Validation of HelioClim-3 version 4, HelioClim-3 version 5 and MACC-RAD using 14 BSRN stations

International audienceThis communication presents the results of a comparison of three satellite-derived databases covering Africa, Europe, Middle East and part of South America, against corresponding 15 min irradiations of very high quality measured by fourteen Baseline Surface Radiation Network (BSRN) stations. The three databases are accessible via the SoDa Service website, and are the two latest versions of HelioClim-3: versions 4 (HC3v4) and 5 (HC3v5), and the MACC-RAD database. The comparison was performed for durations of 15 min, 1 h, 1 day and 1 month for both the global irradiation received on a horizontal surface (GHI) and the direct irradiation received on a plane normal to sun rays (DNI). It is found that the three satellite-derived radiation databases exhibit satisfactory performances. For most of the fourteen locations, HC3v5 surpasses HC3v4 and MACC-RAD, with a bias ranging from-4 to 5% for the GHI and for all tested duration. The correlation coefficient is large for all databases and most often greater than 0.92 for 15 min and 0.98 for daily irradiation for GHI. The RMSE is fairly constant for all locations for 15 min and is approximately 20 kWh m-2 –slightly greater for MACC-RAD.-For daily irradiation, it ranges between 300 and 400 kWh m-2 for HC3v5, 300 and 500 kWh m-2 for HC3v4, and 400 and 550 kWh m-2 for MACC-RAD. Bias for the DNI is larger in absolute values than for GHI for all databases:-12 to 10% for HC3v5. The correlation coefficient is most often greater than 0.68 for 15 min and 0.84 for daily irradiation. The RMSE for 15 min ranges between 46 and 60 kWh m-2 for HC3v5, 46 and 63 kWh m-2 for HC3v4, and 48 and 66 kWh m-2 for MACC-RAD. For daily irradiation, it ranges between 1100 and 1600 kWh m-2 for HC3v5, between 1300 and 1700 kWh m-2 for HC3v4, and between 1000 and 1850 kWh m-2 for MACC-RAD. The MACC-RAD resource show promises provided the model for cloud properties is improved

A Semantic Characterization for ASP Base Revision

International audienceThe paper deals with base revision for Answer Set Programming (ASP). Base revision in classical logic is done by the removal of formulas. Exploiting the non-monotonicity of ASP allows one to propose other revision strategies, namely addition strategy or removal and/or addition strategy. These strategies allow one to define families of rule-based revision operators. The paper presents a semantic characterization of these families of revision operators in terms of answer sets. This semantic characterization allows for equivalently considering the evolution of syntactic logic programs and the evolution of their semantic content. It then studies the logical properties of the proposed operators and gives complexity results

Computing Query Answering With Non-Monotonic Rules: A Case Study of Archaeology Qualitative Spatial Reasoning

International audienceThis paper deals with querying ontology-based knowledge bases equipped with non-monotonic rules through a case study within the framework of Cultural Heritage. It focuses on 3D underwater surveys on the Xlendi wreck which is represented by an OWL2 knowledge base with a large dataset. The paper aims at improving the interactions between the archaeologists and the knowledge base providing new queries that involve non-monotonic rules in order to perform qualitative spatial reasoning. To this end, the knowledge base initially represented in OWL2-QL is translated into an equivalent Answer Set Programming (ASP) program and is enriched with a set of non-monotonic ASP rules suitable to express default and exceptions. An ASP query answering approach is proposed and implemented. Furthermore due to the increased expressiveness of non-monotonic rules it provides spatial reasoning and spatial relations between artifacts query answering which is not possible with query answering languages such as SPARQL and SQWRL

Transcriptomic analysis of the dialogue between Pseudorabies virus and porcine epithelial cells during infection

International audienceBACKGROUND: Transcriptomic approaches are relevant for studying virus-host cell dialogues to better understand the physiopathology of infection and the immune response at the cellular level. Pseudorabies virus (PrV), a porcine Alphaherpesvirus, is a good model for such studies in pig. Since PrV displays a strong tropism for mucous epithelial cells, we developed a kinetics study of PrV infection in the porcine PK15 epithelial cell line. To identify as completely as possible, viral and cellular genes regulated during infection, we simultaneously analyzed PrV and cellular transcriptome modifications using two microarrays i.e. a laboratory-made combined SLA/PrV microarray, consisting of probes for all PrV genes and for porcine genes contained in the Swine Leukocyte Antigen (SLA) complex, and the porcine generic Qiagen-NRSP8 oligonucleotide microarray. We confirmed the differential expression of a selected set of genes by qRT-PCR and flow cytometry. RESULTS: An increase in the number of differentially expressed cellular genes and PrV genes especially from 4 h post-infection (pi) was observed concomitantly with the onset of viral progeny while no early global cellular shutoff was recorded. Many cellular genes were down-regulated from 4 h pi and their number increased until 12 h pi. UL41 transcripts encoding the virion host shutoff protein were first detected as differentially expressed at 8 h pi. The viral gene UL49.5 encoding a TAP inhibitor protein was differentially expressed as soon as 2 h pi, indicating that viral evasion via TAP inhibition may start earlier than the cellular gene shutoff. We found that many biological processes are altered during PrV infection. Indeed, several genes involved in the SLA class I antigenic presentation pathway (SLA-Ia, TAP1, TAP2, PSMB8 and PSMB9), were down-regulated, thus contributing to viral immune escape from this pathway and other genes involved in apoptosis, nucleic acid metabolism, cytoskeleton signaling as well as interferon-mediated antiviral response were also modulated during PrV infection. CONCLUSION: Our results show that the gene expression of both PrV and porcine cells can be analyzed simultaneously with microarrays, providing a chronology of PrV gene transcription, which has never been described before, and a global picture of transcription with a direct temporal link between viral and host gene expression

Diversified rotations in protected vegetable production systems (DiverIMPACTS Practice Abstract)

By relying on these principles, it is possible to design rotations that are more favourable to the preservation of soil health while taking into account the organisational constraints of a farm and economic opportunities

The HelioClim-1 database of daily solar radiation at Earth surface: an example of the benefits of GEOSS Data-CORE

International audienceThe HelioClim-1 database contains daily values of the solar radiation reaching the ground. This GEOSS (Global Earth Observation System of Systems) Data Collection of Open Resources for Everyone (Data-CORE) covers Europe, Africa and the Atlantic Ocean, from 1985 to 2005. It is freely accessible at no cost through the SoDa Service (www.soda-is.com). Several assessments of the HelioClim-1 data against measurements made in meteorological networks reveal that the HelioClim-1 database offers a reliable and accurate knowledge of the solar radiation and its daily, seasonal and annual variations over recent years. The HelioClim-1 data may help in qualifying in situ measurements and may supplement them, thus offering 21 years of accurate daily means of surface solar irradiance. Several published works benefited from openness, availability and accuracy of the HelioClim-1 database in various domains: oceanography, climate, energy production, life cycle analysis, agriculture, forestry, architecture, health and air quality. This demonstration of the benefit of the HelioClim-1 database draws attention to resources open to everyone such as those labeled GEOSS Data-CORE

Transcriptome analysis of porcine PBMCs after in vitro stimulation by LPS or PMA/ionomycin using an expression array targeting the pig immune response

<p>Abstract</p> <p>Background</p> <p>Designing sustainable animal production systems that better balance productivity and resistance to disease is a major concern. In order to address questions related to immunity and resistance to disease in pig, it is necessary to increase knowledge on its immune system and to produce efficient tools dedicated to this species.</p> <p>Results</p> <p>A long-oligonucleotide-based chip referred to as SLA-RI/NRSP8-13K was produced by combining a generic set with a newly designed SLA-RI set that targets all annotated loci of the pig major histocompatibility complex (MHC) region (SLA complex) in both orientations as well as immunity genes outside the SLA complex.</p> <p>The chip was used to study the immune response of pigs following stimulation of porcine peripheral blood mononuclear cells (PBMCs) with lipopolysaccharide (LPS) or a mixture of phorbol myristate acetate (PMA) and ionomycin for 24 hours. Transcriptome analysis revealed that ten times more genes were differentially expressed after PMA/ionomycin stimulation than after LPS stimulation. LPS stimulation induced a general inflammation response with over-expression of SAA1, pro-inflammatory chemokines IL8, CCL2, CXCL5, CXCL3, CXCL2 and CCL8 as well as genes related to oxidative processes (SOD2) and calcium pathways (S100A9 and S100A12). PMA/ionomycin stimulation induced a stronger up-regulation of T cell activation than of B cell activation with dominance toward a Th1 response, including IL2, CD69 and TNFRSF9 (tumor necrosis factor receptor superfamily, member 9) genes. In addition, a very intense repression of THBS1 (thrombospondin 1) was observed. Repression of MHC class I genes was observed after PMA/ionomycin stimulation despite an up-regulation of the gene cascade involved in peptide processing. Repression of MHC class II genes was observed after both stimulations. Our results provide preliminary data suggesting that antisense transcripts mapping to the SLA complex may have a role during immune response.</p> <p>Conclusion</p> <p>The SLA-RI/NRSP8-13K chip was found to accurately decipher two distinct immune response activations of PBMCs indicating that it constitutes a valuable tool to further study immunity and resistance to disease in pig. The transcriptome analysis revealed specific and common features of the immune responses depending on the stimulation agent that increase knowledge on pig immunity.</p

A multi-decade record of high quality fCO2 data in version 3 of the Surface Ocean CO2 Atlas (SOCAT)

The Surface Ocean CO2 Atlas (SOCAT) is a synthesis of quality-controlled fCO2 (fugacity of carbon dioxide) values for the global surface oceans and coastal seas with regular updates. Version 3 of SOCAT has 14.7 million fCO2 values from 3646 data sets covering the years 1957 to 2014. This latest version has an additional 4.6 million fCO2 values relative to version 2 and extends the record from 2011 to 2014. Version 3 also significantly increases the data availability for 2005 to 2013. SOCAT has an average of approximately 1.2 million surface water fCO2 values per year for the years 2006 to 2012. Quality and documentation of the data has improved. A new feature is the data set quality control (QC) flag of E for data from alternative sensors and platforms. The accuracy of surface water fCO2 has been defined for all data set QC flags. Automated range checking has been carried out for all data sets during their upload into SOCAT. The upgrade of the interactive Data Set Viewer (previously known as the Cruise Data Viewer) allows better interrogation of the SOCAT data collection and rapid creation of high-quality figures for scientific presentations. Automated data upload has been launched for version 4 and will enable more frequent SOCAT releases in the future. High-profile scientific applications of SOCAT include quantification of the ocean sink for atmospheric carbon dioxide and its long-term variation, detection of ocean acidification, as well as evaluation of coupled-climate and ocean-only biogeochemical models. Users of SOCAT data products are urged to acknowledge the contribution of data providers, as stated in the SOCAT Fair Data Use Statement. This ESSD (Earth System Science Data) “living data” publication documents the methods and data sets used for the assembly of this new version of the SOCAT data collection and compares these with those used for earlier versions of the data collection (Pfeil et al., 2013; Sabine et al., 2013; Bakker et al., 2014). Individual data set files, included in the synthesis product, can be downloaded here: doi:10.1594/PANGAEA.849770. The gridded products are available here: doi:10.3334/CDIAC/OTG.SOCAT_V3_GRID

Efficacy and Safety of Artemether-Lumefantrine in the Treatment of Acute, Uncomplicated Plasmodium falciparum Malaria: A Pooled Analysis

Randomized trials have confirmed the efficacy and safety of artemether-lumefantrine (AL) for treatment of uncomplicated Plasmodium falciparum malaria. Data from seven studies supported by Novartis (1996–2007), including 647 adults (> 16 years of age, 83.3% completed the study) and 1,332 children (≤ 16 years of age, 89.3% completed the study) with microscopically confirmed uncomplicated P. falciparum malaria and treated with the recommended regimen of AL, were pooled. The 28-day polymerase chain reaction–corrected parasitologic cure rate (primary efficacy endpoint) was 97.1% (495 of 510) in adults and 97.3% (792 of 814) in children (evaluable population). Gametocytemia prevalence after day was 4.2% (23 of 554) in adults and 0.9% (8 of 846) in children. No noteworthy safety signals were observed. Serious adverse events occurred in 1.4% of the adults and 1.3% of the children. This study is the largest data set to date assessing AL therapy for treatment of acute uncomplicated P. falciparum malaria. Artemether-lumefantrine showed high cure rates and rapid resolution of parasitemia, fever, and gametocytemia in adults and children, and showed an excellent safety and tolerability profile

Immunity Traits in Pigs: Substantial Genetic Variation and Limited Covariation

BACKGROUND: Increasing robustness via improvement of resistance to pathogens is a major selection objective in livestock breeding. As resistance traits are difficult or impossible to measure directly, potential indirect criteria are measures of immune traits (ITs). Our underlying hypothesis is that levels of ITs with no focus on specific pathogens define an individual's immunocompetence and thus predict response to pathogens in general. Since variation in ITs depends on genetic, environmental and probably epigenetic factors, our aim was to estimate the relative importance of genetics. In this report, we present a large genetic survey of innate and adaptive ITs in pig families bred in the same environment. METHODOLOGY/PRINCIPAL FINDINGS: Fifty four ITs were studied on 443 Large White pigs vaccinated against Mycoplasma hyopneumoniae and analyzed by combining a principal component analysis (PCA) and genetic parameter estimation. ITs include specific and non specific antibodies, seric inflammatory proteins, cell subsets by hemogram and flow cytometry, ex vivo production of cytokines (IFNα, TNFα, IL6, IL8, IL12, IFNγ, IL2, IL4, IL10), phagocytosis and lymphocyte proliferation. While six ITs had heritabilities that were weak or not significantly different from zero, 18 and 30 ITs had moderate (0.1<h2≤0.4) or high (h2>0.4) heritability values, respectively. Phenotypic and genetic correlations between ITs were weak except for a few traits that mostly include cell subsets. PCA revealed no cluster of innate or adaptive ITs. CONCLUSIONS/SIGNIFICANCE: Our results demonstrate that variation in many innate and adaptive ITs is genetically controlled in swine, as already reported for a smaller number of traits by other laboratories. A limited redundancy of the traits was also observed confirming the high degree of complementarity between innate and adaptive ITs. Our data provide a genetic framework for choosing ITs to be included as selection criteria in multitrait selection programmes that aim to improve both production and health traits