VictorJuiz/thesis huggingface dataset:
"Wounded harts": metaphor and desire in the epic-romances of Tasso, Sidney, and Spenser
Keywords: Torquato Tasso
Edmund Spenser
Early Modern medicine
Renaissance Literature
desire in literature.
body and self
epic-romance
wounds
Philip Sidney
metaphor
Early Modern Literature

If we consider the representation of the body in the epic-romances of Torquato Tasso, Philip Sidney, and Edmund Spenser, certain instances of wounding and laceration emerge as crucial turning points in the development of their respective narratives: Clorinda’s redemptive mutilation, Parthenia’s blood-drenched pallor, Amavia’s disquieting suicide, Venus’s insatiable orifice, Amoret’s “perfect hole.” This thesis affords a detailed comparative study of such passages, contending that the wound assumed a critical metaphoric dimension in sixteenth-century epic-romance literature, particularly in relation to the perceived association between body condition and erotic desire. Along with its function as a marker of martial valor and somatic sacredness, the wound, I argue, increasingly is designated in these epic-romances as an interiorizing apparatus, one liable to accrue at any instance into a surplus of unanticipated meaning. As such, the wound becomes an emblem in these texts of what I call the phenomenology of desire—the equation of consummation and loss—as well as the aesthetic and metaphoric mechanism by which these writers seek to overcome it.
The four chapters of this thesis constitute individual but cumulative points of response to the problem of thinking about desire as a type of wound. For Tasso, a wound poses a challenge to physical, psychological, and spiritual integrity, but its remarkable capacity for aestheticization also allows Tasso to envision it as a synthesizer of sacred and erotic affects. For Sidney, the prospect that a wound could define a body as courageous or pathetic, as sacred or corrupt, became both politically and socially troubling, and the New Arcadia, I argue, proleptically attempts to defend Sidney against interpretations of wounds that register them as manifestations of corrupt desire. For Spenser, body fracture and erotic wounding are analogic (indeed, almost indistinguishable), and The Faerie Queene investigates the prospect that confusing these analogies can become an empowering, even revelatory experience. In each of these epic-romances, a wound serves both a literal and a figurative function and, in this way, is established as the foremost image by which these writers imagine strength and mutilation, affect and heroism, epic and romance as being inextricably bound.
Rydberg ionisation into confined and discrete systems
Keywords: resonant charge transfer
Hydrogen Rydberg atoms
surface ionisation

The energy levels of a hydrogen Rydberg atom approaching a metallic structure are perturbed by the image-charge interaction with the surface. At small atom-surface separations surface ionisation of the Rydberg electron can occur, whereby the electron is transferred to a metal-localised state. In previous studies investigating surface ionisation at bulk metallic surfaces, this state has been part of a conduction band; however this thesis focuses on metallic and structured surfaces where the Rydberg electron transfers into a discrete image-state or hybrid 'well-image state'.
The surface ionisation of hydrogen Rydberg atoms at a Cu(100) projected band-gap surface is investigated experimentally and theoretically. Experimentally, the surface ionisation of an incident beam of hydrogen Rydberg atoms is measured by extraction of the resulting ions. Resonance-enhanced charge transfer is seen for hydrogen Rydberg states that are degenerate with copper-localised image-states. A wavepacket propagation study shows that for on-resonance states the maximum in the surface-ionisation probability is shifted away from the surface by decreasing the collisional velocity.
The discrete hybrid 'well-image states' localised along the surface normal of a thin-film change energy with thin-film thickness. The interaction of hydrogen Rydberg atoms with iron thin films deposited on an insulating substrate is investigated. The preference for electron penetration along the surface normal is seen by the resonance-enhancement of charge transfer at energies where the Rydberg state and well-image state are degenerate. By changing the thickness of the thin film, by in situ depositions, the energies of the well-image state are altered and the Rydberg n-values at which resonances occur, change. At a thickness of 30-monolayer the energetic spacings between the well-image states and the Rydberg states become comparable, and the single well-image state resolution is lost.
A wavepacket-propagation study investigates the interaction of a nanoparticle and low-n hydrogen Rydberg atoms. The nanoparticle has a fully confined potential which at small radii yields well-spaced, fully discrete well-image states. Resonance-enhanced charge transfer occurs when the Rydberg state and the nanoparticle well-image state energy levels are degenerate. However, when there is poor energy matching between the nanoparticle well-image state and the Rydberg atom, no charge transfer is seen i.e. surface ionisation does not occur.
Overall, the work presented here demonstrates the capability of Rydberg-surface studies to identify discrete, high-lying energy levels at specific surfaces.
Investigation of the role of the NLP and TDP1 chromatin associated proteins in transcription control in Trypanosoma brucei
Keywords: epigenetics
chromatin regulation
African trypanosomes

The African trypanosome Trypanosoma brucei evades the immune system of the mammalian host by periodically switching its surface coat which is made up of Variant Surface Glycoprotein (VSG). T. brucei shows monoallelic expression of one VSG out of a repertoire of ~1200 genes with the active VSG gene expressed from one of ~15 telomeric expression sites (ESs). The mechanism behind the monoallelic exclusion of ESs is unclear.
NLP was identified as a novel and essential AT-hook protein binding transcriptionally silent simple sequence repeats in T. brucei. I depleted NLP using RNAi in various T. brucei reporter lines containing an eGFP in different transcriptionally silent areas of the genome and monitored derepression of eGFP using flow cytometry. After NLP knock-down, I observed 45-65 fold derepression of silent ESs, and up to 5 fold derepression of other transcriptionally silent areas. Using chromatin immunoprecipitation (ChIP) I found an enrichment of NLP in certain non-transcribed loci including the rDNA spacers. I also found that blocking NLP synthesis results in a rapid fall in levels of the active VSG transcript. Lastly, I discovered using tandem affinity purification (TAP) followed by mass spectrometry that NLP is a part of a novel TbISWI complex in T. brucei, which also includes two previously unidentified protein partners.
The high mobility group B (HMGB) protein family constitutes a major abundant class of non-histone chromatin associated DNA-binding proteins which play a role in chromatin architecture in a wide range of eukaryotes. In T. brucei, the HMGB protein TDP1, which contains two HMG boxes and one DEK C terminal DNA-binding domain, was first identified as binding to VSG ES promoter oligomer sequences. I report that TDP1 is an essential nuclear protein enriched in the nucleolus and expression site body, and is involved in facilitating transcription. Blocking TDP1 synthesis using RNAi mediated knock-down results in approximately 40-90% reduction in transcription of RNA polymerase I transcribed genes. Using ChIP, I find that TDP1 is enriched in the rDNA and on the active VSG ES in bloodstream form T. brucei. Additionally, the relative proportion of TDP1 binding the procyclin promoter compared with the upstream spacer and downstream EP1 genes is greater in procyclic form compared with bloodstream form T. brucei. Lastly, I performed TAP experiments with TDP1 and found that TDP1 interacts with the core histones. These results indicate that TDP1 is an architectural chromatin protein important for transcription control in T. brucei.
Nella terra di mezzo: cinema e immigrazione in Italia, 1990-2010
Keywords: Migration
Cinema
Italian

The thesis explores the representation of migration to Italy, through the study of a range of films selected for their thematic relevance as much as their aesthetic complexity. Beyond the scope of film analysis, it aims to add a contextualization of the social, political and cultural issues that connect migration and cinema, at the point where film studies and cultural studies converge.
An investigation of reasons for Finland's success in PISA
Keywords: Nordic
comparative education
PISA
Scandinavia
education
Finland

The Programme for International Student Assessment, or PISA, administered by the Organisation for Economic Cooperation and Development, surveyed fifteen-year-olds for the first time in 2000. PISA focuses on mathematics, science, and reading literacy, and intends to undertake a new study every three years. The administration in 2003 added a section that measured problem-solving skills. The results from all three surveys thus far have placed Finland as the highest achieving country in PISA. Finland’s top performances in PISA astonished the educational world. More so than previous cross-national surveys such as TIMSS and PIRLS, PISA has drawn worldwide educational interest towards Finland and its educational system. PISA, unlike TIMSS, does not measure mastery of curriculum, but rather outcomes of education. PISA focuses on real-life applications of knowledge. Triggering global curiosity, the PISA has placed Finland on the itinerary of those wishing to discover the influences behind educational success. This research focuses upon Finland’s historical, cultural, and social context as a part of the Nordic countries and also its immense success in PISA. This project uncovers some of the factors contributing to Finland’s success in education, as indicated by the results in PISA. Finland’s history as a part of both Sweden and Russia has intertwined education with the movement for independence. The struggles after independence, including war and recession, have also reinforced the importance of education within Finnish society. The important status of teachers in Finland, in addition to their high quality, has further enhanced the excellence of the Finnish education system. PISA findings, however, have indicated that the Swedish-speaking Finns score lower than the Finnish-speaking Finns, a phenomenon explored within the research. This project investigates the reasons behind this counterintuitive result. The project incorporates perspectives through interviews with teachers and head teachers from the six sample schools, both Swedish-speaking and Finnish-speaking, Finnish education ministers, PISA creators from the OECD, and Finnish educational researchers and professors responsible for executing PISA in Finland. Their insight, from many different points of view, illuminated different perspectives on PISA and education in Finland.
Mathematical modelling of turbidity currents
Keywords: turbidity currents
density currents
fluid mechanics
mathematical geoscience
gravity currents

Turbidity currents are one of the primary means of transport of sediment in the ocean. They are fast-moving, destructive fluid flows which are able to entrain sediment from the seabed and accelerate downslope in a process known as 'ignition'. In this thesis, we investigate one particular model for turbidity currents; the 'Parker model' of Parker, Pantin and Fukushima (1986), which models the current as a continuous sediment stream and consists of four equations for the depth, velocity, sediment concentration and turbulent kinetic energy of the flow.
We propose two reduced forms of the model; a one-equation velocity model and a two-equation shallow-water model. Both these models give an insight into the dynamics of a turbidity current propagating downstream and we find the slope profile to be particularly influential. Regions of supercritical and subcritical flow are identified and the model is solved through a combination of asymptotic approximations and numerical solutions.
We next consider the dynamics of the four-equation model, which provides a particular focus on Parker's turbulent kinetic energy equation. This equation is found to fail catastrophically and predict complex-valued solutions when the sediment-induced stratification of the current becomes large. We propose a new 'transition' model for turbulent kinetic energy which features a switch from an erosional, turbulent regime to a depositional, stably stratified regime. Finally, the transition model is solved for a series of case studies and a numerical parameter study is conducted in an attempt to answer the question 'when does a turbidity current become extinct?'.
Hedge funds: fees, return revisions, and asset disclosure 
Keywords: Management Companies
Hedge Fund Databases
Hedge Funds
Asset Pricing
Hedge Fund Fees
Revisions
Performance
Assets Under Management
Funds-of-Funds
Voluntary Disclosure
Fraud

This thesis is a collection of three essays on hedge funds with contributions to the empirical understanding of their fees, and their voluntary disclosure of returns and assets under management, using a large consolidation of widely-employed publicly available hedge fund databases.
First, time-series variation in reported fees is analysed using fund launches within hedge fund management companies, and conditioning fees at launch on fund family characteristics. Larger and better performing fund families launch high fee funds. Funds with high management fees at launch do not perform any differently from low fee funds, though funds with high incentive fees marginally outperform. An interval regression technique is proposed to overcome the discrete nature of reported fees.
Secondly, the reliability of voluntary disclosures of financial information is analysed with a different measure of time-variation --- tracking changes to statements of historical performance recorded at different points in time. This uncovers evidence that historical returns are routinely revised. These revisions are not merely random or corrections of earlier mistakes; they are partly forecastable by fund characteristics. Moreover, funds that revise their performance histories, significantly and predictably underperform those that have never revised.
Finally, the availability, and timing, of the selective disclosure of assets under management by funds is examined. More than a third of funds have asset records falling short of returns published. There is evidence of strategic disclosure by funds --- asset reporting drying up after times of fund stress, such as poor performance or outflows. Furthermore, investors should take heed of the greater propensity for shortfall funds to trigger fraud performance flags.
These results suggest that unreliable disclosures: constitute a valuable source of information for current and potential investors; have implications for researchers; and, exhort market regulators to include assets, not just returns, in the debate around mandatory disclosure by financial institutions.
Improving rapid affinity calculations for drug-protein interactions
Keywords: docking
drug-design
water
scoring-function
molecular-modelling
hydrophobicity
simulations

The rationalisation of drug potency using three-dimensional structures of protein-ligand complexes is a central paradigm in medicinal research. For over two decades, a major goal has been to find the rules that accurately relate the structure of any protein-ligand complex to its affinity. Addressing this problem is of great concern to the pharmaceutical industry, which uses virtual screens to computationally assay up to many millions of compounds against a protein target. A fast and trustworthy affinity estimator could potentially streamline the drug discovery process, reducing reliance on expensive wet lab experiments, speeding up the discovery of new hits and aiding lead optimization.
Water plays a critical role in drug-protein interactions. To address the often ambiguous nature of water in binding sites, a water placement method was developed and found to be in good agreement with X-ray crystallography, neutron diffraction data and molecular dynamics simulations. The method is fast and has facilitated a large scale study of the statistics of water in ligand binding sites, as well as the creation of models pertaining to water binding free energies and displacement propensities, which are of particular interest to medicinal chemistry.
Structure-based scoring functions employing the explicit water models were developed. Surprisingly, these attempts were no more accurate than the current state of the art, and the models suffered from the same inadequacies which have plagued all previous scoring functions. This suggests a unifying cause behind scoring function inaccuracy. Accordingly, mathematical analyses on the fundamental uncertainties in structure-based modelling were conducted. Using statistical learning theory and information theory, the existence of inherent errors in empirical scoring functions was proven. Among other results, it was found that even the very best generalised structure-based model is significantly limited in its accuracy, and protein-specific models are always likely to be better. The theoretical framework developed herein hints at modelling strategies that operate at the leading edge of achievable accuracy.
Novel aspects of the reactions of hydrogenases with small molecule inhibitors
Keywords: hydrogenase
electrochemistry

Hydrogenases catalyse the reversible oxidation and production of H₂. They have been the subject of intense interest in recent years since these enzymes, or catalysts inspired by them, may greatly enhance our exploitation of H₂ as an energy carrier in a future ‘green’ H₂-based economy. However, a major challenge to the future use of these catalysts is their reactions with small molecule inhibitors, such as O₂ or CO.
This thesis presents studies using Protein Film Electrochemistry, in which an enzyme is adsorbed onto an electrode to give an electroactive film. Although most hydrogenases are inhibited or irreversibly damaged by even trace O₂, certain O₂-tolerant hydrogenases are unusual in that they are able to sustain H₂ oxidation activity in the presence of O₂. Results outlined in this thesis suggest that the O₂ tolerance of the membrane-bound [NiFe]-hydrogenase from Ralstonia eutropha relies upon O₂ attack generating exclusively the ‘Ready’ inactive state (formed by complete, four-electron reduction of O₂), which subsequently reactivates both rapidly and at high potential. The results contributed to a new explanation for how hydrogenases in certain microbes survive O₂. Electrochemical studies performed on a variant enzyme suggest that a modified proximal FeS cluster plays a role in conferring this O₂ tolerance. Studies of an enzymatic H₂/O₂ fuel cell employing the O₂-tolerant [NiFe]-hydrogenase Hyd1 from Escherichia coli as the anodic catalyst highlight the subtle influence of the reactions of the hydrogenase with O₂ on the power characteristics of the fuel cell under various operating conditions.
This research also identifies straight-chain aldehydes as unprecedented inhibitors of H₂ production by the [FeFe]-hydrogenases. However, some of these results cannot currently be made freely available as they are to be published at a later date in academic journals.
Automated quantitative software verification
Keywords: software verification
software
formal verification
formal methods
verification
quantitative
model checking

Many software systems exhibit probabilistic behaviour, either added explicitly, to improve performance or to break symmetry, or implicitly, through interaction with unreliable networks or faulty hardware. When employed in safety-critical applications, it is important to rigorously analyse the behaviour of these systems. This can be done with a formal verification technique called model checking, which establishes properties of systems by algorithmically considering all execution scenarios. In the presence of probabilistic behaviour, we consider quantitative properties such as "the worst-case probability that the airbag fails to deploy within 10ms", instead of qualitative properties such as "the airbag eventually deploys". Although many model checking techniques exist to verify qualitative properties of software, quantitative model checking techniques typically focus on manually derived models of systems and cannot directly verify software.
In this thesis, we present two quantitative model checking techniques for probabilistic software. The first is a quantitative adaptation of a successful model checking technique called counter-example guided abstraction refinement which uses stochastic two-player games as abstractions of probabilistic software. We show how to achieve abstraction and refinement in a probabilistic setting and investigate theoretical extensions of stochastic two-player game abstractions. Our second technique instruments probabilistic software in such a way that existing, non-probabilistic software verification methods can be used to compute bounds on quantitative properties of the original, uninstrumented software.
Our techniques are the first to target real, compilable software in a probabilistic setting. We present an experimental evaluation of both approaches on a large range of case studies and evaluate several extensions and heuristics. We demonstrate that, with our methods, we can successfully compute quantitative properties of real network clients comprising approximately 1,000 lines of complex ANSI-C code — the verification of such software is far beyond the capabilities of existing quantitative model checking techniques.
Dynamical System Decomposition and Analysis Using Convex Optimization
Keywords: Dynamical systems
Convex optimization

This thesis is concerned with investigating new methods for the analysis of large-scale dynamical systems using convex optimization. The proposed methodology is based on composite Lyapunov theory and is computationally implemented using polynomial programming techniques. The main result of this work is the development of a system decomposition framework that makes it possible to analyze systems that are of such a scale that traditional methods cannot cope with.
We begin by addressing the problem of model invalidation. A barrier certificate method for invalidating models in the presence of uncertain data is presented for both continuous and discrete time models. It is shown how a re-parameterization of the time dependent variables can improve the numerical conditioning of the underlying optimization problem.
The main contribution of this thesis is the development of an automated dynamical system decomposition framework that permits us to verify the stability of systems that typically have a state dimension large enough to render traditional computational methods intractable. The underlying idea is to decompose a system into a set of lower order subsystems connected in feedback in such a manner that composite methods for stability verification may be employed. What is unique about the algorithm presented is that it takes into account both dynamics and the topology of the interconnection graph.
In the first instance we illustrate the methodology with an ecological network and primal Internet congestion control scheme. The versatility of the decomposition framework is also highlighted when it is shown that when applied to a model of the EGF-MAPK signaling pathway it is capable of identifying biologically relevant subsystems in addition to stability verification.
Finally we introduce stability metrics for interconnected dynamical systems based on the theory of dissipativity. We conclude by outlining a clustering based decomposition algorithm that explicitly takes into account the input and output dynamics when determining the system decomposition.