VictorJuiz/thesis huggingface dataset:
The function and evolutionary ecology of intra-sexual aggression in drosophila melanogaster
Keywords: drosophila
aggression

Across the animal kingdom, competition for reproductive resources often results in intra-sexual aggressive contests. The extent to which individuals engage in aggression varies in response to ecological conditions. However, as individuals live and compete in highly complex environments, understanding how aspects of an individual’s ecological surroundings shape aggression is a constantly advancing field with many unresolved questions. Furthermore, while much previous research has focused on male aggression, it is now acknowledged that females fight too, but whether female aggression reflects male aggression in its response to the environment is largely unknown. In this thesis, I use the fruit fly, Drosophila melanogaster, to investigate how the prevailing environment drives short term responses and long term evolutionary change in aggression in both sexes.
Sexual selection plays a key role in shaping traits involved in reproductive competition, such as aggression, and I begin by investigating how the sex ratio influences the operation of sexual selection in males, and whether these patterns are reflected in females. Traditional sexual selection theory predicts that as the sex ratio becomes more biased, the abundant sex should experience stronger sexual selection. I find support for this prediction in males, but, in females, I find sexual selection arising from mating competition to be weak and insensitive to the sex ratio, illustrating differences in intra-sexual competition in the two sexes. I then investigate how aggression evolves in response to the population sex ratio, and find that a male-biased sex ratio increases the propensity for males to focus aggression around food patches but does not influence male aggressive intensity, while a female-biased environment increases the magnitude by which mating elevates female aggression.
Furthermore, kin selection has the potential to shape aggressive interactions, and high population relatedness can reduce harmful aggressive behaviours. I find some evidence that high relatedness can reduce harmful behaviours in D. melanogaster, but find this response to be highly sensitive, with no evidence that it is driven solely by olfactory-based discrimination. Finally, I show that nutrition can determine aggressive ability and motivation, with aggression decreasing in response to food deprivation during development but increasing in response to adult food deprivation.
Sustainability reconsidered: an ethnography of natural dyeing in contemporary Japan
Keywords: Japan
material culture
sustainability
visual anthropology
natural dyeing
Oshima Tsumugi
textiles

Based on twelve months of fieldwork with dyeing craftspeople on the biodiverse island of Amami Ōshima in southern Japan, this thesis explores the complex, often contradictory, intertwining of preservation practices, resource extraction, and access to land that define local relationships with the natural environment. It thereby aims to question widespread discourses about sustainability that assume that small scale ʻtraditionalʼ craft is low impact and therefore more environmentally sustainable. Using apprenticeship methodologies, I reveal that Amamian craft producers are subject to social, economic and bureaucratic pressures, precarities and hierarchies that have equivalences to those widespread in industrial settings. Against a backdrop of uncertainty and instability, my research participants navigate geographically specific practices of ecological care, foraging, cultivating, processing and dyeing and temporally specific experiences of labour migration and lifestyle aspiration. By focusing on their dynamic relationship with local ecologies in order to produce (global) commodities, I was able to study sustaining processes in practice. This in turn forced me to rethink the ideology of sustainability and argue instead for a broader understanding of the extraction, life and value of materials. Value, in this formulation, is not only concentrated on the economic but distributed in ways that benefit the health of a wider conception of community, ecology and sustainability.
Virtually nilpotent mod-𝑝 Iwasawa algebras are catenary
Keywords: completed group rings
Iwasawa algebras
ring theory
noncommutative algebra
compact p-adic analytic groups
catenary rings

Fix a prime 𝑝 > 2. Let G be a nilpotent-by-finite compact 𝑝-adic analytic group, and k a finite field of characteristic 𝑝. We prove that kG is a catenary ring.
Regulation and role of TBX2 and TBX3 in tumour progression
Keywords: Cancer
Tbx3
Melanoma
Tbx2

TBX2 and TBX3 belong to the T-box family of transcription factors and are im- portant in embryonic development and tumourigenesis. Overexpression of TBX2/3 has been observed in several types of cancer, promoting tumour proliferation, senescence bypass and invasiveness.
Given their important contribution to tumour progression, it might be of therapeutic benefit to pharmacologically inhibit their expression for cancer treatment. To identify novel regulators of TBX2/3, we carried out a high throughput screen for FDA-approved drugs that could affect TBX2/3 expression and/or subcellular localisation using melanoma cells ectopically expressing TBX2/3. We identified hit drugs from the initial imaging-base screen and confirmed the results of selected compounds targeting calcineurin.
In addition to the regulation of TBX2/3 protein, to further understand their role in tumour progression, we undertook genome-wide ChIP-seq and RNA-seq experiments to identify potential target genes and explore functional implications. As there is a lack of ChIP-grade TBX2/3 antibodies, we tagged the endogenous proteins with 3xHA using the CRISPR/Cas9 system. The generated cell lines produced high-quality ChIP-seq datasets of TBX2 and TBX3 and revealed the repertoire of binding sites genome-wide. Surprisingly, TBX2 binds to not only T-elements as expected, but also to a subset of E-box sequences bound by USF2. Integrative analysis of ChIP-seq and RNA-seq datasets identified E2F1 as a novel target gene of TBX2 that promotes cell growth.
Last, but not least, we also identified novel cofactors of TBX2, with preliminary data suggesting that TBX2 represses gene expression by interacting with polycomb repressive complex 1, and may be converted to a transactivator when interacting with basis helix-loop-helix transcription factor USF2.
Testing theories of baroclinic adjustment in the laboratory and in simple atmospheric models
Keywords: baroclinic instability
planetary atmospheres
turbulence
geophysical fluid dynamics

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.
A phonological typology of modern Arabic varieties
Keywords: phonology
linguistics
arabic
affixation
metrical structure
stress
prosody
syllable

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.
Digital re-enchantment: tribal belonging, new age science and the search for happiness in a digital detoxing community
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

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.
Old wine in new bottles: a review and analysis of the long shields model- a traditional concept adapted to mitigate human-lion conflict
Keywords: Zimbabwe
Long Shields programme
Impact-evaluation
Human-lion conflict
community-based programme

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.
Understanding convolutional neural networks
Keywords: explainable AI
interpretability
artificial intelligence
machine learning
computer vision

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.
Weighing supermassive black holes with molecular gas kinematics
Keywords: Interstellar medium
Supermassive black holes
Galaxy kinematics
Millimetre astronomy
Galaxies
Interferometry
Galaxy evolution

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.
Improving morphological awareness: Can direct instruction of morphological components and structures improve the quality of KS3 students’ writing in English?
Keywords: MLT 2020
MLT

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.