VictorJuiz/thesis huggingface dataset:
Computation by origami-templated DNA walkers
Keywords: formal languages
DNA computing
nanotechnology

Interactions between DNA molecules can be used to perform computation. These DNA computing systems often use DNA molecules as freely diusing reactants in a well-mixed solution. We demonstrate how DNA walkers tethered to an origami-templated track can perform computation. A DNA walker can block a track that intersects with its own, preventing another walker from stepping down this blocked track. These blockages are primitive operations that can be used to perform computation. This thesis demonstrates how blocking interactions between DNA walkers can evaluate formulae posed in propositional logic.
When anchorages in the track are viewed as networked machines and the DNA walker is viewed as a coordinated message passed between them, DNA walker circuits can be modelled as a distributed system. Techniques from formal veri- cation can be used to check this system for errors, determining the probability with which the system will end up in a certain state. This forms the basis of a compiler that can automatically design a DNA walker circuit that evaluates a given propositional formula within a specied error tolerance. To show how DNA walker circuits can be simplied, we create a propositional logic system called blocking logic that is proven to be both sound and complete.
DNA walker circuits can be implemented and measured experimentally by using fluorescence spectrophotometry to track the position of a walker on the track. To demonstrate proof of principle, circuits were built that implement NOT and NOR operators. To make these circuits operate with minimal error, dierent sources of possible error were investigated and quantied.
Cumulatively, the novel contributions that this thesis makes to the eld are:
• the experimental design and implementation of a DNA computing system that uses DNA walkers,
• probabilistic model checking software that automatically designs these DNA walker circuits,
• a propositional logic system that can simplify a DNA walker circuit to an equivalent circuit that uses fewer tracks.
The circulation of flesh: regional food producing/consuming systems in Southern England 1500BC-AD1086
Keywords: Prehistory
Roman
Medieval
Food
Big-Data
Ceramics

It has become an axiom of British archaeology that the results of developer-funded fieldwork are under-utilised in research and several projects carried out at British universities have attempted to redress this perceived imbalance. These projects, including those on British and Continental prehistory carried out by Richard Bradley, the Roman Rural settlement project, the Fields of Britannia project, John Blair's work on early medieval England and the EngLaId project, of which this thesis forms a component, have all demonstrated beyond doubt the transformative effect of the data produced by developer-funded work on our understanding. However, to date no project has sought to utilise artefact and ecofact data produced by developer-funded work on a similar scale. This thesis is partly an attempt to fill this gap, by using ceramic, animal bone and charred plant data from digital archives generated by developer-funded archaeology, to address a series of questions about food production/consumption over the later prehistoric and early historic periods in Southern England. These three datasets have very varied characteristics and their integration in a single database was, therefore, one of the major challenges of the thesis. However, this also provided the opportunity to ask new questions and to address old questions with new data. The thesis argues that regional ecosystems had a long-term influence on processes of food production/consumption, which displayed considerable continuities across the boundaries of traditional archaeological periods. Landscape, settlement, ceramic, animal bone and charred plant data from three regional case studies, encompassing the Upper Thames Valley, the Middle and Lower Thames Valley and the route of HS1 in Kent were investigated using a Filemaker database and QGIS mapping. It is argued that, while there were long-term continuities in the use of plants and animals, the expression of social relationships expressed in fields, settlements and ceramics followed a cyclical pattern.
Investigating the recombinational response to replication fork barriers in fission yeast
Keywords: Replication restart
Replication Fork Barriers
DNA Replication
Homologous Recombination

Timely completion of DNA replication in each cell cycle is crucial for maintaining genomic integrity. This is often challenged by the presence of various replication fork barriers (RFBs). On collision with a RFB, the fate of the replication fork remains uncertain. In some cases, the integrity of the fork is maintained until the barrier is removed or the fork is rescued by merging with the incoming fork. However, fork stalling can cause dissociation of all of the associated replication proteins (fork collapse). If this occurs, the cell’s recombination machinery can intervene to help restart replication in a process called recombination-dependent replication (RDR).
Programmed protein-DNA barriers like the Replication Terminator Sequence-1 (RTS1) have been used to demonstrate that replication fork blockage can induce recombination. However, it remains unclear how efficiently this recombination gives rise to replication restart and whether the restarted replication fork exhibits the same fidelity as an origin-derived fork. It is also unknown whether accidental replication barriers induce recombination in the same manner as programmed barriers.
In this study, I introduce recombination reporters at various sites downstream of RTS1 to obtain information on both the fidelity and efficiency of replication restart. I find that unlike break induced replication (BIR), the restarted fork gives rise to hyper-recombination at least 75 kb downstream of the barrier. Surprisingly, fork convergence, rather than inducing recombination, acts to prevent or curtail genetic instability associated with RDR. I also investigate a number of genetic factors that have a role in either preventing or promoting genome instability associated with the progression of the restarted fork.
To compare RTS1 with an accidental protein-DNA barrier, a novel site-specific barrier system (called MarBl) was established based on the human mariner transposase, Hsmar1, binding to its transposon end. Replication fork blockage at MarBl strongly induces recombination, more so than at RTS1. This appears to be a general feature of accidental barriers as introduction of the E. coli TusB-TerB site-specific barrier in S. pombe gives rise to a similar effect. Here, I compare and contrast accidental barriers with programmed barriers. I observe that there is very little replication restart, if any, at MarBl measured by direct repeat recombination downstream. This points to the fact that accidental barriers do not trigger fork collapse in the same way as programmed RFBs and that the increased recombination that they cause may be a consequence of the inability of replication forks to terminate correctly, owing to the bi-directional nature of the barrier. Several genetic factors are assessed for their impact on MarBl-induced recombination, which further highlights both similarities and differences with RTS1-induced recombination.
Widening the applicability of permutation inference
Keywords: multi-level block permutation
non-parametric combination
low rank matrix completion
multiple regression
general linear model
surface-based morphometry
brain morphology
Pearson type III distribution
weak exchangeability
gamma distribution
sib-pair design
tail approximation
permutation tests
brain cortical volume
negative binomial distribution
heritability
generalised Pareto distribution
repeated measurements
brain cortical surface area
brain cortical thickness

This thesis is divided into three main parts. In the first, we discuss that, although permutation tests can provide exact control of false positives under the reasonable assumption of exchangeability, there are common examples in which global exchangeability does not hold, such as in experiments with repeated measurements or tests in which subjects are related to each other. To allow permutation inference in such cases, we propose an extension of the well known concept of exchangeability blocks, allowing these to be nested in a hierarchical, multi-level definition. This definition allows permutations that retain the original joint distribution unaltered, thus preserving exchangeability. The null hypothesis is tested using only a subset of all otherwise possible permutations. We do not need to explicitly model the degree of dependence between observations; rather the use of such permutation scheme leaves any dependence intact. The strategy is compatible with heteroscedasticity and can be used with permutations, sign flippings, or both combined. In the second part, we exploit properties of test statistics to obtain accelerations irrespective of generic software or hardware improvements. We compare six different approaches using synthetic and real data, assessing the methods in terms of their error rates, power, agreement with a reference result, and the risk of taking a different decision regarding the rejection of the null hypotheses (known as the resampling risk). In the third part, we investigate and compare the different methods for assessment of cortical volume and area from magnetic resonance images using surface-based methods. Using data from young adults born with very low birth weight and coetaneous controls, we show that instead of volume, the permutation-based non-parametric combination (NPC) of thickness and area is a more sensitive option for studying joint effects on these two quantities, giving equal weight to variation in both, and allowing a better characterisation of biological processes that can affect brain morphology.
The evolutionary consequences of parental effects
Keywords: Evolutionary Biology
Blue tits
Quantitative Genetics

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.
System, gesture, rhetoric: contexts for rethinking tintinnabuli in the music of Arvo Pärt, 1960-1990
Keywords: Estonia
serialism
Embodiment
Rhetoric
Pärt
Film
tintinnabuli
Soviet

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.
A biofilter process for phytoplankton removal prior to potable water treatment works: a field and laboratory study
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

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.
The development of fibre-reinforced ceramic matrix composites of oxide ceramic electrolyte
Keywords: aramid
LAGP
kevlar
3D printing
stereolithography
bijel

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.
Judicial actors as economic regulators
Keywords: economic regulation
judicial behaviour
socio legal studies
judicial activism

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.
Biophysical Studies of Oligonucleotides Containing Duplex Stabilising Modifications
Keywords: DNA
Nucleic Acids
RNA
Crystallography
Labelling of Oligonucleotides
Pyrene

Chemically modified DNA and RNA probes have been used in numerous diagnostic (e.g. fluorogenic PCR and in situ hybridisation) and therapeutic (e.g. exon-skipping and antisense) applications to increase duplex stability and facilitate mismatch discrimination. There is a constant need for well-studied modifications, and to this end X-pyrene was evaluated as a new cytosine analogue that combines enhanced π-stacking, hydrogen bonding and electrostatic interactions to greatly increase the stability of bulged DNA duplexes and DNA/RNA hybrid duplexes. X-pyrene is highly selective for guanine, and even more importantly duplex stability is reduced dramatically when X-pyrene or a neighbouring base is mismatched. NMR and fluorescence studies indicate that the pyrene moiety stacks within the DNA double helix. To enable easier access to this modification, a reductive amination labelling strategy was developed to produce pyrene-functionalised nucleobase analogues which allowed an easier synthesis of X-pyrene. Amino C6 dT was successfully functionalised with this methodology as well, obtaining the duplex stabilising mono- and di-labelled products. Additionally, a much simpler pyrene-modified thymidine monomer (U-pyrene) was selected for further studies. Single and multiple additions of U-pyrene were found to significantly increase the melting temperature of dsDNA without perturbing the B-DNA duplex, as shown by UV and CD spectroscopy. Interestingly, thermodynamic studies showed that four additions of U-pyrene increased the binding constant of a 14-mer oligonucleotide to its complementary strand 10000-fold when compared to the unmodified control. Two oligonucleotides containing a single addition of U-pyrene were also crystallised and their structures were studied by X-ray diffraction. To the author's knowledge these represent the first examples of X-ray crystal structures of a chemically modified pyrene oligonucleotide. They also proved to be of great interest as they highlight the capacity of U-pyrene to facilitate the production of interesting nanostructures.