VictorJuiz/thesis huggingface dataset:
Application of genomic technologies for molecular diagnosis of genetic diseases
Keywords: Macular degeneration
IRD
Molecular diagnostics
NGS
ABCA4
Stargardt
Ohtahara syndrome
Next-generation sequencing
Inherited retinal degeneration

Methods for sequencing deoxyribonucleic acid (DNA) have improved rapidly in the past decade. Recent methods, termed "next-generation sequencing" (NGS), have made sequencing large quantities of DNA economically viable in molecular diagnostics of genetic diseases. This thesis describes some of the first investigations to use NGS for such a purpose.
Several different NGS platforms, each of which differs substantially in terms of sample preparation, chemistry, and sequencing methodology, were tested, in addition to several sequence capture and enrichment technologies that allow sequencing to be targeted, and these combinations were compared to Sanger sequencing. They were each found to have different strengths and weaknesses, which affect their accuracy, reliability, time taken to results, financial cost, and ease of use, but all showed high accuracy and dramatically increased throughput over Sanger sequencing.
NGS was used to identify pathogenic mutations in two groups of patients who had either inherited retinal dystrophies (IRD), or severe early onset epilepsies. NGS was able to identify pathogenic variants, demonstrating the ability of the technology to provide medically useful information for genetically heterogeneous conditions. NGS combined with a novel data analysis pipeline was able to make a secure molecular diagnosis in 25% of a cohort of IRD patients who previously did not have a genetic diagnosis.
The greatest challenge presented by NGS was found to be filtering the vast amounts of data produced to identify potential pathogenic variants. In silico pathogenicity prediction programs were used, but none were 100% accurate. Other methods were also employed to provide further evidence of pathogenicity. These included family based DNA testing for cosegregation of variants with phenotype, and transcript based analysis. In some patients, despite extensive genetic testing, a secure molecular diagnosis could not be made using DNA sequencing technologies, illustrating that challenges still remain in the field of genetic diagnostics.
Climate change v Eurozone crisis: social and economic views of risk in inter-expert risk communication
Keywords: Risk Regulation
Risk Communication
Climate Change
Economic and Monetary Union

This DPhil thesis discusses how two divergent risk conceptions, a 'social view' and an 'economic view' of risk, are constructed through inter-expert risk communication. Different and sometimes contradictory concepts of risk are mobilised in regulatory practice, but the origins of these divergent risk conceptions are not extensively studied. This thesis seeks to unpack this divergence.
Empirically, I analyse risk communication among experts in the European Union (EU) during the creation of two risk regulation standards. The two case studies, one related to the development of the two-degree target of EU climate policies (the climate case) and the other about the negotiation of the excessive deficit criteria of the Maastricht Treaty (the euro case), can shed light on the relations between risk conceptions and inter-expert risk communication. I argue that through risk communication, an initial 'view' of risk can be entrenched and developed into a paradigmatic 'risk conception'. My analysis uses historical and sociological institutionalism, by focusing on path dependence of risk communication and social construction risk conceptions among EU experts.
Through the two case studies, I identify four analytical dimensions of inter-expert risk communication: networks (the institutional setting and relationships between different experts), cultures (the mentalities of experts in relation to discussing risks), dynamics (the actual processes of transmitting and receiving risk messages) and strategies (the rationales supporting the decisions of risk regulation standards). My thematic analysis reveals four key distinct 'features' of social/economic views of risk: expertise (the types of knowledge mobilised), normality (characterising risk as either 'special' or 'routine'), probability (considering risk as either uncertain or calculable) and impact (seeing risk as either negative or positive). I argue that these four features can help explain the construction of risk conceptions, and more broadly, provide an analytical framework for studying how views of risk evolve and interact over time.
Restructuring of education, youth, and citizenship:  an ethnographic study of private higher education in contemporary Singapore
Keywords: Youth citizenship
Singapore
Neoliberal education
Educational class

In spite of widespread critiques about the neoliberalisation of higher education and its production of citizenship in relation to the market, transformation of students into profit-maximising individuals, and the vitalisation of a self-enterprising subjectivity, many of these claims remain under-examined with respect to cultural production. The objective of this research is to explore the neoliberal production of middle-class citizenship through the lens of educated non-elite local youth in Singapore. By combining geographical, sociological and anthropological insights about education and youth, I develop a theoretically informed ethnographic case study to examine how this segment of young people reproduce themselves as middle-class citizens. The research is based on eleven months of fieldwork at a local private institute of higher education, where I hanged around, talked to, and observed Singaporean young people between ages 18 and 25 studying for their first degree.
The ethnographic materials are written up into four substantive papers, demonstrating the ways in which educated non-elite Singaporean youth in private higher education engage with state disseminated ideas around neoliberal accumulation and human capital formation. I argue that these students draw on class-based sensibilities and feelings to produce vibrant forms of normativities, subjectivities, and politics that pose a challenge to dominant assumptions of a "hollowed out" citizenship under neoliberalism. The research makes two overall interventions in geographic and social scientific writings about neoliberal restructuring of higher education and its implications for youth citizenship. First, it cautions against a straightforward claim that neoliberal technologies of control have extended market values into citizenship subjectivity and, with it, the erosion of progressive political projects. Second, it provides a much-needed analysis of middle-class citizenship formation among young people caught at the losing end of a diversifying educational landscape.
Rapid, electrostatic self-assembly of nanoparticles with kelvin probe characterisation
Keywords: nanofabrication
nanoparticles
self-assembly
electrophoresis

The pick-and-place of components to build up complex working machines, such as the robotic arms on automotive assembly lines, has been integral to the enormous success and complexity of modern heavy industry. Modern nanomanufacturing stands in stark contrast to this strategy, reliant instead on the two-dimensional patterning of radiation-sensitive resists to build high-density machines of relative simplicity. The driving goal of our research has thus been to develop a new method of manipulation that would allow the pick-and-place of nanoscale components to mirror that of the assembly lines. A manipulator that could reliably perform this process would open the door to a new age of complex nanomachines.
After analysing the current state-of-the-art in nano-object manipulation, we decided to utilise a combination of voltage-driven electric fields with chemically functional monolayers to achieve this goal. The mechanism was intended to be highly compatible with a Scanning Probe Microscope-style tip that could act as the manipulator tool on such an assembly line. This led to the design of several devices that were intended to capture single nanoparticles from a colloidal suspension, which had a negative surface charge in solution. We used numerical simulations using the Guoy-Chapman model of ionic solutions to determine what electrical and geometrical parameters would create the best devices single particle selectivity. We then describe the fabrication of devices using nanolithography techniques including electron-beam lithography, thin-film deposition and etching. Scanning electron microscopy of these devices after voltage-driven assembly showed that the mechanism had very limited success with few incidences of nanoparticle funnelling. This led through several different troubleshooting analyses of the mechanism that identified a myriad of issues affecting these devices. Ultimately we successfully created a radical new approach that incorporated hydrophobic monolayers with polar surfaces. This method exploited the hydrophobic interaction to overcome the hydrostatic barrier and resulted in repeatable single-particle assembly onto devices in sub 5-minute timeframes.
Another aspect identified in this work was that the electronic state of nano-objects and monolayers on device surfaces is very important, but is difficult to pinpoint even when data sheets are available. We developed an emerging method of open-loop Dual-Harmonic Kelvin Probe Microscopy to identify these materials by their electronic surface potentials, successfully performing measurements in electrolytes where nanomanipulation would take place. This line of research led to novel considerations of how the size of the nanoparticles fundamentally distorts KPM measurements. We identify this as an important and often ignored effect that must be considered when using probes to differentiate between different materials at the nanoscale.
Exploiting the use of induced pluripotent stem cell derived immune cells for immunotherapy
Keywords: Immunotherapy
induced pluripotent stem cells
Dendritic cells
HIV

Immunotherapy traditionally made use of biological agents such as cytokines and monoclonal antibodies. Such first generation therapies lack antigen specificity and fail to induce immunological memory, suggesting that cell therapies may provide the next generation of treatments that are more discerning in their mode of action. Nevertheless, difficulties in obtaining sufficient immunologically-relevant cell types from patients has limited their success. Given that induced pluripotent stem cells (iPSC) may be generated from patients, we have investigated the feasibility of deriving two cell types whose availability is restricted in vivo: regulatory T cells (Tregs) and CD141+ cross-presenting dendritic cells (DCs).
We describe the optimization of protocols for differentiation and purification of CD141+ DCs, focussing on their utility as a therapeutic vaccine for HIV-1. We investigate their phenotype, chemotactic capacity, phagocytic ability and propensity to harbour infectious virus. We also assess their immunostimulatory capacity and ability to cross-present exogenous antigen to MHC class I-restricted T cells.
Our findings led us to speculate that iPSC-derived DCs (iPDCs) possess fetal phenotype, which is characterised by excessive secretion of IL-10 and failure to secrete IL-12, under all but the most stringent conditions. We hypothesised that constitutive secretion of IL-10 may be responsible for maintaining the fetal phenotype, a hypothesis we tested by developing an appropriate mouse model. iPSCs were derived from WT and IL-10-/- mice and were shown to differentiate into iPDCs which recapitulate the fetal phenotype observed among human cells. However, loss of the endogenous Il-10 gene failed to restore full immunogenicity and IL-12 secretion.
Finally, we developed protocols for differentiation of FoxP3+ Tregs from iPSCs, a feat that has not previously been achieved. These findings pave the way for the differentiation of Tregs from iPSCs reprogrammed from antigen-specific pathogenic T cells, thereby creating a source of Tregs with matched specificity for therapeutic intervention.
Cardinal Bessarion and the transmission and interpretation of Plato in the fifteeenth century
Keywords: Interpretation of Plato
Cardinal Bessarion

Cardinal Bessarion came from his native Byzantium and settled in Rome in the mid fifteenth century. He was a Basilian monk and, at the time, a Greek Archbishop. His cultural background was in the rationalist tradition of Greek theology. As the Byzantine Empire succumbed to the invading Turks he made it his mission to preserve as much of Greek cultural heritage as possible. Part of this mission was to set out for the Italians (or Latins as he called them) the teachings of Plato of which they had only scanty knowledge. His work in Calumniatorem Platonis was intended as a defence of Plato's teachings against the criticisms of the militant Aristotelian George of Trebizond. This thesis examines Bessarion's exposition of Plato's teachings in that work on a range of philosophical questions that were litmus tests of theological orthodoxy at the time. It argues that Bessarion's exposition of Plato is heavily interpreted through a prism of later commentaries and thinkers particularly the Neo-Platonists. It shows how these interpretations and Bessarion's use of his sources is determined by his aim of showing that Plato’s philosophy was closer to Christian orthodoxy than Aristotle’s and, therefore, provided a firmer philosophical base than the prevailing Aristotelianism.
Nourishing the nation: manifestations of Catalan national identity through food
Keywords: Culinary identity
Catalanism
Gastronationalism
Catalan cuisine
Anthropology of Food

In this thesis I ask whether food can be used to express Catalan national identity, and if so, in what ways this occurs. In doing so, I consider the lived realities of nationalist movements, rather than simply the ideas and political claims that inform such movements. The Catalan Autonomous Community in northeast Spain is an ideal place to research this issue, due to the strengthening of nationalist sentiments there in light of the rise in support for independence from Spain. I wished to see whether this had any effect on the connections between food and national identity (or gastronationalism).
National identity and food are connected in many diverse and varied ways. Food culture allows us to reflect on national identity as a whole. Themes which commonly appear in nationalist discourse, such as cultural specificity, historicism, or landscape (to name but a few), also inform discussions of national food identity. In the present case, while other markers of identity (e.g. language) are also important, ideals of Catalan nationalism may take the guise of Catalan gastronationalism as well. The current pro-independence movement has had the effect of making Catalans more aware of their cultural symbols, including cuisine, which is now one of many such symbols that can be mobilized for the expression of national identity.
Development of mycobacterial growth inhibition assays for the early evaluation and gating of novel TB vaccine candidates
Keywords: Vaccine
Tuberculosis
MGIA

Tuberculosis poses a serious global health threat, with an estimated 9 million new cases and 1.5 million deaths annually. The current vaccine, BCG, is inadequate but development of an effective alternative is severely hampered by the lack of an immune correlate of protection. Candidate vaccines are currently tested using preclinical animal models such as mice and non-human primates. Large numbers of animals are required and subjected to procedures classified as 'Moderate' in severity. Experiments are long and costly and it is unclear whether outcomes are predictive of efficacy or safety in humans. Work in this thesis describes the optimisation and evaluation of a functional in vitro Mycobacterial Growth Inhibition Assay, the MGIT, which takes into account a range of immune mechanisms and their interactions. Applying this assay, a BCG-induced reduction in mycobacterial growth was detected in humans, NHPs and mice. A correlation was observed between the in vitro MGIT response and in vivo protection from challenge in the mouse and NHP models. There was also concordance between the MGIT and epidemiological data or in vivo outcome in humans. Comparison of whole blood and PBMC compartments indicated that haemoglobin may act as a confounder and suggested a role for complement, but not antibodies, in determining mycobacterial growth. Classical monocytes and CD16- NK cells played a crucial role in PBMC MGIT. Cytokines correlating with mycobacterial growth represented a mixture of subsets, and the immunoregulatory cytokine IL-10 was highly influential. Genes correlating with mycobacterial growth were enriched for the immune response pathway, which included CD14 and HAMP, supporting the importance of monocytes and iron. Although further work is required, the MGIT assay represents a potential correlate of protection that may be applied in preclinical vaccine testing, reducing the number of animals used in challenge experiments and accelerating the development of an effective vaccine.
The impact of adjustment for covariates on meta-analysis of randomised intervention studies for binary outcome
Keywords: covariate adjustment
clinical trials
Adjusted analysis
meta-analysis
binary outcome

Background
Covariate adjustment analysis is often used in epidemiological studies but is less common in randomised controlled trials (RCTs) and RCT meta-analyses. There is a lack of consensus on whether the analysis of RCT data should adjust for important baseline covariates. The estimated treatment effect of a binary covariate can differ when logistic regression is carried out, even when the covariate is balanced between treatment groups.
Objectives
The objectives of this study were to examine the factors that affect the impact of adjusted analysis in different RCT scenarios and to explore the impact of adjusted analysis in RCT meta-analysis.
Methods
Simulation and sampling studies were conducted to identify the factors that affect the impact of using an adjusted logistic regression model. Two covariates, one continuous and one binary, were considered simultaneously. The event rate, treatment effect, binary and continuous variable distributions, covariate prognostic strengths, and correlation between the covariates were varied during the simulations. The impact of adjustment on RCT meta-analysis was investigated using individual participant data obtained from the Perinatal Antiplatelet Review of International Studies. Different methods of performing unadjusted and adjusted meta-analysis were compared.
Results
The simulation results suggest that adjustment only has a notable effect in extreme scenarios, such as a very large treatment effect or highly prognostic covariates. The relative difference between the unadjusted and adjusted odds ratios was found to be larger than 50% under these extreme scenarios. Covariate adjustment is likely to have a small effect on meta-analyses with many studies.
Summary
Adjusted analysis should be carried out by design. Performing adjusted analysis in a meta-analysis can be challenging as sufficient information about the covariates is often not available.
Submesoscale dynamics in the open ocean
Keywords: Anticyclones
Submesoscale

The seasonal cycle of submesoscale flows in the upper ocean is investigated through a series of numerical simulations in an idealised model domain. Subme-soscale processes become stronger as the resolution is increased from 4 km to 0.5 km. There is a seasonal cycle in the magnitude of horizontal buoyancy gradients and horizontal wavenumber spectra consistent with stronger mixed layer insta-bilities developing as the mixed layer deepens and energising the submesoscale. Up to 30% of the mixed layer volume in winter has negative potential vorticity and this negative potential vorticity is found in both mesoscale vortices and filaments. Further investigation of the filaments that arise in anticyclonic eddies show that they are generated in regions of negative potential vorticity and lead to the upwelling of fluid from the thermocline. Symmetric instability is found to be the most likely mechanism. The role of flow curvature is considered and it is shown that the angular velocity of mesoscale eddies, as well as relative vorticity, contributes to their stability. A numerical tracer release experiment shows that the filament generation process leads to downwelling of surface layer flows and a simplified biogeochemical experiment shows that the instability gives rise to much higher primary productivity in mesoscale anticyclones. Observations of a mixed layer front observed in the North Atlantic are presented which has a more diffuse cross-front buoyancy gradient at the surface than lower in the mixed layer and a strong ageostrophic cross-front velocity. The observations are used to motivate two dimensional simulations of Rossby adjustment. These simulations show that as the frontal strength increases the Rossby adjustment phase accounts for an increasing proportion of the restratification. The simulations become much more turbulent over the parameter range for frontal strength. The vertical profile in the observations can be re-produced when the adjustment is simulated with a thermocline, though definitive conclusions are difficult to draw.
Unleashing power: Pathways to inclusion and representation in U.S. AIDS activist organisations
Keywords: Philadelphia
Direct democracy
Activism
The AIDS Coalition to Unleash Power

The thesis proposes a theory for the development of substantive representation among social movement organisations (SMOs). Substantive representation (SR) is the extent to which political institutions advance the policy interests of their constituents, in particular the most disenfranchised. Despite their noble proclamations, institutions of representative democracy often fail to advance the interests of groups who have been ignored and absent at the proverbial table.
The thesis establishes a causal process to explain the divergence in SR outcomes among informal SMOs, or all-volunteer groups that disavow formal hierarchy in favour of egalitarian modes of decision-making. It utilises a case study of the AIDS Coalition to Unleash Power (ACT UP), an umbrella organisation dedicated to ending the HIV/AIDS crisis in the United States and worldwide. It explains an anomalous story of SR attainment through the ACT UP Philadelphia chapter, compared to sister groups in New York City and Boston. The analysis draws from 92 semi-structured interviews, 13 months of participant observation, periodical review, and archival databases.
ACT UP Philadelphia translated common SMO intentions of inclusivity into the uncommon rituals of practice. It forged a deliberate pipeline to invest not only in the presence but also the power of disenfranchised people with HIV, people too dark and poor to interest counterpart groups in other cities. Through an analytic retelling of ACT UP’s history, the thesis argues that the fulfilment of SR depends on the ability of SMOs to appeal to member self-interest. Critically, SMOs can offer material incentives and nurture feelings of debt and obligation: causal steps to recruitment and sustainability of a heterogeneous membership. In building a crucial if contentious core of dissimilar people and partnerships, SMOs can unleash an oft-unrealised power for collective action and SR, by and for disenfranchised peoples who had thought change to be impossible.