VictorJuiz/thesis huggingface dataset:
Network flux analysis of central metabolism in plants

The aim of this thesis was to develop stable-isotope steady-state metabolic flux analysis (MFA) based on 13C labeling to quantify intracellular fluxes of central carbon metabolism in plants. The experiments focus on the analysis of a heterotrophic cell suspension culture of Arabidopsis thaliana (L) Heynh. (ecotype Landsberg erecta). The first objective was to develop a robust methodology based on combining high quality steady-state stable labeling data, metabolic modeling and computational analysis. A comprehensive analysis of the factors that influence the outcome of MFA was undertaken and best practice established. This allowed a critical analysis of the subcellular compartmentation of carbohydrate oxidation in the cell culture. The second objective was to apply the methodology to nutritional perturbations of the cell suspension. A comparison of growth on different nitrogen sources revealed that transfer to an ammonium-free medium: (i) increased flux through the oxidative pentose phosphate pathway (oxPPP) by 10% relative to glucose utilisation; (ii) caused a substantial decrease in entry of carbon into the tricarboxylic acid cycle (TCA); and (iii) increased the carbon conversion efficiency from 55% to 69%. Although growth on nitrate alone might be expected to increase the demand for reductant, the cells responded by decreasing the assimilation of inorganic N. Cells were also grown in media containing different levels of inorganic phosphate (Pi). Comparison of the flux maps showed that decreasing Pi availability: (i) decreased flux through the oxPPP; (ii) increased the proportion of substrate fully oxidised by the TCA cycle; and (iii) decreased carbon conversion efficiency. These changes are consistent with redirection of metabolism away from biosynthesis towards cell maintenance as Pi is depleted. Although published genome-wide transcriptomic and metabolomic studies suggest that Pi starvation leads to the restructuring of carbon and nitrogen metabolism, the current analysis suggests that the impact on metabolic organisation is much less extreme.

Keywords: radiorespirometric
steady state flux analysis
isotopic steady state
flux maps
13C NMR
14N NMR
metabolic flux analysis in plants
metabolic networks
Arabidopsis thaliana
pool correction
phosphate limitation
central carbon metabolism
nitrogen source
systems biology
phosphorus starvation
13C MFA
mathematical modeling
nitrate
metabolic modeling
subcellular compartmentation
stable isotope labelling
suspension cultures
Pi levels
GC-MS
carbon conversion efficiency
carbohydrate oxidation
Advisor: Ratcliffe, R
Kruger, N
Elemental growth of oxide thin films

This thesis reports on the elemental growth of oxide thin films including TiOx, BaOx and BaxTiyOz by Ti/Ba deposition and oxidation. The films were grown on two different substrates, Au(111) and SrTiO₃(001), and studied using a variety of surface characterisation techniques.
On the reconstructed Au(111) surface, three different TiOx structures were obtained with increasing Ti amounts deposited: a (2 × 2) Ti₂O₃ honeycomb structure, a pinwheel structure that is the result of a Moiré pattern, and a triangular island TiO1.30 structure. The structures arise from raised Ti coverages and have increased Ti densities. Although Ba deposited on the reconstructed Au(111) has a weak interaction with the substrate, the BaOx thin films can grow epitaxially and lift the Au(111) reconstruction. Two well-ordered phases, a (6 × 6) and a (2√3 × 2√3) BaOx structure, were obtained which may have octopolar-based surface structures. For Ba & Ti deposition on Au(111), a locally ordered (5 × 5) BaxTiyOz structure was observed in the sub-monolayer regime. What is more interesting is the possible formation of a BaO-TiO surface alloy with short-range ordering achieved by Ba deposition on the (2 × 2) Ti₂O₃-templated Au(111) surface. This is the first time that surface-alloying has been observed for oxides.
When Ti is deposited onto the SrTiO₃(001) surface, it is incorporated into the substrate by forming a variety of Ti-rich SrTiO₃ surface reconstructions, such as c(4 × 2), (6 × 2), (9 × 2) and (√5 ×√5)-R26.6°. Ti deposition provides a completely different route to obtaining these reconstructions at much lower anneal temperatures than the previously reported preparation procedures involving sputtering and annealing the SrTiO₃ sample. Anatase islands with (1 × 3) and (1 × 5) periodicities were also formed by increasing the Ti deposition amount and post-annealing. Reconstructed SrTiO₃ substrate surface has a lattice that differs from the bulk crystal and affects the epitaxial growth of BaO, however, a locally ordered BaOx structure was observed on the sputtered substrate with a growth temperature of 300 °C. Depositing Ba & Ti on SrTiO₃(001) results in the formation of BaOx clusters and the Ti incorporation into the substrate, forming the familiar Ti-rich SrTiO₃ surface reconstructions.

Keywords: barium oxide
barium titanate
titanates
nanostructures
scanning tunnelling microscopy
surface science
Advisor: Castell, M
Contested childhoods: law and social deviance in wartime China, 1937-1945

“Contested Childhoods” links together three major areas of historical inquiry: war and criminality, law and social change, and the law as it relates to children, in the first half of twentieth-century China. The founding of the People’s Republic of China (PRC) in 1949 has eclipsed the historical significance of Chiang Kai-shek’s Nationalist Government and the importance of its role during the wartime period. This study examines how the outbreak of China’s War of Resistance against Japan (1937-1945) served as a crucial catalyst to the construction of ideas of criminality and its relation to children during the wartime period. It examines the different measures by which Chiang Kai-shek’s Nationalist Government (1928-1949) attempted to handle the rise in levels of criminality involving juveniles. The study analyses how an increase in criminality during the wartime period challenged how ideas on and about children and childhood were in understood within Chinese society. Moreover, it argues that wartime conditions served as a crucial catalyst prompted the construction of a new judicial and legal framework that was aimed at delineating the boundaries between childhood and adulthood during this period.

Keywords: China's War of Resistance Against Japan
Kuomintang Government
childhood
law and society
Advisor: Mitter, R
EPR investigations of iron-sulfur cluster relays in enzymes

Electron paramagnetic resonance (EPR) spectroscopy is a powerful tool for obtaining structural information about chemical centres with unpaired electrons. In complex biological systems, EPR spectroscopy can be used to probe these paramagnetic centres and the long-range interactions between them. This thesis investigates two important types of enzymes, and in particular the role of the iron-sulfur electron-transfer centres they contain, with a variety of EPR techniques.
Complex I (NADH:Ubiquinone Oxidoreductase) plays a key role in the electron transfer chain essential to the formation of ATP, and its malfunction has been related to numerous human diseases. It is a giant enzyme that contains the longest relay of iron-sulfur clusters known. EPR experiments conducted on complex I from bovine mitochondria yield crucial insight into the mechanism of efficient long-range electron transfer and bring us a step closer to understanding the functioning of this important complex. Hydrogenases are produced by micro-organisms and catalyse the reversible oxidation of H2. Most hydrogenases, including Hyd-2 from Escherichia coli, are very air-sensitive, but some, including E. coli Hyd-1 and Salmonella Hyd-5, are able to function in the presence of atmospheric levels of O2.
Understanding the origins of this 'O2-tolerance' is of paramount importance if hydrogenases are to be exploited in future energy technologies. In this thesis, native E. coli Hyd-1 and Hyd-2, Salmonella Hyd-5, as well as O2-tolerant and O2-sensitive variants of E. coli Hyd-1 are characterised using EPR. The EPR investigations elucidate properties of the active site and the electron-transfer relay and, in conjunction with other techniques, reveal structural and mechanistic details of how a highly unusual iron-sulfur cluster in the electron-transfer chain enables some hydrogenases to sustain catalytic activity in the presence of O2.

Keywords: Electron paramagnetic resonance
iron-sulfur clusters
enzymes
Advisor: Armstrong, FA
Palaeoceanography and sedimentology of a mid-Cretaceous Greensand

The Upper Albian (mid-Cretaceous) sediments of the Anglo-Paris Basin display a range of condensation phenomena, including glauconitic and phosphoritic sands, glauconitic intraformational pebble beds, and mineralised nodular hardgrounds. These are interpreted as the result of sedimentation rate fluctuations controlled by small-scale relative sea-level changes of at least regional nature. The regional signal was modified by local tectonics, including occasional synsedimentary faulting and the development of thinned successions and complex condensation horizons over broad submarine highs. Candidate sequence boundaries, marine flooding surfaces and systems tracts are proposed. Episodic, high-energy storm events record a spectrum of storm intensities and periodicities in the Upper Greensand Formation. Storm processes interacted with early submarine lithification to produce a suite of pebble-shell beds, simple and amalgamated coquinas, and storm-scoured hardgrounds. Analysis of shell bed fabrics and taphonomy indicates the important role of high-energy storms in generating a distinct event stratigraphy. Stable isotope analysis has detected a positive secular change in carbon-isotopic ratios within carbonates of dispar zone age, resolved as two smaller positive shifts across nodular hardgrounds. This correlates with the development of organic-rich sediments in a range of settings world-wide. Analytical problems, including silica diagenesis, have been addressed by a series of parallel control studies. Geochemical and petrographic analysis has confirmed the widespread development of glauconitic minerals throughout the Upper Greensand, and has been used to investigate grain evolution in a range of lithologies. A review of the global development of the Cretaceous glauconitic facies has been used to compile depositional models for a range of settings. Volumetric calculations of Cretaceous glauconite production rates have shown secular changes, with peak Aptian to Santonian values linked to transgressions across the broad shelf seas which developed globally during this time of rising sea-levels and sea-level highstand.

Advisor: Jenkyns, H
Kennedy, J
Stark deceleration and reactivity of polyatomic molecules and ions at low temperatures

This thesis describes the development of a new experimental technique for studying tunable-collision-energy, quantum state-selected, low-temperature ion-molecule reactions. This has been achieved through the combination of a Stark decelerator for neutral dipolar molecules, and a linear Paul ion trap.
The Stark deceleration process for ND3 was examined in detail, through the analysis of experimental data in combination with newly written molecular dynamics simulation programs. In order to prepare a sample of molecules appropriate for collision studies, additional beamline components were introduced after the decelerator. These components were: two hexapoles, to provide transverse focussing, maximising the molecular density; a molecular buncher, providing increased longitudinal velocity resolution; and a fast-opening shutter, to separate decelerated molecules from undecelerated molecules. The sympathetic-cooling of Xe+ ions and ND+3 ions by laser-cooled, Coulomb crystallised 40Ca+ ions with the ion trap was also studied. In particular, the stable trapping of Xe+ was demonstrated for the first time, and the experimental developments that led to this are discussed.
The work in this thesis represents significant progress towards studying the reaction of tunable-energy ND3 in the |j,mk> = |1,−1> quantum state with cold Xe+ ions. Ion-molecule reactions utilising ND3 molecules electrostatically guided through the Stark decelerator were performed. It was observed that the main source of error in these experiments was in the calculation of the initial number of Xe+ ions that had been sympathetically cooled into the Coulomb crystal. The sensitivity of the crystal morphology to the number of Xe+ ions was evaluated using molecular dynamics simulations. Strategies have been developed to reduce this uncertainty in future studies.
In addition to experimental work, the theory of low temperature ion-molecule reactions has been developed further. The temperature at which classical and quantum mechanical calculations diverge due to purely statistical effects has been investigated using different model intermolecular potentials, for closed-shell and open-shell species, and in the ground and rotationally excited states. From the results of these calculations, several promising candidate reactions have been suggested that might exhibit statistical quantum behaviour at experimentally achievable temperatures.

Keywords: angular momentum
cold and ultracold chemistry
ion trapping
reaction dynamics
Stark deceleration
Advisor: Softley, T
Recent modelling frameworks for systems of interacting particles

In this thesis we study three different modelling frameworks for biological systems of dispersal and combinations thereof. The three frameworks involved are individual-based models, group-level models in the form of partial differential equations (PDEs) and robot swarms. In the first two chapters of the thesis, we present ways of coupling individual based models with PDEs in so-called hybrid models, with the aim of achieving improved performance of simulations. Two classes of such hybrid models are discussed that allow an efficient simulation of multi-species systems of dispersal with reactions, but involve individual resolution for certain species and in certain parts of a computational domain if desired. We generally consider two types of example systems: bacterial chemotaxis and reaction-diffusion systems, and present results in the respective application area as well as general methods. The third chapter of this thesis introduces swarm robotic experiments as an additional tool to study systems of dispersal. In general, those experiments can be used to mimic animal behaviour and to study the impact of local interactions on the group-level dynamics. We concentrate on a target finding problem for groups of robots. We present how PDE descriptions can be adjusted to incorporate the finite turning times observed in the robotic system and that the adjusted models match well with experimental data. In the fourth and last chapter, we consider interactions between robots in the form of hard-sphere collisions and again derive adjusted PDE descriptions. We show that collisions have a significant impact on the speed with which the group spreads across a domain. Throughout these two chapters, we apply a combination of experiments, individual-based simulations and PDE descriptions to improve our understanding of interactions in systems of dispersal.

Keywords: stochastic processes
hybrid models
interacting particles
Advisor: Erban, R
Arginine transport and other determinants of nitric oxide production in human septic shock

The arterial vasodilation seen in human septic shock is conventionally attributed to increased nitric oxide (NO) production, primarily by extrapolation of animal and cellular studies. Little is known of the cellular source of NO in human septic shock. Other mediators, such as carbon monoxide (CO), may modulate NO production, and could also directly contribute to vasodilation.
This study has examined the NO and CO synthetic pathways in peripheral blood mononuclear cells and mesenteric arterial smooth muscle from patients with septic shock, and from non-septic controls.
Peripheral blood mononuclear cells from septic patients had increased NO production, though this was perhaps more modest than expected. The transport of arginine, the substrate for NO synthase, into these cells was increased; this was due to an increase in the activity of one transporter system, y+. mRNA for a protein encoding y+ activity, CAT2B, was increased in these cells. However, mRNA and protein for inducible and endothelial NO synthase was decreased in sepsis, while inducible heme oxygenase (the enzyme responsible for CO production) mRNA and protein was increased.
NO production in arterial smooth muscle from septic patients was reduced, as was mRNA for inducible and endothelial NO synthase, and the arginine transporter CAT1. There was no increase in inducible NO synthase protein, though there were small increases in endothelial NO synthase protein and NO synthase activity. In contrast, both mRNA and protein for inducible heme oxygenase were increased.
These results challenge the assumption that NO is central to the pathogenesis of human sepsis. Negative feedback systems for NO production have been demonstrated in cell models. These may be relatively more important in human sepsis. In addition to forming one of these feedback systems, it may be that CO, more than NO, is responsible for the hypotension observed in these patients.

Advisor: Young, D
The segmentation of sparse MR images

This thesis develops a methodology for the segmentation of anatomical structures within sparse'' MR images. Sparse images were acquired in large numbers prior to the emergence of high-resolution MRI and they form the basis of many long term imaging studies.
The term sparse refers to the fact that the volumetric image has very poor spatial resolution in the direction perpendicular to the slice plane. This leads to a significant degradation in image quality and effectively destroys the spatial continuity of the imaged object. Consequently, generic segmentation schemes --- particularly those based on voxel classification --- will yield poor results unless they have been augmented in some manner.
Our Segmentation approach is based on a deformable simplex mesh surface, which iteratively interpolates extracted boundary point data. Prior information is mobilised at two levels. Boundary points are found using a matching algorithm based on a database of pre-specified piecewise constant models. These models represent possible idealised intensity profiles for the object boundary. In addition to the boundary model, there is a shape template. The template is generated from a training set of pre-segmented structures, which means that only shapes similar to those in the training set will be recovered. The segmentation proceeds in two phases. The first recovers the normal shape component, determined by the training set, whilst the second deforms smoothly from this constrained solution to produce a more veridical boundary representation.
The segmentation scheme is applied to a number of sparse brain images. Qualitative validation --- accomplished by registering the surface extracted from the sparse data to a high resolution scan acquired at the same time-point --- indicates that a good approximation to the underlying boundary is obtainable from such images.

Keywords: symmetry
medical imaging
sparse
MRI
brain
Advisor: Brady, M
Zisserman, A
Reducing domestic energy consumption through behaviour modification

This thesis presents the development of techniques which enable appliance recognition in an Advanced Electricity Meter (AEM) to aid individuals reduce their domestic electricity consumption. The key aspect is to provide immediate and disaggregated information, down to appliance level, from a single point of measurement.
Three sets of features including the short term time domain, time dependent finite state machine behaviour and time of day are identified by monitoring step changes in the power consumption of the home. Associated with each feature set is a membership which depicts the amount to which that feature set is representative of a particular appliance. These memberships are combined in a novel framework to effectively identify individual appliance state changes and hence appliance energy consumption.
An innovative mechanism is developed for generating short term time domain memberships. Hierarchical and nearest neighbour clustering is used to train the AEM by generating appliance prototypes which contain an indication of typical parameters. From these prototypes probabilistic fuzzy memberships and possibilistic fuzzy typicalities are calculated for new data points which correspond to appliance state changes. These values are combined in a weighted geometric mean to produce novel memberships which are determined to be appropriate for the domestic model.
A voltage independent feature space in the short term time domain is developed based on a model of the appliance’s electrical interface. The components within that interface are calculated and these, along with an indication of the appropriate model, form a novel feature set which is used to represent appliances.
The techniques developed are verified with real data and are 99.8% accurate in a laboratory based classification in the short term time domain. The work presented in this thesis demonstrates the ability of the AEM to accurately track the energy consumption of individual appliances.

Keywords: non intrusive appliance load monitoring
fuzzy clustering
smart-meter
disaggregated feedback
membership generation
energy
Advisor: McCulloch, M
Information theoretic resources in quantum theory

Resource identification and quantification is an essential element of both classical and quantum information theory. Entanglement is one of these resources, arising when quantum communication and nonlocal operations are expensive to perform. In the first part of this thesis we quantify the effective entanglement when operations are additionally restricted to account for both fundamental restrictions on operations, such as those arising from superselection rules, as well as experimental errors arising from the imperfections in the apparatus. For an important class of errors we find a linear relationship between the usual and effective higher dimensional generalization of concurrence, a measure of entanglement.
Following the treatment of effective entanglement, we focus on a related concept of nonlocality in the presence of superselection rules (SSR). Here we propose a scheme that may be used to activate nongenuinely multipartite nonlocality, in that a single copy of a state is not multipartite nonlocal, while two or more copies exhibit nongenuinely multipartite nonlocality. The states used exhibit the more powerful genuinely multipartite nonlocality when SSR are not enforced, but not when they are, raising the question of what is needed for genuinely multipartite nonlocality. We show that whenever the number of particles is insufficient, the degrading of genuinely multipartite to nongenuinely multipartite nonlocality is necessary.
While in the first few chapters we focus our attention on understanding the resources present in quantum states, in the final part we turn the picture around and instead treat operations themselves as a resource. We provide our observers with free access to classical operations - ie. those that cannot detect or generate quantum coherence. We show that the operation of interest can then be used to either generate or detect quantum coherence if and only if it violates a particular commutation relation. Using the relative entropy, the commutation relation provides us with a measure of nonclassicality of operations. We show that the measure is a sum of two contributions, the generating power and the distinguishing power, each of which is separately an essential ingredient in quantum communication and information processing. The measure also sheds light on the operational meaning of quantum discord - we show it can be interpreted as the difference in superdense coding capacity between a quantum state and a classical state.

Keywords: entanglement
discord
quantum operations
quantumness
quantum mechanics
quantum information
physics
Advisor: Jaksch, D