VictorJuiz/thesis huggingface dataset:
Mechanics of swelling and damage in brain tissue: a theoretical approach
Keywords: brain edema
soft tissue modelling
Biomechanics
mixture theory

Following trauma, such as an impact injury or stroke, brain tissue can swell. Swelling is the result of water accumulation in the tissue that is driven by pathological changes, such as increased permeability of the capillary walls and osmotic pressure changes within the tissue. Swelling causes increased intracranial pressure and mechanical deformation of the brain tissue, exacerbating the original injury. Furthermore, prolonged local swelling can lead to the spread of damage to the (initially undamaged) surrounding tissue, since compression and increased intracranial pressure may restrict blood flow in this tissue.
In this thesis, we develop mathematical models to examine the consequences of pathophysiological damage mechanisms on the swelling, and associated stress and strain, experienced by brain tissue. Mixture theory is used to represent brain tissue as a mixture of elastic solid, fluid and solutes. This modelling approach allows elastic deformations to be coupled with hydrodynamic pressure and osmotic gradients; the consequences of different mechanisms of damage may then be quantified.
We consider three particular problems motivated by experimental observations of swelling brain tissue. Firstly, we investigate the swelling of isolated, damaged, brain tissue slices; we show that mechanisms leading to an osmotic pressure difference between the tissue slice and its surroundings can explain experimental observations for swollen tissue slices. Secondly, we use our modelling approach to demonstrate that local changes in capillary permeability can cause significant stresses and strains in the surrounding tissue. Thirdly, we investigate the conditions under which a locally swollen, damaged, region can cause compression of the vasculature within the surrounding tissue, and potentially result in damage propagation. To do this, we propose a coupled model for the oxygen concentration within, and mechanical deformation of, brain tissue. We use our model to assess the impact of treatment strategies on damage propagation through the tissue, and show that performing a craniectomy reduces the extent of propagation.
Electronic excitations in semiconductors and insulators using the Sternheimer-GW method
Keywords: Electronic structure
DFT
Many-body perturbation theory
GW
optical properties
Materials Science

In this thesis we describe the extension and implementation of the Sternheimer- GW method to a first-principles pseudopotential framework based on a planewaves basis. The Sternheimer-GW method consists of calculating the GW self-energy operator without resorting to the standard expansion over unoccupied Kohn- Sham electronic states. The Green's function is calculated by solving linear systems for frequencies along the real axis. The screened Coulomb interaction is calculated for frequencies along the imaginary axis using the Sternheimer equa- tion, and analytically continued to the real axis. We exploit novel techniques for generating the frequency dependence of these operators, and discuss the imple- mentation and efficiency of the methodology.
We benchmark our implementation by performing quasiparticle calculations on common insulators and semiconductors, including Si, diamond, LiCl, and SiC. Our calculated quasiparticle energies are in good agreement with the results of fully-converged calculations based on the standard sum-over-states approach and experimental data. We exploit the methodology to calculate the spectral func- tions for silicon and diamond and discuss quasiparticle lifetimes and plasmaronic features in these materials.
We also exploit the methodology to perform quasiparticle calculations on the 2-dimensional transition metal dichalcogenide system molybdenum disulfide (MoS2). We compare the quasiparticle properties for bulk and monolayer MoS2 , and identify significant corrections at the GW level to the LDA bandstructure of these materials. We also discuss changes in the frequency dependence of the electronic screening in the bulk and monolayer systems and relate these changes to the quasiparticle lifetimes and spectral functions in the two limits.
'All the helth and life of the sacraments... I it am': Julian of Norwich and the sacrament of penance
Keywords: Julian of Norwich
penance

This thesis explores a long-neglected area of Julian’s work, namely her devotional and pastoral understanding of the nature of sin and the sacrament of penance. Her two texts reveal a deep concern, set within the context of a rise in lay penitential piety, for those devout who continued to experience a sense of shame and dread of sin, even after confession to a priest. By means of a close comparative reading of Julian's short and long texts of A Revelation of Divine Love, and an examination of a wide range of Middle English devotional texts and manuals, as well as a breadth of Julian scholarship to date, I argue that Julian addresses the devotional and ecclesiastical concerns of late fourteenth-century England in the problem of sin and confession for the ordinary believer. By articulating her revelation in the penitential terms of the manuals of the Church, Julian reveals the extent to which the daily devotional life of 'holy moder church' is the means by which the saving love of Christ is realised and made accessible to the penitent.
Within her writing Julian seeks to reassure her reader that God has dealt with sin and triumphed over the devil but in order to do this she must alter their understanding of a contrition-centred sacrament. For this reason Julian sets up a crisis of understanding within her long text between the 'common teaching of holy church' and her revelation of love. This conflict is deliberately left unresolved in order that, in scholastic terms, two opposing arguments in opposition may jointly illuminate the necessity of sin and penance in bringing the soul to the proper state of humility and the mercy and grace of the loving Lord in forgiveness. In so doing it is argued that, within Julian’s writing, the pastoral process of penance is integral to those who desire a more intimate relationship with God.
The thesis consists of four chapters which first, locates Julian's short and long versions of A Revelation of Divine Love within the climate of the late-fourteenth century; secondly, it charts the rise of the significance of the role of the penitent within the history of penance which led to an increasing lack of confidence within the late fourteenth century in the ability of the confessional encounter to alleviate the sense of sin experienced by some devout souls; thirdly, I analyse the extent to which Julian's short and long version of a Revelation of Divine Love reflect and address this catechetical and penitential climate in her theology of sin and penance; and finally the thesis poses the question of the extent to which Julian's work can be considered as a penitential text which seeks to bring ease and comfort of the assurance of sins forgiven through the everyday practices of the Church. It is concluded that Julian's writing reveals a fascinating and significant contribution to late fourteenth-century thought on penance and brings a fresh reading of Julian's texts.
Chastity on the early modern English stage,  1611-1649  
Keywords: Shakespeare
performance
Milton
John Ford
early modern
chastity

‘Chastity on the Early Modern English Stage’ seeks to explain the relationship between tragicomedy’s brief and short-lived English popularity and the royal cult of chastity which spanned exactly the same historical time-frame. This study attempts to define a cultural movement which influenced the political, religious, social, intellectual, aesthetic, and medical fields in the first half of the seventeenth-century and argues that the narrative tropes which structured, and assisted the spread of, the post-Elizabethan cult of chastity were the same tropes governing the tragicomedies so popular in the period.
The arguments made for tragicomedy are speculatively extended to all generic forms, with the intention of expanding an area of scholarship still dominated by formalist analysis. By focussing on narrative tropes and locating them within both fictional and non-fictional texts and in the presentation and discussion of significant events (from medical discoveries to liturgical arrangements and royal birthing rituals) this thesis aims to illustrate that the human and cosmic visions articulated by different dramatic genres were as relevant to early modern lives outside the theatre as they were to those within it. Genre is thus less a description of a text’s formal characteristics and more a set of truths governing certain human experiences both in texts and in life.
Focussing on Shakespeare’s The Winter’s Tale, two plays by John Ford, Caroline court masques and birthing rituals, Milton’s A Maske and a number of non-professional performances (from the Earl of Castlehaven’s trial to William Harvey’s demonstration of the circulation of the blood), ‘Chastity on the Early Modern English Stage’ describes the four tropes of chastity and their place in tragicomic experience from the death of Elizabeth I to the beheading of Charles I. While Charles’s death and the closure of the theatres are crucial reasons for the abrupt end of the cult of chastity and tragicomedy, this thesis argues that cause must also be attributed to the efforts of pro-Parliamentary and Puritan writers who, throughout the 1630s and 1640s, sought to claim the tropes of chastity for their own rhetoric and cause. Their success resulted in a redefinition of chastity as masculine, individuated, Parliamentarian, Protestant, intellectual, civic and prosaic instead of Catholic, royal, spectacular, feminised, Marian, pietised, and theatrical.
Causal structure in categorical quantum mechanics
Keywords: quantum information
relativity
causal structure

Categorical quantum mechanics is a way of formalising the structural features of quantum theory using category theory. It uses compound systems as the primitive notion, which is formalised by using symmetric monoidal categories. This leads to an elegant formalism for describing quantum protocols such as quantum teleportation. In particular, categorical quantum mechanics provides a graphical calculus that exposes the information flow of such protocols in an intuitive way. However, the graphical calculus also reveals surprising features of these protocols; for example, in the quantum teleportation protocol, information appears to flow `backwards-in-time'. This leads to question of how causal structure can be described within categorical quantum mechanics, and how this might lead to insight regarding the structural compatibility between quantum theory and relativity.
This thesis is concerned with the project of formalising causal structure in categorical quantum mechanics. We begin by studying an abstract view of Bell-type experiments, as described by `no-signalling boxes', and we show that under time-reversal no-signalling boxes generically become signalling. This conflicts with the underlying symmetry of relativistic causal structure. This leads us to consider the framework of categorical quantum mechanics from the perspective of relativistic causal structure. We derive the properties that a symmetric monoidal category must satisfy in order to describe systems in such a background causal structure. We use these properties to define a new type of category, and this provides a formal framework for describing protocols in spacetime. We explore this new structure, showing how it leads to an understanding of the counter-intuitive information flow of protocols in categorical quantum mechanics. We then find that the formal properties of our new structure are naturally related to axioms for reconstructing quantum theory, and we show how a reconstruction scheme based on purification can be formalised using the structures of categorical quantum mechanics. Finally, we discuss the philosophical aspects of using category theory to describe fundamental physics. We consider a recent argument that category-theoretic formulations of physics, such as categorical quantum mechanics, can be used to support a variant of structural realism. We argue against this claim. The work of this thesis suggests instead that the philosophy of categorical quantum mechanics is subtler than either operationalism or realism.
Precedent, commentary, and legal rules in the Madhhab-Law tradition: Ibn Quṭlūbughā's (d. 879/1474) al-Taṣḥīḥ wa-al-tarjīḥ
Keywords: Syria
Egypt
fiqh
madhhab
Islamic jurisprudence
Hanafism
Mamluk
tradition
Islamic law
Hanafi
legal writing

This thesis examines the role that scholarly digests and commentaries played in the formation of legal rules in the Muslim legal institution known as the madhhab. I posit that a shared approach to legal rule-determination, and the respect of juristic precedent that it entails, underlies the jurisprudential processes of all of the four post-classical Sunni madhhabs (the Ḥanafī, Mālikī, Shāfi'ī, and Ḥanbalī), and unites them in a wider ‘madhhab-law tradition’.
Taking the Ḥanafī madhhab as a case study, the thesis analyses a commentary written by the late Mamluk jurist Ibn Quṭlūbughā (d. 879/1474) upon the digest of the celebrated Abbasid-era Abū al-Ḥusayn al-Qudūrī (d. 428/1037). In discussing the madhhab's heritage of precedent, Ibn Quṭlūbughā's commentary weaves an intricate tapestry of quotations and references from previous jurists and works, providing us with insight into how author-scholars reacted to, and interacted with, other jurists over space and time. Chapter 1 provides a short introduction to the lives of Qudūrī and Ibn Quṭlūbughā, and the contexts within which they produced their works. Chapter 2 employs both quantitative and qualitative analysis of the commentary, in order to deduce historical and geographical patterns out of which a periodisation of rule-determination in the Ḥanafī madhhab is proposed. In Chapter 3, Ibn Quṭlūbughā's jurisprudential theory of rule-determination is studied, examining both the justifications and the processes employed by jurists in arriving at a legal rule in the Ḥanafī madhhab. Chapter 4 then turns to the craft of commentary itself, analysing over eighty case examples for the logical relationships, rhetorical devices, and legal arguments that inform the actual practice of rule-determination through commentary. A final chapter then summarises the conclusions, and situates them within a broader discussion as to the nature of the madhhab-law tradition.
Functional analysis of mutations in isocitrate dehydrogenase involved in gliomagenesis
Keywords: Isocitrate Dehydrogenase
glioma
Oncology
glioblastoma
Tumour metabolism.
Cancer

The main subject of my thesis is the investigation of mechanisms of glioma tumorigenesis associated with the recently identified mutations in isocitrate dehydrogenase. Gliomas account for 80% of primary brain cancers. They represent a diverse group of tumours, and are graded from I-IV based on histopathological features. Whilst grade I tumours may be curable with surgery alone, grade II and III gliomas inevitably progress to glioblastoma multiforme (GBM), which is highly resistant to current therapies and carries a very poor prognosis. Despite an improved understanding of the pathways and mechanisms involved in the development of glioma and its progression to grade IV disease, current and novel treatments have so far failed to significantly improve outcome.
Isocitrate dehydrogenase (IDH) enzymes catalyse the oxidative decarboxylation of isocitrate to α-ketoglutarate (α-KG). Somatic mutations in genes encoding IDH1 and IDH2 were first identified in glioma and subsequently in acute myeloid leukemia and other solid tumours. These heterozygous point mutations occur at the arginine residue of the enzymes active site and cause both loss of normal enzyme function and gain-of-function, causing the reduction of α-KG to D-2-hydroxyglutarate (D-2HG), which accumulates. D-2HG may act as an oncometabolite through the inhibition of various α-KG dependent enzymes, stimulating angiogenesis, histone modifications and aberrant DNA methylation. Possibly, IDH1/2 mutations may also cause oncogenic effects through dysregulation of the tricarboxylic acid (TCA) cycle, or by increasing susceptibility to oxidative stress. The exact role of mutant IDH1/2 in tumorigenesis however remains unclear.
In the work outlined in this thesis, I have demonstrated that the expression of mutant IDH1/2 in glioma cell lines leads to 2-HG accumultation and a reduction in α-KG production and results in HIF1α accumulation and a reduction in 5hmC production. Furthermore, the brain-specific expression of mutant Idh1 in mice also results in 2-HG accumulation and reduced α-KG production, whilst a reduction in 5hmC levels are also seen. This data appears to support the theory that IDH1/2 mutant activity results in the inhibition of α-KG dependent enzymes, either through the accumulation of 2-HG or due to a reduction in α-KG levels. The brain-specific expression of mutant Idh1 in mice also results in increased cellular proliferation and an increase in the expression of the neural stem cell marker, nestin. However gliomas do not develop, perhaps suggesting that additional mutations are required in conjunction with those occuring in IDH1/2 in order to initiate tumourigenesis.
Clinically, IDH1/2 mutations may represent a novel therapeutic target in glioma and may also serve as useful diagnostic, prognostic and predictive biomarkers. However, a better understanding of the pathogenesis of mutant IDH is required, to enable effective IDH1/2 directed therapies to be developed in the future.
Elucidating mechanisms of premature ovarian failure using a transgenic mouse model
Keywords: glycans
ovarian physiology
female infertility
oocyte
POF

Premature ovarian failure (POF) is a condition that affects around 1% of women of reproductive age. It is idiopathic in 74-90% of cases and the mechanisms involved remain unclear. Several mouse models of POF have been described, however new models are necessary to understand the aetiology of POF and to hopefully identify candidate molecules that can be used as targets for intervention. A mouse model of POF (DM) occurs from oocyte-specific deletion of two glycosyltransferases encoded by C1galt1 and Mgat1, thus oocytes lack core 1-derived O-glycans and complex N-glycans. DM females have POF by 3 months of age exhibiting follicle depletion, elevated gonadotropins and decreased sex steroids. Female mice are fertile prior to ovarian failure producing a single small litter and thus, the DM model provides an outstanding opportunity to explore the onset of POF. In addition, since ablation of these glycans occurs only in the oocyte generates a progressive ovarian failure and POF, this model provides a unique opportunity to further our understanding of the role of the oocyte in the regulation of ovarian function and fertility. In this thesis, the influence of the abnormal endocrine environment was discarded as the origin of the altered follicle development in DM. In vitro and in vivo analysis of follicle development using follicle culture and the reaggregated chimeric ovary technique has highlighted intra-ovarian factors as responsible for the onset of POF in DM females. Finally, ovary transcriptomic analysis revealed an accumulation of changes in gene expression with age consistent with the DM phenotype. These results have highlighted potential therapies as well as genes and pathways as candidate molecules to try to reverse POF in the DM mouse model.
Aspects of branch groups
Keywords: Branch groups
subgroup structure
commensurability
congruence subgroup property
automorphisms of rooted trees

This thesis is a study of the subgroup structure of some remarkable groups of automorphisms of rooted trees. It is divided into two parts. The main result of the first part is seemingly of an algorithmic nature, establishing that the Gupta--Sidki 3-group G has solvable membership problem. This follows the approach of Grigorchuk and Wilson who showed the same result for the Grigorchuk group. The proof, however, is not algorithmic, and it moreover shows a striking subgroup property of G: that all its infinite finitely generated subgroups are abstractly commensurable with either G or G × G. This is then used to show that G is subgroup separable which, together with some nice presentability properties of G, implies that the membership problem is solvable. The proof of the main theorem is also used to show that G satisfies a "strong fractal" property, in that every infinite finitely generated subgroup acts like G on some rooted subtree.
The second part concerns the subgroup structure of branch and weakly branch groups in general. Motivated by a natural question raised in the first part, a necessary condition for direct products of branch groups to be abstractly commensurable is obtained. From this condition it follows that the Gupta--Sidki 3-group is not abstractly commensurable with its direct square. The first main result in the second part states that any (weakly) branch action of a group on a rooted tree is determined by the subgroup structure of the group. This is then applied to answer a question of Bartholdi, Siegenthaler and Zalesskii, showing that the congruence subgroup property for branch and weakly branch groups is independent of the actions on a tree. Finally, the information obtained on subgroups of branch groups is used to examine which groups have an essentially unique branch action and why this holds.