VictorJuiz/thesis huggingface dataset:
The functional analysis of rare genetic variants in a familial neurodegenerative spectrum disorder

Whole genome sequencing can enable an unbiased approach to the diagnosis and to the understanding of genetic aetiology of neurodegenerative diseases, which are a clinically and genetically heterogeneous group of disorders. Two brothers, originally diagnosed with primary progressive multiple sclerosis (PPMS), displayed an atypical disease progression over a 30-year period with a clinical picture of paresis, ataxia, mental impairment and dysarthria. Late stage fasciculations, absence of sensory symptoms and a follow-up magnetic resonance imaging (MRI) scan showing severe atrophy of the cerebrum, cerebellum and brainstem, but no white matter lesions, called the original diagnosis into question. Given the familial nature and the rarity of this very similar clinical profile, we hypothesised that a rare variant could be contributing to disease. Whole genome sequencing identified three rare variants segregating with disease: a homozygous non-frameshift deletion in the fatty acid 2-hydroxylase (FA2H) gene, an X-bound non-synonymous single nucleotide variant in the adaptor protein-1 complex subunit sigma-2 (AP1S2) gene, and a homozygous frameshift deletion in the mixed lineage kinase domain-like protein (MLKL) gene. Lipidomic analysis using liquid chromatography-tandem mass spectrometry of FA2H variant-expressing cell lines demonstrated no detrimental impact of the deletion in FA2H on protein function. Bioinformatic and computational structural analysis suggested the variant in AP1S2 to be benign. In contrast, the frameshift deletion in MLKL prevents expression of MLKL protein as demonstrated in patient-derived primary cells. The absence of MLKL was shown ex vivo to cause complete deficiency in necroptosis, a recently identified form of programmed cell death that is involved in a spectrum of neurodegenerative diseases. This thesis provides the first clinical case report implicating MLKL and necroptosis deficiency in a neurodegenerative spectrum disorder. The results suggest that current strategies to pursue MLKL inhibition for human therapy should be approached with caution.

Keywords: Genetics
Neuroscience
Advisor: Fugger, L
Dendrou, C
Verifying concurrent systems by approximation

Approximate verification frameworks are an approach to combat the well-known state-space explosion problem. For properties formulated as "no bad state can be reached", an approximate framework can be simply obtained by replacing exact reachability by some over-approximation. These frameworks look for a bad state in this over-approximation. If no bad states are found, the system satisfies the original property; the framework is sound. If a bad state is found, we have an inconclusive result: this bad state might be reachable or not. This permitted incompleteness is a cornerstone of such methods and it is a means to obtain efficiency.
In this thesis, we propose three techniques to approximate reachability. The first analyses small subsystems to capture locally provable relationships between component states. The second and third complement the first by capturing some global system invariants. While the second combines component invariants to estimate whether components can cooperate to reach a system state, the third technique detects token mechanisms and deduces token invariants that approximate reachability.
Moreover, we show how our approximations can give rise to useful frameworks that check deadlock freedom, static properties -- a class of state-based properties we propose -- and CSP's traces and failures refinement expressions. Our evaluation of these frameworks seems to suggest that they can efficiently prove a large spectrum of properties for a variety of systems.
Despite tackling NP-hard problems, our frameworks can be efficiently powered by SAT/SMT solvers. The unsuccessful attempts at using symbolic exploration to precisely check concurrent systems, combined with the success of our frameworks, suggest that the approximations we study are a key factor in harnessing the verification power of these solvers.

Keywords: SMT solving
Symbolic verification
CSP
Static properties
Reachability analysis
Concurrent systems
Refinement checking
SAT solving
Deadlock analysis
Transition systems
Advisor: Roscoe, B
Functional genomics of Ankylosing Spondylitis

This thesis aimed to determine the functional genomic changes specific to Ankylosing Spondylitis (AS) for different disease relevant immune cell types and relate this to disease associated genetic variants. AS is a highly heritable inflammatory disease mainly affecting the spine. Functional genomic approaches at the transcriptomic and epigenetic level in the context of disease are accelerating the understanding of the functional consequences of genetic variation, and how this may impact disease susceptibility and aetiology. Diseaseassociated genetic variants may be active only in certain cell types; therefore understanding the underlying functional mechanisms requires investigation in relevant tissues and cells, and in the disease state. TNF-α inhibition as a current biologic therapy has proved very effective in the majority but not all AS patients. To understand this response further, cell type specific changes in treatment responders were also investigated.
The transcriptomic profile in 15 AS patients with active disease is reported here for six immune blood cell types (CD4+ and CD8+ T cells, CD14+ monocytes, CD16+ neutrophils, NK cells and CD19+ B cells) using RNA-seq, in purified cell types for messenger RNAs, long non-coding RNAs and microRNAs. Enrichment for NF-κB signalling and HDAC Class I signalling was found across cell types, most significantly in CD14+ monocytes and CD16+ neutrophils. The gene expression profile 3 months after commencing anti-TNF therapy is reported for three cell types, providing insights into the molecular basis of treatment response. NEAT1, a long non-coding RNA was found to be correlated with disease activity following anti-TNF therapy (P=0.031) in CD14+ monocytes.
Changes in chromatin accessibility are informative for putative regulatory DNA elements and may inform hypotheses for molecular mechanisms modulated by genetic variation. Here, the chromatin accessibility landscapes in 5 AS patients are established for three cell types using an Assay for Transposase Accessible Chromatin with high-throughput sequencing (ATAC-seq). In CD14+ monocytes, 437 genes were found differentially expressed in AS patients in both RNA-seq and ATAC-seq (observed enrichment P=2.2x10-16). Following TNF-α inhibition therapy, differentially expressed genes in both datasets were found in CD8+ T cells (P= 0.02). PTGER4, a GWAS reported gene was found down-regulated in CD8+ T cells from treated AS patients (FDR=0.0002). Integration of ATAC-seq data with fine-mapped SNPs also revealed a differentially closed chromatin peak in one patient at rs4672505 (locus 2p15), specifically in CD8+ T cells. This SNP may explain the association signal found at this locus, with evidence of regulating B3GNT2. Future work aims to validate these findings in a larger cohort and collect AS specific epigenetic marks using ChIP-seq, along with functional validation of rs4672505 using Capture-C and CRISPR.

Advisor: Knight, J
Bowness, P
Towards the total synthesis of a dolabellane diterpenoid, and studies in synthetic organic electrochemistry

Chapter one begins with an introduction on the dolabellane diterpenoid natural product family, followed by a summary of the most recent total and formal syntheses of dolabellane diterpenoids. Previous work carried out in the Burton group towards the target natural product (1.5), a member of the dolabellane family, will also be discussed. We then discuss our own work towards the natural product target 1.5. Significant progress towards the racemic natural product target has been achieved, and we have isolated the product 1.252 that derives from the key ring-closing metathesis reaction of 1.240. We have also achieved multi-gram syntheses of both enantiomers of an advanced intermediate in the natural product synthesis, and this work is detailed at the end of Chapter one. The synthesis of both enantiomers of the target natural product will be crucial in confirming the absolute configuration of the target natural product, 1.5. Chapter two is focused on the field of synthetic organic electrochemistry, and the work that we have done using this synthetic tool. Although we were ultimately unsuccessful in our stated aim of replacing the manganese(III) based oxidant in the radical cyclisation of substrates containing a dicarbonyl functional group, several observations were made which we expect will guide future research in this area.

Advisor: Burton, J
An analysis of incomplete contacts in partial slip

Fretting fatigue is often the cause of failure in many engineering components. It is of importance in safety critical components subject to extreme loads such as in dovetail joints in jet engines. In order to accurately estimate the life of these components, accurate knowledge of the shear traction and differential strains at the contact interface is required. The loading that these components are subjected to is often complicated (varying normal load, bulk tension and shear force) and needs to be simplified, to ignore the variation in either the bulk tension or the normal load.
The aim of this thesis is to develop a method which estimates the extent and magnitude of slip in incomplete contact problems where the normal load, shear force and bulk tension vary with time.
Three new methods are first presented to solve incomplete contact problems in partial slip. One of these methods - using a dislocation correction to the fully stuck solution - is used to study problems where the normal load is held constant. Then, the problem of a varying normal load and bulk tension is studied in detail using the existing method of a traction correction to the sliding solution. Finally, the distributed dislocation method is used to solve the most general problem involving an incomplete problem with a varying normal load, bulk tension and shear force.

Advisor: Hills, D
Single cell genomics data analyses reveal novel biological insights

Single cell RNA-Seq is one type of single cell –omics experiment. The technology to perform single cell RNA-Seq has recently become available, promising to enable a range of biological investigations, such as identifying cell-to-cell heterogeneity within a cell culture and novel cell types in primary tissues. Despite of these advances, data analytical aspects of this technology was proved to be challenging. Many technical issues and confounders deserve special attention. Only when these are well-understood and accounted for can bioinformatics analyses provide reliable and robust results. The aims of my research were first to comprehensively investigate the analytical aspects of single cell RNA-Seq datasets, and then to apply appropriate analytical methods best suited for each of my two research projects to identify cell-to-cell heterogeneity, in order to answer specific biomedical questions.

Advisor: Ponting, C
Haerty, W
Translational development of MyD88 as a biomarker for selecting patients with lymphoma responsive to histone deacetylase inhibitors

Histone deacetylase inhibitors (HDIs) are promising new agents for the treatment of haematological malignancy including lymphoma. MyD88 expression and secretion of pro-inflammatory cytokines may contribute to the sensitization of cancer cells to HDI. Moreover, MyD88 may be a direct target for HDAC- and BRD- inhibitors. Therefore, both expression level of MyD88 and MyD88 mutation status could serve as potential biomarkers for HDI sensitivity in patient selection.

Keywords: histone deacetylase inhibitors
cancer biomarkers
MyD88
Advisor: La Thangue, N
On certain a priori claims in the foundations of spacetime theories

I critique three a priori claims present in the literature on the foundations of spacetime theories:---
1. Spacetime structure has is chronogeometric significance necessarily.
2. The only candidates for representing physical quantities are objects which can be specified in a coordinate-independent manner.
3. Symmetry- and duality-related models of physical theories may be regarded ab initio as being physically equivalent.

Advisor: Brown, H
Pooley, O
Tissue engineering for the nervous system

Tissue engineering for the brain emerged as a promising therapy for traumatic brain injuries (TBIs) after the discovery of neural stem cells (NSCs) in the subventricular zone (SVZ) and the subgranular zone (SGZ). Combining NSCs with novel bioactive scaffolds may encourage and direct tissue regeneration and ultimately repair tissue damaged due to injuries.
In this thesis, a number of collagen-based scaffolds were fabricated into an interlaced network structure. The scaffolds comprised collagen (Coll), hyaluronic acids (HA) and chondroitin sulfates (CS), where the latter two are commonly-found glycosaminoglycans (GAGs) in the brain’s extracellular matrix (ECM). Our novel tri-interlaced network scaffold, Coll-CS-HA, is the first to be constructed, characterized and tested on NSCs. The synthesis method successfully incorporated HA and/or CS into the interlaced scaffolds, as demonstrated by FTIR, EDX and histology. Compressive testing and SEM also showed that the interlaced scaffolds had consistent and adequate mechanical properties and pore structure suitable for NSC growth.
Further cell biology studies demonstrated excellent biocompatibility of all scaffolds as evidenced by high cell survival. Interlaced scaffolds encouraged higher cell differentiation, shown by a halved nestin expression, a marker for NSCs, compared to Coll. An increase in MAP2 expression, a marker for mature neurons, by 50-100% in proliferation and differentiation was also observed. Coll-CS scaffolds led to an increase in astrocytic differentiation shown by a doubled GFAP expression, which has been related to glial scar formation.
As a result, Coll-HA and Coll-CS-HA may hold therapeutic potential to become candidates for future TBI treatments as they combined the advantage of adequate mechanical properties similar to that of brains, a high neuronal differentiation of around 40%, and a low astrocytic differentiation of around 20%.

Advisor: Czernuszka, J
Szele, F
Analysis and approximation of incompressible chemically reacting non-Newtonian fluids

In this thesis, we consider a system of nonlinear partial differential equations modelling the motion of an incompressible non-Newtonian fluid, which is chemically reacting. The governing system consists of a convection-diffusion equation for the concentration and the generalized Navier-Stokes equations, where the viscosity coeffiicient is a power-law-type function of the shear-rate, and the coupling between the equations results from the concentration-dependence of the power-law index. This system of nonlinear partial differential equations arises in mathematical models of the synovial fluid found in the cavities of moving joints. The only established mathematical result for this model is the existence of weak solutions for the stationary model. As a subsequent mathematical study, we first construct a finite element approximation of the model and perform the mathematical analysis of the numerical method in two and three space dimensions. Key technical tools include discrete counterparts of the Bogovski operator, De Giorgi-type regularity theorem in two dimensions, and the Acerbi-Fusco Lipschitz truncation of Sobolev functions. Then we move to the unsteady problem, and we prove the existence of global weak solutions of the non-stationary model by using the Galerkin method combined with generalized monotone operator theory and parabolic De Giorgi-Nash-Moser theory. As the governing equations involve a nonlinearity with a variable power-law index, our theory exploits the framework of generalized Lebesgue and Sobolev spaces with variable-integrability exponent.

Advisor: Suli, E
‘Teeth and tongue jammed together’: Violence in relationships and its mediation in Freetown, Sierra Leone

Based on 13 months of fieldwork in households, communities, police stations, courts and the prison in Freetown, this thesis extends the classic model of gender complementarity by demonstrating how competing gender ideologies of household, community and state impact on partnerships in urban Sierra Leone that are interlaced with friction and violence.
I utilise the metaphor of ‘teeth and tongue’, to show how love and violence can be coconstitutive. Within various relationship forms, violence is perceived as part of a functional partnership, however, carefully differentiated according to a moral economy of relationships. Legitimated or ‘acceptable’ violence is constitutive of affection and love, whereas transgressive or ‘unacceptable’ violence is reported to household, community or the police.
The thesis argues that to households and communities, violence constitutes a relationship between people which must be cooperatively mediated to maintain social bonds. For state institutions, violence is an act executed by individuals. Here, punishment and imprisonment ruptures relationships and dissolves social bonds.
The thesis is set against the post-conflict and post-TRC watershed where laws were passed to rebuild the state, and to prevent rape, teenage pregnancy and domestic violence. It shows that these laws were inspired by human rights and development discourses but led to the criminalising of young people’s sexual behaviour. By raising the age for sexual consent from 14 to 18, boys now receive prison sentences of up to 15 years for sleeping with underage girlfriends.
The thesis explores how rigid laws rub against contingent social categories and how the criminalisation of sexual relationships clashes with normalisations of violence in speech, acts and relationships. It uncovers that these tensions are based upon different ideals of gender relations and gendered perceptions of violence. The thesis thus offers an ethnographic critique of concepts like love and violence that are often used by academics in ways that fail to capture the vernacular resonances and connotations of the terms in West African popular culture and social life. Based on the framework of competing gender ideologies, the thesis fosters new understandings of the anthropology of violence, love and law.

Keywords: Gender and Generation
Punishment and Confinement
Violence
West Africa
(Human) Rights and Personal Autonomy
Legal Pluralism
Love
Law
Advisor: Pratten, D
Sarro, R
Activation of CD161-expressing T cells in human blood and gut

Human mucosal associated invariant T (MAIT) cells are an important T cell population present in circulation as well as immune privileged sites such as the liver and the gut. They are characterised by a semi-invariant T cell receptor (TCR) and high surface expression levels of CD161 and IL-18Rα, and restriction by the MHC class I-related protein (MR1). Studies have described a broad range of MAIT cell effector functions, including MR1-mediated antibacterial responses and TCR- independent, cytokine-mediated proinflammatory and antiviral properties. How human MAIT cells integrate these signals to exert their effector functions in the gut and in autoimmune and immune-mediated diseases such as inflammatory bowel diseases (IBD) has not been fully described.
In this study, an in vitro approach was used to probe MAIT cell activation, and the roles of the TCR, IL-12/-15/-18, TL1A and type I interferons (IFNs). MAIT cells were shown here to achieve certain effector and antimicrobial functions – measured by IFN-γ / tumour necrosis factor-α release and granzyme B expression – with specific innate cytokine signals. These features were reproduced in gut-derived CD8+ MAIT cells and CD161-expressing CD4+ T cells, whose phenotypes and effector functions may not only be mediated by exogenous TCR/cytokine signals, but also tuned by the gut microenvironment and various cues from IBD.
Furthermore, while TCR triggering was insufficient to drive full activation, gene expression signatures of TCR-triggered MAIT cells showed specific enrichment of tissue-repair functions, and genome-wide comparison of functional responses to TCR-dependent and -independent signals defined novel functions of MAIT cells relevant not only to host defence but also tissue homeostasis.
Overall, these findings indicate the importance of both TCR and inflammatory cytokine signals in promoting effector functions of human CD161-expressing T cells. Further in vitro and in vivo investigations on these gut-derived innate-like CD161+ T cells will be useful to understand their tissue-specific and signal-specific effector functions, as well as their role in various diseases.

Advisor: Klenerman, P
Willberg, C
Magnetic order in functional iron oxides

Developing our understanding of the magnetic order of iron oxides is essential if we are to devise novel, functional magnetic memory devices and sensors. In this thesis we report on the magnetic order of the newly synthesised Y-type hexaferrite Ba0.5Sr1.5Mg2Fe12O22 (BSMFO) and on the remarkable domain morphology of the archetypal iron oxide Fe2O3.
The magnetic phase diagram of BSMFO is studied by lab based characterisation methods and synchrotron techniques. We reveal a series of metastable magnetic structures, characterised by a period commensurate with the crystallographic lattice. We confirm this system is polar below 100 K and exhibits the worlds largest magnetoelectric effect. We perform a Resonant X-ray Diffraction (RXD) experiment to study this effect and show that RXD is sensitive to the magnetic polarity of BSMFO, the order parameter which drives the large magnetoelectric effect observed in this system. Using RXD microdiffraction, we spatially resolve the magnetic polarity domain configuration of BSMFO for the first time. When complemented by dynamic polarisation analysis of the scattered X-ray beam, these results allow us to propose a microscopic mechanism describing the large magnetoelectric effect observed in BSMFO. The RXD techniques demonstrated in this thesis open up a previously unexplored avenue for effectively studying the field-induced phases of the Y-type hexaferrites.
The coupled domain structure of a α-Fe2O3/Co heterostructure is imaged using vector-mapped X-ray PhotoEmission Electron Microscopy. Our measurements reveal an unprecedented network of vortices in the antiferromagnetically ordered α-Fe2O3 layer which imprint, by exchange proximity, into the adjacent Co layer. This work represents the first observation of antiferromagnetic spin vortices in a laterally unconstrained system. These vortices are consistent with the Kibble-Zurek mechanism, originally conceived in the context of cosmology, which describes the formation (and preservation) of topological defects when cooling through a symmetry breaking phase transition. The topological nature of these vortices is exploited to control the domain configuration of our heterostructure by inducing mass vortex-antivortex annihilation. As well as being a suitable system to test the universality of the Kibble-Zurek mechanism, the network of vortices observed in this work have the potential to be incorporated into novel, highly efficient magnetic memory devices.

Keywords: Photoemission Electron Microscopy
Hematite
Magnetoelectrics
Resonant X-ray Diffraction
Hexaferrite
Magnetism
Diffraction
X-ray Diffraction
Multiferroics
Advisor: Radaelli, P