VictorJuiz/thesis huggingface dataset:
Re-formulating the public-private divide in light of the emergence of data dependent utilities under article 6 of the GDPR


This thesis argues that the public sphere should not be confined to states and that data dependent utilities (DDUs) belong in the public sphere. DDUs are essential utilities for social and political engagement which are inherently and fully dependent on processing personal data. In this respect, the thesis challenges the traditional state-centric public-private divide (namely the consideration of the public as the governmental sphere and the private as the non-governmental sphere) in legal frameworks, specifically under article 6 of the General Data Protection Regulation (GDPR) which lays down the lawfulness grounds for personal data processing and is thus the foundation of each personal data processing activity. It argues that this state-centric approach does not respond to the versatile powers of DDUs and instead exacerbates concerns by considering DDUs as private entities and allowing them to arbitrarily apply article 6 in detriment to individuals’ autonomy and democratic values.
In this regard, relying on the res publica example from the Roman Republic era, this thesis offers a novel formula on the constituents of the public sphere which are referred as public features and formulated as: (i) public matters, (ii) public utilities, and (iii) power, as a barrier before the governance and the use of these utilities. The thesis then claims that DDUs share these features, hence they belong in the public sphere; and it argues that once we place them in the public sphere we could only then address the externalities that land both on the individuals and society at large. It then offers a normative account on how the grounds in article 6 of the GDPR – specifically consent, necessity of a performance of a contract, legitimate interest, and public interest grounds should be applied to DDUs considering their public features. As such, the thesis aims to transform these currently toothless lawfulness grounds into functioning ones upon adopting a DDU-targeted approach, thus diminishing DDUs’ exploitative business model.

Keywords: GDPR Art 6
Public Sphere
Data Protection
Data Dependent Utilities
Res Publica
Public-Private Divide
Advisor: Adams-Prassl, J
Williams, R
Causal discovery with ancestral graphs

Graphical models serve as a visual representation that captures the underlying conditional independence relationships within distributions, employing either directed or undirected graphs. In this thesis, we explore maximal ancestral graphs (MAGs), which is an extension to the conventionaldirected acyclic graphs (DAGs). While DAGs excel in illustrating causal relationships, they fail to capture all the conditional independences on the margin in the absence of latent confounders and selection bias. MAGs provide a more comprehensive depiction of complex dependencies by encompassing both direct causal connections and indirect influences stemming from latent variables and selection bias.
The scalability and accuracy of MAG learning algorithms have been some problems due to the complexity of the space of Markov equivalence classes (MECs) of MAGs and instability of scoring criteria. We first use the concept of heads, tails and parametrizing sets to characterize Markov equivalent MAGs. Then we study imsets of MAGs to address the above issues.
The framework of imsets (Studeny, 2006) is an algebraic approach to represent conditional independences. Given the remarkable success of standard imsets within DAGs, where they efficiently represent MECs and offer reliable scoring criteria, we endeavor to extend this framework to MAGs. Through an exploration of 0-1 imsets defined by parametrizing sets, we show under which conditions does this extended `standard imset' of MAGs define the correct model. Consequently, we refine the ordered local Markov property of MAGs (Richardson, 2003), demonstrating that the newly proposed refined Markov property can be constructed in polynomial time if we bound maximal head size.
Finally, we apply the above results to develop novel score-based learning algorithms for MAGs. To efficiently traverse between MECs of MAGs, we identify some important graphical features within MAGs whose independence models are subsets of others. Leveraging the imsets derived from the refined Markov property, we establish a consistent scoring criterion, offering an alternative to BIC by relying solely on estimates of entropy over subsets of variables. Empirical experiments show promising results when compared to state-of-the-art algorithms.

Keywords: causal discovery
graphical model
maximal ancestral graphs
Advisor: Evans, R
Ancient Latin epics in Girolamo Vida's Christiad

The topic of this thesis is the influence of ancient Latin epics on the Christiad, a Neo-Latin epic poem published in 1535 in Cremona and written by an Italian poet and Catholic bishop, Girolamo Vida (circa 1485-1566).
While the impact of Virgil’s Aeneid on Vida’s poem has been studied, it is still in need of further investigation. Likewise, recent scholarship has detected many loci similes between the Christiad on the one hand, and Lucretius’ De Rerum Natura, Ovid’s Metamorphoses, Lucan’s Bellum Civile, Valerius Flaccus’ Argonautica, Silius Italicus’ Punica and Statius’ Thebaid, on the other, without systematically studying the nature of such resemblances.
This thesis argues that many of these loci similes, including borrowings from Virgil, affect the meaning of the Christiad. Vida’s technique covers a wide range of nuances of literary imitation on a hypothetical spectrum that has at its poles, respectively, the inert refashioning of the words of a previous author and the in-depth engagement with the source on an ideological level. Virgil is undoubtedly his favourite model both qualitatively and quantitatively. However, Vida regarded Lucretius and the post-Virgilian epicists of the first century AD as valuable, though problematic, poets and interlocutors.
The first part of the thesis contextualises the Christiad by analysing the role of ancient Latin epics and literary imitation in Italy in the fifteenth and sixteenth Centuries (chapter 1), Vida’s imitative theory and practice in his De Arte Poetica (1527) (chapter 2), and the historical, ideological and intertextual framework of the Christiad (chapter 3). The second part focuses on four major themes, namely knowledge (chapter 4), marvels and miracles (chapter 5), Good and Evil (chapter 6), and Succession (chapter 7), to illustrate the actual presence of ancient epic models in the poem.

Keywords: Neo-Latin
Latin epics
Christian epic
Renaissance
Literary Imitation
Classical Reception
Advisor: Morgan, L
Building a Corpus of Oral Testimonies of the Holocaust: a case study in corpus linguistics and oral history

This dissertation will give an overview of what goes into creating a digital cross- linguistic corpus. Using a case study, I will describe the elements, methodology, and possible research outcomes of building a digital corpus. The case study con- sists of a collection of oral testimonies of Holocaust survivors that have been tran- scribed into a collection of English, Polish, Russian, Czech, and Hungarian texts. Building on existing literature, this dissertation will describe how corpus linguis- tics can make research data more accessible to researchers of many different areas of scholarship. Having given an overview of how a corpus is created and digi- tally distributed, including the range of tools and platforms available for analysing corpora, I will explore two areas of possible research within corpus linguistics: geo-location using named entity recognition programmes, and syntactic analysis of hedging used in oral histories thanks to part of speech tagging. Through build- ing a corpus of Holocaust Oral Testimonies, I hope to demonstrate how digital methods of corpus linguistics can help further interdisciplinary research within the digital humanities.

Keywords: tagged corpus
digital scholarship
oral history
digital humanities
Holocaust studies
corpus linguistics
digital archive
Investigating the cellular role of the deubiquitylating enzyme ZUP1, a novel player in the DNA damage response

The DNA damage response (DDR) is a network of interrelated signal transduction pathways that identify and repair DNA lesions to maintain genome integrity. To coordinate the DDR, cells use post-translational modifications (PTMs) such as ubiquitin to modify and control protein fate and function. Importantly, ubiquitin signalling is a dynamic modification that can be edited or removed from substrates by deubiquitylating enzymes (DUBs). ZUP1 was recently discovered as the founding member of a new DUB class with selectivity against long K63-linked ubiquitin chains and a putative, but poorly defined, role in the DDR. This thesis aimed to improve our understanding of the cellular role of ZUP1 and define which DDR pathway(s) it functions in. To this end, I generated monoclonal ZUP1 knockout (KO) cell lines using CRISPR-Cas9 gene editing and found that these cells were sensitive to genotoxins that induce replication-coupled DNA damage, with hypersensitivity to the interstrand crosslinking agent mitomycin C (MMC), and the PARP inhibitors olaparib and talazoparib. Using the high-content immunofluorescence microscopy technique of quantitative image-based cytometry (QIBC), I then analysed the dynamics of key factors at stressed DNA replication forks and demonstrated that excess generation of ssDNA and persistence of RPA and RAD51 foci underlie the sensitivity of ZUP1 KO cells to MMC. Lastly, I investigated the chemogenetic interactors of ZUP1 in response to MMC in an unbiased manner using genome-wide CRISPR-Cas9 screening and identified potential synergistic interactions between ZUP1 and the factors BRCA2 and HELQ. Collectively, my results suggest that ZUP1 is a novel player in the response to replication-coupled DNA damage and provides new insight into its cellular roles.

Keywords: Interstrand crosslink repair
DNA damage response
Deubiquitylase
DNA repair
Genome-wide CRISPR screen
Advisor: Gibbs-Seymour, I
The use of subwavelength structures to control and enhance the photoacoustic effect

The photoacoustic effect describes the conversion of light to sound, via thermoelastic expansion, and is used extensively in cross-media applications as it combines the favourable properties of light in one medium with the favourable properties of sound in the other. Photoacoustic composites are used for efficient photoacoustic conversion and can be made from planar multilayered structures, comprised of thin layers of optically absorbing media, separated by layers of a thermally-responsive medium. The aim of this project was to formulate a one-dimensional model capable of simulating the acoustic signal generated from a multilayered structure with several absorbing layers. Then, using the model, the effect of subwavelength structures on the generated acoustic signal was investigated for weakly- and strongly-absorbing layers. The transfer-matrix method was used to solve the governing photoacoustic wave equation in the frequency domain and the source function of the second-order differential equation was kept as general as possible so that the user could choose any function to describe the optical absorption profile of the structure. The model was verified by comparing its results with those from previous studies. It was found that acoustic resonant effects could be induced in structures with optically-thin or optically-thick absorbers but that the effect was more pronounced in the spectra of optically-thick absorbers. Furthermore, the features of the frequency spectrum could be explained by considering the poles and zeros of the transfer-matrix when source terms were included. Thus, these observations stimulated the design of a photoacoustic structure with enhanced directivity by using an acoustic high-reflectance coating. The simulated structure was capable of increasing the amplitude of the generated acoustic signal by about 15% at a target frequency, compared to previous methods. These findings indicate that as new photoacoustic composites have reduced dimensions (<10nm), the resonant properties of both light and sound could be utilised to enhance the conversion from optical to acoustic energy.

Keywords: photoacoustics
subwavelength structures
transfer-matrix method
Advisor: Stavrinou, P
Understanding loss of consciousness under general anaesthesia using multimodal neuroimaging

Despite major advancements in consciousness science over the past few decades, how anaesthesia causes loss of consciousness remains incompletely understood and the translation from basic science to clinical practice has been limited. Recent concurrent electroencephalography (EEG) and functional magnetic resonance imaging (FMRI) evidence indicates that a state of complete perception loss is achieved under general anaesthesia when slow wave activity in the brain reaches saturation. Slow wave activity saturation (SWAS) is therefore a potentially clinically relevant end point for titration of anaesthesia.
We have developed a prototype system for titrating anaesthesia to SWAS within an individual. The system features EEG and anaesthesia data input, modelling of slow wave power and detection of SWAS, and visualisation of the model output in a graphical user interface. The prototype system was applied in a patient pre-surgery study (Study 1) which focused on clinical translation of SWAS, and a healthy volunteer EEG-MRI study (Study 2) which focused on experimental validation of SWAS.
We successfully applied the prototype SWAS system in twelve patients (Study 1) and twenty-three healthy volunteers (Study 2). No subjects in either Study 1 or Study 2 were behaviourally responsive when held at SWAS and none had recall of events from when they were held at SWAS.
In Study 2, we also acquired measures of cerebral blood flow (CBF), and resting and task-related FMRI data during wakefulness and when held at SWAS. When held at the SWAS state, CBF was significantly elevated compared to wakefulness. Furthermore, we found that the brain was unresponsive to external stimulation when held at SWAS even when controlling for the observed CBF changes. Finally, we found that this was accompanied by disruption of functional connectivity in the thalamocortical system and in known resting state networks. Our findings provide further evidence that SWAS is a state of perception loss and a clinically relevant target for surgical anaesthesia.

Keywords: loss of consciousness
slow wave activity saturation
neuroimaging
electroencephalography
anaesthesia
consciousness
magnetic resonance imaging
general anaesthesia
neuroscience
Advisor: Warnaby, C
Jbabdi, S
Tracey, I
Branching and fragmenting particle systems in biology

We introduce and study two new classes of branching and fragmenting particle systems in biology. The first class of branching particle systems with interactions model spatially-structured populations with density-dependent birth and death mechanisms. Our spatial model describes spatially heterogeneous populations using point measures, considering birth and death rates based on spatial position and local population density. Notably, our model includes a juvenile phase, where offspring mature with a density-dependent probability. This results in novel scaling limits: an interacting superprocess, a nonlocal partial differential equation (PDE), and a classical PDE (in which the diffusion term is nonlinear). Furthermore, using a lookdown representation, we retain information about genealogies and, in the case of deterministic limiting models, use this to deduce the backwards in time motion of the ancestral lineage of a sampled individual. We observe that knowing the history of the population density is not enough to determine the motion of ancestral lineages in our model.
In our second class of models, motivated by using cell-free DNA (cfDNA) as a biomarker, we capture three mechanisms governing cfDNA fragmentation in the bloodstream. Our Markovian model, FRIME (Fragmentation, Immigration, and Exit), allows the simulation of cfDNA fragment profiles by sampling from its stationary distribution. We validate the model by comparing simulated profiles with mitochondrial and genomic cfDNA fragments, finding consistency with experimental observations. We employ probabilistic tools and the theory of fragmentation processes to establish the first moments of FRIME processes mathematically. This simulation framework improves our computational understanding of DNA fragmentation dynamics in the bloodstream and has the potential to underpin tools for the analysis of liquid biopsy data.

Keywords: fragmentation processes
branching particle system
cell-free DNA
superprocess
lookdown construction
Advisor: Etheridge, A
Analysis of Navier--Stokes--Fokker--Planck systems for incompressible dilute polymeric fluids

We show the existence of large-data global-in-time weak solutions to various classes of coupled bead-spring chain models with finitely extensible nonlinear elastic (FENE) type spring potentials for incompressible dilute polymeric fluids in a bounded domain in Rd, d = 2 or 3. The governing system consists of the transport equation and the Navier--Stokes equation coupled to the Fokker--Planck equation through the elastic extra-stress tensor which is defined by the Kramers expression. The proofs are based on truncating the probability density function and approximating with Galerkin semi-discretizations on the spatial domains. We derive uniform bounds independent of the Galerkin and truncation parameters; then with weak compactness and compensated compactness techniques, we pass to the limits in the sequences of Galerkin approximations and in the truncation level. The technical tools involve using Nikolski\u{\i} norm estimates to derive uniform estimates for fractional time derivatives and using various generalizations of the Aubin--Lions Lemma to deduce strong convergence of approximating sequences. We also apply the Div-Curl Lemma and Vitali's Convergence Theorem to deduce the strong convergence of the sequence of approximations of the probability density function in L1
. We first focus on homogeneous dilute polymeric fluids. The key feature is the polymer-number-density-dependent viscosity coefficient appearing in the Navier--Stokes equation. Then we move on to nonhomogeneous dilute polymeric fluids, featuring the presence of a density-dependent and polymer-number-density-dependent viscosity coefficient in the Navier--Stokes equation and a density-dependent drag coefficient in the Fokker--Planck equation. Finally, we consider nonisothermal homogeneous dilute polymeric fluids. To complete the nonisothermal Navier--Stokes--Fokker--Planck system, the temperature evolution equation is also introduced to form a thermodynamically consistent model. To simplify the nonisothermal model, we present the existence proof in the case of a corotational Fokker--Planck equation.

Keywords: Fokker--Planck equations
Galerkin method
Nonlinear PDEs
Kinetic polymer models
Incompressible Navier--Stokes equations
Advisor: Suli, E
Evolution and function of RHO cell polarity signalling in plants


Since their origin from a unicellular ancestor 630–890 million years ago, the streptophytes, which comprise streptophyte algae and land plants, have evolved mechanisms to develop morphologically complex body plans. Much remains unknown about how such mechanisms evolved and how they regulate plant morphogenesis. To start, I hypothesise that cell polarity signalling, which can spatially regulate fundamental cellular processes like growth and division, contributed to morphological evolution in the streptophytes. In this context, the aim of this thesis is to investigate the evolution and function of RHO Of Plant (ROP) signalling, the plant specific form of the ancient eukaryotic RHO cell polarity signalling. First, I report phylogenetic and sequence analyses resulting in the discovery that ROP signalling genes became established early in the streptophyte lineage, during the period when multicellular filamentous body plans are believed to have evolved from unicellular/colonial forms. Second, by functionally characterising the single ROP gene in the liverwort Marchantia polymorpha, I demonstrate that ROP protein regulates the morphogenesis of complex plant tissues by controlling cell growth, division, and possibly adhesion. Finally, through a series of cross-species complementation experiments with M. polymorpha rop mutants, I show that ROP function has remained largely conserved since the time land plants last shared a common ancestor with the filamentous streptophyte algae, Klebsormidium nitens. Collectively, the findings from this thesis reveal that an ancient signalling mechanism which became established early in the streptophyte lineage is required for the morphogenesis of complex tissues in extant land plants. They also indicate a potential role of ROP signalling function in the morphological evolution of early streptophytes.

Advisor: Dolan, L
P450–Mediated azepane natural product synthesis

Chapter 1 introduces methods and applications for C–H activation, cytochrome P450 enzymes and their uses in synthesis, and the relevant families of compounds in which the present work takes place.
Chapter 2 describes the strategy and the attempts of building the natural product balanol and analogues via C–H amination from enzymatically made substrate, along with new bicyclic lactones synthesised via C–H activation.
Chapter 3 presents progress in the synthesis of the carbon skeleton of the natural product cephalotaxine via an intramolecular Schmidt reaction, along with a significantly improved literature method for assembling the cephalotaxine core.
Chapter 4 explores the P450-catalysed oxidations of the previously made cephalotaxine core structure, to access new analogues of this natural product and to draw a P450-reactivity profile of this molecule.

Keywords: Natural Product - Total Synthesis - Biocatalysis - P450 - C-H Activation - Balanol - Cephalotaxine
Advisor: Robertson, J