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

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

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

Long-term follow-up of IPEX syndrome patients after different therapeutic strategies : an international multicenter retrospective study

Background: Immunodysregulation polyendocrinopathy enteropathy x-linked(IPEX) syndrome is a monogenic autoimmune disease caused by FOXP3 mutations. Because it is a rare disease, the natural history and response to treatments, including allogeneic hematopoietic stem cell transplantation (HSCT) and immunosuppression (IS), have not been thoroughly examined. Objective: This analysis sought to evaluate disease onset, progression, and long-term outcome of the 2 main treatments in long-term IPEX survivors. Methods: Clinical histories of 96 patients with a genetically proven IPEX syndrome were collected from 38 institutions worldwide and retrospectively analyzed. To investigate possible factors suitable to predict the outcome, an organ involvement (OI) scoring system was developed. Results: We confirm neonatal onset with enteropathy, type 1 diabetes, and eczema. In addition, we found less common manifestations in delayed onset patients or during disease evolution. There is no correlation between the site of mutation and the disease course or outcome, and the same genotype can present with variable phenotypes. HSCT patients (n = 58) had a median follow-up of 2.7 years (range, 1 week-15 years). Patients receiving chronic IS (n 5 34) had a median follow-up of 4 years (range, 2 months-25 years). The overall survival after HSCT was 73.2% (95% CI, 59.4-83.0) and after IS was 65.1% (95% CI, 62.8-95.8). The pretreatment OI score was the only significant predictor of overall survival after transplant (P = .035) but not under IS. Conclusions: Patients receiving chronic IS were hampered by disease recurrence or complications, impacting long-term.disease-free survival. When performed in patients with a low OI score, HSCT resulted in disease resolution with better quality of life, independent of age, donor source, or conditioning regimen

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

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

Importance of tree species size dominance and heterogeneity on the productivity of spruce-fir-beech mountain forest stands in Europe

12 Pág.There is concern in the scientific community and among forest managers about potential reductions in the provisioning of forest ecosystem services due to the loss of tree species diversity. Many studies have shown how species diversity influences forest functioning, especially productivity, but the influence of structural diversity, such as tree size heterogeneity, has received much less attention. This study focused on understanding the relationship between stand productivity and several structural characteristics of spruce-fir-beech mountain forest stands in Europe. We used a dataset of 89 long-term plots in spruce-fir-beech forests distributed along the European mountains where the three species, Norway spruce (Picea abies (L.) Karst.), silver fir (Abies alba Mill.) and European beech (Fagus sylvatica L.), represent at least 75% of the basal area. Site-dependent conditions were accounted for in a linear mixed-effect basic model, which related the stand productivity with the morphological, climatic and pedological characteristics. The influence of tree species diversity, tree size heterogeneity, species size dominance, and species overlapping in the size distribution on stand productivity was analysed by adding variables to the basic model one by one and evaluating the change in the Akaike's Information Criterion (AIC). The variables that resulted in significant reductions in the AIC, and that were not correlated with each other, were used to build a model to estimate stand productivity. The model showed that in spruce-fir-beech mixed mountain forests (i) when Norway spruce, silver fir and European beech are evenly present within the size distribution (high evenness) the productivity decreases, (ii) the stand productivity increases when the diameter distribution is skewed to the right (higher numbers of smaller individuals), (iii) the stand productivity increases as the proportion of basal area that is spruce increases, and (iv) stand productivity increases with the variability in diameter. We discuss the implications of our results for the management of spruce-fir-beech mountain forest in Europe and for preserving and increasing the stand productivity of these mixed forests.This study was finalized in the frame of the COST (European Cooperation in Science and Technology) Action CLIMO (Climate-Smart Forestry in Mountain Regions - CA15226) financially supported by the EU Framework Programme for Research and Innovation HORIZON 2020. Additionally, Michal Bosela was supported by the Slovak Research and Development Agency (Slovakia) via the project No. APVV-15-0265. Thomas A. Nagel received support from the Slovenian Research Agency (Slovenia) via the project No. J4-1765. Sitkova Zuzana received support by the Slovak Research and Development Agency (Slovakia) via the project No. APVV-16-0325.Peer reviewe

The diagnosis of severe combined immunodeficiency: Implementation of the PIDTC 2022 Definitions.

BACKGROUND: Shearer et al in 2014 articulated well-defined criteria for the diagnosis and classification of severe combined immunodeficiency (SCID) as part of the Primary Immune Deficiency Treatment Consortiums (PIDTCs) prospective and retrospective studies of SCID. OBJECTIVE: Because of the advent of newborn screening for SCID and expanded availability of genetic sequencing, revision of the PIDTC 2014 Criteria was needed. METHODS: We developed and tested updated PIDTC 2022 SCID Definitions by analyzing 379 patients proposed for prospective enrollment into Protocol 6901, focusing on the ability to distinguish patients with various SCID subtypes. RESULTS: According to PIDTC 2022 Definitions, 18 of 353 patients eligible per 2014 Criteria were considered not to have SCID, whereas 11 of 26 patients ineligible per 2014 Criteria were determined to have SCID. Of note, very low numbers of autologous T cells (<0.05 × 109/L) characterized typical SCID under the 2022 Definitions. Pathogenic variant(s) in SCID-associated genes was identified in 93% of patients, with 7 genes (IL2RG, RAG1, ADA, IL7R, DCLRE1C, JAK3, and RAG2) accounting for 89% of typical SCID. Three genotypes (RAG1, ADA, and RMRP) accounted for 57% of cases of leaky/atypical SCID; there were 13 other rare genotypes. Patients with leaky/atypical SCID were more likely to be diagnosed at more than age 1 year than those with typical SCID lacking maternal T cells: 20% versus 1% (P < .001). Although repeat testing proved important, an initial CD3 T-cell count of less than 0.05 × 109/L differentiated cases of typical SCID lacking maternal cells from leaky/atypical SCID: 97% versus 7% (P < .001). CONCLUSIONS: The PIDTC 2022 Definitions describe SCID and its subtypes more precisely than before, facilitating analyses of SCID characteristics and outcomes