Science.gov

Sample records for convergently evolved enzymes

  1. Evolving hardware as model of enzyme evolution.

    PubMed

    Lahoz-Beltra, R

    2001-06-01

    Organism growth and survival is based on thousands of enzymes organized in networks. The motivation to understand how a large number of enzymes evolved so fast inside cells may be relevant to explaining the origin and maintenance of life on Earth. This paper presents electronic circuits called 'electronic enzymes' that model the catalytic function performed by biological enzymes. Electronic enzymes are the hardware realization of enzymes defined as molecular automata with a finite number of internal conformational states and a set of Boolean operators modelling the active groups of the active site. One of the main features of electronic enzymes is the possibility of evolution finding the proper active site by means of a genetic algorithm yielding a metabolic ring or k-cycle that bears a resemblance to Krebs (k=7) or Calvin (k=4) cycles present in organisms. The simulations are consistent with those results obtained in vitro evolving enzymes based on polymerase chain reaction (PCR) as well as with the general view that suggests the main role of recombination during enzyme evolution. The proposed methodology shows how molecular automata with evolvable features that model enzymes or other processing molecules provide an experimental framework for simulation of the principles governing metabolic pathways evolution and self-organization. PMID:11448522

  2. Divergence and Convergence in Enzyme Evolution*

    PubMed Central

    Galperin, Michael Y.; Koonin, Eugene V.

    2012-01-01

    Comparative analysis of the sequences of enzymes encoded in a variety of prokaryotic and eukaryotic genomes reveals convergence and divergence at several levels. Functional convergence can be inferred when structurally distinct and hence non-homologous enzymes show the ability to catalyze the same biochemical reaction. In contrast, as a result of functional diversification, many structurally similar enzyme molecules act on substantially distinct substrates and catalyze diverse biochemical reactions. Here, we present updates on the ATP-grasp, alkaline phosphatase, cupin, HD hydrolase, and N-terminal nucleophile (Ntn) hydrolase enzyme superfamilies and discuss the patterns of sequence and structural conservation and diversity within these superfamilies. Typically, enzymes within a superfamily possess common sequence motifs and key active site residues, as well as (predicted) reaction mechanisms. These observations suggest that the strained conformation (the entatic state) of the active site, which is responsible for the substrate binding and formation of the transition complex, tends to be conserved within enzyme superfamilies. The subsequent fate of the transition complex is not necessarily conserved and depends on the details of the structures of the enzyme and the substrate. This variability of reaction outcomes limits the ability of sequence analysis to predict the exact enzymatic activities of newly sequenced gene products. Nevertheless, sequence-based (super)family assignments and generic functional predictions, even if imprecise, provide valuable leads for experimental studies and remain the best approach to the functional annotation of uncharacterized proteins from new genomes. PMID:22069324

  3. An analysis of why highly similar enzymes evolve differently.

    PubMed Central

    Majiduddin, Fahd K; Palzkill, Timothy

    2003-01-01

    The TEM-1 and SHV-1 beta-lactamases are important contributors to resistance to beta-lactam antibiotics in gram-negative bacteria. These enzymes share 68% amino acid sequence identity and their atomic structures are nearly superimposable. Extended-spectrum cephalosporins were introduced to avoid the action of these beta-lactamases. The widespread use of antibiotics has led to the evolution of variant TEM and SHV enzymes that can hydrolyze extended-spectrum antibiotics. Despite being highly similar in structure, the TEM and SHV enzymes have evolved differently in response to the selective pressure of antibiotic therapy. Examples of this are at residues Arg164 and Asp179. Among TEM variants, substitutions are found only at position 164, while among SHV variants, substitutions are found only at position 179. To explain this observation, the effects of substitutions at position 164 in both TEM-1 and SHV-1 on antibiotic resistance and on enzyme catalytic efficiency were examined. Competition experiments were performed between mutants to understand why certain substitutions preferentially evolve in response to the selective pressure of antibiotic therapy. The data presented here indicate that substitutions at position Asp179 in SHV-1 and Arg164 in TEM-1 are more beneficial to bacteria because they provide increased fitness relative to either wild type or other mutants. PMID:12618385

  4. Distinct developmental genetic mechanisms underlie convergently evolved tooth gain in sticklebacks

    PubMed Central

    Ellis, Nicholas A.; Glazer, Andrew M.; Donde, Nikunj N.; Cleves, Phillip A.; Agoglia, Rachel M.; Miller, Craig T.

    2015-01-01

    Teeth are a classic model system of organogenesis, as repeated and reciprocal epithelial and mesenchymal interactions pattern placode formation and outgrowth. Less is known about the developmental and genetic bases of tooth formation and replacement in polyphyodonts, which are vertebrates with continual tooth replacement. Here, we leverage natural variation in the threespine stickleback fish Gasterosteus aculeatus to investigate the genetic basis of tooth development and replacement. We find that two derived freshwater stickleback populations have both convergently evolved more ventral pharyngeal teeth through heritable genetic changes. In both populations, evolved tooth gain manifests late in development. Using pulse-chase vital dye labeling to mark newly forming teeth in adult fish, we find that both high-toothed freshwater populations have accelerated tooth replacement rates relative to low-toothed ancestral marine fish. Despite the similar evolved phenotype of more teeth and an accelerated adult replacement rate, the timing of tooth number divergence and the spatial patterns of newly formed adult teeth are different in the two populations, suggesting distinct developmental mechanisms. Using genome-wide linkage mapping in marine-freshwater F2 genetic crosses, we find that the genetic basis of evolved tooth gain in the two freshwater populations is largely distinct. Together, our results support a model whereby increased tooth number and an accelerated tooth replacement rate have evolved convergently in two independently derived freshwater stickleback populations using largely distinct developmental and genetic mechanisms. PMID:26062935

  5. Distinct developmental genetic mechanisms underlie convergently evolved tooth gain in sticklebacks.

    PubMed

    Ellis, Nicholas A; Glazer, Andrew M; Donde, Nikunj N; Cleves, Phillip A; Agoglia, Rachel M; Miller, Craig T

    2015-07-15

    Teeth are a classic model system of organogenesis, as repeated and reciprocal epithelial and mesenchymal interactions pattern placode formation and outgrowth. Less is known about the developmental and genetic bases of tooth formation and replacement in polyphyodonts, which are vertebrates with continual tooth replacement. Here, we leverage natural variation in the threespine stickleback fish Gasterosteus aculeatus to investigate the genetic basis of tooth development and replacement. We find that two derived freshwater stickleback populations have both convergently evolved more ventral pharyngeal teeth through heritable genetic changes. In both populations, evolved tooth gain manifests late in development. Using pulse-chase vital dye labeling to mark newly forming teeth in adult fish, we find that both high-toothed freshwater populations have accelerated tooth replacement rates relative to low-toothed ancestral marine fish. Despite the similar evolved phenotype of more teeth and an accelerated adult replacement rate, the timing of tooth number divergence and the spatial patterns of newly formed adult teeth are different in the two populations, suggesting distinct developmental mechanisms. Using genome-wide linkage mapping in marine-freshwater F2 genetic crosses, we find that the genetic basis of evolved tooth gain in the two freshwater populations is largely distinct. Together, our results support a model whereby increased tooth number and an accelerated tooth replacement rate have evolved convergently in two independently derived freshwater stickleback populations using largely distinct developmental and genetic mechanisms. PMID:26062935

  6. Convergence

    NASA Astrophysics Data System (ADS)

    Darcie, Thomas E.; Doverspike, Robert; Zirngibl, Martin; Korotky, Steven K.

    2005-09-01

    Call for Papers: Convergence The Journal of Optical Networking (JON) invites submissions to a special issue on Convergence. Convergence has become a popular theme in telecommunications, one that has broad implications across all segments of the industry. Continual evolution of technology and applications continues to erase lines between traditionally separate lines of business, with dramatic consequences for vendors, service providers, and consumers. Spectacular advances in all layers of optical networking-leading to abundant, dynamic, cost-effective, and reliable wide-area and local-area connections-have been essential drivers of this evolution. As services and networks continue to evolve towards some notion of convergence, the continued role of optical networks must be explored. One vision of convergence renders all information in a common packet (especially IP) format. This vision is driven by the proliferation of data services. For example, time-division multiplexed (TDM) voice becomes VoIP. Analog cable-television signals become MPEG bits streamed to digital set-top boxes. T1 or OC-N private lines migrate to Ethernet virtual private networks (VPNs). All these packets coexist peacefully within a single packet-routing methodology built on an optical transport layer that combines the flexibility and cost of data networks with telecom-grade reliability. While this vision is appealing in its simplicity and shared widely, specifics of implementation raise many challenges and differences of opinion. For example, many seek to expand the role of Ethernet in these transport networks, while massive efforts are underway to make traditional TDM networks more data friendly within an evolved but backward-compatible SDH/SONET (synchronous digital hierarchy and synchronous optical network) multiplexing hierarchy. From this common underlying theme follow many specific instantiations. Examples include the convergence at the physical, logical, and operational levels of voice and

  7. Rapid divergence and convergence of life-history in experimentally evolved Drosophila melanogaster.

    PubMed

    Burke, Molly K; Barter, Thomas T; Cabral, Larry G; Kezos, James N; Phillips, Mark A; Rutledge, Grant A; Phung, Kevin H; Chen, Richard H; Nguyen, Huy D; Mueller, Laurence D; Rose, Michael R

    2016-09-01

    Laboratory selection experiments are alluring in their simplicity, power, and ability to inform us about how evolution works. A longstanding challenge facing evolution experiments with metazoans is that significant generational turnover takes a long time. In this work, we present data from a unique system of experimentally evolved laboratory populations of Drosophila melanogaster that have experienced three distinct life-history selection regimes. The goal of our study was to determine how quickly populations of a certain selection regime diverge phenotypically from their ancestors, and how quickly they converge with independently derived populations that share a selection regime. Our results indicate that phenotypic divergence from an ancestral population occurs rapidly, within dozens of generations, regardless of that population's evolutionary history. Similarly, populations sharing a selection treatment converge on common phenotypes in this same time frame, regardless of selection pressures those populations may have experienced in the past. These patterns of convergence and divergence emerged much faster than expected, suggesting that intermediate evolutionary history has transient effects in this system. The results we draw from this system are applicable to other experimental evolution projects, and suggest that many relevant questions can be sufficiently tested on shorter timescales than previously thought. PMID:27431916

  8. Convergence

    NASA Astrophysics Data System (ADS)

    Darcie, Thomas E.; Doverspike, Robert; Zirngibl, Martin; Korotky, Steven K.

    2005-09-01

    Call for Papers: Convergence The Journal of Optical Networking (JON) invites submissions to a special issue on Convergence. Convergence has become a popular theme in telecommunications, one that has broad implications across all segments of the industry. Continual evolution of technology and applications continues to erase lines between traditionally separate lines of business, with dramatic consequences for vendors, service providers, and consumers. Spectacular advances in all layers of optical networking-leading to abundant, dynamic, cost-effective, and reliable wide-area and local-area connections-have been essential drivers of this evolution. As services and networks continue to evolve towards some notion of convergence, the continued role of optical networks must be explored. One vision of convergence renders all information in a common packet (especially IP) format. This vision is driven by the proliferation of data services. For example, time-division multiplexed (TDM) voice becomes VoIP. Analog cable-television signals become MPEG bits streamed to digital set-top boxes. T1 or OC-N private lines migrate to Ethernet virtual private networks (VPNs). All these packets coexist peacefully within a single packet-routing methodology built on an optical transport layer that combines the flexibility and cost of data networks with telecom-grade reliability. While this vision is appealing in its simplicity and shared widely, specifics of implementation raise many challenges and differences of opinion. For example, many seek to expand the role of Ethernet in these transport networks, while massive efforts are underway to make traditional TDM networks more data friendly within an evolved but backward-compatible SDH/SONET (synchronous digital hierarchy and synchronous optical network) multiplexing hierarchy. From this common underlying theme follow many specific instantiations. Examples include the convergence at the physical, logical, and operational levels of voice and

  9. Convergence

    NASA Astrophysics Data System (ADS)

    Darcie, Thomas E.; Doverspike, Robert; Zirngibl, Martin; Korotky, Steven K.

    2005-08-01

    Call for Papers: Convergence The Journal of Optical Networking (JON) invites submissions to a special issue on Convergence. Convergence has become a popular theme in telecommunications, one that has broad implications across all segments of the industry. Continual evolution of technology and applications continues to erase lines between traditionally separate lines of business, with dramatic consequences for vendors, service providers, and consumers. Spectacular advances in all layers of optical networking-leading to abundant, dynamic, cost-effective, and reliable wide-area and local-area connections-have been essential drivers of this evolution. As services and networks continue to evolve towards some notion of convergence, the continued role of optical networks must be explored. One vision of convergence renders all information in a common packet (especially IP) format. This vision is driven by the proliferation of data services. For example, time-division multiplexed (TDM) voice becomes VoIP. Analog cable-television signals become MPEG bits streamed to digital set-top boxes. T1 or OC-N private lines migrate to Ethernet virtual private networks (VPNs). All these packets coexist peacefully within a single packet-routing methodology built on an optical transport layer that combines the flexibility and cost of data networks with telecom-grade reliability. While this vision is appealing in its simplicity and shared widely, specifics of implementation raise many challenges and differences of opinion. For example, many seek to expand the role of Ethernet in these transport networks, while massive efforts are underway to make traditional TDM networks more data friendly within an evolved but backward-compatible SDH/SONET (synchronous digital hierarchy and synchronous optical network) multiplexing hierarchy. From this common underlying theme follow many specific instantiations. Examples include the convergence at the physical, logical, and operational levels of voice and

  10. Convergence

    NASA Astrophysics Data System (ADS)

    Darcie, Thomas E.; Doverspike, Robert; Zirngibl, Martin; Korotky, Steven K.

    2005-06-01

    Call for Papers: Convergence The Journal of Optical Networking (JON) invites submissions to a special issue on Convergence. Convergence has become a popular theme in telecommunications, one that has broad implications across all segments of the industry. Continual evolution of technology and applications continues to erase lines between traditionally separate lines of business, with dramatic consequences for vendors, service providers, and consumers. Spectacular advances in all layers of optical networking-leading to abundant, dynamic, cost-effective, and reliable wide-area and local-area connections-have been essential drivers of this evolution. As services and networks continue to evolve towards some notion of convergence, the continued role of optical networks must be explored. One vision of convergence renders all information in a common packet (especially IP) format. This vision is driven by the proliferation of data services. For example, time-division multiplexed (TDM) voice becomes VoIP. Analog cable-television signals become MPEG bits streamed to digital set-top boxes. T1 or OC-N private lines migrate to Ethernet virtual private networks (VPNs). All these packets coexist peacefully within a single packet-routing methodology built on an optical transport layer that combines the flexibility and cost of data networks with telecom-grade reliability. While this vision is appealing in its simplicity and shared widely, specifics of implementation raise many challenges and differences of opinion. For example, many seek to expand the role of Ethernet in these transport networks, while massive efforts are underway to make traditional TDM networks more data friendly within an evolved but backward-compatible SDH/SONET (synchronous digital hierarchy and synchronous optical network) multiplexing hierarchy. From this common underlying theme follow many specific instantiations. Examples include the convergence at the physical, logical, and operational levels of voice and

  11. Convergence

    NASA Astrophysics Data System (ADS)

    Darcie, Thomas E.; Doverspike, Robert; Zirngibl, Martin; Korotky, Steven K.

    2005-05-01

    Call for Papers: Convergence The Journal of Optical Networking (JON) invites submissions to a special issue on Convergence. Convergence has become a popular theme in telecommunications, one that has broad implications across all segments of the industry. Continual evolution of technology and applications continues to erase lines between traditionally separate lines of business, with dramatic consequences for vendors, service providers, and consumers. Spectacular advances in all layers of optical networking-leading to abundant, dynamic, cost-effective, and reliable wide-area and local-area connections-have been essential drivers of this evolution. As services and networks continue to evolve towards some notion of convergence, the continued role of optical networks must be explored. One vision of convergence renders all information in a common packet (especially IP) format. This vision is driven by the proliferation of data services. For example, time-division multiplexed (TDM) voice becomes VoIP. Analog cable-television signals become MPEG bits streamed to digital set-top boxes. T1 or OC-N private lines migrate to Ethernet virtual private networks (VPNs). All these packets coexist peacefully within a single packet-routing methodology built on an optical transport layer that combines the flexibility and cost of data networks with telecom-grade reliability. While this vision is appealing in its simplicity and shared widely, specifics of implementation raise many challenges and differences of opinion. For example, many seek to expand the role of Ethernet in these transport networks, while massive efforts are underway to make traditional TDM networks more data friendly within an evolved but backward-compatible SDH/SONET (synchronous digital hierarchy and synchronous optical network) multiplexing hierarchy. From this common underlying theme follow many specific instantiations. Examples include the convergence at the physical, logical, and operational levels of voice and

  12. Convergence

    NASA Astrophysics Data System (ADS)

    Darcie, Thomas E.; Doverspike, Robert; Zirngibl, Martin; Korotky, Steven K.

    2005-04-01

    Call for Papers: Convergence The Journal of Optical Networking (JON) invites submissions to a special issue on Convergence. Convergence has become a popular theme in telecommunications, one that has broad implications across all segments of the industry. Continual evolution of technology and applications continues to erase lines between traditionally separate lines of business, with dramatic consequences for vendors, service providers, and consumers. Spectacular advances in all layers of optical networking-leading to abundant, dynamic, cost-effective, and reliable wide-area and local-area connections-have been essential drivers of this evolution. As services and networks continue to evolve towards some notion of convergence, the continued role of optical networks must be explored. One vision of convergence renders all information in a common packet (especially IP) format. This vision is driven by the proliferation of data services. For example, time-division multiplexed (TDM) voice becomes VoIP. Analog cable-television signals become MPEG bits streamed to digital set-top boxes. T1 or OC-N private lines migrate to Ethernet virtual private networks (VPNs). All these packets coexist peacefully within a single packet-routing methodology built on an optical transport layer that combines the flexibility and cost of data networks with telecom-grade reliability. While this vision is appealing in its simplicity and shared widely, specifics of implementation raise many challenges and differences of opinion. For example, many seek to expand the role of Ethernet in these transport networks, while massive efforts are underway to make traditional TDM networks more data friendly within an evolved but backward-compatible SDH/SONET (synchronous digital hierarchy and synchronous optical network) multiplexing hierarchy. From this common underlying theme follow many specific instantiations. Examples include the convergence at the physical, logical, and operational levels of voice and

  13. Convergence

    NASA Astrophysics Data System (ADS)

    Darcie, Thomas E.; Doverspike, Robert; Zirngibl, Martin; Korotky, Steven K.

    2005-01-01

    Call for Papers: Convergence

    Guest Editors: Thomas E. Darcie, University of Victoria Robert Doverspike, AT&T Martin Zirngibl, Lucent Technologies

    Coordinating Associate Editor: Steven K. Korotky, Lucent Technologies

    The Journal of Optical Networking (JON) invites submissions to a special issue on Convergence. Convergence has become a popular theme in telecommunications, one that has broad implications across all segments of the industry. Continual evolution of technology and applications continues to erase lines between traditionally separate lines of business, with dramatic consequences for vendors, service providers, and consumers. Spectacular advances in all layers of optical networking-leading to abundant, dynamic, cost-effective, and reliable wide-area and local-area connections-have been essential drivers of this evolution. As services and networks continue to evolve towards some notion of convergence, the continued role of optical networks must be explored. One vision of convergence renders all information in a common packet (especially IP) format. This vision is driven by the proliferation of data services. For example, time-division multiplexed (TDM) voice becomes VoIP. Analog cable-television signals become MPEG bits streamed to digital set-top boxes. T1 or OC-N private lines migrate to Ethernet virtual private networks (VPNs). All these packets coexist peacefully within a single packet-routing methodology built on an optical transport layer that combines the flexibility and cost of data networks with telecom-grade reliability. While this vision is appealing in its simplicity and shared widely, specifics of implementation raise many challenges and differences of opinion. For example, many seek to expand the role of Ethernet in these transport networks, while massive efforts are underway to make traditional TDM networks more data friendly

  14. Convergence

    NASA Astrophysics Data System (ADS)

    Darcie, Thomas E.; Doverspike, Robert; Zirngibl, Martin; Korotky, Steven K.

    2004-12-01

    Convergence has become a popular theme in telecommunications, one that has broad implications across all segments of the industry. Continual evolution of technology and applications continues to erase lines between traditionally separate lines of business, with dramatic consequences for vendors, service providers, and consumers. Spectacular advances in all layers of optical networking-leading to abundant, dynamic, cost-effective, and reliable wide-area and local-area connections-have been essential drivers of this evolution. As services and networks continue to evolve towards some notion of convergence, the continued role of optical networks must be explored. One vision of convergence renders all information in a common packet (especially IP) format. This vision is driven by the proliferation of data services. For example, time-division multiplexed (TDM) voice becomes VoIP. Analog cable-television signals become MPEG bits streamed to digital set-top boxes. T1 or OC-N private lines migrate to Ethernet virtual private networks (VPNs). All these packets coexist peacefully within a single packet-routing methodology built on an optical transport layer that combines the flexibility and cost of data networks with telecom-grade reliability. While this vision is appealing in its simplicity and shared widely, specifics of implementation raise many challenges and differences of opinion. For example, many seek to expand the role of Ethernet in these transport networks, while massive efforts are underway to make traditional TDM networks more data friendly within an evolved but backward-compatible SDH/SONET (synchronous digital hierarchy and synchronous optical network) multiplexing hierarchy. From this common underlying theme follow many specific instantiations. Examples include the convergence at the physical, logical, and operational levels of voice and data, video and data, private-line and virtual private-line, fixed and mobile, and local and long-haul services. These

  15. Convergence

    NASA Astrophysics Data System (ADS)

    Darcie, Thomas E.; Doverspike, Robert; Zirngibl, Martin; Korotky, Steven K.

    2004-12-01

    Convergence has become a popular theme in telecommunications, one that has broad implications across all segments of the industry. Continual evolution of technology and applications continues to erase lines between traditionally separate lines of business, with dramatic consequences for vendors, service providers, and consumers. Spectacular advances in all layers of optical networking-leading to abundant, dynamic, cost-effective, and reliable wide-area and local-area connections-have been essential drivers of this evolution. As services and networks continue to evolve towards some notion of convergence, the continued role of optical networks must be explored. One vision of convergence renders all information in a common packet (especially IP) format. This vision is driven by the proliferation of data services. For example, time-division multiplexed (TDM) voice becomes VoIP. Analog cable-television signals become MPEG bits streamed to digital set-top boxes. T1 or OC-N private lines migrate to Ethernet virtual private networks (VPNs). All these packets coexist peacefully within a single packet-routing methodology built on an optical transport layer that combines the flexibility and cost of data networks with telecom-grade reliability. While this vision is appealing in its simplicity and shared widely, specifics of implementation raise many challenges and differences of opinion. For example, many seek to expand the role of Ethernet in these transport networks, while massive efforts are underway to make traditional TDM networks more data friendly within an evolved but backward-compatible SDH/SONET (synchronous digital hierarchy and synchronous optical network) multiplexing hierarchy. From this common underlying theme follow many specific instantiations. Examples include the convergence at the physical, logical, and operational levels of voice and data, video and data, private-line and virtual private-line, fixed and mobile, and local and long-haul services. These

  16. Convergence

    NASA Astrophysics Data System (ADS)

    Darcie, Thomas E.; Doverspike, Robert; Zirngibl, Martin; Korotky, Steven K.

    2005-03-01

    Call for Papers: Convergence Convergence has become a popular theme in telecommunications, one that has broad implications across all segments of the industry. Continual evolution of technology and applications continues to erase lines between traditionally separate lines of business, with dramatic consequences for vendors, service providers, and consumers. Spectacular advances in all layers of optical networking-leading to abundant, dynamic, cost-effective, and reliable wide-area and local-area connections-have been essential drivers of this evolution. As services and networks continue to evolve towards some notion of convergence, the continued role of optical networks must be explored. One vision of convergence renders all information in a common packet (especially IP) format. This vision is driven by the proliferation of data services. For example, time-division multiplexed (TDM) voice becomes VoIP. Analog cable-television signals become MPEG bits streamed to digital set-top boxes. T1 or OC-N private lines migrate to Ethernet virtual private networks (VPNs). All these packets coexist peacefully within a single packet-routing methodology built on an optical transport layer that combines the flexibility and cost of data networks with telecom-grade reliability. While this vision is appealing in its simplicity and shared widely, specifics of implementation raise many challenges and differences of opinion. For example, many seek to expand the role of Ethernet in these transport networks, while massive efforts are underway to make traditional TDM networks more data friendly within an evolved but backward-compatible SDH/SONET (synchronous digital hierarchy and synchronous optical network) multiplexing hierarchy. From this common underlying theme follow many specific instantiations. Examples include the convergence at the physical, logical, and operational levels of voice and data, video and data, private-line and virtual private-line, fixed and mobile, and local and

  17. Convergence

    NASA Astrophysics Data System (ADS)

    Darcie, Thomas E.; Doverspike, Robert; Zirngibl, Martin; Korotky, Steven K.

    2005-02-01

    Call for Papers: Convergence Convergence has become a popular theme in telecommunications, one that has broad implications across all segments of the industry. Continual evolution of technology and applications continues to erase lines between traditionally separate lines of business, with dramatic consequences for vendors, service providers, and consumers. Spectacular advances in all layers of optical networking-leading to abundant, dynamic, cost-effective, and reliable wide-area and local-area connections-have been essential drivers of this evolution. As services and networks continue to evolve towards some notion of convergence, the continued role of optical networks must be explored. One vision of convergence renders all information in a common packet (especially IP) format. This vision is driven by the proliferation of data services. For example, time-division multiplexed (TDM) voice becomes VoIP. Analog cable-television signals become MPEG bits streamed to digital set-top boxes. T1 or OC-N private lines migrate to Ethernet virtual private networks (VPNs). All these packets coexist peacefully within a single packet-routing methodology built on an optical transport layer that combines the flexibility and cost of data networks with telecom-grade reliability. While this vision is appealing in its simplicity and shared widely, specifics of implementation raise many challenges and differences of opinion. For example, many seek to expand the role of Ethernet in these transport networks, while massive efforts are underway to make traditional TDM networks more data friendly within an evolved but backward-compatible SDH/SONET (synchronous digital hierarchy and synchronous optical network) multiplexing hierarchy. From this common underlying theme follow many specific instantiations. Examples include the convergence at the physical, logical, and operational levels of voice and data, video and data, private-line and virtual private-line, fixed and mobile, and local and

  18. Genome Assembly Improvement and Mapping Convergently Evolved Skeletal Traits in Sticklebacks with Genotyping-by-Sequencing

    PubMed Central

    Glazer, Andrew M.; Killingbeck, Emily E.; Mitros, Therese; Rokhsar, Daniel S.; Miller, Craig T.

    2015-01-01

    Marine populations of the threespine stickleback (Gasterosteus aculeatus) have repeatedly colonized and rapidly adapted to freshwater habitats, providing a powerful system to map the genetic architecture of evolved traits. Here, we developed and applied a binned genotyping-by-sequencing (GBS) method to build dense genome-wide linkage maps of sticklebacks using two large marine by freshwater F2 crosses of more than 350 fish each. The resulting linkage maps significantly improve the genome assembly by anchoring 78 new scaffolds to chromosomes, reorienting 40 scaffolds, and rearranging scaffolds in 4 locations. In the revised genome assembly, 94.6% of the assembly was anchored to a chromosome. To assess linkage map quality, we mapped quantitative trait loci (QTL) controlling lateral plate number, which mapped as expected to a 200-kb genomic region containing Ectodysplasin, as well as a chromosome 7 QTL overlapping a previously identified modifier QTL. Finally, we mapped eight QTL controlling convergently evolved reductions in gill raker length in the two crosses, which revealed that this classic adaptive trait has a surprisingly modular and nonparallel genetic basis. PMID:26044731

  19. Convergence

    NASA Astrophysics Data System (ADS)

    Darcie, Thomas E.; Doverspike, Robert; Zirngibl, Martin; Korotky, Steven K.

    2005-01-01

    Call for Papers: Convergence

    Guest Editors: Thomas E. Darcie, University of Victoria Robert Doverspike, AT&T Martin Zirngibl, Lucent Technologies

    Coordinating Associate Editor: Steven K. Korotky, Lucent Technologies

    The Journal of Optical Networking (JON) invites submissions to a special issue on Convergence. Convergence has become a popular theme in telecommunications, one that has broad implications across all segments of the industry. Continual evolution of technology and applications continues to erase lines between traditionally separate lines of business, with dramatic consequences for vendors, service providers, and consumers. Spectacular advances in all layers of optical networking-leading to abundant, dynamic, cost-effective, and reliable wide-area and local-area connections-have been essential drivers of this evolution. As services and networks continue to evolve towards some notion of convergence, the continued role of optical networks must be explored. One vision of convergence renders all information in a common packet (especially IP) format. This vision is driven by the proliferation of data services. For example, time-division multiplexed (TDM) voice becomes VoIP. Analog cable-television signals become MPEG bits streamed to digital set-top boxes. T1 or OC-N private lines migrate to Ethernet virtual private networks (VPNs). All these packets coexist peacefully within a single packet-routing methodology built on an optical transport layer that combines the flexibility and cost of data networks with telecom-grade reliability. While this vision is appealing in its simplicity and shared widely, specifics of implementation raise many challenges and differences of opinion. For example, many seek to expand the role of Ethernet in these transport networks, while massive efforts are underway to make traditional TDM networks more data friendly

  20. Evolvability

    PubMed Central

    Kirschner, Marc; Gerhart, John

    1998-01-01

    Evolvability is an organism’s capacity to generate heritable phenotypic variation. Metazoan evolution is marked by great morphological and physiological diversification, although the core genetic, cell biological, and developmental processes are largely conserved. Metazoan diversification has entailed the evolution of various regulatory processes controlling the time, place, and conditions of use of the conserved core processes. These regulatory processes, and certain of the core processes, have special properties relevant to evolutionary change. The properties of versatile protein elements, weak linkage, compartmentation, redundancy, and exploratory behavior reduce the interdependence of components and confer robustness and flexibility on processes during embryonic development and in adult physiology. They also confer evolvability on the organism by reducing constraints on change and allowing the accumulation of nonlethal variation. Evolvability may have been generally selected in the course of selection for robust, flexible processes suitable for complex development and physiology and specifically selected in lineages undergoing repeated radiations. PMID:9671692

  1. Effect of time-evolving age and convergence rate of the subducting plate on the Cenozoic adakites and boninites

    NASA Astrophysics Data System (ADS)

    Kim, Yoon-Mi; Lee, Changyeol

    2014-12-01

    Partial melting of subducting oceanic crust expressed as high-Mg volcanic rocks such as adakites and boninites has been actively studied for decades, and Lee and King (2010) reported that time-evolving subduction parameters such as the age and the subduction rate of the converging oceanic plate play important roles in transient partial melting of the subducting oceanic crust (e.g., Aleutians). However, few subduction model experiments have considered time-evolving subduction parameters, posing problems for studies of transient partial melting of subducting oceanic crust in many subduction zones. Therefore, we constructed two-dimensional kinematic-dynamic subduction models for the Izu-Bonin, Mariana, Northeast Japan, Kuril, Tonga, Java-Sunda, and Aleutian subduction zones that account for the last 50 Myr of their evolution. The models include the time-evolving age and convergence rate of the incoming oceanic plate, so the effect of time-evolving subduction parameters on transient partial melting of oceanic crust can be evaluated. Our model calculations revealed that adakites and boninites in the Izu-Bonin and Aleutian subduction zones resulted from transient partial melting of oceanic crust. However, the steady-state subduction model using current subduction parameters did not produce any partial melting of oceanic crust in the aforementioned subduction zones, indicating that time-evolving subduction parameters are crucial for modeling transient eruption of adakites and boninites. Our model calculations confirm that other geological processes such as forearc extension, back-arc opening, mantle plumes and ridge subduction are required for partial melting of the oceanic crust in the Mariana, Northeast Japan, Tonga, and southeastern Java-Sunda subduction zones.

  2. Convergence in feeding posture occurs through different genetic loci in independently evolved cave populations of Astyanax mexicanus.

    PubMed

    Kowalko, Johanna E; Rohner, Nicolas; Linden, Tess A; Rompani, Santiago B; Warren, Wesley C; Borowsky, Richard; Tabin, Clifford J; Jeffery, William R; Yoshizawa, Masato

    2013-10-15

    When an organism colonizes a new environment, it needs to adapt both morphologically and behaviorally to survive and thrive. Although recent progress has been made in understanding the genetic architecture underlying morphological evolution, behavioral evolution is poorly understood. Here, we use the Mexican cavefish, Astyanax mexicanus, to study the genetic basis for convergent evolution of feeding posture. When river-dwelling surface fish became entrapped in the caves, they were confronted with dramatic changes in the availability and type of food source and in their ability to perceive it. In this setting, multiple independent populations of cavefish exhibit an altered feeding posture compared with their ancestral surface forms. We determined that this behavioral change in feeding posture is not due to changes in cranial facial morphology, body depth, or to take advantage of the expansion in the number of taste buds. Quantitative genetic analysis demonstrates that two different cave populations have evolved similar feeding postures through a small number of genetic changes, some of which appear to be distinct. This work indicates that independently evolved populations of cavefish can evolve the same behavioral traits to adapt to similar environmental challenges by modifying different sets of genes. PMID:24085851

  3. Independently evolved upper jaw protrusion mechanisms show convergent hydrodynamic function in teleost fishes.

    PubMed

    Staab, Katie Lynn; Holzman, Roi; Hernandez, L Patricia; Wainwright, Peter C

    2012-05-01

    A protrusible upper jaw has independently evolved multiple times within teleosts and has been implicated in the success of two groups in particular: Acanthomorpha and Cypriniformes. We use digital particle image velocimetry (DPIV) to compare suction feeding flow dynamics in a representative of each of these clades: goldfish and bluegill. Using DPIV, we contrast the spatial pattern of flow, the temporal relationship between flow and head kinematics, and the contribution of jaw protrusion to the forces exerted on prey. As expected, the spatial patterns of flow were similar in the two species. However, goldfish were slower to reach maximal kinematic excursions, and were more flexible in the relative timing of jaw protrusion, other jaw movements and suction flows. Goldfish were also able to sustain flow speeds for a prolonged period of time as compared with bluegill, in part because goldfish generate lower peak flow speeds. In both species, jaw protrusion increased the force exerted on the prey. However, slower jaw protrusion in goldfish resulted in less augmentation of suction forces. This difference in force exerted on prey corresponds with differences in trophic niches and feeding behavior of the two species. The bluegill uses powerful suction to capture insect larvae whereas the goldfish uses winnowing to sort through detritus and sediment. The kinethmoid of goldfish may permit jaw protrusion that is independent of lower jaw movement, which could explain the ability of goldfish to decouple suction flows (due to buccal expansion) from upper jaw protrusion. Nevertheless, our results show that jaw protrusion allows both species to augment the force exerted on prey, suggesting that this is a fundamental benefit of jaw protrusion to suction feeders. PMID:22496281

  4. Recently evolved diversity and convergent radiations of rainforest mahoganies (Meliaceae) shed new light on the origins of rainforest hyperdiversity.

    PubMed

    Koenen, Erik J M; Clarkson, James J; Pennington, Terence D; Chatrou, Lars W

    2015-07-01

    Tropical rainforest hyperdiversity is often suggested to have evolved over a long time-span (the 'museum' model), but there is also evidence for recent rainforest radiations. The mahoganies (Meliaceae) are a prominent plant group in lowland tropical rainforests world-wide but also occur in all other tropical ecosystems. We investigated whether rainforest diversity in Meliaceae has accumulated over a long time or has more recently evolved. We inferred the largest time-calibrated phylogeny for the family to date, reconstructed ancestral states for habitat and deciduousness, estimated diversification rates and modeled potential shifts in macro-evolutionary processes using a recently developed Bayesian method. The ancestral Meliaceae is reconstructed as a deciduous species that inhabited seasonal habitats. Rainforest clades have diversified from the Late Oligocene or Early Miocene onwards. Two contemporaneous Amazonian clades have converged on similar ecologies and high speciation rates. Most species-level diversity of Meliaceae in rainforest is recent. Other studies have found steady accumulation of lineages, but the large majority of plant species diversity in rainforests is recent, suggesting (episodic) species turnover. Rainforest hyperdiversity may best be explained by recent radiations from a large stock of higher level taxa. PMID:26053172

  5. Plant and animal glycolate oxidases have a common eukaryotic ancestor and convergently duplicated to evolve long-chain 2-hydroxy acid oxidases.

    PubMed

    Esser, Christian; Kuhn, Anke; Groth, Georg; Lercher, Martin J; Maurino, Veronica G

    2014-05-01

    Glycolate oxidase (GOX) is a crucial enzyme of plant photorespiration. The encoding gene is thought to have originated from endosymbiotic gene transfer between the eukaryotic host and the cyanobacterial endosymbiont at the base of plantae. However, animals also possess GOX activities. Plant and animal GOX belong to the gene family of (L)-2-hydroxyacid-oxidases ((L)-2-HAOX). We find that all (L)-2-HAOX proteins in animals and archaeplastida go back to one ancestral eukaryotic sequence; the sole exceptions are green algae of the chlorophyta lineage. Chlorophyta replaced the ancestral eukaryotic (L)-2-HAOX with a bacterial ortholog, a lactate oxidase that may have been obtained through the primary endosymbiosis at the base of plantae; independent losses of this gene may explain its absence in other algal lineages (glaucophyta, rhodophyta, and charophyta). We also show that in addition to GOX, plants possess (L)-2-HAOX proteins with different specificities for medium- and long-chain hydroxyacids (lHAOX), likely involved in fatty acid and protein catabolism. Vertebrates possess lHAOX proteins acting on similar substrates as plant lHAOX; however, the existence of GOX and lHAOX subfamilies in both plants and animals is not due to shared ancestry but is the result of convergent evolution in the two most complex eukaryotic lineages. On the basis of targeting sequences and predicted substrate specificities, we conclude that the biological role of plantae (L)-2-HAOX in photorespiration evolved by co-opting an existing peroxisomal protein. PMID:24408912

  6. DNA shuffling method for generating highly recombined genes and evolved enzymes.

    PubMed

    Coco, W M; Levinson, W E; Crist, M J; Hektor, H J; Darzins, A; Pienkos, P T; Squires, C H; Monticello, D J

    2001-04-01

    We introduce a method of in vitro recombination or "DNA shuffling" to generate libraries of evolved enzymes. The approach relies on the ordering, trimming, and joining of randomly cleaved parental DNA fragments annealed to a transient polynucleotide scaffold. We generated chimeric libraries averaging 14.0 crossovers per gene, a several-fold higher level of recombination than observed for other methods. We also observed an unprecedented four crossovers per gene in regions of 10 or fewer bases of sequence identity. These properties allow generation of chimeras unavailable by other methods. We detected no unshuffled parental clones or duplicated "sibling" chimeras, and relatively few inactive clones. We demonstrated the method by molecular breeding of a monooxygenase for increased rate and extent of biodesulfurization on complex substrates, as well as for 20-fold faster conversion of a nonnatural substrate. This method represents a conceptually distinct and improved alternative to sexual PCR for gene family shuffling. PMID:11283594

  7. Chemiluminescence-based pesticide biosensor utilizing the intelligent evolved properties of the enzyme alkaline phosphatase

    SciTech Connect

    Ayyagari, M.; Kamtekar, S.; Pande, R.; Marx, K.; Kumar, J.

    1994-12-31

    A methodology is described for immobilizing the enzyme alkaline phosphatase onto a glass surface using a novel biotinylated copolymer, poly(3-undecylthiophene-co-3- methanoithiophene). A streptavidin conjugate of alkaline phosphatase is used in this study. The biotinylated polymer is attached to the silanized glass surface via hydrophobic interactions and the enzyme is interfaced with the polymer through the classical biotin- streptavidin interaction. Alkaline phosphatase catalyzes the dephosphorylation of a macrocyclic compound, chloro-3-(4-methoxy spiro) (1,2 dioxetane-3-2`-tricyclo-) (3.3.1.1 )-(decani-4-yl) phenyl phosphate, to a species which emits energy by chemiluminescence. This chemiluminescence signal can be detected with a photomultiplier tube for enzymatic catalysis with the biocatalyst both in solution and immobilized on a glass surface. The signal generation is inhibited by the organophosphorus based insecticides such as paraoxon as well as nerve agents. We demonstrate in this study that a number of organophosphorus based insecticides inhibit the enzyme-mediated generation of chemiluminescence signal. This is true for the enzyme conjugate both free in solution and immobilized on a glass surface. In solution, the inhibition resembles the case of a partially uncompetitive system. By this type of inhibition we are able to detect pesticides down to about 50 ppb for the enzyme in solution. The pesticide detection limit of immobilized enzyme is currently being investigated. The enzyme is capable of a number of measurement cycles without significant loss of signal level.

  8. Bioprospecting and evolving alternative xylose and arabinose pathway enzymes for use in Saccharomyces cerevisiae.

    PubMed

    Lee, Sun-Mi; Jellison, Taylor; Alper, Hal S

    2016-03-01

    Bioprospecting is an effective way to find novel enzymes from strains with desirable phenotypes. Such bioprospecting has enabled organisms such as Saccharomyces cerevisiae to utilize nonnative pentose sugars. Yet, the efficiency of this pentose catabolism (especially for the case of arabinose) remains suboptimal. Thus, further pathway optimization or identification of novel, optimal pathways is needed. Previously, we identified a novel set of xylan catabolic pathway enzymes from a superior pentose-utilizing strain of Ustilago bevomyces. These enzymes were used to successfully engineer a xylan-utilizing S. cerevisiae through a blended approach of bioprospecting and evolutionary engineering. Here, we expanded this approach to xylose and arabinose catabolic pathway engineering and demonstrated that bioprospected xylose and arabinose catabolic pathways from U. bevomyces offer alternative choices for enabling efficient pentose catabolism in S. cerevisiae. By introducing a novel set of xylose catabolic genes from U. bevomyces, growth rates were improved up to 85 % over a set of traditional Scheffersomyces stipitis pathway genes. In addition, we suggested an alternative arabinose catabolic pathway which, after directed evolution and pathway engineering, enabled S. cerevisiae to grow on arabinose as a sole carbon source in minimal medium with growth rates upwards of 0.05 h(-1). This pathway represents the most efficient growth of yeast on pure arabinose minimal medium. These pathways provide great starting points for further strain development and demonstrate the utility of bioprospecting from U. bevomyces. PMID:26671616

  9. Lipid peroxidation and antioxidant enzymes activity in Plasmodium vivax malaria patients evolving with cholestatic jaundice

    PubMed Central

    2013-01-01

    Background Plasmodium vivax infection has been considered a benign and self-limiting disease, however, recent studies highlight the association between vivax malaria and life-threatening manifestations. Increase in reactive oxygen species has already been described in vivax malaria, as a result of the increased metabolic rate triggered by the multiplying parasite, and large quantities of toxic redox-active byproducts generated. The present study aimed to study the oxidative stress responses in patients infected with P. vivax, who developed jaundice (hyperbilirubinaemia) in the course of the disease, a common clinical complication related to this species. Methods An evaluation of the lipid peroxidation and antioxidant enzymes profile was performed in 28 healthy individuals and compared with P. vivax infected patients with jaundice, i.e., bilirubin < 51.3 μmol/L (8 patients) or without jaundice (34 patients), on day 1 (D1) and day 14 (D14) after anti-malarial therapy. Results Hyperbilirubinaemia was more frequent among women and patients experiencing their first malarial infection, and lower haemoglobin and higher lactate dehydrogenase levels were observed in this group. Malondialdehyde levels and activity of celuroplasmin and glutathione reductase were increased in the plasma from patients with P. vivax with jaundice compared to the control group on D1. However, the activity of thioredoxin reductase was decreased. The enzymes glutathione reductase, thioredoxin reductase, thiols and malondialdehyde also differed between jaundiced versus non-jaundiced patients. On D14 jaundice and parasitaemia had resolved and oxidative stress biomarkers were very similar to the control group. Conclusion Cholestatic hyperbilirubinaemia in vivax malaria cannot be totally disassociated from malaria-related haemolysis. However, significant increase of lipid peroxidation markers and changes in antioxidant enzymes in patients with P. vivax-related jaundice was observed. These results

  10. Convergence Is Real

    ERIC Educational Resources Information Center

    Enyeart, Mike; Staman, E. Michael; Valdes, Jose J., Jr.

    2007-01-01

    The concept of convergence has evolved significantly during recent years. Today, "convergence" refers to the integration of the communications and computing resources and services that seamlessly traverse multiple infrastructures and deliver content to multiple platforms or appliances. Convergence is real. Those in higher education, and especially…

  11. Enzyme

    MedlinePlus

    Enzymes are complex proteins that cause a specific chemical change in all parts of the body. For ... use them. Blood clotting is another example of enzymes at work. Enzymes are needed for all body ...

  12. Convergent evidences from human and animal studies implicate angiotensin I-converting enzyme activity in cognitive performance in schizophrenia.

    PubMed

    Gadelha, A; Vendramini, A M; Yonamine, C M; Nering, M; Berberian, A; Suiama, M A; Oliveira, V; Lima-Landman, M T; Breen, G; Bressan, R A; Abílio, V; Hayashi, M A F

    2015-01-01

    In schizophrenia (SCZ), higher angiotensin I-converting enzyme (ACE) levels have been reported in patient's blood and cerebrospinal fluid (CSF). Hereby, we propose to explore whether the ACE activity levels are associated to cognitive performance in SCZ. Seventy-two patients with SCZ or schizoaffective disorder diagnosis, and 69 healthy controls (HCs) underwent a cognitive battery with parallel collection of peripheral blood samples to measure ACE activity. Significant higher ACE activity levels were confirmed in the plasma of SCZ patients compared with HCs (Student's t=-5.216; P<0.001). ACE activity significantly correlated to Hopkins delayed recall measures (r=-0.247; P=0.004) and Hopkins total (r=-0.214; P=0.012). Subjects grouped as high ACE activity (above average) had worse performance compared with low ACE activity level group for Hopkins delayed recall measure, even after correction for clinical condition, age, gender and years of education (P=0.029). The adjusted R squared for this final model was 0.343. This result was evident only comparing extreme groups for ACE activity, when splitting the sample in three groups with similar number of subjects. To clarify this finding, we performed an evaluation of the cognitive performance of transgenic mice with three copies of ACE gene in novel object recognition (NOR) test, which showed that such animals presented impairment in NOR (P<0.05) compared with two copies of wild-type animals. The results observed in SCZ patients and animal model suggest both the association of ACE to cognitive deficits in SCZ. This finding may support the evaluation of novel treatment protocols and/or of innovative drugs for specific intervention of cognitive deficits in SCZ envisioning concomitant ACE activity and behavior evaluations. PMID:26645626

  13. Convergence Insufficiency

    MedlinePlus

    ... Eye Terms Conditions Frequently Asked Questions Español Condiciones Chinese Conditions Convergence Insufficiency En Español Read in Chinese What is convergence insufficiency? Convergence insufficiency is the ...

  14. Modularity of Conifer Diterpene Resin Acid Biosynthesis: P450 Enzymes of Different CYP720B Clades Use Alternative Substrates and Converge on the Same Products1[OPEN

    PubMed Central

    Yuen, Macaire M.S.; Bohlmann, Jörg

    2016-01-01

    Cytochrome P450 enzymes of the CYP720B subfamily play a central role in the biosynthesis of diterpene resin acids (DRAs), which are a major component of the conifer oleoresin defense system. CYP720Bs exist in families of up to a dozen different members in conifer genomes and fall into four different clades (I–IV). Only two CYP720B members, loblolly pine (Pinus taeda) PtCYP720B1 and Sitka spruce (Picea sitchensis) PsCYP720B4, have been characterized previously. Both are multisubstrate and multifunctional clade III enzymes, which catalyze consecutive three-step oxidations in the conversion of diterpene olefins to DRAs. These reactions resemble the sequential diterpene oxidations affording ent-kaurenoic acid from ent-kaurene in gibberellin biosynthesis. Here, we functionally characterized the CYP720B clade I enzymes CYP720B2 and CYP720B12 in three different conifer species, Sitka spruce, lodgepole pine (Pinus contorta), and jack pine (Pinus banksiana), and compared their activities with those of the clade III enzymes CYP720B1 and CYP720B4 of the same species. Unlike the clade III enzymes, clade I enzymes were ultimately found not to be active with diterpene olefins but converted the recently discovered, unstable diterpene synthase product 13-hydroxy-8(14)-abietene. Through alternative routes, CYP720B enzymes of both clades produce some of the same profiles of conifer oleoresin DRAs (abietic acid, neoabietic acid, levopimaric acid, and palustric acid), while clade III enzymes also function in the formation of pimaric acid, isopimaric acid, and sandaracopimaric acid. These results highlight the modularity of the specialized (i.e. secondary) diterpene metabolism, which produces conifer defense metabolites through variable combinations of different diterpene synthase and CYP720B enzymes. PMID:26936895

  15. Modularity of Conifer Diterpene Resin Acid Biosynthesis: P450 Enzymes of Different CYP720B Clades Use Alternative Substrates and Converge on the Same Products.

    PubMed

    Geisler, Katrin; Jensen, Niels Berg; Yuen, Macaire M S; Madilao, Lina; Bohlmann, Jörg

    2016-05-01

    Cytochrome P450 enzymes of the CYP720B subfamily play a central role in the biosynthesis of diterpene resin acids (DRAs), which are a major component of the conifer oleoresin defense system. CYP720Bs exist in families of up to a dozen different members in conifer genomes and fall into four different clades (I-IV). Only two CYP720B members, loblolly pine (Pinus taeda) PtCYP720B1 and Sitka spruce (Picea sitchensis) PsCYP720B4, have been characterized previously. Both are multisubstrate and multifunctional clade III enzymes, which catalyze consecutive three-step oxidations in the conversion of diterpene olefins to DRAs. These reactions resemble the sequential diterpene oxidations affording ent-kaurenoic acid from ent-kaurene in gibberellin biosynthesis. Here, we functionally characterized the CYP720B clade I enzymes CYP720B2 and CYP720B12 in three different conifer species, Sitka spruce, lodgepole pine (Pinus contorta), and jack pine (Pinus banksiana), and compared their activities with those of the clade III enzymes CYP720B1 and CYP720B4 of the same species. Unlike the clade III enzymes, clade I enzymes were ultimately found not to be active with diterpene olefins but converted the recently discovered, unstable diterpene synthase product 13-hydroxy-8(14)-abietene. Through alternative routes, CYP720B enzymes of both clades produce some of the same profiles of conifer oleoresin DRAs (abietic acid, neoabietic acid, levopimaric acid, and palustric acid), while clade III enzymes also function in the formation of pimaric acid, isopimaric acid, and sandaracopimaric acid. These results highlight the modularity of the specialized (i.e. secondary) diterpene metabolism, which produces conifer defense metabolites through variable combinations of different diterpene synthase and CYP720B enzymes. PMID:26936895

  16. Convergence Insufficiency

    MedlinePlus

    ... insufficiency? Symptoms of convergence insufficiency include diplopia (double vision) and headaches when reading. Many patients will complain that they have difficulty concentrating on near work (computer, reading, etc.) and that the written word blurs ...

  17. Adenine phosphoribosyltransferase from Sulfolobus solfataricus is an enzyme with unusual kinetic properties and a crystal structure that suggests it evolved from a 6-oxopurine phosphoribosyltransferase.

    PubMed

    Jensen, Kaj Frank; Hansen, Michael Riis; Jensen, Kristine Steen; Christoffersen, Stig; Poulsen, Jens-Christian Navarro; Mølgaard, Anne; Kadziola, Anders

    2015-04-14

    The adenine phosphoribosyltransferase (APRTase) encoded by the open reading frame SSO2342 of Sulfolobus solfataricus P2 was subjected to crystallographic, kinetic, and ligand binding analyses. The enzyme forms dimers in solution and in the crystals, and binds one molecule of the reactants 5-phosphoribosyl-α-1-pyrophosphate (PRPP) and adenine or the product adenosine monophosphate (AMP) or the inhibitor adenosine diphosphate (ADP) in each active site. The individual subunit adopts an overall structure that resembles a 6-oxopurine phosphoribosyltransferase (PRTase) more than known APRTases implying that APRT functionality in Crenarchaeotae has its evolutionary origin in this family of PRTases. Only the N-terminal two-thirds of the polypeptide chain folds as a traditional type I PRTase with a five-stranded β-sheet surrounded by helices. The C-terminal third adopts an unusual three-helix bundle structure that together with the nucleobase-binding loop undergoes a conformational change upon binding of adenine and phosphate resulting in a slight contraction of the active site. The inhibitor ADP binds like the product AMP with both the α- and β-phosphates occupying the 5'-phosphoribosyl binding site. The enzyme shows activity over a wide pH range, and the kinetic and ligand binding properties depend on both pH and the presence/absence of phosphate in the buffers. A slow hydrolysis of PRPP to ribose 5-phosphate and pyrophosphate, catalyzed by the enzyme, may be facilitated by elements in the C-terminal three-helix bundle part of the protein. PMID:25790177

  18. Natural Variants of the KPC-2 Carbapenemase have Evolved Increased Catalytic Efficiency for Ceftazidime Hydrolysis at the Cost of Enzyme Stability

    PubMed Central

    Mehta, Shrenik C.; Rice, Kacie; Palzkill, Timothy

    2015-01-01

    The spread of β-lactamases that hydrolyze penicillins, cephalosporins and carbapenems among Gram-negative bacteria has limited options for treating bacterial infections. Initially, Klebsiella pneumoniae carbapenemase-2 (KPC-2) emerged as a widespread carbapenem hydrolyzing β-lactamase that also hydrolyzes penicillins and cephalosporins but not cephamycins and ceftazidime. In recent years, single and double amino acid substitution variants of KPC-2 have emerged among clinical isolates that show increased resistance to ceftazidime. Because it confers multi-drug resistance, KPC β-lactamase is a threat to public health. In this study, the evolution of KPC-2 function was determined in nine clinically isolated variants by examining the effects of the substitutions on enzyme kinetic parameters, protein stability and antibiotic resistance profile. The results indicate that the amino acid substitutions associated with KPC-2 natural variants lead to increased catalytic efficiency for ceftazidime hydrolysis and a consequent increase in ceftazidime resistance. Single substitutions lead to modest increases in catalytic activity while the double mutants exhibit significantly increased ceftazidime hydrolysis and resistance levels. The P104R, V240G and H274Y substitutions in single and double mutant combinations lead to the largest increases in ceftazidime hydrolysis and resistance. Molecular modeling suggests that the P104R and H274Y mutations could facilitate ceftazidime hydrolysis through increased hydrogen bonding interactions with the substrate while the V240G substitution may enhance backbone flexibility so that larger substrates might be accommodated in the active site. Additionally, we observed a strong correlation between gain of catalytic function for ceftazidime hydrolysis and loss of enzyme stability, which is in agreement with the ‘stability-function tradeoff’ phenomenon. The high Tm of KPC-2 (66.5°C) provides an evolutionary advantage as compared to other

  19. Giant lobelias exemplify convergent evolution

    PubMed Central

    2010-01-01

    Giant lobeliads on tropical mountains in East Africa and Hawaii have highly unusual, giant-rosette growth forms that appear to be convergent on each other and on those of several independently evolved groups of Asteraceae and other families. A recent phylogenetic analysis by Antonelli, based on sequencing the widest selection of lobeliads to date, raises doubts about this paradigmatic example of convergent evolution. Here I address the kinds of evidence needed to test for convergent evolution and argue that the analysis by Antonelli fails on four points. Antonelli's analysis makes several important contributions to our understanding of lobeliad evolution and geographic spread, but his claim regarding convergence appears to be invalid. Giant lobeliads in Hawaii and Africa represent paradigmatic examples of convergent evolution. PMID:20074322

  20. Evolution: convergence in dinosaur crests.

    PubMed

    Hone, David W E

    2015-06-15

    The horned, ceratopsid dinosaurs can be easily split into two major groups based on their cranial structures, but now a new discovery shows that at least one genus 'switched sides' and convergently evolved the form of the other clade. PMID:26079078

  1. Discovery of a Promiscuous Non-Heme Iron Halogenase in Ambiguine Alkaloid Biogenesis: Implication for an Evolvable Enzyme Family for Late-Stage Halogenation of Aliphatic Carbons in Small Molecules.

    PubMed

    Hillwig, Matthew L; Zhu, Qin; Ittiamornkul, Kuljira; Liu, Xinyu

    2016-05-01

    The elucidation of enigmatic enzymatic chlorination timing in ambiguine indole alkaloid biogenesis led to the discovery and characterization of AmbO5 protein as a promiscuous non-heme iron aliphatic halogenase. AmbO5 was shown capable of selectively modifying seven structurally distinct ambiguine, fischerindole and hapalindole alkaloids with chlorine via late-stage aliphatic C-H group functionalization. Cross-comparison of AmbO5 with a previously characterized aliphatic halogenase homolog WelO5 that has a restricted substrate scope led to the identification of a C-terminal sequence motif important for substrate tolerance and specificity. Mutagenesis of 18 residues of WelO5 within the identified sequence motif led to a functional mutant with an expanded substrate scope identical to AmbO5, but an altered substrate specificity from the wild-type enzymes. These observations collectively provide evidence on the evolvable nature of AmbO5/WelO5 enzyme duo in the context of hapalindole-type alkaloid biogenesis and implicate their promise for the future development of designer biocatalysis for the selective late-stage modification of unactivated aliphatic carbon centers in small molecules with halogens. PMID:27027281

  2. Convergent Evolution of Polysaccharide Debranching Defines a Common Mechanism for Starch Accumulation in Cyanobacteria and Plants[W

    PubMed Central

    Cenci, Ugo; Chabi, Malika; Ducatez, Mathieu; Tirtiaux, Catherine; Nirmal-Raj, Jennifer; Utsumi, Yoshinori; Kobayashi, Daiki; Sasaki, Satoshi; Suzuki, Eiji; Nakamura, Yasunori; Putaux, Jean-Luc; Roussel, Xavier; Durand-Terrasson, Amandine; Bhattacharya, Debashish; Vercoutter-Edouart, Anne-Sophie; Maes, Emmanuel; Arias, Maria Cecilia; Palcic, Monica; Sim, Lyann; Ball, Steven G.; Colleoni, Christophe

    2013-01-01

    Starch, unlike hydrosoluble glycogen particles, aggregates into insoluble, semicrystalline granules. In photosynthetic eukaryotes, the transition to starch accumulation occurred after plastid endosymbiosis from a preexisting cytosolic host glycogen metabolism network. This involved the recruitment of a debranching enzyme of chlamydial pathogen origin. The latter is thought to be responsible for removing misplaced branches that would otherwise yield a water-soluble polysaccharide. We now report the implication of starch debranching enzyme in the aggregation of semicrystalline granules of single-cell cyanobacteria that accumulate both glycogen and starch-like polymers. We show that an enzyme of analogous nature to the plant debranching enzyme but of a different bacterial origin was recruited for the same purpose in these organisms. Remarkably, both the plant and cyanobacterial enzymes have evolved through convergent evolution, showing novel yet identical substrate specificities from a preexisting enzyme that originally displayed the much narrower substrate preferences required for glycogen catabolism. PMID:24163312

  3. Do convergent developmental mechanisms underlie convergent phenotypes?

    NASA Technical Reports Server (NTRS)

    Wray, Gregory A.

    2002-01-01

    Convergence is a pervasive evolutionary process, affecting many aspects of phenotype and even genotype. Relatively little is known about convergence in developmental processes, however, nor about the degree to which convergence in development underlies convergence in anatomy. A switch in the ecology of sea urchins from feeding to nonfeeding larvae illustrates how convergence in development can be associated with convergence in anatomy. Comparisons to more distantly related taxa, however, suggest that this association may be limited to relatively close phylogenetic comparisons. Similarities in gene expression during development provide another window into the association between convergence in developmental processes and convergence in anatomy. Several well-studied transcription factors exhibit likely cases of convergent gene expression in distantly related animal phyla. Convergence in regulatory gene expression domains is probably more common than generally acknowledged, and can arise for several different reasons. Copyright 2002 S. Karger AG, Basel.

  4. Enzyme Informatics

    PubMed Central

    Alderson, Rosanna G.; Ferrari, Luna De; Mavridis, Lazaros; McDonagh, James L.; Mitchell, John B. O.; Nath, Neetika

    2012-01-01

    Over the last 50 years, sequencing, structural biology and bioinformatics have completely revolutionised biomolecular science, with millions of sequences and tens of thousands of three dimensional structures becoming available. The bioinformatics of enzymes is well served by, mostly free, online databases. BRENDA describes the chemistry, substrate specificity, kinetics, preparation and biological sources of enzymes, while KEGG is valuable for understanding enzymes and metabolic pathways. EzCatDB, SFLD and MACiE are key repositories for data on the chemical mechanisms by which enzymes operate. At the current rate of genome sequencing and manual annotation, human curation will never finish the functional annotation of the ever-expanding list of known enzymes. Hence there is an increasing need for automated annotation, though it is not yet widespread for enzyme data. In contrast, functional ontologies such as the Gene Ontology already profit from automation. Despite our growing understanding of enzyme structure and dynamics, we are only beginning to be able to design novel enzymes. One can now begin to trace the functional evolution of enzymes using phylogenetics. The ability of enzymes to perform secondary functions, albeit relatively inefficiently, gives clues as to how enzyme function evolves. Substrate promiscuity in enzymes is one example of imperfect specificity in protein-ligand interactions. Similarly, most drugs bind to more than one protein target. This may sometimes result in helpful polypharmacology as a drug modulates plural targets, but also often leads to adverse side-effects. Many cheminformatics approaches can be used to model the interactions between druglike molecules and proteins in silico. We can even use quantum chemical techniques like DFT and QM/MM to compute the structural and energetic course of enzyme catalysed chemical reaction mechanisms, including a full description of bond making and breaking. PMID:23116471

  5. Evolving phenotypic networks in silico.

    PubMed

    François, Paul

    2014-11-01

    Evolved gene networks are constrained by natural selection. Their structures and functions are consequently far from being random, as exemplified by the multiple instances of parallel/convergent evolution. One can thus ask if features of actual gene networks can be recovered from evolutionary first principles. I review a method for in silico evolution of small models of gene networks aiming at performing predefined biological functions. I summarize the current implementation of the algorithm, insisting on the construction of a proper "fitness" function. I illustrate the approach on three examples: biochemical adaptation, ligand discrimination and vertebrate segmentation (somitogenesis). While the structure of the evolved networks is variable, dynamics of our evolved networks are usually constrained and present many similar features to actual gene networks, including properties that were not explicitly selected for. In silico evolution can thus be used to predict biological behaviours without a detailed knowledge of the mapping between genotype and phenotype. PMID:24956562

  6. Searching for convergent evolution in manganese superoxidase dismutase using hydrophobic cluster analysis

    PubMed Central

    Xiang, Heng; Zhang, Ruizhi; Li, Nengzhang; Vossbrinck, Charles R.

    2014-01-01

    There are numerous examples of convergent evolution in nature. Major ecological adaptations such as flight, loss of limbs in vertebrates, pesticide resistance, adaptation to a parasitic way of life, etc., have all evolved more than once, as seen by their analogous functions in separate taxa. But what about protein evolution? Does the environment have a strong enough influence on intracellular processes that enzymes and other functional proteins play, to evolve similar functional roles separately in different organisms? Manganese Superoxide Dismutase (MnSOD) is a manganesedependant metallo-enzyme which plays a crucial role in protecting cells from anti-oxidative stress by eliminating reactive (superoxide) oxygen species. It is a ubiquitous housekeeping enzyme found in nearly all organisms. In this study we compare phylogenies based on MnSOD protein sequences to those based on scores from Hydrophobic Cluster Analysis (HCA). We calculated HCA similarity values for each pair of taxa to obtain a pair-wise distance matrix. A UPGMA tree based on the HCA distance matrix and a common tree based on the primary protein sequence for MnSOD was constructed. Differences between these two trees within animals, enterobacteriaceae, planctomycetes and cyanobacteria are presented and cited as possible examples of convergence. We note that several residue changes result in changes in hydrophobicity at positions which apparently are under the effect of positive selection. PMID:25071412

  7. Convergent evolution of the genomes of marine mammals.

    PubMed

    Foote, Andrew D; Liu, Yue; Thomas, Gregg W C; Vinař, Tomáš; Alföldi, Jessica; Deng, Jixin; Dugan, Shannon; van Elk, Cornelis E; Hunter, Margaret E; Joshi, Vandita; Khan, Ziad; Kovar, Christie; Lee, Sandra L; Lindblad-Toh, Kerstin; Mancia, Annalaura; Nielsen, Rasmus; Qin, Xiang; Qu, Jiaxin; Raney, Brian J; Vijay, Nagarjun; Wolf, Jochen B W; Hahn, Matthew W; Muzny, Donna M; Worley, Kim C; Gilbert, M Thomas P; Gibbs, Richard A

    2015-03-01

    Marine mammals from different mammalian orders share several phenotypic traits adapted to the aquatic environment and therefore represent a classic example of convergent evolution. To investigate convergent evolution at the genomic level, we sequenced and performed de novo assembly of the genomes of three species of marine mammals (the killer whale, walrus and manatee) from three mammalian orders that share independently evolved phenotypic adaptations to a marine existence. Our comparative genomic analyses found that convergent amino acid substitutions were widespread throughout the genome and that a subset of these substitutions were in genes evolving under positive selection and putatively associated with a marine phenotype. However, we found higher levels of convergent amino acid substitutions in a control set of terrestrial sister taxa to the marine mammals. Our results suggest that, whereas convergent molecular evolution is relatively common, adaptive molecular convergence linked to phenotypic convergence is comparatively rare. PMID:25621460

  8. Convergent evolution of the genomes of marine mammals

    USGS Publications Warehouse

    Foote, Andrew D.; Liu, Yue; Thomas, Gregg W.C.; Vinař, Tomáš; Alföldi, Jessica; Deng, Jixin; Dugan, Shannon; van Elk, Cornelis E.; Hunter, Margaret; Joshi, Vandita; Khan, Ziad; Kovar, Christie; Lee, Sandra L.; Lindblad-Toh, Kerstin; Mancia, Annalaura; Nielsen, Rasmus; Qin, Xiang; Qu, Jiaxin; Raney, Brian J.; Vijay, Nagarjun; Wolf, Jochen B. W.; Hahn, Matthew W.; Muzny, Donna M.; Worley, Kim C.; Gilbert, M. Thomas P.; Gibbs, Richard A.

    2015-01-01

    Marine mammals from different mammalian orders share several phenotypic traits adapted to the aquatic environment and therefore represent a classic example of convergent evolution. To investigate convergent evolution at the genomic level, we sequenced and performed de novo assembly of the genomes of three species of marine mammals (the killer whale, walrus and manatee) from three mammalian orders that share independently evolved phenotypic adaptations to a marine existence. Our comparative genomic analyses found that convergent amino acid substitutions were widespread throughout the genome and that a subset of these substitutions were in genes evolving under positive selection and putatively associated with a marine phenotype. However, we found higher levels of convergent amino acid substitutions in a control set of terrestrial sister taxa to the marine mammals. Our results suggest that, whereas convergent molecular evolution is relatively common, adaptive molecular convergence linked to phenotypic convergence is comparatively rare.

  9. Convergent evolution of the genomes of marine mammals

    PubMed Central

    Foote, Andrew D.; Liu, Yue; Thomas, Gregg W.C.; Vinař, Tomáš; Alföldi, Jessica; Deng, Jixin; Dugan, Shannon; van Elk, Cornelis E.; Hunter, Margaret E.; Joshi, Vandita; Khan, Ziad; Kovar, Christie; Lee, Sandra L.; Lindblad-Toh, Kerstin; Mancia, Annalaura; Nielsen, Rasmus; Qin, Xiang; Qu, Jiaxin; Raney, Brian J.; Vijay, Nagarjun; Wolf, Jochen B. W.; Hahn, Matthew W.; Muzny, Donna M.; Worley, Kim C.; Gilbert, M. Thomas P.; Gibbs, Richard A.

    2015-01-01

    Marine mammals from different mammalian orders share several phenotypic traits adapted to the aquatic environment and are therefore a classic example of convergent evolution. To investigate convergent evolution at the genomic level, we sequenced and de novo assembled the genomes of three species of marine mammals (the killer whale, walrus and manatee) from three mammalian orders that share independently evolved phenotypic adaptations to a marine existence. Our comparative genomic analyses found that convergent amino acid substitutions were widespread throughout the genome, and that a subset were in genes evolving under positive selection and putatively associated with a marine phenotype. However, we found higher levels of convergent amino acid substitutions in a control set of terrestrial sister taxa to the marine mammals. Our results suggest that while convergent molecular evolution is relatively common, adaptive molecular convergence linked to phenotypic convergence is comparatively rare. PMID:25621460

  10. Compartments, Customers, or Convergence?: Evolving Challenges to IT Progress

    ERIC Educational Resources Information Center

    Jackson, Gregory A.

    2007-01-01

    For most of the past decade, IT leaders in higher education felt on top of things. Challenges were usually comprehensible and addressable, doing reasonable things yielded reasonable results, and for the most part, IT was a substantial contributor to institutional progress. But these days, IT leaders rarely feel on top of things. Instead, some days…

  11. The Convergence of Intelligences

    NASA Astrophysics Data System (ADS)

    Diederich, Joachim

    Minsky (1985) argued an extraterrestrial intelligence may be similar to ours despite very different origins. ``Problem- solving'' offers evolutionary advantages and individuals who are part of a technical civilisation should have this capacity. On earth, the principles of problem-solving are the same for humans, some primates and machines based on Artificial Intelligence (AI) techniques. Intelligent systems use ``goals'' and ``sub-goals'' for problem-solving, with memories and representations of ``objects'' and ``sub-objects'' as well as knowledge of relations such as ``cause'' or ``difference.'' Some of these objects are generic and cannot easily be divided into parts. We must, therefore, assume that these objects and relations are universal, and a general property of intelligence. Minsky's arguments from 1985 are extended here. The last decade has seen the development of a general learning theory (``computational learning theory'' (CLT) or ``statistical learning theory'') which equally applies to humans, animals and machines. It is argued that basic learning laws will also apply to an evolved alien intelligence, and this includes limitations of what can be learned efficiently. An example from CLT is that the general learning problem for neural networks is intractable, i.e. it cannot be solved efficiently for all instances (it is ``NP-complete''). It is the objective of this paper to show that evolved intelligences will be constrained by general learning laws and will use task-decomposition for problem-solving. Since learning and problem-solving are core features of intelligence, it can be said that intelligences converge despite very different origins.

  12. Evolvable synthetic neural system

    NASA Technical Reports Server (NTRS)

    Curtis, Steven A. (Inventor)

    2009-01-01

    An evolvable synthetic neural system includes an evolvable neural interface operably coupled to at least one neural basis function. Each neural basis function includes an evolvable neural interface operably coupled to a heuristic neural system to perform high-level functions and an autonomic neural system to perform low-level functions. In some embodiments, the evolvable synthetic neural system is operably coupled to one or more evolvable synthetic neural systems in a hierarchy.

  13. Formation of polarity convergences underlying shoot outgrowths.

    PubMed

    Abley, Katie; Sauret-Güeto, Susanna; Marée, Athanasius Fm; Coen, Enrico

    2016-01-01

    The development of outgrowths from plant shoots depends on formation of epidermal sites of cell polarity convergence with high intracellular auxin at their centre. A parsimonious model for generation of convergence sites is that cell polarity for the auxin transporter PIN1 orients up auxin gradients, as this spontaneously generates convergent alignments. Here we test predictions of this and other models for the patterns of auxin biosynthesis and import. Live imaging of outgrowths from kanadi1 kanadi2 Arabidopsis mutant leaves shows that they arise by formation of PIN1 convergence sites within a proximodistal polarity field. PIN1 polarities are oriented away from regions of high auxin biosynthesis enzyme expression, and towards regions of high auxin importer expression. Both expression patterns are required for normal outgrowth emergence, and may form part of a common module underlying shoot outgrowths. These findings are more consistent with models that spontaneously generate tandem rather than convergent alignments. PMID:27478985

  14. Tryptophan-Catabolizing Enzymes – Party of Three

    PubMed Central

    Ball, Helen J.; Jusof, Felicita F.; Bakmiwewa, Supun M.; Hunt, Nicholas H.; Yuasa, Hajime J.

    2014-01-01

    Indoleamine 2,3-dioxygenase (IDO) and tryptophan 2,3-dioxygenase (TDO) are tryptophan-degrading enzymes that have independently evolved to catalyze the first step in tryptophan catabolism via the kynurenine pathway (KP). The depletion of tryptophan and formation of KP metabolites modulates the activity of the mammalian immune, reproductive, and central nervous systems. IDO and TDO enzymes can have overlapping or distinct functions depending on their expression patterns. The expression of TDO and IDO enzymes in mammals differs not only by tissue/cellular localization but also by their induction by distinct stimuli. To add to the complexity, these genes also have undergone duplications in some organisms leading to multiple isoforms of IDO or TDO. For example, many vertebrates, including all mammals, have acquired two IDO genes via gene duplication, although the IDO1-like gene has been lost in some lower vertebrate lineages. Gene duplications can allow the homologs to diverge and acquire different properties to the original gene. There is evidence for IDO enzymes having differing enzymatic characteristics, signaling properties, and biological functions. This review analyzes the evolutionary convergence of IDO and TDO enzymes as tryptophan-catabolizing enzymes and the divergent evolution of IDO homologs to generate an enzyme family with diverse characteristics not possessed by TDO enzymes, with an emphasis on the immune system. PMID:25346733

  15. Gradual neofunctionalization in the convergent evolution of trichomonad lactate and malate dehydrogenases

    PubMed Central

    Steindel, Phillip A.; Chen, Emily H.; Wirth, Jacob D.

    2016-01-01

    Abstract Lactate and malate dehydrogenases (LDH and MDH) are homologous, core metabolic enzymes common to nearly all living organisms. LDHs have evolved convergently from MDHs at least four times, achieving altered substrate specificity by a different mechanism each time. For instance, the LDH of anaerobic trichomonad parasites recently evolved independently from an ancestral trichomonad MDH by gene duplication. LDH plays a central role in trichomonad metabolism by catalyzing the reduction of pyruvate to lactate, thereby regenerating the NAD+ required for glycolysis. Using ancestral reconstruction methods, we identified the biochemical and evolutionary mechanisms responsible for this convergent event. The last common ancestor of these enzymes was a highly specific MDH, similar to modern trichomonad MDHs. In contrast, the LDH lineage evolved promiscuous activity by relaxing specificity in a gradual process of neofunctionalization involving one highly detrimental substitution at the “specificity residue” (R91L) and many additional mutations of small effect. L91 has different functional consequences in LDHs and in MDHs, indicating a prominent role for epistasis. Crystal structures of modern‐day and ancestral enzymes show that the evolution of substrate specificity paralleled structural changes in dimerization and α‐helix orientation. The relatively small “specificity residue” of the trichomonad LDHs can accommodate a range of substrate sizes and may permit solvent to access the active site, both of which promote substrate promiscuity. The trichomonad LDHs present a multi‐faceted counterpoint to the independent evolution of LDHs in other organisms and illustrate the diverse mechanisms by which protein function, structure, and stability coevolve. PMID:26889885

  16. The definition, recognition, and interpretation of convergent evolution, and two new measures for quantifying and assessing the significance of convergence.

    PubMed

    Stayton, C Tristan

    2015-08-01

    Convergent evolution is an important phenomenon in the history of life. Despite this, there is no common definition of convergence used by biologists. Instead, several conceptually different definitions are employed. The primary dichotomy is between pattern-based definitions, where independently evolved similarity is sufficient for convergence, and process-based definitions, where convergence requires a certain process to produce this similarity. The unacknowledged diversity of definitions can lead to problems in evolutionary research. Process-based definitions may bias researchers away from studying or recognizing other sources of independently evolved similarity, or lead researchers to interpret convergent patterns as necessarily caused by a given process. Thus, pattern-based definitions are recommended. Existing measures of convergence are reviewed, and two new measures are developed. Both are pattern based and conceptually minimal, quantifying nothing but independently evolved similarity. One quantifies the amount of phenotypic distance between two lineages that is closed by subsequent evolution; the other simply counts the number of lineages entering a region of phenotypic space. The behavior of these measures is explored in simulations; both show acceptable Type I and Type II error. The study of convergent evolution will be facilitated if researchers are explicit about working definitions of convergence and adopt a standard toolbox of convergence measures. PMID:26177938

  17. Convergence in Multispecies Interactions.

    PubMed

    Bittleston, Leonora S; Pierce, Naomi E; Ellison, Aaron M; Pringle, Anne

    2016-04-01

    The concepts of convergent evolution and community convergence highlight how selective pressures can shape unrelated organisms or communities in similar ways. We propose a related concept, convergent interactions, to describe the independent evolution of multispecies interactions with similar physiological or ecological functions. A focus on convergent interactions clarifies how natural selection repeatedly favors particular kinds of associations among species. Characterizing convergent interactions in a comparative context is likely to facilitate prediction of the ecological roles of organisms (including microbes) in multispecies interactions and selective pressures acting in poorly understood or newly discovered multispecies systems. We illustrate the concept of convergent interactions with examples: vertebrates and their gut bacteria; ectomycorrhizae; insect-fungal-bacterial interactions; pitcher-plant food webs; and ants and ant-plants. PMID:26858111

  18. Adenylate-forming enzymes.

    PubMed

    Schmelz, Stefan; Naismith, James H

    2009-12-01

    Thioesters, amides, and esters are common chemical building blocks in a wide array of natural products. The formation of these bonds can be catalyzed in a variety of ways. For chemists, the use of an activating group is a common strategy and adenylate enzymes are exemplars of this approach. Adenylating enzymes activate the otherwise unreactive carboxylic acid by transforming the normal hydroxyl leaving group into adenosine monophosphate. Recently there have been a number of studies of such enzymes and in this review we suggest a new classification scheme. The review highlights the diversity in enzyme fold, active site architecture, and metal coordination that has evolved to catalyze this particular reaction. PMID:19836944

  19. Prokaryote and eukaryote evolvability.

    PubMed

    Poole, Anthony M; Phillips, Matthew J; Penny, David

    2003-05-01

    The concept of evolvability covers a broad spectrum of, often contradictory, ideas. At one end of the spectrum it is equivalent to the statement that evolution is possible, at the other end are untestable post hoc explanations, such as the suggestion that current evolutionary theory cannot explain the evolution of evolvability. We examine similarities and differences in eukaryote and prokaryote evolvability, and look for explanations that are compatible with a wide range of observations. Differences in genome organisation between eukaryotes and prokaryotes meets this criterion. The single origin of replication in prokaryote chromosomes (versus multiple origins in eukaryotes) accounts for many differences because the time to replicate a prokaryote genome limits its size (and the accumulation of junk DNA). Both prokaryotes and eukaryotes appear to switch from genetic stability to genetic change in response to stress. We examine a range of stress responses, and discuss how these impact on evolvability, particularly in unicellular organisms versus complex multicellular ones. Evolvability is also limited by environmental interactions (including competition) and we describe a model that places limits on potential evolvability. Examples are given of its application to predator competition and limits to lateral gene transfer. We suggest that unicellular organisms evolve largely through a process of metabolic change, resulting in biochemical diversity. Multicellular organisms evolve largely through morphological changes, not through extensive changes to cellular biochemistry. PMID:12689728

  20. Evolvable, reconfigurable hardware for future space systems

    NASA Technical Reports Server (NTRS)

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

    2002-01-01

    This paper overviews Evolvable Hardware (EHW) technology, examining its potential for enhancing survivability and flexibility of future space systems. EHW refers to selfconfiguration of electronic hardware by evolutionary/genetic search mechanisms. Evolvable Hardware can maintain existing functionality in the presence of faults and degradations due to aging, temperature and radiation. It can also configure itself for new functionality when required for mission changes or encountered opportunities. The paper illustrates hardware evolution in silicon using a JPL-designed programmable device reconfigurable at transistor level as the platform and a genetic algorithm running on a DSP as the reconfiguration mechanism. Rapid reconfiguration allows convergence to circuit solutions in the order of seconds. The experiments demonstrate functional recovery from faults as well as from degradation at extreme temperatures indicating the possibility of expanding the operational range of extreme electronics through evolved circuit solutions.

  1. Testing Convergence Versus History: Convergence Dominates Phenotypic Evolution for over 150 Million Years in Frogs.

    PubMed

    Moen, Daniel S; Morlon, Hélène; Wiens, John J

    2016-01-01

    Striking evolutionary convergence can lead to similar sets of species in different locations, such as in cichlid fishes and Anolis lizards, and suggests that evolution can be repeatable and predictable across clades. Yet, most examples of convergence involve relatively small temporal and/or spatial scales. Some authors have speculated that at larger scales (e.g., across continents), differing evolutionary histories will prevent convergence. However, few studies have compared the contrasting roles of convergence and history, and none have done so at large scales. Here we develop a two-part approach to test the scale over which convergence can occur, comparing the relative importance of convergence and history in macroevolution using phylogenetic models of adaptive evolution. We apply this approach to data from morphology, ecology, and phylogeny from 167 species of anuran amphibians (frogs) from 10 local sites across the world, spanning ~160 myr of evolution. Mapping ecology on the phylogeny revealed that similar microhabitat specialists (e.g., aquatic, arboreal) have evolved repeatedly across clades and regions, producing many evolutionary replicates for testing for morphological convergence. By comparing morphological optima for clades and microhabitat types (our first test), we find that convergence associated with microhabitat use dominates frog morphological evolution, producing recurrent ecomorphs that together encompass all sampled species in each community in each region. However, our second test, which examines whether and how much species differ from their inferred optima, shows that convergence is incomplete: that is, phenotypes of most species are still somewhat distant from the estimated optimum for each microhabitat, seemingly because of insufficient time for more complete adaptation (an effect of history). Yet, these effects of history are related to past ecologies, and not clade membership. Overall, our study elucidates the dominant drivers of

  2. REFLECTIONS ON EVOLVING CHANGE.

    PubMed

    Angood, Peter B

    2016-01-01

    Physician leadership is increasingly recognized as pivotal for improved change in health care. Multi-professional care teams, education and leadership are evolving trends that are important for health care's future. PMID:27295737

  3. Evolving Digital Ecological Networks

    PubMed Central

    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). PMID:23533370

  4. Converging shear rheometer

    NASA Astrophysics Data System (ADS)

    Baek, Hyung M.; Mix, Adam W.; Giacomin, A. Jeffrey

    2014-05-01

    For highly viscous fluids that slip in parallel sliding plate rheometers, we want to use a slightly converging flow to suppress this wall slip. In this work, we first attack the steady shear flow of a highly viscous Newtonian fluid between two gently converging plates with no slip boundaries using the equation of motion in cylindrical coordinates, which yields no analytical solution. Then we treat the same problem using the lubrication approximation in Cartesian coordinates to yield exact, explicit solutions for dimensionless velocity, pressure and shear stress. This work deepens our understanding of a drag flow through a gently converging slit of arbitrary convergence angle. We also employ the corotational Maxwell model to explore the role of viscoelasticity in this converging shear flow. We then compare these analytical solutions to finite element calculations for both Newtonian and corotational Maxwell cases. A worked example for determining the Newtonian viscosity using a converging shear rheometer is also included. With this work, we provide the framework for exploring other constitutive equations or other boundary conditions in future work. Our results can also be used to design the linear bearings used for the parallel sliding plate rheometer (SPR). This work can also be used to evaluate the error in the shear stress that is caused by bearing misalignment and specify the parallelism tolerance for the linear bearings incorporated into a SPR.

  5. Transhydrogenase Promotes the Robustness and Evolvability of E. coli Deficient in NADPH Production

    PubMed Central

    Chou, Hsin-Hung; Marx, Christopher J.; Sauer, Uwe

    2015-01-01

    Metabolic networks revolve around few metabolites recognized by diverse enzymes and involved in myriad reactions. Though hub metabolites are considered as stepping stones to facilitate the evolutionary expansion of biochemical pathways, changes in their production or consumption often impair cellular physiology through their system-wide connections. How does metabolism endure perturbations brought immediately by pathway modification and restore hub homeostasis in the long run? To address this question we studied laboratory evolution of pathway-engineered Escherichia coli that underproduces the redox cofactor NADPH on glucose. Literature suggests multiple possibilities to restore NADPH homeostasis. Surprisingly, genetic dissection of isolates from our twelve evolved populations revealed merely two solutions: (1) modulating the expression of membrane-bound transhydrogenase (mTH) in every population; (2) simultaneously consuming glucose with acetate, an unfavored byproduct normally excreted during glucose catabolism, in two subpopulations. Notably, mTH displays broad phylogenetic distribution and has also played a predominant role in laboratory evolution of Methylobacterium extorquens deficient in NADPH production. Convergent evolution of two phylogenetically and metabolically distinct species suggests mTH as a conserved buffering mechanism that promotes the robustness and evolvability of metabolism. Moreover, adaptive diversification via evolving dual substrate consumption highlights the flexibility of physiological systems to exploit ecological opportunities. PMID:25715029

  6. Tangled bank of experimentally evolved Burkholderia biofilms reflects selection during chronic infections.

    PubMed

    Traverse, Charles C; Mayo-Smith, Leslie M; Poltak, Steffen R; Cooper, Vaughn S

    2013-01-15

    How diversity evolves and persists in biofilms is essential for understanding much of microbial life, including the uncertain dynamics of chronic infections. We developed a biofilm model enabling long-term selection for daily adherence to and dispersal from a plastic bead in a test tube. Focusing on a pathogen of the cystic fibrosis lung, Burkholderia cenocepacia, we sequenced clones and metagenomes to unravel the mutations and evolutionary forces responsible for adaptation and diversification of a single biofilm community during 1,050 generations of selection. The mutational patterns revealed recurrent evolution of biofilm specialists from generalist types and multiple adaptive alleles at relatively few loci. Fitness assays also demonstrated strong interference competition among contending mutants that preserved genetic diversity. Metagenomes from five other independently evolved biofilm lineages revealed extraordinary mutational parallelism that outlined common routes of adaptation, a subset of which was found, surprisingly, in a planktonic population. These mutations in turn were surprisingly well represented among mutations that evolved in cystic fibrosis isolates of both Burkholderia and Pseudomonas. These convergent pathways included altered metabolism of cyclic diguanosine monophosphate, polysaccharide production, tricarboxylic acid cycle enzymes, global transcription, and iron scavenging. Evolution in chronic infections therefore may be driven by mutations in relatively few pathways also favored during laboratory selection, creating hope that experimental evolution may illuminate the ecology and selective dynamics of chronic infections and improve treatment strategies. PMID:23271804

  7. Genome-wide signatures of convergent evolution in echolocating mammals

    PubMed Central

    Parker, Joe; Tsagkogeorga, Georgia; Cotton, James A.; Liu, Yuan; Provero, Paolo; Stupka, Elia; Rossiter, Stephen J.

    2013-01-01

    Evolution is typically thought to proceed through divergence of genes, proteins, and ultimately phenotypes1-3. However, similar traits might also evolve convergently in unrelated taxa due to similar selection pressures4,5. Adaptive phenotypic convergence is widespread in nature, and recent results from a handful of genes have suggested that this phenomenon is powerful enough to also drive recurrent evolution at the sequence level6-9. Where homoplasious substitutions do occur these have long been considered the result of neutral processes. However, recent studies have demonstrated that adaptive convergent sequence evolution can be detected in vertebrates using statistical methods that model parallel evolution9,10 although the extent to which sequence convergence between genera occurs across genomes is unknown. Here we analyse genomic sequence data in mammals that have independently evolved echolocation and show for the first time that convergence is not a rare process restricted to a handful of loci but is instead widespread, continuously distributed and commonly driven by natural selection acting on a small number of sites per locus. Systematic analyses of convergent sequence evolution in 805,053 amino acids within 2,326 orthologous coding gene sequences compared across 22 mammals (including four new bat genomes) revealed signatures consistent with convergence in nearly 200 loci. Strong and significant support for convergence among bats and the dolphin was seen in numerous genes linked to hearing or deafness, consistent with an involvement in echolocation. Surprisingly we also found convergence in many genes linked to vision: the convergent signal of many sensory genes was robustly correlated with the strength of natural selection. This first attempt to detect genome-wide convergent sequence evolution across divergent taxa reveals the phenomenon to be much more pervasive than previously recognised. PMID:24005325

  8. Genome-wide signatures of convergent evolution in echolocating mammals.

    PubMed

    Parker, Joe; Tsagkogeorga, Georgia; Cotton, James A; Liu, Yuan; Provero, Paolo; Stupka, Elia; Rossiter, Stephen J

    2013-10-10

    Evolution is typically thought to proceed through divergence of genes, proteins and ultimately phenotypes. However, similar traits might also evolve convergently in unrelated taxa owing to similar selection pressures. Adaptive phenotypic convergence is widespread in nature, and recent results from several genes have suggested that this phenomenon is powerful enough to also drive recurrent evolution at the sequence level. Where homoplasious substitutions do occur these have long been considered the result of neutral processes. However, recent studies have demonstrated that adaptive convergent sequence evolution can be detected in vertebrates using statistical methods that model parallel evolution, although the extent to which sequence convergence between genera occurs across genomes is unknown. Here we analyse genomic sequence data in mammals that have independently evolved echolocation and show that convergence is not a rare process restricted to several loci but is instead widespread, continuously distributed and commonly driven by natural selection acting on a small number of sites per locus. Systematic analyses of convergent sequence evolution in 805,053 amino acids within 2,326 orthologous coding gene sequences compared across 22 mammals (including four newly sequenced bat genomes) revealed signatures consistent with convergence in nearly 200 loci. Strong and significant support for convergence among bats and the bottlenose dolphin was seen in numerous genes linked to hearing or deafness, consistent with an involvement in echolocation. Unexpectedly, we also found convergence in many genes linked to vision: the convergent signal of many sensory genes was robustly correlated with the strength of natural selection. This first attempt to detect genome-wide convergent sequence evolution across divergent taxa reveals the phenomenon to be much more pervasive than previously recognized. PMID:24005325

  9. Multiscale modelling of evolving foams

    NASA Astrophysics Data System (ADS)

    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.

  10. An Evolving Astrobiology Glossary

    NASA Astrophysics Data System (ADS)

    Meech, K. J.; Dolci, W. W.

    2009-12-01

    One of the resources that evolved from the Bioastronomy 2007 meeting was an online interdisciplinary glossary of terms that might not be universally familiar to researchers in all sub-disciplines feeding into astrobiology. In order to facilitate comprehension of the presentations during the meeting, a database driven web tool for online glossary definitions was developed and participants were invited to contribute prior to the meeting. The glossary was downloaded and included in the conference registration materials for use at the meeting. The glossary web tool is has now been delivered to the NASA Astrobiology Institute so that it can continue to grow as an evolving resource for the astrobiology community.

  11. IS THERE CONVERGENCE ACROSS COUNTRIES? A SPATIAL APPROACH

    PubMed Central

    Berry, Heather; Guillen, Mauro F.; Hendi, Arun S.

    2014-01-01

    We analyze convergence across countries over the last half century as a result of globalizing forces. Drawing on theories of modernization, dependency, the world-system, political trade blocs, and the world-society, we consider economic, demographic, knowledge, financial, and political dimensions of convergence. Using a new methodology, we calculate the minimum volume ellipsoid encompassing different groupings of countries, finding that during the 1960–2009 period, countries have not evolved significantly closer or similar to one another, although groups of countries based on their core-periphery status or membership in trade blocs exhibit increasing internal convergence and divergence between one another. PMID:25580035

  12. Formation of polarity convergences underlying shoot outgrowths

    PubMed Central

    Abley, Katie; Sauret-Güeto, Susanna; Marée, Athanasius FM; Coen, Enrico

    2016-01-01

    The development of outgrowths from plant shoots depends on formation of epidermal sites of cell polarity convergence with high intracellular auxin at their centre. A parsimonious model for generation of convergence sites is that cell polarity for the auxin transporter PIN1 orients up auxin gradients, as this spontaneously generates convergent alignments. Here we test predictions of this and other models for the patterns of auxin biosynthesis and import. Live imaging of outgrowths from kanadi1 kanadi2 Arabidopsis mutant leaves shows that they arise by formation of PIN1 convergence sites within a proximodistal polarity field. PIN1 polarities are oriented away from regions of high auxin biosynthesis enzyme expression, and towards regions of high auxin importer expression. Both expression patterns are required for normal outgrowth emergence, and may form part of a common module underlying shoot outgrowths. These findings are more consistent with models that spontaneously generate tandem rather than convergent alignments. DOI: http://dx.doi.org/10.7554/eLife.18165.001 PMID:27478985

  13. Convergent evolution of novel protein function in shrew and lizard venom.

    PubMed

    Aminetzach, Yael T; Srouji, John R; Kong, Chung Yin; Hoekstra, Hopi E

    2009-12-01

    How do proteins evolve novel functions? To address this question, we are studying the evolution of a mammalian toxin, the serine protease BLTX [1], from the salivary glands of the North American shrew Blarina brevicauda. Here, we examine the molecular changes responsible for promoting BLTX toxicity. First, we show that regulatory loops surrounding the BLTX active site have evolved adaptively via acquisition of small insertions and subsequent accelerated sequence evolution. Second, these mutations introduce a novel chemical environment into the catalytic cleft of BLTX. Third, molecular-dynamic simulations show that the observed changes create a novel chemical and physical topology consistent with increased enzyme catalysis. Finally, we show that a toxic serine protease from the Mexican beaded lizard (GTX) [2] has evolved convergently through almost identical functional changes. Together, these results suggest that the evolution of toxicity might be predictable-arising via adaptive structural modification of analogous labile regulatory loops of an ancestral serine protease-and thus might aid in the identification of other toxic proteins. PMID:19879144

  14. Assembly of oxygen-evolving Photosystem II efficiently occurs with the apo-Cytb559 but the holo-Cytb559 accelerates the recovery of a functional enzyme upon photoinhibition.

    PubMed

    Sugiura, Miwa; Nakamura, Makoto; Koyama, Kazumi; Boussac, Alain

    2015-02-01

    Cytb559 in Photosystem II is a heterodimeric b-type cytochrome. The subunits, PsbE and PsbF, consist each in a membrane α-helix. Roles for Cytb559 remain elusive. In Thermosynechococcus elongatus, taking advantage of the robustness of the PSII variant with PsbA3 as the D1 subunit (WT*3), 4 mutants were designed hoping to get mutants nevertheless the obligatory phototrophy of this cyanobacterium. In two of them, an axial histidine ligand of the haem-iron was substituted for either a methionine, PsbE/H23M, which could be potentially a ligand or for an alanine, PsbE/H23A, which cannot. In the other mutants, PsbE/Y19F and PsbE/T26P, the environment around PsbE/H23 was expected to be modified. From EPR, MALDI-TOF and O2 evolution activity measurements, the following results were obtained: Whereas the PsbE/H23M and PsbE/H23A mutants assemble only an apo-Cytb559 the steady-state level of active PSII was comparable to that in WT*3. The lack of the haem or, in PsbE/T26P, conversion of the high-potential into a lower potential form, slowed-down the recovery rate of the O2 activity after high-light illumination but did not affect the photoinhibition rate. This resulted in the following order for the steady-state level of active PSII centers under high-light conditions: PsbE/H23M≈PsbE/H23A< PsbE/Y19F≤PsbE/T26P≤WT*3. These data show i) that the haem has no structural role provided that PsbE and PsbF are present, ii) a lack of correlation between the rate of photoinhibition and the Em of the haem and iii) that the holo-Cytb559 favors the recovery of a functional enzyme upon photoinhibition. PMID:25481108

  15. Converging or Diverging Lens?

    ERIC Educational Resources Information Center

    Branca, Mario

    2013-01-01

    Why does a lens magnify? Why does it shrink objects? Why does this happen? The activities that we propose here are useful in helping us to understand how lenses work, and they show that the same lens can have different magnification capabilities. A converging lens can also act as a diverging lens. (Contains 4 figures.)

  16. Convergence of Arnoldi method

    SciTech Connect

    Nevanlinna, O.

    1994-12-31

    This note summarizes some results on (a monitored version of) the Arnoldi method in Hilbert spaces. The interest in working in infinite dimensional spaces comes partly from the fact that only then can one have meaningful asymptotical statements (which hopefully give some light to the convergence of Arnoldi in large dimensional problems with iteration indices far less than the dimension).

  17. The Convergence Years

    ERIC Educational Resources Information Center

    Kolodzy, Janet; Grant, August E.; DeMars, Tony R.; Wilkinson, Jeffrey S.

    2014-01-01

    The emergence of the Internet, social media, and digital technologies in the twenty-first century accelerated an evolution in journalism and communication that fit under the broad term of convergence. That evolution changed the relationship between news producers and consumers. It broke down the geographical boundaries in defining our communities,…

  18. Self Evolving Modular Network

    NASA Astrophysics Data System (ADS)

    Tokunaga, Kazuhiro; Kawabata, Nobuyuki; Furukawa, Tetsuo

    We propose a novel modular network called the Self-Evolving Modular Network (SEEM). The SEEM has a modular network architecture with a graph structure and these following advantages: (1) new modules are added incrementally to allow the network to adapt in a self-organizing manner, and (2) graph's paths are formed based on the relationships between the models represented by modules. The SEEM is expected to be applicable to evolving functions of an autonomous robot in a self-organizing manner through interaction with the robot's environment and categorizing large-scale information. This paper presents the architecture and an algorithm for the SEEM. Moreover, performance characteristic and effectiveness of the network are shown by simulations using cubic functions and a set of 3D-objects.

  19. Twin Convergence Zones

    NASA Technical Reports Server (NTRS)

    2002-01-01

    NASA's QuikSCAT satellite has confirmed a 30-year old largely unproven theory that there are two areas near the equator where the winds converge year after year and drive ocean circulation south of the equator. By analyzing winds, QuikSCAT has found a year-round southern and northern Intertropical Convergence Zone. This find is important to climate modelers and weather forecasters because it provides more detail on how the oceans and atmosphere interact near the equator. The Intertropical Convergence Zone (ITCZ) is the region that circles the Earth near the equator, where the trade winds of both the Northern and Southern Hemispheres come together. North of the equator, strong sun and warm water of the equator heats the air in the ITCZ, drawing air in from north and south and causing the air to rise. As the air rises it cools, releasing the accumulated moisture in an almost perpetual series of thunderstorms. Satellite data, however, has confirmed that there is an ITCZ north of the equator and a parallel ITCZ south of the equator. Variation in the location of the ITCZ is important to people around the world because it affects the north-south atmospheric circulation, which redistributes energy. It drastically affects rainfall in many equatorial nations, resulting in the wet and dry seasons of the tropics rather than the cold and warm seasons of higher latitudes. Longer term changes in the ITCZ can result in severe droughts or flooding in nearby areas. 'The double ITCZ is usually only identified in the Pacific and Atlantic Oceans on a limited and seasonal basis,' said Timothy Liu, of NASA's Jet Propulsion Laboratory and California Institute of Technology, Pasadena, Calif., and lead researcher on the project. In the eastern Pacific Ocean, the southern ITCZ is usually seen springtime. In the western Atlantic Ocean, the southern ITCZ was recently clearly identified only in the summertime. However, QuikSCAT's wind data has seen the southern ITCZ in all seasons across the

  20. Evolvable Neural Software System

    NASA Technical Reports Server (NTRS)

    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.

  1. Enzyme markers

    MedlinePlus

    ... or defects passed down through families (inherited) can affect how enzymes work. Some enzymes are affected by several genes. Test results are usually reported as a percentage of normal enzyme activity.

  2. Thoughts on the diversity of convergent evolution of bioluminescence on earth

    NASA Astrophysics Data System (ADS)

    Waldenmaier, Hans E.; Oliveira, Anderson G.; Stevani, Cassius V.

    2012-10-01

    The widespread independent evolution of analogous bioluminescent systems is one of the most impressive and diverse examples of convergent evolution on earth. There are roughly 30 extant bioluminescent systems that have evolved independently on Earth, with each system likely having unique enzymes responsible for catalysing the bioluminescent reaction. Bioluminescence is a chemical reaction involving a luciferin molecule and a luciferase or photoprotein that results in the emission of light. Some independent systems utilize the same luciferin, such as the use of tetrapyrrolic compounds by krill and dinoflagellates, and the wide use of coelenterazine by marine organisms, while the enzymes involved are unique. One common thread among all the different bioluminescent systems is the requirement of molecular oxygen. Bioluminescence is found in most forms of life, especially marine organisms. Bioluminescence in known to benefit the organism by: attraction, repulsion, communication, camouflage, and illumination. The marine ecosystem is significantly affected by bioluminescence, the only light found in the pelagic zone and below is from bioluminescent organisms. Transgenic bioluminescent organisms have revolutionized molecular research, medicine and the biotechnology industry. The use of bioluminescence in studying molecular pathways and disease allows for non-invasive and real-time analysis. Bioluminescence-based assays have been developed for several analytes by coupling luminescence to many enzyme-catalysed reactions.

  3. Functional convergence in bat and toothed whale biosonars.

    PubMed

    Madsen, P T; Surlykke, A

    2013-09-01

    Echolocating bats and toothed whales hunt and navigate by emission of sound pulses and analysis of returning echoes to form a self-generated auditory scene. Here, we demonstrate a striking functional convergence in the way these two groups of mammals independently evolved the capability to sense with sound in air and water. PMID:23997187

  4. Converged Librarian/Academic Roles in the 'Wired' University.

    ERIC Educational Resources Information Center

    Dugdale, Christine

    New technologies allow universities to extend pedagogical practices, enhance learning experiences and develop self-managed lifelong learners. To take full advantage of evolving technologies, multi-skilled teaching and development teams are required with a merging and converging of academic and librarian roles. Conclusions are reported from the…

  5. Regolith Evolved Gas Analyzer

    NASA Technical Reports Server (NTRS)

    Hoffman, John H.; Hedgecock, Jud; Nienaber, Terry; Cooper, Bonnie; Allen, Carlton; Ming, Doug

    2000-01-01

    The Regolith Evolved Gas Analyzer (REGA) is a high-temperature furnace and mass spectrometer instrument for determining the mineralogical composition and reactivity of soil samples. REGA provides key mineralogical and reactivity data that is needed to understand the soil chemistry of an asteroid, which then aids in determining in-situ which materials should be selected for return to earth. REGA is capable of conducting a number of direct soil measurements that are unique to this instrument. These experimental measurements include: (1) Mass spectrum analysis of evolved gases from soil samples as they are heated from ambient temperature to 900 C; and (2) Identification of liberated chemicals, e.g., water, oxygen, sulfur, chlorine, and fluorine. REGA would be placed on the surface of a near earth asteroid. It is an autonomous instrument that is controlled from earth but does the analysis of regolith materials automatically. The REGA instrument consists of four primary components: (1) a flight-proven mass spectrometer, (2) a high-temperature furnace, (3) a soil handling system, and (4) a microcontroller. An external arm containing a scoop or drill gathers regolith samples. A sample is placed in the inlet orifice where the finest-grained particles are sifted into a metering volume and subsequently moved into a crucible. A movable arm then places the crucible in the furnace. The furnace is closed, thereby sealing the inner volume to collect the evolved gases for analysis. Owing to the very low g forces on an asteroid compared to Mars or the moon, the sample must be moved from inlet to crucible by mechanical means rather than by gravity. As the soil sample is heated through a programmed pattern, the gases evolved at each temperature are passed through a transfer tube to the mass spectrometer for analysis and identification. Return data from the instrument will lead to new insights and discoveries including: (1) Identification of the molecular masses of all of the gases

  6. From Coexistence to Convergence: Studying Partnerships and Collaboration among Libraries, Archives and Museums

    ERIC Educational Resources Information Center

    Duff, Wendy M.; Carter, Jennifer; Cherry, Joan M.; MacNeil, Heather; Howarth, Lynne C.

    2013-01-01

    Introduction: The convergence of libraries, archives and museums is an evolving phenomenon that has garnered increased attention in the literature and professional practice over the past decade. To date, little research exists documenting the experiences of these institutions as they engage in different forms of collaboration and convergence.…

  7. Knowledge Convergence and Collaborative Learning

    ERIC Educational Resources Information Center

    Jeong, Heisawn; Chi, Michelene T. H.

    2007-01-01

    This paper operationalized the notion of knowledge convergence and assessed quantitatively how much knowledge convergence occurred during collaborative learning. Knowledge convergence was defined as an increase in common knowledge where common knowledge referred to the knowledge that all collaborating partners had. Twenty pairs of college students…

  8. Transistor Level Circuit Experiments using Evolvable Hardware

    NASA Technical Reports Server (NTRS)

    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.

  9. Disparity and convergence in bipedal archosaur locomotion

    PubMed Central

    Bates, K. T.; Schachner, E. R.

    2012-01-01

    This study aims to investigate functional disparity in the locomotor apparatus of bipedal archosaurs. We use reconstructions of hindlimb myology of extant and extinct archosaurs to generate musculoskeletal biomechanical models to test hypothesized convergence between bipedal crocodile-line archosaurs and dinosaurs. Quantitative comparison of muscle leverage supports the inference that bipedal crocodile-line archosaurs and non-avian theropods had highly convergent hindlimb myology, suggesting similar muscular mechanics and neuromuscular control of locomotion. While these groups independently evolved similar musculoskeletal solutions to the challenges of parasagittally erect bipedalism, differences also clearly exist, particularly the distinct hip and crurotarsal ankle morphology characteristic of many pseudosuchian archosaurs. Furthermore, comparative analyses of muscle design in extant archosaurs reveal that muscular parameters such as size and architecture are more highly adapted or optimized for habitual locomotion than moment arms. The importance of these aspects of muscle design, which are not directly retrievable from fossils, warns against over-extrapolating the functional significance of anatomical convergences. Nevertheless, links identified between posture, muscle moments and neural control in archosaur locomotion suggest that functional interpretations of osteological changes in limb anatomy traditionally linked to postural evolution in Late Triassic archosaurs could be constrained through musculoskeletal modelling. PMID:22112652

  10. Design Space Issues for Intrinsic Evolvable Hardware

    NASA Technical Reports Server (NTRS)

    Hereford, James; Gwaltney, David

    2004-01-01

    This paper discusses the problem of increased programming time for intrinsic evolvable hardware (EM) as the complexity of the circuit grows. As the circuit becomes more complex, then more components will be required and a longer programming string, L, is required. We develop equations for the size of the population, n, and the number of generations required for the population to converge, based on L. Our analytical results show that even though the design search space grows as 2L (assuming a binary programming string), the number of circuit evaluations, n*ngen, only grows as O(Lg3), or slightly less than O(L). This makes evolvable techniques a good tool for exploring large design spaces. The major hurdle for intrinsic EHW is evaluation time for each possible circuit. The evaluation time involves downloading the bit string to the device, updating the device configuration, measuring the output and then transferring the output data to the control processor. Each of these steps must be done for each member of the population. The processing time of the computer becomes negligible since the selection/crossover/mutation steps are only done once per generation. Evaluation time presently limits intrinsic evolvable hardware techniques to designing only small or medium-sized circuits. To evolve large or complicated circuits, several researchers have proposed using hierarchical design or reuse techniques where submodules are combined together to form complex circuits. However, these practical approaches limit the search space of available designs and preclude utilizing parasitic coupling or other effects within the programmable device. The practical approaches also raise the issue of why intrinsic EHW techniques do not easily apply to large design spaces, since the analytical results show only an O(L) complexity growth.

  11. Stochastically evolving networks

    NASA Astrophysics Data System (ADS)

    Chan, Derek Y.; Hughes, Barry D.; Leong, Alex S.; Reed, William J.

    2003-12-01

    We discuss a class of models for the evolution of networks in which new nodes are recruited into the network at random times, and links between existing nodes that are not yet directly connected may also form at random times. The class contains both models that produce “small-world” networks and less tightly linked models. We produce both trees, appropriate in certain biological applications, and networks in which closed loops can appear, which model communication networks and networks of human sexual interactions. One of our models is closely related to random recursive trees, and some exact results known in that context can be exploited. The other models are more subtle and difficult to analyze. Our analysis includes a number of exact results for moments, correlations, and distributions of coordination number and network size. We report simulations and also discuss some mean-field approximations. If the system has evolved for a long time and the state of a random node (which thus has a random age) is observed, power-law distributions for properties of the system arise in some of these models.

  12. Fat: an evolving issue

    PubMed Central

    Speakman, John R.; O’Rahilly, Stephen

    2012-01-01

    Summary 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. PMID:22915015

  13. Evolving endoscopic surgery.

    PubMed

    Sakai, Paulo; Faintuch, Joel

    2014-06-01

    Since the days of Albukasim in medieval Spain, natural orifices have been regarded not only as a rather repugnant source of bodily odors, fluids and excreta, but also as a convenient invitation to explore and treat the inner passages of the organism. However, surgical ingenuity needed to be matched by appropriate tools and devices. Lack of technologically advanced instrumentation was a strong deterrent during almost a millennium until recent decades when a quantum jump materialized. Endoscopic surgery is currently a vibrant and growing subspecialty, which successfully handles millions of patients every year. Additional opportunities lie ahead which might benefit millions more, however, requiring even more sophisticated apparatuses, particularly in the field of robotics, artificial intelligence, and tissue repair (surgical suturing). This is a particularly exciting and worthwhile challenge, namely of larger and safer endoscopic interventions, followed by seamless and scarless recovery. In synthesis, the future is widely open for those who use together intelligence and creativity to develop new prototypes, new accessories and new techniques. Yet there are many challenges in the path of endoscopic surgery. In this new era of robotic endoscopy, one will likely need a virtual simulator to train and assess the performance of younger doctors. More evidence will be essential in multiple evolving fields, particularly to elucidate whether more ambitious and complex pathways, such as intrathoracic and intraperitoneal surgery via natural orifice transluminal endoscopic surgery (NOTES), are superior or not to conventional techniques. PMID:24628672

  14. Communicability across evolving networks

    NASA Astrophysics Data System (ADS)

    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.

  15. Evolving synergetic interactions

    PubMed Central

    Wu, Bin; Arranz, Jordi; Du, Jinming; Zhou, Da; Traulsen, Arne

    2016-01-01

    Cooperators forgo their own interests to benefit others. This reduces their fitness and thus cooperators are not likely to spread based on natural selection. Nonetheless, cooperation is widespread on every level of biological organization ranging from bacterial communities to human society. Mathematical models can help to explain under which circumstances cooperation evolves. Evolutionary game theory is a powerful mathematical tool to depict the interactions between cooperators and defectors. Classical models typically involve either pairwise interactions between individuals or a linear superposition of these interactions. For interactions within groups, however, synergetic effects may arise: their outcome is not just the sum of its parts. This is because the payoffs via a single group interaction can be different from the sum of any collection of two-player interactions. Assuming that all interactions start from pairs, how can such synergetic multiplayer games emerge from simpler pairwise interactions? Here, we present a mathematical model that captures the transition from pairwise interactions to synergetic multiplayer ones. We assume that different social groups have different breaking rates. We show that non-uniform breaking rates do foster the emergence of synergy, even though individuals always interact in pairs. Our work sheds new light on the mechanisms underlying such synergetic interactions. PMID:27466437

  16. Evolving synergetic interactions.

    PubMed

    Wu, Bin; Arranz, Jordi; Du, Jinming; Zhou, Da; Traulsen, Arne

    2016-07-01

    Cooperators forgo their own interests to benefit others. This reduces their fitness and thus cooperators are not likely to spread based on natural selection. Nonetheless, cooperation is widespread on every level of biological organization ranging from bacterial communities to human society. Mathematical models can help to explain under which circumstances cooperation evolves. Evolutionary game theory is a powerful mathematical tool to depict the interactions between cooperators and defectors. Classical models typically involve either pairwise interactions between individuals or a linear superposition of these interactions. For interactions within groups, however, synergetic effects may arise: their outcome is not just the sum of its parts. This is because the payoffs via a single group interaction can be different from the sum of any collection of two-player interactions. Assuming that all interactions start from pairs, how can such synergetic multiplayer games emerge from simpler pairwise interactions? Here, we present a mathematical model that captures the transition from pairwise interactions to synergetic multiplayer ones. We assume that different social groups have different breaking rates. We show that non-uniform breaking rates do foster the emergence of synergy, even though individuals always interact in pairs. Our work sheds new light on the mechanisms underlying such synergetic interactions. PMID:27466437

  17. Synchronization in evolving snowdrift game model

    NASA Astrophysics Data System (ADS)

    Huang, Y.; Wu, L.; Zhu, S. Q.

    2009-06-01

    The interaction between the evolution of the game and the underlying network structure with evolving snowdrift game model is investigated. The constructed network follows a power-law degree distribution typically showing scale-free feature. The topological features of average path length, clustering coefficient, degree-degree correlations and the dynamical feature of synchronizability are studied. The synchronizability of the constructed networks changes by the interaction. It will converge to a certain value when sufficient new nodes are added. It is found that initial payoffs of nodes greatly affect the synchronizability. When initial payoffs for players are equal, low common initial payoffs may lead to more heterogeneity of the network and good synchronizability. When initial payoffs follow certain distributions, better synchronizability is obtained compared to equal initial payoff. The result is also true for phase synchronization of nonidentical oscillators.

  18. Enzyme Kinetics.

    ERIC Educational Resources Information Center

    Moe, Owen; Cornelius, Richard

    1988-01-01

    Conveys an appreciation of enzyme kinetic analysis by using a practical and intuitive approach. Discusses enzyme assays, kinetic models and rate laws, the kinetic constants (V, velocity, and Km, Michaels constant), evaluation of V and Km from experimental data, and enzyme inhibition. (CW)

  19. Continuous quality improvement and medical informatics: the convergent synergy.

    PubMed

    Werth, G R; Connelly, D P

    1992-01-01

    Continuous quality improvement (CQI) and medical informatics specialists need to converge their efforts to create synergy for improving health care. Health care CQI needs medical informatics' expertise and technology to build the information systems needed to manage health care organizations according to quality improvement principles. Medical informatics needs CQI's philosophy and methods to build health care information systems that can evolve to meet the changing needs of clinicians and other stakeholders. This paper explores the philosophical basis for convergence of CQI and medical informatics efforts, and then examines a clinical computer workstation development project that is applying a combined approach. PMID:1482948

  20. Homology, convergence and parallelism.

    PubMed

    Ghiselin, Michael T

    2016-01-01

    Homology is a relation of correspondence between parts of parts of larger wholes. It is used when tracking objects of interest through space and time and in the context of explanatory historical narratives. Homologues can be traced through a genealogical nexus back to a common ancestral precursor. Homology being a transitive relation, homologues remain homologous however much they may come to differ. Analogy is a relationship of correspondence between parts of members of classes having no relationship of common ancestry. Although homology is often treated as an alternative to convergence, the latter is not a kind of correspondence: rather, it is one of a class of processes that also includes divergence and parallelism. These often give rise to misleading appearances (homoplasies). Parallelism can be particularly hard to detect, especially when not accompanied by divergences in some parts of the body. PMID:26598721

  1. Consensus in evolving networks of mobile agents

    NASA Astrophysics Data System (ADS)

    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. Series that Converge Absolutely but Don't Converge

    ERIC Educational Resources Information Center

    Kantrowitz, Robert; Schramm, Michael

    2012-01-01

    If a series of real numbers converges absolutely, then it converges. The usual proof requires completeness in the form of the Cauchy criterion. Failing completeness, the result is false. We provide examples of rational series that illustrate this point. The Cantor set appears in connection with one of the examples.

  3. Convergence and non-convergence in ecological, phenotypic, and genetic divergence across replicate population pairs of lake and stream stickleback

    PubMed Central

    Kaeuffer, Renaud; Peichel, Catherine L.; Bolnick, Daniel I.; Hendry, Andrew P.

    2015-01-01

    Convergent (or parallel) evolution provides strong evidence for a deterministic role of natural selection: similar phenotypes evolve when independent populations colonize similar environments. In reality, however, independent populations in similar environments always show some differences: some non-convergent evolution is present. It is therefore important to explicitly quantify the convergent and non-convergent aspects of trait variation, and to investigate the ecological and genetic explanations for each. We performed such an analysis for threespine stickleback (Gasterosteus aculeatus) populations inhabiting lake and stream habitats in independent watersheds. Morphological traits differed in the degree to which lake-stream divergence was convergent across watersheds. Some aspects of this variation were correlated with ecological variables related to diet, presumably reflecting the strength and specifics of divergent selection. Furthermore, a genetic scan revealed some markers that diverged between lakes and streams in many of the watersheds and some that diverged in only a few watersheds. Moreover, some of the lake-stream divergence in genetic markers was associated within some of the lake-stream divergence in morphological traits. Our results suggest that convergent evolution, and deviations from it, are primarily the result of natural selection, which corresponds in only some respect to the dichotomous habitat classifications frequently used in such studies. PMID:22276537

  4. Some Observations on Grid Convergence

    NASA Technical Reports Server (NTRS)

    Salas, manuel D.

    2006-01-01

    It is claimed that current practices in grid convergence studies, particularly in the field of external aerodynamics, are flawed. The necessary conditions to properly establish grid convergence are presented. A theoretical model and a numerical example are used to demonstrate these ideas.

  5. Convergent ablator performance measurements

    SciTech Connect

    Hicks, D. G.; Spears, B. K.; Braun, D. G.; Sorce, C. M.; Celliers, P. M.; Collins, G. W.; Landen, O. L.; Olson, R. E.

    2010-10-15

    The velocity and remaining ablator mass of an imploding capsule are critical metrics for assessing the progress toward ignition of an inertially confined fusion experiment. These and other convergent ablator performance parameters have been measured using a single streaked x-ray radiograph. Traditional Abel inversion of such a radiograph is ill-posed since backlighter intensity profiles and x-ray attenuation by the ablated plasma are unknown. To address this we have developed a regularization technique which allows the ablator density profile {rho}(r) and effective backlighter profile I{sub 0}(y) at each time step to be uniquely determined subject to the constraints that {rho}(r) is localized in radius space and I{sub 0}(y) is delocalized in object space. Moments of {rho}(r) then provide the time-resolved areal density, mass, and average radius (and thus velocity) of the remaining ablator material. These results are combined in the spherical rocket model to determine the ablation pressure and mass ablation rate during the implosion. The technique has been validated on simulated radiographs of implosions at the National Ignition Facility [Miller et al., Nucl. Fusion 44, 228 (2004)] and implemented on experiments at the OMEGA laser facility [Boehly et al., Opt. Commun. 133, 495 (1997)].

  6. Convergent flow stove

    SciTech Connect

    Engblom, D.W.

    1986-02-25

    An apparatus for burning combustible solid organic material such as wood is described in a environment in which combustion is directed downwardly. The apparatus consists of: A. A fuel chamber having a closed upper portion and a major dimension in the vertical direction such that the fuel chamber is generally upright, B. A combustion zone in the lower portion of the fuel chamber defined by a convergent outflow passage at the bottom of the fuel chamber and a pair of walls on opposite sides of the lower portion, the walls being sloped inwardly toward one another at the outflow passage, and the outflow passage comprising a gap between the walls, C. A Hearth element forming each the sloping wall, the hearth element including I. At least one row of spaced slots extending into the interior of the hearth element and a lateral air inlet channel connected to the slots of each row and a source of combustion air, and II. A flue outlet communicating with the outflow passage, the flue outlet including spaced, parallel tubes in the hearth element, with the tubes being juxtaposed the slots and extending perpendicular to the air inlet channels, D. Means connected to the flue outlet to permit exhaustion of flue gases from the apparatus, and E. means for loading fuel into the fuel chamber.

  7. Convergent ablator performance measurements

    NASA Astrophysics Data System (ADS)

    Hicks, D. G.; Spears, B. K.; Braun, D. G.; Olson, R. E.; Sorce, C. M.; Celliers, P. M.; Collins, G. W.; Landen, O. L.

    2010-10-01

    The velocity and remaining ablator mass of an imploding capsule are critical metrics for assessing the progress toward ignition of an inertially confined fusion experiment. These and other convergent ablator performance parameters have been measured using a single streaked x-ray radiograph. Traditional Abel inversion of such a radiograph is ill-posed since backlighter intensity profiles and x-ray attenuation by the ablated plasma are unknown. To address this we have developed a regularization technique which allows the ablator density profile ρ(r ) and effective backlighter profile I0(y) at each time step to be uniquely determined subject to the constraints that ρ(r ) is localized in radius space and I0(y) is delocalized in object space. Moments of ρ(r ) then provide the time-resolved areal density, mass, and average radius (and thus velocity) of the remaining ablator material. These results are combined in the spherical rocket model to determine the ablation pressure and mass ablation rate during the implosion. The technique has been validated on simulated radiographs of implosions at the National Ignition Facility [Miller et al., Nucl. Fusion 44, 228 (2004)] and implemented on experiments at the OMEGA laser facility [Boehly et al., Opt. Commun. 133, 495 (1997)].

  8. Disgust: Evolved Function and Structure

    ERIC Educational Resources Information Center

    Tybur, Joshua M.; Lieberman, Debra; Kurzban, Robert; DeScioli, Peter

    2013-01-01

    Interest in and research on disgust has surged over the past few decades. The field, however, still lacks a coherent theoretical framework for understanding the evolved function or functions of disgust. Here we present such a framework, emphasizing 2 levels of analysis: that of evolved function and that of information processing. Although there is…

  9. Enzymes, Industrial

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Enzymes serve key roles in numerous biotechnology processes and products that are commonly encountered in the forms of food and beverages, cleaning supplies, clothing, paper products, transportation fuels, pharmaceuticals, and monitoring devices. Enzymes can display regio- and stereo-specificity, p...

  10. Understanding Enzymes.

    ERIC Educational Resources Information Center

    Sinnott, M. L.

    1979-01-01

    Describes the way enzymes operate through reaction energetics, and explains that most of the catalytic power of enzymes lies in the strong noncovalent forces responsible for initial binding of substrate, which are only manifested at the transition state of the reaction. (Author/GA)

  11. Soil Enzymes

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The functionality and resilience of natural and managed ecosystems mainly rely on the metabolic abilities of microbial communities, the main source of enzymes in soils. Enzyme mediated reactions are critical in the decomposition of organic matter, cycling of nutrients, and in the breakdown of herbic...

  12. Exceptional Convergent Evolution in a Virus

    PubMed Central

    Bull, J. J.; Badgett, M. R.; Wichman, H. A.; Huelsenbeck, J. P.; Hillis, D. M.; Gulati, A.; Ho, C.; Molineux, I. J.

    1997-01-01

    Replicate lineages of the bacteriophage φX 174 adapted to growth at high temperature on either of two hosts exhibited high rates of identical, independent substitutions. Typically, a dozen or more substitutions accumulated in the 5.4-kilobase genome during propagation. Across the entire data set of nine lineages, 119 independent substitutions occurred at 68 nucleotide sites. Over half of these substitutions, accounting for one third of the sites, were identical with substitutions in other lineages. Some convergent substitutions were specific to the host used for phage propagation, but others occurred across both hosts. Continued adaptation of an evolved phage at high temperature, but on the other host, led to additional changes that included reversions of previous substitutions. Phylogenetic reconstruction using the complete genome sequence not only failed to recover the correct evolutionary history because of these convergent changes, but the true history was rejected as being a significantly inferior fit to the data. Replicate lineages subjected to similar environmental challenges showed similar rates of substitution and similar rates of fitness improvement across corresponding times of adaptation. Substitution rates and fitness improvements were higher during the initial period of adaptation than during a later period, except when the host was changed. PMID:9409816

  13. Why does continental convergence stop

    SciTech Connect

    Hynes, A.

    1985-01-01

    Convergence between India and Asia slowed at 45 Ma when they collided, but continues today. This requires that substantial proportions of the Indian and/or Asian lithospheric mantle are still being subducted. The resulting slab-pull is probably comparable with that from complete lithospheric slabs and may promote continued continental convergence even after collision. Since descending lithospheric slabs are present at all collision zones at the time of collision such continued convergence may be general after continental collisions. It may cease only when there is a major (global) plate reorganization which results in new forces on the convergent continents that may counteract the slab-pull. These inferences may be tested on the late Paleozoic collision between Gondwanaland and Laurasia. This is generally considered to have been complete by mid-Permian time (250 Ma). However, this may be only the time of docking of Gondwanaland with North America, not that of the cessation of convergence. Paleomagnetic polar-wander paths for the Gondwanide continents exhibit consistently greater latitudinal shifts from 250 Ma to 200 Ma than those of Laurasia when corrected for post-Triassic drift, suggesting that convergence continued through late Permian well into the Triassic. It may have been accommodated by crustal thickening under what is now the US Coastal Plain, or by strike-slip faulting. Convergence may have ceased only when Pangea began to fragment again, in which case the cause for its cessation may be related to the cause of continental fragmentation.

  14. Convergent evolution of anti-bat sounds.

    PubMed

    Corcoran, Aaron J; Hristov, Nickolay I

    2014-09-01

    Bats and their insect prey rely on acoustic sensing in predator prey encounters--echolocation in bats, tympanic hearing in moths. Some insects also emit sounds for bat defense. Here, we describe a previously unknown sound-producing organ in Geometrid moths--a prothoracic tymbal in the orange beggar moth (Eubaphe unicolor) that generates bursts of ultrasonic clicks in response to tactile stimulation and playback of a bat echolocation attack sequence. Using scanning electron microscopy and high-speed videography, we demonstrate that E. unicolor and phylogenetically distant tiger moths have evolved serially homologous thoracic tymbal organs with fundamentally similar functional morphology, a striking example of convergent evolution. We compared E. unicolor clicks to that of five sympatric tiger moths and found that 9 of 13 E. unicolor clicking parameters were within the range of sympatric tiger moths. Remaining differences may result from the small size of the E. unicolor tymbal. Four of the five sympatric clicking tiger moth species were unpalatable to bats (0-20% eaten), whereas E. unicolor was palatable to bats (86% eaten). Based on these results, we hypothesize that E. unicolor evolved tymbal organs that mimic the sounds produced by toxic tiger moths when attacked by echolocating bats. PMID:24980483

  15. Spacetimes containing slowly evolving horizons

    SciTech Connect

    Kavanagh, William; Booth, Ivan

    2006-08-15

    Slowly evolving horizons are trapping horizons that are ''almost'' isolated horizons. This paper reviews their definition and discusses several spacetimes containing such structures. These include certain Vaidya and Tolman-Bondi solutions as well as (perturbatively) tidally distorted black holes. Taking into account the mass scales and orders of magnitude that arise in these calculations, we conjecture that slowly evolving horizons are the norm rather than the exception in astrophysical processes that involve stellar-scale black holes.

  16. Natural Selection Promotes Antigenic Evolvability

    PubMed Central

    Graves, Christopher J.; Ros, Vera I. D.; Stevenson, Brian; Sniegowski, Paul D.; Brisson, Dustin

    2013-01-01

    The hypothesis that evolvability - the capacity to evolve by natural selection - is itself the object of natural selection is highly intriguing but remains controversial due in large part to a paucity of direct experimental evidence. The antigenic variation mechanisms of microbial pathogens provide an experimentally tractable system to test whether natural selection has favored mechanisms that increase evolvability. Many antigenic variation systems consist of paralogous unexpressed ‘cassettes’ that recombine into an expression site to rapidly alter the expressed protein. Importantly, the magnitude of antigenic change is a function of the genetic diversity among the unexpressed cassettes. Thus, evidence that selection favors among-cassette diversity is direct evidence that natural selection promotes antigenic evolvability. We used the Lyme disease bacterium, Borrelia burgdorferi, as a model to test the prediction that natural selection favors amino acid diversity among unexpressed vls cassettes and thereby promotes evolvability in a primary surface antigen, VlsE. The hypothesis that diversity among vls cassettes is favored by natural selection was supported in each B. burgdorferi strain analyzed using both classical (dN/dS ratios) and Bayesian population genetic analyses of genetic sequence data. This hypothesis was also supported by the conservation of highly mutable tandem-repeat structures across B. burgdorferi strains despite a near complete absence of sequence conservation. Diversification among vls cassettes due to natural selection and mutable repeat structures promotes long-term antigenic evolvability of VlsE. These findings provide a direct demonstration that molecular mechanisms that enhance evolvability of surface antigens are an evolutionary adaptation. The molecular evolutionary processes identified here can serve as a model for the evolution of antigenic evolvability in many pathogens which utilize similar strategies to establish chronic infections

  17. Structural Organization of Enzymes of the Phenylacetate Catabolic Hybrid Pathway

    PubMed Central

    Grishin, Andrey M.; Cygler, Miroslaw

    2015-01-01

    Aromatic compounds are the second most abundant class of molecules on the earth and frequent environmental pollutants. They are difficult to metabolize due to an inert chemical structure, and of all living organisms, only microbes have evolved biochemical pathways that can open an aromatic ring and catabolize thus formed organic molecules. In bacterial genomes, the phenylacetate (PA) utilization pathway is abundant and represents the central route for degradation of a variety of organic compounds, whose degradation reactions converge at this pathway. The PA pathway is a hybrid pathway and combines the dual features of aerobic metabolism, i.e., usage of both oxygen to open the aromatic ring and of anaerobic metabolism—coenzyme A derivatization of PA. This allows the degradation process to be adapted to fluctuating oxygen conditions. In this review we focus on the structural and functional aspects of enzymes and their complexes involved in the PA degradation by the catabolic hybrid pathway. We discuss the ability of the central PaaABCE monooxygenase to reversibly oxygenate PA, the controlling mechanisms of epoxide concentration by the pathway enzymes, and the similarity of the PA utilization pathway to the benzoate utilization Box pathway and β-oxidation of fatty acids. PMID:26075354

  18. Characterization of Function of the GlgA2 Glycogen/Starch Synthase in Cyanobacterium sp. Clg1 Highlights Convergent Evolution of Glycogen Metabolism into Starch Granule Aggregation.

    PubMed

    Kadouche, Derifa; Ducatez, Mathieu; Cenci, Ugo; Tirtiaux, Catherine; Suzuki, Eiji; Nakamura, Yasunori; Putaux, Jean-Luc; Terrasson, Amandine Durand; Diaz-Troya, Sandra; Florencio, Francisco Javier; Arias, Maria Cecilia; Striebeck, Alexander; Palcic, Monica; Ball, Steven G; Colleoni, Christophe

    2016-07-01

    At variance with the starch-accumulating plants and most of the glycogen-accumulating cyanobacteria, Cyanobacterium sp. CLg1 synthesizes both glycogen and starch. We now report the selection of a starchless mutant of this cyanobacterium that retains wild-type amounts of glycogen. Unlike other mutants of this type found in plants and cyanobacteria, this mutant proved to be selectively defective for one of the two types of glycogen/starch synthase: GlgA2. This enzyme is phylogenetically related to the previously reported SSIII/SSIV starch synthase that is thought to be involved in starch granule seeding in plants. This suggests that, in addition to the selective polysaccharide debranching demonstrated to be responsible for starch rather than glycogen synthesis, the nature and properties of the elongation enzyme define a novel determinant of starch versus glycogen accumulation. We show that the phylogenies of GlgA2 and of 16S ribosomal RNA display significant congruence. This suggests that this enzyme evolved together with cyanobacteria when they diversified over 2 billion years ago. However, cyanobacteria can be ruled out as direct progenitors of the SSIII/SSIV ancestral gene found in Archaeplastida. Hence, both cyanobacteria and plants recruited similar enzymes independently to perform analogous tasks, further emphasizing the importance of convergent evolution in the appearance of starch from a preexisting glycogen metabolism network. PMID:27208262

  19. Self-evolving microstructured systems upon enzymatic catalysis.

    PubMed

    Chopineau, J; Lesieur, S; Carion-Taravella, B; Ollivon, M

    1998-01-01

    The consequences of cell microstructuration on enzyme functions is discussed in the framework of self-evolving microstructured systems. Molecular assemblies of amphiphiles or lipids are spontaneously formed by self-organisation. Among these different structures, reversed micelles, liquid crystalline mesophases and vesicles are hosts for enzymatic reaction studies. Inside a living cell, phospholipid metabolism is responsible for membrane structural modifications; the catalytic behaviour of lipolytic enzymes, mainly phospholipase (PL) A2, is described in relation with structural aspects of biological membranes. The implication in cellular regulation events of PLC and PLD is discussed in relation with the role of their reaction products as second messengers in membrane fusion processes. The in vitro synthesis of dialkyl phosphatidylcholines, via the enzymatic 'salvage pathway' which leads to the formation of vesicles upon phospholipid formation, is considered in relation with autopoiesis. More recent studies on self-evolving systems based on enzyme-surfactants reactions are detailed. The interactions between amphiphilic aggregates and enzymes allow to explore the OG/octanol/water phase diagram. Enzymatic formation of dipalmitoylphosphatidylcholine (DPPC) liposomes and non-ionic surfactant vesicles (NSV), starting from mixed micelles or open structures, finally sets an example of a biomimetic self-evolving system. PMID:9782383

  20. Robustness to Faults Promotes Evolvability: Insights from Evolving Digital Circuits

    PubMed Central

    Nolfi, Stefano

    2016-01-01

    We demonstrate how the need to cope with operational faults enables evolving circuits to find more fit solutions. The analysis of the results obtained in different experimental conditions indicates that, in absence of faults, evolution tends to select circuits that are small and have low phenotypic variability and evolvability. The need to face operation faults, instead, drives evolution toward the selection of larger circuits that are truly robust with respect to genetic variations and that have a greater level of phenotypic variability and evolvability. Overall our results indicate that the need to cope with operation faults leads to the selection of circuits that have a greater probability to generate better circuits as a result of genetic variation with respect to a control condition in which circuits are not subjected to faults. PMID:27409589

  1. Convergent Evolution of Tetrodotoxin-Resistant Sodium Channels in Predators and Prey.

    PubMed

    Toledo, G; Hanifin, C; Geffeney, S; Brodie, E D

    2016-01-01

    Convergent evolution of similar adaptive traits may arise from either common or disparate molecular and physiological mechanisms. The forces that determine the degree of underlying mechanistic similarities across convergent phenotypes are highly debated and poorly understood. Some garter snakes are able to consume newts that possess the channel blocking compound tetrodotoxin (TTX). Despite belonging to unrelated lineages, both the predators and prey have independently evolved remarkably similar physiological mechanisms of resistance to TTX that involve chemical and structural changes in voltage-gated sodium channels (NaV). The evolution of TTX resistance in this predator-prey pair constitutes a natural experiment that allows us to explore the causes of molecular convergence. Here, we review broad patterns of convergence at the level of amino acid changes in NaV channels of animals that evolved TTX resistance and make comparisons to known TTX-resistant channels that did not evolve under the selective pressures imposed by TTX. We conclude that convergence likely stems from the interplay of the target specificity of TTX and functional constraints of NaV that are shared among taxa. These and other factors can limit channel evolution to favor a few functionally permissible paths of adaptation, which can explain the observed predictability of changes to channel structure. By studying the functional causes of convergence in NaV channels, we can further our understanding of the role of these important channel proteins at the center of the evolution of the nervous system. PMID:27586282

  2. Trophic convergence drives morphological convergence in marine tetrapods.

    PubMed

    Kelley, Neil P; Motani, Ryosuke

    2015-01-01

    Marine tetrapod clades (e.g. seals, whales) independently adapted to marine life through the Mesozoic and Caenozoic, and provide iconic examples of convergent evolution. Apparent morphological convergence is often explained as the result of adaptation to similar ecological niches. However, quantitative tests of this hypothesis are uncommon. We use dietary data to classify the feeding ecology of extant marine tetrapods and identify patterns in skull and tooth morphology that discriminate trophic groups across clades. Mapping these patterns onto phylogeny reveals coordinated evolutionary shifts in diet and morphology in different marine tetrapod lineages. Similarities in morphology between species with similar diets-even across large phylogenetic distances-are consistent with previous hypotheses that shared functional constraints drive convergent evolution in marine tetrapods. PMID:25631228

  3. Trophic convergence drives morphological convergence in marine tetrapods

    PubMed Central

    Kelley, Neil P.; Motani, Ryosuke

    2015-01-01

    Marine tetrapod clades (e.g. seals, whales) independently adapted to marine life through the Mesozoic and Caenozoic, and provide iconic examples of convergent evolution. Apparent morphological convergence is often explained as the result of adaptation to similar ecological niches. However, quantitative tests of this hypothesis are uncommon. We use dietary data to classify the feeding ecology of extant marine tetrapods and identify patterns in skull and tooth morphology that discriminate trophic groups across clades. Mapping these patterns onto phylogeny reveals coordinated evolutionary shifts in diet and morphology in different marine tetrapod lineages. Similarities in morphology between species with similar diets—even across large phylogenetic distances—are consistent with previous hypotheses that shared functional constraints drive convergent evolution in marine tetrapods. PMID:25631228

  4. More than one way to be an herbivore: convergent evolution of herbivory using different digestive strategies in prickleback fishes (Stichaeidae).

    PubMed

    German, Donovan P; Sung, Aaron; Jhaveri, Parth; Agnihotri, Ritika

    2015-06-01

    In fishes, the evolution of herbivory has occured within a spectrum of digestive strategies, with two extremes on opposite ends: (i) a rate-maximization strategy characterized by high intake, rapid throughput of food through the gut, and little reliance on microbial digestion or (ii) a yield-maximization strategy characterized by measured intake, slower transit of food through the gut, and more of a reliance on microbial digestion in the hindgut. One of these strategies tends to be favored within a given clade of fishes. Here, we tested the hypothesis that rate or yield digestive strategies can arise in convergently evolved herbivores within a given lineage. In the family Stichaeidae, convergent evolution of herbivory occured in Cebidichthys violaceus and Xiphister mucosus, and despite nearly identical diets, these two species have different digestive physiologies. We found that C. violaceus has more digesta in its distal intestine than other gut regions, has comparatively high concentrations (>11 mM) of short-chain fatty acids (SCFA, the endpoints of microbial fermentation) in its distal intestine, and a spike in β-glucosidase activity in this gut region, findings that, when coupled to long retention times (>20 h) of food in the guts of C. violaceus, suggest a yield-maximizing strategy in this species. X. mucosus showed none of these features and was more similar to its sister taxon, the omnivorous Xiphister atropurpureus, in terms of digestive enzyme activities, gut content partitioning, and concentrations of SCFA in their distal intestines. We also contrasted these herbivores and omnivores with other sympatric stichaeid fishes, Phytichthys chirus (omnivore) and Anoplarchus purpurescens (carnivore), each of which had digestive physiologies consistent with the consumption of animal material. This study shows that rate- and yield-maximizing strategies can evolve in closely related fishes and suggests that resource partitioning can play out on the level of

  5. Origins of stereoselectivity in evolved ketoreductases

    PubMed Central

    Noey, Elizabeth L.; Tibrewal, Nidhi; Jiménez-Osés, Gonzalo; Osuna, Sílvia; Park, Jiyong; Bond, Carly M.; Cascio, Duilio; Liang, Jack; Zhang, Xiyun; Huisman, Gjalt W.; Tang, Yi; Houk, Kendall N.

    2015-01-01

    Mutants of Lactobacillus kefir short-chain alcohol dehydrogenase, used here as ketoreductases (KREDs), enantioselectively reduce the pharmaceutically relevant substrates 3-thiacyclopentanone and 3-oxacyclopentanone. These substrates differ by only the heteroatom (S or O) in the ring, but the KRED mutants reduce them with different enantioselectivities. Kinetic studies show that these enzymes are more efficient with 3-thiacyclopentanone than with 3-oxacyclopentanone. X-ray crystal structures of apo- and NADP+-bound selected mutants show that the substrate-binding loop conformational preferences are modified by these mutations. Quantum mechanical calculations and molecular dynamics (MD) simulations are used to investigate the mechanism of reduction by the enzyme. We have developed an MD-based method for studying the diastereomeric transition state complexes and rationalize different enantiomeric ratios. This method, which probes the stability of the catalytic arrangement within the theozyme, shows a correlation between the relative fractions of catalytically competent poses for the enantiomeric reductions and the experimental enantiomeric ratio. Some mutations, such as A94F and Y190F, induce conformational changes in the active site that enlarge the small binding pocket, facilitating accommodation of the larger S atom in this region and enhancing S-selectivity with 3-thiacyclopentanone. In contrast, in the E145S mutant and the final variant evolved for large-scale production of the intermediate for the antibiotic sulopenem, R-selectivity is promoted by shrinking the small binding pocket, thereby destabilizing the pro-S orientation. PMID:26644568

  6. Origins of stereoselectivity in evolved ketoreductases.

    PubMed

    Noey, Elizabeth L; Tibrewal, Nidhi; Jiménez-Osés, Gonzalo; Osuna, Sílvia; Park, Jiyong; Bond, Carly M; Cascio, Duilio; Liang, Jack; Zhang, Xiyun; Huisman, Gjalt W; Tang, Yi; Houk, Kendall N

    2015-12-22

    Mutants of Lactobacillus kefir short-chain alcohol dehydrogenase, used here as ketoreductases (KREDs), enantioselectively reduce the pharmaceutically relevant substrates 3-thiacyclopentanone and 3-oxacyclopentanone. These substrates differ by only the heteroatom (S or O) in the ring, but the KRED mutants reduce them with different enantioselectivities. Kinetic studies show that these enzymes are more efficient with 3-thiacyclopentanone than with 3-oxacyclopentanone. X-ray crystal structures of apo- and NADP(+)-bound selected mutants show that the substrate-binding loop conformational preferences are modified by these mutations. Quantum mechanical calculations and molecular dynamics (MD) simulations are used to investigate the mechanism of reduction by the enzyme. We have developed an MD-based method for studying the diastereomeric transition state complexes and rationalize different enantiomeric ratios. This method, which probes the stability of the catalytic arrangement within the theozyme, shows a correlation between the relative fractions of catalytically competent poses for the enantiomeric reductions and the experimental enantiomeric ratio. Some mutations, such as A94F and Y190F, induce conformational changes in the active site that enlarge the small binding pocket, facilitating accommodation of the larger S atom in this region and enhancing S-selectivity with 3-thiacyclopentanone. In contrast, in the E145S mutant and the final variant evolved for large-scale production of the intermediate for the antibiotic sulopenem, R-selectivity is promoted by shrinking the small binding pocket, thereby destabilizing the pro-S orientation. PMID:26644568

  7. On the Discovery of Evolving Truth

    PubMed Central

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

    2015-01-01

    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. PMID:26705502

  8. Convergent Evolution of Health Information Management and Health Informatics

    PubMed Central

    Gibson, C. J.; Abrams, K.

    2015-01-01

    Summary Clearly defined boundaries are disappearing among the activities, sources, and uses of health care data and information managed by health information management (HIM) and health informatics (HI) professionals. Definitions of the professional domains and scopes of practice for HIM and HI are converging with the proliferation of information and communication technologies in health care settings. Convergence is changing both the roles that HIM and HI professionals serve in their organizations as well as the competencies necessary for training future professionals. Many of these changes suggest a blurring of roles and responsibilities with increasingly overlapping curricula, job descriptions, and research agendas. Blurred lines in a highly competitive market create confusion for students and employers. In this essay, we provide some perspective on the changing landscape and suggest a course for the future. First we review the evolving definitions of HIM and HI. We next compare the current domains and competencies, review the characteristics as well as the education and credentialing of both disciplines, and examine areas of convergence. Given the current state, we suggest a path forward to strengthen the contributions HIM and HI professionals and educators make to the evolving health care environment. PMID:25848421

  9. Convergent Creativity: From Arthur Cropley (1935-) Onwards

    ERIC Educational Resources Information Center

    Tan, Ai-Girl

    2015-01-01

    Arthur Cropley's view on convergent thinking is reviewed, with reflections on the relations of divergent and convergent processes and the roles of knowledge and convergent creativity. While divergence is about considering and generating multiplicity, possibility, difference, originality, and so on; convergence is about relating, associating,…

  10. Convergence demands by spectacle magnifiers.

    PubMed

    Katz, M

    1996-08-01

    A general equation, c delta = k1b + k2sF, for finding the binocular convergence demands by spectacle magnifiers to view images at any distance is presented. Factor k1 in the equation yields the accommodative demand to view the image; factor k2 determines the actual reduction in convergence demand provided by the vendors' incorporation of base-in prism. When magnifiers from virtual images at finite distances, such as at the least distance of distinct vision or 25 cm, the interpupiliary distance (b), the separation between the lenses and the eyes (d), and the distance between the optical centers of the lenses (s) are basic quantities, according to this equation. The fundamental datum that the vendors should specify is the distance (s) between the optical centers of the lenses, rather than base-in prism. The specification of base-in prism is unrellable when images are formed at finite distances and the frame PD is not equal to the distance IPD. When the image is formed at infinity, that is when the angular magnification M = F/4, the convergence demand by spectacle magnifiers only depends on the separation between the optical centers of the lenses and the lens power, that is, c delta = sF. It is independent of the interpupillary distance (b) and the separation between the lenses and the eyes (d). We also present an equation, to find the disparity of the accommodative/convergence relation caused by spectacle magnifiers. Knowing the demands on convergence and accommodation, the practitioner can probably evaluate the potential for successful adaptation to spectacle magnifiers from routine measurements of positive and negative relative convergence and accommodation. PMID:8869985

  11. Sequentially evolved bilateral epidural haematomas.

    PubMed

    Rochat, P; Johannesen, H H; Poulsgård, L; Bøgeskov, L

    2002-12-01

    Sequentially evolved bilateral epidural haematomas, where the second haematoma evolves after surgical removal of the first haematoma, are rarely reported. We report two cases of this entity. One patient was involved in a road traffic accident and the other was suffering from a head injury after an assault. CT scans showed that both patients had an unilateral epidural haematoma with a thin presumably epidural haemorrhage on the opposite side. Both patients were operated for their epidural haematomas, but did not improve after surgical treatment, and postoperative CT scans revealed evolving of an epidural haematoma on the opposite side. After evacuation of the second epidural haematoma both patients recovered quickly. Sequentially evolved bilateral epidural haematomas are rare, but must be considered in the postoperative intensive care treatment in patients with epidural haematomas. Both cases emphasize the need for intensive care monitoring after an operation for an epidural haematoma and the need for CT scans if the patient does not improve quickly after removal of the haematoma. This is especially important if a small contralateral haematoma is seen on the initial CT scan. PMID:12445923

  12. Slippery Texts and Evolving Literacies

    ERIC Educational Resources Information Center

    Mackey, Margaret

    2007-01-01

    The idea of "slippery texts" provides a useful descriptor for materials that mutate and evolve across different media. Eight adult gamers, encountering the slippery text "American McGee's Alice," demonstrate a variety of ways in which players attempt to manage their attention as they encounter a new text with many resonances. The range of their…

  13. Signing Apes and Evolving Linguistics.

    ERIC Educational Resources Information Center

    Stokoe, William C.

    Linguistics retains from its antecedents, philology and the study of sacred writings, some of their apologetic and theological bias. Thus it has not been able to face squarely the question how linguistic function may have evolved from animal communication. Chimpanzees' use of signs from American Sign Language forces re-examination of language…

  14. Food Enzymes

    ERIC Educational Resources Information Center

    McBroom, Rachel; Oliver-Hoyo, Maria T.

    2007-01-01

    Many students view biology and chemistry as two unrelated, separate sciences; how these courses are generally taught in high schools may do little to change that impression. The study of enzymes provide a great opportunity for both biology and chemistry teachers to share with students the interdisciplinary nature of science. This article describes…

  15. Zinc Enzymes.

    ERIC Educational Resources Information Center

    Bertini, I.; And Others

    1985-01-01

    Discusses the role of zinc in various enzymes concerned with hydration, hydrolysis, and redox reactions. The binding of zinc to protein residues, properties of noncatalytic zinc(II) and catalytic zinc, and the reactions catalyzed by zinc are among the topics considered. (JN)

  16. A comparison of convergently evolved insect silks that share β-sheet molecular structure.

    PubMed

    Church, Jeffrey S; Woodhead, Andrea L; Walker, Andrew A; Sutherland, Tara D

    2014-06-01

    Raspy crickets produce silk webs that are used to build shelters. These webs have been found to consist of both fiber and film components. Raman spectra obtained from both components were found to be very similar for a given species. The protein structure of the fibers and films produced by both species was predominately β-sheet with lesser amounts of β-turns, unordered and α-helical protein also detected. The orientation of the β-sheet backbone in the fiber was determined to be parallel to the fiber axis. Compared to cocoon and dragline silk the orientation distribution exhibits a significant randomly orientated protein component. Amino acid analysis confirmed the presence of glycine, serine, and alanine in both species, which are known to form antiparallel β-sheet structures. Both species, although at significantly different concentrations, where found to contain proline. This amino acid is uncommon in insect silks, and likely involved in increasing fiber elasticity. PMID:24170682

  17. Virulence-Associated Enzymes of Cryptococcus neoformans

    PubMed Central

    Almeida, Fausto; Wolf, Julie M.

    2015-01-01

    Enzymes play key roles in fungal pathogenesis. Manipulation of enzyme expression or activity can significantly alter the infection process, and enzyme expression profiles can be a hallmark of disease. Hence, enzymes are worthy targets for better understanding pathogenesis and identifying new options for combatting fungal infections. Advances in genomics, proteomics, transcriptomics, and mass spectrometry have enabled the identification and characterization of new fungal enzymes. This review focuses on recent developments in the virulence-associated enzymes from Cryptococcus neoformans. The enzymatic suite of C. neoformans has evolved for environmental survival, but several of these enzymes play a dual role in colonizing the mammalian host. We also discuss new therapeutic and diagnostic strategies that could be based on the underlying enzymology. PMID:26453651

  18. Monotonically convergent optimization in quantum control using Krotov's method

    SciTech Connect

    Reich, Daniel M.; Koch, Christiane P.; Ndong, Mamadou

    2012-03-14

    The non-linear optimization method developed by A. Konnov and V. Krotov [Autom. Remote Cont. (Engl. Transl.) 60, 1427 (1999)] has been used previously to extend the capabilities of optimal control theory from the linear to the non-linear Schroedinger equation [S. E. Sklarz and D. J. Tannor, Phys. Rev. A 66, 053619 (2002)]. Here we show that based on the Konnov-Krotov method, monotonically convergent algorithms are obtained for a large class of quantum control problems. It includes, in addition to nonlinear equations of motion, control problems that are characterized by non-unitary time evolution, nonlinear dependencies of the Hamiltonian on the control, time-dependent targets, and optimization functionals that depend to higher than second order on the time-evolving states. We furthermore show that the nonlinear (second order) contribution can be estimated either analytically or numerically, yielding readily applicable optimization algorithms. We demonstrate monotonic convergence for an optimization functional that is an eighth-degree polynomial in the states. For the ''standard'' quantum control problem of a convex final-time functional, linear equations of motion and linear dependency of the Hamiltonian on the field, the second-order contribution is not required for monotonic convergence but can be used to speed up convergence. We demonstrate this by comparing the performance of first- and second-order algorithms for two examples.

  19. Convergent evolution in locomotory patterns of flying and swimming animals.

    PubMed

    Gleiss, Adrian C; Jorgensen, Salvador J; Liebsch, Nikolai; Sala, Juan E; Norman, Brad; Hays, Graeme C; Quintana, Flavio; Grundy, Edward; Campagna, Claudio; Trites, Andrew W; Block, Barbara A; Wilson, Rory P

    2011-01-01

    Locomotion is one of the major energetic costs faced by animals and various strategies have evolved to reduce its cost. Birds use interspersed periods of flapping and gliding to reduce the mechanical requirements of level flight while undergoing cyclical changes in flight altitude, known as undulating flight. Here we equipped free-ranging marine vertebrates with accelerometers and demonstrate that gait patterns resembling undulating flight occur in four marine vertebrate species comprising sharks and pinnipeds. Both sharks and pinnipeds display intermittent gliding interspersed with powered locomotion. We suggest, that the convergent use of similar gait patterns by distinct groups of animals points to universal physical and physiological principles that operate beyond taxonomic limits and shape common solutions to increase energetic efficiency. Energetically expensive large-scale migrations performed by many vertebrates provide common selection pressure for efficient locomotion, with potential for the convergence of locomotory strategies by a wide variety of species. PMID:21673673

  20. Diversity sustains an evolving network

    PubMed Central

    Mehrotra, Ravi; Soni, Vikram; Jain, Sanjay

    2009-01-01

    We study an evolutionary model of a complex system that evolves under catalytic dynamics and Darwinian selection and exhibits spontaneous growth, stasis and then a collapse of its structure. We find that the typical lifetime of the system increases sharply with the diversity of its components or species. We also find that the prime reason for crashes is a naturally occurring internal fragility of the system. This fragility is captured in the network organizational character and is related to a reduced multiplicity of pathways or feedback loops between its components. These results apply to several generalizations of the model as well. This work suggests new parameters for understanding the robustness of evolving molecular networks, ecosystems, societies and markets. PMID:19033136

  1. Evolvable Hardware for Space Applications

    NASA Technical Reports Server (NTRS)

    Lohn, Jason; Globus, Al; Hornby, Gregory; Larchev, Gregory; Kraus, William

    2004-01-01

    This article surveys the research of the Evolvable Systems Group at NASA Ames Research Center. Over the past few years, our group has developed the ability to use evolutionary algorithms in a variety of NASA applications ranging from spacecraft antenna design, fault tolerance for programmable logic chips, atomic force field parameter fitting, analog circuit design, and earth observing satellite scheduling. In some of these applications, evolutionary algorithms match or improve on human performance.

  2. When did oxygenic photosynthesis evolve?

    PubMed

    Buick, Roger

    2008-08-27

    The atmosphere has apparently been oxygenated since the 'Great Oxidation Event' ca 2.4 Ga ago, but when the photosynthetic oxygen production began is debatable. However, geological and geochemical evidence from older sedimentary rocks indicates that oxygenic photosynthesis evolved well before this oxygenation event. Fluid-inclusion oils in ca 2.45 Ga sandstones contain hydrocarbon biomarkers evidently sourced from similarly ancient kerogen, preserved without subsequent contamination, and derived from organisms producing and requiring molecular oxygen. Mo and Re abundances and sulphur isotope systematics of slightly older (2.5 Ga) kerogenous shales record a transient pulse of atmospheric oxygen. As early as ca 2.7 Ga, stromatolites and biomarkers from evaporative lake sediments deficient in exogenous reducing power strongly imply that oxygen-producing cyanobacteria had already evolved. Even at ca 3.2 Ga, thick and widespread kerogenous shales are consistent with aerobic photoautrophic marine plankton, and U-Pb data from ca 3.8 Ga metasediments suggest that this metabolism could have arisen by the start of the geological record. Hence, the hypothesis that oxygenic photosynthesis evolved well before the atmosphere became permanently oxygenated seems well supported. PMID:18468984

  3. Evolving Systems and Adaptive Key Component Control

    NASA Technical Reports Server (NTRS)

    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.

  4. Converging Higher Education Systems in a Global Setting: The Example of France and India

    ERIC Educational Resources Information Center

    Pilkington, Marc

    2014-01-01

    We present a comparative survey between the French and Indian higher education systems. In spite of their respective idiosyncratic features, we show that the two countries have both evolved comprehensively toward a knowledge-based society, in order to ensure the prosperity of their citizens. Secondly, we single out a threefold convergence between…

  5. Evolving Stochastic Learning Algorithm based on Tsallis entropic index

    NASA Astrophysics Data System (ADS)

    Anastasiadis, A. D.; Magoulas, G. D.

    2006-03-01

    In this paper, inspired from our previous algorithm, which was based on the theory of Tsallis statistical mechanics, we develop a new evolving stochastic learning algorithm for neural networks. The new algorithm combines deterministic and stochastic search steps by employing a different adaptive stepsize for each network weight, and applies a form of noise that is characterized by the nonextensive entropic index q, regulated by a weight decay term. The behavior of the learning algorithm can be made more stochastic or deterministic depending on the trade off between the temperature T and the q values. This is achieved by introducing a formula that defines a time-dependent relationship between these two important learning parameters. Our experimental study verifies that there are indeed improvements in the convergence speed of this new evolving stochastic learning algorithm, which makes learning faster than using the original Hybrid Learning Scheme (HLS). In addition, experiments are conducted to explore the influence of the entropic index q and temperature T on the convergence speed and stability of the proposed method.

  6. Bat echolocation calls: adaptation and convergent evolution

    PubMed Central

    Jones, Gareth; Holderied, Marc W

    2007-01-01

    Bat echolocation calls provide remarkable examples of ‘good design’ through evolution by natural selection. Theory developed from acoustics and sonar engineering permits a strong predictive basis for understanding echolocation performance. Call features, such as frequency, bandwidth, duration and pulse interval are all related to ecological niche. Recent technological breakthroughs have aided our understanding of adaptive aspects of call design in free-living bats. Stereo videogrammetry, laser scanning of habitat features and acoustic flight path tracking permit reconstruction of the flight paths of echolocating bats relative to obstacles and prey in nature. These methods show that echolocation calls are among the most intense airborne vocalizations produced by animals. Acoustic tracking has clarified how and why bats vary call structure in relation to flight speed. Bats using broadband echolocation calls adjust call design in a range-dependent manner so that nearby obstacles are localized accurately. Recent phylogenetic analyses based on gene sequences show that particular types of echolocation signals have evolved independently in several lineages of bats. Call design is often influenced more by perceptual challenges imposed by the environment than by phylogeny, and provides excellent examples of convergent evolution. Now that whole genome sequences of bats are imminent, understanding the functional genomics of echolocation will become a major challenge. PMID:17251105

  7. Bat echolocation calls: adaptation and convergent evolution.

    PubMed

    Jones, Gareth; Holderied, Marc W

    2007-04-01

    Bat echolocation calls provide remarkable examples of 'good design' through evolution by natural selection. Theory developed from acoustics and sonar engineering permits a strong predictive basis for understanding echolocation performance. Call features, such as frequency, bandwidth, duration and pulse interval are all related to ecological niche. Recent technological breakthroughs have aided our understanding of adaptive aspects of call design in free-living bats. Stereo videogrammetry, laser scanning of habitat features and acoustic flight path tracking permit reconstruction of the flight paths of echolocating bats relative to obstacles and prey in nature. These methods show that echolocation calls are among the most intense airborne vocalizations produced by animals. Acoustic tracking has clarified how and why bats vary call structure in relation to flight speed. Bats using broadband echolocation calls adjust call design in a range-dependent manner so that nearby obstacles are localized accurately. Recent phylogenetic analyses based on gene sequences show that particular types of echolocation signals have evolved independently in several lineages of bats. Call design is often influenced more by perceptual challenges imposed by the environment than by phylogeny, and provides excellent examples of convergent evolution. Now that whole genome sequences of bats are imminent, understanding the functional genomics of echolocation will become a major challenge. PMID:17251105

  8. Widespread convergence in toxin resistance by predictable molecular evolution

    PubMed Central

    Ujvari, Beata; Casewell, Nicholas R.; Sunagar, Kartik; Arbuckle, Kevin; Wüster, Wolfgang; Lo, Nathan; O’Meally, Denis; Beckmann, Christa; King, Glenn F.; Deplazes, Evelyne; Madsen, Thomas

    2015-01-01

    The question about whether evolution is unpredictable and stochastic or intermittently constrained along predictable pathways is the subject of a fundamental debate in biology, in which understanding convergent evolution plays a central role. At the molecular level, documented examples of convergence are rare and limited to occurring within specific taxonomic groups. Here we provide evidence of constrained convergent molecular evolution across the metazoan tree of life. We show that resistance to toxic cardiac glycosides produced by plants and bufonid toads is mediated by similar molecular changes to the sodium-potassium-pump (Na+/K+-ATPase) in insects, amphibians, reptiles, and mammals. In toad-feeding reptiles, resistance is conferred by two point mutations that have evolved convergently on four occasions, whereas evidence of a molecular reversal back to the susceptible state in varanid lizards migrating to toad-free areas suggests that toxin resistance is maladaptive in the absence of selection. Importantly, resistance in all taxa is mediated by replacements of 2 of the 12 amino acids comprising the Na+/K+-ATPase H1–H2 extracellular domain that constitutes a core part of the cardiac glycoside binding site. We provide mechanistic insight into the basis of resistance by showing that these alterations perturb the interaction between the cardiac glycoside bufalin and the Na+/K+-ATPase. Thus, similar selection pressures have resulted in convergent evolution of the same molecular solution across the breadth of the animal kingdom, demonstrating how a scarcity of possible solutions to a selective challenge can lead to highly predictable evolutionary responses. PMID:26372961

  9. Synchronization in an evolving network

    NASA Astrophysics Data System (ADS)

    Singh, R. K.; Bagarti, Trilochan

    2015-09-01

    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.

  10. Primary enzyme quantitation

    DOEpatents

    Saunders, G.C.

    1982-03-04

    The disclosure relates to the quantitation of a primary enzyme concentration by utilizing a substrate for the primary enzyme labeled with a second enzyme which is an indicator enzyme. Enzyme catalysis of the substrate occurs and results in release of the indicator enzyme in an amount directly proportional to the amount of primary enzyme present. By quantifying the free indicator enzyme one determines the amount of primary enzyme present.

  11. Converging shocks for DSD modelling

    NASA Astrophysics Data System (ADS)

    Matignon, Christophe

    2013-06-01

    Modelling of pyrotechnic systems requires both, a good understanding and precise prediction capabilities of the dynamics of detonation. When using insensitive high explosives IHE (such as TATB-based explosives) the interaction of the detonation front with the confinement can lead to very different detonation velocities. One of the most popular engineering tools used to model this behaviour is the Detonation Shock Dynamics (DSD). In the DSD assumption, the detonation front propagates at a normal shock velocity (Dn) which depends only on its local curvature (κ). For divergent detonations, the DSD limit is very well established both experimentally and theoretically and one can easily propose a model (which obeys the 1D quasi-steady weakly curved detonation theory) to reproduce this behavior. We propose to extend the DSD theory to slightly convergent detonation fronts and to validate it against experimental data. Two series of experiments were carried out. The first series was designed to collect precise information regarding converging detonation. Usually, in such configurations, the detonation is non steady, making precise and simultaneous measurements of velocity and curvature difficult to achieve. The originality of the proposed setup is to drive a self similar convergent detonation at constant speed in an IHE rod by an external explosive tube of greater detonation velocity (allowing an accurate recording of both velocity and curvature). A wide range EOS/reaction rate model (inspired from previous works of Wescott et al.) was then calibrated to reproduce both the strong shock initiation and the newly extended (Dn- κ) law. This model can be used to perform either direct numerical simulation (DNS) on fine resolved mesh grid, or its reduced PZR model (DSD based) on a much coarser grid. This model was then successfully validated against the second series of experiments involving a detonation propagating around an obstacle and exhibiting a non steady converging front

  12. Evolution of albinism in cave planthoppers by a convergent defect in the first step of melanin biosynthesis.

    PubMed

    Bilandžija, Helena; Cetković, Helena; Jeffery, William R

    2012-01-01

    Albinism, the reduction or loss of melanin pigment, is found in many diverse cave-dwelling animals. The mechanisms responsible for loss of melanin pigment are poorly understood. In this study we use a melanogenic substrate assay to determine the position where melanin synthesis is blocked in independently evolved cave planthoppers from Hawaii and Croatia. In this assay, substrates of enzymes responsible for melanin biosynthesis are added to fixed specimens in vitro and their ability to rescue black melanin pigmentation is determined. L-tyrosine, the first substrate in the pathway, did not produce melanin pigment, whereas L-DOPA, the second substrate, restored black pigment. Substrates in combination with enzyme inhibitors were used to test the possibility of additional downstream defects in the pathway. The results showed that downstream reactions leading from L-DOPA and dopamine to DOPA-melanin and dopamine-melanin, the two types of insect melanin, are functional. It is concluded that albinism is caused by a defect in the first step of the melanin synthesis pathway in cave-adapted planthoppers from widely separated parts of the world. However, Western blots indicated that tyrosine hydroxylase (TH), the only enzyme shown to operate at the first step in insects, is present in Hawaiian cave planthoppers. Thus, an unknown factor(s) operating at this step may be important in the evolution of planthopper albinism. In the cavefish Astyanax mexicanus, a genetic defect has also been described at the first step of melanin synthesis suggesting convergent evolution of albinism in both cave-adapted insects and teleosts. PMID:23017027

  13. "Nanoselves": NBIC and the Culture of Convergence

    ERIC Educational Resources Information Center

    Venkatesan, Priya

    2010-01-01

    The subject of this essay is NBIC convergence (nanotechnology, biotechnology, information technology and cognitive science convergence). NBIC convergence is a recurring trope that is dominated by the paradigm of integration of the sciences. It is largely influenced by the considerations of social and economic impact, and it assumes positivism in…

  14. Convergence analysis of combinations of different methods

    SciTech Connect

    Kang, Y.

    1994-12-31

    This paper provides a convergence analysis for combinations of different numerical methods for solving systems of differential equations. The author proves that combinations of two convergent linear multistep methods or Runge-Kutta methods produce a new convergent method of which the order is equal to the smaller order of the two original methods.

  15. Evolving Robust Gene Regulatory Networks

    PubMed Central

    Noman, Nasimul; Monjo, Taku; Moscato, Pablo; Iba, Hitoshi

    2015-01-01

    Design and implementation of robust network modules is essential for construction of complex biological systems through hierarchical assembly of ‘parts’ and ‘devices’. The robustness of gene regulatory networks (GRNs) is ascribed chiefly to the underlying topology. The automatic designing capability of GRN topology that can exhibit robust behavior can dramatically change the current practice in synthetic biology. A recent study shows that Darwinian evolution can gradually develop higher topological robustness. Subsequently, this work presents an evolutionary algorithm that simulates natural evolution in silico, for identifying network topologies that are robust to perturbations. We present a Monte Carlo based method for quantifying topological robustness and designed a fitness approximation approach for efficient calculation of topological robustness which is computationally very intensive. The proposed framework was verified using two classic GRN behaviors: oscillation and bistability, although the framework is generalized for evolving other types of responses. The algorithm identified robust GRN architectures which were verified using different analysis and comparison. Analysis of the results also shed light on the relationship among robustness, cooperativity and complexity. This study also shows that nature has already evolved very robust architectures for its crucial systems; hence simulation of this natural process can be very valuable for designing robust biological systems. PMID:25616055

  16. Mapping convergence points in the initial emergency response to 9/11.

    PubMed

    Bevc, Christine A; Barlau, Ashly N; Passanante, Nick A

    2009-10-01

    In response to extreme events, researchers have recognised the convergence of volunteers, emergency responders, and other individuals and organisations. In 2000, geographer Paul Routledge presented the concept of convergence spaces as a theoretical means to explain social movements. In applying this concept, this paper explores the geographic space in which organisations and individuals converged immediately following the 11 September 2001 attacks on the World Trade Center. The paper begins to answer the question of whether there were in fact any patterns of convergence among the locations utilised by organisations responding to the attacks. Using data collected from field documents, these geographic locations are mapped over 12 days to help identify possible patterns of clustering. Results of this analysis will begin to provide researchers, policy makers and practitioners with a better understanding of how emergency response evolves geographically following an event. PMID:19459903

  17. Biosynthesis of fosfazinomycin is a convergent process†

    PubMed Central

    Huang, Zedu; Wang, Kwo-Kwang A.; Lee, Jaeheon; van der Donk, Wilfred A.

    2014-01-01

    Fosfazinomycin A is a phosphonate natural product in which the C-terminal carboxylate of a Val-Arg dipeptide is connected to methyl 2-hydroxy-2-phosphono-acetate (Me-HPnA) via a unique hydrazide linkage. We report here that Me-HPnA is generated from phosphonoacetaldehyde (PnAA) in three biosynthetic steps through the combined action of an O-methyltransferase (FzmB) and an α-ketoglutarate (α-KG) dependent non-heme iron dioxygenase (FzmG). Unexpectedly, the latter enzyme is involved in two different steps, oxidation of the PnAA to phosphonoacetic acid as well as hydroxylation of methyl 2-phosphonoacetate. The N-methyltransferase (FzmH) was able to methylate Arg-NHNH2 (3) to give Arg-NHNHMe (4), constituting the second segment of the fosfazinomycin molecule. Methylation of other putative intermediates such as desmethyl fosfazinomycin B was not observed. Collectively, our current data support a convergent biosynthetic pathway to fosfazinomycin. PMID:25621145

  18. Primordial evolvability: Impasses and challenges.

    PubMed

    Vasas, Vera; Fernando, Chrisantha; Szilágyi, András; Zachár, István; Santos, Mauro; Szathmáry, Eörs

    2015-09-21

    While it is generally agreed that some kind of replicating non-living compounds were the precursors of life, there is much debate over their possible chemical nature. Metabolism-first approaches propose that mutually catalytic sets of simple organic molecules could be capable of self-replication and rudimentary chemical evolution. In particular, the graded autocatalysis replication domain (GARD) model, depicting assemblies of amphiphilic molecules, has received considerable interest. The system propagates compositional information across generations and is suggested to be a target of natural selection. However, evolutionary simulations indicate that the system lacks selectability (i.e. selection has negligible effect on the equilibrium concentrations). We elaborate on the lessons learnt from the example of the GARD model and, more widely, on the issue of evolvability, and discuss the implications for similar metabolism-first scenarios. We found that simple incorporation-type chemistry based on non-covalent bonds, as assumed in GARD, is unlikely to result in alternative autocatalytic cycles when catalytic interactions are randomly distributed. An even more serious problem stems from the lognormal distribution of catalytic factors, causing inherent kinetic instability of such loops, due to the dominance of efficiently catalyzed components that fail to return catalytic aid. Accordingly, the dynamics of the GARD model is dominated by strongly catalytic, but not auto-catalytic, molecules. Without effective autocatalysis, stable hereditary propagation is not possible. Many repetitions and different scaling of the model come to no rescue. Despite all attempts to show the contrary, the GARD model is not evolvable, in contrast to reflexively autocatalytic networks, complemented by rare uncatalyzed reactions and compartmentation. The latter networks, resting on the creation and breakage of chemical bonds, can generate novel ('mutant') autocatalytic loops from a given set of

  19. Weak {}^* convergence of operator means

    NASA Astrophysics Data System (ADS)

    Romanov, Alexandr V.

    2011-12-01

    For a linear operator U with \\Vert U^n\\Vert \\le \\operatorname{const} on a Banach space X we discuss conditions for the convergence of ergodic operator nets T_\\alpha corresponding to the adjoint operator U^* of U in the {W^*O}-topology of the space \\operatorname{End} X^*. The accumulation points of all possible nets of this kind form a compact convex set L in \\operatorname{End} X^*, which is the kernel of the operator semigroup G=\\overline{\\operatorname{co}}\\,\\Gamma_0, where \\Gamma_0=\\{U_n^*, n \\ge 0\\}. It is proved that all ergodic nets T_\\alpha weakly {}^* converge if and only if the kernel L consists of a single element. In the case of X=C(\\Omega) and the shift operator U generated by a continuous transformation \\varphi of a metrizable compactum \\Omega we trace the relationships among the ergodic properties of U, the structure of the operator semigroups L, G and \\Gamma=\\overline{\\Gamma}_0, and the dynamical characteristics of the semi-cascade (\\varphi,\\Omega). In particular, if \\operatorname{card}L=1, then a) for any \\omega \\in\\Omega the closure of the trajectory \\{\\varphi^n\\omega, n \\ge 0\\} contains precisely one minimal set m, and b) the restriction (\\varphi,m) is strictly ergodic. Condition a) implies the {W^*O}-convergence of any ergodic sequence of operators T_n \\in \\operatorname{End} X^* under the additional assumption that the kernel of the enveloping semigroup E(\\varphi,\\Omega) contains elements obtained from the `basis' family of transformations \\{\\varphi^n, n \\ge 0\\} of the compact set \\Omega by using some transfinite sequence of sequential passages to the limit.

  20. Ecomorphological convergence in planktivorous surgeonfishes.

    PubMed

    Friedman, S T; Price, S A; Hoey, A S; Wainwright, P C

    2016-05-01

    Morphological convergence plays a central role in the study of evolution. Often induced by shared ecological specialization, homoplasy hints at underlying selective pressures and adaptive constraints that deterministically shape the diversification of life. Although midwater zooplanktivory has arisen in adult surgeonfishes (family Acanthuridae) at least four independent times, it represents a clearly specialized state, requiring the capacity to swiftly swim in midwater locating and sucking small prey items. Whereas this diet has commonly been associated with specific functional adaptations in fishes, acanthurids present an interesting case study as all nonplanktivorous species feed by grazing on benthic algae and detritus, requiring a vastly different functional morphology that emphasizes biting behaviours. We examined the feeding morphology in 30 acanthurid species and, combined with a pre-existing phylogenetic tree, compared the fit of evolutionary models across two diet regimes: zooplanktivores and nonzooplanktivorous grazers. Accounting for phylogenetic relationships, the best-fitting model indicates that zooplanktivorous species are converging on a separate adaptive peak from their grazing relatives. Driving this bimodal landscape, zooplanktivorous acanthurids tend to develop a slender body, reduced facial features, smaller teeth and weakened jaw adductor muscles. However, despite these phenotypic changes, model fitting suggests that lineages have not yet reached the adaptive peak associated with plankton feeding even though some transitions appear to be over 10 million years old. These findings demonstrate that the selective demands of pelagic feeding promote repeated - albeit very gradual - ecomorphological convergence within surgeonfishes, while allowing local divergences between closely related species, contributing to the overall diversity of the clade. PMID:26809907

  1. Isotopic Analysis and Evolved Gases

    NASA Technical Reports Server (NTRS)

    Swindle, Timothy D.; Boynton, William V.; Chutjian, Ara; Hoffman, John H.; Jordan, Jim L.; Kargel, Jeffrey S.; McEntire, Richard W.; Nyquist, Larry

    1996-01-01

    Precise measurements of the chemical, elemental, and isotopic composition of planetary surface material and gases, and observed variations in these compositions, can contribute significantly to our knowledge of the source(s), ages, and evolution of solar system materials. The analyses discussed in this paper are mostly made by mass spectrometers or some other type of mass analyzer, and address three broad areas of interest: (1) atmospheric composition - isotopic, elemental, and molecular, (2) gases evolved from solids, and (3) solids. Current isotopic data on nine elements, mostly from in situ analysis, but also from meteorites and telescopic observations are summarized. Potential instruments for isotopic analysis of lunar, Martian, Venusian, Mercury, and Pluto surfaces, along with asteroid, cometary and icy satellites, surfaces are discussed.

  2. Drastic events make evolving networks

    NASA Astrophysics Data System (ADS)

    Ausloos, M.; Lambiotte, R.

    2007-05-01

    Co-authorship networks of neighbouring scientific disciplines, i.e. granular (G) media and networks (N) are studied in order to observe drastic structural changes in evolving networks. The data is taken from arXives. The system is described as coupled networks. By considering the 1995-2005 time interval and scanning the author-article network evolution with a mobile time window, we focus on the properties of the links, as well as on the time evolution of the nodes. They can be in three states, N, G or multi-disciplinary (M). This leads to drastic jumps in a so-called order parameter, i.e. the link proportion of a given type, forming the main island, that reminds of features appearing at percolation and during metastable (aggregation-desaggregation) processes. The data analysis also focuses on the way different kinds (N, G or M) of authors collaborate, and on the kind of the resulting collaboration.

  3. Speech processing: An evolving technology

    SciTech Connect

    Crochiere, R.E.; Flanagan, J.L.

    1986-09-01

    As we enter the information age, speech processing is emerging as an important technology for making machines easier and more convenient for humans to use. It is both an old and a new technology - dating back to the invention of the telephone and forward, at least in aspirations, to the capabilities of HAL in 2001. Explosive advances in microelectronics now make it possible to implement economical real-time hardware for sophisticated speech processing - processing that formerly could be demonstrated only in simulations on main-frame computers. As a result, fundamentally new product concepts - as well as new features and functions in existing products - are becoming possible and are being explored in the marketplace. As the introductory piece to this issue, the authors draw a brief perspective on the evolving field of speech processing and assess the technology in the the three constituent sectors: speech coding, synthesis, and recognition.

  4. Widespread flower color convergence in Solanaceae via alternate biochemical pathways.

    PubMed

    Ng, Julienne; Smith, Stacey D

    2016-01-01

    Phenotypic convergence is rampant throughout the tree of life. While recent studies have made significant progress in ascertaining the proximate mechanisms underlying convergent phenotypes, less is known about the frequency and predictability with which convergent phenotypes arise via the same or multiple pathways at the macroevolutionary scale. We investigated the proximate causes and evolutionary patterns of red flower color in the tomato family, Solanaceae, using large-scale data mining and new sequence data to reconstruct a megaphylogeny of 1341 species. We then combined spectral and anatomical data to assess how many times red flowers have evolved, the relative contribution of different pathways to independent origins of red, and whether the underlying pathway is predicted by phylogenetic relatedness. We estimated at least 30 relatively recent origins of red flowers using anthocyanins, carotenoids, or a dual production of both pigments, with significant phylogenetic signal in the use of anthocyanins and dual production, indicating that closely related red-flowered species tend to employ the same mechanism for coloration. Our study is the first to test whether developmental pathways exhibit phylogenetic signal and implies that historical contingency strongly influences the evolution of new phenotypes. PMID:26224118

  5. Planets in Evolved Binary Systems

    NASA Astrophysics Data System (ADS)

    Perets, Hagai B.

    2011-03-01

    Exo-planets are typically thought to form in protoplanetary disks left over from protostellar disk of their newly formed host star. However, additional planetary formation and evolution routes may exist in old evolved binary systems. Here we discuss the implications of binary stellar evolution on planetary systems in such environments. In these binary systems stellar evolution could lead to the formation of symbiotic stars, where mass is lost from one star and could be transferred to its binary companion, and may form an accretion disk around it. This raises the possibility that such a disk could provide the necessary environment for the formation of a new, second generation of planets in both circumstellar or circumbinary configurations. Pre-existing first generation planets surviving the post-MS evolution of such systems would be dynamically effected by the mass loss in the systems and may also interact with the newly formed disk. Such planets and/or planetesimals may also serve as seeds for the formation of the second generation planets, and/or interact with them, possibly forming atypical planetary systems. Second generation planetary systems should be typically found in white dwarf binary systems, and may show various observational signatures. Most notably, second generation planets could form in environment which are inaccessible, or less favorable, for first generation planets. The orbital phase space available for the second generation planets could be forbidden (in terms of the system stability) to first generation planets in the pre-evolved progenitor binaries. In addition planets could form in metal poor environments such as globular clusters and/or in double compact object binaries. Observations of exo-planets in such forbidden or unfavorable regions could possibly serve to uniquely identify their second generation character. Finally, we point out a few observed candidate second generation planetary systems, including Gl 86, HD 27442 and all of the

  6. Divergent and Convergent Evolution of Fungal Pathogenicity

    PubMed Central

    Shang, Yanfang; Xiao, Guohua; Zheng, Peng; Cen, Kai; Zhan, Shuai; Wang, Chengshu

    2016-01-01

    Fungal pathogens of plants and animals have multifarious effects; they cause devastating damages to agricultures, lead to life-threatening diseases in humans, or induce beneficial effects by reducing insect pest populations. Many virulence factors have been determined in different fungal pathogens; however, the molecular determinants contributing to fungal host selection and adaptation are largely unknown. In this study, we sequenced the genomes of seven ascomycete insect pathogens and performed the genome-wide analyses of 33 species of filamentous ascomycete pathogenic fungi that infect insects (12 species), plants (12), and humans (9). Our results revealed that the genomes of plant pathogens encode more proteins and protein families than the insect and human pathogens. Unexpectedly, more common orthologous protein groups are shared between the insect and plant pathogens than between the two animal group pathogens. We also found that the pathogenicity of host-adapted fungi evolved multiple times, and that both divergent and convergent evolutions occurred during pathogen–host cospeciation thus resulting in protein families with similar features in each fungal group. However, the role of phylogenetic relatedness on the evolution of protein families and therefore pathotype formation could not be ruled out due to the effect of common ancestry. The evolutionary correlation analyses led to the identification of different protein families that correlated with alternate pathotypes. Particularly, the effector-like proteins identified in plant and animal pathogens were strongly linked to fungal host adaptation, suggesting the existence of similar gene-for-gene relationships in fungus–animal interactions that has not been established before. These results well advance our understanding of the evolution of fungal pathogenicity and the factors that contribute to fungal pathotype formation. PMID:27071652

  7. Divergent and Convergent Evolution of Fungal Pathogenicity.

    PubMed

    Shang, Yanfang; Xiao, Guohua; Zheng, Peng; Cen, Kai; Zhan, Shuai; Wang, Chengshu

    2016-01-01

    Fungal pathogens of plants and animals have multifarious effects; they cause devastating damages to agricultures, lead to life-threatening diseases in humans, or induce beneficial effects by reducing insect pest populations. Many virulence factors have been determined in different fungal pathogens; however, the molecular determinants contributing to fungal host selection and adaptation are largely unknown. In this study, we sequenced the genomes of seven ascomycete insect pathogens and performed the genome-wide analyses of 33 species of filamentous ascomycete pathogenic fungi that infect insects (12 species), plants (12), and humans (9). Our results revealed that the genomes of plant pathogens encode more proteins and protein families than the insect and human pathogens. Unexpectedly, more common orthologous protein groups are shared between the insect and plant pathogens than between the two animal group pathogens. We also found that the pathogenicity of host-adapted fungi evolved multiple times, and that both divergent and convergent evolutions occurred during pathogen-host cospeciation thus resulting in protein families with similar features in each fungal group. However, the role of phylogenetic relatedness on the evolution of protein families and therefore pathotype formation could not be ruled out due to the effect of common ancestry. The evolutionary correlation analyses led to the identification of different protein families that correlated with alternate pathotypes. Particularly, the effector-like proteins identified in plant and animal pathogens were strongly linked to fungal host adaptation, suggesting the existence of similar gene-for-gene relationships in fungus-animal interactions that has not been established before. These results well advance our understanding of the evolution of fungal pathogenicity and the factors that contribute to fungal pathotype formation. PMID:27071652

  8. A Quantitative Approach to Assessing System Evolvability

    NASA Technical Reports Server (NTRS)

    Christian, John A., III

    2004-01-01

    When selecting a system from multiple candidates, the customer seeks the one that best meets his or her needs. Recently the desire for evolvable systems has become more important and engineers are striving to develop systems that accommodate this need. In response to this search for evolvability, we present a historical perspective on evolvability, propose a refined definition of evolvability, and develop a quantitative method for measuring this property. We address this quantitative methodology from both a theoretical and practical perspective. This quantitative model is then applied to the problem of evolving a lunar mission to a Mars mission as a case study.

  9. Highly efficient self-replicating RNA enzymes.

    PubMed

    Robertson, Michael P; Joyce, Gerald F

    2014-02-20

    An RNA enzyme has been developed that catalyzes the joining of oligonucleotide substrates to form additional copies of itself, undergoing self-replication with exponential growth. The enzyme also can cross-replicate with a partner enzyme, resulting in their mutual exponential growth and enabling self-sustained Darwinian evolution. The opportunity for inventive evolution within this synthetic genetic system depends on the diversity of the evolving population, which is limited by the catalytic efficiency of the enzyme. Directed evolution was used to improve the efficiency of the enzyme and increase its exponential growth rate to 0.14 min(-1), corresponding to a doubling time of 5 min. This is close to the limit of 0.21 min(-1) imposed by the rate of product release, but sufficient to enable more than 80 logs of growth per day. PMID:24388759

  10. Many Paths to a Common Destination: Morphological Differentiation of a Functionally Convergent Visual Signal.

    PubMed

    Hagman, Mattias; Ord, Terry J

    2016-09-01

    Understanding the interacting outcomes of selection and historical contingency in shaping adaptive evolution remains a challenge in evolutionary biology. While selection can produce convergent outcomes when species occupy similar environments, the unique history of each species can also influence evolutionary trajectories and result in different phenotypic end points. The question is to what extent historical contingency places species on different adaptive pathways and, in turn, the extent to which we can predict evolutionary outcomes. Among lizards there are several distantly related genera that have independently evolved an elaborate extendible dewlap for territorial communication. We conducted a detailed morphological study and employed new phylogenetic comparative methods to investigate the evolution of the underlying hyoid that powers the extension of the dewlap. This analysis showed that there appear to have been multiple phenotypic pathways for evolving a functionally convergent dewlap. The biomechanical complexity that underlies this morphological structure implies that adaptation should have been constrained to a narrow phenotypic pathway. However, multiple adaptive solutions have been possible in apparent response to a common selection pressure. Thus, the phenotypic outcome that subsequently evolved in different genera seems to have been contingent on the history of the group in question. This blurs the distinction between convergent and historically contingent adaptation and suggests that adaptive phenotypic diversity can evolve without the need for divergent natural selection. PMID:27501088

  11. Convergent Validity of the PUTS.

    PubMed

    Brandt, Valerie Cathérine; Beck, Christian; Sajin, Valeria; Anders, Silke; Münchau, Alexander

    2016-01-01

    Premonitory urges are a cardinal feature in Gilles de la Tourette syndrome. Severity of premonitory urges can be assessed with the "Premonitory Urge for Tic Disorders Scale" (PUTS). However, convergent validity of the measure has been difficult to assess due to the lack of other urge measures. We investigated the relationship between average real-time urge intensity assessed by an in-house developed real-time urge monitor (RUM), measuring urge intensity continuously for 5 min on a visual analog scale, and general urge intensity assessed by the PUTS in 22 adult Tourette patients (mean age 29.8 ± 10.3 SD, 19 males). Additionally, underlying factors of premonitory urges assessed by the PUTS were investigated in the adult sample using factor analysis and were replicated in 40 children and adolescents diagnosed with Tourette syndrome (mean age 12.05 ± 2.83 SD, 31 males). Cronbach's α for the PUTS 10 was acceptable (α = 0.79) in the adult sample. Convergent validity between average real-time urge intensity scores (as assessed with the RUM) and the 10-item version of the PUTS (r = 0.64) and the 9-item version of the PUTS (r = 0.66) was good. A factor analysis including the 10 items of the PUTS and average real-time urge intensity scores revealed three factors. One factor included the average real-time urge intensity score and appeared to measure urge intensity, whereas the other two factors can be assumed to reflect the (sensory) quality of urges and subjective control, respectively. The factor structure of the 10 PUTS items alone was replicated in a sample of children and adolescents. The results indicate that convergent validity between the PUTS and the real-time urge assessment monitor is good. Furthermore, the results suggest that the PUTS might assess more than one dimension of urges, and it may be worthwhile developing different subscales of the PUTS assessing premonitory urges in terms of intensity and quality, as well as subjectively

  12. Convergent Validity of the PUTS

    PubMed Central

    Brandt, Valerie Cathérine; Beck, Christian; Sajin, Valeria; Anders, Silke; Münchau, Alexander

    2016-01-01

    Premonitory urges are a cardinal feature in Gilles de la Tourette syndrome. Severity of premonitory urges can be assessed with the “Premonitory Urge for Tic Disorders Scale” (PUTS). However, convergent validity of the measure has been difficult to assess due to the lack of other urge measures. We investigated the relationship between average real-time urge intensity assessed by an in-house developed real-time urge monitor (RUM), measuring urge intensity continuously for 5 min on a visual analog scale, and general urge intensity assessed by the PUTS in 22 adult Tourette patients (mean age 29.8 ± 10.3 SD, 19 males). Additionally, underlying factors of premonitory urges assessed by the PUTS were investigated in the adult sample using factor analysis and were replicated in 40 children and adolescents diagnosed with Tourette syndrome (mean age 12.05 ± 2.83 SD, 31 males). Cronbach’s α for the PUTS 10 was acceptable (α = 0.79) in the adult sample. Convergent validity between average real-time urge intensity scores (as assessed with the RUM) and the 10-item version of the PUTS (r = 0.64) and the 9-item version of the PUTS (r = 0.66) was good. A factor analysis including the 10 items of the PUTS and average real-time urge intensity scores revealed three factors. One factor included the average real-time urge intensity score and appeared to measure urge intensity, whereas the other two factors can be assumed to reflect the (sensory) quality of urges and subjective control, respectively. The factor structure of the 10 PUTS items alone was replicated in a sample of children and adolescents. The results indicate that convergent validity between the PUTS and the real-time urge assessment monitor is good. Furthermore, the results suggest that the PUTS might assess more than one dimension of urges, and it may be worthwhile developing different subscales of the PUTS assessing premonitory urges in terms of intensity and quality, as well as

  13. How do drumlin patterns evolve?

    NASA Astrophysics Data System (ADS)

    Ely, Jeremy; Clark, Chris; Spagnolo, Matteo; Hughes, Anna

    2016-04-01

    The flow of a geomorphic agent over a sediment bed creates patterns in the substrate composed of bedforms. Ice is no exception to this, organising soft sedimentary substrates into subglacial bedforms. As we are yet to fully observe their initiation and evolution beneath a contemporary ice mass, little is known about how patterns in subglacial bedforms develop. Here we study 36,222 drumlins, divided into 72 flowsets, left behind by the former British-Irish Ice sheet. These flowsets provide us with 'snapshots' of drumlin pattern development. The probability distribution functions of the size and shape metrics of drumlins within these flowsets were analysed to determine whether behaviour that is common of other patterned phenomena has occurred. Specifically, we ask whether drumlins i) are printed at a specific scale; ii) grow or shrink after they initiate; iii) stabilise at a specific size and shape; and iv) migrate. Our results indicate that drumlins initiate at a minimum size and spacing. After initiation, the log-normal distribution of drumlin size and shape metrics suggests that drumlins grow, or possibly shrink, as they develop. We find no evidence for stabilisation in drumlin length, supporting the idea of a subglacial bedform continuum. Drumlin migration is difficult to determine from the palaeo-record. However, there are some indications that a mixture of static and mobile drumlins occurs, which could potentially lead to collisions, cannibalisation and coarsening. Further images of modern drumlin fields evolving beneath ice are required to capture stages of drumlin pattern evolution.

  14. Magnetic fields around evolved stars

    NASA Astrophysics Data System (ADS)

    Leal-Ferreira, M.; Vlemmings, W.; Kemball, A.; Amiri, N.; Maercker, M.; Ramstedt, S.; Olofsson, G.

    2014-04-01

    A number of mechanisms, such as magnetic fields, (binary) companions and circumstellar disks have been suggested to be the cause of non-spherical PNe and in particular collimated outflows. This work investigates one of these mechanisms: the magnetic fields. While MHD simulations show that the fields can indeed be important, few observations of magnetic fields have been done so far. We used the VLBA to observe five evolved stars, with the goal of detecting the magnetic field by means of water maser polarization. The sample consists in four AGB stars (IK Tau, RT Vir, IRC+60370 and AP Lyn) and one pPN (OH231.8+4.2). In four of the five sources, several strong maser features were detected allowing us to measure the linear and/or circular polarization. Based on the circular polarization detections, we infer the strength of the component of the field along the line of sight to be between ~30 mG and ~330 mG in the water maser regions of these four sources. When extrapolated to the surface of the stars, the magnetic field strength would be between a few hundred mG and a few Gauss when assuming a toroidal field geometry and higher when assuming more complex magnetic fields. We conclude that the magnetic energy we derived in the water maser regions is higher than the thermal and kinetic energy, leading to the conclusion that, indeed, magnetic fields probably play an important role in shaping Planetary Nebulae.

  15. Submillimeter observations of evolved stars

    NASA Technical Reports Server (NTRS)

    Sopka, R. J.; Hildebrand, R.; Jaffe, D. T.; Gatley, I.; Roellig, T.

    1985-01-01

    Broadband submillimeter observations of thermal emission from several evolved stars have been obtained using the United Kingdom Infrared Telescope on Mauna Kea, Hawaii. The observations were carried out at an effective wavelength of 400 microns in order to estimate the mass loss rates in dust from the stars. Direct estimates of mass loss rates are in the range 10 to the -9th to 10 to the -6th solar mass/yr. Analysis of the spectrum of IRC + 10216 confirmed previous estimates of dust grain emissivity in the range 10-1000 microns. The infrared properties of IRC + 10216 are found to be similar to the carbon rich object CRL 3068. No systematic difference was found between the dust masses of carbon rich and oxygen rich envelopes. The largest mass loss rates in dust were obtained for the bipolar objects OH 231.8 + 4.2 CRL 2688, CRL 618, and NGC 7027. It is suggested that the ratios of gas to dust, and the slopes of the far infrared to submillimeter wavelength continua of these stars objects are probably representative of amorphous rather than crystalline grains.

  16. Circumstellar Crystalline Silicates: Evolved Stars

    NASA Astrophysics Data System (ADS)

    Tartar, Josh; Speck, A. K.

    2008-05-01

    One of the most exciting developments in astronomy in the last 15 years was the discovery of crystalline silicate stardust by the Short Wavelength Spectrometer (SWS) on board of ISO; discovery of the crystalline grains was indeed one of the biggest surprises of the ISO mission. Initially discovered around AGB stars (evolved stars in the range of 0.8 > M/M¤>8) at far-infrared (IR) wavelengths, crystalline silicates have since been seen in many astrophysical environments including young stellar objects (T Tauri and Herbig Ae/Be), comets and Ultra Luminous Infrared Galaxies. Low and intermediate mass stars (LIMS) comprise 95% of the contributors to the ISM, so study of the formation of crystalline silicates is critical to our understanding of the ISM, which is thought to be primarily amorphous (one would expect an almost exact match between the composition of AGB dust shells and the dust in the ISM). Whether the crystalline dust is merely undetectable or amorphized remains a mystery. The FORCAST instrument on SOFIA as well as the PACS instrument on Herschel will provide exciting observing opportunities for the further study of crystalline silicates.

  17. Mosaic Convergence of Rodent Dentitions

    PubMed Central

    Lazzari, Vincent; Charles, Cyril; Tafforeau, Paul; Vianey-Liaud, Monique; Aguilar, Jean-Pierre; Jaeger, Jean-Jacques; Michaux, Jacques; Viriot, Laurent

    2008-01-01

    Background Understanding mechanisms responsible for changes in tooth morphology in the course of evolution is an area of investigation common to both paleontology and developmental biology. Detailed analyses of molar tooth crown shape have shown frequent homoplasia in mammalian evolution, which requires accurate investigation of the evolutionary pathways provided by the fossil record. The necessity of preservation of an effective occlusion has been hypothesized to functionally constrain crown morphological changes and to also facilitate convergent evolution. The Muroidea superfamily constitutes a relevant model for the study of molar crown diversification because it encompasses one third of the extant mammalian biodiversity. Methodology/Principal Findings Combined microwear and 3D-topographic analyses performed on fossil and extant muroid molars allow for a first quantification of the relationships between changes in crown morphology and functionality of occlusion. Based on an abundant fossil record and on a well resolved phylogeny, our results show that the most derived functional condition associates longitudinal chewing and non interlocking of cusps. This condition has been reached at least 7 times within muroids via two main types of evolutionary pathways each respecting functional continuity. In the first type, the flattening of tooth crown which induces the removal of cusp interlocking occurs before the rotation of the chewing movement. In the second type however, flattening is subsequent to rotation of the chewing movement which can be associated with certain changes in cusp morphology. Conclusion/Significance The reverse orders of the changes involved in these different pathways reveal a mosaic evolution of mammalian dentition in which direction of chewing and crown shape seem to be partly decoupled. Either can change in respect to strong functional constraints affecting occlusion which thereby limit the number of the possible pathways. Because convergent

  18. Cosmic Convergence: Art and Science

    NASA Astrophysics Data System (ADS)

    Mayo, Elizabeth A.; Zisholtz, E.; Hilton, H.

    2010-01-01

    The I.P. Stanback Museum and Planetarium is a major educational and teaching resource for South Carolina State University, K-12 schools, other universities and the community of Orangeburg and well beyond. The concept of creating a museum with a planetarium on the campus of SC State was ahead of its time. Today scholars are writing about the unity of creative disciplines. Through its integration of the arts, humanities and sciences, the Stanback, the only art museum with a planetarium at any of the Historically Black Colleges and Universities and one of the few in the nation, stands in the forefront of modern thinking. Cosmic Convergence: Art and Science, opening at the I.P. Stanback Museum and Planetarium in February 2010, will feature the works of Mildred Thompson (1936-2003), a prominent African American artist who worked in the media of painting, drawing, print making, sculpture, and photography. Thompson’s artwork shows the strong influences of her interest in physics, astronomy, and metaphysics as well as music and spiritualism. “My work in the visual arts is, and has always been, a continuous search for understanding. It is an expression of purpose and reflects a personal interpretation of the Universe.” Cosmic Convergence will explore the meeting of Art and Science through Mildred Thompson's work and the scientific basis of that work. The paintings and sculptures of the exhibit will be combined with astronomical images showing both the reality and interpretation of the surrounding Universe. Support for this work was provided by the NSF PAARE program to South Carolina State University under award AST-0750814.

  19. Optimizing convergence rates of alternating minimization reconstruction algorithms for real-time explosive detection applications

    NASA Astrophysics Data System (ADS)

    Bosch, Carl; Degirmenci, Soysal; Barlow, Jason; Mesika, Assaf; Politte, David G.; O'Sullivan, Joseph A.

    2016-05-01

    X-ray computed tomography reconstruction for medical, security and industrial applications has evolved through 40 years of experience with rotating gantry scanners using analytic reconstruction techniques such as filtered back projection (FBP). In parallel, research into statistical iterative reconstruction algorithms has evolved to apply to sparse view scanners in nuclear medicine, low data rate scanners in Positron Emission Tomography (PET) [5, 7, 10] and more recently to reduce exposure to ionizing radiation in conventional X-ray CT scanners. Multiple approaches to statistical iterative reconstruction have been developed based primarily on variations of expectation maximization (EM) algorithms. The primary benefit of EM algorithms is the guarantee of convergence that is maintained when iterative corrections are made within the limits of convergent algorithms. The primary disadvantage, however is that strict adherence to correction limits of convergent algorithms extends the number of iterations and ultimate timeline to complete a 3D volumetric reconstruction. Researchers have studied methods to accelerate convergence through more aggressive corrections [1], ordered subsets [1, 3, 4, 9] and spatially variant image updates. In this paper we describe the development of an AM reconstruction algorithm with accelerated convergence for use in a real-time explosive detection application for aviation security. By judiciously applying multiple acceleration techniques and advanced GPU processing architectures, we are able to perform 3D reconstruction of scanned passenger baggage at a rate of 75 slices per second. Analysis of the results on stream of commerce passenger bags demonstrates accelerated convergence by factors of 8 to 15, when comparing images from accelerated and strictly convergent algorithms.

  20. Voyages Through Time: Everything Evolves

    NASA Astrophysics Data System (ADS)

    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

  1. Submillimeter observations of evolved stars

    SciTech Connect

    Sopka, R.J.; Hildebrand, R.; Jaffe, D.T.; Gatley, I.; Roellig, T.; Werner, M.; Jura, M.; Zuckerman, B.

    1985-07-01

    Broad-band submillimeter observations of the thermal emission from evolved stars have been obtained with the United Kingdom Infrared Telescope on Mauna Kea, Hawaii. These observations, at an effective wavelength of 400 ..mu..m, provide the most direct method for estimating the mass loss rate in dust from these stars and also help to define the long-wavelength thermal spectrum of the dust envelopes. The mass loss rates in dust that we derive range from 10/sup -9/ to 10/sup -6/ M/sub sun/ yr/sup -1/ and are compared with mass loss rates derived from molecular line observations to estimate gas-to-dust ratios in outflowing envelopes. These values are found to be generally compatible with the interstellar gas-to-dust ratio of approx.100 if submillimeter emissivities appropriate to amorphous grain structures are assumed. Our analysis of the spectrum of IRC+10216 confirms previous suggestions that the grain emissivity varies as lambda/sup -1.2/ rather than as lambda/sup -2/ for 10

  2. Convergence of large-deviation estimators.

    PubMed

    Rohwer, Christian M; Angeletti, Florian; Touchette, Hugo

    2015-11-01

    We study the convergence of statistical estimators used in the estimation of large-deviation functions describing the fluctuations of equilibrium, nonequilibrium, and manmade stochastic systems. We give conditions for the convergence of these estimators with sample size, based on the boundedness or unboundedness of the quantity sampled, and discuss how statistical errors should be defined in different parts of the convergence region. Our results shed light on previous reports of "phase transitions" in the statistics of free energy estimators and establish a general framework for reliably estimating large-deviation functions from simulation and experimental data and identifying parameter regions where this estimation converges. PMID:26651644

  3. Early evolution of efficient enzymes and genome organization

    PubMed Central

    2012-01-01

    Background Cellular life with complex metabolism probably evolved during the reign of RNA, when it served as both information carrier and enzyme. Jensen proposed that enzymes of primordial cells possessed broad specificities: they were generalist. When and under what conditions could primordial metabolism run by generalist enzymes evolve to contemporary-type metabolism run by specific enzymes? Results Here we show by numerical simulation of an enzyme-catalyzed reaction chain that specialist enzymes spread after the invention of the chromosome because protocells harbouring unlinked genes maintain largely non-specific enzymes to reduce their assortment load. When genes are linked on chromosomes, high enzyme specificity evolves because it increases biomass production, also by reducing taxation by side reactions. Conclusion The constitution of the genetic system has a profound influence on the limits of metabolic efficiency. The major evolutionary transition to chromosomes is thus proven to be a prerequisite for a complex metabolism. Furthermore, the appearance of specific enzymes opens the door for the evolution of their regulation. Reviewers This article was reviewed by Sándor Pongor, Gáspár Jékely, and Rob Knight. PMID:23114029

  4. Phenotypic and genotypic convergences are influenced by historical contingency and environment in yeast

    PubMed Central

    NIDELET, Thibault; MARTIN, Juliette; LEGRAND, Judith; DILLMANN, Christine; BOURGAIS, Aurélie; de VIENNE, Dominique; SHERLOCK, Gavin; SICARD, Delphine

    2015-01-01

    Different organisms have independently and recurrently evolved similar phenotypic traits at different points throughout history. This phenotypic convergence may be caused by genotypic convergence and constrained by historical contingency. To investigate how convergence may be driven by selection in a particular environment and constrained by history, we analyzed nine life-history traits and four metabolic traits during an experimental evolution of six yeast strains in four different environments. In each of the environments, the population converged towards a different life-history strategy. However, phenotypic convergence was partly associated with the selection of mutations in genes involved in the same pathway. In a fifth of our evolution experiments, mutations in the same gene, BMH1, were selected, in three out of the six ancestral genotypes. Two types of BMH1 mutation with opposite phenotypic effects on several traits were found. The evolution of most traits, as well as the occurrence of BMH1 mutations, was significantly influenced by the ancestral strain. However, this effect could not be easily predicted from ancestors’ phylogeny or past-selection. All together, our data demonstrate that phenotypic and its underlying genotypic convergence depends on a complex interplay between the evolutionary environment, pleiotropy and the ancestor genetic background but are not straightforwardly predicable. PMID:24164389

  5. Convergence dynamics of the Bak Sneppen model: Activity rate and waiting time distribution

    NASA Astrophysics Data System (ADS)

    Tirnakli, Ugur; Lyra, Marcelo L.

    2007-02-01

    In this work, we study the convergence dynamics of two independent random configurations of the Bak-Sneppen model of self-organized criticality evolving under the same external noise. A recently proposed measure of the Hamming distance which considers the minimum difference between displaced configurations is used. The displacement evolves in time intermittently. We compute the jump activity rate and waiting time distribution and report on their asymptotic power-law scaling which characterizes the slow relaxation and the absence of typical length and time scales typical of critical dynamical systems.

  6. Extreme variability in convergence to structural balance in frustrated dynamical systems

    NASA Astrophysics Data System (ADS)

    Singh, Rajeev; Dasgupta, Subinay; Sinha, Sitabhra

    2014-01-01

    In many complex systems, heterogeneous connections can subject constituent elements to conflicting influences, resulting in frustration. Here we show numerically that an initially frustrated system can achieve structural balance by a link adaptation process inspired by Hebb's principle, with interaction strengths evolving in accordance with the dynamical states of its components. In the presence of fluctuations the time required to converge to the balanced state exhibits large dispersion characterized by a bimodal distribution, pointing to an intriguing problem in the study of evolving energy landscapes.

  7. Contrasted patterns of variation and evolutionary convergence at the antiviral OAS1 gene in old world primates.

    PubMed

    Fish, Ian; Boissinot, Stéphane

    2015-09-01

    The oligoadenylate synthetase 1 (OAS1) enzyme acts as an innate sensor of viral infection and plays a major role in the defense against a wide diversity of viruses. Polymorphisms at OAS1 have been shown to correlate with differential susceptibility to several infections of great public health significance, including hepatitis C virus, SARS coronavirus, and West Nile virus. Population genetics analyses in hominoids have revealed interesting evolutionary patterns. In Central African chimpanzee, OAS1 has evolved under long-term balancing selection, resulting in the persistence of polymorphisms since the origin of hominoids, whereas human populations have acquired and retained OAS1 alleles from Neanderthal and Denisovan origin. We decided to further investigate the evolution of OAS1 in primates by characterizing intra-specific variation in four species commonly used as models in infectious disease research: the rhesus macaque, the cynomolgus macaque, the olive baboon, and the Guinea baboon. In baboons, OAS1 harbors a very low level of variation. In contrast, OAS1 in macaques exhibits a level of polymorphism far greater than the genomic average, which is consistent with the action of balancing selection. The region of the enzyme that directly interacts with viral RNA, the RNA-binding domain, contains a number of polymorphisms likely to affect the RNA-binding affinity of OAS1. This strongly suggests that pathogen-driven balancing selection acting on the RNA-binding domain of OAS1 is maintaining variation at this locus. Interestingly, we found that a number of polymorphisms involved in RNA-binding were shared between macaques and chimpanzees. This represents an unusual case of convergent polymorphism. PMID:26156123

  8. Image sharing: evolving solutions in the age of interoperability.

    PubMed

    Mendelson, David S; Erickson, Bradley J; Choy, Garry

    2014-12-01

    Interoperability is a major focus of the quickly evolving world of Health IT. Easy, yet secure and confidential exchange of imaging exams and the associated reports must be a part of the solutions that are implemented. The availability of historical exams is essential in providing a quality interpretation and reducing inappropriate utilization of imaging services. Today, the exchange of imaging exams is most often achieved via a compact disc. We describe the virtues of this solution as well as challenges that have surfaced. Internet- and cloud-based technologies employed for many consumer services can provide a better solution. Vendors are making these solutions available. Standards for Internet-based exchange are emerging. Just as radiology converged on DICOM as a standard to store and view images, we need a common exchange standard. We will review the existing standards and how they are organized into useful workflows through Integrating the Healthcare Enterprise profiles. Integrating the Healthcare Enterprise and standards development processes are discussed. Health care and the domain of radiology must stay current with quickly evolving Internet standards. The successful use of the "cloud" will depend on both the technologies and the policies put into place around them, both of which we discuss. The radiology community must lead the way and provide a solution that works for radiologists and clinicians with use of the electronic medical record. We describe features we believe radiologists should consider when adding Internet-based exchange solutions to their practice. PMID:25467903

  9. Integrating the Human Sciences to Evolve Effective Policies.

    PubMed

    Biglan, Anthony; Cody, Christine

    2013-06-01

    This paper describes an evolutionary perspective on human development and wellbeing and contrasts it with the model of self-interest that is prominent in economics. The two approaches have considerably different implications for how human wellbeing might be improved. Research in psychology, prevention science, and neuroscience is converging on an evolutionary account of the importance of two contrasting suites of social behavior-prosociality vs. antisocial behaviors (crime, drug abuse, risky sexual behavior) and related problems such as depression. Prosociality of individuals and groups evolves in environments that minimize toxic biological and social conditions, promote and richly reinforce prosocial behavior and attitudes, limit opportunities for antisocial behavior, and nurture the pursuit of prosocial values. Conversely, antisocial behavior and related problems emerge in environments that are high in threat and conflict. Over the past 30 years, randomized trials have shown numerous family, school, and community interventions to prevent most problem behaviors and promote prosociality. Research has also shown that poverty and economic inequality are major risk factors for the development of problem behaviors. The paper describes policies that can reduce poverty and benefit youth development. Although it is clear that the canonical economic model of rational self-interest has made a significant contribution to the science of economics, the evidence reviewed here shows that it must be reconciled with an evolutionary perspective on human development and wellbeing if society is going to evolve public policies that advance the health and wellbeing of the entire population. PMID:23833332

  10. Integrating the Human Sciences to Evolve Effective Policies

    PubMed Central

    Biglan, Anthony; Cody, Christine

    2012-01-01

    This paper describes an evolutionary perspective on human development and wellbeing and contrasts it with the model of self-interest that is prominent in economics. The two approaches have considerably different implications for how human wellbeing might be improved. Research in psychology, prevention science, and neuroscience is converging on an evolutionary account of the importance of two contrasting suites of social behavior—prosociality vs. antisocial behaviors (crime, drug abuse, risky sexual behavior) and related problems such as depression. Prosociality of individuals and groups evolves in environments that minimize toxic biological and social conditions, promote and richly reinforce prosocial behavior and attitudes, limit opportunities for antisocial behavior, and nurture the pursuit of prosocial values. Conversely, antisocial behavior and related problems emerge in environments that are high in threat and conflict. Over the past 30 years, randomized trials have shown numerous family, school, and community interventions to prevent most problem behaviors and promote prosociality. Research has also shown that poverty and economic inequality are major risk factors for the development of problem behaviors. The paper describes policies that can reduce poverty and benefit youth development. Although it is clear that the canonical economic model of rational self-interest has made a significant contribution to the science of economics, the evidence reviewed here shows that it must be reconciled with an evolutionary perspective on human development and wellbeing if society is going to evolve public policies that advance the health and wellbeing of the entire population. PMID:23833332

  11. Information and Communication: The New Convergence.

    ERIC Educational Resources Information Center

    Beniger, James R.

    1988-01-01

    Discusses the isolation of the field of communications from other disciplines and the inattention of communications to the increasing convergence on information and communication in other disciplines. Maps the convergence by surveying the authors commonly cited in the fields of cognitive science, humanities, and semiotics. (MS)

  12. New concurrent iterative methods with monotonic convergence

    SciTech Connect

    Yao, Qingchuan

    1996-12-31

    This paper proposes the new concurrent iterative methods without using any derivatives for finding all zeros of polynomials simultaneously. The new methods are of monotonic convergence for both simple and multiple real-zeros of polynomials and are quadratically convergent. The corresponding accelerated concurrent iterative methods are obtained too. The new methods are good candidates for the application in solving symmetric eigenproblems.

  13. Converging finite-strength shocks

    NASA Astrophysics Data System (ADS)

    Axford, R. A.; Holm, D. D.

    1981-01-01

    The converging shock problem was first solved by Guderley and later by Landau and Stanyukovich for infinitely strong shocks in an ideal gas with spherical and cylindrical symmetry. This problem is solved herein for finite-strength shocks and a non-ideal-gas equation of state with an adiabatic bulk modulus of the type Bs= {- v∂ p}/{∂ v| s} = ( p +B) f( v) , where B is a constant with the dimensions of pressure, and f(v) is an arbitrary function of the specific volume. Self-similar profiles of the particle velocity and thermodynamic variables are studied explicitly for two cases with constant specific heat at constant volume; the Tait-Kirkwood-Murnaghan equation, f(v) = constant, and the Walsh equation, f(v) = v/A, where A = constant. The first case reduces to the ideal gas when B = 0. In both cases the flow behind the shock front exhibits an unbalanced buoyant force instability at a critical Mach number which depends upon equation-of-state parameters.

  14. Measuring phonetic convergence in speech production

    PubMed Central

    Pardo, Jennifer S.

    2013-01-01

    Phonetic convergence is defined as an increase in the similarity of acoustic-phonetic form between talkers. Previous research has demonstrated phonetic convergence both when a talker listens passively to speech and while talkers engage in social interaction. Much of this research has focused on a diverse array of acoustic-phonetic attributes, with fewer studies incorporating perceptual measures of phonetic convergence. The current paper reviews research on phonetic convergence in both non-interactive and conversational settings, and attempts to consolidate the diverse array of findings by proposing a paradigm that models perceptual and acoustic measures together. By modeling acoustic measures as predictors of perceived phonetic convergence, this paradigm has the potential to reconcile some of the diverse and inconsistent findings currently reported in the literature. PMID:23986738

  15. Parallel selective pressures drive convergent diversification of phenotypes in pythons and boas.

    PubMed

    Esquerré, Damien; Scott Keogh, J

    2016-07-01

    Pythons and boas are globally distributed and distantly related radiations with remarkable phenotypic and ecological diversity. We tested whether pythons, boas and their relatives have evolved convergent phenotypes when they display similar ecology. We collected geometric morphometric data on head shape for 1073 specimens representing over 80% of species. We show that these two groups display strong and widespread convergence when they occupy equivalent ecological niches and that the history of phenotypic evolution strongly matches the history of ecological diversification, suggesting that both processes are strongly coupled. These results are consistent with replicated adaptive radiation in both groups. We argue that strong selective pressures related to habitat-use have driven this convergence. Pythons and boas provide a new model system for the study of macro-evolutionary patterns of morphological and ecological evolution and they do so at a deeper level of divergence and global scale than any well-established adaptive radiation model systems. PMID:27264195

  16. Convergent transcriptional specializations in the brains of humans and song-learning birds

    PubMed Central

    Pfenning, Andreas R.; Hara, Erina; Whitney, Osceola; Rivas, Miriam V.; Wang, Rui; Roulhac, Petra L.; Howard, Jason T.; Wirthlin, Morgan; Lovell, Peter V.; Ganapathy, Ganeshkumar; Mouncastle, Jacquelyn; Moseley, M. Arthur; Thompson, J. Will; Soderblom, Erik J.; Iriki, Atsushi; Kato, Masaki; Gilbert, M. Thomas P.; Zhang, Guojie; Bakken, Trygve; Bongaarts, Angie; Bernard, Amy; Lein, Ed; Mello, Claudio V.; Hartemink, Alexander J.; Jarvis, Erich D.

    2015-01-01

    Song-learning birds and humans share independently evolved similarities in brain pathways for vocal learning that are essential for song and speech and are not found in most other species. Comparisons of brain transcriptomes of song-learning birds and humans relative to vocal nonlearners identified convergent gene expression specializations in specific song and speech brain regions of avian vocal learners and humans. The strongest shared profiles relate bird motor and striatal song-learning nuclei, respectively, with human laryngeal motor cortex and parts of the striatum that control speech production and learning. Most of the associated genes function in motor control and brain connectivity. Thus, convergent behavior and neural connectivity for a complex trait are associated with convergent specialized expression of multiple genes. PMID:25504733

  17. Did Convergent Protein Evolution Enable Phytoplasmas to Generate 'Zombie Plants'?

    PubMed

    Rümpler, Florian; Gramzow, Lydia; Theißen, Günter; Melzer, Rainer

    2015-12-01

    Phytoplasmas are pathogenic bacteria that reprogram plant development such that leaf-like structures instead of floral organs develop. Infected plants are sterile and mainly serve to propagate phytoplasmas and thus have been termed 'zombie plants'. The developmental reprogramming relies on specific interactions of the phytoplasma protein SAP54 with a small subset of MADS-domain transcription factors. Here, we propose that SAP54 folds into a structure that is similar to that of the K-domain, a protein-protein interaction domain of MADS-domain proteins. We suggest that undergoing convergent structural and sequence evolution, SAP54 evolved to mimic the K-domain. Given the high specificity of resulting developmental alterations, phytoplasmas might be used to study flower development in genetically intractable plants. PMID:26463218

  18. Convergent and divergent mechanisms of sugar recognition across kingdoms

    PubMed Central

    Taylor, Maureen E; Drickamer, Kurt

    2014-01-01

    Protein modules that bind specific oligosaccharides are found across all kingdoms of life from single-celled organisms to man. Different, overlapping and evolving designations for sugar-binding domains in proteins can sometimes obscure common features that often reflect convergent solutions to the problem of distinguishing sugars with closely similar structures and binding them with sufficient affinity to achieve biologically meaningful results. Structural and functional analysis has revealed striking parallels between protein domains with widely different structures and evolutionary histories that employ common solutions to the sugar recognition problem. Recent studies also demonstrate that domains descended from common ancestors through divergent evolution appear more widely across the kingdoms of life than had previously been recognized. PMID:25102772

  19. Convergence and divergence in the evolution of aquatic birds.

    PubMed Central

    Van Tuinen, M.; Butvill, D. B.; Kirsch, J. A.; Hedges, S. B.

    2001-01-01

    Aquatic birds exceed other terrestrial vertebrates in the diversity of their adaptations to aquatic niches. For many species this has created difficulty in understanding their evolutionary origin and, in particular, for the flamingos, hamerkop, shoebill and pelecaniforms. Here, new evidence from nuclear and mitochondrial DNA sequences and DNA-DNA hybridization data indicates extensive morphological convergence and divergence in aquatic birds. Among the unexpected findings is a grouping of flamingos and grebes, species which otherwise show no resemblance. These results suggest that the traditional characters used to unite certain aquatic groups, such as totipalmate feet, foot-propelled diving and long legs, evolved more than once and that organismal change in aquatic birds has proceeded at a faster pace than previously recognized. PMID:11429133

  20. Convergence and divergence in the evolution of aquatic birds.

    PubMed

    Van Tuinen, M; Butvill, D B; Kirsch, J A; Hedges, S B

    2001-07-01

    Aquatic birds exceed other terrestrial vertebrates in the diversity of their adaptations to aquatic niches. For many species this has created difficulty in understanding their evolutionary origin and, in particular, for the flamingos, hamerkop, shoebill and pelecaniforms. Here, new evidence from nuclear and mitochondrial DNA sequences and DNA-DNA hybridization data indicates extensive morphological convergence and divergence in aquatic birds. Among the unexpected findings is a grouping of flamingos and grebes, species which otherwise show no resemblance. These results suggest that the traditional characters used to unite certain aquatic groups, such as totipalmate feet, foot-propelled diving and long legs, evolved more than once and that organismal change in aquatic birds has proceeded at a faster pace than previously recognized. PMID:11429133

  1. The Problem of Evolving a Genetic Code

    ERIC Educational Resources Information Center

    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)

  2. What Technology? Reflections on Evolving Services

    ERIC Educational Resources Information Center

    Collins, Sharon

    2009-01-01

    Each year, the members of the EDUCAUSE Evolving Technologies Committee identify and research the evolving technologies that are having--or are predicted to have--the most direct impact on higher education institutions. The committee members choose the relevant topics, write white papers, and present their findings at the EDUCAUSE annual…

  3. Data Convergence - An Australian Perspective

    NASA Astrophysics Data System (ADS)

    Allen, S. S.; Howell, B.

    2012-12-01

    Coupled numerical physical, biogeochemical and sediment models are increasingly being used as integrators to help understand the cumulative or far field effects of change in the coastal environment. This reliance on modeling has forced observations to be delivered as data streams ingestible by modeling frameworks. This has made it easier to create near real-time or forecasting models than to try to recreate the past, and has lead in turn to the conversion of historical data into data streams to allow them to be ingested by the same frameworks. The model and observation frameworks under development within Australia's Commonwealth and Industrial Research Organisation (CSIRO) are now feeding into the Australian Ocean Data Network's (AODN's) MARine Virtual Laboratory (MARVL) . The sensor, or data stream, brokering solution is centred around the "message" and all data flowing through the gateway is wrapped as a message. Messages consist of a topic and a data object and their routing through the gateway to pre-processors and listeners is determined by the topic. The Sensor Message Gateway (SMG) method is allowing data from different sensors measuring the same thing but with different temporal resolutions, units or spatial coverage to be ingested or visualized seamlessly. At the same time the model output as a virtual sensor is being explored, this again being enabled by the SMG. It is only for two way communications with sensor that rigorous adherence to standards is needed, by accepting existing data in less than ideal formats, but exposing them though the SMG we can move a step closer to the Internet Of Things by creating an Internet of Industries where each vested interest can continue with business as usual, contribute to data convergence and adopt more open standards when investment seems appropriate to that sector or business.Architecture Overview

  4. Convergent bacterial microbiotas in the fungal agricultural systems of insects

    DOE PAGESBeta

    Aylward, Frank O.; Suen, Garret; Biedermann, Peter H. W.; Adams, Aaron S.; Scott, Jarrod J.; Malfatti, Stephanie A.; Glavina del Rio, Tijana; Tringe, Susannah G.; Poulsen, Michael; Raffa, Kenneth F.; et al

    2014-11-18

    The ability to cultivate food is an innovation that has produced some of the most successful ecological strategies on the planet. Although most well recognized in humans, where agriculture represents a defining feature of civilization, species of ants, beetles, and termites have also independently evolved symbioses with fungi that they cultivate for food. Despite occurring across divergent insect and fungal lineages, the fungivorous niches of these insects are remarkably similar, indicating convergent evolution toward this successful ecological strategy. Here, we characterize the microbiota of ants, beetles, and termites engaged in nutritional symbioses with fungi to define the bacterial groups associatedmore » with these prominent herbivores and forest pests. Using culture-independent techniques and the in silico reconstruction of 37 composite genomes of dominant community members, we demonstrate that different insect-fungal symbioses that collectively shape ecosystems worldwide have highly similar bacterial microbiotas comprised primarily of the genera Enterobacter, Rahnella, and Pseudomonas. Although these symbioses span three orders of insects and two phyla of fungi, we show that they are associated with bacteria sharing high whole-genome nucleotide identity. Due to the fine-scale correspondence of the bacterial microbiotas of insects engaged in fungal symbioses, our findings indicate that this represents an example of convergence of entire host-microbe complexes.« less

  5. Convergent bacterial microbiotas in the fungal agricultural systems of insects

    SciTech Connect

    Aylward, Frank O.; Suen, Garret; Biedermann, Peter H. W.; Adams, Aaron S.; Scott, Jarrod J.; Malfatti, Stephanie A.; Glavina del Rio, Tijana; Tringe, Susannah G.; Poulsen, Michael; Raffa, Kenneth F.; Klepzig, Kier D.; Currie, Cameron R.

    2014-11-18

    The ability to cultivate food is an innovation that has produced some of the most successful ecological strategies on the planet. Although most well recognized in humans, where agriculture represents a defining feature of civilization, species of ants, beetles, and termites have also independently evolved symbioses with fungi that they cultivate for food. Despite occurring across divergent insect and fungal lineages, the fungivorous niches of these insects are remarkably similar, indicating convergent evolution toward this successful ecological strategy. Here, we characterize the microbiota of ants, beetles, and termites engaged in nutritional symbioses with fungi to define the bacterial groups associated with these prominent herbivores and forest pests. Using culture-independent techniques and the in silico reconstruction of 37 composite genomes of dominant community members, we demonstrate that different insect-fungal symbioses that collectively shape ecosystems worldwide have highly similar bacterial microbiotas comprised primarily of the genera Enterobacter, Rahnella, and Pseudomonas. Although these symbioses span three orders of insects and two phyla of fungi, we show that they are associated with bacteria sharing high whole-genome nucleotide identity. Due to the fine-scale correspondence of the bacterial microbiotas of insects engaged in fungal symbioses, our findings indicate that this represents an example of convergence of entire host-microbe complexes.

  6. The Defensins Consist of Two Independent, Convergent Protein Superfamilies.

    PubMed

    Shafee, Thomas M A; Lay, Fung T; Hulett, Mark D; Anderson, Marilyn A

    2016-09-01

    The defensin and defensin-like proteins are an extensive group of small, cationic, disulfide-rich proteins found in animals, plants, and fungi and mostly perform roles in host defense. The term defensin was originally used for small mammalian proteins found in neutrophils and was subsequently applied to insect proteins and plant γ-thionins based on their perceived sequence and structural similarity. Defensins are often described as ancient innate immunity molecules and classified as a single superfamily and both sequence alignments and phylogenies have been constructed. Here, we present evidence that the defensins have not all evolved from a single ancestor. Instead, they consist of two analogous superfamilies, and extensive convergent evolution is the source of their similarities. Evidence of common origin necessarily gets weaker for distantly related genes, as is the case for defensins, which are both divergent and small. We show that similarities that have been used as evidence for common origin are all expected by chance in short, constrained, disulfide-rich proteins. Differences in tertiary structure, secondary structure order, and disulfide bond connectivity indicate convergence as the likely source of the similarity. We refer to the two evolutionarily independent groups as the cis-defensins and trans-defensins based on the orientation of the most conserved pair of disulfides. PMID:27297472

  7. Convergent Bacterial Microbiotas in the Fungal Agricultural Systems of Insects

    PubMed Central

    Suen, Garret; Biedermann, Peter H. W.; Adams, Aaron S.; Scott, Jarrod J.; Malfatti, Stephanie A.; Glavina del Rio, Tijana; Tringe, Susannah G.; Poulsen, Michael; Raffa, Kenneth F.; Klepzig, Kier D.

    2014-01-01

    ABSTRACT The ability to cultivate food is an innovation that has produced some of the most successful ecological strategies on the planet. Although most well recognized in humans, where agriculture represents a defining feature of civilization, species of ants, beetles, and termites have also independently evolved symbioses with fungi that they cultivate for food. Despite occurring across divergent insect and fungal lineages, the fungivorous niches of these insects are remarkably similar, indicating convergent evolution toward this successful ecological strategy. Here, we characterize the microbiota of ants, beetles, and termites engaged in nutritional symbioses with fungi to define the bacterial groups associated with these prominent herbivores and forest pests. Using culture-independent techniques and the in silico reconstruction of 37 composite genomes of dominant community members, we demonstrate that different insect-fungal symbioses that collectively shape ecosystems worldwide have highly similar bacterial microbiotas comprised primarily of the genera Enterobacter, Rahnella, and Pseudomonas. Although these symbioses span three orders of insects and two phyla of fungi, we show that they are associated with bacteria sharing high whole-genome nucleotide identity. Due to the fine-scale correspondence of the bacterial microbiotas of insects engaged in fungal symbioses, our findings indicate that this represents an example of convergence of entire host-microbe complexes. PMID:25406380

  8. Convergent Evolution During Local Adaptation to Patchy Landscapes.

    PubMed

    Ralph, Peter L; Coop, Graham

    2015-11-01

    Species often encounter, and adapt to, many patches of similar environmental conditions across their range. Such adaptation can occur through convergent evolution if different alleles arise in different patches, or through the spread of shared alleles by migration acting to synchronize adaptation across the species. The tension between the two reflects the constraint imposed on evolution by the underlying genetic architecture versus how effectively selection and geographic isolation act to inhibit the geographic spread of locally adapted alleles. This paper studies the balance between these two routes to adaptation in a model of continuous environments with patchy selection pressures. We address the following questions: How long does it take for a novel allele to appear in a patch where it is locally adapted through mutation? Or, through migration from another, already adapted patch? Which is more likely to occur, as a function of distance between the patches? What population genetic signal is left by the spread of migrant alleles? To answer these questions we examine the family structure underlying migration-selection equilibrium surrounding an already adapted patch, treating those rare families that reach new patches as spatial branching processes. A main result is that patches further apart than a critical distance will likely evolve independent locally adapted alleles; this distance is proportional to the spatial scale of selection ([Formula: see text], where σ is the dispersal distance and sm is the selective disadvantage of these alleles between patches), and depends linearly on log(sm/μ), where μ is the mutation rate. This provides a way to understand the role of geographic separation between patches in promoting convergent adaptation and the genomic signals it leaves behind. We illustrate these ideas using the convergent evolution of cryptic coloration in the rock pocket mouse, Chaetodipus intermedius, as an empirical example. PMID:26571125

  9. Convergent Evolution During Local Adaptation to Patchy Landscapes

    PubMed Central

    2015-01-01

    Species often encounter, and adapt to, many patches of similar environmental conditions across their range. Such adaptation can occur through convergent evolution if different alleles arise in different patches, or through the spread of shared alleles by migration acting to synchronize adaptation across the species. The tension between the two reflects the constraint imposed on evolution by the underlying genetic architecture versus how effectively selection and geographic isolation act to inhibit the geographic spread of locally adapted alleles. This paper studies the balance between these two routes to adaptation in a model of continuous environments with patchy selection pressures. We address the following questions: How long does it take for a novel allele to appear in a patch where it is locally adapted through mutation? Or, through migration from another, already adapted patch? Which is more likely to occur, as a function of distance between the patches? What population genetic signal is left by the spread of migrant alleles? To answer these questions we examine the family structure underlying migration–selection equilibrium surrounding an already adapted patch, treating those rare families that reach new patches as spatial branching processes. A main result is that patches further apart than a critical distance will likely evolve independent locally adapted alleles; this distance is proportional to the spatial scale of selection (σ/sm, where σ is the dispersal distance and s m is the selective disadvantage of these alleles between patches), and depends linearly on log(s m/μ), where μ is the mutation rate. This provides a way to understand the role of geographic separation between patches in promoting convergent adaptation and the genomic signals it leaves behind. We illustrate these ideas using the convergent evolution of cryptic coloration in the rock pocket mouse, Chaetodipus intermedius, as an empirical example. PMID:26571125

  10. Genetic program based data mining of fuzzy decision trees and methods of improving convergence and reducing bloat

    NASA Astrophysics Data System (ADS)

    Smith, James F., III; Nguyen, ThanhVu H.

    2007-04-01

    A data mining procedure for automatic determination of fuzzy decision tree structure using a genetic program (GP) is discussed. A GP is an algorithm that evolves other algorithms or mathematical expressions. Innovative methods for accelerating convergence of the data mining procedure and reducing bloat are given. In genetic programming, bloat refers to excessive tree growth. It has been observed that the trees in the evolving GP population will grow by a factor of three every 50 generations. When evolving mathematical expressions much of the bloat is due to the expressions not being in algebraically simplest form. So a bloat reduction method based on automated computer algebra has been introduced. The effectiveness of this procedure is discussed. Also, rules based on fuzzy logic have been introduced into the GP to accelerate convergence, reduce bloat and produce a solution more readily understood by the human user. These rules are discussed as well as other techniques for convergence improvement and bloat control. Comparisons between trees created using a genetic program and those constructed solely by interviewing experts are made. A new co-evolutionary method that improves the control logic evolved by the GP by having a genetic algorithm evolve pathological scenarios is discussed. The effect on the control logic is considered. Finally, additional methods that have been used to validate the data mining algorithm are referenced.

  11. Cell biology, molecular embryology, Lamarckian and Darwinian selection as evolvability.

    PubMed

    Hoenigsberg, H

    2003-01-01

    immune system and life as we know it now. We offer the hypothesis that metazoan evolution solved this ancient conflict by evolving an immunogenetic mechanism that responds with rapid Lamarckian efficiency by retaining the ancient reverse transcriptase enzyme (RNACopyright DNA copying discovered by Temin in 1959 (see Temin, 1989) and found in 1970 in RNA tumor viruses by Temin and Baltimore), which can produce cDNA from the genome of an RNA virus that infects the cells. It seems that molecular Lamarckism can survive (Lewin, 1993). PMID:12917798

  12. Systems approaches in understanding evolution and evolvability.

    PubMed

    Agarwal, Sumeet

    2013-12-01

    Systems and network-based approaches are becoming increasingly popular in cellular biology. One contribution of such approaches has been to shed some light on the evolutionary origins of core organisational principles in biological systems, such as modularity, robustness, and evolvability. Models of interactions between genes (epistasis) have also provided insight into how sexual reproduction may have evolved. Additionally, recent work on viewing evolution as a form of learning from the environment has indicated certain bounds on the complexity of the genetic circuits that can evolve within feasible quantities of time and resources. Here we review the key studies and results in these areas, and discuss possible connections between them. In particular, we speculate on the link between the two notions of 'evolvability': the evolvability of a system in terms of how agile it is in responding to novel goals or environments, and the evolvability of certain kinds of gene network functionality in terms of its computational complexity. Drawing on some recent work on the complexity of graph-theoretic problems on modular networks, we suggest that modularity as an organising principle may have its raison d'etre in its ability to enhance evolvability, in both its senses. PMID:24120732

  13. On the Local Convergence of Pattern Search

    NASA Technical Reports Server (NTRS)

    Dolan, Elizabeth D.; Lewis, Robert Michael; Torczon, Virginia; Bushnell, Dennis M. (Technical Monitor)

    2000-01-01

    We examine the local convergence properties of pattern search methods, complementing the previously established global convergence properties for this class of algorithms. We show that the step-length control parameter which appears in the definition of pattern search algorithms provides a reliable asymptotic measure of first-order stationarity. This gives an analytical justification for a traditional stopping criterion for pattern search methods. Using this measure of first-order stationarity, we analyze the behavior of pattern search in the neighborhood of an isolated local minimizer. We show that a recognizable subsequence converges r-linearly to the minimizer.

  14. Photonanomedicine: a convergence of photodynamic therapy and nanotechnology.

    PubMed

    Obaid, Girgis; Broekgaarden, Mans; Bulin, Anne-Laure; Huang, Huang-Chiao; Kuriakose, Jerrin; Liu, Joyce; Hasan, Tayyaba

    2016-07-01

    As clinical nanomedicine has emerged over the past two decades, phototherapeutic advancements using nanotechnology have also evolved and impacted disease management. Because of unique features attributable to the light activation process of molecules, photonanomedicine (PNM) holds significant promise as a personalized, image-guided therapeutic approach for cancer and non-cancer pathologies. The convergence of advanced photochemical therapies such as photodynamic therapy (PDT) and imaging modalities with sophisticated nanotechnologies is enabling the ongoing evolution of fundamental PNM formulations, such as Visudyne®, into progressive forward-looking platforms that integrate theranostics (therapeutics and diagnostics), molecular selectivity, the spatiotemporally controlled release of synergistic therapeutics, along with regulated, sustained drug dosing. Considering that the envisioned goal of these integrated platforms is proving to be realistic, this review will discuss how PNM has evolved over the years as a preclinical and clinical amalgamation of nanotechnology with PDT. The encouraging investigations that emphasize the potent synergy between photochemistry and nanotherapeutics, in addition to the growing realization of the value of these multi-faceted theranostic nanoplatforms, will assist in driving PNM formulations into mainstream oncological clinical practice as a necessary tool in the medical armamentarium. PMID:27328309

  15. Convergent evolution of vascular optimization in kelp (Laminariales).

    PubMed

    Drobnitch, Sarah Tepler; Jensen, Kaare H; Prentice, Paige; Pittermann, Jarmila

    2015-10-01

    Terrestrial plants and mammals, although separated by a great evolutionary distance, have each arrived at a highly conserved body plan in which universal allometric scaling relationships govern the anatomy of vascular networks and key functional metabolic traits. The universality of allometric scaling suggests that these phyla have each evolved an 'optimal' transport strategy that has been overwhelmingly adopted by extant species. To truly evaluate the dominance and universality of vascular optimization, however, it is critical to examine other, lesser-known, vascularized phyla. The brown algae (Phaeophyceae) are one such group--as distantly related to plants as mammals, they have convergently evolved a plant-like body plan and a specialized phloem-like transport network. To evaluate possible scaling and optimization in the kelp vascular system, we developed a model of optimized transport anatomy and tested it with measurements of the giant kelp, Macrocystis pyrifera, which is among the largest and most successful of macroalgae. We also evaluated three classical allometric relationships pertaining to plant vascular tissues with a diverse sampling of kelp species. Macrocystis pyrifera displays strong scaling relationships between all tested vascular parameters and agrees with our model; other species within the Laminariales display weak or inconsistent vascular allometries. The lack of universal scaling in the kelps and the presence of optimized transport anatomy in M. pyrifera raises important questions about the evolution of optimization and the possible competitive advantage conferred by optimized vascular systems to multicellular phyla. PMID:26423844

  16. Photonanomedicine: a convergence of photodynamic therapy and nanotechnology

    NASA Astrophysics Data System (ADS)

    Obaid, Girgis; Broekgaarden, Mans; Bulin, Anne-Laure; Huang, Huang-Chiao; Kuriakose, Jerrin; Liu, Joyce; Hasan, Tayyaba

    2016-06-01

    As clinical nanomedicine has emerged over the past two decades, phototherapeutic advancements using nanotechnology have also evolved and impacted disease management. Because of unique features attributable to the light activation process of molecules, photonanomedicine (PNM) holds significant promise as a personalized, image-guided therapeutic approach for cancer and non-cancer pathologies. The convergence of advanced photochemical therapies such as photodynamic therapy (PDT) and imaging modalities with sophisticated nanotechnologies is enabling the ongoing evolution of fundamental PNM formulations, such as Visudyne®, into progressive forward-looking platforms that integrate theranostics (therapeutics and diagnostics), molecular selectivity, the spatiotemporally controlled release of synergistic therapeutics, along with regulated, sustained drug dosing. Considering that the envisioned goal of these integrated platforms is proving to be realistic, this review will discuss how PNM has evolved over the years as a preclinical and clinical amalgamation of nanotechnology with PDT. The encouraging investigations that emphasize the potent synergy between photochemistry and nanotherapeutics, in addition to the growing realization of the value of these multi-faceted theranostic nanoplatforms, will assist in driving PNM formulations into mainstream oncological clinical practice as a necessary tool in the medical armamentarium.

  17. Acceleration of convergence of vector sequences

    NASA Technical Reports Server (NTRS)

    Sidi, A.; Ford, W. F.; Smith, D. A.

    1986-01-01

    A general approach to the construction of convergence acceleration methods for vector sequence is proposed. Using this approach, one can generate some known methods, such as the minimal polynomial extrapolation, the reduced rank extrapolation, and the topological epsilon algorithm, and also some new ones. Some of the new methods are easier to implement than the known methods and are observed to have similar numerical properties. The convergence analysis of these new methods is carried out, and it is shown that they are especially suitable for accelerating the convergence of vector sequences that are obtained when one solves linear systems of equations iterative. A stability analysis is also given, and numerical examples are provided. The convergence and stability properties of the topological epsilon algorithm are likewise given.

  18. Acceleration of convergence of vector sequences

    NASA Technical Reports Server (NTRS)

    Sidi, A.; Ford, W. F.; Smith, D. A.

    1983-01-01

    A general approach to the construction of convergence acceleration methods for vector sequence is proposed. Using this approach, one can generate some known methods, such as the minimal polynomial extrapolation, the reduced rank extrapolation, and the topological epsilon algorithm, and also some new ones. Some of the new methods are easier to implement than the known methods and are observed to have similar numerical properties. The convergence analysis of these new methods is carried out, and it is shown that they are especially suitable for accelerating the convergence of vector sequences that are obtained when one solves linear systems of equations iteratively. A stability analysis is also given, and numerical examples are provided. The convergence and stability properties of the topological epsilon algorithm are likewise given.

  19. Morphological and molecular convergences in mammalian phylogenetics.

    PubMed

    Zou, Zhengting; Zhang, Jianzhi

    2016-01-01

    Phylogenetic trees reconstructed from molecular sequences are often considered more reliable than those reconstructed from morphological characters, in part because convergent evolution, which confounds phylogenetic reconstruction, is believed to be rarer for molecular sequences than for morphologies. However, neither the validity of this belief nor its underlying cause is known. Here comparing thousands of characters of each type that have been used for inferring the phylogeny of mammals, we find that on average morphological characters indeed experience much more convergences than amino acid sites, but this disparity is explained by fewer states per character rather than an intrinsically higher susceptibility to convergence for morphologies than sequences. We show by computer simulation and actual data analysis that a simple method for identifying and removing convergence-prone characters improves phylogenetic accuracy, potentially enabling, when necessary, the inclusion of morphologies and hence fossils for reliable tree inference. PMID:27585543

  20. Low-Convergence Magnetized Liner Inertial Fusion

    NASA Astrophysics Data System (ADS)

    Slutz, Stephen; Vesey, Roger; Sinars, Daniel; Sefkow, Adam

    2013-10-01

    Numerical simulations indicate that pulsed-power driven liner-implosions could produce substantial fusion yields if the deuterium-tritium (DT) fuel is first magnetized and preheated [S.A. Slutz et al., Phys. Plasmas 17, 056303 (2010)]. As with all inertial fusion, the implosions could be degraded by the Rayleigh-Taylor instability. Since highly convergent implosions are more susceptible to this instability, we have explored the necessary conditions to obtain significant fusion yield with low-convergence liner-implosions. Such low-convergence implosions can be obtained if the fuel is sufficiently preheated and magnetized. We present analytic and numerical studies of laser plasma heating, which indicate that low convergence implosions should be possible with sufficient laser energy. Sandia National Laboratories is a multiprogram laboratory managed and operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Company, for the United States Department of Energy's National Nuclear Security Administration under contra.

  1. Speeding Convergence In Simulations Of Hypersonic Flow

    NASA Technical Reports Server (NTRS)

    Flores, J.; Cheung, S.; Cheer, A.; Hafez, M.

    1991-01-01

    Report describes study aimed at accelerating rates of convergence of iterative schemes for numerical integration of equations of hypersonic flow of viscous and inviscid fluids. Richardson-type overrelaxation method applied.

  2. On Convergent Probability of a Random Walk

    ERIC Educational Resources Information Center

    Lee, Y.-F.; Ching, W.-K.

    2006-01-01

    This note introduces an interesting random walk on a straight path with cards of random numbers. The method of recurrent relations is used to obtain the convergent probability of the random walk with different initial positions.

  3. New convergence estimates for multigrid algorithms

    SciTech Connect

    Bramble, J.H.; Pasciak, J.E.

    1987-10-01

    In this paper, new convergence estimates are proved for both symmetric and nonsymmetric multigrid algorithms applied to symmetric positive definite problems. Our theory relates the convergence of multigrid algorithms to a ''regularity and approximation'' parameter ..cap alpha.. epsilon (0, 1) and the number of relaxations m. We show that for the symmetric and nonsymmetric ..nu.. cycles, the multigrid iteration converges for any positive m at a rate which deteriorates no worse than 1-cj/sup -(1-//sup ..cap alpha..//sup )///sup ..cap alpha../, where j is the number of grid levels. We then define a generalized ..nu.. cycle algorithm which involves exponentially increasing (for example, doubling) the number of smoothings on successively coarser grids. We show that the resulting symmetric and nonsymmetric multigrid iterations converge for any ..cap alpha.. with rates that are independent of the mesh size. The theory is presented in an abstract setting which can be applied to finite element multigrid and finite difference multigrid methods.

  4. Testing Adaptive Hypotheses of Convergence with Functional Landscapes: A Case Study of Bone-Cracking Hypercarnivores

    PubMed Central

    Tseng, Zhijie Jack

    2013-01-01

    Morphological convergence is a well documented phenomenon in mammals, and adaptive explanations are commonly employed to infer similar functions for convergent characteristics. I present a study that adopts aspects of theoretical morphology and engineering optimization to test hypotheses about adaptive convergent evolution. Bone-cracking ecomorphologies in Carnivora were used as a case study. Previous research has shown that skull deepening and widening are major evolutionary patterns in convergent bone-cracking canids and hyaenids. A simple two-dimensional design space, with skull width-to-length and depth-to-length ratios as variables, was used to examine optimized shapes for two functional properties: mechanical advantage (MA) and strain energy (SE). Functionality of theoretical skull shapes was studied using finite element analysis (FEA) and visualized as functional landscapes. The distribution of actual skull shapes in the landscape showed a convergent trend of plesiomorphically low-MA and moderate-SE skulls evolving towards higher-MA and moderate-SE skulls; this is corroborated by FEA of 13 actual specimens. Nevertheless, regions exist in the landscape where high-MA and lower-SE shapes are not represented by existing species; their vacancy is observed even at higher taxonomic levels. Results highlight the interaction of biomechanical and non-biomechanical factors in constraining general skull dimensions to localized functional optima through evolution. PMID:23734244

  5. Interactions between planets and evolved stars

    NASA Astrophysics Data System (ADS)

    Shengbang, Qian; Zhongtao, Han; Fernández Lajús, E.; liying, Zhu; Wenping, Liao; Miloslav, Zejda; Linjia, Li; Voloshina, Irina; Liang, Liu; Jiajia., He

    2016-07-01

    Searching for planetary companions to evolved stars (e.g., white dwarfs (WD) and Cataclysmic Variables (CV)) can provide insight into the interaction between planets and evolved stars as well as on the ultimate fate of planets. We have monitored decades of CVs and their progenitors including some detached WD binaries since 2006 to search for planets orbiting these systems. In the present paper, we will show some observational results of circumbinary planets in orbits around CVs and their progenitors. Some of our findings include planets with the shortest distance to the central evolved binaries and a few multiple planetary systems orbiting binary stars. Finally, by comparing the observational properties of planetary companions to single WDs and WD binaries, the interaction between planets and evolved stars and the ultimate fate of planets are discussed.

  6. Neural mechanisms underlying the evolvability of behaviour

    PubMed Central

    Katz, Paul S.

    2011-01-01

    The complexity of nervous systems alters the evolvability of behaviour. Complex nervous systems are phylogenetically constrained; nevertheless particular species-specific behaviours have repeatedly evolved, suggesting a predisposition towards those behaviours. Independently evolved behaviours in animals that share a common neural architecture are generally produced by homologous neural structures, homologous neural pathways and even in the case of some invertebrates, homologous identified neurons. Such parallel evolution has been documented in the chromatic sensitivity of visual systems, motor behaviours and complex social behaviours such as pair-bonding. The appearance of homoplasious behaviours produced by homologous neural substrates suggests that there might be features of these nervous systems that favoured the repeated evolution of particular behaviours. Neuromodulation may be one such feature because it allows anatomically defined neural circuitry to be re-purposed. The developmental, genetic and physiological mechanisms that contribute to nervous system complexity may also bias the evolution of behaviour, thereby affecting the evolvability of species-specific behaviour. PMID:21690127

  7. International Convergence on Geoscience Cyberinfrastructure

    NASA Astrophysics Data System (ADS)

    Allison, M. L.; Atkinson, R.; Arctur, D. K.; Cox, S.; Jackson, I.; Nativi, S.; Wyborn, L. A.

    2012-04-01

    There is growing international consensus on addressing the challenges to cyber(e)-infrastructure for the geosciences. These challenges include: Creating common standards and protocols; Engaging the vast number of distributed data resources; Establishing practices for recognition of and respect for intellectual property; Developing simple data and resource discovery and access systems; Building mechanisms to encourage development of web service tools and workflows for data analysis; Brokering the diverse disciplinary service buses; Creating sustainable business models for maintenance and evolution of information resources; Integrating the data management life-cycle into the practice of science. Efforts around the world are converging towards de facto creation of an integrated global digital data network for the geosciences based on common standards and protocols for data discovery and access, and a shared vision of distributed, web-based, open source interoperable data access and integration. Commonalities include use of Open Geospatial Consortium (OGC) and ISO specifications and standardized data interchange mechanisms. For multidisciplinarity, mediation, adaptation, and profiling services have been successfully introduced to leverage the geosciences standards which are commonly used by the different geoscience communities -introducing a brokering approach which extends the basic SOA archetype. Principal challenges are less technical than cultural, social, and organizational. Before we can make data interoperable, we must make people interoperable. These challenges are being met by increased coordination of development activities (technical, organizational, social) among leaders and practitioners in national and international efforts across the geosciences to foster commonalities across disparate networks. In doing so, we will 1) leverage and share resources, and developments, 2) facilitate and enhance emerging technical and structural advances, 3) promote

  8. Efficient Controls for Finitely Convergent Sequential Algorithms

    PubMed Central

    Chen, Wei; Herman, Gabor T.

    2010-01-01

    Finding a feasible point that satisfies a set of constraints is a common task in scientific computing: examples are the linear feasibility problem and the convex feasibility problem. Finitely convergent sequential algorithms can be used for solving such problems; an example of such an algorithm is ART3, which is defined in such a way that its control is cyclic in the sense that during its execution it repeatedly cycles through the given constraints. Previously we found a variant of ART3 whose control is no longer cyclic, but which is still finitely convergent and in practice it usually converges faster than ART3 does. In this paper we propose a general methodology for automatic transformation of finitely convergent sequential algorithms in such a way that (i) finite convergence is retained and (ii) the speed of convergence is improved. The first of these two properties is proven by mathematical theorems, the second is illustrated by applying the algorithms to a practical problem. PMID:20953327

  9. Fixing convergence of Gaussian belief propagation

    SciTech Connect

    Johnson, Jason K; Bickson, Danny; Dolev, Danny

    2009-01-01

    Gaussian belief propagation (GaBP) is an iterative message-passing algorithm for inference in Gaussian graphical models. It is known that when GaBP converges it converges to the correct MAP estimate of the Gaussian random vector and simple sufficient conditions for its convergence have been established. In this paper we develop a double-loop algorithm for forcing convergence of GaBP. Our method computes the correct MAP estimate even in cases where standard GaBP would not have converged. We further extend this construction to compute least-squares solutions of over-constrained linear systems. We believe that our construction has numerous applications, since the GaBP algorithm is linked to solution of linear systems of equations, which is a fundamental problem in computer science and engineering. As a case study, we discuss the linear detection problem. We show that using our new construction, we are able to force convergence of Montanari's linear detection algorithm, in cases where it would originally fail. As a consequence, we are able to increase significantly the number of users that can transmit concurrently.

  10. Convergence of a discretized self-adaptive evolutionary algorithm on multi-dimensional problems.

    SciTech Connect

    Hart, William Eugene; DeLaurentis, John Morse

    2003-08-01

    We consider the convergence properties of a non-elitist self-adaptive evolutionary strategy (ES) on multi-dimensional problems. In particular, we apply our recent convergence theory for a discretized (1,{lambda})-ES to design a related (1,{lambda})-ES that converges on a class of seperable, unimodal multi-dimensional problems. The distinguishing feature of self-adaptive evolutionary algorithms (EAs) is that the control parameters (like mutation step lengths) are evolved by the evolutionary algorithm. Thus the control parameters are adapted in an implicit manner that relies on the evolutionary dynamics to ensure that more effective control parameters are propagated during the search. Self-adaptation is a central feature of EAs like evolutionary stategies (ES) and evolutionary programming (EP), which are applied to continuous design spaces. Rudolph summarizes theoretical results concerning self-adaptive EAs and notes that the theoretical underpinnings for these methods are essentially unexplored. In particular, convergence theories that ensure convergence to a limit point on continuous spaces have only been developed by Rudolph, Hart, DeLaurentis and Ferguson, and Auger et al. In this paper, we illustrate how our analysis of a (1,{lambda})-ES for one-dimensional unimodal functions can be used to ensure convergence of a related ES on multidimensional functions. This (1,{lambda})-ES randomly selects a search dimension in each iteration, along which points generated. For a general class of separable functions, our analysis shows that the ES searches along each dimension independently, and thus this ES converges to the (global) minimum.

  11. Vulnerabilities—bibliometric analysis and literature review of evolving concepts

    NASA Astrophysics Data System (ADS)

    Giupponi, Carlo; Biscaro, Claudio

    2015-12-01

    In this work we analyse the evolution of the vulnerability concept in the research streams of climate change adaptation (CCA) and disaster risk reduction (DRR). We combine a traditional literature review with data mining procedures applied to bibliographic databases to reconstruct the history of the concept within various research topics, showing its evolution and convergences over time. To do that, we integrate different methods combining machine learning algorithms with network and cluster analyses to examine a set of 3757 articles, analysing their distinctive features and similarities on the basis of their contents as well as co-authorships. Bibliometric analyses enable the identification of different communities of articles, pinpointing key papers and authors, while literature review makes it possible to assess the concept of vulnerability evolved within and beyond research communities and scientific networks. Moreover, this work examines the role played by documents published by UN institutions (UNDRO, UNISDR, IPCC) in contributing to the evolution of vulnerability and related concepts. Results show that signs of convergence are evident between the two research streams, and that the IPCC reports have played a major role in proposing solutions for unifying definitions of vulnerability. We observe that the phases of preparation of the IPCC reports are very rich in methodological and terminological developments, while after publication, the literature shows evident signs of propagation of the proposed concepts. The DRR research stream developed before the research stream on CCA, but the latter flourished rapidly and became much larger in terms of number of publications. Nevertheless, in terms of contents, adaptation studies and the IPCC have shown increasing adoption of the concepts developed within the disaster research stream, in particular with regard to the interpretation of vulnerability as one of the dimensions of risk.

  12. Evolving efficiency of restraining bends within wet kaolin analog experiments

    NASA Astrophysics Data System (ADS)

    Hatem, Alexandra E.; Cooke, Michele L.; Madden, Elizabeth H.

    2015-03-01

    Restraining bends along strike-slip fault systems evolve by both propagation of new faults and abandonment of fault segments. Scaled analog modeling using wet kaolin allows for qualitative and quantitative observations of this evolution. To explore how bend geometry affects evolution, we model bends with a variety of initial angles, θ, from θ = 0° for a straight fault to θ = 30°. High-angle restraining bends (θ ≥ 20°) overcome initial inefficiencies by abandoning unfavorably oriented restraining segments and propagating multiple new, inwardly dipping, oblique-slip faults that are well oriented to accommodate convergence within the bend. Restraining bends with 0° < θ ≤ 15° maintain activity along the restraining bend segment and grow a single new oblique slip fault on one side of the bend. In all restraining bends, the first new fault propagates at ~5 mm of accumulated convergence. Particle Image Velocimetry analysis provides a complete velocity field throughout the experiments. From these data, we quantify the strike-slip efficiency of the system as the percentage of applied plate-parallel velocity accommodated as slip in the direction of plate motion along faults within the restraining bend. Bends with small θ initially have higher strike-slip efficiency compared to bends with large θ. Although they have different fault geometries, all systems with a 5 cm bend width reach a steady strike-slip efficiency of 80% after 50 mm of applied plate displacement. These experimental restraining bends resemble crustal faults in their asymmetric fault growth, asymmetric topographic gradient, and strike-slip efficiency.

  13. Insolubilization process increases enzyme stability

    NASA Technical Reports Server (NTRS)

    Billingham, J.; Lyn, J.

    1971-01-01

    Enzymes complexed with polymeric matrices contain properties suggesting application to enzyme-controlled reactions. Stability of insolubilized enzyme derivatives is markedly greater than that of soluble enzymes and physical form of insolubilized enzymes is useful in column and batch processes.

  14. The ENZYME data bank.

    PubMed Central

    Bairoch, A

    1994-01-01

    The ENZYME data bank is a repository of information relative to the nomenclature of enzymes. It is primarily based on the recommendations of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (IUBMB) and it contains the following data for each type of characterized enzyme for which an EC (Enzyme Commission) number has been provided: EC number Recommended name Alternative names (if any) Catalytic activity Cofactors (if any) Pointers to the SWISS-PROT protein sequence entrie(s) that correspond to the enzyme (if any) Pointers to human disease(s) associated with a deficiency of the enzyme (if any). PMID:7937072

  15. Ribonuclease P: The Evolution of an Ancient RNA Enzyme

    PubMed Central

    Walker, Scott C.; Engelke, David R.

    2009-01-01

    Ribonuclease P (RNase P) is an ancient and essential endonuclease that catalyses the cleavage of the 5′ leader sequence from precursor tRNAs (pre-tRNAs). The enzyme is one of only two ribozymes which can be found in all kingdoms of life (Bacteria, Archaea, and Eukarya). Most forms of RNase P are ribonucleoproteins; the bacterial enzyme possesses a single catalytic RNA and one small protein. However, in archaea and eukarya the enzyme has evolved an increasingly more complex protein composition, whilst retaining a structurally related RNA subunit. The reasons for this additional complexity are not currently understood. Furthermore, the eukaryotic RNase P has evolved into several different enzymes including a nuclear activity, organellar activities, and the evolution of a distinct but closely related enzyme, RNase MRP, which has different substrate specificities, primarily involved in ribosomal RNA biogenesis. Here we examine the relationship between the bacterial and archaeal RNase P with the eukaryotic enzyme, and summarize recent progress in characterizing the archaeal enzyme. We review current information regarding the nuclear RNase P and RNase MRP enzymes in the eukaryotes, focusing on the relationship between these enzymes by examining their composition, structure and functions. PMID:16595295

  16. Reverse evolution leads to genotypic incompatibility despite functional and active site convergence.

    PubMed

    Kaltenbach, Miriam; Jackson, Colin J; Campbell, Eleanor C; Hollfelder, Florian; Tokuriki, Nobuhiko

    2015-01-01

    Understanding the extent to which enzyme evolution is reversible can shed light on the fundamental relationship between protein sequence, structure, and function. Here, we perform an experimental test of evolutionary reversibility using directed evolution from a phosphotriesterase to an arylesterase, and back, and examine the underlying molecular basis. We find that wild-type phosphotriesterase function could be restored (>10(4)-fold activity increase), but via an alternative set of mutations. The enzyme active site converged towards its original state, indicating evolutionary constraints imposed by catalytic requirements. We reveal that extensive epistasis prevents reversions and necessitates fixation of new mutations, leading to a functionally identical sequence. Many amino acid exchanges between the new and original enzyme are not tolerated, implying sequence incompatibility. Therefore, the evolution was phenotypically reversible but genotypically irreversible. Our study illustrates that the enzyme's adaptive landscape is highly rugged, and different functional sequences may constitute separate fitness peaks. PMID:26274563

  17. Ethanologenic Enzymes of Zymomonas mobilis

    SciTech Connect

    Ingram, Lonnie O'Neal

    1999-03-01

    Zymomonas mobilis is a unique microorganism in being both obligately fermentative and utilizing a Entner-Doudoroff pathway for glycolysis. Glycolytic flux in this organism is readily measured as evolved carbon dioxide, ethanol, or glucose consumed and exceeds 1 {micro}mole glucose/min per mg cell protein. To support this rapid glycolysis, approximately 50% of cytoplasmic protein is devoted to the 13 glycolytic and fermentative enzymes which constitute this central catabolic pathway. Only 1 ATP (net) is produced from each glucose metabolized. During the past grant period, we have completed the characterization of 11 of the 13 glycolytic genes from Z. mobilis together with complementary but separate DOE-fimded research by a former post-dot and collaborator, Dr. Tyrrell Conway. Research funded in my lab by DOE, Division of Energy Biosciences can be divided into three sections: A. Fundamental studies; B. Applied studies and utility; and C. Miscellaneous investigations.

  18. OUTWARD MIGRATION OF JUPITER AND SATURN IN EVOLVED GASEOUS DISKS

    SciTech Connect

    D'Angelo, Gennaro; Marzari, Francesco E-mail: francesco.marzari@pd.infn.it

    2012-09-20

    The outward migration of a pair of resonant-orbit planets, driven by tidal interactions with a gas-dominated disk, is studied in the context of evolved solar nebula models. The planets' masses, M{sub 1} and M{sub 2}, correspond to those of Jupiter and Saturn. Hydrodynamical calculations in two and three dimensions are used to quantify the migration rates and analyze the conditions under which the outward migration mechanism may operate. The planets are taken to be fully formed after 10{sup 6} and before 3 Multiplication-Sign 10{sup 6} years. The orbital evolution of the planets in an evolving disk is then calculated until the disk's gas is completely dissipated. Orbital locking in the 3:2 mean motion resonance may lead to outward migration under appropriate conditions of disk viscosity and temperature. However, resonance locking does not necessarily result in outward migration. This is the case, for example, if convergent migration leads to locking in the 2:1 mean motion resonance, as post-formation disk conditions seem to suggest. Accretion of gas on the planets may deactivate the outward migration mechanism by raising the mass ratio M{sub 2}/M{sub 1} and/or by reducing the accretion rate toward the star, and hence depleting the inner disk. For migrating planets locked in the 3:2 mean motion resonance, there are stalling radii that depend on disk viscosity and on stellar irradiation, when it determines the disk's thermal balance. Planets locked in the 3:2 orbital resonance that start moving outward from within 1-2 AU may reach beyond Almost-Equal-To 5 AU only under favorable conditions. However, within the explored space of disk parameters, only a small fraction-less than a few percent-of the models predict that the interior planet reaches beyond Almost-Equal-To 4 AU.

  19. Enzyme Therapy: Current Perspectives.

    PubMed

    UmaMaheswari, Thiyagamoorthy; Hemalatha, Thiagarajan; Sankaranarayanan, Palavesam; Puvanakrishnan, Rengarajulu

    2016-01-01

    Enzymes control all metabolic processes in human system from simple digestion of food to highly complex immune response. Physiological reactions occuring in healthy individuals are disturbed when enzymes are deficient or absent. Enzymes are administered for normalizing biological function in certain pathologies. Initially, crude proteolytic enzymes were used for the treatment of gastrointestinal disorders. Recent advances have enabled enzyme therapy as a promising tool in the treatment of cardiovascular, oncological and hereditary diseases. Now, a spectrum of other diseases are also covered under enzyme therapy. But, the available information on the use of enzymes as therapeutic agents for different diseases is scanty. This review details the enzymes which have been used to treat various diseases/disorders. PMID:26891548

  20. Convergence of gut microbiomes in myrmecophagous mammals.

    PubMed

    Delsuc, Frédéric; Metcalf, Jessica L; Wegener Parfrey, Laura; Song, Se Jin; González, Antonio; Knight, Rob

    2014-03-01

    Mammals have diversified into many dietary niches. Specialized myrmecophagous (ant- and termite-eating) placental mammals represent a textbook example of evolutionary convergence driven by extreme diet specialization. Armadillos, anteaters, aardvarks, pangolins and aardwolves thus provide a model system for understanding the potential role of gut microbiota in the convergent adaptation to myrmecophagy. Here, we expand upon previous mammalian gut microbiome studies by using high-throughput barcoded Illumina sequencing of the 16S rRNA gene to characterize the composition of gut microbiota in 15 species representing all placental myrmecophagous lineages and their close relatives from zoo- and field-collected samples. We confirm that both diet and phylogeny drive the evolution of mammalian gut microbiota, with cases of convergence in global composition, but also examples of phylogenetic inertia. Our results reveal specialized placental myrmecophages as a spectacular case of large-scale convergence in gut microbiome composition. Indeed, neighbour-net networks and beta-diversity plots based on UniFrac distances show significant clustering of myrmecophagous species (anteaters, aardvarks and aardwolves), even though they belong to phylogenetically distant lineages representing different orders. The aardwolf, which diverged from carnivorous hyenas only in the last 10 million years, experienced a convergent shift in the composition of its gut microbiome to become more similar to other myrmecophages. These results confirm diet adaptation to be a major driving factor of convergence in gut microbiome composition over evolutionary timescales. This study sets the scene for future metagenomic studies aiming at evaluating potential convergence in functional gene content in the microbiomes of specialized mammalian myrmecophages. PMID:24118574

  1. Developments in Enzyme Technology.

    ERIC Educational Resources Information Center

    Chaplin, M. F.

    1984-01-01

    Enzyme technology has a well-established industrial base, with applications that have survived competition. The most prominent applications of enzymes in biotechnology are examined with an explanation of some theoretical background. Topics include extending an enzyme's useful life, partition and diffusion, industrial uses, and therapeutic uses.…

  2. Numerical Convergence In Smoothed Particle Hydrodynamics

    NASA Astrophysics Data System (ADS)

    Zhu, Qirong; Hernquist, Lars; Li, Yuexing

    2015-02-01

    We study the convergence properties of smoothed particle hydrodynamics (SPH) using numerical tests and simple analytic considerations. Our analysis shows that formal numerical convergence is possible in SPH only in the joint limit N → ∞, h → 0, and Nnb → ∞, where N is the total number of particles, h is the smoothing length, and Nnb is the number of neighbor particles within the smoothing volume used to compute smoothed estimates. Previous work has generally assumed that the conditions N → ∞ and h → 0 are sufficient to achieve convergence, while holding Nnb fixed. We demonstrate that if Nnb is held fixed as the resolution is increased, there will be a residual source of error that does not vanish as N → ∞ and h → 0. Formal numerical convergence in SPH is possible only if Nnb is increased systematically as the resolution is improved. Using analytic arguments, we derive an optimal compromise scaling for Nnb by requiring that this source of error balance that present in the smoothing procedure. For typical choices of the smoothing kernel, we find Nnb vpropN 0.5. This means that if SPH is to be used as a numerically convergent method, the required computational cost does not scale with particle number as O(N), but rather as O(N 1 + δ), where δ ≈ 0.5, with a weak dependence on the form of the smoothing kernel.

  3. Grid Convergence for Turbulent Flows(Invited)

    NASA Technical Reports Server (NTRS)

    Diskin, Boris; Thomas, James L.; Rumsey, Christopher L.; Schwoppe, Axel

    2015-01-01

    A detailed grid convergence study has been conducted to establish accurate reference solutions corresponding to the one-equation linear eddy-viscosity Spalart-Allmaras turbulence model for two dimensional turbulent flows around the NACA 0012 airfoil and a flat plate. The study involved three widely used codes, CFL3D (NASA), FUN3D (NASA), and TAU (DLR), and families of uniformly refined structured grids that differ in the grid density patterns. Solutions computed by different codes on different grid families appear to converge to the same continuous limit, but exhibit different convergence characteristics. The grid resolution in the vicinity of geometric singularities, such as a sharp trailing edge, is found to be the major factor affecting accuracy and convergence of discrete solutions, more prominent than differences in discretization schemes and/or grid elements. The results reported for these relatively simple turbulent flows demonstrate that CFL3D, FUN3D, and TAU solutions are very accurate on the finest grids used in the study, but even those grids are not sufficient to conclusively establish an asymptotic convergence order.

  4. Strong convergence for reduced free products

    NASA Astrophysics Data System (ADS)

    Pisier, Gilles

    2016-06-01

    Using an inequality due to Ricard and Xu, we give a different proof of Paul Skoufranis’s recent result showing that the strong convergence of possibly non-commutative random variables X(k) → X is stable under reduced free product with a fixed non-commutative random variable Y. In fact we obtain a more general fact: assuming that the families X(k) = {X i(k)} and Y(k) = {Y j(k)} are ∗-free as well as their limits (in moments) X = {Xi} and Y = {Yj}, the strong convergences X(k) → X and Y(k) → Y imply that of {X(k),Y(k)} to {X,Y }. Phrased in more striking language: the reduced free product is “continuous” with respect to strong convergence. The analogue for weak convergence (i.e. convergence of all moments) is obvious. Our approach extends to the amalgamated free product, left open by Skoufranis.

  5. The correspondence between X-ray bright points and evolving magnetic features in the quiet sun

    NASA Technical Reports Server (NTRS)

    Webb, D. F.; Martin, S. F.; Moses, D.; Harvey, J. W.

    1993-01-01

    The results of a study of X-ray bright points (XBPs) and small-scale evolving magnetic structures are presented. X-ray images obtained during rocket flights, full-disk magnetograms, and time-lapse magnetograms of multiple fields make up the coordinated data set. XBPs were found to be more frequently associated with pre-existing magnetic features of opposite polarity which appeared to be cancelling than with new or emerging flux regions. Most of the XBPs appeared to correspond to opposite polarity magnetic features which were converging towards each other, and some of which had not yet begun cancelling. It is suggested that most XBPs are created when converging flow brings together oppositely directed field lines. This leads to reconnection and heating in the low corona of the newly-formed loops.

  6. Metanetworks of artificially evolved regulatory networks

    NASA Astrophysics Data System (ADS)

    Danacı, Burçin; Erzan, Ayşe

    2016-04-01

    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 evolved populations of Boolean graphs form tree-like giant clusters in genotype space, 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.

  7. Quantifying evolvability in small biological networks

    SciTech Connect

    Nemenman, Ilya; Mugler, Andrew; Ziv, Etay; Wiggins, Chris H

    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.

  8. Distribution characteristics of weighted bipartite evolving networks

    NASA Astrophysics Data System (ADS)

    Zhang, Danping; Dai, Meifeng; Li, Lei; Zhang, Cheng

    2015-06-01

    Motivated by an evolving model of online bipartite networks, we introduce a model of weighted bipartite evolving networks. In this model, there are two disjoint sets of nodes, called user node set and object node set. Edges only exist between two disjoint sets. Edge weights represent the usage amount between a couple of user node and object node. This model not only clinches the bipartite networks' internal mechanism of network growth, but also takes into account the object strength deterioration over time step. User strength and object strength follow power-law distributions, respectively. The weighted bipartite evolving networks have scare-free property in certain situations. Numerical simulations results agree with the theoretical analyses.

  9. Evolving networks in the human epileptic brain

    NASA Astrophysics Data System (ADS)

    Lehnertz, Klaus; Ansmann, Gerrit; Bialonski, Stephan; Dickten, Henning; Geier, Christian; Porz, Stephan

    2014-01-01

    Network theory provides novel concepts that promise an improved characterization of interacting dynamical systems. Within this framework, evolving networks can be considered as being composed of nodes, representing systems, and of time-varying edges, representing interactions between these systems. This approach is highly attractive to further our understanding of the physiological and pathophysiological dynamics in human brain networks. Indeed, there is growing evidence that the epileptic process can be regarded as a large-scale network phenomenon. We here review methodologies for inferring networks from empirical time series and for a characterization of these evolving networks. We summarize recent findings derived from studies that investigate human epileptic brain networks evolving on timescales ranging from few seconds to weeks. We point to possible pitfalls and open issues, and discuss future perspectives.

  10. JavaGenes: Evolving Graphs with Crossover

    NASA Technical Reports Server (NTRS)

    Globus, Al; Atsatt, Sean; Lawton, John; Wipke, Todd

    2000-01-01

    Genetic algorithms usually use string or tree representations. We have developed a novel crossover operator for a directed and undirected graph representation, and used this operator to evolve molecules and circuits. Unlike strings or trees, a single point in the representation cannot divide every possible graph into two parts, because graphs may contain cycles. Thus, the crossover operator is non-trivial. A steady-state, tournament selection genetic algorithm code (JavaGenes) was written to implement and test the graph crossover operator. All runs were executed by cycle-scavagging on networked workstations using the Condor batch processing system. The JavaGenes code has evolved pharmaceutical drug molecules and simple digital circuits. Results to date suggest that JavaGenes can evolve moderate sized drug molecules and very small circuits in reasonable time. The algorithm has greater difficulty with somewhat larger circuits, suggesting that directed graphs (circuits) are more difficult to evolve than undirected graphs (molecules), although necessary differences in the crossover operator may also explain the results. In principle, JavaGenes should be able to evolve other graph-representable systems, such as transportation networks, metabolic pathways, and computer networks. However, large graphs evolve significantly slower than smaller graphs, presumably because the space-of-all-graphs explodes combinatorially with graph size. Since the representation strongly affects genetic algorithm performance, adding graphs to the evolutionary programmer's bag-of-tricks should be beneficial. Also, since graph evolution operates directly on the phenotype, the genotype-phenotype translation step, common in genetic algorithm work, is eliminated.

  11. Endemism and functional convergence across the North American soil mycobiome

    PubMed Central

    Talbot, Jennifer M.; Bruns, Thomas D.; Taylor, John W.; Smith, Dylan P.; Branco, Sara; Glassman, Sydney I.; Erlandson, Sonya; Vilgalys, Rytas; Liao, Hui-Ling; Smith, Matthew E.; Peay, Kabir G.

    2014-01-01

    Identifying the ecological processes that structure communities and the consequences for ecosystem function is a central goal of ecology. The recognition that fungi, bacteria, and viruses control key ecosystem functions has made microbial communities a major focus of this field. Because many ecological processes are apparent only at particular spatial or temporal scales, a complete understanding of the linkages between microbial community, environment, and function requires analysis across a wide range of scales. Here, we map the biological and functional geography of soil fungi from local to continental scales and show that the principal ecological processes controlling community structure and function operate at different scales. Similar to plants or animals, most soil fungi are endemic to particular bioregions, suggesting that factors operating at large spatial scales, like dispersal limitation or climate, are the first-order determinants of fungal community structure in nature. By contrast, soil extracellular enzyme activity is highly convergent across bioregions and widely differing fungal communities. Instead, soil enzyme activity is correlated with local soil environment and distribution of fungal traits within the community. The lack of structure–function relationships for soil fungal communities at continental scales indicates a high degree of functional redundancy among fungal communities in global biogeochemical cycles. PMID:24733885

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

    PubMed Central

    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. PMID:27200076

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

    PubMed

    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. PMID:27200076

  14. Multicloud: Multigrid convergence with a meshless operator

    SciTech Connect

    Katz, Aaron Jameson, Antony

    2009-08-01

    The primary objective of this work is to develop and test a new convergence acceleration technique we call multicloud. Multicloud is well-founded in the mathematical basis of multigrid, but relies on a meshless operator on coarse levels. The meshless operator enables extremely simple and automatic coarsening procedures for arbitrary meshes using arbitrary fine level discretization schemes. The performance of multicloud is compared with established multigrid techniques for structured and unstructured meshes for the Euler equations on two-dimensional test cases. Results indicate comparable convergence rates per unit work for multicloud and multigrid. However, because of its mesh and scheme transparency, multicloud may be applied to a wide array of problems with no modification of fine level schemes as is often required with agglomeration techniques. The implication is that multicloud can be implemented in a completely modular fashion, allowing researchers to develop fine level algorithms independent of the convergence accelerator for complex three-dimensional problems.

  15. Convergence studies in meshfree peridynamic simulations

    DOE PAGESBeta

    Seleson, Pablo; Littlewood, David J.

    2016-04-15

    Meshfree methods are commonly applied to discretize peridynamic models, particularly in numerical simulations of engineering problems. Such methods discretize peridynamic bodies using a set of nodes with characteristic volume, leading to particle-based descriptions of systems. In this article, we perform convergence studies of static peridynamic problems. We show that commonly used meshfree methods in peridynamics suffer from accuracy and convergence issues, due to a rough approximation of the contribution to the internal force density of nodes near the boundary of the neighborhood of a given node. We propose two methods to improve meshfree peridynamic simulations. The first method uses accuratemore » computations of volumes of intersections between neighbor cells and the neighborhood of a given node, referred to as partial volumes. The second method employs smooth influence functions with a finite support within peridynamic kernels. Numerical results demonstrate great improvements in accuracy and convergence of peridynamic numerical solutions, when using the proposed methods.« less

  16. Convergence Estimates for Multidisciplinary Analysis and Optimization

    NASA Technical Reports Server (NTRS)

    Arian, Eyal

    1997-01-01

    A quantitative analysis of coupling between systems of equations is introduced. This analysis is then applied to problems in multidisciplinary analysis, sensitivity, and optimization. For the sensitivity and optimization problems both multidisciplinary and single discipline feasibility schemes are considered. In all these cases a "convergence factor" is estimated in terms of the Jacobians and Hessians of the system, thus it can also be approximated by existing disciplinary analysis and optimization codes. The convergence factor is identified with the measure for the "coupling" between the disciplines in the system. Applications to algorithm development are discussed. Demonstration of the convergence estimates and numerical results are given for a system composed of two non-linear algebraic equations, and for a system composed of two PDEs modeling aeroelasticity.

  17. Mnemonic convergence in the human hippocampus

    PubMed Central

    Backus, Alexander R.; Bosch, Sander E.; Ekman, Matthias; Grabovetsky, Alejandro Vicente; Doeller, Christian F.

    2016-01-01

    The ability to form associations between a multitude of events is the hallmark of episodic memory. Computational models have espoused the importance of the hippocampus as convergence zone, binding different aspects of an episode into a coherent representation, by integrating information from multiple brain regions. However, evidence for this long-held hypothesis is limited, since previous work has largely focused on representational and network properties of the hippocampus in isolation. Here we identify the hippocampus as mnemonic convergence zone, using a combination of multivariate pattern and graph-theoretical network analyses of functional magnetic resonance imaging data from humans performing an associative memory task. We observe overlap of conjunctive coding and hub-like network attributes in the hippocampus. These results provide evidence for mnemonic convergence in the hippocampus, underlying the integration of distributed information into episodic memory representations. PMID:27325442

  18. Mnemonic convergence in the human hippocampus.

    PubMed

    Backus, Alexander R; Bosch, Sander E; Ekman, Matthias; Grabovetsky, Alejandro Vicente; Doeller, Christian F

    2016-01-01

    The ability to form associations between a multitude of events is the hallmark of episodic memory. Computational models have espoused the importance of the hippocampus as convergence zone, binding different aspects of an episode into a coherent representation, by integrating information from multiple brain regions. However, evidence for this long-held hypothesis is limited, since previous work has largely focused on representational and network properties of the hippocampus in isolation. Here we identify the hippocampus as mnemonic convergence zone, using a combination of multivariate pattern and graph-theoretical network analyses of functional magnetic resonance imaging data from humans performing an associative memory task. We observe overlap of conjunctive coding and hub-like network attributes in the hippocampus. These results provide evidence for mnemonic convergence in the hippocampus, underlying the integration of distributed information into episodic memory representations. PMID:27325442

  19. Evolved Massive Stars in the Local Group

    NASA Astrophysics Data System (ADS)

    Drout, M. R.; Massey, P.

    2015-05-01

    In this manuscript we describe a number of recent advances in the study of evolved massive stars in the Local Group, with an emphasis on how representative populations of these stars can be used to test models of massive star evolution. In honor of the 50th anniversary of the Cerro Tololo Inter-American Observatory (CTIO) we attempt to put these finding in some historical context by discussing how our understanding of the various stages in the lives of massive stars has evolved since Cerro Tololo was first selected as the site for the observatory which would become CTIO.

  20. A Stefan problem on an evolving surface

    PubMed Central

    Alphonse, Amal; Elliott, Charles M.

    2015-01-01

    We formulate a Stefan problem on an evolving hypersurface and study the well posedness of weak solutions given L1 data. To do this, we first develop function spaces and results to handle equations on evolving surfaces in order to give a natural treatment of the problem. Then, we consider the existence of solutions for data; this is done by regularization of the nonlinearity. The regularized problem is solved by a fixed point theorem and then uniform estimates are obtained in order to pass to the limit. By using a duality method, we show continuous dependence, which allows us to extend the results to L1 data. PMID:26261364

  1. Dust around main sequence and evolved stars

    NASA Astrophysics Data System (ADS)

    Walker, H. J.; Heinrichsen, I.; Richards, P. J.

    Data for several main sequence and evolved stars, from the photopolarimeter on ISO (ISOPHOT), are presented. Dust shells are resolved for Y CVn and RS Lib at 60mum. Low resolution spectra from ISOPHOT are shown for several evolved stars, and compared to the spectrum of Vega (a stellar photosphere) and HD 169142 (showing emission features from Polycyclic Aromatic Hydrocarbons). W Lyr shows the signature of oxygen-rich circumstellar material around 3mum, V Aql and Y CVn the signature of carbon-rich material.

  2. Precision is essential for efficient catalysis in an evolved Kemp eliminase.

    PubMed

    Blomberg, Rebecca; Kries, Hajo; Pinkas, Daniel M; Mittl, Peer R E; Grütter, Markus G; Privett, Heidi K; Mayo, Stephen L; Hilvert, Donald

    2013-11-21

    Linus Pauling established the conceptual framework for understanding and mimicking enzymes more than six decades ago. The notion that enzymes selectively stabilize the rate-limiting transition state of the catalysed reaction relative to the bound ground state reduces the problem of design to one of molecular recognition. Nevertheless, past attempts to capitalize on this idea, for example by using transition state analogues to elicit antibodies with catalytic activities, have generally failed to deliver true enzymatic rates. The advent of computational design approaches, combined with directed evolution, has provided an opportunity to revisit this problem. Starting from a computationally designed catalyst for the Kemp elimination--a well-studied model system for proton transfer from carbon--we show that an artificial enzyme can be evolved that accelerates an elementary chemical reaction 6 × 10(8)-fold, approaching the exceptional efficiency of highly optimized natural enzymes such as triosephosphate isomerase. A 1.09 Å resolution crystal structure of the evolved enzyme indicates that familiar catalytic strategies such as shape complementarity and precisely placed catalytic groups can be successfully harnessed to afford such high rate accelerations, making us optimistic about the prospects of designing more sophisticated catalysts. PMID:24132235

  3. Using Reaction Mechanism to Measure Enzyme Similarity

    PubMed Central

    O’Boyle, Noel M.; Holliday, Gemma L.; Almonacid, Daniel E.; Mitchell, John B.O.

    2012-01-01

    Summary The concept of reaction similarity has been well-studied in terms of the overall transformation associated with a reaction, but not in terms of mechanism. We present the first method to give a quantitative measure of the similarity of reactions based upon their explicit mechanisms. Two approaches are presented to measure the similarity between individual steps of mechanisms: a fingerprint-based approach which incorporates relevant information on each mechanistic step, and an approach based only on bond formation, cleavage and changes in order. The overall similarity for two reaction mechanisms is then calculated using the Needleman-Wunsch alignment algorithm. An analysis of MACiE, a database of enzyme mechanisms, using our measure of similarity identifies some examples of convergent evolution of chemical mechanism. In many cases mechanism similarity is not reflected by similarity according to the EC system of enzyme classification. In particular, little mechanistic information is conveyed by the class level of the EC. PMID:17400244

  4. Experience and convergence in spiritual direction.

    PubMed

    Evans, Jean

    2015-02-01

    The practice of spiritual direction concerns the human experience of God. As praxis, spiritual direction has a long tradition in Western Christianity. It is a process rooted in spirituality with theology as its foundation. This paper explores the convergences between aspects of philosophy (contemplative awareness), psychology (Rogerian client-centered approach) and phenomenology. There are significant points of convergence between phenomenology and spiritual direction: first, in Ignatius of Loyola's phenomenological approach to his religious experience; second, in the appropriation by spiritual directors of concepts of epochē and empathy; third, in the process of "unpacking" religious experience within a spiritual direction interview. PMID:24469918

  5. Deterministic convergence in iterative phase shifting

    SciTech Connect

    Luna, Esteban; Salas, Luis; Sohn, Erika; Ruiz, Elfego; Nunez, Juan M.; Herrera, Joel

    2009-03-10

    Previous implementations of the iterative phase shifting method, in which the phase of a test object is computed from measurements using a phase shifting interferometer with unknown positions of the reference, do not provide an accurate way of knowing when convergence has been attained. We present a new approach to this method that allows us to deterministically identify convergence. The method is tested with a home-built Fizeau interferometer that measures optical surfaces polished to {lambda}/100 using the Hydra tool. The intrinsic quality of the measurements is better than 0.5 nm. Other possible applications for this technique include fringe projection or any problem where phase shifting is involved.

  6. Surveying The Digital Landscape: Evolving Technologies 2004. The EDUCAUSE Evolving Technologies Committee

    ERIC Educational Resources Information Center

    EDUCAUSE Review, 2004

    2004-01-01

    Each year, the members of the EDUCAUSE Evolving Technologies Committee identify and research the evolving technologies that are having the most direct impact on higher education institutions. The committee members choose the relevant topics, write white papers, and present their findings at the EDUCAUSE annual conference. This year, under the…

  7. A Numerical Study of Strain Partitioning and the Development of Forearc Slivers at Obliquely Convergent Margins

    NASA Astrophysics Data System (ADS)

    Koster, K. L.; Haq, S. S.; Flesch, L. M.

    2012-12-01

    Oblique relative plate motion is common at convergent margins, often with a significant component of margin-parallel motion. At such margins, relative plate motion is often accommodated as spatially distinct margin-normal thrusting and margin-parallel shear, leading to the development of fore-arc slivers. These crustal slivers are bounded trench-ward by thrust faults and arc-ward by a well developed margin-parallel strike-slip fault and are observed in about half of all modern convergent boundaries. Some modestly oblique convergent settings are known to develop fore-arc slivers while some higher obliquity margins fail to effectively partition the margin-parallel component of plate motion in a distinct zone. Analog modeling has shown that pure frictional wedges only produce fore-arc like sliver motion at very high obliquities, however, the presence of ductile layers at depth can localize shear at lower obliquities. We have performed finite-element numerical simulations of oblique convergent wedges, over a wide range of obliquities, governed by viscous behavior at depth in which we solve force-balance equations for Stokes flow using COMSOL Multiphysics to quantify the magnitude and style of stress. Our numerical models reproduce topographic profiles and surface velocity fields of similarly parameterized analog experiments and demonstrate a progressive localization of margin-parallel shear with wedge growth. We also observe the onset and localization of shear in all wedges of non-zero obliquity, which we quantify by comparing the magnitudes of principal compressional and extensional stress tensor axes to constrain the timing of the transition between intermediate and high partitioning of strain in evolving wedges. These results suggest, in conjunction with analog models, that viscous behavior at depth and increase in topography during convergence both work to localize margin-parallel shear in obliquely convergent wedges and gives a mechanism for the development of

  8. Divergent and convergent evolution in metastases suggest treatment strategies based on specific metastatic sites

    PubMed Central

    Cunningham, Jessica J.; Brown, Joel S.; Vincent, Thomas L.

    2015-01-01

    Background and objective: Systemic therapy for metastatic cancer is currently determined exclusively by the site of tumor origin. Yet, there is increasing evidence that the molecular characteristics of metastases significantly differ from the primary tumor. We define the evolutionary dynamics of metastases that govern this molecular divergence and examine their potential contribution to variations in response to targeted therapies. Methodology: Darwinian interactions of transformed cells with the tissue microenvironments at primary and metastatic sites are analyzed using evolutionary game theory. Computational models simulate responses to targeted therapies in different organs within the same patient. Results: Tumor cells, although maximally fit at their primary site, typically have lower fitness on the adaptive landscapes offered by the metastatic sites due to organ-specific variations in mesenchymal properties and signaling pathways. Clinically evident metastases usually exhibit time-dependent divergence from the phenotypic mean of the primary population as the tumor cells evolve and adapt to their new circumstances. In contrast, tumors from different primary sites evolving on identical metastatic adaptive landscapes exhibit phenotypic convergence. Thus, metastases in the liver from different primary tumors and even in different hosts will evolve toward similar adaptive phenotypes. The combination of evolutionary divergence from the primary cancer phenotype and convergence towards similar adaptive strategies in the same tissue cause significant variations in treatment responses particularly for highly targeted therapies. Conclusion and implications: The results suggest that optimal therapies for disseminated cancer must take into account the site(s) of metastatic growth as well as the primary organ. PMID:25794501

  9. Convergent and correlated evolution of major life-history traits in the angiosperm genus Leucadendron (Proteaceae).

    PubMed

    Tonnabel, Jeanne; Mignot, Agnès; Douzery, Emmanuel J P; Rebelo, Anthony G; Schurr, Frank M; Midgley, Jeremy; Illing, Nicola; Justy, Fabienne; Orcel, Denis; Olivieri, Isabelle

    2014-10-01

    Natural selection is expected to cause convergence of life histories among taxa as well as correlated evolution of different life-history traits. Here, we quantify the extent of convergence of five key life-history traits (adult fire survival, seed storage, degree of sexual dimorphism, pollination mode, and seed-dispersal mode) and test hypotheses about their correlated evolution in the genus Leucadendron (Proteaceae) from the fire-prone South African fynbos. We reconstructed a new molecular phylogeny of this highly diverse genus that involves more taxa and molecular markers than previously. This reconstruction identifies new clades that were not detected by previous molecular study and morphological classifications. Using this new phylogeny and robust methods that account for phylogenetic uncertainty, we show that the five life-history traits studied were labile during the evolutionary history of the genus. This diversity allowed us to tackle major questions about the correlated evolution of life-history strategies. We found that species with longer seed-dispersal distances tended to evolve lower pollen-dispersal distance, that insect-pollinated species evolved decreased sexual dimorphism, and that species with a persistent soil seed-bank evolved toward reduced fire-survival ability of adults. PMID:24957971

  10. Project Evolve User-Adopter Manual.

    ERIC Educational Resources Information Center

    Joiner, Lee M.

    An adult basic education (ABE) program for mentally retarded young adults between the ages of 14 and 26 years, Project Evolve can provide education agencies for educationally handicapped children with detailed information concerning an innovative program. The manual format was developed through interviews with professional educators concerning the…

  11. The Evolving Leadership Path of Visual Analytics

    SciTech Connect

    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.

  12. The Evolving Office of the Registrar

    ERIC Educational Resources Information Center

    Pace, Harold L.

    2011-01-01

    A healthy registrar's office will continue to evolve as it considers student, faculty, and institutional needs; staff talents and expectations; technological opportunities; economic realities; space issues; work environments; and where the strategic plan is taking the institution in support of the mission. Several recognized leaders in the field…

  13. Did Language Evolve Like the Vertebrate Eye?

    ERIC Educational Resources Information Center

    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…

  14. Hyper massive black holes in evolved galaxies

    NASA Astrophysics Data System (ADS)

    Romero-Cruz, Fernando J.

    2015-09-01

    From the SDSS DR7 we took a sample of 16733 galaxies which do not show all of the emission lines required to classify their activity according to the classical BPT diagram (Baldwin et al. 1981 PASP). Since they do not show these emission lines they are thought to be evolved enough so to host Hyper Massive Black holes. We compared their statistical properties with other galaxies from the SDSS DR7 which do show emission lines and confirmed that their M-sigma relationship correspond to HMBHs (Gutelkin et al. 2009 ApJ) and also that their SFH confirms evolution. We also analyzed them with a new Diagnostic Diagram in the IR (Coziol et al. 2015 AJ) and found that their position in the IR color space (W3W4 vs W2W3) correspond to AGN activity with current low SF, another confirmation of an evolved galaxy. The position of our final sample in the IR diagram is in the same region in which Holm 15A lies, this galaxy is considered to host the most massive BHs in the nearby universe (Lopez-Cruz et al. 2014 ApJL). The morphology of these galaxies (all of them are classified as elliptical) confirms that they are very evolved. We claim that the hyper massive BH lie in galaxies very evolved and with very low SF and without clear AGN activity in the BPT diagram.

  15. Origins of multicellular evolvability in snowflake yeast.

    PubMed

    Ratcliff, William C; Fankhauser, Johnathon D; Rogers, David W; Greig, Duncan; Travisano, Michael

    2015-01-01

    Complex life has arisen through a series of 'major transitions' in which collectives of formerly autonomous individuals evolve into a single, integrated organism. A key step in this process is the origin of higher-level evolvability, but little is known about how higher-level entities originate and gain the capacity to evolve as an individual. Here we report a single mutation that not only creates a new level of biological organization, but also potentiates higher-level evolvability. Disrupting the transcription factor ACE2 in Saccharomyces cerevisiae prevents mother-daughter cell separation, generating multicellular 'snowflake' yeast. Snowflake yeast develop through deterministic rules that produce geometrically defined clusters that preclude genetic conflict and display a high broad-sense heritability for multicellular traits; as a result they are preadapted to multicellular adaptation. This work demonstrates that simple microevolutionary changes can have profound macroevolutionary consequences, and suggests that the formation of clonally developing clusters may often be the first step to multicellularity. PMID:25600558

  16. Apollo 16 Evolved Lithology Sodic Ferrogabbro

    NASA Technical Reports Server (NTRS)

    Zeigler, Ryan; Jolliff, B. L.; Korotev, R. L.

    2014-01-01

    Evolved lunar igneous lithologies, often referred to as the alkali suite, are a minor but important component of the lunar crust. These evolved samples are incompatible-element rich samples, and are, not surprisingly, most common in the Apollo sites in (or near) the incompatible-element rich region of the Moon known as the Procellarum KREEP Terrane (PKT). The most commonly occurring lithologies are granites (A12, A14, A15, A17), monzogabbro (A14, A15), alkali anorthosites (A12, A14), and KREEP basalts (A15, A17). The Feldspathic Highlands Terrane is not entirely devoid of evolved lithologies, and rare clasts of alkali gabbronorite and sodic ferrogabbro (SFG) have been identified in Apollo 16 station 11 breccias 67915 and 67016. Curiously, nearly all pristine evolved lithologies have been found as small clasts or soil particles, exceptions being KREEP basalts 15382/6 and granitic sample 12013 (which is itself a breccia). Here we reexamine the petrography and geochemistry of two SFG-like particles found in a survey of Apollo 16 2-4 mm particles from the Cayley Plains 62283,7-15 and 62243,10-3 (hereafter 7-15 and 10-3 respectively). We will compare these to previously reported SFG samples, including recent analyses on the type specimen of SFG from lunar breccia 67915.

  17. A Course Evolves-Physical Anthropology.

    ERIC Educational Resources Information Center

    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…

  18. Leadership for Literacy Coaching: Evolving Research

    ERIC Educational Resources Information Center

    Taylor, Rosemarye T.; Moxley, Dale E.

    2008-01-01

    Leadership for literacy coaching is evolving in both the skills of the literacy coaches and the skills of those they coach. Issues of role clarification, communication with administration, and hesitancy to provide authentic feedback are consistently identified. Trends associated with literacy coaching indicate that they continue on their…

  19. Field-evolved resistance to Bt toxins

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Transgenic cotton expressing Bacillus thuringiensis Cry1Ac (Bt cotton) has been used commercially in the United States since 1996. An article by Tabashnik et al. 2008, Nature Biotechnology 26:199-202, states that, for the first time, there is field-evolved Bt resistance in bollworm, Helicoverpa zea...

  20. Organizational Innovation: Current Research and Evolving Concepts

    ERIC Educational Resources Information Center

    Rowe, Lloyd A.; Boise, William B.

    1974-01-01

    A conceptual framework for organizational innovation can evolve from such ideas as the process of innovation, the climate(s) required, the organizational and societal space affected by an innovation, innovation radicalness, and innovation strategies such as organizational development, functional specialization, and periodicity. (Author/WM)

  1. [Families and psychiatry: models and evolving links].

    PubMed

    Frankhauser, Adeline

    2016-01-01

    The role of the families of persons with severe psychiatric disorders (schizophrenia in particular) in the care of their relatives has recently evolved: once seen as pathogenic to be kept at a distance, the family is now recognised by professionals as a partner in the care process. The links between families and psychiatric institutions remain complex and marked by ambivalence and paradoxes. PMID:27157191

  2. Molecular and functional basis of phenotypic convergence in white lizards at White Sands.

    PubMed

    Rosenblum, Erica Bree; Römpler, Holger; Schöneberg, Torsten; Hoekstra, Hopi E

    2010-02-01

    There are many striking examples of phenotypic convergence in nature, in some cases associated with changes in the same genes. But even mutations in the same gene may have different biochemical properties and thus different evolutionary consequences. Here we dissect the molecular mechanism of convergent evolution in three lizard species with blanched coloration on the gypsum dunes of White Sands, New Mexico. These White Sands forms have rapidly evolved cryptic coloration in the last few thousand years, presumably to avoid predation. We use cell-based assays to demonstrate that independent mutations in the same gene underlie the convergent blanched phenotypes in two of the three species. Although the same gene contributes to light phenotypes in these White Sands populations, the specific molecular mechanisms leading to reduced melanin production are different. In one case, mutations affect receptor signaling and in the other, the ability of the receptor to integrate into the melanocyte membrane. These functional differences have important ramifications at the organismal level. Derived alleles in the two species show opposite dominance patterns, which in turn affect their visibility to selection and the spatial distribution of alleles across habitats. Our results demonstrate that even when the same gene is responsible for phenotypic convergence, differences in molecular mechanism can have dramatic consequences on trait expression and ultimately the adaptive trajectory. PMID:20080544

  3. Enzymes for improved biomass conversion

    DOEpatents

    Brunecky, Roman; Himmel, Michael E.

    2016-02-02

    Disclosed herein are enzymes and combinations of the enzymes useful for the hydrolysis of cellulose and the conversion of biomass. Methods of degrading cellulose and biomass using enzymes and cocktails of enzymes are also disclosed.

  4. Grasping convergent evolution in syngnathids: a unique tale of tails.

    PubMed

    Neutens, C; Adriaens, D; Christiaens, J; De Kegel, B; Dierick, M; Boistel, R; Van Hoorebeke, L

    2014-06-01

    Seahorses and pipehorses both possess a prehensile tail, a unique characteristic among teleost fishes, allowing them to grasp and hold onto substrates such as sea grasses. Although studies have focused on tail grasping, the pattern of evolutionary transformations that made this possible is poorly understood. Recent phylogenetic studies show that the prehensile tail evolved independently in different syngnathid lineages, including seahorses, Haliichthys taeniophorus and several types of so-called pipehorses. This study explores the pattern that characterizes this convergent evolution towards a prehensile tail, by comparing the caudal musculoskeletal organization, as well as passive bending capacities in pipefish (representing the ancestral state), pipehorse, seahorse and H. taeniophorus. To study the complex musculoskeletal morphology, histological sectioning, μCT-scanning and phase contrast synchrotron scanning were combined with virtual 3D-reconstructions. Results suggest that the independent evolution towards tail grasping in syngnathids reflects at least two quite different strategies in which the ancestral condition of a heavy plated and rigid system became modified into a highly flexible one. Intermediate skeletal morphologies (between the ancestral condition and seahorses) could be found in the pygmy pipehorses and H. taeniophorus, which are phylogenetically closely affiliated with seahorses. This study suggests that the characteristic parallel myoseptal organization as already described in seahorse (compared with a conical organization in pipefish and pipehorse) may not be a necessity for grasping, but represents an apomorphy for seahorses, as this pattern is not found in other syngnathid species possessing a prehensile tail. One could suggest that the functionality of grasping evolved before the specialized, parallel myoseptal organization seen in seahorses. However, as the grasping system in pipehorses is a totally different one, this cannot be

  5. Grasping convergent evolution in syngnathids: a unique tale of tails

    PubMed Central

    Neutens, C; Adriaens, D; Christiaens, J; De Kegel, B; Dierick, M; Boistel, R; Van Hoorebeke, L

    2014-01-01

    Seahorses and pipehorses both possess a prehensile tail, a unique characteristic among teleost fishes, allowing them to grasp and hold onto substrates such as sea grasses. Although studies have focused on tail grasping, the pattern of evolutionary transformations that made this possible is poorly understood. Recent phylogenetic studies show that the prehensile tail evolved independently in different syngnathid lineages, including seahorses, Haliichthys taeniophorus and several types of so-called pipehorses. This study explores the pattern that characterizes this convergent evolution towards a prehensile tail, by comparing the caudal musculoskeletal organization, as well as passive bending capacities in pipefish (representing the ancestral state), pipehorse, seahorse and H. taeniophorus. To study the complex musculoskeletal morphology, histological sectioning, μCT-scanning and phase contrast synchrotron scanning were combined with virtual 3D-reconstructions. Results suggest that the independent evolution towards tail grasping in syngnathids reflects at least two quite different strategies in which the ancestral condition of a heavy plated and rigid system became modified into a highly flexible one. Intermediate skeletal morphologies (between the ancestral condition and seahorses) could be found in the pygmy pipehorses and H. taeniophorus, which are phylogenetically closely affiliated with seahorses. This study suggests that the characteristic parallel myoseptal organization as already described in seahorse (compared with a conical organization in pipefish and pipehorse) may not be a necessity for grasping, but represents an apomorphy for seahorses, as this pattern is not found in other syngnathid species possessing a prehensile tail. One could suggest that the functionality of grasping evolved before the specialized, parallel myoseptal organization seen in seahorses. However, as the grasping system in pipehorses is a totally different one, this cannot be

  6. Governance Challenges of Technological Systems Convergence

    ERIC Educational Resources Information Center

    Whitman, Jim

    2006-01-01

    The convergence of several technological systems (especially nanotechnology, biotechnology, information technology, and robotics) has now been adopted as a strategic goal by several countries, most notably the United States and those of the European Union. The anticipated benefits and related fears of competitive disadvantage have brought together…

  7. Phonological Convergence in a Contracting Language Variety

    ERIC Educational Resources Information Center

    Bullock, Barbara E.; Gerfen, Chip

    2004-01-01

    Most work investigating the role of convergence in situations of language attrition has focused on the morpho-syntactic restructuring of the dying language variety. A central concern of such research has been untangling the factors driving the restructuring with an eye towards establishing whether the changes observed are best viewed as externally…

  8. The Convergence Coefficient across Political Systems

    PubMed Central

    Schofield, Norman

    2013-01-01

    Formal work on the electoral model often suggests that parties or candidates should locate themselves at the electoral mean. Recent research has found no evidence of such convergence. In order to explain nonconvergence, the stochastic electoral model is extended by including estimates of electoral valence. We introduce the notion of a convergence coefficient, c. It has been shown that high values of c imply that there is a significant centrifugal tendency acting on parties. We used electoral surveys to construct a stochastic valence model of the the elections in various countries. We find that the convergence coefficient varies across elections in a country, across countries with similar regimes, and across political regimes. In some countries, the centripetal tendency leads parties to converge to the electoral mean. In others the centrifugal tendency dominates and some parties locate far from the electoral mean. In particular, for countries with proportional electoral systems, namely, Israel, Turkey, and Poland, the centrifugal tendency is very high. In the majoritarian polities of the United States and Great Britain, the centrifugal tendency is very low. In anocracies, the autocrat imposes limitations on how far from the origin the opposition parties can move. PMID:24385886

  9. Convergence as a Mechanism of Language Change

    ERIC Educational Resources Information Center

    Backus, Ad

    2004-01-01

    This issue of "Bilingualism: Language and Cognition" is about convergence, a type of language change that is contact-induced and results in greater similarity between two languages that are in contact with each other. In Backus (forthcoming), I have attempted an overview of contact-induced language change, focusing on causal factors, on mechanisms…

  10. Culture and Social Psychology: Converging Perspectives

    ERIC Educational Resources Information Center

    Dimaggio, Paul; Markus, Hazel Rose

    2010-01-01

    Views of culture in psychology and sociology have converged markedly in the past two decades. Both have rejected what Adams and Markus (2004) refer to as the "entity" conception of culture--the view that culture is coherent, stable, and located in the heads of collectivities' members--in favor of more supple and dynamic constructs. Culture, in…

  11. Convergence behavior of a new DSMC algorithm.

    SciTech Connect

    Gallis, Michail A.; Rader, Daniel John; Torczynski, John Robert; Bird, Graeme A.

    2008-10-01

    The convergence rate of a new direct simulation Monte Carlo (DSMC) method, termed 'sophisticated DSMC', is investigated for one-dimensional Fourier flow. An argon-like hard-sphere gas at 273.15K and 266.644Pa is confined between two parallel, fully accommodating walls 1mm apart that have unequal temperatures. The simulations are performed using a one-dimensional implementation of the sophisticated DSMC algorithm. In harmony with previous work, the primary convergence metric studied is the ratio of the DSMC-calculated thermal conductivity to its corresponding infinite-approximation Chapman-Enskog theoretical value. As discretization errors are reduced, the sophisticated DSMC algorithm is shown to approach the theoretical values to high precision. The convergence behavior of sophisticated DSMC is compared to that of original DSMC. The convergence of the new algorithm in a three-dimensional implementation is also characterized. Implementations using transient adaptive sub-cells and virtual sub-cells are compared. The new algorithm is shown to significantly reduce the computational resources required for a DSMC simulation to achieve a particular level of accuracy, thus improving the efficiency of the method by a factor of 2.

  12. Collaborative Instructional Strategies to Enhance Knowledge Convergence

    ERIC Educational Resources Information Center

    Draper, Darryl C.

    2015-01-01

    To promote knowledge convergence through collaborative learning activities in groups, this qualitative case study involved a layered approach for the design and delivery of a highly collaborative learning environment incorporating various instructional technologies grounded in learning theory. In a graduate-level instructional technology course,…

  13. Converging Oceaniac Internal Waves, Somalia, Africa

    NASA Technical Reports Server (NTRS)

    1988-01-01

    The arculate fronts of these apparently converging internal waves off the northeast coast of Somalia (11.5N, 51.5E) probably were produced by interaction with two parallel submarine canyons off the Horn of Africa. Internal waves are packets of tidally generated waves traveling within the ocean at varying depths and are not detectable by any surface disturbance.

  14. Professionalization in Universities and European Convergence

    ERIC Educational Resources Information Center

    Vivas, Amparo Jimenez; Hevia, David Menendez Alvarez

    2009-01-01

    The constant assessment of the quality of higher education within the framework of European convergence is a challenge for all those universities that wish their degrees and diplomas to reflect a unified Europe. As is the case in any assessment, change and review process, the quest to improve quality implies measuring achievement of the objectives…

  15. Another Perspective: A Response to "Toward Convergence"

    ERIC Educational Resources Information Center

    Regelski, Thomas A.

    2013-01-01

    This response by Thomas A. Regelski was solicited to complement the lead article in this issue, "Toward Convergence: Adapting Music Education to Contemporary Society and Participatory Culture" by Evan S. Tobias. The author notes that many interesting and vital questions and alternatives that are often studiously ignored, overlooked, or taken for…

  16. A Monotonically Convergent Algorithm for FACTALS.

    ERIC Educational Resources Information Center

    Kiers, Henk A. L.; And Others

    1993-01-01

    A new procedure is proposed for handling nominal variables in the analysis of variables of mixed measurement levels, and a procedure is developed for handling ordinal variables. Using these procedures, a monotonically convergent algorithm is constructed for the FACTALS method for any mixture of variables. (SLD)

  17. Dysregulation of Acetylation Enzymes in Animal Models of Psychostimulant use Disorders: Evolving Stories

    PubMed Central

    Cadet, Jean Lud

    2016-01-01

    Substance use disorders are neuropsychiatric illnesses that have substantial negative biopsychosocial impact. These diseases are defined as compulsive abuse of licit or illicit substances despite adverse medicolegal consequences. Although much research has been conducted to elucidate the pathobiological bases of these disorders, much remains to be done to develop an overarching neurobiological understanding that might be translatable to beneficial pharmacological therapies. Recent advances in epigenetics promise to lead to such an elucidation. Here I provide a brief overview of observations obtained using some models of psychostimulant administration in rodents. The review identifies CREB binding protein (CBP), HDAC1, HDAC2, HADC3, HDAC4, and HDAC5 as important players in the acetylation and deacetylation processes that occur after contingent or non-contingent administration of psychostimulants. These observations are discussed within a framework that suggests a need for better animal models of addiction in order to bring these epigenetic advances to bear on the pharmacological treatment of human addicts. PMID:26813118

  18. Catalyzed enzyme electrodes

    DOEpatents

    Zawodzinski, Thomas A.; Wilson, Mahlon S.; Rishpon, Judith; Gottesfeld, Shimshon

    1993-01-01

    An enzyme electrode is prepared with a composite coating on an electrical conductor. The composite coating is formed from a casting solution of a perfluorosulfonic acid polymer, an enzyme, and a carbon supported catalyst. The solution may be cast directly on the conductor surface or may be formed as a membrane and applied to the surface. The perfluorosulfonic acid ionomer formed from the casting solution provides an insoluble biocompatible protective matrix for the enzyme and acts to retain the enzyme for long term availability in the electrode structure. The carbon supported catalyst provides catalytic sites throughout the layer for the oxidation of hydrogen peroxide from the enzyme reactions. The carbon support then provides a conductive path for establishing an electrical signal to the electrical conductor. In one embodiment, the electrical conductor is a carbon cloth that permits oxygen or other gas to be introduced to the perfluorosulfonic polymer to promote the enzyme reaction independent of oxygen in the solution being tested.

  19. Rational enzyme redesign

    SciTech Connect

    Ornstein, R.L.

    1994-05-01

    Protein engineering is first a means of elucidating structure-function relations in an enzyme, and second, a means of changing a protein to make it serve a different, but generally related, purpose. In principle, one may change the functional characteristics of an enzyme by altering its substrate specificity, kinetics, optimum range of activity, and chemical mechanism. Obviously one cannot make all possible combinations of amino acid changes for even the smallest enzyme, so the essential question is which changes to make. The intent of rational protein/enzyme redesign is to alter a protein/enzyme in a timely and premeditated fashion. This article provides an outline of the process of rational enzyme redesign.

  20. Magnetically responsive enzyme powders

    NASA Astrophysics Data System (ADS)

    Pospiskova, Kristyna; Safarik, Ivo

    2015-04-01

    Powdered enzymes were transformed into their insoluble magnetic derivatives retaining their catalytic activity. Enzyme powders (e.g., trypsin and lipase) were suspended in various liquid media not allowing their solubilization (e.g., saturated ammonium sulfate and highly concentrated polyethylene glycol solutions, ethanol, methanol, 2-propanol) and subsequently cross-linked with glutaraldehyde. Magnetic modification was successfully performed at low temperature in a freezer (-20 °C) using magnetic iron oxides nano- and microparticles prepared by microwave-assisted synthesis from ferrous sulfate. Magnetized cross-linked enzyme powders were stable at least for two months in water suspension without leakage of fixed magnetic particles. Operational stability of magnetically responsive enzymes during eight repeated reaction cycles was generally without loss of enzyme activity. Separation of magnetically modified cross-linked powdered enzymes from reaction mixtures was significantly simplified due to their magnetic properties.

  1. Chloroplast and Cytoplasmic Enzymes

    PubMed Central

    Anderson, Louise E.; Pacold, Ivan

    1972-01-01

    Several peaks of aldolase activity are found in the isoelectric focusing pattern of pea (Pisum sativum) leaf chloroplast extracts. One peak, separated by 0.5 pH unit from the major chloroplast aldolase peak, is found when cytoplasmic extracts are focused. The chloroplast and cytoplasmic enzymes have a pH 7.4 optimum with fructose 1,6-diphosphate. The Michaelis constant for fructose-1,6-diphosphate is 19 μM for the chloroplast, 21 μM for the cytoplasmic enzyme, and for sedoheptulose 1,7-diphosphate, 8 μM for the chloroplast enzyme, 18 μM for the cytoplasmic enzyme. Both enzymes are inhibited by d-glyceraldehyde 3-phosphate and by ribulose 1,5-diphosphate. The similarity in the catalytic properties of the isoenzymes suggests that both enzymes have an amphibolic role in carbon metabolism in the green leaf. PMID:16657968

  2. Catalyzed enzyme electrodes

    SciTech Connect

    Zawodzinski, T.A.; Wilson, M.S.; Rishpon, J.; Gottesfeld, S.

    1992-12-31

    An enzyme electrode is prepared with a composite coating on an electrical conductor. The composite coating is formed from a casting solution of a perfluorosulfonic acid, polymer, an enzyme, and a carbon supported catalyst. The solution may be cast directly on the conductor surface or may be formed as a membrane and applied to the surface. The perfluorosulfonic acid ionomer formed from the casting solution provides an insoluble biocompatible protective matrix for the enzyme and acts to retain the enzyme for long term availability in the electrode structure. The carbon supported catalyst provides catalytic sites throughout the layer for the oxidation of hydrogen peroxide from the enzyme reactions. The carbon support then provides a conductive path for establishing an electrical signal to the electrical conductor. In one embodiment, the electrical conductor is a carbon cloth that permits oxygen or other gas to be introduced to the perfluorosulfonic polymer to promote the enzyme reaction independent of oxygen in the solution being tested.

  3. Catalyzed enzyme electrodes

    SciTech Connect

    Zawodzinski, T.A.; Wilson, M.S.; Rishpon, J.; Gottesfeld, S.

    1993-07-13

    An enzyme electrode is prepared with a composite coating on an electrical conductor. The composite coating is formed from a casting solution of a perfluorosulfonic acid polymer, an enzyme, and a carbon supported catalyst. The solution may be cast directly on the conductor surface or may be formed as a membrane and applied to the surface. The perfluorosulfonic acid ionomer formed from the casting solution provides an insoluble biocompatible protective matrix for the enzyme and acts to retain the enzyme for long term availability in the electrode structure. The carbon supported catalyst provides catalytic sites throughout the layer for the oxidation of hydrogen peroxide from the enzyme reactions. The carbon support then provides a conductive path for establishing an electrical signal to the electrical conductor. In one embodiment, the electrical conductor is a carbon cloth that permits oxygen or other gas to be introduced to the perfluorosulfonic polymer to promote the enzyme reaction independent of oxygen in the solution being tested.

  4. Parental Care: The Key to Understanding Endothermy and Other Convergent Features in Birds and Mammals.

    PubMed

    Farmer

    2000-03-01

    Birds and mammals share a number of features that are remarkably similar but that have evolved independently. One of these characters, endothermy, has been suggested to have played a cardinal role in avian and mammalian evolution. I hypothesize that it is parental care, rather than endothermy, that is the key to understanding the amazing convergence between mammals and birds. Endothermy may have arisen as a consequence of selection for parental care because endothermy enables a parent to control incubation temperature. The remarkable ability of many birds and mammals to sustain vigorous exercise may also have arisen as a consequence of selection for parental care because provisioning of offspring often requires sustained vigorous exercise. Because extensive parental care encompasses a wide range of behaviors, morphology, and physiology, it may be a key innovation that accounts for the majority of convergent avian and mammalian characters. PMID:10718729

  5. Convergent evolution to an aptamer observed in small populations on DNA microarrays

    NASA Astrophysics Data System (ADS)

    Rowe, W.; Platt, M.; Wedge, D. C.; Day, P. J. R.; Kell, D. B.; Knowles, J. D.

    2010-09-01

    The development of aptamers on custom synthesized DNA microarrays, which has been demonstrated in recent publications, can facilitate detailed analyses of sequence and fitness relationships. Here we use the technique to observe the paths taken through sequence-fitness space by three different evolutionary regimes: asexual reproduction, recombination and model-based evolution. The different evolutionary runs are made on the same array chip in triplicate, each one starting from a small population initialized independently at random. When evolving to a common target protein, glucose-6-phosphate dehydrogenase (G6PD), these nine distinct evolutionary runs are observed to develop aptamers with high affinity and to converge on the same motif not present in any of the starting populations. Regime specific differences in the evolutions, such as speed of convergence, could also be observed.

  6. Type I restriction enzymes and their relatives

    PubMed Central

    Loenen, Wil A. M.; Dryden, David T. F.; Raleigh, Elisabeth A.; Wilson, Geoffrey G.

    2014-01-01

    Type I restriction enzymes (REases) are large pentameric proteins with separate restriction (R), methylation (M) and DNA sequence-recognition (S) subunits. They were the first REases to be discovered and purified, but unlike the enormously useful Type II REases, they have yet to find a place in the enzymatic toolbox of molecular biologists. Type I enzymes have been difficult to characterize, but this is changing as genome analysis reveals their genes, and methylome analysis reveals their recognition sequences. Several Type I REases have been studied in detail and what has been learned about them invites greater attention. In this article, we discuss aspects of the biochemistry, biology and regulation of Type I REases, and of the mechanisms that bacteriophages and plasmids have evolved to evade them. Type I REases have a remarkable ability to change sequence specificity by domain shuffling and rearrangements. We summarize the classic experiments and observations that led to this discovery, and we discuss how this ability depends on the modular organizations of the enzymes and of their S subunits. Finally, we describe examples of Type II restriction–modification systems that have features in common with Type I enzymes, with emphasis on the varied Type IIG enzymes. PMID:24068554

  7. NUMERICAL CONVERGENCE IN SMOOTHED PARTICLE HYDRODYNAMICS

    SciTech Connect

    Zhu, Qirong; Li, Yuexing; Hernquist, Lars

    2015-02-10

    We study the convergence properties of smoothed particle hydrodynamics (SPH) using numerical tests and simple analytic considerations. Our analysis shows that formal numerical convergence is possible in SPH only in the joint limit N → ∞, h → 0, and N{sub nb} → ∞, where N is the total number of particles, h is the smoothing length, and N{sub nb} is the number of neighbor particles within the smoothing volume used to compute smoothed estimates. Previous work has generally assumed that the conditions N → ∞ and h → 0 are sufficient to achieve convergence, while holding N{sub nb} fixed. We demonstrate that if N{sub nb} is held fixed as the resolution is increased, there will be a residual source of error that does not vanish as N → ∞ and h → 0. Formal numerical convergence in SPH is possible only if N{sub nb} is increased systematically as the resolution is improved. Using analytic arguments, we derive an optimal compromise scaling for N{sub nb} by requiring that this source of error balance that present in the smoothing procedure. For typical choices of the smoothing kernel, we find N{sub nb} ∝N {sup 0.5}. This means that if SPH is to be used as a numerically convergent method, the required computational cost does not scale with particle number as O(N), but rather as O(N {sup 1} {sup +} {sup δ}), where δ ≈ 0.5, with a weak dependence on the form of the smoothing kernel.

  8. Human Photoreactivating Enzyme

    PubMed Central

    Sutherland, J. C.; Sutherland, B. M.

    1975-01-01

    The action spectrum for photoreactivation by enzymes from human leukocytes and fibroblasts extends from 300 to approximately 600 nm with a maximum near 400 nm. The ability of the human enzymes to utilize light of wavelengths greater than 500 nm suggested that yellow or gold lights conventionally used as safelights for photoreactivation might serve as sources of photoreactivating light for these enzymes. Experiments using lights with a range of spectral outputs confirm that the standard yellow “safe” lights do produce photoreactivation by the human but not the Escherichia coli enzyme. PMID:19211015

  9. Nanostructures for enzyme stabilization

    SciTech Connect

    Kim, Jungbae; Grate, Jay W.; Wang, Ping

    2006-02-02

    The last decade has witnessed notable breakthroughs in nanotechnology with development of various nanostructured materials such as mesoporous materials and nanoparticles. These nanostructures have been used as a host for enzyme immobilization via various approaches, such as enzyme adsorption, covalent attachment, enzyme encapsulation, and sophisticated combinations of methods. This review discusses the stabilization mechanisms behind these diverse approaches; such as confinement, pore size and volume, charge interaction, hydrophobic interaction, and multipoint attachment. In addition, we will introduce recent rigorous approaches to improve the enzyme stability in these nanostructures or develop new nanostructures for the enzyme stabilization. Especially, we will introduce our recent invention of a nanostructure, called single enzyme nanoparticles (SENs). In the form of SENs, each enzyme molecule is surrounded with a nanometer scale network, resulting in stabilization of enzyme activity without any serious limitation for the substrate transfer from solution to the active site. SENs can be further immobilized into mesoporous silica with a large surface area, providing a hierarchical approach for stable, immobilized enzyme systems for various applications, such as bioconversion, bioremediation, and biosensors.

  10. Weak Convergence of a Mass-Structured Individual-Based Model

    SciTech Connect

    Campillo, Fabien; Fritsch, Coralie

    2015-08-15

    We propose a model of chemostat where the bacterial population is individually-based, each bacterium is explicitly represented and has a mass evolving continuously over time. The substrate concentration is represented as a conventional ordinary differential equation. These two components are coupled with the bacterial consumption. Mechanisms acting on the bacteria are explicitly described (growth, division and washout). Bacteria interact via consumption. We set the exact Monte Carlo simulation algorithm of this model and its mathematical representation as a stochastic process. We prove the convergence of this process to the solution of an integro-differential equation when the population size tends to infinity. Finally, we propose several numerical simulations.

  11. Evolved gas analysis of secondary organic aerosols

    SciTech Connect

    Grosjean, D.; Williams, E.L. II; Grosjean, E. ); Novakov, T. )

    1994-11-01

    Secondary organic aerosols have been characterized by evolved gas analysis (EGA). Hydrocarbons selected as aerosol precursors were representative of anthropogenic emissions (cyclohexene, cyclopentene, 1-decene and 1-dodecene, n-dodecane, o-xylene, and 1,3,5-trimethylbenzene) and of biogenic emissions (the terpenes [alpha]-pinene, [beta]-pinene and d-limonene and the sesquiterpene trans-caryophyllene). Also analyzed by EGA were samples of secondary, primary (highway tunnel), and ambient (urban) aerosols before and after exposure to ozone and other photochemical oxidants. The major features of the EGA thermograms (amount of CO[sub 2] evolved as a function of temperature) are described. The usefulness and limitations of EGA data for source apportionment of atmospheric particulate carbon are briefly discussed. 28 refs., 7 figs., 4 tabs.

  12. Traceless protein splicing utilizing evolved split inteins

    PubMed Central

    Lockless, Steve W.; Muir, Tom W.

    2009-01-01

    Split inteins are parasitic genetic elements frequently found inserted into reading frames of essential proteins. Their association and excision restore host protein function through a protein self-splicing reaction. They have gained an increasingly important role in the chemical modification of proteins to create cyclical, segmentally labeled, and fluorescently tagged proteins. Ideally, inteins would seamlessly splice polypeptides together with no remnant sequences and at high efficiency. Here, we describe experiments that identify the branched intermediate, a transient step in the overall splicing reaction, as a key determinant of the splicing efficiency at different splice-site junctions. To alter intein specificity, we developed a cell-based selection scheme to evolve split inteins that splice with high efficiency at different splice junctions and at higher temperatures. Mutations within these evolved inteins occur at sites distant from the active site. We present a hypothesis that a network of conserved coevolving amino acids in inteins mediates these long-range effects. PMID:19541616

  13. Convergent tapering of xylem conduits in different woody species.

    PubMed

    Anfodillo, Tommaso; Carraro, Vinicio; Carrer, Marco; Fior, Claudio; Rossi, Sergio

    2006-01-01

    A recent theoretical model (the West, Brown and Enquist, WBE model) hypothesized that plants have evolved a network of xylem conduits with a tapered structure (narrower conduits distally) which should minimize the cost of water transport from roots to leaves. Specific measurements are required to test the model predictions. We sampled both angiosperms and gymnosperms (50 trees) growing in different environments with heights ranging from 0.5 to 44.4 m, measuring variations of the xylem-conduit diameter from tree top to stem base. In all trees measured, mean hydraulically weighted conduit diameters (Dh) at the tree top were narrower than those at the stem base. In actively growing trees, the longitudinal variation of Dh showed a degree of tapering in agreement with WBE predictions, while trees close to their maximum height showed slightly lower conduit tapering. Comparing different species, a very good correlation was observed between degree of xylem tapering and tree height (r2 = 0.88; P < 0.0001) independently of any other variable (age, site, altitude, etc.). As predicted by WBE, sampled trees seemed to converge towards similar xylem conduit tapering. However, trees approaching their maximum height had a nonoptimal tapering which appeared insufficient to compensate for the progressive increase in tree height. PMID:16411931

  14. Convergent Evolution of Rumen Microbiomes in High-Altitude Mammals.

    PubMed

    Zhang, Zhigang; Xu, Dongming; Wang, Li; Hao, Junjun; Wang, Jinfeng; Zhou, Xin; Wang, Weiwei; Qiu, Qiang; Huang, Xiaodan; Zhou, Jianwei; Long, Ruijun; Zhao, Fangqing; Shi, Peng

    2016-07-25

    Studies of genetic adaptation, a central focus of evolutionary biology, most often focus on the host's genome and only rarely on its co-evolved microbiome. The Qinghai-Tibetan Plateau (QTP) offers one of the most extreme environments for the survival of human and other mammalian species. Yaks (Bos grunniens) and Tibetan sheep (T-sheep) (Ovis aries) have adaptations for living in this harsh high-altitude environment, where nomadic Tibetan people keep them primarily for food and livelihood [1]. Adaptive evolution affects energy-metabolism-related genes in a way that helps these ruminants live at high altitude [2, 3]. Herein, we report convergent evolution of rumen microbiomes for energy harvesting persistence in two typical high-altitude ruminants, yaks and T-sheep. Both ruminants yield significantly lower levels of methane and higher yields of volatile fatty acids (VFAs) than their low-altitude relatives, cattle (Bos taurus) and ordinary sheep (Ovis aries). Ultra-deep metagenomic sequencing reveals significant enrichment in VFA-yielding pathways of rumen microbial genes in high-altitude ruminants, whereas methanogenesis pathways show enrichment in the cattle metagenome. Analyses of RNA transcriptomes reveal significant upregulation in 36 genes associated with VFA transport and absorption in the ruminal epithelium of high-altitude ruminants. Our study provides novel insights into the contributions of microbiomes to adaptive evolution in mammals and sheds light on the biological control of greenhouse gas emissions from livestock enteric fermentation. PMID:27321997

  15. The Convergent Cancer Evolution toward a Single Cellular Destination.

    PubMed

    Chen, Han; He, Xionglei

    2016-01-01

    The essence of Darwin's theory is that evolution is driven by purposeless mutations that are subsequently selected by natural environments, so there is often no predefined destination in organismal evolution. Using gene expressions of 107 cell types, we built a functional space of human cells to trace the evolutionary trajectory of 18 types of solid tumor cancers. We detected a dominant evolving trend toward the functional status of embryonic stem cells (ESC) for approximately 3,000 tumors growing in distinct tissue environments. This pattern remained the same after excluding known cancer/ESC signature genes (∼ 3,000 genes) or excluding all oncogenic gene sets (∼ 12,000 genes) annotated in MSigDB, suggesting a convergent evolution of the overall functional status in cancers. In support of this, the functional distance to ESC served as a common prognostic indicator for cancers of various types, with shorter distance corresponding to poor prognosis, which was true even when randomly selected gene sets were considered. Thus, regardless of the external environments, cancer evolution is a directional process toward a defined cellular destination, a finding reconciling development and evolution, the two seemingly incompatible philosophies both adopted by the cancer research community, and also raising new questions to evolutionary biology. PMID:26464125

  16. The evolving epidemiology of stone disease.

    PubMed

    Roudakova, Ksenia; Monga, Manoj

    2014-01-01

    The epidemiology of kidney stones is evolving - not only is the prevalence increasing, but also the gender gap has narrowed. What drives these changes? Diet, obesity or environmental factors? This article will review the possible explanations for a shift in the epidemiology, with the hope of gaining a better understanding of the extent to which modifiable risk factors play a role on stone formation and what measures may be undertaken for disease prevention in view of these changing trends. PMID:24497682

  17. Nursing administration research: an evolving science.

    PubMed

    Murphy, Lyn Stankiewicz; Scott, Elaine S; Warshawsky, Nora E

    2014-12-01

    The nature and focus of nursing administrative research have evolved over time. Recently, the research agenda has primarily reflected the national health policy agenda. Although nursing research has traditionally been dominated by clinical interests, nursing administrative research has historically addressed the interface of reimbursement, quality, and care delivery systems. This article traces the evolution of nursing administrative research to answer questions relevant to scope, practice, and policy and suggests future directions. PMID:25393136

  18. Quantum games on evolving random networks

    NASA Astrophysics Data System (ADS)

    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.

  19. Chemical evolution of viscously evolving galactic discs

    NASA Technical Reports Server (NTRS)

    Clarke, Catherine J.

    1989-01-01

    The ability of the Lin-Pringle (1987) model of galactic disk formation to reproduce the observed radial distributions of total gas surface density and metals in disk galaxies is investigated. It is found that a satisfactory fit is obtained provided that there exists an outer cut-off to the star-forming disk beyond which gas is allowed to viscously evolve. The metallicity gradient is then established by radial inflow of gas from beyond this cut-off.

  20. Convergence of Newton's method for a single real equation

    NASA Technical Reports Server (NTRS)

    Campbell, C. W.

    1985-01-01

    Newton's method for finding the zeroes of a single real function is investigated in some detail. Convergence is generally checked using the Contraction Mapping Theorem which yields sufficient but not necessary conditions for convergence of the general single point iteration method. The resulting convergence intervals are frequently considerably smaller than actual convergence zones. For a specific single point iteration method, such as Newton's method, better estimates of regions of convergence should be possible. A technique is described which, under certain conditions (frequently satisfied by well behaved functions) gives much larger zones where convergence is guaranteed.

  1. On domains of convergence in optimization problems

    NASA Technical Reports Server (NTRS)

    Diaz, Alejandro R.; Shaw, Steven S.; Pan, Jian

    1990-01-01

    Numerical optimization algorithms require the knowledge of an initial set of design variables. Starting from an initial design x(sup 0), improved solutions are obtained by updating the design iteratively in a way prescribed by the particular algorithm used. If the algorithm is successful, convergence is achieved to a local optimal solution. Let A denote the iterative procedure that characterizes a typical optimization algorithm, applied to the problem: Find x belonging to R(sup n) that maximizes f(x) subject to x belonging to Omega contained in R(sup n). We are interested in problems with several local maxima (x(sub j))(sup *), j=1, ..., m, in the feasible design space Omega. In general, convergence of the algorithm A to a specific solution (x(sub j))(sup *) is determined by the choice of initial design x(sup 0). The domain of convergence D(sub j) of A associated with a local maximum (x(sub j))(sup *) is a subset of initial designs x(sup 0) in Omega such that the sequence (x(sup k)), k=0,1,2,... defined by x(sup k+1) = A(x(sup k)), k=0,1,... converges to (x(sub j))(sup *). The set D(sub j) is also called the basin of attraction of (x(sub j))(sup *). Cayley first proposed the problem of finding the basin of attraction for Newton's method in 1897. It has been shown that the basin of attraction for Newton's method exhibits chaotic behavior in problems with polynomial objective. This implies that there may be regions in the feasible design space where arbitrarily close starting points will converge to different local optimal solutions. Furthermore, the boundaries of the domains of convergence may have a very complex, even fractal structure. In this paper we show that even simple structural optimization problems solved using standard gradient based (first order) algorithms exhibit similar features.

  2. Continuous evaluation of evolving behavioral intervention technologies.

    PubMed

    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. PMID:24050429

  3. Continuous Evaluation of Evolving Behavioral Intervention Technologies

    PubMed Central

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

    2013-01-01

    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. PMID:24050429

  4. Sustained gastrointestinal activity of dendronized polymer-enzyme conjugates

    NASA Astrophysics Data System (ADS)

    Fuhrmann, Gregor; Grotzky, Andrea; Lukić, Ružica; Matoori, Simon; Luciani, Paola; Yu, Hao; Zhang, Baozhong; Walde, Peter; Schlüter, A. Dieter; Gauthier, Marc A.; Leroux, Jean-Christophe

    2013-07-01

    Methods to stabilize and retain enzyme activity in the gastrointestinal tract are investigated rarely because of the difficulty of protecting proteins from an environment that has evolved to promote their digestion. Preventing the degradation of enzymes under these conditions, however, is critical for the development of new protein-based oral therapies. Here we show that covalent conjugation to polymers can stabilize orally administered therapeutic enzymes at different locations in the gastrointestinal tract. Architecturally and functionally diverse polymers are used to protect enzymes sterically from inactivation and to promote interactions with mucin on the stomach wall. Using this approach the in vivo activity of enzymes can be sustained for several hours in the stomach and/or in the small intestine. These findings provide new insight and a firm basis for the development of new therapeutic and imaging strategies based on orally administered proteins using a simple and accessible technology.

  5. A Comparative Mechanical Analysis of Plant and Animal Cells Reveals Convergence across Kingdoms

    PubMed Central

    Durand-Smet, Pauline; Chastrette, Nicolas; Guiroy, Axel; Richert, Alain; Berne-Dedieu, Annick; Szecsi, Judit; Boudaoud, Arezki; Frachisse, Jean-Marie; Bendhamane, Mohammed; Hamant, Oliver; Asnacios, Atef

    2014-01-01

    Plant and animals have evolved different strategies for their development. Whether this is linked to major differences in their cell mechanics remains unclear, mainly because measurements on plant and animal cells relied on independent experiments and setups, thus hindering any direct comparison. In this study we used the same micro-rheometer to compare animal and plant single cell rheology. We found that wall-less plant cells exhibit the same weak power law rheology as animal cells, with comparable values of elastic and loss moduli. Remarkably, microtubules primarily contributed to the rheological behavior of wall-less plant cells whereas rheology of animal cells was mainly dependent on the actin network. Thus, plant and animal cells evolved different molecular strategies to reach a comparable cytoplasmic mechanical core, suggesting that evolutionary convergence could include the internal biophysical properties of cells. PMID:25418292

  6. Evolutionary view of acyl-CoA diacylglycerol acyltransferase (DGAT), a key enzyme in neutral lipid biosynthesis

    PubMed Central

    2011-01-01

    . Overall, the data show that DGAT1 and DGAT2 are present in most eukaryotic organisms and belong to two different gene families. The phylogenetic and evolutionary analyses revealed that DGAT1 and DGAT2 evolved separately, with functional convergence, despite their wide molecular and structural divergence. PMID:21933415

  7. Genome-level and biochemical diversity of the acyl-activating enzyme superfamily in plants

    Technology Transfer Automated Retrieval System (TEKTRAN)

    In higher plants, the superfamily of carboxyl-CoA ligases and related proteins, collectively called acyl activating enzymes (AAEs), has evolved to provide enzymes for many pathways of primary and secondary metabolism and for the conjugation of hormones to amino acids. Across the superfamily there is...

  8. Non-surgical interventions for convergence insufficiency

    PubMed Central

    Scheiman, Mitchell; Gwiazda, Jane; Li, Tianjing

    2014-01-01

    Background Convergence insufficiency is a common eye muscle co-ordination problem in which the eyes have a strong tendency to drift outward (exophoria) when reading or doing close work. Symptoms may include eye strain, headaches, double vision, print moving on the page, frequent loss of place when reading, inability to concentrate, and short attention span. Objectives To systematically assess and synthesize evidence from randomized controlled trials (RCTs) on the effectiveness of non-surgical interventions for convergence insufficiency. Search strategy We searched The Cochrane Library, MEDLINE, EMBASE, Science Citation Index, the metaRegister of Controlled Trials (mRCT) (www.controlled-trials.com) and ClinicalTrials.gov (www.clinicaltrials.gov) on 7 October 2010. We manually searched reference lists and optometric journals. Selection criteria We included RCTs examining any form of non-surgical intervention against placebo, no treatment, sham treatment, or each other. Data collection and analysis Two authors independently assessed eligibility, risk of bias, and extracted data. We performed meta-analyses when appropriate. Main results We included six trials (three in children, three in adults) with a total of 475 participants. We graded four trials at low risk of bias. Evidence from one trial (graded at low risk of bias) suggests that base-in prism reading glasses was no more effective than placebo reading glasses in improving clinical signs or symptoms in children. Evidence from one trial (graded at high risk of bias) suggests that base-in prism glasses using a progressive addition lens design was more effective than progressive addition lens alone in decreasing symptoms in adults. At three weeks of therapy, the mean difference in Convergence Insufficiency Symptoms Survey (CISS) score was −10.24 points (95% confidence interval (CI) −15.45 to −5.03). Evidence from two trials (graded at low risk of bias) suggests that outpatient (or office-based as used in the

  9. Stability of spherical converging shock wave

    SciTech Connect

    Murakami, M.; Sanz, J.; Iwamoto, Y.

    2015-07-15

    Based on Guderley's self-similar solution, stability of spherical converging shock wave is studied. A rigorous linear perturbation theory is developed, in which the growth rate of perturbation is given as a function of the spherical harmonic number ℓ and the specific heats ratio γ. Numerical calculation reveals the existence of a γ-dependent cut-off mode number ℓ{sub c}, such that all the eigenmode perturbations for ℓ > ℓ{sub c} are smeared out as the shock wave converges at the center. The analysis is applied to partially spherical geometries to give significant implication for different ignition schemes of inertial confinement fusion. Two-dimensional hydrodynamic simulations are performed to verify the theory.

  10. Molecular mechanisms involved in convergent crop domestication.

    PubMed

    Lenser, Teresa; Theißen, Günter

    2013-12-01

    Domestication has helped to understand evolution. We argue that, vice versa, novel insights into evolutionary principles could provide deeper insights into domestication. Molecular analyses have demonstrated that convergent phenotypic evolution is often based on molecular changes in orthologous genes or pathways. Recent studies have revealed that during plant domestication the causal mutations for convergent changes in key traits are likely to be located in particular genes. These insights may contribute to defining candidate genes for genetic improvement during the domestication of new plant species. Such efforts may help to increase the range of arable crops available, thus increasing crop biodiversity and food security to help meet the predicted demands of the continually growing global population under rapidly changing environmental conditions. PMID:24035234

  11. Technologies for convergence in the metro network

    NASA Astrophysics Data System (ADS)

    Frankel, Michael Y.

    2005-02-01

    Traditional metro network architectures comprise multiple layers of networking equipment supporting a wide array of services and packet-oriented applications. Among others, these include WDM, SDH, ATM, Ethernet and IP, each requiring its own network elements and associated management solutions to perform its own independent networking functions. While these work well individually, the combined network is cumbersome and inefficient. Recent advancements in network technologies are now changing the way metro networks are designed. Multi-functional consolidation through technology integration and the standardization of protocol inter-networking methods are leading to a converged network solution in support of a diverse set of packet-aware service offerings. This presentation will explore new technologies that are enabling convergence in the metro network, both across layers and across services.

  12. Convergent strand array liquid pumping system

    NASA Technical Reports Server (NTRS)

    Collins, Earl R., Jr. (Inventor)

    1989-01-01

    A surface-tension liquid pumping system is provided by one or more arrays of converging solid monofilament fibers or metal wires (strands) spaced apart at an input end to gather liquid, and gathered close together at the opposite end where menisci forms between wetted strands to force liquid in the direction of convergence of the strands. The liquid pumping system is independent of gravity. It is illustrated as being used in a heat pump having a heating box to vaporize the liquid and a condensing chamber. Condensed liquid is returned by the pumping system to the heating box where it is again vaporized. A vapor tube carries the vapor to the condensing chamber. In that way, a closed system pumps heat from the heating box to the evaporating chamber and from there radiated to the atmosphere.

  13. Antibiotics From Microbes: Converging To Kill

    PubMed Central

    Fischbach, Michael A.

    2011-01-01

    Summary As genetically encoded small molecules, antibiotics are phenotypes that have resulted from mutation and natural selection. Advances in genetics, biochemistry, and bioinformatics have connected hundreds of antibiotics to the gene clusters that encode them, allowing these molecules to be analyzed using the tools of evolutionary biology. This review surveys examples of convergent evolution from microbially produced antibiotics, including the convergence of distinct gene clusters on similar phenotypes and the merger of distinct gene clusters into a single functional unit. Examining antibiotics through an evolutionary lens highlights the versatility of biosynthetic pathways, reveals lessons for combating antibiotic resistance, and provides an entry point for studying the natural roles of these natural products. PMID:19695947

  14. The genetic causes of convergent evolution.

    PubMed

    Stern, David L

    2013-11-01

    The evolution of phenotypic similarities between species, known as convergence, illustrates that populations can respond predictably to ecological challenges. Convergence often results from similar genetic changes, which can emerge in two ways: the evolution of similar or identical mutations in independent lineages, which is termed parallel evolution; and the evolution in independent lineages of alleles that are shared among populations, which I call collateral genetic evolution. Evidence for parallel and collateral evolution has been found in many taxa, and an emerging hypothesis is that they result from the fact that mutations in some genetic targets minimize pleiotropic effects while simultaneously maximizing adaptation. If this proves correct, then the molecular changes underlying adaptation might be more predictable than has been appreciated previously. PMID:24105273

  15. Stability of spherical converging shock wave

    NASA Astrophysics Data System (ADS)

    Murakami, M.; Sanz, J.; Iwamoto, Y.

    2015-07-01

    Based on Guderley's self-similar solution, stability of spherical converging shock wave is studied. A rigorous linear perturbation theory is developed, in which the growth rate of perturbation is given as a function of the spherical harmonic number ℓ and the specific heats ratio γ. Numerical calculation reveals the existence of a γ-dependent cut-off mode number ℓc, such that all the eigenmode perturbations for ℓ > ℓc are smeared out as the shock wave converges at the center. The analysis is applied to partially spherical geometries to give significant implication for different ignition schemes of inertial confinement fusion. Two-dimensional hydrodynamic simulations are performed to verify the theory.

  16. The enzymes of bacterial census and censorship.

    PubMed

    Fast, Walter; Tipton, Peter A

    2012-01-01

    N-Acyl-L-homoserine lactones (AHLs) are a major class of quorum-sensing signals used by Gram-negative bacteria to regulate gene expression in a population-dependent manner, thereby enabling group behavior. Enzymes capable of generating and catabolizing AHL signals are of significant interest for the study of microbial ecology and quorum-sensing pathways, for understanding the systems that bacteria have evolved to interact with small-molecule signals, and for their possible use in therapeutic and industrial applications. The recent structural and functional studies reviewed here provide a detailed insight into the chemistry and enzymology of bacterial communication. PMID:22099187

  17. Arieti and Bowlby: convergence and direct influence.

    PubMed

    Bacciagaluppi, Marco

    2015-09-01

    Arieti was a great specialist of schizophrenia and Bowlby was the initiator of attachment theory. Working independently on the two sides of the Atlantic, they converged on a range of topics, such as evolutionary theory, mourning, trauma, violence, and therapy as art and science. Later, Bowlby exerted a direct influence on Arieti, which Arieti acknowledged in his Love Can Be Found. Finally, the two authors cooperated in the second edition of the American Handbook of Psychiatry. PMID:26356777

  18. Guaranteed convergence of the Hough transform

    NASA Astrophysics Data System (ADS)

    Soffer, Menashe; Kiryati, Nahum

    1995-01-01

    The straight-line Hough Transform using normal parameterization with a continuous voting kernel is considered. It transforms the colinearity detection problem to a problem of finding the global maximum of a two dimensional function above a domain in the parameter space. The principle is similar to robust regression using fixed scale M-estimation. Unlike standard M-estimation procedures the Hough Transform does not rely on a good initial estimate of the line parameters: The global optimization problem is approached by exhaustive search on a grid that is usually as fine as computationally feasible. The global maximum of a general function above a bounded domain cannot be found by a finite number of function evaluations. Only if sufficient a-priori knowledge about the smoothness of the objective function is available, convergence to the global maximum can be guaranteed. The extraction of a-priori information and its efficient use are the main challenges in real global optimization problems. The global optimization problem in the Hough Transform is essentially how fine should the parameter space quantization be in order not to miss the true maximum. More than thirty years after Hough patented the basic algorithm, the problem is still essentially open. In this paper an attempt is made to identify a-priori information on the smoothness of the objective (Hough) function and to introduce sufficient conditions for the convergence of the Hough Transform to the global maximum. An image model with several application dependent parameters is defined. Edge point location errors as well as background noise are accounted for. Minimal parameter space quantization intervals that guarantee convergence are obtained. Focusing policies for multi-resolution Hough algorithms are developed. Theoretical support for bottom- up processing is provided. Due to the randomness of errors and noise, convergence guarantees are probabilistic.

  19. Convergence acceleration of viscous flow computations

    NASA Technical Reports Server (NTRS)

    Johnson, G. M.

    1982-01-01

    A multiple-grid convergence acceleration technique introduced for application to the solution of the Euler equations by means of Lax-Wendroff algorithms is extended to treat compressible viscous flow. Computational results are presented for the solution of the thin-layer version of the Navier-Stokes equations using the explicit MacCormack algorithm, accelerated by a convective coarse-grid scheme. Extensions and generalizations are mentioned.

  20. Design Calculations For NIF Convergent Ablator Experiments

    SciTech Connect

    Olson, R E; Hicks, D G; Meezan, N B; Callahan, D A; Landen, O L; Jones, O S; Langer, S H; Kline, J L; Wilson, D C; Rinderknecht, H; Zylstra, A; Petrasso, R D

    2011-10-25

    The NIF convergent ablation tuning effort is underway. In the early experiments, we have discovered that the design code simulations over-predict the capsule implosion velocity and shock flash rhor, but under-predict the hohlraum x-ray flux measurements. The apparent inconsistency between the x-ray flux and radiography data implies that there are important unexplained aspects of the hohlraum and/or capsule behavior.

  1. Sequences of Rational Numbers Converging to Surds

    ERIC Educational Resources Information Center

    Fletcher, Rodney

    2010-01-01

    In this sequence 1/1, 7/5, 41/29, 239/169 and so on, Thomas notes that the sequence converges to square root of 2. By observation, the sequence of numbers in the numerator of the above sequence, have a pattern of generation which is the same as that in the denominator. That is, the next term is found by multiplying the previous term by six and…

  2. What contribution can international relations make to the evolving global health agenda?

    PubMed

    Davies, Sara E

    2010-01-01

    This article presents two approaches that have dominated International Relations in their approach to the international politics of health. The statist approach, which is primarily security-focused, seeks to link health initiatives to a foreign or defence policy remit. The globalist approach, in contrast, seeks to advance health not because of its intrinsic security value but because it advances the well-being and rights of individuals. This article charts the evolution of these approaches and demonstrates why both have the potential to shape our understanding of the evolving global health agenda. It examines how the statist and globalist perspectives have helped shape contemporary initiatives in global health governance and suggests that there is evidence of an emerging convergence between the two perspectives. This convergence is particularly clear in the articulation of a number of UN initiatives in this area - especially the One World, One Health Strategic Framework and the Oslo Ministerial Declaration (2007) which inspired the first UN General Assembly resolution on global health and foreign policy in 2009 and the UN Secretary-General's note "Global health and foreign policy: strategic opportunities and challenges". What remains to be seen is whether this convergence will deliver on securing states' interest long enough to promote the interests of the individuals who require global efforts to deliver local health improvements. PMID:20882709

  3. Convergent Coarseness Regulation for Segmented Images

    SciTech Connect

    Paglieroni, D W

    2004-05-27

    In segmentation of remotely sensed images, the number of pixel classes and their spectral representations are often unknown a priori. Even with prior knowledge, pixels with spectral components from multiple classes lead to classification errors and undesired small region artifacts. Coarseness regulation for segmented images is proposed as an efficient novel technique for handling these problems. Beginning with an over-segmented image, perceptually similar connected regions are iteratively merged using a method reminiscent of region growing, except the primitives are regions, not pixels. Interactive coarseness regulation is achieved by specifying the area {alpha} of the largest region eligible for merging. A region with area less than {alpha} is merged with the most spectrally similar connected region, unless the regions are perceived as spectrally dissimilar. In convergent coarseness regulation, which requires no user interaction, {alpha} is specified as the total number of pixels in the image, and the coarseness regulation output converges to a steady-state segmentation that remains unchanged as {alpha} is further increased. By applying convergent coarseness regulation to AVIRIS, IKONOS and DigitalGlobe images, and quantitatively comparing computer-generated segmentations to segmentations generated manually by a human analyst, it was found that the quality of the input segmentations was consistently and dramatically improved.

  4. Analysis of Long-Term Anisotropic Convergence in Drifts Excavated in Callovo-Oxfordian Claystone

    NASA Astrophysics Data System (ADS)

    Guayacán-Carrillo, Lina-María; Sulem, Jean; Seyedi, Darius M.; Ghabezloo, Siavash; Noiret, Aurélien; Armand, Gilles

    2016-01-01

    The main purpose of this paper is to analyze the convergence measurements in drifts of the Underground Research Laboratory (URL) of the French National Radioactive Waste Management Agency (Andra), excavated in Callovo-Oxfordian claystone. These measurements show an anisotropic closure, which depends on the drift orientations with respect to the horizontal in situ stresses. This anisotropic character of the deformation is taken into account by assuming that the drifts section evolves following an elliptical shape. The characteristics of the deformed elliptical section are evaluated following the methodology proposed by Vu et al. (Rock Mech Rock Eng 46:231-246, 2013). Then, using the semi-empirical law proposed by Sulem et al. (Int J Rock Mech Min Sci Geomech Abstr 24:145-154, 1987), the convergence evolution is fitted independently for each axis of the ellipse. This method allows to distinguish two effects: the face advance and the time-dependent behavior of the ground. The results for the two drift orientations (along the major horizontal stress and perpendicular to it) show very close values for the parameters describing the time-dependent properties of the ground, the distance of influence of the face, and the extent of the decompressed zone around the drift. Finally, the model is validated by keeping these parameters as constants and by simulating the convergence data on a new drift. It is shown that with a period of about 40 days of convergence monitoring, the model can provide valuable insights for predictions of the convergence evolution in the long term.

  5. On lacunary statistical convergence of order α in probability

    NASA Astrophysics Data System (ADS)

    Işık, Mahmut; Et, Kübra Elif

    2015-09-01

    In this study, we examine the concepts of lacunary statistical convergence of order α in probability and Nθ—convergence of order α in probability. We give some relations connected to these concepts.

  6. Convergence: Human Intelligence The Next 100 Years

    ERIC Educational Resources Information Center

    Fluellen, Jerry E., Jr.

    2005-01-01

    How might human intelligence evolve over the next 100 years? This issue paper explores that idea. First, the paper summarizes five emerging perspectives about human intelligence: Howard Gardner's multiple intelligences theory, Robert Sternberg's triarchic theory of intelligence, Ellen Langer's mindfulness theory, David Perkins' learnable…

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

    NASA Astrophysics Data System (ADS)

    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.

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

    PubMed

    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. PMID:26419865

  9. Enzyme nanoband electrodes

    SciTech Connect

    Wang, J.; Naser, N. ); Renschler, C.L. )

    1993-07-01

    Enzyme nanoelectrodes have been constructed by immobilizing glucose oxidase, alcohol oxidase or tyrosinase onto ultrathin carbon films (of 35-50 nm thickness). The enzyme immobilization is accomplished via entrapment within electropolymerized poly(o-phenylenediamine) coatings. Cyclic voltammetry and controlled-potential amperometry are used to characterize the performance of the new nanoscopic biosensors under different preparation and operation conditions. The resulting electrodes offer convenient and rapid measurements of millimolar substrate concentrations, and (to the best of the authors' knowledge) are the smallest enzyme probes reported to date. 10 refs., 7 figs.

  10. Survivability Is More Fundamental Than Evolvability

    PubMed Central

    Palmer, Michael E.; Feldman, Marcus W.

    2012-01-01

    For a lineage to survive over long time periods, it must sometimes change. This has given rise to the term evolvability, meaning the tendency to produce adaptive variation. One lineage may be superior to another in terms of its current standing variation, or it may tend to produce more adaptive variation. However, evolutionary outcomes depend on more than standing variation and produced adaptive variation: deleterious variation also matters. Evolvability, as most commonly interpreted, is not predictive of evolutionary outcomes. Here, we define a predictive measure of the evolutionary success of a lineage that we call the k-survivability, defined as the probability that the lineage avoids extinction for k generations. We estimate the k-survivability using multiple experimental replicates. Because we measure evolutionary outcomes, the initial standing variation, the full spectrum of generated variation, and the heritability of that variation are all incorporated. Survivability also accounts for the decreased joint likelihood of extinction of sub-lineages when they 1) disperse in space, or 2) diversify in lifestyle. We illustrate measurement of survivability with in silico models, and suggest that it may also be measured in vivo using multiple longitudinal replicates. The k-survivability is a metric that enables the quantitative study of, for example, the evolution of 1) mutation rates, 2) dispersal mechanisms, 3) the genotype-phenotype map, and 4) sexual reproduction, in temporally and spatially fluctuating environments. Although these disparate phenomena evolve by well-understood microevolutionary rules, they are also subject to the macroevolutionary constraint of long-term survivability. PMID:22723844

  11. Production and decay of evolving horizons

    NASA Astrophysics Data System (ADS)

    Nielsen, Alex B.; Visser, Matt

    2006-07-01

    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 spacetime foliations (and hence the horizons) are always spherically symmetric. (2) Furthermore, we adopt Painlevé Gullstrand coordinates (which are well suited to the problem because they are nonsingular at the horizon) in order to simplify the relevant calculations. Of course physics results are ultimately independent of the choice of coordinates, but this particular coordinate system yields a clean physical interpretation of the relevant physics. We find particularly simple forms for surface gravity, and for the first and second law of black hole thermodynamics, in this general evolving horizon situation. Furthermore, we relate our results to Hawking's apparent horizon, Ashtekar and co-worker's isolated and dynamical horizons, and Hayward's trapping horizon. The evolving black hole model discussed here will be of interest, both from an astrophysical viewpoint in terms of discussing growing black holes and from a purely theoretical viewpoint in discussing black hole evaporation via Hawking radiation.

  12. Identification and characterization of D-hydroxyproline dehydrogenase and Delta1-pyrroline-4-hydroxy-2-carboxylate deaminase involved in novel L-hydroxyproline metabolism of bacteria: metabolic convergent evolution.

    PubMed

    Watanabe, Seiya; Morimoto, Daichi; Fukumori, Fumiyasu; Shinomiya, Hiroto; Nishiwaki, Hisashi; Kawano-Kawada, Miyuki; Sasai, Yuuki; Tozawa, Yuzuru; Watanabe, Yasuo

    2012-09-21

    L-hydroxyproline (4-hydroxyproline) mainly exists in collagen, and most bacteria cannot metabolize this hydroxyamino acid. Pseudomonas putida and Pseudomonas aeruginosa convert L-hydroxyproline to α-ketoglutarate via four hypothetical enzymatic steps different from known mammalian pathways, but the molecular background is rather unclear. Here, we identified and characterized for the first time two novel enzymes, D-hydroxyproline dehydrogenase and Δ(1)-pyrroline-4-hydroxy-2-carboxylate (Pyr4H2C) deaminase, involved in this hypothetical pathway. These genes were clustered together with genes encoding other catalytic enzymes on the bacterial genomes. D-hydroxyproline dehydrogenases from P. putida and P. aeruginosa were completely different from known bacterial proline dehydrogenases and showed similar high specificity for substrate (D-hydroxyproline) and some artificial electron acceptor(s). On the other hand, the former is a homomeric enzyme only containing FAD as a prosthetic group, whereas the latter is a novel heterododecameric structure consisting of three different subunits (α(4)β(4)γ(4)), and two FADs, FMN, and [2Fe-2S] iron-sulfur cluster were contained in αβγ of the heterotrimeric unit. These results suggested that the L-hydroxyproline pathway clearly evolved convergently in P. putida and P. aeruginosa. Pyr4H2C deaminase is a unique member of the dihydrodipicolinate synthase/N-acetylneuraminate lyase protein family, and its activity was competitively inhibited by pyruvate, a common substrate for other dihydrodipicolinate synthase/N-acetylneuraminate lyase proteins. Furthermore, disruption of Pyr4H2C deaminase genes led to loss of growth on L-hydroxyproline (as well as D-hydroxyproline) but not L- and D-proline, indicating that this pathway is related only to L-hydroxyproline degradation, which is not linked to proline metabolism. PMID:22833679

  13. Evolvable circuit with transistor-level reconfigurability

    NASA Technical Reports Server (NTRS)

    Stoica, Adrian (Inventor); Salazar-Lazaro, Carlos Harold (Inventor)

    2004-01-01

    An evolvable circuit includes a plurality of reconfigurable switches, a plurality of transistors within a region of the circuit, the plurality of transistors having terminals, the plurality of transistors being coupled between a power source terminal and a power sink terminal so as to be capable of admitting power between the power source terminal and the power sink terminal, the plurality of transistors being coupled so that every transistor terminal to transistor terminal coupling within the region of the circuit comprises a reconfigurable switch.

  14. Earth As an Evolving Planetary System

    NASA Astrophysics Data System (ADS)

    Meert, Joseph G.

    2005-05-01

    ``System'' is an overused buzzword in textbooks covering geological sciences. Describing the Earth as a system of component parts is a reasonable concept, but providing a comprehensive framework for detailing the system is a more formidable task. Kent Condie lays out the systems approach in an easy-to-read introductory chapter in Earth as an Evolving Planetary System. In the book, Condie makes a valiant attempt at taking the mélange of diverse subjects in the solid Earth sciences and weaving them into a coherent tapestry.

  15. Mobile computing acceptance grows as applications evolve.

    PubMed

    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. PMID:11806321

  16. Evolving Black Holes with Wavy Initial Data

    NASA Astrophysics Data System (ADS)

    Kelly, Bernard; Tichy, Wolfgang; Zlochower, Yosef; Campanelli, Manuela; Whiting, Bernard

    2009-05-01

    In Kelly et al. [Phys. Rev. D v. 76, 024008 (2007)], we presented new binary black-hole initial data adapted to puncture evolutions in numerical relativity. This data satisfies the constraint equations to 2.5 post-Newtonian order, and contains a transverse-traceless ``wavy'' metric contribution, violating the standard assumption of conformal flatness. We report on progress in evolving this data with a modern moving-puncture implementation of the BSSN equations in several numerical codes. We will discuss the effect of the new metric terms on junk radiation and continuity of physical radiation extracted.

  17. Present weather and climate: evolving conditions

    USGS Publications Warehouse

    Hoerling, Martin P; Dettinger, Michael; Wolter, Klaus; Lukas, Jeff; Eischeid, Jon K.; Nemani, Rama; Liebmann, Brant; Kunkel, Kenneth E.

    2013-01-01

    This chapter assesses weather and climate variability and trends in the Southwest, using observed climate and paleoclimate records. It analyzes the last 100 years of climate variability in comparison to the last 1,000 years, and links the important features of evolving climate conditions to river flow variability in four of the region’s major drainage basins. The chapter closes with an assessment of the monitoring and scientific research needed to increase confidence in understanding when climate episodes, events, and phenomena are attributable to human-caused climate change.

  18. Evolving techniques for gastrointestinal endoscopic hemostasis treatment.

    PubMed

    Ghassemi, Kevin A; Jensen, Dennis M

    2016-05-01

    With mortality due to gastrointestinal (GI) bleeding remaining stable, the focus on endoscopic hemostasis has been on improving other outcomes such as rebleeding rate, need for transfusions, and need for angiographic embolization or surgery. Over the past few years, a number of devices have emerged to help endoscopically assess and treat bleeding GI lesions. These include the Doppler endoscopic probe, hemostatic powder, and over-the-scope clip. Also, new applications have been described for radiofrequency ablation. In this article, we will discuss these evolving tools and techniques that have been developed, including an analysis of their efficacy and limitations. PMID:26651414

  19. Scar State on Time-evolving Wavepacket

    NASA Astrophysics Data System (ADS)

    Tomiya, Mitsuyoshi; Tsuyuki, Hiroyoshi; Kawamura, Kentaro; Sakamoto, Shoichi; Heller, Eric J.

    2015-09-01

    The scar-like enhancement is found in the accumulation of the time-evolving wavepacket in stadium billiard. It appears close to unstable periodic orbits, when the wavepackets are launched along the orbits. The enhancement is essentially due to the same mechanism of the well-known scar states in stationary eigenstates. The weighted spectral function reveals that the enhancement is the pileup of contributions from scar states on the same periodic orbit. The availavility of the weighted spectrum to the semiclassical approximation is also disscussed.

  20. Independent molecular basis of convergent highland adaptation in maize

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Convergent evolution is the independent evolution of similar traits in different species or lineages of the same species; this often is a result of adaptation to similar environments, a process referred to as convergent adaptation. We investigate here the molecular basis of convergent adaptation in ...

  1. Convergent and Divergent Thinking in the Context of Narrative Mysteries

    ERIC Educational Resources Information Center

    Wenzel, William G.; Gerrig, Richard J.

    2015-01-01

    This project demonstrates how narrative mysteries provide a context in which readers engage in creative cognition. Drawing on the concepts of convergent and divergent thinking, we wrote stories that had either convergent or divergent outcomes. For example, one story had a character give his girlfriend a ring (a convergent outcome), whereas the…

  2. Halophilic enzyme activation induced by salts

    PubMed Central

    Ortega, Gabriel; Laín, Ana; Tadeo, Xavier; López-Méndez, Blanca; Castaño, David; Millet, Oscar

    2011-01-01

    Halophilic archea (halobacteriae) thrive in hypersaline environments, avoiding osmotic shock by increasing the ion concentration of their cytoplasm by up to 3–6 M. To remain folded and active, their constitutive proteins have evolved towards a biased amino acid composition. High salt concentration affects catalytic activity in an enzyme-dependent way and a unified molecular mechanism remains elusive. Here, we have investigated a DNA ligase from Haloferax volcanii (Hv LigN) to show that K+ triggers catalytic activity by preferentially stabilising a specific conformation in the reaction coordinate. Sodium ions, in turn, do not populate such isoform and the enzyme remains inactive in the presence of this co-solute. Our results show that the halophilic amino acid signature enhances the enzyme's thermodynamic stability, with an indirect effect on its catalytic activity. This model has been successfully applied to reengineer Hv LigN into an enzyme that is catalytically active in the presence of NaCl. PMID:22355525

  3. Epistatic interactions between ancestral genotype and beneficial mutations shape evolvability in Pseudomonas aeruginosa.

    PubMed

    Gifford, Danna R; Toll-Riera, Macarena; MacLean, R Craig

    2016-07-01

    The idea that interactions between mutations influence adaptation by driving populations to low and high fitness peaks on adaptive landscapes is deeply ingrained in evolutionary theory. Here, we investigate the impact of epistasis on evolvability by challenging populations of two Pseudomonas aeruginosa clones bearing different initial mutations (in rpoB conferring rifampicin resistance, and the type IV pili gene network) to adaptation to a medium containing l-serine as the sole carbon source. Despite being initially indistinguishable in fitness, populations founded by the two ancestral genotypes reached different fitness following 300 generations of evolution. Genome sequencing revealed that the difference could not be explained by acquiring mutations in different targets of selection; the majority of clones from both ancestors converged on one of the following two strategies: (1) acquiring mutations in either PA2449 (gcsR, an l-serine-metabolism RpoN enhancer binding protein) or (2) protease genes. Additionally, populations from both ancestors converged on loss-of-function mutations in the type IV pili gene network, either due to ancestral or acquired mutations. No compensatory or reversion mutations were observed in RNA polymerase (RNAP) genes, in spite of the large fitness costs typically associated with mutations in rpoB. Although current theory points to sign epistasis as the dominant constraint on evolvability, these results suggest that the role of magnitude epistasis in constraining evolvability may be underappreciated. The contribution of magnitude epistasis is likely to be greatest under the biologically relevant mutation supply rates that make back mutations probabilistically unlikely. PMID:27230588

  4. 2008 GRC Iron Sulfur Enzymes-Conference to be held June 8-13, 2008

    SciTech Connect

    Stephen Cramer, Nancy Ryan Gray

    2009-01-01

    Iron-sulfur proteins are among the most common and ancient enzymes and electron-transfer agents in nature. They play key roles in photosynthesis, respiration, and the metabolism of small molecules such as H2, CO, and N2. The Iron Sulfur Enzyme Gordon Research Conference evolved from an earlier GRC on Nitrogen Fixation that began in 1994. The scope of the current meeting has broadened to include all enzymes or metalloproteins in which Fe-S bonds play a key role. This year's meeting will focus on the biosynthesis of Fe-S clusters, as well as the structure and mechanism of key Fe-S enzymes such as hydrogenase, nitrogenase and its homologues, radical SAM enzymes, and aconitase-related enzymes. Recent progress on the role of Fe-S enzymes in health, disease, DNA/RNA-processing, and alternative bio-energy systems will also be highlighted. This conference will assemble a broad, diverse, and international group of biologists and chemists who are investigating fundamental issues related to Fe-S enzymes, on atomic, molecular, organism, and environmental scales. The topics to be addressed will include: Biosynthesis & Genomics of Fe-S Enzymes; Fundamental Fe-S Chemistry; Hydrogen and Fe-S Enzymes; Nitrogenase & Homologous Fe-S Enzymes; Fe-S Enzymes in Health & Disease; Radical SAM and Aconitase-Related Fe-S Enzymes; Fe-S Enzymes and Synthetic Analogues in BioEnergy; and Fe-S Enzymes in Geochemistry and the Origin of Life.

  5. Enzyme Kinetics in Microgravity

    NASA Astrophysics Data System (ADS)

    Liu, C. C.; Licata, V. J.

    2010-04-01

    The kinetics of some enzymes have been found to be enhanced by the microgravity environment. This is a relatively small effect, but is sufficient to have physiological effects and to impact pharmaceutical therapy in microgravity.

  6. Enzymes in Analytical Chemistry.

    ERIC Educational Resources Information Center

    Fishman, Myer M.

    1980-01-01

    Presents tabular information concerning recent research in the field of enzymes in analytic chemistry, with methods, substrate or reaction catalyzed, assay, comments and references listed. The table refers to 128 references. Also listed are 13 general citations. (CS)

  7. RNA as an Enzyme.

    ERIC Educational Resources Information Center

    Cech, Thomas R.

    1986-01-01

    Reviews current findings that explain RNA's function as an enzyme in addition to being an informational molecule. Highlights recent research efforts and notes changes in the information base on RNA activity. Includes models and diagrams of RNA activity. (ML)

  8. Shaping the outflows of evolved stars

    NASA Astrophysics Data System (ADS)

    Mohamed, Shazrene

    2015-08-01

    Both hot and cool evolved stars, e.g., red (super)giants and Wolf-Rayet stars, lose copious amounts of mass, momentum and mechanical energy through powerful, dense stellar winds. The interaction of these outflows with their surroundings results in highly structured and complex circumstellar environments, often featuring knots, arcs, shells and spirals. Recent improvements in computational power and techniques have led to the development of detailed, multi-dimensional simulations that have given new insight into the origin of these structures, and better understanding of the physical mechanisms driving their formation. In this talk, I will discuss three of the main mechanisms that shape the outflows of evolved stars:- interaction with the interstellar medium (ISM), i.e., wind-ISM interactions- interaction with a stellar wind, either from a previous phase of evolution or the wind from a companion star, i.e., wind-wind interactions- and interaction with a companion star that has a weak or insignicant outflow (e.g., a compact companion such as a neutron star or black hole), i.e., wind-companion interactions.I will also highlight the broader implications and impact of these stellar wind interactions for other phenomena, e.g, for symbiotic and X-ray binaries, supernovae and Gamma-ray bursts.

  9. Caterpillars evolved from onychophorans by hybridogenesis.

    PubMed

    Williamson, Donald I

    2009-11-24

    I reject the Darwinian assumption that larvae and their adults evolved from a single common ancestor. Rather I posit that, in animals that metamorphose, the basic types of larvae originated as adults of different lineages, i.e., larvae were transferred when, through hybridization, their genomes were acquired by distantly related animals. "Caterpillars," the name for eruciforms with thoracic and abdominal legs, are larvae of lepidopterans, hymenopterans, and mecopterans (scorpionflies). Grubs and maggots, including the larvae of beetles, bees, and flies, evolved from caterpillars by loss of legs. Caterpillar larval organs are dismantled and reconstructed in the pupal phase. Such indirect developmental patterns (metamorphoses) did not originate solely by accumulation of random mutations followed by natural selection; rather they are fully consistent with my concept of evolution by hybridogenesis. Members of the phylum Onychophora (velvet worms) are proposed as the evolutionary source of caterpillars and their grub or maggot descendants. I present a molecular biological research proposal to test my thesis. By my hypothesis 2 recognizable sets of genes are detectable in the genomes of all insects with caterpillar grub- or maggot-like larvae: (i) onychophoran genes that code for proteins determining larval morphology/physiology and (ii) sequentially expressed insect genes that code for adult proteins. The genomes of insects and other animals that, by contrast, entirely lack larvae comprise recognizable sets of genes from single animal common ancestors. PMID:19717430

  10. Early formation of evolved asteroidal crust.

    PubMed

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

    2009-01-01

    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. PMID:19129845

  11. Have plants evolved to self-immolate?

    PubMed Central

    Bowman, David M. J. S.; French, Ben J.; Prior, Lynda D.

    2014-01-01

    By definition fire prone ecosystems have highly combustible plants, leading to the hypothesis, first formally stated by Mutch in 1970, that community flammability is the product of natural selection of flammable traits. However, proving the “Mutch hypothesis” has presented an enormous challenge for fire ecologists given the difficulty in establishing cause and effect between landscape fire and flammable plant traits. Individual plant traits (such as leaf moisture content, retention of dead branches and foliage, oil rich foliage) are known to affect the flammability of plants but there is no evidence these characters evolved specifically to self-immolate, although some of these traits may have been secondarily modified to increase the propensity to burn. Demonstrating individual benefits from self-immolation is extraordinarily difficult, given the intersection of the physical environmental factors that control landscape fire (fuel production, dryness and ignitions) with community flammability properties that emerge from numerous traits of multiple species (canopy cover and litter bed bulk density). It is more parsimonious to conclude plants have evolved mechanisms to tolerate, but not promote, landscape fire. PMID:25414710

  12. Netgram: Visualizing Communities in Evolving Networks

    PubMed Central

    Mall, Raghvendra; Langone, Rocco; Suykens, Johan A. K.

    2015-01-01

    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. PMID:26356538

  13. Evolving NASA's Earth Science Data Systems

    NASA Astrophysics Data System (ADS)

    Walter, J.; Behnke, J.; Murphy, K. J.; Lowe, D. R.

    2013-12-01

    NASA's Earth Science Data and Information System Project (ESDIS) is charged with managing, maintaining, and evolving NASA's Earth Observing System Data and Information System (EOSDIS) and is responsible for processing, archiving, and distributing NASA Earth science data. The system supports a multitude of missions and serves diverse science research and other user communities. Keeping up with ever-changing information technology and figuring out how to leverage those changes across such a large system in order to continuously improve and meet the needs of a diverse user community is a significant challenge. Maintaining and evolving the system architecture and infrastructure is a continuous and multi-layered effort. It requires a balance between a "top down" management paradigm that provides a coherent system view and maintaining the managerial, technological, and functional independence of the individual system elements. This presentation will describe some of the key elements of the current system architecture, some of the strategies and processes we employ to meet these challenges, current and future challenges, and some ideas for meeting those challenges.

  14. Overproduction of ligninolytic enzymes

    DOEpatents

    Elisashvili, Vladimir; Kachlishvili, Eva; Torok, Tamas

    2014-06-17

    Methods, compositions, and systems for overproducing ligninolytic enzymes from the basidiomycetous fungus are described herein. As described, the method can include incubating a fungal strain of Cerrena unicolor IBB 303 in a fermentation system having growth medium which includes lignocellulosic material and then cultivating the fungal strain in the fermentation system under conditions wherein the fungus expresses the ligninolytic enzymes. In some cases, the lignocellulosic material is mandarin peel, ethanol production residue, walnut pericarp, wheat bran, wheat straw, or banana peel.

  15. Convergence towards higher standards in international dental education.

    PubMed

    Shanley, Diarmuid B

    2004-01-01

    This paper emanates from the findings of "DentEd" and "DentEdEvolves," two sequential European Union-funded Thematic Network Projects on Dental Education. Despite the existence of EU Directives and Guidelines, which were devised to assure comparable and acceptable standards of dental education and competence gained from training programs, there are serious differences among countries. The differences are greater in those countries about to join an expanding EU, where the stomatological approach to education predominates. Both projects had considerable support and advice from the Association from Dental Education in Europe, the American Dental Education Association and the International Federation of Dental Education Associations. An international effort is now proposed to converge towards higher standards in dental education by agreeing to broad principles for the "Profile of an International Dentist" (see www.dented.org/dresden.php3). The UK's General Dental Council recently adopted its profile of a dentist, which is compatible with and related to the EU's Dental Directives and Guidelines (see www.gdc-uk.org/pdfs/first_five_years_2002.pdf). An agreed profile provides a basis on which to structure a pan-European approach and could be more widely adopted. Dental schools throughout the world might be asked to verify those elements with which their graduates actually comply. It is also intended to use the profile as a basis for a modularized approach that would facilitate students studying elements of their course in different universities as part of an EU drive towards convergence in third- level education. It is not intended to promote a single educational approach. Unfortunately, at this stage, it will have little impact on global ill health, mainly associated with poverty and more recently the HIV/AIDS pandemic. The University of Columbia's Earth Centre has made enormous strides in focusing attention on global health and deprivation. Almost one-sixth of the world

  16. Deadly hairs, lethal feathers--convergent evolution of poisonous integument in mammals and birds.

    PubMed

    Plikus, Maksim V; Astrowski, Aliaksandr A

    2014-07-01

    Hairs and feathers are textbook examples of the convergent evolution of the follicular appendage structure between mammals and birds. While broadly recognized for their convergent thermoregulatory, camouflage and sexual display functions, hairs and feathers are rarely thought of as deadly defence tools. Several recent studies, however, show that in some species of mammals and birds, the integument can, in fact, be a de facto lethal weapon. One mammalian example is provided by African crested rats, which seek for and chew on the bark of plants containing the highly potent toxin, ouabain. These rats then coat their fur with ouabain-containing saliva. For efficient toxin retention, the rodents have evolved highly specialized fenestrated and mostly hollow hair shafts that soak up liquids, which essentially function as wicks. On the avian side of the vertebrate integumental variety spectrum, several species of birds of New Guinea have evolved resistance to highly potent batrachotoxins, which they acquire from their insect diet. While the mechanism of bird toxicity remains obscure, in a recently published issue of the journal, Dumbacher and Menon explore the intriguing idea that to achieve efficient storage of batrachotoxins in their skin, some birds exploit the basic permeability barrier function of their epidermis. Batrachotoxins become preferentially sequestered in their epidermis and are then transferred to feathers, likely through the exploitation of specialized avian lipid-storing multigranular body organelles. Here, we discuss wider implications of this intriguing concept. PMID:24698054

  17. Convergent Evolution of Mechanically Optimal Locomotion in Aquatic Invertebrates and Vertebrates

    PubMed Central

    Bale, Rahul; Neveln, Izaak D.; Bhalla, Amneet Pal Singh

    2015-01-01

    Examples of animals evolving similar traits despite the absence of that trait in the last common ancestor, such as the wing and camera-type lens eye in vertebrates and invertebrates, are called cases of convergent evolution. Instances of convergent evolution of locomotory patterns that quantitatively agree with the mechanically optimal solution are very rare. Here, we show that, with respect to a very diverse group of aquatic animals, a mechanically optimal method of swimming with elongated fins has evolved independently at least eight times in both vertebrate and invertebrate swimmers across three different phyla. Specifically, if we take the length of an undulation along an animal’s fin during swimming and divide it by the mean amplitude of undulations along the fin length, the result is consistently around twenty. We call this value the optimal specific wavelength (OSW). We show that the OSW maximizes the force generated by the body, which also maximizes swimming speed. We hypothesize a mechanical basis for this optimality and suggest reasons for its repeated emergence through evolution. PMID:25919026

  18. Genomics of Rapid Adaptation to Antibiotics: Convergent Evolution and Scalable Sequence Amplification

    PubMed Central

    Laehnemann, David; Peña-Miller, Rafael; Rosenstiel, Philip; Beardmore, Robert; Jansen, Gunther; Schulenburg, Hinrich

    2014-01-01

    Evolutionary adaptation can be extremely fast, especially in response to high selection intensities. A prime example is the surge of antibiotic resistance in bacteria. The genomic underpinnings of such rapid changes may provide information on the genetic processes that enhance fast responses and the particular trait functions under selection. Here, we use experimentally evolved Escherichia coli for a detailed dissection of the genomics of rapid antibiotic resistance evolution. Our new analyses demonstrate that amplification of a sequence region containing several known antibiotic resistance genes represents a fast genomic response mechanism under high antibiotic stress, here exerted by drug combination. In particular, higher dosage of such antibiotic combinations coincided with higher copy number of the sequence region. The amplification appears to be evolutionarily costly, because amplification levels rapidly dropped after removal of the drugs. Our results suggest that amplification is a scalable process, as copy number rapidly changes in response to the selective pressure encountered. Moreover, repeated patterns of convergent evolution were found across the experimentally evolved bacterial populations, including those with lower antibiotic selection intensities. Intriguingly, convergent evolution was identified on different organizational levels, ranging from the above sequence amplification, high variant frequencies in specific genes, prevalence of individual nonsynonymous mutations to the unusual repeated occurrence of a particular synonymous mutation in Glycine codons. We conclude that constrained evolutionary trajectories underlie rapid adaptation to antibiotics. Of the identified genomic changes, sequence amplification seems to represent the most potent, albeit costly genomic response mechanism to high antibiotic stress. PMID:24850796

  19. Convergent evolution and parallelism in plant domestication revealed by an expanding archaeological record

    PubMed Central

    Fuller, Dorian Q; Denham, Tim; Arroyo-Kalin, Manuel; Lucas, Leilani; Stevens, Chris J.; Qin, Ling; Allaby, Robin G.; Purugganan, Michael D.

    2014-01-01

    Recent increases in archaeobotanical evidence offer insights into the processes of plant domestication and agricultural origins, which evolved in parallel in several world regions. Many different crop species underwent convergent evolution and acquired domestication syndrome traits. For a growing number of seed crop species, these traits can be quantified by proxy from archaeological evidence, providing measures of the rates of change during domestication. Among domestication traits, nonshattering cereal ears evolved more quickly in general than seed size. Nevertheless, most domestication traits show similarly slow rates of phenotypic change over several centuries to millennia, and these rates were similar across different regions of origin. Crops reproduced vegetatively, including tubers and many fruit trees, are less easily documented in terms of morphological domestication, but multiple lines of evidence outline some patterns in the development of vegecultural systems across the New World and Old World tropics. Pathways to plant domestication can also be compared in terms of the cultural and economic factors occurring at the start of the process. Whereas agricultural societies have tended to converge on higher population densities and sedentism, in some instances cultivation began among sedentary hunter–gatherers whereas more often it was initiated by mobile societies of hunter–gatherers or herder–gatherers. PMID:24753577

  20. Convergent Evolution of Hemoglobin Function in High-Altitude Andean Waterfowl Involves Limited Parallelism at the Molecular Sequence Level.

    PubMed

    Natarajan, Chandrasekhar; Projecto-Garcia, Joana; Moriyama, Hideaki; Weber, Roy E; Muñoz-Fuentes, Violeta; Green, Andy J; Kopuchian, Cecilia; Tubaro, Pablo L; Alza, Luis; Bulgarella, Mariana; Smith, Matthew M; Wilson, Robert E; Fago, Angela; McCracken, Kevin G; Storz, Jay F

    2015-12-01

    A fundamental question in evolutionary genetics concerns the extent to which adaptive phenotypic convergence is attributable to convergent or parallel changes at the molecular sequence level. Here we report a comparative analysis of hemoglobin (Hb) function in eight phylogenetically replicated pairs of high- and low-altitude waterfowl taxa to test for convergence in the oxygenation properties of Hb, and to assess the extent to which convergence in biochemical phenotype is attributable to repeated amino acid replacements. Functional experiments on native Hb variants and protein engineering experiments based on site-directed mutagenesis revealed the phenotypic effects of specific amino acid replacements that were responsible for convergent increases in Hb-O2 affinity in multiple high-altitude taxa. In six of the eight taxon pairs, high-altitude taxa evolved derived increases in Hb-O2 affinity that were caused by a combination of unique replacements, parallel replacements (involving identical-by-state variants with independent mutational origins in different lineages), and collateral replacements (involving shared, identical-by-descent variants derived via introgressive hybridization). In genome scans of nucleotide differentiation involving high- and low-altitude populations of three separate species, function-altering amino acid polymorphisms in the globin genes emerged as highly significant outliers, providing independent evidence for adaptive divergence in Hb function. The experimental results demonstrate that convergent changes in protein function can occur through multiple historical paths, and can involve multiple possible mutations. Most cases of convergence in Hb function did not involve parallel substitutions and most parallel substitutions did not affect Hb-O2 affinity, indicating that the repeatability of phenotypic evolution does not require parallelism at the molecular level. PMID:26637114

  1. Convergent Evolution of Hemoglobin Function in High-Altitude Andean Waterfowl Involves Limited Parallelism at the Molecular Sequence Level

    PubMed Central

    Natarajan, Chandrasekhar; Projecto-Garcia, Joana; Moriyama, Hideaki; Weber, Roy E.; Muñoz-Fuentes, Violeta; Green, Andy J.; Kopuchian, Cecilia; Tubaro, Pablo L.; Alza, Luis; Bulgarella, Mariana; Smith, Matthew M.; Wilson, Robert E.; Fago, Angela; McCracken, Kevin G.; Storz, Jay F.

    2015-01-01

    A fundamental question in evolutionary genetics concerns the extent to which adaptive phenotypic convergence is attributable to convergent or parallel changes at the molecular sequence level. Here we report a comparative analysis of hemoglobin (Hb) function in eight phylogenetically replicated pairs of high- and low-altitude waterfowl taxa to test for convergence in the oxygenation properties of Hb, and to assess the extent to which convergence in biochemical phenotype is attributable to repeated amino acid replacements. Functional experiments on native Hb variants and protein engineering experiments based on site-directed mutagenesis revealed the phenotypic effects of specific amino acid replacements that were responsible for convergent increases in Hb-O2 affinity in multiple high-altitude taxa. In six of the eight taxon pairs, high-altitude taxa evolved derived increases in Hb-O2 affinity that were caused by a combination of unique replacements, parallel replacements (involving identical-by-state variants with independent mutational origins in different lineages), and collateral replacements (involving shared, identical-by-descent variants derived via introgressive hybridization). In genome scans of nucleotide differentiation involving high- and low-altitude populations of three separate species, function-altering amino acid polymorphisms in the globin genes emerged as highly significant outliers, providing independent evidence for adaptive divergence in Hb function. The experimental results demonstrate that convergent changes in protein function can occur through multiple historical paths, and can involve multiple possible mutations. Most cases of convergence in Hb function did not involve parallel substitutions and most parallel substitutions did not affect Hb-O2 affinity, indicating that the repeatability of phenotypic evolution does not require parallelism at the molecular level. PMID:26637114

  2. Rapid convergent evolution in wild crickets.

    PubMed

    Pascoal, Sonia; Cezard, Timothee; Eik-Nes, Aasta; Gharbi, Karim; Majewska, Jagoda; Payne, Elizabeth; Ritchie, Michael G; Zuk, Marlene; Bailey, Nathan W

    2014-06-16

    The earliest stages of convergent evolution are difficult to observe in the wild, limiting our understanding of the incipient genomic architecture underlying convergent phenotypes. To address this, we capitalized on a novel trait, flatwing, that arose and proliferated at the start of the 21st century in a population of field crickets (Teleogryllus oceanicus) on the Hawaiian island of Kauai. Flatwing erases sound-producing structures on male forewings. Mutant males cannot sing to attract females, but they are protected from fatal attack by an acoustically orienting parasitoid fly (Ormia ochracea). Two years later, the silent morph appeared on the neighboring island of Oahu. We tested two hypotheses for the evolutionary origin of flatwings in Hawaii: (1) that the silent morph originated on Kauai and subsequently introgressed into Oahu and (2) that flatwing originated independently on each island. Morphometric analysis of male wings revealed that Kauai flatwings almost completely lack typical derived structures, whereas Oahu flatwings retain noticeably more wild-type wing venation. Using standard genetic crosses, we confirmed that the mutation segregates as a single-locus, sex-linked Mendelian trait on both islands. However, genome-wide scans using RAD-seq recovered almost completely distinct markers linked with flatwing on each island. The patterns of allelic association with flatwing on either island reveal different genomic architectures consistent with the timing of two mutational events on the X chromosome. Divergent wing morphologies linked to different loci thus cause identical behavioral outcomes--silence--illustrating the power of selection to rapidly shape convergent adaptations from distinct genomic starting points. PMID:24881880

  3. Convergent Margin Structure and a Unifying Concept

    NASA Astrophysics Data System (ADS)

    von Huene, R.; Ranero, C. R.; Scholl, D. W.

    2008-12-01

    Marine observations of the past decade resolve 3 domains of different mechanics in space that probably respond differently from each other during an earthquake cycle. Accretion is common along thickly (>1 km) sedimented trenches and slowly (<50km/myr) converging margins. Erosion is common where convergence is greater which also reduces trench sediment thickness by rapid subduction. However erosion and accretion can be coeval, for instance, subducted seamounts erode the upper plate as adjacent sediment accretes. Trench sediment abundance appears to be a master control of tectonic erosion or accretion. Subducting plate relief and bending, fluid systems, input plate temperature, and material differences seem less important. From recent observations a unifying framework concept to aid interpretations of both accreting and eroding margins is proposed. Over a long term (Ma) the subduction channel accepts a finite amount of material. The excess amount will accrete and a shortage of trench sediment enhances erosion (Cloos and Shreve, 1988). If conditions remain consistent over ~1 Ma periods, the margin configuration becomes typically accretionary or erosional. In each margin segment the short term inter plate friction and material strength changes during the earthquake cycle as proposed by Wang and Hu, 2006. Mechanics probably changes locally during the cycle as well. K. Wang, Y. Hu, Accretionary prisms in subduction earthquake cycles: the theory of dynamic Coulomb wedge, J. Geophys. Res. 111 (2006) B06410, doi:10.1029/2005JB004094. Cloos, M., and R.L. Shreve, (1988), Subduction channel model of prism accretion, melange formation, sediment subduction, and subduction erosion at convergent plate margins: 2. Implications and discussion, Pageoph, v. 129, n. ¾ 501-545

  4. High convergence implosion symmetry in cylindrical hohlraums

    SciTech Connect

    Amendt, P A; Bradley, D K; Hammel, B A; Landen, O L; Suter, L J; Turner, R E; Wallace, R J

    1999-09-01

    High convergence, hohlraum-driven implosions will require control of time-integrated drive asymmetries to 1% levels for ignition to succeed on the NIF. We review how core imaging provides such asymmetry measurement accuracy for the lowest order asymmetry modes, and describe recent improvements in imaging techniques that should allow detection of higher order asymmetry modes. We also present a simple analytic model explaining how the sensitivity of symmetry control to beam pointing scales as we progress from single ring per side Nova cylindrical hohlraum illumination geometries to NIF-like multiple rings per side Omega hohlraum illumination geometries and ultimately to NIF-scale hohlraums.

  5. Convergence Analysis of a Domain Decomposition Paradigm

    SciTech Connect

    Bank, R E; Vassilevski, P S

    2006-06-12

    We describe a domain decomposition algorithm for use in several variants of the parallel adaptive meshing paradigm of Bank and Holst. This algorithm has low communication, makes extensive use of existing sequential solvers, and exploits in several important ways data generated as part of the adaptive meshing paradigm. We show that for an idealized version of the algorithm, the rate of convergence is independent of both the global problem size N and the number of subdomains p used in the domain decomposition partition. Numerical examples illustrate the effectiveness of the procedure.

  6. Convergence of multi-channel effective interactions

    NASA Astrophysics Data System (ADS)

    Wagner, M.; Schaefer, B.-J.; Wambach, J.; Kuo, T. T. S.; Brown, G. E.

    2006-11-01

    A detailed analysis of the convergence properties of the Andreozzi-Lee-Suzuki iteration method, which is used for the calculation of low-momentum effective potentials Vlowk, is presented. After summarizing different modifications of the iteration method for one-flavor channels we introduce a simple model to study the generalization of the iteration method to multi-flavor channels. The failure of a straightforward generalization is discussed. The introduction of a channel-dependent cutoff cures the conceptual and technical problems. This novel method has already been applied successfully for realistic hyperon-nucleon interactions.

  7. On Convergence Acceleration Techniques for Unstructured Meshes

    NASA Technical Reports Server (NTRS)

    Mavriplis, Dimitri J.

    1998-01-01

    A discussion of convergence acceleration techniques as they relate to computational fluid dynamics problems on unstructured meshes is given. Rather than providing a detailed description of particular methods, the various different building blocks of current solution techniques are discussed and examples of solution strategies using one or several of these ideas are given. Issues relating to unstructured grid CFD problems are given additional consideration, including suitability of algorithms to current hardware trends, memory and cpu tradeoffs, treatment of non-linearities, and the development of efficient strategies for handling anisotropy-induced stiffness. The outlook for future potential improvements is also discussed.

  8. Adaptive control: Stability, convergence, and robustness

    NASA Technical Reports Server (NTRS)

    Sastry, Shankar; Bodson, Marc

    1989-01-01

    The deterministic theory of adaptive control (AC) is presented in an introduction for graduate students and practicing engineers. Chapters are devoted to basic AC approaches, notation and fundamental theorems, the identification problem, model-reference AC, parameter convergence using averaging techniques, and AC robustness. Consideration is given to the use of prior information, the global stability of indirect AC schemes, multivariable AC, linearizing AC for a class of nonlinear systems, AC of linearizable minimum-phase systems, and MIMO systems decouplable by static state feedback.

  9. Cubature on Wiener Space: Pathwise Convergence

    SciTech Connect

    Bayer, Christian Friz, Peter K.

    2013-04-15

    Cubature on Wiener space (Lyons and Victoir in Proc. R. Soc. Lond. A 460(2041):169-198, 2004) provides a powerful alternative to Monte Carlo simulation for the integration of certain functionals on Wiener space. More specifically, and in the language of mathematical finance, cubature allows for fast computation of European option prices in generic diffusion models.We give a random walk interpretation of cubature and similar (e.g. the Ninomiya-Victoir) weak approximation schemes. By using rough path analysis, we are able to establish weak convergence for general path-dependent option prices.

  10. Variation in steroid hormone levels among Caribbean Anolis lizards: endocrine system convergence?

    PubMed

    Husak, Jerry F; Lovern, Matthew B

    2014-04-01

    Variation in aggression among species can be due to a number of proximate and ultimate factors, leading to patterns of divergent and convergent evolution of behavior among even closely related species. Caribbean Anolis lizards are well known for their convergence in microhabitat use and morphology, but they also display marked convergence in social behavior and patterns of aggression. We studied 18 Anolis species across six ecomorphs on four different Caribbean islands to test four main hypotheses. We hypothesized that species differences in aggression would be due to species differences in circulating testosterone (T), a steroid hormone implicated in numerous studies across vertebrate taxa as a primary determinant of social behavior; more aggressive species were expected to have higher baseline concentrations of T and corticosterone. We further hypothesized that low-T species would increase T and corticosterone levels during a social challenge. Within three of the four island assemblages studied we found differences in T levels among species within an island that differ in aggression, but in the opposite pattern than predicted: more aggressive species had lower baseline T than the least aggressive species. The fourth island, Puerto Rico, showed the pattern of baseline T levels among species we predicted. There were no patterns of corticosterone levels among species or ecomorphs. One of the two species tested increased T in response to a social challenge, but neither species elevated corticosterone. Our results suggest that it is possible for similarities in aggression among closely related species to evolve via different proximate mechanisms. PMID:24662425

  11. Structural and stratigraphic evolution of Aleutian convergent-margin basins - ridge crest to trench floor

    SciTech Connect

    Scholl, D.W.; Ryan, H.F.; Geist, E.L.; Vallier, T.L.; Stevenson, A.J.; Childs, J.R. )

    1988-02-01

    The Aleutian Ridge lies along nearly 2000 km of the north Pacific's obliquely converging plate boundary with North America. Since middle Eocene time, convergent-margin basins have repeatedly formed here, typically as summit basins along the ridge crest, and as forearc basins on the landward trench slope. Summit and forearc basins formed as a consequence of plate-boundary coupling and the application of compressional and right-lateral shear stresses to the arc massif. Basins typically evolved along shear zones in response to transtensional processes, and as trailing-edge grabens behind rotating blocks of arc massif. In the late Cenozoic, high rates of trench sedimentation led to the growth of an accretionary complex that underthrust forearc basement. Wedging and improved plate coupling elevated and laterally shifted blocks of outer forearc rocks, creating much of the structural framework of the regionally extensive Aleutian Terrace forearc basin. Changes in plate-boundary conditions that affected the ridge's volcanic activity and regional elevation importantly influenced basinal sedimentation. Changes of greatest significance were a major shift in convergence direction and rate about 42 Ma (reduced volcanism), ridge underthrusting by increasingly younger ocean crust in Oligocene and Miocene time (arc elevation), and the combination of more orthogonal underthrusting and the subduction of a dead spreading center 5-10 Ma (arc subsidence).

  12. Structural and stratigraphic evolution of Aleutian convergent-margin basins - Ridge crest to trench floor

    SciTech Connect

    Scholl, D.W.; Ryan, H.F.; Geist, E.L.; Vallier, T.L.

    1988-01-01

    The Aleutian Ridge lies along nearly 2,000 km of the north Pacific's obliquely converging plate boundary with North America. Since middle Eocene time, convergent-margin basins have repeatedly formed here, typically as summit basins along the ridge crest, and as forecarc basins on the landward trench slope. Thick (1-4 km) sequences of terrigenous, hemipelagic, and biogenic debris have accumulated in these depressions, which are mostly intra-arc structures floored by arc-basement rocks. Summit and forearc basins formed as a consequence of plate-boundary coupling and the application of compressional and right-lateral shear stresses to the arc massif. Basins typically evolved along shear zones in response to transtensional processes, and as trailing-edge grabens behind rotating blocks of arc massif. In the late Cenozoic, high rates of trench sedimentation led to the growth of an accretionary complex that underthrust forearc basement. Wedging and improved plate coupling elevated and laterally shifted blocks of outer forearc rocks, creating much of the structural framework of the regionally extensive Aleutian Terrace forearc basin. Changes in plate-boundary conditions that affected the ridge's volcanic activity and regional elevation importantly influenced basinal sedimentation. Changes of greatest significant were a major shift in convergence direction and rate about 42 Ma (reduced volcanism), ridge underthrusting by increasingly younger ocean crust in Oligocena and Miocene time (arc elevation), and the combination of more orthogonal underthrusting and the subduction of a dead spreading center 5-120 Ma (arc subsidence).

  13. Widespread Signals of Convergent Adaptation to High Altitude in Asia and America

    PubMed Central

    Foll, Matthieu; Gaggiotti, Oscar E.; Daub, Josephine T.; Vatsiou, Alexandra; Excoffier, Laurent

    2014-01-01

    Living at high altitude is one of the most difficult challenges that humans had to cope with during their evolution. Whereas several genomic studies have revealed some of the genetic bases of adaptations in Tibetan, Andean, and Ethiopian populations, relatively little evidence of convergent evolution to altitude in different continents has accumulated. This lack of evidence can be due to truly different evolutionary responses, but it can also be due to the low power of former studies that have mainly focused on populations from a single geographical region or performed separate analyses on multiple pairs of populations to avoid problems linked to shared histories between some populations. We introduce here a hierarchical Bayesian method to detect local adaptation that can deal with complex demographic histories. Our method can identify selection occurring at different scales, as well as convergent adaptation in different regions. We apply our approach to the analysis of a large SNP data set from low- and high-altitude human populations from America and Asia. The simultaneous analysis of these two geographic areas allows us to identify several candidate genome regions for altitudinal selection, and we show that convergent evolution among continents has been quite common. In addition to identifying several genes and biological processes involved in high-altitude adaptation, we identify two specific biological pathways that could have evolved in both continents to counter toxic effects induced by hypoxia. PMID:25262650

  14. Distinctive convergence in Australian floral colours seen through the eyes of Australian birds

    PubMed Central

    Burd, Martin; Stayton, C. Tristan; Shrestha, Mani; Dyer, Adrian G.

    2014-01-01

    We used a colour-space model of avian vision to assess whether a distinctive bird pollination syndrome exists for floral colour among Australian angiosperms. We also used a novel phylogenetically based method to assess whether such a syndrome represents a significant degree of convergent evolution. About half of the 80 species in our sample that attract nectarivorous birds had floral colours in a small, isolated region of colour space characterized by an emphasis on long-wavelength reflection. The distinctiveness of this ‘red arm’ region was much greater when colours were modelled for violet-sensitive (VS) avian vision than for the ultraviolet-sensitive visual system. Honeyeaters (Meliphagidae) are the dominant avian nectarivores in Australia and have VS vision. Ancestral state reconstructions suggest that 31 lineages evolved into the red arm region, whereas simulations indicate that an average of five or six lineages and a maximum of 22 are likely to have entered in the absence of selection. Thus, significant evolutionary convergence on a distinctive floral colour syndrome for bird pollination has occurred in Australia, although only a subset of bird-pollinated taxa belongs to this syndrome. The visual system of honeyeaters has been the apparent driver of this convergence. PMID:24573847

  15. Density-Profile Processes Describing Biological Signaling Networks: Almost Sure Convergence to Deterministic Trajectories

    NASA Astrophysics Data System (ADS)

    Fernández, Roberto; Fontes, Luiz R.; Neves, E. Jordão

    2009-09-01

    We introduce jump processes in ℝ k , called density-profile processes, to model biological signaling networks. Our modeling setup describes the macroscopic evolution of a finite-size spin-flip model with k types of spins with arbitrary number of internal states interacting through a non-reversible stochastic dynamics. We are mostly interested on the multi-dimensional empirical-magnetization vector in the thermodynamic limit, and prove that, within arbitrary finite time-intervals, its path converges almost surely to a deterministic trajectory determined by a first-order (non-linear) differential equation with explicit bounds on the distance between the stochastic and deterministic trajectories. As parameters of the spin-flip dynamics change, the associated dynamical system may go through bifurcations, associated to phase transitions in the statistical mechanical setting. We present a simple example of spin-flip stochastic model, associated to a synthetic biology model known as repressilator, which leads to a dynamical system with Hopf and pitchfork bifurcations. Depending on the parameter values, the magnetization random path can either converge to a unique stable fixed point, converge to one of a pair of stable fixed points, or asymptotically evolve close to a deterministic orbit in ℝ k . We also discuss a simple signaling pathway related to cancer research, called p53 module.

  16. Regulatory administrative databases in FDA's Center for Biologics Evaluation and Research: convergence toward a unified database.

    PubMed

    Smith, Jeffrey K

    2013-04-01

    Regulatory administrative database systems within the Food and Drug Administration's (FDA) Center for Biologics Evaluation and Research (CBER) are essential to supporting its core mission, as a regulatory agency. Such systems are used within FDA to manage information and processes surrounding the processing, review, and tracking of investigational and marketed product submissions. This is an area of increasing interest in the pharmaceutical industry and has been a topic at trade association conferences (Buckley 2012). Such databases in CBER are complex, not for the type or relevance of the data to any particular scientific discipline but because of the variety of regulatory submission types and processes the systems support using the data. Commonalities among different data domains of CBER's regulatory administrative databases are discussed. These commonalities have evolved enough to constitute real database convergence and provide a valuable asset for business process intelligence. Balancing review workload across staff, exploring areas of risk in review capacity, process improvement, and presenting a clear and comprehensive landscape of review obligations are just some of the opportunities of such intelligence. This convergence has been occurring in the presence of usual forces that tend to drive information technology (IT) systems development toward separate stovepipes and data silos. CBER has achieved a significant level of convergence through a gradual process, using a clear goal, agreed upon development practices, and transparency of database objects, rather than through a single, discrete project or IT vendor solution. This approach offers a path forward for FDA systems toward a unified database. PMID:23269527

  17. No Genome-Wide Protein Sequence Convergence for Echolocation

    PubMed Central

    Zou, Zhengting; Zhang, Jianzhi

    2015-01-01

    Toothed whales and two groups of bats independently acquired echolocation, the ability to locate and identify objects by reflected sound. Echolocation requires physiologically complex and coordinated vocal, auditory, and neural functions, but the molecular basis of the capacity for echolocation is not well understood. A recent study suggested that convergent amino acid substitutions widespread in the proteins of echolocators underlay the convergent origins of mammalian echolocation. Here, we show that genomic signatures of molecular convergence between echolocating lineages are generally no stronger than those between echolocating and comparable nonecholocating lineages. The same is true for the group of 29 hearing-related proteins claimed to be enriched with molecular convergence. Reexamining the previous selection test reveals several flaws and invalidates the asserted evidence for adaptive convergence. Together, these findings indicate that the reported genomic signatures of convergence largely reflect the background level of sequence convergence unrelated to the origins of echolocation. PMID:25631925

  18. No genome-wide protein sequence convergence for echolocation.

    PubMed

    Zou, Zhengting; Zhang, Jianzhi

    2015-05-01

    Toothed whales and two groups of bats independently acquired echolocation, the ability to locate and identify objects by reflected sound. Echolocation requires physiologically complex and coordinated vocal, auditory, and neural functions, but the molecular basis of the capacity for echolocation is not well understood. A recent study suggested that convergent amino acid substitutions widespread in the proteins of echolocators underlay the convergent origins of mammalian echolocation. Here, we show that genomic signatures of molecular convergence between echolocating lineages are generally no stronger than those between echolocating and comparable nonecholocating lineages. The same is true for the group of 29 hearing-related proteins claimed to be enriched with molecular convergence. Reexamining the previous selection test reveals several flaws and invalidates the asserted evidence for adaptive convergence. Together, these findings indicate that the reported genomic signatures of convergence largely reflect the background level of sequence convergence unrelated to the origins of echolocation. PMID:25631925

  19. Renal cell carcinoma: Evolving and emerging subtypes.

    PubMed

    Crumley, Suzanne M; Divatia, Mukul; Truong, Luan; Shen, Steven; Ayala, Alberto G; Ro, Jae Y

    2013-12-16

    Our knowledge of renal cell carcinoma (RCC) is rapidly expanding. For those who diagnose and treat RCC, it is important to understand the new developments. In recent years, many new renal tumors have been described and defined, and our understanding of the biology and clinical correlates of these tumors is changing. Evolving concepts in Xp11 translocation carcinoma, mucinous tubular and spindle cell carcinoma, multilocular cystic clear cell RCC, and carcinoma associated with neuroblastoma are addressed within this review. Tubulocystic carcinoma, thyroid-like follicular carcinoma of kidney, acquired cystic disease-associated RCC, and clear cell papillary RCC are also described. Finally, candidate entities, including RCC with t(6;11) translocation, hybrid oncocytoma/chromophobe RCC, hereditary leiomyomatosis and RCC syndrome, and renal angiomyoadenomatous tumor are reviewed. Knowledge of these new entities is important for diagnosis, treatment and subsequent prognosis. This review provides a targeted summary of new developments in RCC. PMID:24364021

  20. The evolving classification of renal cell neoplasia.

    PubMed

    Delahunt, Brett; Srigley, John R

    2015-03-01

    The classification of renal cell neoplasia is morphologically based; however, this has evolved over the last 35 years with the incorporation of genetic characteristics into the diagnostic features of some tumors. The 2013 Vancouver classification recognized 17 morphotypes of renal parenchymal malignancy and two benign tumors. This classification included the newly established entities tubulocystic renal cell carcinoma (RCC)), acquired cystic disease-associated RCC, clear cell (tubulo) papillary RCC, microphthalmia transcription factor family translocation RCC and hereditary leiomyomatosis RCC syndrome-associated RCC. In addition to these newly described forms of RCC there are a number of novel tumors that are currently recognized as emerging entities. These are likely to be incorporated into subsequent classifications and include thyroid-like follicular RCC, succinate dehydrogenase B mutation-associated RCC, ALK translocation RCC, tuberous sclerosis complex-associated RCC, and RCC with (angio) leiomyomatous stroma. PMID:25753529

  1. Evolving unipolar memristor spiking neural networks

    NASA Astrophysics Data System (ADS)

    Howard, David; Bull, Larry; De Lacy Costello, Ben

    2015-10-01

    Neuromorphic computing - brain-like computing in hardware - typically requires myriad complimentary metal oxide semiconductor spiking neurons interconnected by a dense mesh of nanoscale plastic synapses. Memristors are frequently cited as strong synapse candidates due to their statefulness and potential for low-power implementations. To date, plentiful research has focused on the bipolar memristor synapse, which is capable of incremental weight alterations and can provide adaptive self-organisation under a Hebbian learning scheme. In this paper, we consider the unipolar memristor synapse - a device capable of non-Hebbian switching between only two states (conductive and resistive) through application of a suitable input voltage - and discuss its suitability for neuromorphic systems. A self-adaptive evolutionary process is used to autonomously find highly fit network configurations. Experimentation on two robotics tasks shows that unipolar memristor networks evolve task-solving controllers faster than both bipolar memristor networks and networks containing constant non-plastic connections whilst performing at least comparably.

  2. Resiliently evolving supply-demand networks

    NASA Astrophysics Data System (ADS)

    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.

  3. Development and the evolvability of human limbs

    PubMed Central

    Young, Nathan M.; Wagner, Günter P.; Hallgrímsson, Benedikt

    2010-01-01

    The long legs and short arms of humans are distinctive for a primate, the result of selection acting in opposite directions on each limb at different points in our evolutionary history. This mosaic pattern challenges our understanding of the relationship of development and evolvability because limbs are serially homologous and genetic correlations should act as a significant constraint on their independent evolution. Here we test a developmental model of limb covariation in anthropoid primates and demonstrate that both humans and apes exhibit significantly reduced integration between limbs when compared to quadrupedal monkeys. This result indicates that fossil hominins likely escaped constraints on independent limb variation via reductions to genetic pleiotropy in an ape-like last common ancestor (LCA). This critical change in integration among hominoids, which is reflected in macroevolutionary differences in the disparity between limb lengths, facilitated selection for modern human limb proportions and demonstrates how development helps shape evolutionary change. PMID:20133636

  4. Finch: A System for Evolving Java (Bytecode)

    NASA Astrophysics Data System (ADS)

    Orlov, Michael; Sipper, Moshe

    The established approach in genetic programming (GP) involves the definition of functions and terminals appropriate to the problem at hand, after which evolution of expressions using these definitions takes place. We have recently developed a system, dubbed FINCH (Fertile Darwinian Bytecode Harvester), to evolutionarily improve actual, extant software, which was not intentionally written for the purpose of serving as a GP representation in particular, nor for evolution in general. This is in contrast to existing work that uses restricted subsets of the Java bytecode instruction set as a representation language for individuals in genetic programming. The ability to evolve Java programs will hopefully lead to a valuable new tool in the software engineer's toolkit.

  5. Pulmonary Sporotrichosis: An Evolving Clinical Paradigm.

    PubMed

    Aung, Ar K; Spelman, Denis W; Thompson, Philip J

    2015-10-01

    In recent decades, sporotrichosis, caused by thermally dimorphic fungi Sporothrix schenckii complex, has become an emerging infection in many parts of the world. Pulmonary infection with S. schenckii still remains relatively uncommon, possibly due to underrecognition. Pulmonary sporotrichosis presents with distinct clinical and radiological patterns in both immunocompetent and immunocompromised hosts and can often result in significant morbidity and mortality despite treatment. Current understanding regarding S. schenckii biology, epidemiology, immunopathology, clinical diagnostics, and treatment options has been evolving in the recent years with increased availability of molecular sequencing techniques. However, this changing knowledge has not yet been fully translated into a better understanding of the clinical aspects of pulmonary sporotrichosis, as such current management guidelines remain unsupported by high-level clinical evidence. This article examines recent advances in the knowledge of sporotrichosis and its application to the difficult challenges of managing pulmonary sporotrichosis. PMID:26398541

  6. Observations of the Dust Around Evolved Stars

    NASA Astrophysics Data System (ADS)

    Walker, H. J.; Heinrichsen, I.; Richards, P. J.

    ISOPHOT has been used to obtain low resolution spectra from 2.5µm to 5µm and 5.8µm to 11.6µm and multi-aperture photometry at 60µm of several evolved stars; oxygen-rich and carbon-rich (including the peculiar carbon-rich stars R CrB and RY Sgr). R CrB was observed early in the ISO mission, 3 weeks after it had been at minimum light. Another spectrum was obtained several months later. The second spectrum shows that the broad plateau (from around 6µm to 8µm) is still present but the flux density has declined from 60Jy to 50Jy. The spectrum for RY Sgr shows the same type of plateau. The multi-aperture data suggest that the dust shells are resolved around R CrB, RY Sgr, Y CVn and RS Lib.

  7. Evolving colon injury management: a review.

    PubMed

    Greer, Lauren T; Gillern, Suzanne M; Vertrees, Amy E

    2013-02-01

    The colon is the second most commonly injured intra-abdominal organ in penetrating trauma. Management of traumatic colon injuries has evolved significantly over the past 200 years. Traumatic colon injuries can have a wide spectrum of severity, presentation, and management options. There is strong evidence that most non-destructive colon injuries can be successfully managed with primary repair or primary anastomosis. The management of destructive colon injuries remains controversial with most favoring resection with primary anastomosis and others favor colonic diversion in specific circumstances. The historical management of traumatic colon injuries, common mechanisms of injury, demographics, presentation, assessment, diagnosis, management, and complications of traumatic colon injuries both in civilian and military practice are reviewed. The damage control revolution has added another layer of complexity to management with continued controversy. PMID:23336650

  8. Properties of evolving e-mail networks

    NASA Astrophysics Data System (ADS)

    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. Regulatory mechanisms link phenotypic plasticity to evolvability.

    PubMed

    van Gestel, Jordi; Weissing, Franz J

    2016-01-01

    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. PMID:27087393

  10. Structural phase transition in evolving networks.

    PubMed

    Kim, Sang-Woo; Noh, Jae Dong

    2009-08-01

    A network as a substrate for dynamic processes may have its own dynamics. We propose a model for networks which evolve together with diffusing particles through a coupled dynamics and investigate emerging structural property. The model consists of an undirected weighted network of fixed mean degree and randomly diffusing particles of fixed density. The weight w of an edge increases by the amount of traffics through its connecting nodes or decreases by a constant factor. Edges are removed with the probability P(rew)=1/(1+w) and replaced by new ones having w=0 at random locations. We find that the model exhibits a structural phase transition between the homogeneous phase characterized by an exponentially decaying degree distribution and the heterogeneous phase characterized by the presence of hubs. The hubs emerge as a consequence of a positive feedback between the particle and the edge dynamics. PMID:19792212

  11. Modelling of the Evolving Stable Boundary Layer

    NASA Astrophysics Data System (ADS)

    Sorbjan, Zbigniew

    2014-06-01

    A single-column model of the evolving stable boundary layer (SBL) is tested for self-similar properties of the flow and effects of ambient forcing. The turbulence closure of the model is diagnostic, based on the K-theory approach, with a semi-empirical form of the mixing length, and empirical stability functions of the Richardson number. The model results, expressed in terms of local similarity scales, are universal functions, satisfied in the entire SBL. Based on similarity expression, a realizability condition is derived for the minimum allowable turbulent heat flux in the SBL. Numerical experiments show that the development of "horse-shoe" shaped, fixed-elevation hodographs in the interior of the SBL around sunrise is controlled by effects imposed by surface thermal forcing.

  12. The Evolving Theory of Evolutionary Radiations.

    PubMed

    Simões, M; Breitkreuz, L; Alvarado, M; Baca, S; Cooper, J C; Heins, L; Herzog, K; Lieberman, B S

    2016-01-01

    Evolutionary radiations have intrigued biologists for more than 100 years, and our understanding of the patterns and processes associated with these radiations continues to grow and evolve. Recently it has been recognized that there are many different types of evolutionary radiation beyond the well-studied adaptive radiations. We focus here on multifarious types of evolutionary radiations, paying special attention to the abiotic factors that might trigger diversification in clades. We integrate concepts such as exaptation, species selection, coevolution, and the turnover-pulse hypothesis (TPH) into the theoretical framework of evolutionary radiations. We also discuss other phenomena that are related to, but distinct from, evolutionary radiations that have relevance for evolutionary biology. PMID:26632984

  13. Renal cell carcinoma: Evolving and emerging subtypes

    PubMed Central

    Crumley, Suzanne M; Divatia, Mukul; Truong, Luan; Shen, Steven; Ayala, Alberto G; Ro, Jae Y

    2013-01-01

    Our knowledge of renal cell carcinoma (RCC) is rapidly expanding. For those who diagnose and treat RCC, it is important to understand the new developments. In recent years, many new renal tumors have been described and defined, and our understanding of the biology and clinical correlates of these tumors is changing. Evolving concepts in Xp11 translocation carcinoma, mucinous tubular and spindle cell carcinoma, multilocular cystic clear cell RCC, and carcinoma associated with neuroblastoma are addressed within this review. Tubulocystic carcinoma, thyroid-like follicular carcinoma of kidney, acquired cystic disease-associated RCC, and clear cell papillary RCC are also described. Finally, candidate entities, including RCC with t(6;11) translocation, hybrid oncocytoma/chromophobe RCC, hereditary leiomyomatosis and RCC syndrome, and renal angiomyoadenomatous tumor are reviewed. Knowledge of these new entities is important for diagnosis, treatment and subsequent prognosis. This review provides a targeted summary of new developments in RCC. PMID:24364021

  14. Microbial communities evolve faster in extreme environments

    PubMed Central

    Li, Sheng-Jin; Hua, Zheng-Shuang; Huang, Li-Nan; Li, Jie; Shi, Su-Hua; Chen, Lin-Xing; Kuang, Jia-Liang; Liu, Jun; Hu, Min; Shu, Wen-Sheng

    2014-01-01

    Evolutionary analysis of microbes at the community level represents a new research avenue linking ecological patterns to evolutionary processes, but remains insufficiently studied. Here we report a relative evolutionary rates (rERs) analysis of microbial communities from six diverse natural environments based on 40 metagenomic samples. We show that the rERs of microbial communities are mainly shaped by environmental conditions, and the microbes inhabiting extreme habitats (acid mine drainage, saline lake and hot spring) evolve faster than those populating benign environments (surface ocean, fresh water and soil). These findings were supported by the observation of more relaxed purifying selection and potentially frequent horizontal gene transfers in communities from extreme habitats. The mechanism of high rERs was proposed as high mutation rates imposed by stressful conditions during the evolutionary processes. This study brings us one stage closer to an understanding of the evolutionary mechanisms underlying the adaptation of microbes to extreme environments. PMID:25158668

  15. Life cycle planning: An evolving concept

    SciTech Connect

    Moore, P.J.R.; Gorman, I.G.

    1994-12-31

    Life-cycle planning is an evolving concept in the management of oil and gas projects. BHP Petroleum now interprets this idea to include all development planning from discovery and field appraisal to final abandonment and includes safety, environmental, technical, plant, regulatory, and staffing issues. This article describes in the context of the Timor Sea, how despite initial successes and continuing facilities upgrades, BHPP came to perceive that current operations could be the victim of early development successes, particularly in the areas of corrosion and maintenance. The search for analogies elsewhere lead to the UK North Sea, including the experiences of Britoil and BP, both of which performed detailed Life of Field studies in the later eighties. These materials have been used to construct a format and content for total Life-cycle plans in general and the social changes required to ensure their successful application in Timor Sea operations and deployment throughout Australia.

  16. Evolving spiking networks with variable resistive memories.

    PubMed

    Howard, Gerard; Bull, Larry; de Lacy Costello, Ben; Gale, Ella; Adamatzky, Andrew

    2014-01-01

    Neuromorphic computing is a brainlike information processing paradigm that requires adaptive learning mechanisms. A spiking neuro-evolutionary system is used for this purpose; plastic resistive memories are implemented as synapses in spiking neural networks. The evolutionary design process exploits parameter self-adaptation and allows the topology and synaptic weights to be evolved for each network in an autonomous manner. Variable resistive memories are the focus of this research; each synapse has its own conductance profile which modifies the plastic behaviour of the device and may be altered during evolution. These variable resistive networks are evaluated on a noisy robotic dynamic-reward scenario against two static resistive memories and a system containing standard connections only. The results indicate that the extra behavioural degrees of freedom available to the networks incorporating variable resistive memories enable them to outperform the comparative synapse types. PMID:23614774

  17. Design Calculations for NIF Convergent Ablator Experiments

    NASA Astrophysics Data System (ADS)

    Olson, R. E.; Callahan, D. A.; Hicks, D. G.; Landen, O. L.; Langer, S. H.; Meezan, N. B.; Spears, B. K.; Widmann, K.; Kline, J. L.; Wilson, D. C.; Petrasso, R. D.; Leeper, R. J.

    2010-11-01

    Design calculations for NIF convergent ablator experiments will be described. The convergent ablator experiments measure the implosion trajectory, velocity, and ablation rate of an x-ray driven capsule and are a important component of the U. S. National Ignition Campaign at NIF. The design calculations are post-processed to provide simulations of the key diagnostics -- 1) Dante measurements of hohlraum x-ray flux and spectrum, 2) streaked radiographs of the imploding ablator shell, 3) wedge range filter measurements of D-He3 proton output spectra, and 4) GXD measurements of the imploded core. The simulated diagnostics will be compared to the experimental measurements to provide an assessment of the accuracy of the design code predictions of hohlraum radiation temperature, capsule ablation rate, implosion velocity, shock flash areal density, and x-ray bang time. Post-shot versions of the design calculations are used to enhance the understanding of the experimental measurements and will assist in choosing parameters for subsequent shots and the path towards optimal ignition capsule tuning. *SNL, LLNL, and LANL are operated under US DOE contracts DE-AC04-94AL85000. DE-AC52-07NA27344, and DE-AC04-94AL85000.

  18. Design calculations for NIF convergent ablator experiments.

    SciTech Connect

    Callahan, Debra; Leeper, Ramon Joe; Spears, B. K.; Zylstra, A.; Seguin, F.; Landen, Otto L.; Petrasso, R. D.; Rinderknecht, H.; Kline, J. L.; Frenje, J.; Wilson, D. C.; Langer, S. H.; Widmann, K.; Meezan, Nathan B.; Hicks, Damien G.; Olson, Richard Edward

    2010-11-01

    Design calculations for NIF convergent ablator experiments will be described. The convergent ablator experiments measure the implosion trajectory, velocity, and ablation rate of an x-ray driven capsule and are a important component of the U. S. National Ignition Campaign at NIF. The design calculations are post-processed to provide simulations of the key diagnostics: (1) Dante measurements of hohlraum x-ray flux and spectrum, (2) streaked radiographs of the imploding ablator shell, (3) wedge range filter measurements of D-He3 proton output spectra, and (4) GXD measurements of the imploded core. The simulated diagnostics will be compared to the experimental measurements to provide an assessment of the accuracy of the design code predictions of hohlraum radiation temperature, capsule ablation rate, implosion velocity, shock flash areal density, and x-ray bang time. Post-shot versions of the design calculations are used to enhance the understanding of the experimental measurements and will assist in choosing parameters for subsequent shots and the path towards optimal ignition capsule tuning.

  19. How evolved psychological mechanisms empower cultural group selection.

    PubMed

    Henrich, Joseph; Boyd, Robert

    2016-01-01

    Driven by intergroup competition, social norms, beliefs, and practices can evolve in ways that more effectively tap into a wide variety of evolved psychological mechanisms to foster group-beneficial behavior. The more powerful such evolved mechanisms are, the more effectively culture can potentially harness and manipulate them to generate greater phenotypic variation across groups, thereby fueling cultural group selection. PMID:27561383

  20. Aminoglycoside Modifying Enzymes

    PubMed Central

    Ramirez, Maria S.; Tolmasky, Marcelo E.

    2010-01-01

    Aminoglycosides have been an essential component of the armamentarium in the treatment of life-threatening infections. Unfortunately, their efficacy has been reduced by the surge and dissemination of resistance. In some cases the levels of resistance reached the point that rendered them virtually useless. Among many known mechanisms of resistance to aminoglycosides, enzymatic modification is the most prevalent in the clinical setting. Aminoglycoside modifying enzymes catalyze the modification at different −OH or −NH2 groups of the 2-deoxystreptamine nucleus or the sugar moieties and can be nucleotidyltranferases, phosphotransferases, or acetyltransferases. The number of aminoglycoside modifying enzymes identified to date as well as the genetic environments where the coding genes are located is impressive and there is virtually no bacteria that is unable to support enzymatic resistance to aminoglycosides. Aside from the development of new aminoglycosides refractory to as many as possible modifying enzymes there are currently two main strategies being pursued to overcome the action of aminoglycoside modifying enzymes. Their successful development would extend the useful life of existing antibiotics that have proven effective in the treatment of infections. These strategies consist of the development of inhibitors of the enzymatic action or of the expression of the modifying enzymes. PMID:20833577

  1. Random-walk enzymes

    NASA Astrophysics Data System (ADS)

    Mak, Chi H.; Pham, Phuong; Afif, Samir A.; Goodman, Myron F.

    2015-09-01

    Enzymes that rely on random walk to search for substrate targets in a heterogeneously dispersed medium can leave behind complex spatial profiles of their catalyzed conversions. The catalytic signatures of these random-walk enzymes are the result of two coupled stochastic processes: scanning and catalysis. Here we develop analytical models to understand the conversion profiles produced by these enzymes, comparing an intrusive model, in which scanning and catalysis are tightly coupled, against a loosely coupled passive model. Diagrammatic theory and path-integral solutions of these models revealed clearly distinct predictions. Comparison to experimental data from catalyzed deaminations deposited on single-stranded DNA by the enzyme activation-induced deoxycytidine deaminase (AID) demonstrates that catalysis and diffusion are strongly intertwined, where the chemical conversions give rise to new stochastic trajectories that were absent if the substrate DNA was homogeneous. The C →U deamination profiles in both analytical predictions and experiments exhibit a strong contextual dependence, where the conversion rate of each target site is strongly contingent on the identities of other surrounding targets, with the intrusive model showing an excellent fit to the data. These methods can be applied to deduce sequence-dependent catalytic signatures of other DNA modification enzymes, with potential applications to cancer, gene regulation, and epigenetics.

  2. Random-walk enzymes

    PubMed Central

    Mak, Chi H.; Pham, Phuong; Afif, Samir A.; Goodman, Myron F.

    2015-01-01

    Enzymes that rely on random walk to search for substrate targets in a heterogeneously dispersed medium can leave behind complex spatial profiles of their catalyzed conversions. The catalytic signatures of these random-walk enzymes are the result of two coupled stochastic processes: scanning and catalysis. Here we develop analytical models to understand the conversion profiles produced by these enzymes, comparing an intrusive model, in which scanning and catalysis are tightly coupled, against a loosely coupled passive model. Diagrammatic theory and path-integral solutions of these models revealed clearly distinct predictions. Comparison to experimental data from catalyzed deaminations deposited on single-stranded DNA by the enzyme activation-induced deoxycytidine deaminase (AID) demonstrates that catalysis and diffusion are strongly intertwined, where the chemical conversions give rise to new stochastic trajectories that were absent if the substrate DNA was homogeneous. The C → U deamination profiles in both analytical predictions and experiments exhibit a strong contextual dependence, where the conversion rate of each target site is strongly contingent on the identities of other surrounding targets, with the intrusive model showing an excellent fit to the data. These methods can be applied to deduce sequence-dependent catalytic signatures of other DNA modification enzymes, with potential applications to cancer, gene regulation, and epigenetics. PMID:26465508

  3. Traveling waves of in vitro evolving RNA.

    PubMed Central

    Bauer, G J; McCaskill, J S; Otten, H

    1989-01-01

    Populations of short self-replicating RNA variants have been confined to one side of a reaction-diffusion traveling wave front propagating along thin capillary tubes containing the Q beta viral enzyme. The propagation speed is accurately measurable with a magnitude of about 1 micron/sec, and the wave persists for hundreds of generations (of duration less than 1 min). Evolution of RNA occurs in the wavefront, as established by front velocity changes and gel electrophoresis of samples drawn from along the capillary. The high population numbers (approximately equal to 10(11], their well-characterized biochemistry, their short generation time, and the constant conditions make the system ideal for evolution experiments. Growth is monitored continuously by excitation of an added RNA-sensitive fluorescent dye, ethidium bromide. An analytic expression for the front velocity is derived for the multicomponent kinetic scheme that reduces, for a high RNA-enzyme binding constant, to the Fisher form v = 2 square root of kappa D, where D is the diffusion constant of the complex and kappa is the low-concentration overall replication rate coefficient. The latter is confirmed as the selective value-determining parameter by numerical solution of a two-species system. Images PMID:2479013

  4. Parallel sites implicate functional convergence of the hearing gene prestin among echolocating mammals.

    PubMed

    Liu, Zhen; Qi, Fei-Yan; Zhou, Xin; Ren, Hai-Qing; Shi, Peng

    2014-09-01

    Echolocation is a sensory system whereby certain mammals navigate and forage using sound waves, usually in environments where visibility is limited. Curiously, echolocation has evolved independently in bats and whales, which occupy entirely different environments. Based on this phenotypic convergence, recent studies identified several echolocation-related genes with parallel sites at the protein sequence level among different echolocating mammals, and among these, prestin seems the most promising. Although previous studies analyzed the evolutionary mechanism of prestin, the functional roles of the parallel sites in the evolution of mammalian echolocation are not clear. By functional assays, we show that a key parameter of prestin function, 1/α, is increased in all echolocating mammals and that the N7T parallel substitution accounted for this functional convergence. Moreover, another parameter, V1/2, was shifted toward the depolarization direction in a toothed whale, the bottlenose dolphin (Tursiops truncatus) and a constant-frequency (CF) bat, the Stoliczka's trident bat (Aselliscus stoliczkanus). The parallel site of I384T between toothed whales and CF bats was responsible for this functional convergence. Furthermore, the two parameters (1/α and V1/2) were correlated with mammalian high-frequency hearing, suggesting that the convergent changes of the prestin function in echolocating mammals may play important roles in mammalian echolocation. To our knowledge, these findings present the functional patterns of echolocation-related genes in echolocating mammals for the first time and rigorously demonstrate adaptive parallel evolution at the protein sequence level, paving the way to insights into the molecular mechanism underlying mammalian echolocation. PMID:24951728

  5. Converging shocks in elastic-plastic solids.

    PubMed

    Ortega, A López; Lombardini, M; Hill, D J

    2011-11-01

    We present an approximate description of the behavior of an elastic-plastic material processed by a cylindrically or spherically symmetric converging shock, following Whitham's shock dynamics theory. Originally applied with success to various gas dynamics problems, this theory is presently derived for solid media, in both elastic and plastic regimes. The exact solutions of the shock dynamics equations obtained reproduce well the results obtained by high-resolution numerical simulations. The examined constitutive laws share a compressible neo-Hookean structure for the internal energy e=e(s)(I(1))+e(h)(ρ,ς), where e(s) accounts for shear through the first invariant of the Cauchy-Green tensor, and e(h) represents the hydrostatic contribution as a function of the density ρ and entropy ς. In the strong-shock limit, reached as the shock approaches the axis or origin r=0, we show that compression effects are dominant over shear deformations. For an isothermal constitutive law, i.e., e(h)=e(h)(ρ), with a power-law dependence e(h) is proportional to ρ(α), shock dynamics predicts that for a converging shock located at r=R(t) at time t, the Mach number increases as M is proportional to [log(1/R)](α), independently of the space index s, where s=2 in cylindrical geometry and 3 in spherical geometry. An alternative isothermal constitutive law with p(ρ) of the arctanh type, which enforces a finite density in the strong-shock limit, leads to M is proportional to R(-(s-1)) for strong shocks. A nonisothermal constitutive law, whose hydrostatic part e(h) is that of an ideal gas, is also tested, recovering the strong-shock limit M is proportional to R(-(s-1)/n(γ)) originally derived by Whitham for perfect gases, where γ is inherently related to the maximum compression ratio that the material can reach, (γ+1)/(γ-1). From these strong-shock limits, we also estimate analytically the density, radial velocity, pressure, and sound speed immediately behind the shock. While the

  6. Converging shocks in elastic-plastic solids

    NASA Astrophysics Data System (ADS)

    López Ortega, A.; Lombardini, M.; Hill, D. J.

    2011-11-01

    We present an approximate description of the behavior of an elastic-plastic material processed by a cylindrically or spherically symmetric converging shock, following Whitham's shock dynamics theory. Originally applied with success to various gas dynamics problems, this theory is presently derived for solid media, in both elastic and plastic regimes. The exact solutions of the shock dynamics equations obtained reproduce well the results obtained by high-resolution numerical simulations. The examined constitutive laws share a compressible neo-Hookean structure for the internal energy e=es(I1)+eh(ρ,ς), where es accounts for shear through the first invariant of the Cauchy-Green tensor, and eh represents the hydrostatic contribution as a function of the density ρ and entropy ς. In the strong-shock limit, reached as the shock approaches the axis or origin r=0, we show that compression effects are dominant over shear deformations. For an isothermal constitutive law, i.e., eh=eh(ρ), with a power-law dependence eh∝ρα, shock dynamics predicts that for a converging shock located at r=R(t) at time t, the Mach number increases as M∝[log(1/R)]α, independently of the space index s, where s=2 in cylindrical geometry and 3 in spherical geometry. An alternative isothermal constitutive law with p(ρ) of the arctanh type, which enforces a finite density in the strong-shock limit, leads to M∝R-(s-1) for strong shocks. A nonisothermal constitutive law, whose hydrostatic part eh is that of an ideal gas, is also tested, recovering the strong-shock limit M∝R-(s-1)/n(γ) originally derived by Whitham for perfect gases, where γ is inherently related to the maximum compression ratio that the material can reach, (γ+1)/(γ-1). From these strong-shock limits, we also estimate analytically the density, radial velocity, pressure, and sound speed immediately behind the shock. While the hydrostatic part of the energy essentially commands the strong-shock behavior, the shear

  7. The ENZYME database in 2000.

    PubMed

    Bairoch, A

    2000-01-01

    The ENZYME database is a repository of information related to the nomenclature of enzymes. In recent years it has became an indispensable resource for the development of metabolic databases. The current version contains information on 3705 enzymes. It is available through the ExPASy WWW server (http://www.expasy.ch/enzyme/ ). PMID:10592255

  8. The ENZYME database in 2000

    PubMed Central

    Bairoch, Amos

    2000-01-01

    The ENZYME database is a repository of information related to the nomenclature of enzymes. In recent years it has became an indispensable resource for the development of metabolic databases. The current version contains information on 3705 enzymes. It is available through the ExPASy WWW server (http://www. expasy.ch/enzyme/ ). PMID:10592255

  9. Cuckoo Search Algorithm Based on Repeat-Cycle Asymptotic Self-Learning and Self-Evolving Disturbance for Function Optimization

    PubMed Central

    Wang, Jie-sheng; Li, Shu-xia; Song, Jiang-di

    2015-01-01

    In order to improve convergence velocity and optimization accuracy of the cuckoo search (CS) algorithm for solving the function optimization problems, a new improved cuckoo search algorithm based on the repeat-cycle asymptotic self-learning and self-evolving disturbance (RC-SSCS) is proposed. A disturbance operation is added into the algorithm by constructing a disturbance factor to make a more careful and thorough search near the bird's nests location. In order to select a reasonable repeat-cycled disturbance number, a further study on the choice of disturbance times is made. Finally, six typical test functions are adopted to carry out simulation experiments, meanwhile, compare algorithms of this paper with two typical swarm intelligence algorithms particle swarm optimization (PSO) algorithm and artificial bee colony (ABC) algorithm. The results show that the improved cuckoo search algorithm has better convergence velocity and optimization accuracy. PMID:26366164

  10. Cuckoo Search Algorithm Based on Repeat-Cycle Asymptotic Self-Learning and Self-Evolving Disturbance for Function Optimization.

    PubMed

    Wang, Jie-sheng; Li, Shu-xia; Song, Jiang-di

    2015-01-01

    In order to improve convergence velocity and optimization accuracy of the cuckoo search (CS) algorithm for solving the function optimization problems, a new improved cuckoo search algorithm based on the repeat-cycle asymptotic self-learning and self-evolving disturbance (RC-SSCS) is proposed. A disturbance operation is added into the algorithm by constructing a disturbance factor to make a more careful and thorough search near the bird's nests location. In order to select a reasonable repeat-cycled disturbance number, a further study on the choice of disturbance times is made. Finally, six typical test functions are adopted to carry out simulation experiments, meanwhile, compare algorithms of this paper with two typical swarm intelligence algorithms particle swarm optimization (PSO) algorithm and artificial bee colony (ABC) algorithm. The results show that the improved cuckoo search algorithm has better convergence velocity and optimization accuracy. PMID:26366164

  11. Convergent evolution of health information management and health informatics: a perspective on the future of information professionals in health care.

    PubMed

    Gibson, C J; Dixon, B E; Abrams, K

    2015-01-01

    Clearly defined boundaries are disappearing among the activities, sources, and uses of health care data and information managed by health information management (HIM) and health informatics (HI) professionals. Definitions of the professional domains and scopes of practice for HIM and HI are converging with the proliferation of information and communication technologies in health care settings. Convergence is changing both the roles that HIM and HI professionals serve in their organizations as well as the competencies necessary for training future professionals. Many of these changes suggest a blurring of roles and responsibilities with increasingly overlapping curricula, job descriptions, and research agendas. Blurred lines in a highly competitive market create confusion for students and employers. In this essay, we provide some perspective on the changing landscape and suggest a course for the future. First we review the evolving definitions of HIM and HI. We next compare the current domains and competencies, review the characteristics as well as the education and credentialing of both disciplines, and examine areas of convergence. Given the current state, we suggest a path forward to strengthen the contributions HIM and HI professionals and educators make to the evolving health care environment. PMID:25848421

  12. Character State Reconstruction of Call Diversity in the Neoconocephalus Katydids Reveals High Levels of Convergence.

    PubMed

    Frederick, Katy; Schul, Johannes

    2016-01-01

    The katydid genus Neoconocephalus is characterized by high diversity of the acoustic communication system. Both male signals and female preferences have been thoroughly studied in the past. This study used Bayesian character state reconstruction to elucidate the evolutionary history of diverse call traits, based on an existing, well supported phylogenetic hypothesis. The most common male call pattern consisted of continuous calls comprising one fast pulse rate; this pattern is the likely ancestral state in this genus. Three lines of call divergence existed among the species of the genus. First, four species had significantly slower pulse rates. Second, five species had alternating pulse periods, resulting in a double pulse rhythm. Third, several species had discontinuous calls, when pulses were grouped into rhythmically repeated verses. Bayesian character state reconstruction revealed that the double-pulse pattern likely evolved convergently five times; the slow pulse rate also evolved four times independently. Discontinuous calls have evolved twice and occur in two clades; each of which contains reversals to the ancestral continuous calls. Pairwise phylogenetically independent contrast analyses among the three call traits found no significant correlations among the character states of the different traits, supporting the independent evolution of the three call traits. PMID:27110432

  13. The evolution of new enzyme function: lessons from xenobiotic metabolizing bacteria versus insecticide-resistant insects

    PubMed Central

    Russell, Robyn J; Scott, Colin; Jackson, Colin J; Pandey, Rinku; Pandey, Gunjan; Taylor, Matthew C; Coppin, Christopher W; Liu, Jian-Wei; Oakeshott, John G

    2011-01-01

    Here, we compare the evolutionary routes by which bacteria and insects have evolved enzymatic processes for the degradation of four classes of synthetic chemical insecticide. For insects, the selective advantage of such degradative activities is survival on exposure to the insecticide, whereas for the bacteria the advantage is simply a matter of access to additional sources of nutrients. Nevertheless, bacteria have evolved highly efficient enzymes from a wide variety of enzyme families, whereas insects have relied upon generalist esterase-, cytochrome P450- and glutathione-S-transferase-dependent detoxification systems. Moreover, the mutant insect enzymes are less efficient kinetically and less diverged in sequence from their putative ancestors than their bacterial counterparts. This presumably reflects several advantages that bacteria have over insects in the acquisition of new enzymatic functions, such as a broad biochemical repertoire from which new functions can be evolved, large population sizes, high effective mutation rates, very short generation times and access to genetic diversity through horizontal gene transfer. Both the insect and bacterial systems support recent theory proposing that new biochemical functions often evolve from ‘promiscuous’ activities in existing enzymes, with subsequent mutations then enhancing those activities. Study of the insect enzymes will help in resistance management, while the bacterial enzymes are potential bioremediants of insecticide residues in a range of contaminated environments. PMID:25567970

  14. Spherically-Convergent, Advanced-Fuel Systems

    NASA Astrophysics Data System (ADS)

    Barnes, D. C.; Nebel, R. A.; Schauer, M. M.; Umstadter, K. R.

    1998-11-01

    Combining nonneutral electron confinement with spherical ion convergence leads to a cm sized reactor volume with high power density.(R. A. Nebel and D. C. Barnes, Fusion Technol.), to appear (1998); D. C. Barnes and R. A. Nebel, Phys. of Plasmas 5, 2498 (1998). This concept is being investigated experimentally,(D. C. Barnes, T. B. Mitchell, and M. M. Schauer, Phys. Plasmas) 4, 1745 (1997). and results will be reported. We argue that D-D operation of such a system offers all the advantages of aneutronic fusion cycles. In particular, no breeding or large tritium inventory is required, and material problems seem tractable based on previous LWR experience. In addition the extremely small unit size leads to a massively modular system which is easily maintained and repaired, suggesting a very high availability. It may also be possible to operate such a system with low or aneutronic fuels. Preliminary work in this direction will be presented.

  15. Converging Intracranial Markers of Conscious Access

    PubMed Central

    Gaillard, Raphaël; Dehaene, Stanislas; Adam, Claude; Clémenceau, Stéphane; Hasboun, Dominique; Baulac, Michel; Cohen, Laurent; Naccache, Lionel

    2009-01-01

    We compared conscious and nonconscious processing of briefly flashed words using a visual masking procedure while recording intracranial electroencephalogram (iEEG) in ten patients. Nonconscious processing of masked words was observed in multiple cortical areas, mostly within an early time window (<300 ms), accompanied by induced gamma-band activity, but without coherent long-distance neural activity, suggesting a quickly dissipating feedforward wave. In contrast, conscious processing of unmasked words was characterized by the convergence of four distinct neurophysiological markers: sustained voltage changes, particularly in prefrontal cortex, large increases in spectral power in the gamma band, increases in long-distance phase synchrony in the beta range, and increases in long-range Granger causality. We argue that all of those measures provide distinct windows into the same distributed state of conscious processing. These results have a direct impact on current theoretical discussions concerning the neural correlates of conscious access. PMID:19296722

  16. Convergent solid-phase synthesis of hirudin.

    PubMed

    Goulas, Spyros; Gatos, Dimitrios; Barlos, Kleomenis

    2006-02-01

    Hirudin variant 1 (HV1), a small protein consisting of 65 amino acids and three disulfide bonds, was synthesized by using Fmoc-based convergent methods on 2-chlorotrityl resin (CLTR). The linear sequence was assembled by the sequential condensation of 7 protected fragments, on the resin-bound 55-65 fragment. The conditions of fragment assembly were carefully studied to determine the most efficient synthetic protocol. Crude reduced [Cys(16, 28)(Acm)]-HV1 thus obtained was easily purified to homogeneity by RP-HPLC. Disulfide bridges were successfully formed by a two-step procedure, involving an oxidative folding step to form Cys(6)-Cys(14) and Cys(22)-Cys(39) linkages, followed by iodine oxidation to form the Cys(16)-Cys(28) bond. The correct disulfide bond alignment was established by peptide mapping using Staphylococcus aureus V8 protease at pH 4.5. PMID:15952245

  17. Relative entropy convergence for depolarizing channels

    NASA Astrophysics Data System (ADS)

    Müller-Hermes, Alexander; Stilck França, Daniel; Wolf, Michael M.

    2016-02-01

    We study the convergence of states under continuous-time depolarizing channels with full rank fixed points in terms of the relative entropy. The optimal exponent of an upper bound on the relative entropy in this case is given by the log-Sobolev-1 constant. Our main result is the computation of this constant. As an application, we use the log-Sobolev-1 constant of the depolarizing channels to improve the concavity inequality of the von Neumann entropy. This result is compared to similar bounds obtained recently by Kim and we show a version of Pinsker's inequality, which is optimal and tight if we fix the second argument of the relative entropy. Finally, we consider the log-Sobolev-1 constant of tensor-powers of the completely depolarizing channel and use a quantum version of Shearer's inequality to prove a uniform lower bound.

  18. Nonlinear Resonance Cones and Converging Plasma Blobs

    NASA Astrophysics Data System (ADS)

    Agmon, Nathan; Pribyl, Patrick; Gekelman, Walter; Wise, Joe; Katz, Cami; Ha, Chis; Baker, Bob

    2013-10-01

    Electric field resonance cones have been shown to create density disturbances in cold, magnetized plasmas. Two circular antennas in the LAPTAG experimental plasma device were used to create converging, nonlinear resonance cones. The nonlinear electrostatic field is produced by large amplitude RF (ERF/nkTe >> 1). A movable probe, powered by a computerized motor and consisting of three mutually orthogonal electric dipoles, is used to measure the electric field of the cones which become distorted at large amplitudes. A 2D movable Langmuir probe was used to determine localized density perturbations after turn-off of the RF power. A density blob moving at 3-5 times the ion sound speed has been observed to propagate away (for at least 20 cm) from the focus of the cone. Two ring antennas produced colliding blobs. The physics of the collision will be described. Work performed at the Basic Plasma Science Facility supported by DOE and NSF.

  19. Positive Cardiovascular Health: A Timely Convergence.

    PubMed

    Labarthe, Darwin R; Kubzansky, Laura D; Boehm, Julia K; Lloyd-Jones, Donald M; Berry, Jarett D; Seligman, Martin E P

    2016-08-23

    Two concepts, positive health and cardiovascular health, have emerged recently from the respective fields of positive psychology and preventive cardiology. These parallel constructs are converging to foster positive cardiovascular health and a growing collaboration between psychologists and cardiovascular scientists to achieve significant improvements in both individual and population cardiovascular health. We explore these 2 concepts and note close similarities in the measures that define them, the health states that they aim to produce, and their intended long-term clinical and public health outcomes. We especially examine subjective health assets, such as optimism, that are a core focus of positive psychology, but have largely been neglected in preventive cardiology. We identify research to date on positive cardiovascular health, discuss its strengths and limitations thus far, and outline directions for further engagement of cardiovascular scientists with colleagues in positive psychology to advance this new field. PMID:27539179

  20. The 1977 intertropical convergence zone experiment

    NASA Technical Reports Server (NTRS)

    Poppoff, I. G. (Editor); Page, W. A. (Editor); Margozzi, A. P. (Editor)

    1979-01-01

    Data are presented from the 1977 Intertropical Convergence Zone (ITCZ) Experiment conducted in the Panama Canal Zone in July 1977. Measurements were made daily over a 16-day period when the ITCZ moved across the Canal Zone. Two aircraft (Learjet and U-2) flew daily and provided data from horizontal traverses at several altitudes to 21.3 km of ozone, temperature, pressure, water vapor, aerosols, fluorocarbons, methane, nitrous oxide, nitric oxide, and nitric acid. Balloonsondes flown four times per day provided data on ozone, wind fields, pressure, temperature, and humidities to altitudes near 30 km. Rocketsondes provided daily data to altitudes near 69 km. Satellite photography provided detailed cloud information. Descriptions of individual experiments and detailed compilations of all results are provided.

  1. Unstable resonators with excited converging wave

    SciTech Connect

    Hodgson, N. ); Weber, H. )

    1990-04-01

    This paper reports the properties of unstable resonators with an additional mirror inside or outside the resonator investigated, both experimentally and theoretically. The additional mirror excites the converging wave, and by this, output coupling is decreased without affecting beam quality. Experiments were performed with a pulsed Nd:YAG system. The theoretical model was based on the coupled Kirchhoff integrals and solved numerically. Agreement between theory and experiments indicates that this kind of resonator provides high focusability and maximum extraction efficiency simultaneously, even with low-gain media. This enables one to apply unstable resonators to solid-state lasers with low small-signal gain, like alexandrite or CW-pumped Nd:YAG.

  2. Convergent evolution in primates and an insectivore

    SciTech Connect

    Boffelli, Dario; Cheng, Jan-Fang; Rubin, Edward M.

    2003-04-16

    The cardiovascular risk factor apolipoprotein(a) (apo(a)) has a puzzling distribution among mammals, its presence being limited to a subset of primates and a member of the insectivore lineage, the hedgehog. To explore the evolutionary history of apo(a), we performed extensive genomic sequence comparisons of multiple species with and without an apo(a) gene product, such as human, baboon, hedgehog, lemurand mouse. This analysis indicated that apo(a) arose independently in a subset of primates, including baboon and human, and an insectivore, the hedgehog, and was not simply lost by species lacking it. The similar structural domains shared by the hedgehog and primate apo(a) indicate that they were formed by a unique molecular mechanism involving the convergent evolution of paralogous genes in these distantspecies.

  3. Improving the Convergence of Reversible Samplers

    NASA Astrophysics Data System (ADS)

    Rey-Bellet, Luc; Spiliopoulos, Konstantinos

    2016-06-01

    In Monte-Carlo methods the Markov processes used to sample a given target distribution usually satisfy detailed balance, i.e. they are time-reversible. However, relatively recent results have demonstrated that appropriate reversible and irreversible perturbations can accelerate convergence to equilibrium. In this paper we present some general design principles which apply to general Markov processes. Working with the generator of Markov processes, we prove that for some of the most commonly used performance criteria, i.e., spectral gap, asymptotic variance and large deviation functionals, sampling is improved for appropriate reversible and irreversible perturbations of some initially given reversible sampler. Moreover we provide specific constructions for such reversible and irreversible perturbations for various commonly used Markov processes, such as Markov chains and diffusions. In the case of diffusions, we make the discussion more specific using the large deviations rate function as a measure of performance.

  4. Parallel C/C++: Convergence or divergence?

    SciTech Connect

    Stanberry, L.

    1993-12-31

    C has been noted for its wide portability. C++ is touted as the next generation C. Both languages, however, have multiple proposals for parallel extensions. For C, this includes two different ANSI sponsored efforts, X3H5 and X3J11.1. Since C++ is itself in the throes of standardization, parallel C++ proposals are finding their audience among MPP vendors and C++ users in an ARPA-sponsored HPC++ consortium. The number of proposals is large and still growing, and questions arise of whether and how these proposals can converge in order to extend/preserve/protect the investment of the user community. In this panel the authors will bring together representatives from the ANSI committees, MPP vendors, and from independent research efforts to discuss the motivation for their respective proposals, to determine the interoperability of the proposals, and to argue for or against merging of proposals for a standard.

  5. Improving the Convergence of Reversible Samplers

    NASA Astrophysics Data System (ADS)

    Rey-Bellet, Luc; Spiliopoulos, Konstantinos

    2016-08-01

    In Monte-Carlo methods the Markov processes used to sample a given target distribution usually satisfy detailed balance, i.e. they are time-reversible. However, relatively recent results have demonstrated that appropriate reversible and irreversible perturbations can accelerate convergence to equilibrium. In this paper we present some general design principles which apply to general Markov processes. Working with the generator of Markov processes, we prove that for some of the most commonly used performance criteria, i.e., spectral gap, asymptotic variance and large deviation functionals, sampling is improved for appropriate reversible and irreversible perturbations of some initially given reversible sampler. Moreover we provide specific constructions for such reversible and irreversible perturbations for various commonly used Markov processes, such as Markov chains and diffusions. In the case of diffusions, we make the discussion more specific using the large deviations rate function as a measure of performance.

  6. Cylindrically converging blast waves in air

    NASA Astrophysics Data System (ADS)

    Matsuo, H.; Nakamura, Y.

    1981-07-01

    Cylindrically converging shock waves are produced by utilizing the detonation of cylindrical explosive shells. The production and the propagation of shock waves are observed by framing and streak camera photographs, and the trajectory of shock propagations is determined by using an electrical ionization probing system. The effect of the quantity of explosives on the stability, or the axial symmetry, of shock fronts and on the strength of shocks produced is investigated. It has been shown that, for practical purposes, the approximation of shock trajectories by Guderley's formulas would be sufficiently acceptable in an unexpectedly wide region near the implosion center, and that the axial symmetry of the shock front is improved by increasing the quantity of explosives, and thus, strong shocks are produced by merely increasing the quantity of explosives. The reflected diverging shock seems to be very stable. Piezoelectric elements have also been used to detect reflected diverging waves.

  7. Comparative Laboratory Evolution of Ordered and Disordered Enzymes*♦

    PubMed Central

    Schulenburg, Cindy; Stark, Yvonne; Künzle, Matthias; Hilvert, Donald

    2015-01-01

    Intrinsically disordered proteins are ubiquitous in nature. To assess potential evolutionary advantages and disadvantages of structural disorder under controlled laboratory conditions, we directly compared the evolvability of weakly active ordered and disordered variants of dihydrofolate reductase by genetic selection. The circularly permuted Escherichia coli enzyme, which exists as a molten globule in the absence of ligands, and a well folded deletion mutant of the Bacillus stearothermophilus enzyme served as starting points. Both scaffolds evolved at similar rates and to similar extents, reaching near-native activity after three rounds of mutagenesis and selection. Surprisingly, however, the starting structural properties of the two scaffolds changed only marginally during optimization. Although the ordered and disordered proteins accumulated distinct sets of mutations, the changes introduced likely improved catalytic efficiency indirectly in both cases by bolstering the network of dynamic conformational fluctuations that productively couple into the reaction coordinate. PMID:25697360

  8. Comparative laboratory evolution of ordered and disordered enzymes.

    PubMed

    Schulenburg, Cindy; Stark, Yvonne; Künzle, Matthias; Hilvert, Donald

    2015-04-10

    Intrinsically disordered proteins are ubiquitous in nature. To assess potential evolutionary advantages and disadvantages of structural disorder under controlled laboratory conditions, we directly compared the evolvability of weakly active ordered and disordered variants of dihydrofolate reductase by genetic selection. The circularly permuted Escherichia coli enzyme, which exists as a molten globule in the absence of ligands, and a well folded deletion mutant of the Bacillus stearothermophilus enzyme served as starting points. Both scaffolds evolved at similar rates and to similar extents, reaching near-native activity after three rounds of mutagenesis and selection. Surprisingly, however, the starting structural properties of the two scaffolds changed only marginally during optimization. Although the ordered and disordered proteins accumulated distinct sets of mutations, the changes introduced likely improved catalytic efficiency indirectly in both cases by bolstering the network of dynamic conformational fluctuations that productively couple into the reaction coordinate. PMID:25697360

  9. The Converged Experience of Risk and Disease

    PubMed Central

    Aronowitz, Robert A

    2009-01-01

    Context: One underappreciated consequence of modern clinical and public health practices is that the experience of being at risk for disease has been converging with the experience of disease itself. This is especially true for certain chronic diseases, in which early diagnosis and aggressive treatment have led to symptom-less and sign-less disease and in which treatments have largely been aimed at altering the disease's future course. Methods: This article reviews the historical scholarship and medical literature pertinent to transformations in the chronic disease and risk experiences. Findings: The experience of chronic disease increasingly resembles or has become indistinguishable from risk because of (1) new clinical interventions that have directly changed the natural history of disease; (2) increased biological, clinical, and epidemiological knowledge about the risk of chronic disease; (3) the recruitment of larger numbers into chronic disease diagnoses via new screening and diagnostic technology and disease definitions; (4) new ways of conceptualizing efficacy; and (5) intense diagnostic testing and medical interventions. Conclusions: The converged experience of risk and disease has led to some unsettling and generally underappreciated consequences that might be subjected to more clinical and policy reflection and response: (1) some puzzling trends in medical decision making, such as the steep and uniform increase in the numbers of women across a broad spectrum of risk/disease in breast cancer who have opted for prophylactic mastectomies; (2) a larger and highly mobilized disease/risk population, resulting in an expanded market for interventions and greater clout for disease advocates; (3) shifts in the perceived severity of the disease, with ripple effects on how people experience and understand their illness and risk of disease; and (4) interventions that promise both to reduce the risk of disease and to treat its symptoms. PMID:19523124

  10. Cooperative target convergence using multiple agents

    SciTech Connect

    Kwok, K.S.; Driessen, B.J.

    1997-10-01

    This work considers the problem of causing multiple (100`s) autonomous mobile robots to converge to a target and provides a follow-the-leader approach to the problem. Each robot has only a limited-range sensor for sending the target and also larger but also limited-range robot-to-robot communication capability. Because of the small amount of information available to the robots, a practical approach to improve convergence to the target is to have a robot follow the robot with the best quality of information. Specifically, each robot emits a signal that informs in-range robots what its status is. A robot has a status value of 0 if it is itself in range of the target. A robot has a status of 1 if it is not in range of the target but is in communication range of a robot that is in range of the target. A robot has a status of 2 if it is not in range of the target but is within range of another robot that has status 1, and so on. Of all the mobile robots that any given robot is in range of, it follows the one with the best status. The emergent behavior is the ant-like trails of robots following each other toward the target. If the robot is not in range of another robot that is either in range of the target or following another robot, the robot will assign-1 to its quality-of-information, and will execute an exhaustive search. The exhaustive search will continue until it encounters either the target or another robot with a nonnegative quality-of-information. The quality of information approach was extended to the case where each robot only has two-bit signals informing it of distance to in-range robots.

  11. Toying with Enzyme Catalysis.

    ERIC Educational Resources Information Center

    Richards, Debbie

    1998-01-01

    Describes a set of manipulatives that are used to establish a secure understanding of the concepts related to the environmental factors that affect the activities of enzymes. Includes a description of the model components and procedures for construction of the model. (DDR)

  12. Photoperiodism and Enzyme Activity

    PubMed Central

    Queiroz, Orlando; Morel, Claudine

    1974-01-01

    Metabolic readjustments after a change from long days to short days appear, in Kalanchoe blossfeldiana, to be achieved through the operation of two main mechanisms: variation in enzyme capacity, and circadian rhythmicity. After a lag time, capacity in phosphoenolpyruvate carboxylase and capacity in aspartate aminotransferase increase exponentially and appear to be allometrically linked during 50 to 60 short days; then a sudden fall takes place in the activity of the former. Malic enzyme and alanine aminotransferase behave differently. Thus, the operation of the two sections of the pathway (before and after the malate step) give rise to a continuously changing functional compartmentation in the pathway. Circadian rhythmicity, on the other hand, produces time compartmentation through phase shifts and variation in amplitude, independently for each enzyme. These characteristics suggest that the operation of a so-called biological clock would be involved. We propose the hypothesis that feedback regulation would be more accurate and efficient when applied to an already oscillating, clock-controlled enzyme system. PMID:16658749

  13. Mismatch repair enhances convergent transcription-induced cell death at trinucleotide repeats by activating ATR.

    PubMed

    Chatterjee, Nimrat; Lin, Yunfu; Wilson, John H

    2016-06-01

    Trinucleotide repeat (TNR) expansion beyond a certain threshold results in some 20 incurable neurodegenerative disorders where disease anticipation positively correlates with repeat length. Long TNRs typically display a bias toward further expansion during germinal transmission from parents to offspring, and then are highly unstable in somatic tissues of affected individuals. Understanding mechanisms of TNR instability will provide insights into disease pathogenesis. Previously, we showed that enhanced convergent transcription at long CAG repeat tracks induces TNR instability and cell death via ATR activation. Components of TC-NER (transcription-coupled nucleotide excision repair) and RNaseH enzymes that resolve RNA/DNA hybrids oppose cell death, whereas the MSH2 component of MMR (mismatch repair) enhances cell death. The exact role of the MMR pathway during convergent transcription-induced cell death at CAG repeats is not well understood. In this study, we show that siRNA knockdowns of MMR components-MSH2, MSH3, MLHI, PMS2, and PCNA-reduce DNA toxicity. Furthermore, knockdown of MSH2, MLH1, and PMS2 significantly reduces the frequency of ATR foci formation. These observations suggest that MMR proteins activate DNA toxicity by modulating ATR foci formation during convergent transcription. PMID:27131875

  14. Generative Representations for Evolving Families of Designs

    NASA Technical Reports Server (NTRS)

    Hornby, Gregory S.

    2003-01-01

    Since typical evolutionary design systems encode only a single artifact with each individual, each time the objective changes a new set of individuals must be evolved. When this objective varies in a way that can be parameterized, a more general method is to use a representation in which a single individual encodes an entire class of artifacts. In addition to saving time by preventing the need for multiple evolutionary runs, the evolution of parameter-controlled designs can create families of artifacts with the same style and a reuse of parts between members of the family. In this paper an evolutionary design system is described which uses a generative representation to encode families of designs. Because a generative representation is an algorithmic encoding of a design, its input parameters are a way to control aspects of the design it generates. By evaluating individuals multiple times with different input parameters the evolutionary design system creates individuals in which the input parameter controls specific aspects of a design. This system is demonstrated on two design substrates: neural-networks which solve the 3/5/7-parity problem and three-dimensional tables of varying heights.

  15. Emerging and Evolving Ovarian Cancer Animal Models

    PubMed Central

    Bobbs, Alexander S; Cole, Jennifer M; Cowden Dahl, Karen D

    2015-01-01

    Ovarian cancer (OC) is the leading cause of death from a gynecological malignancy in the United States. By the time a woman is diagnosed with OC, the tumor has usually metastasized. Mouse models that are used to recapitulate different aspects of human OC have been evolving for nearly 40 years. Xenograft studies in immunocompromised and immunocompetent mice have enhanced our knowledge of metastasis and immune cell involvement in cancer. Patient-derived xenografts (PDXs) can accurately reflect metastasis, response to therapy, and diverse genetics found in patients. Additionally, multiple genetically engineered mouse models have increased our understanding of possible tissues of origin for OC and what role individual mutations play in establishing ovarian tumors. Many of these models are used to test novel therapeutics. As no single model perfectly copies the human disease, we can use a variety of OC animal models in hypothesis testing that will lead to novel treatment options. The goal of this review is to provide an overview of the utility of different mouse models in the study of OC and their suitability for cancer research. PMID:26380555

  16. Regulatory mechanisms link phenotypic plasticity to evolvability

    PubMed Central

    van Gestel, Jordi; Weissing, Franz J.

    2016-01-01

    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. PMID:27087393

  17. Exploring Evolving Media Discourse Through Event Cueing.

    PubMed

    Lu, Yafeng; Steptoe, Michael; Burke, Sarah; Wang, Hong; Tsai, Jiun-Yi; Davulcu, Hasan; Montgomery, Douglas; Corman, Steven R; Maciejewski, Ross

    2016-01-01

    Online news, microblogs and other media documents all contain valuable insight regarding events and responses to events. Underlying these documents is the concept of framing, a process in which communicators act (consciously or unconsciously) to construct a point of view that encourages facts to be interpreted by others in a particular manner. As media discourse evolves, how topics and documents are framed can undergo change, shifting the discussion to different viewpoints or rhetoric. What causes these shifts can be difficult to determine directly; however, by linking secondary datasets and enabling visual exploration, we can enhance the hypothesis generation process. In this paper, we present a visual analytics framework for event cueing using media data. As discourse develops over time, our framework applies a time series intervention model which tests to see if the level of framing is different before or after a given date. If the model indicates that the times before and after are statistically significantly different, this cues an analyst to explore related datasets to help enhance their understanding of what (if any) events may have triggered these changes in discourse. Our framework consists of entity extraction and sentiment analysis as lenses for data exploration and uses two different models for intervention analysis. To demonstrate the usage of our framework, we present a case study on exploring potential relationships between climate change framing and conflicts in Africa. PMID:26529702

  18. Sexual regret: evidence for evolved sex differences.

    PubMed

    Galperin, Andrew; Haselton, Martie G; Frederick, David A; Poore, Joshua; von Hippel, William; Buss, David M; Gonzaga, Gian C

    2013-10-01

    Regret and anticipated regret enhance decision quality by helping people avoid making and repeating mistakes. Some of people's most intense regrets concern sexual decisions. We hypothesized evolved sex differences in women's and men's experiences of sexual regret. Because of women's higher obligatory costs of reproduction throughout evolutionary history, we hypothesized that sexual actions, particularly those involving casual sex, would be regretted more intensely by women than by men. In contrast, because missed sexual opportunities historically carried higher reproductive fitness costs for men than for women, we hypothesized that poorly chosen sexual inactions would be regretted more by men than by women. Across three studies (Ns = 200, 395, and 24,230), we tested these hypotheses using free responses, written scenarios, detailed checklists, and Internet sampling to achieve participant diversity, including diversity in sexual orientation. Across all data sources, results supported predicted psychological sex differences and these differences were localized in casual sex contexts. These findings are consistent with the notion that the psychology of sexual regret was shaped by recurrent sex differences in selection pressures operating over deep time. PMID:23179233

  19. Evolving application of biomimetic nanostructured hydroxyapatite

    PubMed Central

    Roveri, Norberto; Iafisco, Michele

    2010-01-01

    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. PMID:24198477

  20. An evolving model of online bipartite networks

    NASA Astrophysics Data System (ADS)

    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.

  1. How does cognition evolve? Phylogenetic comparative psychology

    PubMed Central

    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

  2. The Evolved Pulsating CEMP Star HD 112869

    NASA Astrophysics Data System (ADS)

    Začs, Laimons; Sperauskas, Julius; Grankina, Aija; Deveikis, Viktoras; Kaminskyi, Bogdan; Pavlenko, Yakiv; Musaev, Faig A.

    2015-04-01

    Radial velocity measurements, BVRC 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 HD 112869 with a 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 HD 112869 appears to be less metal-poor than reported before, [Fe/H] = -2.3 ± 0.2 dex. Carbon-to-oxygen and carbon isotope ratios are found to be extremely high, C/O ≃ 12.6 and12C/13C ≳ 1500, respectively. The s-process elements yttrium and barium are not enhanced, but neodymium appears to be overabundant. The magnesium abundance seems to be lower than the average found for CEMP stars, [Mg/Fe] < +0.4 dex. HD 112869 could be a single low-mass halo star in the stage of asymptotic giant branch evolution.

  3. Minority games, evolving capitals and replicator dynamics

    NASA Astrophysics Data System (ADS)

    Galla, Tobias; Zhang, Yi-Cheng

    2009-11-01

    We discuss a simple version of the minority game (MG) in which agents hold only one strategy each, but in which their capitals evolve dynamically according to their success and in which the total trading volume varies in time accordingly. This feature is known to be crucial for MGs to reproduce stylized facts of real market data. The stationary states and phase diagram of the model can be computed, and we show that the ergodicity breaking phase transition common for MGs, and marked by a divergence of the integrated response, is present also in this simplified model. An analogous majority game turns out to be relatively void of interesting features, and the total capital is found to diverge in time. Introducing a restraining force leads to a model akin to the replicator dynamics of evolutionary game theory, and we demonstrate that here a different type of phase transition is observed. Finally we briefly discuss the relation of this model with one strategy per player to more sophisticated minority games with dynamical capitals and several trading strategies per agent.

  4. Evolving the ingredients for reciprocity and spite

    PubMed Central

    Hauser, Marc; McAuliffe, Katherine; Blake, Peter R.

    2009-01-01

    Darwin never provided a satisfactory account of altruism, but posed the problem beautifully in light of the logic of natural selection. Hamilton and Williams delivered the necessary satisfaction by appealing to kinship, and Trivers showed that kinship was not necessary as long as the originally altruistic act was conditionally reciprocated. From the late 1970s to the present, the kinship theories in particular have been supported by considerable empirical data and elaborated to explore a number of other social interactions such as cooperation, selfishness and punishment, giving us what is now a rich description of the nature of social relationships among organisms. There are, however, two forms of theoretically possible social interactions—reciprocity and spite—that appear absent or nearly so in non-human vertebrates, despite considerable research efforts on a wide diversity of species. We suggest that the rather weak comparative evidence for these interactions is predicted once we consider the requisite socioecological pressures and psychological mechanisms. That is, a consideration of ultimate demands and proximate prerequisites leads to the prediction that reciprocity and spite should be rare in non-human animals, and common in humans. In particular, reciprocity and spite evolved in humans because of adaptive demands on cooperation among unrelated individuals living in large groups, and the integrative capacities of inequity detection, future-oriented decision-making and inhibitory control. PMID:19805432

  5. Are Electronic Cardiac Devices Still Evolving?

    PubMed Central

    Mabo, P.

    2014-01-01

    Summary Objectives The goal of this paper is to review some important issues occurring during the past year in Implantable devices. Methods First cardiac implantable device was proposed to maintain an adequate heart rate, either because the heart’s natural pacemaker is not fast enough, or there is a block in the heart’s electrical conduction system. During the last forty years, pacemakers have evolved considerably and become programmable and allow to configure specific patient optimum pacing modes. Various technological aspects (electrodes, connectors, algorithms diagnosis, therapies, …) have been progressed and cardiac implants address several clinical applications: management of arrhythmias, cardioversion / defibrillation and cardiac resynchronization therapy. Results Observed progress was the miniaturization of device, increased longevity, coupled with efficient pacing functions, multisite pacing modes, leadless pacing and also a better recognition of supraventricular or ventricular tachycardia’s in order to deliver appropriate therapy. Subcutaneous implant, new modes of stimulation (leadless implant or ultrasound lead), quadripolar lead and new sensor or new algorithm for the hemodynamic management are introduced and briefly described. Each times, the main result occurring during the two past years are underlined and repositioned from the history, remaining limitations are also addressed. Conclusion Some important technological improvements were described. Nevertheless, news trends for the future are also considered in a specific session such as the remote follow-up of the patient or the treatment of heart failure by neuromodulation. PMID:25123732

  6. The evolved function of the oedipal conflict.

    PubMed

    Josephs, Lawrence

    2010-08-01

    Freud based his oedipal theory on three clinical observations of adult romantic relationships: (1) Adults tend to split love and lust; (2) There tend to be sex differences in the ways that men and women split love and lust; (3) Adult romantic relationships are unconsciously structured by the dynamics of love triangles in which dramas of seduction and betrayal unfold. Freud believed that these aspects of adult romantic relationships were derivative expressions of a childhood oedipal conflict that has been repressed. Recent research conducted by evolutionary psychologists supports many of Freud's original observations and suggests that Freud's oedipal conflict may have evolved as a sexually selected adaptation for reproductive advantage. The evolution of bi-parental care based on sexually exclusive romantic bonds made humans vulnerable to the costs of sexual infidelity, a situation of danger that seriously threatens monogamous bonds. A childhood oedipal conflict enables humans to better adapt to this longstanding evolutionary problem by providing the child with an opportunity to develop working models of love triangles. On the one hand, the oedipal conflict facilitates monogamous resolutions by creating intense anxiety about the dangers of sexual infidelity and mate poaching. On the other hand, the oedipal conflict in humans may facilitate successful cheating and mate poaching by cultivating a talent for hiding our true sexual intentions from others and even from ourselves. The oedipal conflict in humans may be disguised by evolutionary design in order to facilitate tactical deception in adult romantic relationships. PMID:20840647

  7. Gastric cancer: current and evolving treatment landscape.

    PubMed

    Sun, Weijing; Yan, Li

    2016-01-01

    Gastric (including gastroesophageal junction) cancer is the third leading cause of cancer-related death in the world. In China, an estimated 420,000 patients were diagnosed with gastric cancer in 2011, ranking this malignancy the second most prevalent cancer type and resulting in near 300,000 deaths. The treatment landscape of gastric cancer has evolved in recent years. Although systemic chemotherapy is still the mainstay treatment of metastatic disease, the introduction of agents targeting human epidermal growth factor receptor 2 and vascular endothelial growth factor/vascular endothelia growth factor receptor has brought this disease into the molecular and personalized medicine era. The preliminary yet encouraging clinical efficacy observed with immune checkpoint inhibitors, e.g., anti-programmed cell death protein 1/programmed death-ligand 1, will further shape the treatment landscape for gastric cancer. Molecular characterization of patients will play a critical role in developing new agents, as well as in implementing new treatment options for this disease. PMID:27581465

  8. Tearing Mode Stability of Evolving Toroidal Equilibria

    NASA Astrophysics Data System (ADS)

    Pletzer, A.; McCune, D.; Manickam, J.; Jardin, S. C.

    2000-10-01

    There are a number of toroidal equilibrium (such as JSOLVER, ESC, EFIT, and VMEC) and transport codes (such as TRANSP, BALDUR, and TSC) in our community that utilize differing equilibrium representations. There are also many heating and current drive (LSC and TORRAY), and stability (PEST1-3, GATO, NOVA, MARS, DCON, M3D) codes that require this equilibrium information. In an effort to provide seamless compatibility between the codes that produce and need these equilibria, we have developed two Fortran 90 modules, MEQ and XPLASMA, that serve as common interfaces between these two classes of codes. XPLASMA provides a common equilibrium representation for the heating and current drive applications while MEQ provides common equilibrium and associated metric information needed by MHD stability codes. We illustrate the utility of this approach by presenting results of PEST-3 tearing stability calculations of an NSTX discharge performed on profiles provided by the TRANSP code. Using the MEQ module, the TRANSP equilibrium data are stored in a Fortran 90 derived type and passed to PEST3 as a subroutine argument. All calculations are performed on the fly, as the profiles evolve.

  9. Origins and evolvability of the PAX family.

    PubMed

    Paixão-Côrtes, Vanessa R; Salzano, Francisco M; Bortolini, Maria Cátira

    2015-08-01

    The paired box (PAX) family of transcription/developmental genes plays a key role in numerous stages of embryonic development, as well as in adult organogenesis. There is evidence linking the acquisition of a paired-like DNA binding domain (PD) to domestication of a Tc1/mariner transposon. Further duplication/deletion processes led to at least five paralogous metazoan protein groups, which can be classified into two supergroups, PAXB-like or PAXD-like, using ancestral defining structures; the PD plus an octapeptide motif (OP) and a paired-type homeobox DNA binding domain (PTHD), producing the PD-OP-PTHD structure characteristic of the PAXB-like group, whereas an additional domain, the paired-type homeodomain tail (PHT), is present in the PAXD-like group, producing a PD-OP-PTHD-PHT structure. We examined their patterns of distribution in various species, using both available data and new bioinformatic analyses, including vertebrate PAX genes and their shared and specific functions, as well as inter- and intraspecific variability of PAX in primates. These analyses revealed a relatively conserved PAX network, accompanied by specific changes that led to adaptive novelties. Therefore, both stability and evolvability shaped the molecular evolution of this key transcriptional network. PMID:26321496

  10. Speciation genetics: current status and evolving approaches

    PubMed Central

    Wolf, Jochen B. W.; Lindell, Johan; Backström, Niclas

    2010-01-01

    The view of species as entities subjected to natural selection and amenable to change put forth by Charles Darwin and Alfred Wallace laid the conceptual foundation for understanding speciation. Initially marred by a rudimental understanding of hereditary principles, evolutionists gained appreciation of the mechanistic underpinnings of speciation following the merger of Mendelian genetic principles with Darwinian evolution. Only recently have we entered an era where deciphering the molecular basis of speciation is within reach. Much focus has been devoted to the genetic basis of intrinsic postzygotic isolation in model organisms and several hybrid incompatibility genes have been successfully identified. However, concomitant with the recent technological advancements in genome analysis and a newfound interest in the role of ecology in the differentiation process, speciation genetic research is becoming increasingly open to non-model organisms. This development will expand speciation research beyond the traditional boundaries and unveil the genetic basis of speciation from manifold perspectives and at various stages of the splitting process. This review aims at providing an extensive overview of speciation genetics. Starting from key historical developments and core concepts of speciation genetics, we focus much of our attention on evolving approaches and introduce promising methodological approaches for future research venues. PMID:20439277

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

    PubMed

    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. PMID:23712842

  12. Computational enzyme design

    NASA Astrophysics Data System (ADS)

    Bolon, Daniel N.

    2002-08-01

    The long-term objective of computational enzyme design is the ability to generate efficient protein catalysts for any chemical reaction. This thesis develops and experimentally validates a general computational approach for the design of enzymes with novel function. In order to include catalytic mechanism in protein design, a high-energy state (HES) rotamer (side chain representation) was constructed. In this rotamer, substrate atoms are in a HES. In addition, at least one amino acid side chain is positioned to interact favorably with substrate atoms in their HES and facilitate the reaction. Including an amino acid side chain in the HES rotamer automatically positions substrate relative to a protein scaffold and allows protein design algorithms to search for sequences capable of interacting favorably with the substrate. Because chemical similarity exists between the transition state and the high-energy state, optimizing the protein sequence to interact favorably with the HES rotamer should lead to transition state stabilization. In addition, the HES rotamer model focuses the subsequent computational active site design on a relevant phase space where an amino acid is capable of interacting in a catalytically active geometry with substrate. Using a HES rotamer model of the histidine mediated nucleophilic hydrolysis of p-nitrophenyl acetate, the catalytically inert 108 residue E. coli thioredoxin as a scaffold, and the ORBIT protein design software to compute sequences, an active site scan identified two promising active site designs. Experimentally, both candidate ?protozymes? demonstrated catalytic activity significantly above background. In addition, the rate enhancement of one of these ?protozymes? was the same order of magnitude as the first catalytic antibodies. Because polar groups are frequently buried at enzyme-substrate interfaces, improved modeling of buried polar interactions may benefit enzyme design. By studying native protein structures, rules have been

  13. Monitoring enzyme kinetic behavior of enzyme-quantum dot bioconjugates

    NASA Astrophysics Data System (ADS)

    Claussen, Jonathan C.; Walper, Scott A.; Susumu, Kimihiro; Ancona, Mario G.; Medintz, Igor L.

    2014-05-01

    Luminescent semiconductor nanocrystals or quantum dots (QDs) hold tremendous promise for in vivo biosensing, cellular imaging, theranostics, and smart molecular sensing probes due to their small size and favorable photonic properties such as resistance to photobleaching, size-tunable PL, and large effective Stokes shifts. Herein, we demonstrate how QD-based bioconjugates can be used to enhance enzyme kinetics. Enzyme-substrate kinetics are analyzed for solutions containing both alkaline phosphatase enzymes and QDs with enzyme-to- QD molar ratios of 2, 12, and 24 as well as for a solution containing the same concentration of enzymes but without QDs. The enzyme kinetic paramters Vmax, KM, and Kcat/KM are extracted from the enzyme progress curves via the Lineweaver-Burk plot. Results demonstrate an approximate increase in enzyme efficiency of 5 - 8% for enzymes immobilized on the QD versus free in solution without QD immobilization.

  14. Lower mass limit of an evolving interstellar cloud and chemistry in an evolving oscillatory cloud

    NASA Technical Reports Server (NTRS)

    Tarafdar, S. P.

    1986-01-01

    Simultaneous solution of the equation of motion, equation of state and energy equation including heating and cooling processes for interstellar medium gives for a collapsing cloud a lower mass limit which is significantly smaller than the Jeans mass for the same initial density. The clouds with higher mass than this limiting mass collapse whereas clouds with smaller than critical mass pass through a maximum central density giving apparently similar clouds (i.e., same Av, size and central density) at two different phases of its evolution (i.e., with different life time). Preliminary results of chemistry in such an evolving oscillatory cloud show significant difference in abundances of some of the molecules in two physically similar clouds with different life times. The problems of depletion and short life time of evolving clouds appear to be less severe in such an oscillatory cloud.

  15. Evolution of an Antibiotic Resistance Enzyme Constrained by Stability and Activity Trade-offs

    SciTech Connect

    Wang, Xiaojun; Minasov, George; Shoichet, Brian K.

    2010-03-08

    Pressured by antibiotic use, resistance enzymes have been evolving new activities. Does such evolution have a cost? To investigate this question at the molecular level, clinically isolated mutants of the {beta}-lactamase TEM-1 were studied. When purified, mutant enzymes had increased activity against cephalosporin antibiotics but lost both thermodynamic stability and kinetic activity against their ancestral targets, penicillins. The X-ray crystallographic structures of three mutant enzymes were determined. These structures suggest that activity gain and stability loss is related to an enlarged active site cavity in the mutant enzymes. In several clinically isolated mutant enzymes, a secondary substitution is observed far from the active site (Met182 {yields} Thr). This substitution had little effect on enzyme activity but restored stability lost by substitutions near the active site. This regained stability conferred an advantage in vivo. This pattern of stability loss and restoration may be common in the evolution of new enzyme activity.

  16. Advancing lignocellulose bioconversion through direct assessment of enzyme action on insoluble substrates.

    PubMed

    Goacher, Robyn E; Selig, Michael J; Master, Emma R

    2014-06-01

    Microbial utilization of lignocellulose from plant cell walls is integral to carbon cycling on Earth. Correspondingly, secreted enzymes that initiate lignocellulose depolymerization serve a crucial step in the bioconversion of lignocellulosic biomass to fuels and chemicals. Genome and metagenome sequencing efforts that span the past decade reveal the diversity of enzymes that have evolved to transform lignocellulose from wood, herbaceous plants and grasses. Nevertheless, there are relatively few examples where 'omic' technologies have identified novel enzyme activities or combinations thereof that dramatically improve the economics of lignocellulose bioprocessing and utilization. A likely factor contributing to the discrepancy between sequence-based enzyme discovery and enzyme application is the common practice to screen enzyme candidates based on activity measurements using soluble model compounds. In this context, the development and application of imaging, physicochemical, and spectromicroscopic techniques that allow direct assessment of enzyme action on relevant lignocellulosic substrates is reviewed. PMID:24525082

  17. Poly(ethylene glycol) conjugated enzyme with enhanced hydrophobic compatibility for self-cleaning coatings.

    PubMed

    Zhang, Liting; Wu, Songtao; Buthe, Andreas; Zhao, Xueyan; Jia, Hongfei; Zhang, Songping; Wang, Ping

    2012-11-01

    Enzyme-based smart materials constitute a rapidly growing group of functional materials. Often the natively evolved enzymes are not compatible with hydrophobic synthetic materials, thus significantly limiting the performance of enzymes. This work investigates the use of a polyethylene glycol (PEG)-conjugated detergent enzyme for self-cleaning coatings. As a result, PEG conjugated α-amylase demonstrated a much more homogeneous distribution in polyurethane coatings than the parent native enzyme as detected by both fluorescent microscopy and scanning electron microscopy (SEM) equipped with energy-dispersive X-ray spectroscopy (SEM-EDX). Additionally, the conjugated enzyme showed enhanced retention in the coating and much improved thermal stability with a halflife of 20 days detected at 80 °C and over 350 days under room temperature. Such coating-incorporated enzyme afforded interesting self-cleaning functionality against starch-based stains as examined through a slipping drop test. PMID:23067105

  18. Convergent perturbation theory for lattice models with fermions

    NASA Astrophysics Data System (ADS)

    Sazonov, V. K.

    2016-05-01

    The standard perturbation theory in QFT and lattice models leads to the asymptotic expansions. However, an appropriate regularization of the path or lattice integrals allows one to construct convergent series with an infinite radius of the convergence. In the earlier studies, this approach was applied to the purely bosonic systems. Here, using bosonization, we develop the convergent perturbation theory for a toy lattice model with interacting fermionic and bosonic fields.

  19. Linear perturbations of a Schwarzschild blackhole by thin disc - convergence

    NASA Astrophysics Data System (ADS)

    Čížek, P.; Semerák, O.

    2012-07-01

    In order to find the perturbation of a Schwarzschild space-time due to a rotating thin disc, we try to adjust the method used by [4] in the case of perturbation by a one-dimensional ring. This involves solution of stationary axisymmetric Einstein's equations in terms of spherical-harmonic expansions whose convergence however turned out questionable in numerical examples. Here we show, analytically, that the series are almost everywhere convergent, but in some regions the convergence is not absolute.

  20. [Convergent Care Research: use in developing models of nursing care].

    PubMed

    Rocha, Patrícia Kuerten; do Prado, Marta Lenise; da Silva, Denise Maria Guerreiro Vieira

    2012-01-01

    The present text is a theoretical reflection upon the importance of Nursing care models for the consolidation of this discipline, concerning the contribution of Convergent Care Research (Pesquisa Convergente Assistencial -PCA) in elaborating such models. Beyond this, this article discusses the importance of Convergent Care Research in the convergence of the academic and practical worlds of nursing, which aid towards a safe practice, systematize care, and establish connections between pragmatism and scientism, leading nurses to adopt more solid knowledge construction postures. PMID:23559182

  1. A new look at the convergence of a famous sequence

    NASA Astrophysics Data System (ADS)

    Dobrescu, Mihaela

    2010-12-01

    A new proof for the monotonicity of the sequence ? is given as a special case of a large family of monotomic and bounded, hence convergent sequences. The new proof is based on basic calculus results rather than induction, which makes it accessible to a larger audience including business and life sciences students and faculty. The slow rate of convergence of the two sequences is also discussed, and convergence bounds are found.

  2. Visibility of speech articulation enhances auditory phonetic convergence.

    PubMed

    Dias, James W; Rosenblum, Lawrence D

    2016-01-01

    Talkers automatically imitate aspects of perceived speech, a phenomenon known as phonetic convergence. Talkers have previously been found to converge to auditory and visual speech information. Furthermore, talkers converge more to the speech of a conversational partner who is seen and heard, relative to one who is just heard (Dias & Rosenblum Perception, 40, 1457-1466, 2011). A question raised by this finding is what visual information facilitates the enhancement effect. In the following experiments, we investigated the possible contributions of visible speech articulation to visual enhancement of phonetic convergence within the noninteractive context of a shadowing task. In Experiment 1, we examined the influence of the visibility of a talker on phonetic convergence when shadowing auditory speech either in the clear or in low-level auditory noise. The results suggest that visual speech can compensate for convergence that is reduced by auditory noise masking. Experiment 2 further established the visibility of articulatory mouth movements as being important to the visual enhancement of phonetic convergence. Furthermore, the word frequency and phonological neighborhood density characteristics of the words shadowed were found to significantly predict phonetic convergence in both experiments. Consistent with previous findings (e.g., Goldinger Psychological Review, 105, 251-279, 1998), phonetic convergence was greater when shadowing low-frequency words. Convergence was also found to be greater for low-density words, contrasting with previous predictions of the effect of phonological neighborhood density on auditory phonetic convergence (e.g., Pardo, Jordan, Mallari, Scanlon, & Lewandowski Journal of Memory and Language, 69, 183-195, 2013). Implications of the results for a gestural account of phonetic convergence are discussed. PMID:26358471

  3. Catalytic Promiscuity of the Radical S-adenosyl-L-methionine Enzyme NosL

    PubMed Central

    Ding, Wei; Ji, Xinjian; Li, Yongzhen; Zhang, Qi

    2016-01-01

    Catalytic promiscuity plays a key role in enzyme evolution and the acquisition of novel biological functions. Because of the high reactivity of radical species, in our view enzymes involving radical-mediated mechanisms could intrinsically be more prone to catalytic promiscuity. This mini-review summarizes the recent advances in the study of NosL, a radical S-adenosyl-L-methionine (SAM)-dependent L-tryptophan (L-Trp) lyase. We demonstrate here the interesting chemistry and remarkable catalytic promiscuity of NosL, and attempt to highlight the high evolvability of radical SAM enzymes and the potential to engineer these enzymes for novel and improved activities. PMID:27446906

  4. Early-branching or fast-evolving eukaryotes? An answer based on slowly evolving positions.

    PubMed

    Philippe, H; Lopez, P; Brinkmann, H; Budin, K; Germot, A; Laurent, J; Moreira, D; Müller, M; Le Guyader, H

    2000-06-22

    The current paradigm of eukaryotic evolution is based primarily on comparative analysis of ribosomal RNA sequences. It shows several early-emerging lineages, mostly amitochondriate, which might be living relics of a progressive assembly of the eukaryotic cell. However, the analysis of slow-evolving positions, carried out with the newly developed slow-fast method, reveals that these lineages are, in terms of nucleotide substitution, fast-evolving ones, misplaced at the base of the tree by a long branch attraction artefact. Since the fast-evolving groups are not always the same, depending on which macromolecule is used as a marker, this explains most of the observed incongruent phylogenies. The current paradigm of eukaryotic evolution thus has to be seriously re-examined as the eukaryotic phylogeny is presently best summarized by a multifurcation. This is consistent with the Big Bang hypothesis that all extant eukaryotic lineages are the result of multiple cladogeneses within a relatively brief period, although insufficiency of data is also a possible explanation for the lack of resolution. For further resolution, rare evolutionary events such as shared insertions and/or deletions or gene fusions might be helpful. PMID:10902687

  5. Reverse evolution leads to genotypic incompatibility despite functional and active site convergence

    PubMed Central

    Kaltenbach, Miriam; Jackson, Colin J; Campbell, Eleanor C; Hollfelder, Florian; Tokuriki, Nobuhiko

    2015-01-01

    Understanding the extent to which enzyme evolution is reversible can shed light on the fundamental relationship between protein sequence, structure, and function. Here, we perform an experimental test of evolutionary reversibility using directed evolution from a phosphotriesterase to an arylesterase, and back, and examine the underlying molecular basis. We find that wild-type phosphotriesterase function could be restored (>104-fold activity increase), but via an alternative set of mutations. The enzyme active site converged towards its original state, indicating evolutionary constraints imposed by catalytic requirements. We reveal that extensive epistasis prevents reversions and necessitates fixation of new mutations, leading to a functionally identical sequence. Many amino acid exchanges between the new and original enzyme are not tolerated, implying sequence incompatibility. Therefore, the evolution was phenotypically reversible but genotypically irreversible. Our study illustrates that the enzyme's adaptive landscape is highly rugged, and different functional sequences may constitute separate fitness peaks. DOI: http://dx.doi.org/10.7554/eLife.06492.001 PMID:26274563

  6. Coefficients of convergent multiple Walsh-Paley series

    SciTech Connect

    Plotnikov, Mikhail G

    2012-09-30

    The paper is concerned with the behaviour of the coefficients of multiple Walsh-Paley series that are cube convergent to a finite sum. It is shown that even an everywhere convergent series of this kind may contain coefficients with numbers from a sufficiently large set that grow faster than any preassigned sequence. By Cohen's theorem, this sort of thing cannot happen for multiple trigonometric series that are cube convergent on a set of full measure - their coefficients cannot grow even exponentially. Null subsequences of coefficients are determined for multiple Walsh-Paley series that are cube convergent on a set of definite measure. Bibliography: 18 titles.

  7. Turbulent boundary layer over a convergent and divergent superhydrophobic surface

    NASA Astrophysics Data System (ADS)

    Nadeem, Muhammad; Hwang, Jinyul; Sung, Hyung Jin

    2015-11-01

    Direct numerical simulation (DNS) of spatially developing turbulent boundary layer (TBL) over a convergent and divergent superhydrophobic surface (SHS) was performed. The convergent and divergent SHS was aligned in the streamwise direction. The SHS was modeled as a pattern of slip and no-slip surfaces. For comparison, DNS of TBL over a straight SHS was also carried out. The momentum thickness Reynolds number was varied from 800 to 1400. The gas fraction of the convergent and divergent SHS was the same as that of the straight SHS, keeping the slip area constant. The slip velocity in the convergent SHS was higher than that of the straight SHS. An optimal streamwise length of the convergent and divergent SHS was obtained. The convergent and divergent SHS gave more drag reduction than the straight SHS. The convergent and divergent SHS led to the modification of near wall-turbulent structures, resembling the narrowing and widening streaky structures near the wall. The convergent and divergent SHS had a relatively larger damping effect on near-wall turbulence than the straight SHS. These observations will be further analyzed statistically to demonstrate the effect of the convergent and divergent SHS on the interaction of inner and outer regions of TBL.

  8. Fractal aspects and convergence of Newton`s method

    SciTech Connect

    Drexler, M.

    1996-12-31

    Newton`s Method is a widely established iterative algorithm for solving non-linear systems. Its appeal lies in its great simplicity, easy generalization to multiple dimensions and a quadratic local convergence rate. Despite these features, little is known about its global behavior. In this paper, we will explain a seemingly random global convergence pattern using fractal concepts and show that the behavior of the residual is entirely explicable. We will also establish quantitative results for the convergence rates. Knowing the mechanism of fractal generation, we present a stabilization to the orthodox Newton method that remedies the fractal behavior and improves convergence.

  9. The convergence of health care expenditure in the US states.

    PubMed

    Wang, Zijun

    2009-01-01

    In response to rising health care costs, many have called for more effective regional health policy coordination. In this paper, we address the issue by examining the degree of convergence in per capita health care expenditure and its nine components across the US states from 1980 to 2004. The major finding is the moderate evidence of convergence in total health care expenditure and the diverse performance of the expenditure components regarding convergence. We also find hospital care to be responsible for the bulk of cross-state convergence in total expenditure. The expenditure on prescription drugs is the most important diverging factor. Policy implications of these empirical results are discussed. PMID:18273915

  10. Mesoscopic dynamics of diffusion-influenced enzyme kinetics.

    PubMed

    Chen, Jiang-Xing; Kapral, Raymond

    2011-01-28

    A particle-based mesoscopic model for enzyme kinetics is constructed and used to investigate the influence of diffusion on the reactive dynamics. Enzymes and enzyme-substrate complexes are modeled as finite-size soft spherical particles, while substrate, product, and solvent molecules are point particles. The system is evolved using a hybrid molecular dynamics-multiparticle collision dynamics scheme. Both the nonreactive and reactive dynamics are constructed to satisfy mass, momentum, and energy conservation laws, and reversible reaction steps satisfy detailed balance. Hydrodynamic interactions among the enzymes and complexes are automatically accounted for in the dynamics. Diffusion manifests itself in various ways, notably in power-law behavior in the evolution of the species concentrations. In accord with earlier investigations, regimes where the product production rate exhibits either monotonic or nonmonotonic behavior as a function of time are found. In addition, the species concentrations display both t(-1/2) and t(-3/2) power-law behavior, depending on the dynamical regime under investigation. For high enzyme volume fractions, cooperative effects influence the enzyme kinetics. The time dependent rate coefficient determined from the mass action rate law is computed and shown to depend on the enzyme concentration. Lifetime distributions of substrate molecules newly released in complex dissociation events are determined and shown to have either a power-law form for rebinding to the same enzyme from which they were released or an exponential form for rebinding to different enzymes. The model can be used and extended to explore a variety of issues related concentration effects and diffusion on enzyme kinetics. PMID:21280744

  11. Convergence Insufficiency/Divergence Insufficiency Convergence Excess/Divergence Excess: Some Facts and Fictions

    PubMed Central

    Khawam, Edward; Abiad, Bachir; Boughannam, Alaa; Saade, Joanna; Alameddine, Ramzi

    2015-01-01

    Great discrepancies are often encountered between the distance fixation and the near-fixation esodeviations and exodeviations. They are all attributed to either anomalies of the AC/A ratio or anomalies of the fusional convergence or divergence amplitudes. We report a case with pseudoconvergence insufficiency and another one with pseudoaccommodative convergence excess. In both cases, conv./div. excess and insufficiency were erroneously attributed to anomalies of the AC/A ratio or to anomalies of the fusional amplitudes. Our purpose is to show that numerous factors, other than anomalies in the AC/A ratio or anomalies in the fusional conv. or divergence amplitudes, can contaminate either the distance or the near deviations. This results in significant discrepancies between the distance and the near deviations despite a normal AC/A ratio and normal fusional amplitudes, leading to erroneous diagnoses and inappropriate treatment models. PMID:26351603

  12. Strong convergence and convergence rates of approximating solutions for algebraic Riccati equations in Hilbert spaces

    NASA Technical Reports Server (NTRS)

    Ito, Kazufumi

    1987-01-01

    The linear quadratic optimal control problem on infinite time interval for linear time-invariant systems defined on Hilbert spaces is considered. The optimal control is given by a feedback form in terms of solution pi to the associated algebraic Riccati equation (ARE). A Ritz type approximation is used to obtain a sequence pi sup N of finite dimensional approximations of the solution to ARE. A sufficient condition that shows pi sup N converges strongly to pi is obtained. Under this condition, a formula is derived which can be used to obtain a rate of convergence of pi sup N to pi. The results of the Galerkin approximation is demonstrated and applied for parabolic systems and the averaging approximation for hereditary differential systems.

  13. Molecular determinants of enzyme cold adaptation: comparative structural and computational studies of cold- and warm-adapted enzymes.

    PubMed

    Papaleo, Elena; Tiberti, Matteo; Invernizzi, Gaetano; Pasi, Marco; Ranzani, Valeria

    2011-11-01

    The identification of molecular mechanisms underlying enzyme cold adaptation is a hot-topic both for fundamental research and industrial applications. In the present contribution, we review the last decades of structural computational investigations on cold-adapted enzymes in comparison to their warm-adapted counterparts. Comparative sequence and structural studies allow the definition of a multitude of adaptation strategies. Different enzymes carried out diverse mechanisms to adapt to low temperatures, so that a general theory for enzyme cold adaptation cannot be formulated. However, some common features can be traced in dynamic and flexibility properties of these enzymes, as well as in their intra- and inter-molecular interaction networks. Interestingly, the current data suggest that a family-centered point of view is necessary in the comparative analyses of cold- and warm-adapted enzymes. In fact, enzymes belonging to the same family or superfamily, thus sharing at least the three-dimensional fold and common features of the functional sites, have evolved similar structural and dynamic patterns to overcome the detrimental effects of low temperatures. PMID:21827423

  14. Structure of p-shell nuclei using three-nucleon interactions evolved with the similarity renormalization group

    DOE PAGESBeta

    Jurgenson, E. D.; Maris, P.; Furnstahl, R. J.; Navratil, P.; Ormand, W. E.; Vary, J. P.

    2013-05-13

    The similarity renormalization group (SRG) is used to soften interactions for ab initio nuclear structure calculations by decoupling low- and high-energy Hamiltonian matrix elements. The substantial contribution of both initial and SRG-induced three-nucleon forces requires their consistent evolution in a three-particle basis space before applying them to larger nuclei. While, in principle, the evolved Hamiltonians are unitarily equivalent, in practice the need for basis truncation introduces deviations, which must be monitored. Here we present benchmark no-core full configuration calculations with SRG-evolved interactions in p-shell nuclei over a wide range of softening. As a result, these calculations are used to assessmore » convergence properties, extrapolation techniques, and the dependence of energies, including four-body contributions, on the SRG resolution scale.« less

  15. Structure of p-shell nuclei using three-nucleon interactions evolved with the similarity renormalization group

    SciTech Connect

    Jurgenson, E. D.; Maris, P.; Furnstahl, R. J.; Navratil, P.; Ormand, W. E.; Vary, J. P.

    2013-05-13

    The similarity renormalization group (SRG) is used to soften interactions for ab initio nuclear structure calculations by decoupling low- and high-energy Hamiltonian matrix elements. The substantial contribution of both initial and SRG-induced three-nucleon forces requires their consistent evolution in a three-particle basis space before applying them to larger nuclei. While, in principle, the evolved Hamiltonians are unitarily equivalent, in practice the need for basis truncation introduces deviations, which must be monitored. Here we present benchmark no-core full configuration calculations with SRG-evolved interactions in p-shell nuclei over a wide range of softening. As a result, these calculations are used to assess convergence properties, extrapolation techniques, and the dependence of energies, including four-body contributions, on the SRG resolution scale.

  16. BUBBLE DYNAMICS AT GAS-EVOLVING ELECTRODES

    SciTech Connect

    Sides, Paul J.

    1980-12-01

    Nucleation of bubbles, their growth by diffusion of dissolved gas to the bubble surface and by coalescence, and their detachment from the electrode are all very fast phenomena; furthermore, electrolytically generated bubbles range in size from ten to a few hundred microns; therefore, magnification and high speed cinematography are required to observe bubbles and the phenomena of their growth on the electrode surface. Viewing the action from the front side (the surface on which the bubbles form) is complicated because the most important events occur close to the surface and are obscured by other bubbles passing between the camera and the electrode; therefore, oxygen was evolved on a transparent tin oxide "window" electrode and the events were viewed from the backside. The movies showed that coalescence of bubbles is very important for determining the size of bubbles and in the chain of transport processes; growth by diffusion and by coalescence proceeds in series and parallel; coalescing bubbles cause significant fluid motion close to the electrode; bubbles can leave and reattach; and bubbles evolve in a cycle of growth by diffusion and different modes of coalescence. An analytical solution for the primary potential and current distribution around a spherical bubble in contact with a plane electrode is presented. Zero at the contact point, the current density reaches only one percent of its undisturbed value at 30 percent of the radius from that point and goes through a shallow maximum two radii away. The solution obtained for spherical bubbles is shown to apply for the small bubbles of electrolytic processes. The incremental resistance in ohms caused by sparse arrays of bubbles is given by {Delta}R = 1.352 af/kS where f is the void fraction of gas in the bubble layer, a is the bubble layer thickness, k is the conductivity of gas free electrolyte, and S is the electrode area. A densely populated gas bubble layer on an electrode was modeled as a hexagonal array of

  17. Emergent spacetime in stochastically evolving dimensions

    NASA Astrophysics Data System (ADS)

    Afshordi, Niayesh; Stojkovic, Dejan

    2014-12-01

    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.

  18. Evolving Recommendations on Prostate Cancer Screening.

    PubMed

    Brawley, Otis W; Thompson, Ian M; Grönberg, Henrik

    2016-01-01

    Results of a number of studies demonstrate that the serum prostate-specific antigen (PSA) in and of itself is an inadequate screening test. Today, one of the most pressing questions in prostate cancer medicine is how can screening be honed to identify those who have life-threatening disease and need aggressive treatment. A number of efforts are underway. One such effort is the assessment of men in the landmark Prostate Cancer Prevention Trial that has led to a prostate cancer risk calculator (PCPTRC), which is available online. PCPTRC version 2.0 predicts the probability of the diagnosis of no cancer, low-grade cancer, or high-grade cancer when variables such as PSA, age, race, family history, and physical findings are input. Modern biomarker development promises to provide tests with fewer false positives and improved ability to find high-grade cancers. Stockholm III (STHLM3) is a prospective, population-based, paired, screen-positive, prostate cancer diagnostic study assessing a combination of plasma protein biomarkers along with age, family history, previous biopsy, and prostate examination for prediction of prostate cancer. Multiparametric MRI incorporates anatomic and functional imaging to better characterize and predict future behavior of tumors within the prostate. After diagnosis of cancer, several genomic tests promise to better distinguish the cancers that need treatment versus those that need observation. Although the new technologies are promising, there is an urgent need for evaluation of these new tests in high-quality, large population-based studies. Until these technologies are proven, most professional organizations have evolved to a recommendation of informed or shared decision making in which there is a discussion between the doctor and patient. PMID:27249774

  19. Evolvable Cryogenics (ECRYO) Pressure Transducer Calibration Test

    NASA Technical Reports Server (NTRS)

    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.

  20. Evolvable Lunar Navigation and Communication Constellations

    NASA Astrophysics Data System (ADS)

    Hamera, Kathryn E.; Mosher, T.

    2008-05-01

    Several international space agencies have announced plans for future lunar exploration missions, including orbiters, rovers, and the eventual build-up of a lunar outpost. Each of these missions will have certain communication and navigation requirements. Some missions will explore parts of the lunar environment that are not directly visible to the Earth, and a lunar relay element will be necessary to provide critical communication and navigation support. Previous research has shown the advantages of using halo orbits for a lunar relay. Halo orbit insertion costs are less than those for geostationary orbit, station-keeping costs are minimal, and the Earth is visible for 100% of the spacecraft's orbital period. An example constellation was designed to show the feasibility of a halo orbit constellation. The methodologies used to construct the example constellation can be tailored to design halo orbit constellations to meet the coverage needs of any lunar mission. Additionally, the halo orbits are selected such that low energy-transfers may be used to transfer spacecraft between halo orbits for very small maneuver costs. This follow-on research demonstrates the capability of the constellation to evolve and reconfigure through the use of low-energy transfers. Using low-energy transfers, multiple space agencies can utilize the same lunar relay constellation by reconfiguring the spacecraft to provide optimal coverage for different missions at different times. This research was funded by a grant from NASA's Exploration System Mission Directorate to the Colorado Space Grant Consortium and a Graduate Student Research Fellowship from the National Science Foundation.