VictorJuiz/thesis huggingface dataset:
Geometric morphometric exploration of the skull phenotypic matrix of Columbimorphae (Pteroclidiformes, Mesitornithiformes and Columbiformes): Allometry, heterochrony, ecological factors, modularity, biomechanics, diet, and domestication

This thesis deals with the interplay between developmental constraints and ecomorphological factors in the skull shape evolution in Columbimorphae. Columbimorphae is a group of birds that includes the Mesitornithiformes (mesites), Pteroclidiformes (sandgrouses), and Columbiformes (pigeons and doves). Columbiformes have a wide geographical distribution, exhibit a wide range of body sizes, and have high ecological and morphological diversity. It includes iconic species like the dodo (Raphus cucullatus), the Rodrigues solitaire (Pezophaps solitaria), and the passenger pigeon (Ectopistes migratorius).
This diversity shown in Columbiformes, along with their well resolved phylogenetic relationships makes this clade a good study system to perform macro-evolutionary research. This thesis is focussed on a pluralistic view of phenotypical evolution. For this reason, I tested ecological factors (distribution, body size, centroid size, feeding strategy and biomechanical performance) and developmental factors (allometry, heterochrony, modularity, integration) to examine the skull evolution.
My research sheds light into various evolutionary phenomena, showing that the dodo and the Rodrigues solitaire follow allometry and heterochrony; that modularity and integration are not sufficient to explain the columbiform skull shape; that ecomorphological factors have shaped the pigeon skull; that differences in biomechanical performance are associated with different feeding strategies; that domestication does not only increases the amount of morphological disparity using existent axes of variation but successfully explores and incorporates new axis of variation; and that different phenotypic matrices are not usually comparable and generalizable because matrices of wild Columbiformes, domestic (Columba livia) and feral individuals (C. livia) are unequal and do not share the same axes of variation.
My overall results suggest that both ecomorphology and development influenced the evolution of the pigeon skull. My research also warns against the generalization of species patterns of constraints (modularity and integration) across taxonomic scales.

Keywords: Domestication
Allometry
Evolution
Macroevolution
Modularity
Columba livia
Intrgration
Fancy pigeons
Heterochrony
Pezophaps solitaria
Lines of least evolutionary resistance
dodo
Columbiformes
Geometric morphometrics
Advisor: Friedman, M
Benson, R
Neural world models supporting flexible behaviour

A core component of intelligent behaviour is our ability to flexibly adapt to changes in the external world or internal goals. In order to achieve such flexible behaviour, it has been argued that humans and animals maintain sophisticated internal models – or cognitive maps – of the environment that monitor the state of the world and encode the relationships between objects. This thesis examines 1) how internal models may be monitored and updating in a changing world, and 2) the general principles under which internal models may be learnt, how they may be used for flexible and efficient planning, as well as how they may be generalised to new experiences.
In the first part of the thesis, we investigate the neural substrates of maintaining flexible behaviour in a changing environment. In order to maintain flexibility, the uncertainty in internal models guiding behaviour needs to be increased when the current behavioural strategy no longer accurately reflects the environment. We use functional MRI to measure an internal model representing participants’ beliefs about the state of the world in medial orbitofrontal cortex. We show that changes in pupil diameter – thought to index the neuromodulator noradrenaline – predict increases in uncertainty in this internal model. Anterior cingulate cortex tracked the certainty in participants’ beliefs and predicted changes in pupil diameter. Together these results provide evidence for neuromodulatory control of the flexibility of internal models in dynamic environments.
In the second part of the thesis, we investigate how internal models may be learnt, generalised to novel situations and used for flexible and efficient planning. Cells in the brain that fire when an animal is in certain spatial locations are an internal model of space. They also provide “ground truth” representations of a 2-dimensional environment allowing us to investigate general principles under which they may emerge. We show these cells can be thought of as representing the underlying structure or topology of the environment. We further show how these representations can be used for flexible and efficient planning of arbitrary structures, as well as how they may be generalised to novel situations allowing reuse of previously learnt knowledge. These results suggest the way we process space may be an instance of general coding algorithms responsible for organising knowledge of all different kinds.
Together, these studies demonstrate how neural world models may support flexible behaviours.

Advisor: Behrens, T
O'Reilly, J
Online algorithms for markets

The thesis consists of two parts, both dealing with issues of uncertainty and incentives in markets. In the first part we examine the online properties of markets. In most of the Mechanism Design literature, markets are studied under the assumption that all participants are present at the same time and can seamlessly interact with each other. This may not always be the case in practice. We consider markets where buyers and sellers appear in sequence, one after another, without overlapping and it is the duty of an intermediary to coordinate with them. We take the role of that intermediary and our goal is redistribute items among them to maximise certain objectives, namely the profit, social welfare or gain from trade. We focus on posted price mechanisms, which are robust and truthful. There are two natural, complementary variants of the order of arrival of the agents. In the first case, an adversary dictates their order, but the intermediary has prior, distributional information about their valuations, similar to the prophet inequality setting. In the second, the adversary selects their valuations but their order is a uniformly random permutation. We obtain asymptotically tight worst-case guarantees for both cases, under a competitive analysis benchmark.
In the second part, we study the strategic implications that arise from adding one extra option to the miners participating in the bitcoin proto- col. We propose that when adding a block, miners also have the ability to pay forward an amount to be collected by the first miner who successfully extends their branch, giving them the power to influence the incentives for mining. We formulate a stochastic game for the study of such incentives and show that with this added option, smaller miners can guarantee that the best response of even substantially more powerful miners is to follow the expected behavior intended by the protocol designer. Moreover, pay-forward can be used to alleviate the predicted instability when block rewards are small compared with respect to transaction fees, by smoothing out the variability of the rewards collected from transaction fees.

Keywords: Online Algorithms
Cryptocurrencies
Algorithmic Game Theory
Advisor: Koutsoupias, E
Beauty and the Gods in Archaic Greece

This thesis is about the relationship between the beautiful and the divine in Archaic Greece. By examining the literary, epigraphic and archaeological records, it seeks to understand how ideas, representations and experiences of beauty informed Greek relations with the gods in the Archaic period (c.750-480 BCE). One aim of the thesis is to elucidate the significance of beauty for Archaic conceptions of the gods. The first chapter explores the representation of the beautiful and the divine in Archaic epic, especially Hesiod and Homer, who profoundly affected attitudes to the gods from the Archaic period to late antiquity. How conceptions of beauty and the gods oriented worshippers’ values, actions and the character of their experiences is the focus of the remaining chapters. The second core aim of the thesis, therefore, is to explore the significance of beauty for different forms and contexts of divine worship in Archaic Greece: from musical performances for the gods in chapter two, to developments in sacred architecture in chapter three, to the practice of giving objects to the gods in chapter four. As chapters three and four highlight, the material culture of Greek sanctuaries changed dramatically between the late eighth and early fifth centuries BCE. A central argument of the thesis is that the value and experience of beauty were integral to these changes, which had enduring consequences. Despite its under-representation in scholarship on ancient aesthetics, the Archaic period witnessed a transformation in Greek culture which was pivotal for the religious and aesthetic values, expectations and experiences of later generations of classical antiquity and beyond.

Keywords: Beauty
Archaic Greece
Greek Gods
Advisor: Elsner, J
Metcalf, C
Parker, R
Therapeutic targeting of histone H3 lysine 36 trimethylation-deficient cancers

Histone modifications play diverse and essential roles in the maintenance of genome integrity, as evidenced by the frequency at which different histone marks are dysregulated during tumourigenesis. The trimethylation of histone H3 at lysine 36 (H3K36me3) and SETD2, the enzyme solely responsible for this histone mark, are important in many cellular processes and have been reported to be lost or mutated in cancers. Targeting cells that are deficient in H3K36me3 or SETD2 is therefore an attractive therapeutic strategy for specifically killing tumour cells with minimal effect on normal tissue using the concept of synthetic lethality.
Using a previously reported synthetic lethal interaction between SETD2 and the WEE1 kinase as a starting point, a high-throughput small-molecule compound screen was performed in cells in which SETD2 had been deleted using CRISPR-Cas9 technology. The aim of this screen was to identify two categories of hits: (1) those that enhance the SETD2-WEE1 synthetic lethality (synergy hits) and (2) those that target SETD2-CRISPR cells on their own (novel synthetic lethality hits).
Analysis of the synergy hits focused on histone deacetylases (HDACs), which revealed that the Class I HDACs HDAC1 and HDAC2 had differential effects on the SETD2-WEE1 synthetic lethality. Furthermore, depletion of both HDACs individually led to a significant loss of viability specifically in SETD2-CRISPR cells. The results suggest a putative synthetic lethality between SETD2 and HDAC2 that bears certain similarities to the relationship between SETD2 and WEE1.
The most potent among the novel synthetic lethality hits was a compound called RITA, which demonstrated the ability to target SETD2 deficiency in the form of CRISPR knockout, siRNA knockdown, and naturally occurring mutations. This was accompanied by a striking upregulation and activation of the p53 tumour suppressor, activation of the DNA damage response, cell cycle arrest, and apoptosis. These phenotypes were further associated with increased levels of replication stress markers and reduced replication fork velocity. The potential mechanism of action of this compound was investigated via a number of strategies based on current knowledge of SETD2 and RITA, as well as more exploratory approaches. Overall, the data indicate that perturbations in the G1/S transition and replication stress play key roles in mediating RITA’s cytotoxicity in the context of SETD2 loss.

Keywords: Drug discovery
Epigenetics
Synthetic lethality
Advisor: Humphrey, T
How decisions lead to conflicts – The roles of elephant behaviour and agricultural practices in elephant crop consumption

Elephant crop consumption can have negative direct and indirect consequences for subsistence farmers (e.g. crop losses, livelihood vulnerability, fear) and can result in a reduction in support for the conservation of elephants, which are IUCN classified as vulnerable, and can even result into physical conflicts that can lead to injuries and death of people and elephants. In this thesis, I examine how decisions that elephants make in their movements and foraging behaviour, and farmers make in their mitigation methods, influence elephant crop consumption in the eastern panhandle of the Okavango Delta, Botswana. Chapter 2 shows that elephant corridors are important for exploratory movements of elephants towards the river, and that sexual segregation occurs in elephants’ responses to agricultural fields. Female elephants showed encamped movements in agricultural fields at night and during the dry season, supporting the predation-risk hypothesis, as crop consumption was safest for elephants at these times. Chapter 3 and Chapter 4 suggest that the local natural diet of elephants may be deficient in micronutrients – in particular phosphorus - which indicates that elephants need to consume large amounts of vegetation in order to satisfy their micronutrient levels. This makes crops an optimal alternative, due to their higher levels of absolute phosphorus and dry matter intake. Chapter 5 reveals that one-off inputs of materials to support farmers to deter elephants from their fields do not result in the sustainable mitigation method use desired by providers of materials. In order to empower farmers to live with elephants, external bodies such as government and non-governmental organisations could increase logistical support, and facilitate the improvement of the supply-chain of materials for mitigation methods. Crop consumption mitigation could be improved if sexual segregation in crop consumption patterns are taken into account and crops are harvested earlier (Chapter 2), if alternative micronutrient sources are provided in elephant corridors (Chapter 3 and Chapter 4) and farmers are included in the development and implementation of mitigation method interventions (Chapter 5).
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Advisor: Coulson, T
Songhurst, A
McCulloch, G
Stronza, A
Human genetic variation and the dispersal of Bantu-speaking populations

The expansion of Bantu-speaking agropastoralist populations had a significant impact on the genetic, linguistic, and cultural variation of sub-Saharan Africa. Bantu languages originated in an area close to the present-day border between Cameroon and Nigeria not earlier than 5000 years ago. From their homeland, these languages spread south and east through most of sub-Saharan Africa becoming by far the largest African linguistic family. Even though it is generally accepted that this dispersal was the result of the migration of people, there are still many unanswered questions about the dynamics of this process. The demic consequences of this dispersal are reflected in the relatively high genetic homogeneity observed across most of sub-Saharan Africa populations but its implications on the genetic diversity of the continent are not fully appreciated yet. Incorporating African populations’ genome-wide data available from Prof. Capelli’s research group with previously published data, this thesis addresses and tries to answer some of the questions related to the genetic impact of this dispersal.
I start by addressing the process of admixture between the migrating Bantu speakers and previous inhabitants in south-east Africa.
Rejecting the hypothesis of a potentially pre-Bantu component found in south-east African Bantu-speaking populations as the result of extensive gene flow, I highlight the importance of the demographic dynamics associated with the Bantu dispersal in shaping the genetic diversity of these communities. I then focus on the analysis of the genetic variation observed in sub-Saharan Niger-Congo populations, highlighting the impact of admixture events and the existence of population structure within Bantu speakers, often considered as a genetically homogeneous group. Lastly, I attempt to mask the admixture events I found and reconcile genetics, geography, and linguistics in order to reconstruct the relationships among the Bantu-speaking populations across the continent.
Overall, my results emphasize the diversity observed in Bantu-speaking populations and the impact their rapid dispersal and contact with other communities had on the genetic variation they show.

Keywords: Human genetic variation
Africa
Admixture
Bantu-speaking populations
Advisor: Capelli, C
The impact of everyday violence on identity: an experimental study in Nigeria

“Everyday” violence, such as robbery, burglary, or interpersonal assault, is endemic throughout much of the developing world, yet there has been relatively little research about its effects on social identity and intergroup relations. Using original data collected from an experiment embedded in a survey of over 1,000 people in Lagos, Nigeria, I empirically assess the impact of the acute threat of everyday violence, as well as actual victimization, on social identity, trust, and attitudes about violence and politics.
I find that exposure to everyday violence significantly impacts identity – and that its effects vary considerably depending on whether the individual was “merely” threatened by violence or actually experienced it firsthand. The fear induced by an acute threat of everyday violence is broadly identity-affirming, increasing evaluations of and warmth toward the primary in-group and depressing trust in and attitudes toward the out-group. Actual victimization, however, has the opposite effect, leading to a greater openness toward and trust in the primary out-group. Neither threat nor victimization significantly impacts attitudes about politics or the future use of violence.
Drawing on over 70 interviews with violence-affected-Lagosians, I argue that the way expectations about one’s security and community are defied and then rebuilt may account for this effect. Specifically, I point to three contributing factors: 1) disappointment in the apathetic in-group response; 2) “empathy-born-of-violence;” and 3) positive religious coping. These dynamics play out over time and are largely dependent on interactions with others; in this sense, one’s social environment may significantly shape whether victimization leads to openness to others and to what extent.
This research demonstrates, among other things, the profound and diverse ways in which exposure to everyday violence affects identity, and the importance of incorporating the study of everyday violence into research agendas about the dynamics of identity and conflict.

Keywords: Intergroup Relations
Nigeria
Conflict
Identity
Africa
Violence
Advisor: Cheeseman, N
Harding, R
Using routinely collected data to estimate postoperative complication rates, temporal trends, and geographical variation in Dupuytren's disease surgical management in England

Introduction: Dupuytren's disease (DD) is a common fibro-proliferative condition of the hand and it is usually treated surgically. The primary aim of this thesis was to evaluate DD surgical management in terms of patient characteristics, risk of postoperative complications and reoperation, temporal trend and geographical variation in England. Secondary aim was to investigate the association between DD and non-genetic factors. Methods: A longitudinal population-based cohort study was conducted using Hospital Episode Statistics database. Cumulative incidence and self-controlled case series methods were used to investigate postoperative complications. Directly standardised rates were calculated to evaluate temporal trends and geographical variation of primary Dupuytren’s disease surgery. To investigate the association between DD and non-genetic factors a systematic review was undertaken. Results: Between 1 April 2007 and 31st March 2017, 158,119 DD operative procedures were performed in 121,488 adult patients in England. DD surgery was most commonly performed in male, elderly, white patients living in less financially deprived areas and few comorbidities. Most operations performed were primary limited fasciectomy (LF). There was a significant incidence of local and serious systemic complications following DD surgery. The rate of reoperation was highest after primary percutaneous needle fasciotomy compared to primary LF or dermofasciectomy. There was an overall increasing trend and striking variation in the rates of primary DD surgery in England. A strong association was found between DD and advanced age, male gender, family history of DD, diabetes, heavy alcohol drinking, cigarette smoking and manual work exposure. Conclusions: The study findings have significant clinical importance as they helps to better understand DD surgical management.

Keywords: Complications
Temporal trends
Dupuytren's
Hospital Episode Statistics (HES)
Geographical variation
Advisor: Furniss, D
Prieto-Alhambra, D
Non-polar InGaN quantum dots: polarisation-controlled semiconductor single-photon sources at on-chip temperatures

Polarisation-controlled single-photon sources are at the heart of quantum information applications, e.g. truly secure communication with polarisation-based quantum key distribution protocols, and all-optical quantum computation with logic gates defined by the polarisation states of photons. Non-polar (1120) a-plane InGaN/GaN quantum dots are one of the strongest candidates due to their ability to operate at temperatures similar to those in on-chip conditions, and intrinsic polarisation properties built into the material.
Time-integrated, time-resolved, polarisation-resolved micro-photoluminescence, and Hanbury Brown and Twiss studies are conducted on a-plane QDs fabricated by two different methods, yielding results that are not only a significant step forward in nitride-based single-photon research, but also open up the underexplored field of high-temperature semiconductor quantum dot photophysics. In particular, the first demonstration of ultrafast polarisation-controlled single-photon generation from a semiconductor quantum dot platform at 220K (-53 °C) is achieved, along with an unexpected observation of temperaturedependent fine-structure splitting previously unseen in other systems.
Radiative recombination lifetime and slow-timescale spectral diffusion have been investigated with statistical significance, producing mean values that are on par with stateof- the-art nitride developments in the literature. Combined with efforts from theory collaborators, the insensitivity of radiative lifetime and optical polarisation to differences in the physical dimension, geometry and material composition of the quantum dots has been demonstrated. In particular, a-plane InGaN quantum dots have been shown both theoretically and experimentally to exhibit high polarisation degrees with deterministc axes along nitride crystal directions, from cryogenic to temperatures above 200 K. These developments advance the field of single-photon science and bring the current platform a step closer to on-chip quantum information applications.
Meanwhile, other temperature-dependent optical properties, such as emission intensity quenching, exciton linewidth broadening and phonon-assisted redshift, have been investigated in detail. Parameters relevant to thermally assisted processes in the a-plane platform, including acoustic phonon scattering strengths, typical activation energies of local potential depths and Huang-Rhys factors, have also been evaluated for the first time, thereby facilitating further development of the platform and fundamental research of related photophysics.

Advisor: Taylor, R