VictorJuiz/thesis huggingface dataset:
Chemical tools for the study of epigenetic mechanisms

The overall goal of my work was to develop and apply new chemical methods for the study of epigenetic DNA and protein modifications.
In Chapter 3 the development of Suzuki-Miyaura cross coupling (SMcc) for the post-synthetic modification of DNA is described. DNA modification by SMcc is efficient (4-6h) and proceeds under mild conditions (37°C, pH 8.5). The incorporation of various groups useful for biological investigations is demonstrated using this methodology. Using a photocrosslinker, introduced into the DNA by SMcc capture experiments are performed to identify potential binding partners of modified DNA.
In Chapter 4 a dehydroalanine (Dha) based chemical protein modification method is described that enables the introduction of posttranslational modification (PTM) mimics into histones. The PTM mimics introduced by this method are tested using western- and dot-blot and binding and enzymatic assays, confirming they function as mimics of the natural modifications.
Chapter 5 describes the use of a generated PTM mimics to elucidate the function of O-linked β-Nacetylglucosamine (GlcNAc) of histones in transcriptional regulation. It is shown that GlcNAcylation of Thr-101 on histone H2A can destabilize nucleosome by modulating the H2A/B dimer – H3/H4 tetramer interface.
N- and C-terminal histone tails play an important role in transcriptional regulation. In Chapter 6, nuclear magnetic resonance is used to investigate the structure of the histone H3 N-terminal tail in a nucleosome. The H3 tail, while intrinsically disordered, gains some α-helical character and adopts a compact conformation in a nucleosome context. This H3 tail structure is shown to be modulated by Ser-10 phosphorylation.
The effect of a new covalent DNA modification, 5- hydroxymethylcytosine (5hmC), on transcription factor binding is investigated in Chapter 7. 5hmC influences HIF1α/β, USF and MAX binding to their native recognition sequence, implying involvement of this modification in epigenetic regulation.

Keywords: protein NMR
posttranslational modifications
Epigenetic regulation
DNA modification
Advisor: Davis, B
Schofield, C
A study of scribal practices in early Irish and Anglo-Saxon manuscripts

This thesis describes and accounts for certain innovative scribal practices in Irish and Anglo-Saxon manuscripts of the seventh to ninth centuries, seeing these as both graphic and linguistic phenomena.
Part One deals with the linguistic context in which the scribes were working, examining the general role of grammar during the period and those aspects of grammatical teaching which would most concern the scribe. The presence of Latin as a non-vernacular Church language in Ireland and Anglo- Saxon England resulted in a dependence on and enthusiasm for the study of Latin grammar, and innovations in scribal practice must be seen in the context of this special linguistic environment. Irish grammarians understood their own language in terms of syntactic groups rather than distinct parts of speech: this and other differences between Irish and Latin may have encouraged the practices of separation (and abbreviation) in the copying of Latin, as a means of making the latter easier to read. The traditional teaching of the Latin grammarians on the eight parts of speech was especially popular with Insular grammarians, and this analysis underlies the practice of word separation, but a lack of explicit teaching on word boundaries accounts for the characteristic 'errors' of Insular separation.
Part Two examines the practices of word separation and abbreviation as displayed in early Insular manuscripts. The physical and the linguistic aspects of word separation are considered, and the early development of the practice is described. Standard patterns of separation are seen to reflect Latin morphological teaching. The practice of heavy abbreviation, although modified by various non-linguistic factors such as type of script or the intended function of a book, is basically an orthographical convention which, like the adoption of word separation, brings into the alphabetic system an ideogrammatic element which is symptomatic of a tendency to view Latin primarily as a graphical means of communication.
Linear programming algorithms for detecting separated data in binary logistic regression models

This thesis is a study of the detection of separation among the sample points in binary logistic regression models. We propose a new algorithm for detecting separation and demonstrate empirically that it can be computed fast enough to be used routinely as part of the fitting process for logistic regression models. The parameter estimates of a binary logistic regression model fit using the method of maximum likelihood sometimes do not converge to finite values. This phenomenon (also known as monotone likelihood or infinite parameters) occurs because of a condition among the sample points known as separation. There are two classes of separation. When complete separation is present among the sample points, iterative procedures for maximizing the likelihood tend to break down, when it would be clear that there is a problem with the model. However, when quasicomplete separation is present among the sample points, the iterative procedures for maximizing the likelihood tend to satisfy their convergence criterion before revealing any indication of separation. The new algorithm is based on a linear program with a nonnegative objective function that has a positive optimal value when separation is present among the sample points. We compare several approaches for solving this linear program and find that a method based on determining the feasibility of the dual to this linear program provides a numerically reliable test for separation among the sample points. A simulation study shows that this test can be computed in a similar amount of time as fitting the binary logistic regression model using the method of iteratively reweighted least squares: hence the test is fast enough to be used routinely as part of the fitting procedure. An implementation of our algorithm (as well as the other methods described in this thesis) is available in the R package safeBinaryRegression.

Keywords: binary data
linear programming
infinite parameters
monotone likelihood
logistic regression
Advisor: Ripley, B
Fracture studies in superalloys

This research is concerned with the effects of temperature and frequency on the fatigue crack propagation behaviour. The fatigue behaviour at elevated temperature has been reviewed with emphasis on the mechanisms of propagation proposed to explain the effects of temperature and frequency.
The crack propagation characteristics of a single crystal superalloy have been investigated at various temperatures and frequencies. Determination of the fatigue crack propagation rates was combined with the measurement of crack tip plastic zone sizes and observation of the deformation behaviour.
At elevated temperature, the fatigue crack propagation rates were determined to be dependent on the frequency of loading. At low and high crack growth rates increased crack propagation rates were associated with higher cycling frequencies. At intermediate crack growth rates, the highest propagation rates were associated with the lowest frequency.
Selected area channelling pattern techniques were used to determine the plastic zone sizes and revealed that at high frequencies (>10Hz) the plastic zone sizes at elevated and ambient temperature are similar. With decreasing frequency at elevated temperature creep may lead to increased plastic zone sizes but may also affect the crack tip geometry thereby restricting further effects.
At room temperature crack propagation is observed to occur by shear of the γ' precipitate on <110> {111} resulting in {111} crystallographic facets on the fracture surface. At elevated temperature (>6000 C) however, the crack growth mechanism changes and propagation takes place on {100}. Observations of the dislocation structure indicate that deformation is concentrated within the γ matrix. It is proposed that the observed crack propagation in the γ matrix on {100} arises by the constraints imposed by the surrounding γ' precipitate. A model is presented for the frequency dependence of the intermediate crack growth rate in terms of the observed strain gradients within the plastic zone and the achievement of a critical local fracture strain.

Advisor: Martin, J
Investigation of protective mechanisms of organic coatings by thermal testing and electrochemical techniques

This work investigated the protection of mechanism of organic coatings on steel exposed to 3% sodium chloride solution at 50°C, coupled with the use of electrochemical impedance spectroscopy (EIS) to monitor progress of corrosion and degradation of coating. Unlike Walter, EIS measurement was conducted at 50°C as well as after cooling, and measurements at intermediate temperatures have been used to characterize the dependence of the process involved.
The proposition that corrosion rate is controlled by the ionic resistance of an organic coating has been tested. EIS results were fitted to a model circuit and changes in the film resistance and charge-transfer resistance with temperature were analyzed to deduce activation energies for the processes involved. Surprisingly, the calculated activation energy for coating resistance is significantly lower than the activation energy for the charge transfer resistance. This suggests that ion conduction in the coating, as apparent in an AC measurement, cannot be controlling the corrosion rate.
Potentiostatic pulse tests on coated metal enable iR-corrected polarization curves to be plotted at different temperatures. From this, the activation energy determined from the corrosion currents also higher matches the higher activation energy value calculated from the charge transfer resistance. However, measurements of coating resistance on free films of the same coating also generate higher activation energy values, leaving two possible models that can account for the results.

Keywords: Organic Coating
Thermal Testing
Coating Degradation
Electrochemical Techniques
Advisor: Sykes, J
The House of Guise and the Church, c. 1550-1588

This thesis explores the relationship between a leading French Catholic family and the Church in the second half of the sixteenth century. This is a socio-cultural study rather than an investigation of the French Church during this period, although some insight into the Church is given. The Church is used to provide a focus for an examination of noble experience. The thesis notes that male and female religious were integral members of the family network. The means by which the dynasty maintained an alternative patrimony in the Church is outlined. Consideration is then given to the resources which high ecclesiastical office brought an individual, both tangible - in the form of economic assets - and more theoretical - access to patronage opportunities and influence, which contributed to an individual's power. The economic resources which benefice tenure brought are examined and their management analysed. Patronage is viewed more as an expression of a noble culture of interacting social networks than as a product of a hierarchical power structure. The position of the Lorraine-Guise Cardinals in relation to the French Church is assessed. Their power within the Church was a result of personal qualities rather than institutional structures. The power which came with tenure is discussed, as is any relationship between ecclesiastical and secular power. A final chapter looks at the experience of women religious. Churchmen and women could contribute in certain ways to family interests, but there is no evidence of large-scale despoliation of the Church through ecclesiastical kin.
Studies in the genus Dialium (Cassieae-Caesalpinioideae)

The present study is the first detailed worldwide revision of the whole genus Dialium. The genus has previously been revised and subdivided into infrageneric taxa (with enumeration of species of Africa and the Neotropics only) but their delimitations have been based solely on gross morphology. Therefore, in order to define the taxa, the present study reviewed the gross morphological characters and augmented them with data from anatomy, palynology, cytology and phytochernistry. This made possible a new classification which better reflects the relationships of the infrageneric taxa.
The various characters are reviewed, covering gross morphology, indumentum and other epidermal characters of the leaflets, anatomy of the pulvinus, testa and wood, palynology, cytology and phytochernistry.
The important taxonomic characters in Dialium are pointed out and used to define the genus and infrageneric taxa, as well as in recognising species and varieties. Some taxonomic characters are discussed in relation to geographical distribution in order to explain the present-day occurrence of infrageneric taxa east of, and one species west of, continental Africa. Evolutionary trends are explained based on these taxonomic characters.
The genera in the subtribe Dialiinae are found to be closely inter-related. However, the majority of them are more closely related to each other than they are to Dialium itself. The genera Baudouinia, Eligmocarpus and Mendoravia are taxonomically rather remote from the rest of the Dialiinae and their position needs further evaluation. The subgenus Uittienia is found not to belong to Dialium and has to be reinstated as a monotypic genus but within the same subtribe.
The thesis concludes with a formal taxonomic treatment of Dialium. The arrangement of the infrageneric taxa is such that it reflects their supposed taxonomic relationships. There are no new species described. Previously reduced species and infraspecific taxa are reviewed ana further reductions are made. As a result, only 27 species (4 with varieties) are now recognised out of the previously estimated 40 species.

Advisor: Whitmore, T
Dealignment in Costa Rica

The erosion of partisan identification (i.e. dealignment) and its impact on the declining support for traditional parties has been widely documented in Western countries. However, this phenomenon does not appear to be a Western peculiarity. Costa Rica, Latin America's most stable democracy, seems to be following a similar hitherto unstudied path. The present thesis analyses electoral change in this nation. The study assesses whether Costa Rica is undergoing a long-term electoral change; and if so, how the process could be classified and explained. Moreover, it also evaluates how well the theories developed to explicate electoral change in Western democracies illuminate the Costa Rican case. The thesis is divided into five parts. Part I poses the research's methodological and theoretical framework. Part II contextualises the problem via a historical account of political parties' development, and an assessment of the electoral system. After analysing the main evidence of change in citizens' electoral behaviour and political attitudes, Part III characterises the process. Then, Part IV concentrates on explaining it. Finally, the central findings are presented in Part V. The thesis concludes that: 1) Costa Rica is undergoing a long-term electoral change process. This process can be defined as secular dealignment. 2) In the case studied, the erosion of citizens' partisan identification (partisan dealignment) has resulted in a growing electoral flux and the decline of electoral support for the traditional parties (electoral dealignment). 3) Dealignment in Costa Rica is basically caused by the decline of the PLN's (the country's oldest, most important party) historical loyalties. 4) The PLN's partisan identification is eroding due to the combination and mutual influence of political factors and social transformations. While many of the sociological determinants of dealignment in Costa Rica find parallels in developed democracies, some political factors seem to be specific to this country and most probably to Latin American nations. In general terms, this thesis demonstrates the relevance of in-depth, context-sensitive case studies for comparative electoral research, shows that such studies can be undertaken in Latin America, and highlights the theoretical and empirical benefits of election studies outside advanced industrial democracies.

Advisor: Angell, A
Being, belonging and becoming: a study of gender in the making of post-colonial citizenship in India 1946-1961

Concentrating on the time frame between the establishment of India's Constituent Assembly in 1946, and the passing of the Dowry Prevention Act in 1961, this thesis attempts to write an alternative history of India's transition to Independence, by applying the tools of feminist historiography to this crucial period of citizenship making, as a way of offering new perspectives on the nature, meaning and boundaries of citizenship in post-colonial India. It focuses on a cohort of nationalists and feminists who were leading members of two prominent women's organisations, the All India Women's Conference (AIWC) and the National Federation of Indian Women (NFIW), documenting and analysing the voices and positions of this cohort in some of the key debates around nation building in Nehruvian India. It also traces and analyses the range of activities and struggles engaged in by these two women's organisations - as articulations and expressions of citizenship in practice. The intention in so doing is to address three key questions or areas of exploration. Firstly to analyse and document how gender relations and contemporary understandings of gender difference, both acted upon and were shaped by the emerging identity of the Indian as postcolonial citizen, and how this dynamic interaction was situated within a broader matrix of struggles and competing identities including those of minority rights. Secondly to analyse how the framework of postcolonial Indian citizenship has both created new possibilities for empowerment, but simultaneously set new limitations on how the Indian women's movement was able to imagine itself as a political constituency and the feminist agenda it was able to articulate and pursue. Thirdly to explore how applying a feminist historiography to the story of the construction of postcolonial Indian citizenship calls for the ability to think about the meaning and possibilities of citizenship in new and different ways, to challenge the very conceptual frameworks that define the term.

Advisor: Devji, F
The racial equality proposal at the 1919 Paris Peace Conference

This thesis is a study of the racial equality proposal at the Paris Peace Conference. It explores Japanese motivations for submitting the proposal, and the responses of the British and American governments which eventually defeated it. The thesis uses an analytical framework based on five categories of possible explanations for the proposal: immigration, universal principle, great power status, peace conference politics and bargaining, and domestic politics. The thrust of the analysis contained in the thesis is as follows. For Japan, the proposal meant three things: a means of reaffirming its great power status by securing racial equality with the western great powers in the League of Nations; a justification for Prime Minister Hara whose pro- League position was maintained by a fragile domestic consensus against sceptics in the government and the wider public; and a means of resolving Japanese immigration problems in the United States and British Dominions. But for Japan the proposal was not originally intended as a demand for universal racial equality. For Britain, the proposal was unacceptable because it meant "free immigration" of non-white immigrants into the Dominions. In particular, Australia adamantly opposed it also because of its political significance for Australian public opinion. For the United States, Wilson's determination to create the League of Nations at almost any cost led him to impose a unanimity ruling at the crucial vote on llth April 1919. Other explanations worked in the background. The proposal highlighted the importance of the link between race and great power status for Japan, Japan's insecurity concerning the League of Nations and the West, and Japan's different approach to international relations. Moreover, the failure of the proposal revealed the limits of Wilsonian idealism in that neither Britain nor the United States at that time seriously considered the possibility of universal racial equality.
Assessment of obstetric ultrasound images using machine learning

Ultrasound-based fetal biometry is used to derive important clinical information for identifying IUGR (intra-uterine growth restriction) and managing risk in pregnancy. Accurate and reproducible biometric measurement relies heavily on a good standard image plane. However, qualitative visual assessment, which includes the visual identification of certain anatomical landmarks in the image is prone to inter- and intra-reviewer variability and is also time-consuming to perform. Automated anatomical structure detection is the first step towards the development of a fast and reproducible quality assessment of fetal biometry images. This thesis deals specifically with abdominal scans in the development and evaluation of methods to automatically detect the stomach and the umbilical vein within them.
First, an original method for detecting the stomach and the umbilical vein in fetal abdominal scans was developed using a machine learning framework. A classifier solution was designed with AdaBoost learning algorithm with Haar features extracted from the intensity image. The performance of the new method was compared on different clinically relevant gestational age groups.
Speckle and the low contrast nature of ultrasound images motivated the idea of introducing features extracted from local phase images. Local phase is contrast invariant and has proven to be useful in other ultrasound image analysis application compared with intensity. Nevertheless, it has never been implemented in a machine learning environment before. In our second experiment, local phase features were proven to have higher discriminative power than intensity features which enabled them to be selected as the first weak classifiers with large classifier weight.
Third, a novel approach to improving the speed of the detection was developed using a global feature symmetry map based on local phase to select the candidate locations for the stomach and the umbilical vein. It was coupled with a local intensity-based classifier to form a “hybrid” detector. A nine-fold increase in the average computational speed was recorded along with higher accuracy in the detection of both the anatomical structures.
Quantitative and qualitative evaluations of all the algorithms were presented using 2384 fetal abdominal images retrieved from the image database study of the Oxford Ultrasound Quality Control Unit of the INTERGROWTH-21st project.
Finally, the “hybrid” detection method was evaluated in two potential application scenarios. The first application was clinical scoring in which both the computer algorithm and four experts were asked to record presence or absence of the stomach and the umbilical vein in 400 ultrasound images. The computer-experts agreement was found to be comparable with the inter-expert agreement. The second application concerned selecting the standard image plane from 3D abdominal ultrasound volume. The algorithm was successful in selecting 93.36% of the images plane defined by the expert in 30 ultrasound volumes.

Keywords: fetal ultrasound
image analysis
machine learning
Advisor: Noble, J
Papageorghiou, A