VictorJuiz/thesis huggingface dataset:
Tyche: fortune and chance in Euripides and fifth-century historiography
Keywords: Tyche
Greece
chance
historiography
Thucydides
Euripides
chance in literature
fortune in literature
fortune
Herodotus

This thesis is a study of tychē (success, good or bad fortune, chance, unexpected circumstances) and fortune talk in Greek literature, especially fifth-century tragedy and historiography. This concept is examined as part of popular beliefs about gods and other powers of fate, as an agent in contexts of causation, and as part of fortune talk and the rhetoric of success and failure (exhortation and consolation). It emerges that tychē language, moira language and god talk constitute alternative ways of expressing human uncertainty, ignorance and frailty in the face of the unforeseen future, danger or critical circumstances. The choice of word is important, as it expresses an attitude to events as well as an intellectual explanation of them. Calling events tychē points to their lack of any purpose or shape, and may also suggest the randomness of human life or the transience of all things mortal. Calling events ‘god-sent’ or ‘fated’ points to their acceptance as inevitable and as universal markers of the limits of the human condition. In Homer we find a distinction between broad, or large-scale, patterns of events - which tend to be attributed to the divine - and the small details which occur in their working out, which may be seen as chance circumstances. Similar instances of this juxtaposition of long-term and short-term causation can be found in Herodotus and Euripides. This juxtaposition often takes the form of different perspectives: an ‘as-it-happens’ limited perspective tends to be linked with tychē, whereas an ‘in-retrospect’ and post eventum perspective tends to be linked with the divine or moira. The tychē-gnōmē, tychē-technē and tychē-pronoia tensions occur in a variety of contexts and form part of fifth-century intellectual debates. Euripides, in his use of both fortune talk and god talk as well as in his adaptation of earlier ideas about them, turns out to be the most inclusive and inconclusive tragedian.
Predictive coding inspires effective alternatives to backpropagation
Keywords: neural networks
predictive coding
artificial intelligence
brain-inspired learning, artificial intelligence, neural networks, energy-based networks
energy-based networks

The brain has developed a sophisticated hierarchical structure where information is processed across multiple layers (Van Essen et al. 1992), which is critical for forming abstraction from raw information. Inspired by this, modern machine learning is largely built on deep artificial neural networks (LeCun, Bengio, et al. 2015), where neurons are organized in layers, and synaptic weights connect neurons of different layers. One important piece of learning is to correct errors in one’s predictions, and the hierarchical structure requires spreading the errors in one’s predictions across multiple layers and neurons — creating the core challenge of learning known as “credit assignment” (Lillicrap, Santoro, et al. 2020). How the brain solves credit assignment is a key question to understand learning and for creating artificial learning machines, and many recent studies (Lillicrap, Santoro, et al. 2020; Richards, Lillicrap, et al. 2019; Whittington and Bogacz 2019; Zipser and Andersen 1988; Singer et al. 2018; Whittington, T. H. Muller, et al. 2020; Banino et al. 2018) approached it from the perspective of backpropagation (Werbos 1974; Rumelhart et al. 1985; Parker 1985; LeCun, Bengio, et al. 2015). However, it has been questioned whether it is possible for the brain to implement backpropagation exactly (Crick 1989; Grossberg 1987), and learning in the brain seems to be more efficient than backpropagation in several other critical aspects (Tsividis et al. 2017). On the other hand, neuroscience researchers have developed many biologically plausible models to solve the credit assignment problem (Rao and Ballard 1999; Whittington and Bogacz 2017; Whittington and Bogacz 2019; Lillicrap, Santoro, et al. 2020). However, biologically plausible models are still behind backpropagation in terms of generalization and efficiency. The thesis is inspired by this mismatch: the brain mseems to be more advanced than backpropagation, while biologically plausible models learn no better than machine learning models. Thus, the overall goal of the thesis is to demonstrate biologically plausible models can inspire alternative and potentially better solutions for credit assignment than backpropagation, and we take inspiration mainly from predictive coding (PC). Specifically, I first propose a variant of PC that is equivalent to backpropagation. I then propose that the original PC has advantages over backpropagation, implementing a fundamentally different principle from backpropagation, which I call “prospective configuration”. Inspired by the above two findings, I finally propose another variant of PC that is potentially more efficient than backpropagation and has a similar generalization quality as backpropagation.
The law of nuisance and the rule in Rylands v. Fletcher
Keywords: Rylands v. Fletcher
Rylands versus Fletcher
England
nuisances
law of nuisance

The thesis is concerned with the law of private nuisance and the rule in Rylands v. Fletcher, but not with public or statutory nuisance. It is submitted that every case of nuisance is determinable according to the same general principles. The thesis explores the "state of affairs" concept and who the appropriate defendant is. Knowledge of the state of affairs and foreseeability of harm by the defendant are seen as essential to the formation of liability; the suggestion that there are “intentional (or strict) protected nuisances" and "negligent nuisances" is rejected. The right by nuisance is the right to the ordinary enjoyment of land, and the person entitied to this right is the occupier. The nature of this right and the extent of the remedies available are discussed.
The case of Rylands v. Fletcher is seen as but another nuisance case. All the suggested differences between nuisance and Rylands v. Fletcher are explored and found to be illusory. Theories that Rylands v. Fletcher is an application of the "risk-duty" concept of negligence or of a tort of strict liability for “ultrahazardous activities" are examined but found wanting.
The vague concept of "reasonableness" often associated with nuisance is redefined in terms of a defence of ordinary use; the defendant must prove that the state of affairs was ordinary and that the activity causing harm was reasonably done.(This is the defence to Rylands v. Fletcher often "natural user".) Other defences are statutory authority, consent, and contributory negligence, all of which are analysed. Alleged defences found to be without justification in the light of the juristic basis of nuisance are act of a stranger, Act of God, coming to the nuisance, prescription, and the Fires Prevention (Metropolis) Act 1774, s.86.
The riddle of spiritual pedagogy: how is authoritative spiritual teaching possible?
Keywords: Thomas Aquinas
Wittgenstein
religious language
Anselm
spiritual pedagogy

This thesis asks: can a spiritual teacher be said to teach with authority, as much of the Christian tradition holds and, indeed, requires to continue itself? To answer this question, a secondary question is pursued: what is the relationship of spiritual authority to other types of authoritative teaching? The spiritual pedagogue attempts to form others to live according to God’s will, which is mysterious in principle. Unlike most other disciplines, the spiritual teacher cannot claim authoritative knowledge of the essence of her discipline. Nevertheless, I argue that spiritual teaching authority is a legitimate though limited form of authority, and that a sign of such authority is a self-consciousness of its own limitations.
Drawing on Wittgenstein and Aquinas, I argue that spiritual teaching authority is a riddling form of prudential counsel. Wittgenstein’s account of language within shared activities provides the “rough ground” to speak of the activities associated with spiritual pedagogy while distinguishing the inarticulable mystery at the heart of such teaching. The language of spiritual pedagogy is riddling in Cora Diamond’s sense in that such language fails to make sense but lies within a cultivated, intelligible set of questions and activities. This Wittgensteinian account is joined with Thomas’s two rules for prudential human action, the eternal law of God’s own being, and human reason. The eternal law is, in principle, mysterious yet it formally orders human reason. The spiritual pedagogue becomes authoritative by becoming riddling herself, i.e., by being transformed through her engagement with scripture and tradition in community. This ongoing transformation allows her to creatively and richly speak and act around the riddle of God without ever claiming to solve that riddle.
The Franciscan observants in England, 1482-1559
Keywords: observants
Church history
England
Franciscans

Chapter 1. The early development of the northern European Observant movement and the apparent lack of demand for Franciscan reform in England. The English Observant foundations as products of the interest of the monarchy based upon European court fashion allied to their own dynastic purposes.
Chapter 2. The standards of Apostolic Poverty which the northern Observants professed and the extent to which the English friars lived up to them. Numbers of friars and patterns of recruitment. The extent of royal patronage and its reflection in the court. The friars' intellectual temper.
Chapter 3. Suspicions of Lutheranism at Greenwich and Cardinal Wolsey’s attempts to visit and reform the Greenwich friary in 1524-5. The flight of William Roy and Jerome Barlow to the Continent. Wolsey’s employment of another Greenwich friar, John West to track down English protestants on the Continent and the danger of divided loyalties inherent in external patronage of individual friars.
Chapter 4. Friar William Peto’s sermon before Henry VIII (Easter 1532) and the friars’ opposition to Henry VIII’s divorce and the break with Rome. Thomas Cromwell’s attempts, with the aid of a disaffected faction among the friars led by John Lawrence, to control their public opposition and his ultimate failure. The suppression of the friaries as the consequence of the friars” refusal to accept the Royal Supremacy over the English Church.
Chapter 5. The aftermath of the suppression. The friars were not so brutally treated as Franciscan tradition has alleged and they continued to cause trouble. Their rôle in the 'Pilgrimage of Grace'. The case of friar John Forest and the compilation of a list of former Observants. The refoundation of the convents at Greenwich and Southampton under Queen Mary.
An index of biographical data is appended.
Antigen presentation and T cell regulation by intestinal epithelial cells
Keywords: intestinal epithelial cell
mucosal immunology
antigen presentation
CD4 T cell
MHC class II
non-conventional antigen presenting cell

Major histocompatibility complex (MHC) class II expression by intestinal epithelial cells (IECs) has been described in inflammatory bowel disease patients. However, the role of epithelial antigen presentation in the maintenance of immune homeostasis remains unclear. We determined that colonic IECs possess important features of antigen presenting cells, as they express MHC class II in response to IFNg signalling, are able to take up and to process antigen and express the co-inhibitory molecule programmed death-ligand 1. Using targeted deletion of MHC class II expression in IECs, we demonstrated that colonic IEC antigen presentation plays a minor role in controlling colonic inflammation but might be important in facilitating the resolution of chronic inflammation. Small intestinal IECs express MHC class II at steady state and loss of epithelial antigen presentation at this tissue site resulted in the near loss of CD8aa+ CD4+ IELs. However, the functional consequences of this loss remain to be determined. In addition, we investigated the role of epithelial antigen presentation in modulating regulatory T cell responses and demonstrated that loss of caecal IEC MHC class II expression resulted in increased FoxP3 expression and IL-10 production by H. hepaticus-specific CD4 T cells in H. hepaticus colonised mice during intestinal inflammation. An experimental repeat, characterised by lower caecal IEC MHC class II expression, did not show these CD4 T cell changes, highlighting the importance of the tissue microenvironment in supporting antigenspecific CD4 T cell responses by IECs. To further dissect the importance of epithelial antigen presentation, in vitro colonic organoid and H. hepaticus-specific CD4 T cell co-cultures were established. This co-culture system revealed that IECs activate microbe-specific CD4 T cells in an antigen specific manner and modulate their effector phenotypes and functions. These results show, that IECs can function as non-conventional antigen presenting cells but the functional consequences of epithelial antigen presentation in vivo require further investigations.
Mass photometry: weighing single molecules with interferometric scattering microscopy
Keywords: single molecule
interferometric scattering microscopy
mass photometry
label free

Interferometric scattering microscopy (iSCAT) has emerged in recent years as a highly sensitive imaging technique, capable of detecting the scattering signal even from single unlabelled proteins in suitably designed in vitro single molecule assays where the scattering background is kept to a minimum. Here we present numerical aperture filtering in an iSCAT microscope for enhanced contrast of point-like scatterers, and show that it can lead to improved sensitivity through enabling the use of higher incident light intensities.
We apply this development to measuring the scattering contrast of proteins at the single molecule level. This scattering contrast shows the expected linear dependence on molecular weight, allowing the extraction of mass distributions built up from the quantification of one molecule at a time, an approach we refer to as mass photometry. The mass measured in this way shows ∼2% mass accuracy and ∼2% precision. Distinct species are resolved with a full width at half maximum as low as 20 kDa, although this increases with mass, sufficient for low-order homo-oligomeric resolution. These capabilities are exemplified with measurements of the equilibrium constants for the BanLec- induced aggregation of the HIV protein Env, and dynamic imaging of the early stages of α-synuclein aggregation on supported lipid bilayers. We conclude with a detailed discussion of considerations relevant to the acquisition and analysis of high quality, reproducible mass photometry data.
The effects of microstructure on strength and fracture resistance of nuclear graphite
Keywords: tomography
diffraction
DVC
crystallography
synchrotron
correlation
graphite
elastic strain
x-ray
brittle fracture
neutrons

Cracking from stress concentrations of the graphite neutron moderator, or keyway root cracking, is a potential limit for the lifetime of the UK Advanced Gas-cooled Reactors (AGR), and there is a need to better understand how damage occurs prior to fracture. Gilsocarbon graphite is a heterogeneous and quasi-brittle material, a class that includes concretes and natural materials such as bone. This project has made use of, developed, or participated in the development of advanced neutron and X-ray synchrotron techniques to improve the understanding of the deformation of Gilsocarbon graphite. In-situ High-Resolution Tomography and X-ray Diffraction Mapping has confirmed the non-linearity of graphite deformation in compression of a flattened disc and has highlighted the heterogeneity of the microstructure’s response to stress. To this extent, codes have been written to process and match the DVC and XRD strains and extract comparative strain quantities. A novel in-situ technique and associated post-processing routines have been developed with Neutron Bragg Imaging to investigate grain reorientation, and combined with In-situ Three-dimensional X-ray Diffraction (3DXRD) they reinforced indications that this mechanism is recoverable. In-situ High Speed Synchrotron Tomography provided unique time-resolved observations of crack initiation, propagation and coalescence away from a stress concentration, indicating the prevalence of lenticular cracks. With as much as 72 hours of beamtime, this project has developed reusable techniques and provided unique insight of the damage accommodation in nuclear-grade graphite.
Arbitrage-free neural-SDE market models of traded options
Keywords: option market simulators
quantitative risk management
no-arbitrage
neural-SDE
statistical inference
constrained diffusion processes
option market models

Modelling joint dynamics of liquid vanilla options is crucial for arbitrage-free pricing of illiquid derivatives and managing risks of option trade books. This thesis develops a nonparametric model for the European options book respecting underlying financial constraints while being practically implementable. We derive a state space for prices which are free from static (or model-independent) arbitrage and study the inference problem where a model is learnt from discrete time series data of stock and option prices. We use neural networks as function approximators for the drift and diffusion of the modelled SDE (stochastic differential equation) system, and impose constraints on the neural nets such that no-arbitrage conditions are preserved. In particular, we give methods to calibrate \textit{neural-SDE} models which are guaranteed to satisfy a set of linear inequalities.
We validate our approach with numerical experiments using both (i) synthetic data generated from a Heston stochastic local volatility model and (ii) real world data. In both cases, we assess how well the model captures option price dynamics, and therefore its capacity as a realistic option market simulator. However, the presence of arbitrage in the real world option price data causes difficulties in the calibration of our models, making pre-processing of the data to eliminate arbitrage necessary. We formulate the arbitrage repair as a linear programming (LP) problem, where the no-arbitrage relations are constraints, and the objective is to minimise prices' changes within their bid and ask price bounds. Through empirical studies, we show that the proposed arbitrage repair method gives sparse perturbations on data, and is fast when applied to real world large-scale problems due to the LP formulation. In addition, we show that removing arbitrage from price data by our repair method can improve model calibration with enhanced robustness and reduced calibration error.
Finally, we explore the capacity of the model in two important applications for managing risks of option books, namely the Value-at-Risk (VaR) calculation and hedging. In terms of calculating VaR, we show that our models are more computationally efficient and accurate for evaluating risks of option portfolios, with better coverage performance and less procyclicality than standard filtered historical simulation approaches. In the hedging application, we derive sensitivity and minimum variance based hedging ratios under neural-SDE market models, and compare the performance of hedging various option portfolios with standard Greeks-based hedging under the Black--Scholes model, demonstrating favourable performance of our approach.
Epidemiology and health burdens of antimicrobial resistant bacterial infection in Southeast Asia and impact of antibiotic use on patient survival
Keywords: causal inference
discordant empirical antibiotic
hospital-acquired infection
blood utilisation rate
antimicrobial resistance
application
prospective surveillance

Antimicrobial-resistance (AMR) is a global health concern. Data to support estimates of the AMR health burden are important to guide policy makers in developing appropriate interventions. The objective of this thesis is to improve the understanding of the epidemiology of AMR in low and middle-income countries (LMICs), where data is scarce.
A prospective surveillance study on hospital-acquired infection (HAI) was conducted to estimate excess mortality attributable to AMR infection in a LMIC. Evaluating all types of infections and seven priority bacteria, I estimated that 16.0% of deaths involving bacterial infections were attributable to AMR. This is higher than is observed in high-income countries (HICs).
One of the barriers in sharing AMR data in LMICs is a lack of expertise, time, and resources to analyse the data and write reports. I developed an open-access, offline, and easy-to-use application to fill in this gap. The tool was tested in seven hospitals in seven countries. AMR surveillance reports from those hospitals were shared on an open-access data repository platform and each has a digital object identifier that can be appropriately cited when re-used.
It is known that low blood culture usage can bias the estimates of health burden of AMR. However, the magnitude of this effect is largely unknown. I performed a retrospective study with bootstrap sampling to illustrate the potential magnitude of biases in the estimates of AMR prevalence and incidence rates due to low blood culture utilisation rates.
Finally, using a large retrospective data set, I applied a counterfactual framework to estimate the impact of delays in concordant antibiotic treatments. Attempts were made using observational data to emulate randomised controlled trials that are otherwise unethical to perform.
This thesis describes work which generated data, provided evidence, and created a new tool for quantifying the health burden of AMR infections in LMICs.