Showing papers by "Spanish National Research Council published in 2007"
TL;DR: Whether phylogenetic reconstruction improves after alignment cleaning or not is examined and cleaned alignments produce better topologies although, paradoxically, with lower bootstrap, which indicates that divergent and problematic alignment regions may lead, when present, to apparently better supported although, in fact, more biased topologies.
Abstract: Alignment quality may have as much impact on phylogenetic reconstruction as the phylogenetic methods used. Not only the alignment algorithm, but also the method used to deal with the most problematic alignment regions, may have a critical effect on the final tree. Although some authors remove such problematic regions, either manually or using automatic methods, in order to improve phylogenetic performance, others prefer to keep such regions to avoid losing any information. Our aim in the present work was to examine whether phylogenetic reconstruction improves after alignment cleaning or not. Using simulated protein alignments with gaps, we tested the relative performance in diverse phylogenetic analyses of the whole alignments versus the alignments with problematic regions removed with our previously developed Gblocks program. We also tested the performance of more or less stringent conditions in the selection of blocks. Alignments constructed with different alignment methods (ClustalW, Mafft, and Probcons) were used to estimate phylogenetic trees by maximum likelihood, neighbor joining, and parsimony. We show that, in most alignment conditions, and for alignments that are not too short, removal of blocks leads to better trees. That is, despite losing some information, there is an increase in the actual phylogenetic signal. Overall, the best trees are obtained by maximum-likelihood reconstruction of alignments cleaned by Gblocks. In general, a relaxed selection of blocks is better for short alignment, whereas a stringent selection is more adequate for longer ones. Finally, we show that cleaned alignments produce better topologies although, paradoxically, with lower bootstrap. This indicates that divergent and problematic alignment regions may lead, when present, to apparently better supported although, in fact, more biased topologies.
4,227 citations
TL;DR: A brief history and review of geopolymer technology is presented with the aim of introducing the technology and the vast categories of materials that may be synthesized by alkali activation of aluminosilicates as mentioned in this paper.
Abstract: A brief history and review of geopolymer technology is presented with the aim of introducing the technology and the vast categories of materials that may be synthesized by alkali-activation of aluminosilicates. The fundamental chemical and structural characteristics of geopolymers derived from metakaolin, fly ash and slag are explored in terms of the effects of raw material selection on the properties of geopolymer composites. It is shown that the raw materials and processing conditions are critical in determining the setting behavior, workability and chemical and physical properties of geopolymeric products. The structural and chemical characteristics that are common to all geopolymeric materials are presented, as well as those that are determined by the specific interactions occurring in different systems, providing the ability for tailored design of geopolymers to specific applications in terms of both technical and commercial requirements.
3,302 citations
TL;DR: In this paper, the role of inland water ecosystems in the global carbon cycle has been investigated and it is shown that roughly twice as much C enters inland aquatic systems from land as is exported from land to the sea, roughly equally as inorganic and organic carbon.
Abstract: Because freshwater covers such a small fraction of the Earth’s surface area, inland freshwater ecosystems (particularly lakes, rivers, and reservoirs) have rarely been considered as potentially important quantitative components of the carbon cycle at either global or regional scales. By taking published estimates of gas exchange, sediment accumulation, and carbon transport for a variety of aquatic systems, we have constructed a budget for the role of inland water ecosystems in the global carbon cycle. Our analysis conservatively estimates that inland waters annually receive, from a combination of background and anthropogenically altered sources, on the order of 1.9 Pg C y−1 from the terrestrial landscape, of which about 0.2 is buried in aquatic sediments, at least 0.8 (possibly much more) is returned to the atmosphere as gas exchange while the remaining 0.9 Pg y−1 is delivered to the oceans, roughly equally as inorganic and organic carbon. Thus, roughly twice as much C enters inland aquatic systems from land as is exported from land to the sea. Over prolonged time net carbon fluxes in aquatic systems tend to be greater per unit area than in much of the surrounding land. Although their area is small, these freshwater aquatic systems can affect regional C balances. Further, the inclusion of inland, freshwater ecosystems provides useful insight about the storage, oxidation and transport of terrestrial C, and may warrant a revision of how the modern net C sink on land is described.
3,179 citations
TL;DR: In all cases, enzyme engineering via immobilization techniques is perfectly compatible with other chemical or biological approaches to improve enzyme functions and the final success depend on the availability of a wide battery of immobilization protocols.
3,016 citations
TL;DR: The identification of Snail, ZEB and some basic helix-loop-helix factors as inducers of epithelial–mesenchymal transition (EMT) and potent repressors of E-cadherin expression has opened new avenues of research with potential clinical implications.
Abstract: The molecular mechanisms that underlie tumour progression are still poorly understood, but recently our knowledge of particular aspects of some of these processes has increased. Specifically, the identification of Snail, ZEB and some basic helix-loop-helix (bHLH) factors as inducers of epithelial-mesenchymal transition (EMT) and potent repressors of E-cadherin expression has opened new avenues of research with potential clinical implications.
2,975 citations
TL;DR: It is argued that, although improved accuracy can be delivered through the traditional tasks of trying to build better models with improved data, more robust forecasts can also be achieved if ensemble forecasts are produced and analysed appropriately.
Abstract: Concern over implications of climate change for biodiversity has led to the use of bioclimatic models to forecast the range shifts of species under future climate-change scenarios. Recent studies have demonstrated that projections by alternative models can be so variable as to compromise their usefulness for guiding policy decisions. Here, we advocate the use of multiple models within an ensemble forecasting framework and describe alternative approaches to the analysis of bioclimatic ensembles, including bounding box, consensus and probabilistic techniques. We argue that, although improved accuracy can be delivered through the traditional tasks of trying to build better models with improved data, more robust forecasts can also be achieved if ensemble forecasts are produced and analysed appropriately.
2,624 citations
TL;DR: It is shown that when graphene is epitaxially grown on SiC substrate, a gap of approximately 0.26 eV is produced and it is proposed that the origin of this gap is the breaking of sublattice symmetry owing to the graphene-substrate interaction.
Abstract: Graphene has shown great application potential as the hostmaterial for next-generation electronic devices. However, despite itsintriguing properties, one of the biggest hurdles for graphene to beuseful as an electronic material is the lack of an energy gap in itselectronic spectra. This, for example, prevents the use of graphene inmaking transistors. Although several proposals have been made to open agap in graphene's electronic spectra, they all require complexengineering of the graphene layer. Here, we show that when graphene isepitaxially grown on SiC substrate, a gap of ~;0.26 eV is produced. Thisgap decreases as the sample thickness increases and eventually approacheszero when the number of layers exceeds four. We propose that the originof this gap is the breaking of sublattice symmetry owing to thegraphene-substrate interaction. We believe that our results highlight apromising direction for band gap engineering of graphene.
2,132 citations
TL;DR: The identification of JASMONATE-INSENSITIVE 3 (JAI3) and a family of related proteins named JAZ (jasmonate ZIM-domain), in Arabidopsis thaliana and the existence of a regulatory feed-back loop involving MYC2 and JAZ proteins, which provides a mechanistic explanation for the pulsed response to jasmonate and the subsequent desensitization of the cell.
Abstract: Jasmonates are essential phytohormones for plant development and survival. However, the molecular details of their signalling pathway remain largely unknown. The identification more than a decade ago of COI1 as an F-box protein suggested the existence of a repressor of jasmonate responses that is targeted by the SCF(COI1) complex for proteasome degradation in response to jasmonate. Here we report the identification of JASMONATE-INSENSITIVE 3 (JAI3) and a family of related proteins named JAZ (jasmonate ZIM-domain), in Arabidopsis thaliana. Our results demonstrate that JAI3 and other JAZs are direct targets of the SCF(COI1) E3 ubiquitin ligase and jasmonate treatment induces their proteasome degradation. Moreover, JAI3 negatively regulates the key transcriptional activator of jasmonate responses, MYC2. The JAZ family therefore represents the molecular link between the two previously known steps in the jasmonate pathway. Furthermore, we demonstrate the existence of a regulatory feed-back loop involving MYC2 and JAZ proteins, which provides a mechanistic explanation for the pulsed response to jasmonate and the subsequent desensitization of the cell.
1,991 citations
TL;DR: Target mimicry can be generalized beyond the control of Pi homeostasis, as demonstrated using artificial target mimics and coined to define this mechanism of inhibition of miRNA activity.
Abstract: MicroRNAs (miRNA) regulate key aspects of development and physiology in animals and plants. These regulatory RNAs act as guides of effector complexes to recognize specific mRNA sequences based on sequence complementarity, resulting in translational repression or site-specific cleavage. In plants, most miRNA targets are cleaved and show almost perfect complementarity with the miRNAs around the cleavage site. Here, we examined the non-protein coding gene IPS1 (INDUCED BY PHOSPHATE STARVATION 1) from Arabidopsis thaliana. IPS1 contains a motif with sequence complementarity to the phosphate (Pi) starvation-induced miRNA miR-399, but the pairing is interrupted by a mismatched loop at the expected miRNA cleavage site. We show that IPS1 RNA is not cleaved but instead sequesters miR-399. Thus, IPS1 overexpression results in increased accumulation of the miR-399 target PHO2 mRNA and, concomitantly, in reduced shoot Pi content. Engineering of IPS1 to be cleavable abolishes its inhibitory activity on miR-399. We coin the term 'target mimicry' to define this mechanism of inhibition of miRNA activity. Target mimicry can be generalized beyond the control of Pi homeostasis, as demonstrated using artificial target mimics.
1,767 citations
TL;DR: It is demonstrated that the electronic gap of a graphene bilayer can be controlled externally by applying a gate bias and can be changed from zero to midinfrared energies by using fields of less, approximately < 1 V/nm, below the electric breakdown of SiO2.
Abstract: We demonstrate that the electronic gap of a graphene bilayer can be controlled externally by applying a gate bias. From the magnetotransport data (Shubnikov-de Haas measurements of the cyclotron mass), and using a tight-binding model, we extract the value of the gap as a function of the electronic density. We show that the gap can be changed from zero to midinfrared energies by using fields of less, approximately < 1 V/nm, below the electric breakdown of SiO2. The opening of a gap is clearly seen in the quantum Hall regime.
1,557 citations
Macaulay Institute1, King Juan Carlos University2, University of Montana3, York University4, University of Concepción5, University of Tübingen6, University of Aberdeen7, Duke University8, Institut national de la recherche agronomique9, Spanish National Research Council10, Umeå University11, University of Potsdam12
TL;DR: There is substantial scope for exploring indirect facilitative effects in plant communities, including their impacts on diversity and evolution, and future studies should connect the degree of non-transitivity in plant competitive networks to community diversity and facilitative promotion of species coexistence.
Abstract: Summary 1 Once neglected, the role of facilitative interactions in plant communities has received considerable attention in the last two decades, and is now widely recognized It is timely to consider the progress made by research in this field 2 We review the development of plant facilitation research, focusing on the history of the field, the relationship between plant‐plant interactions and environmental severity gradients, and attempts to integrate facilitation into mainstream ecological theory We then consider future directions for facilitation research 3 With respect to our fundamental understanding of plant facilitation, clarification of the relationship between interactions and environmental gradients is central for further progress, and necessitates the design and implementation of experiments that move beyond the clear limitations of previous studies 4 There is substantial scope for exploring indirect facilitative effects in plant communities, including their impacts on diversity and evolution, and future studies should connect the degree of non-transitivity in plant competitive networks to community diversity and facilitative promotion of species coexistence, and explore how the role of indirect facilitation varies with environmental severity 5 Certain ecological modelling approaches (eg individual-based modelling), although thus far largely neglected, provide highly useful tools for exploring these fundamental processes 6 Evolutionary responses might result from facilitative interactions, and consideration of facilitation might lead to re-assessment of the evolution of plant growth forms
TL;DR: The authors presented a new data set for years of schooling across countries for the 1960-2000 period, constructed from the OECD database on edu- cational attainment and from surveys published by UNESCO.
Abstract: We present a new data set for years of schooling across countries for the 1960-2000 period. The series are constructed from the OECD database on edu- cational attainment and from surveys published by UNESCO. Two features that improve the quality of our data with respect to other series, particularly for series in first-differences, are the use of surveys based on uniform classification systems of education over time, and an intensified use of information by age groups. As a result of the improvement in quality, these new series can be used as a direct substitute for Barro and Lee's (2001; Oxford Economic Papers, 3, 541-563) data in empirical research. In standard cross-country growth regressions we find that our series yield significant coefficients for schooling. In panel data estimates our series are also sig- nificant even when the regressions account for the accumulation of physical capital. Moreover, the estimated macro return is consistent with those reported in labour studies. These results differ from the typical findings of the earlier literature and are a consequence of the reduction in measurement error in the series.
TL;DR: The mutually beneficial interactions between plants and their animal pollinators and seed dispersers have been paramount in the generation of Earth's biodiversity and understanding how coevolution proceeds in these highly diversified mutualisms among free-living species presents a conceptual challenge.
Abstract: The mutually beneficial interactions between plants and their animal pollinators and seed dispersers have been paramount in the generation of Earth's biodiversity. These mutualistic interactions often involve dozens or even hundreds of species that form complex networks of interdependences. Understanding how coevolution proceeds in these highly diversified mutualisms among free-living species presents a conceptual challenge. Recent work has led to the unambiguous conclusion that mutualistic networks are very heterogeneous (the bulk of the species have a few interactions, but a few species are much more connected than expected by chance), nested (specialists interact with subsets of the species with which generalists interact), and built on weak and asymmetric links among species. Both ecological variables (e.g., phenology, local abundance, and geographic range) and past evolutionary history may explain such network patterns. Network structure has important implications for the coexistence and stability of...
TL;DR: The chemistry, catalysts, and challenges involved in the production of biofuels are discussed, allowing us to rapidly transition to a more sustainable economy without large capital investments for new reaction equipment.
Abstract: As petroleum prices continue to increase, it is likely that biofuels will play an ever-increasing role in our energy future. The processing of biomass-derived feedstocks (including cellulosic, starch- and sugar-derived biomass, and vegetable fats) by catalytic cracking and hydrotreating is a promising alternative for the future to produce biofuels, and the existing infrastructure of petroleum refineries is well-suited for the production of biofuels, allowing us to rapidly transition to a more sustainable economy without large capital investments for new reaction equipment. This Review discusses the chemistry, catalysts, and challenges involved in the production of biofuels.
TL;DR: In this paper, a Raman scattering study of wurtzite was carried out over a temperature range from 80 to 750°C, where the second-order Raman features were interpreted in the light of recent ab initio phonon density of states calculations.
Abstract: We present a Raman scattering study of wurtzite $\mathrm{ZnO}$ over a temperature range from 80 to $750\phantom{\rule{03em}{0ex}}\mathrm{K}$ Second-order Raman features are interpreted in the light of recent ab initio phonon density of states calculations The temperature dependence of the Raman intensities allows the assignment of difference modes to be made unambiguously Some weak, sharp Raman peaks are detected whose temperature dependence suggests they may be due to impurity modes High-resolution spectra of the ${E}_{2}^{\mathrm{high}}$, ${A}_{1}(\mathrm{LO})$, and ${E}_{1}(\mathrm{LO})$ modes were recorded, and an analysis of the anharmonicity and lifetimes of these phonons is carried out The ${E}_{2}^{\mathrm{high}}$ mode displays a visibly asymmetric line shape This can be attributed to anharmonic interaction with transverse and longitudinal acoustic phonon combinations in the vicinity of the $K$ point, where the two-phonon density of states displays a sharp edge around the ${E}_{2}^{\mathrm{high}}$ frequency The temperature dependence of the linewidth and frequency of the ${E}_{2}^{\mathrm{high}}$ mode is well described by a perturbation-theory renormalization of the harmonic ${E}_{2}^{\mathrm{high}}$ frequency resulting from the interaction with the acoustic two-phonon density of states In contrast, the ${A}_{1}(\mathrm{LO})$ and ${E}_{1}(\mathrm{LO})$ frequencies lie in a region of nearly flat two-phonon density of states, and they exhibit a nearly symmetric Lorentzian line shape with a temperature dependence that is well accounted for by a dominating asymmetric decay channel
TL;DR: In this paper, the interaction of light with two-dimensional periodic arrays of particles and holes is analyzed and the role of plasmons in these types of structures through analytical considerations.
Abstract: This Colloquium analyzes the interaction of light with two-dimensional periodic arrays of particles and holes. The enhanced optical transmission observed in the latter and the presence of surface modes in patterned metal surfaces is thoroughly discussed. A review of the most significant discoveries in this area is presented first. A simple tutorial model is then formulated to capture the essential physics involved in these phenomena, while allowing analytical derivations that provide deeper insight. Comparison with more elaborated calculations is offered as well. Finally, hole arrays in plasmon-supporting metals are compared to perforated perfect conductors, thus assessing the role of plasmons in these types of structures through analytical considerations. The developments that have been made in nanophotonics areas related to plasmons in nanostructures, extraordinary optical transmission in hole arrays, complete resonant absorption and emission of light, and invisibility in structured metals are illustrated in this Colloquium in a comprehensive, tutorial fashion.
TL;DR: In this article, the main forms of caprine and ovine caseino-macropeptides (CMP), which are the soluble C-terminal derivatives from the action of chymosin on β-casein during the milk clotting process of cheesemaking, have been identified and are a good source of antithrombotic peptides.
TL;DR: This paper examined whether biotic interactions exert a dominant role in governing species distributions at macro-ecological scales, and provided tests for two null hypotheses: (H 0 1) "Biotic interactions do not exert a significant role in explaining current distributions of a particular species of butterfly (clouded Apollo, Parnassius mnemosyne ) in Europe; and ( H 0 2) ''Biotic interaction does not influence the prediction of altered species' ranges under climate change''.
Abstract: Aim There is a debate as to whether biotic interactions exert a dominant role in governing species distributions at macroecological scales. The prevailing idea is that climate is the key limiting factor; thus models that use present-day climate‐species range relationships are expected to provide reasonable means to quantify the impacts of climate change on species distributions. However, there is little empirical evidence that biotic interactions would not constrain species distributions at macroecological scales. We examine this idea, for the first time, and provide tests for two null hypotheses: ( H 0 1) ‐ biotic interactions do not exert a significant role in explaining current distributions of a particular species of butterfly (clouded Apollo, Parnassius mnemosyne ) in Europe; and ( H 0 2) ‐ biotic interactions do not exert a significant role in predictions of altered species’ ranges under climate change.
TL;DR: This critical review provides an up-to-date survey to this new generation of multifunctional open-framework solids, classified into five different sections: magnetic, chiral, conducting, optical, and labile open-frameworks for sensing applications.
Abstract: The literature on open-framework materials has shown numerous examples of porous solids with additional structural, chemical, or physical properties. These materials show promise for applications ranging from sensing, catalysis and separation to multifunctional materials. This critical review provides an up-to-date survey to this new generation of multifunctional open-framework solids. For this, a detailed revision of the different examples so far reported will be presented, classified into five different sections: magnetic, chiral, conducting, optical, and labile open-frameworks for sensing applications. (413 references.)
TL;DR: This work shows that films of La (0.1)Bi(0.9)MnO(3) (LBMO) are ferromagnetic and ferroelectric, and retain both ferroic properties down to a thickness of 2 nm, and represents an advance over the original four-state memory concept based on multiferroics.
Abstract: Multiferroics are singular materials that can exhibit simultaneously electric and magnetic orders. Some are ferroelectric and ferromagnetic and provide the opportunity to encode information in electric polarization and magnetization to obtain four logic states. However, such materials are rare and schemes allowing a simple electrical readout of these states have not been demonstrated in the same device. Here, we show that films of La0.1Bi0.9MnO3 (LBMO) are ferromagnetic and ferroelectric, and retain both ferroic properties down to a thickness of 2 nm. We have integrated such ultrathin multiferroic films as barriers in spin-filter-type tunnel junctions that exploit the magnetic and ferroelectric degrees of freedom of LBMO. Whereas ferromagnetism permits read operations reminiscent of magnetic random access memories (MRAM), the electrical switching evokes a ferroelectric RAM write operation. Significantly, our device does not require the destructive ferroelectric readout, and therefore represents an advance over the original four-state memory concept based on multiferroics.
TL;DR: Modulation of plant defense responses occurs, potentially through cross-talk between salicylic acid and jasmonate dependent signaling pathways, and may impact plant responses to potential enemies by priming the tissues for a more efficient activation of defense mechanisms.
TL;DR: In this article, the authors used electron beams instead of photons to detect plasmons as resonance peaks in the energy-loss spectra of sub-nanometre electron beams rastered on nanoparticles of well-defined geometrical parameters.
Abstract: Understanding how light interacts with matter at the nanometre scale is a fundamental issue in optoelectronics and nanophotonics. In particular, many applications (such as bio-sensing, cancer therapy and all-optical signal processing) rely on surface-bound optical excitations in metallic nanoparticles. However, so far no experimental technique has been capable of imaging localized optical excitations with sufficient resolution to reveal their dramatic spatial variation over one single nanoparticle. Here, we present a novel method applied on silver nanotriangles, achieving such resolution by recording maps of plasmons in the near-infrared/visible/ultraviolet domain using electron beams instead of photons. This method relies on the detection of plasmons as resonance peaks in the energy-loss spectra of subnanometre electron beams rastered on nanoparticles of well-defined geometrical parameters. This represents a significant improvement in the spatial resolution with which plasmonic modes can be imaged, and provides a powerful tool in the development of nanometre-level optics.
TL;DR: It is shown that plastic responses to abiotic factors are reduced under situations of conservative resource use in stressful and unpredictable habitats, and that extreme levels in a given abiotic factor can negatively influence Plastic responses to another factor.
Abstract: Phenotypic plasticity is considered the major means by which plants cope with environmental heterogeneity. Although ubiquitous in nature, actual phenotypic plasticity is far from being maximal. This has been explained by the existence of internal limits to its expression. However, phenotypic plasticity takes place within an ecological context and plants are generally exposed to multifactor environments and to simultaneous interactions with many species. These external, ecological factors may limit phenotypic plasticity or curtail its adaptive value, but seldom have they been considered because limits to plasticity have typically addressed factors internal to the plant. We show that plastic responses to abiotic factors are reduced under situations of conservative resource use in stressful and unpredictable habitats, and that extreme levels in a given abiotic factor can negatively influence plastic responses to another factor. We illustrate how herbivory may limit plant phenotypic plasticity because damaged plants can only rarely attain the optimal phenotype in the challenging environment. Finally, it is examined how phenotypic changes involved in trait-mediated interactions can entail costs for the plant in further interactions with other species in the community. Ecological limits to plasticity must be included in any realistic approach to understand the evolution of plasticity in complex environments and to predict plant responses to global change.
TL;DR: Findings identify transcriptional control of PTEN and regulation of the PI3K-AKT pathway as key elements of the leukemogenic program activated by NOTCH1 and provide the basis for the design of new therapeutic strategies for T-ALL.
Abstract: Gain-of-function mutations in NOTCH1 are common in T-cell lymphoblastic leukemias and lymphomas (T-ALL), making this receptor a promising target for drugs such as γ-secretase inhibitors, which block a proteolytic cleavage required for NOTCH1 activation. However, the enthusiasm for these therapies has been tempered by tumor resistance and the paucity of information on the oncogenic programs regulated by oncogenic NOTCH1. Here we show that NOTCH1 regulates the expression of PTEN (encoding phosphatase and tensin homolog) and the activity of the phosphoinositol-3 kinase (PI3K)-AKT signaling pathway in normal and leukemic T cells. Notch signaling and the PI3K-AKT pathway synergize in vivo in a Drosophila melanogaster model of Notch-induced tumorigenesis, and mutational loss of PTEN is associated with human T-ALL resistance to pharmacological inhibition of NOTCH1. Overall, these findings identify transcriptional control of PTEN and regulation of the PI3K-AKT pathway as key elements of the leukemogenic program activated by NOTCH1 and provide the basis for the design of new therapeutic strategies for T-ALL.
TL;DR: Using caesium-137 and carbon inventory measurements from a large-scale survey, consistent evidence is found for an erosion-induced sink of atmospheric carbon equivalent to approximately 26% of the carbon transported by erosion.
Abstract: Agricultural soil erosion is thought to perturb the global carbon cycle, but estimates of its effect range from a source of 1 petagram per year(-1) to a sink of the same magnitude. By using caesium-137 and carbon inventory measurements from a large-scale survey, we found consistent evidence for an erosion-induced sink of atmospheric carbon equivalent to approximately 26% of the carbon transported by erosion. Based on this relationship, we estimated a global carbon sink of 0.12 (range 0.06 to 0.27) petagrams of carbon per year(-1) resulting from erosion in the world's agricultural landscapes. Our analysis directly challenges the view that agricultural erosion represents an important source or sink for atmospheric CO2.
TL;DR: The Fifth Data Release (DR5) of the Sloan Digital Sky Survey (SDSS) was released in 2005 June and represents the completion of the SDSS-I project as mentioned in this paper, which includes five-band photometric data for 217 million objects selected over 8000 deg 2 and 1,048,960 spectra of galaxies, quasars, and stars selected from 5713 deg 2 of imaging data.
Abstract: This paper describes the Fifth Data Release (DR5) of the Sloan Digital Sky Survey (SDSS). DR5 includes all survey quality data taken through 2005 June and represents the completion of the SDSS-I project (whose successor, SDSS-II, will continue through mid-2008). It includes five-band photometric data for 217 million objects selected over 8000 deg^2 and 1,048,960 spectra of galaxies, quasars, and stars selected from 5713 deg^2 of that imaging data. These numbers represent a roughly 20% increment over those of the Fourth Data Release; all the data from previous data releases are included in the present release. In addition to "standard" SDSS observations, DR5 includes repeat scans of the southern equatorial stripe, imaging scans across M31 and the core of the Perseus Cluster of galaxies, and the first spectroscopic data from SEGUE, a survey to explore the kinematics and chemical evolution of the Galaxy. The catalog database incorporates several new features, including photometric redshifts of galaxies, tables of matched objects in overlap regions of the imaging survey, and tools that allow precise computations of survey geometry for statistical investigations.
TL;DR: The results support a model for ABA affecting JA biosynthesis in the activation of defenses against this oomycete, and reveal an unexpected overrepresentation of ABA response elements in promoters of P. irregulare–responsive genes.
Abstract: Analyses of Arabidopsis thaliana defense response to the damping-off oomycete pathogen Pythium irregulare show that resistance to P. irregulare requires a multicomponent defense strategy. Penetration represents a first layer, as indicated by the susceptibility of pen2 mutants, followed by recognition, likely mediated by ERECTA receptor-like kinases. Subsequent signaling of inducible defenses is predominantly mediated by jasmonic acid (JA), with insensitive coi1 mutants showing extreme susceptibility. In contrast with the generally accepted roles of ethylene and salicylic acid cooperating with or antagonizing, respectively, JA in the activation of defenses against necrotrophs, both are required to prevent disease progression, although much less so than JA. Meta-analysis of transcriptome profiles confirmed the predominant role of JA in activation of P. irregulare–induced defenses and uncovered abscisic acid (ABA) as an important regulator of defense gene expression. Analysis of cis-regulatory sequences also revealed an unexpected overrepresentation of ABA response elements in promoters of P. irregulare–responsive genes. Subsequent infections of ABA-related and callose-deficient mutants confirmed the importance of ABA in defense, acting partly through an undescribed mechanism. The results support a model for ABA affecting JA biosynthesis in the activation of defenses against this oomycete.
University of Zurich1, University of Adelaide2, National Institute of Standards and Technology3, Johns Hopkins University4, University of Illinois at Urbana–Champaign5, Texas A&M University6, Lamont–Doherty Earth Observatory7, Stockholm University8, Commonwealth Scientific and Industrial Research Organisation9, Rice University10, Chinese Academy of Sciences11, Binghamton University12, Ohio State University13, University of Denver14, University of Hawaii at Manoa15, University of Bonn16, Environment Canada17, Massachusetts Institute of Technology18, Chimie ParisTech19, Institut national de la recherche agronomique20, Martin Luther University of Halle-Wittenberg21, Spanish National Research Council22, Newcastle University23
TL;DR: In this paper, the authors conducted a comprehensive intercomparison of this type (multimethod, multilab, and multisample), focusing mainly on methods used for soil and sediment BC studies.
Abstract: Black carbon (BC), the product of incomplete combustion of fossil fuels and biomass (called elemental carbon (EC) in atmospheric sciences), was quantified in 12 different materials by 17 laboratories from different disciplines, using seven different methods. The materials were divided into three classes: (1) potentially interfering materials, (2) laboratory-produced BC-rich materials, and (3) BC-containing environmental matrices (from soil, water, sediment, and atmosphere). This is the first comprehensive intercomparison of this type (multimethod, multilab, and multisample), focusing mainly on methods used for soil and sediment BC studies. Results for the potentially interfering materials (which by definition contained no fire-derived organic carbon) highlighted situations where individual methods may overestimate BC concentrations. Results for the BC-rich materials (one soot and two chars) showed that some of the methods identified most of the carbon in all three materials as BC, whereas other methods identified only soot carbon as BC. The different methods also gave widely different BC contents for the environmental matrices. However, these variations could be understood in the light of the findings for the other two groups of materials, i.e., that some methods incorrectly identify non-BC carbon as BC, and that the detection efficiency of each technique varies across the BC continuum. We found that atmospheric BC quantification methods are not ideal for soil and sediment studies as in their methodology these incorporate the definition of BC as light-absorbing material irrespective of its origin, leading to biases when applied to terrestrial and sedimentary materials. This study shows that any attempt to merge data generated via different methods must consider the different, operationally defined analytical windows of the BC continuum detected by each technique, as well as the limitations and potential biases of each technique. A major goal of this ring trial was to provide a basis on which to choose between the different BC quantification methods in soil and sediment studies. In this paper we summarize the advantages and disadvantages of each method. In future studies, we strongly recommend the evaluation of all methods analyzing for BC in soils and sediments against the set of BC reference materials analyzed here.
TL;DR: Four threshold criteria are compared for a wide range of sample sizes and prevalences, modeling a virtual species in order to avoid the omnipresent error sources that the use of real species data implies.
Abstract: For many applications the continuous prediction afforded by species distribution modeling must be converted to a map of presence or absence, so a threshold probability indicative of species presence must be fixed. Because of the bias in probability outputs due to frequency of presences (prevalence), a fixed threshold value, such as 0.5, does not usually correspond to the threshold above which the species is more likely to be present. In this paper four threshold criteria are compared for a wide range of sample sizes and prevalences, modeling a virtual species in order to avoid the omnipresent error sources that the use of real species data implies. In general, sensitivity–specificity difference minimizer and sensitivity–specificity sum maximizer criteria produced the most accurate predictions. The widely-used 0.5 fixed threshold and Kappa-maximizer criteria are the worst ones in almost all situations. Nevertheless, whatever the criteria used, the threshold value chosen and the research goals that determined its choice must be stated.