VictorJuiz/thesis huggingface dataset:
POP-type rhodium complexes in amine borane dehydropolymerisation

This thesis explores the catalytic dehydropolymerisation of N-methylamine borane, H3B·NMeH2, to form N-methylpolyaminoborane, (H2BNMeH)n, using POP-type rhodium complexes based upon the {Rh(Xantphos-iPr)}+ and {Rh(DPEphos)}+ fragments. A comparison of these metal-ligand frameworks provides a structure/activity relationship in order to gain mechanistic insight into the H3B·NMeH2 dehydropolymerisation process.
Chapter 2 describes the synthesis of a suitable {Rh(Xantphos-iPr)}+ precatalyst for H3B·NMeH2 dehydropolymerisation. Its reactivity with H3B·NMeH2 is examined by NMR spectroscopy, and independent synthetic routes to the complexes observed are described. From this, a dimetalloborylene is isolated and crystallographically characterised. The kinetics of H3B·NMeH2 dehydrogenation and (H2BNMeH)n growth using the {Rh(Xantphos-iPr)}+ fragment are reported in Chapter 3, which combined with the speciation studies in Chapter 2, allows for a mechanistic proposal for dehydropolymerisation. The formation and subsequent deprotonation of a boronium cation is postulated to lead to the monomer, H2B=NMeH, which forms (H2BNMeH)n via an on-metal end-chain propagation mechanism.
In Chapter 4 the focus shifts to synthesise a suitable {Rh(DPEphos)}+ precatalyst for H3B·NMeH2 dehydropolymerisation. Here, speciation studies of the {Rh(DPEphos)}+ fragment with H3B·NMeH2 enables the observation of bimetallic complexes, one of which is considered an amidodiboryl complex. An in-depth dehydropolymerisation kinetic study using the {Rh(DPEphos)}+ system is undertaken in Chapter 5, and strong dependence of (H2BNMeH)n molecular weight on H2 pressure and catalyst loading indicates that an on-metal coordination/dehydrogenation/insertion mechanism operates, contrasting that proposed for the {Rh(Xantphos-iPr)}+ system. The bimetallic amidodiboryl complex described in Chapter 4 and NMeH2-derived {Rh(DPEphos)}+ species are also tested in catalysis, and appear close in identity to the true active catalytic species, due to the lack of induction period observed prior to H2 evolution.

Keywords: Rhodium
Catalysis
Amine borane
Dehydropolymerisation
Polyaminoborane
Advisor: Weller, A
The role of ZNRF3 in testis determination

In mammals, the presence or absence of SRY primarily determines whether the gonad will develop as a testis or an ovary – a process known as sex determination. Downstream of SRY, the testis and ovarian pathways diverge and mutually antagonise each other to ensure a robust switch in gonadal fate. One such interaction is well characterised in mice, between the ovary-promoting gene, Wnt4 and the testis-determining gene, Fgf9. The mutual repression of these two genes has recently been shown to be crucial for mouse sex determination. However, there is currently little evidence for how this interaction between the male and female pathways, and others required for sex determination, may be controlled at the molecular level.
Differences/disorders of sex development (DSDs) are a group of rare human conditions in which chromosomal and anatomical sex are discordant. Exome screens of DSD patients exhibiting gonadal dysgenesis can be used to identify candidate genes. In one such screen, 2 independent mutations were found in ZNRF3. ZNRF3 is a WNT-signalling antagonist which functions by downregulating the number of Frizzled receptors available on the plasma membrane. WNT4 is expressed in pregranulosa cells and plays a key role in ovarian development through promotion of beta-catenin-dependent gene transcription. This thesis demonstrates that Znrf3 plays an important role in testis determination in the mouse. Znrf3 is required to suppress the ovarian-pathway, and when removed from the testis causes partial or full XY sex reversal associated with ectopic activation of WNT/ beta-catenin signaling. Moreover, use of a sensitized genetic background allows generation of sex-reversed XY female mice carrying a single copy of a Znrf3 null allele. ZNRF3 may therefore play a key role in mediating the mutually antagonistic interactions between the testis and ovarian pathways, in both mice and in humans.

Keywords: sex determination
embryonic
znrf3
gonad
testis
gonadal development
developmental biology
Advisor: Greenfield, A
Categorical operational physics

Many insights into the quantum world can be found by studying it from amongst more general operational theories of physics. In this thesis, we develop an approach to the study of such theories purely in terms of the behaviour of their processes, as described mathematically through the language of category theory. This extends a framework for quantum processes known as categorical quantum mechanics (CQM) due to Abramsky and Coecke.
We first consider categorical frameworks for operational theories. We introduce a notion of such theory, based on those of Chiribella, D'Ariano and Perinotti (CDP), but more general than the probabilistic ones typically considered. We establish a correspondence between these and what we call operational categories, using features introduced by Jacobs et al. in effectus theory, an area of categorical logic to which we provide an operational interpretation. We then see how to pass to a broader category of super-causal processes, allowing for the powerful diagrammatic features of CQM.
Next we study operational theories themselves. We survey numerous principles that a theory may satisfy, treating them in a basic diagrammatic setting, and relating notions from probabilistic theories, CQM and effectus theory. We provide a new description of superpositions in the category of pure quantum processes, using this to give an abstract construction of the category of Hilbert spaces and linear maps.
Finally, we reconstruct finite-dimensional quantum theory itself. More broadly, we give a recipe for recovering a class of generalised quantum theories, before instantiating it with operational principles inspired by an earlier reconstruction due to CDP. This reconstruction is fully categorical, not requiring the usual technical assumptions of probabilistic theories. Specialising to such theories recovers both standard quantum theory and that over real Hilbert spaces.

Keywords: Dagger kernel
Phased coproduct
Operational theory
Categorical quantum mechanics
Quantum reconstruction
Purification
Dagger compact category
Advisor: Coecke, B
Heunen, C
‘We meet and mingle separately:’ religion, identity, and the anthropology of Catholicism in Chilón, Chiapas

The history of Christianity in Mexico is a complex one. Despite four centuries of Catholicism, what is meant by “being Catholic” remains an elusive question. My thesis examines how an inculturated Catholicism is practiced in a particular corner of southern Mexico where the majority self-identify themselves as indigenous. The central concern of this thesis is how religious beliefs and practices structure society in ways that simultaneously reproduce the indigenous Tseltal worldview while encompassing the Spanish-speaking ladino culture, with the moral order of one sphere merging with the other. My thesis demonstrates how patterns of social behavior are inextricably linked to the ways they practice their Catholicism, demonstrating the fluidity of boundaries between indigenous custom, ladino tradition, and Catholic orthodoxy.

Advisor: Rival, L
Gellner, D
Evaluation of biodegradable magnesium alloys for orthopaedic applications

The use of bio-materials in medical applications has risen exponentially in recent years, where applications range from the treatment of early stage disease to implants for major trauma. Particularly, research on biodegradable metallic materials have demonstrated potential step-change technologies which may revolutionise the treatment of broken bones. Implants made with biodegradable metals are significantly stronger than their polymer counterparts. They are also fully biodegradable in vivo, removing the need for secondary surgery. After a decade of laboratory and early translational research, these new materials are now showing significant clinical potential with the ability to create a paradigm shift in the way we treat musculoskeletal conditions.
To contribute to the clinical translation of the biodegradable metals, this thesis explored the biological response to a novel biodegradable Mg5wt%Ca-1wt%Zn alloy developed for orthopaedic repair, to study the bone remodelling process and assess the potential of the new implant. The main objectives of the research were to explore the impact of active Mg alloy biodegradation on the OB cells cultured in a perfusion bioreactor system and to further understand the bone healing process in and around a degrading Mg alloy by assessing angiogenesis and coupled osteogenesis at the Mg alloy implanted site.
Results demonstrate that the simulated key aspects of the in vivo environment recapitulated in these studies such as blood flow-induced magnesium corrosion, hydrogen evolution, and local pH change, contribute to a statistically significant increase in cellular proliferation and differentiation in the presence of degrading Mg alloys. The released ions from both fast and slowly degrading alloy showed a positive effect on the progress of bone formation. However, fast corroding alloy showed a detrimental effect on osteoblast cells, while osteoblast proliferation and differentiation were improved by released metal ions from optimized alloy with a much slower corrosion rate. These findings suggested that the release of metal ions consisting of Mg, Ca and Zn also sufficiently stimulate the bone formation process. In vivo experimental results observed using second harmonic generation and immunohistological staining confirmed that the optimized mechanical properties and corrosion rate of Mg-5wt%wt%Ca alloy leads to release of metallic Mg, Ca and Zn ions at a rate that facilitate both angiogenesis and coupled osteogenesis for better bone healing without causing adverse effect at the implantation site. To conclude, this thesis tests a new in vivo model system to evaluate biodegradable metals and validate the potential of the newly developed Mg-Ca-Zn alloy as orthopaedic implant material. Furthermore, this work supports ongoing development and refinement of biodegradable metal systems to act as crucial portal technology with potential to revolutionize a myriad of clinical applications.

Advisor: Edwards, J
Glyn-Jones, S
Mechanistic studies of rhodium-catalysed intermolecular hydroacylation

Chapter 1 – Introduction: The concept of rhodium-catalysed intermolecular hydroacylation is introduced. The research that has led to significant improvements in substrate scope and catalytic activity are described, with the reactions being classified into three sub-groups: aldehyde-tethered hydroacylation, alkene-tethered hydroacylation and non-tethered hydroacylation. The mechanistic studies that have facilitated these developments are then detailed.
Chapter 2 – Mechanistic Studies of β-Amido Aldehyde Hydroacylation: One of the recent developments in aldehyde-tethered hydroacylation has been the use of β-amido aldehyde substrates. This chapter describes the mechanistic studies of the reaction of a β-amido aldehyde substrate with 1-octyne, catalysed by the Rh(I)-complex [Rh(cis-κ2-P,P-DPEPhos)(acetone)2][BArF4].
Chapter 3 – Cyclotrimerisation and Optimisation of Hydroacylation: In chapter 2, cyclotrimerisation of 1-ocytne was discovered to be a competitive side-reaction with hydroacylation under certain conditions. The mechanism of the cyclotrimerisation reaction is explored with the pre-catalyst [Rh(cis-κ2-P,P-DPEPhos)(acetone)2][BArF4], and the point at which the reactions become competitive is discovered. This understanding is then used to optimize the catalyst loading, reagent stoichiometry, reaction concentration and reaction temperature, leading to the realisation of an exceptionally efficient, and selective, gram-scale hydroacylation process.
Chapter 4 – Non-tethered Aldehyde Hydroacylation of Acrylates: The discovery of a non-tethered aldehyde Tishchenko reaction catalysed by [Rh(Cy2PCH2PCy2)(η6-fluoroarene)][AlOF4] complexes, in weakly coordinating fluoroarene solvents is described. The subsequent discovery and optimization of a hydroacylation reaction of non-tethered aldehydes with acrylates, catalysed by a {Rh(DPEPhos)}+ catalyst system in 1,2-difluorobenzene is detailed.

Keywords: Acyl-hydride
Cyclotrimirisation
Enone
Alkyne
Kinetics
Rhodium
Catalysis
Aldehyde
Hydroacylation
Advisor: Weller, A
Willis, M
Early and multiple entry to GCSE mathematics and the implications for examination standards

GCSEs are high stakes assessments in England generally taken by students aged 16. The results are put to several uses: they allow students access to further opportunities and are used to judge the performance of schools. While students are expected to take GCSEs once aged 16, this thesis explores an alternative approach – early and multiple examination entry (EMEE). This approach rose in prominence between 2007 and 2013 for GCSE English and mathematics, before changes to accountability measures in September 2013 meant that single entry once again became the norm.
A multiphase mixed methods design was used focusing on EMEE in GCSE mathematics. The first (quantitative) phase showed that early entry increased from 2007 to 2011, generally due to weaker students and students from lower performing schools increasingly entering early. The second (qualitative) phase suggested that the rise in EMEE was due to the pressure of performance measures driving behaviour in schools, encouraging EMEE and associated teaching practices. The third (quantitative) phase suggested that EMEE was likely to have implications for examination outcomes, potentially leading to increased outcomes (i.e. higher grades) at the cohort level.
The findings are considered in terms of the implications for examination standards, drawing on the theoretical literature relating to how examination standards are defined. While the comparable outcomes approach in England implies a causal definition of standards, the rise and subsequent decline of EMEE challenges this definition, raising questions about how standards can be maintained in the presence of EMEE.
Although the prevalence of EMEE has now declined in England, many of the issues identified here are likely to transcend EMEE and have wider implications. Thus, this thesis contributes to the literature relating to the effects of accountability measures on schools’ behaviour and how examination standards are defined, in addition to adding to the existing, albeit limited literature, focusing on EMEE.

Keywords: Early entry
Assessment
mathematics
GCSE
Advisor: Strand, S
Baird, J
Using molecular epidemiology to investigate HIV transmission and prevention efforts

The Human Immunodeficiency Virus (HIV) is a retrovirus that causes HIV infection and, if untreated, leads to Acquired Immunodeficiency Syndrome (AIDS) and death. An estimated 36.7 million people in the world are HIV-infected; around 10% of them live in Europe. In this thesis I use molecular epidemiology in combination with mathematical modelling and traditional epidemiological analysis to describe HIV transmission dynamics and to assess various HIV prevention strategies, which might help to inform public health decisions.
I start by characterizing the explosive HIV growth in people who inject drugs (PWID) in Russia and Ukraine in the 1990s in Chapter 2. I chose those settings as a model system in which to study HIV transmission in PWID in the absence of prevention. I then use my estimates to build a mathematical model that can be used to evaluate preventive measures during HIV outbreaks in PWID.
In Chapter 3 I analyse newly-generated HIV-1 subtype A genetic sequences from Ukraine and apply a novel method to show how HIV spread among Ukrainian regions shifted after the initiation of war on the country’s eastern borders. I show that, since 2014, HIV is moving westwards, carried by large-scale human migration.
In Chapter 4 I created the largest Ukrainian subtype B (the second most prevalent HIV-1 subtype in Ukraine) dataset to date, and show how the virus distribution changed in the country over the last 15 years. I then simulated phylogenies under scenarios similar to the Ukrainian subtype A and subtype B epidemics, to study the performance of various phylodynamic models that are used to estimate changes in HIV population size and transmission dynamics from virus gene sequences.
Finally, Chapter 5 describes the molecular epidemiological profiles of the two most prevalent HIV-1 subtypes in Portugal, subtypes B and G. I use novel phylodynamic approaches to trace and compare the effect of various public health interventions on the transmission dynamics of these subtypes, given their different transmission group composition.

Keywords: Phylodynamics
Eastern Europe
HIV
Advisor: Faria, N
Pybus, O
The legacy of muscular Judaism: Jewish-Israeli identity through sport

This thesis examines how Israel’s identity as a Jewish state is expressed through sport, using both archival and historical sources and ethnographic fieldwork. My primary contribution to the literature builds upon the history of muscular Judaism in order to develop a longitudinal perspective demonstrating how the body continues to provide a source of social and political capital, both reflecting and confronting identity. I show how sport is a platform for identity negotiation, a position which necessarily confronts certain other issues, including ethnoreligious divisions, Jewish sectarianism, nationalism and Israeli control of the Palestinian territories. Consequently, a second focus is the degree to which sport may be used for normalising relationships within Israel, primarily, secular Jewish-Israeli and Palestinian- Israeli relationships.
I explore the nexus of sport and identity within Israel through three ethnographic chapters, each exploring different themes through expanding but interconnecting perspectives within local, national and international spheres respectively. In the first ethnographic chapter (4), I show how community-based sport fits within the greater normalisation debate, viewing its successes and failures in response to the prevailing Jewish state. As professional football has had an integral role in modern Israeli history, Chapter 5 takes a fresh perspective on football culture, primarily seeing fans as a form of scaffolding upholding state institutions. The final ethnographic chapter (6) looks beyond Israel’s borders, adopting the perspective of the state to see how athletes legitimise and broker Jewish identity on an international scale.
Ultimately, I find that, akin to Nordau’s concept of muscular Judaism, sport continues to be productive for negotiating identity within Israel. Sport, however, reflects underlying socio-political patterns, and as such, the different areas of sport explored in the respective chapters have complementary strengths and spheres of influence for confronting and brokering Jewish-Israeli identity with the Diaspora, the Arab Middle East and recursively with itself.

Keywords: Israel-Palestine
Sport-for-peace
Identity
Middle East
Track 2 Diplomacy
Advisor: Parkin, R
A model-theoretic approach to the arithmetic of global fields

This thesis assembles some new results in the field arithmetic of various classes of fields, including global fields, models of the common first-order theory of algebraic extensions of global fields, and fields of finite transcendence degree over their prime field. Most of the results stem from a very simple technique for first-order definitions in fields, based on the satisfaction of a first-order sentence in a family of finite extensions of the ground field. In the first two chapters, we develop this technique to associate existentially definable sets to central simple algebras and Pfister forms, respectively.
We then use these tools to obtain results on global fields, their algebraic extensions, fields elementarily equivalent to ultraproducts thereof, and finitely generated fields. We study valuations on such fields, and notably obtain a large class of examples of fields without Self-Embedded Residue, a natural notion that arises in the study of definable valuations.
Subsequently, we focus on the study of a single global field, where we obtain new definability results. Most importantly, we show that non-solubility of a polynomial equation in one variable over the global field is expressible as an existential condition on the coefficients. This also yields consequences in algebraic geometry over the given field.
After a category-theoretic interlude in the model theory of absolute Galois groups, the final chapter investigates p-valuations on fields. We introduce a notion of generalised Stufe in this context, and prove an interpretability result for spaces of p-valuations in situations of interest.

Keywords: Field Arithmetic
Definability in Fields
Model Theory of Fields
Advisor: Koenigsmann, J
Breast cancer radiotherapy: exposure of the heart and lungs

Breast cancer radiotherapy can cause heart disease and lung cancer, with the risks increasing with the incidental radiation dose to the heart or lungs. To derive appropriate strategies for limiting the risks to future patients, detailed estimates of the radiation doses involved are required.
Radiation-induced heart disease
An atlas for cardiac substructure (segment) contouring on radiotherapy planning scans was developed. The atlas was used to estimate segment doses for 470 women irradiated in Denmark or Sweden during 1958-2001 who had developed ischaemic heart disease with known segment location of cardiac injury, thus enabling an assessment as to which segments are sensitive to radiation.
Cardiac radiation doses were estimated for 771 women irradiated in the Netherlands during 1970 to 2009. The doses form the basis of three case-control studies characterising the relationship between cardiac dose and the risks of subsequent ischaemic heart disease, valvular heart disease and heart failure in young women (median age 50 years).
Radiation-induced lung cancer
Lung doses were estimated for ~40,000 women irradiated for breast cancer in 75 randomised trials. The doses were used to estimate the dose-response relationship for incident lung cancer. A systematic review of modern breast cancer regimens published worldwide during 2010-2015 was also performed. The modern typical doses found in these studies were combined with the estimated dose-response relationship to estimate absolute risks of lung cancer for women irradiated today.
Irradiation of the internal mammary chain
It has been recently shown that internal mammary chain irradiation improves survival but irradiating this region can expose the heart and lungs to several Gy radiation dose. To inform resource allocation, the percentage of women in one cancer centre who met current international criteria for IMC radiotherapy was investigated. Information on cardiovascular risk factors was also collected.
Finally, a phase II clinical trial proposal was developed aiming to investigate if proton beam therapy reduces acute cardiac injury compared to modern X-ray treatment.

Advisor: Taylor, C
Darby, S
Rahimi, K