Navigating the PDF/A Standard: A Case Study of Theses in Oxford's Institutional Repository

The PDF/A (Portable Document Format–Archival) was established by the International Organization of Standardization as the ISO 19005 standard for long-term preservation of electronic documents. In a case study of the Oxford institutional repository theses collection, PDF/A was evaluated as a possible format for standardizing theses disseminated online. While the ISO requirements of a well-formed PDF/A promises sustainability and easy recovery of content, the case study uncovered that the standard restricts some document features from being incorporated into a well-formed PDF/A. Non-conformances to the standard are found across electronic theses and dissertations, from non-Latin glyphs used in scientific and language papers to embedded content, such as images. A further complication for achieving ISO 19005 compliance is that, despite non-conformance to the ISO standard, validation tools do not always catch non-conformance errors in documents which claim to conform to PDF/A. While PDF/A is a logical solution for long-term digital preservation, the stringent standard prevents some content which is frequently used in academic research from conforming to the ISO 19005 standard

The impact of modelling method selection on predicted extent and distribution of deep-sea benthic assemblages

Predictive modelling of deep-sea species and assemblages with multibeam acoustic datasets as input variables is now a key tool in the provision of maps upon which spatial planning and management of the marine environment can be based. However, with a multitude of methods available, advice is needed on the best methods for the task at hand. In this study, we predictively modelled the distribution and extent of three vulnerable marine ecosystems (VMEs) at the assemblage level (‘Lophelia pertusa reef frameworks’; ‘Stylasterids and lobose sponges’; and ‘Xenophyophore fields’) on the eastern flank of Rockall Bank, using three modelling methods: MaxEnt; RandomForests classification with multiple assemblages (gRF); and RandomForests classification with the presence/absence of a single VME (saRF). Performance metrics indicated that MaxEnt performed the best, but all models were considered valid. All three methods broadly agreed with regard to broad patterns in distribution. However, predicted extent presented a variation of up to 35 % between the different methods, and clear differences in predicted distribution were observed. We conclude that the choice of method is likely to influence the results of predicted maps, potentially impacting political decisions about deep-sea VME conservation

Evaluation of benthic assemblage structure in the NAFO regulatory area with regard to the protection of VME

This article presents the results from the analysis of data acquired during the NEREIDA survey programme (2009-2010) around the Flemish Cap and the tail of the Grand Banks of Newfoundland (NAFO Regulatory Area). Biological samples were collected using a mega box-core, which were processed for the extraction and identification of benthic macrofauna. A suite of physical samples and environmental measurements was also collected for evaluation. Analyses revealed the presence of benthic assemblages that were indicative of Vulnerable Marine Ecosystems (VME). VME indicative assemblages were present mostly outside of the fishing footprint. A simple habitat suitability model identified areas that are likely to accommodate VME indicative assemblages. Areas with the greatest potential to accommodate VME assemblages closely correspond with areas already managed for the protection of VME, where bottom-contact fishing practices are presently excluded. Such results support the notion that existing bottom-fishery exclusion zones should continue to be enforced for the long-term protection of VME.En prensa2,277

Reconstructing baselines: use of habitat suitability modelling to predict pre-fishing condition of a Vulnerable Marine Ecosystem

As industrialized fishing activities have moved into deeper water, the recognition of Vulnerable Marine Ecosystems (VMEs) has become important for the protection of the deep-sea. Our limited knowledge on the past and present distribution of VMEs hinders our ability to manage bottom fisheries effectively. This study investigated whether accounting for bottom fishing intensity (derived from Vessel Monitoring System records) as a predictor in habitat suitability models can (1) improve predictions of, and (2) provide estimates for a pre-fishing baseline for the distribution and biomass of a VME indicator taxon. Random Forest models were applied to presence/absence and biomass of Geodia sponges and environmental variables with and without bottom fishing intensity. The models including fishing were further used to predict distribution and biomass of Geodia to a pre-fishing scenario. Inclusion of fishing pressure as a predictive term significantly improved model performance for both sponge presence and biomass. This study has demonstrated a way to produce a more accurate picture of the current distribution of VMEs in the study area. The pre-fishing scenario predictions also identified areas of suitable Geodia habitat that are currently impacted by fishing, suggesting that sponge habitat and biomass have been impacted by bottom trawling activities.1054-3139Versión del editor2,27

Testing the Potential for Predictive Modeling and Mapping and Extending Its Use as a Tool for Evaluating Management Scenarios and Economic Valuation in the Baltic Sea (PREHAB)

Peer reviewe

Distribution of Vulnerable Marine Ecosystems at the South Sandwich Islands: Results From the Blue Belt Discovery Expedition 99 Deep-Water Camera Surveys

The South Sandwich Islands (SSI) are a chain of volcanic islands located to the east of the Scotia Sea, approximately 700 km south-east of South Georgia. To date, knowledge of the SSI benthic environment remains limited. In this context, the Blue Belt Programme conducted a scientific survey in the SSI Marine Protected Area (MPA) during February/March 2019 to examine the biodiversity and distribution of benthic communities and their potential vulnerability to licensed longline research fisheries. Here we report results from analysis of multibeam echosounder (MBES) data and drop camera imagery data collected in selected locations around the SSI. A total of eight vulnerable marine ecosystem (VME) indicator morphotaxa were mapped along the slopes of the SSI, showing a substantial variation in taxon composition and frequency of occurrence, both along bathymetric and latitudinal gradients. Our results suggest that VME indicator taxa are mostly restricted to waters shallower than 700 m. As such, based on our present understanding of the region’s benthic environment the MPA, as currently established, offers effective protection for the majority of the VME indicator taxa

Mutation of praR in Rhizobium leguminosarum enhances root biofilms, improving nodulation competitiveness by increased expression of attachment proteins

Summary In Rhizobium leguminosarum bv. viciae, quorumsensing is regulated by CinR, which induces the cinIS operon. CinI synthesizes an AHL, whereas CinS inactivates PraR, a repressor. Mutation of praR enhanced biofilms in vitro. We developed a light (lux)-dependent assay of rhizobial attachment to roots and demonstrated that mutation of praR increased biofilms on pea roots. The praR mutant out-competed wild-type for infection of pea nodules in mixed inoculations. Analysis of gene expression by microarrays and promoter fusions revealed that PraR represses its own transcription and mutation of praR increased expression of several genes including those encoding secreted proteins (the adhesins RapA2, RapB and RapC, two cadherins and the glycanase PlyB), the polysaccharide regulator RosR, and another protein similar to PraR. PraR bound to the promoters of several of these genes indicating direct repression. Mutations in rapA2, rapB, rapC, plyB, the cadherins or rosR did not affect the enhanced root attachment or nodule competitiveness of the praR mutant. However combinations of mutations in rapA, rapB and rapC abolished the enhanced attachment and nodule competitiveness. We conclude that relief of PraR-mediated repression determines a lifestyle switch allowing the expression of genes that are important for biofilm formation on roots and the subsequent initiation of infection of legume roots

Defining the target population to make marine image-based biological data FAIR

Marine imaging studies have unique constraints on the data collected requiring a tool for defining the biological scope to facilitate data discovery, quality evaluation, sharing and reuse. Defining the ‘target population’ is way of scoping biological sampling or observations by setting the pool of organisms to be observed or sampled. It is used in survey design and planning, to determine statistical inference, and is critical for data interpretation and reuse (both images and derived data). We designed a set of attributes for defining and recording the target population in biological studies using marine photography, incorporating ecological and environmental delineation and marine imaging method constraints. We describe how this definition may be altered and recorded at different phases of a project. The set of attributes records the definition of the target population in a structured metadata format to enhance data FAIRness. It is designed as an extension to the image FAIR Digital Objects metadata standard, and we map terms to other biological data standards where possible. This set of attributes serves a need to update ecological metadata to align with new remotely-sensed data, and can be applied to other remotely-sensed ecological image data

Antarctic extreme events

There is increasing evidence that fossil-fuel burning, and consequential global heating of 1.1°C to date, has led to the increased occurrence and severity of extreme environmental events. It is well documented how such events have impacted society outside Antarctica through enhanced levels of rainfall and flooding, heatwaves and wildfires, drought and water/food shortages and episodes of intense cooling. Here, we briefly examine evidence for extreme events in Antarctica and the Southern Ocean across a variety of environments and timescales. We show how vulnerable natural Antarctic systems are to extreme events and highlight how governance and environmental protection of the continent must take them into account. Given future additional heating of at least 0.4°C is now unavoidable (to contain heating to the “Paris Agreement 1.5°C” scenario), and may indeed be higher unless drastic action is successfully taken on reducing greenhouse gas emissions to net zero by mid-Century, we explain it is virtually certain that future Antarctic extreme events will be more pronounced than those observed to date