Combination of DROOL rules and Protégé knowledge bases in the ONTO-H annotation tool

ONTO-H is a semi-automatic collaborative tool for the semantic annotation of documents, built as a Protégé 3.0 tab plug-in. Among its multiple functionalities aimed at easing the document annotation process, ONTO-H uses a rule-based system to create cascading annotations out from a single drag and drop operation from a part of a document into an already existing concept or instance of the domain ontology being used for annotation. It also gives support to the detection of name conflicts and instance duplications in the creation of the annotations. The rule system runs on top of the open source rule engine DROOLS and is connected to the domain ontology used for annotation by means of an ad-hoc programmed Java proxy

New plasmid calibrators for geminivirus-resistant (EMB-PV051-1 event) common bean (Phaseolus vulgaris L.) quantitation using simplex and duplex qPCR.

The geminivirus-resistant common bean, Embrapa 5.1, was the first commercial genetically modified (GM) event developed in Latin America by the Brazilian Agricultural Research Corp.. Therein novel standard reference plasmids were constructed for species-specific (pLEC) and event-specific (pFGM) qualitative and quantitative detection of Embrapa 5.1 GM common bean. To establish these plasmids as certified reference materials (CRM) for Embrapa 5.1 GM common bean, two DNA extraction protocols, simplex and duplex qPCR using two different operators (experimenters) were tested. The efficiency values ranged from 92% to 110% for the simplex and duplex reactions considering both operators. The limit of detection was enough to detect at least 0.1% GM content. These plasmids are suitable to be used as CRM for Embrapa 5.1 GM common bean. They will be useful for survey of food labels for compliance with legislation about GMO content in Brazil and in other countries where GM common bean is not yet approved for commercialization

Locomotor performance of closely related Tropidurus species: relationships with physiological parameters and ecological divergence

Tropidurid lizards have colonized a variety of Brazilian open environments without remarkable morphological variation, despite ecological and structural differences among habitats used. This study focuses on two Tropidurus sister-species that, despite systematic proximity and similar morphology, exhibit great ecological divergence and a third ecologically generalist congeneric species providing an outgroup comparison. We quantified jumping capacity and sprint speed of each species on sand and rock to test whether ecological divergence was also accompanied by differences in locomotor performance. Relevant physiological traits possibly associated with locomotor performance metabolic scopes and fiber type composition, power output and activity of the enzymes citrate synthase, pyruvate kinase and lactate dehydrogenase of the iliofibularis muscle - were also compared among the three Tropidurus species. We found that the two sister-species exhibited remarkable differences in jumping performance, while Tropidurus oreadicus, the more distantly related species, exhibited intermediate values. Tropidurus psamonastes, a species endemic to sand dunes, exhibited high absolute sprint speeds on sand, jumped rarely and possessed a high proportion of glycolytic fibers and low activity of citrate synthase. The sister-species Tropidurus itambere, endemic to rocky outcrops, performed a large number of jumps and achieved lower absolute sprint speed than T. psamonastes. This study provides evidence of rapid divergence of locomotor parameters between sister-species that use different substrates, which is only partially explained by variation in physiological parameters of the iliofibularis muscle

Monitoring of the Eyjafjalla volcanic plume at four lidar stations over the Iberian Peninsula: 6 to 8 May 2010

Lidar measurements were performed in the framework of the EARLINET and SPALINET networks during the eruption of Eyjafjalla volcano (Iceland) since 14 April 2010. The profiles of the aerosol optical properties, namely backscatter and extinction coefficients, lidar ratio and Angström exponent, show the presence of volcanic aerosol layers over all SPALINET stations since 5 May. The volcanic particles were monitored both within the planetary boundary layer and in decoupled layers up to 8 km agl over the Iberian Peninsula. This is the first time that the spatial and temporal distributions of volcanic aerosols have been studied with active remote sensing techniques over the Iberian Peninsula.Postprint (published version

Characterization of atmospheric aerosols for a long-range transport of biomass-burning from North America over the Iberian Peninsula

This work presents the characterization of atmospheric aerosols performed over the Iberian Peninsula in the framework of EARLINET for a special episode on 20th August 2007. The assessment of aerosol radiative impact requires an accurate determination of their optical and microphysical properties, which are presented here for a variety of instrumentation including passive remote sensors, as sun-photometers, and active systems both ground-based and on board CALIPSO satellite. Measurements highlight the presence of a multilayered structure with a well-defined planetary boundary layer and biomass-particles in elevated layers, extending up to 7 km asl over the central Iberian Peninsula, and even higher, up to 9 km asl, at the southeastern part of the peninsula. Lidar computations reveal a contribution to the aerosol optical depth around 10-40% for these biomass-burning particles, with backscatter-related AngströPostprint (published version

The Pierre Auger Observatory III: Other Astrophysical Observations

Astrophysical observations of ultra-high-energy cosmic rays with the Pierre Auger ObservatoryComment: Contributions to the 32nd International Cosmic Ray Conference, Beijing, China, August 201

Highlights from the Pierre Auger Observatory

The Pierre Auger Observatory is the world's largest cosmic ray observatory. Our current exposure reaches nearly 40,000 km$^2$ str and provides us with an unprecedented quality data set. The performance and stability of the detectors and their enhancements are described. Data analyses have led to a number of major breakthroughs. Among these we discuss the energy spectrum and the searches for large-scale anisotropies. We present analyses of our X$_{max}$ data and show how it can be interpreted in terms of mass composition. We also describe some new analyses that extract mass sensitive parameters from the 100% duty cycle SD data. A coherent interpretation of all these recent results opens new directions. The consequences regarding the cosmic ray composition and the properties of UHECR sources are briefly discussed.Comment: 9 pages, 12 figures, talk given at the 33rd International Cosmic Ray Conference, Rio de Janeiro 201

A search for point sources of EeV photons

Measurements of air showers made using the hybrid technique developed with the fluorescence and surface detectors of the Pierre Auger Observatory allow a sensitive search for point sources of EeV photons anywhere in the exposed sky. A multivariate analysis reduces the background of hadronic cosmic rays. The search is sensitive to a declination band from -85{\deg} to +20{\deg}, in an energy range from 10^17.3 eV to 10^18.5 eV. No photon point source has been detected. An upper limit on the photon flux has been derived for every direction. The mean value of the energy flux limit that results from this, assuming a photon spectral index of -2, is 0.06 eV cm^-2 s^-1, and no celestial direction exceeds 0.25 eV cm^-2 s^-1. These upper limits constrain scenarios in which EeV cosmic ray protons are emitted by non-transient sources in the Galaxy.Comment: 28 pages, 10 figures, accepted for publication in The Astrophysical Journa

Reconstruction of inclined air showers detected with the Pierre Auger Observatory

We describe the method devised to reconstruct inclined cosmic-ray air showers with zenith angles greater than $60^\circ$ detected with the surface array of the Pierre Auger Observatory. The measured signals at the ground level are fitted to muon density distributions predicted with atmospheric cascade models to obtain the relative shower size as an overall normalization parameter. The method is evaluated using simulated showers to test its performance. The energy of the cosmic rays is calibrated using a sub-sample of events reconstructed with both the fluorescence and surface array techniques. The reconstruction method described here provides the basis of complementary analyses including an independent measurement of the energy spectrum of ultra-high energy cosmic rays using very inclined events collected by the Pierre Auger Observatory.Comment: 27 pages, 19 figures, accepted for publication in Journal of Cosmology and Astroparticle Physics (JCAP

A microRNA Cluster Controls Fat Cell Differentiation and Adipose Tissue Expansion By Regulating SNCG

The H19X-encoded miR-424(322)/503 cluster regulates multiple cellular functions. Here, it is reported for the first time that it is also a critical linchpin of fat mass expansion. Deletion of this miRNA cluster in mice results in obesity, while increasing the pool of early adipocyte progenitors and hypertrophied adipocytes. Complementary loss and gain of function experiments and RNA sequencing demonstrate that miR-424(322)/503 regulates a conserved genetic program involved in the differentiation and commitment of white adipocytes. Mechanistically, it is demonstrated that miR-424(322)/503 targets gamma-Synuclein (SNCG), a factor that mediates this program rearrangement by controlling metabolic functions in fat cells, allowing adipocyte differentiation and adipose tissue enlargement. Accordingly, diminished miR-424(322) in mice and obese humans co-segregate with increased SNCG in fat and peripheral blood as mutually exclusive features of obesity, being normalized upon weight loss. The data unveil a previously unknown regulatory mechanism offat mass expansion tightly controlled by the miR-424(322)/503 through SNCG.Peer reviewe