VictorJuiz/thesis huggingface dataset:
Understanding the role of Toll signalling in Drosophila midgut stem cell proliferation.
Keywords: notch signalling
microbiome
toll signalling
gut immunology
dysplasia
immunofluorescence
intestinal stem cells
innate immunity
drosophila
JNK signalling

The intestinal epithelium is a site of complex interaction between microbiome, epithelial cells, and the immune system through a multidirectional crosstalk achieved using signalling molecules and metabolites secreted by the microbiome and host cells. This cross talk maintains epithelial turnover and the gut microbial population while integrating nutrient absorption and host defence. In this context, innate immune pathways have been extensively studied to understand their role in the maintenance of microbial and epithelial homeostasis and to study the response against infections and stress. In mammals, Toll-Like Receptors (TLRs) have been widely researched for their role in maintaining the commensals and influencing the epithelial regeneration. However, the complexity of mammalian systems and inability to standardize the models makes it challenging to study interactions of TLRs with different pathways in the gut. The immune and developmental pathways involved in epithelial plasticity are evolutionarily conserved. Therefore, using Drosophila melanogaster as a model organism, we aim to understand the role of Toll signalling in regulating epithelial turnover during infection. To this end, we used a constitutively active form of Toll receptor to mimic Toll activation. Our results reveal that, the canonical Toll pathway was involved in the intestinal stem cell (ISC) proliferation. It also led to the enteroblasts getting blocked from differentiating and/or (mis)differentiating that caused accumulation of esg+ cells in the gut resulting in dysplasia. We found that the Jun N-terminal kinase (JNK) pathway was acting downstream of Toll in mediating Toll-induced dysplasia. Moreover, the developmental pathway Notch, had a potential antagonistic role upstream or in parallel to the Toll pathway. Taken together our results place Toll as the signalling element to integrate epithelial renewal and immune response.
“Girls should be ready for anything”: time, learning and aspiration among hostel girls in Lahore  
Keywords: girls
hope
hostel
migration
adolescence
aspiration
women
Pakistan
uncertainty

This thesis explores the lives of a group of young, middle-class women living in a privately-run girls’ hostel in Lahore. The key question that this thesis seeks to address is the meaning of this stage in the lives of young women. A temporary period of accommodation in an urban hostel while studying is increasingly conceptualised as part of the life course for middle-class young women, bracketed by childhood in the natal household and married, virilocal adulthood. What does it mean to move to the city alone as a young Pakistani woman, and how do these women understand the experience of being a ‘hostellite’?
Based on nearly nine months of close-range participant observation, I tell the stories of some of the women who lived alongside me in the hostel. I describe how the journeys they make from rural areas to the city become conceptualised as journeys from asynchronous cultural ‘backwardness’ to a distinctively gendered and classed modernity, embodied in bodily techniques, cultural competencies and practices of consumption. Against global narratives celebrating the liberatory potential of education and work for supposedly constrained and oppressed Muslim women in the Global South, my thesis shows the pressure placed upon these subjects in the process of becoming groomed, as they experience hardship, humiliation and loneliness and learn to cultivate endurance (bardasht) and patience (sabr) as key attributes of hostellite life.
In this thesis I reflect critically upon the ethical and methodological decisions that have influenced my research practice, particularly in the context of the Covid-19 pandemic. I seek to show how these issues have influenced my research and writing, and how questions of absence, incompleteness and ethical refusal have shaped my thesis.
Imagining Germany abroad, c. 1920-1950. Women writers, photographers, exiles, Nazis
Keywords: Nazi Germany
subjectivity
gender
Weimar Republic

This thesis explores the lives of a small selection of individual German women who pursued professions as writers, journalists, or photojournalists, and whose work saw them spend significant periods of time abroad between 1920 and 1950. These women were unalike in important ways: they held diverging political beliefs, pursued different personal and professional goals, and travelled abroad in contradictory directions. At the same time, they shared a strong sense of independence and individuality, unanimously considered themselves to be modern women, and were each committed to their own imagined version of the German nation.
I argue that centring the individual and subjective experiences of these heterogeneous women highlights the extent to which they remoulded abstract cultural frameworks, especially gender and national identity, first and foremost to suit their own purposes. Those purposes varied widely, but in their shared insistence on individuality, independence, and social relevance, they revealed themselves to be part of a fluid and emerging cohort of emancipated women who were aware of being unconventional, but who nonetheless had a wide range of complex possible life paths to choose from. Their loyalty to imagined versions of German modernity was paramount to their otherwise malleable sense of nationhood because it created openings they might not have found otherwise and bestowed external meaning on their choices. They thus often looked towards the future more than they did the past. At the same time, that the lives these women chose to live were available to them was due to their privileged social background and liberal education more than to contemporary events.
The research project is important, because it probes the complex relationship between individuals and their wider cultural context without flattening out either personality or agency. Especially in the case of Nazi Germany, the question of how cultural context and individual subjectivities intersect is one that continues to excite scholarly interest.
Generalisation and expressiveness for over-parameterised neural networks
Keywords: generalisation bounds
expressiveness
over-parameterised networks

Over-parameterised modern neural networks owe their success to two fundamental properties: expressive power and generalisation capability. The former refers to the model's ability to fit a large variety of data sets, while the latter enables the network to extrapolate patterns from training examples and apply them to previously unseen data. This thesis addresses a few challenges related to these two key properties.
The fact that over-parameterised networks can fit any data set is not always indicative of their practical expressiveness. This is the object of the first part of this thesis, where we delve into how the input information can get lost when propagating through a deep architecture, and we propose as an easily implementable possible solution the introduction of suitable scaling factors and residual connections.
The second part of this thesis focuses on generalisation. The reason why modern neural networks can generalise well to new data without overfitting, despite being over-parameterised, is an open question that is currently receiving considerable attention in the research community. We explore this subject from information-theoretic and PAC-Bayesian viewpoints, proposing novel learning algorithms and generalisation bounds.
A fluid-solid coupled heat transfer methodology as applied to rotating cavities
Keywords: computational fluid dynamics
turbulence modelling
rotating cavities
conjugate heat transfer
large eddy simulation

Conjugate heat transfer (CHT), which captures the thermal interaction between the fluid and solid domains, is important for an accurate computational aerothermal analysis when there are temperature dependent fluid domain physics. In the rotating cavities in compressor internal air systems, there is a need to understand the unsteady buoyancy-driven flow and heat transfer so that the disk radial expansion (and hence change in blade tip clearance) throughout the flight cycle can be predicted. Despite the inherently conjugate nature of rotating cavity flows, coupled analyses are rare due to the challenges of using CHT with unsteady methods.
In this thesis, it is shown that it is necessary to use wall-resolved large eddy simulation (LES) to accurately capture the fluid domain flow structures, and to use CHT to capture the interaction of the wall heating conditions and the cavity aerodynamics. The main challenge in LES-CHT is that the timescale in the solid is significantly larger than in the fluid. Many current state-of-the-art methods try to address this by accelerating the solid domain timescale to achieve a temporally converged solution, before switching to a non-accelerated solid solution that is assumed to be correct. However, this is not the case - it is demonstrated in a simplified conduction analysis that these current time domain CHT methods still introduce a long-lasting error in the solid domain temperature.
As a result, a new multiscale framework for LES-CHT has been developed, building on an existing closely coupled methodology. Non-local interactions from coherent low frequency temperature fluctuations are calculated with a time-spectral solid domain solution and turbulent higher frequency fluctuations are accounted for using a wall transfer function approach, reformulated to simplify its application. This is the only framework that can consistently deal with the fluid-solid timescale disparity and capture all timescales of wall temperature fluctuation.
The novel framework is used in first-of-their-kind LES-CHT computations on rotating cavities, evidencing framework efficacy and providing further evidence of the previously observed issues with other LES-CHT methods. An examination of the effect of CHT on the flow structures within the rotating cavity found that thermally induced near-disk vortical instabilities are seen to only form when there is strong local heating. This effect has not been previously observed and illustrates the value of the multiscale framework for deriving new insights into heat transfer in gas turbines.
Gradient accelerated cosmology
Keywords: statistical inference
gaussian processes
auto-differentiation
cosmology
angular power spectra
Hamiltonian Monte Carlo

Cosmology is currently sitting on a ticking time bomb that will result in an unprecedented explosion in the quantity and quality of data. In preparation, physicists are starting to incorporate into their theoretical predictions more of the physical, observational and instrumental effects which, until now, could be overlooked. In practice, this translates into a dramatic increase in the number of parameters that future analyses will have to consider. This combination of large data sets with complex models will (and in many cases already does) overwhelm the inference methods we currently use to constrain the values of these parameters. In this thesis, we propose two solutions to this problem. First, we show how gradient-based inference algorithms can dramatically speed up the numerical marginalisation of high dimensional parameter spaces. Second, we show how analytical marginalisation schemes, such as the Laplace ap- proximation, can achieve similar speed increases. Crucially, both these methods rely on having access to computationally affordable gradients of the cosmological models, stressing the importance of developing differen- tiable analyses pipelines for future cosmological surveys.
A critical-ethical politics for transnational commercial English language teaching: conjectures, contradictions, affects, and possible just futures
Keywords: reparative justice
English language teaching
gig work
social justice
platform economy
racial capitalism
semiotics
colonial capitalism
language ideologies
Filipino English teachers
commercial ELT
transnational labour
ELT

This thesis aims to promote a critical-ethical politics for transnational commercial English language teaching. This type of politics seeks to liberate TESOL researchers and practitioners from the ‘totalising system’ (Dussel, 2013) that continues to model English language education after the ‘hegemonic ontology’ or normative ideal: the white/Anglo-American/native English speaker, which reflects deep-seated colonial and racial logics and inflicts a range of material, epistemic, and affective injustices on language-minoritised racialised communities. The study that I present here focuses on a particular community of English language users, i.e., Filipino English teachers, the cost-effective and cost-efficient lifeline of the lucrative multi-billion dollar English language education market in East and Southeast Asia. These teachers tread a very fine line between privilege and marginalisation, and experience day-to-day exclusion and oppression by virtue of their ‘non-nativeness,’ nationality, racial background, and skin colour.
The study was carried out via year-long online fieldwork in the Philippines, which involved compiling and analysing a corpus of online publicity, marketing, and lesson materials from 37 ELT platforms, and semi-structured interviews with 50 Filipino English teachers. I adopted an abductive and interpretive approach to data analysis that I call critical-ethical semiotics, which involves the metasemiotic construal of the teachers as a starting point or site of ideological work (Gal & Irvine, 2019). This approach, commensurate with de-coloniality (Quijano, 2000a,b; Grosfoguel, 2011), Marxist (Simpson, 2023), critical post-structuralist (Chong, 2009; Flores & Rosa, 2015; Tajima, 2018), and trans-ontological perspectives (Dussel, 2013; Táíwò, 2022a), allows for the critical and ethical examination of the hegemonic ontology, as it were, from the outside (Mills, 2018). It is my hope that the critical-ethical perspectives and approaches developed in this study will help forge a new pathway forward in TESOL – one that will lead us towards a more just and sustainable future for language education.
Regeneration of the cardiac conduction system
Keywords: Remodelling
Electrical Conduction
Connexin
Single-cell RNA-sequencing
Arrhythmia
Heart Regeneration
3D Imaging
Myocardial Infarction
Purkinje

Arrhythmias are a hallmark of myocardial infarction (MI) and increase mortality risk for patients. The cardiac conduction system is increasingly implicated in arrhythmias but how it is altered following MI is not well understood. I hypothesised that there is an impairment of the conduction system in adult infarcted hearts whereas it is rapidly restored in regenerative neonatal hearts to maintain normal rhythm.
In this thesis, I demonstrate complete conduction system restoration during neonatal mouse heart regeneration, versus pathological remodelling at non-regenerative stages that map onto the adult heart wound-healing response. By developing tissue-cleared whole- organ imaging and analysis approaches, I initially performed the first description and quantitative characterisation of the intact 3D architecture of the post-natal murine ventricular conduction system. Next, following MI injury, I identified global disruption to the His/Purkinje network, disorganised bundling of conduction fibres and regional loss of connexin-40 one week after birth which contrasted with regeneration of the network and restoration of fibres at immediate post-natal stages. Enriched single-cell RNA-sequencing revealed distinct transcriptional signatures of infarcted regenerating versus non-regenerating conduction cells. I identified that conduction cells undergo transition at a transcriptional and protein level to regenerate the network, as compared to sustained electrical alterations during fibrotic repair. I found that this manifests functionally via transition from normal rhythm to pathological conduction delay beyond the regenerative window. Finally, modelling the non- regenerative phenotype in the infarcted human heart implicated these changes as causative for bundle branch block and increased dyssynchrony of ventricular contraction, as is observed in MI patients.
Collectively, the findings of this thesis characterise conduction system growth and maturation following birth, identify pathophysiological electrical remodelling in the His/Purkinje network after MI, elucidate the cellular and molecular profiles of the regenerating conduction system, and demonstrate the consequence of MI-induced conduction system damage for clinical arrhythmogenesis.
When rebels turn protesters: demobilized insurgents and social uprisings in Colombia
Keywords: Farc
protests
social movements
paro nacional
rebel politics
peace process
contentious politics
Colombia

Following civil conflict peace agreements, societies often continue to experience political volatility. Cleavages that provided reasons for some society segments to seek armed action may still exist, and violence might have increased political polarization. Consequently, peace process societies often face diverse expressions of discontent, including mass protests. This raises the question of if and how demobilized armed group members behave in such protests. Are they willing to participate and use protests as a new form to articulate their interests and political demands? What implications does their participation have for protest dynamics and political stability? How does the rest of society react to such protest participation?
This thesis explores these questions by examining the participation of demobilized members of the FARC guerrilla group in Colombia during mass protest waves following the country's 2016 peace agreement. The thesis contains three research articles. Article 1 is theory-testing and explores through qualitative field research in Colombia, including 94 interviews, to which extent existing social movement theories explain variations in former rebels' participation during mass protests, finding that existing links to protesting communities, integration into networks of former comrades, and perceived security risks had the most influence on former rebels' mobilization decision. Building upon the same 94 interviews, Article 2 is theory-building and examines the implications of former FARC rebels' protest participation, finding that their involvement reduced violence levels, enhanced their societal reintegration, and led to a professionalization of the protests. Finally, Article 3 provides an online survey experiment to assess how the protest participation of former FARC members and alleged links to vandalism alter public opinion, finding that former rebels' involvement reduces public support for protests but that vandalism weighs heavier. The analyses speak to the social movement and demobilized rebel literature and highlight the benefits of bridging these two literature streams.
Simulating chemical reactivity using machine learning potentials and umbrella sampling
Keywords: ACE
Python
umbrella sampling
machine learning potentials
molecular dynamics

Dynamic simulations of reactions enable prediction of mechanisms and explanation of chemical phenomena. Traditional methods of simulation include ab initio molecular dynamics (AIMD), which is generally accurate but expensive, and force field methods, which are fast but often unsuitable for exploring bond breaking or forming processes. Machine learning potentials (MLPs) have emerged as a promising tool for exploring dynamics at the accuracy of quantum mechanics and a fraction of the cost of AIMD. However, training often requires many data points and expert knowledge. In this thesis, we introduce strategies to efficiently train and use MLPs to study a range of chemical processes, utilising and extending the umbrella sampling (US) methodology. Chapter 2 presents a training strategy for the generation of MLPs along with the gap-train and mlp-train Python packages developed during this thesis, which automate training and enhanced sampling. In Chapter 3, we illustrate the use of the ACE MLP to study terpene reactions. The generated MLPs accurately predict free energy and product ratios, providing good agreement with experiment and previous computational studies. We explore a proposed bifurcation of a sesquiterpene, using MLPs to confirm its existence. Nuclear quantum effects are introduced using path integral molecular dynamics and MLPs, highlighting examples where quantum dynamics affect the free energy and product ratios in hydrogen migration reactions. Chapter 4 presents a series of metrics to quantify the convergence and overlap in US. We study the influence of overlap on free energy for analytic, MLP and protein systems, finding an overlap of 15% is sufficient to converge free energy. Finally, in Chapter 5, attempts to develop an adaptive US scheme are presented, along with a Python package, adaptiveus, to automate the process.
Wide-bandgap halide perovskite materials for photovoltaic and optoelectronic applications
Keywords: atomic layer deposition
degradation
light-emitting diode
pinhole
solar cell
lead
photovoltaic
selective
formamidinium
bromide
optoelectronic
perovskite
cesium
iodide
ALD
LED
halide

With increasing global surface temperatures due to greenhouse gas emissions from human activity, the global society is in urgent need of pivoting the energy system towards low or zero-emission energy sources. Photovoltaic solar energy has the potential to deliver substantial emission reductions and is expected to make up a major portion of the energy mix in the remainder of the 21st century. Over the last decade, halide perovskite materials have shown great promise in bolstering and diversifying photovoltaic solar technologies, as well as the potential for efficient and colour-pure light-emitting diodes.
Leaps of progress have been made on halide perovskite-based single-junction and tandem solar cell technologies, but triple-junction solar cells, which theoretically could provide an even higher power conversion efficiency, are still in the infancy. For mainly perovskite-based triple-junctions to reach the highest realistic power conversion efficiencies, top cell bandgaps in the range 1.95 to 2.05 eV are required. Herein, we review the achievements and progress that have been made on the topic of perovskite triple-junction solar cells and the important wide-bandgap (2 eV) top cell. We then go on to characterize our FAPb(Br0.7I0.3)3-based 2.0 eV single-junction solar cells. We identify the main reasons for VOC-loss in these cells and look into the effect of halide segregation on the performance. Finding that nonradiative recombination in the bulk is the main cause of VOC-loss and that halide segregation may be significantly more detrimental to the JSC than the VOC. Further, we investigate halide segregation and degradation trends in isolated films of this 2 eV material under the influence of different atmospheres. We observe untypical wavelength-shifts in the photoluminescence spectrum which may be linked to iodide-depletion under light exposure.
Finally, we improve the performance of our green perovskite LEDs by introducing a novel composite p-contact comprising the organic hole-transporting polymer TFB deposited by solution processing and Al2O3 deposited by atomic layer deposition. Due to the different chemical reactivity of the trimethyl aluminium precursor of the ALD process towards the oxide surface groups and the TFB polymer, the Al2O3 has the dual function of being able to insulate any bare patches of the underlying transparent conducting oxide electrode, which were not adequately covered during the TFB processing, and intergrow in the porosities of the TFB layer and cause a swelling, further blocking any potential nonradiative recombination sites.