Open Research Exeter - University of Exeter
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Decadal and spatially complete global surface chlorophyll-<i>a</i> data record from satellite and BGC-Argo observations
No full textDecadal-scale satellite-based climate data records of chlorophyll-a (chl-a), an essential climate variable, are now readily available at high accuracy and precision. These data are being extensively used for research and, increasingly, for operational services. However, these observations rely on availability of sunlight and the satellite sensor being able to view the ocean, so there are gaps in data due to the presence of clouds and more widely during the polar winter. This is an issue when spatially complete data are needed for global climate studies, or as inputs to machine learning methods and for data assimilation. Whilst addressing cloud cover is well studied, methodologies to overcome missing data due to the polar winter has received little attention and simple approaches to overcome these gaps can lead to unrealistic values. Biogeochemical Argo (BGC-Argo) floats have widely been deployed, and they represent an opportunity to address these gaps. We present an approach that combines BGC-Argo data and a satellite chl-a climate data record to produce a spatially and temporally complete, global monthly chl-a record between 1997–2024 at 0.25° spatial resolution. Clouds gaps were filled using an established spatial kriging approach. Polar wintertime chl-a were reconstructed using relative changes between the wintertime BGC-Argo chl-a, and the previous autumntime or next springtime satellite observations, for individual hemispheres. Uncertainties were calculated on a per-pixel basis to retain the underlying uncertainty fields in the climate data record and were modified to account for the uncertainties related to the gap filling. The seasonal cycles in the resulting polar data are consistent with light availability. Clear interannual and inter-hemisphere variability in the wintertime chl-a were observed. Independent assessment of solely the gap filled wintertime chl-a estimates against in situ data (N=201 total) indicates that the accuracy and precision of the underlying satellite data, a key component of a climate data record, are maintained. The 26 year global and spatially complete chl-a data, that are consistent with the underlying climate data record can be downloaded from Zenodo (https://doi.org/10.5281/zenodo.15689006, Ford et al., 2025b).</p
Understanding immune priming in Pacific oysters: A multi-omics exploration of transcriptomic, epigenetic and microbiome regulation: supplemental files for the thesis by Sarah Woodsford
No full textThese are the supplemental data files associated with PhD thesis: "Immune priming in Pacific oysters: A multi-omics exploration of transcriptomic, epigenetic and microbiome regulation", by Sarah Woodsford.Thesis abstractAquaculture has a fundamental role to play in global food security, given the limitations for increase of captures from global fisheries and the pressures they pose on the natural environment. Infectious disease remains an important limitation for the aquaculture industry both because it is financially costly and contributes towards poor animal welfare. For molluscs, widespread mass-mortalities of Pacific oysters (Magallana gigas) have occurred in recent years linked to infection with the bacterial pathogen Vibrio aestuarianus. Disease in farmed oysters is difficult to prevent or to treat and, in this context, immune priming has been proposed as a method to increase resistance to disease, and has been reported to be effective for viral pathogens. However, it is unknown whether an immune response can be primed in oysters to provide protection against Vibrio aestuarianus upon secondary challenge. This thesis aimed to address this knowledge gap and explored the hypothesis that epigenetic and microbiome processes are involved in sustaining long-lasting immune system memory.In order to identify a period of DNA methylation reprogramming, and therefore a candidate window of epigenome malleability, Pacific oyster embryos were exposed to the methylation inhibitor 5-azacytidine at different temporal intervals throughout early development (Chapter 2). A period of methylation inhibitor sensitivity was observed up to approximately 11 hours post fertilisation, which is indicative of a window of methylome reprogramming. Further periods of reprogramming and/or epigenetic sensitivity may exist after this window, but their presence and precise timing was not explored.Pacific oysters were primed with heat-inactivated Vibrio aestuarianus via 24-hour bath exposure at either the larval or young spat stage, then challenged with the non-attenuated form of the pathogen at six months old. A multi-omics approach involving RNA-Seq, 16S amplicon sequencing and whole genome bisulphite sequencing was utilised to interrogate whether immune priming resulted in long-lasting molecular alterations to the oyster transcriptome, microbiome and epigenome (Chapters 3-5). For naïve oysters, transcriptomic analysis evidenced that Vibrio aestuarianus had an immunosuppressant effect on 6-month-old oyster spat, despite high survival rates and no significant alterations in oyster microbiota suggesting spat were not susceptible to disease. Immune priming at either the larval or young spat stage resulted in lasting alterations in the oyster transcriptome, microbiome and epigenome that were sustained for up to five months after the priming took place. Lasting transcriptional alterations were identified in pathways including complement, protein modification and phagocytosis, with upregulation of these pathways suggesting faster pathogen recognition upon challenge. The oyster transcriptome, microbiome and epigenome appeared to remain malleable after metamorphosis, although larval priming appeared to be more beneficial in terms of increasing within-sample microbial diversity.Together, this thesis demonstrates that acquired immunity can be primed in Pacific oysters against Vibrio aestuarianus at either the larval or spat stage and suggests that epigenetics may be responsible for the continued alteration of transcriptional and microbiome regulation after priming. However, it remains unclear how long this acquired pathogen memory may persist for and whether priming during a window of epigenome malleability will enhance adult survival against the virulent pathogen. Overall, this work highlights the potential to utilise sensitive windows during early life to manipulate the microbiome and epigenome in order to induce lasting memory for use in disease control within bivalve molluscs. Future research is required to clarify the precise causative mechanisms of the effects seen, whether transgenerational immunological memory can be primed against Vibrio aestuarianus, and evaluate the feasibility of this approach for building pathogen resistance within invertebrate aquaculture settings.</p
BOWIE-ALIGN: Sub-solar C/O ratio and metallicity atmosphere of the misaligned hot Jupiter HAT-P-30 b
No full textWe present the JWST NIRSpec/G395H transmission spectrum of the misaligned hot Jupiter HAT-P-30b from 2.8–5.2 m as part of the BOWIE-ALIGN survey, a comparative survey designed to probe the link between planet formation and atmospheric composition in samples of misaligned and aligned hot Jupiters orbiting F-type stars. Through independent data reductions and retrieval analyses, we find evidence for absorption features of H2O and CO2 in the atmosphere of HAT-P-30 b. Our retrieved abundances are consistent with equilibrium chemistry, from which we infer a sub-solar C/O ratio (0.16–0.45), and sub-solar and sub-stellar metallicity (0.2–0.8×solar, compared to a stellar metallicity of 1.1–1.6×solar), with muted spectral features. This composition challenges formation models of continuous migration and accretion within a steady disc of stellar metallicity, and could be the result of low C/O ratio gas accretion within the water ice line, low metallicity accretion due to the trapping of volatiles further out in the disc, or the combined accretion of low metallicity gas and carbon-poor solids.</p
Moral certainty and the wrongness of killing: a non-propositional view
No full textIn 2008 I published a paper making the case that Wittgenstein’s On Certainty reflections can be fruitfully extended to cast light on the foundations of our moral lives and practices. My primary example was that the wrongness of killing is a basic moral certainty. This proposal has come in for sustained criticism, with critics arguing that there is can and can be no such moral certainty. In this paper, I respond to the dominant line of critique, which I call ‘the exceptions objection’ to the wrongness of killing being a basic moral certainty. My diagnosis shows that, and how, this objection is predicated on a ‘propositional’ (mis)interpretation of the concept of basic certainty. In its stead, I present and develop an opposing ‘non-propositional’ conception, which is crucial to seeing aright the claim that the wrongness of killing is a basic moral certainty.</p
Practitioners' responses to Saunders and Roth's ten talking points for organising for change
No full textThis collection of papers combines practitioners’ responses to the Ten Talking Points. Neate
(Shelter) reflects on practices like subversive humanitarianism, useful for rebuilding trust in
charities. Kogbara (Place Matters) discusses the role of formal institutions in social change ecosystems and highlights the need for hope. McCallum (Greenpeace) focuses on the diversification and localisation of Greenpeace’s activist base, which affects its decision-making. Saunders and Roth reply to the issues raised by the practitioners</p
Simulating scotomas and exploring assistive strategies for diabetic retinopathy vision loss
No full textBackground and Aims: This study presents a new computer-based simulation system designed to replicate the experience of central scotomas, a common visual impairment in diabetic retinopathy. The aim is to examine how these blind spots affect daily tasks such as reading and object search, while also reviewing emerging assistive technologies designed to mitigate their impact. The literature review covers six key areas: (1) artificial scotoma simulation, (2) search performance with visual field deficits, (3) reading impairment due to blind spots, (4) VR-based vision loss simulations, (5) visual aid technologies, and (6) broader research on visual field defects. Methods: A real-time scotoma simulation was developed using a standard display with custom eye-tracking software built in OpenCV. To enhance realism, a 50ms delay was introduced between eye movement and scotoma repositioning, and a smooth floating motion was added to mimic natural visual arti-fact behavior. The simulation is also compatible with Virtual Reality (VR) headsets for immersive testing. Central scotomas were modeled to represent cotton wool spots typical in diabetic retinopathy. Assistive algorithms were incorporated using visual remapping techniques. Results: Three remapping strategies were implemented: no correction, square remapping, and circular warp remapping. These approaches were tested for their effectiveness in improving functional vision during tasks such as reading, searching, driving, and cooking. Both hard-edge and soft-edge scotomas were modeled to reflect real-world variability in blind spot appearance and progression. Conclusions: Preliminary feedback from ophthalmology experts supports this system’s potential. Future work will refine simulation accuracy using direct input from patients with vision loss.</p
Castles and Communities: Using the taskscape to explore the attitudes, activities, and lived experience of wider communities in castle landscapes between 1050 - 1550.
No full textThis thesis utilises the concept of the taskscape to explore the impact of the medieval castle in England on lived experiences in the landscapes surrounding them between 1050 to 1550. Recent shifts in the focus of castle studies have demonstrated the need to focus on castles as sites of everyday activities, inclusive of a range of social experiences beyond those of the elite occupants. These insights will be gained through the use of the taskscape, viewing the medieval world as a series of mutually attentive interlocking temporalities, helping contextualise the castle within ongoing dwelling.
In order to bridge the divide between theory and methodology, a integrative methodology is suggested, using geographical information systems to approach the sensory and temporal dimensions of tasks. The form of the landscape is modelled using a retrogressive analysis of historic maps and LiDAR imagery. Portable Antiquity Scheme data, excavations, and historical and archaeologically attested sites and places are then integrated into a model of the physical and social topography of the medieval world. Visibility and movement analysis then informs analysis of the motion and sensory experiences inherent to the performance of dwelling tasks.
This methodology is applied to three pairs of case studies, helping focus on different dimensions of the taskscape, whilst also reflecting the variations in castle and landscape form across dispersed, nucleated, rural, and urban settings. Ultimately, three conclusions are reached. Firstly, everyday movements of materials and individuals around the castle ensured that it maintained a central place within the lived experience of non-elite communities, and consequently in their production of identity. Secondly the castle adopted long term temporalities of memory, geology, and natural rhythms into a display of social hierarchies and parallel temporalities. Finally, the impact of the castle was relative to the strength, intensity, and momentum of surrounding tasks.</p
Realizing phage therapy in the UK
No full textOn 25 November 2025, the international phage therapy research and biotechnology communities gathered in Liverpool, UK, to discuss progress in implementing clinical phage therapies and the latest technological breakthroughs in phage biology and engineering, while UK regulators and health agencies provided the latest guidance.</p
Persistence of coral reef structures into the twenty-first century
No full textCoral reefs provide important socioecological services but are vulnerable to climate change, which shifts the balance between the production and erosion of calcium carbonate (CaCO3). In this Review, we summarize understanding of reef accretion, describe the mechanisms of carbonate production and erosion, and consider the effects of future ocean warming and acidification on key reef-building and eroding taxa. The combined stressors of climate change substantially reduce net carbonate production, with a more pronounced effect on calcifying algae than corals. However, declining coral cover driven by marine heatwaves and mass bleaching will probably be the dominant determinant of future reef carbonate budgets, and thus only reefs with thermally adapted populations are predicted to maintain the ability to sustain positive CaCO3 production under climate change, even if calcareous algal cover increases. As carbonate budgets become net negative in the future, the longevity of pre-existing reef frameworks remains unknown and understudied owing to the timescales required to meaningfully assess framework removal rates. Improving estimates of the rates of biologically driven framework loss and chemical dissolution will also be important in better predicting future reef persistence. Key knowledge gaps exist in understanding the effects of deoxygenation on coral reefs, as well as the influence of climate change on understudied sediment-producing taxa such as foraminifera and tropical molluscs.</p
Domestic revolutionaries: subverting hierarchies of influence in Joseph Conrad and Pío Baroja
No full textJoseph Conrad was already well-known in Spanish intellectual circles before the translation of several of his works into Spanish in the mid-1920s, following a commemoration of the Polish émigré author in the Madrid literary review Revista de Occidente in 1924. Inspired by Conrad’s writing, the Basque author Pío Baroja collected a substantial number of his volumes in the library at his house ‘Itzea’ (in Vera de Bidasoa, Navarra), with several in French translation. Among them was the French edition of The Secret Agent (1907), published as L’Agent secret (Paris: Mercure de France, 1912). This article seeks to update the long-established critical framing of the influence of Anglophone literature on Baroja (Alberich 1966; Lecuona Lerchundi, 1993; Murphy 2004 and 2020). It provides a comparative approach to striking parallels between literary representations of revolutionary activity in London and Madrid in Conrad’s The Secret Agent and two closely contemporaneous novels by Pío Baroja: La dama errante (The Wandering Lady) (1908) and La ciudad de la niebla (The City of Fog) (1909). Through a focus on sceptical engagements by each author with theories of criminal and racial anthropology, this analysis explores parallels between the two writers’ literary works beyond existing hierarchies of appropriation and direct influence.</p