VictorJuiz/thesis huggingface dataset:
The structure of the Tamil verb
Keywords: tamil
verb

The study of the verbal forms occurring in the Cankam texts (date about 50 B.C. - 250 A.D.) reveals that at least two of them namely kalittokai and paripātal possess forms of later origin. In the language of the other sixteen texts, many distinct features of the Old Tamil have been observed. The development of the Tamil language began to take a new turn from the period of kalittokai. Therefore the Old Tamil features as seen in the verbal forms of the earlier texts are of much importance especially to understand the true nature of the Dravidian verb.
Continued in thesis ...
Ultra-sensitive molecular detection of explosives
Keywords: Conductive polymer
Vapour sensing
Nanoparticles
Explosives
Percolation

Explosives detection plays an important role in both military and civilian applications. However, the detection of explosive vapours remains challenging because of the low vapour pressures of explosive materials. The aim of this project is to develop a system for the ultra-sensitive molecular detection of explosives. The sensor is based on a percolation network of conductive polymers, supported on a scaffold of gold nanoparticles. By operating the sensor at the percolation threshold a higher sensitivity can be achieved compared to more traditional polymer thin film based sensors.
The first component of the sensor, the gold nanoparticle scaffold, was created by dewetting a gold thin film. The nanoparticle size and separation were controlled by controlling the initial gold thin film thickness and the annealing time and temperature. Furthermore, stepwise resistance changes were observed during gold deposition and annealing. Next, conductive polymers were deposited on the gold nanoparticle scaffolds, creating polymer networks ranging from thin films to networks close to the percolation threshold. Additionally, simulations were used to confirm that a sensor based on a percolation network has a higher sensitivity than a thin film based sensor. Finally, initial testing of sensors with various polymer coverages in the presence of ammonia has provided a proof of concept of a sensor based on a percolation network of conductive polymers.
Novel self-expanding stent retractors for neuroendoscopy
Keywords: nitinol
tubular retractor
finite element analysis
neuroendoscopy
self-expanding stent
minimally invasive

This thesis reports on the development of a novel self-expanding stent retractor (SESR), one that could replace the rigid tubular retractors in common use for minimally invasive neuroendoscopy. The thesis begins with a comprehensive literature review, focusing on existing neuroendoscopy techniques and devices that treat deep brain lesions. The motivation behind this project, including its potential scientific and practical value, is set out clearly. The main body of the thesis describes three different activities.
The first part presents preliminary studies on brain tissue that have been conducted to set up an appropriate medium for SESR deployment. A finite element model of brain tissue phantom was built in Abaqus/Explicit and several surgical scenarios were simulated. The finite element model was validated through comparisons with existing simulation results, data from the literature review and experimental measurements. It is found that the pressure required to create a 16mm diameter corridor in the brain tissue phantom through radial expansion is 2.089 kPa.
The second part of the thesis explains the process of designing and analysing the SESR. Conceptual designs identify the dimensions, materials, and functions of SESR, along with its accessory components. Theoretical analysis found a range for geometric design based on z shape stent radial pressure. Finite element analysis was applied to thoroughly study single z shape stents and SESRs, identifying 5-crown stent SESR (wire diameter 0.31mm to 0.33mm) and 10-crown stent SESR (wire diameter 0.34mm to 0.36mm) to be suitable designs for neuroendoscopy deployment. Finally, prototypes were manufactured and experiments conducted to validate these results of finite element analysis.
The third part of the thesis explores the SESRs' deployment in brain tissue. In both finite element analysis and in vitro experiments, SESRs created access corridors in the brain tissue phantom similar in efficacy to those by rigid tubular retractors, while reducing the pressure on surrounding tissue. By changing SESR’s radial pressure along its longitudinal direction, alternative deployment shapes were also attainable, which suggested suitability for varying surgical needs.
In summary this thesis demonstrates that the proposed novel self-expanding stent retractor is a viable design with potential to reduce tissue damage during surgical use.
Statistical mechanics of colloids and active matter in and out of equilibrium
Keywords: Cell swimming
Active Matter
Statistical Mechanics
Nematic liquid crystals
Biophysics

Thermal and viscous forces compete for dominance at the microscopic length-scales which govern the behaviour of many soft or biological systems. We study three systems of increasing complexity with the central goal of understanding the statistical or hydrodynamic nature of their mechanics.
First we study experiments that have been conducted on ferromagnetic colloidal rods. At equilibrium, the magnetically pinned rod is observed to randomly flip between two orientational states, which our theoretical analysis shows is due to a competition between entropic and Hamiltonian forces. We show analytically how entropic forces can arise by considering the coupling between observed and unobserved variables of a system.
Experiments in which a rod is driven out of equilibrium by a rotating field display three phases of steady-state behaviour as a function of driving frequency. Using Brownian dynamics simulations we match the lower critical frequency to the experimentally obtained values, showing that thermal fluctuations play an important role in this regime and propose a simple argument to demonstrate that hydrodynamic interactions between the substrate and rod affect the upper critical frequency.
We then turn to the biophysical topic of cell locomotion in viscoelastic media. In order to study how bacterial flagella interact with similarly-sized polymers in their environment, we construct a Stokesian dynamics model of a helical filament and bead--spring polymer. Simulating their interaction first for a pinned--rotating helix, then for a swimming helix, we demonstrate that large polymers become hydrodynamically entrained by the flagellum and coil around it, causing both pinned and swimming flagella to expend more work. For the swimming helix, this results in a reduction of swimming speed on average.
Finally, we consider an active nematic fluid confined to a channel and show that the inclusion of a passive colloid induces a global state of coherent flow maintained by the intrinsic activity of the system. This flow is persistent, and transports the colloid with it along the channel. By this mechanism, a passive colloid is able to spontaneously induce its own transport through an otherwise quiescent fluid.
Investigation into the relationship between PARPs in DNA repair and synthetic lethality with homologous recombination deficiency
Keywords: DNA Repair
PARP
Genome Stability

The genome of each cell is under constant threat from various forms of DNA damage. In order to protect themselves from this danger, cells possess a number of pathways able to resolve DNA lesions. The addition of poly(ADPribose) is a post-translational modification produced by attaching successive ADP-ribose moieties to a protein acceptor, forming long chains. Enzymes called poly(ADP-ribose) polymerases (PARPs) catalyse the production of these modifications, and a number of different PARPs have been linked to the process of DNA repair, including PARP1, PARP2 and PARP3. How these enzymes might function together to facilitate the repair of different lesions is unclear. Furthermore, inhibitors that target these enzymes are in clinical use for their ability to kill homologous recombination deficient tumour cells, through a mechanism of synthetic lethality. Which subset of PARPs is necessary to inhibit to achieve maximum efficacy of these agents has not been assessed.
I use genome editing to generate cells disrupted for these PARPs in different combinations. Whilst loss of PARP1 compromises cellular tolerance to homologous recombination deficiency, this is independent of the status of PARP2 and PARP3, indicating the development of PARP1-specific inhibitors may hold therapeutic potential. In contrast to these observations, I uncover strong redundancy between PARP1 and PARP2 in the repair of damaged DNA bases through the base excision repair (BER) pathway. I also identify BER independent roles of both PARP1 and PARP2 in resolving replication forks that have collided with BER-intermediates, through promoting the stability of Rad51 nucleofilaments via an Fbh1-dependent mechanism. Thus PARP1 and PARP2 perform two closely-linked functions in response to cellular base damage promoting resolution of these lesions directly through BER, and stabilising replication forks which have encountered BER intermediates.
Greeks, Jews, heretics, and the Church of God
Keywords: Catholicity
Late Antiquity
Disciplina Arcani
Christianization
Orthodoxy
Catechesis
Ecclesiology
Baptism

The following study seeks to explore the subjects of Christianisation and Christian identity during the transitional period of the fourth century from an ecclesiological perspective, and argues that the very question of Christian identity is, indeed, an ecclesiological one. It approaches the subject through the writings of Cyril of Jerusalem, specifically his Catechetical Lectures, the earliest complete catechetical programme that has come down to us, making it an invaluable resource for anyone hoping to understand the Catholic Church’s efforts to preserve and construct its identity in the wake of Constantine’s formal conversion to its faith. Moreover, Cyril, who became bishop of the Holy City around 350, affords us a unique perspective on the question at hand, teaching as he did from the “very centre of the earth”, following the creation of a Christian holy land and pilgrimage centre in the midst of what remained a largely pagan province, and in a city still central to Judaism. The ability to possess the sites and relics associated with the life of Christ and the Prophets for the first time in Christian history not only made the drama of salvation tangible in Jerusalem like nowhere else, but raised new and important questions around the extent to which this sacred topography was compatible with Christianity's departure from the temple-centred worship of the Old Testament. It also provides valuable insight into the relationship between the local and the universal as regards notions of the Church’s catholicity, Cyril's definition of καθολική in his eighteenth lecture arguably being the earliest.
Membership of the Church, and therefore Christian identity, is for Cyril primarily ontological, defined and effected through mysteriological participation, with baptism — the believer's death, rebirth, and union with Christ — representing the dividing line between insider and outsider, a fact enforced by the so-called Disciplina Arcani, by which all knowledge of the Church's sacraments were jealously guarded from the unbaptised. The thesis explores how this notion of ontological membership underpins and informs Cyril's dealings with the various groups against which he sought to define his own community — the Greeks, Jews, and heretics — while also looking at the ecclesiological significance of the baptismal act itself.
Depot-specific mechanisms determining human fat distribution
Keywords: Adipose

Body fat distribution is a strong determinant of human metabolic health but the mechanisms underpinning regional deposition of white adipose tissue (WAT) remain poorly understood. WAT also exhibits striking depot-specific functional properties. The aim of this project was to investigate the potential role of specific candidate genes implicated in regulating WAT development and/or function in a depot-specific manner. Cartilage oligomeric matrix protein (COMP) is an extracellular matrix protein that is highly differentially expressed between subcutaneous abdominal and gluteal WAT but has primarily been studied in the context of bone biology. WAT COMP expression was found to be significantly up-regulated in obesity; COMP expression in preadipocytes was increased by glucocorticoids; and COMP promoted adipogenesis in (immortalised) subcutaneous abdominal and gluteal preadipocytes.
Building on a finding during the COMP study, bone morphogenetic protein (BMP)-2 was identified as another candidate. BMP2 exerts positive adipogenic effects in murine models and a recent genome-wide association study meta-analysis identified a significant association between BMP2 and body fat distribution. BMP2 was found to exert a pro-adipogenic effect specifically in subcutaneous abdominal preadipocytes, with this effect requiring activation of SMAD1/5/8 signalling via type 1 BMP receptors. These data identify BMP2 as a novel depot-specific regulator of human adipogenesis.
Particularly lipid-laden cells were formed when conventional adipogenic medium was supplemented with fatty acids; these cells were captured, de-differentiated (DFAT) and expanded to generate immortalised abdominal and gluteal DFAT cells. These DFAT cells exhibit a greatly enhanced adipogenic potential compared to the mixed stromovascular (SVF) population from which they derive and retained an intrinsic memory of their anatomical origin. The use of DFAT cells is likely to represent a valid and enhanced model system to study various depot-specific aspects of WAT biology such as adipogenesis. Overall, the data from this thesis emphasise the striking depot-specific biology exhibited by WAT and provide novel insights into the mechanisms governing the regional distribution of WAT in humans.
Trade, development and resilience: an archaeology of contemporary livelihoods in Turkana, northern Kenya
Keywords: Kenya
Turkana
fishing
farming
herding
anthropology
development
pastoralism
trade
raiding
ethnography
contemporary archaeology
pastoralist history
history
Africa
archaeology
resilience
pastoral economy

The recent history of the Turkana of northern Kenya has rarely been explored in detail, a fact that corresponds with, and to a large extent facilitates, their regular portrayal in the popular press as passive, unchanging and therefore vulnerable in the face of ongoing and ensuing socio-economic transformations. Such visions of the Turkana and the region in which they live have, via their manifestation in the policies and practices of development-orientated interventions, actively inhibited (although never fully arrested) the fulfilment of various local desires and aspirations over the years. In addressing these topics, this thesis provides some hitherto largely unexplored and unrecognised historical context to the many socio-economic and political issues surrounding Turkana’s ongoing development. It discusses interdisciplinary research which combined archaeological and ethnographic techniques and was undertaken amongst communities engaged in the most prominent livelihoods that have historically underlain the Turkana pastoral economy: fishing (akichem), cultivation (akitare), herding (akiyok) and raiding (aremor). In doing so, it draws attention to some of the ways in which these communities have actively and dynamically negotiated broad economic, environmental and political transformations over the last century and beyond, thereby providing a picture of social change and long-term continuity that might serve as a means for a more critical assessment of regional development over the coming years.
By weaving together a series of historical narratives that emerge from a consideration of the changing production, use and exchange of material culture, the thesis builds an understanding of Turkana’s history that diverges from more standard, implicitly accepted notions of recent change in such regions of the world that envisage globalisation purely as a process of convergence or homogenisation. Its central argument, which it demonstrates using various examples, is that seemingly disruptive transformations in daily practices, social institutions, livelihoods and systems of livelihood interaction can be envisaged as articulations of longer-term continuities, emerging from a set of durable yet open-ended dispositions within Turkana society and culture. Moreover, rather than being built on a stable, passive repertoire of cultural knowledge, the thesis shows that this capacity for change is established upon a dynamic generative process where value systems and institutions are reconfigured to the same extent as daily practices and skills, as knowledge is continually reconstituted and recast in relation to the shifting constraints and possibilities of daily life. It thus characterises this process as a form of resilience that is deeply rooted in and determinant of the Turkana pastoral economy.
Application of engineered T cell receptors to investigate the failure of cytotoxic T lymphocytes to eliminate the HIV reservoir
Keywords: HIV
Reservoir
Immunology
T cells

HIV establishes a reservoir comprising long lived, latently infected CD4+ T cells and monocytic cells early during primary infection. This population represents a major barrier to an HIV cure. This thesis aimed to investigate the role of the immunological synapse in the failure of cytotoxic T lymphocytes (CTLs) to eliminate the HIV reservoir and the potential for engineered bispecific Immune-mobilising monoclonal T cell receptors Against Viruses (ImmTAV) to overcome this by redirecting fully functional CD8+ T cells against viral targets.
A primary cell model of latency was used to investigate the expression of HIV Gag on latently infected cells and their susceptibility to ImmTAV-mediated elimination. A subset of cells expressed low levels of Gag without spreading infection and ImmTAV-redirected healthy donor CD8+ T cells were able to eliminate up to 40% of infected cells without latency reversal. CD8+ T cells from chronic HIV infected (CHI) donors showed impaired antiviral activity even with ImmTAV redirection.
To investigate this further, confocal microscopy was used to study immunological synapse formation using primary CD8+ T cells from HIV-negative and CHI donors. CD8+ T cells from CHI donors were able to form conjugates with virus-infected cells but exhibited impaired synapse maturation, indicated by reduced Zap70 localisation, delayed microtubule-organising centre polarisation and impaired perforin recruitment to the synapse. ImmTAV redirection partially overcame these defects.
Finally, the impact of antiretroviral agents on T cell mitochondrial function was explored. Exposure to zidovudine increased mitochondrial reactive oxygen species production and susceptibility to apoptosis. However, there was no evidence of impaired mitophagy.
These data show that defects in CD4+/CD8+ T cell synapse maturation contribute to HIV persistence but nevertheless suggest that a subset of HIV reservoir cells may be susceptible to ImmTAV-mediated elimination. The therapeutic potential of ImmTAVs may depend in part on correction of CD8+ T cell exhaustion.
Picturesque urban planning - Tunbridge Wells and the suburban ideal
Keywords: Picturesque

This study addresses the development of the English suburb in the second quarter of the nineteenth century. Its proposition is that suburbs were where people wanted to live, and not just to avoid the dirt and disease of the city. They had an appeal beyond the practical. Whether it was a feeling of security, independence, oneness with nature, or of living in 'a place apart', there was an emotional, culturally-conditioned attraction.
The specific focus is on the development of the Calverley estate in Tunbridge Wells. The point is not that Calverley was typical, but that it represented a suburban 'ideal'. It was created by a London developer, John Ward, to be just such a 'place apart', an idyllic retreat for a wealthy metropolitan middle class.
The study starts by considering Ward's 'vision' for Calverley. Ward had been a major investor in Regent’s Park. The study suggests that Calverley, with its 'picturesque' landscape setting, mirrored the fantasy world created by John Nash in Regent's Park. In Calverley, though, Ward and his architect, Decimus Burton, built individual houses in gardens, a model for what was later to become 'a universal suburbia'.
A second section considers what attracted Ward's customers. It suggests four influences: the notion of the Picturesque; historical associations; idealised visions of the countryside; and the appeal of certain architectural styles.
The final part then examines those customers in more detail. They were not drawn from the existing residents of Tunbridge Wells, but were metropolitan/cosmopolitan incomers (70% of them women). They could have lived anywhere. The study uses five themes of suburban historiography: movement, control, separation, withdrawal and identity, to show how they moulded the physical and social space around them to further achieve their ideal; to create, in the words of one advertisement, this 'enviable little English Elysium'.
Crystallization properties of molecular materials: prediction and rule extraction by machine learning
Keywords: Crystallization
Powder diffraction

Crystallization is an increasingly important process in a variety of applications from drug development to single crystal X-ray diffraction structure determination. However, while there is a good deal of research into prediction of molecular crystal structure, the factors that cause a molecule to be crystallizable have so far remained poorly understood.
The aim of this project was to answer the seemingly straightforward question: can we predict how easily a molecule will crystallize? The Cambridge Structural Database contains almost a million examples of materials from the scientific literature that have crystallized. Models for the prediction of crystallization propensity of organic molecular materials were developed by training machine learning algorithms on carefully curated sets of molecules which are either observed or not observed to crystallize, extracted from a database of commercially available molecules. The models were validated computationally and experimentally, while feature extraction methods and high resolution powder diffraction studies were used to understand the molecular and structural features that determine the ease of crystallization. This led to the development of a new molecular descriptor which encodes information about the conformational flexibility of a molecule.
The best models gave error rates of less than 5% for both cross-validation data and previously-unseen test data, demonstrating that crystallization propensity can be predicted with a high degree of accuracy. Molecular size, flexibility and nitrogen atom environments were found to be the most influential factors in determining the ease of crystallization, while microstructural features determined by powder diffraction showed almost no correlation with the model predictions. Further predictions on co-crystals show scope for extending the methodology to other relevant applications.