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  1. Revealing the underlying drivers of disaster risk: a global analysis

    Science.gov (United States)

    Peduzzi, Pascal

    2017-04-01

    Disasters events are perfect examples of compound events. Disaster risk lies at the intersection of several independent components such as hazard, exposure and vulnerability. Understanding the weight of each component requires extensive standardisation. Here, I show how footprints of past disastrous events were generated using GIS modelling techniques and used for extracting population and economic exposures based on distribution models. Using past event losses, it was possible to identify and quantify a wide range of socio-politico-economic drivers associated with human vulnerability. The analysis was applied to about nine thousand individual past disastrous events covering earthquakes, floods and tropical cyclones. Using a multiple regression analysis on these individual events it was possible to quantify each risk component and assess how vulnerability is influenced by various hazard intensities. The results show that hazard intensity, exposure, poverty, governance as well as other underlying factors (e.g. remoteness) can explain the magnitude of past disasters. Analysis was also performed to highlight the role of future trends in population and climate change and how this may impacts exposure to tropical cyclones in the future. GIS models combined with statistical multiple regression analysis provided a powerful methodology to identify, quantify and model disaster risk taking into account its various components. The same methodology can be applied to various types of risk at local to global scale. This method was applied and developed for the Global Risk Analysis of the Global Assessment Report on Disaster Risk Reduction (GAR). It was first applied on mortality risk in GAR 2009 and GAR 2011. New models ranging from global assets exposure and global flood hazard models were also recently developed to improve the resolution of the risk analysis and applied through CAPRA software to provide probabilistic economic risk assessments such as Average Annual Losses (AAL

  2. Risk analysis reveals global hotspots for marine debris ingestion by sea turtles

    NARCIS (Netherlands)

    Schuyler, Qamar A.; Wilcox, Chris; Townsend, Kathy A.; Wedemeyer-Strombel, Kathryn R.; Balazs, George; van Sebille, Erik|info:eu-repo/dai/nl/304831921; Hardesty, Britta Denise

    2016-01-01

    Plastic marine debris pollution is rapidly becoming one of the critical environmental concerns facing wildlife in the 21st century. Here we present a risk analysis for plastic ingestion by sea turtles on a global scale. We combined global marine plastic distributions based on ocean drifter data with

  3. Risk Analysis Reveals Global Hotspots for Marine Debris Ingestion by Sea Turtles

    Science.gov (United States)

    Schuyler, Q. A.; Wilcox, C.; Townsend, K.; Wedemeyer-Strombel, K.; Balazs, G.; van Sebille, E.; Hardesty, B. D.

    2016-02-01

    Plastic marine debris pollution is rapidly becoming one of the critical environmental concerns facing wildlife in the 21st century. Here we present a risk analysis for plastic ingestion by sea turtles on a global scale. We combined global marine plastic distributions based on ocean drifter data with sea turtle habitat maps to predict exposure levels to plastic pollution. Empirical data from necropsies of deceased animals were then utilised to assess the consequence of exposure to plastics. We modelled the risk (probability of debris ingestion) by incorporating exposure to debris and consequence of exposure, and included life history stage, species of sea turtle, and date of stranding observation as possible additional explanatory factors. Life history stage is the best predictor of debris ingestion, but the best-fit model also incorporates encounter rates within a limited distance from stranding location, marine debris predictions specific to the date of the stranding study, and turtle species. There was no difference in ingestion rates between stranded turtles vs. those caught as bycatch from fishing activity, suggesting that stranded animals are not a biased representation of debris ingestion rates in the background population. Oceanic life-stage sea turtles are at the highest risk of debris ingestion, and olive ridley turtles are the most at-risk species. The regions of highest risk to global sea turtle populations are off of the east coasts of the USA, Australia, and South Africa; the east Indian Ocean, and Southeast Asia. Model results can be used to predict the number of sea turtles globally at risk of debris ingestion. Based on currently available data, initial calculations indicate that up to 52% of sea turtles may have ingested debris.

  4. Risk analysis reveals global hotspots for marine debris ingestion by sea turtles.

    Science.gov (United States)

    Schuyler, Qamar A; Wilcox, Chris; Townsend, Kathy A; Wedemeyer-Strombel, Kathryn R; Balazs, George; van Sebille, Erik; Hardesty, Britta Denise

    2016-02-01

    Plastic marine debris pollution is rapidly becoming one of the critical environmental concerns facing wildlife in the 21st century. Here we present a risk analysis for plastic ingestion by sea turtles on a global scale. We combined global marine plastic distributions based on ocean drifter data with sea turtle habitat maps to predict exposure levels to plastic pollution. Empirical data from necropsies of deceased animals were then utilised to assess the consequence of exposure to plastics. We modelled the risk (probability of debris ingestion) by incorporating exposure to debris and consequence of exposure, and included life history stage, species of sea turtle and date of stranding observation as possible additional explanatory factors. Life history stage is the best predictor of debris ingestion, but the best-fit model also incorporates encounter rates within a limited distance from stranding location, marine debris predictions specific to the date of the stranding study and turtle species. There is no difference in ingestion rates between stranded turtles vs. those caught as bycatch from fishing activity, suggesting that stranded animals are not a biased representation of debris ingestion rates in the background population. Oceanic life-stage sea turtles are at the highest risk of debris ingestion, and olive ridley turtles are the most at-risk species. The regions of highest risk to global sea turtle populations are off of the east coasts of the USA, Australia and South Africa; the east Indian Ocean, and Southeast Asia. Model results can be used to predict the number of sea turtles globally at risk of debris ingestion. Based on currently available data, initial calculations indicate that up to 52% of sea turtles may have ingested debris. © 2015 John Wiley & Sons Ltd.

  5. Global meta-analysis reveals low consistency of biodiversity congruence relationships.

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    Westgate, Martin J; Barton, Philip S; Lane, Peter W; Lindenmayer, David B

    2014-05-21

    Knowledge of the number and distribution of species is fundamental to biodiversity conservation efforts, but this information is lacking for the majority of species on earth. Consequently, subsets of taxa are often used as proxies for biodiversity; but this assumes that different taxa display congruent distribution patterns. Here we use a global meta-analysis to show that studies of cross-taxon congruence rarely give consistent results. Instead, species richness congruence is highest at extreme spatial scales and close to the equator, while congruence in species composition is highest at large extents and grain sizes. Studies display highest variance in cross-taxon congruence when conducted in areas with dissimilar areal extents (for species richness) or latitudes (for species composition). These results undermine the assumption that a subset of taxa can be representative of biodiversity. Therefore, researchers whose goal is to prioritize locations or actions for conservation should use data from a range of taxa.

  6. Global transcriptome analysis of spore formation in Myxococcus xanthus reveals a locus necessary for cell differentiation

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    Treuner-Lange Anke

    2010-04-01

    Full Text Available Abstract Background Myxococcus xanthus is a Gram negative bacterium that can differentiate into metabolically quiescent, environmentally resistant spores. Little is known about the mechanisms involved in differentiation in part because sporulation is normally initiated at the culmination of a complex starvation-induced developmental program and only inside multicellular fruiting bodies. To obtain a broad overview of the sporulation process and to identify novel genes necessary for differentiation, we instead performed global transcriptome analysis of an artificial chemically-induced sporulation process in which addition of glycerol to vegetatively growing liquid cultures of M. xanthus leads to rapid and synchronized differentiation of nearly all cells into myxospore-like entities. Results Our analyses identified 1 486 genes whose expression was significantly regulated at least two-fold within four hours of chemical-induced differentiation. Most of the previously identified sporulation marker genes were significantly upregulated. In contrast, most genes that are required to build starvation-induced multicellular fruiting bodies, but which are not required for sporulation per se, were not significantly regulated in our analysis. Analysis of functional gene categories significantly over-represented in the regulated genes, suggested large rearrangements in core metabolic pathways, and in genes involved in protein synthesis and fate. We used the microarray data to identify a novel operon of eight genes that, when mutated, rendered cells unable to produce viable chemical- or starvation-induced spores. Importantly, these mutants displayed no defects in building fruiting bodies, suggesting these genes are necessary for the core sporulation process. Furthermore, during the starvation-induced developmental program, these genes were expressed in fruiting bodies but not in peripheral rods, a subpopulation of developing cells which do not sporulate

  7. Global Analysis of miRNA Gene Clusters and Gene Families Reveals Dynamic and Coordinated Expression

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    Li Guo

    2014-01-01

    Full Text Available To further understand the potential expression relationships of miRNAs in miRNA gene clusters and gene families, a global analysis was performed in 4 paired tumor (breast cancer and adjacent normal tissue samples using deep sequencing datasets. The compositions of miRNA gene clusters and families are not random, and clustered and homologous miRNAs may have close relationships with overlapped miRNA species. Members in the miRNA group always had various expression levels, and even some showed larger expression divergence. Despite the dynamic expression as well as individual difference, these miRNAs always indicated consistent or similar deregulation patterns. The consistent deregulation expression may contribute to dynamic and coordinated interaction between different miRNAs in regulatory network. Further, we found that those clustered or homologous miRNAs that were also identified as sense and antisense miRNAs showed larger expression divergence. miRNA gene clusters and families indicated important biological roles, and the specific distribution and expression further enrich and ensure the flexible and robust regulatory network.

  8. Quantitative analysis of proteome and lipidome dynamics reveals functional regulation of global lipid metabolism

    DEFF Research Database (Denmark)

    Casanovas, Albert; Sprenger, Richard R; Tarasov, Kirill

    2015-01-01

    Elucidating how and to what extent lipid metabolism is remodeled under changing conditions is essential for understanding cellular physiology. Here, we analyzed proteome and lipidome dynamics to investigate how regulation of lipid metabolism at the global scale supports remodeling of cellular...

  9. Global gene expression analysis of the zoonotic parasite Trichinella spiralis revealed novel genes in host parasite interaction.

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    Xiaolei Liu

    Full Text Available BACKGROUND: Trichinellosis is a typical food-borne zoonotic disease which is epidemic worldwide and the nematode Trichinella spiralis is the main pathogen. The life cycle of T. spiralis contains three developmental stages, i.e. adult worms, new borne larva (new borne L1 larva and muscular larva (infective L1 larva. Stage-specific gene expression in the parasites has been investigated with various immunological and cDNA cloning approaches, whereas the genome-wide transcriptome and expression features of the parasite have been largely unknown. The availability of the genome sequence information of T. spiralis has made it possible to deeply dissect parasite biology in association with global gene expression and pathogenesis. METHODOLOGY AND PRINCIPAL FINDINGS: In this study, we analyzed the global gene expression patterns in the three developmental stages of T. spiralis using digital gene expression (DGE analysis. Almost 15 million sequence tags were generated with the Illumina RNA-seq technology, producing expression data for more than 9,000 genes, covering 65% of the genome. The transcriptome analysis revealed thousands of differentially expressed genes within the genome, and importantly, a panel of genes encoding functional proteins associated with parasite invasion and immuno-modulation were identified. More than 45% of the genes were found to be transcribed from both strands, indicating the importance of RNA-mediated gene regulation in the development of the parasite. Further, based on gene ontological analysis, over 3000 genes were functionally categorized and biological pathways in the three life cycle stage were elucidated. CONCLUSIONS AND SIGNIFICANCE: The global transcriptome of T. spiralis in three developmental stages has been profiled, and most gene activity in the genome was found to be developmentally regulated. Many metabolic and biological pathways have been revealed. The findings of the differential expression of several protein

  10. A global analysis of bird plumage patterns reveals no association between habitat and camouflage

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    Marius Somveille

    2016-11-01

    Full Text Available Evidence suggests that animal patterns (motifs function in camouflage. Irregular mottled patterns can facilitate concealment when stationary in cluttered habitats, whereas regular patterns typically prevent capture during movement in open habitats. Bird plumage patterns have predominantly converged on just four types—mottled (irregular, scales, bars and spots (regular—and habitat could be driving convergent evolution in avian patterning. Based on sensory ecology, we therefore predict that irregular patterns would be associated with visually noisy closed habitats and that regular patterns would be associated with open habitats. Regular patterns have also been shown to function in communication for sexually competing males to stand-out and attract females, so we predict that male breeding plumage patterns evolved in both open and closed habitats. Here, taking phylogenetic relatedness into account, we investigate ecological selection for bird plumage patterns across the class Aves. We surveyed plumage patterns in 80% of all avian species worldwide. Of these, 2,756 bird species have regular and irregular plumage patterns as well as habitat information. In this subset, we tested whether adult breeding/non-breeding plumages in each sex, and juvenile plumages, were associated with the habitat types found within the species’ geographical distributions. We found no evidence for an association between habitat and plumage patterns across the world’s birds and little phylogenetic signal. We also found that species with regular and irregular plumage patterns were distributed randomly across the world’s eco-regions without being affected by habitat type. These results indicate that at the global spatial and taxonomic scale, habitat does not predict convergent evolution in bird plumage patterns, contrary to the camouflage hypothesis.

  11. A global analysis of bird plumage patterns reveals no association between habitat and camouflage.

    Science.gov (United States)

    Somveille, Marius; Marshall, Kate L A; Gluckman, Thanh-Lan

    2016-01-01

    Evidence suggests that animal patterns (motifs) function in camouflage. Irregular mottled patterns can facilitate concealment when stationary in cluttered habitats, whereas regular patterns typically prevent capture during movement in open habitats. Bird plumage patterns have predominantly converged on just four types-mottled (irregular), scales, bars and spots (regular)-and habitat could be driving convergent evolution in avian patterning. Based on sensory ecology, we therefore predict that irregular patterns would be associated with visually noisy closed habitats and that regular patterns would be associated with open habitats. Regular patterns have also been shown to function in communication for sexually competing males to stand-out and attract females, so we predict that male breeding plumage patterns evolved in both open and closed habitats. Here, taking phylogenetic relatedness into account, we investigate ecological selection for bird plumage patterns across the class Aves. We surveyed plumage patterns in 80% of all avian species worldwide. Of these, 2,756 bird species have regular and irregular plumage patterns as well as habitat information. In this subset, we tested whether adult breeding/non-breeding plumages in each sex, and juvenile plumages, were associated with the habitat types found within the species' geographical distributions. We found no evidence for an association between habitat and plumage patterns across the world's birds and little phylogenetic signal. We also found that species with regular and irregular plumage patterns were distributed randomly across the world's eco-regions without being affected by habitat type. These results indicate that at the global spatial and taxonomic scale, habitat does not predict convergent evolution in bird plumage patterns, contrary to the camouflage hypothesis.

  12. Global analysis of biosynthetic gene clusters reveals vast potential of secondary metabolite production in Penicillium species

    DEFF Research Database (Denmark)

    Nielsen, Jens Christian; Grijseels, Sietske; Prigent, Sylvain

    2017-01-01

    Filamentous fungi produce a wide range of bioactive compounds with important pharmaceutical applications, such as antibiotic penicillins and cholesterol-lowering statins. However, less attention has been paid to fungal secondary metabolites compared to those from bacteria. In this study, we...... sequenced the genomes of 9 Penicillium species and, together with 15 published genomes, we investigated the secondary metabolism of Penicillium and identified an immense, unexploited potential for producing secondary metabolites by this genus. A total of 1,317 putative biosynthetic gene clusters (BGCs) were......-referenced the predicted pathways with published data on the production of secondary metabolites and experimentally validated the production of antibiotic yanuthones in Penicillia and identified a previously undescribed compound from the yanuthone pathway. This study is the first genus-wide analysis of the genomic...

  13. Global analysis of threat status reveals higher extinction risk in tropical than in temperate bird sister species

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    Reif Jiří

    2016-06-01

    Full Text Available Given increasing pressures upon biodiversity, identification of species’ traits related to elevated extinction risk is useful for more efficient allocation of limited resources for nature conservation. Despite its need, such a global analysis was lacking in the case of birds. Therefore, we performed this exercise for avian sister species using information about their global extinction risk from IUCN Red List. We focused on 113 pairs of sister species, each containing a threatened and an unthreatened species to factor out the effects of common evolutionary history on the revealed relationship. We collected data on five traits with expected relationships to species’ extinction risk based on previous studies performed at regional or national levels: breeding habitat (recognizing forest, grassland, wetland and oceanic species, latitudinal range position (temperate and tropics species, migration strategy (migratory and resident species, diet (carnivorous, insectivorous, herbivorous and omnivorous species and body mass. We related the extinction risk using IUCN threat level categories to species’ traits using generalised linear mixed effects models expecting lower risk for forest, temperate, omnivorous and smaller-bodied species. Our expectation was confirmed only in the case of latitudinal range position, as we revealed higher threat level for tropical than for temperate species. This relationship was robust to different methods of threat level expression and cannot be explained by a simple association of high bird species richness with the tropical zone. Instead, it seems that tropical species are more threatened because of their intrinsic characteristics such as slow life histories, adaptations to stable environments and small geographic ranges. These characteristics are obviously disadvantageous in conditions of current human-induced environmental perturbations. Moreover, given the absence of habitat effects, our study indicates that such

  14. Global phylogeography with mixed-marker analysis reveals male-mediated dispersal in the endangered scalloped hammerhead shark (Sphyrna lewini.

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    Toby S Daly-Engel

    Full Text Available The scalloped hammerhead shark, Sphyrna lewini, is a large endangered predator with a circumglobal distribution, observed in the open ocean but linked ontogenetically to coastal embayments for parturition and juvenile development. A previous survey of maternal (mtDNA markers demonstrated strong genetic partitioning overall (global Φ(ST = 0.749 and significant population separations across oceans and between discontinuous continental coastlines.We surveyed the same global range with increased sample coverage (N = 403 and 13 microsatellite loci to assess the male contribution to dispersal and population structure. Biparentally inherited microsatellites reveal low or absent genetic structure across ocean basins and global genetic differentiation (F(ST = 0.035 over an order of magnitude lower than the corresponding measures for maternal mtDNA lineages (Φ(ST = 0.749. Nuclear allelic richness and heterozygosity are high throughout the Indo-Pacific, while genetic structure is low. In contrast, allelic diversity is low while population structure is higher for populations at the ends of the range in the West Atlantic and East Pacific.These data are consistent with the proposed Indo-Pacific center of origin for S. lewini, and indicate that females are philopatric or adhere to coastal habitats while males facilitate gene flow across oceanic expanses. This study includes the largest sampling effort and the most molecular loci ever used to survey the complete range of a large oceanic predator, and findings emphasize the importance of incorporating mixed-marker analysis into stock assessments of threatened and endangered shark species.

  15. Analysis of global gene expression in Brachypodium distachyon reveals extensive network plasticity in response to abiotic stress.

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    Henry D Priest

    Full Text Available Brachypodium distachyon is a close relative of many important cereal crops. Abiotic stress tolerance has a significant impact on productivity of agriculturally important food and feedstock crops. Analysis of the transcriptome of Brachypodium after chilling, high-salinity, drought, and heat stresses revealed diverse differential expression of many transcripts. Weighted Gene Co-Expression Network Analysis revealed 22 distinct gene modules with specific profiles of expression under each stress. Promoter analysis implicated short DNA sequences directly upstream of module members in the regulation of 21 of 22 modules. Functional analysis of module members revealed enrichment in functional terms for 10 of 22 network modules. Analysis of condition-specific correlations between differentially expressed gene pairs revealed extensive plasticity in the expression relationships of gene pairs. Photosynthesis, cell cycle, and cell wall expression modules were down-regulated by all abiotic stresses. Modules which were up-regulated by each abiotic stress fell into diverse and unique gene ontology GO categories. This study provides genomics resources and improves our understanding of abiotic stress responses of Brachypodium.

  16. Systems-level analysis of age-related macular degeneration reveals global biomarkers and phenotype-specific functional networks

    Science.gov (United States)

    2012-01-01

    Background Age-related macular degeneration (AMD) is a leading cause of blindness that affects the central region of the retinal pigmented epithelium (RPE), choroid, and neural retina. Initially characterized by an accumulation of sub-RPE deposits, AMD leads to progressive retinal degeneration, and in advanced cases, irreversible vision loss. Although genetic analysis, animal models, and cell culture systems have yielded important insights into AMD, the molecular pathways underlying AMD's onset and progression remain poorly delineated. We sought to better understand the molecular underpinnings of this devastating disease by performing the first comparative transcriptome analysis of AMD and normal human donor eyes. Methods RPE-choroid and retina tissue samples were obtained from a common cohort of 31 normal, 26 AMD, and 11 potential pre-AMD human donor eyes. Transcriptome profiles were generated for macular and extramacular regions, and statistical and bioinformatic methods were employed to identify disease-associated gene signatures and functionally enriched protein association networks. Selected genes of high significance were validated using an independent donor cohort. Results We identified over 50 annotated genes enriched in cell-mediated immune responses that are globally over-expressed in RPE-choroid AMD phenotypes. Using a machine learning model and a second donor cohort, we show that the top 20 global genes are predictive of AMD clinical diagnosis. We also discovered functionally enriched gene sets in the RPE-choroid that delineate the advanced AMD phenotypes, neovascular AMD and geographic atrophy. Moreover, we identified a graded increase of transcript levels in the retina related to wound response, complement cascade, and neurogenesis that strongly correlates with decreased levels of phototransduction transcripts and increased AMD severity. Based on our findings, we assembled protein-protein interactomes that highlight functional networks likely to be

  17. Meta-analysis of global transcriptomics reveals conserved genetic pathways of Quercetin and Tannic acid mediated longevity in C. elegans

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    Kerstin ePietsch

    2012-04-01

    Full Text Available Recent research has highlighted that the polyphenols Quercetin and Tannic acid are capable of extending the lifespan of C. elegans. To gain a deep understanding of the underlying molecular genetics, we analyzed the global transcriptional patterns of nematodes exposed to Quercetin or Tannic acid concentrations that are non-effective (in lifespan extension, lifespan extending or toxic. By means of an intricate meta-analysis it was possible to compare the transcriptomes of polyphenol exposure to recently published data sets derived from i longevity mutants or ii infection. This detailed comparative in silico analysis facilitated the identification of compound specific and overlapping transcriptional profiles and allowed the formulation of mechanistic models of Quercetin and Tannic acid mediated longevity. Lifespan extension due to Quercetin was predominantly driven by the metabolome, TGF-beta signaling, Insulin-like signaling and the p38 MAPK pathway and Tannic acid’s impact involved, in part, the amino acid metabolism and was modulated by the TGF-beta and the p38 MAPK pathways. DAF-12, which integrates TGF-beta and Insulin-like downstream signaling, therefore seems to be a crucial regulator for both polyphenols.

  18. Promoter Analysis Reveals Globally Differential Regulation of Human Long Non-Coding RNA and Protein-Coding Genes

    KAUST Repository

    Alam, Tanvir

    2014-10-02

    Transcriptional regulation of protein-coding genes is increasingly well-understood on a global scale, yet no comparable information exists for long non-coding RNA (lncRNA) genes, which were recently recognized to be as numerous as protein-coding genes in mammalian genomes. We performed a genome-wide comparative analysis of the promoters of human lncRNA and protein-coding genes, finding global differences in specific genetic and epigenetic features relevant to transcriptional regulation. These two groups of genes are hence subject to separate transcriptional regulatory programs, including distinct transcription factor (TF) proteins that significantly favor lncRNA, rather than coding-gene, promoters. We report a specific signature of promoter-proximal transcriptional regulation of lncRNA genes, including several distinct transcription factor binding sites (TFBS). Experimental DNase I hypersensitive site profiles are consistent with active configurations of these lncRNA TFBS sets in diverse human cell types. TFBS ChIP-seq datasets confirm the binding events that we predicted using computational approaches for a subset of factors. For several TFs known to be directly regulated by lncRNAs, we find that their putative TFBSs are enriched at lncRNA promoters, suggesting that the TFs and the lncRNAs may participate in a bidirectional feedback loop regulatory network. Accordingly, cells may be able to modulate lncRNA expression levels independently of mRNA levels via distinct regulatory pathways. Our results also raise the possibility that, given the historical reliance on protein-coding gene catalogs to define the chromatin states of active promoters, a revision of these chromatin signature profiles to incorporate expressed lncRNA genes is warranted in the future.

  19. A global analysis of the impacts of urbanization on bird and plant diversity reveals key anthropogenic drivers.

    Science.gov (United States)

    Aronson, Myla F J; La Sorte, Frank A; Nilon, Charles H; Katti, Madhusudan; Goddard, Mark A; Lepczyk, Christopher A; Warren, Paige S; Williams, Nicholas S G; Cilliers, Sarel; Clarkson, Bruce; Dobbs, Cynnamon; Dolan, Rebecca; Hedblom, Marcus; Klotz, Stefan; Kooijmans, Jip Louwe; Kühn, Ingolf; Macgregor-Fors, Ian; McDonnell, Mark; Mörtberg, Ulla; Pysek, Petr; Siebert, Stefan; Sushinsky, Jessica; Werner, Peter; Winter, Marten

    2014-04-07

    Urbanization contributes to the loss of the world's biodiversity and the homogenization of its biota. However, comparative studies of urban biodiversity leading to robust generalities of the status and drivers of biodiversity in cities at the global scale are lacking. Here, we compiled the largest global dataset to date of two diverse taxa in cities: birds (54 cities) and plants (110 cities). We found that the majority of urban bird and plant species are native in the world's cities. Few plants and birds are cosmopolitan, the most common being Columba livia and Poa annua. The density of bird and plant species (the number of species per km(2)) has declined substantially: only 8% of native bird and 25% of native plant species are currently present compared with estimates of non-urban density of species. The current density of species in cities and the loss in density of species was best explained by anthropogenic features (landcover, city age) rather than by non-anthropogenic factors (geography, climate, topography). As urbanization continues to expand, efforts directed towards the conservation of intact vegetation within urban landscapes could support higher concentrations of both bird and plant species. Despite declines in the density of species, cities still retain endemic native species, thus providing opportunities for regional and global biodiversity conservation, restoration and education.

  20. A global analysis of the impacts of urbanization on bird and plant diversity reveals key anthropogenic drivers

    Science.gov (United States)

    Aronson, Myla F. J.; La Sorte, Frank A.; Nilon, Charles H.; Katti, Madhusudan; Goddard, Mark A.; Lepczyk, Christopher A.; Warren, Paige S.; Williams, Nicholas S. G.; Cilliers, Sarel; Clarkson, Bruce; Dobbs, Cynnamon; Dolan, Rebecca; Hedblom, Marcus; Klotz, Stefan; Kooijmans, Jip Louwe; Kühn, Ingolf; MacGregor-Fors, Ian; McDonnell, Mark; Mörtberg, Ulla; Pyšek, Petr; Siebert, Stefan; Sushinsky, Jessica; Werner, Peter; Winter, Marten

    2014-01-01

    Urbanization contributes to the loss of the world's biodiversity and the homogenization of its biota. However, comparative studies of urban biodiversity leading to robust generalities of the status and drivers of biodiversity in cities at the global scale are lacking. Here, we compiled the largest global dataset to date of two diverse taxa in cities: birds (54 cities) and plants (110 cities). We found that the majority of urban bird and plant species are native in the world's cities. Few plants and birds are cosmopolitan, the most common being Columba livia and Poa annua. The density of bird and plant species (the number of species per km2) has declined substantially: only 8% of native bird and 25% of native plant species are currently present compared with estimates of non-urban density of species. The current density of species in cities and the loss in density of species was best explained by anthropogenic features (landcover, city age) rather than by non-anthropogenic factors (geography, climate, topography). As urbanization continues to expand, efforts directed towards the conservation of intact vegetation within urban landscapes could support higher concentrations of both bird and plant species. Despite declines in the density of species, cities still retain endemic native species, thus providing opportunities for regional and global biodiversity conservation, restoration and education. PMID:24523278

  1. Global phosphoproteomic analysis of human skeletal muscle reveals a network of exercise-regulated kinases and AMPK substrates

    DEFF Research Database (Denmark)

    Hoffman, Nolan J; Parker, Benjamin L; Chaudhuri, Rima

    2015-01-01

    -intensity exercise bout, revealing 1,004 unique exercise-regulated phosphosites on 562 proteins. These included substrates of known exercise-regulated kinases (AMPK, PKA, CaMK, MAPK, mTOR), yet the majority of kinases and substrate phosphosites have not previously been implicated in exercise signaling. Given...

  2. Global gene transcriptome analysis in vaccinated cattle revealed a dominant role of IL-22 for protection against bovine tuberculosis.

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    Sabin Bhuju

    2012-12-01

    Full Text Available Bovine tuberculosis (bTB is a chronic disease of cattle caused by Mycobacterium bovis, a member of the Mycobacterium tuberculosis complex group of bacteria. Vaccination of cattle might offer a long-term solution for controlling the disease and priority has been given to the development of a cattle vaccine against bTB. Identification of biomarkers in tuberculosis research remains elusive and the goal is to identify host correlates of protection. We hypothesized that by studying global gene expression we could identify in vitro predictors of protection that could help to facilitate vaccine development. Calves were vaccinated with BCG or with a heterologous BCG prime adenovirally vectored subunit boosting protocol. Protective efficacy was determined after M. bovis challenge. RNA was prepared from PPD-stimulated PBMC prepared from vaccinated-protected, vaccinated-unprotected and unvaccinated control cattle prior to M. bovis challenge and global gene expression determined by RNA-seq. 668 genes were differentially expressed in vaccinated-protected cattle compared with vaccinated-unprotected and unvaccinated control cattle. Cytokine-cytokine receptor interaction was the most significant pathway related to this dataset with IL-22 expression identified as the dominant surrogate of protection besides INF-γ. Finally, the expression of these candidate genes identified by RNA-seq was evaluated by RT-qPCR in an independent set of PBMC samples from BCG vaccinated and unvaccinated calves. This experiment confirmed the importance of IL-22 as predictor of vaccine efficacy.

  3. Global gene expression analysis of canine osteosarcoma stem cells reveals a novel role for COX-2 in tumour initiation.

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    Pang, Lisa Y; Gatenby, Emma L; Kamida, Ayako; Whitelaw, Bruce A; Hupp, Ted R; Argyle, David J

    2014-01-01

    Osteosarcoma is the most common primary bone tumour of both children and dogs. It is an aggressive tumour in both species with a rapid clinical course leading ultimately to metastasis. In dogs and children distant metastasis occurs in >80% of individuals treated by surgery alone. Both canine and human osteosarcoma has been shown to contain a sub-population of cancer stem cells (CSCs), which may drive tumour growth, recurrence and metastasis, suggesting that naturally occurring canine osteosarcoma could act as a preclinical model for the human disease. Here we report the successful isolation of CSCs from primary canine osteosarcoma, as well as established cell lines. We show that these cells can form tumourspheres, and demonstrate relative resistance to chemotherapy. We demonstrate similar results for the human osteosarcma cell lines, U2OS and SAOS2. Utilizing the Affymetrix canine microarray, we are able to definitively show that there are significant differences in global gene expression profiles of isolated osteosarcoma stem cells and the daughter adherent cells. We identified 13,221 significant differences (p = 0.05), and significantly, COX-2 was expressed 141-fold more in CSC spheres than daughter adherent cells. To study the role of COX-2 expression in CSCs we utilized the COX-2 inhibitors meloxicam and mavacoxib. We found that COX-2 inhibition had no effect on CSC growth, or resistance to chemotherapy. However inhibition of COX-2 in daughter cells prevented sphere formation, indicating a potential significant role for COX-2 in tumour initiation.

  4. Global gene expression analysis of canine osteosarcoma stem cells reveals a novel role for COX-2 in tumour initiation.

    Directory of Open Access Journals (Sweden)

    Lisa Y Pang

    Full Text Available Osteosarcoma is the most common primary bone tumour of both children and dogs. It is an aggressive tumour in both species with a rapid clinical course leading ultimately to metastasis. In dogs and children distant metastasis occurs in >80% of individuals treated by surgery alone. Both canine and human osteosarcoma has been shown to contain a sub-population of cancer stem cells (CSCs, which may drive tumour growth, recurrence and metastasis, suggesting that naturally occurring canine osteosarcoma could act as a preclinical model for the human disease. Here we report the successful isolation of CSCs from primary canine osteosarcoma, as well as established cell lines. We show that these cells can form tumourspheres, and demonstrate relative resistance to chemotherapy. We demonstrate similar results for the human osteosarcma cell lines, U2OS and SAOS2. Utilizing the Affymetrix canine microarray, we are able to definitively show that there are significant differences in global gene expression profiles of isolated osteosarcoma stem cells and the daughter adherent cells. We identified 13,221 significant differences (p = 0.05, and significantly, COX-2 was expressed 141-fold more in CSC spheres than daughter adherent cells. To study the role of COX-2 expression in CSCs we utilized the COX-2 inhibitors meloxicam and mavacoxib. We found that COX-2 inhibition had no effect on CSC growth, or resistance to chemotherapy. However inhibition of COX-2 in daughter cells prevented sphere formation, indicating a potential significant role for COX-2 in tumour initiation.

  5. Global histone analysis by mass spectrometry reveals a high content of acetylated lysine residues in the malaria parasite Plasmodium falciparum

    DEFF Research Database (Denmark)

    Trelle, Morten Beck; Salcedo-Amaya, Adriana M; Cohen, Adrian

    2009-01-01

    Post-translational modifications (PTMs) of histone tails play a key role in epigenetic regulation of gene expression in a range of organisms from yeast to human, however, little is known about histone proteins from the parasite that causes malaria in humans, Plasmodium falciparum. We characterize...... comprehensive map of histone modifications in Plasmodium falciparum and highlight the utility of tandem MS for detailed analysis of peptides containing multiple PTMs....

  6. Global impacts from improved tropical forages: A meta-analysis revealing overlooked benefits and costs, evolving values and new priorities

    Directory of Open Access Journals (Sweden)

    Douglas S. White

    2013-09-01

    Full Text Available El uso más amplio y el desempeño mejorado de forrajes tropicales sembrados pueden cambiar sustancialmente los paisajes social, económico y ambiental. Mediante la revisión de estudios relacionados con el impacto de forrajes tropicales publicados en las últimas dos décadas, este artículo muestra cómo las prioridades de desarrollo cambiantes han influido en los tipos de impactos que se están documentando. Se utilizó un meta-análisis para examinar 98 estudios de acuerdo con: (i la envergadura de los efectos reportados en relación con los objetivos de desarrollo de equidad social, crecimiento económico y sostenibilidad ambiental; (ii el alcance de los efectos, que van desde impactos a mediano plazo a más largo plazo; y (iii la precisión de medición (identificación, descripción o cuantificación de los impactos. Se han evaluado impactos para menos de la mitad de los 118 millones de hectáreas con forrajes mejorados que se encuentran documentados. Aunque Brasil representa el 86% de la superficie sembrada que se conoce, los informes de adopción de tecnología son, en general, irregulares, lo cual afecta a la precisión de las estimaciones globales. Más del 80% de los estudios relacionados con el impacto de forrajes tropicales reportaron efectos económicos, mientras que menos del 20% son estimaciones cuantitativas del impacto económico a largo plazo. Métodos y supuestos de valoración inconsistentes impidieron sumar, en forma válida, el impacto económico total. Se reportaron efectos sociales en menos del 60% de los estudios, y se enfatizaron los resultados a nivel de los hogares en cuanto a género y trabajo. La mayoría de los efectos reportados fueron no cuantitativos. Los efectos ambientales fueron reportados un poco más frecuentemente que los efectos sociales, con aumentos recientes en las estimaciones cuantitativas de la acumulación de carbono. Pocos estudios analizaron las ventajas y desventajas. Aproximadamente el 15% de

  7. Global Transcriptome Analysis Reveals Distinct Aluminum-Tolerance Pathways in the Al-Accumulating Species Hydrangea macrophylla and Marker Identification.

    Directory of Open Access Journals (Sweden)

    Haixia Chen

    Full Text Available Hydrangea (Hydrangea macrophylla is a well known Al-accumulating plant, showing a high level of aluminum (Al tolerance and accumulation. Although the physiological mechanisms for detoxification of Al and the roles of Al in blue hydrangea sepals have been reported, the molecular mechanisms of Al tolerance and accumulation are poorly understood in hydrangea. In this study, we conducted a genome-wide transcriptome analysis of Al-response genes in the roots and leaves of hydrangea by RNA sequencing (RNA-seq. The assembly of hydrangea transcriptome provides a rich source for gene identification and mining molecular markers, including single nucleotide polymorphism (SNP and simple sequence repeat (SSR. A total of 401,215 transcripts with an average length of 810.77 bp were assembled, generating 256,127 unigenes. After annotation, 4,287 genes in the roots and 730 genes in the leaves were up-regulated by Al exposure, while 236 genes in the roots and 719 genes in the leaves were down-regulated, respectively. Many transporters, including MATE and ABC families, were involved in the process of Al-citrate complex transporting from the roots in hydrangea. A plasma membrane Al uptake transporter, Nramp aluminum transporter was up-regulated in roots and leaves under Al stress, indicating it may play an important role in Al tolerance by reducing the level of toxic Al. Although the exact roles of these candidate genes remain to be examined, these results provide a platform for further functional analysis of the process of detoxification of Al in hydrangea.

  8. Global MYCN transcription factor binding analysis in neuroblastoma reveals association with distinct E-box motifs and regions of DNA hypermethylation.

    LENUS (Irish Health Repository)

    Murphy, Derek M

    2009-01-01

    BACKGROUND: Neuroblastoma, a cancer derived from precursor cells of the sympathetic nervous system, is a major cause of childhood cancer related deaths. The single most important prognostic indicator of poor clinical outcome in this disease is genomic amplification of MYCN, a member of a family of oncogenic transcription factors. METHODOLOGY: We applied MYCN chromatin immunoprecipitation to microarrays (ChIP-chip) using MYCN amplified\\/non-amplified cell lines as well as a conditional knockdown cell line to determine the distribution of MYCN binding sites within all annotated promoter regions. CONCLUSION: Assessment of E-box usage within consistently positive MYCN binding sites revealed a predominance for the CATGTG motif (p<0.0016), with significant enrichment of additional motifs CATTTG, CATCTG, CAACTG in the MYCN amplified state. For cell lines over-expressing MYCN, gene ontology analysis revealed enrichment for the binding of MYCN at promoter regions of numerous molecular functional groups including DNA helicases and mRNA transcriptional regulation. In order to evaluate MYCN binding with respect to other genomic features, we determined the methylation status of all annotated CpG islands and promoter sequences using methylated DNA immunoprecipitation (MeDIP). The integration of MYCN ChIP-chip and MeDIP data revealed a highly significant positive correlation between MYCN binding and DNA hypermethylation. This association was also detected in regions of hemizygous loss, indicating that the observed association occurs on the same homologue. In summary, these findings suggest that MYCN binding occurs more commonly at CATGTG as opposed to the classic CACGTG E-box motif, and that disease associated over expression of MYCN leads to aberrant binding to additional weaker affinity E-box motifs in neuroblastoma. The co-localization of MYCN binding and DNA hypermethylation further supports the dual role of MYCN, namely that of a classical transcription factor affecting the

  9. Global mRNA expression analysis in myosin II deficient strains of Saccharomyces cerevisiae reveals an impairment of cell integrity functions

    Directory of Open Access Journals (Sweden)

    Rivera-Molina Félix E

    2008-01-01

    Full Text Available Abstract Background The Saccharomyces cerevisiae MYO1 gene encodes the myosin II heavy chain (Myo1p, a protein required for normal cytokinesis in budding yeast. Myo1p deficiency in yeast (myo1Δ causes a cell separation defect characterized by the formation of attached cells, yet it also causes abnormal budding patterns, formation of enlarged and elongated cells, increased osmotic sensitivity, delocalized chitin deposition, increased chitin synthesis, and hypersensitivity to the chitin synthase III inhibitor Nikkomycin Z. To determine how differential expression of genes is related to these diverse cell wall phenotypes, we analyzed the global mRNA expression profile of myo1Δ strains. Results Global mRNA expression profiles of myo1Δ strains and their corresponding wild type controls were obtained by hybridization to yeast oligonucleotide microarrays. Results for selected genes were confirmed by real time RT-PCR. A total of 547 differentially expressed genes (p ≤ 0.01 were identified with 263 up regulated and 284 down regulated genes in the myo1Δ strains. Gene set enrichment analysis revealed the significant over-representation of genes in the protein biosynthesis and stress response categories. The SLT2/MPK1 gene was up regulated in the microarray, and a myo1Δslt2Δ double mutant was non-viable. Overexpression of ribosomal protein genes RPL30 and RPS31 suppressed the hypersensitivity to Nikkomycin Z and increased the levels of phosphorylated Slt2p in myo1Δ strains. Increased levels of phosphorylated Slt2p were also observed in wild type strains under these conditions. Conclusion Following this analysis of global mRNA expression in yeast myo1Δ strains, we conclude that 547 genes were differentially regulated in myo1Δ strains and that the stress response and protein biosynthesis gene categories were coordinately regulated in this mutant. The SLT2/MPK1 gene was confirmed to be essential for myo1Δ strain viability, supporting that the up

  10. Switch of Sensitivity Dynamics Revealed with DyGloSA Toolbox for Dynamical Global Sensitivity Analysis as an Early Warning for System's Critical Transition

    Science.gov (United States)

    Baumuratova, Tatiana; Dobre, Simona; Bastogne, Thierry; Sauter, Thomas

    2013-01-01

    Systems with bifurcations may experience abrupt irreversible and often unwanted shifts in their performance, called critical transitions. For many systems like climate, economy, ecosystems it is highly desirable to identify indicators serving as early warnings of such regime shifts. Several statistical measures were recently proposed as early warnings of critical transitions including increased variance, autocorrelation and skewness of experimental or model-generated data. The lack of automatized tool for model-based prediction of critical transitions led to designing DyGloSA – a MATLAB toolbox for dynamical global parameter sensitivity analysis (GPSA) of ordinary differential equations models. We suggest that the switch in dynamics of parameter sensitivities revealed by our toolbox is an early warning that a system is approaching a critical transition. We illustrate the efficiency of our toolbox by analyzing several models with bifurcations and predicting the time periods when systems can still avoid going to a critical transition by manipulating certain parameter values, which is not detectable with the existing SA techniques. DyGloSA is based on the SBToolbox2 and contains functions, which compute dynamically the global sensitivity indices of the system by applying four main GPSA methods: eFAST, Sobol's ANOVA, PRCC and WALS. It includes parallelized versions of the functions enabling significant reduction of the computational time (up to 12 times). DyGloSA is freely available as a set of MATLAB scripts at http://bio.uni.lu/systems_biology/software/dyglosa. It requires installation of MATLAB (versions R2008b or later) and the Systems Biology Toolbox2 available at www.sbtoolbox2.org. DyGloSA can be run on Windows and Linux systems, -32 and -64 bits. PMID:24367574

  11. Switch of sensitivity dynamics revealed with DyGloSA toolbox for dynamical global sensitivity analysis as an early warning for system's critical transition.

    Science.gov (United States)

    Baumuratova, Tatiana; Dobre, Simona; Bastogne, Thierry; Sauter, Thomas

    2013-01-01

    Systems with bifurcations may experience abrupt irreversible and often unwanted shifts in their performance, called critical transitions. For many systems like climate, economy, ecosystems it is highly desirable to identify indicators serving as early warnings of such regime shifts. Several statistical measures were recently proposed as early warnings of critical transitions including increased variance, autocorrelation and skewness of experimental or model-generated data. The lack of automatized tool for model-based prediction of critical transitions led to designing DyGloSA - a MATLAB toolbox for dynamical global parameter sensitivity analysis (GPSA) of ordinary differential equations models. We suggest that the switch in dynamics of parameter sensitivities revealed by our toolbox is an early warning that a system is approaching a critical transition. We illustrate the efficiency of our toolbox by analyzing several models with bifurcations and predicting the time periods when systems can still avoid going to a critical transition by manipulating certain parameter values, which is not detectable with the existing SA techniques. DyGloSA is based on the SBToolbox2 and contains functions, which compute dynamically the global sensitivity indices of the system by applying four main GPSA methods: eFAST, Sobol's ANOVA, PRCC and WALS. It includes parallelized versions of the functions enabling significant reduction of the computational time (up to 12 times). DyGloSA is freely available as a set of MATLAB scripts at http://bio.uni.lu/systems_biology/software/dyglosa. It requires installation of MATLAB (versions R2008b or later) and the Systems Biology Toolbox2 available at www.sbtoolbox2.org. DyGloSA can be run on Windows and Linux systems, -32 and -64 bits.

  12. Global and system-specific resting-state fMRI fluctuations are uncorrelated: principal component analysis reveals anti-correlated networks.

    Science.gov (United States)

    Carbonell, Felix; Bellec, Pierre; Shmuel, Amir

    2011-01-01

    The influence of the global average signal (GAS) on functional-magnetic resonance imaging (fMRI)-based resting-state functional connectivity is a matter of ongoing debate. The global average fluctuations increase the correlation between functional systems beyond the correlation that reflects their specific functional connectivity. Hence, removal of the GAS is a common practice for facilitating the observation of network-specific functional connectivity. This strategy relies on the implicit assumption of a linear-additive model according to which global fluctuations, irrespective of their origin, and network-specific fluctuations are super-positioned. However, removal of the GAS introduces spurious negative correlations between functional systems, bringing into question the validity of previous findings of negative correlations between fluctuations in the default-mode and the task-positive networks. Here we present an alternative method for estimating global fluctuations, immune to the complications associated with the GAS. Principal components analysis was applied to resting-state fMRI time-series. A global-signal effect estimator was defined as the principal component (PC) that correlated best with the GAS. The mean correlation coefficient between our proposed PC-based global effect estimator and the GAS was 0.97±0.05, demonstrating that our estimator successfully approximated the GAS. In 66 out of 68 runs, the PC that showed the highest correlation with the GAS was the first PC. Since PCs are orthogonal, our method provides an estimator of the global fluctuations, which is uncorrelated to the remaining, network-specific fluctuations. Moreover, unlike the regression of the GAS, the regression of the PC-based global effect estimator does not introduce spurious anti-correlations beyond the decrease in seed-based correlation values allowed by the assumed additive model. After regressing this PC-based estimator out of the original time-series, we observed robust anti

  13. Transcriptome analysis of an mvp mutant reveals important changes in global gene expression and a role for methyl jasmonate in vernalization and flowering in wheat.

    Science.gov (United States)

    Diallo, Amadou Oury; Agharbaoui, Zahra; Badawi, Mohamed A; Ali-Benali, Mohamed Ali; Moheb, Amira; Houde, Mario; Sarhan, Fathey

    2014-06-01

    The einkorn wheat mutant mvp-1 (maintained vegetative phase 1) has a non-flowering phenotype caused by deletions including, but not limited to, the genes CYS, PHYC, and VRN1. However, the impact of these deletions on global gene expression is still unknown. Transcriptome analysis showed that these deletions caused the upregulation of several pathogenesis-related (PR) and jasmonate-responsive genes. These results suggest that jasmonates may be involved in flowering and vernalization in wheat. To test this hypothesis, jasmonic acid (JA) and methyl jasmonate (MeJA) content in mvp and wild-type plants was measured. The content of JA was comparable in all plants, whereas the content of MeJA was higher by more than 6-fold in mvp plants. The accumulation of MeJA was also observed in vernalization-sensitive hexaploid winter wheat during cold exposure. This accumulation declined rapidly once plants were deacclimated under floral-inductive growth conditions. This suggests that MeJA may have a role in floral transition. To confirm this result, we treated vernalization-insensitive spring wheat with MeJA. The treatment delayed flowering with significant downregulation of both TaVRN1 and TaFT1 genes. These data suggest a role for MeJA in modulating vernalization and flowering time in wheat. © The Author 2014. Published by Oxford University Press on behalf of the Society for Experimental Biology.

  14. The use of global transcriptional analysis to reveal the biological and cellular events involved in distinct development phases of Trichophyton rubrum conidial germination

    Directory of Open Access Journals (Sweden)

    Ding Guohui

    2007-04-01

    Full Text Available Abstract Background Conidia are considered to be the primary cause of infections by Trichophyton rubrum. Results We have developed a cDNA microarray containing 10250 ESTs to monitor the transcriptional strategy of conidial germination. A total of 1561 genes that had their expression levels specially altered in the process were obtained and hierarchically clustered with respect to their expression profiles. By functional analysis, we provided a global view of an important biological system related to conidial germination, including characterization of the pattern of gene expression at sequential developmental phases, and changes of gene expression profiles corresponding to morphological transitions. We matched the EST sequences to GO terms in the Saccharomyces Genome Database (SGD. A number of homologues of Saccharomyces cerevisiae genes related to signalling pathways and some important cellular processes were found to be involved in T. rubrum germination. These genes and signalling pathways may play roles in distinct steps, such as activating conidial germination, maintenance of isotropic growth, establishment of cell polarity and morphological transitions. Conclusion Our results may provide insights into molecular mechanisms of conidial germination at the cell level, and may enhance our understanding of regulation of gene expression related to the morphological construction of T. rubrum.

  15. Global Analysis of Nonlinear Dynamics

    CERN Document Server

    Luo, Albert

    2012-01-01

    Global Analysis of Nonlinear Dynamics collects chapters on recent developments in global analysis of non-linear dynamical systems with a particular emphasis on cell mapping methods developed by Professor C.S. Hsu of the University of California, Berkeley. This collection of contributions prepared by a diverse group of internationally recognized researchers is intended to stimulate interests in global analysis of complex and high-dimensional nonlinear dynamical systems, whose global properties are largely unexplored at this time. This book also: Presents recent developments in global analysis of non-linear dynamical systems Provides in-depth considerations and extensions of cell mapping methods Adopts an inclusive style accessible to non-specialists and graduate students Global Analysis of Nonlinear Dynamics is an ideal reference for the community of nonlinear dynamics in different disciplines including engineering, applied mathematics, meteorology, life science, computational science, and medicine.  

  16. Haplotype Analysis of the Pre-harvest Sprouting Resistance Locus Phs-A1 Reveals a Causal Role of TaMKK3-A in Global Germplasm.

    Science.gov (United States)

    Shorinola, Oluwaseyi; Balcárková, Barbara; Hyles, Jessica; Tibbits, Josquin F G; Hayden, Matthew J; Holušova, Katarina; Valárik, Miroslav; Distelfeld, Assaf; Torada, Atsushi; Barrero, Jose M; Uauy, Cristobal

    2017-01-01

    Pre-harvest sprouting (PHS) is an important cause of quality loss in many cereal crops and is particularly prevalent and damaging in wheat. Resistance to PHS is therefore a valuable target trait in many breeding programs. The Phs-A1 locus on wheat chromosome arm 4AL has been consistently shown to account for a significant proportion of natural variation to PHS in diverse mapping populations. However, the deployment of sprouting resistance is confounded by the fact that different candidate genes, including the tandem duplicated Plasma Membrane 19 ( PM19 ) genes and the mitogen-activated protein kinase kinase 3 ( TaMKK3-A) gene, have been proposed to underlie Phs-A1 . To further define the Phs-A1 locus, we constructed a physical map across this interval in hexaploid and tetraploid wheat. We established close proximity of the proposed candidate genes which are located within a 1.2 Mb interval. Genetic characterization of diverse germplasm used in previous genetic mapping studies suggests that TaMKK3-A , and not PM19 , is the major gene underlying the Phs-A1 effect in European, North American, Australian and Asian germplasm. We identified the non-dormant TaMKK3-A allele at low frequencies within the A-genome diploid progenitor Triticum urartu genepool, and show an increase in the allele frequency in modern varieties. In United Kingdom varieties, the frequency of the dormant TaMKK3-A allele was significantly higher in bread-making quality varieties compared to feed and biscuit-making cultivars. Analysis of exome capture data from 58 diverse hexaploid wheat accessions identified fourteen haplotypes across the extended Phs-A1 locus and four haplotypes for TaMKK3-A . Analysis of these haplotypes in a collection of United Kingdom and Australian cultivars revealed distinct major dormant and non-dormant Phs-A1 haplotypes in each country, which were either rare or absent in the opposing germplasm set. The diagnostic markers and haplotype information reported in the study will

  17. Haplotype Analysis of the Pre-harvest Sprouting Resistance Locus Phs-A1 Reveals a Causal Role of TaMKK3-A in Global Germplasm

    Directory of Open Access Journals (Sweden)

    Oluwaseyi Shorinola

    2017-09-01

    Full Text Available Pre-harvest sprouting (PHS is an important cause of quality loss in many cereal crops and is particularly prevalent and damaging in wheat. Resistance to PHS is therefore a valuable target trait in many breeding programs. The Phs-A1 locus on wheat chromosome arm 4AL has been consistently shown to account for a significant proportion of natural variation to PHS in diverse mapping populations. However, the deployment of sprouting resistance is confounded by the fact that different candidate genes, including the tandem duplicated Plasma Membrane 19 (PM19 genes and the mitogen-activated protein kinase kinase 3 (TaMKK3-A gene, have been proposed to underlie Phs-A1. To further define the Phs-A1 locus, we constructed a physical map across this interval in hexaploid and tetraploid wheat. We established close proximity of the proposed candidate genes which are located within a 1.2 Mb interval. Genetic characterization of diverse germplasm used in previous genetic mapping studies suggests that TaMKK3-A, and not PM19, is the major gene underlying the Phs-A1 effect in European, North American, Australian and Asian germplasm. We identified the non-dormant TaMKK3-A allele at low frequencies within the A-genome diploid progenitor Triticum urartu genepool, and show an increase in the allele frequency in modern varieties. In United Kingdom varieties, the frequency of the dormant TaMKK3-A allele was significantly higher in bread-making quality varieties compared to feed and biscuit-making cultivars. Analysis of exome capture data from 58 diverse hexaploid wheat accessions identified fourteen haplotypes across the extended Phs-A1 locus and four haplotypes for TaMKK3-A. Analysis of these haplotypes in a collection of United Kingdom and Australian cultivars revealed distinct major dormant and non-dormant Phs-A1 haplotypes in each country, which were either rare or absent in the opposing germplasm set. The diagnostic markers and haplotype information reported in the

  18. Satellite-detected fluorescence reveals global physiology of ocean phytoplankton

    Directory of Open Access Journals (Sweden)

    M. J. Behrenfeld

    2009-05-01

    Full Text Available Phytoplankton photosynthesis links global ocean biology and climate-driven fluctuations in the physical environment. These interactions are largely expressed through changes in phytoplankton physiology, but physiological status has proven extremely challenging to characterize globally. Phytoplankton fluorescence does provide a rich source of physiological information long exploited in laboratory and field studies, and is now observed from space. Here we evaluate the physiological underpinnings of global variations in satellite-based phytoplankton chlorophyll fluorescence. The three dominant factors influencing fluorescence distributions are chlorophyll concentration, pigment packaging effects on light absorption, and light-dependent energy-quenching processes. After accounting for these three factors, resultant global distributions of quenching-corrected fluorescence quantum yields reveal a striking consistency with anticipated patterns of iron availability. High fluorescence quantum yields are typically found in low iron waters, while low quantum yields dominate regions where other environmental factors are most limiting to phytoplankton growth. Specific properties of photosynthetic membranes are discussed that provide a mechanistic view linking iron stress to satellite-detected fluorescence. Our results present satellite-based fluorescence as a valuable tool for evaluating nutrient stress predictions in ocean ecosystem models and give the first synoptic observational evidence that iron plays an important role in seasonal phytoplankton dynamics of the Indian Ocean. Satellite fluorescence may also provide a path for monitoring climate-phytoplankton physiology interactions and improving descriptions of phytoplankton light use efficiencies in ocean productivity models.

  19. Global Expression Profiling and Pathway Analysis of Mouse Mammary Tumor Reveals Strain and Stage Specific Dysregulated Pathways in Breast Cancer Progression.

    Science.gov (United States)

    Mei, Yan; Yang, Jun-Ping; Lang, Yan-Hong; Peng, Li-Xia; Yang, Ming-Ming; Liu, Qin; Meng, Dong-Fang; Zheng, Li-Sheng; Qiang, Yuan-Yuan; Xu, Liang; Li, Chang-Zhi; Wei, Wen-Wen; Niu, Ting; Peng, Xing-Si; Yang, Qin; Lin, Fen; Hu, Hao; Xu, Hong-Fa; Huang, Bi-Jun; Wang, Li-Jing; Qian, Chao-Nan

    2018-05-01

    It is believed that the alteration of tissue microenvironment would affect cancer initiation and progression. However, little is known in terms of the underlying molecular mechanisms that would affect the initiation and progression of breast cancer. In the present study, we use two murine mammary tumor models with different speeds of tumor initiation and progression for whole genome expression profiling to reveal the involved genes and signaling pathways. The pathways regulating PI3K-Akt signaling and Ras signaling were activated in Fvb mice and promoted tumor progression. Contrastingly, the pathways regulating apoptosis and cellular senescence were activated in Fvb.B6 mice and suppressed tumor progression. We identified distinct patterns of oncogenic pathways activation at different stages of breast cancer, and uncovered five oncogenic pathways that were activated in both human and mouse breast cancers. The genes and pathways discovered in our study would be useful information for other researchers and drug development.

  20. Global transcriptome analysis reveals extensive gene remodeling, alternative splicing and differential transcription profiles in non-seed vascular plant Selaginella moellendorffii.

    Science.gov (United States)

    Zhu, Yan; Chen, Longxian; Zhang, Chengjun; Hao, Pei; Jing, Xinyun; Li, Xuan

    2017-01-25

    Selaginella moellendorffii, a lycophyte, is a model plant to study the early evolution and development of vascular plants. As the first and only sequenced lycophyte to date, the genome of S. moellendorffii revealed many conserved genes and pathways, as well as specialized genes different from flowering plants. Despite the progress made, little is known about long noncoding RNAs (lncRNA) and the alternative splicing (AS) of coding genes in S. moellendorffii. Its coding gene models have not been fully validated with transcriptome data. Furthermore, it remains important to understand whether the regulatory mechanisms similar to flowering plants are used, and how they operate in a non-seed primitive vascular plant. RNA-sequencing (RNA-seq) was performed for three S. moellendorffii tissues, root, stem, and leaf, by constructing strand-specific RNA-seq libraries from RNA purified using RiboMinus isolation protocol. A total of 176 million reads (44 Gbp) were obtained from three tissue types, and were mapped to S. moellendorffii genome. By comparing with 22,285 existing gene models of S. moellendorffii, we identified 7930 high-confidence novel coding genes (a 35.6% increase), and for the first time reported 4422 lncRNAs in a lycophyte. Further, we refined 2461 (11.0%) of existing gene models, and identified 11,030 AS events (for 5957 coding genes) revealed for the first time for lycophytes. Tissue-specific gene expression with functional implication was analyzed, and 1031, 554, and 269 coding genes, and 174, 39, and 17 lncRNAs were identified in root, stem, and leaf tissues, respectively. The expression of critical genes for vascular development stages, i.e. formation of provascular cells, xylem specification and differentiation, and phloem specification and differentiation, was compared in S. moellendorffii tissues, indicating a less complex regulatory mechanism in lycophytes than in flowering plants. The results were further strengthened by the evolutionary trend of

  1. Global Analysis of the Fungal Microbiome in Cystic Fibrosis Patients Reveals Loss of Function of the Transcriptional Repressor Nrg1 as a Mechanism of Pathogen Adaptation.

    Science.gov (United States)

    Kim, Sang Hu; Clark, Shawn T; Surendra, Anuradha; Copeland, Julia K; Wang, Pauline W; Ammar, Ron; Collins, Cathy; Tullis, D Elizabeth; Nislow, Corey; Hwang, David M; Guttman, David S; Cowen, Leah E

    2015-11-01

    The microbiome shapes diverse facets of human biology and disease, with the importance of fungi only beginning to be appreciated. Microbial communities infiltrate diverse anatomical sites as with the respiratory tract of healthy humans and those with diseases such as cystic fibrosis, where chronic colonization and infection lead to clinical decline. Although fungi are frequently recovered from cystic fibrosis patient sputum samples and have been associated with deterioration of lung function, understanding of species and population dynamics remains in its infancy. Here, we coupled high-throughput sequencing of the ribosomal RNA internal transcribed spacer 1 (ITS1) with phenotypic and genotypic analyses of fungi from 89 sputum samples from 28 cystic fibrosis patients. Fungal communities defined by sequencing were concordant with those defined by culture-based analyses of 1,603 isolates from the same samples. Different patients harbored distinct fungal communities. There were detectable trends, however, including colonization with Candida and Aspergillus species, which was not perturbed by clinical exacerbation or treatment. We identified considerable inter- and intra-species phenotypic variation in traits important for host adaptation, including antifungal drug resistance and morphogenesis. While variation in drug resistance was largely between species, striking variation in morphogenesis emerged within Candida species. Filamentation was uncoupled from inducing cues in 28 Candida isolates recovered from six patients. The filamentous isolates were resistant to the filamentation-repressive effects of Pseudomonas aeruginosa, implicating inter-kingdom interactions as the selective force. Genome sequencing revealed that all but one of the filamentous isolates harbored mutations in the transcriptional repressor NRG1; such mutations were necessary and sufficient for the filamentous phenotype. Six independent nrg1 mutations arose in Candida isolates from different patients

  2. Global Analysis of the Fungal Microbiome in Cystic Fibrosis Patients Reveals Loss of Function of the Transcriptional Repressor Nrg1 as a Mechanism of Pathogen Adaptation.

    Directory of Open Access Journals (Sweden)

    Sang Hu Kim

    2015-11-01

    Full Text Available The microbiome shapes diverse facets of human biology and disease, with the importance of fungi only beginning to be appreciated. Microbial communities infiltrate diverse anatomical sites as with the respiratory tract of healthy humans and those with diseases such as cystic fibrosis, where chronic colonization and infection lead to clinical decline. Although fungi are frequently recovered from cystic fibrosis patient sputum samples and have been associated with deterioration of lung function, understanding of species and population dynamics remains in its infancy. Here, we coupled high-throughput sequencing of the ribosomal RNA internal transcribed spacer 1 (ITS1 with phenotypic and genotypic analyses of fungi from 89 sputum samples from 28 cystic fibrosis patients. Fungal communities defined by sequencing were concordant with those defined by culture-based analyses of 1,603 isolates from the same samples. Different patients harbored distinct fungal communities. There were detectable trends, however, including colonization with Candida and Aspergillus species, which was not perturbed by clinical exacerbation or treatment. We identified considerable inter- and intra-species phenotypic variation in traits important for host adaptation, including antifungal drug resistance and morphogenesis. While variation in drug resistance was largely between species, striking variation in morphogenesis emerged within Candida species. Filamentation was uncoupled from inducing cues in 28 Candida isolates recovered from six patients. The filamentous isolates were resistant to the filamentation-repressive effects of Pseudomonas aeruginosa, implicating inter-kingdom interactions as the selective force. Genome sequencing revealed that all but one of the filamentous isolates harbored mutations in the transcriptional repressor NRG1; such mutations were necessary and sufficient for the filamentous phenotype. Six independent nrg1 mutations arose in Candida isolates from

  3. Global Liver Proteome Analysis Using iTRAQ Reveals AMPK-mTOR-Autophagy Signaling Is Altered by Intrauterine Growth Restriction in Newborn Piglets.

    Science.gov (United States)

    Long, Baisheng; Yin, Cong; Fan, Qiwen; Yan, Guokai; Wang, Zhichang; Li, Xiuzhi; Chen, Changqing; Yang, Xingya; Liu, Lu; Zheng, Zilong; Shi, Min; Yan, Xianghua

    2016-04-01

    Intrauterine growth restriction (IUGR) impairs fetal growth and development, perturbs nutrient metabolism, and increases the risk of developing diseases in postnatal life. However, the underlying mechanisms by which IUGR affects fetal liver development and metabolism remain incompletely understood. Here, we applied a high-throughput proteomics approach and biochemical analysis to investigate the impact of IUGR on the liver of newborn piglets. As a result, we identified 78 differentially expressed proteins in the three biological replicates, including 31 significantly up-regulated proteins and 47 significantly down-regulated proteins. Among them, a majority of differentially expressed proteins were related to nutrient metabolism and mitochondrial function. Additionally, many significantly down-regulated proteins participated in the mTOR signaling pathway and the phagosome maturation signaling pathway. Further analysis suggested that glucose concentration and hepatic glycogen storage were both reduced in IUGR newborn piglets, which may contribute to AMPK activation and mTORC1 inhibition. However, AMPK activation and mTORC1 inhibition failed to induce autophagy in the liver of IUGR neonatal pigs. A possible reason is that PP2Ac, a potential candidate in autophagy regulation, is significantly down-regulated in the liver of IUGR newborn piglets. These findings may provide implications for preventing and treating IUGR in human beings and domestic animals.

  4. Global Genome Comparative Analysis Reveals Insights of Resistome and Life-Style Adaptation of Pseudomonas putida Strain T2-2 in Oral Cavity

    Directory of Open Access Journals (Sweden)

    Xin Yue Chan

    2014-01-01

    Full Text Available Most Pseudomonas putida strains are environmental microorganisms exhibiting a wide range of metabolic capability but certain strains have been reported as rare opportunistic pathogens and some emerged as multidrug resistant P. putida. This study aimed to assess the drug resistance profile of, via whole genome analysis, P. putida strain T2-2 isolated from oral cavity. At the same time, we also compared the nonenvironmental strain with environmentally isolated P. putida. In silico comparative genome analysis with available reference strains of P. putida shows that T2-2 has lesser gene counts on carbohydrate and aromatic compounds metabolisms, which suggested its little versatility. The detection of its edd gene also suggested T2-2’s catabolism of glucose via ED pathway instead of EMP pathway. On the other hand, its drug resistance profile was observed via in silico gene prediction and most of the genes found were in agreement with drug-susceptibility testing in laboratory by automated VITEK 2. In addition, the finding of putative genes of multidrug resistance efflux pump and ATP-binding cassette transporters in this strain suggests a multidrug resistant phenotype. In summary, it is believed that multiple metabolic characteristics and drug resistance in P. putida strain T2-2 helped in its survival in human oral cavity.

  5. Introduction to global analysis

    CERN Document Server

    Kahn, Donald W

    2007-01-01

    This text introduces the methods of mathematical analysis as applied to manifolds, including the roles of differentiation and integration, infinite dimensions, Morse theory, Lie groups, and dynamical systems. 1980 edition.

  6. Global analysis of estrogen receptor beta binding to breast cancer cell genome reveals an extensive interplay with estrogen receptor alpha for target gene regulation

    Directory of Open Access Journals (Sweden)

    Papa Maria

    2011-01-01

    Full Text Available Abstract Background Estrogen receptors alpha (ERα and beta (ERβ are transcription factors (TFs that mediate estrogen signaling and define the hormone-responsive phenotype of breast cancer (BC. The two receptors can be found co-expressed and play specific, often opposite, roles, with ERβ being able to modulate the effects of ERα on gene transcription and cell proliferation. ERβ is frequently lost in BC, where its presence generally correlates with a better prognosis of the disease. The identification of the genomic targets of ERβ in hormone-responsive BC cells is thus a critical step to elucidate the roles of this receptor in estrogen signaling and tumor cell biology. Results Expression of full-length ERβ in hormone-responsive, ERα-positive MCF-7 cells resulted in a marked reduction in cell proliferation in response to estrogen and marked effects on the cell transcriptome. By ChIP-Seq we identified 9702 ERβ and 6024 ERα binding sites in estrogen-stimulated cells, comprising sites occupied by either ERβ, ERα or both ER subtypes. A search for TF binding matrices revealed that the majority of the binding sites identified comprise one or more Estrogen Response Element and the remaining show binding matrixes for other TFs known to mediate ER interaction with chromatin by tethering, including AP2, E2F and SP1. Of 921 genes differentially regulated by estrogen in ERβ+ vs ERβ- cells, 424 showed one or more ERβ site within 10 kb. These putative primary ERβ target genes control cell proliferation, death, differentiation, motility and adhesion, signal transduction and transcription, key cellular processes that might explain the biological and clinical phenotype of tumors expressing this ER subtype. ERβ binding in close proximity of several miRNA genes and in the mitochondrial genome, suggests the possible involvement of this receptor in small non-coding RNA biogenesis and mitochondrial genome functions. Conclusions Results indicate that the

  7. Global optimization and sensitivity analysis

    International Nuclear Information System (INIS)

    Cacuci, D.G.

    1990-01-01

    A new direction for the analysis of nonlinear models of nuclear systems is suggested to overcome fundamental limitations of sensitivity analysis and optimization methods currently prevalent in nuclear engineering usage. This direction is toward a global analysis of the behavior of the respective system as its design parameters are allowed to vary over their respective design ranges. Presented is a methodology for global analysis that unifies and extends the current scopes of sensitivity analysis and optimization by identifying all the critical points (maxima, minima) and solution bifurcation points together with corresponding sensitivities at any design point of interest. The potential applicability of this methodology is illustrated with test problems involving multiple critical points and bifurcations and comprising both equality and inequality constraints

  8. Global analysis studies and applications

    CERN Document Server

    Gliklikh, Yuri; Vershik, A

    1992-01-01

    This volume (a sequel to LNM 1108, 1214, 1334 and 1453) continues the presentation to English speaking readers of the Voronezh University press series on Global Analysis and Its Applications. The papers are selected fromtwo Russian issues entitled "Algebraic questions of Analysis and Topology" and "Nonlinear Operators in Global Analysis". CONTENTS: YuE. Gliklikh: Stochastic analysis, groups of diffeomorphisms and Lagrangian description of viscous incompressible fluid.- A.Ya. Helemskii: From topological homology: algebras with different properties of homological triviality.- V.V. Lychagin, L.V. Zil'bergleit: Duality in stable Spencer cohomologies.- O.R. Musin: On some problems of computational geometry and topology.- V.E. Nazaikinskii, B.Yu. Sternin, V.E.Shatalov: Introduction to Maslov's operational method (non-commutative analysis and differential equations).- Yu.B. Rudyak: The problem of realization of homology classes from Poincare up to the present.- V.G. Zvyagin, N.M. Ratiner: Oriented degree of Fredholm...

  9. Convex analysis and global optimization

    CERN Document Server

    Tuy, Hoang

    2016-01-01

    This book presents state-of-the-art results and methodologies in modern global optimization, and has been a staple reference for researchers, engineers, advanced students (also in applied mathematics), and practitioners in various fields of engineering. The second edition has been brought up to date and continues to develop a coherent and rigorous theory of deterministic global optimization, highlighting the essential role of convex analysis. The text has been revised and expanded to meet the needs of research, education, and applications for many years to come. Updates for this new edition include: · Discussion of modern approaches to minimax, fixed point, and equilibrium theorems, and to nonconvex optimization; · Increased focus on dealing more efficiently with ill-posed problems of global optimization, particularly those with hard constraints;

  10. Flows method in global analysis

    International Nuclear Information System (INIS)

    Duong Minh Duc.

    1994-12-01

    We study the gradient flows method for W r,p (M,N) where M and N are Riemannian manifold and r may be less than m/p. We localize some global analysis problem by constructing gradient flows which only change the value of any u in W r,p (M,N) in a local chart of M. (author). 24 refs

  11. Global sensitivity analysis by polynomial dimensional decomposition

    Energy Technology Data Exchange (ETDEWEB)

    Rahman, Sharif, E-mail: rahman@engineering.uiowa.ed [College of Engineering, The University of Iowa, Iowa City, IA 52242 (United States)

    2011-07-15

    This paper presents a polynomial dimensional decomposition (PDD) method for global sensitivity analysis of stochastic systems subject to independent random input following arbitrary probability distributions. The method involves Fourier-polynomial expansions of lower-variate component functions of a stochastic response by measure-consistent orthonormal polynomial bases, analytical formulae for calculating the global sensitivity indices in terms of the expansion coefficients, and dimension-reduction integration for estimating the expansion coefficients. Due to identical dimensional structures of PDD and analysis-of-variance decomposition, the proposed method facilitates simple and direct calculation of the global sensitivity indices. Numerical results of the global sensitivity indices computed for smooth systems reveal significantly higher convergence rates of the PDD approximation than those from existing methods, including polynomial chaos expansion, random balance design, state-dependent parameter, improved Sobol's method, and sampling-based methods. However, for non-smooth functions, the convergence properties of the PDD solution deteriorate to a great extent, warranting further improvements. The computational complexity of the PDD method is polynomial, as opposed to exponential, thereby alleviating the curse of dimensionality to some extent.

  12. Cool seafloor hydrothermal springs reveal global geochemical fluxes

    Science.gov (United States)

    Wheat, C. Geoffrey; Fisher, Andrew T.; McManus, James; Hulme, Samuel M.; Orcutt, Beth N.

    2017-10-01

    We present geochemical data from the first samples of spring fluids from Dorado Outcrop, a basaltic edifice on 23 M.y. old seafloor of the Cocos Plate, eastern Pacific Ocean. These samples were collected from the discharge of a cool hydrothermal system (CHS) on a ridge flank, where typical reaction temperatures in the volcanic crust are low (2-20 °C) and fluid residence times are short. Ridge-flank hydrothermal systems extract 25% of Earth's lithospheric heat, with a global discharge rate equivalent to that of Earth's river discharge to the ocean; CHSs comprise a significant fraction of this global flow. Upper crustal temperatures around Dorado Outcrop are ∼15 °C, the calculated residence time is V, U, Mg, phosphate, Si and Li are different. Applying these observed differences to calculated global CHS fluxes results in chemical fluxes for these ions that are ≥15% of riverine fluxes. Fluxes of K and B also may be significant, but better analytical resolution is required to confirm this result. Spring fluids also have ∼50% less dissolved oxygen (DO) than bottom seawater. Calculations of an analytical model suggest that the loss of DO occurs primarily (>80%) within the upper basaltic crust by biotic and/or abiotic consumption. This calculation demonstrates that permeable pathways within the upper crust can support oxic water-rock interactions for millions of years.

  13. Spaceflight Alters Bacterial Gene Expression and Virulence and Reveals Role for Global Regulator Hfq

    Science.gov (United States)

    Wilson, J. W.; Ott, C. M.; zuBentrup, K. Honer; Ramamurthy R.; Quick, L.; Porwollik, S.; Cheng, P.; McClellan, M.; Tsaprailis, G.; Radabaugh, T.; hide

    2007-01-01

    A comprehensive analysis of both the molecular genetic and phenotypic responses of any organism to the spaceflight environment has never been accomplished due to significant technological and logistical hurdles. Moreover, the effects of spaceflight on microbial pathogenicity and associated infectious disease risks have not been studied. The bacterial pathogen Salmonella typhimurium was grown aboard Space Shuttle mission STS-115 and compared to identical ground control cultures. Global microarray and proteomic analyses revealed 167 transcripts and 73 proteins changed expression with the conserved RNA-binding protein Hfq identified as a likely global regulator involved in the response to this environment. Hfq involvement was confirmed with a ground based microgravity culture model. Spaceflight samples exhibited enhanced virulence in a murine infection model and extracellular matrix accumulation consistent with a biofilm. Strategies to target Hfq and related regulators could potentially decrease infectious disease risks during spaceflight missions and provide novel therapeutic options on Earth.

  14. A Global Synthesis Reveals Gaps in Coastal Habitat Restoration Research

    Directory of Open Access Journals (Sweden)

    Y. Stacy Zhang

    2018-04-01

    Full Text Available Coastal ecosystems have drastically declined in coverage and condition across the globe. To combat these losses, marine conservation has recently employed habitat restoration as a strategy to enhance depleted coastal ecosystems. For restoration to be a successful enterprise, however, it is necessary to identify and address potential knowledge gaps and review whether the field has tracked scientific advances regarding best practices. This enables managers, researchers, and practitioners alike to more readily establish restoration priorities and goals. We synthesized the peer-reviewed, published literature on habitat restoration research in salt marshes, oyster reefs, and seagrasses to address three questions related to restoration efforts: (i How frequent is cross-sector authorship in coastal restoration research? (ii What is the geographic distribution of coastal restoration research? and (iii Are abiotic and biotic factors equally emphasized in the literature, and how does this vary with time? Our vote-count survey indicated that one-third of the journal-published studies listed authors from at least two sectors, and 6% listed authors from all three sectors. Across all habitat types, there was a dearth of studies from Africa, Asia, and South America. Finally, despite many experimental studies demonstrating that species interactions can greatly affect the recovery and persistence of coastal foundation species, only one-fourth of the studies we examined discussed their effects on restoration. Combined, our results reveal gaps and discrepancies in restoration research that should be addressed in order to further propel coastal restoration science.

  15. Global lower mesospheric water vapor revealed by LIMS observations

    Science.gov (United States)

    Gordley, L. L.; Russell, J. M., III; Remsberg, E. E.

    1985-01-01

    The Limb Infrared Monitor of the Stratospheric water vapor channel data analysis has been extended from the 1. mb level (about 48 km) to the .3 mb level (about 60 km) through a radiance averaging procedure and better understanding of systematic errors. The data show H2O mixing ratio peaks near the .5 mb level varying from 4 to 7 ppmv with latitude and season. Above this level the mixing ratio drops off quickly with altitude, but, due to experimental uncertainties, at an uncertain rate. The stratospheric results are virtually the same as determined from the archived LIMS results with a tropical hygropause and enhanced H2O concentration in the lower levels at high winter latitudes.

  16. Conserved regulators of nucleolar size revealed by global phenotypic analyses.

    Science.gov (United States)

    Neumüller, Ralph A; Gross, Thomas; Samsonova, Anastasia A; Vinayagam, Arunachalam; Buckner, Michael; Founk, Karen; Hu, Yanhui; Sharifpoor, Sara; Rosebrock, Adam P; Andrews, Brenda; Winston, Fred; Perrimon, Norbert

    2013-08-20

    Regulation of cell growth is a fundamental process in development and disease that integrates a vast array of extra- and intracellular information. A central player in this process is RNA polymerase I (Pol I), which transcribes ribosomal RNA (rRNA) genes in the nucleolus. Rapidly growing cancer cells are characterized by increased Pol I-mediated transcription and, consequently, nucleolar hypertrophy. To map the genetic network underlying the regulation of nucleolar size and of Pol I-mediated transcription, we performed comparative, genome-wide loss-of-function analyses of nucleolar size in Saccharomyces cerevisiae and Drosophila melanogaster coupled with mass spectrometry-based analyses of the ribosomal DNA (rDNA) promoter. With this approach, we identified a set of conserved and nonconserved molecular complexes that control nucleolar size. Furthermore, we characterized a direct role of the histone information regulator (HIR) complex in repressing rRNA transcription in yeast. Our study provides a full-genome, cross-species analysis of a nuclear subcompartment and shows that this approach can identify conserved molecular modules.

  17. Conserved Regulators of Nucleolar Size Revealed by Global Phenotypic Analyses

    Science.gov (United States)

    Neumüller, Ralph A.; Gross, Thomas; Samsonova, Anastasia A.; Vinayagam, Arunachalam; Buckner, Michael; Founk, Karen; Hu, Yanhui; Sharifpoor, Sara; Rosebrock, Adam P.; Andrews, Brenda; Winston, Fred; Perrimon, Norbert

    2014-01-01

    Regulation of cell growth is a fundamental process in development and disease that integrates a vast array of extra- and intracellular information. A central player in this process is RNA polymerase I (Pol I), which transcribes ribosomal RNA (rRNA) genes in the nucleolus. Rapidly growing cancer cells are characterized by increased Pol I–mediated transcription and, consequently, nucleolar hypertrophy. To map the genetic network underlying the regulation of nucleolar size and of Pol I–mediated transcription, we performed comparative, genome-wide loss-of-function analyses of nucleolar size in Saccharomyces cerevisiae and Drosophila melanogaster coupled with mass spectrometry–based analyses of the ribosomal DNA (rDNA) promoter. With this approach, we identified a set of conserved and nonconserved molecular complexes that control nucleolar size. Furthermore, we characterized a direct role of the histone information regulator (HIR) complex in repressing rRNA transcription in yeast. Our study provides a full-genome, cross-species analysis of a nuclear subcompartment and shows that this approach can identify conserved molecular modules. PMID:23962978

  18. Global Analysis of Minimal Surfaces

    CERN Document Server

    Dierkes, Ulrich; Tromba, Anthony J

    2010-01-01

    Many properties of minimal surfaces are of a global nature, and this is already true for the results treated in the first two volumes of the treatise. Part I of the present book can be viewed as an extension of these results. For instance, the first two chapters deal with existence, regularity and uniqueness theorems for minimal surfaces with partially free boundaries. Here one of the main features is the possibility of 'edge-crawling' along free parts of the boundary. The third chapter deals with a priori estimates for minimal surfaces in higher dimensions and for minimizers of singular integ

  19. Global analysis of muon decay measurements

    International Nuclear Information System (INIS)

    Gagliardi, C.A.; Tribble, R.E.; Williams, N.J.

    2005-01-01

    We have performed a global analysis of muon decay measurements to establish model-independent limits on the space-time structure of the muon decay matrix element. We find limits on the scalar, vector, and tensor coupling of right- and left-handed muons to right- and left-handed electrons. The limits on those terms that involve the decay of right-handed muons to left-handed electrons are more restrictive than in previous global analyses, while the limits on the other nonstandard model interactions are comparable. The value of the Michel parameter η found in the global analysis is -0.0036±0.0069, slightly more precise than the value found in a more restrictive analysis of a recent measurement. This has implications for the Fermi coupling constant G F

  20. Global Analysis of a Planetary Gear Train

    Directory of Open Access Journals (Sweden)

    Tongjie Li

    2014-01-01

    Full Text Available By using the Poincaré-like cell-to-cell mapping method and shooting method, the global characteristics of a planetary gear train are studied based on the torsional vibration model with errors of transmission, time-varying meshing stiffness, and multiple gear backlashes. The study results reveal that the planetary with a certain set of parameters has four coexisting periodic orbits, which are P-1, P-2, P-4, and P-8, respectively. P-1 and P-2 motions are not of long-term stability, P-8 motion is of local stability, and P-4 motion is of global stability. Shooting method does not have the capacity of searching coexisting periodic orbits in a global scope, and it is easy to omit some periodic orbits which are far away from the main gropes of periodic orbits.

  1. Population Genetic Analysis Reveals a High Genetic Diversity in the Brazilian Cryptococcus gattii VGII Population and Shifts the Global Origin from the Amazon Rainforest to the Semi-arid Desert in the Northeast of Brazil.

    Science.gov (United States)

    Souto, Ana C P; Bonfietti, Lucas X; Ferreira-Paim, Kennio; Trilles, Luciana; Martins, Marilena; Ribeiro-Alves, Marcelo; Pham, Cau D; Martins, Liline; Dos Santos, Wallace; Chang, Marilene; Brito-Santos, Fabio; Santos, Dayane C S; Fortes, Silvana; Lockhart, Shawn R; Wanke, Bodo; Melhem, Márcia S C; Lazéra, Márcia S; Meyer, Wieland

    2016-08-01

    Cryptococcus neoformans and Cryptococcus gattii are responsible globally for almost one million cryptococcosis cases yearly, mostly in immunocompromised patients, such as those living with HIV. Infections due to C. gattii have mainly been described in tropical and subtropical regions, but its adaptation to temperate regions was crucial in the species evolution and highlighted the importance of this pathogenic yeast in the context of disease. Cryptococcus gattii molecular type VGII has come to the forefront in connection with an on-going emergence in the Pacific North West of North America. Taking into account that previous work pointed towards South America as an origin of this species, the present work aimed to assess the genetic diversity within the Brazilian C. gattii VGII population in order to gain new insights into its origin and global dispersal from the South American continent using the ISHAM consensus MLST typing scheme. Our results corroborate the finding that the Brazilian C. gattii VGII population is highly diverse. The diversity is likely due to recombination generated from sexual reproduction, as evidenced by the presence of both mating types in clinical and environmental samples. The data presented herein strongly supports the emergence of highly virulent strains from ancestors in the Northern regions of Brazil, Amazonia and the Northeast. Numerous genotypes represent a link between Brazil and other parts of the world reinforcing South America as the most likely origin of the C. gattii VGII subtypes and their subsequent global spread, including their dispersal into North America, where they caused a major emergence.

  2. A second life for old data: Global patterns in pollution ecology revealed from published observational studies

    Energy Technology Data Exchange (ETDEWEB)

    Kozlov, Mikhail V., E-mail: mikoz@utu.fi [Section of Ecology, University of Turku, 20014 Turku (Finland); Zvereva, Elena L. [Section of Ecology, University of Turku, 20014 Turku (Finland)

    2011-05-15

    A synthesis of research on the responses of terrestrial biota (1095 effect sizes) to industrial pollution (206 point emission sources) was conducted to reveal regional and global patterns from small-scale observational studies. A meta-analysis, in combination with other statistical methods, showed that the effects of pollution depend on characteristics of the specific polluter (type, amount of emission, duration of impact on biota), the affected organism (trophic group, life history), the level at which the response was measured (organism, population, community), and the environment (biome, climate). In spite of high heterogeneity in responses, we have detected several general patterns. We suggest that the development of evolutionary adaptations to pollution is a common phenomenon and that the harmful effects of pollution on terrestrial ecosystems are likely to increase as the climate warms. We argue that community- and ecosystem-level responses to pollution should be explored directly, rather than deduced from organism-level studies. - Research synthesis demonstrated that the harmful effects of pollution on terrestrial ecosystems are likely to increase as the climate warms.

  3. A second life for old data: Global patterns in pollution ecology revealed from published observational studies

    International Nuclear Information System (INIS)

    Kozlov, Mikhail V.; Zvereva, Elena L.

    2011-01-01

    A synthesis of research on the responses of terrestrial biota (1095 effect sizes) to industrial pollution (206 point emission sources) was conducted to reveal regional and global patterns from small-scale observational studies. A meta-analysis, in combination with other statistical methods, showed that the effects of pollution depend on characteristics of the specific polluter (type, amount of emission, duration of impact on biota), the affected organism (trophic group, life history), the level at which the response was measured (organism, population, community), and the environment (biome, climate). In spite of high heterogeneity in responses, we have detected several general patterns. We suggest that the development of evolutionary adaptations to pollution is a common phenomenon and that the harmful effects of pollution on terrestrial ecosystems are likely to increase as the climate warms. We argue that community- and ecosystem-level responses to pollution should be explored directly, rather than deduced from organism-level studies. - Research synthesis demonstrated that the harmful effects of pollution on terrestrial ecosystems are likely to increase as the climate warms.

  4. Global Analysis of Photosynthesis Transcriptional Regulatory Networks

    Science.gov (United States)

    Imam, Saheed; Noguera, Daniel R.; Donohue, Timothy J.

    2014-01-01

    Photosynthesis is a crucial biological process that depends on the interplay of many components. This work analyzed the gene targets for 4 transcription factors: FnrL, PrrA, CrpK and MppG (RSP_2888), which are known or predicted to control photosynthesis in Rhodobacter sphaeroides. Chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) identified 52 operons under direct control of FnrL, illustrating its regulatory role in photosynthesis, iron homeostasis, nitrogen metabolism and regulation of sRNA synthesis. Using global gene expression analysis combined with ChIP-seq, we mapped the regulons of PrrA, CrpK and MppG. PrrA regulates ∼34 operons encoding mainly photosynthesis and electron transport functions, while CrpK, a previously uncharacterized Crp-family protein, regulates genes involved in photosynthesis and maintenance of iron homeostasis. Furthermore, CrpK and FnrL share similar DNA binding determinants, possibly explaining our observation of the ability of CrpK to partially compensate for the growth defects of a ΔFnrL mutant. We show that the Rrf2 family protein, MppG, plays an important role in photopigment biosynthesis, as part of an incoherent feed-forward loop with PrrA. Our results reveal a previously unrealized, high degree of combinatorial regulation of photosynthetic genes and significant cross-talk between their transcriptional regulators, while illustrating previously unidentified links between photosynthesis and the maintenance of iron homeostasis. PMID:25503406

  5. Global analysis of photosynthesis transcriptional regulatory networks.

    Directory of Open Access Journals (Sweden)

    Saheed Imam

    2014-12-01

    Full Text Available Photosynthesis is a crucial biological process that depends on the interplay of many components. This work analyzed the gene targets for 4 transcription factors: FnrL, PrrA, CrpK and MppG (RSP_2888, which are known or predicted to control photosynthesis in Rhodobacter sphaeroides. Chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq identified 52 operons under direct control of FnrL, illustrating its regulatory role in photosynthesis, iron homeostasis, nitrogen metabolism and regulation of sRNA synthesis. Using global gene expression analysis combined with ChIP-seq, we mapped the regulons of PrrA, CrpK and MppG. PrrA regulates ∼34 operons encoding mainly photosynthesis and electron transport functions, while CrpK, a previously uncharacterized Crp-family protein, regulates genes involved in photosynthesis and maintenance of iron homeostasis. Furthermore, CrpK and FnrL share similar DNA binding determinants, possibly explaining our observation of the ability of CrpK to partially compensate for the growth defects of a ΔFnrL mutant. We show that the Rrf2 family protein, MppG, plays an important role in photopigment biosynthesis, as part of an incoherent feed-forward loop with PrrA. Our results reveal a previously unrealized, high degree of combinatorial regulation of photosynthetic genes and significant cross-talk between their transcriptional regulators, while illustrating previously unidentified links between photosynthesis and the maintenance of iron homeostasis.

  6. Global processing takes time: A meta-analysis on local-global visual processing in ASD.

    Science.gov (United States)

    Van der Hallen, Ruth; Evers, Kris; Brewaeys, Katrien; Van den Noortgate, Wim; Wagemans, Johan

    2015-05-01

    What does an individual with autism spectrum disorder (ASD) perceive first: the forest or the trees? In spite of 30 years of research and influential theories like the weak central coherence (WCC) theory and the enhanced perceptual functioning (EPF) account, the interplay of local and global visual processing in ASD remains only partly understood. Research findings vary in indicating a local processing bias or a global processing deficit, and often contradict each other. We have applied a formal meta-analytic approach and combined 56 articles that tested about 1,000 ASD participants and used a wide range of stimuli and tasks to investigate local and global visual processing in ASD. Overall, results show no enhanced local visual processing nor a deficit in global visual processing. Detailed analysis reveals a difference in the temporal pattern of the local-global balance, that is, slow global processing in individuals with ASD. Whereas task-dependent interaction effects are obtained, gender, age, and IQ of either participant groups seem to have no direct influence on performance. Based on the overview of the literature, suggestions are made for future research. (c) 2015 APA, all rights reserved).

  7. Carbon emission intensity in electricity production: A global analysis

    International Nuclear Information System (INIS)

    Ang, B.W.; Su, Bin

    2016-01-01

    We study changes in the aggregate carbon intensity (ACI) for electricity at the global and country levels. The ACI is defined as the energy-related CO_2 emissions in electricity production divided by the electricity produced. It is a performance indicator since a decrease in its value is a desirable outcome from the environmental and climate change viewpoints. From 1990 to 2013, the ACI computed at the global level decreased only marginally. However, fairly substantial decreases were observed in many countries. This apparent anomaly arises from a geographical shift in global electricity production with countries having a high ACI increasingly taking up a larger electricity production share. It is found that globally and in most major electricity producing countries, reduction in their ACI was due mainly to improvements in the thermal efficiency of electricity generation rather than to fuel switching. Estimates of the above-mentioned effects are made using LMDI decomposition analysis. Our study reveals several challenges in reducing global CO_2 emissions from the electricity production sector although technically the reduction potential for the sector is known to be great. - Highlights: •Variations of aggregate carbon intensity (ACI) for electricity of world countries are analysed. •Main drivers of changes in ACI of major electricity producing countries are studied using index decomposition analysis. •Geographical shift in electricity production had a significant impact on global ACI. •Improvements in the thermal efficiency of generation were the main driver of reduction in ACI.

  8. [18F]DPA 714 PET Imaging Reveals Global Neuroinflammation in Zika Virus Infected Mice

    Science.gov (United States)

    2017-09-12

    with neurotropic viruses and the evaluation of therapeutics being developed for treatment of infectious diseases. Keywords: Zika virus , Animal...18F]DPA-714 PET Imaging Reveals Global Neuroinflammation in Zika Virus - Infected Mice Kyle Kuszpit1†, Bradley S. Hollidge2†, Xiankun Zeng3, Robert...Running Head: PET Imaging of Zika Virus -Induced Neuroinflammation Manuscript Category: Article Affiliations: 1Molecular and Translational

  9. Whole-genome analysis of mRNA decay in Plasmodium falciparum reveals a global lengthening of mRNA half-life during the intra-erythrocytic development cycle.

    Science.gov (United States)

    Shock, Jennifer L; Fischer, Kael F; DeRisi, Joseph L

    2007-01-01

    The rate of mRNA decay is an essential element of post-transcriptional regulation in all organisms. Previously, studies in several organisms found that the specific half-life of each mRNA is precisely related to its physiologic role, and plays an important role in determining levels of gene expression. We used a genome-wide approach to characterize mRNA decay in Plasmodium falciparum. We found that, globally, rates of mRNA decay increase dramatically during the asexual intra-erythrocytic developmental cycle. During the ring stage of the cycle, the average mRNA half-life was 9.5 min, but this was extended to an average of 65 min during the late schizont stage of development. Thus, a major determinant of mRNA decay rate appears to be linked to the stage of intra-erythrocytic development. Furthermore, we found specific variations in decay patterns superimposed upon the dominant trend of progressive half-life lengthening. These variations in decay pattern were frequently enriched for genes with specific cellular functions or processes. Elucidation of Plasmodium mRNA decay rates provides a key element for deciphering mechanisms of genetic control in this parasite, by complementing and extending previous mRNA abundance studies. Our results indicate that progressive stage-dependent decreases in mRNA decay rate function are a major determinant of mRNA accumulation during the schizont stage of intra-erythrocytic development. This type of genome-wide change in mRNA decay rate has not been observed in any other organism to date, and indicates that post-transcriptional regulation may be the dominant mechanism of gene regulation in P. falciparum.

  10. Global plastic models for computerized structural analysis

    International Nuclear Information System (INIS)

    Roche, R.L.; Hoffmann, A.

    1977-01-01

    In many types of structures, it is possible to use generalized stresses (like membrane forces, bending moment, torsion moment...) to define a yield surface for a part of the structure. Analysis can be achieved by using the HILL's principle and a hardening rule. The whole formulation is said 'Global Plastic Model'. Two different global models are used in the CEASEMT system for structural analysis, one for shell analysis and the other for piping analysis (in plastic or creep field). In shell analysis the generalized stresses chosen are the membrane forces and bending (including torsion) moments. There is only one yield condition for a normal to the middle surface and no integration along the thickness is required. In piping analysis, the choice of generalized stresses is bending moments, torsional moment, hoop stress and tension stress. There is only a set of stresses for a cross section and no integration over the cross section area is needed. Connected strains are axis curvature, torsion, uniform strains. The definition of the yield surface is the most important item. A practical way is to use a diagonal quadratic function of the stress components. But the coefficients are depending of the shape of the pipe element, especially for curved segments. Indications will be given on the yield functions used. Some examples of applications in structural analysis are added to the text

  11. Finite element application to global reactor analysis

    International Nuclear Information System (INIS)

    Schmidt, F.A.R.

    1981-01-01

    The Finite Element Method is described as a Coarse Mesh Method with general basis and trial functions. Various consequences concerning programming and application of Finite Element Methods in reactor physics are drawn. One of the conclusions is that the Finite Element Method is a valuable tool in solving global reactor analysis problems. However, problems which can be described by rectangular boxes still can be solved with special coarse mesh programs more efficiently. (orig.) [de

  12. Conference on Convex Analysis and Global Optimization

    CERN Document Server

    Pardalos, Panos

    2001-01-01

    There has been much recent progress in global optimization algo­ rithms for nonconvex continuous and discrete problems from both a theoretical and a practical perspective. Convex analysis plays a fun­ damental role in the analysis and development of global optimization algorithms. This is due essentially to the fact that virtually all noncon­ vex optimization problems can be described using differences of convex functions and differences of convex sets. A conference on Convex Analysis and Global Optimization was held during June 5 -9, 2000 at Pythagorion, Samos, Greece. The conference was honoring the memory of C. Caratheodory (1873-1950) and was en­ dorsed by the Mathematical Programming Society (MPS) and by the Society for Industrial and Applied Mathematics (SIAM) Activity Group in Optimization. The conference was sponsored by the European Union (through the EPEAEK program), the Department of Mathematics of the Aegean University and the Center for Applied Optimization of the University of Florida, by th...

  13. Dynamical Analysis of the Global Warming

    Directory of Open Access Journals (Sweden)

    J. A. Tenreiro Machado

    2012-01-01

    Full Text Available Global warming is a major concern nowadays. Weather conditions are changing, and it seems that human activity is one of the main causes. In fact, since the beginning of the industrial revolution, the burning of fossil fuels has increased the nonnatural emissions of carbon dioxide to the atmosphere. Carbon dioxide is a greenhouse gas that absorbs the infrared radiation produced by the reflection of the sunlight on the Earth’s surface, trapping the heat in the atmosphere. Global warming and the associated climate changes are being the subject of intensive research due to their major impact on social, economic, and health aspects of human life. This paper studies the global warming trend in the perspective of dynamical systems and fractional calculus, which is a new standpoint in this context. Worldwide distributed meteorological stations and temperature records for the last 100 years are analysed. It is shown that the application of Fourier transforms and power law trend lines leads to an assertive representation of the global warming dynamics and a simpler analysis of its characteristics.

  14. A hybrid approach for global sensitivity analysis

    International Nuclear Information System (INIS)

    Chakraborty, Souvik; Chowdhury, Rajib

    2017-01-01

    Distribution based sensitivity analysis (DSA) computes sensitivity of the input random variables with respect to the change in distribution of output response. Although DSA is widely appreciated as the best tool for sensitivity analysis, the computational issue associated with this method prohibits its use for complex structures involving costly finite element analysis. For addressing this issue, this paper presents a method that couples polynomial correlated function expansion (PCFE) with DSA. PCFE is a fully equivalent operational model which integrates the concepts of analysis of variance decomposition, extended bases and homotopy algorithm. By integrating PCFE into DSA, it is possible to considerably alleviate the computational burden. Three examples are presented to demonstrate the performance of the proposed approach for sensitivity analysis. For all the problems, proposed approach yields excellent results with significantly reduced computational effort. The results obtained, to some extent, indicate that proposed approach can be utilized for sensitivity analysis of large scale structures. - Highlights: • A hybrid approach for global sensitivity analysis is proposed. • Proposed approach integrates PCFE within distribution based sensitivity analysis. • Proposed approach is highly efficient.

  15. Global meta-analysis of transcriptomics studies.

    Directory of Open Access Journals (Sweden)

    José Caldas

    Full Text Available Transcriptomics meta-analysis aims at re-using existing data to derive novel biological hypotheses, and is motivated by the public availability of a large number of independent studies. Current methods are based on breaking down studies into multiple comparisons between phenotypes (e.g. disease vs. healthy, based on the studies' experimental designs, followed by computing the overlap between the resulting differential expression signatures. While useful, in this methodology each study yields multiple independent phenotype comparisons, and connections are established not between studies, but rather between subsets of the studies corresponding to phenotype comparisons. We propose a rank-based statistical meta-analysis framework that establishes global connections between transcriptomics studies without breaking down studies into sets of phenotype comparisons. By using a rank product method, our framework extracts global features from each study, corresponding to genes that are consistently among the most expressed or differentially expressed genes in that study. Those features are then statistically modelled via a term-frequency inverse-document frequency (TF-IDF model, which is then used for connecting studies. Our framework is fast and parameter-free; when applied to large collections of Homo sapiens and Streptococcus pneumoniae transcriptomics studies, it performs better than similarity-based approaches in retrieving related studies, using a Medical Subject Headings gold standard. Finally, we highlight via case studies how the framework can be used to derive novel biological hypotheses regarding related studies and the genes that drive those connections. Our proposed statistical framework shows that it is possible to perform a meta-analysis of transcriptomics studies with arbitrary experimental designs by deriving global expression features rather than decomposing studies into multiple phenotype comparisons.

  16. Global plastic models for computerized structural analysis

    International Nuclear Information System (INIS)

    Roche, R.; Hoffmann, A.

    1977-01-01

    Two different global models are used in the CEASEMT system for structural analysis, one for the shells analysis and the other for piping analysis (in plastic or creep field). In shell analysis the generalized stresses choosed are the membrane forces Nsub(ij) and bending (including torsion) moments Msub(ij). There is only one yield condition for a normal (to the middle surface) and no integration along the thickness is required. In piping analysis, the choice of generalized stresses is: bending moments, torsional moments, Hoop stress and tension stress. There is only a set of stresses for a cross section and non integration over the cross section area is needed. Connected strains are axis curvature, torsion, uniform strains. The definition of the yield surface is the most important item. A practical way is to use a diagonal quadratic fonction of the stress components. But the coefficients are depending of the shape of the pipe element, especially for curved segments. Indications will be given on the yield fonctions used. Some examples of applications in structural analysis are added to the text [fr

  17. Global Food Security Support Analysis Data (GFSAD) Crop Mask 2010 Global 1 km V001

    Data.gov (United States)

    National Aeronautics and Space Administration — The NASA Making Earth System Data Records for Use in Research Environments (MEaSUREs) Global Food Security Support Analysis Data (GFSAD) Crop Mask Global 1 kilometer...

  18. Global terrestrial water storage connectivity revealed using complex climate network analyses

    Science.gov (United States)

    Sun, A. Y.; Chen, J.; Donges, J.

    2015-07-01

    Terrestrial water storage (TWS) exerts a key control in global water, energy, and biogeochemical cycles. Although certain causal relationship exists between precipitation and TWS, the latter quantity also reflects impacts of anthropogenic activities. Thus, quantification of the spatial patterns of TWS will not only help to understand feedbacks between climate dynamics and the hydrologic cycle, but also provide new insights and model calibration constraints for improving the current land surface models. This work is the first attempt to quantify the spatial connectivity of TWS using the complex network theory, which has received broad attention in the climate modeling community in recent years. Complex networks of TWS anomalies are built using two global TWS data sets, a remote sensing product that is obtained from the Gravity Recovery and Climate Experiment (GRACE) satellite mission, and a model-generated data set from the global land data assimilation system's NOAH model (GLDAS-NOAH). Both data sets have 1° × 1° grid resolutions and cover most global land areas except for permafrost regions. TWS networks are built by first quantifying pairwise correlation among all valid TWS anomaly time series, and then applying a cutoff threshold derived from the edge-density function to retain only the most important features in the network. Basinwise network connectivity maps are used to illuminate connectivity of individual river basins with other regions. The constructed network degree centrality maps show the TWS anomaly hotspots around the globe and the patterns are consistent with recent GRACE studies. Parallel analyses of networks constructed using the two data sets reveal that the GLDAS-NOAH model captures many of the spatial patterns shown by GRACE, although significant discrepancies exist in some regions. Thus, our results provide further measures for constraining the current land surface models, especially in data sparse regions.

  19. Global sensitivity analysis using polynomial chaos expansions

    International Nuclear Information System (INIS)

    Sudret, Bruno

    2008-01-01

    Global sensitivity analysis (SA) aims at quantifying the respective effects of input random variables (or combinations thereof) onto the variance of the response of a physical or mathematical model. Among the abundant literature on sensitivity measures, the Sobol' indices have received much attention since they provide accurate information for most models. The paper introduces generalized polynomial chaos expansions (PCE) to build surrogate models that allow one to compute the Sobol' indices analytically as a post-processing of the PCE coefficients. Thus the computational cost of the sensitivity indices practically reduces to that of estimating the PCE coefficients. An original non intrusive regression-based approach is proposed, together with an experimental design of minimal size. Various application examples illustrate the approach, both from the field of global SA (i.e. well-known benchmark problems) and from the field of stochastic mechanics. The proposed method gives accurate results for various examples that involve up to eight input random variables, at a computational cost which is 2-3 orders of magnitude smaller than the traditional Monte Carlo-based evaluation of the Sobol' indices

  20. Global sensitivity analysis using polynomial chaos expansions

    Energy Technology Data Exchange (ETDEWEB)

    Sudret, Bruno [Electricite de France, R and D Division, Site des Renardieres, F 77818 Moret-sur-Loing Cedex (France)], E-mail: bruno.sudret@edf.fr

    2008-07-15

    Global sensitivity analysis (SA) aims at quantifying the respective effects of input random variables (or combinations thereof) onto the variance of the response of a physical or mathematical model. Among the abundant literature on sensitivity measures, the Sobol' indices have received much attention since they provide accurate information for most models. The paper introduces generalized polynomial chaos expansions (PCE) to build surrogate models that allow one to compute the Sobol' indices analytically as a post-processing of the PCE coefficients. Thus the computational cost of the sensitivity indices practically reduces to that of estimating the PCE coefficients. An original non intrusive regression-based approach is proposed, together with an experimental design of minimal size. Various application examples illustrate the approach, both from the field of global SA (i.e. well-known benchmark problems) and from the field of stochastic mechanics. The proposed method gives accurate results for various examples that involve up to eight input random variables, at a computational cost which is 2-3 orders of magnitude smaller than the traditional Monte Carlo-based evaluation of the Sobol' indices.

  1. Updated Global Analysis of Higgs Couplings

    CERN Document Server

    Ellis, John

    2013-01-01

    There are many indirect and direct experimental indications that the new particle H discovered by the ATLAS and CMS Collaborations has spin zero and (mostly) positive parity, and that its couplings to other particles are correlated with their masses. Beyond any reasonable doubt, it is a Higgs boson, and here we examine the extent to which its couplings resemble those of the single Higgs boson of the Standard Model. Our global analysis of its couplings to fermions and massive bosons determines that they have the same relative sign as in the Standard Model. We also show directly that these couplings are highly consistent with a dependence on particle masses that is linear to within a few %, and scaled by the conventional electroweak symmetry-breaking scale to within 10%. We also give constraints on loop-induced couplings, on the total Higgs decay width, and on possible invisible decays of the Higgs boson under various assumptions.

  2. Global Surface Warming Hiatus Analysis Data

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — These data were used to conduct the study of the global surface warming hiatus, an apparent decrease in the upward trend of global surface temperatures since 1998....

  3. Analysis of Globalization, the Planet and Education

    Science.gov (United States)

    Tsegay, Samson Maekele

    2016-01-01

    Thorough the framework of theories analyzing globalization and education, this paper focuses on the intersection among globalization, the environment and education. This paper critically analyzes how globalization could affect environmental devastation, and explore the role of pedagogies that could foster planetary citizenship by exposing…

  4. Characteristics of the tomato chromoplast revealed by proteomic analysis

    OpenAIRE

    Barsan, Cristina; Sanchez-Bel, Paloma; Rombaldi, César Valmor; Egea, Isabel; Rossignol, Michel; Kuntz, Marcel; Zouine, Mohamed; Latché, Alain; Bouzayen, Mondher; Pech, Jean-Claude

    2010-01-01

    Chromoplasts are non-photosynthetic specialized plastids that are important in ripening tomato fruit (Solanum lycopersicum) since, among other functions, they are the site of accumulation of coloured compounds. Analysis of the proteome of red fruit chromoplasts revealed the presence of 988 proteins corresponding to 802 Arabidopsis unigenes, among which 209 had not been listed so far in plastidial databanks. These data revealed several features of the chromoplast. Proteins of lipid metabolism ...

  5. Stability of fundamental couplings: A global analysis

    Science.gov (United States)

    Martins, C. J. A. P.; Pinho, A. M. M.

    2017-01-01

    Astrophysical tests of the stability of fundamental couplings are becoming an increasingly important probe of new physics. Motivated by the recent availability of new and stronger constraints we update previous works testing the consistency of measurements of the fine-structure constant α and the proton-to-electron mass ratio μ =mp/me (mostly obtained in the optical/ultraviolet) with combined measurements of α , μ and the proton gyromagnetic ratio gp (mostly in the radio band). We carry out a global analysis of all available data, including the 293 archival measurements of Webb et al. and 66 more recent dedicated measurements, and constraining both time and spatial variations. While nominally the full data sets show a slight statistical preference for variations of α and μ (at up to two standard deviations), we also find several inconsistencies between different subsets, likely due to hidden systematics and implying that these statistical preferences need to be taken with caution. The statistical evidence for a spatial dipole in the values of α is found at the 2.3 sigma level. Forthcoming studies with facilities such as ALMA and ESPRESSO should clarify these issues.

  6. The global land rush: what the evidence reveals about scale and geography

    Energy Technology Data Exchange (ETDEWEB)

    Cotula, Lorenzo; Polack, Emily

    2012-04-15

    In developing countries, millions of people depend on land for their food and livelihoods. But a global 'land rush' — moves to acquire large tracts of land across the world — is increasing competition for this vital resource. A growing body of evidence points to the scale, geography, players and key characteristics of the phenomenon. Some of this is based on media reports and some on country level inventories. Much of the data cannot be compared due to variations in methodology, timescale and the differing criteria for what makes a land deal. Further improving data and analysis is critical. But while exact numbers will keep changing, all evidence indicates that land acquisitions are happening quickly and on a large scale. So we urgently need to get on with developing appropriate responses.

  7. Spring and Its Global Echo: Quantitative Analysis

    Directory of Open Access Journals (Sweden)

    A. V. Korotayev

    2017-01-01

    Full Text Available It is shown that the Arab Spring acted as a trigger for a global wave of socio-political destabilization, which signifi cantly exceeded the scale of the Arab Spring itself and affected absolutely all world-system zones. Only in 2011 the growth of the global number of largescale anti-government demonstrations, riots and political strikes was to a high degree (although not entirely due to their growth in the Arab world. In the ensuing years, the Arab countries rather made a negative contribution to a very noticeable further increase in the global number of large-scale anti-government demonstrations, riots and general strikes (the global intensity of all these three important types of socio-political destabilization continued to grow despite the decline in the Arab world. Thus, for all these three important indicators of sociopolitical destabilization, the scale of the global echo of the Arab Spring has overshadowed the scale of the Arab Spring itself. Only as regards the fourth considered indicator (major terrorist attacks / guerrilla warfare the scale of the global echo for the entire period considered did not overshadow the scale of the Arab Spring (and, incidentally, «Winter» - and in 2014-2015 Arab countries continued to make a disproportionate contribution to the historically record global values of this sad indicator – global number of major terrorist attacks/ guerilla warfare. To conclude, triggered by the Arab Spring, the global wave of socio-political destabilization led after 2010 to a very signifi cant growth of socio-political instability in absolutely all World System zones. However, this global destabilization wave manifested itself in different World System zones in different ways and not completely synchronously.

  8. Modelling and analysis of global coal markets

    International Nuclear Information System (INIS)

    Trueby, Johannes

    2013-01-01

    International Steam Coal Trade. In this paper, we analyse steam coal market equilibria in the years 2006 and 2008 by testing for two possible market structure scenarios: perfect competition and an oligopoly setup with major exporters competing in quantities. The assumed oligopoly scenario cannot explain market equilibria for any year. While we find that the competitive model simulates market equilibria well in 2006, the competitive model is not able to reproduce real market outcomes in 2008. The analysis shows that not all available supply capacity was utilised in 2008. We conclude that either unknown capacity bottlenecks or more sophisticated non-competitive strategies were the cause for the high prices in 2008. Chapter 4 builds upon the findings of the analysis in chapter 3 and adds a more detailed representation of domestic markets. The corresponding essay is titled Nations as Strategic Players in Global Commodity Markets: Evidence from World Coal Trade. In this chapter we explore the hypothesis that export policies and trade patterns of national players in the steam coal market are consistent with non-competitive market behaviour. We test this hypothesis by developing a static equilibrium model which is able to model coal producing nations as strategic players. We explicitly account for integrated seaborne trade and domestic markets. The global steam coal market is simulated under several imperfect market structure setups. We find that trade and prices of a China - Indonesia duopoly fits the real market outcome best and that real Chinese export quotas in 2008 were consistent with simulated exports under a Cournot-Nash strategy. Chapter 5 looks at the long-term effect of Chinese energy system planning decisions. The time horizon is 2006 to 2030. The analysis in this chapter combines a dynamic equilibrium model with the scenario analysis technique. The corresponding essay is titled Coal Lumps vs. Electrons: How Do Chinese Bulk Energy Transport Decisions Affect the Global

  9. Modelling and analysis of global coal markets

    Energy Technology Data Exchange (ETDEWEB)

    Trueby, Johannes

    2013-01-17

    International Steam Coal Trade. In this paper, we analyse steam coal market equilibria in the years 2006 and 2008 by testing for two possible market structure scenarios: perfect competition and an oligopoly setup with major exporters competing in quantities. The assumed oligopoly scenario cannot explain market equilibria for any year. While we find that the competitive model simulates market equilibria well in 2006, the competitive model is not able to reproduce real market outcomes in 2008. The analysis shows that not all available supply capacity was utilised in 2008. We conclude that either unknown capacity bottlenecks or more sophisticated non-competitive strategies were the cause for the high prices in 2008. Chapter 4 builds upon the findings of the analysis in chapter 3 and adds a more detailed representation of domestic markets. The corresponding essay is titled Nations as Strategic Players in Global Commodity Markets: Evidence from World Coal Trade. In this chapter we explore the hypothesis that export policies and trade patterns of national players in the steam coal market are consistent with non-competitive market behaviour. We test this hypothesis by developing a static equilibrium model which is able to model coal producing nations as strategic players. We explicitly account for integrated seaborne trade and domestic markets. The global steam coal market is simulated under several imperfect market structure setups. We find that trade and prices of a China - Indonesia duopoly fits the real market outcome best and that real Chinese export quotas in 2008 were consistent with simulated exports under a Cournot-Nash strategy. Chapter 5 looks at the long-term effect of Chinese energy system planning decisions. The time horizon is 2006 to 2030. The analysis in this chapter combines a dynamic equilibrium model with the scenario analysis technique. The corresponding essay is titled Coal Lumps vs. Electrons: How Do Chinese Bulk Energy Transport Decisions Affect the Global

  10. Genome and metagenome enabled analyses reveal new insight into the global biogeography and potential urea utilization in marine Thaumarchaeota.

    Science.gov (United States)

    Ahlgren, N.; Parada, A. E.; Fuhrman, J. A.

    2016-02-01

    Marine Thaumarchaea are an abundant, important group of marine microbial communities as they fix carbon, oxidize ammonium, and thus contribute to key N and C cycles in the oceans. From an enrichment culture, we have sequenced the complete genome of a new Thaumarchaeota strain, SPOT01. Analysis of this genome and other Thaumarchaeal genomes contributes new insight into its role in N cycling and clarifies the broader biogeography of marine Thaumarchaeal genera. Phylogenomics of Thaumarchaeota genomes reveal coherent separation into clusters roughly equivalent to the genus level, and SPOT01 represents a new genus of marine Thaumarchaea. Competitive fragment recruitment of globally distributed metagenomes from TARA, Ocean Sampling Day, and those generated from a station off California shows that the SPOT01 genus is often the most abundant genus, especially where total Thaumarchaea are most abundant in the overall community. The SPOT01 genome contains urease genes allowing it to use an alternative form of N. Genomic and metagenomic analysis also reveal that among planktonic genomes and populations, the urease genes in general are more frequently found in members of the SPOT01 genus and another genus dominant in deep waters, thus we predict these two genera contribute most significantly to urea utilization among marine Thaumarchaea. Recruitment also revealed broader biogeographic and ecological patterns of the putative genera. The SPOT01 genus was most abundant at colder temperatures (45 degrees). The genus containing Nitrosopumilus maritimus had the highest temperature range, and the genus containing Candidatus Nitrosopelagicus brevis was typically most abundant at intermediate temperatures and intermediate latitudes ( 35-45 degrees). Together these genome and metagenome enabled analyses provide significant new insight into the ecology and biogeochemical contributions of marine archaea.

  11. Core microbial functional activities in ocean environments revealed by global metagenomic profiling analyses.

    Directory of Open Access Journals (Sweden)

    Ari J S Ferreira

    Full Text Available Metagenomics-based functional profiling analysis is an effective means of gaining deeper insight into the composition of marine microbial populations and developing a better understanding of the interplay between the functional genome content of microbial communities and abiotic factors. Here we present a comprehensive analysis of 24 datasets covering surface and depth-related environments at 11 sites around the world's oceans. The complete datasets comprises approximately 12 million sequences, totaling 5,358 Mb. Based on profiling patterns of Clusters of Orthologous Groups (COGs of proteins, a core set of reference photic and aphotic depth-related COGs, and a collection of COGs that are associated with extreme oxygen limitation were defined. Their inferred functions were utilized as indicators to characterize the distribution of light- and oxygen-related biological activities in marine environments. The results reveal that, while light level in the water column is a major determinant of phenotypic adaptation in marine microorganisms, oxygen concentration in the aphotic zone has a significant impact only in extremely hypoxic waters. Phylogenetic profiling of the reference photic/aphotic gene sets revealed a greater variety of source organisms in the aphotic zone, although the majority of individual photic and aphotic depth-related COGs are assigned to the same taxa across the different sites. This increase in phylogenetic and functional diversity of the core aphotic related COGs most probably reflects selection for the utilization of a broad range of alternate energy sources in the absence of light.

  12. Core microbial functional activities in ocean environments revealed by global metagenomic profiling analyses.

    KAUST Repository

    Ferreira, Ari J S

    2014-06-12

    Metagenomics-based functional profiling analysis is an effective means of gaining deeper insight into the composition of marine microbial populations and developing a better understanding of the interplay between the functional genome content of microbial communities and abiotic factors. Here we present a comprehensive analysis of 24 datasets covering surface and depth-related environments at 11 sites around the world\\'s oceans. The complete datasets comprises approximately 12 million sequences, totaling 5,358 Mb. Based on profiling patterns of Clusters of Orthologous Groups (COGs) of proteins, a core set of reference photic and aphotic depth-related COGs, and a collection of COGs that are associated with extreme oxygen limitation were defined. Their inferred functions were utilized as indicators to characterize the distribution of light- and oxygen-related biological activities in marine environments. The results reveal that, while light level in the water column is a major determinant of phenotypic adaptation in marine microorganisms, oxygen concentration in the aphotic zone has a significant impact only in extremely hypoxic waters. Phylogenetic profiling of the reference photic/aphotic gene sets revealed a greater variety of source organisms in the aphotic zone, although the majority of individual photic and aphotic depth-related COGs are assigned to the same taxa across the different sites. This increase in phylogenetic and functional diversity of the core aphotic related COGs most probably reflects selection for the utilization of a broad range of alternate energy sources in the absence of light.

  13. Core microbial functional activities in ocean environments revealed by global metagenomic profiling analyses.

    KAUST Repository

    Ferreira, Ari J S; Siam, Rania; Setubal, Joã o C; Moustafa, Ahmed; Sayed, Ahmed; Chambergo, Felipe S; Dawe, Adam S; Ghazy, Mohamed A; Sharaf, Hazem; Ouf, Amged; Alam, Intikhab; Abdel-Haleem, Alyaa M; Lehvä slaiho, Heikki; Ramadan, Eman; Antunes, André ; Stingl, Ulrich; Archer, John A.C.; Jankovic, Boris R; Sogin, Mitchell; Bajic, Vladimir B.; El-Dorry, Hamza

    2014-01-01

    Metagenomics-based functional profiling analysis is an effective means of gaining deeper insight into the composition of marine microbial populations and developing a better understanding of the interplay between the functional genome content of microbial communities and abiotic factors. Here we present a comprehensive analysis of 24 datasets covering surface and depth-related environments at 11 sites around the world's oceans. The complete datasets comprises approximately 12 million sequences, totaling 5,358 Mb. Based on profiling patterns of Clusters of Orthologous Groups (COGs) of proteins, a core set of reference photic and aphotic depth-related COGs, and a collection of COGs that are associated with extreme oxygen limitation were defined. Their inferred functions were utilized as indicators to characterize the distribution of light- and oxygen-related biological activities in marine environments. The results reveal that, while light level in the water column is a major determinant of phenotypic adaptation in marine microorganisms, oxygen concentration in the aphotic zone has a significant impact only in extremely hypoxic waters. Phylogenetic profiling of the reference photic/aphotic gene sets revealed a greater variety of source organisms in the aphotic zone, although the majority of individual photic and aphotic depth-related COGs are assigned to the same taxa across the different sites. This increase in phylogenetic and functional diversity of the core aphotic related COGs most probably reflects selection for the utilization of a broad range of alternate energy sources in the absence of light.

  14. Multitarget global sensitivity analysis of n-butanol combustion.

    Science.gov (United States)

    Zhou, Dingyu D Y; Davis, Michael J; Skodje, Rex T

    2013-05-02

    A model for the combustion of butanol is studied using a recently developed theoretical method for the systematic improvement of the kinetic mechanism. The butanol mechanism includes 1446 reactions, and we demonstrate that it is straightforward and computationally feasible to implement a full global sensitivity analysis incorporating all the reactions. In addition, we extend our previous analysis of ignition-delay targets to include species targets. The combination of species and ignition targets leads to multitarget global sensitivity analysis, which allows for a more complete mechanism validation procedure than we previously implemented. The inclusion of species sensitivity analysis allows for a direct comparison between reaction pathway analysis and global sensitivity analysis.

  15. Integrated risk analysis of global climate change

    International Nuclear Information System (INIS)

    Shlyakhter, Alexander; Wilson, Richard; Valverde A, L.J. Jr.

    1995-01-01

    This paper discusses several factors that should be considered in integrated risk analyses of global climate change. We begin by describing how the problem of global climate change can be subdivided into largely independent parts that can be linked together in an analytically tractable fashion. Uncertainty plays a central role in integrated risk analyses of global climate change. Accordingly, we consider various aspects of uncertainty as they relate to the climate change problem. We also consider the impacts of these uncertainties on various risk management issues, such as sequential decision strategies, value of information, and problems of interregional and intergenerational equity. (author)

  16. Global sensitivity analysis in wind energy assessment

    Science.gov (United States)

    Tsvetkova, O.; Ouarda, T. B.

    2012-12-01

    Wind energy is one of the most promising renewable energy sources. Nevertheless, it is not yet a common source of energy, although there is enough wind potential to supply world's energy demand. One of the most prominent obstacles on the way of employing wind energy is the uncertainty associated with wind energy assessment. Global sensitivity analysis (SA) studies how the variation of input parameters in an abstract model effects the variation of the variable of interest or the output variable. It also provides ways to calculate explicit measures of importance of input variables (first order and total effect sensitivity indices) in regard to influence on the variation of the output variable. Two methods of determining the above mentioned indices were applied and compared: the brute force method and the best practice estimation procedure In this study a methodology for conducting global SA of wind energy assessment at a planning stage is proposed. Three sampling strategies which are a part of SA procedure were compared: sampling based on Sobol' sequences (SBSS), Latin hypercube sampling (LHS) and pseudo-random sampling (PRS). A case study of Masdar City, a showcase of sustainable living in the UAE, is used to exemplify application of the proposed methodology. Sources of uncertainty in wind energy assessment are very diverse. In the case study the following were identified as uncertain input parameters: the Weibull shape parameter, the Weibull scale parameter, availability of a wind turbine, lifetime of a turbine, air density, electrical losses, blade losses, ineffective time losses. Ineffective time losses are defined as losses during the time when the actual wind speed is lower than the cut-in speed or higher than the cut-out speed. The output variable in the case study is the lifetime energy production. Most influential factors for lifetime energy production are identified with the ranking of the total effect sensitivity indices. The results of the present

  17. State of the Climate - Global Analysis

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — The State of the Climate is a collection of periodic summaries recapping climate-related occurrences on both a global and national scale. The State of the Climate...

  18. Global metabolomics reveals potential urinary biomarkers of esophageal squamous cell carcinoma for diagnosis and staging

    Science.gov (United States)

    Xu, Jing; Chen, Yanhua; Zhang, Ruiping; He, Jiuming; Song, Yongmei; Wang, Jingbo; Wang, Huiqing; Wang, Luhua; Zhan, Qimin; Abliz, Zeper

    2016-10-01

    We performed a metabolomics study using liquid chromatography-mass spectrometry (LC-MS) combined with multivariate data analysis (MVDA) to discriminate global urine profiles in urine samples from esophageal squamous cell carcinoma (ESCC) patients and healthy controls (NC). Our work evaluated the feasibility of employing urine metabolomics for the diagnosis and staging of ESCC. The satisfactory classification between the healthy controls and ESCC patients was obtained using the MVDA model, and obvious classification of early-stage and advanced-stage patients was also observed. The results suggest that the combination of LC-MS analysis and MVDA may have potential applications for ESCC diagnosis and staging. We then conducted LC-MS/MS experiments to identify the potential biomarkers with large contributions to the discrimination. A total of 83 potential diagnostic biomarkers for ESCC were screened out, and 19 potential biomarkers were identified; the variations between the differences in staging using these potential biomarkers were further analyzed. These biomarkers may not be unique to ESCCs, but instead result from any malignant disease. To further elucidate the pathophysiology of ESCC, we studied related metabolic pathways and found that ESCC is associated with perturbations of fatty acid β-oxidation and the metabolism of amino acids, purines, and pyrimidines.

  19. Land Tenure, Gender, and Globalization : Research and Analysis ...

    International Development Research Centre (IDRC) Digital Library (Canada)

    Land Tenure, Gender, and Globalization : Research and Analysis from Africa, Asia, and Latin America. Couverture du livre Land Tenure, Gender, and Globalization : Research and Analysis from Africa. Directeur(s) : Dzodzi Tsikata et Pamela Golah. Maison(s) d'édition : Zubaan, CRDI. 29 août 2009. ISBN : 9788189884727.

  20. Metagenomes Reveal Global Distribution of Bacterial Steroid Catabolism in Natural, Engineered, and Host Environments

    Directory of Open Access Journals (Sweden)

    Johannes Holert

    2018-01-01

    Full Text Available Steroids are abundant growth substrates for bacteria in natural, engineered, and host-associated environments. This study analyzed the distribution of the aerobic 9,10-seco steroid degradation pathway in 346 publically available metagenomes from diverse environments. Our results show that steroid-degrading bacteria are globally distributed and prevalent in particular environments, such as wastewater treatment plants, soil, plant rhizospheres, and the marine environment, including marine sponges. Genomic signature-based sequence binning recovered 45 metagenome-assembled genomes containing a majority of 9,10-seco pathway genes. Only Actinobacteria and Proteobacteria were identified as steroid degraders, but we identified several alpha- and gammaproteobacterial lineages not previously known to degrade steroids. Actino- and proteobacterial steroid degraders coexisted in wastewater, while soil and rhizosphere samples contained mostly actinobacterial ones. Actinobacterial steroid degraders were found in deep ocean samples, while mostly alpha- and gammaproteobacterial ones were found in other marine samples, including sponges. Isolation of steroid-degrading bacteria from sponges confirmed their presence. Phylogenetic analysis of key steroid degradation proteins suggested their biochemical novelty in genomes from sponges and other environments. This study shows that the ecological significance as well as taxonomic and biochemical diversity of bacterial steroid degradation has so far been largely underestimated, especially in the marine environment.

  1. Global Transcription Profiling Reveals Comprehensive Insights into Hypoxic Response in Arabidopsis1[w

    Science.gov (United States)

    Liu, Fenglong; VanToai, Tara; Moy, Linda P.; Bock, Geoffrey; Linford, Lara D.; Quackenbush, John

    2005-01-01

    Plants have evolved adaptation mechanisms to sense oxygen deficiency in their environments and make coordinated physiological and structural adjustments to enhance their hypoxic tolerance. To gain insight into how plants respond to low-oxygen stress, gene expression profiling using whole-genome DNA amplicon microarrays was carried out at seven time points over 24 h, in wild-type and transgenic PSAG12:ipt Arabidopsis (Arabidopsis thaliana) plants under normoxic and hypoxic conditions. Transcript levels of genes involved in glycolysis and fermentation pathways, ethylene synthesis and perception, calcium signaling, nitrogen utilization, trehalose metabolism, and alkaloid synthesis were significantly altered in response to oxygen limitation. Analysis based on gene ontology assignments suggested a significant down-regulation of genes whose functions are associated with cell walls, nucleosome structures, water channels, and ion transporters and a significant up-regulation of genes involved in transcriptional regulation, protein kinase activity, and auxin responses under conditions of oxygen shortage. Promoter analysis on a cluster of up-regulated genes revealed a significant overrepresentation of the AtMYB2-binding motif (GT motif), a sugar response element-like motif, and a G-box-related sequence, and also identified several putative anaerobic response elements. Finally, quantitative real-time polymerase chain reactions using 29 selected genes independently verified the microarray results. This study represents one of the most comprehensive analyses conducted to date investigating hypoxia-responsive transcriptional networks in plants. PMID:15734912

  2. Global transcription profiling reveals comprehensive insights into hypoxic response in Arabidopsis.

    Science.gov (United States)

    Liu, Fenglong; Vantoai, Tara; Moy, Linda P; Bock, Geoffrey; Linford, Lara D; Quackenbush, John

    2005-03-01

    Plants have evolved adaptation mechanisms to sense oxygen deficiency in their environments and make coordinated physiological and structural adjustments to enhance their hypoxic tolerance. To gain insight into how plants respond to low-oxygen stress, gene expression profiling using whole-genome DNA amplicon microarrays was carried out at seven time points over 24 h, in wild-type and transgenic P(SAG12):ipt Arabidopsis (Arabidopsis thaliana) plants under normoxic and hypoxic conditions. Transcript levels of genes involved in glycolysis and fermentation pathways, ethylene synthesis and perception, calcium signaling, nitrogen utilization, trehalose metabolism, and alkaloid synthesis were significantly altered in response to oxygen limitation. Analysis based on gene ontology assignments suggested a significant down-regulation of genes whose functions are associated with cell walls, nucleosome structures, water channels, and ion transporters and a significant up-regulation of genes involved in transcriptional regulation, protein kinase activity, and auxin responses under conditions of oxygen shortage. Promoter analysis on a cluster of up-regulated genes revealed a significant overrepresentation of the AtMYB2-binding motif (GT motif), a sugar response element-like motif, and a G-box-related sequence, and also identified several putative anaerobic response elements. Finally, quantitative real-time polymerase chain reactions using 29 selected genes independently verified the microarray results. This study represents one of the most comprehensive analyses conducted to date investigating hypoxia-responsive transcriptional networks in plants.

  3. Is globalization healthy: a statistical indicator analysis of the impacts of globalization on health.

    Science.gov (United States)

    Martens, Pim; Akin, Su-Mia; Maud, Huynen; Mohsin, Raza

    2010-09-17

    It is clear that globalization is something more than a purely economic phenomenon manifesting itself on a global scale. Among the visible manifestations of globalization are the greater international movement of goods and services, financial capital, information and people. In addition, there are technological developments, more transboundary cultural exchanges, facilitated by the freer trade of more differentiated products as well as by tourism and immigration, changes in the political landscape and ecological consequences. In this paper, we link the Maastricht Globalization Index with health indicators to analyse if more globalized countries are doing better in terms of infant mortality rate, under-five mortality rate, and adult mortality rate. The results indicate a positive association between a high level of globalization and low mortality rates. In view of the arguments that globalization provides winners and losers, and might be seen as a disequalizing process, we should perhaps be careful in interpreting the observed positive association as simple evidence that globalization is mostly good for our health. It is our hope that a further analysis of health impacts of globalization may help in adjusting and optimising the process of globalization on every level in the direction of a sustainable and healthy development for all.

  4. Is globalization healthy: a statistical indicator analysis of the impacts of globalization on health

    Directory of Open Access Journals (Sweden)

    Martens Pim

    2010-09-01

    Full Text Available Abstract It is clear that globalization is something more than a purely economic phenomenon manifesting itself on a global scale. Among the visible manifestations of globalization are the greater international movement of goods and services, financial capital, information and people. In addition, there are technological developments, more transboundary cultural exchanges, facilitated by the freer trade of more differentiated products as well as by tourism and immigration, changes in the political landscape and ecological consequences. In this paper, we link the Maastricht Globalization Index with health indicators to analyse if more globalized countries are doing better in terms of infant mortality rate, under-five mortality rate, and adult mortality rate. The results indicate a positive association between a high level of globalization and low mortality rates. In view of the arguments that globalization provides winners and losers, and might be seen as a disequalizing process, we should perhaps be careful in interpreting the observed positive association as simple evidence that globalization is mostly good for our health. It is our hope that a further analysis of health impacts of globalization may help in adjusting and optimising the process of globalization on every level in the direction of a sustainable and healthy development for all.

  5. Global Proteome Analysis of Leptospira interrogans

    Science.gov (United States)

    Comparative global proteome analyses were performed on Leptospira interrogans serovar Copenhageni grown under conventional in vitro conditions and those mimicking in vivo conditions (iron limitation and serum presence). Proteomic analyses were conducted using iTRAQ and LC-ESI-tandem mass spectrometr...

  6. Event-related potentials reveal increased distraction by salient global objects in older adults

    DEFF Research Database (Denmark)

    Wiegand, Iris; Finke, Kathrin; Töllner, Thomas

    Age-related changes in visual functions influence how older individuals perceive and react upon objects in their environment. In particular, older individuals might be more distracted by highly salient, irrelevant information. Kanizsa figures induce a ‘global precedence’ effect, which reflects...... a processing advantage for salient whole-object representations relative to configurations of local elements not inducing a global form. We investigated event-related potential (ERP) correlates of age-related decline in visual abilities, and specifically, distractibility by salient global objects in visual...

  7. Globalization

    DEFF Research Database (Denmark)

    Plum, Maja

    Globalization is often referred to as external to education - a state of affair facing the modern curriculum with numerous challenges. In this paper it is examined as internal to curriculum; analysed as a problematization in a Foucaultian sense. That is, as a complex of attentions, worries, ways...... of reasoning, producing curricular variables. The analysis is made through an example of early childhood curriculum in Danish Pre-school, and the way the curricular variable of the pre-school child comes into being through globalization as a problematization, carried forth by the comparative practices of PISA...

  8. Comparison of global sensitivity analysis techniques and importance measures in PSA

    International Nuclear Information System (INIS)

    Borgonovo, E.; Apostolakis, G.E.; Tarantola, S.; Saltelli, A.

    2003-01-01

    This paper discusses application and results of global sensitivity analysis techniques to probabilistic safety assessment (PSA) models, and their comparison to importance measures. This comparison allows one to understand whether PSA elements that are important to the risk, as revealed by importance measures, are also important contributors to the model uncertainty, as revealed by global sensitivity analysis. We show that, due to epistemic dependence, uncertainty and global sensitivity analysis of PSA models must be performed at the parameter level. A difficulty arises, since standard codes produce the calculations at the basic event level. We discuss both the indirect comparison through importance measures computed for basic events, and the direct comparison performed using the differential importance measure and the Fussell-Vesely importance at the parameter level. Results are discussed for the large LLOCA sequence of the advanced test reactor PSA

  9. Current issues and challenges in global analysis of parton distributions

    International Nuclear Information System (INIS)

    Tung, Wu-Ki

    2007-01-01

    A new implementation of precise perturbative QCD calculation of deep inelastic scattering structure functions and cross sections, incorporating heavy quark mass effects, is applied to the global analysis of the full HERA I data sets on NC and CC cross sections, in conjunction with other experiments. Improved agreement between the NLO QCD theory and the global data sets are obtained. Comparison of the new results to that of previous analysis based on conventional zero-mass parton formalism is made. Exploratory work on implications of new fixed-target neutrino scattering and Drell-Yan data on global analysis is also discussed. (author)

  10. Global transcriptional profiling of Burkholderia pseudomallei under salt stress reveals differential effects on the Bsa type III secretion system

    Directory of Open Access Journals (Sweden)

    Singsuksawat Ekapot

    2010-06-01

    Full Text Available Abstract Background Burkholderia pseudomallei is the causative agent of melioidosis where the highest reported incidence world wide is in the Northeast of Thailand, where saline soil and water are prevalent. Moreover, recent reports indicate a potential pathogenic role for B. pseudomallei in cystic fibrosis lung disease, where an increased sodium chloride (NaCl concentration in airway surface liquid has been proposed. These observations raise the possibility that high salinity may represent a favorable niche for B. pseudomallei. We therefore investigated the global transcriptional response of B. pseudomallei to increased salinity using microarray analysis. Results Transcriptome analysis of B. pseudomallei under salt stress revealed several genes significantly up-regulated in the presence of 320 mM NaCl including genes associated with the bsa-derived Type III secretion system (T3SS. Microarray data were verified by reverse transcriptase-polymerase chain reactions (RT-PCR. Western blot analysis confirmed the increased expression and secretion of the invasion-associated type III secreted proteins BipD and BopE in B. pseudomallei cultures at 170 and 320 mM NaCl relative to salt-free medium. Furthermore, salt-treated B. pseudomallei exhibited greater invasion efficiency into the lung epithelial cell line A549 in a manner partly dependent on a functional Bsa system. Conclusions B. pseudomallei responds to salt stress by modulating the transcription of a relatively small set of genes, among which is the bsa locus associated with invasion and virulence. Expression and secretion of Bsa-secreted proteins was elevated in the presence of exogenous salt and the invasion efficiency was enhanced. Our data indicate that salinity has the potential to influence the virulence of B. pseudomallei.

  11. Mapping the global health employment market: an analysis of global health jobs.

    Science.gov (United States)

    Keralis, Jessica M; Riggin-Pathak, Brianne L; Majeski, Theresa; Pathak, Bogdan A; Foggia, Janine; Cullinen, Kathleen M; Rajagopal, Abbhirami; West, Heidi S

    2018-02-27

    The number of university global health training programs has grown in recent years. However, there is little research on the needs of the global health profession. We therefore set out to characterize the global health employment market by analyzing global health job vacancies. We collected data from advertised, paid positions posted to web-based job boards, email listservs, and global health organization websites from November 2015 to May 2016. Data on requirements for education, language proficiency, technical expertise, physical location, and experience level were analyzed for all vacancies. Descriptive statistics were calculated for the aforementioned job characteristics. Associations between technical specialty area and requirements for non-English language proficiency and overseas experience were calculated using Chi-square statistics. A qualitative thematic analysis was performed on a subset of vacancies. We analyzed the data from 1007 global health job vacancies from 127 employers. Among private and non-profit sector vacancies, 40% (n = 354) were for technical or subject matter experts, 20% (n = 177) for program directors, and 16% (n = 139) for managers, compared to 9.8% (n = 87) for entry-level and 13.6% (n = 120) for mid-level positions. The most common technical focus area was program or project management, followed by HIV/AIDS and quantitative analysis. Thematic analysis demonstrated a common emphasis on program operations, relations, design and planning, communication, and management. Our analysis shows a demand for candidates with several years of experience with global health programs, particularly program managers/directors and technical experts, with very few entry-level positions accessible to recent graduates of global health training programs. It is unlikely that global health training programs equip graduates to be competitive for the majority of positions that are currently available in this field.

  12. Global qualitative analysis of a quartic ecological model

    NARCIS (Netherlands)

    Broer, Hendrik; Gaiko, Valery A.

    2010-01-01

    in this paper we complete the global qualitative analysis of a quartic ecological model. In particular, studying global bifurcations of singular points and limit cycles, we prove that the corresponding dynamical system has at most two limit cycles. (C) 2009 Elsevier Ltd. All rights reserved.

  13. "Competing Conceptions of Globalization" Revisited: Relocating the Tension between World-Systems Analysis and Globalization Analysis

    Science.gov (United States)

    Clayton, Thomas

    2004-01-01

    In recent years, many scholars have become fascinated by a contemporary, multidimensional process that has come to be known as "globalization." Globalization originally described economic developments at the world level. More specifically, scholars invoked the concept in reference to the process of global economic integration and the seemingly…

  14. Global analysis of the protection status of the world's forests

    DEFF Research Database (Denmark)

    Schmitt, Christine B.; Burgess, Neil David; Coad, Lauren

    2009-01-01

    This study presents a global analysis of forest cover and forest protection. An updated Global Forest Map (using MODIS2005) provided a current assessment of forest cover within 20 natural forest types. This map was overlaid onto WWF realms and ecoregions to gain additional biogeographic information...... on forest distribution. Using the 2008 World Database on Protected Areas, percentage forest cover protection was calculated globally, within forest types, realms and ecoregions, and within selected areas of global conservation importance. At the 10% tree cover threshold, global forest cover was 39 million...... km2. Of this, 7.7% fell within protected areas under IUCN management categories I-IV. With the inclusion of IUCN categories V and VI, the level of global forest protection increased to 13.5%. Percentage forest protection (IUCN I-IV) varied greatly between realms from 5.5% (Palearctic) to 13...

  15. Revealing the Socio-technical Design of Global e-businesses

    DEFF Research Database (Denmark)

    Kampf, Constance Elizabeth

    2012-01-01

    Global e-businesses such as Google, Amazon and E-bay affect both users and society. How can we begin to understand this duality in the socio-technical affordances of e-business? This paper examines a digital art performance as an example of the tensions between capitalist businesses and the public...... of socio-technical design and using dimensions of transparency to understand technology based Internet business, positing global Internet business as having two levels of socio-technical design—1) the micro level, dealing with user interaction, and 2) the macro level, dealing with the social design...

  16. Global change revealed by palaeolimnological records from remote lakes: a review

    Czech Academy of Sciences Publication Activity Database

    Catalan, J.; Pla-Rabés, S.; Wolfe, A. P.; Smol, J. P.; Rühland, K. M.; Anderson, N. J.; Kopáček, Jiří; Stuchlík, E.; Schmidt, R.; Koinig, K. A.; Camarero, L.; Flower, R. J.; Heiri, O.; Kameník, C.; Korhola, A.; Leavitt, P. R.; Psenner, R.; Renberg, I.

    2013-01-01

    Roč. 49, č. 3 (2013), s. 513-535 ISSN 0921-2728 R&D Projects: GA ČR(CZ) GA526/09/0567 Institutional support: RVO:60077344 Keywords : palaeolimnology * sediments * acidifications * heavy metals * global change Subject RIV: DA - Hydrology ; Limnology Impact factor: 2.139, year: 2013

  17. Community Analysis of Global Financial Markets

    Directory of Open Access Journals (Sweden)

    Irena Vodenska

    2016-05-01

    Full Text Available We analyze the daily returns of stock market indices and currencies of 56 countries over the period of 2002–2012. We build a network model consisting of two layers, one being the stock market indices and the other the foreign exchange markets. Synchronous and lagged correlations are used as measures of connectivity and causality among different parts of the global economic system for two different time intervals: non-crisis (2002–2006 and crisis (2007–2012 periods. We study community formations within the network to understand the influences and vulnerabilities of specific countries or groups of countries. We observe different behavior of the cross correlations and communities for crisis vs. non-crisis periods. For example, the overall correlation of stock markets increases during crisis while the overall correlation in the foreign exchange market and the correlation between stock and foreign exchange markets decrease, which leads to different community structures. We observe that the euro, while being central during the relatively calm period, loses its dominant role during crisis. Furthermore we discover that the troubled Eurozone countries, Portugal, Italy, Greece and Spain, form their own cluster during the crisis period.

  18. Proteomics Reveals Global Regulation of Protein SUMOylation by ATM and ATR Kinases during Replication Stress

    Directory of Open Access Journals (Sweden)

    Stephanie Munk

    2017-10-01

    Full Text Available The mechanisms that protect eukaryotic DNA during the cumbersome task of replication depend on the precise coordination of several post-translational modification (PTM-based signaling networks. Phosphorylation is a well-known regulator of the replication stress response, and recently an essential role for SUMOs (small ubiquitin-like modifiers has also been established. Here, we investigate the global interplay between phosphorylation and SUMOylation in response to replication stress. Using SUMO and phosphoproteomic technologies, we identify thousands of regulated modification sites. We find co-regulation of central DNA damage and replication stress responders, of which the ATR-activating factor TOPBP1 is the most highly regulated. Using pharmacological inhibition of the DNA damage response kinases ATR and ATM, we find that these factors regulate global protein SUMOylation in the protein networks that protect DNA upon replication stress and fork breakage, pointing to integration between phosphorylation and SUMOylation in the cellular systems that protect DNA integrity.

  19. Genomic analysis of primordial dwarfism reveals novel disease genes.

    Science.gov (United States)

    Shaheen, Ranad; Faqeih, Eissa; Ansari, Shinu; Abdel-Salam, Ghada; Al-Hassnan, Zuhair N; Al-Shidi, Tarfa; Alomar, Rana; Sogaty, Sameera; Alkuraya, Fowzan S

    2014-02-01

    Primordial dwarfism (PD) is a disease in which severely impaired fetal growth persists throughout postnatal development and results in stunted adult size. The condition is highly heterogeneous clinically, but the use of certain phenotypic aspects such as head circumference and facial appearance has proven helpful in defining clinical subgroups. In this study, we present the results of clinical and genomic characterization of 16 new patients in whom a broad definition of PD was used (e.g., 3M syndrome was included). We report a novel PD syndrome with distinct facies in two unrelated patients, each with a different homozygous truncating mutation in CRIPT. Our analysis also reveals, in addition to mutations in known PD disease genes, the first instance of biallelic truncating BRCA2 mutation causing PD with normal bone marrow analysis. In addition, we have identified a novel locus for Seckel syndrome based on a consanguineous multiplex family and identified a homozygous truncating mutation in DNA2 as the likely cause. An additional novel PD disease candidate gene XRCC4 was identified by autozygome/exome analysis, and the knockout mouse phenotype is highly compatible with PD. Thus, we add a number of novel genes to the growing list of PD-linked genes, including one which we show to be linked to a novel PD syndrome with a distinct facial appearance. PD is extremely heterogeneous genetically and clinically, and genomic tools are often required to reach a molecular diagnosis.

  20. Proteomics Reveals Global Regulation of Protein SUMOylation by ATM and ATR Kinases during Replication Stress

    DEFF Research Database (Denmark)

    Munk, Stephanie; Sigurðsson, Jón Otti; Xiao, Zhenyu

    2017-01-01

    The mechanisms that protect eukaryotic DNA during the cumbersome task of replication depend on the precise coordination of several post-translational modification (PTM)-based signaling networks. Phosphorylation is a well-known regulator of the replication stress response, and recently an essentia....... They analyze changes in the SUMO and phosphoproteome after MMC and hydroxyurea treatments and find that the DNA damage response kinases ATR and ATM globally regulate SUMOylation upon replication stress and fork breakage....

  1. Global analysis of urban surface water supply vulnerability

    International Nuclear Information System (INIS)

    Padowski, Julie C; Gorelick, Steven M

    2014-01-01

    This study presents a global analysis of urban water supply vulnerability in 71 surface-water supplied cities, with populations exceeding 750 000 and lacking source water diversity. Vulnerability represents the failure of an urban supply-basin to simultaneously meet demands from human, environmental and agricultural users. We assess a baseline (2010) condition and a future scenario (2040) that considers increased demand from urban population growth and projected agricultural demand. We do not account for climate change, which can potentially exacerbate or reduce urban supply vulnerability. In 2010, 35% of large cities are vulnerable as they compete with agricultural users. By 2040, without additional measures 45% of cities are vulnerable due to increased agricultural and urban demands. Of the vulnerable cities in 2040, the majority are river-supplied with mean flows so low (1200 liters per person per day, l/p/d) that the cities experience ‘chronic water scarcity’ (1370 l/p/d). Reservoirs supply the majority of cities facing individual future threats, revealing that constructed storage potentially provides tenuous water security. In 2040, of the 32 vulnerable cities, 14 would reduce their vulnerability via reallocating water by reducing environmental flows, and 16 would similarly benefit by transferring water from irrigated agriculture. Approximately half remain vulnerable under either potential remedy. (letter)

  2. COMPARATIVE ANALYSIS OF GLOBAL TERTIARY EDUCATIONAL SYSTEMS

    Directory of Open Access Journals (Sweden)

    Ciumas Cristina

    2013-07-01

    Full Text Available Higher education system occupies a special place in the policy of each nation. Regardless of geographical location, socio-economic or cultural differences, the need to improve the education offered for population by facilitating access to higher education becomes more and more important. Providing a suitable framework for the personal development of each student is expensive and involves high amounts of money. From the analyses carried out we couldn\\'t identify the substantial differences between the way it is structured and organized education system worldwide. However, we were able to identify a number of common elements that create a global University System. The need to invest in human resources through structural reforms in each country is present, and therefore a higher indention to pay greater attention to the development of the higher education system. In our work we decided to analyze education systems in countries like United States of America (USA, United Kingdom (GB, China (CHN, Germany (DE, France (FR, Russian Federation (RU, Japan (JPN average values recorded for EU-27 and last but not least Romania (RO. Although the investment in the University system is hard to quantify, it is unanimously acknowledged that a country can achieve a competitive advantage in international relations through a very well prepared and trained personnel. The countries reviewed in this paper have different policies when it comes to financial support of the University System. If Germany and France have decided to get involved directly in supporting the system by allocating the necessary funds from the State budget, another European country, the United Kingdom, decided to apply a policy diametrically opposite, similar to that existing in the USA and cover in a lesser degree the needs of universities in Government funds. Regardless of the policy adopted the results are intended to be the same: facilitating access to university education, a high quality of

  3. Dual African origins of global Aedes aegypti s.l. populations revealed by mitochondrial DNA.

    Directory of Open Access Journals (Sweden)

    Michelle Moore

    Full Text Available Aedes aegypti is the primary global vector to humans of yellow fever and dengue flaviviruses. Over the past 50 years, many population genetic studies have documented large genetic differences among global populations of this species. These studies initially used morphological polymorphisms, followed later by allozymes, and most recently various molecular genetic markers including microsatellites and mitochondrial markers. In particular, since 2000, fourteen publications and four unpublished datasets have used sequence data from the NADH dehydrogenase subunit 4 mitochondrial gene to compare Ae. aegypti collections and collectively 95 unique mtDNA haplotypes have been found. Phylogenetic analyses in these many studies consistently resolved two clades but no comprehensive study of mtDNA haplotypes have been made in Africa, the continent in which the species originated.ND4 haplotypes were sequenced in 426 Ae. aegypti s.l. from Senegal, West Africa and Kenya, East Africa. In Senegal 15 and in Kenya 7 new haplotypes were discovered. When added to the 95 published haplotypes and including 6 African Aedes species as outgroups, phylogenetic analyses showed that all but one Senegal haplotype occurred in a basal clade while most East African haplotypes occurred in a second clade arising from the basal clade. Globally distributed haplotypes occurred in both clades demonstrating that populations outside Africa consist of mixtures of mosquitoes from both clades.Populations of Ae. aegypti outside Africa consist of mosquitoes arising from one of two ancestral clades. One clade is basal and primarily associated with West Africa while the second arises from the first and contains primarily mosquitoes from East Africa.

  4. Multifaceted diversity-area relationships reveal global hotspots of mammalian species, trait and lineage diversity.

    Science.gov (United States)

    Mazel, Florent; Guilhaumon, François; Mouquet, Nicolas; Devictor, Vincent; Gravel, Dominique; Renaud, Julien; Cianciaruso, Marcus Vinicius; Loyola, Rafael Dias; Diniz-Filho, José Alexandre Felizola; Mouillot, David; Thuiller, Wilfried

    2014-08-01

    To define biome-scale hotspots of phylogenetic and functional mammalian biodiversity (PD and FD, respectively) and compare them to 'classical' hotspots based on species richness (SR) only. Global. SR, PD & FD were computed for 782 terrestrial ecoregions using distribution ranges of 4616 mammalian species. We used a set of comprehensive diversity indices unified by a recent framework that incorporates the species relative coverage in each ecoregion. We build large-scale multifaceted diversity-area relationships to rank ecoregions according to their levels of biodiversity while accounting for the effect of area on each diversity facet. Finally we defined hotspots as the top-ranked ecoregions. While ignoring species relative coverage led to a relative good congruence between biome top ranked SR, PD and FD hotspots, ecoregions harboring a rich and abundantly represented evolutionary history and functional diversity did not match with top ranked ecoregions defined by species richness. More importantly PD and FD hotspots showed important spatial mismatches. We also found that FD and PD generally reached their maximum values faster than species richness as a function of area. The fact that PD/FD reach faster their maximal value than SR may suggest that the two former facets might be less vulnerable to habitat loss than the latter. While this point is expected, it is the first time that it is quantified at global scale and should have important consequences in conservation. Incorporating species relative coverage into the delineation of multifaceted hotspots of diversity lead to weak congruence between SR, PD and FD hotspots. This means that maximizing species number may fail at preserving those nodes (in the phylogenetic or functional tree) that are relatively abundant in the ecoregion. As a consequence it may be of prime importance to adopt a multifaceted biodiversity perspective to inform conservation strategies at global scale.

  5. Intergenic DNA sequences from the human X chromosome reveal high rates of global gene flow

    Directory of Open Access Journals (Sweden)

    Wall Jeffrey D

    2008-11-01

    Full Text Available Abstract Background Despite intensive efforts devoted to collecting human polymorphism data, little is known about the role of gene flow in the ancestry of human populations. This is partly because most analyses have applied one of two simple models of population structure, the island model or the splitting model, which make unrealistic biological assumptions. Results Here, we analyze 98-kb of DNA sequence from 20 independently evolving intergenic regions on the X chromosome in a sample of 90 humans from six globally diverse populations. We employ an isolation-with-migration (IM model, which assumes that populations split and subsequently exchange migrants, to independently estimate effective population sizes and migration rates. While the maximum effective size of modern humans is estimated at ~10,000, individual populations vary substantially in size, with African populations tending to be larger (2,300–9,000 than non-African populations (300–3,300. We estimate mean rates of bidirectional gene flow at 4.8 × 10-4/generation. Bidirectional migration rates are ~5-fold higher among non-African populations (1.5 × 10-3 than among African populations (2.7 × 10-4. Interestingly, because effective sizes and migration rates are inversely related in African and non-African populations, population migration rates are similar within Africa and Eurasia (e.g., global mean Nm = 2.4. Conclusion We conclude that gene flow has played an important role in structuring global human populations and that migration rates should be incorporated as critical parameters in models of human demography.

  6. Integrating abundance and functional traits reveals new global hotspots of fish diversity.

    Science.gov (United States)

    Stuart-Smith, Rick D; Bates, Amanda E; Lefcheck, Jonathan S; Duffy, J Emmett; Baker, Susan C; Thomson, Russell J; Stuart-Smith, Jemina F; Hill, Nicole A; Kininmonth, Stuart J; Airoldi, Laura; Becerro, Mikel A; Campbell, Stuart J; Dawson, Terence P; Navarrete, Sergio A; Soler, German A; Strain, Elisabeth M A; Willis, Trevor J; Edgar, Graham J

    2013-09-26

    Species richness has dominated our view of global biodiversity patterns for centuries. The dominance of this paradigm is reflected in the focus by ecologists and conservation managers on richness and associated occurrence-based measures for understanding drivers of broad-scale diversity patterns and as a biological basis for management. However, this is changing rapidly, as it is now recognized that not only the number of species but the species present, their phenotypes and the number of individuals of each species are critical in determining the nature and strength of the relationships between species diversity and a range of ecological functions (such as biomass production and nutrient cycling). Integrating these measures should provide a more relevant representation of global biodiversity patterns in terms of ecological functions than that provided by simple species counts. Here we provide comparisons of a traditional global biodiversity distribution measure based on richness with metrics that incorporate species abundances and functional traits. We use data from standardized quantitative surveys of 2,473 marine reef fish species at 1,844 sites, spanning 133 degrees of latitude from all ocean basins, to identify new diversity hotspots in some temperate regions and the tropical eastern Pacific Ocean. These relate to high diversity of functional traits amongst individuals in the community (calculated using Rao's Q), and differ from previously reported patterns in functional diversity and richness for terrestrial animals, which emphasize species-rich tropical regions only. There is a global trend for greater evenness in the number of individuals of each species, across the reef fish species observed at sites ('community evenness'), at higher latitudes. This contributes to the distribution of functional diversity hotspots and contrasts with well-known latitudinal gradients in richness. Our findings suggest that the contribution of species diversity to a range of

  7. Analysis reveals potential rangeland impacts if Williamson Act eliminated

    Directory of Open Access Journals (Sweden)

    William C. Wetzel

    2012-10-01

    Full Text Available California budget cuts have resulted in dramatic reductions in state funding for the Williamson Act, a land protection program that reduces property taxes for the owners of 15 million acres of California farms and rangeland. With state reimbursements to counties eliminated, the decision to continue Williamson Act contracts lies with individual counties. We investigated the consequences of eliminating the Williamson Act, using a geospatial analysis and a mail questionnaire asking ranchers for plans under a hypothetical elimination scenario. The geospatial analysis revealed that 72% of rangeland parcels enrolled in Williamson Act contracts contained habitat important for statewide conservation goals. Presented with the elimination scenario, survey respondents reported an intention to sell 20% of their total 496,889 acres. The tendency of survey participants to respond that they would sell land was highest among full-time ranchers with low household incomes and without off-ranch employment. A majority (76% of the ranchers who reported that they would sell land predicted that the buyers would develop it for nonagricultural uses, suggesting substantial changes to California's landscape in a future without the Williamson Act.

  8. Multilocus analysis reveals three candidate genes for Chinese migraine susceptibility.

    Science.gov (United States)

    An, X-K; Fang, J; Yu, Z-Z; Lin, Q; Lu, C-X; Qu, H-L; Ma, Q-L

    2017-08-01

    Several genome-wide association studies (GWASs) in Caucasian populations have identified 12 loci that are significantly associated with migraine. More evidence suggests that serotonin receptors are also involved in migraine pathophysiology. In the present study, a case-control study was conducted in a cohort of 581 migraine cases and 533 ethnically matched controls among a Chinese population. Eighteen polymorphisms from serotonin receptors and GWASs were selected, and genotyping was performed using a Sequenom MALDI-TOF mass spectrometry iPLEX platform. The genotypic and allelic distributions of MEF2D rs2274316 and ASTN2 rs6478241 were significantly different between migraine patients and controls. Univariate and multivariate analysis revealed significant associations of polymorphisms in the MEF2D and ASTN2 genes with migraine susceptibility. MEF2D, PRDM16 and ASTN2 were also found to be associated with migraine without aura (MO) and migraine with family history. And, MEF2D and ASTN2 also served as genetic risk factors for the migraine without family history. The generalized multifactor dimensionality reduction analysis identified that MEF2D and HTR2E constituted the two-factor interaction model. Our study suggests that the MEF2D, PRDM16 and ASTN2 genes from GWAS are associated with migraine susceptibility, especially MO, among Chinese patients. It appears that there is no association with serotonin receptor related genes. © 2017 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  9. Comparative analysis reveals the underlying mechanism of vertebrate seasonal reproduction.

    Science.gov (United States)

    Ikegami, Keisuke; Yoshimura, Takashi

    2016-02-01

    Animals utilize photoperiodic changes as a calendar to regulate seasonal reproduction. Birds have highly sophisticated photoperiodic mechanisms and functional genomics analysis in quail uncovered the signal transduction pathway regulating avian seasonal reproduction. Birds detect light with deep brain photoreceptors. Long day (LD) stimulus induces secretion of thyroid-stimulating hormone (TSH) from the pars tuberalis (PT) of the pituitary gland. PT-derived TSH locally activates thyroid hormone (TH) in the hypothalamus, which induces gonadotropin-releasing hormone (GnRH) and hence gonadotropin secretion. However, during winter, low temperatures increase serum TH for adaptive thermogenesis, which accelerates germ cell apoptosis by activating the genes involved in metamorphosis. Therefore, TH has a dual role in the regulation of seasonal reproduction. Studies using TSH receptor knockout mice confirmed the involvement of PT-derived TSH in mammalian seasonal reproduction. In addition, studies in mice revealed that the tissue-specific glycosylation of TSH diversifies its function in the circulation to avoid crosstalk. In contrast to birds and mammals, one of the molecular machineries necessary for the seasonal reproduction of fish are localized in the saccus vasculosus from the photoreceptor to the neuroendocrine output. Thus, comparative analysis is a powerful tool to uncover the universality and diversity of fundamental properties in various organisms. Copyright © 2015 Elsevier Inc. All rights reserved.

  10. Analysis and Research on Several Global Subdivision Grids

    Directory of Open Access Journals (Sweden)

    SONG Shuhua

    2016-12-01

    Full Text Available In order to solve the problem that lacking of an unified organization frame about global remote sensing satellite image data, this paper introduces serval global subdivision grids as the unified organization frame for remote sensing image. Based on the characteristics of remote sensing image data, this paper analyzes and summarizes the design principles and difficulties of the organization frame. Based on analysis and comparison with these grids, GeoSOT is more suitable as the unified organization frame for remote sensing image. To provide a reference for the global remote sensing image organization.

  11. In situ imaging reveals the biomass of giant protists in the global ocean.

    Science.gov (United States)

    Biard, Tristan; Stemmann, Lars; Picheral, Marc; Mayot, Nicolas; Vandromme, Pieter; Hauss, Helena; Gorsky, Gabriel; Guidi, Lionel; Kiko, Rainer; Not, Fabrice

    2016-04-28

    Planktonic organisms play crucial roles in oceanic food webs and global biogeochemical cycles. Most of our knowledge about the ecological impact of large zooplankton stems from research on abundant and robust crustaceans, and in particular copepods. A number of the other organisms that comprise planktonic communities are fragile, and therefore hard to sample and quantify, meaning that their abundances and effects on oceanic ecosystems are poorly understood. Here, using data from a worldwide in situ imaging survey of plankton larger than 600 μm, we show that a substantial part of the biomass of this size fraction consists of giant protists belonging to the Rhizaria, a super-group of mostly fragile unicellular marine organisms that includes the taxa Phaeodaria and Radiolaria (for example, orders Collodaria and Acantharia). Globally, we estimate that rhizarians in the top 200 m of world oceans represent a standing stock of 0.089 Pg carbon, equivalent to 5.2% of the total oceanic biota carbon reservoir. In the vast oligotrophic intertropical open oceans, rhizarian biomass is estimated to be equivalent to that of all other mesozooplankton (plankton in the size range 0.2-20 mm). The photosymbiotic association of many rhizarians with microalgae may be an important factor in explaining their distribution. The previously overlooked importance of these giant protists across the widest ecosystem on the planet changes our understanding of marine planktonic ecosystems.

  12. Large-scale analysis of Arabidopsis transcription reveals a basal co-regulation network

    Directory of Open Access Journals (Sweden)

    Chamovitz Daniel A

    2009-09-01

    Full Text Available Abstract Background Analyses of gene expression data from microarray experiments has become a central tool for identifying co-regulated, functional gene modules. A crucial aspect of such analysis is the integration of data from different experiments and different laboratories. How to weigh the contribution of different experiments is an important point influencing the final outcomes. We have developed a novel method for this integration, and applied it to genome-wide data from multiple Arabidopsis microarray experiments performed under a variety of experimental conditions. The goal of this study is to identify functional globally co-regulated gene modules in the Arabidopsis genome. Results Following the analysis of 21,000 Arabidopsis genes in 43 datasets and about 2 × 108 gene pairs, we identified a globally co-expressed gene network. We found clusters of globally co-expressed Arabidopsis genes that are enriched for known Gene Ontology annotations. Two types of modules were identified in the regulatory network that differed in their sensitivity to the node-scoring parameter; we further showed these two pertain to general and specialized modules. Some of these modules were further investigated using the Genevestigator compendium of microarray experiments. Analyses of smaller subsets of data lead to the identification of condition-specific modules. Conclusion Our method for identification of gene clusters allows the integration of diverse microarray experiments from many sources. The analysis reveals that part of the Arabidopsis transcriptome is globally co-expressed, and can be further divided into known as well as novel functional gene modules. Our methodology is general enough to apply to any set of microarray experiments, using any scoring function.

  13. Systemic sclerosis: a world wide global analysis.

    Science.gov (United States)

    Coral-Alvarado, Paola; Pardo, Aryce L; Castaño-Rodriguez, Natalia; Rojas-Villarraga, Adriana; Anaya, Juan-Manuel

    2009-07-01

    The objective of this study was to analyze epidemiological tendencies of systemic sclerosis (SSc) around the world in order to identify possible local variations in the presentation and occurrence of the disease. A systematic review of the literature was performed through electronic databases using the keywords "Systemic Sclerosis" and "Clinical Characteristics." Out of a total of 167 articles, 41 were included in the analysis. Significant differences in the mean age at the time of diagnosis, subsets of SSc, clinical characteristics, and presence of antibodies were found between different regions of the word. Because variations in both additive and nonadditive genetic factors and the environmental variance are specific to the investigated population, ethnicity and geography are important characteristics to be considered in the study of SSc and other autoimmune diseases.

  14. Recurrence quantification analysis of global stock markets

    Science.gov (United States)

    Bastos, João A.; Caiado, Jorge

    2011-04-01

    This study investigates the presence of deterministic dependencies in international stock markets using recurrence plots and recurrence quantification analysis (RQA). The results are based on a large set of free float-adjusted market capitalization stock indices, covering a period of 15 years. The statistical tests suggest that the dynamics of stock prices in emerging markets is characterized by higher values of RQA measures when compared to their developed counterparts. The behavior of stock markets during critical financial events, such as the burst of the technology bubble, the Asian currency crisis, and the recent subprime mortgage crisis, is analyzed by performing RQA in sliding windows. It is shown that during these events stock markets exhibit a distinctive behavior that is characterized by temporary decreases in the fraction of recurrence points contained in diagonal and vertical structures.

  15. Mechanistic Differences in Neuropathic Pain Modalities Revealed by Correlating Behavior with Global Expression Profiling

    Directory of Open Access Journals (Sweden)

    Enrique J. Cobos

    2018-01-01

    Full Text Available Chronic neuropathic pain is a major morbidity of neural injury, yet its mechanisms are incompletely understood. Hypersensitivity to previously non-noxious stimuli (allodynia is a common symptom. Here, we demonstrate that the onset of cold hypersensitivity precedes tactile allodynia in a model of partial nerve injury, and this temporal divergence was associated with major differences in global gene expression in innervating dorsal root ganglia. Transcripts whose expression change correlates with the onset of cold allodynia were nociceptor related, whereas those correlating with tactile hypersensitivity were immune cell centric. Ablation of TrpV1 lineage nociceptors resulted in mice that did not acquire cold allodynia but developed normal tactile hypersensitivity, whereas depletion of macrophages or T cells reduced neuropathic tactile allodynia but not cold hypersensitivity. We conclude that neuropathic pain incorporates reactive processes of sensory neurons and immune cells, each leading to distinct forms of hypersensitivity, potentially allowing drug development targeted to each pain type.

  16. Global, exact cosmic microwave background data analysis using Gibbs sampling

    International Nuclear Information System (INIS)

    Wandelt, Benjamin D.; Larson, David L.; Lakshminarayanan, Arun

    2004-01-01

    We describe an efficient and exact method that enables global Bayesian analysis of cosmic microwave background (CMB) data. The method reveals the joint posterior density (or likelihood for flat priors) of the power spectrum C l and the CMB signal. Foregrounds and instrumental parameters can be simultaneously inferred from the data. The method allows the specification of a wide range of foreground priors. We explicitly show how to propagate the non-Gaussian dependency structure of the C l posterior through to the posterior density of the parameters. If desired, the analysis can be coupled to theoretical (cosmological) priors and can yield the posterior density of cosmological parameter estimates directly from the time-ordered data. The method does not hinge on special assumptions about the survey geometry or noise properties, etc., It is based on a Monte Carlo approach and hence parallelizes trivially. No trace or determinant evaluations are necessary. The feasibility of this approach rests on the ability to solve the systems of linear equations which arise. These are of the same size and computational complexity as the map-making equations. We describe a preconditioned conjugate gradient technique that solves this problem and demonstrate in a numerical example that the computational time required for each Monte Carlo sample scales as n p 3/2 with the number of pixels n p . We use our method to analyze the data from the Differential Microwave Radiometer on the Cosmic Background Explorer and explore the non-Gaussian joint posterior density of the C l from the Differential Microwave Radiometer on the Cosmic Background Explorer in several projections

  17. Global Analysis of Heat Shock Response in Desulfovibrio vulgaris Hildenborough.

    Energy Technology Data Exchange (ETDEWEB)

    Chhabra, S.R.; He, Q.; Huang, K.H.; Gaucher, S.P.; Alm, E.J.; He,Z.; Hadi, M.Z.; Hazen, T.C.; Wall, J.D.; Zhou, J.; Arkin, A.P.; Singh, A.K.

    2005-09-16

    Desulfovibrio vulgaris Hildenborough belongs to a class ofsulfate-reducing bacteria (SRB) and is found ubiquitously in nature.Given the importance of SRB-mediated reduction for bioremediation ofmetal ion contaminants, ongoing research on D. vulgaris has been in thedirection of elucidating regulatory mechanisms for this organism under avariety of stress conditions. This work presents a global view of thisorganism's response to elevated growth temperature using whole-celltranscriptomics and proteomics tools. Transcriptional response (1.7-foldchange or greater; Z>1.5) ranged from 1,135 genes at 15 min to 1,463genes at 120 min for a temperature up-shift of 13oC from a growthtemperature of 37oC for this organism and suggested both direct andindirect modes of heat sensing. Clusters of orthologous group categoriesthat were significantly affected included posttranslationalmodifications; protein turnover and chaperones (up-regulated); energyproduction and conversion (down-regulated), nucleotide transport,metabolism (down-regulated), and translation; ribosomal structure; andbiogenesis (down-regulated). Analysis of the genome sequence revealed thepresence of features of both negative and positive regulation whichincluded the CIRCE element and promoter sequences corresponding to thealternate sigma factors ?32 and ?54. While mechanisms of heat shockcontrol for some genes appeared to coincide with those established forEscherichia coli and Bacillus subtilis, the presence of unique controlschemes for several other genes was also evident. Analysis of proteinexpression levels using differential in-gel electrophoresis suggestedgood agreement with transcriptional profiles of several heat shockproteins, including DnaK (DVU0811), HtpG (DVU2643), HtrA (DVU1468), andAhpC (DVU2247). The proteomics study also suggested the possibility ofposttranslational modifications in the chaperones DnaK, AhpC, GroES(DVU1977), and GroEL (DVU1976) and also several periplasmic ABCtransporters.

  18. Global approach of emergency response, reflection analysis

    International Nuclear Information System (INIS)

    Velasco Garcia, E.; Garcia Ahumada, F.; Albaladejo Vidal, S.

    1998-01-01

    The emergency response management approach must be dealt with adequately within company strategy, since a badly managed emergency situation can adversely affect a company, not only in terms of asset, but also in terms of the negative impact on its credibility, profitability and image. Thereby, it can be said that there are three main supports to manage the response in an emergency situation. a) Diagnosis b) Prognosis. c) Communications. To reach these capabilities it is necessary a co-ordination of different actions at the following levels. i. Facility Operation implies Local level. ii. Facility Property implies National level iii. Local Authority implies Local level iv. National Authority implies National level Taking into account all the last, these following functions must be covered: a) Management: incorporating communication, diagnosis and prognosis areas. b) Decision: incorporating communication and information means. c) Services: in order to facilitate the decision, as well as the execution of this decision. d) Analysis: in order to facilitate the situations that make easier to decide. e) Documentation: to seek the information for the analysts and decision makers. (Author)

  19. Global phosphoproteome profiling reveals unanticipated networks responsive to cisplatin treatment of embryonic stem cells

    DEFF Research Database (Denmark)

    Pines, Alex; Kelstrup, Christian D; Vrouwe, Mischa G

    2011-01-01

    (stable isotope labeling by amino acids in cell culture)-labeled murine embryonic stem cells with the anticancer drug cisplatin. Network and pathway analyses indicated that processes related to the DNA damage response and cytoskeleton organization were significantly affected. Although the ATM (ataxia...... rearrangements. Integration of transcriptomic and proteomic data revealed a poor correlation between changes in the relative levels of transcripts and their corresponding proteins, but a large overlap in affected pathways at the levels of mRNA, protein, and phosphoprotein. This study provides an integrated view...

  20. Molecular analysis of sourdough reveals Lactobacillus mindensis sp. nov.

    Science.gov (United States)

    Ehrmann, Matthias A; Müller, Martin R A; Vogel, Rudi F

    2003-01-01

    Genotypic fingerprinting to analyse the bacterial flora of an industrial sourdough revealed a coherent group of strains which could not be associated with a valid species. Comparative 16S rDNA sequence analysis showed that these strains formed a homogeneous cluster distinct from their closest relatives, Lactobacillus farciminis, Lactobacillus alimentarius and Lactobacillus kimchii. To characterize them further, physiological (sugar fermentation, formation of DL-lactate, hydrolysis of arginine, growth temperature, CO2 production) and chemotaxonomic properties have been determined. The DNA G +C content was 37.5 0.2 mol%. The peptidoglycan was of the lysine-D-iso-asparagine (L-Lys-D-Asp) type. The strains were homofermentative, Gram-positive, catalase-negative, non-spore-forming, non-motile rods. They were found as a major stable component of a rye flour sourdough fermentation. Physiological, biochemical as well as genotypic data suggested them to be a new species of the genus Lactobacillus. This was confirmed by DNA-DNA hybridization of genomic DNA, and the name Lactobacillus mindensis is proposed. The type strain of this species is DSM 14500T (=LMG 21508T).

  1. Global/local methods for probabilistic structural analysis

    Science.gov (United States)

    Millwater, H. R.; Wu, Y.-T.

    1993-04-01

    A probabilistic global/local method is proposed to reduce the computational requirements of probabilistic structural analysis. A coarser global model is used for most of the computations with a local more refined model used only at key probabilistic conditions. The global model is used to establish the cumulative distribution function (cdf) and the Most Probable Point (MPP). The local model then uses the predicted MPP to adjust the cdf value. The global/local method is used within the advanced mean value probabilistic algorithm. The local model can be more refined with respect to the g1obal model in terms of finer mesh, smaller time step, tighter tolerances, etc. and can be used with linear or nonlinear models. The basis for this approach is described in terms of the correlation between the global and local models which can be estimated from the global and local MPPs. A numerical example is presented using the NESSUS probabilistic structural analysis program with the finite element method used for the structural modeling. The results clearly indicate a significant computer savings with minimal loss in accuracy.

  2. Optimizing human activity patterns using global sensitivity analysis.

    Science.gov (United States)

    Fairchild, Geoffrey; Hickmann, Kyle S; Mniszewski, Susan M; Del Valle, Sara Y; Hyman, James M

    2014-12-01

    Implementing realistic activity patterns for a population is crucial for modeling, for example, disease spread, supply and demand, and disaster response. Using the dynamic activity simulation engine, DASim, we generate schedules for a population that capture regular (e.g., working, eating, and sleeping) and irregular activities (e.g., shopping or going to the doctor). We use the sample entropy (SampEn) statistic to quantify a schedule's regularity for a population. We show how to tune an activity's regularity by adjusting SampEn, thereby making it possible to realistically design activities when creating a schedule. The tuning process sets up a computationally intractable high-dimensional optimization problem. To reduce the computational demand, we use Bayesian Gaussian process regression to compute global sensitivity indices and identify the parameters that have the greatest effect on the variance of SampEn. We use the harmony search (HS) global optimization algorithm to locate global optima. Our results show that HS combined with global sensitivity analysis can efficiently tune the SampEn statistic with few search iterations. We demonstrate how global sensitivity analysis can guide statistical emulation and global optimization algorithms to efficiently tune activities and generate realistic activity patterns. Though our tuning methods are applied to dynamic activity schedule generation, they are general and represent a significant step in the direction of automated tuning and optimization of high-dimensional computer simulations.

  3. Integrative analysis of RNA, translation, and protein levels reveals distinct regulatory variation across humans.

    Science.gov (United States)

    Cenik, Can; Cenik, Elif Sarinay; Byeon, Gun W; Grubert, Fabian; Candille, Sophie I; Spacek, Damek; Alsallakh, Bilal; Tilgner, Hagen; Araya, Carlos L; Tang, Hua; Ricci, Emiliano; Snyder, Michael P

    2015-11-01

    Elucidating the consequences of genetic differences between humans is essential for understanding phenotypic diversity and personalized medicine. Although variation in RNA levels, transcription factor binding, and chromatin have been explored, little is known about global variation in translation and its genetic determinants. We used ribosome profiling, RNA sequencing, and mass spectrometry to perform an integrated analysis in lymphoblastoid cell lines from a diverse group of individuals. We find significant differences in RNA, translation, and protein levels suggesting diverse mechanisms of personalized gene expression control. Combined analysis of RNA expression and ribosome occupancy improves the identification of individual protein level differences. Finally, we identify genetic differences that specifically modulate ribosome occupancy--many of these differences lie close to start codons and upstream ORFs. Our results reveal a new level of gene expression variation among humans and indicate that genetic variants can cause changes in protein levels through effects on translation. © 2015 Cenik et al.; Published by Cold Spring Harbor Laboratory Press.

  4. Developmental Reorganization of the Core and Extended Face Networks Revealed by Global Functional Connectivity.

    Science.gov (United States)

    Wang, Xu; Zhu, Qi; Song, Yiying; Liu, Jia

    2017-08-28

    Prior studies on development of functional specialization in human brain mainly focus on age-related increases in regional activation and connectivity among regions. However, a few recent studies on the face network demonstrate age-related decrease in face-specialized activation in the extended face network (EFN), in addition to increase in activation in the core face network (CFN). Here we used a voxel-based global brain connectivity approach to investigate whether development of the face network exhibited both increase and decrease in network connectivity. We found the voxel-wise resting-state functional connectivity (FC) within the CFN increased with age in bilateral posterior superior temporal sulcus, suggesting the integration of the CFN during development. Interestingly, the FC of the voxels in the EFN to the right fusiform face area and occipital face area decreased with age, suggesting that the CFN segregated from the EFN during development. Moreover, the age-related connectivity in the CFN was related to behavioral performance in face processing. Overall, our study demonstrated developmental reorganization of the face network achieved by both integration within the CFN and segregation of the CFN from the EFN, which may account for the simultaneous increases and decreases in neural activation during the development of the face network. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  5. Cross-species global proteomics reveals conserved and unique processes in Phytophthora sojae and P. ramorum

    Energy Technology Data Exchange (ETDEWEB)

    Savidor, Alon [ORNL; Donahoo, Ryan S [ORNL; Hurtado-Gonzales, Oscar [University of Tennessee, Knoxville (UTK); Land, Miriam L [ORNL; Shah, Manesh B [ORNL; Lamour, Kurt H [ORNL; McDonald, W Hayes [ORNL

    2008-08-01

    Phytophthora ramorum and Phytophthora sojae are destructive plant pathogens. Phytophthora sojae has a narrow host range whereas P. ramorum has a wide host range. A global proteomic comparison of the vegetative (mycelium) and infective (germinating-cyst) life-stages of P. sojae and P. ramorum was conducted to identify candidate proteins involved in host range, early infection and vegetative growth. Sixty-two candidates for early infection, 26 candidates for vegetative growth, and numerous proteins that may be involved in defining host specificity were identified. In addition, common life stage proteomic trends between the organisms were observed. In mycelia, proteins involved in transport and metabolism of amino acids, carbohydrates and other small molecules were up-regulated. In the germinating cysts, up-regulated proteins associated with lipid transport and metabolism, cytoskeleton and protein synthesis were observed. It appears that the germinating cyst catabolizes lipid reserves through the -oxidation pathway to drive the extensive protein synthesis necessary to produce the germ tube and initiate infection. Once inside the host, the pathogen switches to vegetative growth, where energy is derived from glycolysis and utilized for synthesis of amino acids and other molecules that assist survival in the plant tissue.

  6. RNAi Reveals Phase-Specific Global Regulators of Human Somatic Cell Reprogramming

    Directory of Open Access Journals (Sweden)

    Cheng-Xu Delon Toh

    2016-06-01

    Full Text Available Incomplete knowledge of the mechanisms at work continues to hamper efforts to maximize reprogramming efficiency. Here, we present a systematic genome-wide RNAi screen to determine the global regulators during the early stages of human reprogramming. Our screen identifies functional repressors and effectors that act to impede or promote the reprogramming process. Repressors and effectors form close interacting networks in pathways, including RNA processing, G protein signaling, protein ubiquitination, and chromatin modification. Combinatorial knockdown of five repressors (SMAD3, ZMYM2, SFRS11, SAE1, and ESET synergistically resulted in ∼85% TRA-1-60-positive cells. Removal of the novel splicing factor SFRS11 during reprogramming is accompanied by rapid acquisition of pluripotency-specific spliced forms. Mechanistically, SFRS11 regulates exon skipping and mutually exclusive splicing of transcripts in genes involved in cell differentiation, mRNA splicing, and chromatin modification. Our study provides insights into the reprogramming process, which comprises comprehensive and multi-layered transcriptional, splicing, and epigenetic machineries.

  7. Anthropogenic osmium in rain and snow reveals global-scale atmospheric contamination.

    Science.gov (United States)

    Chen, Cynthia; Sedwick, Peter N; Sharma, Mukul

    2009-05-12

    Osmium is one of the rarer elements in seawater, with typical concentration of approximately 10 x 10(-15) g g(-1) (5.3 x 10(-14) mol kg(-1)). The osmium isotope composition ((187)Os/(188)Os ratio) of deep oceans is 1.05, reflecting a balance between inputs from continental crust (approximately 1.3) and mantle/cosmic dust (approximately 0.13). Here, we show that the (187)Os/(188)Os ratios measured in rain and snow collected around the world range from 0.16 to 0.48, much lower than expected (>1), but similar to the isotope composition of ores (approximately 0.2) that are processed to extract platinum and other metals to be used primarily in automobile catalytic converters. Present-day surface seawater has a lower (187)Os/(188)Os ratio (approximately 0.95) than deep waters, suggesting that human activities have altered the isotope composition of the world's oceans and impacted the global geochemical cycle of osmium. The contamination of the surface ocean is particularly remarkable given that osmium has few industrial uses. The pollution may increase with growing demand for platinum-based catalysts.

  8. Archetypal analysis of diverse Pseudomonas aeruginosa transcriptomes reveals adaptation in cystic fibrosis airways

    Science.gov (United States)

    2013-01-01

    Background Analysis of global gene expression by DNA microarrays is widely used in experimental molecular biology. However, the complexity of such high-dimensional data sets makes it difficult to fully understand the underlying biological features present in the data. The aim of this study is to introduce a method for DNA microarray analysis that provides an intuitive interpretation of data through dimension reduction and pattern recognition. We present the first “Archetypal Analysis” of global gene expression. The analysis is based on microarray data from five integrated studies of Pseudomonas aeruginosa isolated from the airways of cystic fibrosis patients. Results Our analysis clustered samples into distinct groups with comprehensible characteristics since the archetypes representing the individual groups are closely related to samples present in the data set. Significant changes in gene expression between different groups identified adaptive changes of the bacteria residing in the cystic fibrosis lung. The analysis suggests a similar gene expression pattern between isolates with a high mutation rate (hypermutators) despite accumulation of different mutations for these isolates. This suggests positive selection in the cystic fibrosis lung environment, and changes in gene expression for these isolates are therefore most likely related to adaptation of the bacteria. Conclusions Archetypal analysis succeeded in identifying adaptive changes of P. aeruginosa. The combination of clustering and matrix factorization made it possible to reveal minor similarities among different groups of data, which other analytical methods failed to identify. We suggest that this analysis could be used to supplement current methods used to analyze DNA microarray data. PMID:24059747

  9. Simulation analysis of globally integrated logistics and recycling strategies

    Energy Technology Data Exchange (ETDEWEB)

    Song, S.J.; Hiroshi, K. [Hiroshima Inst. of Tech., Graduate School of Mechanical Systems Engineering, Dept. of In formation and Intelligent Systems Engineering, Hiroshima (Japan)

    2004-07-01

    This paper focuses on the optimal analysis of world-wide recycling activities associated with managing the logistics and production activities in global manufacturing whose activities stretch across national boundaries. Globally integrated logistics and recycling strategies consist of the home country and two free trading economic blocs, NAFTA and ASEAN, where significant differences are found in production and disassembly cost, tax rates, local content rules and regulations. Moreover an optimal analysis of globally integrated value-chain was developed by applying simulation optimization technique as a decision-making tool. The simulation model was developed and analyzed by using ProModel packages, and the results help to identify some of the appropriate conditions required to make well-performed logistics and recycling plans in world-wide collaborated manufacturing environment. (orig.)

  10. Isotope analysis reveals foraging area dichotomy for atlantic leatherback turtles.

    Directory of Open Access Journals (Sweden)

    Stéphane Caut

    Full Text Available BACKGROUND: The leatherback turtle (Dermochelys coriacea has undergone a dramatic decline over the last 25 years, and this is believed to be primarily the result of mortality associated with fisheries bycatch followed by egg and nesting female harvest. Atlantic leatherback turtles undertake long migrations across ocean basins from subtropical and tropical nesting beaches to productive frontal areas. Migration between two nesting seasons can last 2 or 3 years, a time period termed the remigration interval (RI. Recent satellite transmitter data revealed that Atlantic leatherbacks follow two major dispersion patterns after nesting season, through the North Gulf Stream area or more eastward across the North Equatorial Current. However, information on the whole RI is lacking, precluding the accurate identification of feeding areas where conservation measures may need to be applied. METHODOLOGY/PRINCIPAL FINDINGS: Using stable isotopes as dietary tracers we determined the characteristics of feeding grounds of leatherback females nesting in French Guiana. During migration, 3-year RI females differed from 2-year RI females in their isotope values, implying differences in their choice of feeding habitats (offshore vs. more coastal and foraging latitude (North Atlantic vs. West African coasts, respectively. Egg-yolk and blood isotope values are correlated in nesting females, indicating that egg analysis is a useful tool for assessing isotope values in these turtles, including adults when not available. CONCLUSIONS/SIGNIFICANCE: Our results complement previous data on turtle movements during the first year following the nesting season, integrating the diet consumed during the year before nesting. We suggest that the French Guiana leatherback population segregates into two distinct isotopic groupings, and highlight the urgent need to determine the feeding habitats of the turtle in the Atlantic in order to protect this species from incidental take by

  11. Quantitative flux analysis reveals folate-dependent NADPH production

    Science.gov (United States)

    Fan, Jing; Ye, Jiangbin; Kamphorst, Jurre J.; Shlomi, Tomer; Thompson, Craig B.; Rabinowitz, Joshua D.

    2014-06-01

    ATP is the dominant energy source in animals for mechanical and electrical work (for example, muscle contraction or neuronal firing). For chemical work, there is an equally important role for NADPH, which powers redox defence and reductive biosynthesis. The most direct route to produce NADPH from glucose is the oxidative pentose phosphate pathway, with malic enzyme sometimes also important. Although the relative contribution of glycolysis and oxidative phosphorylation to ATP production has been extensively analysed, similar analysis of NADPH metabolism has been lacking. Here we demonstrate the ability to directly track, by liquid chromatography-mass spectrometry, the passage of deuterium from labelled substrates into NADPH, and combine this approach with carbon labelling and mathematical modelling to measure NADPH fluxes. In proliferating cells, the largest contributor to cytosolic NADPH is the oxidative pentose phosphate pathway. Surprisingly, a nearly comparable contribution comes from serine-driven one-carbon metabolism, in which oxidation of methylene tetrahydrofolate to 10-formyl-tetrahydrofolate is coupled to reduction of NADP+ to NADPH. Moreover, tracing of mitochondrial one-carbon metabolism revealed complete oxidation of 10-formyl-tetrahydrofolate to make NADPH. As folate metabolism has not previously been considered an NADPH producer, confirmation of its functional significance was undertaken through knockdown of methylenetetrahydrofolate dehydrogenase (MTHFD) genes. Depletion of either the cytosolic or mitochondrial MTHFD isozyme resulted in decreased cellular NADPH/NADP+ and reduced/oxidized glutathione ratios (GSH/GSSG) and increased cell sensitivity to oxidative stress. Thus, although the importance of folate metabolism for proliferating cells has been long recognized and attributed to its function of producing one-carbon units for nucleic acid synthesis, another crucial function of this pathway is generating reducing power.

  12. In vivo Host-Pathogen Interaction as Revealed by Global Proteomic Profiling of Zebrafish Larvae

    Directory of Open Access Journals (Sweden)

    Francisco Díaz-Pascual

    2017-07-01

    immersion. We demonstrated the suitability of zebrafish embryos as a model for in vivo host-pathogen based proteomic studies in P. aeruginosa. Our global proteomic profiling identifies novel molecular signatures that give systematic insight into zebrafish-Pseudomonas interaction.

  13. Finite-time analysis of global projective synchronization on coloured ...

    Indian Academy of Sciences (India)

    A novel finite-time analysis is given to investigate the global projective synchronization on coloured networks. Some less conservative conditions are derived by utilizing finite-time control techniques and Lyapunov stability theorem. In addition, two illustrative numerical simulations are provided to verify the effectiveness of ...

  14. Global and Local Sensitivity Analysis Methods for a Physical System

    Science.gov (United States)

    Morio, Jerome

    2011-01-01

    Sensitivity analysis is the study of how the different input variations of a mathematical model influence the variability of its output. In this paper, we review the principle of global and local sensitivity analyses of a complex black-box system. A simulated case of application is given at the end of this paper to compare both approaches.…

  15. Methods for global sensitivity analysis in life cycle assessment

    NARCIS (Netherlands)

    Groen, Evelyne A.; Bokkers, Eddy; Heijungs, Reinout; Boer, de Imke J.M.

    2017-01-01

    Purpose: Input parameters required to quantify environmental impact in life cycle assessment (LCA) can be uncertain due to e.g. temporal variability or unknowns about the true value of emission factors. Uncertainty of environmental impact can be analysed by means of a global sensitivity analysis to

  16. Ecological network analysis on global virtual water trade.

    Science.gov (United States)

    Yang, Zhifeng; Mao, Xufeng; Zhao, Xu; Chen, Bin

    2012-02-07

    Global water interdependencies are likely to increase with growing virtual water trade. To address the issues of the indirect effects of water trade through the global economic circulation, we use ecological network analysis (ENA) to shed insight into the complicated system interactions. A global model of virtual water flow among agriculture and livestock production trade in 1995-1999 is also built as the basis for network analysis. Control analysis is used to identify the quantitative control or dependency relations. The utility analysis provides more indicators for describing the mutual relationship between two regions/countries by imitating the interactions in the ecosystem and distinguishes the beneficiary and the contributor of virtual water trade system. Results show control and utility relations can well depict the mutual relation in trade system, and direct observable relations differ from integral ones with indirect interactions considered. This paper offers a new way to depict the interrelations between trade components and can serve as a meaningful start as we continue to use ENA in providing more valuable implications for freshwater study on a global scale.

  17. Error Analysis of Determining Airplane Location by Global Positioning System

    OpenAIRE

    Hajiyev, Chingiz; Burat, Alper

    1999-01-01

    This paper studies the error analysis of determining airplane location by global positioning system (GPS) using statistical testing method. The Newton Rhapson method positions the airplane at the intersection point of four spheres. Absolute errors, relative errors and standard deviation have been calculated The results show that the positioning error of the airplane varies with the coordinates of GPS satellite and the airplane.

  18. Genetic diversity and relationship of global faba bean (Vicia faba L.) germplasm revealed by ISSR markers.

    Science.gov (United States)

    Wang, Hai-Fei; Zong, Xu-Xiao; Guan, Jian-Ping; Yang, Tao; Sun, Xue-Lian; Ma, Yu; Redden, Robert

    2012-03-01

    Genetic diversity and relationships of 802 faba bean (Vicia faba L.) landraces and varieties from different geographical locations of China and abroad were examined using ISSR markers. A total of 212 repeatable amplified bands were generated with 11 ISSR primers, of which 209 were polymorphic. Accessions from North China showed highest genetic diversity, while accessions from central China showed low level of diversity. Chinese spring faba bean germplasm was clearly separated from Chinese winter faba bean, based on principal component analysis and UPGMA clustering analysis. Winter accessions from Zhejiang (East China), Jiangxi (East China), Sichuan (Southwest China) and Guizhou (Southwest China) were quite distinct to that from other provinces in China. Great differentiation between Chinese accessions and those from rest of the world was shown with a UPGMA dendrogram. AMOVA analyses demonstrated large variation and differentiation within and among groups of accessions from China. As a continental geographic group, accessions from Europe were genetically closer to those from North Africa. Based on ISSR data, grouping results of accessions from Asia, Europe and Africa were obviously associated with their geographical origin. The overall results indicated that the genetic relationship of faba bean germplasm was closely associated with their geographical origin and their ecological habit.

  19. Reconstruction of the yeast Snf1 kinase regulatory network reveals its role as a global energy regulator

    Science.gov (United States)

    Usaite, Renata; Jewett, Michael C; Oliveira, Ana Paula; Yates, John R; Olsson, Lisbeth; Nielsen, Jens

    2009-01-01

    Highly conserved among eukaryotic cells, the AMP-activated kinase (AMPK) is a central regulator of carbon metabolism. To map the complete network of interactions around AMPK in yeast (Snf1) and to evaluate the role of its regulatory subunit Snf4, we measured global mRNA, protein and metabolite levels in wild type, Δsnf1, Δsnf4, and Δsnf1Δsnf4 knockout strains. Using four newly developed computational tools, including novel DOGMA sub-network analysis, we showed the benefits of three-level ome-data integration to uncover the global Snf1 kinase role in yeast. We for the first time identified Snf1's global regulation on gene and protein expression levels, and showed that yeast Snf1 has a far more extensive function in controlling energy metabolism than reported earlier. Additionally, we identified complementary roles of Snf1 and Snf4. Similar to the function of AMPK in humans, our findings showed that Snf1 is a low-energy checkpoint and that yeast can be used more extensively as a model system for studying the molecular mechanisms underlying the global regulation of AMPK in mammals, failure of which leads to metabolic diseases. PMID:19888214

  20. A global overview of drought and heat-induced tree mortality reveals emerging climate change risks for forests

    Science.gov (United States)

    Allen, Craig D.; Macalady, A.K.; Chenchouni, H.; Bachelet, D.; McDowell, N.; Vennetier, Michel; Kitzberger, T.; Rigling, A.; Breshears, D.D.; Hogg, E.H.(T.); Gonzalez, P.; Fensham, R.; Zhang, Z.; Castro, J.; Demidova, N.; Lim, J.-H.; Allard, G.; Running, S.W.; Semerci, A.; Cobb, N.

    2010-01-01

    Greenhouse gas emissions have significantly altered global climate, and will continue to do so in the future. Increases in the frequency, duration, and/or severity of drought and heat stress associated with climate change could fundamentally alter the composition, structure, and biogeography of forests in many regions. Of particular concern are potential increases in tree mortality associated with climate-induced physiological stress and interactions with other climate-mediated processes such as insect outbreaks and wildfire. Despite this risk, existing projections of tree mortality are based on models that lack functionally realistic mortality mechanisms, and there has been no attempt to track observations of climate-driven tree mortality globally. Here we present the first global assessment of recent tree mortality attributed to drought and heat stress. Although episodic mortality occurs in the absence of climate change, studies compiled here suggest that at least some of the world's forested ecosystems already may be responding to climate change and raise concern that forests may become increasingly vulnerable to higher background tree mortality rates and die-off in response to future warming and drought, even in environments that are not normally considered water-limited. This further suggests risks to ecosystem services, including the loss of sequestered forest carbon and associated atmospheric feedbacks. Our review also identifies key information gaps and scientific uncertainties that currently hinder our ability to predict tree mortality in response to climate change and emphasizes the need for a globally coordinated observation system. Overall, our review reveals the potential for amplified tree mortality due to drought and heat in forests worldwide.

  1. Global metabolomic profiling reveals an association of metal fume exposure and plasma unsaturated fatty acids.

    Directory of Open Access Journals (Sweden)

    Yongyue Wei

    Full Text Available Welding-associated air pollutants negatively affect the health of exposed workers; however, their molecular mechanisms in causing disease remain largely unclear. Few studies have systematically investigated the systemic toxic effects of welding fumes on humans.To explore the effects of welding fumes on the plasma metabolome, and to identify biomarkers for risk assessment of welding fume exposure.The two-stage, self-controlled exploratory study included 11 boilermakers from a 2011 discovery panel and 8 boilermakers from a 2012 validation panel. Plasma samples were collected pre- and post-welding fume exposure and analyzed by chromatography/mass spectrometry.Eicosapentaenoic or docosapentaenoic acid metabolic changes post-welding were significantly associated with particulate (PM2.5 exposure (p<0.05. The combined analysis by linear mixed-effects model showed that exposure was associated with a statistically significant decline in metabolite change of eicosapentaenoic acid [β(95% CI = -0.013(-0.022 ≈ -0.004; p = 0.005], docosapentaenoic acid n3 [β(95% CI = -0.010(-0.018 ≈ -0.002; p = 0.017], and docosapentaenoic acid n6 [β(95% CI = -0.007(-0.013 ≈ -0.001; p = 0.021]. Pathway analysis identified an association of the unsaturated fatty acid pathway with exposure (p Study-2011 = 0.025; p Study-2012 = 0.021; p Combined = 0.009. The functional network built by these fatty acids and their interactive genes contained significant enrichment of genes associated with various diseases, including neoplasms, cardiovascular diseases, and lipid metabolism disorders.High-dose exposure of metal welding fumes decreases unsaturated fatty acids with an exposure-response relationship. This alteration in fatty acids is a potential biological mediator and biomarker for exposure-related health disorders.

  2. Genetic analysis of Aedes albopictus (Diptera, Culicidae) reveals a deep divergence in the original regions.

    Science.gov (United States)

    Ruiling, Zhang; Tongkai, Liu; Zhendong, Huang; Guifen, Zhuang; Dezhen, Ma; Zhong, Zhang

    2018-05-02

    Aedes albopictus has been described as one of the 100 worst invasive species in the world. This mosquito originated from southeastern Asia and currently has a widespread presence in every continent except Antarctica. The rapid global expansion of Ae. albopictus has increased public health concerns about arbovirus-related disease threats. Adaptation, adaption to novel areas is a biological challenge for invasive species, and the underlying processes can be studied at the molecular level. In this study, genetic analysis was performed using mitochondrial gene NADH dehydrogenase subunit 5 (ND5), based on both native and invasive populations. Altogether, 38 haplotypes were detected with H1 being the dominant and widely distributed in 21 countries. Both phylogenetic and network analyses supported the existence of five clades, with only clade I being involved in the subsequent global spread of Asian tiger mosquito. The other four clades (II, III, IV and V) were restricted to their original regions, which could be ancestral populations that had diverged from clade I in the early stages of evolution. Neutrality tests suggested that most of the populations had experienced recent expansion. Analysis of molecular variance and the population-pair statistic F ST revealed that most populations lacked genetic structure, while high variability was detected within populations. Multiple and independent human-mediated introductions may explain the present results. Copyright © 2018 Elsevier B.V. All rights reserved.

  3. A general first-order global sensitivity analysis method

    International Nuclear Information System (INIS)

    Xu Chonggang; Gertner, George Zdzislaw

    2008-01-01

    Fourier amplitude sensitivity test (FAST) is one of the most popular global sensitivity analysis techniques. The main mechanism of FAST is to assign each parameter with a characteristic frequency through a search function. Then, for a specific parameter, the variance contribution can be singled out of the model output by the characteristic frequency. Although FAST has been widely applied, there are two limitations: (1) the aliasing effect among parameters by using integer characteristic frequencies and (2) the suitability for only models with independent parameters. In this paper, we synthesize the improvement to overcome the aliasing effect limitation [Tarantola S, Gatelli D, Mara TA. Random balance designs for the estimation of first order global sensitivity indices. Reliab Eng Syst Safety 2006; 91(6):717-27] and the improvement to overcome the independence limitation [Xu C, Gertner G. Extending a global sensitivity analysis technique to models with correlated parameters. Comput Stat Data Anal 2007, accepted for publication]. In this way, FAST can be a general first-order global sensitivity analysis method for linear/nonlinear models with as many correlated/uncorrelated parameters as the user specifies. We apply the general FAST to four test cases with correlated parameters. The results show that the sensitivity indices derived by the general FAST are in good agreement with the sensitivity indices derived by the correlation ratio method, which is a non-parametric method for models with correlated parameters

  4. Globalization

    Directory of Open Access Journals (Sweden)

    Tulio Rosembuj

    2006-12-01

    Full Text Available There is no singular globalization, nor is the result of an individual agent. We could start by saying that global action has different angles and subjects who perform it are different, as well as its objectives. The global is an invisible invasion of materials and immediate effects.

  5. Globalization

    OpenAIRE

    Tulio Rosembuj

    2006-01-01

    There is no singular globalization, nor is the result of an individual agent. We could start by saying that global action has different angles and subjects who perform it are different, as well as its objectives. The global is an invisible invasion of materials and immediate effects.

  6. Safety-oriented global analysis of reactor dynamics

    International Nuclear Information System (INIS)

    Belhadj, M.; Aldemir, T.

    1992-01-01

    It is well known that the asymptotic solutions of the non-linear systems encountered in reactor dynamics can change from stable to periodic or from periodic to chaotic with a very small change in system parameters and/or initial conditions. In that respect, determination of the domains of attraction (DOAs) in the state-space that contains the asymptotic solutions and the identification of the basins of attraction (BOAs) and lead to these DOAs usually requires a global analysis of reactor dynamics (as opposed to a local analysis through perturbation theory). From the standpoint of safety, the DOAs indicate whether the reactor behavior remains within the imposed constraints or not, and the BOAs show which initial conditions lead to safe operation. Due to the lack of a general theory, often the only feasible method for the global analysis of nonlinear systems is the direct integration of governing equations. However, direct integration can be computationally prohibitive, particularly if there is uncertainty on the values of the system parameters to be used in the analysis, and/or asymptotic system behavior is chaotic. In a recent study, a global analysis algorithm was presented to determine the structure of DOAs (and their probability distribution when there is uncertainty on the system parameters) more quickly than by direct integration. This paper shows how the new algorithm can be expanded to determine the BOAs of reactor dynamics equations as well as their DOAs

  7. Global robust exponential stability analysis for interval recurrent neural networks

    International Nuclear Information System (INIS)

    Xu Shengyuan; Lam, James; Ho, Daniel W.C.; Zou Yun

    2004-01-01

    This Letter investigates the problem of robust global exponential stability analysis for interval recurrent neural networks (RNNs) via the linear matrix inequality (LMI) approach. The values of the time-invariant uncertain parameters are assumed to be bounded within given compact sets. An improved condition for the existence of a unique equilibrium point and its global exponential stability of RNNs with known parameters is proposed. Based on this, a sufficient condition for the global robust exponential stability for interval RNNs is obtained. Both of the conditions are expressed in terms of LMIs, which can be checked easily by various recently developed convex optimization algorithms. Examples are provided to demonstrate the reduced conservatism of the proposed exponential stability condition

  8. The Global Acetylome of the Human Pathogen Vibrio cholerae V52 Reveals Lysine Acetylation of Major Transcriptional Regulators

    DEFF Research Database (Denmark)

    Jers, Carsten; Ravikumar, Vaishnavi; Lezyk, Mateusz Jakub

    2018-01-01

    Protein lysine acetylation is recognized as an important reversible post translational modification in all domains of life. While its primary roles appear to reside in metabolic processes, lysine acetylation has also been implicated in regulating pathogenesis in bacteria. Several global lysine...... acetylome analyses have been carried out in various bacteria, but thus far there have been no reports of lysine acetylation taking place in the important human pathogen Vibrio cholerae. In this study, we analyzed the lysine acetylproteome of the human pathogen V. cholerae V52. By applying a combination...... in direct regulation of virulence in V. cholerae were acetylated. In conclusion, this is the first global protein lysine acetylome analysis of V. cholerae and should constitute a valuable resource for in-depth studies of the impact of lysine acetylation in pathogenesis and other cellular processes....

  9. Lattice Boltzmann methods for global linear instability analysis

    Science.gov (United States)

    Pérez, José Miguel; Aguilar, Alfonso; Theofilis, Vassilis

    2017-12-01

    Modal global linear instability analysis is performed using, for the first time ever, the lattice Boltzmann method (LBM) to analyze incompressible flows with two and three inhomogeneous spatial directions. Four linearization models have been implemented in order to recover the linearized Navier-Stokes equations in the incompressible limit. Two of those models employ the single relaxation time and have been proposed previously in the literature as linearization of the collision operator of the lattice Boltzmann equation. Two additional models are derived herein for the first time by linearizing the local equilibrium probability distribution function. Instability analysis results are obtained in three benchmark problems, two in closed geometries and one in open flow, namely the square and cubic lid-driven cavity flow and flow in the wake of the circular cylinder. Comparisons with results delivered by classic spectral element methods verify the accuracy of the proposed new methodologies and point potential limitations particular to the LBM approach. The known issue of appearance of numerical instabilities when the SRT model is used in direct numerical simulations employing the LBM is shown to be reflected in a spurious global eigenmode when the SRT model is used in the instability analysis. Although this mode is absent in the multiple relaxation times model, other spurious instabilities can also arise and are documented herein. Areas of potential improvements in order to make the proposed methodology competitive with established approaches for global instability analysis are discussed.

  10. Comparative proteomics and codon substitution analysis reveal mechanisms of differential resistance to hypoxia in congeneric snails

    KAUST Repository

    Mu, Huawei; Sun, Jin; Cheung, Siu Gin; Fang, Ling; Zhou, Haiyun; Luan, Tiangang; Zhang, Huoming; Wong, Chris K.C.; Qiu, Jian-Wen

    2017-01-01

    Although high-throughput proteomics has been widely applied to study mechanisms of environmental adaptation, the conclusions from studies that are based on one species can be confounded by phylogeny. We compare the freshwater snail Pomacea canaliculata (a notorious invasive species) and its congener Pomacea diffusa (a non-invasive species) to understand the molecular mechanisms of their differential resistance to hypoxia. A 72-h acute exposure experiment showed that P. canaliculata is more tolerant to hypoxia than P. diffusa. The two species were then exposed to three levels of dissolved oxygen (6.7, 2.0 and 1.0mgL−1) for 8h, and their gill proteins were analyzed using iTRAQ-coupled LC-MS/MS. The two species showed striking differences in protein expression profiles, with the more hypoxia tolerant P. canaliculata having more up-regulated proteins in signal transduction and down-regulated proteins in glycolysis and the tricarboxylic acid cycle. Evolutionary analysis revealed five orthologous genes encoding differentially expressed proteins having clear signal of positive selection, indicating selection has acted on some of the hypoxia responsive genes. Our case study has highlighted the potential of integrated proteomics and comparative evolutionary analysis for understanding the genetic basis of adaptation to global environmental change in non-model species. SignificanceRapid globalization in recent decades has greatly facilitated species introduction around the world. Successfully established introduced species, so-called invasive species, have threatened the invaded ecosystems. There has been substantial interest in studying how invasive species respond to extreme environmental conditions because the results can help not only predict their range of expansion and manage their impact, but also may reveal the adaptive mechanisms underlying their invasiveness. Our study has adopted a comparative approach to study the differential physiological and proteomic

  11. Comparative proteomics and codon substitution analysis reveal mechanisms of differential resistance to hypoxia in congeneric snails

    KAUST Repository

    Mu, Huawei

    2017-11-06

    Although high-throughput proteomics has been widely applied to study mechanisms of environmental adaptation, the conclusions from studies that are based on one species can be confounded by phylogeny. We compare the freshwater snail Pomacea canaliculata (a notorious invasive species) and its congener Pomacea diffusa (a non-invasive species) to understand the molecular mechanisms of their differential resistance to hypoxia. A 72-h acute exposure experiment showed that P. canaliculata is more tolerant to hypoxia than P. diffusa. The two species were then exposed to three levels of dissolved oxygen (6.7, 2.0 and 1.0mgL−1) for 8h, and their gill proteins were analyzed using iTRAQ-coupled LC-MS/MS. The two species showed striking differences in protein expression profiles, with the more hypoxia tolerant P. canaliculata having more up-regulated proteins in signal transduction and down-regulated proteins in glycolysis and the tricarboxylic acid cycle. Evolutionary analysis revealed five orthologous genes encoding differentially expressed proteins having clear signal of positive selection, indicating selection has acted on some of the hypoxia responsive genes. Our case study has highlighted the potential of integrated proteomics and comparative evolutionary analysis for understanding the genetic basis of adaptation to global environmental change in non-model species. SignificanceRapid globalization in recent decades has greatly facilitated species introduction around the world. Successfully established introduced species, so-called invasive species, have threatened the invaded ecosystems. There has been substantial interest in studying how invasive species respond to extreme environmental conditions because the results can help not only predict their range of expansion and manage their impact, but also may reveal the adaptive mechanisms underlying their invasiveness. Our study has adopted a comparative approach to study the differential physiological and proteomic

  12. Political priority of global oral health: an analysis of reasons for international neglect.

    Science.gov (United States)

    Benzian, Habib; Hobdell, Martin; Holmgren, Christopher; Yee, Robert; Monse, Bella; Barnard, Johannes T; van Palenstein Helderman, Wim

    2011-06-01

    Global Oral Health suffers from a lack of political attention, particularly in low- and middle-income countries. This paper analyses the reasons for this political neglect through the lens of four areas of political power: the power of the ideas, the power of the issue, the power of the actors, and the power of the political context (using a modified Political Power Framework by Shiffman and Smith. Lancet370 [2007] 1370). The analysis reveals that political priority for global oral health is low, resulting from a set of complex issues deeply rooted in the current global oral health sector, its stakeholders and their remit, the lack of coherence and coalescence; as well as the lack of agreement on the problem, its portrayal and possible solutions. The shortcomings and weaknesses demonstrated in the analysis range from rather basic matters, such as defining the issue in an agreed way, to complex and multi-levelled issues concerning appropriate data collection and agreement on adequate solutions. The political priority of Global Oral Health can only be improved by addressing the underlying reasons that resulted in the wide disconnection between the international health discourse and the small sector of Global Oral Health. We hope that this analysis may serve as a starting point for a long overdue, broad and candid international analysis of political, social, cultural, communication, financial and other factors related to better prioritisation of oral health. Without such an analysis and the resulting concerted action the inequities in Global Oral Health will grow and increasingly impact on health systems, development and, most importantly, human lives. © 2011 FDI World Dental Federation.

  13. Global analysis of cloud field coverage and radiative properties, using morphological methods and MODIS observations

    Directory of Open Access Journals (Sweden)

    R. Z. Bar-Or

    2011-01-01

    Full Text Available The recently recognized continuous transition zone between detectable clouds and cloud-free atmosphere ("the twilight zone" is affected by undetectable clouds and humidified aerosol. In this study, we suggest to distinguish cloud fields (including the detectable clouds and the surrounding twilight zone from cloud-free areas, which are not affected by clouds. For this classification, a robust and simple-to-implement cloud field masking algorithm which uses only the spatial distribution of clouds, is presented in detail. A global analysis, estimating Earth's cloud field coverage (50° S–50° N for 28 July 2008, using the Moderate Resolution Imaging Spectroradiometer (MODIS data, finds that while the declared cloud fraction is 51%, the global cloud field coverage reaches 88%. The results reveal the low likelihood for finding a cloud-free pixel and suggest that this likelihood may decrease as the pixel size becomes larger. A global latitudinal analysis of cloud fields finds that unlike oceans, which are more uniformly covered by cloud fields, land areas located under the subsidence zones of the Hadley cell (the desert belts, contain proper areas for investigating cloud-free atmosphere as there is 40–80% probability to detect clear sky over them. Usually these golden-pixels, with higher likelihood to be free of clouds, are over deserts. Independent global statistical analysis, using MODIS aerosol and cloud products, reveals a sharp exponential decay of the global mean aerosol optical depth (AOD as a function of the distance from the nearest detectable cloud, both above ocean and land. Similar statistical analysis finds an exponential growth of mean aerosol fine-mode fraction (FMF over oceans when the distance from the nearest cloud increases. A 30 km scale break clearly appears in several analyses here, suggesting this is a typical natural scale of cloud fields. This work shows different microphysical and optical properties of cloud fields

  14. The Analysis of the Impact of Globalization on Employment in Ukraine

    Directory of Open Access Journals (Sweden)

    Gryshkin Vadym O.

    2016-08-01

    Full Text Available The aim of the article is analyzing the impact of globalization on employment in Ukraine and studying foreign experience in regulation of the labor market under conditions of globalization. The theoretical aspects of employment of population at the stage of market transformation of economy have been analyzed. The comprehensive analysis of the current state of employment in Ukraine has been conducted. The dynamics of the main indicators of employment of population and labor migration has been considered and analyzed. The shortcomings in the mechanism of employment regulation are revealed and measures to overcome them on the basis of the positive experience of developed countries are proposed. The necessity of adapting the foreign experience to the Ukrainian realities and the possibility of its use in the national territory is justified. The main tasks of the state policy on regulating the employment of Ukraine’s population under conditions of globalization are presented.

  15. 8000-year monsoonal record from Himalaya revealing reinforcement of tropical and global climate systems since mid-Holocene.

    Science.gov (United States)

    Srivastava, Pradeep; Agnihotri, Rajesh; Sharma, Deepti; Meena, Narendra; Sundriyal, Y P; Saxena, Anju; Bhushan, Ravi; Sawlani, R; Banerji, Upasana S; Sharma, C; Bisht, P; Rana, N; Jayangondaperumal, R

    2017-11-06

    We provide the first continuous Indian Summer Monsoon (ISM) climate record for the higher Himalayas (Kedarnath, India) by analyzing a 14 C-dated peat sequence covering the last ~8000 years, with ~50 years temporal resolution. The ISM variability inferred using various proxies reveal striking similarity with the Greenland ice core (GISP2) temperature record and rapid denitrification changes recorded in the sediments off Peru. The Kedarnath record provides compelling evidence for a reorganization of the global climate system taking place at ~5.5 ka BP possibly after sea level stabilization and the advent of inter-annual climate variability governed by the modern ENSO phenomenon. The ISM record also captures warm-wet and cold-dry conditions during the Medieval Climate Anomaly and Little Ice Age, respectively.

  16. Structural analysis of a ship on global aspect using ANSYS

    Science.gov (United States)

    Rahman, M. Muzibur; Kamol, Rajia Sultana; Islam, Reyana

    2017-12-01

    Ship is a complex geometry which undergoes a combination of loadings such as hydrostatic, hydrodynamic, wind, wave etc. at sea and thus adequate strength in a ship has always been one of the most challenging tasks for the ship designers. International Maritime Organization (IMO) and classification societies are providing the standards to ensure the adequacy of strength for the ship against all demands throughout its service life. Thus, structural analysis is needed to assess the overall strength of hull, and the means in this regard are based on finite element method which may be applied either local or global aspect of the ship. This paper is an attempt to carry out the structural analysis of a ship in global aspect using ANSYS software to locate the most stress concentration and deformed area, which will have ultimate effect on fatigue fracture.

  17. Globalization

    OpenAIRE

    Andru?cã Maria Carmen

    2013-01-01

    The field of globalization has highlighted an interdependence implied by a more harmonious understanding determined by the daily interaction between nations through the inducement of peace and the management of streamlining and the effectiveness of the global economy. For the functioning of the globalization, the developing countries that can be helped by the developed ones must be involved. The international community can contribute to the institution of the development environment of the gl...

  18. The Future of the Global Environment: A Model-based Analysis Supporting UNEP's First Global Environment Outlook

    NARCIS (Netherlands)

    Bakkes JA; Woerden JW van; Alcamo J; Berk MM; Bol P; Born GJ van den; Brink BJE ten; Hettelingh JP; Langeweg F; Niessen LW; Swart RJ; United Nations Environment; MNV

    1997-01-01

    This report documents the scenario analysis in UNEP's first Global Environment Outlook, published at the same time as the scenario analysis. This Outlook provides a pilot assessment of developments in the environment, both global and regional, between now and 2015, with a further projection to

  19. An Analysis of Yip's Global Strategy Model, Using Coca-Cola ...

    African Journals Online (AJOL)

    Analysis of the selected business cases suggest a weak fit between the Yip model of a truly Global strategy ... like Coca-Cola in the beverage industry for effective implementation of a global strategy. ... Keywords: Global Strategy, Leadership.

  20. Omics approaches on fresh-cut lettuce reveal global molecular responses to sodium hypochlorite and peracetic acid treatment.

    Science.gov (United States)

    Daddiego, Loretta; Bianco, Linda; Capodicasa, Cristina; Carbone, Fabrizio; Dalmastri, Claudia; Daroda, Lorenza; Del Fiore, Antonella; De Rossi, Patrizia; Di Carli, Mariasole; Donini, Marcello; Lopez, Loredana; Mengoni, Alessio; Paganin, Patrizia; Perrotta, Gaetano; Bevivino, Annamaria

    2018-01-01

    Lettuce is a leafy vegetable that is extensively commercialized as a ready-to-eat product because of its widespread use in human nutrition as salad. It is well known that washing treatments can severely affect the quality and shelf-life of ready-to-eat vegetables. The study presented here evaluated the effect of two washing procedures on fresh-cut lettuce during storage. An omics approach was applied to reveal global changes at molecular level induced by peracetic acid washing in comparison with sodium hypochlorite treatment. Microbiological analyses were also performed to quantify total bacterial abundance and composition. The study revealed wide metabolic alterations induced by the two sanitizers. In particular, transcriptomic and proteomic analyses pointed out a number of transcripts and proteins differentially accumulated in response to peracetic acid washing, mainly occurring on the first day of storage. In parallel, different microbiota composition and significant reduction in total bacterial load following washing were also observed. The results provide useful information for the fresh-cut industry to select an appropriate washing procedure preserving fresh-like attributes as much as possible during storage of the end product. Molecular evidence indicated peracetic acid to be a valid alternative to sodium hypochlorite as sanitizer solution. © 2017 Society of Chemical Industry. © 2017 Society of Chemical Industry.

  1. A global sensitivity analysis approach for morphogenesis models

    KAUST Repository

    Boas, Sonja E. M.

    2015-11-21

    Background Morphogenesis is a developmental process in which cells organize into shapes and patterns. Complex, non-linear and multi-factorial models with images as output are commonly used to study morphogenesis. It is difficult to understand the relation between the uncertainty in the input and the output of such ‘black-box’ models, giving rise to the need for sensitivity analysis tools. In this paper, we introduce a workflow for a global sensitivity analysis approach to study the impact of single parameters and the interactions between them on the output of morphogenesis models. Results To demonstrate the workflow, we used a published, well-studied model of vascular morphogenesis. The parameters of this cellular Potts model (CPM) represent cell properties and behaviors that drive the mechanisms of angiogenic sprouting. The global sensitivity analysis correctly identified the dominant parameters in the model, consistent with previous studies. Additionally, the analysis provided information on the relative impact of single parameters and of interactions between them. This is very relevant because interactions of parameters impede the experimental verification of the predicted effect of single parameters. The parameter interactions, although of low impact, provided also new insights in the mechanisms of in silico sprouting. Finally, the analysis indicated that the model could be reduced by one parameter. Conclusions We propose global sensitivity analysis as an alternative approach to study the mechanisms of morphogenesis. Comparison of the ranking of the impact of the model parameters to knowledge derived from experimental data and from manipulation experiments can help to falsify models and to find the operand mechanisms in morphogenesis. The workflow is applicable to all ‘black-box’ models, including high-throughput in vitro models in which output measures are affected by a set of experimental perturbations.

  2. A global sensitivity analysis approach for morphogenesis models.

    Science.gov (United States)

    Boas, Sonja E M; Navarro Jimenez, Maria I; Merks, Roeland M H; Blom, Joke G

    2015-11-21

    Morphogenesis is a developmental process in which cells organize into shapes and patterns. Complex, non-linear and multi-factorial models with images as output are commonly used to study morphogenesis. It is difficult to understand the relation between the uncertainty in the input and the output of such 'black-box' models, giving rise to the need for sensitivity analysis tools. In this paper, we introduce a workflow for a global sensitivity analysis approach to study the impact of single parameters and the interactions between them on the output of morphogenesis models. To demonstrate the workflow, we used a published, well-studied model of vascular morphogenesis. The parameters of this cellular Potts model (CPM) represent cell properties and behaviors that drive the mechanisms of angiogenic sprouting. The global sensitivity analysis correctly identified the dominant parameters in the model, consistent with previous studies. Additionally, the analysis provided information on the relative impact of single parameters and of interactions between them. This is very relevant because interactions of parameters impede the experimental verification of the predicted effect of single parameters. The parameter interactions, although of low impact, provided also new insights in the mechanisms of in silico sprouting. Finally, the analysis indicated that the model could be reduced by one parameter. We propose global sensitivity analysis as an alternative approach to study the mechanisms of morphogenesis. Comparison of the ranking of the impact of the model parameters to knowledge derived from experimental data and from manipulation experiments can help to falsify models and to find the operand mechanisms in morphogenesis. The workflow is applicable to all 'black-box' models, including high-throughput in vitro models in which output measures are affected by a set of experimental perturbations.

  3. Three-dimensional Crustal Structure beneath the Tibetan Plateau Revealed by Multi-scale Gravity Analysis

    Science.gov (United States)

    Xu, C.; Luo, Z.; Sun, R.; Li, Q.

    2017-12-01

    The Tibetan Plateau, the largest and highest plateau on Earth, was uplifted, shorten and thicken by the collision and continuous convergence of the Indian and Eurasian plates since 50 million years ago, the Eocene epoch. Fine three-dimensional crustal structure of the Tibetan Plateau is helpful in understanding the tectonic development. At present, the ordinary method used for revealing crustal structure is seismic method, which is inhibited by poor seismic station coverage, especially in the central and western plateau primarily due to the rugged terrain. Fortunately, with the implementation of satellite gravity missions, gravity field models have demonstrated unprecedented global-scale accuracy and spatial resolution, which can subsequently be employed to study the crustal structure of the entire Tibetan Plateau. This study inverts three-dimensional crustal density and Moho topography of the Tibetan Plateau from gravity data using multi-scale gravity analysis. The inverted results are in agreement with those provided by the previous works. Besides, they can reveal rich tectonic development of the Tibetan Plateau: (1) The low-density channel flow can be observed from the inverted crustal density; (2) The Moho depth in the west is deeper than that in the east, and the deepest Moho, which is approximately 77 km, is located beneath the western Qiangtang Block; (3) The Moho fold, the directions of which are in agreement with the results of surface movement velocities estimated from Global Positioning System, exists clearly on the Moho topography.This study is supported by the National Natural Science Foundation of China (Grant No. 41504015), the China Postdoctoral Science Foundation (Grant No. 2015M572146), and the Surveying and Mapping Basic Research Programme of the National Administration of Surveying, Mapping and Geoinformation (Grant No. 15-01-08).

  4. A genetic analysis of segregation distortion revealed by molecular ...

    Indian Academy of Sciences (India)

    Journal of Genetics, Vol. 90, No. ... Segregation analysis was based on 64 molecular markers, including 26 .... FHB of RIL populations was controlled by quantitative trait ... The authors acknowledge financial support by the National Basic.

  5. Global sensitivity analysis in stochastic simulators of uncertain reaction networks.

    Science.gov (United States)

    Navarro Jimenez, M; Le Maître, O P; Knio, O M

    2016-12-28

    Stochastic models of chemical systems are often subjected to uncertainties in kinetic parameters in addition to the inherent random nature of their dynamics. Uncertainty quantification in such systems is generally achieved by means of sensitivity analyses in which one characterizes the variability with the uncertain kinetic parameters of the first statistical moments of model predictions. In this work, we propose an original global sensitivity analysis method where the parametric and inherent variability sources are both treated through Sobol's decomposition of the variance into contributions from arbitrary subset of uncertain parameters and stochastic reaction channels. The conceptual development only assumes that the inherent and parametric sources are independent, and considers the Poisson processes in the random-time-change representation of the state dynamics as the fundamental objects governing the inherent stochasticity. A sampling algorithm is proposed to perform the global sensitivity analysis, and to estimate the partial variances and sensitivity indices characterizing the importance of the various sources of variability and their interactions. The birth-death and Schlögl models are used to illustrate both the implementation of the algorithm and the richness of the proposed analysis method. The output of the proposed sensitivity analysis is also contrasted with a local derivative-based sensitivity analysis method classically used for this type of systems.

  6. Global sensitivity analysis in stochastic simulators of uncertain reaction networks

    KAUST Repository

    Navarro, María

    2016-12-26

    Stochastic models of chemical systems are often subjected to uncertainties in kinetic parameters in addition to the inherent random nature of their dynamics. Uncertainty quantification in such systems is generally achieved by means of sensitivity analyses in which one characterizes the variability with the uncertain kinetic parameters of the first statistical moments of model predictions. In this work, we propose an original global sensitivity analysis method where the parametric and inherent variability sources are both treated through Sobol’s decomposition of the variance into contributions from arbitrary subset of uncertain parameters and stochastic reaction channels. The conceptual development only assumes that the inherent and parametric sources are independent, and considers the Poisson processes in the random-time-change representation of the state dynamics as the fundamental objects governing the inherent stochasticity. A sampling algorithm is proposed to perform the global sensitivity analysis, and to estimate the partial variances and sensitivity indices characterizing the importance of the various sources of variability and their interactions. The birth-death and Schlögl models are used to illustrate both the implementation of the algorithm and the richness of the proposed analysis method. The output of the proposed sensitivity analysis is also contrasted with a local derivative-based sensitivity analysis method classically used for this type of systems.

  7. Phylogenetic analysis reveals multiple introductions of Cynodon species in Australia.

    Science.gov (United States)

    Jewell, M; Frère, C H; Harris-Shultz, K; Anderson, W F; Godwin, I D; Lambrides, C J

    2012-11-01

    The distinction between native and introduced flora within isolated land masses presents unique challenges. The geological and colonisation history of Australia, the world's largest island, makes it a valuable system for studying species endemism, introduction, and phylogeny. Using this strategy we investigated Australian cosmopolitan grasses belonging to the genus Cynodon. While it is believed that seven species of Cynodon are present in Australia, no genetic analyses have investigated the origin, diversity and phylogenetic history of Cynodon within Australia. To address this gap, 147 samples (92 from across Australia and 55 representing global distribution) were sequenced for a total of 3336bp of chloroplast DNA spanning six genes. Data showed the presence of at least six putatively introduced Cynodon species (C. transvaalensis, C. incompletus, C. hirsutus, C. radiatus, C. plectostachyus and C. dactylon) in Australia and suggested multiple recent introductions. C. plectostachyus, a species often confused with C. nlemfuensis, was not previously considered to be present in Australia. Most significantly, we identified two common haplotypes that formed a monophyletic clade diverging from previously identified Cynodon species. We hypothesise that these two haplotypes may represent a previously undescribed species of Cynodon. We provide further evidence that two Australian native species, Brachyachne tenella and B. convergens belong in the genus Cynodon and, therefore, argue for the taxonomic revision of the genus Cynodon. Copyright © 2012 Elsevier Inc. All rights reserved.

  8. Mixed kernel function support vector regression for global sensitivity analysis

    Science.gov (United States)

    Cheng, Kai; Lu, Zhenzhou; Wei, Yuhao; Shi, Yan; Zhou, Yicheng

    2017-11-01

    Global sensitivity analysis (GSA) plays an important role in exploring the respective effects of input variables on an assigned output response. Amongst the wide sensitivity analyses in literature, the Sobol indices have attracted much attention since they can provide accurate information for most models. In this paper, a mixed kernel function (MKF) based support vector regression (SVR) model is employed to evaluate the Sobol indices at low computational cost. By the proposed derivation, the estimation of the Sobol indices can be obtained by post-processing the coefficients of the SVR meta-model. The MKF is constituted by the orthogonal polynomials kernel function and Gaussian radial basis kernel function, thus the MKF possesses both the global characteristic advantage of the polynomials kernel function and the local characteristic advantage of the Gaussian radial basis kernel function. The proposed approach is suitable for high-dimensional and non-linear problems. Performance of the proposed approach is validated by various analytical functions and compared with the popular polynomial chaos expansion (PCE). Results demonstrate that the proposed approach is an efficient method for global sensitivity analysis.

  9. Global health initiative investments and health systems strengthening: a content analysis of global fund investments.

    Science.gov (United States)

    Warren, Ashley E; Wyss, Kaspar; Shakarishvili, George; Atun, Rifat; de Savigny, Don

    2013-07-26

    Millions of dollars are invested annually under the umbrella of national health systems strengthening. Global health initiatives provide funding for low- and middle-income countries through disease-oriented programmes while maintaining that the interventions simultaneously strengthen systems. However, it is as yet unclear which, and to what extent, system-level interventions are being funded by these initiatives, nor is it clear how much funding they allocate to disease-specific activities - through conventional 'vertical-programming' approach. Such funding can be channelled to one or more of the health system building blocks while targeting disease(s) or explicitly to system-wide activities. We operationalized the World Health Organization health system framework of the six building blocks to conduct a detailed assessment of Global Fund health system investments. Our application of this framework framework provides a comprehensive quantification of system-level interventions. We applied this systematically to a random subset of 52 of the 139 grants funded in Round 8 of the Global Fund to Fight AIDS, Tuberculosis and Malaria (totalling approximately US$1 billion). According to the analysis, 37% (US$ 362 million) of the Global Fund Round 8 funding was allocated to health systems strengthening. Of that, 38% (US$ 139 million) was for generic system-level interventions, rather than disease-specific system support. Around 82% of health systems strengthening funding (US$ 296 million) was allocated to service delivery, human resources, and medicines & technology, and within each of these to two to three interventions. Governance, financing, and information building blocks received relatively low funding. This study shows that a substantial portion of Global Fund's Round 8 funds was devoted to health systems strengthening. Dramatic skewing among the health system building blocks suggests opportunities for more balanced investments with regard to governance, financing, and

  10. Methodology for global nonlinear analysis of nuclear systems

    International Nuclear Information System (INIS)

    Cacuci, D.G.; Cacuci, G.L.

    1987-01-01

    This paper outlines a general method for globally computing the crucial features of nonlinear problems: bifurcations, limit points, saddle points, extrema (maxima and minima); our method also yields the local sensitivities (i.e., first order derivatives) of the system's state variables (e.g., fluxes, power, temperatures, flows) at any point in the system's phase space. We also present an application of this method to the nonlinear BWR model discussed in Refs. 8 and 11. The most significant novel feature of our method is the recasting of a general mathematical problem comprising three aspects: (1) nonlinear constrained optimization, (2) sensitivity analysis, into a fixed point problem of the form F[u(s), λ(s)] = 0 whose global zeros and singular points are related to the special features (i.e., extrema, bifurcations, etc.) of the original problem

  11. Global analysis of a renewable micro hydro power generation plant

    Science.gov (United States)

    Rahman, Md. Shad; Nabil, Imtiaz Muhammed; Alam, M. Mahbubul

    2017-12-01

    Hydroelectric power or Hydropower means the power generated by the help of flowing water with force. It is one the best source of renewable energy in the world. Water evaporates from the earth's surface, forms clouds, precipitates back to earth, and flows toward the ocean. Hydropower is considered a renewable energy resource because it uses the earth's water cycle to generate electricity. As far as Global is concerned, only a small fraction of electricity is generated by hydro-power. The aim of our analysis is to demonstrate and observe the hydropower of the Globe in micro-scale by our experimental setup which is completely new in concept. This paper consists of all the Global and National Scenario of Hydropower. And how we can more emphasize the generation of Hydroelectric power worldwide.

  12. Network analysis reveals multiscale controls on streamwater chemistry

    Science.gov (United States)

    Kevin J. McGuire; Christian E. Torgersen; Gene E. Likens; Donald C. Buso; Winsor H. Lowe; Scott W. Bailey

    2014-01-01

    By coupling synoptic data from a basin-wide assessment of streamwater chemistry with network-based geostatistical analysis, we show that spatial processes differentially affect biogeochemical condition and pattern across a headwater stream network. We analyzed a high-resolution dataset consisting of 664 water samples collected every 100 m throughout 32 tributaries in...

  13. Fluorescent Protein-Based Ca2+ Sensor Reveals Global, Divalent Cation-Dependent Conformational Changes in Cardiac Troponin C.

    Directory of Open Access Journals (Sweden)

    Myriam A Badr

    Full Text Available Cardiac troponin C (cTnC is a key effector in cardiac muscle excitation-contraction coupling as the Ca2+ sensing subunit responsible for controlling contraction. In this study, we generated several FRET sensors for divalent cations based on cTnC flanked by a donor fluorescent protein (CFP and an acceptor fluorescent protein (YFP. The sensors report Ca2+ and Mg2+ binding, and relay global structural information about the structural relationship between cTnC's N- and C-domains. The sensors were first characterized using end point titrations to decipher the response to Ca2+ binding in the presence or absence of Mg2+. The sensor that exhibited the largest responses in end point titrations, CTV-TnC, (Cerulean, TnC, and Venus was characterized more extensively. Most of the divalent cation-dependent FRET signal originates from the high affinity C-terminal EF hands. CTV-TnC reconstitutes into skinned fiber preparations indicating proper assembly of troponin complex, with only ~0.2 pCa unit rightward shift of Ca2+-sensitive force development compared to WT-cTnC. Affinity of CTV-TnC for divalent cations is in agreement with known values for WT-cTnC. Analytical ultracentrifugation indicates that CTV-TnC undergoes compaction as divalent cations bind. C-terminal sites induce ion-specific (Ca2+ versus Mg2+ conformational changes in cTnC. Our data also provide support for the presence of additional, non-EF-hand sites on cTnC for Mg2+ binding. In conclusion, we successfully generated a novel FRET-Ca2+ sensor based on full length cTnC with a variety of cellular applications. Our sensor reveals global structural information about cTnC upon divalent cation binding.

  14. Global tractography with embedded anatomical priors for quantitative connectivity analysis

    Directory of Open Access Journals (Sweden)

    Alia eLemkaddem

    2014-11-01

    Full Text Available The main assumption of fiber-tracking algorithms is that fiber trajectories are represented by paths of highest diffusion, which is usually accomplished by following the principal diffusion directions estimated in every voxel from the measured diffusion MRI data. The state-of-the-art approaches, known as global tractography, reconstruct all the fiber tracts of the whole brain simultaneously by solving a global energy minimization problem. The tractograms obtained with these algorithms outperform any previous technique but, unfortunately, the price to pay is an increased computational cost which is not suitable in many practical settings, both in terms of time and memory requirements. Furthermore, existing global tractography algorithms suffer from an important shortcoming that is crucial in the context of brain connectivity analyses. As no anatomical priors are used during in the reconstruction process, the recovered fiber tracts are not guaranteed to connect cortical regions and, as a matter of fact, most of them stop prematurely in the white matter. This does not only unnecessarily slow down the estimation procedure and potentially biases any subsequent analysis but also, most importantly, prevents the de facto quantification of brain connectivity. In this work, we propose a novel approach for global tractography that is specifically designed for connectivity analysis applications by explicitly enforcing anatomical priors of the tracts in the optimization and considering the effective contribution of each of them, i.e. volume, to the acquired diffusion MRI image. We evaluated our approach on both a realistic diffusion MRI phantom and in-vivo data, and also compared its performance to existing tractography aloprithms.

  15. Correlation analyses revealed global microRNA-mRNA expression associations in human peripheral blood mononuclear cells.

    Science.gov (United States)

    Wang, Lan; Zhu, Jiang; Deng, Fei-Yan; Wu, Long-Fei; Mo, Xing-Bo; Zhu, Xiao-Wei; Xia, Wei; Xie, Fang-Fei; He, Pei; Bing, Peng-Fei; Qiu, Ying-Hua; Lin, Xiang; Lu, Xin; Zhang, Lei; Yi, Neng-Jun; Zhang, Yong-Hong; Lei, Shu-Feng

    2018-02-01

    MicroRNAs (miRNAs) can regulate gene expression through binding to complementary sites in the 3'-untranslated regions of target mRNAs, which will lead to existence of correlation in expression between miRNA and mRNA. However, the miRNA-mRNA correlation patterns are complex and remain largely unclear yet. To establish the global correlation patterns in human peripheral blood mononuclear cells (PBMCs), multiple miRNA-mRNA correlation analyses and expression quantitative trait locus (eQTL) analysis were conducted in this study. We predicted and achieved 861 miRNA-mRNA pairs (65 miRNAs, 412 mRNAs) using multiple bioinformatics programs, and found global negative miRNA-mRNA correlations in PBMC from all 46 study subjects. Among the 861 pairs of correlations, 19.5% were significant (P correlation network was complex and highlighted key miRNAs/genes in PBMC. Some miRNAs, such as hsa-miR-29a, hsa-miR-148a, regulate a cluster of target genes. Some genes, e.g., TNRC6A, are regulated by multiple miRNAs. The identified genes tend to be enriched in molecular functions of DNA and RNA binding, and biological processes such as protein transport, regulation of translation and chromatin modification. The results provided a global view of the miRNA-mRNA expression correlation profile in human PBMCs, which would facilitate in-depth investigation of biological functions of key miRNAs/mRNAs and better understanding of the pathogenesis underlying PBMC-related diseases.

  16. The Future of the Global Environment: A Model-based Analysis Supporting UNEP's First Global Environment Outlook

    OpenAIRE

    Bakkes JA; Woerden JW van; Alcamo J; Berk MM; Bol P; Born GJ van den; Brink BJE ten; Hettelingh JP; Langeweg F; Niessen LW; Swart RJ; United Nations Environment Programme (UNEP), Nairobi, Kenia; MNV

    1997-01-01

    This report documents the scenario analysis in UNEP's first Global Environment Outlook, published at the same time as the scenario analysis. This Outlook provides a pilot assessment of developments in the environment, both global and regional, between now and 2015, with a further projection to 2050. The study was carried out in support of the Agenda 21 interim evaluation, five years after 'Rio' and ten years after 'Brundtland'. The scenario analysis is based on only one scenario, Conventional...

  17. Global Sensitivity Analysis of Environmental Models: Convergence, Robustness and Validation

    Science.gov (United States)

    Sarrazin, Fanny; Pianosi, Francesca; Khorashadi Zadeh, Farkhondeh; Van Griensven, Ann; Wagener, Thorsten

    2015-04-01

    Global Sensitivity Analysis aims to characterize the impact that variations in model input factors (e.g. the parameters) have on the model output (e.g. simulated streamflow). In sampling-based Global Sensitivity Analysis, the sample size has to be chosen carefully in order to obtain reliable sensitivity estimates while spending computational resources efficiently. Furthermore, insensitive parameters are typically identified through the definition of a screening threshold: the theoretical value of their sensitivity index is zero but in a sampling-base framework they regularly take non-zero values. There is little guidance available for these two steps in environmental modelling though. The objective of the present study is to support modellers in making appropriate choices, regarding both sample size and screening threshold, so that a robust sensitivity analysis can be implemented. We performed sensitivity analysis for the parameters of three hydrological models with increasing level of complexity (Hymod, HBV and SWAT), and tested three widely used sensitivity analysis methods (Elementary Effect Test or method of Morris, Regional Sensitivity Analysis, and Variance-Based Sensitivity Analysis). We defined criteria based on a bootstrap approach to assess three different types of convergence: the convergence of the value of the sensitivity indices, of the ranking (the ordering among the parameters) and of the screening (the identification of the insensitive parameters). We investigated the screening threshold through the definition of a validation procedure. The results showed that full convergence of the value of the sensitivity indices is not necessarily needed to rank or to screen the model input factors. Furthermore, typical values of the sample sizes that are reported in the literature can be well below the sample sizes that actually ensure convergence of ranking and screening.

  18. Sensitization trajectories in childhood revealed by using a cluster analysis

    DEFF Research Database (Denmark)

    Schoos, Ann-Marie M.; Chawes, Bo L.; Melen, Erik

    2017-01-01

    Prospective Studies on Asthma in Childhood 2000 (COPSAC2000) birth cohort with specific IgE against 13 common food and inhalant allergens at the ages of ½, 1½, 4, and 6 years. An unsupervised cluster analysis for 3-dimensional data (nonnegative sparse parallel factor analysis) was used to extract latent......BACKGROUND: Assessment of sensitization at a single time point during childhood provides limited clinical information. We hypothesized that sensitization develops as specific patterns with respect to age at debut, development over time, and involved allergens and that such patterns might be more...... biologically and clinically relevant. OBJECTIVE: We sought to explore latent patterns of sensitization during the first 6 years of life and investigate whether such patterns associate with the development of asthma, rhinitis, and eczema. METHODS: We investigated 398 children from the at-risk Copenhagen...

  19. Fractal analysis reveals reduced complexity of retinal vessels in CADASIL.

    Directory of Open Access Journals (Sweden)

    Michele Cavallari

    2011-04-01

    Full Text Available The Cerebral Autosomal Dominant Arteriopathy with Subcortical Infarcts and Leukoencephalopathy (CADASIL affects mainly small cerebral arteries and leads to disability and dementia. The relationship between clinical expression of the disease and progression of the microvessel pathology is, however, uncertain as we lack tools for imaging brain vessels in vivo. Ophthalmoscopy is regarded as a window into the cerebral microcirculation. In this study we carried out an ophthalmoscopic examination in subjects with CADASIL. Specifically, we performed fractal analysis of digital retinal photographs. Data are expressed as mean fractal dimension (mean-D, a parameter that reflects complexity of the retinal vessel branching. Ten subjects with genetically confirmed diagnosis of CADASIL and 10 sex and age-matched control subjects were enrolled. Fractal analysis of retinal digital images was performed by means of a computer-based program, and the data expressed as mean-D. Brain MRI lesion volume in FLAIR and T1-weighted images was assessed using MIPAV software. Paired t-test was used to disclose differences in mean-D between CADASIL and control groups. Spearman rank analysis was performed to evaluate potential associations between mean-D values and both disease duration and disease severity, the latter expressed as brain MRI lesion volumes, in the subjects with CADASIL. The results showed that mean-D value of patients (1.42±0.05; mean±SD was lower than control (1.50±0.04; p = 0.002. Mean-D did not correlate with disease duration nor with MRI lesion volumes of the subjects with CADASIL. The findings suggest that fractal analysis is a sensitive tool to assess changes of retinal vessel branching, likely reflecting early brain microvessel alterations, in CADASIL patients.

  20. Penicillium simile sp. nov. revealed by morphological and phylogenetic analysis.

    Science.gov (United States)

    Davolos, Domenico; Pietrangeli, Biancamaria; Persiani, Anna Maria; Maggi, Oriana

    2012-02-01

    The morphology of three phenetically identical Penicillium isolates, collected from the bioaerosol in a restoration laboratory in Italy, displayed macro- and microscopic characteristics that were similar though not completely ascribable to Penicillium raistrickii. For this reason, a phylogenetic approach based on DNA sequencing analysis was performed to establish both the taxonomic status and the evolutionary relationships of these three peculiar isolates in relation to previously described species of the genus Penicillium. We used four nuclear loci (both rRNA and protein coding genes) that have previously proved useful for the molecular investigation of taxa belonging to the genus Penicillium at various evolutionary levels. The internal transcribed spacer region (ITS1-5.8S-ITS2), domains D1 and D2 of the 28S rDNA, a region of the tubulin beta chain gene (benA) and part of the calmodulin gene (cmd) were amplified by PCR and sequenced. Analysis of the rRNA genes and of the benA and cmd sequence data indicates the presence of three isogenic isolates belonging to a genetically distinct species of the genus Penicillium, here described and named Penicillium simile sp. nov. (ATCC MYA-4591(T)  = CBS 129191(T)). This novel species is phylogenetically different from P. raistrickii and other related species of the genus Penicillium (e.g. Penicillium scabrosum), from which it can be distinguished on the basis of morphological trait analysis.

  1. Economic impact analysis for global warming: Sensitivity analysis for cost and benefit estimates

    International Nuclear Information System (INIS)

    Ierland, E.C. van; Derksen, L.

    1994-01-01

    Proper policies for the prevention or mitigation of the effects of global warming require profound analysis of the costs and benefits of alternative policy strategies. Given the uncertainty about the scientific aspects of the process of global warming, in this paper a sensitivity analysis for the impact of various estimates of costs and benefits of greenhouse gas reduction strategies is carried out to analyze the potential social and economic impacts of climate change

  2. Subfield profitability analysis reveals an economic case for cropland diversification

    Science.gov (United States)

    Brandes, E.; McNunn, G. S.; Schulte, L. A.; Bonner, I. J.; Muth, D. J.; Babcock, B. A.; Sharma, B.; Heaton, E. A.

    2016-01-01

    Public agencies and private enterprises increasingly desire to achieve ecosystem service outcomes in agricultural systems, but are limited by perceived conflicts between economic and ecosystem service goals and a lack of tools enabling effective operational management. Here we use Iowa—an agriculturally homogeneous state representative of the Maize Belt—to demonstrate an economic rationale for cropland diversification at the subfield scale. We used a novel computational framework that integrates disparate but publicly available data to map ˜3.3 million unique potential management polygons (9.3 Mha) and reveal subfield opportunities to increase overall field profitability. We analyzed subfield profitability for maize/soybean fields during 2010-2013—four of the most profitable years in recent history—and projected results for 2015. While cropland operating at a loss of US 250 ha-1 or more was negligible between 2010 and 2013 at 18 000-190 000 ha (profitable areas, incorporating conservation management that breaks even (e.g., planting low-input perennials), into low-yielding portions of fields could increase overall cropland profitability by 80%. This approach is applicable to the broader region and differs substantially from the status quo of ‘top-down’ land management for conservation by harnessing private interest to align profitability with the production of ecosystem services.

  3. Proteomics Analysis Reveals Previously Uncharacterized Virulence Factors in Vibrio proteolyticus

    Directory of Open Access Journals (Sweden)

    Ann Ray

    2016-07-01

    Full Text Available Members of the genus Vibrio include many pathogens of humans and marine animals that share genetic information via horizontal gene transfer. Hence, the Vibrio pan-genome carries the potential to establish new pathogenic strains by sharing virulence determinants, many of which have yet to be characterized. Here, we investigated the virulence properties of Vibrio proteolyticus, a Gram-negative marine bacterium previously identified as part of the Vibrio consortium isolated from diseased corals. We found that V. proteolyticus causes actin cytoskeleton rearrangements followed by cell lysis in HeLa cells in a contact-independent manner. In search of the responsible virulence factor involved, we determined the V. proteolyticus secretome. This proteomics approach revealed various putative virulence factors, including active type VI secretion systems and effectors with virulence toxin domains; however, these type VI secretion systems were not responsible for the observed cytotoxic effects. Further examination of the V. proteolyticus secretome led us to hypothesize and subsequently demonstrate that a secreted hemolysin, belonging to a previously uncharacterized clan of the leukocidin superfamily, was the toxin responsible for the V. proteolyticus-mediated cytotoxicity in both HeLa cells and macrophages. Clearly, there remains an armory of yet-to-be-discovered virulence factors in the Vibrio pan-genome that will undoubtedly provide a wealth of knowledge on how a pathogen can manipulate host cells.

  4. Comparative Genomic Analysis Reveals Ecological Differentiation in the Genus Carnobacterium.

    Science.gov (United States)

    Iskandar, Christelle F; Borges, Frédéric; Taminiau, Bernard; Daube, Georges; Zagorec, Monique; Remenant, Benoît; Leisner, Jørgen J; Hansen, Martin A; Sørensen, Søren J; Mangavel, Cécile; Cailliez-Grimal, Catherine; Revol-Junelles, Anne-Marie

    2017-01-01

    Lactic acid bacteria (LAB) differ in their ability to colonize food and animal-associated habitats: while some species are specialized and colonize a limited number of habitats, other are generalist and are able to colonize multiple animal-linked habitats. In the current study, Carnobacterium was used as a model genus to elucidate the genetic basis of these colonization differences. Analyses of 16S rRNA gene meta-barcoding data showed that C. maltaromaticum followed by C. divergens are the most prevalent species in foods derived from animals (meat, fish, dairy products), and in the gut. According to phylogenetic analyses, these two animal-adapted species belong to one of two deeply branched lineages. The second lineage contains species isolated from habitats where contact with animal is rare. Genome analyses revealed that members of the animal-adapted lineage harbor a larger secretome than members of the other lineage. The predicted cell-surface proteome is highly diversified in C. maltaromaticum and C. divergens with genes involved in adaptation to the animal milieu such as those encoding biopolymer hydrolytic enzymes, a heme uptake system, and biopolymer-binding adhesins. These species also exhibit genes for gut adaptation and respiration. In contrast, Carnobacterium species belonging to the second lineage encode a poorly diversified cell-surface proteome, lack genes for gut adaptation and are unable to respire. These results shed light on the important genomics traits required for adaptation to animal-linked habitats in generalist Carnobacterium .

  5. Proteomic Analysis of Hylocereus polyrhizus Reveals Metabolic Pathway Changes

    Directory of Open Access Journals (Sweden)

    Qingzhu Hua

    2016-09-01

    Full Text Available Red dragon fruit or red pitaya (Hylocereus polyrhizus is the only edible fruit that contains betalains. The color of betalains ranges from red and violet to yellow in plants. Betalains may also serve as an important component of health-promoting and disease-preventing functional food. Currently, the biosynthetic and regulatory pathways for betalain production remain to be fully deciphered. In this study, isobaric tags for relative and absolute quantitation (iTRAQ-based proteomic analyses were used to reveal the molecular mechanism of betalain biosynthesis in H. polyrhizus fruits at white and red pulp stages, respectively. A total of 1946 proteins were identified as the differentially expressed between the two samples, and 936 of them were significantly highly expressed at the red pulp stage of H. polyrhizus. RNA-seq and iTRAQ analyses showed that some transcripts and proteins were positively correlated; they belonged to “phenylpropanoid biosynthesis”, “tyrosine metabolism”, “flavonoid biosynthesis”, “ascorbate and aldarate metabolism”, “betalains biosynthesis” and “anthocyanin biosynthesis”. In betalains biosynthesis pathway, several proteins/enzymes such as polyphenol oxidase, CYP76AD3 and 4,5-dihydroxy-phenylalanine (DOPA dioxygenase extradiol-like protein were identified. The present study provides a new insight into the molecular mechanism of the betalain biosynthesis at the posttranscriptional level.

  6. Drivers of wetland conversion: a global meta-analysis.

    Science.gov (United States)

    van Asselen, Sanneke; Verburg, Peter H; Vermaat, Jan E; Janse, Jan H

    2013-01-01

    Meta-analysis of case studies has become an important tool for synthesizing case study findings in land change. Meta-analyses of deforestation, urbanization, desertification and change in shifting cultivation systems have been published. This present study adds to this literature, with an analysis of the proximate causes and underlying forces of wetland conversion at a global scale using two complementary approaches of systematic review. Firstly, a meta-analysis of 105 case-study papers describing wetland conversion was performed, showing that different combinations of multiple-factor proximate causes, and underlying forces, drive wetland conversion. Agricultural development has been the main proximate cause of wetland conversion, and economic growth and population density are the most frequently identified underlying forces. Secondly, to add a more quantitative component to the study, a logistic meta-regression analysis was performed to estimate the likelihood of wetland conversion worldwide, using globally-consistent biophysical and socioeconomic location factor maps. Significant factors explaining wetland conversion, in order of importance, are market influence, total wetland area (lower conversion probability), mean annual temperature and cropland or built-up area. The regression analyses results support the outcomes of the meta-analysis of the processes of conversion mentioned in the individual case studies. In other meta-analyses of land change, similar factors (e.g., agricultural development, population growth, market/economic factors) are also identified as important causes of various types of land change (e.g., deforestation, desertification). Meta-analysis helps to identify commonalities across the various local case studies and identify which variables may lead to individual cases to behave differently. The meta-regression provides maps indicating the likelihood of wetland conversion worldwide based on the location factors that have determined historic

  7. Gas Hydrate-Sediment Morphologies Revealed by Pressure Core Analysis

    Science.gov (United States)

    Holland, M.; Schultheiss, P.; Roberts, J.; Druce, M.

    2006-12-01

    Analysis of HYACINTH pressure cores collected on IODP Expedition 311 and NGHP Expedition 1 showed gas hydrate layers, lenses, and veins contained in fine-grained sediments as well as gas hydrate contained in coarse-grained layers. Pressure cores were recovered from sediments on the Cascadia Margin off the North American West Coast and in the Krishna-Godavari Basin in the Western Bay of Bengal in water depths of 800- 1400 meters. Recovered cores were transferred to laboratory chambers without loss of pressure and nondestructive measurements were made at in situ pressures and controlled temperatures. Gamma density, P-wave velocity, and X-ray images showed evidence of grain-displacing and pore-filling gas hydrate in the cores. Data highlights include X-ray images of fine-grained sediment cores showing wispy subvertical veins of gas hydrate and P-wave velocity excursions corresponding to grain-displacing layers and pore-filling layers of gas hydrate. Most cores were subjected to controlled depressurization experiments, where expelled gas was collected, analyzed for composition, and used to calculate gas hydrate saturation within the core. Selected cores were stored under pressure for postcruise analysis and subsampling.

  8. Comparative proteomic analysis reveals heart toxicity induced by chronic arsenic exposure in rats

    International Nuclear Information System (INIS)

    Huang, Qingyu; Xi, Guochen; Alamdar, Ambreen; Zhang, Jie; Shen, Heqing

    2017-01-01

    Arsenic is a widespread metalloid in the environment, which poses a broad spectrum of adverse effects on human health. However, a global view of arsenic-induced heart toxicity is still lacking, and the underlying molecular mechanisms remain unclear. By performing a comparative quantitative proteomic analysis, the present study aims to investigate the alterations of proteome profile in rat heart after long-term exposure to arsenic. As a result, we found that the abundance of 81 proteins were significantly altered by arsenic treatment (35 up-regulated and 46 down-regulated). Among these, 33 proteins were specifically associated with cardiovascular system development and function, including heart development, heart morphology, cardiac contraction and dilation, and other cardiovascular functions. It is further proposed that the aberrant regulation of 14 proteins induced by arsenic would disturb cardiac contraction and relaxation, impair heart morphogenesis and development, and induce thrombosis in rats, which is mediated by the Akt/p38 MAPK signaling pathway. Overall, these findings will augment our knowledge of the involved mechanisms and develop useful biomarkers for cardiotoxicity induced by environmental arsenic exposure. - Highlights: • Arsenic exposure has been associated with a number of adverse health effects. • The molecular mechanisms involved in arsenic-induced cardiotoxicity remain unclear. • Differential proteins were identified in arsenic-exposed rat heart by proteomics. • Arsenic induces heart toxicity through the Akt/p38 MAPK signaling pathway. - Label-free quantitative proteomic analysis of rat heart reveals putative mechanisms and biomarkers for arsenic-induced cardiotoxicity.

  9. The identification of model effective dimensions using global sensitivity analysis

    International Nuclear Information System (INIS)

    Kucherenko, Sergei; Feil, Balazs; Shah, Nilay; Mauntz, Wolfgang

    2011-01-01

    It is shown that the effective dimensions can be estimated at reasonable computational costs using variance based global sensitivity analysis. Namely, the effective dimension in the truncation sense can be found by using the Sobol' sensitivity indices for subsets of variables. The effective dimension in the superposition sense can be estimated by using the first order effects and the total Sobol' sensitivity indices. The classification of some important classes of integrable functions based on their effective dimension is proposed. It is shown that it can be used for the prediction of the QMC efficiency. Results of numerical tests verify the prediction of the developed techniques.

  10. The identification of model effective dimensions using global sensitivity analysis

    Energy Technology Data Exchange (ETDEWEB)

    Kucherenko, Sergei, E-mail: s.kucherenko@ic.ac.u [CPSE, Imperial College London, South Kensington Campus, London SW7 2AZ (United Kingdom); Feil, Balazs [Department of Process Engineering, University of Pannonia, Veszprem (Hungary); Shah, Nilay [CPSE, Imperial College London, South Kensington Campus, London SW7 2AZ (United Kingdom); Mauntz, Wolfgang [Lehrstuhl fuer Anlagensteuerungstechnik, Fachbereich Chemietechnik, Universitaet Dortmund (Germany)

    2011-04-15

    It is shown that the effective dimensions can be estimated at reasonable computational costs using variance based global sensitivity analysis. Namely, the effective dimension in the truncation sense can be found by using the Sobol' sensitivity indices for subsets of variables. The effective dimension in the superposition sense can be estimated by using the first order effects and the total Sobol' sensitivity indices. The classification of some important classes of integrable functions based on their effective dimension is proposed. It is shown that it can be used for the prediction of the QMC efficiency. Results of numerical tests verify the prediction of the developed techniques.

  11. Combinatorial-topological framework for the analysis of global dynamics

    Science.gov (United States)

    Bush, Justin; Gameiro, Marcio; Harker, Shaun; Kokubu, Hiroshi; Mischaikow, Konstantin; Obayashi, Ippei; Pilarczyk, Paweł

    2012-12-01

    We discuss an algorithmic framework based on efficient graph algorithms and algebraic-topological computational tools. The framework is aimed at automatic computation of a database of global dynamics of a given m-parameter semidynamical system with discrete time on a bounded subset of the n-dimensional phase space. We introduce the mathematical background, which is based upon Conley's topological approach to dynamics, describe the algorithms for the analysis of the dynamics using rectangular grids both in phase space and parameter space, and show two sample applications.

  12. Combinatorial-topological framework for the analysis of global dynamics.

    Science.gov (United States)

    Bush, Justin; Gameiro, Marcio; Harker, Shaun; Kokubu, Hiroshi; Mischaikow, Konstantin; Obayashi, Ippei; Pilarczyk, Paweł

    2012-12-01

    We discuss an algorithmic framework based on efficient graph algorithms and algebraic-topological computational tools. The framework is aimed at automatic computation of a database of global dynamics of a given m-parameter semidynamical system with discrete time on a bounded subset of the n-dimensional phase space. We introduce the mathematical background, which is based upon Conley's topological approach to dynamics, describe the algorithms for the analysis of the dynamics using rectangular grids both in phase space and parameter space, and show two sample applications.

  13. An Analysis of Historical Global Warming and Social Engagement

    OpenAIRE

    Train, Joseph; Roizenman, David; Damiani, Seth; Rochwerg, Ronny

    2018-01-01

    The goal of this paper is to determine whether there is a correlation between awareness of global warming, and where global warming occurs. This theory is carried out by analyzing maps containing various forms of data that have to do with global warming, such as precipitation and surface temperature, and comparing it with a map of engagement from tweets which mention global warming. This paper found that there is no solid correlation between mentioning global warming in tweets and global warm...

  14. A meta-analysis of global urban land expansion.

    Science.gov (United States)

    Seto, Karen C; Fragkias, Michail; Güneralp, Burak; Reilly, Michael K

    2011-01-01

    The conversion of Earth's land surface to urban uses is one of the most irreversible human impacts on the global biosphere. It drives the loss of farmland, affects local climate, fragments habitats, and threatens biodiversity. Here we present a meta-analysis of 326 studies that have used remotely sensed images to map urban land conversion. We report a worldwide observed increase in urban land area of 58,000 km(2) from 1970 to 2000. India, China, and Africa have experienced the highest rates of urban land expansion, and the largest change in total urban extent has occurred in North America. Across all regions and for all three decades, urban land expansion rates are higher than or equal to urban population growth rates, suggesting that urban growth is becoming more expansive than compact. Annual growth in GDP per capita drives approximately half of the observed urban land expansion in China but only moderately affects urban expansion in India and Africa, where urban land expansion is driven more by urban population growth. In high income countries, rates of urban land expansion are slower and increasingly related to GDP growth. However, in North America, population growth contributes more to urban expansion than it does in Europe. Much of the observed variation in urban expansion was not captured by either population, GDP, or other variables in the model. This suggests that contemporary urban expansion is related to a variety of factors difficult to observe comprehensively at the global level, including international capital flows, the informal economy, land use policy, and generalized transport costs. Using the results from the global model, we develop forecasts for new urban land cover using SRES Scenarios. Our results show that by 2030, global urban land cover will increase between 430,000 km(2) and 12,568,000 km(2), with an estimate of 1,527,000 km(2) more likely.

  15. Ultra-deep sequencing reveals high prevalence and broad structural diversity of hepatitis B surface antigen mutations in a global population.

    Science.gov (United States)

    Gencay, Mikael; Hübner, Kirsten; Gohl, Peter; Seffner, Anja; Weizenegger, Michael; Neofytos, Dionysios; Batrla, Richard; Woeste, Andreas; Kim, Hyon-Suk; Westergaard, Gaston; Reinsch, Christine; Brill, Eva; Thu Thuy, Pham Thi; Hoang, Bui Huu; Sonderup, Mark; Spearman, C Wendy; Pabinger, Stephan; Gautier, Jérémie; Brancaccio, Giuseppina; Fasano, Massimo; Santantonio, Teresa; Gaeta, Giovanni B; Nauck, Markus; Kaminski, Wolfgang E

    2017-01-01

    The diversity of the hepatitis B surface antigen (HBsAg) has a significant impact on the performance of diagnostic screening tests and the clinical outcome of hepatitis B infection. Neutralizing or diagnostic antibodies against the HBsAg are directed towards its highly conserved major hydrophilic region (MHR), in particular towards its "a" determinant subdomain. Here, we explored, on a global scale, the genetic diversity of the HBsAg MHR in a large, multi-ethnic cohort of randomly selected subjects with HBV infection from four continents. A total of 1553 HBsAg positive blood samples of subjects originating from 20 different countries across Africa, America, Asia and central Europe were characterized for amino acid variation in the MHR. Using highly sensitive ultra-deep sequencing, we found 72.8% of the successfully sequenced subjects (n = 1391) demonstrated amino acid sequence variation in the HBsAg MHR. This indicates that the global variation frequency in the HBsAg MHR is threefold higher than previously reported. The majority of the amino acid mutations were found in the HBV genotypes B (28.9%) and C (25.4%). Collectively, we identified 345 distinct amino acid mutations in the MHR. Among these, we report 62 previously unknown mutations, which extends the worldwide pool of currently known HBsAg MHR mutations by 22%. Importantly, topological analysis identified the "a" determinant upstream flanking region as the structurally most diverse subdomain of the HBsAg MHR. The highest prevalence of "a" determinant region mutations was observed in subjects from Asia, followed by the African, American and European cohorts, respectively. Finally, we found that more than half (59.3%) of all HBV subjects investigated carried multiple MHR mutations. Together, this worldwide ultra-deep sequencing based genotyping study reveals that the global prevalence and structural complexity of variation in the hepatitis B surface antigen have, to date, been significantly underappreciated.

  16. A Global Sensitivity Analysis Methodology for Multi-physics Applications

    Energy Technology Data Exchange (ETDEWEB)

    Tong, C H; Graziani, F R

    2007-02-02

    Experiments are conducted to draw inferences about an entire ensemble based on a selected number of observations. This applies to both physical experiments as well as computer experiments, the latter of which are performed by running the simulation models at different input configurations and analyzing the output responses. Computer experiments are instrumental in enabling model analyses such as uncertainty quantification and sensitivity analysis. This report focuses on a global sensitivity analysis methodology that relies on a divide-and-conquer strategy and uses intelligent computer experiments. The objective is to assess qualitatively and/or quantitatively how the variabilities of simulation output responses can be accounted for by input variabilities. We address global sensitivity analysis in three aspects: methodology, sampling/analysis strategies, and an implementation framework. The methodology consists of three major steps: (1) construct credible input ranges; (2) perform a parameter screening study; and (3) perform a quantitative sensitivity analysis on a reduced set of parameters. Once identified, research effort should be directed to the most sensitive parameters to reduce their uncertainty bounds. This process is repeated with tightened uncertainty bounds for the sensitive parameters until the output uncertainties become acceptable. To accommodate the needs of multi-physics application, this methodology should be recursively applied to individual physics modules. The methodology is also distinguished by an efficient technique for computing parameter interactions. Details for each step will be given using simple examples. Numerical results on large scale multi-physics applications will be available in another report. Computational techniques targeted for this methodology have been implemented in a software package called PSUADE.

  17. Changes in cod muscle proteins during frozen storage revealed by proteome analysis and multivariate data analysis

    DEFF Research Database (Denmark)

    Kjærsgård, Inger Vibeke Holst; Nørrelykke, M.R.; Jessen, Flemming

    2006-01-01

    Multivariate data analysis has been combined with proteomics to enhance the recovery of information from 2-DE of cod muscle proteins during different storage conditions. Proteins were extracted according to 11 different storage conditions and samples were resolved by 2-DE. Data generated by 2-DE...... was subjected to principal component analysis (PCA) and discriminant partial least squares regression (DPLSR). Applying PCA to 2-DE data revealed the samples to form groups according to frozen storage time, whereas differences due to different storage temperatures or chilled storage in modified atmosphere...... light chain 1, 2 and 3, triose-phosphate isomerase, glyceraldehyde-3-phosphate dehydrogenase, aldolase A and two ?-actin fragments, and a nuclease diphosphate kinase B fragment to change in concentration, during frozen storage. Application of proteomics, multivariate data analysis and MS/MS to analyse...

  18. Globalization

    OpenAIRE

    F. Gerard Adams

    2008-01-01

    The rapid globalization of the world economy is causing fundamental changes in patterns of trade and finance. Some economists have argued that globalization has arrived and that the world is “flat†. While the geographic scope of markets has increased, the author argues that new patterns of trade and finance are a result of the discrepancies between “old†countries and “new†. As the differences are gradually wiped out, particularly if knowledge and technology spread worldwide, the t...

  19. Differential network analysis reveals genetic effects on catalepsy modules.

    Directory of Open Access Journals (Sweden)

    Ovidiu D Iancu

    Full Text Available We performed short-term bi-directional selective breeding for haloperidol-induced catalepsy, starting from three mouse populations of increasingly complex genetic structure: an F2 intercross, a heterogeneous stock (HS formed by crossing four inbred strains (HS4 and a heterogeneous stock (HS-CC formed from the inbred strain founders of the Collaborative Cross (CC. All three selections were successful, with large differences in haloperidol response emerging within three generations. Using a custom differential network analysis procedure, we found that gene coexpression patterns changed significantly; importantly, a number of these changes were concordant across genetic backgrounds. In contrast, absolute gene-expression changes were modest and not concordant across genetic backgrounds, in spite of the large and similar phenotypic differences. By inferring strain contributions from the parental lines, we are able to identify significant differences in allelic content between the selected lines concurrent with large changes in transcript connectivity. Importantly, this observation implies that genetic polymorphisms can affect transcript and module connectivity without large changes in absolute expression levels. We conclude that, in this case, selective breeding acts at the subnetwork level, with the same modules but not the same transcripts affected across the three selections.

  20. Network analysis reveals distinct clinical syndromes underlying acute mountain sickness.

    Directory of Open Access Journals (Sweden)

    David P Hall

    Full Text Available Acute mountain sickness (AMS is a common problem among visitors at high altitude, and may progress to life-threatening pulmonary and cerebral oedema in a minority of cases. International consensus defines AMS as a constellation of subjective, non-specific symptoms. Specifically, headache, sleep disturbance, fatigue and dizziness are given equal diagnostic weighting. Different pathophysiological mechanisms are now thought to underlie headache and sleep disturbance during acute exposure to high altitude. Hence, these symptoms may not belong together as a single syndrome. Using a novel visual analogue scale (VAS, we sought to undertake a systematic exploration of the symptomatology of AMS using an unbiased, data-driven approach originally designed for analysis of gene expression. Symptom scores were collected from 292 subjects during 1110 subject-days at altitudes between 3650 m and 5200 m on Apex expeditions to Bolivia and Kilimanjaro. Three distinct patterns of symptoms were consistently identified. Although fatigue is a ubiquitous finding, sleep disturbance and headache are each commonly reported without the other. The commonest pattern of symptoms was sleep disturbance and fatigue, with little or no headache. In subjects reporting severe headache, 40% did not report sleep disturbance. Sleep disturbance correlates poorly with other symptoms of AMS (Mean Spearman correlation 0.25. These results challenge the accepted paradigm that AMS is a single disease process and describe at least two distinct syndromes following acute ascent to high altitude. This approach to analysing symptom patterns has potential utility in other clinical syndromes.

  1. Demographic analysis reveals gradual senescence in the flatworm Macrostomum lignano

    Directory of Open Access Journals (Sweden)

    Braeckman Bart P

    2009-07-01

    Full Text Available Abstract Free-living flatworms ("Turbellaria" are appropriate model organisms to gain better insight into the role of stem cells in ageing and rejuvenation. Ageing research in flatworms is, however, still scarce. This is partly due to culture difficulties and the lack of a complete set of demographic data, including parameters such as median lifespan and age-specific mortality rate. In this paper, we report on the first flatworm survival analysis. We used the species Macrostomum lignano, which is an emerging model for studying the reciprocal influence between stem cells, ageing and rejuvenation. This species has a median lifespan of 205 ± 13 days (average ± standard deviation [SD] and a 90th percentile lifespan of 373 ± 32 days. The maximum lifespan, however, is more than 745 days, and the average survival curve is characterised by a long tail because a small number of individuals lives twice as long as 90% of the population. Similar to earlier observations in a wide range of animals, in M. lignano the age-specific mortality rate increases exponentially, but levels off at the oldest ages. To compare the senescence of M. lignano with that of other ageing models, we determined the mortality rate doubling time, which is 0.20 ± 0.02 years. As a result, we can conclude that M. lignano shows gradual senescence at a rate similar to the vertebrate ageing models Rattus norvegicus and Mus musculus. We argue that M. lignano is a suitable model for ageing and rejuvenation research, and especially for the role of stem cells in these processes, due to its accessible stem cell system and regeneration capacity, and the possibility of combining stem cell studies with demographic analyses.

  2. Network analysis reveals multiscale controls on streamwater chemistry

    Science.gov (United States)

    McGuire, Kevin J.; Torgersen, Christian E.; Likens, Gene E.; Buso, Donald C.; Lowe, Winsor H.; Bailey, Scott W.

    2014-01-01

    By coupling synoptic data from a basin-wide assessment of streamwater chemistry with network-based geostatistical analysis, we show that spatial processes differentially affect biogeochemical condition and pattern across a headwater stream network. We analyzed a high-resolution dataset consisting of 664 water samples collected every 100 m throughout 32 tributaries in an entire fifth-order stream network. These samples were analyzed for an exhaustive suite of chemical constituents. The fine grain and broad extent of this study design allowed us to quantify spatial patterns over a range of scales by using empirical semivariograms that explicitly incorporated network topology. Here, we show that spatial structure, as determined by the characteristic shape of the semivariograms, differed both among chemical constituents and by spatial relationship (flow-connected, flow-unconnected, or Euclidean). Spatial structure was apparent at either a single scale or at multiple nested scales, suggesting separate processes operating simultaneously within the stream network and surrounding terrestrial landscape. Expected patterns of spatial dependence for flow-connected relationships (e.g., increasing homogeneity with downstream distance) occurred for some chemical constituents (e.g., dissolved organic carbon, sulfate, and aluminum) but not for others (e.g., nitrate, sodium). By comparing semivariograms for the different chemical constituents and spatial relationships, we were able to separate effects on streamwater chemistry of (i) fine-scale versus broad-scale processes and (ii) in-stream processes versus landscape controls. These findings provide insight on the hierarchical scaling of local, longitudinal, and landscape processes that drive biogeochemical patterns in stream networks.

  3. Network analysis reveals multiscale controls on streamwater chemistry.

    Science.gov (United States)

    McGuire, Kevin J; Torgersen, Christian E; Likens, Gene E; Buso, Donald C; Lowe, Winsor H; Bailey, Scott W

    2014-05-13

    By coupling synoptic data from a basin-wide assessment of streamwater chemistry with network-based geostatistical analysis, we show that spatial processes differentially affect biogeochemical condition and pattern across a headwater stream network. We analyzed a high-resolution dataset consisting of 664 water samples collected every 100 m throughout 32 tributaries in an entire fifth-order stream network. These samples were analyzed for an exhaustive suite of chemical constituents. The fine grain and broad extent of this study design allowed us to quantify spatial patterns over a range of scales by using empirical semivariograms that explicitly incorporated network topology. Here, we show that spatial structure, as determined by the characteristic shape of the semivariograms, differed both among chemical constituents and by spatial relationship (flow-connected, flow-unconnected, or Euclidean). Spatial structure was apparent at either a single scale or at multiple nested scales, suggesting separate processes operating simultaneously within the stream network and surrounding terrestrial landscape. Expected patterns of spatial dependence for flow-connected relationships (e.g., increasing homogeneity with downstream distance) occurred for some chemical constituents (e.g., dissolved organic carbon, sulfate, and aluminum) but not for others (e.g., nitrate, sodium). By comparing semivariograms for the different chemical constituents and spatial relationships, we were able to separate effects on streamwater chemistry of (i) fine-scale versus broad-scale processes and (ii) in-stream processes versus landscape controls. These findings provide insight on the hierarchical scaling of local, longitudinal, and landscape processes that drive biogeochemical patterns in stream networks.

  4. ACE2 Global Digital Elevation Model : User Analysis

    Science.gov (United States)

    Smith, R. G.; Berry, P. A. M.; Benveniste, J.

    2013-12-01

    Altimeter Corrected Elevations 2 (ACE2), first released in October 2009, is the Global Digital Elevation Model (GDEM) created by fusing the high accuracy of over 100 million altimeter retracked height estimates, derived primarily from the ERS-1 Geodetic Mission, with the high frequency content available within the near-global Shuttle Radar Topography Mission. This novel ACE2 GDEM is freely available at 3”, 9”, 30” and 5' and has been distributed via the web to over 680 subscribers. This paper presents the results of a detailed analysis of geographical distribution of subscribed users, along with fields of study and potential uses. Investigations have also been performed to determine the most popular spatial resolutions and the impact these have on the scope of data downloaded. The analysis has shown that, even though the majority of users have come from Europe and America, a significant number of website hits have been received from South America, Africa and Asia. Registered users also vary widely, from research institutions and major companies down to individual hobbyists looking at data for single projects.

  5. Global patterns of materials use. A socioeconomic and geophysical analysis

    Energy Technology Data Exchange (ETDEWEB)

    Steinberger, Julia K.; Krausmann, Fridolin; Eisenmenger, Nina [Institute of Social Ecology Vienna, IFF, University of Klagenfurt, Schottenfeldgasse 29, A-1070 Wien (Austria)

    2010-03-15

    Human use of materials is a major driver of global environmental change. The links between materials use and economic development are central to the challenge of decoupling of materials use and economic growth (dematerialization). This article presents a new global material flow dataset compiled for the year 2000, covering 175 countries, including both extraction and trade flows, and comprising four major material categories: biomass, construction minerals, fossil energy carriers and ores/industrial minerals. First, we quantify the variability and distributional inequality (Gini coefficients) in international material consumption. We then measure the influence of the drivers population, GDP, land area and climate. This analysis yields international income elasticities of material use. Finally, we examine the coupling between material flows, and between income and material productivity, measured in economic production per tonne material consumed. Material productivity is strongly coupled to income, and may thus not be suitable as an international indicator of environmental progress - a finding which we relate to the economic inelasticity of material consumption. The results demonstrate striking differences between the material groups. Biomass is the most equitably distributed resource, economically the most inelastic, and is not correlated to any of the mineral materials. The three mineral material groups are closely coupled to each other and economic activity, indicating that the challenge of dematerializing industrial economies may require fundamental structural transformation. Our analysis provides a first systematic investigation of international differences in material use and their drivers, and thus serves as the basis for more detailed future work. (author)

  6. Phylogenetic analysis of ferlin genes reveals ancient eukaryotic origins

    Directory of Open Access Journals (Sweden)

    Lek Monkol

    2010-07-01

    Full Text Available Abstract Background The ferlin gene family possesses a rare and identifying feature consisting of multiple tandem C2 domains and a C-terminal transmembrane domain. Much currently remains unknown about the fundamental function of this gene family, however, mutations in its two most well-characterised members, dysferlin and otoferlin, have been implicated in human disease. The availability of genome sequences from a wide range of species makes it possible to explore the evolution of the ferlin family, providing contextual insight into characteristic features that define the ferlin gene family in its present form in humans. Results Ferlin genes were detected from all species of representative phyla, with two ferlin subgroups partitioned within the ferlin phylogenetic tree based on the presence or absence of a DysF domain. Invertebrates generally possessed two ferlin genes (one with DysF and one without, with six ferlin genes in most vertebrates (three DysF, three non-DysF. Expansion of the ferlin gene family is evident between the divergence of lamprey (jawless vertebrates and shark (cartilaginous fish. Common to almost all ferlins is an N-terminal C2-FerI-C2 sandwich, a FerB motif, and two C-terminal C2 domains (C2E and C2F adjacent to the transmembrane domain. Preservation of these structural elements throughout eukaryotic evolution suggests a fundamental role of these motifs for ferlin function. In contrast, DysF, C2DE, and FerA are optional, giving rise to subtle differences in domain topologies of ferlin genes. Despite conservation of multiple C2 domains in all ferlins, the C-terminal C2 domains (C2E and C2F displayed higher sequence conservation and greater conservation of putative calcium binding residues across paralogs and orthologs. Interestingly, the two most studied non-mammalian ferlins (Fer-1 and Misfire in model organisms C. elegans and D. melanogaster, present as outgroups in the phylogenetic analysis, with results suggesting

  7. Global sensitivity analysis of multiscale properties of porous materials

    Science.gov (United States)

    Um, Kimoon; Zhang, Xuan; Katsoulakis, Markos; Plechac, Petr; Tartakovsky, Daniel M.

    2018-02-01

    Ubiquitous uncertainty about pore geometry inevitably undermines the veracity of pore- and multi-scale simulations of transport phenomena in porous media. It raises two fundamental issues: sensitivity of effective material properties to pore-scale parameters and statistical parameterization of Darcy-scale models that accounts for pore-scale uncertainty. Homogenization-based maps of pore-scale parameters onto their Darcy-scale counterparts facilitate both sensitivity analysis (SA) and uncertainty quantification. We treat uncertain geometric characteristics of a hierarchical porous medium as random variables to conduct global SA and to derive probabilistic descriptors of effective diffusion coefficients and effective sorption rate. Our analysis is formulated in terms of solute transport diffusing through a fluid-filled pore space, while sorbing to the solid matrix. Yet it is sufficiently general to be applied to other multiscale porous media phenomena that are amenable to homogenization.

  8. Risk-analysis of global climate tipping points

    Energy Technology Data Exchange (ETDEWEB)

    Frieler, Katja; Meinshausen, Malte; Braun, N [Potsdam Institute for Climate Impact Research e.V., Potsdam (Germany). PRIMAP Research Group; and others

    2012-09-15

    vulnerable to climate change impacts. Here we focus on tipping elements within the physical / biological system. In the following two sections, we briefly highlight some of our methodological research regarding global mean precipitation and regional climate change. These methodological developments provided the underpinning for our subsequent analysis of individual large-scale climate impacts, as e.g. mass losses of the Greenland ice sheet, the release of greenhouse gases by the thawing of permafrost regions or the threat of coral reefs by high ocean temperatures.

  9. Transcriptional regulation of rod photoreceptor homeostasis revealed by in vivo NRL targetome analysis.

    Directory of Open Access Journals (Sweden)

    Hong Hao

    Full Text Available A stringent control of homeostasis is critical for functional maintenance and survival of neurons. In the mammalian retina, the basic motif leucine zipper transcription factor NRL determines rod versus cone photoreceptor cell fate and activates the expression of many rod-specific genes. Here, we report an integrated analysis of NRL-centered gene regulatory network by coupling chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-Seq data from Illumina and ABI platforms with global expression profiling and in vivo knockdown studies. We identified approximately 300 direct NRL target genes. Of these, 22 NRL targets are associated with human retinal dystrophies, whereas 95 mapped to regions of as yet uncloned retinal disease loci. In silico analysis of NRL ChIP-Seq peak sequences revealed an enrichment of distinct sets of transcription factor binding sites. Specifically, we discovered that genes involved in photoreceptor function include binding sites for both NRL and homeodomain protein CRX. Evaluation of 26 ChIP-Seq regions validated their enhancer functions in reporter assays. In vivo knockdown of 16 NRL target genes resulted in death or abnormal morphology of rod photoreceptors, suggesting their importance in maintaining retinal function. We also identified histone demethylase Kdm5b as a novel secondary node in NRL transcriptional hierarchy. Exon array analysis of flow-sorted photoreceptors in which Kdm5b was knocked down by shRNA indicated its role in regulating rod-expressed genes. Our studies identify candidate genes for retinal dystrophies, define cis-regulatory module(s for photoreceptor-expressed genes and provide a framework for decoding transcriptional regulatory networks that dictate rod homeostasis.

  10. Systematic Prioritization and Integrative Analysis of Copy Number Variations in Schizophrenia Reveal Key Schizophrenia Susceptibility Genes

    Science.gov (United States)

    Luo, Xiongjian; Huang, Liang; Han, Leng; Luo, Zhenwu; Hu, Fang; Tieu, Roger; Gan, Lin

    2014-01-01

    Schizophrenia is a common mental disorder with high heritability and strong genetic heterogeneity. Common disease-common variants hypothesis predicts that schizophrenia is attributable in part to common genetic variants. However, recent studies have clearly demonstrated that copy number variations (CNVs) also play pivotal roles in schizophrenia susceptibility and explain a proportion of missing heritability. Though numerous CNVs have been identified, many of the regions affected by CNVs show poor overlapping among different studies, and it is not known whether the genes disrupted by CNVs contribute to the risk of schizophrenia. By using cumulative scoring, we systematically prioritized the genes affected by CNVs in schizophrenia. We identified 8 top genes that are frequently disrupted by CNVs, including NRXN1, CHRNA7, BCL9, CYFIP1, GJA8, NDE1, SNAP29, and GJA5. Integration of genes affected by CNVs with known schizophrenia susceptibility genes (from previous genetic linkage and association studies) reveals that many genes disrupted by CNVs are also associated with schizophrenia. Further protein-protein interaction (PPI) analysis indicates that protein products of genes affected by CNVs frequently interact with known schizophrenia-associated proteins. Finally, systematic integration of CNVs prioritization data with genetic association and PPI data identifies key schizophrenia candidate genes. Our results provide a global overview of genes impacted by CNVs in schizophrenia and reveal a densely interconnected molecular network of de novo CNVs in schizophrenia. Though the prioritized top genes represent promising schizophrenia risk genes, further work with different prioritization methods and independent samples is needed to confirm these findings. Nevertheless, the identified key candidate genes may have important roles in the pathogenesis of schizophrenia, and further functional characterization of these genes may provide pivotal targets for future therapeutics and

  11. Integrated Analysis of Alzheimer's Disease and Schizophrenia Dataset Revealed Different Expression Pattern in Learning and Memory.

    Science.gov (United States)

    Li, Wen-Xing; Dai, Shao-Xing; Liu, Jia-Qian; Wang, Qian; Li, Gong-Hua; Huang, Jing-Fei

    2016-01-01

    Alzheimer's disease (AD) and schizophrenia (SZ) are both accompanied by impaired learning and memory functions. This study aims to explore the expression profiles of learning or memory genes between AD and SZ. We downloaded 10 AD and 10 SZ datasets from GEO-NCBI for integrated analysis. These datasets were processed using RMA algorithm and a global renormalization for all studies. Then Empirical Bayes algorithm was used to find the differentially expressed genes between patients and controls. The results showed that most of the differentially expressed genes were related to AD whereas the gene expression profile was little affected in the SZ. Furthermore, in the aspects of the number of differentially expressed genes, the fold change and the brain region, there was a great difference in the expression of learning or memory related genes between AD and SZ. In AD, the CALB1, GABRA5, and TAC1 were significantly downregulated in whole brain, frontal lobe, temporal lobe, and hippocampus. However, in SZ, only two genes CRHBP and CX3CR1 were downregulated in hippocampus, and other brain regions were not affected. The effect of these genes on learning or memory impairment has been widely studied. It was suggested that these genes may play a crucial role in AD or SZ pathogenesis. The different gene expression patterns between AD and SZ on learning and memory functions in different brain regions revealed in our study may help to understand the different mechanism between two diseases.

  12. Global sensitivity analysis of computer models with functional inputs

    International Nuclear Information System (INIS)

    Iooss, Bertrand; Ribatet, Mathieu

    2009-01-01

    Global sensitivity analysis is used to quantify the influence of uncertain model inputs on the response variability of a numerical model. The common quantitative methods are appropriate with computer codes having scalar model inputs. This paper aims at illustrating different variance-based sensitivity analysis techniques, based on the so-called Sobol's indices, when some model inputs are functional, such as stochastic processes or random spatial fields. In this work, we focus on large cpu time computer codes which need a preliminary metamodeling step before performing the sensitivity analysis. We propose the use of the joint modeling approach, i.e., modeling simultaneously the mean and the dispersion of the code outputs using two interlinked generalized linear models (GLMs) or generalized additive models (GAMs). The 'mean model' allows to estimate the sensitivity indices of each scalar model inputs, while the 'dispersion model' allows to derive the total sensitivity index of the functional model inputs. The proposed approach is compared to some classical sensitivity analysis methodologies on an analytical function. Lastly, the new methodology is applied to an industrial computer code that simulates the nuclear fuel irradiation.

  13. Global Proteomics Revealed Klebsiella pneumoniae Induced Autophagy and Oxidative Stress in Caenorhabditis elegans by Inhibiting PI3K/AKT/mTOR Pathway during Infection

    Directory of Open Access Journals (Sweden)

    Arumugam Kamaladevi

    2017-09-01

    Full Text Available The enterobacterium, Klebsiella pneumoniae invades the intestinal epithelium of humans by interfering with multiple host cell response. To uncover a system-level overview of host response during infection, we analyzed the global dynamics of protein profiling in Caenorhabditis elegans using quantitative proteomics approach. Comparison of protein samples of nematodes exposed to K. pneumoniae for 12, 24, and 36 h by 2DE revealed several changes in host proteome. A total of 266 host-encoded proteins were identified by 2DE MALDI-MS/MS and LC-MS/MS and the interacting partners of the identified proteins were predicted by STRING 10.0 analysis. In order to understand the interacting partners of regulatory proteins with similar or close pI ranges, a liquid IEF was performed and the isolated fractions containing proteins were identified by LC-MS/MS. Functional bioinformatics analysis on identified proteins deciphered that they were mostly related to the metabolism, dauer formation, apoptosis, endocytosis, signal transduction, translation, developmental, and reproduction process. Gene enrichment analysis suggested that the metabolic process as the most overrepresented pathway regulated against K. pneumoniae infection. The dauer-like formation in infected C. elegans along with intestinal atrophy and ROS during the physiological analysis indicated that the regulation of metabolic pathway is probably through the involvement of mTOR. Immunoblot analysis supported the above notion that the K. pneumoniae infection induced protein mis-folding in host by involving PI3Kinase/AKT-1/mTOR mediated pathway. Furthermore, the susceptibility of pdi-2, akt-1, and mTOR C. elegans mutants confirmed the role and involvement of PI3K/AKT/mTOR pathway in mediating protein mis-folding which appear to be translating the vulnerability of host defense toward K. pneumoniae infection.

  14. Global Analysis of Solar Neutrino Oscillations Including SNO CC Measurement

    CERN Document Server

    Bahcall, J N; Peña-Garay, C; Bahcall, John N; Peña-Garay, Carlos

    2001-01-01

    For active and sterile neutrinos, we present the globally allowed solutions for two neutrino oscillations. We include the SNO CC measurement and all other relevant solar neutrino and reactor data. Five active neutrino oscillation solutions (LMA, LOW, SMA, VAC, and Just So2) are currently allowed at 3 sigma; three sterile neutrino solutions (Just So2, SMA, and VAC) are allowed at 3 sigma. The goodness of fit is satisfactory for all eight solutions. We also investigate the robustness of the allowed solutions by carrying out global analyses with and without: 1) imposing solar model constraints on the 8B neutrino flux, 2) including the Super-Kamiokande spectral energy distribution and day-night data, 3) using an enhanced CC cross section for deuterium (due to radiative corrections), and 4) a optimistic, hypothetical reduction by a factor of three of the error of the SNO CC rate. For every analysis strategy used in this paper, the most favored solutions all involve large mixing angles: LMA, LOW, or VAC. The favore...

  15. Global Analysis of RNA Secondary Structure in Two Metazoans

    Directory of Open Access Journals (Sweden)

    Fan Li

    2012-01-01

    Full Text Available The secondary structure of RNA is necessary for its maturation, regulation, processing, and function. However, the global influence of RNA folding in eukaryotes is still unclear. Here, we use a high-throughput, sequencing-based, structure-mapping approach to identify the paired (double-stranded RNA [dsRNA] and unpaired (single-stranded RNA [ssRNA] components of the Drosophila melanogaster and Caenorhabditis elegans transcriptomes, which allows us to identify conserved features of RNA secondary structure in metazoans. From this analysis, we find that ssRNAs and dsRNAs are significantly correlated with specific epigenetic modifications. Additionally, we find key structural patterns across protein-coding transcripts that indicate that RNA folding demarcates regions of protein translation and likely affects microRNA-mediated regulation of mRNAs in animals. Finally, we identify and characterize 546 mRNAs whose folding pattern is significantly correlated between these metazoans, suggesting that their structure has some function. Overall, our findings provide a global assessment of RNA folding in animals.

  16. Global transcriptome analysis of developing chickpea (Cicer arietinum L.) seeds.

    Science.gov (United States)

    Pradhan, Seema; Bandhiwal, Nitesh; Shah, Niraj; Kant, Chandra; Gaur, Rashmi; Bhatia, Sabhyata

    2014-01-01

    Understanding developmental processes, especially in non-model crop plants, is extremely important in order to unravel unique mechanisms regulating development. Chickpea (C. arietinum L.) seeds are especially valued for their high carbohydrate and protein content. Therefore, in order to elucidate the mechanisms underlying seed development in chickpea, deep sequencing of transcriptomes from four developmental stages was undertaken. In this study, next generation sequencing platform was utilized to sequence the transcriptome of four distinct stages of seed development in chickpea. About 1.3 million reads were generated which were assembled into 51,099 unigenes by merging the de novo and reference assemblies. Functional annotation of the unigenes was carried out using the Uniprot, COG and KEGG databases. RPKM based digital expression analysis revealed specific gene activities at different stages of development which was validated using Real time PCR analysis. More than 90% of the unigenes were found to be expressed in at least one of the four seed tissues. DEGseq was used to determine differentially expressing genes which revealed that only 6.75% of the unigenes were differentially expressed at various stages. Homology based comparison revealed 17.5% of the unigenes to be putatively seed specific. Transcription factors were predicted based on HMM profiles built using TF sequences from five legume plants and analyzed for their differential expression during progression of seed development. Expression analysis of genes involved in biosynthesis of important secondary metabolites suggested that chickpea seeds can serve as a good source of antioxidants. Since transcriptomes are a valuable source of molecular markers like simple sequence repeats (SSRs), about 12,000 SSRs were mined in chickpea seed transcriptome and few of them were validated. In conclusion, this study will serve as a valuable resource for improved chickpea breeding.

  17. Global transcriptome analysis of developing chickpea (Cicer arietinum L. seeds

    Directory of Open Access Journals (Sweden)

    Seema ePradhan

    2014-12-01

    Full Text Available Understanding developmental processes, especially in non-model crop plants, is extremely important in order to unravel unique mechanisms regulating development. Chickpea (C. arietinum L. seeds are especially valued for their high carbohydrate and protein content. Therefore, in order to elucidate the mechanisms underlying seed development in chickpea, deep sequencing of transcriptomes from four developmental stages was undertaken. In this study, next generation sequencing platform was utilised to sequence the transcriptome of four distinct stages of seed development in chickpea. About 1.3 million reads were generated which were assembled into 51,099 unigenes by merging the de novo and reference assemblies. Functional annotation of the unigenes was carried out using the Uniprot, COG and KEGG databases. RPKM based digital expression analysis revealed specific gene activities at different stages of development which was validated using Real time PCR analysis. More than 90% of the unigenes were found to be expressed in at least one of the four seed tissues. DEGseq was used to determine differentially expressing genes which revealed that only 6.75% of the unigenes were differentially expressed at various stages. Homology based comparison revealed 17.5% of the unigenes to be putatively seed specific. Transcription factors were predicted based on HMM profiles built using TF sequences from five legume plants and analysed for their differential expression during progression of seed development. Expression analysis of genes involved in biosynthesis of important secondary metabolites suggested that chickpea seeds can serve as a good source of antioxidants. Since transcriptomes are a valuable source of molecular markers like simple sequence repeats (SSRs, about 12,000 SSRs were mined in chickpea seed transcriptome and few of them were validated. In conclusion, this study will serve as a valuable resource for improved chickpea breeding.

  18. A global analysis of NMR distance constraints from the PDB

    International Nuclear Information System (INIS)

    Vranken, Wim

    2007-01-01

    Information obtained from Nuclear Magnetic Resonance (NMR) experiments is encoded as a set of constraint lists when calculating three-dimensional structures for a protein. With the amount of constraint data from the world wide Protein Data Bank (wwPDB) that is now available, it is possible to do a global, large-scale analysis using only information from the constraints, without taking the coordinate information into account. This article describes such an analysis of distance constraints from NOE data based on a set of 1834 NMR PDB entries containing 1909 protein chains. In order to best represent the quality and extent of the data that is currently deposited at the wwPDB, only the original data as deposited by the authors was used, and no attempt was made to 'clean up' and further interpret this information. Because the constraint lists provide a single set of data, and not an ensemble of structural solutions, they are easier to analyse and provide a reduced form of structural information that is relevant for NMR analysis only. The online resource resulting from this analysis makes it possible to check, for example, how often a particular contact occurs when assigning NOESY spectra, or to find out whether a particular sequence fragment is likely to be difficult to assign. In this respect it formalises information that scientists with experience in spectrum analysis are aware of but cannot necessarily quantify. The analysis described here illustrates the importance of depositing constraints (and all other possible NMR derived information) along with the structure coordinates, as this type of information can greatly assist the NMR community

  19. Analysis of a global database containing tritium in precipitation

    Energy Technology Data Exchange (ETDEWEB)

    Buckley, R. L. [Savannah River Site (SRS), Aiken, SC (United States); Rabun, R. L. [Savannah River Site (SRS), Aiken, SC (United States); Heath, M. [Savannah River Site (SRS), Aiken, SC (United States)

    2016-02-17

    The International Atomic Energy Agency (IAEA) directed the collection of tritium in water samples from the mid-1950s to 2009. The Global Network of Isotopes in Precipitation (GNIP) data examined the airborne movement of isotope releases to the environment, with an objective of collecting spatial data on the isotope content of precipitation across the globe. The initial motivation was to monitor atmospheric thermonuclear test fallout through tritium, deuterium, and oxygen isotope concentrations, but after the 1970s the focus changed to being an observation network of stable hydrogen and oxygen isotope data for hydrologic studies. The GNIP database provides a wealth of tritium data collections over a long period of time. The work performed here primarily examined data features in the past 30 years (after much of the effects of above-ground nuclear testing in the late 1950s to early 1960s decayed away), revealing potentially unknown tritium sources. The available data at GNIP were reorganized to allow for evaluation of trends in the data both temporally and spatially. Several interesting cases were revealed, including relatively high measured concentrations in the Atlantic and Indian Oceans, Russia, Norway, as well as an increase in background concentration at a collector in South Korea after 2004. Recent data from stations in the southeastern United States nearest to the Savannah River Site do not indicate any high values. Meteorological impacts have not been considered in this study. Further research to assess the likely source location of interesting cases using transport simulations and/or literature searches is warranted.

  20. Global review of open access risk assessment software packages valid for global or continental scale analysis

    Science.gov (United States)

    Daniell, James; Simpson, Alanna; Gunasekara, Rashmin; Baca, Abigail; Schaefer, Andreas; Ishizawa, Oscar; Murnane, Rick; Tijssen, Annegien; Deparday, Vivien; Forni, Marc; Himmelfarb, Anne; Leder, Jan

    2015-04-01

    Over the past few decades, a plethora of open access software packages for the calculation of earthquake, volcanic, tsunami, storm surge, wind and flood have been produced globally. As part of the World Bank GFDRR Review released at the Understanding Risk 2014 Conference, over 80 such open access risk assessment software packages were examined. Commercial software was not considered in the evaluation. A preliminary analysis was used to determine whether the 80 models were currently supported and if they were open access. This process was used to select a subset of 31 models that include 8 earthquake models, 4 cyclone models, 11 flood models, and 8 storm surge/tsunami models for more detailed analysis. By using multi-criteria analysis (MCDA) and simple descriptions of the software uses, the review allows users to select a few relevant software packages for their own testing and development. The detailed analysis evaluated the models on the basis of over 100 criteria and provides a synopsis of available open access natural hazard risk modelling tools. In addition, volcano software packages have since been added making the compendium of risk software tools in excess of 100. There has been a huge increase in the quality and availability of open access/source software over the past few years. For example, private entities such as Deltares now have an open source policy regarding some flood models (NGHS). In addition, leaders in developing risk models in the public sector, such as Geoscience Australia (EQRM, TCRM, TsuDAT, AnuGA) or CAPRA (ERN-Flood, Hurricane, CRISIS2007 etc.), are launching and/or helping many other initiatives. As we achieve greater interoperability between modelling tools, we will also achieve a future wherein different open source and open access modelling tools will be increasingly connected and adapted towards unified multi-risk model platforms and highly customised solutions. It was seen that many software tools could be improved by enabling user

  1. Dynamical analysis of the global business-cycle synchronization.

    Science.gov (United States)

    Lopes, António M; Tenreiro Machado, J A; Huffstot, John S; Mata, Maria Eugénia

    2018-01-01

    This paper reports the dynamical analysis of the business cycles of 12 (developed and developing) countries over the last 56 years by applying computational techniques used for tackling complex systems. They reveal long-term convergence and country-level interconnections because of close contagion effects caused by bilateral networking exposure. Interconnectivity determines the magnitude of cross-border impacts. Local features and shock propagation complexity also may be true engines for local configuration of cycles. The algorithmic modeling proves to represent a solid approach to study the complex dynamics involved in the world economies.

  2. Dynamical analysis of the global business-cycle synchronization

    Science.gov (United States)

    2018-01-01

    This paper reports the dynamical analysis of the business cycles of 12 (developed and developing) countries over the last 56 years by applying computational techniques used for tackling complex systems. They reveal long-term convergence and country-level interconnections because of close contagion effects caused by bilateral networking exposure. Interconnectivity determines the magnitude of cross-border impacts. Local features and shock propagation complexity also may be true engines for local configuration of cycles. The algorithmic modeling proves to represent a solid approach to study the complex dynamics involved in the world economies. PMID:29408909

  3. Global sensitivity analysis using low-rank tensor approximations

    International Nuclear Information System (INIS)

    Konakli, Katerina; Sudret, Bruno

    2016-01-01

    In the context of global sensitivity analysis, the Sobol' indices constitute a powerful tool for assessing the relative significance of the uncertain input parameters of a model. We herein introduce a novel approach for evaluating these indices at low computational cost, by post-processing the coefficients of polynomial meta-models belonging to the class of low-rank tensor approximations. Meta-models of this class can be particularly efficient in representing responses of high-dimensional models, because the number of unknowns in their general functional form grows only linearly with the input dimension. The proposed approach is validated in example applications, where the Sobol' indices derived from the meta-model coefficients are compared to reference indices, the latter obtained by exact analytical solutions or Monte-Carlo simulation with extremely large samples. Moreover, low-rank tensor approximations are confronted to the popular polynomial chaos expansion meta-models in case studies that involve analytical rank-one functions and finite-element models pertinent to structural mechanics and heat conduction. In the examined applications, indices based on the novel approach tend to converge faster to the reference solution with increasing size of the experimental design used to build the meta-model. - Highlights: • A new method is proposed for global sensitivity analysis of high-dimensional models. • Low-rank tensor approximations (LRA) are used as a meta-modeling technique. • Analytical formulas for the Sobol' indices in terms of LRA coefficients are derived. • The accuracy and efficiency of the approach is illustrated in application examples. • LRA-based indices are compared to indices based on polynomial chaos expansions.

  4. Analysis of Global Urban Temperature Trends and Urbanization Impacts

    Science.gov (United States)

    Lee, K. I.; Ryu, J.; Jeon, S. W.

    2018-04-01

    Due to urbanization, urban areas are shrinking green spaces and increasing concrete, asphalt pavement. So urban climates are different from non-urban areas. In addition, long-term macroscopic studies of urban climate change are becoming more important as global urbanization affects global warming. To do this, it is necessary to analyze the effect of urbanization on the temporal change in urban temperature with the same temperature data and standards for urban areas around the world. In this study, time series analysis was performed with the maximum, minimum, mean and standard values of surface temperature during the from 1980 to 2010 and analyzed the effect of urbanization through linear regression analysis with variables (population, night light, NDVI, urban area). As a result, the minimum value of the surface temperature of the urban area reflects an increase by a rate of 0.28K decade-1 over the past 31 years, the maximum value reflects an increase by a rate of 0.372K decade-1, the mean value reflects an increase by a rate of 0.208 decade-1, and the standard deviation reflects a decrease by rate of 0.023K decade-1. And the change of surface temperature in urban areas is affected by urbanization related to land cover such as decrease of greenery and increase of pavement area, but socioeconomic variables are less influential than NDVI in this study. This study are expected to provide an approach to future research and policy-planning for urban temperature change and urbanization impacts.

  5. Oceanic mantle rocks reveal evidence for an ancient, 1.2-1.3 Ga global melting event

    Science.gov (United States)

    Dijkstra, A. H.; Sergeev, D.; McTaminey, L.; Dale, C. W.; Meisel, T. C.

    2011-12-01

    It is now increasingly being recognized that many oceanic peridotites are refertilized harzburgites, and that the refertilization often masks an extremely refractory character of the original mantle rock 'protolith'. Oceanic peridotites are, when the effects of melt refertilization are undone, often too refractory to be simple mantle melting residues after the extraction of mid-ocean ridge basalts at a spreading center. Rhenium-osmium isotope analysis is a powerful method to look through the effects of refertilization and to obtain constraints on the age of the melting that produced the refractory mantle protolith. Rhenium-depletion model ages of such anomalously refractory oceanic mantle rocks - found as abyssal peridotites or as mantle xenoliths on ocean islands - are typically >1 Ga, i.e., much older than the ridge system at which they were emplaced. In my contribution I will show results from two case studies of refertilized anciently depleted mantle rocks (Macquarie Island 'abyssal' peridotites and Lanzarote mantle xenoliths). Interestingly, very refractory oceanic mantle rocks from sites all around the world show recurring evidence for a Mesoproterozoic (~1.2-1.3 Ga) melting event [1]. Therefore, oceanic mantle rocks seem to preserve evidence for ancient melting events of global significance. Alternatively, such mantle rocks may be samples of rafts of ancient continental lithospheric mantle. Laser-ablation osmium isotope 'dating' of large populations of individual osmium-bearing alloys from mantle rocks is the key to better constrain the nature and significance of these ancient depletion events. Osmium-bearing alloys form when mantle rocks are melted to high-degrees. We have now extracted over >250 detrital osmium alloys from placer gold occurrences in the river Rhine. These alloys are derived from outcrops of ophiolitic mantle rocks in the Alps, which include blocks of mantle rocks emplaced within the Tethys Ocean, and ultramafic lenses of unknown

  6. Satellite Imagery Analysis for Automated Global Food Security Forecasting

    Science.gov (United States)

    Moody, D.; Brumby, S. P.; Chartrand, R.; Keisler, R.; Mathis, M.; Beneke, C. M.; Nicholaeff, D.; Skillman, S.; Warren, M. S.; Poehnelt, J.

    2017-12-01

    The recent computing performance revolution has driven improvements in sensor, communication, and storage technology. Multi-decadal remote sensing datasets at the petabyte scale are now available in commercial clouds, with new satellite constellations generating petabytes/year of daily high-resolution global coverage imagery. Cloud computing and storage, combined with recent advances in machine learning, are enabling understanding of the world at a scale and at a level of detail never before feasible. We present results from an ongoing effort to develop satellite imagery analysis tools that aggregate temporal, spatial, and spectral information and that can scale with the high-rate and dimensionality of imagery being collected. We focus on the problem of monitoring food crop productivity across the Middle East and North Africa, and show how an analysis-ready, multi-sensor data platform enables quick prototyping of satellite imagery analysis algorithms, from land use/land cover classification and natural resource mapping, to yearly and monthly vegetative health change trends at the structural field level.

  7. Importance measures in global sensitivity analysis of nonlinear models

    International Nuclear Information System (INIS)

    Homma, Toshimitsu; Saltelli, Andrea

    1996-01-01

    The present paper deals with a new method of global sensitivity analysis of nonlinear models. This is based on a measure of importance to calculate the fractional contribution of the input parameters to the variance of the model prediction. Measures of importance in sensitivity analysis have been suggested by several authors, whose work is reviewed in this article. More emphasis is given to the developments of sensitivity indices by the Russian mathematician I.M. Sobol'. Given that Sobol' treatment of the measure of importance is the most general, his formalism is employed throughout this paper where conceptual and computational improvements of the method are presented. The computational novelty of this study is the introduction of the 'total effect' parameter index. This index provides a measure of the total effect of a given parameter, including all the possible synergetic terms between that parameter and all the others. Rank transformation of the data is also introduced in order to increase the reproducibility of the method. These methods are tested on a few analytical and computer models. The main conclusion of this work is the identification of a sensitivity analysis methodology which is both flexible, accurate and informative, and which can be achieved at reasonable computational cost

  8. Accuracy analysis of the 2014–2015 Global Shuttle Radar ...

    Indian Academy of Sciences (India)

    1KIIT University, Bhubaneswar 751 024, India. 2Continental ... Global Shuttle Radar Topography Mission (SRTM) data products have been widely used in Earth. Sciences ..... tional GNSS Service in a changing landscape of Global. Navigation ...

  9. The world as the new local clinic: a critical analysis of three discourses of global medical competency.

    Science.gov (United States)

    Martimianakis, Maria Athina Tina; Hafferty, Frederic W

    2013-06-01

    The effects of globalization on health are the focus of administrators, educators, policy makers and researchers as they work to consider how best to train and regulate health professionals to practice in a globalized world. This study explores what happens to constructs such as medical competence when the context of medical practice is discursively expanded to include the whole world. An archive of texts was assembled (1970-2011) totaling 1100 items and analyzed using a governmentality approach. Texts were included that articulated rationales for pursuing global education activities, and/or that implicitly or explicitly took a position on medical competencies in relation to practicing medicine in international or culturally diverse contexts, or in dealing with health issues as global concerns. The analysis revealed three distinct visions, representative of a primarily western mentality, for preparing physicians to practice in a globalized world: the universal global physician, the culturally versed global physician and the global physician advocate. Each has its own epistemological relationship to globalization and is supported by an evidence base. All three discourses are active and productive, sometimes within the same context. However, the discourse of the universal global physician is currently the most established. The challenge to policy makers and educators in evolving regulatory frameworks and curricula that are current and relevant necessitates a better understanding of the socio-political effects of globalization on medical education, and the ethical, political, cultural and scientific issues underlying efforts to prepare students to practice competently in a globalized world. Copyright © 2013 Elsevier Ltd. All rights reserved.

  10. Visualization and analysis of eddies in a global ocean simulation

    Energy Technology Data Exchange (ETDEWEB)

    Williams, Sean J [Los Alamos National Laboratory; Hecht, Matthew W [Los Alamos National Laboratory; Petersen, Mark [Los Alamos National Laboratory; Strelitz, Richard [Los Alamos National Laboratory; Maltrud, Mathew E [Los Alamos National Laboratory; Ahrens, James P [Los Alamos National Laboratory; Hlawitschka, Mario [UC DAVIS; Hamann, Bernd [UC DAVIS

    2010-10-15

    Eddies at a scale of approximately one hundred kilometers have been shown to be surprisingly important to understanding large-scale transport of heat and nutrients in the ocean. Due to difficulties in observing the ocean directly, the behavior of eddies below the surface is not very well understood. To fill this gap, we employ a high-resolution simulation of the ocean developed at Los Alamos National Laboratory. Using large-scale parallel visualization and analysis tools, we produce three-dimensional images of ocean eddies, and also generate a census of eddy distribution and shape averaged over multiple simulation time steps, resulting in a world map of eddy characteristics. As expected from observational studies, our census reveals a higher concentration of eddies at the mid-latitudes than the equator. Our analysis further shows that mid-latitude eddies are thicker, within a range of 1000-2000m, while equatorial eddies are less than 100m thick.

  11. Relative Quantitative Proteomic Analysis of Brucella abortus Reveals Metabolic Adaptation to Multiple Environmental Stresses.

    Science.gov (United States)

    Zai, Xiaodong; Yang, Qiaoling; Yin, Ying; Li, Ruihua; Qian, Mengying; Zhao, Taoran; Li, Yaohui; Zhang, Jun; Fu, Ling; Xu, Junjie; Chen, Wei

    2017-01-01

    Brucella spp. are facultative intracellular pathogens that cause chronic brucellosis in humans and animals. The virulence of Brucella primarily depends on its successful survival and replication in host cells. During invasion of the host tissue, Brucella is simultaneously subjected to a variety of harsh conditions, including nutrient limitation, low pH, antimicrobial defenses, and extreme levels of reactive oxygen species (ROS) via the host immune response. This suggests that Brucella may be able to regulate its metabolic adaptation in response to the distinct stresses encountered during its intracellular infection of the host. An investigation into the differential proteome expression patterns of Brucella grown under the relevant stress conditions may contribute toward a better understanding of its pathogenesis and adaptive response. Here, we utilized a mass spectrometry-based label-free relative quantitative proteomics approach to investigate and compare global proteomic changes in B. abortus in response to eight different stress treatments. The 3 h short-term in vitro single-stress and multi-stress conditions mimicked the in vivo conditions of B. abortus under intracellular infection, with survival rates ranging from 3.17 to 73.17%. The proteomic analysis identified and quantified a total of 2,272 proteins and 74% of the theoretical proteome, thereby providing wide coverage of the B. abortus proteome. By including eight distinct growth conditions and comparing these with a control condition, we identified a total of 1,221 differentially expressed proteins (DEPs) that were significantly changed under the stress treatments. Pathway analysis revealed that most of the proteins were involved in oxidative phosphorylation, ABC transporters, two-component systems, biosynthesis of secondary metabolites, the citrate cycle, thiamine metabolism, and nitrogen metabolism; constituting major response mechanisms toward the reconstruction of cellular homeostasis and metabolic

  12. Relative Quantitative Proteomic Analysis of Brucella abortus Reveals Metabolic Adaptation to Multiple Environmental Stresses

    Directory of Open Access Journals (Sweden)

    Xiaodong Zai

    2017-11-01

    Full Text Available Brucella spp. are facultative intracellular pathogens that cause chronic brucellosis in humans and animals. The virulence of Brucella primarily depends on its successful survival and replication in host cells. During invasion of the host tissue, Brucella is simultaneously subjected to a variety of harsh conditions, including nutrient limitation, low pH, antimicrobial defenses, and extreme levels of reactive oxygen species (ROS via the host immune response. This suggests that Brucella may be able to regulate its metabolic adaptation in response to the distinct stresses encountered during its intracellular infection of the host. An investigation into the differential proteome expression patterns of Brucella grown under the relevant stress conditions may contribute toward a better understanding of its pathogenesis and adaptive response. Here, we utilized a mass spectrometry-based label-free relative quantitative proteomics approach to investigate and compare global proteomic changes in B. abortus in response to eight different stress treatments. The 3 h short-term in vitro single-stress and multi-stress conditions mimicked the in vivo conditions of B. abortus under intracellular infection, with survival rates ranging from 3.17 to 73.17%. The proteomic analysis identified and quantified a total of 2,272 proteins and 74% of the theoretical proteome, thereby providing wide coverage of the B. abortus proteome. By including eight distinct growth conditions and comparing these with a control condition, we identified a total of 1,221 differentially expressed proteins (DEPs that were significantly changed under the stress treatments. Pathway analysis revealed that most of the proteins were involved in oxidative phosphorylation, ABC transporters, two-component systems, biosynthesis of secondary metabolites, the citrate cycle, thiamine metabolism, and nitrogen metabolism; constituting major response mechanisms toward the reconstruction of cellular

  13. The global burden of dengue: an analysis from the Global Burden of Disease Study 2013

    NARCIS (Netherlands)

    J.D. Stanaway (Jeffrey D.); D.S. Shepard (Donald); E.A. Undurraga (Eduardo); Halasa, Y.A. (Yara A); L.E. Coffeng (Luc); Brady, O.J. (Oliver J); Hay, S.I. (Simon I); Bedi, N. (Neeraj); I.M. Bensenor (Isabela M.); C.A. Castañeda-Orjuela (Carlos A); T.-W. Chuang (Ting-Wu); K.B. Gibney (Katherine B); Z.A. Memish (Ziad); A. Rafay (Anwar); K.N. Ukwaja (Kingsley N); N. Yonemoto (Naohiro); C.J.L. Murray (Christopher)

    2016-01-01

    textabstractBackground Dengue is the most common arbovirus infection globally, but its burden is poorly quantified. We estimated dengue mortality, incidence, and burden for the Global Burden of Disease Study 2013. Methods We modelled mortality from vital registration, verbal autopsy, and

  14. Globalization and Shanghai Model: A Retrospective and Prospective Analysis

    Directory of Open Access Journals (Sweden)

    Linsun Cheng

    2012-11-01

    Full Text Available Intended to shed light on the debate on the results of globalization and providebetter understanding of the influences of globalization upon China as well as theworld, this article traces the history of Shanghai’s economic globalization over thepast 170 years since 1843 and demonstrates the benefits and problems Shanghaireceived from (or connected to its economic globalization. Divided into threesections (Globalization, de-globalization and re-globalization of Shanghai’s economy;Manufacturing-Oriented vs. Tertiary-oriented—Shanghai’s Double PriorityStrategy of Economic Growth; Free market, state enterprises, and Shanghai’s mixedeconomy the article summarizes and analyzes several characteristics that madeShanghai a unique model in the history of globalization: In adapting and adoptinginevitable economic globalization, Shanghai created its unique model of economicdevelopment—widely embracing economic globalization; placing Shanghai’seconomy on a solid foundation of both strong modern manufacturing and strongtertiary industry (consisting of finance and insurance, real estate, transportations,post and telecommunication, wholesale and retailing; and creating a mixedeconomic structure with hybrid of private and state owned enterprises. TheShanghai model proves that globalization has been an unavoidable trend as scienceand technology have made the world “smaller” and “smaller.” Actively engaging intoeconomic globalization is the only way for Shanghai, as well as many developingcountries, to accelerate its economic growth.

  15. GLobal Ocean Data Analysis Project (GLODAP) version 1.1 (NODC Accession 0001644)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — The GLobal Ocean Data Analysis Project (GLODAP) is a cooperative effort to coordinate global synthesis projects funded through NOAA/DOE and NSF as part of the Joint...

  16. Application of machine learning methods to histone methylation ChIP-Seq data reveals H4R3me2 globally represses gene expression

    Science.gov (United States)

    2010-01-01

    Background In the last decade, biochemical studies have revealed that epigenetic modifications including histone modifications, histone variants and DNA methylation form a complex network that regulate the state of chromatin and processes that depend on it including transcription and DNA replication. Currently, a large number of these epigenetic modifications are being mapped in a variety of cell lines at different stages of development using high throughput sequencing by members of the ENCODE consortium, the NIH Roadmap Epigenomics Program and the Human Epigenome Project. An extremely promising and underexplored area of research is the application of machine learning methods, which are designed to construct predictive network models, to these large-scale epigenomic data sets. Results Using a ChIP-Seq data set of 20 histone lysine and arginine methylations and histone variant H2A.Z in human CD4+ T-cells, we built predictive models of gene expression as a function of histone modification/variant levels using Multilinear (ML) Regression and Multivariate Adaptive Regression Splines (MARS). Along with extensive crosstalk among the 20 histone methylations, we found H4R3me2 was the most and second most globally repressive histone methylation among the 20 studied in the ML and MARS models, respectively. In support of our finding, a number of experimental studies show that PRMT5-catalyzed symmetric dimethylation of H4R3 is associated with repression of gene expression. This includes a recent study, which demonstrated that H4R3me2 is required for DNMT3A-mediated DNA methylation--a known global repressor of gene expression. Conclusion In stark contrast to univariate analysis of the relationship between H4R3me2 and gene expression levels, our study showed that the regulatory role of some modifications like H4R3me2 is masked by confounding variables, but can be elucidated by multivariate/systems-level approaches. PMID:20653935

  17. Global/local methods research using a common structural analysis framework

    Science.gov (United States)

    Knight, Norman F., Jr.; Ransom, Jonathan B.; Griffin, O. H., Jr.; Thompson, Danniella M.

    1991-01-01

    Methodologies for global/local stress analysis are described including both two- and three-dimensional analysis methods. These methods are being developed within a common structural analysis framework. Representative structural analysis problems are presented to demonstrate the global/local methodologies being developed.

  18. A global sensitivity analysis of crop virtual water content

    Science.gov (United States)

    Tamea, S.; Tuninetti, M.; D'Odorico, P.; Laio, F.; Ridolfi, L.

    2015-12-01

    The concepts of virtual water and water footprint are becoming widely used in the scientific literature and they are proving their usefulness in a number of multidisciplinary contexts. With such growing interest a measure of data reliability (and uncertainty) is becoming pressing but, as of today, assessments of data sensitivity to model parameters, performed at the global scale, are not known. This contribution aims at filling this gap. Starting point of this study is the evaluation of the green and blue virtual water content (VWC) of four staple crops (i.e. wheat, rice, maize, and soybean) at a global high resolution scale. In each grid cell, the crop VWC is given by the ratio between the total crop evapotranspiration over the growing season and the crop actual yield, where evapotranspiration is determined with a detailed daily soil water balance and actual yield is estimated using country-based data, adjusted to account for spatial variability. The model provides estimates of the VWC at a 5x5 arc minutes and it improves on previous works by using the newest available data and including multi-cropping practices in the evaluation. The model is then used as the basis for a sensitivity analysis, in order to evaluate the role of model parameters in affecting the VWC and to understand how uncertainties in input data propagate and impact the VWC accounting. In each cell, small changes are exerted to one parameter at a time, and a sensitivity index is determined as the ratio between the relative change of VWC and the relative change of the input parameter with respect to its reference value. At the global scale, VWC is found to be most sensitive to the planting date, with a positive (direct) or negative (inverse) sensitivity index depending on the typical season of crop planting date. VWC is also markedly dependent on the length of the growing period, with an increase in length always producing an increase of VWC, but with higher spatial variability for rice than for

  19. Cross-covariance based global dynamic sensitivity analysis

    Science.gov (United States)

    Shi, Yan; Lu, Zhenzhou; Li, Zhao; Wu, Mengmeng

    2018-02-01

    For identifying the cross-covariance source of dynamic output at each time instant for structural system involving both input random variables and stochastic processes, a global dynamic sensitivity (GDS) technique is proposed. The GDS considers the effect of time history inputs on the dynamic output. In the GDS, the cross-covariance decomposition is firstly developed to measure the contribution of the inputs to the output at different time instant, and an integration of the cross-covariance change over the specific time interval is employed to measure the whole contribution of the input to the cross-covariance of output. Then, the GDS main effect indices and the GDS total effect indices can be easily defined after the integration, and they are effective in identifying the important inputs and the non-influential inputs on the cross-covariance of output at each time instant, respectively. The established GDS analysis model has the same form with the classical ANOVA when it degenerates to the static case. After degeneration, the first order partial effect can reflect the individual effects of inputs to the output variance, and the second order partial effect can reflect the interaction effects to the output variance, which illustrates the consistency of the proposed GDS indices and the classical variance-based sensitivity indices. The MCS procedure and the Kriging surrogate method are developed to solve the proposed GDS indices. Several examples are introduced to illustrate the significance of the proposed GDS analysis technique and the effectiveness of the proposed solution.

  20. Global analysis of small molecule binding to related protein targets.

    Directory of Open Access Journals (Sweden)

    Felix A Kruger

    2012-01-01

    Full Text Available We report on the integration of pharmacological data and homology information for a large scale analysis of small molecule binding to related targets. Differences in small molecule binding have been assessed for curated pairs of human to rat orthologs and also for recently diverged human paralogs. Our analysis shows that in general, small molecule binding is conserved for pairs of human to rat orthologs. Using statistical tests, we identified a small number of cases where small molecule binding is different between human and rat, some of which had previously been reported in the literature. Knowledge of species specific pharmacology can be advantageous for drug discovery, where rats are frequently used as a model system. For human paralogs, we demonstrate a global correlation between sequence identity and the binding of small molecules with equivalent affinity. Our findings provide an initial general model relating small molecule binding and sequence divergence, containing the foundations for a general model to anticipate and predict within-target-family selectivity.

  1. Global sensitivity analysis for models with spatially dependent outputs

    International Nuclear Information System (INIS)

    Iooss, B.; Marrel, A.; Jullien, M.; Laurent, B.

    2011-01-01

    The global sensitivity analysis of a complex numerical model often calls for the estimation of variance-based importance measures, named Sobol' indices. Meta-model-based techniques have been developed in order to replace the CPU time-expensive computer code with an inexpensive mathematical function, which predicts the computer code output. The common meta-model-based sensitivity analysis methods are well suited for computer codes with scalar outputs. However, in the environmental domain, as in many areas of application, the numerical model outputs are often spatial maps, which may also vary with time. In this paper, we introduce an innovative method to obtain a spatial map of Sobol' indices with a minimal number of numerical model computations. It is based upon the functional decomposition of the spatial output onto a wavelet basis and the meta-modeling of the wavelet coefficients by the Gaussian process. An analytical example is presented to clarify the various steps of our methodology. This technique is then applied to a real hydrogeological case: for each model input variable, a spatial map of Sobol' indices is thus obtained. (authors)

  2. Uncertainty in the global oceanic CO2 uptake induced by wind forcing: quantification and spatial analysis

    Directory of Open Access Journals (Sweden)

    A. Roobaert

    2018-03-01

    Full Text Available The calculation of the air–water CO2 exchange (FCO2 in the ocean not only depends on the gradient in CO2 partial pressure at the air–water interface but also on the parameterization of the gas exchange transfer velocity (k and the choice of wind product. Here, we present regional and global-scale quantifications of the uncertainty in FCO2 induced by several widely used k formulations and four wind speed data products (CCMP, ERA, NCEP1 and NCEP2. The analysis is performed at a 1°  ×  1° resolution using the sea surface pCO2 climatology generated by Landschützer et al. (2015a for the 1991–2011 period, while the regional assessment relies on the segmentation proposed by the Regional Carbon Cycle Assessment and Processes (RECCAP project. First, we use k formulations derived from the global 14C inventory relying on a quadratic relationship between k and wind speed (k = c ⋅ U102; Sweeney et al., 2007; Takahashi et al., 2009; Wanninkhof, 2014, where c is a calibration coefficient and U10 is the wind speed measured 10 m above the surface. Our results show that the range of global FCO2, calculated with these k relationships, diverge by 12 % when using CCMP, ERA or NCEP1. Due to differences in the regional wind patterns, regional discrepancies in FCO2 are more pronounced than global. These global and regional differences significantly increase when using NCEP2 or other k formulations which include earlier relationships (i.e., Wanninkhof, 1992; Wanninkhof et al., 2009 as well as numerous local and regional parameterizations derived experimentally. To minimize uncertainties associated with the choice of wind product, it is possible to recalculate the coefficient c globally (hereafter called c∗ for a given wind product and its spatio-temporal resolution, in order to match the last evaluation of the global k value. We thus performed these recalculations for each wind product at the resolution and time period of our study

  3. Uncertainty in the global oceanic CO2 uptake induced by wind forcing: quantification and spatial analysis

    Science.gov (United States)

    Roobaert, Alizée; Laruelle, Goulven G.; Landschützer, Peter; Regnier, Pierre

    2018-03-01

    The calculation of the air-water CO2 exchange (FCO2) in the ocean not only depends on the gradient in CO2 partial pressure at the air-water interface but also on the parameterization of the gas exchange transfer velocity (k) and the choice of wind product. Here, we present regional and global-scale quantifications of the uncertainty in FCO2 induced by several widely used k formulations and four wind speed data products (CCMP, ERA, NCEP1 and NCEP2). The analysis is performed at a 1° × 1° resolution using the sea surface pCO2 climatology generated by Landschützer et al. (2015a) for the 1991-2011 period, while the regional assessment relies on the segmentation proposed by the Regional Carbon Cycle Assessment and Processes (RECCAP) project. First, we use k formulations derived from the global 14C inventory relying on a quadratic relationship between k and wind speed (k = c ṡ U102; Sweeney et al., 2007; Takahashi et al., 2009; Wanninkhof, 2014), where c is a calibration coefficient and U10 is the wind speed measured 10 m above the surface. Our results show that the range of global FCO2, calculated with these k relationships, diverge by 12 % when using CCMP, ERA or NCEP1. Due to differences in the regional wind patterns, regional discrepancies in FCO2 are more pronounced than global. These global and regional differences significantly increase when using NCEP2 or other k formulations which include earlier relationships (i.e., Wanninkhof, 1992; Wanninkhof et al., 2009) as well as numerous local and regional parameterizations derived experimentally. To minimize uncertainties associated with the choice of wind product, it is possible to recalculate the coefficient c globally (hereafter called c∗) for a given wind product and its spatio-temporal resolution, in order to match the last evaluation of the global k value. We thus performed these recalculations for each wind product at the resolution and time period of our study but the resulting global FCO2 estimates

  4. Quantitative genome-wide genetic interaction screens reveal global epistatic relationships of protein complexes in Escherichia coli.

    Directory of Open Access Journals (Sweden)

    Mohan Babu

    2014-02-01

    Full Text Available Large-scale proteomic analyses in Escherichia coli have documented the composition and physical relationships of multiprotein complexes, but not their functional organization into biological pathways and processes. Conversely, genetic interaction (GI screens can provide insights into the biological role(s of individual gene and higher order associations. Combining the information from both approaches should elucidate how complexes and pathways intersect functionally at a systems level. However, such integrative analysis has been hindered due to the lack of relevant GI data. Here we present a systematic, unbiased, and quantitative synthetic genetic array screen in E. coli describing the genetic dependencies and functional cross-talk among over 600,000 digenic mutant combinations. Combining this epistasis information with putative functional modules derived from previous proteomic data and genomic context-based methods revealed unexpected associations, including new components required for the biogenesis of iron-sulphur and ribosome integrity, and the interplay between molecular chaperones and proteases. We find that functionally-linked genes co-conserved among γ-proteobacteria are far more likely to have correlated GI profiles than genes with divergent patterns of evolution. Overall, examining bacterial GIs in the context of protein complexes provides avenues for a deeper mechanistic understanding of core microbial systems.

  5. Global analysis of general SU(2) x SU(2) x U(1) models with precision data

    Energy Technology Data Exchange (ETDEWEB)

    Hsieh, Ken; Yu, Jiang-Hao; Yuan, C.P. [Michigan State Univ., East Lansing, MI (United States). Dept. of Physics and Astronomy; Schmitz, Kai [Deutsches Elektronen-Synchrotron (DESY), Hamburg (Germany); Michigan State Univ., East Lansing, MI (United States). Dept. of Physics and Astronomy

    2010-05-15

    We present the results of a global analysis of a class of models with an extended electroweak gauge group of the form SU(2) x SU(2) x U(1), often denoted as G(221) models, which include as examples the left-right, the lepto-phobic, the hadro-phobic, the fermio-phobic, the un-unified, and the non-universal models. Using an effective Lagrangian approach, we compute the shifts to the coeffcients in the electroweak Lagrangian due to the new heavy gauge bosons, and obtain the lower bounds on the masses of the Z' and W' bosons. The analysis of the electroweak parameter bounds reveals a consistent pattern of several key observables that are especially sensitive to the effects of new physics and thus dominate the overall shape of the respective parameter contours. (orig.)

  6. Global analysis of general SU(2) x SU(2) x U(1) models with precision data

    International Nuclear Information System (INIS)

    Hsieh, Ken; Yu, Jiang-Hao; Yuan, C.P.; Schmitz, Kai; Michigan State Univ., East Lansing, MI

    2010-05-01

    We present the results of a global analysis of a class of models with an extended electroweak gauge group of the form SU(2) x SU(2) x U(1), often denoted as G(221) models, which include as examples the left-right, the lepto-phobic, the hadro-phobic, the fermio-phobic, the un-unified, and the non-universal models. Using an effective Lagrangian approach, we compute the shifts to the coeffcients in the electroweak Lagrangian due to the new heavy gauge bosons, and obtain the lower bounds on the masses of the Z' and W' bosons. The analysis of the electroweak parameter bounds reveals a consistent pattern of several key observables that are especially sensitive to the effects of new physics and thus dominate the overall shape of the respective parameter contours. (orig.)

  7. Global processing takes time: A meta-analysis on local-global visual processing in ASD

    OpenAIRE

    Van der Hallen, Ruth; Evers, Kris; Brewaeys, K.; Van Den Noortgate, Wim; Wagemans, Johan

    2015-01-01

    What does an individual with autism spectrum disorder (ASD) perceive first: the forest or the trees? In spite of 30 years of research and influential theories like the weak central coherence (WCC) theory and the enhanced perceptual functioning (EPF) account, the interplay of local and global visual processing in ASD remains only partly understood. Research findings vary in indicating a local processing bias or a global processing deficit, and often contradict each other. We have applied a for...

  8. Global Analysis of Palmitoylated Proteins in Toxoplasma gondii.

    Science.gov (United States)

    Foe, Ian T; Child, Matthew A; Majmudar, Jaimeen D; Krishnamurthy, Shruthi; van der Linden, Wouter A; Ward, Gary E; Martin, Brent R; Bogyo, Matthew

    2015-10-14

    Post-translational modifications (PTMs) such as palmitoylation are critical for the lytic cycle of the protozoan parasite Toxoplasma gondii. While palmitoylation is involved in invasion, motility, and cell morphology, the proteins that utilize this PTM remain largely unknown. Using a chemical proteomic approach, we report a comprehensive analysis of palmitoylated proteins in T. gondii, identifying a total of 282 proteins, including cytosolic, membrane-associated, and transmembrane proteins. From this large set of palmitoylated targets, we validate palmitoylation of proteins involved in motility (myosin light chain 1, myosin A), cell morphology (PhIL1), and host cell invasion (apical membrane antigen 1, AMA1). Further studies reveal that blocking AMA1 palmitoylation enhances the release of AMA1 and other invasion-related proteins from apical secretory organelles, suggesting a previously unrecognized role for AMA1. These findings suggest that palmitoylation is ubiquitous throughout the T. gondii proteome and reveal insights into the biology of this important human pathogen. Copyright © 2015 Elsevier Inc. All rights reserved.

  9. MRSA: a density-equalizing mapping analysis of the global research architecture.

    Science.gov (United States)

    Addicks, Johann P; Uibel, Stefanie; Jensen, Anna-Maria; Bundschuh, Matthias; Klingelhoefer, Doris; Groneberg, David A

    2014-09-30

    Methicillin-resistant Staphylococcus aureus (MRSA) has evolved as an alarming public health thread due to its global spread as hospital and community pathogen. Despite this role, a scientometric analysis has not been performed yet. Therefore, the NewQIS platform was used to conduct a combined density-equalizing mapping and scientometric study. As database, the Web of Science was used, and all entries between 1961 and 2007 were analyzed. In total, 7671 entries were identified. Density equalizing mapping demonstrated a distortion of the world map for the benefit of the USA as leading country with a total output of 2374 publications, followed by the UK (1030) and Japan (862). Citation rate analysis revealed Portugal as leading country with a rate of 35.47 citations per article, followed by New Zealand and Denmark. Country cooperation network analyses showed 743 collaborations with US-UK being most frequent. Network citation analyses indicated the publications that arose from the cooperation of USA and France as well as USA and Japan as the most cited (75.36 and 74.55 citations per collaboration article, respectively). The present study provides the first combined density-equalizing mapping and scientometric analysis of MRSA research. It illustrates the global MRSA research architecture. It can be assumed that this highly relevant topic for public health will achieve even greater dimensions in the future.

  10. UNEARTHING GLOBAL FINANCIAL INCLUSION LEVELS AND ANALYSIS OF FINANCIAL INCLUSION AS A MEDIATING FACTOR IN GLOBAL HUMAN DEVELOPMENT

    Directory of Open Access Journals (Sweden)

    Roshny Unnikrishnan

    2015-04-01

    Full Text Available This study is a result of the author’s inquisition to unearth the current values of Global Financial Inclusion and its relationship with economic growth measured by Gross Domestic product(GDP and human development measured by United Nations Human Development Index (HDI. The Financial Inclusion (FI levels are measured using Index for Financial Inclusion .The relationship between GDP and HDI with FI as mediator, using multiple regression, is validated on a global level based on data of 162 countries for the year 2011. An overall global mediation analysis is undertaken to establish Financial Inclusion as a mediating factor and partial mediation on human development is validated. The study is valid and unique in the global context of income inequality prevailing in developed, developing and underdeveloped countries as it validates the argument that an impressive GDP performance does not ensure equity in economic growth.

  11. Analysis of global water vapour trends from satellite measurements in the visible spectral range

    Directory of Open Access Journals (Sweden)

    S. Mieruch

    2008-02-01

    Full Text Available Global water vapour total column amounts have been retrieved from spectral data provided by the Global Ozone Monitoring Experiment (GOME flying on ERS-2, which was launched in April 1995, and the SCanning Imaging Absorption spectroMeter for Atmospheric CHartographY (SCIAMACHY onboard ENVISAT launched in March 2002. For this purpose the Air Mass Corrected Differential Optical Absorption Spectroscopy (AMC-DOAS approach has been used. The combination of the data from both instruments provides us with a long-term global data set spanning more than 11 years with the potential of extension up to 2020 by GOME-2 data on MetOp.

    Using linear and non-linear methods from time series analysis and standard statistics the trends of H2O columns and their errors have been calculated. In this study, factors affecting the trend such as the length of the time series, the magnitude of the variability of the noise, and the autocorrelation of the noise are investigated. Special emphasis has been placed on the calculation of the statistical significance of the observed trends, which reveal significant local changes from −5% per year to +5% per year. These significant trends are distributed over the whole globe. Increasing trends have been calculated for Greenland, East Europe, Siberia and Oceania, whereas decreasing trends have been observed for the northwest USA, Central America, Amazonia, Central Africa and the Arabian Peninsular.

  12. Bacterial meningitis: a density-equalizing mapping analysis of the global research architecture.

    Science.gov (United States)

    Pleger, Niklas; Kloft, Beatrix; Quarcoo, David; Zitnik, Simona; Mache, Stefanie; Klingelhoefer, Doris; Groneberg, David A

    2014-09-30

    Bacterial meningitis is caused by a variety of pathogens and displays an important public health threat all over the world. Despite the necessity to develop customized public health-related research projects, a thorough study of global meningitis research is not present, so far. Therefore, the aim of this study was a combined density-equalizing and scientometric study. To evaluate the scientific efforts of bibliometric methods, density-equalizing algorithms and large-scale data analysis of the Web of Science were applied in the period between 1900 and 2007. From this, 7998 publications on bacterial meningitis have been found. With a number of 2698, most publications have been written by U.S. authors, followed by the UK (912), Germany (749) and France (620). This dominance can also be shown in the international cooperation. The specific citation analyses reveal that the nation with the highest average citation rate (citations per publications) was Norway (26.36), followed by Finland (24.16) and the U.S. (24.06). This study illustrates the architecture of global research on bacterial meningitis and points to the need for customized research programs with a focus on local public health issues in countries with a low development index, but high incidences, to target this global public health problem.

  13. Comparative proteomic and metabolomic analysis reveal the antiosteoporotic molecular mechanism of icariin from Epimedium brevicornu maxim.

    Science.gov (United States)

    Xue, Liming; Jiang, Yiping; Han, Ting; Zhang, Naidan; Qin, Luping; Xin, Hailiang; Zhang, Qiaoyan

    2016-11-04

    Icariin, a principal flavonoid glycoside of Epimedium brevicornu Maxim, has been widely proved to possess antiosteoporotic activity with promoting bone formation and decreasing bone resorption. However, the involving mechanisms remain unclear. To clear a global insight of signal pathways involved in anti-osteoporotic mechanism of icariin at proteins and metabolites level by integrating the proteomics and NMR metabonomics, in a systems biology approach. Mice were divided into sham, OVX model and icariin-treated OVX group, after 90 days treatment, difference gel electrophoresis combined with MALDI-TOF/TOF proteomics analysis on bone femur and serum metabolomics were carried out for monitor intracellular processes and elucidate anti-osteoporotic mechanism of icariin. Osteoblast and osteoclast were applied to evaluate the potential signal pathways. Twenty three proteins in bone femur, and 8 metabolites in serum, were significantly altered and identified, involving in bone remodeling, energy metabolism, cytoskeleton, lipid metabolism, MAPK signaling, Ca 2+ signaling et, al. Furthermore, animal experiment show icariin could enhance the BMD and BMC, decrease CTX-I level in ovariectomized mice. The mitochondrial membrane potential and the intracellular ATP levels were increased significantly, and the cytoskeleton were improved in icariin-treatment osteoblast and osteoclast. Icariin also increased mRNA expression of Runx2 and osterix of OB, decreased CTR and CAII mRNA expression and protein expression of P38 and JNK. However, icariin did not reveal any inhibition of the collagenolytic activity of cathepsin K, mRNA expression of MMP-9 and protein expression of ERK in osteoclast. we consider icariin as multi-targeting compounds for treating with osteoporosis, involve initiating osteoblastogenesis, inhibiting adipogenesis, and preventing osteoclast differentiation. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

  14. Advancing Collaborative Climate Studies through Globally Distributed Geospatial Analysis

    Science.gov (United States)

    Singh, R.; Percivall, G.

    2009-12-01

    Infrastructure and the broader GEOSS architecture. Of specific interest to this session is the work on geospatial workflows and geo-processing and data discovery and access. CCIP demonstrates standards-based interoperability between geospatial applications in the service of Climate Change analysis. CCIP is planned to be a yearly exercise. It consists of a network of online data services (WCS, WFS, SOS), analysis services (WPS, WCPS, WMS), and clients that exercise those services. In 2009, CCIP focuses on Australia, and the initial application of existing OGC services to climate studies. The results of the 2009 CCIP will serve as requirements for more complex geo-processing services to be developed for CCIP 2010. The benefits of CCIP include accelerating the implementation of the GCOS, and building confidence that implementations using multi-vendor interoperable technologies can help resolve vexing climate change questions. AIP-2: Architecture Implementation Pilot, Phase 2 CCIP: Climate Challenge Integration Plugfest GEO: Group on Earth Observations GEOSS: Global Earth Observing System of Systems GCOS: Global Climate Observing System OGC: Open Geospatial Consortium SOS: Sensor Observation Service WCS: Web Coverage Service WCPS: Web Coverage Processing Service WFS: Web Feature Service WMS: Web Mapping Service

  15. Global Sensitivity Analysis for multivariate output using Polynomial Chaos Expansion

    International Nuclear Information System (INIS)

    Garcia-Cabrejo, Oscar; Valocchi, Albert

    2014-01-01

    Many mathematical and computational models used in engineering produce multivariate output that shows some degree of correlation. However, conventional approaches to Global Sensitivity Analysis (GSA) assume that the output variable is scalar. These approaches are applied on each output variable leading to a large number of sensitivity indices that shows a high degree of redundancy making the interpretation of the results difficult. Two approaches have been proposed for GSA in the case of multivariate output: output decomposition approach [9] and covariance decomposition approach [14] but they are computationally intensive for most practical problems. In this paper, Polynomial Chaos Expansion (PCE) is used for an efficient GSA with multivariate output. The results indicate that PCE allows efficient estimation of the covariance matrix and GSA on the coefficients in the approach defined by Campbell et al. [9], and the development of analytical expressions for the multivariate sensitivity indices defined by Gamboa et al. [14]. - Highlights: • PCE increases computational efficiency in 2 approaches of GSA of multivariate output. • Efficient estimation of covariance matrix of output from coefficients of PCE. • Efficient GSA on coefficients of orthogonal decomposition of the output using PCE. • Analytical expressions of multivariate sensitivity indices from coefficients of PCE

  16. Global analysis of ICRF wave coupling on Tore Supra

    International Nuclear Information System (INIS)

    Goniche, M.; Bremond, S.; Colas, L.

    2003-01-01

    The Tore Supra tokamak is equipped with a multi-megawatt ion cyclotron range of frequency (ICRF) system for heating and current drive. The coupling of the fast wave to the plasma, characterized by the distributed coupling resistance along the radiating straps, is a crucial issue in order to launch large RF powers. Many factors can have an effect on ICRF wave coupling. Quantitative prediction from theoretical modelling requires the knowledge of the local inhomogeneous plasma density profile in front of the antenna for running sophisticated antenna codes. In this work, we have rather followed a 'global' approach, based on Tore Supra experimental results, for the parametric study of the coupling resistance. From a large data base covering seven experimental campaigns (∼2250 shots), a scaling law of the coupling resistance including the main parameters of the plasma and of the antenna configuration is established. This approach is found to be reliable for the analysis of coupling in the different scenarios: He/D 2 gas filling, gas/pellets for plasma fuelling, plasma leaning on inner wall/low field side limiter, limiter/ergodic divertor configuration, minority heating/direct electron heating. From one scenario to another, a significant variation of the coefficients of the scaling law is found. The study of these variations allows to get some insight on the main physical mechanisms which influence the ICRF wave coupling in a tokamak operation, such as the wall conditioning and recycling conditions, RF sheaths or frequency. (author)

  17. Introduction to global analysis minimal surfaces in Riemannian manifolds

    CERN Document Server

    Moore, John Douglas

    2017-01-01

    During the last century, global analysis was one of the main sources of interaction between geometry and topology. One might argue that the core of this subject is Morse theory, according to which the critical points of a generic smooth proper function on a manifold M determine the homology of the manifold. Morse envisioned applying this idea to the calculus of variations, including the theory of periodic motion in classical mechanics, by approximating the space of loops on M by a finite-dimensional manifold of high dimension. Palais and Smale reformulated Morse's calculus of variations in terms of infinite-dimensional manifolds, and these infinite-dimensional manifolds were found useful for studying a wide variety of nonlinear PDEs. This book applies infinite-dimensional manifold theory to the Morse theory of closed geodesics in a Riemannian manifold. It then describes the problems encountered when extending this theory to maps from surfaces instead of curves. It treats critical point theory for closed param...

  18. Learner Analysis Framework for Globalized E-Learning

    Science.gov (United States)

    Saxena, Mamta

    2010-01-01

    The digital shift to technology-mediated modes of instructional delivery and the increased global connectivity has led to the rise in globalized e-learning programs. Educational institutions face multiple challenges as they seek to design effective, engaging and culturally competent instruction for an increasingly diverse learner population. The…

  19. An Analysis of Globalization and Higher Education in Malaysia

    Science.gov (United States)

    Arokiasamy, Anantha Raj A.

    2011-01-01

    This study aims to examine the impact of globalization on private higher education in Malaysia. The impact of globalization and the development of knowledge-based economy have caused much dramatic change to the character and functions of higher education in Malaysia. The major trend is the reforming and restructuring of private higher education in…

  20. Global Proteome Analysis of the NCI-60 Cell Line Panel

    Directory of Open Access Journals (Sweden)

    Amin Moghaddas Gholami

    2013-08-01

    Full Text Available The NCI-60 cell line collection is a very widely used panel for the study of cellular mechanisms of cancer in general and in vitro drug action in particular. It is a model system for the tissue types and genetic diversity of human cancers and has been extensively molecularly characterized. Here, we present a quantitative proteome and kinome profile of the NCI-60 panel covering, in total, 10,350 proteins (including 375 protein kinases and including a core cancer proteome of 5,578 proteins that were consistently quantified across all tissue types. Bioinformatic analysis revealed strong cell line clusters according to tissue type and disclosed hundreds of differentially regulated proteins representing potential biomarkers for numerous tumor properties. Integration with public transcriptome data showed considerable similarity between mRNA and protein expression. Modeling of proteome and drug-response profiles for 108 FDA-approved drugs identified known and potential protein markers for drug sensitivity and resistance. To enable community access to this unique resource, we incorporated it into a public database for comparative and integrative analysis (http://wzw.tum.de/proteomics/nci60.

  1. Global carbon monoxide cycle: Modeling and data analysis

    Science.gov (United States)

    Arellano, Avelino F., Jr.

    The overarching goal of this dissertation is to develop robust, spatially and temporally resolved CO sources, using global chemical transport modeling, CO measurements from Climate Monitoring and Diagnostic Laboratory (CMDL) and Measurement of Pollution In The Troposphere (MOPITT), under the framework of Bayesian synthesis inversion. To rigorously quantify the CO sources, I conducted five sets of inverse analyses, with each set investigating specific methodological and scientific issues. The first two inverse analyses separately explored two different CO observations to estimate CO sources by region and sector. Under a range of scenarios relating to inverse methodology and data quality issues, top-down estimates using CMDL CO surface and MOPITT CO remote-sensed measurements show consistent results particularly on a significantly large fossil fuel/biofuel (FFBF) emission in East Asia than present bottom-up estimates. The robustness of this estimate is strongly supported by forward and inverse modeling studies in the region particularly from TRansport and Chemical Evolution over the Pacific (TRACE-P) campaign. The use of high-resolution measurement for the first time in CO inversion also draws attention to a methodology issue that the range of estimates from the scenarios is larger than posterior uncertainties, suggesting that estimate uncertainties may be underestimated. My analyses highlight the utility of top-down approach to provide additional constraints on present global estimates by also pointing to other discrepancies including apparent underestimation of FFBF from Africa/Latin America and biomass burning (BIOM) sources in Africa, southeast Asia and north-Latin America, indicating inconsistencies on our current understanding of fuel use and land-use patterns in these regions. Inverse analysis using MOPITT is extended to determine the extent of MOPITT information and estimate monthly regional CO sources. A major finding, which is consistent with other

  2. Reconstruction of the yeast Snf1 kinase regulatory network reveals its role as a global energy regulator

    DEFF Research Database (Denmark)

    Usaite, Renata; Jewett, Michael Christopher; Soberano de Oliveira, Ana Paula

    2009-01-01

    Highly conserved among eukaryotic cells, the AMP-activated kinase (AMPK) is a central regulator of carbon metabolism. To map the complete network of interactions around AMPK in yeast (Snf1) and to evaluate the role of its regulatory subunit Snf4, we measured global mRNA, protein and metabolite...

  3. Development of a Sampling-Based Global Sensitivity Analysis Workflow for Multiscale Computational Cancer Models

    Science.gov (United States)

    Wang, Zhihui; Deisboeck, Thomas S.; Cristini, Vittorio

    2014-01-01

    There are two challenges that researchers face when performing global sensitivity analysis (GSA) on multiscale in silico cancer models. The first is increased computational intensity, since a multiscale cancer model generally takes longer to run than does a scale-specific model. The second problem is the lack of a best GSA method that fits all types of models, which implies that multiple methods and their sequence need to be taken into account. In this article, we therefore propose a sampling-based GSA workflow consisting of three phases – pre-analysis, analysis, and post-analysis – by integrating Monte Carlo and resampling methods with the repeated use of analysis of variance (ANOVA); we then exemplify this workflow using a two-dimensional multiscale lung cancer model. By accounting for all parameter rankings produced by multiple GSA methods, a summarized ranking is created at the end of the workflow based on the weighted mean of the rankings for each input parameter. For the cancer model investigated here, this analysis reveals that ERK, a downstream molecule of the EGFR signaling pathway, has the most important impact on regulating both the tumor volume and expansion rate in the algorithm used. PMID:25257020

  4. Economic analysis of the global polio eradication initiative.

    Science.gov (United States)

    Duintjer Tebbens, Radboud J; Pallansch, Mark A; Cochi, Stephen L; Wassilak, Steven G F; Linkins, Jennifer; Sutter, Roland W; Aylward, R Bruce; Thompson, Kimberly M

    2010-12-16

    The global polio eradication initiative (GPEI), which started in 1988, represents the single largest, internationally coordinated public health project to date. Completion remains within reach, with type 2 wild polioviruses apparently eradicated since 1999 and fewer than 2000 annual paralytic poliomyelitis cases of wild types 1 and 3 reported since then. This economic analysis of the GPEI reflects the status of the program as of February 2010, including full consideration of post-eradication policies. For the GPEI intervention, we consider the actual pre-eradication experience to date followed by two distinct potential future post-eradication vaccination policies. We estimate GPEI costs based on actual and projected expenditures and poliomyelitis incidence using reported numbers corrected for underreporting and model projections. For the comparator, which assumes only routine vaccination for polio historically and into the future (i.e., no GPEI), we estimate poliomyelitis incidence using a dynamic infection transmission model and costs based on numbers of vaccinated children. Cost-effectiveness ratios for the GPEI vs. only routine vaccination qualify as highly cost-effective based on standard criteria. We estimate incremental net benefits of the GPEI between 1988 and 2035 of approximately 40-50 billion dollars (2008 US dollars; 1988 net present values). Despite the high costs of achieving eradication in low-income countries, low-income countries account for approximately 85% of the total net benefits generated by the GPEI in the base case analysis. The total economic costs saved per prevented paralytic poliomyelitis case drive the incremental net benefits, which become positive even if we estimate the loss in productivity as a result of disability as below the recommended value of one year in average per-capita gross national income per disability-adjusted life year saved. Sensitivity analysis suggests that the finding of positive net benefits of the GPEI remains

  5. Polycystic ovary syndrome: analysis of the global research architecture using density equalizing mapping.

    Science.gov (United States)

    Brüggmann, Dörthe; Berges, Lea; Klingelhöfer, Doris; Bauer, Jan; Bendels, Michael; Louwen, Frank; Jaque, Jenny; Groneberg, David A

    2017-06-01

    Polycystic ovary syndrome (PCOS) is the most common cause of female infertility worldwide. Although the related research output is constantly growing, no detailed global map of the scientific architecture has so far been created encompassing quantitative, qualitative, socioeconomic and gender aspects. We used the NewQIS platform to assess all PCOS-related publications indexed between 1900 and 2014 in the Web of Science, and applied density equalizing mapping projections, scientometric techniques and economic benchmarking procedures. A total of 6261 PCOS-specific publications and 703 international research collaborations were found. The USA was identified as the most active country in total and collaborative research activity. In the socioeconomic analysis, the USA was also ranked first (25.49 PCOS-related publications per gross domestic product [GDP]/capita), followed by the UK, Italy and Greece. When research activity was related to population size, Scandinavian countries and Greece were leading the field. For many highly productive countries, gender analysis revealed a high ratio of female scientists working on PCOS with the exception of Japan. In this study, we have created the first picture of global PCOS research, which largely differs from other gynaecologic conditions and indicates that most related research and collaborations originate from high-income countries. Copyright © 2017 Reproductive Healthcare Ltd. Published by Elsevier Ltd. All rights reserved.

  6. A reflective discussion: questions about globalization and multiculturalism in nursing as revealed during a student/staff exchange programme.

    Science.gov (United States)

    Graham, Iain; Norman, Linda

    2008-06-01

    The purpose of this paper is to present elements of a discussion on the discipline of nursing that arose from a student-faculty exchange programme, as a reflection of the experiences the students and faculty had during the 3-year exchange. It suggests that the globalization of health and the international migration of nurses might prove to be an opportunity for nurses to learn more about nursing practice. It became apparent to the participants that the phenomenon of nursing, although understood by them all, was not easy to describe, and words used in Swedish, Finnish or British or American English were often not easy to interpret or explain. These reflections were noted by the authors when the group came together to plan the programme and design experiences for the participants. We were concerned how nursing could contribute to health-care improvement globally if it wasn't universally understood within the four countries concerned.

  7. Global architecture of gestational diabetes research: density-equalizing mapping studies and gender analysis.

    Science.gov (United States)

    Brüggmann, Dörthe; Richter, Theresa; Klingelhöfer, Doris; Gerber, Alexander; Bundschuh, Matthias; Jaque, Jenny; Groneberg, David A

    2016-04-04

    Gestational diabetes mellitus (GDM) is associated with substantial morbidity for mothers and their offspring. While clinical and basic research activities on this important disease grow constantly, there is no concise analysis of global architecture of GDM research. Hence, it was the objective of this study to assess the global scientific performance chronologically, geographically and in relation to existing research networks and gender distribution of publishing authors. On the basis of the New Quality and Quantity Indices in Science (NewQIS) platform, scientometric methods were combined with modern visualizing techniques such as density equalizing mapping, and the Web of Science database was used to assess GDM-related entries from 1900 to 2012. Twelve thousand five hundred four GDM-related publications were identified and analyzed. The USA (4295 publications) and the UK (1354 publications) dominated the field concerning research activity, overall citations and country-specific Hirsch-Index, which quantified the impact of a country's published research on the scientific community. Semi-qualitative indices such as country-specific citation rates ranked New Zealand and the UK at top positions. Annual collaborative publications increased steeply between the years 1990 and 2012 (71 to 1157 respectively). Subject category analysis pointed to a minor interest of public health issues in GDM research. Gender analysis in terms of publication authorship revealed a clear dominance of the male gender until 2005; then a trend towards gender equity started and the activity of female scientists grew visibly in many countries. The country-specific gender analysis revealed large differences, i.e. female scientists dominated the scientific output in the USA, whereas the majority of research was published by male authors in countries such as Japan. This study provides the first global sketch of GDM research architecture. While North-American and Western-European countries were

  8. Global sensitivity analysis in stochastic simulators of uncertain reaction networks

    KAUST Repository

    Navarro, Marí a; Le Maitre, Olivier; Knio, Omar

    2016-01-01

    sources are independent, and considers the Poisson processes in the random-time-change representation of the state dynamics as the fundamental objects governing the inherent stochasticity. A sampling algorithm is proposed to perform the global sensitivity

  9. The credibility challenge for global fluvial flood risk analysis

    NARCIS (Netherlands)

    Trigg, M.A.; Birch, C.E.; Neal, J.C.; Bates, P.D.; Smith, A.; Sampson, C.C.; Yamazaki, D.; Hirabayashi, Y.; Pappenberger, F.; Dutra, E.; Ward, P.J.; Winsemius, H.C.; Salamon, P.; Dottori, F.; Rudari, R.; Kappes, M.S.; Simpson, A.L.; Hadzilacos, G.; Fewtrell, T.J.

    2016-01-01

    Quantifying flood hazard is an essential component of resilience planning, emergency response, and mitigation, including insurance. Traditionally undertaken at catchment and national scales, recently, efforts have intensified to estimate flood risk globally to better allow consistent and equitable

  10. Globalization and health: a framework for analysis and action.

    Science.gov (United States)

    Woodward, D.; Drager, N.; Beaglehole, R.; Lipson, D.

    2001-01-01

    Globalization is a key challenge to public health, especially in developing countries, but the linkages between globalization and health are complex. Although a growing amount of literature has appeared on the subject, it is piecemeal, and suffers from a lack of an agreed framework for assessing the direct and indirect health effects of different aspects of globalization. This paper presents a conceptual framework for the linkages between economic globalization and health, with the intention that it will serve as a basis for synthesizing existing relevant literature, identifying gaps in knowledge, and ultimately developing national and international policies more favourable to health. The framework encompasses both the indirect effects on health, operating through the national economy, household economies and health-related sectors such as water, sanitation and education, as well as more direct effects on population-level and individual risk factors for health and on the health care system. Proposed also is a set of broad objectives for a programme of action to optimize the health effects of economic globalization. The paper concludes by identifying priorities for research corresponding with the five linkages identified as critical to the effects of globalization on health. PMID:11584737

  11. Determinants of renewable energy growth: A global sample analysis

    International Nuclear Information System (INIS)

    Aguirre, Mariana; Ibikunle, Gbenga

    2014-01-01

    We investigate factors influencing country-level renewable energy growth by applying FEVD and PCSE estimation methods in a unique sample analysis. With a longer time series (1990–2010) and a broader sample size of countries (including Brazil, Russia, India, China and South Africa) than previous studies, our results reveal new insights. The results suggest that certain government-backed energy policies impede renewable energy investments, thus implying significant failures in policy design. These policies may be failing mainly because of uncertainty and the likelihood of discontinuity. Weak voluntary approaches are introduced in order to satisfy public demand for more sustainable investments and programmes; we find that these may have negative influences on the growth of renewables as well. The insight gained is consistent over the estimation methods employed. - Highlights: • Some public energy policies are shown to impede renewable energy investments; this implies failure in policy design. • Environmental concern is shown to drive renewables investment but energy security concerns do not seem to influence renewables investment. • Results suggest that countries are likely to reduce renewables commitments when under pressure to ensure energy supply. • Results seem to underscore the policy lobbying strength of the traditional energy mix industries

  12. Global health initiative investments and health systems strengthening: a content analysis of global fund investments

    OpenAIRE

    Warren, Ashley E; Wyss, Kaspar; Shakarishvili, George; Atun, Rifat; de Savigny, Don

    2013-01-01

    Background: Millions of dollars are invested annually under the umbrella of national health systems strengthening. Global health initiatives provide funding for low- and middle-income countries through disease-oriented programmes while maintaining that the interventions simultaneously strengthen systems. However, it is as yet unclear which, and to what extent, system-level interventions are being funded by these initiatives, nor is it clear how much funding they allocate to disease-specific a...

  13. Applying machine learning to global surface ocean and seabed data to reveal the controls on the distribution of deep-sea sediments

    Science.gov (United States)

    Dutkiewicz, Adriana; Müller, Dietmar; O'Callaghan, Simon

    2017-04-01

    World's ocean basins contain a rich and nearly continuous record of environmental fluctuations preserved as different types of deep-sea sediments. The sediments represent the largest carbon sink on Earth and its largest geological deposit. Knowing the controls on the distribution of these sediments is essential for understanding the history of ocean-climate dynamics, including changes in sea-level and ocean circulation, as well as biological perturbations. Indeed, the bulk of deep-sea sediments comprises the remains of planktonic organisms that originate in the photic zone of the global ocean implying a strong connection between the seafloor and the sea surface. Machine-learning techniques are perfectly suited to unravelling these controls as they are able to handle large sets of spatial data and they often outperform traditional spatial analysis approaches. Using a support vector machine algorithm we recently created the first digital map of seafloor lithologies (Dutkiewicz et al., 2015) based on 14,400 surface samples. This map reveals significant deviations in distribution of deep-sea lithologies from hitherto hand-drawn maps based on far fewer data points. It also allows us to explore quantitatively, for the first time, the relationship between oceanographic parameters at the sea surface and lithologies on the seafloor. We subsequently coupled this global point sample dataset of 14,400 seafloor lithologies to bathymetry and oceanographic grids (sea-surface temperature, salinity, dissolved oxygen and dissolved inorganic nutrients) and applied a probabilistic Gaussian process classifier in an exhaustive combinatorial fashion (Dutkiewicz et al., 2016). We focused on five major lithologies (calcareous sediment, diatom ooze, radiolarian ooze, clay and lithogenous sediment) and used a computationally intensive five-fold cross-validation, withholding 20% of the data at each iteration, to assess the predictive performance of the machine learning method. We find that

  14. Rotavirus - Global research density equalizing mapping and gender analysis.

    Science.gov (United States)

    Köster, Corinna; Klingelhöfer, Doris; Groneberg, David A; Schwarzer, Mario

    2016-01-02

    Rotaviruses are the leading reason for dehydration and severe diarrheal disease and in infants and young children worldwide. An increasing number of related publications cause a crucial challenge to determine the relevant scientific output. Therefore, scientometric analyses are helpful to evaluate quantity as well as quality of the worldwide research activities on Rotavirus. Up to now, no in-depth global scientometric analysis relating to Rotavirus publications has been carried out. This study used scientometric tools and the method of density equalizing mapping to visualize the differences of the worldwide research effort referring to Rotavirus. The aim of the study was to compare scientific output geographically and over time by using an in-depth data analysis and New quality and quantity indices in science (NewQIS) tools. Furthermore, a gender analysis was part of the data interpretation. We retrieved all Rotavirus-related articles, which were published on "Rotavirus" during the time period from 1900 to 2013, from the Web of Science by a defined search term. These items were analyzed regarding quantitative and qualitative aspects, and visualized with the help of bibliometric methods and the technique of density equalizing mapping to show the differences of the worldwide research efforts. This work aimed to extend the current NewQIS platform. The 5906 Rotavirus associated articles were published in 138 countries from 1900 to 2013. The USA authored 2037 articles that equaled 34.5% of all published items followed by Japan with 576 articles and the United Kingdom - as the most productive representative of the European countries - with 495 articles. Furthermore, the USA established the most cooperations with other countries and was found to be in the center of an international collaborative network. We performed a gender analysis of authors per country (threshold was set at a publishing output of more than 100 articles by more than 50 authors whose names could be

  15. Global sensitivity analysis of DRAINMOD-FOREST, an integrated forest ecosystem model

    Science.gov (United States)

    Shiying Tian; Mohamed A. Youssef; Devendra M. Amatya; Eric D. Vance

    2014-01-01

    Global sensitivity analysis is a useful tool to understand process-based ecosystem models by identifying key parameters and processes controlling model predictions. This study reported a comprehensive global sensitivity analysis for DRAINMOD-FOREST, an integrated model for simulating water, carbon (C), and nitrogen (N) cycles and plant growth in lowland forests. The...

  16. Indian Handicrafts in Globalization Times: An analysis of Global-Local Dynamics

    Directory of Open Access Journals (Sweden)

    Pradeep Kumar Jena

    2010-12-01

    Full Text Available Globalization – which refers to the growing integration of societies, economies and cultures around the world, has become one of the most hotly-debated topics and key area of research among the policy makers, statesmen, corporate, politicians and academia respectively over the past few years. As India opens up her doors to the multinationals during the era of economic reform and liberalized market, putting an end to the ‘license raj’, it is not only the economies that often meet in the global market sphere, but also the people and cultures, which bring a new dimension to the multi-cultural setting. What we can see in present day modern world is that there is always a cross-cultural interaction between the ‘local’ and ‘global’ and the much discussed ‘global village’, is now not just a possibility but a reality despite many contradictions. Talking about Indian Handicrafts, which constitutes a significant segment of the decentralized sector of the economy, its export has reached at a commendable height. Indian folk art and crafts which are the integral parts of the Indian culture and tradition, are in high demand among the western consumers. Again, foreign fashion industry borrows a great deal from Indian appliquéd motifs Saree designs, an ethnic Indian wear. Needless to say, the borders between the world cultures are now eroding out and becoming irrelevant, therefore prompting to call it as a deterritorialized world.But notwithstanding, the real concern for many of us is that, can the ‘local’ really meet with the ‘global’ by truly sustaining its localness? The biggest problem in the Indian Handicraft industry is that the village craftsmen remain concerned that with free trade and mass production, hand-made products from other parts of the world will out price the products of their hard labour. So the basic question arises, is globalization a panacea for every human problems that the mother earth is facing now? With a

  17. Bibliometric analysis of global environmental assessment research in a 20-year period

    Energy Technology Data Exchange (ETDEWEB)

    Li, Wei, E-mail: weili@bnu.edu.cn; Zhao, Yang

    2015-01-15

    Based on the samples of 113,468 publications on environmental assessment (EA) from the past 20 years, we used a bibliometric analysis to study the literature in terms of trends of growth, subject categories and journals, international collaboration, geographic distribution of publications, and scientific research issues. By applying thresholds to network centralities, a core group of countries can be distinguished as part of the international collaboration network. A frequently used keywords analysis found that the priority in assessment would gradually change from project environmental impact assessment (EIA) to strategic environmental assessment (SEA). Decision-theoretic approaches (i.e., environmental indicator selection, life cycle assessment, etc.), along with new technologies and methods (i.e., the geographic information system and modeling) have been widely applied in the EA research field over the past 20 years. Hot spots such as “biodiversity” and “climate change” have been emphasized in current EA research, a trend that will likely continue in the future. The h-index has been used to evaluate the research quality among countries all over the world, while the improvement of developing countries' EA systems is becoming a popular research topic. Our study reveals patterns in scientific outputs and academic collaborations and serves as an alternative and innovative way of revealing global research trends in the EA research field.

  18. Bibliometric analysis of global environmental assessment research in a 20-year period

    International Nuclear Information System (INIS)

    Li, Wei; Zhao, Yang

    2015-01-01

    Based on the samples of 113,468 publications on environmental assessment (EA) from the past 20 years, we used a bibliometric analysis to study the literature in terms of trends of growth, subject categories and journals, international collaboration, geographic distribution of publications, and scientific research issues. By applying thresholds to network centralities, a core group of countries can be distinguished as part of the international collaboration network. A frequently used keywords analysis found that the priority in assessment would gradually change from project environmental impact assessment (EIA) to strategic environmental assessment (SEA). Decision-theoretic approaches (i.e., environmental indicator selection, life cycle assessment, etc.), along with new technologies and methods (i.e., the geographic information system and modeling) have been widely applied in the EA research field over the past 20 years. Hot spots such as “biodiversity” and “climate change” have been emphasized in current EA research, a trend that will likely continue in the future. The h-index has been used to evaluate the research quality among countries all over the world, while the improvement of developing countries' EA systems is becoming a popular research topic. Our study reveals patterns in scientific outputs and academic collaborations and serves as an alternative and innovative way of revealing global research trends in the EA research field

  19. Supplementary Material for: A global sensitivity analysis approach for morphogenesis models

    KAUST Repository

    Boas, Sonja; Navarro, Marí a; Merks, Roeland; Blom, Joke

    2015-01-01

    ) represent cell properties and behaviors that drive the mechanisms of angiogenic sprouting. The global sensitivity analysis correctly identified the dominant parameters in the model, consistent with previous studies. Additionally, the analysis provided

  20. Global Proteomic Analysis Reveals an Exclusive Role of Thylakoid Membranes in Bioenergetics of a Model Cyanobacterium

    Energy Technology Data Exchange (ETDEWEB)

    Liberton, Michelle; Saha, Rajib; Jacobs, Jon M.; Nguyen, Amelia Y.; Gritsenko, Marina A.; Smith, Richard D.; Koppenaal, David W.; Pakrasi, Himadri B.

    2016-04-07

    Cyanobacteria are photosynthetic microbes with highly differentiated membrane systems. These organisms contain an outer membrane, plasma membrane, and an internal system of thylakoid membranes where the photosynthetic and respiratory machinery are found. This existence of compartmentalization and differentiation of membrane systems poses a number of challenges for cyanobacterial cells in terms of organization and distribution of proteins to the correct membrane system. Proteomics studies have long sought to identify the components of the different membrane systems, and to date about 450 different proteins have been attributed to either the plasma membrane or thylakoid membrane. Given the complexity of these membranes, many more proteins remain to be identified in these membrane systems, and a comprehensive catalog of plasma membrane and thylakoid membrane proteins is needed. Here we describe the identification of 635 proteins in Synechocystis sp. PCC 6803 by quantitative iTRAQ isobaric labeling; of these, 459 proteins were localized to the plasma membrane and 176 were localized to the thylakoid membrane. Surprisingly, we found over 2.5 times the number of unique proteins identified in the plasma membrane compared to the thylakoid membrane. This suggests that the protein composition of the thylakoid membrane is more homogeneous than the plasma membrane, consistent with the role of the plasma membrane in diverse cellular processes including protein trafficking and nutrient import, compared to a more specialized role for the thylakoid membrane in cellular energetics. Overall, the protein composition of the Synechocystis 6803 plasma membrane and thylakoid membrane is quite similar to the E.coli plasma membrane and Arabidopsis thylakoid membrane, respectively. Synechocystis 6803 can therefore be described as a gram-negative bacterium that has an additional internal membrane system that fulfils the energetic requirements of the cell.

  1. Global Transcriptomic Analysis Reveals the Mechanism of Phelipanche aegyptiaca Seed Germination.

    Science.gov (United States)

    Yao, Zhaoqun; Tian, Fang; Cao, Xiaolei; Xu, Ying; Chen, Meixiu; Xiang, Benchun; Zhao, Sifeng

    2016-07-15

    Phelipanche aegyptiaca is one of the most destructive root parasitic plants of Orobanchaceae. This plant has significant impacts on crop yields worldwide. Conditioned and host root stimulants, in particular, strigolactones, are needed for unique seed germination. However, no extensive study on this phenomenon has been conducted because of insufficient genomic information. Deep RNA sequencing, including de novo assembly and functional annotation was performed on P. aegyptiaca germinating seeds. The assembled transcriptome was used to analyze transcriptional dynamics during seed germination. Key gene categories involved were identified. A total of 274,964 transcripts were determined, and 53,921 unigenes were annotated according to the NR, GO, COG, KOG, and KEGG databases. Overall, 5324 differentially expressed genes among dormant, conditioned, and GR24-treated seeds were identified. GO and KEGG enrichment analyses demonstrated numerous DEGs related to DNA, RNA, and protein repair and biosynthesis, as well as carbohydrate and energy metabolism. Moreover, ABA and ethylene were found to play important roles in this process. GR24 application resulted in dramatic changes in ABA and ethylene-associated genes. Fluridone, a carotenoid biosynthesis inhibitor, alone could induce P. aegyptiaca seed germination. In addition, conditioning was probably not the indispensable stage for P. aegyptiaca, because the transcript level variation of MAX2 and KAI2 genes (relate to strigolactone signaling) was not up-regulated by conditioning treatment.

  2. Global Transcriptomic Analysis Reveals the Mechanism of Phelipanche aegyptiaca Seed Germination

    OpenAIRE

    Zhaoqun Yao; Fang Tian; Xiaolei Cao; Ying Xu; Meixiu Chen; Benchun Xiang; Sifeng Zhao

    2016-01-01

    Phelipanche aegyptiaca is one of the most destructive root parasitic plants of Orobanchaceae. This plant has significant impacts on crop yields worldwide. Conditioned and host root stimulants, in particular, strigolactones, are needed for unique seed germination. However, no extensive study on this phenomenon has been conducted because of insufficient genomic information. Deep RNA sequencing, including de novo assembly and functional annotation was performed on P. aegyptiaca germinating seeds...

  3. Global Transcriptomic Analysis Reveals the Mechanism of Phelipanche aegyptiaca Seed Germination

    Directory of Open Access Journals (Sweden)

    Zhaoqun Yao

    2016-07-01

    Full Text Available Phelipanche aegyptiaca is one of the most destructive root parasitic plants of Orobanchaceae. This plant has significant impacts on crop yields worldwide. Conditioned and host root stimulants, in particular, strigolactones, are needed for unique seed germination. However, no extensive study on this phenomenon has been conducted because of insufficient genomic information. Deep RNA sequencing, including de novo assembly and functional annotation was performed on P. aegyptiaca germinating seeds. The assembled transcriptome was used to analyze transcriptional dynamics during seed germination. Key gene categories involved were identified. A total of 274,964 transcripts were determined, and 53,921 unigenes were annotated according to the NR, GO, COG, KOG, and KEGG databases. Overall, 5324 differentially expressed genes among dormant, conditioned, and GR24-treated seeds were identified. GO and KEGG enrichment analyses demonstrated numerous DEGs related to DNA, RNA, and protein repair and biosynthesis, as well as carbohydrate and energy metabolism. Moreover, ABA and ethylene were found to play important roles in this process. GR24 application resulted in dramatic changes in ABA and ethylene-associated genes. Fluridone, a carotenoid biosynthesis inhibitor, alone could induce P. aegyptiaca seed germination. In addition, conditioning was probably not the indispensable stage for P. aegyptiaca, because the transcript level variation of MAX2 and KAI2 genes (relate to strigolactone signaling was not up-regulated by conditioning treatment.

  4. Global Proteomic Analysis Reveals an Exclusive Role of Thylakoid Membranes in Bioenergetics of a Model Cyanobacterium

    Energy Technology Data Exchange (ETDEWEB)

    Liberton, Michelle; Saha, Rajib; Jacobs, Jon M.; Nguyen, Amelia Y.; Gritsenko, Marina A.; Smith, Richard D.; Koppenaal, David W.; Pakrasi, Himadri B.

    2016-04-07

    Cyanobacteria are photosynthetic microbes with highlydifferentiated membrane systems. These organisms contain an outer membrane, plasma membrane, and an internal system of thylakoid membranes where the photosynthetic and respiratory machinery are found. This existence of compartmentalization and differentiation of membrane systems poses a number of challenges for cyanobacterial cells in terms of organization and distribution of proteins to the correct membrane system. Proteomics studies have long sought to identify the components of the different membrane systems in cyanobacteria, and to date about 450 different proteins have been attributed to either the plasma membrane or thylakoid membrane. Given the complexity of these membranes, many more proteins remain to be identified, and a comprehensive catalogue of plasma membrane and thylakoid membrane proteins is needed. Here we describe the identification of 635 differentially localized proteins in Synechocystis sp. PCC 6803 by quantitative iTRAQ isobaric labeling; of these, 459 proteins were localized to the plasma membrane and 176 were localized to the thylakoid membrane. Surprisingly, we found over 2.5 times the number of unique proteins identified in the plasma membrane compared with the thylakoid membrane. This suggests that the protein composition of the thylakoid membrane is more homogeneous than the plasma membrane, consistent with the role of the plasma membrane in diverse cellular processes including protein trafficking and nutrient import, compared with a more specialized role for the thylakoid membrane in cellular energetics. Thus, our data clearly define the two membrane systems with distinct functions. Overall, the protein compositions of the Synechocystis 6803 plasma membrane and thylakoid membrane are quite similar to that of the plasma membrane of Escherichia coli and thylakoid membrane of Arabidopsis chloroplasts, respectively. Synechocystis 6803 can therefore be described as a Gram-negative bacterium with an additional internal membrane system that fulfills the energetic requirements of the cell.

  5. Diurnal Cycling Transcription Factors of Pineapple Revealed by Genome-Wide Annotation and Global Transcriptomic Analysis.

    Science.gov (United States)

    Sharma, Anupma; Wai, Ching Man; Ming, Ray; Yu, Qingyi

    2017-09-01

    Circadian clock provides fitness advantage by coordinating internal metabolic and physiological processes to external cyclic environments. Core clock components exhibit daily rhythmic changes in gene expression, and the majority of them are transcription factors (TFs) and transcription coregulators (TCs). We annotated 1,398 TFs from 67 TF families and 80 TCs from 20 TC families in pineapple, and analyzed their tissue-specific and diurnal expression patterns. Approximately 42% of TFs and 45% of TCs displayed diel rhythmic expression, including 177 TF/TCs cycling only in the nonphotosynthetic leaf tissue, 247 cycling only in the photosynthetic leaf tissue, and 201 cycling in both. We identified 68 TF/TCs whose cycling expression was tightly coupled between the photosynthetic and nonphotosynthetic leaf tissues. These TF/TCs likely coordinate key biological processes in pineapple as we demonstrated that this group is enriched in homologous genes that form the core circadian clock in Arabidopsis and includes a STOP1 homolog. Two lines of evidence support the important role of the STOP1 homolog in regulating CAM photosynthesis in pineapple. First, STOP1 responds to acidic pH and regulates a malate channel in multiple plant species. Second, the cycling expression pattern of the pineapple STOP1 and the diurnal pattern of malate accumulation in pineapple leaf are correlated. We further examined duplicate-gene retention and loss in major known circadian genes and refined their evolutionary relationships between pineapple and other plants. Significant variations in duplicate-gene retention and loss were observed for most clock genes in both monocots and dicots. © The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  6. Global analysis of plastid diversity reveals apicomplexan-related lineages in coral reefs

    Czech Academy of Sciences Publication Activity Database

    Janouškovec, J.; Horák, Aleš; Barott, K. L.; Rohwer, F. L.; Keeling, P. J.

    2012-01-01

    Roč. 22, č. 13 (2012), R518-R519 ISSN 0960-9822 Institutional support: RVO:60077344 Keywords : DINOFLAGELLATE * ORIGIN * LIFE Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 9.494, year: 2012

  7. A Snapshot of the World of Global Multinationals – An Industry Based Analysis of Fortune Global 500 Companies

    Directory of Open Access Journals (Sweden)

    Ogrean Claudia

    2017-08-01

    Full Text Available For better or for worse, the “corporations rule the world” assertion is nowadays more actual and accurate than ever before, as multinational companies represent the undisputable engine of the globalization process, and the latter continuously (recreates the background against which global multinationals are flourishing, while reinforcing their “domination”. Since 1995, the Fortune Global 500 ranking (FG 500 annually provides a comprehensive and eloquent image of the world of global multinationals; the merits of the FG 500 ranking go beyond the synchronic approach of the characteristics of global multinationals (in terms of revenues, profits, assets and employees - by sector, industry and country, as it also favors diachronic analysis and comparisons - which are essential for strategists in identifying evolving trends and substantiating corporate strategies able to lead to sustainable competitiveness. The paper aims to determine the contribution of sectors to FG 500 ranking in 2016, on one hand, and to emphasize on some industry-based dynamics in FG 500 - by comparatively analyzing the 2016 and 1996 rankings, on the other hand.

  8. Global Analysis, Interpretation and Modelling: An Earth Systems Modelling Program

    Science.gov (United States)

    Moore, Berrien, III; Sahagian, Dork

    1997-01-01

    The Goal of the GAIM is: To advance the study of the coupled dynamics of the Earth system using as tools both data and models; to develop a strategy for the rapid development, evaluation, and application of comprehensive prognostic models of the Global Biogeochemical Subsystem which could eventually be linked with models of the Physical-Climate Subsystem; to propose, promote, and facilitate experiments with existing models or by linking subcomponent models, especially those associated with IGBP Core Projects and with WCRP efforts. Such experiments would be focused upon resolving interface issues and questions associated with developing an understanding of the prognostic behavior of key processes; to clarify key scientific issues facing the development of Global Biogeochemical Models and the coupling of these models to General Circulation Models; to assist the Intergovernmental Panel on Climate Change (IPCC) process by conducting timely studies that focus upon elucidating important unresolved scientific issues associated with the changing biogeochemical cycles of the planet and upon the role of the biosphere in the physical-climate subsystem, particularly its role in the global hydrological cycle; and to advise the SC-IGBP on progress in developing comprehensive Global Biogeochemical Models and to maintain scientific liaison with the WCRP Steering Group on Global Climate Modelling.

  9. Application of wavelet analysis in determining the periodicity of global warming

    Science.gov (United States)

    Feng, Xiao

    2018-04-01

    In the last two decades of the last century, the global average temperature has risen by 0.48 ° C over 100 years ago. Since then, global warming has become a hot topic. Global warming will have complex and potential impacts on humans and the Earth. However, the negative impacts far outweigh the positive impacts. The most obvious external manifestation of global warming is temperature. Therefore, this study uses wavelet analysis study the characteristics of temperature time series, solve the periodicity of the sequence, find out the trend of temperature change and predict the extent of global warming in the future, so as to take the necessary precautionary measures.

  10. Bird and bat species' global vulnerability to collision mortality at wind farms revealed through a trait-based assessment.

    Science.gov (United States)

    Thaxter, Chris B; Buchanan, Graeme M; Carr, Jamie; Butchart, Stuart H M; Newbold, Tim; Green, Rhys E; Tobias, Joseph A; Foden, Wendy B; O'Brien, Sue; Pearce-Higgins, James W

    2017-09-13

    Mitigation of anthropogenic climate change involves deployments of renewable energy worldwide, including wind farms, which can pose a significant collision risk to volant animals. Most studies into the collision risk between species and wind turbines, however, have taken place in industrialized countries. Potential effects for many locations and species therefore remain unclear. To redress this gap, we conducted a systematic literature review of recorded collisions between birds and bats and wind turbines within developed countries. We related collision rate to species-level traits and turbine characteristics to quantify the potential vulnerability of 9538 bird and 888 bat species globally. Avian collision rate was affected by migratory strategy, dispersal distance and habitat associations, and bat collision rates were influenced by dispersal distance. For birds and bats, larger turbine capacity (megawatts) increased collision rates; however, deploying a smaller number of large turbines with greater energy output reduced total collision risk per unit energy output, although bat mortality increased again with the largest turbines. Areas with high concentrations of vulnerable species were also identified, including migration corridors. Our results can therefore guide wind farm design and location to reduce the risk of large-scale animal mortality. This is the first quantitative global assessment of the relative collision vulnerability of species groups with wind turbines, providing valuable guidance for minimizing potentially serious negative impacts on biodiversity. © 2017 The Author(s).

  11. Transcriptome analysis reveals key differentially expressed genes involved in wheat grain development

    Directory of Open Access Journals (Sweden)

    Yonglong Yu

    2016-04-01

    Full Text Available Wheat seed development is an important physiological process of seed maturation and directly affects wheat yield and quality. In this study, we performed dynamic transcriptome microarray analysis of an elite Chinese bread wheat cultivar (Jimai 20 during grain development using the GeneChip Wheat Genome Array. Grain morphology and scanning electron microscope observations showed that the period of 11–15 days post-anthesis (DPA was a key stage for the synthesis and accumulation of seed starch. Genome-wide transcriptional profiling and significance analysis of microarrays revealed that the period from 11 to 15 DPA was more important than the 15–20 DPA stage for the synthesis and accumulation of nutritive reserves. Series test of cluster analysis of differential genes revealed five statistically significant gene expression profiles. Gene ontology annotation and enrichment analysis gave further information about differentially expressed genes, and MapMan analysis revealed expression changes within functional groups during seed development. Metabolic pathway network analysis showed that major and minor metabolic pathways regulate one another to ensure regular seed development and nutritive reserve accumulation. We performed gene co-expression network analysis to identify genes that play vital roles in seed development and identified several key genes involved in important metabolic pathways. The transcriptional expression of eight key genes involved in starch and protein synthesis and stress defense was further validated by qRT-PCR. Our results provide new insight into the molecular mechanisms of wheat seed development and the determinants of yield and quality.

  12. Mass Cytometry and Topological Data Analysis Reveal Immune Parameters Associated with Complications after Allogeneic Stem Cell Transplantation

    Directory of Open Access Journals (Sweden)

    Tadepally Lakshmikanth

    2017-08-01

    Full Text Available Human immune systems are variable, and immune responses are often unpredictable. Systems-level analyses offer increased power to sort patients on the basis of coordinated changes across immune cells and proteins. Allogeneic stem cell transplantation is a well-established form of immunotherapy whereby a donor immune system induces a graft-versus-leukemia response. This fails when the donor immune system regenerates improperly, leaving the patient susceptible to infections and leukemia relapse. We present a systems-level analysis by mass cytometry and serum profiling in 26 patients sampled 1, 2, 3, 6, and 12 months after transplantation. Using a combination of machine learning and topological data analyses, we show that global immune signatures associated with clinical outcome can be revealed, even when patients are few and heterogeneous. This high-resolution systems immune monitoring approach holds the potential for improving the development and evaluation of immunotherapies in the future.

  13. The role of energy-service demand reduction in global climate change mitigation: Combining energy modelling and decomposition analysis

    International Nuclear Information System (INIS)

    Kesicki, Fabian; Anandarajah, Gabrial

    2011-01-01

    In order to reduce energy-related CO 2 emissions different options have been considered: energy efficiency improvements, structural changes to low carbon or zero carbon fuel/technologies, carbon sequestration, and reduction in energy-service demands (useful energy). While efficiency and technology options have been extensively studied within the context of climate change mitigation, this paper addresses the possible role of price-related energy-service demand reduction. For this analysis, the elastic demand version of the TIAM-UCL global energy system model is used in combination with decomposition analysis. The results of the CO 2 emission decomposition indicate that a reduction in energy-service demand can play a limited role, contributing around 5% to global emission reduction in the 21st century. A look at the sectoral level reveals that the demand reduction can play a greater role in selected sectors like transport contributing around 16% at a global level. The societal welfare loss is found to be high when the price elasticity of demand is low. - Highlights: → A reduction in global energy-service demand can contribute around 5% to global emission reduction in the 21st century. → The role of demand is a lot higher in transport than in the residential sector. → Contribution of demand reduction is higher in early periods of the 21st century. → Societal welfare loss is found to be high when the price elasticity of demand is low. → Regional shares in residual emissions vary under different elasticity scenarios.

  14. The role of energy-service demand reduction in global climate change mitigation: Combining energy modelling and decomposition analysis

    Energy Technology Data Exchange (ETDEWEB)

    Kesicki, Fabian, E-mail: fabian.kesicki.09@ucl.ac.uk [UCL Energy Institute, University College London, 14 Upper Woburn Place, London, WC1H 0NN (United Kingdom); Anandarajah, Gabrial [UCL Energy Institute, University College London, 14 Upper Woburn Place, London, WC1H 0NN (United Kingdom)

    2011-11-15

    In order to reduce energy-related CO{sub 2} emissions different options have been considered: energy efficiency improvements, structural changes to low carbon or zero carbon fuel/technologies, carbon sequestration, and reduction in energy-service demands (useful energy). While efficiency and technology options have been extensively studied within the context of climate change mitigation, this paper addresses the possible role of price-related energy-service demand reduction. For this analysis, the elastic demand version of the TIAM-UCL global energy system model is used in combination with decomposition analysis. The results of the CO{sub 2} emission decomposition indicate that a reduction in energy-service demand can play a limited role, contributing around 5% to global emission reduction in the 21st century. A look at the sectoral level reveals that the demand reduction can play a greater role in selected sectors like transport contributing around 16% at a global level. The societal welfare loss is found to be high when the price elasticity of demand is low. - Highlights: > A reduction in global energy-service demand can contribute around 5% to global emission reduction in the 21st century. > The role of demand is a lot higher in transport than in the residential sector. > Contribution of demand reduction is higher in early periods of the 21st century. > Societal welfare loss is found to be high when the price elasticity of demand is low. > Regional shares in residual emissions vary under different elasticity scenarios.

  15. Analysis of textbooks in terms of interpretation of global issues

    OpenAIRE

    Brodníček, Daniel

    2017-01-01

    In the contemporary world, when the whole world is connected, the fact saying that anything what happens on the other side of the world does not have influence to our lives is not truthful anymore. We live in an era of globalization. Therefore, it is important to focus on the global issues already at school and also on the way in which they concern us. However, it should be borne in the mind that, the most important thing is the way, how teachers explain it to their students. The main aim of ...

  16. Differential proteomic analysis reveals novel links between primary metabolism and antibiotic production in Amycolatopsis balhimycina

    DEFF Research Database (Denmark)

    Gallo, G.; Renzone, G.; Alduina, R.

    2010-01-01

    A differential proteomic analysis, based on 2-DE and MS procedures, was performed on Amycolatopsis balhimycina DSM5908, the actinomycete producing the vancomycin-like antibiotic balhimycin. A comparison of proteomic profiles before and during balhimycin production characterized differentially...... available over the World Wide Web as interactive web pages (http://www.unipa.it/ampuglia/Abal-proteome-maps). Functional clustering analysis revealed that differentially expressed proteins belong to functional groups involved in central carbon metabolism, amino acid metabolism and protein biosynthesis...... intermediates, were upregulated during antibiotic production. qRT-PCR analysis revealed that 8 out of 14 upregulated genes showed a positive correlation between changes at translational and transcriptional expression level. Furthermore, proteomic analysis of two nonproducing mutants, restricted to a sub...

  17. Facilitation of the PED analysis of large molecules by using global coordinates.

    Science.gov (United States)

    Jamróz, Michał H; Ostrowski, Sławomir; Dobrowolski, Jan Cz

    2015-10-05

    Global coordinates have been found to be useful in the potential energy distribution (PED) analyses of the following large molecules: [13]-acene and [33]-helicene. The global coordinate is defined based on much distanced fragments of the analysed molecule, whereas so far, the coordinates used in the analysis were based on stretchings, bendings, or torsions of the adjacent atoms. It has been shown that the PED analyses performed using the global coordinate and the classical ones can lead to exactly the same PED contributions. The global coordinates may significantly improve the facility of the analysis of the vibrational spectra of large molecules. Copyright © 2015 Elsevier B.V. All rights reserved.

  18. Using team cognitive work analysis to reveal healthcare team interactions in a birthing unit

    OpenAIRE

    Ashoori, Maryam; Burns, Catherine M.; d'Entremont, Barbara; Momtahan, Kathryn

    2014-01-01

    Cognitive work analysis (CWA) as an analytical approach for examining complex sociotechnical systems has shown success in modelling the work of single operators. The CWA approach incorporates social and team interactions, but a more explicit analysis of team aspects can reveal more information for systems design. In this paper, Team CWA is explored to understand teamwork within a birthing unit at a hospital. Team CWA models are derived from theories and models of teamworkand leverage the exis...

  19. Proteomic analysis of three gonad types of swamp eel reveals genes differentially expressed during sex reversal

    OpenAIRE

    Sheng, Yue; Zhao, Wei; Song, Ying; Li, Zhigang; Luo, Majing; Lei, Quan; Cheng, Hanhua; Zhou, Rongjia

    2015-01-01

    A variety of mechanisms are engaged in sex determination in vertebrates. The teleost fish swamp eel undergoes sex reversal naturally and is an ideal model for vertebrate sexual development. However, the importance of proteome-wide scanning for gonad reversal was not previously determined. We report a 2-D electrophoresis analysis of three gonad types of proteomes during sex reversal. MS/MS analysis revealed a group of differentially expressed proteins during ovary to ovotestis to testis transf...

  20. A Global Analysis of the Relationship between Farmed Seaweed Production and Herbivorous Fish Catch.

    Directory of Open Access Journals (Sweden)

    E James Hehre

    Full Text Available Globally, farmed seaweed production is expanding rapidly in shallow marine habitats. While seaweed farming provides vital income to millions of artisanal farmers, it can negatively impact shallow coral reef and seagrass habitats. However, seaweed farming may also potentially provide food subsidies for herbivorous reef fish such as the Siganidae, a valuable target family, resulting in increased catch. Comparisons of reef fish landings across the central Philippines revealed that the catch of siganids was positively correlated to farmed seaweed production whilst negatively correlated to total reef fish catch over the same period of time. We tested the generality of this pattern by analysing seaweed production, siganid catch, and reef fish catch for six major seaweed-producing countries in the tropics. We hypothesized that increased seaweed production would correspond with increased catch of siganids but not other reef fish species. Analysis of the global data showed a positive correlation between farmed seaweeds and siganids in Southeast Asia (Indonesia, Malaysia, and the Philippines but not Africa (Tanzania and Zanzibar, or the Western Pacific (Fiji. In Southeast Asia, siganid catch increased disproportionately faster with seaweed production than did reef fish catch. Low continuity, sporadic production and smaller volumes of seaweed farming may explain the differences.

  1. A Global Analysis of the Relationship between Farmed Seaweed Production and Herbivorous Fish Catch.

    Science.gov (United States)

    Hehre, E James; Meeuwig, Jessica J

    2016-01-01

    Globally, farmed seaweed production is expanding rapidly in shallow marine habitats. While seaweed farming provides vital income to millions of artisanal farmers, it can negatively impact shallow coral reef and seagrass habitats. However, seaweed farming may also potentially provide food subsidies for herbivorous reef fish such as the Siganidae, a valuable target family, resulting in increased catch. Comparisons of reef fish landings across the central Philippines revealed that the catch of siganids was positively correlated to farmed seaweed production whilst negatively correlated to total reef fish catch over the same period of time. We tested the generality of this pattern by analysing seaweed production, siganid catch, and reef fish catch for six major seaweed-producing countries in the tropics. We hypothesized that increased seaweed production would correspond with increased catch of siganids but not other reef fish species. Analysis of the global data showed a positive correlation between farmed seaweeds and siganids in Southeast Asia (Indonesia, Malaysia, and the Philippines) but not Africa (Tanzania and Zanzibar), or the Western Pacific (Fiji). In Southeast Asia, siganid catch increased disproportionately faster with seaweed production than did reef fish catch. Low continuity, sporadic production and smaller volumes of seaweed farming may explain the differences.

  2. Biodiversity's big wet secret: the global distribution of marine biological records reveals chronic under-exploration of the deep pelagic ocean.

    Directory of Open Access Journals (Sweden)

    Thomas J Webb

    Full Text Available BACKGROUND: Understanding the distribution of marine biodiversity is a crucial first step towards the effective and sustainable management of marine ecosystems. Recent efforts to collate location records from marine surveys enable us to assemble a global picture of recorded marine biodiversity. They also effectively highlight gaps in our knowledge of particular marine regions. In particular, the deep pelagic ocean--the largest biome on Earth--is chronically under-represented in global databases of marine biodiversity. METHODOLOGY/PRINCIPAL FINDINGS: We use data from the Ocean Biogeographic Information System to plot the position in the water column of ca 7 million records of marine species occurrences. Records from relatively shallow waters dominate this global picture of recorded marine biodiversity. In addition, standardising the number of records from regions of the ocean differing in depth reveals that regardless of ocean depth, most records come either from surface waters or the sea bed. Midwater biodiversity is drastically under-represented. CONCLUSIONS/SIGNIFICANCE: The deep pelagic ocean is the largest habitat by volume on Earth, yet it remains biodiversity's big wet secret, as it is hugely under-represented in global databases of marine biological records. Given both its value in the provision of a range of ecosystem services, and its vulnerability to threats including overfishing and climate change, there is a pressing need to increase our knowledge of Earth's largest ecosystem.

  3. Revealing the equivalence of two clonal survival models by principal component analysis

    International Nuclear Information System (INIS)

    Lachet, Bernard; Dufour, Jacques

    1976-01-01

    The principal component analysis of 21 chlorella cell survival curves, adjusted by one-hit and two-hit target models, lead to quite similar projections on the principal plan: the homologous parameters of these models are linearly correlated; the reason for the statistical equivalence of these two models, in the present state of experimental inaccuracy, is revealed [fr

  4. Using team cognitive work analysis to reveal healthcare team interactions in a birthing unit.

    Science.gov (United States)

    Ashoori, Maryam; Burns, Catherine M; d'Entremont, Barbara; Momtahan, Kathryn

    2014-01-01

    Cognitive work analysis (CWA) as an analytical approach for examining complex sociotechnical systems has shown success in modelling the work of single operators. The CWA approach incorporates social and team interactions, but a more explicit analysis of team aspects can reveal more information for systems design. In this paper, Team CWA is explored to understand teamwork within a birthing unit at a hospital. Team CWA models are derived from theories and models of teamwork and leverage the existing CWA approaches to analyse team interactions. Team CWA is explained and contrasted with prior approaches to CWA. Team CWA does not replace CWA, but supplements traditional CWA to more easily reveal team information. As a result, Team CWA may be a useful approach to enhance CWA in complex environments where effective teamwork is required. This paper looks at ways of analysing cognitive work in healthcare teams. Team Cognitive Work Analysis, when used to supplement traditional Cognitive Work Analysis, revealed more team information than traditional Cognitive Work Analysis. Team Cognitive Work Analysis should be considered when studying teams.

  5. Using team cognitive work analysis to reveal healthcare team interactions in a birthing unit

    Science.gov (United States)

    Ashoori, Maryam; Burns, Catherine M.; d'Entremont, Barbara; Momtahan, Kathryn

    2014-01-01

    Cognitive work analysis (CWA) as an analytical approach for examining complex sociotechnical systems has shown success in modelling the work of single operators. The CWA approach incorporates social and team interactions, but a more explicit analysis of team aspects can reveal more information for systems design. In this paper, Team CWA is explored to understand teamwork within a birthing unit at a hospital. Team CWA models are derived from theories and models of teamworkand leverage the existing CWA approaches to analyse team interactions. Team CWA is explained and contrasted with prior approaches to CWA. Team CWA does not replace CWA, but supplements traditional CWA to more easily reveal team information. As a result, Team CWA may be a useful approach to enhance CWA in complex environments where effective teamwork is required. Practitioner Summary: This paper looks at ways of analysing cognitive work in healthcare teams. Team Cognitive Work Analysis, when used to supplement traditional Cognitive Work Analysis, revealed more team information than traditional Cognitive Work Analysis. Team Cognitive Work Analysis should be considered when studying teams PMID:24837514

  6. Global phylogenetic analysis of contemporary aleutian mink disease viruses (AMDVs)

    DEFF Research Database (Denmark)

    Ryt-Hansen, Pia; Hagberg, E. E.; Chriél, Mariann

    2017-01-01

    a strain originating from Sweden. In contrast, we did not identify any potential source for the other and more widespread outbreak strain. To the authors knowledge this is the first major global phylogenetic study of contemporary AMDV partial NS1 sequences. The study proved that partial NS1 sequencing can...

  7. Maximum-entropy clustering algorithm and its global convergence analysis

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    Constructing a batch of differentiable entropy functions touniformly approximate an objective function by means of the maximum-entropy principle, a new clustering algorithm, called maximum-entropy clustering algorithm, is proposed based on optimization theory. This algorithm is a soft generalization of the hard C-means algorithm and possesses global convergence. Its relations with other clustering algorithms are discussed.

  8. The yield gap of global grain production: A spatial analysis

    NARCIS (Netherlands)

    Neumann, K.; Verburg, P.H.; Stehfest, E.; Muller, C.

    2010-01-01

    Global grain production has increased dramatically during the past 50 years, mainly as a consequence of intensified land management and introduction of new technologies. For the future, a strong increase in grain demand is expected, which may be fulfilled by further agricultural intensification

  9. Characterization and global analysis of a family of Poisson structures

    International Nuclear Information System (INIS)

    Hernandez-Bermejo, Benito

    2006-01-01

    A three-dimensional family of solutions of the Jacobi equations for Poisson systems is characterized. In spite of its general form it is possible the explicit and global determination of its main features, such as the symplectic structure and the construction of the Darboux canonical form. Examples are given

  10. Characterization and global analysis of a family of Poisson structures

    Energy Technology Data Exchange (ETDEWEB)

    Hernandez-Bermejo, Benito [Escuela Superior de Ciencias Experimentales y Tecnologia, Edificio Departamental II, Universidad Rey Juan Carlos, Calle Tulipan S/N, 28933 (Mostoles), Madrid (Spain)]. E-mail: benito.hernandez@urjc.es

    2006-06-26

    A three-dimensional family of solutions of the Jacobi equations for Poisson systems is characterized. In spite of its general form it is possible the explicit and global determination of its main features, such as the symplectic structure and the construction of the Darboux canonical form. Examples are given.

  11. A comparability analysis of global burden sharing GHG reduction scenarios

    International Nuclear Information System (INIS)

    Ciscar, Juan-Carlos; Saveyn, Bert; Soria, Antonio; Szabo, Laszlo; Van Regemorter, Denise; Van Ierland, Tom

    2013-01-01

    The distribution of the mitigation burden across countries is a key issue regarding the post-2012 global climate policies. This article explores the economic implications of alternative allocation rules, an assessment made in the run-up to the COP15 in Copenhagen (December 2009). We analyse the comparability of the allocations across countries based on four single indicators: GDP per capita, GHG emissions per GDP, GHG emission trends in the recent past, and population growth. The multi-sectoral computable general equilibrium model of the global economy, GEM-E3, is used for that purpose. Further, the article also compares a perfect carbon market without transaction costs with the case of a gradually developing carbon market, i.e. a carbon market with (gradually diminishing) transaction costs. - Highlights: ► Burden sharing of global mitigation efforts should consider equity and efficiency. ► The comparability of allocations across countries is based on four indicators. ► The four indicators are GDP/capita, GHG/GDP, population growth, and GHG trend. ► Any possible agreement on effort comparability needs a combination of indicators. ► We analyse the role played by the degree of flexibility in global carbon trading

  12. Climate Prediction Center (CPC) Global Land Surface Air Temperature Analysis

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — A station observation-based global land monthly mean surface air temperature dataset at 0.5 0.5 latitude-longitude resolution for the period from 1948 to the present...

  13. The Global Physical Inactivity Pandemic: An Analysis of Knowledge Production

    Science.gov (United States)

    Piggin, Joe; Bairner, Alan

    2016-01-01

    In July 2012, "The Lancet" announced a pandemic of physical inactivity and a global call to action to effect change. The worldwide pandemic is said to be claiming millions of lives every year. Asserting that physical inactivity is pandemic is an important moment. Given the purported scale and significance of physical inactivity around…

  14. The Global Financial Crisis: Analysis and Policy Implications

    Science.gov (United States)

    2009-05-12

    Ministerio de Economia y Finanzas Publicas. Instituto Nacional de Estadistica y Censos (INDEC). Utilizacion de la Capacidid Instalada en la Industria...2008 and International Monetary Fund. Global Markets Monitor. March 17, 2009. 102 Republica Argentina. Ministerio de Economia y Finanzas Publicas

  15. Climate Prediction Center (CPC) Global Land Surface Air Temperature Analysis

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — A station observation-based global land monthly mean surface air temperature dataset at 0.5 x 0.5 latitude-longitude resolution for the period from 1948 to the...

  16. Methodological considerations for global analysis of cellular FLIM/FRET measurements

    Science.gov (United States)

    Adbul Rahim, Nur Aida; Pelet, Serge; Kamm, Roger D.; So, Peter T. C.

    2012-02-01

    Global algorithms can improve the analysis of fluorescence energy transfer (FRET) measurement based on fluorescence lifetime microscopy. However, global analysis of FRET data is also susceptible to experimental artifacts. This work examines several common artifacts and suggests remedial experimental protocols. Specifically, we examined the accuracy of different methods for instrument response extraction and propose an adaptive method based on the mean lifetime of fluorescent proteins. We further examined the effects of image segmentation and a priori constraints on the accuracy of lifetime extraction. Methods to test the applicability of global analysis on cellular data are proposed and demonstrated. The accuracy of global fitting degrades with lower photon count. By systematically tracking the effect of the minimum photon count on lifetime and FRET prefactors when carrying out global analysis, we demonstrate a correction procedure to recover the correct FRET parameters, allowing us to obtain protein interaction information even in dim cellular regions with photon counts as low as 100 per decay curve.

  17. Global-Local Analysis and Optimization of a Composite Civil Tilt-Rotor Wing

    Science.gov (United States)

    Rais-Rohani, Masound

    1999-01-01

    This report gives highlights of an investigation on the design and optimization of a thin composite wing box structure for a civil tilt-rotor aircraft. Two different concepts are considered for the cantilever wing: (a) a thin monolithic skin design, and (b) a thick sandwich skin design. Each concept is examined with three different skin ply patterns based on various combinations of 0, +/-45, and 90 degree plies. The global-local technique is used in the analysis and optimization of the six design models. The global analysis is based on a finite element model of the wing-pylon configuration while the local analysis uses a uniformly supported plate representing a wing panel. Design allowables include those on vibration frequencies, panel buckling, and material strength. The design optimization problem is formulated as one of minimizing the structural weight subject to strength, stiffness, and d,vnamic constraints. Six different loading conditions based on three different flight modes are considered in the design optimization. The results of this investigation reveal that of all the loading conditions the one corresponding to the rolling pull-out in the airplane mode is the most stringent. Also the frequency constraints are found to drive the skin thickness limits, rendering the buckling constraints inactive. The optimum skin ply pattern for the monolithic skin concept is found to be (((0/+/-45/90/(0/90)(sub 2))(sub s))(sub s), while for the sandwich skin concept the optimal ply pattern is found to be ((0/+/-45/90)(sub 2s))(sub s).

  18. Archetypal analysis of diverse Pseudomonas aeruginosa transcriptomes reveals adaptation in cystic fibrosis airways

    DEFF Research Database (Denmark)

    Thøgersen, Juliane Charlotte; Mørup, Morten; Pedersen, Søren Damkiær

    2013-01-01

    is to introduce a method for DNA microarray analysis that provides an intuitive interpretation of data through dimension reduction and pattern recognition. We present the first “Archetypal Analysis” of global gene expression. The analysis is based on microarray data from five integrated studies of Pseudomonas...... aeruginosa isolated from the airways of cystic fibrosis patients. RESULTS: Our analysis clustered samples into distinct groups with comprehensible characteristics since the archetypes representing the individual groups are closely related to samples present in the data set. Significant changes in gene....... This suggests positive selection in the cystic fibrosis lung environment, and changes in gene expression for these isolates are therefore most likely related to adaptation of the bacteria. CONCLUSIONS: Archetypal analysis succeeded in identifying adaptive changes of P. aeruginosa. The combination of clustering...

  19. Optogenetic Activation of the Sensorimotor Cortex Reveals "Local Inhibitory and Global Excitatory" Inputs to the Basal Ganglia.

    Science.gov (United States)

    Ozaki, Mitsunori; Sano, Hiromi; Sato, Shigeki; Ogura, Mitsuhiro; Mushiake, Hajime; Chiken, Satomi; Nakao, Naoyuki; Nambu, Atsushi

    2017-12-01

    To understand how information from different cortical areas is integrated and processed through the cortico-basal ganglia pathways, we used optogenetics to systematically stimulate the sensorimotor cortex and examined basal ganglia activity. We utilized Thy1-ChR2-YFP transgenic mice, in which channelrhodopsin 2 is robustly expressed in layer V pyramidal neurons. We applied light spots to the sensorimotor cortex in a grid pattern and examined neuronal responses in the globus pallidus (GP) and entopeduncular nucleus (EPN), which are the relay and output nuclei of the basal ganglia, respectively. Light stimulation typically induced a triphasic response composed of early excitation, inhibition, and late excitation in GP/EPN neurons. Other response patterns lacking 1 or 2 of the components were also observed. The distribution of the cortical sites whose stimulation induced a triphasic response was confined, whereas stimulation of the large surrounding areas induced early and late excitation without inhibition. Our results suggest that cortical inputs to the GP/EPN are organized in a "local inhibitory and global excitatory" manner. Such organization seems to be the neuronal basis for information processing through the cortico-basal ganglia pathways, that is, releasing and terminating necessary information at an appropriate timing, while simultaneously suppressing other unnecessary information. © The Author 2017. Published by Oxford University Press.

  20. Global Prevalence of Elder Abuse: A Meta-analysis and Meta-regression.

    Science.gov (United States)

    Ho, C Sh; Wong, S Y; Chiu, M M; Ho, R Cm

    2017-06-01

    Elder abuse is increasingly recognised as a global public health and social problem. There has been limited inter-study comparison of the prevalence and risk factors for elder abuse. This study aimed to estimate the pooled and subtype prevalence of elder abuse worldwide and identify significant associated risk factors. We conducted a meta-analysis and meta-regression of 34 population-based and 17 non-population-based studies. The pooled prevalences of elder abuse were 10.0% (95% confidence interval, 5.2%-18.6%) and 34.3% (95% confidence interval, 22.9%-47.8%) in population-based studies and third party- or caregiver-reported studies, respectively. Being in a marital relationship was found to be a significant moderator using random-effects model. This meta-analysis revealed that third parties or caregivers were more likely to report abuse than older abused adults. Subgroup analyses showed that females and those resident in non-western countries were more likely to be abused. Emotional abuse was the most prevalent elder abuse subtype and financial abuse was less commonly reported by third parties or caregivers. Heterogeneity in the prevalence was due to the high proportion of married older adults in the sample. Subgroup analysis showed that cultural factors, subtypes of abuse, and gender also contributed to heterogeneity in the pooled prevalence of elder abuse.

  1. Global economic activity and crude oil prices. A cointegration analysis

    International Nuclear Information System (INIS)

    He, Yanan; Wang, Shouyang; Lai, Kin Keung

    2010-01-01

    This paper empirically investigates the cointegrating relationship between crude oil prices and global economic activity. The Kilian economic index is used as an indicator of global economic activity. Based on a supply-demand framework and the cointegration theory, we find that real futures prices of crude oil are cointegrated with the Kilian economic index and a trade weighted US dollar index, and crude oil prices are influenced significantly by fluctuations in the Kilian economic index through both long-run equilibrium conditions and short-run impacts. We also develop an empirically stable, data-coherent and single-equation error-correction model (ECM) which has sensible economic properties. Empirical results based on the ECM show that the adjustment implied by a permanent change in the Kilian economic index is a relatively drawn-out process. (author)

  2. Structure analysis of the global metabolic regulator Crc from Pseudomonas aeruginosa.

    Science.gov (United States)

    Wei, Yong; Zhang, Heng; Gao, Zeng-Qiang; Xu, Jian-Hua; Liu, Quan-Sheng; Dong, Yu-Hui

    2013-01-01

    The global metabolic regulator catabolite repression control (Crc) has recently been found to modulate the susceptibility to antibiotics and virulence in the opportunistic pathogen Pseudomonas aeruginosa and been suggested as a nonlethal target for novel antimicrobials. In P. aeruginosa, Crc couples with the CA motifs from the small RNA CrcZ to form a post-transcriptional regulator system and is removed from the 5'-end of the target mRNAs. In this study, we first reported the crystal structure of Crc from P. aeruginosa refined to 2.20 Å. The structure showed that it consists of two halves with similar overall topology and there are 11 β strands surrounded by 13 helices, forming a four-layered α/β-sandwich. The circular dichroism spectroscopy revealed that it is thermostable in solution and shares similar characteristics to that in crystal. Comprehensive structural analysis and comparison with the homologies of Crc showed high similarity with several known nucleases and consequently may be classified into a member exodeoxyribonuclease III. However, it shows distinct substrate specificity (RNA as the preferred substrate) compared to these DNA endonucleases. Structural comparisons also revealed potential RNA recognition and binding region mainly consisting of five flexible loops. Our structure study provided the basis for the future application of Crc as a target to develop new antibiotics. Copyright © 2012 International Union of Biochemistry and Molecular Biology, Inc.

  3. Global analysis of epigenetic regulation of gene expression in response to drought stress in Sorghum.

    Energy Technology Data Exchange (ETDEWEB)

    Reddy, Anireddy [Colorado State Univ., Fort Collins, CO (United States); Ben-Hur, Asa [Colorado State Univ., Fort Collins, CO (United States)

    2017-11-22

    Abiotic stresses including drought are major limiting factors of crop yields and cause significant crop losses. Acquisition of stress tolerance to abiotic stresses requires coordinated regulation of a multitude of biochemical and physiological changes, and most of these changes depend on alterations in gene expression. The goal of this work is to perform global analysis of differential regulation of gene expression and alternative splicing, and their relationship with chromatin landscape in drought sensitive and tolerant cultivars. our Iso-Seq study revealed transcriptome-wide full-length isoforms at an unprecedented scale with over 11000 novel splice isoforms. Additionally, we uncovered alternative polyadenylation sites of ~11000 expressed genes and many novel genes. Overall, Iso-Seq results greatly enhanced sorghum gene annotations that are not only useful in analyzing all our RNA-seq, ChIP-seq and ATAC-seq data but also serve as a great resource to the plant biology community. Our studies identified differentially expressed genes and splicing events that are correlated with the drought-resistant phenotype. An association between alternative splicing and chromatin accessibility was also revealed. Several computational tools developed here (TAPIS and iDiffIR) have been made freely available to the research community in analyzing alternative splicing and differential alternative splicing.

  4. Hydropower versus irrigation—an analysis of global patterns

    Science.gov (United States)

    Zeng, Ruijie; Cai, Ximing; Ringler, Claudia; Zhu, Tingju

    2017-03-01

    Numerous reservoirs around the world provide multiple flow regulation functions; key among these are hydroelectricity production and water releases for irrigation. These functions contribute to energy and food security at national, regional and global levels. While reservoir operations for hydroelectricity production might support irrigation, there are also well-known cases where hydroelectricity production reduces water availability for irrigated food production. This study assesses these relationships at the global level using machine-learning techniques and multi-source datasets. We find that 54% of global installed hydropower capacity (around 507 thousand Megawatt) competes with irrigation. Regions where such competition exists include the Central United States, northern Europe, India, Central Asia and Oceania. On the other hand, 8% of global installed hydropower capacity (around 79 thousand Megawatt) complements irrigation, particularly in the Yellow and Yangtze River Basins of China, the East and West Coasts of the United States and most river basins of Southeast Asia, Canada and Russia. No significant relationship is found for the rest of the world. We further analyze the impact of climate variables on the relationships between hydropower and irrigation. Reservoir flood control functions that operate under increased precipitation levels appear to constrain hydroelectricity production in various river basins of the United States, South China and most basins in Europe and Oceania. On the other hand, increased reservoir evaporative losses and higher irrigation requirements due to higher potential evaporation levels may lead to increased tradeoffs between irrigation and hydropower due to reduced water availability in regions with warmer climates, such as India, South China, and the Southern United States. With most reservoirs today being built for multiple purposes, it is important for policymakers to understand and plan for growing tradeoffs between key

  5. Analysis of Roanoke Region Weather Patterns Under Global Teleconnections

    OpenAIRE

    LaRocque, Eric John

    2006-01-01

    This work attempts to relate global teleconnections, through physical phenomena such as the El Nino-Southern Oscillation (ENSO), Artic Oscillation (AO), North Atlantic Oscillation (NAO), and the Pacific North American (PNA) pattern to synoptic-scale weather patterns and precipitation in the Roanoke, Virginia region. The first chapter describes the behavior of the El Nino-Southern Oscillation (ENSO) by implementing non-homogeneous and homogeneous Markov Chain models on a monthly time series o...

  6. The Global Financial Crisis: Analysis and Policy Implications

    Science.gov (United States)

    2009-10-02

    tariffs and new non-tariff measures (non-automatic licenses, reference prices, etc.) affecting merchandise trade. The WTO also compiled a list of new...stores, restaurants , and bars and could cost more than 40,000 jobs. Closing the assembly line in Fremont marks the end of large-scale auto manufacturing...and the 20- City Composite is down 29.1%. March 31. The World Trade Organization (WTO) predicted that the volume of global merchandise trade would

  7. Economic-Social Analysis of Global Illicit Drug Trade

    OpenAIRE

    Salahedin Ghaderi

    2003-01-01

    Political unstability, less respect to the role of law, low life standards and suitable conditions for poppy/coca cultivation, have all affected on growing illicit drug international trafficking. Colombia is the center for global cocaine industry. Colombians had to use ship in the Carribean but now they pass Mexico where the costs are half of using ship. Mexican traffickers permit that the domestic poppy plants turned into herion, Colombian cocaine transited to USA and methamephtamine manufac...

  8. The Global Financial and Economic Crisis: Analysis and Policy Implications

    Science.gov (United States)

    2009-02-20

    Takeover Plan. Bloomberg. October 21, 2008 and Latin American Monitor: Southern Cone. January 2009. 77 Republica Argentina. Ministerio de Economia y...Finanzas Publicas. Instituto Nacional de Estadistica y Censos. Intercambio Comercial Argentino. Buenos Aires, January 28, 2009. 78 Global Insight...fund a rescue of Bank of America which guarantees $118 billion in troubled assets. January 6. Chile announced a $4 billion stimulus package

  9. Vertically mounted bifacial photovoltaic modules: A global analysis

    International Nuclear Information System (INIS)

    Guo, Siyu; Walsh, Timothy Michael; Peters, Marius

    2013-01-01

    Bifacial PV (photovoltaic) modules have recently come to increasing attention and various system designs have been investigated. In this paper, a global comparison is made between vertically mounted bifacial modules facing East–West and conventionally mounted mono-facial modules. An analytical method is used to calculate the radiation received by these two module configurations. It is found that the answer to the question which of these two module configurations performs better strongly depends on three factors: (i) the latitude, (ii) the local diffuse fraction and (iii) the albedo. In a subsequent part of the paper, the minimum albedo required to result in a better performance for vertically mounted bifacial modules is calculated for every place in the world. The calculation is based on measured data of the diffuse light fraction and the results are shown in the form of a global map. Finally, the albedo requirements are compared with the measured global albedo distribution. The calculation allows a distinct decision which module configuration is more suitable for a certain place in the world. The result is also shown as a map defining the corresponding areas. - Highlights: • Vertically mounted bifacial module and conventionally monofacial module are compared. • The key factors affecting the performance of the two configurations are investigated. • Which module configuration is more suitable for each place is shown in a world map. • The minimum albedo for bifacial modules to have a better performance is calculated

  10. Global analysis of anthropogenic debris ingestion by sea turtles.

    Science.gov (United States)

    Schuyler, Qamar; Hardesty, Britta Denise; Wilcox, Chris; Townsend, Kathy

    2014-02-01

    Ingestion of marine debris can have lethal and sublethal effects on sea turtles and other wildlife. Although researchers have reported on ingestion of anthropogenic debris by marine turtles and implied incidences of debris ingestion have increased over time, there has not been a global synthesis of the phenomenon since 1985. Thus, we analyzed 37 studies published from 1985 to 2012 that report on data collected from before 1900 through 2011. Specifically, we investigated whether ingestion prevalence has changed over time, what types of debris are most commonly ingested, the geographic distribution of debris ingestion by marine turtles relative to global debris distribution, and which species and life-history stages are most likely to ingest debris. The probability of green (Chelonia mydas) and leatherback turtles (Dermochelys coriacea) ingesting debris increased significantly over time, and plastic was the most commonly ingested debris. Turtles in nearly all regions studied ingest debris, but the probability of ingestion was not related to modeled debris densities. Furthermore, smaller, oceanic-stage turtles were more likely to ingest debris than coastal foragers, whereas carnivorous species were less likely to ingest debris than herbivores or gelatinovores. Our results indicate oceanic leatherback turtles and green turtles are at the greatest risk of both lethal and sublethal effects from ingested marine debris. To reduce this risk, anthropogenic debris must be managed at a global level. © 2013 The Authors. Conservation Biology published by Wiley Periodicals, Inc., on behalf of the Society for Conservation Biology.

  11. Global energy futures and human development: a framework for analysis

    International Nuclear Information System (INIS)

    Pasternak, A.D.

    2001-01-01

    This paper explores the relationship between measures of human well-being and consumption of energy and electricity. A correlation is shown between the United Nations Human Development Index (HDI) and annual per- capita electricity consumption for 60 populous countries comprising 90% of the world population. In this correlation, HDI reaches a maximum value when electricity consumption is about 4,000 kWh per person per year, well below consumption levels for most developed countries but also well above the level for developing countries. The correlation with electricity use is better than with total primary energy use. Global electricity consumption associated with a ''Human Development Scenario'' is estimated by adding to U.S. Department of Energy projections for the year 2020 increments of additional electricity consumption sufficient to reach 4,000 kWh per capita on a country-by-country basis. A roughly constant ratio of primary energy consumption to electric energy consumption is observed for countries with high levels of electricity use, and this ratio is used to estimate global primary energy consumption in the Human Development Scenario. The Human Development Scenario implies significantly greater global consumption of electricity and primary energy than do projections for 2020 by the DOE and others. (author)

  12. Global energy futures and human development: a framework for analysis

    Energy Technology Data Exchange (ETDEWEB)

    Pasternak, A.D. [Lawrence Livermore National Lab., CA (United States)

    2001-07-01

    This paper explores the relationship between measures of human well-being and consumption of energy and electricity. A correlation is shown between the United Nations Human Development Index (HDI) and annual per- capita electricity consumption for 60 populous countries comprising 90% of the world population. In this correlation, HDI reaches a maximum value when electricity consumption is about 4,000 kWh per person per year, well below consumption levels for most developed countries but also well above the level for developing countries. The correlation with electricity use is better than with total primary energy use. Global electricity consumption associated with a ''Human Development Scenario'' is estimated by adding to U.S. Department of Energy projections for the year 2020 increments of additional electricity consumption sufficient to reach 4,000 kWh per capita on a country-by-country basis. A roughly constant ratio of primary energy consumption to electric energy consumption is observed for countries with high levels of electricity use, and this ratio is used to estimate global primary energy consumption in the Human Development Scenario. The Human Development Scenario implies significantly greater global consumption of electricity and primary energy than do projections for 2020 by the DOE and others. (author)

  13. EXPLORATORY DATA ANALYSIS AND MULTIVARIATE STRATEGIES FOR REVEALING MULTIVARIATE STRUCTURES IN CLIMATE DATA

    Directory of Open Access Journals (Sweden)

    2016-12-01

    Full Text Available This paper is on data analysis strategy in a complex, multidimensional, and dynamic domain. The focus is on the use of data mining techniques to explore the importance of multivariate structures; using climate variables which influences climate change. Techniques involved in data mining exercise vary according to the data structures. The multivariate analysis strategy considered here involved choosing an appropriate tool to analyze a process. Factor analysis is introduced into data mining technique in order to reveal the influencing impacts of factors involved as well as solving for multicolinearity effect among the variables. The temporal nature and multidimensionality of the target variables is revealed in the model using multidimensional regression estimates. The strategy of integrating the method of several statistical techniques, using climate variables in Nigeria was employed. R2 of 0.518 was obtained from the ordinary least square regression analysis carried out and the test was not significant at 5% level of significance. However, factor analysis regression strategy gave a good fit with R2 of 0.811 and the test was significant at 5% level of significance. Based on this study, model building should go beyond the usual confirmatory data analysis (CDA, rather it should be complemented with exploratory data analysis (EDA in order to achieve a desired result.

  14. Genome Wide Transcriptome Analysis reveals ABA mediated response in Arabidopsis during Gold (AuCl4- treatment

    Directory of Open Access Journals (Sweden)

    Devesh eShukla

    2014-11-01

    Full Text Available The unique physico-chemical properties of gold nanoparticles (AuNPs find manifold applications in diagnostics, medicine and catalysis. Chemical synthesis produces reactive AuNPs and generates hazardous by-products. Alternatively, plants can be utilized to produce AuNPs in an eco-friendly manner. To better control the biosynthesis of AuNPs, we need to first understand the detailed molecular response induced by AuCl4- In this study, we carried out global transcriptome analysis in root tissue of Arabidopsis grown for 12- hours in presence of gold solution (HAuCl4 using the novel unbiased Affymetrix exon array. Transcriptomics analysis revealed differential regulation of a total of 704 genes and 4900 exons. Of these, 492 and 212 genes were up- and downregulated, respectively. The validation of the expressed key genes, such as glutathione-S-transferases, auxin responsive genes, cytochrome P450 82C2, methyl transferases, transducin (G protein beta subunit, ERF transcription factor, ABC, and MATE transporters, was carried out through quantitative RT-PCR. These key genes demonstrated specific induction under AuCl4- treatment relative to other heavy metals, suggesting a unique plant-gold interaction. GO enrichment analysis reveals the upregulation of processes like oxidative stress, glutathione binding, metal binding, transport, and plant hormonal responses. Changes predicted in biochemical pathways indicated major modulation in glutathione mediated detoxification, flavones and derivatives, and plant hormone biosynthesis. Motif search analysis identified a highly significant enriched motif, ACGT, which is an abscisic acid responsive core element (ABRE, suggesting the possibility of ABA- mediated signaling. Identification of abscisic acid response element (ABRE points to the operation of a predominant signaling mechanism in response to AuCl4- exposure. Overall, this study presents a useful picture of plant-gold interaction with an identification of

  15. Genesis of Twin Tropical Cyclones as Revealed by a Global Mesoscale Model: The Role of Mixed Rossby Gravity Waves

    Science.gov (United States)

    Shen, Bo-Wen; Tao, Wei-Kuo; Lin, Yuh-Lang; Laing, Arlene

    2012-01-01

    In this study, it is proposed that twin tropical cyclones (TCs), Kesiny and 01A, in May 2002 formed in association with the scale interactions of three gyres that appeared as a convectively coupled mixed Rossby gravity (ccMRG) wave during an active phase of the Madden-Julian Oscillation (MJO). This is shown by analyzing observational data, including NCEP reanalysis data and METEOSAT 7 IR satellite imagery, and performing numerical simulations using a global mesoscale model. A 10-day control run is initialized at 0000 UTC 1 May 2002 with grid-scale condensation but no sub-grid cumulus parameterizations. The ccMRG wave was identified as encompassing two developing and one non-developing gyres, the first two of which intensified and evolved into the twin TCs. The control run is able to reproduce the evolution of the ccMRG wave and thus the formation of the twin TCs about two and five days in advance as well as their subsequent intensity evolution and movement within an 8-10 day period. Five additional 10-day sensitivity experiments with different model configurations are conducted to help understand the interaction of the three gyres, leading to the formation of the TCs. These experiments suggest the improved lead time in the control run may be attributed to the realistic simulation of the ccMRG wave with the following processes: (1) wave deepening (intensification) associated with a reduction in wavelength and/or the intensification of individual gyres, (2) poleward movement of gyres that may be associated with boundary layer processes, (3) realistic simulation of moist processes at regional scales in association with each of the gyres, and (4) the vertical phasing of low- and mid-level cyclonic circulations associated with a specific gyre.

  16. Body-size structure of Central Iberian mammal fauna reveals semidesertic conditions during the middle Miocene Global Cooling Event.

    Directory of Open Access Journals (Sweden)

    Iris Menéndez

    Full Text Available We developed new quantitative palaeoclimatic inference models based on the body-size structure of mammal faunas from the Old World tropics and applied them to the Somosaguas fossil site (middle Miocene, central Iberian Peninsula. Twenty-six mammal species have been described at this site, including proboscideans, ungulates, carnivores, insectivores, lagomorphs and rodents. Our analyses were based on multivariate and bivariate regression models correlating climatic data and body-size structure of 63 modern mammal assemblages from Sub-Saharan Africa and the Indian subcontinent. The results showed an average temperature of the coldest month higher than 26°C for the Somosaguas fossil site, a mean annual thermal amplitude around 10°C, a drought length of 10 months, and an annual total precipitation greater than 200 mm per year, which are climate conditions typical of an ecotonal zone between the savanna and desert biomes. These results are congruent with the aridity peaks described over the middle Aragonian of Spain and particularly in the local biozone E, which includes Somosaguas. The aridity increase detected in this biozone is associated with the Middle Miocene Global Cooling Event. The environment of Somosaguas around 14 Ma was similar to the current environment in the Sahel region of North Africa, the Horn of Africa, the boundary area between the Kalahari and the Namib in Southern Africa, south-central Arabia, or eastern Pakistan and northwestern India. The distribution of modern vegetation in these regions follows a complex mosaic of plant communities, dominated by scattered xerophilous shrublands, semidesert grasslands, and vegetation linked to seasonal watercourses and ponds.

  17. Body-size structure of Central Iberian mammal fauna reveals semidesertic conditions during the middle Miocene Global Cooling Event.

    Science.gov (United States)

    Menéndez, Iris; Gómez Cano, Ana R; García Yelo, Blanca A; Domingo, Laura; Domingo, M Soledad; Cantalapiedra, Juan L; Blanco, Fernando; Hernández Fernández, Manuel

    2017-01-01

    We developed new quantitative palaeoclimatic inference models based on the body-size structure of mammal faunas from the Old World tropics and applied them to the Somosaguas fossil site (middle Miocene, central Iberian Peninsula). Twenty-six mammal species have been described at this site, including proboscideans, ungulates, carnivores, insectivores, lagomorphs and rodents. Our analyses were based on multivariate and bivariate regression models correlating climatic data and body-size structure of 63 modern mammal assemblages from Sub-Saharan Africa and the Indian subcontinent. The results showed an average temperature of the coldest month higher than 26°C for the Somosaguas fossil site, a mean annual thermal amplitude around 10°C, a drought length of 10 months, and an annual total precipitation greater than 200 mm per year, which are climate conditions typical of an ecotonal zone between the savanna and desert biomes. These results are congruent with the aridity peaks described over the middle Aragonian of Spain and particularly in the local biozone E, which includes Somosaguas. The aridity increase detected in this biozone is associated with the Middle Miocene Global Cooling Event. The environment of Somosaguas around 14 Ma was similar to the current environment in the Sahel region of North Africa, the Horn of Africa, the boundary area between the Kalahari and the Namib in Southern Africa, south-central Arabia, or eastern Pakistan and northwestern India. The distribution of modern vegetation in these regions follows a complex mosaic of plant communities, dominated by scattered xerophilous shrublands, semidesert grasslands, and vegetation linked to seasonal watercourses and ponds.

  18. SVD identifies transcript length distribution functions from DNA microarray data and reveals evolutionary forces globally affecting GBM metabolism.

    Directory of Open Access Journals (Sweden)

    Nicolas M Bertagnolli

    Full Text Available To search for evolutionary forces that might act upon transcript length, we use the singular value decomposition (SVD to identify the length distribution functions of sets and subsets of human and yeast transcripts from profiles of mRNA abundance levels across gel electrophoresis migration distances that were previously measured by DNA microarrays. We show that the SVD identifies the transcript length distribution functions as "asymmetric generalized coherent states" from the DNA microarray data and with no a-priori assumptions. Comparing subsets of human and yeast transcripts of the same gene ontology annotations, we find that in both disparate eukaryotes, transcripts involved in protein synthesis or mitochondrial metabolism are significantly shorter than typical, and in particular, significantly shorter than those involved in glucose metabolism. Comparing the subsets of human transcripts that are overexpressed in glioblastoma multiforme (GBM or normal brain tissue samples from The Cancer Genome Atlas, we find that GBM maintains normal brain overexpression of significantly short transcripts, enriched in transcripts that are involved in protein synthesis or mitochondrial metabolism, but suppresses normal overexpression of significantly longer transcripts, enriched in transcripts that are involved in glucose metabolism and brain activity. These global relations among transcript length, cellular metabolism and tumor development suggest a previously unrecognized physical mode for tumor and normal cells to differentially regulate metabolism in a transcript length-dependent manner. The identified distribution functions support a previous hypothesis from mathematical modeling of evolutionary forces that act upon transcript length in the manner of the restoring force of the harmonic oscillator.

  19. Global Analysis of Anthropogenic Debris Ingestion by Sea Turtles

    Science.gov (United States)

    Schuyler, Qamar; Hardesty, Britta Denise; Wilcox, Chris; Townsend, Kathy

    2014-01-01

    Ingestion of marine debris can have lethal and sublethal effects on sea turtles and other wildlife. Although researchers have reported on ingestion of anthropogenic debris by marine turtles and implied incidences of debris ingestion have increased over time, there has not been a global synthesis of the phenomenon since 1985. Thus, we analyzed 37 studies published from 1985 to 2012 that report on data collected from before 1900 through 2011. Specifically, we investigated whether ingestion prevalence has changed over time, what types of debris are most commonly ingested, the geographic distribution of debris ingestion by marine turtles relative to global debris distribution, and which species and life-history stages are most likely to ingest debris. The probability of green (Chelonia mydas) and leatherback turtles (Dermochelys coriacea) ingesting debris increased significantly over time, and plastic was the most commonly ingested debris. Turtles in nearly all regions studied ingest debris, but the probability of ingestion was not related to modeled debris densities. Furthermore, smaller, oceanic-stage turtles were more likely to ingest debris than coastal foragers, whereas carnivorous species were less likely to ingest debris than herbivores or gelatinovores. Our results indicate oceanic leatherback turtles and green turtles are at the greatest risk of both lethal and sublethal effects from ingested marine debris. To reduce this risk, anthropogenic debris must be managed at a global level. Análisis Global de la Ingesta de Residuos Antropogénicos por Tortugas Marinas La ingesta de residuos marinos puede tener efectos letales y subletales sobre las tortugas marinas y otros animales. Aunque hay investigadores que han reportado la ingesta de residuos antropogénicos por tortugas marinas y la incidencia de la ingesta de residuos ha incrementado con el tiempo, no ha habido una síntesis global del fenómeno desde 1985. Por esto analizamos 37 estudios publicados, desde

  20. Global health worker salary estimates: an econometric analysis of global earnings data.

    Science.gov (United States)

    Serje, Juliana; Bertram, Melanie Y; Brindley, Callum; Lauer, Jeremy A

    2018-01-01

    Human resources are consistently cited as a leading contributor to health care costs; however the availability of internationally comparable data on health worker earnings for all countries is a challenge for estimating the costs of health care services. This paper describes an econometric model using cross sectional earnings data from the International Labour Organization (ILO) that the World Health Organizations (WHO)-Choosing Interventions that are Cost-effective programme (CHOICE) has used to prepare estimates of health worker earnings (in 2010 USD) for all WHO member states. The ILO data contained 324 observations of earnings data across 4 skill levels for 193 countries. Using this data, along with the assumption that data were missing not at random, we used a Heckman two stage selection model to estimate earning data for each of the 4 skill levels for all WHO member states. It was possible to develop a prediction model for health worker earnings for all countries for which GDP data was available. Health worker earnings vary both within country due to skill level, as well as across countries. As a multiple of GDP per capita, earnings show a negative correlation with GDP-that is lower income countries pay their health workers relatively more than higher income countries. Limited data on health worker earnings is a limiting factor in estimating the costs of global health programmes. It is hoped that these estimates will support robust health care intervention costings and projections of resources needs over the Sustainable Development Goal period.

  1. Discourse Analysis of Domination of the Global Human Rights

    Directory of Open Access Journals (Sweden)

    Nasrin Mosaffa

    2012-11-01

    Full Text Available In this article, we are attempting to answer the question of how the Global Human Rights as an idea which is in accordance with common sense took shape. The conceptual and theoretical framework and research method of this exploration is based on discourse analysis and in step with Laclu and Mouffe's agenda. Therefore, phenomenon of Human Rights in the present analysis is thought of as a discourse. This discourse, granted temporary stability to central signs such as human dignity, liberty, equality, tolerance that their meanings were being fluctuated in World War II, around nodal point of “Human Rights” and has been dominated in the agenda of International Politics. This discourse, of course was validated by exclusion and rejection of other means of these signs. The ultimate goal of this study is to show the contingent and the historical of phenomenon of Human Rights. ما در مقالۀ حاضر در صدد پاسخ گفتن به این پرسش هستیم که چگونه حقوق بشر جهانی به مثابۀ انگاره‌ای مطابق با عقل سلیم شکل گرفت. چارچوب مفهومی، نظری و روش تحقیق این کاوش، تحلیل گفتمانی و همگام با دستورکار لاکلا و موف است. پدیدۀ حقوق بشر در تحلیل حاضر به صورت گفتمانی تصور می‌شود. این گفتمان، نشانه‌های محوری چون کرامت انسانی، آزادی، برابری، مدارا را که معنایشان‌ در زمان جنگ جهانی دوم در حال شناورشدن بود، حول دال مرکزی «حقوق بشر» ثبات موقت بخشیده و در دستورکار سیاست بین‌الملل مسلط ساخته است. البته این گفتمان با برون‌گذاری و طرد سایر معانی از این نشانه‌ها اعتبار یافت. هدف نهایی این مطالعه، نشان دادن

  2. The Community College and a Rising Global Imaginary: An Analysis of Practical Reasoning, 1950-2013

    Science.gov (United States)

    Ayers, David F.; Palmadessa, Allison L.

    2015-01-01

    Through an analysis of 245 issues of the "Community College Journal" published between 1950 and 2013, we show how three discourses--international understanding and geopolitics, economic competitiveness, and global citizenship--informed practical reasoning about a rising global imaginary and its implications for the community college. By…

  3. The Determination of Children's Knowledge of Global Lunar Patterns from Online Essays Using Text Mining Analysis

    Science.gov (United States)

    Cheon, Jongpil; Lee, Sangno; Smith, Walter; Song, Jaeki; Kim, Yongjin

    2013-01-01

    The purpose of this study was to use text mining analysis of early adolescents' online essays to determine their knowledge of global lunar patterns. Australian and American students in grades five to seven wrote about global lunar patterns they had discovered by sharing observations with each other via the Internet. These essays were analyzed for…

  4. Sequence analysis of serum albumins reveals the molecular evolution of ligand recognition properties.

    Science.gov (United States)

    Fanali, Gabriella; Ascenzi, Paolo; Bernardi, Giorgio; Fasano, Mauro

    2012-01-01

    Serum albumin (SA) is a circulating protein providing a depot and carrier for many endogenous and exogenous compounds. At least seven major binding sites have been identified by structural and functional investigations mainly in human SA. SA is conserved in vertebrates, with at least 49 entries in protein sequence databases. The multiple sequence analysis of this set of entries leads to the definition of a cladistic tree for the molecular evolution of SA orthologs in vertebrates, thus showing the clustering of the considered species, with lamprey SAs (Lethenteron japonicum and Petromyzon marinus) in a separate outgroup. Sequence analysis aimed at searching conserved domains revealed that most SA sequences are made up by three repeated domains (about 600 residues), as extensively characterized for human SA. On the contrary, lamprey SAs are giant proteins (about 1400 residues) comprising seven repeated domains. The phylogenetic analysis of the SA family reveals a stringent correlation with the taxonomic classification of the species available in sequence databases. A focused inspection of the sequences of ligand binding sites in SA revealed that in all sites most residues involved in ligand binding are conserved, although the versatility towards different ligands could be peculiar of higher organisms. Moreover, the analysis of molecular links between the different sites suggests that allosteric modulation mechanisms could be restricted to higher vertebrates.

  5. A structural homologue of colipase in black mamba venom revealed by NMR floating disulphide bridge analysis.

    Science.gov (United States)

    Boisbouvier, J; Albrand, J P; Blackledge, M; Jaquinod, M; Schweitz, H; Lazdunski, M; Marion, D

    1998-01-01

    The solution structure of mamba intestinal toxin 1 (MIT1), isolated from Dendroaspis polylepis polylepis venom, has been determined. This molecule is a cysteine-rich polypeptide exhibiting no recognised family membership. Resistance to MIT1 to classical specific endoproteases produced contradictory NMR and biochemical information concerning disulphide-bridge topology. We have used distance restraints allowing ambiguous partners between S atoms in combination with NMR-derived structural information, to correctly determine the disulphide-bridge topology. The resultant solution structure of MIT1, determined to a resolution of 0.5 A, reveals an unexpectedly similar global fold with respect to colipase, a protein involved in fatty acid digestion. Colipase exhibits an analogous resistance to endoprotease activity, indicating for the first time the possible topological origins of this biochemical property. The biochemical and structural homology permitted us to propose a mechanically related digestive function for MIT1 and provides novel information concerning snake venom protein evolution. Copyright 1998 Academic Press.

  6. Forest responses to tropospheric ozone and global climate change: an analysis.

    Science.gov (United States)

    Kickert, R N; Krupa, S V

    1990-01-01

    In this paper an analysis is provided on: what we know, what we need to know, and what we need to do, to further our understanding of the relationships between tropospheric ozone (O(3)), global climate change and forest responses. The relationships between global geographic distributions of forest ecosystems and potential geographic regions of high photochemical smog by the year 2025 AD are described. While the emphasis is on the effects of tropospheric O(3) on forest ecosystems, discussion is presented to understand such effects in the context of global climate change. One particular strong point of this paper is the audit of published surface O(3) data by photochemical smog region that reveals important forest/woodland geographic regions where little or no O(3) data exist even though the potential threat to forests in those regions appears to be large. The concepts and considerations relevant to the examination of ecosystem responses as a whole, rather than simply tree stands alone are reviewed. A brief argument is provided to stimulate the modification of the concept of simple cause and effect relationships in viewing total ecosystems. Our knowledge of O(3) exposure and its effects on the energy, nutrient and hydrological flow within the ecosystem are described. Modeling strategies for such systems are reviewed. A discussion of responses of forests to potential multiple climatic changes is provided. An important concept in this paper is that changes in water exchange processes throughout the hydrological cycle can be used as early warning indicators of forest responses to O(3). Another strength of this paper is the integration of information on structural and functional processes of ecosystems and their responses to O(3). An admitted weakness of this analysis is that the information on integrated ecosystem responses is based overwhelmingly on the San Bernardino Forest ecosystem research program of the 1970s because of a lack of similar studies. In the final

  7. Rich club analysis in the Alzheimer's disease connectome reveals a relatively undisturbed structural core network.

    Science.gov (United States)

    Daianu, Madelaine; Jahanshad, Neda; Nir, Talia M; Jack, Clifford R; Weiner, Michael W; Bernstein, Matt A; Thompson, Paul M

    2015-08-01

    Diffusion imaging can assess the white matter connections within the brain, revealing how neural pathways break down in Alzheimer's disease (AD). We analyzed 3-Tesla whole-brain diffusion-weighted images from 202 participants scanned by the Alzheimer's Disease Neuroimaging Initiative-50 healthy controls, 110 with mild cognitive impairment (MCI) and 42 AD patients. From whole-brain tractography, we reconstructed structural brain connectivity networks to map connections between cortical regions. We tested whether AD disrupts the "rich club" - a network property where high-degree network nodes are more interconnected than expected by chance. We calculated the rich club properties at a range of degree thresholds, as well as other network topology measures including global degree, clustering coefficient, path length, and efficiency. Network disruptions predominated in the low-degree regions of the connectome in patients, relative to controls. The other metrics also showed alterations, suggesting a distinctive pattern of disruption in AD, less pronounced in MCI, targeting global brain connectivity, and focusing on more remotely connected nodes rather than the central core of the network. AD involves severely reduced structural connectivity; our step-wise rich club coefficients analyze points to disruptions predominantly in the peripheral network components; other modalities of data are needed to know if this indicates impaired communication among non rich club regions. The highly connected core was relatively preserved, offering new evidence on the neural basis of progressive risk for cognitive decline. © 2015 Wiley Periodicals, Inc.

  8. Global Analysis, Interpretation, and Modelling: First Science Conference

    Science.gov (United States)

    Sahagian, Dork

    1995-01-01

    Topics considered include: Biomass of termites and their emissions of methane and carbon dioxide - A global database; Carbon isotope discrimination during photosynthesis and the isotope ratio of respired CO2 in boreal forest ecosystems; Estimation of methane emission from rice paddies in mainland China; Climate and nitrogen controls on the geography and timescales of terrestrial biogeochemical cycling; Potential role of vegetation feedback in the climate sensitivity of high-latitude regions - A case study at 6000 years B.P.; Interannual variation of carbon exchange fluxes in terrestrial ecosystems; and Variations in modeled atmospheric transport of carbon dioxide and the consequences for CO2 inversions.

  9. Word-wide meta-analysis of Quercus forests ectomycorrhizal fungal diversity reveals southwestern Mexico as a hotspot.

    Science.gov (United States)

    García-Guzmán, Olimpia Mariana; Garibay-Orijel, Roberto; Hernández, Edith; Arellano-Torres, Elsa; Oyama, Ken

    2017-11-01

    Quercus is the most diverse genus of ectomycorrhizal (ECM) host plants; it is distributed in the Northern and Southern Hemispheres, from temperate to tropical regions. However, their ECM communities have been scarcely studied in comparison to those of conifers. The objectives of this study were to determine the richness of ECM fungi associated with oak forests in the Cuitzeo basin in southwestern Mexico; and to determine the level of richness, potential endemism and species similarity among ECM fungal communities associated with natural oak forests worldwide through a meta-analysis. The ITS DNA sequences of ECM root tips from 14 studies were included in the meta-analysis. In total, 1065 species of ECM fungi have been documented worldwide; however, 812 species have been only found at one site. Oak forests in Europe contain 416 species, Mexico 307, USA 285, and China 151. Species with wider distributions are Sebacinaceae sp. SH197130, Amanita subjunquillea, Cenococcum geophilum, Cortinarius decipiens, Russula hortensis, R. risigallina, R. subrubescens, Sebacinaceae sp. SH214607, Tomentella ferruginea, and T. lapida. The meta-analysis revealed (1) that Mexico is not only a hotspot for oak species but also for their ECM mycobionts. (2) There is a particularly high diversity of ECM Pezizales in oak seasonal forests from western USA to southwestern Mexico. (3) The oak forests in southwestern Mexico have the largest number of potential endemic species. (4) Globally, there is a high turnover of ECM fungal species associated with oaks, which indicates high levels of alpha and beta diversity in these communities.

  10. Morphometric differences in planum temporale in schizophrenia and bipolar disorder revealed by statistical analysis of Labeled Cortical Depth Maps

    Directory of Open Access Journals (Sweden)

    J Tilak eRatnanather

    2014-08-01

    Full Text Available Differences in cortical thickness in the lateral temporal lobe, including the planum temporale (PT, have been reported in MRI studies of schizophrenia (SCZ and bipolar disorder (BPD patients. Most of these studies have used a single-valued global or local measure for thickness. However, additional and complementary information can be obtained by generating Labelled Cortical Depth Maps (LCDMs, which are distances of labeled gray matter voxels from the nearest point on the gray/white matter (inner cortical surface. Statistical analyses of pooled and censored LCDM distances reveal subtle differences in PT between SCZ and BPD groups from data generated by Ratnanather et al. (Schizophrenia Research, http://dx.doi.org/10.1016/j.schres.2013.08.014. These results confirm that the left PT (LPT is more sensitive than the right PT in distinguishing between SCZ, BPD and healthy controls. Also confirmed is a strong gender effect, with a thicker PT seen in males than in females. The differences between groups at smaller distances in the LPT revealed by pooled and censored LCDM analysis suggest that SCZ and BPD have different effects on the cortical mantle close to the gray/white matter surface. This is consistent with reported subtle changes in the cortical mantle observed in postmortem studies.

  11. Mars Global Surveyor Ka-Band Frequency Data Analysis

    Science.gov (United States)

    Morabito, D.; Butman, S.; Shambayati, S.

    2000-01-01

    The Mars Global Surveyor (MGS) spacecraft, launched on November 7, 1996, carries an experimental space-to-ground telecommunications link at Ka-band (32 GHz) along with the primary X-band (8.4 GHz) downlink. The signals are simultaneously transmitted from a 1.5-in diameter parabolic high gain antenna (HGA) on MGS and received by a beam-waveguide (BWG) R&D 34-meter antenna located in NASA's Goldstone Deep Space Network (DSN) complex near Barstow, California. The projected 5-dB link advantage of Ka-band relative to X-band was confirmed in previous reports using measurements of MGS signal strength data acquired during the first two years of the link experiment from December 1996 to December 1998. Analysis of X-band and Ka-band frequency data and difference frequency (fx-fka)/3.8 data will be presented here. On board the spacecraft, a low-power sample of the X-band downlink from the transponder is upconverted to 32 GHz, the Ka-band frequency, amplified to I-W using a Solid State Power Amplifier, and radiated from the dual X/Ka HGA. The X-band signal is amplified by one of two 25 W TWTAs. An upconverter first downconverts the 8.42 GHz X-band signal to 8 GHz and then multiplies using a X4 multiplier producing the 32 GHz Ka-band frequency. The frequency source selection is performed by an RF switch which can be commanded to select a VCO (Voltage Controlled Oscillator) or USO (Ultra-Stable Oscillator) reference. The Ka-band frequency can be either coherent with the X-band downlink reference or a hybrid combination of the USO and VCO derived frequencies. The data in this study were chosen such that the Ka-band signal is purely coherent with the X-band signal, that is the downconverter is driven by the same frequency source as the X-band downlink). The ground station used to acquire the data is DSS-13, a 34-meter BWG antenna which incorporates a series of mirrors inside beam waveguide tubes which guide the energy to a subterranean pedestal room, providing a stable environment

  12. Global Bedload Flux Modeling and Analysis in Large Rivers

    Science.gov (United States)

    Islam, M. T.; Cohen, S.; Syvitski, J. P.

    2017-12-01

    Proper sediment transport quantification has long been an area of interest for both scientists and engineers in the fields of geomorphology, and management of rivers and coastal waters. Bedload flux is important for monitoring water quality and for sustainable development of coastal and marine bioservices. Bedload measurements, especially for large rivers, is extremely scarce across time, and many rivers have never been monitored. Bedload measurements in rivers, is particularly acute in developing countries where changes in sediment yields is high. The paucity of bedload measurements is the result of 1) the nature of the problem (large spatial and temporal uncertainties), and 2) field costs including the time-consuming nature of the measurement procedures (repeated bedform migration tracking, bedload samplers). Here we present a first of its kind methodology for calculating bedload in large global rivers (basins are >1,000 km. Evaluation of model skill is based on 113 bedload measurements. The model predictions are compared with an empirical model developed from the observational dataset in an attempt to evaluate the differences between a physically-based numerical model and a lumped relationship between bedload flux and fluvial and basin parameters (e.g., discharge, drainage area, lithology). The initial study success opens up various applications to global fluvial geomorphology (e.g. including the relationship between suspended sediment (wash load) and bedload). Simulated results with known uncertainties offers a new research product as a valuable resource for the whole scientific community.

  13. Global Analysis of Climate Change Projection Effects on Atmospheric Rivers

    Science.gov (United States)

    Espinoza, Vicky; Waliser, Duane E.; Guan, Bin; Lavers, David A.; Ralph, F. Martin

    2018-05-01

    A uniform, global approach is used to quantify how atmospheric rivers (ARs) change between Coupled Model Intercomparison Project Phase 5 historical simulations and future projections under the Representative Concentration Pathway (RCP) 4.5 and RCP8.5 warming scenarios. The projections indicate that while there will be 10% fewer ARs in the future, the ARs will be 25% longer, 25% wider, and exhibit stronger integrated water vapor transports (IVTs) under RCP8.5. These changes result in pronounced increases in the frequency (IVT strength) of AR conditions under RCP8.5: 50% (25%) globally, 50% (20%) in the northern midlatitudes, and 60% (20%) in the southern midlatitudes. The models exhibit systematic low biases across the midlatitudes in replicating historical AR frequency ( 10%), zonal IVT ( 15%), and meridional IVT ( 25%), with sizable intermodel differences. A more detailed examination of six regions strongly impacted by ARs suggests that the western United States, northwestern Europe, and southwestern South America exhibit considerable intermodel differences in projected changes in ARs.

  14. Comparative analysis of fungal genomes reveals different plant cell wall degrading capacity in fungi

    Science.gov (United States)

    2013-01-01

    Background Fungi produce a variety of carbohydrate activity enzymes (CAZymes) for the degradation of plant polysaccharide materials to facilitate infection and/or gain nutrition. Identifying and comparing CAZymes from fungi with different nutritional modes or infection mechanisms may provide information for better understanding of their life styles and infection models. To date, over hundreds of fungal genomes are publicly available. However, a systematic comparative analysis of fungal CAZymes across the entire fungal kingdom has not been reported. Results In this study, we systemically identified glycoside hydrolases (GHs), polysaccharide lyases (PLs), carbohydrate esterases (CEs), and glycosyltransferases (GTs) as well as carbohydrate-binding modules (CBMs) in the predicted proteomes of 103 representative fungi from Ascomycota, Basidiomycota, Chytridiomycota, and Zygomycota. Comparative analysis of these CAZymes that play major roles in plant polysaccharide degradation revealed that fungi exhibit tremendous diversity in the number and variety of CAZymes. Among them, some families of GHs and CEs are the most prevalent CAZymes that are distributed in all of the fungi analyzed. Importantly, cellulases of some GH families are present in fungi that are not known to have cellulose-degrading ability. In addition, our results also showed that in general, plant pathogenic fungi have the highest number of CAZymes. Biotrophic fungi tend to have fewer CAZymes than necrotrophic and hemibiotrophic fungi. Pathogens of dicots often contain more pectinases than fungi infecting monocots. Interestingly, besides yeasts, many saprophytic fungi that are highly active in degrading plant biomass contain fewer CAZymes than plant pathogenic fungi. Furthermore, analysis of the gene expression profile of the wheat scab fungus Fusarium graminearum revealed that most of the CAZyme genes related to cell wall degradation were up-regulated during plant infection. Phylogenetic analysis also

  15. Ferricyanide-based analysis of aqueous lignin suspension revealed sequestration of water-soluble lignin moieties

    OpenAIRE

    Joshua, CJ; Simmons, BA; Singer, SW

    2016-01-01

    © 2016 The Royal Society of Chemistry. This study describes the application of a ferricyanide-based assay as a simple and inexpensive assay for rapid analysis of aqueous lignin samples. The assay measures the formation of Prussian blue from the redox reaction between a mixture of potassium ferricyanide and ferric chloride, and phenolic hydroxyl groups of lignin or lignin-derived phenolic moieties. This study revealed that soluble lignin moieties exhibited stronger ferricyanide reactivity than...

  16. Global analysis of the techno-economic potential of renewable energy hybrid systems on small islands

    International Nuclear Information System (INIS)

    Blechinger, P.; Cader, C.; Bertheau, P.; Huyskens, H.; Seguin, R.; Breyer, C.

    2016-01-01

    Globally, small islands below 100,000 inhabitants represent a large number of diesel based mini-grids. With volatile fossil fuel costs which are most likely to increase in the long-run and competitive renewable energy technologies the introduction of such sustainable power generation system seems a viable and environmental friendly option. Nevertheless the implementation of renewable energies on small islands is quite low based on high transaction costs and missing knowledge according to the market potential. Our work provides a global overview on the small island landscape showing the respective population, economic activity, energy demand, and fuel costs for almost 1800 islands with approximately 20 million inhabitants currently supplied by 15 GW of diesel plants. Based on these parameters a detailed techno-economic assessment of the potential integration of solar PV, wind power, and battery storage into the power supply system was performed for each island. The focus on solar and wind was set due to the lack of data on hydro and geothermal potential for a global island study. It revealed that almost 7.5 GW of photovoltaic and 14 GW of wind power could be economically installed and operated on these islands reducing the GHG-emissions and fuel consumption by approximately 50%. In total numbers more than 20 million tons of GHG emissions can be reduced by avoiding the burning of 7.8 billion liters of diesel per year. Cost savings of around 9 USDct/kWh occur on average by implementing these capacities combined with 5.8 GWh of battery storage. This detailed techno-economic evaluation of renewable energies enables policy makers and investors to facilitate the implementation of clean energy supply systems on small islands. To accelerate the implementation of this enormous potential we give specific policy recommendations such as the introduction of proper regulations. - Highlights: • GIS analysis has identified approximately 1800 small island energy systems with

  17. Cost analysis of small hydroelectric power plants components and preliminary estimation of global cost

    International Nuclear Information System (INIS)

    Basta, C.; Olive, W.J.; Antunes, J.S.

    1990-01-01

    An analysis of cost for each components of Small Hydroelectric Power Plant, taking into account the real costs of these projects is shown. It also presents a global equation which allows a preliminary estimation of cost for each construction. (author)

  18. GHRSST Level 4 AVHRR_AMSR_OI Global Blended Sea Surface Temperature Analysis (GDS version 1)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — A Group for High Resolution Sea Surface Temperature (GHRSST) global Level 4 sea surface temperature analysis produced daily on a 0.25 degree grid at the NOAA...

  19. GHRSST Level 4 MW_OI Global Foundation Sea Surface Temperature analysis (GDS version 2)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — A Group for High Resolution Sea Surface Temperature (GHRSST) global Level 4 sea surface temperature analysis produced daily on a 0.25 degree grid at Remote Sensing...

  20. Characterization of global microRNA expression reveals oncogenic potential of miR-145 in metastatic colorectal cancer

    International Nuclear Information System (INIS)

    Arndt, Greg M; Retzlaff, Kathy; Bittner, Anton; Raponi, Mitch; Dossey, Lesley; Cullen, Lara M; Lai, Angela; Druker, Riki; Eisbacher, Michael; Zhang, Chunyan; Tran, Nham; Fan, Hongtao

    2009-01-01

    MicroRNAs (MiRNAs) are short non-coding RNAs that control protein expression through various mechanisms. Their altered expression has been shown to be associated with various cancers. The aim of this study was to profile miRNA expression in colorectal cancer (CRC) and to analyze the function of specific miRNAs in CRC cells. MirVana miRNA Bioarrays were used to determine the miRNA expression profile in eight CRC cell line models, 45 human CRC samples of different stages, and four matched normal colon tissue samples. SW620 CRC cells were stably transduced with miR-143 or miR-145 expression vectors and analyzed in vitro for cell proliferation, cell differentiation and anchorage-independent growth. Signalling pathways associated with differentially expressed miRNAs were identified using a gene set enrichment analysis. The expression analysis of clinical CRC samples identified 37 miRNAs that were differentially expressed between CRC and normal tissue. Furthermore, several of these miRNAs were associated with CRC tumor progression including loss of miR-133a and gain of miR-224. We identified 11 common miRNAs that were differentially expressed between normal colon and CRC in both the cell line models and clinical samples. In vitro functional studies indicated that miR-143 and miR-145 appear to function in opposing manners to either inhibit or augment cell proliferation in a metastatic CRC model. The pathways targeted by miR-143 and miR-145 showed no significant overlap. Furthermore, gene expression analysis of metastatic versus non-metastatic isogenic cell lines indicated that miR-145 targets involved in cell cycle and neuregulin pathways were significantly down-regulated in the metastatic context. MiRNAs showing altered expression at different stages of CRC could be targets for CRC therapies and be further developed as potential diagnostic and prognostic analytes. The identified biological processes and signalling pathways collectively targeted by co-expressed miRNAs in

  1. Uncertainties propagation and global sensitivity analysis of the frequency response function of piezoelectric energy harvesters

    Science.gov (United States)

    Ruiz, Rafael O.; Meruane, Viviana

    2017-06-01

    The goal of this work is to describe a framework to propagate uncertainties in piezoelectric energy harvesters (PEHs). These uncertainties are related to the incomplete knowledge of the model parameters. The framework presented could be employed to conduct prior robust stochastic predictions. The prior analysis assumes a known probability density function for the uncertain variables and propagates the uncertainties to the output voltage. The framework is particularized to evaluate the behavior of the frequency response functions (FRFs) in PEHs, while its implementation is illustrated by the use of different unimorph and bimorph PEHs subjected to different scenarios: free of uncertainties, common uncertainties, and uncertainties as a product of imperfect clamping. The common variability associated with the PEH parameters are tabulated and reported. A global sensitivity analysis is conducted to identify the Sobol indices. Results indicate that the elastic modulus, density, and thickness of the piezoelectric layer are the most relevant parameters of the output variability. The importance of including the model parameter uncertainties in the estimation of the FRFs is revealed. In this sense, the present framework constitutes a powerful tool in the robust design and prediction of PEH performance.

  2. Global Regulatory T-Cell Research from 2000 to 2015: A Bibliometric Analysis.

    Directory of Open Access Journals (Sweden)

    Yin Zongyi

    Full Text Available We aimed to analyze the global scientific output of regulatory T-cell (Treg research and built a model to qualitatively and quantitatively evaluate publications from 2000 to 2015. Data were obtained from the Web of Science Core Collection (WoSCC of Thomson Reuters on January 1, 2016. The bibliometric method and Citespace III were used to analyze authors, journals, publication outputs, institutions, countries, research areas, research hotspots, and trends. In total, we identified 35,741 publications on Treg research from 2000 to 2015, and observed that the annual publication rate increased with time. The Journal of Immunology published the highest number of articles, the leading country was the USA, and the leading institute was Harvard University. Sakaguchi, Hori, Fontenot, and Wang were the top authors in Treg research. Immunology accounted for the highest number of publications, followed by oncology, experimental medicine, cell biology, and hematology. Keyword analysis indicated that autoimmunity, inflammation, cytokine, gene expression, foxp3, and immunotherapy were the research hotspots, whereas autoimmune inflammation, gene therapy, granzyme B, RORγt, and th17 were the frontiers of Treg research. This bibliometric analysis revealed that Treg-related studies are still research hotspots, and that Treg-related clinical therapies are the research frontiers; however, further study and collaborations are needed worldwide. Overall, our findings provide valuable information for the editors of immunology journals to identify new perspectives and shape future research directions.

  3. Transcriptomic profiling of interacting nasal staphylococci species reveals global changes in gene and non-coding RNA expression

    DEFF Research Database (Denmark)

    Hermansen, Grith Miriam Maigaard; Sazinas, Pavelas; Kofod, Ditte

    2018-01-01

    Interspecies interactions between bacterial pathogens and the commensal microbiota can influence disease outcome. In the nasal cavities, Staphylococcus epidermidis has been shown to be a determining factor for Staphylococcus aureus colonization and biofilm formation. However, the interaction...... between S. epidermidis and S. aureus has mainly been described by phenotypic analysis, and little is known about how this interaction modulates gene expression.This study aimed to determine the interactome of nasal S. aureus and S. epidermidis isolates to understand the molecular effect of interaction...... also identified putative non-coding RNAs (ncRNAs) and, interestingly, detected a putative ncRNA transcribed antisense to esp, the serine protease of S. epidermidis, that has previously been shown to inhibit nasal colonization of S. aureus. In our study, the gene encoding Esp and the antisense nc...

  4. Global stability analysis of epidemiological models based on Volterra–Lyapunov stable matrices

    International Nuclear Information System (INIS)

    Liao Shu; Wang Jin

    2012-01-01

    Highlights: ► Global dynamics of high dimensional dynamical systems. ► A systematic approach for global stability analysis. ► Epidemiological models of environment-dependent diseases. - Abstract: In this paper, we study the global dynamics of a class of mathematical epidemiological models formulated by systems of differential equations. These models involve both human population and environmental component(s) and constitute high-dimensional nonlinear autonomous systems, for which the global asymptotic stability of the endemic equilibria has been a major challenge in analyzing the dynamics. By incorporating the theory of Volterra–Lyapunov stable matrices into the classical method of Lyapunov functions, we present an approach for global stability analysis and obtain new results on some three- and four-dimensional model systems. In addition, we conduct numerical simulation to verify the analytical results.

  5. COMPARATIVE ANALYSIS OF RUSSIA’S AND CHINA’S PARTICIPATING IN GLOBAL GOVERNANCE INSTITUTIONS EXPERIENCE

    Directory of Open Access Journals (Sweden)

    Vladimir E. Petrovskiy

    2015-01-01

    Full Text Available The article deals with the comparative analysis of Russian and Chinese participation in the current system of global governance, and in its reform. The author views participation of the respective countries in the system of global governance as part of their foreign policy and foreign policy strategy. He shows common and distinctive features of conceptual and practical approaches towards global governance defined by specific features of Russia’s and China’s history, economic development, political culture and traditions. Based on this comparative analysis, the author speculates on the future trends of participation of the two countries in the global governance system, in the spheres of global economy and international security, and on the future trends of their policy coordination in these respective areas.

  6. Allosteric effects in bacteriophage HK97 procapsids revealed directly from covariance analysis of cryo EM data.

    Science.gov (United States)

    Xu, Nan; Veesler, David; Doerschuk, Peter C; Johnson, John E

    2018-05-01

    The information content of cryo EM data sets exceeds that of the electron scattering potential (cryo EM) density initially derived for structure determination. Previously we demonstrated the power of data variance analysis for characterizing regions of cryo EM density that displayed functionally important variance anomalies associated with maturation cleavage events in Nudaurelia Omega Capensis Virus and the presence or absence of a maturation protease in bacteriophage HK97 procapsids. Here we extend the analysis in two ways. First, instead of imposing icosahedral symmetry on every particle in the data set during the variance analysis, we only assume that the data set as a whole has icosahedral symmetry. This change removes artifacts of high variance along icosahedral symmetry axes, but retains all of the features previously reported in the HK97 data set. Second we present a covariance analysis that reveals correlations in structural dynamics (variance) between the interior of the HK97 procapsid with the protease and regions of the exterior (not seen in the absence of the protease). The latter analysis corresponds well with hydrogen deuterium exchange studies previously published that reveal the same correlation. Copyright © 2018 Elsevier Inc. All rights reserved.

  7. Drivers of Wetland Conversion: a Global Meta-Analysis

    NARCIS (Netherlands)

    van Asselen, S.; Verburg, P.H.; Vermaat, J.E.; Janse, J.

    2013-01-01

    Meta-analysis of case studies has become an important tool for synthesizing case study findings in land change. Meta-analyses of deforestation, urbanization, desertification and change in shifting cultivation systems have been published. This present study adds to this literature, with an analysis

  8. Global metabolite analysis of yeast: evaluation of sample preparation methods

    DEFF Research Database (Denmark)

    Villas-Bôas, Silas Granato; Højer-Pedersen, Jesper; Åkesson, Mats Fredrik

    2005-01-01

    Sample preparation is considered one of the limiting steps in microbial metabolome analysis. Eukaryotes and prokaryotes behave very differently during the several steps of classical sample preparation methods for analysis of metabolites. Even within the eukaryote kingdom there is a vast diversity...

  9. Global duricrust on Mars - Analysis of remote-sensing data

    Science.gov (United States)

    Jakosky, B. M.; Christensen, P. R.

    1986-01-01

    A study is conducted of the infrared thermal emission, radio thermal emission, and radar reflection data sets with the objective to obtain a simple and self-consistent model for the Mars surface. The results are compared with in situ observations at the Viking Lander sites. Attention is given to thermal inertia values, the abundance of surface rocks, radar/thermal correlations, diurnal temperature deviations, and radio emission data. It is suggested that all of the global remote-sensing data sets considered can be reconciled on the basis of variations in the degree of formation of a case-hardened crust or duricrust. On the other hand, no other model which has been proposed in conjunction with any individual data set can satisfy all of the constraints discussed.

  10. Herbal medicine research and global health: an ethical analysis.

    Science.gov (United States)

    Tilburt, Jon C; Kaptchuk, Ted J

    2008-08-01

    Governments, international agencies and corporations are increasingly investing in traditional herbal medicine research. Yet little literature addresses ethical challenges in this research. In this paper, we apply concepts in a comprehensive ethical framework for clinical research to international traditional herbal medicine research. We examine in detail three key, underappreciated dimensions of the ethical framework in which particularly difficult questions arise for international herbal medicine research: social value, scientific validity and favourable risk-benefit ratio. Significant challenges exist in determining shared concepts of social value, scientific validity and favourable risk-benefit ratio across international research collaborations. However, we argue that collaborative partnership, including democratic deliberation, offers the context and process by which many of the ethical challenges in international herbal medicine research can, and should be, resolved. By "cross-training" investigators, and investing in safety-monitoring infrastructure, the issues identified by this comprehensive framework can promote ethically sound international herbal medicine research that contributes to global health.

  11. DNA Barcode Analysis of Thrips (Thysanoptera) Diversity in Pakistan Reveals Cryptic Species Complexes.

    Science.gov (United States)

    Iftikhar, Romana; Ashfaq, Muhammad; Rasool, Akhtar; Hebert, Paul D N

    2016-01-01

    Although thrips are globally important crop pests and vectors of viral disease, species identifications are difficult because of their small size and inconspicuous morphological differences. Sequence variation in the mitochondrial COI-5' (DNA barcode) region has proven effective for the identification of species in many groups of insect pests. We analyzed barcode sequence variation among 471 thrips from various plant hosts in north-central Pakistan. The Barcode Index Number (BIN) system assigned these sequences to 55 BINs, while the Automatic Barcode Gap Discovery detected 56 partitions, a count that coincided with the number of monophyletic lineages recognized by Neighbor-Joining analysis and Bayesian inference. Congeneric species showed an average of 19% sequence divergence (range = 5.6% - 27%) at COI, while intraspecific distances averaged 0.6% (range = 0.0% - 7.6%). BIN analysis suggested that all intraspecific divergence >3.0% actually involved a species complex. In fact, sequences for three major pest species (Haplothrips reuteri, Thrips palmi, Thrips tabaci), and one predatory thrips (Aeolothrips intermedius) showed deep intraspecific divergences, providing evidence that each is a cryptic species complex. The study compiles the first barcode reference library for the thrips of Pakistan, and examines global haplotype diversity in four important pest thrips.

  12. Performance analysis of tracked panel according to predicted global radiation

    International Nuclear Information System (INIS)

    Chang, T.P.

    2009-01-01

    In this paper, the performance of a south facing single-axis tracked panel was analyzed according to global radiation predicted by empirical model. Mathematic expressions appropriate for single-axis tracking system were derived to calculate the radiation on it. Instantaneous increments of solar energy collected by the tracked panel relative to fixed panel are illustrated. The validity of the empirical model to Taiwan area will also be examined with the actual irradiation data observed in Taipei. The results are summarized as follows: the gains made by the tracked panel relative to a fixed panel are between 20.0% and 33.9% for four specified days of year, between 20.9% and 33.2% for the four seasons and 27.6% over the entire year. For latitudes below 65 deg., the yearly optimal tilt angle of a fixed panel is close to 0.8 times latitude, the irradiation ratio of the tracked panel to the fixed panel is about 1.3, which are smaller than the corresponding values calculated from extraterrestrial radiation, suggesting us that the installation angle should be adjusted toward a flatter angle and that the gain of the tracked panel will reduce while it works in cloudy climate or in air pollution environment. Although the captured radiation increases with the maximal rotation angle of panel, but the benefit on the global radiation case is still not so good as that on extraterrestrial radiation case. The irradiation data observed is much less than the data predicted by the empirical model, however the trend of fitting curve to the observed data is somewhat in agreement with that to the predicted one; the yearly gain is 14.3% when a tracked panel is employed throughout the year.

  13. A global equilibrium analysis of co-firing coal and solid recovered fuel

    DEFF Research Database (Denmark)

    Wu, Hao; Glarborg, Peter; Jappe Frandsen, Flemming

    Global equilibrium calculations have been performed to study the behavior of ash forming species in cocombustion of a bituminous coal and a solid recovered fuel (SRF). It revealed that co-combustion of coal and 25% SRF (weight basis) could significantly reduce the formation of NaCl (g) and KCl (g...

  14. The online database MaarjAM reveals global and ecosystemic distribution patterns in arbuscular mycorrhizal fungi (Glomeromycota).

    Science.gov (United States)

    Opik, M; Vanatoa, A; Vanatoa, E; Moora, M; Davison, J; Kalwij, J M; Reier, U; Zobel, M

    2010-10-01

    • Here, we describe a new database, MaarjAM, that summarizes publicly available Glomeromycota DNA sequence data and associated metadata. The goal of the database is to facilitate the description of distribution and richness patterns in this group of fungi. • Small subunit (SSU) rRNA gene sequences and available metadata were collated from all suitable taxonomic and ecological publications. These data have been made accessible in an open-access database (http://maarjam.botany.ut.ee). • Two hundred and eighty-two SSU rRNA gene virtual taxa (VT) were described based on a comprehensive phylogenetic analysis of all collated Glomeromycota sequences. Two-thirds of VT showed limited distribution ranges, occurring in single current or historic continents or climatic zones. Those VT that associated with a taxonomically wide range of host plants also tended to have a wide geographical distribution, and vice versa. No relationships were detected between VT richness and latitude, elevation or vascular plant richness. • The collated Glomeromycota molecular diversity data suggest limited distribution ranges in most Glomeromycota taxa and a positive relationship between the width of a taxon's geographical range and its host taxonomic range. Inconsistencies between molecular and traditional taxonomy of Glomeromycota, and shortage of data from major continents and ecosystems, are highlighted.

  15. Integration and global analysis of isothermal titration calorimetry data for studying macromolecular interactions.

    Science.gov (United States)

    Brautigam, Chad A; Zhao, Huaying; Vargas, Carolyn; Keller, Sandro; Schuck, Peter

    2016-05-01

    Isothermal titration calorimetry (ITC) is a powerful and widely used method to measure the energetics of macromolecular interactions by recording a thermogram of differential heating power during a titration. However, traditional ITC analysis is limited by stochastic thermogram noise and by the limited information content of a single titration experiment. Here we present a protocol for bias-free thermogram integration based on automated shape analysis of the injection peaks, followed by combination of isotherms from different calorimetric titration experiments into a global analysis, statistical analysis of binding parameters and graphical presentation of the results. This is performed using the integrated public-domain software packages NITPIC, SEDPHAT and GUSSI. The recently developed low-noise thermogram integration approach and global analysis allow for more precise parameter estimates and more reliable quantification of multisite and multicomponent cooperative and competitive interactions. Titration experiments typically take 1-2.5 h each, and global analysis usually takes 10-20 min.

  16. Global Transcriptome Analysis of Aedes aegypti Mosquitoes in Response to Zika Virus Infection.

    Science.gov (United States)

    Etebari, Kayvan; Hegde, Shivanand; Saldaña, Miguel A; Widen, Steven G; Wood, Thomas G; Asgari, Sassan; Hughes, Grant L

    2017-01-01

    Zika virus (ZIKV) of the Flaviviridae family is a recently emerged mosquito-borne virus that has been implicated in the surge of the number of microcephaly instances in South America. The recent rapid spread of the virus led to its declaration as a global health emergency by the World Health Organization. The virus is transmitted mainly by the mosquito Aedes aegypti , which is also the vector of dengue virus; however, little is known about the interactions of the virus with the mosquito vector. In this study, we investigated the transcriptome profiles of whole A. aegypti mosquitoes in response to ZIKV infection at 2, 7, and 14 days postinfection using transcriptome sequencing. Results showed changes in the abundance of a large number of transcripts at each time point following infection, with 18 transcripts commonly changed among the three time points. Gene ontology analysis revealed that most of the altered genes are involved in metabolic processes, cellular processes, and proteolysis. In addition, 486 long intergenic noncoding RNAs that were altered upon ZIKV infection were identified. Further, we found changes of a number of potential mRNA target genes correlating with those of altered host microRNAs. The outcomes provide a basic understanding of A. aegypti responses to ZIKV and help to determine host factors involved in replication or mosquito host antiviral response against the virus. IMPORTANCE Vector-borne viruses pose great risks to human health. Zika virus has recently emerged as a global threat, rapidly expanding its distribution. Understanding the interactions of the virus with mosquito vectors at the molecular level is vital for devising new approaches in inhibiting virus transmission. In this study, we embarked on analyzing the transcriptional response of Aedes aegypti mosquitoes to Zika virus infection. Results showed large changes in both coding and long noncoding RNAs. Analysis of these genes showed similarities with other flaviviruses, including

  17. Comparative genomics reveals diversified CRISPR-Cas systems of globally distributed Microcystis aeruginosa, a freshwater bloom-forming cyanobacterium

    Directory of Open Access Journals (Sweden)

    Chen eYang

    2015-05-01

    Full Text Available Microcystis aeruginosa is one of the most common and dominant bloom-forming cyanobacteria in freshwater lakes around the world. Microcystis cells can produce toxic secondary metabolites, such as microcystins, which are harmful to human health. Two M. aeruginosa strains were isolated from two highly eutrophic lakes in China and their genomes were sequenced. Comparative genomic analysis was performed with the 12 other available M. aeruginosa genomes and closely related unicellular cyanobacterium. Each genome of M. aeruginosa containing at least one clustered regularly interspaced short palindromic repeat (CRISPR locus and total 71 loci were identified, suggesting it is ubiquitous in M. aeruginosa genomes. In addition to the previously reported subtype I-D cas gene sets, three CAS subtypes I-A, III-A and III-B were identified and characterized in this study. Seven types of CRISPR direct repeat have close association with CAS subtype, confirming that different and specific secondary structures of CRISPR repeats are important for the recognition, binding and process of corresponding cas gene sets. Homology search of the CRISPR spacer sequences provides a history of not only resistance to bacteriophages and plasmids known to be associated with M. aeruginosa, but also the ability to target much more exogenous genetic material in the natural environment. These adaptive and heritable defense mechanisms play a vital role in keeping genomic stability and self-maintenance by restriction of horizontal gene transfer. Maintaining genomic stability and modulating genomic plasticity are both important evolutionary strategies for M. aeruginosa in adaptation and survival in various habitats.

  18. Data-Independent Acquisition-Based Quantitative Proteomic Analysis Reveals Potential Biomarkers of Kidney Cancer.

    Science.gov (United States)

    Song, Yimeng; Zhong, Lijun; Zhou, Juntuo; Lu, Min; Xing, Tianying; Ma, Lulin; Shen, Jing

    2017-12-01

    Renal cell carcinoma (RCC) is a malignant and metastatic cancer with 95% mortality, and clear cell RCC (ccRCC) is the most observed among the five major subtypes of RCC. Specific biomarkers that can distinguish cancer tissues from adjacent normal tissues should be developed to diagnose this disease in early stages and conduct a reliable prognostic evaluation. Data-independent acquisition (DIA) strategy has been widely employed in proteomic analysis because of various advantages, including enhanced protein coverage and reliable data acquisition. In this study, a DIA workflow is constructed on a quadrupole-Orbitrap LC-MS platform to reveal dysregulated proteins between ccRCC and adjacent normal tissues. More than 4000 proteins are identified, 436 of these proteins are dysregulated in ccRCC tissues. Bioinformatic analysis reveals that multiple pathways and Gene Ontology items are strongly associated with ccRCC. The expression levels of L-lactate dehydrogenase A chain, annexin A4, nicotinamide N-methyltransferase, and perilipin-2 examined through RT-qPCR, Western blot, and immunohistochemistry confirm the validity of the proteomic analysis results. The proposed DIA workflow yields optimum time efficiency and data reliability and provides a good choice for proteomic analysis in biological and clinical studies, and these dysregulated proteins might be potential biomarkers for ccRCC diagnosis. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  19. Recent adaptive events in human brain revealed by meta-analysis of positively selected genes.

    Directory of Open Access Journals (Sweden)

    Yue Huang

    Full Text Available BACKGROUND AND OBJECTIVES: Analysis of positively-selected genes can help us understand how human evolved, especially the evolution of highly developed cognitive functions. However, previous works have reached conflicting conclusions regarding whether human neuronal genes are over-represented among genes under positive selection. METHODS AND RESULTS: We divided positively-selected genes into four groups according to the identification approaches, compiling a comprehensive list from 27 previous studies. We showed that genes that are highly expressed in the central nervous system are enriched in recent positive selection events in human history identified by intra-species genomic scan, especially in brain regions related to cognitive functions. This pattern holds when different datasets, parameters and analysis pipelines were used. Functional category enrichment analysis supported these findings, showing that synapse-related functions are enriched in genes under recent positive selection. In contrast, immune-related functions, for instance, are enriched in genes under ancient positive selection revealed by inter-species coding region comparison. We further demonstrated that most of these patterns still hold even after controlling for genomic characteristics that might bias genome-wide identification of positively-selected genes including gene length, gene density, GC composition, and intensity of negative selection. CONCLUSION: Our rigorous analysis resolved previous conflicting conclusions and revealed recent adaptation of human brain functions.

  20. Global methylation profiling of lymphoblastoid cell lines reveals epigenetic contributions to autism spectrum disorders and a novel autism candidate gene, RORA, whose protein product is reduced in autistic brain

    Science.gov (United States)

    Nguyen, AnhThu; Rauch, Tibor A.; Pfeifer, Gerd P.; Hu, Valerie W.

    2010-01-01

    Autism is currently considered a multigene disorder with epigenetic influences. To investigate the contribution of DNA methylation to autism spectrum disorders, we have recently completed large-scale methylation profiling by CpG island microarray analysis of lymphoblastoid cell lines derived from monozygotic twins discordant for diagnosis of autism and their nonautistic siblings. Methylation profiling revealed many candidate genes differentially methylated between discordant MZ twins as well as between both twins and nonautistic siblings. Bioinformatics analysis of the differentially methylated genes demonstrated enrichment for high-level functions including gene transcription, nervous system development, cell death/survival, and other biological processes implicated in autism. The methylation status of 2 of these candidate genes, BCL-2 and retinoic acid-related orphan receptor alpha (RORA), was further confirmed by bisulfite sequencing and methylation-specific PCR, respectively. Immunohistochemical analyses of tissue arrays containing slices of the cerebellum and frontal cortex of autistic and age- and sex-matched control subjects revealed decreased expression of RORA and BCL-2 proteins in the autistic brain. Our data thus confirm the role of epigenetic regulation of gene expression via differential DNA methylation in idiopathic autism, and furthermore link molecular changes in a peripheral cell model with brain pathobiology in autism.—Nguyen, A., Rauch, T. A., Pfeifer, G. P., Hu, V. W. Global methylation profiling of lymphoblastoid cell lines reveals epigenetic contributions to autism spectrum disorders and a novel autism candidate gene, RORA, whose protein product is reduced in autistic brain. PMID:20375269

  1. The Europa Global Geologic Map

    Science.gov (United States)

    Leonard, E. J.; Patthoff, D. A.; Senske, D. A.; Collins, G. C.

    2018-06-01

    The Europa Global Geologic Map reveals three periods in Europa's surface history as well as an interesting distribution of microchaos. We will discuss the mapping and the interesting implications of our analysis of Europa's surface.

  2. Transcriptomic analysis of human retinal detachment reveals both inflammatory response and photoreceptor death.

    Directory of Open Access Journals (Sweden)

    Marie-Noëlle Delyfer

    Full Text Available BACKGROUND: Retinal detachment often leads to a severe and permanent loss of vision and its therapeutic management remains to this day exclusively surgical. We have used surgical specimens to perform a differential analysis of the transcriptome of human retinal tissues following detachment in order to identify new potential pharmacological targets that could be used in combination with surgery to further improve final outcome. METHODOLOGY/PRINCIPAL FINDINGS: Statistical analysis reveals major involvement of the immune response in the disease. Interestingly, using a novel approach relying on coordinated expression, the interindividual variation was monitored to unravel a second crucial aspect of the pathological process: the death of photoreceptor cells. Within the genes identified, the expression of the major histocompatibility complex I gene HLA-C enables diagnosis of the disease, while PKD2L1 and SLCO4A1 -which are both down-regulated- act synergistically to provide an estimate of the duration of the retinal detachment process. Our analysis thus reveals the two complementary cellular and molecular aspects linked to retinal detachment: an immune response and the degeneration of photoreceptor cells. We also reveal that the human specimens have a higher clinical value as compared to artificial models that point to IL6 and oxidative stress, not implicated in the surgical specimens studied here. CONCLUSIONS/SIGNIFICANCE: This systematic analysis confirmed the occurrence of both neurodegeneration and inflammation during retinal detachment, and further identifies precisely the modification of expression of the different genes implicated in these two phenomena. Our data henceforth give a new insight into the disease process and provide a rationale for therapeutic strategies aimed at limiting inflammation and photoreceptor damage associated with retinal detachment and, in turn, improving visual prognosis after retinal surgery.

  3. Network analysis of oyster transcriptome revealed a cascade of cellular responses during recovery after heat shock.

    Directory of Open Access Journals (Sweden)

    Lingling Zhang

    Full Text Available Oysters, as a major group of marine bivalves, can tolerate a wide range of natural and anthropogenic stressors including heat stress. Recent studies have shown that oysters pretreated with heat shock can result in induced heat tolerance. A systematic study of cellular recovery from heat shock may provide insights into the mechanism of acquired thermal tolerance. In this study, we performed the first network analysis of oyster transcriptome by reanalyzing microarray data from a previous study. Network analysis revealed a cascade of cellular responses during oyster recovery after heat shock and identified responsive gene modules and key genes. Our study demonstrates the power of network analysis in a non-model organism with poor gene annotations, which can lead to new discoveries that go beyond the focus on individual genes.

  4. The Revealed Competitiveness of Major Ports in the East Asian Region: An Additive Market Share Analysis

    Directory of Open Access Journals (Sweden)

    Tae Seung Kim

    2015-12-01

    Full Text Available In the single cargo market, the ordinary market share analysis method has been the representative tool for revealed competitiveness analysis. This paper develops and employs an applied market share index called the additive market share (AMS. Data are collected from 15 major container ports for the 1998-2013 period. In comparison to the results of an ordinary market share analysis, the highest AMS is observed for the Bohai Rim port cluster from 2008, not for the Yangtze River cluster or the Pearl River cluster. There are substitutable relationships between Yangtze River and non-Chinese ports and between Pearl River and Bohai Rim ports from 2001. Finally, there is an internal competition at Pearl River and Yangtze River ports, whereas Bohai Rim and non-Chinese ports show internally complementary relationships.

  5. Accelerator mass spectrometry: ultrasensitive analysis of global science

    International Nuclear Information System (INIS)

    Tuniz, C.; Bird, J.B.; Fink, D.; Herzog, G.F.

    1998-01-01

    Accelerator mass spectrometry (AMS), an innovative analytical technique, measures rare atoms at unprecedented levels of sensitivity, revolutionizing the science of radiocarbon dating and accessing new environmental tracers and chronometers. AMS can study extraterrestrial materials, the earth sciences, the future of the global environment, and the history of mankind. The Shroud of Turin, meteorites from Mars, the crown of Charlemagne, and ancient air trapped in Antarctic ice indicate some of the samples on which AMS has been applied. This book has compiled the diverse set of scientific literature into a single volume, suitable as a text or resource on the major AMS-related outcomes, issues, and methods. It explains how scientists and researchers succeeded in counting Carbon-14 atoms at an extraordinary level, examines the impact of AMS on the branches of scientific technology and historical research, provides an understanding of the chronology and significance of past and present environmental changes, details the advances in AMS equipment, technology, and methods as well as the expansion of AMS research

  6. Economic-Social Analysis of Global Illicit Drug Trade

    Directory of Open Access Journals (Sweden)

    Salahedin Ghaderi

    2003-11-01

    Full Text Available Political unstability, less respect to the role of law, low life standards and suitable conditions for poppy/coca cultivation, have all affected on growing illicit drug international trafficking. Colombia is the center for global cocaine industry. Colombians had to use ship in the Carribean but now they pass Mexico where the costs are half of using ship. Mexican traffickers permit that the domestic poppy plants turned into herion, Colombian cocaine transited to USA and methamephtamine manufactured and distributed. Golden triangle in southeast Asia is one of the major regions for opium poppy cultivation. This region has seen many guerrilla warfare for selling illicit drugs especially in Myanmar. Manufactured hroin is usually dealt in Thailand. Golden Crescent region in southwest Asia has a suitable climate for opium poppy cultivation which provides necessay money for purchasing needed weapons by rival groups in northwestern border provinces of Afghanistan and Pakistan. Nigeria is one of the main centers for transporting heroin from Golden Crescent and cocaine from Brazil. Dominics run cocaine trade in New York and New England and Afro-American criminal organizations conduct heroin trading in big cities such as New york, Detroit, Chicago, Phila Delphia and Washington. Street trading of illicit drugs is mainly done by cultural or commanding gangs. Illicit drug traffickers apply many methods to laundering their profits including money exchange, smurfs, electronic transferring, and faced firms (the firms that are only registered.

  7. A global water supply reservoir yield model with uncertainty analysis

    International Nuclear Information System (INIS)

    Kuria, Faith W; Vogel, Richard M

    2014-01-01

    Understanding the reliability and uncertainty associated with water supply yields derived from surface water reservoirs is central for planning purposes. Using a global dataset of monthly river discharge, we introduce a generalized model for estimating the mean and variance of water supply yield, Y, expected from a reservoir for a prespecified reliability, R, and storage capacity, S assuming a flow record of length n. The generalized storage–reliability–yield (SRY) relationships reported here have numerous water resource applications ranging from preliminary water supply investigations, to economic and climate change impact assessments. An example indicates how our generalized SRY relationship can be combined with a hydroclimatic model to determine the impact of climate change on surface reservoir water supply yields. We also document that the variability of estimates of water supply yield are invariant to characteristics of the reservoir system, including its storage capacity and reliability. Standardized metrics of the variability of water supply yields are shown to depend only on the sample size of the inflows and the statistical characteristics of the inflow series. (paper)

  8. Multisteps Global Kinetic Analysis of MSW Slow Pyrolysis

    Directory of Open Access Journals (Sweden)

    Dwi Aries Himawanto

    2013-12-01

    Full Text Available The goal of this research is to find relationships between single components slow pyrolysis characteristics and mixed component slow pyrolysis characteristics of segregated municipal solid wastes (MSW. The material of this research consists of organic wastes (bamboo wastes and banana leaves wastes and inorganic wastes (styrofoam wastes and snack wrapping wastes. The materials which used to study were the unprosessing waste. The samples were collected, dried and crushed until passing 20 mesh shieves then characterized in self manufactured macro balance. The thermogravimetry analyses were done to find the MSW slow pyrolysis characteristics. The 20 gram sample was placed in the furnace whose temperature is increased with 10 0C/min heating rate until reached 400 0 final temperature and held for 30 minutes before the sample is cooled into room temperature. One hundred ml/min nitrogen introduced from the bottom of furnace as a swept gas. The results of the research show that the global kinetic method could be used to predict the MSW single component activation energy but it should be modified to calculate the mixed sample activation energy . The predictive activation energy values which calculated based on weighed sum of single component have 18.5 % deviations if compared with experimental result.

  9. Global Analysis of Ecosystem Evapotranspiration Response to Precipitation Deficits

    Science.gov (United States)

    He, Bin; Wang, Haiyan; Guo, Lanlan; Liu, Junjie

    2017-12-01

    Changes in ecosystem evapotranspiration (ET) due to precipitation deficits (PD) can relieve or aggravate soil moisture shortages, thus impacting drought severity. Previous findings have conflicted with regard to response of ET to PD. The present study relies on a global land ET synthesis data set (ETsyn) and observations from eddy-covariance towers (ETobs) to thoroughly examine the sensitivity of ET to PD, which is represented by the standardized precipitation index. There was a contrast in the response to PD between arid and humid ecosystems. ETsyn of arid ecosystems was typically reduced promptly in response to a reduction of precipitation, while ETsyn in humid ecosystems experienced a two-staged change: First, there was an enhancement, and then a reduction associated with persisting PD. Compared with ETsyn, ETobs suggests the occurrence of a more significant ET transition in response to PD. In arid ecosystems, ET typically negatively correlated with low PD, but this was limited by a large PD. Findings from this study are crucial for understanding the role of ET in drought evolution.

  10. De novo transcriptome and small RNA analysis of two Chinese willow cultivars reveals stress response genes in Salix matsudana.

    Directory of Open Access Journals (Sweden)

    Guodong Rao

    Full Text Available Salix matsudana Koidz. is a deciduous, rapidly growing, and drought resistant tree and is one of the most widely distributed and commonly cultivated willow species in China. Currently little transcriptomic and small RNAomic data are available to reveal the genes involve in the stress resistant in S. matsudana. Here, we report the RNA-seq analysis results of both transcriptome and small RNAome data using Illumina deep sequencing of shoot tips from two willow variants(Salix. matsudana and Salix matsudana Koidz. cultivar 'Tortuosa'. De novo gene assembly was used to generate the consensus transcriptome and small RNAome, which contained 106,403 unique transcripts with an average length of 944 bp and a total length of 100.45 MB, and 166 known miRNAs representing 35 miRNA families. Comparison of transcriptomes and small RNAomes combined with quantitative real-time PCR from the two Salix libraries revealed a total of 292 different expressed genes(DEGs and 36 different expressed miRNAs (DEMs. Among the DEGs and DEMs, 196 genes and 24 miRNAs were up regulated, 96 genes and 12 miRNA were down regulated in S. matsudana. Functional analysis of DEGs and miRNA targets showed that many genes were involved in stress resistance in S. matsudana. Our global gene expression profiling presents a comprehensive view of the transcriptome and small RNAome which provide valuable information and sequence resources for uncovering the stress response genes in S. matsudana. Moreover the transcriptome and small RNAome data provide a basis for future study of genetic resistance in Salix.

  11. Revealed preferences towards the appraisal of orphan drugs in Poland - multi criteria decision analysis.

    Science.gov (United States)

    Kolasa, Katarzyna; Zwolinski, Krzysztof Miroslaw; Zah, Vladimir; Kaló, Zoltán; Lewandowski, Tadeusz

    2018-04-27

    A Multi Criteria Decision Analysis (MCDA) technique was adopted to reveal the preferences of the Appraisal Body of the Polish HTA agency towards orphan drugs (OMPs). There were 34 positive and 23 negative HTA recommendations out of 54 distinctive drug-indication pairs. The MCDA matrix consisted of 13 criteria, seven of which made the most impact on the HTA process. Appraisal of clinical evidence, cost of therapy, and safety considerations were the main contributors to the HTA guidance, whilst advancement of technology and manufacturing costs made the least impact. MCDA can be regarded as a valuable tool for revealing decision makers' preferences in the healthcare sector. Given that only roughly half of all criteria included in the MCDA matrix were deemed to make an impact on the HTA process, there is certainly some room for improvement with respect to the adaptation of a new approach towards the value assessment of OMPs in Poland.

  12. Proteome-wide analysis of arginine monomethylation reveals widespread occurrence in human cells

    DEFF Research Database (Denmark)

    Larsen, Sara C; Sylvestersen, Kathrine B; Mund, Andreas

    2016-01-01

    to the frequency of somatic mutations at arginine methylation sites throughout the proteome, we observed that somatic mutations were common at arginine methylation sites in proteins involved in mRNA splicing. Furthermore, in HeLa and U2OS cells, we found that distinct arginine methyltransferases differentially...... kidney 293 cells, indicating that the occurrence of this modification is comparable to phosphorylation and ubiquitylation. A site-level conservation analysis revealed that arginine methylation sites are less evolutionarily conserved compared to arginines that were not identified as modified...... as coactivator-associated arginine methyltransferase 1 (CARM1)] or PRMT1 increased the RNA binding function of HNRNPUL1. High-content single-cell imaging additionally revealed that knocking down CARM1 promoted the nuclear accumulation of SRSF2, independent of cell cycle phase. Collectively, the presented human...

  13. Transcriptional Network Analysis Reveals Drought Resistance Mechanisms of AP2/ERF Transgenic Rice

    Directory of Open Access Journals (Sweden)

    Hongryul Ahn

    2017-06-01

    Full Text Available This study was designed to investigate at the molecular level how a transgenic version of rice “Nipponbare” obtained a drought-resistant phenotype. Using multi-omics sequencing data, we compared wild-type rice (WT and a transgenic version (erf71 that had obtained a drought-resistant phenotype by overexpressing OsERF71, a member of the AP2/ERF transcription factor (TF family. A comprehensive bioinformatics analysis pipeline, including TF networks and a cascade tree, was developed for the analysis of multi-omics data. The results of the analysis showed that the presence of OsERF71 at the source of the network controlled global gene expression levels in a specific manner to make erf71 survive longer than WT. Our analysis of the time-series transcriptome data suggests that erf71 diverted more energy to survival-critical mechanisms related to translation, oxidative response, and DNA replication, while further suppressing energy-consuming mechanisms, such as photosynthesis. To support this hypothesis further, we measured the net photosynthesis level under physiological conditions, which confirmed the further suppression of photosynthesis in erf71. In summary, our work presents a comprehensive snapshot of transcriptional modification in transgenic rice and shows how this induced the plants to acquire a drought-resistant phenotype.

  14. Transcriptome Analysis of Polyhydroxybutyrate Cycle Mutants Reveals Discrete Loci Connecting Nitrogen Utilization and Carbon Storage in Sinorhizobium meliloti.

    Science.gov (United States)

    D'Alessio, Maya; Nordeste, Ricardo; Doxey, Andrew C; Charles, Trevor C

    2017-01-01

    Polyhydroxybutyrate (PHB) and glycogen polymers are produced by bacteria as carbon storage compounds under unbalanced growth conditions. To gain insights into the transcriptional mechanisms controlling carbon storage in Sinorhizobium meliloti , we investigated the global transcriptomic response to the genetic disruption of key genes in PHB synthesis and degradation and in glycogen synthesis. Under both nitrogen-limited and balanced growth conditions, transcriptomic analysis was performed with genetic mutants deficient in PHB synthesis ( phbA , phbB , phbAB , and phbC ), PHB degradation ( bdhA , phaZ , and acsA2 ), and glycogen synthesis ( glgA1 ). Three distinct genomic regions of the pSymA megaplasmid exhibited altered expression in the wild type and the PHB cycle mutants that was not seen in the glycogen synthesis mutant. An Fnr family transcriptional motif was identified in the upstream regions of a cluster of genes showing similar transcriptional patterns across the mutants. This motif was found at the highest density in the genomic regions with the strongest transcriptional effect, and the presence of this motif upstream of genes in these regions was significantly correlated with decreased transcript abundance. Analysis of the genes in the pSymA regions revealed that they contain a genomic overrepresentation of Fnr family transcription factor-encoding genes. We hypothesize that these loci, containing mostly nitrogen utilization, denitrification, and nitrogen fixation genes, are regulated in response to the intracellular carbon/nitrogen balance. These results indicate a transcriptional regulatory association between intracellular carbon levels (mediated through the functionality of the PHB cycle) and the expression of nitrogen metabolism genes. IMPORTANCE The ability of bacteria to store carbon and energy as intracellular polymers uncouples cell growth and replication from nutrient uptake and provides flexibility in the use of resources as they are available to

  15. Global classification of human facial healthy skin using PLS discriminant analysis and clustering analysis.

    Science.gov (United States)

    Guinot, C; Latreille, J; Tenenhaus, M; Malvy, D J

    2001-04-01

    Today's classifications of healthy skin are predominantly based on a very limited number of skin characteristics, such as skin oiliness or susceptibility to sun exposure. The aim of the present analysis was to set up a global classification of healthy facial skin, using mathematical models. This classification is based on clinical, biophysical skin characteristics and self-reported information related to the skin, as well as the results of a theoretical skin classification assessed separately for the frontal and the malar zones of the face. In order to maximize the predictive power of the models with a minimum of variables, the Partial Least Square (PLS) discriminant analysis method was used. The resulting PLS components were subjected to clustering analyses to identify the plausible number of clusters and to group the individuals according to their proximities. Using this approach, four PLS components could be constructed and six clusters were found relevant. So, from the 36 hypothetical combinations of the theoretical skin types classification, we tended to a strengthened six classes proposal. Our data suggest that the association of the PLS discriminant analysis and the clustering methods leads to a valid and simple way to classify healthy human skin and represents a potentially useful tool for cosmetic and dermatological research.

  16. Discrete non-parametric kernel estimation for global sensitivity analysis

    International Nuclear Information System (INIS)

    Senga Kiessé, Tristan; Ventura, Anne

    2016-01-01

    This work investigates the discrete kernel approach for evaluating the contribution of the variance of discrete input variables to the variance of model output, via analysis of variance (ANOVA) decomposition. Until recently only the continuous kernel approach has been applied as a metamodeling approach within sensitivity analysis framework, for both discrete and continuous input variables. Now the discrete kernel estimation is known to be suitable for smoothing discrete functions. We present a discrete non-parametric kernel estimator of ANOVA decomposition of a given model. An estimator of sensitivity indices is also presented with its asymtotic convergence rate. Some simulations on a test function analysis and a real case study from agricultural have shown that the discrete kernel approach outperforms the continuous kernel one for evaluating the contribution of moderate or most influential discrete parameters to the model output. - Highlights: • We study a discrete kernel estimation for sensitivity analysis of a model. • A discrete kernel estimator of ANOVA decomposition of the model is presented. • Sensitivity indices are calculated for discrete input parameters. • An estimator of sensitivity indices is also presented with its convergence rate. • An application is realized for improving the reliability of environmental models.

  17. Transcriptome analysis reveals the regulation of brassinosteroids on petal growth in Gerbera hybrida

    Directory of Open Access Journals (Sweden)

    Gan Huang

    2017-05-01

    Full Text Available Gerbera hybrida is a cut-flower crop of global importance, and an understanding of the mechanisms underlying petal development is vital for the continued commercial development of this plant species. Brassinosteroids (BRs, a class of phytohormones, are known to play a major role in cell expansion, but their effect on petal growth in G. hybrida is largely unexplored. In this study, we found that the brassinolide (BL, the most active BR, promotes petal growth by lengthening cells in the middle and basal regions of petals, and that this effect on petal growth was greater than that of gibberellin (GA. The RNA-seq (high-throughput cDNA sequencing technique was employed to investigate the regulatory mechanisms by which BRs control petal growth. A global transcriptome analysis of the response to BRs in petals was conducted and target genes regulated by BR were identified. These differentially expressed genes (DEGs include various transcription factors (TFs that were activated during the early stage (0.5 h of BL treatment, as well as cell wall proteins whose expression was regulated at a late stage (10 h. BR-responsive DEGs are involved in multiple plant hormone signal pathways, hormone biosynthesis and biotic and abiotic stress responses, showing that the regulation of petal growth by BRs is a complex network of processes. Thus, our study provides new insights at the transcriptional level into the molecular mechanisms of BR regulation of petal growth in G. hybrida.

  18. Waterpipe tobacco smoking legislation and policy enactment: a global analysis.

    Science.gov (United States)

    Jawad, Mohammed; El Kadi, Lama; Mugharbil, Sanaa; Nakkash, Rima

    2015-03-01

    (1) To review how current global tobacco control policies address regulation of waterpipe tobacco smoking (WTS). (2) To identify features associated with enactment and enforcement of WTS legislation. (1) Legislations compiled by Tobacco Control Laws (www.tobaccocontrollaws.org). (2) Weekly news articles by 'Google Alerts' (www.google.com/alerts) from July 2013 to August 2014. (1) Countries containing legislative reviews, written by legal experts, were included. Countries prohibiting tobacco sales were excluded. (2) News articles discussing aspects of the WHO FCTC were included. News articles related to electronic-waterpipe, crime, smuggling, opinion pieces or brief mentions of WTS were excluded. (1) Two reviewers independently abstracted the definition of "tobacco product" and/or "smoking". Four tobacco control domains (smokefree law, misleading descriptors, health warning labels and advertising/promotion/sponsorship) were assigned one of four categories based on the degree to which WTS had specific legislation. (2) Two investigators independently assigned at least one theme and associated subtheme to each news article. (1) Reviewed legislations of 62 countries showed that most do not address WTS regulation but instead rely on generic tobacco/smoking definitions to cover all tobacco products. Where WTS was specifically addressed, no additional legislative guidance accounted for the unique way it is smoked, except for in one country specifying health warnings on waterpipe apparatuses (2) News articles mainly reported on noncompliance with public smoking bans, especially in India, Pakistan and the UK. A regulatory framework evaluated for effectiveness and tailored for the specificities of WTS needs to be developed. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://group.bmj.com/group/rights-licensing/permissions.

  19. Comparative analysis reveals that polyploidy does not decelerate diversification in fish.

    Science.gov (United States)

    Zhan, S H; Glick, L; Tsigenopoulos, C S; Otto, S P; Mayrose, I

    2014-02-01

    While the proliferation of the species-rich teleost fish has been ascribed to an ancient genome duplication event at the base of this group, the broader impact of polyploidy on fish evolution and diversification remains poorly understood. Here, we investigate the association between polyploidy and diversification in several fish lineages: the sturgeons (Acipenseridae: Acipenseriformes), the botiid loaches (Botiidae: Cypriniformes), Cyprininae fishes (Cyprinidae: Cypriniformes) and the salmonids (Salmonidae: Salmoniformes). Using likelihood-based evolutionary methodologies, we co-estimate speciation and extinction rates associated with polyploid vs. diploid fish lineages. Family-level analysis of Acipenseridae and Botiidae revealed no significant difference in diversification rates between polyploid and diploid relatives, while analysis of the subfamily Cyprininae revealed higher polyploid diversification. Additionally, order-level analysis of the polyploid Salmoniformes and its diploid sister clade, the Esociformes, did not support a significantly different net diversification rate between the two groups. Taken together, our results suggest that polyploidy is generally not associated with decreased diversification in fish - a pattern that stands in contrast to that previously observed in plants. While there are notable differences in the time frame examined in the two studies, our results suggest that polyploidy is associated with different diversification patterns in these two major branches of the eukaryote tree of life. © 2014 The Authors. Journal of Evolutionary Biology © 2014 European Society For Evolutionary Biology.

  20. Multilocus sequence analysis of nectar pseudomonads reveals high genetic diversity and contrasting recombination patterns.

    Science.gov (United States)

    Alvarez-Pérez, Sergio; de Vega, Clara; Herrera, Carlos M

    2013-01-01

    The genetic and evolutionary relationships among floral nectar-dwelling Pseudomonas 'sensu stricto' isolates associated to South African and Mediterranean plants were investigated by multilocus sequence analysis (MLSA) of four core housekeeping genes (rrs, gyrB, rpoB and rpoD). A total of 35 different sequence types were found for the 38 nectar bacterial isolates characterised. Phylogenetic analyses resulted in the identification of three main clades [nectar groups (NGs) 1, 2 and 3] of nectar pseudomonads, which were closely related to five intrageneric groups: Pseudomonas oryzihabitans (NG 1); P. fluorescens, P. lutea and P. syringae (NG 2); and P. rhizosphaerae (NG 3). Linkage disequilibrium analysis pointed to a mostly clonal population structure, even when the analysis was restricted to isolates from the same floristic region or belonging to the same NG. Nevertheless, signatures of recombination were observed for NG 3, which exclusively included isolates retrieved from the floral nectar of insect-pollinated Mediterranean plants. In contrast, the other two NGs comprised both South African and Mediterranean isolates. Analyses relating diversification to floristic region and pollinator type revealed that there has been more unique evolution of the nectar pseudomonads within the Mediterranean region than would be expected by chance. This is the first work analysing the sequence of multiple loci to reveal geno- and ecotypes of nectar bacteria.

  1. Multilocus Sequence Analysis of Nectar Pseudomonads Reveals High Genetic Diversity and Contrasting Recombination Patterns

    Science.gov (United States)

    Álvarez-Pérez, Sergio; de Vega, Clara; Herrera, Carlos M.

    2013-01-01

    The genetic and evolutionary relationships among floral nectar-dwelling Pseudomonas ‘sensu stricto’ isolates associated to South African and Mediterranean plants were investigated by multilocus sequence analysis (MLSA) of four core housekeeping genes (rrs, gyrB, rpoB and rpoD). A total of 35 different sequence types were found for the 38 nectar bacterial isolates characterised. Phylogenetic analyses resulted in the identification of three main clades [nectar groups (NGs) 1, 2 and 3] of nectar pseudomonads, which were closely related to five intrageneric groups: Pseudomonas oryzihabitans (NG 1); P. fluorescens, P. lutea and P. syringae (NG 2); and P. rhizosphaerae (NG 3). Linkage disequilibrium analysis pointed to a mostly clonal population structure, even when the analysis was restricted to isolates from the same floristic region or belonging to the same NG. Nevertheless, signatures of recombination were observed for NG 3, which exclusively included isolates retrieved from the floral nectar of insect-pollinated Mediterranean plants. In contrast, the other two NGs comprised both South African and Mediterranean isolates. Analyses relating diversification to floristic region and pollinator type revealed that there has been more unique evolution of the nectar pseudomonads within the Mediterranean region than would be expected by chance. This is the first work analysing the sequence of multiple loci to reveal geno- and ecotypes of nectar bacteria. PMID:24116076

  2. Analysis of global multiscale finite element methods for wave equations with continuum spatial scales

    KAUST Repository

    Jiang, Lijian; Efendiev, Yalchin; Ginting, Victor

    2010-01-01

    In this paper, we discuss a numerical multiscale approach for solving wave equations with heterogeneous coefficients. Our interest comes from geophysics applications and we assume that there is no scale separation with respect to spatial variables. To obtain the solution of these multiscale problems on a coarse grid, we compute global fields such that the solution smoothly depends on these fields. We present a Galerkin multiscale finite element method using the global information and provide a convergence analysis when applied to solve the wave equations. We investigate the relation between the smoothness of the global fields and convergence rates of the global Galerkin multiscale finite element method for the wave equations. Numerical examples demonstrate that the use of global information renders better accuracy for wave equations with heterogeneous coefficients than the local multiscale finite element method. © 2010 IMACS.

  3. Analysis of global multiscale finite element methods for wave equations with continuum spatial scales

    KAUST Repository

    Jiang, Lijian

    2010-08-01

    In this paper, we discuss a numerical multiscale approach for solving wave equations with heterogeneous coefficients. Our interest comes from geophysics applications and we assume that there is no scale separation with respect to spatial variables. To obtain the solution of these multiscale problems on a coarse grid, we compute global fields such that the solution smoothly depends on these fields. We present a Galerkin multiscale finite element method using the global information and provide a convergence analysis when applied to solve the wave equations. We investigate the relation between the smoothness of the global fields and convergence rates of the global Galerkin multiscale finite element method for the wave equations. Numerical examples demonstrate that the use of global information renders better accuracy for wave equations with heterogeneous coefficients than the local multiscale finite element method. © 2010 IMACS.

  4. Genome-wide analysis of the Dof transcription factor gene family reveals soybean-specific duplicable and functional characteristics.

    Directory of Open Access Journals (Sweden)

    Yong Guo

    Full Text Available The Dof domain protein family is a classic plant-specific zinc-finger transcription factor family involved in a variety of biological processes. There is great diversity in the number of Dof genes in different plants. However, there are only very limited reports on the characterization of Dof transcription factors in soybean (Glycine max. In the present study, 78 putative Dof genes were identified from the whole-genome sequence of soybean. The predicted GmDof genes were non-randomly distributed within and across 19 out of 20 chromosomes and 97.4% (38 pairs were preferentially retained duplicate paralogous genes located in duplicated regions of the genome. Soybean-specific segmental duplications contributed significantly to the expansion of the soybean Dof gene family. These Dof proteins were phylogenetically clustered into nine distinct subgroups among which the gene structure and motif compositions were considerably conserved. Comparative phylogenetic analysis of these Dof proteins revealed four major groups, similar to those reported for Arabidopsis and rice. Most of the GmDofs showed specific expression patterns based on RNA-seq data analyses. The expression patterns of some duplicate genes were partially redundant while others showed functional diversity, suggesting the occurrence of sub-functionalization during subsequent evolution. Comprehensive expression profile analysis also provided insights into the soybean-specific functional divergence among members of the Dof gene family. Cis-regulatory element analysis of these GmDof genes suggested diverse functions associated with different processes. Taken together, our results provide useful information for the functional characterization of soybean Dof genes by combining phylogenetic analysis with global gene-expression profiling.

  5. Human threats to sandy beaches: A meta-analysis of ghost crabs illustrates global anthropogenic impacts.

    Science.gov (United States)

    Schlacher, Thomas A.; Lucrezi, Serena; Connolly, Rod M.; Peterson, Charles H.; Gilby, Ben L.; Maslo, Brooke; Olds, Andrew D.; Walker, Simon J.; Leon, Javier X.; Huijbers, Chantal M.; Weston, Michael A.; Turra, Alexander; Hyndes, Glenn A.; Holt, Rebecca A.; Schoeman, David S.

    2016-02-01

    Beach and coastal dune systems are increasingly subjected to a broad range of anthropogenic pressures that on many shorelines require significant conservation and mitigation interventions. But these interventions require reliable data on the severity and frequency of adverse ecological impacts. Such evidence is often obtained by measuring the response of 'indicator species'. Ghost crabs are the largest invertebrates inhabiting tropical and subtropical sandy shores and are frequently used to assess human impacts on ocean beaches. Here we present the first global meta-analysis of these impacts, and analyse the design properties and metrics of studies using ghost-crabs in their assessment. This was complemented by a gap analysis to identify thematic areas of anthropogenic pressures on sandy beach ecosystems that are under-represented in the published literature. Our meta-analysis demonstrates a broad geographic reach, encompassing studies on shores of the Pacific, Indian, and Atlantic Oceans, as well as the South China Sea. It also reveals what are, arguably, two major limitations: i) the near-universal use of proxies (i.e. burrow counts to estimate abundance) at the cost of directly measuring biological traits and bio-markers in the organism itself; and ii) descriptive or correlative study designs that rarely extend beyond a simple 'compare and contrast approach', and hence fail to identify the mechanistic cause(s) of observed contrasts. Evidence for a historically narrow range of assessed pressures (i.e., chiefly urbanisation, vehicles, beach nourishment, and recreation) is juxtaposed with rich opportunities for the broader integration of ghost crabs as a model taxon in studies of disturbance and impact assessments on ocean beaches. Tangible advances will most likely occur where ghost crabs provide foci for experiments that test specific hypotheses associated with effects of chemical, light and acoustic pollution, as well as the consequences of climate change (e

  6. Crystal structure analysis reveals functional flexibility in the selenocysteine-specific tRNA from mouse.

    Directory of Open Access Journals (Sweden)

    Oleg M Ganichkin

    Full Text Available Selenocysteine tRNAs (tRNA(Sec exhibit a number of unique identity elements that are recognized specifically by proteins of the selenocysteine biosynthetic pathways and decoding machineries. Presently, these identity elements and the mechanisms by which they are interpreted by tRNA(Sec-interacting factors are incompletely understood.We applied rational mutagenesis to obtain well diffracting crystals of murine tRNA(Sec. tRNA(Sec lacking the single-stranded 3'-acceptor end ((ΔGCCARNA(Sec yielded a crystal structure at 2.0 Å resolution. The global structure of (ΔGCCARNA(Sec resembles the structure of human tRNA(Sec determined at 3.1 Å resolution. Structural comparisons revealed flexible regions in tRNA(Sec used for induced fit binding to selenophosphate synthetase. Water molecules located in the present structure were involved in the stabilization of two alternative conformations of the anticodon stem-loop. Modeling of a 2'-O-methylated ribose at position U34 of the anticodon loop as found in a sub-population of tRNA(Secin vivo showed how this modification favors an anticodon loop conformation that is functional during decoding on the ribosome. Soaking of crystals in Mn(2+-containing buffer revealed eight potential divalent metal ion binding sites but the located metal ions did not significantly stabilize specific structural features of tRNA(Sec.We provide the most highly resolved structure of a tRNA(Sec molecule to date and assessed the influence of water molecules and metal ions on the molecule's conformation and dynamics. Our results suggest how conformational changes of tRNA(Sec support its interaction with proteins.

  7. Understanding the Role of the Master Regulator XYR1 in Trichoderma reesei by Global Transcriptional Analysis

    Science.gov (United States)

    dos Santos Castro, Lilian; de Paula, Renato G.; Antoniêto, Amanda C. C.; Persinoti, Gabriela F.; Silva-Rocha, Rafael; Silva, Roberto N.

    2016-01-01

    We defined the role of the transcriptional factor—XYR1—in the filamentous fungus Trichoderma reesei during cellulosic material degradation. In this regard, we performed a global transcriptome analysis using RNA-Seq of the Δxyr1 mutant strain of T. reesei compared with the parental strain QM9414 grown in the presence of cellulose, sophorose, and glucose as sole carbon sources. We found that 5885 genes were expressed differentially under the three tested carbon sources. Of these, 322 genes were upregulated in the presence of cellulose, while 367 and 188 were upregulated in sophorose and glucose, respectively. With respect to genes under the direct regulation of XYR1, 30 and 33 are exclusive to cellulose and sophorose, respectively. The most modulated genes in the Δxyr1 belong to Carbohydrate-Active Enzymes (CAZymes), transcription factors, and transporters families. Moreover, we highlight the downregulation of transporters belonging to the MFS and ABC transporter families. Of these, MFS members were mostly downregulated in the presence of cellulose. In sophorose and glucose, the expression of these transporters was mainly upregulated. Our results revealed that MFS and ABC transporters could be new players in cellulose degradation and their role was shown to be carbon source-dependent. Our findings contribute to a better understanding of the regulatory mechanisms of XYR1 to control cellulase gene expression in T. reesei in the presence of cellulosic material, thereby potentially enhancing its application in several biotechnology fields. PMID:26909077

  8. Sharing tools and best practice in Global Sensitivity Analysis within academia and with industry

    Science.gov (United States)

    Wagener, T.; Pianosi, F.; Noacco, V.; Sarrazin, F.

    2017-12-01

    We have spent years trying to improve the use of global sensitivity analysis (GSA) in earth and environmental modelling. Our efforts included (1) the development of tools that provide easy access to widely used GSA methods, (2) the definition of workflows so that best practice is shared in an accessible way, and (3) the development of algorithms to close gaps in available GSA methods (such as moment independent strategies) and to make GSA applications more robust (such as convergence criteria). These elements have been combined in our GSA Toolbox, called SAFE (www.safetoolbox.info), which has up to now been adopted by over 1000 (largely) academic users worldwide. However, despite growing uptake in academic circles and across a wide range of application areas, transfer to industry applications has been difficult. Initial market research regarding opportunities and barriers for uptake revealed a large potential market, but also highlighted a significant lack of knowledge regarding state-of-the-art methods and their potential value for end-users. We will present examples and discuss our experience so far in trying to overcome these problems and move beyond academia in distributing GSA tools and expertise.

  9. High-speed image analysis reveals chaotic vibratory behaviors of pathological vocal folds

    Energy Technology Data Exchange (ETDEWEB)

    Zhang Yu, E-mail: yuzhang@xmu.edu.c [Key Laboratory of Underwater Acoustic Communication and Marine Information Technology of the Ministry of Education, Xiamen University, Xiamen Fujian 361005 (China); Shao Jun [Shanghai EENT Hospital of Fudan University, Shanghai (China); Krausert, Christopher R. [Department of Surgery, Division of Otolaryngology - Head and Neck Surgery, University of Wisconsin School of Medicine and Public Health, Madison, WI 53792-7375 (United States); Zhang Sai [Key Laboratory of Underwater Acoustic Communication and Marine Information Technology of the Ministry of Education, Xiamen University, Xiamen Fujian 361005 (China); Jiang, Jack J. [Shanghai EENT Hospital of Fudan University, Shanghai (China); Department of Surgery, Division of Otolaryngology - Head and Neck Surgery, University of Wisconsin School of Medicine and Public Health, Madison, WI 53792-7375 (United States)

    2011-01-15

    Research highlights: Low-dimensional human glottal area data. Evidence of chaos in human laryngeal activity from high-speed digital imaging. Traditional perturbation analysis should be cautiously applied to aperiodic high speed image signals. Nonlinear dynamic analysis may be helpful for understanding disordered behaviors in pathological laryngeal systems. - Abstract: Laryngeal pathology is usually associated with irregular dynamics of laryngeal activity. High-speed imaging facilitates direct observation and measurement of vocal fold vibrations. However, chaotic dynamic characteristics of aperiodic high-speed image data have not yet been investigated in previous studies. In this paper, we will apply nonlinear dynamic analysis and traditional perturbation methods to quantify high-speed image data from normal subjects and patients with various laryngeal pathologies including vocal fold nodules, polyps, bleeding, and polypoid degeneration. The results reveal the low-dimensional dynamic characteristics of human glottal area data. In comparison to periodic glottal area series from a normal subject, aperiodic glottal area series from pathological subjects show complex reconstructed phase space, fractal dimension, and positive Lyapunov exponents. The estimated positive Lyapunov exponents provide the direct evidence of chaos in pathological human vocal folds from high-speed digital imaging. Furthermore, significant differences between the normal and pathological groups are investigated for nonlinear dynamic and perturbation analyses. Jitter in the pathological group is significantly higher than in the normal group, but shimmer does not show such a difference. This finding suggests that the traditional perturbation analysis should be cautiously applied to high speed image signals. However, the correlation dimension and the maximal Lyapunov exponent reveal a statistically significant difference between normal and pathological groups. Nonlinear dynamic analysis is capable of

  10. High-speed image analysis reveals chaotic vibratory behaviors of pathological vocal folds

    International Nuclear Information System (INIS)

    Zhang Yu; Shao Jun; Krausert, Christopher R.; Zhang Sai; Jiang, Jack J.

    2011-01-01

    Research highlights: → Low-dimensional human glottal area data. → Evidence of chaos in human laryngeal activity from high-speed digital imaging. → Traditional perturbation analysis should be cautiously applied to aperiodic high speed image signals. → Nonlinear dynamic analysis may be helpful for understanding disordered behaviors in pathological laryngeal systems. - Abstract: Laryngeal pathology is usually associated with irregular dynamics of laryngeal activity. High-speed imaging facilitates direct observation and measurement of vocal fold vibrations. However, chaotic dynamic characteristics of aperiodic high-speed image data have not yet been investigated in previous studies. In this paper, we will apply nonlinear dynamic analysis and traditional perturbation methods to quantify high-speed image data from normal subjects and patients with various laryngeal pathologies including vocal fold nodules, polyps, bleeding, and polypoid degeneration. The results reveal the low-dimensional dynamic characteristics of human glottal area data. In comparison to periodic glottal area series from a normal subject, aperiodic glottal area series from pathological subjects show complex reconstructed phase space, fractal dimension, and positive Lyapunov exponents. The estimated positive Lyapunov exponents provide the direct evidence of chaos in pathological human vocal folds from high-speed digital imaging. Furthermore, significant differences between the normal and pathological groups are investigated for nonlinear dynamic and perturbation analyses. Jitter in the pathological group is significantly higher than in the normal group, but shimmer does not show such a difference. This finding suggests that the traditional perturbation analysis should be cautiously applied to high speed image signals. However, the correlation dimension and the maximal Lyapunov exponent reveal a statistically significant difference between normal and pathological groups. Nonlinear dynamic

  11. Correction: Comparative analysis of fungal genomes reveals different plant cell wall degrading capacity in fungi

    Science.gov (United States)

    2014-01-01

    Abstract The version of this article published in BMC Genomics 2013, 14: 274, contains 9 unpublished genomes (Botryobasidium botryosum, Gymnopus luxurians, Hypholoma sublateritium, Jaapia argillacea, Hebeloma cylindrosporum, Conidiobolus coronatus, Laccaria amethystina, Paxillus involutus, and P. rubicundulus) downloaded from JGI website. In this correction, we removed these genomes after discussion with editors and data producers whom we should have contacted before downloading these genomes. Removing these data did not alter the principle results and conclusions of our original work. The relevant Figures 1, 2, 3, 4 and 6; and Table 1 have been revised. Additional files 1, 3, 4, and 5 were also revised. We would like to apologize for any confusion or inconvenience this may have caused. Background Fungi produce a variety of carbohydrate activity enzymes (CAZymes) for the degradation of plant polysaccharide materials to facilitate infection and/or gain nutrition. Identifying and comparing CAZymes from fungi with different nutritional modes or infection mechanisms may provide information for better understanding of their life styles and infection models. To date, over hundreds of fungal genomes are publicly available. However, a systematic comparative analysis of fungal CAZymes across the entire fungal kingdom has not been reported. Results In this study, we systemically identified glycoside hydrolases (GHs), polysaccharide lyases (PLs), carbohydrate esterases (CEs), and glycosyltransferases (GTs) as well as carbohydrate-binding modules (CBMs) in the predicted proteomes of 94 representative fungi from Ascomycota, Basidiomycota, Chytridiomycota, and Zygomycota. Comparative analysis of these CAZymes that play major roles in plant polysaccharide degradation revealed that fungi exhibit tremendous diversity in the number and variety of CAZymes. Among them, some families of GHs and CEs are the most prevalent CAZymes that are distributed in all of the fungi analyzed

  12. Multiplatform analysis of 12 cancer types reveals molecular classification within and across tissues of origin

    DEFF Research Database (Denmark)

    Hoadley, Katherine A; Yau, Christina; Wolf, Denise M

    2014-01-01

    Recent genomic analyses of pathologically defined tumor types identify "within-a-tissue" disease subtypes. However, the extent to which genomic signatures are shared across tissues is still unclear. We performed an integrative analysis using five genome-wide platforms and one proteomic platform...... on 3,527 specimens from 12 cancer types, revealing a unified classification into 11 major subtypes. Five subtypes were nearly identical to their tissue-of-origin counterparts, but several distinct cancer types were found to converge into common subtypes. Lung squamous, head and neck, and a subset...

  13. Analysis of the behavior of students in the global network

    Directory of Open Access Journals (Sweden)

    Buha Vesna V.

    2016-01-01

    Full Text Available The subject of this research is to analyze the way in which students use content on the Internet. The emphasis is on the educational and informational needs of students in the selected statistical sample. Internet sites are structured according to the preferences of students. In this sense, have been explicitly included in the analysis of educational content, information, and entertainment. After a field study on a sample of 238 students conducted a quantitative analysis and qualitative assessment derived. Data were processed in SPSS software. The results showed how students estimate the total amount of time you spend on the Internet. Conclusions also apply to the assessment of the same time, as a possible limiting factors in terms of contacts, which have to do with real social environment. Data evaluation is based on the need to analyze the habits and behavior of students on the Internet as well as their organization of time in relation to the Work-life balance.

  14. Global Carbon Fiber Composites Supply Chain Competitiveness Analysis

    Energy Technology Data Exchange (ETDEWEB)

    Sujit Das, Josh Warren, Devin West, Susan M. Schexnayder

    2016-05-01

    This analysis identifies key opportunities in the carbon fiber supply chain where resources and investments can help advance the clean energy economy. The report focuses on four application areas — wind energy, aerospace, automotive, and pressure vessels — that top the list of industries using carbon fiber and carbon fiber reinforced polymers. For each of the four application areas, the report addresses the supply and demand trends within that sector, supply chain, and costs of carbon fiber and components.

  15. Comparative proteomic analysis reveals heart toxicity induced by chronic arsenic exposure in rats

    DEFF Research Database (Denmark)

    Huang, Qingyu; Xi, Guochen; Alamdar, Ambreen

    2017-01-01

    Arsenic is a widespread metalloid in the environment, which poses a broad spectrum of adverse effects on human health. However, a global view of arsenic-induced heart toxicity is still lacking, and the underlying molecular mechanisms remain unclear. By performing a comparative quantitative...... proteomic analysis, the present study aims to investigate the alterations of proteome profile in rat heart after long-term exposure to arsenic. As a result, we found that the abundance of 81 proteins were significantly altered by arsenic treatment (35 up-regulated and 46 down-regulated). Among these, 33...... proteins were specifically associated with cardiovascular system development and function, including heart development, heart morphology, cardiac contraction and dilation, and other cardiovascular functions. It is further proposed that the aberrant regulation of 14 proteins induced by arsenic would disturb...

  16. Global sensitivity analysis using a Gaussian Radial Basis Function metamodel

    International Nuclear Information System (INIS)

    Wu, Zeping; Wang, Donghui; Okolo N, Patrick; Hu, Fan; Zhang, Weihua

    2016-01-01

    Sensitivity analysis plays an important role in exploring the actual impact of adjustable parameters on response variables. Amongst the wide range of documented studies on sensitivity measures and analysis, Sobol' indices have received greater portion of attention due to the fact that they can provide accurate information for most models. In this paper, a novel analytical expression to compute the Sobol' indices is derived by introducing a method which uses the Gaussian Radial Basis Function to build metamodels of computationally expensive computer codes. Performance of the proposed method is validated against various analytical functions and also a structural simulation scenario. Results demonstrate that the proposed method is an efficient approach, requiring a computational cost of one to two orders of magnitude less when compared to the traditional Quasi Monte Carlo-based evaluation of Sobol' indices. - Highlights: • RBF based sensitivity analysis method is proposed. • Sobol' decomposition of Gaussian RBF metamodel is obtained. • Sobol' indices of Gaussian RBF metamodel are derived based on the decomposition. • The efficiency of proposed method is validated by some numerical examples.

  17. Principal component analysis of global warming with respect to CO{sub 2} emission in Nigeria: an exploratory study

    Energy Technology Data Exchange (ETDEWEB)

    Igwenagu, C.M. [Enugu State University of Science and Technology (Nigeria). Dept. of Industrial Mathematics, Applied Statistics and Demography

    2011-07-01

    This study has examined the position of Nigeria in relation to carbon dioxide (CO{sub 2}) emission in readiness for emission trading as proposed in the Kyoto protocol as a measure of reducing global warming. It was discovered that Nigeria emits only 0.4% of the world's total CO{sub 2} emission indicating that they will be possible sellers of emission as contained in the Kyoto protocol. Fifty countries were selected for the analysis and some possible correlates of CO{sub 2} were considered. Correlation analysis and principal component analysis revealed that gross domestic product and industrial output accounted for 93% of the total variation. Based on this, a very low economic activity is being experienced in the country.

  18. Gender inequality and HIV transmission: a global analysis.

    Science.gov (United States)

    Richardson, Eugene T; Collins, Sean E; Kung, Tiffany; Jones, James H; Hoan Tram, Khai; Boggiano, Victoria L; Bekker, Linda-Gail; Zolopa, Andrew R

    2014-01-01

    The HIV pandemic disproportionately impacts young women. Worldwide, young women aged 15-24 are infected with HIV at rates twice that of young men, and young women alone account for nearly a quarter of all new HIV infections. The incommensurate HIV incidence in young - often poor - women underscores how social and economic inequalities shape the HIV epidemic. Confluent social forces, including political and gender violence, poverty, racism, and sexism impede equal access to therapies and effective care, but most of all constrain the agency of women. HIV prevalence data was compiled from the 2010 UNAIDS Global Report. Gender inequality was assessed using the 2011 United Nations Human Development Report Gender Inequality Index (GII). Logistic regression models were created with predominant mode of transmission (heterosexual vs. MSM/IDU) as the dependent variable and GII, Muslim vs. non-Muslim, Democracy Index, male circumcision rate, log gross national income (GNI) per capita at purchasing power parity (PPP), and region as independent variables. There is a significant correlation between having a predominantly heterosexual epidemic and high gender inequality across all models. There is not a significant association between whether a country is predominantly Muslim, has a high/low GNI at PPP, has a high/low circumcision rate, and its primary mode of transmission. In addition, there are only three countries that have had a generalized epidemic in the past but no longer have one: Cambodia, Honduras, and Eritrea. GII data are available only for Cambodia and Honduras, and these countries showed a 37 and 34% improvement, respectively, in their Gender Inequality Indices between 1995 and 2011. During the same period, both countries reduced their HIV prevalence below the 1% threshold of a generalized epidemic. This represents limited but compelling evidence that improvements in gender inequality can lead to the abatement of generalized epidemics. Gender inequality is an

  19. Global species delimitation and phylogeography of the circumtropical ‘sexy shrimp’ Thor amboinensis reveals a cryptic species complex and secondary contact in the Indo-West Pacific

    KAUST Repository

    Titus, Benjamin M.

    2018-04-27

    Aim The “sexy shrimp” Thor amboinensis is currently considered a single circumtropical species. However, the tropical oceans are partitioned by hard and soft barriers to dispersal, providing ample opportunity for allopatric speciation. Herein, we test the null hypothesis that T. amboinensis is a single global species, reconstruct its global biogeographical history, and comment on population‐level patterns throughout the Tropical Western Atlantic. Location Coral reefs in all tropical oceans. Methods Specimens of Thor amboinensis were obtained through field collection and museum holdings. We used one mitochondrial (COI) and two nuclear (NaK, enolase) gene fragments for global species delimitation and phylogenetic analyses (n = 83 individuals, 30 sample localities), while phylogeographical reconstruction in the TWA was based on COI only (n = 303 individuals, 10 sample localities). Results We found evidence for at least five cryptic lineages (9%–22% COI pairwise sequence divergence): four in the Indo‐West Pacific and one in the Tropical Western Atlantic. Phylogenetic reconstruction revealed that endemic lineages from Japan and the South Central Pacific are more closely related to the Tropical Western Atlantic lineage than to a co‐occurring lineage that is widespread throughout the Indo‐West Pacific. Concatenated and species tree phylogenetic analyses differ in the placement of an endemic Red Sea lineage and suggest alternate dispersal pathways into the Atlantic. Phylogeographical reconstruction throughout the Tropical Western Atlantic reveals little genetic structure over more than 3,000 km. Main conclusions Thor amboinensis is a species complex that has undergone a series of allopatric speciation events and whose members are in secondary contact in the Indo‐West Pacific. Nuclear‐ and mitochondrial‐ gene phylogenies show evidence of introgression between lineages inferred to have been separated more than 20 Ma. Phylogenetic discordance between

  20. Re-Analysis of Metagenomic Sequences from Acute Flaccidmyelitis Patients Reveals Alternatives to Enterovirus D68 Infection

    Science.gov (United States)

    2015-07-13

    caused in some cases by infection with enterovirus D68. We found that among the patients whose symptoms were previously attributed to enterovirus D68...distribution is unlimited. Re-analysis of metagenomic sequences from acute flaccidmyelitis patients reveals alternatives to enterovirus D68...Street Baltimore, MD 21218 -2685 ABSTRACT Re-analysis of metagenomic sequences from acute flaccidmyelitis patients reveals alternatives to enterovirus

  1. VNTR analysis reveals unexpected genetic diversity within Mycoplasma agalactiae, the main causative agent of contagious agalactia

    Directory of Open Access Journals (Sweden)

    Ayling Roger D

    2008-11-01

    Full Text Available Abstract Background Mycoplasma agalactiae is the main cause of contagious agalactia, a serious disease of sheep and goats, which has major clinical and economic impacts. Previous studies of M. agalactiae have shown it to be unusually homogeneous and there are currently no available epidemiological techniques which enable a high degree of strain differentiation. Results We have developed variable number tandem repeat (VNTR analysis using the sequenced genome of the M. agalactiae type strain PG2. The PG2 genome was found to be replete with tandem repeat sequences and 4 were chosen for further analysis. VNTR 5 was located within the hypothetical protein MAG6170 a predicted lipoprotein. VNTR 14 was intergenic between the hypothetical protein MAG3350 and the hypothetical protein MAG3340. VNTR 17 was intergenic between the hypothetical protein MAG4060 and the hypothetical protein MAG4070 and VNTR 19 spanned the 5' end of the pseudogene for a lipoprotein MAG4310 and the 3' end of the hypothetical lipoprotein MAG4320. We have investigated the genetic diversity of 88 M. agalactiae isolates of wide geographic origin using VNTR analysis and compared it with pulsed field gel electrophoresis (PFGE and random amplified polymorphic DNA (RAPD analysis. Simpson's index of diversity was calculated to be 0.324 for PFGE and 0.574 for VNTR analysis. VNTR analysis revealed unexpected diversity within M. agalactiae with 9 different VNTR types discovered. Some correlation was found between geographical origin and the VNTR type of the isolates. Conclusion VNTR analysis represents a useful, rapid first-line test for use in molecular epidemiological analysis of M. agalactiae for outbreak tracing and control.

  2. Multilocus sequence analysis (MLSA) of Bradyrhizobium strains: revealing high diversity of tropical diazotrophic symbiotic bacteria.

    Science.gov (United States)

    Delamuta, Jakeline Renata Marçon; Ribeiro, Renan Augusto; Menna, Pâmela; Bangel, Eliane Villamil; Hungria, Mariangela

    2012-04-01

    Symbiotic association of several genera of bacteria collectively called as rhizobia and plants belonging to the family Leguminosae (=Fabaceae) results in the process of biological nitrogen fixation, playing a key role in global N cycling, and also bringing relevant contributions to the agriculture. Bradyrhizobium is considered as the ancestral of all nitrogen-fixing rhizobial species, probably originated in the tropics. The genus encompasses a variety of diverse bacteria, but the diversity captured in the analysis of the 16S rRNA is often low. In this study, we analyzed twelve Bradyrhizobium strains selected from previous studies performed by our group for showing high genetic diversity in relation to the described species. In addition to the 16S rRNA, five housekeeping genes (recA, atpD, glnII, gyrB and rpoB) were analyzed in the MLSA (multilocus sequence analysis) approach. Analysis of each gene and of the concatenated housekeeping genes captured a considerably higher level of genetic diversity, with indication of putative new species. The results highlight the high genetic variability associated with Bradyrhizobium microsymbionts of a variety of legumes. In addition, the MLSA approach has proved to represent a rapid and reliable method to be employed in phylogenetic and taxonomic studies, speeding the identification of the still poorly known diversity of nitrogen-fixing rhizobia in the tropics.

  3. Metagenomic analysis reveals that modern microbialites and polar microbial mats have similar taxonomic and functional potential

    Directory of Open Access Journals (Sweden)

    Richard Allen White III

    2015-09-01

    Full Text Available Within the subarctic climate of Clinton Creek, Yukon, Canada, lies an abandoned and flooded open-pit asbestos mine that harbors rapidly growing microbialites. To understand their formation we completed a metagenomic community profile of the microbialites and their surrounding sediments. Assembled metagenomic data revealed that bacteria within the phylum Proteobacteria numerically dominated this system, although the relative abundances of taxa within the phylum varied among environments. Bacteria belonging to Alphaproteobacteria and Gammaproteobacteria were dominant in the microbialites and sediments, respectively. The microbialites were also home to many other groups associated with microbialite formation including filamentous cyanobacteria and dissimilatory sulfate-reducing Deltaproteobacteria, consistent with the idea of a shared global microbialite microbiome. Other members were present that are typically not associated with microbialites including Gemmatimonadetes and iron-oxidizing Betaproteobacteria, which participate in carbon metabolism and iron cycling. Compared to the sediments, the microbialite microbiome has significantly more genes associated with photosynthetic processes (e.g., photosystem II reaction centers, carotenoid and chlorophyll biosynthesis and carbon fixation (e.g., CO dehydrogenase. The Clinton Creek microbialite communities had strikingly similar functional potentials to non-lithifying microbial mats from the Canadian High Arctic and Antarctica, but are functionally distinct, from non-lithifying mats or biofilms from Yellowstone. Clinton Creek microbialites also share metabolic genes (R2 0.900. These metagenomic profiles from an anthropogenic microbialite-forming ecosystem provide context to microbialite formation on a human-relevant timescale.

  4. Comprehensive resistome analysis reveals the prevalence of NDM and MCR-1 in Chinese poultry production.

    Science.gov (United States)

    Wang, Yang; Zhang, Rongmin; Li, Jiyun; Wu, Zuowei; Yin, Wenjuan; Schwarz, Stefan; Tyrrell, Jonathan M; Zheng, Yongjun; Wang, Shaolin; Shen, Zhangqi; Liu, Zhihai; Liu, Jianye; Lei, Lei; Li, Mei; Zhang, Qidi; Wu, Congming; Zhang, Qijing; Wu, Yongning; Walsh, Timothy R; Shen, Jianzhong

    2017-02-06

    By 2030, the global population will be 8.5 billion, placing pressure on international poultry production, of which China is a key producer 1 . From April 2017, China will implement the withdrawal of colistin as a growth promoter, removing over 8,000 tonnes per year from the Chinese farming sector 2 . To understand the impact of banning colistin and the epidemiology of multi-drug-resistant (MDR) Escherichia coli (using bla NDM and mcr-1 as marker genes), we sampled poultry, dogs, sewage, wild birds and flies. Here, we show that mcr-1, but not bla NDM , is prevalent in hatcheries, but bla NDM quickly contaminates flocks through dogs, flies and wild birds. We also screened samples directly for resistance genes to understand the true breadth and depth of the environmental and animal resistome. Direct sample testing for bla NDM and mcr-1 in hatcheries, commercial farms, a slaughterhouse and supermarkets revealed considerably higher levels of positive samples than the bla NDM - and mcr-1-positive E. coli, indicating a substantial segment of unseen resistome-a phenomenon we have termed the 'phantom resistome'. Whole-genome sequencing identified common bla NDM -positive E. coli shared among farms, flies, dogs and farmers, providing direct evidence of carbapenem-resistant E. coli transmission and environmental contamination.

  5. Proteomes and Ubiquitylomes Analysis Reveals the Involvement of Ubiquitination in Protein Degradation in Petunias1

    Science.gov (United States)

    Liu, Juanxu; Wei, Qian; Wang, Rongmin; Yang, Weiyuan; Ma, Yueyue; Chen, Guoju

    2017-01-01

    Petal senescence is a complex programmed process. It has been demonstrated previously that treatment with ethylene, a plant hormone involved in senescence, can extensively alter transcriptome and proteome profiles in plants. However, little is known regarding the impact of ethylene on posttranslational modification (PTM) or the association between PTM and the proteome. Protein degradation is one of the hallmarks of senescence, and ubiquitination, a major PTM in eukaryotes, plays important roles in protein degradation. In this study, we first obtained reference petunia (Petunia hybrida) transcriptome data via RNA sequencing. Next, we quantitatively investigated the petunia proteome and ubiquitylome and the association between them in petunia corollas following ethylene treatment. In total, 51,799 unigenes, 3,606 proteins, and 2,270 ubiquitination sites were quantified 16 h after ethylene treatment. Treatment with ethylene resulted in 14,448 down-regulated and 6,303 up-regulated unigenes (absolute log2 fold change > 1 and false discovery rate petunia. Several putative ubiquitin ligases were up-regulated at the protein and transcription levels. Our results showed that the global proteome and ubiquitylome were negatively correlated and that ubiquitination could be involved in the degradation of proteins during ethylene-mediated corolla senescence in petunia. Ethylene regulates hormone signaling transduction pathways at both the protein and ubiquitination levels in petunia corollas. In addition, our results revealed that ethylene increases the ubiquitination levels of proteins involved in endoplasmic reticulum-associated degradation. PMID:27810942

  6. Life history of the Harlequin ladybird, Harmonia axyridis; a global meta-analysis

    NARCIS (Netherlands)

    Raak-van den Berg, C.L.; Hemerik, A.; Werf, van der W.; Jong, de P.W.; Lenteren, van J.C.

    2017-01-01

    Data collected en used for a meta analysis on life history data of H. axyridis. And the resulting 20 best models for each life history characteristic. Published in the paper: Life history of the Harlequin ladybird, Harmonia axyridis; a global meta-analysis.

  7. The use of 'macro' legal analysis in the development of global environmental governance

    OpenAIRE

    Turner, Stephen

    2016-01-01

    This talk will discuss the challenges that are faced by lawyers in assessing the constituent elements of global environmental governance. It takes into account the different and sometimes disparate approaches that have been taken to the subject and the different interpretations of the term ‘global environmental governance’ itself. It suggests that in the face of such challenges an approach which includes ‘macro’ legal analysis should be developed to ensure that all relevant factors are includ...

  8. Multi-variant pathway association analysis reveals the importance of genetic determinants of estrogen metabolism in breast and endometrial cancer susceptibility.

    Directory of Open Access Journals (Sweden)

    Yen Ling Low

    2010-07-01

    Full Text Available Despite the central role of estrogen exposure in breast and endometrial cancer development and numerous studies of genes in the estrogen metabolic pathway, polymorphisms within the pathway have not been consistently associated with these cancers. We posit that this is due to the complexity of multiple weak genetic effects within the metabolic pathway that can only be effectively detected through multi-variant analysis. We conducted a comprehensive association analysis of the estrogen metabolic pathway by interrogating 239 tagSNPs within 35 genes of the pathway in three tumor samples. The discovery sample consisted of 1,596 breast cancer cases, 719 endometrial cancer cases, and 1,730 controls from Sweden; and the validation sample included 2,245 breast cancer cases and 1,287 controls from Finland. We performed admixture maximum likelihood (AML-based global tests to evaluate the cumulative effect from multiple SNPs within the whole metabolic pathway and three sub-pathways for androgen synthesis, androgen-to-estrogen conversion, and estrogen removal. In the discovery sample, although no single polymorphism was significant after correction for multiple testing, the pathway-based AML global test suggested association with both breast (p(global = 0.034 and endometrial (p(global = 0.052 cancers. Further testing revealed the association to be focused on polymorphisms within the androgen-to-estrogen conversion sub-pathway, for both breast (p(global = 0.008 and endometrial cancer (p(global = 0.014. The sub-pathway association was validated in the Finnish sample of breast cancer (p(global = 0.015. Further tumor subtype analysis demonstrated that the association of the androgen-to-estrogen conversion sub-pathway was confined to postmenopausal women with sporadic estrogen receptor positive tumors (p(global = 0.0003. Gene-based AML analysis suggested CYP19A1 and UGT2B4 to be the major players within the sub-pathway. Our study indicates that the composite

  9. Proteomic analysis of three gonad types of swamp eel reveals genes differentially expressed during sex reversal.

    Science.gov (United States)

    Sheng, Yue; Zhao, Wei; Song, Ying; Li, Zhigang; Luo, Majing; Lei, Quan; Cheng, Hanhua; Zhou, Rongjia

    2015-05-18

    A variety of mechanisms are engaged in sex determination in vertebrates. The teleost fish swamp eel undergoes sex reversal naturally and is an ideal model for vertebrate sexual development. However, the importance of proteome-wide scanning for gonad reversal was not previously determined. We report a 2-D electrophoresis analysis of three gonad types of proteomes during sex reversal. MS/MS analysis revealed a group of differentially expressed proteins during ovary to ovotestis to testis transformation. Cbx3 is up-regulated during gonad reversal and is likely to have a role in spermatogenesis. Rab37 is down-regulated during the reversal and is mainly associated with oogenesis. Both Cbx3 and Rab37 are linked up in a protein network. These datasets in gonadal proteomes provide a new resource for further studies in gonadal development.

  10. Proteomic analysis of MG132-treated germinating pollen reveals expression signatures associated with proteasome inhibition.

    Directory of Open Access Journals (Sweden)

    Candida Vannini

    Full Text Available Chemical inhibition of the proteasome has been previously found to effectively impair pollen germination and tube growth in vitro. However, the mediators of these effects at the molecular level are unknown. By performing 2DE proteomic analysis, 24 differentially expressed protein spots, representing 14 unique candidate proteins, were identified in the pollen of kiwifruit (Actinidia deliciosa germinated in the presence of the MG132 proteasome inhibitor. qPCR analysis revealed that 11 of these proteins are not up-regulated at the mRNA level, but are most likely stabilized by proteasome inhibition. These differentially expressed proteins are predicted to function in various pathways including energy and lipid metabolism, cell wall synthesis, protein synthesis/degradation and stress responses. In line with this evidence, the MG132-induced changes in the proteome were accompanied by an increase in ATP and ROS content and by an alteration in fatty acid composition.

  11. Time-frequency wavelet analysis of the interrelationship between the global macro assets and the fear indexes

    Science.gov (United States)

    Abid, Fathi; Kaffel, Bilel

    2018-01-01

    Understanding the interrelationships of the global macro assets is crucial for global macro investing. This paper investigates the local variance and the interconnection between the stock, gold, oil, Forex and the implied volatility markets in the time/frequency domains using the wavelet methodology, including the wavelet power spectrum, the wavelet squared coherence and phase difference, the wavelet multiple correlation and cross-correlation. The univariate analysis reveals that, in some crisis periods, underlying asset markets present the same pattern in terms of the wavelet power spectrum indicating high volatility for the medium scale, and that for the other market stress periods, volatility behaves differently. Moreover, unlike the underlying asset markets, the implied volatility markets are characterized by high power regions across the entire period, even in the absence of economic events. Bivariate results show a bidirectional relationship between the underlying assets and their corresponding implied volatility indexes, and a steady co-movement between the stock index and its corresponding fear index. Multiple correlation analysis indicates a strong correlation between markets at high scales with evidence of a nearly perfect integration for a period longer than a year. In addition, the hedging strategies based on the volatility index lead to an increase in portfolio correlation. On the other hand, the results from multiple cross-correlations reveal that the lead-lag effect starts from the medium scale and that the VIX (stock market volatility index) index is the potential leader or follower of the other markets.

  12. Co-occurrence correlations of heavy metals in sediments revealed using network analysis.

    Science.gov (United States)

    Liu, Lili; Wang, Zhiping; Ju, Feng; Zhang, Tong

    2015-01-01

    In this study, the correlation-based study was used to identify the co-occurrence correlations among metals in marine sediment of Hong Kong, based on the long-term (from 1991 to 2011) temporal and spatial monitoring data. 14 stations out of the total 45 marine sediment monitoring stations were selected from three representative areas, including Deep Bay, Victoria Harbour and Mirs Bay. Firstly, Spearman's rank correlation-based network analysis was conducted as the first step to identify the co-occurrence correlations of metals from raw metadata, and then for further analysis using the normalized metadata. The correlations patterns obtained by network were consistent with those obtained by the other statistic normalization methods, including annual ratios, R-squared coefficient and Pearson correlation coefficient. Both Deep Bay and Victoria Harbour have been polluted by heavy metals, especially for Pb and Cu, which showed strong co-occurrence with other heavy metals (e.g. Cr, Ni, Zn and etc.) and little correlations with the reference parameters (Fe or Al). For Mirs Bay, which has better marine sediment quality compared with Deep Bay and Victoria Harbour, the co-occurrence patterns revealed by network analysis indicated that the metals in sediment dominantly followed the natural geography process. Besides the wide applications in biology, sociology and informatics, it is the first time to apply network analysis in the researches of environment pollutions. This study demonstrated its powerful application for revealing the co-occurrence correlations among heavy metals in marine sediments, which could be further applied for other pollutants in various environment systems. Copyright © 2014 Elsevier Ltd. All rights reserved.

  13. Large scale aggregate microarray analysis reveals three distinct molecular subclasses of human preeclampsia.

    Science.gov (United States)

    Leavey, Katherine; Bainbridge, Shannon A; Cox, Brian J

    2015-01-01

    Preeclampsia (PE) is a life-threatening hypertensive pathology of pregnancy affecting 3-5% of all pregnancies. To date, PE has no cure, early detection markers, or effective treatments short of the removal of what is thought to be the causative organ, the placenta, which may necessitate a preterm delivery. Additionally, numerous small placental microarray studies attempting to identify "PE-specific" genes have yielded inconsistent results. We therefore hypothesize that preeclampsia is a multifactorial disease encompassing several pathology subclasses, and that large cohort placental gene expression analysis will reveal these groups. To address our hypothesis, we utilized known bioinformatic methods to aggregate 7 microarray data sets across multiple platforms in order to generate a large data set of 173 patient samples, including 77 with preeclampsia. Unsupervised clustering of these patient samples revealed three distinct molecular subclasses of PE. This included a "canonical" PE subclass demonstrating elevated expression of known PE markers and genes associated with poor oxygenation and increased secretion, as well as two other subclasses potentially representing a poor maternal response to pregnancy and an immunological presentation of preeclampsia. Our analysis sheds new light on the heterogeneity of PE patients, and offers up additional avenues for future investigation. Hopefully, our subclassification of preeclampsia based on molecular diversity will finally lead to the development of robust diagnostics and patient-based treatments for this disorder.

  14. Evolutionary Meta-Analysis of Association Studies Reveals Ancient Constraints Affecting Disease Marker Discovery

    Science.gov (United States)

    Dudley, Joel T.; Chen, Rong; Sanderford, Maxwell; Butte, Atul J.; Kumar, Sudhir

    2012-01-01

    Genome-wide disease association studies contrast genetic variation between disease cohorts and healthy populations to discover single nucleotide polymorphisms (SNPs) and other genetic markers revealing underlying genetic architectures of human diseases. Despite scores of efforts over the past decade, many reproducible genetic variants that explain substantial proportions of the heritable risk of common human diseases remain undiscovered. We have conducted a multispecies genomic analysis of 5,831 putative human risk variants for more than 230 disease phenotypes reported in 2,021 studies. We find that the current approaches show a propensity for discovering disease-associated SNPs (dSNPs) at conserved genomic positions because the effect size (odds ratio) and allelic P value of genetic association of an SNP relates strongly to the evolutionary conservation of their genomic position. We propose a new measure for ranking SNPs that integrates evolutionary conservation scores and the P value (E-rank). Using published data from a large case-control study, we demonstrate that E-rank method prioritizes SNPs with a greater likelihood of bona fide and reproducible genetic disease associations, many of which may explain greater proportions of genetic variance. Therefore, long-term evolutionary histories of genomic positions offer key practical utility in reassessing data from existing disease association studies, and in the design and analysis of future studies aimed at revealing the genetic basis of common human diseases. PMID:22389448

  15. Global gene expression analysis for evaluation and design of biomaterials

    Directory of Open Access Journals (Sweden)

    Nobutaka Hanagata, Taro Takemura and Takashi Minowa

    2010-01-01

    Full Text Available Comprehensive gene expression analysis using DNA microarrays has become a widespread technique in molecular biological research. In the biomaterials field, it is used to evaluate the biocompatibility or cellular toxicity of metals, polymers and ceramics. Studies in this field have extracted differentially expressed genes in the context of differences in cellular responses among multiple materials. Based on these genes, the effects of materials on cells at the molecular level have been examined. Expression data ranging from several to tens of thousands of genes can be obtained from DNA microarrays. For this reason, several tens or hundreds of differentially expressed genes are often present in different materials. In this review, we outline the principles of DNA microarrays, and provide an introduction to methods of extracting information which is useful for evaluating and designing biomaterials from comprehensive gene expression data.

  16. Global Carbon Fiber Composites Supply Chain Competitiveness Analysis

    Energy Technology Data Exchange (ETDEWEB)

    Das, Sujit [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Warren, Josh [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); West, Devin [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Schexnayder, Susan M. [Univ. of Tennessee, Knoxville, TN (United States)

    2016-05-01

    This study identifies key opportunities in the carbon fiber supply chain where the United States Department of Energy's Office of Energy Efficiency and Renewable Energy resources and investments can help the United States achieve or maintain a competitive advantage. The report focuses on four application areas--wind energy, aerospace, automotive, and pressure vessels--that top the list of industries using carbon fiber and carbon fiber reinforced polymers and are also particularly relevant to EERE's mission. For each of the four application areas, the report addresses the supply and demand trends within that sector, supply chain, and costs of carbon fiber and components, all contributing to a competitiveness assessment that addresses the United States' role in future industry growth. This report was prepared by researchers at Oak Ridge National Laboratory and the University of Tennessee for the Clean Energy Manufacturing Analysis Center.

  17. Global gene expression analysis for evaluation and design of biomaterials

    International Nuclear Information System (INIS)

    Hanagata, Nobutaka; Takemura, Taro; Minowa, Takashi

    2010-01-01

    Comprehensive gene expression analysis using DNA microarrays has become a widespread technique in molecular biological research. In the biomaterials field, it is used to evaluate the biocompatibility or cellular toxicity of metals, polymers and ceramics. Studies in this field have extracted differentially expressed genes in the context of differences in cellular responses among multiple materials. Based on these genes, the effects of materials on cells at the molecular level have been examined. Expression data ranging from several to tens of thousands of genes can be obtained from DNA microarrays. For this reason, several tens or hundreds of differentially expressed genes are often present in different materials. In this review, we outline the principles of DNA microarrays, and provide an introduction to methods of extracting information which is useful for evaluating and designing biomaterials from comprehensive gene expression data. (topical review)

  18. Global analysis of the sporulation pathway of Clostridium difficile.

    Science.gov (United States)

    Fimlaid, Kelly A; Bond, Jeffrey P; Schutz, Kristin C; Putnam, Emily E; Leung, Jacqueline M; Lawley, Trevor D; Shen, Aimee

    2013-01-01

    The Gram-positive, spore-forming pathogen Clostridium difficile is the leading definable cause of healthcare-associated diarrhea worldwide. C. difficile infections are difficult to treat because of their frequent recurrence, which can cause life-threatening complications such as pseudomembranous colitis. The spores of C. difficile are responsible for these high rates of recurrence, since they are the major transmissive form of the organism and resistant to antibiotics and many disinfectants. Despite the importance of spores to the pathogenesis of C. difficile, little is known about their composition or formation. Based on studies in Bacillus subtilis and other Clostridium spp., the sigma factors σ(F), σ(E), σ(G), and σ(K) are predicted to control the transcription of genes required for sporulation, although their specific functions vary depending on the organism. In order to determine the roles of σ(F), σ(E), σ(G), and σ(K) in regulating C. difficile sporulation, we generated loss-of-function mutations in genes encoding these sporulation sigma factors and performed RNA-Sequencing to identify specific sigma factor-dependent genes. This analysis identified 224 genes whose expression was collectively activated by sporulation sigma factors: 183 were σ(F)-dependent, 169 were σ(E)-dependent, 34 were σ(G)-dependent, and 31 were σ(K)-dependent. In contrast with B. subtilis, C. difficile σ(E) was dispensable for σ(G) activation, σ(G) was dispensable for σ(K) activation, and σ(F) was required for post-translationally activating σ(G). Collectively, these results provide the first genome-wide transcriptional analysis of genes induced by specific sporulation sigma factors in the Clostridia and highlight that diverse mechanisms regulate sporulation sigma factor activity in the Firmicutes.

  19. Statistical Analysis of Development Trends in Global Renewable Energy

    Directory of Open Access Journals (Sweden)

    Marina D. Simonova

    2016-01-01

    Full Text Available The article focuses on the economic and statistical analysis of industries associated with the use of renewable energy sources in several countries. The dynamic development and implementation of technologies based on renewable energy sources (hereinafter RES is the defining trend of world energy development. The uneven distribution of hydrocarbon reserves, increasing demand of developing countries and environmental risks associated with the production and consumption of fossil resources has led to an increasing interest of many states to this field. Creating low-carbon economies involves the implementation of plans to increase the proportion of clean energy through renewable energy sources, energy efficiency, reduce greenhouse gas emissions. The priority of this sector is a characteristic feature of modern development of developed (USA, EU, Japan and emerging economies (China, India, Brazil, etc., as evidenced by the inclusion of the development of this segment in the state energy strategies and the revision of existing approaches to energy security. The analysis of the use of renewable energy, its contribution to value added of countries-producers is of a particular interest. Over the last decade, the share of energy produced from renewable sources in the energy balances of the world's largest economies increased significantly. Every year the number of power generating capacity based on renewable energy is growing, especially, this trend is apparent in China, USA and European Union countries. There is a significant increase in direct investment in renewable energy. The total investment over the past ten years increased by 5.6 times. The most rapidly developing kinds are solar energy and wind power.

  20. Inequalities in global health inequalities research: A 50-year bibliometric analysis (1966-2015)

    Science.gov (United States)

    Pericàs, Juan M.; Benach, Joan

    2018-01-01

    Background Increasing evidence shows that health inequalities exist between and within countries, and emphasis has been placed on strengthening the production and use of the global health inequalities research, so as to improve capacities to act. Yet, a comprehensive overview of this evidence base is still needed, to determine what is known about the global and historical scientific production on health inequalities to date, how is it distributed in terms of country income groups and world regions, how has it changed over time, and what international collaboration dynamics exist. Methods A comprehensive bibliometric analysis of the global scientific production on health inequalities, from 1966 to 2015, was conducted using Scopus database. The historical and global evolution of the study of health inequalities was considered, and through joinpoint regression analysis and visualisation network maps, the preceding questions were examined. Findings 159 countries (via authorship affiliation) contributed to this scientific production, three times as many countries than previously found. Scientific output on health inequalities has exponentially grown over the last five decades, with several marked shift points, and a visible country-income group affiliation gradient in the initiation and consistent publication frequency. Higher income countries, especially Anglo-Saxon and European countries, disproportionately dominate first and co-authorship, and are at the core of the global collaborative research networks, with the Global South on the periphery. However, several country anomalies exist that suggest that the causes of these research inequalities, and potential underlying dependencies, run deeper than simply differences in country income and language. Conclusions Whilst the global evidence base has expanded, Global North-South research gaps exist, persist and, in some cases, are widening. Greater understanding of the structural determinants of these research

  1. Proteomic analysis of maize grain development using iTRAQ reveals temporal programs of diverse metabolic processes.

    Science.gov (United States)

    Yu, Tao; Li, Geng; Dong, Shuting; Liu, Peng; Zhang, Jiwang; Zhao, Bin

    2016-11-04

    Grain development in maize is an essential process in the plant's life cycle and is vital for use of the plant as a crop for animals and humans. However, little is known regarding the protein regulatory networks that control grain development. Here, isobaric tag for relative and absolute quantification (iTRAQ) technology was used to analyze temporal changes in protein expression during maize grain development. Maize grain proteins and changes in protein expression at eight developmental stages from 3 to 50 d after pollination (DAP) were performed using iTRAQ-based proteomics. Overall, 4751 proteins were identified; 2639 of these were quantified and 1235 showed at least 1.5-fold changes in expression levels at different developmental stages and were identified as differentially expressed proteins (DEPs). The DEPs were involved in different cellular and metabolic processes with a preferential distribution to protein synthesis/destination and metabolism categories. A K-means clustering analysis revealed coordinated protein expression associated with different functional categories/subcategories at different development stages. Our results revealed developing maize grain display different proteomic characteristics at distinct stages, such as numerous DEPs for cell growth/division were highly expressed during early stages, whereas those for starch biosynthesis and defense/stress accumulated in middle and late stages, respectively. We also observed coordinated expression of multiple proteins of the antioxidant system, which are essential for the maintenance of reactive oxygen species (ROS) homeostasis during grain development. Particularly, some DEPs, such as zinc metallothionein class II, pyruvate orthophosphate dikinase (PPDK) and 14-3-3 proteins, undergo major changes in expression at specific developmental stages, suggesting their roles in maize grain development. These results provide a valuable resource for analyzing protein function on a global scale and also

  2. Strategies for assessing proton linkage to bimolecular interactions by global analysis of isothermal titration calorimetry data

    International Nuclear Information System (INIS)

    Coussens, Nathan P.; Schuck, Peter; Zhao, Huaying

    2012-01-01

    Highlights: ► We demonstrate the usefulness of global analysis of ITC data for proton-linked binding study. ► Various experimental strategies are evaluated for their information content. ► Data at multiple temperatures might improve the precision of binding parameters. ► Methods for detailed error analysis of parameter uncertainties are discussed. ► By global modeling, an uncertainty in molecular concentrations can be accounted for. - Abstract: Isothermal titration calorimetry (ITC) is a traditional and powerful method for studying the linkage of ligand binding to proton uptake or release. The theoretical framework has been developed for more than two decades and numerous applications have appeared. In the current work, we explored strategic aspects of experimental design. To this end, we simulated families of ITC data sets that embed different strategies with regard to the number of experiments, range of experimental pH, buffer ionization enthalpy, and temperature. We then re-analyzed the families of data sets in the context of global analysis, employing a proton linkage binding model implemented in the global data analysis platform SEDPHAT, and examined the information content of all data sets by a detailed statistical error analysis of the parameter estimates. In particular, we studied the impact of different assumptions about the knowledge of the exact concentrations of the components, which in practice presents an experimental limitation for many systems. For example, the uncertainty in concentration may reflect imperfectly known extinction coefficients and stock concentrations or may account for different extents of partial inactivation when working with proteins at different pH values. Our results show that the global analysis can yield reliable estimates of the thermodynamic parameters for intrinsic binding and protonation, and that in the context of the global analysis the exact molecular component concentrations may not be required. Additionally

  3. The future of the global environment. A model-based analysis supporting UNEP's first global environment outlook

    International Nuclear Information System (INIS)

    Bakkes, J.; Van Woerden, J.; Alcamo, J.; Berk, M.; Bol, P.; Van den Born, G.J.; Ten Brink, B.; Hettelingh, J.P.; Niessen, L.; Langeweg, F.; Swart, R.

    1997-01-01

    Integrated assessments in support of environmental policy have been applied to a number of countries and regions, and to international negotiations. UNEP's first Global Environment Outlook (GEO-1) can be seen as a step towards making the tool of integrated assessment more widely available as a means for focusing action. This technical report documents RIVM's contribution to the GEO-1 report, focusing on the subject 'looking ahead'. It is illustrated that a 'what if' analysis helps to look beyond the delays in environmental and resource processes. This report illustrates that integrated assessment and modelling techniques can be excellent tools for environment and development policy-setting. The methodology, however, will need to be further developed and adapted to the realities and expectations of diverse regions, incorporating alternative policy strategies and development scenarios. This report focuses primarily on the period 1970-2015, because reliable historical data are often only generally available from 1970 onwards and the year 2015 is believed to match the time perspective of decision-makers. The findings of the analysis are reported in terms of six regions, corresponding with the division of the UNEP regional offices. Questions asked are: how will socioeconomic driving forces affect freshwater and land resources, and how will these changes mutually interact, and why are these changes important for society? Chapter 2 deals with the development of the social and economic driving forces. In the Chapters 3 and 4 it is discussed how this pressure influences selected aspects of the environment. Chapter 3 alone addresses the importance of selected elements of the interacting global element cycles for environmental quality, while Chapter 4 addresses land resources, their potential for food production and associated dependence on freshwater resources. The impacts on selected components of natural areas (Chapter 5) and society (Chapter 6) are subsequently addressed

  4. RNA-Seq Analysis Reveals MAPKKK Family Members Related to Drought Tolerance in Maize

    Science.gov (United States)

    Ren, Wen; Yang, Fengling; He, Hang; Zhao, Jiuran

    2015-01-01

    The mitogen-activated protein kinase (MAPK) cascade is an evolutionarily conserved signal transduction pathway that is involved in plant development and stress responses. As the first component of this phosphorelay cascade, mitogen-activated protein kinase kinase kinases (MAPKKKs) act as adaptors linking upstream signaling steps to the core MAPK cascade to promote the appropriate cellular responses; however, the functions of MAPKKKs in maize are unclear. Here, we identified 71 MAPKKK genes, of which 14 were novel, based on a computational analysis of the maize (Zea mays L.) genome. Using an RNA-seq analysis in the leaf, stem and root of maize under well-watered and drought-stress conditions, we identified 5,866 differentially expressed genes (DEGs), including 8 MAPKKK genes responsive to drought stress. Many of the DEGs were enriched in processes such as drought stress, abiotic stimulus, oxidation-reduction, and metabolic processes. The other way round, DEGs involved in processes such as oxidation, photosynthesis, and starch, proline, ethylene, and salicylic acid metabolism were clearly co-expressed with the MAPKKK genes. Furthermore, a quantitative real-time PCR (qRT-PCR) analysis was performed to assess the relative expression levels of MAPKKKs. Correlation analysis revealed that there was a significant correlation between expression levels of two MAPKKKs and relative biomass responsive to drought in 8 inbred lines. Our results indicate that MAPKKKs may have important regulatory functions in drought tolerance in maize. PMID:26599013

  5. Analysis of Sea Ice Cover Sensitivity in Global Climate Model

    Directory of Open Access Journals (Sweden)

    V. P. Parhomenko

    2014-01-01

    Full Text Available The paper presents joint calculations using a 3D atmospheric general circulation model, an ocean model, and a sea ice evolution model. The purpose of the work is to analyze a seasonal and annual evolution of sea ice, long-term variability of a model ice cover, and its sensitivity to some parameters of model as well to define atmosphere-ice-ocean interaction.Results of 100 years simulations of Arctic basin sea ice evolution are analyzed. There are significant (about 0.5 m inter-annual fluctuations of an ice cover.The ice - atmosphere sensible heat flux reduced by 10% leads to the growth of average sea ice thickness within the limits of 0.05 m – 0.1 m. However in separate spatial points the thickness decreases up to 0.5 m. An analysis of the seasonably changing average ice thickness with decreasing, as compared to the basic variant by 0.05 of clear sea ice albedo and that of snow shows the ice thickness reduction in a range from 0.2 m up to 0.6 m, and the change maximum falls for the summer season of intensive melting. The spatial distribution of ice thickness changes shows, that on the large part of the Arctic Ocean there was a reduction of ice thickness down to 1 m. However, there is also an area of some increase of the ice layer basically in a range up to 0.2 m (Beaufort Sea. The 0.05 decrease of sea ice snow albedo leads to reduction of average ice thickness approximately by 0.2 m, and this value slightly depends on a season. In the following experiment the ocean – ice thermal interaction influence on the ice cover is estimated. It is carried out by increase of a heat flux from ocean to the bottom surface of sea ice by 2 W/sq. m in comparison with base variant. The analysis demonstrates, that the average ice thickness reduces in a range from 0.2 m to 0.35 m. There are small seasonal changes of this value.The numerical experiments results have shown, that an ice cover and its seasonal evolution rather strongly depend on varied parameters

  6. Forest Loss in Protected Areas and Intact Forest Landscapes: A Global Analysis.

    Science.gov (United States)

    Heino, Matias; Kummu, Matti; Makkonen, Marika; Mulligan, Mark; Verburg, Peter H; Jalava, Mika; Räsänen, Timo A

    2015-01-01

    In spite of the high importance of forests, global forest loss has remained alarmingly high during the last decades. Forest loss at a global scale has been unveiled with increasingly finer spatial resolution, but the forest extent and loss in protected areas (PAs) and in large intact forest landscapes (IFLs) have not so far been systematically assessed. Moreover, the impact of protection on preserving the IFLs is not well understood. In this study we conducted a consistent assessment of the global forest loss in PAs and IFLs over the period 2000-2012. We used recently published global remote sensing based spatial forest cover change data, being a uniform and consistent dataset over space and time, together with global datasets on PAs' and IFLs' locations. Our analyses revealed that on a global scale 3% of the protected forest, 2.5% of the intact forest, and 1.5% of the protected intact forest were lost during the study period. These forest loss rates are relatively high compared to global total forest loss of 5% for the same time period. The variation in forest losses and in protection effect was large among geographical regions and countries. In some regions the loss in protected forests exceeded 5% (e.g. in Australia and Oceania, and North America) and the relative forest loss was higher inside protected areas than outside those areas (e.g. in Mongolia and parts of Africa, Central Asia, and Europe). At the same time, protection was found to prevent forest loss in several countries (e.g. in South America and Southeast Asia). Globally, high area-weighted forest loss rates of protected and intact forests were associated with high gross domestic product and in the case of protected forests also with high proportions of agricultural land. Our findings reinforce the need for improved understanding of the reasons for the high forest losses in PAs and IFLs and strategies to prevent further losses.

  7. Improving Crop Yield and Nutrient Use Efficiency via Biofertilization—A Global Meta-analysis

    Directory of Open Access Journals (Sweden)

    Lukas Schütz

    2018-01-01

    Full Text Available The application of microbial inoculants (biofertilizers is a promising technology for future sustainable farming systems in view of rapidly decreasing phosphorus stocks and the need to more efficiently use available nitrogen (N. Various microbial taxa are currently used as biofertilizers, based on their capacity to access nutrients from fertilizers and soil stocks, to fix atmospheric nitrogen, to improve water uptake or to act as biocontrol agents. Despite the existence of a considerable knowledge on effects of specific taxa of biofertilizers, a comprehensive quantitative assessment of the performance of biofertilizers with different traits such as phosphorus solubilization and N fixation applied to various crops at a global scale is missing. We conducted a meta-analysis to quantify benefits of biofertilizers in terms of yield increase, nitrogen and phosphorus use efficiency, based on 171 peer reviewed publications that met eligibility criteria. Major findings are: (i the superiority of biofertilizer performance in dry climates over other climatic regions (yield response: dry climate +20.0 ± 1.7%, tropical climate +14.9 ± 1.2%, oceanic climate +10.0 ± 3.7%, continental climate +8.5 ± 2.4%; (ii meta-regression analyses revealed that yield response due to biofertilizer application was generally small at low soil P levels; efficacy increased along higher soil P levels in the order arbuscular mycorrhizal fungi (AMF, P solubilizers, and N fixers; (iii meta-regressions showed that the success of inoculation with AMF was greater at low organic matter content and at neutral pH. Our comprehensive analysis provides a basis and guidance for proper choice and application of biofertilizers.

  8. Ontology-based meta-analysis of global collections of high-throughput public data.

    Directory of Open Access Journals (Sweden)

    Ilya Kupershmidt

    2010-09-01

    Full Text Available The investigation of the interconnections between the molecular and genetic events that govern biological systems is essential if we are to understand the development of disease and design effective novel treatments. Microarray and next-generation sequencing technologies have the potential to provide this information. However, taking full advantage of these approaches requires that biological connections be made across large quantities of highly heterogeneous genomic datasets. Leveraging the increasingly huge quantities of genomic data in the public domain is fast becoming one of the key challenges in the research community today.We have developed a novel data mining framework that enables researchers to use this growing collection of public high-throughput data to investigate any set of genes or proteins. The connectivity between molecular states across thousands of heterogeneous datasets from microarrays and other genomic platforms is determined through a combination of rank-based enrichment statistics, meta-analyses, and biomedical ontologies. We address data quality concerns through dataset replication and meta-analysis and ensure that the majority of the findings are derived using multiple lines of evidence. As an example of our strategy and the utility of this framework, we apply our data mining approach to explore the biology of brown fat within the context of the thousands of publicly available gene expression datasets.Our work presents a practical strategy for organizing, mining, and correlating global collections of large-scale genomic data to explore normal and disease biology. Using a hypothesis-free approach, we demonstrate how a data-driven analysis across very large collections of genomic data can reveal novel discoveries and evidence to support existing hypothesis.

  9. Improving Crop Yield and Nutrient Use Efficiency via Biofertilization—A Global Meta-analysis

    Science.gov (United States)

    Schütz, Lukas; Gattinger, Andreas; Meier, Matthias; Müller, Adrian; Boller, Thomas; Mäder, Paul; Mathimaran, Natarajan

    2018-01-01

    The application of microbial inoculants (biofertilizers) is a promising technology for future sustainable farming systems in view of rapidly decreasing phosphorus stocks and the need to more efficiently use available nitrogen (N). Various microbial taxa are currently used as biofertilizers, based on their capacity to access nutrients from fertilizers and soil stocks, to fix atmospheric nitrogen, to improve water uptake or to act as biocontrol agents. Despite the existence of a considerable knowledge on effects of specific taxa of biofertilizers, a comprehensive quantitative assessment of the performance of biofertilizers with different traits such as phosphorus solubilization and N fixation applied to various crops at a global scale is missing. We conducted a meta-analysis to quantify benefits of biofertilizers in terms of yield increase, nitrogen and phosphorus use efficiency, based on 171 peer reviewed publications that met eligibility criteria. Major findings are: (i) the superiority of biofertilizer performance in dry climates over other climatic regions (yield response: dry climate +20.0 ± 1.7%, tropical climate +14.9 ± 1.2%, oceanic climate +10.0 ± 3.7%, continental climate +8.5 ± 2.4%); (ii) meta-regression analyses revealed that yield response due to biofertilizer application was generally small at low soil P levels; efficacy increased along higher soil P levels in the order arbuscular mycorrhizal fungi (AMF), P solubilizers, and N fixers; (iii) meta-regressions showed that the success of inoculation with AMF was greater at low organic matter content and at neutral pH. Our comprehensive analysis provides a basis and guidance for proper choice and application of biofertilizers. PMID:29375594

  10. Improving Crop Yield and Nutrient Use Efficiency via Biofertilization-A Global Meta-analysis.

    Science.gov (United States)

    Schütz, Lukas; Gattinger, Andreas; Meier, Matthias; Müller, Adrian; Boller, Thomas; Mäder, Paul; Mathimaran, Natarajan

    2017-01-01

    The application of microbial inoculants (biofertilizers) is a promising technology for future sustainable farming systems in view of rapidly decreasing phosphorus stocks and the need to more efficiently use available nitrogen (N). Various microbial taxa are currently used as biofertilizers, based on their capacity to access nutrients from fertilizers and soil stocks, to fix atmospheric nitrogen, to improve water uptake or to act as biocontrol agents. Despite the existence of a considerable knowledge on effects of specific taxa of biofertilizers, a comprehensive quantitative assessment of the performance of biofertilizers with different traits such as phosphorus solubilization and N fixation applied to various crops at a global scale is missing. We conducted a meta-analysis to quantify benefits of biofertilizers in terms of yield increase, nitrogen and phosphorus use efficiency, based on 171 peer reviewed publications that met eligibility criteria. Major findings are: (i) the superiority of biofertilizer performance in dry climates over other climatic regions (yield response: dry climate +20.0 ± 1.7%, tropical climate +14.9 ± 1.2%, oceanic climate +10.0 ± 3.7%, continental climate +8.5 ± 2.4%); (ii) meta-regression analyses revealed that yield response due to biofertilizer application was generally small at low soil P levels; efficacy increased along higher soil P levels in the order arbuscular mycorrhizal fungi (AMF), P solubilizers, and N fixers; (iii) meta-regressions showed that the success of inoculation with AMF was greater at low organic matter content and at neutral pH. Our comprehensive analysis provides a basis and guidance for proper choice and application of biofertilizers.

  11. Ontology-based meta-analysis of global collections of high-throughput public data.

    Science.gov (United States)

    Kupershmidt, Ilya; Su, Qiaojuan Jane; Grewal, Anoop; Sundaresh, Suman; Halperin, Inbal; Flynn, James; Shekar, Mamatha; Wang, Helen; Park, Jenny; Cui, Wenwu; Wall, Gregory D; Wisotzkey, Robert; Alag, Satnam; Akhtari, Saeid; Ronaghi, Mostafa

    2010-09-29

    The investigation of the interconnections between the molecular and genetic events that govern biological systems is essential if we are to understand the development of disease and design effective novel treatments. Microarray and next-generation sequencing technologies have the potential to provide this information. However, taking full advantage of these approaches requires that biological connections be made across large quantities of highly heterogeneous genomic datasets. Leveraging the increasingly huge quantities of genomic data in the public domain is fast becoming one of the key challenges in the research community today. We have developed a novel data mining framework that enables researchers to use this growing collection of public high-throughput data to investigate any set of genes or proteins. The connectivity between molecular states across thousands of heterogeneous datasets from microarrays and other genomic platforms is determined through a combination of rank-based enrichment statistics, meta-analyses, and biomedical ontologies. We address data quality concerns through dataset replication and meta-analysis and ensure that the majority of the findings are derived using multiple lines of evidence. As an example of our strategy and the utility of this framework, we apply our data mining approach to explore the biology of brown fat within the context of the thousands of publicly available gene expression datasets. Our work presents a practical strategy for organizing, mining, and correlating global collections of large-scale genomic data to explore normal and disease biology. Using a hypothesis-free approach, we demonstrate how a data-driven analysis across very large collections of genomic data can reveal novel discoveries and evidence to support existing hypothesis.

  12. Complex history of admixture during citrus domestication revealed by genome analysis

    Energy Technology Data Exchange (ETDEWEB)

    Wu, G. Albert; Prochnik, Simon; Jenkins, Jerry; Salse, Jerome; Hellsten, Uffe; Murat, Florent; Perrier, Xavier; Ruiz, Manuel; Scalabrin, Simone; Terol, Javier; Takita, Marco Aur& #233; lio,; Labadie, Karine; Poulain, Julie; Couloux, Arnaud; Jabbari, Kamel; Cattonaro, Federica; Fabbro, Cristian Del; Pinosio, Sara; Zuccolo, Andrea; Chapman, Jarrod; Grimwood, Jane; Tadeo, Francisco; Estornell, Leandro H.; Mu?oz-Sanz, Juan V.; Ibanez, Victoria; Herrero-Ortega, Amparo; Aleza, Pablo; P& #233; rez, Juli& #225; n P& #233; rez,; Ramon, Daniel; Brunel, Dominique; Luro, Francois; Chen, Chunxian; Farmerie, William G.; Desany, Brian; Kodira, Chinnappa; Mohiuddin, Mohammed; Harkins, Tim; Fredrikson, Karin; Burns, Paul; Lomsadze, Alexandre; Borodovsky, Mark; Reforgiato, Giuseppe; Freitas-Astua, Juliana; Quetier, Francis; Navarro, Luis; Roose, Mikeal; Wincker, Patrick; Schmutz, Jeremy; Morgante, Michele; Machado, Marcos Antonio; Talon, Manuel; Jaillon, Olivier; Ollitrault, Patrick; Gmitter, Frederick; Rokhsar, Daniel

    2014-06-30

    Although Citrus is the most globally significant tree fruit, its domestication history is poorly understood. Cultivated citrus types are believed to comprise selections from and/or hybrids of several wild progenitor species, but the identities of these progenitors, and their contribution to modern cultivars, remain controversial. Here we report the genomes of a collection of mandarins, pummelos, and oranges, including a high quality reference sequence from a haploid Clementine mandarin. By comparative genome analysis we show that these cultivated types can be derived from two progenitor species. Cultivated pummelos represent selections from a single progenitor species C. maxima. Unexpectedly, however, we find that cultivated mandarins are introgressions of C. maxima into a distinct second population that we identify with the ancestral wild mandarin species C. reticulata. Sweet and sour oranges are found to be interspecific hybrids. Sweet orange, the most widely cultivated citrus, arose as the offspring of previously admixed individuals. In contrast, sour (or Seville) orange is an F1 hybrid of pure C. maxima and C. reticulata parents, implying that wild mandarins were part of the early breeding germplasm. Surprisingly, we also find that a wild Chinese mandarin from Mangshan, China shows substantial sequence divergence from C. reticulata and appears to represent a distinct taxon. Understanding the relationships and phylogeny of cultivated citrus through genome analysis will clarify taxonomic relationships and enable previously inconceivable opportunities for sequence-directed genetic improvement. Citrus are widely consumed worldwide as juice or fresh fruit, providing important sources of vitamin C and other health-promoting compounds. Global production in 2012 exceeded 86 million metric tons, with an estimated value of US$9 billion (http://www.fas.usda.gov/psdonline/circulars/citrus.pdf). The very narrow genetic diversity of cultivated citrus makes it highly

  13. Global Proteome Analysis Identifies Active Immunoproteasome Subunits in Human Platelets*

    Science.gov (United States)

    Klockenbusch, Cordula; Walsh, Geraldine M.; Brown, Lyda M.; Hoffman, Michael D.; Ignatchenko, Vladimir; Kislinger, Thomas; Kast, Juergen

    2014-01-01

    The discovery of new functions for platelets, particularly in inflammation and immunity, has expanded the role of these anucleate cell fragments beyond their primary hemostatic function. Here, four in-depth human platelet proteomic data sets were generated to explore potential new functions for platelets based on their protein content and this led to the identification of 2559 high confidence proteins. During a more detailed analysis, consistently high expression of the proteasome was discovered, and the composition and function of this complex, whose role in platelets has not been thoroughly investigated, was examined. Data set mining resulted in identification of nearly all members of the 26S proteasome in one or more data sets, except the β5 subunit. However, β5i, a component of the immunoproteasome, was identified. Biochemical analyses confirmed the presence of all catalytically active subunits of the standard 20S proteasome and immunoproteasome in human platelets, including β5, which was predominantly found in its precursor form. It was demonstrated that these components were assembled into the proteasome complex and that standard proteasome as well as immunoproteasome subunits were constitutively active in platelets. These findings suggest potential new roles for platelets in the immune system. For example, the immunoproteasome may be involved in major histocompatibility complex I (MHC I) peptide generation, as the MHC I machinery was also identified in our data sets. PMID:25146974

  14. Global proteome analysis identifies active immunoproteasome subunits in human platelets.

    Science.gov (United States)

    Klockenbusch, Cordula; Walsh, Geraldine M; Brown, Lyda M; Hoffman, Michael D; Ignatchenko, Vladimir; Kislinger, Thomas; Kast, Juergen

    2014-12-01

    The discovery of new functions for platelets, particularly in inflammation and immunity, has expanded the role of these anucleate cell fragments beyond their primary hemostatic function. Here, four in-depth human platelet proteomic data sets were generated to explore potential new functions for platelets based on their protein content and this led to the identification of 2559 high confidence proteins. During a more detailed analysis, consistently high expression of the proteasome was discovered, and the composition and function of this complex, whose role in platelets has not been thoroughly investigated, was examined. Data set mining resulted in identification of nearly all members of the 26S proteasome in one or more data sets, except the β5 subunit. However, β5i, a component of the immunoproteasome, was identified. Biochemical analyses confirmed the presence of all catalytically active subunits of the standard 20S proteasome and immunoproteasome in human platelets, including β5, which was predominantly found in its precursor form. It was demonstrated that these components were assembled into the proteasome complex and that standard proteasome as well as immunoproteasome subunits were constitutively active in platelets. These findings suggest potential new roles for platelets in the immune system. For example, the immunoproteasome may be involved in major histocompatibility complex I (MHC I) peptide generation, as the MHC I machinery was also identified in our data sets. © 2014 by The American Society for Biochemistry and Molecular Biology, Inc.

  15. QTL global meta-analysis: are trait determining genes clustered?

    Directory of Open Access Journals (Sweden)

    Adelson David L

    2009-04-01

    Full Text Available Abstract Background A key open question in biology is if genes are physically clustered with respect to their known functions or phenotypic effects. This is of particular interest for Quantitative Trait Loci (QTL where a QTL region could contain a number of genes that contribute to the trait being measured. Results We observed a significant increase in gene density within QTL regions compared to non-QTL regions and/or the entire bovine genome. By grouping QTL from the Bovine QTL Viewer database into 8 categories of non-redundant regions, we have been able to analyze gene density and gene function distribution, based on Gene Ontology (GO with relation to their location within QTL regions, outside of QTL regions and across the entire bovine genome. We identified a number of GO terms that were significantly over represented within particular QTL categories. Furthermore, select GO terms expected to be associated with the QTL category based on common biological knowledge have also proved to be significantly over represented in QTL regions. Conclusion Our analysis provides evidence of over represented GO terms in QTL regions. This increased GO term density indicates possible clustering of gene functions within QTL regions of the bovine genome. Genes with similar functions may be grouped in specific locales and could be contributing to QTL traits. Moreover, we have identified over-represented GO terminology that from a biological standpoint, makes sense with respect to QTL category type.

  16. Global sensitivity analysis for fuzzy inputs based on the decomposition of fuzzy output entropy

    Science.gov (United States)

    Shi, Yan; Lu, Zhenzhou; Zhou, Yicheng

    2018-06-01

    To analyse the component of fuzzy output entropy, a decomposition method of fuzzy output entropy is first presented. After the decomposition of fuzzy output entropy, the total fuzzy output entropy can be expressed as the sum of the component fuzzy entropy contributed by fuzzy inputs. Based on the decomposition of fuzzy output entropy, a new global sensitivity analysis model is established for measuring the effects of uncertainties of fuzzy inputs on the output. The global sensitivity analysis model can not only tell the importance of fuzzy inputs but also simultaneously reflect the structural composition of the response function to a certain degree. Several examples illustrate the validity of the proposed global sensitivity analysis, which is a significant reference in engineering design and optimization of structural systems.

  17. Ensuring dynamic strategic fit of firms that compete globally in alliances and networks: proposing the Global SNA - Strategic Network Analysis - framework

    Directory of Open Access Journals (Sweden)

    T. Diana L. Van Aduard de Macedo-Soares

    2011-02-01

    Full Text Available In order to sustain their competitive advantage in the current increasingly globalized and turbulent context, more and more firms are competing globally in alliances and networks that oblige them to adopt new managerial paradigms and tools. However, their strategic analyses rarely take into account the strategic implications of these alliances and networks, considering their global relational characteristics, admittedly because of a lack of adequate tools to do so. This paper contributes to research that seeks to fill this gap by proposing the Global Strategic Network Analysis - SNA - framework. Its purpose is to help firms that compete globally in alliances and networks to carry out their strategic assessments and decision-making with a view to ensuring dynamic strategic fit from both a global and relational perspective.

  18. Multilocus sequence typing analysis reveals that Cryptococcus neoformans var. neoformans is a recombinant population.

    Science.gov (United States)

    Cogliati, Massimo; Zani, Alberto; Rickerts, Volker; McCormick, Ilka; Desnos-Ollivier, Marie; Velegraki, Aristea; Escandon, Patricia; Ichikawa, Tomoe; Ikeda, Reiko; Bienvenu, Anne-Lise; Tintelnot, Kathrin; Tore, Okan; Akcaglar, Sevim; Lockhart, Shawn; Tortorano, Anna Maria; Varma, Ashok

    2016-02-01

    Cryptococcus neoformans var. neoformans (serotype D) represents about 30% of the clinical isolates in Europe and is present less frequently in the other continents. It is the prevalent etiological agent in primary cutaneous cryptococcosis as well as in cryptococcal skin lesions of disseminated cryptococcosis. Very little is known about the genotypic diversity of this Cryptococcus subtype. The aim of this study was to investigate the genotypic diversity among a set of clinical and environmental C. neoformans var. neoformans isolates and to evaluate the relationship between genotypes, geographical origin and clinical manifestations. A total of 83 globally collected C. neoformans var. neoformans isolates from Italy, Germany, France, Belgium, Denmark, Greece, Turkey, Thailand, Japan, Colombia, and the USA, recovered from different sources (primary and secondary cutaneous cryptococcosis, disseminated cryptococcosis, the environment, and animals), were included in the study. All isolates were confirmed to belong to genotype VNIV by molecular typing and they were further investigated by MLST analysis. Maximum likelihood phylogenetic as well as network analysis strongly suggested the existence of a recombinant rather than a clonal population structure. Geographical origin and source of isolation were not correlated with a specific MLST genotype. The comparison with a set of outgroup C. neoformans var. grubii isolates provided clear evidence that the two varieties have different population structures. Copyright © 2016 Elsevier Inc. All rights reserved.