VictorJuiz/thesis huggingface dataset:
Investigating protective mechanisms of anti-sporozoite vaccines

Malaria remains a leading cause of childhood mortality, thereby highlighting the need for an effective vaccine. R21 is a virus-like particle-based (VLP-based) vaccine displaying the immunodominant NANP repeat region of the circumsporozoite protein (CSP) of Plasmodium falciparum. R21 is biosimilar to the current leading malaria vaccine candidate, RTS,S, in that CSP epitopes are found on the VLP surface. However RTS,S has a higher ratio of unbound Hepatitis B surface antigen (HBsAg) than CSP.
R21/Matrix M (R21/MM) was initially manufactured in Oxford with a C-tag for purification, but is now manufactured at the Serum Institute India (SII) without a C-tag. The products made using the two manufacturing processes elicit comparable immunogenicity and efficacy among malaria naïve adults in the UK using comparable dose regimens.
Three doses of R21/MM produce comparable immunogenicity in adults in the UK, Kenya and Burkina Faso, all with different transmission settings. Anti-NANP antibodies were comparable to antibodies measured in protected malaria naïve adults immunised with RTS,S/AS01. A fractional third dose and delayed fractional third dose whereby a third dose of one-fifth did not improve ELISA-measured antibody titres or efficacy. However, a delayed third dose administered at 5 months increased antibody avidity. Among R21/MM immunised malaria naïve adults anti-NANP IgG titres greater than 1100EU and anti-C term IgG greater than 1100EU were associated with protection.
R21/MM was examined in infants in both Kenya (low relatively consistent transmission) and Burkina Faso (seasonal transmission). Infants in both countries, who were administered the same dose, produced comparable antibody titres. Infants immunised with the higher dose adjuvant (50µg MM) produced higher antibody titres and functional antibodies as compared to low dose adjuvant (25µg), irrespective of the dose of R21. Furthermore, three doses of R21/MM and a booster administered 12 months later produced efficacy that met WHO's desired vaccine efficacy of 75% by 2030.
Both RTS,S and R21 induce high anti-NANP IgG responses following a 3-dose primary series regimen and after a boost. Anti-NANP IgG durability measured twelve months after primary series and boost were improved in R21 immunised infants. In addition, HBsAg titres were 8-fold higher with RTS,S. Increased CSP antibody durability and high cytophilic subclass antibody responses may contribute to the effectiveness of the R21 vaccine.
High protection and immunogenicity to CSP antigens induced by R21 along with large-scale manufacturing and reduced cost from the SII will support R21 for the Phase III study and aid WHO pre-qualification approval following the recent positive recommendation. Additional effective vaccines to accompany RTS,S will help alleviate supply help contribute towards increasing demand and, ultimately, reduce morbidity and mortality from malaria amongst the most vulnerable populations.

Keywords: infectious diseases
immunology
Malaria
vaccine
Advisor: Ewer, K
Hill, A
Geologic processes that control sourcing and migration of subsurface helium


There is an ever-pressing need to find more helium (He) because 1) it is an essential resource for modern life, 2) reserves are dwindling faster than He accumulations are discovered, and 3) new He projects are delayed. The motivation for this work is to provide updated frameworks on the geologic processes and migration mechanisms of He in the mid-continent USA, using noble gas geochemistry, structural geology and geophysics. The Colorado Plateau field area (Four Corners area), USA was chosen to represent a moderate tectonic activity environment, and Yellowstone (and its environs), USA, were chosen to represent a very tectonically active region and to investigate the impact of heat on gas release. In the Four Corners area, utilizing bulk gas and isotopes of hydrocarbons, non-hydrocarbons, and noble gases (n=31), we construct mass balance and noble gas fractionation models that provide evidence for advective fault-controlled systems responsible for basement sourced He accumulations. Regarding Yellowstone, utilizing heat flow data, bulk gas, and isotopes of non-hydrocarbons and noble gases (n=43), we quantify gas origin, fluid flow, and heat influence in a regional context using noble gas heat and fractionation models. We show a poor relationship regarding He and heat flow on a regional scale for Yellowstone, and we propose that localized heat sources are important in releasing He trapped in minerals. Our prediction of fault-controlled He-systems in the Four Corners area is corroborated with high-resolution geophysical data that shows a strong non-random relationship with He-rich occurrences and structural features (faults/intrusions) and historical He-well data (n=94). Based on the distributions of these relationships, we create a regional probabilistic predictive He map to reduce exploration risk. Additional work utilizing soil gas data (n=1974), was used to construct a higher-resolution localized predictive model calibrated with real-world data illustrating areas that are higher-likelihood of containing He-rich gas.

Keywords: helium exploration
structural geology
noble gas and stable isotope geochemistry
helium sources and migration
crustal-fluid interactions
statistical models
helium systems
Advisor: Ballentine, C
Cartwright, J
Rights appropriated to a scheme: trusts, partnerships and deceased estates compared

This thesis focusses on English standard fixed trusts, English partnerships and English deceased estates. It examines some similarities and differences. These three institutions share at least two important features. The first is that they all involve rights being appropriated, in the totality of the jural relations to which those rights give rise, to a scheme. The second is that the scheme defines the rights of the beneficiaries in all three cases as subject to the priority claims of the scheme’s managers and the scheme’s creditors. If those claims exceed the assets of the fund, both during the scheme’s existence and at its end, then the beneficiaries will be left with nothing. In this sense, the rights of trust beneficiaries, partners and legatees are residual. They are residual because the scheme beneficiaries’ interests are vindicated after those of the scheme’s manager and the scheme’s creditors. At its core, the interest held by the scheme beneficiaries in these three cases is the same: a right to due administration of the scheme. That right exists because the scheme’s beneficiaries have a practical interest in seeking the scheme’s enforcement. Although the core interest held by trust beneficiaries, partners and legatees is the same, there are important conceptual differences in the nature of these three institutions, which may justify their separate treatment in certain contexts. With partnerships, the doctrine of ostensible authority provides an important difference with the standard fixed trust, whereas the fact that a legatee’s interest is subject to the priority claims of both the deceased’s general creditors and the executor’s scheme creditors offers a valid criterion of distinction with the interest of a standard trust beneficiary.

Keywords: rights appropriated to a scheme
trusts
schemes
Advisor: McFarlane, B
Whom? The effect of target agent on motivation to help, hurt, or understand

This thesis is about the social psychology of motivation: When do we go out of our way to help an individual other than ourselves? In the studies that follow, I explore how what we know about that other person—whether they are a member of an in-group or out-group, whether we perceive them to be similar to ourselves—modulates our willingness to exert effort on their behalf (i.e., prosocial motivation). I investigate these effects of different target agents on motivation not only for helping behaviour, but also for one's willingness to harm others or to better understand the contents of their minds. I use a combination of experimental and computational methods to address these questions in twelve studies across five empirical chapters.
The studies presented in this thesis can be divided into two parts. In the first part, I investigate the role of prosocial motivation in reward-seeking behaviour. How do we value rewards for others, depending on what we know about who that other person is? How do those valuations change our willingness to exert effort on another's behalf? This line of research represents an advancement on an existing paradigm, the Prosocial Effort Task (Lockwood et al., 2017; Lockwood et al., 2021), to extend findings about prosocial motivation to help an anonymous other—about whom no social identifying information is provided—to various kinds of target agents, such as members of one's in- or out-group. In the second part, I develop my own novel paradigm designed to assess individual differences in accuracy and perceived effort for performing mental state inferences by neurotypical adults. I investigate the possibility of these stimuli for detecting differences in theory of mind ability, depending on what social information is given about the target mind. Are people less willing to exert effort when making inferences about out-group minds? I end with a discussion of possible future directions for a research program investigating this kind of intergroup theory of mind.

Keywords: Minimal Groups
Prosocial Motivation
Empathy
Theory of Mind
Advisor: Apps, M
Bird, G
Mesolimbic dopamine and circuit level mechanisms in action initiation and restraint 

Beneficial decision making does not just involve selecting which action to make based on anticipated future reward but also being able to withhold responding at appropriate times. Mesolimbic dopamine is associated with both reward processing and the activation of reward seeking action. Yet an understanding of how phasic dopamine signals may influence reward guided action, and how extended circuits may act in concert with dopamine when action must be controlled, remains lacking. To probe these questions, we applied different causal manipulations within a common behavioural paradigm – a reward-guided Go/No-Go task – where animals must either restrain or enact action to obtain different sizes of reward. In Chapter 3 we demonstrate that transient activation of VTA dopamine neurons can promote action over inaction, in a manner dependent on the magnitude of activation and its timing relative to task relevant cues. Though effects on behaviour were observed most strongly on trials receiving stimulation, we also found stimulation influenced within-session behavioural strategy, biasing animals towards premature action as the session progressed. In Chapter 4, we show that the ability to successfully restrain action depends on prelimbic and infralimbic, but not the medial orbital, subregions of the medial prefrontal cortex. However, while pharmacological inactivation of prelimbic and infralimbic cortex both increased premature responses on No-Go trials, analysis of the patterns of errors showed distinct contributions of these areas to action restraint. Conversely all three subregions are shown to be crucial for executing the correct action sequence for reward. In Chapter 5 we determined that potentiating endocannabinoid signalling did not boost motivation as had been observed in simpler behavioural paradigms, but rather selectively increased the likelihood of entering into an unfocused state when needing to complete the Go trial action sequence to gain reward. Together, this thesis demonstrates the capacity for phasic dopamine signals to causally influence reward guided action, and highlights how medial prefrontal circuits and the endocannabinoid system contribute to the initiation and restraint of action, key information for progressing towards an integrated understanding of the systems governing appropriate action control.

Keywords: action control
action restraint
medial prefrontal cortex
reward seeking action
decision making
endocannabinoid signaling
mesolimbic dopamine
Advisor: Walton, M
Bannerman, D
Extraverted developmentalism: the political logic of special economic zones in Angola and Ethiopia

The African growth spurt of the 2000s and 2010s saw a resurgence of developmental ambitions. Special economic zones (SEZs) stood out as one of the main industrial policy instruments deployed during this period. This thesis seeks to elucidate the reasons for the diffusion of SEZs, variations in SEZ design, and quality of implementation, focusing on the cases of Angola and Ethiopia, two of Africa’s most assertive post-liberation regimes.
I contend that the logic of industrial policymaking in African post-liberation regimes can be conceived of as the outcome of political struggles carried out within a shared set of ideas, policy “styles”, and opportunities for unequal exchange with the outside world, or “extraversion”. Industrial policy therefore derives from the interaction between domestic political dynamics, regimes’ historically inherited ideational dispositions, and changes to the global political economy.
To bear out this argument, I trace the trajectory of SEZ policy in Angola and Ethiopia, drawing on over 130 elite interviews, archival data, and proprietary surveys of SEZ firms. I show that recourse to SEZs and differences in their design can be explained by how pre-existing developmentalist ambitions were fuelled by an enabling external economic conjuncture, particularly the rise of China. Policy styles in turn left their mark on the progression of SEZ policy: the EPRDF’s “disputatious” policy style assigned great importance to theorization and learning, ensuring that SEZs’ technical quality improved over time. In contrast, the MPLA’s “bifurcated” policy style featured a gap between developmentalist aspirations and the reality of pervasive rent-seeking, leading to an essentially unchanged, and failed, agenda.
By highlighting the role of shared ideas in shaping industrial policy, explaining their historical and political origins, and examining the impact of a changing global political economy, this thesis contributes to the study of authoritarianism and the comparative political economy of industrialization.

Keywords: post-liberation regimes
political economy of development
industrial policy
African politics
special economic zones
Advisor: Soares de Oliveira, R
Discovery and investigation of high-capacity cathode materials for next generation Li-ion batteries

Lithium ion (Li-ion) batteries are the current state of the art for electrochemical energy storage and there is increasing demand for Li-ion batteries with a higher energy density. To achieve such a goal, cathode materials with higher capacity are required. Layered lithium rich (Li-rich) cathode materials are considered as a potential cathode candidate for future high capacity Li-ion batteries, mainly due to their large reversibly capacity of about 250 mAh g-1. However, the underlying chemistry of these materials remains unclear. The goal of this D.Phil. project is to investigate the underlying chemistry of these materials, especially the origin of the extra capacity; then to explore new Li-rich cathode materials with high capacities.
The Resorcinol - Formaldehyde gel (R-F gel) method was selected from three different synthesis methods for preparing the layered Li-rich materials, as the material obtained by this method presented stable and enhanced electrochemical performance. By using a variety of characterization methodologies, a detailed study on the 1st cycle of Li1.2Ni0.13Co0.13Mn0.54O2, an archetypal example of layered Li-rich materials, were carried out and the extra capacity was attributed to a reversible oxygen redox process. A model of this oxygen redox process was also proposed, suggesting the balance between ionicity and covalency of metal-oxygen (M-O) bond is essential for activating this reversible oxygen redox. Additionally, a study of the binder effects on a layered Li-rich cathode was carried out. It was demonstrated that different binders used in electrodes would influence the electrochemical performance of the layered Li-rich cathode.
A subsequent work was to synthesize and investigate Li1.2Mn0.4Ti0.4O2, a disordered rock-salt Li-rich material, which also exhibits enormous capacity and 1st cycle load curve similar to the layered Li-rich materials. A reversible oxygen redox process was demonstrated to be responsible for its extra capacity by using a variety of characterization methodologies. Moreover, the rock-salt structure was found remaining stable in the 1st cycle. The study of disordered rock-salt Li1.2Mn0.4Ti0.4O2 brings a new perspective to the study of oxygen redox in Li-rich cathode materials.

Advisor: Bruce, PG
Safety quantification in gene editing experiments using machine learning on rationally designed feature spaces

With ongoing development of the CRISPR/Cas programmable nuclease system, applications in the area of \textit{in vivo} therapeutic gene editing are increasingly within reach. However, non-negligible off-target effects remain a major concern for clinical applications. Even though a multitude of off-target cleavage datasets have been published, a comprehensive, transparent overview tool has not yet been established. The first part of this thesis presents the creation of crisprSQL (http://www.crisprsql.com), a large, diverse, interactive and bioinformatically enhanced collection of CRISPR/Cas9 off-target cleavage studies aimed at enriching the fields of cleavage profiling, gene editing safety analysis and transcriptomics.
Having established this data source, we use it to train novel deep learning algorithms and explore feature encodings for off-target prediction, systematically sampling the resulting model space in order to find optimal models and inform future modelling efforts. We lay emphasis on physically informed features which capture the biological environment of the cleavage site, hence terming our approach piCRISPR. We find that our best-performing model highlights the importance of sequence context and chromatin accessibility for cleavage prediction and compares favourably with state-of-the-art prediction performance. We further show that our novel, environmentally sensitive features are crucial to accurate prediction on sequence-identical locus pairs, making them highly relevant for clinical guide design.
We then turn our attention to the cell-intrinsic repair mechanisms that follow CRISPR/Cas-induced cleavage and provide a prediction algorithm for the outcome genotype distribution based on thermodynamic features of the DNA repair process. In a pioneering approach, we utilise structural calculations for the generation of these features and show that this novel approach surpasses published outcome prediction algorithms within our testing regime. Through interpretation of the trained model, we elucidate the thermodynamic factors driving DNA repair and provide a computational tool that allows experts to assess the severity of the genotypic changes predicted for a given edit.
Together, these efforts provide a comprehensive, one-stop computational source to assess and improve CRISPR/Cas9 gene editing safety.

Keywords: computational biology
CRISPR
gene editing
machine learning
Advisor: Minary, P
MALDI and SIMS microscope mode imaging mass spectrometry

Mass spectrometry imaging (MSI) is a powerful tool, mapping the spatial distribution of molecules with micron or sub-micron resolutions using their molecular mass. Microscope MSI is a great technique with a high throughput, but is used less commonly than microprobe MSI as it achieves lower mass and spatial resolution. This thesis presents methods for improving the mass and spatial resolution with a microscope MSI instrument, as well as expanding the imaging field of view. A new microscope MSI instrument is also presented, utilising secondary ion mass spectrometry (SIMS).
Using a reflectron ToF mass spectrometer, by generating a stronger field, the spatial resolution can be increased from 13 ± 1 μm o 8 ± 1 μm experimentally, and could potentially reach <7 μm according to simulations. Variable magnification has been explored in simulation, and the application of an additional einzel lens proved capable of changing the magnification from ×92 to ×20, which can expand the field of view from 270 μm to 1242 μm. This can increase the scope of the instrument by acquiring larger images first, with a <50 μm spatial resolution and ~ 2,500 mass resolution, before increasing the magnification on a region of interest and attaining higher resolution data. Such a feature would be very desirable in commercial applications and improve the throughput of the instrument.
Using a Timepix3 camera, the timing precision can be improved by using a more intense trigger, reaching a 4.5 ns full width half maximum (FWHM). Through the use of time-over-threshold data, mass peaks can be reduced from a FWHM of 50 μm to 32 μm, improving the attainable mass resolution with the Timepix3 camera, bringing it closer to the true mass resolution of the instrument.
A SIMS ToF mass spectrometer has been presented, taking a similar design to the reflectron ToF instrument. Work was done to characterise this instrument in order for it to be used in tandem with the reflectron ToF mass spectrometer.

Keywords: MSI
microscope imaging mass spectrometry
imaging mass spectrometry
SIMS
MALDI
Advisor: Brouard, M
Inferring brain network dynamics of MEG and EEG in healthy aging and Alzheimer’s disease

Alzheimer’s disease (AD) has long been encumbered by a lack of clinically effective biomarkers, which has impeded its early-stage detection and relegated diagnostic practices to symptom-based observations. Amidst the ongoing quest to discover novel biomarkers with enhanced clinical utility, this thesis aims to elucidate the prospect of static and dynamic changes in brain network features, derived from electroencephalography (EEG) and magnetoencephalography (MEG), to explicate the earliest changes in the brain caused by AD.
The first component of the thesis contrasts MEG and EEG in capturing age-related effects within the healthy aging datasets and validates the methodologies initially designed for MEG for their application to EEG. We demonstrate that while both modalities reveal analogous age effects in static power spectra and narrow-band power, MEG exhibits higher sensitivity to age effects in various brain network features within source space. The adopted analysis techniques successfully replicated previously documented healthy aging effects, substantiating their credibility in inferring transient resting-state network (RSN) dynamics from M/EEG data.
Leveraging the findings above, the second component of the thesis focuses on identifying modality-specific biomarkers for mild cognitive impairment (MCI) and early-stage AD from resting-state M/EEG. The reproducibility of known biomarkers --- evident in static RSN features and the posterior default mode network --- is confirmed in our dataset. Furthermore, we show that the dynamic effects of MCI and early-stage AD in the wide-band power and temporal dynamics of RSNs can be recognized as potential AD biomarkers. These results are among the first to demonstrate the statistically significant effects of prodromal AD in resting-state M/EEG.
Together, our findings provide a concrete case that M/EEG-derived static and dynamic RSN features can potentially be reliable and clinically meaningful biomarkers. This research propels the field towards refining early detection mechanisms for AD, laying a foundation for ensuing research to build upon, and steering future diagnostic practices towards enhanced efficacy.

Keywords: electroencephalography
aging
magnetoencephalography
Alzheimer's disease
brain network dynamics
Advisor: Woolrich, M
Gohil, C
van Es, M