VictorJuiz/thesis huggingface dataset:
Liquid-liquid phase separation of germline proteins
Keywords: Biomolecular condensates
Intrinsically disordered proteins
Ddx4
Liquid-liquid phase separation
Evolution
Piwi

Spatial organization of chemical processes is a widely accepted requirement for living systems. Cells have developed a great variety of mechanisms to achieve spatial and temporal organization of which many rely on lipid membranes to separate biochemical processes from bulk phases. However, studies in recent years have shown that membraneless organelles are highly dynamic entities that can organize and facilitate chemical reactions. Membraneless organelles are known to consist of a diverse population of different proteins and nucleic acids. Many studies focus on the phase behaviour and properties of single protein regions. We therefore investigated the phase behaviour of more complex systems using the well-characterized germ granule protein Ddx4 and the uncharacterized N-terminal regions of Piwi proteins. We show that the interplay of these disordered regions has differential effects on the phase properties and the propensity to phase separate. Furthermore, we find that liquidliquid phase separation of Piwi protein N-terminal regions is dependent on folded domains. The evolution of disordered proteins is not well understood and experimental data is scarce. Therefore, we compared the phase behaviour of human germ granule proteins to Drosophila melanogaster proteins. We show that the propensity to phase separate, phase properties and interactions of composite systems are evolutionarily conserved between Homo sapiens and Drosophila melanogaster homologues, even though sequence similarity is remarkably low.
Deep learning for communication: emergence, recognition and synthesis
Keywords: lipreading
speech
lipnet
communication
machine learning
deep learning

Human intelligence is a social phenomenon tightly coupled to the act and process of communication. Ever since the early prehistoric period, humans have been able to communicate amongst themselves at an unprecedented and unparalleled level compared to all other living species. Communication led humans to develop media such as the spoken and written word to effectively convey the meanings of concrete and abstract concepts, and still today a substantial part of human life is spent communicating and sharing information. The scientific study of communication began in Classical Greece with the work of Aristotle and was to evolve through time into the work on information theory by Claude E. Shannon. This work proposes three novel methods for studying the processes of emergence, recognition, synthesis and enhancement of communication, using recent advances in deep learning. The first method investigates the emergence of communication among agents, and introduces a differentiable way of learning communication protocols. The second studies speech recognition in visual verbal communication, and for the first time solves sentence-level lipreading with deep neural networks trained end-to-end. The third and final method proposes a meta-learning approach for sample efficient verbal communication via text-to-speech synthesis. This thesis advances deep learning in these areas, and defines the premises for the creation of novel technologies for the greater good of society.
Adventures in low-valent germanium chemistry
Keywords: Cationic
Small molecule activation
Main group
Germanium

This thesis explores the use of boryl, terphenyl and amido ligands in a variety of interesting areas of low-valent germanium chemistry.
In Chapter 1, a general introduction to the state of the art in this field is provided. The ligands that have proven pivotal in recent decades in germanium chemistry are introduced, and the developments that they have facilitated are then described. Finally, the field of germanium cations is introduced.
In Chapter 2, the general methods deployed in this thesis’ work are described; modified literature procedures for the syntheses of a variety of starting materials that were used in this work are also detailed.
In Chapter 3, the synthesis of novel germylium-ylidenes is examined, utilising a strategy of chloride abstraction from chlorogermylenes substituted by a combination of N-heterocyclic carbene and anionic ligand. The structural characterisation of the first isolable germylium-ylidenes featuring boryl, terphenyl, primary amido, and borylamido ligands is reported, and the influence of these ligands on the structure of these compounds is discussed in detail. For instance, concerning terphenyl-substituted cations, the effect of subtle variation in ligand steric bulk is explored, in terms of changing the degree of aggregation, and leading to secondary interactions with the ligand peripheries.
In Chapter 4, the reactivity of these germylium-ylidenes is then explored. The first activation of E-H bonds by isolable germylium-ylidenes is reported, as well as novel onward reactivity of some of the products as a result of their charge. For instance, oxidative addition of certain cations with ammonia leads to a subsequent elimination. Attempts towards the synthesis of multiple bonds is described, and the novel compounds this leads to discussed; for instance, reaction of a boryl-substituted cation with trimethylsilylazide leads to the formation of the first germylium azide.
In Chapter 5, the synthesis of compounds featuring boryl-substituted germanium-transition metal bonds
is investigated, and the first examples of such compounds for the cases of molybdenum, cobalt and iron are reported.
In Chapter 6, conclusions are drawn from the work of this thesis, and suggestions for future work are made.
Due diligence on conservation organisations: what should we be asking?
Keywords: conservation
organisational effectiveness
non-profit organisation
barriers
typology

This inductive study explores what criteria could be used to identify conservation organisations more likely to achieve their goals. In addition to information gathered from the academic and grey literature, primary data was obtained from three main sources: semi-structured interviews with 74 conservation practitioners; an online survey completed by 154 conservation practitioners; and review of 35 non-profit organisational effectiveness frameworks.
Interviews identified barriers to conservation success, allowing a typology of barriers to be developed. Risks to success can be internal (arising inside an organisation), external (completely outside of an organisation’s control) or operational (outside of individual organisational control, but within the control of the conservation community). Because the list was long, statistical procedures were applied to the survey data to reduce the number of barriers needed to understand operating context.
The framework review and survey explored organisational deficiencies that might present internal barriers to effectiveness. I found four dimensions to an effective organisation: governance; finance; leadership; and management. There was less agreement as to which criteria are present in effective organisations. Differences between frameworks used to guide effectiveness and those used to judge it were noted and discussed. Finally, survey results were compared to framework review results to compare viewpoints on effectiveness criteria. Ranked lists were not significantly different, but correlation between them was weak.
This study provides the first empirically based conceptual model of barriers to conservation as perceived by conservation practitioners, and a first attempt to identify which barriers, internal and external, may be most important in identifying more effective conservation organisations. My findings also suggest that current criteria applied in funding decisions might be counter-productive: insisting on the presence of unproven effectiveness criteria stretches already pressurised conservation organisations even further and hampers their effectiveness. Instead, the donors could collaborate more and work towards less onerous and untested methods of decision- making.
Discrimination in modern asymmetric conflict: a Christian moral analysis
Keywords: Discrimination
Collateral Damage
Just War
Improvised Explosive Device
Double Effect
Modern Asymmetric Conflict

The task of discrimination in war is a non-static phenomenon. It changes with the character of war, which itself changes with developments in cultures, international relations, how states organise for war, innovations in doctrines, technologies and tactics etc. Fundamental changes to war’s character necessitate some moral revision, and modern asymmetric conflict (MAC) is the latest fundamental change. MAC is characterised by forces from developed countries fighting unconventional, often non-state adversaries that flout moral and legal norms, and deliberately exploit immoral, unlawful and repugnant tactics.
My analysis of the relevant ethics of Paul Ramsey, the US Conference of Catholic Bishops and James Turner Johnson – which, respectively, treats the form of war most similar to MAC, addresses an earlier fundamental change in the character of war, and comprises an important assessment of MAC – as well as touching on other Christian and secular contributions, discerns that there is insufficient Christian moral guidance to address the questions raised about discrimination in MAC. Thinking out of Christian just-war tradition, I focus on the Improvised Explosive Device (IED) network to expose novel ethical issues concerning discrimination in MAC. I argue that by not revealing their combatant status, those enabling the prosecution of IED attacks, and by extension broader combat functions, should lose or at least jeopardise any absolute non-combatant immunity.
I then proceed to explain how conventional forces can discriminate morally, while their irregular and less scrupulous adversaries do not. This includes enhancing the rule of double effect by exploiting predictive analytics; overcoming the enemy’s erosion of non-combatant immunity and the inviolability of national borders; empowering soldiers to act discriminately through a simple, moral foundation; equalising the legal accountability of the opposing forces, rather than unfairly pursuing soldiers only from developed countries; and, finally, establishing a level of military supererogation that reflects this new form of conflict, where minimising civilian casualties is a key measure of success.
Motion estimation using radiofrequency scattering of a parallel transmit coil for cardiac magnetic resonance imaging at 7T
Keywords: S-Matrix
Radiofrequency Scattering
Motion Estimation

Magnetic resonance imaging (MRI) at ultra-high magnetic field strengths offers an increased signal-to-noise ratio (SNR) and has the potential to boost the MR image resolution. Cardiovascular applications remain challenging, as high-resolution image acquisitions are still too slow to capture a fast moving organ like the heart. Synchronisation of the acquisition to the heart motion is necessary to acquire an image over several consecutive heartbeats. The current gold-standard method for cardiac synchronisation is the electrocardiogram (ECG), which measures the electrical activity of the heart. Magnetohydrodynamic effects of the blood flow interfere with the ECG measurement and can affect reliable gating, which is particularly significant at higher magnetic field strengths.
The work of this thesis presents new motion estimation methods that are based on radiofrequency (RF) scattering of a parallel-transmit coil and directly assess the heart motion, independent of the electrical activity of the heart. A cardiac motion signal is derived with a high SNR and with a number of potential gating features, which have a high accuracy when compared to ECG gating. No additional motion-monitoring hardware is needed other than the commercially available pTx system. Different RF pulse designs are proposed to integrate the scattering measurements into the normal MR image acquisition to estimate cardiac and respiratory motion in real-time on the MRI scanner. The integrated cardiac-respiratory motion framework is combined with a new MR imaging acquisition strategy to acquire high-resolution, 3D images of the heart during free breathing.
Endohedral fullerenes as standards for portable atomic clocks
Keywords: Endohedral fullerene
Electron paramagnetic resonance
Allan deviation
Atomic clock
N@C60
EPR
Frequency reference
Electron spin resonance
ESR
High-pressure EPR
Solid-state
SWaP
Magnetic resonance
Quantum
Spectrometer

Highly stable and accurate frequency sources underpin a wide range of modern technologies. For many applications, there is a need to develop clocks with low size, weight and power (SWaP). Significant effort has been expended in miniaturising existing atomic clock architectures, but the various limitations inherent to contemporary designs incentivise further exploration of novel architectures.
Here, I investigate endohedral fullerenes as possible frequency references in future portable atomic clocks. Firstly, I detail the instrumentation developed to acquire the low-field data presented in this thesis. I then show that the endohedral fullerene 15N@C60 possesses a magnetic field-insensitive "clock transition" with fclock ≈ 38.6 MHz at a field Bclock ≈ 0.8 mT. This measurement is the first observation of a clock transition in a molecular spin system at room temperature, and it enables me to estimate the stability of an fullerene-based clock. The predicted performance is very poor, and I discuss potential strategies to address this problem.
I also investigate the hyperfine coupling as a function of pressure. The measured shift (dA/dP ≈ 3.5 × 10-4 Hz Pa-1) is too small to be a useful tunable parameter with which to offset the temperature coefficient of a fullerene-based atomic clock. However, it does ensure that such a clock would be reasonably insensitive to atmospheric pressure fluctuations. Using this datum I make the first experimental estimate of the compressibility of an isolated fullerene cage.
On the basis of the research performed in this thesis, I believe that the outlook for fullerene-based frequency standards is poor. They are fundamentally limited by their low frequency clock transitions and broad linewidths relative to the atomic frequency standards used in contemporary portable atomic clocks. This is due to their small hyperfine interaction and the coupling between the electron spin and degrees of freedom that are absent in atomic systems.
Authoritarian regimes and the co-optation of Islam: Kazakhstan and Russia
Keywords: Islam
co-optation
subnational
Kazakhstan
authoritarian regimes
Russia
religion and politics
authoritarianism
CIS

National and subnational authoritarian regimes with Muslim majorities prefer to co-opt rather than repress Islam in order to bolster their legitimacy, limit bargaining partners, deter mobilization, and gather information. Authoritarian regimes also elect to co-opt other potential sources of opposition besides religion due to similar incentives. Religion, however, is a unique source of potential opposition given its high salience relative to other forms of identity. Repression or overt co-optation of the majority religious identity holds a higher potential to foster an opposition movement based on religious identity. In order to deter this threat, national and subnational regimes frequently create a separate religious institution for Islam. Kazakhstan, a national authoritarian regime, and Tatarstan, Russia, a subnational authoritarian regime, both attempt to co-opt the majority religious group, Islam, through quasi-governmental agencies. Quasi-governmental agencies reduce transparency and provide a semblance of official distance between co-optation efforts and the regime. However, the different layer of institutional structures between national and subnational authoritarian regimes spurs each type of regime to pursue different strategies. Given the regime juxtaposition between Tatarstan and Russia, Tatarstan more frequently pursues co-optation through unofficial and extra-legal means. Alternatively, a higher level of institutions does not exist in Kazakhstan. Thus, there is a higher degree of harmony between the law and policies on religion. In addition to using a quasi-governmental agency, both regimes attempt to securitize Islam by framing regime associated religious sources as the panacea to extremism and other negative influences. Muslims in Kazakhstan were more likely than Muslims in Tatarstan to report using religious sources approved by the regime. This is likely because Kazakhstan had a wider array of tools at hand to co-opt Islam. However, a majority of Muslims in neither case cited securitization narratives to justify why they chose to use governmental religious sources.
A witness to pain: Samuel Beckett and post-war Francophone drama
Keywords: suffering
war
France
Beckett
pain
Francophone

This thesis examines how Beckett stages physical pain in his early theatre plays, arguing that Eleutheria (1947, pub. 1995), En attendant Godot/Waiting for Godot (1952/1954), Fin de partie/Endgame (1957), Happy Days/Oh les beaux jours (1961/1963), Play/Comédie (1964) and Not I/Pas moi (1972/1975) generate intensely sceptical readings of sympathetic or redemptive forms of witnessing. These plays raise questions about our capacity both to communicate our own physical suffering, and to comprehend – or in some cases even to perceive – another’s pain. They prompt us to interrogate the utopian ideas of empathetic witnessing and of the theatre auditorium as a site of intimate communion, which were popularised after World War II and which still linger in public consciousness and contemporary criticism. Bringing together Anglophone and Francophone scholarship, this project resituates Beckett’s early plays in the long aftermath of World War II in France, reading them as part of a post-war drive in Francophone literature to formulate new ways of negotiating the extreme wartime and post-war experience of witnessing others’ pain. I offer a comparison of Beckett’s plays with the work of four contemporary Francophone artists: Albert Camus, Pablo Picasso, Eugène Ionesco, and Marguerite Duras, each of whom, like Beckett, lived out World War II in France as non-native non-combatants. I explore how these plays construct a live encounter with the human body within the paradoxically intimate distance of the theatre auditorium, drawing the spectators’ own responses unsettlingly into question. This comparative examination combines close textual analysis with consideration of recorded audience responses to the staging details of specific productions, ranging from Roger Blin’s 1953 première production of En attendant Godot at the Théâtre de Babylone through to Vahid Rahbani’s unlicensed 2005 staging of Eleutheria in Tehran and Jess Thom’s 2018 staging of Not I at the Battersea Arts Centre.
Quantitative analysis of complex materials using non-negative matrix factorisation
Keywords: Metropolis Monte Carlo
Total scattering
Pari distribution function
Non-negative matrix factorisation
Multivariate analysis
Complex materials

The properties of a material are unquestionably linked to its structure. Thus, in or- der to wholly understand, or even predict, a material’s properties we must establish a complete understanding of its structure. Developing this understanding becomes particularly challenging when a material comprises multiple components. Experi- mental measurements of complex materials are often complicated as they contain contributions from different components, and interpreting measurements of complex materials in terms of their individual components is a well established problem. This thesis concerns a newly developed multivariate analysis technique designed to break up experimental datasets and describe them in terms of a number of indi- vidual components. The algorithm at the heart of this is called Matrix Metropolis Factorisation (MMF)—it combines Metropolis Monte Carlo minimisation into a non- negative matrix factorisation algorithm to produce a robust and versatile method for decomposing experimental datasets. This thesis comprises applications of this methodology to the structural characterisation of complex materials. Active pharmaceutical ingredients (APIs) are often intentionally prepared in an amorphous form to improve drug solubility and bioavailability. Total scattering and PDF measurements have been used to study these disordered materials. I then show how MMF analysis of PDF data enables: (i) structural characterisation of the amorphous API in a complex preparation, (ii) determination of the maximum API loading level capable of inhibiting crystallisation, and (iii) identification of drug design strategies for improving stability of the amorphous form. Next, a number of mixed-metal framework materials are considered. Through MMF analysis of infrared spectroscopy data the distribution of neighbouring cations pairs is determined as a function of composition for three formate perovskite families, and Cd-doped ZIF-8. Atomistic pictures of domain formation are developed for each material which may, in principle, enable tuning of ferroelectric and sorption behaviour. Finally, I identify the existence of a locally ordered domain structure that persists above the magnetic ordering temperature of a simple cubic ferromagnet. MMF analysis of radial spin-correlation function data was used to determine regions of ferromagnetic order within a largely disordered paramagnetic phase. The systems considered each have complex structures that are governed by short- range interactions and can be described in terms of a small number of components. In each case, MMF analysis is used to identify these components, including those that cannot be measured in isolation. Fundamentally the same methodology is applied to data from different experimental techniques to probe the local structure of each system.