VictorJuiz/thesis huggingface dataset:
Nonparametric Involutive Markov Chain Monte Carlo: a MCMC algorithm for universal probabilistic programming
Keywords: HMC
MCMC
involutive MCMC
probabilistic programming
inference algorithm

Probabilistic programming, the idea to write probabilistic models as computer programs, has proven to be a powerful tool for statistical analysis thanks to the computation power of built-in inference algorithms. Developing suitable inference algorithms that work for arbitrary programs in a Turing-complete probabilistic programming language (PPL) has become increasingly important. This thesis presents the Nonparametric Involutive Markov chain Monte Carlo (NP-iMCMC) framework for the construction of MCMC inference machines for nonparametric models that can be expressed in Turing-complete PPLs. Relying on the tree representable structure of probabilistic programs, the NP-iMCMC algorithm automates the trans-dimensional movement in the sampling process and only requires the specification of proposal distributions and mappings on fixed dimensional spaces which are provided by inferences like the popular Hamiltonian Monte Carlo (HMC). We gave a theoretical justification for the NP-iMCMC algorithm and put NP-iMCMC into action by introducing the Nonparametric HMC (NP-HMC) algorithm, a nonparametric variant of the HMC sampler. This NP-HMC sampler works out-of-the-box and can be applied to virtually all useful probabilistic models. We further improved NP-HMC by applying the techniques specified for NP-iMCMC to construct irreversible extensions that have shown significant performance improvements against other existing inference methods.
Generating tools for the characterisation of cell surface proteins
Keywords: x-ray crystallography
uncoordinated-5 receptor (UNC5)
protein-protein interaction
nanobody
glypican-3 (GPC3)

Cell migration depends on cell surface molecules that work together to define the precise direction and position of the migrating cell. To understand the cells’ communication with their environment, the signaling networks that are formed between cell surface proteins are being explored. The determination of the structures of the individual proteins, as well as the complexes they form, is essential for the comprehension of these signaling networks. Recently, an interaction between the morphogen receptor Glypican 3 (GPC3) and the Uncoordinated-5 receptor D (Unc5D) was discovered. The crystal structure of the complex revealed an octamer of four GPC3 and four Unc5D molecules. Evidence in the literature about the two proteins points to a function of this newly discovered interaction in cell migration.
In my DPhil project, I developed tools to characterise the GPC3-Unc5D interaction and understand its role in cell migration. Nanobodies against GPC3 were characterised, and their effects on the GPC3-Unc5 interaction were investigated using biochemical, biophysical, and structural biology techniques. Two nanobodies were identified as potential research tools, one that enhances and one that inhibits the GPC3-Unc5 interaction. They were effectively employed in functional in vitro and in vivo experiments, which revealed the importance of the GPC3-Unc5 interaction in neuronal cell migration during cortical development and in neuroblastoma collective cell migration. In addition to the nanobodies, I also contributed to the design and characterisation of non-binding GPC3 and Unc5 mutants. These mutants were used as tools, together with the nanobodies, in functional experiments, and their contribution was critical for understanding the Unc5-GPC3 complex function in vivo.
In a side project during my DPhil, I worked on an adhesion G-protein coupled receptor (GPCR). This adhesion GPCR has functions in cell-cell communication through its intracellular signaling and adhesion properties, and data indicate its important role in the central nervous system development. In this project, I worked towards the structural characterisation of this adhesion GPCR and the protein construct design, expression and purification for this project are presented in this thesis.
British policy towards Israel and the Arab-Israeli dispute, 1951-1954
Keywords: conflict
dispute
Great Britain
Arab-Israeli dispute
Arab-Israeli conflict
Israeli
Arab
Israel
Arab-Israeli
foreign relations

Written from the perspective of a student of British diplomatic history, rather than that of an orientalist, this thesis questions the unidimensional assumption, based mainly upon the literature about the Suez Crisis of 1956 and its origins, that the British, and Eden in particular, were more sympathetic to the Arab States, if not altogether hostile to Israel, in the early nineteen-fifties.
The method adopted in the writing of this thesis is thematic rather than chronological. Six principle themes have been selected, with the introduction and particularly the conclusion attempting to put the six chapters into a coherent whole. This thesis is based predominantly on the profusion of primary material available in the Public Record Office in London and the more modest quantity of documents in the Israel State Archives in Jerusalem.
How can GIS contribute to the development of 'Powerful Knowledge' in the Geography Curriculum?
Keywords: MLT
MLT 2021

This investigation examines Michael Young’s concept of powerful knowledge and considers whether Geographical information systems (GIS) present an opportunity for accessing such knowledge in the geography curriculum. The concept of powerful knowledge may produce fresh impetus to encourage more use of GIS in secondary education if the benefits are visible. To this end, the study also investigates the ease to which GIS tasks can be implemented in lessons. This small-scale evaluative project takes a class of year Nine students through a mapping exercise using ESRI’s ArcGIS interface, and then by way of questionnaires determines whether the knowledge accessed could be seen to be powerful, using Maude’s (2018) ideas as a framework. Similarly, interviews with a colleague establish whether such lessons could and should be incorporated into the syllabus more regularly. Results suggest that GIS and digital mapping allow pupils to access knowledge which could be considered powerful and that both practitioner and pupils enjoyed their completion. The project concludes by proposing that GIS activities be used more in geography lessons, whilst appreciating that some of the historical barriers to their implementation no longer exist.
Examining the extent and role of implicit bias within the religious education classroom
Keywords: MLT
MLT 2021

Implicit biases within education exist amongst both staff and students. The primary reasons for such biases exist due to the postcolonial condition, which has resulted in colonial influence that is systemically embedded amongst institutions such as schools. Within the context of the religious education classroom, using the Harvard Implicit Associations Test (IAT) education practitioners have the ability to measure and reduce the implicit biases demonstrated by staff and students. Students and staff tend to demonstrate implicit biases which demonstrate an automatic preference towards majority races and religions, but using decolonised models of curricula, staff have the potential to reduce such biases.
What impact does linking the affective dimensions of teaching to behavioural, cognitive and emotional engagement have on key stage four boys? 
Keywords: MLT
MLT 2021

Student engagement in a school context is often spoken about in a holistic sense rather than specific types of engagement. The aim of this practitioner research is to establish how breaking engagement into three different types - cognitive, behavioural and emotional - impacts on each type of engagement and engagement as a whole. This study investigates how the different engagement types interrelate through classroom-based strategy implementation and is measured through qualitative and quantitative data taken prior to and post strategy. The strategies applied are all dimensions that are within the control of the individual classroom teacher. This research will help practitioners and researchers to gain a further understanding into specific engagement types and strategies that can be used within the classroom and how to use them most effectively. The study found that increasing emotional engagement had the largest increase on engagement overall, whereas focussing solely on cognitive engagement can be detrimental to the other engagement types. The study took place in 2019, pre-pandemic, and the results may be different had the study been undertaken during, or following, the disruption of the pandemic.
In what ways does pupil consultation improve teaching and learning within a Humanities department?
Keywords: MLT
MLT 2021

The research investigates the opportunities that can arise for the improvement of teaching and learning through the use of student consultation. The key theme that emerges from the literature is that if it is implemented correctly, student consultation can bring many benefits to both teachers and students. This small-scale evaluation project was designed to understand if benefits could be seen through a pilot study in the Humanities department of my school over the course of an 8-week period. The research project was hampered by the impacts of COVID-19 and so only parts of the data collection could take place. Analysis was undertaken and links can be seen between the literature and the data collected with key themes emerging that often agreed with previous research. Students had constructive pieces of advice for the improvement of teaching strategies, prep setting strategies and marking and feedback, which suggests that if a complete research cycle was undertaken, positive strides could be made towards the improvement of teaching and learning.
Novel phosphorus precursors to group III-V semiconductor nanoparticles
Keywords: ZnS
characterisation
QDs
core shell
nanocrystal
InP
phosphinecarboxamide
indium phosphide
magic-sized clusters
phosphorus precursor
quantum dot
InP QD
heterostructured
seminconductor
zinc sulfide
air-stable phosphorus precursor
nanoparticle
synthesis
PH3
phosphine
shell
phosphaurea
air stable
InP/ZnS
clusters
precursor
photoluminescence
in-situ

The development of novel phosphorus precursors to group III-V semiconductor nanoparticles is described in this thesis. An overview of semiconductor nanoparticles, colloquially referred to as quantum dots (QDs), is presented in Chapter 1, including strategies for the preparation of InP QDs from typical phosphorus precursors.
Chapter 2 explores the reactivity of the parent phosphinecarboxamide (H2PC(O)NH2) in solution towards common InP QD precursors. The preparation of InP clusters and a novel N-functionalised phosphinecarboxamide using H2PC(O)NH2 is discussed. Both H2PC(O)NH2 and N-functionalised phosphinecarboxamides are found to be effective sources of PH3 in solution upon thermal decomposition in pyridine at 105oC.
Chapter 3 describes the use of an N-functionalised phosphinecarboxamide as a novel air-stable phosphorus precursor to core/shell In(Zn)P/ZnS QDs. A synthetic protocol is optimised to afford core/shell In(Zn)P/ZnS QDs with size-dependant photoluminescence emission maxima between 550 and 650 nm, with full width at half maxima (FWHM) between 68 and 128 nm.
Chapter 4 explores the reactivity of N-, N,N-, and P-functionalised phosphinecarboxamides in solution. The effect of phosphinecarboxamide side-chain functionalisation on reactivity is also discussed.
Finally, Chapter 5 discusses the use of functionalised phosphinecarboxamides for the preparation of In(Zn)P/ZnS QDs and the unique size control that they afford. Carboxylate functionalised phosphinecarboxamides are used to prepare core/shell In(Zn)P/ZnS QDs with size-dependant photoluminescence emission maxima between 550 and 620 nm and FWHM between 83 and 114 nm. Additionally, the unexpected use of a P-functionalised phosphinecarboxamide as an air-stable precursor to size-uniform InP QDs is described, which display a photoluminescence maximum at 546 nm and a FWHM of 75 nm.
Structural and biophysical study of the KlebC import mechanism
Keywords: bacteriocin
gram-negative bacteria cell envelope

The cell envelope of Gram-negative bacteria hosts many different protein machineries. These protein machineries are used by bacteria to perform different functions, such as cell division and nutrient acquisition. TolC is a trimeric protein that anchors at the OM and extends into the periplasm. TolC is used as a channel forexporting protein toxins and xenobiotics out of the cell but is also hijacked by bacteriocins as an import channel. This unique double-sided function of TolC has drawn interest to understand its roles in different biological processes and apply them to combat increasingly serious global antimicrobial crisis. The exploitation of TolC by a group B bacteriocin, KlebC, was studied using biochemical, biophysical and structural methods. It was previously discovered that the Ton system, known for its role in nutrient acquisition, is required to uptake KlebC into cells. Although the interactions between different group B bacteriocins and their outer membrane receptors have been elucidated, there has been no published studies on the interaction between group B bacteriocins and periplasmic TonB. This study has successfully demonstrated binding between KlebC and TonB, by analytical size exclusion chromatography and isothermal titration calorimetry. A binding affinity of 66 μM was measured between KlebC and TonB. The structure of the complex waspredicted by Alphafold 2.0 and validated by mutational approaches. To fully understand the uptake mechanism of KlebC, the ternary KlebC translocon (KlebC-TolC-TonB) was assembled in nanodiscs. Grids, containing the KlebC translocon, wereoptimised for single-particle cryogenic electron microscopy data collection and analysis for future structure determination of the complex.
A qualitative examination of cybercriminal governance in China
Keywords: criminal governance
criminal cooperation
cybercrime
extra-legal governance
organised crime in China

Profit-driven cybercrime has evolved into a sophisticated industry, inflicting millions of dollars in losses on the world economy. However, limited research has been conducted on the extra-legal governance of this industry, particularly in China, one of the world's most prominent cybercrime hotspots. This study, based on comprehensive fieldwork in China from 2020 to 2022 and an analysis of both primary and secondary data, seeks to address this gap. It endeavours to answer the question: How is the cybercrime industry governed in China? In line with previous research on extra-legal governance, this study finds that Chinese cybercriminals have developed a series of private governance systems, encompassing both self-governance and third-party governance, to facilitate their business interactions. In addition, this study offered three main new findings that can be added to our understanding of extra-legal governance. Firstly, self-governance is notably effective in online marketplaces due to the swift transmission of information, thus diminishing the necessity for third-party governance in the cybercrime market and the use of violence. Secondly, cybercriminal firms tend to be less predatory than traditional criminal firms, likely attributed to the reduced need for territorial resources. Lastly, cybercriminals can relocate to countries where protectors are present and continue their illicit activities remotely, with protection being more likely offered when the inflicted harm does not impact the protector's own country’s residents, and the political and economic gains outweigh the costs. This availability of protection could potentially elucidate the ongoing global dispersion of cybercriminals.
How do we teach a knowledge rich primary science curriculum in an exciting way?
Keywords: MLT
MLT 2021

Research has shown that fewer pupils are choosing to pursue science in the later years of their education. One key reason for this is that pupils’ attitudes towards learning science become more negative. Debate exists about when this reported decline occurs, but some suggest that pupils’ attitudes to science begin to change towards the end of their primary education. One way to counteract this may be through teaching exciting lessons that are rich in scientific knowledge. This study interviewed year 5/6 pupils (ages 9-11), surveyed primary school teachers and conducted an intervention lesson series, which pupils were surveyed on, to explore ways of making knowledge rich science lessons exciting for pupils. Three task types were investigated during the intervention lesson series: talk tasks, inquiry-based learning and drama. The findings showed that all three task types made science lessons exciting for the pupils but to differing degrees, with drama tasks proving especially effective. This study also found that practical activities were highly important to both pupils and teachers for making science learning exciting, although it highlighted potential issues surrounding the effectiveness of how practical activities are used in science lessons. Issues surrounding the teaching of science such as time, space, resources and topics, were also raised and explored. The findings have impacted the future approach to science at the setting school.
Dynamics of the subpolar North Atlantic ocean circulation—the role of surface forcing and topography
Keywords: streamfunction
North Atlantic
ocean modelling
barotropic
vorticity
large-scale ocean circulation

The ocean is a fundamental component of the global climate system, acting as a colossal sink of heat and carbon dioxide. Its effectiveness as a sink is enhanced by the transport of these tracers into the deep ocean by the Atlantic Meridional Overturning Circulation (AMOC). Hence, due to its location near the northern terminus of the AMOC, the subpolar North Atlantic plays a crucial role within the global climate system. Unfortunately, this is a fiendishly difficult region to model. As such, a better understanding of the physical mechanisms setting the large-scale flow at these latitudes is required.
In this thesis, the roles played by wind stress, surface buoyancy forcing, and topography in determining the mean barotropic and overturning circulations in the subpolar North Atlantic Ocean are explored. An idealised model of the region is introduced, and the response of the mean circulation to different combinations of wind, buoyancy forcing and bathymetry is presented. The overturning circulations in both depth, and density, space are split into shear, Ekman, and external mode components.
A novel diagnostic is then derived allowing for the isolation of the force balances controlling the large-scale flow. This diagnostic is based on the previously proposed rotational momentum framework, whereby the rotational component of an applied force is extracted in the form of a set of force func- tions. An error in the original derivation of this framework is highlighted which limits its utility to domains without topography. A new derivation generalising the approach to apply to domains with arbitrary topography is presented, and the derived force functions are related to the barotropic and overturning circulations.
This diagnostic is then applied to the aforementioned experiments, allowing the dominant force balances in each to be identified. A key result emerging from this analysis is that the presence of sloping sidewalls drastically alters the dominant force balance in the mean barotropic circulation.
The enantioselective total synthesis of Sealutomicin C
Keywords: sealutomicin
natural product synthesis
total synthesis

This thesis is divided into six chapters and concerns the successful total synthesis of the natural product sealutomicin C. Chapter 1 provides an overview of anthraquinone-fused enediyne natural products, the sealutomicin natural products, and other related cycloaromatised natural products. Chapter 1 also discusses prior work carried out in the Burton group by previous group member Dr Sean Guggiari towards the synthesis of the natural product unciaphenol, which bears structural similarities to sealutomicin C.
Chapter 2 details work undertaken to prepare lactone-fused chiral dihydroquinolines, using methodology developed by Dr Guggiari to construct the chiral dihydroquinoline scaffold. Chapter 3 discusses the use of these lactone-fused dihydroquinolines as substrates in a key organolithium mediated cyclisation to construct the core of enantiomeric sealutomicin C. Chapter 3 also discusses efforts to elaborate this core, resulting in the synthesis of tris-benzyl protected enantiomeric sealutomicin C.
Chapter 4 concerns the application of the chemistry developed in Chapters 2 and 3 to the synthesis of the correct enantiomer of sealutomicin C, culminating in a successful first-generation synthesis of the target natural product. Chapter 5 presents a shorter and more streamlined second-generation synthesis of sealutomicin C, improving on the work described in Chapters 2 – 4 by employing a more efficient protecting group strategy. Finally, Chapter 6 summarises our achievements and suggests potential strategies to apply the chemistry developed here to the synthesis of the structurally related natural products sealutomicins B and D.
Big data in viral hepatitis
Keywords: electronic health records
Hepatitis B virus
epidemiology
real world data

Chronic infection with hepatitis B virus is one of the leading global causes of chronicliver disease, specifically primary liver cancer. The population is not well characterisedin the United Kingdom, with evidence gaps including lack of characterisation of theinfected population, the burden of comorbid disease and risk factors for progressionto liver cancer. Antiviral treatment eligibility and coverage across the diseasepopulation is unclear, as are impacts of COVID-19 and health policy on viralsurveillance and vaccination. This thesis presents results from analyses undertakenacross multiple electronic health record databases in the United Kingdom to addressthese gaps.
Systematic literature review and meta-analysis were undertaken to appraise previousstudies describing epidemiology and investigating primary liver cancer risk factors.Subsequently the largest cohort of chronically infected individuals to date wascharacterised in the QResearch database. The chronic hepatitis B virus population inthe United Kingdom has been characterised as a young, ethnically diverse andsocioeconomically deprived population of individuals. Risk factors for primary livercancer included male sex, increasing age and comorbidities. A protective associationof statin use with risk of primary liver cancer was observed.
In the NIHR HIC database, antiviral treatment coverage across individuals with chronichepatitis B virus was quantified, reporting treatment initiation practices in line withclinical recommendations. The impact of COVID-19 on surveillance was quantified,reporting a decrease in surveillance as compared to the pre-COVID-19 era.Surveillance has not recovered to pre-COVID coverage. In the Clinical PracticeResearch Datalink database, it was demonstrated hepatitis B virus vaccinationcoverage has both increased since the compounds introduction as a universalcomponent in 2017 and has remained high despite the COVID-19 pandemic.
These results have clinical relevance to both care pathways and researchinvestigations. They may facilitate improvements in clinical management, resourceallocation and future investigations.