Direction Générale Déléguée aux Ressources

Old-growth tropical forests harbor an immense diversity of tree species but are rapidly being cleared, while secondary forests that regrow on abandoned agricultural lands increase in extent. We assess how tree species richness and composition recover during secondary succession across gradients in environmental conditions and anthropogenic disturbance in an unprecedented multisite analysis for the Neotropics. Secondary forests recover remarkably fast in species richness but slowly in species composition. Secondary forests take a median time of five decades to recover the species richness of old-growth forest (80% recovery after 20 years) based on rarefaction analysis. Full recovery of species composition takes centuries (only 34% recovery after 20 years). A dual strategy that maintains both old-growth forests and species-rich secondary forests is therefore crucial for biodiversity conservation in human-modified tropical landscapes.

Abstract The tri-axial search-coil magnetometer (SCM) belongs to the FIELDS instrumentation suite on the Magnetospheric Multiscale (MMS) mission (Torbert et al. in Space Sci. Rev. (2014), this issue). It provides the three magnetic components of the waves from 1 Hz to 6 kHz in particular in the key regions of the Earth’s magnetosphere namely the subsolar region and the magnetotail. Magnetospheric plasmas being collisionless, such a measurement is crucial as the electromagnetic waves are thought to provide a way to ensure the conversion from magnetic to thermal and kinetic energies allowing local or global reconfigurations of the Earth’s magnetic field. The analog waveforms provided by the SCM are digitized and processed inside the digital signal processor (DSP), within the Central Electronics Box (CEB), together with the electric field data provided by the spin-plane double probe (SDP) and the axial double probe (ADP). On-board calibration signal provided by DSP allows the verification of the SCM transfer function once per orbit. Magnetic waveforms and on-board spectra computed by DSP are available at different time resolution depending on the selected mode. The SCM design is described in details as well as the different steps of the ground and in-flight calibrations.

Source Agritrop Cirad (https://agritrop.cirad.fr/595484/)

Comment arrivons-nous a dessiner le cours de notre vie ? Etre sujet de son existence - une conquete historique - implique un travail complexe, eprouvant et risque. L'auteur nous ouvre les portes de la petite fabrique a s'inventer. Delivre des cadres traditionnels, l'individu moderne tombe en panne sitot qu'il ne croit plus a sa propre histoire : l'analyse ouvre sur la question de l'identite. Une notion devenue omnipresente sans etre jamais clairement definie. Apres un bilan critique de l'histoire du concept, Jean-Claude Kaufmann nous propose une theorie, ancree dans l'actualite la plus vive. Pour le meilleur et pour le pire, nous sommes desormais entres dans l'âge des identites.

Abstract Background Ecological research now deals increasingly with the effects of noise pollution on biodiversity. Indeed, many studies have shown the impacts of anthropogenic noise and concluded that it is potentially a threat to the persistence of many species. The present work is a systematic map of the evidence of the impacts of all anthropogenic noises (industrial, urban, transportation, etc.) on biodiversity. This report describes the mapping process and the evidence base with summary figures and tables presenting the characteristics of the selected articles. Methods The method used was published in an a priori protocol. Searches included peer-reviewed and grey literature published in English and French. Two online databases were searched using English terms and search consistency was assessed with a test list. Supplementary searches were also performed (using search engines, a call for literature and searching relevant reviews). Articles were screened through three stages (titles, abstracts, full-texts). No geographical restrictions were applied. The subject population included all wild species (plants and animals excluding humans) and ecosystems. Exposures comprised all types of man-made sounds in terrestrial and aquatic media, including all contexts and sound origins (spontaneous or recorded sounds, in situ or laboratory studies, etc.). All relevant outcomes were considered (space use, reproduction, communication, etc.). Then, for each article selected after full-text screening, metadata were extracted on key variables of interest (species, types of sound, outcomes, etc.). Review findings Our main result is a database that includes all retrieved literature on the impacts of anthropogenic noise on species and ecosystems, coded with several markers (sources of noise, species concerned, types of impacts, etc.). Our search produced more than 29,000 articles and 1794 were selected after the three screening stages (1340 studies (i.e. primary research), 379 reviews, 16 meta-analyses). Some articles (n = 19) are written in French and all others are in English. This database is available as an additional file of this report. It provides an overview of the current state of knowledge. It can be used for primary research by identifying knowledge gaps or in view of further analysis, such as systematic reviews. It can also be helpful for scientists and researchers as well as for practitioners, such as managers of transportation infrastructure. Conclusion The systematic map reveals that the impacts of anthropogenic noises on species and ecosystems have been researched for many years. In particular, some taxonomic groups (mammals, birds, fishes), types of noise (transportation, industrial, abstract) and outcomes (behavioural, biophysiological, communication) have been studied more than others. Conversely, less knowledge is available on certain species (amphibians, reptiles, invertebrates), noises (recreational, military, urban) and impacts (space use, reproduction, ecosystems). The map does not assess the impacts of anthropogenic noise, but it can be the starting point for more thorough synthesis of evidence. After a critical appraisal, the included reviews and meta-analyses could be exploited, if reliable, to transfer the already synthesized knowledge into operational decisions to reduce noise pollution and protect biodiversity.

Canadian Journal on Aging / La Revue canadienne du vieillissement - Volume 34, Number 3, September/septembre 2015

International audience

We provide a quantitative description of the French national herbarium vascular plants collection dataset. Held at the Muséum national d'histoire naturelle, Paris, it currently comprises records for 5,400,000 specimens, representing 90% of the estimated total of specimens. Ninety nine percent of the specimen entries are linked to one or more images and 16% have field-collecting information available. This major botanical collection represents the results of over three centuries of exploration and study. The sources of the collection are global, with a strong representation for France, including overseas territories, and former French colonies. The compilation of this dataset was made possible through numerous national and international projects, the most important of which was linked to the renovation of the herbarium building. The vascular plant collection is actively expanding today, hence the continuous growth exhibited by the dataset, which can be fully accessed through the GBIF portal or the MNHN database portal (available at: https://science.mnhn.fr/institution/mnhn/collection/p/item/search/form). This dataset is a major source of data for systematics, global plants macroecological studies or conservation assessments.

The house mouse (Mus musculus) represents the extreme of globalization of invasive mammals. However, the timing and basis of its origin and early phases of dispersal remain poorly documented. To track its synanthropisation and subsequent invasive spread during the develoment of complex human societies, we analyzed 829 Mus specimens from 43 archaeological contexts in Southwestern Asia and Southeastern Europe, between 40,000 and 3,000 cal. BP, combining geometric morphometrics numerical taxonomy, ancient mitochondrial DNA and direct radiocarbon dating. We found that large late hunter-gatherer sedentary settlements in the Levant, c. 14,500 cal. BP, promoted the commensal behaviour of the house mouse, which probably led the commensal pathway to cat domestication. House mouse invasive spread was then fostered through the emergence of agriculture throughout the Near East 12,000 years ago. Stowaway transport of house mice to Cyprus can be inferred as early as 10,800 years ago. However, the house mouse invasion of Europe did not happen until the development of proto urbanism and exchange networks - 6,500 years ago in Eastern Europe and 4000 years ago in Southern Europe - which in turn may have driven the first human mediated dispersal of cats in Europe.

Although it is possible to increase confidence in free and open source software by reviewing its source code, trusting code is not the same as trusting its executable counterparts. This article examines reproducible builds, an approach that can determine whether generated binaries correspond to the original source code.

The SHARC Interest Group of the Research Data Alliance was established to improve research crediting and rewarding mechanisms for scientists who wish to organise their data (and material resources) for community sharing. This requires that data are findable and accessible on the Web, and comply with shared standards making them interoperable and reusable in alignment with the FAIR principles. It takes considerable time, energy, expertise and motivation. It is imperative to facilitate the processes to encourage scientists to share their data. To that aim, supporting FAIR principles compliance processes and increasing the human understanding of FAIRness criteria – i.e., promoting FAIRness literacy – and not only the machine-readability of the criteria, are critical steps in the data sharing process. Appropriate human-understandable criteria must be the first identified in the FAIRness assessment processes and roadmap. This paper reports on the lessons learned from the RDA SHARC Interest Group on identifying the processes required to prepare FAIR implementation in various communities not specifically data skilled, and on the procedures and training that must be deployed and adapted to each practice and level of understanding. These are essential milestones in developing adapted support and credit back mechanisms not yet in place.

BACKGROUND: The coffee species Coffea canephora is commercially identified as "Conilon" when produced in Brazil, or "Robusta" when produced elsewhere in the world. It represents approximately 40 % of coffee production worldwide. While the genetic diversity of wild C. canephora has been well studied in the past, only few studies have addressed the genetic diversity of currently cultivated varieties around the globe. Vietnam is the largest Robusta producer in the world, while Mexico is the only Latin American country, besides Brazil, that has a significant Robusta production. Knowledge of the genetic origin of Robusta cultivated varieties in countries as important as Vietnam and Mexico is therefore of high interest. RESULTS: Through the use of Sequencing-based diversity array technology-DArTseq method-on a collection of C. canephora composed of known accessions and accessions cultivated in Vietnam and Mexico, 4,021 polymorphic SNPs were identified. We used a multivariate analysis using SNP data from reference accessions in order to confirm and further fine-tune the genetic diversity of C. canephora. Also, by interpolating the data obtained for the varieties from Vietnam and Mexico, we determined that they are closely related to each other, and identified that their genetic origin is the Robusta Congo - Uganda group. CONCLUSIONS: The genetic characterization based on SNP markers of the varieties grown throughout the world, increased our knowledge on the genetic diversity of C. canephora, and contributed to the understanding of the genetic background of varieties from very important coffee producers. Given the common genetic origin of the Robusta varieties cultivated in Vietnam, Mexico and Uganda, and the similar characteristics of climatic areas and relatively high altitude where they are grown, we can state that the Vietnamese and the Mexican Robusta have the same genetic potential to produce good cup quality.

Most agricultural research organizations strive to address societal challenges and contribute to positive societal impacts. Fulfilling this ambition involves embedding a culture of impact in organizational culture, which, in our view, entails three main elements: understanding the role of the research community in contributing to impacts over the long term within the systems in which it operates; equipping researchers to support positive change; and implementing strategies that allow the culture of impact to percolate at various levels of the organization. To build just such a culture, in the past 8 years, Cirad, the French Agricultural Research Center for International Development, embarked on a transformational process, from which we draw key lessons. Building a culture of impact requires fostering transdisciplinary dialogue on the multiple roles of researchers, on their contribution to societal impacts, and on the relevance of this reflection. This involves adapting from pre-existing visions, interactions, and practices. Formalization in the organization's strategy and the action of leading change agents foster its institutionalization. Strengthening capacity to build shared visions of change and collective processes in research design, implementation, and evaluation while respecting the diversity of profiles and approaches in the organization favors appropriation. This requires adequate funding at the project, institutional and funding bodies level, and targeted communication to ensure buy-in by internal and external change agents. We argue that a culture of impact is a reflective culture and long-term dynamics that aims to overcome the dichotomy between research and development and bring agricultural research closer to societal needs.

To simulate the end-of-life behavior of cladding tubes during the first phase of a LOCA transient, one may assume that the main effect of a long service exposure on the cladding deformation behavior during LOCA arises from the hydrogen uptake associated with the cladding oxidation at high burn-up. Thus, the recent metallurgical studies and EDGAR [2] tests performed on pre-hydrided Zr-base alloys are presented. The influence of hydrogen has been studied for concentrations ranging from ∼ 100 up to ∼1000 (weight) ppm on FramatomeANP low-tin Zy-4, M4 (ZrSnFeV), and M5™(ZrNbO) alloys. The decrease of the α/β phase transformation temperatures with the increase of the hydrogen content is noticeable and has been quantified, and then modeled, for both quasi-equilibrium (calorimetry) and dynamic (dilatometry) conditions for heating rates up to 100°C/s. Some complementary microstructural examinations on hydrided samples, beforehand partially transformed into β phase, have been performed to get a better insight of the metallurgical features associated with the hydrogen effects. Finally, the EDGAR thermal-mechanical test results are presented and discussed. The alloys have been tested under steady state conditions of pressure and temperature, on the one hand, and with continuous heating (thermal ramps) on the other. The results show that the mechanical behavior cannot be explained solely by the effect of hydrogen on the shift of the α/β phase transformation temperatures, but that hydrogen modifies also the creep behavior and the burst criterion, especially in the a domain, and in the lower α+β temperature range. As a result, hydrogen decreases the creep strength and the ductility of the materials, the effect being greater for higher hydrogen content. All these data are used to model the thermal-mechanical behavior of the hydrided cladding tubes in order to simulate the LOCA behavior of the clad after long-term in-service exposure. Finally, preliminary thermal ramp tests under uniaxial loading performed on irradiated Zy-4 are presented and compared to the behavior of non-irradiated as-received and hydrided Zy-4. These last experiments were made to validate the assumption that the main effect of a long service exposure on the cladding deformation behavior during the first phase of LOCA is mainly linked to the hydrogen uptake associated with the cladding oxidation.

Abstract. We use satellite observations from IASI (Infrared Atmospheric Sounding Interferometer) on board the MetOp-A satellite to evaluate the springtime daily variations in lower-tropospheric ozone over east Asia. The availability of semi-independent columns of ozone from the surface up to 12 km simultaneously with CO columns provides a powerful observational data set to diagnose the processes controlling tropospheric ozone enhancement on synoptic scales. By combining IASI observations with meteorological reanalyses from ERA-Interim, we develop an analysis method based only on IASI ozone and CO observations to identify the respective roles of the stratospheric source and the photochemical source in ozone distribution and variations over east Asia. The succession of low- and high-pressure systems drives the day-to-day variations in lower-tropospheric ozone. A case study analysis of one frontal system and one cut-off low system in May 2008 shows that reversible subsiding and ascending ozone transfers in the upper-troposphere–lower-stratosphere (UTLS) region, due to the tropopause perturbations occurring in the vicinity of low-pressure systems, impact free and lower-tropospheric ozone over large regions, especially north of 40° N, and largely explain the ozone enhancement observed with IASI for these latitudes. Irreversible stratosphere–troposphere exchanges of ozone-rich air masses occur more locally in the southern and southeastern flanks of the trough. The contribution to the lower-tropospheric ozone column is difficult to dissociate from the tropopause perturbations generated by weather systems. For regions south of 40° N, a significant correlation has been found between lower-tropospheric ozone and carbon monoxide (CO) observations from IASI, especially over the North China Plain (NCP). Considering carbon monoxide observations as a pollutant tracer, the O3–CO correlation indicates that the photochemical production of ozone from primary pollutants emitted over such large polluted regions significantly contributes to the ozone enhancements observed in the lower troposphere via IASI. When low-pressure systems circulate over the NCP, stratospheric and pollution sources play a concomitant role in the ozone enhancement. IASI's 3-D observational capability allows the areas in which each source dominates to be determined. Moreover, the studied cut-off low system has enough potential convective capacity to uplift pollutants (ozone and CO) and to transport them to Japan. The increase in the enhancement ratio of ozone to CO from 0.16 on 12 May over the North China Plain to 0.28 over the Sea of Japan on 14 May indicates photochemical processing during the plume transport.

Background: The prevalence of chronic pain and sleep disturbances substantially increases with age. Pharmacotherapy remains the primary treatment option for these health issues. However, side effects and drug interactions are difficult to control in elderly individuals. Aims: The objective of this study was to assess the feasibility of conducting a randomized sham-controlled trial and to collect preliminary data on the efficacy of transcranial direct current stimulation (tDCS) to reduce pain and improve sleep in older adults suffering from chronic pain. Methods: Fourteen elderly individuals (mean age 71±7 years) suffering from chronic pain and sleep complaints were randomized to receive either anodal tDCS, applied over the primary motor cortex (2 mA, 20 minutes), or sham tDCS, for 5 consecutive days. Pain was measured with visual analog scales, pain logbooks and questionnaires, while sleep was assessed with actigraphy, sleep diaries and questionnaires. Results: There were no missing data for pain and sleep measures, except for actigraphy, that generated several missing data. Blinding was maintained throughout the study, for both the evaluator and participants. Active but not sham tDCS significantly reduced pain ( P <0.05). No change was observed in sleep parameters, in both the active and sham tDCS groups (all P ≥0.18). Conclusion: The present study provides guidelines for the implementation of future tDCS studies in larger populations of elderly individuals. M1 anodal tDCS in this population appears to be effective to reduce pain, but not to improve sleep. Keywords: transcranial direct current stimulation, tDCS, pain, sleep, elderly, actigraphy, aging

Magnetic resonance imaging of the thoracolumbar spine showed complete fatty degeneration of the lumbar erector spinae muscles in a woman who had complained of chronic lower back pain for 5 years and of progressive weakness of the lower limbs for 1 year. Neuromuscular examination of the lower limbs showed no obvious anomaly, and there was no camptocormia. Serum creatine kinase levels were increased (six- to ninefold); electrodiagnostic examination revealed no activity at rest or during effort in the erector spinae muscles and was normal in proximal and distal muscles of the limbs. Muscle computed tomography revealed mild fatty degeneration of thigh and gastrocnemius muscles, and histopathology of the deltoid muscle showed dystrophic features and complete lack of dysferlin. Molecular analysis identified a homozygous disease-causing mutation in the gene encoding dysferlin. Because there were no similar cases in the family, the final diagnosis was sporadic limb-girdle muscular dystrophy type 2B. Overall, this case report shows that the lumbar and lower thoracic of erector spinae muscles may display complete fatty degeneration without the occurrence of camptocormia, with primary dysferlin deficiency as a possible cause.

A series of eight patients with isolated clinical and electrophysiological sensory deficit related to neuralgic amyotrophy (NA) is reported. NA was diagnosed by clinical and electrodiagnostic features and disease course. Imaging and laboratory investigations excluded other disorders. The results showed mild to severe involvement of eight individual sensory nerves: lateral antebrachial cutaneous nerve lesions in three instances and partial lesions of the median nerve in five cases. Our findings suggest that isolated clinical and electrodiagnostic sensory involvement in NA is not exceptional but rather is unrecognized. The pattern of these nerve lesions agrees with the most typical pattern of NA, which is a mononeuritis or mononeuritis multiplex. The present study also shows that the spectrum of NA is diverse and may vary from pure motor to pure sensory deficit, according to the nature of the involved nerve fibers.

Introduit à Madagascar au début du 19e siècle, le giroflier est originaire des îles Moluques en Indonésie. Malgré la sensibilité de l’essence aux risques météorologiques, tels les cyclones, et aux attaques d’un parasite local, andretra, et malgré la production variable de clous de girofle d’une année sur l’autre, son adaptation aux conditions écologiques de la côte Est de Madagascar, notamment dans la région d’Analanjirofo, est remarquable. Très vite adoptée par les paysans (certains venus s’installer mais la plupart autochtones), ceux-ci l’ont intégrée dans leurs systèmes de culture en complément aux cultures vivrières (riz, surtout) et de rapport (café et vanille). Aujourd’hui, le marché du clou de girofle est une source de revenus réguliers pour les ménages et leur assure la sécurité ali- mentaire. Le giroflier donne deux produits de grande valeur économique, le clou de girofle, le bouton floral séché, et l’huile essentielle de girofle produite par distillation des feuilles, dont Madagascar est le premier exportateur mondial. Avec la vanille, les produits du giro- flier représentent les premiers produits agri- coles d’exportation, parfois les deuxièmes, de Madagascar. Les clous de girofle s’exportent surtout en Indonésie, où ils entrent dans la fabrication d’une cigarette locale appelée kretek. Un petit volume s’exporte vers les pays du nord sous forme d’épice. L’huile essentielle de girofle est distillée dans une multitude d'alambics rudimentaires dans toute la région de pro- duction. La qualité de l’huile essentielle dépend de sa teneur en eugénol, molécule mise en œuvre dans de nombreux secteurs éco- nomiques, dont l’industrie des cosmétiques, la pharmaceutique humaine et vétérinaire et l’in- dustrie alimentaire. Le giroflier de Madagascar semble représenter un exemple d’intégration réussie d’une nouvelle culture dans un système de cultures existant. Cependant, les plantations de girofliers vieillissent et les conditions de leur renouvellement ne sont pas pleinement présentes. Alors que le marché du clou de girofle dépend fortement de la demande indonésienne, les perspectives sont prometteuses sur le marché mondial des épices et des produits contenant de l’eugénol. De ce fait, les pratiques actuelles et les possibilités d’adaptation et de développement du secteur Malgache de la girofle doivent être étudiées de près pour assurer l’équilibre futur entre les marchés et les besoins des paysans en termes de gestion de la ressource et de sa valorisation.

Abstract Ocean acidification (OA) and its subsequent changes in seawater carbonate chemistry are threatening the survival of calcifying organisms. Due to their use of calcium carbonate to build their shells, marine molluscs are particularly vulnerable. This study investigated the effect of CO2-induced OA on adult European abalone (Haliotis tuberculata) using a multi-parameter approach. Biological (survival, growth), physiological (pHT of haemolymph, phagocytosis, metabolism, gene expression), and structural responses (shell strength, nano-indentation measurements, Scanning electron microscopy imaging of microstructure) were evaluated throughout a 5-month exposure to ambient (8.0) and low (7.7) pH conditions. During the first 2 months, the haemolymph pH was reduced, indicating that abalone do not compensate for the pH decrease of their internal fluid. Overall metabolism and immune status were not affected, suggesting that abalone maintain their vital functions when facing OA. However, after 4 months of exposure, adverse effects on shell growth, calcification, microstructure, and resistance were highlighted, whereas the haemolymph pH was compensated. Significant reduction in shell mechanical properties was revealed at pH 7.7, suggesting that OA altered the biomineral architecture leading to a more fragile shell. It is concluded that under lower pH, abalone metabolism is maintained at a cost to growth and shell integrity. This may impact both abalone ecology and aquaculture.