Growth analysis of an aged Turkey oak coppice under conversion into high forest

Most Italian research concerning the conversion of coppices analyse growth response at the stand level and adopt absolute growth as reference metric. Nonetheless, inter-individual interactions are lost when averaging tree level information at the stand level. Moreover, absolute growth ignores the initial size of individuals under comparison, the growth of large trees will thus always outperform that of small trees, and nothing can be inferred about tree-to-tree competition.We modelled the growth response after conversion thinning at the tree level using relative growth rate as a function of the initial diameter of individuals, stand density and time. Twenty years later, thinned treatments still yielded larger growth than the reference unthinned aged coppice. In the first 10-year period, the relative growth rate in all treatments decreased with increasing tree size. In the second 10-year period, the relative growth rate still decreased with increasing tree size in thinned treatments, whereas in the unthinned aged coppice, it increased with increasing tree size.The model we applied shows to what extent released individuals have grown in relation to their size and, at same time, provides information on their competitive state in relation to the overall density of stands over time

The conservation status assessment of Natura 2000 forest habitats in Europe: capabilities, potentials and challenges of national forest inventories data

This article is part of the topical collection on Forest information for bioeconomy outlooks at European level- Key message - There is a need to improve the consistency of international information concerning the conservation status assessment of the species and habitat types in the Natura 2000 reports. National Forest Inventories could contribute towards a more objective and harmonised assessment although their use shows some challenges as low precision for rare or small area habitats. Recommendations for a set of 12 structural and functional indicators are provided. - Context - There are differences among Member States as regards applying conservation status assessment and priorities according to the Directive on the conservation of natural habitats (Habitats Directive). - Aims -This paper aims to analyse the consistency as regards forest habitat types reporting and the use and suitability of National Forest Inventories (NFIs) to assess their conservation status, as well as to provide recommendations for harmonised assessments through NFIs. - Methods - A survey was carried out concerning the use of NFI data to report within the commitments of the Habitat Directive. The survey covered 13 European countries, accounting for 62% of forest habitat area. Additionally, case studies were carried out in four countries. - Results -The identification of forest habitat types and the set of quantitative and/or qualitative indicators differ between countries. The use of NFI data is being considered in seven countries and it is expected to increase for the 2013–2018 reporting period. The main challenges reported of use of NFI data are related to the habitat identification and their mapping, and the monitoring frequency, design and costs (i.e. rare or small area habitats). - Conclusion - It is necessary to improve the comparability of the conservation status assessments between countriesinfo:eu-repo/semantics/publishedVersio

Assessing forest availability for wood supply in Europe

The quantification of forests available for wood supply (FAWS) is essential for decision-making with regard to the maintenance and enhancement of forest resources and their contribution to the global carbon cycle. The provision of harmonized forest statistics is necessary for the development of forest associated policies and to support decision-making. Based on the National Forest Inventory (NFI) data from 13 European countries, we quantify and compare the areas and aboveground dry biomass (AGB) of FAWS and forest not available for wood supply (FNAWS) according to national and reference definitions by determining the restrictions and associated thresholds considered at country level to classify forests as FAWS or FNAWS. FAWS represent between 75 and 95 % of forest area and AGB for most of the countries in this study. Economic restrictions are the main factor limiting the availability of forests for wood supply, accounting for 67 % of the total FNAWS area and 56 % of the total FNAWS AGB, followed by environmental restrictions. Profitability, slope and accessibility as economic restrictions, and protected areas as environmental restrictions are the factors most frequently considered to distinguish between FAWS and FNAWS. With respect to the area of FNAWS associated with each type of restriction, an overlap among the restrictions of 13.7 % was identified. For most countries, the differences in the FNAWS areas and AGB estimates between national and reference definitions ranged from 0 to 5 %. These results highlight the applicability and reliability of a FAWS reference definition for most of the European countries studied, thereby facilitating a consistent approach to assess forests available for supply for the purpose of international reportinginfo:eu-repo/semantics/publishedVersio

BioMaS: a modular pipeline for Bioinformatic analysis of Metagenomic AmpliconS

Background: Substantial advances in microbiology, molecular evolution and biodiversity have been carried out in recent years thanks to Metagenomics, which allows to unveil the composition and functions of mixed microbial communities in any environmental niche. If the investigation is aimed only at the microbiome taxonomic structure, a target-based metagenomic approach, here also referred as Meta-barcoding, is generally applied. This approach commonly involves the selective amplification of a species-specific genetic marker (DNA meta-barcode) in the whole taxonomic range of interest and the exploration of its taxon-related variants through High-Throughput Sequencing (HTS) technologies. The accessibility to proper computational systems for the large-scale bioinformatic analysis of HTS data represents, currently, one of the major challenges in advanced Meta-barcoding projects.; Results: BioMaS (Bioinformatic analysis of Metagenomic AmpliconS) is a new bioinformatic pipeline designed to support biomolecular researchers involved in taxonomic studies of environmental microbial communities by a completely automated workflow, comprehensive of all the fundamental steps, from raw sequence data upload and cleaning to final taxonomic identification, that are absolutely required in an appropriately designed Meta-barcoding HTS-based experiment. In its current version, BioMaS allows the analysis of both bacterial and fungal environments starting directly from the raw sequencing data from either Roche 454 or Illumina HTS platforms, following two alternative paths, respectively. BioMaS is implemented into a public web service available at https://recasgateway.ba.infn.it/ and is also available in Galaxy at http://galaxy.cloud.ba.infn.it:8080 (only for Illumina data).; Conclusion: BioMaS is a friendly pipeline for Meta-barcoding HTS data analysis specifically designed for users without particular computing skills. A comparative benchmark, carried out by using a simulated dataset suitably designed to broadly represent the currently known bacterial and fungal world, showed that BioMaS outperforms QIIME and MOTHUR in terms of extent and accuracy of deep taxonomic sequence assignments.Peer ReviewedPostprint (published version

Hematopoietic Cell Transplantation in Patients With Primary Immune Regulatory Disorders (PIRD): A Primary Immune Deficiency Treatment Consortium (PIDTC) Survey.

Primary Immune Regulatory Disorders (PIRD) are an expanding group of diseases caused by gene defects in several different immune pathways, such as regulatory T cell function. Patients with PIRD develop clinical manifestations associated with diminished and exaggerated immune responses. Management of these patients is complicated; oftentimes immunosuppressive therapies are insufficient, and patients may require hematopoietic cell transplant (HCT) for treatment. Analysis of HCT data in PIRD patients have previously focused on a single gene defect. This study surveyed transplanted patients with a phenotypic clinical picture consistent with PIRD treated in 33 Primary Immune Deficiency Treatment Consortium centers and European centers. Our data showed that PIRD patients often had immunodeficient and autoimmune features affecting multiple organ systems. Transplantation resulted in resolution of disease manifestations in more than half of the patients with an overall 5-years survival of 67%. This study, the first to encompass disorders across the PIRD spectrum, highlights the need for further research in PIRD management

Harmonised projections of future forest resources in Europe

Data PaperAbstract • Key message A dataset of forest resource projections in 23 European countries to 2040 has been prepared for fores trelated policy analysis and decision-making. Due to applying harmonised definitions, while maintaining country-specific forestry practices, the projections should be usable from national to international levels. The dataset can be accessed at https://doi.org/10.5061/dryad.4t880qh. The associated metadata are available at https://metadata-afs.nancy.inra.fr/ geonetwork/srv/eng/catalog.search#/metadata/8f93e0d6-b524-43bd-bdb8-621ad5ae6fa9info:eu-repo/semantics/publishedVersio

Preexisting autoantibodies to type I IFNs underlie critical COVID-19 pneumonia in patients with APS-1

Patients with biallelic loss-of-function variants of AIRE suffer from autoimmune polyendocrine syndrome type-1 (APS-1) and produce a broad range of autoantibodies (auto-Abs), including circulating auto-Abs neutralizing most type I interferons (IFNs). These auto-Abs were recently reported to account for at least 10% of cases of life-threatening COVID-19 pneumonia in the general population. We report 22 APS-1 patients from 21 kindreds in seven countries, aged between 8 and 48 yr and infected with SARS-CoV-2 since February 2020. The 21 patients tested had auto-Abs neutralizing IFN-α subtypes and/or IFN-ω; one had anti–IFN-β and another anti–IFN-ε, but none had anti–IFN-κ. Strikingly, 19 patients (86%) were hospitalized for COVID-19 pneumonia, including 15 (68%) admitted to an intensive care unit, 11 (50%) who required mechanical ventilation, and four (18%) who died. Ambulatory disease in three patients (14%) was possibly accounted for by prior or early specific interventions. Preexisting auto-Abs neutralizing type I IFNs in APS-1 patients confer a very high risk of life-threatening COVID-19 pneumonia at any age.publishedVersio

Assessing forest availability for wood supply in Europe

14 Pág.The quantification of forests available for wood supply (FAWS) is essential for decision-making with regard to the maintenance and enhancement of forest resources and their contribution to the global carbon cycle. The provision of harmonized forest statistics is necessary for the development of forest associated policies and to support decision-making. Based on the National Forest Inventory (NFI) data from 13 European countries, we quantify and compare the areas and aboveground dry biomass (AGB) of FAWS and forest not available for wood supply (FNAWS) according to national and reference definitions by determining the restrictions and associated thresholds considered at country level to classify forests as FAWS or FNAWS. FAWS represent between 75 and 95 % of forest area and AGB for most of the countries in this study. Economic restrictions are the main factor limiting the availability of forests for wood supply, accounting for 67 % of the total FNAWS area and 56 % of the total FNAWS AGB, followed by environmental restrictions. Profitability, slope and accessibility as economic restrictions, and protected areas as environmental restrictions are the factors most frequently considered to distinguish between FAWS and FNAWS. With respect to the area of FNAWS associated with each type of restriction, an overlap among the restrictions of 13.7 % was identified. For most countries, the differences in the FNAWS areas and AGB estimates between national and reference definitions ranged from 0 to 5 %. These results highlight the applicability and reliability of a FAWS reference definition for most of the European countries studied, thereby facilitating a consistent approach to assess forests available for supply for the purpose of international reporting.This research was supported by the Specific contract n. 18 “Use of National Forest Inventories data to estimate area and above ground biomass in European forests not available for wood supply” in the context of the Framework contract for the provision of forest data and services supporting the European Forest Data Centre 2012/ S 78-127532 of 21/04/2012 of the Joint Research Centre of the European Commission; the EG-013-72 agreement of the Ministry of Agriculture, Fisheries and Food (MAPA) and the INIA belonging to the Spanish Ministry of Science and Innovation (MICINN); and the project No.APVV-15-0265 granted by the Slovak Research and Development Agency.Peer reviewe