Amélioration des références techniques pour les rotations à base de Cucurbitacées et Solanacées en culture Biologique sous abris (projet OptiAbriBio)

En maraîchage biologique sous abri, les cultures de solanacées et cucurbitacées occupent un place prédominante car il s'agit de productions essentielles et incoutournables, en circuit court comme en circuit long. Cette situation induit cependant des difficultés dans la mise en oeuvre de rotations et assolements diversifiés, pratique fondamentale en agriculture biologique. Les rotations courtes et intensives sous abri, et le retour fréquent des solanacées et cucurbitacées, peuvent engendrer de réelles difficultés sanitaires car elles peuvent favoriser le développement de ravageurs et maladies telluriques ou aériens. Il est donc essentiel de choisir les espèces et variétés les plus adaptés à ce contexte, qui permettront d'assurer les meilleurs résultats agronomiques grâce à leur rusticité et/ou leur potentiel de résistance aux pathogènes, tout en respectant les exigences spécifiques de la filière AB : semences biologiques privilégiées, diversité variétale (variétés populations et hybrides F1), qualités commerciale et organoleptique, ... Les objectifs du projet sont de : - Proposer des solutions techniques pour améliorer la résilience et la durabilité des systèmes maraîchers sous abris vis à vis des problèmes sanitaires, - Evaluer et caractériser le matériel végétal disponible en Agriculture Biologique pour les cultures de solanacées et cucurbitacées sous abri, afin de permettre aux producteurs de disposer d'un matériel végétal adapté et performant dans ces conditions de cultures spécifiques, pour une valorisation en circuit court et en circuit long

hydrographr: An R package for scalable hydrographic data processing

1. Freshwater ecosystems are considered biodiversity hotspots, but assessing the spatial distribution of species remains challenging. One major obstacle lies in the complex geospatial processing of large amounts of data, such as stream network, sub-catchment and basin data, that are necessary for addressing the longitudinal connectivity among water bodies. Workflows thus need to be scalable, especially when working across large spatial extents and at high spatial resolution. This in turn requires advanced command-line GIS skills and programming language integration, which often poses a challenge for freshwater researchers. 2. To address this challenge, we developed the package hydrographr that provides scalable hydrographic data processing in R. The package contains functions for downloading data of the high-resolution Hydrography90m dataset, processing, reading and extracting information, as well as assessing network distances and connectivity. While the functions are, by default, tailored toward the Hydrography90m data, they can also be generalised toward other data and purposes, such as efficient cropping and merging of raster and vector data, point-raster extraction, raster reclassification and data aggregation. The package depends on the open-source software GDAL/OGR, GRASS-GIS and the AWK programming language in the Linux environment, allowing a seamless language integration. Since the data is processed outside R, hydrographr allows creating scalable geo-processing workflows. 3. We illustrate the hydrographr functions using two workflows that focus on (i) a freshwater species distribution modelling approach, and (ii) assessing stream connectivity given the fragmentation by dams. We also provide a detailed guide for the initial installation of the required software. Windows users need to first enable the Windows Subsystem for Linux (WSL) feature, and can then follow the same software installation as Linux users. hydrographr is maintained on GitHub at https://github.com/glowabio/hydrographr. 4. hydrographr provides a set of key functions for processing freshwater geospatial data. We expect that the package will support the freshwater-related research communities given the easy-to-use wrapper functions that allow capitalizing on powerful open-source command-line software, which may otherwise require a steep learning curve. Users can thus perform large-scale freshwater-specific longitudinal connectivity and network analyses across large geographic extents while staying within the R environment

The global EPTO database: Worldwide occurrences of aquatic insects

Motivation: Aquatic insects comprise 64% of freshwater animal diversity and are widely used as bioindicators to assess water quality impairment and freshwater eco-system health, as well as to test ecological hypotheses. Despite their importance, a comprehensive, global database of aquatic insect occurrences for mapping freshwater biodiversity in macroecological studies and applied freshwater research is missing. We aim to fill this gap and present the Global EPTO Database, which includes world-wide geo- referenced aquatic insect occurrence records for four major taxa groups: Ephemeroptera, Plecoptera, Trichoptera and Odonata (EPTO).Main type of variables contained: A total of 8,368,467 occurrence records globally, of which 8,319,689 (99%) are publicly available. The records are attributed to the cor-responding drainage basin and sub-catchment based on the Hydrography90m dataset and are accompanied by the elevation value, the freshwater ecoregion and the pro-tection status of their location. Spatial location and grain: The database covers the global extent, with 86% of the observation records having coordinates with at least four decimal digits (11.1 m preci-sion at the equator) in the World Geodetic System 1984 (WGS84) coordinate refer-ence system.Time period and grain: Sampling years span from 1951 to 2021. Ninety- nine percent of the records have information on the year of the observation, 95% on the year and month, while 94% have a complete date. In the case of seven sub-datasets, exact dates can be retrieved upon communication with the data contributors. Major taxa and level of measurement: Ephemeroptera, Plecoptera, Trichoptera and Odonata, standardized at the genus taxonomic level. We provide species names for 7,727,980 (93%) records without further taxonomic verification.Software format: The entire tab-separated value (.csv) database can be downloaded and visualized at https://glowabio.org/project/epto_database/ . Fifty individual data-sets are also available at https://fred.igb-berlin.de, while six datasets have restricted access. For the latter, we share metadata and the contact details of the authors

The three Rs of river ecosystem resilience : Resources, recruitment, and refugia

This review article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Use of Self-Archived VersionResilience in river ecosystems requires that organisms must persist in the face of highly dynamic hydrological and geomorphological variations. Disturbance events such as floods and droughts are postulated to shape life history traits that support resilience, but river management and conservation would benefit from greater understanding of the emergent effects in communities of river organisms. We unify current knowledge of taxonomic-, phylogenetic-, and trait-based aspects of river communities that might aid the identification and quantification of resilience mechanisms. Temporal variations in river productivity, physical connectivity, and environmental heterogeneity resulting from floods and droughts are highlighted as key characteristics that promote resilience in these dynamic ecosystems. Three community-wide mechanisms that underlie resilience are (a) partitioning (competition/facilitation) of dynamically varying resources, (b) dispersal, recolonization, and recruitment promoted by connectivity, and (c) functional redundancy in communities promoted by resource heterogeneity and refugia. Along with taxonomic and phylogenetic identity, biological traits related to feeding specialization, dispersal ability, and habitat specialization mediate organism responses to disturbance. Measures of these factors might also enable assessment of the relative contributions of different mechanisms to community resilience. Interactions between abiotic drivers and biotic aspects of resource use, dispersal, and persistence have clear implications for river conservation and management. To support these management needs, we propose a set of taxonomic, phylogenetic, and life-history trait metrics that might be used to measure resilience mechanisms. By identifying such indicators, our proposed framework can enable targeted management strategies to adapt river ecosystems to global change

The recovery of European freshwater biodiversity has come to a halt

Owing to a long history of anthropogenic pressures, freshwater ecosystems are among the most vulnerable to biodiversity loss1. Mitigation measures, including wastewater treatment and hydromorphological restoration, have aimed to improve environmental quality and foster the recovery of freshwater biodiversity2. Here, using 1,816 time series of freshwater invertebrate communities collected across 22 European countries between 1968 and 2020, we quantified temporal trends in taxonomic and functional diversity and their responses to environmental pressures and gradients. We observed overall increases in taxon richness (0.73% per year), functional richness (2.4% per year) and abundance (1.17% per year). However, these increases primarily occurred before the 2010s, and have since plateaued. Freshwater communities downstream of dams, urban areas and cropland were less likely to experience recovery. Communities at sites with faster rates of warming had fewer gains in taxon richness, functional richness and abundance. Although biodiversity gains in the 1990s and 2000s probably reflect the effectiveness of water-quality improvements and restoration projects, the decelerating trajectory in the 2010s suggests that the current measures offer diminishing returns. Given new and persistent pressures on freshwater ecosystems, including emerging pollutants, climate change and the spread of invasive species, we call for additional mitigation to revive the recovery of freshwater biodiversity.publishedVersio

Variation in Structure and Process of Care in Traumatic Brain Injury: Provider Profiles of European Neurotrauma Centers Participating in the CENTER-TBI Study.

INTRODUCTION: The strength of evidence underpinning care and treatment recommendations in traumatic brain injury (TBI) is low. Comparative effectiveness research (CER) has been proposed as a framework to provide evidence for optimal care for TBI patients. The first step in CER is to map the existing variation. The aim of current study is to quantify variation in general structural and process characteristics among centers participating in the Collaborative European NeuroTrauma Effectiveness Research in Traumatic Brain Injury (CENTER-TBI) study. METHODS: We designed a set of 11 provider profiling questionnaires with 321 questions about various aspects of TBI care, chosen based on literature and expert opinion. After pilot testing, questionnaires were disseminated to 71 centers from 20 countries participating in the CENTER-TBI study. Reliability of questionnaires was estimated by calculating a concordance rate among 5% duplicate questions. RESULTS: All 71 centers completed the questionnaires. Median concordance rate among duplicate questions was 0.85. The majority of centers were academic hospitals (n = 65, 92%), designated as a level I trauma center (n = 48, 68%) and situated in an urban location (n = 70, 99%). The availability of facilities for neuro-trauma care varied across centers; e.g. 40 (57%) had a dedicated neuro-intensive care unit (ICU), 36 (51%) had an in-hospital rehabilitation unit and the organization of the ICU was closed in 64% (n = 45) of the centers. In addition, we found wide variation in processes of care, such as the ICU admission policy and intracranial pressure monitoring policy among centers. CONCLUSION: Even among high-volume, specialized neurotrauma centers there is substantial variation in structures and processes of TBI care. This variation provides an opportunity to study effectiveness of specific aspects of TBI care and to identify best practices with CER approaches

Multi-decadal improvements in the ecological quality of European rivers are not consistently reflected in biodiversity metrics

Humans impact terrestrial, marine and freshwater ecosystems, yet many broad-scale studies have found no systematic, negative biodiversity changes (for example, decreasing abundance or taxon richness). Here we show that mixed biodiversity responses may arise because community metrics show variable responses to anthropogenic impacts across broad spatial scales. We first quantified temporal trends in anthropogenic impacts for 1,365 riverine invertebrate communities from 23 European countries, based on similarity to least-impacted reference communities. Reference comparisons provide necessary, but often missing, baselines for evaluating whether communities are negatively impacted or have improved (less or more similar, respectively). We then determined whether changing impacts were consistently reflected in metrics of community abundance, taxon richness, evenness and composition. Invertebrate communities improved, that is, became more similar to reference conditions, from 1992 until the 2010s, after which improvements plateaued. Improvements were generally reflected by higher taxon richness, providing evidence that certain community metrics can broadly indicate anthropogenic impacts. However, richness responses were highly variable among sites, and we found no consistent responses in community abundance, evenness or composition. These findings suggest that, without sufficient data and careful metric selection, many common community metrics cannot reliably reflect anthropogenic impacts, helping explain the prevalence of mixed biodiversity trends.We thank J. England for assistance with calculating ecological quality and the biomonitoring indices in the UK. Funding for authors, data collection and processing was provided by the European Union Horizon 2020 project eLTER PLUS (grant number 871128). F.A. was supported by the Swiss National Science Foundation (grant numbers 310030_197410 and 31003A_173074) and the University of Zurich Research Priority Program Global Change and Biodiversity. J.B. and M.A.-C. were funded by the European Commission, under the L‘Instrument Financier pour l’Environnement (LIFE) Nature and Biodiversity program, as part of the project LIFE-DIVAQUA (LIFE18 NAT/ES/000121) and also by the project ‘WATERLANDS’ (PID2019-107085RB-I00) funded by the Ministerio de Ciencia, Innovación y Universidades (MCIN) and Agencia Estatal de Investigación (AEI; MCIN/AEI/10.13039/501100011033/ and by the European Regional Development Fund (ERDF) ‘A way of making Europe’. N.J.B. and V.P. were supported by the Lithuanian Environmental Protection Agency (https://aaa.lrv.lt/) who collected the data and were funded by the Lithuanian Research Council (project number S-PD-22-72). J.H. was supported by the Academy of Finland (grant number 331957). S.C.J. acknowledges funding by the Leibniz Competition project Freshwater Megafauna Futures and the German Federal Ministry of Education and Research (Bundesministerium für Bildung und Forschung or BMBF; 033W034A). A.L. acknowledges funding by the Spanish Ministry of Science and Innovation (PID2020-115830GB-100). P.P., M.P. and M.S. were supported by the Czech Science Foundation (GA23-05268S and P505-20-17305S) and thank the Czech Hydrometeorological Institute and the state enterprises Povodí for the data used to calculate ecological quality metrics from the Czech surface water monitoring program. H.T. was supported by the Estonian Research Council (number PRG1266) and by the Estonian national program ‘Humanitarian and natural science collections’. M.J.F. acknowledges the support of Fundação para a Ciência e Tecnologia, Portugal, through the projects UIDB/04292/2020 and UIDP/04292/2020 granted to the Marine and Environmental Sciences Centre, LA/P/0069/2020 granted to the Associate Laboratory Aquatic Research Network (ARNET), and a Call Estímulo ao Emprego Científico (CEEC) contract.Peer reviewe

The recovery of European freshwater biodiversity has come to a halt

Owing to a long history of anthropogenic pressures, freshwater ecosystems are among the most vulnerable to biodiversity loss1. Mitigation measures, including wastewater treatment and hydromorphological restoration, have aimed to improve environmental quality and foster the recovery of freshwater biodiversity2. Here, using 1,816 time series of freshwater invertebrate communities collected across 22 European countries between 1968 and 2020, we quantified temporal trends in taxonomic and functional diversity and their responses to environmental pressures and gradients. We observed overall increases in taxon richness (0.73% per year), functional richness (2.4% per year) and abundance (1.17% per year). However, these increases primarily occurred before the 2010s, and have since plateaued. Freshwater communities downstream of dams, urban areas and cropland were less likely to experience recovery. Communities at sites with faster rates of warming had fewer gains in taxon richness, functional richness and abundance. Although biodiversity gains in the 1990s and 2000s probably reflect the effectiveness of water-quality improvements and restoration projects, the decelerating trajectory in the 2010s suggests that the current measures offer diminishing returns. Given new and persistent pressures on freshwater ecosystems, including emerging pollutants, climate change and the spread of invasive species, we call for additional mitigation to revive the recovery of freshwater biodiversity.N. Kaffenberger helped with initial data compilation. Funding for authors and data collection and processing was provided by the EU Horizon 2020 project eLTER PLUS (grant agreement no. 871128); the German Federal Ministry of Education and Research (BMBF; 033W034A); the German Research Foundation (DFG FZT 118, 202548816); Czech Republic project no. P505-20-17305S; the Leibniz Competition (J45/2018, P74/2018); the Spanish Ministerio de Economía, Industria y Competitividad—Agencia Estatal de Investigación and the European Regional Development Fund (MECODISPER project CTM 2017-89295-P); Ramón y Cajal contracts and the project funded by the Spanish Ministry of Science and Innovation (RYC2019-027446-I, RYC2020-029829-I, PID2020-115830GB-100); the Danish Environment Agency; the Norwegian Environment Agency; SOMINCOR—Lundin mining & FCT—Fundação para a Ciência e Tecnologia, Portugal; the Swedish University of Agricultural Sciences; the Swiss National Science Foundation (grant PP00P3_179089); the EU LIFE programme (DIVAQUA project, LIFE18 NAT/ES/000121); the UK Natural Environment Research Council (GLiTRS project NE/V006886/1 and NE/R016429/1 as part of the UK-SCAPE programme); the Autonomous Province of Bolzano (Italy); and the Estonian Research Council (grant no. PRG1266), Estonian National Program ‘Humanitarian and natural science collections’. The Environment Agency of England, the Scottish Environmental Protection Agency and Natural Resources Wales provided publicly available data. We acknowledge the members of the Flanders Environment Agency for providing data. This article is a contribution of the Alliance for Freshwater Life (www.allianceforfreshwaterlife.org).Peer reviewe

Extracorporeal Membrane Oxygenation for Severe Acute Respiratory Distress Syndrome associated with COVID-19: An Emulated Target Trial Analysis.

RATIONALE: Whether COVID patients may benefit from extracorporeal membrane oxygenation (ECMO) compared with conventional invasive mechanical ventilation (IMV) remains unknown. OBJECTIVES: To estimate the effect of ECMO on 90-Day mortality vs IMV only Methods: Among 4,244 critically ill adult patients with COVID-19 included in a multicenter cohort study, we emulated a target trial comparing the treatment strategies of initiating ECMO vs. no ECMO within 7 days of IMV in patients with severe acute respiratory distress syndrome (PaO2/FiO2 <80 or PaCO2 ≥60 mmHg). We controlled for confounding using a multivariable Cox model based on predefined variables. MAIN RESULTS: 1,235 patients met the full eligibility criteria for the emulated trial, among whom 164 patients initiated ECMO. The ECMO strategy had a higher survival probability at Day-7 from the onset of eligibility criteria (87% vs 83%, risk difference: 4%, 95% CI 0;9%) which decreased during follow-up (survival at Day-90: 63% vs 65%, risk difference: -2%, 95% CI -10;5%). However, ECMO was associated with higher survival when performed in high-volume ECMO centers or in regions where a specific ECMO network organization was set up to handle high demand, and when initiated within the first 4 days of MV and in profoundly hypoxemic patients. CONCLUSIONS: In an emulated trial based on a nationwide COVID-19 cohort, we found differential survival over time of an ECMO compared with a no-ECMO strategy. However, ECMO was consistently associated with better outcomes when performed in high-volume centers and in regions with ECMO capacities specifically organized to handle high demand. This article is open access and distributed under the terms of the Creative Commons Attribution Non-Commercial No Derivatives License 4.0 (http://creativecommons.org/licenses/by-nc-nd/4.0/)

Variation in general supportive and preventive intensive care management of traumatic brain injury: a survey in 66 neurotrauma centers participating in the Collaborative European NeuroTrauma Effectiveness Research in Traumatic Brain Injury (CENTER-TBI) study

Abstract Background General supportive and preventive measures in the intensive care management of traumatic brain injury (TBI) aim to prevent or limit secondary brain injury and optimize recovery. The aim of this survey was to assess and quantify variation in perceptions on intensive care unit (ICU) management of patients with TBI in European neurotrauma centers. Methods We performed a survey as part of the Collaborative European NeuroTrauma Effectiveness Research in Traumatic Brain Injury (CENTER-TBI) study. We analyzed 23 questions focused on: 1) circulatory and respiratory management; 2) fever control; 3) use of corticosteroids; 4) nutrition and glucose management; and 5) seizure prophylaxis and treatment. Results The survey was completed predominantly by intensivists (n = 33, 50%) and neurosurgeons (n = 23, 35%) from 66 centers (97% response rate). The most common cerebral perfusion pressure (CPP) target was > 60 mmHg (n = 39, 60%) and/or an individualized target (n = 25, 38%). To support CPP, crystalloid fluid loading (n = 60, 91%) was generally preferred over albumin (n = 15, 23%), and vasopressors (n = 63, 96%) over inotropes (n = 29, 44%). The most commonly reported target of partial pressure of carbon dioxide in arterial blood (PaCO2) was 36–40 mmHg (4.8–5.3 kPa) in case of controlled intracranial pressure (ICP) < 20 mmHg (n = 45, 69%) and PaCO2 target of 30–35 mmHg (4–4.7 kPa) in case of raised ICP (n = 40, 62%). Almost all respondents indicated to generally treat fever (n = 65, 98%) with paracetamol (n = 61, 92%) and/or external cooling (n = 49, 74%). Conventional glucose management (n = 43, 66%) was preferred over tight glycemic control (n = 18, 28%). More than half of the respondents indicated to aim for full caloric replacement within 7 days (n = 43, 66%) using enteral nutrition (n = 60, 92%). Indications for and duration of seizure prophylaxis varied, and levetiracetam was mostly reported as the agent of choice for both seizure prophylaxis (n = 32, 49%) and treatment (n = 40, 61%). Conclusions Practice preferences vary substantially regarding general supportive and preventive measures in TBI patients at ICUs of European neurotrauma centers. These results provide an opportunity for future comparative effectiveness research, since a more evidence-based uniformity in good practices in general ICU management could have a major impact on TBI outcome