VictorJuiz/thesis huggingface dataset:
Volcanic ash in the atmosphere

This thesis presents new work on the characterisation of volcanic ash in the atmosphere. The eruption of Eyjafjallajökull in 2010 brought the issue of ash in the atmosphere into sharp focus. Radiative transfer models used in remote sensing and hazard assessment of volcanic ash require knowledge of ash optical parameters, which are governed by the spectral complex refractive index (n + ik: where n is the real and k is the imaginary part). By investigating the relationship between volcanic ash composition and refractive index, a new parameterisation has been developed which will aid in the detection and quantification of hazardous ash clouds. It has been tested on retrievals from three recent eruptions using Infrared Atmospheric Sounding Interferometer (IASI) satellite data. The eruptions of Chaitén (Chile) in May 2008, Okmok (Aleutian Peninsula) in July 2008 and Grímsvötn (Iceland) in May 2011 allowed the testing and application of the parameterisation on a range of compositions, demonstrating that use of a parameterised index may significantly improve the retrieval of mass loading, a crucial parameter for assessing hazards to health, infrastructure and aviation. Direct sampling techniques are required to supplement satellite observations in order to ground-truth remote sensing techniques. A study of aerosol samples collected in the UK when the ash plume of Eyjafjallajökull was overhead has demonstrated that volcanic ash is chemically detectable above urban particulate matter, and that ash surface chemistry plays an important role in transporting heavy metals, which may have implications for remote sensing.

Keywords: Refractive index
Volcanic aerosols
Volcanic ash
Optical properties
Air quality
Chemical composition
Advisor: Mather, T
Pyle, D
Collective behaviour of chemotactic microorganisms in a viscous environment

The aim of this DPhil thesis is the investigation of collective effects that can occur in a colony of interacting bacteria. The non-equilibrium dynamics of living organisms can lead to fascinating patterns and behaviours which cannot be found in equilibrium systems. It is our goal to obtain a better understanding of bacterial colonies and to develop a general theoretical description for living systems undergoing chemotaxis.
Some types of bacteria are able to release chemical attractants to their environ- ment, which enables them to sense each other and to form biofilms in a coordinated way. E. Coli, for example, secrete aspartate if succinate is present, which diffuses in their environment and enables interactions. In the first part of the thesis we will derive a general model for bacteria or cells that interact with each other via chemo- taxis and also undergo divisions. Using Renormalization Group calculations we will show that division and chemotactic terms are of the same relevance, and that the competition between them can lead to a rich phase diagram and a transition from controlled behaviour to uncontrolled growth.
In the second chapter, we will examine microorganism interaction in the limit where the secreted particles are effectively non-diffusive. On a surface, Pseudomonas aeruginosa bacteria leave a trail of polysaccharides behind them, which is followed by other P. aeruginosa bacteria [1,2]. These interactions between individuals can lead to a local accumulation and spatial correlations of bacteria [3, 4], which are important at the early stages of the biofilm formation. Starting with a generic single microorganism, we will derive the underlying equations of motion. As an important qualitative feature, we will obtain trail alignment with the gradient in addition to a trail-dependent velocity in conventional chemotaxis. Using a simplified version of the model, we will analytically investigate the effects of autochemotaxis with a self-deposited trail and show that it can lead to enhanced rotational diffusion and even trapping. However, if a microorganism is following an existing trail, it can also lead to oscillatory behaviour and to perpendicular trail escapes. We will then compare the full model to experimental results and find that it can both explain single-bacteria behaviour and collective microcolony formation of P. aeruginosa. The collective polysaccharide distributions can also be understood within the framework of a simple calculation inspired by network theory, which gives surprisingly good results.

Advisor: Golestanian, R
Free-flight kinematics of diptera

Insect flight is a complex behaviour that goes beyond pure mechanism. Integrating genetics, morphology, physiology, sensorimotor control, kinematics and aerodynamics, researching the multiform nature of insect flight is of great scientific interest and also a challenge. Consequently, exploring different strategies for reducing the dimensionality of large flight datasets to uncover meaningful relationships is critical to furthering our understanding of insect flight biomechanics. The aim of my DPhil is to explore different strategies for analysing large datasets of free-flight kinematics in three Dipteran species: Drosophila melanogaster (fruit fly), Calliphora vicina (blowfly) and Eristalis tenax (drone fly). In Chapter 2, I critically evaluate the k-means clustering algorithm as a means of partitioning dipteran body kinematics, and show that it is an unsuitable target for body kinematic data that shifts continuously. In Chapter 3, I show that sexual dimorphism in fruit flies affects their wing beat kinematics beyond size dimorphism. In Chapter 4, I used the k-nearest neighbour clustering algorithm to develop a way of predicting the gear stops that blowflies engage in based on their wing beat kinematics. In Chapter 5, I contrast the wing beat kinematics and aerodynamic profile of all three species. Overall, my thesis shows firstly, that fruit flies, blowflies and drone flies occupy distinct kinematic morphospaces, and secondly, that careful consideration should be given to the choice of technique used to reduce the dimensionality of the data.

Keywords: biomechanics
insect flight
kinematics
Advisor: Walker, S
Taylor, G
Improving hip fracture outcomes using routinely collected health data

Hip fracture is associated with high morbidity and mortality but outcomes can be improved through dedicated clinical pathways that deliver evidence-based multidisciplinary care. The National Hip Fracture Database (NHFD) is a national clinical audit that exists to improve hip fracture care by providing hospital-level performance data through online dashboards and an annual report. The aim of this thesis was to explore how national clinical audit can improve hip fracture care and outcomes.
In Chapter 2, a systematic review found little existing evidence to show that releasing performance data into the public domain can change healthcare decisions, clinical performance, or patient outcomes. Importantly, the evidence could not exclude an effect and it seems likely that data will continue to be released to the public in efforts to improve performance. Chapter 3 shows that specific identification of performance outliers is relatively insensitive to the model used for risk-adjustment and may not be enhanced by routine linkage of the NHFD to other datasets.
In Chapter 4, an interrupted time series and difference-in-differences study did not find any evidence that introduction of the NHFD alone improved performance measures or patient outcomes. However, integration of the NHFD with the Hip Fracture Best Practice Tariff (BPT) - which pays hospitals a supplement for meeting evidence-based care standards - was associated with marked and sustained improvements across both performance measures and patient outcomes. This suggests that an integrated system for rewarding best practice can improve outcomes beyond that of a voluntary audit of national clinical standards.
The BPT rewards hospitals for meeting seven care standards. In Chapter 5, an observational study using NHFD data found substantial deviation from national guidance around provision of total hip arthroplasty (THA), which is not yet a BPT standard. Under-provision of THA appears to disproportionately affect patients living in deprived areas and those presenting to hospital at weekends.
One possible reason for under-provision of THA is that the evidence is uncertain. There is concern that randomised trials may overstate the advantages of THA when used in routine clinical practice. However, Chapter 6 combined meta-analysis of trial data with a propensity score matched cohort study using the NHFD and did not find evidence that outcomes were worse outside clinical trials. Importantly, both studies reported an association between THA and reduced 12-month mortality, which clearly requires urgent further investigation.
This thesis shows that the NHFD is a valuable resource both for auditing standards of care and embedding studies aimed at learning from the outcomes of patients with hip fractures. If the findings in Chapter 6 are supported by further work, the provision of THA to eligible patients should be considered as a future quality standard that must be met for payment of the BPT.

Advisor: Perry, D
Judge, A
Gabbe, B
Costa, M
Scanning micro-photoluminescence studies of GaAs photonic crystals and perovskite structures

The first part of this thesis focuses on a novel design of photonic crystal microcavity coupled to InGaAs quantum dots. Such coupled dot-cavity systems can be used as enhanced single photon sources for quantum information applications and more complicated arrangements could even be used as optical switches in a quantum computer. A photolithography process is used to fabricate these cavities, allowing them to overcome many of the difficulties involved in achieving reliable dot-cavity coupling in traditional e-beam defined cavities.
Theoretical FDTD simulations are used to predict the Q factor and mode volume (1.44 (λ0/n)3) of this cavity design. The fabrication process is given in detail, and micro-photoluminescence measurements are used to verify successful cavity fabrication. A success rate of 85% is achieved with Q factors as high as 7.4 × 103 at a wavelength of around 1.25 µm. These cavities are shown to have comparable performance to existing designs such as L3 and Notomi cavities fabricated using e-beam lithography.
The second part covers studies of four different polycrystalline perovskite films with compositions of the form FA0.83Cs0.17Pb(BrxI1-x)3 and varying bromine fraction x ∈ {0.1, 0.2, 0.3, 0.4}. These perovskites are promising candidates for commercially scalable photovoltaic applications and have received a great deal of scientific interest over the past decade. This particular composition has been shown to have improved stability and optoelectronic properties compared to other perovskites.
Micro-photoluminescence mapping is used to study the temperature dependence and structure of these samples. The diffusion lengths are found to be in the range from 2 µm to 5 µm, and evidence of photon recycling over longer distances is identified. Time-resolved photoluminescence measurements are carried out at cryogenic temperatures to study the carrier decay dynamics. A theoretical model of the decay process is developed and fitted to the data. Both excitons and free carriers are found to contribute to the emission, with the 10% bromine sample having the highest exciton binding energy.

Advisor: Taylor, R
The dramatic ecologies of As You Like It

This thesis reads As You Like It’s various cultural perspectives as dramatic ecologies. At their intersections, where characters describe and respond to each other, they combine and clash, exposing linguistic and dramatic traces of these ecologies, which appear as multidimensional signs – words, ideas, and mythical archetypes leading to multiple narrative subtexts. They create polysemic sites of possible interpretations, introducing potentially related but non-identical realities, simultaneously copresent in the forest playspace, constructing the conditions for emerging subjectivities. My analysis is both historical, attending to the unique cultural issues of each character’s world, and critical, considering the resonances of verbal repetitions and conceptual dissonances, foregrounding imbricated issues such as technology’s cultural impact, class conflict, women’s literacy, and Elizabethan race relations. My research is intertextual, addressing the play’s literary and historical precursors, including Ovid’s Metamorphoses, Lodge’s Rosalind, The Fairie Queene and Sidney’s Arcadia, as well as intratextual, considering the interaction of these discourses as they connect in Arden.
Beginning with Jaques, I address the forest’s Ovidian, Pythagorean cosmology, before exploring Touchstone’s contrasting approach to time and technology, and the influences of Rabelais and commedia dell’arte in the clown’s ecology, with its emphasis on conditionality. Chapter three analyses Corin’s work ethic (both social and physical), his cultural relativism, his role as guide to the forest society, and his poetic language, with its links to the tradition of classical and Elizabethan literary pastoral. Chapter four traces race and writing in Phoebe’s ecology, emphasising her role as social scapegoat, and chapter five considers Orlando’s heroic encounter with regard to its potential relevance for the other characters’ intertwined psychic journeys. Chapter six addresses Rosalind’s alchemical shapeshifting and literary self-expression as she negotiates Elizabethan gender norms; inhabiting the contrasting interpellations of other ecologies, she exemplifies the exiles’ citational, emergent subjectivity, which parallels audience responses to interpretive possibilities.

Keywords: ecology
form; formalism
gender
intertextuality
class
myth
race
heteroglossia
slavery
archetype
subjectivity
ecocriticism
interpretation
Advisor: Palfrey, S
Antiviral and immunomodulatory activities of iminosugars: candidate therapeutics for arbovirus infections

The antiviral efficacy of iminosugars with glucose-stereochemistry has been demonstrated against a broad range of enveloped viruses possessing N-glycoproteins. This antiviral activity is primarily understood to be mediated by competitive inhibition of endoplasmic reticulum (ER) α-glucosidases, leading to a reduction in functional viral glycoprotein folding and infectious virion production.
Dengue virus (DENV) is one such virus for which iminosugar efficacy has previously been established. Here, the antiviral efficacy of N-8’-2’’-tetrahydrofuranyl-octyl-deoxynojirimycin (2THO-DNJ) is evaluated against DENV infection of primary human monocyte-derived macrophages (MDMΦs). The potential for iminosugars to impact stages of the DENV infection cycle in addition to virion secretion is considered, and DNJ-derivative iminosugars are demonstrated to inhibit DENV replication in primary human immune cells for the first time. Alongside DENV, iminosugar efficacy against Zika virus (ZIKV) is investigated, finding important differences in the iminosugar susceptibility and ER α-glucosidase dependence of the two viruses.
Moving away from flaviviruses, the potential for iminosugars to be employed against the emerging Crimean-Congo haemorrhagic fever virus is considered, through use of the little-characterised ‘surrogate’ Hazara virus (HAZV). Despite possession of N-glycoproteins, a lack of iminosugar antiviral activity is observed in HAZV-infected SW13 cells.
Common to viral haemorrhagic fevers and certain other disease states is a strong pro-inflammatory, pathological immune response. Immunomodulatory activity of iminosugars has previously been reported, but with a limited range of stimuli used. Here, the impact of iminosugars on cytokine responses to both viral infection and stimulation of MDMΦs with a spectrum of pattern-associated molecular patterns (PAMPs) is investigated, with secretion of biologically functional TNF-α the major read-out. The suppressive effects of DNJ-derivative iminosugars on TNF-α secretion are broadly conserved across stimuli, supporting previous findings that iminosugar immunomodulatory activity is not dependent on viral replication or restricted to PAMPs of a viral origin. In contrast, the galactostereochemistry iminosugar N-nonyl-deoxygalactonojirimycin had more selective effects on cytokine production than the corresponding DNJ-derivative. Preliminary mechanistic investigations considering potential effects of iminosugars on TLR signalling pathways are conducted.
Overall, this thesis explores exciting new features and nuances of iminosugar activities relevant for treating viral infections and combatting a wider range of inflammatory conditions.

Advisor: Zitzmann, N
Influence of the upper stratosphere on polar vortex variability

The polar vortex is a band of strong westerly winds that forms each winter and encircles the pole, high up in the atmosphere in a region known as the stratosphere. However this band of winds is not stable in the northern hemisphere, and often dramatically disintegrates in events known as sudden stratospheric warmings (SSWs). When SSWs happen they influence the weather occurring below, often leading to cold winters for northern Europe. SSWs are driven by the vertical propagation of waves from lower down in the atmosphere. Recent studies have suggested that the winds in the upper tropical and subtropical stratosphere may affect how these waves propagate, and whether they are able to influence the development of SSWs.
In this thesis I investigate the various contributions different parts of the atmosphere make to the evolution of the SSW in the winter of 2008/9 by fixing different areas of the atmosphere to reality in a computer model, whilst letting the polar vortex evolve freely and comparing its evolution to reality. Fixing the lower atmosphere in this way prescribes the wave forcing entering the stratosphere, but this is not found to be enough on its own to generate an SSW close to that seen in 2008/9. Neither is fixing the upper stratosphere, above the polar vortex. It is only when the winds in the upper tropical stratosphere are fixed in addition to that of the lower atmosphere that a similar SSW occurs, consistent with the idea that this area of the atmosphere is important for determining the evolution of SSWs by affecting wave propagation.

Keywords: Atmosphere
Stratosphere
Sudden Stratospheric Warmings
Seasonal forecasting
Numerical weather prediction
Stratospheric Sudden Warmings
Nudging
Polar vortex
Atmospheric waves
Advisor: Gray, L
Knight, J
Between Hindu and Indian: the nationalist thought of Lala Lajpat Rai

This thesis undertakes the first ever systematic intellectual study of the nationalist thought of Lala Lajpat Rai. In doing so, it strongly contests the dominant scholarly interpretation of his nationalist thought as representing the nascent stage of Savarkarite Hindutva. Through a fine-grained textual analysis of his entire oeuvre on nationhood, it uncovers the multiple, internally distinct nationalist narratives that Lajpat Rai articulated in the four broad historical phases of his intellectual life. These reveal that while for much of his life, he switched between ‘Indian nation’- and ‘Hindu nation’-based nationalist narratives, in the latter phase of his life, he settled firmly into narratives grounded in the notion of a ‘secular’ Indian nation.
In unearthing Lajpat Rai’s complicated intellectual trajectory, this study makes larger intellectual claims. By demonstrating that, despite apparent similarities with Hindutva, his own ‘Hindu nation’-based narratives remained substantially distinct, it draws attention to the variegated nature of ‘Hindu nationalism’. By showing that Lajpat Rai eventually moved towards Indian nationalist narratives, it further undermines the assumption that all ideas of Hindu nationhood necessarily culminate in Hindutva. By outlining the different internal structures of his Indian nationalist narratives, this thesis uncovers space for properly discerning the internally differentiated nature of ‘Indian nationalism’. In recognising commonalities across his different ‘Hindu’ and ‘Indian’ nationalist narratives, it rejects the sharp binary conventionally drawn the two, and by showing that Lajpat Rai endeavoured to organise a ‘communal’ politics to establish a ‘secular’ Indian nation-state, it reveals how ‘communalism’ can be engineered in service of a ‘secular’ Indian nation. Finally, instead of reading Lajpat Rai’s thought through the purposes for which others might have utilised it, this study insists on understanding it in its own right, thus constituting an argument that the political thought of a thinker must be understood independently of reductionist teleological narratives.

Keywords: secularism
Hindu nationalism
Hindu communalism
Indian nationalism
Arya Samaj
Hindu Mahasabha
political representation
Hindutva
caste system
Advisor: Devji, F
Life in space

For nearly half a century, inclusive fitness theory has formed a bedrock of whole-organism biology. It has helped explain social behaviours across the tree of life, including, via the major transitions view of evolution, the history of life itself. However, some significant questions remain. In this thesis, I consider challenges at the frontiers of inclusive fitness, in time, theory, and space. Specifically: (i) I study the evolution of cooperation early in the history of life. I develop models of simple molecular replicators, resolving previously puzzling results and identifying important life-history features of replicators for cooperation. (ii) I use kin selection models to develop a framework for understanding RNA cooperation and guiding empirical work on the origins of life. (iii) I develop and test a new hypothesis for the origin of the genome, the first major transition in individuality. (iv) I address criticisms of inclusive fitness theory, developing conceptual arguments for why it is a useful tool despite its flaws. (v) I show that recent mathematical criticisms of inclusive fitness misapplied inclusive fitness, and extend their models, recovering inclusive fitness maximisation. I provide formal arguments for a broader range of the theory's application than previously thought by some mathematical biologists. (vi) I show that a recent paper about the effects of divorce on honest signalling in birds miscalculated inclusive fitness, and develop a formal model that predicts an effect of inclusive fitness on signalling in birds, which is supported by the data. (vii) Finally, I consider the universality of natural selection and major transitions in individuality, demonstrating how evolutionary theory can be used as a powerful tool in astrobiology. As a whole, this body of work extends the range of inclusive fitness theory’s application earlier in evolutionary time, to a wider range of biological scenarios, and further in space.

Advisor: West, S