VictorJuiz/thesis huggingface dataset:
The architecture of rights
Keywords: Philosophy of Law
Philosophy of Rights
Hohfeld
Legal Philosophy
Rights
Jurisprudence

This thesis concerns the various concepts of rights and philosophical accounts of them. Chapter 1 addresses some methodological issues affecting analytic legal philosophy and the philosophy of rights. Chapter 2 distinguishes between two kinds of philosophical accounts of rights: models and theories. Models outline the 'conceptually basic' types of rights, their differences, and their relationships with other kinds of 'normative positions' (e.g., duties, liabilities, etc.). Theories of rights serve two roles: first, to posit a supposed ultimate purpose for all rights; second, to provide criteria for determining what counts as 'a right' in the first place. The chapter also criticises both monistic models (ones positing only a single basic kind) for being under-inclusive and a subset of pluralistic ones (those positing several basic kinds) as over-inclusive.
Chapter 3 clarifies the concepts of rights exercise, enforcement, remedying, and vindication. Chapter 4 explains the Interest-Will Theories of rights debate, while Chapter 5 argues that its constituents are irredeemably flawed, unnecessary, and under-inclusive. Chapter 6 further analyses the concept of rights enforceability, showing why legal rights are not invariably enforceable by legal powers. It then explains why wholly unenforceable legal rights nonetheless constitute 'imperfect' or defective cases. Chapter 7 argues there are more ways to enforce legal rights than just via powers, elucidating two such modes: legal rights can generally be claimed or invoked using legal liberties in private and social circumstances. While Chapter 8 shows why it might not always be possible to make liberty-based claims or invocations of right, it also provides reasons for thinking that legal rights that cannot be enforced in these ways are also imperfect.
Atomic structure and dynamics study of defects in graphene by aberration-corrected transmission electron microscope
Keywords: graphene

Graphene has grabbed enormous research attention due to its multiple unique properties. These properties, however, can be strongly influenced by lattice imperfections. Aberration corrected transmission electron microscopy (AC-TEM) is one of the leading methods to image two-dimensional materials at the atomic level. This thesis addresses the issue of structure and dynamics characterization of dislocations and grain boundaries (GBs) in graphene with single atom sensitivity using the state-of-the-art AC-TEM in Department of Materials, University of Oxford.
My first goal is to understand the interaction between dislocation and the edge of graphene. When a dislocation is located near an edge, a decrease in the rippling and increase of the in-plane rotation occurs relative to the dislocations in the bulk. The increased in-plane rotation near the edge causes bond rotations at the edge of graphene to reduce the overall strain in the system. Dislocations are highly stable and remain fixed in their position even when located within a few lattice spacings from the graphene edge.
With the aid of an in situ heating holder, the high temperature behavior of dislocations is then investigated. Control of temperature enables the differentiation of electron beam induced effects and thermally driven processes. An analysis of the dislocation movement shows both climb and glide processes, including new complex pathways for migration and large nanoscale rapid jumps between fixed positions in the lattice. The improved understanding of the high temperature dislocation movement provides insights into annealing processes in graphene and the behavior of defects with increased heat.
The in situ heterogeneous nucleation and growth of graphene are also studied within the AC-TEM. The growth mechanism consists of alternating carbon cluster attachment and indentation filling to maintain a uniform growth front of lowest energy. The highly polycrystalline graphene seed is found to evolve with time into a higher order crystalline structure. The motion of GBs is discontinuous and mediated by both bond rotation and atom evaporation. These results provide insights into the formation of crystalline seed domains that are generated during bottom-up graphene synthesis.
Finally, the formation, reconfiguration and annihilation of GB loops are demonstrated. It is shown that the GB loop cannot fully relaxed under electron beam irradiation with its terminal state being isolated dislocations far apart from each other. Line defects composed of several adjacent excess-atom defects can be found during the reconfiguration process. This work gives detailed information about the stability and behavior of large GB loops in two dimensional materials.
Model or mirage?
Keywords: Oil
Institutions
Ghana
Good governance

Despite significant growth in the number of “good governance” initiatives promising to generate optimum developmental outcomes in resource-rich countries, there is surprisingly little empirical information about their sector and country-specific dynamics. This thesis focusses on how external “good governance” norms and institutions interact with domestic actors and organisations to shape the institutional landscape of resource-rich countries. This objective is pursued by means of an in-depth case study of Ghana, a Sub-Saharan African nation that has become a middle-sized exporter of crude oil since January 2011. More specifically, it scrutinises two major reform efforts designed to steer the country’s oil industry towards a developmental direction: the Extractive Industries Transparency Initiative (EITI), an international auditing and multi-stakeholder oversight mechanism, and the Public Interest and Accountability Committee, a home-grown citizens’ oversight initiative in Ghana. The analytical lens employed in the study is based on comparative political economy and comparative institutional analysis. They are employed to make sense of the dialectic between the promise of corrective “good governance” measures and the mirage of reform outcomes in the Ghanaian oil sector. The main argument advanced here is that “good governance” solutions in the oil industry are essentially weak instruments, due to their inability to grapple with deep-seated instrumental politics, perverse institutional environment, and elite capture that continue to undermine reform in Ghana. This point is adduced to highlight the shortcomings of the “good governance” agenda. The thesis draws from multiple data sources, collected through semi-structured interviews with various stakeholders, public officials, NGOs and community activists, development agencies, and oil companies. These are complemented by archival research, documentary sources, non-participant observation, and workshops.
Harnessing demographic data for cross-scale analysis of forest dynamics
Keywords: Demography
Vital rates
Forest dynamics
Integral Projection Models
Ash dieback
Tropical trees

Forests are a critical biome but are under threat from unprecedented global change. The need to understand forest dynamics across spatial, temporal and biological scales has never been greater. Critical to this will be understanding how the demographic rates of individuals translate into patterns of species diversity, biomass and carbon turnover at much larger scales.
In this thesis, I present a modelling framework focussed on demography. In Chapter 2, I introduce methods for translating forest inventory data into population models that account for the size-dependency of vital rates and persistent differences in individual performance.
Outbreaks of forest pest and pathogens are increasing in frequency and severity, with consequences for biodiversity and forest structure. In Chapter 3, I explore the impact of ash dieback on the community dynamics of a British woodland, describing a spatially explicit individual based model that captures the effect of an opening of the canopy on local competitive interactions.
Chapter 4 introduces methods to infer the impact of historical deer herbivory on the juvenile survival of forest trees. The approach is generalisable and could be applied to any forest in which patterns of regeneration and community structure have been impacted by periodic disturbance (e.g. forest fires).
Finding meaningful ways of incorporating species diversity into global vegetation models is increasingly recognised as a research priority. In Chapter 5, I explore the diversity of demographic rates in a tropical forest community and identify groups of species with similar life history strategies. I discuss the potential of integrating demographic and physiological traits as a way to aggregate species for inclusion in global models.
In summary, translating measurements of individuals into population dynamics provides opportunities to both explore small-scale community responses to disturbance events, and to feed into much larger scale vegetation models.
Impact of drops upon surfaces with complex morphology
Keywords: Wetting
Hydrodynamics

Drop impacts are ubiquitous in nature forming a vital pathway for the transport of liquids, primarily water, and any dissolved substances. The axisymmetric impact of drops has been heavily studied but less work has been done on droplet impacts in which axial symmetry is broken. To analyse such impacts we used a two phase lattice Boltzmann code capable of simulating high density differences
.
We studied the impact of droplets on cylindrical surfaces, with radius of curvature similar to that of the drop. We found that the symmetry breaking nature of these surfaces leads to droplets bouncing faster and in elongated shapes. The origin of this eﬀect is a positive feedback mechanism through which the momentum asymmetry resulting from the impact grows during retraction.
We next looked at how varying the size of the cylinder affected this phenomenon. We found that smaller cylinders increased the contact time reduction, as long as they were still bigger than the droplet, but that below this limit the drop contacted the ﬂat surface and entered a new regime.
The work was expanded to look at other types of bouncing asymmetry, using a simple, exactly solvable Lagrangian model. We found that contact time reduction can result from an asymmetric droplet shape, an initially asymmetric velocity or if the surface has an asymmetric drag.
A study of the impact of liquid drops containing embedded air bubbles was also undertaken. This was found to lead to jet formation from the bottom of the bubble. We showed how the jet velocity depended on the physical parameters of the drop and impact. In particular the jet formation was very sensitive to the position of the air bubble inside the drop.
Development and characterisation of a cold molecule source and ion trap for studying cold ion-molecule chemistry
Keywords: Ion trapping
Low-temperature physics
Molecular beams
Reaction dynamics
Cold chemistry
Ammonia
Laser cooling

A novel apparatus, combining buffer-gas cooling, electrostatic velocity selection and ion trapping, has been constructed and characterised. This apparatus is designed to investigate cold ion-molecule chemistry in the laboratory, at a variable translational and internal (rotational) temperature. This improves on previous experiments with translationally cold but rotationally hot molecule sources. The ability to vary the rotational temperature of cold molecules will allow for the experimental investigation of post-Langevin capture theories.
Pharmacoproteomic characterisation of human colon and rectal cancer
Keywords: QUASAR 2
proteomics
mass spectrometry
CPTAC
colorectal cancer
patient stratification
CRC65

Colorectal cancer (CRC) is one of the top three most common cancers and among the top four causes of cancer-related deaths worldwide (Torre et al., 2015). CRC patients are well characterised on the transcriptome and proteome level, but proteomics data on representative cell lines as model systems for pre-clinical drug sensitivity studies lag behind. Here, label-free quantitative mass spectrometry was used to characterise the kinomes and full proteomes of 65 CRC cell lines, collectively termed the CRC65 cell line panel. This data was integrated with proteomics data on patient samples, as well as public transcriptome and drug sensitivity datasets, which were reanalysed from raw data in order to unify and streamline the data processing. Protein/mRNA ratios were constant across these datasets, enabling linear prediction of protein abundance from mRNA abundance after appropriate adjustment, which was used for mRNA-guided missing value imputation. An exploration of secondary imputation methods prompted the development of a complementary method for minimum-guided missing value imputation. Combining the proteomics datasets on cell lines and patients led to the discovery of integrated proteomic subtypes of CRC and enabled the identification of representative cell lines for each of them. Modelling publicly available dose-response data generated by four large-scale drug sensitivity studies as a function of kinome/full proteome profiles fuelled the prediction of drug sensitivity for cell lines and patients, allowed the identification of drugs differentially effective between the different integrated proteomic subtypes and revealed MERTK as a predictive biomarker for resistance towards MEK1/2 inhibitors. This predictive role of MERTK was subsequently confirmed using in vitro experiments, while immunohistochemistry of TMAs from 1,074 tumours generated as part of the QUASAR2 clinical trial unveiled that MERTK is also a prognostic biomarker in CRC. This dataset will be made available to the scientific community to facilitate the design of prospective clinical studies.
Has the sweeping revisionism of the Arian Controversy gone too far in sidelining the real theological and political dispute that shaped Christian doctrine?
Keywords: revisionism

The last three decades have produced a number of publications devoted to the revision of Athanasius of Alexandria's "Arian Controversy". The fruits of this re-evaluation highlight the complexities of post-Nicene theology long ignored in the shadow of Athanasius' crude "Arian" versus "orthodox" binary. It is now widely accepted in patristic studies that "Arian" was not a self-designation nor was the presbyter who lent his name to the heresy all that crucial a figure.
A handful of scholars have moved beyond these helpful developments to revise the "Arian Controversy" out of existence. For some, "Arianism” was a rhetorical construct of a power hungry and abusive bishop who indiscriminately branded his personal opponents. Likewise, this revisionist thesis dismisses the activity of any "Eusebians", opting for the complete rejection of conflicting "parties". What remains is not alternate theologies and a genuine dispute, but a phantasmal "Athanasian Arianism". This dissertation analyzes this re-shaping of the post-Nicene years and offers a modest remonstrance to the most extreme aspects of the "Arian Controversy" revision. The study does not want to return to a place of Athanasian hagiography, but rather argue that "Arian" served as a useful polemical heuristic to identify a distinct theology that the bishop (and others) found unacceptable. After outlining the erosion of the "Arian Controversy", the thesis marshals evidence supporting a substantive theological dispute over which divergent networks clashed. In this vein, the work wants to recapture a genuine historical theology in that not everything is reducible to politics. The thesis argues that there is a responsible way of reading Athanasius' charged polemic.
A computational investigation of the electrocardiogram with healthy and diseased human ventricles
Keywords: Simulation
QRS complex
Ventricles
Electrocardiogram
Activation sequence

Cardiovascular diseases are the leading cause of death worldwide, and are estimated to kill over 17 million people each year, about 31% of all deaths. In the clinic, the first diagnostic procedure for a suspected cardiac abnormality is often acquisition of an electrocardiogram (ECG), which measures the electrical potential of the heart at the body surface. Understanding the mechanisms underlying generation of the ECG waveforms is crucial for optimal clinical benefit. Computer simulations possess several strengths as a tool to gain this understanding, particularly in terms of human-specificity, flexibility, repeatability, and ethics.
The ventricles make up the majority of the cardiac volume and are therefore responsible for the majority of ECG waveforms. Ventricular disorders are the most life-threatening, because the ventricles are responsible for pumping blood to the body. Due to their size it has only recently become possible to perform biophysically detailed simulations of the ventricles and torso using supercomputers.
In this thesis, multiscale, mathematical models of the ventricles and torso using the Chaste software library are simulated on high performance computing systems. A description is included of the performance enhancements made in Chaste to improve resource efficiency and accelerate job turnaround, particularly in data storage and the auxiliary tasks of post-processing and data conversion. A novel model of ventricular activation is presented and parametrized using multi-modal human data, and successfully used to simulate normal and pathological QRS complexes. Similarly, repolarization gradients are imposed based on the literature and result in a variety of T waves. Finally, the developed human whole-ventricular and torso models are utilized to gain new insights into possible ionic mechanisms underlying the clinical manifestations of the early repolarization syndrome.
Overall, this thesis presents a novel framework for simulation of the human ECG using high performance computers, with possible applications in basic science and computational medicine.
High-spin impurities and surface acoustic waves in piezoelectric crystals for spin-lattice coupling
Keywords: Surface acoustic wave
Spin

In this thesis we investigate various aspects of SAW devices and strain sensitive spin species in ZnO and LiNbO3 for coupling surface acoustic waves to spin ensembles.
Firstly, we performed a series of ESR experiments exploring the potential of Fe3+ impurities in ZnO for spin-lattice coupling. This spin system has already been identified as a high potential quantum technology component due to its long coherence time. We show that the system also has good properties for spin-lattice coupling experiments, with a strain-coupling parameter G33 = 280 ± 5GHz/strain, which is about 16 times larger than the largest reported for NV centres in diamond. We found that the LEFE effect as well as the spin Hamiltonian parameter D have a linear temperature dependence. As the relative change in each coincide, this strongly supports the notion that the modification of D by an electric field is a multiplicative effect rather than an additive one, D = D0(1 + κΕ). The LEFE coefficient we measured is several times larger for Fe3+:ZnO than for Mn2+:ZnO.
Secondly, we have fabricated and characterised SAW devices on bulk ZnO crystals and Fe doped lithium niobate. We found that the nominally pure ZnO was conductive at room temperature due to n-type intrinsic doping, and electrical losses inhibited any transmission through a SAW delay line above T = 200K. The one-port resonator measured down to milli-Kelvin temperatures showed excellent quality factors of up to Q &sime; 1.5 × 105 in its superconducting state.
Finally, we performed a surface acoustic wave spin resonance (SAWSR) experiment using a one-port SAW resonator fabricated on Fe2+:LN. We observed a clear signal at T &sime; 25 K, at a field near the expected one for a Δms = 2 transition between the |−1〉 and |+1〉 states. We concluded it to be a transition induced by acoustic coupling since the signal intensity did not tend to zero when the magnetic field was parallel to the crystal anisotropy axis. Furthermore, this tells us that the coupling is due to a modulation of the E zero-field splitting parameter rather than D. We investigated the dependence on microwave power and found the saturation limit. We performed a measurement of Fe3+:LN as well to reassure ourselves that the resonance is not magnetically excited by the field around the IDT.
On the identifiability of highly parameterised models of physical processes
Keywords: Structural Unidentifiability
Covariance quantification
Practical Unidentifiability
Region-of-attraction analysis

This thesis is concerned with drawing out high-level insight from otherwise complex mathematical models of physical processes. This is achieved through detailed analysis of model behaviour as constituent parameters are varied. A particular focus is the well-posedness of parameter estimation from noisy data, and its relationship to the parametric sensitivity properties of the model. Other topics investigated include the verification of model performance properties over large ranges of parameters, and the simplification of models based upon their response to parameter perturbation. Several methodologies are proposed, which account for various model classes. However, shared features of the models considered include nonlinearity, parameters with considerable scope for variability, and experimental data corrupted by significant measurement uncertainty.
We begin by considering models described by systems of nonlinear ordinary differen- tial equations with parameter dependence. Model output, in this case, can only be obtained by numerical integration of the relevant equations. Therefore, assessment of model behaviour over tracts of parameter space is usually carried out by repeated model simulation over a grid of parameter values. We instead reformulate this as- sessment as an algebraic problem, using polynomial programming techniques. The result is an algorithm that produces parameter-dependent algebraic functions that are guaranteed to bound user-defined aspects of model behaviour over parameter space.
We then consider more general classes of parameter-dependent model. A theoretical framework is constructed through which we can explore the duality between model sensitivity to non-local parameter perturbations, and the well-posedness of parameter estimation from significantly noisy data. This results in an algorithm that can uncover functional relations on parameter space over which model output is insensitive and parameters cannot be estimated. The methodology used derives from techniques of nonlinear optimal control. We use this algorithm to simplify benchmark models from the systems biology literature. Specifically, we uncover features such as fast-timescale subsystems and redundant model interactions, together with the sets of parameter values over which the features are valid.
We finally consider parameter estimation in models that are acknowledged to im- perfectly describe the modelled process. We show that this invalidates standard statistical theory associated with uncertainty quantification of parameter estimates. Alternative theory that accounts for this situation is then developed, resulting in a computationally tractable approximation of the covariance of a parameter estimate with respect to noise-induced fluctuation of experimental data.