Les set vides del paper: formats de presentació i models de distribució en línia dels treballs publicats en revistes científiques digitals

Study of the publication models and the means of accessing scientific literature in the current environment of digital communication and the web. The text introduces the concept of journal article as a well-defined and stable unit within the publishing world, and as a nucleus on which professional and scholarly communication has been based since its beginnings in the 17th century. The transformation of scientific communication that the digital world has enabled is analysed. Descriptions are provided of some of the practices undertaken by authors, research organisations, publishers and library-related institutions as a response to the new possibilities being unveiled for articles, both as products as well as for their creation and distribution processes. These transformations affect the very nature of articles as a minimal unit -both unique and stable- of scientific communication. The article concludes by noting that under varying documentary forms of publisher aggregation and bibliographic control -sometimes simultaneously and, even, apparently contradictory- there flourishes a more pluralistic type of scientific communication. This pluralism offers: more possibilities for communication among authors; fewer levels of intermediaries such as agents that intervene and provide added value to the products; greater availability for users both economically speaking and from the point of view of access; and greater interaction and wealth of contents, thanks to the new hypertext and multimedia possibilities.

Semiclassical image potential at a solid surface

A surface dielectric function of a semi-infinite plane-bounded metal is defined in the spirit of the plasmon-pole dielectric function of the bulk. It is modeled in such a way that the surface-plasmon dispersion relation is recovered for small momentum transfer. This function is employed to compute the image potential at all distances outside the surface. Interaction with bulk modes is neglected for simplicity and clarity. The interaction of a massive point charge with a metal surface is also considered in the context of a boson model for surface-plasmon excitation. We present a new definition of the image potential for this case.

Formation and distribution of point defects on a disclination line near a free nematic interface

Point defects of opposite signs can alternately nucleate on the -1/2 disclination line that forms near the free surface of a confined nematic liquid crystal. We show the existence of metastable configurations consisting of periodic repetitions of such defects. These configurations are characterized by a minimal interdefect spacing that is seen to depend on sample thickness and on an applied electric field. The time evolution of the defect distribution suggests that the defects attract at small distances and repel at large distances.

Ground- and excited-state properties of M-center oxygen vacancy aggregates in the bulk and the surface of MgO

Aggregates of oxygen vacancies (F centers) represent a particular form of point defects in ionic crystals. In this study we have considered the combination of two oxygen vacancies, the M center, in the bulk and on the surface of MgO by means of cluster model calculations. Both neutral and charged forms of the defect M and M+ have been taken into account. The ground state of the M center is characterized by the presence of two doubly occupied impurity levels in the gap of the material; in M+ centers the highest level is singly occupied. For the ground-state properties we used a gradient corrected density functional theory approach. The dipole-allowed singlet-to-singlet and doublet-to-doublet electronic transitions have been determined by means of explicitly correlated multireference second-order perturbation theory calculations. These have been compared with optical transitions determined with the time-dependent density functional theory formalism. The results show that bulk M and M+ centers give rise to intense absorptions at about 4.4 and 4.0 eV, respectively. Another less intense transition at 1.3 eV has also been found for the M+ center. On the surface the transitions occur at 1.6 eV (M+) and 2 eV (M). The results are compared with recently reported electron energy loss spectroscopy spectra on MgO thin films.

GSVA: gene set variation analysis for microarray and RNA-seq data

Gene set enrichment (GSE) analysis is a popular framework for condensing information from gene expression profiles into a pathway or signature summary. The strengths of this approach over single gene analysis include noise and dimension reduction, as well as greater biological interpretability. As molecular profiling experiments move beyond simple case-control studies, robust and flexible GSE methodologies are needed that can model pathway activity within highly heterogeneous data sets. To address this challenge, we introduce Gene Set Variation Analysis (GSVA), a GSE method that estimates variation of pathway activity over a sample population in an unsupervised manner. We demonstrate the robustness of GSVA in a comparison with current state of the art sample-wise enrichment methods. Further, we provide examples of its utility in differential pathway activity and survival analysis. Lastly, we show how GSVA works analogously with data from both microarray and RNA-seq experiments. GSVA provides increased power to detect subtle pathway activity changes over a sample population in comparison to corresponding methods. While GSE methods are generally regarded as end points of a bioinformatic analysis, GSVA constitutes a starting point to build pathway-centric models of biology. Moreover, GSVA contributes to the current need of GSE methods for RNA-seq data. GSVA is an open source software package for R which forms part of the Bioconductor project and can be downloaded at http://www.bioconductor.org.

Surface-enhanced laser desorption/ionisation time-of-flight mass spectrometry: A tool to predict pork quality

Expression of water soluble proteins of fresh pork Longissimus thoracis from 4 pure breed pigs (Duroc, Large White, Landrace, and Piétrain) was studied to identify candidate protein markers for meat quality. Surface-enhanced laser desorption/ionisation time-of-flight mass spectrometry (SELDI-TOF-MS) was used to obtain the soluble protein profiles of Longissimus thoracis muscles. The pure breeds showed differences among the studied meat quality traits (pHu, drip loss, androstenone, marbling, intramuscular fat, texture, and moisture), but no significant differences were detected in sensory analysis. Associations between protein peaks obtained with SELDI-TOF-MS and meat quality traits, mainly water holding capacity, texture and skatole were observed. Of these peaks, a total of 10 peaks from CM10 array and 6 peaks from Q10 array were candidate soluble protein markers for pork loin quality. The developed models explained a limited proportion of the variability, however they point out interesting relationships between protein expression and meat quality

Real-time tree-foliage surface estimation using a ground laser scanner

The optimization of most pesticide and fertilizer applications is based on overall grove conditions. In this work we measurements. Recently, Wei [9, 10] used a terrestrial propose a measurement system based on a ground laser scanner to LIDAR to measure tree height, width and volume developing estimate the volume of the trees and then extrapolate their foliage a set of experiments to evaluate the repeatability and surface in real-time. Tests with pear trees demonstrated that the accuracy of the measurements, obtaining a coefficient of relation between the volume and the foliage can be interpreted as variation of 5.4% and a relative error of 4.4% in the linear with a coefficient of correlation (R) of 0.81 and the foliar estimation of the volume but without real-time capabilities. surface can be estimated with an average error less than 5 %.

Characterisation of the LMS200 laser beam under the influence of blockage surfaces. Influence on 3D scanning of tree orchards

The geometric characterisation of tree orchards is a high-precision activity comprising the accurate measurement and knowledge of the geometry and structure of the trees. Different types of sensors can be used to perform this characterisation. In this work a terrestrial LIDAR sensor (SICK LMS200) whose emission source was a 905-nm pulsed laser diode was used. Given the known dimensions of the laser beam cross-section (with diameters ranging from 12 mm at the point of emission to 47.2 mm at a distance of 8 m), and the known dimensions of the elements that make up the crops under study (flowers, leaves, fruits, branches, trunks), it was anticipated that, for much of the time, the laser beam would only partially hit a foreground target/object, with the consequent problem of mixed pixels or edge effects. Understanding what happens in such situations was the principal objective of this work. With this in mind, a series of tests were set up to determine the geometry of the emitted beam and to determine the response of the sensor to different beam blockage scenarios. The main conclusions that were drawn from the results obtained were: (i) in a partial beam blockage scenario, the distance value given by the sensor depends more on the blocked radiant power than on the blocked surface area; (ii) there is an area that influences the measurements obtained that is dependent on the percentage of blockage and which ranges from 1.5 to 2.5 m with respect to the foreground target/object. If the laser beam impacts on a second target/object located within this range, this will affect the measurement given by the sensor. To interpret the information obtained from the point clouds provided by the LIDAR sensors, such as the volume occupied and the enclosing area, it is necessary to know the resolution and the process for obtaining this mesh of points and also to be aware of the problem associated with mixed pixels.

Tailoring the surface density of silicon nanocrystals embedded in SiOx single layers

In this article, we explore the possibility of modifying the silicon nanocrystal areal density in SiOx single layers, while keeping constant their size. For this purpose, a set of SiOx monolayers with controlled thickness between two thick SiO2 layers has been fabricated, for four different compositions (x=1, 1.25, 1.5, or 1.75). The structural properties of the SiO x single layers have been analyzed by transmission electron microscopy (TEM) in planar view geometry. Energy-filtered TEM images revealed an almost constant Si-cluster size and a slight increase in the cluster areal density as the silicon content increases in the layers, while high resolution TEM images show that the size of the Si crystalline precipitates largely decreases as the SiO x stoichiometry approaches that of SiO2. The crystalline fraction was evaluated by combining the results from both techniques, finding a crystallinity reduction from 75% to 40%, for x = 1 and 1.75, respectively. Complementary photoluminescence measurements corroborate the precipitation of Si-nanocrystals with excellent emission properties for layers with the largest amount of excess silicon. The integrated emission from the nanoaggregates perfectly scales with their crystalline state, with no detectable emission for crystalline fractions below 40%. The combination of the structural and luminescence observations suggests that small Si precipitates are submitted to a higher compressive local stress applied by the SiO2 matrix that could inhibit the phase separation and, in turn, promotes the creation of nonradiative paths.

Response of the Thermal Conductivity as a Function of Water Content of a Burnt Mediterranean Loam Soil

The purpose of this research is to explore the variability on the soil thermal conductivity -λ- after a prescribe fire, and to assess the effects of the ashes on the heat transfer once it"s were incorporated into the soil matrix. Sampling plot was located in the Montgrí Massif (NE of Spain). A set of 42 soil samples between surface and 5 cm depth was collected before and after the fire. To characterize the soil chemical and physical variables were analyzed. To determine the vari-ability on the soil λ a dry-out curve per scenario (before and after fire) was determined. SoilRho® method based on ASTM D-5334-08 which was validated by LabFerrer was used. Soil thermal conductivity has shown changes in their values. Indeed, in all moisture scenarios the values of soil λ decreased after soil was burnt. The critical point in the rela-tionship ϴ (λ) for the soil after fire which always was stronger than soil before to be burnt. Soil with"white" ashes showed a high thermal conductivity. An X-Ray diffractometry analysis allowed to clarify and to verify these results. To sum up, we could say that thermal conductivity presents changes when the scenario changes, i.e. before and after to be burnt. On the other hand, the volume of ashes incorporated on the soil increased the differences between no burnt and burnt soil, showing even some improvements on the heat transfer when water content started to govern the process.

Molecular dynamics simulation of the spherical electrical double layer of a soft nanoparticle. Effect of the surface and counterion valence

Molecular dynamics simulations were performed to study the ion and water distribution around a spherical charged nanoparticle. A soft nanoparticle model was designed using a set of hydrophobic interaction sites distributed in six concentric spherical layers. In order to simulate the effect of charged functionalyzed groups on the nanoparticle surface, a set of charged sites were distributed in the outer layer. Four charged nanoparticle models, from a surface charge value of −0.035 Cm−2 to − 0.28 Cm−2, were studied in NaCl and CaCl2 salt solutions at 1 M and 0.1 M concentrations to evaluate the effect of the surface charge, counterion valence, and concentration of added salt. We obtain that Na + and Ca2 + ions enter inside the soft nanoparticle. Monovalent ions are more accumulated inside the nanoparticle surface, whereas divalent ions are more accumulated just in the plane of the nanoparticle surface sites. The increasing of the the salt concentration has little effect on the internalization of counterions, but significantly reduces the number of water molecules that enter inside the nanoparticle. The manner of distributing the surface charge in the nanoparticle (uniformly over all surface sites or discretely over a limited set of randomly selected sites) considerably affects the distribution of counterions in the proximities of the nanoparticle surface.

Effect of the surface charge discretization on electric double layers. A Monte Carlo simulation study

The structure of the electric double layer in contact with discrete and continuously charged planar surfaces is studied within the framework of the primitive model through Monte Carlo simulations. Three different discretization models are considered together with the case of uniform distribution. The effect of discreteness is analyzed in terms of charge density profiles. For point surface groups,a complete equivalence with the situation of uniformly distributed charge is found if profiles are exclusively analyzed as a function of the distance to the charged surface. However, some differences are observed moving parallel to the surface. Significant discrepancies with approaches that do not account for discreteness are reported if charge sites of finite size placed on the surface are considered.