VictorJuiz/thesis huggingface dataset:
Sand ramps as late Quaternary palaeoenvironmental archives: analysis from Southern Africa

Sand ramps are widespread but understudied landforms which have the potential to provide detailed palaeoenvironmental information in dryland regions. This thesis investigates the utility of sand ramps as late Quaternary palaeoenvironmental archives by addressing two research questions: (1) What are the main controls on sand ramp formation in southern Africa? (2) What does the sand ramp record tell us about late Quaternary palaeoenvironments in southern Africa?
The distribution of sand ramps in southern Africa was surveyed using Google EarthTM and 75 features were identified in southern Namibia. Ten of these sand ramps, and an additional feature from South Africa, were studied in the field. Sediments and morphology were mapped and a total of 64 OSL dates, 96 sediment samples, 10 heavy mineral assemblages and OSL sensitivity data from 8 samples were examined.
The distribution of sand ramps suggests formation is dependent on (1) sediment supply, (2) accommodation space, (3) persistent unidirectional wind and (4) a variable semi-arid to arid climate. Chronologies and sediment analyses indicate individual sand ramp accumulation is locally controlled by sediment supply modulated by the availability, and nature, of the accommodation space. Comparison between the Namibian and South African sand ramps suggests considerable regional variation in the factors controlling sediment supply.
The Namibian sand ramps show an affinity to local ephemeral river channels. Periods of dated sand ramp activity in multiple features are interpreted as periods of increased regional fluvial activity. Significant activity occurred at &Tilde;21-12 ka (with peaks at 21-18.5 ka and 14.5-12 ka), &Tilde;8.5-7.5 ka and &Tilde;2 ka. Some activity is also indicated at 85-65 ka and 45-35 ka. These results correspond well to regional records.
Overall, this study demonstrates that sand ramps can provide palaeoclimatic information on both the local and regional scale but only if a number of caveats are taken into consideration.

Keywords: Sand ramp
OSL
aeolian geomorphology
Quaternary
Namibia
Advisor: Thomas, D
Bailey, R
Movement synchrony, social bonding and pro-sociality in ontogeny

Human sociality, with its wide scope, early ontogeny and pervasiveness across cultures, is remarkable from an evolutionary perspective. We form bonds with other individuals and live in large social groups. We help, empathise with and share our resources with others, who are unfamiliar and genetically unrelated to us. It has been suggested that interpersonal coordination and rhythmic synchronisation of movements may be one proximate mechanism that enables such widespread human sociality and facilitates cooperation. In the last decade, considerable research has examined the effect of movement synchrony on social bonding and cooperation. However, when this thesis started, there was virtually no experimental study investigating the ontogeny of the movement synchrony-social bonding link, which is proposed to have deep evolutionary roots and important, long-lasting consequences in social life.
This thesis aims to investigate the effects of movement synchrony on social bonding and cooperative behaviour across different time points in ontogeny. Three experimental studies were conducted examining infancy, early childhood and middle childhood. Each study explored a different aspect of social bonding and cooperation based on the motor, social and cognitive developments that mark that age group.
Study 1a found that at 12 months of age, infants prefer individuals who move in synchrony with them, when the individuals are social entities, but not when they are non-social. Study 1b showed no preferences for synchrony at 9 months in either social or non-social contexts, however. Study 2 revealed that in early childhood, performing synchronous movements actively with a peer facilitates helping behaviour among the children, as well as eye contact and mutual smiling during the interaction. Finally, Study 3 showed that the social bonding effects of movement synchrony applied to inter- group settings and that performing synchronous movements with out-groups increased bonding towards the out-group in middle childhood.
This thesis followed an interdisciplinary, integrative and naturalistic approach, where (i) literature from a wide range of disciplines motivated and guided the present research; (ii) links between motor, social and cognitive aspects of development, which are often investigated separately, are formed; and (iii) the experiments were designed in ways that represent the real-life occurrences of the investigated phenomena. The current findings provide the first substantial evidence that movement synchrony facilitates social bonding and cooperation in childhood and thereby provides a foundation for future research.

Keywords: children
movement synchrony
social cognition
infants
dance and rhythm
intergroup behaviour
minimal group paradigm
cooperation
motor coordination
helping behavior
social preferences
Advisor: Cohen, E
Functional characterisation of key residues in the photopigment melanopsin

Melanopsin (Opn4) is the opsin photopigment of intrinsically photosensitive retinal ganglion cells (ipRGCs). It has a conserved opsin structure and activation mechanism, yet demonstrates unusual functional properties that suggest it will possess unique structure-function relationships. The aim of this thesis was to characterise key OPN4 residues by examining the impact of non-synonymous mutations on melanopsin function. A genotype-driven screen of a chemically-mutagenized mouse archive led to the identification of a novel Opn4 mutant, S310A, located at a known opsin spectral tuning site. Action spectra from ipRGC and pupil light responses (PLR) of Opn4S310A mice revealed no change in wavelength of peak sensitivity. However, Opn4S310A PLR was significantly less sensitive at longer wavelengths, consistent with a short-wavelength shift in spectral sensitivity. This suggests S310A acts as a spectral tuning site in melanopsin. Next, the impact of naturally-occurring missense variants in human melanopsin (hOPN4) was examined in vitro. Fluorescent calcium imaging of 16 hOPN4 variants expressed in HEK293 cells revealed four hOPN4 variants abolished or attenuated responses to light (Y146C, R168C, G208S and S308F). These variants were located in conserved opsin motifs for chromophore binding or hydrogen-bond networks, functional roles apparently shared by melanopsin. Finally, two hOPN4 single nucleotide polymorphisms (SNPs) P10L and T394I, associated with abnormal non-image forming behaviour in humans, were explored in vivo. Using targeted viral-delivery of hOPN4 SNPs to mouse ipRGCs, a range of OPN4-driven behaviours, such as circadian photoentrainment and pupil light responses, were found to be comparable with hOPN4 WT control. Multi-electrode array recordings of ipRGCs transduced with hOPN4 T394I virus had significantly attenuated sensitivity and faster response offset, indicating this site may be functionally important for melanopsin activity but compensatory rod and cone input limits changes to non-image forming behaviour.

Keywords: ipRGC
Opsin
Single Nucleotide Polymorphism
G-protein coupled receptor
Melanopsin
Missense Mutation
Photopigment
Pupillometry
Spectral Tuning
Multi-electrode array
Opn4
Adeno-associated virus
Circadian Rhythms
Advisor: Hankins, M
Peirson, S
The evolutionary ecology of animal information use and social dominance

Organisms are frequently faced with uncertainty regarding how best to exploit vital resources, and may benefit from collecting information about their distribution through space and time. However, the ways in which competition over resources might systematically facilitate or constrain an individual's ability to use information has been largely overlooked. In this thesis, I develop a conceptual framework for considering how the distribution of limited resources might underpin interdependencies between competition and information use. I focus on the evolutionary ecology of relationships between social dominance and social information use. I begin with an observational study of wild chacma baboons (Papio ursinus) suggesting that, when resources can be monopolised, individuals with low competitive ability are limited in their ability to use social information. Building on these findings, I then develop a general model exploring selection on social information use in a competitive context across three axes of 'resource ecology' (scarcity, depletion rate, monopolisability). This study makes predictions regarding the resource conditions under which competitive ability might constrain social information use, and the potential importance of social information use in the evolution of social dominance. I go on to test these predictions in chacma baboons using a field experiment. This experiment also explores whether the predictability of resource distribution might facilitate the decoupling of social information use from the competitive context in which it was collected. Taken together, these findings provide general insights into the combinations of ecological conditions and behavioural mechanisms that should underpin the benefits of social dominance. I end by building a simple population matrix model to study social dominance using an eco-evolutionary approach, in which feedback loops between ecological and evolutionary processes are considered. By modelling relationships between dominance rank and survival, reproduction, inheritance, and development, I am able to derive estimates of long-term fitness associated with dominance. Using these estimates, I generate predictions regarding how dominance hierarchies should impact the dynamics of group stability, viability, and fission.

Keywords: individual differences
inequality
social evolution
information use
game theory
social dominance
competition
exploitation
evolutionary demography
evolutionary ecology
social behaviour
Advisor: Coulson, T
Cowlishaw, G
Rowcliffe, M
Thesis on behavioural asset pricing and portfolio choice

This thesis presents three papers in the field of behavioural financial economics and financial econometrics.
The first paper, entitled "Optimistic versus Pessimistic–Optimal Judgemental Bias with Reference Point" develops a model of reference-dependent assessment of subjective beliefs in which the loss-averse people optimally choose expectation as the reference point to balance the current felicity from the optimistic anticipation and the future disappointment from the realization. The choice of over-optimism or over-pessimism depends on the real chance of success and optimistic decision makers prefer receiving early information. In the portfolio choice problem, pessimistic investors tend to trade conservatively. However, they might trade aggressively if they are sophisticated enough to recognise the biases as low expectation can reduce their fear of loss.
The second paper, entitled "Information and Dynamic Trading with Gambler's Fallacy", develops a multi-period stock trading model in which there are two types of investors–"rational" type and "gambler's fallacy" type, both observe the public signal about the fundamental value each period. The rational investor holds correct beliefs on the stochastic process of the signal, whereas the gambler's fallacy investor falsely believes that the sequence of signals should exhibit systematic reversals. Both types of investors trade against each other to speculate the future price changes, based on their inferences about the fundamental value. This paper explores the competitive equilibrium, in which both types of investors have model consistent expectations adjusted for the heterogeneity in their beliefs about the signal generating process. The thesis examines the dynamics of prices, returns, optimal portfolios and trading volumes in reaction to the information flow. Consistent with empirical evidence, the market in this model exhibits short-run momentum and long-run reversal. It is also demonstrated that the equilibrium price is more close to the valuation of the gambler's fallacy type.
Finally, the third empirical paper entitled "Regime Switching in Financial Market and Portfolio Choice" considers a variety of regime switching models with time varying transition probabilities for the joint distribution of stocks and bonds returns. Paper results support a two-regime univariate model for stocks with ISM and P/E ratio as leading predictors for the transition probabilities and support the fixed transition probability model for univariate distribution of bond returns. Under joint distribution assumption, the model selects a three regime model with ISM, unemployment rate and P/E ratio as predictors for the time varying transition probabilities. Even though both fixed and time varying transition probability models identify three regimes in the financial market, however, the time varying transition probability model provides better out of sample predictions, based on the regime-dependent portfolio performance.

Advisor: Crawford, V
Mukerji, S
Ozsoylev, H
Nature and narratives; landscapes, plants and animals in Palaiologan vernacular literature

This thesis identifies the role of nature within Palaiologan entertainment literature. The texts on which this thesis focuses include a selection of the Palaiologan novels, namely the Achilleid, Velthandros and Chrysandza, Kallimachos and Chrysorroi and Livistros and Rodamni, as well as two other, more satirical works, The Synaxarion of the Honourable Donkey, and An Entertaining Tale of Quadrupeds. These texts seem to be different from earlier works in which nature is prominent, utilising such material in an innovative way. The study of these texts provides us with information both on the Byzantine view of the natural world and on the use of literature during a particularly troubled period of Byzantine history. My main questions therefore are how nature is portrayed in these texts and what can this tell us about the society that produced them. The study of these vernacular texts indicates that the natural world is given a prominent place in the literature of the period, using landscapes, plants and animals in diverse ways to express assorted ideas, or to stress particular aspects of the stories. The animals and landscapes provide hints of the plot to the audience, which the authors sometimes then subvert. The authors draw on earlier Greek material, but parallels with literature from other cultures show similarities which imply a shared medieval perspective on nature with local differences.

Keywords: Byzantine
Ecocriticism
Advisor: Lauxtermann, M
From the Andes to the coast: human mobility and diet in the Atacama desert during the late intermediate period (ad 900-1450)

The Late Intermediate Period in northern Chile has been strongly influenced by the mobility models of vertical archipelago and the gyratory mobility. The vertical archipelago model proposes altiplano colonies would have lived in the lowlands controlling trade and distributing economic resources. The gyratory mobility suggests trade was rather controlled by pastoralist groups from the highlands, travelling across the Andes using llama caravans. Following new studies on stable isotope analysis for the LIP in the Atacama Desert, there is little evidence to support the colonies hypothesis. For this reason, the aim of this thesis is to evaluate the presence of colonies and specialised highland pastoralist groups in the lowlands of northern Chile through the use of δ13C, δ15N, δ18O and 87Sr/86Sr as well as radiocarbon dating. Human remains were analysed for tooth enamel, bone collagen, bone apatite, and hair-keratin. A second aim of the thesis was to provide new analysis of archaeological plants and animals of the area. Plants results present incredibly high δ15N values for the crops, suggesting use of fertilisers on them, probably seabird guano from the coast. This is also supported by the absence of a marine reservoir effect on the radiocarbon dates, reflected in the lack of offset between paired dates of bone collagen and textiles in individuals enriched in 15N.
The results obtained for the human remains suggest there is no evidence to support neither the 'colony' hypothesis nor the gyratory mobility model. However, a small number of outlier individuals for δ13C, δ15N, δ18O and 87Sr/86Sr suggest a non-local origin. Mobility patterns were diverse and flexible including female and male individuals that moved at different moments of their life (infancy and adulthood). This study shows that dietary patterns in the Atacama Desert during the LIP were associated with strong local traditions.

Advisor: Lee-Thorp, J
Schulting, R
Methods to jointly analyze multiple phenotypes

Linear mixed models (LMMs) have re-emerged as a central tool in statistical genetics. Fixed effects capture genetic variants tested for association. Random effects leverage aggregate relatedness while remaining agnostic to specific genetic mechanisms, naturally modeling heritability and controlling for polygenic background and confounding from population or family structure in genome-wide association studies (GWAS). Multiple random effects can partition heritability amongst many biologically meaningful variance components (VCs).
Concurrently, genetic studies have begun to analyze multiple traits. This can improve power by adding data and can inform the path from genotype to phenotype, e.g. with graphical models, pleiotropy detection or endophenotyping. Multi-trait analyses are natural for biobanks and high-throughput phenotypic measurements like gene expression, medical images or metabolites.
Following these advances, this thesis develops three multi-trait mixed models. phenix imputes missing phenotype data by modifying probabilistic matrix factorization to incorporate genetic relatedness. General linear mixed models (GLMMs) generalize and unify multi-VC, multi-trait and likelihood-penalized mixed models. Finally, compressive mixed models (CMMs) combine the two, obtaining the imputation and computational benefits of phenix and the heritability estimation and multi-VC capabilities of GLMMs.
phenix essentially always outperforms all competitors in imputation and can improve GWAS power. GLMMs accurately estimate heritability despite (measured) confounders, can improve phenotype prediction, and increase gene-based, multi-trait association signal. CMMs regularly improve prediction, scale to thousands of phenotypes, and can uncover plausible GWAS hits entirely missed by LMMs. Altogether, multi-trait mixed models are invaluable for intrinsically multitrait tasks, like phenotype imputation and low-rank decomposition, and, surprisingly, can be much faster than LMMs; however, I find only small, and inconsistent, benefits for single-trait-oriented objectives like heritability estimation and out-of-sample prediction.
The challenges in this thesis are primarily computational. Naively, multi-trait approaches model an N × P matrix of P phenotypes measured on N samples as a long Gaussian vector, inducing prohibitive O(N3P3) computations. Fortunately, the parsimonious matrix normals underlying mixed models enable simpler O(N3+P3) expressions. This is summarized by a new decomposition for positive semidefinite tensor products that, under a crucial assumption, facilitates cheap evaluation of ubiquitous low-level operations like multiplication.

Advisor: Marchini, J
The characterisation of mycobacterial control profiles and underlying immune signatures in patients with latent tuberculosis infection and active disease

Despite the progress that has been made with global control programmes, tuberculosis (TB) remains a significant challenge to health. Better diagnostics, shorter and more effective treatment regimens and improved vaccines are urgently needed. There is also increasing awareness of the need to tackle the huge burden of latent TB infection, which is estimated to affect one-third of the global population. Targeted preventative therapy is the pragmatic solution to this problem. Unfortunately, current diagnostics lack the necessary resolution to accurately identify individuals at risk of progressing to active TB disease. It has recently been proposed that TB exists on a continuous spectrum, which likely represents the dynamic interaction between the host and pathogen. Delineating this spectrum may identify individuals at risk of disease reactivation who would benefit from targeted treatment. The work presented in this thesis describes the novel use of an ex vivo whole blood functional assay to measure the capacity of individuals with active TB disease and latent infection to control mycobacterial growth. The assay identified differential functional responses that discriminated between conventional diagnostic groups, but also showed considerable overlap. Enhanced mycobacterial growth control occurred in patients with active TB disease, which may reflect a general state of immune activation. The wide range of responses seen among latently infected patients is consistent with the concept of a spectrum of infection. Characterisation of different control profiles was undertaken using a multi-platform approach. Differential gene expression was dominated by type I interferon and inflammatory signatures seen in active TB patients and some individuals with latent TB. Clustering analysis showed clear associations with functional responses. Cytokine and chemokine studies revealed strong correlations with mycobacterial growth control. Finally, increases in inflammatory monocytes, polyfunctional T cells, activated and atypical memory B cells and IgG1 responses all demonstrated correlations or associations with functional responses. These findings have potential application in developing a biosignature for TB reactivation and predictive models of risk that warrant further investigation.

Advisor: McShane, H
Formation and growth of fibrous mineral veins in mudrocks during burial and uplift

Fibrous mineral veins are extremely important structures in mudrocks because they represent phases of geological activity that occurred after the deposition of the host rocks. They are, therefore, crucial for unravelling the geological history, especially for analyzing postdepositional tectonism, diagenesis, and associated physical and chemical conditions. This research focuses on the investigation of fibrous mineral (gypsum and calcite) veins in mudrocks, using integrated field, petrographic, and geochemical methods. The aim is to obtain a better understanding of mineral vein systems in fine-grained rocks over spatial scales ranging from reservoir to microns, regarding the timing, formation mechanism, vein growth, fluid and stress conditions, fluid-rock interaction, and their expressions in vein texture. The results reveal that fibrous mineral veins are produced during different stages of basin evolution.
Fibrous calcite veins in Lower Jurassic shales in the Wessex Basin have a diagenetic growth history during early burial of the sediments. In contrast, the formation of satin spar veins in the Triassic marls of the Bristol Channel Basin is closely associated with tectonic compression during basin uplift. However, both the gypsum veins and calcite veins owe their origin to overpressure and incremental fibre growth in closed systems, with their textures exhibiting similar antitaxial characteristics. Host rock lithology, defined by mineral components, fabrics and mechanical properties, mainly controls the development of the veins. The research highlights the kinematic implications of fibre orientations for host rock deformation and the EBSD measurement of crystallographic orientations of fibres for the analysis of paleo-stress state during fibre growth. Evidence for the force of crystallization exerted by mineral fibres, which has largely been ignored in previous studies, are revealed based on field and petrographic observations. The vein systems presented in this research provide an analogue for future studies on sub-seismic scale fracture/vein characterization and prediction in mudrocks either as caprock or source rocks for hydrocarbons.

Advisor: Cartwright, J