VictorJuiz/thesis huggingface dataset:
Challenging the orthodox view of human rights
Keywords: Human Rights
Political theory

The concept of human rights holds a distinctive significance in political practice, yet philosophers remain divided over the nature of these rights. The Orthodox View defines human rights as moral rights possessed by all individuals simply in virtue of their humanity. Proponents of this view claim that the contemporary idea of human rights is a continuation of the natural rights project of the eighteenth century and shares many of its basic philosophical assumptions.
This thesis argues that the Orthodox View is no longer an appropriate characterisation of the concept of human rights we find in current domestic and international practice. It also rejects recent alternatives offered by supporters of the Political View, who define human rights by particular functions they serve, specifically their role(s) in acting as benchmarks for the legitimacy of states or triggers of international concern.
I propose instead a new 'Political Justification View' of human rights, which states that human rights are demands which challenge unjustifiable political-institutional orders, which are the concern of all people, and which protect the equal standing of individuals in political decisions that affect the collective or individual good. This view better captures the diversity of practices that employ the term 'human rights', whilst also explaining its innovative power as a moral language that enables individuals to challenge the official institutional order under whose authority they live.
Finally, I argue that within this broader view of human rights there are two distinct moral concepts which pertain to different parts of human rights practice: Domestic Human Rights and International Legitimacy Rights. Separating these two concepts is helpful in resolving long-standing debates about whether human rights are properly thought of as minimalist moral concerns of legitimacy or broader social goals to be achieved through political institutions.
The role of innate lymphoid cells in intestinal inflammation
Keywords: Inflammatory bowel disease
Innate lymphoid cells

A breakdown of intestinal homeostasis due to dysregulated immune responses against intestinal bacteria underlies the pathogenesis of inflammatory bowel disease (IBD) in genetically susceptible individuals. Amongst mucosal immune cells, innate lymphoid cells (ILCs) are a heterogeneous group of cells whose functions in pathogenic inflammatory processes in the intestine are beginning to emerge from experimental murine models. However, less is known about the role of ILCs in chronic intestinal inflammation in humans.
In this thesis, human ILCs were examined in the context of IBD and potential mechanisms by which these cells may contribute to IBD pathogenesis were investigated. We identified phenotypically and functionally distinct ILC1, ILC2 and ILC3 populations in the human intestinal lamina propria and peripheral blood and found that ILCs enriched for expression of IL-17A and IFNγ accumulated in the inflamed intestine, potentially through increased in situ proliferation and chemokine-mediated recruitment from blood. Based on their in situ localization, we investigated potential functional interactions between ILCs and CD4+ T cells and found that a proportion of human ILCs in peripheral blood and the intestinal lamina propria expressed HLA-DR and co-stimulatory molecules. ILCs were capable of taking up and processing protein antigen at levels equivalent to B cells, but in contrast to monocytes, antigen-pulsed ILCs failed to activate antigen-specific memory CD4+ T cells in vitro. Reciprocal activation between ILCs and monocytes enhanced the antigen-presenting potential and bactericidal capacity of myeloid cells and induced upregulation of co-stimulatory ligand expression by ILCs. This innate activation loop resulted in an augmentation of CD4+ T cell activation.
These findings extend our knowledge of the complex interactions between human ILCs and other key immune cell populations, and suggest mechanisms by which rare ILCs may contribute to the pathogenesis of IBD by augmenting myeloid cell and CD4+ T cell responses.
The politics of implementing e-government for development: the ecology of games shaping property tax administration in Bangalore city, India
Keywords: Ecology of Games
Strategic Choice Architecture
Political Game Theory
Behavioural Economics
Design-Actuality Gap Model

The recent global diffusion of information and communications technologies (ICTs) has raised expectations for technological change to support socio-economic progress and political reform in the developing as well as the developed world. Particularly prominent is the promise of ICT platforms and applications that enable innovations in electronic government (e-government), since their implementation and use in the public sector are often linked to organizational and administrative reforms.
Much has been written about e-government within a growing stream of literature on ICT for development, generating countervailing perspectives where optimistic, technocratic approaches are countered by far more sceptical standpoints on technological innovation. This body of work is not without its limitations: a large proportion has been anecdotal in its style and overly deterministic in its logic, with far less being empirical, and there is a tendency for models offered up by scholarly research to neglect the actual attitudes, choices and behaviour of the wide array of actors involved in the implementation and use of new technology in real organisations.
To address these shortcomings, this research sought to focus on an empirical case study surrounding the implementation and use of an electronic property tax collection system in Bangalore, India between 1998 and 2008. Early work reinforced the need to move beyond technologically deterministic explanations of the project, prompting the study to draw on the theoretical perspective of the 'Ecology of Games' which (being close to theories of New Institutionalism) recognises the importance of a multitude of diverse motives and individualistic behaviour as key factors influencing organisational reform and institutional change.
This thesis thus contributes not just to an understanding of the role of ICTs in administrative reform in development, but towards an emerging body of research that is critical of managerial rationalism for an organization as a whole, and sensitive to an ecology of actors and motivations within the organisation. The core research findings of the work question the received wisdom prevalent in current political and development discourse that all actors on such projects, operating within a given game arena or game ecology possess a global, rational perspective on the role of technology, both in government and within their particular domain specialism; suggesting that both scholars of e-government and top management would do well to recognise and seek to understand the complex web of varying actor interests and motivations inherent within ICT-fordevelopment projects.
In vitro, in silico and in vivo studies of the structure and conformational dynamics of DNA Polymerase I
Keywords: single-molecule spectroscopy
in-cell FRET
single-molecule FRET

DNA polymerases are a family of molecular machines involved in high-fidelity DNA replication and repair, of which DNA polymerase I (Pol) is one the best-characterized members. Pol is a strand-displacing polymerase responsible for Okazaki fragment synthesis and base-excision repair in bacteria; it consists of three protein domains, which harbour its 5’-3' polymerase, 3’-5’ exonuclease and 5’ endonuclease activities.

In the first part of the thesis, we use a combination of single-molecule Förster resonance energy transfer (smFRET) and rigid-body docking to probe the structure of Pol bound to its gapped-DNA substrate. We show that the DNA substrate is highly bent in the complex, and that the downstream portion of the DNA is partly unwound. Using all-atom molecular dynamics (MD) simulations, we identify residues in the polymerase important for strand displacement and for downstream DNA binding. Moreover, we use coarse-grained simulations to investigate the dynamics of the gapped-DNA substrate alone, allowing us to propose a model for specific recognition and binding of gapped DNA by Pol.

In the second part of the thesis, we focus on the catalytically important conformational change in Pol that involves the closing of the ‘fingers’ subdomain of the protein around an incoming nucleotide. We make use of the energy decomposition method (EDM) to predict the stability-determining residues for the closed and open conformations of Pol, and test their relevance by site-directed mutagenesis. We apply the unnatural amino acid approach and a single-molecule FRET assay of Pol fingers-closing, to show that substitutions in the stability-determining residues significantly affect the conformational equilibrium of Pol.

In the final part of the thesis, we attempt to study Pol in its native environment of the living cell. We make use of the recently developed method of internalization by electroporation, and optimize it for organically labelled proteins. We demonstrate the internalization and single-molecule tracking of Pol, and provide preliminary data of intra-molecular FRET in Pol, both at the single-cell and single-molecule levels. Finally, by measuring smFRET within an internalized gapped-DNA construct, we observe DNA binding and bending by endogenous Pol, confirming the physiological relevance of our in vitro Pol-DNA structure.
Efficiency and other-regarding preferences in information and job-referral networks
Keywords: lab-in-the-field experiment
public goods
social networks
other-regarding preferences

In this thesis I study how networks are formed and I analyse the strategies that well-connected individuals adopt in public good games on a network.

In chapter one I study an artefactual field experiment in rural India which tests whether farmers can create efficient networks in a repeated link formation game, and whether group categorisation increases the frequency of in-group links and reduces network efficiency. I find that the efficiency of the networks formed in the experiment is significantly lower than the efficiency which could be achieved under selfish, rational play. When information about group membership is disclosed, in-group links are chosen more frequently, while the efficiency of network structure is not significantly affected.

Using a job-referral network experiment in an urban area of Ethiopia, I investigate in chapter two whether individuals create new links with the least connected players in the network. In a first treatment, competition for job-referrals makes it in the player’s interest to link with the least connected partners. In this treatment, links to the least connected players are significantly more likely than links to better connected individuals. In a second treatment, connections only affect the welfare of the new partner. Choosing the least connected player minimises inequality and maximises aggregate efficiency. This may motivate other-regarding players. In this treatment, however, links to least connected partners are not significantly more likely than links to other players.

In chapter three I explore the characteristics that individuals value in the people they approach for advice. Using cross-sectional data on cocoa farmers in Ghanaian villages and a matched lottery experiment, I find an association between the difference in the aversion to risk of two farmers and the probability that one farmer is interested in the advice of the other farmer.

In chapter four I study a one-shot public good game in rural India between farmers connected by a star network. Contributions by the centre of the star have a larger impact on aggregate payoffs than contributions by the spoke players. I use the strategy method to study whether the centre of the star contributes more than the average of the spokes. In selected sessions, I disclose participants’ expectations about the choices of the centre of star. I find that the centre player contributes just as much as the average of the spokes, and that he is influenced by the expectations that other players hold about his decisions.
Three-dimensional aligned fibrillar scaffolds -- fabrication and characterization
Keywords: electrospinning
multiphoton
second harmonic generation

Aligned fibrillar scaffolds (AFSs) have been widely studied for their application in regenerative medicine, providing possible transplantable tissue replacements for nerve, spinal cord, tendon, ligament, muscle, etc. However, researches in AFSs are technically challenging mainly due to the complex fabrication and characterization processes, especially when the AFSs are made to be fully three-dimensional (3D). As the structure is linked to the quality and function of the engineered tissue product, there is an urgent need for novel techniques to characterize AFSs non-invasively and non-destructively and to link their characteristics to their functions and outcome.

In this thesis AFS fabrication and characterization were explored. By combining second harmonic generation (SHG) imaging, multiphoton microscopy (MPM), and various image processing tools, the whole process of 3D tissue characterization could be achieved in a non-invasive, precise, and quantitative way. A proof-of-concept AFS with blended fibers made of polycaprolactone and porcine gelatin was used to demonstrate the feasibility of implementing such a strategy. The data indicated that, in terms of scaffold characterization, the proposed MPM method was capable of measuring the porosity of homogenous scaffolds precisely from deconvolved 3D images. Furthermore, the method could also be used to illustrate the orientation of the aligned nanofibers. Next, when SH-SY5Y neurons were cultured on the AFS, the MPM imaging was capable of evaluating the cell viability ratio, cell-localization in AFS, and neurite outgrowth. This provided guidance for selecting the alignment method for AFS functional recovery. Lastly, when employing this non-invasive imaging-based characterization method, it was possible to illustrate the relationship between the alignment of collagen arrays in decellularized corneal stroma and the transparency. In summary, the proposed strategy can provide some essential scaffold/tissue properties (such as alignment of fiber, porosity of scaffold, and cell viability ratio) quantitatively and non-invasively, which will help both scaffold processing design and characterization.
Absolute distance interferometry capable of long-term high frequency measurements of fast targets
Keywords: absorption spectroscopy
laser interferometry
absolute distance measurement
metrology

This thesis presents two novel absolute distance measurement techniques which expand the recently developed dynamic frequency scanning interferometry method [1][2][3]. Preliminary work to improve the frequency referencing of the techniques will also be reported.
The first method was developed to eliminate gaps in the distance measurement which were present in previous approaches and is referred to as continuous frequency scanning interferometry (continuous FSI). This technique has been successfully demonstrated on stationary targets at a range of 2.5–5 m and moving targets at speeds around 2 mm/s and 8 mm/s.
The second method is referred to as enhanced continuous FSI (enhanced CFSI). It addresses one of the main limitations of the continuous FSI technique by greatly increasing the allowable target motion speed. Proof of principle measurements of enhanced continuous FSI have been performed at speeds of up to 16 mm/s and are presented here.
The improved frequency referencing technique uses an optical nanofibre to perform saturated absorption spectroscopy of acetylene-13. The equipment, experimental procedure and preliminary results are presented.
Ultrasound segmentation tools and their application to assess fetal nutritional health
Keywords: Live Wire
shape model
Feature Asymmetry
analytic signal
monogenic signal

Maternal diet can have a great impact on the health and development of the fetus. Poor fetal nutrition has been linked to the development of a set of conditions in later life, such as coronary heart disease, type 2 diabetes and hypertension, while restricted growth can result in hypogylcemia, hypocalcemia, hypothermia, polycythemia, hyperbilirubinemia and cerebral palsy. High alcohol consumption during pregnancy can result in Fetal Alcohol Syndrome, a condition that can cause growth retardation, lowered intelligence and craniofacial defects. Current biometric assessment of the fetus involves size-based measures which may not accurately portray the state of fetal development, since they cannot differentiate cases of small-but-healthy or large-but-unhealthy fetuses.

This thesis aims to outline a set of more appropriate measures of accurately capturing the state of fetal development. Specifically, soft tissue area and liver volume measurement are examined, followed by facial shape characterisation.

A number of tools are presented which aim to allow clinicians to achieve accurate segmentations of these landmark regions. These are modifications on the Live Wire algorithm, an interactive segmentation method in which the user places a number of anchor points and a minimum cost path is calculated between the previous anchor point and the cursor. This focuses on giving the clinician intuitive control over the exact position of the segmented contour.

These modifications are FA-S Live Wire, which utilises Feature Asymmetry and a weak shape constraint, ASP Live Wire, which is a 3D expansion of Live Wire, and FA-O Live Wire, which uses Feature Asymmtery and Local Orientation to guide the segmentation process. These have been designed with each of the specific biometric landmarks in mind.

Finally, a method of characterising fetal face shape is proposed, using a combination of the segmentation methods described here and a simple shape model with a parameterised b-spline meshing approach to facial surface representation.
Linear optics quantum computing with single photons from an atom-cavity system
Keywords: single photons
cavity QED
linear optics quantum computing
quantum information
atomic physics

One of today’s challenges to realise computing based on quantum mechanics is to reliably and scalably encode information in quantum systems. Here, we present a photon source to on-demand deliver photonic quantum bits of information based on a strongly coupled atom-cavity system. The source operates intermittently for periods of up to 100 μs, with a single-photon repetition rate of 1 MHz, and an intra-cavity production efficiency of up to 85%. Our ability to arbitrarily control the photons’ wavepackets and phase profiles, together with long coherence times of 500 ns, allows to store time-bin encoded quantum information within a single photon. To do so, the spatio-temporal envelope of a single photon is sub-divided in d time bins which allows for the delivery of arbitrary qu-d-its. This is done with a fidelity of > 95% for qubits, and 94% for qutrits verified using a newly developed time-resolved quantum-homodyne measurement technique.

Additionally, we combine two separate fields of quantum physics by using our deterministic single-photon source to seed linear optics quantum computing (LOQC) circuits. As a step towards quantum networking, it is shown that this photon source can be combined with quantum gates, namely a chip-integrated beam splitter, a controlled-NOT (CNOT) gate as well as a CNOT4 gate. We use this CNOT4 gate to entangle photons deterministically emitted from our source and observe non-classical correlations between events separated by periods exceeding the travel time across the chip by three orders of magnitude. Additionally, we use time-bin encoded qubits to systematically study the de- and re-phasing of quantum states as well as the the effects of time-varying internal phases in photonic quantum circuits.
Unconscious Christianity: a neglected element in Dietrich Bonhoeffer's late theology
Keywords: Dietrich Bonhoeffer

In this thesis I argue that unconscious Christianity (unbewußtes Christentum), referred to by Dietrich Bonhoeffer in several of his later writings, is a significant idea in his late theology. There has as yet been no in-depth study of this theological concept as it appears in Bonhoeffer's work, and I therefore aim with this thesis to begin a new conversation in Bonhoeffer studies on this important topic. Bonhoeffer does not offer a definition of unconscious Christianity, but by analysing the ways in which he uses the term in his writing, I offer a constructed definition of unconscious Christianity as used by Bonhoeffer. The first three chapters of the thesis build towards this definition with a close analysis of each relevant text. By examining unconscious Christianity alongside other theological ideas in Bonhoeffer's prison writing, I show how an awareness and understanding of unconscious Christianity adds depth to readings of Bonhoeffer's late work. This thesis also clarifies the differences between unconscious Christianity and religionless Christianity, and shows how unconscious Christianity fits alongside the other, more widely-studied, concepts present in the later writings, such as the world come of age. This work demonstrates that there is movement within Bonhoeffer's thoughts on unconscious Christianity and points to Bonhoeffer's readiness to allow his personal circumstances to inform his theology. It also shows how unconscious Christianity represents a shift within Bonhoeffer's theology. This thesis also makes the subsidiary point that Bonhoeffer's prison fiction should be considered as theological writing. Through it Bonhoeffer addresses not only unconscious Christianity as discussed in this thesis, but many other issues that reoccur in his theological prison letters. I conclude by showing how an understanding of unconscious Christianity is beneficial not only for Bonhoeffer studies, but for contemporary theology more widely.
Investigations into the structure, function and pharmacology of TREK K2P potassium channels
Keywords: ion channels
pharmacology
TREK-2
mechano-sensitivity
TREK-1
polymodal gating
patch clamp electrophysiology
TRAAK
K2P
norfluoxetine

TREK channels are polymodal potassium channels which act as integrators of diverse chemical and physical stimuli to dynamically control the cellular membrane potential. How the channels sense different stimuli, and how this is transduced to channel gating is not fully understood. Here I report the results of electrophysiological investigations into the structure-function relationship and pharmacology of TREK channels. Firstly, the mechanism of action of plant derived alkylamides at TREK-1 was found to be complex and assay-context dependent. Subsequent studies of TREK-2, guided by recent X-ray crystal structures, provide novel insights into the mechanisms of gating in mechano-, temperature-, arachidonic acid- and pH-modulation. Studying the effect of these different gating stimuli, and the effects of different gating mutations on the potency of state-dependent inhibitors reveals the existence of multiple, distinct open conformations. The results of these studies are consolidated into a structural model for polymodal gating in TREK channels.