VictorJuiz/thesis huggingface dataset:
Towards an effective vaccine against Plasmodium vivax malaria

Over seventy vaccines are now licensed against more than thirty pathogens, but despite a century of effort, the malaria parasite is not among them. In the meantime, effective drugs and anti-mosquito measures notwithstanding, millions still suffer and die from of a disease which belongs in the history books. The reasons are largely political and economic, malaria is a neglected disease of the poor, but also scientific; a parasite as protean as Plasmodium is not easy to pin down with a vaccine.
It has been known for over a hundred years that almost a billion people on the world’s most malarial continent are ‘naturally immune’ to Plasmodium vivax (P. vivax) malaria. I can think of no other human pathogen with such an ancient and continental-scale natural experiment to inspire research. The source of this immunity was discovered, over forty years ago, to be due to the lack of the Duffy antigen on the surface of red blood cells. The parasite must bind to this Duffy antigen, using its ‘Duffy-binding protein’ (DBP), in order to invade the erythrocyte. Despite this ‘Achilles heel’ of P. vivax being known about for decades, it was not until 2014 that it was first targeted in a human vaccine trial. This long overdue trial of a P. vivax DBP (PvDBP) vaccine provided the source material for, and the starting point of, this DPhil Thesis. The extreme polymorphism of malaria antigens, such as PvDBP, poses a great challenge to vaccine design, but new approaches are emerging to tackle this and it is one of these, known as ‘epitope-focused vaccinology’, that I pursue in this Thesis. I report the production of the first panel of vaccine-induced human monoclonal antibodies (mAb) against PvDBP and, through testing in functional assays using both P. vivax and a transgenic Plasmodium knowlesi line, the discovery of a broadly-neutralising mAb. X-ray crystallographic studies have identified its epitope on PvDBP and the process of re-engineering the PvDBP vaccine to place this conserved and critical epitope in the immune system’s spotlight has begun.

Advisor: Draper, S
Higgins, M
Empirical performance of simple statistical inference-type models with feature extraction in comparison to modern machine learning methods concerning regression and classification problems

While most statistical methods used in the industry are of simple structure -- like decision trees and logistic regression -- many machine learning competitions are won by modern complex methods, which also outperformed the more simple methods in previous benchmark studies. In these benchmark studies, the results were usually obtained over raw and unprocessed datasets. In practice, when developing a model, a feature extraction is performed first to create non-redundant and useful covariates for the model. This is especially important for the simple methods, which often require approximately linear features without severe outliers.
In this thesis, we investigate the performance of modern machine learning methods on raw data, without any additionally extracted features, in comparison to simpler and more interpretable models on data together with feature extraction. For this purpose we employ certain preprocessing and feature extraction algorithms to objectively approximate this task over 32 different datasets.
Our results show that, for classification problems, the simple methods perform almost as well as the more complex methods. This is true for both binary classification, regarding the metric area under the ROC curve, and for multiclass classification with regards to the weighted F1 Score metric.
In our regression problems, the modern methods outperform the simpler methods and seem superior to the more interpretable methods in terms of their respective R-squared or explained variance.
We suspect that the difference between classification and regression problems might be due to the evaluation metrics used; specifically how they react to the monotonicity or linearity of the extracted features, but more research is necessary to investigate this difference.

Keywords: classification
performance
empirical
benchmark
interpretable model
regression
black box model
Advisor: Graf, F
Cohen, S
Malware ecologies: a politics of cybersecurity

Computation, in popular imaginations, is at perennial risk of infection from the tools of nefarious hackers, commonly referred to as malware. Today, malware pervade and perform a crucial and constitutive role in the insecurities of contemporary life from financial transactions, to ‘critical national infrastructures’ – such as electricity, water, and transportation – to devices in our ‘smart’ homes and cities, and even to potential ‘cyberwar.’ Yet, critical security research has rarely turned its attention to malware. In contrast, I explore malware and their politics, situated and extended beyond, an (auto)ethnographic study of the malware analysis laboratory of the UK endpoint protection business, Sophos. I argue that malware are currently processed through a patho-logic that conflate organic and non-organic materialities, permitting analogies between biology and computation, and are generative of particular forms of security that relegate malware to the intent of their authors. I explore how endpoint protection businesses are imbibed with these logics in order to attend to how malware are analysed, detected, and curated beyond them. By drawing on my method of ‘becoming-analyst,’ I critically reflect on how malware become known, are responded to by ad hoc political groups, and can assist in rethinking the role of computational agency in geography, international relations, security studies, and beyond. I instead conceive of malware as performative political actors making limited choices in broader computational ecologies. I therefore advocate for an eco-logical repositioning of malware, where cyberspace is not simply a neutral domain; but is central to the formation of choice that gives space for malware to be political. With four cases – Conficker, Stuxnet, the Dukes, and WannaCry / (Not)Petya – I write new stories on how malware are encountered and dealt with in the twenty-first century. In doing so, I challenge contemporary discourses of cybersecurity to ask if conventional notions of who and what (per)form security are adequate, and how these are reconfigured through a radical 'more-than-human' politics, where malware are not just objects of security, but are active participants in its production and negotiation.

Keywords: Agency
Cybersecurity
Geography
Malware
Cyberspace
Advisor: McCormack, D
Greenhough, B
The ritual of churching of women after childbirth in Denmark, 1500-1900

This thesis traces the ritual of churching of women after childbirth in Lutheran Denmark which has hitherto been marginalised in scholarship. Rooted in Levitical childbirth impurity and closely linked to the Feast of the Purification of the Virgin Mary, churching was a troublesome legacy for Lutheran reformers because initially it fell short of supporting the objective of elevating marriage as the cornerstone of society and propounding procreation as the foremost duty of virtuous mothers. Reformers solved the problem by retaining a mandatory lying-in whilst remodelling churching as a thanksgiving ritual shorn of Catholic sacramentals. Yet notions of childbirth uncleanness were not immediately eradicated, and mothers reacted by reshaping the ritual to fit with their own religiosity. The ritual of churching therefore offers fresh insight into the reception of Lutheran reform at parish level.
Rediscovering the rite through hymns, sermons, clerical and legal papers, narratives and material culture, this study demonstrates that churching not only served to reintegrate the mother into Church and society after childbirth but it was also a social marker for the married mother and helped to reinforce communal bonds. For the unmarried mother, however, her route back to Church and society was through church discipline. If churching thus afforded the clergy the means to shame the unwed, a married mother could well use the rite to punish an unpopular clergyman by withholding the churching fee or behaving aggressively during the ceremony. This insight adds a new facet to the scholarship of the complex power relationship between parishioners and clergy in early modern Denmark. From the eighteenth century onwards, churching was rarely performed in urban areas. Far from becoming obsolete, however, this thesis demonstrates that rural churching continued to thrive well into the nineteenth century and, in some areas, even into the first half of the twentieth century.

Keywords: Church rituals
Motherhood
Church discipline
Scandinavia
Churching
Advisor: Roper, L
The magic lantern in Japan: transnational technology across the long nineteenth century

This thesis presents a history of the magic lantern in Japan from the late eighteenth to the early twentieth century. From the first recorded appearance of the magic lantern in the 1770s, Japanese intellectual figures such as Ōtsuki Gentaku were fascinated by the device and positioned it within a wider discourse on epistemology, knowledge about nature, and the study of the human body. This helped to lay the groundwork for the emergence of localised groups of domestic magic lantern producers in the early nineteenth century, which supported, in turn, the unprecedented country-wide popularity of magic lantern shows in the latter half of the 1800s and early 1900s. With different versions of the device in production and circulation, the technology found use in the hands of a variety of state and non-state historical actors, linking it to both broad societal changes and the everyday lives of Japanese people in this period.
This work, the first detailed study of the topic in English, traces not only the development of the magic lantern as a physical instrument in Japan, but also the expanding web of intellectual, social, economic, cultural, and political developments that hinged on or were otherwise profoundly shaped by connections to this unique technology. As well as elucidating the significance of the magic lantern beyond the spheres of visual culture and pre-cinema history, the thesis uses the device to tell a story from beyond the prevailing narratives of global technological and intellectual development. By analysing the ways that this single technology was imported, ascribed meaning, manufactured, and used over a significant timeframe – the “long” nineteenth century – it is possible to consider Japanese history outside of the conventional divide of “early modern” Tokugawa Japan and “modern” Meiji Japan. This new technological history decentres the influence of the West and the state, revealing instead the far-reaching importance of transnational, often non-state connections and networks to major trends in areas such as technological and cultural production, epistemology, humanitarianism, and political discourse.

Keywords: Japanese History
History of Science and Technology
Advisor: Konishi, S
Development of NMR methodology for the study of complex molecular and biomolecular systems

Nuclear magnetic resonance (NMR) is amongst the most powerful and versatile spectroscopic tools for characterising biological systems. A key advantage of NMR techniques is that in addition to being sensitive to structural features of biomolecules through their chemical shift, chemical exchange and relaxation processes allow dynamic molecular properties to be studied. Techniques have also been developed to facilitate the characterisation of translational diffusion with NMR, through the application of pulsed field gradients.
In this thesis we develop and apply NMR methods for studying biomolecular systems. Firstly, in Chapter 2, we introduce an experimental protocol and model for the analysis of cellular systems from the diffusional properties of the water within them. In addition to reporting diffusion coefficients, this analysis also provides information on cell radii, abundance and permeability. A drawback of NMR compared to other spectroscopic techniques is its relative insensitivity. One way of improving this is through chemical exchange saturation transfer (CEST) experiments where the presence of lowly concentrated species is effectively read out through its interactions with a highly concentrated species. In Chapter 3 we show how this experiment can be used to follow changes in a range of solution properties. The diffusion and CEST experiments are combined in Chapter 4, where we introduce the novel diffusion-weighted CEST experiment. Here, the diffusion weighting is used to differentiate between compartments, while the CEST component of the experiment characterises properties of each of the compartments.
In Chapters 5 and 6, modern NMR techniques are used to characterise dynamical features of 15N-labelled proteins. Experiments employed in this section include a fast dynamics analysis as well as CPMG and R1ρ relaxation dispersion experiments. Collectively, these experiments provide important insights into the behaviour of the proteins with atomic-level resolution.

Keywords: Nuclear Magnetic Resonance (NMR)
Advisor: Baldwin, A
Flow and combustion in direct injection spark ignition engines

The goal of producing more efficient internal combustion engines has led to the use of more advanced technologies and operating strategies. As a result, Computational Fluid Dynamics (CFD) is now a standard tool that is used to optimise the design of new combustion systems. Validation of these numerical simulations is essential, especially for the prediction of in- cylinder flow, which is known to have a profound effect on mixture preparation and combustion. Therefore, high quality, in-cylinder flow measurements are required to aid the validation process and the design of new combustion systems.
This work outlines the development of an optical engine test facility and the installation of a high-speed Particle Image Velocimetry (PIV) system that provides in-cylinder flow measurements with high spatial and temporal resolution over a large range of crank angles. The system is capable of producing measurements at a maximum rate of 3.7 kHz at full resolution and a total of 6000 frame pairs in a single experiment. Additional improvements to the system for specific application to IC engines have been outlined, including the use of variable inter-frame delay and methods of scatter minimisation.
To aid the validation of CFD simulations, metrics known as the Weighted Relevance Index (WRI) and the Weighted Magnitude Index (WMI), have been developed to quantify differences between flow fields in terms of both alignment and magnitude. These have been combined to produce a third metric, the Combined Magnitude and Relevance Index (CMRI), that produces a single value that rates the similarity of two flow fields. The application of these metrics has been demonstrated by investigating the differences between velocity measurements and CFD RANS simulations in the central tumble plane for three test conditions. The metrics were able to determine regions of the flow field that were significantly different between simulation and experiment, which would not be highlighted by conventional metrics.
Flow field measurements were also made during the induction and compression strokes of firing cycles to investigate the effect of in-cylinder flow structures on cycle-by-cycle variations in combustion. The cycles were separated into subsets conditioned on burn rate, as indicated by in-cylinder pressure measurements. The WRI and WMI were then used to compare the conditionally averaged flow fields of fast and slow burning cycles. From this analysis, it was possible to determine regions of the flow that have a significant effect on the rate of combustion. Simultaneous combustion imaging showed that the flames for slow burning cycles tended to grow asymmetrically towards the exhaust valves. In contrast, the flames of fast burning cycles were convected away from the spark plug and grew rapidly in all directions.

Keywords: Laser Diagnostics
Internal combustion engines
Combustion
Advisor: Stone, R
Teens, screens and well-being: an improved approach

Concerns about emergent technologies form a continuous cycle: they appear when a new technology surpasses a certain popularity threshold and stop once a newer technology prompts the cycle to restart. Currently, society is concerned about teenage digital technology and social media use, which is feared to negatively impact well-being. While there has been a flurry of research in the area, remarkably little consensus has been reached. I argue in this thesis that such a lack of consensus stems from a lack of methodological rigour. Using innovations put forth by psychology’s recent credibility revolution, I devise an improved methodological framework for the study of emergent technologies. I then apply it to investigate digital technology and social media use’s association with decreased adolescent well-being, using large-scale secondary datasets from the United Kingdom, Ireland and the United States. My first study implements a methodological approach called Specification Curve Analysis, which tackles analytical flexibility by illustrating how diverse analytical approaches can produce a wide range of numerical outcomes. Furthermore, I develop a comparison specification method to put the size of the associations found into perspective. My second study focuses on diversifying measurement and implements an explicit exploratory and confirmatory hypothesis testing framework. Lastly, my third study utilises high-quality longitudinal data to highlight the bidirectional and individual nature of the effects of interest. All studies indicate that previous systematic reviews overestimated the negative link between digital technology use and well-being. It is however still unclear whether the small, complex and inherently multivariate relationship found in this thesis should engender widespread policy change.

Keywords: Specification Curve Analysis
Open Science
Adolescents
Digital Technology
Well-Being
Social Media
Advisor: Dunbar, R
Bishop, D
Advanced gas turbine cooling: double-wall turbine cooling technologies in turbine NGV/blade applications

The drive to increase the thermal efficiency and specific power output of the gas turbine results in increasing turbine temperatures which necessitate active cooling of the turbine blades. High performance cooling systems are required which achieve the necessary blade life requirements whilst minimising coolant consumption. This thesis explores one potential turbine cooling system advancement termed the double-wall, effusion cooled system which is envisaged to find application in areas where high cooling performance is required.
Single wall effusion cooling performance is initially investigated given its importance in the double-wall system. An experimental investigation is performed and used to validate a computational model. A two-dimensional superposition method for predicting effusion cooling performance is presented and validated based upon the experimental and computational data.
The superposition method was used as part of a computationally light, decoupled conjugate method which was developed to predict the cooling performance of double-wall geometries. This decoupled method was used to assess several developed double-wall geometries. Those geometries which exhibited preferable cooling characteristic were manufactured for testing in a novel experimental facility, designed and commissioned as part of the thesis work. The facility incorporates several features to improve the quality of data obtained and matches several relevant non-dimensional parameters. The facility was used to obtain both overall effectiveness and film effectiveness results for five flat plate, double-wall geometries. This data was then used to infer the convective cooling performance of each geometry at varying coolant flow rates, with preferable cooling features identified. The results indicate the high cooling performance achieved in double-wall, effusion cooled geometries.
Two computational methods were used to replicate the experimental setup utilising boundary conditions obtained from the facility. The first was a fully conjugate solver, and the second was a modified form of the developed decoupled method. The results from both sets of simulations compared favourably with the experimental data. The decoupled conjugate method was particularly encouraging given the vast reduction in simulation time required when compared to the fully conjugate solver.
Thermomechanical analyses were performed to identify how various geometric features influence the stress field developed under thermal load, which has direct implication on blade lifespan. The work was successful in indicating certain double-wall configurations which could reduce the magnitude of the stresses.

Keywords: Heat Exchangers
Heat Transfer
Turbine Cooling
Gas Turbines
Turbomachinery
Aerodynamics
Advisor: Ireland, P
A battlefield of memory: the Nakba and the Holocaust as exclusive victimhood narratives

Situated in the post-Oslo era, this work constitutes a parallel analysis of the collective transmission of the foundational pasts in Israeli-Jewish and Palestinian society, respectively the Holocaust and the Nakba. Through the application of postmodern criticism to Maurice Halbwachs’ unitary understanding of group memory transmission, this thesis exposes the existence and perpetuation of exclusive and ethnocentric victimhood narratives that provide the theoretical foundations for an ensuing minimization of the out-group’s past. Divided into three sections, which correspond to the examined realms of memory transmission, a range of qualitative research methods are used to analyze the conveyed narrative across the established realms of collective memory transmission: official state education, commemorative acts and mass mediation. Beyond an analysis of the depiction of the primary history events in the societies’ curricula, mass media and commemorative institutes, semi-structured interviews with (former) memory agents and participant observation testify to the interplay between elites’ historical conceptions and the transmitted narrative.
While illustrating the universal plasticity of memory construction in coherence with contemporary political and societal needs, this work emphasizes the effects of the intractable Israeli-Palestinian conflict on the contemporary contextualization of the primary historical events and the ensuing subversion of the other’s past. Much like the original scenes of the watersheds and the principal actors, this thesis demonstrates that the exclusionary bases of Palestinian and Israeli victimhood narratives differ. The invocation of an exclusive Jewish Holocaust suffering thus is not unique to Israeli society; nevertheless, a consistent framing of a particularistic Zionist Holocaust victimhood narrative in the context of the Middle East conflict has stymied acknowledgement of the Palestinian catastrophe, deemed an inherent challenge to the ongoing redemptive nature of the Israeli state. An exclusive Palestinian victimhood narrative, conversely, has materialized in direct response to the opponent’s foundational memory. Rather than solely underlining an understanding of Israeli-Jewish political usage of the Holocaust, this thesis reveals that the retaliatory nature that characterizes the exclusive Palestinian narrative derives from its application as an interpretative framework –– an ‘ongoing Nakba’ –– which sheds light on the Palestinians’ marginalization and, consequently, demands a screening out of any past suffering of those held responsible.

Keywords: Israel
Advisor: Rogan, E
Waxman, Z