VictorJuiz/thesis huggingface dataset:
Studies in peptide synthesis

One of the most important considerations in peptide synthesis is the avoidance of loss of optical activity at the asymmetric centres of the amino-acids when these are condensed together. This racemisation is undesirable not only because it limits the yield of required product but also because the presence of even traces of racemates or disaster- eoisomers may inhibit crystallisation of a peptide, thus rendering purification more difficult.
The most commonly employed amino protecting group, the benzyloxycarbonyl group, confers a remarkable optical stability upon the amino-acid which it protects, and the observation that a benzyloxycarbonyl amino-acid may be coupled without danger of racemisation under conditions which may cause considerable loss of activity when the benzyloxycarbonyldi-peptide, so formed, is coupled further, led to a much greater awareness of the problem. Thus, in 1955, North and Young initiated a study of coupling reactions from the point of view of racemisation, using the condensation of acetyl- L-leucine with glycine ester as a model reaction. They found that the azide procedure was remarkably free from the danger of racemisation but other procedures, including those which have been postulated to involve amino-activation, may result in considerable loss of activity.
[Please see pdf. for full abstract.]
Applications of optical-cavity-based spectroscopic techniques in the condensed phase

Cavity ring-down spectroscopy (CRDS) and cavity enhanced absorption spectroscopy (CEAS) are two well-established absorption spectroscopic techniques originally developed for gas-phase samples. Condensed-phase applications of these techniques still remain rare, complicated as they are by additional background losses induced by condensed-phase samples as well as the intracavity components in which the sample is constrained. This thesis is concerned with the development and application of optical-cavity-based techniques in the condensed phase.
Polarization-dependent evanescent wave CRDS (EW-CRDS) has been used to study the molecular orientation at the solid/air and solid/liquid interfaces. An increase in average orientation angle with respect to the surface normal has been observed for both methylene blue and coumarin molecules as a function of coverage at the fused silica/air interface. An orientation-angle-dependent photobleaching of pyridin molecules at the fused silica/methanol interface have also been observed. EW-CRDS has also been used to monitor slow in situ photobleaching of thin dye films deposited on the prism surface. The photobleaching dynamics is interpreted as a combination of first- and second-order processes.
A significant fraction of this thesis has been devoted to studying magnetic field effects (MFEs) on the kinetics of the radical pair (RP) reactions in solution, in an effort to understand the ability of animals to sense the geomagnetic field. Two novel optical-cavity-based techniques – broadband CEAS (BBCEAS) and CRDS have been developed for this purpose. BBCEAS uses a supercontinuum (SC) source as the cavity light source and a CCD camera as photodetector, enabling simultaneous acquisition of absorption spectrum across the whole visible region (400 – 800 nm). In CRDS, a tunable optical parametric oscillator has been used as the cavity light source. Combined with the switching of external magnetic field (SEMF) method, this technique allows the decay kinetics of the geminate RPs to be monitored, with nanosecond resolution. Both BBCEAS and CRDS provide sensitivity superior to single-pass transient absorption (TA), a technique traditionally used in the MFE studies. A series of photochemical systems have been studied by BBCEAS and CRDS, respectively, among which, the MFEs of drosophila melanogaster cryptochrome has been observed. Importantly, this is the first time an MFE has been observed in an animal cryptochrome, and provides key supporting evidence for the cryptochrome hypothesis of magnetoreception in animals. Besides the optical-cavity-based techniques, a novel fluorescence detection method of MFEs has also been demonstrated. This technique proved ultrahigh sensitivity when applicable.

Keywords: molecular orientation
evanescent wave CRDS
magnetic field effects
cavity ring-down spectroscopy
cryptochrome
broadband CEAS
laser spectroscopy
cavity enhanced absorption spectroscopy
radical pair
photobleaching
optical cavity
fluorescence
Advisor: Mackenzie, S
Religious life for women from the twelfth century to the middle of the fourteenth century with special reference to the English foundations of the Order of Fontevraud

The Order of Fontevraud, founded in 1100 by the hermit/preacher Robert of Arbrisssel was the only twelfth-century women's order incorporating into its structure a group of chaplains and lay brothers whose specific role was to serve the nuns. This thesis examines the origins of the order and demonstrates that the English foundations were a stage in its development, closely linked to its Angevin connections. Each of the two houses established in England c.l 150 was founded and patronised by supporters of Henry Plantagenet. Westwood, founded by the de Say family, lesser barons from Herefordshire, received a modest endowment. Nuneaton, founded by the magnate Robert, earl of Leicester, was richly endowed. Twenty years later Henry II expelled the Benedictine community from Amesbury replacing it with a group from Fontevraud, thus founding the third house. A fourth, Grovebury, is not treated; it was never a foundation for women.
I have studied the process of endowment and shown that the wealth and status of the founder in no small measure determined the future prosperity of the foundation. The internal organisation of the Fontevraud houses has been explored, in particular the balance between local autonomy and dependence on the mother house. As well, I have examined recruitment and shown that this, too, reflected on the circumstances of foundation.
My main focus has been on the economy of these three houses, their income and expenditure and the exploitation of their assets. The nuns are seen as a group of women who were dynamic and creative in managing their affairs. This has not precluded an investigation into the spiritual, and in particular, the liturgical dimension of life in the English foundations. Fundamentally the Order of Fontevraud is presented as an opportunity for noble women of England in the twelfth and thirteenth centuries to live religious life in a new order, one renowned for its strict interpretation of the Rule of St Benedict and for the prayerfumess of its members, and one in which women were manifestly in control of their own destinies.
Fluorescence microscopy investigation on residual stresses in alumina-based ceramics

Grinding/polishing and indentation induced residual stresses were measured by confocal Cr3+ fluorescence microscopy with high spatial resolution (~2 μm),obtaining local stress variation information rather than the mean stress averaged over a large sampling volume as is measured by other techniques.
Due to the translucency of alumina materials, a substantial portion of the fluorescence signal comes from beneath the surface of the specimen. A probe response function (PRF) was developed taking account of microscope resolution, refraction, absorption and scattering, to quantitatively describe where the collected signal came from. It described the fluorescence intensity variations against defocus distance very well for a range of materials including sapphire, ruby, polycrystalline alumina and AI2O3/SiC nanocomposites.
Large variations in the residual stresses on ground and polished surfaces were observed, owing to the surface fracture and pullouts. The broad peaks and narrow peaks separated from the spectra collected near the ground/polished surfaces physically represented the two distinct regions in the ground region: a plastically deformed surface layer and the elastically deformed material underneath. A model for the residual stress field taking into account the pullout was proposed using an array of virtual dislocations. The model agreed with the experimental results well when the PRF was included. Tensile stresses were detected on the ground surfaces of polycrystalline aluminas and 2 vol.% SiC nanocomposite, but not on the polished surfaces of polycrystalline aluminas or ground surfaces of 5 and 10 vol.% SiC nanocomposites. This was explained in terms of difference in the amount of pullouts on the surfaces. The depth of deformation was deeper in the ground polycrystalline alumina compared to the polished condition; the depth of deformation in alumina and the AI2O>sub>3
/SiC nanocomposites were similar (~1 μm) while the compressive stresses in the nanocomposites were greater owing to the reduction in pullout. The main difference between ground alumina and AI2O3/SiC nanocomposites was the brittle fracture behavior rather than the plastic deformation.
Line scans and area mapping were carried out on 1 kg loaded Vickers indentations of alumina-based ceramics. Tensile stresses were found at the tips of radial cracks and lateral cracks and compressive stresses were found around the indent impression. The line scan results in the elastic regions agreed qualitatively with Yoffe's model and the quantitative discrepancy was attributed mainly to the cracking that relaxed the stresses. The differences in residual stresses between alumina and AI2O3/SiC nanocomposites were small if measured with high spatial resolution but it would be exaggerated with lower resolution.

Advisor: Todd, R
Cationic titanium amidinate and guanidinate complexes

This Thesis describes the synthesis and characterisation of half-sandwich complexes supported by κ1-amidinate and κ1-guanidinate ligands as well as the cationic species produced on activation. The chemistry of the cationic species is detailed and DFT studies which have also been carried out to elucidate the bonding in relevant complexes are also presented.

Keywords: catalysis
Titanium
Inorganic chemistry
Advisor: Mountford, P
Decisions under uncertainty: common processes in birds, fish and humans

Decision making is a framework we impose on a vast universe of possible behaviors to better understand the advantages and disadvantages of acting in different ways. Decisions under uncertainty are of particular interest because stochasticity is a feature of environments both today and throughout evolutionary history. As a result, we might expect decision makers (DMs) to have evolved mechanisms to handle variability. In this dissertation, I examine common decision processes in several model species: European starlings (Sturnus vulgaris), Banded tetras (Astyanax fasciatus) and humans (Homo sapiens). The broad range of approaches discussed include currencies DMs are expected to maximize (Risk Sensitivity Theory, Expected Utility), the currencies DMs do maximize (e.g. long versus short term rate maximizing models), the representation of outcomes in memory (Scalar Expectancy Theory) as well as explicit choice mechanisms (Sequential Choice Model). The first section of this thesis discusses responses to risk, offering humans and starlings choices between options which deliver certain or variable outcomes. Starlings demonstrate sensitivity to changes in the probability of variable outcomes and strong support for local rate maximization. Humans appear similarly sensitive to their own accuracy when task difficulty is varied. When the DM’s affective state was manipulated, neither humans nor starlings exhibit changes in risk preferences, but the effectiveness of these manipulations used could not be confirmed. Another topic of inquiry is the effect of the DM’s state at the time of valuation learning. State dependent valuation learning is demonstrated for the first time in a fish species, but Within Trial Contrast is not observed in starlings. Lastly, two experiments find strong support for the Sequential Choice Model, a promising new model of the mechanism of choice. Taken together, these experiments offer a glimpse into shared decision processes, but leave open questions about the mechanisms through which value is acquired.

Keywords: Decision Making
Sturnus vulgaris
Animal Behaviour
Starlings
Decision Making in Animals
Comparative Cognition
Advisor: Kacelnik, A
Modelling technology in agriculture and manufacturing using cross-country panel data

Why do we observe such dramatic differences in labour productivity across countries in the macro data? This thesis argues that the growth empirics literature oversimplifies the complexity of the production process across countries and neglects data cross-section and time-series properties, leading to bias in the empirical estimates. Chapter 1 presents two general empirical frameworks for cross-country productivity analysis and demonstrates that they encompass the growth empirics literature of the past decades. We introduce our central argument of cross-country heterogeneity in the impact of observables and unobservables on output and develop this against the background of the pertinent time-series and cross-section properties of macro panel data. Chapter 2 uses data from 48 countries to estimate manufacturing production functions. We discuss standard and novel estimators, focusing on their treatment of parameter heterogeneity and data time-series and cross-section properties. We develop the Augmented Mean Group (AMG) estimator and show its similarity to the Pesaran (2006) Common Correlated Effects (CCE) approach. Our results confirm parameter heterogeneity across countries in the impact of observable inputs on output. We check the robustness of this finding and highlight its implications for empirical measures of TFP. Chapter 3 investigates the heterogeneity of agricultural production technology using data for 128 countries. We develop an extension to the CCE estimators which allows us to suggest that TFP is structured such that countries with similar agro-climatic environment are influenced by the same unobserved factors. This finding offers a possible explanation for the failure of technology-transfer from advanced countries of the temperate 'North' to developing countries of the arid/equatorial 'South'. Our Monte Carlo simulations in Chapter 4 investigate the performance of the AMG, CCE and standard (micro-)panel estimators. Failure to account for cross-section dependence is shown to result in serious distortion of the empirical estimates. We highlight scenarios in which the AMG is biased and offer simple remedies.

Keywords: common factor model
cross-country productivity analysis
nonstationary panel econometrics
technology heterogeneity
Advisor: Teal, F
Bond, S
Half spaghetti- half Knödel: cultural division through the lens of language learning

South Tyrol, which is situated on the border between Austria and Italy, has been considered a 'peace model' by many nation-states since the creation of the province's autonomy statutes. The objective of these statutes was to allow for minority protection of the German- and Ladin-speaking communities while also permitting Austria to be the 'protector' of South Tyrol even though the province is situated in Italy. Another bi-product of these statutes was the creation of the 'separate but equal' education system, which allowed the German-, Italian- and Ladin-speaking communities to have individual schools in order to protect their culture and language identity.
In the past several decades, there has been an increase in 'mixed' marriages with members of differing language groups producing bilingual children. Additionally, civil service positions now require that all applicants have a mandatory comprehension of the L2, or in some cases L3, in order to apply for certain posts. As the education system tries to adjust to local concerns regarding the insufficient teaching of the L2 in monolingual education, the concept of South Tyrol as a 'peace model' is brought into question.
In this thesis, I examine how the South Tyrolean school system is reflective of society at large as its divided education mirrors the current fissures existent amongst the language communities. With parents looking for alternative measures to instruct their children in the L2, some residents would prefer a bilingual schooling option to encourage inter-group assimilation.
Furthermore, I discuss, outside of education, external social factors in the region which impact L2 learning creating language learning 'blocks' and 'victim' versus 'conqueror' mentalities. The objective of this research is to try and understand how South Tyrol continues to be in transition as the province adjusts to more bilingualism despite the historical need to preserve the language minorities.

Keywords: bilingualism
borders
education
multilingualism
South Tyrol
second language acquisition
Austria
language minorities
Italy
Advisor: Parkin, R
Ethical issues in the use of magnetic resonance imaging of the brain in newborn infants with hypoxic-ischaemic encephalopathy

Infants with hypoxic-ischaemic encephalopathy (birth asphyxia) have a high risk of death or disability. Those with poor prognosis are sometimes allowed to die after withdrawal of intensive care. In recent years, doctors have used new types of brain scan, magnetic resonance imaging (MRI), to predict the type and severity of impairment if the infant survives and to help with such decisions. In this thesis, I analyse the issues arising from the use of MRI for prognostication and decision-making in newborn infants. I argue that previous prognostic research has been hampered by a failure to identify and focus on the most important practical question and that this contributes to uncertainty in practice. I outline recommendations for improving research. I then look at existing guidelines about withdrawal of life-sustaining treatment. I identify several problems with these guidelines; they are vague and fail to provide practical guidance, they provide little or no genuine scope for parental involvement in decisions, and they give no weight to the interests of others. I argue that parental interests should be given some weight in decisions for newborn infants. I develop a new model of decision-making that, using the concept of a Restricted Life, attempts to set out clearly the boundaries of parental discretion in decision-making. I argue that where infants are predicted to have severe cognitive or very severe physical impairment parents should be permitted to request either withdrawal or continuation of treatment. I justify this model on the basis of overlapping interests, (prognostic, experiential and moral) uncertainty, asymmetrical harms, and the burden of care. In the conclusion, I set out a guideline for the use of MRI in newborn infants with hypoxic-ischaemic encephalopathy. I suggest that this guideline would provide a more robust, coherent and practical basis for decision-making in newborn intensive care.

Keywords: euthanasia
disability
cerebral palsy
decision-making
neuroethics
intellectual disability
Prognosis
Birth asphyxia
withdrawing treatment
neonatal intensive care
neuroimaging
medical ethics
Withholding treatment
MRI
Magnetic Resonance imaging
applied ethics
decision theory
Hypoxic ischaemic encephalopathy
Brain injury
Newborn infant
prognosis
Advisor: Hope, T
Savulescu, J
The place of the inns in the commercial life of London and western England, 1660-1760

The economic history of England has long been dominated by the Industrial Revolution, examining its degree of uniqueness, and its longer-term implications for both the domestic economy and that of the nations whose advance to the modern industrial state took place rather later. In this study , scholars have tended to concentrate on the period after 1750, often dismissing the previous century rather naively in terms of 'preconditions' for industrial growth. Relatively few have looked at the later seventeenth and early eighteenth centuries in depth, except in the fields of public finance and overseas trade. For most purposes, the century before the Industrial Revolution is still, in Professor Fisher's words, a 'Dark Age'.
One sector of the economy, the retail trade and retailing institutions, has been generally deprived of scholarly attention. Apart from the development of the great chain stores in the nineteenth century, the bulk of our knowledge of the sector of the economy stems from research conducted prior to 1920. While age is hardly synonymous with a lack of quality, the time had clearly come for some revision. As scholars such as Professor Eversley have come to stress the significance of changing patterns of consumption in the home market to the Industrial Revolution, this sector of the economy has increasingly demanded more research.
[Abstract continued in thesis]

Keywords: Inns
When two worldviews meet

Over the past thirty years, academic dialogues on the relationships between the sciences and religions have flourished, albeit primarily within Judeo-Christian historical, theological and philosophical contexts. Can a Hindu tradition be brought into this dialogue? The Bhāgavata Purāṇa is one of the most well-known sacred texts of India, and biology, Darwinism in particular, has become one of the most spirited areas of the science and religion dialogue in academia, as well as in the popular media. This thesis examines the possibility, scope and foundational topics involved in a dialogue between Vaiṣṇava-Hindu theology as found in the Bhāgavata, and the theoretical, philosophical and theological issues surrounding contemporary biology.
To examine the possibility and scope of a Bhāgavata-science dialogue, I focus on the theological, ontological, epistemological and teleological presuppositions that each tradition bring to the study of nature, outlining the similarities and differences in their approaches. I establish the grounds for further discussion through a comparative analysis of terms such as "consciousness," "knowledge" and "goal of knowledge"; as they appear in the Bhāgavata and noteworthy Darwinian texts.
My argument is that although prima facie the two traditions appear different in their philosophical, scientific and theological approaches, there are a number of areas of common interest and parallels, especially in their epistemologies and teleologies. In the case of genuine differences, such as their views on the ontology of consciousness, I demonstrate the possibility of reconciliation. Clarifying the conceptual differences, establishing parallels and demonstrating areas of common interests opens the possibility and widens the scope for further dialogue.

Keywords: Epistemology
Hinduism
Biology
Consciousness
Teleology
Ontology
Bhagavata Purana
Darwinism
Advisor: Brooke, JH
Clooney, FX