VictorJuiz/thesis huggingface dataset:
Nucleic acid structures as transcriptional and epigenetic regulators in health and disease

DNA and RNA structures are involved in major biological processes, such as regulating gene expression, and can play an important role in cancer and neurodegenerative diseases.
Huntington’s disease (HD) is the most common monogenic neurological disorder caused by the expanded and unstable CAG trinucleotide repeat in the first exon of the huntingtin gene (HTT). The pathology of HD has been traditionally associated with the mutant HTT protein, which confers toxic gain of function leading to dysfunction and death of neurons. However, recent evidence indicates that at least part of the gain of function may operate at the RNA level.
In the first part of this thesis, the transcriptional and epigenetic regulation of the HTT gene in HD is investigated. It is shown that expanded CAG repeats of endogenous HTT transcript adopt double-stranded RNA structures that lead to RNA Polymerase II transcriptional repression and heterochromatin formation of the HTT gene in cis, providing a molecular link between dsRNA and the pathology of expansion diseases.
Double-stranded RNA is a key player in numerous Biological activities in cells, however little is known about the proteins that bind to dsRNA. Therefore, a proteomics approach was established, employing the dsRNA pull-down to identify dsRNA-binding proteins in control and HD fibroblast cells. Analysis of the dsRNA interactome indicated that interaction with the top candidate ENO1 is enriched in HD and promotes dsRNA-mediated transcriptional repression of the HTT gene.
This thesis work also elucidates on the importance of RNA/DNA hybrids in cancer as their accumulation is a major cause for genomic instability. The research demonstrated that cancer cells overexpressing oncogenes such as HRASV12, lead to increased RNA synthesis and RNA/DNA hybrid accumulation that can be correlated with replication stress. These events lead to DNA damage, revealing a strong link between R-loop-mediated genome instability and human disease.
Overall, nucleic acid structures and their interactors could determine the ability of a single gene product to perform multiple functions, as potential disease modifiers and future targets to modulate diseases.

Advisor: Wood, M
Students' and teachers’ beliefs about second language vocabulary learning: Using congruence and friction to predict outcomes in a Mexican EFL context

This mixed-methods study investigated students’ and teachers’ beliefs about vocabulary learning, the relationship between student and teacher beliefs, and whether the nature of this relationship is related to vocabulary development among students. Previous research has investigated the relationship between students’ beliefs and learning outcomes, but little research has been conducted comparing students’ and teachers’ beliefs, especially not within the context of vocabulary learning.
The study involved two groups of participants: students and teachers. The student participant group consisted of 110 first-year high-school students studying English at a bilingual private high school in Mexico. The teacher participant group included their 4 English teachers and 4 teachers at a comparable bilingual private high school. Student and teacher beliefs about vocabulary learning were identified by means of two sets of instruments: equivalent questionnaires and interview schedules, given midway through their semester. Near the end of their course, students also completed a test of vocabulary depth, measuring acquisition of lexical items covered in class during the semester in which the self-report data were collected. The analysis of the quantitative data consisted of descriptive statistics, exploratory factor analysis, non-parametric comparison of mean ranks, and hierarchical multiple regression, while the qualitative data were content-analysed.
The results revealed a three-factor structure for interpreting students’ vocabulary-related beliefs. Overall, across these three factors there was a high degree of agreement between teacher and student responses with no significant differences found between them. However, interview data pointed to some areas where teachers and students might hold differing views. Crucially, a measure of the extent to which students disagree with their teacher was found to predict a small portion of the variance in student vocabulary scores.
The results of this study may therefore be of benefit in second language instruction if they convince teachers of the importance of recognizing their students’ beliefs about language learning, and the importance of rationalizing their actions in the classroom to their students.

Keywords: Teacher beliefs
EFL
Student beliefs
Advisor: Baffoe-Djan, J
Teaching robots where to drive using real world data

In this work we teach a robot where to drive from measured, real world data. In Chapter 1 we measure energy usage on a pedestrian robot and use high-level, publically available maps to predict energy con- sumption on unobserved routes with a heteroscedastic Gaussian Process model. These energy predictions can be used to make route-planning decisions in energy constrained situations, for example by learning to avoid areas with rough surfaces or that are likely to be crowded. Our method performs well, particularly in its ability to capture uncertainty in the data, however it is reliant on well annotated maps.
In Chapter 2 we consider the case where well annotated maps and good prior information about an environment are not available. Again we use measured, real world data by introducing vertical variance in a laser pointcloud as a proxy for drivability which can be labelled automatically in an online setting. We propose a method for using this online stream of data in a computationally efficient manner to learn where to drive. We then test this method against models trained in other environments and an existing method which utilises the most recent data.

Advisor: Posner, I
Of mice and MenB: assessing the immune mechanisms underlying meningococcal capsular group B vaccines in mice

Neisseria meningitidis is the causative agent of invasive meningococcal disease (IMD) which claims between 50,000 and 135,000 lives worldwide annually. Disease caused by the capsular group B meningococcus (MenB) is the leading cause of infectious death in UK infants. A four component vaccine, 4CMenB, has been developed to prevent IMD caused by this capsular group, but is associated with a high incidence of fever in infants and requires multiple doses to induce adequate protection. A novel adenovirus-based vaccine encoding the MenB factor H binding protein (fHbp) with an N-terminal signal sequence (Ad-fHbp) has been developed at the Oxford Vaccine Group and was found to induce high titres of protective antibody after a single dose in mice. The central aims of the work presented in this thesis were to elucidate the immune mechanisms underlying the reactogenicity of 4CMenB and the immunogenicity of Ad-fHbp. ‘Systems vaccinology’ has provided many insights into vaccine-induced responses by combining high-throughput sequencing with conventional immunogenicity assays to characterise the gene signatures and immunological pathways underlying them. However, the RNA- sequencing (RNA-seq) component of such studies can be compromised by the impact of computational choices on the final differential gene expression (DGE) call. A novel DGE pipeline was developed in the present study to mitigate the impact of this computational ‘noise’. A ‘systems’ approach was then taken to comparatively assess 4CMenB vaccine combinations and components in order to determine the cause of fever in a mouse immunisation model. Using a combination of RNA-seq, temperature, and inflammation markers, the reactogenicity was ultimately attributed to the membrane-bound endotoxin contained in the outer membrane vesicle component of the vaccine. To explore the phenomenon of the early, sustained protective immune response induced by Ad-fHbp, a panel of N-terminal signal sequence insertion/deletion variants of the antigen were comparatively assessed for in vitro expression from mammalian cells and for immunogenicity in mice. The full-length sequence demonstrated superior early expression and induction of bactericidal antibody and was also found to significantly boost antigen-specific T cell responses when incorporated ahead of other adenovirus-encoded bacterial antigens, highlighting it’s potential as an immune-enhancing sequence element for other viral vectored vaccine transgenes. Finally, antigen-specific immunological pathways were defined for the fHbp transgene product by comparative transcriptomics. The work presented in this thesis contributes to our understanding of what constitutes a well-tolerated and immunogenic meningococcal vaccine.

Keywords: Outer membrane vesicles
Viral vectored vaccine
RNA-seq
Noise
Systems vaccinology
Immunological pathways
Signal sequence
Molecular determinants
Fever
Advisor: Dold, C
Transport models for non-isobaric electrolytes

Conventionally, transport models employed for describing processes in electrochemical devices have been developed for liquid electrolytes under isobaric conditions. The assumption of constant pressure starts to break down for solid or other viscoelastic electrolytes, which respond to internal or external stress and strain changes in a fundamentally different way. Mechanical effects and their coupling with charge and mass transfer have, therefore, become a key area of research. The present work focuses on the Nafion ionomers used in polymer electrolyte membrane (PEM) fuel cells. The tendency of these membranes to swell upon solvent sorption in spatially constrained environments, when viewed in conjunction with the delicate water balance necessary for optimum operation and the durability requirements from the cell stacks, makes for a perfect case study of non-isobaric transport in electrolytes.
The thermodynamics underlying the transport model for a viscoelastic electrolyte such as a hydrated Nafion membrane was recently revisited by the authors. A membrane (or more generally, a solid) can store energy in the form of elastic work obtained from deformation of the material, in addition to the pV compressive work, heat work, and electrochemical work; this introduces deformation stress as an additional intensive variable. Conservation laws for material, momentum, and energy, local equilibrium conditions, as well as material and momentum flux constitutive laws, have been developed using basic principles of classical and irreversible thermodynamics to maintain congruency with this modified basis of thermodynamic intensive variables.
Electrochemical impedance spectroscopy (EIS) response of the model has been studied within the new framework to gain insight into electrochemical/mechanical coupling. EIS concentrates on the first-order effects and identifies the various time-scales, length-scales, and the dominant ranges of the modelled physical phenomena. For instance, current-induced pressure variations at high frequencies (˜ MHz) were found to manifest as resonance peaks on Bode plots, which can partially explain the high-frequency inductance observed in Nafion systems. Further, a parameter study was performed to assess which material and mechanical properties are necessary to enhance or downplay stress effects in the model.

Advisor: Monroe, C
Behaviour orders: preventive and/or punitive measures?

This thesis enquires into the nature of behaviour orders; specifically, it seeks to establish whether they are preventive and/or punitive. In 1998, Parliament introduced the anti-social behaviour order (ASBO), an order granted in a civil court that imposed ostensibly preventive conditions – such as curfews – on its recipient. Breach of a condition was an offence. This hybrid model was meant to overcome the supposedly unique difficulties of addressing anti-social behaviour through the criminal law. There has since been a proliferation of behaviour orders that take the form of or forms similar to the now repealed ASBO. At present, there are 33 such orders that target behaviours ranging from community nuisance to violent offending.
Behaviour orders are often described as preventive by courts and commentators. The central contention of this thesis is that though all behaviour orders are preventive, many are also punitive. The importance of this contention lies in the consequences of both classifications. Heightened safeguards, such as the presumption of innocence, must be employed when a trial may result in punishment. The current processes for the imposition of behaviour orders fall short of these standards. In addition, the thesis argues comparable safeguards should precede the imposition of preventive measures imposed by the state when these measures are coercive and based on a risk assessment. Again, such safeguards are not routinely employed before behaviour orders are imposed. In making out this argument, the thesis develops a new taxonomy of behaviour orders; offers new insight into both domestic judgments on behaviour orders and related decisions of the European Court of Human Rights; and critically engages with the concepts of punishment and prevention themselves.

Keywords: prevention
behaviour orders
punishment
Advisor: Zedner, L
High resolution characterisation of oxidation mechanisms in polycrystalline nickel based superalloys

In order to withstand the demanding conditions experienced at the heart of modern jet turbine engines, nickel based superalloys must combine extreme strength with resistance to temperature-dependent degradation mechanisms such as oxidation and fatigue. This is increasingly becoming a priority, as operating temperatures continue to be pushed higher due to tighter fuel economy and emissions targets.
A new generation of high temperature, damage tolerant superalloys has been developed which balances all of these properties through careful control of composition. For further alloy development, the relationship between oxidation kinetics and alloy composition must be established. Two elements in particular have been focussed on – titanium and niobium. Both of these elements are vital for maintaining high temperature strength; however Ti has been experimentally shown to increase rates of oxidation, while Nb has been implicated in accelerating dwell fatigue crack growth.
In order to study these composition-property relationships, a family of near identical superalloys have been created with varying titanium/niobium ratio, and subsequently characterised. Oxidation kinetics were studied using thermogravimetric analysis, which confirmed the link between titanium and oxidation, while also creating oxide scales for further characterisation. A variety of high-resolution techniques have been used to analyse these oxide scales on the smallest scales, revealing the location of titanium – some was found dissolved in chromia oxide scales as expected – but much more was found segregated to grain boundaries within the oxide. Ion transport along these grain boundaries may explain the oxidation kinetics better than the lattice diffusion mechanism previously assumed.
A number of fatigue crack tips also underwent examination, in an attempt to shed light on the mechanism by which niobium encourages dwell fatigue. While no evidence could be found for this, a number of analysis techniques have been developed and refined to hopefully aid these efforts in future.

Keywords: Atom Probe
Oxidation
Dwell Fatigue
Oxidation Mechanisms
Alloy design
Superalloys
Advisor: Moody, M
Bagot, P
Reed, R
Mechanisms for novel multidimensional choices in prefrontal cortex

In this thesis the cognitive and neuro-computational bases of novel value-based decision-making in non-human primates are studied. Humans routinely perform choices among options that have not previously been experienced, using value expectations derived from their component attributes. Animal studies, however, are typically performed after extensive training ensuring familiarity with the task. Here we show how Rhesus macaques can readily perform value-guided choices among novel stimuli – if their components are known. An economic analysis of subjective biases is provided. Neuroimaging and causal techniques are then used to uncover a network centred in anterior medial frontal cortex (AMFC) underlying adaptive novel decisions. A first experiment, using fMRI with a binary decision task, reveals that orbitofrontal cortex is equally modulated by value in novel and familiar choices, but in contrast AMFC and dorsolateral prefrontal cortex (dlPFC) show a markedly different pattern of responses between conditions. A second experiment, using fMRI and single option trials, reveals how AMFC and dlPFC, but no other regions, encode representations of abstract value independent from its components (reward magnitude and probability), appearing across sessions with exposure to the novel options. Additionally, a pattern of hexagonal symmetry is found in AMFC activity, indicating a grid-like encoding of two-dimensional value space. Such a code provides a mechanistic explanation of how novel options’ values may be computed. A last experiment confirms this by showing that transiently disrupting AMFC with focused transcranial ultrasound impairs the use of an integrated representation of value when novel decisions are made. Together, these experiments bridge neuroscientific studies in humans and monkeys and reveal a neural basis for novel decision-making that has not previously been investigated in either species.

Keywords: Primate
Novel choice
Ultrasound
Grid cells
Inference
fMRI
Advisor: Rushworth, M
Designing novel modulators selective for the intermediate conductance calcium activated potassium channel

Reduction of systemic vascular resistance by dilation of resistance arteries, is a powerful method of blood pressure reduction. Endothelium derived hyperpolarisation is a major vasorelaxant pathway in resistance arteries, dependant on the activation of endothelium Ca2+ activated K+ (KCa) channels. Existing positive modulators of KCa channels act by stabilising the protein-protein interaction of the KCa channel gating complex, involving the Ca2+ sensing protein, calmodulin (CaM). Herein describes an investigation of the KCa channel positive modulator binding cavity, the rational design of next generation positive modulators, and developments towards a biophysical screening assay.
A homology model of the intermediate conductance (IKCa3.1) channel positive modulator binding cavity was generated, docked with existing positive modulators and scrutinised for the rational design of novel next generation analogues. A set of modulator analogues, capable of hydrogen bonding to an IKCa3.1 specific serine residue, were designed and synthesised. These analogues were tested for KCa channel modulation via their vasorelaxant activities by ex vivo artery wire myography. During this assessment, a novel and unknown vasorelaxant effect, unrelated to KCa channels, was discovered.
The IKCa3.1 gating complex proteins, CaM and the channel CaM binding domain (CaMBD), were expressed for biophysical investigation. Several techniques were designed, developed and evaluated as a modulator screening assay. In differential scanning fluorimetry (DSF), existing KCa channel positive modulators produced a significant effect, potentially enabling the observation of direct gating complex stabilisation. Native protein mass spectrometry observed oligomerisation of the gating complex in solution and could be used in future to confirm modulator binding and so the DSF results. This would be the first biophysical assay able to identify KCa channel ligands; a powerful tool for the development of increasingly potent and selective positive modulators.

Advisor: Conway, S
Donohoe, T
Garland, C
Hypoxia related function in human osteoarthritic cartilage

Articular cartilage is an avascular tissue, and therefore, at least in large animals, functions in a hypoxic environment. In healthy human cartilage, chondrocytes exhibit a well-adapted hypoxic response. Previous work in our laboratory has shown that hypoxia in healthy human articular chondrocytes (HACs) increases anabolic function (SOX9, COL2A1, ACAN) via HIF-2α and decreases catabolism (reducing MMP13 and ADAMTS5) predominantly via HIF-1α. Inhibition of HIF-targeting hydroxylase PHD2 was also identified as a potential means to induce cartilage repair by enhancing HIF-2α levels subsequently increasing anabolism via SOX9.
In contrast, evidence from murine studies has suggested HIF-2α as a catabolic regulator in the progression of OA, targeting key catabolic enzymes MMP13 and ADAMTS5, thus indicating HIF-2α as a potentially relevant therapeutic target in OA. The role of hypoxia and HIF activity in human OA cartilage and chondrocytes is less clearly understood, and hence was the focus of the current study.
In this study the general response of key cartilage genes, in primary OA HACs, to hypoxia are shown to be beneficial to the chondrocyte phenotype (as it is in healthy HACs). Hypoxia in OA HACs increases levels of SOX9 by 125% and subsequently increases the downstream cartilage matrix gene COL2A1 by 215% compared to levels observed in normoxia. Additionally, it is reported that the hypoxia-mediated downregulation of MMP13 and ADAMTS5 by 32% and 45% respectively. However, it is noted that TIMP3 is not induced by hypoxia in OA HACs indicating a potentially reduced protective capacity compared to healthy cartilage. Interestingly, it is observed that HIF-1α is the predominant isoform responsible for the induction of SOX9 in OA HACs (as opposed to HIF-2α in healthy HACs) noting the depletion of HIF-1α reduces SOX9 by 54% and 61% in normoxia and hypoxia respectively. Importantly, results represent no evidence of a HIF-2α dependent induction of catabolic factors in OA HACs, but rather a potentially anti-catabolic role reducing ADAMTS5 and MMP13 levels by 111% and 78% respectively in hypoxia. Furthermore, the results shows that, whilst PHD2 depletion on its own is insufficient, combined HIF-targeting hydroxylase inhibition (via DMOG) can enhance the beneficial effects of hypoxia observed in OA HACs (increasing SOX9 levels 2.36 fold above typically observed by hypoxia alone). Therefore, a combined inhibition of the PHDs represents a potential means of increasing cartilage matrix production in an OA setting.

Advisor: Murphy, C