VictorJuiz/thesis huggingface dataset:
Identifying apoplastic plant proteins involved in plant-pathogen interactions on the basis of their evolutionary profile

To sustainably feed a growing global population, yield can be increased by reducing crop losses to plant pathogens. During infection of plants, several pathogens attempt to colonise the intercellular space, the apoplast. Apoplastic defence against attempted invasions includes the secretion of defence-related proteins, turning the apoplast into a molecular battlefield. While few apoplastic hydrolases have been characterised in plant immunity, many secreted proteins remain uncharacterised. Thus, in order to improve our understanding of apoplastic plant defence responses, we aimed to identify novel apoplastic proteins involved in immunity in this thesis. We combined comparative proteomics with molecular evolution and bioluminescence-based high-throughput disease assays. First, to identify core extracellular tomato proteins in immune responses, we studied apoplastic fluids (AF) of different biotic stress-induced tomato species S.lycopersicum, S.peruvianum and S.pennellii by mass spectrometry (MS). We identified that P69 subtilases were the most abundant proteins in tomato AFs during defence. Molecular evolution studies further implicated P69 subtilases in plant immunity and implicated another 20 biotic stress-induced tomato proteins under positive selection in plant immunity. Second, we compared apoplastic proteomic landscapes between tomato species and N.benthamiana, G.max and A.thaliana which marked distinct differences in profiles of accumulating defence proteins, implicating subtilases from G.max and chitinases from tomato species in plant immunity. Third, we established a bioluminescence-based, high-throughput disease assay for the N.benthamiana-Pseudomonas syringae pv. tomato (Pto) pathosystem, but failed to identify increased immunity in N.benthamiana against Pto for three proteins implicated in plant immunity, including P69B. Last, we used AlphaFold2 multimer as a high-throughput in silico screening tool to identify inhibitor-enzyme complexes from the plant-pathogen interface and identified 13 novel, putative hydrolase inhibitors, including six putative P69B inhibitors. This thesis has contributed to understanding apoplastic defence responses by identifying proteins implicated in plant immunity.

Keywords: plant immunity
molecular evolution
proteomics
positive selection
apoplast
Advisor: Van der hoorn, R
The 'other' side of memory: the survival of pro-regime memorialisation in democratic Chile (1990-2020)

The thesis investigates the conditions that explain the survival of pro-regime memorialisation in democratic Chile (1990 – 2020). A pro-regime memory site is a monument, memorial or symbolic marker (e.g., street name) built to celebrate a past authoritarian government. In Chile, these sites either praise the military coup of 11th of September 1973, glorify General Augusto Pinochet’s 17-year dictatorship (1973 – 1990), or celebrate Military Junta members and civil collaborators. Their survival – that is, their maintenance by authorities (city councils, judicial actors) – is a striking phenomenon in a context in which victims’ human rights memorials dominate the public space. To enhance the internal validity of the thesis, the elimination of pro-regime memorials is also investigated. The thesis elaborates a theoretical framework to explain the survival and elimination outcome, with four and five conditions, respectively. Using Qualitative Comparative Analysis (QCA), the research minimised the presence and absence of these conditions in a sample of 17 cases of pro-regime memorials. It obtained a parsimonious solution for both outcomes (survival and elimination). The QCA procedure uncovered that the survival of pro-regime memorialisation is explained by the presence of “Walls” (veto players), and a combination of “Silence” (absence of external intervention by NGOs and victims’ associations) and “Local and/or Institutional Support” (support towards the site’s survival by local communities and State institutions). Likewise, the elimination of pro-regime memorialisation is explained by the rejection of the site by the local community, or by a combination of civil society pressure and the presence of “Windows of Opportunity” (centre-left or left-wing city councils, or judges receptive to human rights). The results highlight the continued relevance of veto players in the survival of pro-regime memorialisation. The findings also emphasise the prominence of civil society, particularly local communities, in advancing both the survival and elimination of pro-regime memory sites in Chile.

Keywords: right-wing
collective memory
Chile
pro-regime memorialisation
transitional justice
memorialisation
veto players
memory sites
pinochetismo
Advisor: Payne, L
Organic semiconducting polymers for organic electrochemical transistors with bioelectronic applications

Organic electrochemical transistors (OECTs) are a promising technology for bioelectronic devices, with applications in neuromorphic computing and sensing in healthcare settings. The active component enabling an OECT is the organic mixed ionic-electronic conductor (OMIEC), the optimisation of which is critical for realising high-performing devices. This thesis further develops structure-property relationships of OMIECs, by exploring their electrochemical activity and OECT performance.
This work aims to understand in greater depth the effectiveness of currently employed approaches, as well as proposing novel design strategies and additional factors that impact the performance of OECTs. By using both a p-type polythiophene and an n-type naphthalene diimide (NDI)-based polymer, the impact of purity and molecular weight were investigated. It was found that whilst molecular weight has negligible impact on OECT performance, the degree of purity, specifically the removal of palladium, is able to improve both OECT performance by over seven times. Next, a novel series of n-type NDI-based copolymers were designed, with the aim of improving the degree of delocalisation, and therefore electron mobility. Reducing the size of the comonomer and improving planarity, by utilising vinyl and alkynyl motifs, was observed to increase the degree of crystallinity and improve the OECT electron mobility by over 200 times compared to the typical thiophene comonomer, to achieve a mobility of 2.40 x 10-2 cm2 V-1 s-1. The final series was designed as a model system to better understand the ionic conductivity of OMIECs, by employing the electronically insulating pyromellitic diimide (PMDI) unit for a series of copolymers. By varying the hydrophilic sidechain content and composition, it was found that the capacitance is proportional to the percentage of sidechains that are hydrophilic, providing this segment terminates the sidechain.

Advisor: McCulloch, I
Massive amplitudes from twistors on the worldsheet

The subject of this thesis are ambitwistor string models that describe massive particles by gauging currents to implement a symmetry reduction. Because the amplitude formulae one obtains as correlators in these models are really reductions of the ones presented in [1, 2], the body of the thesis will open with a discussion of properties and features of the six-dimensional superamplitudes that the massive formulae will inherit. Two different instances of symmetry reduction in the ambitwistor string will be considered. The first is a massive version of the RNS ambitwistor string. This provides a derivation of massive amplitude formulae that have support on massive scattering equations such as the ones predicted by Dolan and Goddard [3] and Naculich [4], together with a solid understanding of mass assignment both to external and propagating particles. The second consists of four dimensional twistorial models that will be shown to have an alternative interpretation as theories of maps into the phase space of complexified massive particles. This representation is more suitable to describe supersymmetric theories, such as the Coulomb branch of N = 4 sYM. An interesting class of theories is presented, which is obtained by symmetry reduction along the R-symmetry generators. For supergravity, this produces CSS gauged supergravities in four dimensions. In these theories a novel instance of ‘massive’ double copy structure arises.

Advisor: Mason, LJ
Navigating coercive control: making sense of police response to a legislative intervention

The legislative intervention that criminalised controlling or coercive behaviour in England and Wales attempted to shift policing from focusing on discrete incidents of physical violence to identifying a pattern of abusive behaviour. This thesis examines how the police have navigated the criminalisation of coercive control and translated the legislation into practice. The findings address a gap in the literature by including an in-depth qualitative analysis that considers both the individual and joint role of the police in responding to coercive control, interrogating how officers negotiate the challenges presented by the legislation. This study is informed by a theoretical framework that considers the influence of officers’ understanding, interpersonal interactions, multi-agency working, and organisational and legal context on their discretionary practice.
Drawing on qualitative data from interviews, case files, and observations, and quantitative police- recorded outcome data, the analysis shows how evidential and victim engagement challenges contribute to an entrenched perception of the coercive control offence as intractable. The legislation induced a conflict between organisational objectives, available resources, and safeguarding responsibilities for officers. This conflict facilitated officers’ working practice to use their discretion to pursue alternative offences or protective measures. For some officers, the legislation also served an educative function concerning the risks associated with coercive control. Furthermore, those officers who overcame the barriers to practice utilised professional curiosity and the resources of their colleagues and partners. These findings inform the policing, domestic abuse, coercive control, and socio-legal literature, using a case study of coercive control to demonstrate how a legislative intervention is interpreted and translated into practice through a process of negotiated discretion.

Keywords: coercive control
domestic abuse
policing
policy
legislation
intimate partner violence
Advisor: Condry, R
English Catholic literary culture, 1640-1660 

This thesis is the first study of English Catholic literary culture produced during the 1640s and 1650s. It investigates how different Catholic communities responded creatively to the civil wars and Revolution. I argue that recovering this diverse literature provides new insights into both the longue durée of early modern Catholicism and the canonical authors of the English Revolution. Contrary to prevailing scholarly assumptions, I demonstrate that Catholics were not uniformly or unequivocally royalist, but sustained the tradition of Catholic resistance, adapting the writings of militant Elizabethan Jesuits, such as Robert Persons, for new circumstances. The complex allegiances of English Catholic writers can help us reconsider the traditional literary history of the mid-seventeenth century, which categorizes genres and forms using polarised polemical labels. This thesis interrogates the relationship between literary style and religious and political identity. The first three chapters discuss how Catholics deployed genres often associated with stereotypes of Cavaliers, republicans, and royalists. I analyse verse miscellanies compiled by a group of gentry families; tyrant tragedies by the celebrated Jesuit dramatist, Joseph Simons, revived for performance at the English College, Rome, in the 1640s; and tragicomedies staged at St. Omers College after the regicide. Cross-confessional similarity and difference, as the fourth chapter shows, preoccupied Richard Crashaw and his fellow exiled Catholic converts, who reflected imaginatively on the relationship between style and identity in poetry and polemical life-writing. The final chapter suggests that Catholic arguments for toleration, especially by Thomas White, alias Blacklo, challenged confessional distinctions by borrowing ideas and idiolects from across the political spectrum and by disguising the writers’ own Catholic commitments. This thesis contends that confessional and political identities were ascribed to literary styles through contested and contingent acts of rhetoric and interpretation. It recovers a thriving transnational literary culture and proposes new ways of reading post-Reformation literary politics.

Keywords: Baroque
exile
early modern Catholicism
English Revolution
English Civil Wars
Advisor: Kewes, P
Davidson, P
Justifying precedent in law

This thesis aims to provide a philosophical foundation for the practice of following precedent in law. It argues that legal systems should adopt a practice of precedent that advances the Rule of Law instead of one that advances other values at the cost of undermining this ideal. This practice is called ‘precedent-following’. In virtue of precedent-following, later courts treat relevant precedents as normative legal facts favouring, and sometimes requiring, the same decision as before. A distinctive feature of precedent-following is that later courts always have a legal reason for following relevant precedent, even if the precedent is morally suboptimal, so long as it is not evil. This reason is by default non-obligatory. But a legal system may further advance the Rule of Law by imposing an obligation on later courts, in some cases, to follow relevant precedent. Thus, depending on whether courts have a non-obligatory legal reason or a legal obligation to follow relevant precedent, two modes of precedential reasoning may be distinguished. These are the persuasive and the authoritative modes. The thesis explains the pros and cons of the two modes and shows how some of their drawbacks can be managed in order to realise conflicting values, such as the value of not entrenching morally deficient decisions in the law. The thesis argues that, in a jurisdiction under the authoritative mode, the law should authorise a later court that is bound by a morally deficient precedent to either follow the precedent or exercise an equitable in conformity with certain conditions. This power, it is argued, would contribute to the justification of the authoritative mode, as courts would have an additional mechanism for dealing with morally deficient precedents. Thereby, it is argued, this power might also allow courts to avoid distinguishing morally deficient precedents in a disingenuous way, which is a way of enhancing the legitimacy of the common law.

Keywords: precedent
equitable power
rule of law
morally deficient precedents
modes of precedential reasoning
stare decisis
Modelling droplet impact in fluid-structure interaction problems

The impact of a liquid droplet onto a deformable substrate is a physical phenomenon that appears ubiquitously in both natural and industrial contexts. The fluid-structure interaction between the droplet and the substrate results in a complex and highly nonlinear system, and is a significant modelling challenge. In this thesis, analytical and numerical modelling techniques for these systems are presented with the aim of providing physical insight and quantitative predictions on the dynamics of the droplet as the properties of the substrate are changed.
In Chapter 1, we motivate the thesis by outlining relevant real-world scenarios involving droplet impact onto deformable substrates, and present a review of the existing literature. In Chapter 2, we setup the canonical droplet impact system that will be used throughout the thesis, including the statement of governing equations, non-dimensionalisation and any assumptions that apply throughout. We present an analytical model for this system in Chapter 3, where we exploit the small timescale of impact phenomena to derive a matched asymptotic solution based on Wagner's theory of impact. To validate the analytical model and investigate regimes which Wagner theory cannot reach, a numerical modelling technique is then considered in Chapter 4, where we use the volume-of-fluid method to conduct direct numerical simulations of the system. We present a novel approach to model the fluid-structure interaction within a two-phase scenario by employing a moving frame coordinate transformation. In Chapters 5 and 6, we apply the previously developed models to study droplet impact onto a spring-supported plate and an elastic membrane, respectively. We find how the deformation of the substrate affects the dynamics of the droplet via slowing down the spreading, decreasing the pressure and reducing the amount of fluid ejected across the substrate. By making use of both modelling techniques, we explore a wide range of substrates by varying the elasticity, tension, mass and dampening properties of the substrate. We then quantify how changing these physical properties of the substrate affects the dynamics of the droplet and in turn the displacement of the substrate during the impact process. Finally, in Chapter 7, we summarise the main results and discuss directions for further work.

Keywords: fluid mechanics
droplets
matched asymptotics
applied mathematics
fluid-structure interaction
droplet impact
Wagner theory
direct numerical simulation
Advisor: Oliver, J
Cimpeanu, R
Moore, M
Biomarkers of motor network excitability in amyotrophic lateral sclerosis

Increased cortical excitability, associated with brain motor network alterations, has been consistently implicated in the pathology of amyotrophic lateral sclerosis (ALS). This thesis considers the application of multi-modal magnetic resonance imaging (MRI) to explore motor network excitability in ALS.
Chapter 3 describes a novel functional MRI (fMRI) study measuring motor task associated cortical activation and between-region functional connectivity in ALS. This showed hyper-activation in non-motor regions in rapidly progressive ALS. I also showed brain motor network connectivity remodelling linked to measures of functional decline across all ALS patients.
Chapter 4 describes a novel magnetic resonance spectroscopic imaging (MRSI) technique that quantifies neurochemical excitatory and inhibitory ‘tone’ with fine spatial resolution. I validated this technique in a cohort of healthy adults to describe physiological variation in excitability ‘set-points’ between motor regions and hemispheres, age-associated changes, and the relationship between excitability and motor network connectivity.
Chapter 5 applies the same MRSI technique to a cohort including ALS patients and presymptomatic carriers of the ALS-causing C9orf72 -HRE mutation. I found altered excitatory and inhibitory tone in both ALS and C9orf72 -HRE carriers, a novel finding with a notably lateralised pattern between the hemispheres. A disinhibited ‘hot-spot’ in the left motor hand area may precede disease in C9orf72 -HRE carriers.
Chapter 6 integrates these task-fMRI and MRSI motor network excitability biomarkers using modern data science techniques. This generated a multifactorial marker reflecting changes most prominent in established ALS, as well as a more specific marker of motor cortex activation lateralisation that improved differentiation of presymptomatic individuals.
Motor network excitability alterations in ALS and presymptomatic disease are multifaceted, reflecting an early stage of compensated vulnerability, followed by established neurodegeneration with accompanying functional reorganisation. My findings argue for the inclusion of MRI-based techniques measuring motor network excitability in future translational studies in ALS and presymptomatic disease.

Keywords: magnetic resonance imaging
motor network
functional mri
magnetic resonance spectroscopy
amyotrophic lateral sclerosis
Advisor: Turner, M
Stagg, C
Demography and social structure of water vole 
populations: implications for restoration


Water voles (Arvicola terrestris) are semi-aquatic rodents which mainly inhabit linear ranges bordering water-courses and are an endangered species in the United Kingdom. Habitat loss and predation from American mink have resulted in lowland populations that are increasingly becoming fragmented and spatially isolated. Conservation measures for water voles may therefore include habitat restoration and re-introduction.
The main objective of this thesis was to study the interactions between habitat quality, population demography, social structure and dispersal biology of water voles in extant populations, providing information with which to produce practical guidelines for habitat restoration and re-introduction.
Higher population densities were associated with larger quantities of available forage, larger growth rates, heavier individuals and smaller range-lengths of both males and females. Population densities apparently responded to increased food resources. Increasing widths of riparian habitat may, therefore, increase numbers of individuals within water vole populations.
Males were apparently non-territorial at all population densities studied, and their range sizes limited by a maximum number of females they could overlap, possibly resulting from aggressive interactions with other males and females. The geographical location of females' territories and males' ranges constantly drifted. The degree to which female territories drifted was smaller at a high population density site than at a low density site. At even higher densities, female territories may potentially reach a minimum size and cease drifting. Female territory sizes apparently reached a maximum size at low population densities. Ideal spacing of release pens for reintroducing females should lie between these minimum and maximum range sizes.
A decline in numbers of females at one study site during radio-tracking was associated with male-biased birth sex ratios. Stress caused by radio-collars could have resulted in maternal sex ratio adjustment. Radio-tracking of water vole populations may, therefore, be inappropriate in some cases.

Advisor: Macdonald, D