VictorJuiz/thesis huggingface dataset:
Bilayer formation with fluorinated amphiphiles and applications in membrane protein studies
Keywords: Bilayer
Membrane proteins
Lipids
Membranes
Fluorinated amphiphiles
Electrophsyiology

Every cell is enclosed by a membrane which gives structure to the cell and allows for the passage of nutrients and wastes into and out of the cell. Membranes are made up of amphiphilic lipid molecules, with one water-soluble end, and one hydrophobic end. Naturally occurring and synthetic membranes are made up of double-chained amphiphiles derived from hydrocarbons. Recently, a novel class of amphiphilic molecules derived from fluorocarbons have been reported. The properties of fluorinated amphiphiles are very different to that of hydrocarbon based amphiphiles. Fluorinated amphiphiles have been previously reported to be useful in the studies of membrane proteins. In this thesis, we explore some novel uses of fluorinated amphiphiles.
Chapter one: Provides a comprehensive review of the properties of fluorocarbon-based amphiphiles and discusses the existing uses of fluorinated amphiphiles in biochemical and biomedical research.
Chapter two: Describes some of the important materials and methods used in this thesis including a detailed description of the proteins used and the working principles behind the techniques used in the study.
Chapter three: Looks at the stability of pre-formed planar lipid bilayers in the presence of fluorinated amphiphiles (F-amphiphiles), and characterizes the behaviour of alpha-haemolysin and other proteins in liposomes and planar lipid bilayers in the presence of F-amphiphiles. We found that F-amphiphiles have an inhibitory effect on the insertion of protein into lipid bilayers, and this property has been exploited to control the number of proteins in the bilayer.
Chapter four: Using droplet interface bilayers, we investigate the electrical properties and behaviour of protein(s) in bilayers formed by F-amphiphiles. The results obtained with fluorinated bilayers are compared with results obtained in conventional DPhPC lipid bilayers. This is the first ever report to carry out such an investigation and it provides insights into the formation, stability and utility of fluorinated bilayers.
Chapter five: In Chapter five, we explore another aspect of droplet interface bilayers: the feasibility of using droplet interface bilayers to screen for membrane protein libraries. I have chosen to focus on certain fundamental aspects of the screening process that are sufficient to establish the feasibility of the method and to act as the proof of concept.
Chapter six: Summarizes all the important results in the thesis and discusses some possible future directions of this project.
Advanced materials for plasma facing components in fusion devices
Keywords: functionally graded coatings
graded coatings
VPS steel
plasma facing components
JET
nano-indentation
vacuum plasma spraying
functionally gradient coatings
ITER
fusion
residual stress
FGMs
FGM
functionally graded materials
FEA
PFCs
diverter
tungsten
VPS W
first wall
tokamak
finite element analysis
VPS
W

This thesis describes the design, manufacture and characterisation of thick vacuum plasma sprayed tungsten (W) coatings on steel substrates. Fusion is a potentially clean, sustainable, energy source in which nuclear energy is generated via the release of internal energy from nuclei. In order to fuse nuclei the Coulomb barrier must be breached - requiring extreme temperatures or pressures – akin to creating a ‘star in a box’. Tungsten is a promising candidate material for future fusion reactors due to a high sputtering threshold and melting temperature. However, the large coefficient of thermal expansion mismatch with reactor structural steels such as the low activation steel Eurofer’97 is a major manufacturing and in-service problem. A vacuum plasma spraying approach for the manufacture of tungsten and tungsten/steel graded coatings has been developed successfully. The use of graded coatings and highly textured 3D interface surfi-sculpt substrates has been investigated to allow the deposition of thick plasma sprayed tungsten coatings on steel substrates. Finite element models have been developed to understand the residual stresses that develop in W/steel systems and made use of experimental measurements of coating thermal history during manufacture and elastic moduli measured by nano-indentation. For both the graded and surfi-sculpt coating, the models have been used to understand the mechanism of residual stress redistribution and relief in comparison with simple W on steel coatings, particularly by consideration of stored strain energy. In the case of surfi-sculpt W coatings, the patterned substrate gave rise to regular stress concentrating features, and allowed 2mm thick W coatings to be produced reproducibly without delamination. Preliminary through thickness residual stress measurements were compared to model predictions and provided tentative evidence of significant W coating stress relief by regulated coating segmentation.
Treating the children of the poor: institutions and the construction of medical authority in eighteenth-century London
Keywords: London
London Foundling Hospital
children
medicine
paediatrics

It is commonly accepted that, prior to the rise of paediatric medicine as a formal medical specialisation in the nineteenth and twentieth centuries, medical care of children was primarily conducted by women in the context of the household. However, as this thesis argues, there was vibrant medical interest in children prior to the development of formalized paediatric medicine. Over the course of the eighteenth century, a network of medical practitioners interested in children’s health sought to establish their authority over the subject and, in doing so, devoted increased attention to children, channelling general medical interest into the basis for future medical specialisation.
As this thesis argues, medical authority over children’s health was gradually constructed over the eighteenth century through printed texts, institutional experience, medical understandings of disease, and efforts to devise therapeutic practices suitable to children. Key to these developments were the efforts made by medical men to supplant women as authorities on children’s health. Also crucial was the role played by institutions in providing spaces for medical practitioners to encounter children. Institutions, such as the Dispensary for the Infant Poor and the London Foundling Hospital, increased the opportunities for medical practitioners to gain experience treating child patients. As this thesis demonstrates, it was the children of the poor who provided medical practitioners with the hands-on experience necessary to bolster their emerging claims of authority. As such, institutions and poor children both had essential roles to play in the development of medical interest in children, and the translation of that interest into claims of medical authority.
Scanning probe microscopy and electrochemical studies of deposition on electrode surfaces
Keywords: voltammetry
BDD
AFM
nucleation
deposition
SPM
electrochemistry

SPM, optical microscopy, and electrochemical techniques are used to study a range of electrochemical deposition processes on carbon electrodes, particularly those associated with diffusion-controlled multiple nucleation. Anodic stripping voltammetry for analytical measurements using solid electrodes is addressed in the light of limitations arising from electrode heterogeneity, electrode morphology, inhibited electrodeposition, and incomplete stripping of deposited metal. It is shown, using direct imaging of electrode surfaces, that each of the preceding factors may produce significant deviations from ideal electrode behaviour. The electrochemical nucleation of silver on BDD is examined. Data are obtained for the nucleation rate by interpretation of the deposition voltammetry, and by inspection of in-situ optical microscopic images. The particle distributions are analyzed and a stochastic model of nucleation developed. A model for the potentiostatic nucleation and three dimensional growth of deposits on an electrode surface under hydrodynamic conditions is examined. A wall-tube and stirred cell are used to generate conditions in which the diffusion layer thickness is in the range 10 – 40 μm. It is shown that the model provides excellent fits to the experimental data. A previously unrecognised correlation between the morphology of the PbO2 deposits and their electrocatalytic activity is established. The morphology of the films are observed as a function of time and potential using in-situ AFM. Nanotrench arrays are fabricated on HOPG surfaces. Cyclic voltammetry in simple redox couples is used to provide experimental evidence that the voltammetric response of a graphite electrode is solely due to the edge plane sites, with the basal plane sites having no measurable contribution. Nanotrenches are used as templates in a simple method for generating random assemblies of metal nanobands. This method is shown to be effective for generating gold, silver and copper nanowires. The electrochemical properties of the array are investigated via cyclic voltammetry.
Using metamorphic modelling techniques to investigate the thermal and structural evolution of the Himalayan-Karakoram-Tibetan orogen
Keywords: Karakoram
Red River shear zone
Himalaya
metamorphic petrology
Tibet
plate tectonics

Metamorphic rocks constitute a vast volumetric proportion of the Earth’s continental lithosphere and are invaluable recorders of the mechanisms and rates of deformation and metamorphism that occur at the micro-, meso- and macro-scale. As such, they have the potential to provide detailed insight into important tectonic processes such as the subductive transport of material into, and back from, mantle depths and also folding, faulting and thickening of crust that occurs during collisional orogeny. The Himalayan-Karakoram-Tibetan orogen is the youngest and most prominent example of a continent-continent collisional mountain belt on Earth today and is a product of the on-going convergence of the Indian and Asian plates that initiated in the Early Eocene. Thus, it provides an exceptional natural laboratory for the investigation of such processes. Recent advances in the computational ability to replicate natural mineral assemblages through a variety of metamorphic modelling techniques have led to improvements in the amount (and quality) of petrographic data that may be obtained from a typical metamorphic rock. In this study, phase equilibria modelling (pseudosection construction) using THERMOCALC, amongst other techniques, has been integrated with in-situ U–Pb and Th–Pb geochronology of accessory monazite in order to constrain the tectonothermal evolution of four regions intimately associated with the Himalayan-Karakoram-Tibetan orogen. These regions comprise the Karakoram metamorphic complex (north Pakistan), the Tso Morari massif (north-west India), the eastern Himalayan syntaxis (south-east Tibet) and the Day Nui Con Voi metamorphic core complex of the Red River shear zone (North Vietnam). Each case study documents previously unreported metamorphic, magmatic or deformational events that are associated with the India-Asia collision. These data have allowed original interpretations to be made regarding the tectonic evolution of each individual region as well as the large-scale evolution of the Himalayan-Karakoram-Tibetan orogenic system as a whole.
The evolution of a conception of citizenly duty towards military service 1854–1914: a study of London press discourse
Keywords: militia
national service
Victorian
duty
volunteers
conscription
citizenship
obligation
military service
enlistment

This dissertation investigates how personal military service, which during the immensely popular Crimean War of 1854-6 was regarded as the business only of an abstract and lowly soldier-class, had by the eve of the Great War taken on the aspect of a clear and universal citizenly duty in London press discourse. It utilises text-searchable digitised newspaper archives to exhaustively review the whole body of relevant press debate in thirteen key London periodicals, identifying key shifts and trends in press conceptions of civilian military obligation over the six decades between the outbreak of the Crimean War in 1854 and the eve of the Great War in 1914. The analytical narrative that emerges highlights the importance of key events, including the Crimean War, Indian Mutiny, wars of Prussian expansionism, and Boer War, in promoting and shaping the coherent conception of citizenly duty towards military service that would go on to underpin not only the mass enlistments of 1914 but also the acceptance of conscription in 1916. It suggests also the important role of broader cultural and political trends – in particular, the advent of militarist Imperialism, the growing legitimacy of the state, the shift towards a more collectivist ‘social democratic’ liberalism, and the emergence of ‘contractual’ theories of citizenship – in facilitating a reconciliation between the military imperative towards mass civilian military participation and existing liberal values and ideologies. This dissertation reveals that the societal consensus on the duty to enlist in 1914 was by no means a foregone cultural conclusion, nor indeed the relic of an earlier heroic age, but rather the dynamic product of evolution and contestation over six decades. The present study not only provides vital context to our understanding of the ‘rush to the colours’ of 1914, but also represents the first historical investigation of an important and much-neglected aspect of the relationship between war and society.
On the origin, morphology and kinematics of molecular gas in early-type galaxies
Keywords: kinematics
early-type
galaxies
morphology
molecular Ggs

In this thesis I present new interferometric 12CO observations of 30 early-type galaxies (ETGs). These galaxies were the brightest ~2/3 of CO detected ETGs from the complete, volume limited Atlas3D survey. By including literature data I construct the largest ever sample of mapped ETGs, containing 41 objects, and use this sample to analyse the morphology, kinematics and origin of the molecular gas.
Many of the galaxies in this sample have relaxed molecular discs, but polar structures, rings, bars and disturbed gas distributions are also present. Around half of the galaxies have molecular gas that follows the stellar light profile, similar to molecular gas in spirals, while others have molecular gas excesses, truncations, rings or composite profiles. The molecular gas extent is smaller in absolute terms in ETGs than in late-type galaxies, but the size distributions are similar once scaled by the galaxies optical/stellar characteristic scalelengths. Cluster environments, however, lead to systems having denser, more compact molecular reservoirs.
I find that molecular gas is an excellent kinematic tracer, even in high-mass ETGs, and thus molecules may be the kinematic tracer of choice for probing the M/L evolution of galaxies over cosmic-time. I use this knowledge to construct the first ever early-type CO Tully-Fisher relation, and show that it is offset from the Tully-Fisher relation of spirals by 0.98±0.22 magnitudes at Ks-band.
I find that a third of my sample galaxies have their molecular and ionised gas kinematically misaligned with respect to the stars, setting a strong lower limit on the importance of externally acquired gas (e.g. from mergers and cold accretion). The origin of the molecular gas seems to depend strongly on environment, with externally acquired material being common in the field but nearly completely absent in Virgo. Furthermore, my results suggest that galaxy mass may be an important independent factor associated with the origin of the gas, with the most massive fast-rotating galaxies in our sample always having kinematically aligned gas.
The evolution and development of left/right asymmetry in the Lophotrochozoa
Keywords: Lophotrochozoa
TGF
Asymmetry
Nodal

Left/right (L/R) asymmetries, differences in morphology between the otherwise mirrored left- and right-hand sides of the body, are found in animals across the Bilateria. For many years it was thought that the mechanisms for establishment of these asymmetries had evolved separately in the three superphyla that constitute the Bilateria, but the discovery in 2009 that the TGF-beta ligand Nodal shares a conserved role in the Deuterostomia and Lophotrochozoa has re-ignited debate and interest in this field. In this thesis, work examining the establishment and maintenance of L/R asymmetries in the lophotrochozoan superphylum is presented, aimed at uncovering the wider conservation of these pathways across the Bilateria.
Illumina sequencing and a range of de novo assembly techniques were used to derive genomic and transcriptomic data respectively for two primary model organisms, the limpet Patella vulgata and the serpulid annelid Pomatoceros lamarckii. Additionally, collaborative work lead to the derivation of transcriptomes for two other mollusc species and the genome of the monogont rotifer Brachionus plicatilis. A range of analysis was performed on these novel resources and is detailed here, with particular reference to the transcription factor cassettes contained in these datasets.
These sequence resources formed the basis for examination of the breaking of initial symmetry in these model organisms. Known read-outs of correct establishment of L/R asymmetry, the expression of genes Nodal and Pitx on the right of the body, were codified in the course of normal development in P. vulgata. Pharmacological inhibitors of genes implicated in the establishment of L/R asymmetry, particularly ATPase ion channels, were then applied to embryos. After development, markers of normal development were assayed for signs of bilateral inversion. Although radialised phenotypes were observed, it is unclear whether these are specifically the result of L/R asymmetry defects. The localisation of ATPase mRNA and serotonin, often posited as a small molecule potential morphogen, were also assayed, although no conclusions could be drawn as to a role in the establishment of L/R asymmetry for these molecules, counter to some evidence from vertebrates.
Once symmetry is broken, the TGF-beta pathway is responsible for the communication, specification and maintenance of tissue identity across the L/R axis. The novel sequence resources described in this thesis provided a comprehensive window into this signalling cassette, and detailed here is a treatment of the TGF-beta pathway within the Lophotrochozoa. Ligand diversity has increased markedly in some clades, while signal transduction and regulatory steps are relatively unchanged.
This work has increased our knowledge of lophotrochozoan biology and particularly the mechanisms underpinning the establishment of asymmetry in this under-researched clade, however, much remains to be discovered about the ultimate origin of asymmetry itself.
Analysis of human non-canonical 3’end formation signals
Keywords: human non-canonical 3' end formation signals
3'end cleavage and polyadenylation
human pre-mRNA 3'end processing
A-rich 3'end formation signals

Cleavage and polyadenylation are essential pre-mRNA processing reactions maturing the 3’end of almost all protein encoding eukaryotic mRNAs. Analysis of the sequences required for cleavage and polyadenylation in the human melanocortin 4 receptor (MC4R) and the human transcription factors JUNB and JUND pre-mRNAs revealed that, at least for some mammalian genes, 3’end processing of the primary transcript is independent of previously described auxiliary sequence elements located upstream or downstream of the core poly(A) sequences. The analysis of the MC4R poly(A) site, contrary to the current understanding of mammalian poly(A) sites, showed that mutations of the AUUAAA hexamer sequence had no effect on 3’end processing levels while mutations in the short DSE severely reduced cleavage efficiency. The MC4R poly(A) site uses a potent DSE and to direct maximal cleavage efficiency requires only a short upstream adenosine rich sequence. Furthermore, analysis of the endogenous A-rich human JUNB poly(A) signal validated upstream A-rich core sequences as genuine 3’end formation directing sequences in human non-canonical 3’end formation signals. The results show that a minimal human poly(A) site, similar to yeast and plants, can be defined by an adenosine rich sequence adjacent to a U/GU-rich sequence element and a cleavage site. These findings further imply that some human non-canonical poly(A) sites may be recognised via a similar DSE-dependent mechanism and may not require additional auxiliary sequence elements. Finally, results on the analysis of the EDF1 poly(A) signal show that, in a spliced environment, A-rich sequences are also 3’end formation effectors but depend on an competent upstream splicing reaction for efficient definition of the 3’end processing site.
Effect of shear patterns and EPS on fouling in microfiltration
Keywords: shear
microfiltration
EPS

Concentration polarisation and fouling reduce performance as well as increase costs. In order to mitigate these effects, understanding the cause and effects of these phenomena is crucial. It has been hypothesized, and to a certain extent shown, that amelioration of fouling can be achieved through the use of time varying shear for example use of air-sparging or sharp changes in crossflow velocity. Nevertheless the effect of shear on membrane fouling, in particular its effect on the foulant deposition and the transmission of small molecules in microfiltration, is not well understood.
The goal of this project was to achieve an understanding of various foulant be- haviour. The work was divided into two parts. Firstly, the observations of fouling by freshwater algae, Chlorella Sorokiniana, were carried out at Nanyang Technolo- gical University, Singapore. Observations using macroscopic parameters were ex- amined with an optical non-invasive observation technique called Direct Observa- tion Through Membrane (DOTM). The result yielded a novel relationship between operating flux, crossflow velocity and transmission of extracellular polysaccharide. Interestingly shear was shown to have positive as well as negative effects on fouling of microfiltration membrane. The analysis of permeate has clearly shown that a maximisation of shear rate was not ideal.
The second part was concerned with observations of the effect of shear patterns on membrane fouling using newly fabricated special membrane filtration cell, Direct Shear Stress Test Cell (DSSTC), designed to fit an Anton Paar rheometer and op- erate at constant flux. Unlike the-constant-shear-filtration cells, one could impose a very wide variety of shear regimes including intermittent sharp changes of direction and sinusoidal oscillations in the DSSTC. The effect of shear patterns on transmis- sion and fouling of a model polysaccharide (Dextran Blue) through microfiltration membranes was carried out at various conditions. Again, the results showed that the maximisation of shear rate was not ideal. The effect of shear patterns and EPS on fouling by yeast suspension was also studied using the DSSTC. The benefit of oscillatory shear is foulant dependent. For example, square wave oscillatory shear led to lower relative fouling for yeast EPS, but it resulted in higher relative fouling for unwashed yeast.