PROCESSING CONSERVATION INDICATORS WITH OPEN SOURCE TOOLS: LESSONS LEARNED FROM THE DIGITAL OBSERVATORY FOR PROTECTED AREAS

The European Commission has a commitment to open data and the support of open source software and standards. We present lessons learnt while populating and supporting the web and map services that underly the Joint Research Centre's Digital Observatory for Protected Areas. Challenges include: large datasets with highly complex geometries; topological inconsistencies, compounded by reprojection for equal-area calculations; multiple different representations of the same geographical entities, for example coastlines; licensing requirement to continuously update indicators to respond to monthly changes in the authoritative data. In order to compute and publish an array of indicators, we used a range of open source tools including GRASS, R, python, GDAL, PostGIS, geometry libraries for Hadoop, Geoserver, Geonode, and Mapserver. In addition we assessed the value of the commercial ArcGIS Pro software and the Google Earth Engine platform. We describe the lessons that we learnt in building and documenting a usable and repeatable workflow,highlighting weak spots and workarounds., Code for our processing workflows will be shared via github and key process flows will be shared via a VRE to allow reproducible research while complying with data redistribution restrictions from the data providers. Our final goal is to move the entire processing chain to open source tools and share it as a versioned resource

Protected areas in the world's ecoregions:how well connected are they?

Protected areas (PAs) are the main instrument for biodiversity conservation, which has triggered the development of numerous indicators and assessments on their coverage, performance and efficiency. The connectivity of the PA networks at a global scale has however been much less explored; previous studies have either focused on particular regions of the world or have only considered some types of PAs. Here we present, and globally assess, ProtConn, an indicator of PA connectivity that (i) quantifies the percentage of a study region covered by protected connected lands, (ii) can be partitioned in several components depicting different categories of land (unprotected, protected or transboundary) through which movement between protected locations may occur, (iii) is easy to communicate, to compare with PA coverage and to use in the assessment of global targets for PA systems. We apply ProtConn to evaluate the connectivity of the PA networks in all terrestrial ecoregions of the world as of June 2016, considering a range of median dispersal distances (1–100 km) encompassing the dispersal abilities of the large majority of terrestrial vertebrates. We found that 9.3% of the world is covered by protected connected lands (average for all the world's ecoregions) for a reference dispersal distance of 10 km, increasing up to 11.7% for the largest dispersal distance considered of 100 km. These percentages are considerably smaller than the global PA coverage of 14.7%, indicating that the spatial arrangement of PAs is only partially successful in ensuring connectivity of protected lands. The connectivity of PAs largely differed across ecoregions. Only about a third of the world's ecoregions currently meet the Aichi Target of having 17% of the terrestrial realm covered by well-connected systems of PAs. Finally, our findings suggest that PAs with less strict management objectives (allowing the sustainable use of resources) may play a fundamental role in upholding the connectivity of the PA systems. Our analyses and indicator make it possible to identify where on the globe additional efforts are most needed in expanding or reinforcing the connectivity of PA systems, and can be also used to assess whether newly designated sites provide effective connectivity gains in the PA system by acting as corridors or stepping stones between other PAs. The results of the ProtConn indicator are available, together with a suite of other global PA indicators, in the Digital Observatory for Protected Areas of the Joint Research Centre of the European Commission

Global trends in protected area connectivity from 2010 to 2018

Connectivity of protected areas (PAs) is needed to ensure the long-term persistence of biodiversity and ecosystem service delivery. The Convention on Biological Diversity agreed in 2010 to have 17% of land covered by well-connected PA systems by 2020 (Aichi Target 11). We here globally assess, for all countries, the trends in terrestrial PA connectivity every other year from 2010 to 2018 using the ProtConn indicator, which quantifies how well the PA systems are designed to support connectivity. The percentage of protected connected land (ProtConn) has increased globally from 6.5% in 2010 to 7.7% in 2018. Oceania experienced the largest recent increase in PA connectivity, whereas Asia is the only content with a lower ProtConn in 2018 than in 2010. Globally, the relative increase in the percentage of protected connected land (ProtConn) is nearly twice that of the percentage of land under protection (PA coverage), due to clear improvements in the design of PA systems for connectivity in many regions. The connectivity of the PA networks has become more dependent on the permeability of the unprotected landscape matrix in between PAs and on the coordinated management of adjacent PAs with different designations and of transboundary PA linkages. The relatively slow recent increase in PA connectivity globally (2016–2018) raises doubt as to whether connectivity targets will be met by 2020, and suggests that considerable further action is required to promote better-connected PA systems globally, including the expansion of the PA systems to cover key areas for connectivity in many countries and regions

Biophysical characterization of protected areas globally through optimized image segmentation and classification

Protected areas (PAs) need to be assessed systematically according to biodiversity values and threats in order to support decision-making processes. For this, PAs can be characterized according to their species, ecosystems and threats, but such information is often difficult to access and usually not comparable across regions. There are currently over 200,000 PAs in the world, and assessing these systematically according to their ecological values remains a huge challenge. However, linking remote sensing with ecological modelling can help to overcome some limitations of conservation studies, such as the sampling bias of biodiversity inventories. The aim of this paper is to introduce eHabitat+, a habitat modelling service supporting the European Commission's Digital Observatory for Protected Areas, and specifically to discuss a component that systematically stratifies PAs into different habitat functional types based on remote sensing data. eHabitat+ uses an optimized procedure of automatic image segmentation based on several environmental variables to identify the main biophysical gradients in each PA. This allows a systematic production of key indicators on PAs that can be compared globally. Results from a few case studies are illustrated to show the benefits and limitations of this open-source tool

Identifying unique areas in the Congo Basin for conservation

A major challenge in conservation biology is to identify areas to be protected in priority. With the hypotheses in mind that areas presenting unique environmental features when compared to their surroundings are more likely 1) to be vulnerable to changes and 2) hosting relatively more specialized species, we performed a global analysis to identify singular forested areas and further explored the relationship of those areas with forest bird richness and endemism. Using a moving window of 50 x 50 km, we computed, across the earth's surface, on a grid of 5 x 5 km resolution the probabilities for each cell to find similar biophysical features elsewhere in the window. The input variables were, NDVI and NDWI, slope, and the percentages of grassland and tree covers. This systematic screening allowed us to map areas presenting unique features and to further correlate this information with the level of the correlation between bird endemism and species richness. At the global scale, we found the forested biomes of the Congo Basin, namely the Tropical & Subtropical Moist Broadleaf Forests and the Tropical & Subtropical Grasslands, Savannas & Shrublands among the most homogeneous ones for what concern our environmental variables. While it is well-known that the Tropical Moist Forest is the biome holding the biggest diversity in terms of bird-species richness, the relationship between biomes and endemism levels is less documented. If we found that more than half of our variables explained bird endemism for the moist forests, such characterization of the level of endemism was not straightforward for other biomes. More relevant to the identification of potential new areas to focus on for biodiversity conservation, we found that the Tropical and Subtropical Moist Broadleaf Forests shown little ecological heterogeneity and consequently present only a few unique areas. Interestingly, while we found that the relationship between endemism and areas presenting unique environmental features was not obvious for most forested ecosystems, we found a significant relationship between endemism and habitat uniqueness for the Tropical and Subtropical Moist Broadleaf Forest. It is the purpose of this contribution to discuss further our preliminary results and to contrast our findings with the current distribution of protected areas in the Congo Basin. (Texte integral

The Digital Observatory for Protected Areas (DOPA) Explorer 1.0

The Digital Observatory for Protected Areas (DOPA) has been developed to support the European Union’s efforts in strengthening our capacity to mobilize and use biodiversity data, information and forecasts so that they are readily accessible to policymakers, managers, experts and other users. Conceived as a set of web based services, DOPA provides a broad set of free and open source tools to assess, monitor and even forecast the state of and pressure on protected areas at local, regional and global scale. DOPA Explorer 1.0 is a web based interface available in four languages (EN, FR, ES, PT) providing simple means to explore the nearly 16,000 protected areas that are at least as large as 100 km2. Distinguishing between terrestrial, marine and mixed protected areas, DOPA Explorer 1.0 can help end users to identify those with most unique ecosystems and species, and assess the pressures they are exposed to because of human development. Recognized by the UN Convention on Biological Diversity (CBD) as a reference information system, DOPA Explorer is based on the best global data sets available and provides means to rank protected areas at the country and ecoregion levels. Inversely, DOPA Explorer indirectly highlights the protected areas for which information is incomplete. We finally invite the end-users of DOPA to engage with us through the proposed communication platforms to help improve our work to support the safeguarding of biodiversity

Refractory chronic GVHD emerging after splenectomy in a marrow transplant recipient with accelerated phase CML

We report a 39-year-old female patient who underwent HLA-identical sibling allogeneic BMT for CML in accelerated phase. Severe pancytopenia refractory to G-CSF associated with progressive splenomegaly and RBC/ platelet transfusion dependency were present from day + 60 after BMT. MRD assessed by FISH and RT-PCR multiplex for BCR-ABL rearrangement was negative, and complete chimerism was documented by VNTR on days + 100, + 180, + 360 and 2 years after BMT. Splenectomy was performed on day + 225 and pancytopenia resolved but chronic extensive graft-versus-host disease developed, with hepatic cholestasis, diffuse scleroderma and sicca-like syndrome. She was sequentially and progressively treated with different immunosuppressive therapy combinations with no clear benefit. On day + 940, she presented with infection over the previously present ulcers on both limbs, which culminated in septic shock and death on day + 1041. We conclude that, although splenectomy may reverse poor graft function after allogeneic BMT, hyposplenism may trigger or worsen chronic extensive GVHD leading to increased morbidity and mortality.Hosp São Paulo, São Paulo, BrazilHosp São Paulo, São Paulo, BrazilWeb of Scienc

Synthesis and Crystallographic Characterization of a Maleimide Derivative of Tryptamine

While mechanosynthesis of the target compound, 1-[2-(1H-indol-3-yl)-ethyl]-pyrrole-2,5-dione, C14 H12 N2 O2, did not yield the desired product, it instead resulted in an open intermediate. On the other hand, synthesis starting from the activated maleic anhydride yielded the final maleimide compound. The outcome of the mechanosynthesis has been evaluated by powder X-ray diffraction, and structures of both the final product and open intermediate have been confirmed using single-crystal crystallography