VictorJuiz/thesis huggingface dataset:
Total scattering studies of orbital disorder in strongly-correlated transition-metal oxides

Transition metal oxides are a family of materials where the physical properties are determined by the strong interplay between orbitals, spins, and electron charge. This thesis aims to understand the local orbital ordering and its relation to the physical properties. Both neutron and X-ray total scattering data have been collected and analysed using a small box approach to obtain specific information about the orbital ordering and its relation to the physical properties within three canonical systems: the spin-glass material Y2Mo2O7; the parent endmember compound, LaMnO3, of the doped manganites showing colossal magneto resistance (CMR); and a related series of different compositions, namely La1-xCaxMnO3.
Y2Mo2O7 consist of Jahn-Teller active Mo4+ ions which occupy corner-sharing tetrahedra in a frustrated pyrochlore lattice. In most pyrochlore oxides both frustration and positional disorder must be present to show spin-glass behaviour. In this thesis I present how the Mo4+ ions on each frustrated tetrahedron dimerise, leading to structural disorder on the Mo site large enough to drive the spin-glass state in Y2Mo2O7.
LaMnO3 undergoes a canonical orbital order/disorder transition at ~750K which is the same as the transition that precedes CMR itself in doped manganites. Here I find a discontinuity in local structure that indicates a fundamental change in the type of orbital arrangement at the transition. In the analysis of the transition I realise the difficulty of discriminating between local structure models when static and dynamic disorder are strongly coupled. Nevertheless, my data show a subtle but consistent preference for the anisotropic Potts model. La1-xCaxMnO3 is of high interest because of its ability to show CMR. Here, I synthesised nine different sample compositions, using the citric gel method. I present a discontinuity in local structure as a function of composition similar to the observed orbital order/disorder transition in LaMnO3. An extended study of the local structure of La0.5Ca0.5MnO3 composition as a function of temperature is presented.
This study indicates that there is a difference in the sample composition depending on which synthesis method used. However, the study shows that Goodenough’s CO/OO model for the ground state of La0.5Ca0.5MnO3 is too simplified and suggests that a different model may represent the low temperature state better.

Advisor: Godwin, A
Ideo-affective politics and the construction of U.S. foreign policy

This thesis asks, how it is possible that in five years, from 1945 to 1950, the United States reoriented its foreign policy to allow for a total Cold War mobilization, one that included both policy elites and the public? At a broader theoretical level, this thesis investigates how public mobilization operates and explores the consequences – both intended and unintended – of pursuing certain mobilization strategies, especially affectively-laden ones. Drawing on constructivist theorizing and recent scholarship on affect and emotions, I advance a theory of “ideo-affective politics,” or the political use of ideas and emotions, and outline a three-part conceptual pathway of foreign policy change: ramping-tampingrevamping. “Ramping” refers to the deliberate strategic cultivation of public emotions for the purposes of public persuasion; “tamping” to the strategic efforts at calming public sentiment and restoring the balance between elite and public structures of feeling when the latter is no longer politically advantageous; and “revamping” to the reconstitution of the initiating elite actor’s ideo-affective approach for either strategic or genuine reasons. Using a form of affectively-sensitive discourse analysis and process tracing, I examine archival, published, and secondary materials to trace the construction of the Cold War along this pathway, from the ramping up of public emotions in 1947 with the Truman Doctrine and its accompanying campaign, to the failed attempts to tamp down those same emotions (due to the creative capacities of emotions and the strategic maneuvering of political opponents) when confronted with the “shocks of 1949”, to the revamping of the administration’s own ideo-affective beliefs to match the newly reconstituted public structure of feeling in the face of the North Korean invasion in 1950. I argue that in strategically ramping up public emotions in 1947, the Truman administration unleashed dynamics that they could no longer control, laying the foundations for the reconstitution of their beliefs and interests to a Cold War footing by 1950. In examining this in-depth case, this thesis provides both a new explanation for the beginning of the Cold War and a new conceptual pathway for explicating the relationship between ideas and emotions in politics, highlighting the ways that emotions can be both strategic assets and dynamic phenomena that result in constraining structures.

Advisor: Dill, J
Hall, T
The aetiology and pathogenesis of rectal prolapse

It is still an enigma that some patients develop rectal prolapse whilst others with similar risk factors do not. Biomechanical assessment of the skin may provide further insight into the aetiology of this complex condition. Components of connective tissue other than collagen have been found to be involved in patients with rectal prolapse. Elastin fibres are an abundant and integral part of many extracellular matrices and are especially critical for providing the property of elastic recoil to tissues. The significance of elastin fibres is clearly reflected by the numerous human conditions in which a skin phenotype occurs as a result of elastin fibre abnormalities. The organization of elastic fibres differs between controls and subsets of patients with rectal prolapse, and their importance for maintaining the structural and functional integrity of the pelvic floor has been demonstrated in transgenic mice, with animals which have a null mutation in fibulin-5 (Fbln5¡/¡) developing prolapse. This study aimed to compare fibulin-5 expression in the skin of patients with and without rectal prolapse. Between January 2013 and February 2014, skin specimens were obtained during surgery from 20 patients with rectal prolapse and from 21 without prolapse undergoing surgery for other indications. Fibroblasts from the skin were cultured and the level of fibulin-5 expression was determined on cultured fibroblasts, isolated from these specimens by quantitative real-time polymerase chain reaction. Immunohistochemistry was performed on fixed tissue specimens to assess fibulin-5 expression. Orcein staining measured expression levels of elastin in the skin, and Image J. Tensile tests were performed using the Zwick Roell device, with custom ceramic clamps. For statistical analysis, Student's t test was used. Fibulin-5 mRNA expression and fibulin-5 staining intensity were significantly lower in young male patients with rectal prolapse compared with age matched controls [fibulin-5 mean _ SD mRNA relative units, 1.1 _ 0.41 vs 0.53 _ 0.22, P = 0.001; intensity score, median (range), 2 (0–3) vs 1 (0–3), P = 0.05]. There were no significant differences in the expression of fibulin-5 in women with rectal prolapse compared with controls. Histological analysis of prolapse vs control showed percentage dermal elastin fibres of 9 vs 5.8 % (p=0.001) in males and 6.5 vs 5.3 % (p=0.05) in females. Patients with more severe prolapse (external) had a significantly (p=0.05) higher percentage dermal elastin fibres 6.9 vs 6.1 % than internal prolapse. Young's modulus of patients with prolapse was lower in males (3.3 vs 2.8, p=0.05) and females (3.1 vs 2.7, p=0.05). Patients with prolapse have a higher concentration of elastin fibres in the skin, and these differences are quantitatively demonstrated through mechanical testing. This suggests that the aetiology may be a result of a dysfunction of elastin fibre assembly. Fibulin-5 may be implicated in the aetiology of rectal prolapse in a subgroup of young male patients.

Advisor: Jones, O
Mortensen, N
Hydrogen-driven hydrocarbon oxidation by cytochrome P450 enzymes

P450BM3 (CYP102A1) from Bacillus megaterium is a 119 kDa, 1,046-residue polypeptide with the FAD/FMN reductase domain fused to the C-terminus of the haem domain and, as such it is catalytically self-sufficient; only NADPH and oxygen are required for monooxygenase activity. P450BM3 is a sub-terminal fatty acid hydroxylase, but generations of CYP102A1 engineering allowed them to be used in, e.g. drug metabolism and alkane oxidation. This thesis describes protein engineering of P450BM3 and altering reaction conditions to enhance C1 – C8 alkane oxidation activities, with the long-term goal of oxidising methane, and using the hydrogen-driven cofactor regeneration system to drive these reactions. Catalytic hydrocarbon oxidation under mild conditions is highly desirable in fuel synthesis and energy applications. Methane is a greenhouse gas and its effect can be minimised if methane is selectively oxidised to methanol, which can be used as a liquid fuel or feedstock. The R47L/Y51F, KT2, I401P and A330P mutants, which previously showed higher activities for a wide range of substrates, were used as templates to build a library of mutants. The R47L/Y51F/KT2/A330P mutant (RT2/AP) showed total turnover number (TTN) of 680 ± 10 under atmospheric pressure at ambient temperature for propane oxidation, and the TTN improved by 16-fold under 5 bar propane pressure (TTN is defined as the maximum number of moles of substrate converted per mole of P450BM3). TTN values of 14,250 ± 1,370 (KU4/AP) and 920 ± 50 (KU3/AP) were observed under 5 bar propane and 8 bar ethane, respectively, at ambient temperature. The effect of adding an inert perfluorocarboxylic acid (PFC), which resembles the structures of natural substrates and constrains small alkanes to bind closer to the haem, was investigated. The R47L/Y51F/N70S/M237L/A328V mutant (RL/YF/NMA) with PFC11 gave a TTN of 13,590 ± 30 under 5 bar propane at ambient temperature. Higher TTNs of 26,320 ± 1,010 for propane and 1,440 ± 70 for ethane oxidation were observed for the RL/YF/NMA mutant at 4 °C due to improved aqueous alkane solubility. Octane and propane oxidations were performed using a hydrogen-driven NADP+ recycling system without changing the selectivity of products, although the observed propane oxidation activity was 15% of the glucose/GDH cofactor recycling system.

Advisor: Wong, L
Vincent, K
Automatic inference for higher-order probabilistic programs

Probabilistic models used in quantitative sciences have historically co-evolved with methods for performing inference: specific modeling assumptions are made not because they are appropriate to the application domain, but because they are required to leverage existing software packages or inference methods. The intertwined nature of modeling and computational concerns leaves much of the promise of probabilistic modeling out of reach for data scientists, forcing practitioners to turn to off-the-shelf solutions. The emerging field of probabilistic programming aims to reduce the technical and cognitive overhead for writing and designing novel probabilistic models, by introducing a specialized programming language as an abstraction barrier between modeling and inference.
The aim of this thesis is to develop inference algorithms that scale well and are applicable to broad model families. We focus particularly on methods that can be applied to models written in general-purpose higher-order probabilistic programming languages, where programs may make use of recursion, arbitrary deterministic simulation, and higher-order functions to create more accurate models of an application domain. In a probabilistic programming system, probabilistic models are defined using a modeling language; a backend implements generic inference methods applicable to any model written in this language. Probabilistic programs — models — can be written without concern for how inference will later be performed.
We begin by considering several existing probabilistic programming languages, their design choices, and tradeoffs. We then demonstrate how programs written in higher-order languages can be used to define coherent probability models, describing possible approaches to inference, and providing explicit algorithms for efficient implementations of both classic and novel inference methods based on and extending sequential Monte Carlo. This is followed by an investigation into the use of variational inference methods within higher-order probabilistic programming languages, with application to policy learning, adaptive importance sampling, and amortization of inference.

Advisor: Wood, F
Migrant remittances and democracy

How do migrant remittances affect the prospects for democracy in receiving states? In this thesis, I use a range of methods including statistical analysis of macro-economic and micro-level survey data and qualitative interviews to investigate this question. I use cross-national data, barometer surveys from the Middle East, sub-Saharan Africa and post-Communist countries and 63 interviews conducted with remittance recipients in Jordan and Tunisia.
I find that remittances from migrants in democratic states are associated with political liberalisation and the downfall of authoritarian regimes, but that remittances from migrants in non-democratic states are not. An important causal mechanism is that of protests: remittances from democratic countries fuel protests in authoritarian regimes. On the individual level, I show that remittances are associated with greater non-electoral political participation because recipients perceive themselves to have higher levels of economic security. I also find that financial remittances from democratic countries are accompanied by and reinforce the transmission of social remittances in the form of pro-democratic political norms.
In addition to the main findings, I present the first evidence for electoral remittance cycles in authoritarian regimes, clarify our knowledge about how and why remittances affect different forms of political participation and add to our understanding of the political dimensions of social remittances.

Advisor: McLean, I
Synthesis, characterization and catalytic activity of graphene promoted metal / metal oxide composite catalysts on direct propylene oxidation

The catalytic oxidation of hydrocarbons such as propylene is of a major economic importance. The products of their oxidation are used daily in our life and the uses are expanding to other products. However, the oxidation processes are sometimes accompanied by various by-products that are environmentally unfriendly. Nowadays, the calling for greener production processes is louder than ever due to the emission of greenhouse gases and the other environmental pollutants. Therefore, a search for a capable catalyst to improve the process with a minimal environmental impact was set as a goal in this project.
We report herein the use of graphene as a promoter for different supports for the direct gaseous oxidation of propylene. Graphene, when added to the catalyst, can facilitate the production of acrolein through synergetic effects. Despite the fact that acrolein can be produced solely on graphene, the activity of the graphene was greatly improved when it was used as a support for the metals. The conversion had risen from 1% for graphene to 11% when graphene is loaded with 5% Cu. The increase of metal content can clearly increase the conversion.
Typically, Cu-G-Al2O3 and Cu-G produced acrolein with up to 52% selectivity and 11% conversion. TEM, XPS and NH3-TPD characterization showed enhanced metal support interaction with acidic sites of graphene.

Advisor: Tsang, E
Putting marine microbes on the map: determining the global distribution of marine picophytoplankton using a combination of satellite and field data

Picophytoplanktonic cells (0.2-2 μm) are the dominant phytoplankters in the largest marine biomes on Earth: the subtropical gyres. The overaching aim of this thesis is to develop algorithms that use remote-sensing observables to map the distribution of the smallest and most abundant member of picophytoplankton, Prochlorococcus, and assess its contribution to the marine carbon cycle. To understand how the photoacclimatory status and growth of Prochlorococcus and its sister genera Synechococcus are influenced by light and nutrients, experiments were conducted in the South Atlantic Gyre (SAG). Results from the manipulation experiments show that, in the central region of the SAG, nutrient addition can induce marked changes in the optical properties of Prochlorococcus cells when subjected to saturating light levels, leading to a decrease in cell abundance, whereas at the gyre periphery no substantive changes in cell growth or optical characteristics were observed. Since light plays a central role in shaping the distribution of cyanobacteria, an empirical algorithm based on relationships between Prochlorococcus abundance and remotely-sensed observables was developed. The outputs were then used in a modified primary production model to predict the vertical distribution of carbon fixation by Prochlorococcus. The models estimate that &Tilde; 3.4 x 1027 Prochlorococcus cells in the global ocean fix 4.7 Gt C year-1. Most of the cell biomass and primary productivity is concentrated in the subtropical gyres and areas near the Equatorial Convergence, and 61% of the carbon fixation occurs in the upper water column (0-45 metres), where only 43% of the cells reside. However, in the gyres, carbon fixation is highest (62%) in deeper layers (45-200m), and both cell abundance and carbon fixation show marked seasonal patterns. The models developed in this study provide an unprecedented view of the vertical distribution of Prochlorococcus cells and their corresponding rates of carbon fixation in the global ocean.

Keywords: climate change
marine ecology
phytoplankton
ecological modelling
Prochlorococcus
photoacclimation
Advisor: Bouman, H
First cast the beam from thine own eye: the condemnation at the University of Paris 1241/4

In 1241/4 the theology masters at the university at Paris, their chancellor, Odo of Châteauroux, and bishop, William of Auvergne, condemned ten propositions against theological truth. Unlike other such condemnations, particularly at Paris in 1277, modern scholars have largely ignored it. This study attempts to remedy this neglect. It aims to view the condemnation in its contemporary context, concentrating on contemporary texts or those available in the period. The study’s main focus is not the condemnation itself. Instead it seeks to set it against the background of wider doctrinal, intellectual, institutional and historical developments within the emerging 'university'. The study's conclusions are three-fold. First, the period 1200-1240 combined a developing focus of Paris theologians on using their learning for preaching (fostered by their faculty's inclusion of the mendicant orders) with a rapid and sometimes divergent development of doctrine. This latter was based on long-term biblical enigmas and patristic discussions, now sharpened by external 'threats', including from newly-translated Aristotelian texts and the views of groups deemed heretical. There were also increasing concerns over Greek theology and the Jews. Second, while no single influence appears dominant in the choice of articles, they follow closely the major statement of catholic principles in the first canon of Lateran IV in 1215. The content and order of the propositions is too close to be coincidental. Read in this light, the condemnation served to cement Lateran IV within the theology faculty. Third, however, this was not just for internal self-discipline. 1241/4 was the point when the faculty itself 'came of age' - it aspired to leadership in catholic doctrine according to Lateran IV’s principles, seeing its role as external as much as internal. For this, it needed 'to cast the beam from its own eye before seeing clearly to remove the mote from its brother's'.

Keywords: Heresy
Lateran IV
William of Auvergne
Development of Theology Faculty at University of Paris in the first half of the thirteenth century
Role of Paris theologians in the 1240s
Advisor: Kempshall, M
Assessment of the role of cannabinoid receptor 2 in innate immune cell trafficking during acute inflammation

Activation of the cannabinoid receptor CB2 has been shown to induce directed leukocyte migration and inhibit leukocyte chemotaxis towards CC chemokines. However, the role that CB2 plays in regulating macrophage chemotaxis remains understudied. Using a real-time chemotaxis assay and a panel of chemically diverse CB2 agonists, I set out to examine whether CB2 modulates primary macrophage chemotaxis. Of 14 agonists tested, only a subset acted as bona fide macrophage chemoattractants. Surprisingly, despite being pertussis toxin-sensitive, neither pharmacological inhibition nor genetic ablation of CB2 had any effect on CB2 agonist-induced macrophage chemotaxis. Furthermore, the activation of CB2 had no effect on CCL2 or CCL5- induced macrophage chemotaxis. Therefore, the activation of CB2 does not inhibit CC chemokine-induced macrophage migration and a non-CB1/CB2, Gi/o-coupled GPCR must transduce CB2 agonist-induced macrophage chemotaxis. To identify the GPCR responsible, I examined primary murine macrophage GPCR expression and found that they express 124 non-sensory GPCRs. Functional screening of candidate receptors demonstrated that the putative cannabinoid receptors GPR18 and GPR55 and the lipid binding GPCRs LPAR1&5, CYSLTR1&2 and GPER1, were not responsible for CB2 agonist-induced macrophage chemotaxis. Alongside, a ligand-directed virtual screen, combined with functional testing, uncovered a novel chemotaxis positive chemical scaffold. Importantly, compounds in this series containing a photoaffinity label retained activity and will aid in the identification of the target(s) responsible for CB2 agonist-induced macrophage chemotaxis in future photocrosslinking experiments. Finally, I assessed whether CB2 controls innate immune cell recruitment in vivo using the zymosan-induced dorsal air pouch inflammation model and animals genetically deleted for CB2. I found that CB2-/- mice had increased air pouch neutrophil and monocyte numbers, as well as pro-inflammatory mediators, during the acute inflammatory phase. Interestingly, mixed bone marrow chimera experiments demonstrated that lack of CB2 specifically in the myeloid population is responsible for increased neutrophil trafficking. Therefore these data demonstrate that CB2 acts to regulate neutrophil recruitment during the acute inflammatory response.

Keywords: Inflammation
Chemotaxis
Cannabinoids
Advisor: Greaves, D