Large-scale dynamics associated with clustering of extratropical cyclones affecting Western Europe

Some recent winters in Western Europe have been characterized by the occurrence of multiple extratropical cyclones following a similar path. The occurrence of such cyclone clusters leads to large socio-economic impacts due to damaging winds, storm surges, and floods. Recent studies have statistically characterized the clustering of extratropical cyclones over the North Atlantic and Europe and hypothesized potential physical mechanisms responsible for their formation. Here we analyze 4 months characterized by multiple cyclones over Western Europe (February 1990, January 1993, December 1999, and January 2007). The evolution of the eddy driven jet stream, Rossby wave-breaking, and upstream/downstream cyclone development are investigated to infer the role of the large-scale flow and to determine if clustered cyclones are related to each other. Results suggest that optimal conditions for the occurrence of cyclone clusters are provided by a recurrent extension of an intensified eddy driven jet toward Western Europe lasting at least 1 week. Multiple Rossby wave-breaking occurrences on both the poleward and equatorward flanks of the jet contribute to the development of these anomalous large-scale conditions. The analysis of the daily weather charts reveals that upstream cyclone development (secondary cyclogenesis, where new cyclones are generated on the trailing fronts of mature cyclones) is strongly related to cyclone clustering, with multiple cyclones developing on a single jet streak. The present analysis permits a deeper understanding of the physical reasons leading to the occurrence of cyclone families over the North Atlantic, enabling a better estimation of the associated cumulative risk over Europe.

Climate perspective on the large-scale circulation associated with the transition of the first South Atlantic hurricane

The landfall of Cyclone Catarina on the Brazilian coast in March 2004 became known as the first documented hurricane in the South Atlantic Ocean, promoting a new view oil how large-scale features can contribute to tropical transition. The aim of this paper is to put the large-scale circulation associated with Catarina`s transition in climate perspective. This is discussed in the light of a robust pattern of spatial correlations between thermodynamic and dynamic variables of importance for hurricane formation. A discussion on how transition mechanisms respond to the present-day circulation is presented. These associations help in understanding why Catarina was formed in a region previously thought to be hurricane-free. Catarina developed over a large-scale area of thermodynamically favourable air/sea temperature contrast. This aspect explains the paradox that such a rare system developed when the sea surface temperature was slightly below average. But, although thermodynamics played an important role, it is apparent that Catarina would not have formed without the key dynamic interplay triggered by a high latitude blocking. The blocking was associated with an extreme positive phase of the Southern Annular Mode (SAM) both hemispherically and locally, and the nearby area where Catarina developed is found to be more cyclonic during the positive phase of the SAM. A conceptual model is developed and a `South Atlantic index` is introduced as a useful diagnostic of potential conditions leading to tropical transition in the area, where large-scale indices indicate trends towards more favourable atmospheric conditions for tropical cyclone formation. Copyright (c) 2008 Royal Meteorological Society

Influence of multi-scale landscape structure on the occurrence of carnivorous mammals in a human-modified savanna, Brazil

So Paulo is the most developed state in Brazil and contains few fragments of native ecosystems, generally surrounded by intensive agriculture lands. Despite this, some areas still shelter large native animals. We aimed at understanding how medium and large carnivores use a mosaic landscape of forest/savanna and agroecosystems, and how the species respond to different landscape parameters (percentage of landcover and edge density), in a multi-scale perspective. The response variables were: species richness, carnivore frequency and frequency for the three most recorded species (Puma concolor, Chrysocyon brachyurus and Leopardus pardalis). We compared 11 competing models using Akaike`s information criterion (AIC) and assessed model support using weight of AIC. Concurrent models were combinations of landcover types (native vegetation, ""cerrado"" formations, ""cerrado"" and eucalypt plantation), landscape feature (percentage of landcover and edge density) and spatial scale. Herein, spatial scale refers to the radius around a sampling point defining a circular landscape. The scales analyzed were 250 (fine), 1,000 (medium) and 2,000 m (coarse). The shape of curves for response variables (linear, exponential and power) was also assessed. Our results indicate that species with high mobility, P. concolor and C. brachyurus, were best explained by edge density of the native vegetation at a coarse scale (2,000 m). The relationship between P. concolor and C. brachyurus frequency had a negative power-shaped response to explanatory variables. This general trend was also observed for species richness and carnivore frequency. Species richness and P. concolor frequency were also well explained by a second concurrent model: edge density of cerrado at the fine (250 m) scale. A different response was recorded for L. pardalis, as the frequency was best explained for the amount of cerrado at the fine (250 m) scale. The curve of response was linearly positive. The contrasting results (P. concolor and C. brachyurus vs L. pardalis) may be due to the much higher mobility of the two first species, in comparison with the third. Still, L. pardalis requires habitat with higher quality when compared with other two species. This study highlights the importance of considering multiple spatial scales when evaluating species responses to different habitats. An important and new finding was the prevalence of edge density over the habitat extension to explain overall carnivore distribution, a key information for planning and management of protected areas.

Resilience of protein-protein interaction networks as determined by their large-scale topological features

The relationship between the structure and function of biological networks constitutes a fundamental issue in systems biology. Particularly, the structure of protein-protein interaction networks is related to important biological functions. In this work, we investigated how such a resilience is determined by the large scale features of the respective networks. Four species are taken into account, namely yeast Saccharomyces cerevisiae, worm Caenorhabditis elegans, fly Drosophila melanogaster and Homo sapiens. We adopted two entropy-related measurements (degree entropy and dynamic entropy) in order to quantify the overall degree of robustness of these networks. We verified that while they exhibit similar structural variations under random node removal, they differ significantly when subjected to intentional attacks (hub removal). As a matter of fact, more complex species tended to exhibit more robust networks. More specifically, we quantified how six important measurements of the networks topology (namely clustering coefficient, average degree of neighbors, average shortest path length, diameter, assortativity coefficient, and slope of the power law degree distribution) correlated with the two entropy measurements. Our results revealed that the fraction of hubs and the average neighbor degree contribute significantly for the resilience of networks. In addition, the topological analysis of the removed hubs indicated that the presence of alternative paths between the proteins connected to hubs tend to reinforce resilience. The performed analysis helps to understand how resilience is underlain in networks and can be applied to the development of protein network models.

The structure of the asteroid 4 Vesta as revealed by models of planet-scale collisions

Asteroid 4Vesta seems to be a major intact protoplanet, with a surface composition similar to that of the HED (howardite-eucrite-diogenite) meteorites. The southern hemisphere is dominated by a giant impact scar, but previous impact models have failed to reproduce the observed topography. The recent discovery that Vesta's southern hemisphere is dominated by two overlapping basins provides an opportunity to model Vesta's topography more accurately. Here we report three-dimensional simulations of Vesta's global evolution under two overlapping planet-scale collisions. We closely reproduce its observed shape, and provide maps of impact excavation and ejecta deposition. Spiral patterns observed in the younger basin Rheasilvia, about one billion years old, are attributed to Coriolis forces during crater collapse. Surface materials exposed in the north come from a depth of about 20kilometres, according to our models, whereas materials exposed inside the southern double-excavation come from depths of about 60-100kilometres. If Vesta began as a layered, completely differentiated protoplanet, then our model predicts large areas of pure diogenites and olivine-rich rocks. These are not seen, possibly implying that the outer 100kilometres or so of Vesta is composed mainly of a basaltic crust (eucrites) with ultramafic intrusions (diogenites).

Concept, design and implementation of a cardiovascular gene-centric 50 k SNP array for large-scale genomic association studies.

A wealth of genetic associations for cardiovascular and metabolic phenotypes in humans has been accumulating over the last decade, in particular a large number of loci derived from recent genome wide association studies (GWAS). True complex disease-associated loci often exert modest effects, so their delineation currently requires integration of diverse phenotypic data from large studies to ensure robust meta-analyses. We have designed a gene-centric 50 K single nucleotide polymorphism (SNP) array to assess potentially relevant loci across a range of cardiovascular, metabolic and inflammatory syndromes. The array utilizes a "cosmopolitan" tagging approach to capture the genetic diversity across approximately 2,000 loci in populations represented in the HapMap and SeattleSNPs projects. The array content is informed by GWAS of vascular and inflammatory disease, expression quantitative trait loci implicated in atherosclerosis, pathway based approaches and comprehensive literature searching. The custom flexibility of the array platform facilitated interrogation of loci at differing stringencies, according to a gene prioritization strategy that allows saturation of high priority loci with a greater density of markers than the existing GWAS tools, particularly in African HapMap samples. We also demonstrate that the IBC array can be used to complement GWAS, increasing coverage in high priority CVD-related loci across all major HapMap populations. DNA from over 200,000 extensively phenotyped individuals will be genotyped with this array with a significant portion of the generated data being released into the academic domain facilitating in silico replication attempts, analyses of rare variants and cross-cohort meta-analyses in diverse populations. These datasets will also facilitate more robust secondary analyses, such as explorations with alternative genetic models, epistasis and gene-environment interactions.

A local electrostatic change is the cause of the large-scale protein conformation shift in bacteriorhodopsin

During light-driven proton transport bacteriorhodopsin shuttles between two protein conformations. A large-scale structural change similar to that in the photochemical cycle is produced in the D85N mutant upon raising the pH, even without illumination. We report here that (i) the pKa values for the change in crystallographic parameters and for deprotonation of the retinal Schiff base are the same, (ii) the retinal isomeric configuration is nearly unaffected by the protein conformation, and (iii) preventing rotation of the C13—C14 double bond by replacing the retinal with an all-trans locked analogue makes little difference to the Schiff base pKa. We conclude that the direct cause of the conformational shift is destabilization of the structure upon loss of interaction of the positively charged Schiff base with anionic residues that form its counter-ion.

The past and the future fate of the universe and the formation of structure in it

The history and the ultimate future fate of the universe as a whole depend on how much the expansion of the universe is decelerated by its own mass. In particular, whether the expansion of the universe will ever come to a halt can be determined from the past expansion. However, the mass density in the universe does not only govern the expansion history and the curvature of space, but in parallel also regulates the growth of hierarchical structure, including the collapse of material into the dense, virialized regions that we identify with galaxies. Hence, the formation of galaxies and their clustered distribution in space depend not only on the detailed physics of how stars are formed but also on the overall structure of the universe. Recent observational efforts, fueled by new large, ground-based telescopes and the Hubble Space Telescope, combined with theoretical progress, have brought us to the verge of determining the expansion history of the universe and space curvature from direct observation and to linking this to the formation history of galaxies.

On the possibility of coherently stimulated recombination and cosmological structure generation: cosmological consequences.

Given a specific physical mechanism for instabilities during cosmological recombination discussed in an earlier paper, we examine the nonlinear growth of density structures to form fractal-like structural patterns out to the horizon scale at that epoch (approximately 200 Mpc today). A model for such fractal patterns is presented. Such effects could explain observed large-scale structure patterns and the formation of objects at high z, while keeping microwave background anisotropies at the observed minimal levels. We also discuss possible microwave background implications of such a transition and note a potentially observable spectral signature at lambda approximately 0.18 mm as well as a weak line near the peak in the microwave background.

Large-scale clustering measurements with photometric redshifts: comparing the dark matter haloes of X-ray AGN, star-forming and passive galaxies at z ≈ 1

We combine multi-wavelength data in the AEGIS-XD and C-COSMOS surveys to measure the typical dark matter halo mass of X-ray selected active galactic nuclei (AGN) [L_X(2–10 keV) > 10^42 erg s^− 1] in comparison with far-infrared selected star-forming galaxies detected in the Herschel/PEP survey (PACS Evolutionary Probe; L_IR > 10^11 L_⊙) and quiescent systems at z ≈ 1. We develop a novel method to measure the clustering of extragalactic populations that uses photometric redshift probability distribution functions in addition to any spectroscopy. This is advantageous in that all sources in the sample are used in the clustering analysis, not just the subset with secure spectroscopy. The method works best for large samples. The loss of accuracy because of the lack of spectroscopy is balanced by increasing the number of sources used to measure the clustering. We find that X-ray AGN, far-infrared selected star-forming galaxies and passive systems in the redshift interval 0.6 < z < 1.4 are found in haloes of similar mass, log M_DMH/(M_⊙ h^−1) ≈ 13.0. We argue that this is because the galaxies in all three samples (AGN, star-forming, passive) have similar stellar mass distributions, approximated by the J-band luminosity. Therefore, all galaxies that can potentially host X-ray AGN, because they have stellar masses in the appropriate range, live in dark matter haloes of log M_DMH/(M_⊙ h^−1) ≈ 13.0 independent of their star formation rates. This suggests that the stellar mass of X-ray AGN hosts is driving the observed clustering properties of this population. We also speculate that trends between AGN properties (e.g. luminosity, level of obscuration) and large-scale environment may be related to differences in the stellar mass of the host galaxies.

The large scale distribution of galaxies in the Shapley Supercluster

We present new results of our wide-field redshift survey of galaxies in a 182 square degree region of the Shapley Supercluster (SSC) based on observations with the FLAIR-II spectrograph on the UK Schmidt Telescope (UKST). In this paper we present new measurements to give a total sample of redshifts for 710 bright (R less than or equal to 16.6) galaxies, of which 464 are members of the SSC (8000 < υ < 18 000 km s(-1)). Our data reveal that the main plane of the SSC (upsilon approximate to 14 500 km s(-1)) extends further than previously realised, filling the whole extent of our survey region of 10 degrees by 20 degrees on the sky (35 Mpc by 70 Mpc, for H-0 = 75 km s(-1) Mpc(-1)). There is also a significant structure associated with the slightly nearer Abell 3571 cluster complex (upsilon approximate to 12 000 km s(-1)) with a caustic structure evident out to a radius of 6 Mpc. These galaxies seem to link two previously identified sheets of galaxies and establish a connection with a third one at (V) over bar = 15 000 km s(-1) near RA = 13(h). They also tend to fill the gap of galaxies between the foreground Hydra-Centaurus region and the more distant SSC. We calculate galaxy overdensities of 5.0+/-0.1 over the 182 square degree region surveyed and 3.3+.-0.1 in a 159 square degree region excluding rich clusters. Over the large region of our survey the inter-cluster galaxies make up 46 per cent of all galaxies in the SSC region and may contribute a similar amount of mass to the cluster galaxies.

Toward an atomistic understanding of the immune synapse:large-scale molecular dynamics simulation of a membrane-embedded TCR-pMHC-CD4 complex

T-cell activation requires interaction of T-cell receptors (TCR) with peptide epitopes bound by major histocompatibility complex (MHC) proteins. This interaction occurs at a special cell-cell junction known as the immune or immunological synapse. Fluorescence microscopy has shown that the interplay among one agonist peptide-MHC (pMHC), one TCR and one CD4 provides the minimum complexity needed to trigger transient calcium signalling. We describe a computational approach to the study of the immune synapse. Using molecular dynamics simulation, we report here on a study of the smallest viable model, a TCR-pMHC-CD4 complex in a membrane environment. The computed structural and thermodynamic properties are in fair agreement with experiment. A number of biomolecules participate in the formation of the immunological synapse. Multi-scale molecular dynamics simulations may be the best opportunity we have to reach a full understanding of this remarkable supra-macromolecular event at a cell-cell junction.

Large-scale molecular dynamics simulations of HLA-A*0201 complexed with a tumor-specific antigenic peptide:can the α3 and β2m domains be neglected?

Large-scale massively parallel molecular dynamics (MD) simulations of the human class I major histo-compatibility complex (MHC) protein HLA-A*0201 bound to a decameric tumor-specific antigenic peptide GVY-DGREHTV were performed using a scalable MD code on high-performance computing platforms. Such computational capabilities put us in reach of simulations of various scales and complexities. The supercomputing resources available Large-scale massively parallel molecular dynamics (MD) simulations of the human class I major histocompatibility complex (MHC) protein HLA-A*0201 bound to a decameric tumor-specific antigenic peptide GVYDGREHTV were performed using a scalable MD code on high-performance computing platforms. Such computational capabilities put us in reach of simulations of various scales and complexities. The supercomputing resources available for this study allow us to compare directly differences in the behavior of very large molecular models; in this case, the entire extracellular portion of the peptide–MHC complex vs. the isolated peptide binding domain. Comparison of the results from the partial and the whole system simulations indicates that the peptide is less tightly bound in the partial system than in the whole system. From a detailed study of conformations, solvent-accessible surface area, the nature of the water network structure, and the binding energies, we conclude that, when considering the conformation of the α1–α2 domain, the α3 and β2m domains cannot be neglected. © 2004 Wiley Periodicals, Inc. J Comput Chem 25: 1803–1813, 2004

Spatial scale and abundance patterns of large fish communities in freshwater marshes of the Florida Everglades

Anthropogenic habitat alterations and water-management practices have imposed an artificial spatial scale onto the once contiguous freshwater marshes of the Florida Everglades. To gain insight into how these changes may affect biotic communities, we examined whether variation in the abundance and community structure of large fishes (SL . 8 cm) in Everglades marshes varied more at regional or intraregional scales, and whether this variation was related to hydroperiod, water depth, floating mat volume, and vegetation density. From October 1997 to October 2002, we used an airboat electrofisher to sample large fishes at sites within three regions of the Everglades. Each of these regions is subject to unique watermanagement schedules. Dry-down events (water depth , 10 cm) occurred at several sites during spring in 1999, 2000, 2001, and 2002. The 2001 dry-down event was the most severe and widespread. Abundance of several fishes decreased significantly through time, and the number of days post-dry-down covaried significantly with abundance for several species. Processes operating at the regional scale appear to play important roles in regulating large fishes. The most pronounced patterns in abundance and community structure occurred at the regional scale, and the effect size for region was greater than the effect size for sites nested within region for abundance of all species combined, all predators combined, and each of the seven most abundant species. Non-metric multi-dimensional scaling revealed distinct groupings of sites corresponding to the three regions. We also found significant variation in community structure through time that correlated with the number of days post-dry-down. Our results suggest that hydroperiod and water management at the regional scale influence large fish communities of Everglades marshes.