Detection of coccolithophore blooms with biogeochemical‐argo floats

Coccolithophores (calcifying phytoplankton) form extensive blooms in temperate and subpolar oceans as evidenced from ocean-color satellites. This study examines the potential to detect coccolithophore blooms with BioGeoChemical-Argo (BGC-Argo) floats, autonomous ocean profilers equipped with bio-optical and physicochemical sensors. We first matched float data to ocean-color satellite data of calcite concentration to select floats that sampled coccolithophore blooms. We identified two floats in the Southern Ocean, which measured the particulate beam attenuation coefficient (c(p)) in addition to two core BGC-Argo variables, Chlorophyll-a concentration ([Chl-a]) and the particle backscattering coefficient (b(bp)). We show that coccolithophore blooms can be identified from floats by distinctively high values of (1) the b(bp)/c(p) ratio, a proxy for the refractive index of suspended particles, and (2) the b(bp)/[Chl-a] ratio, measurable by any BGC-Argo float. The latter thus paves the way to global investigations of environmental control of coccolithophore blooms and their role in carbon export. Plain Language Summary Coccolithophores are a group of phytoplankton that form an armor of calcite plates. Coccolithophores may form intense blooms which can be identified from space by so-called ocean-color satellites, providing global images of the color of the surface ocean. BioGeoChemical-Argo (BGC-Argo) floats, robots profiling down to 2,000 m with a variety of physicochemical and bio-optical sensors, present an increasingly attractive and cost-effective platform to study phytoplankton blooms and their impact on oceanic biogeochemical cycles. We show that coccolithophore blooms can be detected by BGC-Argo floats with high confidence, hence providing a new way to study them at the global scale as well as their role in sinking carbon. Key Points We matched profiling float trajectories with ocean-color satellite observations of coccolithophore blooms Two simple bio-optical indices permitted successful identification of coccolithophore blooms from floats in the Southern Ocean A method for identifying coccolithophore blooms at the global scale is proposed using regional thresholds of bio-optical float measurement

The relative importance of phytoplankton aggregates and zooplankton fecal pellets to carbon export: insights from free-drifting sediment trap deployments in naturally iron-fertilised waters near the Kerguelen Plateau

The first KErguelen Ocean and Plateau compared Study (KEOPS1), conducted in the naturally iron-fertilised Kerguelen bloom, demonstrated that fecal material was the main pathway for exporting carbon to the deep ocean during summer (January–February 2005), suggesting a limited role of direct export via phytodetrital aggregates. The KEOPS2 project reinvestigated this issue during the spring bloom initiation (October–November 2011), when zooplankton communities may exert limited grazing pressure, and further explored the link between carbon flux, export efficiency and dominant sinking particles depending upon surface plankton community structure. Sinking particles were collected in polyacrylamide gel-filled and standard free-drifting sediment traps (PPS3/3), deployed at six stations between 100 and 400 m, to examine flux composition, particle origin and their size distributions. Results revealed an important contribution of phytodetrital aggregates (49 ± 10 and 45 ± 22% of the total number and volume of particles respectively, all stations and depths averaged). This high contribution dropped when converted to carbon content (30 ± 16% of total carbon, all stations and depths averaged), with cylindrical fecal pellets then representing the dominant fraction (56 ± 19%).At 100 and 200 m depth, iron- and biomass-enriched sites exhibited the highest carbon fluxes (maxima of 180 and 84 ± 27 mg C m-2 d-1, based on gel and PPS3/3 trap collection respectively), especially where large fecal pellets dominated over phytodetrital aggregates. Below these depths, carbon fluxes decreased (48 ± 21% decrease on average between 200 and 400 m), and mixed aggregates composed of phytodetritus and fecal matter dominated, suggesting an important role played by physical aggregation in deep carbon export.Export efficiencies determined from gels, PPS3/3 traps and 234Th disequilibria (200 m carbon flux/net primary productivity) were negatively correlated to net primary productivity with observed decreases from ~ 0.2 at low-iron sites to ~ 0.02 at high-iron sites. Varying phytoplankton communities and grazing pressure appear to explain this negative relationship. Our work emphasises the need to consider detailed plankton communities to accurately identify the controls on carbon export efficiency, which appear to include small spatio-temporal variations in ecosystem structure

The relative importance of phytoplankton aggregates and zooplankton fecal pellets to carbon export: insights from free-drifting sediment trap deployments in naturally iron-fertilised waters near the Kerguelen Plateau

The first KErguelen Ocean and Plateau compared Study (KEOPS1), conducted in the naturally iron-fertilised Kerguelen bloom, demonstrated that fecal material was the main pathway for exporting carbon to the deep ocean during summer (January–February 2005), suggesting a limited role of direct export via phytodetrital aggregates. The KEOPS2 project reinvestigated this issue during the spring bloom initiation (October–November 2011), when zooplankton communities may exert limited grazing pressure, and further explored the link between carbon flux, export efficiency and dominant sinking particles depending upon surface plankton community structure. Sinking particles were collected in polyacrylamide gel-filled and standard free-drifting sediment traps (PPS3/3), deployed at six stations between 100 and 400 m, to examine flux composition, particle origin and their size distributions. Results revealed an important contribution of phytodetrital aggregates (49+/-10 and 45+/-22% of the total number and volume of particles respectively, all stations and depths averaged). This high contribution dropped when converted to carbon content (30+/-16% of total carbon, all stations and depths averaged), with cylindrical fecal pellets then representing the dominant fraction (56+/-19 %). At 100 and 200m depth, iron- and biomass-enriched sites exhibited the highest carbon fluxes (maxima of 180 and 84+/- 27 mgCm-2 d-1, based on gel and PPS3/3 trap collection respectively), especially where large fecal pellets dominated over phytodetrital aggregates. Below these depths, carbon fluxes decreased (48+/-21%decrease on average between 200 and 400 m), and mixed aggregates composed of phytodetritus and fecal matter dominated, suggesting an important role played by physical aggregation in deep carbon export. Export efficiencies determined from gels, PPS3/3 traps and 234Th disequilibria (200m carbon flux/net primary productivity) were negatively correlated to net primary productivity with observed decreases from ~0.2 at low-iron sites to ~0.02 at high-iron sites. Varying phytoplankton communities and grazing pressure appear to explain this negative relationship. Our work emphasises the need to consider detailed plankton communities to accurately identify the controls on carbon export efficiency, which appear to include small spatio-temporal variations in ecosystem structure

Surveyed common data access policies preferences amongst European Reference Networks

Background: Data sharing amongst existing Rare Disease (RD) registries, even though being a process that presents multiple barriers, would enrich and ease research, as well as facilitate interoperability between the registries themselves. Methods: To understand their preferences on sharing data, we surveyed 24 European Reference Networks (ERNs) from the RD Domain. Results: The answers show that most ERNs are willing to share a set of Common Data Elements for free with authenticated users at an aggregated or pseudonymized level the moment the data is collected. The one exception is the industry sector, to which ERNs prefer to ask for a fee. Objective: Our aim is to create a reference for how most RD registries are willing to share their data, improving the ability of other stakeholders to make informed decisions to make their data interoperable.</p

Surveyed common data access policies preferences amongst European Reference Networks

Background: Data sharing amongst existing Rare Disease (RD) registries, even though being a process that presents multiple barriers, would enrich and ease research, as well as facilitate interoperability between the registries themselves. Methods: To understand their preferences on sharing data, we surveyed 24 European Reference Networks (ERNs) from the RD Domain. Results: The answers show that most ERNs are willing to share a set of Common Data Elements for free with authenticated users at an aggregated or pseudonymized level the moment the data is collected. The one exception is the industry sector, to which ERNs prefer to ask for a fee. Objective: Our aim is to create a reference for how most RD registries are willing to share their data, improving the ability of other stakeholders to make informed decisions to make their data interoperable.</p

Surveyed common data access policies preferences amongst European Reference Networks

Background: Data sharing amongst existing Rare Disease (RD) registries, even though being a process that presents multiple barriers, would enrich and ease research, as well as facilitate interoperability between the registries themselves. Methods: To understand their preferences on sharing data, we surveyed 24 European Reference Networks (ERNs) from the RD Domain. Results: The answers show that most ERNs are willing to share a set of Common Data Elements for free with authenticated users at an aggregated or pseudonymized level the moment the data is collected. The one exception is the industry sector, to which ERNs prefer to ask for a fee. Objective: Our aim is to create a reference for how most RD registries are willing to share their data, improving the ability of other stakeholders to make informed decisions to make their data interoperable.</p

Animated Edge Textures in Node-Link Diagrams: a Design Space and Initial Evaluation

International audienceNetwork edge data attributes are usually encoded using color, opacity, stroke thickness and stroke pattern, or some combination thereof. In addition to these static variables, it is also possible to animate dynamic particles flowing along the edges. This opens a larger design space of animated edge textures, featuring additional visual encodings that have potential not only in terms of visual mapping capacity but also playfulness and aesthetics. Such animated edge textures have been used in several commercial and design-oriented visualizations, but to our knowledge almost always in a relatively ad hoc manner. We introduce a design space and Web-based framework for generating animated edge textures, and report on an initial evaluation of particle properties – particle speed, pattern and frequency – in terms of visual perception

Towards FAIRification of sensitive and fragmented rare disease patient data:challenges and solutions in European reference network registries

INTRODUCTION: Rare disease patient data are typically sensitive, present in multiple registries controlled by different custodians, and non-interoperable. Making these data Findable, Accessible, Interoperable, and Reusable (FAIR) for humans and machines at source enables federated discovery and analysis across data custodians. This facilitates accurate diagnosis, optimal clinical management, and personalised treatments. In Europe, twenty-four European Reference Networks (ERNs) work on rare disease registries in different clinical domains. The process and the implementation choices for making data FAIR (‘FAIRification’) differ among ERN registries. For example, registries use different software systems and are subject to different legal regulations. To support the ERNs in making informed decisions and to harmonise FAIRification, the FAIRification steward team was established to work as liaisons between ERNs and researchers from the European Joint Programme on Rare Diseases. RESULTS: The FAIRification steward team inventoried the FAIRification challenges of the ERN registries and proposed solutions collectively with involved stakeholders to address them. Ninety-eight FAIRification challenges from 24 ERNs’ registries were collected and categorised into “training” (31), “community” (9), “modelling” (12), “implementation” (26), and “legal” (20). After curating and aggregating highly similar challenges, 41 unique FAIRification challenges remained. The two categories with the most challenges were “training” (15) and “implementation” (9), followed by “community” (7), and then “modelling” (5) and “legal” (5). To address all challenges, eleven types of solutions were proposed. Among them, the provision of guidelines and the organisation of training activities resolved the “training” challenges, which ranged from less-technical “coffee-rounds” to technical workshops, from informal FAIR Games to formal hackathons. Obtaining implementation support from technical experts was the solution type for tackling the “implementation” challenges. CONCLUSION: This work shows that a dedicated team of FAIR data stewards is an asset for harmonising the various processes of making data FAIR in a large organisation with multiple stakeholders. Additionally, multi-levelled training activities are required to accommodate the diverse needs of the ERNs. Finally, the lessons learned from the experience of the FAIRification steward team described in this paper may help to increase FAIR awareness and provide insights into FAIRification challenges and solutions of rare disease registries. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13023-022-02558-5

Euro plus Med-Checklist Notulae, 11

This is the eleventh of a series of miscellaneous contributions, by various authors, where hitherto unpublished data relevant to both the Med-Checklist and the Euro+Med (or Sisyphus) projects are presented. This instalment deals with the families Anacardiaceae, Asparagaceae (incl. Hyacinthaceae), Bignoniaceae, Cactaceae, Compositae, Cruciferae, Cyperaceae, Ericaceae, Gramineae, Labiatae, Leguminosae, Orobanchaceae, Polygonaceae, Rosaceae, Solanaceae and Staphyleaceae. It includes new country and area records and taxonomic and distributional considerations for taxa in Bidens, Campsis, Centaurea, Cyperus, Drymocallis, Engem, Hoffmannseggia, Hypopitys, Lavandula, Lithraea, Melilotus, Nicotiana, Olimarabidopsis, Opuntia, Orobanche, Phelipanche, Phragmites, Rumex, Salvia, Schinus, Staphylea, and a new combination in Drimia.Peer reviewe

OP0137 GENOME-WIDE WHOLE-BLOOD TRANSCRIPTOME PROFILING IN A LARGE EUROPEAN COHORT OF SYSTEMIC SCLEROSIS PATIENTS

Background:The analysis of annotated transcripts from genome-wide expression studies data is of paramount importance to understand the molecular phenomena underlying the occurrence of complex diseases, such as systemic sclerosis (SSc).Objectives:To perform whole-blood transcriptome and pathway analysis on whole-blood (WB) RNA collected in two cohorts of European SSc patients. Via a discovery and validation strategy we aimed at characterizing the molecular pathways that differentiate SSc from controls and that are reproducible in geographically diverse populations.Methods:WB samples from 252 controls and 162 SSc patients were collected in RNA stabilizers. Patients were divided into a discovery (n=79; Southern Europe) and validation cohort (n=83; Central-Western Europe). RNA sequencing was performed by an Illumina assay. Functional annotations of Reactome pathways were performed with the FAIME algorithm. In parallel, a immunophenotyping analysis on 28 circulating cell populations was assessed. We then tested: the presence of differentially expressed genes or pathways and the correlation between absolute cell counts and RNA transcripts/FAIME scores in regression models. Results significant in both populations were considered as replicated.Results:A total of 15224 genes and 1277 related functional pathways were available for analysis. Among these, 99 genes and 225 pathways were significant in both sets. The heatmap in figure shows the relative expression of replicated pathways and the distribution of cases and controls (red and green bars). Among the significant pathways we found a deregulation in: type-I IFN, TLR-cascade and signalling, function of the tumor suppressor p53 protein, platelet degranulation and activation. Correlation analysis showed that the count of several cell subtypes is jointly associated with RNA transcripts or FAIME scores with strong differences in relation to the geographical origin of samples; neutrophils emerged as the major determinant of gene expression in SSc-whole-blood samples.Conclusion:We discovered a set of differentially expressed genes and pathways that could be validated in two independent sets of SSc patients highlighting a number of deregulated molecular processes that have relevance for the pathogenesis of autoimmunity and SSc.Acknowledgments:This work was supported by EU/EFPIA/Innovative Medicines Initiative Joint Undertaking PRECISESADS grant No. 115565.Disclosure of Interests:Lorenzo Beretta Grant/research support from: Pfizer, Guillermo Barturen: None declared, Barbara Vigone: None declared, Chiara Bellocchi: None declared, Nicolas Hunzelmann: None declared, Ellen Delanghe: None declared, László Kovács: None declared, Ricard Cervera: None declared, Maria Gerosa: None declared, Rafaela Ortega Castro: None declared, Isabel Almeida: None declared, Divi Cornec: None declared, Carlo Chizzolini Consultant of: Boehringer Ingelheim, Roche, Jacques-Olivier Pers: None declared, Zuzanna Makowska Employee of: Bayer AG, Anne buttgereit Employee of: Bayer AG, Ralf Lesche Employee of: Bayer, Martin Kerick: None declared, Marta Alarcon-Riquelme: None declared, Javier Martin Ibanez: None declare