VictorJuiz/thesis huggingface dataset:
Advancements in galactic chemical evolution

In this thesis we examine several improvements which can be made to the canonical under- standing of Galactic Chemical Evolution (GCE) models in light of modern developments in stellar physics and new modelling techniques. Not only is GCE a vital component of our understanding of the history and composition of the universe in its own right, but since it incorporates physics on the scale of the cosmological to the subatomic, it may also be used as an independent probe and constraint on physics across many different fields.
We develop two brand new, state-of-the-art models for studying galactic chemical evo- lution under two differing paradigms: the Simple Analytical Chemical Evolution Model (sacem) which allows for rapid and complete scans of the high-dimensional parameter space associated with GCE, and the updated version of the Radial Migration in Chemical Evolution Simulation (RAMICES II), which emulates the underlying physics chemical evolution as faithfully, and completely, as possible.
These models allow us to investigate the origin of r-process nucleosynthesis within the Milky Way, in particular, identifying the ability of 'collapsar' events to contribute meaningfully to the global r-process budget. Utilising the sacem code, we are able to evaluate in excess of 1012 potential models of the galaxy, and evaluate them against intentionally weak constrains on the resulting chemical and temporal properties, and hence provide a strong upper bound on the ability of such events to contribute to the r-process abundance of the Milky Way at late times.
We study the impact of advances in stellar evolution modelling on GCE models, utilising new rotationally-resolved stellar evolution codes and nucleosynthetic yield grids. We show that the output from these new stellar models is fundamentally irreconcilable with observed data, and hence develop a number of tools which allow future stellar modelling to be rapidly diagnosed as incompatible, providing a new constraint on the internal evolution of stellar bodies.
Finally, we apply our new RAMICES II model to briefly study the phenomena of metallicity- offset, strongly peaked curves in the gas-phase abundance diagrams – so called 'caustics' – and how these imprint themselves in non-trivial ways on the stellar abundance plane, using them to inform future studies of both r-process nucleosynthesis and the assembly history of the galaxy.

Keywords: ISM
Collapsars
Stellar Parameters
Neutron Star Mergers
Galactic Chemical Evolution
Galaxies
r-Process
Chemical Abundances
Nucleosynthesis
Advisor: Schoenrich, R
Magorrian, J
Informational self-determination in context: privacy and data protection in the age of big data and surveillance capitalism

This thesis focuses on the problem of widespread and sophisticated data collection and processing by private commercial entities, and the threat these practices pose to individual rights and freedoms. This work is directly concerned with European data protection law, and the fundamental rights to privacy and data protection. Particular emphasis will be placed upon the right to informational self-determination, which seeks to ensure individual persons, or ‘data subjects’, are able to exercise control over their personal data. As will be discussed, this concept is of crucial importance in this context, and is overwhelmingly threatened by the social, economic and technological circumstances of the information age.
The initial discussion will elaborate the problematic nature of the data economy, including the unprecedented scale of this issue and its detrimental consequences. Thereafter, this account will explore fundamental rights, proceeding with the right to privacy, which – despite its renowned importance – is significantly limited and thus unable to effectively respond to a threat of this character. The focus will then turn to data protection, and the need to recognise this right’s independent value distinct from privacy. Informational self-determination is essential in this regard, as the importance of data protection is demonstrated through its unique potential to: confer data subject control; and address the overarching power imbalances which currently render such control unfeasible. The success of data protection law relies upon fully developing both of these aspects. Legislative developments have made valid progress with respect to the former, but failed thus far to sufficiently address the latter. Therefore, the final chapter of this thesis will discuss how data protection can evolve to confront the information and power asymmetries of the digital age, in order to create an environment in which individual persons are both protected and empowered.

Keywords: Data Protection
Technology
Human Rights
Privacy
Law
Dressed to the nines, stripped to the bones: the symbology and rhetoric of YHWH’s acts of investiture and divestiture of dress in prophetic literature

The last four years has seen a renewed interest in dress in biblical studies. Much of this work focuses on dress as object – what it is, looks like, and who wears it. A consequence of this is the symbolic and rhetorical function of dress in metaphors being reduced to its function in “real life.” In response, I treat dress as subject. My research explores the conceptualization of dress and nakedness in prophetic texts within the Hebrew Bible where YHWH is the investor/divestor of dress, and personified Jerusalem/Zion is the recipient of his actions. The texts include Jeremiah 13:18-27; Isaiah 52:1-2, 7-10; 61:10-11; Ezekiel 16:35-43. My work distinguishes itself from previous scholarship through its interpretive shift from what dress is to what it is doing. To my knowledge, no one has studied acts of investiture and divestiture of dress in prophetic literature. I argue that the conceptualization of dress grants meaning and function to the suffering and destruction of the 6th century BCE. My philological methodology brings dress into focus by exploring how the movements of it on or off Jerusalem/Zion are crucial to understanding her as woman and city. At the same time, the shift to what dress is doing and my focus on it as a concept allows me to identify constellations that hold these metaphors together with respect to suffering and destruction. Through Jerusalem/Zion, a divine/prophetic perspective on suffering is made recognizable: the conceptualization of dress reorients the audiences to see suffering and destruction as the place of self-reckoning, shame, and unbeing (Jeremiah 13 and Ezekiel 16), or as the moment of transformation, revelation, and recovery (Isaiah 52 and 61). I conclude that acts of investiture and divestiture are crucial to the audiences’ identity and formation and effacement and deformation. Dress and its conceptualization are a means of perception management.

Keywords: transformation
acts of clothing
nakedness
shame
acts of unclothing
ancient Near East
exile
Israel
suffering
Judah
clothing
divestiture
identity
dress
agency
destruction
investiture
Advisor: Southwood, K
Autofictional trauma in post-Imperial Portuguese literature

This thesis aims to situate the work of three contemporary Portuguese female authors, Lídia Jorge, Isabela Figueiredo, and Dulce Maria Cardoso, within the autofictional genre in order to interrogate how the trauma of their own personal experience of the Colonial Wars and decolonisation era is reflected within their writing. Drawing on the theoretical framework of Vincent Colonna, I propose that each of the works investigated can be positioned along a spectrum of autofictionality, due to the proximity or distance of the authors from their respective narrators and protagonists. I contend that an autofictional blurring of fact and fiction within A Costa dos Murmúrios (1988), Caderno de Memórias Coloniais (2009, 2015), and O Retorno (2011) is a productive strategy for the depiction of trauma and enables the traumatic memories of the authors to bleed onto the page, albeit from a protected distance.
This study draws on close textual analysis to assess the breadth, and severity, of the physical and mental trauma experienced during the Colonial Wars and decolonisation epoch. This thesis is careful to give equal weight to protagonists of different genders, with an integral dimension of the analysis being its innovative focus on masculinities. My close reading develops across four chapters, traversing themes of photography, gender, and sexuality, and examines the traumatic implications of this period ranging from PTSD and suicide to sexual assault. My assessment of a range of protagonists highlights that, through their depiction of trauma, Jorge, Figueiredo and Cardoso explode and problematise nostalgic notions of the Portuguese empire and Estado Novo ideologies of imperial power. This study questions the possibility of survival and recovery proposed by the three authors, not only for their traumatised characters, but also for themselves, and culminates with a reading of these works as a “protected” and cathartic reliving of trauma.

Keywords: autofiction
post-imperial
portuguese literature
gender
trauma
Advisor: Alonso, C
Atropisomeric fragments in drug discovery and probe compound development

This thesis describes work on the use of atropisomeric biaryl compounds in fragment-based drug discovery (FBDD) and probe compound development.
Part I describes the investigation of derivatisation methodologies and fragment growth methodologies to generate axially chiral biarylpyrimidines with high rotational barriers, for potential incorporation in FBDD screening libraries. We explored 6 derivatisation methodologies, yielding 23 examples. When carried out on enantioenriched substrates, conservation of the enantiomeric ratio was observed and the compounds displayed high enantiomeric stability in most cases (ΔG > 30 kcal/mol).
Part II describes the exploitation of axially chiral biarylpyrimidine fragments to synthesise molecular probes for KRas G12C covalent inhibition, following the discovery of sotorasib (AMG 510). Probe 120 was synthesised, assessed in biological studies, and optimised to lead to probe 150, active against KRas G12C in the low micromolar range as a racemate.

Keywords: Fragment Based Drug Discovery
Synthesis
Atropisomerism
Advisor: Brennan, P
Smith, M
Novel molecular MRI approaches to the detection of brain metastasis


Secondary brain cancer (brain metastasis) is a leading cause of cancer morbidity and mortality. As treatments for primary tumours and systemic metastatic disease improve, the significance of brain metastasis as a cause of death increases. The poor survival of patients with brain metastasis is partly attributed to the unique microenvironment of the brain, includes the blood-brain barrier (BBB), which limits penetration of systemics cancer therapies and imaging contrast agents, and partly to the late stage of diagnosis. Current diagnosis relies on breakdown of the BBB, which only occurs at later stages of metastasis progression and, thus, delaying the introduction of potential treatments. To address this critical issue, development of novel molecular magnetic resonance imaging (MRI) contrast agents for the detection of brain metastasis at the early stages of formation was the overall focus of this thesis.
Inflammation is a hallmark of many neurological disorders, and expression of cell adhesion molecules on blood vessels is a key component of this process. Brain endothelial activation can readily be targeted by iron oxide particles in vivo and unmasked using routine MRI acquisition methods. A number of different types of iron oxide particles, MRI sequences and magnetic field strengths have been used previously for visualising this endothelial activation. Hence, in this thesis, the initial aim was to optimise each of these parameters to further improve molecular MRI in mouse brain.
Endothelial activation is also an early event in the development of brain metastasis. Two adhesion molecules, activated leukocyte cell adhesion molecule (ALCAM) and E selectin, were assessed in brain metastasis models from three primary tumours (breast, melanoma and lung) as potential biomarkers for detection of brain micrometastases in the preclinical models. Iron oxide based microparticles against these surrogate biomarkers of brain metastases were developed, validated and applied in vivo.
The results of this work demonstrated that targeting both ALCAM and E selectin can reveal brain metastases at the microscopic level, and before conventional imaging methods. The advances in our ability to detect early brain metastatic stages using molecular MRI, and the presented contrast agents in this body of work is likely to yield substantial improvements in patient survival.

Keywords: brain metastasis
vascular cell adhesion molecule (VCAM-1)
activated leukocyte cell adhesion molecule (ALCAM)
inflammation
magnetic resonance imaging
E-selectin
molecular imaging
Advisor: Sibson, N
Systems-driven improvements to radar-only ego-motion estimation

Ego-motion estimation in robotics is typically performed with cameras or laser sensors using established techniques that have proven successful in a variety of applications. While these advances have expanded the capabilities of autonomous systems, they are limited by sensor hardware that is adversely affected by poor weather and lighting conditions. Sensing with radar offers a robust means to perceive the environment in even the harshest conditions where these optical sensors fail.
This thesis presents strategic improvements to a radar-only ego-motion estimation pipeline to extend its utility as a core component in an autonomous system. By leveraging information pertaining to the context in which the sensor is used, we offer a means to reduce processing time by filtering out spurious returns, predict failure using an introspective component, and estimate ego-motion with much greater accuracy by considering motion constraints.
The first contribution uses a weakly-supervised approach to train a neural network that filters out radar returns not likely to correspond to static objects in the scene. By passing only those returns that are useful for ego-motion estimation, processing times are reduced by a factor of 2.36. Secondly, we propose a system that interprets the information encoded within the data association algorithm such that the overall confidence in a match between two radar landmark sets can be determined. A classifier is trained to distinguish between strong and weak correspondences and flag poor performance prior to taking action, reducing failure frequency by 24.7 %. Finally, we present a method which leverages information regarding the physical constraints of the robot platform to refine landmark correspondences. We discard those that suggest extreme ego-motion when under the assumption that the vehicle traverses paths of constant curvature. This includes a way to estimate relative pose from a single landmark observed twice, and reduces translational error in odometry by 45.94%.
In each instance, validation is performed on real data captured from a vehicle-mounted scanning radar to measure the performance improvement of the proposed subsystem against a baseline Radar Odometry (RO) system. Through these data-driven advances, we seek to further the use of radar as a navigation sensor, so as to enable our robots to roam with greater efficiency, safety, and accuracy than before.

Advisor: Newman, P
A second-quantised Shannon theory

Shannon's theory of information laid the groundwork for the rapid developments in information and communications technologies over the last century. Yet, it assumed that information carriers were described by the laws of classical physics, whilst at the most fundamental level, nature obeys the laws of quantum physics. Quantum Shannon theory, which describes information carriers as quantum states, has led to a new era of possibilities, such as perfectly secure cryptography without pre-established keys. Yet, there is a sense in which this transition from classical to quantum is incomplete. Traditionally, quantum Shannon theory has focused on scenarios where the internal states of information carriers are quantum, whilst their trajectories in spacetime have still been assumed to be classical.
This work presents a second level of quantisation where both the information itself and its propagation in spacetime are treated in a quantum fashion. The second-quantised Shannon theory describes the possibility of a single particle being simultaneously transmitted through multiple communication channels in a quantum superposition. The framework is developed using the tools of higher-order transformations and quantum resource theories, formally quantifying the resources required for communication between a sender and receiver in this setting.
The advantages of the second-quantised theory are illustrated in a series of examples, showcasing various counterintuitive phenomena that occur when information is simultaneously transmitted through multiple communication channels. In particular, when a single particle travels in a quantum superposition through two alternative transmission lines, the noisy processes in the two lines can destructively interfere, leading to a cleaner communication channel overall. Various different scenarios are encompassed in the framework, including transmission through a superposition of both independent and correlated channels, as well as through large-scale communication networks. This work concludes with a study of the robustness of these protocols to errors and a discussion of recent experimental demonstrations of their associated communication advantages.

Keywords: superposition of channels
Shannon theory
quantum information
indefinite causal order
quantum circuits
quantum communication
vacuum extension
quantum computation
quantum Shannon theory
time-correlated channels
interference of quantum channels
coherent control
quantum supermaps
higher-order processes
quantum foundations
resource theories
Advisor: Chiribella, G
Epidemiology of a sexually transmittable herpesvirus, the Mustelid gammaherpesvirus 1 (MusGHV-1), and its link to reproductive health and physiological stress in European badgers (Meles meles)

Along with virulence and transmissibility, pathogen transmission mode can be decisive on host-pathogen dynamics, where sexually transmitted infections (STIs) are predicted to be more likely to drive vulnerable host population to extinction than infections transmitted mainly through other routes. Despite STIs being common among animals, and often associated with sterility, STIs have been poorly studied in wild animals. As a background introduction to the current state of knowledge about wildlife STIs, in Chapter 1 I reviewed studies reporting STIs in wild musteloids; a group substantially ignored in previous STI reviews. The high proportion of reported cases associated with reproductive diseases and failure, and disproportionally investigation effort in wild populations highlight the need for further research, especially in species of conservation concern. I established the need for systematic wild mammal host-STI models to better understand the actual impact of STIs on wildlife health and population dynamics. In Chapter 2, I laid the foundations for investigating a sexually transmittable pathogen, the Mustelid gammaherpesvirus 1 (MusGHV-1), in free-ranging European badgers (Meles meles), and reported that MusGHV-1 reactivation has a negative effect on female pregnancy success, but not on male sperm abundance. In Chapter 3, I explored influential host risk factors associated with higher MusGHV-1 shedding, such as age, body conditions and sex. In Chapter 4, I explored the effect of MusGHV-1 coinfection with a zoonotic bacterial pathogen, Clostridium perfringens. MusGHV-1 reactivation causes a predisposition to C. perfringens overgrowth in the gut, especially when infected with a novel MusGHV-1 variant. This led me to further explore the genetic and phenotypic differences between the two MusGHV-1 variants identified in this badger population in Chapter 5. I found social group-biased MusGHV-1 variant frequencies and blood viral load differences, implying different functional virulence between the two variants. In Chapter 6, I identified that weather-related stress experienced during prenatal life exacerbate the likelihood of MusGHV-1 reactivation in adulthood. Collectively, these chapters reveal the potential for host responses to viral STI’s to be complex, hinging on individual demographics, coinfection status, environmental conditions, and the viral strain involved; all factors needing proper consideration when attempting to mitigate the role of disease in conservation ecology.

Keywords: conservation
molecular epidemiology
STD
climate change
Wildlife disease
Advisor: Macdonald, D
Buesching, C
Francois, S
Sin, S
Identifying regulators of chronic myeloid leukaemic (CML) stem cell quiescence and discovering effective novel therapies for CML relapse

Chronic myeloid leukaemia (CML) is a myeloproliferative neoplasm characterised by the presence of Philadelphia (Ph) chromosome. The standard treatment is tyrosine kinase inhibitors (TKI), while they achieve remission in many patients, the majority will relapse on cessation of therapy. This indicates that TKI do not ablate the CML stem cells. In this study, I analysed a single-cell transcriptome dataset of CML stem cells published in our lab [1] and other public datasets trying to identify candidate targets that may mediate stem cells resistance to TKI. Growth Arrest Specific 2 (GAS2) was the ‘top hit’ and therefore the candidate I took forward for functional validation.
I first sought to develop an efficient gene knock-down (KD) or knock-out (KO) strategy. Four approaches were compared: 1. Inducible lentiviral shRNA, 2. Constitutive lentiviral shRNA, 3. Single Cas9-sgRNA ribonucleoprotein (RNP) complex, 4. Dual Cas9-sgRNA RNPs. Comparing all approaches, constitutive shRNA achieved 67.2% of successfully transduced eYFP+ cells, 86.2% reduction of GAS2 mRNA level in CML CD34+ cells and was used for further experiments.
My preliminary functional analysis suggested that GAS2KD reduced quiescence and increased cell proliferation in both cell lines and primary CML CD34+ cells. Then I repeated lentiviral shRNA transduction in different CML samples. Slightly higher proliferation index occurred in the GAS2KD group than controlKD group. No significant changes in apoptosis or lineage differentiation were noted in GAS2KD group vs. controlKD group. In summary, knock-down of GAS2 modestly reduced the number of quiescent CML stem cells, suggesting potential therapeutic efficacy against TKI resistant CML stem cells. Further in vitro and in vivo studies are needed to validate and extend this observation.

Keywords: CML stem cell
Tyrosine kinase inhibitor resistance
Quiescence
Advisor: Mead, A
Psaila, B