VictorJuiz/thesis huggingface dataset:
Finite-frequency tomography using regional P-waves, with application to the western Pacific upper mantle
Keywords: Seismology
Axisem
Geophysics
Seismic Inversion
Full waveform
Tomography
Sensitivity Kernels
MC Kernel
P-waves
western Pacific
Triplications
Subduction
Upper Mantle

This thesis aims to present the data measurement process, waveform modelling, full waveform sensitivity measurements, and inversion workflow, required to produce a P-wave tomography of the upper mantle, including the mantle transition zone, down to 1000km depth.
Improved seismic velocity models are needed: many tomography models do not include regional travel-time datasets. This is because the first arrivals identified in travel-time datasbases are not enough on their own to seismically sample the mantle transition zone. Sharp velocity gradients at the top (410km) and bottom (660km) of the mantle transition zone induce triplications in body waves. This means that there is more than one possible path between source and receiver for a given waveform: these can range from a topside reflection off the 410km discontinuity, through to refraction at the base of the 660km discontinuity. It is therefore difficult to attribute the first arrival time in a body waveform to its true path in an automated manner, as needed for tomography. This is heightened by discrepancies between the assumed reference background model for data processing and inversion, with respect to the true background model: therefore, seismic travel-times must be measured relative to synthetic data based on full waveform modelling. A limited number of regional body wave velocity models based on the full seismic waveform exist, which can provide sufficient seismic illumination of the mantle transition zone, a known barrier for subducting oceanic lithosphere.
In this study I present JEABOX, a P-wave tomography of the western Pacific upper mantle, using the joint inversion of existing teleseismic P-wave travel times based on multifrequency cross-correlation, with regional P-wave measurements between 14-30 degrees epicentral distance. I calculate Born sensitivity kernels for these latter triplicated data using the MC Kernel software based on the spectral element solver, Axisem. I showcase the integration of these novel triplicated data and their sensitivity kernels into a tried-and-tested finite-frequency tomography workflow, to perform joint inversion of teleseismic data and Dahlen kernels with regional travel-times and MC Kernels, to produce a hybridised P-wave velocity model based on Axisem, the first tomography of its kind.
The resulting model corroborates several major seismic structures observed across western Pacific subduction zones in previous studies, including what appears to be slab stagnation beneath the Kuril and Japan trenches, and steep subduction under the Izu-Bonin trench. In the southern hemisphere, seismic signatures imply protracted subduction beneath the Sunda-Java trench under Borneo and surrounding area. Future work will tectonically interpret the JEABOX model in full.
Practical Bayesian optimisation for hyperparameter tuning
Keywords: Hyperparameter tuning
Bayesian optimisation
Machine learning
Global search
Gaussian process

Advances in machine learning have had, and continue to have, a profound effect on scientific research and industrial activities. We are able to uncover insights contained within large troves of data and develop models to solve problems that seemed infeasible until recently. Before we can train a model, we have to define high-level properties, also known as the model’s hyperparameters. Examples include the architecture of a neural network, the class and parameters of a stochastic optimisation algorithm, the number of trees in a random forest or the kernel in a Gaussian process. One of the key challenges in developing good machine learning models is choosing good values for these hyperparameters.
Evaluating the quality of a set of hyperparameters is usually computationally costly, as it requires us to first train a model specified by the hyperparameters before we can evaluate a score. The computational costs of scoring a configuration means that we want to perform this hyperparameter search with as few trials as possible. Bayesian optimisation (BO) is a general-purpose efficient global optimisation technique that has proven to be remarkably effective for many expensive optimisation tasks, including hyperparameter tuning. This thesis brings together multiple contributions aimed at making BO more practically applicable, focussing on uncertain-input measurements as well as model hyperparameter tuning.
The case of data with input noise is relevant when we are modelling (or finding extremal values of) a quantity defined on a spatial grid. We undertake a comparative study evaluating existing uncertain-input GP methods, and develop a novel approach based on the unscented transform that outperforms existing uncertain-input methods. We then address the question of parallelising BO to make optimal use of available computing resources. We develop a novel class of methods for asynchronous parallel BO, and demonstrate empirically the benefits of our approach, as well as more generally showing the advantages of asynchronous over synchronous BO.
Finally, we propose a new framework for dealing with a mixture of categorical and continuous hyperparameters. With few exceptions, model hyperparameters consist of both categorical and continuous variables, but BO approaches have mainly focussed on continuous search spaces. We present a novel framework that combines multi-armed bandits with continuous BO methods and leverages each of their strengths to achieve state-of-the-art performance on real-world optimisation tasks.
Energy harvesting by using ferroelectric switching
Keywords: electroceramic
energy harvesting
transducer
piezoelectric
ferroelectric/ferroelastic switching

The aim of the current work is to develop a novel energy harvesting method by using ferroelectric/ferroelastic switching and to establish a practical prototype device with stability and robustness. The results are expected to provide a deep mechanistic understanding of the polarization state in ferroelectrics and assist in the improvement of transducers’ performance in practical applications.
Ferroelectric/ferroelastic switching, which can generate greater energies and charge flows than those of piezoelectrics has attracted increased interest to improve transducers’ performance in recent years. However, the challenges of nonlinearity, fatigue degradation and the difficulty of driving an electrical cycle by stress have limited ferroelectrics’ use in energy harvesting applications. In the current work, by using a simple model of switching, a working cycle that could generate electrical energy from a harmonically varying source of stress is explored. The cycle uses depolarization by stress, followed by repolarization with combined electromechanical loading. A harvesting electric field and bias electric field are imposed to ensure a stable repeatable working cycle during the depolarization process and repolarization process, respectively. The bias electric field, which is much less than the coercive field, provides a preferred direction of repolarization. The conversion efficiency of this cycle is estimated and improvements to the cycle are explored by adjusting the electrical and mechanical field amplitudes.
The current work then explores a novel and robust ferroelectric energy harvester based on partial ferroelectric switching. The device is of simple construction and achieves a per-cycle energy density of about 1mJ/cm3, orders of magnitude greater than that of typical piezoelectrics. Instead of using an external electrical bias field, the internal residual electric fields, generated during a partial depoling of an electroceramic, are adopted to provide ‘memory’ of a preferred direction for repolarizing it. A crucial feature is the control of residual stress by poling the active material in stages, first in a mechanically unconstrained state, then adhered to a substrate before completing the poling process. Then the method works by partially depolarizing a poled ferroelectric using a single application of tensile stress, and then using cycles of compression to vary the polarization state. It is shown that only periodic compressive stress is needed to induce the energy harvesting cycles, yielding unique and promising mechanical attributes that limit fatigue or fracture during cyclic loading. The results show this prototype device operating stably over 0.5×106 cycles at low frequency. The explorations of various polarization states and resistive electrical loads are also carried out to improve the performance for further practical applications.
Site-selective strategies for the biological investigation of glycoproteins
Keywords: protein modifications
glycogenesis
site-selective
proteoglycans
glycoproteins
tag-and-modify
glycosaminoglycans

Protein glycosylation is a post-translational modification that modulates numerous intracellular pathways and extracellular events. However, the study of glycosylated proteins is challenging since these are naturally produced as heterogeneous mixtures of different glycoforms. Moreover, isolation and characterisation of single glycoforms is not always feasible, and the chemical synthesis of such complex biomolecules is often impossible. Although several glycan-protein ligation methods have emerged in recent years, there is still significant progress to be made for the generation of true, homogeneous glycoform-mimics. This doctoral thesis aims at expanding the current toolbox used for the site-selective glycosylation of proteins with strategies that generate ‘near-native’ glycosidic linkages.
The ‘tag-and-modify’ approach has been widely recognized as a powerful method for the site-selective chemical modification of proteins. Herein, the application of this methodology for the synthesis of proteoglycan (PG)-mimics is described. A natural PG was homogeneously ‘tagged’ via enzymatic trimming of its glycosaminoglycan (GAG) chain, and a biocompatible radical ligation was developed to install a priming sugar. The minimally ‘modified’ PG was subjected to enzymatic GAG-polymerization and this allowed the unprecedented access to remodeled PG-analogues. Optimised conditions for the on-protein GAG-extension revealed interesting aspects pertaining to the activity of the employed GAG-synthase. Future work should reveal the utility of such methodology towards understanding the extent to which variously engineered GAGs affect the biological activity of their corresponding PG glycoforms.
In our work we also explored a cysteine (Cys)-based ‘tag-and-modify’ strategy for the generation of a homogeneous N-glycoprotein-mimic. We found that the presumed disulfide reshuffling of the native Cys-residues had impeded the site-specific chemical glycosylation at the inserted Cys-tag. Lastly, our focus turned towards further investigating the protein that uses the high energy glucose (Glc)-donor UDP-Glc to initiate, via autoglucosylation, the biosynthesis of glycogen. Close inspection of both its self-extended glycoforms and the more complex glucosylation states generated by the downstream enzymatic partners raised exciting new questions about the basic mechanisms of glycogenesis and glycogenolysis.
Cortical regulation of sleep
Keywords: cerebral cortex
sleep
layer 5 pyramidal neurons
mouse
sleep homeostasis
DREADDs

Sleep is vital but the regulation of sleep is poorly understood. Over the past decades, several subcortical regions in the mammalian brain have been identified, which promote wakefulness or sleep and constitute a ‘sleep switch’. The neurophysiology of the circadian clock, with the suprachiasmatic nucleus of the hypothalamus at its centre, has also been elucidated. However, it is still unclear how the brain tracks the accumulating sleep debt during wakefulness and adjusts the duration and intensity of sleep accordingly. This core process of sleep regulation, termed ‘sleep homeostasis’, remains enigmatic. The cortex engages in characteristic oscillations during sleep that serve as electroencephalographic (EEG) markers of rapid eye movement (REM) and non-rapid eye movement (NREM) sleep. Slow waves, the hallmark of NREM sleep, indicate the depth of sleep and are used to determine the level of the homeostatic process. The aim of my DPhil project was to probe in mice whether cortex, and in particular neocortical layer 5 pyramidal neurons, contribute to the regulation of slow waves and sleep.
This project was divided into three subprojects. First, I present laminar recordings of neocortical activity during sleep in wild type mice, which suggest that layer 5 actively drives slow waves. Next, I describe the validation of a chemogenetic tool, which I initially planned to use for the manipulation of layer 5 pyramidal neurons. These experiments revealed unexpected effects of the chemogenetic actuators clozapine-N-oxide (CNO) and Compound 21 (Cmpd21) on sleep in wild type mice, which do not express designer receptors exclusively activated by designer drugs (DREADDs). Finally, I present extensive work on ‘cortical SNAP25-ablated’ (Rbp4-Cre;Ai14;Snap25fl/fl) mice, which served as a model for chronic silencing of neocortical layer 5 pyramidal and archicortical dentate gyrus granule cells. These mice displayed changes in neocortical dynamics during NREM sleep, a strong increase in wakefulness, and a reduced homeostatic response to sleep deprivation, while circadian measures were unaltered.
Together, my work suggests that the cortex may play an essential role in the regulation of sleep oscillations, architecture, and homeostasis. Further investigation into the cortical regulation of sleep could reveal neural circuits and molecular mechanisms underlying sleep homeostasis and identify novel targets for the manipulation of sleep in the clinic.
Strongly-coupled QFTs from string theory
Keywords: String Theory
Holography
Supersymmetric Quantum Field Theory
Strongly-coupled Quantum Field Theory
Generalized Global Symmetries
Brane-webs

Strongly-coupled regimes of quantum field theory (QFT) are notoriously challenging to explore. In this thesis, which is divided into two parts, I address the question from a string theoretic perspective. I will focus on methods to map out the RG-flow, symmetries and phase structure, first taking a holographic point of view, then within the context of geometric engineering and brane-webs.
Holography constitutes a profound and potent way to describe strongly-coupled QFTs, especially when combined with sophisticated geometric techniques, and modern tools from QFT such as generalized global symmetries and their 't Hooft anomalies. In chapter 3 I will present our work on the gravitational dual of I/c-extremization for a 1d/2d N=(0,2) theory in the presence of a holomorphically varying axio-dilaton. This generalization makes the analysis suitable for F-theory supergravity solutions, and establishes a correspondence of the two extremization principles furnished by M/F-theory duality. In chapter 4 we develop new holographic methods to compute anomalies of discrete higher-form symmetries, and derive the topological field theory (TFT), which matches these anomalies in the infra-red (IR). This interplay of holography and generalized global symmetries shines new light on the topological sector of supergravity theories and its physical implications. We illustrate the approach in a rich non-conformal holographic setting, which flows to confining N=1 SU(N) Super-Yang Mills (SYM) in the IR, focusing on the 1-form symmetry and its mixed 0-/1-form symmetry anomaly, which is closely related to chiral symmetry breaking in gapped confining vacua.
Geometric engineering and brane-webs enable us to realize a vast array of superconformal field theories (SCFTs) whose salient features would otherwise be out of reach. In my research, I have focused on 5d N=1 SCFTs, which are intrinsically non-perturbative. In chapters 6 and 7 we establish a comprehensive description of 5d SCFTs in terms of Generalized Toric Polygons (GTPs) and map out their moduli space. Using the duality with brane-webs and insights from toric geometry we parametrize the extended Coulomb branch (CB) and determine an algorithm to compute the magnetic quiver (MQ) describing the Higgs branch (HB). We then apply these methods to all 5d SCFTs that flow to single gauge node theories in the IR with anti-symmetric and fundamental matter. Finally, in chapter 8 we identify a correspondence between 5d extended CB deformations and 3d Fayet-Iliopoulos (FI) deformations in the MQ, which elucidates how changes in the geometry of the HB are implemented as we move along the extended CB.
Latin loanwords in Greek documentary papyri (c. 30 BCE to c. 200 CE)
Keywords: Eastern Desert
Latin loanwords in Greek
language contact
borrowing
papyri
Oxyrhynchus
Roman Egypt

Ancient Greek hosted hundreds of Latin loanwords (e.g. κεντουρίων ‘centurion’) as a result of contact between Greeks and Romans. Because previous studies of Latin loanwords have mostly concentrated on chronology, morphology, and lexicon, there has been no systematic investigation of their introduction and spread in specific contexts and the motives behind their choice or avoidance. This thesis is the first work to address such questions. It uses a large corpus of Greek texts, the papyri of early Roman Egypt (c. 30 BCE to c. 200 CE), a place that did not have much prior exposure to Latin, as they are generally closer to everyday language than literature and present numerous first attestations of loans with a high density and frequency.
The dissertation includes an introduction laying the linguistic and methodological groundwork and four chapters. The first two focus on a military-influenced setting, the Eastern Desert of Egypt with forts (Didymoi and Krokodilo) and quarries (Mons Claudianus), and the other two on an urban setting in the Nile valley, the city of Oxyrhynchus. Being at the opposite ends of a scale of Romanness and military influence, the two settings might have presented diametrically opposed linguistic outcomes. In fact, most findings are valid for both. Only the players and a few tendencies differ: if in the Desert loanwords spread from within the community, from the higher ranks and the military administration, in Oxyrhynchus loanwords at first enter the community mainly from outside, reaching it from a larger centre, Alexandria. But general trends are observable in both settings. Documents show that military loanwords are usually the first large group of loans to enter military and civilian settings alike. Loanwords are by and large introduced by a select and generally bilingual minority and spread through society mainly through a top- down process. This process is faster in smaller societies and slower in larger ones. The introduction and choice of loanwords is not usually the consequence of a deliberate policy, and loans are deliberately chosen, preferred, or avoided in specific cases only. This analysis deepens our knowledge of Latin influence on Greek in a newly conquered, Greek-speaking region like Egypt and furthers our understanding of Latin-Greek language contact and its consequences.
The incorporation of Dalits into India’s business economy & its implications for social and economic policies
Keywords: Social Exclusion
Business Economy
Discrimination
Entrepreneurship
Uttar Pradesh
India
Dalit
Spatial Analysis
Mixed Methods
Policy Studies

Even after six and a half decades since Indian Independence, Dalits (ex-untouchables and oppressed castes) continue to experience caste-based discrimination and social exclusion in social as well as economic life. This research examines the incorporation of Dalits into the business economy - how they enter the market as owners of businesses rather than as wage-workers. The research has three key objectives: first, to analyse the spatial and sectoral patterns and variation of Dalit’s incorporation; second, to explain factors and processes affecting their entry; and third, to analyse the implications of key social and economic policies on Dalits’ incorporation.
This doctoral research project uses mixed methods, moves between different scales and deploys a wide range of evidence. The research estimates ‘indices of participation’ and produces a series of maps to show patterns and trajectories. It uses spatial econometric techniques to model quantifiable factors affecting Dalits’ entry. It relies on qualitative methods for individual case studies to unravel other factors and processes. Using Schaffer’s policy analysis framework, the research examines the politics of affirmative policies for Dalit businesses in the agenda-setting, the establishing of procedures and rules, and resource mobilisation.
The study revealed that the trajectory of Dalits’ incorporation is uneven and the spatial patterns across several sectors and regions show persistent under-representation. Urbanisation is the most significant predictor of Dalits’ incorporation. Dalits’ entry into the business is conditioned by the interactions of opportunities and resources and by the barriers created by subtle forms of exclusionary and discriminatory practices inherent in social structures, market institutions and the state. The study also found that the politics of patronage, of bureaucratic inefficiency, underinvestment and procrastination, and of domination of the business interests of higher castes are mutually reinforcing. This research has clear policy significance from the perspectives of equity and inclusiveness in the business economy.
Societal selection and historical materialism
Keywords: Analytical Marxism
Marxism
Political Theory
Socialism
Historical Materialism

This DPhil thesis is an attempt to provide a detailed account of Marx’s theory of history which relies on a quasi-Darwinian mechanism. Building on the debate around G.A. Cohen’s Karl Marx’s Theory of History: A Defence, I argue that a selective mechanism between societies can underpin some of the key theses of historical materialism. In societal selection, the view I propose, greater development of the forces of production leads to a competitive advantage for those wielding these forces. Therefore, societies which adopt more developed forces of production ̶ or relations of production which foster the development of the forces of production -̶ will tend to be those that succeed, expand and impose their practices on others, at the expense of societies with less developed forces. This, in a manner similar to natural selection, creates a broad tendency for forces of production to develop and for relations which enable further development of these forces to emerge. This thesis will not just be and account of this process, which has already been presented in a more limited form by others; it will also attempt to detail the mechanisms underlying this process in order to tease out what a historical materialism that is based on societal selection would look like. How do forces of production translate into advantage in (generally military) competition? What is the role of imitation and human intention in the theory? How do the mechanisms of historical materialism play themselves out? What account does this theory have of class struggle and human agency? What kinds of predictions would this theory yield? Answering these questions will not only provide a more complete view of historical materialism but also address the critiques levied against this selectionist view. The goal of this thesis is to propose a detailed theory which can provide a compelling account of human history.