VictorJuiz/thesis huggingface dataset:
Beyond translation technique:  linguistic approaches to the Septuagint’s translation of the Aramaic verbal system in Old Greek Daniel, Theodotion Daniel, and 2 Esdras

This thesis applies four distinct linguistic methods to the philological data mined from translation technique of the Aramaic verbal system in Old Greek Daniel, Theodotion Daniel, and 2 Esdras. After briefly setting the present work within the context of previous studies (ch. 1), an exhaustive catalogue of the Aramaic verbal forms and their Greek translations occur, followed by the Greek forms and the Aramaic forms they translate (ch. 2). Chapter 3 applies linguistic typology and typological studies of tense, aspect, and modality (TAM) to the enigmatic Aramaic prefix conjugation (PC). Chapter 4 uses the concepts of language contact to explore Aramaic dialect differences (both lexical and grammatical) between the Aramaic of the Bible and the spoken Aramaic of the translators. Chapter 5 applies the concepts of idiolect as developed in forensic linguistics to Greek verbal syntax in the pluses of Old Greek Daniel, which in turn informs our understanding of the textual problem that is Old Greek Daniel 4-6. Chapter 6 problematizes minority translation equivalents in terms of Relevance Theory, showing how translators’ use aspectual choice functions as a procedural constraint to guide their readers toward intended inferences. The closing chapter (ch. 7) reviews the conclusions of the work and suggests new avenues for research.

Keywords: Greek Verb
Translation Technique
Relevance Theory
Linguistic Typology
Aspect
Verbal Syntax
Forensic Linguistic
Aramaic Verb
Tense
and Modality
Language Contact
Advisor: Joosten, J
Molecular networks regulating T cell  responses at barrier sites

Inflammatory bowel disease is a complex syndrome characterized by chronic inflammation of the intestine with an unclear aetiology. GWAS and preclinical studies revealed how IL-23 is one of the main drivers of the deranged Th17 inflammatory response that characterizes this disease, although the molecular and cellular pathways involved are still unclear. With a combination of in vitro and in vivo systems, in this study we identified Timp1 and Ltb4r1 as IL-23-induced genes in Th17 cells and tested their pathogenic potential in IL-23/Th17 driven intestinal inflammation. Timp1-/- and Ltb4r1-/- mice were tested in models of T-cell dependent colitis showing minimal impact on overall inflammation and Th17 cytokines production. With this study we also showed how another gene of interest, Dgat1, was enriched in CD4+ T cells and Foxp3+ Tregs at barrier sites. While Dgat1 deficiency in CD4+ cells did not have an impact on T cell induced colitis, mice carrying the specific ablation of Dgat1 in Foxp3 expressing cells developed a systemic type 2 inflammatory response characterized by accumulation of GATA3+ Foxp3+ Tregs at barrier sites and high levels of serum IgE. Thus, with our study we identified a novel role for barrier site Tregs in inducing immune tolerance through DGAT1. Finally, we investigated the effect of IL-23 signalling on intestinal Th2 cells. Our data suggest that IL-23, while sustaining Th17 inflammation, restrains the activity of intestinal Th2 cells. Using an adoptive T cell transfer model of colitis, we observed a cell intrinsic inhibitory effect of IL-23 on Th2 cells, suggesting that in the intestine, the Th17/Th2 balance is controlled by IL-23. With this study we revealed new insights in the complex regulation of inflammatory responses at barrier sites, where the function of T cells and Tregs is tightly regulated to maintain homeostasis.

Advisor: Powrie, F
Swift's art of allusion

The thesis is a study of Jonathan Swift’s library and reading, and a literary-critical examination of his art of allusion. Much scholarship on eighteenth-century literature seeks to affirm its formal clarity and decorum, perceiving — particularly in Augustan poetry — a strain for order and scholarly care. The claim of this thesis is that Swift provided an alternative to, and a critique of, these standards in literature, alluding to other texts with the kinds of obliquity, parody, and playful misanthropy which were germane both to his own writing and to satire as a genre.
The introduction examines Swift’s obligations at Marsh’s Library, Dublin, showing how he seems to have capitalised on opportunities to steal books and re-use fragments from them. This opens up a discussion of what constitutes a literary allusion, and how satirists such as Swift are invested at once in unsettling an allusion’s plausibility and expanding its possibilities. Chapter 1 immediately responds to these claims, showing how Swift subjected his scholarly editions of ancient writers to processes of breaking and remaking. It reveals his fondness for scholarly errors and distortions of mythology, and his attraction to areas of pseudo-learning which he could inhabit and parody. Chapter 2 pursues a closely-related argument in relation to Swift’s reading of modern literature, looking at the ways in which Swift ignored or affected ignorance of literature written in his own time: alluding, often, to their opening lines, or to cant phrases.
Chapter 3 shows how Swift’s allusions rejected any concept of literary dependance or gratitude; and depended, instead, on his own mock-tyrannical behaviour. The chapter takes special interest in Swift’s reading of classic accounts of tyranny, suggesting that many of his most eccentric allusions were thinly-veiled parodies of his own unfriendly characteristics. Chapter 4, a study of Swift’s allusions to the King James Bible, builds on this work, and examines the range of allusive practices to which he subjected passages of scripture, situating him in a context of clerical learning in eighteenth-century Dublin, and as a Dean in the Church of Ireland.
The thesis closes with an account of the ‘hint’ in eighteenth-century literature (an important word for an allusion in the period), showing how Swift related to a much wider context of allusive practice. The conclusion examines some of the ways in which Swift himself was alluded to, both in England and Ireland, and suggests that one of his legacies to satire was a species of obscurity that derived its local energies from genuinely acquired forces of erudition.

Keywords: literary criticism
allusion
Swift
eighteenth-century
satire
Advisor: Johnston, F
Experimental investigation of accelerator beam dynamics with a linear Paul trap

This thesis describes a range of experiments performed using a linear Paul trap to investigate the transverse beam dynamics of intense hadron accelerators. Due to the complexity of the dynamics in intense hadron accelerators, it is advantageous to use a scaled experiment to gain insight into these machines. A Paul trap is used to study accelerator dynamics, as the Hamiltonians of the two systems are equivalent.
The IBEX Paul trap at the Rutherford Appleton Laboratory, Oxfordshire, has been commissioned. The first trapping of argon ions is observed, and the system is characterised, developing an understanding of the ion creation process, ion lifetime, longitudinal temperature, transverse emittance, and the process of ion extraction from the trap. A Faraday cup and MCP are used as diagnostics for the trap and are calibrated carefully to detect accurately the number of ions confined.
Both the IBEX and S-POD (Hiroshima University, Japan) linear Paul traps are used to study space-charge-driven resonances quantitatively for the first time. The particle-in-cell code Warp is used to gain a deeper understanding of the experiment and to assist with the interpretation of results. Values are extracted describing the location of the greatest ion loss in tune space for a given intensity for equal transverse tunes. These values are compared to values predicted both analytically and through simulation.
In the second half of this thesis, a design for a novel particle accelerator is considered, using the theory of Nonlinear Integrable Optics (NIO). In NIO, a highly nonlinear magnet is inserted into a linear lattice (known as a T-insert), resulting in regular and bounded particle motion. Detailed studies are undertaken to ascertain whether a simpler version of this theory, Quasi-Integrable nonlinear Optics (QIO), can be tested in a Paul trap.
A T-insert lattice is designed to meet the constraints of QIO, as well as the constraints imposed by the IBEX hardware. A number of these lattices are tested on the IBEX trap, confirming that enough ions are confined to study QIO in the presence of space-charge forces and that it is possible to create a T-insert with sufficient precision. To verify that the T-insert lattice created within the Paul trap meets the conditions for QIO, a method to measure the beta function in a Paul trap has been designed and tested.
Finally, a series of simulations are presented, showing that with a simple upgrade to the IBEX trap it is possible to create an octupole potential of high-enough quality to test QIO, while also retaining the ability to create a high-quality quadrupole to make the T-insert lattice. The impact of misalignment and scraping within the trap on the dynamic aperture and tune spread is studied using Warp. The resistance of the lattice to resonant excitation is investigated.
The experimental and simulation studies described show that QIO can be tested in a Paul trap, and pave the way for a range of studies of this exciting concept.

Keywords: Nonlinear Integrable Optics
Paul Trap
Accelerator Physics
Transverse Dynamics
Advisor: Sheehy, S
Magnetism in topological materials

Notions of topology are of considerable interest currently in physics, especially in the way topology influences the electronic properties of crystalline solids. This thesis concerns the experimental investigation of four different magnetic materials, which have been predicted to display a strong interplay between magnetism and the topology of the electronic band structure.
I demonstrate that EuCd2Sb2, below TN= 7.4 K, displays an A-type anti-ferromagnetic order on the Eu sub-lattice with a magnetic propagation vector of k=(0,0,1/2). I also establish that the C3 rotational symmetry along the crystal c axis (essential for the stabilisation of band crossings called Dirac nodes) is broken by the in-plane orientation of the Eu moments.
Following the initial discoveries of crystalline solids which can host topologically-protected band crossings called Weyl nodes, there is now a need for better material realisations, ideally comprising a single pair of nodes located at or very close to the Fermi level and in an energy window free from other overlapping bands. I propose that EuCd2As2, in a magnetic field of B >1.6 T along the c axis, to be such a system. This material is of general interest as it represents the simplest possible Weyl semimetal, and is therefore a model system for fundamental investigations of Weyl physics.
I refute the proposition that semimetallic YbMnBi2 hosts Weyl nodes induced by the time-reversal symmetry breaking mechanism. Furthermore, the full magnetic excitation spectrum of YbMnBi2, which has been mapped for the first time, demonstrates that the magnetic order of the Mn sub-lattice is weakly coupled to the charge carriers in the Bi square net.
Finally, the complex magnetic order of the Mn sub-lattice in Mn3Ge has been elucidated for the first time. This will shed light on the origin of the large anomalous Hall effect in Mn3Ge, which is unusual for an antiferromagnet.

Keywords: Magnetism
Weyl
Topology
Advisor: Boothroyd, A
Optimizing an AAV-CRISPR system for retinal gene therapy

Introduction: CRISPR/Cas9 is a bacterial defence system which evolved to cleave and deactivate bacteriophage DNA. The elements involved in the CRISPR/Cas9 system may be modified for gene therapy. CRISPR/Cas9 consists of two components, a single guide RNA (sgRNA) and a Cas9 protein. The sgRNA allows for sequence-specific binding. “Active” Cas9 creates a double-stranded break in the target region while the “deactivated” form can inhibit transcription. CRISPR/Cas9 can be packaged within adeno-associated viral vectors, which opens the possibility of using CRISPR/Cas9 to target mutations in the retina. We examine several optimizations to the AAV-CRISPR/Cas9 system in vitro in HEK293-eGFP cells.
Materials and Methods: We compare the effects of sgRNA orientation in both active SaCas9 constructs and deactivated SaCas9 constructs with the KRAB repressor (dSaCas9-KRAB). We also examine the cleavage ability of GeoCas9.
Results: There was no difference in Cas9 and sgRNA levels between the in cis and in trans SaCas9 constructs. We also found no difference in Cas9 levels, sgRNA levels, and target knock-down between the cis and trans orientations of the dSaCas9-KRAB constructs. For GeoCas9, we found that DNA cleavage levels were undetectable, despite confirmed expression of both sgRNA and GeoCas9 protein.
Conclusion: When delivering CRISPR/Cas9 in an AAV-based expression cassette, the efficacy appears unrelated to the orientation of the sgRNA (in cis or in trans) relative to the Cas9 gene. Furthermore, GeoCas9 may not be as efficacious as SaCas9, since it was unable to cleave DNA detectably in similar experiments.

Keywords: Gene therapy
Retinal degeneration
CRISPR/Cas9
Retina
Advisor: MacLaren, R
Exotic phases of interacting Majorana fermions and parafermions

In this thesis exotic phases of models preserving the symmetries of the one-dimensional quantum Ising and three-state Potts chains are considered, the natural habitats of Majorana fermions and parafermions, respectively. Along with numerical techniques, conformal field theory (CFT) is used to study the resulting physics.
Chapter 1 gives an introduction to the field and explains the basics of the numerical techniques to be used throughout the thesis. CFT is briefly introduced in Chapter 2 before the key results necessary for the thesis are given.
In Chapter 3, self-dual interactions are added to the critical Ising model, giving a range of different phases. A tricritical Ising point separates the Ising phase from an order-disorder coexistence phase on the chirally symmetric line, while a supersymmetric line provides the transition to an incommensurate phase in the general model. The model is solved exactly on a free-fermionic line giving insight into the points where only numerical analysis can be performed. This is supplemented by Appendix A, where the qualitative difference between similar perturbations is considered.
Chapters 4 and 5 consider models with the symmetries of the three-state Potts model. Various phases are found including an order-disorder coexistence phase, a second critical Potts phase, a "not-A" phase, and a representation symmetry protected topological phase. The effect of lattice momentum on the stability of phases and the connection with conformal field theory operators is studied. Lattice realizations of several CFTs are found, such as the tricritical Potts CFT and a CFT expressible in two different forms, either in terms of a boson and fermion, or Potts and tricritical Ising CFTs.

Keywords: Conformal Field Theory
Majorana fermions
Duality
Parafermions
Advisor: Fendley, P
Palaeogenomics of animal domestication: computational modelling of ancestry, demography and selection

The study of animal domestication is in the midst of a genomic revolution, as technological advances dramatically increase the availability of DNA sequence data from ancient and modern domestic populations. For the first time, palaeogenomic datasets are being produced of sufficient size and scope to directly observe anthropological and evolutionary processes through time; from the emergence of domestic animals in the Neolithic, to the formation of modern breeds in the Victorian era.
This thesis applies computational modelling of ancient and modern DNA to infer ancestry, demography, and selection in domestic cattle (Bos taurus), horses (Equus ferus caballus), and dogs (Canis familiaris).
Chapter 1 reviews the substantial contribution palaeogenomics has made to the study of animal domestication, and details the latest theoretical and empirical advances, alongside individual profiles of sixteen major domestic species.
Chapter 2 reconstructs the allele frequency trajectories of genetic variants linked to quantitative traits in genome-wide associations studies (GWAS) of cattle and horses. Using a Bayesian modelling approach, and a dataset of more than 350 ancient genomes spread across the last 10,000 years, the age of the allele under selection for thousands of GWAS variants is inferred, along with the selection coefficients for hundreds of polygenic traits.
Chapter 3 analyses the first ancient genome-wide DNA from pre-contact North American dogs. Admixture analyses show that the earliest American dogs were not independently domesticated, and originated from a population of arctic dogs in Eastern Siberia. These dogs likely accompanied humans during the peopling of the continent, and rapidly diversified after their arrival, until their sudden replacement following the arrival of European colonists. Remarkably, their most closely related living relatives are now an 8,000-year-old contagious cancer clone known as Canine Transmissible Venereal Tumour (CTVT).
Chapter 4 presents an ancestry analysis of a rare breed of humpless, dwarf shorthorn cattle from the remote island of Socotra, in the Arabian Sea. Admixture analyses show that contrary to published hypotheses, these cattle are predominantly Eurasian taurine (Bos taurus) in ancestry, with only minimal African taurine heritage, and preliminary results indicate possible admixture with a basal clade of zebu cattle (Bos indicus).

Keywords: domestication
bioinformatics
aDNA
palaeogenomics
Advisor: Larson, G
Dynamic SLAM, object reconstruction, shape and pose prediction for 3D scene understanding

Advances in 3-dimensional (3D) computer vision have tremendously impacted the way that humans and computers interact. Applications of 3D vision, such as virtual reality video games and robotics are underpinned by a range of computer vision competencies, including pose estimation, mapping and semantic understanding. However, many challenging research problems remain, three of which are the focus of this work.
Firstly, the difficult task of dense mapping in dynamic environments is tackled, utilising a novel scene representation allowing dynamic and static components to be handled separately. This approach demonstrates improved pose estimation accuracy in dynamic scenes, compared to established reconstruction approaches. The second topic of this Thesis is 3D object reconstruction, with a novel representation and formulation that provides online error correction. This approach demonstrates improved reconstruction quality and geometric accuracy compared to both a start of the art method and a vanilla approach. The final focus of this work is the simultaneous inference of object shape and pose in large scale, outdoor environments. The approach taken regresses shape and pose in a combined supervised/weakly-supervised manner, utilising a combination of Convolutional Neural Networks and Gaussian Processes.
This Thesis provides a foundation for further research in this area. However, immediate applications are evident. The motion segmentation and dense mapping approach allows for operation in previously prohibitive scenarios, such as robotics. The 3D object reconstruction work is applicable to the collection of geometrically consistent 3D object data. Finally, the simultaneous inference of shape and pose is applicable to modelling scenarios of specific semantic interest, where an entire scene need not be reconstructed, preliminarily demonstrating potential for large scale, semi-dense, geometric mapping.

Advisor: Torr, P
Prisacariu, V
Role of diabetes mellitus in atrial fibrillation and potential new treatments

Chapter 1 explains the relative importance of diabetes mellitus (DM) and cardiovascular complications in a global perspective. It then describes the current understanding of how diabetic cardiomyopathy develops and what the underlying mechanisms are. Afterwards, atrial fibrillation (AF), another DM-related complication, is presented followed by the description of the main related pathological mechanisms. Finally, the chapter discusses the therapeutic potential of tetrahydrobiopterin (BH4) as a cofactor of nitric oxide synthase (NOS). Chapter 2 describes in full detail all methods used in the experimental work of this research thesis. Chapter 3 shows that the myocardial overexpression of the rate-limiting enzyme for the synthesis of BH4, GTP cyclohydrolase 1 (GCH1), in mice (mGCH1-Tg) prevents the development of left ventricular (LV) diastolic dysfunction in the presence of streptozotocin (STZ)-induced diabetes. Interestingly, the mechanism underpinning this beneficial effect is not suppression of myocardial superoxide production, prevention of BH4 oxidation and restoration of coupled NOS activity, or reduction of interstitial myocardial fibrosis. Instead, the overexpression of GCH1 with an associated increase in the myocardial BH4 level and myocardial NOS activity prevents myocardial energetic impairment in diabetic hearts by increasing glucose uptake via the insulin-independent glucose transporter 1 (GLUT-1). Chapter 4 explores the atrial electrophysiological characteristics of STZ diabetic mice. Diabetic mice have increased risk for in vivo pacing-induced AF, enlarged relative atrial size and impaired in vivo atrial conduction, as indicated by prolonged ECG PQ interval. Furthermore, experiments in isolated whole atria demonstrate a significant focal increase in fibrosis in the medial part of the right atrium, which results in a significant decrease in the conduction velocity in the same area followed by an increase in the conduction wave-front heterogeneity in the left atrium. Chapter 5 investigates the electrophysiological phenotype of the mGCH1-Tg mice. The transgenic mice have lower heart rates, they spontaneously develop AV nodal escape rhythm, and have prolonged ECG QT interval. The underlying mechanisms for those changes are a global decrease in the atrial conduction velocity, decrease in the conduction through the AV node, as well an increase in the action potential duration (APD). Furthermore, oral BH4 treatment was also tested in diabetic mice, but it did not decrease the risk of AF or improved LV diastolic dysfunction significantly. Chapter 6 summarises the key results and presents the relative impact of each finding. It also discusses the main limitations of the study as well as future research directions.

Keywords: atrial fibrillation
diabetes mellitus
tetrahydrobiopterin
Advisor: Casadei, B
Carnicer, R