VictorJuiz/thesis huggingface dataset:
A model-based statistical approach to functional MRI group studies

Functional Magnetic Resonance Imaging (fMRI) is a noninvasive imaging method that reflects local changes in brain activity. FMRI group studies involves the analysis of the functional images acquired for each of a group of subjects under the same experimental conditions.
We propose a spatial marked point-process model for the activation patterns of the subjects in a group study. Each pattern is described as the sum of individual centres of activation. The marked point-process that we propose allows the researcher to enforce repulsion between all pairs of centres of an individual subject that are within a specified minimum distance of each other. It also allows the researcher to enforce attraction between similarly-located centres from different subjects. This attraction helps to compensate for the misalignment of corresponding functional areas across subjects and is a novel method of addressing the problem of imperfect inter-subject registration of functional images. We use a Bayesian framework and choose prior distributions according to current understanding of brain activity. Simulation studies and exploratory studies of our reference dataset are used to fine-tune the prior distributions. We perform inference via Markov chain Monte Carlo.
The fitted model gives a summary of the activation in terms of its location, height and size. We use this summary both to identify brain regions that were activated in response to the stimuli under study and to quantify the discrepancies between the activation maps of subjects. Applied to our reference dataset, our measure is successful in separating out those subjects with activation patterns that do not agree with the overall group pattern. In addition, our measure is sensitive to subjects with a large number of activation centres relative to the other subjects in the group. The activation summary given by our model makes it possible to pursue a range of inferential questions that cannot be addressed with ease by current model-based approaches.

Keywords: Markov chain Monte Carlo
Spatial Point Processes
Bayesian Approach
Functional MRI Group Studies
Advisor: Ripley, B
Peptide targeting by spontaneous isopeptide bond formation

Peptide fusion tags are fundamental for the identification, detection, and capture of proteins in biological assays. Commonly used peptide fusion tags rely on temporary non-covalent interactions for binding, which can put constraints on assay sensitivity. Here, peptide fusion tags were developed that could specifically interact with protein binding partners via spontaneous and irreversible isopeptide bond formation. To develop covalently interacting peptide-protein pairs, outer-membrane proteins from Gram-positive bacteria that form autocatalyzed intramolecular isopeptide bonds were dissected to generate a short peptide fragment and a protein binding partner. Initially, the major pilin subunit Spy0128 from Streptococcus pyogenes was split to develop the 16 residue isopeptag peptide and the 31 kDa pilin-C protein partner. The isopeptag:pilin-C pair were able to react via spontaneous isopeptide bond formation between an Asn residue in isopeptag and a Lys residue in pilin-C without the requirement for any accessory factors, and with a yield of 60% after a 72 hr reaction. Reconstitution between the isopeptag:pilin-C pair was robust and occurred under all biologically relevant conditions tested, and also in the complex environment of a bacterial cytosol and on the surface of mammalian cells. A similar approach was also used to dissect the small CnaB2 domain that is part of the large FbaB fibronectin-binding protein from S. pyogenes. This led to the development of a more efficient peptide-protein pair, which was rationally modified to generate the highly optimized SpyTag:SpyCatcher pair. SpyTag is a 13 amino acid peptide with a reactive Asp that forms a spontaneous intermolecular isopeptide bond with a Lys present in the 12 kDa SpyCatcher binding partner. In a reaction with SpyTag, over 40% of SpyCatcher was depleted after 1 min and SpyCatcher could no longer be detected after 2 hr. The SpyTag and SpyCatcher reaction did not require any accessory factors and proceeded efficiently at a range of biologically relevant temperatures, pH values, concentrations, buffer compositions, and in the presence of commonly used detergents. The SpyTag:SpyCatcher technology was also used for specific cell surface labelling on mammalian cell membranes. SpyTag and SpyCatcher are both composed of the regular 20 amino acids and can therefore be genetically encoded as fusion constructs for a variety of in vitro and in vivo applications. Potential applications of the SpyTag:SpyCatcher technology include specific cell surface labelling, the development of novel protein architectures, and the covalent and irreversible capture of target proteins in biological assays.

Keywords: covalent
adhesin
isopeptide
tag
Streptococcus Pyogenes
split protein
peptide
pilin
Advisor: Howarth, M
The ASD equations in split signature and hypersymplectic geometry

This thesis is mainly concerned with the study of hypersymplectic structures in gauge theory. These structures arise via applications of the hypersymplectic quotient construction to the action of the gauge group on certain spaces of connections and Higgs fields.
Motivated by Kobayashi-Hitchin correspondences in the case of hyperkähler moduli spaces, we first study the relationship between hypersymplectic, complex and paracomplex quotients in the spirit of Kirwan's work relating Kähler quotients to GIT quotients. We then study dimensional reductions of the ASD equations on 𝐑2,2. We discuss a version of twistor theory for hypersymplectic manifolds, which we use to put the ASD equations into Lax form.
Next, we study Schmid's equations from the viewpoint of hypersymplectic quotients and examine the local product structure of the moduli space. Then we turn towards the integrability aspects of this system. We deduce various properties of the spectral curve associated to a solution and provide explicit solutions with cyclic symmetry.
Hitchin's harmonic map equations are the split signature analogue of the self-duality equations on a Riemann surface, in which case it is known that there is a smooth hyperkähler moduli space. In the case at hand, we cannot expect to obtain a globally well-behaved moduli space. However, we are able to construct a smooth open set of solutions with small Higgs field, on which we then analyse the hypersymplectic geometry. In particular, we exhibit the local product structures and the family of complex structures. This is done by interpreting the equations as describing certain geodesics on the moduli space of unitary connections. Using this picture we relate the degeneracy locus to geodesics with conjugate endpoints.
Finally, we present a split signature version of the ADHM construction for so-called split signature instantons on S2 × S2, which can be given an interpretation as a hypersymplectic quotient.

Keywords: Gauge Theory
Moment Map
Symplectic Geometry
special Holonomy
Moduli Space
Hypersymplectic Geometry
Advisor: Dancer, A
Plants, power, possibility: maneuvering the medical landscape in response to chronic illness and uncertainty

This thesis is concerned with plants, chronic illness and medicine in Oku, Northwest Region, Cameroon. I focus on patient strategies to obtain effective medical outcomes, and on how such outcomes may be obtained through seeking traditional medicine in Oku. I argue that biomedical notions of efficacy do not appropriately represent the central and diverse roles that plants play in traditional medicine nor do they correctly represent how people in Oku evaluate the efficacy of plant-based traditional medicine. I argue instead that efficacy must be understood in terms of the emic concept of power. This power is understood to be located in the Oku landscape, which is still uniquely forested and said to embody powerful ancestral spirits. With plants as the primary tangible material of power, and traditional doctors in Oku as those who claim exclusive rights to manipulate and disperse such power, I discuss traditional medicine in Oku as a system wherein power from the natural landscape is drawn upon to challenge harmful powers feared to derive from the social arena.
Using the pragmatic and phenomenological approaches, I show how patients evaluate the efficacy of a medical treatment based on their bodily experiences, and how their actions, as revealed in their therapeutic trajectories, reveal their satisfaction or dissatisfaction with a given diagnosis and/or therapy. I discuss how enduring illness generates and exacerbates bodily, treatment-outcome, social, and psychological uncertainties. In this context, effective outcomes can be understood as those which address and limit these uncertainties and anxieties while offering ways to imagine hopeful prognoses. This thesis then outlines the major sources of uncertainty, people’s responses to such uncertainties, and what people might achieve in terms of limiting uncertainties by seeking traditional medicine in Oku.

Keywords: plants
Cameroon
chronic illness
uncertainty
traditional medicine
medical anthropology
malaria
biomedicine in rural Cameroon
Africa.
social and cultural anthropology
co-infections
Advisor: Hsu, E
Pratten, D
Cardamom, class and change in a Limbu village in east Nepal

This thesis investigates the history of economic differentiation in a Limbu village in east Nepal. By examining three historically overlapping productive processes - subsistence agriculture, cash crop cardamom cultivation, and international migration - this thesis shows how each productive process has contributed in different ways to the acceleration of economic differentiation. In particular this thesis focuses on cardamom cultivation which first provided a means to transform significantly the lives of a large section of Limbu society. Introduced into the village by a local inhabitant in 1968, and thereafter spread throughout the whole Kabeli river valley and beyond, the cardamom plant has given many households access to considerable cash. This has enabled some households to purchase property in the plains, send their children to English-medium private schools, and send sons abroad for work. Households with little or no cardamom however, have fallen into increasing indebtedness, losing access to land and becoming increasingly dependent on wage labour for survival. The thesis also discusses international labour migration, which has more recently become another important and lucrative productive process for a certain proportion of the village. This has resulted in the rapid growth of a dispersed village in Jhapa in the plains, which has become a hub for international migrants as well as a symbol of the hopes and aspirations of villagers. This has brought about yet further economic differentiation between households that have been able to finance visas for work abroad, and those that continue to struggle day to day. Despite the increased integration of the village with a national and global market, the continued existence of Limbu language and cultural practises emphasizes the active role villagers have played in shaping their current condition.

Keywords: rural inequality
social change
class
anthropology
economic anthropology
Nepal
Limbu
cash crop
cardamom
Advisor: Gellner, D
Rival, L
The role of the BBSome in  Trypanosoma brucei

In humans, 7 genes causing the cilia-related disorder Bardet-Biedl syndrome (BBS) encode proteins that form a complex, named the BBSome. The highly conserved 7 BBSome components facilitate ciliary membrane biogenesis by sorting and transporting specific membrane proteins to the ciliary membrane. The BBSome subunits are also conserved in the protozoan parasite Trypanosoma brucei, the causative agent of African sleeping sickness. T. brucei has been used as a model organism providing huge insight into basal body/flagella biology; it is therefore a good candidate for further analysis of BBSome function.
Even though it has been suggested that BBSome traffics specific ciliary membrane proteins to the ciliary membrane in mammalian cells, we still do not know whether the function is universal or present in T. brucei. In my thesis, I have focused on the most conserved BBSome protein, BBS5, to characterize its localisation and function in flagella formation in T. brucei. Through bioinformatics, I identified that BBS5 was predicted to possess a predicted lipid binding domain which is not present in the other BBSome components, and that the diseases causing residues are most conserved in BBS5. Moreover, I generated a cell line in which endogenous BBS5 was tagged with TY-epitope and GFP to assess the localisation, which was found to be in transition zone of the flagellum. In order to investigate the function of BBS5 in the flagellum formation, RNAi mediated knockdown of BBS5 was then performed. Knockdown of BBS5 did not cause any defect in cell morphology and flagellum formation, indicating that BBS5 is not required for flagellum formation in T. brucei. This thesis provides the first insight into the localisation of BBS5 in T. brucei, and may shed the light on the importance of the transition zone proteins in T. brucei, where selection of proteins to enter the flagellum membrane may take place.

Keywords: Trypanosoma brucei
Advisor: Gull, K
Gluenz, E
The moral status of civil disobedience

This dissertation examines the moral character of civil disobedience. The discussion begins with a conceptual analysis of civil disobedience which eschews standard definitions in favour of a paradigm case approach, highlighting a parallel between the communicative aspects of civil disobedience and the communicative aspects of lawful punishment by the state. Foundations for a moral evaluation of civil disobedience are then laid down through, first, an examination of the nature of wrongdoing and justification, and second, a critique of contemporary defences of political obligation. The absence of political obligation, it is argued, does not immediately justify civil disobedience even in reprehensible regimes because, in all contexts, adherence to the law and disobedience of the law must be judged on the basis of their character and consequences. Various considerations relevant to the justifiability of civil disobedience are then examined before the discussion turns to the three principal claims defended in this thesis. The first is that people have a moral right to engage in civil disobedience irrespective of both the political regime and the merits of their cause. The second is that the reasons for which people engage in civil disobedience may be understood in terms of a pursuit of ideals. When motivated by a deep commitment to the genuine ideals of their society, disobedients may be said to demonstrate responsible citizenship. The third claim is that the law should treat disobedients differently from other offenders. When civil disobedience is morally justified, and sometimes when it is not, the law has reason to be lenient to its practitioners. In defending these claims, this discussion critiques not only the 'classical' narrow conception of civil disobedience as a public, non-violent, conscientious breach of law for which disobedients are willing to be punished, but also broader conceptions of civil disobedience which take a modest view of its justifiability and accord it limited status as a moral right.

Advisor: Raz, J
Tasioulas, J
The differential effects of teacher code-switching on the vocabulary acquisition of adult and young EFL learners: a study in the Korean context

In Second Language Acquisition (SLA)literature there has been a considerable theoretical debate over the issue of teachers’ use of the students’ first language, a phenomenon sometimes referred to as ‘code-switching’. Yet to date there has been little study of the effect of teachers’ use of code-switching (CS) on the second language learning itself. Therefore the aim of this research was to study the effect of teachers’ CS on the learning of English word meanings by two age groups – 19- and 12-year–old EFL students in Korea. To this end, this study implemented a quasi-experimental design but conducive to ecological validity, drawing on intact EFL classrooms of two kinds: one with monolingual English teachers (English-only condition) and the other with bilingual teachers who speak mainly English but occasionally switch to Korean to explain unknown English words (CS condition). Under these two different instructional types, the participants – 286 adult and 443 young learners – were encouraged to learn previously unknown English words, drawn from reading texts, through their teachers’ explanations. The study also employed a participant questionnaire and follow-up interviews, so as to shed light on the issue of teacher CS from the learners’ perspective. The results reveal that, for both age groups, the teachers’ CS by and large yielded better learning results, in terms of vocabulary gains, than English-only instruction. However, an inspection of the effect sizes further shows that young learners, compared with adult ones, might benefit from the CS environment to an even greater degree in the learning of vocabulary. The findings from the questionnaire and interviews further suggest that this differential effect of teachers’ CS might be due to the young learners’ overwhelming preference for teachers’ CS in learning English. These differences both in results and learner perceptions are explained as resulting from proficiency levels on the one hand and levels of learning experience on the other. Having discovered these differential effects of teachers’ CS on the two age groups, the findings of the present thesis call for a reconsideration of pedagogical decisions regarding L2-only instruction, in particular for young L2 learners.

Keywords: vocabulary acquisition
second language acquisition
EFL in Korea
age in SLA
English language teaching
code-switching
Advisor: Macaro, E
Popular literature and reading habits in Britain, 1914-1950

This thesis is an examination of the mass-market publishing industry in Britain after the First World War and of the 'literature' read by the lower-middle and working classes: novels and weekly magazines. We chronicle the development of the industry both generally and through the experiences of three publishers, examine the activity and motivations of the reading public and consider the treatment of contemporary issues and attitudes within popular fiction as a useful barometer for the historian.
There are seven chapters. Chapter 1 considers the period before 1914 in order to provide the necessary background for an understanding of the focus of this study, 1914-1950. The origins of the popular publishing industry and Wilkie Collins' 'Unknown Public' are examined and continuities with post-1914 popular literature traced. In Chapter 2 a broad overview of our period is conducted: the development of the industry and of the market, the influence of war and the depression, and the effect on reading of the growth of other leisure activities. Chapters 3 and 5 look at the reading habits of adults and children/adolescents from the lower-middle and working classes. In both cases contemporaries and readers themselves seemed to think 'escapism' was paramount in the selection of 'light' fiction and there was therefore a significant continuity between child and adult reading. Finally, Chapters 4, 6 and 7 focus on the histories and influence of three publishers of popular fiction during this period. These include two of the most successful (Mills and Boon, D.C. Thomson) and in contrast, a prominent but declining firm (The Religious Tract Society). In each case the complex relationship between market forces and editorial policies is discussed. We conclude that a reciprocal relationship existed between publisher and reader, with the latter dictating much of what was published. Popular fiction, moreover, served to reinforce predominant stereotypes and ideological views of society rather than to impose specific doctrine.
Remote sounding of the atmosphere of Titan

The Composite Infrared Spectrometer (CIRS) instrument onboard the Cassini spacecraft will be used to probe the atmosphere and surface of Saturn's giant moon Titan. This thesis describes an investigation of the capabilities of CIRS as a remote sounding instrument.
To enable infrared spectra to be computed, a radiative transfer code has been adapted for Titan's atmosphere. The atmospheric model, including gases and aerosol particles, was refined by comparison of synthetic spectra with results from the IRIS instrument of the Voyager 1 spacecraft.
Characteristics of the instrument have been deduced from laboratory measurements. The size and shape of the field of view was found for the mid-infrared detectors. A Fourier code was developed to transform the raw data (interferograms). Blackbody spectra taken with the flight instrument were analysed to calculate the noise equivalent radiance for the detectors of all three focal planes.
Finally, the data regarding instrument performance was used in combination with the predictive radiative transfer code to consider in detail the extent to which gaseous bands and other spectral features will be observable for a variety of limb and nadir viewing modes. Current observing strategies are reviewed and recommendations for scientific emphasis in the light of the actual instrument performance are made.

Keywords: infrared spectroscopy
CIRS instrument
Cassini spacecraft
remote sensing
Titan
Advisor: Taylor, FW
Some problems in combinatorial geometry

This thesis is in two parts. The first two chapters deal with infinite matroids and the remaining three chapters with finite matroids.
Chapter 1 has two main results. Firstly we prove that there is no duality function on the class of independence spaces which behaves like duality for finite matroids. Secondly we determine the unique class of preindependence spaces which contains the class of independence spaces and is closed under restriction, contraction and the natural duality function. Two other results of this chapter answer questions of Higgs and Welsh on infinite matroids.
The main result of Chapter 2 is a counter-example to a 1967 conjecture of Nash-Williams concerning packing disjoint spanning trees in countably infinite graphs.
In the third chapter we prove matroid analogues of various bounds on the chromatic number of a graph due to Matula, Szekeres and Wilf, and Brooks. These matroid results sharpen earlier bounds of Heron and Lindstrőm. In the second half of the chapter we answer a number of questions of Mullin and Stanton related to the critical problem for binary matroids.
In Chapter 4 we prove the binary case of a matroid conjecture of Welsh which is a natural analogue of Gallai's theorem that the vertex-stability and vertex-covering numbers of a graph G sum to the number of vertices of G.
The Tutte polynomial of a graph is known to be related to the bond percolation model on the graph. In Chapter 5 we introduce a basic abstraction of classical percolation theory, namely percolation on clutters. We give new and simpler proofs of several results of Hammersley and bound the percolation probability above and below. One of the main results shows that the theory of the Tutte polynomial cannot be extended from matroids to arbitrary clutters.

Advisor: Welsh, D