VictorJuiz/thesis huggingface dataset:
2D ultrasound elastography as a functional measure of healing of the Achilles tendon in vivo
Keywords: elastography
Achilles
ultrasound
strain
healing
rupture
tendon

The Achilles tendon is the largest tendon in the human body, which elastically stores and releases energy to facilitate walking and running. Tendons can suffer from a range of pathologies, most notably that of complete rupture, which affects athletes, physically active workers and the aged. There is a growing demand for in vivo methods of objectively measuring tendon health for aiding diagnosis, monitoring therapy and for assessment of new treatments. Knowledge of the changes in mechanical properties during the healing process is also limited and new methods to accurately and consistently estimate these could provide insights into the healing process and guide future research efforts.
This thesis presents the development and use of 2D ultrasound elastography, a quantitative strain estimation imaging technique, as a tool to measure changes in the tensile mechanical properties of the Achilles tendon. This technique performs frame-to-frame block matching of image texture to track motion in an ultrasound signal sequence and create a strain estimation field from the spatial derivative of the motion. Elastography in the image-lateral direction of sagittal plane scans is of particular interest as this is in line with the longitudinal axis of the tendon, but presents extra accuracy issues from out of plane motion and lower image spatial resolution. Tendon rupture also presents unique problems to image acquisition and analysis- patient pain and safety are important considerations and disruption of the ultrasound texture can make 2D motion tracking more difficult.
A new 2D elastography block matching algorithm, named `AutoQual', was developed to enable accurate tracking of motion in the image-lateral direction and reduce the impact of artefacts and errors common with damaged Achilles tendons image sequences. It was shown to outperform a multiscale block matching method when tested using ultrasound sequences from
Screening for inhibitors of and novel proteins within the homologous recombination DNA repair pathway
Keywords: small-molecule
High-throughput screening
DNA damage
RNAi

The homologous recombination (HR) pathway of DNA repair is essential for the faithful repair of double-stranded DNA breaks (DSBs) in all organisms and as such helps maintain genomic stability. Furthermore, HR is instrumental in the cellular response to exogenous DNA damaging agents such as those used in the clinic for chemo- and radiotherapy. HR in humans is a complex, incompletely understood process involving numerous stages and diverse biochemical activities. Advancing our knowledge of the HR pathway in humans aids the understanding of how chemo- and radiotherapies act and may be used to develop novel therapeutic strategies. Recent studies have identified inhibition of HR as one of the mechanisms via which a number of recently developed chemotherapeutics have their effect. Accordingly, the clinical potential of HR inhibitors is under investigation. My work has centred around the identification of both novel HR proteins and novel, small molecule HR inhibitors. To further these aims, I have successfully employed high-throughput RNAi and small molecule screening strategies. RNAi screens are commonly used to identify genes involved in a given cellular process via genetic loss of function, whilst small molecule, cell based screens are a powerful tool in the drug discovery process.
Cancer metabolic pathways regulated by hypoxia
Keywords: glycogen
microRNA
hypoxia
Cancer metabolism

Metabolic reprogramming in cancer cells provides energy and important metabolites required to sustain tumour proliferation. Hypoxia represents a hostile environment that can encourage these transformations and other adaptive responses that contribute to poor prognosis and resistance to radiation and chemotherapy. Hypoxic signatures associated with worse prognosis were previously derived in different cancer types, and led to the selection of two candidates with potential metabolic implications, namely the mir210-putuative target iron-sulfur scaffold protein ISCU and glycogen phosphorylase (PYGL). Firstly, it was verified that the hypoxia-induced miR-210 targets ISCU. Iron-sulfur clusters represent cofactors for key enzymes involved in Krebs cycle and electron transport chain. Downregulation of ISCU was associated with the induction of reactive oxygen species (ROS) and reduced mitochondrial complex I and aconitase activity, caused a shift to glycolysis in normoxia and enhanced cell survival. This indicates that the induction of a single microRNA, miR-210, can mediate a new mechanism of adaptation to hypoxia, by regulating mitochondrial function via iron-sulfur cluster metabolism and free radical generation. Secondly, it was found that changes in PYGL expression reflect a characteristic upregulation of glycogen metabolism in hypoxia in both tumour xenografts and in cancer cell lines. More specifically, hypoxia stimulates glycogen accumulation and its utilisation, as well as the concurrent upregulation of several glycogen-metabolizing enzymes such as glycogen synthase (GYS1) and PYGL. PYGL depletion led to glycogen accumulation in hypoxic cells, increased intracellular levels of ROS, and a reduction in proliferation due to a p53-dependent induction of senescence. Furthermore, depletion of PYGL was associated with markedly impaired tumorigenesis in vivo. Finally, metabolic analyses indicated that glycogen degradation by PYGL is important for the optimal functioning of the pentose phosphate pathway. Collectively, this study shows the contribution of two important pathways to the metabolic adaptations induced by hypoxia.
Single channel Kondo physics in triple quantum dots
Keywords: quantum dots
triple quantum dots
condensed matter theory

In this thesis we investigate a system of three tunnel-coupled quantum dots, arranged in a triangular geometry and attached to a single metallic conduction band, using both analytic and semi-analytic methods and the numerical renormalisation group technique. This is the simplest coupled quantum dot system to exhibit frustration. We study three different models of the triple quantum dot device: a mirror symmetric arrangement of dots in which only one dot is connected to the conduction band, a triple quantum dot system in which only one dot is connected to the conduction band without a plane of mirror symmetry and a mirror symmetric arrangement of quantum dots in which all three dots are coupled to the conduction band. We study these models over a wide range of parameter space, and in both the presence and absence of a magnetic field.
Both antiferromagnetic and ferromagnetic Kondo effects are observed, and in all three models we find that the system contains at least two phases, and so a number of quantum phase transitions may be observed, associated in some cases with significant changes in the low temperature conductance through the triple quantum dot device. In addition to zero-field Kondo physics, a number of field induced Kondo effects are also observed. Both first order quantum phase transitions and Kosterlitz-Thouless phase transitions are observed. We use both symmetry arguments and low energy effective models which we derive to explain and understand both the position of and type of phase boundary that is observed in each case, and perturbative methods are used to accurately predict Kondo temperatures for a wide range of systems.
Investigations of open-shell open-shell Van der Waals complexes
Keywords: microwave spectroscopy
open-shell
ab initio
radicals
Van der Waals complexes

The question posed in this work is how one would model and predict the rotational spectrum of open-shell open-shell van der Waals complexes. There are two secondary questions that arise: the nature of radical-radical interactions in such systems and the modelling of the large amplitude motion of the constituent molecules. Four different systems were studied in this work, each providing part of the answer to the main question.
Starting with the large amplitude motion, there are two theoretical approaches that may be adopted: to either model the whole complex as a semi-rigid molecule, or to perform quantum dynamical calculations. We recorded and analysed the rotational spectrum (using Fourier transform microwave spectroscopy) of the molecule of tertiary butyl acetate (TBAc) which exhibits a high degree of internal rotation; and of the weakly-bound complex between a neon atom and a nitrogen dioxide molecule (Ne-NO2). We used the semi-rigid approach for TBAc and the quantum dynamical approach for Ne-NO2. We also explored the compatibility of these two approaches. Moreover, we were able to predict and analyse the fine and hyperfine structure of the Ne-NO2 spectrum using spherical tensor operator algebra and the results of our dynamics calculations.
To explore the nature of the interactions in an radical-radical van der Waals complex we calculated the PESs of the possible states that the complex may be formed in, when an oxygen and a nitrogen monoxide molecule meet on a plane using a number of high level ab initio methods. Finally, our conclusions were tested and applied when we performed the angular quantum dynamics to predict the rotational spectrum of the complex between an oxygen and a nitrogen dioxide molecule, and account for the effect of nuclear spin statistics in that system.
Nutrient limitation of marine phytoplankton
Keywords: Biogeochemistry
Physiology
Phytoplankton
nutrients

Phytoplankton across the majority of the world’s oceans are thought to be limited by the availability of either nitrate or iron (Fe). However, the spatial resolution of experiments confirming this is low. Two thesis chapters present the results of bottle enrichment experiments at high spatial resolution across (i) the South Subtropical Convergence (SSTC) in the South Atlantic, and (ii) the Scotia Sea-Drake Passage sector of the Southern Ocean. These studies have added detail to the boundaries of limiting nutrients in these regions. Patterns of Fast Repetition Rate fluorometry (FRRf) derived parameters, physiological regulation of these parameters including influences of community structure, and the environmental controls driving them are analysed. Given its role as an essential micronutrient, there has been much effort in constraining potential sources of bioavailable Fe to the ocean, with one such source receiving recent interest: erupted ash from volcanoes. Bottle-scale ash-incubation experiments alongside conventional iron additions and laboratory ash-leaching experiments were conducted, the results of which suggest phytoplankton would respond strongly to ash deposition in the High Nitrate, Low Chlorophyll (HNLC) areas of the Southern Ocean. Particularly notable was the evidence these experiments provided for potential (co-)limitation of phytoplankton in these waters by the micronutrient manganese. The first three chapters of this thesis highlight a number of biogeochemical implications of trace metal stress, particularly that of Fe stress. Therefore, the ability to map the oceanographic extent of Fe-stressed regions using remote sensing would represent a particularly useful advance in marine biogeochemistry. Theoretically it could be possible to map Fe stress from space using satellite images of chlorophyll fluorescence, yet there are important uncertainties that need to be addressed before this can be carried out. In particular, a better understanding of the midday non-photochemical quenching driven reductions in chlorophyll fluorescence occurring at the time satellite images are captured is required. Analysis of over 200 non-photochemical quenching experiments collected over three research cruises, has allowed us to explore non-photochemical quenching and its relevance for using sunlight induced chlorophyll fluorescence to assess broad patterns of Fe stress. Our results have confirmed that satellite fluorescence quantum yields have the potential to reveal broad regions of Fe stress, however a dynamic non-photochemical quenching correction derived from our experiments and analysis was necessary to achieve this.
A Bayesian chromosome painting approach to detect signals of incomplete positive selection in sequence data : applications to 1000 genomes
Keywords: Natural Selection
Bayesian
Hidden Markov Models
Sequence Analysis

Methods to detect patterns of variation associated with ongoing positive selection often focus on identifying regions of the genome with extended haplotype homozygosity - indicative of recently shared ancestry. Whilst these have been shown to be powerful they have two major challenges.
First, these methods are constructed to detect variation associated with a classical selective sweep; a single haplotype background gets swept up to a higher than expected frequency given its age. Recently studies have shown that other forms of positive selection, e.g. selection on standing variation, may be more prevalent than previous thought. Under such evolution, a mutation that is already segregating in the population becomes beneficial, possibly as a result of an environmental change. The second challenge with these methods is that they base their inference on non-parametric tests of significance which can result in uncontrolled false positive rates.
We tackle these problems using two approaches. First, by exploiting a widely used model in population genomics we construct a new approach to detect regions where a subset of the chromosomes are much more related than expected genome-wide. Using this metric we show that it is sensitive to both classical selective sweeps, and to soft selective sweeps, e.g. selection on standing variation. Second, building on existing methods, we construct a Bayesian test which bi-partitions chromosomes at every position based on their allelic type and tests for association between chromosomes carrying one allele and significantly reduced time to common ancestor.
Using simulated data we show that this approach results in a powerful, fast, and robust approach to detect signals of positive selection in sequence data. Moreover by comparing our model to existing techniques we show that we have similar power to detect recent classical selective sweeps, and considerably greater power to detect soft selective sweeps.
We apply our method, ABACUS, to three human populations using data from the 1000 Genome Project. Using existing and novel candidates of positive selection, we show that the results between ABACUS and existing methods are comparable in regions of classical selection, and are arguably superior in regions that show evidence for recent selection on standing variation.
Characterization of RNA aptamers that bind to HIV-1 gp120
Keywords: gp120
HIV-1
aptamer

RNA aptamers with 2'-fluoro-pyrimidine chemistry were previously selected by in vitro evolution to bind to monomeric HIV-1 gp120 from the R5 strain BaL. A group of 36 novel aptamers were cloned and sequenced from the heterogeneous pool and were tested for their ability to bind to gp120. The diversity of the RNA secondary structure of these, and 27 aptamers isolated previously, was analysed using a bioinformatics approach. This showed that eight aptamers contain a common branched motif, and RNA mutagenesis indicated that this structure is probably required for gp120 binding. Chemically synthesised derivatives of one such aptamer, B40, were designed and tested for binding to gp120. Truncation was found to decrease their binding, but the introduction of point mutations to stabilise the branched conformation and 2'-O-dimethylallyl-modified residues to stabilise helices increased binding to levels greater than that of the parental aptamer. The aptamer epitope on gp120 was mapped by testing aptamer binding to alanine-scanning mutants and deletion mutants of gp120 using a novel plate-based assay. This study showed that the aptamer binding site overlaps with the CCR5 epitope and is confined to four key residues at the base of the V3 loop, one of which is highly conserved. This finding may account for the observation that a number of aptamers were shown previously to neutralise a range of HIV-1 R5 clinical isolates in PBMC cultures. Interestingly however, the aptamer was unable to neutralise HIV-1 pseudovirus in a cell line, which is most likely due to the increased levels of cell-surface CCR5 in cell lines compared to PBMC. Future work should focus on identifying the structure and epitopes of other anti-gp120 aptamers as well as testing neutralisation of HIV-1, HIV-2 and SIV by the B40-derived aptamers. These aptamers can be used as tools to investigate the HIV-1 entry pathway and also have the potential to be developed as anti-HIV-1 microbicides.
Cyberattacks in international relations
Keywords: international law
norms
cyberwar
international relations
cyberdeterrence
deterrence
cyber
cybersecurity
cyberattacks

New methods of conflict and coercion can prompt tectonic shifts in the international system, reconfiguring power, institutions, and norms of state behavior. Cyberattacks, coercive acts that disrupt or destroy the digital infrastructure on which states increasingly rely, have the potential to be such a tool — but only if put into practice. This study examines which forces in the international system might restrain state use of cyberattacks, even when they are militarily advantageous. To do so I place this novel technology in the context of existing international regimes, employing an analogical approach that identifies the salient aspects of cyberattacks, and compares them to prior weapons and tactics that share those attributes. Specifically, this study considers three possible restraints on state behavior: rationalist deterrence, the jus ad bellum regime governing the resort to force, and incompatibility with the jus in bello canon of law defining just conduct in war. First, I demonstrate that cyberattacks frustrate conventional deterrence models, and invite, instead, a novel form of proto-competition I call ‘structural deterrence.’ Recognizing that states have not yet grounded their sweeping claims about the acceptability of cyberattacks in any formal analysis, I consider evidence from other prohibited uses of force or types of weaponry to defining whether cyberattacks are ‘legal’ in peacetime or ‘usable’ in wartime. Whereas previous studies of cyberattacks have focused primarily on policy guidance for a single state or limited analysis of the letter of international law, this study explicitly relates international law to state decision-making and precedent. It draws together previously disparate literature across strategic studies, international law, and diplomatic history to offer conclusions applicable beyond any single technology, and of increasing importance as states’ dependence on technology grows.
Closure games: the politics of clubs in international society
Keywords: Mobility Dampeners
G20
G8
G7
Family of Civilised Nations
Standard of Civilisation
Status
Closure Theory
International Society
Great Powers
Entry
Exclusion
Credentialism.
G-Summitry
Inclusion
Social Closure
Incorporation

This thesis develops a theory of international social closure to examine (i) the politics of membership in status groups – or, clubs – in international society and (ii) the persistence of clubs in international society. This thesis offers new concepts to improve the English School’s understanding of international society, its expansion, and its reproduction. In so doing it also addresses limitations and gaps in the IR status literature and the global governance and diplomacy literatures concerned with clubs and networks. This thesis analyses strategies of exclusion, entry, and incorporation used by actors to deny, attempt, or grant inclusion into clubs as well as the institutional contexts underpinning those clubs. Specifically, this research undertakes a study of instances of exclusion, entry, and incorporation in the context of three clubs: the Family of Civilised Nations, the Great Powers club, and G-summitry. In the first two cases, this research relies primarily on secondary sources while in the case of G-summitry it presents original empirical research gathered through archival research, interviews, and ethnographic participant observation. This thesis presents four main conclusions about the operation of closure: (i) the logics of different closure games are defined by overarching normative institutions of international society; (ii) despite a collectivist closure rule, closure in international society is predominantly individualistic; (iii) actors seeking entry tend to employ deferential entry strategies that reproduce a stratified status quo order; and (iv) incorporation promotes stratification along both functional and cultural lines. This thesis also draws three specific conclusions that run counter to much current scholarship: (i) contemporary international society is neither more open nor less hierarchical than nineteenth century international society; (ii) hierarchy is reproduced to a large degree by entry and incorporation strategies rather than exclusion strategies; and (iii) closure does not run along a ‘west versus the rest’ fault line.
Regeneration of the retina by stem cell transplantation therapy
Keywords: transplantation
retinal degeneration
retina
blindness
vision
ophthalmology
visual sciences
stem cell

One strategy to restore vision in retinitis pigmentosa and related retinal degenerations is by cell replacement. Typically, patients lose vision when the outer retinal photoreceptor layer is lost, and so the therapeutic ideal would be to restore vision at this stage of disease. It is not currently known if a degenerate retina lacking the outer nuclear layer of photoreceptor cells would allow the survival, maturation and reconnection of replacement photoreceptors, as prior studies used hosts with a pre-existing outer nuclear layer at the time of treatment. Here, using a murine model of severe human retinitis pigmentosa at a stage when no host rod cells remain, transplanted rod precursors are shown to reform an anatomically distinct and appropriately polarised outer nuclear layer. A trilaminar nuclear organisation is returned to the rd1 hosts that had only two retinal layers before treatment. The newly introduced rod precursor cells were able to resume their developmental programme in the degenerate host niche to become mature rods with light- sensitive outer segments, and reconnected with host neurons downstream. Visual function, assayed in the same animals before and after transplantation, was restored in animals with zero rod function at baseline. These observations suggest that a cell therapy approach may reconstitute a light-sensitive cell layer de novo and hence repair a structurally damaged visual circuit. Rather than placing discrete photoreceptors amongst pre-existing host outer retinal cells, total photoreceptor layer reconstruction may provide a clinically relevant model to investigate cell-based strategies for retinal repair.