VictorJuiz/thesis huggingface dataset:
Voices in the dark: energy and the politics of living in refugee camps

This thesis examines two central issues: firstly, how energy is valued and perceived by refugees and humanitarian practitioners, and, secondly, how energy is accessed and governed in refugee camps. It draws on empirical evidence collected from households, enterprises and humanitarian operations in Kenyan and Rwandan camps to argue that energy is of critical importance for refugee life. The thesis shows how energy is valued for social and practical reasons, with refugees often finding and securing their own access to energy. Small and informal enterprises within camps are the main providers of energy access for refugee homes and businesses, especially when institutional actors fail to meet needs. Within community facilities and humanitarian operations, provision of energy is intermittent and often absent. While refugee users and enterprises are aware of the value of energy, humanitarians undervalue its importance. Using a theoretical framing centred around the politics of living, the research critically questions the role of humanitarian agencies and argues that energy in camps is always political. In other words, humanitarians make choices about the distribution of resources and access to energy in a way that restricts energy activities and this has notably political effects.

Keywords: politics of living
forced migration
ethnography
renewable energy
refugee camps
Advisor: Eyre, N
Scott-Smith, T
The reality of Eternal Recurrence

This thesis presents a novel account of Nietzsche’s idea of Eternal Recurrence of the Same (ER). I argue that ER should be understood neither as theoretical cosmology, nor hypothetical thought-experiment, but as metaphysical interpretation of reality.
The thesis is composed of four chapters. In chapter 1 I argue that certain motivations underlying the consensus views on how to interpret ER are unfounded assumptions that need not be made. I discuss these motivations and their discursive consequences with a view to opening the way for metaphysical, non-theoretical understandings of ER. Thus, I dispel possibilities that ER is not literal by removing the assumptions I believe ground them.
In chapter 2 I examine Nietzsche’s attitude to science in order to show that his criticism for all theoretical science as an adherent of the ascetic ideal leads to the conclusion that ER could not be a theoretical account of the universe. Following from this, I argue that the unpublished “proofs” for ER and zeitatomenlehre note are not supporting a physical theory but are alternative experimental interpretations of reality set within a scientific paradigm.
In chapter 3 I move to an outline of Nietzsche’s metaphysical and interpretative way of understanding reality, specifically in relation to his appropriation of Heraclitan ideology to describe the world metaphysically, and use of Dionysos through a particular interpretative lens. I show that the Heraclitan and Dionysian are linked and are linked in relation to ER, pointing towards the sense in which I argue one ought to understand ER: as a metaphysical interpretation of reality, graspable only through the Dionysian perspective.
In chapter 4 I turn to a close exegesis of the key passages on ER to show that they evidence a metaphysical ER, set within Dionysian interpretation of reality. I argue that close analysis is required to draw out the way Nietzsche expresses the Dionysian interpretative nature of ER in vividly depicting the experience of coming to realise it.

Keywords: Eternal Recurrence
Reality
Metaphysical
Interpretation
Origin of science
Nietzsche
Exegesis
Intensity-dependent effects in the Accelerator Test Facility 2 and extrapolation to future electron-positron linear colliders

The high energy physics community considers electron-positron linear colliders in order to complement the results obtained at the Large Hadron Collider. In order to achieve the design luminosity above 1034 cm-2s-1, these linear colliders require a nanometer beam size at the Interaction Point (IP). The electron and positron beams are transported inside the Beam Delivery Systems (BDS) from the linear accelerators (LINACS) to the IP. The beam is focused by two strong quadrupoles in the Final Focus System (FFS) where chromatic effects and aberrations are corrected thanks to a local chromaticity correction scheme. Two projects are being studied now, the International Linear Collider (ILC) and the Compact Linear Collider (CLIC). Their FFS and the local chromaticity correction are being tested at the Accelerator Test Facility 2 (ATF2) at KEK in Japan. This test facility has been studying this matter for more than 20 years, achieving two of its main goals: obtaining a stable beam size around 37 nm at the IP and an orbit stabilisation with a nanometer precision at the IP. However, these goals were achieved at 10% of the nominal beam intensity. Indeed, when increasing the beam intensity, the beam becomes more unstable and its size grows. This is mainly due to wakefields in the ATF2 extraction line. Ultra-relativistic electrons going through the beam pipe interact with the surrounding structure and create an electromagnetic field, the wakefield. This field interacts with electrons inside the same bunch (short-range wakefield) but also with electrons in the following bunches (long-range wakefield). In ATF2, one considers that bellows, flanges and cavity BPMs are the main sources of wakefield. This effect results in increasing significantly the beam size at the IP. This thesis will show the impact of these intensity-dependent effects inside ATF2 and how to mitigate them. It will also show the impact of the same intensity-dependent effects in future electron-positron linear colliders, the ILC and CLIC.

Keywords: wakefields
CLIC
short-range
PLACET
CERN
ATF2
GdfidL
ILC
Intensity-dependent effects
long-range
Advisor: Burrows, P
The role of YAP and cell of origin during the progression of pancreatic neoplastic lesions to invasive ductal adenocarcinoma

Pancreatic ductal adenocarcinoma (PDAC) is considered one of the most fatal cancer types with a very low survival rate. The development of dysplasia in normal ductal epithelium is the initiating step of the disease, which then undergoes multiple grades of pancreatic intraepithelial neoplasia (PanIN) lesions before developing into invasive adenocarcinoma. KRAS mutations occur during early stages of malignant transformation and act as a critical event in both initiating and maintaining PDAC development. Alongside, an oncogene, YAP, is emerging to play a role in the facilitation of neoplastic precursor lesions to invasive cancer in KRAS mutated pancreas. Canonically, YAP’s activation is negatively regulated by the tumour suppressive Hippo pathway by inhibiting the protein’s nuclear localisation. In order to elucidate the mechanism by which YAP promotes early progression of PanIN lesions, I explored the association of YAP with the components of KRAS-mediated MAPK signalling pathway. Firstly, I show an association between YAP and phosphorylated ERK1/2 both in pancreatic cancer cells and low-grade PanIN lesions of Kras-mutated mice. In these PanIN lesions, I demonstrate the nuclear expression of YAP to be heterogeneous and associate this with PanIN lesions’ origin from different cell types. I show ductal-derived precursor lesions in Kras mutated mice and PDAC in human samples to positively correlate with high nuclear expression of YAP. To further understand this role of YAP in ductal-derived PDAC, I establish YAP depleted 3D pancreatic organoid system isolated from ductal cells of Kras mutated mouse pancreas. From this study, I present the potential role of YAP as a useful marker to identify ductal-derived PanIN lesions and PDAC.

Keywords: KRAS
pancreatic cancer
YAP
Pancreatic ductal adenocarcinoma
oncogene
Genetically engineered mouse model
Advisor: O’Neill, E
miRNA biogenesis and developmental phase transition in the liverwort M. polymorpha

microRNAs (miRNAs) are important regulators of gene expression and plant development. Some miRNAs, together with their target genes, have conserved functions among the major land plant lineages. An important miRNA-regulated developmental pathway is the ageing pathway that controls the juvenile to adult transition and the vegetative to reproductive transition in flowering plants. This thesis presents evidence that the function of HASTY (HST), a regulator of the ageing pathway through miRNA processing in the flowering plant Arabidopsis thaliana, is conserved in the bryophyte Marchantia polymorpha. MpHST negatively regulates the timing of the reproductive transition in male M. polymorpha, which is consistent with AtHST inhibiting phase transitions in A. thaliana. In contrary, MpHST positively regulates the reproductive transition in female M. polymorpha plants. This suggests a sex-specific function of MpHST in the dioecious liverwort and presents a new aspect of phase change regulation. This thesis also reports that another core regulator of miRNA biogenesis, DICER-LIKE 1 (DCL1), controls growth, morphogenesis and organ differentiation through miRNA processing in M. polymorpha, as it does in angiosperms. Moreover, a novel role was discovered for MpDCL1 – MpDCL1 represses the reproductive phase transition in the absence of the normally required far-red light inductive signal. This occurs in a sex-dependent manner – similar to the requirement of MpHST to delay phase transition in male plants, MpDCL1 represses phase change under non-inductive conditions in male plants. I propose that miRNAs, including sex-specific miRNAs, are involved in controlling phase change in the early divergent embryophyte M. polymorpha. This suggests that HST-regulated phase change operated in the common ancestor of liverworts and angiosperms, one of the first land plants.

Keywords: HASTY
M. polymorpha
rhizoid development
DICER-LIKE1
reproductive phase transition
miRNA biogenesis
gametangiophores
Advisor: Dolan, L
Degradation-aware optimal control of grid-connected lithium-ion batteries

With the accelerating deployment of intermittent renewable energy sources, the need for balancing on the power system is ever increasing. Even though lithium-ion (Li-ion) batteries are not yet cost-competitive with other solutions for most applications, the number of grid-connected Li-ion batteries is expected to increase sharply in the coming years.
Due to the sunk costs of the upfront investment, understanding the lifetime of a battery is crucial for the business case. Nevertheless, predicting the lifetime of a battery is not straightforward. Many degradation mechanisms reduce the total energy which can be stored in a battery, thus decreasing its lifetime. This thesis begins with an extensive literature review into the causes of this battery degradation, both qualitatively and quantitatively. Various physics-based degradation models are combined into one flexible battery degradation model which is used to study which mechanisms cause degradation under which operating conditions.
The model is then carefully formulated for optimisation in a power system application. While a battery makes revenue from trading power on the day-ahead market, it degrades. The physics-based model is used to optimise the usage profile of the battery, determining when to buy power (charging the battery) and when to sell (discharging the battery), in order to maximise revenue while minimising degradation. These optimal profiles are compared to profiles which are obtained using state-of-the-art economic optimisation models.
Finally, Li-ion batteries were cycled with different usage profiles in an experimental validation. The battery degradation was measured monthly, while the revenue each battery could make was also tracked. It is shown that the usage profiles determined by the physics-based model outperform the profiles from conventional optimisation models. The revenue can be increased by 17% while at the same time decreasing the degradation by 31%. This implies that such physics-based models can increase the revenue and the lifetime of grid-connected batteries, increasing the net profit by over 300%.

Keywords: Degradation
Techno-economic assessment
Optimisation
Lifetime prediction
Lithium ion batteries
Advisor: Howey, D
Mulder, G
Building synaptic plasticity rules that learn generalisation-apt neuronal architectures

One of the hallmarks of intelligent behaviour is the ability to generalise, i.e. to make use of information from specific experiences to solve unencountered scenarios. Here I focus on the generalisation task of transitive inference, which tests the ability to infer that stimulus A is preferable to C, based solely on previous training that A is preferred over B and B is preferred over C. Such inference tasks are thought to be performed by hippocampal-entorhinal circuits and rely heavily on recurrent and conjunctive connectivity to bind associated stimuli. Notably, a 3-layer recurrent neural network model called REMERGE (Kumaran & McClelland, 2012) can solve the transitive inference task through recall dynamics in a circuit that also relies on recurrent and conjunctive connectivity. However, it is not clear how the architecture could be constructed by a learning rule. Here, I develop a biologically plausible non-linear Hebbian plasticity rule to build REMERGE’s connectivity starting from an all-to-all architecture. I separate the problem of learning the complete architecture into two parts: 1 - how to learn input connections and 2 - how to learn output connections. For the first part, I design a learning rule that forms connections from coincidentally stimulated inputs to separated conjunctive units in the hidden layer. Learning the second set of weights requires a more complex rule that takes into account a reward signal if the choice was correct, allowing only connections that lead to reward to be strengthened. Ultimately, the results predict a reorganisation of recurrent activity flow across training by potentiating feedforward and feedback connections in hippocampal-entorhinal stimulus pathways, and the need of reward-dependent plasticity to form connections to response neurons. My model bridges the gap between conceptual models of generalisation and how to learn them through biologically plausible plasticity rules.

Keywords: pattern separation
synaptic plasticity
memory
generalisation
Advisor: Manohar, S
Vogels, T
Gilded wreaths of the late Classical and Hellenistic periods

This thesis is the first major piece of research in the last 30 years to focus specifically on gilded wreaths. It is the result of close study of some 170 wreaths in Greece and Southern Italy, dating to the Late Classical and Hellenistic periods. This allowed the wreaths to be classified into seven main types, the earliest of which were found in Macedonia in Northern Greece. Wreaths of a different design, making more use of clay and less of copper, are also presented, which are mainly from central and southern Greece. The wreaths from Southern Italy make a useful contrast, similar in many ways to the material in Greece, but with some resemblance to earlier items from Italy such as wreath-diadems. The materials used to make the wreaths have been analysed with hand-held XRF and, in some instances, a Scanning Electron Microscope; the results are presented here for the first time. Very little analytical work has been done before on gilded wreaths, which made use of a range of materials including copper, gold and clay. Most of the wreaths are in fragments and not on view in the museums, and so are described in some detail, with illustrations, in the catalogue. The wreaths raise intriguing questions as to why they were buried in graves but appear not to have been used in sanctuaries. They are found with males and females, young and old - did they have some sort of apotropaic function, or did they mark the status of the individual? Could they have marked various stages in life (rites de passage), such as adolescence, marriage, giving birth and death? Gilded wreaths are found often in multiples in Macedonia, sometimes with solid gold wreaths, raising further questions as to why the deceased and their families felt it necessary for them to be buried with more than one wreath. Did the wreaths have a religious significance, or were the relatives simply seeking to show their wealth in consigning this valuable material to the grave? Is it possible to tell whether their use was solely funerary, or could they have been worn also by the living? Some answers to these many questions are put forward.

Keywords: origin
oak
wreaths
wire
analysis
Gilding
ancient Greek world
technology
pigments
gold leaf
kaolin
significance
textiles
Scanning Electron Microscope
ivy
XRF
Hellenistic
myrtle
copper
Raman
Advisor: Stamatopoulou, M
Doherty, C
Privacy: a political approach

This thesis is concerned with two central questions on the subject of privacy: (1) how should we conceptualize privacy? And (2), on what basis can laws and regulations to protect privacy be justified? The goal of this thesis is to provide an account of privacy that is both more persuasive than existing accounts and more capable of meeting the challenges to privacy in the modern day.
The first part of the thesis advances the argument that privacy is a normatively dependent concept. A normatively dependent concept is defined as a concept that relies on outside normative frameworks for its meaning or value. This thesis argues that privacy has this quality because it exists in a relationship of opposition to “the public” and thus lacks any essential characteristic other than being not-public, not-visible, or not in the common view. An examination of four historic reformulations of what it means to be private, spanning two thousand years of western history, confirms that privacy has shifted considerably over time and that attempts to essentialize it are misplaced. In addition, the modern disarray of the privacy debate—characterized by deep disagreement over both the definition and the purpose of privacy—reflects privacy’s normative dependence and in particular reveals our over-reliance on liberal-individualist conceptions of privacy that wrongly prioritize consent and control.
The second part of this thesis argues for adopting a wholly new approach to understanding privacy: the political approach. More specifically, this thesis argues for abandoning traditional liberal frameworks in favor of demonstrating how privacy supports central features of modern democracies, such as the ability to form a distinct political identity, the right to free expression, and the right of free assembly. Furthermore, this thesis argues that democracy even presupposes an “epistemic veil” of privacy around citizens, which motivates the practices of deliberation and voting. It can thus be shown that a commitment to democracy entails a commitment to certain privacy rights—a finding that circumvents the difficulty in establishing a common basis for privacy protections by appealing to all citizens who live under democratic regimes. In abandoning familiar understandings of privacy, the political approach to privacy does away with the problematic emphasis on consent, adapts privacy to an ever-changing surveillance environment, addresses prominent critiques of privacy rights, and provides a common basis of justification for future privacy legislation.

Keywords: privacy
privacy policy
privacy and democracy
history of privacy
concept of privacy
Advisor: Bejan, T
Protein folding investigated by NMR spectroscopy

Proteins are biological molecules that perform diverse cellular roles, including metabolizing energy sources to regulating the acidity of blood. The collective actions of proteins and their interactions with nucleic acids at the molecular level enable life at the macroscopic level. If protein folding is delayed or has faltered, unwanted associations between exposed hydrophobic amino acids can lead to cytotoxic protein aggregation, which is implicated in diseases such as Parkinson’s, Alzheimer’s, and type II diabetes. However, cells have armed themselves with an evolutionarily conserved defense mechanism to combat protein misfolding: a class of proteins known as molecular chaperones that can recognize misfolded, aggregation-prone proteins and either correctly refold them or target them for degradation and recycling.
The focus of this thesis is to understand aspects of protein folding and the activity of molecular chaperones at the atomic level. Nuclear magnetic resonance (NMR) spectroscopy methods have been applied to characterize the molecular chaperone HSP27. My results reveal that HSP27 locally unfolds upon monomerization and becomes highly active. Further, I characterize a single amino acid variant of HSP27 implicated in the onset of Charcot-Marie-Tooth disease, a commonly inherited motor neuropathy, and find to be devoid of chaperone activity, while also forming oligomers that are significantly larger than the wild-type protein.
Rapid pressure-jump NMR experiments are developed and deployed to monitor protein folding with millisecond resolution via the protection from solvent exchange. These data provide insight into the folding mechanism of a pressure-sensitized variant of ubiquitin. The extent of cis-proline formation is characterized in unfolded proteins with NMR, and the degree of polypeptide collapse in low denaturant conditions is probed by translational diffusion. Finally, the accuracy and precision of Carr-Purcell-Meiboom-Gill relaxation dispersion, a powerful NMR method to investigate transiently populated folding intermediates, is analyzed in the presence of limited input data.

Keywords: small heat-shock proteins
NMR spectroscopy
protein folding
molecular chaperones
Advisor: Baldwin, A
Bax, A
Benesch, J
Applications of single-cell Raman microspectroscopy in bacteria metabolism and physiology

Bacteria play important roles in almost all ecosystems, including the natural environment and the human body, and they are extremely abundant and versatile. New generations of sequencing technologies can provide phylogenetic diversity and metagenomic profiling of microbial communities, but metabolic functions of individual microbes and their molecular mechanisms are often elusive, owing to the limited culturability and the complexity of microbial communities.
Single-cell Raman microspectroscopy (SCRM) is label-free vibrational spectroscopy that measures a collection of molecular vibrations coming from all biomolecules in a single bacterial cell. This thesis emphasises the capabilities of SCRM in a wide spectrum of applications for investigating bacterial metabolism and physiology. SCRM is applied to study bacterial phenotypes in a symbiotic setting with a plant host. SCRM is combined with deuterium-isotope-probing (DIP) and applied to study carbon metabolism in pure cultures, as well as in vivo metabolic adaptations by human-invasive pathogens. Especially, the power of single-cell analysis in studies of heterogeneous bacterial populations is explored and highlighted.
This thesis also outlines an analytical pipeline to standardise and automate the process of spectral analysis in SCRM studies, from data tidying and data preprocessing to a variety of analytical approaches for either exploratory or diagnostic purposes. By following the established pipeline and executing the developed programming script, single-cell Raman analysis can be performed in a simple and rapid manner.
To conclude, by applying SCRM to provide intrinsic biochemical fingerprints of individual bacterial cells and connecting SCRM with the power of computational analysis, this thesis provides the possibility of probing bacterial metabolism and physiological states in ever-changing and multifaceted ecological settings.

Keywords: Raman spectroscopy
Single cell
Bacteria metabolism
Advisor: Huang, W