VictorJuiz/thesis huggingface dataset:
Colour and cloud structure in the atmospheres of the giant planets

For decades, the origin of colour-carrying compounds ('chromophores') in Jupiter and Saturn's atmospheres has remained elusive. Changes in colour are often associated with cyclical meteorological events ('upheavals') on Jupiter. Multiple datasets were obtained from the VLT/MUSE instrument between 2014 and 2018, each containing spatially-resolved spectra of Jupiter and Saturn between 0.48um and 0.93um. We describe the analysis of these datasets to characterise Jovian and Saturnian chromophores and to retrieve abundance profiles of aerosol and gaseous ammonia. Through limb-darkening analysis of Jupiter's NEB, we retrieved chromophore optical constants similar to the laboratory chromophore of (Carlson et al. [2016] Icarus 274, 106-115). These also provided a good fit to spectra of the Great Red Spot, but not to spectra of Jupiter's zones. We applied these chromophore optical constants to other regions of Jupiter, and found that red haze in the NTBs was initially associated with elevated aerosol abundances, but remained in the atmosphere long after upwelling had subsided. We verified previous findings of colour and haze structure changes relating to the shrinkage of the Great Red Spot, where we retrieved the altitude of the chromophore layer at the tropopause. We found no evidence of changes to the cloud structure of Oval BA to explain its fade in colour in 2018. An equivalent retrieval of chromophore optical constants from Saturn's NEB resulted in an absorption spectrum similar to the laboratory chromophore of (Noy et al. [1981] JGR:Oceans 86, 11985-11988), which we located just above Saturn's tropospheric haze. However, we found considerable variability in Saturn spectra that was not entirely consistent with a single chromophore compound. We believe that this work provides a significant contribution to our understanding of both colour and tropospheric aerosol structure on Jupiter and Saturn, and sheds light on the origin of spatial and temporal changes in the visible appearance of the two planets.

Keywords: Outer Planets
Giant Planets
Jupiter
Cloud
Radiative Transfer
Saturn
Chromophore
Atmospheres
Advisor: Irwin, P
Developing treatments for rhodopsin-related dominant retinitis pigmentosa

Mutations in the rhodopsin gene are one of the most common causes of autosomal dominant retinitis pigmentosa (ADRP) and there is at present no treatment available. In this thesis, three potential treatments were developed and tested in a RhoP23H/+ knock-in mouse model.
In the first, animals were housed in red cages which acted as long-pass light filters. This resulted in a significant slowing in the rate of both rod and cone photoreceptor degeneration as determined anatomically using non-invasive in vivo imaging and immunohistochemistry, and functionally by dark- and light-adapted electroretinography.
In the second, efficient adeno-associated viral (AAV) vectors expressing wild type human rhodopsin were manufactured and injected subretinally in RhoP23H/+ mice to test the hypothesis that overexpression of the normal protein might overcome the effect of the P23H mutant. No structural or functional rescue effect was however observed.
The final treatment strategy involved development of artificial mirtrons to suppress expression of endogenous rhodopsin. Mirtrons are novel RNA interference effectors that are spliced from mRNA transcripts. Both efficient mirtrons and a codon modified mirtron-resistant version of the human rhodopsin coding sequence were designed and validated in vitro. These elements were then combined under the control of a single rhodopsin promoter within AAVs as knockdown/replacement gene therapy vectors for ADRP. Subretinal injection in the RhoP23H/+ mouse resulted in mouse-to-human rhodopsin mRNA replacement, and this was associated with a modest rescue effect when injected at a dose of 2x108 gc. This represents the first use of an artificial mirtron to induce gene knockdown in vivo.

Keywords: Retina
Gene therapy
AAV
Rhodopsin
Inherited retinal disease
Mirtron
Retinitis pigmentosa
Advisor: MacLaren, R
Topochemical reduction and doping of some complex iridium oxides

The main body of the work is focussed on the topochemical reduction of iridium containing oxides which adopt the perovskite or the n = 1 Ruddlesden-Popper structures. The second part of this work is focussed on the doping of Sr2FeIrO6.
The topochemical reduction chemistry of some 3d/Ir containing oxides was investigated using the group I/II hydrides as reducing agents. These reactions were successful however the by-products of reaction could not be removed without decomposing the reduced phases. To overcome these issues new reduction methods were developed.
Reduction of the double perovskite Sr2FeIrO6 with 5%/95% H2/N2 resulted in the formation of Sr2FeIrO4. At temperatures above 115 K Sr2FeIrO4 adopts a highly symmetric infinite-layer structure that consists of a rigorously ordered array of vertex sharing IrIIO4 and FeIIO4 units. The structure distorts with the onset of magnetic order. At above 115 K the spins in Sr2FeIrO4 are strongly interacting but frustrated. At 115 K the spins in Sr2FeIrO4 order resulting in a canted-antiferromagnetic state that is highly unusual and is dominated by Ir-Ir and Fe-Fe exchange interactions.
To extend this work we synthesised and reduced Sr2Fe0.5Ir0.5O4. Sr2Fe0.5Ir0.5O4 adopts the archetypal n=1 Ruddlesden-Popper structure. Magnetisation data suggest Sr2Fe0.5Ir0.5O4 may have two magnetic transitions however the structure is paracrystalline so the magnetic structures cannot be determined. Reduction of Sr2Fe0.5Ir0.5O4 using a zirconium getter resulted in the formation of Sr2Fe0.5Ir0.5O3. The structure of Sr2Fe0.5Ir0.5O3 is the layered analogue of the infinite-layer structure.
The reduction of the solid-solution CaMn0.5Ir0.5O3 was achieved using a NaH getter reaction and resulted in the formation of CaMn0.5Ir0.5O2.5. The B-site disorder present in CaMn0.5Ir0.5O3 is retained in CaMn0.5Ir0.5O2.5 and the oxide vacancies introduced are also disordered. CaMn0.5Ir0.5O2.5 is the first example of IrIII in a topochemically reduced phase and the first example of square pyramidal IrIII.
The final set of phases that were synthesised and reduced were LaxSr2-xCo0.5Ir0.5O4 (x = 0, 0.5). These n=1 Ruddlesden-Popper phases were reduced using a zirconium getter reaction to form LaxSr2-xCo0.5Ir0.5O3 (x = 0, 0.5). Similarly other Ruddlesden-Popper phases and reduced analogues, LaxSr2-xCo0.5Ir0.5O3 (x = 0, 0.5) are paracrystalline so accurate structural determination is difficult however refinements suggest these phases could have a distorted anion structure.
The doping chemistry of Sr2FeIrO6 was investigated by doping the double perovskite with low levels of Ca, Ba, Ga and La. Structural analysis showed that the doped samples undergo phase separation and consist of an I1̅ phase and a P21/n phase. Magnetisation data suggest that the doped samples have two magnetic transitions. The second transition is to a type-II antiferromagnetically ordered state similar to that of Sr2FeIrO6. It is not clear what causes the first transition but Fe Mössbauer data show it is not due to Fe-based spins, indicating a jeff ≠ 0state for IrV.

Advisor: Hayward, M
An optimisation framework for magnetic resonance fingerprinting

Magnetic Resonance Fingerprinting (MRF) is an efficient quantitative MRI technique for simultaneously mapping multiple tissue or system properties. This thesis presents a framework for optimising the acquisition parameter schedules of a Spin-Echo (SE) Echo Planar Imaging (EPI) MRF pulse sequence, with a view to an application to tracking oedema in acute stroke.
Reference quantitative MRI methods were implemented and used for validations of the SE EPI MRF acquisitions. For this purpose a custom phantom was built with relaxation parameters spanning those typical of in vivo grey and white matter. Inversion recovery and spin-echo sequences were used to provide gold standard maps of T1 and T2, respectively. A 3D DREAM protocol was used for B1+ mapping and gradient-echo sequences provided B0 off-resonance measurements. Balanced SSFP and FISP MRF sequences were also implemented, with spiral readouts and acquisition parameters similar to those of literature examples.
The framework was designed to optimise the SE EPI MRF excitation flip angles, repetition times and the temporal positioning of inversion pulses. Many of the optimisation parameters were flexible and user-specified, such as the targeted T1 and T2 and the evaluation metric. Single-slice and 10-slice schedules were optimised using fmincon and genetic algorithms from MATLAB toolboxes and custom cost functions based on Monte Carlo error simulations.
Ten-slice SE EPI MRF schedules requiring 8 seconds and 20 seconds per slice were compared experimentally, with the longer schedules providing the better T1 and T2 accuracy and precision. However, both sets of schedules were unable to fit B1+ accurately, necessitating the use of a separately acquired B1+ map to correct the dictionary flip angles. Experimental phantom results with B1+ correction demonstrated agreement with the theoretical accuracy improvements predicted for the optimised schedules but undesired reductions in precision were observed. Those phantom results suggested that the fmincon schedule marginally outperformed the corresponding genetic algorithm schedule, showing maximum biases of 16.5% for T1 and 4.6% for T2 and maximum spreads of 16.3% for T1 and 14.3% for T2. The FISP MRF sequence provided the best all-round performance.

Advisor: Jezzard, P
Kennedy, J
The politics of dam resurgence: high modernist statebuilding and the emerging powers in Africa

Following a decade from the mid-1990s that saw a near cessation in dam building, the infrastructure has returned. This phenomenon is controversial because dams’ social and environmental impacts, economic costs and development ineffectiveness have been well evidenced. This timely analysis of the dam resurgence asks why and how this trend is happening. It studies three individual dams in Rwanda and Tanzania with Indian, Brazilian and World Bank involvement respectively. Primarily qualitative analysis interrogates three conceptual levels of these projects: The international enabling companies and financiers; driving national governments; and each dam site’s locale. Addressing a literature bias towards materialist explanations, theoretical analysis uses a lens of high modernist ideology. Research finds depoliticising and expert-centric applied high modernist ideas in the case study dams’ justifications, decision-making and knowledge-production. This entailed a singular focus on electricity generation and short-sightedness to these dams’ socio-environmental impacts. However, the thesis also demonstrates the presence of dam reforms and evidences their influence on each case’s discourse and practice. Given reformist policies’ foundation in oppositional principles, the thesis proposes an ideological bricolage with high modernism to describe the rationales and practices of its case studies of dam resurgence; a moulding of past high modernism with new reformist idea-practices. This significantly furthers the social science literature on the dam resurgence, describing and explaining the era’s complexity, its limited but important change and array of, increasingly corporate, actors. Through the case study research, the thesis also furthers understanding of the emerging powers’ presence and influence in Africa. Moreover, it contributes to analysis on the growing number of illiberal modernisation projects across the continent. The dam-building resurgence in Rwanda and Tanzania and its ideological bricolage both demonstrates and nuances this trend. Intersection with these themes ensures the thesis advances understanding of the ideology, politics and geography of development.

Advisor: de Oliveira, R
Agricultural development, mechanization, and rental markets: theory and empirics from Ghana

The subject of this thesis is the process of agricultural mechanization in the tropical farming systems of Ghana. Three original research papers are presented which explore separate research questions with different methodological approaches. All three papers draw upon detailed empirical analysis of the decisions by farm households over the use of tractor plowing in cereal-producing farming systems of Ghana. This empirical analysis informs our theoretical understandings of mechanization, its use, and its impacts.
The questions considered are: (i) to what extent can the patterns of agricultural mechanization be explained by changes in population, urbanization, and agro-ecological conditions? (ii) Given the heterogeneity of conditions and farming systems, is it right to assume that mechanization will reduce the labour requirements for production? What is the impact of mechanization on other farming decisions and productivity? And (iii) what role do informal institutions and social capital play in facilitating access to more productive technologies by farmers of all scales?
By revisiting the theories of mechanization developed in the1960s through to the 1980s, the first paper argues that farmers’ technology adoption decisions continue to be linked to system-wide drivers such as population change and urbanization. The second paper argues that farmers are taking up tractor plowing in this production system in large part because of the advantage it confers in shortening the required time for land preparation, even as mechanization has little impact on post-planting farm practices, which remain highly labour intensive. The final paper examines the market for tractor plowing services, which is the primary mode of access to mechanized technology for farmers in Ghana. I argue that the social embeddedness of farmers in rural Ghana is key to the functioning of the market for tractor services, allowing communities to manage spatial externalities and time constraints.

Keywords: technology adoption
mechanization
social institutions
Africa
agricultural development
Ghana
farming systems
Advisor: Gollin, D
Fu, X
Content in thought and perception

This thesis addresses a debate within the philosophy of perception between so-called conceptualists and nonconceptualists. Its principal thesis is that the intentional content of a perceptual experience is the content of a thought that a reflective subject is in a position to think if she has the experience. I call this claim, endorsed by conceptualists, the thesis of content congruence. Two principal lines of argument are put forward for this thesis. The first, ‘simple’ argument contends that a perceptual experience is a state in which it perceptually appears to the subject that things are thus and so; that a reflective subject who has an experience is in a position to think that things are thus and so; and that the subject in question, in doing so, thinks a thought with the same content as her experience. The second line of argument appeals to the role of perceptual experience in intentional explanation of observational beliefs. It makes the case that such explanation presumes that there is a non-trivial, non-vacuous law linking perceptual experiences with observational beliefs, and argues that an adherent of content congruence is significantly better placed to formulate such a law (consistently with her view) than her ‘content nonconceptualist’ opponent.
The thesis of content congruence has often been associated in the literature with the thesis of state conceptualism, i.e. the claim that the representational capacities in virtue of the activation of which a perceptual experience has the content it has are conceptual. I reject the latter, and explain why we should not expect the denial of that claim, i.e. state nonconceptualism, to be incompatible with content congruence. I defend moreover the thesis of content congruence against the objection that it confuses sense and reference, and the objection that it leads to a viciously circular or otherwise inadequate account of observational or demonstrative concepts.

Advisor: Williamson, T
Campbell, J
Studying galaxy evolution with modern radio surveys

Modern radio surveys are transforming our view of the extragalactic sky, observing both Star Forming Galaxies (SFGs) and Active Galactic Nuclei (AGN) over large fractions of the history of the Universe. This allows us to investigate their evolution. In Chapter 2, I investigate how the relationship between galaxies and their dark matter environments evolves, through studying their angular clustering. Using the VLA 3 GHz COSMOS Survey (Smolcic et al., 2017a,b), I find that AGN reside in more massive haloes than SFGs and that radiatively inefficient AGN tend to reside in more massive haloes than their efficient counterparts. I investigate this further, in Chapter 3, by parameterising the Conditional Luminosity Function (CLF), which links environment to the luminosity distribution of these sources. This is novel at radio frequencies. From this, I study how the typical properties of galaxies vary with environment (or luminosity), again concluding that inefficient AGN reside in the most massive haloes, but that the halo mass supporting AGN and SFGs is smaller at higher redshifts. In Chapter 4, I investigate whether the multi-wavelength source extraction software ProFound (Robotham et al., 2018) can accurately quantify the flux densities of radio sources, irrespective of morphology. This is especially important for modern telescopes with a combination of long and short baselines. I find that Pro- Found is able to outperform commonly used software (PyBDSF and AEGEAN) when complex morphologies are considered and perform competitively when modelling sources with smooth morphologies. Finally, in Chapter 5, I present the deepest low frequency (144 MHz) observations of the XMM-LSS field, using LOFAR. This provides a low frequency catalogue which can be used in conjunction with higher frequency radio surveys. Combining the work of this Thesis will enable greater understanding of the relationship between galaxies and their environments, using future deep extragalactic radio surveys and this is discussed in Chapter 6.

Keywords: Radio Astronomy
Large Scale Structure
Advisor: Jarvis, M
‘Brotherly strangers’: historicising and disaggregating Kenya and Zambia’s relations with China (1961-2000)

This thesis examines post-colonial Kenya and Zambia’s relations with the People’s Republic of China from ideological, political, economic and social perspectives, encompassing encounters between Kenyans, Zambians and Chinese as well as between their states. China’s growing significance in Africa is a popular subject in the press and academia but hitherto has been little analysed from a historical dimension. Through the triangulation of the global Cold War, African history, and Chinese history, the thesis examines the encounters, conflicts, and dynamics of China-Kenya/Zambia relations from 1961 until 2000, as well as the basis on which historical narratives regarding Chinese encounters with Kenyans/Zambians have been constructed. In doing so, it explains the on-going development of these relationships and sheds light on the historical underpinnings – or lack thereof – on contemporary China-Africa relations.
The thesis title, ‘brotherly strangers’, identifies two key ostensibly contradictory aspects of China-Africa relations: ‘strangers’ in the sense of their diverse historical trajectories, but ‘brotherly’ in terms of an asserted shared historical lineage of western domination. The dynamics of their changing relations across a wide span of time are examined by the comparative studies of Kenya and Zambia’s respective relations with China. From a Chinese state perspective, Zambia has been primarily of political/strategic importance, whereas Kenya, although politically estranged and even hostile, has been of greater economic significance. Their distinctive historical legacies, and the variation in China’s relations with specific African states, challenges both the ‘taken for granted’ role of the China-Africa historical lineage in contemporary analyses, as well as its tendency to assume uniformity in these relationships.

Keywords: China-Africa
African history
Cold War
Advisor: Larmer, M
The muscle-type nicotinic acetylcholine receptor in health and disease

Myasthenic syndromes are characterised by weakness and increased fatigability due to an impairment of neuromuscular transmission. Autoimmune or genetic factors compromise the function of muscle-type nicotinic acetylcholine receptors (AChRs), which have two isoforms composed of five subunits in muscle – fetal AChRs have a γ- and adult AChRs have an ε-subunit. Rapsyn is another key component of the postsynaptic molecular machinery required for neuromuscular transmission. It directly interacts with AChRs and is required for AChR clustering at the neuromuscular junction (NMJ).
The NMJ is one of the most widely studied synapses but there are still aspects of normal NMJ development and function that need to be better understood. In this work, patch clamp experiments on muscle (TE671/CN21) and non-muscle cells (HEK293) were performed to elucidate AChR function under different physiological and pathological conditions. The adult AChR isoform recovered faster from desensitisation compared to the fetal AChR. Rapsyn was shown to induce AChR aggregation in TE671/CN21 and HEK293 cells and facilitated recovery kinetics in both fetal and adult AChRs in the muscle cell line. Rapsyn also increased the sensitivity for myasthenia gravis (MG) sera to inhibit adult AChR currents, and confined current inhibition to sera with AChR autoantibodies only. Finally, the novel αL251R mutation found in a patient with congenital myasthenic syndrome (CMS) was shown to be associated with a voltage-dependent conversion of AChR ion selectivity from cationic to anionic, transforming the receptor into an inhibitory channel.
This work provides an evaluation of the functional impact of rapsyn on AChRs and helps to understand better the significance of the developmental switch from the fetal to the adult isoform. The data suggest that rapsyn is important for the analysis of the functional effect of MG sera on AChRs, and show novel functional effects of a new CMS mutation that sheds light on AChR function.

Advisor: Beeson, D
Webster, R
Vincent, A