. Given a multi-set of intervals, their intersection is captured by certain equality conditions on the encoding of the nodes. Following that, it turns out that the problem of evaluating an IJQ on an input database containing intervals can be reduced to the problem of evaluating a union of CQs on a database containing scalars and vice versa. Such reductions lead to upper and lower bounds for the data complexity of Boolean IJQs, given upper and lower bounds for the data complexity Boolean CQs. The upper bounds are obtained using a reduction called forward reduction, which reduces any Boolean IJQ to a disjunction of Boolean CQs. The lower bounds are obtained by a reduction called backward reduction, in which any Boolean CQ from the aforementioned disjunction is reduced to the input Boolean IJQ. Overall, the two findings suggest that a Boolean IJQ is as difficult as the forward disjunctions' most difficult Boolean CQ. Last but not least, this thesis identifies an interesting subclass of Boolean IJQs that admit quasi-linear time computation in data complexity. They are referred to as ι-acyclic IJQs.

Keywords: intersection joins
iota acyclicity
complexity
Advisor: Benedikt, M
Olteanu, D
Advanced deep active learning & data subset selection: unifying principles with information-theory intuitions

At its core, this thesis aims to enhance the practicality of deep learning by improving the label and training efficiency of deep learning models. To this end, we investigate data subset selection techniques, specifically active learning and active sampling, grounded in information-theoretic principles. Active learning improves label efficiency, while active sampling enhances training efficiency.
Supervised deep learning models often require extensive training with labeled data. Label acquisition can be expensive and time-consuming, and training large models is resource-intensive, hindering the adoption outside academic research and "big tech."
Existing methods for data subset selection in deep learning often rely on heuristics or lack a principled information-theoretic foundation. In contrast, this thesis examines several objectives for data subset selection and their applications within deep learning, striving for a more principled approach inspired by information theory.
We begin by disentangling epistemic and aleatoric uncertainty in single forward-pass deep neural networks, which provides helpful intuitions and insights into different forms of uncertainty and their relevance for data subset selection. We then propose and investigate various approaches for active learning and data subset selection in (Bayesian) deep learning. Finally, we relate various existing and proposed approaches to approximations of information quantities in weight or prediction space.
Underpinning this work is a principled and practical notation for information-theoretic quantities that includes both random variables and observed outcomes. This thesis demonstrates the benefits of working from a unified perspective and highlights the potential impact of our contributions to the practical application of deep learning.

Keywords: active learning
uncertainty estimation
Bayesian deep learning
deep learning
information theory
active sampling
out of distribution detection
data subset selection
Advisor: Gal, Y