VictorJuiz/thesis huggingface dataset:
Modelling species invasions in heterogeneous landscapes

Biological invasions are devastating ecosystems and economies world-wide, while many native species' survival depends on their ability to track climate change. Characterising the spread of biological populations is therefore of utmost importance, and can be studied with spatially explicit, discrete-time integrodifference equations (IDEs), which reflect numerous species' processes of demography and dispersal. While spatial variation has often been ignored when implementing IDE models, real landscapes are rarely spatially uniform and environmental variation is crucial in determining biological spread.
To address this, we use novel methods to characterise population spread in heterogeneous landscapes. Asymptotic analysis is used for highly fragmented landscapes, where habitat patches are isolated and smaller than the dispersal scale, and in landscapes with low environmental variation, where the ecological parameters vary by no more than a small factor from their mean values. We find that the choice of dispersal kernel determines the effect of landscape structure on spreading speed, indicating that accurately fitting a kernel to data is important in accurately predicting speed. For the low-variation case, the spreading speeds in the heterogeneous and homogeneous landscapes differ by &straightepsilon;2, where &straightepsilon; governs the degree of variation, suggesting that in many cases, a simpler homogeneous model gives similar spread rates.
For irregular landscapes, analytical methods become intractable and numerical simulation is needed to predict spread. Accurate simulation requires high spatial resolution, which, using existing techniques, requires prohibitive amounts of computational resources (RAM, CPU etc). We overcome this by developing and implementing a novel algorithm that uses adaptive mesh refinement. The approximations and simulation algorithm produce accurate results, with the adaptive algorithm providing large improvements in efficiency without significant losses of accuracy compared to non-adaptive simulations. Hence, the adaptive algorithm enables faster simulation at previously unfeasible scales and resolutions, permitting novel areas of scientific research in species spread modelling.

Keywords: Landscape Heterogeneity
Integrodifference Equations
Biological Invasions
Advisor: Gaffney, E
White, S
Bullock, J
English vocabulary learning through watching YouTube videos and reading blog posts

Research on the Online Informal Learning of English has found that social media can facilitate language learning, mainly in the domain of vocabulary. It does so not only by providing the necessary language input, but also through the unique ways in which social media platforms encourage interaction between the user and the content as well as with other users. The present study investigated English vocabulary acquisition from engagement with two different types of social media: blog posts and video blogs. It also explored how learners make use of the unique opportunities for user-content and user-user interaction offered by these media. For this purpose, screen-captures of participants engaging with the blog posts and videoblogs were collected.
The results showed that incidental vocabulary learning occurred, in approximately equal amounts, from reading blog posts and watching video blogs. They also revealed that different types of vocabulary knowledge were gained from the two input modalities. Written input was found to promote greater gains in orthographic knowledge than videos. In turn, the videos promoted greater recognition and recall of the target words' meaning and recall of their grammatical function. The analysis of the screen-captures indicated that learners did not often make use of the unique features offered by the blog and video platforms. The findings are discussed in the wider context of user engagement with social media and virtual communities.

Keywords: informal learning
blog
YouTube
online language learning
online resources
incidental vocabulary acquisition
videoblog
Advisor: Woore, R
Probing GPCR-Gα interactions: a functional study by EM and SPR

The G protein-coupled receptor (GPCR), neurotensin receptor type 1 (NTS1), is pharmacologically important and activated by the tridecapeptide hormone, neurotensin (NT), initiating a cascade of interactions through G proteins to effect cellular responses. The mechanisms by which these occur have only recently begun to be examined structurally, and standard assays involving downstream effectors or radioactive GTPγS G protein activation to describe GPCR-G protein interactions do not assay the interactions directly. Two methods have been used here to study the interaction of NTS1 with the signalling partners, Gαs and Gαi1. A novel DNA-nanotechnological approach for preparing samples for electron microscopy (EM) has been used to study NTS1 and Gαi1, both separately and complexed, on a functionalised 2D DNA lattice, providing the first direct evidence of this interaction. Single particle reconstruction methods were used to determine a structure of NTS1 at a resolution of ~15 Å, a structure of Gαi1 at ~ 15 Å, and the interaction of Gαi1 with NTS1 has been observed using EM.
A further nanotechnological approach, using the increasingly popular method of reconstitution of membrane proteins in nanodiscs, has been used to study NTS1-Gαs and NTS1-Gαi1 interactions, using EM and surface plasmon resonance (SPR). The ligand (NT) affinity of detergent-solubilised NTS1 and NTS1 reconstituted into nanodiscs was &Tilde;1 nM, and for the first time, the affinity of binding of Gαi1 and Gαs to NTS1 was directly measured and determined as 15 nM and 31 nM, respectively. These results will facilitate cryo-EM studies on GPCRs with interacting partners, using a tethering system that both activates the GPCR and maintains it in a concentrated form within a restricted, two-dimensional plane; and also will aid a wealth of mutational and lipid-dependent studies whereby the effect on coupling and GPCR-protein interactions of specific residues and lipid types can be directly measured. This thesis primarily demonstrates the development and effective application of a biophysical methodology for measuring the coupling kinetics of GPCRs to G proteins; as well as demonstrating that this coupling can be visually evidenced under EM using gold-labelled G proteins.

Keywords: electron microscopy
surface plasmon resonance
G proteins
GPCRs
biosensors
Advisor: Watts, A
Inclusive teaching: why every child matters in your classroom and strategies to deploy to ensure this happens within drama

Inclusion is a term which ensures that all students have equal access to the classroom in order to increase their life chances. This research aimed to explore how having an inclusive classroom could influence how students felt about their learning but also to find specific strategies to use to ensure that inclusion occurred. The literature found that inclusion was difficult to define as it had so many subcategories of Special Educational Needs which suggested different strategies. It also found that all students (both with and without Special Educational Needs) thrive in an inclusive environment. The research through surveys and focus groups to both students and inclusion staff was successful in finding out four key points: students felt working in groups was inclusive; students wanted to feel included by their teachers; instruction sheets aided inclusive learning and; students who enjoyed lessons felt more included. Overall this small study of 274 students was successful in finding out about inclusion in my own classroom. The findings could provide the basis for further studies by independent researchers in order to explore whether the four key findings are a key theme across more students and more schools.

Keywords: Inclusive teaching
MLT
MLT2016
Harnessing parent power: to what extent can parental engagement enhance the development of growth mindset in secondary school children?

This study has focussed on how parental engagement can be used as an intervention to develop a growth mindset in young adolescent boys.
The research frame has been a case study approach designed to gather data that is rich enough to analyse a mediated act as complex as parenting. Therefore, the methods have been mixed and varied to enable thorough triangulation and have included semi-structured interviews, questionnaires, diaries, informal observation, drawing and pictures. The intervention period itself lasted six months.
The context is set within a co-educational, fee paying, independent boarding school which is non-selective and provides bursarial assistance to those from lower socio-economic backgrounds; four local day boys in year 9 were randomly selected from a targeted group as the case study students.
Many schools involve parents via emails and newsletters, reports and parents’ evenings, all of which serve to relay information in a useful and important way. However, in a complex and ever changing world I propose that schools must get more creative to strengthen the learning culture around each child. Parental participation in schools, particularly parental engagement (where parents are empowered to further develop their child’s learning dispositions at home) can have huge effects on that child’s lifetime achievement.
All students developed a more incremental mindset as a result of the parental intervention albeit to varying degrees. The main factors that influenced the degree of progress were upheaval within the family unit and how the strategies we employed by the parents. Unsurprisingly, I found that parents experience responsible parenting to be challenging, and that they were very grateful for support and guidance. Providing autonomy was found to be an important factor in successful strategies with the young adolescents, as was working in a careful manner via questioning, using process oriented praise and collaborative, learning-orientated, goal setting; all of which were best deployed in a light-touch manner.
The project sat within a whole school initiative to engage pupils, teachers and parents in strategies to develop learner self-sufficiency, as part of a collective culture, within a community of learning. The process and reflections of all involved within this project will help to develop our continued focus on a wholeness approach and continue to dissolve the boundaries between the silos of traditional educational practice and perceived responsibility.

Keywords: MLT2016
MLT
The hieratic ritual books of Pawerem (P. BM EA 10252 and P. BM EA 10081) from the late 4th century BC

The following thesis submitted for the DPhil in Oriental Studies (Egyptology) is the editio princeps of the ritual texts preserved on two hieratic papyri from the British Museum, P. BM EA 10252 and P. BM EA 10081. In the first part of the thesis, overall questions concerning the textual corpus are answered. These deal with the information concerning the acquisition of the papyri, the material aspects of the two manuscripts, the layout of the texts, the different hands and scribal divisions attested on them, the date and provenance of the papyri, their later owner including a discussion of information about him and his connection to the objects, a discussion of the content and context of the compositions, their grammar and orthography, and an investigation of the translations and later added glosses. The second part is the edition of the ritual texts including the hieroglyphic transcription of the hieratic texts, transliteration, translation, and line-to-line commentary. In addition, a detailed palaeography as well as a synopsis for those compositions of which none exists so far is provided. It is concluded that what have previously been designated as two separate papyri containing liturgical texts for the god Osiris were originally a single papyrus roll (P. BM EA 10252 + 10081) that can be described as an Osirian ritual handbook for the performance of the Khoiak-festival in the temple of Karnak at Thebes, dated to 307/6 BC due to a colophon written by a priest called Pay.

Advisor: Smith, M
Evaluating aerosol administration of a candidate TB vaccine, MVA85A, as a way to induce potent local cellular immune responses and avoid anti-vector immunity

There is an urgent need for a better vaccine against TB than BCG, which confers variable protection against pulmonary TB. Heterologous prime-boost regimens with viral vector vaccines are a leading strategy for TB vaccine development. MVA85A is a viral vector candidate TB vaccine designed to boost BCG. This phase I clinical trial was designed to evaluate whether alternating aerosol and intradermal routes of vaccination can improve Ag85A immunogenicity; maybe by circumventing local anti- MVA immunity. Thirty-six BCG-vaccinated healthy UK adults received two MVA85A vaccinations one month apart as heterologous (aerosol-intradermal or intradermalaerosol) or homologous prime-boost (intradermal-intradermal). Bronchoscopies with bronchoalveolar lavages (BAL) were performed 7 days after each vaccination. Delivering MVA85A by aerosol as a priming immunisation was well tolerated and highly immunogenic. Boosting an intradermal MVA85A prime with an aerosolised MVA85A vaccination led to transient respiratory and systemic adverse events which resulted in vaccinations in this group ceasing. Aerosolised MVA85A induced potent Ag85A-specific T cell responses in mucosal and systemic compartments; and suggested a potential for dose sparing with this route. The intradermal-aerosol regimen boosted Ag85A-specific cellular immune responses in systemic and lung mucosal compartments. Serum antibodies to Ag85A and MVA were only detected after intradermal vaccination. Anti-Ag85A antibodies in serum were boosted by a second intradermal vaccination. The findings of this trial are important for the development of aerosolised TB vaccines but also for new viral vector vaccines for other respiratory pathogens.

Advisor: McShane, H
Bettinson, H
Satti, I
Outsider cosmology and studio practice

This D.Phil constitutes an investigation led by studio practice and supported by archival and desk-based research into knowledge production through the building of complex cosmologies; specifically those created de novo in visual art practice and ‘outsider science’ oeuvres. It considers how these cosmologies relate to mainstream science, definitions of outsider art, and other complex cultural systems such as alchemy. Through a more detailed analysis of the work of the British artist John Latham and American outsider cosmologist James Carter, the thesis undertakes this investigation through discussions on the development of these systems and a consideration of the epistemologies these cosmologies reveal. The studio practice elements drive this investigation forward by interrogating themes including the relationship between culture and complex systems, alchemical epistemology, and the struggle to relate to unintuitive science.

Keywords: outsider art
art
outsider science
Foucault
James Carter
John Latham
cosmology
epistemology
Advisor: Grayson, R
Catling, B
Human cardiac magnetic resonance spectroscopy

The status of the myocardial “high energy phosphate” metabolism is a sensitive marker of the occurrence and progression of heart failure. Magnetic resonance spectroscopy enables non-invasive, direct and potentially quantitative measurements of the phosphate containing metabolites present in the human myocardium. This thesis is primarily concerned with the creation of measurement techniques for cardiac phosphorus magnetic resonance spectroscopy (31P-MRS) at the 7 tesla field strength.
Chapter 1 provides an overview of the physical basis of magnetic resonance spectroscopy, the myocardial high energy phosphate metabolism, and the clinical relevance of the technique.
Chapter 2 describes the advantage of 7 tesla scanners over lower field strengths. The radio frequency coil hardware is characterised experimentally. The multivoxel spectroscopy methods used throughout the thesis are described.
Chapter 3 details the implementation of an open source spectroscopy fitting program. It is validated against previous closed-source implementations. The program’s use is demonstrated in several clinical studies of heart failure, and to improve a previously implemented 1H spectroscopy coil combination method.
In Chapter 4 the measurement of inorganic phosphate in the presence of overlapping peaks is attempted. Suppression of overlapping peaks, originating from the blood, is tried using Bo gradients, then saturation transfer. The myocardial pH of hypertrophic cardiomyopathy patients is measured.
Chapter 5 describes the effect of creatine kinase catalysed chemical exchange on the 31P-MRS spectrum. A survey of methods suitable for measuring creatine kinase kinetics at 7 tesla is made. Multi-parametric fitting of variable repetition time saturation transfer data is explored in simulation and experiment.
Chapter 6 describes the re-implementation and extension, for dynamic measurements, of the triple repetition time saturation transfer method for two clinical studies at 3 tesla. The creatine kinase forward rate constant is measured in heart failure and healthy cohorts, at rest, and during cardiac stress.
In Chapter 7 a Bloch-Siegert B1 mapping sequence is implemented for 31P-MRS. An optimal Bloch-Siegert method for X-nuclear spectroscopy is calculated. B1maps are validated in skeletal muscle and collected in 5 volunteer’s hearts.
Chapter 8 uses the Bloch-Siegert B1 mapping sequence and the four angle saturation transfer method to implement creatine kinase rate measurement at 7 tesla. The first 3D localised creatine kinase rate measurements in the human myocardium are achieved in 10 volunteers.

Keywords: 31P
Human cardiac spectrsocopy
Phosphorus spectroscopy
Advisor: Rodgers, C
Robson, M
Incorporating spatial and temporal variability in analyses of the relationship between biodiversity and ecosystem functioning

In the last few decades, a growing literature has examined how biodiversity influences ecosystem functioning. This body of work has greatly improved our understanding of ecosystem functioning and its modulation by biodiversity. In particular, there is nowa- days large consensus that biodiversity increases ecosystem productivity, and stabilises ecosystems.
Early investigations were largely theoretical or involved simple experiments run in laboratory conditions, but over time biodiversity ecosystem-functioning experiments evolved to more realistic field experiments that better represent the real conditions found in natural ecosystems. In particular, these experiments are often run on larger spatial scales and over longer time frames allowing for the effect of environmental heterogeneity and temporal fluctuations to be explored.
The designs of these experiments evolved along with the questions addressed in this field of research. However, the analytical tools used in the analyses of these experi- ments followed a slightly different path. In particular, most of the metrics currently used to analyse biodiversity ecosystem functioning experiments are not entirely suited to properly deal with the complexity of modern designs as they make a number of assumptions that are not met any more.
In my thesis I developed a unified framework, based on the tailored use of Linear Mixed Effects Models, to analyse biodiversity-ecosystem functioning experiments such that the new complexities of these experiments can be taken into account. This thesis aimed to bring the focus of the analysis back to the biological interpretation of the results. I successfully applied my approach to several data sets.
The framework developed here is expected to improve greatly our understanding of ecosystem functioning and how biodiversity modulates it. It also sheds new light on past research in this field. The great flexibility of the new approach makes it possible to let these experiments to evolve such that new biological questions can be addressed.

Keywords: Biodiversity ecosystem-functioning experiments
Ecological statistics
Advisor: Hector, A
Gadd45g and mammalian testis determination

Mammalian sex is determined by the presence or absence of Sry. This gene, located on the Y chromosome, promotes the development of a testis from the biopotential gonad by initiating a transcriptional programme that results in Sertoli cell formation. SRY is required to reach a specific threshold level during a critical time-period in order to induce the testicular differentiation pathway. We have previously shown that XY mouse embryos lacking Growth arrest and DNA damage inducible 45 gamma (Gadd45g) exhibit gonadal sex reversal due to a delay in Sry expression.
Efforts to study the role of GADD45γ in sex determination have been stymied by the lack of a working antibody. As an alternative, I have produced a BAC transgene produces a similar expression profile to endogenous Gadd45g. This BAC was also shown to rescue the sex reversal found in B6-YPOS gonads, though further research is required to understand the molecular mechanisms through which this occurs. As a result, this BAC was chosen for modification using BAC recombineering to contain the sequence for a poly-His/FLAG epitope tag. Though this edited BAC was generated successfully, no transgenic lines have yet been produced.
Members of the Gadd45 family have previously been associated with active DNA demethylation. Assuch, I have conducted whole genome bisulphite sequencing on DNA from XY wild-type, XX wild-type and XY Gadd45g-/- embryos at the 18 tail somite stage, where Sry expression is at its peak. Gadd45g and Sry are only expressed in the somatic cells of the gonads, which have been purified through fluorescence-activated flow cytometry using the transgenic line Sf1-EGFP. Due to the low number of cells that are purified from the embryonic gonad at this stage, sequencing libraries were generated using post-bisulphite adaptor tagging (PBAT). Analysis of the acquired sequences revealed that there are no significant differences between the methylomes of XY wild-type, XX wild-type and XY Gadd45g-/- mutant gonadal somatic cells. It therefore appears that GADD45γ does not have a role in establishing the methylome at this particular stage of sex determination.

Advisor: Greenfield, A
Christian, H
Cox, R