easyDAS: Automatic creation of DAS servers

Background: The Distributed Annotation System (DAS) has proven to be a successful way to publish and share biological data. Although there are more than 750 active registered servers from around 50 organizations, setting up a DAS server comprises a fair amount of work, making it difficult for many research groups to share their biological annotations. Given the clear advantage that the generalized sharing of relevant biological data is for the research community it would be desirable to facilitate the sharing process. Results: Here we present easyDAS, a web-based system enabling anyone to publish biological annotations with just some clicks. The system, available at http://www.ebi.ac.uk/panda-srv/easydas is capable of reading different standard data file formats, process the data and create a new publicly available DAS source in a completely automated way. The created sources are hosted on the EBI systems and can take advantage of its high storage capacity and network connection, freeing the data provider from any network management work. easyDAS is an open source project under the GNU LGPL license. Conclusions: easyDAS is an automated DAS source creation system which can help many researchers in sharing their biological data, potentially increasing the amount of relevant biological data available to the scientific community.Postprint (published version

Meson-exchange currents and quasielastic predictions for charged-current neutrino-12C scattering in the superscaling approach

We evaluate and discuss the impact of meson-exchange currents (MECs) on charged-current quasielastic neutrino cross sections. We consider the nuclear transverse response arising from two-particle two-hole states excited by the action of electromagnetic, purely isovector meson-exchange currents in a fully relativistic framework based on the work by the Torino Collaboration [A. D. Pace, M. Nardi, W. M. Alberico, T. W. Donnelly, and A. Molinari, Nucl. Phys. A726, 303 (2003)]. An accurate parametrization of this MEC response as a function of the momentum and energy transfers involved is presented. Results of neutrino-nucleus cross sections using this MEC parametrization together with a recent scaling approach for the one-particle one-hole contributions (named SuSAv2) are compared with experimental data (MiniBooNE, MINERvA, NOMAD and T2K Collaborations).Comment: 16 pages, 19 figure

Microporosity in aluminium foams

We studied microporosity in the metallic matrix of aluminium foams produced by the powder metallurgical route both with and without application of a blowing agent. Microporosity was studied in situ in liquid metal foams as well as ex situ in the solidified microstructures. In situ studies were carried out using synchrotron X rays. Quantitative analyses of the amount and distribution of microporosity inside cell walls, Plateau borders and nodes were performed on 2D micrographs and on 3D reconstructed volumes generated by X ray tomography. We studied the influence of alloying elements, blowing agent and holding time on the amount and type of micropores. The mechanisms of microporosity formation and the evolution of microporosity via diffusion of hydrogen and by coalescence are discussed. It was observed that alloy composition and holding time have a strong influence on microporosity. Different possible strategies to control microporosity are suggeste

In vitro and in vivo anti-Trypanosoma cruzi activity of new arylamine Mannich base-type derivatives

Chagas disease is a neglected tropical disease with 6-7 million people infected worldwide and there is no effective treatment. Therefore, there is an urgent need to continue researching in order to discover novel therapeutic alternatives. We present a series of arylaminoketone derivatives as means of identifying new drugs to treat Chagas disease in the acute phase with greater activity, less toxicity and with a larger spectrum of action than that corresponding to the reference drug benznidazole. Indexes of high selectivity found in vitro formed the basis for later in vivo assays in BALB/c mice. Murine model results show that compounds 3, 4, 7 and 10 induced a remarkable decrease in parasitemia levels in acute phase and the parasitemia reactivation following immunosuppression, and curative rates were higher than with benznidazole. These high anti-parasitic activities encourage us to propose these compounds as promising molecules for developing an easy to synthesize anti-Chagas agent

In vitro antileishmanial activity and iron superoxide dismutase inhibition of arylamine Mannich base derivatives

Leishmaniasis is one of the world’s most neglected diseases, and it has a worldwide prevalence of 12 million. There are no effective human vaccines for its prevention, and treatment is hampered by outdated drugs. Therefore, research aiming at the development of new therapeutic tools to fight Leishmaniasis remains a crucial goal today. With this purpose in mind, we present twenty arylaminoketone derivatives with a very interesting in vitro and in vivo efficacy against Trypanosoma cruzi that have now been studied against promastigote and amastigote forms of L. infantum, L. donovani and L. braziliensis strains. Six out of the twenty Mannich base-type derivatives showed Selectivity Index between 39 and 2337 times higher in the amastigote form than the reference drug glucantime. These six derivatives affected the parasite infectivity rates; the result was lower parasite infectivity rates than glucantime tested at a IC25 dose. In addition, these derivatives were substantially more active against the three Leishmania species tested than glucantime. The mechanism of action of these compounds has been studied, showing a greater alteration in glucose catabolism and leading to greater levels of Fe-SOD (iron superoxide dismutase) inhibition. These molecules could be potential candidates for Leishmaniasis chemotherapy

Physiological lentiviral vectors for the generation of improved CAR-T cells

Anti-CD19 chimeric antigen receptor (CAR)-T cells have achieved impressive outcomes for the treatment of relapsed and refractory B-lineage neoplasms. However, important limitations still remain due to severe adverse events (i.e., cytokine release syndrome and neuroinflammation) and relapse of 40%-50% of the treated patients. Most CAR-T cells are generated using retroviral vectors with strong promoters that lead to high CAR expression levels, tonic signaling, premature exhaustion, and overstimulation, reducing efficacy and increasing side effects. Here, we show that lentiviral vectors (LVs) expressing the transgene through a WAS gene promoter (AW-LVs) closely mimic the T cell receptor (TCR)/CD3 expression kinetic upon stimulation. These AW-LVs can generate improved CAR-T cells as a consequence of their moderate and TCR-like expression profile. Compared with CAR-T cells generated with human elongation factor alpha (EF1 alpha)-driven-LVs, AW-CAR-T cells exhibited lower tonic signaling, higher proportion of naive and stem cell memory T cells, less exhausted phenotype, and milder secretion of tumor necrosis factor alpha (TNF-alpha) and interferon (IFN)-gamma after efficient destruction of CD19(+) lymphoma cells, both in vitro and in vivo. Moreover, we also showed their improved efficiency using an in vitro CD19(+) pancreatic tumor model. We finally demonstrated the feasibility of large-scale manufacturing of AW-CAR-T cells in guanosine monophosphate (GMP)-like conditions. Based on these data, we propose the use of AWLVs for the generation of improved CAR-T products

Earthworm management in tropical agroecosystems

Ecological and demographic parameters of 26 species of native and exotic earthworms species common in tropical agroecosystems, with large environmental tolerance and/or extended distribution were investigated. Principal component analysis (PCA) isolated four groups : (i) large native endogeic and anecic species (16-32 g individual fresh wt) with long generation time (2-4 years), low fecundity (0.5-3.1 cocoons/year/adult) and one hatchling per cocoon ; (ii) medium size species (1.2-6 g) endogeic mesohumic, with intermediate fecundity (1.3-45 cocoons/year/adult) ; (iii) small species (0.17-1.25 g f.w.) mainly endogeic polyhumic, with short generation time (3-7 months), intermediate fecundity (10-68 cocoons/year/adult) and one hatchling per cocoon ; and (iv) generally small (80-150 mg f.w.) species mainly exotic and epigeic, with short generation time (1-3 months), very high fecundity (50-350 cocoons/year/adult) and up to three hatchlings per cocoon. Casts may be either large globular or small granular. The selective investigations of large organic particles and small mineral particles (clays) concentrates total organic matter in the casts. There is an intense mineralization rate of nitrogen in the casts (6-29% of organic N), exotic worms seeming to be less efficient than natives at mineralizing N. The mineral phosphorus content of casts is always at least 30% higher than in the non-ingested soil. All these worms ingest daily, on average, three times their own weight of soil at the adult stage (1-9) and much more when juvenile ; up to 1000 Mg dry soil/ha may transit yearly through earthworm guts. (Résumé d'auteur

67P/C-G inner coma dust properties from 2.2 au inbound to 2.0 auoutbound to the Sun

GIADA (Grain Impact Analyzer and Dust Accumulator) on-board the Rosetta space probe is designed to measure the momentum, mass and speed of individual dust particles escaping the nucleus of comet 67P/Churyumov-Gerasimenko (hereafter 67P). From 2014 August to 2016 June, Rosetta escorted comet 67P during its journey around the Sun. Here, we focus on GIADA data taken between 2015 January and 2016 February which included 67P's perihelion passage. To better understand cometary activity and more specifically the presence of dust structures in cometary comae, we mapped the spatial distribution of dust density in 67P's coma. In this manner, we could track the evolution of high-density regions of coma dust and their connections with nucleus illumination conditions, namely tracking 67P's seasons. We also studied the link between dust particle speeds and their masses with respect to heliocentric distance, i.e. the level of cometary activity. This allowed us to derive a global and a local correlation of the dust particles' speed distribution with respect to the H2O production rate. © 2016 The Authors.Peer Reviewe

GIADA: its status after the Rosetta cruise phase and on-ground activity in support of the encounter with comet 67P/Churyumov-Gerasimenko

GIADA (Grain Impact Analyser and Dust Accumulator) on-board the Rosetta mission to comet 67P/Churyumov-Gerasimenko was designed to study the physical and dynamical properties of dust particles ejected by the comet during the encounter. In this paper we report the results of the analysis of data collected by GIADA during the past seven years of the cruise phase. During this period the GIADA detection subsystems were switched on for periodic in-flight payload checkouts to monitor their state of-health including potential changes in its performance that could affect its data collection. Only slight variations in sensitivity and dynamical range were identified that will not affect the GIADA measurement capability during the Rosetta comet encounter and rendezvous phase. The GIADA microbalance system detected the presence of low-volatility material over a period of about 169 days when the GIADA cover remained partially opened. It is highly probable that this material originated from the spacecraft itself, as a spacecraft’s outgassing was observed by the ROSINA mass spectrometer (on-board Rosetta) during the cruise phase. The identification of the low-volatility mass deposited on the microbalances as self-contamination will allow us to evaluate the mass rate background to be subtracted from the GIADA science data. These results obtained from GIADA cruise data analysis coupled with laboratory calibration data obtained from measurements using the GIADA spare model for selected cometary dust analogs will be the basis for the interpretation of the GIADA scientific data

Effectiveness of habitat management in the recovery of low-density populations of wild rabbit.

Understanding the relationship between spatial patterns of landscape attributes and population presence and abundance is essential for understanding population processes as well as supporting management and conservation strategies. This study evaluates the influence of three factors: environment, habitat management, and season on the presence and abundance of the wild rabbit (Oryctolagus cuniculus), an important prey species for Mediterranean endangered predator species. To address this issue, we estimated wild rabbit presence and abundance by latrine counting in transects located in 45 plots within a 250×250 m grid from June 2007 until June 2009 in a 1,200 ha hunting area in southern Portugal.We then analyzed how wild rabbit presence and abundance correlatewith the aforementioned factors. Our results showed that the main variable influencing wild rabbit presence and abundance was the distance to the artificial warrens. North and northeast slope directions were negatively related to wild rabbit presence. Conversely, rabbit presence was positively correlated with short distances to ecotone, artificial warrens, and spring. Regarding rabbit abundance, in addition to artificial warrens, soft soils, bushes, and season also had a positive effect. We found that environmental variables, management practices, and season each affect wild rabbit presence and abundance differently at a home range scale in low-density population. Thus, our major recommendations are reducing the distance to artificial warrens and ecotone, ideally to less than 100 m, and promoting habitat quality improvement on slopes with plenty of sun exposure