Showing papers by "Spanish National Research Council published in 2010"

A Multiscalar Drought Index Sensitive to Global Warming: The Standardized Precipitation Evapotranspiration Index

Abstract: The authors propose a new climatic drought index: the standardized precipitation evapotranspiration index (SPEI). The SPEI is based on precipitation and temperature data, and it has the advantage of combining multiscalar character with the capacity to include the effects of temperature variability on drought assessment. The procedure to calculate the index is detailed and involves a climatic water balance, the accumulation of deficit/surplus at different time scales, and adjustment to a log-logistic probability distribution. Mathematically, the SPEI is similar to the standardized precipitation index (SPI), but it includes the role of temperature. Because the SPEI is based on a water balance, it can be compared to the self-calibrated Palmer drought severity index (sc-PDSI). Time series of the three indices were compared for a set of observatories with different climate characteristics, located in different parts of the world. Under global warming conditions, only the sc-PDSI and SPEI identified an...

A Draft Sequence of the Neandertal Genome

Abstract: Neandertals, the closest evolutionary relatives of present-day humans, lived in large parts of Europe and western Asia before disappearing 30,000 years ago. We present a draft sequence of the Neandertal genome composed of more than 4 billion nucleotides from three individuals. Comparisons of the Neandertal genome to the genomes of five present-day humans from different parts of the world identify a number of genomic regions that may have been affected by positive selection in ancestral modern humans, including genes involved in metabolism and in cognitive and skeletal development. We show that Neandertals shared more genetic variants with present-day humans in Eurasia than with present-day humans in sub-Saharan Africa, suggesting that gene flow from Neandertals into the ancestors of non-Africans occurred before the divergence of Eurasian groups from each other.

Review of Particle Physics

Abstract: This biennial Review summarizes much of particle physics. Using data from previous editions, plus 2158 new measurements from 551 papers, we list, evaluate, and average measured properties of gauge bosons, leptons, quarks, mesons, and baryons. We also summarize searches for hypothetical particles such as Higgs bosons, heavy neutrinos, and supersymmetric particles. All the particle properties and search limits are listed in Summary Tables. We also give numerous tables, figures, formulae, and reviews of topics such as the Standard Model, particle detectors, probability, and statistics. Among the 108 reviews are many that are new or heavily revised including those on neutrino mass, mixing, and oscillations, QCD, top quark, CKM quark-mixing matrix, V-ud & V-us, V-cb & V-ub, fragmentation functions, particle detectors for accelerator and non-accelerator physics, magnetic monopoles, cosmological parameters, and big bang cosmology.

The Photodetector Array Camera and Spectrometer (PACS) on the Herschel Space Observatory

Abstract: The Photodetector Array Camera and Spectrometer (PACS) is one of the three science instruments on ESA's far infrared and submil- limetre observatory. It employs two Ge:Ga photoconductor arrays (stressed and unstressed) with 16 × 25 pixels, each, and two filled silicon bolometer arrays with 16 × 32 and 32 × 64 pixels, respectively, to perform integral-field spectroscopy and imaging photom- etry in the 60−210 μm wavelength regime. In photometry mode, it simultaneously images two bands, 60−85 μ mo r 85−125 μ ma nd 125−210 μm, over a field of view of ∼1.75 � × 3.5 � , with close to Nyquist beam sampling in each band. In spectroscopy mode, it images afi eld of 47 �� × 47 �� , resolved into 5 × 5 pixels, with an instantaneous spectral coverage of ∼ 1500 km s −1 and a spectral resolution of ∼175 km s −1 . We summarise the design of the instrument, describe observing modes, calibration, and data analysis methods, and present our current assessment of the in-orbit performance of the instrument based on the performance verification tests. PACS is fully operational, and the achieved performance is close to or better than the pre-launch predictions.

The Herschel-SPIRE instrument and its in-flight performance

Abstract: The Spectral and Photometric Imaging REceiver (SPIRE), is the Herschel Space Observatory`s submillimetre camera and spectrometer It contains a three-band imaging photometer operating at 250, 350 and 500 mu m, and an imaging Fourier-transform spectrometer (FTS) which covers simultaneously its whole operating range of 194-671 mu m (447-1550 GHz) The SPIRE detectors are arrays of feedhorn-coupled bolometers cooled to 03 K The photometer has a field of view of 4' x 8', observed simultaneously in the three spectral bands Its main operating mode is scan-mapping, whereby the field of view is scanned across the sky to achieve full spatial sampling and to cover large areas if desired The spectrometer has an approximately circular field of view with a diameter of 26' The spectral resolution can be adjusted between 12 and 25 GHz by changing the stroke length of the FTS scan mirror Its main operating mode involves a fixed telescope pointing with multiple scans of the FTS mirror to acquire spectral data For extended source measurements, multiple position offsets are implemented by means of an internal beam steering mirror to achieve the desired spatial sampling and by rastering of the telescope pointing to map areas larger than the field of view The SPIRE instrument consists of a cold focal plane unit located inside the Herschel cryostat and warm electronics units, located on the spacecraft Service Module, for instrument control and data handling Science data are transmitted to Earth with no on-board data compression, and processed by automatic pipelines to produce calibrated science products The in-flight performance of the instrument matches or exceeds predictions based on pre-launch testing and modelling: the photometer sensitivity is comparable to or slightly better than estimated pre-launch, and the spectrometer sensitivity is also better by a factor of 15-2

Beyond Intercalation-Based Li-Ion Batteries: The State of the Art and Challenges of Electrode Materials Reacting Through Conversion Reactions

Abstract: Despite the imminent commercial introduction of Li-ion batteries in electric drive vehicles and their proposed use as enablers of smart grids based on renewable energy technologies, an intensive quest for new electrode materials that bring about improvements in energy density, cycle life, cost, and safety is still underway. This Progress Report highlights the recent developments and the future prospects of the use of phases that react through conversion reactions as both positive and negative electrode materials in Li-ion batteries. By moving beyond classical intercalation reactions, a variety of low cost compounds with gravimetric specific capacities that are two-to-five times larger than those attained with currently used materials, such as graphite and LiCoO(2), can be achieved. Nonetheless, several factors currently handicap the applicability of electrode materials entailing conversion reactions. These factors, together with the scientific breakthroughs that are necessary to fully assess the practicality of this concept, are reviewed in this report.

Baryon Acoustic Oscillations in the Sloan Digital Sky Survey Data Release 7 Galaxy Sample

Abstract: The spectroscopic Sloan Digital Sky Survey (SDSS) Data Release 7 (DR7) galaxy sample represents the final set of galaxies observed using the original SDSS target selection criteria. We analyse the clustering of galaxies within this sample, including both the luminous red galaxy and main samples, and also include the 2-degree Field Galaxy Redshift Survey data. In total, this sample comprises 893 319 galaxies over 9100 deg(2). Baryon acoustic oscillations (BAO) are observed in power spectra measured for different slices in redshift; this allows us to constrain the distance-redshift relation at multiple epochs. We achieve a distance measure at redshift z = 0.275, of r(s)(z(d))/D-V(0.275) = 0.1390 +/- 0.0037 (2.7 per cent accuracy), where r(s)(z(d)) is the comoving sound horizon at the baryon-drag epoch, D-V(z) equivalent to [(1 + z)(2)D(A)(2)cz/H(z)](1/3), D-A(z) is the angular diameter distance and H(z) is the Hubble parameter. We find an almost independent constraint on the ratio of distances D-V(0.35)/D-V(0.2) = 1.736 +/- 0.065, which is consistent at the 1.1 sigma level with the best-fitting Lambda cold dark matter model obtained when combining our z = 0.275 distance constraint with the Wilkinson Microwave Anisotropy Probe 5-year (WMAP5) data. The offset is similar to that found in previous analyses of the SDSS DR5 sample, but the discrepancy is now of lower significance, a change caused by a revised error analysis and a change in the methodology adopted, as well as the addition of more data. Using WMAP5 constraints on Omega(b)h(2) and Omega(c) h(2), and combining our BAO distance measurements with those from the Union supernova sample, places a tight constraint on Omega(m) = 0.286 +/- 0.018 and H-0 = 68.2 +/- 2.2 km s(-1) Mpc(-1) that is robust to allowing Omega(k) not equal 0 and omega not equal -1. This result is independent of the behaviour of dark energy at redshifts greater than those probed by the BAO and supernova measurements. Combining these data sets with the full WMAP5 likelihood constraints provides tight constraints on both Omega(k) = -0.006 +/- 0.008 and omega = -0.97 +/- 0.10 for a constant dark energy equation of state.

Amazonia Through Time: Andean Uplift, Climate Change, Landscape Evolution, and Biodiversity

Abstract: The Amazonian rainforest is arguably the most species-rich terrestrial ecosystem in the world, yet the timing of the origin and evolutionary causes of this diversity are a matter of debate. We review the geologic and phylogenetic evidence from Amazonia and compare it with uplift records from the Andes. This uplift and its effect on regional climate fundamentally changed the Amazonian landscape by reconfiguring drainage patterns and creating a vast influx of sediments into the basin. On this “Andean” substrate, a region-wide edaphic mosaic developed that became extremely rich in species, particularly in Western Amazonia. We show that Andean uplift was crucial for the evolution of Amazonian landscapes and ecosystems, and that current biodiversity patterns are rooted deep in the pre-Quaternary.

Scenarios for global biodiversity in the 21st Century

Abstract: Quantitative scenarios are coming of age as a tool for evaluating the impact of future socioeconomic development pathways on biodiversity and ecosystem services. We analyze global terrestrial, freshwater, and marine biodiversity scenarios using a range of measures including extinctions, changes in species abundance, habitat loss, and distribution shifts, as well as comparing model projections to observations. Scenarios consistently indicate that biodiversity will continue to decline over the 21st century. However, the range of projected changes is much broader than most studies suggest, partly because there are major opportunities to intervene through better policies, but also because of large uncertainties in projections.

Energy gaps and a zero-field quantum Hall effect in graphene by strain engineering

Abstract: Owing to the fact that graphene is just one atom thick, it has been suggested that it might be possible to control its properties by subjecting it to mechanical strain. New analysis indicates not only this, but that pseudomagnetic behaviour and even zero-field quantum Hall effects could be induced in graphene under realistic amounts of strain. Among many remarkable qualities of graphene, its electronic properties attract particular interest owing to the chiral character of the charge carriers, which leads to such unusual phenomena as metallic conductivity in the limit of no carriers and the half-integer quantum Hall effect observable even at room temperature1,2,3. Because graphene is only one atom thick, it is also amenable to external influences, including mechanical deformation. The latter offers a tempting prospect of controlling graphene’s properties by strain and, recently, several reports have examined graphene under uniaxial deformation4,5,6,7,8. Although the strain can induce additional Raman features7,8, no significant changes in graphene’s band structure have been either observed or expected for realistic strains of up to ∼15% (refs 9, 10, 11). Here we show that a designed strain aligned along three main crystallographic directions induces strong gauge fields12,13,14 that effectively act as a uniform magnetic field exceeding 10 T. For a finite doping, the quantizing field results in an insulating bulk and a pair of countercirculating edge states, similar to the case of a topological insulator15,16,17,18,19,20. We suggest realistic ways of creating this quantum state and observing the pseudomagnetic quantum Hall effect. We also show that strained superlattices can be used to open significant energy gaps in graphene’s electronic spectrum.

The SMOS Mission: New Tool for Monitoring Key Elements ofthe Global Water Cycle

Abstract: It is now well understood that data on soil moisture and sea surface salinity (SSS) are required to improve meteorological and climate predictions. These two quantities are not yet available globally or with adequate temporal or spatial sampling. It is recognized that a spaceborne L-band radiometer with a suitable antenna is the most promising way of fulfilling this gap. With these scientific objectives and technical solution at the heart of a proposed mission concept the European Space Agency (ESA) selected the Soil Moisture and Ocean Salinity (SMOS) mission as its second Earth Explorer Opportunity Mission. The development of the SMOS mission was led by ESA in collaboration with the Centre National d'Etudes Spatiales (CNES) in France and the Centro para el Desarrollo Tecnologico Industrial (CDTI) in Spain. SMOS carries a single payload, an L-Band 2-D interferometric radiometer operating in the 1400-1427-MHz protected band . The instrument receives the radiation emitted from Earth's surface, which can then be related to the moisture content in the first few centimeters of soil over land, and to salinity in the surface waters of the oceans. SMOS will achieve an unprecedented maximum spatial resolution of 50 km at L-band over land (43 km on average over the field of view), providing multiangular dual polarized (or fully polarized) brightness temperatures over the globe. SMOS has a revisit time of less than 3 days so as to retrieve soil moisture and ocean salinity data, meeting the mission's science objectives. The caveat in relation to its sampling requirements is that SMOS will have a somewhat reduced sensitivity when compared to conventional radiometers. The SMOS satellite was launched successfully on November 2, 2009.

Genetic history of an archaic hominin group from Denisova Cave in Siberia

Abstract: Using DNA extracted from a finger bone found in Denisova Cave in southern Siberia, we have sequenced the genome of an archaic hominin to about 1.9-fold coverage. This individual is from a group that shares a common origin with Neanderthals. This population was not involved in the putative gene flow from Neanderthals into Eurasians; however, the data suggest that it contributed 4–6% of its genetic material to the genomes of present-day Melanesians. We designate this hominin population ‘Denisovans’ and suggest that it may have been widespread in Asia during the Late Pleistocene epoch. A tooth found in Denisova Cave carries a mitochondrial genome highly similar to that of the finger bone. This tooth shares no derived morphological features with Neanderthals or modern humans, further indicating that Denisovans have an evolutionary history distinct from Neanderthals and modern humans.

Erosion of lizard diversity by climate change and altered thermal niches.

Abstract: It is predicted that climate change will cause species extinctions and distributional shifts in coming decades, but data to validate these predictions are relatively scarce Here, we compare recent and historical surveys for 48 Mexican lizard species at 200 sites Since 1975, 12% of local populations have gone extinct We verified physiological models of extinction risk with observed local extinctions and extended projections worldwide Since 1975, we estimate that 4% of local populations have gone extinct worldwide, but by 2080 local extinctions are projected to reach 39% worldwide, and species extinctions may reach 20% Global extinction projections were validated with local extinctions observed from 1975 to 2009 for regional biotas on four other continents, suggesting that lizards have already crossed a threshold for extinctions caused by climate change

The integrative future of taxonomy.

Abstract: Taxonomy is the biological discipline that identifies, describes, classifies and names extant and extinct species and other taxa. Nowadays, species taxonomy is confronted with the challenge to fully incorporate new theory, methods and data from disciplines that study the origin, limits and evolution of species. Integrative taxonomy has been proposed as a framework to bring together these conceptual and methodological developments. Here we review perspectives for an integrative taxonomy that directly bear on what species are, how they can be discovered, and how much diversity is on Earth. We conclude that taxonomy needs to be pluralistic to improve species discovery and description, and to develop novel protocols to produce the much-needed inventory of life in a reasonable time. To cope with the large number of candidate species revealed by molecular studies of eukaryotes, we propose a classification scheme for those units that will facilitate the subsequent assembly of data sets for the formal description of new species under the Linnaean system, and will ultimately integrate the activities of taxonomists and molecular biologists.

Biodiversity of the Mediterranean Sea: estimates, patterns and threats

Abstract: Trabajo presentado en el 39th CIESM Congress, celebrado en Venecia, Italia, del 10 al 14 de mayo de 2010

Accurate masses and radii of normal stars: Modern results and applications

Abstract: This article presents and discusses a critical compilation of accurate, fundamental determinations of stellar masses and radii. We have identified 95 detached binary systems containing 190 stars (94 eclipsing systems, and α Centauri) that satisfy our criterion that the mass and radius of both stars be known within errors of ±3% accuracy or better. All of them are non-interacting systems, and so the stars should have evolved as if they were single. This sample more than doubles that of the earlier similar review by Andersen (Astron Astrophys Rev 3:91–126, 1991), extends the mass range at both ends and, for the first time, includes an extragalactic binary. In every case, we have examined the original data and recomputed the stellar parameters with a consistent set of assumptions and physical constants. To these we add interstellar reddening, effective temperature, metal abundance, rotational velocity and apsidal motion determinations when available, and we compute a number of other physical parameters, notably luminosity and distance. These accurate physical parameters reveal the effects of stellar evolution with unprecedented clarity, and we discuss the use of the data in observational tests of stellar evolution models in some detail. Earlier findings of significant structural differences between moderately fast-rotating, mildly active stars and single stars, ascribed to the presence of strong magnetic and spot activity, are confirmed beyond doubt. We also show how the best data can be used to test prescriptions for the subtle interplay between convection, diffusion, and other non-classical effects in stellar models. The amount and quality of the data also allow us to analyse the tidal evolution of the systems in considerable depth, testing prescriptions of rotational synchronisation and orbital circularisation in greater detail than possible before. We show that the formulae for pseudo-synchronisation of stars in eccentric orbits predict the observed rotations quite well, except for very young and/or widely separated stars. Deviations do occur, however, especially for stars with convective envelopes. The superior data set finally demonstrates that apsidal motion rates as predicted from General Relativity plus tidal theory are in good agreement with the best observational data. No reliable binary data exist, which challenge General Relativity to any significant extent. The new data also enable us to derive empirical calibrations of M and R for single (post-) main-sequence stars above $${0.6\,M_{\odot}}$$ . Simple, polynomial functions of T eff, log g and [Fe/H] yield M and R within errors of 6 and 3%, respectively. Excellent agreement is found with independent determinations for host stars of transiting extrasolar planets, and good agreement with determinations of M and R from stellar models as constrained by trigonometric parallaxes and spectroscopic values of T eff and [Fe/H]. Finally, we list a set of 23 interferometric binaries with masses known to be better than 3%, but without fundamental radius determinations (except α Aur). We discuss the prospects for improving these and other stellar parameters in the near future.

Strain-Induced Pseudo–Magnetic Fields Greater Than 300 Tesla in Graphene Nanobubbles

Abstract: Recent theoretical proposals suggest that strain can be used to engineer graphene electronic states through the creation of a pseudo-magnetic field. This effect is unique to graphene because of its massless Dirac fermion-like band structure and particular lattice symmetry (C3v). Here, we present experimental spectroscopic measurements by scanning tunneling microscopy of highly strained nanobubbles that form when graphene is grown on a platinum (111) surface. The nanobubbles exhibit Landau levels that form in the presence of strain-induced pseudo-magnetic fields greater than 300 tesla. This demonstration of enormous pseudo-magnetic fields opens the door to both the study of charge carriers in previously inaccessible high magnetic field regimes and deliberate mechanical control over electronic structure in graphene or so-called "strain engineering."

The Biodiversity of the Mediterranean Sea: Estimates, Patterns, and Threats

Abstract: The Mediterranean Sea is a marine biodiversity hot spot. Here we combined an extensive literature analysis with expert opinions to update publicly available estimates of major taxa in this marine ecosystem and to revise and update several species lists. We also assessed overall spatial and temporal patterns of species diversity and identified major changes and threats. Our results listed approximately 17,000 marine species occurring in the Mediterranean Sea. However, our estimates of marine diversity are still incomplete as yet—undescribed species will be added in the future. Diversity for microbes is substantially underestimated, and the deep-sea areas and portions of the southern and eastern region are still poorly known. In addition, the invasion of alien species is a crucial factor that will continue to change the biodiversity of the Mediterranean, mainly in its eastern basin that can spread rapidly northwards and westwards due to the warming of the Mediterranean Sea. Spatial patterns showed a general decrease in biodiversity from northwestern to southeastern regions following a gradient of production, with some exceptions and caution due to gaps in our knowledge of the biota along the southern and eastern rims. Biodiversity was also generally higher in coastal areas and continental shelves, and decreases with depth. Temporal trends indicated that overexploitation and habitat loss have been the main human drivers of historical changes in biodiversity. At present, habitat loss and degradation, followed by fishing impacts, pollution, climate change, eutrophication, and the establishment of alien species are the most important threats and affect the greatest number of taxonomic groups. All these impacts are expected to grow in importance in the future, especially climate change and habitat degradation. The spatial identification of hot spots highlighted the ecological importance of most of the western Mediterranean shelves (and in particular, the Strait of Gibraltar and the adjacent Alboran Sea), western African coast, the Adriatic, and the Aegean Sea, which show high concentrations of endangered, threatened, or vulnerable species. The Levantine Basin, severely impacted by the invasion of species, is endangered as well. This abstract has been translated to other languages (File S1).

Optical excitations in electron microscopy

Abstract: This review discusses how low-energy, valence excitations created by swift electrons can render information on the optical response of structured materials with unmatched spatial resolution. Electron microscopes are capable of focusing electron beams on sub-nanometer spots and probing the target response either by analyzing electron energy losses or by detecting emitted radiation. Theoretical frameworks suited to calculate the probability of energy loss and light emission (cathodoluminescence) are revisited and compared with experimental results. More precisely, a quantum-mechanical description of the interaction between the electrons and the sample is discussed, followed by a powerful classical dielectric approach that can be in practice applied to more complex systems. We assess the conditions under which classical and quantum-mechanical formulations are equivalent. The excitation of collective modes such as plasmons is studied in bulk materials, planar surfaces, and nanoparticles. Light emission induced by the electrons is shown to constitute an excellent probe of plasmons, combining sub-nanometer resolution in the position of the electron beam with nanometer resolution in the emitted wavelength. Both electron energy-loss and cathodoluminescence spectroscopies performed in a scanning mode of operation yield snap shots of plasmon modes in nanostructures with fine spatial detail as compared to other existing imaging techniques, thus providing an ideal tool for nanophotonics studies.

Vitamin C Is an Ideal Substitute for Hydrazine in the Reduction of Graphene Oxide Suspensions

Abstract: The preparation of solution-processable graphene from graphite oxide typically involves a hydrazine reduction step, but the use of such a reagent in the large-scale implementation of this approach is not desirable due to its high toxicity. Here, we compare the deoxygenation efficiency of graphene oxide suspensions by different reductants (sodium borohydride, pyrogallol, and vitamin C, in addition to hydrazine), as well as by heating the suspensions under alkaline conditions. In almost all cases, the degree of reduction attainable and the subsequent restoration of relevant properties (e.g., electrical conductivity) lag significantly behind those achieved with hydrazine. Only vitamin C is found to yield highly reduced suspensions in a way comparable to those provided by hydrazine. Stable suspensions of vitamin C-reduced graphene oxide can be prepared not only in water but also in common organic solvents, such as N,N-dimethylformamide (DMF) or N-methyl-2-pyrrolidone (NMP). These results open the perspective ...

Current-driven spin torque induced by the Rashba effect in a ferromagnetic metal layer

Abstract: Methods to manipulate the magnetization of ferromagnets by means of local electric fields or current-induced spin transfer torque allow the design of integrated spintronic devices with reduced dimensions and energy consumption compared with conventional magnetic field actuation. An alternative way to induce a spin torque using an electric current has been proposed based on intrinsic spin-orbit magnetic fields and recently realized in a strained low-temperature ferromagnetic semiconductor. Here we demonstrate that strong magnetic fields can be induced in ferromagnetic metal films lacking structure inversion symmetry through the Rashba effect. Owing to the combination of spin-orbit and exchange interactions, we show that an electric current flowing in the plane of a Co layer with asymmetric Pt and AlO(x) interfaces produces an effective transverse magnetic field of 1 T per 10(8) A cm(-2). Besides its fundamental significance, the high efficiency of this process makes it a realistic candidate for room-temperature spintronic applications.

Notes on the characterization of prokaryote strains for taxonomic purposes.

Abstract: Taxonomy relies on three key elements: characterization, classification and nomenclature. All three elements are dynamic fields, but each step depends on the one which precedes it. Thus, the nomenclature of a group of organisms depends on the way they are classified, and the classification (among other elements) depends on the information gathered as a result of characterization. While nomenclature is governed by the Bacteriological Code, the classification and characterization of prokaryotes is an area that is not formally regulated and one in which numerous changes have taken place in the last 50 years. The purpose of the present article is to outline the key elements in the way that prokaryotes are characterized, with a view to providing an overview of some of the pitfalls commonly encountered in taxonomic papers.

TranslatorX: multiple alignment of nucleotide sequences guided by amino acid translations

Abstract: We present TranslatorX, a web server designed to align protein-coding nucleotide sequences based on their corresponding amino acid translations. Many comparisons between biological sequences (nucleic acids and proteins) involve the construction of multiple alignments. Alignments represent a statement regarding the homology between individual nucleotides or amino acids within homologous genes. As protein-coding DNA sequences evolve as triplets of nucleotides (codons) and it is known that sequence similarity degrades more rapidly at the DNA than at the amino acid level, alignments are generally more accurate when based on amino acids than on their corresponding nucleotides. TranslatorX novelties include: (i) use of all documented genetic codes and the possibility of assigning different genetic codes for each sequence; (ii) a battery of different multiple alignment programs; (iii) translation of ambiguous codons when possible; (iv) an innovative criterion to clean nucleotide alignments with GBlocks based on protein information; and (v) a rich output, including Jalview-powered graphical visualization of the alignments, codon-based alignments coloured according to the corresponding amino acids, measures of compositional bias and first, second and third codon position specific alignments. The TranslatorX server is freely available at http://translatorx.co.uk.

Circuit quantum electrodynamics in the ultrastrong-coupling regime

Abstract: The Jaynes–Cummings model describes the interaction between a two-level system and a small number of photons. It is now shown that the model breaks down in the regime of ultrastrong coupling between light and matter. The spectroscopic response of a superconducting artificial atom in a waveguide resonator indicates higher-order processes.

Light passing through subwavelength apertures

Abstract: This review provides a perspective on the recent developments in the transmission of light through subwavelength apertures in metal films. The main focus is on the phenomenon of extraordinary optical transmission in periodic hole arrays, discovered over a decade ago. It is shown that surface electromagnetic modes play a key role in the emergence of the resonant transmission. These modes are also shown to be at the root of both the enhanced transmission and beaming of light found in single apertures surrounded by periodic corrugations. This review describes both the theoretical and experimental aspects of the subject. For clarity, the physical mechanisms operating in the different structures considered are analyzed within a common theoretical framework. Several applications based on the transmission properties of subwavelength apertures are also addressed.

Viral mutation rates.

Abstract: Accurate estimates of virus mutation rates are important to understand the evolution of the viruses and to combat them. However, methods of estimation are varied and often complex. Here, we critically review over 40 original studies and establish criteria to facilitate comparative analyses. The mutation rates of 23 viruses are presented as substitutions per nucleotide per cell infection (s/n/c) and corrected for selection bias where necessary, using a new statistical method. The resulting rates range from 10 8 to10 6 s/n/c for DNA viruses and from 10 6 to 10 4 s/n/c for RNA viruses. Similar to what has been shown previously for DNA viruses, there appears to be a negative correlation between mutation rate and genome size among RNA viruses, but this result requires further experimental testing. Contrary to some suggestions, the mutation rate of retroviruses is not lower than that of other RNA viruses. We also show that nucleotide substitutions are on average four times more common than insertions/deletions (indels). Finally, we provide estimates of the mutation rate per nucleotide per strand copying, which tends to be lower than that per cell infection because some viruses undergo several rounds of copying per cell, particularly double-stranded DNA viruses. A regularly updated virus mutation rate data set will be available at www.uv.es/rsanjuan/virmut.

How well do we understand the impacts of alien species on ecosystem services? A pan-European, cross-taxa assessment

Abstract: Recent comprehensive data provided through the DAISIE project (www.europe-aliens.org) have facilitated the development of the first pan-European assessment of the impacts of alien plants, vertebrates, and invertebrates – in terrestrial, freshwater, and marine environments – on ecosystem services. There are 1094 species with documented ecological impacts and 1347 with economic impacts. The two taxonomic groups with the most species causing impacts are terrestrial invertebrates and terrestrial plants. The North Sea is the maritime region that suffers the most impacts. Across taxa and regions, ecological and economic impacts are highly correlated. Terrestrial invertebrates create greater economic impacts than ecological impacts, while the reverse is true for terrestrial plants. Alien species from all taxonomic groups affect “supporting”, “provisioning”, “regulating”, and “cultural” services and interfere with human well-being. Terrestrial vertebrates are responsible for the greatest range of impacts, and these are widely distributed across Europe. Here, we present a review of the financial costs, as the first step toward calculating an estimate of the economic consequences of alien species in Europe.