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Sample records for genes evolve faster

  1. Mammals evolve faster on smaller islands.

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    Millien, Virginie

    2011-07-01

    Island mammals often display remarkable evolutionary changes in size and morphology. Both theory and empirical data support the hypothesis that island mammals evolve at faster rates than their mainland congeners. It is also often assumed that the island effect is stronger and that evolution is faster on the smallest islands. I used a dataset assembled from the literature to test these assumptions for the first time. I show that mammals on smaller islands do indeed evolve more rapidly than mammals on larger islands, and also evolve by a greater amount. These results fit well the theory of an evolutionary burst due to the opening of new ecological opportunities on islands. This evolutionary burst is expected to be the strongest on the smallest islands where the contrast between the island and the mainland environments is the most dramatic.

  2. New Technology Makes Gene Mapping Cheaper, Faster

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    ... https://medlineplus.gov/news/fullstory_164255.html New Technology Makes Gene Mapping Cheaper, Faster: Study Researchers decoded ... they've developed a much cheaper and faster technology for mapping the genetic makeup of a living ...

  3. Faster-X Evolution of Gene Expression in Drosophila

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    Meisel, Richard P.; Malone, John H.; Clark, Andrew G.

    2012-01-01

    DNA sequences on X chromosomes often have a faster rate of evolution when compared to similar loci on the autosomes, and well articulated models provide reasons why the X-linked mode of inheritance may be responsible for the faster evolution of X-linked genes. We analyzed microarray and RNA–seq data collected from females and males of six Drosophila species and found that the expression levels of X-linked genes also diverge faster than autosomal gene expression, similar to the “faster-X” effect often observed in DNA sequence evolution. Faster-X evolution of gene expression was recently described in mammals, but it was limited to the evolutionary lineages shortly following the creation of the therian X chromosome. In contrast, we detect a faster-X effect along both deep lineages and those on the tips of the Drosophila phylogeny. In Drosophila males, the dosage compensation complex (DCC) binds the X chromosome, creating a unique chromatin environment that promotes the hyper-expression of X-linked genes. We find that DCC binding, chromatin environment, and breadth of expression are all predictive of the rate of gene expression evolution. In addition, estimates of the intraspecific genetic polymorphism underlying gene expression variation suggest that X-linked expression levels are not under relaxed selective constraints. We therefore hypothesize that the faster-X evolution of gene expression is the result of the adaptive fixation of beneficial mutations at X-linked loci that change expression level in cis. This adaptive faster-X evolution of gene expression is limited to genes that are narrowly expressed in a single tissue, suggesting that relaxed pleiotropic constraints permit a faster response to selection. Finally, we present a conceptional framework to explain faster-X expression evolution, and we use this framework to examine differences in the faster-X effect between Drosophila and mammals. PMID:23071459

  4. Evolution of evolvability in gene regulatory networks.

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    Anton Crombach

    Full Text Available Gene regulatory networks are perhaps the most important organizational level in the cell where signals from the cell state and the outside environment are integrated in terms of activation and inhibition of genes. For the last decade, the study of such networks has been fueled by large-scale experiments and renewed attention from the theoretical field. Different models have been proposed to, for instance, investigate expression dynamics, explain the network topology we observe in bacteria and yeast, and for the analysis of evolvability and robustness of such networks. Yet how these gene regulatory networks evolve and become evolvable remains an open question. An individual-oriented evolutionary model is used to shed light on this matter. Each individual has a genome from which its gene regulatory network is derived. Mutations, such as gene duplications and deletions, alter the genome, while the resulting network determines the gene expression pattern and hence fitness. With this protocol we let a population of individuals evolve under Darwinian selection in an environment that changes through time. Our work demonstrates that long-term evolution of complex gene regulatory networks in a changing environment can lead to a striking increase in the efficiency of generating beneficial mutations. We show that the population evolves towards genotype-phenotype mappings that allow for an orchestrated network-wide change in the gene expression pattern, requiring only a few specific gene indels. The genes involved are hubs of the networks, or directly influencing the hubs. Moreover, throughout the evolutionary trajectory the networks maintain their mutational robustness. In other words, evolution in an alternating environment leads to a network that is sensitive to a small class of beneficial mutations, while the majority of mutations remain neutral: an example of evolution of evolvability.

  5. Sperm competition and the coevolution of pre- and postcopulatory traits: Weapons evolve faster than testes among onthophagine dung beetles.

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    Simmons, Leigh W; Fitzpatrick, John L

    2016-05-01

    Reproductive competition generates episodes of both pre- and postcopulatory sexual selection. Theoretical models of sperm competition predict that as the fitness gains from expenditure on the weapons of male combat increase, males should increase their expenditure on weapons and decrease their expenditure on traits that contribute to competitive fertilization success. Although traits subject to sexual selection are known to have accelerated evolutionary rates of phenotypic divergence, it is not known whether the competing demands of investment into pre- and postcopulatory traits affect their relative rates of evolutionary divergence. We use a comparative approach to estimate the rates of divergence in pre- and postcopulatory traits among onthophagine dung beetles. Weapons evolved faster than body size while testes mass and sperm length evolved more slowly than body size, suggesting that precopulatory competition is the stronger episode of sexual selection acting on these beetles. Although horns evolved faster than testes, evolutionary increases in horn length were not associated with evolutionary reductions in testes mass. Our data for onthophagines support the notion that in taxa where males are unable to monopolize paternity, expenditure on both weapons and testes should both be favored.

  6. How the gene ontology evolves.

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    Leonelli, Sabina; Diehl, Alexander D; Christie, Karen R; Harris, Midori A; Lomax, Jane

    2011-08-05

    Maintaining a bio-ontology in the long term requires improving and updating its contents so that it adequately captures what is known about biological phenomena. This paper illustrates how these processes are carried out, by studying the ways in which curators at the Gene Ontology have hitherto incorporated new knowledge into their resource. Five types of circumstances are singled out as warranting changes in the ontology: (1) the emergence of anomalies within GO; (2) the extension of the scope of GO; (3) divergence in how terminology is used across user communities; (4) new discoveries that change the meaning of the terms used and their relations to each other; and (5) the extension of the range of relations used to link entities or processes described by GO terms. This study illustrates the difficulties involved in applying general standards to the development of a specific ontology. Ontology curation aims to produce a faithful representation of knowledge domains as they keep developing, which requires the translation of general guidelines into specific representations of reality and an understanding of how scientific knowledge is produced and constantly updated. In this context, it is important that trained curators with technical expertise in the scientific field(s) in question are involved in supervising ontology shifts and identifying inaccuracies.

  7. Having your cake and eating it - Staphylococcus aureus small colony variants can evolve faster growth rate without losing their antibiotic resistance

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    Gerrit Brandis

    2017-08-01

    Full Text Available Staphylococcus aureus can produce small colony variants (SCVs during infections. These cause significant clinical problems because they are difficult to detect in standard microbiological screening and are associated with persistent infections. The major causes of the SCV phenotype are mutations that inhibit respiration by inactivation of genes of the menadione or hemin biosynthesis pathways. This reduces the production of ATP required to support fast growth. Importantly, it also decreases cross-membrane potential in SCVs, resulting in decreased uptake of cationic compounds, with reduced susceptibility to aminoglycoside antibiotics as a consequence. Because SCVs are slow-growing (mutations in men genes are associated with growth rates in rich medium ~30% of the wild-type growth rate bacterial cultures are very susceptible to rapid takeover by faster-growing mutants (revertants or suppressors. In the case of reversion, the resulting fast growth is obviously associated with the loss of antibiotic resistance. However, direct reversion is relatively rare due to the very small genetic target size for such mutations. We explored the phenotypic consequences of SCVs evolving faster growth by routes other than direct reversion, and in particular whether any of those routes allowed for the maintenance of antibiotic resistance. In a recent paper (mBio 8: e00358-17 we demonstrated the existence of several different routes of SCV evolution to faster growth, one of which maintained the antibiotic resistance phenotype. This discovery suggests that SCVs might be more adaptable and problematic that previously thought. They are capable of surviving as a slow-growing persistent form, before evolving into a significantly faster-growing form without sacrificing their antibiotic resistance phenotype.

  8. Gene Essentiality Is a Quantitative Property Linked to Cellular Evolvability.

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    Liu, Gaowen; Yong, Mei Yun Jacy; Yurieva, Marina; Srinivasan, Kandhadayar Gopalan; Liu, Jaron; Lim, John Soon Yew; Poidinger, Michael; Wright, Graham Daniel; Zolezzi, Francesca; Choi, Hyungwon; Pavelka, Norman; Rancati, Giulia

    2015-12-03

    Gene essentiality is typically determined by assessing the viability of the corresponding mutant cells, but this definition fails to account for the ability of cells to adaptively evolve to genetic perturbations. Here, we performed a stringent screen to assess the degree to which Saccharomyces cerevisiae cells can survive the deletion of ~1,000 individual "essential" genes and found that ~9% of these genetic perturbations could in fact be overcome by adaptive evolution. Our analyses uncovered a genome-wide gradient of gene essentiality, with certain essential cellular functions being more "evolvable" than others. Ploidy changes were prevalent among the evolved mutant strains, and aneuploidy of a specific chromosome was adaptive for a class of evolvable nucleoporin mutants. These data justify a quantitative redefinition of gene essentiality that incorporates both viability and evolvability of the corresponding mutant cells and will enable selection of therapeutic targets associated with lower risk of emergence of drug resistance. Copyright © 2015 Elsevier Inc. All rights reserved.

  9. The Evolving Definition of the Term "Gene".

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    Portin, Petter; Wilkins, Adam

    2017-04-01

    This paper presents a history of the changing meanings of the term "gene," over more than a century, and a discussion of why this word, so crucial to genetics, needs redefinition today. In this account, the first two phases of 20th century genetics are designated the "classical" and the "neoclassical" periods, and the current molecular-genetic era the "modern period." While the first two stages generated increasing clarity about the nature of the gene, the present period features complexity and confusion. Initially, the term "gene" was coined to denote an abstract "unit of inheritance," to which no specific material attributes were assigned. As the classical and neoclassical periods unfolded, the term became more concrete, first as a dimensionless point on a chromosome, then as a linear segment within a chromosome, and finally as a linear segment in the DNA molecule that encodes a polypeptide chain. This last definition, from the early 1960s, remains the one employed today, but developments since the 1970s have undermined its generality. Indeed, they raise questions about both the utility of the concept of a basic "unit of inheritance" and the long implicit belief that genes are autonomous agents. Here, we review findings that have made the classic molecular definition obsolete and propose a new one based on contemporary knowledge. Copyright © 2017 by the Genetics Society of America.

  10. EVOLVE

    CERN Document Server

    Deutz, André; Schütze, Oliver; Legrand, Pierrick; Tantar, Emilia; Tantar, Alexandru-Adrian

    2017-01-01

    This book comprises nine selected works on numerical and computational methods for solving multiobjective optimization, game theory, and machine learning problems. It provides extended versions of selected papers from various fields of science such as computer science, mathematics and engineering that were presented at EVOLVE 2013 held in July 2013 at Leiden University in the Netherlands. The internationally peer-reviewed papers include original work on important topics in both theory and applications, such as the role of diversity in optimization, statistical approaches to combinatorial optimization, computational game theory, and cell mapping techniques for numerical landscape exploration. Applications focus on aspects including robustness, handling multiple objectives, and complex search spaces in engineering design and computational biology.

  11. Evolvability and hierarchy in rewired bacterial gene networks

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    Isalan, Mark; Lemerle, Caroline; Michalodimitrakis, Konstantinos; Beltrao, Pedro; Horn, Carsten; Raineri, Emanuele; Garriga-Canut, Mireia; Serrano, Luis

    2009-01-01

    Sequencing DNA from several organisms has revealed that duplication and drift of existing genes have primarily molded the contents of a given genome. Though the effect of knocking out or over-expressing a particular gene has been studied in many organisms, no study has systematically explored the effect of adding new links in a biological network. To explore network evolvability, we constructed 598 recombinations of promoters (including regulatory regions) with different transcription or σ-factor genes in Escherichia coli, added over a wild-type genetic background. Here we show that ~95% of new networks are tolerated by the bacteria, that very few alter growth, and that expression level correlates with factor position in the wild-type network hierarchy. Most importantly, we find that certain networks consistently survive over the wild-type under various selection pressures. Therefore new links in the network are rarely a barrier for evolution and can even confer a fitness advantage. PMID:18421347

  12. Microcephaly genes evolved adaptively throughout the evolution of eutherian mammals.

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    Montgomery, Stephen H; Mundy, Nicholas I

    2014-06-05

    Genes associated with the neurodevelopmental disorder microcephaly display a strong signature of adaptive evolution in primates. Comparative data suggest a link between selection on some of these loci and the evolution of primate brain size. Whether or not either positive selection or this phenotypic association are unique to primates is unclear, but recent studies in cetaceans suggest at least two microcephaly genes evolved adaptively in other large brained mammalian clades. Here we analyse the evolution of seven microcephaly loci, including three recently identified loci, across 33 eutherian mammals. We find extensive evidence for positive selection having acted on the majority of these loci not just in primates but also across non-primate mammals. Furthermore, the patterns of selection in major mammalian clades are not significantly different. Using phylogenetically corrected comparative analyses, we find that the evolution of two microcephaly loci, ASPM and CDK5RAP2, are correlated with neonatal brain size in Glires and Euungulata, the two most densely sampled non-primate clades. Together with previous results, this suggests that ASPM and CDK5RAP2 may have had a consistent role in the evolution of brain size in mammals. Nevertheless, several limitations of currently available data and gene-phenotype tests are discussed, including sparse sampling across large evolutionary distances, averaging gene-wide rates of evolution, potential phenotypic variation and evolutionary reversals. We discuss the implications of our results for studies of the genetic basis of brain evolution, and explicit tests of gene-phenotype hypotheses.

  13. Assembly of evolved ligninolytic genes in Saccharomyces cerevisiae

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    Gonzalez-Perez, David; Alcalde, Miguel

    2014-01-01

    The ligninolytic enzymatic consortium produced by white-rot fungi is one of the most efficient oxidative systems found in nature, with many potential applications that range from the production of 2nd generation biofuels to chemicals synthesis. In the current study, two high redox potential oxidoreductase fusion genes (laccase -Lac- and versatile peroxidase -Vp-) that had been evolved in the laboratory were re-assembled in Saccharomyces cerevisiae. First, cell viability and secretion were assessed after co-transforming the Lac and Vp genes into yeast. Several expression cassettes were inserted in vivo into episomal bi-directional vectors in order to evaluate inducible promoter and/or terminator pairs of different strengths in an individual and combined manner. The synthetic white-rot yeast model harboring Vp(GAL1/CYC1)-Lac(GAL10/ADH1) displayed up to 1000 and 100 Units per L of peroxidase and laccase activity, respectively, representing a suitable point of departure for future synthetic biology studies. PMID:24830983

  14. Faster T-cell development following gene therapy compared with haploidentical HSCT in the treatment of SCID-X1.

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    Touzot, Fabien; Moshous, Despina; Creidy, Rita; Neven, Bénédicte; Frange, Pierre; Cros, Guilhem; Caccavelli, Laure; Blondeau, Johanna; Magnani, Alessandra; Luby, Jean-Marc; Ternaux, Brigitte; Picard, Capucine; Blanche, Stéphane; Fischer, Alain; Hacein-Bey-Abina, Salima; Cavazzana, Marina

    2015-06-04

    During the last decade, gene therapy via ex vivo gene transfer into autologous hematopoietic stem cells has emerged as a convincing therapy for severe combined immunodeficiency caused by ILR2G mutation (SCID-X1) despite the occurrence of genotoxicity caused by the integration of first-generation retroviral vectors. However, the place of gene therapy among the therapeutic armamentarium remains to be defined. We retrospectively analyze and compare clinical outcomes and immune reconstitution in 13 consecutive SCID-X1 patients having undergone haploidentical hematopoietic stem cell transplantation (HSCT) and 14 SCID-X1 patients treated with gene therapy over the same period at a single center level: the Necker Children's Hospital (Paris, France). Our results show a clear advantage in terms of T-cell development of gene therapy over HSCT with a mismatched donor. Patients treated with gene therapy display a faster T-cell reconstitution and a better long-term thymic output. Interestingly, this advantage of gene therapy vs haploidentical HSCT seems to be independent of the existence of clinical graft-versus-host disease in the latter condition. If data of safety are confirmed over the long term, gene therapy for SCID-X1 appears to be an equal, if not superior, alternative to haploidentical HSCT.

  15. Copy number change: evolving views on gene amplification.

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    Elliott, Kathryn T; Cuff, Laura E; Neidle, Ellen L

    2013-07-01

    The rapid pace of genomic sequence analysis is increasing the awareness of intrinsically dynamic genetic landscapes. Gene duplication and amplification (GDA) contribute to adaptation and evolution by allowing DNA regions to expand and contract in an accordion-like fashion. This process affects diverse aspects of bacterial infection, including antibiotic resistance and host-pathogen interactions. In this review, microbial GDA is discussed, primarily using recent bacterial examples that demonstrate medical and evolutionary consequences. Interplay between GDA and horizontal gene transfer further impact evolutionary trajectories. Complementing the discovery of gene duplication in clinical and environmental settings, experimental evolution provides a powerful method to document genetic change over time. New methods for GDA detection highlight both its importance and its potential application for genetic engineering, synthetic biology and biotechnology.

  16. Evolving DNA motifs to predict GeneChip probe performance

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    Harrison AP

    2009-03-01

    Full Text Available Abstract Background Affymetrix High Density Oligonuclotide Arrays (HDONA simultaneously measure expression of thousands of genes using millions of probes. We use correlations between measurements for the same gene across 6685 human tissue samples from NCBI's GEO database to indicated the quality of individual HG-U133A probes. Low correlation indicates a poor probe. Results Regular expressions can be automatically created from a Backus-Naur form (BNF context-free grammar using strongly typed genetic programming. Conclusion The automatically produced motif is better at predicting poor DNA sequences than an existing human generated RE, suggesting runs of Cytosine and Guanine and mixtures should all be avoided.

  17. Rapidly Evolving Mitochondrial Genome and Directional Selection in Mitochondrial Genes in the Parasitic Wasp Nasonia (Hymenoptera: Pteromalidae)

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    Raychoudhury, Rhitoban; Lavrov, Dennis V.; Werren, John H.

    2008-01-01

    We sequenced the nearly complete mtDNA of 3 species of parasitic wasps, Nasonia vitripennis (2 strains), Nasonia giraulti, and Nasonia longicornis, including all 13 protein-coding genes and the 2 rRNAs, and found unusual patterns of mitochondrial evolution. The Nasonia mtDNA has a unique gene order compared with other insect mtDNAs due to multiple rearrangements. The mtDNAs of these wasps also show nucleotide substitution rates over 30 times faster than nuclear protein-coding genes, indicating among the highest substitution rates found in animal mitochondria (normally <10 times faster). A McDonald and Kreitman test shows that the between-species frequency of fixed replacement sites relative to silent sites is significantly higher compared with within-species polymorphisms in 2 mitochondrial genes of Nasonia, atp6 and atp8, indicating directional selection. Consistent with this interpretation, the Ka/Ks (nonsynonymous/synonymous substitution rates) ratios are higher between species than within species. In contrast, cox1 shows a signature of purifying selection for amino acid sequence conservation, although rates of amino acid substitutions are still higher than for comparable insects. The mitochondrial-encoded polypeptides atp6 and atp8 both occur in F0F1ATP synthase of the electron transport chain. Because malfunction in this fundamental protein severely affects fitness, we suggest that the accelerated accumulation of replacements is due to beneficial mutations necessary to compensate mild-deleterious mutations fixed by random genetic drift or Wolbachia sweeps in the fast evolving mitochondria of Nasonia. We further propose that relatively high rates of amino acid substitution in some mitochondrial genes can be driven by a “Compensation-Draft Feedback”; increased fixation of mildly deleterious mutations results in selection for compensatory mutations, which lead to fixation of additional deleterious mutations in nonrecombining mitochondrial genomes, thus

  18. Evolving expression patterns of the homeotic gene Scr in insects.

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    Passalacqua, Karla D; Hrycaj, Steven; Mahfooz, Najmus; Popadic, Aleksandar

    2010-01-01

    While the mRNA expression patterns of homeotic genes have been examined in numerous arthropod species, data on their protein accumulation is extremely limited. To address this gap, we analyzed the protein expression pattern of the hox gene Sex combs reduced (Scr) in six hemimetabolous insects from four divergent orders (Thysanura, Orthoptera, Dictyoptera and Hemiptera). Our comparative analysis reveals that the original domain of SCR expression was likely confined to the head and then subsequently moved into the prothorax (T1) in winged insect lineages. The data also show a trend toward the posteriorization of the anterior boundary of SCR expression in the head, which starts in the mandibles (Thysanura) and then gradually shifts to the maxillary (Orthoptera) and labial segments (Dictyoptera and Hemiptera), respectively. In Thermobia (firebrat) and Oncopeltus (milkweed bug) we also identify instances where SCR protein is not detected in regions where mRNA is expressed. This finding suggests the presence of a post-transcriptional regulatory mechanism of Scr in these species. Finally, we show that SCR expression in insect T1 legs is highly variable and exhibits divergent patterning even among related species. In addition, signal in the prothoracic legs of more basal insect lineages cannot be associated with any T1 specific features, indicating that the acquisition of SCR in this region preceded any apparent gain of function. Overall, our results show that Scr expression has diverged considerably among hemimetabolous lineages and establish a framework for subsequent analyses to determine its role in the evolution of the insect head and prothorax.

  19. A plant virus evolved by acquiring multiple nonconserved genes to extend its host range

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    Tatineni, Satyanarayana; Robertson, Cecile J.; Garnsey, Stephen M.; Dawson, William O.

    2011-01-01

    Viruses have evolved as combinations of genes whose products interact with cellular components to produce progeny virus throughout the plants. Some viral genes, particularly those that are involved in replication and assembly, tend to be relatively conserved, whereas other genes that have evolved for interactions with the specific host for movement and to counter host–defense systems tend to be less conserved. Closteroviridae encode 1–5 nonconserved ORFs. Citrus tristeza virus (CTV), a Closterovirus, possesses nonconserved p33, p18, and p13 genes that are expendable for systemic infection of the two laboratory hosts, Citrus macrophylla and Mexican lime. In this study, we show that the extended host range of CTV requires these nonconserved genes. The p33 gene was required to systemically infect sour orange and lemon trees, whereas either the p33 or the p18 gene was sufficient for systemic infection of grapefruit trees and the p33 or the p13 gene was sufficient for systemic infection of calamondin plants. Thus, these three genes are required for systemic infection of the full host range of CTV, but different genes were specific for different hosts. Remarkably, either of two genes was sufficient for infection of some citrus hybrids. These findings suggest that CTV acquired multiple nonconserved genes (p33, p18, and p13) and, as a result, gained the ability to interact with multiple hosts, thus extending its host range during the course of evolution. These results greatly extend the complexity of known virus–plant interactions. PMID:21987809

  20. Cloning of novel rice blast resistance genes from two rapidly evolving NBS-LRR gene families in rice.

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    Guo, Changjiang; Sun, Xiaoguang; Chen, Xiao; Yang, Sihai; Li, Jing; Wang, Long; Zhang, Xiaohui

    2016-01-01

    Most rice blast resistance genes (R-genes) encode proteins with nucleotide-binding site (NBS) and leucine-rich repeat (LRR) domains. Our previous study has shown that more rice blast R-genes can be cloned in rapidly evolving NBS-LRR gene families. In the present study, two rapidly evolving R-gene families in rice were selected for cloning a subset of genes from their paralogs in three resistant rice lines. A total of eight functional blast R-genes were identified among nine NBS-LRR genes, and some of these showed resistance to three or more blast strains. Evolutionary analysis indicated that high nucleotide diversity of coding regions served as important parameters in the determination of gene resistance. We also observed that amino-acid variants (nonsynonymous mutations, insertions, or deletions) in essential motifs of the NBS domain contribute to the blast resistance capacity of NBS-LRR genes. These results suggested that the NBS regions might also play an important role in resistance specificity determination. On the other hand, different splicing patterns of introns were commonly observed in R-genes. The results of the present study contribute to improving the effectiveness of R-gene identification by using evolutionary analysis method and acquisition of novel blast resistance genes.

  1. Faster-X adaptive protein evolution in house mice.

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    Kousathanas, Athanasios; Halligan, Daniel L; Keightley, Peter D

    2014-04-01

    The causes of the large effect of the X chromosome in reproductive isolation and speciation have long been debated. The faster-X hypothesis predicts that X-linked loci are expected to have higher rates of adaptive evolution than autosomal loci if new beneficial mutations are on average recessive. Reproductive isolation should therefore evolve faster when contributing loci are located on the X chromosome. In this study, we have analyzed genome-wide nucleotide polymorphism data from the house mouse subspecies Mus musculus castaneus and nucleotide divergence from Mus famulus and Rattus norvegicus to compare rates of adaptive evolution for autosomal and X-linked protein-coding genes. We found significantly faster adaptive evolution for X-linked loci, particularly for genes with expression in male-specific tissues, but autosomal and X-linked genes with expression in female-specific tissues evolve at similar rates. We also estimated rates of adaptive evolution for genes expressed during spermatogenesis and found that X-linked genes that escape meiotic sex chromosome inactivation (MSCI) show rapid adaptive evolution. Our results suggest that faster-X adaptive evolution is either due to net recessivity of new advantageous mutations or due to a special gene content of the X chromosome, which regulates male function and spermatogenesis. We discuss how our results help to explain the large effect of the X chromosome in speciation.

  2. Rapidly evolving mitochondrial genome and directional selection in mitochondrial genes in the parasitic wasp nasonia (hymenoptera: pteromalidae).

    Science.gov (United States)

    Oliveira, Deodoro C S G; Raychoudhury, Rhitoban; Lavrov, Dennis V; Werren, John H

    2008-10-01

    We sequenced the nearly complete mtDNA of 3 species of parasitic wasps, Nasonia vitripennis (2 strains), Nasonia giraulti, and Nasonia longicornis, including all 13 protein-coding genes and the 2 rRNAs, and found unusual patterns of mitochondrial evolution. The Nasonia mtDNA has a unique gene order compared with other insect mtDNAs due to multiple rearrangements. The mtDNAs of these wasps also show nucleotide substitution rates over 30 times faster than nuclear protein-coding genes, indicating among the highest substitution rates found in animal mitochondria (normally mitochondrial genes of Nasonia, atp6 and atp8, indicating directional selection. Consistent with this interpretation, the Ka/Ks (nonsynonymous/synonymous substitution rates) ratios are higher between species than within species. In contrast, cox1 shows a signature of purifying selection for amino acid sequence conservation, although rates of amino acid substitutions are still higher than for comparable insects. The mitochondrial-encoded polypeptides atp6 and atp8 both occur in F0F1ATP synthase of the electron transport chain. Because malfunction in this fundamental protein severely affects fitness, we suggest that the accelerated accumulation of replacements is due to beneficial mutations necessary to compensate mild-deleterious mutations fixed by random genetic drift or Wolbachia sweeps in the fast evolving mitochondria of Nasonia. We further propose that relatively high rates of amino acid substitution in some mitochondrial genes can be driven by a "Compensation-Draft Feedback"; increased fixation of mildly deleterious mutations results in selection for compensatory mutations, which lead to fixation of additional deleterious mutations in nonrecombining mitochondrial genomes, thus accelerating the process of amino acid substitutions.

  3. Evolving gene regulatory networks into cellular networks guiding adaptive behavior: an outline how single cells could have evolved into a centralized neurosensory system.

    Science.gov (United States)

    Fritzsch, Bernd; Jahan, Israt; Pan, Ning; Elliott, Karen L

    2015-01-01

    Understanding the evolution of the neurosensory system of man, able to reflect on its own origin, is one of the major goals of comparative neurobiology. Details of the origin of neurosensory cells, their aggregation into central nervous systems and associated sensory organs and their localized patterning leading to remarkably different cell types aggregated into variably sized parts of the central nervous system have begun to emerge. Insights at the cellular and molecular level have begun to shed some light on the evolution of neurosensory cells, partially covered in this review. Molecular evidence suggests that high mobility group (HMG) proteins of pre-metazoans evolved into the definitive Sox [SRY (sex determining region Y)-box] genes used for neurosensory precursor specification in metazoans. Likewise, pre-metazoan basic helix-loop-helix (bHLH) genes evolved in metazoans into the group A bHLH genes dedicated to neurosensory differentiation in bilaterians. Available evidence suggests that the Sox and bHLH genes evolved a cross-regulatory network able to synchronize expansion of precursor populations and their subsequent differentiation into novel parts of the brain or sensory organs. Molecular evidence suggests metazoans evolved patterning gene networks early, which were not dedicated to neuronal development. Only later in evolution were these patterning gene networks tied into the increasing complexity of diffusible factors, many of which were already present in pre-metazoans, to drive local patterning events. It appears that the evolving molecular basis of neurosensory cell development may have led, in interaction with differentially expressed patterning genes, to local network modifications guiding unique specializations of neurosensory cells into sensory organs and various areas of the central nervous system.

  4. Rodent-specific alternative exons are more frequent in rapidly evolving genes and in paralogs

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    Mironov Andrey A

    2009-06-01

    Full Text Available Abstract Background Alternative splicing is an important mechanism for generating functional and evolutionary diversity of proteins in eukaryotes. Here, we studied the frequency and functionality of recently gained, rodent-specific alternative exons. Results We projected the data about alternative splicing of mouse genes to the rat, human, and dog genomes, and identified exons conserved in the rat genome, but missing in more distant genomes. We estimated the frequency of rodent-specific exons while controlling for possible residual conservation of spurious exons. The frequency of rodent-specific exons is higher among predominantly skipped exons and exons disrupting the reading frame. Separation of all genes by the rate of sequence evolution and by gene families has demonstrated that rodent-specific cassette exons are more frequent in rapidly evolving genes and in rodent-specific paralogs. Conclusion Thus we demonstrated that recently gained exons tend to occur in fast-evolving genes, and their inclusion rate tends to be lower than that of older exons. This agrees with the theory that gain of alternative exons is one of the major mechanisms of gene evolution.

  5. The impact of gene expression variation on the robustness and evolvability of a developmental gene regulatory network.

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    David A Garfield

    2013-10-01

    Full Text Available Regulatory interactions buffer development against genetic and environmental perturbations, but adaptation requires phenotypes to change. We investigated the relationship between robustness and evolvability within the gene regulatory network underlying development of the larval skeleton in the sea urchin Strongylocentrotus purpuratus. We find extensive variation in gene expression in this network throughout development in a natural population, some of which has a heritable genetic basis. Switch-like regulatory interactions predominate during early development, buffer expression variation, and may promote the accumulation of cryptic genetic variation affecting early stages. Regulatory interactions during later development are typically more sensitive (linear, allowing variation in expression to affect downstream target genes. Variation in skeletal morphology is associated primarily with expression variation of a few, primarily structural, genes at terminal positions within the network. These results indicate that the position and properties of gene interactions within a network can have important evolutionary consequences independent of their immediate regulatory role.

  6. Adaptive Representations for Improving Evolvability, Parameter Control, and Parallelization of Gene Expression Programming

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    Nigel P. A. Browne

    2010-01-01

    Full Text Available Gene Expression Programming (GEP is a genetic algorithm that evolves linear chromosomes encoding nonlinear (tree-like structures. In the original GEP algorithm, the genome size is problem specific and is determined through trial and error. In this work, a method for adaptive control of the genome size is presented. The approach introduces mutation, transposition, and recombination operators that enable a population of heterogeneously structured chromosomes, something the original GEP algorithm does not support. This permits crossbreeding between normally incompatible individuals, speciation within a population, increases the evolvability of the representations, and enhances parallel GEP. To test our approach, an assortment of problems were used, including symbolic regression, classification, and parameter optimization. Our experimental results show that our approach provides a solution for the problem of self-adaptive control of the genome size of GEP's representation.

  7. Identification of fast-evolving genes in the scleractinian coral Acropora using comparative EST analysis.

    Directory of Open Access Journals (Sweden)

    Akira Iguchi

    Full Text Available To identify fast-evolving genes in reef-building corals, we performed direct comparative sequence analysis with expressed sequence tag (EST datasets from two acroporid species: Acropora palmata from the Caribbean Sea and A. millepora from the Great Barrier Reef in Australia. Comparison of 589 independent sequences from 1,421 A. palmata contigs, with 10,247 A. millepora contigs resulted in the identification of 196 putative homologues. Most of the homologous pairs demonstrated high amino acid similarities (over 90%. Comparisons of putative homologues showing low amino acid similarities (under 90% among the Acropora species to the near complete datasets from two other cnidarians (Hydra magnipapillata and Nematostella vectensis implied that some were non-orthologous. Within 86 homologous pairs, 39 exhibited dN/dS ratios significantly less than 1, suggesting that these genes are under purifying selection associated with functional constraints. Eight independent genes showed dN/dS ratios exceeding 1, while three deviated significantly from 1, suggesting that these genes may play important roles in the adaptive evolution of Acropora. Our results also indicated that CEL-III lectin was under positive selection, consistent with a possible role in immunity or symbiont recognition. Further studies are needed to clarify the possible functions of the genes under positive selection to provide insight into the evolutionary process of corals.

  8. Hidden Markov induced Dynamic Bayesian Network for recovering time evolving gene regulatory networks

    Science.gov (United States)

    Zhu, Shijia; Wang, Yadong

    2015-12-01

    Dynamic Bayesian Networks (DBN) have been widely used to recover gene regulatory relationships from time-series data in computational systems biology. Its standard assumption is ‘stationarity’, and therefore, several research efforts have been recently proposed to relax this restriction. However, those methods suffer from three challenges: long running time, low accuracy and reliance on parameter settings. To address these problems, we propose a novel non-stationary DBN model by extending each hidden node of Hidden Markov Model into a DBN (called HMDBN), which properly handles the underlying time-evolving networks. Correspondingly, an improved structural EM algorithm is proposed to learn the HMDBN. It dramatically reduces searching space, thereby substantially improving computational efficiency. Additionally, we derived a novel generalized Bayesian Information Criterion under the non-stationary assumption (called BWBIC), which can help significantly improve the reconstruction accuracy and largely reduce over-fitting. Moreover, the re-estimation formulas for all parameters of our model are derived, enabling us to avoid reliance on parameter settings. Compared to the state-of-the-art methods, the experimental evaluation of our proposed method on both synthetic and real biological data demonstrates more stably high prediction accuracy and significantly improved computation efficiency, even with no prior knowledge and parameter settings.

  9. Hidden Markov induced Dynamic Bayesian Network for recovering time evolving gene regulatory networks.

    Science.gov (United States)

    Zhu, Shijia; Wang, Yadong

    2015-12-18

    Dynamic Bayesian Networks (DBN) have been widely used to recover gene regulatory relationships from time-series data in computational systems biology. Its standard assumption is 'stationarity', and therefore, several research efforts have been recently proposed to relax this restriction. However, those methods suffer from three challenges: long running time, low accuracy and reliance on parameter settings. To address these problems, we propose a novel non-stationary DBN model by extending each hidden node of Hidden Markov Model into a DBN (called HMDBN), which properly handles the underlying time-evolving networks. Correspondingly, an improved structural EM algorithm is proposed to learn the HMDBN. It dramatically reduces searching space, thereby substantially improving computational efficiency. Additionally, we derived a novel generalized Bayesian Information Criterion under the non-stationary assumption (called BWBIC), which can help significantly improve the reconstruction accuracy and largely reduce over-fitting. Moreover, the re-estimation formulas for all parameters of our model are derived, enabling us to avoid reliance on parameter settings. Compared to the state-of-the-art methods, the experimental evaluation of our proposed method on both synthetic and real biological data demonstrates more stably high prediction accuracy and significantly improved computation efficiency, even with no prior knowledge and parameter settings.

  10. Faster Than Light Communication

    CERN Document Server

    Michalski, M

    1999-01-01

    If it is possible to measure any photon at arbitrary polarization state with the probability arbitrary close to 1, we can force photon from entangled photon pair to be measured in desired state and project the second photon to the parallel state. Measurement performed on the second photon (which is arbitrary far away from the first) makes possible faster than light communication.

  11. Writing faster Python

    CERN Document Server

    CERN. Geneva

    2016-01-01

    Did you know that Python preallocates integers from -5 to 257 ? Reusing them 1000 times, instead of allocating memory for a bigger integer, can save you a couple of milliseconds of code’s execution time. If you want to learn more about this kind of optimizations then, … well, probably this presentation is not for you :) Instead of going into such small details, I will talk about more "sane" ideas for writing faster code. After a very brief overview of how to optimize Python code (rule 1: don’t do this; rule 2: don’t do this yet; rule 3: ok, but what if I really want to do this ?), I will show simple and fast ways of measuring the execution time and finally, discuss examples of how some code structures could be improved. You will see: - What is the fastest way of removing duplicates from a list - How much faster your code is when you reuse the built-in functions instead of trying to reinvent the wheel - What is faster than the good ol’ for loop - If the lookup is faster in a list or a set (and w...

  12. Genome-Wide Analysis in Three Fusarium Pathogens Identifies Rapidly Evolving Chromosomes and Genes Associated with Pathogenicity.

    Science.gov (United States)

    Sperschneider, Jana; Gardiner, Donald M; Thatcher, Louise F; Lyons, Rebecca; Singh, Karam B; Manners, John M; Taylor, Jennifer M

    2015-05-19

    Pathogens and hosts are in an ongoing arms race and genes involved in host-pathogen interactions are likely to undergo diversifying selection. Fusarium plant pathogens have evolved diverse infection strategies, but how they interact with their hosts in the biotrophic infection stage remains puzzling. To address this, we analyzed the genomes of three Fusarium plant pathogens for genes that are under diversifying selection. We found a two-speed genome structure both on the chromosome and gene group level. Diversifying selection acts strongly on the dispensable chromosomes in Fusarium oxysporum f. sp. lycopersici and on distinct core chromosome regions in Fusarium graminearum, all of which have associations with virulence. Members of two gene groups evolve rapidly, namely those that encode proteins with an N-terminal [SG]-P-C-[KR]-P sequence motif and proteins that are conserved predominantly in pathogens. Specifically, 29 F. graminearum genes are rapidly evolving, in planta induced and encode secreted proteins, strongly pointing toward effector function. In summary, diversifying selection in Fusarium is strongly reflected as genomic footprints and can be used to predict a small gene set likely to be involved in host-pathogen interactions for experimental verification. © The Author(s) 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  13. Preparing for faster filling

    CERN Multimedia

    CERN Bulletin

    2010-01-01

    Following the programmed technical stop last week, operators focussed on preparing the machine for faster filling, which includes multibunch injection and a faster pre-cycle phase.   The LHC1 screen shot during the first multibunch injection operation. The LHC operational schedule incorporates a technical stop for preventive maintenance roughly every six weeks of stable operation, during which several interventions on the various machines are carried out. Last week these included the replacement of a faulty magnet in the SPS pre-accelerator, which required the subsequent re-setting of the system of particle extraction and transfer to the LHC. At the end of last week, all the machines were handed back for operation and work could start on accommodating all the changes made into the complex systems in order for normal operation to be resumed. These ‘recovery’ operations continued through the weekend and into this week. At the beginning of this week, operators succeeded in pro...

  14. Faster than Light Neutrinos

    Institute of Scientific and Technical Information of China (English)

    Jarah Evslin

    2011-01-01

    In September, the OPERA experiment in Italy claimed to have observed neutrinos which travel faster than light. Strong experimental constraints are placed by neutrinos observed from the supernova SN1987A and from various terrestrial and astrophysical measurements of synchrotron radiation. I will review the many experimental and theoretical challenges faced by any theory which attempts to explain this result, and speculate on just which theories may succeed.

  15. Mammalian X chromosome inactivation evolved as a dosage-compensation mechanism for dosage-sensitive genes on the X chromosome.

    Science.gov (United States)

    Pessia, Eugénie; Makino, Takashi; Bailly-Bechet, Marc; McLysaght, Aoife; Marais, Gabriel A B

    2012-04-03

    How and why female somatic X-chromosome inactivation (XCI) evolved in mammals remains poorly understood. It has been proposed that XCI is a dosage-compensation mechanism that evolved to equalize expression levels of X-linked genes in females (2X) and males (1X), with a prior twofold increase in expression of X-linked genes in both sexes ("Ohno's hypothesis"). Whereas the parity of X chromosome expression between the sexes has been clearly demonstrated, tests for the doubling of expression levels globally along the X chromosome have returned contradictory results. However, changes in gene dosage during sex-chromosome evolution are not expected to impact on all genes equally, and should have greater consequences for dosage-sensitive genes. We show that, for genes encoding components of large protein complexes (≥ 7 members)--a class of genes that is expected to be dosage-sensitive--expression of X-linked genes is similar to that of autosomal genes within the complex. These data support Ohno's hypothesis that XCI acts as a dosage-compensation mechanism, and allow us to refine Ohno's model of XCI evolution. We also explore the contribution of dosage-sensitive genes to X aneuploidy phenotypes in humans, such as Turner (X0) and Klinefelter (XXY) syndromes. X aneuploidy in humans is common and is known to have mild effects because most of the supernumerary X genes are inactivated and not affected by aneuploidy. Only genes escaping XCI experience dosage changes in X-aneuploidy patients. We combined data on dosage sensitivity and XCI to compute a list of candidate genes for X-aneuploidy syndromes.

  16. Adult Drosophila melanogaster evolved for antibacterial defense invest in infection-induced expression of both humoral and cellular immunity genes

    Directory of Open Access Journals (Sweden)

    McGraw Elizabeth A

    2011-08-01

    Full Text Available Abstract Background While the transcription of innate immunity genes in response to bacterial infection has been well-characterised in the Drosophila model, we recently demonstrated the capacity for such transcription to evolve in flies selected for improved antibacterial defense. Here we use this experimental system to examine how insects invest in constitutive versus infection-induced transcription of immunity genes. These two strategies carry with them different consequences with respect to energetic and pleiotropic costs and may be more or less effective in improving defense depending on whether the genes contribute to humoral or cellular aspects of immunity. Findings Contrary to expectation we show that selection preferentially increased the infection-induced expression of both cellular and humoral immunity genes. Given their functional roles, infection induced increases in expression were expected for the humoral genes, while increases in constitutive expression were expected for the cellular genes. We also report a restricted ability to improve transcription of immunity genes that is on the order of 2-3 fold regardless of total transcription level of the gene. Conclusions The evolved increases in infection-induced expression of the cellular genes may result from specific cross talk with humoral pathways or from generalised strategies for enhancing immunity gene transcription. A failure to see improvements in constitutive expression of the cellular genes suggests either that increases might come at too great a cost or that patterns of expression in adults are decoupled from the larval phase where increases would be most effective. The similarity in fold change increase across all immunity genes may suggest a shared mechanism for the evolution of increased transcription in small, discrete units such as duplication of cis-regulatory elements.

  17. Horizontal gene transfer: essentiality and evolvability in prokaryotes, and roles in evolutionary transitions [version 1; referees: 2 approved

    Directory of Open Access Journals (Sweden)

    Eugene V. Koonin

    2016-07-01

    Full Text Available The wide spread of gene exchange and loss in the prokaryotic world has prompted the concept of ‘lateral genomics’ to the point of an outright denial of the relevance of phylogenetic trees for evolution. However, the pronounced coherence congruence of the topologies of numerous gene trees, particularly those for (nearly universal genes, translates into the notion of a statistical tree of life (STOL, which reflects a central trend of vertical evolution. The STOL can be employed as a framework for reconstruction of the evolutionary processes in the prokaryotic world. Quantitatively, however, horizontal gene transfer (HGT dominates microbial evolution, with the rate of gene gain and loss being comparable to the rate of point mutations and much greater than the duplication rate. Theoretical models of evolution suggest that HGT is essential for the survival of microbial populations that otherwise deteriorate due to the Muller’s ratchet effect. Apparently, at least some bacteria and archaea evolved dedicated vehicles for gene transfer that evolved from selfish elements such as plasmids and viruses. Recent phylogenomic analyses suggest that episodes of massive HGT were pivotal for the emergence of major groups of organisms such as multiple archaeal phyla as well as eukaryotes. Similar analyses appear to indicate that, in addition to donating hundreds of genes to the emerging eukaryotic lineage, mitochondrial endosymbiosis severely curtailed HGT. These results shed new light on the routes of evolutionary transitions, but caution is due given the inherent uncertainty of deep phylogenies.

  18. When slower is faster

    CERN Document Server

    Gershenson, Carlos

    2015-01-01

    The slower is faster (SIF) effect occurs when a system performs worse when its components try to be better. Thus, a moderate individual efficiency actually leads to a better systemic performance. The SIF effect takes place in a variety of phenomena. We review studies and examples of the SIF effect in pedestrian dynamics, vehicle traffic, traffic light control, logistics, public transport, social dynamics, ecological systems, and adaptation. Drawing on these examples we generalize common features of the SIF effect and suggest possible future lines of research.

  19. Evolution of hydra, a recently evolved testis-expressed gene with nine alternative first exons in Drosophila melanogaster.

    Directory of Open Access Journals (Sweden)

    Shou-Tao Chen

    2007-07-01

    Full Text Available We describe here the Drosophila gene hydra that appears to have originated de novo in the melanogaster subgroup and subsequently evolved in both structure and expression level in Drosophila melanogaster and its sibling species. D. melanogaster hydra encodes a predicted protein of approximately 300 amino acids with no apparent similarity to any previously known proteins. The syntenic region flanking hydra on both sides is found in both D. ananassae and D. pseudoobscura, but hydra is found only in melanogaster subgroup species, suggesting that it originated less than approximately 13 million y ago. Exon 1 of hydra has undergone recurrent duplications, leading to the formation of nine tandem alternative exon 1s in D. melanogaster. Seven of these alternative exons are flanked on their 3' side by the transposon DINE-1 (Drosophila interspersed element-1. We demonstrate that at least four of the nine duplicated exon 1s can function as alternative transcription start sites. The entire hydra locus has also duplicated in D. simulans and D. sechellia. D. melanogaster hydra is expressed most intensely in the proximal testis, suggesting a role in late-stage spermatogenesis. The coding region of hydra has a relatively high Ka/Ks ratio between species, but the ratio is less than 1 in all comparisons, suggesting that hydra is subject to functional constraint. Analysis of sequence polymorphism and divergence of hydra shows that it has evolved under positive selection in the lineage leading to D. melanogaster. The dramatic structural changes surrounding the first exons do not affect the tissue specificity of gene expression: hydra is expressed predominantly in the testes in D. melanogaster, D. simulans, and D. yakuba. However, we have found that expression level changed dramatically (approximately >20-fold between D. melanogaster and D. simulans. While hydra initially evolved in the absence of nearby transposable element insertions, we suggest that the subsequent

  20. Evolution in the fast lane: rapidly evolving sex-related genes in Drosophila.

    Science.gov (United States)

    Haerty, Wilfried; Jagadeeshan, Santosh; Kulathinal, Rob J; Wong, Alex; Ravi Ram, Kristipati; Sirot, Laura K; Levesque, Lisa; Artieri, Carlo G; Wolfner, Mariana F; Civetta, Alberto; Singh, Rama S

    2007-11-01

    A large portion of the annotated genes in Drosophila melanogaster show sex-biased expression, indicating that sex and reproduction-related genes (SRR genes) represent an appreciable component of the genome. Previous studies, in which subsets of genes were compared among few Drosophila species, have found that SRR genes exhibit unusual evolutionary patterns. Here, we have used the newly released genome sequences from 12 Drosophila species, coupled to a larger set of SRR genes, to comprehensively test the generality of these patterns. Among 2505 SRR genes examined, including ESTs with biased expression in reproductive tissues and genes characterized as involved in gametogenesis, we find that a relatively high proportion of SRR genes have experienced accelerated divergence throughout the genus Drosophila. Several testis-specific genes, male seminal fluid proteins (SFPs), and spermatogenesis genes show lineage-specific bursts of accelerated evolution and positive selection. SFP genes also show evidence of lineage-specific gene loss and/or gain. These results bring us closer to understanding the details of the evolutionary dynamics of SRR genes with respect to species divergence.

  1. Longer - Faster - Purer

    CERN Multimedia

    Caroline Duc

    2013-01-01

    The MR-ToF-MS, a new ion trap, has been integrated into ISOLTRAP, the experiment that performs accurate mass measurements on short-lived nuclides produced at ISOLDE. When used as a mass separator and spectrometer, it extends ISOLTRAP’s experimental reach towards the limits of nuclear stability.   Susanne Kreim, the ISOLTRAP local group leader at CERN in front of a part of the ISOLTRAP device. When mass measurement experiments like ISOLTRAP* are placed in an on-line radioactive ion-beam facility they face a major challenge: the efficient and fast transfer of the nuclide of interest to the location where the mass measurement is performed. The biggest yield of one selected nuclide, without contaminants, needs to be transferred to the set-up as quickly as possible in order to measure its mass with the greatest precision. Recently, the ISOLTRAP collaboration installed a new device that provides a faster separation of isobars.** It has significantly improved ISOLTRAP’s purificat...

  2. Cheetahs have 4 serum amyloid a genes evolved through repeated duplication events.

    Science.gov (United States)

    Chen, Lei; Une, Yumi; Higuchi, Keiichi; Mori, Masayuki

    2012-01-01

    Amyloid A (AA) amyloidosis is a leading cause of mortality in captive cheetahs (Acinonyx jubatus). We performed genome walking and PCR cloning and revealed that cheetahs have 4 SAA genes (provisionally named SAA1A, SAA1B, SAA3A, and SAA3B). In addition, we identified multiple nucleotide polymorphisms in the 4 SAA genes by screening 51 cheetahs. The polymorphisms defined 4, 7, 6, and 4 alleles for SAA1A, SAA3A, SAA1B, and SAA3B, respectively. Pedigree analysis of the inheritance of genotypes for the SAA genes revealed that specific combinations of alleles for the 4 SAA genes cosegregated as a unit (haplotype) in pedigrees, indicating that the 4 genes were linked on the same chromosome. Notably, cheetah SAA1A and SAA1B were highly homologous in their nucleotide sequences. Likewise, SAA3A and SAA3B genes were homologous. These observations suggested a model for the evolution of the 4 SAA genes in cheetahs in which duplication of an ancestral SAA gene first gave rise to SAA1 and SAA3. Subsequently, each gene duplicated one more time, uniquely making 4 genes in the cheetah genome. The monomorphism of the cheetah SAA1A protein might be one of the factors responsible for the high incidence of AA amyloidosis in this species.

  3. Rapidly evolving marmoset MSMB genes are differently expressed in the male genital tract

    Directory of Open Access Journals (Sweden)

    Ceder Yvonne

    2009-09-01

    Full Text Available Abstract Background Beta-microseminoprotein, an abundant component in prostatic fluid, is encoded by the potential tumor suppressor gene MSMB. Some New World monkeys carry several copies of this gene, in contrast to most mammals, including humans, which have one only. Here we have investigated the background for the species difference by analyzing the chromosomal organization and expression of MSMB in the common marmoset (Callithrix jacchus. Methods Genes were identified in the Callithrix jacchus genome database using bioinformatics and transcripts were analyzed by RT-PCR and quantified by real time PCR in the presence of SYBR green. Results The common marmoset has five MSMB: one processed pseudogene and four functional genes. The latter encompass homologous genomic regions of 32-35 kb, containing the genes of 12-14 kb and conserved upstream and downstream regions of 14-19 kb and 3-4 kb. One gene, MSMB1, occupies the same position on the chromosome as the single human gene. On the same chromosome, but several Mb away, is another MSMB locus situated with MSMB2, MSMB3 and MSMB4 arranged in tandem. Measurements of transcripts demonstrated that all functional genes are expressed in the male genital tract, generating very high transcript levels in the prostate. The transcript levels in seminal vesicles and testis are two and four orders of magnitude lower. A single gene, MSMB3, accounts for more than 90% of MSMB transcripts in both the prostate and the seminal vesicles, whereas in the testis around half of the transcripts originate from MSMB2. These genes display rapid evolution with a skewed distribution of mutated nucleotides; in MSMB2 they affect nucleotides encoding the N-terminal Greek key domain, whereas in MSMB3 it is the C-terminal MSMB-unique domain that is affected. Conclusion Callitrichide monkeys have four functional MSMB that are all expressed in the male genital tract, but the product from one gene, MSMB3, will predominate in seminal

  4. Multiple Cis-Acting Sequences Contribute to Evolved Regulatory Variation for Drosophila Adh Genes

    Science.gov (United States)

    Fang, X. M.; Brennan, M. D.

    1992-01-01

    Drosophila affinidisjuncta and Drosophila hawaiiensis are closely related species that display distinct tissue-specific expression patterns for their homologous alcohol dehydrogenase genes (Adh genes). In Drosophila melanogaster transformants, both genes are expressed at high levels in the larval and adult fat bodies, but the D. affinidisjuncta gene is expressed 10-50-fold more strongly in the larval and adult midguts and Malpighian tubules. The present study reports the mapping of cis-acting sequences contributing to the regulatory differences between these two genes in transformants. Chimeric genes were constructed and introduced into the germ line of D. melanogaster. Stage- and tissue-specific expression patterns were determined by measuring steady-state RNA levels in larvae and adults. Three portions of the promoter region make distinct contributions to the tissue-specific regulatory differences between the native genes. Sequences immediately upstream of the distal promoter have a strong effect in the adult Malpighian tubules, while sequences between the two promoters are relatively important in the larval Malpighian tubules. A third gene segment, immediately upstream of the proximal promoter, influences levels of the proximal Adh transcript in all tissues and developmental stages examined, and largely accounts for the regulatory difference in the larval and adult midguts. However, these as well as other sequences make smaller contributions to various aspects of the tissue-specific regulatory differences. In addition, some chimeric genes display aberrant RNA levels for the whole organism, suggesting close physical association between sequences involved in tissue-specific regulatory differences and those important for Adh expression in the larval and adult fat bodies. PMID:1644276

  5. Identifying time-delayed gene regulatory networks via an evolvable hierarchical recurrent neural network.

    Science.gov (United States)

    Kordmahalleh, Mina Moradi; Sefidmazgi, Mohammad Gorji; Harrison, Scott H; Homaifar, Abdollah

    2017-01-01

    The modeling of genetic interactions within a cell is crucial for a basic understanding of physiology and for applied areas such as drug design. Interactions in gene regulatory networks (GRNs) include effects of transcription factors, repressors, small metabolites, and microRNA species. In addition, the effects of regulatory interactions are not always simultaneous, but can occur after a finite time delay, or as a combined outcome of simultaneous and time delayed interactions. Powerful biotechnologies have been rapidly and successfully measuring levels of genetic expression to illuminate different states of biological systems. This has led to an ensuing challenge to improve the identification of specific regulatory mechanisms through regulatory network reconstructions. Solutions to this challenge will ultimately help to spur forward efforts based on the usage of regulatory network reconstructions in systems biology applications. We have developed a hierarchical recurrent neural network (HRNN) that identifies time-delayed gene interactions using time-course data. A customized genetic algorithm (GA) was used to optimize hierarchical connectivity of regulatory genes and a target gene. The proposed design provides a non-fully connected network with the flexibility of using recurrent connections inside the network. These features and the non-linearity of the HRNN facilitate the process of identifying temporal patterns of a GRN. Our HRNN method was implemented with the Python language. It was first evaluated on simulated data representing linear and nonlinear time-delayed gene-gene interaction models across a range of network sizes and variances of noise. We then further demonstrated the capability of our method in reconstructing GRNs of the Saccharomyces cerevisiae synthetic network for in vivo benchmarking of reverse-engineering and modeling approaches (IRMA). We compared the performance of our method to TD-ARACNE, HCC-CLINDE, TSNI and ebdbNet across different network

  6. The impact of gene expression analysis on evolving views of avian brain organization.

    Science.gov (United States)

    Montiel, Juan F; Molnár, Zoltán

    2013-11-01

    Recent studies have presented data on adult and developing avian brain organization. Jarvis et al. ([2013] J Comp Neurol. 521:3614-3665) identify four pallial and two subpallial gene expression domains and demonstrate that the mesopallium and adjoining divisions of the hyperpallium (hyperpallium intercalatum and hyperpallium densocellulare), have very similar gene expression profiles to each other, distinct from those of the nidopallium, the arcopallium, and the more distant divisions of the hyperpallium (hyperpallium apicale). The study proposes an update of the current nomenclature (Jarvis et al. [2005] Nat Rev Neurosci. 6:151-159). The authors perform densitometric quantifications of the in situ expression of 50 selected genes, use correlations of distances between vectors that represent these gene expression patterns within the 23 avian brain regions of their study, and group them according to similarity in their expression profiles. The generated cluster tree further supports their argument for a new terminology. The authors hypothesize that the mesopallium and adjoining divisions of the hyperpallium have a common developmental origin, and in the accompanying paper (Chen et al. [2013] J Comp Neurol. 521:3666-3701) show that these structures/subdivisions initially form continuous gene expression domains. With subsequent development these domains fold into distinct subdivisions in the dorsal and ventral avian pallium, forming mirror images to each other. Jarvis et al. ([2013] J Comp Neurol. 521:3614-3665) also demonstrate interesting principles of the functional organization of the avian brain by showing that specific sensory stimulation or motor behavior elicits gene expression in functional units perpendicular to the axis of the gene expression reversal and compare their arrangements and cell types with mammalian cortical columns.

  7. Fructan Biosynthetic and Breakdown Enzymes in Dicots Evolved From Different Invertases. Expression of Fructan Genes Throughout Chicory Development

    Directory of Open Access Journals (Sweden)

    Wim Van den Ende

    2002-01-01

    Full Text Available Fructans are fructose-based oligo- and polymers that serve as reserve carbohydrates in many plant species. The biochemistry of fructan biosynthesis in dicots has been resolved, and the respective cDNAs have been cloned. Recent progress has now succeeded in elucidating the biochemistry and molecular biology of fructan biodegradation in chicory, an economically important species used for commercial inulin extraction. Unlike fructan biosynthetic genes that originated from vacuolar-type invertase, fructan exohydrolases (FEHs seem to have evolved from a cell-wall invertase ancestor gene that later obtained a low iso-electric point and a vacuolar targeting signal. Expression analysis reveals that fructan enzymes are controlled mainly at the transcriptional level. Using chicory as a model system, northern analysis was consistent with enzymatic activity measurements and observed carbohydrate changes throughout its development.

  8. Evolving lessons on nanomaterial-coated viral vectors for local and systemic gene therapy.

    Science.gov (United States)

    Kasala, Dayananda; Yoon, A-Rum; Hong, Jinwoo; Kim, Sung Wan; Yun, Chae-Ok

    2016-07-01

    Viral vectors are promising gene carriers for cancer therapy. However, virus-mediated gene therapies have demonstrated insufficient therapeutic efficacy in clinical trials due to rapid dissemination to nontarget tissues and to the immunogenicity of viral vectors, resulting in poor retention at the disease locus and induction of adverse inflammatory responses in patients. Further, the limited tropism of viral vectors prevents efficient gene delivery to target tissues. In this regard, modification of the viral surface with nanomaterials is a promising strategy to augment vector accumulation at the target tissue, circumvent the host immune response, and avoid nonspecific interactions with the reticuloendothelial system or serum complement. In the present review, we discuss various chemical modification strategies to enhance the therapeutic efficacy of viral vectors delivered either locally or systemically. We conclude by highlighting the salient features of various nanomaterial-coated viral vectors and their prospects and directions for future research.

  9. Host mitochondrial association evolved in the human parasite Toxoplasma gondii via neofunctionalization of a gene duplicate

    Science.gov (United States)

    In Toxoplasma gondii, an intracellular parasite of humans and other warm-blooded animals, the ability to associate with host mitochondria (HMA) is driven by a locally expanded gene family that encodes multiple mitochondrial association factor 1 (MAF1) proteins. The importance of copy number in the e...

  10. The Spatial Association of Gene Expression Evolves from Synchrony to Asynchrony and Stochasticity with Age

    Science.gov (United States)

    Zhang, Xinmin; Wu, Bin; Liu, Xiaoyu; Shen, Ziyin

    2011-01-01

    For multicellular organisms, different tissues coordinate to integrate physiological functions, although this systematically and gradually declines in the aging process. Therefore, an association exists between tissue coordination and aging, and investigating the evolution of tissue coordination with age is of interest. In the past decade, both common and heterogeneous aging processes among tissues were extensively investigated. The results on spatial association of gene changes that determine lifespan appear complex and paradoxical. To reconcile observed commonality and heterogeneity of gene changes among tissues and to address evolution feature of tissue coordination with age, we introduced a new analytical strategy to systematically analyze genome-wide spatio-temporal gene expression profiles. We first applied the approach to natural aging process in three species (Rat, Mouse and Drosophila) and then to anti-aging process in Mouse. The results demonstrated that temporal gene expression alteration in different tissues experiences a progressive association evolution from spatial synchrony to asynchrony and stochasticity with age. This implies that tissue coordination gradually declines with age. Male mice showed earlier spatial asynchrony in gene expression than females, suggesting that male animals are more prone to aging than females. The confirmed anti-aging interventions (resveratrol and caloric restriction) enhanced tissue coordination, indicating their underlying anti-aging mechanism on multiple tissue levels. Further, functional analysis suggested asynchronous DNA/protein damage accumulation as well as asynchronous repair, modification and degradation of DNA/protein in tissues possibly contributes to asynchronous and stochastic changes of tissue microenvironment. This increased risk for a variety of age-related diseases such as neurodegeneration and cancer that eventually accelerate organismal aging and death. Our study suggests a novel molecular event

  11. A complete mitochondrial genome of wheat (Triticum aestivum cv. Chinese Yumai), and fast evolving mitochondrial genes in higher plants

    Indian Academy of Sciences (India)

    Peng Cui; Huitao Liu; Qiang Lin; Feng Ding; Guoyin Zhuo; Songnian Hu; Dongcheng Liu; Wenlong Yang; Kehui Zhan; Aimin Zhang; Jun Yu

    2009-12-01

    Plant mitochondrial genomes, encoding necessary proteins involved in the system of energy production, play an important role in the development and reproduction of the plant. They occupy a specific evolutionary pattern relative to their nuclear counterparts. Here, we determined the winter wheat (Triticum aestivum cv. Chinese Yumai) mitochondrial genome in a length of 452 and 526 bp by shotgun sequencing its BAC library. It contains 202 genes, including 35 known protein-coding genes, three rRNA and 17 tRNA genes, as well as 149 open reading frames (ORFs; greater than 300 bp in length). The sequence is almost identical to the previously reported sequence of the spring wheat (T. aestivum cv. Chinese Spring); we only identified seven SNPs (three transitions and four transversions) and 10 indels (insertions and deletions) between the two independently acquired sequences, and all variations were found in non-coding regions. This result confirmed the accuracy of the previously reported mitochondrial sequence of the Chinese Spring wheat. The nucleotide frequency and codon usage of wheat are common among the lineage of higher plant with a high AT-content of 58%. Molecular evolutionary analysis demonstrated that plant mitochondrial genomes evolved at different rates, which may correlate with substantial variations in metabolic rate and generation time among plant lineages. In addition, through the estimation of the ratio of non-synonymous to synonymous substitution rates between orthologous mitochondrion-encoded genes of higher plants, we found an accelerated evolutionary rate that seems to be the result of relaxed selection.

  12. Polymorphism in interleukin-7 receptor [alpha] gene is associated with faster CD4+ T-cell recovery after initiation of combination antiretroviral therapy

    DEFF Research Database (Denmark)

    Hartling, Hans Jakob; Thørner, Lise W; Erikstrup, Christian;

    2014-01-01

    OBJECTIVES: To investigate single-nucleotide polymorphisms (SNPs) in the gene encoding interleukin-7 receptor α (IL7RA) as predictors for CD4⁺ T-cell change after initiation of combination antiretroviral therapy (cART) in HIV-infected whites. DESIGN: SNPs in IL7RA were determined in the Danish HIV...

  13. Mycobacterium tuberculosis modulates the gene interactions to activate the HIV replication and faster disease progression in a co-infected host.

    Science.gov (United States)

    Toor, Jaideep S; Singh, Sukhvinder; Sharma, Aman; Arora, Sunil K

    2014-01-01

    Understanding of the chronic immune activation, breakdown of immune defense and synergistic effect between HIV and Mycobacterium tuberculosis (Mtb) may provide essential information regarding key factors involved in the pathogenesis of HIV disease. In this study, we aimed to highlight a few of the immunological events that may influence and accelerate the progression of HIV disease in the presence of co-infecting Mtb. A cross-sectional study was performed on cohorts, including anti-tubercular therapy (ATT) naïve active pulmonary tuberculosis (PTB) patients, antiretroviral therapy (ART) naïve HIV-1 infected individuals at different stages of disease, ATT and ART naïve HIV-PTB co-infected individuals and healthy controls. A significantly higher T-regulatory cell (Treg) frequency coupled with the high FoxP3 expression in the CD4 T-cells indicated an immunosuppressive environment in the advance stage of HIV-1 infection. This is further substantiated by high HO-1 expression favoring TB co-infection. Functionally, this change in Treg frequency in HIV-1 infected individuals correlated well with suppression of T-cell proliferation. Mtb infection seems to facilitate the expansion of the Treg pool along with increased expression of FoxP3, specifically the variant-1, as evident from the data in HIV-1 co-infected as well as in patients with only PTB. A significantly lower expression of HO-1 in co-infected individuals compared to patients with only HIV-infection having comparable CD4 count correlated well with increased expression of CCR5 and CxCR4 as well as NF-κB and inflammatory cytokines IL-6 and TNF-α, which collectively may contribute to enhanced viral replication and increased cell death, hence faster disease progression in co-infected individuals.

  14. Mycobacterium tuberculosis modulates the gene interactions to activate the HIV replication and faster disease progression in a co-infected host.

    Directory of Open Access Journals (Sweden)

    Jaideep S Toor

    Full Text Available Understanding of the chronic immune activation, breakdown of immune defense and synergistic effect between HIV and Mycobacterium tuberculosis (Mtb may provide essential information regarding key factors involved in the pathogenesis of HIV disease. In this study, we aimed to highlight a few of the immunological events that may influence and accelerate the progression of HIV disease in the presence of co-infecting Mtb. A cross-sectional study was performed on cohorts, including anti-tubercular therapy (ATT naïve active pulmonary tuberculosis (PTB patients, antiretroviral therapy (ART naïve HIV-1 infected individuals at different stages of disease, ATT and ART naïve HIV-PTB co-infected individuals and healthy controls. A significantly higher T-regulatory cell (Treg frequency coupled with the high FoxP3 expression in the CD4 T-cells indicated an immunosuppressive environment in the advance stage of HIV-1 infection. This is further substantiated by high HO-1 expression favoring TB co-infection. Functionally, this change in Treg frequency in HIV-1 infected individuals correlated well with suppression of T-cell proliferation. Mtb infection seems to facilitate the expansion of the Treg pool along with increased expression of FoxP3, specifically the variant-1, as evident from the data in HIV-1 co-infected as well as in patients with only PTB. A significantly lower expression of HO-1 in co-infected individuals compared to patients with only HIV-infection having comparable CD4 count correlated well with increased expression of CCR5 and CxCR4 as well as NF-κB and inflammatory cytokines IL-6 and TNF-α, which collectively may contribute to enhanced viral replication and increased cell death, hence faster disease progression in co-infected individuals.

  15. Genomic analysis of isolates from the United Kingdom 2012 pertussis outbreak reveals that vaccine antigen genes are unusually fast evolving.

    Science.gov (United States)

    Sealey, Katie L; Harris, Simon R; Fry, Norman K; Hurst, Laurence D; Gorringe, Andrew R; Parkhill, Julian; Preston, Andrew

    2015-07-15

    A major outbreak of whooping cough, or pertussis, occurred in 2012 in the United Kingdom (UK), with nearly 10 000 laboratory-confirmed cases and 14 infant deaths attributed to pertussis. A worldwide resurgence of pertussis has been linked to switch to the use of acellular pertussis vaccines and the evolution of Bordetella pertussis away from vaccine-mediated immunity. We have conducted genomic analyses of multiple strains from the UK outbreak. We show that the UK outbreak was polyclonal in nature, caused by multiple distinct but closely related strains. Importantly, we demonstrate that acellular vaccine antigen-encoding genes are evolving at higher rates than other surface protein-encoding genes. This was true even prior to the introduction of pertussis vaccines but has become more pronounced since the introduction of the current acellular vaccines. The fast evolution of vaccine antigen-encoding genes has serious consequences for the ability of current vaccines to continue to control pertussis. © The Author 2014. Published by Oxford University Press on behalf of the Infectious Diseases Society of America. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  16. Cytoplasmic-genetic male sterility gene provides direct evidence for some hybrid rice recently evolving into weedy rice.

    Science.gov (United States)

    Zhang, Jingxu; Lu, Zuomei; Dai, Weimin; Song, Xiaoling; Peng, Yufa; Valverde, Bernal E; Qiang, Sheng

    2015-05-27

    Weedy rice infests paddy fields worldwide at an alarmingly increasing rate. There is substantial evidence indicating that many weedy rice forms originated from or are closely related to cultivated rice. There is suspicion that the outbreak of weedy rice in China may be related to widely grown hybrid rice due to its heterosis and the diversity of its progeny, but this notion remains unsupported by direct evidence. We screened weedy rice accessions by both genetic and molecular marker tests for the cytoplasmic male sterility (CMS) genes (Wild abortive, WA, and Boro type, BT) most widely used in the production of indica and japonica three-line hybrid rice as a diagnostic trait of direct parenthood. Sixteen weedy rice accessions of the 358 tested (4.5%) contained the CMS-WA gene; none contained the CMS-BT gene. These 16 accessions represent weedy rices recently evolved from maternal hybrid rice derivatives, given the primarily maternal inheritance of this trait. Our results provide key direct evidence that hybrid rice can be involved in the evolution of some weedy rice accessions, but is not a primary factor in the recent outbreak of weedy rice in China.

  17. Superparamagnetic Nanoparticles and RNAi-Mediated Gene Silencing: Evolving Class of Cancer Diagnostics and Therapeutics

    Directory of Open Access Journals (Sweden)

    Sanchareeka Dey

    2012-01-01

    Full Text Available The ever increasing death of patients affected by various types of fatal cancers is of concern worldwide. Curative attempts by radiation/chemotherapy and surgery are often a failure in the long run. Moreover, adverse side effects of such treatments burden the patients with painful survival at the last phase of their life. The failure of early diagnosis is one of the root causes of the problem. Intensive research activities are being pursued in reputed laboratories across the globe to find superior diagnostics and therapeutics. Over the last decade, a number of publications have highlighted RNA interference based silencing of cancer-related gene expression as a promising technology to tackle the aforesaid problems. Superparamagnetic iron oxide nanoparticles (SPIONs are reported to be excellent vehicles for short-interfering RNA (siRNA. The SPION-siRNA conjugate is biocompatible, stable, and amenable to specific targeting and can cross the blood brain barrier. The issues related to their synthesis, surface properties, delivery, tracking, imaging in relevance to cancer diagnostic and therapeutic, and so forth demand an extensive review, and we have addressed these aspects in this paper. The future prospects of the technology have also been traced.

  18. Phylogeny of ultra-rapidly evolving dinoflagellate chloroplast genes: a possible common origin for sporozoan and dinoflagellate plastids.

    Science.gov (United States)

    Zhang, Z; Green, B R; Cavalier-Smith, T

    2000-07-01

    Complete chloroplast 23S rRNA and psbA genes from five peridinin-containing dinoflagellates (Heterocapsa pygmaea, Heterocapsa niei, Heterocapsa rotun-data, Amphidinium carterae, and Protoceratium reticulatum) were amplified by PCR and sequenced; partial sequences were obtained from Thoracosphaera heimii and Scrippsiella trochoidea. Comparison with chloroplast 23S rRNA and psbA genes of other organisms shows that dinoflagellate chloroplast genes are the most divergent and rapidly evolving of all. Quartet puzzling, maximum likelihood, maximum parsimony, neighbor joining, and LogDet trees were constructed. Intersite rate variation and invariant sites were allowed for with quartet puzzling and neighbor joining. All psbA and 23S rRNA trees showed peridinin-containing dinoflagellate chloroplasts as monophyletic. In psbA trees they are related to those of chromists and red algae. In 23S rRNA trees, dinoflagellates are always the sisters of Sporozoa (apicomplexans); maximum likelihood analysis of Heterocapsa triquetra 16S rRNA also groups the dinoflagellate and sporozoan sequences, but the other methods were inconsistent. Thus, dinoflagellate chloroplasts may actually be related to sporozoan plastids, but the possibility of reproducible long-branch artifacts cannot be strongly ruled out. The results for all three genes fit the idea that dinoflagellate chloroplasts originated from red algae by a secondary endosymbiosis, possibly the same one as for chromists and Sporozoa. The marked disagreement between 16S rRNA trees using different phylogenetic algorithms indicates that this is a rather poor molecule for elucidating overall chloroplast phylogeny. We discuss possible reasons why both plastid and mitochondrial genomes of alveolates (Dinozoa, Sporozoa and Ciliophora) have ultra-rapid substitution rates and a proneness to unique genomic rearrangements.

  19. Rapidly Evolving Genes Are Key Players in Host Specialization and Virulence of the Fungal Wheat Pathogen Zymoseptoria tritici (Mycosphaerella graminicola.

    Directory of Open Access Journals (Sweden)

    Stephan Poppe

    2015-07-01

    Full Text Available The speciation of pathogens can be driven by divergent host specialization. Specialization to a new host is possible via the acquisition of advantageous mutations fixed by positive selection. Comparative genome analyses of closely related species allows for the identification of such key substitutions via inference of genome-wide signatures of positive selection. We previously used a comparative genomics framework to identify genes that have evolved under positive selection during speciation of the prominent wheat pathogen Zymoseptoria tritici (synonym Mycosphaerella graminicola. In this study, we conducted functional analyses of four genes exhibiting strong signatures of positive selection in Z. tritici. We deleted the four genes in Z. tritici and confirm a virulence-related role of three of the four genes ΔZt80707, ΔZt89160 and ΔZt103264. The two mutants ΔZt80707 and ΔZt103264 show a significant reduction in virulence during infection of wheat; the ΔZt89160 mutant causes a hypervirulent phenotype in wheat. Mutant phenotypes of ΔZt80707, ΔZt89160 and ΔZt103264 can be restored by insertion of the wild-type genes. However, the insertion of the Zt80707 and Zt89160 orthologs from Z. pseudotritici and Z. ardabiliae do not restore wild-type levels of virulence, suggesting that positively selected substitutions in Z. tritici may relate to divergent host specialization. Interestingly, the gene Zt80707 encodes also a secretion signal that targets the protein for cell secretion. This secretion signal is however only transcribed in Z. tritici, suggesting that Z. tritici-specific substitutions relate to a new function of the protein in the extracellular space of the wheat-Z. tritici interaction. Together, the results presented here highlight that Zt80707, Zt103264 and Zt89160 represent key genes involved in virulence and host-specific disease development of Z. tritici. Our findings illustrate that evolutionary predictions provide a powerful tool

  20. Rapidly Evolving Genes Are Key Players in Host Specialization and Virulence of the Fungal Wheat Pathogen Zymoseptoria tritici (Mycosphaerella graminicola)

    Science.gov (United States)

    Poppe, Stephan; Dorsheimer, Lena; Happel, Petra; Stukenbrock, Eva Holtgrewe

    2015-01-01

    The speciation of pathogens can be driven by divergent host specialization. Specialization to a new host is possible via the acquisition of advantageous mutations fixed by positive selection. Comparative genome analyses of closely related species allows for the identification of such key substitutions via inference of genome-wide signatures of positive selection. We previously used a comparative genomics framework to identify genes that have evolved under positive selection during speciation of the prominent wheat pathogen Zymoseptoria tritici (synonym Mycosphaerella graminicola). In this study, we conducted functional analyses of four genes exhibiting strong signatures of positive selection in Z. tritici. We deleted the four genes in Z. tritici and confirm a virulence-related role of three of the four genes ΔZt80707, ΔZt89160 and ΔZt103264. The two mutants ΔZt80707 and ΔZt103264 show a significant reduction in virulence during infection of wheat; the ΔZt89160 mutant causes a hypervirulent phenotype in wheat. Mutant phenotypes of ΔZt80707, ΔZt89160 and ΔZt103264 can be restored by insertion of the wild-type genes. However, the insertion of the Zt80707 and Zt89160 orthologs from Z. pseudotritici and Z. ardabiliae do not restore wild-type levels of virulence, suggesting that positively selected substitutions in Z. tritici may relate to divergent host specialization. Interestingly, the gene Zt80707 encodes also a secretion signal that targets the protein for cell secretion. This secretion signal is however only transcribed in Z. tritici, suggesting that Z. tritici-specific substitutions relate to a new function of the protein in the extracellular space of the wheat-Z. tritici interaction. Together, the results presented here highlight that Zt80707, Zt103264 and Zt89160 represent key genes involved in virulence and host-specific disease development of Z. tritici. Our findings illustrate that evolutionary predictions provide a powerful tool for the

  1. GeneEvolve: a fast and memory efficient forward-time simulator of realistic whole-genome sequence and SNP data.

    Science.gov (United States)

    Tahmasbi, Rasool; Keller, Matthew C

    2017-01-15

    Computer simulations are excellent tools for understanding the evolutionary and genetic consequences of complex processes that cannot be analytically predicted and for creating realistic genetic data. There are many software packages that simulate genetic data, but they are typically not fast or memory efficient enough to simulate realistic, individual-level genome-wide SNP/sequence data. GeneEvolve is a user-friendly and efficient population genetics simulator that handles complex evolutionary and life history scenarios and generates individual-level phenotypes and realistic whole-genome sequence or SNP data. GeneEvolve runs forward-in-time, which allows it to provide a wide range of scenarios for mating systems, selection, population size and structure, migration, recombination and environmental effects. The software is designed to use as input data from real or previously simulated phased haplotypes, allowing it to mimic very closely the properties of real genomic data. GeneEvolve is freely available at https://github.com/rtahmasbi/GeneEvolve CONTACT: Rasool.Tahmasbi@Colorado.eduSupplementary information: Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  2. Adaptation of Escherichia coli to glucose promotes evolvability in lactose.

    Science.gov (United States)

    Phillips, Kelly N; Castillo, Gerardo; Wünsche, Andrea; Cooper, Tim F

    2016-02-01

    The selective history of a population can influence its subsequent evolution, an effect known as historical contingency. We previously observed that five of six replicate populations that were evolved in a glucose-limited environment for 2000 generations, then switched to lactose for 1000 generations, had higher fitness increases in lactose than populations started directly from the ancestor. To test if selection in glucose systematically increased lactose evolvability, we started 12 replay populations--six from a population subsample and six from a single randomly selected clone--from each of the six glucose-evolved founder populations. These replay populations and 18 ancestral populations were evolved for 1000 generations in a lactose-limited environment. We found that replay populations were initially slightly less fit in lactose than the ancestor, but were more evolvable, in that they increased in fitness at a faster rate and to higher levels. This result indicates that evolution in the glucose environment resulted in genetic changes that increased the potential of genotypes to adapt to lactose. Genome sequencing identified four genes--iclR, nadR, spoT, and rbs--that were mutated in most glucose-evolved clones and are candidates for mediating increased evolvability. Our results demonstrate that short-term selective costs during selection in one environment can lead to changes in evolvability that confer longer term benefits.

  3. Cobalamin-Independent Methionine Synthase (MetE): A Face-to-Face Double Barrel that Evolved by Gene Duplication

    Energy Technology Data Exchange (ETDEWEB)

    Pejcha, Robert; Ludwig, Martha L. (Michigan)

    2010-03-08

    Cobalamin-independent methionine synthase (MetE) catalyzes the transfer of a methyl group from methyltetrahydrofolate to L-homocysteine (Hcy) without using an intermediate methyl carrier. Although MetE displays no detectable sequence homology with cobalamin-dependent methionine synthase (MetH), both enzymes require zinc for activation and binding of Hcy. Crystallographic analyses of MetE from T. maritima reveal an unusual dual-barrel structure in which the active site lies between the tops of the two ({beta}{alpha}){sub 8} barrels. The fold of the N-terminal barrel confirms that it has evolved from the C-terminal polypeptide by gene duplication; comparisons of the barrels provide an intriguing example of homologous domain evolution in which binding sites are obliterated. The C-terminal barrel incorporates the zinc ion that binds and activates Hcy. The zinc-binding site in MetE is distinguished from the (Cys){sub 3}Zn site in the related enzymes, MetH and betaine-homocysteine methyltransferase, by its position in the barrel and by the metal ligands, which are histidine, cysteine, glutamate, and cysteine in the resting form of MetE. Hcy associates at the face of the metal opposite glutamate, which moves away from the zinc in the binary E {center_dot} Hcy complex. The folate substrate is not intimately associated with the N-terminal barrel; instead, elements from both barrels contribute binding determinants in a binary complex in which the folate substrate is incorrectly oriented for methyl transfer. Atypical locations of the Hcy and folate sites in the C-terminal barrel presumably permit direct interaction of the substrates in a ternary complex. Structures of the binary substrate complexes imply that rearrangement of folate, perhaps accompanied by domain rearrangement, must occur before formation of a ternary complex that is competent for methyl transfer.

  4. Zero bugs and program faster

    CERN Document Server

    Thompson, Kate

    2015-01-01

    A book about programming, improving skill, and avoiding mistakes. The author spent two years researching every bug avoidance technique she could find. This book contains the best of them. If you want to program faster, with fewer bugs, and write more secure code, buy this book! "This is the best book I have ever read." - Anonymous reviewer "Four score and seven years ago this book helped me debug my server code." -Abraham Lincoln "Would my Javascript have memory leaks without this book? Would fishes fly without water?" -Socrates "This book is the greatest victory since the Spanish Armada, and the best about programming." -Queen Elizabeth

  5. NCYM, a Cis-antisense gene of MYCN, encodes a de novo evolved protein that inhibits GSK3β resulting in the stabilization of MYCN in human neuroblastomas.

    Directory of Open Access Journals (Sweden)

    Yusuke Suenaga

    2014-01-01

    Full Text Available The rearrangement of pre-existing genes has long been thought of as the major mode of new gene generation. Recently, de novo gene birth from non-genic DNA was found to be an alternative mechanism to generate novel protein-coding genes. However, its functional role in human disease remains largely unknown. Here we show that NCYM, a cis-antisense gene of the MYCN oncogene, initially thought to be a large non-coding RNA, encodes a de novo evolved protein regulating the pathogenesis of human cancers, particularly neuroblastoma. The NCYM gene is evolutionally conserved only in the taxonomic group containing humans and chimpanzees. In primary human neuroblastomas, NCYM is 100% co-amplified and co-expressed with MYCN, and NCYM mRNA expression is associated with poor clinical outcome. MYCN directly transactivates both NCYM and MYCN mRNA, whereas NCYM stabilizes MYCN protein by inhibiting the activity of GSK3β, a kinase that promotes MYCN degradation. In contrast to MYCN transgenic mice, neuroblastomas in MYCN/NCYM double transgenic mice were frequently accompanied by distant metastases, behavior reminiscent of human neuroblastomas with MYCN amplification. The NCYM protein also interacts with GSK3β, thereby stabilizing the MYCN protein in the tumors of the MYCN/NCYM double transgenic mice. Thus, these results suggest that GSK3β inhibition by NCYM stabilizes the MYCN protein both in vitro and in vivo. Furthermore, the survival of MYCN transgenic mice bearing neuroblastoma was improved by treatment with NVP-BEZ235, a dual PI3K/mTOR inhibitor shown to destabilize MYCN via GSK3β activation. In contrast, tumors caused in MYCN/NCYM double transgenic mice showed chemo-resistance to the drug. Collectively, our results show that NCYM is the first de novo evolved protein known to act as an oncopromoting factor in human cancer, and suggest that de novo evolved proteins may functionally characterize human disease.

  6. Gene expression analysis of parthenogenetic embryonic development of the pea aphid, Acyrthosiphon pisum, suggests that aphid parthenogenesis evolved from meiotic oogenesis.

    Directory of Open Access Journals (Sweden)

    Dayalan G Srinivasan

    Full Text Available Aphids exhibit a form of phenotypic plasticity, called polyphenism, in which genetically identical females reproduce sexually during one part of the life cycle and asexually (via parthenogenesis during the remainder of the life cycle. The molecular basis for aphid parthenogenesis is unknown. Cytological observations of aphid parthenogenesis suggest that asexual oogenesis evolved either through a modification of meiosis or from a mitotic process. As a test of these alternatives, we assessed the expression levels and expression patterns of canonical meiotic recombination and germline genes in the sexual and asexual ovaries of the pea aphid, Acyrthosiphon pisum. We observed expression of all meiosis genes in similar patterns in asexual and sexual ovaries, with the exception that some genes encoding Argonaute-family members were not expressed in sexual ovaries. In addition, we observed that asexual aphid tissues accumulated unspliced transcripts of Spo11, whereas sexual aphid tissues accumulated primarily spliced transcripts. In situ hybridization revealed Spo11 transcript in sexual germ cells and undetectable levels of Spo11 transcript in asexual germ cells. We also found that an obligately asexual strain of pea aphid produced little spliced Spo11 transcript. Together, these results suggest that parthenogenetic oogenesis evolved from a meiosis-like, and not a mitosis-like, process and that the aphid reproductive polyphenism may involve a modification of Spo11 gene activity.

  7. AS3MT-mediated tolerance to arsenic evolved by multiple independent horizontal gene transfers from bacteria to eukaryotes

    DEFF Research Database (Denmark)

    Palmgren, Michael; Engström, Karin; Hallström, Björn M.

    2017-01-01

    Organisms have evolved the ability to tolerate toxic substances in their environments, often by producing metabolic enzymes that efficiently detoxify the toxicant. Inorganic arsenic is one of the most toxic and carcinogenic substances in the environment, but many organisms, including humans......, metabolise inorganic arsenic to less toxic metabolites. This multistep process produces mono-, di-, and trimethylated arsenic metabolites, which the organism excretes. In humans, arsenite methyltransferase (AS3MT) appears to be the main metabolic enzyme that methylates arsenic. In this study, we examined...... during evolution. These findings are supported by the observation that genetic variation in AS3MT correlates with the capacity to methylate arsenic. Adaptation to arsenic thus serves as a model for how organisms evolve to survive under toxic conditions....

  8. Novel and Recently Evolved MicroRNA Clusters Regulate Expansive F-BOX Gene Networks through Phased Small Interfering RNAs in Wild Diploid Strawberry.

    Science.gov (United States)

    Xia, Rui; Ye, Songqing; Liu, Zongrang; Meyers, Blake C; Liu, Zhongchi

    2015-09-01

    The wild strawberry (Fragaria vesca) has recently emerged as an excellent model for cultivated strawberry (Fragaria × ananassa) as well as other Rosaceae fruit crops due to its short seed-to-fruit cycle, diploidy, and sequenced genome. Deep sequencing and parallel analysis of RNA ends were used to identify F. vesca microRNAs (miRNAs) and their target genes, respectively. Thirty-eight novel and 31 known miRNAs were identified. Many known miRNAs targeted not only conserved mRNA targets but also developed new target genes in F. vesca. Significantly, two new clusters of miRNAs were found to collectively target 94 F-BOX (FBX) genes. One of the miRNAs in the new cluster is 22 nucleotides and triggers phased small interfering RNA production from six FBX genes, which amplifies the silencing to additional FBX genes. Comparative genomics revealed that the main novel miRNA cluster evolved from duplications of FBX genes. Finally, conserved trans-acting siRNA pathways were characterized and confirmed with distinct features. Our work identified novel miRNA-FBX networks in F. vesca and shed light on the evolution of miRNAs/phased small interfering RNA networks that regulate large gene families in higher plants. © 2015 American Society of Plant Biologists. All Rights Reserved.

  9. Faster than Hermitian Time Evolution

    Directory of Open Access Journals (Sweden)

    Carl M. Bender

    2007-12-01

    Full Text Available For any pair of quantum states, an initial state $|I angle$ and afinal quantum state $|F angle$, in a Hilbert space, there are many Hamiltonians $H$ under which $|I angle$ evolves into $|F angle$. Let us impose the constraint that the difference between the largest and smallest eigenvalues of $H$, $E_{max}$ and $E_{min}$, is held fixed. We can then determine the Hamiltonian $H$ that satisfies this constraint and achieves the transformation from the initial state to the final state in the least possible time $au$. For Hermitian Hamiltonians, $au$ has a nonzero lower bound. However, amongnon-Hermitian ${cal PT}$-symmetric Hamiltonians satisfying the same energy constraint, $au$ can be made arbitrarily small without violating the time-energy uncertainty principle. The minimum value of $au$ can be made arbitrarily small because for ${cal PT}$-symmetric Hamiltonians the path from the vector $|I angle$ to the vector $|F angle$, as measured using the Hilbert-space metric appropriate for this theory, can be made arbitrarily short. The mechanism described here is similar to that in general relativity in whichthe distance between two space-time points can be made small if they are connected by a wormhole. This result may have applications in quantum computing.

  10. Clustering of two genes putatively involved in cyanate detoxification evolved recently and independently in multiple fungal lineages

    Science.gov (United States)

    Fungi that have the enzymes cyanase and carbonic anhydrase show a limited capacity to detoxify cyanate, a fungicide employed by both plants and humans. Here, we describe a novel two-gene cluster that comprises duplicated cyanase and carbonic anhydrase copies, which we name the CCA gene cluster, trac...

  11. Clustering of two genes putatively involved in cyanate detoxification evolved recently and independently in multiple fungal lineages.

    Science.gov (United States)

    Elmore, M Holly; McGary, Kriston L; Wisecaver, Jennifer H; Slot, Jason C; Geiser, David M; Sink, Stacy; O'Donnell, Kerry; Rokas, Antonis

    2015-03-01

    Fungi that have the enzymes cyanase and carbonic anhydrase show a limited capacity to detoxify cyanate, a fungicide employed by both plants and humans. Here, we describe a novel two-gene cluster that comprises duplicated cyanase and carbonic anhydrase copies, which we name the CCA gene cluster, trace its evolution across Ascomycetes, and examine the evolutionary dynamics of its spread among lineages of the Fusarium oxysporum species complex (hereafter referred to as the FOSC), a cosmopolitan clade of purportedly clonal vascular wilt plant pathogens. Phylogenetic analysis of fungal cyanase and carbonic anhydrase genes reveals that the CCA gene cluster arose independently at least twice and is now present in three lineages, namely Cochliobolus lunatus, Oidiodendron maius, and the FOSC. Genome-wide surveys within the FOSC indicate that the CCA gene cluster varies in copy number across isolates, is always located on accessory chromosomes, and is absent in FOSC's closest relatives. Phylogenetic reconstruction of the CCA gene cluster in 163 FOSC strains from a wide variety of hosts suggests a recent history of rampant transfers between isolates. We hypothesize that the independent formation of the CCA gene cluster in different fungal lineages and its spread across FOSC strains may be associated with resistance to plant-produced cyanates or to use of cyanate fungicides in agriculture.

  12. Evidence That Loss-of-Function Filaggrin Gene Mutations Evolved in Northern Europeans to Favor Intracutaneous Vitamin D3 Production

    DEFF Research Database (Denmark)

    Thyssen, Jacob P; Bikle, Daniel D; Elias, Peter M

    2014-01-01

    Skin pigmentation lightened progressively to a variable extent, as modern humans emigrated out of Africa, but extreme lightening occurred only in northern Europeans. Yet, loss of pigmentation alone cannot suffice to sustain cutaneous vitamin D3 (VD3) formation at the high latitudes of northern...... Europe. We hypothesized that loss-of-function mutations in the epidermal structural protein, filaggrin (FLG), could have evolved to sustain adequate VD3 status. Loss of FLG results in reduced generation of trans-urocanic acid, the principal endogenous ultraviolet-B (UV-B) filter in lightly...... UV-B penetration and intracutaneous VD3 formation, the latitude-dependent gradient in FLG mutations, likely together with other concurrent mutations in VD3 metabolic pathways, provide a non-pigment-based mechanism that sustains higher levels of circulating VD3 in northern Europeans. At the time...

  13. Detection of the gene encoding the small subunit of the CO dehydrogenase enzyme in the H{sub 2}-evolving bacterium Rubrivivax gelatinosus CBS

    Energy Technology Data Exchange (ETDEWEB)

    Kish, A.; Levin, D. [Victoria Univ., BC (Canada)]|[Victoria Univ., BC (Canada)

    2001-06-01

    A purple non-sulfur bacterium, Rubrivivax gelatinosus CBS presents great opportunities, on a commercial scale, for the biological hydrogen production. A water-gas shift reaction is catalyzed when the bacterium is cultured in the presence of carbon oxide in the dark. The result is carbon monoxide (and water) being shifted into hydrogen (H{sub 2}) and carbon dioxide in near stoichiometric quantities. The production of hydrogen as a clean alternative fuel could be accomplished by using carbon monoxide generated from gasified waste biomass, using the bacterial water-gas shift reaction for that purpose. The characterization of three key enzymes and the genes encoding them was performed in a closely related purple non-sulfur bacterium called Rhodospirillum rubrum. They were: (1) a carbon monoxide dehydrogenase (CODH), (2) the ferredoxin-like electron-carrier small subunit of the CODH enzyme, and (3) an hydrogen-evolving hydrogenase. A transcriptional unit separate from the genes encoding the CODH and its ferredoxin-like small subunit encode the genes for the hydrogenase. A fragment of the Rhodospirillum rubrum ferredoxin-like subunit gene was amplified through the use of a polymerase chain reaction. Southern blots of restriction endonuclease digested genomic deoxyribonucleic acid (DNA) extracted from Rubrivivax gelatinosus CBS was probed with the fragment of the Rhodospirillum rubrum previously amplified using the polymerase chain reaction. Confirmation of the identification is being confirmed, while the gene is sequenced. 25 refs., 2 figs.

  14. Chloroplast biogenesis-associated nuclear genes: Control by plastid signals evolved prior to their regulation as part of photomorphogenesis.

    Directory of Open Access Journals (Sweden)

    Alison C HIlls

    2015-12-01

    Full Text Available The assembly of photosynthetically-competent chloroplasts occurs in angiosperm seedlings when first exposed to light, and is due to the control by light of photosynthesis-associated nuclear genes (PhANGs, also dependent upon plastid-to-nucleus biogenic communication signals. The relationship between light- and plastid signal-regulation of PhANGs is close but poorly understood. In contrast, many conifers green in the dark and the promoter of a pine PhANG, Lhcb, is active in the dark in tobacco. Here we show that the activity of this promoter in tobacco is sensitive to plastid photobleaching, or to the inhibition of plastid translation in the light or the dark, and the same interventions reduce expression of the native gene in pine seedlings, demonstrating classic plastid biogenic signalling in gymnosperms. Furthermore, Arabidopsis mutations causing defective plastid biogenesis suppress the effect in darkness of mutations in COP1 and DET1, repressors of photomorphogenesis, for the expression of several PhANGs but not a photosynthesis-unrelated, light-regulated gene. GLK transcriptional regulators mediate the response of LHCB but not of other tested PhANGs. We propose gain of the ability by repressors of photomorphogenesis to suppress the response of PhANG promoters to positive plastid biogenic signals in the dark to have contributed to the evolution of light control of chloroplast biogenesis.

  15. FASTER Test Reactor Preconceptual Design Report

    Energy Technology Data Exchange (ETDEWEB)

    Grandy, C. [Argonne National Lab. (ANL), Argonne, IL (United States); Belch, H. [Argonne National Lab. (ANL), Argonne, IL (United States); Brunett, A. J. [Argonne National Lab. (ANL), Argonne, IL (United States); Heidet, F. [Argonne National Lab. (ANL), Argonne, IL (United States); Hill, R. [Argonne National Lab. (ANL), Argonne, IL (United States); Hoffman, E. [Argonne National Lab. (ANL), Argonne, IL (United States); Jin, E. [Argonne National Lab. (ANL), Argonne, IL (United States); Mohamed, W. [Argonne National Lab. (ANL), Argonne, IL (United States); Moisseytsev, A. [Argonne National Lab. (ANL), Argonne, IL (United States); Passerini, S. [Argonne National Lab. (ANL), Argonne, IL (United States); Sienicki, J. [Argonne National Lab. (ANL), Argonne, IL (United States); Sumner, T. [Argonne National Lab. (ANL), Argonne, IL (United States); Vilim, R. [Argonne National Lab. (ANL), Argonne, IL (United States); Hayes, S. [Argonne National Lab. (ANL), Argonne, IL (United States)

    2016-03-31

    The FASTER test reactor plant is a sodium-cooled fast spectrum test reactor that provides high levels of fast and thermal neutron flux for scientific research and development. The 120MWe FASTER reactor plant has a superheated steam power conversion system which provides electrical power to a local grid allowing for recovery of operating costs for the reactor plant.

  16. FASTER test reactor preconceptual design report summary

    Energy Technology Data Exchange (ETDEWEB)

    Grandy, C. [Argonne National Lab. (ANL), Argonne, IL (United States); Belch, H. [Argonne National Lab. (ANL), Argonne, IL (United States); Brunett, A. [Argonne National Lab. (ANL), Argonne, IL (United States); Heidet, F. [Argonne National Lab. (ANL), Argonne, IL (United States); Hill, R. [Argonne National Lab. (ANL), Argonne, IL (United States); Hoffman, E. [Argonne National Lab. (ANL), Argonne, IL (United States); Jin, E. [Argonne National Lab. (ANL), Argonne, IL (United States); Mohamed, W. [Argonne National Lab. (ANL), Argonne, IL (United States); Moisseytsev, A. [Argonne National Lab. (ANL), Argonne, IL (United States); Passerini, S. [Argonne National Lab. (ANL), Argonne, IL (United States); Sienicki, J. [Argonne National Lab. (ANL), Argonne, IL (United States); Sumner, T. [Argonne National Lab. (ANL), Argonne, IL (United States); Vilim, R. [Argonne National Lab. (ANL), Argonne, IL (United States); Hayes, Steven [Argonne National Lab. (ANL), Argonne, IL (United States)

    2016-02-29

    The FASTER reactor plant is a sodium-cooled fast spectrum test reactor that provides high levels of fast and thermal neutron flux for scientific research and development. The 120MWe FASTER reactor plant has a superheated steam power conversion system which provides electrical power to a local grid allowing for recovery of operating costs for the reactor plant.

  17. Protein coalitions in a core mammalian biochemical network linked by rapidly evolving proteins

    Directory of Open Access Journals (Sweden)

    Tsoka Sophia

    2011-05-01

    Full Text Available Abstract Background Cellular ATP levels are generated by glucose-stimulated mitochondrial metabolism and determine metabolic responses, such as glucose-stimulated insulin secretion (GSIS from the β-cells of pancreatic islets. We describe an analysis of the evolutionary processes affecting the core enzymes involved in glucose-stimulated insulin secretion in mammals. The proteins involved in this system belong to ancient enzymatic pathways: glycolysis, the TCA cycle and oxidative phosphorylation. Results We identify two sets of proteins, or protein coalitions, in this group of 77 enzymes with distinct evolutionary patterns. Members of the glycolysis, TCA cycle, metabolite transport, pyruvate and NADH shuttles have low rates of protein sequence evolution, as inferred from a human-mouse comparison, and relatively high rates of evolutionary gene duplication. Respiratory chain and glutathione pathway proteins evolve faster, exhibiting lower rates of gene duplication. A small number of proteins in the system evolve significantly faster than co-pathway members and may serve as rapidly evolving adapters, linking groups of co-evolving genes. Conclusions Our results provide insights into the evolution of the involved proteins. We find evidence for two coalitions of proteins and the role of co-adaptation in protein evolution is identified and could be used in future research within a functional context.

  18. Identification of a novel PNMA-MS1 gene in marsupials suggests the LTR retrotransposon-derived PNMA genes evolved differently in marsupials and eutherians.

    Science.gov (United States)

    Iwasaki, Sawa; Suzuki, Shunsuke; Pelekanos, Matthew; Clark, Helen; Ono, Ryuichi; Shaw, Geoff; Renfree, Marilyn B; Kaneko-Ishino, Tomoko; Ishino, Fumitoshi

    2013-10-01

    Two major gene families derived from Ty3/Gypsy long terminal repeat (LTR) retrotransposons were recently identified in mammals. The sushi-ichi retrotransposon homologue (SIRH) family comprises 12 genes: 11 in eutherians including Peg10 and Peg11/Rtl1 that have essential roles in the eutherian placenta and 1 that is marsupial specific. Fifteen and 12 genes were reported in the second gene family, para-neoplastic antigen MA (PNMA), in humans and mice, respectively, although their biological functions and evolutionary history remain largely unknown. Here, we identified two novel candidate PNMA genes, PNMA-MS1 and -MS2 in marsupials. Like all eutherian-specific PNMA genes, they exhibit the highest homology to a Gypsy12_DR (DR, Danio rerio) Gag protein. PNMA-MS1 is conserved in both Australian and South American marsupial species, the tammar wallaby and grey short-tailed opossum. However, no PNMA-MS1 orthologue was found in eutherians, monotremes or non-mammalian vertebrates. PNMA-MS1 was expressed in the ovary, mammary gland and brain during development and growth in the tammar, suggesting that PNMA-MS1 may have acquired a marsupial-specific function. However, PNMA-MS2 seems to be a pseudogene. The absence of marsupial orthologues of eutherian PNMA genes suggests that the retrotransposition events of the Gypsy12_DR-related retrotransposons that gave rise to the PNMA family occurred after the divergence of marsupials and eutherians.

  19. FASTER: an unsupervised fully automated sleep staging method for mice.

    Science.gov (United States)

    Sunagawa, Genshiro A; Séi, Hiroyoshi; Shimba, Shigeki; Urade, Yoshihiro; Ueda, Hiroki R

    2013-06-01

    Identifying the stages of sleep, or sleep staging, is an unavoidable step in sleep research and typically requires visual inspection of electroencephalography (EEG) and electromyography (EMG) data. Currently, scoring is slow, biased and prone to error by humans and thus is the most important bottleneck for large-scale sleep research in animals. We have developed an unsupervised, fully automated sleep staging method for mice that allows less subjective and high-throughput evaluation of sleep. Fully Automated Sleep sTaging method via EEG/EMG Recordings (FASTER) is based on nonparametric density estimation clustering of comprehensive EEG/EMG power spectra. FASTER can accurately identify sleep patterns in mice that have been perturbed by drugs or by genetic modification of a clock gene. The overall accuracy is over 90% in every group. 24-h data are staged by a laptop computer in 10 min, which is faster than an experienced human rater. Dramatically improving the sleep staging process in both quality and throughput FASTER will open the door to quantitative and comprehensive animal sleep research. © 2013 The Authors Genes to Cells © 2013 by the Molecular Biology Society of Japan and Wiley Publishing Asia Pty Ltd.

  20. Changes in G+C content of a neutrally evolving gene under a non-reversible dynamics measured by computer simulations based on experimental evolution data

    Directory of Open Access Journals (Sweden)

    Adriana Brunstein

    2004-01-01

    Full Text Available To evaluate the effects of non-reversibility on compositional base changes and the distribution of branch lengths along a phylogeny, we extended, by means of computer simulations, our previous sequential PCR in vitro evolution experiment. In that study a 18S rRNA gene evolved neutrally for 280 generations and a homogeneous non-stationary model of base substitution based on a non-reversible dynamics was built from the in vitro evolution data to describe the observed pattern of nucleotide substitutions. Here, the process was extended to 840 generations without selection, using the model parameters calculated from the in vitro evolution experiment. We observed that under a non-reversible model the G+C content of the sequences significantly increases when compared to simulations with a reversible model. The values of mean and variance of the branch lengths are reduced under a non-reversible dynamics although they follow a Poisson distribution. We conclude that the major implication of non-reversibility is the overall decrease of branch lengths, although no transition from a stochastic to an ordered process is observed. According to our model the result of this neutral process will be the increase in the G+C content of the descendant sequences with an overall decrease in the frequency of substitutions.

  1. Particles That Travel Faster than Light?

    Science.gov (United States)

    Newton, Roger G.

    1970-01-01

    A discussion of the possible existence of tachyons, particles that travel faster than light, and their theoretical properties. Suggests that if tachyons were found, the consequences for relativity theory, quantum mechanics and the concept of casuality would be far-reaching. Concludes that the final answer rests with the experimentalist.…

  2. Bacteriophage ΦM1 of Pectobacterium evolves to escape two bifunctional Type III toxin-antitoxin and abortive infection systems through mutations in a single viral gene.

    Science.gov (United States)

    Blower, Tim R; Chai, Ray; Przybilski, Rita; Chindhy, Shahzad; Fang, Xinzhe; Kidman, Samuel E; Tan, Hui; Luisi, Ben F; Fineran, Peter C; Salmond, George P C

    2017-02-03

    Some bacteria, when infected by their viral parasites (bacteriophages), undergo a suicidal response that also terminates productive viral replication (abortive infection; Abi). This response can be viewed as an altruistic act protecting the uninfected bacterial clonal population. Abortive infection can occur through the action of Type III protein-RNA toxin-antitoxin (TA) systems, such as ToxINPa from the phytopathogen, Pectobacterium atrosepticum Rare spontaneous mutants evolved in the generalized transducing phage, ΦM1, which escaped ToxINPa-mediated abortive infection in P. atrosepticum ΦM1 is a member of the Podoviridae and member of the "KMV-like viruses", a subset of the T7 supergroup. Genomic sequencing of ΦM1 escape mutants revealed single-base changes which clustered in a single open reading frame. The "escape" gene product, M1-23, was highly toxic to the host bacterium when over-expressed, but mutations in M1-23 that enabled an escape phenotype caused M1-23 to be less toxic. M1-23 is encoded within the DNA metabolism modular section of the phage genome, and when it was over-expressed, it co-purified with the host nucleotide excision repair protein, UvrA. While the M1-23 protein interacted with UvrA in co-immunoprecipitation assays, a UvrA mutant strain still aborted ΦM1, suggesting that the interaction is not critical for the Type III TA Abi activity. Additionally, ΦM1 escaped a heterologous Type III TA system (TenpINPl) from Photorhabdus luminescens (reconstituted in P. atrosepticum) through mutations in the same protein, M1-23. The mechanistic action of M1-23 is currently unknown but further analysis of this protein could provide insights into the mode of activation of both systems.

  3. Faster and Low Power Twin Precision Multiplier

    CERN Document Server

    Sreedeep, V; Kittur, Harish M

    2011-01-01

    In this work faster unsigned multiplication has been achieved by using a combination of High Performance Multiplication [HPM] column reduction technique and implementing a N-bit multiplier using 4 N/2-bit multipliers (recursive multiplication) and acceleration of the final addition using a hybrid adder. Low power has been achieved by using clock gating technique. Based on the proposed technique 16 and 32-bit multipliers are developed. The performance of the proposed multiplier is analyzed by evaluating the delay, area and power, with TCBNPHP 90 nm process technology on interconnect and layout using Cadence NC launch, RTL compiler and ENCOUNTER tools. The results show that the 32-bit proposed multiplier is as much as 22% faster, occupies only 3% more area and consumes 30% lesser power with respect to the recently reported twin precision multiplier.

  4. Faster than Nyquist signaling algorithms to silicon

    CERN Document Server

    Dasalukunte, Deepak; Rusek, Fredrik; Anderson, John B

    2014-01-01

    This book addresses the challenges and design trade-offs arising during the hardware design of Faster-than-Nyquist (FTN) signaling transceivers. The authors describe how to design for coexistence between the FTN system described and Orthogonal frequency-division multiplexing (OFDM) systems, enabling readers to design FTN specific processing blocks as add-ons to the conventional transceiver chain.   • Provides a comprehensive introduction to Faster-than-Nyquist (FTN) signaling transceivers, covering both theory and hardware implementation; • Enables readers to design systems that achieve bandwidth efficiency by making better use of the available spectrum resources; • Describes design techniques to achieve 2x improvement in bandwidth usage with similar performance as that of an OFDM system.  

  5. Pigeons home faster through polluted air

    OpenAIRE

    Zhongqiu Li; Franck Courchamp; Daniel T. Blumstein

    2016-01-01

    Air pollution, especially haze pollution, is creating health issues for both humans and other animals. However, remarkably little is known about how animals behaviourally respond to air pollution. We used multiple linear regression to analyse 415 pigeon races in the North China Plain, an area with considerable air pollution, and found that while the proportion of pigeons successfully homed was not influenced by air pollution, pigeons homed faster when the air was especially polluted. Our resu...

  6. Faster than light, slower than time

    Energy Technology Data Exchange (ETDEWEB)

    Rucker, R. (Randolph-Macon Women' s College, Lynchburg, VA (USA). Dept. of Mathematics)

    1981-10-01

    The problem with faster-than-light travel is that, in the framework of Special Relativity, it is logically equivalent to time-travel. The problem with time-travel is that it leads to two types of paradoxes. The paradoxes, and the various means of skirting them, are all discussed here. Virtually all the examples are drawn from science-fiction novels, which are a large and neglected source of thought-experiments.

  7. CORSIKA modifications for faster background generation

    Science.gov (United States)

    Jero, Kyle

    2016-04-01

    CORSIKA is a simulation program for extensive air showers initiated by high energy cosmic particles. These air showers create the majority of the muons and neutrinos which neutrino that telescopes detect and are considered a background signature in searches for astrophysical neutrinos. This contribution will discuss changes to CORSIKA which allow for faster high energy background simulation. The theory, implementation, application, and performance of these modifications will be presented.

  8. CORSIKA modifications for faster background generation

    Directory of Open Access Journals (Sweden)

    Jero Kyle

    2016-01-01

    Full Text Available CORSIKA is a simulation program for extensive air showers initiated by high energy cosmic particles. These air showers create the majority of the muons and neutrinos which neutrino that telescopes detect and are considered a background signature in searches for astrophysical neutrinos. This contribution will discuss changes to CORSIKA which allow for faster high energy background simulation. The theory, implementation, application, and performance of these modifications will be presented.

  9. Compressing bitmap indexes for faster search operations

    Energy Technology Data Exchange (ETDEWEB)

    Wu, Kesheng; Otoo, Ekow J.; Shoshani, Arie

    2002-04-25

    In this paper, we study the effects of compression on bitmap indexes. The main operations on the bitmaps during query processing are bitwise logical operations such as AND, OR, NOT, etc. Using the general purpose compression schemes, such as gzip, the logical operations on the compressed bitmaps are much slower than on the uncompressed bitmaps. Specialized compression schemes, like the byte-aligned bitmap code(BBC), are usually faster in performing logical operations than the general purpose schemes, but in many cases they are still orders of magnitude slower than the uncompressed scheme. To make the compressed bitmap indexes operate more efficiently, we designed a CPU-friendly scheme which we refer to as the word-aligned hybrid code (WAH). Tests on both synthetic and real application data show that the new scheme significantly outperforms well-known compression schemes at a modest increase in storage space. Compared to BBC, a scheme well-known for its operational efficiency, WAH performs logical operations about 12 times faster and uses only 60 percent more space. Compared to the uncompressed scheme, in most test cases WAH is faster while still using less space. We further verified with additional tests that the improvement in logical operation speed translates to similar improvement in query processing speed.

  10. Analyzing Evolving Social Network 2 (EVOLVE2)

    Science.gov (United States)

    2015-04-01

    COVERED (From - To) JUN 2012 – OCT 2014 4. TITLE AND SUBTITLE ANALYZING EVOLVING SOCIAL NETWORKS 2 (EVOLVE2) 5a. CONTRACT NUMBER FA8750-12-2-0186... jazz 198 2742 274 0.14 connect 1095 7825 783 0.014 hep-th 8710 14254 1425 0.0003 netscience 1461 2742 274 0.0013 imdb 6260 98235 9824 0.005 technological

  11. Phylogeny of the arthropod endosymbiont Wolbachia based on the wsp gene

    NARCIS (Netherlands)

    Meer, van M.M.M.; Witteveldt, J.; Stouthamer, R.

    1999-01-01

    Bacteria of the genus Wolbachia (Rickettsiae) are widespread in arthropods and can induce cytoplasmic incompatibility (CI), thelytoky (T) or feminization (F) in their host. Recent research on the wsp gene of mainly CI inducing Wolbachia has shown that this gene evolves at a much faster rate than pre

  12. Faster Case Retrieval Using Hash Indexing Technique

    OpenAIRE

    2011-01-01

    The main objective of case retrieval is to scan and to map the most similar old cases in case base with a new problem. Beside accurateness, the time taken to retrieve case is also important. With the increasing number of cases in case base, the retrieval task is becoming more challenging where faster retrieval time and good accuracy are the main aim. Traditionally, sequential indexing method has been applied to search for possible cases in case base. This technique worked fast when the number...

  13. Better Faster Noise with the GPU

    DEFF Research Database (Denmark)

    Wyvill, Geoff; Frisvad, Jeppe Revall

    Filtered noise [Perlin 1985] has, for twenty years, been a fundamental tool for creating functional texture and it has many other applications; for example, animating water waves or the motion of grass waving in the wind. Perlin noise suffers from a number of defects and there have been many atte...... attempts to create better or faster noise but Perlin’s ‘Gradient Noise’ has consistently proved to be the best compromise between speed and quality. Our objective was to create a better noise cheaply by use of the GPU....

  14. Faster Algorithms on Branch and Clique Decompositions

    Science.gov (United States)

    Bodlaender, Hans L.; van Leeuwen, Erik Jan; van Rooij, Johan M. M.; Vatshelle, Martin

    We combine two techniques recently introduced to obtain faster dynamic programming algorithms for optimization problems on graph decompositions. The unification of generalized fast subset convolution and fast matrix multiplication yields significant improvements to the running time of previous algorithms for several optimization problems. As an example, we give an O^{*}(3^{ω/2k}) time algorithm for Minimum Dominating Set on graphs of branchwidth k, improving on the previous O *(4 k ) algorithm. Here ω is the exponent in the running time of the best matrix multiplication algorithm (currently ω< 2.376). For graphs of cliquewidth k, we improve from O *(8 k ) to O *(4 k ). We also obtain an algorithm for counting the number of perfect matchings of a graph, given a branch decomposition of width k, that runs in time O^{*}(2^{ω/2k}). Generalizing these approaches, we obtain faster algorithms for all so-called [ρ,σ]-domination problems on branch decompositions if ρ and σ are finite or cofinite. The algorithms presented in this paper either attain or are very close to natural lower bounds for these problems.

  15. Development of the FASTER Wheeled Bevameter

    Science.gov (United States)

    Richter, L.; Eder, V.; Hoheneder, W.; Imhof, B.; Lewinger, W.; Ransom, S.; Saaj, C.; Weclewski, P.; Waclavicek, R.,

    2014-04-01

    This paper describes the development of a Wheeled Bevameter (WB) within the FASTER project (Forward Acquisition of Soil and Terrain Data for Exploration Rovers), funded by the European Union's FP7 programme. In FASTER, novel and innovative concepts for in situ forward sensing of soil properties and terrain conditions in the planned path of a planetary rover are developed. Terrain strength measurements for assessment of the mobility of crosscountry vehicles have decades of heritage on Earth, but typically trafficability of terrains is only gauged by human operators ahead of vehicle operations rather than in-line by probes deployed from the vehicle itself, as is intended for FASTER. For FASTER, a Wheeled Bevameter (WB) has been selected as the terrain sensing instrument for the vehicle. Wheeled Bevameters are suitable for terrain measurements while driving but traditionally have mostly been employed on terrestrial vehicles to evaluate particular wheel designs. The WB as conceived in FASTER uses a dedicated, passive-rolling test wheel (‚test wheel') placed on the terrain as the loading device to enable to determine bearing strength, compressive strength and shear strength of the terrain immediately ahead of the vehicle, as well as rover-terrain interaction parameters used in semi-empirical vehicle-terrain traction models. The WB includes a placement mechanism for the test wheel. The test wheel would remain lowered onto the ground during nominal rover motion, including when climbing and descending slopes. During normal operations, the placement mechanism assumes the function of a passive suspension of the wheel, allowing it to follow the terrain contour. Quantities measured with the WB are: test wheel sinkage (through a laser sensor), test wheel vertical load, test wheel horizontal reaction force, and test wheel rotation rate. Measurements are performed while the rover is in motion. Measured test wheel rotation rate (with appropriate corrections for slight skid) can

  16. Fat: an evolving issue

    Directory of Open Access Journals (Sweden)

    John R. Speakman

    2012-09-01

    Work on obesity is evolving, and obesity is a consequence of our evolutionary history. In the space of 50 years, we have become an obese species. The reasons why can be addressed at a number of different levels. These include separating between whether the primary cause lies on the food intake or energy expenditure side of the energy balance equation, and determining how genetic and environmental effects contribute to weight variation between individuals. Opinion on whether increased food intake or decreased energy expenditure drives the obesity epidemic is still divided, but recent evidence favours the idea that food intake, rather than altered expenditure, is most important. There is more of a consensus that genetics explains most (probably around 65% of weight variation between individuals. Recent advances in genome-wide association studies have identified many polymorphisms that are linked to obesity, yet much of the genetic variance remains unexplained. Finding the causes of this unexplained variation will be an impetus of genetic and epigenetic research on obesity over the next decade. Many environmental factors – including gut microbiota, stress and endocrine disruptors – have been linked to the risk of developing obesity. A better understanding of gene-by-environment interactions will also be key to understanding obesity in the years to come.

  17. Hot water can freeze faster than cold?!?

    CERN Document Server

    Jeng, M

    2005-01-01

    We review the Mpemba effect, where intially hot water freezes faster than initially cold water. While the effect appears impossible at first sight, it has been seen in numerous experiments, was reported on by Aristotle, Francis Bacon, and Descartes, and has been well-known as folklore around the world. It has a rich and fascinating history, which culminates in the dramatic story of the secondary school student, Erasto Mpemba, who reintroduced the effect to the twentieth century scientific community. The phenomenon, while simple to describe, is deceptively complex, and illustrates numerous important issues about the scientific method: the role of skepticism in scientific inquiry, the influence of theory on experiment and observation, the need for precision in the statement of a scientific hypothesis, and the nature of falsifiability. We survey proposed theoretical mechanisms for the Mpemba effect, and the results of modern experiments on the phenomenon. Studies of the observation that hot water pipes are more ...

  18. Backward Evolving Quantum States

    CERN Document Server

    Vaidman, L

    2006-01-01

    The basic concept of the two-state vector formalism, which is the time symmetric approach to quantum mechanics, is the backward evolving quantum state. However, due to the time asymmetry of the memory's arrow of time, the possible ways to manipulate a backward evolving quantum state differ from those for a standard, forward evolving quantum state. The similarities and the differences between forward and backward evolving quantum states regarding the no-cloning theorem, nonlocal measurements, and teleportation are discussed. The results are relevant not only in the framework of the two-state vector formalism, but also in the framework of retrodictive quantum theory.

  19. Evolving sensitivity balances Boolean Networks.

    Directory of Open Access Journals (Sweden)

    Jamie X Luo

    Full Text Available We investigate the sensitivity of Boolean Networks (BNs to mutations. We are interested in Boolean Networks as a model of Gene Regulatory Networks (GRNs. We adopt Ribeiro and Kauffman's Ergodic Set and use it to study the long term dynamics of a BN. We define the sensitivity of a BN to be the mean change in its Ergodic Set structure under all possible loss of interaction mutations. In silico experiments were used to selectively evolve BNs for sensitivity to losing interactions. We find that maximum sensitivity was often achievable and resulted in the BNs becoming topologically balanced, i.e. they evolve towards network structures in which they have a similar number of inhibitory and excitatory interactions. In terms of the dynamics, the dominant sensitivity strategy that evolved was to build BNs with Ergodic Sets dominated by a single long limit cycle which is easily destabilised by mutations. We discuss the relevance of our findings in the context of Stem Cell Differentiation and propose a relationship between pluripotent stem cells and our evolved sensitive networks.

  20. The type F6 neurotoxin gene cluster locus of group II clostridium botulinum has evolved by successive disruption of two different ancestral precursors.

    Science.gov (United States)

    Carter, Andrew T; Stringer, Sandra C; Webb, Martin D; Peck, Michael W

    2013-01-01

    Genome sequences of five different Group II (nonproteolytic) Clostridium botulinum type F6 strains were compared at a 50-kb locus containing the neurotoxin gene cluster. A clonal origin for these strains is indicated by the fact that sequences were identical except for strain Eklund 202F, with 10 single-nucleotide polymorphisms and a 15-bp deletion. The essential topB gene encoding topoisomerase III was found to have been split by the apparent insertion of 34.4 kb of foreign DNA (in a similar manner to that in Group II C. botulinum type E where the rarA gene has been disrupted by a neurotoxin gene cluster). The foreign DNA, which includes the intact 13.6-kb type F6 neurotoxin gene cluster, bears not only a newly introduced topB gene but also two nonfunctional botulinum neurotoxin gene remnants, a type B and a type E. This observation combined with the discovery of bacteriophage integrase genes and IS4 elements suggest that several rounds of recombination/horizontal gene transfer have occurred at this locus. The simplest explanation for the current genotype is that the ancestral bacterium, a Group II C. botulinum type B strain, received DNA firstly from a strain containing a type E neurotoxin gene cluster, then from a strain containing a type F6 neurotoxin gene cluster. Each event disrupted the previously functional neurotoxin gene. This degree of successive recombination at one hot spot is without precedent in C. botulinum, and it is also the first description of a Group II C. botulinum genome containing more than one neurotoxin gene sequence.

  1. Faster and Simpler Minimal Conflicting Set Identification

    CERN Document Server

    Ouangraoua, Aida

    2012-01-01

    Let C be a finite set of N elements and R = r_1,r_2,..., r_m a family of M subsets of C. A subset X of R verifies the Consecutive Ones Property (C1P) if there exists a permutation P of C such that each r_i in X is an interval of P. A Minimal Conflicting Set (MCS) S is a subset of R that does not verify the C1P, but such that any of its proper subsets does. In this paper, we present a new simpler and faster algorithm to decide if a given element r in R belongs to at least one MCS. Our algorithm runs in O(N^2M^2 + NM^7), largely improving the current O(M^6N^5 (M+N)^2 log(M+N)) fastest algorithm of [Blin {\\em et al}, CSR 2011]. The new algorithm is based on an alternative approach considering minimal forbidden induced subgraphs of interval graphs instead of Tucker matrices.

  2. Faster Energy Efficient Column Compression Multiplication

    CERN Document Server

    Ramkumar, B

    2011-01-01

    In this work we demonstrate that faster, energy efficient, column compression multiplication, can be achieved by using a combination of two design techniques: partitioning of the partial products into two parts for independent parallel column compression and acceleration of the final addition using a hybrid adder proposed in this work. In order to demonstrate the efficacy of the techniques we have chosen the Dadda multiplier as an example. Based on the proposed techniques 8, 16, 32 and 64-bit Dadda multipliers are developed and compared with the regular Dadda multiplier. The performance of the proposed multiplier is analyzed by evaluating the delay, area and power, with 180 nm process technologies on interconnect and layout using industry standard design and layout tools. The result analysis shows that the 64-bit regular Dadda multiplier is as much as 41.1% slower than the proposed multiplier and requires only 1.4% and 3.7% less area and power respectively. Also the power-delay product of the proposed design ...

  3. Why are halo coronal mass ejections faster?

    Institute of Scientific and Technical Information of China (English)

    Qing-Min Zhang; Yang Guo; Peng-Fei Chen; Ming-De Ding; Cheng Fang

    2010-01-01

    Halo coronal mass ejections(CMEs)have been to be significantly faster than normal CMEs,which is a long-standing puzzle.In order to solve the puzzle,we first investigate the observed properties of 31 limb CMEs that clearly display loopshaped frontal loops.The observational results show a strong tendency that slower CMEs are weaker in white-light intensity.Then,we perform a Monte Carlo simulation of 20000 artificial limb CMEs that have an average velocity of~523 km s-1.The Thomson scattering of these events is calculated when they are assumed to be observed as limb and halo events,respectively.It is found that the white-light intensity of many slow CMEs becomes remarkably reduced when they turn from being viewed as a limb event to being viewed as a halo event.When the intensity is below the background solar wind fluctuation,it is assumed that they would be missed by coronagraphs.The average velocity of"detectable"halo CMEs is~922 km s-1,very close to the observed value.This also indicates that wider events are more likely to be recorded.The results soundly suggest that the higher average velocity of halo CMEs is due to that a majority of slow events and some of narrow fast events carrying less material are so faint that they are blended with the solar wind fluctuations,and therefore are not observed.

  4. Functional modules of sigma factor regulons guarantee adaptability and evolvability

    Science.gov (United States)

    Binder, Sebastian C.; Eckweiler, Denitsa; Schulz, Sebastian; Bielecka, Agata; Nicolai, Tanja; Franke, Raimo; Häussler, Susanne; Meyer-Hermann, Michael

    2016-02-01

    The focus of modern molecular biology turns from assigning functions to individual genes towards understanding the expression and regulation of complex sets of molecules. Here, we provide evidence that alternative sigma factor regulons in the pathogen Pseudomonas aeruginosa largely represent insulated functional modules which provide a critical level of biological organization involved in general adaptation and survival processes. Analysis of the operational state of the sigma factor network revealed that transcription factors functionally couple the sigma factor regulons and significantly modulate the transcription levels in the face of challenging environments. The threshold quality of newly evolved transcription factors was reached faster and more robustly in in silico testing when the structural organization of sigma factor networks was taken into account. These results indicate that the modular structures of alternative sigma factor regulons provide P. aeruginosa with a robust framework to function adequately in its environment and at the same time facilitate evolutionary change. Our data support the view that widespread modularity guarantees robustness of biological networks and is a key driver of evolvability.

  5. Genes that escape X-inactivation in humans have high intraspecific variability in expression, are associated with mental impairment but are not slow evolving.

    Science.gov (United States)

    Zhang, Yuchao; Castillo-Morales, Atahualpa; Jiang, Min; Zhu, Yufei; Hu, Landian; Urrutia, Araxi O; Kong, Xiangyin; Hurst, Laurence D

    2013-12-01

    In female mammals most X-linked genes are subject to X-inactivation. However, in humans some X-linked genes escape silencing, these escapees being candidates for the phenotypic aberrations seen in polyX karyotypes. These escape genes have been reported to be under stronger purifying selection than other X-linked genes. Although it is known that escape from X-inactivation is much more common in humans than in mice, systematic assays of escape in humans have to date employed only interspecies somatic cell hybrids. Here we provide the first systematic next-generation sequencing analysis of escape in a human cell line. We analyzed RNA and genotype sequencing data obtained from B lymphocyte cell lines derived from Europeans (CEU) and Yorubans (YRI). By replicated detection of heterozygosis in the transcriptome, we identified 114 escaping genes, including 76 not previously known to be escapees. The newly described escape genes cluster on the X chromosome in the same chromosomal regions as the previously known escapees. There is an excess of escaping genes associated with mental retardation, consistent with this being a common phenotype of polyX phenotypes. We find both differences between populations and between individuals in the propensity to escape. Indeed, we provide the first evidence for there being both hyper- and hypo-escapee females in the human population, consistent with the highly variable phenotypic presentation of polyX karyotypes. Considering also prior data, we reclassify genes as being always, never, and sometimes escape genes. We fail to replicate the prior claim that genes that escape X-inactivation are under stronger purifying selection than others.

  6. Modeling Evolving Innovation Networks

    OpenAIRE

    Koenig, Michael D.; Battiston, Stefano; Schweitzer, Frank

    2007-01-01

    We develop a new framework for modeling innovation networks which evolve over time. The nodes in the network represent firms, whereas the directed links represent unilateral interactions between the firms. Both nodes and links evolve according to their own dynamics and on different time scales. The model assumes that firms produce knowledge based on the knowledge exchange with other firms, which involves both costs and benefits for the participating firms. In order to increase their knowledge...

  7. Faster exon assembly by sparse spliced alignment

    CERN Document Server

    Tiskin, Alexander

    2007-01-01

    Assembling a gene from candidate exons is an important problem in computational biology. Among the most successful approaches to this problem is \\emph{spliced alignment}, proposed by Gelfand et al., which scores different candidate exon chains within a DNA sequence of length $m$ by comparing them to a known related gene sequence of length n, $m = \\Theta(n)$. Gelfand et al.\\ gave an algorithm for spliced alignment running in time O(n^3). Kent et al.\\ considered sparse spliced alignment, where the number of candidate exons is O(n), and proposed an algorithm for this problem running in time O(n^{2.5}). We improve on this result, by proposing an algorithm for sparse spliced alignment running in time O(n^{2.25}). Our approach is based on a new framework of \\emph{quasi-local string comparison}.

  8. Evolving digital ecological networks.

    Science.gov (United States)

    Fortuna, Miguel A; Zaman, Luis; Wagner, Aaron P; Ofria, Charles

    2013-01-01

    "It is hard to realize that the living world as we know it is just one among many possibilities" [1]. Evolving digital ecological networks are webs of interacting, self-replicating, and evolving computer programs (i.e., digital organisms) that experience the same major ecological interactions as biological organisms (e.g., competition, predation, parasitism, and mutualism). Despite being computational, these programs evolve quickly in an open-ended way, and starting from only one or two ancestral organisms, the formation of ecological networks can be observed in real-time by tracking interactions between the constantly evolving organism phenotypes. These phenotypes may be defined by combinations of logical computations (hereafter tasks) that digital organisms perform and by expressed behaviors that have evolved. The types and outcomes of interactions between phenotypes are determined by task overlap for logic-defined phenotypes and by responses to encounters in the case of behavioral phenotypes. Biologists use these evolving networks to study active and fundamental topics within evolutionary ecology (e.g., the extent to which the architecture of multispecies networks shape coevolutionary outcomes, and the processes involved).

  9. Evolving digital ecological networks.

    Directory of Open Access Journals (Sweden)

    Miguel A Fortuna

    Full Text Available "It is hard to realize that the living world as we know it is just one among many possibilities" [1]. Evolving digital ecological networks are webs of interacting, self-replicating, and evolving computer programs (i.e., digital organisms that experience the same major ecological interactions as biological organisms (e.g., competition, predation, parasitism, and mutualism. Despite being computational, these programs evolve quickly in an open-ended way, and starting from only one or two ancestral organisms, the formation of ecological networks can be observed in real-time by tracking interactions between the constantly evolving organism phenotypes. These phenotypes may be defined by combinations of logical computations (hereafter tasks that digital organisms perform and by expressed behaviors that have evolved. The types and outcomes of interactions between phenotypes are determined by task overlap for logic-defined phenotypes and by responses to encounters in the case of behavioral phenotypes. Biologists use these evolving networks to study active and fundamental topics within evolutionary ecology (e.g., the extent to which the architecture of multispecies networks shape coevolutionary outcomes, and the processes involved.

  10. Metschnikowia Species Share a Pool of Diverse rRNA Genes Differing in Regions That Determine Hairpin-Loop Structures and Evolve by Reticulation.

    Directory of Open Access Journals (Sweden)

    Matthias Sipiczki

    Full Text Available Modern taxonomy of yeasts is mainly based on phylogenetic analysis of conserved DNA and protein sequences. By far the most frequently used sequences are those of the repeats of the chromosomal rDNA array. It is generally accepted that the rDNA repeats of a genome have identical sequences due to the phenomenon of sequence homogenisation and can thus be used for identification and barcoding of species. Here we show that the rDNA arrays of the type strains of Metschnikowia andauensis and M. fructicola are not homogenised. Both have arrays consisting of diverse repeats that differ from each other in the D1/D2 domains by up to 18 and 25 substitutions. The variable sites are concentrated in two regions that correspond to back-folding stretches of hairpin loops in the predicted secondary structure of the RNA molecules. The substitutions do not alter significantly the overall hairpin-loop structure due to wobble base pairing at sites of C-T transitions and compensatory mutations in the complementary strand of the hairpin stem. The phylogenetic and network analyses of the cloned sequences revealed that the repeats had not evolved in a vertical tree-like way but reticulation might have shaped the rDNA arrays of both strains. The neighbour-net analysis of all cloned sequences of the type strains and the database sequences of different strains further showed that these species share a continuous pool of diverse repeats that appear to evolve by reticulate evolution.

  11. MHC class I genes in a New World primate, the cotton-top tamarin (Saguinus oedipus), have evolved by an active process of loci turnover.

    Science.gov (United States)

    Cadavid, L F; Mejía, B E; Watkins, D I

    1999-03-01

    Lymphocytes of a New World primate, the cotton-top tamarin (Saguinus oedipus), express classical G-related major histocompatibility complex (MHC) class I molecules with unusually limited polymorphism and variability. Three G-related loci, an F locus, an E locus, and two pseudogenes (So-N1 and So-N3) have been identified by cDNA library screening and extensive PCR analysis of both cDNA and genomic DNA from the cotton-top tamarin. Furthermore, each genus of the subfamily Callitrichinae (tamarins and marmosets) appears to express its own unique set of MHC class I genes, likely due to a rapid turnover of loci. The rapid emergence of unique MHC class I genes in the Callitrichinae genera, resulting from an active process of duplication and inactivation of loci, may account for the limited diversity of the MHC class I genes in the cotton-top tamarin. To determine the nature of the entire complement of MHC class I genes in the cotton-top tamarin, we synthesized a genomic DNA library and screened it with MHC class I-specific probes. We isolated nine new MHC class I pseudogenes from this library. These newly isolated tamarin G-related MHC class I pseudogenes are not closely related to any of their functional counterparts in the tamarin, suggesting that they do not share a recent common ancestral gene with the tamarin's currently expressed MHC class I loci. In addition, these tamarin sequences display a high rate of nonsynonymous substitutions in their putative peptide binding region. This indicates that the genes from which they have derived were likely subject to positive selection and, therefore, were once functional. Our data support the notion that an extremely high rate of loci turnover is largely responsible for the limited diversity of the MHC class I genes in the cotton-top tamarin.

  12. De novo transcriptome assembly facilitates characterisation of fast-evolving gene families, MHC class I in the bank vole (Myodes glareolus).

    Science.gov (United States)

    Migalska, M; Sebastian, A; Konczal, M; Kotlík, P; Radwan, J

    2017-04-01

    The major histocompatibility complex (MHC) plays a central role in the adaptive immune response and is the most polymorphic gene family in vertebrates. Although high-throughput sequencing has increasingly been used for genotyping families of co-amplifying MHC genes, its potential to facilitate early steps in the characterisation of MHC variation in nonmodel organism has not been fully explored. In this study we evaluated the usefulness of de novo transcriptome assembly in characterisation of MHC sequence diversity. We found that although de novo transcriptome assembly of MHC I genes does not reconstruct sequences of individual alleles, it does allow the identification of conserved regions for PCR primer design. Using the newly designed primers, we characterised MHC I sequences in the bank vole. Phylogenetic analysis of the partial MHC I coding sequence (2-4 exons) of the bank vole revealed a lack of orthology to MHC I of other Cricetidae, consistent with the high gene turnover of this region. The diversity of expressed alleles was characterised using ultra-deep sequencing of the third exon that codes for the peptide-binding region of the MHC molecule. High allelic diversity was demonstrated, with 72 alleles found in 29 individuals. Interindividual variation in the number of expressed loci was found, with the number of alleles per individual ranging from 5 to 14. Strong signatures of positive selection were found for 8 amino acid sites, most of which are inferred to bind antigens in human MHC, indicating conservation of structure despite rapid sequence evolution.

  13. Regulation of ascorbate biosynthesis in green algae has evolved to enable rapid stress-induced response via the VTC2 gene encoding GDP-l-galactose phosphorylase.

    Science.gov (United States)

    Vidal-Meireles, André; Neupert, Juliane; Zsigmond, Laura; Rosado-Souza, Laise; Kovács, László; Nagy, Valéria; Galambos, Anikó; Fernie, Alisdair R; Bock, Ralph; Tóth, Szilvia Z

    2017-04-01

    Ascorbate (vitamin C) plays essential roles in stress resistance, development, signaling, hormone biosynthesis and regulation of gene expression; however, little is known about its biosynthesis in algae. In order to provide experimental proof for the operation of the Smirnoff-Wheeler pathway described for higher plants and to gain more information on the regulation of ascorbate biosynthesis in Chlamydomonas reinhardtii, we targeted the VTC2 gene encoding GDP-l-galactose phosphorylase using artificial microRNAs. Ascorbate concentrations in VTC2 amiRNA lines were reduced to 10% showing that GDP-l-galactose phosphorylase plays a pivotal role in ascorbate biosynthesis. The VTC2 amiRNA lines also grow more slowly, have lower chlorophyll content, and are more susceptible to stress than the control strains. We also demonstrate that: expression of the VTC2 gene is rapidly induced by H2 O2 and (1) O2 resulting in a manifold increase in ascorbate content; in contrast to plants, there is no circadian regulation of ascorbate biosynthesis; photosynthesis is not required per se for ascorbate biosynthesis; and Chlamydomonas VTC2 lacks negative feedback regulation by ascorbate in the physiological concentration range. Our work demonstrates that ascorbate biosynthesis is also highly regulated in Chlamydomonas albeit via mechanisms distinct from those previously described in land plants.

  14. Methods Evolved by Observation

    Science.gov (United States)

    Montessori, Maria

    2016-01-01

    Montessori's idea of the child's nature and the teacher's perceptiveness begins with amazing simplicity, and when she speaks of "methods evolved," she is unveiling a methodological system for observation. She begins with the early childhood explosion into writing, which is a familiar child phenomenon that Montessori has written about…

  15. No evidence for faster male hybrid sterility in population crosses of an intertidal copepod (Tigriopus californicus).

    Science.gov (United States)

    Willett, Christopher S

    2008-06-01

    Two different forces are thought to contribute to the rapid accumulation of hybrid male sterility that has been observed in many inter-specific crosses, namely the faster male and the dominance theories. For male heterogametic taxa, both faster male and dominance would work in the same direction to cause the rapid evolution of male sterility; however, for taxa lacking differentiated sex chromosomes only the faster male theory would explain the rapid evolution of male hybrid sterility. It is currently unknown what causes the faster evolution of male sterility, but increased sexual selection on males and the sensitivity of genes involved in male reproduction are two hypotheses that could explain the observation. Here, patterns of hybrid sterility in crosses of genetically divergent copepod populations are examined to test potential mechanisms of faster male evolution. The study species, Tigriopus californicus, lacks differentiated, hemizygous sex chromosomes and appears to have low levels of divergence caused by sexual selection acting upon males. Hybrid sterility does not accumulate more rapidly in males than females in these crosses suggesting that in this taxon male reproductive genes are not inherently more prone to disruption in hybrids.

  16. Rapid evolution of antimicrobial peptide genes in an insect host-social parasite system.

    Science.gov (United States)

    Erler, Silvio; Lhomme, Patrick; Rasmont, Pierre; Lattorff, H Michael G

    2014-04-01

    Selection, as a major driver for evolution in host-parasite interactions, may act on two levels; the virulence of the pathogen, and the hosts' defence system. Effectors of the host defence system might evolve faster than other genes e.g. those involved in adaptation to changes in life history or environmental fluctuations. Host-parasite interactions at the level of hosts and their specific social parasites, present a special setting for evolutionarily driven selection, as both share the same environmental conditions and pathogen pressures. Here, we study the evolution of antimicrobial peptide (AMP) genes, in six host bumblebee and their socially parasitic cuckoo bumblebee species. The selected AMP genes evolved much faster than non-immune genes, but only defensin-1 showed significant differences between host and social parasite. Nucleotide diversity and codon-by-codon analyses confirmed that purifying selection is the main selective force acting on bumblebee defence genes.

  17. Improved Evolvability in Genetic Programming with Polyandry

    Directory of Open Access Journals (Sweden)

    Anisa Waganda Ragalo

    2013-12-01

    Full Text Available This paper proposes Polyandry, a new nature-inspired modification to canonical Genetic Programming (GP. Polyandry aims to improve evolvability in GP. Evolvability is a critically important GP trait, the maintenance of which determines the arrival of the GP at the global optimum solution. Specifically evolvability is defined as the ability of the genetic operators employed in GP to produce offspring that are fitter than their parents. When GP fails to exhibit evolvability, further adaptation of the GP individuals towards the global optimum solution becomes impossible. Polyandry improves evolvability by improving the typically disruptive standard GP crossover operator. The algorithm employs a dual strategy towards this goal. The chief part of this strategy is an incorporation of genetic material from multiple mating partners into broods of offspring. Given such a brood, the offspring in the brood then compete according to a culling function, which we make equivalent to the main GP fitness function. Polyandry’s incorporation of genetic material from multiple GP individuals into broods of offspring represents a more aggressive search for building block information. This characteristic of the algorithm leads to an advanced explorative capability in both GP structural space and fitness space. The second component of the Polyandry strategy is an attempt at multiple crossover points, in order to find crossover points that minimize building block disruption from parents to offspring. This strategy is employed by a similar algorithm, Brood Recombination. We conduct experiments to compare Polyandry with the canonical GP. Our experiments demonstrate that Polyandry consistently exhibits better evolvability than the canonical GP. As a consequence, Polyandry achieves higher success rates and finds solutions faster than the latter. The result of these observations is that given certain brood size settings, Polyandry requires less computational effort to

  18. The impact of AAV capsid-specific T cell responses on design and outcome of clinical gene transfer trials with recombinant AAV vectors - an evolving controversy.

    Science.gov (United States)

    Ertl, Hildegund Cj; High, Katherine A

    2017-01-02

    Recombinant adenovirus-associated (rAAV) vectors due to their ease of construction, wide tissue tropism and lack of pathogenicity remain at the forefront for long-term gene replacement therapy. In spite of very encouraging pre-clinical results, clinical trials were initially unsuccessful; expression of the rAAV vector-delivered therapeutic protein was transient. Loss of expression was linked to an expansion of AAV capsid-specific T cell responses, leading to the hypothesis that rAAV vectors recall pre-existing memory T cells that had been induced by natural infections with AAV together with a helper virus. Although this was hotly debated at first, AAV capsid-specific T cell responses were observed in several gene transfer trials that used high doses of rAAV vectors. Subsequent trials designed to circumvent these T cell responses through the use of immunosuppressive drugs, rAAV vectors based on rare serotypes or modified to allow for therapeutic levels of the transgene product at low, non-immunogenic vector doses are now successful in correcting debilitating diseases.

  19. Colder environments did not select for a faster metabolism during experimental evolution of Drosophila melanogaster.

    Science.gov (United States)

    Alton, Lesley A; Condon, Catriona; White, Craig R; Angilletta, Michael J

    2017-01-01

    The effect of temperature on the evolution of metabolism has been the subject of debate for a century; however, no consistent patterns have emerged from comparisons of metabolic rate within and among species living at different temperatures. We used experimental evolution to determine how metabolism evolves in populations of Drosophila melanogaster exposed to one of three selective treatments: a constant 16°C, a constant 25°C, or temporal fluctuations between 16 and 25°C. We tested August Krogh's controversial hypothesis that colder environments select for a faster metabolism. Given that colder environments also experience greater seasonality, we also tested the hypothesis that temporal variation in temperature may be the factor that selects for a faster metabolism. We measured the metabolic rate of flies from each selective treatment at 16, 20.5, and 25°C. Although metabolism was faster at higher temperatures, flies from the selective treatments had similar metabolic rates at each measurement temperature. Based on variation among genotypes within populations, heritable variation in metabolism was likely sufficient for adaptation to occur. We conclude that colder or seasonal environments do not necessarily select for a faster metabolism. Rather, other factors besides temperature likely contribute to patterns of metabolic rate over thermal clines in nature. © 2016 The Author(s). Evolution © 2016 The Society for the Study of Evolution.

  20. EVOLVE 2014 International Conference

    CERN Document Server

    Tantar, Emilia; Sun, Jian-Qiao; Zhang, Wei; Ding, Qian; Schütze, Oliver; Emmerich, Michael; Legrand, Pierrick; Moral, Pierre; Coello, Carlos

    2014-01-01

    This volume encloses research articles that were presented at the EVOLVE 2014 International Conference in Beijing, China, July 1–4, 2014.The book gathers contributions that emerged from the conference tracks, ranging from probability to set oriented numerics and evolutionary computation; all complemented by the bridging purpose of the conference, e.g. Complex Networks and Landscape Analysis, or by the more application oriented perspective. The novelty of the volume, when considering the EVOLVE series, comes from targeting also the practitioner’s view. This is supported by the Machine Learning Applied to Networks and Practical Aspects of Evolutionary Algorithms tracks, providing surveys on new application areas, as in the networking area and useful insights in the development of evolutionary techniques, from a practitioner’s perspective. Complementary to these directions, the conference tracks supporting the volume, follow on the individual advancements of the subareas constituting the scope of the confe...

  1. Evolvable Neural Software System

    Science.gov (United States)

    Curtis, Steven A.

    2009-01-01

    The Evolvable Neural Software System (ENSS) is composed of sets of Neural Basis Functions (NBFs), which can be totally autonomously created and removed according to the changing needs and requirements of the software system. The resulting structure is both hierarchical and self-similar in that a given set of NBFs may have a ruler NBF, which in turn communicates with other sets of NBFs. These sets of NBFs may function as nodes to a ruler node, which are also NBF constructs. In this manner, the synthetic neural system can exhibit the complexity, three-dimensional connectivity, and adaptability of biological neural systems. An added advantage of ENSS over a natural neural system is its ability to modify its core genetic code in response to environmental changes as reflected in needs and requirements. The neural system is fully adaptive and evolvable and is trainable before release. It continues to rewire itself while on the job. The NBF is a unique, bilevel intelligence neural system composed of a higher-level heuristic neural system (HNS) and a lower-level, autonomic neural system (ANS). Taken together, the HNS and the ANS give each NBF the complete capabilities of a biological neural system to match sensory inputs to actions. Another feature of the NBF is the Evolvable Neural Interface (ENI), which links the HNS and ANS. The ENI solves the interface problem between these two systems by actively adapting and evolving from a primitive initial state (a Neural Thread) to a complicated, operational ENI and successfully adapting to a training sequence of sensory input. This simulates the adaptation of a biological neural system in a developmental phase. Within the greater multi-NBF and multi-node ENSS, self-similar ENI s provide the basis for inter-NBF and inter-node connectivity.

  2. Conserved regulation of p53 network dosage by microRNA-125b occurs through evolving miRNA-target gene pairs.

    Directory of Open Access Journals (Sweden)

    Minh T N Le

    2011-09-01

    Full Text Available MicroRNAs regulate networks of genes to orchestrate cellular functions. MiR-125b, the vertebrate homologue of the Caenorhabditis elegans microRNA lin-4, has been implicated in the regulation of neural and hematopoietic stem cell homeostasis, analogous to how lin-4 regulates stem cells in C. elegans. Depending on the cell context, miR-125b has been proposed to regulate both apoptosis and proliferation. Because the p53 network is a central regulator of both apoptosis and proliferation, the dual roles of miR-125b raise the question of what genes in the p53 network might be regulated by miR-125b. By using a gain- and loss-of-function screen for miR-125b targets in humans, mice, and zebrafish and by validating these targets with the luciferase assay and a novel miRNA pull-down assay, we demonstrate that miR-125b directly represses 20 novel targets in the p53 network. These targets include both apoptosis regulators like Bak1, Igfbp3, Itch, Puma, Prkra, Tp53inp1, Tp53, Zac1, and also cell-cycle regulators like cyclin C, Cdc25c, Cdkn2c, Edn1, Ppp1ca, Sel1l, in the p53 network. We found that, although each miRNA-target pair was seldom conserved, miR-125b regulation of the p53 pathway is conserved at the network level. Our results lead us to propose that miR-125b buffers and fine-tunes p53 network activity by regulating the dose of both proliferative and apoptotic regulators, with implications for tissue stem cell homeostasis and oncogenesis.

  3. A case study for effects of operational taxonomic units from intracellular endoparasites and ciliates on the eukaryotic phylogeny: phylogenetic position of the haptophyta in analyses of multiple slowly evolving genes.

    Directory of Open Access Journals (Sweden)

    Hisayoshi Nozaki

    Full Text Available Recent multigene phylogenetic analyses have contributed much to our understanding of eukaryotic phylogeny. However, the phylogenetic positions of various lineages within the eukaryotes have remained unresolved or in conflict between different phylogenetic studies. These phylogenetic ambiguities might have resulted from mixtures or integration from various factors including limited taxon sampling, missing data in the alignment, saturations of rapidly evolving genes, mixed analyses of short- and long-branched operational taxonomic units (OTUs, intracellular endoparasite and ciliate OTUs with unusual substitution etc. In order to evaluate the effects from intracellular endoparasite and ciliate OTUs co-analyzed on the eukaryotic phylogeny and simplify the results, we here used two different sets of data matrices of multiple slowly evolving genes with small amounts of missing data and examined the phylogenetic position of the secondary photosynthetic chromalveolates Haptophyta, one of the most abundant groups of oceanic phytoplankton and significant primary producers. In both sets, a robust sister relationship between Haptophyta and SAR (stramenopiles, alveolates, rhizarians, or SA [stramenopiles and alveolates] was resolved when intracellular endoparasite/ciliate OTUs were excluded, but not in their presence. Based on comparisons of character optimizations on a fixed tree (with a clade composed of haptophytes and SAR or SA, disruption of the monophyly between haptophytes and SAR (or SA in the presence of intracellular endoparasite/ciliate OTUs can be considered to be a result of multiple evolutionary reversals of character positions that supported the synapomorphy of the haptophyte and SAR (or SA clade in the absence of intracellular endoparasite/ciliate OTUs.

  4. Measurably evolving populations

    DEFF Research Database (Denmark)

    Drummond, Alexei James; Pybus, Oliver George; Rambaut, Andrew

    2003-01-01

    processes through time. Populations for which such studies are possible � measurably evolving populations (MEPs) � are characterized by sufficiently long or numerous sampled sequences and a fast mutation rate relative to the available range of sequence sampling times. The impact of sequences sampled through...... time has been most apparent in the disciplines of RNA viral evolution and ancient DNA, where they enable us to estimate divergence times without paleontological calibrations, and to analyze temporal changes in population size, population structure and substitution rates. Thus, MEPs could increase our...

  5. Evolving XSLT stylesheets

    CERN Document Server

    Zorzano, Nestor; Laredo, J L J; Sevilla, J P; Garcia, Pablo; Merelo, J J

    2007-01-01

    This paper introduces a procedure based on genetic programming to evolve XSLT programs (usually called stylesheets or logicsheets). XSLT is a general purpose, document-oriented functional language, generally used to transform XML documents (or, in general, solve any problem that can be coded as an XML document). The proposed solution uses a tree representation for the stylesheets as well as diverse specific operators in order to obtain, in the studied cases and a reasonable time, a XSLT stylesheet that performs the transformation. Several types of representation have been compared, resulting in different performance and degree of success.

  6. Induction of deletion mutation onompR gene ofSalmonella enterica serovar Typhi isolates from asymptomatic typhoid carriers to evolve attenuated strains for vaccine development

    Institute of Scientific and Technical Information of China (English)

    Senthilkumar B; Anbarasu K; Senbagam D; Rajasekarapandian M

    2014-01-01

    Objective:To develop attenuated strains ofSalmonella enterica serovar Typhi(S. typhi) for the candidate vaccine by osmolar stress.Methods:S. typhiSS3 andSS5 strains were isolated from asymptomatic typhoid carriers inNamakkal,TamilNadu,India.Both strains were grown inLB (LuriaBertani) medium supplemented with various concentration ofNaCl(0.1-0.7M) respectively. The effect of osmolar stress was determined at molecular level byPCR usingMGR06 andMGR 07 primers corresponding to ompR with chromosomalDNA of S. typhiSS3 andSS5 strains. Attenuation by osmolar stress results in deletion mutation of theS. typhi strains was determined by agglutination assays, precipitation method,SDSPAGE analysis and by animal models. Results:The799 bp amplifiedompRgene product from wild typeS. typhiSS3 andSS5 illustrate the presence of virulent gene.Interestingly, there was only a282 bp amplified product fromS. typhiSS3 andSS5 grown in the presence of0.5,0.6 and0.7MNaCl.This illustrates the occurrence of deletion mutation inompRgene at high concentration ofNaCl.Furthermore, both the wild-type and mutantS. typhi outer membraneSDS-PAGE profile reveals the differences in the expression ofompF,ompC andompA proteins.In mice, wild type and mutant strains lethal dose (LD50) were determined.The mice died within72 h when both the wild type strains were injected intraperitoneally with3 logCFU.mL-1.When the mice were injected with the mutants in same dosage, no clinical symptoms were observed; whereas the serum antibody titre was elicited within two weeks indicated that the mutants have the ability to induce protective humoral immune response.These results suggest thatS. typhiSS3 andSS5 may be used as good candidate strains for the development of live attenuated vaccine against salmonellosis.Conclusions:This study demonstrates that theS. typhistrains were attenuated and could be good vaccine candidates in future.

  7. Faster-than-Light Particles: A Review of Tachyon Characteristics.

    Science.gov (United States)

    1980-10-01

    A-DlAO9(4 529 RAND CORP SANTA MNtICA CA F/6 20/S FASTER-THAN-LIBI4T PARTICLES: A REVIEW OF TACHYON CHARACTERISTIC--ETCWU) OCT B0 E A PUSCHER F49620...77-C-0023 UNCLASSIFIED RAI0IN-1530-AF N. I nmui ininmuuuI LEVEL A RAND NOTE FASTER-THAN-LIGHT PARTICLES: A REVIEW OF ) ( TACHYON CHARACTERISTICS Edward...RECIPIENT’S CATALOG NUMBER 4TIT LE ( d Subtitle) TYPE OF REPORT & PERIOD COVERED ( Faster-than-Light Particles: A Review of /Interim -i Tachyon

  8. Positive selection at reproductive ADAM genes with potential intercellular binding activity.

    Science.gov (United States)

    Glassey, Barb; Civetta, Alberto

    2004-05-01

    Many genes with a role in reproduction, including those implicated in fertilization and spermatogenesis, have been shown to evolve at a faster rate relative to genes associated with other functions and tissues. These survey studies usually group a wide variety of genes with different characteristics and evolutionary histories as reproductive genes based on their site of expression or function. We have examined the molecular evolution of the ADAM (a disintegrin and metalloprotease) gene family, a structurally and functionally diverse group of genes expressed in reproductive and somatic tissue to test whether a variety of protein characteristics such as phylogenetic clusters, tissue of expression, and proteolytic and adhesive function can group fast evolving ADAM genes. We found that all genes were evolving under purifying selection (d(N)/d(S) < 1), although reproductive ADAMs, including those implicated in fertilization and spermatogenesis, evolved at the fastest rate. Genes with a role in binding to cell receptors in endogenous tissue appear to be evolving under purifying selection, regardless of the tissue of expression. In contrast, positive selection of codon sites in the disintegrin/cysteine-rich adhesion domains was detected exclusively in ADAMs 2 and 32, two genes expressed in the testis with a potential role in sperm-egg adhesion. Positive selection was detected in the transmembrane/cytosolic tail region of ADAM genes expressed in a variety of tissues.

  9. Cortex Matures Faster in Youths With Highest IQ

    Science.gov (United States)

    ... Current Issue Past Issues Research News From NIH Cortex Matures Faster in Youths With Highest IQ Past ... scans showed that their brains' outer mantle, or cortex, thickens more rapidly during childhood, reaching its peak ...

  10. Evolving Procurement Organizations

    DEFF Research Database (Denmark)

    Bals, Lydia; Laine, Jari; Mugurusi, Godfrey

    Procurement has to find further levers and advance its contribution to corporate goals continuously. This places pressure on its organization in order to facilitate its performance. Therefore, procurement organizations constantly have to evolve in order to match these demands. A conceptual model...... putting the structural elements in focus is derived from the analysis of two case companies, which extends the existing literature and opens new avenues for future research. The findings highlight the importance of taking a contingency perspective on procurement organization, understanding the internal...... and external contingency factors and having a more detailed look at the structural dimensions chosen, beyond the well-known characteristics of centralization, formalization, participation, specialization, standardization and size. From a theoretical perspective, it opens up insights that can be leveraged...

  11. FTEC: a coalescent simulator for modeling faster than exponential growth

    OpenAIRE

    Reppell, Mark; Boehnke, Michael; Zöllner, Sebastian

    2012-01-01

    Summary: Recent genetic studies as well as recorded history point to massive growth in human population sizes during the recent past. To model and understand this growth accurately we introduce FTEC, an easy-to-use coalescent simulation program capable of simulating haplotype samples drawn from a population that has undergone faster than exponential growth. Samples drawn from a population that has undergone faster than exponential growth show an excess of very rare variation and more rapid LD...

  12. Quantifying evolvability in small biological networks

    Energy Technology Data Exchange (ETDEWEB)

    Nemenman, Ilya [Los Alamos National Laboratory; Mugler, Andrew [COLUMBIA UNIV; Ziv, Etay [COLUMBIA UNIV; Wiggins, Chris H [COLUMBIA UNIV

    2008-01-01

    The authors introduce a quantitative measure of the capacity of a small biological network to evolve. The measure is applied to a stochastic description of the experimental setup of Guet et al. (Science 2002, 296, pp. 1466), treating chemical inducers as functional inputs to biochemical networks and the expression of a reporter gene as the functional output. The authors take an information-theoretic approach, allowing the system to set parameters that optimise signal processing ability, thus enumerating each network's highest-fidelity functions. All networks studied are highly evolvable by the measure, meaning that change in function has little dependence on change in parameters. Moreover, each network's functions are connected by paths in the parameter space along which information is not significantly lowered, meaning a network may continuously change its functionality without completely losing it along the way. This property further underscores the evolvability of the networks.

  13. A slowly evolving host moves first in symbiotic interactions

    Science.gov (United States)

    Damore, James; Gore, Jeff

    2011-03-01

    Symbiotic relationships, both parasitic and mutualistic, are ubiquitous in nature. Understanding how these symbioses evolve, from bacteria and their phages to humans and our gut microflora, is crucial in understanding how life operates. Often, symbioses consist of a slowly evolving host species with each host only interacting with its own sub-population of symbionts. The Red Queen hypothesis describes coevolutionary relationships as constant arms races with each species rushing to evolve an advantage over the other, suggesting that faster evolution is favored. Here, we use a simple game theoretic model of host- symbiont coevolution that includes population structure to show that if the symbionts evolve much faster than the host, the equilibrium distribution is the same as it would be if it were a sequential game where the host moves first against its symbionts. For the slowly evolving host, this will prove to be advantageous in mutualisms and a handicap in antagonisms. The model allows for symbiont adaptation to its host, a result that is robust to changes in the parameters and generalizes to continuous and multiplayer games. Our findings provide insight into a wide range of symbiotic phenomena and help to unify the field of coevolutionary theory.

  14. Rapidly Evolving Giant Dermatofibroma

    Directory of Open Access Journals (Sweden)

    K. J. Lang

    2010-01-01

    Full Text Available Dermatofibroma, also known as “fibrous histiocytoma”, is a benign dermal or subcutaneous poorly circumscribed proliferation of spindle-shaped fibroblasts and macrophages in the dermis. Although it is commonly present as a brownish nodule the legs of females, it may also arise on the upper extremities, trunk, and rarely on the head. The exact pathogenesis is unclear. However, it is widely believed that the originating insult to the dermis is a folliculitis, an arthropod bite, or an unspecified initial inflammatory condition. Giant dermatofibromas of greater than 5 cm in diameter are rare, with only 22 cases reported in the literature. We present a case of a rapidly evolving pedunculated mass in the groin of a male patient. Histological examination confirmed this to be a giant dermatofibroma. Though this specimen cannot is not confirmed as such, the cellular subtype is sometimes present as a larger lesion with anecdotal reports of local recurrence and distant metastases. The clinical and radiological features which were somewhat suspicious of malignancy are considered in the context of the definitive pathological diagnosis of a benign lesion.

  15. Communicability across evolving networks.

    Science.gov (United States)

    Grindrod, Peter; Parsons, Mark C; Higham, Desmond J; Estrada, Ernesto

    2011-04-01

    Many natural and technological applications generate time-ordered sequences of networks, defined over a fixed set of nodes; for example, time-stamped information about "who phoned who" or "who came into contact with who" arise naturally in studies of communication and the spread of disease. Concepts and algorithms for static networks do not immediately carry through to this dynamic setting. For example, suppose A and B interact in the morning, and then B and C interact in the afternoon. Information, or disease, may then pass from A to C, but not vice versa. This subtlety is lost if we simply summarize using the daily aggregate network given by the chain A-B-C. However, using a natural definition of a walk on an evolving network, we show that classic centrality measures from the static setting can be extended in a computationally convenient manner. In particular, communicability indices can be computed to summarize the ability of each node to broadcast and receive information. The computations involve basic operations in linear algebra, and the asymmetry caused by time's arrow is captured naturally through the noncommutativity of matrix-matrix multiplication. Illustrative examples are given for both synthetic and real-world communication data sets. We also discuss the use of the new centrality measures for real-time monitoring and prediction.

  16. Evolving a photosynthetic organelle

    Directory of Open Access Journals (Sweden)

    Nakayama Takuro

    2012-04-01

    Full Text Available Abstract The evolution of plastids from cyanobacteria is believed to represent a singularity in the history of life. The enigmatic amoeba Paulinella and its 'recently' acquired photosynthetic inclusions provide a fascinating system through which to gain fresh insight into how endosymbionts become organelles. The plastids, or chloroplasts, of algae and plants evolved from cyanobacteria by endosymbiosis. This landmark event conferred on eukaryotes the benefits of photosynthesis - the conversion of solar energy into chemical energy - and in so doing had a huge impact on the course of evolution and the climate of Earth 1. From the present state of plastids, however, it is difficult to trace the evolutionary steps involved in this momentous development, because all modern-day plastids have fully integrated into their hosts. Paulinella chromatophora is a unicellular eukaryote that bears photosynthetic entities called chromatophores that are derived from cyanobacteria and has thus received much attention as a possible example of an organism in the early stages of organellogenesis. Recent studies have unlocked the genomic secrets of its chromatophore 23 and provided concrete evidence that the Paulinella chromatophore is a bona fide photosynthetic organelle 4. The question is how Paulinella can help us to understand the process by which an endosymbiont is converted into an organelle.

  17. Evolving paradigms in pharmacovigilance.

    Science.gov (United States)

    Brewster, Wendy; Gibbs, Trevor; Lacroix, Karol; Murray, Alison; Tydeman, Michael; Almenoff, June

    2006-05-01

    All medicines have adverse effects as well as benefits. The aim of pharmacovigilance is to protect public health by monitoring medicines to identify and evaluate issues and ensure that the overall benefits outweigh the potential risks. The tools and processes used in pharmacovigilance are continually evolving. Increasingly sophisticated tools are being designed to evaluate safety data from clinical trials to enhance the likelihood of detecting safety signals ahead of product registration. Methods include integration of safety data throughout development, meta-analytical techniques, quantitative and qualitative methods for evaluation of adverse event data and graphical tools to explore laboratory and biometric data. Electronic data capture facilitates monitoring of ongoing studies so that it is possible to promptly identify potential issues and manage patient safety. In addition, GSK employs a number of proactive methods for post-marketing signal detection and knowledge management using state-of-the-art statistical and analytical tools. Using these tools, together with safety data collected through pharmacoepidemiologic studies, literature and spontaneous reporting, potential adverse drug reactions can be better identified in marketed products. In summary, the information outlined in this paper provides a valuable benchmark for risk management and pharmacovigilance in pharmaceutical development.

  18. A faster switching regime for zenithal bistable nematic displays

    Energy Technology Data Exchange (ETDEWEB)

    Rudin, J

    1997-12-01

    A simpler and faster switching regime for Zenithal Bistable Nematic displays is reported. A cell, based on homeotropic alignment of nematic liquid crystal over a continuous blazed monograting on one surface, can be switched using bipolar pulses an order of magnitude faster than monopolar pulses of the same voltage. We propose that this regime relies on simple dielectric coupling to drive the cell into a higher energy state with a long pulse time, and the relaxation into a lower energy state after the creation of surface defects from a shorter applied pulse. Although flexoelectric effects are observed, they do not form the basis of state selection as was proposed for the monopolar pulses

  19. Apparent faster than light propagation from light sterile neutrinos

    CERN Document Server

    Hannestad, Steen

    2011-01-01

    Recent data from the OPERA experiment seem to point to neutrinos propagating faster than light. One possible physics explanation for such a result is the existence of light sterile neutrinos which can propagate in a higher dimensional bulk and achieve apparent superluminal velocities when measured by an observer confined to the 4D brane of the standard model. Such a model has the advantage of easily being able to explain the non-observation of superluminal neutrinos from SN1987A. Here we discuss the phenomenological implications of such a model and show that it can provide an explanation for the observed faster than light propagation of neutrinos.

  20. Secure and Faster Clustering Environment for Advanced Image Compression

    Directory of Open Access Journals (Sweden)

    D.Kesavaraja

    2010-11-01

    Full Text Available Cloud computing provides ample opportunity in many areas such as fastest image transmission, secure and efficient imaging as a service. In general users needs faster and secure service. Usually Image Compression Algorithms are not working faster. In spite of several ongoing researches, Conventional Compression and its Algorithms might not be able to run faster. So, we perform comparative study of three image compression algorithm and their variety of features and factors to choose best among them for cluster processing. After choosing a best one it can be applied for a cluster computing environment to run parallel image compression for faster processing. This paper is the real time implementation of a Distributed Image Compression in Clustering of Nodes. In cluster computing, security is also more important factor. So, we propose a Distributed Intrusion Detection System to monitors all the nodes in cluster . If an intrusion occur in node processing then take an prevention step based on RIC (Robust Intrusion Control Method. We demonstrate the effectiveness and feasibility of our method on a set of satellite images for defense forces. The efficiency ratio of this computation process is 91.20.

  1. New analytical approaches for faster or greener phytochemical analyses

    NARCIS (Netherlands)

    Shen, Y.

    2015-01-01

    Summary Chapter 1 provides a short introduction into the constraints of phytochemical analysis. In order to make them faster, less laborious and greener, there is a clear scope for miniaturized and simplified sample preparation, solvent-free extractions and the use

  2. New analytical approaches for faster or greener phytochemical analyses

    NARCIS (Netherlands)

    Shen, Y.

    2015-01-01

    Summary Chapter 1 provides a short introduction into the constraints of phytochemical analysis. In order to make them faster, less laborious and greener, there is a clear scope for miniaturized and simplified sample preparation, solvent-free extractions and the use

  3. Angular Momentum Transport via Internal Gravity Waves in Evolving Stars

    CERN Document Server

    Fuller, Jim; Cantiello, Matteo; Brown, Ben

    2014-01-01

    Recent asteroseismic advances have allowed for direct measurements of the internal rotation rates of many sub-giant and red giant stars. Unlike the nearly rigidly rotating Sun, these evolved stars contain radiative cores that spin faster than their overlying convective envelopes, but slower than they would in the absence of internal angular momentum transport. We investigate the role of internal gravity waves in angular momentum transport in evolving low mass stars. In agreement with previous results, we find that convectively excited gravity waves can prevent the development of strong differential rotation in the radiative cores of Sun-like stars. As stars evolve into sub-giants, however, low frequency gravity waves become strongly attenuated and cannot propagate below the hydrogen burning shell, allowing the spin of the core to decouple from the convective envelope. This decoupling occurs at the base of the sub-giant branch when stars have surface temperatures of roughly 5500 K. However, gravity waves can s...

  4. Toward an Evolved Concept of Landrace.

    Science.gov (United States)

    Casañas, Francesc; Simó, Joan; Casals, Joan; Prohens, Jaime

    2017-01-01

    The term "landrace" has generally been defined as a cultivated, genetically heterogeneous variety that has evolved in a certain ecogeographical area and is therefore adapted to the edaphic and climatic conditions and to its traditional management and uses. Despite being considered by many to be inalterable, landraces have been and are in a constant state of evolution as a result of natural and artificial selection. Many landraces have disappeared from cultivation but are preserved in gene banks. Using modern selection and breeding technology tools to shape these preserved landraces together with the ones that are still cultivated is a further step in their evolution in order to preserve their agricultural significance. Adapting historical landraces to present agricultural conditions using cutting-edge breeding technology represents a challenging opportunity to use them in a modern sustainable agriculture, as an immediate return on the investment is highly unlikely. Consequently, we propose a more inclusive definition of landraces, namely that they consist of cultivated varieties that have evolved and may continue evolving, using conventional or modern breeding techniques, in traditional or new agricultural environments within a defined ecogeographical area and under the influence of the local human culture. This includes adaptation of landraces to new management systems and the unconscious or conscious selection made by farmers or breeders using available technology. In this respect, a mixed selection system might be established in which farmers and other social agents develop evolved landraces from the variability generated by public entities.

  5. canEvolve: a web portal for integrative oncogenomics.

    Directory of Open Access Journals (Sweden)

    Mehmet Kemal Samur

    Full Text Available BACKGROUND & OBJECTIVE: Genome-wide profiles of tumors obtained using functional genomics platforms are being deposited to the public repositories at an astronomical scale, as a result of focused efforts by individual laboratories and large projects such as the Cancer Genome Atlas (TCGA and the International Cancer Genome Consortium. Consequently, there is an urgent need for reliable tools that integrate and interpret these data in light of current knowledge and disseminate results to biomedical researchers in a user-friendly manner. We have built the canEvolve web portal to meet this need. RESULTS: canEvolve query functionalities are designed to fulfill most frequent analysis needs of cancer researchers with a view to generate novel hypotheses. canEvolve stores gene, microRNA (miRNA and protein expression profiles, copy number alterations for multiple cancer types, and protein-protein interaction information. canEvolve allows querying of results of primary analysis, integrative analysis and network analysis of oncogenomics data. The querying for primary analysis includes differential gene and miRNA expression as well as changes in gene copy number measured with SNP microarrays. canEvolve provides results of integrative analysis of gene expression profiles with copy number alterations and with miRNA profiles as well as generalized integrative analysis using gene set enrichment analysis. The network analysis capability includes storage and visualization of gene co-expression, inferred gene regulatory networks and protein-protein interaction information. Finally, canEvolve provides correlations between gene expression and clinical outcomes in terms of univariate survival analysis. CONCLUSION: At present canEvolve provides different types of information extracted from 90 cancer genomics studies comprising of more than 10,000 patients. The presence of multiple data types, novel integrative analysis for identifying regulators of oncogenesis, network

  6. A Conceptual Framework for Understanding Faster-Than-Light Neutrinos

    CERN Document Server

    Sakk, Eric

    2012-01-01

    Recent experiments have led to the production of neutrinos with transit times indicating the appearance of traveling faster than the speed of light. In this paper, we present a conceptual framework to understand how faster-than-light events involving neutrinos (as indicated by time-of-flight) might occur. We propose that observations of this kind do not violate the special theory of relativity; instead, they only help to provide evidence in support of the general theory of relativity at quantum scales. Specifically, given the relativistic effects of the neutrino on its local spacetime environment, we demonstrate that the measured time-of-flight at the macroscopic level is attributable to a decrease in the effective path length traversed by the neutrino.

  7. Multiple object tracking using the shortest path faster association algorithm.

    Science.gov (United States)

    Xi, Zhenghao; Liu, Heping; Liu, Huaping; Yang, Bin

    2014-01-01

    To solve the persistently multiple object tracking in cluttered environments, this paper presents a novel tracking association approach based on the shortest path faster algorithm. First, the multiple object tracking is formulated as an integer programming problem of the flow network. Then we relax the integer programming to a standard linear programming problem. Therefore, the global optimum can be quickly obtained using the shortest path faster algorithm. The proposed method avoids the difficulties of integer programming, and it has a lower worst-case complexity than competing methods but better robustness and tracking accuracy in complex environments. Simulation results show that the proposed algorithm takes less time than other state-of-the-art methods and can operate in real time.

  8. Multiple Object Tracking Using the Shortest Path Faster Association Algorithm

    Directory of Open Access Journals (Sweden)

    Zhenghao Xi

    2014-01-01

    Full Text Available To solve the persistently multiple object tracking in cluttered environments, this paper presents a novel tracking association approach based on the shortest path faster algorithm. First, the multiple object tracking is formulated as an integer programming problem of the flow network. Then we relax the integer programming to a standard linear programming problem. Therefore, the global optimum can be quickly obtained using the shortest path faster algorithm. The proposed method avoids the difficulties of integer programming, and it has a lower worst-case complexity than competing methods but better robustness and tracking accuracy in complex environments. Simulation results show that the proposed algorithm takes less time than other state-of-the-art methods and can operate in real time.

  9. Boundary conditions on faster-than-light transportation systems

    Science.gov (United States)

    Bennett, Gary L.; Knowles, H. B.

    1993-01-01

    In order to be consistent with current physical theories, any proposal of a faster-than light (FTL) transportation system must satisfy several critical conditions. It must predict the mass, space, and time dimensional changes predicted by relativity physics when velocity falls below the speed of light. It must also not violate causality, and remain consistent with quantum physics in the limit of microscopic systems. It is also essential that the proposal conserve energy.

  10. Why does hydronium diffuse faster than hydroxide in liquid water?

    Science.gov (United States)

    Zheng, Lixin; Santra, Biswajit; Distasio, Robert; Klein, Michael; Car, Roberto; Wu, Xifan

    Experiments show that the hydronium ion (H3O+) diffuses much faster than the hydroxide ion (OH-) in liquid water. ab initio molecular dynamics (AIMD) simulations correctly associated the diffusion mechanism to proton transfer (PT) but have been unable so far to clearly identify the reason for the faster diffusion of hydronium compared to hydroxide, as the diffusion rate was found to depend sensitively on the adopted functional approximation. We carried out AIMD simulations of the solvated water ions using a van der Waals (vdW) inclusive PBE0 hybrid density functional. It is found that not only hydronium diffuses faster than hydroxide but also the absolute rates agree with experiment. The fast diffusion of H3O+ occurs via concerted PT that enables the ion to jump across several H-bonded molecules in successful transfer events; in contrast, such concerted motion is significantly hindered in OH- where the ion is easily trapped in a hyper-coordination configuration (a local solvation structure that forbids PT). As a result multiple PT events are rare and the diffusion of OH- is significantly slowed down. Such a clear difference between the two ions results from the combined effect of vdW interactions and self-interaction correction. Doe SciDac: DE-SC0008626 and DE-SC0008726.

  11. Optimization as side-effect of evolving allelopathic diversity

    NARCIS (Netherlands)

    Pagie, L.; Hogeweg, P.

    2002-01-01

    Many bacteria carry gene complexes that code for a toxin-antidote pair, e.g. colicin systems. Such gene complexes can be advantageous for its host by killing competitor bacteria while the antidote protects the host. However, in order to evolve a novel and useful toxin first a proper antidote must be

  12. Marshal: Maintaining Evolving Models Project

    Data.gov (United States)

    National Aeronautics and Space Administration — SIFT proposes to design and develop the Marshal system, a mixed-initiative tool for maintaining task models over the course of evolving missions. Marshal-enabled...

  13. Review of Evolving Planet [game

    Directory of Open Access Journals (Sweden)

    Shawn Graham

    2016-11-01

    Full Text Available A review of Evolving Planet is an agent-based model situated in the archaeology of hominin dispersal, wrapped in the trappings of a casual video game. In Evolving Planet, a terrestrial world has been discovered, replete with artefacts and sites from a now-extinct intelligent species, dubbed the 'Lovans'. You (the player are the distinguished archaeologist sent from Earth to oversee a project trying to work out why the 'Lovans' became extinct.

  14. Review of Evolving Planet [game

    OpenAIRE

    Shawn Graham

    2016-01-01

    A review of Evolving Planet is an agent-based model situated in the archaeology of hominin dispersal, wrapped in the trappings of a casual video game. In Evolving Planet, a terrestrial world has been discovered, replete with artefacts and sites from a now-extinct intelligent species, dubbed the 'Lovans'. You (the player) are the distinguished archaeologist sent from Earth to oversee a project trying to work out why the 'Lovans' became extinct.

  15. Drosophila X-Linked Genes Have Lower Translation Rates than Autosomal Genes.

    Science.gov (United States)

    Zhang, Zhenguo; Presgraves, Daven C

    2016-02-01

    In Drosophila, X-linked and autosomal genes achieve comparable expression at the mRNA level. Whether comparable X-autosome gene expression is realized at the translational and, ultimately, the protein levels is, however, unknown. Previous studies suggest the possibility of higher translation rates for X-linked genes owing to stronger usage of preferred codons. In this study, we use public ribosome profiling data from Drosophila melanogaster to infer translation rates on the X chromosome versus the autosomes. We find that X-linked genes have consistently lower ribosome densities than autosomal genes in S2 cells, early embryos, eggs, and mature oocytes. Surprisingly, the lower ribosome densities of X-linked genes are not consistent with faster translation elongation but instead imply slower translation initiation. In particular, X-linked genes have sequence features known to slow translation initiation such as stronger mRNA structure near start codons and longer 5'-UTRs. Comparison to outgroup species suggests that stronger mRNA structure is an evolved feature of Drosophila X chromosomes. Finally, we find that the magnitude of the X-autosome difference in ribosome densities is smaller for genes encoding members of protein complexes, suggesting that stoichiometry constrains the evolution of translation rates. In sum, our analyses suggest that Drosophila X-linked genes have evolved lower translation rates than autosomal genes despite stronger usage of preferred codons.

  16. Women cross the 'Catalina Channel' faster than men.

    Science.gov (United States)

    Knechtle, Beat; Rosemann, Thomas; Rüst, Christoph Alexander

    2015-01-01

    Open-water ultra-distance swimming has a long history where the 'English Channel' (~33 km) was crossed in 1875 for the first time. Nowadays, the three most challenging open-water swims worldwide are the 21-miles (34 km) 'English Channel Swim', the 20.1-miles (32.2 km) 'Catalina Channel Swim' and the 28.5-miles (45.9 km) 'Manhattan Island Marathon Swim', also called the 'Triple Crown of Open Water Swimming'. Recent studies showed that women were able to achieve men's performance in the 'English Channel Swim' or to even outperform men in the 'Manhattan Island Marathon Swim'. However, the analysis of the 'Catalina Channel Swim' as part of the 'Triple Crown of Open Water Swimming' is missing. We investigated performance and sex difference in performance for successful women and men crossing the 'Catalina Channel' between 1927 and 2014. The fastest woman ever was ~22 min faster than the fastest man ever. Although the three fastest women ever were ~20 min faster than the three fastest men ever, the difference reached not statistical significance (p > 0.05). Similarly for the ten fastest ever, the ~1 min difference for women was not significant (p > 0.05). However, when the swimming times of the annual fastest women (n = 39) and the annual fastest men (n = 50) competing between 1927 and 2014 were compared, women (651 ± 173 min) were 52.9 min (16 ± 12%) faster than men (704 ± 279 min) (p Catalina Channel' faster than the annual fastest men. The non-linear decrease in swimming times suggests that female and male swimmers have reached a limit in this event. However, the linear decrease in the sex difference may indicate that women continuously narrow the gap to men.

  17. 20 Recipes for Programming MVC 3 Faster, Smarter Web Development

    CERN Document Server

    Munro, Jamie

    2011-01-01

    There's no need to reinvent the wheel every time you run into a problem with ASP.NET's Model-View-Controller (MVC) framework. This concise cookbook provides recipes to help you solve tasks many web developers encounter every day. Each recipe includes the C# code you need, along with a complete working example of how to implement the solution. Learn practical techniques for applying user authentication, providing faster page reloads, validating user data, filtering search results, and many other issues related to MVC3 development. These recipes help you: Restrict access to views with password

  18. Robustness of a bisimulation-type faster-than preorder

    Directory of Open Access Journals (Sweden)

    Katrin Iltgen

    2009-11-01

    Full Text Available TACS is an extension of CCS where upper time bounds for delays can be specified. Luettgen and Vogler defined three variants of bismulation-type faster-than relations and showed that they all three lead to the same preorder, demonstrating the robustness of their approach. In the present paper, the operational semantics of TACS is extended; it is shown that two of the variants still give the same preorder as before, underlining robustness. An explanation is given why this result fails for the third variant. It is also shown that another variant, which mixes old and new operational semantics, can lead to smaller relations that prove the same preorder.

  19. Faster magnet sorting with a threshold acceptance algorithm

    Science.gov (United States)

    Lidia, Steve; Carr, Roger

    1995-02-01

    We introduce here a new technique for sorting magnets to minimize the field errors in permanent magnet insertion devices. Simulated annealing has been used in this role, but we find the technique of threshold acceptance produces results of equal quality in less computer time. Threshold accepting would be of special value in designing very long insertion devices, such as long free electron lasers (FELs). Our application of threshold acceptance to magnet sorting showed that it converged to equivalently low values of the cost function, but that it converged significantly faster. We present typical cases showing time to convergence for various error tolerances, magnet numbers, and temperature schedules.

  20. Faster than light motion does not imply time travel

    CERN Document Server

    Andréka, H; Németi, I; Stannett, M; Székely, G

    2014-01-01

    Seeing the many examples in the literature of causality violations based on faster-than- light (FTL) signals one naturally thinks that FTL motion leads inevitably to the possibility of time travel. We show that this logical inference is invalid by demonstrating a model, based on (3+1)-dimensional Minkowski spacetime, in which FTL motion is permitted (in every direction without any limitation on speed) yet which does not admit time travel. Moreover, the Principle of Relativity is true in this model in the sense that all observers are equivalent. In short, FTL motion does not imply time travel after all.

  1. Faster Broadband, but Who Needs It'?

    Institute of Scientific and Technical Information of China (English)

    2011-01-01

    According to New York Times on October 24, the global mobile industry is making the same leap of faith with Long Term Evolution, the technology behind the super-fast wireless broadband net- works now being switched on around the world. In October, mobile operators are building 174 LTE networks in 64 countries, according to the GSA Association, an industry group of net- work equipment makers based in Zurich. With its faster speed and greater capacity to handle the explosive growth in mobile data traffic, operators are wagering that LTE will be critical to future profitability.

  2. Even Faster Web Sites Performance Best Practices for Web Developers

    CERN Document Server

    Souders, Steve

    2009-01-01

    Performance is critical to the success of any web site, and yet today's web applications push browsers to their limits with increasing amounts of rich content and heavy use of Ajax. In this book, Steve Souders, web performance evangelist at Google and former Chief Performance Yahoo!, provides valuable techniques to help you optimize your site's performance. Souders' previous book, the bestselling High Performance Web Sites, shocked the web development world by revealing that 80% of the time it takes for a web page to load is on the client side. In Even Faster Web Sites, Souders and eight exp

  3. Bone fracture consolidates faster with low-power laser

    Energy Technology Data Exchange (ETDEWEB)

    Trelles, M.A.; Mayayo, E.

    1987-01-01

    Low-power laser radiation is currently used in the treatment of pain and osteoarticular inflammation. However, the mechanisms of the laser biostimulating effects on tissue are still not completely understood. With laser treatment, we have achieved activation of osseous regeneration in human bone fractures. After 7 years of positive clinical control in human beings, we decided to start an experimental study of fractures in the tibia of mice, histologically controlling its reparation after exposure to 632 nm. He/Ne laser in doses of 2.4 Joules in one point was used. The radiation was directly applied to the area of fracture in a series of 12 treatments (one treatment every second day). By optic microscope we observed, in the treated animals, an important increase in vascularization and faster formation of osseous tissue with a dense trabecular net compared to the control group, which presented only chondroid tissue and poor vascularization corresponding to an earlier stage of bone consolidation (controls were also analyzed by electron microscopy). Potentially, the laser effect might modulate the function of osteocytes, promoting faster metabolism and reaction of bone callus.

  4. Faster Acquisition Technique for Software-defined GPS Receivers

    Directory of Open Access Journals (Sweden)

    M. Venu Gopala Rao

    2015-03-01

    Full Text Available Acquisition is a most important process and a challenge task for identifying visible satellites, coarse values of carrier frequency, and code phase of the satellite signals in designing software defined Global positioning system (GPS receiver. This paper presents a new, simple, efficient and faster GPS acquisition via sub-sampled fast Fourier transform (ssFFT. The proposed algorithm exploits the recently developed sparse FFT (or sparse IFFT that computes in sub-linear time. Further it uses the property of fourier transforms (FT: Aliasing a signal in the time domain corresponds to sub-sampling it in the frequency domain, and vice versa. The ssFFT is an FFT algorithm that computes sub-sampled version of the data by an integer factor ‘d’, and hence, the computational complexity is proportionately reduced by a factor of ‘d log d’ compared to conventional FFT-based algorithms for any length of the input GPS signal. The simulation results show that the proposed ssFFT based GPS acquisition computation is 8.5571 times faster than the conventional FFT-based acquisition computation time. The implementation of this method in an FPGA provides very fast processing of incoming GPS samples that satisfies real-time positioning requirements.Defence Science Journal, Vol. 65, No. 1, January 2015, pp.5-11, DOI:http://dx.doi.org/10.14429/dsj.65.5579

  5. ZKBoo: Faster Zero-Knowledge for Boolean Circuits

    DEFF Research Database (Denmark)

    Giacomelli, Irene; Madsen, Jesper; Orlandi, Claudio

    2016-01-01

    ms (resp. 5ms), with a proof size of 444KB. Our techniques are based on the “MPC-in-the-head” approach to zero-knowledge of Ishai et al. (IKOS), which has been successfully used to achieve significant asymp- totic improvements. Our contributions include: ◦ A thorough analysis of the different...... variants of IKOS, which highlights their pros and cons for practically rele- vant soundness parameters; ◦ A generalization and simplification of their approach, which leads to faster Σ-protocols (that can be made non-interactive using the Fiat-Shamir heuristic) for state- ments of the form “I know x...... such that y = φ (x)” (where φ is a circuit and y a public value); ◦ A case study, where we provide explicit protocols, implementations and benchmarking of zero-knowledge protocols for the SHA-1 and SHA-256 circuits....

  6. Climbing favours the tripod gait over alternative faster insect gaits

    Science.gov (United States)

    Ramdya, Pavan; Thandiackal, Robin; Cherney, Raphael; Asselborn, Thibault; Benton, Richard; Ijspeert, Auke Jan; Floreano, Dario

    2017-02-01

    To escape danger or catch prey, running vertebrates rely on dynamic gaits with minimal ground contact. By contrast, most insects use a tripod gait that maintains at least three legs on the ground at any given time. One prevailing hypothesis for this difference in fast locomotor strategies is that tripod locomotion allows insects to rapidly navigate three-dimensional terrain. To test this, we computationally discovered fast locomotor gaits for a model based on Drosophila melanogaster. Indeed, the tripod gait emerges to the exclusion of many other possible gaits when optimizing fast upward climbing with leg adhesion. By contrast, novel two-legged bipod gaits are fastest on flat terrain without adhesion in the model and in a hexapod robot. Intriguingly, when adhesive leg structures in real Drosophila are covered, animals exhibit atypical bipod-like leg coordination. We propose that the requirement to climb vertical terrain may drive the prevalence of the tripod gait over faster alternative gaits with minimal ground contact.

  7. Group chasing tactics: how to catch a faster prey

    Science.gov (United States)

    Janosov, Milán; Virágh, Csaba; Vásárhelyi, Gábor; Vicsek, Tamás

    2017-05-01

    We propose a bio-inspired, agent-based approach to describe the natural phenomenon of group chasing in both two and three dimensions. Using a set of local interaction rules we created a continuous-space and discrete-time model with time delay, external noise and limited acceleration. We implemented a unique collective chasing strategy, optimized its parameters and studied its properties when chasing a much faster, erratic escaper. We show that collective chasing strategies can significantly enhance the chasers’ success rate. Our realistic approach handles group chasing within closed, soft boundaries—in contrast with the periodic ones in most published literature—and resembles several properties of pursuits observed in nature, such as emergent encircling or the escaper’s zigzag motion.

  8. Faster Rates for training Max-Margin Markov Networks

    CERN Document Server

    Zhang, Xinhua; Vishwanathan, S V N

    2010-01-01

    Structured output prediction is an important machine learning problem both in theory and practice, and the max-margin Markov network (\\mcn) is an effective approach. All state-of-the-art algorithms for optimizing \\mcn\\ objectives take at least $O(1/\\epsilon)$ number of iterations to find an $\\epsilon$ accurate solution. Recent results in structured optimization suggest that faster rates are possible by exploiting the structure of the objective function. Towards this end \\citet{Nesterov05} proposed an excessive gap reduction technique based on Euclidean projections which converges in $O(1/\\sqrt{\\epsilon})$ iterations on strongly convex functions. Unfortunately when applied to \\mcn s, this approach does not admit graphical model factorization which, as in many existing algorithms, is crucial for keeping the cost per iteration tractable. In this paper, we present a new excessive gap reduction technique based on Bregman projections which admits graphical model factorization naturally, and converges in $O(1/\\sqrt{...

  9. [Faster, higher, stronger: knowledge about old and new doping substances].

    Science.gov (United States)

    Pieters, Toine; de Hon, Olivier

    2013-01-01

    Physicians should possess specific diagnostic and pharmacotherapeutic skills in order to recognize symptoms associated with doping use. It is important to be on the alert in athletes and fitness enthusiasts for physical and psychological changes due to use of anabolic steroids such as acne, stretch marks, gynecomastia, signs of acromegaly, irascibility and lethargy. Stimulants such as amphetamines, ephedrine and cocaine lead to fat loss and increased alertness; their main side effects are cardiac problems, behavioural changes and addiction. In addition to anabolic steroids and stimulants, erythropoietin, growth hormone, diuretics and glucocorticoids are regularly used to improve sport performance. In cycling, a biological passport will be used in an attempt to detect doping use. In future, the Olympic motto 'citius, altius, fortius' (faster, higher, stronger) will have ground-breaking consequences for the performance and health of top athletes.

  10. Thermal and evolved gas analyzer

    Science.gov (United States)

    Williams, M. S.; Boynton, W. V.; James, R. L.; Verts, W. T.; Bailey, S. H.; Hamara, D. K.

    1998-01-01

    The Thermal and Evolved Gas Analyzer (TEGA) instrument will perform calorimetry and evolved gas analysis on soil samples collected from the Martian surface. TEGA is one of three instruments, along with a robotic arm, that form the Mars Volatile and Climate Survey (MVACS) payload. The other instruments are a stereo surface imager, built by Peter Smith of the University of Arizona and a meteorological station, built by JPL. The MVACS lander will investigate a Martian landing site at approximately 70 deg south latitude. Launch will take place from Kennedy Space Center in January, 1999. The TEGA project started in February, 1996. In the intervening 24 months, a flight instrument concept has been designed, prototyped, built as an engineering model and flight model, and tested. The instrument performs laboratory-quality differential-scanning calorimetry (DSC) over the temperature range of Mars ambient to 1400K. Low-temperature volatiles (water and carbon dioxide ices) and the carbonates will be analyzed in this temperature range. Carbonates melt and evolve carbon dioxide at temperatures above 600 C. Evolved oxygen (down to a concentration of 1 ppm) is detected, and C02 and water vapor and the isotopic variations of C02 and water vapor are detected and their concentrations measured. The isotopic composition provides important tests of the theory of solar system formation.

  11. Evolving Objects for Software Engineering

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    This paper is concerned with evolving objects method for softwaredesign that can adapt to the changing environments and requirements automatically. We presen t system architecture with objects library, where there are objects based on dom ain ontologies. We define some genetic operators for objects, and discuss how to apply these genetic operators on objects to get new objects, which can satisfy new requirements.

  12. Ground Data System Risk Mitigation Techniques for Faster, Better, Cheaper Missions

    Science.gov (United States)

    Catena, John J.; Saylor, Rick; Casasanta, Ralph; Weikel, Craig; Powers, Edward I. (Technical Monitor)

    2000-01-01

    With the advent of faster, cheaper, and better missions, NASA Projects acknowledged that a higher level of risk was inherent and accepted with this approach. It was incumbent however upon each component of the Project whether spacecraft, payload, launch vehicle, or ground data system to ensure that the mission would nevertheless be an unqualified success. The Small Explorer (SMEX) program's ground data system (GDS) team developed risk mitigation techniques to achieve these goals starting in 1989. These techniques have evolved through the SMEX series of missions and are practiced today under the Triana program. These techniques are: (1) Mission Team Organization--empowerment of a closeknit ground data system team comprising system engineering, software engineering, testing, and flight operations personnel; (2) Common Spacecraft Test and Operational Control System--utilization of the pre-launch spacecraft integration system as the post-launch ground data system on-orbit command and control system; (3) Utilization of operations personnel in pre-launch testing--making the flight operations team an integrated member of the spacecraft testing activities at the beginning of the spacecraft fabrication phase; (4) Consolidated Test Team--combined system, mission readiness and operations testing to optimize test opportunities with the ground system and spacecraft; and (5). Reuse of Spacecraft, Systems and People--reuse of people, software and on-orbit spacecraft throughout the SMEX mission series. The SMEX ground system development approach for faster, cheaper, better missions has been very successful. This paper will discuss these risk management techniques in the areas of ground data system design, implementation, test, and operational readiness.

  13. Simultaneous development of laparoscopy and robotics provides acceptable perioperative outcomes and shows robotics to have a faster learning curve and to be overall faster in rectal cancer surgery: analysis of novice MIS surgeon learning curves.

    Science.gov (United States)

    Melich, George; Hong, Young Ki; Kim, Jieun; Hur, Hyuk; Baik, Seung Hyuk; Kim, Nam Kyu; Sender Liberman, A; Min, Byung Soh

    2015-03-01

    Laparoscopy offers some evidence of benefit compared to open rectal surgery. Robotic rectal surgery is evolving into an accepted approach. The objective was to analyze and compare laparoscopic and robotic rectal surgery learning curves with respect to operative times and perioperative outcomes for a novice minimally invasive colorectal surgeon. One hundred and six laparoscopic and 92 robotic LAR rectal surgery cases were analyzed. All surgeries were performed by a surgeon who was primarily trained in open rectal surgery. Patient characteristics and perioperative outcomes were analyzed. Operative time and CUSUM plots were used for evaluating the learning curve for laparoscopic versus robotic LAR. Laparoscopic versus robotic LAR outcomes feature initial group operative times of 308 (291-325) min versus 397 (373-420) min and last group times of 220 (212-229) min versus 204 (196-211) min-reversed in favor of robotics; major complications of 4.7 versus 6.5 % (NS), resection margin involvement of 2.8 versus 4.4 % (NS), conversion rate of 3.8 versus 1.1 (NS), lymph node harvest of 16.3 versus 17.2 (NS), and estimated blood loss of 231 versus 201 cc (NS). Due to faster learning curves for extracorporeal phase and total mesorectal excision phase, the robotic surgery was observed to be faster than laparoscopic surgery after the initial 41 cases. CUSUM plots demonstrate acceptable perioperative surgical outcomes from the beginning of the study. Initial robotic operative times improved with practice rapidly and eventually became faster than those for laparoscopy. Developing both laparoscopic and robotic skills simultaneously can provide acceptable perioperative outcomes in rectal surgery. It might be suggested that in the current milieu of clashing interests between evolving technology and economic constrains, there might be advantages in embracing both approaches.

  14. Innovations for competitiveness: European views on "better-faster-cheaper"

    Science.gov (United States)

    Atzei, A.; Groepper, P.; Novara, M.; Pseiner, K.

    1999-09-01

    The paper elaborates on " lessons learned" from two recent ESA workshops, one focussing on the role of Innovation in the competitiveness of the space sector and the second on technology and engineering aspects conducive to better, faster and cheaper space programmes. The paper focuses primarily on four major aspects, namely: a) the adaptations of industrial and public organisations to the global market needs; b) the understanding of the bottleneck factors limiting competitiveness; c) the trends toward new system architectures and new engineering and production methods; d) the understanding of the role of new technology in the future applications. Under the pressure of market forces and the influence of many global and regional players, applications of space systems and technology are becoming more and more competitive. It is well recognised that without major effort for innovation in industrial practices, organisations, R&D, marketing and financial approaches the European space sector will stagnate and loose its competence as well as its competitiveness. It is also recognised that a programme run according to the "better, faster, cheaper" philosophy relies on much closer integration of system design, development and verification, and draws heavily on a robust and comprehensive programme of technology development, which must run in parallel and off-line with respect to flight programmes. A company's innovation capabilities will determine its future competitive advantage (in time, cost, performance or value) and overall growth potential. Innovation must be a process that can be counted on to provide repetitive, sustainable, long-term performance improvements. As such, it needs not depend on great breakthroughs in technology and concepts (which are accidental and rare). Rather, it could be based on bold evolution through the establishment of know-how, application of best practices, process effectiveness and high standards, performance measurement, and attention to

  15. Coupled oscillators on evolving networks

    Science.gov (United States)

    Singh, R. K.; Bagarti, Trilochan

    2016-12-01

    In this work we study coupled oscillators on evolving networks. We find that the steady state behavior of the system is governed by the relative values of the spread in natural frequencies and the global coupling strength. For coupling strong in comparison to the spread in frequencies, the system of oscillators synchronize and when coupling strength and spread in frequencies are large, a phenomenon similar to amplitude death is observed. The network evolution provides a mechanism to build inter-oscillator connections and once a dynamic equilibrium is achieved, oscillators evolve according to their local interactions. We also find that the steady state properties change by the presence of additional time scales. We demonstrate these results based on numerical calculations studying dynamical evolution of limit-cycle and van der Pol oscillators.

  16. Mandelbrot Law of Evolving Networks

    Institute of Scientific and Technical Information of China (English)

    REN Xue-Zao; YANG Zi-Mo; WANG Bing-Hong; ZHOU Tao

    2012-01-01

    We show that the degree distribution of a growing network with linear preferential attachment approximately follows the Mandelbrot law,and propose an analytical method based on a recursive formula that can be used to obtain a more accurate expression of the shifting coefficient.Simulations demonstrate the advantages of our method. This work provides a possible mechanism leading to the Mandelbrot law of evolving networks,and refines the mainstream analytical methods for the shifting coefficient.

  17. A Calculus of Evolving Objects

    Directory of Open Access Journals (Sweden)

    M. Dezani-Ciancaglini

    2008-01-01

    Full Text Available The demands of developing modern, highly dynamic applications have led to an increasing interest in dynamic programming languages and mechanisms. Not only must applications evolve over time, but the object models themselves may need to be adapted to the requirements of different run-time contexts. Class-based models and prototype-based models, for example, may need to co-exist to meet the demands of dynamically evolving applications. Multi-dimensional dispatch, fine-grained and dynamic software composition, and run-time evolution of behaviour are further examples of diverse mechanisms which may need to co-exist in a dynamically evolving run-time environment. How can we model the semantics of these highly dynamic features, yet still offer some reasonable safety guarantees?To this end we present an original calculus in which objects can adapt their behaviour at run-time. Both objects and environments are represented by first-class mappings between variables and values. Message sends are dynamically resolved to method calls. Variables may be dynamically bound, making it possible to model a variety of dynamic mechanisms within the same calculus. Despite the highly dynamic nature of the calculus, safety properties are assured by a type assignment system.

  18. Ranking in evolving complex networks

    Science.gov (United States)

    Liao, Hao; Mariani, Manuel Sebastian; Medo, Matúš; Zhang, Yi-Cheng; Zhou, Ming-Yang

    2017-05-01

    Complex networks have emerged as a simple yet powerful framework to represent and analyze a wide range of complex systems. The problem of ranking the nodes and the edges in complex networks is critical for a broad range of real-world problems because it affects how we access online information and products, how success and talent are evaluated in human activities, and how scarce resources are allocated by companies and policymakers, among others. This calls for a deep understanding of how existing ranking algorithms perform, and which are their possible biases that may impair their effectiveness. Many popular ranking algorithms (such as Google's PageRank) are static in nature and, as a consequence, they exhibit important shortcomings when applied to real networks that rapidly evolve in time. At the same time, recent advances in the understanding and modeling of evolving networks have enabled the development of a wide and diverse range of ranking algorithms that take the temporal dimension into account. The aim of this review is to survey the existing ranking algorithms, both static and time-aware, and their applications to evolving networks. We emphasize both the impact of network evolution on well-established static algorithms and the benefits from including the temporal dimension for tasks such as prediction of network traffic, prediction of future links, and identification of significant nodes.

  19. Evolving Systems and Adaptive Key Component Control

    Science.gov (United States)

    Frost, Susan A.; Balas, Mark J.

    2009-01-01

    We propose a new framework called Evolving Systems to describe the self-assembly, or autonomous assembly, of actively controlled dynamical subsystems into an Evolved System with a higher purpose. An introduction to Evolving Systems and exploration of the essential topics of the control and stability properties of Evolving Systems is provided. This chapter defines a framework for Evolving Systems, develops theory and control solutions for fundamental characteristics of Evolving Systems, and provides illustrative examples of Evolving Systems and their control with adaptive key component controllers.

  20. Advanced Ultrasonic Diagnosis of Extremity Trauma: The Faster Exam

    Science.gov (United States)

    Dulchavsky, S. A.; Henry, S. E.; Moed, B. R.; Diebel, L. N.; Marshburn, T.; Hamilton, D. R.; Logan, J.; Kirkpatrick, A. W.; Williams, D. R.

    2002-01-01

    Ultrasound is of prO)len accuracy in abdominal and thoracic trauma and may be useful to diagnose extremity injury in situations where radiography is not available such as military and space applications. We prospectively evaluated the utility of extremity , ultrasound performed by trained, non-physician personnel in patients with extremity trauma, to simulate remote aerospace or military applications . Methods: Patients with extremity trauma were identified by history, physical examination, and radiographic studies. Ultrasound examination was performed bilaterally by nonphysician personnel with a portable ultrasound device using a 10-5 MHz linear probe, Images were video-recorded for later analysis against radiography by Fisher's exact test. The average time of examination was 4 minutes. Ultrasound accurately diagnosed extremity, injury in 94% of patients with no false positive exams; accuracy was greater in mid-shaft locations and least in the metacarpa/metatarsals. Soft tissue/tendon injury was readily visualized . Extremity ultrasound can be performed quickly and accurately by nonphysician personnel with excellent accuracy. Blinded verification of the utility of ultrasound in patients with extremity injury should be done to determine if Extremity and Respiratory evaluation should be added to the FAST examination (the FASTER exam) and verify the technique in remote locations such as military and aerospace applications.

  1. Causal events enter awareness faster than non-causal events

    Science.gov (United States)

    Wagemans, Johan; de-Wit, Lee

    2017-01-01

    Philosophers have long argued that causality cannot be directly observed but requires a conscious inference (Hume, 1967). Albert Michotte however developed numerous visual phenomena in which people seemed to perceive causality akin to primary visual properties like colour or motion (Michotte, 1946). Michotte claimed that the perception of causality did not require a conscious, deliberate inference but, working over 70 years ago, he did not have access to the experimental methods to test this claim. Here we employ Continuous Flash Suppression (CFS)—an interocular suppression technique to render stimuli invisible (Tsuchiya & Koch, 2005)—to test whether causal events enter awareness faster than non-causal events. We presented observers with ‘causal’ and ‘non-causal’ events, and found consistent evidence that participants become aware of causal events more rapidly than non-causal events. Our results suggest that, whilst causality must be inferred from sensory evidence, this inference might be computed at low levels of perceptual processing, and does not depend on a deliberative conscious evaluation of the stimulus. This work therefore supports Michotte’s contention that, like colour or motion, causality is an immediate property of our perception of the world. PMID:28149698

  2. A Faster Algorithm for Quasi-convex Integer Polynomial Optimization

    CERN Document Server

    Hildebrand, Robert

    2010-01-01

    We present a faster exponential-time algorithm for integer optimization over quasi-convex polynomials. We study the minimization of a quasi-convex polynomial subject to s quasi-convex polynomial constraints and integrality constraints for all variables. The new algorithm is an improvement upon the best known algorithm due to Heinz (Journal of Complexity, 2005). A lower time complexity is reached through applying a stronger ellipsoid rounding method and applying a recent advancement in the shortest vector problem to give a smaller exponential-time complexity of a Lenstra-type algorithm. For the bounded case, our algorithm attains a time-complexity of s (r l M d)^{O(1)} 2^{2n\\log_2(n) + O(n)} when M is a bound on the number of monomials in each polynomial and r is the binary encoding length of a bound on the feasible region. In the general case, s l^{O(1)} d^{O(n)} 2^{2n\\log_2(n)}. In each we assume d>=2 is a bound on the total degree of the polynomials and l bounds the maximum binary encoding size of the input...

  3. Globalization of Behavioral Risks Needs Faster Diffusion of Interventions

    Directory of Open Access Journals (Sweden)

    Shahul Ebrahim, MD, MSc, PhD

    2007-04-01

    Full Text Available International trade, population migration, changes in living conditions (i.e., consumption transition, nutritional transition, and changes in production, marketing, and availability of consumer goods (i.e., production transition have brought about continuous and rapid changes in the human environment. Such changes have improved the health and economic status of many people in developing countries. At the same time, a parallel phenomenon is occurring: the rapid emergence and expansion of modifiable risk behaviors. These behaviors adversely affect the national health of developing countries and that of future generations because of their impact on maternal, child, and adolescent health. Furthermore, these behaviors are increasing at a faster rate than interventions to curb their growth are being implemented. We discuss the current status of five modifiable risk behaviors — alcohol consumption, tobacco use, overweight and obesity, low fruit and vegetable consumption, and physical inactivity — to emphasize the need for global advocacy and local action to enhance policy formulation and diffusion of interventions necessary to moderate the spread of these behaviors.

  4. Learning Faster by Discovering and Exploiting Object Similarities

    Directory of Open Access Journals (Sweden)

    Tadej Janež

    2013-03-01

    Full Text Available In this paper we explore the question: “Is it possible to speed up the learning process of an autonomous agent by performing experiments in a more complex environment (i.e., an environment with a greater number of different objects?” To this end, we use a simple robotic domain, where the robot has to learn a qualitative model predicting the change in the robot’s distance to an object. To quantify the environment’s complexity, we defined cardinal complexity as the number of objects in the robot’s world, and behavioural complexity as the number of objects’ distinct behaviours. We propose Error reduction merging (ERM, a new learning method that automatically discovers similarities in the structure of the agent’s environment. ERM identifies different types of objects solely from the data measured and merges the observations of objects that behave in the same or similar way in order to speed up the agent’s learning. We performed a series of experiments in worlds of increasing complexity. The results in our simple domain indicate that ERM was capable of discovering structural similarities in the data which indeed made the learning faster, clearly superior to conventional learning. This observed trend occurred with various machine learning algorithms used inside the ERM method.

  5. Faster and More Accurate Sequence Alignment with SNAP

    CERN Document Server

    Zaharia, Matei; Curtis, Kristal; Fox, Armando; Patterson, David; Shenker, Scott; Stoica, Ion; Karp, Richard M; Sittler, Taylor

    2011-01-01

    We present the Scalable Nucleotide Alignment Program (SNAP), a new short and long read aligner that is both more accurate (i.e., aligns more reads with fewer errors) and 10-100x faster than state-of-the-art tools such as BWA. Unlike recent aligners based on the Burrows-Wheeler transform, SNAP uses a simple hash index of short seed sequences from the genome, similar to BLAST's. However, SNAP greatly reduces the number and cost of local alignment checks performed through several measures: it uses longer seeds to reduce the false positive locations considered, leverages larger memory capacities to speed index lookup, and excludes most candidate locations without fully computing their edit distance to the read. The result is an algorithm that scales well for reads from one hundred to thousands of bases long and provides a rich error model that can match classes of mutations (e.g., longer indels) that today's fast aligners ignore. We calculate that SNAP can align a dataset with 30x coverage of a human genome in le...

  6. Faster, More Reproducible DESI-MS for Biological Tissue Imaging

    Science.gov (United States)

    Tillner, Jocelyn; Wu, Vincen; Jones, Emrys A.; Pringle, Steven D.; Karancsi, Tamas; Dannhorn, Andreas; Veselkov, Kirill; McKenzie, James S.; Takats, Zoltan

    2017-10-01

    A new, more robust sprayer for desorption electrospray ionization (DESI) mass spectrometry imaging is presented. The main source of variability in DESI is thought to be the uncontrolled variability of various geometric parameters of the sprayer, primarily the position of the solvent capillary, or more specifically, its positioning within the gas capillary or nozzle. If the solvent capillary is off-center, the sprayer becomes asymmetrical, making the geometry difficult to control and compromising reproducibility. If the stiffness, tip quality, and positioning of the capillary are improved, sprayer reproducibility can be improved by an order of magnitude. The quality of the improved sprayer and its potential for high spatial resolution imaging are demonstrated on human colorectal tissue samples by acquisition of images at pixel sizes of 100, 50, and 20 μm, which corresponds to a lateral resolution of 40-60 μm, similar to the best values published in the literature. The high sensitivity of the sprayer also allows combination with a fast scanning quadrupole time-of-flight mass spectrometer. This provides up to 30 times faster DESI acquisition, reducing the overall acquisition time for a 10 mm × 10 mm rat brain sample to approximately 1 h. Although some spectral information is lost with increasing analysis speed, the resulting data can still be used to classify tissue types on the basis of a previously constructed model. This is particularly interesting for clinical applications, where fast, reliable diagnosis is required. [Figure not available: see fulltext.

  7. DNF Sparsification and a Faster Deterministic Counting Algorithm

    CERN Document Server

    Gopala, Parikshit; Reingold, Omer

    2012-01-01

    Given a DNF formula on n variables, the two natural size measures are the number of terms or size s(f), and the maximum width of a term w(f). It is folklore that short DNF formulas can be made narrow. We prove a converse, showing that narrow formulas can be sparsified. More precisely, any width w DNF irrespective of its size can be $\\epsilon$-approximated by a width $w$ DNF with at most $(w\\log(1/\\epsilon))^{O(w)}$ terms. We combine our sparsification result with the work of Luby and Velikovic to give a faster deterministic algorithm for approximately counting the number of satisfying solutions to a DNF. Given a formula on n variables with poly(n) terms, we give a deterministic $n^{\\tilde{O}(\\log \\log(n))}$ time algorithm that computes an additive $\\epsilon$ approximation to the fraction of satisfying assignments of f for $\\epsilon = 1/\\poly(\\log n)$. The previous best result due to Luby and Velickovic from nearly two decades ago had a run-time of $n^{\\exp(O(\\sqrt{\\log \\log n}))}$.

  8. Chromosomal redistribution of male-biased genes in mammalian evolution with two bursts of gene gain on the X chromosome.

    Science.gov (United States)

    Zhang, Yong E; Vibranovski, Maria D; Landback, Patrick; Marais, Gabriel A B; Long, Manyuan

    2010-10-05

    Mammalian X chromosomes evolved under various mechanisms including sexual antagonism, the faster-X process, and meiotic sex chromosome inactivation (MSCI). These forces may contribute to nonrandom chromosomal distribution of sex-biased genes. In order to understand the evolution of gene content on the X chromosome and autosome under these forces, we dated human and mouse protein-coding genes and miRNA genes on the vertebrate phylogenetic tree. We found that the X chromosome recently acquired a burst of young male-biased genes, which is consistent with fixation of recessive male-beneficial alleles by sexual antagonism. For genes originating earlier, however, this pattern diminishes and finally reverses with an overrepresentation of the oldest male-biased genes on autosomes. MSCI contributes to this dynamic since it silences X-linked old genes but not X-linked young genes. This demasculinization process seems to be associated with feminization of the X chromosome with more X-linked old genes expressed in ovaries. Moreover, we detected another burst of gene originations after the split of eutherian mammals and opossum, and these genes were quickly incorporated into transcriptional networks of multiple tissues. Preexisting X-linked genes also show significantly higher protein-level evolution during this period compared to autosomal genes, suggesting positive selection accompanied the early evolution of mammalian X chromosomes. These two findings cast new light on the evolutionary history of the mammalian X chromosome in terms of gene gain, sequence, and expressional evolution.

  9. Chromosomal redistribution of male-biased genes in mammalian evolution with two bursts of gene gain on the X chromosome.

    Directory of Open Access Journals (Sweden)

    Yong E Zhang

    Full Text Available Mammalian X chromosomes evolved under various mechanisms including sexual antagonism, the faster-X process, and meiotic sex chromosome inactivation (MSCI. These forces may contribute to nonrandom chromosomal distribution of sex-biased genes. In order to understand the evolution of gene content on the X chromosome and autosome under these forces, we dated human and mouse protein-coding genes and miRNA genes on the vertebrate phylogenetic tree. We found that the X chromosome recently acquired a burst of young male-biased genes, which is consistent with fixation of recessive male-beneficial alleles by sexual antagonism. For genes originating earlier, however, this pattern diminishes and finally reverses with an overrepresentation of the oldest male-biased genes on autosomes. MSCI contributes to this dynamic since it silences X-linked old genes but not X-linked young genes. This demasculinization process seems to be associated with feminization of the X chromosome with more X-linked old genes expressed in ovaries. Moreover, we detected another burst of gene originations after the split of eutherian mammals and opossum, and these genes were quickly incorporated into transcriptional networks of multiple tissues. Preexisting X-linked genes also show significantly higher protein-level evolution during this period compared to autosomal genes, suggesting positive selection accompanied the early evolution of mammalian X chromosomes. These two findings cast new light on the evolutionary history of the mammalian X chromosome in terms of gene gain, sequence, and expressional evolution.

  10. Adaptive synonymous mutations in an experimentally evolved Pseudomonas fluorescens population

    DEFF Research Database (Denmark)

    Bailey, Susan; Hinz, Aaron; Kassen, Rees

    2014-01-01

    in an experimentally evolved population of Pseudomonas fluorescens. We show experimentally that these mutations increase fitness by an amount comparable to non-synonymous mutations and that the fitness increases stem from increased gene expression. These results provide unequivocal evidence that synonymous mutations...

  11. Regulatory mechanisms link phenotypic plasticity to evolvability.

    Science.gov (United States)

    van Gestel, Jordi; Weissing, Franz J

    2016-04-18

    Organisms have a remarkable capacity to respond to environmental change. They can either respond directly, by means of phenotypic plasticity, or they can slowly adapt through evolution. Yet, how phenotypic plasticity links to evolutionary adaptability is largely unknown. Current studies of plasticity tend to adopt a phenomenological reaction norm (RN) approach, which neglects the mechanisms underlying plasticity. Focusing on a concrete question - the optimal timing of bacterial sporulation - we here also consider a mechanistic approach, the evolution of a gene regulatory network (GRN) underlying plasticity. Using individual-based simulations, we compare the RN and GRN approach and find a number of striking differences. Most importantly, the GRN model results in a much higher diversity of responsive strategies than the RN model. We show that each of the evolved strategies is pre-adapted to a unique set of unseen environmental conditions. The regulatory mechanisms that control plasticity therefore critically link phenotypic plasticity to the adaptive potential of biological populations.

  12. Rate of evolution in brain-expressed genes in humans and other primates.

    Directory of Open Access Journals (Sweden)

    Hurng-Yi Wang

    2007-02-01

    Full Text Available Brain-expressed genes are known to evolve slowly in mammals. Nevertheless, since brains of higher primates have evolved rapidly, one might expect acceleration in DNA sequence evolution in their brain-expressed genes. In this study, we carried out full-length cDNA sequencing on the brain transcriptome of an Old World monkey (OWM and then conducted three-way comparisons among (i mouse, OWM, and human, and (ii OWM, chimpanzee, and human. Although brain-expressed genes indeed appear to evolve more rapidly in species with more advanced brains (apes > OWM > mouse, a similar lineage effect is observable for most other genes. The broad inclusion of genes in the reference set to represent the genomic average is therefore critical to this type of analysis. Calibrated against the genomic average, the rate of evolution among brain-expressed genes is probably lower (or at most equal in humans than in chimpanzee and OWM. Interestingly, the trend of slow evolution in coding sequence is no less pronounced among brain-specific genes, vis-à-vis brain-expressed genes in general. The human brain may thus differ from those of our close relatives in two opposite directions: (i faster evolution in gene expression, and (ii a likely slowdown in the evolution of protein sequences. Possible explanations and hypotheses are discussed.

  13. Rate of Evolution in Brain-Expressed Genes in Humans and Other Primates

    Science.gov (United States)

    Wang, Hurng-Yi; Chien, Huan-Chieh; Osada, Naoki; Hashimoto, Katsuyuki; Sugano, Sumio; Gojobori, Takashi; Chou, Chen-Kung; Tsai, Shih-Feng; Wu, Chung-I; Shen, C.-K. James

    2007-01-01

    Brain-expressed genes are known to evolve slowly in mammals. Nevertheless, since brains of higher primates have evolved rapidly, one might expect acceleration in DNA sequence evolution in their brain-expressed genes. In this study, we carried out full-length cDNA sequencing on the brain transcriptome of an Old World monkey (OWM) and then conducted three-way comparisons among (i) mouse, OWM, and human, and (ii) OWM, chimpanzee, and human. Although brain-expressed genes indeed appear to evolve more rapidly in species with more advanced brains (apes > OWM > mouse), a similar lineage effect is observable for most other genes. The broad inclusion of genes in the reference set to represent the genomic average is therefore critical to this type of analysis. Calibrated against the genomic average, the rate of evolution among brain-expressed genes is probably lower (or at most equal) in humans than in chimpanzee and OWM. Interestingly, the trend of slow evolution in coding sequence is no less pronounced among brain-specific genes, vis-à-vis brain-expressed genes in general. The human brain may thus differ from those of our close relatives in two opposite directions: (i) faster evolution in gene expression, and (ii) a likely slowdown in the evolution of protein sequences. Possible explanations and hypotheses are discussed. PMID:17194215

  14. The 'E' factor -- evolving endodontics.

    Science.gov (United States)

    Hunter, M J

    2013-03-01

    Endodontics is a constantly developing field, with new instruments, preparation techniques and sealants competing with trusted and traditional approaches to tooth restoration. Thus general dental practitioners must question and understand the significance of these developments before adopting new practices. In view of this, the aim of this article, and the associated presentation at the 2013 British Dental Conference & Exhibition, is to provide an overview of endodontic methods and constantly evolving best practice. The presentation will review current preparation techniques, comparing rotary versus reciprocation, and question current trends in restoration of the endodontically treated tooth.

  15. Synchronization in an evolving network

    CERN Document Server

    Singh, R K

    2015-01-01

    In this work we study the dynamics of Kuramoto oscillators on a stochastically evolving network whose evolution is governed by the phases of the individual oscillators and degree distribution. Synchronization is achieved after a threshold connection density is reached. This cumulative effect of topology and dynamics has many real-world implications, where synchronization in a system emerges as a collective property of its components in a self-organizing manner. The synchronous state remains stable as long as the connection density remains above the threshold value, with additional links providing resilience against network fluctuations.

  16. Evolving understanding of the evolution of herbicide resistance.

    Science.gov (United States)

    Gressel, Jonathan

    2009-11-01

    A greater number of, and more varied, modes of resistance have evolved in weeds than in other pests because the usage of herbicides is far more extensive than the usage of other pesticides, and because weed seed output is so great. The discovery and development of selective herbicides are more problematic than those of insecticides and fungicides, as these must only differentiate between plant and insect or pathogen. Herbicides are typically selective between plants, meaning that before deployment there are already some crops possessing natural herbicide resistance that weeds could evolve. The concepts of the evolution of resistance and the mechanisms of delaying resistance have evolved as nature has continually evolved new types of resistance. Major gene target-site mutations were the first types to evolve, with initial consideration devoted mainly to them, but slowly 'creeping' resistance, gradually accruing increasing levels of resistance, has become a major force owing to an incremental accumulation of genetic changes in weed populations. Weeds have evolved mechanisms unknown even in antibiotic as well as other drug and pesticide resistances. It is even possible that cases of epigenetic 'remembered' resistances may have appeared.

  17. Stability of Evolving Multiagent Systems.

    Science.gov (United States)

    De Wilde, P; Briscoe, G

    2011-08-01

    A multiagent system is a distributed system where the agents or nodes perform complex functions that cannot be written down in analytic form. Multiagent systems are highly connected, and the information they contain is mostly stored in the connections. When agents update their state, they take into account the state of the other agents, and they have access to those states via the connections. There is also external user-generated input into the multiagent system. As so much information is stored in the connections, agents are often memory less. This memory-less property, together with the randomness of the external input, has allowed us to model multiagent systems using Markov chains. In this paper, we look at multiagent systems that evolve, i.e., the number of agents varies according to the fitness of the individual agents. We extend our Markov chain model and define stability. This is the start of a methodology to control multiagent systems. We then build upon this to construct an entropy-based definition for the degree of instability (entropy of the limit probabilities), which we used to perform a stability analysis. We then investigated the stability of evolving agent populations through simulation and show that the results are consistent with the original definition of stability in nonevolving multiagent systems, proposed by Chli and De Wilde. This paper forms the theoretical basis for the construction of digital business ecosystems, and applications have been reported elsewhere.

  18. Are hourly precipitation extremes increasing faster than daily precipitation extremes?

    Science.gov (United States)

    Barbero, Renaud; Fowler, Hayley; Blenkinsop, Stephen; Lenderink, Geert

    2016-04-01

    Extreme precipitation events appear to be increasing with climate change in many regions of the world, including the United States. These extreme events have large societal impacts, as seen during the recent Texas-Oklahoma flooding in May 2015 which caused several billion in damages and left 47 deaths in its path. Better understanding of past changes in the characteristics of extreme rainfall events is thus critical for reliable projections of future changes. Although it has been documented in several studies that daily precipitation extremes are increasing across parts of the contiguous United States, very few studies have looked at hourly extremes. However, this is of primary importance as recent studies on the temperature scaling of extreme precipitation have shown that increases above the Clausius-Clapeyron (~ 7% °C-1) are possible for hourly precipitation. In this study, we used hourly precipitation data (HPD) from the National Climatic Data Center and extracted more than 1,000 stations across the US with more than 40 years of data spanning the period 1950-2010. As hourly measurements are often associated with a range of issues, the data underwent multiple quality control processes to exclude erroneous data. While no significant changes were found in annual maximum precipitation using both hourly and daily resolution datasets, significant increasing trends in terms of frequency of episodes exceeding present-day 95th percentiles of wet hourly/daily precipitation were observed across a significant portion of the US. The fraction of stations with significant increasing trends falls outside the confidence interval range during all seasons but the summer. While less than 12% of stations exhibit significant trends at the daily scale in the wintertime, more than 45% of stations, mostly clustered in central and Northern United States, show significant increasing trends at the hourly scale. This suggests that short-duration storms have increased faster than daily

  19. Flight loss linked to faster molecular evolution in insects.

    Science.gov (United States)

    Mitterboeck, T Fatima; Adamowicz, Sarah J

    2013-09-22

    The loss of flight ability has occurred thousands of times independently during insect evolution. Flight loss may be linked to higher molecular evolutionary rates because of reductions in effective population sizes (Ne) and relaxed selective constraints. Reduced dispersal ability increases population subdivision, may decrease geographical range size and increases (sub)population extinction risk, thus leading to an expected reduction in Ne. Additionally, flight loss in birds has been linked to higher molecular rates of energy-related genes, probably owing to relaxed selective constraints on energy metabolism. We tested for an association between insect flight loss and molecular rates through comparative analysis in 49 phylogenetically independent transitions spanning multiple taxa, including moths, flies, beetles, mayflies, stick insects, stoneflies, scorpionflies and caddisflies, using available nuclear and mitochondrial protein-coding DNA sequences. We estimated the rate of molecular evolution of flightless (FL) and related flight-capable lineages by ratios of non-synonymous-to-synonymous substitutions (dN/dS) and overall substitution rates (OSRs). Across multiple instances of flight loss, we show a significant pattern of higher dN/dS ratios and OSRs in FL lineages in mitochondrial but not nuclear genes. These patterns may be explained by relaxed selective constraints in FL ectotherms relating to energy metabolism, possibly in combination with reduced Ne.

  20. Evolving networks by merging cliques

    Science.gov (United States)

    Takemoto, Kazuhiro; Oosawa, Chikoo

    2005-10-01

    We propose a model for evolving networks by merging building blocks represented as complete graphs, reminiscent of modules in biological system or communities in sociology. The model shows power-law degree distributions, power-law clustering spectra, and high average clustering coefficients independent of network size. The analytical solutions indicate that a degree exponent is determined by the ratio of the number of merging nodes to that of all nodes in the blocks, demonstrating that the exponent is tunable, and are also applicable when the blocks are classical networks such as Erdös-Rényi or regular graphs. Our model becomes the same model as the Barabási-Albert model under a specific condition.

  1. Peripartum hysterectomy: an evolving picture.

    LENUS (Irish Health Repository)

    Turner, Michael J

    2012-02-01

    Peripartum hysterectomy (PH) is one of the obstetric catastrophes. Evidence is emerging that the role of PH in modern obstetrics is evolving. Improving management of postpartum hemorrhage and newer surgical techniques should decrease PH for uterine atony. Rising levels of repeat elective cesarean deliveries should decrease PH following uterine scar rupture in labor. Increasing cesarean rates, however, have led to an increase in the number of PHs for morbidly adherent placenta. In the case of uterine atony or rupture where PH is required, a subtotal PH is often sufficient. In the case of pathological placental localization involving the cervix, however, a total hysterectomy is required. Furthermore, the involvement of other pelvic structures may prospectively make the diagnosis difficult and the surgery challenging. If resources permit, PH for pathological placental localization merits a multidisciplinary approach. Despite advances in clinical practice, it is likely that peripartum hysterectomy will be more challenging for obstetricians in the future.

  2. Axial Spondyloarthritis: An Evolving Concept

    Directory of Open Access Journals (Sweden)

    Nelly Ziadé

    2015-07-01

    Full Text Available Axial spondyloarthritis (AxSpA is the prototype of a family of inter-related yet heterogeneous diseases sharing common clinical and genetic manifestations: the spondyloarthritides (SpAs. The condition mainly affects the sacroiliac joints and axial skeleton, and has a clear classification scheme, wider epidemiological data, and distinct therapeutic guidelines when compared with other SpAs. However, the concept of AxSpA has not been immutable over time and has evolved tremendously on many levels over the past decades. This review identifies the evolution of the AxSpA concept at two levels. First, at the level of classification, the old classifications and rationales leading to the current Assessment of SpondyloArthritis international Society (ASAS classification are reviewed, and the advantages and drawbacks are discussed. Second, at the therapeutic level, current and future treatments are described and treatment strategies are discussed.

  3. The evolving Gleason grading system.

    Science.gov (United States)

    Chen, Ni; Zhou, Qiao

    2016-02-01

    The Gleason grading system for prostate adenocarcinoma has evolved from its original scheme established in the 1960s-1970s, to a significantly modified system after two major consensus meetings conducted by the International Society of Urologic Pathology (ISUP) in 2005 and 2014, respectively. The Gleason grading system has been incorporated into the WHO classification of prostate cancer, the AJCC/UICC staging system, and the NCCN guidelines as one of the key factors in treatment decision. Both pathologists and clinicians need to fully understand the principles and practice of this grading system. We here briefly review the historical aspects of the original scheme and the recent developments of Gleason grading system, focusing on major changes over the years that resulted in the modern Gleason grading system, which has led to a new "Grade Group" system proposed by the 2014 ISUP consensus, and adopted by the 2016 WHO classification of tumours of the prostate.

  4. Mandelbrot Law of Evolving Networks

    CERN Document Server

    Ren, Xue-Zao; Wang, Bing-Hong; Zhou, Tao

    2011-01-01

    Degree distributions of many real networks are known to follow the Mandelbrot law, which can be considered as an extension of the power law that determined by not only the power-law exponent, but also the shifting coefficient. Although the shifting coefficient highly affect the shape of distribution, it receives less attention in the literature and in fact, mainstream analytical method based on backward or forward difference will lead to considerable deviation to its value. In this article, we show that the degree distribution of a growing network with linear preferential attachment approximately follows the Mandelbrot law. We propose an analytical method based on a recursive formula that can obtain a more accurate expression of the shifting coefficient than the previous methods. Simulations demonstrate the advantages of our method. This work provides a possible mechanism leading to the Mandelbrot law of evolving networks, and refines the mainstream analytical methods for the shifting coefficient.

  5. A faster immunofluorescence assay for tracking infection progress of human cytomegalovirus

    Institute of Scientific and Technical Information of China (English)

    Yingliang Duan; Lingfeng Miao; Hanqing Ye; Cuiqing Yang; Bishi Fu; Philip H.Schwartz; Simon Rayner; Elizabeth A.Fortunato; Min-Hua Luo

    2012-01-01

    Immunofluorescence assay (IFA) is one of the most frequently used methods in the biological sciences and clinic diagnosis,but it is expensive and time-consuming.To overcome these limitations,we developed a faster and more cost-effective IFA (f-IFA) by modifying the standard IFA,and applied this method to track the progression of human cytomegalovirus (HCMV) infection in different cells.The f-IFA that we developed not only saves time,but also dramatically reduces the quantity of antibody (Ab),which will facilitate the application of IFA in clinic diagnosis,f-IFA requires only 15 min for blocking,10 min incubation for each primary and secondary Abs,followed by 1 min extensive wash after each incubation.Only 25 μl of diluted Ab solution was needed for each coverslip at the primary and secondary Ab incubation steps.In addition,all steps were performed at room temperature.This f-IFA has been applied successfully to follow virion entry (pp65) and expression of viral genes (IE1,UL44,and pp65) in order to track the details of HCMV infection process.We found that ~0.5% HCMV-infected T98G cells formed multiple-micronuclei (IE1 and nucleus staining) and had virus shedding (pp65 staining) by f-IFA,which could not be detected by the traditional IFA.Our results indicated that f-IFA is a sensitive,convenient,fast,and cost-effective method for investigating the details of virus infection progress,especially HCMV infection.The faster and cost-effective feature with higher sensitivity and specilieity implies that f-IFA has potential applications in clinical diagnosis.

  6. Antibiotic-Resistant Neisseria gonorrhoeae Spread Faster with More Treatment, Not More Sexual Partners.

    Directory of Open Access Journals (Sweden)

    Stephanie M Fingerhuth

    2016-05-01

    Full Text Available The sexually transmitted bacterium Neisseria gonorrhoeae has developed resistance to all antibiotic classes that have been used for treatment and strains resistant to multiple antibiotic classes have evolved. In many countries, there is only one antibiotic remaining for empirical N. gonorrhoeae treatment, and antibiotic management to counteract resistance spread is urgently needed. Understanding dynamics and drivers of resistance spread can provide an improved rationale for antibiotic management. In our study, we first used antibiotic resistance surveillance data to estimate the rates at which antibiotic-resistant N. gonorrhoeae spread in two host populations, heterosexual men (HetM and men who have sex with men (MSM. We found higher rates of spread for MSM (0.86 to 2.38 y-1, mean doubling time: 6 months compared to HetM (0.24 to 0.86 y-1, mean doubling time: 16 months. We then developed a dynamic transmission model to reproduce the observed dynamics of N. gonorrhoeae transmission in populations of heterosexual men and women (HMW and MSM. We parameterized the model using sexual behavior data and calibrated it to N. gonorrhoeae prevalence and incidence data. In the model, antibiotic-resistant N. gonorrhoeae spread with a median rate of 0.88 y-1 in HMW and 3.12 y-1 in MSM. These rates correspond to median doubling times of 9 (HMW and 3 (MSM months. Assuming no fitness costs, the model shows the difference in the host population's treatment rate rather than the difference in the number of sexual partners explains the differential spread of resistance. As higher treatment rates result in faster spread of antibiotic resistance, treatment recommendations for N. gonorrhoeae should carefully balance prevention of infection and avoidance of resistance spread.

  7. Antibiotic-Resistant Neisseria gonorrhoeae Spread Faster with More Treatment, Not More Sexual Partners.

    Science.gov (United States)

    Fingerhuth, Stephanie M; Bonhoeffer, Sebastian; Low, Nicola; Althaus, Christian L

    2016-05-01

    The sexually transmitted bacterium Neisseria gonorrhoeae has developed resistance to all antibiotic classes that have been used for treatment and strains resistant to multiple antibiotic classes have evolved. In many countries, there is only one antibiotic remaining for empirical N. gonorrhoeae treatment, and antibiotic management to counteract resistance spread is urgently needed. Understanding dynamics and drivers of resistance spread can provide an improved rationale for antibiotic management. In our study, we first used antibiotic resistance surveillance data to estimate the rates at which antibiotic-resistant N. gonorrhoeae spread in two host populations, heterosexual men (HetM) and men who have sex with men (MSM). We found higher rates of spread for MSM (0.86 to 2.38 y-1, mean doubling time: 6 months) compared to HetM (0.24 to 0.86 y-1, mean doubling time: 16 months). We then developed a dynamic transmission model to reproduce the observed dynamics of N. gonorrhoeae transmission in populations of heterosexual men and women (HMW) and MSM. We parameterized the model using sexual behavior data and calibrated it to N. gonorrhoeae prevalence and incidence data. In the model, antibiotic-resistant N. gonorrhoeae spread with a median rate of 0.88 y-1 in HMW and 3.12 y-1 in MSM. These rates correspond to median doubling times of 9 (HMW) and 3 (MSM) months. Assuming no fitness costs, the model shows the difference in the host population's treatment rate rather than the difference in the number of sexual partners explains the differential spread of resistance. As higher treatment rates result in faster spread of antibiotic resistance, treatment recommendations for N. gonorrhoeae should carefully balance prevention of infection and avoidance of resistance spread.

  8. QERx- A Faster than Real-Time Emulator for Space Processors

    Science.gov (United States)

    Carvalho, B.; Pidgeon, A.; Robinson, P.

    2012-08-01

    Developing software for space systems is challenging. Especially because, in order to be sure it can cope with the harshness of the environment and the imperative requirements and constrains imposed by the platform were it will run, it needs to be tested exhaustively. Software Validation Facilities (SVF) are known to the industry and developers, and provide the means to run the On-Board Software (OBSW) in a realistic environment, allowing the development team to debug and test the software.But the challenge is to be able to keep up with the performance of the new processors (LEON2 and LEON3), which need to be emulated within the SVF. Such processor emulators are also used in Operational Simulators, used to support mission preparation and train mission operators. These simulators mimic the satellite and its behaviour, as realistically as possible. For test/operational efficiency reasons and because they will need to interact with external systems, both these uses cases require the processor emulators to provide real-time, or faster, performance.It is known to the industry that the performance of previously available emulators is not enough to cope with the performance of the new processors available in the market. SciSys approached this problem with dynamic translation technology trying to keep costs down by avoiding a hardware solution and keeping the integration flexibility of full software emulation.SciSys presented “QERx: A High Performance Emulator for Software Validation and Simulations” [1], in a previous DASIA event. Since then that idea has evolved and QERx has been successfully validated. SciSys is now presenting QERx as a product that can be tailored to fit different emulation needs. This paper will present QERx latest developments and current status.

  9. Recommendation in evolving online networks

    Science.gov (United States)

    Hu, Xiao; Zeng, An; Shang, Ming-Sheng

    2016-02-01

    Recommender system is an effective tool to find the most relevant information for online users. By analyzing the historical selection records of users, recommender system predicts the most likely future links in the user-item network and accordingly constructs a personalized recommendation list for each user. So far, the recommendation process is mostly investigated in static user-item networks. In this paper, we propose a model which allows us to examine the performance of the state-of-the-art recommendation algorithms in evolving networks. We find that the recommendation accuracy in general decreases with time if the evolution of the online network fully depends on the recommendation. Interestingly, some randomness in users' choice can significantly improve the long-term accuracy of the recommendation algorithm. When a hybrid recommendation algorithm is applied, we find that the optimal parameter gradually shifts towards the diversity-favoring recommendation algorithm, indicating that recommendation diversity is essential to keep a high long-term recommendation accuracy. Finally, we confirm our conclusions by studying the recommendation on networks with the real evolution data.

  10. CERN internal communication is evolving

    CERN Multimedia

    2016-01-01

    CERN news will now be regularly updated on the CERN People page (see here).      Dear readers, All over the world, communication is becoming increasingly instantaneous, with news published in real time on websites and social networks. In order to keep pace with these changes, CERN's internal communication is evolving too. From now on, you will be informed of what’s happening at CERN more often via the “CERN people” page, which will frequently be updated with news. The Bulletin is following this trend too: twice a month, we will compile the most important articles published on the CERN site, with a brand-new layout. You will receive an e-mail every two weeks as soon as this new form of the Bulletin is available. If you have interesting news or stories to share, tell us about them through the form at: https://communications.web.cern.ch/got-story-cern-website​. You can also find out about news from CERN in real time...

  11. Multiscale modelling of evolving foams

    Science.gov (United States)

    Saye, R. I.; Sethian, J. A.

    2016-06-01

    We present a set of multi-scale interlinked algorithms to model the dynamics of evolving foams. These algorithms couple the key effects of macroscopic bubble rearrangement, thin film drainage, and membrane rupture. For each of the mechanisms, we construct consistent and accurate algorithms, and couple them together to work across the wide range of space and time scales that occur in foam dynamics. These algorithms include second order finite difference projection methods for computing incompressible fluid flow on the macroscale, second order finite element methods to solve thin film drainage equations in the lamellae and Plateau borders, multiphase Voronoi Implicit Interface Methods to track interconnected membrane boundaries and capture topological changes, and Lagrangian particle methods for conservative liquid redistribution during rearrangement and rupture. We derive a full set of numerical approximations that are coupled via interface jump conditions and flux boundary conditions, and show convergence for the individual mechanisms. We demonstrate our approach by computing a variety of foam dynamics, including coupled evolution of three-dimensional bubble clusters attached to an anchored membrane and collapse of a foam cluster.

  12. Faster, safer, and better DNA purification by ultracentrifugation using GelRed stain and development of mismatch oligo DNA for genome walking.

    Science.gov (United States)

    Kasajima, Ichiro; Ohtsubo, Norihiro; Sasaki, Katsutomo

    2014-01-01

    Purification of plant DNA involves lengthy ultracentrifugation using ethidium bromide. Here, ultracentrifugation method is improved by staining with GelRed. The resulting method is faster, safer and of higher sensitivity. Purified DNA quality was confirmed by treatment with restriction enzymes and isolation of gene promoters. New type of long adaptor with mismatch sequence was also developed for promoter isolation.

  13. Local synteny and codon usage contribute to asymmetric sequence divergence of Saccharomyces cerevisiae gene duplicates

    Directory of Open Access Journals (Sweden)

    Bergthorsson Ulfar

    2011-09-01

    Full Text Available Abstract Background Duplicated genes frequently experience asymmetric rates of sequence evolution. Relaxed selective constraints and positive selection have both been invoked to explain the observation that one paralog within a gene-duplicate pair exhibits an accelerated rate of sequence evolution. In the majority of studies where asymmetric divergence has been established, there is no indication as to which gene copy, ancestral or derived, is evolving more rapidly. In this study we investigated the effect of local synteny (gene-neighborhood conservation and codon usage on the sequence evolution of gene duplicates in the S. cerevisiae genome. We further distinguish the gene duplicates into those that originated from a whole-genome duplication (WGD event (ohnologs versus small-scale duplications (SSD to determine if there exist any differences in their patterns of sequence evolution. Results For SSD pairs, the derived copy evolves faster than the ancestral copy. However, there is no relationship between rate asymmetry and synteny conservation (ancestral-like versus derived-like in ohnologs. mRNA abundance and optimal codon usage as measured by the CAI is lower in the derived SSD copies relative to ancestral paralogs. Moreover, in the case of ohnologs, the faster-evolving copy has lower CAI and lowered expression. Conclusions Together, these results suggest that relaxation of selection for codon usage and gene expression contribute to rate asymmetry in the evolution of duplicated genes and that in SSD pairs, the relaxation of selection stems from the loss of ancestral regulatory information in the derived copy.

  14. Evolving Superantigens of Staphylococcus Aureus

    Science.gov (United States)

    2000-01-01

    20000302 m (81 ELSEVIER FEMS Immunology and Medical Microbiology 27 (2000) 1-7 IMMUNOLOGY AND MEDICAL MICROBIOLOGY www.fems-microbiology.org...DISTRIBUTION STATEMENT A Approved for Public Release Distribution Unlimited R.G. Ulrich IFEMS Immunology and Medical Microbiology 27 (2000) 1-7 w...nonessential gene products that are R.G. Ulrich IFEMS Immunology and Medical Microbiology 27 (2000) 1-7 selectively expressed and result in lower host

  15. ECG Sensor Card with Evolving RBP Algorithms for Human Verification

    Science.gov (United States)

    Tseng, Kuo-Kun; Huang, Huang-Nan; Zeng, Fufu; Tu, Shu-Yi

    2015-01-01

    It is known that cardiac and respiratory rhythms in electrocardiograms (ECGs) are highly nonlinear and non-stationary. As a result, most traditional time-domain algorithms are inadequate for characterizing the complex dynamics of the ECG. This paper proposes a new ECG sensor card and a statistical-based ECG algorithm, with the aid of a reduced binary pattern (RBP), with the aim of achieving faster ECG human identity recognition with high accuracy. The proposed algorithm has one advantage that previous ECG algorithms lack—the waveform complex information and de-noising preprocessing can be bypassed; therefore, it is more suitable for non-stationary ECG signals. Experimental results tested on two public ECG databases (MIT-BIH) from MIT University confirm that the proposed scheme is feasible with excellent accuracy, low complexity, and speedy processing. To be more specific, the advanced RBP algorithm achieves high accuracy in human identity recognition and is executed at least nine times faster than previous algorithms. Moreover, based on the test results from a long-term ECG database, the evolving RBP algorithm also demonstrates superior capability in handling long-term and non-stationary ECG signals. PMID:26307995

  16. ECG Sensor Card with Evolving RBP Algorithms for Human Verification

    Directory of Open Access Journals (Sweden)

    Kuo-Kun Tseng

    2015-08-01

    Full Text Available It is known that cardiac and respiratory rhythms in electrocardiograms (ECGs are highly nonlinear and non-stationary. As a result, most traditional time-domain algorithms are inadequate for characterizing the complex dynamics of the ECG. This paper proposes a new ECG sensor card and a statistical-based ECG algorithm, with the aid of a reduced binary pattern (RBP, with the aim of achieving faster ECG human identity recognition with high accuracy. The proposed algorithm has one advantage that previous ECG algorithms lack—the waveform complex information and de-noising preprocessing can be bypassed; therefore, it is more suitable for non-stationary ECG signals. Experimental results tested on two public ECG databases (MIT-BIH from MIT University confirm that the proposed scheme is feasible with excellent accuracy, low complexity, and speedy processing. To be more specific, the advanced RBP algorithm achieves high accuracy in human identity recognition and is executed at least nine times faster than previous algorithms. Moreover, based on the test results from a long-term ECG database, the evolving RBP algorithm also demonstrates superior capability in handling long-term and non-stationary ECG signals.

  17. ECG Sensor Card with Evolving RBP Algorithms for Human Verification.

    Science.gov (United States)

    Tseng, Kuo-Kun; Huang, Huang-Nan; Zeng, Fufu; Tu, Shu-Yi

    2015-08-21

    It is known that cardiac and respiratory rhythms in electrocardiograms (ECGs) are highly nonlinear and non-stationary. As a result, most traditional time-domain algorithms are inadequate for characterizing the complex dynamics of the ECG. This paper proposes a new ECG sensor card and a statistical-based ECG algorithm, with the aid of a reduced binary pattern (RBP), with the aim of achieving faster ECG human identity recognition with high accuracy. The proposed algorithm has one advantage that previous ECG algorithms lack-the waveform complex information and de-noising preprocessing can be bypassed; therefore, it is more suitable for non-stationary ECG signals. Experimental results tested on two public ECG databases (MIT-BIH) from MIT University confirm that the proposed scheme is feasible with excellent accuracy, low complexity, and speedy processing. To be more specific, the advanced RBP algorithm achieves high accuracy in human identity recognition and is executed at least nine times faster than previous algorithms. Moreover, based on the test results from a long-term ECG database, the evolving RBP algorithm also demonstrates superior capability in handling long-term and non-stationary ECG signals.

  18. Evolvability Search: Directly Selecting for Evolvability in order to Study and Produce It

    OpenAIRE

    Mengistu, Henok; Lehman, Joel Anthony; Clune, Jeff

    2016-01-01

    One hallmark of natural organisms is their significant evolvability, i.e.,their increased potential for further evolution. However, reproducing such evolvability in artificial evolution remains a challenge, which both reduces the performance of evolutionary algorithms and inhibits the study of evolvable digital phenotypes. Although some types of selection in evolutionary computation indirectly encourage evolvability, one unexplored possibility is to directly select for evolvability. To do so,...

  19. Voyages Through Time: Everything Evolves

    Science.gov (United States)

    Pendleton, Y. J.; Tarter, J. C.; DeVore, E. K.; O'Sullivan, K. A.; Taylor, S. M.

    2001-12-01

    Evolutionary change is a powerful framework for studying our world and our place therein. It is a recurring theme in every realm of science: over time, the universe, the planet Earth, life, and human technologies all change, albeit on vastly different scales. Evolution offers scientific explanations for the age-old question, "Where did we come from?" In addition, historical perspectives of science show how our understanding has evolved over time. The complexities of all of these systems will never reveal a "finished" story. But it is a story of epic size, capable of inspiring awe and of expanding our sense of time and place, and eminently worthy of investigating. This story is the basis of Voyages Through Time. Voyages Through Time (VTT), provides teachers with not only background science content and pedagogy, but also with materials and resources for the teaching of evolution. The six modules, Cosmic Evolution, Planetary Evolution, Origin of Life, Evolution of Life, Hominid Evolution, and Evolution of Technology, emphasize student inquiry, and promote the nature of science, as recommended in the NSES and BSL. The modules are unified by the overarching theme of evolution and the meta questions: "What is changing?" "What is the rate of change?" and "What is the mechanism of change?" Determination of student outcomes for the project required effective collaboration of scientists, teachers, students and media specialists. The broadest curricula students outcomes are 1) an enjoyment of science, 2) an understanding of the nature of science, especially the understanding of evidence and re-evaluation, and 3) key science content. The curriculum is being developed by the SETI Institute, NASA Ames Research Center, California Academy of Sciences, and San Francisco State University, and is funded by the NSF (IMD 9730693), with support form Hewlett-Packard Company, The Foundation for Microbiology, Combined Federated Charities, NASA Astrobiology Institute, and NASA Fundamental

  20. Faster increases in human life expectancy could lead to slower population aging.

    Directory of Open Access Journals (Sweden)

    Warren C Sanderson

    Full Text Available Counterintuitively, faster increases in human life expectancy could lead to slower population aging. The conventional view that faster increases in human life expectancy would lead to faster population aging is based on the assumption that people become old at a fixed chronological age. A preferable alternative is to base measures of aging on people's time left to death, because this is more closely related to the characteristics that are associated with old age. Using this alternative interpretation, we show that faster increases in life expectancy would lead to slower population aging. Among other things, this finding affects the assessment of the speed at which countries will age.

  1. Faster Increases in Human Life Expectancy Could Lead to Slower Population Aging

    Science.gov (United States)

    2015-01-01

    Counterintuitively, faster increases in human life expectancy could lead to slower population aging. The conventional view that faster increases in human life expectancy would lead to faster population aging is based on the assumption that people become old at a fixed chronological age. A preferable alternative is to base measures of aging on people’s time left to death, because this is more closely related to the characteristics that are associated with old age. Using this alternative interpretation, we show that faster increases in life expectancy would lead to slower population aging. Among other things, this finding affects the assessment of the speed at which countries will age. PMID:25876033

  2. Evolving concepts in primary sclerosing cholangitis.

    Science.gov (United States)

    Krones, Elisabeth; Graziadei, Ivo; Trauner, Michael; Fickert, Peter

    2012-03-01

    Patients suffering from primary sclerosing cholangitis (PSC) show considerable differences regarding clinical manifestations (i.e. large duct versus small-duct PSC, presence or absence of concomitant inflammatory bowel disease), disease progression, risk for malignancy and response to therapy, raising the question whether PSC may represent a mixed bag of diseases of different aetiologies. The growing list of secondary causes and diseases 'mimicking' or even overlapping with PSC (e.g. IgG4-associated sclerosing cholangitis), which frequently causes problems in clear-cut discrimination from classic PSC and the emerging knowledge about potential disease modifier genes (e.g. variants of CFTR, TGR5 and MDR3) support such a conceptual view. In addition, PSC in children differs significantly from PSC in adults in several aspects resulting in distinct therapeutic concepts. From a clinical perspective, appropriate categorization and careful differential diagnosis are essential for the management of concerned patients. Therefore, the aim of the current review is to summarize current and evolving pathophysiological concepts and to provide up-to-date perspectives including future treatment strategies for PSC.

  3. Identification of a gene for an ancient cytokine, interleukin 15-like, in mammals; interleukins 2 and 15 co-evolved with this third family member, all sharing binding motifs for IL-15Rα.

    Science.gov (United States)

    Dijkstra, Johannes M; Takizawa, Fumio; Fischer, Uwe; Friedrich, Maik; Soto-Lampe, Veronica; Lefèvre, Christophe; Lenk, Matthias; Karger, Axel; Matsui, Taei; Hashimoto, Keiichiro

    2014-02-01

    Interleukins 2 and 15 (IL-2 and IL-15) are highly differentiated but related cytokines with overlapping, yet also distinct functions, and established benefits for medical drug use. The present study identified a gene for an ancient third IL-2/15 family member in reptiles and mammals, interleukin 15-like (IL-15L), which hitherto was only reported in fish. IL-15L genes with intact open reading frames (ORFs) and evidence of transcription, and a recent past of purifying selection, were found for cattle, horse, sheep, pig and rabbit. In human and mouse the IL-15L ORF is incapacitated. Although deduced IL-15L proteins share only ~21 % overall amino acid identity with IL-15, they share many of the IL-15 residues important for binding to receptor chain IL-15Rα, and recombinant bovine IL-15L was shown to interact with IL-15Rα indeed. Comparison of sequence motifs indicates that capacity for binding IL-15Rα is an ancestral characteristic of the IL-2/15/15L family, in accordance with a recent study which showed that in fish both IL-2 and IL-15 can bind IL-15Rα. Evidence reveals that the species lineage leading to mammals started out with three similar cytokines IL-2, IL-15 and IL-15L, and that later in evolution (1) IL-2 and IL-2Rα receptor chain acquired a new and specific binding mode and (2) IL-15L was lost in several but not all groups of mammals. The present study forms an important step forward in understanding this potent family of cytokines, and may help to improve future strategies for their application in veterinarian and human medicine.

  4. Evolving evolutionary algorithms using linear genetic programming.

    Science.gov (United States)

    Oltean, Mihai

    2005-01-01

    A new model for evolving Evolutionary Algorithms is proposed in this paper. The model is based on the Linear Genetic Programming (LGP) technique. Every LGP chromosome encodes an EA which is used for solving a particular problem. Several Evolutionary Algorithms for function optimization, the Traveling Salesman Problem and the Quadratic Assignment Problem are evolved by using the considered model. Numerical experiments show that the evolved Evolutionary Algorithms perform similarly and sometimes even better than standard approaches for several well-known benchmarking problems.

  5. When is the helicopter faster? A comparison of helicopter and ground ambulance transport times.

    Science.gov (United States)

    Diaz, Marco A; Hendey, Gregory W; Bivins, Herbert G

    2005-01-01

    A retrospective analysis of 7,854 ground ambulance and 1,075 helicopter transports was conducted. The 911-hospital arrival intervals for three transport methods were compared: ground, helicopter dispatched simultaneously with ground unit, and helicopter dispatched nonsimultaneously after ground unit response. Compared with ground transports, simultaneously dispatched helicopter transports had significantly shorter 911-hospital arrival intervals at all distances greater than 10 miles from the hospital. Nonsimultaneously dispatched helicopter transport was significantly faster than ground at distances greater than 45 miles, and simultaneous helicopter dispatch was faster than nonsimultaneous at virtually all distances. Ground transport was significantly faster than either air transport modality at distances less than 10 miles from the hospital. Ground ambulance transport provided the shortest 911-hospital arrival interval at distances less than 10 miles from the hospital. At distances greater than 10 miles, simultaneously dispatched air transport was faster. Nonsimultaneous dispatched helicopter transport was faster than ground if greater than 45 miles from the hospital.

  6. Evolving Technologies: A View to Tomorrow

    Science.gov (United States)

    Tamarkin, Molly; Rodrigo, Shelley

    2011-01-01

    Technology leaders must participate in strategy creation as well as operational delivery within higher education institutions. The future of higher education--the view to tomorrow--is irrevocably integrated and intertwined with evolving technologies. This article focuses on two specific evolving technologies: (1) alternative IT sourcing; and (2)…

  7. Evolving Technologies: A View to Tomorrow

    Science.gov (United States)

    Tamarkin, Molly; Rodrigo, Shelley

    2011-01-01

    Technology leaders must participate in strategy creation as well as operational delivery within higher education institutions. The future of higher education--the view to tomorrow--is irrevocably integrated and intertwined with evolving technologies. This article focuses on two specific evolving technologies: (1) alternative IT sourcing; and (2)…

  8. The Problem of Evolving a Genetic Code

    Science.gov (United States)

    Woese, Carl R.

    1970-01-01

    Proposes models for the evolution of the genetic code and translation mechanisms. Suggests that the translation process is so complex and precise that it must have evolved in many stages, and that the evolution of the code was influenced by the constraints imposed by the evolving translation mechanism. (EB)

  9. The Computational Complexity of Evolving Systems

    NARCIS (Netherlands)

    Verbaan, P.R.A.

    2006-01-01

    Evolving systems are systems that change over time. Examples of evolving systems are computers with soft-and hardware upgrades and dynamic networks of computers that communicate with each other, but also colonies of cooperating organisms or cells within a single organism. In this research, several m

  10. Mechanical Determinants of Faster Change of Direction and Agility Performance in Female Basketball Athletes.

    Science.gov (United States)

    Spiteri, Tania; Newton, Robert U; Binetti, Molly; Hart, Nicolas H; Sheppard, Jeremy M; Nimphius, Sophia

    2015-08-01

    Change of direction (COD) and agility require the integration of multiple components to produce a faster performance. However, the mechanisms contributing to a faster performance without the confounding factor of athlete expertise or gender is currently unknown. Therefore, the purpose of this study was to assess body composition, strength, and kinetic profile required for a faster COD and agility performance across multiple directional changes. Six faster and 6 slower (n = 12) elite female basketball athletes completed a maximal dynamic back squat; eccentric and concentric only back squat; isometric midthigh pull; whole-body scan to determine lean, fat, and total mass; 505 COD test; T-test; and a multidirectional agility test over in-ground force plates to obtain relevant kinetic measures. Group (faster and slower) by test (2 × 3) multivariate analyses of variance with follow-up analyses of variance were conducted to examine differences between faster and slower groups and each COD and agility test (p ≤ 0.05). Faster athletes during the 505 COD test produced significantly greater vertical force (p = 0.002) and eccentric and isometric strength capacity (p = 0.001). Faster agility and T-test athletes demonstrated significantly shorter contact times (p = 0.001), greater propulsive impulse (p = 0.02), isometric strength, and relative lean mass compared with slower athletes. Differences between faster athletes across each test seem to be attributed to the mechanical demands of the directional change, increasing force and impulse application as the degree of directional change increased. These findings indicate that different mechanical properties are required to produce a faster COD and agility performances, and the importance of a greater strength capacity to enable greater mechanical adjustment through force production and body control, during different directional changes.

  11. Reading faster

    OpenAIRE

    Paul Nation

    2009-01-01

    This article describes the visual nature of the reading process as it relates to reading speed. It points out that there is a physical limit on normal reading speed and beyond this limit the reading process will be different from normal reading where almost every word is attended to. The article describes a range of activities for developing reading fluency, and suggests how the development of fluency can become part of a reading programme.

  12. Reading faster

    Directory of Open Access Journals (Sweden)

    Paul Nation

    2009-12-01

    Full Text Available This article describes the visual nature of the reading process as it relates to reading speed. It points out that there is a physical limit on normal reading speed and beyond this limit the reading process will be different from normal reading where almost every word is attended to. The article describes a range of activities for developing reading fluency, and suggests how the development of fluency can become part of a reading programme.

  13. Gene

    Data.gov (United States)

    U.S. Department of Health & Human Services — Gene integrates information from a wide range of species. A record may include nomenclature, Reference Sequences (RefSeqs), maps, pathways, variations, phenotypes,...

  14. Evolution of trappin genes in mammals

    Directory of Open Access Journals (Sweden)

    Furutani Yutaka

    2010-01-01

    Full Text Available Abstract Background Trappin is a multifunctional host-defense peptide that has antiproteolytic, antiinflammatory, and antimicrobial activities. The numbers and compositions of trappin paralogs vary among mammalian species: human and sheep have a single trappin-2 gene; mouse and rat have no trappin gene; pig and cow have multiple trappin genes; and guinea pig has a trappin gene and two other derivativegenes. Independent duplications of trappin genes in pig and cow were observed recently after the species were separated. To determine whether these trappin gene duplications are restricted only to certain mammalian lineages, we analyzed recently-developed genome databases for the presence of duplicate trappin genes. Results The database analyses revealed that: 1 duplicated trappin multigenes were found recently in the nine-banded armadillo; 2 duplicated two trappin genes had been found in the Afrotherian species (elephant, tenrec, and hyrax since ancient days; 3 a single trappin-2 gene was found in various eutherians species; and 4 no typical trappin gene has been found in chicken, zebra finch, and opossum. Bayesian analysis estimated the date of the duplication of trappin genes in the Afrotheria, guinea pig, armadillo, cow, and pig to be 244, 35, 11, 13, and 3 million-years ago, respectively. The coding regions of trappin multigenes of almadillo, bovine, and pig evolved much faster than the noncoding exons, introns, and the flanking regions, showing that these genes have undergone accelerated evolution, and positive Darwinian selection was observed in pig-specific trappin paralogs. Conclusion These results suggest that trappin is an eutherian-specific molecule and eutherian genomes have the potential to form trappin multigenes.

  15. Significant Comparative Characteristics between Orphan and Nonorphan Genes in the Rice (Oryza sativa L. Genome

    Directory of Open Access Journals (Sweden)

    Wen-Jiu Guo

    2007-01-01

    Full Text Available Microsatellites are short tandem repeats of one to six bases in genomic DNA. As microsatellites are highly polymorphic and play a vital role in gene function and recombination, they are an attractive subject for research in evolution and in the genetics and breeding of animals and plants. Orphan genes have no known homologs in existing databases. Using bioinformatic computation and statistical analysis, we identified 19,26 orphan genes in the rice (Oryza sativa ssp. Japanica cv. Nipponbare proteome. We found that a larger proportion of orphan genes are expressed after sexual maturation and under environmental pressure than nonorphan genes. Orphan genes generally have shorter protein lengths and intron size, and are faster evolving. Additionally, orphan genes have fewer PROSITE patterns with larger pattern sizes than those in nonorphan genes. The average microsatellite content and the percentage of trinucleotide repeats in orphan genes are also significantly higher than in nonorphan genes. Microsatellites are found less often in PROSITE patterns in orphan genes. Taken together, these orphan gene characteristics suggest that microsatellites play an important role in orphan gene evolution and expression.

  16. Bed bugs evolved unique adaptive strategy to resist pyrethroid insecticides.

    Science.gov (United States)

    Zhu, Fang; Gujar, Hemant; Gordon, Jennifer R; Haynes, Kenneth F; Potter, Michael F; Palli, Subba R

    2013-01-01

    Recent advances in genomic and post-genomic technologies have facilitated a genome-wide analysis of the insecticide resistance-associated genes in insects. Through bed bug, Cimex lectularius transcriptome analysis, we identified 14 molecular markers associated with pyrethroid resistance. Our studies revealed that most of the resistance-associated genes functioning in diverse mechanisms are expressed in the epidermal layer of the integument, which could prevent or slow down the toxin from reaching the target sites on nerve cells, where an additional layer of resistance (kdr) is possible. This strategy evolved in bed bugs is based on their unique morphological, physiological and behavioral characteristics and has not been reported in any other insect species. RNA interference-aided knockdown of resistance associated genes showed the relative contribution of each mechanism towards overall resistance development. Understanding the complexity of adaptive strategies employed by bed bugs will help in designing the most effective and sustainable bed bug control methods.

  17. Insect sex determination: it all evolves around transformer.

    Science.gov (United States)

    Verhulst, Eveline C; van de Zande, Louis; Beukeboom, Leo W

    2010-08-01

    Insects exhibit a variety of sex determining mechanisms including male or female heterogamety and haplodiploidy. The primary signal that starts sex determination is processed by a cascade of genes ending with the conserved switch doublesex that controls sexual differentiation. Transformer is the doublesex splicing regulator and has been found in all examined insects, indicating its ancestral function as a sex-determining gene. Despite this conserved function, the variation in transformer nucleotide sequence, amino acid composition and protein structure can accommodate a multitude of upstream sex determining signals. Transformer regulation of doublesex and its taxonomic distribution indicate that the doublesex-transformer axis is conserved among all insects and that transformer is the key gene around which variation in sex determining mechanisms has evolved.

  18. Molecular Mechanisms and Evolutionary Processes Contributing to Accelerated Divergence of Gene Expression on the Drosophila X Chromosome

    Science.gov (United States)

    Coolon, Joseph D.; Stevenson, Kraig R.; McManus, C. Joel; Yang, Bing; Graveley, Brenton R.; Wittkopp, Patricia J.

    2015-01-01

    In species with a heterogametic sex, population genetics theory predicts that DNA sequences on the X chromosome can evolve faster than comparable sequences on autosomes. Both neutral and nonneutral evolutionary processes can generate this pattern. Complex traits like gene expression are not predicted to have accelerated evolution by these theories, yet a “faster-X” pattern of gene expression divergence has recently been reported for both Drosophila and mammals. Here, we test the hypothesis that accelerated adaptive evolution of cis-regulatory sequences on the X chromosome is responsible for this pattern by comparing the relative contributions of cis- and trans-regulatory changes to patterns of faster-X expression divergence observed between strains and species of Drosophila with a range of divergence times. We find support for this hypothesis, especially among male-biased genes, when comparing different species. However, we also find evidence that trans-regulatory differences contribute to a faster-X pattern of expression divergence both within and between species. This contribution is surprising because trans-acting regulators of X-linked genes are generally assumed to be randomly distributed throughout the genome. We found, however, that X-linked transcription factors appear to preferentially regulate expression of X-linked genes, providing a potential mechanistic explanation for this result. The contribution of trans-regulatory variation to faster-X expression divergence was larger within than between species, suggesting that it is more likely to result from neutral processes than positive selection. These data show how accelerated evolution of both coding and noncoding sequences on the X chromosome can lead to accelerated expression divergence on the X chromosome relative to autosomes. PMID:26041937

  19. Identifying the Right Disease Targets to Develop Better Drugs, Faster | NIH MedlinePlus the Magazine

    Science.gov (United States)

    ... JavaScript on. Identifying the Right Disease Targets to Develop Better Drugs, Faster Past Issues / Spring 2014 Table ... a-dozen pharmaceutical companies are now racing to develop drugs that lower cholesterol by blocking PCSK9. Are ...

  20. Questions Students Ask: How Can a Downhill Skier Move Faster than a Sky Diver?

    Science.gov (United States)

    Armenti, Angelo, Jr.

    1984-01-01

    Discusses the relationship of gravity, coefficient of friction, surface area, and Newton's second law to explain the physics involved in downhill skiers being able to move faster than sky divers in free fall. (JM)

  1. WSC-07: Evolving the Web Services Challenge

    NARCIS (Netherlands)

    Blake, M. Brian; Cheung, William K.W.; Jaeger, Michael C.; Wombacher, Andreas

    2007-01-01

    Service-oriented architecture (SOA) is an evolving architectural paradigm where businesses can expose their capabilities as modular, network-accessible software services. By decomposing capabilities into modular services, organizations can share their offerings at multiple levels of granularity whil

  2. Robot navigation system using intrinsic evolvable hardware

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    Recently there has been great interest in the idea that evolvable system based on the principle of ar tifcial intelligence can be used to continuously and autonomously adapt the behaviour of physically embedded systems such as autonomous mobile robots and intelligent home devices. Meanwhile, we have seen the introduc tion of evolvable hardware(EHW): new integrated electronic circuits that are able to continuously evolve to a dapt the chages in the environment implemented by evolutionary algorithms such as genetic algorithm(GA)and reinforcement learning. This paper concentrates on developing a robotic navigation system whose basic behav iours are obstacle avoidance and light source navigation. The results demonstrate that the intrinsic evolvable hardware system is able to create the stable robotiiuc behaviours as required in the real world instead of the tra ditional hardware systems.

  3. Evolvability Characterization in the Context of SOA

    Science.gov (United States)

    Arciniegas H., Jose L.; Dueñas L., Juan C.

    Service-Oriented Architecture (SOA) is an architectural style which promotes reuse of self-contained services. These self-contained services allow a better consideration of software quality characteristics as they can be independently analyzed. In our work, the evolvability quality characteristic has been considered, due to its impact in the stages of Maintenance and Evolution (M&E) for the software enterprises. Three goals are underlined in this paper: first, the relationship between SOA and quality characteristics focusing on a precise definition of evolvability of a software product from the SOA perspective, second a M&E model for SOA, and finally, some experiences are presented in order to assess evolvability in real software products. Two case studies have been executed: the first one analyzing the evolvability of the OSGi framework. And in the second case, the model is used in local Small and Medium Enterprises (SMEs), where an improvement process has been executed.

  4. Acquiring Evolving Technologies: Web Services Standards

    Science.gov (United States)

    2016-06-30

    2006 Carnegie Mellon University Acquiring Evolving Technologies: Web Services Standards Harry L. Levinson Software Engineering Institute Carnegie...Acquiring Evolving Technologies: Web Services Standards 5a. CONTRACT NUMBER 5b. GRANT NUMBER 5c. PROGRAM ELEMENT NUMBER 6. AUTHOR(S) 5d. PROJECT...NUMBER OF PAGES 22 19a. NAME OF RESPONSIBLE PERSON a. REPORT unclassified b. ABSTRACT unclassified c. THIS PAGE unclassified Standard Form

  5. The effect of scale-free topology on the robustness and evolvability of genetic regulatory networks

    OpenAIRE

    Greenbury, Sam F.; Johnston, Iain G.; Matthew A Smith; Doye, Jonathan P. K.; Louis, Ard A.

    2010-01-01

    Abstract We investigate how scale-free (SF) and Erdos-Renyi (ER) topologies affect the interplay between evolvability and robustness of model gene regulatory networks with Boolean threshold dynamics. In agreement with Oikonomou and Cluzel (2006) we find that networks with SFin topologies, that is SF topology for incoming nodes and ER topology for outgoing nodes, are significantly more evolvable towards specific oscillatory targets than networks with ER topology for both incoming an...

  6. Molecular evolution of the exon 2 of CHS genes and the possibility of its application to plant phylogenetic analysis

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    The exon 2 of chalcone synthase (CHS) gene is relatively conserved during evolution.In this study,three exon 2 fragments from two species in gymnosperm (Cycas panzhihuaensis,Ginkgo biloba) and seven from four species in angiosperm (Magnolia denudata,Salix babylonica,Nymphaea tetragona,Camellia japonica) have been amplified by PCR from genomic DNA and sequenced.Together with other 73 sequences of CHS collected from EMBL database and literature,these sequences,which embrace 19 families of gymnosperm and angiosperm,have been analyzed for their phylogenetic relations by parsimony method.The result indicated that sequences from the same systematic family usually grouped together except those from Theaceae,Magnoliaceae and Nymphaeaceae.The relative rate test revealed the rate heterogeneity of CHS genes among the families.For the nucleotide substitution the sequences from Asteraceae and Solanaceae evolve faster than those from the other families analyzed while the sequences from Poaceae,Asteraceae and Solanaceae evolve faster for the nonsynonymous substitution.These results suggest that the duplication and extinction events of CHS genes are different among systematic families,therefore it seems impractical to look for orthologous sequences from CHS genes to study plant phylogeny at the family level and/or above.However,it is possible to do so below the family level.

  7. Reliability of genetic networks is evolvable

    Science.gov (United States)

    Braunewell, Stefan; Bornholdt, Stefan

    2008-06-01

    Control of the living cell functions with remarkable reliability despite the stochastic nature of the underlying molecular networks—a property presumably optimized by biological evolution. We ask here to what extent the ability of a stochastic dynamical network to produce reliable dynamics is an evolvable trait. Using an evolutionary algorithm based on a deterministic selection criterion for the reliability of dynamical attractors, we evolve networks of noisy discrete threshold nodes. We find that, starting from any random network, reliability of the attractor landscape can often be achieved with only a few small changes to the network structure. Further, the evolvability of networks toward reliable dynamics while retaining their function is investigated and a high success rate is found.

  8. Metanetworks of artificially evolved regulatory networks

    CERN Document Server

    Danacı, Burçin

    2014-01-01

    We study metanetworks arising in genotype and phenotype spaces, in the context of a model population of Boolean graphs evolved under selection for short dynamical attractors. We define the adjacency matrix of a graph as its genotype, which gets mutated in the course of evolution, while its phenotype is its set of dynamical attractors. Metanetworks in the genotype and phenotype spaces are formed, respectively, by genetic proximity and by phenotypic similarity, the latter weighted by the sizes of the basins of attraction of the shared attractors. We find that populations of evolved networks form giant clusters in genotype space, have Poissonian degree distributions but exhibit hierarchically organized $k$-core decompositions, while random populations of Boolean graphs are typically so far removed from each other genetically that they cannot form a metanetwork. In phenotype space, the metanetworks of evolved populations are super robust both under the elimination of weak connections and random removal of nodes. ...

  9. Statistics of Evolving Populations and Their Relevance to Flood Risk

    Institute of Scientific and Technical Information of China (English)

    Robert E.Criss

    2016-01-01

    ABSTRACT:Statistical methods are commonly used to evaluate natural populations and environmen-tal variables, yet these must recognize temporal trends in population character to be appropriate in an evolving world. New equations presented here define the statistical measures of aggregate historical populations affected by linear changes in population means and standard deviations. These can be used to extract the statistical character of present-day populations, needed to define modern variability and risk, from tables of historical data that are dominated by measurements made when conditions were different. As an example, many factors such as climate change and in-channel structures are causing flood levels to rise, so realistic estimation of future flood levels must take such secular changes into ac-count. The new equations provide estimates of water levels for“100-year”floods in the USA Midwest that are 0.5 to 2 m higher than official calculations that routinely assume population stationarity. These equations also show that flood levels will continue to rise by several centimeters per year. This rate is nearly ten times faster than the rise of sea level, and thus represents one of the fastest and most damag-ing rates of change that is documented by robust data.

  10. Spin-orbit coupling for tidally evolving super-Earths

    CERN Document Server

    Rodríguez, Adrián; Michtchenko, Tatiana A; Hussmann, Hauke

    2012-01-01

    We investigate the spin behavior of close-in rocky planets and the implications for their orbital evolution. Considering that the planet rotation evolves under simultaneous actions of the torque due to the equatorial deformation and the tidal torque, both raised by the central star, we analyze the possibility of temporary captures in spin-orbit resonances. The results of the numerical simulations of the exact equations of motions indicate that, whenever the planet rotation is trapped in a resonant motion, the orbital decay and the eccentricity damping are faster than the ones in which the rotation follows the so-called pseudo-synchronization. Analytical results obtained through the averaged equations of the spin-orbit problem show a good agreement with the numerical simulations. We apply the analysis to the cases of the recently discovered hot super-Earths Kepler-10 b, GJ 3634 b and 55 Cnc e. The simulated dynamical history of these systems indicates the possibility of capture in several spin-orbit resonances...

  11. Temporal Heterogeneities Increase the Prevalence of Epidemics on Evolving Networks

    CERN Document Server

    Rocha, Luis Enrique Correa

    2012-01-01

    Empirical studies suggest that contact patterns follow heterogeneous inter-event times, meaning that intervals of high activity are followed by periods of inactivity. Combined with birth and death of individuals, these temporal constraints affect the spread of infections in a non-trivial way and are dependent on the particular contact dynamics. We propose a stochastic model to generate temporal networks where vertices make instantaneous contacts following heterogeneous inter-event times, and leave and enter the system at fixed rates. We study how these temporal properties affect the prevalence of an infection and estimate R0, the number of secondary infections, by modeling simulated infections (SIR, SI and SIS) co-evolving with the network structure. We find that heterogeneous contact patterns cause earlier and larger epidemics on the SIR model in comparison to homogeneous scenarios. In case of SI and SIS, the epidemics is faster in the early stages (up to 90% of prevalence) followed by a slowdown in the asym...

  12. The Evolving Flow of Jupiter's White Ovals and Adjacent Cyclones

    CERN Document Server

    Choi, David S; Vasavada, Ashwin R; 10.1016/j.icarus.2009.10.013

    2013-01-01

    We present results regarding the dynamical meteorology of Jupiter's White Ovals at different points in their evolution. Starting from the era with three White Ovals FA, BC, and DE (Galileo), continuing to the post-merger epoch with only one Oval BA (Cassini), and finally to Oval BA's current reddened state (New Horizons), we demonstrate that the dynamics of their flow have similarly evolved along with their appearance. The northern periphery of Oval BA increased in speed by 20 m/s from Cassini to New Horizons, ending up at a speed nearly identical to that of the northern periphery of Oval DE during Galileo. However, the peak speeds along the southern rim of the newly formed Oval BA were consistently faster than the corresponding speeds in Oval DE, and they increased still further between Cassini and New Horizons, ending up at ~140 to 150 m/s. The modest strengthening of the winds in Oval BA, the appearance of red aerosols, and the appearance of a turbulent, cyclonic feature to Oval BA's northwest create a str...

  13. Population level analysis of evolved mutations underlying improvements in plant hemicellulose and cellulose fermentation by Clostridium phytofermentans.

    Directory of Open Access Journals (Sweden)

    Supratim Mukherjee

    Full Text Available The complexity of plant cell walls creates many challenges for microbial decomposition. Clostridium phytofermentans, an anaerobic bacterium isolated from forest soil, directly breaks down and utilizes many plant cell wall carbohydrates. The objective of this research is to understand constraints on rates of plant decomposition by Clostridium phytofermentans and identify molecular mechanisms that may overcome these limitations.Experimental evolution via repeated serial transfers during exponential growth was used to select for C. phytofermentans genotypes that grow more rapidly on cellobiose, cellulose and xylan. To identify the underlying mutations an average of 13,600,000 paired-end reads were generated per population resulting in ∼300 fold coverage of each site in the genome. Mutations with allele frequencies of 5% or greater could be identified with statistical confidence. Many mutations are in carbohydrate-related genes including the promoter regions of glycoside hydrolases and amino acid substitutions in ABC transport proteins involved in carbohydrate uptake, signal transduction sensors that detect specific carbohydrates, proteins that affect the export of extracellular enzymes, and regulators of unknown specificity. Structural modeling of the ABC transporter complex proteins suggests that mutations in these genes may alter the recognition of carbohydrates by substrate-binding proteins and communication between the intercellular face of the transmembrane and the ATPase binding proteins.Experimental evolution was effective in identifying molecular constraints on the rate of hemicellulose and cellulose fermentation and selected for putative gain of function mutations that do not typically appear in traditional molecular genetic screens. The results reveal new strategies for evolving and engineering microorganisms for faster growth on plant carbohydrates.

  14. The sound of an evolving floating sculpture

    CERN Document Server

    Seibold, Benjamin

    2012-01-01

    Commissioned by MIT's in-house artist Jane Philbrick, we evolve an abstract 2D surface (resembling Marta Pan's 1961 "Sculpture Flottante I") under mean curvature, all the while calculating the eigenmodes and eigenvalues of the Laplace-Beltrami operator on the resulting shapes. These are then synthesized into a sound-wave embodying the "swan song" of the surfaces as the evolve to points and vanish. The surface is approximated by a triangulation, and we present a robust approach to approximate the normal directions and the mean curvature. The resulting video and sound-track were parts in the Jane Philbrick's exhibition "Everything Trembles" in Lund, Sweden, 2009.

  15. Interactively Evolving Compositional Sound Synthesis Networks

    DEFF Research Database (Denmark)

    Jónsson, Björn Þór; Hoover, Amy K.; Risi, Sebastian

    2015-01-01

    While the success of electronic music often relies on the uniqueness and quality of selected timbres, many musicians struggle with complicated and expensive equipment and techniques to create their desired sounds. Instead, this paper presents a technique for producing novel timbres that are evolved......, CPPNs can theoretically compute any function and can build on those present in traditional synthesizers (e.g. square, sawtooth, triangle, and sine waves functions) to produce completely novel timbres. Evolved with NeuroEvolution of Augmenting Topologies (NEAT), the aim of this paper is to explore...

  16. How the first biopolymers could have evolved.

    Science.gov (United States)

    Abkevich, V I; Gutin, A M; Shakhnovich, E I

    1996-01-01

    In this work, we discuss a possible origin of the first biopolymers with stable unique structures. We suggest that at the prebiotic stage of evolution, long organic polymers had to be compact to avoid hydrolysis and had to be soluble and thus must not be exceedingly hydrophobic. We present an algorithm that generates such sequences for model proteins. The evolved sequences turn out to have a stable unique structure, into which they quickly fold. This result illustrates the idea that the unique three-dimensional native structures of first biopolymers could have evolved as a side effect of nonspecific physicochemical factors acting at the prebiotic stage of evolution. PMID:8570645

  17. Evolving Intelligent Systems Methodology and Applications

    CERN Document Server

    Angelov, Plamen; Kasabov, Nik

    2010-01-01

    From theory to techniques, the first all-in-one resource for EIS. There is a clear demand in advanced process industries, defense, and Internet and communication (VoIP) applications for intelligent yet adaptive/evolving systems. Evolving Intelligent Systems is the first self- contained volume that covers this newly established concept in its entirety, from a systematic methodology to case studies to industrial applications. Featuring chapters written by leading world experts, it addresses the progress, trends, and major achievements in this emerging research field, with a strong emphasis on th

  18. Self-Adaptation in Evolving Systems

    CERN Document Server

    Stephens, C R; Mora, J; Waelbroeck, H

    1997-01-01

    A theoretical and experimental analysis is made of the effects of self-adaptation in a simple evolving system. Specifically, we consider the effects of coding the mutation and crossover probabilities of a genetic algorithm evolving in certain model fitness landscapes. The resultant genotype-phenotype mapping is degenerate, there being no direct selective advantage for one probability versus another. We show that the action of mutation and crossover breaks this degeneracy leading to an induced symmetry breaking among the genotypic synonyms. We demonstrate that this induced symmetry breaking allows the system to self-adapt in a time dependent environment.

  19. Selection of orphan Rhs toxin expression in evolved Salmonella enterica serovar Typhimurium.

    Directory of Open Access Journals (Sweden)

    Sanna Koskiniemi

    2014-03-01

    Full Text Available Clonally derived bacterial populations exhibit significant genotypic and phenotypic diversity that contribute to fitness in rapidly changing environments. Here, we show that serial passage of Salmonella enterica serovar Typhimurium LT2 (StLT2 in broth, or within a mouse host, results in selection of an evolved population that inhibits the growth of ancestral cells by direct contact. Cells within each evolved population gain the ability to express and deploy a cryptic "orphan" toxin encoded within the rearrangement hotspot (rhs locus. The Rhs orphan toxin is encoded by a gene fragment located downstream of the "main" rhs gene in the ancestral strain StLT2. The Rhs orphan coding sequence is linked to an immunity gene, which encodes an immunity protein that specifically blocks Rhs orphan toxin activity. Expression of the Rhs orphan immunity protein protects ancestral cells from the evolved lineages, indicating that orphan toxin activity is responsible for the observed growth inhibition. Because the Rhs orphan toxin is encoded by a fragmented reading frame, it lacks translation initiation and protein export signals. We provide evidence that evolved cells undergo recombination between the main rhs gene and the rhs orphan toxin gene fragment, yielding a fusion that enables expression and delivery of the orphan toxin. In this manner, rhs locus rearrangement provides a selective advantage to a subpopulation of cells. These observations suggest that rhs genes play important roles in intra-species competition and bacterial evolution.

  20. Evolvability Search: Directly Selecting for Evolvability in order to Study and Produce It

    DEFF Research Database (Denmark)

    Mengistu, Henok; Lehman, Joel Anthony; Clune, Jeff

    2016-01-01

    One hallmark of natural organisms is their significant evolvability, i.e.,their increased potential for further evolution. However, reproducing such evolvability in artificial evolution remains a challenge, which both reduces the performance of evolutionary algorithms and inhibits the study of ev...

  1. The faster country in Economic Development must be an International Center of Economy

    Institute of Scientific and Technical Information of China (English)

    杜晓军

    2005-01-01

    The purpose of this study was to research the effects of faster pace of economic development and the reason why international economic centers are rapidly changed. The study analyzes the historical facts and materials concerning economic development from ancient times to the present, and analyzes the reason why one country or area becomes an international economic center. Then it concludes that if one nation or area's economy develops faster than that of other areas or nations, this nation or area must become the international economic center in a certain time.

  2. The Faster, Better, Cheaper Approach to Space Missions: An Engineering Management Assessment

    Science.gov (United States)

    Hamaker, Joe

    2000-01-01

    This paper describes, in viewgraph form, the faster, better, cheaper approach to space missions. The topics include: 1) What drives "Faster, Better, Cheaper"? 2) Why Space Programs are Costly; 3) Background; 4) Aerospace Project Management (Old Culture); 5) Aerospace Project Management (New Culture); 6) Scope of Analysis Limited to Engineering Management Culture; 7) Qualitative Analysis; 8) Some Basic Principles of the New Culture; 9) Cause and Effect; 10) "New Ways of Doing Business" Survey Results; 11) Quantitative Analysis; 12) Recent Space System Cost Trends; 13) Spacecraft Dry Weight Trend; 14) Complexity Factor Trends; 15) Cost Normalization; 16) Cost Normalization Algorithm; 17) Unnormalized Cost vs. Normalized Cost; and 18) Concluding Observations.

  3. Dedicated workspaces: Faster resumption times and reduced cognitive load in sequential multitasking

    DEFF Research Database (Denmark)

    Jeuris, Steven; Bardram, Jakob Eyvind

    2016-01-01

    Studies show that virtual desktops have become a widespread approach to window management within desktop environments. However, despite their success, there is no experimental evidence of their effect on multitasking. In this paper, we present an experimental study incorporating 16 participants...... to perform the same tasks. Results show that adopting virtual desktops as dedicated workspaces allows for faster task resumption (10 s faster on average) and reduced cognitive load during sequential multitasking. Within our experiment the majority of users already benefited from using dedicated workspaces...

  4. Real-time vehicle detection and tracking in video based on faster R-CNN

    Science.gov (United States)

    Zhang, Yongjie; Wang, Jian; Yang, Xin

    2017-08-01

    Vehicle detection and tracking is a significant part in auxiliary vehicle driving system. Using the traditional detection method based on image information has encountered enormous difficulties, especially in complex background. To solve this problem, a detection method based on deep learning, Faster R-CNN, which has very high detection accuracy and flexibility, is introduced. An algorithm of target tracking with the combination of Camshift and Kalman filter is proposed for vehicle tracking. The computation time of Faster R-CNN cannot achieve realtime detection. We use multi-thread technique to detect and track vehicle by parallel computation for real-time application.

  5. Mass Loss and Variability in Evolved Stars

    OpenAIRE

    Marengo, Massimo

    2014-01-01

    Mass loss and variability are two linked, fundamental properties of evolved stars. In this paper I review our current understanding of these processes, with a particular focus on how observations and models are used to constrain reliable mass loss prescriptions for stellar evolution and population synthesis models.

  6. Views on Evolvability of Embedded Systems

    NARCIS (Netherlands)

    Laar, P. van de; Punter, T.

    2011-01-01

    Evolvability, the ability to respond effectively to change, represents a major challenge to today's high-end embedded systems, such as those developed in the medical domain by Philips Healthcare. These systems are typically developed by multi-disciplinary teams, located around the world, and are in

  7. Systems of Accumulation and the Evolving MEC

    NARCIS (Netherlands)

    S. Ashman (Sam); B. Fine (Ben); S.A. Newman (Susan)

    2013-01-01

    textabstractThe limitations of the Developmental State Paradigm were discussed in the introductory chapter to this volume. This chapter offers an alternative approach to the DSP through use of the notion of systems of (capital) accumulation and its specific application to South Africa’s evolving pol

  8. Evolving Random Forest for Preference Learning

    DEFF Research Database (Denmark)

    Abou-Zleikha, Mohamed; Shaker, Noor

    2015-01-01

    This paper introduces a novel approach for pairwise preference learning through a combination of an evolutionary method and random forest. Grammatical evolution is used to describe the structure of the trees in the Random Forest (RF) and to handle the process of evolution. Evolved random forests...

  9. Satcom access in the Evolved Packet Core

    NARCIS (Netherlands)

    Cano Soveri, M.D.; Norp, A.H.J.; Popova, M.P.

    2011-01-01

    Satellite communications (Satcom) networks are increasingly integrating with terrestrial communications networks, namely Next Generation Networks (NGN). In the area of NGN the Evolved Packet Core (EPC) is a new network architecture that can support multiple access technologies. When Satcom is consid

  10. Satcom access in the evolved packet core

    NARCIS (Netherlands)

    Cano, M.D.; Norp, A.H.J.; Popova, M.P.

    2012-01-01

    Satellite communications (Satcom) networks are increasingly integrating with terrestrial communications networks, namely Next Generation Networks (NGN). In the area of NGN the Evolved Packet Core (EPC) is a new network architecture that can support multiple access technologies. When Satcom is consid

  11. Thermal and Evolved-Gas Analyzer Illustration

    Science.gov (United States)

    2008-01-01

    This is a computer-aided drawing of the Thermal and Evolved-Gas Analyzer, or TEGA, on NASA's Phoenix Mars Lander. The Phoenix Mission is led by the University of Arizona, Tucson, on behalf of NASA. Project management of the mission is by NASA's Jet Propulsion Laboratory, Pasadena, Calif. Spacecraft development is by Lockheed Martin Space Systems, Denver.

  12. Market theories evolve, and so do markets

    OpenAIRE

    Friedman, Daniel

    2007-01-01

    Responding to Mirowski's target article, this paper discusses some intellectual currents of 1970s-1990s and offers suggestions on measuring market performance, on including automated agents as market participants, on evolving new market formats, and on dealing with highly differentiated goods. (c) 2006 Elsevier B.V. All rights reserved.

  13. Information Spreading in Stationary Markovian Evolving Graphs

    CERN Document Server

    Clementi, Andrea; Pasquale, Francesco; Silvestri, Riccardo

    2011-01-01

    Markovian evolving graphs are dynamic-graph models where the links among a fixed set of nodes change during time according to an arbitrary Markovian rule. They are extremely general and they can well describe important dynamic-network scenarios. We study the speed of information spreading in the "stationary phase" by analyzing the completion time of the "flooding mechanism". We prove a general theorem that establishes an upper bound on flooding time in any stationary Markovian evolving graph in terms of its node-expansion properties. We apply our theorem in two natural and relevant cases of such dynamic graphs. "Geometric Markovian evolving graphs" where the Markovian behaviour is yielded by "n" mobile radio stations, with fixed transmission radius, that perform independent random walks over a square region of the plane. "Edge-Markovian evolving graphs" where the probability of existence of any edge at time "t" depends on the existence (or not) of the same edge at time "t-1". In both cases, the obtained upper...

  14. A Course Evolves-Physical Anthropology.

    Science.gov (United States)

    O'Neil, Dennis

    2001-01-01

    Describes the development of an online physical anthropology course at Palomar College (California) that evolved from online tutorials. Discusses the ability to update materials on the Web more quickly than in traditional textbooks; creating Web pages that are readable by most Web browsers; test security issues; and clarifying ownership of online…

  15. Mass Loss and Variability in Evolved Stars

    OpenAIRE

    Marengo, Massimo

    2014-01-01

    Mass loss and variability are two linked, fundamental properties of evolved stars. In this paper I review our current understanding of these processes, with a particular focus on how observations and models are used to constrain reliable mass loss prescriptions for stellar evolution and population synthesis models.

  16. Did Language Evolve Like the Vertebrate Eye?

    Science.gov (United States)

    Botha, Rudolf P.

    2002-01-01

    Offers a critical appraisal of the way in which the idea that human language or some of its features evolved like the vertebrate eye by natural selection is articulated in Pinker and Bloom's (1990) selectionist account of language evolution. Argues that this account is less than insightful because it fails to draw some of the conceptual…

  17. Research Notes Openness and Evolvability Legal Assessment

    Science.gov (United States)

    2016-08-01

    enforceable? Are interface providers (granule vendors) legally required to disclose (including license) semantic characteristics of their interfaces to...not be possible to adequately maintain and evolve the supporting material. Similarly, if the tool is proprietary to a related entity (such as the

  18. Páramo is the world’s fastest evolving and coolest biodiversity hotspot

    Directory of Open Access Journals (Sweden)

    Santiago eMadriñán

    2013-10-01

    Full Text Available Understanding the processes that cause speciation is a key aim of evolutionary biology. Lineages or biomes that exhibit recent and rapid diversification are ideal model systems for determining these processes. Species rich biomes reported to be of relatively recent origin, i.e., since the beginning of the Miocene, include Mediterranean ecosystems such as the California Floristic Province, oceanic islands such as the Hawaiian archipelago and the Neotropical high elevation ecosystem of the Páramos. Páramos constitute grasslands above the forest tree-line (at elevations of c. 2800–4700 m with high species endemism. Organisms that occupy this ecosystem are a likely product of unique adaptations to an extreme environment that evolved during the last three to five million years when the Andes reached an altitude that was capable of sustaining this type of vegetation. We compared net diversification rates of lineages in fast evolving biomes using 73 dated molecular phylogenies. Based on our sample, we demonstrate that average net diversification rates of Páramo plant lineages are faster than those of other reportedly fast evolving hotspots and that the faster evolving lineages are more likely to be found in Páramos than the other hotspots. Páramos therefore represent the ideal model system for studying diversification processes. Most of the speciation events that we observed in the Páramos (144 out of 177 occurred during the Pleistocene possibly due to the effects of species range contraction and expansion that may have resulted from the well-documented climatic changes during that period. Understanding these effects will assist with efforts to determine how future climatic changes will impact plant populations.

  19. Páramo is the world's fastest evolving and coolest biodiversity hotspot

    Science.gov (United States)

    Madriñán, Santiago; Cortés, Andrés J.; Richardson, James E.

    2013-01-01

    Understanding the processes that cause speciation is a key aim of evolutionary biology. Lineages or biomes that exhibit recent and rapid diversification are ideal model systems for determining these processes. Species rich biomes reported to be of relatively recent origin, i.e., since the beginning of the Miocene, include Mediterranean ecosystems such as the California Floristic Province, oceanic islands such as the Hawaiian archipelago and the Neotropical high elevation ecosystem of the Páramos. Páramos constitute grasslands above the forest tree-line (at elevations of c. 2800–4700 m) with high species endemism. Organisms that occupy this ecosystem are a likely product of unique adaptations to an extreme environment that evolved during the last three to five million years when the Andes reached an altitude that was capable of sustaining this type of vegetation. We compared net diversification rates of lineages in fast evolving biomes using 73 dated molecular phylogenies. Based on our sample, we demonstrate that average net diversification rates of Páramo plant lineages are faster than those of other reportedly fast evolving hotspots and that the faster evolving lineages are more likely to be found in Páramos than the other hotspots. Páramos therefore represent the ideal model system for studying diversification processes. Most of the speciation events that we observed in the Páramos (144 out of 177) occurred during the Pleistocene possibly due to the effects of species range contraction and expansion that may have resulted from the well-documented climatic changes during that period. Understanding these effects will assist with efforts to determine how future climatic changes will impact plant populations. PMID:24130570

  20. The aldehyde dehydrogenase, AldA, is essential for L-1,2-propanediol utilization in laboratory-evolved Escherichia coli

    DEFF Research Database (Denmark)

    Aziz, Ramy K.; Monk, Jonathan M.; Andrews, Kathleen A.;

    2017-01-01

    is highly conserved among members of the family Enterobacteriacea. To test this hypothesis, we first performed computational model simulation, which confirmed the essentiality of the aldA gene for 1,2-PDO utilization by the evolved PDO-degrading E. coli. Next, we deleted the aldA gene from the evolved...

  1. Development and implementation of a camera system for faster area reduction

    NARCIS (Netherlands)

    Jong, W. de; Schavemaker, J.G.M.; Breuers, M.G.J.; Baan, J.; Schleijpen, H.M.A.

    2004-01-01

    This paper describes the development and implementation of a low cost camera system that uses polarisation features of visible light for faster area reduction. The camera system will be mounted on a mechanical minefield area reduction asset, namely an AT mine roller of The HALO Trust. The automatic

  2. Faster Simulation Methods for the Nonstationary Random Vibrations of Non-linear MDOF Systems

    DEFF Research Database (Denmark)

    Askar, A.; Köylüo, U.; Nielsen, Søren R.K.

    1996-01-01

    . Such a treatment offers higher rates of convergence, faster speed and higher accuracy. These procedures are compared to the direct Monte Carlo simulation procedure, which uses a fourth order Runge-Kutta scheme with the white noise process approximated by a broad band Ruiz-Penzien broken line process...

  3. Faster Simulation Methods for the Non-Stationary Random Vibrations of Non-Linear MDOF Systems

    DEFF Research Database (Denmark)

    Askar, A.; Köylüoglu, H. U.; Nielsen, Søren R. K.

    . Such a treatment offers higher rates of convergence, faster speed and higher accuracy. These procedures are compared to the direct Monte Carlo simulation procedure, which uses a fourth order Runge-Kutta scheme with the white noise process approximated by a broad band Ruiz-Penzien broken line process...

  4. Approximating fixed points of generalized nonexpansive mappings via faster iteration schemes

    Directory of Open Access Journals (Sweden)

    Anupam Sharma

    2014-09-01

    Full Text Available In this paper, we approximate fixed points of generalized nonexpansive mappings in Banach spaces under relatively faster iteration schemes and also prove some weak and strong convergence theorems. Our results generalize and improve several previously known results of the existing literature.

  5. Exploiting hydrophobic borohydride-rich ionic liquids as faster-igniting rocket fuels.

    Science.gov (United States)

    Liu, Tianlin; Qi, Xiujuan; Huang, Shi; Jiang, Linhai; Li, Jianling; Tang, Chenglong; Zhang, Qinghua

    2016-02-01

    A family of hydrophobic borohydride-rich ionic liquids was developed, which exhibited the shortest ignition delay times of 1.7 milliseconds and the lowest viscosity (10 mPa s) of hypergolic ionic fluids, demonstrating their great potential as faster-igniting rocket fuels to replace toxic hydrazine derivatives in liquid bipropellant formulations.

  6. Rapid evolution of the sequences and gene repertoires of secreted proteins in bacteria.

    Directory of Open Access Journals (Sweden)

    Teresa Nogueira

    Full Text Available Proteins secreted to the extracellular environment or to the periphery of the cell envelope, the secretome, play essential roles in foraging, antagonistic and mutualistic interactions. We hypothesize that arms races, genetic conflicts and varying selective pressures should lead to the rapid change of sequences and gene repertoires of the secretome. The analysis of 42 bacterial pan-genomes shows that secreted, and especially extracellular proteins, are predominantly encoded in the accessory genome, i.e. among genes not ubiquitous within the clade. Genes encoding outer membrane proteins might engage more frequently in intra-chromosomal gene conversion because they are more often in multi-genic families. The gene sequences encoding the secretome evolve faster than the rest of the genome and in particular at non-synonymous positions. Cell wall proteins in Firmicutes evolve particularly fast when compared with outer membrane proteins of Proteobacteria. Virulence factors are over-represented in the secretome, notably in outer membrane proteins, but cell localization explains more of the variance in substitution rates and gene repertoires than sequence homology to known virulence factors. Accordingly, the repertoires and sequences of the genes encoding the secretome change fast in the clades of obligatory and facultative pathogens and also in the clades of mutualists and free-living bacteria. Our study shows that cell localization shapes genome evolution. In agreement with our hypothesis, the repertoires and the sequences of genes encoding secreted proteins evolve fast. The particularly rapid change of extracellular proteins suggests that these public goods are key players in bacterial adaptation.

  7. Adaptive evolution of the lactose utilization network in experimentally evolved populations of Escherichia coli.

    Directory of Open Access Journals (Sweden)

    Selwyn Quan

    2012-01-01

    Full Text Available Adaptation to novel environments is often associated with changes in gene regulation. Nevertheless, few studies have been able both to identify the genetic basis of changes in regulation and to demonstrate why these changes are beneficial. To this end, we have focused on understanding both how and why the lactose utilization network has evolved in replicate populations of Escherichia coli. We found that lac operon regulation became strikingly variable, including changes in the mode of environmental response (bimodal, graded, and constitutive, sensitivity to inducer concentration, and maximum expression level. In addition, some classes of regulatory change were enriched in specific selective environments. Sequencing of evolved clones, combined with reconstruction of individual mutations in the ancestral background, identified mutations within the lac operon that recapitulate many of the evolved regulatory changes. These mutations conferred fitness benefits in environments containing lactose, indicating that the regulatory changes are adaptive. The same mutations conferred different fitness effects when present in an evolved clone, indicating that interactions between the lac operon and other evolved mutations also contribute to fitness. Similarly, changes in lac regulation not explained by lac operon mutations also point to important interactions with other evolved mutations. Together these results underline how dynamic regulatory interactions can be, in this case evolving through mutations both within and external to the canonical lactose utilization network.

  8. Motivational salience signal in the basal forebrain is coupled with faster and more precise decision speed.

    Science.gov (United States)

    Avila, Irene; Lin, Shih-Chieh

    2014-03-01

    The survival of animals depends critically on prioritizing responses to motivationally salient stimuli. While it is generally believed that motivational salience increases decision speed, the quantitative relationship between motivational salience and decision speed, measured by reaction time (RT), remains unclear. Here we show that the neural correlate of motivational salience in the basal forebrain (BF), defined independently of RT, is coupled with faster and also more precise decision speed. In rats performing a reward-biased simple RT task, motivational salience was encoded by BF bursting response that occurred before RT. We found that faster RTs were tightly coupled with stronger BF motivational salience signals. Furthermore, the fraction of RT variability reflecting the contribution of intrinsic noise in the decision-making process was actively suppressed in faster RT distributions with stronger BF motivational salience signals. Artificially augmenting the BF motivational salience signal via electrical stimulation led to faster and more precise RTs and supports a causal relationship. Together, these results not only describe for the first time, to our knowledge, the quantitative relationship between motivational salience and faster decision speed, they also reveal the quantitative coupling relationship between motivational salience and more precise RT. Our results further establish the existence of an early and previously unrecognized step in the decision-making process that determines both the RT speed and variability of the entire decision-making process and suggest that this novel decision step is dictated largely by the BF motivational salience signal. Finally, our study raises the hypothesis that the dysregulation of decision speed in conditions such as depression, schizophrenia, and cognitive aging may result from the functional impairment of the motivational salience signal encoded by the poorly understood noncholinergic BF neurons.

  9. Histone variant innovation in a rapidly evolving chordate lineage

    Directory of Open Access Journals (Sweden)

    Jansen Pascal WTC

    2011-07-01

    Full Text Available Abstract Background Histone variants alter the composition of nucleosomes and play crucial roles in transcription, chromosome segregation, DNA repair, and sperm compaction. Modification of metazoan histone variant lineages occurs on a background of genome architecture that shows global similarities from sponges to vertebrates, but the urochordate, Oikopleura dioica, a member of the sister group to vertebrates, exhibits profound modification of this ancestral architecture. Results We show that a histone complement of 47 gene loci encodes 31 histone variants, grouped in distinct sets of developmental expression profiles throughout the life cycle. A particularly diverse array of 15 male-specific histone variants was uncovered, including a testes-specific H4t, the first metazoan H4 sequence variant reported. Universal histone variants H3.3, CenH3, and H2A.Z are present but O. dioica lacks homologs of macroH2A and H2AX. The genome encodes many H2A and H2B variants and the repertoire of H2A.Z isoforms is expanded through alternative splicing, incrementally regulating the number of acetylatable lysine residues in the functionally important N-terminal "charge patch". Mass spectrometry identified 40 acetylation, methylation and ubiquitylation posttranslational modifications (PTMs and showed that hallmark PTMs of "active" and "repressive" chromatin were present in O. dioica. No obvious reduction in silent heterochromatic marks was observed despite high gene density in this extraordinarily compacted chordate genome. Conclusions These results show that histone gene complements and their organization differ considerably even over modest phylogenetic distances. Substantial innovation among all core and linker histone variants has evolved in concert with adaptation of specific life history traits in this rapidly evolving chordate lineage.

  10. Evolving Quantum Circuits using Genetic Algorithms

    CERN Document Server

    Prashant

    2005-01-01

    This paper describes an application of genetic algorithm for evolving quantum computing circuits. The circuits use reversible one qubit and two qubit gates which are applied on a multi-qubit system having some initial state. The genetic algorithm automatically searches the space and comes out with the appropriate circuit design, which yields desired output state. The fitness function used matches the output with desired output and the search stops when it is found. The fitness value becomes higher if the output is close to the desired output. The paper briefly discusses the operation of a quantum gate over the multi-qubit system. The paper also demonstrates some examples of the evolved circuits using the algorithm.

  11. A novel evolving model for power grids

    Institute of Scientific and Technical Information of China (English)

    2010-01-01

    In this paper,a novel power grid evolving model,which can well describe the evolving property of power grids,is presented. Based on the BA model,motivated by the fact that in real power grids,connectivity of node not only depends on its degree,but also is influenced by many uncertain factors,so we introduce the subconnection factor K for each node. Using the mean-field theory,we get the analytical expression of power-law degree distribution with the exponent γ∈ (3,∞ ). Finally,simulation results show that the new model can provide a satisfactory description for empirical characteristics of power network,and power network falls somewhere in between scale-free network and uncertain network.

  12. Evolvement Complexity in an Artificial Stock Market

    Institute of Scientific and Technical Information of China (English)

    YANG Chun-Xia; ZHOU Tao; ZHOU Pei-Ling; LIU Jun; TANG Zi-Nan

    2005-01-01

    @@ An artificial stock market is established based on the multi-agent model.Each agent has a limited memory of the history of stock price, and will choose an action according to its memory and trading strategy.The trading strategy of each agent evolves ceaselessly as a result of a self-teaching mechanism.The simulation results exhibit that large events are frequent in the fluctuation of the stock price generated by the present model when compared with a normal process, and the price returns distribution is a L関y distribution in the central part followed by an approximately exponential truncation.In addition, by defining a variable to gauge the evolvement complexity of this system, we have found a phase cross-over from simple-phase to complex-phase along with the increase of the number of individuals, which may be a ubiquitous phenomenon in multifarious real-life systems.

  13. Architecture for Pseudo Acausal Evolvable Embedded Systems

    CERN Document Server

    Abubakr, Mohd

    2007-01-01

    Advances in semiconductor technology are contributing to the increasing complexity in the design of embedded systems. Architectures with novel techniques such as evolvable nature and autonomous behavior have engrossed lot of attention. This paper demonstrates conceptually evolvable embedded systems can be characterized basing on acausal nature. It is noted that in acausal systems, future input needs to be known, here we make a mechanism such that the system predicts the future inputs and exhibits pseudo acausal nature. An embedded system that uses theoretical framework of acausality is proposed. Our method aims at a novel architecture that features the hardware evolability and autonomous behavior alongside pseudo acausality. Various aspects of this architecture are discussed in detail along with the limitations.

  14. Dust obscuration by an evolving galaxy population

    Science.gov (United States)

    Najita, Joan; Silk, Joseph; Wachter, Kenneth W.

    1990-01-01

    The effect of an evolving luminosity function (LF) on the ability of foreground galaxies to obscure background sources is discussed, using the Press-Schechter/CDM standard evolving LF model. Galaxies are modeled as simplified versions of local spirals and Poisson statistics are used to estimate the fraction of sky covered by intervening dusty galaxies and the mean optical depths due to these galaxies. The results are compared to those obtained in the case of nonevolving luminosity function in a low-density universe. It is found that evolution of the galaxy LF does not allow the quasar dust obscuration hypothesis to be sustained for dust disks with plausible sizes. Even in a low-density universe, where evolution at z = less than 10 is unimportant, large disk radii are needed to achieve the desired obscuring effect. The mean fraction of sky covered is presented as a function of the redshift z along with adequate diagram illustrations.

  15. Interactively Evolving Compositional Sound Synthesis Networks

    DEFF Research Database (Denmark)

    Jónsson, Björn Þór; Hoover, Amy K.; Risi, Sebastian

    2015-01-01

    While the success of electronic music often relies on the uniqueness and quality of selected timbres, many musicians struggle with complicated and expensive equipment and techniques to create their desired sounds. Instead, this paper presents a technique for producing novel timbres that are evolved...... by the musician through interactive evolutionary computation. Each timbre is produced by an oscillator, which is represented by a special type of artificial neural network (ANN) called a compositional pattern producing network (CPPN). While traditional ANNs compute only sigmoid functions at their hidden nodes......, CPPNs can theoretically compute any function and can build on those present in traditional synthesizers (e.g. square, sawtooth, triangle, and sine waves functions) to produce completely novel timbres. Evolved with NeuroEvolution of Augmenting Topologies (NEAT), the aim of this paper is to explore...

  16. Quantum games on evolving random networks

    Science.gov (United States)

    Pawela, Łukasz

    2016-09-01

    We study the advantages of quantum strategies in evolutionary social dilemmas on evolving random networks. We focus our study on the two-player games: prisoner's dilemma, snowdrift and stag-hunt games. The obtained result show the benefits of quantum strategies for the prisoner's dilemma game. For the other two games, we obtain regions of parameters where the quantum strategies dominate, as well as regions where the classical strategies coexist.

  17. Quantum games on evolving random networks

    CERN Document Server

    Pawela, Łukasz

    2015-01-01

    We study the advantages of quantum strategies in evolutionary social dilemmas on evolving random networks. We focus our study on the two-player games: prisoner's dilemma, snowdrift and stag-hunt games. The obtained result show the benefits of quantum strategies for the prisoner's dilemma game. For the other two games, we obtain regions of parameters where the quantum strategies dominate, as well as regions where the classical strategies coexist.

  18. The evolving epidemiology of inflammatory bowel disease.

    LENUS (Irish Health Repository)

    Shanahan, Fergus

    2009-07-01

    Epidemiologic studies in inflammatory bowel disease (IBD) include assessments of disease burden and evolving patterns of disease presentation. Although it is hoped that sound epidemiologic studies provide aetiological clues, traditional risk factor-based epidemiology has provided limited insights into either Crohn\\'s disease or ulcerative colitis etiopathogenesis. In this update, we will summarize how the changing epidemiology of IBD associated with modernization can be reconciled with current concepts of disease mechanisms and will discuss studies of clinically significant comorbidity in IBD.

  19. Circumstellar Molecular Spectra towards Evolved Stars

    CERN Document Server

    Bakker, E J

    1997-01-01

    In this paper we discuss the relevance of, and possible scientific gains which can be acquired from studying circumstellar molecular spectra toward evolved stars. Where can we expect circumstellar molecular spectra, why would we want to study these spectra, which molecules might be present, and what can we learn from these studies? We present an overview of reported detections, and discuss some of the results.

  20. Evolving economic architecture in East Asia

    OpenAIRE

    Kawai, Masahiro

    2007-01-01

    This paper examines how East Asia's economic architecture has been evolving over the last ten years and how it will shape itself in the future. With the progress of market-driven economic integration, East Asian economies have developed various cooperative initiatives for trade and finance, including free trade agreements (FTAs), the Chiang Mai Initiative, the Economic Review and Policy Dialogue, and the Asian Bond Markets Initiative. The paper suggests policy directions for greater regional ...

  1. Continual Learning through Evolvable Neural Turing Machines

    DEFF Research Database (Denmark)

    Lüders, Benno; Schläger, Mikkel; Risi, Sebastian

    2016-01-01

    Continual learning, i.e. the ability to sequentially learn tasks without catastrophic forgetting of previously learned ones, is an important open challenge in machine learning. In this paper we take a step in this direction by showing that the recently proposed Evolving Neural Turing Machine (ENTM......) approach is able to perform one-shot learning in a reinforcement learning task without catastrophic forgetting of previously stored associations....

  2. The Evolving Leadership Path of Visual Analytics

    Energy Technology Data Exchange (ETDEWEB)

    Kluse, Michael; Peurrung, Anthony J.; Gracio, Deborah K.

    2012-01-02

    This is a requested book chapter for an internationally authored book on visual analytics and related fields, coordianted by a UK university and to be published by Springer in 2012. This chapter is an overview of the leadship strategies that PNNL's Jim Thomas and other stakeholders used to establish visual analytics as a field, and how those strategies may evolve in the future.

  3. Evolving Information Filtering for Personalized Information Service

    Institute of Scientific and Technical Information of China (English)

    田范江; 李丛蓉; 王鼎兴

    2001-01-01

    Information filtering (IF) systems are important for personalized information service. However, most current IF systems suffer from low quality and long training time. In this paper, a refined evolving information filtering method is presented. This method describes user's information need from multi-aspects and improves filtering quality through a process like natural selection. Experimental result shows this method can shorten training time, improve filtering quality, and reduce the relevance between filtering results and training sequence.

  4. Evolving networks:from topology to dynamics

    Institute of Scientific and Technical Information of China (English)

    Zhengping FAN; Guanrong CHEN; King Tim KO

    2004-01-01

    A multi-local-world model is introduced to describe the evolving networks that have a localization property such as the Intemet. Based on this model, we show that the traffic load defined by "betweenness centrality" on the multi-local-world scale-free networks' model also follows a power law form. In this kind of network, a few vertices have heavier loads and so play more important roles than the others in the network.

  5. Continuous evaluation of evolving behavioral intervention technologies.

    Science.gov (United States)

    Mohr, David C; Cheung, Ken; Schueller, Stephen M; Hendricks Brown, C; Duan, Naihua

    2013-10-01

    Behavioral intervention technologies (BITs) are web-based and mobile interventions intended to support patients and consumers in changing behaviors related to health, mental health, and well-being. BITs are provided to patients and consumers in clinical care settings and commercial marketplaces, frequently with little or no evaluation. Current evaluation methods, including RCTs and implementation studies, can require years to validate an intervention. This timeline is fundamentally incompatible with the BIT environment, where technology advancement and changes in consumer expectations occur quickly, necessitating rapidly evolving interventions. However, BITs can routinely and iteratively collect data in a planned and strategic manner and generate evidence through systematic prospective analyses, thereby creating a system that can "learn." A methodologic framework, Continuous Evaluation of Evolving Behavioral Intervention Technologies (CEEBIT), is proposed that can support the evaluation of multiple BITs or evolving versions, eliminating those that demonstrate poorer outcomes, while allowing new BITs to be entered at any time. CEEBIT could be used to ensure the effectiveness of BITs provided through deployment platforms in clinical care organizations or BIT marketplaces. The features of CEEBIT are described, including criteria for the determination of inferiority, determination of BIT inclusion, methods of assigning consumers to BITs, definition of outcomes, and evaluation of the usefulness of the system. CEEBIT offers the potential to collapse initial evaluation and postmarketing surveillance, providing ongoing assurance of safety and efficacy to patients and consumers, payers, and policymakers.

  6. Breast cancer management: Past, present and evolving

    Directory of Open Access Journals (Sweden)

    M Akram

    2012-01-01

    Full Text Available Breast cancer is known from ancient time,and the treatment strategy evolved as our understanding of the disease changed with time. In 460 BC Hippocrates described breast cancer as a humoral disease and presently after a lot of studies breast cancer is considered as a local disease with systemic roots. For most of the twentieth century Halsted radical mastectomy was the "established and standardized operation for cancer of the breast in all stages, early or late". New information about tumor biology and its behavior suggested that less radical surgery might be just as effective as the more extensive one. Eventually, with the use of adjuvant therapy likeradiation and systemic therapy, the extent of surgical resection in the breast and axilla got reduced further and led to an era of breast conservation. The radiation treatment of breast cancer has evolved from 2D to 3D Conformal and to accelarated partial breast irradiation, aiming to reduce normal tissue toxicity and overall treatment time. Systemic therapy in the form of hormone therapy, chemotherapy and biological agents is now a well-established modality in treatment of breast cancer. The current perspective of breast cancer management is based on the rapidly evolving and increasingly integrated study on the genetic, molecular , biochemical and cellular basis of disease. The challenge for the future is to take advantage of this knowledge for the prediction of therapeutic outcome and develop therapies and rapidly apply more novel biologic therapeutics.

  7. Transistor Level Circuit Experiments using Evolvable Hardware

    Science.gov (United States)

    Stoica, A.; Zebulum, R. S.; Keymeulen, D.; Ferguson, M. I.; Daud, Taher; Thakoor, A.

    2005-01-01

    The Jet Propulsion Laboratory (JPL) performs research in fault tolerant, long life, and space survivable electronics for the National Aeronautics and Space Administration (NASA). With that focus, JPL has been involved in Evolvable Hardware (EHW) technology research for the past several years. We have advanced the technology not only by simulation and evolution experiments, but also by designing, fabricating, and evolving a variety of transistor-based analog and digital circuits at the chip level. EHW refers to self-configuration of electronic hardware by evolutionary/genetic search mechanisms, thereby maintaining existing functionality in the presence of degradations due to aging, temperature, and radiation. In addition, EHW has the capability to reconfigure itself for new functionality when required for mission changes or encountered opportunities. Evolution experiments are performed using a genetic algorithm running on a DSP as the reconfiguration mechanism and controlling the evolvable hardware mounted on a self-contained circuit board. Rapid reconfiguration allows convergence to circuit solutions in the order of seconds. The paper illustrates hardware evolution results of electronic circuits and their ability to perform under 230 C temperature as well as radiations of up to 250 kRad.

  8. Markov Chain-based Degree Distributions of Evolving Networks

    Institute of Scientific and Technical Information of China (English)

    Xiang Xing KONG; Zhen Ting HOU; Ding Hua SHI; Quan Rong CHEN; Qing Gui ZHAO

    2012-01-01

    In this paper,we study a class of stochastic processes,called evolving network Markov chains,in evolving networks. Our approach is to transform the degree distribution problem of an evolving network to a corresponding problem of evolving network Markov chains.We investigate the evolving network Markov chains,thereby obtaining some exact formulas as well as a precise criterion for determining whether the steady degree distribution of the evolving network is a power-law or not.With this new method,we finally obtain a rigorous,exact and unified solution of the steady degree distribution of the evolving network.

  9. eVolver: an optimization engine for evolving protein sequences to stabilize the respective structures.

    Science.gov (United States)

    Brylinski, Michal

    2013-07-31

    Many structural bioinformatics approaches employ sequence profile-based threading techniques. To improve fold recognition rates, homology searching may include artificially evolved amino acid sequences, which were demonstrated to enhance the sensitivity of protein threading in targeting midnight zone templates. We describe implementation details of eVolver, an optimization algorithm that evolves protein sequences to stabilize the respective structures by a variety of potentials, which are compatible with those commonly used in protein threading. In a case study focusing on LARG PDZ domain, we show that artificially evolved sequences have quite high capabilities to recognize the correct protein structures using standard sequence profile-based fold recognition. Computationally design protein sequences can be incorporated in existing sequence profile-based threading approaches to increase their sensitivity. They also provide a desired linkage between protein structure and function in in silico experiments that relate to e.g. the completeness of protein structure space, the origin of folds and protein universe. eVolver is freely available as a user-friendly webserver and a well-documented stand-alone software distribution at http://www.brylinski.org/evolver.

  10. Rapidly evolving and luminous transients from Pan-STARRS1

    Energy Technology Data Exchange (ETDEWEB)

    Drout, M. R.; Chornock, R.; Soderberg, A. M.; Sanders, N. E.; McKinnon, R.; Milisavljevic, D.; Margutti, R.; Berger, E.; Calkins, M.; Fong, W.; Kirshner, R. P.; Lunnan, R. [Harvard-Smithsonian Center for Astrophysics, 60 Garden Street, Cambridge, MA 02138 (United States); Rest, A. [Space Telescope Science Institute, 3700 San Martin Drive, Baltimore, MD 21218 (United States); Foley, R. J. [Astronomy Department, University of Illinois at Urbana-Champaign, 1002 West Green Street, Urbana, IL 61801 (United States); Gezari, S. [Department of Astronomy, University of Maryland, College Park, MD 20742-2421 (United States); Huber, M. E. [Institute for Astronomy, University of Hawaii at Manoa, Honolulu, HI 96822 (United States); Kankare, E.; Mattila, S. [Finnish Centre for Astronomy with ESO (FINCA), University of Turku, Väisäläntie 20, FI-21500 Piikkiö (Finland); Leibler, C. [Department of Astronomy and Astrophysics, University of California, Santa Cruz, CA 95060 (United States); Marion, G. H., E-mail: mdrout@cfa.harvard.edu [Department of Astronomy, University of Texas at Austin, Austin, TX 78712 (United States); and others

    2014-10-10

    In the past decade, several rapidly evolving transients have been discovered whose timescales and luminosities are not easily explained by traditional supernovae (SNe) models. The sample size of these objects has remained small due, at least in part, to the challenges of detecting short timescale transients with traditional survey cadences. Here we present the results from a search within the Pan-STARRS1 Medium Deep Survey (PS1-MDS) for rapidly evolving and luminous transients. We identify 10 new transients with a time above half-maximum (t {sub 1/2}) of less than 12 days and –16.5 > M > –20 mag. This increases the number of known events in this region of SN phase space by roughly a factor of three. The median redshift of the PS1-MDS sample is z = 0.275 and they all exploded in star-forming galaxies. In general, the transients possess faster rise than decline timescale and blue colors at maximum light (g {sub P1} – r {sub P1} ≲ –0.2). Best-fit blackbodies reveal photospheric temperatures/radii that expand/cool with time and explosion spectra taken near maximum light are dominated by a blue continuum, consistent with a hot, optically thick, ejecta. We find it difficult to reconcile the short timescale, high peak luminosity (L > 10{sup 43} erg s{sup –1}), and lack of UV line blanketing observed in many of these transients with an explosion powered mainly by the radioactive decay of {sup 56}Ni. Rather, we find that many are consistent with either (1) cooling envelope emission from the explosion of a star with a low-mass extended envelope that ejected very little (<0.03 M {sub ☉}) radioactive material, or (2) a shock breakout within a dense, optically thick, wind surrounding the progenitor star. After calculating the detection efficiency for objects with rapid timescales in the PS1-MDS we find a volumetric rate of 4800-8000 events yr{sup –1} Gpc{sup –3} (4%-7% of the core-collapse SN rate at z = 0.2).

  11. Evolution of the CNS myelin gene regulatory program.

    Science.gov (United States)

    Li, Huiliang; Richardson, William D

    2016-06-15

    Myelin is a specialized subcellular structure that evolved uniquely in vertebrates. A myelinated axon conducts action potentials many times faster than an unmyelinated axon of the same diameter; for the same conduction speed, the unmyelinated axon would need a much larger diameter and volume than its myelinated counterpart. Hence myelin speeds information transfer and saves space, allowing the evolution of a powerful yet portable brain. Myelination in the central nervous system (CNS) is controlled by a gene regulatory program that features a number of master transcriptional regulators including Olig1, Olig2 and Myrf. Olig family genes evolved from a single ancestral gene in non-chordates. Olig2, which executes multiple functions with regard to oligodendrocyte identity and development in vertebrates, might have evolved functional versatility through post-translational modification, especially phosphorylation, as illustrated by its evolutionarily conserved serine/threonine phospho-acceptor sites and its accumulation of serine residues during more recent stages of vertebrate evolution. Olig1, derived from a duplicated copy of Olig2 in early bony fish, is involved in oligodendrocyte development and is critical to remyelination in bony vertebrates, but is lost in birds. The origin of Myrf orthologs might be the result of DNA integration between an invading phage or bacterium and an early protist, producing a fusion protein capable of self-cleavage and DNA binding. Myrf seems to have adopted new functions in early vertebrates - initiation of the CNS myelination program as well as the maintenance of mature oligodendrocyte identity and myelin structure - by developing new ways to interact with DNA motifs specific to myelin genes. This article is part of a Special Issue entitled SI: Myelin Evolution.

  12. The evolvability of growth form in a clonal seaweed.

    Science.gov (United States)

    Monro, Keyne; Poore, Alistair G B

    2009-12-01

    Although modular construction is considered the key to adaptive growth or growth-form plasticity in sessile taxa (e.g., plants, seaweeds and colonial invertebrates), the serial expression of genes in morphogenesis may compromise its evolutionary potential if growth forms emerge as integrated wholes from module iteration. To explore the evolvability of growth form in the red seaweed, Asparagopsis armata, we estimated genetic variances, covariances, and cross-environment correlations for principal components of growth-form variation in contrasting light environments. We compared variance-covariance matrices across environments to test environmental effects on heritable variation and examined the potential for evolutionary change in the direction of plastic responses to light. Our results suggest that growth form in Asparagopsis may constitute only a single genetic entity whose plasticity affords only limited evolutionary potential. We argue that morphological integration arising from modular construction may constrain the evolvability of growth form in Asparagopsis, emphasizing the critical distinction between genetic and morphological modularity in this and other modular taxa.

  13. An experimental study of the "faster-is-slower" effect using mice under panic

    Science.gov (United States)

    Lin, Peng; Ma, Jian; Liu, Tianyang; Ran, Tong; Si, Youliang; Li, Tao

    2016-06-01

    A number of crowd accidents in last decades have attracted the interests of scientists in the study of self-organized behavior of crowd under extreme conditions. The faster-is-slower effect is one of the most referenced behaviors in pedestrian dynamics. However, this behavior has not been experimentally verified yet. A series of experiments with mice under panic were conducted in a bi-dimensional space. The mice were trained to be familiar with the way of escape. A varying number of joss sticks were used to produce different levels of stimulus to drive the mice to escape. The evacuation process was video-recorded for further analysis. The experiment found that the escape times significantly increased with the levels of stimulus due to the stronger competition of selfish mice in panic condition. The faster-is-slower effect was experimentally verified. The probability distributions of time intervals showed a power law and the burst sizes exhibited an exponential behavior.

  14. National health expenditure projections, 2013-23: faster growth expected with expanded coverage and improving economy.

    Science.gov (United States)

    Sisko, Andrea M; Keehan, Sean P; Cuckler, Gigi A; Madison, Andrew J; Smith, Sheila D; Wolfe, Christian J; Stone, Devin A; Lizonitz, Joseph M; Poisal, John A

    2014-10-01

    In 2013 health spending growth is expected to have remained slow, at 3.6 percent, as a result of the sluggish economic recovery, the effects of sequestration, and continued increases in private health insurance cost-sharing requirements. The combined effects of the Affordable Care Act's coverage expansions, faster economic growth, and population aging are expected to fuel health spending growth this year and thereafter (5.6 percent in 2014 and 6.0 percent per year for 2015-23). However, the average rate of increase through 2023 is projected to be slower than the 7.2 percent average growth experienced during 1990-2008. Because health spending is projected to grow 1.1 percentage points faster than the average economic growth during 2013-23, the health share of the gross domestic product is expected to rise from 17.2 percent in 2012 to 19.3 percent in 2023.

  15. Forty Years Research of Faster-Than-Light——Review and Prospects

    Institute of Scientific and Technical Information of China (English)

    HuangZhixun

    2005-01-01

    Since the early work of O. M. Bilanuik and B. C. Sudarshan in 1962 and G. Feinberg in 1967, the research work on the faster-than-light (superluminal) has been performed in the world, such as in USA, Europe and China. In this paper, the development stages of the study are presented, which include beginning stage, transitional stage and experimental stage. Based on the Einstein's paper in 1905, the velocities greater than that of light had no possibility of existence. However, in the Einstein's papers of 1907 it was founded that the superluminal signal speed could not be refuted absolutely. In this paper, the studies on velocities are classified. The definition of General Information Speed is suggested, which will ease the discussion. After reviewing the researches of 1962-2004, it can be concluded that the faster-than-light is a realizable scientific statement.

  16. Faster-is-slower effect in escaping ants revisited: Ants do not behave like humans

    OpenAIRE

    Parisi, Daniel R.; Soria, Sabrina A; Josens, Roxana

    2014-01-01

    In this work we studied the trajectories, velocities and densities of ants when egressing under controlled levels of stress produced by a chemical repellent at different concentrations. We found that, unlike other animals escaping under life-and-death conditions and pedestrian simulations, ants do not produce a higher density zone near the exit door. Instead, ants are uniformly distributed over the available space allowing for efficient evacuations. Consequently, the faster-is-slower effect o...

  17. The Trans-Gompertz Function: An Alternative to the Logistic Growth Function with Faster Growth.

    Science.gov (United States)

    Kozusko, F; Bourdeau, M

    2015-12-01

    The growth characteristics of the recently derived Trans-Gompertz function are compared to those of the Generalized Logistic function. Both functions are defined by one shaping parameter and one rate parameter. The functions are matched at a specified point on the growth curve by equating both the first and second derivatives. Analysis shows that the matched Trans-Gompertz function will have grown at a faster rate with a larger inflection point ratio.

  18. How could the Gompertz-Makeham law evolve.

    Science.gov (United States)

    Golubev, A

    2009-05-01

    In line with the origin of life from the chemical world, biological mortality kinetics is suggested to originate from chemical decomposition kinetics described by the Arrhenius equation k = A*exp(-E/RT). Another chemical legacy of living bodies is that, by using the appropriate properties of their constituent molecules, they incorporate all their potencies, including adverse ones. In early evolution, acquiring an ability to use new molecules to increase disintegration barrier E might be associated with new adverse interactions, yielding products that might accumulate in organisms and compromise their viability. Thus, the main variable of the Arrhenius equation changed from T in chemistry to E in biology; mortality turned to rise exponentially as E declined with increasing age; and survivorship patterns turned to feature slow initial and fast late descent making the bulk of each finite cohort to expire within a short final period of its lifespan. Numerical modelling shows that such acquisition of new functions associated with faster functional decline may increase the efficiency of investing resources into progeny, in line with the antagonistic pleiotropy theory of ageing. Any evolved time trajectories of functional changes were translated into changes in mortality through exponent according to the generalised Gompertz-Makeham law mu = C(t)+Lambda*exp[-E(t)], which is reduced to the conventional form when E(t) = E0-gammat and C is constant. The proposed model explains the origin of the linear mid-age functional decline followed by its deceleration at later ages and the positive correlation between the initial vitality and the rate of ageing.

  19. Infevers: an evolving mutation database for auto-inflammatory syndromes.

    Science.gov (United States)

    Touitou, Isabelle; Lesage, Suzanne; McDermott, Michael; Cuisset, Laurence; Hoffman, Hal; Dode, Catherine; Shoham, Nitza; Aganna, Ebun; Hugot, Jean-Pierre; Wise, Carol; Waterham, Hans; Pugnere, Denis; Demaille, Jacques; Sarrauste de Menthiere, Cyril

    2004-09-01

    The Infevers database (http://fmf.igh.cnrs.fr/infevers/) was established in 2002 to provide investigators with access to a central source of information about all sequence variants associated with periodic fevers: Familial Mediterranean fever (FMF), TNF Receptor Associated Periodic Syndrome (TRAPS), Hyper IgD Syndrome (HIDS), Familial Cold Autoinflammatory Syndrome/Muckle-Wells Syndrome/Chronic Infantile Neurological Cutaneous and Articular Syndrome (FCAS/MWS/CINCA). The prototype of this group of disorders is FMF, a recessive disease characterized by recurrent bouts of unexplained inflammation. FMF is the pivotal member of an expanding family of autoinflammatory disorders, a new term coined to describe illnesses resulting from a defect of the innate immune response. Therefore, we decided to extend the Infevers database to genes connected with autoinflammatory diseases. We present here the biological content of the Infevers database, including the introduction of two new entries: Crohn/Blau and Pyogenic sterile arthritis, pyoderma gangrenosum and acne (PAPA syndrome). Infevers has a range of query capabilities, allowing for simple or complex interrogation of the database. Currently, the database contains 291 sequence variants in related genes (MEFV, TNFRSF1A, MVK, CARD15, PSTPIP1, and CIAS1), consisting of published data and personal communications, which has revealed or refined the preferential mutational sites for each gene. This database will continue to evolve in its content and to improve in its presentation.

  20. Modeling promoter grammars with evolving hidden Markov models

    DEFF Research Database (Denmark)

    Won, Kyoung-Jae; Sandelin, Albin; Marstrand, Troels Torben

    2008-01-01

    MOTIVATION: Describing and modeling biological features of eukaryotic promoters remains an important and challenging problem within computational biology. The promoters of higher eukaryotes in particular display a wide variation in regulatory features, which are difficult to model. Often several...... factors are involved in the regulation of a set of co-regulated genes. If so, promoters can be modeled with connected regulatory features, where the network of connections is characteristic for a particular mode of regulation. RESULTS: With the goal of automatically deciphering such regulatory structures......, we present a method that iteratively evolves an ensemble of regulatory grammars using a hidden Markov Model (HMM) architecture composed of interconnected blocks representing transcription factor binding sites (TFBSs) and background regions of promoter sequences. The ensemble approach reduces the risk...

  1. Forces shaping the fastest evolving regions in the human genome

    DEFF Research Database (Denmark)

    Pollard, Katherine S; Salama, Sofie R; King, Bryan;

    2006-01-01

    Comparative genomics allow us to search the human genome for segments that were extensively changed in the last approximately 5 million years since divergence from our common ancestor with chimpanzee, but are highly conserved in other species and thus are likely to be functional. We found 202 gen...... contributed to accelerated evolution of the fastest evolving elements in the human genome.......Comparative genomics allow us to search the human genome for segments that were extensively changed in the last approximately 5 million years since divergence from our common ancestor with chimpanzee, but are highly conserved in other species and thus are likely to be functional. We found 202...... genomic elements that are highly conserved in vertebrates but show evidence of significantly accelerated substitution rates in human. These are mostly in non-coding DNA, often near genes associated with transcription and DNA binding. Resequencing confirmed that the five most accelerated elements...

  2. Evolvability Is an Evolved Ability: The Coding Concept as the Arch-Unit of Natural Selection.

    Science.gov (United States)

    Janković, Srdja; Ćirković, Milan M

    2016-03-01

    Physical processes that characterize living matter are qualitatively distinct in that they involve encoding and transfer of specific types of information. Such information plays an active part in the control of events that are ultimately linked to the capacity of the system to persist and multiply. This algorithmicity of life is a key prerequisite for its Darwinian evolution, driven by natural selection acting upon stochastically arising variations of the encoded information. The concept of evolvability attempts to define the total capacity of a system to evolve new encoded traits under appropriate conditions, i.e., the accessible section of total morphological space. Since this is dependent on previously evolved regulatory networks that govern information flow in the system, evolvability itself may be regarded as an evolved ability. The way information is physically written, read and modified in living cells (the "coding concept") has not changed substantially during the whole history of the Earth's biosphere. This biosphere, be it alone or one of many, is, accordingly, itself a product of natural selection, since the overall evolvability conferred by its coding concept (nucleic acids as information carriers with the "rulebook of meanings" provided by codons, as well as all the subsystems that regulate various conditional information-reading modes) certainly played a key role in enabling this biosphere to survive up to the present, through alterations of planetary conditions, including at least five catastrophic events linked to major mass extinctions. We submit that, whatever the actual prebiotic physical and chemical processes may have been on our home planet, or may, in principle, occur at some time and place in the Universe, a particular coding concept, with its respective potential to give rise to a biosphere, or class of biospheres, of a certain evolvability, may itself be regarded as a unit (indeed the arch-unit) of natural selection.

  3. Evolvability Is an Evolved Ability: The Coding Concept as the Arch-Unit of Natural Selection

    Science.gov (United States)

    Janković, Srdja; Ćirković, Milan M.

    2016-03-01

    Physical processes that characterize living matter are qualitatively distinct in that they involve encoding and transfer of specific types of information. Such information plays an active part in the control of events that are ultimately linked to the capacity of the system to persist and multiply. This algorithmicity of life is a key prerequisite for its Darwinian evolution, driven by natural selection acting upon stochastically arising variations of the encoded information. The concept of evolvability attempts to define the total capacity of a system to evolve new encoded traits under appropriate conditions, i.e., the accessible section of total morphological space. Since this is dependent on previously evolved regulatory networks that govern information flow in the system, evolvability itself may be regarded as an evolved ability. The way information is physically written, read and modified in living cells (the "coding concept") has not changed substantially during the whole history of the Earth's biosphere. This biosphere, be it alone or one of many, is, accordingly, itself a product of natural selection, since the overall evolvability conferred by its coding concept (nucleic acids as information carriers with the "rulebook of meanings" provided by codons, as well as all the subsystems that regulate various conditional information-reading modes) certainly played a key role in enabling this biosphere to survive up to the present, through alterations of planetary conditions, including at least five catastrophic events linked to major mass extinctions. We submit that, whatever the actual prebiotic physical and chemical processes may have been on our home planet, or may, in principle, occur at some time and place in the Universe, a particular coding concept, with its respective potential to give rise to a biosphere, or class of biospheres, of a certain evolvability, may itself be regarded as a unit (indeed the arch-unit) of natural selection.

  4. Evolving Networks with Nonlinear Assignment of Weight

    Institute of Scientific and Technical Information of China (English)

    TANG Chao; TANG Yi

    2006-01-01

    We propose a weighted evolving network model in which the underlying topological structure is still driven by the degree according to the preferential attachment rule while the weight assigned to the newly established edges is dependent on the degree in a nonlinear form. By varying the parameter α that controls the function determining the assignment of weight, a wide variety of power-law behaviours of the total weight distributions as well as the diversity of the weight distributions of edges are displayed. Variation of correlation and heterogeneity in the network is illustrated as well.

  5. The tree length of an evolving coalescent

    CERN Document Server

    Pfaffelhuber, Peter; Weisshaupt, Heinz

    2009-01-01

    A well-established model for the genealogy of a large population in equilibrium is Kingman's coalescent. For the population together with its genealogy evolving in time, this gives rise to a time-stationary tree-valued process. We study the sum of the branch lengths, briefly denoted as tree length, and prove that the (suitably compensated) sequence of tree length processes converges, as the population size tends to infinity, to a limit process with cadlag paths, infinite infinitesimal variance, and a Gumbel distribution as its equilibrium.

  6. Logistic Regression for Evolving Data Streams Classification

    Institute of Scientific and Technical Information of China (English)

    YIN Zhi-wu; HUANG Shang-teng; XUE Gui-rong

    2007-01-01

    Logistic regression is a fast classifier and can achieve higher accuracy on small training data. Moreover,it can work on both discrete and continuous attributes with nonlinear patterns. Based on these properties of logistic regression, this paper proposed an algorithm, called evolutionary logistical regression classifier (ELRClass), to solve the classification of evolving data streams. This algorithm applies logistic regression repeatedly to a sliding window of samples in order to update the existing classifier, to keep this classifier if its performance is deteriorated by the reason of bursting noise, or to construct a new classifier if a major concept drift is detected. The intensive experimental results demonstrate the effectiveness of this algorithm.

  7. Strength dynamics of weighted evolving networks

    Institute of Scientific and Technical Information of China (English)

    Wu Jian-Jun; Gao Zi-You; Sun Hui-Jun

    2007-01-01

    In this paper, a simple model for the strength dynamics of weighted evolving networks is proposed to characterize the weighted networks. By considering the congestion effects, this approach can yield power law strength distribution appeared on the many real weighted networks, such as traffic networks, internet networks. Besides, the relationship between strength and degree is given. Numerical simulations indicate that the strength distribution is strongly related to the strength dynamics decline. The model also provides us with a better description of the real weighted networks.

  8. SALT Spectroscopy of Evolved Massive Stars

    Science.gov (United States)

    Kniazev, A. Y.; Gvaramadze, V. V.; Berdnikov, L. N.

    2017-06-01

    Long-slit spectroscopy with the Southern African Large Telescope (SALT) of central stars of mid-infrared nebulae detected with the Spitzer Space Telescope and Wide-Field Infrared Survey Explorer (WISE) led to the discovery of numerous candidate luminous blue variables (cLBVs) and other rare evolved massive stars. With the recent advent of the SALT fiber-fed high-resolution echelle spectrograph (HRS), a new perspective for the study of these interesting objects is appeared. Using the HRS we obtained spectra of a dozen newly identified massive stars. Some results on the recently identified cLBV Hen 3-729 are presented.

  9. Mobile computing acceptance grows as applications evolve.

    Science.gov (United States)

    Porn, Louis M; Patrick, Kelly

    2002-01-01

    Handheld devices are becoming more cost-effective to own, and their use in healthcare environments is increasing. Handheld devices currently are being used for e-prescribing, charge capture, and accessing daily schedules and reference tools. Future applications may include education on medications, dictation, order entry, and test-results reporting. Selecting the right handheld device requires careful analysis of current and future applications, as well as vendor expertise. It is important to recognize the technology will continue to evolve over the next three years.

  10. SALT spectroscopy of evolved massive stars

    CERN Document Server

    Kniazev, A Y; Berdnikov, L N

    2016-01-01

    Long-slit spectroscopy with the Southern African Large Telescope (SALT) of central stars of mid-infrared nebulae detected with the Spitzer Space Telescope and Wide-field Infrared Survey Explorer (WISE) led to the discovery of numerous candidate luminous blue variables (cLBVs) and other rare evolved massive stars. With the recent advent of the SALT fibre-fed high-resolution echelle spectrograph (HRS), a new perspective for the study of these interesting objects is appeared. Using the HRS we obtained spectra of a dozen newly identified massive stars. Some results on the recently identified cLBV Hen 3-729 are presented.

  11. Evolving NoSQL Databases Without Downtime

    OpenAIRE

    Saur, Karla; Dumitraş, Tudor; Hicks, Michael

    2015-01-01

    NoSQL databases like Redis, Cassandra, and MongoDB are increasingly popular because they are flexible, lightweight, and easy to work with. Applications that use these databases will evolve over time, sometimes necessitating (or preferring) a change to the format or organization of the data. The problem we address in this paper is: How can we support the evolution of high-availability applications and their NoSQL data online, without excessive delays or interruptions, even in the presence of b...

  12. Will the Amaranthus tuberculatus Resistance Mechanism to PPO-Inhibiting Herbicides Evolve in Other Amaranthus Species?

    Directory of Open Access Journals (Sweden)

    Chance W. Riggins

    2012-01-01

    Full Text Available Resistance to herbicides that inhibit protoporphyrinogen oxidase (PPO has been slow to evolve and, to date, is confirmed for only four weed species. Two of these species are members of the genus Amaranthus L. Previous research has demonstrated that PPO-inhibitor resistance in A. tuberculatus (Moq. Sauer, the first weed to have evolved this type of resistance, involves a unique codon deletion in the PPX2 gene. Our hypothesis is that A. tuberculatus may have been predisposed to evolving this resistance mechanism due to the presence of a repetitive motif at the mutation site and that lack of this motif in other amaranth species is why PPO-inhibitor resistance has not become more common despite strong herbicide selection pressure. Here we investigate inter- and intraspecific variability of the PPX2 gene—specifically exon 9, which includes the mutation site—in ten amaranth species via sequencing and a PCR-RFLP assay. Few polymorphisms were observed in this region of the gene, and intraspecific variation was observed only in A. quitensis. However, sequencing revealed two distinct repeat patterns encompassing the mutation site. Most notably, A. palmeri S. Watson possesses the same repetitive motif found in A. tuberculatus. We thus predict that A. palmeri will evolve resistance to PPO inhibitors via the same PPX2 codon deletion that evolved in A. tuberculatus.

  13. Impact of duplicate gene copies on phylogenetic analysis and divergence time estimates in butterflies

    Directory of Open Access Journals (Sweden)

    Liswi Saif W

    2009-05-01

    Full Text Available Abstract Background The increase in availability of genomic sequences for a wide range of organisms has revealed gene duplication to be a relatively common event. Encounters with duplicate gene copies have consequently become almost inevitable in the context of collecting gene sequences for inferring species trees. Here we examine the effect of incorporating duplicate gene copies evolving at different rates on tree reconstruction and time estimation of recent and deep divergences in butterflies. Results Sequences from ultraviolet-sensitive (UVRh, blue-sensitive (BRh, and long-wavelength sensitive (LWRh opsins,EF-1α and COI were obtained from 27 taxa representing the five major butterfly families (5535 bp total. Both BRh and LWRh are present in multiple copies in some butterfly lineages and the different copies evolve at different rates. Regardless of the phylogenetic reconstruction method used, we found that analyses of combined data sets using either slower or faster evolving copies of duplicate genes resulted in a single topology in agreement with our current understanding of butterfly family relationships based on morphology and molecules. Interestingly, individual analyses of BRh and LWRh sequences also recovered these family-level relationships. Two different relaxed clock methods resulted in similar divergence time estimates at the shallower nodes in the tree, regardless of whether faster or slower evolving copies were used, with larger discrepancies observed at deeper nodes in the phylogeny. The time of divergence between the monarch butterfly Danaus plexippus and the queen D. gilippus (15.3–35.6 Mya was found to be much older than the time of divergence between monarch co-mimic Limenitis archippus and red-spotted purple L. arthemis (4.7–13.6 Mya, and overlapping with the time of divergence of the co-mimetic passionflower butterflies Heliconius erato and H. melpomene (13.5–26.1 Mya. Our family-level results are congruent with

  14. De novo ORFs in Drosophila are important to organismal fitness and evolved rapidly from previously non-coding sequences.

    Directory of Open Access Journals (Sweden)

    Josephine A Reinhardt

    Full Text Available How non-coding DNA gives rise to new protein-coding genes (de novo genes is not well understood. Recent work has revealed the origins and functions of a few de novo genes, but common principles governing the evolution or biological roles of these genes are unknown. To better define these principles, we performed a parallel analysis of the evolution and function of six putatively protein-coding de novo genes described in Drosophila melanogaster. Reconstruction of the transcriptional history of de novo genes shows that two de novo genes emerged from novel long non-coding RNAs that arose at least 5 MY prior to evolution of an open reading frame. In contrast, four other de novo genes evolved a translated open reading frame and transcription within the same evolutionary interval suggesting that nascent open reading frames (proto-ORFs, while not required, can contribute to the emergence of a new de novo gene. However, none of the genes arose from proto-ORFs that existed long before expression evolved. Sequence and structural evolution of de novo genes was rapid compared to nearby genes and the structural complexity of de novo genes steadily increases over evolutionary time. Despite the fact that these genes are transcribed at a higher level in males than females, and are most strongly expressed in testes, RNAi experiments show that most of these genes are essential in both sexes during metamorphosis. This lethality suggests that protein coding de novo genes in Drosophila quickly become functionally important.

  15. Specificity of genome evolution in experimental populations of Escherichia coli evolved at different temperatures

    Science.gov (United States)

    Deatherage, Daniel E.; Kepner, Jamie L.; Bennett, Albert F.; Lenski, Richard E.; Barrick, Jeffrey E.

    2017-01-01

    Isolated populations derived from a common ancestor are expected to diverge genetically and phenotypically as they adapt to different local environments. To examine this process, 30 populations of Escherichia coli were evolved for 2,000 generations, with six in each of five different thermal regimes: constant 20 °C, 32 °C, 37 °C, 42 °C, and daily alternations between 32 °C and 42 °C. Here, we sequenced the genomes of one endpoint clone from each population to test whether the history of adaptation in different thermal regimes was evident at the genomic level. The evolved strains had accumulated ∼5.3 mutations, on average, and exhibited distinct signatures of adaptation to the different environments. On average, two strains that evolved under the same regime exhibited ∼17% overlap in which genes were mutated, whereas pairs that evolved under different conditions shared only ∼4%. For example, all six strains evolved at 32 °C had mutations in nadR, whereas none of the other 24 strains did. However, a population evolved at 37 °C for an additional 18,000 generations eventually accumulated mutations in the signature genes strongly associated with adaptation to the other temperature regimes. Two mutations that arose in one temperature treatment tended to be beneficial when tested in the others, although less so than in the regime in which they evolved. These findings demonstrate that genomic signatures of adaptation can be highly specific, even with respect to subtle environmental differences, but that this imprint may become obscured over longer timescales as populations continue to change and adapt to the shared features of their environments. PMID:28202733

  16. Noncoding sequences from the slowly evolving chloroplast inverted repeat in addition to rbcL data do not support gnetalean affinities of angiosperms.

    Science.gov (United States)

    Goremykin, V; Bobrova, V; Pahnke, J; Troitsky, A; Antonov, A; Martin, W

    1996-02-01

    We developed PCR primers against highly conserved regions of the rRNA operon located within the inverted repeat of the chloroplast genome and used these to amplify the region spanning from the 3' terminus of the 23S rRNA gene to the 5' terminus of the 5S rRNA gene. The sequence of this roughly 500-bp region, which includes the 4.5S rRNA gene and two chloroplast intergenic transcribed spacer regions (cpITS2 and cpITS3), was determined from 20 angiosperms, 7 gymnosperms, and 16 ferns (21,700 bp). Sequences for the large subunit of ribulose bisphosphate carboxylase/oxygenase (rbcL) from the same or confamilial genera were analyzed in both separate and combined data sets. Due to the low substitution rate in the inverted repeat region, noncoding sequences in the cpITS region are not saturated with substitutions, in contrast to synonymous sites in rbcL, which are shown to evolve roughly six times faster than noncoding cpITS sequences. Several length polymorphisms with very clear phylogenetic distributions were detected in the data set. Results of phylogenetic analyses provide very strong bootstrap support for monophyly of both spermatophytes and angiosperms. No support for a sister group relationship between Gnetales and angiosperms in either cpITS or rbcL data was found. Rather, weak bootstrap support for monophyly of gymnosperms studied and for a basal position for the aquatic angiosperm Nymphaea among angiosperms studied was observed. Noncoding sequences from the inverted repeat region of chloroplast DNA appear suitable for study of land plant evolution.

  17. The evolving role of the transfusion practitioner.

    Science.gov (United States)

    Miller, Kristy; Akers, Christine; Davis, Amanda K; Wood, Erica; Hennessy, Clare; Bielby, Linley

    2015-04-01

    Much of the recent work in transfusion practice has shifted to focus on the patient, after efforts over previous decades to ensure the quality and safety of blood products. After the commencement of hemovigilance and transfusion practice improvement programs, the introduction of transfusion practitioners (TP) into health care services and blood centers has continued to increase worldwide. Since this relatively new role was introduced, much work of the TP has focused on patient and staff education, adverse events, transfusion governance, and monitoring of transfusion practices within organizations. The complex nature of the transfusion process makes the TP an integral link in the transfusion chain. Together with hospital transfusion teams and committees, the TP works collaboratively to facilitate the transfusion change management programs and initiatives. Recently, the TP role has evolved to include an emphasis on patient blood management and, to some extent, is shaped by national standards and regulations. These established roles of the TP, together with the ever-changing field of transfusion medicine, provide new opportunities and challenges for a role that is continuing to evolve worldwide. Copyright © 2015 Elsevier Inc. All rights reserved.

  18. Netgram: Visualizing Communities in Evolving Networks.

    Directory of Open Access Journals (Sweden)

    Raghvendra Mall

    Full Text Available Real-world complex networks are dynamic in nature and change over time. The change is usually observed in the interactions within the network over time. Complex networks exhibit community like structures. A key feature of the dynamics of complex networks is the evolution of communities over time. Several methods have been proposed to detect and track the evolution of these groups over time. However, there is no generic tool which visualizes all the aspects of group evolution in dynamic networks including birth, death, splitting, merging, expansion, shrinkage and continuation of groups. In this paper, we propose Netgram: a tool for visualizing evolution of communities in time-evolving graphs. Netgram maintains evolution of communities over 2 consecutive time-stamps in tables which are used to create a query database using the sql outer-join operation. It uses a line-based visualization technique which adheres to certain design principles and aesthetic guidelines. Netgram uses a greedy solution to order the initial community information provided by the evolutionary clustering technique such that we have fewer line cross-overs in the visualization. This makes it easier to track the progress of individual communities in time evolving graphs. Netgram is a generic toolkit which can be used with any evolutionary community detection algorithm as illustrated in our experiments. We use Netgram for visualization of topic evolution in the NIPS conference over a period of 11 years and observe the emergence and merging of several disciplines in the field of information processing systems.

  19. BOOK REVIEW: OPENING SCIENCE, THE EVOLVING GUIDE ...

    Science.gov (United States)

    The way we get our funding, collaborate, do our research, and get the word out has evolved over hundreds of years but we can imagine a more open science world, largely facilitated by the internet. The movement towards this more open way of doing and presenting science is coming, and it is not taking hundreds of years. If you are interested in these trends, and would like to find out more about where this is all headed and what it means to you, consider downloding Opening Science, edited by Sönke Bartling and Sascha Friesike, subtitled The Evolving Guide on How the Internet is Changing Research, Collaboration, and Scholarly Publishing. In 26 chapters by various authors from a range of disciplines the book explores the developing world of open science, starting from the first scientific revolution and bringing us to the next scientific revolution, sometimes referred to as “Science 2.0”. Some of the articles deal with the impact of the changing landscape of how science is done, looking at the impact of open science on Academia, or journal publishing, or medical research. Many of the articles look at the uses, pitfalls, and impact of specific tools, like microblogging (think Twitter), social networking, and reference management. There is lots of discussion and definition of terms you might use or misuse like “altmetrics” and “impact factor”. Science will probably never be completely open, and Twitter will probably never replace the journal article,

  20. Collapse of cooperation in evolving games.

    Science.gov (United States)

    Stewart, Alexander J; Plotkin, Joshua B

    2014-12-09

    Game theory provides a quantitative framework for analyzing the behavior of rational agents. The Iterated Prisoner's Dilemma in particular has become a standard model for studying cooperation and cheating, with cooperation often emerging as a robust outcome in evolving populations. Here we extend evolutionary game theory by allowing players' payoffs as well as their strategies to evolve in response to selection on heritable mutations. In nature, many organisms engage in mutually beneficial interactions and individuals may seek to change the ratio of risk to reward for cooperation by altering the resources they commit to cooperative interactions. To study this, we construct a general framework for the coevolution of strategies and payoffs in arbitrary iterated games. We show that, when there is a tradeoff between the benefits and costs of cooperation, coevolution often leads to a dramatic loss of cooperation in the Iterated Prisoner's Dilemma. The collapse of cooperation is so extreme that the average payoff in a population can decline even as the potential reward for mutual cooperation increases. Depending upon the form of tradeoffs, evolution may even move away from the Iterated Prisoner's Dilemma game altogether. Our work offers a new perspective on the Prisoner's Dilemma and its predictions for cooperation in natural populations; and it provides a general framework to understand the coevolution of strategies and payoffs in iterated interactions.

  1. BOOK REVIEW: OPENING SCIENCE, THE EVOLVING GUIDE ...

    Science.gov (United States)

    The way we get our funding, collaborate, do our research, and get the word out has evolved over hundreds of years but we can imagine a more open science world, largely facilitated by the internet. The movement towards this more open way of doing and presenting science is coming, and it is not taking hundreds of years. If you are interested in these trends, and would like to find out more about where this is all headed and what it means to you, consider downloding Opening Science, edited by Sönke Bartling and Sascha Friesike, subtitled The Evolving Guide on How the Internet is Changing Research, Collaboration, and Scholarly Publishing. In 26 chapters by various authors from a range of disciplines the book explores the developing world of open science, starting from the first scientific revolution and bringing us to the next scientific revolution, sometimes referred to as “Science 2.0”. Some of the articles deal with the impact of the changing landscape of how science is done, looking at the impact of open science on Academia, or journal publishing, or medical research. Many of the articles look at the uses, pitfalls, and impact of specific tools, like microblogging (think Twitter), social networking, and reference management. There is lots of discussion and definition of terms you might use or misuse like “altmetrics” and “impact factor”. Science will probably never be completely open, and Twitter will probably never replace the journal article,

  2. Novel cooperation experimentally evolved between species.

    Science.gov (United States)

    Harcombe, William

    2010-07-01

    Cooperation violates the view of "nature red in tooth and claw" that prevails in our understanding of evolution, yet examples of cooperation abound. Most work has focused on maintenance of cooperation within a single species through mechanisms such as kin selection. The factors necessary for the evolutionary origin of aiding unrelated individuals such as members of another species have not been experimentally tested. Here, I demonstrate that cooperation between species can be evolved in the laboratory if (1) there is preexisting reciprocation or feedback for cooperation, and (2) reciprocation is preferentially received by cooperative genotypes. I used a two species system involving Salmonella enterica ser. Typhimurium and an Escherichia coli mutant unable to synthesize an essential amino acid. In lactose media Salmonella consumes metabolic waste from E. coli, thus creating a mechanism of reciprocation for cooperation. Growth in a spatially structured environment assured that the benefits of cooperation were preferentially received by cooperative genotypes. Salmonella evolved to aid E. coli by excreting a costly amino acid, however this novel cooperation disappeared if the waste consumption or spatial structure were removed. This study builds on previous work to demonstrate an experimental origin of interspecific cooperation, and to test the factors necessary for such interactions to arise.

  3. Early formation of evolved asteroidal crust.

    Science.gov (United States)

    Day, James M D; Ash, Richard D; Liu, Yang; Bellucci, Jeremy J; Rumble, Douglas; McDonough, William F; Walker, Richard J; Taylor, Lawrence A

    2009-01-08

    Mechanisms for the formation of crust on planetary bodies remain poorly understood. It is generally accepted that Earth's andesitic continental crust is the product of plate tectonics, whereas the Moon acquired its feldspar-rich crust by way of plagioclase flotation in a magma ocean. Basaltic meteorites provide evidence that, like the terrestrial planets, some asteroids generated crust and underwent large-scale differentiation processes. Until now, however, no evolved felsic asteroidal crust has been sampled or observed. Here we report age and compositional data for the newly discovered, paired and differentiated meteorites Graves Nunatak (GRA) 06128 and GRA 06129. These meteorites are feldspar-rich, with andesite bulk compositions. Their age of 4.52 +/- 0.06 Gyr demonstrates formation early in Solar System history. The isotopic and elemental compositions, degree of metamorphic re-equilibration and sulphide-rich nature of the meteorites are most consistent with an origin as partial melts from a volatile-rich, oxidized asteroid. GRA 06128 and 06129 are the result of a newly recognized style of evolved crust formation, bearing witness to incomplete differentiation of their parent asteroid and to previously unrecognized diversity of early-formed materials in the Solar System.

  4. Accelerated rates of protein evolution in barley grain and pistil biased genes might be legacy of domestication.

    Science.gov (United States)

    Shi, Tao; Dimitrov, Ivan; Zhang, Yinling; Tax, Frans E; Yi, Jing; Gou, Xiaoping; Li, Jia

    2015-10-01

    Traits related to grain and reproductive organs in grass crops have been under continuous directional selection during domestication. Barley is one of the oldest domesticated crops in human history. Thus genes associated with the grain and reproductive organs in barley may show evidence of dramatic evolutionary change. To understand how artificial selection contributes to protein evolution of biased genes in different barley organs, we used Digital Gene Expression analysis of six barley organs (grain, pistil, anther, leaf, stem and root) to identify genes with biased expression in specific organs. Pairwise comparisons of orthologs between barley and Brachypodium distachyon, as well as between highland and lowland barley cultivars mutually indicated that grain and pistil biased genes show relatively higher protein evolutionary rates compared with the median of all orthologs and other organ biased genes. Lineage-specific protein evolutionary rates estimation showed similar patterns with elevated protein evolution in barley grain and pistil biased genes, yet protein sequences generally evolve much faster in the lowland barley cultivar. Further functional annotations revealed that some of these grain and pistil biased genes with rapid protein evolution are related to nutrient biosynthesis and cell cycle/division. Our analyses provide insights into how domestication differentially shaped the evolution of genes specific to different organs of a crop species, and implications for future functional studies of domestication genes.

  5. Criticality is an emergent property of genetic networks that exhibit evolvability.

    Directory of Open Access Journals (Sweden)

    Christian Torres-Sosa

    Full Text Available Accumulating experimental evidence suggests that the gene regulatory networks of living organisms operate in the critical phase, namely, at the transition between ordered and chaotic dynamics. Such critical dynamics of the network permits the coexistence of robustness and flexibility which are necessary to ensure homeostatic stability (of a given phenotype while allowing for switching between multiple phenotypes (network states as occurs in development and in response to environmental change. However, the mechanisms through which genetic networks evolve such critical behavior have remained elusive. Here we present an evolutionary model in which criticality naturally emerges from the need to balance between the two essential components of evolvability: phenotype conservation and phenotype innovation under mutations. We simulated the Darwinian evolution of random Boolean networks that mutate gene regulatory interactions and grow by gene duplication. The mutating networks were subjected to selection for networks that both (i preserve all the already acquired phenotypes (dynamical attractor states and (ii generate new ones. Our results show that this interplay between extending the phenotypic landscape (innovation while conserving the existing phenotypes (conservation suffices to cause the evolution of all the networks in a population towards criticality. Furthermore, the networks produced by this evolutionary process exhibit structures with hubs (global regulators similar to the observed topology of real gene regulatory networks. Thus, dynamical criticality and certain elementary topological properties of gene regulatory networks can emerge as a byproduct of the evolvability of the phenotypic landscape.

  6. Faster Smith-Waterman database searches with inter-sequence SIMD parallelisation

    Directory of Open Access Journals (Sweden)

    Rognes Torbjørn

    2011-06-01

    Full Text Available Abstract Background The Smith-Waterman algorithm for local sequence alignment is more sensitive than heuristic methods for database searching, but also more time-consuming. The fastest approach to parallelisation with SIMD technology has previously been described by Farrar in 2007. The aim of this study was to explore whether further speed could be gained by other approaches to parallelisation. Results A faster approach and implementation is described and benchmarked. In the new tool SWIPE, residues from sixteen different database sequences are compared in parallel to one query residue. Using a 375 residue query sequence a speed of 106 billion cell updates per second (GCUPS was achieved on a dual Intel Xeon X5650 six-core processor system, which is over six times more rapid than software based on Farrar's 'striped' approach. SWIPE was about 2.5 times faster when the programs used only a single thread. For shorter queries, the increase in speed was larger. SWIPE was about twice as fast as BLAST when using the BLOSUM50 score matrix, while BLAST was about twice as fast as SWIPE for the BLOSUM62 matrix. The software is designed for 64 bit Linux on processors with SSSE3. Source code is available from http://dna.uio.no/swipe/ under the GNU Affero General Public License. Conclusions Efficient parallelisation using SIMD on standard hardware makes it possible to run Smith-Waterman database searches more than six times faster than before. The approach described here could significantly widen the potential application of Smith-Waterman searches. Other applications that require optimal local alignment scores could also benefit from improved performance.

  7. Faster self-paced rate of drinking for alcohol mixed with energy drinks versus alcohol alone.

    Science.gov (United States)

    Marczinski, Cecile A; Fillmore, Mark T; Maloney, Sarah F; Stamates, Amy L

    2017-03-01

    The consumption of alcohol mixed with energy drinks (AmED) has been associated with higher rates of binge drinking and impaired driving when compared with alcohol alone. However, it remains unclear why the risks of use of AmED are heightened compared with alcohol alone even when the doses of alcohol consumed are similar. Therefore, the purpose of this laboratory study was to investigate if the rate of self-paced beverage consumption was faster for a dose of AmED versus alcohol alone using a double-blind, within-subjects, placebo-controlled study design. Participants (n = 16) of equal gender who were social drinkers attended 4 separate test sessions that involved consumption of alcohol (1.97 ml/kg vodka) and energy drinks, alone and in combination. On each test day, the dose assigned was divided into 10 cups. Participants were informed that they would have a 2-h period to consume the 10 drinks. After the self-paced drinking period, participants completed a cued go/no-go reaction time (RT) task and subjective ratings of stimulation and sedation. The results indicated that participants consumed the AmED dose significantly faster (by ∼16 min) than the alcohol dose. For the performance task, participants' mean RTs were slower in the alcohol conditions and faster in the energy-drink conditions. In conclusion, alcohol consumers should be made aware that rapid drinking might occur for AmED beverages, thus heightening alcohol-related safety risks. The fast rate of drinking may be related to the generalized speeding of responses after energy-drink consumption. (PsycINFO Database Record (c) 2017 APA, all rights reserved).

  8. Faster native vowel discrimination learning in musicians is mediated by an optimization of mnemonic functions.

    Science.gov (United States)

    Elmer, Stefan; Greber, Marielle; Pushparaj, Arethy; Kühnis, Jürg; Jäncke, Lutz

    2017-09-01

    The ability to discriminate phonemes varying in spectral and temporal attributes constitutes one of the most basic intrinsic elements underlying language learning mechanisms. Since previous work has consistently shown that professional musicians are characterized by perceptual and cognitive advantages in a variety of language-related tasks, and since vowels can be considered musical sounds within the domain of speech, here we investigated the behavioral and electrophysiological correlates of native vowel discrimination learning in a sample of professional musicians and non-musicians. We evaluated the contribution of both the neurophysiological underpinnings of perceptual (i.e., N1/P2 complex) and mnemonic functions (i.e., N400 and P600 responses) while the participants were instructed to judge whether pairs of native consonant-vowel (CV) syllables manipulated in the first formant transition of the vowel (i.e., from /tu/ to /to/) were identical or not. Results clearly demonstrated faster learning in musicians, compared to non-musicians, as reflected by shorter reaction times and higher accuracy. Most notably, in terms of morphology, time course, and voltage strength, this steeper learning curve was accompanied by distinctive N400 and P600 manifestations between the two groups. In contrast, we did not reveal any group differences during the early stages of auditory processing (i.e., N1/P2 complex), suggesting that faster learning was mediated by an optimization of mnemonic but not perceptual functions. Based on a clear taxonomy of the mnemonic functions involved in the task, results are interpreted as pointing to a relationship between faster learning mechanisms in musicians and an optimization of echoic (i.e., N400 component) and working memory (i.e., P600 component) functions. Copyright © 2017 Elsevier Ltd. All rights reserved.

  9. Faster Simulation Methods for the Non-Stationary Random Vibrations of Non-Linear MDOF Systems

    DEFF Research Database (Denmark)

    Askar, A.; Köylüoglu, H. U.; Nielsen, Søren R. K.;

    In this paper semi-analytical forward-difference Monte Carlo simulation procedures are proposed for the determination of the lower order statistics and the Joint Probability Density Function (JPDF) of the stochastic response of geometrically nonlinear multi-degree-of-freedom structural systems....... Such a treatment offers higher rates of convergence, faster speed and higher accuracy. These procedures are compared to the direct Monte Carlo simulation procedure, which uses a fourth order Runge-Kutta scheme with the white noise process approximated by a broad band Ruiz-Penzien broken line process...

  10. Evaluating Zeolite-Modified Sensors: towards a faster set of chemical sensors

    Science.gov (United States)

    Berna, A. Z.; Vergara, A.; Trincavelli, M.; Huerta, R.; Afonja, A.; Parkin, I. P.; Binions, R.; Trowell, S.

    2011-09-01

    The responses of zeolite-modified sensors, prepared by screen printing layers of chromium titanium oxide (CTO), were compared to unmodified tin oxide sensors using amplitude and transient responses. For transient responses we used a family of features, derived from the exponential moving average (EMA), to characterize chemo-resistive responses. All sensors were tested simultaneously against 20 individual volatile compounds from four chemical groups. The responses of the two types of sensors showed some independence. The zeolite-modified CTO sensors discriminated compounds better using either amplitude response or EMA features and CTO-modified sensors also responded three times faster.

  11. Two-ply channels for faster wicking in paper-based microfluidic devices.

    Science.gov (United States)

    Camplisson, Conor K; Schilling, Kevin M; Pedrotti, William L; Stone, Howard A; Martinez, Andres W

    2015-12-01

    This article describes the development of porous two-ply channels for paper-based microfluidic devices that wick fluids significantly faster than conventional, porous, single-ply channels. The two-ply channels were made by stacking two single-ply channels on top of each other and were fabricated entirely out of paper, wax and toner using two commercially available printers, a convection oven and a thermal laminator. The wicking in paper-based channels was studied and modeled using a modified Lucas-Washburn equation to account for the effect of evaporation, and a paper-based titration device incorporating two-ply channels was demonstrated.

  12. Hybrid incompatibility is acquired faster in annual than in perennial species of sunflower and tarweed.

    Science.gov (United States)

    Owens, Gregory L; Rieseberg, Loren H

    2014-03-01

    Hybrid sterility is an important species barrier, especially in plants where hybrids can often form between divergent taxa. Here we explore how life history affects the acquisition of hybrid sterility in two groups in the sunflower family. We analyzed genetic distance and F1 pollen sterility for interspecific crosses in annual and perennial groups. We find that reproductive isolation is acquired in a steady manner and that annual species acquire hybrid sterility barriers faster than perennial species. Potential causes of the observed sterility pattern are discussed.

  13. Forces shaping the fastest evolving regions in the human genome.

    Directory of Open Access Journals (Sweden)

    Katherine S Pollard

    2006-10-01

    Full Text Available Comparative genomics allow us to search the human genome for segments that were extensively changed in the last approximately 5 million years since divergence from our common ancestor with chimpanzee, but are highly conserved in other species and thus are likely to be functional. We found 202 genomic elements that are highly conserved in vertebrates but show evidence of significantly accelerated substitution rates in human. These are mostly in non-coding DNA, often near genes associated with transcription and DNA binding. Resequencing confirmed that the five most accelerated elements are dramatically changed in human but not in other primates, with seven times more substitutions in human than in chimp. The accelerated elements, and in particular the top five, show a strong bias for adenine and thymine to guanine and cytosine nucleotide changes and are disproportionately located in high recombination and high guanine and cytosine content environments near telomeres, suggesting either biased gene conversion or isochore selection. In addition, there is some evidence of directional selection in the regions containing the two most accelerated regions. A combination of evolutionary forces has contributed to accelerated evolution of the fastest evolving elements in the human genome.

  14. The Evolving Diagnostic and Genetic Landscapes of Autism Spectrum Disorder.

    Science.gov (United States)

    Ziats, Mark N; Rennert, Owen M

    2016-01-01

    The autism spectrum disorders (ASD) are a heterogeneous set of neurodevelopmental syndromes defined by impairments in verbal and non-verbal communication, restricted social interaction, and the presence of stereotyped patterns of behavior. The prevalence of ASD is rising, and the diagnostic criteria and clinical perspectives on the disorder continue to evolve in parallel. Although the majority of individuals with ASD will not have an identifiable genetic cause, almost 25% of cases have identifiable causative DNA variants. The rapidly improving ability to identify genetic mutations because of advances in next generation sequencing, coupled with previous epidemiological studies demonstrating high heritability of ASD, have led to many recent attempts to identify causative genetic mutations underlying the ASD phenotype. However, although hundreds of mutations have been identified to date, they are either rare variants affecting only a handful of ASD patients, or are common variants in the general population conferring only a small risk for ASD. Furthermore, the genes implicated thus far are heterogeneous in their structure and function, hampering attempts to understand shared molecular mechanisms among all ASD patients; an understanding that is crucial for the development of targeted diagnostics and therapies. However, new work is beginning to suggest that the heterogeneous set of genes implicated in ASD may ultimately converge on a few common pathways. In this review, we discuss the parallel evolution of our diagnostic and genetic understanding of autism spectrum disorders, and highlight recent attempts to infer common biology underlying this complicated syndrome.

  15. Meiosis evolves: adaptation to external and internal environments.

    Science.gov (United States)

    Bomblies, Kirsten; Higgins, James D; Yant, Levi

    2015-10-01

    306 I. 306 II. 307 III. 312 IV. 317 V. 318 319 References 319 SUMMARY: Meiosis is essential for the fertility of most eukaryotes and its structures and progression are conserved across kingdoms. Yet many of its core proteins show evidence of rapid or adaptive evolution. What drives the evolution of meiosis proteins? How can constrained meiotic processes be modified in response to challenges without compromising their essential functions? In surveying the literature, we found evidence of two especially potent challenges to meiotic chromosome segregation that probably necessitate adaptive evolutionary responses: whole-genome duplication and abiotic environment, especially temperature. Evolutionary solutions to both kinds of challenge are likely to involve modification of homologous recombination and synapsis, probably via adjustments of core structural components important in meiosis I. Synthesizing these findings with broader patterns of meiosis gene evolution suggests that the structural components of meiosis coevolve as adaptive modules that may change in primary sequence and function while maintaining three-dimensional structures and protein interactions. The often sharp divergence of these genes among species probably reflects periodic modification of entire multiprotein complexes driven by genomic or environmental changes. We suggest that the pressures that cause meiosis to evolve to maintain fertility may cause pleiotropic alterations of global crossover rates. We highlight several important areas for future research. © 2015 The Authors. New Phytologist © 2015 New Phytologist Trust.

  16. Constantly evolving safety assessment protocols for GM foods.

    Science.gov (United States)

    Sesikeran, B; Vasanthi, Siruguri

    2008-01-01

    he introduction of GM foods has led to the evolution of a food safety assessment paradigm that establishes safety of the GM food relative to its conventional counterpart. The GM foods currently approved and marketed in several countries have undergone extensive safety testing under a structured safety assessment framework evolved by international organizations like FAO, WHO, Codex and OECD. The major elements of safety assessment include molecular characterization of inserted genes and stability of the trait, toxicity and allergenicity potential of the expressed substances, compositional analysis, potential for gene transfer to gut microflora and unintentional effects of the genetic modification. As more number and type of food crops are being brought under the genetic modification regime, the adequacy of existing safety assessment protocols for establishing safety of these foods has been questioned. Such crops comprise GM crops with higher agronomic vigour, nutritional or health benefit/ by modification of plant metabolic pathways and those expressing bioactive substances and pharmaceuticals. The safety assessment challenges of these foods are the potential of the methods to detect unintentional effects with higher sensitivity and rigor. Development of databases on food compositions, toxicants and allergens is currently seen as an important aid to development of safety protocols. With the changing global trends in genetic modification technology future challenge would be to develop GM crops with minimum amount of inserted foreign DNA so as to reduce the burden of complex safety assessments while ensuring safety and utility of the technology.

  17. Evolved Mechanisms Versus Underlying Conditional Relations

    Directory of Open Access Journals (Sweden)

    Astorga Miguel López

    2015-03-01

    Full Text Available The social contracts theory claims that, in social exchange circumstances, human reasoning is not necessarily led by logic, but by certain evolved mental mechanisms that are useful for catching offenders. An emblematic experiment carried out with the intention to prove this thesis is the first experiment described by Fiddick, Cosmides, and Tooby in their paper of 2000. Lopez Astorga has questioned that experiment claiming that its results depend on an underlying conditional logical form not taken into account by Fiddick, Cosmides, and Tooby. In this paper, I propose an explanation alternative to that of Lopez Astorga, which does not depend on logical forms and is based on the mental models theory. Thus, I conclude that this other alternative explanation is one more proof that the experiment in question does not demonstrate the fundamental thesis of the social contracts theory.

  18. Evolving Classifiers: Methods for Incremental Learning

    CERN Document Server

    Hulley, Greg

    2007-01-01

    The ability of a classifier to take on new information and classes by evolving the classifier without it having to be fully retrained is known as incremental learning. Incremental learning has been successfully applied to many classification problems, where the data is changing and is not all available at once. In this paper there is a comparison between Learn++, which is one of the most recent incremental learning algorithms, and the new proposed method of Incremental Learning Using Genetic Algorithm (ILUGA). Learn++ has shown good incremental learning capabilities on benchmark datasets on which the new ILUGA method has been tested. ILUGA has also shown good incremental learning ability using only a few classifiers and does not suffer from catastrophic forgetting. The results obtained for ILUGA on the Optical Character Recognition (OCR) and Wine datasets are good, with an overall accuracy of 93% and 94% respectively showing a 4% improvement over Learn++.MT for the difficult multi-class OCR dataset.

  19. Quantum mechanics in an evolving Hilbert space

    CERN Document Server

    Artacho, Emilio

    2016-01-01

    Many basis sets for electronic structure calculations evolve with varying external parameters, such as moving atoms in dynamic simulations, giving rise to extra derivative terms in the dynamical equations. Here we revisit these derivatives in the context of differential geometry, thereby obtaining a more transparent formalisation, and a geometrical perspective for better understanding the resulting equations. The effect of the evolution of the basis set within the spanned Hilbert space separates explicitly from the effect of the turning of the space itself when moving in parameter space, as the tangent space turns when moving in a curved space. New insights are obtained using familiar concepts in that context such as the Riemann curvature. The differential geometry is not strictly that for curved spaces as in general relativity, a more adequate mathematical framework being provided by fibre bundles. The language used here, however, will be restricted to tensors and basic quantum mechanics. The local gauge imp...

  20. THE J STRUCTURE IN ECONOMIC EVOLVING PROCESS

    Institute of Scientific and Technical Information of China (English)

    FANG Fukang; CHEN Qinghua

    2003-01-01

    The economic evolution exhibits complexity. Behind the variable and fiuctuant economic data there exists basic characters and rules. One basic structure in economic evolving process called as "J" structure is studied by us. This kind of structure exists in a wide area, such as economic growth, technology innovation, international trade, education, human capital, ecology and environment etc. From the view of economic evolution, J structure has the character that system should suffer the pressure of initial investment with profit decreasing but get larger return afterwards. It is a kind of adaptation in complex economic systems; it reflects the adaptive and reformative ability of the system under the surrounding change. We illustrate the J structure by discussing economic growth. Based on a two-dimension dynamic system the geometric character and mechanism of J structure are studied, also the phase graphs with its condition are given. Also some further works are discussed.

  1. Design of Evolvable Hardware for Robotic Navigation

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    This paper presents an integrated on-line learning system toevolve programmabl e logic array (PLA) controllers for navigating an autonomous robot in a two-dime n sional environment. The integrated on-line learning system consists of two lear n ing modules: one is the module of reinforcement learning based on temporal-diff e rence learning based on genetic algorithms, and the other is the module of evolu tionary learning based on genetic algorithms. The control rules extracted from t he module of reinforcement learning can be used as input to the module of evolut ionary learning, and quickly implemented by the PLA through on-line evolution. T he on-line evolution has shown promise as a method of learning systems in compl e x environment. The evolved PLA controllers can successfully navigate the robot t o a target in the two-dimensional environment while avoiding collisions with ra ndomly positioned obstacles.

  2. Production and decay of evolving horizons

    CERN Document Server

    Visser, M; Nielsen, Alex; Visser, Matt

    2006-01-01

    We consider a simple physical model for an evolving horizon that is strongly interacting with its environment, exchanging arbitrarily large quantities of matter with its environment in the form of both infalling material and outgoing Hawking radiation. We permit fluxes of both lightlike and timelike particles to cross the horizon, and ask how the horizon grows and shrinks in response to such flows. We place a premium on providing a clear and straightforward exposition with simple formulae. To be able to handle such a highly dynamical situation in a simple manner we make one significant physical restriction, that of spherical symmetry, and two technical mathematical restrictions: (1) We choose to slice the spacetime in such a way that the space-time foliations (and hence the horizons) are always spherically symmetric. (2) Furthermore we adopt Painleve-Gullstrand coordinates (which are well suited to the problem because they are nonsingular at the horizon) in order to simplify the relevant calculations. We find...

  3. Epidemic spreading on evolving signed networks

    CERN Document Server

    Saeedian, M; Jafari, G R; Kertesz, J

    2016-01-01

    Most studies of disease spreading consider the underlying social network as obtained without the contagion, though epidemic influences peoples willingness to contact others: A friendly contact may be turned to unfriendly to avoid infection. We study the susceptible-infected (SI) disease spreading model on signed networks, in which each edge is associated with a positive or negative sign representing the friendly or unfriendly relation between its end nodes. In a signed network, according to Heiders theory, edge signs evolve such that finally a state of structural balance is achieved, corresponding to no frustration in physics terms. However, the danger of infection affects the evolution of its edge signs. To describe the coupled problem of the sign evolution and disease spreading, we generalize the notion of structural balance by taking into account the state of the nodes. We introduce an energy function and carry out Monte-Carlo simulations on complete networks to test the energy landscape, where we find loc...

  4. Resiliently evolving supply-demand networks

    CERN Document Server

    Rubido, Nicolás; Baptista, Murilo S

    2013-01-01

    The ability to design a transport network such that commodities are brought from suppliers to consumers in a steady, optimal, and stable way is of great importance for nowadays distribution systems. In this Letter, by using the circuit laws of Kirchhoff and Ohm, we provide the exact capacities of the edges that an optimal supply-demand network should have to operate stably under perturbations. The perturbations we consider are the evolution of the connecting topology, the decentralisation of hub sources or sinks, and the intermittence of suppliers/consumers characteristics. We analyse these conditions and the impact of our results, both on the current UK power-grid structure and on numerically generated evolving archetypal network topologies.

  5. Resiliently evolving supply-demand networks.

    Science.gov (United States)

    Rubido, Nicolás; Grebogi, Celso; Baptista, Murilo S

    2014-01-01

    The ability to design a transport network such that commodities are brought from suppliers to consumers in a steady, optimal, and stable way is of great importance for distribution systems nowadays. In this work, by using the circuit laws of Kirchhoff and Ohm, we provide the exact capacities of the edges that an optimal supply-demand network should have to operate stably under perturbations, i.e., without overloading. The perturbations we consider are the evolution of the connecting topology, the decentralization of hub sources or sinks, and the intermittence of supplier and consumer characteristics. We analyze these conditions and the impact of our results, both on the current United Kingdom power-grid structure and on numerically generated evolving archetypal network topologies.

  6. The Evolving Structure of Galactic Disks

    CERN Document Server

    Martel, H; McGee, S; Gibson, B; Kawata, D; Martel, Hugo; Brook, Chris; Gee, Sean Mc; Gibson, Brad

    2005-01-01

    Observations suggest that the structural parameters of disk galaxies have not changed greatly since redshift 1. We examine whether these observations are consistent with a cosmology in which structures form hierarchically. We use SPH/N-body galaxy-scale simulations to simulate the formation and evolution of Milky-Way-like disk galaxies by fragmentation, followed by hierarchical merging. The simulated galaxies have a thick disk, that forms in a period of chaotic merging at high redshift, during which a large amount of alpha-elements are produced, and a thin disk, that forms later and has a higher metallicity. Our simulated disks settle down quickly and do not evolve much since redshift z~1, mostly because no major mergers take place between z=1 and z=0. During this period, the disk radius increases (inside-out growth) while its thickness remains constant. These results are consistent with observations of disk galaxies at low and high redshift.

  7. Ensuring Query Compatibility with Evolving XML Schemas

    CERN Document Server

    Genevès, Pierre; Quint, Vincent

    2008-01-01

    During the life cycle of an XML application, both schemas and queries may change from one version to another. Schema evolutions may affect query results and potentially the validity of produced data. Nowadays, a challenge is to assess and accommodate the impact of theses changes in rapidly evolving XML applications. This article proposes a logical framework and tool for verifying forward/backward compatibility issues involving schemas and queries. First, it allows analyzing relations between schemas. Second, it allows XML designers to identify queries that must be reformulated in order to produce the expected results across successive schema versions. Third, it allows examining more precisely the impact of schema changes over queries, therefore facilitating their reformulation.

  8. Properties of evolving e-mail networks

    Science.gov (United States)

    Wang, Juan; de Wilde, Philippe

    2004-12-01

    Computer viruses spread by attaching to an e-mail message and sending themselves to users whose addresses are in the e-mail address book of the recipients. Here we investigate a simple model of an evolving e-mail network, with nodes as e-mail address books of users and links as the records of e-mail addresses in the address books. Within specific periods, some new links are generated and some old links are deleted. We study the statistical properties of this e-mail network and observe the effect of the evolution on the structure of the network. We also find that the balance between the generation procedure and deletion procedure is dependent on different parameters of the model.

  9. Language as a coordination tool evolves slowly

    Science.gov (United States)

    2016-01-01

    Social living ultimately depends on coordination between group members, and communication is necessary to make this possible. We suggest that this might have been the key selection pressure acting on the evolution of language in humans and use a behavioural coordination model to explore the impact of communication efficiency on social group coordination. We show that when language production is expensive but there is an individual benefit to the efficiency with which individuals coordinate their behaviour, the evolution of efficient communication is selected for. Contrary to some views of language evolution, the speed of evolution is necessarily slow because there is no advantage in some individuals evolving communication abilities that much exceed those of the community at large. However, once a threshold competence has been achieved, evolution of higher order language skills may indeed be precipitate. PMID:28083091

  10. A local-world evolving hypernetwork model

    Science.gov (United States)

    Yang, Guang-Yong; Liu, Jian-Guo

    2014-01-01

    Complex hypernetworks are ubiquitous in the real system. It is very important to investigate the evolution mechanisms. In this paper, we present a local-world evolving hypernetwork model by taking into account the hyperedge growth and local-world hyperedge preferential attachment mechanisms. At each time step, a newly added hyperedge encircles a new coming node and a number of nodes from a randomly selected local world. The number of the selected nodes from the local world obeys the uniform distribution and its mean value is m. The analytical and simulation results show that the hyperdegree approximately obeys the power-law form and the exponent of hyperdegree distribution is γ = 2 + 1/m. Furthermore, we numerically investigate the node degree, hyperedge degree, clustering coefficient, as well as the average distance, and find that the hypernetwork model shares the scale-free and small-world properties, which shed some light for deeply understanding the evolution mechanism of the real systems.

  11. Evolving roles of highly successful mentors.

    Science.gov (United States)

    Melanson, Mark A

    2007-01-01

    This article was written groom mentors, old and new, by identifying the evolving roles that highly successful mentors in order to share wisdom with their protégés. First aspiring mentors need to become subject matter experts in their profession by achieving the relevant benchmarks of mastery in their career fields. Next, they must win the coveted role of respected leader by being trustworthy and putting the development of others first. The mastery of knowledge and earning of respect must also be balanced by genuine humility if the mentor is to be effective in sharing what he or she knows. Highly successful mentors are teachers, plain and simple, and they are most effective in this role when they have a deep passion for teaching. By properly using reflection, adroit mentors look back upon their many adventures and carefully select critical stories to share with their protégés. While outstanding mentors have a lot to say, they need to spend most of their time listening to those they mentor to ensure that they understand their protégés' individualized needs and goals. To help protégés through the setbacks and disappointments that can accompany an Army career, high-speed mentors need to don the role of optimistic cheerleaders, encouraging those they mentor and restoring hope. Once a striving mentor has finally reached the summit of mentoring and is a trusted counselor, he or she must continue to nurture and protect this fragile, but most influential role. Lastly, great mentors need to be consummate students of both their profession and mentoring so that they remain vital and responsive to those they mentor. In closing, it is hoped that by considering and embracing these evolving roles, dedicated students of mentoring will derive a deeper satisfaction and have greater success in this critically important leadership responsibility.

  12. Evolving circuits in seconds: experiments with a stand-alone board-level evolvable system

    Science.gov (United States)

    Stoica, A.; Zebulum, R. S.; Ferguson, M. I.; Keymeulen, D.; Duong, V.; Guo, X.

    2002-01-01

    The purpose of this paper is twofold: first, to illustrate a stand-alone board-level evolvable system (SABLES) and its performance, and second to illustrate some problems that occur during evolution with real hardware in the loop, or when the intention of the user is not completely reflected in the fitness function.

  13. Domain Organization in Clostridium botulinum Neurotoxin Type E is Unique: Its Implication in Faster Translocation

    Energy Technology Data Exchange (ETDEWEB)

    Kumaran, D.; Eswaramoorthy, S; Furey, W; Navaza, J; Sax, M; Swaminathan, S

    2009-01-01

    Clostridium botulinum produces seven antigenically distinct neurotoxins [C. botulinum neurotoxins (BoNTs) A-G] sharing a significant sequence homology. Based on sequence and functional similarity, it was believed that their three-dimensional structures will also be similar. Indeed, the crystal structures of BoNTs A and B exhibit similar fold and domain association where the translocation domain is flanked on either side by binding and catalytic domains. Here, we report the crystal structure of BoNT E holotoxin and show that the domain association is different and unique, although the individual domains are similar to those of BoNTs A and B. In BoNT E, both the binding domain and the catalytic domain are on the same side of the translocation domain, and all three have mutual interfaces. This unique association may have an effect on the rate of translocation, with the molecule strategically positioned in the vesicle for quick entry into cytosol. Botulism, the disease caused by BoNT E, sets in faster than any other serotype because of its speedy internalization and translocation, and the present structure offers a credible explanation. We propose that the translocation domain in other BoNTs follows a two-step process to attain translocation-competent conformation as in BoNT E. We also suggest that this translocation-competent conformation in BoNT E is a probable reason for its faster toxic rate compared to BoNT A. However, this needs further experimental elucidation.

  14. Faster recovery of a diatom from UV damage under ocean acidification.

    Science.gov (United States)

    Wu, Yaping; Campbell, Douglas A; Gao, Kunshan

    2014-11-01

    Diatoms are the most important group of primary producers in marine ecosystems. As oceanic pH declines and increased stratification leads to the upper mixing layer becoming shallower, diatoms are interactively affected by both lower pH and higher average exposures to solar ultraviolet radiation. The photochemical yields of a model diatom, Phaeodactylum tricornutum, were inhibited by ultraviolet radiation under both growth and excess light levels, while the functional absorbance cross sections of the remaining photosystem II increased. Cells grown under ocean acidification (OA) were less affected during UV exposure. The recovery of PSII under low photosynthetically active radiation was much faster than in the dark, indicating that photosynthetic processes were essential for the full recovery of photosystem II. This light dependent recovery required de novo synthesized protein. Cells grown under ocean acidification recovered faster, possibly attributable to higher CO₂ availability for the Calvin cycle producing more resources for repair. The lower UV inhibition combined with higher recovery rate under ocean acidification could benefit species such as P.tricornutum, and change their competitiveness in the future ocean. Copyright © 2014 Elsevier B.V. All rights reserved.

  15. Analysis of the faster-than-Nyquist optimal linear multicarrier system

    Science.gov (United States)

    Marquet, Alexandre; Siclet, Cyrille; Roque, Damien

    2017-02-01

    Faster-than-Nyquist signalization enables a better spectral efficiency at the expense of an increased computational complexity. Regarding multicarrier communications, previous work mainly relied on the study of non-linear systems exploiting coding and/or equalization techniques, with no particular optimization of the linear part of the system. In this article, we analyze the performance of the optimal linear multicarrier system when used together with non-linear receiving structures (iterative decoding and direct feedback equalization), or in a standalone fashion. We also investigate the limits of the normality assumption of the interference, used for implementing such non-linear systems. The use of this optimal linear system leads to a closed-form expression of the bit-error probability that can be used to predict the performance and help the design of coded systems. Our work also highlights the great performance/complexity trade-off offered by decision feedback equalization in a faster-than-Nyquist context. xml:lang="fr"

  16. Faster Proton dynamics of water on SnO2 compared to TiO2.

    Energy Technology Data Exchange (ETDEWEB)

    Kumar, Nitin [ORNL; Kent, Paul R [ORNL; Bandura, Andrei V. [St. Petersburg State University, St. Petersburg, Russia; Kubicki, James D. [Pennsylvania State University; Wesolowski, David J [ORNL; Cole, David R [ORNL; Sofo, Jorge O. [Pennsylvania State University

    2011-01-01

    Proton jump processes in the hydration layer on the iso-structural TiO2 rutile (110) and SnO2 cassiterite (110) surfaces were studied with density functional theory molecular dynamics. We find that the proton jump rate is more than three times faster on cassiterite compared with rutile. A local analysis based on the correlation between the stretching band of the O H vibrations and the strength of H-bonds indicates that the faster proton jump activity on cassiterite is produced by a stronger H-bond formation between the surface and the hydration layer above the surface. The origin of the increased H-bond strength on cassiterite is a combined effect of stronger covalent bonding and stronger electrostatic interactions due to differences of its electronic structure. The bridging oxygens form the strongest H-bonds between the surface and the hydration layer. This higher proton jump rate is likely to affect reactivity and catalytic activity on the surface. A better understanding of its origins will enable methods to control these rates. 2011 American Institute of Physics. [doi:10.1063/1.3509386

  17. Ear Detection under Uncontrolled Conditions with Multiple Scale Faster Region-Based Convolutional Neural Networks

    Directory of Open Access Journals (Sweden)

    Yi Zhang

    2017-04-01

    Full Text Available Ear detection is an important step in ear recognition approaches. Most existing ear detection techniques are based on manually designing features or shallow learning algorithms. However, researchers found that the pose variation, occlusion, and imaging conditions provide a great challenge to the traditional ear detection methods under uncontrolled conditions. This paper proposes an efficient technique involving Multiple Scale Faster Region-based Convolutional Neural Networks (Faster R-CNN to detect ears from 2D profile images in natural images automatically. Firstly, three regions of different scales are detected to infer the information about the ear location context within the image. Then an ear region filtering approach is proposed to extract the correct ear region and eliminate the false positives automatically. In an experiment with a test set of 200 web images (with variable photographic conditions, 98% of ears were accurately detected. Experiments were likewise conducted on the Collection J2 of University of Notre Dame Biometrics Database (UND-J2 and University of Beira Interior Ear dataset (UBEAR, which contain large occlusion, scale, and pose variations. Detection rates of 100% and 98.22%, respectively, demonstrate the effectiveness of the proposed approach.

  18. Faster in-plane switching and reduced rotational viscosity characteristics in a graphene-nematic suspension

    Science.gov (United States)

    Basu, Rajratan; Kinnamon, Daniel; Skaggs, Nicole; Womack, James

    2016-05-01

    The in-plane switching (IPS) for a nematic liquid crystal (LC) was found to be considerably faster when the LC was doped with dilute concentrations of monolayer graphene flakes. Additional studies revealed that the presence of graphene reduced the rotational viscosity of the LC, permitting the nematic director to respond quicker in IPS mode on turning the electric field on. The studies were carried out with several graphene concentrations in the LC, and the experimental results coherently suggest that there exists an optimal concentration of graphene, allowing a reduction in the IPS response time and rotational viscosity in the LC. Above this optimal graphene concentration, the rotational viscosity was found to increase, and consequently, the LC no longer switched faster in IPS mode. The presence of graphene suspension was also found to decrease the LC's pretilt angle significantly due to the π-π electron stacking between the LC molecules and graphene flakes. To understand the π-π stacking interaction, the anchoring mechanism of the LC on a CVD grown monolayer graphene film on copper substrate was studied by reflected crossed polarized microscopy. Optical microphotographs revealed that the LC alignment direction depended on monolayer graphene's hexagonal crystal structure and its orientation.

  19. Partial Refactorization in Sparse Matrix Solution: A New Possibility for Faster Nonlinear Finite Element Analysis

    Directory of Open Access Journals (Sweden)

    Qi Song

    2013-01-01

    Full Text Available This paper proposes a partial refactorization for faster nonlinear analysis based on sparse matrix solution, which is nowadays the default solution choice in finite element analysis and can solve finite element models up to millions degrees of freedom. Among various fill-in’s reducing strategies for sparse matrix solution, the graph partition is in general the best in terms of resultant fill-ins and floating-point operations and furthermore produces a particular graph of sparse matrix that prevents local change of entries from wide spreading in factorization. Based on this feature, an explicit partial triangular refactorization with local change is efficiently constructed with limited additional storage requirement in row-sparse storage scheme. The partial refactorization of the changed stiffness matrix inherits a big percentage of the original factor and is carried out only on partial factor entries. The proposed method provides a new possibility for faster nonlinear analysis and is mainly suitable for material nonlinear problems and optimization problems. Compared to full factorization, it can significantly reduce the factorization time and can make nonlinear analysis more efficient.

  20. Faster non-renal clearance of metoprolol in streptozotocin-induced diabetes mellitus rats.

    Science.gov (United States)

    Lee, Unji; Lee, Inchul; Lee, Byung K; Kang, Hee E

    2013-11-20

    Metoprolol is a selective β1-adrenergic receptor antagonist metabolized by hepatic cytochrome P450s (CYPs). In this study, we evaluated pharmacokinetic changes following intravenous (i.v.) and oral metoprolol in rats with diabetes mellitus induced by streptozotocin (DMIS). Metoprolol has an intermediate hepatic extraction ratio in rats (0.586-0.617), and it is assumed that the liver is exclusively responsible for metoprolol metabolism. Thus, the hepatic clearance, CL(H) (the non-renal clearance, CL(NR)) of metoprolol depends on the hepatic blood flow rate (Q(H)), the free fraction in plasma (f(p)), and in vitro hepatic intrinsic clearance, CL(int). After i.v. administration of 1.5 mg/kg metoprolol to DMIS rats, its CLNR was 40.9% faster than control animals. This could be due to a significantly faster QH because hepatic CL(int) and fp were comparable between the two groups of rats due to unchanged hepatic CYP2D activity. After oral administration of 1.5 mg/kg metoprolol to DMIS rats, gastrointestinal absorption was >99% of the oral dose for both groups, while the area under the curve (AUC) was 27.9% smaller, which could be caused by the greater hepatic metabolism seen in the i.v. study. These findings have potential therapeutic implications, assuming that the DMIS rats qualitatively reflect similar changes in patients with diabetes.

  1. Better, Faster, Cheaper: Getting the Most Out of High-Throughput Screening with Zebrafish.

    Science.gov (United States)

    Truong, Lisa; Simonich, Michael T; Tanguay, Robert L

    2016-01-01

    The field of toxicology is undergoing a vast change with high-throughput (HT) approaches that rapidly query huge swaths of chemico-structural space for bioactivity and hazard potential. Its practicality is due in large part to switching from high-cost, low-throughput mammalian models to faster and cheaper alternatives. We believe this is an improved approach because the immense breadth of the resulting data sets a foundation for predictive structure-activity-based toxicology. Moreover, rapidly uncovering structure-related bioactivity drives better decisions about where to commit resources to drill down to a mechanism, or pursue commercial leads. While hundreds of different in vitro toxicology assays can collectively serve as an alternative to mammalian animal model testing, far greater efficiency and ultimately more relevant data are obtained from the whole animal. The developmental zebrafish, with its well-documented advantages over many animal models, is now emerging as a true biosensor of chemical activity. Herein, we draw on nearly a decade of experience developing high-throughput toxicology screens in the developmental zebrafish to summarize the best practices in fulfilling the better, faster, cheaper goals. We include optimization and harmonization of dosing volume, exposure paradigms, chemical solubility, chorion status, experimental duration, endpoint definitions, and statistical analysis.

  2. General strength and kinetics: fundamental to sprinting faster in cross country skiing?

    Science.gov (United States)

    Stöggl, T; Müller, E; Ainegren, M; Holmberg, H-C

    2011-12-01

    To determine relationships between general strength, maximal skiing speed (V(max)), pole and leg kinetics and kinematics, 16 male elite skiers underwent three V(max) tests in double poling, diagonal stride and V2 on a treadmill. The analyzed skiing speeds and leg and arm kinetics were among the highest ever recorded. Relationships between general strength exercises and V(max) were technique dependent. Power output in bench press and bench pull were related to V(max) in DP and diagonal stride, whereas each 1 repetition maximum was related to V2. Isometric squats were not associated with V(max) in all three techniques, whereas jump height and rate of force development during squat jump were. Analysis of kinetics and kinematics revealed that it was not exclusively the magnitude of applied forces during skiing, but the timing and proper instant of force application were major factors discriminating between faster and slower skiers. For all techniques, the faster skiers used different skiing strategies when approaching V(max) when compared with the slower skiers. General strength and power per se seem not to be major determinants of performance in elite skiers, whereas coordination of these capacities within the different and complex skiing movements seems to be the discriminating factor.

  3. Erythrocytes retain hypoxic adenosine response for faster acclimatization upon re-ascent

    Science.gov (United States)

    Song, Anren; Zhang, Yujin; Han, Leng; Yegutkin, Gennady G.; Liu, Hong; Sun, Kaiqi; D'Alessandro, Angelo; Li, Jessica; Karmouty-Quintana, Harry; Iriyama, Takayuki; Weng, Tingting; Zhao, Shushan; Wang, Wei; Wu, Hongyu; Nemkov, Travis; Subudhi, Andrew W.; Jameson-Van Houten, Sonja; Julian, Colleen G.; Lovering, Andrew T.; Hansen, Kirk C.; Zhang, Hong; Bogdanov, Mikhail; Dowhan, William; Jin, Jianping; Kellems, Rodney E.; Eltzschig, Holger K.; Blackburn, Michael; Roach, Robert C.; Xia, Yang

    2017-01-01

    Faster acclimatization to high altitude upon re-ascent is seen in humans; however, the molecular basis for this enhanced adaptive response is unknown. We report that in healthy lowlanders, plasma adenosine levels are rapidly induced by initial ascent to high altitude and achieved even higher levels upon re-ascent, a feature that is positively associated with quicker acclimatization. Erythrocyte equilibrative nucleoside transporter 1 (eENT1) levels are reduced in humans at high altitude and in mice under hypoxia. eENT1 deletion allows rapid accumulation of plasma adenosine to counteract hypoxic tissue damage in mice. Adenosine signalling via erythrocyte ADORA2B induces PKA phosphorylation, ubiquitination and proteasomal degradation of eENT1. Reduced eENT1 resulting from initial hypoxia is maintained upon re-ascent in humans or re-exposure to hypoxia in mice and accounts for erythrocyte hypoxic memory and faster acclimatization. Our findings suggest that targeting identified purinergic-signalling network would enhance the hypoxia adenosine response to counteract hypoxia-induced maladaptation. PMID:28169986

  4. “Highly evolvable malaria vectors: the genomes of 16 Anopheles mosquitoes”

    Science.gov (United States)

    Neafsey, Daniel E.; Waterhouse, Robert M.; Abai, Mohammad R.; Aganezov, Sergey S.; Alekseyev, Max A.; Allen, James E.; Amon, James; Arcà, Bruno; Arensburger, Peter; Artemov, Gleb; Assour, Lauren A.; Basseri, Hamidreza; Berlin, Aaron; Birren, Bruce W.; Blandin, Stephanie A.; Brockman, Andrew I.; Burkot, Thomas R.; Burt, Austin; Chan, Clara S.; Chauve, Cedric; Chiu, Joanna C.; Christensen, Mikkel; Costantini, Carlo; Davidson, Victoria L.M.; Deligianni, Elena; Dottorini, Tania; Dritsou, Vicky; Gabriel, Stacey B.; Guelbeogo, Wamdaogo M.; Hall, Andrew B.; Han, Mira V.; Hlaing, Thaung; Hughes, Daniel S.T.; Jenkins, Adam M.; Jiang, Xiaofang; Jungreis, Irwin; Kakani, Evdoxia G.; Kamali, Maryam; Kemppainen, Petri; Kennedy, Ryan C.; Kirmitzoglou, Ioannis K.; Koekemoer, Lizette L.; Laban, Njoroge; Langridge, Nicholas; Lawniczak, Mara K.N.; Lirakis, Manolis; Lobo, Neil F.; Lowy, Ernesto; MacCallum, Robert M.; Mao, Chunhong; Maslen, Gareth; Mbogo, Charles; McCarthy, Jenny; Michel, Kristin; Mitchell, Sara N.; Moore, Wendy; Murphy, Katherine A.; Naumenko, Anastasia N.; Nolan, Tony; Novoa, Eva M.; O'Loughlin, Samantha; Oringanje, Chioma; Oshaghi, Mohammad A.; Pakpour, Nazzy; Papathanos, Philippos A.; Peery, Ashley N.; Povelones, Michael; Prakash, Anil; Price, David P.; Rajaraman, Ashok; Reimer, Lisa J.; Rinker, David C.; Rokas, Antonis; Russell, Tanya L.; Sagnon, N'Fale; Sharakhova, Maria V.; Shea, Terrance; Simão, Felipe A.; Simard, Frederic; Slotman, Michel A.; Somboon, Pradya; Stegniy, Vladimir; Struchiner, Claudio J.; Thomas, Gregg W.C.; Tojo, Marta; Topalis, Pantelis; Tubio, José M.C.; Unger, Maria F.; Vontas, John; Walton, Catherine; Wilding, Craig S.; Willis, Judith H.; Wu, Yi-Chieh; Yan, Guiyun; Zdobnov, Evgeny M.; Zhou, Xiaofan; Catteruccia, Flaminia; Christophides, George K.; Collins, Frank H.; Cornman, Robert S.; Crisanti, Andrea; Donnelly, Martin J.; Emrich, Scott J.; Fontaine, Michael C.; Gelbart, William; Hahn, Matthew W.; Hansen, Immo A.; Howell, Paul I.; Kafatos, Fotis C.; Kellis, Manolis; Lawson, Daniel; Louis, Christos; Luckhart, Shirley; Muskavitch, Marc A.T.; Ribeiro, José M.; Riehle, Michael A.; Sharakhov, Igor V.; Tu, Zhijian; Zwiebel, Laurence J.; Besansky, Nora J.

    2015-01-01

    Variation in vectorial capacity for human malaria among Anopheles mosquito species is determined by many factors, including behavior, immunity, and life history. To investigate the genomic basis of vectorial capacity and explore new avenues for vector control, we sequenced the genomes of 16 anopheline mosquito species from diverse locations spanning ~100 million years of evolution. Comparative analyses show faster rates of gene gain and loss, elevated gene shuffling on the X chromosome, and more intron losses, relative to Drosophila. Some determinants of vectorial capacity, such as chemosensory genes, do not show elevated turnover, but instead diversify through protein-sequence changes. This dynamism of anopheline genes and genomes may contribute to their flexible capacity to take advantage of new ecological niches, including adapting to humans as primary hosts. PMID:25554792

  5. The evolving energy budget of accretionary wedges

    Science.gov (United States)

    McBeck, Jessica; Cooke, Michele; Maillot, Bertrand; Souloumiac, Pauline

    2017-04-01

    The energy budget of evolving accretionary systems reveals how deformational processes partition energy as faults slip, topography uplifts, and layer-parallel shortening produces distributed off-fault deformation. The energy budget provides a quantitative framework for evaluating the energetic contribution or consumption of diverse deformation mechanisms. We investigate energy partitioning in evolving accretionary prisms by synthesizing data from physical sand accretion experiments and numerical accretion simulations. We incorporate incremental strain fields and cumulative force measurements from two suites of experiments to design numerical simulations that represent accretionary wedges with stronger and weaker detachment faults. One suite of the physical experiments includes a basal glass bead layer and the other does not. Two physical experiments within each suite implement different boundary conditions (stable base versus moving base configuration). Synthesizing observations from the differing base configurations reduces the influence of sidewall friction because the force vector produced by sidewall friction points in opposite directions depending on whether the base is fixed or moving. With the numerical simulations, we calculate the energy budget at two stages of accretion: at the maximum force preceding the development of the first thrust pair, and at the minimum force following the development of the pair. To identify the appropriate combination of material and fault properties to apply in the simulations, we systematically vary the Young's modulus and the fault static and dynamic friction coefficients in numerical accretion simulations, and identify the set of parameters that minimizes the misfit between the normal force measured on the physical backwall and the numerically simulated force. Following this derivation of the appropriate material and fault properties, we calculate the components of the work budget in the numerical simulations and in the

  6. On the Critical Role of Divergent Selection in Evolvability

    Directory of Open Access Journals (Sweden)

    Joel Lehman

    2016-08-01

    Full Text Available An ambitious goal in evolutionary robotics is to evolve increasingly complex robotic behaviors with minimal human design effort. Reaching this goal requires evolutionary algorithms that can unlock from genetic encodings their latent potential for evolvability. One issue clouding this goal is conceptual confusion about evolvability, which often obscures the aspects of evolvability that are important or desirable. The danger from such confusion is that it may establish unrealistic goals for evolvability that prove unproductive in practice. An important issue separate from conceptual confusion is the common misalignment between selection and evolvability in evolutionary robotics. While more expressive encodings can represent higher-level adaptations (e.g. sexual reproduction or developmental systems that increase long-term evolutionary potential (i.e. evolvability, realizing such potential requires gradients of fitness and evolvability to align. In other words, selection is often a critical factor limiting increasing evolvability. Thus, drawing from a series of recent papers, this article seeks to both (1 clarify and focus the ways in which the term evolvability is used within artificial evolution, and (2 argue for the importance of one type of selection, i.e. divergent selection, for enabling evolvability. The main argument is that there is a fundamental connection between divergent selection and evolvability (on both the individual and population level that does not hold for typical goal-oriented selection. The conclusion is that selection pressure plays a critical role in realizing the potential for evolvability, and that divergent selection in particular provides a principled mechanism for encouraging evolvability in artificial evolution.

  7. Relationship among phenotypic plasticity, phenotypic fluctuations, robustness, and evolvability; Waddington's legacy revisited under the spirit of Einstein

    Indian Academy of Sciences (India)

    Kunihiko Kaneko

    2009-10-01

    Questions on possible relationship between phenotypic plasticity and evolvability, and that between robustness and evolution have been addressed over decades in the field of evolution-development. Based on laboratory evolution experiments and numerical simulations of gene expression dynamics model with an evolving transcription network, we propose quantitative relationships on plasticity, phenotypic fluctuations, and evolvability. By introducing an evolutionary stability assumption on the distribution of phenotype and genotype, the proportionality among phenotypic plasticity against environmental change, variances of phenotype fluctuations of genetic and developmental origins, and evolution speed is obtained. The correlation between developmental robustness to noise and evolutionary robustness to mutation is analysed by simulations of the gene network model. These results provide quantitative formulation on canalization and genetic assimilation, in terms of fluctuations of gene expression levels.

  8. Faster-is-slower effect in escaping ants revisited: Ants do not behave like humans

    CERN Document Server

    Parisi, Daniel R; Josens, Roxana

    2014-01-01

    In this work we studied the trajectories, velocities and densities of ants when egressing under controlled levels of stress produced by a chemical repellent at different concentrations. We found that, unlike other animals escaping under life-and-death conditions and pedestrian simulations, ants do not produce a higher density zone near the exit door. Instead, ants are uniformly distributed over the available space allowing for efficient evacuations. Consequently, the faster-is-slower effect observed in ants (Soria et al., 2012) is clearly of a different nature to that predicted by de social force model. In the case of ants, the minimum evacuation time is correlated with the lower probability of taking backward steps. Thus, as biological model ants have important differences that make their use inadvisable for the design of human facilities.

  9. Faster growth of the major prokaryotic versus eukaryotic CO2 fixers in the oligotrophic ocean.

    Science.gov (United States)

    Zubkov, Mikhail V

    2014-04-29

    Because maintenance of non-scalable cellular components--membranes and chromosomes--requires an increasing fraction of energy as cell size decreases, miniaturization comes at a considerable energetic cost for a phytoplanktonic cell. Consequently, if eukaryotes can use their superior energetic resources to acquire nutrients with more or even similar efficiency compared with prokaryotes, larger unicellular eukaryotes should be able to achieve higher growth rates than smaller cyanobacteria. Here, to test this hypothesis, we directly compare the intrinsic growth rates of phototrophic prokaryotes and eukaryotes from the equatorial to temperate South Atlantic using an original flow cytometric (14)CO2-tracer approach. At the ocean basin scale, cyanobacteria double their biomass twice as frequently as the picoeukaryotes indicating that the prokaryotes are faster growing CO2 fixers, better adapted to phototrophic living in the oligotrophic open ocean-the most extensive biome on Earth.

  10. Pain hypersensitivity in congenital blindness is associated with faster central processing of C-fibre input

    DEFF Research Database (Denmark)

    Slimani, H.; Plaghki, L.; Ptito, M.

    2016-01-01

    Background We have recently shown that visual deprivation from birth exacerbates responses to painful thermal stimuli. However, the mechanisms underlying pain hypersensitivity in congenital blindness are unclear. Methods To study the contribution of Aδ- and C-fibres in pain perception, we measured...... thresholds and response times to selective C- and Aδ-fibre activation in congenitally blind, late blind and normally sighted participants. Ultrafast constant-temperature heat pulses were delivered to the hand with a CO2 laser using an interleaved adaptive double staircase procedure. Participants were...... instructed to respond as quickly as possible when detecting a laser-induced sensation. We used a 650 ms cut-off criterion to distinguish fast Aδ- from slow C-fibre–mediated sensations. Results Congenitally blind participants showed significantly faster reaction times to C- but not to Aδ...

  11. Small-amplitude swimmers can self-propel faster in viscoelastic fluids

    CERN Document Server

    Riley, Emily E

    2015-01-01

    Many small organisms self-propel in viscous fluids using travelling wave-like deformation of their bodies or appendages. Examples include small nematodes moving through soil using whole-body undulations or spermatozoa swimming through mucus using flagellar waves. When self-propulsion occurs in a non-Newtonian fluid, one fundamental question is whether locomotion will occur faster or slower than in a Newtonian environment. Here we consider the general problem of swimming using small-amplitude periodic waves in a viscoelastic fluid described by the classical Oldroyd-B constitutive relationship. Using Taylor's swimming sheet model, we show that if all travelling waves move in the same direction, the locomotion speed of the organism is systematically decreased. However, if we allow waves to travel in two opposite directions, we show that this can lead to enhancement of the swimming speed, which is physically interpreted as due to asymmetric viscoelastic damping of waves with different frequencies. A change of the...

  12. Faster is More Different: Mean-Field Dynamics of Innovation Diffusion

    CERN Document Server

    Baek, Seung Ki; Kim, Mina

    2013-01-01

    Based on a recent model of paradigm shifts by Bornholdt et al., we studied mean-field opinion dynamics in an infinite population where an infinite number of ideas compete simultaneously with their values publicly known. We found that a highly innovative society is not characterized by heavy concentration in highly valued ideas: Rather, ideas are more broadly distributed in a more innovative society with faster progress, provided that the rate of adoption is constant, which suggests a positive correlation between innovation and technological disparity. Furthermore, the distribution is generally skewed in such a way that the fraction of innovators is substantially smaller than has been believed in conventional innovation-diffusion theory based on normality. Thus, the typical adoption pattern is predicted to be asymmetric with slow saturation in the ideal situation, which is compared with empirical data sets.

  13. A Faster Routing Scheme for Stationary Wireless Sensor Networks - A Hybrid Approach

    CERN Document Server

    Norman, Jasmine; Roja, P Prapoorna; 10.5121/ijasuc.2010.1101

    2010-01-01

    A wireless sensor network consists of light-weight, low power, small size sensor nodes. Routing in wireless sensor networks is a demanding task. This demand has led to a number of routing protocols which efficiently utilize the limited resources available at the sensor nodes. Most of these protocols are either based on single hop routing or multi hop routing and typically find the minimum energy path without addressing other issues such as time delay in delivering a packet, load balancing, and redundancy of data. Response time is very critical in environment monitoring sensor networks where typically the sensors are stationary and transmit data to a base station or a sink node. In this paper a faster load balancing routing protocol based on location with a hybrid approach is proposed.

  14. New models for the evolution of central stars of planetary nebulae: Faster and Brighter

    CERN Document Server

    Bertolami, Marcelo M Miller

    2016-01-01

    The post-asymptotic giant branch (AGB) phase is arguably one of the least understood phases of the evolution of low- and intermediate- mass stars. The recent post-AGB evolutionary sequences computed by Miller Bertolami (2016) are at least three to ten times faster than those previously published by Vassiliadis & Wood (1994) and Bloecker (1995) which have been used in a large number of studies. This is true for the whole mass and metallicity range. The new models are also $\\sim$0.1-0.3 dex brighter than the previous models with similar remnant masses. In this short article we comment on the main reasons behind these differences, and discuss possible implications for other studies of post-AGB stars or planetary nebulae.

  15. Faster is more different: mean-field dynamics of innovation diffusion.

    Directory of Open Access Journals (Sweden)

    Seung Ki Baek

    Full Text Available Based on a recent model of paradigm shifts by Bornholdt et al., we studied mean-field opinion dynamics in an infinite population where an infinite number of ideas compete simultaneously with their values publicly known. We found that a highly innovative society is not characterized by heavy concentration in highly valued ideas: Rather, ideas are more broadly distributed in a more innovative society with faster progress, provided that the rate of adoption is constant, which suggests a positive correlation between innovation and technological disparity. Furthermore, the distribution is generally skewed in such a way that the fraction of innovators is substantially smaller than has been believed in conventional innovation-diffusion theory based on normality. Thus, the typical adoption pattern is predicted to be asymmetric with slow saturation in the ideal situation, which is compared with empirical data sets.

  16. Evolving role of MRI in Crohn's disease.

    Science.gov (United States)

    Yacoub, Joseph H; Obara, Piotr; Oto, Aytekin

    2013-06-01

    MR enterography is playing an evolving role in the evaluation of small bowel Crohn's disease (CD). Standard MR enterography includes a combination of rapidly acquired T2 sequence, balanced steady-state acquisition, and contrast enhanced T1-weighted gradient echo sequence. The diagnostic performance of these sequences has been shown to be comparable, and in some respects superior, to other small bowel imaging modalities. The findings of CD on MR enterography have been well described in the literature. New and emerging techniques such as diffusion-weighted imaging (DWI), dynamic contrast enhanced MRI (DCE-MRI), cinematography, and magnetization transfer, may lead to improved accuracy in characterizing the disease. These advanced techniques can provide quantitative parameters that may prove to be useful in assessing disease activity, severity, and response to treatment. In the future, MR enterography may play an increasing role in management decisions for patients with small bowel CD; however, larger studies are needed to validate these emerging MRI parameters as imaging biomarkers.

  17. UKAEA'S evolving contract philosophy

    Energy Technology Data Exchange (ETDEWEB)

    Nicol, R. D. [UK Atomic Energy Authority, UKAEA, Harwell, Oxfordshire (United Kingdom)

    2003-07-01

    The United Kingdom Atomic Energy Authority (UKAEA) has gone through fundamental change over the last ten years. At the heart of this change has been UKAEA's relationship with the contracting and supply market. This paper describes the way in which UKAEA actively developed the market to support the decommissioning programme, and how the approach to contracting has evolved as external pressures and demands have changed. UKAEA's pro-active approach to industry has greatly assisted the development of a healthy, competitive market for services supporting decommissioning in the UK. There have been difficult changes and many challenges along the way, and some retrenchment was necessary to meet regulatory requirements. Nevertheless, UKAEA has sustained a high level of competition - now measured in terms of competed spend as a proportion of competable spend - with annual out-turns consistently over 80%. The prime responsibility for market development will pass to the new Nuclear Decommissioning Authority (NDA) in 2005, as the owner, on behalf of the Government, of the UK's civil nuclear liabilities. The preparatory work for the NDA indicates that the principles established by UKAEA will be carried forward. (author)

  18. On the Discovery of Evolving Truth.

    Science.gov (United States)

    Li, Yaliang; Li, Qi; Gao, Jing; Su, Lu; Zhao, Bo; Fan, Wei; Han, Jiawei

    2015-08-01

    In the era of big data, information regarding the same objects can be collected from increasingly more sources. Unfortunately, there usually exist conflicts among the information coming from different sources. To tackle this challenge, truth discovery, i.e., to integrate multi-source noisy information by estimating the reliability of each source, has emerged as a hot topic. In many real world applications, however, the information may come sequentially, and as a consequence, the truth of objects as well as the reliability of sources may be dynamically evolving. Existing truth discovery methods, unfortunately, cannot handle such scenarios. To address this problem, we investigate the temporal relations among both object truths and source reliability, and propose an incremental truth discovery framework that can dynamically update object truths and source weights upon the arrival of new data. Theoretical analysis is provided to show that the proposed method is guaranteed to converge at a fast rate. The experiments on three real world applications and a set of synthetic data demonstrate the advantages of the proposed method over state-of-the-art truth discovery methods.

  19. THE EVOLVING CONCEPT OF SUSTAINABLE AGRICULTURE

    Directory of Open Access Journals (Sweden)

    PETRONELA-SONIA NEDEA

    2012-11-01

    Full Text Available Over the years, the definition of sustainability in development literature has varied widely and broadened in scope. The concept arose in response to economic growth models that characterized development approaches over the last half century. It was eventually recognized that such models did not adequately address social inequalities and led to environmental degradation. The concept gained wider use after the World Commission on Environment and Development published "Our common future" (Brundtland 1987. The economic, social, political and ecological dimensions of the rural environment are complex and have multiple implications, starting with theoretical and practical reasons. The process of urbanization that takes place at world-wide level has become one of the global problems of mankind, because of the disparities created between the countryside and the city, which arematerialized in the cultural, economical and social aspects that are synthesized in the terms of urban and rural civilizations, which define the different realities of the geographical space. Because the concept of sustainable agriculture is still evolving, this paper reviews the ideas, practices and policies that make the basis ofsustainable agriculture concept, in order to suggest to others practical steps that may be appropriate for them in moving toward sustainable agriculture.

  20. Epidemic spreading on evolving signed networks

    Science.gov (United States)

    Saeedian, M.; Azimi-Tafreshi, N.; Jafari, G. R.; Kertesz, J.

    2017-02-01

    Most studies of disease spreading consider the underlying social network as obtained without the contagion, though epidemic influences people's willingness to contact others: A "friendly" contact may be turned to "unfriendly" to avoid infection. We study the susceptible-infected disease-spreading model on signed networks, in which each edge is associated with a positive or negative sign representing the friendly or unfriendly relation between its end nodes. In a signed network, according to Heider's theory, edge signs evolve such that finally a state of structural balance is achieved, corresponding to no frustration in physics terms. However, the danger of infection affects the evolution of its edge signs. To describe the coupled problem of the sign evolution and disease spreading, we generalize the notion of structural balance by taking into account the state of the nodes. We introduce an energy function and carry out Monte Carlo simulations on complete networks to test the energy landscape, where we find local minima corresponding to the so-called jammed states. We study the effect of the ratio of initial friendly to unfriendly connections on the propagation of disease. The steady state can be balanced or a jammed state such that a coexistence occurs between susceptible and infected nodes in the system.

  1. Consensus in evolving networks of mobile agents

    Science.gov (United States)

    Baronchelli, Andrea; Díaz-Guilera, Albert

    2012-02-01

    Populations of mobile and communicating agents describe a vast array of technological and natural systems, ranging from sensor networks to animal groups. Here, we investigate how a group-level agreement may emerge in the continuously evolving networks defined by the local interactions of the moving individuals. We adopt a general scheme of motion in two dimensions and we let the individuals interact through the minimal naming game, a prototypical scheme to investigate social consensus. We distinguish different regimes of convergence determined by the emission range of the agents and by their mobility, and we identify the corresponding scaling behaviors of the consensus time. In the same way, we rationalize also the behavior of the maximum memory used during the convergence process, which determines the minimum cognitive/storage capacity needed by the individuals. Overall, we believe that the simple and general model presented in this talk can represent a helpful reference for a better understanding of the behavior of populations of mobile agents.

  2. Stability of Evolving Multi-Agent Systems

    CERN Document Server

    De Wilde, Philippe; 10.1109/TSMCB.2011.2110642

    2011-01-01

    A Multi-Agent System is a distributed system where the agents or nodes perform complex functions that cannot be written down in analytic form. Multi-Agent Systems are highly connected, and the information they contain is mostly stored in the connections. When agents update their state, they take into account the state of the other agents, and they have access to those states via the connections. There is also external, user-generated input into the Multi-Agent System. As so much information is stored in the connections, agents are often memory-less. This memory-less property, together with the randomness of the external input, has allowed us to model Multi-Agent Systems using Markov chains. In this paper, we look at Multi-Agent Systems that evolve, i.e. the number of agents varies according to the fitness of the individual agents. We extend our Markov chain model, and define stability. This is the start of a methodology to control Multi-Agent Systems. We then build upon this to construct an entropy-based defi...

  3. Evolving Galaxies in a Hierachical Universe

    Science.gov (United States)

    Hahn, Changhoon

    2017-01-01

    Observations of galaxies using large surveys (SDSS, COSMOS, PRIMUS, etc.) have firmly established a global view of galaxy properties out to z~1. Galaxies are broadly divided into two classes: blue, typically disk-like star forming galaxies and red, typically elliptical quiescent ones with little star formation. The star formation rates (SFR) and stellar masses of star forming galaxies form an empirical relationship referred to as the "star formation main sequence". Over cosmic time, this sequence undergoes significant decline in SFR and causes the overall cosmic star formation decline. Simultaneously, physical processes cause significant fractions of star forming galaxies to "quench" their star formation. Hierarchical structure formation and cosmological models provide precise predictions of the evolution of the underying dark matter, which serve as the foundation for these detailed trends and their evolution. Whatever trends we observe in galaxy properties can be interpreted within the narrative of the underlying dark matter and halo occupation framework. More importantly, through careful statistical treatment and precise measurements, this connection can be utilized to better constrain and understand key elements of galaxy evolution. In this spirit, for my dissertation I connect observations of evolving galaxy properties to the framework of the hierarchical Universe and use it to better understand physical processes responsible for the cessation of star formation in galaxies. For instance, through this approach, I constrain the quenching timescale of central galaxies and find that they are significantly longer than the quenching timescale of satellite galaxies.

  4. Evolving Decision Rules to Predict Investment Opportunities

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    This paper is motivated by the interest in finding significant movements in financial stock prices. However, when the number of profitable opportunities is scarce, the prediction of these cases is difficult. In a previous work, we have introduced evolving decision rules (EDR) to detect financial opportunities. The objective of EDR is to classify the minority class (positive cases) in imbalanced environments. EDR provides a range of classifications to find the best balance between not making mistakes and not missing opportunities. The goals of this paper are: 1) to show that EDR produces a range of solutions to suit the investor's preferences and 2) to analyze the factors that benefit the performance of EDR. A series of experiments was performed. EDR was tested using a data set from the London Financial Market. To analyze the EDR behaviour, another experiment was carried out using three artificial data sets, whose solutions have different levels of complexity. Finally, an illustrative example was provided to show how a bigger collection of rules is able to classify more positive cases in imbalanced data sets. Experimental results show that: 1) EDR offers a range of solutions to fit the risk guidelines of different types of investors, and 2) a bigger collection of rules is able to classify more positive cases in imbalanced environments.

  5. Evolving application of biomimetic nanostructured hydroxyapatite

    Directory of Open Access Journals (Sweden)

    Norberto Roveri

    2010-11-01

    Full Text Available Norberto Roveri, Michele IafiscoLaboratory of Environmental and Biological Structural Chemistry (LEBSC, Dipartimento di Chimica ‘G. Ciamician’, Alma Mater Studiorum, Università di Bologna, Bologna, ItalyAbstract: By mimicking Nature, we can design and synthesize inorganic smart materials that are reactive to biological tissues. These smart materials can be utilized to design innovative third-generation biomaterials, which are able to not only optimize their interaction with biological tissues and environment, but also mimic biogenic materials in their functionalities. The biomedical applications involve increasing the biomimetic levels from chemical composition, structural organization, morphology, mechanical behavior, nanostructure, and bulk and surface chemical–physical properties until the surface becomes bioreactive and stimulates cellular materials. The chemical–physical characteristics of biogenic hydroxyapatites from bone and tooth have been described, in order to point out the elective sides, which are important to reproduce the design of a new biomimetic synthetic hydroxyapatite. This review outlines the evolving applications of biomimetic synthetic calcium phosphates, details the main characteristics of bone and tooth, where the calcium phosphates are present, and discusses the chemical–physical characteristics of biomimetic calcium phosphates, methods of synthesizing them, and some of their biomedical applications.Keywords: hydroxyapatite, nanocrystals, biomimetism, biomaterials, drug delivery, remineralization

  6. Evolving application of biomimetic nanostructured hydroxyapatite.

    Science.gov (United States)

    Roveri, Norberto; Iafisco, Michele

    2010-11-09

    By mimicking Nature, we can design and synthesize inorganic smart materials that are reactive to biological tissues. These smart materials can be utilized to design innovative third-generation biomaterials, which are able to not only optimize their interaction with biological tissues and environment, but also mimic biogenic materials in their functionalities. The biomedical applications involve increasing the biomimetic levels from chemical composition, structural organization, morphology, mechanical behavior, nanostructure, and bulk and surface chemical-physical properties until the surface becomes bioreactive and stimulates cellular materials. The chemical-physical characteristics of biogenic hydroxyapatites from bone and tooth have been described, in order to point out the elective sides, which are important to reproduce the design of a new biomimetic synthetic hydroxyapatite. This review outlines the evolving applications of biomimetic synthetic calcium phosphates, details the main characteristics of bone and tooth, where the calcium phosphates are present, and discusses the chemical-physical characteristics of biomimetic calcium phosphates, methods of synthesizing them, and some of their biomedical applications.

  7. How does cognition evolve? Phylogenetic comparative psychology

    Science.gov (United States)

    Matthews, Luke J.; Hare, Brian A.; Nunn, Charles L.; Anderson, Rindy C.; Aureli, Filippo; Brannon, Elizabeth M.; Call, Josep; Drea, Christine M.; Emery, Nathan J.; Haun, Daniel B. M.; Herrmann, Esther; Jacobs, Lucia F.; Platt, Michael L.; Rosati, Alexandra G.; Sandel, Aaron A.; Schroepfer, Kara K.; Seed, Amanda M.; Tan, Jingzhi; van Schaik, Carel P.; Wobber, Victoria

    2014-01-01

    Now more than ever animal studies have the potential to test hypotheses regarding how cognition evolves. Comparative psychologists have developed new techniques to probe the cognitive mechanisms underlying animal behavior, and they have become increasingly skillful at adapting methodologies to test multiple species. Meanwhile, evolutionary biologists have generated quantitative approaches to investigate the phylogenetic distribution and function of phenotypic traits, including cognition. In particular, phylogenetic methods can quantitatively (1) test whether specific cognitive abilities are correlated with life history (e.g., lifespan), morphology (e.g., brain size), or socio-ecological variables (e.g., social system), (2) measure how strongly phylogenetic relatedness predicts the distribution of cognitive skills across species, and (3) estimate the ancestral state of a given cognitive trait using measures of cognitive performance from extant species. Phylogenetic methods can also be used to guide the selection of species comparisons that offer the strongest tests of a priori predictions of cognitive evolutionary hypotheses (i.e., phylogenetic targeting). Here, we explain how an integration of comparative psychology and evolutionary biology will answer a host of questions regarding the phylogenetic distribution and history of cognitive traits, as well as the evolutionary processes that drove their evolution. PMID:21927850

  8. How does cognition evolve? Phylogenetic comparative psychology.

    Science.gov (United States)

    MacLean, Evan L; Matthews, Luke J; Hare, Brian A; Nunn, Charles L; Anderson, Rindy C; Aureli, Filippo; Brannon, Elizabeth M; Call, Josep; Drea, Christine M; Emery, Nathan J; Haun, Daniel B M; Herrmann, Esther; Jacobs, Lucia F; Platt, Michael L; Rosati, Alexandra G; Sandel, Aaron A; Schroepfer, Kara K; Seed, Amanda M; Tan, Jingzhi; van Schaik, Carel P; Wobber, Victoria

    2012-03-01

    Now more than ever animal studies have the potential to test hypotheses regarding how cognition evolves. Comparative psychologists have developed new techniques to probe the cognitive mechanisms underlying animal behavior, and they have become increasingly skillful at adapting methodologies to test multiple species. Meanwhile, evolutionary biologists have generated quantitative approaches to investigate the phylogenetic distribution and function of phenotypic traits, including cognition. In particular, phylogenetic methods can quantitatively (1) test whether specific cognitive abilities are correlated with life history (e.g., lifespan), morphology (e.g., brain size), or socio-ecological variables (e.g., social system), (2) measure how strongly phylogenetic relatedness predicts the distribution of cognitive skills across species, and (3) estimate the ancestral state of a given cognitive trait using measures of cognitive performance from extant species. Phylogenetic methods can also be used to guide the selection of species comparisons that offer the strongest tests of a priori predictions of cognitive evolutionary hypotheses (i.e., phylogenetic targeting). Here, we explain how an integration of comparative psychology and evolutionary biology will answer a host of questions regarding the phylogenetic distribution and history of cognitive traits, as well as the evolutionary processes that drove their evolution.

  9. The Evolving Luminosity Function of Red Galaxies

    CERN Document Server

    Brown, M J I; Jannuzi, B T; Brand, K; Benson, A J; Brodwin, M; Croton, D J; Eisenhardt, P R M; Brown, Michael J. I.; Dey, Arjun; Jannuzi, Buell T.; Brand, Kate; Benson, Andrew J.; Brodwin, Mark; Croton, Darren J.; Eisenhardt, Peter R.

    2006-01-01

    We trace the assembly history of red galaxies since z=1, by measuring their evolving space density with the B-band luminosity function. Our sample of 39599 red galaxies, selected from 6.96 square degrees of imaging from the NOAO Deep Wide-Field and Spitzer IRAC Shallow surveys, is an order of magnitude larger, in size and volume, than comparable samples in the literature. We measure a higher space density of z=0.9 red galaxies than some of the recent literature, in part because we account for the faint yet significant galaxy flux which falls outside of our photometric aperture. The B-band luminosity density of red galaxies, which effectively measures the evolution of ~L* galaxies, increases by only 36 percent from z=0 to z=1. If red galaxy stellar populations have faded by 1.24 B-band magnitudes since z=1, the stellar mass contained within the red galaxy population has roughly doubled over the past 8 Gyr. This is consistent with star-forming galaxies being transformed into ~L* red galaxies after a decline in ...

  10. Extreme insular dwarfism evolved in a mammoth.

    Science.gov (United States)

    Herridge, Victoria L; Lister, Adrian M

    2012-08-22

    The insular dwarfism seen in Pleistocene elephants has come to epitomize the island rule; yet our understanding of this phenomenon is hampered by poor taxonomy. For Mediterranean dwarf elephants, where the most extreme cases of insular dwarfism are observed, a key systematic question remains unresolved: are all taxa phyletic dwarfs of a single mainland species Palaeoloxodon antiquus (straight-tusked elephant), or are some referable to Mammuthus (mammoths)? Ancient DNA and geochronological evidence have been used to support a Mammuthus origin for the Cretan 'Palaeoloxodon' creticus, but these studies have been shown to be flawed. On the basis of existing collections and recent field discoveries, we present new, morphological evidence for the taxonomic status of 'P'. creticus, and show that it is indeed a mammoth, most probably derived from Early Pleistocene Mammuthus meridionalis or possibly Late Pliocene Mammuthus rumanus. We also show that Mammuthus creticus is smaller than other known insular dwarf mammoths, and is similar in size to the smallest dwarf Palaeoloxodon species from Sicily and Malta, making it the smallest mammoth species known to have existed. These findings indicate that extreme insular dwarfism has evolved to a similar degree independently in two elephant lineages.

  11. The Role of Trends in Evolving Networks

    CERN Document Server

    Mokryn, Osnat; Shavitt, Yuval

    2013-01-01

    Modeling complex networks has been the focus of much research for over a decade. Preferential attachment (PA) is considered a common explanation to the self organization of evolving networks, suggesting that new nodes prefer to attach to more popular nodes. The PA model results in broad degree distributions, found in many networks, but cannot explain other common properties such as: The growth of nodes arriving late and Clustering (community structure). Here we show that when the tendency of networks to adhere to trends is incorporated into the PA model, it can produce networks with such properties. Namely, in trending networks, newly arriving nodes may become central at random, forming new clusters. In particular, we show that when the network is young it is more susceptible to trends, but even older networks may have trendy new nodes that become central in their structure. Alternatively, networks can be seen as composed of two parts: static, governed by a power law degree distribution, and a dynamic part go...

  12. The evolved pulsating CEMP star HD112869

    CERN Document Server

    Začs, L; Grankina, A; Deveikis, V; Kaminskyi, B; Pavlenko, Y; Musaev, F

    2015-01-01

    Radial velocity measurements, $BVR_C$ photometry, and high-resolution spectroscopy in the wavelength region from blue to near infrared are employed in order to clarify the evolutionary status of the carbon-enhanced metal-poor star HD112869 with unique ratio of carbon isotopes in the atmosphere. An LTE abundance analysis was carried out using the method of spectral synthesis and new self consistent 1D atmospheric models. The radial velocity monitoring confirmed semiregular variations with a peak-to-peak amplitude of about 10 km $s^{-1}$ and a dominating period of about 115 days. The light, color and radial velocity variations are typical of the evolved pulsating stars. The atmosphere of HD112869 appears to be less metal-poor than reported before, [Fe/H] = -2.3 $\\pm$0.2 dex. Carbon to oxygen and carbon isotope ratios are found to be extremely high, C/O $\\simeq$ 12.6 and $^{12}C/^{13}C \\gtrsim$ 1500, respectively. The s-process elements yttrium and barium are not enhanced, but neodymium appears to be overabundan...

  13. Evolving epidemiology of HIV-associated malignancies.

    Science.gov (United States)

    Shiels, Meredith S; Engels, Eric A

    2017-01-01

    The purpose of this review is to describe the epidemiology of cancers that occur at an elevated rate among people with HIV infection in the current treatment era, including discussion of the cause of these cancers, as well as changes in cancer incidence and burden over time. Rates of Kaposi sarcoma, non-Hodgkin lymphoma and cervical cancer have declined sharply in developed countries during the highly active antiretroviral therapy era, but remain elevated 800-fold, 10-fold and four-fold, respectively, compared with the general population. Most studies have reported significant increases in liver cancer rates and decreases in lung cancer over time. Although some studies have reported significant increases in anal cancer rates and declines in Hodgkin lymphoma rates, others have shown stable incidence. Declining mortality among HIV-infected individuals has resulted in the growth and aging of the HIV-infected population, causing an increase in the number of non-AIDS-defining cancers diagnosed each year in HIV-infected people. The epidemiology of cancer among HIV-infected people has evolved since the beginning of the HIV epidemic with particularly marked changes since the introduction of modern treatment. Public health interventions aimed at prevention and early detection of cancer among HIV-infected people are needed.

  14. Properties of asymmetrically evolved community networks

    Institute of Scientific and Technical Information of China (English)

    Cui Di; Gao Zi-You; Zheng Jian-Feng

    2009-01-01

    This paper studies a simple asymmetrically evolved community network with a combination of preferential at-tachment and random properties. An important issue about community networks is to discover the different utility increments of two nodes, where the utility is introduced to investigate the asymmetrical effect of connecting two nodes. On the other hand, the connection of two nodes in community networks can be classified as two nodes belonging to the same or to different communities. The simulation results show that the model can reproduce a power-law utility distribution P(u)~ u-σ,σ=2+ 1/p, which can be obtained by using mean-field approximation methods. Furthermore, the model exhibits exponential behaviour with respect to small values of a parameter denoting the random effect in our model at the low-utility region and a power-law feature with respect to big values of this parameter at the high-utility region, which is in good agreement with theoretical analysis. This kind of community network can reproduce a unique utility distribution by theoretical and numerical analysis.

  15. Evolving paradigms in multifocal breast cancer.

    Science.gov (United States)

    Salgado, Roberto; Aftimos, Philippe; Sotiriou, Christos; Desmedt, Christine

    2015-04-01

    The 7th edition of the TNM defines multifocal breast cancer as multiple simultaneous ipsilateral and synchronous breast cancer lesions, provided they are macroscopically distinct and measurable using current traditional pathological and clinical tools. According to the College of American Pathologists (CAP), the characterization of only the largest lesion is considered sufficient, unless the grade and/or histology are different between the lesions. Here, we review three potentially clinically relevant aspects of multifocal breast cancers: first, the importance of a different intrinsic breast cancer subtype of the various lesions; second, the emerging awareness of inter-lesion heterogeneity; and last but not least, the potential introduction of bias in clinical trials due to the unrecognized biological diversity of these cancers. Although the current strategy to assess the lesion with the largest diameter has clearly its advantages in terms of costs and feasibility, this recommendation may not be sustainable in time and might need to be adapted to be compliant with new evolving paradigms in breast cancer.

  16. An evolving model of online bipartite networks

    Science.gov (United States)

    Zhang, Chu-Xu; Zhang, Zi-Ke; Liu, Chuang

    2013-12-01

    Understanding the structure and evolution of online bipartite networks is a significant task since they play a crucial role in various e-commerce services nowadays. Recently, various attempts have been tried to propose different models, resulting in either power-law or exponential degree distributions. However, many empirical results show that the user degree distribution actually follows a shifted power-law distribution, the so-called Mandelbrot’s law, which cannot be fully described by previous models. In this paper, we propose an evolving model, considering two different user behaviors: random and preferential attachment. Extensive empirical results on two real bipartite networks, Delicious and CiteULike, show that the theoretical model can well characterize the structure of real networks for both user and object degree distributions. In addition, we introduce a structural parameter p, to demonstrate that the hybrid user behavior leads to the shifted power-law degree distribution, and the region of power-law tail will increase with the increment of p. The proposed model might shed some lights in understanding the underlying laws governing the structure of real online bipartite networks.

  17. Women's oral health: the evolving science.

    Science.gov (United States)

    Sinkford, Jeanne C; Valachovic, Richard W; Harrison, Sonja G

    2008-02-01

    The evidence base for women's oral health is emerging from legislative action, clinical research, and survey documentation. The Women's Health in the Dental School Curriculum study (1999) followed a similar study (1996) of medical school curricula. Both of these major efforts resulted from statutory mandates in the National Institutes of Health Revitalization Act of 1993 (updated October 2000). A major study of the Institute of Medicine (IOM) National Academy of Sciences in 2001 concluded that "the study of sex differences is evolving into a mature science." This IOM study documented the scientific basis for gender-related policy and research and challenged the dental research enterprise to conduct collaborative, cross-disciplinary research on gender-related issues in oral health, disease, and disparities. This report chronicles some of the factors that have and continue to influence concepts of women's oral health in dental education, research, and practice. Gender issues related to women's health are no longer restricted to reproductive issues but are being considered across the life span and include psychosocial factors that impact women's health and treatment outcomes.

  18. Faster heart rate and muscular oxygen uptake kinetics in type 2 diabetes patients following endurance training.

    Science.gov (United States)

    Koschate, Jessica; Drescher, Uwe; Brinkmann, Christian; Baum, Klaus; Schiffer, Thorsten; Latsch, Joachim; Brixius, Klara; Hoffmann, Uwe

    2016-11-01

    Cardiorespiratory kinetics were analyzed in type 2 diabetes patients before and after a 12-week endurance exercise-training intervention. It was hypothesized that muscular oxygen uptake and heart rate (HR) kinetics would be faster after the training intervention and that this would be detectable using a standardized work rate protocol with pseudo-random binary sequences. The cardiorespiratory kinetics of 13 male sedentary, middle-aged, overweight type 2 diabetes patients (age, 60 ± 8 years; body mass index, 33 ± 4 kg·m(-2)) were tested before and after the 12-week exercise intervention. Subjects performed endurance training 3 times a week on nonconsecutive days. Pseudo-random binary sequences exercise protocols in combination with time series analysis were used to estimate kinetics. Greater maxima in cross-correlation functions (CCFmax) represent faster kinetics of the respective parameter. CCFmax of muscular oxygen uptake (pre-training: 0.31 ± 0.03; post-training: 0.37 ± 0.1, P = 0.024) and CCFmax of HR (pre-training: 0.25 ± 0.04; post-training: 0.29 ± 0.06, P = 0.007) as well as peak oxygen uptake (pre-training: 24.4 ± 4.7 mL·kg(-1)·min(-1); post-training: 29.3 ± 6.5 mL·kg(-1)·min(-1), P = 0.004) increased significantly over the course of the exercise intervention. In conclusion, kinetic responses to changing work rates in the moderate-intensity range are similar to metabolic demands occurring in everyday habitual activities. Moderate endurance training accelerated the kinetic responses of HR and muscular oxygen uptake. Furthermore, the applicability of the used method to detect these accelerations was demonstrated.

  19. Cone-Beam Computed Tomography (CBCT) Versus CT in Lung Ablation Procedure: Which is Faster?

    Energy Technology Data Exchange (ETDEWEB)

    Cazzato, Roberto Luigi, E-mail: r.cazzato@unicampus.it; Battistuzzi, Jean-Benoit, E-mail: j.battistuzzi@bordeaux.unicancer.fr; Catena, Vittorio, E-mail: vittoriocatena@gmail.com [Institut Bergonié, Department of Radiology (France); Grasso, Rosario Francesco, E-mail: r.grasso@unicampus.it; Zobel, Bruno Beomonte, E-mail: b.zobel@unicampus.it [Università Campus Bio-Medico di Roma, Department of Radiology and Diagnostic Imaging (Italy); Schena, Emiliano, E-mail: e.schena@unicampus.it [Università Campus Bio-Medico di Roma, Unit of Measurements and Biomedical Instrumentations, Biomedical Engineering Laboratory (Italy); Buy, Xavier, E-mail: x.buy@bordeaux.unicancer.fr; Palussiere, Jean, E-mail: j.palussiere@bordeaux.unicancer.fr [Institut Bergonié, Department of Radiology (France)

    2015-10-15

    AimTo compare cone-beam CT (CBCT) versus computed tomography (CT) guidance in terms of time needed to target and place the radiofrequency ablation (RFA) electrode on lung tumours.Materials and MethodsPatients at our institution who received CBCT- or CT-guided RFA for primary or metastatic lung tumours were retrospectively included. Time required to target and place the RFA electrode within the lesion was registered and compared across the two groups. Lesions were stratified into three groups according to their size (<10, 10–20, >20 mm). Occurrences of electrode repositioning, repositioning time, RFA complications, and local recurrence after RFA were also reported.ResultsForty tumours (22 under CT, 18 under CBCT guidance) were treated in 27 patients (19 male, 8 female, median age 67.25 ± 9.13 years). Thirty RFA sessions (16 under CBCT and 14 under CT guidance) were performed. Multivariable linear regression analysis showed that CBCT was faster than CT to target and place the electrode within the tumour independently from its size (β = −9.45, t = −3.09, p = 0.004). Electrode repositioning was required in 10/22 (45.4 %) tumours under CT guidance and 5/18 (27.8 %) tumours under CBCT guidance. Pneumothoraces occurred in 6/14 (42.8 %) sessions under CT guidance and in 6/16 (37.5 %) sessions under CBCT guidance. Two recurrences were noted for tumours receiving CBCT-guided RFA (2/17, 11.7 %) and three after CT-guided RFA (3/19, 15.8 %).ConclusionCBCT with live 3D needle guidance is a useful technique for percutaneous lung ablation. Despite lesion size, CBCT allows faster lung RFA than CT.

  20. The Development of Functional Overreaching Is Associated with a Faster Heart Rate Recovery in Endurance Athletes.

    Directory of Open Access Journals (Sweden)

    Anaël Aubry

    Full Text Available The aim of the study was to investigate whether heart rate recovery (HRR may represent an effective marker of functional overreaching (f-OR in endurance athletes.Thirty-one experienced male triathletes were tested (10 control and 21 overload subjects before (Pre, and immediately after an overload training period (Mid and after a 2-week taper (Post. Physiological responses were assessed during an incremental cycling protocol to exhaustion, including heart rate, catecholamine release and blood lactate concentration. Ten participants from the overload group developed signs of f-OR at Mid (i.e. -2.1 ± 0.8% change in performance associated with concomitant high perceived fatigue. Additionally, only the f-OR group demonstrated a 99% chance of increase in HRR during the overload period (+8 ± 5 bpm, large effect size. Concomitantly, this group also revealed a >80% chance of decreasing blood lactate (-11 ± 14%, large, plasma norepinephrine (-12 ± 37%, small and plasma epinephrine peak concentrations (-51 ± 22%, moderate. These blood measures returned to baseline levels at Post. HRR change was negatively correlated to changes in performance, peak HR and peak blood metabolites concentrations.These findings suggest that i a faster HRR is not systematically associated with improved physical performance, ii changes in HRR should be interpreted in the context of the specific training phase, the athletes perceived level of fatigue and the performance response; and, iii the faster HRR associated with f-OR may be induced by a decreased central command and by a lower chemoreflex activity.

  1. The FASTER Approach: A New Tool for Calculating Real-Time Tsunami Flood Hazards

    Science.gov (United States)

    Wilson, R. I.; Cross, A.; Johnson, L.; Miller, K.; Nicolini, T.; Whitmore, P.

    2014-12-01

    In the aftermath of the 2010 Chile and 2011 Japan tsunamis that struck the California coastline, emergency managers requested that the state tsunami program provide more detailed information about the flood potential of distant-source tsunamis well ahead of their arrival time. The main issue is that existing tsunami evacuation plans call for evacuation of the predetermined "worst-case" tsunami evacuation zone (typically at a 30- to 50-foot elevation) during any "Warning" level event; the alternative is to not call an evacuation at all. A solution to provide more detailed information for secondary evacuation zones has been the development of tsunami evacuation "playbooks" to plan for tsunami scenarios of various sizes and source locations. To determine a recommended level of evacuation during a distant-source tsunami, an analytical tool has been developed called the "FASTER" approach, an acronym for factors that influence the tsunami flood hazard for a community: Forecast Amplitude, Storm, Tides, Error in forecast, and the Run-up potential. Within the first couple hours after a tsunami is generated, the National Tsunami Warning Center provides tsunami forecast amplitudes and arrival times for approximately 60 coastal locations in California. At the same time, the regional NOAA Weather Forecast Offices in the state calculate the forecasted coastal storm and tidal conditions that will influence tsunami flooding. Providing added conservatism in calculating tsunami flood potential, we include an error factor of 30% for the forecast amplitude, which is based on observed forecast errors during recent events, and a site specific run-up factor which is calculated from the existing state tsunami modeling database. The factors are added together into a cumulative FASTER flood potential value for the first five hours of tsunami activity and used to select the appropriate tsunami phase evacuation "playbook" which is provided to each coastal community shortly after the forecast

  2. Emergent spacetime in stochastically evolving dimensions

    Directory of Open Access Journals (Sweden)

    Niayesh Afshordi

    2014-12-01

    Full Text Available Changing the dimensionality of the space–time at the smallest and largest distances has manifold theoretical advantages. If the space is lower dimensional in the high energy regime, then there are no ultraviolet divergencies in field theories, it is possible to quantize gravity, and the theory of matter plus gravity is free of divergencies or renormalizable. If the space is higher dimensional at cosmological scales, then some cosmological problems (including the cosmological constant problem can be attacked from a completely new perspective. In this paper, we construct an explicit model of “evolving dimensions” in which the dimensions open up as the temperature of the universe drops. We adopt the string theory framework in which the dimensions are fields that live on the string worldsheet, and add temperature dependent mass terms for them. At the Big Bang, all the dimensions are very heavy and are not excited. As the universe cools down, dimensions open up one by one. Thus, the dimensionality of the space we live in depends on the energy or temperature that we are probing. In particular, we provide a kinematic Brandenberger–Vafa argument for how a discrete causal set, and eventually a continuum (3+1-dim spacetime along with Einstein gravity emerges in the Infrared from the worldsheet action. The (3+1-dim Planck mass and the string scale become directly related, without any compactification. Amongst other predictions, we argue that LHC might be blind to new physics even if it comes at the TeV scale. In contrast, cosmic ray experiments, especially those that can register the very beginning of the shower, and collisions with high multiplicity and density of particles, might be sensitive to the dimensional cross-over.

  3. Quantum mechanics in an evolving Hilbert space

    Science.gov (United States)

    Artacho, Emilio; O'Regan, David D.

    2017-03-01

    Many basis sets for electronic structure calculations evolve with varying external parameters, such as moving atoms in dynamic simulations, giving rise to extra derivative terms in the dynamical equations. Here we revisit these derivatives in the context of differential geometry, thereby obtaining a more transparent formalization, and a geometrical perspective for better understanding the resulting equations. The effect of the evolution of the basis set within the spanned Hilbert space separates explicitly from the effect of the turning of the space itself when moving in parameter space, as the tangent space turns when moving in a curved space. New insights are obtained using familiar concepts in that context such as the Riemann curvature. The differential geometry is not strictly that for curved spaces as in general relativity, a more adequate mathematical framework being provided by fiber bundles. The language used here, however, will be restricted to tensors and basic quantum mechanics. The local gauge implied by a smoothly varying basis set readily connects with Berry's formalism for geometric phases. Generalized expressions for the Berry connection and curvature are obtained for a parameter-dependent occupied Hilbert space spanned by nonorthogonal Wannier functions. The formalism is applicable to basis sets made of atomic-like orbitals and also more adaptative moving basis functions (such as in methods using Wannier functions as intermediate or support bases), but should also apply to other situations in which nonorthogonal functions or related projectors should arise. The formalism is applied to the time-dependent quantum evolution of electrons for moving atoms. The geometric insights provided here allow us to propose new finite-difference time integrators, and also better understand those already proposed.

  4. Emergent spacetime in stochastically evolving dimensions

    Energy Technology Data Exchange (ETDEWEB)

    Afshordi, Niayesh [Perimeter Institute for Theoretical Physics, 31 Caroline St. N., Waterloo, ON, N2L 2Y5 (Canada); Department of Physics and Astronomy, University of Waterloo, Waterloo, ON, N2L 3G1 (Canada); HEPCOS, Department of Physics, SUNY at Buffalo, Buffalo, NY 14260-1500 (United States); Stojkovic, Dejan, E-mail: ds77@buffalo.edu [Perimeter Institute for Theoretical Physics, 31 Caroline St. N., Waterloo, ON, N2L 2Y5 (Canada); HEPCOS, Department of Physics, SUNY at Buffalo, Buffalo, NY 14260-1500 (United States)

    2014-12-12

    Changing the dimensionality of the space–time at the smallest and largest distances has manifold theoretical advantages. If the space is lower dimensional in the high energy regime, then there are no ultraviolet divergencies in field theories, it is possible to quantize gravity, and the theory of matter plus gravity is free of divergencies or renormalizable. If the space is higher dimensional at cosmological scales, then some cosmological problems (including the cosmological constant problem) can be attacked from a completely new perspective. In this paper, we construct an explicit model of “evolving dimensions” in which the dimensions open up as the temperature of the universe drops. We adopt the string theory framework in which the dimensions are fields that live on the string worldsheet, and add temperature dependent mass terms for them. At the Big Bang, all the dimensions are very heavy and are not excited. As the universe cools down, dimensions open up one by one. Thus, the dimensionality of the space we live in depends on the energy or temperature that we are probing. In particular, we provide a kinematic Brandenberger–Vafa argument for how a discrete causal set, and eventually a continuum (3+1)-dim spacetime along with Einstein gravity emerges in the Infrared from the worldsheet action. The (3+1)-dim Planck mass and the string scale become directly related, without any compactification. Amongst other predictions, we argue that LHC might be blind to new physics even if it comes at the TeV scale. In contrast, cosmic ray experiments, especially those that can register the very beginning of the shower, and collisions with high multiplicity and density of particles, might be sensitive to the dimensional cross-over.

  5. Evolvable Cryogenics (ECRYO) Pressure Transducer Calibration Test

    Science.gov (United States)

    Diaz, Carlos E., Jr.

    2015-01-01

    This paper provides a summary of the findings of recent activities conducted by Marshall Space Flight Center's (MSFC) In-Space Propulsion Branch and MSFC's Metrology and Calibration Lab to assess the performance of current "state of the art" pressure transducers for use in long duration storage and transfer of cryogenic propellants. A brief historical narrative in this paper describes the Evolvable Cryogenics program and the relevance of these activities to the program. This paper also provides a review of three separate test activities performed throughout this effort, including: (1) the calibration of several pressure transducer designs in a liquid nitrogen cryogenic environmental chamber, (2) the calibration of a pressure transducer in a liquid helium Dewar, and (3) the calibration of several pressure transducers at temperatures ranging from 20 to 70 degrees Kelvin (K) using a "cryostat" environmental chamber. These three separate test activities allowed for study of the sensors along a temperature range from 4 to 300 K. The combined data shows that both the slope and intercept of the sensor's calibration curve vary as a function of temperature. This homogeneous function is contrary to the linearly decreasing relationship assumed at the start of this investigation. Consequently, the data demonstrates the need for lookup tables to change the slope and intercept used by any data acquisition system. This ultimately would allow for more accurate pressure measurements at the desired temperature range. This paper concludes with a review of a request for information (RFI) survey conducted amongst different suppliers to determine the availability of current "state of the art" flight-qualified pressure transducers. The survey identifies requirements that are most difficult for the suppliers to meet, most notably the capability to validate the sensor's performance at temperatures below 70 K.

  6. Professional Music Training and Novel Word Learning: From Faster Semantic Encoding to Longer-lasting Word Representations

    OpenAIRE

    Dittinger, Eva,; Barbaroux, Mylène; D'Imperio, Mariapaola; Jäncke, Lutz; Elmer, Stefan; Besson, Mireille

    2016-01-01

    On the basis of previous results showing that music training positively influences different aspects of speech perception and cognition, the aim of this series of experiments was to test the hypothesis that adult professional musicians would learn the meaning of novel words through picture-word associations more efficiently than controls without music training (i.e., fewer errors and faster RTs). We also expected musicians to show faster changes in brain electrical activity than controls, in ...

  7. Bioinformatics methods for identifying candidate disease genes

    NARCIS (Netherlands)

    Driel, M.A. van; Brunner, H.G.

    2006-01-01

    With the explosion in genomic and functional genomics information, methods for disease gene identification are rapidly evolving. Databases are now essential to the process of selecting candidate disease genes. Combining positional information with disease characteristics and functional information i

  8. Mitotic Exit Control as an Evolved Complex System

    Energy Technology Data Exchange (ETDEWEB)

    Bosl, W; Li, R

    2005-04-25

    The exit from mitosis is the last critical decision a cell has to make during a division cycle. A complex regulatory system has evolved to evaluate the success of mitotic events and control this decision. Whereas outstanding genetic work in yeast has led to rapid discovery of a large number of interacting genes involved in the control of mitotic exit, it has also become increasingly difficult to comprehend the logic and mechanistic features embedded in the complex molecular network. Our view is that this difficulty stems in part from the attempt to explain mitotic exit control using concepts from traditional top-down engineering design, and that exciting new results from evolutionary engineering design applied to networks and electronic circuits may lend better insights. We focus on four particularly intriguing features of the mitotic exit control system: the two-stepped release of Cdc14; the self-activating nature of Tem1 GTPase; the spatial sensor associated with the spindle pole body; and the extensive redundancy in the mitotic exit network. We attempt to examine these design features from the perspective of evolutionary design and complex system engineering.

  9. Faster than classical quantum algorithm for dense formulas of exact satisfiability and occupation problems

    Science.gov (United States)

    Mandrà, Salvatore; Giacomo Guerreschi, Gian; Aspuru-Guzik, Alán

    2016-07-01

    We present an exact quantum algorithm for solving the Exact Satisfiability problem, which belongs to the important NP-complete complexity class. The algorithm is based on an intuitive approach that can be divided into two parts: the first step consists in the identification and efficient characterization of a restricted subspace that contains all the valid assignments of the Exact Satisfiability; while the second part performs a quantum search in such restricted subspace. The quantum algorithm can be used either to find a valid assignment (or to certify that no solution exists) or to count the total number of valid assignments. The query complexities for the worst-case are respectively bounded by O(\\sqrt{{2}n-{M\\prime }}) and O({2}n-{M\\prime }), where n is the number of variables and {M}\\prime the number of linearly independent clauses. Remarkably, the proposed quantum algorithm results to be faster than any known exact classical algorithm to solve dense formulas of Exact Satisfiability. As a concrete application, we provide the worst-case complexity for the Hamiltonian cycle problem obtained after mapping it to a suitable Occupation problem. Specifically, we show that the time complexity for the proposed quantum algorithm is bounded by O({2}n/4) for 3-regular undirected graphs, where n is the number of nodes. The same worst-case complexity holds for (3,3)-regular bipartite graphs. As a reference, the current best classical algorithm has a (worst-case) running time bounded by O({2}31n/96). Finally, when compared to heuristic techniques for Exact Satisfiability problems, the proposed quantum algorithm is faster than the classical WalkSAT and Adiabatic Quantum Optimization for random instances with a density of constraints close to the satisfiability threshold, the regime in which instances are typically the hardest to solve. The proposed quantum algorithm can be straightforwardly extended to the generalized version of the Exact Satisfiability known as Occupation

  10. Robustness promotes evolvability of thermotolerance in an RNA virus

    Directory of Open Access Journals (Sweden)

    Turner Paul E

    2008-08-01

    Full Text Available Abstract Background The ability for an evolving population to adapt to a novel environment is achieved through a balance of robustness and evolvability. Robustness is the invariance of phenotype in the face of perturbation and evolvability is the capacity to adapt in response to selection. Genetic robustness has been posited, depending on the underlying mechanism, to either decrease the efficacy of selection, or increase the possibility of future adaptation. However, the true effect of genetic robustness on evolvability in biological systems remains uncertain. Results Here we demonstrate that genetic robustness increases evolvability of thermotolerance in laboratory populations of the RNA virus φ6. We observed that populations founded by robust clones evolved greater resistance to heat shock, relative to populations founded by brittle (less-robust clones. Thus, we provide empirical evidence for the idea that robustness can promote evolvability in this environment, and further suggest that evolvability can arise indirectly via selection for robustness, rather than through direct selective action. Conclusion Our data imply that greater tolerance of mutational change is associated with virus adaptability in a new niche, a finding generally relevant to evolutionary biology, and informative for elucidating how viruses might evolve to emerge in new habitats and/or overcome novel therapies.

  11. Rapidly evolving microorganisms with high biofuel tolerance

    Science.gov (United States)

    Vyawahare, Saurabh; Zhang, Qiucen; Lang, Wendy; Austin, Robert

    2012-02-01

    Replacing non-renewable energy sources is one of the biggest and most exciting challenges of our generation. Algae and bacteria are poised to become major renewable biofuels if strains can be developed that provide a high,consistent and robust yield of oil. One major stumbling block towards this goal is the lack of tolerance to high concentrations of biofuels like isobutanol. Using traditional bioengineering techniques to remedy this face the hurdle of identifying the correct pathway or gene to modify. But the multiplicity of interactions inside a cell makes it very hard to determine what to modify a priori. Instead, we propose a technology that does not require prior knowledge of the genes or pathways to modify. In our approach that marries microfabrication and ecology, spatial heterogeneity is used as a knob to speed up evolution in the desired direction. Recently, we have successfully used this approach to demonstrate the rapid emergence of bacterial antibiotic resistance in as little as ten hours. Here, we describe our experimental results in developing new strains of micro-organisms with high oil tolerance. Besides biofuel production, our work is also relevant to oil spill clean-ups.

  12. The effect of scale-free topology on the robustness and evolvability of genetic regulatory networks.

    Science.gov (United States)

    Greenbury, Sam F; Johnston, Iain G; Smith, Matthew A; Doye, Jonathan P K; Louis, Ard A

    2010-11-01

    We investigate how scale-free (SF) and Erdos-Rényi (ER) topologies affect the interplay between evolvability and robustness of model gene regulatory networks with Boolean threshold dynamics. In agreement with Oikonomou and Cluzel (2006) we find that networks with SF(in) topologies, that is SF topology for incoming nodes and ER topology for outgoing nodes, are significantly more evolvable towards specific oscillatory targets than networks with ER topology for both incoming and outgoing nodes. Similar results are found for networks with SF(both) and SF(out) topologies. The functionality of the SF(out) topology, which most closely resembles the structure of biological gene networks (Babu et al., 2004), is compared to the ER topology in further detail through an extension to multiple target outputs, with either an oscillatory or a non-oscillatory nature. For multiple oscillatory targets of the same length, the differences between SF(out) and ER networks are enhanced, but for non-oscillatory targets both types of networks show fairly similar evolvability. We find that SF networks generate oscillations much more easily than ER networks do, and this may explain why SF networks are more evolvable than ER networks are for oscillatory phenotypes. In spite of their greater evolvability, we find that networks with SF(out) topologies are also more robust to mutations (mutational robustness) than ER networks. Furthermore, the SF(out) topologies are more robust to changes in initial conditions (environmental robustness). For both topologies, we find that once a population of networks has reached the target state, further neutral evolution can lead to an increase in both the mutational robustness and the environmental robustness to changes in initial conditions.

  13. Rapidly-Evolving and Luminous Transients from Pan-STARRS1

    CERN Document Server

    Drout, M R; Soderberg, A M; Sanders, N E; McKinnon, R; Rest, A; Foley, R J; Milisavljevic, D; Margutti, R; Berger, E; Calkins, M; Fong, W; Gezari, S; Huber, M E; Kankare, E; Kirshner, R P; Leibler, C; Lunnan, R; Mattila, S; Marion, G H; Narayan, G; Riess, A G; Roth, K C; Scolnic, D; Smartt, S J; Tonry, J L; Burgett, W S; Hodapp, K W; Jedicke, R; Kaiser, N; Magnier, E A; Metcalfe, N; Morgan, J S; Price, P A; Waters, C

    2014-01-01

    In the past decade, several rapidly-evolving transients have been discovered whose timescales and luminosities are not easily explained by traditional supernovae (SN) models. The sample size of these objects has remained small due, at least in part, to the challenge of detecting short timescale transients with traditional survey cadences. Here we present the results from a search within the Pan-STARRS1 Medium Deep Survey (PS1-MDS) for rapidly-evolving and luminous transients. We identify 10 new transients with a time above half-maximum of less than 12 days and -16.5 > M > -20 mag. This increases the number of known events in this region of SN phase space by roughly a factor of three. The median redshift of the PS1-MDS sample is z=0.275 and they all exploded in star forming galaxies. In general, the transients possess faster rise than decline timescale and blue colors at maximum light (g - r 10^43 erg/s), and lack of UV line blanketing observed in many of these transients with an explosion powered mainly by t...

  14. Encoding Systems and Evolved Message Processing: Pictures Enable Action, Words Enable Thinking

    Directory of Open Access Journals (Sweden)

    Annie Lang

    2015-09-01

    Full Text Available This paper, based on theories of ecological perception, embodied motivated cognition, and evolutionary psychology, proposes that pictures elicit evolved biologically imperative responses more quickly and thoroughly than do words. These biologically imperative responses are directly responsible for evolved automatic reactions away from biological threats (e.g. escaping predators, avoiding disease and noxious stimuli and towards opportunities (e.g. consuming food, approaching mates, finding shelter in the environment. When elicited, these responses take time to occur and may delay or interfere with other types of behavior. Thus, when environmental information is presented in pictures (which should elicit larger biological responses than words biological responses should interfere more with higher order tasks like information processing and cognitive decision-making. To test this proposition we designed an experiment in which participants performed speeded categorizations of 60 pairs of matched pleasant and unpleasant environmental opportunities and threats. They categorized the items based on their form (is this a word or a picture? or based on how the picture made them feel (is this pleasant or unpleasant to you?. If pictures do elicit greater biologically imperative responses than their word counterparts, participants should be able to make form decisions faster than feeling decisions, especially when presented with words rather than pictures and especially when the words and pictures have less biological relevance. This main proposition was supported. Implications for this proposition in terms of communication theory are discussed.

  15. Hippocampal brain volume is associated with faster facial emotion identification in older adults: preliminary results

    Directory of Open Access Journals (Sweden)

    Sarah M Szymkowicz

    2016-08-01

    Full Text Available Fast correct identification of facial emotions is highly relevant for successful social interactions. Research suggests that older, compared to young, adults experience increased difficulty with face and emotion processing skills. While functional neuroimaging studies suggest age differences in neural processing of faces and emotions, evidence about age-associated structural brain changes and their involvement in face and emotion processing is scarce. Using structural magnetic resonance imaging, this study investigated the extent to which volumes of frontal and temporal brain structures were related to reaction time in accurate identification of facial emotions in 30 young and 30 older adults. Volumetric segmentation was performed using FreeSurfer and gray matter volumes from frontal and temporal regions were extracted. Analyses of covariance models with response time as the dependent variable and age group and regional volume, and their interaction, as independent variables were conducted, controlling for total intracranial volume. Results indicated that, in older adults, larger hippocampal volumes were associated with faster correct facial emotion identification. These preliminary observations suggest that greater volume in brain regions associated with face and emotion processing contributes to improved facial emotion identification performance in aging.

  16. Faster Heart Rate Recovery With Increased RPE: Paradoxical Responses After an 87-km Ultramarathon.

    Science.gov (United States)

    Mann, Theresa N; Platt, Cathrin E; Lamberts, Robert P; Lambert, Michael I

    2015-12-01

    The aim of this study was to determine the relationship between heart rate recovery (HRR) and an acute training "overload" by comparing HRR responses before and after an ultramarathon road race. Ten runners completed a standardized laboratory protocol ∼7 days before and between 2 and 4 days after participating in the 87-km Comrades Marathon. The protocol included muscle pain ratings, a 5-bound test, and 20 minutes of treadmill exercise at 70% of maximal oxygen uptake followed by 15 minutes of recovery. Respiratory gases and heart rate measurements were used to calculate steady-state exercise responses, HRR, and excess postexercise oxygen consumption (EPOC), and participants also provided a rating of perceived exertion (RPE) during exercise. The RPE was significantly increased (13 ± 2 vs. 11 ± 1) (p EPOC. Although previous studies have shown that faster HRR reflected an "adapted" state with enhanced training status, the current findings suggest that this may not always be the case. It follows that changes in HRR should be considered in the context of other factors, such as recent training load and RPE during submaximal exercise.

  17. Relaxed Linearized Algorithms for Faster X-Ray CT Image Reconstruction.

    Science.gov (United States)

    Nien, Hung; Fessler, Jeffrey A

    2016-04-01

    Statistical image reconstruction (SIR) methods are studied extensively for X-ray computed tomography (CT) due to the potential of acquiring CT scans with reduced X-ray dose while maintaining image quality. However, the longer reconstruction time of SIR methods hinders their use in X-ray CT in practice. To accelerate statistical methods, many optimization techniques have been investigated. Over-relaxation is a common technique to speed up convergence of iterative algorithms. For instance, using a relaxation parameter that is close to two in alternating direction method of multipliers (ADMM) has been shown to speed up convergence significantly. This paper proposes a relaxed linearized augmented Lagrangian (AL) method that shows theoretical faster convergence rate with over-relaxation and applies the proposed relaxed linearized AL method to X-ray CT image reconstruction problems. Experimental results with both simulated and real CT scan data show that the proposed relaxed algorithm (with ordered-subsets [OS] acceleration) is about twice as fast as the existing unrelaxed fast algorithms, with negligible computation and memory overhead.

  18. "Feeling younger, walking faster": subjective age and walking speed in older adults.

    Science.gov (United States)

    Stephan, Yannick; Sutin, Angelina R; Terracciano, Antonio

    2015-10-01

    Walking speed is a key vital sign in older people. Given the implications of slower gait speed, a large literature has identified health-related, behavioral, cognitive, and biological factors that moderate age-related decline in mobility. The present study aims to contribute to existing knowledge by examining whether subjective age, how old or young individuals experience themselves to be relative to their chronological age, contributes to walking speed. Participants were drawn from the 2008 and 2012 waves of the Health and Retirement Study (HRS, N = 2970) and the 2011 and 2013 waves of the National Health and Aging Trends Study (NHATS, N = 5423). In both the HRS and the NHATS, linear regression analysis revealed that a younger subjective age was associated with faster walking speed at baseline and with less decline over time, controlling for age, sex, education, and race. These associations were partly accounted for by depressive symptoms, disease burden, physical activity, cognition, body mass index, and smoking. Additional analysis revealed that feeling younger than one's age was associated with a reduced risk of walking slower than the frailty-related threshold of 0.6 m/s at follow-up in the HRS. The present study provides novel and consistent evidence across two large prospective studies for an association between the subjective experience of age and walking speed of older adults. Subjective age may help identify individuals at risk for mobility limitations in old age and may be a target for interventions designed to mitigate functional decline.

  19. Human actuarial aging increases faster when background death rates are lower: a consequence of differential heterogeneity?

    Science.gov (United States)

    Hawkes, Kristen; Smith, Ken R; Blevins, James K

    2012-01-01

    Many analyses of human populations have found that age-specific mortality rates increase faster across most of adulthood when overall mortality levels decline. This contradicts the relationship often expected from Williams' classic hypothesis about the effects of natural selection on the evolution of senescence. More likely, much of the within-species difference in actuarial aging is not due to variation in senescence, but to the strength of filters on the heterogeneity of frailty in older survivors. A challenge to this differential frailty hypothesis was recently posed by an analysis of life tables from historical European populations and traditional societies that reported variation in actuarial aging consistent with Williams' hypothesis after all. To investigate the challenge, we reconsidered those cases and aging measures. Here we show that the discrepancy depends on Ricklefs' aging rate measure, ω, which decreases as mortality levels drop because it is an index of mortality level itself, not the rate of increase in mortality with age. We also show unappreciated correspondence among the parameters of Gompertz-Makeham and Weibull survival models. Finally, we compare the relationships among mortality parameters of the traditional societies and the historical series, providing further suggestive evidence that differential heterogeneity has strong effects on actuarial aging.

  20. Emotion, Etmnooi, or Emitoon?--Faster lexical access to emotional than to neutral words during reading.

    Science.gov (United States)

    Kissler, Johanna; Herbert, Cornelia

    2013-03-01

    Cortical processing of emotional words differs from that of neutral words. Using EEG event-related potentials (ERPs), the present study examines the functional stage(s) of this differentiation. Positive, negative, and neutral nouns were randomly mixed with pseudowords and letter strings derived from words within each valence and presented for reading while participants' EEG was recorded. Results indicated emotion effects in the N1 (110-140 ms), early posterior negativity (EPN, 216-320) and late positive potential (LPP, 432-500 ms) time windows. Across valence, orthographic word-form effects occurred from about 180 ms after stimulus presentation. Crucially, in emotional words, lexicality effects (real words versus pseudowords) were identified from 216 ms, words being more negative over posterior cortex, coinciding with EPN effects, whereas neutral words differed from pseudowords only after 320 ms. Emotional content affects word processing at pre-lexical, lexical and post-lexical levels, but remarkably lexical access to emotional words is faster than access to neutral words. Copyright © 2012 Elsevier B.V. All rights reserved.

  1. Growing coral larger and faster: micro-colony-fusion as a strategy for accelerating coral cover.

    Science.gov (United States)

    Forsman, Zac H; Page, Christopher A; Toonen, Robert J; Vaughan, David

    2015-01-01

    Fusion is an important life history strategy for clonal organisms to increase access to shared resources, to compete for space, and to recover from disturbance. For reef building corals, fragmentation and colony fusion are key components of resilience to disturbance. Observations of small fragments spreading tissue and fusing over artificial substrates prompted experiments aimed at further characterizing Atlantic and Pacific corals under various conditions. Small (∼1-3 cm(2)) fragments from the same colony spaced regularly over ceramic tiles resulted in spreading at rapid rates (e.g., tens of square centimeters per month) followed by isogenic fusion. Using this strategy, we demonstrate growth, in terms of area encrusted and covered by living tissue, of Orbicella faveolata, Pseudodiploria clivosa, and Porites lobata as high as 63, 48, and 23 cm(2) per month respectively. We found a relationship between starting and ending size of fragments, with larger fragments growing at a faster rate. Porites lobata showed significant tank effects on rates of tissue spreading indicating sensitivity to biotic and abiotic factors. The tendency of small coral fragments to encrust and fuse over a variety of surfaces can be exploited for a variety of applications such as coral cultivation, assays for coral growth, and reef restoration.

  2. Growing coral larger and faster: micro-colony-fusion as a strategy for accelerating coral cover

    Directory of Open Access Journals (Sweden)

    Zac H. Forsman

    2015-10-01

    Full Text Available Fusion is an important life history strategy for clonal organisms to increase access to shared resources, to compete for space, and to recover from disturbance. For reef building corals, fragmentation and colony fusion are key components of resilience to disturbance. Observations of small fragments spreading tissue and fusing over artificial substrates prompted experiments aimed at further characterizing Atlantic and Pacific corals under various conditions. Small (∼1–3 cm2 fragments from the same colony spaced regularly over ceramic tiles resulted in spreading at rapid rates (e.g., tens of square centimeters per month followed by isogenic fusion. Using this strategy, we demonstrate growth, in terms of area encrusted and covered by living tissue, of Orbicella faveolata, Pseudodiploria clivosa, and Porites lobata as high as 63, 48, and 23 cm2 per month respectively. We found a relationship between starting and ending size of fragments, with larger fragments growing at a faster rate. Porites lobata showed significant tank effects on rates of tissue spreading indicating sensitivity to biotic and abiotic factors. The tendency of small coral fragments to encrust and fuse over a variety of surfaces can be exploited for a variety of applications such as coral cultivation, assays for coral growth, and reef restoration.

  3. Are OPERA neutrinos faster than light because of non-inertial reference frames?

    CERN Document Server

    Germana, Claudio

    2012-01-01

    Recent results from the OPERA experiment reported a neutrino beam traveling faster than light. The experiment measured the neutrino time of flight (TOF) over a baseline from the CERN to the Gran Sasso site. The neutrino beam arrives 60 ns earlier than a light ray would do. Because the result has an enormous impact on science, it might be worth double-checking the time definitions with respect to the non-inertial system in which the neutrino travel time was measured. Potential problems in the OPERA data analysis connected with the definition of the reference frame and time synchronization are emphasized. We aim to investigate the synchronization of non-inertial clocks on Earth by relating this time to the proper time of an inertial observer at Solar System Barycenter(SSB). The Tempo2 software was used to time-stamp events observed on the geoid with respect to the SSB inertial observer time. Neutrino results from OPERA might carry the fingerprint of non-inertial effects. The CERN-Gran Sasso clock synchronizatio...

  4. What Makes You Go Faster?: The Effect of Reward on Speeded Action under Risk

    Directory of Open Access Journals (Sweden)

    Xing-jie Chen

    2017-06-01

    Full Text Available Evaluating the potential reward and risk associated with a choice of action plays an important role in everyday decision making. However, the details behind how reward and risk affect the decisions for actions remain unclear. The present study investigates the influence of reward and risk on a decision to make a speeded motor response. One hundred and ten college students performed a Speed-Rewarded Go-NoGo task during which they were rewarded proportionally based on the speed and accuracy of their response. On each trial, the magnitude of potential reward and the probability of a forthcoming Go signal (Go-probability were presented prior to the Go or NoGo signal. Personality traits, such as risk taking and impulsive tendencies, were measured to determine their contribution in explaining individual differences in task performance. The results showed that larger amount of rewards can motivate people to respond faster, and this effect was modulated by the assessed risk, suggesting that decisions for actions are based on a systematic trade-off between rewards and risks. Moreover, when the assessed risk was high, individuals with greater risk taking and impulsive tendencies did not adequately adjust their behavior across different reward levels. These findings shed light on the mechanistic understanding of the effect of reward and risk on decisions for a speeded action.

  5. Faster-Than-Real-Time Simulation of Lithium Ion Batteries with Full Spatial and Temporal Resolution

    Directory of Open Access Journals (Sweden)

    Sandip Mazumder

    2013-01-01

    Full Text Available A one-dimensional coupled electrochemical-thermal model of a lithium ion battery with full temporal and normal-to-electrode spatial resolution is presented. Only a single pair of electrodes is considered in the model. It is shown that simulation of a lithium ion battery with the inclusion of detailed transport phenomena and electrochemistry is possible with faster-than-real-time compute times. The governing conservation equations of mass, charge, and energy are discretized using the finite volume method and solved using an iterative procedure. The model is first successfully validated against experimental data for both charge and discharge processes in a LixC6-LiyMn2O4 battery. Finally, it is demonstrated for an arbitrary rapidly changing transient load typical of a hybrid electric vehicle drive cycle. The model is able to predict the cell voltage of a 15-minute drive cycle in less than 12 seconds of compute time on a laptop with a 2.33 GHz Intel Pentium 4 processor.

  6. Soft robotics: a review and progress towards faster and higher torque actuators (presentation video)

    Science.gov (United States)

    Shepherd, Robert

    2014-03-01

    Last year, nearly 160,000 industrial robots were shipped worldwide—into a total market valued at 26 Bn (including hardware, software, and peripherals).[1] Service robots for professional (e.g., defense, medical, agriculture) and personal (e.g., household, handicap assistance, toys, and education) use accounted for 16,000 units, 3.4 Bn and 3,000,000 units, $1.2 Bn respectively.[1] The vast majority of these robotic systems use fully actuated, rigid components that take little advantage of passive dynamics. Soft robotics is a field that is taking advantage of compliant actuators and passive dynamics to achieve several goals: reduced design, manufacturing and control complexity, improved energy efficiency, more sophisticated motions, and safe human-machine interactions to name a few. The potential for societal impact is immense. In some instances, soft actuators have achieved commercial success; however, large scale adoption will require improved methods of controlling non-linear systems, greater reliability in their function, and increased utility from faster and more forceful actuation. In my talk, I will describe efforts from my work in the Whitesides group at Harvard to prove sophisticated motions in these machines using simple controls, as well capabilities unique to soft machines. I will also describe the potential for combinations of different classes of soft actuators (e.g., electrically and pneumatically actuated systems) to improve the utility of soft robots. 1. World Robotics - Industrial Robots 2013, 2013, International Federation of Robotics.

  7. Small-amplitude swimmers can self-propel faster in viscoelastic fluids.

    Science.gov (United States)

    Riley, Emily E; Lauga, Eric

    2015-10-01

    Many small organisms self-propel in viscous fluids using travelling wave-like deformations of their bodies or appendages. Examples include small nematodes moving through soil using whole-body undulations or spermatozoa swimming through mucus using flagellar waves. When self-propulsion occurs in a non-Newtonian fluid, one fundamental question is whether locomotion will occur faster or slower than in a Newtonian environment. Here we consider the general problem of swimming using small-amplitude periodic waves in a viscoelastic fluid described by the classical Oldroyd-B constitutive relationship. Using Taylor's swimming sheet model, we show that if all travelling waves move in the same direction, the locomotion speed of the organism is systematically decreased. However, if we allow waves to travel in two opposite directions, we show that this can lead to enhancement of the swimming speed, which is physically interpreted as due to asymmetric viscoelastic damping of waves with different frequencies. A change of the swimming direction is also possible. By analysing in detail the cases of swimming using two or three travelling waves, we demonstrate that swimming can be enhanced in a viscoelastic fluid for all Deborah numbers below a critical value or, for three waves or more, only for a finite, non-zero range of Deborah numbers, in which case a finite amount of elasticity in the fluid is required to increase the swimming speed.

  8. A robust adaptive sampling method for faster acquisition of MR images.

    Science.gov (United States)

    Vellagoundar, Jaganathan; Machireddy, Ramasubba Reddy

    2015-06-01

    A robust adaptive k-space sampling method is proposed for faster acquisition and reconstruction of MR images. In this method, undersampling patterns are generated based on magnitude profile of a fully acquired 2-D k-space data. Images are reconstructed using compressive sampling reconstruction algorithm. Simulation experiments are done to assess the performance of the proposed method under various signal-to-noise ratio (SNR) levels. The performance of the method is better than non-adaptive variable density sampling method when k-space SNR is greater than 10dB. The method is implemented on a fully acquired multi-slice raw k-space data and a quality assurance phantom data. Data reduction of up to 60% is achieved in the multi-slice imaging data and 75% is achieved in the phantom imaging data. The results show that reconstruction accuracy is improved over non-adaptive or conventional variable density sampling method. The proposed sampling method is signal dependent and the estimation of sampling locations is robust to noise. As a result, it eliminates the necessity of mathematical model and parameter tuning to compute k-space sampling patterns as required in non-adaptive sampling methods. Copyright © 2015 Elsevier Inc. All rights reserved.

  9. In a warmer Arctic, mosquitoes avoid increased mortality from predators by growing faster.

    Science.gov (United States)

    Culler, Lauren E; Ayres, Matthew P; Virginia, Ross A

    2015-09-22

    Climate change is altering environmental temperature, a factor that influences ectothermic organisms by controlling rates of physiological processes. Demographic effects of warming, however, are determined by the expression of these physiological effects through predator-prey and other species interactions. Using field observations and controlled experiments, we measured how increasing temperatures in the Arctic affected development rates and mortality rates (from predation) of immature Arctic mosquitoes in western Greenland. We then developed and parametrized a demographic model to evaluate how temperature affects survival of mosquitoes from the immature to the adult stage. Our studies showed that warming increased development rate of immature mosquitoes (Q10 = 2.8) but also increased daily mortality from increased predation rates by a dytiscid beetle (Q10 = 1.2-1.5). Despite increased daily mortality, the model indicated that faster development and fewer days exposed to predators resulted in an increased probability of mosquito survival to the adult stage. Warming also advanced mosquito phenology, bringing mosquitoes into phenological synchrony with caribou. Increases in biting pests will have negative consequences for caribou and their role as a subsistence resource for local communities. Generalizable frameworks that account for multiple effects of temperature are needed to understand how climate change impacts coupled human-natural systems.

  10. The cost of defeat: Capuchin groups travel further, faster and later after losing conflicts with neighbors.

    Science.gov (United States)

    Crofoot, Margaret C

    2013-09-01

    Although competition between social groups is central to hypotheses about the evolution of human social organization, competitive interactions among group-mates are thought to play a more dominant role in shaping the behavior and ecology of other primate species. However, few studies have directly tested the impact of intergroup conflicts in non-human primates. What is the cost of defeat? To address this question, the movements of six neighboring white-faced capuchin (Cebus capucinus) social groups living on Barro Colorado Island, Panama were tracked simultaneously using an Automated Radio Telemetry System (ARTS), for a period of six months. Groups moved 13% (441 m) further on days they lost interactions compared with days they won interactions. To cover these larger distances, they traveled faster, stopped less frequently, and remained active later in the evening. Defeat also caused groups to alter their patterns of space use. Losing groups had straighter travel paths than winning groups, larger net displacements and were more likely to change their sleeping site. These results demonstrate that losing groups pay increased travel costs and suggest that they forage in low-quality areas. They provide some of the first direct evidence that intergroup conflicts have important energetic consequences for members of competitively unsuccessful primate social groups. A better understanding of how intergroup competition impacts patterns of individual fitness is thus needed to clarify the role that this group-level process plays in shaping the evolution of human- and non-human primate behavior.

  11. Booze, Bars, and Bystander Behavior: People who Consumed Alcohol Help Faster in the Presence of Others.

    Directory of Open Access Journals (Sweden)

    Marco eVan Bommel

    2016-02-01

    Full Text Available People help each other less often and less quickly when bystanders are present. In this paper, we propose that alcohol consumption could attenuate or reverse this so-called bystander effect. Alcohol impairs people cognitively and perceptually, leading them to think less about the presence of others and behave less inhibited. Moreover, alcohol makes people more prone to see the benefits of helping and not the costs. To provide an initial test of these lines of reasoning, we invited visitors of bars in Amsterdam to join our study at a secluded spot at the bar. We manipulated bystander presence, and at the end of the study, we measured alcohol consumption. When participants took their seats, the experimenter dropped some items. We measured how many items were picked up and how quickly participants engaged in helping. Results revealed that alcohol did not influence the bystander effect in terms of the amount of help given. But importantly, it did influence the bystander effect in terms of response times: People who consumed alcohol actually came to aid faster in the presence of others.

  12. Hippocampal Brain Volume Is Associated with Faster Facial Emotion Identification in Older Adults: Preliminary Results.

    Science.gov (United States)

    Szymkowicz, Sarah M; Persson, Jonas; Lin, Tian; Fischer, Håkan; Ebner, Natalie C

    2016-01-01

    Quick correct identification of facial emotions is highly relevant for successful social interactions. Research suggests that older, compared to young, adults experience increased difficulty with face and emotion processing skills. While functional neuroimaging studies suggest age differences in neural processing of faces and emotions, evidence about age-associated structural brain changes and their involvement in face and emotion processing is scarce. Using structural magnetic resonance imaging (MRI), this study investigated the extent to which volumes of frontal and temporal brain structures were related to reaction time in accurate identification of facial emotions in 30 young and 30 older adults. Volumetric segmentation was performed using FreeSurfer and gray matter volumes from frontal and temporal regions were extracted. Analysis of covariances (ANCOVAs) models with response time (RT) as the dependent variable and age group and regional volume, and their interaction, as independent variables were conducted, controlling for total intracranial volume (ICV). Results indicated that, in older adults, larger hippocampal volumes were associated with faster correct facial emotion identification. These preliminary observations suggest that greater volume in brain regions associated with face and emotion processing contributes to improved facial emotion identification performance in aging.

  13. Faster poleward range shifts in moths with more variable colour patterns

    Science.gov (United States)

    Forsman, Anders; Betzholtz, Per-Eric; Franzén, Markus

    2016-11-01

    Range shifts have been documented in many organisms, and climate change has been implicated as a contributing driver of latitudinal and altitudinal range modifications. However, little is known about what species trait(s) allow for faster environmental tracking and improved capacity for distribution expansions. We used data for 416 species of moths, and show that range limits in Sweden have shifted to the north by on average 52.4 km per decade between 1973 and 2014. When also including non-expanding species, average expansion rate was 23.2 km per decade. The rate of boundary shifts increased with increasing levels of inter-individual variation in colour patterns and decreased with increasing latitude. The association with colour patterns indicate that variation in this functionally important trait enables species to cope with novel and changing conditions. Northern range limits also increased with average abundance and decreased with increasing year-to-year abundance fluctuations, implicating production of dispersers as a driver of range dynamics. Studies of terrestrial animals show that rates of poleward shifts differ between taxonomic groups, increase over time, and depend on study duration and latitude. Knowledge of how distribution shifts change with time, location, and species characteristics may improve projections of responses to climate change and aid the protection of biodiversity.

  14. Booze, Bars, and Bystander Behavior: People Who Consumed Alcohol Help Faster in the Presence of Others.

    Science.gov (United States)

    van Bommel, Marco; van Prooijen, Jan-Willem; Elffers, Henk; Van Lange, Paul A M

    2016-01-01

    People help each other less often and less quickly when bystanders are present. In this paper, we propose that alcohol consumption could attenuate or reverse this so-called bystander effect. Alcohol impairs people cognitively and perceptually, leading them to think less about the presence of others and behave less inhibited. Moreover, alcohol makes people more prone to see the benefits of helping and not the costs. To provide an initial test of these lines of reasoning, we invited visitors of bars in Amsterdam to join our study at a secluded spot at the bar. We manipulated bystander presence, and at the end of the study, we measured alcohol consumption. When participants took their seats, the experimenter dropped some items. We measured how many items were picked up and how quickly participants engaged in helping. Results revealed that alcohol did not influence the bystander effect in terms of the amount of help given. But importantly, it did influence the bystander effect in terms of response times: people who consumed alcohol actually came to aid faster in the presence of others.

  15. Decadally cycling soil carbon is more sensitive to warming than faster-cycling soil carbon.

    Science.gov (United States)

    Lin, Junjie; Zhu, Biao; Cheng, Weixin

    2015-12-01

    The response of soil organic carbon (SOC) pools to globally rising surface temperature crucially determines the feedback between climate change and the global carbon cycle. However, there is a lack of studies investigating the temperature sensitivity of decomposition for decadally cycling SOC which is the main component of total soil carbon stock and the most relevant to global change. We tackled this issue using two decadally (13) C-labeled soils and a much improved measuring system in a long-term incubation experiment. Results indicated that the temperature sensitivity of decomposition for decadally cycling SOC (>23 years in one soil and >55 years in the other soil) was significantly greater than that for faster-cycling SOC (<23 or 55 years) or for the entire SOC stock. Moreover, decadally cycling SOC contributed substantially (35-59%) to the total CO2 loss during the 360-day incubation. Overall, these results indicate that the decomposition of decadally cycling SOC is highly sensitive to temperature change, which will likely make this large SOC stock vulnerable to loss by global warming in the 21st century and beyond.

  16. Real-time 3D medical structure segmentation using fast evolving active contours

    Science.gov (United States)

    Wang, Xiaotao; Wang, Qiang; Hao, Zhihui; Xu, Kuanhong; Guo, Ping; Ren, Haibing; Jang, Wooyoung; Kim, Jung-bae

    2014-03-01

    Segmentation of 3D medical structures in real-time is an important as well as intractable problem for clinical applications due to the high computation and memory cost. We propose a novel fast evolving active contour model in this paper to reduce the requirements of computation and memory. The basic idea is to evolve the brief represented dynamic contour interface as far as possible per iteration. Our method encodes zero level set via a single unordered list, and evolves the list recursively by adding activated adjacent neighbors to its end, resulting in active parts of the zero level set moves far enough per iteration along with list scanning. To guarantee the robustness of this process, a new approximation of curvature for integer valued level set is proposed as the internal force to penalize the list smoothness and restrain the list continual growth. Besides, list scanning times are also used as an upper hard constraint to control the list growing. Together with the internal force, efficient regional and constrained external forces, whose computations are only performed along the unordered list, are also provided to attract the list toward object boundaries. Specially, our model calculates regional force only in a narrowband outside the zero level set and can efficiently segment multiple regions simultaneously as well as handle the background with multiple components. Compared with state-of-the-art algorithms, our algorithm is one-order of magnitude faster with similar segmentation accuracy and can achieve real-time performance for the segmentation of 3D medical structures on a standard PC.

  17. How well will stacked transgenic pest/herbicide resistances delay pests from evolving resistance?

    Science.gov (United States)

    Gressel, Jonathan; Gassmann, Aaron J; Owen, Micheal Dk

    2017-01-01

    Resistance has evolved to single transgenic traits engineered into crops for arthropod and herbicide resistances, and can be expected to evolve to the more recently introduced pathogen resistances. Combining transgenes against the same target pest is being promoted as the solution to the problem. This solution will work if used pre-emptively, but where resistance has evolved to one member of a stack, resistance should easily evolve for the second gene in most cases. We propose and elaborate criteria that could be used to evaluate the value of stacked traits for pest resistance management. Stacked partners must: target the same pest species; be in a tandem construct to preclude segregation; be synchronously expressed in the same tissues; have similar tissue persistence; target pest species that are still susceptible to at least two stacked partners. Additionally, transgene products must not be degraded in the same manner, and there should be a lack of cross-resistance to stacked transgenes or to their products. With stacked herbicide resistance transgenes, both herbicides must be used and have the same persistence. If these criteria are followed, and integrated with other pest management practices, resistance may be considerably delayed. © 2016 Society of Chemical Industry.

  18. Faster, better, and cheaper” at NASA: Lessons learned in managing and accepting risk

    Science.gov (United States)

    Paxton, Larry J.

    2007-11-01

    Can Earth observing missions be done "better, faster and cheaper"? In this paper I explore the management and technical issues that arose from the attempt to do things "faster, better and cheaper" at NASA. The FBC mantra lead to some failures and, more significantly, an increase in the cadence of missions. Mission cadence is a major enabler of innovation and the driver for the training and testing of the next generation of managers, engineers, and scientists. A high mission cadence is required to maintain and develop competence in mission design, management, and execution and, for an exploration-driven organization, to develop and train the next generation of leaders: the time between missions must be short enough that careers span the complete life of more than a few missions. This process reduces risk because the "lessons learned" are current and widely held. Increasing the cadence of missions has the added benefit of reducing the pressure to do everything on one particular mission thus reducing mission complexity. Since failures are inevitable in such a complex endeavor, a higher mission cadence has the advantage of providing some resiliency to the scientific program the missions support. Some failures are avoidable (often only in hindsight) but most are due to some combination of interacting factors. This interaction is often only appreciated as a potential failure mode after the fact. There is always the pressure to do more with less: the scope of the project may become too ambitious or the management and oversight of the project may be reduced to fit the money allocated, or the project time line may be lengthened due to external factors (launcher availability, budgetary constraints) without a concomitant increase in the total funding. This leads to increased risk. Risks are always deemed acceptable until they change from a "risk" to a "failure mode". Identifying and managing those risks are particularly difficult when the activities are dispersed

  19. Faster but Less Careful Prehension in Presence of High, Rather than Low, Social Status Attendees.

    Directory of Open Access Journals (Sweden)

    Carlo Fantoni

    Full Text Available Ample evidence attests that social intention, elicited through gestures explicitly signaling a request of communicative intention, affects the patterning of hand movement kinematics. The current study goes beyond the effect of social intention and addresses whether the same action of reaching to grasp an object for placing it in an end target position within or without a monitoring attendee's peripersonal space, can be moulded by pure social factors in general, and by social facilitation in particular. A motion tracking system (Optotrak Certus was used to record motor acts. We carefully avoided the usage of communicative intention by keeping constant both the visual information and the positional uncertainty of the end target position, while we systematically varied the social status of the attendee (a high, or a low social status in separated blocks. Only thirty acts performed in the presence of a different social status attendee, revealed a significant change of kinematic parameterization of hand movement, independently of the attendee's distance. The amplitude of peak velocity reached by the hand during the reach-to-grasp and the lift-to-place phase of the movement was larger in the high rather than in the low social status condition. By contrast, the deceleration time of the reach-to-grasp phase and the maximum grasp aperture was smaller in the high rather than in the low social status condition. These results indicated that the hand movement was faster but less carefully shaped in presence of a high, but not of a low social status attendee. This kinematic patterning suggests that being monitored by a high rather than a low social status attendee might lead participants to experience evaluation apprehension that informs the control of motor execution. Motor execution would rely more on feedforward motor control in the presence of a high social status human attendee, vs. feedback motor control, in the presence of a low social status attendee.

  20. Automated PDF highlighting to support faster curation of literature for Parkinson's and Alzheimer's disease.

    Science.gov (United States)

    Wu, Honghan; Oellrich, Anika; Girges, Christine; de Bono, Bernard; Hubbard, Tim J P; Dobson, Richard J B

    2017-01-01

    Neurodegenerative disorders such as Parkinson's and Alzheimer's disease are devastating and costly illnesses, a source of major global burden. In order to provide successful interventions for patients and reduce costs, both causes and pathological processes need to be understood. The ApiNATOMY project aims to contribute to our understanding of neurodegenerative disorders by manually curating and abstracting data from the vast body of literature amassed on these illnesses. As curation is labour-intensive, we aimed to speed up the process by automatically highlighting those parts of the PDF document of primary importance to the curator. Using techniques similar to those of summarisation, we developed an algorithm that relies on linguistic, semantic and spatial features. Employing this algorithm on a test set manually corrected for tool imprecision, we achieved a macro F 1 -measure of 0.51, which is an increase of 132% compared to the best bag-of-words baseline model. A user based evaluation was also conducted to assess the usefulness of the methodology on 40 unseen publications, which reveals that in 85% of cases all highlighted sentences are relevant to the curation task and in about 65% of the cases, the highlights are sufficient to support the knowledge curation task without needing to consult the full text. In conclusion, we believe that these are promising results for a step in automating the recognition of curation-relevant sentences. Refining our approach to pre-digest papers will lead to faster processing and cost reduction in the curation process. https://github.com/KHP-Informatics/NapEasy.

  1. Faster onset of action with topical levocabastine than with oral cetirizine

    Directory of Open Access Journals (Sweden)

    Michel A. Drouin

    1995-01-01

    Full Text Available This international multicentre, open-label, parallel-group trial was undertaken to compare the therapeutic efficacy and tolerability of topical levocabastine and oral cetirizine in patients with perennial allergic rhinoconjunctivitis, with particular reference to the comparative onset of action of the two drugs. A total of 207 patients were randomized to receive either levocabastine nasal spray (0.5 mg/ml, two sprays in each nostril twice daily plus levocabastine eye drops as required (0.5 mg/ml, one drop in each eye twice daily p.r.n. or cetirizine orally (10 mg once daily with a treatment duration of 2 weeks. Onset of action was found to be significantly more rapid with levocabastine than with cetirizine for both nasal and ocular symptoms (p < 0.001. Within 15 min of study drug administration, 36% of levocabastine-treated patients reported relief from nasal symptoms and 32% relief from ocular symptoms compared with 10% and 17% of patients on cetirizine, respectively. At 1 h, the percentages of patients reporting relief were 76% and 38% for nasal symptoms, and 81% and 48% for ocular symptoms in the levocabastine and cetirizine treatment groups, respectively. At 8 h there were no differences between the two treatments. Overall therapeutic efficacy was found to be comparable in the two treatment groups over the 2-week study period with no significant intergroup differences in symptom severity or global therapeutic efficacy. Both drugs were well tolerated with no significant differences in the incidence or type of adverse reactions between the two groups. In conclusion, levocabastine eye drops and nasal spray are as effective and well tolerated as oral cetirizine for the treatment of perennial allergic rhinoconjunctivitis with the advantage of a significantly faster onset of action for both nasal and ocular symptoms.

  2. Slower Perception Followed by Faster Lexical Decision in Longer Words: A Diffusion Model Analysis.

    Science.gov (United States)

    Oganian, Yulia; Froehlich, Eva; Schlickeiser, Ulrike; Hofmann, Markus J; Heekeren, Hauke R; Jacobs, Arthur M

    2015-01-01

    Effects of stimulus length on reaction times (RTs) in the lexical decision task are the topic of extensive research. While slower RTs are consistently found for longer pseudo-words, a finding coined the word length effect (WLE), some studies found no effects for words, and yet others reported faster RTs for longer words. Moreover, the WLE depends on the orthographic transparency of a language, with larger effects in more transparent orthographies. Here we investigate processes underlying the WLE in lexical decision in German-English bilinguals using a diffusion model (DM) analysis, which we compared to a linear regression approach. In the DM analysis, RT-accuracy distributions are characterized using parameters that reflect latent sub-processes, in particular evidence accumulation and decision-independent perceptual encoding, instead of typical parameters such as mean RT and accuracy. The regression approach showed a decrease in RTs with length for pseudo-words, but no length effect for words. However, DM analysis revealed that the null effect for words resulted from opposing effects of length on perceptual encoding and rate of evidence accumulation. Perceptual encoding times increased with length for words and pseudo-words, whereas the rate of evidence accumulation increased with length for real words but decreased for pseudo-words. A comparison between DM parameters in German and English suggested that orthographic transparency affects perceptual encoding, whereas effects of length on evidence accumulation are likely to reflect contextual information and the increase in available perceptual evidence with length. These opposing effects may account for the inconsistent findings on WLEs.

  3. Slower perception followed by faster lexical decision in longer words: a diffusion model analysis

    Directory of Open Access Journals (Sweden)

    Yulia eOganian

    2016-01-01

    Full Text Available Effects of stimulus length on reaction times (RTs in the lexical decision task are the topic of extensive research. While slower RTs are consistently found for longer pseudo-words, a finding coined the word length effect (WLE, some studies found no effects for words, and yet others reported faster RTs for longer words. Moreover, the WLE depends on the orthographic transparency of a language, with larger effects in more transparent orthographies. Here we investigate processes underlying the WLE in lexical decision in German-English bilinguals using a diffusion model (DM analysis, which we compared to a linear regression approach. In the DM analysis, RT-accuracy distributions are characterized using parameters that reflect latent sub-processes, in particular evidence accumulation and decision-independent perceptual encoding, instead of typical parameters such as mean RT and accuracy. The regression approach showed a decrease in RTs with length for pseudo-words, but no length effect for words. However, DM analysis revealed that the null effect for words resulted from opposing effects of length on perceptual encoding and rate of evidence accumulation. Perceptual encoding times increased with length for words and pseudo-words, whereas the rate of evidence accumulation increased with length for real words but decreased for pseudo-words. A comparison between DM parameters in German and English suggested that orthographic transparency affects perceptual encoding, whereas effects of length on evidence accumulation are likely to reflect contextual information and the increase in available perceptual evidence with length. These opposing effects may account for the inconsistent findings on word length effects.

  4. Natural enemies act faster than endophytic fungi in population control of cereal aphids.

    Science.gov (United States)

    Härri, Simone A; Krauss, Jochen; Müller, Christine B

    2008-05-01

    1. Fast-growing populations of phytophagous insects can be limited by the presence of natural enemies and by alkaloids that are produced by symbiotic associations of many temperate grass species with endophytic fungi. It is unclear if and how acquired plant defences derived from endophytic fungi interact with natural enemies to affect phytophagous insect populations. 2. To assess the relative importance of endophytic fungi compared to that of natural enemies on the population dynamics of phytophagous insects, we carried out a fully factorial field experiment, in which the presence of natural enemies and the presence of endophytic fungi were manipulated simultaneously. Target colonies of aphids were monitored for 8 weeks starting from their natural appearance in the field to the end of the aphid season. 3. We show that on Lolium perenne increased natural enemy densities reduced the individual numbers of two common cereal aphids, Rhopalosiphum padi and Metopolophium festucae. 4. The presence of the endophytic fungi Neotyphodium lolii reduced the number of M. festucae but did not affect the number of R. padi. The reduction in R. padi numbers by predators and parasitoids was not influenced by the presence of endophytes. For adult M. festucae, however, the negative effects of natural enemies were significant only in the absence of endophytes. 5. Over the duration of the experiment, the effect of natural enemies on aphid colony growth was much stronger than the effect of the endophytic fungi N. lolii, presumably because predator and parasitoid action on aphid colonies is much faster than any effects of endophytes. 6. Our results demonstrate that with simultaneous action of acquired endosymbionts and natural enemies, both factors can control aphid colony growth but they generally act independently of each other.

  5. Faster oxygen atom transfer catalysis with a tungsten dioxo complex than with its molybdenum analog.

    Science.gov (United States)

    Arumuganathan, T; Mayilmurugan, Ramasamy; Volpe, Manuel; Mösch-Zanetti, Nadia C

    2011-08-21

    The synthesis and characterization of a series of molybdenum ([MoO(2)Cl(L(n))]; L(1) (1), L(2) (3)) and tungsten ([WO(2)Cl(L(n))]; L(1) (2), L(2) (4)) dioxo complexes (L(1) = 1-methyl-4-(2-hydroxybenzyl)-1,4-diazepane and L(2) = 1-methyl-4-(2-hydroxy-3,5-di-tert-butylbenzyl)-1,4-diazepane) of tridentate aminomonophenolate ligands HL(1) and HL(2) are reported. The ligands were obtained by reductive amination of 1-methyl-1,4-diazepane with the corresponding aldehyde. Complexes 3 and 4 were obtained by the reaction of [MO(2)Cl(2)(dme)(n)] (M = Mo, n = 0; W, n = 1) with the corresponding ligand in presence of a base, whereas for the preparation of 1 and 2 the ligands were deprotonated by KH prior to the addition to the metal. They were characterized by NMR and IR spectroscopy, by cyclic voltammetry, mass spectrometry, elemental analysis and by single-crystal X-ray diffraction analysis. Solid-state structures of the molybdenum and tungsten cis-dioxo complexes reveal hexa-coordinate metal centers surrounded by two oxo groups, a chloride ligand and by the tridentate monophenolate ligand which coordinates meridionally through its [ONN] donor set. In the series of compounds 1-4, complexes 3 and 4 have been used as catalysts for the oxygen atom transfer reaction between dimethyl sulfoxide (DMSO) and trimethyl phosphine (PMe(3)). Surprisingly, faster oxygen atom transfer (OAT) reactivity has been observed for the tungsten complex [WO(2)Cl(L(2))] (4) in comparison to its molybdenum analog [MoO(2)Cl(L(2))] (3) at room temperature. The kinetic results are discussed and compared in terms of their reactivity. This journal is © The Royal Society of Chemistry 2011

  6. A new concept in orthodontics: faster and healthier tooth movement by regularly consuming xyilitol chewing gum

    Directory of Open Access Journals (Sweden)

    Haryono Utomo

    2007-12-01

    Full Text Available Xylitol was first discovered in the 19th century, it wasn’t until the 1960’s that commercial production was first implemented. Recent studies showed that xylitol chewing gum is beneficial for preventing caries and periodontal disease. Therefore, it is also advantageous for orthodontic treatment, especially the fixed orthodontics patients who have difficulties in acquiring optimal oral health, particularly periodontal health which important in remodeling. However, how consuming xylitol chewing gum may stimulate tooth movement and preventing root resorption is still unclear. It is suggested that chewing activities may stimulate tooth movement, since jaw hypofunction leads to lower mineral apposition and bone function; and narrow periodontal ligament (PDL. These conditions may lead to impaired remodeling process, and increases the susceptibility of root resorption during orthodontic tooth movement. Moreover, since stimulation of the PDL could be mechanoreceptive (i.e. chewing action or nociceptive (i.e. painful stimulation, periodontal nerve fibers are supposed to play an important role in bone remodeling. It is supported by a study which revealed that during tooth movement, the galanin-containing immunoreactive nerve fibers, a part of primary sensory neurons in the PDL is increasing. Galanin is able to induce osteoclast differentiation that needed for bone resorption in orthodontic treatment. The objective of this study is to elucidate a new concept in using xylitol chewing gum as an excellent media to have a faster and healthier orthodontic movement. Since continuous chewing stimulates the PDL which enhances tooth movement, improves oral health, and prevents root resorption; it is concluded that this concept is possible.

  7. Self-control forecasts better psychosocial outcomes but faster epigenetic aging in low-SES youth.

    Science.gov (United States)

    Miller, Gregory E; Yu, Tianyi; Chen, Edith; Brody, Gene H

    2015-08-18

    There are persistent socioeconomic disparities in many aspects of child development in America. Relative to their affluent peers, children of low socioeconomic status (SES) complete fewer years of education, have a higher prevalence of health problems, and are convicted of more criminal offenses. Based on research indicating that low self-control underlies some of these disparities, policymakers have begun incorporating character-skills training into school curricula and social services. However, emerging data suggest that for low-SES youth, self-control may act as a "double-edged sword," facilitating academic success and psychosocial adjustment, while at the same time undermining physical health. Here, we examine this hypothesis in a five-wave study of 292 African American teenagers from rural Georgia. From ages 17 to 20 y, we assessed SES and self-control annually, along with depressive symptoms, substance use, aggressive behavior, and internalizing problems. At age 22 y, we obtained DNA methylation profiles of subjects' peripheral blood mononuclear cells. These data were used to measure epigenetic aging, a methylation-derived biomarker reflecting the disparity between biological and chronological aging. Among high-SES youth, better mid-adolescent self-control presaged favorable psychological and methylation outcomes. However, among low-SES youth, self-control had divergent associations with these outcomes. Self-control forecasted lower rates of depressive symptoms, substance use, aggressive behavior, and internalizing problems but faster epigenetic aging. These patterns suggest that for low-SES youth, resilience is a "skin-deep" phenomenon, wherein outward indicators of success can mask emerging problems with health. These findings have conceptual implications for models of resilience, and practical implications for interventions aimed at ameliorating social and racial disparities.

  8. Computing exponentially faster: implementing a non-deterministic universal Turing machine using DNA.

    Science.gov (United States)

    Currin, Andrew; Korovin, Konstantin; Ababi, Maria; Roper, Katherine; Kell, Douglas B; Day, Philip J; King, Ross D

    2017-03-01

    The theory of computer science is based around universal Turing machines (UTMs): abstract machines able to execute all possible algorithms. Modern digital computers are physical embodiments of classical UTMs. For the most important class of problem in computer science, non-deterministic polynomial complete problems, non-deterministic UTMs (NUTMs) are theoretically exponentially faster than both classical UTMs and quantum mechanical UTMs (QUTMs). However, no attempt has previously been made to build an NUTM, and their construction has been regarded as impossible. Here, we demonstrate the first physical design of an NUTM. This design is based on Thue string rewriting systems, and thereby avoids the limitations of most previous DNA computing schemes: all the computation is local (simple edits to strings) so there is no need for communication, and there is no need to order operations. The design exploits DNA's ability to replicate to execute an exponential number of computational paths in P time. Each Thue rewriting step is embodied in a DNA edit implemented using a novel combination of polymerase chain reactions and site-directed mutagenesis. We demonstrate that the design works using both computational modelling and in vitro molecular biology experimentation: the design is thermodynamically favourable, microprogramming can be used to encode arbitrary Thue rules, all classes of Thue rule can be implemented, and non-deterministic rule implementation. In an NUTM, the resource limitation is space, which contrasts with classical UTMs and QUTMs where it is time. This fundamental difference enables an NUTM to trade space for time, which is significant for both theoretical computer science and physics. It is also of practical importance, for to quote Richard Feynman 'there's plenty of room at the bottom'. This means that a desktop DNA NUTM could potentially utilize more processors than all the electronic computers in the world combined, and thereby outperform the world

  9. Responses of cardiac natriuretic peptides after paroxysmal supraventricular tachycardia: ANP surges faster than BNP and CNP.

    Science.gov (United States)

    Kuo, Jen-Yuan; Wang, An-Mei; Chang, Sheng-Hsiung; Hung, Chung-Lieh; Chen, Chun-Yen; Shih, Bing-Fu; Yeh, Hung-I

    2016-03-15

    Atrial natriuretic peptide (ANP) secretion increases after 30 min of paroxysmal supraventricular tachycardia (PSVT). Whether this phenomenon also applies to brain or C-type natriuretic peptides (BNP or CNP) remains unknown. Blood samples of 18 patients (41 ± 11 yr old; 4 men) with symptomatic PSVT and normal left ventricular systolic function (ejection fraction 65 ± 6%) were collected from the coronary sinus (CS) and the femoral artery (FA) before and 30 min after the induction, and 30 min after the termination of PSVT. The results showed that the ANP levels rose steeply after the PSVT and then reduced at 30 min after the termination (baseline vs. post-PSVT vs. posttermination: CS: 34.0 ± 29.6 vs. 74.1 ± 42.3 vs. 46.1 ± 32.9; FA: 5.9 ± 3.24 vs. 28.2 ± 20.7 vs. 10.0 ± 4.6 pg/ml; all P tachycardia (BNP, 10.2 ± 6.4 vs. 11.3 ± 7.1 vs. 11.8 ± 7.9; CNP, 4.5 ± 1.2 vs. 4.9 ± 1.4 vs. 5.0 ± 1.4 pg/ml; all P < 0.05). The rise of BNP and CNP in FA was similarly less sharp after the PSVT and remained stationary after the termination. PSVT exerted differential effects on cardiac natriuretic peptide levels. ANP increased greater after a 30-min induced PSVT, but dropped faster after termination of PSVT, compared with BNP and CNP.

  10. Faster diffraction-based overlay measurements with smaller targets using 3D gratings

    Science.gov (United States)

    Li, Jie; Kritsun, Oleg; Liu, Yongdong; Dasari, Prasad; Volkman, Catherine; Hu, Jiangtao

    2012-03-01

    Diffraction-based overlay (DBO) technologies have been developed to address the overlay metrology challenges for 22nm technology node and beyond. Most DBO technologies require specially designed targets that consist of multiple measurement pads, which consume too much space and increase measurement time. The traditional empirical approach (eDBO) using normal incidence spectroscopic reflectometry (NISR) relies on linear response of the reflectance with respect to overlay displacement within a small range. It offers convenience of quick recipe setup since there is no need to establish a model. However it requires three or four pads per direction (x or y) which adds burden to throughput and target size. Recent advances in modeling capability and computation power enabled mDBO, which allows overlay measurement with reduced number of pads, thus reducing measurement time and DBO target space. In this paper we evaluate the performance of single pad mDBO measurements using two 3D targets that have different grating shapes: squares in boxes and L-shapes in boxes. Good overlay sensitivities are observed for both targets. The correlation to programmed shifts and image-based overlay (IBO) is excellent. Despite the difference in shapes, the mDBO results are comparable for square and L-shape targets. The impact of process variations on overlay measurements is studied using a focus and exposure matrix (FEM) wafer. Although the FEM wafer has larger process variations, the correlation of mDBO results with IBO measurements is as good as the normal process wafer. We demonstrate the feasibility of single pad DBO measurements with faster throughput and smaller target size, which is particularly important in high volume manufacturing environment.

  11. Action-effect congruence during observational learning leads to faster action sequence learning.

    Science.gov (United States)

    Horvath, Jared C; Gray, Zachary; Schilberg, Lukas; Vidrin, Ilya; Pascual-Leone, Alvaro

    2015-01-01

    Common coding theory suggests that any action (pressing a piano key) is intimately linked with its resultant sensory effect (an auditory musical tone). We conducted two experiments to explore the effect of varying auditory action-effect patterns during complex action learning. In Experiment 1, participants were assigned to 1 of 4 groups, watched a silent video of a hand playing a sequence on a piano keyboard with no auditory action effect (observation) and were asked to practise and perform the sequence on an identical keyboard with varying action effects (reproduction). During reproduction, Group 1 heard no auditory tones (identical to observed video), Group 2 heard typical scale-ascending piano tones with each key press, Group 3 heard fixed but out-of-sequence piano tones with each key press, and Group 4 heard random piano tones with each key press. In Experiment two, new participants were assigned to 1 of 2 groups and watched an identical video; however, the video in this experiment contained typical, scale-ascending piano sounds. During reproduction, Group 1 heard no auditory tones while Group 2 heard typical, scale-ascending piano tones with each key press (identical to observed video). Our results showed that participants whose action-effect patterns during reproduction matched those in the observed video learned the action sequence faster than participants whose action-effect patterns during reproduction differed from those in the observed video. Additionally, our results suggest that adding an effect during reproduction (when one is absent during observation) is somewhat more detrimental to action sequence learning than removing an effect during reproduction (when one is present during observation).

  12. Faster processing of multiple spatially-heterodyned direct to digital holograms

    Science.gov (United States)

    Hanson, Gregory R [Clinton, TN; Bingham, Philip R [Knoxville, TN

    2008-09-09

    Systems and methods are described for faster processing of multiple spatially-heterodyned direct to digital holograms. A method includes of obtaining multiple spatially-heterodyned holograms, includes: digitally recording a first spatially-heterodyned hologram including spatial heterodyne fringes for Fourier analysis; digitally recording a second spatially-heterodyned hologram including spatial heterodyne fringes for Fourier analysis; Fourier analyzing the recorded first spatially-heterodyned hologram by shifting a first original origin of the recorded first spatially-heterodyned hologram including spatial heterodyne fringes in Fourier space to sit on top of a spatial-heterodyne carrier frequency defined as a first angle between a first reference beam and a first object beam; applying a first digital filter to cut off signals around the first original origin and performing an inverse Fourier transform on the result; Fourier analyzing the recorded second spatially-heterodyned hologram by shifting a second original origin of the recorded second spatially-heterodyned hologram including spatial heterodyne fringes in Fourier space to sit on top of a spatial-heterodyne carrier frequency defined as a second angle between a second reference beam and a second object beam; and applying a second digital filter to cut off signals around the second original origin and performing an inverse Fourier transform on the result, wherein digitally recording the first spatially-heterodyned hologram is completed before digitally recording the second spatially-heterodyned hologram and a single digital image includes both the first spatially-heterodyned hologram and the second spatially-heterodyned hologram.

  13. Faster Synthesis of Beta-Diketonate Ternary Europium Complexes: Elapsed Times & Reaction Yields

    Science.gov (United States)

    Lima, Nathalia B. D.; Silva, Anderson I. S.; Gerson, P. C.; Gonçalves, Simone M. C.; Simas, Alfredo M.

    2015-01-01

    β-diketonates are customary bidentate ligands in highly luminescent ternary europium complexes, such as Eu(β-diketonate)3(L)2, where L stands for a nonionic ligand. Usually, the syntheses of these complexes start by adding, to an europium salt such as EuCl3(H2O)6, three equivalents of β-diketonate ligands to form the complexes Eu(β-diketonate)3(H2O)2. The nonionic ligands are subsequently added to form the target complexes Eu(β-diketonate)3(L)2. However, the Eu(β-diketonate)3(H2O)2 intermediates are frequently both difficult and slow to purify by recrystallization, a step which usually takes a long time, varying from days to several weeks, depending on the chosen β-diketonate. In this article, we advance a novel synthetic technique which does not use Eu(β-diketonate)3(H2O)2 as an intermediate. Instead, we start by adding 4 equivalents of a monodentate nonionic ligand L straight to EuCl3(H2O)6 to form a new intermediate: EuCl3(L)4(H2O)n, with n being either 3 or 4. The advantage is that these intermediates can now be easily, quickly, and efficiently purified. The β-diketonates are then carefully added to this intermediate to form the target complexes Eu(β-diketonate)3(L)2. For the cases studied, the 20-day average elapsed time reduced to 10 days for the faster synthesis, together with an improvement in the overall yield from 42% to 69%. PMID:26710103

  14. Computing exponentially faster: implementing a non-deterministic universal Turing machine using DNA

    Science.gov (United States)

    Currin, Andrew; Korovin, Konstantin; Ababi, Maria; Roper, Katherine; Kell, Douglas B.; Day, Philip J.

    2017-01-01

    The theory of computer science is based around universal Turing machines (UTMs): abstract machines able to execute all possible algorithms. Modern digital computers are physical embodiments of classical UTMs. For the most important class of problem in computer science, non-deterministic polynomial complete problems, non-deterministic UTMs (NUTMs) are theoretically exponentially faster than both classical UTMs and quantum mechanical UTMs (QUTMs). However, no attempt has previously been made to build an NUTM, and their construction has been regarded as impossible. Here, we demonstrate the first physical design of an NUTM. This design is based on Thue string rewriting systems, and thereby avoids the limitations of most previous DNA computing schemes: all the computation is local (simple edits to strings) so there is no need for communication, and there is no need to order operations. The design exploits DNA's ability to replicate to execute an exponential number of computational paths in P time. Each Thue rewriting step is embodied in a DNA edit implemented using a novel combination of polymerase chain reactions and site-directed mutagenesis. We demonstrate that the design works using both computational modelling and in vitro molecular biology experimentation: the design is thermodynamically favourable, microprogramming can be used to encode arbitrary Thue rules, all classes of Thue rule can be implemented, and non-deterministic rule implementation. In an NUTM, the resource limitation is space, which contrasts with classical UTMs and QUTMs where it is time. This fundamental difference enables an NUTM to trade space for time, which is significant for both theoretical computer science and physics. It is also of practical importance, for to quote Richard Feynman ‘there's plenty of room at the bottom’. This means that a desktop DNA NUTM could potentially utilize more processors than all the electronic computers in the world combined, and thereby outperform the world

  15. Faster but Less Careful Prehension in Presence of High, Rather than Low, Social Status Attendees.

    Science.gov (United States)

    Fantoni, Carlo; Rigutti, Sara; Piccoli, Valentina; Sommacal, Elena; Carnaghi, Andrea

    2016-01-01

    Ample evidence attests that social intention, elicited through gestures explicitly signaling a request of communicative intention, affects the patterning of hand movement kinematics. The current study goes beyond the effect of social intention and addresses whether the same action of reaching to grasp an object for placing it in an end target position within or without a monitoring attendee's peripersonal space, can be moulded by pure social factors in general, and by social facilitation in particular. A motion tracking system (Optotrak Certus) was used to record motor acts. We carefully avoided the usage of communicative intention by keeping constant both the visual information and the positional uncertainty of the end target position, while we systematically varied the social status of the attendee (a high, or a low social status) in separated blocks. Only thirty acts performed in the presence of a different social status attendee, revealed a significant change of kinematic parameterization of hand movement, independently of the attendee's distance. The amplitude of peak velocity reached by the hand during the reach-to-grasp and the lift-to-place phase of the movement was larger in the high rather than in the low social status condition. By contrast, the deceleration time of the reach-to-grasp phase and the maximum grasp aperture was smaller in the high rather than in the low social status condition. These results indicated that the hand movement was faster but less carefully shaped in presence of a high, but not of a low social status attendee. This kinematic patterning suggests that being monitored by a high rather than a low social status attendee might lead participants to experience evaluation apprehension that informs the control of motor execution. Motor execution would rely more on feedforward motor control in the presence of a high social status human attendee, vs. feedback motor control, in the presence of a low social status attendee.

  16. Laplacian Estrada and normalized Laplacian Estrada indices of evolving graphs.

    Directory of Open Access Journals (Sweden)

    Yilun Shang

    Full Text Available Large-scale time-evolving networks have been generated by many natural and technological applications, posing challenges for computation and modeling. Thus, it is of theoretical and practical significance to probe mathematical tools tailored for evolving networks. In this paper, on top of the dynamic Estrada index, we study the dynamic Laplacian Estrada index and the dynamic normalized Laplacian Estrada index of evolving graphs. Using linear algebra techniques, we established general upper and lower bounds for these graph-spectrum-based invariants through a couple of intuitive graph-theoretic measures, including the number of vertices or edges. Synthetic random evolving small-world networks are employed to show the relevance of the proposed dynamic Estrada indices. It is found that neither the static snapshot graphs nor the aggregated graph can approximate the evolving graph itself, indicating the fundamental difference between the static and dynamic Estrada indices.

  17. Laplacian Estrada and normalized Laplacian Estrada indices of evolving graphs.

    Science.gov (United States)

    Shang, Yilun

    2015-01-01

    Large-scale time-evolving networks have been generated by many natural and technological applications, posing challenges for computation and modeling. Thus, it is of theoretical and practical significance to probe mathematical tools tailored for evolving networks. In this paper, on top of the dynamic Estrada index, we study the dynamic Laplacian Estrada index and the dynamic normalized Laplacian Estrada index of evolving graphs. Using linear algebra techniques, we established general upper and lower bounds for these graph-spectrum-based invariants through a couple of intuitive graph-theoretic measures, including the number of vertices or edges. Synthetic random evolving small-world networks are employed to show the relevance of the proposed dynamic Estrada indices. It is found that neither the static snapshot graphs nor the aggregated graph can approximate the evolving graph itself, indicating the fundamental difference between the static and dynamic Estrada indices.

  18. RNA structural analysis by evolving SHAPE chemistry.

    Science.gov (United States)

    Spitale, Robert C; Flynn, Ryan A; Torre, Eduardo A; Kool, Eric T; Chang, Howard Y

    2014-01-01

    RNA is central to the flow of biological information. From transcription to splicing, RNA localization, translation, and decay, RNA is intimately involved in regulating every step of the gene expression program, and is thus essential for health and understanding disease. RNA has the unique ability to base-pair with itself and other nucleic acids to form complex structures. Hence the information content in RNA is not simply its linear sequence of bases, but is also encoded in complex folding of RNA molecules. A general chemical functionality that all RNAs have is a 2'-hydroxyl group in the ribose ring, and the reactivity of the 2'-hydroxyl in RNA is gated by local nucleotide flexibility. In other words, the 2'-hydroxyl is reactive at single-stranded and conformationally flexible positions but is unreactive at nucleotides constrained by base-pairing. Recent efforts have been focused on developing reagents that modify RNA as a function of RNA 2' hydroxyl group reactivity. Such RNA structure probing techniques can be read out by primer extension in experiments termed RNA SHAPE (selective 2'- hydroxyl acylation and primer extension). Herein, we describe the efforts devoted to the design and utilization of SHAPE probes for characterizing RNA structure. We also describe current technological advances that are being applied to utilize SHAPE chemistry with deep sequencing to probe many RNAs in parallel. The merging of chemistry with genomics is sure to open the door to genome-wide exploration of RNA structure and function.

  19. RNA Structural Analysis by Evolving SHAPE Chemistry

    Science.gov (United States)

    Spitale, Robert C.; Flynn, Ryan A.; Torre, Eduardo A.; Kool, Eric T.; Chang, Howard Y.

    2017-01-01

    RNA is central to the flow of biological information. From transcription to splicing, RNA localization, translation, and decay, RNA is intimately involved in regulating every step of the gene expression program, and is thus essential for health and understanding disease. RNA has the unique ability to base-pair with itself and other nucleic acids to form complex structures. Hence the information content in RNA is not simply its linear sequence of bases, but is also encoded in complex folding of RNA molecules. A general chemical functionality that all RNAs have is a 2’-hydroxyl group in the ribose ring, and the reactivity of the 2'-hydroxyl in RNA is gated by local nucleotide flexibility. In other words, the 2'-hydroxyl is reactive at single-stranded and conformationally flexible positions but is unreactive at nucleotides constrained by base pairing. Recent efforts have been focused on developing reagents that modify RNA as a function of RNA 2’ hydroxyl group flexibility. Such RNA structure probing techniques can be read out by primer extension in experiments termed RNA SHAPE (Selective 2’ Hydroxyl Acylation and Primer Extension). Herein we describe the efforts devoted to the design and utilization of SHAPE probes for characterizing RNA structure. We also describe current technological advances that are being used to utilize SHAPE chemistry with deep sequencing to probe many RNAs in parallel. The merger of chemistry with genomics is sure to open the door to genome-wide exploration of RNA structure and function. PMID:25132067

  20. Faster convergence of imaginary time evolution tensor network algorithms by recycling the environment

    CERN Document Server

    Phien, Ho N; Vidal, Guifré

    2014-01-01

    We propose an environment recycling scheme to speed up a class of tensor network algorithms that produce an approximation to the ground state of a local Hamiltonian by simulating an evolution in imaginary time. Specifically, we consider the time-evolving block decimation (TEBD) algorithm applied to infinite systems in 1D and 2D, where the ground state is encoded, respectively, in a matrix product state (MPS) and in a projected entangled-pair state (PEPS). An important ingredient of the TEBD algorithm (and a main computational bottle-neck, especially with PEPS in 2D) is the computation of the so-called environment, which is used to determine how to optimally truncate the bond indices of the tensor network so that their dimension is kept constant. In current algorithms, the environment is computed at each step of the imaginary time evolution, to account for the changes that the time evolution introduces in the many-body state represented by the tensor network. Our key insight is that close to convergence, most ...

  1. Rapid evolution of dispersal ability makes biological invasions faster and more variable

    Science.gov (United States)

    Ochocki, Brad M.; Miller, Tom E. X.

    2017-01-01

    Genetic variation in dispersal ability may result in the spatial sorting of alleles during range expansion. Recent theory suggests that spatial sorting can favour the rapid evolution of life history traits at expanding fronts, and therefore modify the ecological dynamics of range expansion. Here we test this prediction by disrupting spatial sorting in replicated invasions of the bean beetle Callosobruchus maculatus across homogeneous experimental landscapes. We show that spatial sorting promotes rapid evolution of dispersal distance, which increases the speed and variability of replicated invasions: after 10 generations of range expansion, invasions subject to spatial sorting spread 8.9% farther and exhibit 41-fold more variable spread dynamics relative to invasions in which spatial sorting is suppressed. Correspondingly, descendants from spatially evolving invasions exhibit greater mean and variance in dispersal distance. Our results reveal an important role for rapid evolution during invasion, even in the absence of environmental filters, and argue for evolutionarily informed forecasts of invasive spread by exotic species or climate change migration by native species. PMID:28128215

  2. Spiders appear to move faster than non-threatening objects regardless of one's ability to block them.

    Science.gov (United States)

    Witt, Jessica K; Sugovic, Mila

    2013-07-01

    We examined whether perception of a threatening object - a spider - was more accurate than of a non-threatening object. An accurate perception could promote better survival than a biased perception. However, if biases encourage faster responses and more appropriate behaviors, then under the right circumstances, perceptual biases could promote better survival. We found that spiders appeared to be moving faster than balls and ladybugs. Furthermore, the perceiver's ability to act on the object also influenced perceived speed: the object looked faster when it was more difficult to block. Both effects--the threat of the object and the perceiver's blocking abilities--acted independently from each other. The results suggest effects of multiple types of affordances on perception of speed.

  3. NASA's Space Launch System: An Evolving Capability for Exploration An Evolving Capability for Exploration

    Science.gov (United States)

    Creech, Stephen D.; Crumbly, Christopher M.; Robinson, Kimerly F.

    2016-01-01

    A foundational capability for international human deep-space exploration, NASA's Space Launch System (SLS) vehicle represents a new spaceflight infrastructure asset, creating opportunities for mission profiles and space systems that cannot currently be executed. While the primary purpose of SLS, which is making rapid progress towards initial launch readiness in two years, will be to support NASA's Journey to Mars, discussions are already well underway regarding other potential utilization of the vehicle's unique capabilities. In its initial Block 1 configuration, capable of launching 70 metric tons (t) to low Earth orbit (LEO), SLS is capable of propelling the Orion crew vehicle to cislunar space, while also delivering small CubeSat-class spacecraft to deep-space destinations. With the addition of a more powerful upper stage, the Block 1B configuration of SLS will be able to deliver 105 t to LEO and enable more ambitious human missions into the proving ground of space. This configuration offers opportunities for launching co-manifested payloads with the Orion crew vehicle, and a class of secondary payloads, larger than today's CubeSats. Further upgrades to the vehicle, including advanced boosters, will evolve its performance to 130 t in its Block 2 configuration. Both Block 1B and Block 2 also offer the capability to carry 8.4- or 10-m payload fairings, larger than any contemporary launch vehicle. With unmatched mass-lift capability, payload volume, and C3, SLS not only enables spacecraft or mission designs currently impossible with contemporary EELVs, it also offers enhancing benefits, such as reduced risk, operational costs and/or complexity, shorter transit time to destination or launching large systems either monolithically or in fewer components. This paper will discuss both the performance and capabilities of Space Launch System as it evolves, and the current state of SLS utilization planning.

  4. Diverse CRISPRs evolving in human microbiomes.

    Directory of Open Access Journals (Sweden)

    Mina Rho

    Full Text Available CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats loci, together with cas (CRISPR-associated genes, form the CRISPR/Cas adaptive immune system, a primary defense strategy that eubacteria and archaea mobilize against foreign nucleic acids, including phages and conjugative plasmids. Short spacer sequences separated by the repeats are derived from foreign DNA and direct interference to future infections. The availability of hundreds of shotgun metagenomic datasets from the Human Microbiome Project (HMP enables us to explore the distribution and diversity of known CRISPRs in human-associated microbial communities and to discover new CRISPRs. We propose a targeted assembly strategy to reconstruct CRISPR arrays, which whole-metagenome assemblies fail to identify. For each known CRISPR type (identified from reference genomes, we use its direct repeat consensus sequence to recruit reads from each HMP dataset and then assemble the recruited reads into CRISPR loci; the unique spacer sequences can then be extracted for analysis. We also identified novel CRISPRs or new CRISPR variants in contigs from whole-metagenome assemblies and used targeted assembly to more comprehensively identify these CRISPRs across samples. We observed that the distributions of CRISPRs (including 64 known and 86 novel ones are largely body-site specific. We provide detailed analysis of several CRISPR loci, including novel CRISPRs. For example, known streptococcal CRISPRs were identified in most oral microbiomes, totaling ∼8,000 unique spacers: samples resampled from the same individual and oral site shared the most spacers; different oral sites from the same individual shared significantly fewer, while different individuals had almost no common spacers, indicating the impact of subtle niche differences on the evolution of CRISPR defenses. We further demonstrate potential applications of CRISPRs to the tracing of rare species and the virus exposure of individuals

  5. Microbiota and diabetes: an evolving relationship.

    Science.gov (United States)

    Tilg, Herbert; Moschen, Alexander R

    2014-09-01

    The gut microbiota affects numerous biological functions throughout the body and its characterisation has become a major research area in biomedicine. Recent studies have suggested that gut bacteria play a fundamental role in diseases such as obesity, diabetes and cardiovascular disease. Data are accumulating in animal models and humans suggesting that obesity and type 2 diabetes (T2D) are associated with a profound dysbiosis. First human metagenome-wide association studies demonstrated highly significant correlations of specific intestinal bacteria, certain bacterial genes and respective metabolic pathways with T2D. Importantly, especially butyrate-producing bacteria such as Roseburia intestinalis and Faecalibacterium prausnitzii concentrations were lower in T2D subjects. This supports the increasing evidence, that butyrate and other short-chain fatty acids are able to exert profound immunometabolic effects. Endotoxaemia, most likely gut-derived has also been observed in patients with metabolic syndrome and T2D and might play a key role in metabolic inflammation. A further hint towards an association between microbiota and T2D has been derived from studies in pregnancy showing that major gut microbial shifts occurring during pregnancy affect host metabolism. Interestingly, certain antidiabetic drugs such as metformin also interfere with the intestinal microbiota. Specific members of the microbiota such as Akkermansia muciniphila might be decreased in diabetes and when administered to murines exerted antidiabetic effects. Therefore, as a 'gut signature' becomes more evident in T2D, a better understanding of the role of the microbiota in diabetes might provide new aspects regarding its pathophysiological relevance and pave the way for new therapeutic principles.

  6. Ploidy dynamics and evolvability in fungi

    Science.gov (United States)

    Stone, Neil

    2016-01-01

    Rapid responses to acute stresses are essential for stress survival and are critical to the ability of fungal pathogens to adapt to new environments or hosts. The rapid emergence of drug resistance is used as a model for how fungi adapt and survive stress conditions that inhibit the growth of progenitor cells. Aneuploidy and loss of heterozygosity (LOH), which are large-scale genome shifts involving whole chromosomes or chromosome arms, occur at higher frequency than point mutations and have the potential to mediate stress survival. Furthermore, the stress of exposure to an antifungal drug can induce elevated levels of LOH and can promote the formation of aneuploids. This occurs via mitotic defects that first produce tetraploid progeny with extra spindles, followed by chromosome mis-segregation. Thus, drug exposure induces elevated levels of aneuploidy, which can alter the copy number of genes that improve survival in a given stress or drug. Selection then acts to increase the proportion of adaptive aneuploids in the population. Because aneuploidy is a common property of many pathogenic fungi, including those posing emerging threats to plants, animals and humans, we propose that aneuploid formation and LOH often accompanying it contribute to the rapid generation of diversity that can facilitate the emergence of fungal pathogens to new environmental niches and/or new hosts, as well as promote antifungal drug resistance that makes emerging fungal infections ever more difficult to contain. This article is part of the themed issue ‘Tackling emerging fungal threats to animal health, food security and ecosystem resilience’. PMID:28080987

  7. Online System for Faster Multipoint Linkage Analysis via Parallel Execution on Thousands of Personal Computers

    OpenAIRE

    Silberstein, M.; Tzemach, A.; Dovgolevsky, N.; Fishelson, M.; Schuster, A.; Geiger, D.

    2006-01-01

    Computation of LOD scores is a valuable tool for mapping disease-susceptibility genes in the study of Mendelian and complex diseases. However, computation of exact multipoint likelihoods of large inbred pedigrees with extensive missing data is often beyond the capabilities of a single computer. We present a distributed system called “SUPERLINK-ONLINE,” for the computation of multipoint LOD scores of large inbred pedigrees. It achieves high performance via the efficient parallelization of the ...

  8. Ascomycota has a faster evolutionary rate and higher species diversity than Basidiomycota

    Institute of Scientific and Technical Information of China (English)

    Lumbsch; H.; THORSTEN

    2010-01-01

    Differences in rates of nucleotide or amino acid substitutions among major groups of organisms are repeatedly found and well documented. A growing body of evidence suggests a link between the rate of neutral molecular change within populations and the evolution of species diversity. More than 98% of terrestrial fungi belong to the phyla Ascomycota or Basidiomycota. The former is considerably richer in number of species than the latter. We obtained DNA sequences of 21 protein-coding genes from the lichenized fungus Rhizoplaca chrysoleuca and used them together with sequences from GenBank for subsequent analyses. Three datasets were used to test rate discrepancies between Ascomycota and Basidiomycota and that within Ascomycota: (i) 13 taxa including 105 protein-coding genes, (ii) nine taxa including 21 protein-coding genes, and (iii) nuclear LSU rDNA of 299 fungal species. Based on analyses of the 105 protein-coding genes and nuclear LSU rDNA datasets, we found that the evolutionary rate was higher in Ascomycota than in Basidiomycota. The differences in substitution rates between Ascomycota and Basidiomycota were significant. Within Ascomycota, the species-rich Sordariomycetes has the fastest evolutionary rate, while Leotiomycetes has the slowest. Our results indicate that the main contribution to the higher substitution rates in Ascomycota does not come from mutualism, ecological conditions, sterility, metabolic rate or shorter generation time, but is possibly caused by the founder effect. This is another example of the correlation between species number and evolutionary rates, which is consistent with the hypothesis that the founder effect is responsible for accelerated substitution rates in diverse clades.

  9. Evolving regulatory paradigm for proarrhythmic risk assessment for new drugs.

    Science.gov (United States)

    Vicente, Jose; Stockbridge, Norman; Strauss, David G

    Fourteen drugs were removed from the market worldwide because their potential to cause torsade de pointes (torsade), a potentially fatal ventricular arrhythmia. The observation that most drugs that cause torsade block the potassium channel encoded by the human ether-à-go-go related gene (hERG) and prolong the heart rate corrected QT interval (QTc) on the ECG, led to a focus on screening new drugs for their potential to block the hERG potassium channel and prolong QTc. This has been a successful strategy keeping torsadogenic drugs off the market, but has resulted in drugs being dropped from development, sometimes inappropriately. This is because not all drugs that block the hERG potassium channel and prolong QTc cause torsade, sometimes because they block other channels. The regulatory paradigm is evolving to improve proarrhythmic risk prediction. ECG studies can now use exposure-response modeling for assessing the effect of a drug on the QTc in small sample size first-in-human studies. Furthermore, the Comprehensive in vitro Proarrhythmia Assay (CiPA) initiative is developing and validating a new in vitro paradigm for cardiac safety evaluation of new drugs that provides a more accurate and comprehensive mechanistic-based assessment of proarrhythmic potential. Under CiPA, the prediction of proarrhythmic potential will come from in vitro ion channel assessments coupled with an in silico model of the human ventricular myocyte. The preclinical assessment will be checked with an assessment of human phase 1 ECG data to determine if there are unexpected ion channel effects in humans compared to preclinical ion channel data. While there is ongoing validation work, the heart rate corrected J-Tpeak interval is likely to be assessed under CiPA to detect inward current block in presence of hERG potassium channel block.

  10. A faster running speed is associated with a greater body weight loss in 100-km ultra-marathoners.

    Science.gov (United States)

    Knechtle, Beat; Knechtle, Patrizia; Wirth, Andrea; Alexander Rüst, Christoph; Rosemann, Thomas

    2012-01-01

    In 219 recreational male runners, we investigated changes in body mass, total body water, haematocrit, plasma sodium concentration ([Na(+)]), and urine specific gravity as well as fluid intake during a 100-km ultra-marathon. The athletes lost 1.9 kg (s = 1.4) of body mass, equal to 2.5% (s = 1.8) of body mass (P running speed (r = -0.16, P running speed (r = 0.42, P 0.05). In conclusion, faster runners lost more body mass, runners lost more body mass when they drank less fluid, and faster runners drank more fluid than slower runners.

  11. Are OPERA neutrinos faster than light because of non-inertial reference frames?

    Science.gov (United States)

    Germanà, C.

    2012-02-01

    Context. Recent results from the OPERA experiment reported a neutrino beam traveling faster than light. The challenging experiment measured the neutrino time of flight (TOF) over a baseline from the CERN to the Gran Sasso site, concluding that the neutrino beam arrives ~60 ns earlier than a light ray would do. Because the result, if confirmed, has an enormous impact on science, it might be worth double-checking the time definitions with respect to the non-inertial system in which the neutrino travel time was measured. An observer with a clock measuring the proper time τ free of non-inertial effects is the one located at the solar system barycenter (SSB). Aims: Potential problems in the OPERA data analysis connected with the definition of the reference frame and time synchronization are emphasized. We aim to investigate the synchronization of non-inertial clocks on Earth by relating this time to the proper time of an inertial observer at SSB. Methods: The Tempo2 software was used to time-stamp events observed on the geoid with respect to the SSB inertial observer time. Results: Neutrino results from OPERA might carry the fingerprint of non-inertial effects because they are timed by terrestrial clocks. The CERN-Gran Sasso clock synchronization is accomplished by applying corrections that depend on special and general relativistic time dilation effects at the clocks, depending on the position of the clocks in the solar system gravitational well. As a consequence, TOF distributions are centered on values shorter by tens of nanoseconds than expected, integrating over a period from April to December, longer if otherwise. It is worth remarking that the OPERA runs have always been carried out from April/May to November. Conclusions: If the analysis by Tempo2 holds for the OPERA experiment, the excellent measurement by the OPERA collaboration will turn into a proof of the general relativity theory in a weak field approximation. The analysis presented here is falsifiable

  12. Second generation stationary digital breast tomosynthesis system with faster scan time and wider angular span.

    Science.gov (United States)

    Calliste, Jabari; Wu, Gongting; Laganis, Philip E; Spronk, Derrek; Jafari, Houman; Olson, Kyle; Gao, Bo; Lee, Yueh Z; Zhou, Otto; Lu, Jianping

    2017-09-01

    The aim of this study was to characterize a new generation stationary digital breast tomosynthesis system with higher tube flux and increased angular span over a first generation system. The linear CNT x-ray source was designed, built, and evaluated to determine its performance parameters. The second generation system was then constructed using the CNT x-ray source and a Hologic gantry. Upon construction, test objects and phantoms were used to characterize system resolution as measured by the modulation transfer function (MTF), and artifact spread function (ASF). The results indicated that the linear CNT x-ray source was capable of stable operation at a tube potential of 49 kVp, and measured focal spot sizes showed source-to-source consistency with a nominal focal spot size of 1.1 mm. After construction, the second generation (Gen 2) system exhibited entrance surface air kerma rates two times greater the previous s-DBT system. System in-plane resolution as measured by the MTF is 7.7 cycles/mm, compared to 6.7 cycles/mm for the Gen 1 system. As expected, an increase in the z-axis depth resolution was observed, with a decrease in the ASF from 4.30 mm to 2.35 mm moving from the Gen 1 system to the Gen 2 system as result of an increased angular span. The results indicate that the Gen 2 stationary digital breast tomosynthesis system, which has a larger angular span, increased entrance surface air kerma, and faster image acquisition time over the Gen 1 s-DBT system, results in higher resolution images. With the detector operating at full resolution, the Gen 2 s-DBT system can achieve an in-plane resolution of 7.7 cycles per mm, which is better than the current commercial DBT systems today, and may potentially result in better patient diagnosis. © 2017 American Association of Physicists in Medicine.

  13. Evidence for shifts to faster growth strategies in the new ranges of invasive alien plants

    Science.gov (United States)

    Leishman, Michelle R; Cooke, Julia; Richardson, David M; Newman, Jonathan

    2014-01-01

    novel environment commonly results in a reduction in the top-down constraint imposed by herbivores on growth, allowing plants to shift towards a faster growth strategy which may result in an increase in population size and spread and consequently to invasive success. PMID:25558090

  14. How Language Evolved%语言如何进化

    Institute of Scientific and Technical Information of China (English)

    Michael C. Corballis

    2007-01-01

    人类语言具有复杂多变的递归结构,漫长的物种进化过程中唯独人类精通语言.语言的进化始于大约两百万年前的"更新世时期",语言在当时作为一种认知适应对于人类应对自然界带给人类的挑战(如动物掠食与森林毁坏)有很大帮助.人类进化过程中学习与文化因素形成一种选择压力促使人际交流语法化,人际交流语法化引发大脑容量增加,然而,最初的语言进化与基因无关.学习与文化压力也使交流的媒介依次变为手语模式、表情模式与语言模式.交流媒介的逐渐变化最终导致了FOXP2基因突变,FOXP2基因突变让智人具有了自主的言语能力.与地球上其它的人科动物相比,人类的语言能力使人类在进化中具有明显的优势.%Language, with its complex recursive structure, is almost certainly a uniquely human capacity. I argue that it evolved over the past 2 million years during the Pleistocene epoch, as part of a cognitive adaptation to deforestation and predation from dangerous killer animals on the African savanna. Rather than postulate any specific genes for language, I suggest that there was systematic selection for increase in brain size, allowing for more complex social cognition, including the "grammaticalization" of communication through learning and cultural pressures. Parallel to this development, the medium of communication changed gradually from a manual mode to a facial and then vocal mode, culmination in a mutation of the FOXP2 gene that gave our own species,Homo sapiens, the capacity for autonomous speech. This final switch may explain the so-called "human revolution," leading to the dominance of humans on the planet, and the demise of other species of the genus Homo.

  15. Adapting Morphology to Multiple Tasks in Evolved Virtual Creatures

    DEFF Research Database (Denmark)

    Lessin, Dan; Fussell, Don; Miikkulainen, Risto

    2014-01-01

    The ESP method for evolving virtual creatures (Lessin et al., 2013) consisted of an encapsulation mechanism to preserve learned skills, a human-designed syllabus to build higherlevel skills by combining lower-level skills systematically, and a pandemonium mechanism to resolve conflicts between...... encapsulated skills in a single creature’s brain. Previous work with ESP showed that it is possible to evolve much more complex behavior than before, even when fundamental morphology (i.e., skeletal segments and joints) was evolved only for the first skill. This paper introduces a more general form of ESP...

  16. Heterogeneous edge weights promote epidemic diffusion in weighted evolving networks

    Science.gov (United States)

    Duan, Wei; Song, Zhichao; Qiu, Xiaogang

    2016-08-01

    The impact that the heterogeneities of links’ weights have on epidemic diffusion in weighted networks has received much attention. Investigating how heterogeneous edge weights affect epidemic spread is helpful for disease control. In this paper, we study a Reed-Frost epidemic model in weighted evolving networks. Our results indicate that a higher heterogeneity of edge weights leads to higher epidemic prevalence and epidemic incidence at earlier stage of epidemic diffusion in weighted evolving networks. In addition, weighted evolving scale-free networks come with a higher epidemic prevalence and epidemic incidence than unweighted scale-free networks.

  17. Evolving role of pharmaceutical physicians in the industry: Indian perspective

    Directory of Open Access Journals (Sweden)

    Anant Patil

    2012-01-01

    Full Text Available The Indian pharmaceutical industry, like any other industry, has undergone significant change in the last decade. The role of a Medical advisor has always been of paramount importance in the pharmaceutical companies in India. On account of the evolving medical science and the competitive environment, the medical advisor′s role is also increasingly becoming critical. In India, with changes in regulatory rules, safety surveillance, and concept of medical liaisons, the role of the medical advisor is evolving continuously and is further likely to evolve in the coming years in important areas like health economics, public private partnerships, and strategic planning.

  18. Evolving Connectionist System Based Role Allocation for Robotic Soccer

    OpenAIRE

    Huang, L.; Song, Q.; Kasabov, N

    2008-01-01

    Robotic soccer is an intelligent system where a group of mobile robots are controlled to perform soccer play (http://www.fira.net). The allocation of a suitable role for each robot in a team is a key for the success of the play. The paper treats this issue as one of pattern classification, and solves it with an Evolving classification function (ECF), a special evolving connectionist system (ECOS). A robot's role is determined by and evolves with the states of system ( robots and target ) in r...

  19. Self-Evolvable Systems Machine Learning in Social Media

    CERN Document Server

    Iordache, Octavian

    2012-01-01

    This monograph presents key method to successfully manage the growing  complexity of systems  where conventional engineering and scientific methodologies and technologies based on learning and adaptability come to their limits and new ways are nowadays required. The transition from adaptable to evolvable and finally to self-evolvable systems is highlighted, self-properties such as self-organization, self-configuration, and self-repairing are introduced and challenges and limitations of the self-evolvable engineering systems are evaluated.

  20. GC-biased gene conversion impacts ribosomal DNA evolution in vertebrates, angiosperms, and other eukaryotes.

    Science.gov (United States)

    Escobar, Juan S; Glémin, Sylvain; Galtier, Nicolas

    2011-09-01

    Ribosomal DNA (rDNA) is one of the most conserved genes in eukaryotes. The multiples copies of rDNA in the genome evolve in a concerted manner, through unequal crossing over and/or gene conversion, two mechanisms related to homologous recombination. Recombination increases local GC content in several organisms through a process known as GC-biased gene conversion (gBGC). gBGC has been well characterized in mammals, birds, and grasses, but its phylogenetic distribution across the tree of life is poorly understood. Here, we test the hypothesis that recombination affects the evolution of base composition in 18S rDNA and examine the reliability of this thoroughly studied molecule as a marker of gBGC in eukaryotes. Phylogenetic analyses of 18S rDNA in vertebrates and angiosperms reveal significant heterogeneity in the evolution of base composition across both groups. Mammals, birds, and grasses experience increases in the GC content of the 18S rDNA, consistent with previous genome-wide analyses. In addition, we observe increased GC contents in Ostariophysi ray-finned fishes and commelinid monocots (i.e., the clade including grasses), suggesting that the genomes of these two groups have been affected by gBGC. Polymorphism analyses in rDNA confirm that gBGC, not mutation bias, is the most plausible explanation for these patterns. We also find that helix and loop sites of the secondary structure of ribosomal RNA do not evolve at the same pace: loops evolve faster than helices, whereas helices are GC richer than loops. We extend analyses to major lineages of eukaryotes and suggest that gBGC might have also affected base composition in Giardia (Diplomonadina), nudibranch gastropods (Mollusca), and Asterozoa (Echinodermata).