TriAnnot: A Versatile and High Performance Pipeline for the Automated Annotation of Plant Genomes

In support of the international effort to obtain a reference sequence of the bread wheat genome and to provide plant communities dealing with large and complex genomes with a versatile, easy-to-use online automated tool for annotation, we have developed the TriAnnot pipeline. Its modular architecture allows for the annotation and masking of transposable elements, the structural, and functional annotation of protein-coding genes with an evidence-based quality indexing, and the identification of conserved non-coding sequences and molecular markers. The TriAnnot pipeline is parallelized on a 712 CPU computing cluster that can run a 1-Gb sequence annotation in less than 5 days. It is accessible through a web interface for small scale analyses or through a server for large scale annotations. The performance of TriAnnot was evaluated in terms of sensitivity, specificity, and general fitness using curated reference sequence sets from rice and wheat. In less than 8 h, TriAnnot was able to predict more than 83% of the 3,748 CDS from rice chromosome 1 with a fitness of 67.4%. On a set of 12 reference Mb-sized contigs from wheat chromosome 3B, TriAnnot predicted and annotated 93.3% of the genes among which 54% were perfectly identified in accordance with the reference annotation. It also allowed the curation of 12 genes based on new biological evidences, increasing the percentage of perfect gene prediction to 63%. TriAnnot systematically showed a higher fitness than other annotation pipelines that are not improved for wheat. As it is easily adaptable to the annotation of other plant genomes, TriAnnot should become a useful resource for the annotation of large and complex genomes in the future

The PREDICTS database: a global database of how local terrestrial biodiversity responds to human impacts

Biodiversity continues to decline in the face of increasing anthropogenic pressures such as habitat destruction, exploitation, pollution and introduction of alien species. Existing global databases of species’ threat status or population time series are dominated by charismatic species. The collation of datasets with broad taxonomic and biogeographic extents, and that support computation of a range of biodiversity indicators, is necessary to enable better understanding of historical declines and to project – and avert – future declines. We describe and assess a new database of more than 1.6 million samples from 78 countries representing over 28,000 species, collated from existing spatial comparisons of local-scale biodiversity exposed to different intensities and types of anthropogenic pressures, from terrestrial sites around the world. The database contains measurements taken in 208 (of 814) ecoregions, 13 (of 14) biomes, 25 (of 35) biodiversity hotspots and 16 (of 17) megadiverse countries. The database contains more than 1% of the total number of all species described, and more than 1% of the described species within many taxonomic groups – including flowering plants, gymnosperms, birds, mammals, reptiles, amphibians, beetles, lepidopterans and hymenopterans. The dataset, which is still being added to, is therefore already considerably larger and more representative than those used by previous quantitative models of biodiversity trends and responses. The database is being assembled as part of the PREDICTS project (Projecting Responses of Ecological Diversity In Changing Terrestrial Systems – www.predicts.org.uk).We make site-level summary data available alongside this article. The full database will be publicly available in 2015

Formaliser l’expérience. Écrits professionnels et Écrits poétiques

Le présent article n’est pas un essai théorique. Dans le cadre de l’intervention en entreprise, l’ergonome produit des documents écrits. Ils répondent à un objectif précis : transformer leur situation de travail pour réduire les effets indésirables sur la santé des opérateurs. Ces rapports d’étude ne peuvent contenir tout de l’expérience humaine acquise sur chaque terrain. Des « surplus » ne peuvent être exploités que dans des écrits personnels réalisés dans un autre cadre. Le texte n’a d’autre prétention que de témoigner et mettre en forme une expérience singulière d’écriture.The present article is not a theoretical essay. Within the framework of his intervention in the firm, the ergonomist produces written documents. They meet a specific aim : transforming their working position so as to reduce the unwanted effets on the health of operators. These study reports cannot include all the human experience acquired on each field. « Surpluses » cannot be exploited except in personal writing achieved in another context. The text does not have any other claim but that of testifying and of giving shape to a unique writing experience

Communiquer... les mots de l'expérience

Demande patronale, construction de métier ou de collectifs, l’expérience du travail ne git pas dans les consciences, en mots prêts à l’emploi. Aujourd’hui, de nombreux acteurs interviennent en entreprise et développent des échanges avec les individus et les équipes au travail… Dans quelles conditions – heureuses, malheureuses -, est assurée cette mise en mots, cette mise en discours

Correlation Analysis between Employee Productivity, Absenteeism and Illnesses in BPO Industry.

With the expansion of Business Process Outsourcing (BPO) in the Philippines, this study was initiated to understand the effect of illnesses on absenteeism and productivity among employees. The secondary data, from January to December 2022, from the onsite clinic of AMAZON was used in this study. The top three illnesses, aggregated illnesses, namely Upper Respiratory Tract Infection, Nervous System Illnesses and ENT Illness data collected, were statistically tested. As a result, it was noted that aggregated illnesses increased the effect on employee productivity based on absenteeism. Also, among the top three illnesses, Nervous System Illnesses increased the effect on absenteeism of employees in the company

Interventions d'entreprises de BTP sur sites industriels a risques : la prevention en question

Available at INIST (FR), Document Supply Service, under shelf-number : RP 13000 / INIST-CNRS - Institut de l'Information Scientifique et TechniqueSIGLEFRFranc

Conditions de travail sur les chantiers de bucheronnage Modernisation des entreprises d'exploitation forestiere et evolution de la filiere bois

Available at INIST (FR), Document Supply Service, under shelf-number : AR 15256 (1); AR 15256 (2) / INIST-CNRS - Institut de l'Information Scientifique et TechniqueSIGLEFRFranc

Une analyse des grandes visions prospectives internationales sur le devenir de l’environnement : l’étude ScénEnvi

International audienceTo contribute to French scientific planning in the environmental sciences, a study of major scenarios from around the world on the possible futures for the environment was made under the auspices of Alliance AllEnvi. For the more than 300 scenarios analyzed, governance and the economy turned out to be the major factors for differentiating them. Eleven families of scenarios were placed in three groups : decline, no priority for the environment, and priority for the environment. The first two groups correspond to a severely deteriorated environment, but the third has a more encouraging outcome despite the inefficiency of certain orientations. A detailed analysis of the methodology and findings is proposed while focusing on the factors “environment” and “sciences and technology”, which are decisive for AllEnvi.Pour contribuer à la programmation scientifique française dans le domaine des sciences de l’environnement, une étude des grandes visions de prospective à travers le monde sur les devenirs possibles de l’environnement a été entreprise dans le cadre de l’Alliance AllEnvi. Plus de 300 scénarios ont été analysés, révélant la prédominance de la gouvernance et de l’économie comme facteurs différenciant ces scénarios. La démarche a défini 11 familles de scénarios regroupant les différentes tendances qui se structurent en 3 groupes : le déclin, l’absence de priorité environnementale et la priorité accordée à l’environnement. Si les deux premiers groupes correspondent à des dégradations plus ou moins sévères de l’environnement, le troisième conduit à des résultats plutôt encourageants, même si certaines orientations s’avèrent in fine peu efficaces. Une analyse détaillée de la démarche déployée et des résultats obtenus est proposée ici en apportant une attention particulière aux facteurs « Environnement » et « Sciences et Technologie », qui sont structurants pour les missions d’AllEnvi

The effectiveness of Neolithic sickles in the Middle East: an experimental approach

In the Near East "sickles" or "glossy pieces" occur for the first time during the Natufian period. These tools are either "sickle blades" or "sickle elements". "Sickle blades" are used hafted or hand-held as single cutting tools. "Sickle elements" are inserted in a haft in order to create a composite instrument. When sickles are made from flint, they are easily recognized since they usually bear a macroscopic gloss that covers a wide area on both sides of the tool. Experimental and microscopic studies have shown that the majority of these tools were used as sickles to harvest cereals or, less frequently, soft siliceous plants such as reeds and typha. Macroscopic glosses of different natures develop on various occasions, for example: on elements mounted on threshing sledges; when limestone is worked with the addition of water; when humid clay is scraped; etc. When sickle elements are made from obsidian, no macroscopic gloss develops and use wear is rarely observed with the naked eye. In this case, the worn area on the tool presents a mat aspect and abrasion features. Such tools are rarely recognized as such. Sometimes, abrasion features are erroneously interpreted as harvesting marks