VictorJuiz/thesis huggingface dataset:
Admixture history of the South African "Coloured" populations
Keywords: Vereenigde Oostindische Compagnie
Slave Trade
Colonialism
KhoeSan
single nucleotide polymorphism
African
Admixture
Creole
Linkage disequilibrium

Admixed people formed from colonial era migrations are a major feature of present-day diversity. In Southern Africa, establishment of the Dutch Cape Colony instigated the so-called "Coloured" communities, associated, essentialistically, with 'mixed descent'. This multi-way admixture involved diverse regional groups producing a fascinating genetic story. In this thesis I develop further the history of the Cape Colony admixture using genome-wide SNP chip data.
In chapter 4 I characterise the ancestry of 733 Cape Town "Coloured" individuals, identifying specific contributions using haplotype coalescence. I find no substructure despite identifying 11 ancestral contributions. Results concur with historic accounts of South Asian, European, African KhoeSan and Bantu-speakers, and South-East Asian contributions from slaves, indigenous people and settlers. Signals from known slaving regions are detected as is a previously unknown Central European and Iberian contribution. In chapter 5 I explore evidence of admixture events and sources using linkage-disequilibrium decay curve fitting for the above dataset. Results indicate recent, continuous admixture pre-dating the Cape Colony. Europeans, South-East Asians and the KhoeSan are likely sources for the pre-Colonial signals possibly reflecting shipwrecks along the coast. I find no clear evidence for Southern Bantu and Malagasy contributions to the South African Coloured (SAC).
In chapter 6, I evaluate geographic expansion and admixture in the "Coloured" sub-identity: Cape Malay, Griekwa and Baster. I genotype 116 new individuals. Geography and ethnicity correlate with genetics but inconsistently. Griekwa and Cape Malay show evidence of gene flow with geographic neighbouring communities while the Namibian Baster are the clearest example of endogamy, associated with isolation and inbreeding.
Novel and challenging aspects are added to our understanding of the "Coloured" communities. This work highlights that admixture pre-dates the arrival of settlers and how social identities are formed along more dynamic processes than simple admixture proportions.
Modelling the short-T2* signal in the liver with ultrashort echo time magnetic resonance imaging (UTE-MRI)
Keywords: UTE
tendon
R2*
fibrosis
T2*
short T2*
collagen
ultrashort echo time
liver
frequency

Liver fibrosis, a consequence of most chronic liver diseases, is characterised by collagen deposition. Collagen has a short-T2* signal that is undetectable with conventional magnetic resonance (MR) sequences. However, collagen signal is measurable with the ultrashort echo time (UTE) sequence, which can achieve an echo time of less than 1 ms. This thesis explored the modelling of the short-T2* signal in the liver with UTE.
Given the implication of collagen in liver disease, MR signal properties, including the R2* and resonant frequency shift, were investigated in oriented collagen. Ex vivo measurements were performed at 3 T in tendon, an example of oriented collagen. Furthermore, the R2* of collagen was investigated in phantoms in vitro.
The UTE sequence was optimised for in vivo imaging on the Siemens Trio 3-T and Prisma 3-T scanners. On the Trio, optimisations included reduced gradient spoiling, the use of a double-echo vs. a single-echo acquisition and the use of spatial saturation. Calibrations were performed on the Prisma for the bandwidth, radiofrequency coil and minimum TE.
From the R2* and resonant frequency shift of tendon, an R2* model was developed for describing isotropic collagen and free water in the liver. Other exponential models were also considered, accounting for short-T2* signal. UTE acquisitions were performed to measure R2* signal in the liver from healthy subjects and liver-disease patients in vivo. The models were used to fit the R2* signal and the most appropriate model was selected. Subsequently, the repeatability and reproducibility of the short-T2* signal fraction were evaluated. Comparisons of the short-T2* signal fraction were made between healthy subjects and patients.
Given the selected model for the short-T2* signal in the liver, potential sources of short-T2* signal were discussed. Future work involves the identification of the constituent(s) giving rise to the short-T2* signal in the liver.
'The Hotel de Luxe': the architectural and social significance of the 'grand hotel' in London 1860-1910
Keywords: history of travel
production of space
architectural history
waiter
history of tourism
luxury hotel
social history
restaurant
housekeeper
chef
luxury

The London grand hotel or hotel de luxe was a new building type, designed to provide luxury for a changing society. These venues were located at the intersection of public and private, and composed of a series of potentially contradictory characteristics. They combined an idealised past with the excitement of the future. They promised an experience of consumption rooted in traditional status which was also innovative. ‘Modern’ in terms of up-to-date technology, they also exhibited the modernity of shifting hierarchies and identities in an urbanised, industrialised society. Their desirability was associated with the excitement of the foreign, but also with their practical role as a convenient base . Monuments to wealth and fashion which constantly adapted, grand hotels both responded to and reshaped identity and social culture.
Luxury is complex and elusive, defined according to place, time and person. Chapter I sets this thesis in the context of other examinations of the concept, its inherent duality as economic fact and medium to communicate social relationships, and its connection to the production of space. It argues for a set of characteristics of luxury around which the thesis is structured. Chapter II: Grandeur examines the hotels’ physical reality, size and status. Chapter III: Magic considers the representational encounter, promoted through a narrative of magical transformation. Chapter IV: Exclusivity examines the tensions between this crucial aspect of luxury and the need to attract clients, balanced via tangible and intangible thresholds of plan, design, and staff performance. Chapter V: Cosmopolitanism considers the attractions of foreign cultures, visible in the public-facing staff and in the gastro-cosmopolitanism of restaurants. Chapter VI: Comfort addresses the influence of changing ideas of physical and social comfort on public and guest rooms, and the new, private bathroom. Chapter VIII: Modernity examines the hidden production systems of luxury, and the social modernity on display in palm courts, where men and women could enjoy novel experiences in a new interior. Combined, these characteristics created the grand hotel.
Rediscovering Rubén Darío through translation
Keywords: Modernismo
Spanish American Literature
Translation
Rubén Darío
Poetry
Multilingualism

Despite being widely considered one of the most important writers of the Spanish language, Rubén Darío is scarcely known in the English-speaking world. This thesis addresses the question of his obscurity. By approaching Darío’s oeuvre through translation, it sheds light on the history of his reception in English and on the multilingualism of his writing. In addition, it offers new renderings of the modernista’s poetry alongside a critical discussion of the translation of poetry with a view to improving its practice.
The thesis is divided into three different sections which correspond to three different ways of applying translation to the study of Darío’s oeuvre. Section I offers a reading of Darío’s work with an emphasis on his use of translation in his writing, thereby revealing its multilingualism. Section II centres on translation as a critical issue: it analyses the history of Darío’s reception in English by considering historical, cultural, and poetic differences between Spanish- and English-language literature from the turn of the nineteenth century to the present. In addition, it offers a critical discussion of the theory of the translation of poetry vis-à-vis Darío’s writing. Section III puts translation into practice both by offering new renderings of the Nicaraguan’s poetry as well as discussing the issues that arise when looking at existing versions.
This thesis argues that the translation of poetry is by and large literary imitation across languages. In this regard, some of the key elements of Darío’s poetry, notably its prosody, have not been rendered successfully into English; nevertheless, cultural and historical differences between Spanish- and English-language literary traditions, rather than linguistic, have impacted on its reception more heavily.
Recurrent neural networks for time series prediction
Keywords: Machine Learning
Recurrent neural networks
Forecasting
Time series
Gaussian Process
Probabilistic
Neural networks
LSTM
Transfer learning

Attempting to predict the future long precedes the time where we could first quantify much of our present. But nowadays, performing long-term and reliable time series forecasting remains as relevant as ever across a vast number of application domains, including astronomy, healthcare, meteorology, physiology, energy systems, econometrics, finance and sociology, amongst many others. Practitioners act upon these forecasts, and it is thus mandatory that such forecasts are accompanied by well-calibrated uncertainty assessments so as to enable a better-informed decision-making process.
This thesis proposes a novel time series forecasting framework, namely a scalable and general-purpose recurrent neural network approach which provides probabilistic predictions. Our method recasts time series forecasting as a symbolic sequence learning task by introducing a discrete encoding scheme over measurements. Such symbol sequence tasks have been most successfully dealt with by Long Short-Term Memory (LSTM) models and extensions, such as the sequence-to-sequence model, which form the core of our methodology. This presentation is accompanied by a large-scale experiment where we show the effectiveness of our method over 45 different datasets in comparison with state-of-the-art baselines, such as Gaussian Process Regression (GPR).
Crucially, our framework also offers a number of extensions that address a broad range of use cases beyond univariate time series prediction. For example, we show how predictive densities over the occurrence of critical events within a predictive horizon can be inferred from our forecasts. Whereas this requires access to labelled data, we provide a complementary method for recognising and labelling prototypical time series segments on the basis of the feature embedding learnt by our neural networks. Such motifs can subsequently be used to build predictive densities and characterise time series. Lastly, we extend our framework to allow for multivariate forecasting, enabling efficient inference of joint predictive densities over multiple correlated time series.
Finally, time series data scarcity constrains the choice of a forecasting model, especially as over-parameterised models such as recurrent neural networks cannot generalise from limited data. In this thesis, we propose a novel approach to infer accurate and reliable predictive distributions from scarce time series data. We achieve this through a recurrent neural network approach that infers a joint feature representation over the space of quantised time series by means of a compilation of auxiliary datasets. Cross-task knowledge transfer is readily enabled by assuming an ordinal regression approach, as quantised time series can then be characterised in terms of their ordinal bin sequences.
A third way: Muslim arguments for secular nationalism in mid-twentieth century North India
Keywords: Pakistan
Pashtuns
Indian Muslims
Secularism
Kashmir
Sheikh Abdullah
Abul Kalam Azad
Abdul Ghaffar Khan
Indian nationalism

From the late colonial period, three eminent Indian Muslim nationalists—Abul Kalam Azad, Sheikh Mohammad Abdullah, and Abdul Ghaffar Khan—conceived of a third way to nationalism which had till now been ignored by historians. Drawing confidence from the nationwide strength of the Muslim community and/or presence of their overwhelmingly Muslim regional homelands, these thinker-politicians abjured the separatism of Mohammad Ali Jinnah’s Muslim League and embraced an Indian national movement for the establishment of a secular republic. However, since they wished to avoid being reduced to a subordinate role within the Indian nation from the subject position of minority, they insisted on imagining it in terms of socio-cultural parity between Hindu and Muslim. This separated them from their colleagues Jawaharlal Nehru and M.K. Gandhi who had little need to concern themselves with this question. Nevertheless, by refusing to make religion a determinant of nationality while still retaining it within the public space, this thought must be understood as part of India’s broader secular nationalist tradition.
This endeavour—to establish an unequivocally Indian nationalism marked by Hindu-Muslim equality—did not preclude substantial differences between Azad, Abdullah, and Ghaffar Khan. How they imagined the Indian nation was informed by their contrasting ethnolinguistic inheritances and whether their respective Muslim constituencies—Hindustani, Kashmiri, and Pashtun—occupied the position of a regional majority or minority. But these figures understood that their principle of Indian equality had meaning for other groups, too; they were not parochial thinkers. Therefore, what this thesis uncovers is a new set of perspectives on major South Asian debates about: majority and minority; national history and culture; secularism; and subidentities and their political representation. And by placing these in dialogue with alternative secular and communal nationalisms, it contributes to a wider discussion about the meaning of political concepts in India and Pakistan.
Peripheral T cell responses to immunotherapy treatment in metastatic melanoma
Keywords: Melanoma
Immunotherapy
Checkpoint inhibitor
T cell

Immune checkpoint inhibitor treatment has revolutionised treatment for cancers such as malignant melanoma, producing durable responses in patients with metastatic malignancy. Despite this progress, responses are still only seen in a subset of patients and the phenotype and specificity of the T cells responsible for determining efficacy remain poorly characterised. A better understanding of T cell behaviour during immunotherapy treatment is required to identify markers of response and resistance and to predict effective combination strategies. To address this, we performed longitudinal peripheral immune monitoring of metastatic melanoma patients receiving checkpoint inhibitor therapy. By integrating a variety of single-cell analysis approaches including mass cytometry, MHC Class I tetramer staining, single-cell fluorescence activated cell sorting and single-cell RNAsequencing, we were able to track and analyse in detail tumour-specific T cell responses in the periphery over time. Accumulation of activated effector CD8+ T cells expressing CD38 and HLA-DR was observed in response to treatment, was more pronounced with combination anti-CTLA-4/anti-PD-1 treatment than anti-PD-1 monotherapy, and was correlated with treatment outcome. Activated cells were enriched in tumour-specific compared to microbial-specific T cells, with diversification and expansion of the tumour but not microbial-specific response observed over the course of treatment. This was accompanied by transient alterations in the functional avidity of T cell clones specific for the common tumour-associated antigen MART-1. Single-cell RNA-seq revealed substantial heterogeneity in the transcriptional profile of tumour-specific T cells during therapy with transient activation and persistence of specific clonotypes observed. These results demonstrate both the feasibility of monitoring tumour-specific T cells mobilised in response to immunotherapy in the periphery, and provide insights into the mechanisms underpinning therapeutic efficacy of combination checkpoint blockade. The results also have implications for the identification of T cells and TCR clonotypes with maximum therapeutic potential for other therapeutic strategies such as adoptive cell therapies.
Refractory body-centred cubic high-entropy alloys for nuclear fusion
Keywords: High-entropy alloys
Nuclear Fusion

In this work refractory High-Entropy Alloys (HEAs) have been investigated for application as Plasma Facing Components in nuclear fusion reactors. Sample fabrication was guided by optimising composition in order to maximise the Ω parameter, which has been previously identified as correlating with the stability of solidsolution microstructures. Arc melting was used to fabricate billets of TiVZrHfTa, TiVZrTa, and TiVTa, each of equiatomic and optimised compositions. These samples were analysed by XRD and SEM in the as-cast condition and after being annealed at 1400 ◦C for twenty four hours. The matrix of each sample was found to be BCC, and each contained secondary phases with either BCC, HCP, or rocksalt crystal structures. The latter of these phases was found to be a carbonitride, formed from an air leak that occurred during melting. Finite-Element Analysis of thermal transport in arc-melted billets has shown that cooling rates generated are rapid, and even more so in smaller billets. Smaller 10 g billets of equiatomic alloys were found to have much lower volume fractions of secondary phases than as-cast 50 g counterparts, and this has been attributed to the differences in solidification and cooling conditions. The modelling also demonstrated large variations in cooling rate throughout larger 50 g billets, and so the effect of this on as-cast microstructures was also investigated. It was found that the differences in cooling rate was sufficient to create variations in microstructures, with an increase of 10% volume fraction of the carbonitride phase between the bottom and top of the billet, along with a large increase in porosity. The main conclusion of this portion of the thesis is that arc melting plays a larger role in determining as-cast microstructures than previously thought. Two ion-implantation experiments were run into four different alloys of TiVZrHfTa up to damages of 0.6 and 3.5dpa. Nanoindentation has then been used to show there is no measurable change in hardness, despite a strong reaction being found in a vanadium control sample. Separately, these alloys were used to demonstrate the efficacy and limitation of using a new nanoindentation technique called Express indentation, which rapidly makes thousands of indents in order to map the hardness and modulus of materials.
Insights into the mechanisms of asymmetric phase-transfer catalysis
Keywords: spirobiindanone
kinetics
phase-transfer catalysis
organic chemistry
enantioselective

This thesis describes work conducted towards the study of the mechanisms of asymmetric cation-directed phase-transfer catalysis (PTC).
Chapter 1 introduces the field of PTC, including its general mechanisms, utility in an asymmetric context, and previous kinetic and mechanistic studies. Despite being a well-established technique in organic chemistry, the precise mechanisms of enantioselective phase-transfer reactions, particularly those effected by cinchona alkaloid-derived catalysts are not fully understood.
In Chapter 2, we found that studying enantioselective phase-transfer reactions effected by cinchona alkaloid-derived catalysts proved to be both practically and intellectually demanding. The manner in which the reactions were practically conducted had significant bearings on the kinetic behaviour that was exhibited. Primarily, we developed robust methods that enabled the collection of reliable, reproducible kinetic data from polyphasic heterogeneous reaction systems.
Chapter 3 describes the kinetic and mechanistic study of a phase-transfer catalysed intramolecular C-acylation reaction. Deconvolution of the mechanism involved a series of practical kinetic investigations, evaluation of theoretical models, and further experimental interrogation. The final mechanistic hypothesis highlighted a series of processes concerning catalyst activation and regeneration, which were rate-determining in this system.
Chapter 4 presents a concise summary and conclusion to the thesis, and Chapters 5 to 10 describe experimental details and provide supporting information.
Systematics of Andean Lupinus L. and the origin of L. mutabilis Sweet
Keywords: Radiation
Lupinus
Phylogeny
Species diversification
Molecular phylogeny
Character evolution
Plant diversification
Leaf morphology
Andes
Lupin
Classification
Seed size
Domestication
Taxonomic accounts
Evolution

This thesis contributes to the central goals of systematics - the inventory of species, building the tree of life and understanding evolutionary processes - through a descriptive taxonomic study, molecular phylogenetic analysis and morphological survey of the genus Lupinus L.
Lupinus comprises ca. 290 annual and perennial species placed in the Genistoid clade of the Papilionoid legumes. In this study three new DNA sequence datasets are used to reconstruct species relationships. The new phylogeny is used to investigate character evolution, species diversification, domestication and as the basis for a new infrageneric classification.
Approaches to plant species-level phylogeny reconstruction and criteria for selecting DNA sequence loci are evaluated from a theoretical standpoint, and experimental work to develop hypervariable nuclear DNA sequence loci is presented.
The comparative morphology of Lupinus species is investigated and presented. This includesstudies of seed coats, cotyledons, leaves, and chromosomes. Optimisation of these data onto the 3-locus phylogeny reveals congruence between chromosome number and geographyand shows that non-digitate leaves have evolved twice independently within Lupinus.
Evolutionary rates analysis is used to estimate divergence times for clades and to investigate the tempo of species diversification. Notably, a strongly supported clade representing ca. 81 Andean species is estimated to be 1.18-1.76 Myr, implying a diversification rate of 2.49-3.72 species per Myr. This exceeds previous estimates for plants providing the most spectacular example of explosive plant species diversification documented to date.
Lupin species have been independently domesticated as grain legume crops in the Old and New Worlds. The origins of the Andean domesticate, L. mutabilis, are investigated. Lack of resolution amongst the Andean species, attributable to exceptionally rapid species diversification, meant that the progenitor(s) of L. mutabilis could not be firmly established. However, four Andean species are tentatively identified as closely related to L. mutabilis based on morphology. A taxonomic account of these species is presented.
Finally, a new infrageneric classification based on morphological diagnosability monophyly is proposed.