VictorJuiz/thesis huggingface dataset:
Assessing phytoplankton biogeography and photophysiology in the Atlantic Basin 
Keywords: phytoplankton
ecology
photophysiology
North Atlantic
succession

Phytoplankton play a key role in the geochemical cycles of the Earth, are responsible for 50% of global carbon fixation, and through this, provide almost all of the energy for the entire marine trophic system. Understanding the dynamics of phytoplankton, and the species composition in relation to environmental factors is therefore of great importance. In this thesis a range of techniques to identify phytoplankton groups that use accessory pigment data obtained from high performance liquid chromatography are compared. While fixed indicator pigment:chl-a ratio approaches provide a quick and simple way of estimating phytoplankton distributions either on the basis of size-class or taxonomic group, the more sophisticated iterative approach of CHEMTAX divides the biomass into more categories and allows more flexibility to adapt to changes in indicator pigment:chl-a ratios caused by environmental variability. Combined with flow cytometric cell counts, depth-dependent trends in the intracellular concentration and composition of phytoplankton pigments can be identified. These data show an exponential decrease in the ratio of carbon-to-chlorophyll with depth, in response to decreasing light intensity. The relative as well as absolute concentrations of phytoplankton pigments are also seen to change with depth, particularly under stratified conditions, with the ratio of zeaxanthin to chlorophyll-a decreasing with increasing depth, and the ratio of chlorophyll-b to chlorophyll-a increasing. Cluster analysis is used to identify the main phytoplankton populations in the North West Atlantic, with communities of large, fucoxanthin-containing phytoplankton dominating in spring when mixing is strong, before being replaced by smaller cells upon the onset of stratification. The links between trends in phytoplankton photophysiology and abiotic conditions are also explored, with temperature being found to be the most important forcing factor. Size-class specific relationships between phytoplankton photosynthetic rates and temperature are identified, with the potential for use in remotely-sensed models of primary production.
Investigating the role of a dynamic actin cytoskeleton and its regulators for HIV-1 entry in macrophages.
Keywords: GTPases
actin cytoskeleton
gene-expression systems
ientiviral vectors
virology

Macrophages are one of the three main human cell types infected by HIV-1. They are highly plastic cells requiring a dynamic actin cytoskeleton for their role in development, homeostasis, tissue repair and immunity. For HIV-1, disrupting actin in macrophages is detrimental in that it leads to a complete block of viral uptake and reduces reverse transcription but, significantly, not fusion. Rho GTPases (Rac1, RhoA and Cdc42) regulate many aspects of actin dynamics including those required for endocytosis. Using a pharmacological approach, it was shown that Rac1 along with Rho GTPase effectors Pak1 and N-WASP are important for productive HIV-1 entry in macrophages. However, pharmacological inhibitors aren’t available for many host factors and may have off-target effects. To overcome this, expression of dominant negative (DN) Rho GTPases was attempted in human stem cell-derived macrophages (esMDMs). While DN Rac1 expressing esMDMs were successfully generated, this was not possible for the other two. DN Rac1 expressing esMDMs, as expected, had less filamentous actin and reduced dextran uptake compared to control esMDMs. In contrast to the pharmacological studies, HIV-1 infection studies in Rac1 DN esMDMs revealed a significant increase in HIV-1 fusion, reverse transcription and nuclear import, which could be due to reduced filamentous actin leading to a slower rate of endocytosis thereby allowing more time for viral fusion within endocytic vesicles. Surprisingly, reduced HIV-1 gene expression was observed in Rac1 DN esMDMs. This was corroborated by transfection studies implicating Rho GTPases in LTR driven gene expression. To overcome the ineffectiveness of RhoA and Cdc42 DN constitutive gene expression in esMDMs, an inducible lentiviral gene expression system based on the use of a constitutive promoter and a FLEx switch mediating irreversible DNA inversions was generated. The novel FLEx vector was the first system shown to induce transgene expression in esMDMs albeit at a very low efficiency.
The mechanics of growth and residual stress in biological cylinders
Keywords: morphoelasticity
residual stress
mechanobiology

Biological tissue differs from other materials in many ways. Perhaps the most crucial difference is its ability to grow. Growth processes may give rise to stresses that exist in a body in the absence of applied loads and these are known as residual stresses. Residual stress is present in many biological systems and can have important consequences on the mechanical response of a body. Mathematical models of biological structures must therefore be able to capture accurately the effects of differential growth and residual stress, since greater understanding of the roles of these phenomena may have applications in many fields.
In addition to residual stresses, biological structures often have a complex morphology. The theory of 3-D elasticity is analytically tractable in modelling mechanical properties in simple geometries such as a cylinder. On the other hand, rod theory is well-suited for geometrically-complex deformations, but is unable to account for residual stress.
In this thesis, we aim to develop a map between the two frameworks. Firstly, we use 3-D elasticity to determine effective mechanical properties of a growing cylinder and map them into an effective rod. Secondly, we consider a growing filament embedded in an elastic foundation. Here, we estimate the degree of transverse reinforcement the foundation confers on the filament in terms of its material properties. Finally, to gain a greater understanding of the role of residual stress in biological structures, we consider a case study: the chameleon's tongue. In particular we consider the role of residual stress and anisotropy in aiding the rapid projection of the tongue during prey capture. We construct a mechanical model of the tongue and use it to investigate a proposed mechanism of projection by means of an energy balance argument.
"Why bother? It's gonna hurt me": the role of interpersonal cognitive biases in the development of anxiety and depression
Keywords: CBM
CBM-I
depression
cognitive bias
anxiety
adolescence
adolescents
interpretive bias

Child and adolescent mood and anxiety symptoms are common and debilitating, with long-term effects on well-being. Research presented in this thesis examines interpersonal cognitive factors in the emergence of anxious and depressive symptoms in late childhood through to early adulthood. The thesis considers this issue using three main approaches. For the first, data are presented showing that biases in the appraisals of social situations are the aspects of interpersonal cognition most closely associated with emotional symptoms. For the second, longitudinal twin data are used to examine genetic and environmental origins of these interpersonal cognitive biases and their temporal prediction of symptoms across a 2-year period. Data show that interpersonal cognitive factors are strongly influenced by non-shared environmental factors, and moreover, predict symptoms across time. The final section of the thesis comprises four studies using Cognitive Bias Modification of Interpretations (CBM-I) training methodology to show that both positive and negative interpretive biases for interpersonal information can be induced in adolescents. Positive biases are shown to persist for at least 24 hours after training, and induced positive and negative biases are shown to differentially predict anxious responses to an experimental stressor. Evidence is also provided to suggest that effects following training positive interpretive biases may transfer to other cognitive measures, namely appraisals of ambiguous emotional faces. Finally, data tentatively show that CBM-I training may be useful in reducing negative interpretations of interpersonal information made by 11-year-old children undergoing the transition to secondary school. In summary, studies in this thesis support the contribution of cognitive biases to mood and anxiety symptoms in childhood and adolescence. They further extend this knowledge by suggesting that these reflect individual-specific (non-shared) environmental risks to predict symptoms across time. These biases may also be amenable to change through training interventions, with some - albeit weak - effects on other cognitive outcomes.
Modelling and reconstruction of events in SNO+ related to future searches for lepton and baryon number violation
Keywords: nucleon decay
neutrino
SNO+
neutrinoless double beta decay
proton decay

SNO+ is a liquid scintillator experiment whose physics goals include measurements of solar neutrinos, reactor anti-neutrinos, geo neutrinos and double beta decay. During an initial water phase, it will also search for invisible modes of nucleon decay.
This thesis investigates methods of improving the detector's sensitivity to the baryon and lepton violating processes of neutrinoless double beta decay and invisible nucleon decay. It does this through an improved scintillator model, allowing the sensitivity of the detector with different loading techniques to be evaluated, through a new background rejection technique, capable of increasing the active volume of the detector, and with the development of improved position fitters, achieving resolutions of approximately 10 cm in scintillator and 25 cm in water.
The sensitivity of SNO+ to invisible modes of nucleon decay is explored, predicting, after one month of data, a limit of τ > 1.38 x 1030 years on the decay of neutrons and of τ > 1.57 x 1030 years on the decay of protons.
Older single gay men: questioning the master narrative of coupledom
Keywords: older gay men
qualitative research
ageing and life course
singlehood
life story
sexuality

This thesis fills an important research gap in the sociology of ageing and life course, and the sociology of sexualities and intimacies by exploring the understudied experience of singlehood among older gay men. It is a qualitative study based on semi-structured in-depth life story interviews conducted with 25 self-identified gay men over the age of 50 who live in England and have been single for most of their lives.
The primary objective of the study is to investigate how older single gay men interpret and assign meanings to their lives in later life. In considering the role of narratives in bridging structure and agency, the thesis suggests that the older gay men’s narratives of singlehood need to be understood with reference to the master narrative in society that privileges couplehood. The master narrative undoubtedly informed and at times overshadowed the ways in which the older gay men understood their lives. But at the same time this thesis finds that the research participants engaged with the master narrative in a variety of creative ways – they did not only adopt, but also adapted and subverted the dominant story line.
These counter-stories do not only reproduce, but have the potential to reinvent, the meanings of relationships in contemporary societies. To achieve this, resources were needed in reframing the master narrative. From a life course perspective the thesis suggests that the older gay men’s earlier life experiences and current social locations influenced the narratives they told. Only some of the older single gay men were able to (re-)claim sexual citizenship while others were denied this. In addition, the older gay men’s story-telling was filled with ambivalence and ambiguities. As a whole, the thesis sees the older gay men’s stories as displaying agency within structure.
Incoherent neutron scattering studies of select inorganic systems
Keywords: inelastic neutron scattering
neutron compton scattering
dynamics

Spectroscopic measurements are detailed within this thesis, utilising incoherent neutron scattering to examine the dynamics of various condensed-matter systems, from nanosecond to sub-femtosecond timescales. The body of this work is divided into two distinct areas of research.
I. Nuclear Momentum Measurements of Multiple Masses
Deep inelastic neutron scattering (DINS) is used to probe the nuclear momentum distributions and kinetic energies of individual atomic species in sodium hydride (both in bulk and as nanoparticulates within a silica matrix), enriched lithium-7 fluoride and lithium tetra-ammoniate. Extension of DINS to examine heavier (M>4amu) nuclei is detailed, accomplished by the application of a simple stoichiometric fixing technique within the standard DINS theory and analysis protocols. The validity and accuracy of such simultaneous measurements are discussed.
II. The Dynamics of Coordinated Ammonia in Zeolite A
Inelastic neutron scattering (INS) and quasielastic neutron scattering (QENS) are utilised in the examination of vibrational and stochastic dynamics of the ammonia molecule, as coordinated to the internal surface of a zeolite host. Both sodium and copper-exchanged forms of zeolite-A are studied, with proton-weighted, low energy phonon-modes and rotational processes being observed and assigned.
Archaic trade in the northern Aegean: the case of Methone in Pieria, Greece
Keywords: Ancient Macedonia
Ancient Euboeans
Archaic Greece
Trade
Amphorae
Ancient Greek Colonies of the Northern Aegean
Ancient Commerce
Methone
Geography and History of Ancient Macedonia

Recent discoveries near the village of Nea Agathoupoli, in Pieria, Greece have revealed the remains of an ancient town, identifiable with the ancient town of Methone, a putative Eretrian colony founded, according to Plutarch, in ca. 733 BC. From the material excavated so far, the town’s zenith was in the Late Geometric and Archaic periods, well documented by the high amounts of imports from all regions of the ancient world, especially by imported transport vessels. The significant percentage of transport amphorae in comparison to that of fine pottery strongly indicates the settlement's commercial character and suggests that Methone was operating as a redistribution centre which supplied Macedonia's hinterland with goods. This study is based on unpublished pottery analyzed here, for the first time. Among the regions, whose products are most popular in Methone are Chios and Athens, although more Eastern Greek towns such as Samos and Miletus had trading relations with Methone, too. Settlers from the these regions may have established themselves in Methone, but the initiative for the foundation of the town was, most probably, taken by Euboeans, whose activity in the Northern Aegean, in the Geometric period, was strong. Alongside the abundant imported vessels, a large amount of locally made transport vessels was unearthed. These early archaic amphora types (early 6th century BC), which have also been found in other sites in the Northern Aegean and possibly Northern Ionia, have been known in literature by my study. The discovery of these local transport vessels reveals participation by the local population in trading transactions and manufacture of a product which was packaged and circulated among the Northern Aegean towns. A mixed cultural environment starts to form in archaic Methone and includes Euboeans, Eastern Greeks, local Thracians and others, including Macedonian neighbours. Having emerged as the most powerful military force of the area, the Macedonians residing in nearby Bottiaia, constantly expanding, were, arguably, involved in the commercial activities at Methone. This study suggests that because of Methone's geographical location and proximity to the capital of the Macedonian kingdom, Aigai (modern Vergina), Methone functioned as the capital's face to the sea, as the royal harbour of Macedonia, until it was destroyed by Philip II, in 354 BC when all activities related to trade moved to neighbouring Pydna. Methone's finds together with other Northern Aegean settlements mentioned in this study reveal how important, even indispensable, this part of the ancient world was to the commercial networks of the archaic Mediterranean. The Northern Aegean is, therefore, not only well integrated into networks connecting southern and Eastern Greece, Egypt and the Levantine coast, but constitutes a vital part of them from the 8th century BC, onwards.
Within the limits: respectability, class and gender in Hyderabad
Keywords: education
social mobility
middle class
caste
gender
India

Drawing on twelve months of fieldwork in suburban Hyderabad, India, this thesis contributes to emerging debates on the Indian new middle classes and postcolonial middle classes more generally. I challenge images of a homogenous middle class enjoying the benefits of liberalization by highlighting the diversity in wealth, lifestyle and access to opportunities within this class sector. Contrary to the pervasive image of a hedonistic and morally corrupt new middle class, I assert the centrality of moral discourses to the construction of middle-class identity in Hyderabad. Middle-class Hyderabadis engage in moral discourses of ‘respectability’ and ‘open-mindedness’ in relation to caste, consumption, education, and women’s public and domestic roles. These discourses of morality are central to the reproduction of class and gender inequality as successfully balancing the demands of respectability and open-mindedness is particularly difficult for those with fewer resources such as the lower middle class and for women who are expected to embody authentic Indianness in their demure comportment, ‘traditional’ attire and commitment to ‘Indian’ family values, but are also liable to being judged ‘backward’ if their clothing and lack of education and paid employment are seen to be in conflict with fashion and open-mindedness. The focus on balance and compromise in middle-class Hyderabadis’ narratives echoes other work on postcolonial middle classes that has emphasised people’s efforts to adhere to local notions of respectable behaviour that are central to national identities while also attempting to align themselves with a ‘modern’ global consumer culture. In contrast to much of this literature, however, I challenge the notion that modernity and tradition, the local and the global are objects of desire in and of themselves and instead argue that they function as important reference points in discourses that legitimate the dominant position of men and those of upper class-caste status.
Development of proton magnetic resonance spectroscopy in human heart at 3 Tesla
Keywords: creatine
cardiac magnetic resonace spectroscopy
quantification
3 Tesla
lipid

Cardiovascular magnetic resonance imaging (MRI) is a well established technique in clinical cardiology. Different MRI sequences are routinely used to assess cardiac anatomy, function, viability and other parameters that aid diagnosing cardiac disease. Conversely, cardiac magnetic resonance spectroscopy (MRS), the only available method for a non-invasive study of human cardiac metabolism, has not evolved into a clinical tool yet. The combination of both techniques holds great potential to gain insight into the causality of cardiomyopathy diseases or other medical conditions with high cardiovascular risk profile, like diabetes or obesity and improve the clinical management of cardiac diseases.
Nowadays, high field clinical MR systems have the great potential of improving the low spatial and temporal resolution and reproducibility of MRS. The aim of this thesis was to develop and implement a cardiac 1H-MRS method at 3 T that can be applied in clinical routine for the assessment of creatine and lipid levels in the human myocardium. The methodological developments to advance cardiac MRS are presented first. A robust 1H-MRS method comprising an optimized single-voxel technique, phased-array coil combination routine, optimized water suppression, breath-hold averaging and post-processing methods were developed. First, reproducibility and feasibility of the method were validated in vivo by acquiring 1H-MRS of the liver in almost one hundred healthy subjects. Subsequently, myocardial lipids levels were obtained in healthy volunteers by single breath-hold 1H-MRS triggered to mid-diastole, showing good reproducibility in an acquisition time less than 12 s. The good spectral resolution achieved using this method was demonstrated by the ability to differentiate for the first time two pools of myocardial lipids in spectra from the septum of patients with suspected myocardial lipid excess. Finally, creatine levels for healthy volunteers were investigated using multiple breath-hold acquisitions. Thus, this study shows the practicality and feasibility to incorporate this rapid cardiac 1H-MRS method into clinical studies of the human myocardium.
The prediction of surface settlements due to tunnelling in soft ground
Keywords: settlement
tunnelling

The investigation of various soil models for the prediction of surface settlement profiles due to the excavation of a single tunnel in soft ground is described in this thesis. Both analytical and numerical methods are used. Emphasis is placed on the establishment of the width of the predicted settlement trough. In the analytical analysis the ground is assumed to be an elastic halfspace. The problem is approached using two methods: (i) the application of a line load to model the uplift of soil caused by the excavation; (ii) the application of Sagaseta's method which models the soil deformation due to ground loss. For the numerical analysis of the tunnelling problem, the finite element program OXFEM is used. Finite element modelling for the simulation of tunnelling is investigated. The mesh size used in the analysis found to have an important impact on the computed results. Parametric studies using linear elastic and elastic-plastic models are carried out. The effect of stress and strain amplitudes on the behaviour of soil is also investigated. The non-linear elastic model assumes a power law between the elastic moduli and the mean effective stress, and represents the increase of stiffness with increasing stress amplitudes in the elastic region of the soil. The effect of strain amplitudes on the behaviour of soil is considered using an elastic-plastic model with nested yield loci and an outer von Mises surface. Both models have been implemented in OXFEM, and parametric studies on tunnelling are carried out using both models. Comparison between the computed results and existing empirical values of the widths of settlement troughs were carried out.