VictorJuiz/thesis huggingface dataset:
Gyrokinetic turbulence and transport in the Mega Ampere Spherical Tokamak

In this thesis we consider energy transport due to turbulence in the Mega Ampere Spherical Tokamak (MAST), using a multi-scale framework based on local δf gyrokinetics. Transport is modelled globally by means of local flux-tube simulations at each magnetic flux surface. In view of the evidence indicating that turbulent ion transport can be substantially suppressed by rotation shear, our flux tubes span only electron-gyroradius scales. This both simplifies our physics model and reduces the computational resource requirements to a manageable level. Our electrostatic simulations of a MAST H-mode discharge exhibit turbulent electron heat transport comparable with experiment in the outer core region, and are broadly consistent with the paradigm of an electron temperature profile governed by pedestal height and critical electron temperature gradient. Neoclassical transport dominates the ions, and is also comparable with experiment. The two species are decoupled in the sense that the collisional equilibration between ions and electrons is small compared to the sources across most of the plasma.
Focusing on a single flux surface in this region, still using both kinetic electrons and kinetic ions, we find that at early simulation times the heat flux "quasi-saturates" with the turbulence dominated by streamer-like radially elongated structures. However, the zonal fluctuation component continues to grow slowly until much later times, eventually leading to a new saturated state dominated by the zonal component.
Simplifying further to an adiabatic ion model (which shows the same slow evolution behaviour), we find that in the final saturated state (which determines the macroscopic energy transport) the electron heat flux is approximately proportional to the collision rate. We outline an explanation of this effect based on zonalnonzonal interactions and a scaling of the zonal damping rate with electron-ion collisionality. Improved energy confinement with decreasing collisionality has previously been observed experimentally in STs, and is favourable towards the performance of future devices, which are expected to be hotter and thus less collisional.

Advisor: Schekochihin, A
Incremental generative models for syntactic and semantic natural language processing

This thesis investigates the role of linguistically-motivated generative models of syntax and semantic structure in natural language processing (NLP). Syntactic well-formedness is crucial in language generation, but most statistical models do not account for the hierarchical structure of sentences. Many applications exhibiting natural language understanding rely on structured semantic representations to enable querying, inference and reasoning. Yet most semantic parsers produce domain-specific or inadequately expressive representations.
We propose a series of generative transition-based models for dependency syntax which can be applied as both parsers and language models while being amenable to supervised or unsupervised learning. Two models are based on Markov assumptions commonly made in NLP: The first is a Bayesian model with hierarchical smoothing, the second is parameterised by feed-forward neural networks. The Bayesian model enables careful analysis of the structure of the conditioning contexts required for generative parsers, but the neural network is more accurate. As a language model the syntactic neural model outperforms both the Bayesian model and n-gram neural networks, pointing to the complementary nature of distributed and structured representations for syntactic prediction. We propose approximate inference methods based on particle filtering. The third model is parameterised by recurrent neural networks (RNNs), dropping the Markov assumptions. Exact inference with dynamic programming is made tractable here by simplifying the structure of the conditioning contexts.
We then shift the focus to semantics and propose models for parsing sentences to labelled semantic graphs. We introduce a transition-based parser which incrementally predicts graph nodes (predicates) and edges (arguments). This approach is contrasted against predicting top-down graph traversals. RNNs and pointer networks are key components in approaching graph parsing as an incremental prediction problem. The RNN architecture is augmented to condition the model explicitly on the transition system configuration. We develop a robust parser for Minimal Recursion Semantics, a linguistically-expressive framework for compositional semantics which has previously been parsed only with grammar-based approaches. Our parser is much faster than the grammar-based model, while the same approach improves the accuracy of neural Abstract Meaning Representation parsing.

Keywords: Dependency Parsing
Deep Learning
Semantic Parsing
Generative Models
Parsing
Language Modelling
Incremental Parsing
Advisor: Blunsom, P
Physical phenomena in metal-organic frameworks: mechanical, vibrational, and dielectric response

This thesis entails the utilisation of ab initio density functional theory (DFT) in conjunction with neutron and synchrotron spectroscopy to study the mechanical, vibrational, and dielectric response of metal-organic framework (MOF) materials at the molecular level. MOFs are crystalline materials with nanoscale porosity, which have garnered immense scientific and technological interest for a wide variety of innovative engineering applications.
One part of the thesis involves using low-frequency lattice vibrations to characterise the various physical motions that are possible for framework materials. These collective modes detected at terahertz (THz) frequencies have been used to reveal a broad range of exciting possibilities. New evidence has been established to demonstrate that THz modes are intrinsically linked to anomalous elasticity underpinning gate-opening and pore-breathing mechanisms, and to shear-induced phase transitions and the onset of structural instability. The phenomenon of molecular rotor mechanisms and trampoline-like motions are also observed, along with the first experimental confirmation of coordinated shear dynamics. Additionally, a new method to characterise the effects of temperature, and hence thermally-induced structural amorphisation is reported.
Finally, for the first time, the frequency-dependent (dynamic) dielectric response of MOF materials, across the extended infrared (IR) spectral region was reported. The results were obtained from experimental synchrotron radiation IR reflectivity and DFT to reveal the low-&kcy; dielectric response of MOFs and established structure-property trends that highlight them as promising systems for microelectronic device applications.

Keywords: Vibrational Spectroscopy
Metal-Organic Frameworks
Terahertz Vibrations
Inelastic Neutron Scattering
Mechanical Properties
Density Functional Theory
Synchrotron Infrared Spectroscopy
Raman Spectroscopy
Response Properties
Dielectric Response
Advisor: Tan, J
The role of lung tissue-resident memory T cells in protection against tuberculosis

Tuberculosis (TB) is a global health problem, which is proving extremely difficult to control in the absence of an effective vaccine. Bacille Calmette-Guérin (BCG), the only vaccine currently licensed against TB, demonstrates variable efficacy in humans and cattle. A greater understanding of what constitutes a protective host immune response is required in order to aid the development of improved vaccines. Tissue-resident memory T cells (TRM) are a recently-identified subset of T cells, which may represent an important aspect of protective immunity to TB. This thesis aims to characterise the role of lung TRM in BCG-induced protection against TB. In a mouse model, intravascular staining allowed discrimination between lung-vascular and lung-parenchymal T cells. Experiments demonstrated that BCG vaccination induced a population of antigen-specific lung-parenchymal CD4+ T cells, a putative tissue-resident population. This lung-parenchymal population was significantly increased in frequency following mucosal BCG vaccination, compared to systemic BCG vaccination. This correlated with enhanced protection against Mycobacterium tuberculosis (M.tb) infection in the lungs of mice receiving mucosal BCG, compared to those receiving systemic BCG. Mucosal BCG induced lung-parenchymal CD4+ T cells with enhanced proliferative capacity and a PD1+KLRG1- cell-surface phenotype, a memory-like phenotype associated with improved protection against M.tb infection. These cells may represent a BCG-induced lung TRM population responsible for the enhanced protection observed following mucosal BCG. Overall, this thesis highlights the potential of mucosal vaccination to elicit lung TRM and identifies this as a possible immunological mechanism underlying enhanced protection against M.tb infection. These cells may constitute an important target for future vaccination strategies.

Keywords: T cell immunology
Tuberculosis
BCG vaccine
Tissue-resident memory
Advisor: McShane, H
Hogarth, P
Crustal structure, gravity anomalies and subsidence history of the Parnaíba cratonic basin, Northeast Brazil

Cratonic basins cover more than 10% of Earth's continental surface area, yet their origin remains enigmatic. In this thesis a suite of new and legacy geophysical and geological data are integrated to constrain the origin of the Parnaíba basin, a cratonic basin in Northeast Brazil. These data include a 1400 km long, deep (20 s two-way travel time) seismic reflection profile, five +/- 110 km offset wide-angle split-spread receiver gathers, gravity anomaly, and well data.
In the centre of the basin, the depth to pre-Paleozoic basement is &Tilde; 3.3 km, a zone of midcrustal reflectivity (MCR) can be traced laterally for &Tilde; 250 km at depths between 17-25 km and Moho depth is &Tilde; 42 +/- 2 km. Gravity and P-wave modelling suggests that the MCR represents the upper surface of a high density (2985 kg m3) and Vp (6.7–7.0 km s-1) lower crustal body, likely of magmatic origin. Backstripping of well data shows a concave up decreasing tectonic subsidence, similar in form to that commonly observed in rift-type basins. It is shown, however, that the seismic and gravity data are inconsistent with an extensional origin. It is shown that an intrusive body in the lower crust that has loaded and flexed the surface of the crust, combined with sediment loading, provides a satisfactory fit to the observed gravity anomaly, sediment thickness and basin shape. A buried load model is also consistent with seismic data, which suggest that the Moho is as deep or deeper beneath the basin centre than its flanks and accounts for at least part of the tectonic subsidence through a viscoelastic stress relaxation that occurs in the lithosphere following load emplacement.
Comparative analysis of the Michigan and Congo basins shows gravity data from these basins is also consistent with a lower crustal mass excess, while subsidence analysis shows viscoelastic stress relaxation may also contribute to their early subsidence histories. However, unlike Parnaíba, both of these basins appear to have been subjected to secondary tectonic processes that obscure the primary 'cratonic basin' subsidence signals. Parnaíba basin, therefore, offers an excellent record for the investigation of cratonic basin formation.

Keywords: Sedimentary basin
Gravity modelling
Seismic refraction
Cratonic
Backstripping
Subsidence analysis
Seismic reflection
Advisor: Watts, T
Daly, M
The Thob yig gsal ba'i me long by Dza-ya Paṇḍita Blo-bzang 'phrin-las (1642-1715): an enquiry into biographies as lineage history

This thesis centres on a text belonging to a rich but understudied genre of Tibetan Buddhist literature known as thob yig or gsan yig, 'records of teachings received'. Their undeniable value has been acknowledged by scholars who utilised them as supplementary material for research on biographies, transmission lineages and authentication of Buddhist texts. However, extensive studies of thob yigs as the focal topic of research are few and scarce. Chronologically, these texts form the "biography" of Tibetan Buddhism since the very beginning of sectarian Buddhism in Tibet. The primary purpose of these texts is to document in detail the transmission lineages through which major religious practices and teachings were passed down.
The main text investigated for this thesis is titled the "Thob yig gsal ba'i me long" and was compiled by the 17th century Khalkha Mongolian monk-scholar Dza-ya Paṇḍita Blo-bzang 'phrin-las (1642-1715). He who was one of the most distinguished Mongolian Tibetan Buddhist masters of his time and still occupies one of the highest positions amongst the ranks of Mongolian monk-scholars to have emerged throughout history. Unlike simpler examples of its genre, Dza-ya Paṇḍita's thob yig also includes relevant information on tantric and monastic precepts, instructions and consecrations, expositions on doctrine and practice, meditation guidelines, historical events, and autobiographical and biographical material related to important female and male Buddhist figures. Though catching the attention of scholars both in and outside of Mongolia as an important work for the study of Tibetan Buddhism, to date, it has never been studied in detail.
This thesis attempts to remedy the lack of study of this vast work. The focus here being the aspect of rnam thar, 'biography" in Dza-ya Paṇḍita's thob yig. These life stories totalling around 227 form the structural backbone of the work and is the feature which makes the Thob yig gsal ba'i me long a truly unique example of its genre. The chapters of this thesis investigate a selection of rnam thars belonging to Dza-ya Paṇḍita's own teacher and contemporaries, as well as the author's rang rnam, 'autobiography'. Through thus analysis, the goal of this thesis is to demonstrate what these life stories reveal about the author's outlook on the chaotic 17th century period, his vision of an exemplary Dge-lugs tradition, the manifestation of Dza-ya Paṇḍita's relentless devotion to Buddhism in the narratives he composes, and how this work and its contents fits into the larger context of Tibetan Buddhist writing.

Advisor: Roesler, U
Identifying mechanisms involved in the resistance of homologous recombination defective Dictyostelium cells to ART inhibitors

Poly(ADP-ribose) polymerase (PARP) inhibitors (PARPi) are toxic to cells with defects in homologous recombination (HR), which is exploited in the clinic as therapy of BRCA1/2-mutated tumours. Although the concept of synthetic lethality between PARPi and HR deficiency is well-known, the exact mechanisms resulting in cell death are still unclear. Here, we establish Dictyostelium as model to investigate the molecular basis of synthetic lethality of HR dysfunction with PARPi. We show that disrupting the HR-critical factor exonuclease I (exo1) sensitises Dictyostelium cells to PARPi. We further identify that HR inhibition is toxic for cells disrupted in the single-strand break responding PARP Adprt2, whereas an additional loss of the non-homologous end-joining (NHEJ)-promoting PARP Adprt1a renders cells resistant to the treatment. Accordingly, a defect in NHEJ suppresses PARPi toxicity to HR-defective exo1- strains which is not dependent on the alternative NHEJ (alt-NHEJ) factors Lig3 and PolQ but instead due to re-activation of HR. Furthermore, inhibiting Mre11 re-sensitises dnapkcs-exo1- cells to PARPi, indicating that redundancy between nucleases induce PARPi resistance. To identify further mechanims that suppress PARPi toxicity to HR-defective cells, we perform a screen to select for PARPi-resistant exo1- cells. Using whole genome sequencing we detect mutations that might be accountable for the tolerance of HR-compromised cells to PARPi. Taken together, our data indicate that NHEJ drives the toxicity of PARPi in the absence of HR and that its disruption results in PARPi resistance due to nuclease redundancy, which restores HR.

Advisor: Lakin, N
Collaboration of Ezh2 and Runx1 inactivating mutations in malignant haematopoiesis

Extensive efforts have shed light on the identity and biology of cancer stem cells, required and sufficient for the propagation of hematological malignancies and solid tumours. Much less is understood about the closely related issue as to the identity and properties of the normal stem and progenitor cells targeted by oncogenic lesions, and how the nature of the targeted cell might impact on the biology and clinical picture of the resulting cancer. To address this, we developed a mouse model allowing targeted inactivation of Ezh2 and Runx1 to different haematopoietic compartments. Inactivating mutations of EZH2 and RUNX1 frequently co-occur in haematological malignancies with markedly different phenotypes including myelodysplastic syndrome (MDS) and early thymic progenitor (ETP) leukaemia.
Inactivation of Ezh2 and Runx1 in adult haematopoietic stem cells (HSCs) resulted in perturbed haematopoiesis leading to development of an MDS-like disease. Unexpectedly, this MDS phenotype could be fully reproduced when Ezh2 and Runx1 inactivation was targeted to multipotent progenitors (MPPs) using Flt3-Cre. Furthermore, the disease was transplantable by MPPs, but not more committed progenitor populations, demonstrating that MDS tumour propagating potential is not exclusive to intrinsically self-renewing HSCs.
Targeting Ezh2 and Runx1 inactivation to early lympho-myeloid progenitors did not result in an MDS phenotype. These mice showed a marked expansion of ETPs within the thymus, combined with a block in thymocyte differentiation. These expanded ETPs displayed transcriptional features characteristic of ETP leukaemia, a treatment-resistant acute leukaemia subtype hypothesised to originate from ETPs. Combination of inactivation of Ezh2 and Runx1 in ETPs with the constitutively activating Flt3-ITD signalling mutation resulted in an aggressive lympho-myeloid acute leukaemia, which could be propagated by the expanded ETP population. These findings demonstrate the potential of lympho-myeloid progenitors such as ETPs to become leukaemia stem cells which propagate a disease retaining lympho-myeloid features.
We used this novel ETP leukaemia model to explore therapeutic targeting of Ezh2-inactivated ETP leukaemias using inhibitors of the bromodomain and extra terminal (BET) proteins. Aberrant transcription resulting from epigenetic changes induced by Ezh2 loss could be reversed by BET inhibitors, and these compounds showed therapeutic efficacy against both mouse and human ETP leukaemias in vitro and in vivo.

Keywords: Myelodysplastic syndrome
Leukaemia
Advisor: Mead, A
Jacobsen, S
Melodic exchange and musical violence in the thirteenth-century jeu-parti

The thirteenth-century jeu-parti was a sung debate between two or more poet singers. In the jeu-parti, singers exchanged stanzas composed to the same melody, rhyme scheme and syllable count. What else was exchanged in the composition, performance and inscription of the jeu-parti? Grounded in a definition of violence as the non-consensual deployment of power on a subject, this thesis investigates whether any modes of exchange in the jeu-parti were non-consensual, and therefore violent. The form of the jeu-parti has the potential for what Žižek calls ‘symbolic violence’, in which the structures and meaning of one trouvère’s song are appropriated and undermined by their opponent. This symbolic violence is discussed throughout the thesis. Several early jeux-partis are contrafacts of other trouvère songs. They were created in an aristocratic milieu that was deeply, and often violently, divided; contrafacture stages these aristocratic disputes and animates the form of the jeu-parti, which itself was created in a process of successive contrafacture. Later jeux-partis do not have the same context of aristocratic dispute, but are nevertheless a platform for symbolic violence. This is manifest in jeux-partis melodies, which are frequently tonally divided. In the interaction between textual structures and divided tonal structures, trouvères were able to enact symbolic violence against one another by subverting their opponent’s tonal arguments. Furthermore, the jeu-parti was performed and created in a cultural context that praised violent acts. Set against the cultural backdrop of chivalric literature and rituals, the disputatio, the trial by inquest, the tournament, the joust, and scientific and lyric definitions of sound as the product of a violent act, the jeu-parti was a genre through which violent practices could be praised, defined, and censured.

Keywords: jeu-parti
music analysis
trouvère
violence
Advisor: Leach, E
Beyond the politics of labelling: exploring the cessation clauses for Rwandan and Eritrean refugees through semiotics

Academics have for decades written on the need to interrogate the labels upon which the field of Refugee and Forced Migration Studies has been founded. At the centre of these discussions has been theorising around the 'integrity' and 'content' of the refugee label itself, with foundational texts expounding the need to take nothing about the meaning and purpose of this label for granted. This is evidently important in popular accounts, where the term's misuse fuels anti-immigrant sentiments and societal mistrust, as well as for the futures of these populations, as multiple interpretations of their status affect attempts to negotiate durable solutions to their plight. Without denying the importance of these theoretical accounts, or the incredibly rich literature that has emerged on account of them, this thesis suggests that much of the theorising on labelling to date has lacked a clear theoretical framework around which to structure otherwise critical observations vis-à-vis the performative and malleable characteristics of language.
It therefore introduces semiotic theories and methodologies as an approach for making sense of these manifold interpretations and their relationships to each other, and to explore what impacts this has on negotiations over refugees' futures. Associated theories are used to explain the controversial negotiations that surrounded the invocation of the Cessation Clause for Eritrean refugees in Sudan in 2002, and the ongoing attempts to apply Cessation to Rwandan refugees in Uganda. Both processes were mired by controversy, and yet almost no literature exists detailing when, why and how they unfolded as they did. Disaggregating the refugee 'label' through the semiotic frameworks provided by Saussure and Barthes helps explain the conceptual and spatial dissonance that plagued attempts to conclude these protracted refugee situations.
Through doing so, this thesis seeks to make three main contributions. First, it provides these extended accounts of how decisions to apply Cessation are arrived at, thereby filling an empirical gap in literature on this process. Second, it presents a heuristic framework rooted in linguistic theories to explain how certain words and objects – including the refugee label - can see their meanings transformed and bourgeon over time, the mechanisms through which this distortion occurs and is accommodated within discussions over the treatment of refugees, and the implications that the application of this theoretical framework has for how we understand particular incidents of decision-making within the refugee regime. Third, these theoretical approaches are shown to result in key challenges to how the role, content and function of the word refugee have been conceptualised to date.

Keywords: Rwanda
Politics
Forced Migration
Uganda
Eritrea
Refugees
Semiotics
Advisor: Scott-Smith, T
Betts, A