VictorJuiz/thesis huggingface dataset:
The history of the Society of Jesus in Colombia, 1844-1861
Keywords: Jesuits in Colombia
Catholic Church in Colombia
The Society of Jesus

This thesis examines the activity of the Jesuits in Colombia during the nineteenth century; it demonstrates how their return to the country in 1844 became a highly controversial political issue until 1884, when the national government authorized their permanent residence. The Jesuits were established in the country from 1844 to 1850, and then from 1858 to 1861. These two short sojourns generated significant debate between the Conservative and Liberal parties. The first return of the Jesuits coincided with the formation of these two parties and the debate over the separation of Church and State. It was after the Guerra de los Supremos, with the defeat of the Liberal Party and victory for the Conservative Party, that the latter passed a law on mission schools that allowed the return of the Society after its exile during colonial times.
The Liberals considered the law of April 1842 to be a tactic used by the Conservatives to empower their political project, and when the Jesuits arrived in the country, the Liberal Party started a campaign against them in Congress and through the press. As the invitation for their return to New Granada had been issued by the Conservative government, Liberals considered them to be allies of the Conservatives and deserving of their political antipathy.
The decrees issued regarding the return of the Jesuits clearly stated that they were to be assigned to Colegios de Misiones and Casas de Escala (Rest Residences) in mission territories. The Superior General of the order in Rome and the ecclesiastical authorities in Colombia interpreted the law as justifying the work of the Jesuits in establishing missions among the indigenous people and also in education in general.
Eladio Urisarri, the official in Rome in charge of arranging the return of the Jesuits, supported this interpretation, but the latent ambiguity was a continual issue.
The thesis analyses these episodes within the context of the republic’s politics and the state of the Colombian Church at the time, and examines the Jesuits’s experiences in Bogotá and the other dioceses where they were present.
Evildoing: an attack on morality
Keywords: conatus
end of morality
fundamentals of morality
evil
evildoing
attack on morality

This thesis presents a comprehensive theory of evildoing as an attack on morality, grounded in objective morality. It introduces evildoing as a distinct category of immorality, arguing that it is the relationship of evil acts to the core of morality that distinguishes them from ordinary wrongdoing. Two projects are undertaken: to provide an account of morality that can ground a theory of evildoing that is both objective and capable of systematically accommodating the diverse phenomena and definitions of evil acts, and to articulate and defend the attack on morality theory of evildoing. The challenge of the first project is met by a minimalist account of morality, structured by what I call the fundamentals of morality. The thesis defends a particular substantive account of these fundamentals, underpinned by the idea of conatus as the end of morality. Ultimately, it is conatus as the striving to persist in existence and prosper inherent in human beings that justifies the objectivity of the fundamentals of morality and with it the objectivity of the theory of evildoing, for it is these fundamentals that are attacked when we speak of an ‘attack on morality.’ Specifying and defending the conditions necessary for such an attack is the task of the second part of the thesis. An act constitutes evildoing, or an attack on morality, when it is wrong, results in serious harm to others, originates in an intention based on the correct belief that the act will cause or risk such harm, and where the perpetrator’s mental states and/or the act’s consequences are antagonistic to the realization of morality via one or more of its fundamentals.
Comprehensive assessment of the role of DNA methylation in obesity and type 2 diabetes
Keywords: Epigenetics
Genomics
DNA Methylation
Obesity
T2D
Epigenomics
EWAS

Obesity and type 2 diabetes (T2D) are major risk factors for cardiovascular and other diseases and are currently undergoing an increase in global prevalence. The work presented in my thesis addresses the role epigenetics, specifically DNA methylation, plays in the susceptibility to obesity and T2D and deals with methodological issues in the analysis of DNA methylation data.
I first combined epigenome-wide DNA methylation data across 38 adipose tissue samples with corresponding SNP and mRNA data for the same subjects. At 5% false discovery rate (FDR), methylation of 149 regions associated with at least one cis-SNP. When 19 of the 149 regions were tested for association in an additional 181 independent samples, five regions replicated. These results indicate a genetic influence on DNA methylation in adipose tissue.
I then analysed 90 epigenome-wide methylation samples taken from 15 South Asian controls and 30 T2D cases participating in the LOLIPOP study at two time points ∼7 years apart. I found global differences at both follow-up and baseline between the normal glucose tolerant and T2D groups, as well as strong differences with aging. I further used the main EpiMigrant data from 2,687 individuals, with 36 samples measured in duplicate to assess approaches to quality control, data normalisation and batch correction through control probe adjustment. A null hypothesis for epigenome-wide association studies (EWAS) by permutation testing and I investigated the effects of correlation between individual methylation markers.
Using the developed methods, I carried out an EWAS of body mass index (BMI) with subsequent meta-analysis amongst 10,261 individuals of European and South Asian ancestry. DNA methylation markers at 187 genetic loci were associated with BMI. Mendelian randomisation experiments suggested that association of DNA methylation with BMI is the consequence of BMI.
Lastly, I tested haplotypes of 85 SNPs currently known to be associated with T2D and 118 SNPs associated with obesity traits for an enrichment of CpG creating or abrogating SNPs and found that 9 T2D and 23 obesity SNPs showed a significant difference in CpG count between the SNP alleles as established by permutation testing. Amongst these is FTO, a locus which has been previously been shown to have a haplotype-specific methylation effect.
My work provides novel insights into the role of DNA methylation in metabolic diseases. The methods that I developed to robustly detect association are flexible and scalable and will further be useful for larger, future EWAS.
Software architecture for capturing clinical information in hadron therapy and the design of an ion beam for radiobiology
Keywords: slow extraction
model-driven engineering
health informatics
evidence based medicine
data capture
case report form
ion beam
beam transport
radiobiology
synchrotron
charged particle therapy
software architectures
domain-specific model
markov model
metamodel
system description languages

Hadron Therapy (HT) exploits properties of ion radiation to gain therapeutic advantages over existing photon-based forms of external radiation therapy. However, its relative superiority and cost-effectiveness have not been proven for all clinical situations. Establishing a robust evidence base for the development of best treatment practices is one of the major challenges for the field. This thesis investigates two research infrastructures for building this essential evidence.
First, the thesis develops main components of a metadata-driven software architecture for the collection of clinical information and its analysis. This architecture acknowledges the diversity in the domain and supports data interoperability by sharing information models. Their compliance to common metamodels guarantees that primary data and analysis results can be interpreted outside of the immediate production context. This is a fundamental necessity for all aspects of the evidence creation process. A metamodel of data capture forms is developed with unique properties to support data collection and documentation in this architecture. The architecture's potential to support complex analysis processes is demonstrated with the help of a novel metamodel for Markov model based simulations, as used for the synthesis of evidence in health-economic assessments. The application of both metamodels is illustrated on the example of HT.
Since the biological effect of particle radiation is a major source of uncertainty in HT, in its second part, this thesis undertakes first investigations towards a new research facility for bio-medical experiments with ion beams. It examines the feasibility of upgrading LEIR, an existing accelerator at the European Organisation for Nuclear Research (CERN), with a new slow extraction and investigates transport of the extracted beam to future experiments. Possible configurations for the slow-resonant extraction process are identified, and designs for horizontal and vertical beam transport lines developed. The results of these studies indicate future research directions towards a new ion beam facility for biomedical research.
Coevolutionary adaptation in mutualisms
Keywords: adaptation
mutualism
social evolution
cooperation
coevolution

Natural selection favours those individuals that respond best to novel features of their selective environment. For many, a critical challenge is responding to evolutionary change in mutualistic species. These responses create complex feedbacks, so only coevolutionary approaches are able to fully answer key questions about the maintenance or disruption of mutualistic behaviour, and explain the range of mechanisms that allow individuals to benefit from these associations. I first consider the hypothesis that economic models studying multiple classes of traders, where each trader seeks to optimise its own payoffs will yield insights into mutualistic systems. I show that individuals can be favoured to discriminate amongst potential partners based on the price for which they provide resources. Then, I show that market mechanisms can maintain cooperation and drive specialisation in mutualistic systems. I extend this market model to allow individuals to restrict a mutualistic partner's access to resources, and show that this strategy can stabilise cooperation and increase the fitness of both partners. I also explicitly incorporate relatedness in my market model. I show that high relatedness sometimes increases cooperativeness in members of a mutualistic species, but sometimes decreases cooperativeness as it narrow the scope for partner choice to maintain cooperation. Having studied market mechanisms, I consider indiscriminate costly help to members of another species. I discover that this trait can be favoured by natural selection and can be classified as either altruism between or altruism within species. Finally, I consider a framework for analysing coevolved phenotypic responses to a partner's cooperativeness, a challenging process to model. I demonstrate that this framework can yield firm predictions about behaviour whenever partners hold private information about their costs and benefits.
Stable moduli spaces of manifolds
Keywords: 57R50
57R15
55P47
57M07
MSC Classification: 57R90
55R40
57R56

In this thesis we make several contributions to the theory of moduli spaces of smooth manifolds, especially in dimension two.
In Chapter 2 (joint with Soren Galatius) we give a new geometric proof of a generalisation of the Madsen-Weiss theorem, which does not rely on the tangential structure under investigation having homological stability. This allows us to compute the stable homology of moduli spaces of surfaces equipped with many different tangential structures.
In Chapter 3 we give a general approach to homological stability problems, especially focused on stability for moduli spaces of surfaces with tangential structure. We give a sufficient condition for a structure to exhibit homological stability, and thus obtain stability ranges for many tangential structures of current interest (orientations, maps to a simply-connected background space, etc.), which match or improve the previously known ranges in all cases.
In Chapter 4 we define and study the cobordism category of submanifolds of a fixed background manifold, and extend the work of Galatius-Madsen-Tillmann-Weiss to identify the homotopy type of these categories. We describe several applications of this theory.
In Chapter 5 we compute the stable (co)homology of the non-orientable mapping class group, and find a family of geometrically-defined torsion cohomology classes. This is in contrast to the oriented mapping class group, where few are known.
In Chapter 6 (joint with Johannes Ebert) we study the divisibility of certain characteristic classes of bundles of unoriented surfaces introduced by Wahl, analogues of the Miller-Morita-Mumford classes for unoriented surfaces. We show them to be indivisible in the free quotient of cohomology.
Numerical modelling of real-time sub-structure testing
Keywords: dynamic testing
real-time sub-structure testing

Current dynamic testing methods can prove unrealistic due to the scale at which test components are modelled, the rate at which they are loaded or the boundary conditions to which they are subjected. A new test method, termed "Real-Time Sub-Structure Testing" seeks to provide a more realistic testing environment for energy dissipative components. The method tests structural components at full or large scale and in real-time. The physical test interacts with a computer model of the structure surrounding the test component. In this way, the in-situ behaviour of the test component is evaluated in relation to the overall structural response. The testing method requires fast and realistic modelling of the surrounding structure and a rapid interaction with the physical test specimen. For these reasons, a new non-linear finite element method has been proposed in order to model the surrounding structure behaviour efficiently. The method uses the Central Difference Method time stepping integration scheme together with a newly devised basis. The proposed basis consists of the structure’s elastic modes and additional Ritz vectors, which are calculated from the inelastic static displacement shapes of the structure. The displacement shapes correspond to the same static spatial distribution of loading as the intended dynamic excitation, and are intended to characterise the inelastic behaviour of the structure. The method has been validated against a Newmark event to event algorithm as well as Drain2DX. The non-linear dynamic response of a propped cantilever beam and portal frame structure was investigated. The response evaluated by the algorithm agrees closely with both validation analyses. The new algorithm was also shown to be faster than the Newmark procedure in simple benchmark tests. In addition, a numerical model of the testing apparatus has been developed in order to simulate complete tests for the purposes of testing procedure development and validation. The model is developed using Matlab Simulink. Parameters for the model are deduced from published data, experimental component tests and open loop step response calibrations. The model behaviour was found to be very sensitive to the parameters used. However, after calibration against open loop tests the model reproduces the observed laboratory behaviour to a good degree of accuracy. In an attempt to predict the behaviour of an actual test, the laboratory model has been coupled with the new structural solution algorithm to simulate a virtual test. The simulated results compare well with experimentally observed data demonstrating the usefulness of the overall simulation as a test modelling tool.
The peoples of Britain: population genetics, archaeology and linguistics
Keywords: archaeology
genetics
population
Britain
history
demography

The history of peoples has always evoked a great deal of both academic and popular interest, and the peoples of Britain, with its island position and semi-mythic serial invasions, have evoked as much as any. As most of the period during which Britain has been inhabited by modern humans lies in prehistory, archaeology has long been the best method for elucidating the past. In recent years, however, genetics has come to complement the reconstruction of peoples' pasts, with its ability to trace lineal human biology instead of transferable human culture.
The purpose of this thesis is to assess population genetics systems of Britain against the backdrop of archaeologically determined history, informed for later periods by linguistics, and attempt to ascertain any marked congruities or incongruities between this history and modern genetic data. The genetic datasets included in this work are the People of the British Isles Project collection, and some ancillary cohorts from surrounding countries. The genetic systems assessed include mitochondrial DNA, classical marker genes, lactase, pigmentation genes and some phenotypes, and finally a suite of candidate genes for determining normal facial variation. In a self-contained section, the principle of relating population genetic data to population histories is illustrated by a study focusing on Central Asia (a larger area), but using fewer genetic markers.
The chosen markers systems overall reveal modest amounts of genetic differentiation among different groups in Britain, but consistently highlight Wales and Orkney especially as relatively distanced from the rest of Britain. This is in keeping with the historically quite isolated state of the former, and the comparatively recent heavy influx of Norse Vikings in the latter. Further details are observable from subsets of this study: all are discussed in the context of archaeological and linguistic evidence.
These findings provide support and foundation for a forthcoming study from the People of the British Isles Project, using a genome-wide SNP approach rather than selected markers, which will likely increase the nuance of this initial picture and contribute further to answering specific questions regarding Britain's past.
Intertextualidades bíblicas en "Celestina"
Keywords: Christian humanism
Celestina
the bible in literature

The Bible serves as a source for Celestina, but biblical references and reminiscences in the text do not derive from the Scriptures themselves, but from secondary and even tertiary sources. These represent the typical medium of access to the Bible of laymen and, in the case of Celestina, of a very specific group of laymen: university members, which formed the original audience of the work and shared a same way of reading it. Therefore, biblical intertextuality in Celestina is defined by the relation of university members to these sources.
When analysed from the perspective of university readers, Celestina becomes a pseudo-contemplative work to which the principles of visual mental representation of affective meditation apply. If read making use of these principles, the didactic and moralising message of the preliminary texts is confirmed and Celestina reveals itself as an admonitory tale against carnal love. Moreover, it appears as a counterfeit sentimental romance, concretely, a reply to "Cárcel de amor", to contemporary love habits and to courtly customs.
In addition, reading Celestina from the perspective of an university audience offers a new view on the misuse of biblical references. Instead of being representative of a heterodox attitude toward the Scriptures, these function as a condemnation of the bad use of auctoritates in dialectic contexts. As a result, Celestina can be related to a reformist current in the university world, which was particularly critical to Scholasticism and its teaching methodology. In this sense, Celestina aligns itself with Humanism and, specifically with Christian Humanism.
Finally, analysing Celestina from the point of view of university readers explains why a work, which had been originally conceived as a didactic and moralising text, was criticised in the sixteenth century for being inmmoral: audience and times had changed.
Molecular studies of stiff skin-causing mutations in fibrillin-1
Keywords: integrins
Fibrillin
Extracellular matrix

Fibrillin-1 is the main component of the 10-12 nm microfibrils, which are found in several elastic and non-elastic tissues. Human fibrillin-1 contains multiple calcium-binding epidermal growth factor-like (cbEGF) domains interspersed with transforming growth factor β-binding protein-like (TB) domains. TB4 domain contains a flexible RGD loop which mediates cell adhesion via αVβ3, α5β1 and αVβ6 integrins. Mutations which introduce amino acid substitutions into TB4 are associated with a wide spectrum of diseases such as Marfan syndrome (MFS), ectopia lentis, Stiff skin syndrome (SSS). Amino acid substitutions such as W1570C, C1564S and C1577G in the TB4 domain have been found to cause SSS. The upstream TB5 domain has been predicted to modulate integrin binding and a deletion in the domain has been found in Weill-Marchesani syndrome (WMS), phenotype of which is similar to SSS (skin fibrosis and short stature), thereby suggesting that the underlying pathogenic mechanism might be similar.
This study has used cellular, biochemical and biophysical methods to investigate the effects of SSS substitutions C1564S and W1570C on domain structure and function and compared it to a MFS substitution C1564Y in the TB4 domain and WMS deletion in the TB5 domain. Effects of the SSS mutations on structure of the domains were studied using limited proteolysis, nuclear magnetic resonance spectroscopy and calcium chelation experiments. Subsequently, the ability of human fibroblasts to secrete wild-type and mutant fibrillin-1 was examined to identify the effect of the mutations on the trafficking of the protein. Finally, cell binding assays and SPR was employed to investigate the effect of disease-causing mutations on fibrillin-1/integrin interactions.
The results demonstrate that the SSS mutations affect TB4-cbEGF23 interface and calcium-binding to cbEGF23 but do not alter secretion of recombinant fibrillin-1 mutant fragments from the cell. On the other hand, intracellular retention was observed for MFS substitution C1564Y which was shown to be more susceptible to proteolysis than SSS substitution C1564S. WMS deletion also gives rise to partial retention of the recombinant fragment, suggesting a different pathogenic mechanism for these disorders. Cell binding assays and surface plasmon resonance (SPR) experiments show that SSS mutations affect binding to αvβ3 integrin, but not αvβ6 integrin suggesting that selectively impaired integrin interactions may contribute to pathogenesis of SSS.