VictorJuiz/thesis huggingface dataset:
Clinical studies on enteric fever
Keywords: Trial Design
Fluoroquinolones
Enteric fever
Paratyphoid
Patient Reported Outcome
Randomised Controlled Trials
Blood Culture
Salmonella Typhi
Patient Perception
Salmonella Paratyphi A
Sample Size
Typhoid
Randomisation
Ofloxacin
Chloramphenicol
Gatifloxacin

I performed two randomised controlled trials (RCTs) to determine the best treatments for enteric fever in Kathmandu, Nepal, an area with a high proportion of nalidixic acid resistant S. Typhi and S. Paratyphi A isolates.
I recruited 844 patients with suspected enteric fever to compare chloramphenicol versus gatifloxacin. 352 patients were culture confirmed. 14/175 patients treated with chloramphenicol and 12/177 patients treated with gatifloxacin experienced treatment failure (HR=0.86 (95% CI 0.40 to 1.86), p=0.70). The median times to fever clearance were 3.95 and 3.90 days, respectively (HR=1.06 [CI 0.86 to 1.32], p=0.59).
The second RCT compared ofloxacin versus gatifloxacin and recruited 627 patients. Of the 170 patients infected with nalidixic acid resistant strains, the number of patients with treatment failure was 6/83 in the ofloxacin group and 5/87 in the gatifloxacin group (Hazard Ratio, HR=0.81, 95% CI 0.25 to 2.65; p=0.73); the median times to fever clearance were 4.7 and 3.3 days respectively (HR=1.59 [CI 1.16 to 2.18], p=0.004).
I compared conventional blood culture against an electricity free culture approach. 66 of 304 patients with suspected enteric fever were positive for S. Typhi or S. Paratyphi A, 55 (85%) isolates were identified by the conventional blood culture and 60 (92%) isolates were identified by the experimental method. The percentages of positive and negative agreement for diagnosis of enteric fever were 90.9% and 96.0%, respectively. This electricity free blood culture system may have utility in resource-limited settings or potentially in disaster relief and refugee camps.
I performed a literature review of RCTs of enteric fever which showed that trial design varied greatly. I was interested in the perspective of patients and what they regarded as cure. 1,481 patients were interviewed at the start of treatment, 860 (58%) reported that the resolution of fever would mean cure to them. At the completion of treatment, 877/1,448 (60.6%) reported that they felt cured when fever was completely gone. We suggest that fever clearance time is the best surrogate for clinical cure in patients with enteric fever and should be used as the primary outcome in future RCTs for the treatment of enteric fever.
Tests of community assembly across spatial scales in Neotropical birds
Keywords: phylogeny
Amazon
Andes
biogeography
South America
community ecology
birds

Species diversity varies dramatically across the surface of the Earth. A key step in the accumulation of species diversity is the ability of species to coexist in biological communities. Thus, identifying the mechanisms underlying community assembly is a major challenge for ecologists seeking to explain patterns in species diversity and composition. Recently some consensus has been reached on the set of processes that influence community assembly: speciation, demographic stochasticity, niche-based fitness trade-offs among species and dispersal. However, it is unclear how the importance of a particular process changes with spatial scale, which interactions exist among processes at large spatial scales and the extent to which niche-based resource partitioning among species explains differences in diversity among communities. Neotropical birds offer an ideal opportunity to address these uncertainties because of their high diversity and the existence of detailed information on their evolutionary history and ecology. In this thesis, I first use trait and phylogenetic metrics of community structure to show that both habitat filtering and interspecific competition shape community composition at the scale of individual bird territories (~1-2 ha). Second, I use simulations of community assembly to show that trait-based metrics of community structure outperform phylogenetic metrics for detecting niche-based community assembly, and that both sets of metrics often have low power when multiple processes influence community composition. Third, taking a trait-based, species-level approach, I show that both habitat filtering and interspecific competition influence species occurrence at regional scales (~75000 km2), and interact with dispersal ability so that their effect on species occurrence is increased for species with greater dispersal ability. Finally, using a combination of trait- and isotope-based methods to quantify resource partitioning, I show that species' niche widths do not change and niche overlap is reduced at high compared to low species richness. Taken together, these results suggest that both habitat filtering and interspecific competition (i.e. niche-based processes) influence community assembly from local to regional scales. However, at least at regional scales, the degree to which these processes are important for determining the occurrence of any given species depends on that species's dispersal ability. They also suggest, based on niche-based interspecific competition influencing community composition, that differences in species richness among communities are in part explained by differences among sites in the breadth of available niche space, not by increased ecological specialisation or niche overlap.
Searches for supersymmetric partners of the bottom and top quarks with the ATLAS detector
Keywords: ATLAS
Sbottom
Stop
Supersymmetry
Large Hadron Collider

Supersymmetry is a promising candidate theory that could solve the hierarchy problem and explain the dark matter density in the Universe. The ATLAS experiment at the Large Hadron Collider is sensitive to a variety of such supersymmetric models. This thesis reports on a search for pair production of the supersymmetric scalar partners of bottom and top quarks in 20.1 fb−1 of pp collisions at a centre-of-mass energy of 8 TeV using the ATLAS experiment. The study focuses on final states with large missing transverse momentum, no electrons or muons and two jets identified as originating from a b-quark. This final state can be produced in a R-parity conserving minimal supersymmetric scenario, assuming that the scalar bottom decays exclusively to a bottom quark and a neutralino and the scalar top decays to a bottom quark and a chargino, with a small mass difference with the neutralino. As no signal is observed above the Standard Model expectation, competitive exclusion limits are set on scalar bottom and top production, surpassing previously existing limits. Sbottom masses up to 640 GeV are excluded at 95% CLs for neutralino masses of up to 150 GeV. Differences in mass between ~b1 and ~X01 larger than 50 GeV are excluded up to sbottom masses of 300 GeV. In the case of stop pair production and decay ~t1 → b + ~X±1 and ~X±1 → ~X01 + W* with mass differences &triangle;m = m~X±1 − m~X01 = 5 GeV (20 GeV), stop masses up to 580 GeV (440 GeV) are excluded for m~X01 = 100 GeV. Neutralino masses up to 280 GeV (230 GeV) are excluded for m~t1 = 420 GeV for &triangle;m = 5 GeV (20 GeV). In an extension of this analysis, sbottom quarks cascade-decaying to at least a Higgs boson are searched for in final states with large missing transverse momentum, at least 3 b-tagged jets and no electrons or muons, using neural network discriminants.
Regulation of TGFbeta-activated-kinase 1 (TAK1) in nuclear factor-kB and tumour necrosis factor/Eiger signalling in Drosophila melanogaster.
Keywords: apoptosis
A20
TNF
innate immunity

Drosophila TGFbeta-Activating-Kinase 1 (dTAK1) is an essential component of both the Immune Deficiency (IMD) innate immune and TNF/Eiger apoptotic cascades. The IMD and JNK pathways bifurcate at the level of dTAK1. Hence, elucidating the regulatory mechanism of dTAK1 is pertinent to understanding the regulation of both innate immunity and apoptosis.
In this study, Trabid was identified as a novel negative regulator of the Drosophila IMD pathway. Trabid interacted with dTAK1 and decreased K63-linked ubiquitination, thereby reducing immune signalling. Three tandem Npl4 Zinc Fingers (NZF) and C518 were required for Trabid activity. Lysines 142 & 156 were identified as the K63 Ub acceptor sites of dTAK1, required for K63-linked ubiquitination and signalling. Also, results show Lys 156 functioned as the K48 Ub acceptor site. Further, the ZF domain of TAK1-associated Binding Protein 2 (dTAB2) was important in modulating dTAK1 K63-linked ubiquitination and thereby the immune signal. These results indicate an elaborate and multi-tiered mechanism for regulating dTAK1 activity and modulating the immune signal.
Further, Ariadne-2 (Ari-2) was identified as a novel component of the Drosophila TNF/Eiger pathway which functioned at the level of dTAK1. Results indicate that Ari-2 is essential for normal development and longevity. It enhances the apoptotic signal when concomitantly over-expressed with Eiger. Further, Ari-2 interacts with dTAK1, dTAB2 and dTRAF2 which are all implicated in TNF/Eiger signalling. Thus, evidence supports the hypothesis that Ari-2 functions as an adaptor, involved in assembling a distinct signalling complex which transduces the apoptotic signal without activating immunity.
The role of congruence in policy priorities between citizens and elites in citizens' political attitudes and behaviour
Keywords: Satisfaction with democracy
Political Representation
Voter Turnout
Policy priorities

This thesis shows that citizens whose policy concerns are higher on political elites' agendas are more likely to be satisfied with democracy and to vote in elections. It develops a theoretical framework to explain the influence of the previously neglected variable priority congruence on democratic satisfaction and turnout and provides empirical evidence for it. The thesis thereby makes significant contributions to our knowledge about the ingredients of democratic legitimacy.
Previous research shows that political representation, as measured by proximity between citizens' and elites' policy positions, is linked to democratic satisfaction. In this thesis, it is argued that congruence in priorities has a similar effect because citizens are likely to perceive elites who emphasise their concerns as responsive to societal needs and public opinion. The empirical analyses suggest that democratic satisfaction is indeed influenced by priority congruence, yet less so amongst more politically sophisticated individuals as well as in younger democracies and countries with lower levels of democracy and governance. These differences are probably due to variation in citizens' expectations towards elite behaviour and the democratic system.
Elite attention to citizens' concerns moreover influences their decision to turn out in elections. If voters' issue priorities are salient in the campaign, they are likely to perceive the election to be more important. Moreover, they will find it easier to evaluate parties and make their vote choice. These mechanisms are shown to be less relevant amongst partisans, since party attachment mobilises voters and facilitates their vote choice. Again, previous policy-based explanations of turnout focus on positions, largely ignoring priorities.
The hypotheses are tested through statistical analysis of data from voter and candidate surveys as well as media content analyses. The data come from all 27 European Union countries in 2009, whereby several hypotheses are only tested in Germany due to data availability.
Essays on unconventional monetary policy and long-term government debt
Keywords: Monetary Union
Monetary Policy
Quantitative Easing
Portfolio Choice

This thesis studies the optimal conduct of unconventional monetary policy in the form of purchases of long-term government debt by the central bank and, motivated by this policy tool, the evolution of long-term government debt holdings in household portfolios over the course of the life cycle. It is comprised of three self-contained chapters.
The first chapter investigates whether it can be beneficial for central banks to use the unconventional tool even when the main policy rate is not constrained by the zero lower bound. A friction in the interaction between households and banks allows central bank purchases of long-term government debt to reduce long-term interest rates and thus to stimulate economic activity. If debt purchases and conventional short-term interest rate policy are coordinated in an appropriate way, the central bank is able to reduce the volatility of output and inflation.
In the second chapter, the role that unconventional monetary policy can play in a currency union is analysed. A model is laid out, in which two countries form a currency union with a common central bank but separate and uncoordinated fiscal policy institutions. When monetary policy is implemented only through the common short-term interest rate, the central bank is unable to respond effectively to country-specific shocks. Due to segmentation in the market for long-term government debt, the yield on long-term debt can differ across countries. As a result, a monetary policy authority that can rely on bond purchases is able to address idiosyncratic shocks reflected in volatility of the natural terms of trade more effectively and to achieve higher welfare than one that cannot make use of this instrument.
The final chapter studies the long-term government bond share in household portfolios over the course of the life cycle. US data from the Survey of Consumer Finances suggests that participation in the market for long-term government debt first increases and later decreases as agents approach the retirement age. The portfolio share conditional on participation is non-decreasing over the working life. These stylised facts can be explained by means of a portfolio choice model in which agents are subject to aggregate risk through asset returns as well as idiosyncratic risk through labour income and the stochastic events of retirement and death.
Storytelling in late antique epic: a study of the narrator in Nonnus of Panopolis' Dionysiaca
Keywords: epic poetry
Nonnus
Nonnus of Panopolis
Dionysiaca
reception of Homeric literature
ancient greek literature
storytelling
literary devices
narratology

This thesis is a narratological study of Nonnus of Panopolis' Dionysiaca, focussing on the figure of the narrator whose interventions reveal much about his relationship to his predecessors and his own conception of story-telling. Although he presents himself as a follower of Homer, whom he mentions by name in his poem, the Dionysiaca are clearly influenced by a much wider range of sources of inspiration. The study of narratological interventions brings to light the narrator's relationship with Homer, between imitation and innovation. The way he renews and transforms epic narratorial devices attests to his literary skills as he strives for ποικιλία in his poem. His interventions hint at sources of inspiration other than Homer, such as lyric poetry, historiography, and didactic epic. Another innovation is the way the narrator intervenes not to draw the narratee's attention to the contents of his text, but to underline his own role as story-teller. Some interventions signal a change in tone or the integration of another genre; the expected proems and invocations to the Muse become spaces for a display of ingeniousness, a discussion of the sources and a reflection on the role of the poet.
The efforts made by the Nonnian narrator to renew well known devices also denotes his mindfulness of his narratee, whom he involves in the story through metaleptic devices, or by drawing on a shared cultural background to enhance the narrative with allusions to extradiegetic references.
The study of narratorial interventions proves that the Dionysiaca were not written only in an attempt to recreate a Homeric epic, but are a compendium of influences, genres, and myths, encompassing the influence of a thousand years of Greek literature.
Static pile-soil-pile interaction in offshore pile groups
Keywords: foundations
piles
offshore

This thesis is a theoretical study, using both finite element and boundary element methods, of the behaviour of single-piles and pile groups under vertical and lateral loading. It offers an improved understanding of the soil-structure interaction that occurs in pile groups, particularly closely spaced piles subjected to lateral loads. The potential of a two- dimensional idealisation of what is a three-dimensional problem is demonstrated by achieving real insight into the complex nature of pile-soil and pile-soil-pile interaction in pile groups. A new load transfer mechanism is presented for a rigid, axially loaded vertical pile. From this an improvement is then derived to the analytical solution for pile head settlement given by Randolph and Wroth (1978). The improved mechanism has the further merit that it can be applied also to solutions for flexible piles and pile groups. The improved analytical solution is further adapted in the development of two correcting layers specifically for vertically loaded piles to model infinite boundaries in the finite element model. The correcting layers help in establishing superiority of the finite element method over the boundary element method. To model pile-soil interaction, a purely cohesive interface element is developed and then validated by performing various two-dimensional test problems, including stability analysis of flat surface footings. Footing-soil interface tension is successfully modelled in this way - an outcome that entails a significant modification to the Hansen (1970) bearing capacity solution. Stability analysis is also carried out of conical footings using a three-dimensional finite element model: the results help to explain the applicability of the existing bearing capacity theories to conical footings. The ultimate lateral soil reaction is determined and various pile loading stages are investigated through parametric studies. Study of the stage immediately following pile installation (i.e. the consolidation stage) highlights the need to develop an effective stress analysis for laterally loaded piles. Pile-soil interaction is studied using the cohesive interface element presented earlier, which proves to be quite successful in smoothing out the stress discontinuities around the pile. A new material model for frictional soils is presented, and validated by using it to model an extension test: it captures well post-peak behaviour and takes care of the effects of dilation on the response of laterally loaded piles. Finally, mechanisms of interaction in closely spaced pile groups are studied. Simple analytical expressions are derived which quantify the effects of interaction. A new method of analysis is presented for single-piles and pile groups which offers a considerable degree of reliability without having to do either impossibly expensive full scale field tests or prohibitively expensive full three-dimensional analysis using the currently available computers.
Seamus Heaney and society, 1964 - 1994
Keywords: Northern Ireland
Heaney
society
poetry

The contexts of Seamus Heaney's writing have been routinely noted but their critical interrogation has, to date, been limited. This thesis resituates Heaney's work to reassert the significance of his writing in its varied times and places. Its aim is to revive the web of connections within which Heaney's work was written, published, and received, and this accounts for the "society" of the title. While the idea of society as entity remains important, the word is employed primarily as a capacious guiding principle. Society's adjective, social, is always connected: to be "social" in any sense is always to be implicated in a wider context or contexts.
A central ambition has been to reappraise Heaney's work in relation to the situation in Northern Ireland during the three decades under consideration. A trend in criticism has been to offer reductive contextual accounts which risk depreciating the value of a historicist approach. This thesis demonstrates instead how Heaney's work is implicated in textual, cultural, and institutional networks which were themselves conditioned by the unique circumstances in Northern Ireland. It considers: the London publishing scene on which his work emerged; his relationship to Belfast mediated through television documentary; his radio work for the BBC Northern Ireland Schools Service; his relationship to Derry mediated through photography; and ideas of audience, address, and redress in his Oxford lectures. Participating in the increasingly interdisciplinary treatment of literature within and beyond Irish Studies, the literary analysis at the heart of this project is undertaken within a broader framework of cultural criticism.
The significance of this contribution lies not solely in its acts of historical recovery, but in the critical reorientation these permit. By locating Heaney as a respondent in varied public arenas we can understand the genesis not only of his work but of the international establishment literary figure he became.
Analysis of SMN function in development and Nedd4, a putative modifier of Parkinson's disease, in Drosophila melanogaster
Keywords: Parkinson's disease
Drosophila
SMN

Neurological diseases are devastating illnesses that affect over one billion people worldwide. Drosophila melanogaster provides a genetically tractable system in which to study gene function and the mechanisms of pathogenesis of neurological diseases. In this study I have investigated the function of survival motor neuron (SMN), the causative gene in the neuromuscular disease spinal muscular atrophy (SMA), in growth and differentiation in Drosophila. In addition, I have used the fruit fly to investigate a putative modifier of a previously characterised Drosophila model of Parkinson's disease.
Spinal muscular atrophy is an autosomal recessive neurological disease that is characterised by motor neuron loss resulting in muscle weakness. The disease is caused by the deletion or mutation of the survival motor neuron (SMN) gene. In Drosophila, SMN was found to be highly expressed in dividing tissues and a reduction in SMN levels resulted in growth defects, stem cell defects and developmental delay. SMN was also shown to regulate chromosome morphology of the endocycling nurse cells of the female germline. Therefore it appears that SMN has a role in growth control and development in Drosophila.
Parkinson's disease is a common disorder that results in widespread neurodegeneration with a predilection for dopaminergic neuron loss resulting in movement defects. A defining neuropathological feature of the disease is the presence of alpha-synuclein containing inclusions. Using a Drosophila model of PD, I have shown that specific alpha-synuclein-induced phenotypes in the fly can be suppressed by the overexpression of the E3 ubiquitin ligase, Nedd4.
Spectral data for G-Higgs bundles
Keywords: Hitchin fibration
spectral data
Higgs bundles

We develop a new geometric method of understanding principal G-Higgs bundles through their spectral data, for G a real form of a complex Lie group. In particular, we consider the case of G a split real form, as well as G = SL(2,R), U(p,p), SU(p,p), and Sp(2p,2p). Further, we give some applications of our results, and discuss open questions.