VictorJuiz/thesis huggingface dataset:
Explanation from neural networks

Neural networks have frequently been found to give accurate solutions to hard classification problems. However neural networks do not make explained classifications because the class boundaries are implicitly defined by the network weights, and these weights do not lend themselves to simple analysis. Explanation is desirable because it gives problem insight both to the designer and to the user of the classifier.
Many methods have been suggested for explaining the classification given by a neural network, but they all suffer from one or more of the following disadvantages:
a lack of equivalence between the network and the explanation;
the absence of a probability framework required to express the uncertainty present in the data;
a restriction to problems with binary or coarsely discretised features;
reliance on axis-aligned rules, which are intrinsically poor at describing the boundaries generated by neural networks.
The structure of the solution presented in this thesis rests on the following steps:
Train a standard neural network to estimate the class conditional probabilities. Bayes’ rule then defines the optimal class boundaries.
Obtain an explicit representation of these class boundaries using a piece-wise linearisation technique. Note that the class boundaries are otherwise only implicitly defined by the network weights.
Obtain a safe but possibly partial description of this explicit representation using rules based upon the city-block distance to a prototype pattern.
The methods required to achieve the last two represent novel work which seeks to explain the answers given by a proven neural network solution to the classification problem.
Taxonomy, biodiversity, and ecology of Apusozoa (Protozoa)

Apusozoa (Protozoa) is a phylum of heterotrophic gliding zooflagellates of unknown taxonomic affiliation, commonly observed in environmental samples. Almost nothing was previously known about the diversity and ecology of apusozoan species though, as bacterivores, they are probably important functional constituents within microbial assemblages.
We explored apusozoan morphological and genetic diversity, ecology, and related methodological questions. By culturing environmental material from a range of habitats, we isolated and maintained monocultures of both previously described apusozoan orders, Apusomonadida (apusomonads) and Planomonadida (planomonads). For planomonads, we present a revised taxonomy based on morphology, ultrastructure, and 18S rDNA genetic differences. We describe nine new species and new genera Nutomonas and Fabomonas, and demonstrate ITS2 rDNA secondary structure analysis for species delineation.
During our culturing effort, we also isolated two genotypes of a previously unknown flagellate group, shown here to belong to a novel third apusozoan order, Mantamonadida. We designed molecular probes specific to all three orders and applied them to environmental DNA, detecting novel 18S and ITS1 rDNA lineages in a range of habitats.
We mined publically available metagenomic and metatranscriptomic sequence databases using 18S rDNA of described species as seeds, identifying hundreds of sequences with affinities to all three orders. Phylogenies featuring newly retrieved lineages with previously described species suggest that direct sequencing of transcriptomic material is more effective than amplification-dependent methods at detecting rare cells in mixed microbial assemblages.
Finally, to test potential future applications of our newly isolated strains, we ran microcosm experiments examining the effect of protozoan (Cercozoa) grazing on the structure of bacterial assemblages, demonstrating that closely related and morphologically similar species can have different impacts on their prey base.
Taken together, by combining traditional culturing and modern molecular methods, this thesis drastically improves our understanding of apusozoan diversity and sets the scene for future work using next-generation sequencing and ecologically driven functional experiments.
A comparative study of die attach strategies for use in harsh environments

Well-logging and aerospace applications require electronics capable of withstanding elevated temperature operation. A key element of high temperature packaging technology is the Si die attach material, and a comparative study of two die attach systems for use in harsh environment has been performed.
Die bond sample packages, using commercial adhesives and an Au-Si eutectic solder, have been manufactured and were subsequently thermally exposed for various times at 250 and 300°C respectively. The adhesive die bond packages comprised a high temperature co-fired ceramic (HTCC) substrate with W, Ni and Au metallisations whereas the Au-Si die bond packages used thick film Au metallised on a Al₂O₃ substrate. Optimisation of the eutectic die bonding parameters was successfully performed for the Au-Si system by an experimental design method, which improved mean and spread of maximum bonded areas and consequently, the shear load to failure. Bonded area was systematically assessed by scanning acoustic microscopy (SAM) followed by digital image analysis (DIA).
Accelerated testing comprised thermal cycling and thermal shock and although showing some degradation, Au-2wt%Si die bonds were surprisingly robust, showing excellent subsequent stability during industrial device testing investigations.
Product publics and the early moments of nascent markets

Product markets have been found to be socially constructed as industry logics, product ontologies and organising visions. Information intermediaries play an important field-level role in determining the categories and ontologies of emerging products. Within shared cognitive structures, sellers and buyers come together in mutual understandings on how products are used, what features are important and what counts as value.
Although market information is often legitimated through objective scientific methodologies, it can also appear as uncertain knowledge, or rumour. Contrary to the often seen conception of rumour as crowd-like behavioural contagion, it is presented here as an informal message lacking a reliable sponsor that is developed in an uncertain situation, but still may be subject to critical reasoning.
This thesis investigates the ambiguity around the fuzzy front-end of product markets, as social media and blogs that trade in rumour and proposition before any official announcement by firms. Through a process of improvised news, these online collectivities, as product publics, deliberate and collectively generate expectations as meaning structures. By tracking discourse from tech blogs, I trace the emergence of meaning in the tablet device product ontology. This occurred well before product introductions by firms who eventually came to form the market.
In the hall of the flop king: two applications of perverse coherent sheaves to Donaldson-Thomas invariants

This thesis contains two main results. The first is a comparison formula for the Donaldson-Thomas invariants of two (complex, smooth and projective) Calabi-Yau threefolds related by a flop; the second is a proof of the projective case of the Crepant Resolution Conjecture for Donaldson-Thomas invariants, as stated by Bryan, Cadman and Young.
Both results rely on Bridgeland’s category of perverse coherent sheaves, which is the heart of a t-structure in the derived category of the given Calabi-Yau variety. The first formula is a consequence of various identities in an appropriate motivic Hall algebra followed by an implementation of the integration morphism (using the technology of Joyce and Song). Our proof of the crepant resolution conjecture is a quick and elegant application of the first formula in the context of the derived McKay correspondence of Bridgeland, King and Reid. The first chapter is introductory and is followed by two chapters of background material. The last two chapters are devoted to the proofs of the main results.
The uses of Anglo-Saxon manuscripts, c. 1066-1200

This thesis examines the uses of Anglo-Saxon manuscripts in the 150 years immediately following the Norman Conquest. By focusing on the most common types of use evident in the manuscripts, it explores how readers actually interacted with books. It also treats manuscripts as cultural artefacts through which it is possible to observe the literary and social consequences of the Conquest. The Introduction summarises our current understanding of the literary culture of this transitional period. Chapter II, ‘Destruction and Conservation’, examines claims that Norman elites destroyed Anglo-Saxon manuscripts; finding these claims unjustified, it investigates the circumstances in which manuscripts were lost and identifies how readers evaluated the contents of pre-Conquest books. Chapter III, ‘The Movement of Pre-Conquest Manuscripts’, looks at the consequent loan, exchange and sale of pre-Conquest manuscripts after 1066. Chapter IV, ‘Updating Pre-Conquest Manuscripts’, discusses difficulties which Norman readers encountered with pre-Conquest books, including script, abbreviation, orthography and textual redaction, and examines how these technical features could be modernised. It also investigates more practical modernisations to liturgical books, chronicles and cartularies. Chapter V, ‘Glossing and Annotating’, concerns readers’ reactions to the texts found in pre-Conquest manuscripts, particularly vernacular homilies and translations. It argues that the post-Conquest classroom was essentially trilingual, though Latin became the lingua franca. Chapter VI, ‘Record-Keeping in Pre-Conquest Manuscripts’, explores the use of pre-Conquest manuscripts – copies of the gospels, liturgical books and patristic texts – as repositories for records. Chapter VII, ‘The Veneration of Pre-Conquest Manuscripts’, continues this exploration of the symbolic capital of pre-Conquest books by examining how Norman churchmen supported the veneration of particular manuscripts as secondary relics, and introduced new traditions regarding other books. The Conclusion refocuses the findings of this thesis on two key issues: early medieval reading practices and English literature between 1066 and 1200.
Shocked single crystals studied via nanosecond Laue diffraction and molecular dynamics

Under shock compression it is believed that crystalline materials undergo complex, rapid, micro-structural changes to relieve the large applied shear stresses. The mechanisms involved, such as dislocation flow and deformation twinning, under the generated high strain rates are not fully understood and in situ measurements of defects have proven elusive. This work presents the development of a nanosecond x-ray diffraction technique based on the white-light Laue method, and its first use in studying shock compressed copper. Observations of diffuse scattering are interpreted as stress-dependent lattice rotations due to dislocation glide. The results are compared with MD simulations of shocks in copper which are shown not to agree. Simulations of tantalum, shocked along the [001] axis, are demonstrated to undergo deformation twinning. A novel order parameter for identifying twin variants is developed and the deformation twinning mechanism under shock compression is identified.
Intensional type theory for higher-order contingentism

Things could have been different, but could it also have been different what things there are? It is natural to think so, since I could have failed to be born, and it is natural to think that I would then not have been anything. But what about entities like propositions, properties and relations? Had I not been anything, would there have been the property of being me? In this thesis, I formally develop and assess views according to which it is both contingent what individuals there are and contingent what propositions, properties and relations there are. I end up rejecting these views, and conclude that even if it is contingent what individuals there are, it is necessary what propositions, properties and relations there are.
Call the view that it is contingent what individuals there are first-order contingentism, and the view that it is contingent what propositions, properties and relations there are higher-order contingentism. I bring together the three major contributions to the literature on higher-order contingentism, which have been developed largely independently of each other, by Kit Fine, Robert Stalnaker, and Timothy Williamson. I show that a version of Stalnaker's approach to higher-order contingentism was already explored in much more technical detail by Fine, and that it stands up well to the major challenges against higher-order contingentism posed by Williamson.
I further show that once a mistake in Stalnaker's development is corrected, each of his models of contingently existing propositions corresponds to the propositional fragment of one of Fine's more general models of contingently existing propositions, properties and relations, and vice versa. I also show that Stalnaker's theory of contingently existing propositions is in tension with his own theory of counterfactuals, but not with one of the main competing theories, proposed by David Lewis.
Finally, I connect higher-order contingentism to expressive power arguments against first-order contingentism. I argue that there are intelligible distinctions we draw with talk about "possible things", such as the claim that there are uncountably many possible stars. Since first-order contingentists hold that there are no possible stars apart from the actual stars, they face the challenge of paraphrasing such talk. I show that even in an infinitary higher-order modal logic, the claim that there are uncountably many possible stars can only be paraphrased if higher-order contingentism is false. I therefore conclude that even if first-order contingentism is true, higher-order contingentism is false.
Monolayers of cationic surfectants at the air-water and oil-water interfaces

Monolayers of the cationic surfactant hexadecyltrimethylammonium halide (CTAX, where X = F¯, Cl¯, Br¯, and I¯) have been studied at the air-water and oilwater interfaces. At the air-water interface, the effects of the halide counterion and the addition of counterion were investigated. Sum-frequency spectroscopy (SFS), ellipsometry, and surface tensiometry indicated that the counterion changed the efficiency and effectiveness of the surfactant, both decreasing in the order of Br¯> Cl¯>F¯. The addition of salt in the form of 0.1 M KX was found to reduce the cmc but had little effect on the limiting area per molecule attained at the cmc, which increased from 44 Å2 for CTAB to 65 Å2 for CTAC and ca. 94 Å2 for CTAF. Neither SFS nor ellipsometry provided any firm evidence for specific effects of the halide ions on the structure of the surfactant monolayers. For CTAB monolayers in the absence of excess electrolyte, the effect of area per molecule on the sum-frequency (SF) spectra was studied.
Mixed monolayers of CTAB and tetradecane at the air-water interface exhibit a first-order phase transition from a conformationally disordered to a conformationally ordered state as the temperature is lowered. The phase transition occurs ca. 11 °C above the bulk melting point of tetradecane.
A new experimental arrangement is described for acquiring SF spectra from surfactants at the oil-water interface. The key features of this approach are the stabilisation of a thin oil film between a sapphire prism and an aqueous phase, and the use of total internal reflection to enhance the total signal and discriminate against signals from other interfaces in the system. With this new methodology, the first SF vibrational spectra of surfactant monolayers at an alkane-water interface were obtained. Surface tensiometry was used to characterise the monolayers further. The structure of CTAB monolayers at the hexadecane-water interface was determined by SFS and compared with monolayers of CTAB at the air-water interface. At low concentrations, CTAB/hexadecane showed the expected features in the C-H stretching region, characteristic of a conformationally disordered monolayer. As the bulk concentration approached the critical micelle concentration, the spectra changed to one characteristic of a more ordered, upright conformation. Ellipsometric measurements supported this conclusion. This qualitative structural change is not observed in analogous monolayers at the air-water interface or CCl4-water interface, or in surfactant solutions in contact with a hydrophobic solid surface.
Ion gradients and fluxes in isolated liver cells

The overall aim of this thesis was to establish relationships between the ion content of isolated rat hepatocytes and metabolic processes such as glucose synthesis and fructose metabolism. In addition, a closely related subject, that of the mechanism of maintenance of the alleged ammonia gradient in liver, was also investigated.
Isolated rat hepatocytes were separated from the incubation medium for estimation of intracellular ion and metabolite values. Cell volume was estimated both from wet weight, dry weight and inulin space of cells, and from distribution of tritiated water between cells and medium. Cell volume increased in conditions where intracellular accumulation of amino acids occurred and when cells were treated anaerobically. The specific inhibitor of the Na-K ATPase, ouabain, did not affect cell volume.
Hepatocyte K+ and Na+ content, and K+ turnover, were estimated in conditions of added substrates such as fructose, lactate, NH4C1, ethanol, asparagine, glutamine and alanine. Change in turnover of cell K+, estimated with 42K+, was not directly related to change in rate of metabolic processes such as glucose or urea synthesis. However, in all conditions in which increased cell volume occurred and in which amino acids were accumulated, K+ turnover was increased. The effect of added alanine on cell ion and alanine content was examined in detail with special reference to the effects of ouabain and insulin.
Metabolism of added fructose led to redistribution of cell and medium inorganic phosphate. Movement of phosphate was concomitant with change in intracellular K+ and Na+ content.
Intracellular [ammonia] in isolated hepatocytes incubated without additions was 60 times greater than that of the medium. This constitutes an ammonia gradient only if intracellular ammonia was free in solution and not bound. Mechanisms which might be involved in maintaining high intracellular [ammonial] were investigated.
Modes of presence in the contemporary sculptural encounter 

This thesis examines the manifestation of ‘presence’ in contemporary sculpture and the nature of the viewer’s encounter. In particular, it investigates the ways in which inert materials are transformed into objects that appear to possess life. Presence has been considered in terms of the image in different media; however, this thesis shows that a work does not have to be figurative for presence to be evoked. Through a detailed investigation of individual artworks, each of the chapters explores different ways in which presence manifests itself. The identification of diverse examples across time and place reveals unexpected similarities between modes of presence observed in ancient and religious sculpture and the practices of making and viewing art in the contemporary sculptural encounter. The thesis examines the shared agency between artist and materials, and how this manifests itself as presence; how presence operates when the site and the viewer become part of the work; and how materials are activated through specific beliefs or through an intervention made to their form or context. It aims to show that these different layers are interconnected and that together they determine the nature of presence.
Synthetic applications of arene chromium tricarbonyl complexes

This thesis investigates the use of arene chromium complexes as phenyl cation synthons in the synthesis of homochiral N-phenylamino esters, and the dianion formation of a series of complexed aryl ethers.
Chapter 1 reviews the properties of arene chromium tricarbonyl complexes and discusses in detail the ability of some of these complexes to undergo nucleophilic aromatic substitution.
Chapter 2 outlines the biological importance of homochiral N-phenylamino esters. The N-phenylation of a series of amino alcohols are first investigated both by direct reaction of haloarene complexes with amino alcohols and also via a Smiles rearrangement of an aryl ether derivative. In addition, methodology is developed for the synthesis of a series of homochiral N-phenyl-α-amino esters and N-phenyl-β-amino esters. The synthetic strategy is then applied to the synthesis of some N-phenyl-β-lactams, in particular (+)SCH 48461.
Chapter 3 reviews the directed metallation of complexed and uncomplexed arene compounds and discusses the mechanism involved. The generation of dianions in a series of complexed aryl ethers is investigated. Regioselective deprotonation is observed using different alkyllithium bases and the degree of dianion formation is confirmed by electrophilic quench of the dianionic intermediates with CD3OD and TMSC1.
In search of the Dioskouroi: image, myth and cult

This study explores the Greeks' experience of the Dioskouroi before the arrival of the Romans, stimulated by Cicero's assertion (Cic. Nat.D. 3.15(39)) that by his time they were worshipped widely in Greece, possibly more than the Olympians: from the archaeological evidence, a surprising claim. The task is complicated by the brothers' different incarnations in different places and at different times, and the variability and patchiness of the evidence for the period, from Homeric times to c. 146 BC. To address this (explained in Chapter 1), the study is designed around examining the evidence in selected locations over time, with an underlying theme of comparing the archaeological with the literary evidence, much of which is Roman. An overview of the evidence from literature, images and buildings sets the stage (Chapter 2). The association of Kastor and Polydeukes with 'Lakedaimon' in the literature, from Homer onwards, led the study to focus primarily on Sparta and the Peloponnese (Chapter 3), looking closely also at Sparta's near neighbours, Messene and Argos. It then looks at evidence from Thera, Kyrene and Naukratis (Chapter 4), in order to include some of the earliest material evidence we have of cult of the Dioskouroi in Greek settlements, which also have associations with Sparta and Lakonia; evidence from Thasos is included too. The final chapter considers the findings and assesses the usefulness of the methodology. The paucity of architectural evidence for major monuments and buildings specifically dedicated to the Dioskouroi, except in centres where Greeks gathered from different places for trade or religious reasons, may be explained if the primary location of their cult was the individual household, buildings only being needed for dedications to the brothers by Greeks away from home. It could also explain the seeming mismatch between Cicero's statement and the archaeological record.

Keywords: Ancient Greek cult
Archaeology
Dioskouroi
Advisor: Parker, R
Kurtz, DC