Showing papers by "Technical University of Madrid published in 2016"

The FAIR Guiding Principles for scientific data management and stewardship

Abstract: There is an urgent need to improve the infrastructure supporting the reuse of scholarly data. A diverse set of stakeholders—representing academia, industry, funding agencies, and scholarly publishers—have come together to design and jointly endorse a concise and measureable set of principles that we refer to as the FAIR Data Principles. The intent is that these may act as a guideline for those wishing to enhance the reusability of their data holdings. Distinct from peer initiatives that focus on the human scholar, the FAIR Principles put specific emphasis on enhancing the ability of machines to automatically find and use the data, in addition to supporting its reuse by individuals. This Comment is the first formal publication of the FAIR Principles, and includes the rationale behind them, and some exemplar implementations in the community.

The Gaia mission

Abstract: Gaia is a cornerstone mission in the science programme of the EuropeanSpace Agency (ESA). The spacecraft construction was approved in 2006, following a study in which the original interferometric concept was changed to a direct-imaging approach. Both the spacecraft and the payload were built by European industry. The involvement of the scientific community focusses on data processing for which the international Gaia Data Processing and Analysis Consortium (DPAC) was selected in 2007. Gaia was launched on 19 December 2013 and arrived at its operating point, the second Lagrange point of the Sun-Earth-Moon system, a few weeks later. The commissioning of the spacecraft and payload was completed on 19 July 2014. The nominal five-year mission started with four weeks of special, ecliptic-pole scanning and subsequently transferred into full-sky scanning mode. We recall the scientific goals of Gaia and give a description of the as-built spacecraft that is currently (mid-2016) being operated to achieve these goals. We pay special attention to the payload module, the performance of which is closely related to the scientific performance of the mission. We provide a summary of the commissioning activities and findings, followed by a description of the routine operational mode. We summarise scientific performance estimates on the basis of in-orbit operations. Several intermediate Gaia data releases are planned and the data can be retrieved from the Gaia Archive, which is available through the Gaia home page.

Gaia Data Release 1 Summary of the astrometric, photometric, and survey properties

Abstract: Context. At about 1000 days after the launch of Gaia we present the first Gaia data release, Gaia DR1, consisting of astrometry and photometry for over 1 billion sources brighter than magnitude 20.7. Aims: A summary of Gaia DR1 is presented along with illustrations of the scientific quality of the data, followed by a discussion of the limitations due to the preliminary nature of this release. Methods: The raw data collected by Gaia during the first 14 months of the mission have been processed by the Gaia Data Processing and Analysis Consortium (DPAC) and turned into an astrometric and photometric catalogue. Results: Gaia DR1 consists of three components: a primary astrometric data set which contains the positions, parallaxes, and mean proper motions for about 2 million of the brightest stars in common with the Hipparcos and Tycho-2 catalogues - a realisation of the Tycho-Gaia Astrometric Solution (TGAS) - and a secondary astrometric data set containing the positions for an additional 1.1 billion sources. The second component is the photometric data set, consisting of mean G-band magnitudes for all sources. The G-band light curves and the characteristics of 3000 Cepheid and RR Lyrae stars, observed at high cadence around the south ecliptic pole, form the third component. For the primary astrometric data set the typical uncertainty is about 0.3 mas for the positions and parallaxes, and about 1 mas yr-1 for the proper motions. A systematic component of 0.3 mas should be added to the parallax uncertainties. For the subset of 94 000 Hipparcos stars in the primary data set, the proper motions are much more precise at about 0.06 mas yr-1. For the secondary astrometric data set, the typical uncertainty of the positions is 10 mas. The median uncertainties on the mean G-band magnitudes range from the mmag level to0.03 mag over the magnitude range 5 to 20.7. Conclusions: Gaia DR1 is an important milestone ahead of the next Gaia data release, which will feature five-parameter astrometry for all sources. Extensive validation shows that Gaia DR1 represents a major advance in the mapping of the heavens and the availability of basic stellar data that underpin observational astrophysics. Nevertheless, the very preliminary nature of this first Gaia data release does lead to a number of important limitations to the data quality which should be carefully considered before drawing conclusions from the data.

A century of trends in adult human height

Abstract: Being taller is associated with enhanced longevity, and higher education and earnings. We reanalysed 1472 population-based studies, with measurement of height on more than 18.6 million participants to estimate mean height for people born between 1896 and 1996 in 200 countries. The largest gain in adult height over the past century has occurred in South Korean women and Iranian men, who became 20.2 cm (95% credible interval 17.5–22.7) and 16.5 cm (13.3–19.7) taller, respectively. In contrast, there was little change in adult height in some sub-Saharan African countries and in South Asia over the century of analysis. The tallest people over these 100 years are men born in the Netherlands in the last quarter of 20th century, whose average heights surpassed 182.5 cm, and the shortest were women born in Guatemala in 1896 (140.3 cm; 135.8–144.8). The height differential between the tallest and shortest populations was 19-20 cm a century ago, and has remained the same for women and increased for men a century later despite substantial changes in the ranking of countries.

AVclass : A Tool for Massive Malware Labeling

Abstract: Labeling a malicious executable as a variant of a known family is important for security applications such as triage, lineage, and for building reference datasets in turn used for evaluating malware clustering and training malware classification approaches. Oftentimes, such labeling is based on labels output by antivirus engines. While AV labels are well-known to be inconsistent, there is often no other information available for labeling, thus security analysts keep relying on them. However, current approaches for extracting family information from AV labels are manual and inaccurate. In this work, we describe AVclass, an automatic labeling tool that given the AV labels for a, potentially massive, number of samples outputs the most likely family names for each sample. AVclass implements novel automatic techniques to address 3 key challenges: normalization, removal of generic tokens, and alias detection. We have evaluated AVclass on 10 datasets comprising 8.9 M samples, larger than any dataset used by malware clustering and classification works. AVclass leverages labels from any AV engine, e.g., all 99 AV engines seen in VirusTotal, the largest engine set in the literature. AVclass’s clustering achieves F1 measures up to 93.9 on labeled datasets and clusters are labeled with fine-grained family names commonly used by the AV vendors. We release AVclass to the community.

Linked Open Vocabularies (LOV): a gateway to reusable semantic vocabularies on the Web

Abstract: One of the major barriers to the deployment of Linked Data is the difficulty that data publishers have in determining which vocabularies to use to describe the semantics of data. This system report describes Linked Open Vocabularies (LOV), a high quality catalogue of reusable vocabularies for the description of data on the Web. The LOV initiative gathers and makes visible indicators that have not been previously harvested such as the interconnections between vocabularies, version history along with past and current referent (individual or organization). LOV goes beyond existing Semantic Web vocabulary search engines and takes into consideration the value's property type, matched with a query, to improve vocabulary terms scoring. By providing an extensive range of data access methods (SPARQL endpoint, API, data dump or UI), we try to facilitate the reuse of well-documented vocabularies in the Linked Data ecosystem. We conclude that the adoption in many applications and methods of LOV shows the benefits of such a set of vocabularies and related features to aid the design and publication of data on the Web.

Med-CORDEX initiative for Mediterranean climate studies

Abstract: The Mediterranean is expected to be one of the most prominent and vulnerable climate change “hot spots” of the 21st century, and the physical mechanisms underlying this finding are still not clear. Furthermore complex interactions and feedbacks involving ocean-atmosphere-land-biogeochemical processes play a prominent role in modulating the climate and environment of the Mediterranean region on a range of spatial and temporal scales. Therefore it is critical to provide robust climate change information for use in Vulnerability/Impact/Adaptation assessment studies considering the Mediterranean as a fully coupled environmental system. The Med-CORDEX initiative aims at coordinating the Mediterranean climate modeling community towards the development of fully coupled regional climate simulations, improving all relevant components of the system, from atmosphere and ocean dynamics to land surface, hydrology and biogeochemical processes. The primary goals of Med-CORDEX are to improve understanding of past climate variability and trends, and to provide more accurate and reliable future projections, assessing in a quantitative and robust way the added value of using high resolution and coupled regional climate models. The coordination activities and the scientific outcomes of Med-CORDEX can produce an important framework to foster the development of regional earth system models in several key regions worldwide.

A fast pathway for fear in human amygdala

Abstract: A fast, subcortical pathway to the amygdala is thought to have evolved to enable rapid detection of threat. This pathway's existence is fundamental for understanding nonconscious emotional responses, but has been challenged as a result of a lack of evidence for short-latency fear-related responses in primate amygdala, including humans. We recorded human intracranial electrophysiological data and found fast amygdala responses, beginning 74-ms post-stimulus onset, to fearful, but not neutral or happy, facial expressions. These responses had considerably shorter latency than fear responses that we observed in visual cortex. Notably, fast amygdala responses were limited to low spatial frequency components of fearful faces, as predicted by magnocellular inputs to amygdala. Furthermore, fast amygdala responses were not evoked by photographs of arousing scenes, which is indicative of selective early reactivity to socially relevant visual information conveyed by fearful faces. These data therefore support the existence of a phylogenetically old subcortical pathway providing fast, but coarse, threat-related signals to human amygdala.

A non negative matrix factorization for collaborative filtering recommender systems based on a Bayesian probabilistic model

Abstract: In this paper we present a novel technique for predicting the tastes of users in recommender systems based on collaborative filtering. Our technique is based on factorizing the rating matrix into two non negative matrices whose components lie within the range 0, 1 with an understandable probabilistic meaning. Thanks to this decomposition we can accurately predict the ratings of users, find out some groups of users with the same tastes, as well as justify and understand the recommendations our technique provides.

High-Speed Railway Communications: From GSM-R to LTE-R

Abstract: High-speed railways (HSRs) improve the quality of rail services, yield greater customer satisfaction, and help to create socioeconomically balanced societies [1]. This highly efficient transport mode creates significant challenges in terms of investment, technology, industry, and environment. To handle increasing traffic, ensure passenger safety, and provide real-time multimedia information, a new communication system for HSR is required. In the last decade, public networks have been evolving from voice-centric second-generation systems, e.g., Global System for Mobile Communications (GSM) with limited capabilities, to fourth-generation (4G) broad-band systems that offer higher data rates, e.g., long-term evolution (LTE). It is thus relevant for HSR to replace the current GSM-railway (GSM-R) technology with the next-generation railway-dedicated communication system providing improved capacity and capability.

Biological Indices for Soil Quality Evaluation: Perspectives and Limitations

Abstract: Soil quality is threatened by the increase in human population and by the fact that most of the cultivable land is intensively used. The initial interest in this topic focused on defining soil quality but shifted into how to measure soil quality in the late 1990s. There is a general agreement that soil biochemical, microbiological and biological properties are more suitable than physical and/or chemical properties for the purpose of estimating alterations in soil quality and hence soil degradation. To date, most studies have used microbial biomass, soil respiration and enzymatic activities to obtain soil quality indices, whereas less focus has been given to soil fauna (microarthropods and nematodes). This article aims to do a critical review of soil quality indices based on soil biological and biochemical activities, mainly microbial biomass, soil respiration and the activity of several enzymes. Limitations within the database of articles that are focussed on broad scale application of soil quality indices include the difficulty of selecting the highest quality soils for comparison purposes, lack of standardisation of analytical methods, and inclusion of an insufficient number of soil types and ecosystems. There is a need to validate soil quality indices, both, spatially and temporally and to explore the use of indices that integrate faunal and microbial measurements

Unlocking the bacterial and fungal communities assemblages of sugarcane microbiome.

Abstract: Plant microbiome and its manipulation herald a new era for plant biotechnology with the potential to benefit sustainable crop production. However, studies evaluating the diversity, structure and impact of the microbiota in economic important crops are still rare. Here we describe a comprehensive inventory of the structure and assemblage of the bacterial and fungal communities associated with sugarcane. Our analysis identified 23,811 bacterial OTUs and an unexpected 11,727 fungal OTUs inhabiting the endophytic and exophytic compartments of roots, shoots, and leaves. These communities originate primarily from native soil around plants and colonize plant organs in distinct patterns. The sample type is the primary driver of fungal community assemblage, and the organ compartment plays a major role in bacterial community assemblage. We identified core bacterial and fungal communities composed of less than 20% of the total microbial richness but accounting for over 90% of the total microbial relative abundance. The roots showed 89 core bacterial families, 19 of which accounted for 44% of the total relative abundance. Stalks are dominated by groups of yeasts that represent over 12% of total relative abundance. The core microbiome described here comprise groups whose biological role underlies important traits in plant growth and fermentative processes.

Population structure in the model grass Brachypodium distachyon is highly correlated with flowering differences across broad geographic areas

Abstract: The small, annual grass (L.) Beauv., a close relative of wheat ( L.) and barley ( L.), is a powerful model system for cereals and bioenergy grasses. Genome-wide association studies (GWAS) of natural variation can elucidate the genetic basis of complex traits but have been so far limited in by the lack of large numbers of well-characterized and sufficiently diverse accessions. Here, we report on genotyping-by-sequencing (GBS) of 84 , seven , and three accessions with diverse geographic origins including Albania, Armenia, Georgia, Italy, Spain, and Turkey. Over 90,000 high-quality single-nucleotide polymorphisms (SNPs) distributed across the Bd21 reference genome were identified. Our results confirm the hybrid nature of the genome, which appears as a mosaic of -like and -like sequences. Analysis of more than 50,000 SNPs for the accessions revealed three distinct, genetically defined populations. Surprisingly, these genomic profiles are associated with differences in flowering time rather than with broad geographic origin. High levels of differentiation in loci associated with floral development support the differences in flowering phenology between populations. Genome-wide association studies combining genotypic and phenotypic data also suggest the presence of one or more photoperiodism, circadian clock, and vernalization genes in loci associated with flowering time variation within populations. Our characterization elucidates genes underlying population differences, expands the germplasm resources available for , and illustrates the feasibility and limitations of GWAS in this model grass.

Survival trade-offs in plant roots during colonization by closely related beneficial and pathogenic fungi

Abstract: The sessile nature of plants forced them to evolve mechanisms to prioritize their responses to simultaneous stresses, including colonization by microbes or nutrient starvation. Here, we compare the genomes of a beneficial root endophyte, Colletotrichum tofieldiae and its pathogenic relative C. incanum, and examine the transcriptomes of both fungi and their plant host Arabidopsis during phosphate starvation. Although the two species diverged only 8.8 million years ago and have similar gene arsenals, we identify genomic signatures indicative of an evolutionary transition from pathogenic to beneficial lifestyles, including a narrowed repertoire of secreted effector proteins, expanded families of chitin-binding and secondary metabolism-related proteins, and limited activation of pathogenicity-related genes in planta. We show that beneficial responses are prioritized in C. tofieldiae-colonized roots under phosphate-deficient conditions, whereas defense responses are activated under phosphate-sufficient conditions. These immune responses are retained in phosphate-starved roots colonized by pathogenic C. incanum, illustrating the ability of plants to maximize survival in response to conflicting stresses.

A multi-scale hierarchical framework for developing understanding of river behaviour to support river management

Abstract: This paper introduces this special issue of Aquatic Sciences. It outlines a multi-scale, hierarchical framework for developing process-based understanding of catchment to reach hydromorphology that can aid design and delivery of sustainable river management solutions. The framework was developed within the REFORM (REstoring rivers FOR effective catchment Management) project, funded by the European Union’s FP7 Programme. Specific aspects of this ‘REFORM framework’ and some applications are presented in other papers in this special issue. The REFORM framework is founded on previous hierarchical frameworks, sixteen examples of which are reviewed. However, the REFORM framework has some particular properties that reflect the European context for which it was developed. The framework delineates regional landscapes into nested spatial units at catchment, landscape unit, segment, reach, geomorphic unit and finer scales. Reaches, regardless of their ‘naturalness’, are assigned to a river type based on valley confinement, planform and bed material. Indicators are quantified at each spatial scale to feed three groups of assessments. First, contemporary indicators at reach and geomorphic unit scales investigate present processes, forms and human pressures within each reach. These feed assessments of present reach hydromorphological function/alteration, including whether the reach is functioning appropriately for its type; riparian corridor function and alteration; and hydromorphological adjustment. Second, indicators at catchment to segment scales investigate water and sediment production and delivery to reaches and how these are affected by human pressures now and in the past. These are used to construct an inventory of changes over space and time. Third, historical reach and geomorphic unit scale indicators are used to construct the trajectory of reach-scale changes. Contemporary reach-scale assessments, space–time inventory, and trajectory of changes are then combined to establish how river reaches of different type, subject to different human pressures, and located in different environmental contexts behave in response to changes at all considered spatial scales. These support forecasts of the likely responses of reaches to future scenarios (e.g., changes in climate, land cover, channel interventions).

Characterization of the structure, dynamics, and productivity of mixed-species stands: review and perspectives

Abstract: The growth and yield of mixed-species stands has become an important topic of research since there are certain advantages of this type of forest as regards functions and services. However, the concepts and methods used to characterize mixed stands need to be understood, as well as harmonized and standardized. In this review we have compiled a set of measures, indices, and methods at stand level to characterize the structure, dynamics, and productivity of mixed stands, and we discuss the pros and cons of their application in growth and yield studies. Parameters for the characterization of mixed stand structure such as stand density, species composition, horizontal (intermingling) and vertical tree distribution pattern, tree size distribution, and age composition are described, detailing the potential as well as the constraints of these parameters for understanding resource capture, use, and efficiency in mixed stands. Furthermore, a set of stand-level parameters was evaluated to characterize the dynamics of mixed stands, e.g. height growth and space partitioning, self- and alien-thinning, and growth partitioning among trees. The deviations and changes in the behaviour of the analysed parameters in comparison with pure stand conditions due to inter-specific interactions are of particular interest. As regards stand productivity, we reviewed site productivity indices, the growth–density relationship in mixed stands as well as methods to compare productivity in mixed versus monospecific stands. Finally, we discuss the main problems associated with the methodology such as up-scaling from tree to stand level as well as the relevance of standardized measures and methods for improving forest growth and yield research in mixed stands. The main challenges are also outlined, especially the need for qualitatively sound data.

A Survey on Underwater Acoustic Sensor Network Routing Protocols

Abstract: Underwater acoustic sensor networks (UASNs) have become more and more important in ocean exploration applications, such as ocean monitoring, pollution detection, ocean resource management, underwater device maintenance, etc. In underwater acoustic sensor networks, since the routing protocol guarantees reliable and effective data transmission from the source node to the destination node, routing protocol design is an attractive topic for researchers. There are many routing algorithms have been proposed in recent years. To present the current state of development of UASN routing protocols, we review herein the UASN routing protocol designs reported in recent years. In this paper, all the routing protocols have been classified into different groups according to their characteristics and routing algorithms, such as the non-cross-layer design routing protocol, the traditional cross-layer design routing protocol, and the intelligent algorithm based routing protocol. This is also the first paper that introduces intelligent algorithm-based UASN routing protocols. In addition, in this paper, we investigate the development trends of UASN routing protocols, which can provide researchers with clear and direct insights for further research.

Cuticle Structure in Relation to Chemical Composition: Re-assessing the Prevailing Model

Abstract: The surface of most aerial plant organs is covered with a cuticle that provides protection against multiple stress factors including dehydration. Interest on the nature of this external layer dates back to the beginning of the 19th century and since then, several studies facilitated a better understanding of cuticular chemical composition and structure. The prevailing undertanding of the cuticle as a lipidic, hydrophobic layer which is independent from the epidermal cell wall underneath stems from the concept developed by Brongniart and von Mohl during the first half of the 19th century. Such early investigations on plant cuticles attempted to link chemical composition and structure with the existing technologies, and have not been directly challenged for decades. Beginning with a historical overview about the development of cuticular studies, this review is aimed at critically assessing the information available on cuticle chemical composition and structure, considering studies performed with cuticles and isolated cuticular chemical components. The concept of the cuticle as a lipid layer independent from the cell wall is subsequently challenged, based on the existing literature, and on new findings pointing towards the cell wall nature of this layer, also providing examples of different leaf cuticle structures. Finally, the need for a re-assessment of the chemical and structural nature of the plant cuticle is highlighted, considering its cell wall nature and variability among organs, species, developmental stages, and biotic and abiotic factors during plant growth.

Unique membrane properties and enhanced signal processing in human neocortical neurons

Abstract: The advanced cognitive capabilities of the human brain are often attributed to our recently evolved neocortex. However, it is not known whether the basic building blocks of the human neocortex, the pyramidal neurons, possess unique biophysical properties that might impact on cortical computations. Here we show that layer 2/3 pyramidal neurons from human temporal cortex (HL2/3 PCs) have a specific membrane capacitance (Cm) of ~0.5 µF/cm2, half of the commonly accepted 'universal' value (~1 µF/cm2) for biological membranes. This finding was predicted by fitting in vitro voltage transients to theoretical transients then validated by direct measurement of Cm in nucleated patch experiments. Models of 3D reconstructed HL2/3 PCs demonstrated that such low Cm value significantly enhances both synaptic charge-transfer from dendrites to soma and spike propagation along the axon. This is the first demonstration that human cortical neurons have distinctive membrane properties, suggesting important implications for signal processing in human neocortex.

Hydrology needed to manage droughts: the 2015 European case

Abstract: It is generally accepted that drought is one of the most costly weather-related natural hazards. In 2015, a long-lasting drought hit Europe, particularly affecting central and eastern Europe. In some regions it was the driest (North Slovakia) and in others (Czech Republic and Poland) it was the second driest summer of the last 50 years (following 2003). Key questions are: (i) how extreme are these events, not only in terms of hydro-meteorological characteristics but also impacts? and (ii) how are these impacts managed?

From massive access to cooperation: lessons learned and proven results of a hybrid xMOOC/cMOOC pedagogical approach to MOOCs

Abstract: The low completion rate for Massive Open Online Courses (MOOCs), averaging 10 % across total enrolment, highlights a need for close analysis of the underlying formative model. The methodology used here involves cooperation among MOOC participants to introduce new resources through social networks and the integration of these resources with previous teacher materials. The paper describes two MOOCs on distinct topics using this methodology and implemented on the same platform. The observed outcomes indicate increased completion rates for both courses as compared with other MOOCs developed on the same platform. Additionally, although participants in the two MOOCs differed in profile and personal goals, they reported similar perceptions of the quality of the learning experience, which was influenced by the knowledge management approach developed in the proposed methodology.

A Conceptual Model of Vegetation–hydrogeomorphology Interactions Within River Corridors

Abstract: This is the peer reviewed version of the following article: M. GURNELL, D. CORENBLITc, D. GARCIA DE JALON, M. GONZALEZ DEL TANAGO, R. C. GRABOWSKI, M. T. O’HARE, M. SZEWCZYK (2015) A conceptual model of vegetationhydrogeomorphology interactions within river corridors. River Research and Applications (early view), which has been published in final form at 10.1002/rra.2928. This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Self-Archiving.