VictorJuiz/thesis huggingface dataset:
High resolution CMB physics

This thesis presents the measurement of the cosmic microwave background (CMB) power spectrum for the Atacama Cosmology Telescope (ACT) experiment and its polarized upgrade, ACTPol. I present the tools that I have developed for constructing unbiased and nearly optimal statistical estimators. I discuss how to separate the cosmological and the astrophysical signal and how to characterize instrumental systematics. The goal of this work is to obtain accurate power spectra measurement that can be used for cosmological parameter estimation.
I first present the analysis of the complete ACT data set. The high resolution of the telescope allows us to recover power spectra to &ell; = 10000. I report the measurement of the power spectra at 148 GHz and 218 GHz, as well as the cross-frequency spectrum between the two channels. The power spectrum measurement is consistent with the ΛCDM model and a basic foreground model.
I then present the cross correlation of maps from the Atacama Cosmology Telescope with maps from the Planck satellite in two overlapping regions covering 592 square degrees. I find excel- lent agreement between the two datasets at both frequencies, quantified using the variance of the residuals between the ACT power spectra and the ACT×Planck cross-spectra.
The next generation of CMB experiments are focused on measuring its polarization. I present efficient algorithms for CMB lensing simulation and power spectrum estimation for flat-sky CMB polarization maps.
Finally, I discuss the first temperature and polarization power spectra measurement from the ACTPol experiment. They are the first attempt to measure the polarization of the CMB at high resolution.

Keywords: Cosmic Microwave Background
Advisor: Dunkley, J
Heart function in mouse models of muscular dystrophy

Duchenne muscular dystrophy (DMD) is an X-linked recessive disease caused, in most cases, by the complete absence of the 427 kD cytoskeletal protein, dystrophin. Without dystrophin, the dystrophin-associated protein complex (DAPC) does not form and the plasma membrane is destabilised. There is no effective treatment and affected individuals die from respiratory failure and cardiomyopathy by age 30. This thesis describes experiments in which in vivo cardiac function was measured using non-invasive magnetic resonance imaging in a number of mouse models relevant to muscular dystrophy. As syncoilin forms a link from the DAPC to the cytoskeleton, it was postulated in Chapter 3 that the syncoilin knockout mouse would have cardiac defects similar to those caused by the loss of dystrophin. However, the loss of syncoilin did not alter the protein levels of its binding partners, measured by western blotting, and caused no defect in heart function or structure, measured using histological staining. Similarly, in Chapter 4, a mouse with a mutation in the transient receptor potential channel canonical type 3 (TRPC3), a receptor/stretch-activated cation channel thought to be involved in the pathogenesis of DMD, was found to have no functional or morphological cardiac defect. In the mdx mouse, a mouse model of DMD that lacks dystrophin, cardiomyopathy was prevented by either increasing levels of the dystrophin related protein, utrophin, or of dystrophin, in the diaphragm, which thereby restored diaphragm function. In Chapter 5 it was found that in a transgenic mdx mouse in which utrophin was over-expressed in skeletal muscle and diaphragm, but not in the heart, cardiac function was restored to wild-type levels. However, histologically the transgenic heart showed more fibrosis and immune cell infiltration than that of untreated mdx controls. In Chapter 6 it was found that in mdx mice treated with a peptide-conjugated phosphorodiamidate morpholino oligomer (PPMO), that resulted in high dystrophin restoration in skeletal muscle and diaphragm only, cardiac function was also restored to wild-type levels. In Chapter 6 it was also found that in dystrophin/utrophin-deficient double-knockout (dKO) mice, a more severely affected animal model of DMD, treatment with a PPMO again produced high levels of dystrophin only in skeletal muscle and diaphragm, and once more restored cardiac function to wild-type levels. In the dKO mouse, there was no difference in heart function between treatment of the diaphragm plus the heart and treatment of the diaphragm alone. Restoration of diaphragm and other respiratory muscle function, irrespective of the method used, was sufficient to prevent cardiomyopathy in dystrophic mice. The novel mechanism of treating respiratory muscles to prevent cardiomyopathy in dystrophic mice has implications for the study of heart function in the current DMD mouse models and suggests a new approach to treatment.

Keywords: DMD
muscular dystrophy
heart function
Advisor: Davies, K
Clarke, K
Branch groups and automata

The focus of this thesis is finitely generated subgroups of the automorphism group of an infinite spherically homogeneous rooted tree (regular or irregular). The first chapter introduces the topic and outlines the main results. The second chapter provides definitions of the terminology used, and also some preliminary results. The third chapter introduces a group that appears to be a promising candidate for a finitely generated group of infinite upper rank with finite upper
p
-rank for all primes
p
. It goes on to demonstrate that in fact this group has infinite upper
p
-rank for all primes
p
. As a by-product of this construction, we obtain a finitely generated branch group with quotients that are virtually-(free abelian of rank
n
) for arbitrarily large
n
. The fourth chapter gives a complete classification of ternary automata with
C
2
-action at the root, and a partial classification of ternary automata with
C
3
-action at the root. The concept of a `windmill automaton' is introduced in this chapter, and a complete classification of binary windmill automata is given. The fifth chapter contains a detailed study of the non-abelian ternary automata with
C
3
-action at the root. It also contains some conjectures about possible isomorphisms between these groups.

Keywords: Automata
Automaton
Advisor: Segal, D
The roles of Flrt2 and Flrt3 cell surface proteins during mouse development

Embryos morphogenesis relies on the interactions between different tissues and their constituent cells. These interactions are controlled by different signalling and adhesion molecules, such as the Fibronectin Leucine-rich Repeat transmembrane (Flrt) family of proteins. The closely related Flrt2 and Flrt3 share 45% amino acid sequence identity, and show several sites of co-expression in the developing mouse embryo. Experiments in this laboratory have shown that mice deficient in either one of Flrt2 or Flrt3 are embryonic lethal due to cardiac insufficiency, and structural defect in the AVE and a fusion failure of the lateral body walls of the embryo respectively. The highly conserved structural features shared between Flrt2 and Flrt3 suggest possible shared functional roles between the two closely related genes. The aims of this study were first to generate a Flrt2 and Flrt3 double mutant embryos, and examine the hypothesis that the two genes function cooperatively at sites of their co-expression. The second goal was to generate a Flrt2 LacZ reporter and a conditional alleles, using the EUCOMM/KOMP resource, to further analyse Flrt2 expression patterns and function.
Flrt2 and Flrt3 double mutant embryos were embryonic lethal at embryonic day (E) 10. The genetic experiment designed in this study suggests that Flrt3 seems to function in cooperation with Flrt2, to maintain tissue integrity in the developing mouse embryo as loss of both exhibits a more severe phenotype than the single mutants, and has a more severe impact on the embryonic development.
The Flrt2 LacZ reporter and conditional alleles generated in this study were shown to be useful tools in dissecting Flrt2 expression patterns, and can be used in further experiments to study the expression of Flrt2 in particular sites that have not been studied or extensively mentioned in the literature, or in site-specific deletion of Flrt2 in tissues where Flrt2 is expressed but the function has not been elucidated.

Keywords: cell biology
Advisor: Robertson, E
A semisynthetic protein nanoreactor for single-molecule chemistry

The covalent chemistry of individual reactants bound within a protein nanopore can be monitored by observing the ionic current flow through the pore, which acts as a nanoreactor responding to bond-making and bond-breaking events. However, chemistry investigated in this way has been largely confined to the reactions of thiolates, presented by the side chains of cysteine residues. The introduction of unnatural amino acids would provide a large variety of reactive side chains with which additional single-molecule chemistry could be investigated.
An efficient method to incorporate unnatural amino acid is semisynthesis, which allows site-specific modification with a chemically-defined functional group. However, relatively little work has been done on engineered membrane proteins. This deficiency stems from attributes inherent to proteins that interact with lipid bilayer, notably the poor solubility in aqueous buffer.
In the present work, four different derivatives α-hemolysin (αHL) monomer were obtained either by two- or three-way native chemical ligation. The semisynthetic αHL monomers were successfully refolded to heptameric pores and used as nanoreactors to study single-molecule chemistry. The semisynthetic pores show similar biophysical properties to native αHL pores obtained from an in vitro transcription and translation technique. Interestingly, when αHL pores with one semisynthetic subunit containing a terminal alkyne group were used to study Cu(I)-catalyzed azide-alkyne cycloaddition, a long-lived intermediate in the reaction was directly observed.

Keywords: single-molecule chemistry
semisynthesis
CuAAC
alpha-hemolysin
Advisor: Bayley, H
Individual differences in complex grammar acquisition: causes and consequences

A longitudinal study lasting 3.5 years was conducted to investigate complex grammar development, focusing on acquisition of the passive and type 3 conditionals, and its relationship with a number of domain-general, domain-specific and environmental factors.
128 children (M = 5 years 10 months) were tested at the beginning and towards the end of each school year starting from Year 1. The administered measures included established tests of fluid intelligence, short-term and working memory, seriation, grammar, vocabulary, literacy and arithmetic, plus newly-developed tests of passive and conditional sentence acquisition, and arithmetic word problem solving.
It was demonstrated that grammar acquisition is not complete even when children start Year 4 of primary school (M = 8 years 7 months), when the current study was completed. At that time, 32% of children have not acquired type 3 conditionals and 89% showed no understanding of centre-embedded sentences. However, only 3% showed no passive sentence acquisition.
Fluid intelligence, verbal STM and WM, ability to seriate, vocabulary and parental education level were all found to contribute to individual differences in complex grammar acquisition, independently of age differences and, where relevant, independently of non-verbal ability. There were differences between the passives and the conditionals in their relationship to these variables.
Complex grammar development was found to be a significant predictor of reading comprehension, spelling and arithmetic performance, independently of age, non-verbal ability, verbal STM and WM.
The findings demonstrate the inter-relatedness of higher cognitive functions, particularly domain-general with domain-specific ones. Modularity in its strictest sense (informational encapsulation, functional isolation) is not present in normally developing brains. Educational applications of the results are discussed.

Keywords: language development
arithmetic learning
cognitive development
literacy learning
grammar acquisition
neuroconstructivism
mathematical development
Advisor: Mellanby, J
McLeod, P
Portfolio Selection in Incomplete Markets with Utility Maximisation

The problem of maximizing the expected utility is well understood in the context of a complete financial market. This dissertation studies the same problem in an arbitrage-free yet incomplete market. Jin and Zhou have characterized the set of the terminal wealths that can be replicated by admissible portfolios. The problem is then transformed into a static optimization problem. It is proved that the terminal wealth is attainable for all utility functions when the market parameters are deterministic. The optimal portfolio is obtained explicitly when the utility function is logarithmic even if the market parameters follow stochastic processes. However we do not succeed in extending this result to the power utility function.
Politics, property, and progress

This thesis attempts to provide an account of radical thought in Britain, 1760 to 1815, by way of a study of the tracts, pamphlets and articles of the major radical ideologues. It begins by examining the assumptions made by the radicals in respect of nature and human nature, material and moral progress, and liberty and equality. The differences revealed in relation to the basic assumptions are then analysed in the context of the major questions of politics, property and progress. On the issue of political liberty distinctions are made between mixed constitutionalist radicals and republicans, democratic or otherwise, and between those who adopted a "radical" as opposed to a "moderate" approach to voting rights. Special attention is given to Thomas Spence's and William Godwin's views on decentralization and democracy and to the radical case for an armed citizenry. Regarding property and progress a major distinction is drawn between agrarian and commercial radicals according to attitudes taken on the emergence and development of modern commercial society. The different versions of the agrarian alternative are considered and the reformist, communitarian and revolutionary approaches to agrarianism examined. In relation to commercial radicalism a distinction is drawn between Smithian and artisan approaches to the meaning of equality of opportunity and connected with a change in the social composition of the radical movement in the 1790s. A chapter is devoted to James Burgh who synthesized aspects of agrarianism and commercial radicalism. The final section of the thesis considers the alternatives proposed for the achievement of radical ends. A distinction is drawn between reformers and revolutionaries and two chapters given over to consideration of the special contributions of William Godwin and the young Coleridge. It is concluded that radical ideology is best understood as a synthesis of civic humanism and Lockean liberalism and that the class perceptions of particular radicals are important in understanding the different ways they develop the radical case.
Electron paramagnetic resonance studies of artificial supramolecular structures and biological systems

The research described in this thesis employs a variety of Electron Paramagnetic Resonance (EPR) techniques for the study of the electronic and structural properties of artificial supramolecular porphyrin systems and of protein complexes of biological relevance.
The electron delocalisation in the cationic radical and photoexcited triplet states of linear and cyclic Π-conjugated multiporphyrin arrays was investigated. In the radical cations, information on the extent of delocalisation can be inferred from the measurement of hyperfine couplings, either indirectly from the continuous wave EPR spectrum or directly using pulsed hyperfine EPR techniques. The results of room temperature EPR experiments showed complete delocalisation of the electron on the timescale of the EPR experiments, but frozen solution EPR measurements revealed localisation onto mainly two to three porphyrin units in the larger porphyrin systems.
Information on the delocalisation of the triplet state in the same porphyrin systems is contained both in the hyperfine couplings and in the zero-field splitting (ZFS) interaction. The results outlined in this thesis show that the hyperfine couplings provide a much more accurate estimate of the extent of delocalisation. The trends in proton and nitrogen hyperfine couplings with the size of the porphyrin systems indicate uneven spin density distributions over the linear arrays, but complete delocalisation in the cyclic systems. Time-resolved EPR and magnetophotoselection experiments have shown a reorientation of the zero-field splitting tensor between a single porphyrin unit and longer linear arrays, resulting in alignment of the main optical transition moment and the Z axis of the ZFS tensor.
Continuous wave and pulsed dipolar EPR techniques were employed for the determination of the structure of two different protein complexes, the homomultimeric twin-arginine translocase A (TatA) protein channel and the ferredoxin-P450 complex of the electron transport chain in Novosphingobium aromaticivorans. The interaction between nitroxide spin labels introduced at different positions of the TatA monomer was investigated in the complex reconstituted in detergent micelles by analysing the dipolar broadening of the EPR spectra and the results of three- and four-pulse Double Electron-Electron Resonance (DEER) measurements. In combination with results from NMR and molecular dynamics calculations, a structure for the channel complex was proposed.
The structure of the ferredoxin-cytochrome P450 complex was investigated by orientation-selective DEER between nitroxide labels introduced on the cytochrome P450 protein and the iron-sulfur cluster of the ferredoxin. The distance and orientation information contained in the experimental DEER data was interpreted in terms of a structural model of the protein complex by orientation-selective DEER simulations combined with a modelling approach based on protein-protein docking.

Keywords: hyperfine interaction
ENDOR
triplet state
EPR
protein structure
radical cation
DEER
porphyrins
HYSCORE
Advisor: Timmel, C
Single photon generation and quantum computing with integrated photonics

Photonics has consistently played an important role in the investigation of quantum-enhanced technologies and the corresponding study of fundamental quantum phenomena. The majority of these experiments have relied on the free space propagation of light between bulk optical components. This relatively simple and flexible approach often provides the fastest route to small proof-of-principle demonstrations. Unfortunately, such experiments occupy significant space, are not inherently phase stable, and can exhibit significant scattering loss which severely limits their use. Integrated photonics offers a scalable route to building larger quantum states of light by surmounting these barriers.
In the first half of this thesis, we describe the operation of on-chip heralded sources of single photons. Loss plays a critical role in determining whether many quantum technologies have any hope of outperforming their classical analogues. Minimizing loss leads us to choose Spontaneous Four-Wave Mixing (SFWM) in a silica waveguide for our source design; silica exhibits extremely low scattering loss and emission can be efficiently coupled to the silica chips and fibers that are widely used in quantum optics experiments. We show there is a straightforward route to maximizing heralded photon purity by minimizing the spectral correlations between emitted photon pairs. Fabrication of identical sources on a large scale is demonstrated by a series of high-visibility interference experiments. This architecture offers a promising route to the construction of nonclassical states of higher photon number by operating many on-chip SFWM sources in parallel.
In the second half, we detail one of the first proof-of-principle demonstrations of a new intermediate model of quantum computation called boson sampling. While likely less powerful than a universal quantum computer, boson sampling machines appear significantly easier to build and may allow the first convincing demonstration of a quantum-enhanced computation in the not-distant future. Boson sampling requires a large interferometric network which are challenging to build with bulk optics, we therefore perform our experiment on-chip. We model the effect of loss on our postselected experiment and implement a circuit characterization technique that accounts for this loss. Experimental imperfections, including higher-order emission from our photon pair sources and photon distinguishability, are modeled and found to explain the sampling error observed in our experiment.

Keywords: integrated optics
boson sampling
quantum computing
quantum optics
heralded single photon source
Advisor: Walmsley, IA
The effects of farm size and management system on agricultural production in Iran

During the last two decades two major government policies aimed at bringing structural changes in the system of land tenure in Iran have been implemented. The first was the Land Reform of 1962-66, which transferred the ownership of the land from the large landlords to the peasant and tribal producers. But during the late-sixties and the seventies a second major structural change in the system of land tenure was proposed by the government, this time aimed at the destruction of the already existing peasant, tribal and capitalist producers and the creation of very large-scale agricultural corporations. As the main objective of this policy was to bring about substantial increases in agricultural production and productivities, it is the purpose of this dissertation to examine whether these very large-scale corporations are more productive systems than the already existing autonomous producers. As the proponents of the very large-scale farms argue in terms of gains from economies of scale in very large units and of the superiority of the trained and skilled corporate managers to the family managed peasant farmers, in this dissertation an attempt has been made to examine the effect on productivity of (a) farm size and (b) management system. The following procedure has been adopted to examine the subject.
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Town and Gown: Amateurs and Academics.

This investigation into the origin of a collection of nineteenth century lanternslides revealed evidence of the social, intellectual and cultural importance of various scientific societies in Oxford, and the contributions made by those involved, particularly the creator of the lanternslides, H. M. J. Underhill, (1855–1920). Evidence gathered from primary sources showed a fluidity of relationships between the supposed ‘town and gown’ in late nineteenth century Oxford which consisted of a community of citizens, amateurs and academics, all of whom were linked by a growing interest in the real and mythological British past. Following a discussion of the key intellectual and social influences in Britain during the latter half of the nineteenth century, including the implications of the emerging evidence of an ancient human past, the thesis focuses on individual case studies. They illustrate the roles of overlooked or neglected individuals whose work contributed to the growth of today’s discipline of British prehistory. Several people, now forgotten, including Underhill were contemporaries of Arthur Evans and Edward Tylor whose social circumstances made it easier for them to become prominent academics. The results of this research indicate that a new approach is required in the history of archaeology; one that would draw attention to the vital contributions made by forgotten or overlooked individuals, societies and popular publications. Further attention to these issues will shed new light on the way that prehistoric archaeology moved from an antiquarian pastime to an academic discipline between 1850 and 1900.

Keywords: intellectual history
local societies Underhill
Oxford
social
British prehistory
lanternslides
amateur archaeology
Advisor: Gosden, C