The GRAPE aerosol retrieval algorithm

The aerosol component of the Oxford-Rutherford Aerosol and Cloud (ORAC) combined cloud and aerosol retrieval scheme is described and the theoretical performance of the algorithm is analysed. ORAC is an optimal estimation retrieval scheme for deriving cloud and aerosol properties from measurements made by imaging satellite radiometers and, when applied to cloud free radiances, provides estimates of aerosol optical depth at a wavelength of 550 nm, aerosol effective radius and surface reflectance at 550 nm. The aerosol retrieval component of ORAC has several incarnations – this paper addresses the version which operates in conjunction with the cloud retrieval component of ORAC (described by Watts et al., 1998), as applied in producing the Global Retrieval of ATSR Cloud Parameters and Evaluation (GRAPE) data-set.

Shifts in metabolic scaling, production, and efficiency across major evolutionary transitions of life

The diversification of life involved enormous increases in size and complexity. The evolutionary transitions from prokaryotes to unicellular eukaryotes to metazoans were accompanied by major innovations inmetabolicdesign.Hereweshowthat thescalingsofmetabolic rate, population growth rate, and production efficiency with body size have changed across the evolutionary transitions.Metabolic rate scales with body mass superlinearly in prokaryotes, linearly in protists, and sublinearly inmetazoans, so Kleiber’s 3/4 power scaling law does not apply universally across organisms. The scaling ofmaximum population growth rate shifts from positive in prokaryotes to negative in protists and metazoans, and the efficiency of production declines across these groups.Major changes inmetabolic processes duringtheearlyevolutionof life overcameexistingconstraints, exploited new opportunities, and imposed new constraints. The 3.5 billion year history of life on earth was characterized by

A 3D cloud-construction algorithm for the EarthCARE satellite mission

This article presents and assesses an algorithm that constructs 3D distributions of cloud from passive satellite imagery and collocated 2D nadir profiles of cloud properties inferred synergistically from lidar, cloud radar and imager data. It effectively widens the active–passive retrieved cross-section (RXS) of cloud properties, thereby enabling computation of radiative fluxes and radiances that can be compared with measured values in an attempt to perform radiative closure experiments that aim to assess the RXS. For this introductory study, A-train data were used to verify the scene-construction algorithm and only 1D radiative transfer calculations were performed. The construction algorithm fills off-RXS recipient pixels by computing sums of squared differences (a cost function F) between their spectral radiances and those of potential donor pixels/columns on the RXS. Of the RXS pixels with F lower than a certain value, the one with the smallest Euclidean distance to the recipient pixel is designated as the donor, and its retrieved cloud properties and other attributes such as 1D radiative heating rates are consigned to the recipient. It is shown that both the RXS itself and Moderate Resolution Imaging Spectroradiometer (MODIS) imagery can be reconstructed extremely well using just visible and thermal infrared channels. Suitable donors usually lie within 10 km of the recipient. RXSs and their associated radiative heating profiles are reconstructed best for extensive planar clouds and less reliably for broken convective clouds. Domain-average 1D broadband radiative fluxes at the top of theatmosphere(TOA)for (21 km)2 domains constructed from MODIS, CloudSat andCloud–Aerosol Lidar and Infrared Pathfinder Satellite Observations (CALIPSO) data agree well with coincidental values derived from Clouds and the Earth’s Radiant Energy System (CERES) radiances: differences betweenmodelled and measured reflected shortwave fluxes are within±10Wm−2 for∼35% of the several hundred domains constructed for eight orbits. Correspondingly, for outgoing longwave radiation∼65% are within ±10Wm−2.

Gene duplication and an accelerated evolutionary rate in 11S globulin genes are associated with higher protein synthesis in dicots as compared to monocots

Background: Seed storage proteins are a major source of dietary protein, and the content of such proteins determines both the quantity and quality of crop yield. Significantly, examination of the protein content in the seeds of crop plants shows a distinct difference between monocots and dicots. Thus, it is expected that there are different evolutionary patterns in the genes underlying protein synthesis in the seeds of these two groups of plants. Results: Gene duplication, evolutionary rate and positive selection of a major gene family of seed storage proteins (the 11S globulin genes), were compared in dicots and monocots. The results, obtained from five species in each group, show more gene duplications, a higher evolutionary rate and positive selections of this gene family in dicots, which are rich in 11S globulins, but not in the monocots. Conclusion: Our findings provide evidence to support the suggestion that gene duplication and an accelerated evolutionary rate may be associated with higher protein synthesis in dicots as compared to monocots.

The North Atlantic jet stream under climate change and its relation to the NAO and EA patterns

This paper describes recent variations of the North Atlantic eddy-driven jet stream and analyzes the mean response of the jet to anthropogenic forcing in climate models. Jet stream changes are analyzed both using a direct measure of the near-surface westerly wind maximum and using an EOF-based approach. This allows jet stream changes to be related to the widely used leading patterns of variability: the North Atlantic Oscillation (NAO) and East Atlantic (EA) pattern. Viewed in NAO–EA state space, isolines of jet latitude and speed resemble a distorted polar coordinate system, highlighting the dependence of the jet stream quantities on both spatial patterns. Some differences in the results of the two methods are discussed, but both approaches agree on the general characteristics of the climate models. While there is some agreement between models on a poleward shift of the jet stream in response to anthropogenic forcing, there is still considerable spread between different model projections, especially in winter. Furthermore, the model responses to forcing are often weaker than their biases when compared to a reanalysis. Diagnoses of jet stream changes can be sensitive to the methodologies used, and several aspects of this are also discussed.

An improvement in clear-air turbulence forecasting based on spontaneous imbalance theory: the ULTURB algorithm

Recent research has shown that Lighthill–Ford spontaneous gravity wave generation theory, when applied to numerical model data, can help predict areas of clear-air turbulence. It is hypothesized that this is the case because spontaneously generated atmospheric gravity waves may initiate turbulence by locally modifying the stability and wind shear. As an improvement on the original research, this paper describes the creation of an ‘operational’ algorithm (ULTURB) with three modifications to the original method: (1) extending the altitude range for which the method is effective downward to the top of the boundary layer, (2) adding turbulent kinetic energy production from the environment to the locally produced turbulent kinetic energy production, and, (3) transforming turbulent kinetic energy dissipation to eddy dissipation rate, the turbulence metric becoming the worldwide ‘standard’. In a comparison of ULTURB with the original method and with the Graphical Turbulence Guidance second version (GTG2) automated procedure for forecasting mid- and upper-level aircraft turbulence ULTURB performed better for all turbulence intensities. Since ULTURB, unlike GTG2, is founded on a self-consistent dynamical theory, it may offer forecasters better insight into the causes of the clear-air turbulence and may ultimately enhance its predictability.

Divergent evolutionary pattern of starch biosynthetic pathway genes in grasses and dicots

Starch is the most widespread and abundant storage carbohydrate in crops and its production is critical to both crop yield and quality. As regards the starch content in the seeds of crop plants, there are distinct difference between grasses (Poaceae) and dicots. However, few studies have described the evolutionary pattern of genes in the starch biosynthetic pathway in these two groups of plants. In this study, therefore, an attempt was made to compare the evolutionary rate, gene duplication and selective pattern of the key genes involved in this pathway between the two groups, using five grasses and five dicots as materials. The results showed (i) distinct differences in patterns of gene duplication and loss between grasses and dicots; duplication in grasses mainly occurred prior to the divergence of grasses, whereas duplication mostly occurred in individual species within the dicots; there is less gene loss in grasses than in dicots; (ii) a considerably higher evolutionary rate in grasses than in dicots in most gene families analyzed; (iii) evidence of a different selective pattern between grasses and dicots; positive selection may have occurred asymmetrically in grasses in some gene families, e.g. AGPase small subunit. Therefore, we deduced that gene duplication contributes to, and a higher evolutionary rate is associated with, the higher starch content in grasses. In addition, two novel aspects of the evolution of the starch biosynthetic pathway were observed.

An elastic net orthogonal forward regression algorithm

In this paper we propose an efficient two-level model identification method for a large class of linear-in-the-parameters models from the observational data. A new elastic net orthogonal forward regression (ENOFR) algorithm is employed at the lower level to carry out simultaneous model selection and elastic net parameter estimation. The two regularization parameters in the elastic net are optimized using a particle swarm optimization (PSO) algorithm at the upper level by minimizing the leave one out (LOO) mean square error (LOOMSE). Illustrative examples are included to demonstrate the effectiveness of the new approaches.

Evolutionary developmental biology: impact on systematic theory and practice, and the contribution of systematics

Evolutionary developmental genetics brings together systematists, morphologists and developmental geneticists; it will therefore impact on each of these component disciplines. The goals and methods of phylogenetic analysis are reviewed here, and the contribution of evolutionary developmental genetics to morphological systematics, in terms of character conceptualisation and primary homology assessment, is discussed. Evolutionary developmental genetics, like its component disciplines phylogenetic systematics and comparative morphology, is concerned with homology concepts. Phylogenetic concepts of homology and their limitations are considered here, and the need for independent homology statements at different levels of biological organisation is evaluated. The role of systematics in evolutionary developmental genetics is outlined. Phylogenetic systematics and comparative morphology will suggest effective sampling strategies to developmental geneticists. Phylogenetic systematics provides hypotheses of character evolution (including parallel evolution and convergence), stimulating investigations into the evolutionary gains and losses of morphologies. Comparative morphology identifies those structures that are not easily amenable to typological categorisation, and that may be of particular interest in terms of developmental genetics. The concepts of latent homology and genetic recall may also prove useful in the evolutionary interpretation of developmental genetic data.

The music instinct: the evolutionary basis of musicality

Why does music pervade our lives and those of all known human beings living today and in the recent past? Why do we feel compelled to engage in musical activity, or at least simply enjoy listening to music even if we choose not to actively participate? I argue that this is because musicality—communication using variations in pitch, rhythm, dynamics and timbre, by a combination of the voice, body (as in dance), and material culture—was essential to the lives of our pre-linguistic hominin ancestors. As a consequence we have inherited a desire to engage with music, even if this has no adaptive benefit for us today as a species whose communication system is dominated by spoken language. In this article I provide a summary of the arguments to support this view.

Evolutionary dynamics of Staphylococcus aureus during progression from carriage to disease

Whole-genome sequencing offers new insights into the evolution of bacterial pathogens and the etiology of bacterial disease. Staph- ylococcus aureus is a major cause of bacteria-associated mortality and invasive disease and is carried asymptomatically by 27% of adults. Eighty percent of bacteremias match the carried strain. How- ever, the role of evolutionary change in the pathogen during the progression from carriage to disease is incompletely understood. Here we use high-throughput genome sequencing to discover the genetic changes that accompany the transition from nasal carriage to fatal bloodstream infection in an individual colonized with meth- icillin-sensitive S. aureus. We found a single, cohesive population exhibiting a repertoire of 30 single-nucleotide polymorphisms and four insertion/deletion variants. Mutations accumulated at a steady rate over a 13-mo period, except for a cluster of mutations preceding the transition to disease. Although bloodstream bacteria differed by just eight mutations from the original nasally carried bacteria, half of those mutations caused truncation of proteins, including a prema- ture stop codon in an AraC-family transcriptional regulator that has been implicated in pathogenicity. Comparison with evolution in two asymptomatic carriers supported the conclusion that clusters of pro- tein-truncating mutations are highly unusual. Our results demon- strate that bacterial diversity in vivo is limited but nonetheless detectable by whole-genome sequencing, enabling the study of evolutionary dynamics within the host. Regulatory or structural changes that occur during carriage may be functionally important for pathogenesis; therefore identifying those changes is a crucial step in understanding the biological causes of invasive bacterial disease.