VictorJuiz/thesis huggingface dataset:
On the importance of feedback in the stream-fed high redshift universe

Cosmological hydrodynamic simulations have shown that galaxies are fed by dense, cold gas streams at high redshift. However, the presence of such gas has never been observationally confirmed.
Using the Horizon- MareNostrum simulation, I examined whether cold flows are detectable with low-ionisation metal absorption lines, such as C II 1334. It is concluded that due to their low metallicity and density, it is extremely difficult to prove/disprove the presence of cold flows using the metal absorption lines.
Revisiting the acquisition of angular momentum in disc galaxies using high resolution simulations, I found that at the time of accretion, gas and dark matter do carry a similar amount of specific angular momentum which is systematically and significantly higher (at minimum by a factor of 2) than that of the dark matter halo as a whole. Whereas cold streams directly deposit this large amount of angular momentum within a sphere of radius r~0.1 Rvir, dark matter particles easily pass through the central region, depositing their angular momentum over a much more spatially extended region.
As a result, in our simulations neither the total specific angular momentum of the baryons nor its radial profile ever follows that of the virialised dark matter halo, contrary to what is typically assumed in the standard theory of disc galaxy formation. In order to better understand the formation of disc galaxies and the missing baryon problem in a LCDM universe, continuous, collective galactic winds are implemented. It is demonstrated that stellar feedback processes are able to suppress star formation by ~30% at z=3, compared to that from the run without feedback sources, but it still produces an unrealistic central peak in the rotation curve. Although inclusion of hypernovae further suppresses star formation, it is unable to quench the formation of low-angular momentum stars enough to remove the peaked rotation curves at high redshift.
Finally, feedback from active galactic nuclei turns out to be effective at suppressing star formation in massive galaxies at 1

Keywords: High Redshift Universe
Galaxy Formation
Advisor: Slyz, A
Devriendt, J
Wind tunnel modelling of buoyant plumes

The short range dispersion in the atmosphere of buoyant gases, such as hot air or natural gas, may be hazardous and dangerous. The available methods for studying this problem were reviewed. Wind tunnel studies were considered to be the most suitable method for studying near-field dispersion, and methods for accurately modelling the nearfield behaviour of a buoyant plume of gas were examined. The experiments were performed in the Oxford University 4m x 2m low speed wind tunnel at a model scale of 1:200. The mean trajectory and rate of spread of a buoyant plume from a 60 m high (full-scale) stack were measured in the presence of a simulated natural wind.
The exact similarity requirements were derived from dimensional analysis and from the equations of motion. In practice, it is not possible to match all the necessary dimensionless groups and exact scaling of the exit gas density ratio and the exit Reynolds number is often relaxed. A series of experiments was performed to examine the effect of these two groups on mean plume behaviour, with the intention of providing guidance for correct simulation of plume dispersion at reduced-scale.
The exit density ratio was found to have little effect on the near-field plume behaviour, provided all the other dimensionless groups were matched. Plumes with low Reynolds number were found to rise significantly higher than plumes with higher 'turbulent' Reynolds numbers. This difference in trajectory could not be correlated with the plume exit momentum flux.
The effect of the cross-flow on near-field dispersion was examined by performing experiments in four different simulations of the earth's atmospheric boundary-layer. The behaviour of the plume was found to be sensitive to both the velocity profile and the turbulence intensity of the cross-flow. To study dispersion in the wind tunnel, the cross-flow should be an accurate simulation of the velocity profile and turbulence intensity components of the natural wind.

Advisor: Thornton, G
The entrance-portico in the architecture of Great Britain, 1630-1850

This thesis attempts to account for the appearance, persistence, and eventual decline of an architectural motif, derived from ancient pagan temples, widely used as the principal feature on an increasing variety of building types in Britain, during the period 1630 to 1850.
The thesis seeks to do this by defining both the word 'portico' and the architectural forms to which, historically, it was applied, and by examining the religious, political, social, and stylistic contexts in which the portico, as a metaphor for the temple, was utilized.
The rationalization within the Vitruvian-Christian tradition of the ancient temple's pagan connotations; the portico's intrinsic capacity to symbolize virtue, distinction, and authority; the changing perceptions of the idea of the temple; and the different nature and sources of both the authority and the architectural style which the portico expressed, are investigated. Architecturally, the portico expressed grandeur, centrality, and an entry; it controlled, defined, and gave focus to urban space.
Introduced to Britain by Inigo Jones, and based on classical Roman and Palladian models but with Salomonic overtones, the portico initially symbolized Stuart dynastic claims to divine kingship. As political and economic power shifted to an aristocratic oligarchy, the temple that was Britain, Rome's heir, symbolized a church and state united, and the secular virtues of the Augustan age. Palladio's fusion of Roman temple and villa provided the model for the oligarchy's power base, the porticoed country house. Archaeology and politics combined, first to project mercantile opulence through imperial Roman-inspired neo-classicism, then the more fundamental qualities of the Greek temple. The Pantheon gave way to the Parthenon; the temple of private wealth to the imagined temple of democracy.
After epitomizing the characteristic early nineteenth-century public style, the too-pagan Greek portico succumbed - as did the classical ideal - in the anarchy of styles, to the Gothic.
The genetics of handedness and dyslexia

The population level bias towards right-handedness in humans implies left-hemisphere dominance for fine motor control. Left-handedness and reduced cerebral asymmetry have been linked to neurodevelopmental disorders such as dyslexia. Understanding the biology of these traits at a genetic level is crucial for understanding the relationship between handedness and neurodevelopmental disorders.
Here I present genome-wide association study (GWAS) meta-analyses for both relative hand skill (handedness, n = 728) and reading-related traits (n = 548) in individuals with dyslexia. I uncovered a genome-wide significant association in an intron of PCSK6 associated with relative hand skill. PCSK6 is a protease that cleaves NODAL proprotein into an active form, and NODAL determines the development of left/right (LR) asymmetry in bilaterians. I performed pathway analyses of the GWAS data that revealed handedness is determined in part by the mechanisms that establish left/right (LR) asymmetry early in development, such as NODAL signalling and ciliogenesis. This finding replicated in a general population cohort unaffected with neurodevelopmental disorders (n = 2,666).
A key stage in LR asymmetry development is the rotation of cilia that creates a leftward flow of NODAL. Candidate genes for dyslexia are involved in both neuronal migration and ciliogenesis. Ciliopathies can cause not only LR body asymmetry phenotypes, but also cerebral midline phenotypes such as an absent corpus callosum. Furthermore, I identified a genome-wide significant association with non-word reading located in an intron of MAP1B, a gene involved in neuronal migration that causes an absent corpus callosum when disrupted in mice. However, this finding did not replicate in two independent cohorts with dyslexia (n = 156 & 199), or in the general population cohort (n = 2,359). Though these cohorts had inadequate reading measures and poorly matched ascertainment for dyslexia.
I also performed copy number variation (CNV) pathway and burden analyses of 920 individuals with dyslexia and 1,366 unselected controls, but did not find that rare CNVs play a major role in the etiology of dyslexia.
Based on these results I propose that common variants in genes responsible for ciliogenesis and corpus callosum development influence traits such as handedness and reading ability.

Keywords: Handedness
CNV
Dyslexia
Genome-wide association study
Genetics
Genomics
Advisor: Monaco, A
Webber, C
Morris, A
Halogen bonding interlocked host systems for recognition and sensing of anions

This thesis describes the synthesis of halogen bonding receptors for integration within interlocked anion host systems.
Chapter 1 introduces the field of supramolecular chemistry, with a particular focus on anion recognition and sensing, halogen bonding, and the synthesis of mechanically interlocked structures.
Chapter 2 describes the preparation and anion binding properties of carbazole-based receptor molecules. A systematic anion binding study on a series of halogen- and hydrogen-bonding 3,6-bis-triazolium carbazole acyclic receptors is described initially, followed by the development of a halogen bonding rotaxane. The anion and metal complexation properties of acyclic and macrocyclic systems incorporating the 1,8-bis-triazole carbazole motif are also presented.
Chapter 3 details the synthesis and anion complexation investigations of halogen and hydrogen bonding naphthalene-based acyclic and interlocked rotaxane host molecules.
Chapter 4 presents receptors based on the 4,4'-bis-triazole-2,2'-bipyridyl motif. A halogen bonding rhenium(I) bipyridyl complex is exploited in the development of a rotaxane host system which optically senses anions via luminescence purely through halogen bonding interactions. The anion recognition and sensing properties of diquat-based receptors are also investigated, and shown to exhibit optical and electrochemical responses to anions.
Chapter 5 summarises the major conclusions from Chapters 2-4.
Chapter 6 describes the experimental procedures used in the work, and includes characterisation data for the synthesised compounds.
Supplementary information relating to crystallographic data, and absorption, luminescence and electrochemical studies, is provided in the Appendices.

Keywords: rotaxane
anion
halogen bonding
Advisor: Beer, P
Immune modulation in normal and pathological human pregnancy

The first half of this thesis addressed the clinical question of whether the phenotype of peripheral immune cells is affected by the normal menstrual cycle and whether there are differences in women with recurrent unexplained miscarriage. In chapter 2, a mid-luteal type 1 shift was demonstrated in NKdim and cytotoxic T cells in the menstrual cycle. In addition, women with recurrent miscarriage had increased numbers of type 1 (IL-18R+) cytotoxic lymphocytes and an increased number of NKdim and NKbright cells in the mid-luteal phase of the cycle.
The shift to type 2 immunity seen in normal pregnancy has been previously identified from the second half of the first trimester. In chapter 3 this type 2 shift was seen in NK and T cells as early as 9 days post implantation. ST2L (the ligand for IL-33 and a marker of type 2 cells) was consistently up regulated at this very early stage post implantation in women who were pregnant.
The second half of this thesis investigated IL-33 and ST2 in normal and pathological pregnancy. In chapter 4 it was shown that circulating IL-33 did not change over the course of pregnancy but that sST2 (the soluble decoy receptor) increased significantly in the 3rd trimester of normal pregnancy. Both IL-33 and ST2 were variably expressed by the pre-implantation human blastocyst, as well as by the 1st and 3rd trimester placenta.
Finally, chapter 5 showed a potential role for ST2 in pre-eclampsia, an inflammatory disease of pregnancy. sST2 was significantly elevated in the third trimester in women who went on to develop pre-eclampsia even prior to the onset of disease. Using an in vitro model of placental perfusion, it was shown that sST2 can be secreted by the placenta, suggesting that sST2 may play a significant role in pregnancies complicated by this disease.

Keywords: immunology
pregnancy
recurrent miscarriage
NK cells
IL-33
ST2
implantation
Advisor: Sargent, I
Child, T
Distributive justice and global public goods

Public goods are goods that are non-rival and non-excludable. One person enjoying the benefits of a public good will not reduce the value of the good for others. And nobody within a particular population can be excluded from enjoying those benefits. While we often think of the relevant population being co-citizens of a state - national defence is taken to be the archetypal public good - in recent years the importance of public goods that benefit individuals across different countries has increasingly been recognised. We can refer to these as "global public goods".
When global public goods are supplied, various costs and benefits are generated, and these costs and benefits can be shared among countries in different ways. This thesis explores how justice requires us to share them; I develop a theory of distributive justice for global public goods. I begin by developing two principles for assigning the costs and benefits of supplying public goods within a state, and then argue that these should, for the most part, also govern the distribution of costs and benefits arising from global public good production. Finally, I assess how certain private goods that the supply of public goods make possible should be shared among states. The fact that these goods rely for their production on the supply of global public goods, I argue, will affect the principles of distributive justice that should govern these.

Keywords: global public goods
distributive justice
global justice
Advisor: Miller, D
Mutational analysis of membrane traffic in Arabidopsis thaliana

To identify novel and essential components of the plant membrane trafficking mechanisms, Arabidopsis membrane trafficking mutants from fluorescent protein-based forward genetic screens were characterized. First, four novel glutathione synthase (GSH2) mutant alleles featured swollen endoplasmic reticulum (ER)-derived bodies that accumulated a soluble secretory marker. Consistent with the role of GSH2 in glutathione biosynthesis, the loss-of-function mutant alleles exhibited gamma-glutamylcysteine (γ-EC) hyperaccumulation and glutathione deficiency. The aberrant ER morphology was ascribed to the γ-EC accumulation. Redox-sensitive fluorescent protein revealed that gsh2 seedlings maintained a reduced cytoplasm at steady state but were more sensitive to oxidative challenge. Second, Mut 21 was a conditional mutant that accumulated a secretory marker in the alkalized apoplast at restrictive temperature (31˚C). The mutant was identified as carrying a mutant allele of tuftelin-interacting protein 11 (TFIP11), which has been implicated in regulating redifferentiation and cell proliferation through a cytokinin signalling pathway. Hence, it was postulated that the changes in response to cytokinin affect auxin-mediated acidification of the apoplast. Third, Mut 43 was a conditional mutant that accumulated a soluble secretory marker in the ER and unidentified punctate structures at restrictive temperature, and exhibited perturbations in ER export of a soluble protein marker. Moreover, the mutant showed severe growth defects and abnormal radial root swelling in the apical elongation zone. A mutation identification method through deep-sequencing of the wild-type siblings in outcrossed heterozygous mutant families was developed and tested in Mut 43. At the time when this thesis was prepared, bioinformatic analysis has assigned Mut 43 to the bottom arm of chromosome two and predicted a 300kb mapping interval based on the observed bias in single nucleotide polymorphism ratios. This work demonstrates the feasibility of using forward genetics to study plant-specific aspects of membrane trafficking mechanisms and incorporates new technology to streamline the process of gene identification.

Keywords: forward genetics
Arabidopsis thaliana
membrane trafficking
Advisor: Moore, I
Econometric Issues in Forward-Looking Monetary Models.

Recently, single equation approaches for estimating structural models have become popular in the monetary economics literature. In particular, single-equation Generalized Method Moments estimators have been used for estimating forward-looking models with rational expectations. Two important examples are found in Clarida, Galí, and Gertler (1998) for the estimation of forward-looking Taylor rules and in Galí and Gertler (1999) for the estimation of a forward-looking model for inflation dynamics. In this thesis, we address the issues of identification which have been overlooked due to the incompleteness of the single-equation formulations. We provide extensions to existing results on the properties of GMM estimators and inference under weak identification, pertaining to situations in which only functions of the parameters of interest are identified, and structural residuals exhibit negative autocorrelation. We also characterize the power of the Hansen test to detect mis-specification, and address the issues arising from using too many irrelevant instruments as well as from general corrections for residual autocorrelation, beyond what is implied by the maintained model. In general, we show that the non-modelled variables cannot be weakly exogenous for the parameters of interest, and that they are informative about the identification and mis-specification of the model. Modelling the reduced form helps identify pathological situations in which the structural parameters are weakly identified and the GMM estimators are inconsistent and biased in the direction of OLS.We also find the OLS bias to be increasing in the number of over-identifying instruments, even when the latter are irrelevant, thus demonstrating the dangers of using too many potentially irrelevant instruments. Finally, with regards to the "New Phillips curve", we conclude that, for the US economy, this model is either un-identified or mis-specified, casting doubts on its utility as a model of inflation dynamics.
Interaction of proteins with oligo(ethylene glycol) self-assembled monolayers

The aim of this thesis is the study of protein resistant oligo(ethylene glycol) (OEG) self-assembled monolayers (SAMs) using in situ techniques, such as neutron reflectivity (NR), polarisation modulation infrared spectroscopy (PMIR) and small-angle x-ray scattering (SAXS). In order to elucidate the mechanisms that lead to the nonfouling properties of these SAMs, the SAM-water, protein-protein and protein-SAM interactions have been studied separately.
NR measurements, focused on the solid-liquid interface between OEG SAMs and water, show clear evidence of an extended layer with reduced density water. The reduction in density is up to 10% compared to the bulk value, and extends up to 5 nm into the bulk. The effective area (density reduction x length) of this reduced density water layer did not significantly change when the temperature was reduced to 5°C. In a complementary study, the interaction of water with protein-resistant HS(CHV2)11(OCH2CH2)3OMe monolayers was examined using in and ex situ PMIR. In particular, shifts in the position of the characteristic C-O-C stretching vibration were observed after the monolayers had been exposed to water. The shift in frequency increased when the SAM was observed in direct contact with a thin layer of water. It was found that the magnitude of the shift also depended on the surface coverage of the SAM. These results suggest a rather strong interaction of oligo(ethylene glycol) SAMs with water and indicate the penetration of water into the upper region of the monolayer. These findings indicate the presence of a tightly bound water layer at the SAM-water interface.
Further NR studies of the interface between OEG SAMs and a highly concentrated protein solution revealed an oscillating protein density profile. A protein depleted region of about 4-5 nm close to the SAM was followed by a more densely populated region of 5-6 nm. These oscillations were then rapidly damped out until the bulk value was reached. The influence of temperature and salt concentration on the protein density profile was small, indicating a rather minor contribution of electrostatic interactions to the protein repulsive force. SAXS measurements of OEG coated gold colloids mixed with proteins in solution did also not show any pronounced salt concentration dependence of the colloid-protein interaction.
The strong association of water with the SAM and the layer of tightly bound water, together with the lack of electrostatic repulsion, suggest that the adsorption of proteins is energetically hindered by the presence of a strongly bound hydration layer.

Advisor: Schreiber, F
Characterisation of cytoplasmic uridyl transferases in yeast and human cells

Regulation of gene expression by terminal addition of uridyl residues to RNA substrates has recently emerged as a widespread phenomenon in eukaryotes. Studies in organisms ranging from fission yeast to human cells have shown that uridylation of RNA 3' ends stimulates rapid RNA degradation. However, many questions regarding the specificity of the uridyl transferases, the broad range of their substrates and the consequences of their loss are still unanswered. In light of this, the uridyl transferases Cid1 in Schizosaccharomyces pombe and ZCCHC11 in human cells and their roles in the regulation of gene expression were further characterised in this study. To begin with, the biochemistry of the Cid1 protein complex responsible for uridylation in Schizosaccharomyces pombe was analysed in more detail by mass spectrometry and in vitro assays. These experiments provided insights into the modulation of Cid1 activity by accessory factors. Next, the role of the human uridyl transferase ZCCHC11 in the regulation of replication- dependent histone mRNAs was examined. Results showed that ZCCHC11 is required for efficient destabilisation of histone mRNAs following inhibition or completion of DNA replication. In agreement with this finding, cDNA sequencing experiments showed that ZCCHC11-mediated uridylation is particularly prevalent at the end of S phase. Finally, this thesis also explored the phenotype resulting from ZCCHC11 knock-down with respect to the human cell cycle. Depletion of ZCCHC11 led to the occurrence of DNA damage and activation of the DNA integrity checkpoint, which in turn resulted in cell cycle delay. Taken together, the data presented in this thesis extend current knowledge of the uridyl transferases and their actions in fission yeast and human cells and provide a link between RNA regulation and cell cycle control.

Keywords: uridylation
cell cylce
ZCCHC11
Cid1
Advisor: Norbury, C