A Semantic-Based Approach to Attain Reproducibility of Computational Environments in Scientic Work ows: A Case Study

Reproducible research in scientic work ows is often addressed by tracking the provenance of the produced results. While this approach allows inspecting intermediate and nal results, improves understanding, and permits replaying a work ow execution, it does not ensure that the computational environment is available for subsequent executions to reproduce the experiment. In this work, we propose describing the resources involved in the execution of an experiment using a set of semantic vocabularies, so as to conserve the computational environment. We dene a process for documenting the work ow application, management system, and their dependencies based on 4 domain ontologies. We then conduct an experimental evaluation sing a real work ow application on an academic and a public Cloud platform. Results show that our approach can reproduce an equivalent execution environment of a predened virtual machine image on both computing platforms

Synaptotagmin-1 membrane binding is driven by the C2B domain and assisted cooperatively by the C2A domain

Synaptotagmin interaction with anionic lipid (phosphatidylserine/phosphatidylinositol) containing membranes, both in the absence and presence of calcium ions (Ca2+), is critical to its central role in orchestrating neurotransmitter release. The molecular surfaces involved, namely the conserved polylysine motif in the C2B domain and Ca2+-binding aliphatic loops on both C2A and C2B domains, are known. Here we use surface force apparatus combined with systematic mutational analysis of the functional surfaces to directly measure Syt1-membrane interaction and fully map the site-binding energetics of Syt1 both in the absence and presence of Ca2+. By correlating energetics data with the molecular rearrangements measured during confinement, we find that both C2 domains cooperate in membrane binding, with the C2B domain functioning as the main energetic driver, and the C2A domain acting as a facilitator.Fil: Gruget, Clémence. Ecole Normale Supérieure; FranciaFil: Bello, Oscar Daniel. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mendoza. Instituto de Histología y Embriología de Mendoza Dr. Mario H. Burgos. Universidad Nacional de Cuyo. Facultad de Ciencias Médicas. Instituto de Histología y Embriología de Mendoza Dr. Mario H. Burgos; ArgentinaFil: Coleman, Jeff. University of Yale. School of Medicine; Estados UnidosFil: Krishnakumar, Shyam S.. University of Yale. School of Medicine; Estados UnidosFil: Perez, Eric. Ecole Normale Supérieure; FranciaFil: Rothman, James E.. University of Yale. School of Medicine; Estados UnidosFil: Pincet, Frederic. Ecole Normale Supérieure; Francia. University of Yale. School of Medicine; Estados UnidosFil: Donaldson, Stephen H.. Ecole Normale Supérieure; Franci

Magnetic and elastic anisotropy in magnetorheological elastomers using nickel-based nanoparticles and nanochains

Nickel (Ni) based nanoparticles and nanochains were incorporated as fillers in polydimethylsiloxane (PDMS) elastomers and then these mixtures were thermally cured in the presence of a uniform magnetic field. In this way, macroscopically structured-anisotropic PDMS-Ni based magnetorheological composites were obtained with the formation of pseudo-chains-like structures (referred as needles) oriented in the direction of the applied magnetic field when curing. Nanoparticles were synthesized at room temperature, under air ambient atmosphere (open air, atmospheric pressure) and then calcined at 400 °C (in air atmosphere also). The size distribution was obtained by fitting SAXS experiments with a polydisperse hard spheres model and a Schulz-Zimm distribution, obtaining a size distribution centered at (10.0 - 0.6) nm with polydispersivity given by sigma= (8.0 ± 0.2) nm. The SAXS, XRD and TEM experiments are consistent with single crystal nanoparticles of spherical shape (average particle diameter obtained by TEM: (12 ± 1) nm). Nickel-based nanochains (average diameter: 360 nm; average length: 3 mm, obtained by SEM; aspect ratio=length/diameter ~10) were obtained at 85 ºC and ambient atmosphere (open air, atmospheric pressure). The magnetic properties of Ni-based nanoparticles and nanochains at room temperature are compared and discussed in terms of surface and size effects. Both Ni-based nanoparticles and nanochains were used as fillers for obtaining the PDMS structured magnetorheological composites, observing the presence of oriented needles. Magnetization curves, ferromagnetic resonance spectra (FMR) and strain-stress curves of low filler´s loading composites (2% w/w of fillers) were determined as functions of the relative orientation respect to the needles. The results indicate that even at low loadings it is possible to obtain magnetorheological composites with anisotropic properties, with larger anisotropy when using nanochains. For instance, the magnetic remanence, the FMR-resonance field and the elastic response to compression are higher when measured parallel to the needles (about 30% with nanochains as fillers). Analogously, the elastic response is also anisotropic, with larger anisotropy when using nanochains as fillers. Therefore, all experiments performed confirm the high potential of nickel nanochains to induce anisotropic effects in magnetorheological materials.Fil: Landa, Romina Ailín. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinacion Administrativa Ciudad Universitaria. Instituto de Química Física de los Materiales del Medioambiente y Energía; Argentina;Fil: P Soledad Antonel. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinacion Administrativa Ciudad Universitaria. Instituto de Química Física de los Materiales del Medioambiente y Energía; Argentina;Fil: Mariano M. Ruiz. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinacion Administrativa Ciudad Universitaria. Instituto de Química Física de los Materiales del Medioambiente y Energía; Argentina;Fil: Oscar E Pérez. Universidad de Buenos Aires. Facultad de Cs.exactas y Naturales. Departamento de Industrias;Fil: Alejandro Butera. Comisión Nacional de Energía Atómica;Fil: Guillermo Jorge. Universidad Nacional de General Sarmiento;Fil: Cristiano L. P. Oliveira. Instituto de Física, Universidade De São Paulo; Brasil;Fil: Martín Negri. Universidad de Buenos Aires. Facultad de Cs.exactas y Naturales. Departamento de Industrias

Augmented Reticular Thalamic Bursting and Seizures in Scn1a-Dravet Syndrome

Loss of function in the Scn1a gene leads to a severe epileptic encephalopathy called Dravet syndrome (DS). Reduced excitability in cortical inhibitory neurons is thought to be the major cause of DS seizures. Here, in contrast, we show enhanced excitability in thalamic inhibitory neurons that promotes the non-convulsive seizures that are a prominent yet poorly understood feature of DS. In a mouse model of DS with a loss of function in Scn1a, reticular thalamic cells exhibited abnormally long bursts of firing caused by the downregulation of calcium-activated potassium SK channels. Our study supports a mechanism in which loss of SK activity causes the reticular thalamic neurons to become hyperexcitable and promote non-convulsive seizures in DS. We propose that reduced excitability of inhibitory neurons is not global in DS and that non-GABAergic mechanisms such as SK channels may be important targets for treatment

Carbon Aerogel-Supported Nickel and Iron for Gasification Gas Cleaning. Part I: Ammonia Adsorption

Biomass gasification is a promising way to obtain green energy, but the gas composition makes it unsuitable for use in traditional technologies (i.e., IC engine). Gas purification over nickel and/or iron catalysts is an attractive alternative. Cellulose-based carbon aerogels (CAGs) have shown suitable physical chemical properties for use as catalyst supports. In this work, nickel and iron catalysts are supported on CAG made from cellulose microfibers. Microfibers were impregnated with (NH4)(2)SO4 to increase the mass yield. Carbonization was evaluated at different heating rates, maximum temperatures, and dwell times to generate CAGs. Resulting chars were characterized by N-2 adsorption, X-ray diffraction (XRD), and Raman spectroscopy. The CAG with better properties (specific surface, pore size, thermal resistance) was impregnated with the metal precursor salt via incipient wetness and treated with H-2. Catalysts were characterized by transmission electron microscopy (TEM), XRD, N-2 adsorption, and inductively coupled plasma optical emission spectrometry (ICP-OES). Ammonia adsorption was studied over CAG and catalysts to estimate the thermodynamic parameters. The impregnation with ((NH4)(2)SO4 improves thermal resistance of the char obtained from carbonization. The catalysts exhibit higher adsorption capacity than CAG (without metal), indicating chemical interaction between ammonia and metals. The metal-ammonia interaction is stronger on Fe than on Ni catalyst, which is consistent with reported theoretical calculations

Assessment of stress and nutritional biomarkers in cultured Octopus vulgaris paralarvae: Effects of geographical origin and dietary regime

The common octopus (Octopus vulgaris) is a promising species for aquaculture diversification, but massive mortality during the first life-cycle stages (paralarvae) is the main bottleneck for its commercial production in captivity. The aim of this study was to assess stress and nutritional condition biomarkers (HSP70, ROS enzymes and lipid peroxidation) (RNA/DNA, RNA/protein, protein/DNA and protein) inO.vulgarisparalarvae from different geographical origins and fed withArtemiaenriched with marine phospholipids or microalgae (control group). To this end paralarvae were cultured for 30days, in three different centres in Spain (Tarragona-Mediterranean area, Tenerife-Central Atlantic area and Vigo-North Atlantic area), under the same protocol, and fed onArtemiaenriched with marine phospholipids (LC60) (Marine Lecithin LC 60®, PhosphoTech Laboratoires) or microalgae (control group). Dry weight and most biomarkers analysed in hatchlings showed significant differences related to their origin (centre). Fifteen day old paralarvae presented significant differences in specific growth rate (SGR) associated with their dietary regime, and also showed differences in biomarkers associated both with their geographical origin and dietary regime. The results suggest that the SGR of paralarvae were positively influenced by LC60, promoting growth and in agreement with the results of nutritional condition biomarkers (nucleic acids ratios). The antioxidant defences against oxidative damage were also boosted in the LC60 paralarvae group, possibly as a result of the elevated content in highly polyunsaturated fatty acids. In addition, the partial correlations found between biomarkers varied according to diet. However, no positive effect of LC60 on survival was observed. The high variability found among geographical origins, despite the use of the same rearing protocol, highlights the need to clarify the sources of such variability

Piezo and magneto resistance of magnetically oriented dispersions of magnetic particles covered with silver in bulk and screen-printed elastomer polymers

1) Synthesis and characterization of oxide@Ag particles that are simultaneously magnetic and conductive 2) Elaboration of composites: dispersion of particles in organic matrix: silicone (PDMS) or thermoplastic (ethylcellulose + wax) 3) Screen printing of composite paste on alumina substrate 4) Curing under controllable and orientable magnetic field Composite materials with a thermoplastic matrix may be re-melted an aligned again

Phase behaviour of Ag2CrO4 under compression: Structural, vibrational, and optical properties

This document is the Accepted Manuscript version of a Published Work that appeared in final form in Journal of Physical Chemistry C, copyright © American Chemical Society after peer review and technical editing by the publisher. To access the final edited and published work see http://dx.doi.org/10.1021/jp401524sWe have performed an experimental study of the crystal structure, lattice dynamics, and optical properties of silver chromate (Ag2CrO4) at ambient temperature and high pressures. In particular, the crystal structure, Raman-active phonons, and electronic band gap have been accurately determined. When the initial orthorhombic Pnma Ag2CrO4 structure (phase I) is compressed up to 4.5 GPa, a previously undetected phase (phase II) has been observed with a 0.95% volume collapse. The structure of phase II can be indexed to a similar orthorhombic cell as phase I, and the transition can be considered to be an isostructural transition. This collapse is mainly due to the drastic contraction of the a axis (1.3%). A second phase transition to phase III occurs at 13 GPa to a structure not yet determined. First-principles calculations have been unable to reproduce the isostructural phase transition, but they propose the stabilization of a spinel-type structure at 11 GPa. This phase is not detected in experiments probably because of the presence of kinetic barriers. Experiments and calculations therefore seem to indicate that a new structural and electronic description is required to model the properties of silver chromate.This study was supported by the Spanish government MEC under grants MAT2010-21270-C04-01/03/04 and CTQ2009-14596-C02-01, by the Comunidad de Madrid and European Social Fund (S2009/PPQ1551 4161893), by the MALTA Consolider Ingenio 2010 project (CSD2007-00045), and by the Vicerrectorado de Investigacion y Desarrollo of the Universidad Politecnica de Valencia (UPV2011-0914 PAID-05-11 and UPV2011-0966 PAID-06-11). A.M. and P.R.-H. acknowledge computing time provided by Red Espanola de Supercomputacion (RES) and MALTA-Cluster. J.A.S. acknowledges Juan de la Cierva Fellowship Program for its financial support. Diamond and ALBA Synchrotron Light Sources are acknowledged for provisions of beam time. We also thank Drs. Peral, Popescu, and Fauth for technical support.Santamaría Pérez, D.; Bandiello, E.; Errandonea, D.; Ruiz-Fuertes, J.; Gomis Hilario, O.; Sans, JÁ.; Manjón Herrera, FJ.... (2013). Phase behaviour of Ag2CrO4 under compression: Structural, vibrational, and optical properties. Journal of Physical Chemistry C. 117(23):12239-12248. https://doi.org/10.1021/jp401524sS12239122481172