VictorJuiz/thesis huggingface dataset:
Development and non-equilibrium functions of a supramolecular oscillator

Lipids are an important class of chemicals which appear simple in isolation, but collectively show complex supramolecular dynamics. Biology uses lipids ubiquitously and this thesis demonstrates ways in which chemical systems of lipids can emulate traits found in living systems. The primary theme of this thesis is how synthetic, metastable lipids can generate unexpected complexity, for example through emergent selection mechanisms and unique chemically oscillating systems.
Chapter 1 gives a general introduction to self-reproducing lipids both in the context of prebiotic chemistry and as a source of valuable systems-level behaviour. Physical autocatalysis is introduced and presented as a central principle in origins of life research and for related applications. Special consideration is given towards the generation of structural complexity and out-of-equilibrium concepts, both which are important hallmarks of life.
Chapter 2 describes an investigation into competition between self-reproducing lipids. Mixtures of lipids which continuously form and breakdown over time revealed two selection mechanisms, one of which involved an unexpected reaction pathway for some lipids, at the expense of competitors. This work showed new ways that simple chemicals may have become dominant species in prebiotic environments.
Chapter 3 introduces a unique supramolecular oscillator based upon autocatalytic micelles. The development of this system and its core principles are discussed in detail. Supported by high resolution kinetics and other control experiments, the underpinning mechanism of the oscillator is explored. This system has several properties which set it apart from other chemical oscillators and will be a source of interesting chemical systems in the future.
In Chapter 4, the responsivity of the oscillator is used to transduce information in waves of chemical concentration. Fine control over the frequency and period over the waveforms is shown. Chapter 5 uses the oscillator to guide the transport of chemical cargo between phases, as a demonstration of the potential spatiotemporal control that is possible with such systems.

Keywords: organic synthesis
supramolecular
autocatalysis
systems chemistry
origin of life
Advisor: Fletcher, S
Do leaders matter? International conflict, leader traits, and leader selection

Why do leaders start conflicts? The bulk of IR tends to look outside of leaders, focusing on institutional and structural forces. Where there is more uncertainty is whether the factors within leaders might also influence their decision to start conflicts. Thus, this thesis asks the question: To what extent do the personal traits of leaders influence their decision to start international conflicts? Recent literature has found that several traits of leaders strongly predict conflict initiation, such as military experience and age. However, these findings may be biased if leaders with these traits are more likely to be selected into environments where the probability of conflict is greater. Yet, this problem of selection has not been given enough attention in previous research. To deal with the problem of selection, I develop a unique strategy, which I call the “counterfactual leader strategy.” The core idea of this strategy is that each time a leader is selected in reality, there is a counterfactual world in which someone else was selected instead. I call these individuals “counterfactual leaders” and the traits of these individual can be used as a “placebo” to indirectly test for bias. Since the counterfactual leaders' traits should not be associated with conflict initiation, any association reveals bias in the traits of leaders. Using an original dataset on leaders and counterfactual leaders between 1945 and 2004, I find that several traits of counterfactual leaders predict conflict in the same way as those traits among leaders. I argue this is because states that frequently engage in conflict are more likely to have candidates with these traits due to demographics and thus have a higher probability of selecting a leader with one, even if by chance. Therefore, I argue traits do not influence leaders’ decision to start conflicts, and what matters instead is the environment they are selected into.

Keywords: leaders
counterfactual
leader selection
international conflict
Advisor: Johnson, D
Commenting on ancient texts: interpreters and their audience in the Graeco-Roman world

The present study offers the first comprehensive work on papyrus commentaries in the context of ancient scholarship. Each chapter treats a different aspect of these texts. In Chapter 1 I provide the reader with a general overview of the main features of ancient commentaries in terms of content and layout, analysing a selection of examples focusing on different literary genres and comparing them to their modern counterparts. In Chapter 2 I study the material characteristics of papyrus commentaries, i.e. handwriting, use of the recto / verso, presence / absence of abbreviations, corrections, lectional and critical signs, and physical reinforcements of the papyrus. Chapter 3 takes into account the other main ‘exegetical typologies’ (treatises, marginal annotations, paraphrases, hypotheses, diegeseis), and studies in particular their similarities and differences with respect to commentaries. Finally, Chapter 4 investigates the contexts of production, use, and safekeeping of papyrus commentaries, i.e. whether they could belong to students, teachers, or scholars, and could be kept in public or private libraries and collections. This study intends to offer a better understanding of how ancient people read and studied their ‘classics’ in the light of the fundamental testimony of papyrus fragments.

Keywords: papyrology
ancient Egypt
bibliology
Greek paleography
commentaries
classical philology
ancient scholarship
Advisor: Hutchinson, G
Colomo, D
An edition of Svipdagsmál

Section I of this thesis establishes a text of the two Old Norse poems Gróugaldr and Fjǫlsvinnsmál, known collectively as Svipdagsmál (Sv). Previous editions are surveyed, discussing their use of the two MSS upon which the emended text offered by this edition is based, Stockholm Papp. 15 8vo and Rask 21 a (I.1). Reasons are given for the choice of these two MSS (out of the forty six MSS known to the editor) and the two MSS are described (I.2). The emended and normalised text is accompanied by a translation and summary apparatus (I.3), followed by a Commentary (I.4). A reconstruction is attempted of the history of the MS tradition (I.5). This reconstruction is based on computer collation of the MSS and database analysis of the collation, together with external evidence where available. The reconstruction confirms the choice of Stockholm Papp. 15 8vo and Rask 21 a: most of the other MSS appear descended from one of these two.
Section II gathers together analogues to the poems in Celtic, Icelandic and Scandinavian ballad tradition. The story was earlier an Irish mythical tale, itself an adaptation of an international popular tale of the "giant's daughter" type (II.2). Traces of this original tale are to be found in Icelandic popular tradition (II.3). The Scandinavian Ungen Svendal ballads seem derived from Sv itself (II.4).
Section III analyses the poet's use of Old Norse poetic and mythological materials. The poems are skilful studies in Eddic style (III.2) and the poet shows a deliberate creativity in the adaptation and invention of mythological material (III.3-5).
Evidence is presented for a date of composition in the early thirteenth century (IV.1). A study of the art of the poems shows a poet of rare skill (IV.2).

Keywords: Old Norse
Old Norse poetry
Svipdagsmál
edition
manuscripts
Advisor: Dronke, UM
Measurement of oscillations in solar boron-8 neutrinos and studies of optical scattering in the SNO+ detector

SNO+ is a large-scale liquid scintillator experiment based in Sudbury, Canada, capable of probing many aspects of neutrinos. One major property of interest is the neutrino’s ability to oscillate between different flavours, an indirect demonstration that neutrinos must have mass.
This thesis performs the first ever measurement of oscillations from 8B solar neutrinos in the scintillator phase of SNO+. Assuming the current global fit flux of 8 B solar neutrinos, the neutrino oscillation parameter theta_12 was measured to be 38.9 degrees +8.0-7.9 degrees, using an initial 80.6 days of data. This result is consistent with the current global fit result of 33.44 degrees +0.77-0.74 degrees. A sensitivity study indicates that the precision of this result is capable of improving by at least a factor of two within two years of livetime.
On top of this, substantial improvements were made to all aspects of the optical calibration system known as SMELLIE. This is a series of optical-wavelength lasers whose light is emitted from optical fibres attached to the edge of the SNO+ detector. By developing a new analysis, this system was able to measure the scintillator extinction lengths as a function of wavelength and time in-situ for the first time. A new analysis was also built and demonstrated to observe changes in scattering and scintillator re-emission properties of the scintillator as a function of time and wavelength. Alongside this, major upgrades were made to both the hardware and simulation of the SMELLIE system, enabling higher-quality data to be taken, and simulations to be made with much greater speed.

Keywords: optical calibration
Bayesian Analysis
neutrino
particle physics
MCMC
neutrino oscillations
SNO+
solar neutrinos
Advisor: Reichold, A
Uneven pathways: three novel mechanisms of intergenerational transmission of (dis)advantages

This thesis advances the understanding of the socioeconomic inequalities in children’s development by examining three novel mechanisms of intergenerational transmission of (dis)advantages. These channels are founded on a dynamic understanding of the process of social reproduction. Each one is illustrated with reference to the cases of the UK or the US.
The first empirical chapter examines how parents respond to their children’s early physical health problems and delves into the enduring consequences of these parental responses. Using twins fixed effects models, the findings reveal that, on average, parents exhibit negative responses when their children face early health problems, and that these responses have a lasting negative impact on the children’s educational achievements. Surprisingly, the effect of health problems on parental responses does not vary across socioeconomic groups. The second study examines whether mothers adapt their level of cognitive stimulation as a response to children’s developmental declines, and whether this is a socially stratified process. The results obtained from a series of two-way fixed effects and fixed effects counterfactual models indicate that, on average, mothers respond to their children’s skills declines by reducing their cognitive stimulation. This pattern is especially pronounced within impoverished families or those with low educational levels. In the final empirical chapter of this thesis, attention shifts to exploring whether mothers’ occupation-specific skills influence the process of development of their children. Exploiting changes in mothers’ jobs during their children’s upbringing, the results suggest that mothers’ mathematical occupation-specific skills have a positive effect on children’s mathematical ability and that high-SES children especially benefit from the skills upgrading of their mothers.
This dissertation discusses the substantive implications of each of these mechanisms and tests them empirically. It is only by disentangling the complex combination of channels through which inequality is transmitted across generations that appropriate policy responses can be elaborated.

Keywords: inequality
social stratification
intergenerational transmission of advantage
child development
Advisor: Monden, C
Evolution of phenotypic diversity

Phenotypic diversity, also known as phenotypic heterogeneity, occurs when individuals within a species have different phenotypes. Phenotypic diversity plays a crucial role in adaptation, and understanding how it is maintained is fundamental for comprehending the complexity of life. In this thesis, I use theoretical approaches to investigate different mechanisms that support the selection for variation. Specifically: (1) I model the optimal degree of coordination in the division of labour in a non-clonal population, and predict that communication between individuals would be less frequent in a population with low relatedness; (2) I show that the temporal scale of abiotic environmental fluctuations can play a crucial role in favouring a monomorphic or polymorphic population, that short-term variation selects for diversity, but long-term variation selects against it; (3) I develop and test a new form of cheating strategy that manipulates other social group members and find that it can lead to arms-race-like dynamics, which can help explain the genetic complication found in nature; (4) I construct a general model to incorporate different properties in experimental setups and provide general principles for when the cheater-cooperator ratio remains stable and when oscillations occur; (5) I examine how comparative studies, an important tool for validating theoretical predictions, have quantified abiotic environments and highlight the potential problem with correlating climatic quantities and using environmental predictability. Taken together, this body of work extends our knowledge on phenotypic diversity and identifies several promising research directions related to eco-evolutionary feedbacks.

Advisor: West, S
Cooper, G
Investigating the role of suppressed hydrolases during Pseudomonas syringae infection

The apoplast, the extracellular space outside the plasma membrane of plant cells, is an important battleground for plant-pathogen interactions. Plants secrete hydrolytic enzymes into this space which are targeted by pathogen inhibitors. Previous work used activity-based protein profiling coupled to mass-spectrometry (ABPP-MS) to monitor hydrolase dynamics in the apoplast of Nicotiana benthamiana upon infection with virulent Pseudomonas syringae pv. tomato DC3000. This work detected 171 hydrolase activities, including 60 that were suppressed upon bacterial infection. We hypothesised that suppression by a bacterial inhibitor may have evolved in response to a role in immunity for some of these hydrolases.
This thesis aimed to uncover novel immune hydrolases by testing six of the suppressed hydrolases for their role in plant immunity using ‘agromonas’ assays. We identified NbPR3, a glycosyl hydrolase with a role in bacterial immunity despite its annotation as an endochitinase. We identified a Nicotiana-specific substitution in the catalytic general base of NbPR3 that is essential for this resistance function. A hypothesis-driven approach to identify the substrate of NbPR3 uncovered a potential role in release of a bacterial elicitor to trigger the oxidative burst.
We also identified NbRD21, a papain-like cysteine protease whose function in bacterial resistance appears to be dependent on effector-triggered immunity. We used transient NbRD21 expression combined with rd21 knockout by CRISPR-Cas9 to test potential mechanisms of NbRD21 function. Proteomics data uncovered a role for NbRD21 in processing of receptor-like kinases.
Finally, we developed a high-throughput assay for monitoring NbRD21 activity and used it to confirm that NbRD21 is inhibited during P. syringae infection. We presented evidence that the inhibitor is novel, likely proteinaceous, and produced by multiple bacterial species. Overall, this work has identified two novel and distinct plant immune hydrolases, demonstrating the potential of ABPP-MS to uncover molecular plant-pathogen interactions in the apoplast.

Keywords: plants
proteases
plant immunity
Advisor: Van der Hoorn, R
Sweetlove, L
Synthetic studies towards sesquiterpenoids

Chapter 1 explores synthetic efforts carried out during this project towards α-bulnesene. Several radical cyclisation methods are discussed for constructing the 5,7-fused bicyclic framework. A concise and enantiospecific route to 5-epi-α-bulnesene, combining a new reductive rearrangement method, is presented.
Chapter 2 focuses on the total synthesis of daphnenoid A. A unique strategy towards this cage-like tetracyclic structure is developed via an intramolecular Diels–Alder reaction and a 20-step synthesis leading to an advanced intermediate to daphnenoid A is presented.

Keywords: total synthesis
sesquiterpenoid
Advisor: Robertson, J
Bayesian inference for biological time series

Inferring the parameters of time series models from observed data is essential across many areas of science. Bayesian statistics provides a powerful framework for this purpose, but significant challenges arise when time series models are misspecified due to complexities in the underlying process (e.g., heterogeneity in the modelled population, or when parameter values fluctuate over time), inaccurate numerical approximation of the forward model (e.g., in models involving differential equations), or the presence of non-stationary, non-independent error terms. We introduce a series of models and computational strategies for dealing with misspecification in time series inference problems, with a particular focus on time series problems arising in epidemiology and problems involving ordinary differential equations.
The models and inference strategies discussed include: 1. A generalisation of the Poisson renewal model to allow heterogeneous behaviour between local and imported cases, which we use to show that accounting for such heterogeneous behaviour is essential for accurate inference of the time-varying reproduction number (Rt); 2. A Bayesian nonparametric approach to flexibly learn time variation in Rt, which we show is capable of learning accurate and precise estimates of the parameter; 3. Estimates of the gradient and the error in the log-likelihood arising from numerical approximation of differential equations derived from a posteriori error analysis; and 4. A flexible noise process accommodating correlated and heteroscedastic error terms and whose form can be inferred from time series data using kernel functions. We motivate our methodological innovation by a comprehensive examination of the biases in inference that result from insufficiently accurate numerical approximation of differential equations, as well as time series inverse problems and models drawn from epidemiology, hydrology, and cardiac electrophysiology.

Advisor: Gavaghan, D
Lambert, B
Robinson, M
Lok Lei, C
Shrines and special graves in Britain and Ireland c.600-850

This thesis offers a reappraisal of the development of the cult of the saints in Britain and Ireland in the period 600-850, by situating the written, sculptural, and archaeological evidence for saints’ graves in the context of wider patterns of funerary practice between the fifth and ninth centuries. It also argues that there was great variety in the way that saints’ remains were presented in this period. The experience of visiting shrines depended on the audience, aspirations, and functions of the cult, as well as the cultural and economic context of the church in which it was situated. Saints’ graves were part of a spectrum of special graves that existed in the early medieval Insular world. Before the later seventh century, special graves were found at church sites and in traditional cemeteries, or in isolated landscape contexts. By the eighth century, special graves were created almost exclusively within ecclesiastical contexts. However, even within church sites the distinction between the grave of a saint and that of another honoured individual was not always obvious and unchanging. The location of the grave and the way it was marked was not necessarily a reliable indicator of saintly status. By comparing saints’ graves with other kinds of special graves, the similarities of form and function are revealed, demonstrating that the cult of the saints was adapted to local contexts and incorporated existing practices. The thesis argues that the influence of local burial practices and funerary monuments explains the variation in the types of shrines across Britain and Ireland as well as the unique forms of Insular shrines. This argument modifies and updates previous understandings of the development of the cult of the saints which have over-emphasised the influence of Frankish and Late Antique Mediterranean forms and neglected the contribution of Insular traditions.

Keywords: Christianity
shrines
conversion
funerary practice
special graves
early medieval
Ireland
Britain
cemeteries
cult of the saints
religious change
stone sculpture
Advisor: Gittos, H
Blair, W
Neural mechanisms of state-dependent sensory processing

A key purpose of the central nervous system is to transform sensation into action. During this process, identical stimuli can cause variable behavioural responses because of changes in the condition -- or, state -- of the brain. This response variability is a common phenomenon, yet the underlying neural mechanisms of how sensory information differentially interacts with varying network states remain obscure. In this thesis, we consider three such mechanisms in depth: inhibition stabilisation, neural variability and predictive learning. First, we analyse all-optical experiments where we were able to simultaneously record and insert neural activity in somatosensory cortex in vivo. Our results show that population activity is stabilised by inhibition, thereby allowing faint sensory stimulation to be detected and propagated downstream. In mice trained to detect these stimuli, we further observe that the neural variability across neurons modulated their perceptual performance, whereas this effect did not occur during passive stimulation. Therefore, maximising the cortical signal-to-noise ratio of behaviourally relevant stimuli is critical to facilitate activity propagation and perception. Separately, in a study of artificial neural networks, we demonstrate that it is advantageous for networks to continuously predict upcoming sensory information, as this facilitates learning of more complex working memory tasks. This could explain recent experimental findings showing that cortical neurons engage in predictive learning even when reward is absent. In sum, this thesis explores how sensory information interacts with ongoing neural activity in both biological and artificial neural networks, and explains mechanisms that underpin the variability of our behavioural response.

Keywords: recurrent neural networks
decoding
all-optical microscopy
calcium imaging
neural variability
perception
working memory
E/I balance
optogenetics
Advisor: Packer, A