VictorJuiz/thesis huggingface dataset:
Dengue diagnostics and therapeutic interventions in Viet Nam

Dengue is a major public health problem that affects tens of millions of people annually in tropical and sub-tropical countries. This acute viral infection happens to be severe and even life threatening but there is still no available drug or vaccine. Previous studies have noted early higher viral burden in patients who develop more severe symptoms suggesting that administration of a potent and safe antiviral may prevent progression to severe dengue. To verify this hypothesis, we have conducted the first RCT directed towards reducing the viral burden in vivo by administrating chloroquine (CQ), a cheap and well-tolerated drug that inhibits DENV in vitro with concentrations achievable in vivo, to 307 Vietnamese adults with suspected dengue (257 of them were laboratory-confirmed cases). Unfortunately, we did not see an effect of CQ on the duration of infection. However in patients treated with CQ, we observed a trend towards a lower incidence of severe forms. We did not find any differences in the immune response that can explain this trend. We also found more adverse events, primarily vomiting, with CQ. In addition, we have explored the relationships between clinical features, antibody responses and virological markers in these patients. We found that the early magnitude of viremia is positively associated with disease severity and there are serotype dependent differences in infection kinetics. We found as well that DENV was cleared faster and earlier in patients with secondary infections. To complete this study, we have also evaluated 2 rapid lateral flow tests for the diagnosis of dengue in a panel of plasma samples from 245 RT-PCR confirmed dengue patients and 47 with other febrile illnesses. Our data suggest that the NS1 test component of these tests are highly specific and have similar levels of sensitivity (~60%). Both NS1 assays were significantly more sensitive for primary than secondary dengue. The IgM parameter in the SD Duo test improved overall test sensitivity without compromising specificity. All these findings are of major importance for further anti-viral drug testing.

Keywords: Viet Nam
clinical trial
point-of-care systems
antiviral agents
dengue
neglected tropical diseases
virology
diagnostic
Advisor: Simmons, C
Farrar, J
Sensor-based motion planning via nonsmooth analysis

In this thesis we present a novel approach to sensor-based motion planning developed using the mathematical tools provided by the field of nonsmooth analysis. The work is based on a broad body of background material developed using the tools of differential topology (smooth analysis), that is limited to simple cases like a point or circular robot. Nonsmooth analysis is required to extend this background work to the case of a polygonal robot moving amidst polygonal obstacles.
We present a detailed nonsmooth analysis of the distance function for arbitrary configuration spaces and use this analysis to develop a planner for a rotating and translating polygonal mobile robot. Using the tools of nonsmooth analysis, we then describe a one-dimensional nonsmooth roadmap of the robot's freespace called the Nonsmooth Critical Set + Nonsmooth Generalised Voronoi Graph (NCRIT+NGVG) where the robot is equidistant to a number of obstacles, in a critical configuration or passing between two obstacles. We then use the related field of nonsmooth control theory to develop several provably stable control laws for following and exploring the nonsmooth roadmap. Finally, we implement a motion planner in simulation and for a real polygonal mobile robot, thus verifying the utility and practicality of the nonsmooth roadmap.

Advisor: Cameron, S
When scientists meet the public: an investigation into citizen cyberscience

Citizen Cyberscience Projects (CCPs) are projects mediated through the Internet, in which teams of scientists recruit members of the public (volunteers) to assist in scientific research, typically through the processing of large quantities of data. This thesis presents qualitative ethnographic case studies of the communities that have formed around two such projects, climateprediction.net and Galaxy Zoo. By considering these social actors in the broader contexts in which they are situated (historical, institutional, social, scientific), I discuss the co-shaping of the interests of these actors, the nature of the relationships amongst these actors, and the infrastructure of the projects and the purposes and nature of the scientific work performed.
The thesis focusses on two relationships in particular. The first is that between scientists and volunteers, finding that, although scientists in both projects are concerned with treating volunteers with respect, there are nevertheless considerable differences between the projects. These are related to a number of interconnecting factors, including the particular contexts in which each project is embedded, the nature of the scientific work that volunteers are asked to undertake, the possibilities and challenges for the future development of the projects as perceived by the scientists, and the tools at the disposal of the respective teams of scientists for mediating relationships with volunteers. The second is amongst the volunteers themselves. This thesis argues that volunteers are heterogeneous, from disparate backgrounds, and that they sustain their involvement in CCPs for very different purposes. In particular, they seek to pursue these through the way they negotiate and construct their relationships with other volunteers, drawing on particular features of the project to do so.
This thesis contributes to two fields. The first is to Citizen Cyberscience itself, with a view to improving the running of such projects. Some social studies have already been conducted of CCPs to this end, and this thesis both extends the analysis of some of these pre-existing studies and also problematizes aspects of CCPs that these studies had not considered. I discuss the significance of my findings for those involved in setting up and running a CCP, and present some recommendations for practice. The second field is Science and Technology Studies, in particular studies of public engagement with scientific and technological decision- and knowledge-making processes. The modes of engagement found in CCPs differ in key ways from those that have already been documented in the existing literature (in particular, different power relationships) and thus offer new ways of understanding how the public might be engaged successfully in such processes.

Keywords: Science and Technology Studies
citizen science
climate science
virtual ethnography
astronomy
Advisor: Carusi, A
Jirotka, M
Neutron scattering and praseodymium suppression of superconductivity

PrBa2Cu3O6+x is anomalous among the compounds which can be made by substituting different rare-earth ions for yttrium (Y) in YBa2Cu3O6+x:it is the only compound which has the same structure as YBa2Cu3O6+x, and yet does not superconduct. This unusual property makes it an important system to study, since the differences between the two compounds could produce theoretical insights into the mechanisms of cuprate, or high-temperature, superconductivity. This thesis describes neutron scattering investigations of the magnetic properties of PrBa2Cu3O6+x.
I have investigated the magnetic ordering in well-characterised, single-crystal samples, both with and without Al-contamination. In the data analysis, proper account is taken of the sample mosaicity and the different intrinsic peak shapes encountered. Some of the most striking new characteristics reported here are that (i), there is a clear interaction between the Pr ions and the Cu-O2 planes, (ii), the ordered Pr moments tilt away from the c-axis (as suggested previously by Mossbauer spectroscopy), and (iii), there is two-dimensional ordering in the Al-containing crystals. I show how observed trends in the magnetic ordering, as O- and Al-contents vary, may be understood in terms of charge redistribution involving the hybridisation of the Pr ions.
I have also examined the crystal field transitions of the praseodymium ion. Because of the difficulties previously encountered in measuring these in PrBa2Cu3O6+x, I have used instead the compounds PrO2 and Y0.3Pr0.7Ba2Cu4O8, which contain praseodymium in a chemically similar environment. Y0.3Pr0.7Ba2Cu4O8 shows the same broadening effects as PrBa2Cu3O6+x; PrO2 shows signs of mixed-valency, with temperature-dependent lifetime effects. The application of symmetry considerations and the point-charge model to the crystal field measurements is considered in some detail.

Advisor: Boothroyd, A
Molecular Rydberg dynamics

A simple theory relating the dynamics of electrons to the long-range properties of the molecular ionic core is developed for asymmetric top molecules in general and water in particular. It is combined with the molecular version of multichannel quantum defect theory developed by Fano and Jungen and applied to the resonance-enhanced multiphoton ionization spectra of Child and Glab (M. S. Child and W. G. Glab, J. Chem. Phys., 2001, 112, 3754-3765), the mass-analysed threshold ionization spectra of Dickinson et al. (H. Dickinson, S. R. Mackenzie and T. P. Softley, Phys. Chem. Chem. Phys., 2000, 2, 4669-4675) and the as-yet unpublished work of Glab on the photoelectron branching ratios of the nd and nf Rydberg lines of the water molecule. The effect of resonances between electronic and rotational motion in Rydberg molecules is investigated using multichannel quantum defect theory with special reference to the time-resolved wave packet experiments of Smith et al. (R. A. L. Smith, J. R. R. Verlet, E. D. Boleat, V. G. Stavros and H. H. Fielding, Faraday Discuss., 2000, 115, 63-70).

Keywords: quantum defect theory
electronic spectroscopy
Rydberg molecule
Advisor: Child, M
Static analyses over weak memory

Writing concurrent programs with shared memory is often not trivial. Correctly synchronising the threads and handling the non-determinism of executions require a good understanding of the interleaving semantics. Yet, interleavings are not sufficient to model correctly the executions of modern, multicore processors. These executions follow rules that are weaker than those observed by the interleavings, often leading to reorderings in the sequence of updates and readings from memory; the executions are subject to a weaker memory consistency. Reorderings can produce executions that would not be observable with interleavings, and these possible executions also depend on the architecture that the processors implement. It is therefore necessary to locate and understand these reorderings in the context of a program running, or to prevent them in an automated way.
In this dissertation, we aim to automate the reasoning behind weak memory consistency and perform transformations over the code so that developers need not to consider all the specifics of the processors when writing concurrent programs. We claim that we can do automatic static analysis for axiomatically-defined weak memory models. The method that we designed also allows re-use of automated verification tools like model checkers or abstract interpreters that were not designed for weak memory consistency, by modification of the input programs.
We define an abstraction in detail that allows us to reason statically about weak memory models over programs. We locate the parts of the code where the semantics could be affected by the weak memory consistency. We then provide a method to explicitly reveal the resulting reorderings so that usual verification techniques can handle the program semantics under a weaker memory consistency. We finally provide a technique that synthesises synchronisations so that the program would behave as if only interleavings were allowed. We finally test these approaches on artificial and real software. We justify our choice of an axiomatic model with the scalability of the approach and the runtime performance of the programs modified by our method.

Keywords: weak memory
concurrency
memory fence
static analysis
Advisor: Kroening, D
Ouaknine, J
Alglave, J
Intersection types and higer-order model checking

Higher-order recursion schemes are systems of equations that are used to define finite and infinite labelled trees. Since, as Ong has shown, the trees defined have a decidable monadic second order theory, recursion schemes have drawn the attention of research in program verification, where they sit naturally as a higher-order, functional analogue of Boolean programs. Driven by applications, fragments have been studied, algorithms developed and extensions proposed; the emerging theme is called higher-order model checking. Kobayashi has pioneered an approach to higher-order model checking using intersection types, from which many recent advances have followed. The key is a characterisation of model checking as a problem of intersection type assignment. This dissertation contributes to both the theory and practice of the intersection type approach.
A new, fixed-parameter polynomial-time decision procedure is described for the alternating trivial automaton fragment of higher-order model checking. The algorithm uses a novel, type-directed form of abstraction refinement, in which behaviours of the scheme are distinguished according to the intersection types that they inhabit. Furthermore, by using types to reason about acceptance and rejection simultaneously, the algorithm is able to converge on a solution from two sides. An implementation, Preface, and an extensive body of evidence demonstrate empirically that the algorithm scales well to schemes of several thousand rules. A comparison with other tools on benchmarks derived from current practice and the related literature puts it well beyond the state-of-the-art.
A generalisation of the intersection type approach is presented in which higher-order model checking is seen as an instance of exact abstract interpretation. Intersection type assignment is used to characterise a general class of safety checking problems, defined independently of any particular representation (such as automata) for a class of recursion schemes built over arbitrary constants. Decidability of any problem in the class is an immediate corollary. Moreover, the work looks beyond whole-program verification, the traditional territory of model checking, by giving a natural treatment of higher-type properties, which are sets of functions.

Keywords: software verification
intersection types
model checking
Advisor: Ong, C
Optical diagnostics and combustion analysis in a gasoline direct injection engine

Gasoline Direct Injection (GDI) engines work with stratified charge at part load and burn with lean mixtures in order to save fuel, whilst at full load, the fuel and air mix homogeneously for maximum power output. The higher compression ratio and the absence of throttling are two of the most significant benefits of GDI engines. The key issues facing GDI combustion include in-cylinder mixture preparation and post-combustion soot formation. This work was intended to investigate these aspects and was undertaken on a dedicated Jaguar single-cylinder optical GDI engine with a spray-guided combustion system. The spray-guided concept does not rely as much on charge motion or piston design, and can avoid wall-wetting effects so as to reduce engine emissions. Relevant engine control hardware and data acquisition equipment were commissioned. Data/image processing software was also developed to suit the measurements.
A data-processing case study with data from a small two-stroke glow ignition engine has been conducted to develop a method to combine the burn rate and heat release analyses in the study of engines with premixed charge but compression ignition. Difficulties such as unknown ignition timing and polytropic index have been addressed. Results for all operating conditions have shown good correlations between the two methods.
The technique of quantitative planar laser-induced fluorescence is useful for measuring 2-D fuel distribution in GDI engines. The relevant physics and literature were reviewed in depth. A multi-component fuel was designed to give reasonable co-evaporation characteristics with tracers matching different fuel fractions. The absorption and fluorescence features of each fuel component and tracer were characterised. Optimisation of hardware and signal-to-noise ratio was performed. A recirculating loop was set up for the calibration of the technique.
The technique of colour-ratio pyrometry (CRP) for estimating the temperature and loading of soot was applied on the GDI engine. Critical features of the candidate CCD colour camera including its spectral response and noise behaviours were fully studied. Validation tests with reference sources together with an error analysis suggested an accuracy of ±50K within the combustion temperature range. Engine combustion images were then taken under various operating conditions. Temperature estimates were shown to be insensitive to the concentration of soot. Simulation with a thermodynamic modelling package, ISIS, was introduced for comparison with the experimental data. With careful tuning, ISIS gave outputs comparable to the CRP and proved to be a cost-effective tool to study GDI engines. High-speed combustion imaging was carried out using a CMOS camera, allowing the study of flame properties as well as crank-angle resolved CRP. By using a lens in the piston crown to give full bore optical access and appropriate image processing, the flame front could be detected reliably throughout the main combustion process.

Advisor: Stone, R
Gifts to the Gods: Aparchai, Dekatai and related offerings in Archaic and Classical Greece

This study is about one of the most ubiquitous and yet little studied aspects of ancient Greek religion, the offering of so-called ‘first-fruits’ (aparchai) and tithes (dekatai) in Archaic and Classical Greece (c.700-300 B.C.). A widespread and traditional custom all over Greece and the Greek Mediterranean, the offering of ‘first-fruits’ and tithes entailed using a portion of the proceeds from a diversity of human activities (such as craft-work, fishing, trade, military expeditions) to present something to the gods. I look at the different kinds of aparchai and dekatai offered to the Greek gods by individuals and states under various circumstances, the various contexts in which the language and practice of making such offerings were used, the deployment of this religious custom in politics, and the transformation of a voluntary practice into a religious obligation. Ultimately, however, my major concern is with questions of religious psychology: why people should bring aparchai and dekatai to the gods, and what motivations and expectations they might have had. Because it was such a commonplace practice, the custom has been taken simply as a given in both ancient and modern scholarship; and no attempt has been made to explain its religious significance. By drawing on current anthropological studies of gift-giving, I argue that that aparchai and dekatai do not merely give to the gods, but give back to the gods some of the benefits granted by the divinities in the first place, reflecting first and foremost a sense of dependence on the divine. I suggest that the offering of aparchai and dekatai may be thought of as a means of settling men’s debts to, and thereby maintaining good relations with, the gods, who were considered the sources of both goods and evils. I challenge the emphasis, common in modern scholarship, on material returns as the central motive behind the act of bringing gifts to the gods. Instead I suggest that the study of gift-giving between humans and the divine should embrace the possibility that psychological feelings of dependence on and gratitude to the gods might also have been involved.

Keywords: Greek Religion
aparchai
first-fruits
dekatai
tithes
Advisor: Parker, R
Centring on the Margins: Migration Control in Malta, Cyprus and the European Union

Why does the European Union focus on controlling irregular immigration at the external border? The emphasis presents a paradox as most irregular migrants in the EU arrive through legal channels and subsequently overstay or violate the conditions of their visa. In order to explore this paradox, the thesis examines two case studies, Malta and Cyprus. As small island states on the Union’s southern periphery, the two are ostensibly unable to resist the transfer of migration controls and asylum responsibility to the EU’s external borders. Yet, employing nonmaterial power, namely by highlighting the perceived migration pressures they are under, the two states have successfully attracted significant financial and practical support from other member states. In doing so, they have influenced policymaking within EU migration governance, but have ultimately reinforced the emphasis on controlling irregular immigration at the external border by portraying the phenomenon as a crisis.
This thesis not only sheds light on the interaction between the EU and the two states under investigation, but combines three levels of analysis – the regional, national, and local. The crisis narrative detrimentally affects the migrant and refugee populations as it encourages the adoption of restrictive and deterrent measures rather than ensuring access to rights and long-term integration. Nevertheless, this population is not without agency. It is their individual decisions to move across national borders without state authorisation that in the aggregate both compels states into dialogue about the issue and provides the basis for the dynamic between the EU and these two member states.

Keywords: migration control
borders
migrant agency
Cyprus
power
irregular immigration
Malta
European Union
small states
Advisor: Nicolaidis, K
Duvell, F
Banach spaces with few operators and multiplier results

The construction of a non-separable reflexive Banach space on which every operator is the sum of a scalar multiple of the identity operator and an operator of separable range is presented.
Using a result of Rao, a sufficient condition is given for Banach spaces with smooth norms to be decomposable.
It is shown that operators on Banach spaces of co-dimension one in their biduals are the sum of a scalar multiple of the identity operator and a weakly compact operator. The Banach spaces of bounded operators L(11, 1p) (1p
, 1r), 1 < p ≤ r ≤ p1 < ꝏ, where 1/p + 1/p1 = 1, are shown to be primary.
The spaces of bounded diagonal operators and compact diagonal operators on a seminormalized Schauder basis β, the multiplier algebras Ld
(X, β) and Kd(X, β), are introduced and studied. New examples of these multiplier algebras are presented and a theorem of Sersouri is extended. A necessary and sufficient condition is given for co to embed in Kd(X, β). A sufficient condition is given on a semi-normalized Schauder basis β of a reflexive hereditarily indecomposable Banach space Y to ensure that Kd(Y, β) has the RNP. It is shown that the algebra Ld(X, β) is semisimple and that on the algebra Kd(X, β) derivations are automatically continuous.
By representing diagonal operators as stochastic processes a general method of constructing multiplier algebras is given. A non trivial multiplier invariance for the normalized Haar basis of L1[0,1] is proved.