VictorJuiz/thesis huggingface dataset:
Crisis and form in Ingeborg Bachmann's late verse and prose: an aesthetic examination of the poetic drafts of the 1960s
Keywords: 1960s
prose
Todesarten
poetry
Ingeborg Bachmann
women's writing
crisis
post-1945 literature
experimental writing
German literature

This thesis demonstrates the aesthetic impact of crisis on Ingeborg Bachmann's late verse and prose. It examines poetic drafts written during a period of personal breakdown in the 1960s, which have largely been received as documents of personal suffering, and identifies these texts as a radical stage of writing that was to prove formally significant for Bachmann's development of the prose "Todesarten"-Projekt. This thesis draws on the new material made available with the publication of these poetic drafts to chart the genesis of Bachmann's acclaimed late oeuvre. By selecting and grouping lyric fragments, the thesis defines recurrent features in this verse and accounts for the texts as a body of writing that forms a radical, yet undocumented, part of this oeuvre. In terms of both their form and of their content, the fragmentary drafts are shown to reflect new engagement with aspects of experience conventionally excluded from High Art. In light of Bachmann's growing preoccupation with the need for aesthetic engagement in the post-war era, close readings reveal how she set about taking her subjective suffering as a basis for a critique of the social order. The thesis outlines how, during the 1960s, Bachmann pioneered a symptomatic expressive mode that - in the disrupted form of the writing - found an indirect means of manifesting the wider origins of subjective disturbance. The ambiguous aesthetic status of these poetic drafts, which were never finished by Bachmann, is related to an inability to establish structural distance from crisis in lyric form. Building on its readings of the poetic drafts, the thesis traces Bachmann's prose experimentation with the same motifs. It identifies how, ultimately, the prose medium enabled the author to resolve problems of aesthetic form raised in the verse. Parallels with the work of other writers and thinkers illuminate the development of a reflexive mode where sophisticated aesthetic strategies enable the oblique expression of cultural critique.
Protein loop structure prediction
Keywords: protein loop
protein
computational biology
protein structure prediction
bioinformatics
protein loop structure prediction

This dissertation concerns the study and prediction of loops in protein structures.
Proteins perform crucial functions in living organisms. Despite their importance, we are currently unable to predict their three dimensional structure accurately.
Loops are segments that connect regular secondary structures of proteins. They tend to be located on the surface of proteins and often interact with other biological agents. As loops are generally subject to more frequent mutations than the rest of the protein, their sequences and structural conformations can vary significantly even within the same protein family. Although homology modelling is the most accurate computational method for protein structure prediction, difficulties still arise in predicting protein loops. Protein loop structure prediction is therefore a bottleneck in solving the protein structure prediction problem.
Reflecting on the success of homology modelling, I implement an improved version of a database search method, FREAD. I show how sequence similarity as quantified by environment specific substitution scores can be used to significantly improve loop prediction.
FREAD performs appreciably better for an identifiable subset of loops (two thirds of shorter loops and half of the longer loops tested) than ab initio methods; FREAD's predictive ability is length independent. In general, it produces results within 2Å root mean square deviation (RMSD) from the native conformations, compared to an average of over 10Å for loop length 20 for any of the other tested ab initio methods.
I then examine FREAD’s predictive ability on a specific type of loops called complementarity determining regions (CDRs) in antibodies. CDRs consist of six hypervariable loops and form the majority of the antigen binding site. I examine CDR loop structure prediction as a general case of loop structure prediction problem. FREAD achieves accuracy similar to specific CDR predictors. However, it fails to accurately predict CDR-H3, which is known to be the most challenging CDR. Various FREAD versions including FREAD with contact information (ConFREAD) are examined. The FREAD variants improve predictions for CDR-H3 on homology models and docked structures.
Lastly, I focus on the local properties of protein loops and demonstrate that the protein loop structure prediction problem is a local protein folding problem. The end-to-end distance of loops (loop span) follows a distinctive frequency distribution, regardless of secondary structure elements connected or the number of residues in the loop. I show that the loop span distribution follows a Maxwell-Boltzmann distribution.
Based on my research, I propose future directions in protein loop structure prediction including estimating experimentally undetermined local structures using FREAD, multiple loop structure prediction using contact information and a novel ab initio method which makes use of loop stretch.
Game semantics based equivalence checking of higher-order programs
Keywords: verification
Higher-order programs
Game semantics
equivalence checking

This thesis examines the use of game semantics for the automatic equivalence checking of higher-order programs. Game semantics has proved to be a powerful method for constructing fully abstract models of logics and programming languages. Furthermore, the concrete nature of the semantics lends itself to algorithmic analysis. The game-semantic model can be used to identify fragments of languages which have a decidable observational equivalence problem. We investigate decidability results for different languages as well as the efficiency of these algorithms in practice.
First we consider the call-by-value higher-order language with state, RML. This can be viewed as a canonical restriction of Standard ML to ground-type references. The O-strict fragment of RML is the largest set of type sequents for which, in the game-semantic denotation, justification pointers from O-moves are always uniquely reconstructible from the underlying move sequence. The O-strict fragment is surprisingly expressive, including higher-order types and difficult examples from the literature. By representing strategies as Visibly Pushdown Automata (VPA) we show that observational equivalence of O-strict terms is decidable (and in fact is ExpTime-complete). We then consider extensions of the O-strict fragment. Adding general recursion or using most non-O-strict types leads to undecidability. However, a limited form of recursion can be added while still preserving decidability (although the full power of DPDA is required).
Next we examine languages with non-local control. This involves adding call/cc to our language and is known to correspond to dropping the game-semantic bracketing condition. In the call-by-name game-semantic model of Idealized Algol (IA), in which answers cannot justify questions, the visibility condition still implies a form of weak bracketing. By making bracketing violations explicit we show that we can still model the entire third-order fragment using VPA.
We have also implemented tools based on these algorithms. Our model checkers Homer and Hector perform equivalence checking for third-order IA and O-strict RML respectively. Homer uses a naive explicit state method whereas Hector takes advantage of on-the-fly model checking. Our tools perform well on small yet challenging examples. On negative instances, the on-the-fly approach allows Hector to outperform Homer. To improve their performance, we also consider using ideas from symbolic execution. We propose a representation for finite automata using transitions labelled with formulas and guards which aims to take advantage of the symmetries of the game-semantic model so that strategies can be represented compactly. We refer to this representation as Symbolically Executed Automata (SEA). Using SEA allows much larger data types to be handled but is not as effective on larger examples with small data types.
Words and artworks in the twelfth century and beyond. The thirteenth-century manuscript Marcianus gr. 524 and the twelfth-century dedicatory epigrams on works of art
Keywords: 12th century Byzantium
epigrams on works of art
Manuel Komnenos
marc. gr. 524
word and image
Constantinople

The thesis is divided into three sections. The first section discusses the manuscript Marcianus graecus 524, the second looks at the Greek text of the dedicatory epigrams on works of art from the same manuscript, and the third puts these texts in their context. In the first part, the compilation of the manuscript is analysed. I suggest that the manuscript was copied mainly by one individual scribe living in Constantinople at the end of the thirteenth century. He copied the quires individually, but at some point he put all these quires together, added new quires, and compiled an anthology of poetry. The scribe’s connection to the Planudean School and the Petra monastery in Constantinople is discussed. Although their relationship remains inconclusive, the manuscript provides evidence regarding the literary interests of late-thirteenth-century intellectuals. The second part contains thirty-five unpublished dedicatory epigrams on works of art. New readings are offered for the text of previously published epigrams. The third section analyses the dedicatory epigrams on works of art in their context. The first chapter of this section discusses the epigrams as Gebrauchstexte, i.e. texts with a practical use. The difference between epigrams intended to be inscribed and epigrams intended to be performed is highlighted. In the next chapter of this part, La poésie de l’objet, the composition of the dedicatory epigrams is discussed. The conventional character of the epigrams suggests that the poetics express the ritual aspect of the epigram. The last chapter considers the texts from a more pragmatic angle. After a short discussion of the objects on which the epigrams were written, the mechanisms of the twelfth-century art market are presented based on evidence taken mainly from the epigrams. At the end of this part, conclusions are drawn on the understanding of these texts in the twelfth century.
Community, women and selfhood in the writings of Michel Leiris and Carlo Emilio Gadda
Keywords: Self
Carlo Emilio Gadda
Community
Identity
Women
Michel Leiris

This study sets out to uncover the thus far unexplored affinities between the works of Carlo Emilio Gadda and Michel Leiris, two key figures of twentieth-century literature whose place within the broader European literary panorama has been largely overlooked. Through an inquiry into three interconnected areas – the question of 'community'; the relationship between male self and female other; and writing as a space in which a fractured experience of subjectivity is both played out and exposed – I argue that their works are underpinned by a parallel tension, between a nostalgia for a lost experience of unity and a recognition of its impossibility within a fractured modernity.
Chapter One examines the relationship between the individual and the communal. With a focus on Gadda's Giornale di guerra e di prigionia, and Leiris's involvement in a series of key intellectual, literary and political societies of the 1930s and 1940s, it argues that while both authors were drawn to a form of communal integration, both were ultimately thwarted in their attempts to reinstate it. Chapter Two continues this inquiry into the relationship between self and other through an examination of the dysfunctional relationship between individual (male) self and (female) other. With a focus on Leiris's L'Age d'homme and Gadda's Quer pasticciaccio brutto de via Merulana, it questions the extent to which any authentic relationship between male self and female other is ruled out, and examines the association between sexuality and fear that underpins their approach to the sphere of the female at large. The final chapter examines the implications of the authors' shared loss of faith in the notion of a unified, authentic experience of selfhood for their approach to the literary act itself.
Through a study of these three key areas, this study thus sets out to respond to the need for further contextualisation of these two key figures of the twentieth-century European literary panorama, in the conviction that a comparative examination will shed new light both on their individual works and on their shared affinity with a number of key tenets of twentieth-century European thought.
Tax incentives, R&amp;D; and productivity
Keywords: R&amp;D
productivity
tax
policy evaluation
applied microeconomics

This thesis explores the causal relationships between tax incentives, research and development (R&D;) and productivity. Using R&D; survey data from the United Kingdom (UK) Office for National Statistics and administrative data on corporation tax returns from HM Revenue and Customs, I first conduct empirical analyses of tax incentive policies for R&D;, and then estimate the elasticity of output with respect to firms' own R&D; efforts as well as external R&D; performed by neighboring firms in technology and product space. In the first two chapters which focus on tax incentive policies and their evaluation, I am able to identify the policy effect of interest by exploiting two significant reforms in the UK in 2002 and 2008. I find that tax incentives had a positive and significant stimulating effect on businesses' R&D; spending. I argue that the availability of a quasi-experimental set up helps in better identifying the policy impact. The production function estimation exercise in the third chapter shows that double counting of R&D; human resources and materials in the production function causes the elasticity of output with respect to the firms' own R&D; to be substantially underestimated. I also find that the R&D; done in multi-unit enterprise groups is productive for the production facilities which themselves do not perform R&D.; The Jaffe (1986) and Bloom et al. (2013) measures of external R&D;, which account for closeness of firms in technology and product space can be constructed and included in the production function in the spirit of Griliches (1979). I find that the point estimate for the elasticity of output with respect to firms' own R&D; is around 3 percent and statistically significant. Evidence is mixed regarding the productivity effects of R&D; carried out by competitors in the product market or neighboring firms in technology space. The detailed data sets used in this study offer valuable resources for empirical work on R&D; and productivity.
Construction and characterisation of MRI coils for vessel wall imaging at 7 tesla
Keywords: MRI coils
MR safety
RF simulation
vessel wall imaging
RF safety
RF coils
RF coil construction
array characterisation
RF arrays

Atherosclerotic plaques in the bifurcation of the carotid artery vessels can pose a significant stroke risk from stenosis, thrombosis and emboli, or plaque rupture. However, the possibility of the latter depends on the structure of the plaque and its stability. So far, the assessment of such depositions, and the evaluation of the risk they pose, is not satisfactory with 3 Tesla black blood imaging. It is expected that the SNR increase at 7 Tesla, together with an appropriate and patient-safe RF coil, will result in higher resolution images that would help in better assessing the composition of atherosclerotic plaques in vessel walls. A custom-built neck array was designed and constructed, with the aim of investigating the benefits of the higher field strength using DANTE-prepared black blood imaging.
A 4-channel transmit array was designed to generate the required B&plus;1 field for the DANTE module to be used. A separate close fitting 4-channel receive array was preferred for improved SNR and parallel (receive) imaging. Geometric, active, passive as well as preamp decoupling schemes were employed for adequate isolation between the arrays and their channels. Electromagnetic simulation software, Semcad X (SPEAG, Zurich), was used for safety assessment with human phantoms (Virtual population). The E fields for 1 W transmission per channel were calculated for each element for a worst case SAR estimation. The transmission power limits per channel were set according to the 10g SAR limit set in IEC 60601. For simulation validation, temperature measurements and surface heat mapping were performed on a meat phantom. Finally, a healthy male subject was scanned using a protocol consisting of B1 mapping, RF shimming at an ROI, and 2D and 3D DANTE prepared Gradient Echo (GRE).
The worst-case heating scenario, as defined in the methods section, generated a maximum local SAR of 7.65 W/kg for 1 Watt per channel input. Thus, for 1st level mode (20W/kg max), the power limit was set at 2.6 W per channel. The heating profile was similar to that simulated and the measured temperature increase was within a ±10% margin relative to the simulation. The global SAR power limit per channel was found to be higher (i.e. more allowed power) than the worst case local SAR power limit, and thus did not impose additional power penalty. The resolution achieved was 0.6 mm isotropic for the 3D protocol and 0.6 by 0.6 by 2.5 mm for the 2D protocol. The average SNR was measured within the vessel wall location of the two carotid arteries and found to be 27±6 for the DANTE images and for the static tissue closer to the skin the SNR was 55±2.
In conclusion, a 4Tx/4Rx coil was designed to target the carotid arteries operating under pTx mode and a black blood imaging sequence was implemented for blood signal suppression and vessel wall imaging. The initial results from the subject and phantom imaging show satisfactory blood suppression and spatial resolution.
Towards the development of direct methodology to enantioenriched α-alkylated aldehydes
Keywords: tropinone
oxazolidine
tropane
alkylation
enantioselective
diastereoselective
pyrrolidine
enamine
computation
DFT
auxiliary
aldehyde
asymmetric

Enantiopure α-alkyl-substituted aldehydes are widely recognised as important building blocks in synthesis. Despite this, methods to prepare such substrates are limited. Strategically, asymmetric intermolecular SN2 α-alkylation represents a highly straightforward transformation, but still remains an elusive feat. This thesis describes efforts to address this challenge, with attempted access to enantioenriched α-alkyl aldehydes by way of C-alkylation of chiral, non-racemic, hindered aldenamines using simple alkyl halides. Enamines derived from four types of auxiliary (a tropane, an oxazolidine, a pyrrolidine and a homotropane) have been prepared, and their alkylation profile examined.
While the desired levels of asymmetric induction were not attained, use of the tropane and homotropane auxiliaries, which differ only by a single methylene group, interestingly, gave complimentary diastereocontrol during alkylation with EtI. The observed stereoselectivity is supported by density functional studies performed for ethylation of both enamines.
Additionally, in the course of preparing the homotropane a highly efficient asymmetric synthesis of a homotropinone bearing gem-α-substitution has been developed.
Innate immune responses to tuberculosis vaccines
Keywords: immunology
MVA
microarray
vaccine
TB

Tuberculosis, caused by infection with Mycobacterium tuberculosis (M.tb), remains a global health problem. Drug resistance and high rates of HIV infection have fuelled the pandemic and, although a vaccine exists, its ability to protect from pulmonary tuberculosis varies between 0 and 80%. Bacille Calmette Guerin (BCG) has been administered to billions worldwide yet its protective mechanisms remain unknown, as do the reasons for its failure to protect in many parts of the world. Modified Vaccinia virus Ankara expressing antigen 85A (MVA85A) is a novel candidate vaccine designed to boost immune responses to BCG and improve protection. An aim of this thesis has been to characterise the innate immune response to an MVA85A boosting vaccination in both UK adults and South African infants. In the former, volunteers develop a strong innate response following vaccination however this does not always translate into a robust adaptive response to antigen 85A (Ag85A), which is determined in part by Treg expansion and the nuclear protein HMGB1 signaling through the TLR1-2-6 axis. By contrast, not all South Africa infants mount a strong innate immune response to MVA85A yet this response is correlated with the magnitude of the adaptive response. The immune response to BCG in both populations is also characterised and an association found between increased production of IL-17, IL-22 and IFN-γ in response to BCG stimulation and control of mycobacterial growth. The results presented here further the knowledge on the links between innate and adaptive responses to vaccination with BCG and MVA85A and the variation in mechanisms involved in different populations.
Geometric and probabilistic aspects of groups with hyperbolic features
Keywords: random walk
hyperbolic

The main objects of interest in this thesis are relatively hyperbolic groups. We will study some of their geometric properties, and we will be especially concerned with geometric properties of their boundaries, like linear connectedness, avoidability of parabolic points, etc. Exploiting such properties will allow us to construct, under suitable hypotheses, quasi-isometric embeddings of hyperbolic planes into relatively hyperbolic groups and quasi-isometric embeddings of relatively hyperbolic groups into products of trees. Both results have applications to fundamental groups of 3-manifolds.
We will also study probabilistic properties of relatively hyperbolic groups and of groups containing hyperbolic directions'' despite not being relatively hyperbolic, like mapping class groups, Out(Fn), CAT(0) groups and subgroups of the above. In particular, we will show that the elements that generate the hyperbolic directions'' (hyperbolic elements in relatively hyperbolic groups, pseudo-Anosovs in mapping class groups, fully irreducible elements in Out(Fn) and rank one elements in CAT(0) groups) are generic in the corresponding groups (provided at least one exists, in the case of CAT(0) groups, or of proper subgroups). We also study how far a random path can stray from a geodesic in the context of relatively hyperbolic groups and mapping class groups, but also of groups acting on a relatively hyperbolic space. We will apply this, for example, to show properties of random triangles.