VictorJuiz/thesis huggingface dataset:
Testing theories of baroclinic adjustment in the laboratory and in simple atmospheric models

The mean state of the Earth’s climate is the result of a balance between the destabilising effect of radiative forcing and the dynamics which transport heat through the atmosphere. The contribution of baroclinic instability to maintaining this balance is not quantitatively well understood. Two prominent groups of existing ideas which attempt to explain the effect of baroclinic eddies on the mean state are baroclinic adjustment and geostrophic turbulence theories. The former suggests that the efficiency of eddy transport increases rapidly with imposed forcing such that the system adjusts to some preferred neutral state and only small departures from this state are allowed. The latter implies that the efficiency of eddy transport is set locally by an eddy diffusivity which varies smoothly with the forcing.
This thesis describes the use of a new approach, centred on a novel configuration of a lab experiment, to provide insights useful for understanding the impacts of various instabilities on the dynamical equilibration of the thermal structure of the atmosphere. The lab experiment is a new rotating annulus configuration particularly suited to studying meridional heat transfer as its thermal structure is representative of that observed in Earth’s atmosphere. Within this thesis we describe the development of a three dimensional simulation of this experiment using the dynamical core of the Met Office Unified Model. The main advantages of using this model are that the numerics can be tested against the experimental data and the same model can be used to simulate Earth-like atmospheres.
Our findings suggest that the theories of baroclinic adjustment and geostrophic turbulence may apply in different regimes which are described by the size of the baroclinic deformation radius relative to the domain size. We found this behaviour to be consistent between simulations of the annulus experiments and simulations of idealised planetary atmospheres.

Keywords: baroclinic instability
planetary atmospheres
turbulence
geophysical fluid dynamics
Advisor: Read, PL
A phonological typology of modern Arabic varieties

Modern Arabic colloquial varieties exhibit signiﬁcant phonological variation that has only partially been incorporated into previous typological eﬀorts. This thesis motivates a phonological typology of sixteen modern varieties, exploring not just the crucial ingredients of the phonological grammar including syllable and foot structure, but also the lexical and postlexical nature of prosodic structure.
I argue that there are two axes for phonological variation in Arabic: Tolerance and Repair, that is, varieties diﬀer in terms of which types of syllables they tolerate and in how they repair violations of syllable structure, and these axes do not covary. In terms of Tolerance, varieties diﬀer in acceptance of quantity. Varieties that permit long segments have restrictions on the segmental level, whereas varieties that do not have restrictions on the moraic level, and varieties that allow long consonants or clusters but not long vowels have restrictions on the X-slot tier. In addition to the canonical 2 or 3 elements, individual varieties may also permit an extra element in their medial syllable rime according to variety-speciﬁc restrictions including coronality, fast speech, and sonority. As such, this typology provides mechanisms to account for the data in each and every variety, rather than merely providing a canonical set of features that not all varieties ﬁt.
Repair is concerned with how violations of syllable structure are repaired in terms of epenthesis direction and the licensing of word edge extrasyllabic segments. I propose that catalectic moras are required to incorporate extrasyllabic material across the word. The Onset/Coda distinction can therefore be expressed as whether the extrasyllabic material is incorporated as the onset or coda of a syllable containing a catalectic mora. Epenthesis occurs where the catalectic mora is not permitted to surface without overt segmental material. The diﬀerence between domain edge behaviour therefore follows from this — where the catalectic mora is the peripheral element, the surface cluster is permitted; but where it is non-peripheral, epenthesis occurs as the catalectic mora is ﬁlled by an epenthetic vowel. ‘Extreme’ Onset/Coda varieties are those that permit catalectic moras word-internally in domain edge syllables.
Furthermore, I explore the prosodic word structure of Arabic, ﬁnding that there is a preference for aﬃxes to attach after a stressed syllable that accounts for lengthening phenomena and apparent stress exceptions.
This thesis demonstrates that there are constraints on both the input and output of the phonological grammar, and that the variation rests on the acceptability or violation of the constraints. Thus, the Arabic typology emphasizes two aspects: ﬁrst, variation in phonology is not just on the surface, and second, abstract quantitative analyses including catalexis are fundamental to our understanding of how prosodic structure can survive across a range of dialects.

Keywords: phonology
linguistics
arabic
affixation
metrical structure
stress
prosody
syllable
Advisor: Lahiri, A
Digital re-enchantment: tribal belonging, new age science and the search for happiness in a digital detoxing community

Our digital era is no less “human” or “authentic” than any other time in history, yet many people feel that the opposite is true. This study investigates Camp Grounded’s digital detox and summer camp for adults as an example of the “social fact” of anti-tech narratives, and as an opportunity to better understand how we live with technology today.
Why do people attend a digital detox, and what happens when they return to their digital lives? This ethnography of a digital detoxing community views detoxing as a symptom of Weber’s “disenchantment,” an isolating and meaningless modern existence, which can be countered through New Age “re-enchantment.”
At Camp Grounded, digital detoxers hope to recreate the experience of tribal life, using imaginaries of neuroscience to envision the dangerous, unnatural, and “disenchanted” world they live in. At camp, detoxers feel a spiritual connection to nature, to each other, and a deeply rooted sense of belonging to the human race. Returning to their digital lives after their time in the woods, digital detoxers are inspired to prioritise their personal growth and happiness.
This research explores how people can have their own understandings of categories like “use" and "non use" of technology, how science is used and misused by people in everyday life, and the ways in which people imagine technology to be harmful.

Keywords: psychology
wellness
mindfulness
enchantment
digital anthropology
new age spirituality
california
community
social media
technology
neuroscience
digital detoxing
mental health
ethnography
digital detox
disenchantment
new age
san francisco bay area
Advisor: Eynon, R
Old wine in new bottles: a review and analysis of the long shields model- a traditional concept adapted to mitigate human-lion conflict

Conflict with humans over livestock is a major threat to lion (Panthera leo) populations across their range in Africa. Lions kill livestock, a major source of livelihood for marginalised communities, and farmers kill lions in return. How to effectively mitigate this conflict remains a major conservation challenge till this day. In this thesis, I evaluate the effectiveness of the Long Shields Community Guardian programme (in short: Long Shields programme), a community-based, non-lethal human-lion conflict intervention that seeks to mitigate the impacts from lions by encouraging farmers to adopt behaviours that reduce the risk of livestock depredation. Specially, I examine (a) baseline attitudes towards lions and lion conservation; (b) attitudes towards lions before and after the implementation of the Long Shields programme; (c) trends in livestock losses to lions before and after the implementation of the Long Shields programme, and (d) barriers that prevented the adoption of the Long Shields programme. My results reveal that farmers’ attitudes towards lions are strongly negative and seem to be influenced by perceived losses rather than the actual losses to lions. Attitudes varied based on the geographic location where the farmer lived as well as the farmer’s ethnic group (Chapter 2). Subsequently, I detected a positive shift in attitudes of farmers that were part of the Long Shields programme (i.e., treatment group), including those that were part of the control group but exchanged information with their peers in the treatment group, than those of farmers in the control group (Chapter 3). My results also revealed that farmers that were part of the Long Shields programme experienced a significant reduction (up to 40%) in livestock loss to lions since the start of this programme in 2013, compared to the period 2008-2012 before the programme was initiated, while livestock losses increased for farmers that were not part of this programme. The number of lions killed annually due to retaliatory killing by farmers also declined by 41% since the implementation of the programme in 2013 (Chapter 4). My results also revealed that although the Long Shields programme was effective and well perceived by the majority of participants, a minority of farmers in the programme area continued to suffer higher livestock losses to lions than did others. Continuance of higher livestock losses to lions, despite all efforts from the programme personnel, seemed to be influenced by various barriers such as poor communication, negative attitudes towards the programme, and lack of trust in the programme itself, and in some cases, the programme personnel (Chapter 5). Although here we focus on human-lion conflict, our evaluation design and overall findings are applicable to other human-carnivore conflicts situations in other areas.

Keywords: Zimbabwe
Long Shields programme
Impact-evaluation
Human-lion conflict
community-based programme
Advisor: van der Meer, E
Macdonald, D
Loveridge, A
To piperidines and beyond

This thesis describes the development of synthetic routes to investigate the relative and absolute stereochemistry of a number of piperidine alkaloids isolated from Microcos Paniculata. This thesis then goes on to explore an intramolecular Diels-Alder reaction, and explores its applicability to natural product synthesis.
Chapter 1 introduces the biological significance of piperidine alkaloids, followed by a brief review of noteworthy chemical syntheses of piperidine and (piperidine-containing) natural products.
Chapter 2 describes the isolation of Microcosamine A, and previous synthetic efforts towards the alkaloid. The chapter then describes the development and optimisation of a synthetic route to the alkaloid, culminating with independent verification of its relative and absolute configuration.
Chapter 3 describes the isolation, synthesis, and independent assessment of relative and absolute configuration of Microgrewiapines AꟷC, natural products from Microcos Paniculata.
Chapter 4 presents corrected 1H NMR data for the originally isolated sample of the alkaloid microconine. The asymmetric synthesis of the two C(3) epimeric forms of this compound are presented which allow the unambiguous assignment of relative and absolute configuration.
Chapter 5 describes the exploration of an intramolecular Diels Alder reaction using substrates derived from the amine ring opening of benzene oxide. Initial experiments use N-substituted allyl amines, which perform a ring opening and spontaneous cycloaddition in 1 step to yield racemic tricycles. Later an enantiopure route is developed utilising ring opening with a chiral amine.
Chapter 6 contains full experimental procedures and characterisation data for all compounds synthesised in Chapters 2–5.

Advisor: Davies, S
Russell, A
Understanding convolutional neural networks

In the past decade, deep learning has fueled a number of exciting developments in artificial intelligence (AI). However, as deep learning is increasingly being applied to high-impact domains, like medical diagnosis or autonomous driving, the impact of its failures also increases. Because of their high complexity (i.e. they are typically composed of millions of parameters), deep learning models are difficult to interpret. Thus, there is a great need for tools that help us understand how such models make their decisions. In this thesis, we introduce several methods for understanding convolutional neural networks (CNNs), the class of deep learning models that is typically applied to visual data — i.e. images and videos. Our techniques span three approaches to understanding a model: 1. describing the relationship between its inputs and outputs; 2. characterizing correlations between a model’s inputs and its internal representation; and 3. using visualization tools to easily and efficiently explore aspects of a model.
First, we tackle the attribution problem of identifying the parts of a model’s input (i.e. image regions) that are most responsible for its output decision. We present two techniques — meaningful perturbations and extremal perturbations – which work by perturbing the input image and learning the regions that when edited out, most affect the model’s prediction. Second, we seek to understand how semantic concepts, from different kinds of textures to various kinds of objects, are recognized by network parameters (a.k.a. neurons). We introduce Net2Vec, a novel paradigm that reveals how combinations of internal neurons encode specific concepts. Lastly, similar to how a stethoscope is used to explore the internal behavior of different parts of the body, we introduce a novel visualization technique — interactive similarity overlays — that allows an AI researcher or developer to quickly and easily explore the internal representation of a model. Together, these methods enable us to scientifically understand the external behavior of CNNs as well as their inner workings.

Keywords: explainable AI
interpretability
artificial intelligence
machine learning
computer vision
Advisor: Vedaldi, A
Weighing supermassive black holes with molecular gas kinematics

Supermassive black hole (SMBH) masses correlate tightly with various properties of their host galaxies, implying close co-evolution. However, the mass measurements underpinning this conclusion have large uncertainties and are limited by selection biases. With the advent of modern millimetre/sub-millimetre interferometers, molecular gas dynamics are now suitable tracers of the SMBH-dominated regions of galaxy potentials.
In this thesis, I present new mass measurements for the SMBHs in the nuclei of the local elliptical galaxies NGC 524 and NGC 7052. These measurements exploit exceptionally high angular resolution observations of carbon monoxide (CO) J=2−1 emission using the Atacama Large Millimeter/sub-millimeter Array (ALMA). I refine earlier dynamical modelling methods, allowing for non-axisymmetric gas distributions and accounting for previously underestimated formal uncertainties when fitting models with very large numbers of constraints. The measurement in NGC 524 is consistent with an earlier stellar dynamical measurement, while that in NGC 7052 shows that an earlier gas dynamical measurement underestimated the SMBH mass (possibly by neglecting pressure support). The dynamical models of these galaxies also reveal a small inflow/warp in NGC 524, and that the central hole in NGC 7052 is consistent with the region within which tidal forces disrupt molecular clouds.
Using spatially-integrated CO spectra from both single-dish telescopes and interferometers I further show a correlation exists between large-scale CO emission line widths and SMBH masses. This new correlation is no less tight than most, allowing it to be used to estimate SMBH masses in the absence of the (often harder to obtain) data required to exploit tighter correlations.
Finally, I discuss the dynamical features revealed in new ALMA observations of 11 other SMBH mass measurement candidate galaxies, and estimate the SMBH masses in the three most promising.
This thesis demonstrates the potential of molecular gas dynamics to advance our understanding of SMBH–host coevolution, and indicates the next steps in understanding the molecular contribution to AGN fuelling and feedback.

Keywords: Interstellar medium
Supermassive black holes
Galaxy kinematics
Millimetre astronomy
Galaxies
Interferometry
Galaxy evolution
Advisor: Bureau, M
Improving morphological awareness: Can direct instruction of morphological components and structures improve the quality of KS3 students’ writing in English?

Over the course of my teaching career, I have observed that in order to excel in English, the ability to expressively use a nuanced and wide vocabulary is fundamental. However, in my experience, many students’ expressive vocabulary knowledge is lacking, meaning that they cannot express themselves in writing with precision, or critique literature with the flair and nuance expected to access higher attainment scores and grades. Students’ work often relies on the use of the same turns of phrases or repeated sentence stems which have been taught as scaffolds and thus when writing, these stock phrases limit the students’ ability to creatively express themselves or their literary interpretations. In order to address this, my research explores the use of morphology as a means to unlock access to a wider range of vocabulary for students to use in their writing and to improve their knowledge of the way morphological components work in order to foster ‘word consciousness’ (Graves, 2016). Carlisle et al (2010) maintain that there has been a ‘growing interest in the role of morphological awareness in literacy acquisition’ (p. 464) but at the same time it is clear that the role that vocabulary, and I would argue specifically knowledge of the morphological components of English plays in the quality of students’ written compositions has received little attention particularly in the secondary school context (Olinghouse & Wilson, 2013).
To address this, my research consisted of an intervention of one lesson per week for all Key Stage 3 students. Each lesson focused on the use of either affixes or roots which were linked by a common theme. To assess the impact of the intervention, I used pre-intervention summative assessments which were compared with post intervention summatively assessed work. Additionally, I used online questionnaires to gather qualitative data about the intervention from students and staff. Overall, the intervention was designed to ‘heighten students’ awareness of the morphological structure of words’ (Carlisle, McBride-Chang, Nagy, & Nunes, 2010, p. 478) in order to determine whether this can have a significant impact on writing performance.
The results of the intervention were mixed and superficially did not have the impact I had hoped in terms of an improvement in the summative assessment data. Despite this, the general attitude from the students towards the intervention was positive and succeeded to a certain degree in terms of raising ‘word consciousness’ and a general interest in morphology. I recognise that there is still more to do in this area of research and would advise a longitudinal approach to a study of the link between morphological awareness and its impact on writing in the future.

Keywords: MLT 2020
MLT
Investigating the effects of IFNγ signalling on transcriptional, epigenetic and enhancer landscapes

IFNγ signalling can have contradictory roles in a tumour microenvironment. Predominantly, IFNγ has an anti-tumour function, activating the immune system against the cancer. However, pro-tumour activities of IFNγ have also been observed. Its choice between the two opposing outcomes appears to be context dependent and the mechanism instructing this choice isn’t well understood. One prevailing determinant comes from the IFNγ-induced upregulation of PD-L1, an immunosuppressive ligand. Binding of PD-L1 to its receptor, PD-1, inhibits immune cells despite the presence of other activating signals, enabling cancer immune evasion. Increased knowledge of IFNγ-induced gene expression within cancer cells, including the regulation of PD-L1, would enable a more accurate prediction of IFNγ’s behaviour in the tumour microenvironment.
This thesis examines the effect of IFNγ signalling on the transcriptional, epigenetic and enhancer landscape in a hepatocellular carcinoma cell line, Hep3B. Using a variety of genome-wide sequencing techniques, I find that IFNγ orchestrates differential gene expression and enhancer activity dynamically in at least three distinct phases within 24 hrs of treatment. IFNγ treatments were found to regulate more enhancers than genes, with a large proportion of these enhancers becoming primed but not fully activated. Capture-C, a 3C based technique, revealed that IFNγ treatments significantly increase promoter:enhancer interactions, adding a further level of gene regulation.
IFNγ treatments induced upregulation of PD-L1 in Hep3B cells. Capture-C revealed that the PD-L1 promoter interacts with the closest neighbouring promoter and a CTCF site downstream of the gene. Neither of these interactions appeared to regulate IFNγ-induced PD-L1 expression. Instead, this thesis proposes that the proximal promoter may be sufficient for IFNγ-induced upregulation of PD-L1. Altogether, this study increases our understanding of IFNγ-induced gene regulation.

Keywords: gene expression
regulatory elements
IFNγ
enhancers
PD-L1
Advisor: Mellor, J
Atomic force microscope-based methods for the nano-mechanical characterisation of hydrogels and other viscoelastic polymeric materials for biomedical applications

Hydrogels, porous hydrated polymeric materials, are being increasingly used in biomedical applications. The mechanical properties of hydrogels play an important role in the success of many of these applications (e.g. tissue engineering and drug delivery), and can be modulated by external stimuli and/or by changing hydrogel structure and composition. Therefore, it is important to measure and understand these mechanical properties at cellular length scales (nano/micro-scale) to improve the efficacy of hydrogels in biomedical applications.
Hydrogels are often studied in terms of their elasticity. In this thesis, elastic properties of hydrogels were studied in terms of their elasticity via Atomic Force Microscopy (AFM) quasi-static micro-indentations. It is important to consider that hydrogels are not just elastic, but exhibit viscoelasticity, a time-dependent mechanical behaviour typical of hydrogels and polymeric materials in general. In this thesis, a novel AFM-based technique was developed to measure nano/micro-scale viscoelasticity.
First, changes in the local elastic properties of chitosan (a biopolymer) hydrogels in response to an external magnetic field were measured, demonstrating magneto-mechanical coupling. Second, this coupling was further explored by incorporating magnetic nanowires into the hydrogels. Both experiments suggest this coupling could be exploited to control hydrogel mechanics. Third, elasticity of hydrogels based on fullerenes was measured, and depended on the size of the fullerene used. Hydrogel elasticity in all three experiments matched that of biological tissues, suggesting biomechanical compatibility. The possibility of controlling hydrogel properties either by external stimuli or by composition, opens the door for all three of these materials to be used for therapeutic applications. Lastly, a novel technique based on photothermal excitation of the AFM cantilever was developed and proved to quantify viscoelasticity of polymeric materials over a frequency range up to five orders of magnitude (0.2 Hz to 20200 Hz), in good agreement with macroscopic data, revealing a promising tool for the viscoelastic characterisation of hydrogels.

Keywords: magneto-mechanical coupling
fullerene
polymeric materials
mechanical properties
AFM
viscoelasticity
hydrogels
biomedical applications
atomic force microscopy
elasticity
polymers
chitosan
Advisor: Antoranz Contera, S