VictorJuiz/thesis huggingface dataset:
The evolutionary consequences of parental effects

Parents modulate the phenotypes of their offspring, beyond the effects of the genes they pass on. These parental effects can have impacts on the fitnesses of those offspring, as well as the fitness of the parents themselves. Parental investment in offspring is expected to be under antagonistic selection through its beneficial effects to offspring, and its detrimental effects on the parent's own fitness. Evolutionary conflict over parental care is therefore expected to occur, and may cause evolutionary stasis. Furthermore, selection is also expected to act on offspring traits, in order to maximise offspring fitness within a given parental environment, generating predictions of parent-offspring coadaptation.
I tested the predictions of conflict and coadaptation in parent-offspring interactions, using a population of blue tits (Cyanistes caeruleus), a species in which adults provide biparental care to their offspring. I found evolutionary conflict over offspring body mass, which may explain stasis in this trait. I also used a cross-fostering design to test for coadaptation between parents and offspring, and siblings. I did not find evidence for parent-offspring coadaptation, nor did I find that siblings were important through either direct interactions, or in mediating parent-offspring interactions, suggesting that there is little family coadaptation in this species. In addition, I investigated whether a maternal effect on hatching time was a passive consequence of environmental changes, or was an anticipatory maternal effect actively placed in eggs to manipulate hatching time. The results from this analysis suggest the latter to be the case, and mothers appear to actively manipulate offspring hatching time to reduce the extent of hatching asynchrony, which may reduce fitness costs to the offspring.
By measuring the effects of interactions between individuals on phenotypes and fitness measures, I was able to show how parental effects on offspring can affect evolutionary dynamics. Such evidence of evolutionary conflicts has not previously been found, due to methodological issues with the ways in which selection has been measured. Thus, I highlight how gaps in knowledge about the evolutionary consequences of parental effects can be addressed using appropriate statistical tools and measures of fitness.

Keywords: Evolutionary Biology
Blue tits
Quantitative Genetics
Advisor: Hadfield, J
Sheldon, B
System, gesture, rhetoric: contexts for rethinking tintinnabuli in the music of Arvo Pärt, 1960-1990

This thesis addresses critical strategies that have been used, or might be used, to approach Pärt's tintinnabuli music. It has three main objectives: to question prevalent narratives drawn around the tintinnabuli concept, to suggest interpretative frameworks that could yield fresh insights into that concept's 'meaning', and to introduce new and neglected materials to anglophone Pärt discourse. In studying the mediating role of the tintinnabuli scholar, I also confront some of the ethical challenges associated with research on living composers. This project places special emphasis on localised narratives of production and influence in Pärt's music, and draws extensively on Estonian primary source material. A major hermeneutic guide has been the composer's 1994 description of seeking ‘the appropriate system for the gesture’, and this idea figures in each of the four main chapters. Chapter 1 describes and questions existing knowledge around tintinnabuli, approaching this task through a study of "Wenn Bach Bienen Gezüchtet Hätte …", a work chosen for its critically fertile 'cusp’ status. Chapter 2 concentrates on Pärt's explorations of 'Soviet serialism' from 1960-3, engaging with withdrawn and film scores in addition to the well-known "Nekrolog". I discuss this music in terms of a complex freedom-constraint interplay, and suggest links to the tintinnabuli style. Taking "Sarah Was Ninety Years Old" as a case study, Chapter 3 turns to listener-oriented frameworks of musical meaning. I offer an experiential reading of the piece that places tintinnabuli in dialogue with body-based theories of cognition. Lastly, Chapter 4 addresses texted tintinnabuli. I build up a reading of "Miserere" in terms of 'musical rhetoric', comparing Pärt's compositional strategies to those used by Josquin des Prez in the 1503 motet "Miserere Mei, Deus". I also consider the implications of music-rhetorical analogy for wider understandings of the 'tintinnabuli' concept.

Keywords: Estonia
serialism
Embodiment
Rhetoric
Pärt
Film
tintinnabuli
Soviet
Advisor: Grimley, D
Biophysical studies on the structure-function relationship of membrane-active peptides

It is becoming evident that protein conformation and function are sensitive to the local environment. Structural models are often reported, out of technical necessity, in environments only partially related to the native environment of the protein of interest. This is a major challenge for structural biology of membrane proteins, which are predicted to be highly sensitive to their local environment. The structural plasticity of membrane-active alpha helical peptides and proteins is explored in native-like model membranes in this thesis. On the one hand, alpha helical antimicrobial peptides (AMPs) and their destructive membrane insertion mode are characterised, and on the other, the viroporin p7 (Hepatitis C Virus), expected to form oligomeric channels, is investigated in a endoplasmic reticulum mimicking model membrane.
(I) AMPs: An engineering approach, which alters the antimicrobial insertion motif, is used to characterise distinct structure-function relationships linked between the primary and secondary peptide structures. Data is presented on different timescales and resolutions in order to understand the direct peptide location and orientation with respect to the membrane normal using solid-state NMR. Equally important are the global effects on the membrane bilayer and bacteria examined using atomic force microscopy (AFM) and fluorescence microscopy. Detailed dynamical changes and membrane order are explored by continuous wave EPR and solid-state NMR. Design principles that altered a pore-forming transmembrane AMP into a sequence that develops its potency in the membrane interface and shows broadspectrum antimicrobial activity are reported.
(II) Different structural models of p7 have been reported in the literature, most of which are in a detergent or organic solvent environment. A single-constraint approach is presented in order to probe their plausibility in an endoplasmic reticulum-like model membrane using pulsed EPR. This is combined with angular constraints from solid-state NMR experiments in the same membrane composition. The results point towards an ensemble hairpin structure in the environment probed. Further to this, the drug-membrane interaction of the p7 inhibitor, NN-DNJ (an iminosugar), is investigated, and a membrane interaction is observed with a pKa of 6.3 for the membrane-partitioned inhibitor.
Both systems are described in simplified models. While not yielding high resolution structures, these models are still an important consideration for the understanding of protein structure, topology and oligomerisation, which directly relates to protein function. The functionalities of the two systems explored in this thesis differ significantly, AMPs are naturally occurring antibiotics that compromise membrane integrity, whereas p7, with a defined channel architecture, is essential to the viral life cycle of Hepatitis C Virus. Hence, a structural spectrum of membrane-activity with relevance to infectious diseases is explored.

Advisor: Watts, A
The synthesis and characterisation of high performance electrode materials for Li-ion batteries

With the worlds demand for electricity constantly growing, energy storage technologies, and lithium-ion batteries in particular, are becoming increasingly important. One of the most significant issues concerning Li-ion batteries is that of safety. Graphite is the most commonly used anode material, however, due to its very low operating voltage vs Li+/Li0, reactive lithium can plate on the electrode surface, this is especially an issue for large batteries for use in electric vehicles. It would be useful to have an anode that operates at a higher voltage than graphite, but not at such a high voltage as to limit the overall potential of the cell.
To this end the focus of this thesis is the development of an anode material that operate at 1 V vs Li+/Li0. The lithium metal sulphides have previously demonstrated that they reversibly intercalate lithium at &Tilde; 1 V, but the reported performance is poor. Here LiVS2 is reinvestigated and optimised to display significantly improved electrochemical properties. At a rate of 100 mAg-1 a reversible capacity of over 200 mAhg-1 is achieved compared to less than 150 mAhg-1 previously reported, capacity retention is also considerably enhanced. LiVS2 deintercalates Li+ at the high voltage of 1.3 V, therefore attention is turned to LiV0.5Ti0.5S2 which intercalates Li+ at 0.9 V and deintercalation occurs at 0.9 V. The performance of LiV0.5Ti0.5S2 is optimised and the electrochemical process by which LiV0.5Ti0.5S2 operates is fully investigated. LiV0.5Ti0.5S2 displays a low irreversible capacity loss, low polarisation, good rate capabilities and good capacity retention.
As LiV0.5Ti0.5S2 operates at &Tilde; 1 V higher than graphite it is important to match it with a high voltage cathode so the overall potential of the cell is not significantly reduced. The lithium rich mixed metal oxides have been the focus of much research over the last 15 years and here they are investigated using a resorcinol-formaldehyde gel synthesis. 0.5Li2MnO3:0.5LiNi0.5Mn0.5O2 and 0.6Li2MnO3:0.4Li(Ni1/3Mn1/3Co1/3)O2 are both successfully synthesised and demonstrate excellent electrochemical performance. The specific capacities and capacity retention of both materials at a rate of 150 mAg-1 are excellent and better than virtually all previously reported materials of this type. Neutron diffraction was carried out on both materials to monitor structural changes on cycling.
Finally, LiV0.5Ti0.5S2 and the lithium-rich mixed metal oxides are combined in full 'rocking- chair' lithium-ion cells to successfully show that both materials can be used in practical lithium-ion batteries.

Advisor: Bruce, P
Armstrong, R
Homo theurgos: freedom according to John Zizioulas and Nikolai Berdyaev

For both John Zizioulas (1931), prominent Greek theologian, and Nikolai Berdyaev (1874–1948), renowned Russian religious philosopher, freedom is the question of ontology, i.e., freedom is about absolute otherness. Since to be is to act, and because to act means to create, we are only as long as we are capable of creating a radically unique reality. Being unique, our creation appears to every other person, including God, as a new reality. However, theistic theology claims that God added nothing to Himself by the creation of the world. Since according to this scenario human person cannot add anything to Being, we cannot speak about her ontological freedom. The doctrine of the divine image seems to be incompatible with the theistic concept of the divine omnipotence. Inquiry into the human freedom is therefore inevitably intertwined with the question of how God is God. Zizioulas's concept of the divine omnipotence does not envisage a space of freedom that God provides for human person from which she could create surplus in being. The French philosopher Etienne Gilson is therefore right when he writes that 'homo faber can never become homo creator because, having only a received being he cannot produce what he himself is not.' Berdyaev on the other hand locates the origin of our being in the Bottomless freedom or the Ungrund. The Bottomless freedom is Godhead from which both freedom of the divine Persons and that of the human person originate. Berdyaev explains that person can never create another person (something that is possible only for God). However, because person in spite of being created is not causally determined by the Creator, she can create her radically unique reality and thus realize her ontological freedom. Clearly, homo faber can never become homo creator (creator of other personalities), but this does not preclude person’s power to create surplus in being and to be homo theurgos.

Advisor: Zachhuber, J
Pattison, G
Ethics for rational animals: a study of the cognitive psychology at the basis of Aristotle’s ethics.

Aristotle is, at the same time, a student of psychology and a student of ethics. He takes the two disciplines to be linked: the ethicist should know something about the human soul. In this thesis, I start from a study of Aristotle’s cognitive theory to shed new light on his account of virtue, moral education and practical wisdom. I draw three main conclusions. First, I argue that eliminating certain false evaluative appearances is necessary to achieve virtue. It is widely assumed that achieving virtue requires eliminating vicious desires. I show that it also requires eliminating the false evaluative appearances that give rise to vicious desires. Second, I show that moral education addresses first and foremost the workings of our perceptual-recognitional faculties. Moral education trains us to recognise fine things (kala) perceptually. Third, I argue that Aristotle develops a notion of practical wisdom (phron&emacr;sis) as a distinctive kind of rational excellence. Unlike other rational excellences, practical wisdom is persuasive as well as discriminative.
Although its goal is to reconstruct Aristotle's views on the links between ethics and psychology, this study is not guided by historical interest only. Some details of Aristotle’s cognitive theory are outdated. However, his observations on attention, on rational and non-rational cognition, and on practical and theoretical thought are always deep and often persuasive. The theory of virtue, practical rationality and moral education Aristotle develops taking into account these observations is controversial, but it continues to call for our close philosophical consideration and assessment.

Advisor: Coope, U
Moss, J
A biofilter process for phytoplankton removal prior to potable water treatment works: a field and laboratory study

Phytoplankton blooms compromise the quality of freshwater ecosystems and the efficient processing of water by treatment works worldwide. This research aims to determine whether in-situ filamentous biofiltration processes mediated by living roots and synthetic filters as media can reduce or remove the phytoplankton loading (micro-algae and cyanobacteria) prior to a potable water treatment works intake.
The underlying biofiltration mechanisms were investigated using field and laboratory studies. A novel macroscale biofilter with three plant species, named the "Living-Filter", installed in Farmoor II reservoir, UK, was surveyed weekly for physicochemical and biological variables under continuous flow conditions during 17 weeks. The efficiency of a mesoscale biofilter using the aquatic plant Phalaris arundinacea and synthetic filters, was tested with Microcystis aeruginosa under continuous flow conditions and in batch experiments. The 'simultaneous allelochemical method' was developed for quantifying allelochemicals from Phalaris in aqueous samples. Microscale studies were used to investigate biofilter allelochemical release in response to environmental stressors and Microcystis growth inhibition in filtered and unfiltered aqueous root exudate.
Results demonstrate that the removal of phytoplankton biomass by physical mechanisms has a removal efficiency of ≤45% in the "Living-Filter" (filamentous biofilter plus synthetic fabric) and that the removal of Microcystis biomass using only biofilters was 25%. Chemical mechanisms that reduce Microcystis cell numbers are mediated by allelochemicals released from biofilter roots. Root exudate treatments on Microcystis revealed that Microcystis growth is inhibited by allelochemicals, not by nutrient competition, and that protists and invertebrates play a role in removing Microcystis.
Filamentous biofilters can remove phytoplankton biomass by physical, chemical and biological mechanisms. Biofilters and synthetic filters in combination improve removal efficiency. Application of macroscale biofilters prior to potable water treatment works benefits the ecosystem. Plant properties, biofilter size to surface water ratio, and retention time must be considered to maximise the benefits of biofiltration processes.

Keywords: Phalaris arundinacea
HPLC
Algal control
Macrocosm
Floating treatment wetland
Biofilter
Reed bed
Phytoplankton removal
Batch experiments
Microcosm
Mesocosm
Microcystis
Root exudate
Living-Filter
Continuous flow
Allelochemicals
Advisor: Hughes, J
Hankins, N
A stochastic Dollo model for lateral transfer

Lateral transfer, a process whereby species exchange evolutionary traits through non-ancestral relationships, is a frequent source of model misspecification in phylogenetic inference. Lateral transfer obscures the phylogenetic signal in the data — the signal of the taxa ancestry — as the histories of affected traits are mosaics of the species phylogeny and may conflict with the underlying phylogeny. We control for the effect of lateral transfer in a Stochastic Dollo model and a Bayesian setting. We infer rooted phylogenetic trees. Our likelihood is highly intractable as its parameters are given by the solution of a sequence of systems of differential equations which represent the expected evolution of traits along a tree and grow exponentially in dimension with the number of taxa under consideration. We construct an accurate parameter approximation framework, and from this we derive an efficient exact-approximate inference scheme. We illustrate our method on data sets of lexical traits in Eastern Polynesian and Indo-European languages and obtain improved fits over the corresponding model without lateral transfer.

Advisor: Nicholls, G
The development of fibre-reinforced ceramic matrix composites of oxide ceramic electrolyte

Flammable solvents contained in liquid electrolytes pose a serious safety risk when used in lithium batteries. Oxide ceramic electrolytes are a safer alternative, but suffer from inadequate mechanical properties and ionic conductivity. Thin electrolyte layers resolve the issue of conductance, but accentuate the detrimental mechanical properties of oxide ceramics. The presented work has investigated oxide ceramic electrolyte reinforcement in composite electrolytes for all-solid-state batteries.
Fabricating oxide ceramic electrolytes with engineered microstructure enabled development of a reinforced composite. This approach is based on the formation of 3D- porous ceramics via stereolithography printing of polymer templates from designed cubic, gyroid, diamond and bijel architectures. The microstructural parameters of templates were analysed and modified using computational techniques. Infiltration of the prepared 3D-porous electrolyte with polymeric-fibre reinforcement created the reinforced composite electrolyte. The prepared ceramic composite showed excellent reproduction of the template microstructure, good retention of ionic conductivity and enhanced mechanical properties.
The final composite was composed of NASICON-type Li1.6Al0.6Ge1.4(PO4)3 oxide ceramic electrolyte and epoxy and aramid fibre reinforcement. The gyroid architecture was computationally determined as having the optimal stress transfer efficiency between two phases. The printed gyroid polymer template gave excellent pore microstructure reproduction in ceramic that had 3D-interconnected porosity, high relative density and the most uniform thickness distribution. The ceramic matrix porosity allowed for complete infiltration of reinforcement by aramid and epoxy forming the fibre-reinforced ceramic matrix composite. The interpenetrating composite microstructure with ceramic and epoxy gave a flexural strength increase of 45.65 MPa compared to the ceramic. Unfortunately, the infiltration procedure of aramid-epoxy reinforcement did not realise the full tensile strength potential of aramid fibres.

Keywords: aramid
LAGP
kevlar
3D printing
stereolithography
bijel
Advisor: Bruce, P
Judicial actors as economic regulators

This DPhil thesis explores judicial activism in economic telecommunications regulation. It enquires into what factors explain its occurrence. Two debates in different strands of literature –and gaps in them- inspire the research. A first one is that various theories attempt to explain judicial activism, but no general agreement can be found on what factors actually have key explanatory power. The second gap is that the literature on regulation usually considers judicial actors as having a role in the enforcement or accountability stages of the regulatory process but largely ignore the role that they could have in the development of regulation.
Empirically, I analyse judicial activism in relation to economic telecommunications regulation through an exploratory comparative study. The two countries, Chile and the UK, are chosen because they have similarities and differences that made them interesting for a comparative project, such as having different legal systems (common and continental law) and having a different political history but similar approaches to regulating telecommunications (privatisation and liberalisation). Through a critical analysis of interviews and of final decisions made by judicial actors in both countries, I explore whether the factors the relevant literature argues explain judicial activism actually do explain judicial activism in the two case studies, whether other factors not found in the literature are important in explaining judicial activism, and - most importantly - how these factors interact.
Through the analysis based on the case studies I reach three main conclusions. First, that judicial activism is a jurisdiction specific phenomenon and different factors are found to explain it in each case. Second, the different factors that explain judicial activism – I argue - play different roles. Some are argued to act as enabling factors of judicial activism while others explain judicial activism in an immediate manner, which I call direct drivers. Finally, I argue that the findings of this thesis contribute to debates in different strands of literature, such as legal theory, and specifically descriptive accounts of adjudication.

Keywords: economic regulation
judicial behaviour
socio legal studies
judicial activism
Advisor: Lange, B
Decker, C