VictorJuiz/thesis huggingface dataset:
Modelling residual stresses and deformation in metal at different scales
Keywords: finite element analysis
x-ray diffraction
neutron diffraction

This thesis is devoted to the numerical and experimental investigation of residual stress and deformation in polycrystalline metallic alloys at different scales. The emphasis in the current study is placed on establishing the connection between the simulation of deformation by the Finite Element (FE) method and experimental characterisation by synchrotron X-Ray Diffraction (XRD). Of particular importance is the interpretation of modelling results and their validation by careful comparison with experimental data. The concept of eigenstrain was used extensively throughout the report to study the residual elastic strain distributions and their sources. A pseudo-thermal strain FE procedure was used systematically to simulate the residual stress states in samples and engineering components of different shape and dimensionality. The case of 1-D strain variation was considered using the example of a plastically bent bar. The direct and inverse problems of eigenstrain analysis were solved, and validated experimentally by the use of XRD and EDM slitting methods. A novel 2-D discrete inverse eigenstrain algorithm was proposed and implemented to reconstruct the residual stress distribution in a worn rail head. The link between the residual stress and deformation history was studied via thermo-mechanical modelling of the Linear Friction Welding (LFW) process. To advance the understanding of polycrystalline deformation behaviour across the scales, a crystal plasticity model was employed to simulate the elastic-plastic deformation behaviour of Ti-6Al-4V alloy. A post-processor was developed to extract the average elastic strains for orientation-specific grain groups and to compare them with XRD data. A “peak constructor” post-processor was developed that utilised the knowledge of both the elastic strain and dislocation density. In a further development step, a strain gradient crystal plasticity formulation was adopted to account for the local dislocation evolution. Intra-granular deformation analysis was carried out and micro-beam Laue experimental diffraction technique was used for validation. Thus, local lattice arrangement was studied at the microscopic, intragranular scale. Special attention was paid to the phenomenon of Laue spot “streaking”, indicative of the local lattice misorientation caused by dislocation activity during deformation. The results presented in this thesis contributed to the fundamental understanding of the residual stress and deformation in polycrystalline metallic alloys and lead to more than 20 publications in peer-reviewed journals and conference proceedings, which are listed in the Appendix.
Gender mainstreaming in development organisations: policy, practice and institutional change
Keywords: development organisations
feminism
gender and development
mainstreaming
gender

‘Gender and Development’ (GAD) is currently seen as the dominant theoretical model within international development for promoting social justice and equality for women. As a consequence, many development organisations are undertaking gender mainstreaming. The most interesting fact about the vast number of analyses about gender mainstreaming is the consistency with which they tell of GAD influenced policies failing to implement GAD approaches in practice. This should raise suspicion rather than simple condemnation. It is time to ask: ‘How are, often very progressive, gender policies and strategies consistently silenced across the range of organisational contexts?’ This thesis focuses upon the contemporary process of gender mainstreaming in development organisations – a term that specifically refers to a ‘process of organisational change’ that aims to explicitly develop the ‘use of GAD approaches within all projects and programmes’ of development institutions in order to achieve ‘a vision of development that creates gender equitable social change’ in society. Moreover, it takes an approach that specifically details the ‘organisational process’ element of change inferred in the term. As such, this thesis uses the literature of organisational culture as a lens to make previously unnoticed and submerged sites of conflict and acts of resistance visible, allowing an understanding to be gained of how gender mainstreaming has so consistently faced a policy-practice impasse. It develops this analysis using an in-depth case study of Oxfam GB and demonstrates that the process of gender mainstreaming in the organisation has resulted in the removal of ‘responsibility for’ implementing GAD approaches among staff in the organisation. It goes on to highlight that the unwillingness of development organisations and practitioners to recognise gender mainstreaming as an explicitly feminist and political process of change directly couched at the level of the organisation and not just at the level of the actual development project (or society more widely) has resulted in the ‘process of organisational change’ becoming rationalised and technical rather than personal and politically charged. In reaching this understanding of gender mainstreaming, the thesis develops an awareness of organisational change processes and highlights that ‘norms’ and ‘values’ in organisations are often confused. This confusion has led to an ineffective process of change in institutions as well as a poor conceptualisation and practice of gender mainstreaming in international development.
Digital signal processing methods for large-N, low-frequency radio telescopes
Keywords: FPGA
beamforming
radio astronomy
interferometry
X-Engine
correlator
BEST-2
direct imaging
SKA
Square Kilometre Array

Current attempts to make precision measurements of the HI power spectrum at high redshifts have led to the construction of several low-frequency, large-N, interferometric arrays. The computational demands of digital correlators required by these arrays present a significant challenge. These demands stem from the treatment of radio telescopes as collections of two-element interferometers, which results in the need to multiply O(N2) pairs of antenna signals in an N-element array. Given the unparalleled flexibility offered by modern digital processing systems, it is apt to consider whether a different way of treating the signals from antennas in an array might be fruitful in current and future radio telescopes. Such methods potentially avoid the unfavourable N2 scaling of computation rate with array size.
In this thesis I examine the prospect of using direct-imaging methods to map the sky without first generating correlation matrices. These methods potentially provide great computational savings by creating images using efficient, FFT-based algorithms. This thesis details the design and deployment of such a system for the Basic Element of SKA Training II (BEST-2) array in Medicina, Italy. Here the 32-antenna BEST-2 array is used as a test bed for comparison of FX correlation and direct-imaging systems, and to provide a frontend for a real-time transient event detection pipeline.
Even in the case of traditional O(N2) correlation methods, signal processing algorithms can be significantly optimized to deliver large performance gains. In this thesis I present a new mechanism for optimizing the cross-correlation operation on Field Programmable Gate Array (FPGA) hardware. This implementation is shown to achieve a 75% reduction in multiplier usage, and has a variety of benefits over existing optimization strategies.
Finally, this thesis turns its focus towards The Square Kilometre Array (SKA). When constructed, the SKA will be the world's largest radio telescope and will comprise a variety of arrays targeting different observing frequencies and science goals. The low-frequency component of the SKA (SKA-low) will feature ~250,000 individual antennas, sub-divided into a number of stations. This thesis explores the impact of the station size on the computational requirements of SKA-low, investigating the optimal array configuration and signal processing realizations.
Mental files
Keywords: philosohy of mind
de jure coreference
mental files
singular thought
philosophy of language

It is often supposed that we can make progress understanding singular thought about objects by claiming that thinkers use ‘mental files’. However, the proposal is rarely subject to sustained critical evaluation. This thesis aims to clarify and critique the claim that thinkers use mental files.
In my introductory first chapter, I motivate my subsequent discussion by introducing the claim that thinkers deploy modes of presentation in their thought about objects, and lay out some of my assumptions and terminology. In the second chapter, I introduce mental files, responding to the somewhat fragmented files literature by setting out a core account of files, and outlining different ways of implementing the claim that thinkers use mental files. I highlight pressing questions about the synchronic and diachronic individuation conditions for files.
In chapters three and four, I explore whether ‘de jure coreference’ can be used to give synchronic individuation conditions on mental files. I explore existing characterisations of de jure coreference before presenting my own, but conclude that de jure coreference does not give a useful account of the synchronic individuation conditions on files. In chapter five, I consider the proposal that thinkers must sometimes trade on the coreference of their mental representations, and argue that we can give synchronic individuation conditions on files in terms of trading on coreference. In chapter six, I bring together the account of files developed so far, compare it to the most developed theory of mental files published to date, and defend my account from the objection that it is circular. In chapter seven, I explore routes for giving diachronic individuation conditions on mental files. In my concluding chapter, I distinguish the core account of files from the idea that the file metaphor should be taken seriously. I suggest that my investigation of the consequences of the core account has shown that the file metaphor is unhelpful, and I outline reasons to exercise caution when using ‘files’ terminology.
Investigating the role of iASPP and ASPP2 in human carcinoma
Keywords: carcinoma
ASPP

The apoptotic function of p53 is specifically regulated by iASPP and ASPP2 and their additional modulation of p63, a key regulator of squamous epithelial homeostasis, has been demonstrated in mice. In this study the role of iASPP and ASPP2 in human carcinomas was explored with a particular focus on the development of squamous cell carcinomas.
The predominant expression of cytoplasmic ASPP2 is seen in the superficial, terminally differentiated cell layers of normal squamous epithelia and its loss is documented in areas of dysplasia and in squamous cell carcinomas. In addition the absence of nuclear ASPP2 in association with human papillomavirus infection suggests it could be a novel viral target.
Furthermore in a novel mouse model of lung tumourigenesis, the somatic deletion of ASPP2 is shown to promote the over expression of markers associated with specific lung progenitor cells and to be associated with the development of non small cell lung carcinomas.
Conversely nuclear iASPP expression is seen in p63 expressing, replication competent, basal and parabasal squamous epithelial cells and is increased in areas of dysplasia and in squamous cell carcinomas. Moreover the combination of nuclear iASPP, p63 and loss of ASPP2 expression is seen to be associated with cell survival and characterises the invasive edges of lingual squamous cell carcinomas.
The novel interaction of iASPP with ERα is also demonstrated together with the negative impact of nuclear iASPP on ER positive breast cancer survival, potentially identifying iASPP as a novel player in estrogen signalling and an important factor in breast tumourigenesis.
Together the data presented here provide significant corroborative evidence implicating ASPP2 and iASPP in tumourigenesis. Specifically ASPP2 is shown to promote cellular differentiation and inhibit the expansion of proliferative populations whereas nuclear iASPP promotes the survival of potentially neoplastic clones. It is likely that the balance of these proteins is a key factor in determining individual cell fate decisions.
Trajectories of Peircean philosophical theology :
Keywords: Charles Sanders Peirce
Robert C. Neville
Scriptural Reasoning
Peter Ochs
Nested Continua

The writings of the American pragmatist thinker Charles S. Peirce (1839-1914) provide resources for what this thesis calls the “nested continua model” of theological interpretation. A diagrammatic demonstration of iconic relational logic akin to Peirce’s Existential Graphs, the nested continua model is imagined as a series of concentric circles graphed upon a two-dimensional plane. When faced with some problem of interpretation, one may draw discrete markings that signify that problem’s logical distinctions, then represent in the form of circles successive contexts by which these distinctions may be examined in relation to one another, arranged ordinally at relative degrees of specificity and vagueness, aesthetic intensity and concrete reasonableness. Drawing from Peter Ochs’s Scriptural Reasoning model of interfaith dialogue and Robert C. Neville’s axiology of thinking—each of which makes creative use of Peirce’s logic—this project aims to achieve an analytical unity between these two thinkers’ projects, which can then be addressed to further theological ends. The model hinges between diagrammatic and ameliorative functions, honing its logic to disclose contexts in which its theological or metaphysical claims might, if needed, be revised. Such metaphysical claims include love as that which unites feeling with intelligibility, hell as imprisonment within an opaque circle of interpretation whose distorted reflections render violence upon oneself and others, and the divine as both the center of aesthetic creativity and outermost horizon from which our many layers of interpretive criteria emerge. These are claims made from a particular identity in a particular cultural context, but the logical rules upon which they are based are accessible to all, and the hope of the model is to help people overcome problems of interpretation and orient themselves toward eternity without ignoring the world around them.
A model-based statistical approach to functional MRI group studies
Keywords: Markov chain Monte Carlo
Spatial Point Processes
Bayesian Approach
Functional MRI Group Studies

Functional Magnetic Resonance Imaging (fMRI) is a noninvasive imaging method that reflects local changes in brain activity. FMRI group studies involves the analysis of the functional images acquired for each of a group of subjects under the same experimental conditions.
We propose a spatial marked point-process model for the activation patterns of the subjects in a group study. Each pattern is described as the sum of individual centres of activation. The marked point-process that we propose allows the researcher to enforce repulsion between all pairs of centres of an individual subject that are within a specified minimum distance of each other. It also allows the researcher to enforce attraction between similarly-located centres from different subjects. This attraction helps to compensate for the misalignment of corresponding functional areas across subjects and is a novel method of addressing the problem of imperfect inter-subject registration of functional images. We use a Bayesian framework and choose prior distributions according to current understanding of brain activity. Simulation studies and exploratory studies of our reference dataset are used to fine-tune the prior distributions. We perform inference via Markov chain Monte Carlo.
The fitted model gives a summary of the activation in terms of its location, height and size. We use this summary both to identify brain regions that were activated in response to the stimuli under study and to quantify the discrepancies between the activation maps of subjects. Applied to our reference dataset, our measure is successful in separating out those subjects with activation patterns that do not agree with the overall group pattern. In addition, our measure is sensitive to subjects with a large number of activation centres relative to the other subjects in the group. The activation summary given by our model makes it possible to pursue a range of inferential questions that cannot be addressed with ease by current model-based approaches.
Peptide targeting by spontaneous isopeptide bond formation
Keywords: covalent
adhesin
isopeptide
tag
Streptococcus Pyogenes
split protein
peptide
pilin

Peptide fusion tags are fundamental for the identification, detection, and capture of proteins in biological assays. Commonly used peptide fusion tags rely on temporary non-covalent interactions for binding, which can put constraints on assay sensitivity. Here, peptide fusion tags were developed that could specifically interact with protein binding partners via spontaneous and irreversible isopeptide bond formation. To develop covalently interacting peptide-protein pairs, outer-membrane proteins from Gram-positive bacteria that form autocatalyzed intramolecular isopeptide bonds were dissected to generate a short peptide fragment and a protein binding partner. Initially, the major pilin subunit Spy0128 from Streptococcus pyogenes was split to develop the 16 residue isopeptag peptide and the 31 kDa pilin-C protein partner. The isopeptag:pilin-C pair were able to react via spontaneous isopeptide bond formation between an Asn residue in isopeptag and a Lys residue in pilin-C without the requirement for any accessory factors, and with a yield of 60% after a 72 hr reaction. Reconstitution between the isopeptag:pilin-C pair was robust and occurred under all biologically relevant conditions tested, and also in the complex environment of a bacterial cytosol and on the surface of mammalian cells. A similar approach was also used to dissect the small CnaB2 domain that is part of the large FbaB fibronectin-binding protein from S. pyogenes. This led to the development of a more efficient peptide-protein pair, which was rationally modified to generate the highly optimized SpyTag:SpyCatcher pair. SpyTag is a 13 amino acid peptide with a reactive Asp that forms a spontaneous intermolecular isopeptide bond with a Lys present in the 12 kDa SpyCatcher binding partner. In a reaction with SpyTag, over 40% of SpyCatcher was depleted after 1 min and SpyCatcher could no longer be detected after 2 hr. The SpyTag and SpyCatcher reaction did not require any accessory factors and proceeded efficiently at a range of biologically relevant temperatures, pH values, concentrations, buffer compositions, and in the presence of commonly used detergents. The SpyTag:SpyCatcher technology was also used for specific cell surface labelling on mammalian cell membranes. SpyTag and SpyCatcher are both composed of the regular 20 amino acids and can therefore be genetically encoded as fusion constructs for a variety of in vitro and in vivo applications. Potential applications of the SpyTag:SpyCatcher technology include specific cell surface labelling, the development of novel protein architectures, and the covalent and irreversible capture of target proteins in biological assays.
The ASD equations in split signature and hypersymplectic geometry
Keywords: Gauge Theory
Moment Map
Symplectic Geometry
special Holonomy
Moduli Space
Hypersymplectic Geometry

This thesis is mainly concerned with the study of hypersymplectic structures in gauge theory. These structures arise via applications of the hypersymplectic quotient construction to the action of the gauge group on certain spaces of connections and Higgs fields.
Motivated by Kobayashi-Hitchin correspondences in the case of hyperkähler moduli spaces, we first study the relationship between hypersymplectic, complex and paracomplex quotients in the spirit of Kirwan's work relating Kähler quotients to GIT quotients. We then study dimensional reductions of the ASD equations on 𝐑2,2. We discuss a version of twistor theory for hypersymplectic manifolds, which we use to put the ASD equations into Lax form.
Next, we study Schmid's equations from the viewpoint of hypersymplectic quotients and examine the local product structure of the moduli space. Then we turn towards the integrability aspects of this system. We deduce various properties of the spectral curve associated to a solution and provide explicit solutions with cyclic symmetry.
Hitchin's harmonic map equations are the split signature analogue of the self-duality equations on a Riemann surface, in which case it is known that there is a smooth hyperkähler moduli space. In the case at hand, we cannot expect to obtain a globally well-behaved moduli space. However, we are able to construct a smooth open set of solutions with small Higgs field, on which we then analyse the hypersymplectic geometry. In particular, we exhibit the local product structures and the family of complex structures. This is done by interpreting the equations as describing certain geodesics on the moduli space of unitary connections. Using this picture we relate the degeneracy locus to geodesics with conjugate endpoints.
Finally, we present a split signature version of the ADHM construction for so-called split signature instantons on S2 × S2, which can be given an interpretation as a hypersymplectic quotient.
Plants, power, possibility: maneuvering the medical landscape in response to chronic illness and uncertainty
Keywords: plants
Cameroon
chronic illness
uncertainty
traditional medicine
medical anthropology
malaria
biomedicine in rural Cameroon
Africa.
social and cultural anthropology
co-infections

This thesis is concerned with plants, chronic illness and medicine in Oku, Northwest Region, Cameroon. I focus on patient strategies to obtain effective medical outcomes, and on how such outcomes may be obtained through seeking traditional medicine in Oku. I argue that biomedical notions of efficacy do not appropriately represent the central and diverse roles that plants play in traditional medicine nor do they correctly represent how people in Oku evaluate the efficacy of plant-based traditional medicine. I argue instead that efficacy must be understood in terms of the emic concept of power. This power is understood to be located in the Oku landscape, which is still uniquely forested and said to embody powerful ancestral spirits. With plants as the primary tangible material of power, and traditional doctors in Oku as those who claim exclusive rights to manipulate and disperse such power, I discuss traditional medicine in Oku as a system wherein power from the natural landscape is drawn upon to challenge harmful powers feared to derive from the social arena.
Using the pragmatic and phenomenological approaches, I show how patients evaluate the efficacy of a medical treatment based on their bodily experiences, and how their actions, as revealed in their therapeutic trajectories, reveal their satisfaction or dissatisfaction with a given diagnosis and/or therapy. I discuss how enduring illness generates and exacerbates bodily, treatment-outcome, social, and psychological uncertainties. In this context, effective outcomes can be understood as those which address and limit these uncertainties and anxieties while offering ways to imagine hopeful prognoses. This thesis then outlines the major sources of uncertainty, people’s responses to such uncertainties, and what people might achieve in terms of limiting uncertainties by seeking traditional medicine in Oku.