VictorJuiz/thesis huggingface dataset:
Discontinuous Galerkin discretisation in time of the second-order hyperbolic PDEs
Keywords: Discontinuous Galerkin method
Discontinuous time stepping
Numerical analysis
Finite element method
second-order hyperbolic PDEs
Nonlinear PDEs

A discontinuous Galerkin (DG) time-stepping method is presented for solving second-order hyperbolic partial differential equations (PDEs). The proposed numerical method combines the hp
-version discontinuous Galerkin finite element method (hp-DGFEM) in the time direction with an H1(Ω)-conforming finite element approximation for the spatial variables. We start with the construction and analysis of the discontinuous-in-time scheme to linear hyperbolic PDEs of second order in Chapter 2. Our analysis shows that this method is consistent and stable, with arbitrarily high-order convergence rates in the temporal domain for sufficiently smooth solutions. Error bounds in both energy and L2 norms are derived. These error estimates show that this method allows for a broad range of hp-refinement strategies with varying time step sizes and polynomial degrees, thus having the potential to give exponential rates of convergence. Numerical experiments on linear wave equations and elastodynamics systems show significant gains in accuracy over existing time integration schemes.
We then extend this DG time-stepping method to approximate solutions of second-order quasilinear hyperbolic systems in Chapter 3. In particular, we study the nonlinear elastodynamics problem. The resulting numerical scheme is stable and convergent, and we derive a priori error bounds at nodal points in the L2-norm for sufficiently regular solutions. Numerical experiments on a nonlinear elastodynamics problem with smooth solutions demonstrate the convergence rates.
Chapter 4 further applies this discontinuous-in-time scheme to a nonlinear damped equation, which is derived from Maxwell's equations by assuming a linearly polarised wave propagating on an infinite cylindrical domain. Again, we show a priori error estimates of the solutions at the nodal points in this chapter. Numerical experiments on nonlinear wave equations illustrate and confirm these theoretical findings.
Exploring the ring-forming chemistry of yndiamides
Keywords: Yndiamide

Yndiamides are a uniquely capable class of doubly heteroatom-substituted alkynes which provide access to many diverse nitrogen-rich structures. This thesis describes the development of new ring-forming reactions of yndiamides. In the course of this work three project areas have been explored:
1. A cycloisomerisation transformation to form fused pyrroles, using either gold-catalysis or by heating in the absence of a catalyst (Chapter 2).
2. Two rhodium-catalysed [2+2+2] cyclotrimerisation reactions which form 1,2-diaminobenzene derivatives (Chapter 3). Mechanistic studies on this reaction were also carried out using computational methods (Chapter 4).
3. Catalytic methods to synthesise diaminopyridine and diaminopyridone derivatives from yndiamides. (Chapter 5).
Childcare arrangements and the role of childcare policy provisions in Romania
Keywords: Romania
childcare
childcare policy
childcare arrangements

The focus of the thesis is the exploration of young children’s routine childcare arrangements and the role played by childcare policy provisions (in cash, in time and in kind, through services) in shaping these arrangements in the Romanian context. Through the narratives of 68 family carers in 37 urban and rural Romanian households in multi-ethnic Transylvania, the study investigates the household level processes whereby young children’s care arrangements come to be and explores the ways in which the design of and access to childcare policy provisions might shape young children’s routine care arrangements. In doing so, the thesis reconceptualises the term childcare arrangements and provides a descriptive account of ten different routine arrangements for the care of young children. Through an inductive analysis of carer narratives, the thesis also develops a heuristic tool – hierarchies of care ideals – that lies at the heart of a refined explanatory framework pertaining to the conception and implementation of individual care arrangements. This framework complements existing analytic models that have been developed to explain mothers’ employment and care related decisions during their children’s early years. Building on this inductively developed framework, the thesis expands on the role that different childcare policy provisions were said to play in shaping households’ childcare choices. The thesis reveals that the designs of policy provisions and households’ access to different benefits directly shape young children’s care arrangements. Furthermore, through the analysis of narrative pairs available for most households in the study, the thesis explores the gendered ways in which mothers and fathers narratively constructed agency in relation to decision-making about children’s care arrangements. Finally, the thesis proposes three real-type decision-making models described by carers in the study, revealing the dynamic nature of household decision-making in relation to children’s care arrangements.
Methods of deference in human rights adjudication
Keywords: burden of proof
standard of review
margin of discretion
judicial deference
separation of powers
public law
constitutional theory
judicial restraint
administrative law
constitutional law
judicial reasoning
constitutional rights
human rights adjudication
proportionality
margin of appreciation

The phenomenon of judicial deference to the executive or legislature in human rights adjudication has elicited extensive scholarly discussions. Whilst much has been written on whether and when courts should defer, this thesis is the first to systematically probe two questions regarding how courts should defer.
The first is what devices courts should use to express the various reasons for deference. I explain that in jurisdictions that satisfy certain background conditions (which include the jurisdictions whose case law this thesis draws upon, namely, Canada, Hong Kong, Ireland, Israel, New Zealand and United Kingdom), courts have three sets of grounds for deference: grounds that relate to arriving at correct outcomes on the rights issue in question, to respect for constitutional legitimacy, and to the achievement of other aspects of the common good that courts should take into account in adjudication. Noting that courts have at their disposal six devices for exercising deference – the burden of proof, standard of proof, standard of review, giving of weight to views, choice of interpretation and choice of remedy – I argue that sometimes specific devices must be used because other devices are unable to express, or express to the appropriate degree, the reasons for deference in a particular instance.
The second question that this thesis examines is how the methods of determining when and how to defer can be made more practicable for judges and litigants without undue compromise of those methods’ ability to fulfil the reasons for deference in a particular case. I propose four techniques for striking a balance between these two considerations: the use of rules, presumptions and factorial analysis; mapping certain normative considerations for deference onto specific devices; developing clear and reliable indicators of deference; and developing finite scales for various devices and levels of scrutiny that combine devices.
Multi-robot coordination under temporal uncertainty
Keywords: multi-robot systems
spatiotemporal uncertainty
Markov Automata
planning under uncertainty
temporal uncertainty
multi-robot task allocation
formal verification
continuous-time Markov chain
discrete-event simulation

Sources of temporal uncertainty affect the duration and start time of robot actions during execution. For example, mobile robots may slip on uneven terrain, slowing them down. The presence of multiple robots in the environment contributes towards temporal uncertainty, as robot interactions such as congestion affect navigation performance. Existing multi-robot coordination solutions often disregard temporal uncertainty through simplifying assumptions such as fixed, identical action durations, which simplifies the problem at the cost of inefficient execution-time behaviour. To synthesise multi-robot behaviour that is robust to unexpected temporal disturbances, we must explicitly capture temporal uncertainty during coordination. In this thesis, we present techniques for effective multi-robot coordination under temporal uncertainty. To represent temporal uncertainty, we construct probabilistic models of action duration for each spatiotemporal situation an action may be executed in. With this, we build formal multi-robot models which accurately capture asynchronous robot execution in continuous time. We then develop planning and task allocation solutions which reason over the effects of temporal uncertainty to synthesise efficient multi-robot behaviour. Further, we consider the problem of policy evaluation, i.e. evaluating properties of synthesised multi-robot behaviour prior to execution, and present two approaches which trade between the accuracy of the model and the solution methods used for policy evaluation. Empirically, our methods outperform solutions which ignore temporal uncertainty, use simplified models, or constrain robot behaviour to reduce temporal uncertainty.
Essays on information regimes and uncertainty in emerging economies
Keywords: infrastructure
World Bank
Brazil
electricity
economic development

This thesis contains three papers studying the behavioural response of firms, households and investors in emerging economies to changes in expectations and uncertainty. The first paper investigates how economic agents change their consumption and investment behaviour to news about unanticipated changes to power sector plans by exploiting a novel dataset for the identification of news shocks in a vector– autoregression. While there is an immediate expectations–driven GDP response to a surprise capacity addition in OECD economies, this positive output effect is absent in developing and emerging countries. Firms and households in developing countries respond to failed power projects by immediately reducing investments and are also subjected to lower economic growth as a result relative to the pre–disappointment period. The second paper examines regulatory uncertainty as a barrier affecting infrastructure service investments and quality in Brazil. Exploiting a quasi–natural experiment for identification, it finds that electric utilities partially shielded from uncertainty significantly increase their irreversible investments in electricity distribution infrastructure. This response is qualitatively consistent with optimal behaviour as prescribed by real options theory. The third paper uses an autoregressive distributed lag model and finds that sovereign and corporate bond yields in emerging economies exhibit a long–run relationship that is not explained by economic conditions, firm fundamentals, bond properties, or external factors affecting emerging countries. The paper identifies perceived transfer risks by investors as the key channel. Investors’ perceived transfer risks lead corporate and sovereign bond yields to co–move and generally converge. The introduction and conclusion of the thesis further explain common themes.
Essays on electoral institutions
Keywords: electoral systems
legislative careers
comparative politics
institutionalism
preferential voting
political geography

Do electoral systems matter for the outcomes of democratic politics beyond their well-known relationship to party systems? This thesis presents three studies on the consequences of electoral institutions, highlighting how they shape incentives and opportunities for political actors operating at the intra-party level. The first article considers how the spatial representativeness of legislatures - i.e. the extent to which MPs from different parts of the country are equally represented - varies with constituency and ballot structure. The paper proposes a novel measurement to gauge the descriptive representation of places in parliaments and develops a theoretical framework linking spatial representation to parties' incentives and voters' ability to elect local MPs. Consistently with the theory, the analysis finds that mixed-member systems and preferential voting mechanisms are associated with more geographically representative parliaments. The second paper asks whether sub-national legislators' likelihood to run for the national parliament is influenced by the electoral system through which they were elected. Leveraging within-legislature variation in electoral rules across German State parliaments, I find that list-PR MPs are more likely to attempt ‘level hopping’ than single-member district legislators. It is argued that this depends on the lower levels of electoral security of the former, and to the more direct accountability of the latter to local (s)electorates. The third paper develops a theoretical model of preference vote distribution in preferential-list PR system, extending the approach behind Taagepera and Shugart's Seat Product Model to intra-party competition. I show that the share of preference votes for the first-ranked and last-eligible candidates, as well as the effective number of candidates in a list, can be accurately predicted in expectation as functions of institutional variables. Overall, the thesis makes contributions in terms of measurement, data and theory towards a broader and richer understanding of the intra-party effects of electoral institutions.
Studies for upgrading and optimising the CLEAR beamline, and generating uniform electron-beam profiles for irradiation experiments
Keywords: irradiation facility
compact linear collider
FLASH radiotherapy
accelerator physics
VHEE
photoinjector

Irradiation facilities around the world are used to investigate the effect of high-energy particle beams on electronics, to study the makeup of historical objects and art, and for medical applications, notably radiotherapy. The CERN Linear Electron Accelerator for Research (CLEAR) is an irradiation facility that produces 200 MeV beams of electrons with parameters tuned to the needs of users.
One of the most commonly requested beam parameters is for bunch lengths of less than 1 ps, which was not previously possible for high-charge bunches. In this thesis, the ability to compress high-charge bunches to sub-ps bunch lengths, using the velocity bunching technique, is shown in simulation. The simulations are then verified with experimental measurements taken at CLEAR. The ability to reduce the emittance of the beam during compression is also presented.
Potential upgrades to the CLEAR facility are proposed, namely a new laser system and the installation of an additional klystron. The benefits of these upgrades are explored in simulation, demonstrating that they would allow the production of shorter bunches, with lower energy spread, and lower emittance.
It is shown that by using a modified version of the CLEAR photoinjector it is possible to produce bunches with a uniform transverse profile using a simple Gaussian laser with a 1 ps pulse length. A compact irradiation facility was proposed consisting of the CLEAR photoinjector, an X-band linac using cavities similar to those developed for the Compact Linear Collider, and a quadrupole matching section. It was shown that such a facility could produce beams of different sizes with uniform beam profiles. The stability of such a facility was investigated, demonstrating that beam jitters do not significantly reduce beam uniformity.
The mechanisms of HIF-2α action in the carotid body
Keywords: HIF
paraganglioma
ARNT
carotid body
hypoxia
pheochromocytoma
acute oxygen sensing

The carotid body (CB) is an arterial chemoreceptor central to ventilatory adaptations to reduced oxygen arterial pressure (hypoxia) and responds both rapidly, by increasing ventilation within seconds of the drop in O2 saturation, and chronically, by potentiating the acute hypoxic ventilatory response (HVR), which is associated with CB hyperplasia. Mechanisms behind these adaptations are not fully understood, but the Hypoxia Inducible Factor (HIF) signalling pathway has been implicated in mediating the CB chronic response to hypoxia. Indeed, HIF-2α isoform has been found to be very highly expressed in the CB.
Using a recently developed pharmacological HIF-2α inhibitor (PT2385), we demonstrate that HIF-2α is necessary for the CB-mediated acclimatisation to chronic hypoxia, and plays a major role in acute HVR (Chapter 2). The response to PT2385 was blocked in mice with HIF-2α S305M mutation, obstructing binding of allosteric inhibitors without altering the HIF transcriptional function, demonstrating that the PT2385 effects are on-target to HIF-2α (Chapter 3). Further, a hypomorphic ventilatory phenotype was found in S305M mutants (Chapter 3), suggesting a potential HIF-β-independent role of HIF-2α in CB function. This was investigated in Arnt1/2dKO mice, which showed incomplete loss of CB responses to chronic hypoxia with Arnt1/2 loss in adulthood (Chapter 4). The role of G-protein signalling regulators: RGS4 and RGS5, which are highly CB-enriched and reportedly HIF-target genes, was further investigated using genetic models, and demonstrated a function of RGS5 in ventilatory acclimatisation to hypoxia, uncovering a potential HIF-2α downstream mediator (Chapter 5).
Finally, the role of HIF-2α in sympathoadrenal tumours was investigated by developmental, tyrosine-hydroxylase-expressing cell-restricted Phd2 inactivation (Chapter 6). This study showed that HIF-2α stabilisation (due to Phd2 inactivation) preserves the chromaffin cells in an ‘immature’, noradrenergic state, with induction of CB-specific genes, and is sufficient to preserve acute oxygen sensitivity of chromaffin cells, typically only found in neonates.
Together, presented results demonstrate that HIF-2α is both necessary and sufficient for oxygen sensitivity in the carotid body and related tissues, and provides insight into the possible transcriptional and HIF-β-independent mechanisms of HIF-2α action in hypoxia.
The Bay of Biscay as a sphere of interaction (2900-1100 BC): big data and big thinking in the Bronze Age
Keywords: Atlantic Europe
Bronze Age
metalwork
archaeological theory
Bay of Biscay
sailing

This study is about the flow of metalwork around the Bay of Biscay between the Chalcolithic and the Middle Bronze Age. The Bay of Biscay is understood as the waterbody between northern Iberia and western Atlantic France. This study addresses three questions. How were the different regions of the Bay of Biscay connected to each other during the Bronze Age, what routes were used to travel between them and what was the nature of the connections identified? To answer them in Chapter 2 the routes employed to travel around the Bay in the longue-durée are identified. In Chapters 3, 4 and 5 the distribution of metalwork is analysed to understand how the Bay’s regions were connected to each other during the periods studied. Finally, Chapter 6 discusses the possible nature of those connections and what routes might have been employed at the different moments of the Bronze Age.
Investigating mechanisms of TDP-43 toxicity in cellular models of amyotrophic lateral sclerosis
Keywords: neurodegeneration

Amyotrophic lateral sclerosis (ALS) is a fatal, neurodegenerative disorder for which there is currently no cure. TDP-43 cytoplasmic mislocalisation and aggregation are the pathological hallmarks of the disease, and mutations in the gene encoding TDP-43, TARDBP, have been observed in a small number of ALS cases. Given this, it is hoped that modelling TARDBP mutations may provide early mechanistic insight into the disease process. Here, I examine the effects of the pathogenic TDP-43 M337V mutation on cellular phenotypes in an mESC-MN model of ALS. In TDP-43 M337V mESC-MNs, I observed reduced viability, both in unstressed and oxidative stressed conditions, and impaired stress granule formation in response to oxidative stress compared to TDP-43 WT controls. Interestingly, these changes were observed without evidence of TDP-43 cytoplasmic mislocalisation in TDP-43 M337V mESC-MNs when compared to TDP-43 WT controls. Increasing culture duration did not significantly alter synaptic protein expression or exacerbate phenotypes observed at earlier time points. Analysis of cellular energy metabolism revealed significantly reduced glycolysis in TDP-43 M337V mESC-MNs compared to TDP-43 WT controls in response to oxidative stress. Following oxidative stress, treatment with terazosin, which has previously been shown to significantly improve viability in our TDP-43 M337V mESC-MNs, significantly increased glycolysis whilst reducing mitochondrial respiration in TDP-43 M337V mESC-MNs. Finally, analysis of axonal transport in unstressed conditions using live imaging microscopy, revealed significantly impaired bi-directional transport of mitochondria and signalling endosomes in TDP-43 M337V mESC-MNs compared to TDP-43 WT controls. Overall, this work identifies relevant, ALS-associated phenotypes in the TDP-43 M337V mESC-MN model, which provides a valuable high-throughput system for investigating disease mechanisms and screening potential therapeutic compounds.
Evolutionary biology of members of the viral kingdom Bamfordvirae
Keywords: mavericks/polintons
virophages
paleovirology
vertebrates
dsDNA viruses

Members of the viral kingdom Bamfordvirae arguably represent the most diverse lineage of viruses infecting eukaryotes. They comprise the Nucleocytoplasmic Large DNA viruses (NCLDVs), virophages, adenoviruses, Maverick/Polintons and Polinton-like viruses. Most elements encode a conserved module of genes involved in capsid formation: two jelly-roll fold capsid proteins, an FtsK-HerA DNA-packaging ATPase and an adenoviral-like protease. However, over the course of evolution, these viruses diversified to an unprecedented extent by numerous gene gains and losses, replacement of the ancestral replicase and acquisition of integrases. I investigated aspects of the evolutionary biology of this viral kingdom by combining results from paleovirology, phylogenetics, mathematical modelling and computational simulations. First, I show that Mavericks have undergone frequent cross-species transmissions and the genes involved in capsid formation are under strong purifying selection. These observations imply that Mavericks are endogenous viruses and not merely transposons. Maverick viruses were estimated to have infected vertebrates for at least 419 million years. Next, I found support for an alternative evolutionary scenario for the origin of the bamfordviruses of eukaryotes, which is at odds with the nuclear-escape hypothesis (origin from a Maverick-like element that escaped from the nucleus). The topology of the phylogenetic tree suggests that this viral lineage has infected eukaryotes for > 1 billion years. By modelling the interactions between cells, viruses and virophages, I argue that the virophage entry mechanism is potentially the main driver of the different integration patterns observed for Mavirus/Spuntik-like virophages. Theoretical analyses also supported the role of virophage inhibition, programmed cell-death and multicellularity as effective antiviral mechanisms in microbial eukaryotes. Finally, I explored the evolutionary biology of two Maverick integrations found in the human genome, which integrated at least ~102 million years ago. These results shed light on the ancient interactions of viruses with eukaryotes, and present new questions and hypotheses open for investigation.