VictorJuiz/thesis huggingface dataset:
Time and Tillich: re-examining salvation through the lens of relativity

Time is often neglected in conversations between science and religion. As this thesis engages time and theology within the theological framework provided by Paul Tillich’s Systematic Theology, it is a step towards addressing this oversight. In this work I use Tillich’s method of correlation as my overarching structure, a theological methodology which is explicitly designed to encourage the continuous evolution of theology in dialogue with pressing questions from the culture in which that theology is to be received. My approach is fundamentally one of constructive engagement, meaning I am not concerned with proving or disproving any theological, philosophical, or scientific claims; rather, this thesis engages time and theology with the aim of fostering a constructive dialogue. The method of correlation involves locating specific cultural concerns, the so-called philosophical question, and providing a theological response, termed the theological answer. To this end, this thesis begins with the physics and metaphysics of time, especially Einstein’s Relativity Theories, and argues that these give good reason to accept a B-theory of time in which time does not pass and reality is comprised of a block universe. The philosophical question that arises is this: how can change be understood within this static temporal metaphysic? This question is highly important for any doctrine of salvation that requires a transformation in time. I then explore Systematic Theology, with a particular focus on Tillich’s treatment of salvation, time, and history, as these are the foundations of my theological answer. Finally, the thesis argues that given a B-theory of time, a salvation-transformation is best understood as a form of qualitative, phenomenological change, rather than a robust ontological change. I use concepts from the philosophy of temporal experience to make this argument, ultimately concluding that the individual’s transformation from fallen to saved is one of mind-dependent becoming.

Keywords: Science and Religion
Special Relativity
General Relativity
Philosophy of Religion
Salvation
Paul Tillich
Time
Advisor: McGrath, A
Saving nature or nation in the Kachin Hills: an ethnography of encounters

Amid decades of ethno-political war, northernmost Burma’s Kachin people have increasingly come into encounters with international projects for grabbing or saving local nature. Drawing on eighteen months of ethnographic fieldwork in 2017–2019, this thesis explores encounters between the Kachin ethno-national movement and outside-led projects of resource extraction and nature conservation. The thesis argues for ethnographic approaches that do not assume certain outcomes, but instead foreground diversely situated, contradictory, and empathic voices – both local and from outside – to explain why such encounters can lead to clash, collaboration, disconnect, or other pathways. The studied encounters showed many-sided disconnect, distrust, outreach, and collaboration amid war, driven by different sides’ comparable senses of emergency over saving natures or nations. Telling such stories of many-sided encounters can help anthropology in addressing analytical and ethical challenges when representing multi-scale conflict, conspiracy accusations, and ecological destruction.

Advisor: Rival, L
Development of affinity and fluorescent probes to elucidate the mechanism of small molecule modulators of neurogenesis

Neurogenesis is an endogenous neuroprotective mechanism that mainly occurs in two neurogenic niches of the adult mammalian brain. In neurodegenerative diseases, such as Parkinson’s disease and Alzheimer’s disease, adult neurogenesis is often impaired. For these diseases, pharmacological stimulation of the de novo production of neurons in the stem cell niches of the brain is a promising regenerative therapy. OXS-N1 was previously identified as a hit neurogenic compound through an in vitro phenotypic screen. It increased neurogenesis in murine neural stem cells (NSCs) in vitro and in wild-type mice in vivo after oral administration. The aim of this DPhil work is to identify the molecular target(s) of OXS-N1 and the mechanism of its neurogenic activity through a chemoproteomics approach.
A series of affinity probes was synthesised to assess the molecular interactions of OXS-N1 through affinity-based protein profiling (AfBPP). Vimentin was identified as the molecular target of OXS-N1 through pull-down studies and mass spectrometry analysis. Using fluorescent-tagged OXS-N1 derivatives, OXS-N1 was found to localise primarily in the cytoplasm, correlating to the known subcellular localisation of vimentin. It was found to directly bind to vimentin in live NSCs, without causing significant disassembly or aggregation of vimentin filaments. The protein-ligand binding was further validated using waterLOGSY and intact protein mass spectrometry. Reported literature vimentin binders also increased neurogenesis in vitro, showing that vimentin modulation could be used in future neuroregenerative therapies.

Keywords: Neurogenesis
Affinity-based Protein Profiling
Chemical Probes
Chemical Proteomics
Target Identification
Advisor: Russell, A
Changing meanings of megalithic monuments in the Upper Baram, Sarawak, Malaysian Borneo

This thesis examines contemporary engagements with the megalithic monuments in the Upper Baram region of Sarawak, Malaysian Borneo. It proceeds from the premise that over the long term, despite being objects that originated in the past, megalithic monuments are capable of accumulating new meanings as a result of their interactions with different groups of people in different times and contexts. Through a combination of archaeological, historical and anthropological investigations, this thesis identifies the various new meanings that the megalithic monuments in the Upper Baram have acquired since they were last erected traditionally around the middle of the 20th century, and further, how these meanings have changed over the years. Over the last seventy years, the megalithic monuments have transformed from being the outcomes of a living tradition of commemorating important people and events to being objects associated with the past, particularly in their association with pre-Christian or traditional (now abandoned) practices, and treatment as archaeological objects. Moreover, this thesis examines the megalithic monuments’ present-day significance as cultural heritage, and as objects that provide local communities − the Kelabit and the Sa’ban − with a sense of identity and belonging to the land. This thesis also shows the creation and recreation of the meanings of the megalithic monuments in the Upper Baram to be the products of historical and contemporary processes that are tied to the political, social, economic and environmental changes that the region and its inhabitants have experienced since colonial times to the present day. This thesis concludes that the meanings of the megalithic monuments in the Upper Baram are fluid and ever-changing. As social, political and economic constructs of particular times, the meanings of the megalithic monuments should further be regarded as an ongoing process that will continue into the near and distant future, for as long as the megalithic remains continue to exist, in the physical world, as well as in the minds of people. As a study that focuses on local and contemporary interactions with the megalithic monuments, this thesis has provided an up-to-date ethnography that broadens understanding of the social significance of megalithic monuments as multivalent objects, and contributes to the wider issue of how people relate to and make meanings of objects from the past.

Keywords: Archaeology
Megalith
Sarawak
Monument
Borneo
Advisor: Gosden, C
The structural transformation of the military public sphere: war, knowledge, and military elites in West Germany, 1940-1989

The history of the Federal Republic of Germany is generally told as one of liberalisation. Denazification and demilitarisation in the immediate post-war years were long regarded as having founded a new liberal-democratic state, worthy of “the West”. The armed forces, too, were said to have been cleansed of the old militaristic spirit and imbued with a new ethos. But repeated scandals suggest that military institutions were, and remain, resilient to civilian control. The thesis argues that this is the result of continued organising by networks of conservative soldiers. They dominated military and military-adjacent structures and organised various kinds of networks and associations to preserve their power over military decision-making and younger generations of officers. The thesis sketches the evolution of these networks over five decades and shows just how they organised for various political, social, and economic causes and thus preserved their influence. Military historical knowledge played a foundational role as old military elites initially organised for the purposes of distilling their war-time experiences, particularly that of the Eastern Front, which was to be mobilised for a coming war with the Soviet Union. Although they never mounted a fundamental challenge to the new political order, the networks endured for decades after this initial impetus, and the thesis follows them as they shift position and structure and compete for power and influence. The last two chapters in particular show how they pushed back against the emergence of more progressive voices from the 1970s onwards. The endurance of their power suggests that the story of strong liberal tendencies within the post-war West German armed forces is in urgent need of revision.

Keywords: Second World War
Eastern Front
Federal Republic of Germany
Public Sphere
Advisor: Wilson, P
Investigating the role of BRCA2 in the maintenance of chromosomal stability

Genetic information is preserved across cell divisions by the faithful transmission of chromosomes. Mutations in the BRCA2 gene predispose individuals to breast and ovarian cancers. BRCA2-deficient cells are characterised by an aberrant structure and number of chromosomes. The former phenotype has been generally explained by the BRCA2 function in the DNA repair, through the homologous recombination (HR) pathway mediated by RAD51 recombinase. However, it is not fully understood how BRCA2 deficiency leads to an abnormal number of chromosomes. Proper chromosome segregation in mitosis requires the orderly assembly of kinetochore components at specific DNA regions of chromosomes, called centromeres. Due to their complex structure, centromeres are particularly susceptible to DNA damage, which in turn can lead to abnormal chromosomal rearrangements. Despite the importance of maintaining centromere integrity, the mechanism protecting centromeric DNA remains largely unknown. Throughout my research, I explored the function that BRCA2 may play in the protection and formation of centromeres.
In this thesis, the role of BRCA2 at centromeres was investigated using three experimental approaches. Firstly, I utilised a previously established human HT1080 cell line carrying a small extra-chromosome, called the alphoid-tetO HAC, engineered from synthetic centromeric alphoid DNA arrays. Using this system, I showed that BRCA2 is important for the faithful transmission of the HAC during the cell division, whereas the same conclusion could not be drawn for other HR factors, such as RAD51. Interestingly, however, I observed that tethering the RAD51 binding motif of BRCA2, BRC4, to the HAC negatively impacted on the HAC maintenance. Secondly, the impact of BRCA2 depletion on endogenous centromeres was investigated in HeLa cells. Using immunofluorescence experiments, I found no clear evidence that BRCA2 protects centromeric DNA from damage, but unexpectedly observed that the removal of BRCA2 changed the chromatin status and the centromeres formation. Lastly, I generated CRISPR-modified HCT116 cell lines, in which endogenous BRCA2 is tandem tagged with a fluorescent protein and an auxin-inducible degron (AID). This cell line is a novel tool to study the localisation and functions of BRCA2 at every stage of the cell cycle. Using this system, I observed that BRCA2 partially localised at kinetochores and centromeres in interphase.
Based on the results presented in this thesis, I propose that BRCA2 may have a DNA-repair independent function at centromeres. BRCA2 may be important for chromatin remodelling, which can affect the centromere and kinetochore formation. These findings shed light on the BRCA2 function and suggest new ways by which BRCA2 may promote chromosome maintenance.

Keywords: BRCA2
chromosomal stability
centromere
kinetochore
human artificial chromosome (HAC)
Advisor: Esashi, F
Laser-based high heat flux testing for power exhaust in fusion devices

One of the critical challenges in realizing fusion energy is the survival and cooling of the Plasma Facing Components (PFCs) in the extreme environment (>1000°C and constant neutron bombardment). In the DEMOnstration Power Plant (DEMO), the divertor must endure steady state loads of 10MWm2and transient thermal cycling up to 20MWm2. Novel target designs are needed to cope with this thermal load.
An optics system was designed to replicate the thermal environment in DEMO. A new facility, coined the Oxford Laser Heating Facility (OLAHF), has been established for laser-based heating tests. A Compound Parabolic Concentrator (CPC) was designed to focus the power from four laser modules to greater than 5MWm2 onto a target that absorbs 98.9% of the incident light. Numerical, thermomechanical studies on the steady-state performance confirmed that the deformation of the CPC does not exceed 0.4 mm and that the maximum temperature of the glass is less than 30°C.
A novel divertor target, termed the Spiral Plate Module (SPM), was designed to meet the fusion-relevant requirements. The geometry of the SPM was initially optimized by a one-dimensional model, the results of which showed a good correlation to Computational Fluid Dynamics (CFD) studies. The SPM achieved the lowest walloverheat (τs) and dimensionless mass flow rate (m∗) of any target design considered, and showed good hydraulic performance such that the power needed to pump the coolant is only 0.32% of the incident heat flux.
Lastly, a method was created to control the lasers and monitor the processes within OLAHF. Through a number of Labview panels, the operator can vary the laser power in time and record and store experimental data, and the program will send a warning or shut down all systems (depending on severity) if there is a possibility of harm to the hardware or users.

Keywords: divertor
fusion
laser
Advisor: Nicholas, J
Ireland, P
Neuropsychological deficits of visuospatial attention: subtypes, clinical utility, and underlying mechanisms

Visuospatial neglect is a common neuropsychological syndrome characterised by consis- tently lateralised spatial attentional deficits. The purpose of this thesis is to investigate patterns of heterogeneity within visuospatial neglect, to determine this syndrome’s underlying mechanisms, and to investigate the practical utility of considering this heterogeneity within clinical settings.
Chapter Two presents a critical analysis of common neglect assessment methods and in- vestigates the utility of neglect severity metrics which can be extracted from neuropsychological measures. Chapter Three analyses behavioural heterogeneity in neglect dyslexia to investigate the relationship between reading-related and domain-general neglect impairments. Chapter Four presents three case studies characterising representation-level neglect dyslexia in order to evalu- ate existing models of spatial attention. Chapter Five presents a detailed, lesion-mapping analysis of visuospatial neglect deficits aiming to determine whether right neglect is anatomically homolo- gous to left-lateralised neglect. Finally, Chapter Six analyses the relationship between the occur- rence of acute neglect and poor long term recovery outcomes to determine whether the specific behavioural phenotype of acute neglect impairment acts as a useful prognostic indicator.
The findings of these data chapters are then cumulatively discussed to extend fundamental understanding of the neglect syndrome, establish a novel conceptualisation of representation- level neglect dyslexia, evaluate current neglect-related clinical practices, and clarify the recovery outcome of stroke survivors exhibiting acute neglect impairment.

Keywords: Visual Neglect
Cognitive Impairment
Neuropsychology
Stroke
Attention
Advisor: Demeyere, N
Modelling the neural coding of natural sounds in the auditory cortex

When neurons fire in the auditory cortex what do they represent? What is the form of transformation that sound stimuli go through in order to produce activity in the auditory cortex? Studying how neural activity changes in response to a stimulus parameter, e.g. the level or frequency of sound, has been a way to address such questions in the past. In more recent times, an alternative approach has been to measure the responses of cortical neurons to natural stimuli. Here, we investigate the responses of neurons in ferret auditory cortex, recorded using extracellular electrode probes, to a diverse collection of natural sounds using models that aim to capture many aspects of the information transformation process from the ear to the cortex. We use the method of encoding - whereby we build functional transformations that predict neural responses from the sound stimulus, and also of decoding - whereby we build functional transformations that estimate the stimulus from neural responses. Our primary goal has been to focus our modelling effort to produce mechanistic and interpretive insights into auditory processing in the brain. Firstly, we examine to what extent biological details matter in making a model of the auditory periphery that provides input to the cortex. Secondly, we study possible biological mechanisms underlying the temporal receptive fields of auditory cortical neurons. Thirdly, we ask whether neural populations in the auditory cortex represent the past or future of ongoing sound stimuli. We found that simple models are well suited for models of auditory encoding in the brain, and that stimulus history in linear receptive fields of auditory neurons can be explained by a dynamic network model, and also that a population of neurons might contain non-linearities that enable them to predict the future. These results will improve our understanding of some of the fundamental questions relating to neural coding in the auditory system.

Keywords: decoding stimuli from neural responses
predicting neural responses
encoding models of neural responses
models of the auditory periphery
predicting the future inputs
neural network model of neural response
auditory cortex
predictive information in the brain
predicting responses to natural sounds
Marr’s levels of analysis
Advisor: Willmore, B
King, A
Harper, N
Genomic regulation and molecular pathways of X chromosome inactivation

X chromosome inactivation (XCI) is a process by which one X chromosome in female mammals is silenced to equalise the dosage of X-linked gene expression between XX females and XY males. XCI is initiated by a long non-coding RNA (lncRNA), Xist, expressed from the future inactive X chromosome (Xi) during embryonic development. Xist spreads in cis to coat the chromosome and recruits molecular pathways which modify the underlying chromatin from an active to a repressive state, leading to complete transcriptional silencing of almost all genes on Xi. XCI is an important paradigm for lncRNA-directed gene repression and its study can inform our understanding of mechanisms of chromatin regulation more widely.
This thesis presents an experimental characterisation of iXist-ChrX, a cellular model that recapitulates the establishment of XCI during early mouse development. I perform quantitative, high-resolution and allele-specific genomic analyses of Xist-mediated changes to chromatin over time courses of Xist induction, providing novel insights into the cis-regulatory features that influence variable silencing dynamics on a gene-by-gene basis. A key finding from these analyses is that slow-silencing genes and genes which escape complete inactivation are marked by binding motifs for the transcription factor YY1. I also document a pilot scRNA-seq experiment to address questions of cellular heterogeneity in Xist-mediated gene silencing and lay the foundations for future investigations at single-cell resolution.
In further experiments, I use CRISPR-Cas9 genome editing to interrogate two key molecular pathways acting downstream of Xist. By disrupting SPEN and Polycomb pathways individually and in combination in iXist-ChrX cells, I dissect the relative contributions of each pathway and demonstrate that they act in parallel, through distinct mechanisms of chromatin modification, and additively to silence X-linked genes. These experiments also reveal that both SPEN and PCGF3/5-PRC1 have secondary roles in ensuring correct localisation of Xist RNA over Xi, and highlight an interplay with cellular differentiation important for the complete establishment of silencing during the later stages of XCI.

Keywords: polycomb
Xist
genomics
gene silencing
X chromosome inactivation
gene regulation
chromatin
long non-coding RNA
Advisor: Brockdorff, N
Identifying and exploiting structures for reliable deep learning

Deep learning research has recently witnessed an impressively fast-paced progress in a wide range of tasks including computer vision, natural language processing, and reinforcement learning. The extraordinary performance of these systems often gives the impression that they can be used to revolutionise our lives for the better. However, as recent works point out, these systems suffer from several issues that make them unreliable for use in the real world, including vulnerability to adversarial attacks (Szegedy et al. [243]), tendency to memorise noise (Zhang et al. [286]), being over-confident on incorrect predictions (miscalibration) (Guo et al. [99]), and unsuitability for handling private data (Gilad-Bachrach et al. [88]). In this the- sis, we look at each of these issues in detail, investigate their causes, and propose computationally cheap algorithms for mitigating them in practice.
To do this, we identify structures in deep neural networks that can be exploited to mitigate the above causes of unreliability of deep learning algorithms. In Chapter 4, we show that minimising a property of matrices, called stable rank, for individual weight matrix in a neural network reduces the tendency of the network to memorise noise without sacrificing its performance on noiseless data.
In Chapter 5, we prove that memorising label noise or doing improper representation learning makes achieving adversarial robustness impossible. Chapter 6 shows that a low-rank prior on the representation space of neural networks increases the robustness of neural networks to adversarial perturbations without inducing any tradeoff with accuracy in practice.
In Chapter 7, we highlight the use of focal loss, which weights loss components from individual samples differentially by how well the neural network classifies each of them, as an alternative loss function to cross-entropy for minimising miscalibration in neural networks.
In Chapter 8, we first define a new framework called Encrypted Prediction As A Service (EPAAS) along with a set of computational and privacy constraints. Then we propose the use of a Fully Homomorphic Encryption [84] scheme which can be used with a Binary neural network [61], along with a set of algebraic and computational tricks, to satisfy all our conditions for EPAAS while being computationally efficient.

Keywords: regularisation
encyrpted prediction
calibration
generalisation
benign overfitting
adversarial robustness
label noise
machine learning
Advisor: Kanade, VN
Torr, P