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  • American Institute of Physics (AIP)  (241,959)
  • Periodicals Archive Online (PAO)  (190,459)
  • Public Library of Science (PLoS)
Collection
Publisher
Years
  • 1
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    American Institute of Physics (AIP)
    Online: 1(1).2016 –
    Publisher: American Institute of Physics (AIP)
    Electronic ISSN: 2378-0967
    Topics: Physics
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  • 2
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    American Institute of Physics (AIP)
    Online: 1.2013 –
    Publisher: American Institute of Physics (AIP)
    Electronic ISSN: 2166-532X
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
    Keywords: Werkstoffkunde
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  • 3
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    American Institute of Physics (AIP)
    Online: 1(1).2014 –
    Publisher: American Institute of Physics (AIP)
    Electronic ISSN: 1931-9401
    Topics: Physics
    Keywords: Allgemeine Physik
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  • 4
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    American Institute of Physics (AIP)
    Online: 1.1962 –
    Publisher: American Institute of Physics (AIP)
    Print ISSN: 0003-6951
    Electronic ISSN: 1077-3118
    Topics: Physics
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  • 5
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    American Institute of Physics (AIP)
    Online: 1.1975 – 29.2003
    Formerly as: Soviet Astronomy / Letters. A translation of the Astronomical journal of the Soviet Academy of Sciences of the USSR  (1975–1992)
    Publisher: American Institute of Physics (AIP)
    Print ISSN: 0360-0327 , 1063-7737
    Topics: Physics
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  • 6
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    American Institute of Physics (AIP)
    Online: 1.1969 – 34.2002
    Publisher: American Institute of Physics (AIP)
    Print ISSN: 0002-7537
    Topics: Physics
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  • 7
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    American Institute of Physics (AIP)
    Online: 1(1).1970 –
    Publisher: American Institute of Physics (AIP)
    Print ISSN: 0094-243X
    Electronic ISSN: 1551-7616
    Topics: Physics
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  • 8
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    American Crystallographic Association (ACA) | American Institute of Physics (AIP)
    Online: 1(1).2014 –
    Publisher: American Crystallographic Association (ACA) , American Institute of Physics (AIP)
    Electronic ISSN: 2329-7778
    Topics: Physics
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  • 9
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    American Institute of Physics (AIP)
    Online: 1.1933 –
    Publisher: American Institute of Physics (AIP)
    Print ISSN: 0021-9606
    Electronic ISSN: 1089-7690
    Topics: Chemistry and Pharmacology , Physics
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  • 10
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    American Institute of Physics (AIP)
    Online: 36.2004 –
    Publisher: American Institute of Physics (AIP)
    Print ISSN: 0148-5857
    Topics: Physics
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  • 11
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    American Institute of Physics (AIP) | American Crystallographic Association (ACA)
    Online: 1.2011 –
    Publisher: American Institute of Physics (AIP) , American Crystallographic Association (ACA)
    Electronic ISSN: 2158-3226
    Topics: Physics
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  • 12
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    American Institute of Physics (AIP)
    Online: 1.1991 –
    Publisher: American Institute of Physics (AIP)
    Print ISSN: 1054-1500
    Electronic ISSN: 1089-7682
    Topics: Physics
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  • 13
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    American Institute of Physics (AIP) | IEEE Computer Society | Institute of Electrical and Electronics Engineers (IEEE)
    Online: 1.1999 –
    Publisher: American Institute of Physics (AIP) , IEEE Computer Society , Institute of Electrical and Electronics Engineers (IEEE)
    Print ISSN: 1521-9615
    Electronic ISSN: 1558-366X
    Topics: Computer Science , Natural Sciences in General , Technology
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  • 14
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    American Institute of Physics (AIP)
    Online: 1.1958 –
    Formerly as: Physics of Fluids A: Fluid Dynamics ; Physics of Fluids B: Plasma Physics  (1989–1993)
    Publisher: American Institute of Physics (AIP)
    Print ISSN: 0031-9171 , 1070-6631
    Electronic ISSN: 1089-7666
    Topics: Physics
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  • 15
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    American Institute of Physics (AIP)
    Online: 1(1).1989 – 5(12).1993
    Online: 1(1).1989 – 5(12).1993
    Publisher: American Institute of Physics (AIP)
    Print ISSN: 0899-8213
    Topics: Physics
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  • 16
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    Public Library of Science (PLoS)
    Online: 1.2003 –
    Publisher: Public Library of Science (PLoS)
    Print ISSN: 1544-9173
    Electronic ISSN: 1545-7885
    Topics: Biology
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  • 17
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    American Institute of Physics (AIP)
    Online: 1.2009 –
    Publisher: American Institute of Physics (AIP)
    Electronic ISSN: 1941-7012
    Topics: Energy, Environment Protection, Nuclear Power Engineering
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  • 18
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    Society of Rheology (SoR) | American Institute of Physics (AIP)
    Online: 1(1).1929 –
    Formerly as: Transactions of the Society of Rheology  (1957–1977)
    Publisher: Society of Rheology (SoR) , American Institute of Physics (AIP)
    Print ISSN: 0038-0032 , 0097-0360 , 0148-6055
    Electronic ISSN: 1520-8516
    Topics: Physics
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  • 19
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    Public Library of Science (PLoS)
    Online: 1.2005 –
    Publisher: Public Library of Science (PLoS)
    Print ISSN: 1553-734X
    Electronic ISSN: 1553-7358
    Topics: Biology , Computer Science
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  • 20
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    Public Library of Science (PLoS) | PubMed Central
    Online: 1.2009 – 10.2018
    Publisher: Public Library of Science (PLoS) , PubMed Central
    Electronic ISSN: 2157-3999
    Topics: Medicine , Natural Sciences in General
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  • 21
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    American Institute of Physics (AIP)
    Online: 52.1999 –
    Print: 39(7).1986 – 45.1992 (Location: A17, Kompaktmagazin, 58/6-7)
    Print: 44.1991 – 63.2010 (Location: A43, Archiv)
    Print: 46.1993 – 71.2018 (Location: A17, Kompaktmagazin, 58/6-7)
    Publisher: American Institute of Physics (AIP)
    Print ISSN: 0031-9228
    Electronic ISSN: 1945-0699
    Topics: Physics
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  • 22
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    American Institute of Physics (AIP)
    Online: 1.1960 –
    Publisher: American Institute of Physics (AIP)
    Print ISSN: 0022-2488
    Electronic ISSN: 1089-7658
    Topics: Mathematics , Physics
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  • 23
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    American Institute of Physics (AIP)
    Online: 1(1).1989 – 5(12).1993
    Online: 1(1).1989 – 5(12).1993
    Publisher: American Institute of Physics (AIP)
    Print ISSN: 0899-8221
    Topics: Physics
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  • 24
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    American Institute of Physics (AIP)
    Online: 1.1994 –
    Publisher: American Institute of Physics (AIP)
    Print ISSN: 1070-664X
    Electronic ISSN: 1089-7674
    Topics: Physics
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  • 25
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    Public Library of Science (PLoS)
    Online: 1.2005 –
    Publisher: Public Library of Science (PLoS)
    Print ISSN: 1553-7390
    Electronic ISSN: 1553-7404
    Topics: Biology
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  • 26
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    Laser Institute of America (LIA) | American Institute of Physics (AIP)
    Online: 1(1).1988 –
    Publisher: Laser Institute of America (LIA) , American Institute of Physics (AIP)
    Print ISSN: 1042-346X
    Electronic ISSN: 1938-1387
    Topics: Physics
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  • 27
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    American Institute of Physics (AIP)
    Online: 1.1931 –
    Formerly as: Physics  (1931–1936)
    Publisher: American Institute of Physics (AIP)
    Print ISSN: 0021-8979
    Electronic ISSN: 1089-7550
    Topics: Physics
    Acronym: JAP
    Abbreviation: J Appl Phys
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  • 28
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    American Institute of Physics (AIP) | früher: Elsevier
    Online: 1(1).2016 –
    Publisher: American Institute of Physics (AIP) , früher: Elsevier
    Print ISSN: 2468-2047
    Electronic ISSN: 2468-080X
    Topics: Physics
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  • 29
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    American Institute of Physics (AIP)
    Online: 23.1997 –
    Publisher: American Institute of Physics (AIP)
    Print ISSN: 1063-777X
    Electronic ISSN: 1090-6517
    Topics: Physics
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  • 30
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    American Institute of Physics (AIP)
    Online: 1.1930 –
    Print: 28.1957 – 41.1970 (Location: A18, ---)
    Formerly as: Review of Scientific Instruments with Physics News and Views  (1933–1938)
    Publisher: American Institute of Physics (AIP)
    Print ISSN: 0034-6748
    Electronic ISSN: 1089-7623
    Topics: Electrical Engineering, Measurement and Control Technology , Physics
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  • 31
    Publication Date: 2022-05-25
    Description: © 2005 Sullivan et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The definitive version was published in PLoS Biology 3 (2005): e144, doi:10.1371/journal.pbio.0030144.
    Description: The oceanic cyanobacteria Prochlorococcus are globally important, ecologically diverse primary producers. It is thought that their viruses (phages) mediate population sizes and affect the evolutionary trajectories of their hosts. Here we present an analysis of genomes from three Prochlorococcus phages: a podovirus and two myoviruses. The morphology, overall genome features, and gene content of these phages suggest that they are quite similar to T7-like (P-SSP7) and T4-like (P-SSM2 and P-SSM4) phages. Using the existing phage taxonomic framework as a guideline, we examined genome sequences to establish ‘‘core’’ genes for each phage group. We found the podovirus contained 15 of 26 core T7-like genes and the two myoviruses contained 43 and 42 of 75 core T4-like genes. In addition to these core genes, each genome contains a significant number of ‘‘cyanobacterial’’ genes, i.e., genes with significant best BLAST hits to genes found in cyanobacteria. Some of these, we speculate, represent ‘‘signature’’ cyanophage genes. For example, all three phage genomes contain photosynthetic genes (psbA, hliP) that are thought to help maintain host photosynthetic activity during infection, as well as an aldolase family gene (talC) that could facilitate alternative routes of carbon metabolism during infection. The podovirus genome also contains an integrase gene (int) and other features that suggest it is capable of integrating into its host. If indeed it is, this would be unprecedented among cultured T7-like phages or marine cyanophages and would have significant evolutionary and ecological implications for phage and host. Further, both myoviruses contain phosphate-inducible genes (phoH and pstS) that are likely to be important for phage and host responses to phosphate stress, a commonly limiting nutrient in marine systems. Thus, these marine cyanophages appear to be variations of two well-known phages—T7 and T4—but contain genes that, if functional, reflect adaptations for infection of photosynthetic hosts in low-nutrient oceanic environments.
    Description: This research was supported by the US DOE under grant numbers DEFG02– 99ER62814 and DE-FG02–02ER63445, and the National Science Foundation under grant number OCE-9820035 (to SWC).
    Keywords: Oceanic cyanobacteria ; Prochlorococcus phages
    Repository Name: Woods Hole Open Access Server
    Type: Article
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  • 32
    Publication Date: 2022-05-25
    Description: © 2006 Bordenstein et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The definitive version was published in PLoS Pathogens 2(2006): e43, doi:10.1371/journal.ppat.0020043.
    Description: By manipulating arthropod reproduction worldwide, the heritable endosymbiont Wolbachia has spread to pandemic levels. Little is known about the microbial basis of cytoplasmic incompatibility (CI) except that bacterial densities and percentages of infected sperm cysts associate with incompatibility strength. The recent discovery of a temperate bacteriophage (WO-B) of Wolbachia containing ankyrin-encoding genes and virulence factors has led to intensifying debate that bacteriophage WO-B induces CI. However, current hypotheses have not considered the separate roles that lytic and lysogenic phage might have on bacterial fitness and phenotype. Here we describe a set of quantitative approaches to characterize phage densities and its associations with bacterial densities and CI. We enumerated genome copy number of phage WO-B and Wolbachia and CI penetrance in supergroup A- and B-infected males of the parasitoid wasp Nasonia vitripennis. We report several findings: (1) variability in CI strength for A-infected males is positively associated with bacterial densities, as expected under the bacterial density model of CI, (2) phage and bacterial densities have a significant inverse association, as expected for an active lytic infection, and (3) CI strength and phage densities are inversely related in A-infected males; similarly, males expressing incomplete CI have significantly higher phage densities than males expressing complete CI. Ultrastructural analyses indicate that approximately 12% of the A Wolbachia have phage particles, and aggregations of these particles can putatively occur outside the Wolbachia cell. Physical interactions were observed between approximately 16% of the Wolbachia cells and spermatid tails. The results support a low to moderate frequency of lytic development in Wolbachia and an overall negative density relationship between bacteriophage and Wolbachia. The findings motivate a novel phage density model of CI in which lytic phage repress Wolbachia densities and therefore reproductive parasitism. We conclude that phage, Wolbachia, and arthropods form a tripartite symbiotic association in which all three are integral to understanding the biology of this widespread endosymbiosis. Clarifying the roles of lytic and lysogenic phage development in Wolbachia biology will effectively structure inquiries into this research topic.
    Description: This work was supported by grants from the NASA Astrobiology Institute (NNA04CC04A) and National Institutes of Health (R01 GM62626-01) to JJW, and by the Marine Biological Laboratory's Program in Global Infectious Diseases, funded by the Ellison Medical Foundation, to SRB.
    Repository Name: Woods Hole Open Access Server
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  • 33
    Publication Date: 2022-05-25
    Description: © 2006 Parfrey et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The definitive version was published in PLoS Genetics 2 (2006): e220, doi:10.1371/journal.pgen.0020220.
    Description: Perspectives on the classification of eukaryotic diversity have changed rapidly in recent years, as the four eukaryotic groups within the five-kingdom classification—plants, animals, fungi, and protists—have been transformed through numerous permutations into the current system of six ‘‘supergroups.’’ The intent of the supergroup classification system is to unite microbial and macroscopic eukaryotes based on phylogenetic inference. This supergroup approach is increasing in popularity in the literature and is appearing in introductory biology textbooks. We evaluate the stability and support for the current six-supergroup classification of eukaryotes based on molecular genealogies. We assess three aspects of each supergroup: (1) the stability of its taxonomy, (2) the support for monophyly (single evolutionary origin) in molecular analyses targeting a supergroup, and (3) the support for monophyly when a supergroup is included as an out-group in phylogenetic studies targeting other taxa. Our analysis demonstrates that supergroup taxonomies are unstable and that support for groups varies tremendously, indicating that the current classification scheme of eukaryotes is likely premature. We highlight several trends contributing to the instability and discuss the requirements for establishing robust clades within the eukaryotic tree of life.
    Description: This work is supported by the National Science Foundation Assembling the Tree of Life grant (043115) to DB, DJP, and LAK.
    Repository Name: Woods Hole Open Access Server
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  • 34
    Publication Date: 2022-05-25
    Description: This is an open-access article distributed under the terms of the Creative Commons Public Domain dedication. The definitive version was published in PLoS Biology 4 (2006): e383, doi:10.1371/journal.pbio.0040383.
    Description: Presented here is the complete genome sequence of Thiomicrospira crunogena XCL-2, representative of ubiquitous chemolithoautotrophic sulfur-oxidizing bacteria isolated from deep-sea hydrothermal vents. This gammaproteobacterium has a single chromosome (2,427,734 base pairs), and its genome illustrates many of the adaptations that have enabled it to thrive at vents globally. It has 14 methyl-accepting chemotaxis protein genes, including four that may assist in positioning it in the redoxcline. A relative abundance of coding sequences (CDSs) encoding regulatory proteins likely control the expression of genes encoding carboxysomes, multiple dissolved inorganic nitrogen and phosphate transporters, as well as a phosphonate operon, which provide this species with a variety of options for acquiring these substrates from the environment. Thiom. crunogena XCL-2 is unusual among obligate sulfur-oxidizing bacteria in relying on the Sox system for the oxidation of reduced sulfur compounds. The genome has characteristics consistent with an obligately chemolithoautotrophic lifestyle, including few transporters predicted to have organic allocrits, and Calvin-Benson-Bassham cycle CDSs scattered throughout the genome.
    Description: This work was performed under the auspices of the United States Department of Energy by Lawrence Livermore National Laboratory, University of California, under contract W-7405-ENG-48. Genome closure was funded in part by a University of South Florida Innovative Teaching Grant (to KMS). KMS, SKF, and CAK gratefully acknowledge support from the United States Department of Agriculture Higher Education Challenge Grants Program (Award # 20053841115876). SMS kindly acknowledges support through a fellowship received from the Hanse Wissenschaftskolleg in Delmenhorst, Germany (http://www.h-w-k.de). MH was supported by a Woods Hole Oceanographic Institution postdoctoral scholarship.
    Repository Name: Woods Hole Open Access Server
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  • 35
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    Public Library of Science (PLoS)
    Publication Date: 2022-05-25
    Description: © 2004 Jennifer J. Wernegreen. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The definitive version was published in PLoS Biology 2 (2004): e68, doi:10.1371/journal.pbio.0020068.
    Description: Symbiosis, an interdependent relationship between two species, is an important driver of evolutionary novelty and ecological diversity. Microbial symbionts in particular have been major evolutionary catalysts throughout the 4 billion years of life on earth and have largely shaped the evolution of complex organisms. Endosymbiosis is a specifi c type of symbiosis in which one—typically microbial—partner lives within its host and represents the most intimate contact between interacting organisms. Mitochondria and chloroplasts, for example, result from endosymbiotic events of lasting significance that extended the range of acceptable habitats for life. The wide distribution of intracellular bacteria across diverse hosts and marine and terrestrial habitats testifies to the continued importance of endosymbiosis in evolution. Among multicellular organisms, insects as a group form exceptionally diverse associations with microbial associates, including bacteria that live exclusively within host cells and undergo maternal transmission to offspring. These microbes have piqued the interest of evolutionary biologists because they represent a wide spectrum of evolutionary strategies, ranging from obligate mutualism to reproductive parasitism (Buchner 1965; Ishikawa 2003) (Box 1; Table 1).
    Description: JJW gratefully acknowledges the support of the National Institutes of Health (R01 GM62626-01), the National Science Foundation (DEB 0089455), the National Aeronautics and Space Administration Astrobiology Institute (NNA04CC04A), and the Josephine Bay Paul and C. Michael Paul Foundation.
    Keywords: Endosymbiosis ; Endosymbiosis manipulation
    Repository Name: Woods Hole Open Access Server
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  • 36
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    Public Library of Science (PLoS)
    In:  EPIC3PLOS ONE, Public Library of Science (PLoS), 15(8), pp. e0237704-e0237704, ISSN: 1932-6203
    Publication Date: 2023-06-21
    Description: Since plastics degrade very slowly, they remain in the environment on much longer timescales than most natural organic substrates and provide a novel habitat for colonization by bacterial communities. The spectrum of relationships between plastics and bacteria, however, is little understood. The first objective of this study was to examine plastics as substrates for communities of Bacteria in estuarine surface waters. We used next-generation sequencing of the 16S rRNA gene to characterize communities from plastics collected in the field, and over the course of two colonization experiments, from biofilms that developed on plastic (low-density polyethylene, high-density polyethylene, polypropylene, polycarbonate, polystyrene) and glass substrates placed in the environment. Both field sampling and colonization experiments were conducted in estuarine tributaries of the lower Chesapeake Bay. As a second objective, we concomitantly analyzed biofilms on plastic substrates to ascertain the presence and abundance of Vibrio spp. bacteria, then isolated three human pathogens, V. cholerae, V. parahaemolyticus, and V. vulnificus, and determined their antibiotic-resistant profiles. In both components of this study, we compared our results with analyses conducted on paired samples of estuarine water. This research adds to a nascent literature that suggests environmental factors govern the development of bacterial communities on plastics, more so than the characteristics of the plastic substrates themselves. In addition, this study is the first to culture three pathogenic vibrios from plastics in estuaries, reinforcing and expanding upon earlier reports of plastic pollution as a habitat for Vibrio species. The antibiotic resistance detected among the isolates, coupled with the longevity of plastics in the aqueous environment, suggests biofilms on plastics have potential to persist and serve as focal points of potential pathogens and horizontal gene transfer.
    Repository Name: EPIC Alfred Wegener Institut
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  • 37
    Publication Date: 2023-06-21
    Description: Multiomics approaches need to be applied in the central Arctic Ocean to benchmark biodiversity change and to identify novel species and their genes. As part of MOSAiC, EcoOmics will therefore be essential for conservation and sustainable bioprospecting in one of the least explored ecosystems on Earth.
    Repository Name: EPIC Alfred Wegener Institut
    Type: Article , NonPeerReviewed
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  • 38
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    Public Library of Science (PLoS)
    In:  PLoS ONE vol. 9 no. 12, pp. e115750-e115750
    Publication Date: 2024-01-12
    Keywords: Multidisciplinary
    Repository Name: National Museum of Natural History, Netherlands
    Type: info:eu-repo/semantics/article
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  • 39
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    Public Library of Science (PLoS)
    In:  EPIC3PLOS ONE, Public Library of Science (PLoS), 18(8), pp. e0290437-e0290437, ISSN: 1932-6203
    Publication Date: 2023-08-31
    Description: Due to its involvement in numerous feedbacks, sea ice plays a crucial role not only for polar climate but also at global scale. We analyse state-of-the-art observed, reconstructed, and modelled sea-ice concentration (SIC) together with sea surface temperature (SST) to disentangle the influence of different forcing factors on the variability of these coupled fields. Canonical Correlation Analysis provides distinct pairs of coupled Arctic SIC–Atlantic SST variability which are linked to prominent oceanic and atmospheric modes of variability over the period 1854–2017. The first pair captures the behaviour of the Atlantic meridional overturning circulation (AMOC) while the third and can be associated with the North Atlantic Oscillation (NAO) in a physically consistent manner. The dominant global SIC–Atlantic SST coupled mode highlights the contrast between the responses of Arctic and Antarctic sea ice to changes in AMOC over the 1959–2021 period. Model results indicate that coupled SST–SIC patterns can be associated with changes in ocean circulation. We conclude that a correct representation of AMOC-induced coupled SST–SIC variability in climate models is essential to understand the past, present and future sea-ice evolution.
    Repository Name: EPIC Alfred Wegener Institut
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  • 40
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    Public Library of Science (PLoS)
    In:  EPIC3PLOS ONE, Public Library of Science (PLoS), 17(9), pp. e0273623-e0273623, ISSN: 1932-6203
    Publication Date: 2023-10-23
    Description: While the output of a team is evident, the productivity of each team member is typically not readily identifiable. In this paper we consider the problem of measuring the productivity of team members. We propose a new concept of coworker productivity, which we refer to as eigenvalue productivity (EVP). We demonstrate the existence and uniqueness of our concept and show that it possesses several desirable properties. Also, we suggest a procedure for specifying the required productivity matrix of a team, and illustrate the operational practicability of EVP by means of three examples representing different types of available data.
    Repository Name: EPIC Alfred Wegener Institut
    Type: Article , peerRev
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  • 41
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    In:  EPIC3PLOS ONE, Public Library of Science (PLoS), 18(7), pp. e0286036-e0286036, ISSN: 1932-6203
    Publication Date: 2023-08-01
    Description: Euphausia superba is a key species of the Southern Ocean, impacted by climate change and human exploitation. Understanding how these changes affect the distribution and abundance of krill is crucial for generating projections of change for Southern Ocean ecosystems. Krill growth is an important indicator of habitat suitability and a series of models have been developed and used to examine krill growth potential at different spatial and temporal scales. The available models have been developed using a range of empirical and mechanistic approaches, providing alternative perspectives and comparative analyses of the key processes influencing krill growth. Here we undertake an intercomparison of a suite of the available models to understand their sensitivities to major driving variables. This illustrates that the results are strongly determined by the model structure and technical characteristics, and the data on which they were developed and validated. Our results emphasize the importance of assessing the constraints and requirements of individual krill growth models to ensure their appropriate application. The study also demonstrates the value of the development of alternative modelling approaches to identify key processes affecting the dynamics of krill. Of critical importance for modelling the growth of krill is appropriately assessing and accounting for differences in estimates of food availability resulting from alternative methods of observation. We suggest that an intercomparison approach is particularly valuable in the development and application of models for the assessment of krill growth potential at circumpolar scales and for future projections. As another result of the intercomparison, the implementations of the models used in this study are now publicly available for future use and analyses.
    Repository Name: EPIC Alfred Wegener Institut
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  • 42
    Publication Date: 2024-02-07
    Description: Phylogeographic patterns and sex-biased dispersal were studied in riverine populations of West Indian (Trichechus manatus) and Amazonian manatees (T. inunguis) in South America, using 410bp D-loop (Control Region, Mitochondrial DNA) sequences and 15 nuclear microsatellite loci. This multi-locus approach was key to disentangle complex patterns of gene flow among populations. D-loop analyses revealed population structuring among all Colombian rivers for T. manatus, while microsatellite data suggested no structure. Two main populations of T. inunguis separating the Colombian and Peruvian Amazon were supported by analysis of the D-loop and microsatellite data. Overall, we provide molecular evidence for differences in dispersal patterns between sexes, demonstrating male-biased gene flow dispersal in riverine manatees. These results are in contrast with previously reported levels of population structure shown by microsatellite data in marine manatee populations, revealing low habitat restrictions to gene flow in riverine habitats, and more significant dispersal limitations for males in marine environments. © 2012 Satizábal et al.
    Repository Name: EPIC Alfred Wegener Institut
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  • 43
    Publication Date: 2024-02-28
    Description: The superfamily Orthalicoidea comprises approximately 2,000 species of terrestrial gastropods, mostly concentrated in the Neotropics but also present in southern Africa and Oceania. We provide a multi-marker molecular phylogeny of this superfamily, reassessing its \nfamily- and genus-level classification. We exclude two families from the group, Odontostomidae and Vidaliellidae, transferring them to Rhytidoidea based on their phylogenetic relationships as recovered herein. Two new families are recognized herein as members of \nOrthalicoidea, Tomogeridae and Cyclodontinidae fam. nov. The family Megaspiridae and \nthe subfamily Prestonellinae are paraphyletic but are retained herein for taxonomic stability. \nThe subfamily Placostylinae is synonymized with Bothriembryontinae. The new genera \nAlterorhinus gen. nov. and Sanniostracus gen. nov. containing some Brazilian species are \ndescribed here to better reflect the phylogeny. The fossil record and paleobiogeographic \nhistory of the group is explored under the new phylogenetic framework.
    Repository Name: National Museum of Natural History, Netherlands
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  • 44
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    Public Library of Science (PLoS)
    In:  PLOS Computational Biology vol. 19 no. 10, pp. e1011541-e1011541
    Publication Date: 2024-03-12
    Description: Insect population numbers and biodiversity have been rapidly declining with time, and monitoring \nthese trends has become increasingly important for conservation measures to be \neffectively implemented. But monitoring methods are often invasive, time and resource \nintense, and prone to various biases. Many insect species produce characteristic sounds \nthat can easily be detected and recorded without large cost or effort. Using deep learning \nmethods, insect sounds from field recordings could be automatically detected and classified \nto monitor biodiversity and species distribution ranges. We implement this using recently \npublished datasets of insect sounds (up to 66 species of Orthoptera and Cicadidae) and \nmachine learning methods and evaluate their potential for acoustic insect monitoring. We \ncompare the performance of the conventional spectrogram-based audio representation \nagainst LEAF, a new adaptive and waveform-based frontend. LEAF achieved better classification \nperformance than the mel-spectrogram frontend by adapting its feature extraction \nparameters during training. This result is encouraging for future implementations of deep \nlearning technology for automatic insect sound recognition, especially as larger datasets \nbecome available.
    Repository Name: National Museum of Natural History, Netherlands
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  • 45
    Publication Date: 2024-03-29
    Description: Ecological indicators for monitoring strategies are expected to combine three major characteristics: ecological significance, statistical credibility, and cost-effectiveness. Strategies based on stranding networks rank highly in cost-effectiveness, but their ecological significance and statistical credibility are disputed. Our present goal is to improve the value of stranding data as population indicator as part of monitoring strategies by constructing the spatial and temporal null hypothesis for strandings. The null hypothesis is defined as: small cetacean distribution and mortality are uniform in space and constant in time. We used a drift model to map stranding probabilities and predict stranding patterns of cetacean carcasses under H0 across the North Sea, the Channel and the Bay of Biscay, for the period 1990–2009. As the most common cetacean occurring in this area, we chose the harbour porpoise Phocoena phocoena for our modelling. The difference between these strandings expected under H0 and observed strandings is defined as the stranding anomaly. It constituted the stranding data series corrected for drift conditions. Seasonal decomposition of stranding anomaly suggested that drift conditions did not explain observed seasonal variations of porpoise strandings. Long-term stranding anomalies increased first in the southern North Sea, the Channel and Bay of Biscay coasts, and finally the eastern North Sea. The hypothesis of changes in porpoise distribution was consistent with local visual surveys, mostly SCANS surveys (1994 and 2005). This new indicator could be applied to cetacean populations across the world and more widely to marine megafauna.
    Repository Name: National Museum of Natural History, Netherlands
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  • 46
    Publication Date: 2024-04-09
    Description: Biodiversity loss is a major global challenge and minimizing extinction rates is the goal of several multilateral environmental agreements. Policy decisions require comprehensive, spatially explicit information on species’ distributions and threats. We present an analysis of the conservation status of 14,669 European terrestrial, freshwater and marine species (ca. 10% of the continental fauna and flora), including all vertebrates and selected groups of invertebrates and plants. Our results reveal that 19% of European species are threatened with extinction, with higher extinction risks for plants (27%) and invertebrates (24%) compared to vertebrates (18%). These numbers exceed recent IPBES (Intergovernmental Platform on Biodiversity and Ecosystem Services) assumptions of extinction risk. Changes in agricultural practices and associated habitat loss, overharvesting, pollution and development are major threats to biodiversity. Maintaining and restoring sustainable land and water use practices is crucial to minimize future biodiversity declines.
    Repository Name: National Museum of Natural History, Netherlands
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  • 47
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    Public Library of Science (PLoS)
    In:  EPIC3PLOS ONE, Public Library of Science (PLoS), 19(4), pp. e0300138-e0300138, ISSN: 1932-6203
    Publication Date: 2024-04-26
    Description: Using the climate model CLIMBER-X, we present an efficient method for assimilating the temporal evolution of surface temperatures for the last deglaciation covering the period 22000 to 6500 years before the present. The data assimilation methodology combines the data and the underlying dynamical principles governing the climate system to provide a state estimate of the system, which is better than that which could be obtained using just the data or the model alone. In applying an ensemble Kalman filter approach, we make use of the advances in the parallel data assimilation framework (PDAF), which provides parallel data assimilation functionality with a relatively small increase in computation time. We find that the data assimilation solution depends strongly on the background evolution of the decaying ice sheets rather than the assimilated temperatures. Two different ice sheet reconstructions result in a different deglacial meltwater history, affecting the large-scale ocean circulation and, consequently, the surface temperature. We find that the influence of data assimilation is more pronounced on regional scales than on the global mean. In particular, data assimilation has a stronger effect during millennial warming and cooling phases, such as the Bølling-Allerød and Younger Dryas, especially at high latitudes with heterogeneous temperature patterns. Our approach is a step toward a comprehensive paleo-reanalysis on multi-millennial time scales, including incorporating available paleoclimate data and accounting for their uncertainties in representing regional climates.
    Repository Name: EPIC Alfred Wegener Institut
    Type: Article , peerRev
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  • 48
    Publication Date: 2015-08-11
    Description: We demonstrate the real-time observation of phonon-polariton propagation in ferroelectric LiNbO 3 using a single-shot spectroscopic setup that employs an echelon mirror. The echelon mirror provides a spatially encoded time delay for the probe pulse; therefore, the ultrafast transient behavior of materials can be detected on a single-shot basis. Using optical Kerr gate apparatus, forward and backward propagating E -mode phonon-polaritons were simultaneously induced via an impulsive stimulated Raman scattering process, and subsequently, their dynamics were readily mapped in time-frequency space using heterodyne detection. The two phonon-polaritons appeared on opposite sides of the central probe wavelength and were symmetrically imaged against the ordinary and extraordinary probe lights. By taking into account coupling of the lowest E -mode phonon-polariton to a low-frequency relaxational mode, not only the phonon-polariton dispersion but also the wavevector dependence of the damping rate was unveiled and quantitatively evaluated.
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  • 49
    Publication Date: 2015-08-11
    Description: This is the report on trap states in enhancement-mode AlGaN/GaN/AlGaN double heterostructures high electron mobility transistors by fluorine plasma treatment with different GaN channel layer thicknesses. Compared with the thick GaN channel layer sample, the thin one has smaller 2DEG concentration, lower electron mobility, lower saturation current, and lower peak transconductance, but it has a higher threshold voltage of 1.2 V. Deep level transient spectroscopy measurements are used to obtain the accurate capture cross section of trap states. By frequency dependent capacitance and conductance measurements, the trap state density of (1.98–2.56) × 10 12  cm −2 eV −1 is located at E T in a range of (0.37–0.44) eV in the thin sample, while the trap state density of (2.3–2.92) × 10 12  cm −2 eV −1 is located at E T in a range of (0.33–0.38) eV in the thick one. It indicates that the trap states in the thin sample are deeper than those in the thick one.
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  • 50
    Publication Date: 2015-08-11
    Description: Vertically aligned nanocomposite (VAN) (La 0.7 Sr 0.3 MnO 3 ) 1−x :(CeO 2 ) x (LSMO:CeO 2 ) thin films have been grown on SrTiO 3 (001) substrates by pulsed laser deposition. Tunable magnetoresistance properties as well as microstructures are demonstrated in these VAN films by modulating the film composition (x = 0, 0.3, 0.4, 0.45, 0.5, and 0.55). The sample of x = 0.3 shows a large low-field magnetoresistance (LFMR) in a high temperature range, i.e., over 10% at the range of 280 K to 320 K under 1 T and with a peak value of ∼13.5% at 310 K. In addition, a vast enhancement of LFMR in a low temperature range of 20–150 K with peak of ≈34.3% at 45 K for 1 T could be achieved with x = 0.5. The enhanced LFMR properties can be attributed to both the phase boundary induced spin fluctuation and the magnetic tunneling effect through vertical ferromagnetic/insulator/ferromagnetic structures. The observed enhanced LFMR performance, especially at high temperatures, as well as its simple growth method, offers a great potential for LSMO:CeO 2 nanocomposites to be used in spintronic devices in a large temperature range.
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    Electronic ISSN: 1089-7550
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  • 51
    Publication Date: 2015-08-11
    Description: We present a new generalized scaling relationship accounting for relaxation processes of both the real and the imaginary parts of the complex dielectric permittivity data in a wide temperature range of dielectric media. It has been successfully used for experimental data related to various dynamics in liquid crystalline phases of: 4-bromobenzylidene-4′-pentyloxyanilin, 4-bromobenzylidene-4′-hexyloxyaniline, 4′-butyl-4-(2-methylbutoxy) azoxybenzene, and 4-ethyl-4′-octylazoxybenzene. Moreover, the scaling was checked for the theoretical data of Dissado-Hill cluster model. A comparison with earlier scaling, proposed by Nagel and Dendzik, is given.
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  • 52
    Publication Date: 2015-08-11
    Description: Focusing of surface phonon-polaritons propagating toward the tip of a cone and the edge of a wedge is theoretically analyzed and compared. Based on Maxwell's equations, explicit expressions for the dispersion relations in each structure are determined and solved numerically for a propagation parameter driving the surface phonon-polariton energy density. For conical and wedge structures of SiO 2 , it is found that: (1) the cone (wedge) supports the polariton focusing only for aperture angles in the interval 18 ° – 68 ° ( 21 ° – 51 ° ), and within the range of excitation frequencies from 32.1 THz (31.5 THz) to 33.9 THz (33.9 THz). In this frequency interval, the real part of the SiO 2 permittivity is negative and the presence of polaritons is significant. (2) The polariton focusing efficiency of both the cone and wedge reaches its maximum values at the critical frequency f cr = 33.6  THz and at different aperture angles of about α opt = 45 ° and α opt = 30 ° , respectively. (3) When the polaritons travel from 100 nm to 5 nm toward the tip of the cone with this optimum angle, their Poynting vector increases by a factor of 12, which is about four times larger than the corresponding one provided by the wedge and indicates that the cone is more efficient than the wedge for the focusing of surface phonon-polaritons.
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  • 53
    Publication Date: 2015-08-11
    Description: Surface plasmons can squeeze light into a deep-subwavelength space and generate abundant hot electrons in the nearby metallic regions, enabling a new paradigm of photoconversion by the way of hot electron collection. Unlike the visible spectral range concerned in previous literatures, we focus on the communication band and design the infrared hot-electron photodetectors with plasmonic metal-insulator-metal configuration by using full-wave finite-element method. Titanium dioxide-silver Schottky interface is employed to boost the low-energy infrared photodetection. The photodetection sensitivity is strongly improved by enhancing the plasmonic excitation from a rationally engineered metallic grating, which enables a strong unidirectional photocurrent. With a five-step electrical simulation, the optimized device exhibits an unbiased responsivity of ∼0.1 mA/W and an ultra-narrow response band (FWHM = 4.66 meV), which promises to be a candidate as the compact photodetector operating in communication band.
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  • 54
    Publication Date: 2015-08-11
    Description: A two-step method that combines homogeneous electron beam (EB) irradiation and thermal annealing has been developed to enhance the thermoelectric properties of nanocrystalline bismuth selenium telluride thin films. The thin films, prepared using a flash evaporation method, were treated with EB irradiation in a N 2 atmosphere at room temperature and an acceleration voltage of 0.17 MeV. Thermal annealing was performed under Ar/H 2 (5%) at 300 °C for 60 min. X-ray diffraction was used to determine that compositional phase separation between bismuth telluride and bismuth selenium telluride developed in the thin films exposed to higher EB doses and thermal annealing. We propose that the phase separation was induced by fluctuations in the distribution of selenium atoms after EB irradiation, followed by the migration of selenium atoms to more stable sites during thermal annealing. As a result, thin film crystallinity improved and mobility was significantly enhanced. This indicates that the phase separation resulting from the two-step method enhanced, rather than disturbed, the electron transport. Both the electrical conductivity and the Seebeck coefficient were improved following the two-step method. Consequently, the power factor of thin films that underwent the two-step method was enhanced to 20 times (from 0.96 to 21.0  μ W/(cm K 2 ) that of the thin films treated with EB irradiation alone.
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  • 55
    Publication Date: 2015-08-11
    Description: In this study, we developed a new method for in-situ pressure determination in multi-anvil, high-pressure apparatus using an acoustic travel time approach within the framework of acoustoelasticity. The ultrasonic travel times of polycrystalline Al 2 O 3 were calibrated against NaCl pressure scale up to 15 GPa and 900 °C in a Kawai-type double-stage multi-anvil apparatus in conjunction with synchrotron X-radiation, thereby providing a convenient and reliable gauge for pressure determination at ambient and high temperatures. The pressures derived from this new travel time method are in excellent agreement with those from the fixed-point methods. Application of this new pressure gauge in an offline experiment revealed a remarkable agreement of the densities of coesite with those from the previous single crystal compression studies under hydrostatic conditions, thus providing strong validation for the current travel time pressure scale. The travel time approach not only can be used for continuous in-situ pressure determination at room temperature, high temperatures, during compression and decompression, but also bears a unique capability that none of the previous scales can deliver, i.e., simultaneous pressure and temperature determination with a high accuracy (±0.16 GPa in pressure and ±17 °C in temperature). Therefore, the new in-situ Al 2 O 3 pressure gauge is expected to enable new and expanded opportunities for offline laboratory studies of solid and liquid materials under high pressure and high temperature in multi-anvil apparatus.
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  • 56
    Publication Date: 2015-08-11
    Description: We report a novel method of determining the average Néel relaxation time and its temperature dependence by calculating derivatives of the measured time dependence of temperature for a frozen ferrofluid exposed to an alternating magnetic field. The ferrofluid, composed of dextran-coated Fe 3 O 4 nanoparticles (diameter 13.7 nm ± 4.7 nm), was synthesized via wet chemical precipitation and characterized by x-ray diffraction and transmission electron microscopy. An alternating magnetic field of constant amplitude ( H 0 = 20 kA/m) driven at frequencies of 171 kHz, 232 kHz, and 343 kHz was used to determine the temperature dependent magnetic energy absorption rate in the temperature range from 160 K to 210 K. We found that the specific absorption rate of the ferrofluid decreased monotonically with temperature over this range at the given frequencies. From these measured data, we determined the temperature dependence of the Néel relaxation time and estimate a room-temperature magnetocrystalline anisotropy constant of 40 kJ/m 3 , in agreement with previously published results.
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  • 57
    Publication Date: 2015-08-11
    Description: We propose a concurrent multiscale molecular dynamics for molecular systems in order to apply macroscale mechanical boundary conditions such as traction and average displacement for solid state materials, which is difficult to do in traditional molecular dynamics where boundary conditions are applied in terms of forces and displacements on selected particles. The multiscale model is systematically constructed in terms of multiscale structures of kinematics, force field, and dynamical equations. The idea is to extend the Anderson-Parrinello-Rahman molecular dynamics to the cases that have arbitrary finite domain and boundary, thus the model is capable of solving inhomogeneous, non-equilibrium problems. The macroscale stress loading on a representative volume element with periodic boundary condition is generalized to all kinds of macroscale mechanical boundary conditions. Unlike most multiscale techniques, our theory is aimed at understanding fundamental physics rather than achieving computing efficiency. Examples of problems with prescribed average displacements and surface tractions are presented to demonstrate the validity of the proposed multiscale molecular dynamics.
    Print ISSN: 0021-9606
    Electronic ISSN: 1089-7690
    Topics: Chemistry and Pharmacology , Physics
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  • 58
    Publication Date: 2015-08-11
    Description: We study the effect of chain rigidity on the behavior of semiflexible polymers in the vicinity of flat walls in a slit, and of surfactants at the liquid-liquid interface between immiscible liquids. Using molecular dynamics simulations, it is demonstrated that the impact of bending angle forces is particularly strong within the depletion layer at the phase boundary whereas at distance R e away from the interface, where R e is the mean distance between the ends of a semiflexible chain, the contribution of these non-local triplet interactions to pressure tensor virtually disappears. The present study also demonstrates that growing stiffness of the macromolecules leads to an increase in surface tension and total pressure.
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  • 59
    Publication Date: 2015-08-11
    Description: Quantum-chemical computations of nuclear quadrupole-coupling parameters for 24 open-shell states of small molecules based on non-relativistic and spin-free exact two-component (SFX2C) relativistic equation-of-motion coupled-cluster (EOM-CC) as well as spin-orbital-based restricted open-shell Hartree-Fock coupled-cluster (ROHF-CC) methods are reported. Relativistic effects, the performance of the EOM-CC and ROHF-CC methods for treating electron correlation, as well as basis-set convergence have been carefully analyzed. Consideration of relativistic effects is necessary for accurate calculations on systems containing third-row (K-Kr) and heavier elements, as expected, and the SFX2C approach is shown to be a useful cost-effective option here. Further, it is demonstrated that the EOM-CC methods constitute flexible and accurate alternatives to the ROHF-CC methods in the calculations of nuclear quadrupole-coupling parameters for open-shell states.
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  • 60
    Publication Date: 2015-08-11
    Description: We study the continuity of an abstract generalization of the maximum-entropy inference—a maximizer. It is defined as a right-inverse of a linear map restricted to a convex body which uniquely maximizes on each fiber of the linear map a continuous function on the convex body. Using convex geometry we prove, amongst others, the existence of discontinuities of the maximizer at limits of extremal points not being extremal points themselves and apply the result to quantum correlations. Further, we use numerical range methods in the case of quantum inference which refers to two observables. One result is a complete characterization of points of discontinuity for 3 × 3 matrices.
    Print ISSN: 0022-2488
    Electronic ISSN: 1089-7658
    Topics: Mathematics , Physics
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  • 61
    Publication Date: 2015-08-11
    Description: A quantum two-path interferometer allows for direct measurement of the transmission phase shift of an electron, providing useful information on coherent scattering problems. In mesoscopic systems, however, the two-path interference is easily smeared by contributions from other paths, and this makes it difficult to observe the true transmission phase shift. To eliminate this problem, multi-terminal Aharonov-Bohm (AB) interferometers have been used to derive the phase shift by assuming that the relative phase shift of the electrons between the two paths is simply obtained when a smooth shift of the AB oscillations is observed. Nevertheless, the phase shifts using such a criterion have sometimes been inconsistent with theory. On the other hand, we have used an AB ring contacted to tunnel-coupled wires and acquired the phase shift consistent with theory when the two output currents through the coupled wires oscillate with well-defined anti-phase. Here, we investigate thoroughly these two criteria used to ensure a reliable phase measurement, the anti-phase relation of the two output currents, and the smooth phase shift in the AB oscillation. We confirm that the well-defined anti-phase relation ensures a correct phase measurement with a quantum two-path interference. In contrast, we find that even in a situation where the anti-phase relation is less well-defined, the smooth phase shift in the AB oscillation can still occur but does not give the correct transmission phase due to contributions from multiple paths. This indicates that the phase relation of the two output currents in our interferometer gives a good criterion for the measurement of the true transmission phase, while the smooth phase shift in the AB oscillation itself does not.
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  • 62
    Publication Date: 2015-08-11
    Description: The stability of a long scale equilibrium vortex structure to short scale perturbations is studied in a strongly coupled dusty plasma in the framework of a generalized hydrodynamic model. It is shown that the free energy associated with the velocity shear of the vortex can drive secondary instabilities consisting of transverse shear waves when the resonance condition between the vortex rotation frequency and the secondary wave frequency is met. Such a process can transfer energy from the long scale vortex to the short scale secondary wave and thereby provide a saturation mechanism for long scale vortices in plasmas in a manner analogous to that in neutral fluids.
    Print ISSN: 1070-664X
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  • 63
    Publication Date: 2015-08-11
    Description: A laser produced high-Z plasma in which an energy balance is achieved due to radiation emission and radiative heat transfer supports ion acoustic instability. A linear dispersion relation is derived, and instability is compared to the radiation cooling instability [R. G. Evans, Plasma Phys. Controlled Fusion 27 , 751 (1985)]. Under conditions of indirect drive fusion experiments, the driving term for the instability is the radiative heat flux and, in particular, the density dependence of the radiative heat conductivity. A specific example of thermal Bremsstrahlung radiation source has been considered. This instability may lead to plasma jet formation and anisotropic x-ray generation, thus affecting inertial confinement fusion related experiments.
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  • 64
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    In: PLoS ONE
    Publication Date: 2015-08-11
    Description: by Cheng-Jui Lin, Tai-Cherng Liou, Chi-Feng Pan, Pei-Chen Wu, Fang-Ju Sun, Hsuan-Liang Liu, Han-Hsiang Chen, Chih-Jen Wu Evidence has shown that indoxyl sulfate (IS) and p-cresyl sulfate (PCS) may be alternative predictors of clinical outcomes in chronic kidney disease (CKD). Both toxins are derived from the gastrointestinal tract and metabolised in the liver. However, it is unclear whether the liver affects the production of IS and PCS. Here, we explore the association between IS and PCS levels in liver cirrhosis and a CKD-based cohort (N = 115). Liver and kidney function was assessed and classified by a Child-Pugh score (child A–C) and a modified version of the Modification of Diet in Renal Disease (MDRD) equation (Stages 1–4), respectively. An animal model was also used to confirm the two toxin levels in a case of liver fibrosis. In patients with early liver cirrhosis (child A), IS and PCS were significantly associated with CKD stages. In contrast, serum IS and PCS did not significantly change in advanced liver cirrhosis (child C). A stepwise multiple linear regression analysis also showed that T-PCS was significantly associated with stages of liver cirrhosis after adjusting for other confounding factors (B = -2.29, p = 0.012). Moreover, the serum and urine levels of T-PCS and T-IS were significantly lower in rats with liver failure than in those without ( p
    Electronic ISSN: 1932-6203
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  • 65
    Publication Date: 2015-08-11
    Description: The present paper is devoted to simulation of nonlinear disintegration of a localized perturbation into ion-acoustic solitons train in a plasma with hot electrons and cold ions. A Gaussian initial perturbation is used to model the localized perturbation. For this purpose, first, we reduce fluid system of equations to a Korteweg de-Vries equation by the following well-known assumptions. (i) On the ion-acoustic evolution time-scale, the electron velocity distribution function (EVDF) is assumed to be stationary. (ii) The calculation is restricted to small amplitude cases. Next, in order to generalize the model to finite amplitudes cases, the evolution of EVDF is included. To this end, a hybrid code is designed to simulate the case, in which electrons dynamics is governed by Vlasov equation, while cold ions dynamics is, like before, studied by the fluid equations. A comparison between the two models shows that although the fluid model is capable of demonstrating the general features of the process, to have a better insight into the relevant physics resulting from the evolution of EVDF, the use of kinetic treatment is of great importance.
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  • 66
    Publication Date: 2015-08-11
    Description: by Guangde Zhang, Hongbo Shi, Lin Wang, Meng Zhou, Zhenzhen Wang, Xiaoxia Liu, Liang Cheng, Weimin Li, Xueqi Li Myocardial infarction (MI) is a severe coronary artery disease and a leading cause of mortality and morbidity worldwide. However, the molecular mechanisms of MI have yet to be fully elucidated. In this study, we compiled MI-related genes, MI-related microRNAs (miRNAs) and known human transcription factors (TFs), and we then identified 1,232 feed-forward loops (FFLs) among these miRNAs, TFs and their co-regulated target genes through integrating target prediction. By merging these FFLs, the first miRNA and TF mediated regulatory network for MI was constructed, from which four regulators (SP1, ESR1, miR-21-5p and miR-155-5p) and three regulatory modules that might play crucial roles in MI were then identified. Furthermore, based on the miRNA and TF mediated regulatory network and literature survey, we proposed a pathway model for miR-21-5p, the miR-29 family and SP1 to demonstrate their potential co-regulatory mechanisms in cardiac fibrosis, apoptosis and angiogenesis. The majority of the regulatory relations in the model were confirmed by previous studies, which demonstrated the reliability and validity of this miRNA and TF mediated regulatory network. Our study will aid in deciphering the complex regulatory mechanisms involved in MI and provide putative therapeutic targets for MI.
    Electronic ISSN: 1932-6203
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  • 67
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    In: PLoS ONE
    Publication Date: 2015-08-11
    Description: by Dominik Eichin, Juha P. Laurila, Sirpa Jalkanen, Marko Salmi The ectoenzyme CD73 catalyzes the hydrolysis of AMP, and is one of the most important producers of extracellular adenosine. On regulatory T cells, CD73 is necessary for immunosuppressive functions, and on Th17 cells CD73-generated adenosine exerts anti-inflammatory effects. However, the expression and function of CD73 in pro-inflammatory M1 and in immunosuppressive M2 macrophages is largely unknown. Here we show that CD73 expression and enzyme activity were induced in in vitro polarized pro-inflammatory human M(LPS+TNF) monocytes/macrophages, while CD73 was absent from immunosuppressive M(IL-4+M-CSF)-polarized macrophages. Inhibition of CD73 activity with the inhibitor AMPCP did not affect the polarization of human monocytes. In mice, CD73 was present on resident peritoneal macrophages. In striking contrast, elicited peritoneal macrophages remained CD73 negative regardless of their polarization towards either a pro-inflammatory M(LPS) or anti-inflammatory M(IL-4c) direction. Finally, the ability of peritoneal macrophages to polarize to pro- and anti-inflammatory cells was perfectly normal in CD73-deficient mice in vivo . These data indicate that, in contrast to other major leukocyte subpopulations, CD73 activity on macrophages does not play a major role in their polarization and that in mice host CD73 on any cell type is not required in vivo for peritoneal macrophage polarization towards either a pro- or an anti-inflammatory direction.
    Electronic ISSN: 1932-6203
    Topics: Medicine , Natural Sciences in General
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  • 68
    Publication Date: 2015-08-11
    Description: by Hui San Ong, Mohd Syafiq Rahim, Mohd Firdaus-Raih, Effirul Ikhwan Ramlan The unique programmability of nucleic acids offers alternative in constructing excitable and functional nanostructures. This work introduces an autonomous protocol to construct DNA Tetris shapes (L-Shape, B-Shape, T-Shape and I-Shape) using modular DNA blocks. The protocol exploits the rich number of sequence combinations available from the nucleic acid alphabets, thus allowing for diversity to be applied in designing various DNA nanostructures. Instead of a deterministic set of sequences corresponding to a particular design, the protocol promotes a large pool of DNA shapes that can assemble to conform to any desired structures. By utilising evolutionary programming in the design stage, DNA blocks are subjected to processes such as sequence insertion, deletion and base shifting in order to enrich the diversity of the resulting shapes based on a set of cascading filters. The optimisation algorithm allows mutation to be exerted indefinitely on the candidate sequences until these sequences complied with all the four fitness criteria. Generated candidates from the protocol are in agreement with the filter cascades and thermodynamic simulation. Further validation using gel electrophoresis indicated the formation of the designed shapes. Thus, supporting the plausibility of constructing DNA nanostructures in a more hierarchical, modular, and interchangeable manner.
    Electronic ISSN: 1932-6203
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  • 69
    Publication Date: 2015-08-11
    Description: by Nima Toosizadeh, Jane Mohler, David G. Armstrong, Talal K. Talal, Bijan Najafi Poor balance control and increased fall risk have been reported in people with diabetic peripheral neuropathy (DPN). Traditional body sway measures are unable to describe underlying postural control mechanism. In the current study, we used stabilogram diffusion analysis to examine the mechanism under which balance is altered in DPN patients under local-control (postural muscle control) and central-control (postural control using sensory cueing). DPN patients and healthy age-matched adults over 55 years performed two 15-second Romberg balance trials. Center of gravity sway was measured using a motion tracker system based on wearable inertial sensors, and used to derive body sway and local/central control balance parameters. Eighteen DPN patients (age = 65.4±7.6 years; BMI = 29.3±5.3 kg/m 2 ) and 18 age-matched healthy controls (age = 69.8±2.9; BMI = 27.0±4.1 kg/m 2 ) with no major mobility disorder were recruited. The rate of sway within local-control was significantly higher in the DPN group by 49% (healthy local-control slope = 1.23±1.06×10 -2 cm 2 /sec, P
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  • 70
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    Public Library of Science (PLoS)
    In: PLoS ONE
    Publication Date: 2015-08-11
    Description: by Raphael H. Heiberger Today´s connected world allows people to gather information in shorter intervals than ever before, widely monitored by massive online data sources. As a dramatic economic event, recent financial crisis increased public interest for large companies considerably. In this paper, we exploit this change in information gathering behavior by utilizing Google query volumes as a "bad news" indicator for each corporation listed in the Standard and Poor´s 100 index. Our results provide not only an investment strategy that gains particularly in times of financial turmoil and extensive losses by other market participants, but reveal new sectoral patterns between mass online behavior and (bearish) stock market movements. Based on collective attention shifts in search queries for individual companies, hence, these findings can help to identify early warning signs of financial systemic risk. However, our disaggregated data also illustrate the need for further efforts to understand the influence of collective attention shifts on financial behavior in times of regular market activities with less tremendous changes in search volumes.
    Electronic ISSN: 1932-6203
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  • 71
    Publication Date: 2015-08-11
    Description: by Sea H. Kim, Birendra Babu Adhikari, Siobanth Cruz, Michael P. Schramm, Joe A. Vinson, Vasanthy Narayanaswami The objective of this study is to transport and deliver resveratrol to intracellular sites using apolipoprotein E3 (apoE3). Reconstituted high-density lipoprotein (rHDL) bearing resveratrol (rHDL/res) was prepared using phospholipids and the low-density lipoprotein receptor (LDLr)-binding domain of apoE3. Biophysical characterization revealed that resveratrol was partitioned into the phospholipid bilayer of discoidal rHDL/res particles (~19 nm diameter). Co-immunoprecipitation studies indicated that the LDLr-binding ability of apoE3 was retained. Cellular uptake of resveratrol to intracellular sites was evaluated in glioblastoma A-172 cells by direct fluorescence using chemically synthesized NBD-labeled resveratrol (res/NBD) embedded in rHDL/res. Competition and inhibition studies indicate that the uptake is by receptor mediated endocytosis via the LDLr, with co-localization of apoE3 and res/NBD in late endosomes/lysosomes. We propose that rHDL provides an ideal hydrophobic milieu to sequester resveratrol and that rHDL containing apoE3 serves as an effective “nanovehicle” to transport and deliver resveratrol to targeted intracellular sites.
    Electronic ISSN: 1932-6203
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  • 72
    Publication Date: 2015-08-11
    Description: by JunLi Liu, YiHu Wang, ShuJun Song, XiJie Wang, YaYa Qin, ShaoYan Si, YanChuan Guo Purpose Collagen peptides (CPs) and calcium citrate are commonly used as bone health supplements for treating osteoporosis. However, it remains unknown whether the combination of oral bovine CPs with calcium citrate is more effective than administration of either agent alone. Methods Forty 12-week-old Sprague-Dawley rats were randomly divided into five groups ( n = 8) for once-daily intragastric administration of different treatments for 3 months at 3 months after ovariectomy (OVX) as follows: sham + vehicle; OVX + vehicle; OVX + 750 mg/kg CP; OVX + CP-calcium citrate (75 mg/kg); OVX + calcium citrate (75 mg/kg). After euthanasia, the femurs were removed and analyzed by dual energy X-ray absorptiometry and micro-computed tomography, and serum samples were analyzed for bone metabolic markers. Results OVX rats supplemented with CPs or CP-calcium citrate showed osteoprotective effects, with reductions in the OVX-induced decreases in their femoral bone mineral density. Moreover, CP-calcium citrate prevented trabecular bone loss, improved the microarchitecture of the distal femur, and significantly inhibited bone loss with increased bone volume, connectivity density, and trabecular number compared with OVX control rats. CP or CP-calcium citrate administration significantly increased serum procollagen type I N-terminal propeptide levels and reduced serum bone-specific alkaline phosphatase, osteocalcin, and C-telopeptide of type I collagen levels. Conclusions Our data indicate that combined oral administration of bovine CPs with calcium citrate inhibits bone loss in OVX rats. The present findings suggest that combined oral administration of bovine CPs with calcium citrate is a promising alternative for reducing bone loss in osteopenic postmenopausal women.
    Electronic ISSN: 1932-6203
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  • 73
    Publication Date: 2015-08-11
    Description: Coherence oscillations measured in two-dimensional (2D) electronic spectra of pigment-protein complexes may have electronic, vibrational, or mixed-character vibronic origins, which depend on the degree of electronic-vibrational mixing. Oscillations from intrapigment vibrations can obscure the inter-site coherence lifetime of interest in elucidating the mechanisms of energy transfer in photosynthetic light-harvesting. Huang-Rhys factors ( S ) for low-frequency vibrations in Chlorophyll and Bacteriochlorophyll are quite small ( S ≤ 0.05), so it is often assumed that these vibrations influence neither 2D spectra nor inter-site coherence dynamics. In this work, we explore the influence of S within this range on the oscillatory signatures in simulated 2D spectra of a pigment heterodimer. To visualize the inter-site coherence dynamics underlying the 2D spectra, we introduce a formalism which we call the “site-probe response.” By comparing the calculated 2D spectra with the site-probe response, we show that an on-resonance vibration with Huang-Rhys factor as small as S = 0.005 and the most strongly coupled off-resonance vibrations ( S = 0.05) give rise to long-lived, purely vibrational coherences at 77 K. We moreover calculate the correlation between optical pump interactions and subsequent entanglement between sites, as measured by the concurrence. At 77 K, greater long-lived inter-site coherence and entanglement appear with increasing S . This dependence all but vanishes at physiological temperature, as environmentally induced fluctuations destroy the vibronic mixing.
    Electronic ISSN: 1931-9223
    Topics: Chemistry and Pharmacology , Physics
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  • 74
    Publication Date: 2015-08-11
    Description: We demonstrate high precision controllability of the magnetization reversal nucleation process in [Co/Pd] 8 multilayer films consisting of two sets of bilayers with high and low perpendicular anisotropy, respectively. The anisotropy of the entire film is set by the degree of Co/Pd interfacial mixing during deposition which provides fine control of the anisotropy of an individual bilayer in the multilayer stack. The relative number of each type of bilayer is used to select the magnetisation reversal behavior such that changing one bilayer changes the properties of the entire multilayer through anisotropy averaging. A simple extension to the sputtering protocol would provide multilayer films with fully graded anisotropy, while maintaining a constant saturation magnetization opening new possibilities for the creation of highly engineered multilayer structures for spin torque devices and future magnetic recording media.
    Print ISSN: 0021-8979
    Electronic ISSN: 1089-7550
    Topics: Physics
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  • 75
    Publication Date: 2015-08-11
    Description: Coherence oscillations measured in two-dimensional (2D) electronic spectra of pigment-protein complexes may have electronic, vibrational, or mixed-character vibronic origins, which depend on the degree of electronic-vibrational mixing. Oscillations from intrapigment vibrations can obscure the inter-site coherence lifetime of interest in elucidating the mechanisms of energy transfer in photosynthetic light-harvesting. Huang-Rhys factors ( S ) for low-frequency vibrations in Chlorophyll and Bacteriochlorophyll are quite small ( S ≤ 0.05), so it is often assumed that these vibrations influence neither 2D spectra nor inter-site coherence dynamics. In this work, we explore the influence of S within this range on the oscillatory signatures in simulated 2D spectra of a pigment heterodimer. To visualize the inter-site coherence dynamics underlying the 2D spectra, we introduce a formalism which we call the “site-probe response.” By comparing the calculated 2D spectra with the site-probe response, we show that an on-resonance vibration with Huang-Rhys factor as small as S = 0.005 and the most strongly coupled off-resonance vibrations ( S = 0.05) give rise to long-lived, purely vibrational coherences at 77 K. We moreover calculate the correlation between optical pump interactions and subsequent entanglement between sites, as measured by the concurrence. At 77 K, greater long-lived inter-site coherence and entanglement appear with increasing S . This dependence all but vanishes at physiological temperature, as environmentally induced fluctuations destroy the vibronic mixing.
    Print ISSN: 0021-9606
    Electronic ISSN: 1089-7690
    Topics: Chemistry and Pharmacology , Physics
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  • 76
    Publication Date: 2015-08-11
    Description: Electrochemical in operando X-ray diffraction (XRD) is a powerful method to analyze structural changes of energy storage materials while inserting/de-inserting charge carriers, such as Li- or Na-ions, into/from a host structure. The design of an XRD in operando cell is presented, which enables the use of thin (6 μ m) aluminum foil as X-ray window as a non-toxic alternative to conventional beryllium windows. Owing to the reduced thickness, diffraction patterns and their changes during cycling can be observed with excellent quality, which was demonstrated for two cathode materials for sodium-ion batteries in a half-cell set-up, P2-Na 0.7 MnO 2 and Na 2.55 V 6 O 16 ⋅ 0.6H 2 O.
    Print ISSN: 0034-6748
    Electronic ISSN: 1089-7623
    Topics: Electrical Engineering, Measurement and Control Technology , Physics
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  • 77
    Publication Date: 2015-08-12
    Description: We present a method for noninvasively imaging the hand joints using a three-dimensional (3D) photoacoustic imaging (PAI) system. This 3D PAI system utilizes cylindrical scanning in data collection and virtual-detector concept in image reconstruction. The maximum lateral and axial resolutions of the PAI system are 70  μ m and 240  μ m. The cross-sectional photoacoustic images of a healthy joint clearly exhibited major internal structures including phalanx and tendons, which are not available from the current photoacoustic imaging methods. The in vivo PAI results obtained are comparable with the corresponding 3.0 T MRI images of the finger joint. This study suggests that the proposed method has the potential to be used in early detection of joint diseases such as osteoarthritis.
    Print ISSN: 0003-6951
    Electronic ISSN: 1077-3118
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  • 78
    Publication Date: 2015-08-12
    Description: We show how to levitate a liquid droplet above a plasma. Submitting a conductive droplet to a voltage larger than 50 V, we get a levitation regime that looks like the one obtained with the well-known thermal Leidenfrost effect, except that light is emitted from beneath the droplet. Spectroscopic analysis shows that this light is emitted by a cold and dense plasma and also that lines coming from the cathode plate material are present revealing a local cathodic sputtering effect. We examine the conditions for the levitation to occur and show that the levitation is essentially of thermal origin. Assuming a stationary heat transfer, we present a model that accounts well for the observed levitation conditions. In particular, stable levitation is shown to be possible for thin cathode plates only.
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  • 79
    Publication Date: 2015-08-12
    Description: We have performed atomistic simulations of the phonon-limited high field carrier transport in ⟨ 110 ⟩ Si nanowires with small diameter. The carrier drift velocities are obtained from a direct solution of the non-linear Boltzmann transport equation. The relationship between the drift velocity and the electric field considerably depends on the carrier, temperature, and diameter of the nanowires. In particular, the threshold between the linear and non-linear regimes exhibits important variations. The drift velocity reaches a maximum value and then drops. These trends can be related to the effects of quantum confinement on the band structure of the nanowires. We also discuss the impact of the different phonon modes and show that high-energy phonons can, unexpectedly, increase the drift velocity at a high electric field.
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  • 80
    Publication Date: 2015-08-12
    Description: Ion implantation is proposed to produce self-standing bent monocrystals. A Si sample 0.2 mm thick was bent to a radius of curvature of 10.5 m. The sample curvature was characterized by interferometric measurements; the crystalline quality of the bulk was tested by X-ray diffraction in transmission geometry through synchrotron light at ESRF (Grenoble, France). Dislocations induced by ion implantation affect only a very superficial layer of the sample, namely, the damaged region is confined in a layer 1  μ m thick. Finally, an elective application of a deformed crystal through ion implantation is here proposed, i.e., the realization of a crystalline undulator to produce X-ray beams.
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  • 81
    Publication Date: 2015-08-12
    Description: One-dimensional (1D) nanotubes of Nd 0.1 Bi 0.9 FeO 3 (NBFO) with an inner diameter of ∼50 nm were synthesized via sol-gel based electrospinning without template assistant. The phases, morphologies, crystalline structures, and magnetic properties of these 1D nanostructures were characterized by means of X-ray diffraction, scanning electron microscopy, transmission electron microscopy and SQUID, respectively. It was found that the calcination condition plays a crucial role in determining the morphologies and the magnetic properties. Interestingly, these 1D NBFO nanotubes exhibit wasp-waisted magnetic hysteresis with a lower coercivity and larger saturation magnetization, which were prevalent in natural rocks and artificial composite materials. The origin of these wasp-waisted hysteresis loops was discussed.
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  • 82
    Publication Date: 2015-08-12
    Description: Atmospheric pressure pulsed helium plasma jets are utilized for plasma-cell interactions. The effect of operating parameters such as applied voltage, pulse repetition frequency, and duty ratio on the generation of specific reactive oxygen and nitrogen species in gas and liquid phases and within cells is investigated. The apoptotic changes detected by terminal deoxynucleotidyl transferase (TdT)-mediated dUTP nick-end labeling assay in cells caused by plasma exposure are observed to correlate well with the levels of extracellular and intracellular reactive oxygen and nitrogen species.
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  • 83
    Publication Date: 2015-08-12
    Description: We report photovoltaic response of highly transparent graphene/BiFe 0.95 Si 0.05 O 3 (BFSiO)/ITO/glass derived from bottom-up spin coating technique. The device exhibits short-circuit-current (I SC 0.75 mA) with 1000 fold upsurge and open-circuit-voltage (V OC  ∼ 0.45 V) under standard AM 1.5 illumination through graphene. In combination, I SC of 0.63 mA and V OC of 0.35 V for same illumination through ITO, reveals the prospects of harvesting indoor light. Also, crystallographic structure, red shift in band gap, leakage behavior, and ferroelectric characteristics of BFSiO thin films are reported. Reproducible transient response of I SC and V OC with quick switching (
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  • 84
    Publication Date: 2015-08-12
    Description: Physical insights on the hydrodynamics and locomotion of self-propelled nanowire motor under nonequilibrium steady state are investigated using finite element method in accordance with hybrid molecular dynamics/multiparticle collision dynamics and rigid body dynamics. Nanowire motor is discretized into finite segments, and forces of solvent molecule acting on the motor are assumed to be the sum of forces acting on all segments of the motor. We show that the locomotion of nanowire motor is mainly determined by the imbalance forces acting on the catalytic and noncatalytic segments. The average velocity along the axis increases significantly as a function of time prior to reaching equilibrium. The length of nanowire motor shows negligible effect on the velocity of the motor. Preliminary experimental results are provided to validate the current model.
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  • 85
    Publication Date: 2015-08-12
    Description: Ultrahigh density periodically ordered magnetic yttrium iron garnet (Y 3 Fe 5 O 12 , YIG) nanodot arrays have been prepared by pulsed laser deposition through an ultrathin alumina mask (UTAM). UTAM having periodically ordered circularly shaped holes with 350 nm in diameter, 450 nm in inter-pore distance, and 700 nm in height has been prepared on silicon substrate. Furthermore, the microstructure and magnetic properties of YIG nanodot arrays have been characterized. Nanodot arrays with a sharp distribution in diameter centered at 340 nm with standard deviation of 10 nm have been fabricated. Moreover, typical hysteresis loops and ferromagnetic resonance spectra in in-plane and out-of-plane revealed that this unique structure greatly influences the magnetics properties of YIG. First, coercivity of YIG nanodot arrays in in-plane was increased about from 15 Oe of YIG films to 500 Oe. Then, the degree of uniformity about nanodot height decided that two or more resonance peaks in out-of-plane were detected in the spectra. The peak-to-peak linewidth values were about 94 Oe and 40 Oe in the parallel and perpendicular directions, respectively, which indicated that the values were larger by the two-magnon scattering. Consequently, this pattering method creates opportunities for studying physics in oxide nanomagnets and may be applied in spin-wave devices.
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  • 86
    Publication Date: 2015-08-12
    Description: We report on the tuning of the optical properties of II-VI-material-based microcavity samples, which is achieved by depositing Ag films on top of the structures. The micro-reflectivity spectra show a spectral shift of the sample resonance dependent on the metal layer thickness. By comparison of the experimental findings with the theoretical calculations applying the transfer matrix method on a metal-dielectric mirror structure, the influence of the metal layer particularly with regard to its partial oxidation was explored. Tamm plasmon modes are created at the interface between an open cavity with three ZnSe quantum wells and a metal layer on top. When tuning the excitonic emission relative to the mode by changing the sample temperature, an anticrossing of the resonances was observed. This is a clear indication that the strong coupling regime has been achieved in that sample configuration yielding a Rabi splitting of 18.5 meV. These results are promising for the realization of polariton-based optical devices with a rather simple sample configuration.
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  • 87
    Publication Date: 2015-08-12
    Description: As urbanization continues across the globe, cities face significant challenges and opportunities to grow in ways that reduce carbon emissions while providing high quality of life. An EcoPartnership between the cities of Portland, Oregon, USA and Kunming, China is designed to accelerate the exchange of policies and strategies for low-carbon development. Kunming successfully implemented China's first bus-rapid transit system (BRT); Portland is currently analyzing the feasibility of BRT. Portland relies on an urban growth boundary (UGB) as a key policy to guide growth management; Kunming is evaluating the feasibility of a UGB. Both cities are investing in infrastructure for bicycle networks. Key characteristics of successful collaboration include shared substantive priorities; familiarity with the institutional context and roles of the individuals involved; a good match in the responsibilities of the participating agencies and individuals; interpersonal rapport and trust; and the persistence of the collaboration over time.
    Electronic ISSN: 1941-7012
    Topics: Energy, Environment Protection, Nuclear Power Engineering
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  • 88
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    Public Library of Science (PLoS)
    In: PLoS ONE
    Publication Date: 2015-08-09
    Description: by Jennifer Choe Bush, Peter Christopher Pantelis, Xavier Morin Duchesne, Sebastian Alexander Kagemann, Daniel Patrick Kennedy We present a novel “Gaze-Replay” paradigm that allows the experimenter to directly test how particular patterns of visual input—generated from people’s actual gaze patterns—influence the interpretation of the visual scene. Although this paradigm can potentially be applied across domains, here we applied it specifically to social comprehension. Participants viewed complex, dynamic scenes through a small window displaying only the foveal gaze pattern of a gaze “donor.” This was intended to simulate the donor’s visual selection, such that a participant could effectively view scenes “through the eyes” of another person. Throughout the presentation of scenes presented in this manner, participants completed a social comprehension task, assessing their abilities to recognize complex emotions. The primary aim of the study was to assess the viability of this novel approach by examining whether these Gaze-Replay windowed stimuli contain sufficient and meaningful social information for the viewer to complete this social perceptual and cognitive task. The results of the study suggested this to be the case; participants performed better in the Gaze-Replay condition compared to a temporally disrupted control condition, and compared to when they were provided with no visual input. This approach has great future potential for the exploration of experimental questions aiming to unpack the relationship between visual selection, perception, and cognition.
    Electronic ISSN: 1932-6203
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  • 89
    Publication Date: 2015-08-09
    Description: by David G. Warnock, Daniel G. Bichet, Myrl Holida, Ozlem Goker-Alpan, Kathy Nicholls, Mark Thomas, Francois Eyskens, Suma Shankar, Mathews Adera, Sheela Sitaraman, Richie Khanna, John J. Flanagan, Brandon A. Wustman, Jay Barth, Carrolee Barlow, Kenneth J. Valenzano, David J. Lockhart, Pol Boudes, Franklin K. Johnson Trial Registration ClinicalTrials.gov NCT01196871
    Electronic ISSN: 1932-6203
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  • 90
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    Public Library of Science (PLoS)
    In: PLoS ONE
    Publication Date: 2015-08-12
    Description: by Clementine Menz, Mahroo K. Parsi, Julian R. J. Adams, Mohamed A. Sideek, Zlatko Kopecki, Allison J. Cowin, Mark A. Gibson Latent transforming growth factor-beta-1 binding protein-2 (LTBP-2) belongs to the fibrillin-LTBP superfamily of extracellular matrix proteins. LTBPs and fibrillins are involved in the sequestration and storage of latent growth factors, particularly transforming growth factor β (TGF-β), in tissues. Unlike other LTBPs, LTBP-2 does not covalently bind TGF-β, and its molecular functions remain unclear. We are screening LTBP-2 for binding to other growth factors and have found very strong saturable binding to fibroblast growth factor-2 (FGF-2) (Kd = 1.1 nM). Using a series of recombinant LTBP-2 fragments a single binding site for FGF-2 was identified in a central region of LTBP-2 consisting of six tandem epidermal growth factor-like (EGF-like) motifs (EGFs 9–14). This region was also shown to contain a heparin/heparan sulphate-binding site. FGF-2 stimulation of fibroblast proliferation was completely negated by the addition of 5-fold molar excess of LTBP-2 to the assay. Confocal microscopy showed strong co-localisation of LTBP-2 and FGF-2 in fibrotic keloid tissue suggesting that the two proteins may interact in vivo. Overall the study indicates that LTBP-2 is a potent inhibitor of FGF-2 that may influence FGF-2 bioactivity during wound repair particularly in fibrotic tissues.
    Electronic ISSN: 1932-6203
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  • 91
    Publication Date: 2015-08-12
    Description: by Xinwei Shi, Hao Liu, Jing Cao, Qing Liu, Guiju Tang, Wanlu Liu, Haiyi Liu, Dongrui Deng, Fuyuan Qiao, Yuanyuan Wu Objective Extravillous trophoblast (EVT) cells invade the endometrium and the maternal spiral arterioles during the first trimester. Mammary Serine Protease Inhibitor (Maspin, SERPINB5) plays a putative role in regulating the invasive activity of cytotrophoblasts. The maspin gene is silenced in various cancers by an epigenetic mechanism that involves aberrant cytosine methylation. We investigated the effect of the methylation status of the maspin promoter on the maspin expression and the aggressiveness of EVT cells. Methods Western blotting was used to detect the maspin protein expression in EVT cells upon hypoxia. The proliferative ability, the apoptosis rate and the migration and invasiveness were measured with Cell Counting Kit-8 assay, Flow Cytometry technology and Transwell methods. Subsequently, we treated cells with recombinant maspin protein. The methylation degree of maspin promoter region upon hypoxia/ decitabine was detected by bisulfite sequencing PCR and methylation-specific PCR. Finally, we explored the effects of decitabine on maspin protein expression and the aggressiveness of EVT cells. Results Hypoxia effectively increased maspin protein expression in EVT cells and significantly inhibited their aggressiveness. The addition of recombinant maspin protein inhibited this aggressiveness. Decitabine reduced the methylation in the maspin promoter region and effectively increased the maspin protein expression, which significantly weakened the migration and invasiveness of EVT cells. Discussion The methylation status of the maspin promoter is an important factor that affects the migration and invasion of EVT cells during early pregnancy. A decrease in the methylation status can inhibit the migration and invasion of EVT cells to affect placentation and can result in the ischemia and hypoxia of placenta.
    Electronic ISSN: 1932-6203
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  • 92
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    In: PLoS ONE
    Publication Date: 2015-08-12
    Description: by Jun-Ha Hwang, Mi Ran Byun, A. Rum Kim, Kyung Min Kim, Hang Jun Cho, Yo Han Lee, Juwon Kim, Mi Gyeong Jeong, Eun Sook Hwang, Jeong-Ho Hong Mesenchymal stem cell (MSC) differentiation is regulated by the extracellular matrix (ECM) through activation of intracellular signaling mediators. The stiffness of the ECM was shown to be an important regulatory factor for MSC differentiation, and transcriptional coactivator with PDZ-binding motif (TAZ) was identified as an effector protein for MSC differentiation. However, the detailed underlying mechanism regarding the role of ECM stiffness and TAZ in MSC differentiation is not yet fully understood. In this report, we showed that ECM stiffness regulates MSC fate through ERK or JNK activation. Specifically, a stiff hydrogel matrix stimulates osteogenic differentiation concomitant with increased nuclear localization of TAZ, but inhibits adipogenic differentiation. ERK and JNK activity was significantly increased in cells cultured on a stiff hydrogel. TAZ activation was induced by ERK or JNK activation on a stiff hydrogel because exposure to an ERK or JNK inhibitor significantly decreased the nuclear localization of TAZ, indicating that ECM stiffness-induced ERK or JNK activation is important for TAZ-driven osteogenic differentiation. Taken together, these results suggest that ECM stiffness regulates MSC differentiation through ERK or JNK activation.
    Electronic ISSN: 1932-6203
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  • 93
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    Public Library of Science (PLoS)
    In: PLoS ONE
    Publication Date: 2015-08-12
    Description: by Maria Cecilia P. Moura, Steven J. Smith, David B. Belzer Residential buildings are a key driver of energy consumption and also impact transportation and land-use. Energy consumption in the residential sector accounts for one-fifth of total U.S. energy consumption and energy-related CO 2 emissions, with floor space a major driver of building energy demands. In this work a consistent, vintage-disaggregated, annual long-term series of U.S. housing stock and residential floor space for 1891–2010 is presented. An attempt was made to minimize the effects of the incompleteness and inconsistencies present in the national housing survey data. Over the 1891–2010 period, floor space increased almost tenfold, from approximately 24,700 to 235,150 million square feet, corresponding to a doubling of floor space per capita from approximately 400 to 800 square feet. While population increased five times over the period, a 50% decrease in household size contributed towards a tenfold increase in the number of housing units and floor space, while average floor space per unit remains surprisingly constant, as a result of housing retirement dynamics. In the last 30 years, however, these trends appear to be changing, as household size shows signs of leveling off, or even increasing again, while average floor space per unit has been increasing. GDP and total floor space show a remarkably constant growth trend over the period and total residential sector primary energy consumption and floor space show a similar growth trend over the last 60 years, decoupling only within the last decade.
    Electronic ISSN: 1932-6203
    Topics: Medicine , Natural Sciences in General
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  • 94
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    Public Library of Science (PLoS)
    In: PLoS ONE
    Publication Date: 2015-08-12
    Description: by Yi-Ling Chen, Shiun Chang, Ting-Ting Chen, Chien-Kuo Lee Dendritic cells (DCs), including conventional DCs (cDCs) and plasmacytoid DCs (pDCs) are critical for initiating and controlling the immune response. However, study of DC, particularly pDC, function is hampered by their low frequency in lymphoid organs, and existing methods for in vitro DC generation preferentially favor the production of cDCs over pDCs. Here, we demonstrated that pDCs could be efficiently generated in vitro from common lymphoid progenitors (CLPs) using Flt3 ligand (FL) in three different culture systems, namely feeder-free, BM-feeder and AC-6-feeder. This was in stark contrast to common DC progenitors (CDPs), in which cDCs were prominently generated under the same conditions. Moreover, the efficiency and function of pDCs generated from these three systems varied. While AC-6 system showed the greatest ability to support pDC development from CLPs, BM-feeder system was able to develop pDCs with better functionality. pDCs could also be expanded in vivo using hydrodynamic gene transfer of FL, which was further enhanced by the combined treatment of FL and IFN-α. Interestingly, IFN-α selectively promoted the proliferation of CLPs and not CDPs, which might contribute to enhanced pDC development. Together, we have defined conditions for in vitro and in vivo generation of pDCs, which may be useful for investigating the biology of pDCs.
    Electronic ISSN: 1932-6203
    Topics: Medicine , Natural Sciences in General
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  • 95
    Publication Date: 2015-08-12
    Description: The duplication-divergence network model is generally thought to incorporate key ingredients underlying the growth and evolution of protein-protein interaction networks. Properties of the model have been elucidated through numerous simulation studies. However, a comprehensive theoretical study of the model is lacking. Here, we derived analytic expressions for quantities describing key characteristics of the network—the average degree, the degree distribution, the clustering coefficient, and the neighbor connectivity—in the mean-field, large- N limit of an extended version of the model, duplication-divergence complemented with heterodimerization and addition. We carried out extensive simulations and verified excellent agreement between simulation and theory except for one partial case. All four quantities obeyed power-laws even at moderate network size ( N ∼ 10 4 ), except the degree distribution, which had an additional exponential factor observed to obey power-law. It is shown that our network model can lead to the emergence of scale-free property and hierarchical modularity simultaneously, reproducing the important topological properties of real protein-protein interaction networks.
    Print ISSN: 1054-1500
    Electronic ISSN: 1089-7682
    Topics: Physics
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  • 96
    Publication Date: 2015-08-12
    Description: by Andrew Erwin, Frank C. Sup In this paper, a novel haptic feedback scheme, used for accurately positioning a 1DOF virtual wrist prosthesis through sensory substitution, is presented. The scheme employs a three-node tactor array and discretely and selectively modulates the stimulation frequency of each tactor to relay 11 discrete haptic stimuli to the user. Able-bodied participants were able to move the virtual wrist prosthesis via a surface electromyography based controller. The participants evaluated the feedback scheme without visual or audio feedback and relied solely on the haptic feedback alone to correctly position the hand. The scheme was evaluated through both normal (perpendicular) and shear (lateral) stimulations applied on the forearm. Normal stimulations were applied through a prototype device previously developed by the authors while shear stimulations were generated using an ubiquitous coin motor vibrotactor. Trials with no feedback served as a baseline to compare results within the study and to the literature. The results indicated that using normal and shear stimulations resulted in accurately positioning the virtual wrist, but were not significantly different. Using haptic feedback was substantially better than no feedback. The results found in this study are significant since the feedback scheme allows for using relatively few tactors to relay rich haptic information to the user and can be learned easily despite a relatively short amount of training. Additionally, the results are important for the haptic community since they contradict the common conception in the literature that normal stimulation is inferior to shear. From an ergonomic perspective normal stimulation has the potential to benefit upper limb amputees since it can operate at lower frequencies than shear-based vibrotactors while also generating less noise. Through further tuning of the novel haptic feedback scheme and normal stimulation device, a compact and comfortable sensory substitution device for upper limb amputees might be created.
    Electronic ISSN: 1932-6203
    Topics: Medicine , Natural Sciences in General
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  • 97
    Publication Date: 2015-08-09
    Description: by Aparajita Chatterjee, Daniel M. Ratner, Christopher M. Ryan, Patricia J. Johnson, Barry R. O’Keefe, W. Evan Secor, Deborah J. Anderson, Phillips W. Robbins, John Samuelson Trichomonas vaginalis causes vaginitis and increases the risk of HIV transmission by heterosexual sex, while Tritrichomonas foetus causes premature abortion in cattle. Our goals were to determine the effects, if any, of anti-retroviral lectins, which are designed to prevent heterosexual transmission of HIV, on adherence of Trichomonas to ectocervical cells and on Tritrichomonas infections in a mouse model. We show that Trichomonas Asn-linked glycans ( N -glycans), like those of HIV, bind the mannose-binding lectin (MBL) that is part of the innate immune system. N -glycans of Trichomonas and Tritrichomonas bind anti-retroviral lectins (cyanovirin-N and griffithsin) and the 2G12 monoclonal antibody, each of which binds HIV N -glycans. Binding of cyanovirin-N appears to be independent of susceptibility to metronidazole, the major drug used to treat Trichomonas . Anti-retroviral lectins, MBL, and galectin-1 cause Trichomonas to self-aggregate and precipitate. The anti-retroviral lectins also increase adherence of ricin-resistant mutants, which are less adherent than parent cells, to ectocervical cell monolayers and to organotypic EpiVaginal tissue cells. Topical application of either anti-retroviral lectins or yeast N -glycans decreases by 40 to 70% the recovery of Tritrichomonas from the mouse vagina. These results, which are explained by a few simple models, suggest that the anti-retroviral lectins have a modest potential for preventing or treating human infections with Trichomonas .
    Electronic ISSN: 1932-6203
    Topics: Medicine , Natural Sciences in General
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  • 98
    Publication Date: 2015-08-09
    Description: by Suzan J. W. Robroek, Anne Rongen, Coos H. Arts, Ferdy W. H. Otten, Alex Burdorf, Merel Schuring Background Individuals with lower socioeconomic status are at increased risk of involuntary exit from paid employment. To give sound advice for primary prevention in the workforce, insight is needed into the role of mediating factors between socioeconomic status and labour force participation. Therefore, it is aimed to investigate the influence of health status, lifestyle-related factors and work characteristics on educational differences in exit from paid employment. Methods 14,708 Dutch employees participated in a ten-year follow-up study during 1999–2008. At baseline, education, self-perceived health, lifestyle (smoking, alcohol, sports, BMI) and psychosocial (demands, control, rewards) and physical work characteristics were measured by questionnaire. Employment status was ascertained monthly based on tax records. The relation between education, health, lifestyle, work-characteristics and exit from paid employment through disability benefits, unemployment, early retirement and economic inactivity was investigated by competing risks regression analyses. The mediating effects of these factors on educational differences in exit from paid employment were tested using a stepwise approach. Results Lower educated workers were more likely to exit paid employment through disability benefits (SHR:1.84), unemployment (SHR:1.74), and economic inactivity (SHR:1.53) but not due to early retirement (SHR:0.92). Poor or moderate health, an unhealthy lifestyle, and unfavourable work characteristics were associated with disability benefits and unemployment, and an unhealthy lifestyle with economic inactivity. Educational differences in disability benefits were explained for 40% by health, 31% by lifestyle, and 12% by work characteristics. For economic inactivity and unemployment, up to 14% and 21% of the educational differences could be explained, particularly by lifestyle-related factors. Conclusions There are educational differences in exit from paid employment, which are partly mediated by health, lifestyle and work characteristics, particularly for disability benefits. Health promotion and improving working conditions seem important measures to maintain a productive workforce, particularly among workers with a low education.
    Electronic ISSN: 1932-6203
    Topics: Medicine , Natural Sciences in General
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  • 99
    Publication Date: 2015-08-12
    Description: by SK Hafizul Islam, Muhammad Khurram Khan, Xiong Li Over the past few years, secure and privacy-preserving user authentication scheme has become an integral part of the applications of the healthcare systems. Recently, Wen has designed an improved user authentication system over the Lee et al.’s scheme for integrated electronic patient record (EPR) information system, which has been analyzed in this study. We have found that Wen’s scheme still has the following inefficiencies: (1) the correctness of identity and password are not verified during the login and password change phases; (2) it is vulnerable to impersonation attack and privileged-insider attack; (3) it is designed without the revocation of lost/stolen smart card; (4) the explicit key confirmation and the no key control properties are absent, and (5) user cannot update his/her password without the help of server and secure channel. Then we aimed to propose an enhanced two-factor user authentication system based on the intractable assumption of the quadratic residue problem (QRP) in the multiplicative group. Our scheme bears more securities and functionalities than other schemes found in the literature.
    Electronic ISSN: 1932-6203
    Topics: Medicine , Natural Sciences in General
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  • 100
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    Public Library of Science (PLoS)
    In: PLoS ONE
    Publication Date: 2015-08-12
    Description: by Sherif H. Elmeligy Abdelhamid, Chris J. Kuhlman, Madhav V. Marathe, Henning S. Mortveit, S. S. Ravi Discrete dynamical systems are used to model various realistic systems in network science, from social unrest in human populations to regulation in biological networks. A common approach is to model the agents of a system as vertices of a graph, and the pairwise interactions between agents as edges. Agents are in one of a finite set of states at each discrete time step and are assigned functions that describe how their states change based on neighborhood relations. Full characterization of state transitions of one system can give insights into fundamental behaviors of other dynamical systems. In this paper, we describe a discrete graph dynamical systems (GDSs) application called GDSCalc for computing and characterizing system dynamics. It is an open access system that is used through a web interface. We provide an overview of GDS theory. This theory is the basis of the web application; i.e., an understanding of GDS provides an understanding of the software features, while abstracting away implementation details. We present a set of illustrative examples to demonstrate its use in education and research. Finally, we compare GDSCalc with other discrete dynamical system software tools. Our perspective is that no single software tool will perform all computations that may be required by all users; tools typically have particular features that are more suitable for some tasks. We situate GDSCalc within this space of software tools.
    Electronic ISSN: 1932-6203
    Topics: Medicine , Natural Sciences in General
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