Mapping the universe in three dimensions

The determination of the three-dimensional layout of galaxies is critical to our understanding of the evolution of galaxies and the structures in which they lie, to our determination of the fundamental parameters of cosmology, and to our understanding of both the past and future histories of the universe at large. The mapping of the large scale structure in the universe via the determination of galaxy red shifts (Doppler shifts) is a rapidly growing industry thanks to technological developments in detectors and spectrometers at radio and optical wavelengths. First-order application of the red shift-distance relation (Hubble’s law) allows the analysis of the large-scale distribution of galaxies on scales of hundreds of megaparsecs. Locally, the large-scale structure is very complex but the overall topology is not yet clear. Comparison of the observed red shifts with ones expected on the basis of other distance estimates allows mapping of the gravitational field and the underlying total density distribution. The next decade holds great promise for our understanding of the character of large-scale structure and its origin.

Cyclically-arranged, storm-controlled, prograding lithosomes in Messinian terrigenous shelves (Bajo Segura Basin, western Mediterranean)

This work focuses on a Messinian shallow-marine terrigenous unit, termed the La Virgen Formation, which forms part of the sedimentary infill of the Bajo Segura Basin (Betic margin of the western Mediterranean). This formation was deposited during a high sea level phase prior to the onset of the Messinian Salinity Crisis. Stratigraphically, it comprises a prograding stack of sandstone lithosomes alternating with marly intervals (1st-order cyclicity). These lithosomes are characterized by a homoclinal geometry that tapers distally, and interfinger with pelagic sediments rich in planktonic and benthic microfauna (Torremendo Formation). An analysis of sedimentary facies of each lithosome reveals a repetitive succession of sandy storm beds (tempestites), occasionally amalgamated, which are separated by thin marly layers (2nd-order cyclicity). Each storm bed contains internal erosional surfaces (3rd-order cyclicity) that delimit sets of laminae. Two categories of storm beds have been differentiated. The first one includes layers formed below storm wave base (SWB), characterized by traction structures associated to unidirectional flows (scoured base, planar lamination, and parting lineation). The second category consists of layers deposited above the SWB which display typical high regime oscillatory flow structures (swaley and hummocky cross lamination). In both cases, the ichnological record is characterized by an oligotypic association of Ophiomorpha nodosa, which can be interpreted as the result of allochthonous tracemakers (crustaceans) transported during storm events together with the sediment. The benthic microfauna in the marly intervals that separate the sandstone lithosomes (1st-order cyclicity) indicates that the storm ebb surges were deposited at depths ranging from those of inner shelf settings (with Elphidium spp. and Cibicides lobatulus) to those of outer shelf (with Valvulineria complanata and Uvigerina cylindrica). At the distal end of the sandstone lithosomes, the planktonic microfauna is characterized by a high content of taxa indicative of warm-oligotrophic waters (Globigerinoides obliquus and Globigerinoides bulloideus). In contrast, in the marly intervals, the microfauna is dominated by species typical of cold-eutrophic waters (Globigerina and Neogloboquadrina). This alternation of planktic foraminiferal assemblages is interpreted as being the expression of climatic cycles, in which every episode of progradation of tempestite-dominated lithosomes corresponds to maximum insolation and warm waters, whereas episodes of marly deposition correspond to minimal insolation and cold waters. The 1st-order cyclicity recorded in the La Virgen Formation, in a context of terrigenous storm-dominated shelf, corresponds to sapropel/homogeneous marl cycles formed in a pelagic basin (Torremendo Fm). These cycles in pelagic sediments are commonplace throughout the Mediterranean during the Messinian and reflect precession orbital changes: repeated periods of maximum insolation – minimum precession (sapropels) and minimal insolation – maximum precession (homogeneous marls). The fact that the example of terrigenous unit studied herein is coetaneous with the well-developed reef complexes in the Mediterranean basins points out the importance of sediment supply in the formation of large-scale sandy lithosomes. This is a crucial aspect to understanding reservoir genesis as well as lateral stratigraphic relationships with potential seal and/or source rocks.

PRELIMINARY RESULTS OF A LARGE-SCALE TREE INVENTORY OF UPLAND RAIN FOREST IN THE CENTRAL AMAZON

A large-scale inventory of trees > 10cm DBH was conducted in the upland "terra firme" rain forest of the Distrito Agropecuário da SUFRAMA (Manaus Free Zone Authority Agricultural District) approximately 65Km north of the city of Manaus (AM), Srasil. Thegeneral appearance and structure of the forest is described together with local topography and soil texture. Thepreliminary results of the Inventory provide a minimum estimate of 698 tree species in 53 families in the 40Km radius sampled, including 17 undescribed species. Themost numerically abundant families, Lecythidaceae, Leguminosae, 5apotaceae and Burseraceae as also among the most species rich families. One aspect of this diverse assemblage is the proliferation of species within certain genera, Including 26 genera In 17 families with 6 or more species or morphospecies. Most species have very low abundances of less than 1 tree per hectare. While more abundant species do exist at densities ranging up to a mean of 12 trees per ha, many have clumped distributions leading to great variation in local species abundance. The degree of similarity between hectare samples based int the Coefficient of Community similarity Index varies widely over different sample hectares for five ecologically different families. Soil texture apparently plays a significant role In determining species composition in the different one hectare plots examined while results for other variable were less consistent. Greater differences in similarity indices are found for comparisons with a one hectare sample within the same formation approximately 40Km to the south. It is concluded that homogeneity of tree community composition within this single large and diverse yet continuous upland forest formation can not be assumed.

The co-evolution of social institutions, demography, and large-scale human cooperation.

Human cooperation is typically coordinated by institutions, which determine the outcome structure of the social interactions individuals engage in. Explaining the Neolithic transition from small- to large-scale societies involves understanding how these institutions co-evolve with demography. We study this using a demographically explicit model of institution formation in a patch-structured population. Each patch supports both social and asocial niches. Social individuals create an institution, at a cost to themselves, by negotiating how much of the costly public good provided by cooperators is invested into sanctioning defectors. The remainder of their public good is invested in technology that increases carrying capacity, such as irrigation systems. We show that social individuals can invade a population of asocials, and form institutions that support high levels of cooperation. We then demonstrate conditions where the co-evolution of cooperation, institutions, and demographic carrying capacity creates a transition from small- to large-scale social groups.

A comparative study of Java and C performance in two large-scale parallel applications

In the 1990s the Message Passing Interface Forum defined MPI bindings for Fortran, C, and C++. With the success of MPI these relatively conservative languages have continued to dominate in the parallel computing community. There are compelling arguments in favour of more modern languages like Java. These include portability, better runtime error checking, modularity, and multi-threading. But these arguments have not converted many HPC programmers, perhaps due to the scarcity of full-scale scientific Java codes, and the lack of evidence for performance competitive with C or Fortran. This paper tries to redress this situation by porting two scientific applications to Java. Both of these applications are parallelized using our thread-safe Java messaging system—MPJ Express. The first application is the Gadget-2 code, which is a massively parallel structure formation code for cosmological simulations. The second application uses the finite-domain time-difference method for simulations in the area of computational electromagnetics. We evaluate and compare the performance of the Java and C versions of these two scientific applications, and demonstrate that the Java codes can achieve performance comparable with legacy applications written in conventional HPC languages. Copyright © 2009 John Wiley & Sons, Ltd.

Recent patterns of change in vegetation structure and tree composition of British broadleaved woodland: evidence from large-scale surveys

Evidence is presented of widespread changes in structure and species composition between the 1980s and 2003–2004 from surveys of 249 British broadleaved woodlands. Structural components examined include canopy cover, vertical vegetation profiles, field-layer cover and deadwood abundance. Woods were located in 13 geographical localities and the patterns of change were examined for each locality as well as across all woods. Changes were not uniform throughout the localities; overall, there were significant decreases in canopy cover and increases in sub-canopy (2–10 m) cover. Changes in 0.5–2 m vegetation cover showed strong geographic patterns, increasing in western localities, but declining or showing no change in eastern localities. There were significant increases in canopy ash Fraxinus excelsior and decreases in oak Quercus robur/petraea. Shrub layer ash and honeysuckle Lonicera periclymenum increased while birch Betula spp. hawthorn Crataegus monogyna and hazel Corylus avellana declined. Within the field layer, both bracken Pteridium aquilinum and herbs increased. Overall, deadwood generally increased. Changes were consistent with reductions in active woodland management and changes in grazing and browsing pressure. These findings have important implications for sustainable active management of British broadleaved woodlands to meet silvicultural and biodiversity objectives.

Structure formation in the presence of dark energy perturbations

We study non-linear structure formation in the presence of dark energy. The influence of dark energy on the growth of large-scale cosmological structures is exerted both through its background effect on the expansion rate, and through its perturbations. In order to compute the rate of formation of massive objects we employ the spherical collapse formalism, which we generalize to include fluids with pressure. We show that the resulting non-linear evolution equations are identical to the ones obtained in the pseudo-Newtonian approach to cosmological perturbations, in the regime where an equation of state serves to describe both the background pressure relative to density, and the pressure perturbations relative to the density perturbations. We then consider a wide range of constant and time-dependent equations of state (including phantom models) parametrized in a standard way, and study their impact on the non-linear growth of structure. The main effect is the formation of dark energy structure associated with the dark matter halo: non-phantom equations of state induce the formation of a dark energy halo, damping the growth of structures; phantom models, on the other hand, generate dark energy voids, enhancing structure growth. Finally, we employ the Press-Schechter formalism to compute how dark energy affects the number of massive objects as a function of redshift (number counts).

Large-scale protein structure modeling of the Saccharomyces cerevisiae genome

The function of a protein generally is determined by its three-dimensional (3D) structure. Thus, it would be useful to know the 3D structure of the thousands of protein sequences that are emerging from the many genome projects. To this end, fold assignment, comparative protein structure modeling, and model evaluation were automated completely. As an illustration, the method was applied to the proteins in the Saccharomyces cerevisiae (baker’s yeast) genome. It resulted in all-atom 3D models for substantial segments of 1,071 (17%) of the yeast proteins, only 40 of which have had their 3D structure determined experimentally. Of the 1,071 modeled yeast proteins, 236 were related clearly to a protein of known structure for the first time; 41 of these previously have not been characterized at all.

Control of ordered structure and morphology of large-pore periodic mesoporous organosilicas by inorganic salt

Highly ordered rodlike periodic mesoporous organosilicas (PMO) were successfully synthesized using 1.2-bis(trimethoxysilyl)ethane as an precursor and triblock copolymer P123 as a template at low acid concentration and in the presence of inorganic salts (KCl). The role of acid and salt as well as the effects of synthesis temperature and reactant mole ratio in the control of morphology and the formation of ordered mesostructure was systematically examined. It was found that the addition of inorganic salt can dramatically expand the range of the synthesis parameters to produce highly ordered PMO structure and improve the quality of PMO materials. The morphology of PMOs was significantly dependent on the induction time for precipitation. The uniform PMO rods can only be synthesized in a narrow range of acid and salt concentrations. The results also show that the optimized salt concentration (I M) and low acidity (0.167 M) were beneficial to the formation of not only highly ordered mesostructure but also rodlike morphology. Increasing acidity resulted in fast hydrolysis reaction and short rod or plate-like particles. Highly ordered rod can also be prepared at low temperature (35 degrees C) with high salt amount (1.5 M) or high temperature (45 degrees C) with low salt amount (0.5 M). Optimum reactant molar composition at 40 degrees C is 0.035P123:8KCl:1.34HCI:444H(2)O:1.0bis(trimethoxysilyl)ethane. Lower or higher SiO2/PI23 ratio led to the formation of uniform meso-macropores or pore-blocking effect. (c) 2005 Elsevier Inc. All rights reserved.

Large-scale ecological restoration of high-diversity tropical forests in SE Brazil

The complex interactions among endangered ecosystems, landowners` interests, and different models of land tenure and use, constitute an important series of challenges for those seeking to maintain and restore biodiversity and augment the flow of ecosystem services. Over the past 10 years, we have developed a data-based approach to address these challenges and to achieve medium and large-scale ecological restoration of riparian areas on private lands in the state of Sao Paulo, southeastern Brazil. Given varying motivations for ecological restoration, the location of riparian areas within landholdings, environmental zoning of different riparian areas, and best-practice restoration methods were developed for each situation. A total of 32 ongoing projects, covering 527,982 ha, were evaluated in large sugarcane farms and small mixed farms, and six different restoration techniques have been developed to help upscale the effort. Small mixed farms had higher portions of land requiring protection as riparian areas (13.3%), and lower forest cover of riparian areas (18.3%), than large sugarcane farms (10.0% and 36.9%, respectively for riparian areas and forest cover values). In both types of farms, forest fragments required some degree of restoration. Historical anthropogenic degradation has compromised forest ecosystem structure and functioning, despite their high-diversity of native tree and shrub species. Notably, land use patterns in riparian areas differed markedly. Large sugarcane farms had higher portions of riparian areas occupied by highly mechanized agriculture, abandoned fields, and anthropogenic wet fields created by siltation in water courses. In contrast, in small mixed crop farms, low or non-mechanized agriculture and pasturelands were predominant. Despite these differences, plantations of native tree species covering the entire area was by far the main restoration method needed both by large sugarcane farms (76.0%) and small mixed farms (92.4%), in view of the low resilience of target sites, reduced forest cover, and high fragmentation, all of which limit the potential for autogenic restoration. We propose that plantations should be carried out with a high-diversity of native species in order to create biologically viable restored forests, and to assist long-term biodiversity persistence at the landscape scale. Finally, we propose strategies to integrate the political, socio-economic and methodological aspects needed to upscale restoration efforts in tropical forest regions throughout Latin America and elsewhere. (C) 2010 Elsevier BA/. All rights reserved.

Combustion of alternative biomass fuels in a domestic boiler and in a large-scale furnace

Programa Doutoral em Engenharia Mecânica.

Climate oscillations and species interactions: large-scale congruence but regional differences in the phylogeographic structures of an alpine plant and its monophagous insect

Aim. To predict the fate of alpine interactions involving specialized species, using a monophagous beetle and its host-plant as a case study. Location. The Alps. Methods. We investigated genetic structuring of the herbivorous beetle Oreina gloriosa and its specific host-plant Peucedanum ostruthium. We used genome fingerprinting (in the insect and the plant) and sequence data (in the insect) to compare the distribution of the main gene pools in the two associated species and to estimate divergence time in the insect, a proxy for the temporal origin of the interaction. We quantified the similarity in spatial genetic structures by performing a Procrustes analysis, a tool from the shape theory. Finally, we simulated recolonization of an empty space analogous to the deglaciated Alps just after ice retreat by two lineages from two species showing unbalanced dependence, to examine how timing of the recolonization process, as well as dispersal capacities of associated species, could explain the observed pattern. Results. Contrasting with expectations based on their asymmetrical dependence, patterns in the beetle and plant were congruent at a large scale. Exceptions occurred at a regional scale in areas of admixture, matching known suture zones in Alpine plants. Simulations using a lattice-based model suggested these empirical patterns arose during or soon after recolonization, long after the estimated origin of the interaction c. 0.5 million years ago. Main conclusions. Species-specific interactions are scarce in alpine habitats because glacial cycles have limited opportunities for coevolution. Their fate, however, remains uncertain under climate change. Here we show that whereas most dispersal routes are paralleled at large scale, regional incongruence implies that the destinies of the species might differ under changing climate. This may be a consequence of the host-dependence of the beetle that locally limits the establishment of dispersing insects.

Density-based hierarchical clustering of pyro-sequences on a large scale--the case of fungal ITS1.

MOTIVATION: Analysis of millions of pyro-sequences is currently playing a crucial role in the advance of environmental microbiology. Taxonomy-independent, i.e. unsupervised, clustering of these sequences is essential for the definition of Operational Taxonomic Units. For this application, reproducibility and robustness should be the most sought after qualities, but have thus far largely been overlooked. RESULTS: More than 1 million hyper-variable internal transcribed spacer 1 (ITS1) sequences of fungal origin have been analyzed. The ITS1 sequences were first properly extracted from 454 reads using generalized profiles. Then, otupipe, cd-hit-454, ESPRIT-Tree and DBC454, a new algorithm presented here, were used to analyze the sequences. A numerical assay was developed to measure the reproducibility and robustness of these algorithms. DBC454 was the most robust, closely followed by ESPRIT-Tree. DBC454 features density-based hierarchical clustering, which complements the other methods by providing insights into the structure of the data. AVAILABILITY: An executable is freely available for non-commercial users at ftp://ftp.vital-it.ch/tools/dbc454. It is designed to run under MPI on a cluster of 64-bit Linux machines running Red Hat 4.x, or on a multi-core OSX system. CONTACT: dbc454@vital-it.ch or nicolas.guex@isb-sib.ch.

Effect of ENSO phase on large-scale snow water equivalent distribution in a GCM

Understanding links between the El Nino-Southern Oscillation (ENSO) and snow would be useful for seasonal forecasting, but also for understanding natural variability and interpreting climate change predictions. Here, a 545-year run of the general circulation model HadCM3, with prescribed external forcings and fixed greenhouse gas concentrations, is used to explore the impact of ENSO on snow water equivalent (SWE) anomalies. In North America, positive ENSO events reduce the mean SWE and skew the distribution towards lower values, and vice versa during negative ENSO events. This is associated with a dipole SWE anomaly structure, with anomalies of opposite sign centered in western Canada and the central United States. In Eurasia, warm episodes lead to a more positively skewed distribution and the mean SWE is raised. Again, the opposite effect is seen during cold episodes. In Eurasia the largest anomalies are concentrated in the Himalayas. These correlations with February SWE distribution are seen to exist from the previous June-July-August (JJA) ENSO index onwards, and are weakly detected in 50-year subsections of the control run, but only a shifted North American response can be detected in the anaylsis of 40 years of ERA40 reanalysis data. The ENSO signal in SWE from the long run could still contribute to regional predictions although it would be a weak indicator only