Perturbations in the carbon budget of the tropics

The carbon budget of the tropics has been perturbed as a result of human influences. Here, we attempt to construct a ‘bottom-up’ analysis of the biological components of the budget as they are affected by human activities. There are major uncertainties in the extent and carbon content of different vegetation types, the rates of land-use change and forest degradation, but recent developments in satellite remote sensing have gone far towards reducing these uncertainties. Stocks of carbon as biomass in tropical forests and woodlands add up to 271 ± 16 Pg with an even greater quantity of carbon as soil organic matter. Carbon loss from deforestation, degradation, harvesting and peat fires is estimated as 2.01 ± 1.1 Pg annum(−1); while carbon gain from forest and woodland growth is 1.85 ± 0.09 Pg annum(−1). We conclude that tropical lands are on average a small carbon source to the atmosphere, a result that is consistent with the ‘top-down’ result from measurements in the atmosphere. If they were to be conserved, they would be a substantial carbon sink. Release of carbon as carbon dioxide from fossil fuel burning in the tropics is 0.74 Pg annum(−1) or 0.57 MgC person(−1) annum(−1), much lower than the corresponding figures from developed regions of the world

Model d’atenció a la salut de les persones trans*

Persones trans; Atenció a la salut; Identitat de gènerePersonas trans; Atención a la salud; Identidad de géneroTrans people; Health care; Gender identityL'objectiu d'aquest document és l'ordenació de la cartera de serveis de l’atenció a la salut de les persones trans en el seu procés de transició en la identitat de gènere sentida a càrrec del sistema sanitari públic de Catalunya a partir d’un model consensuat i d’un protocol clínic marc per a l’atenció de la salut

ABRomics: A Galaxy-based one health antimicrobial resistance platform

International audienceAntibiotic resistance (ABR) is a major global public health issue designated for urgent action by international institutions, especially regarding the emergence and the global dissemination of multidrug-resistant bacteria (MDRB) and antibiotic resistance genes (ARGs) carried by mobile genetic elements. They are widely transmitted between humans, animals, and the environmental domains, without borders, calling for a One Health perspective on ABR. Whole genome sequencing (WGS) is used for molecular typing purposes at the highest resolution. It provides the genome sequences required for the identification of ARGs as well as mutations leading to a decrease in antibiotic susceptibility. Tracking transmissions of outbreaks and identifying sources of contamination is achievable with WGS data combined with epidemiological information. Ensuring the sharing of high-quality sequence data alongside interoperable curated metadata is a key requirement for understanding the spatiotemporal patterns of dissemination of MDRB and ARGs. Today, systematic genome sequencing and bioinformatics analyses partially address such major issues. However, the remaining major bottlenecks are data sharing and comparable results across multiple centers and labs. The ABRomics project aims to develop a secure One Health, online platform to make MDRB genomics, metagenomics data, and their metadata accessible to a network of researchers including epidemiologists, clinical microbiologists, and the wider research community. The ABRomics platform is a free, secure web-based (Django) service designed to facilitate collaboration between experts working on ABR. It offers a user-friendly interface for carrying out Galaxy-based bioinformatics analyses on both private and public sequencing data. It integrates project management functionalities so that users can store their biological sequence data and retrieve the results of launched analyses. ABRomics offers standardized Galaxy workflows to run ABR analyses of sequencing data from pathogenic strains (e.g. ARG detection, sequence typing, virulence factor detection, etc). These workflows have been submitted to Intergalactic Workflow Commission (IWC) and are documented with tutorials on the Galaxy Training Network. In ABRomics background, the UseGalaxy France server is used to schedule jobs via django-to-galaxy (a Django library to communicate with Galaxy API), allowing users to launch complex multi-step scientific workflows on the French Bioinformatics Institute (IFB) Core Cluster. The platform also offers an interface for cross-referencing and enriching results with other information and omics data. An Application Programming Interface (API) is available for integration with other systems, enabling the ABRomics platform to achieve interoperability. In this talk, we will present ABRomics, the secure multisectorial, open-access, online platform that analyzes (meta-)genomic data relating to ABR. We will also present the plans for the ABRomics platform to enable tracking of spatio-temporal dissemination of ABR from bacterial genomes and metagenomes, thereby improving surveillance and research in antimicrobial resistance

ABRomics - a digital platform on antimicrobial resistance to store, integrate, analyze and share multi-omics data

International audienceAntibiotic resistance (ABR) is a major public health issue prioritized for mitigation by major international institutions, especially regarding the emergence and the global dissemination of multidrug resistant (MDR) isolates and of antibiotic resistance genes (ARGs) carried by mobile genetic elements. They are also transmitted between humans, animals and the environment, without borders. The evolution of ABR is a complex process with multiple selective forces in different environments.Genome sequences, which contain all the genetic information of an organism, can be used for molecular typing purposes with the highest resolution, the identification of ARGs and their genetic supports as well as mutations leading to a decrease in antibiotic susceptibility. Combined with epidemiological information, bacterial Whole Genome Sequencing (WGS) can enable tracking transmissions of outbreaks and identifying a source of contamination. Reinforcing the sharing of high-quality sequence data for diagnostic and epidemiological applications, together with interoperable and curated metadata, which can be integrated with other omics data, is a key requirement for understanding the complexity of spatiotemporal patterns of pathogen and ARGs transmission between compartments.Today, if more systematic genome sequencing and bioinformatics analysis can partially address such major issues, data sharing and comparison across centers, together with standardization of analytical workflows remain major bottlenecks. The ABRomics project aims to develop a secure One Health, online platform to make bacterial infectious disease (meta)genomics data and their associated clinical and epidemiological metadata accessible to a meta-network of researchers including epidemiologists, clinical microbiologists and the wider research community. It should provide the diverse communities with a user-friendly platform to store, share and analyze genomic information together with their metadata. It will also serve as a data brokering hub to ease the submission of data sequences into international repositories.The platform will meet two main objectives:1. Establish a repository of structured, interoperable, standardized, and well-annotated multi-omics microbiology data with tailored mathematical and bioinformatics tools that can be used to answer specific research questions related to ABR.2. Establish a shared platform to facilitate retrospective and prospective surveillance of ABRs in human and veterinary medicine, including environmental and food isolates, to enable near-real-time surveillance of pathogen transmission and outbreaks with actionable results for public health authorities. FAIR (Findable, Accessible, Interoperable and Reusable) data management procedures will enable retrospective studies.We will present here the ongoing development of the three main modules of the ABRomics platform architecture: (i) ABRomics-BIOINFO: an IT infrastructure with high capacity of data storage and data analysis, accessible to users under defined rules and offering a general software environment, both HPC and Cloud environments, (ii) ABRomics-DB: an integrated multi-omics microbiological databases for the Human-Animal-Environment sectors, and (iii) ABRomics-WF: standard tools and pipelines for (semi) automatic analysis of NGS data from pathogenic strains.The ABRomics project is led by the Institut Français de Bioinformatique (IFB), the Institut Pasteur and is made up of a consortium of 45 specialized teams belonging to the main French research organizations

ABRomics - an open access online platform on antimicrobial resistance to store, integrate, analyze and share multi-omics data

International audienceAntibiotic resistance (ABR) is a major public health issue prioritized for mitigation by international institutions. Multidrug resistant bacteria (MDRB) and Antibiotic Resistance Genes (ARGs) carried by mobile genetic elements spread between the human, animal, and environmental sectors. Whole Genome Sequencing (WGS) is used for molecular typing purposes at the highest resolution. It provides identification of ARGs and their genetic supports as well as mutations leading to a decrease in antibiotic susceptibility. Epidemiological and WGS data are used for tracking MDRB in hospital outbreaks but also across the animal and environmental sectors. Sharing and interoperability of high-quality data (sequence and metadata) are key requirements for addressing the spatio-temporal dissemination of MDRB. To this aim, the French Priority Plan on ABR has funded the development of an online, open platform dedicated to antibiotic resistance.We are establishing a repository of structured, interoperable, standardized, and well-annotated multi-omics data with tailored mathematical and bioinformatics tools to answer generic and specific research questions related to ABR. The ABRomics platform includes standardized pipelines to run ABR analyses of WGS from pathogenic strains supported with integrated databases (ARG, sequence types [ST], virulence factors [VF]). Uploading data, launching pipelines, viewing and cross-referencing enriched results will be achieved through easy-to-use web interfaces. ABRomics ß-version integrating the ABR detection genomic pipeline and other markers such as ST, and VF will be available in summer 2023. Core-genome multi-locus sequence typing, relationships between strains and metagenomics pipelines will next be made available

ABRomics - an open access online platform on antimicrobial resistance to store, integrate, analyze and share multi-omics data

International audienceAntibiotic resistance (ABR) is a major public health issue prioritized for mitigation by international institutions. Multidrug resistant bacteria (MDRB) and Antibiotic Resistance Genes (ARGs) carried by mobile genetic elements spread between the human, animal, and environmental sectors. Whole Genome Sequencing (WGS) is used for molecular typing purposes at the highest resolution. It provides identification of ARGs and their genetic supports as well as mutations leading to a decrease in antibiotic susceptibility. Epidemiological and WGS data are used for tracking MDRB in hospital outbreaks but also across the animal and environmental sectors. Sharing and interoperability of high-quality data (sequence and metadata) are key requirements for addressing the spatio-temporal dissemination of MDRB. To this aim, the French Priority Plan on ABR has funded the development of an online, open platform dedicated to antibiotic resistance.We are establishing a repository of structured, interoperable, standardized, and well-annotated multi-omics data with tailored mathematical and bioinformatics tools to answer generic and specific research questions related to ABR. The ABRomics platform includes standardized pipelines to run ABR analyses of WGS from pathogenic strains supported with integrated databases (ARG, sequence types [ST], virulence factors [VF]). Uploading data, launching pipelines, viewing and cross-referencing enriched results will be achieved through easy-to-use web interfaces. ABRomics ß-version integrating the ABR detection genomic pipeline and other markers such as ST, and VF will be available in summer 2023. Core-genome multi-locus sequence typing, relationships between strains and metagenomics pipelines will next be made available

ABRomics: An integrated multi-omics platform for antibiotic resistance research and public health

International audienceIntroduction and objectivesAntibiotic resistance (ABR) is a major public health issue prioritized for mitigation by international institutions. Multidrug resistant bacteria (MDRB) and Antibiotic Resistance Genes (ARGs) carried by mobile genetic elements spread between the human, animal, and environmental sectors. Whole Genome Sequencing (WGS) is used for molecular typing purposes at the highest resolution. It provides identification of ARGs and their genetic supports as well as mutations leading to a decrease in antibiotic susceptibility. Epidemiological and WGS data are used for tracking MDRB in hospital outbreaks but also across the animal and environmental sectors.Sharing and interoperability of high-quality data (sequence and metadata) are key requirements for addressing the spatio-temporal dissemination of MDRB. To this aim, the French Priority Plan on ABR has funded the development of an online, open platform dedicated to antibiotic resistance research and public health. MethodsWe are establishing a repository of structured, interoperable, standardized, and well-annotated multi-omics data with standard workflow analysis (Galaxy pipelines) to answer generic questions related to ABR, and tailored mathematical and bioinformatics tools to address more specific research questions. To access the platform, we are designing a web interface to also facilitate and combine the surveillance of ABR in the three sectors. FAIR (Findable, Accessible, Interoperable and Reusable) data management procedures will enable retrospective studies.The ABRomics platform is hosted at the French Bioinformatics Institute (www.francebioinformatique.fr) with a high capacity of analysis and 2 petabytes data storage.Results and conclusionsThe ABRomics platform includes standardized pipelines to run ABR analyses of WGS from pathogenic strains of interest for ABR, with integrated databases (ARG, sequence types [ST], virulence factors [VF]). Uploading data, launching pipelines, viewing and cross-referencing enriched results is achieved through easy-to-use web interfaces.ABRomics ß-version integrating the ABR detection genomic pipeline and other markers such as ST, and VF will be made available to the consortium in autumn 2023 and to the whole microbial research community in the beginning of 2024. Core-genome multi-locus sequence typing, relationships between strains and metagenomics pipelines will next be made available

ABRomics - an open access online platform on antimicrobial resistance to store, integrate, analyze and share multi-omics data

International audienceAntibiotic resistance (ABR) is a major public health issue prioritized for mitigation by international institutions. Multidrug resistant bacteria (MDRB) and Antibiotic Resistance Genes (ARGs) carried by mobile genetic elements spread between the human, animal, and environmental sectors. Whole Genome Sequencing (WGS) is used for molecular typing purposes at the highest resolution. It provides identification of ARGs and their genetic supports as well as mutations leading to a decrease in antibiotic susceptibility. Epidemiological and WGS data are used for tracking MDRB in hospital outbreaks but also across the animal and environmental sectors. Sharing and interoperability of high-quality data (sequence and metadata) are key requirements for addressing the spatio-temporal dissemination of MDRB. To this aim, the French Priority Plan on ABR has funded the development of an online, open platform dedicated to antibiotic resistance.We are establishing a repository of structured, interoperable, standardized, and well-annotated multi-omics data with tailored mathematical and bioinformatics tools to answer generic and specific research questions related to ABR. The ABRomics platform includes standardized pipelines to run ABR analyses of WGS from pathogenic strains supported with integrated databases (ARG, sequence types [ST], virulence factors [VF]). Uploading data, launching pipelines, viewing and cross-referencing enriched results will be achieved through easy-to-use web interfaces. ABRomics ß-version integrating the ABR detection genomic pipeline and other markers such as ST, and VF will be available in summer 2023. Core-genome multi-locus sequence typing, relationships between strains and metagenomics pipelines will next be made available

ABRomics: An integrated multi-omics platform for antibiotic resistance research and public health

International audienc

ABRomics - an open access online platform on antimicrobial resistance to store, integrate, analyze and share multi-omics data

International audienceAntibiotic resistance (ABR) is a major public health issue prioritized for mitigation by international institutions. Multidrug resistant bacteria (MDRB) and Antibiotic Resistance Genes (ARGs) carried by mobile genetic elements spread between the human, animal, and environmental sectors. Whole Genome Sequencing (WGS) is used for molecular typing purposes at the highest resolution. It provides identification of ARGs and their genetic supports as well as mutations leading to a decrease in antibiotic susceptibility. Epidemiological and WGS data are used for tracking MDRB in hospital outbreaks but also across the animal and environmental sectors. Sharing and interoperability of high-quality data (sequence and metadata) are key requirements for addressing the spatio-temporal dissemination of MDRB. To this aim, the French Priority Plan on ABR has funded the development of an online, open platform dedicated to antibiotic resistance.We are establishing a repository of structured, interoperable, standardized, and well-annotated multi-omics data with tailored mathematical and bioinformatics tools to answer generic and specific research questions related to ABR. The ABRomics platform includes standardized pipelines to run ABR analyses of WGS from pathogenic strains supported with integrated databases (ARG, sequence types [ST], virulence factors [VF]). Uploading data, launching pipelines, viewing and cross-referencing enriched results will be achieved through easy-to-use web interfaces. ABRomics ß-version integrating the ABR detection genomic pipeline and other markers such as ST, and VF will be available in summer 2023. Core-genome multi-locus sequence typing, relationships between strains and metagenomics pipelines will next be made available