VictorJuiz/thesis huggingface dataset:
A molecular toolkit for high-throughput identification of competitive and effective rhizobial strains
Keywords: Molecular biology
Sustainable agriculture
Microbiology
Environmental agriculture
Plant sciences

Legumes tend to become nodulated by highly competitive but not necessarily effective rhizobial strains, resulting in less optimal plant growth. Research focused on the identification of both competitive and highly effective nitrogen-fixing strains has been limited because, so far, the only way to test competitive rhizobial strains has been to isolate individual strains and compare them one at a time in large-scale plant growth assays.
We have developed a library of novel reporter plasmids (Plasmid IDs) compatible with Golden Gate cloning which consist of i) a promoter-probe vector (pOGG026) suitable for studies where antibiotic selection is not possible, ii) the maker gene sfGFP under the control of a synthetic consensus promoter (psNifH) to drive nodule-specific expression in biovars and strains of Rhizobium leguminosarum and which can be used as a proxy for nitrogenase activity assays, and iii) a 12-nucleotide specific sequence to mark R. leguminosarum strains.
Additionally, we developed reporter plasmids that express biomarkers, such as gusA, celB and mCherry suitable for rhizobial screening in the rhizosphere. The plasmid pOGG026 allowed us to develop a new plasmid-based system to mark Rhizobium strains with GusA/CelB and evaluate their competitiveness.
Results demonstrated the proof of concept of Plasmid IDs as a tool for high-throughput identification of competitive and effective rhizobial strains.
The application of this tool in a competition assay among eighty-four Tagged-strains, in non-sterilised agricultural soil containing indigenous rhizobia, allowed us to identify an effective and super competitive strain, in addition to mixed nodules occupied by up to four Tagged-strains. This tool has the potential to revolutionise the search for elite indigenous rhizobia, by reducing the costs involved in identifying competitive and effective rhizobial strains.
Modelling and simulation of phenotypic variability in cardiac tissue and application to stem cell-derived cardiomyocytes
Keywords: Safety pharmacology
Computational biology
Bidomain equations
Cardiac electrophysiology

Prediction of the safety of a novel pharmaceutical compound at the earliest possible stage of development is of great importance for drug discovery. Cardiac side-effects are a particular cause for concern, with several drugs such as Terfenadine and Cisapride having being withdrawn from the market due to adverse events. Investigation of the properties of novel compounds can be facilitated by the use of in silico models, which can provide a high-throughput and low-cost method of translating the known effects of a novel compound on multiple ion channels to effects on tissue-level electrophysiology.
In this thesis, we examine the case of monolayers of human stem cell-derived cardiomyocytes (hSC-CMs). In recent years, experimental systems utilising such monolayers have become more widely used, especially following their inclusion in the Comprehensive in vitro Proarrhythmia Assay (CiPA) initiative. In contrast to cells found in the adult heart, hSC-CMs beat spontaneously and are not necessarily spatially segregated by their subtype, or phenotype. These properties mean that the overall electrophysiological activity of a monolayer is sensitive to the spatial arrangement of the different types of cells. The simulation framework must therefore permit different spatial distributions of phenotypes.
The first part of this thesis is dedicated to the development of a simulation framework for modelling monolayers of hSC-CMs that incorporate phenotypic variability. While tissue containing regions of distinct cell types can be modelled using the bidomain equations, this approach is not computationally efficient when the cells are well-mixed. We test a novel approach, the homogenised phenotypes model, where the homogenisation process that underpins the bidomain equations is carried out over a small unit that contains two cell types.
In the second part of this thesis, we utilise the homogenised phenotypes model in simulations of the micro-electrode array, a device which is used to record extracellular field potentials from a monolayer of hSC-CMs, and compare our simulation predictions with experimental recordings. We investigate how variability in cellular phenotype and the distribution of these phenotypes throughout the monolayer affects the field potential, how this variability is manifest in simulations of drug block, and discuss the implications of our findings for the safety assessment process.
Hypoxia and HIF signalling in the epicardium during development and regeneration
Keywords: Hypoxia
HIF signalling
Myocardial infarction
Epicardium
Heart failure
Cardiovascular disease

Heart failure is a major cause of death worldwide due to the inability of the mammalian heart to regenerate after injury. The neonatal mouse heart however mounts a substantial regenerative response; though this capacity is lost one week after birth. The epicardium, which is activated in response to injury, becomes quiescent during this time-frame and may, therefore, be involved in the loss of regenerative potential. Another key change that occurs in the heart after birth is the transition to a post-natal circulation, meaning it becomes less hypoxic. Hypoxia inducible factor (HIF) is a transcription factor, which is activated in response to hypoxia and significantly, activated HIF can directly bind to and upregulate expression of Wt1, the master regulator of epicardial activation via epithelial-to-mesenchymal transition (EMT). I, therefore, sought to investigate a functional requirement for hypoxia and HIF-signalling in the activation of the epicardium during murine heart development and neonatal cardiac regeneration.
In the developing heart, co-expression of WT1 with hypoxyprobe at embryonic stages (E)16.5 and E18.5 indicated the epicardium is hypoxic at later stages of embryogenesis. Epicardial-specific loss of Hif1-alpha or Hif2-alpha during development led to decreased epicardial activation and EMT which impacted on coronary vessel development and myocardial compaction. Furthermore, stabilisation of HIF in epicardial explant cultures, via genetic ablation of prolyl hydroxylase domain 2 gene (Phd2), or chemical inhibition of PHD enzymes via FG-4592 (also known as Roxadustat), resulted in enhanced EMT, implicating a role for HIF signalling in epicardial activation. Whilst the epicardium becomes quiescent within the first postnatal week, stabilisation of HIF signalling after birth through loss of Phd2 was sufficient to maintain activation of the epicardium. Moreover, genetic knock-down and pharmacological (treatment with FG-4592) inhibition of PHD2 to stabilise HIF augmented the epicardial response to injury and preliminary results suggested an improvement in the regenerative response.
Further analysis into the full impact on neonatal cardiac regeneration, and transition to the injured adult heart, is required. Nevertheless, FG-4592, which is already in clinical trials for patients with anaemia, presents a potential novel therapeutic approach to improve cardiac repair in human patients following myocardial infarction.
Family and familiarity in flies
Keywords: Drosophila melanogaster
Kin selection
Sexual conflict
Kin discrimination

The concept of gene-centred evolution and subsequent inclusive fitness theory provided a formal framework in which to study the adaptation of social behaviours. It highlighted the role of relatedness between individuals in mediating both cooperation and conflict. However, social behaviours can be difficult to study, particularly among animals in the wild. Drosophila melanogaster has been studied as a model organism for over a century, and we have a deep understanding of its genetics, development and physiology. Furthermore, its short lifespan, small size and fast reproduction rate make it an ideal laboratory animal. Yet we currently know very little about how relatedness affects social behaviours in this species. In this thesis, I aim to contribute to our knowledge of kin selection and recognition in Drosophila melanogaster, developing its use as a model organism for studying inclusive fitness.
In Chapter 2, I examine the role of relatedness on adult sexual behaviours, namely how male-male relatedness mediates sexual harm to females. I distinguish the roles of genetic relatedness and larval social familiarity, and find that familiarity alone is not sufficient and genetic relatedness is required to reduce sexual conflict. However, male intrasexual interactions are important, as in Chapter 3, I find no effect of relatedness when males are presented to the female sequentially rather than simultaneously.
In Chapters 4 and 5, I consider the effect of relatedness on larval social behaviours, which have thus far been understudied compared to their adult counterparts. Contrary to predictions from inclusive fitness theory, in Chapter 4 I find that larvae benefit from developing in unrelated, rather than related, groups. This is possibly due to the increased genetic diversity and therefore behavioural diversity in unrelated groups, reducing direct competition. In Chapter 5, I additionally show that larvae prefer to cannibalise unrelated and unfamiliar conspecific victims, which may have strong fitness consequences for both adult and larval behaviour.
This thesis provides new evidence that relatedness, over and above social familiarity, mediates both adult and larval behaviours in Drosophila melanogaster, allowing us further to develop this species as a model organism for kin selection.
Coherent combination of mismatched fibre lasers - steps towards real world applications
Keywords: Filled aperture combination
Ultrafast Laser
Photonic crystal fibre
Laser

Large arrays of coherently-combined Quasi-Continuous-Wave (QCW) fibre lasers have been identified as a plausible solution to creating high-repetition rate (~1 kHz), high-wall-plug efficiency lasers capable of driving a wakefield for accelerator applications. The coherent combination of four near-identical Photonic Crystal Fibre (PCF) lasers to produce laser pulses with pulse energies of 5.7 mJ and peak powers of 22 GW has been successfully demonstrated by other groups. Extensions of the four PCF experiment also demonstrated the coherent combination of 8 photonic crystal fibres to attain pulse energies of 12 mJ and peak powers of 35 GW. However, these PCFs were near-identical in length, core size, fibre structure and dopant concentration. Work done in Oxford focused on the coherent combination of fibre lasers which were unmatched in length, core size, internal structure and dopant concentration. The aim was to identify the point at which the fibre differences caused the combining efficiency to degrade. Potentially, this information would be used to identify the tolerance levels required for the large-scale manufacture of the fibres needed to construct a facility-scale laser system for laser-wakefield acceleration.
This thesis covers the coherent combination of mismatched PCFs, a scenario which could occur during the construction of a facility-scale terawatt laser system. Here, hundreds or potentially thousands of PCFs could be purchased from different manufacturers, each of whom use their own methods of manufacture and tolerances. An investigation into the challenges associated with combining two highly-mismatched PCFs was performed, with the PCFs chosen to be very different to exaggerate any effects which could degrade their coherent combination. This work resulted in the successful coherent combination of these highly-mismatched PCFs, with a measured degree of linear polarisation of 85.9 ± 0.5 % and a fraction of available beam power of 93.0 ± 0.5 %. Also, supporting work investigated the difference between simulation and measurement in explaining the observed degree of linear-polarisation of the combined-beam.
Security analysis of behavioural biometrics for continuous authentication
Keywords: security
eye movements
authentication
biometrics

In recent years, behavioural biometrics have become increasingly popular, with many types of behaviour being explored for the purpose of user authentication. Some of the most common examples are keystroke dynamics, mouse movements, touchscreen inputs and human gait.
Unlike physiological biometrics (e.g., fingerprints), behavioural biometrics are often believed to be relatively hard for adversaries to collect, but nevertheless have been subject to active attacks, including presentation, signal injection and imitation attacks.
In this thesis, we take a holistic view on the design, evaluation and security analysis of behavioural biometric recognition systems. First, we underline their usefulness by designing a novel authentication system based on distinctive eye movement behaviour. We evaluate this system under different adversary models and show that eye movements can be used for both user authentication and judging a user's task familiarity. Drawing from insights gained from this project, we go beyond the state of the art to develop metrics and methodologies that more accurately reflect a system's real-world performance and security. This approach is centred around reflecting a biometric's systematic false negatives (i.e., attackers that consistently go undetected) more accurately.
A frequent focus of related work is how to present previously obtained biometric data to a behavioural authentication system (e.g., through imitation or mimicry attacks). However, the challenge of obtaining this data in the first place is far less explored. In this thesis, we perform a series of experiments to judge the usefulness of biometric data collected through a variety of sources. The idea is to measure the security impact of the plethora of biometric data that is involuntarily created through our day-to-day interactions with diverse systems.
The evolution of exoskeleton moulting in Trilobita
Keywords: Cambrian
Euarthropoda
Behaviour
Trilobita
Ecdysis
Exoskeleton
Moulting

Moulting is the process of replacing an exoskeleton. The exoskeleton provides protection but must be periodically moulted for growth, development, and repair. Moulting is therefore intrinsic to ontogeny, but is risky and energetically-expensive, meaning the morphology and behaviours of an animal are also important. Ecdysozoa (e.g. Euarthropoda, Nematoida) are united by moulting, but Euarthropoda (e.g. insects, crustaceans) have particularly tough, usually reinforced, exoskeletons. Correspondingly they have a high preservation potential and exceptional fossil record. Amongst arthropods, the extinct trilobites were extraordinarily abundant and diverse, with an unparalleled fossil record. Both trilobite carcasses and moults are abundant, and when correctly identified these moults inform on many aspects of evolutionary history. Trilobites were both extremely inter- and intraspecifically variable in their moulting compared to other euarthropods. By examining trilobite moults we can reconstruct and contrast moulting behaviours to other groups to explore the ways in which moulting has affected trilobite evolutionary history.
This thesis illustrates the importance of moulting to the evolution of trilobite, and euarthropod, life history. First, I provide a review of published information on trilobite moulting, and discuss the importance of accurate moult identification. I then present a broad-scale database of trilobite behavioural and morphological data, which is used to quantitatively answer “how variable was trilobite moulting behaviour, and is this linked to differences in morphology?” Case studies then explore the detailed moulting information available from Konservat-Lagerstätten (focusing on the early Cambrian Emu Bay Shale); the association between moulting and morphology through trilobite ontogenetic history (by describing the development of Dalmanitina); and show that the process of moulting has been conserved throughout euarthropod evolution (by describing a complete moulting sequence of Symphysurus). The manuscripts constituting this thesis demonstrate the trilobite fossil record of moulting is an important source of information that can inform on the evolutionary history of development, behaviour, ecology, and morphology in this influential group.
Design of single-shot longitudinal bunch profile monitor based on analysis of coherent smith-purcell radiation
Keywords: Smith-Purcell Radiation
Longitudinal Beam Diagnostics
Terahertz Radiation

The spectral analysis of coherent Smith-Purcell radiation (cSPr) is a promising new longitudinal diagnostic technique. This thesis presents a conceptual design for a single-shot, non-destructive, coherent Smith-Purcell radiation monitor and investigates the challenges of realising this type of diagnostic.
It is proposed to use the polarization of coherent Smith Purcell radiation in order to distinguish it from background radiation. A series of experimental studies are carried out at the 8MeV electron accelerator LUCX (KEK, Japan) in order to measure the polarization of cSPr.
An experimental setup is developed for measuring the frequency and polarization of low intensity THz frequency signals in accelerator environments. The frequency measurements are made with a Fabry-Perot interferometer, using wire grid polarizers as beamsplitters. The operation of this interferometer is shown to be comparable to classic interferometer designs.
The results show cSPr to be highly polarized and easily distinguishable from unpolarized background radiation. Suggestions are made to improve the experimental setup in order to obtain more detailed measurements in the future.
An investigation into the number and distribution of detection channels required in the cSPr monitor is also carried out. This demonstrates that significant savings in space and cost can be made by optimising the design for specific accelerator environments.
Identifying and prioritising interventions to reduce emergency hospital admissions
Keywords: hospital
hospitalisation
umbrella review
unscheduled admission
unplanned admission
hospitalization
overview
hospital admission
emergency admission

The aim of this thesis was to identify and prioritise evidence-based interventions that reduce emergency hospital admissions and explore their implementation in clinical practice. To achieve its aim, this thesis first identified evidence-based interventions that reduce emergency admissions using a systematic review of systematic reviews. Second, it determined which of the evidence-based interventions had been recommended in national clinical guidelines, developed into quality of care indicators, and featured in national audits in England. Thirdly, it explored the extent to which evidence- and guideline-based interventions were being optimally utilised in primary care in the United Kingdom. Fourthly, it evaluated an innovative access to care initiative implemented in primary care to reduce hospital admissions. Fifthly, it explored the use of evidence by decision makers when designing and implementing local interventions as part of national campaigns to reduce admissions. Overall, the findings showed that there are a variety of evidence-based interventions that reduce emergency hospital admission rates. However, the thesis showed gaps in the promotion and use of these interventions in clinical practice in the United Kingdom. It also demonstrated that increasing access to primary care using innovative interventions may not be an effective or evidence-based approach to reducing hospitalisations. Stakeholders seeking to reduce admission rates may consider optimising use of the evidence- and guideline-based interventions prioritised in this thesis. This may be done using existing quality improvement infrastructure or by developing or expanding health care services that feature the interventions. Furthermore, efforts should be made to robustly evaluate novel interventions implemented in clinical practice to reduce hospital admissions. The results of such evaluations should be systematically disseminated to facilitate peer-peer learning, avoid duplicated efforts, and promote use of evidence-based interventions.
Sonodynamic therapy of hypoxic tumours
Keywords: Sonodynamic Therapy
Hypoxia
Bubble

Improvements in cancer therapies have enabled a steady increase in the five-year survival rates of patients with most tumour types. Yet, some highly aggressive tumours still present resistance to conventional cancer therapies. One of the explanations for this has been ascribed to the low levels of oxygen seen in the tumours’ vicinity. In this manuscript, the development of sonodynamic therapy to enable the treatment of hypoxic pancreatic tumours is presented. With this technique, low intensity ultrasound is used to activate oxygen-loaded microbubbles in order to provide oxygen in hypoxic lesions and enable their treatment using an ultrasound-responsive drug: Rose Bengal.
An investigation on mechanisms demonstrated that light generated from collapsing microbubbles allows the activation of Rose Bengal during ultrasound exposure. Several acoustic parameters were also evaluated to understand their impact on treatment. To enhance the delivery of oxygen and the sonodynamic effect, magnetic targeting of microbubbles was enabled by incorporating iron oxide nanoparticles within their coating. Thus, an external magnetic field focused at the tumour can be used to target this therapy. A structural analysis of microbubbles as drug and oxygen carrier was then undertaken to optimise the system’s stability and performance. An evaluation of this method in preclinical in vivo experiments demonstrated that magnetically targeted sonodynamic therapy with oxygen microbubbles and Rose Bengal enabled a decrease in size of hypoxic pancreatic tumours in a murine model. Therefore, this thesis presents promising results for the treatment of hypoxic tumours using sonodynamic therapy, as well as key mechanistic and parametric results to enable the further optimisation of this method for clinical use.