VictorJuiz/thesis huggingface dataset:
HSV-1 amplicons; a non-integrating, high transgene capacity tool for the generation and differentiation of induced pluripotent stem cells

Induced pluripotent stem (iPS) cells are valuable for generating patient-specific disease models. Many reprogramming systems have been developed however some technological concerns remain including insertional mutagenesis caused by integrating viruses, low efficiency and low transgene capacity.
Herpes simplex virus type-1 (HSV-1) amplicons address the main limitations of current reprogramming methods as they are non-integrating and have a large transgene capacity of 150 Kb. In addition HSV-1 amplicons have a high transduction efficiency in both primary fibroblasts and iPS cells. We have developed three sets of HSV-1 amplicons to reprogram fibroblasts to iPS cells, directly differentiate fibroblasts to dopaminergic neurons and aid dopaminergic neuron differentiation from iPS cells.
1) We constructed and characterised a set of HSV-1 reprogramming amplicons, which express the reprogramming factors Oct-4, Sox-2, Klf-4, C-Myc, Nanog and Lin28. These vectors were capable of generating partially reprogrammed colonies as confirmed by RT-PCR analysis of pluripotency factors. We were unable to generate fully reprogrammed colonies and our results suggest that this is due to an induction of the p53 pathway.
2) We constructed an HSV-1 direct differentiation amplicon containing the polycistronic cassette Mash-1, Nurr-1 and Lmx1a. All elements were functional however we were unable to generate dopaminergic neurons.
3) We constructed and characterised a set of HSV-1 neuronal differentiation amplicons expressing the neuronal transcription factors Nurr-1, Lmx1a, FoxA2 and PitX3. We employed a 96 well differentiation protocol and transduced the differentiating cultures with our neuronal amplicons to try and improve dopaminergic neuron efficiency. Transduction at early time points in the protocol resulted in a significant increase in TH positive neurons.

Advisor: Wade-Martins, R
James, W
Political theory as moral philosophy

I argue against the claim that normative political theory is ‘autonomous’ with respect to moral philosophy. I take the simple view that political theory is a form of moral philosophy, and is differentiated by pragmatic rather than theoretically significant criteria. I defend this view by criticizing arguments for the autonomy thesis. In the first three chapters I introduce and analyse the autonomy thesis and provide a framework for understanding the various claims that are made in the literature. In Chapters 4 to 8 I proceed to criticize a series of arguments for the autonomy thesis. In Chapter 4 I explain why Kant’s division of morality into ethics and right is not as useful as it may seem to those who wish to defend the autonomy thesis, and argues that Arthur Ripstein gives no reason to think that political philosophy is autonomous that can be endorsed independently of commitment to a Kantian normative theory. In Chapter 5 I examine the political liberal argument for the autonomy thesis, concluding that even if a freestanding political conception of justice can be regarded as autonomous, it does not follow that political philosophy can also. Chapters 6 to 8 tackle various political realist arguments for the autonomy thesis. In Chapter 6 I argue that political theory is not required to deal with empirical facts in any way that distinguishes it from moral philosophy, and any argument for its autonomy that is based on a prior claim about the purpose of political theorizing would be question-begging. In Chapters 7 and 8 I provide various arguments against the idea that there is a distinctively political form of normativity, and diagnose some of the mistaken assumptions about morality that I take to lie at the heart of the realist case. In Chapter 9 I conclude.

Keywords: autonomy of politics
autonomy of political philosophy
autonomy of political theory
Advisor: Stemplowska, Z
Gardner, J
The right to food and trade law in the external relations of the European Union with developing countries

The European Union has exclusive competence to negotiate trade agreements with third countries. Using this competence the European Commission developed an extensive policy to conclude free trade agreements with numerous countries around the world. These agreements include regulation of the import and export of food products and also involve developing countries prone to hunger and malnutrition. This thesis investigates the recent trade agreements between the European Union and developing countries from the perspective of the human right to adequate food. This thesis demonstrates that the clauses on import and export of food products of such agreements limit the capacity of the developing countries involved to realise the right to food of their citizens. This outcome does not take into account the normative content of the right to food as contained in international human rights law and is dismissive of the references to human rights contained in European Union funding treaties and in the previous agreements between the European Union and developing countries. This thesis also demonstrates that this outcome is mainly an autonomous policy decision of the European Union and its trade partners independent from the obligations of World Trade Organization law. The thesis concludes with several proposals of reform to conciliate the external trade objectives of the European Union with the human right to adequate food.
A position-sensing system for the top PMT array in the LUX-ZEPLIN dark matter experiment

LUX-ZEPLIN (LZ) is a next-generation liquid xenon dark matter detection experiment, searching for direct interactions with WIMPs. As it is a low-background experiment using high-purity xenon, the sensors installed to monitor the experiment must be custom-made from a short list of acceptable materials. This includes the position sensors that will monitor the relative position of the top photomultiplier tube (PMT) array with respect to the cryostat vessel that surrounds it. LZ will operate at around -100°C, so must undergo a significant cooling period, during which the vessel that supports the PMT array is expected to shrink. It is crucial to monitor this.
The capacitive position sensors couple a change in relative position to a change in capacitance. However, the size of the LZ detector necessitates the use of cables around 12m long to read out this signal. These cables will have a capacitance themselves of around 1 nanofarad, which can vary as the cable environment changes, while the sensor capacitances are around a thousand times smaller, so small variations in the cable capacitance could be misinterpreted as changes in position. To combat this, we created a novel feedback circuit for the sensor readout electronics, designed to suppress the effect of the cable capacitance.
To monitor precisely the position of the PMT array with respect to the cryostat vessel, we will use six position sensors mounted as a Gough-Stewart Platform Mechanism (GSPM) between the PMT truss and the cryostat vessel. The use of six sensors in this configuration will enable the reconstruction of all six degrees of freedom of the position of the PMT array. I have developed an algorithm that returns these six values given input from the position sensors. The six capacitive sensors connected as a GSPM, with the novel readout electronics, form the system of position sensors that will be used in the LUX-ZEPLIN experiment.

Advisor: Kraus, H
Forest histories and nuclear futures: mapping resources, value, and change in southern Tanzania

At a time when an estimated one-quarter of UNESCO sites of natural world heritage are threatened by existing or proposed extractive projects, this thesis explores the histories and futures in and around sub-Saharan Africa’s oldest and largest wilderness area, where Tanzania’s first uranium mine is quiet as it completes its sixth year of delays. Today’s contested perceptions of the future of the UNESCO World Heritage Site Selous Game Reserve are a product of the social construction of wilderness that has been developed and applied over time to African landscapes through (post)colonial models of conservation. While the rationale for conservationists’ opposition to extraction has been articulated, this thesis examines the historical dynamics of local expectations of extraction.
The thesis argues that the multiplicity of valued resources at stake in and around the mine demands an approach that takes into account uranium, but also wildlife, land, and water. This natural resource intersectionality also reflects the scales at hand: a mineral deposit containing globally significant amounts of uranium, a wilderness area the size of Switzerland, and the infinite lifespan of uranium’s radioactive decay. Ultimately, the study maps the ways that the incursion of mining activities is destabilizing the local order. Across scales of space and time, the Selous emerges, not as a primordial forest wilderness, but instead as a sacrifice zone, set aside for de-territorialization, discipline, and extraction. I demonstrate that it is the heritagization process that helps to re-imagine, and therefore re-create, the past, but also that it projects particular ambitions ahead: an imagined, pristine Selous woodland of past, intervening in the present, and influencing the future of the Reserve. I investigate the conceptual nexus between conservation and extraction, challenging simplistic narratives which place the two in opposition. As the mine languishes, the thesis provides evidence from neighbouring villages suggesting that despite seemingly universal support for the mine, there is uncertainty and ambivalence toward the future, with or without uranium.

Advisor: Sarro, R
Quantum groups at q=0, a Tannakian reconstruction theorem for IndBanach spaces, and analytic analogues of quantum groups

This thesis is divided into the following three parts.
A categorical reconstruction of crystals and quantum groups at q = 0. The quantum co-ordinate algebra Aq(&gfr;) associated to a KacMoody Lie algebra g forms a Hopf algebra whose comodules are direct sums of finite dimensional irreducible Uq(&gfr;) modules. In Part I we investigate whether an analogous result is true when q = 0. We classify crystal bases as coalgebras over a comonadic functor on the category of pointed sets and encode the monoidal structure of crystals into a bicomonadic structure. In doing this we prove that there is no coalgebra in the category of pointed sets whose comodules are equivalent to crystal bases. We then construct a bialgebra over &Zopf; whose based comodules are equivalent to crystals, which we conjecture is linked to Lusztig’s quantum group at v = ∞.
A Tannakian Reconstruction Theorem for IndBanach Spaces. Classically, Tannaka-Krein duality allows us to reconstruct a (co)algebra from its category of representation. In Part II we present an approach that allows us to generalise this theory to the setting of Banach spaces. This leads to several interesting applications in the directions of analytic quantum groups, bounded cohomology and Galois descent. A large portion of Part II is dedicated to such examples.
On analytic analogues of quantum groups. In Part III we present a new construction of analytic analogues of quantum groups over non-Archimedean fields and construct braided monoidal categories of their representations. We do this by constructing analytic Nichols algebras and use Majid’s double-bosonisation construction to glue them together. We then go on to study the rigidity of these analytic quantum groups as algebra deformations of completed enveloping algebras through bounded cohomology. This provides the first steps towards a p-adic Drinfel'd-Kohno Theorem, which should relate this work to Furusho's p-adic Drinfel'd associators. Finally, we adapt these constructions to working over Archimedean fields.

Keywords: Quantum Groups
Crystal Bases
Advisor: Kremnitzer, K
Radiation dosimetry for studying the late effects of radiotherapy

Evidence that radiation-related cardiovascular disease and second primary cancers can occur in cancer survivors following radiation therapy (RT) has emerged from several independent sources. Cardiotoxicity and second cancers are of particular concern for patients with good prognosis, such as those with Hodgkin lymphoma (HL). HL patients are among the youngest to receive RT, which means that those who are cured of their cancer have decades-long natural life-expectancies during which treatment-related long-term toxicities may cause years of excess morbidity or premature mortality. A considerable amount of research has been conducted to investigate the risk of radiation-related cardiotoxicity and second cancers. However, there are still substantial gaps in knowledge. It is therefore important to improve our understanding regarding these risks and develop treatment approaches and survivorship care to minimise their impact on patients’ quality of life. In this thesis, I have investigated the risk of congestive heart failure (CHF) in a cohort of 2619 HL survivors and presented, for the first time, dose-response relationships for risk of CHF versus cardiac radiation doses. I also validated the radiation dosimetry method used to estimate the cardiac doses in this study as well as for other reconstruction methods, versus a gold standard based on the patients’ own computed tomography scans. Additionally, I investigated what effect the dose reconstruction errors had on the dose-response relationships. I then focused on modern RT methods and specifically on proton RT. Based on published dose-response relationships (including that developed in this thesis) I predicted cardiovascular and second cancer risks for patients treated with advanced RT. This thesis has provided new knowledge in the study of late effects in HL patients who were treated decades ago as well as for patients treated more recently with advanced RT methods. The results here can be used to facilitate progress towards personalised RT in terms of choosing the appropriate RT method by integrating individualised risk prediction in advanced RT treatment planning. The research here provides the basis for further work towards evidence-based case selection for HL patients for the first NHS proton therapy centres in the UK, opening in 2018-2021.

Keywords: Retrospective dosimetry
Radiation-related cardiac disease
Hodgkin lymphoma
Advisor: Darby, S
Cutter, D
Van Den Heuvel, F
Aznar, M
Human and environmental change at North Atlantic coastal settlements, ca. AD 900-1700: a chronological perspective

How environmental change affects human settlement is a research question that is becoming increasingly important to us in the twenty-first century. The North Atlantic, from ca. AD 900-1800, is currently one of the most well-studied regions and times for answering this research question. Norse exploration of the North Atlantic and subsequent colonisation and settlement – both short- and long-term – of the various islands there has been interpreted as a narrative of adaptation to new and changing environmental conditions. Although there is a relative wealth of archaeological and environmental data from the region, chronology remains an area needing further study. This thesis synthesises a wide range of scientific chronological data – constructing new chronologies for two small-scale landscapes in case studies from Iceland and Orkney, and then using Bayesian modelling to derive new analyses from published dating information throughout the region – in order to work towards a cohesive narrative of North Atlantic settlement and adaptation that includes scientific chronologies.

Advisor: Griffiths, D
Pollard, M
The contagion of desire: two case studies of appropriation art

My doctoral thesis is comprised of two bodies of research: two artworks taking the form of installations (videos, audio recordings, textiles, texts), which will be exhibited for viva.
Femme Fabrications, 2016, is made from research into the American artist Joseph Cornell’s (1903-1972) source materials held in the Smithsonian American Art Museum alongside research on Jean Wilkinson’s 1977 book Flower Fabrications.
A series of textile works encased in silk lined boxes trace my step-by-step construction of a rose from organdie. The floral emblem of the white rose (dried), ‘death is preferable to a loss of innocence’ , becomes an editing device, which I use to consider a number of possible recipients for the rose, such as Cornell himself. Spoken word audio recordings, which ruminate on how his sexuality pertain to the criteria of the rose are edited together with home-camcorder video footage of the house that Cornell lived in for most of his life - the house he made the entirety of his artworks within.
Central to The Cesspool of Rapture, 2017, are moving-image studies of zippers, stains, rips, abrasions, openings, and closings in a series of dresses made by the American couturier Charles James (1906-1978). These videos register and move through the material research, the garments, at alternating speeds. The changing speed is registered in sound by clicks synced to each individual frame. It is at times violent and at other times tentative and gentle as the uncovering of the damage to the dresses unfolds. Audio recordings of James explicating his interests in eroticism and sexuality persistently interject the footage.
This work includes the installation of a series of reconstructions of James’s 1932 Taxi dress. Its black linen body is reconfigured and abstracted as the splayed design makes unfinished seams and unzipped zippers visible.
In each artwork I configure viewing and consuming as a mode of authorship. I show how these diverse processes of identification become authored acts. When drawn into intimate relation with the leftover material of these historical authors, my contamination proves deviant: I gain possession of the capacity to speak for them, to expose, idolise, misrepresent, and fictionalise them. My thesis is composed of this group of methodologies, which were found and developed within the production of the artworks.

Keywords: Joseph Cornell
Clothes
Rose
Fiction
Voice
Zipper
Art Writing
Installation Art
Couture
Appropriation Art
Sexuality
Video Art
Charles James
Desire
Advisor: Price, E
Palmer, K
Magnetic effects in astrophysically relevant laboratory plasmas

Astrophysics typically uses observation, theory and simulation to further the understanding of the cosmos. By using high power lasers, scaled astrophysical events can be created in the laboratory.
This thesis describes laboratory results based on two different astrophysical phenomena, particle acceleration and the turbulent dynamo mechanism, both of which are governed by magnetic fields.
Particle acceleration is commonly seen at astrophysical shocks. The exact mechanism of this acceleration, especially for electrons, remains unclear. One possible method of electron acceleration is through lower hybrid turbulence, a phenomena observed at the interaction between the Solar wind and a comet. The results from a laboratory experiment demonstrate the observation of electron acceleration via lower hybrid waves. Lower hybrid waves require an external magnetic field to generate the necessary electron accelerating instability.
Magnetic fields themselves are ubiquitous throughout the universe. Having generated seed fields through, for example an astrophysical shock, these magnetic fields can be ampliflied through the turbulent dynamo mechanism. To generate the dynamo mechanism within the laboratory, two plasma jets are collided. A new Faraday rotation diagnostic, for magnetic field measurements, was added to the suite of diagnostics characterizing the turbulent plasma. The setup, calibration and analysis for the Faraday rotation diagnostic is new to the OMEGA laser facility and dynamo experiment. The results from this new Faraday rotation diagnostic and Thomson scattering diagnostic allow the plasma parameters and evolution of the jets to be fully characterized.
Finally, the thesis is concluded by drawing these results together.

Advisor: Gregori, G
Islamic finance: the convergence of faith, capital, and power

This dissertation assesses how Islamic finance fares as an example of ‘civil compromise’ in Islamic law. By focusing on the Islamic project finance sector, my research examines how the industry’s main stakeholders (representing faith, capital, and power) cooperate and compete to bring about this compromise through the ‘Game of Islamic Bank Bargains’.
The Islamic finance industry is a work in progress, and while it has made some significant strides, it is still a niche in the global conventional financial order rather than an alternative to it. It has fallen short of fulfilling its originally-stated social justice aspirations, but has provided a previously unavailable form of banking and finance for Muslims to transact, at least formalistically, in accordance with widely-believed tenets of their faith. Thus, those who hold up Islamic finance as a universal panacea or dismiss it outright as a fraud have both got it wrong. It is neither. It is, rather, a complex myriad of incentives and aspirations of a multitude of stakeholders muddled together across numerous geographies and evolving incrementally and constantly. 
The state of the industry is the result of how the stakeholders (the shariah scholars, lawyers, bankers, government officials, and customers) have pursued their self-interest in the Game of Islamic Bank Bargains. My research examines who are the ‘winners’ and ‘losers’ of this game, and what religious, commercial, and political factors have influenced this outcome. I assess what may incentivise the incumbent ‘winners’ to guide the Islamic finance industry away from a formal and legalistic approach towards one that also incorporates principles from Islamic economics. I explore how the ‘losers’—whose interests are not accounted for due to their lack of sufficient financial and political clout—can sway the outcome of the game in their favour.

Keywords: Islamic banking and finance
Shariah finance
Civil Compromise
Shariah scholars
Islamic bankers
Advisor: Kurkchiyan, M