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  • Public Library of Science (PLoS)
  • Annual Reviews
Collection
Years
  • 1
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    Annual Reviews
    Online: 1.1970 – 47.2016
    Online: 1.1970 – 47.2016
    Formerly as: Annual Review of Ecology and Systematics  (1970–2002)
    Publisher: Annual Reviews
    Print ISSN: 0066-4162 , 1543-592X
    Electronic ISSN: 1545-2069
    Topics: Biology
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  • 2
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    Annual Reviews | JSTOR
    Online: 1.2009 – 5.2013
    Publisher: Annual Reviews , JSTOR
    Print ISSN: 1941-1367
    Electronic ISSN: 1941-1375
    Topics: Economics
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  • 3
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    Annual Reviews
    Online: 1.2013 – 4.2016
    Online: 1.2013 – 4.2016
    Publisher: Annual Reviews
    Print ISSN: 2165-8102
    Electronic ISSN: 2165-8110
    Topics: Biology
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  • 4
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    Annual Reviews
    Online: 1.2008 – 9.2016
    Online: 1.2008 – 9.2016
    Publisher: Annual Reviews
    Print ISSN: 1936-1327
    Electronic ISSN: 1936-1335
    Topics: Chemistry and Pharmacology
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  • 5
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    Annual Reviews
    Online: 1.2009 – 8.2016
    Online: 1.2009 – 8.2016
    Publisher: Annual Reviews
    Print ISSN: 1941-1405
    Electronic ISSN: 1941-0611
    Topics: Biology , Geosciences
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  • 6
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    Annual Reviews
    Online: 1.1932 – 85.2016
    Online: 1.1932 – 85.2016
    Publisher: Annual Reviews
    Print ISSN: 0066-4154
    Electronic ISSN: 1545-4509
    Topics: Biology , Chemistry and Pharmacology
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  • 7
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    Annual Reviews
    Online: 1.1952 –
    Online: 1.1952 –
    Formerly as: Annual Review of Nuclear Science  (1952–1977)
    Publisher: Annual Reviews
    Print ISSN: 0066-4243 , 0163-8998
    Electronic ISSN: 1545-4134
    Topics: Physics
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  • 8
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    Annual Reviews
    Online: 1.1971 – 46.2016
    Online: 1.1971 – 46.2016
    Formerly as: Annual Review of Materials Science  (1971–2000)
    Publisher: Annual Reviews
    Print ISSN: 0084-6600 , 1531-7331
    Electronic ISSN: 1545-4118
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
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  • 9
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    Annual Reviews
    Online: 1.1978 – 39.2016
    Online: 1.1978 – 39.2016
    Publisher: Annual Reviews
    Print ISSN: 0147-006X
    Electronic ISSN: 1545-4126
    Topics: Biology , Medicine
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  • 10
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    Annual Reviews
    Online: 1973 – 1996
    Publisher: Annual Reviews
    Print ISSN: 0084-6597
    Electronic ISSN: 1545-4495
    Topics: Geosciences , Physics
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  • 11
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    Annual Reviews | JSTOR
    Online: 1.2009 – 5.2013
    Publisher: Annual Reviews , JSTOR
    Print ISSN: 1941-1383
    Electronic ISSN: 1941-1391
    Topics: Economics
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  • 12
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    Annual Reviews
    Online: 1.2014 – 3.2016
    Online: 1.2014 – 3.2016
    Publisher: Annual Reviews
    Print ISSN: 2326-8298
    Electronic ISSN: 2326-831X
    Topics: Mathematics
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  • 13
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    Annual Reviews
    Online: 1.1986 – 4.1990
    Online: 1.1986 – 4.1990
    Publisher: Annual Reviews
    Print ISSN: 8756-7016
    Electronic ISSN: 8756-7016
    Topics: Computer Science
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  • 14
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    Annual Reviews
    Online: 1.1973 –
    Print: 8.1980 – 46.2018 (Location: A17, Kompaktmagazin, 5/6-7)
    Publisher: Annual Reviews
    Print ISSN: 0084-6597
    Electronic ISSN: 1545-4495
    Topics: Geosciences , Physics
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  • 15
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    Annual Reviews
    Online: 1.1983 – 34.2016
    Online: 1.1983 – 34.2016
    Publisher: Annual Reviews
    Print ISSN: 0732-0582
    Electronic ISSN: 1545-3278
    Topics: Biology , Medicine
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  • 16
    Formerly as: Annual Review of Biophysics and Biomolecular Structure ; Annual Review of Biophysics and Biophysical Chemistry ; Annual Review of Biophysics and Bioengineering  (1972–2007)
    Publisher: Annual Reviews
    Print ISSN: 0084-6589 , 0883-9182 , 1056-8700 , 1936-122X
    Electronic ISSN: 1545-4266 , 1936-1238
    Topics: Biology , Physics
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  • 17
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    Annual Reviews
    Online: 1.1999 – 18.2016
    Online: 1.1999 – 18.2016
    Online: 1.2021 –
    Publisher: Annual Reviews
    Print ISSN: 1523-9829
    Electronic ISSN: 1545-4274
    Topics: Medicine , Technology
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  • 18
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    Annual Reviews
    Online: 1.1947 – 70.2016
    Online: 1.1947 – 70.2016
    Publisher: Annual Reviews
    Print ISSN: 0066-4227
    Electronic ISSN: 1545-3251
    Topics: Biology
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  • 19
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    Annual Reviews
    Online: 1.1939 – 78.2016
    Online: 1.1939 – 78.2016
    Publisher: Annual Reviews
    Print ISSN: 0066-4278
    Electronic ISSN: 1545-1585
    Topics: Biology , Medicine
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  • 20
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    Annual Reviews
    Online: 1.2000 –
    Online: 1.2021 –
    Publisher: Annual Reviews
    Print ISSN: 1527-8204
    Electronic ISSN: 1545-293X
    Topics: Biology
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  • 21
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    Annual Reviews
    Online: 1.1963 – 54.2016
    Online: 1.1963 – 54.2016
    Publisher: Annual Reviews
    Print ISSN: 0066-4286
    Electronic ISSN: 1545-2107
    Topics: Biology , Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
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  • 22
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    Annual Reviews
    Online: 1.1972 – 45.2016
    Online: 1.1972 – 45.2016
    Publisher: Annual Reviews
    Print ISSN: 0084-6570
    Electronic ISSN: 1545-4290
    Topics: Biology , Ethnic Sciences
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  • 23
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    Annual Reviews
    Online: 1.1976 –
    Online: 1.1976 –
    Formerly as: Annual Review of Energy and the Environment ; Annual Review of Energy  (1976–2002)
    Publisher: Annual Reviews
    Print ISSN: 0362-1626 , 1056-3466 , 1543-5938
    Electronic ISSN: 1545-2050
    Topics: Energy, Environment Protection, Nuclear Power Engineering
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  • 24
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    Annual Reviews
    Online: 1.1969 – 48.2016
    Online: 1.1969 – 48.2016
    Publisher: Annual Reviews
    Print ISSN: 0066-4189
    Electronic ISSN: 1545-4479
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics , Physics
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  • 25
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    Annual Reviews
    Online: 1.1967 – 50.2016
    Online: 1.1967 – 50.2016
    Publisher: Annual Reviews
    Print ISSN: 0066-4197
    Electronic ISSN: 1545-2948
    Topics: Biology
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  • 26
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    Annual Reviews
    Online: 1.1963 – 54.2016
    Online: 1.1963 – 54.2016
    Publisher: Annual Reviews
    Print ISSN: 0066-4146
    Electronic ISSN: 1545-4282
    Topics: Physics
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  • 27
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    Annual Reviews
    Online: 1963 – 1995
    Publisher: Annual Reviews
    Print ISSN: 0066-4146
    Electronic ISSN: 1545-4282
    Topics: Physics
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  • 28
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    Annual Reviews
    Online: 1.1981 – 36.2016
    Online: 1.1981 – 36.2016
    Publisher: Annual Reviews
    Print ISSN: 0199-9885
    Electronic ISSN: 1545-4312
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
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  • 29
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    Annual Reviews
    Online: 1.2017 –
    Publisher: Annual Reviews
    Electronic ISSN: 2472-3428
    Topics: Biology , Medicine
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  • 30
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    Annual Reviews
    Online: 1.1985 – 32.2016
    Online: 1.1985 – 32.2016
    Formerly as: Annual Review of Cell Biology  (1985–1994)
    Publisher: Annual Reviews
    Print ISSN: 0743-4634 , 1081-0706
    Electronic ISSN: 1530-8995
    Topics: Biology , Medicine
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  • 31
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    Annual Reviews
    Online: 1.2010 – 7.2016
    Online: 1.2010 – 7.2016
    Publisher: Annual Reviews
    Print ISSN: 1947-5454
    Electronic ISSN: 1947-5462
    Topics: Physics
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  • 32
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    Annual Reviews
    Online: 1.2009 – 5.2013
    Publisher: Annual Reviews
    Print ISSN: 1941-1340
    Electronic ISSN: 1941-1359
    Topics: Economics
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  • 33
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    Annual Reviews
    Online: 1.1956 – 61.2016
    Online: 1.1956 – 61.2016
    Publisher: Annual Reviews
    Print ISSN: 0066-4170
    Electronic ISSN: 1545-4487
    Topics: Biology
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  • 34
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    Annual Reviews
    Online: 1.1950 – 67.2016
    Online: 1.1950 – 67.2016
    Publisher: Annual Reviews
    Print ISSN: 0066-426X
    Electronic ISSN: 1545-1593
    Topics: Chemistry and Pharmacology , Physics
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  • 35
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    Annual Reviews
    Online: 1.1961 – 56.2016
    Online: 1.1961 – 56.2016
    Formerly as: Annual Review of Pharmacology  (1961–1975)
    Publisher: Annual Reviews
    Print ISSN: 0066-4251 , 0362-1642
    Electronic ISSN: 1545-4304
    Topics: Chemistry and Pharmacology , Medicine
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  • 36
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    Annual Reviews
    Online: 1.1950 – 67.2016
    Online: 1.1950 – 67.2016
    Formerly as: Annual Review of Plant Physiology and Plant Molecular Biology ; Annual Review of Plant Physiology  (1950–2001)
    Publisher: Annual Reviews
    Print ISSN: 0066-4294 , 1040-2519 , 1543-5008
    Electronic ISSN: 1545-2123
    Topics: Biology
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  • 37
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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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  • 38
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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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  • 39
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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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  • 40
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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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  • 41
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    Annual Reviews
    Online: 2017 –
    Publisher: Annual Reviews
    Description: What is known? What isn’t known? Knowable Magazine, the digital publication from Annual Reviews, seeks to make that knowledge accessible to all. Knowable Magazine explores the real-world significance of scholarly work through a journalistic lens. We report on the current state of play across a wide variety of fields — from agriculture to high-energy physics; biochemistry to water security; the origins of the universe to psychology. Review articles written by leading scholars from the 50 Annual Reviews journals serve as springboards for stories in Knowable Magazine. Through in-depth features, explainers, articles, essays, interviews, infographics, slideshows, and comics, Knowable Magazine presents insights from research to a broader audience. The content is published under a CC BY-ND copyright license, and the Annual Reviews journal articles featured in Knowable Magazine are free to all for a limited period. Knowable Magazine content is thoroughly researched, reported, edited, copy-edited and fact-checked. Review articles in Annual Review journals provide ideas, but editorial decisions and reporting decisions are made by the magazine staff, guided by what will best inform and intrigue readers.
    Electronic ISSN: 2575-4459
    Topics: Natural Sciences in General
    Keywords: Allgemeine Naturwissenschaften ; Forschung
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  • 42
    Publication Date: 2019-07-17
    Description: The public health, tourism, fisheries, and ecosystem impacts from harmful algal blooms (HABs) have all increased over the past few decades. This has led to heightened scientific and regulatory attention, and the development of many new technologies and approaches for research and management. This, in turn, is leading to significant paradigm shifts with regard to, e.g.,our interpretation of the phytoplankton species concept (strain variation), the dogma of their apparent cosmopolitanism, the role of bacteria and zooplankton grazing in HABs, and our approaches to investigating the ecological and genetic basis for the production of toxins and allelochemicals. Increasingly,eutrophication and climate change are viewed andmanaged as multifactorial environmental stressors that will further challenge managers of coastal resources and those responsible for protecting human health. Here we review HABscience with an eye toward new concepts and approaches,emphasizing, where possible, the unexpected yet promising new directions that research has taken in this diverse field.
    Repository Name: EPIC Alfred Wegener Institut
    Type: Article , isiRev
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  • 43
    Publication Date: 2022-05-25
    Description: Author Posting. © Annual Reviews, 2003. This article is posted here by permission of Annual Reviews for personal use, not for redistribution. The definitive version was published in Annual Review of Environment and Resources 28 (2003): 521-558, doi:10.1146/annurev.energy.28.011503.163443.
    Description: Agriculture and industrial development have led to inadvertent changes in the natural carbon cycle. As a consequence, concentrations of carbon dioxide and other greenhouse gases have increased in the atmosphere and may lead to changes in climate. The current challenge facing society is to develop options for future management of the carbon cycle. A variety of approaches has been suggested: direct reduction of emissions, deliberate manipulation of the natural carbon cycle to enhance sequestration, and capture and isolation of carbon from fossil fuel use. Policy development to date has laid out some of the general principles to which carbon management should adhere. These are summarized as: how much carbon is stored, by what means, and for how long. To successfully manage carbon for climate purposes requires increased understanding of carbon cycle dynamics and improvement in the scientific capabilities available for measurement as well as for policy needs. The specific needs for scientific information to underpin carbon cycle management decisions are not yet broadly known. A stronger dialogue between decision makers and scientists must be developed to foster improved application of scientific knowledge to decisions. This review focuses on the current knowledge of the carbon cycle, carbon measurement capabilities (with an emphasis on the continental scale) and the relevance of carbon cycle science to carbon sequestration goals.
    Description: The National Center for Atmospheric Research is supported by the National Science Foundation.
    Keywords: Carbon sequestration ; Measurement techniques ; Climate ; Kyoto protocol
    Repository Name: Woods Hole Open Access Server
    Type: Article
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  • 44
    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
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  • 45
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    Annual Reviews
    Publication Date: 2022-05-25
    Description: Author Posting. © Annual Reviews, 2006. This article is posted here by permission of Annual Reviews for personal use, not for redistribution. The definitive version was published in Annual Review of Fluid Mechanics 38 (2006): 395-425, doi:10.1146/annurev.fluid.38.050304.092129.
    Description: Over the past four decades, the combination of in situ and remote sensing observations has demonstrated that long nonlinear internal solitary-like waves are ubiquitous features of coastal oceans. The following provides an overview of the properties of steady internal solitary waves and the transient processes of wave generation and evolution, primarily from the point of view of weakly nonlinear theory, of which the Korteweg-de Vries equation is the most frequently used example. However, the oceanographically important processes of wave instability and breaking, generally inaccessible with these models, are also discussed. Furthermore, observations often show strongly nonlinear waves whose properties can only be explained with fully nonlinear models.
    Description: KRH acknowledges support from NSF and ONR and an Independent Study Award from the Woods Hole Oceanographic Institution. WKM acknowledges support from NSF and ONR, which has made his work in this area possible, in close collaboration with former graduate students at Scripps Institution of Oceanography and MIT.
    Keywords: Solitary waves ; Nonlinear waves ; Stratified flow ; Physical Oceanography
    Repository Name: Woods Hole Open Access Server
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  • 46
    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.
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  • 47
    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.
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  • 48
    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.
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  • 49
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    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
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  • 50
    Publication Date: 2022-05-25
    Description: First published online as a Review in Advance on October 24, 2005. (Some corrections may occur before final publication online and in print)
    Description: Author Posting. © Annual Reviews, 2005. This article is posted here by permission of Annual Reviews for personal use, not for redistribution. The definitive version was published in Annual Review of Physiology 68 (2006): 22.1-22.29, doi:10.1146/annurev.physiol.68.040104.105418.
    Description: Superfast muscles of vertebrates power sound production. The fastest, the swimbladder muscle of toadfish, generates mechanical power at frequencies in excess of 200 Hz. To operate at these frequencies, the speed of relaxation has had to increase approximately 50-fold. This increase is accomplished by modifications of three kinetic traits: (a) a fast calcium transient due to extremely high concentration of sarcoplasmic reticulum (SR)-Ca2+ pumps and parvalbumin, (b) fast off-rate of Ca2+ from troponin C due to an alteration in troponin, and (c) fast cross-bridge detachment rate constant (g, 50 times faster than that in rabbit fast-twitch muscle) due to an alteration in myosin. Although these three modifications permit swimbladder muscle to generate mechanical work at high frequencies (where locomotor muscles cannot), it comes with a cost: The high g causes a large reduction in attached force-generating cross-bridges, making the swimbladder incapable of powering low-frequency locomotory movements. Hence the locomotory and sound-producing muscles have mutually exclusive designs.
    Description: This work was made possible by support from NIH grants AR38404 and AR46125 as well as the University of Pennsylvania Research Foundation.
    Keywords: Parvalbumin ; Ca2+ release ; Ca2+ uptake ; Cross-bridges ; Adaptation ; Sound production ; Whitman Center
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  • 51
    Publication Date: 2022-10-27
    Description: This paper is not subject to U.S. copyright. The definitive version was published in Sherwood, C. R., van Dongeren, A., Doyle, J., Hegermiller, C. A., Hsu, T.-J., Kalra, T. S., Olabarrieta, M., Penko, A. M., Rafati, Y., Roelvink, D., van der Lugt, M., Veeramony, J., & Warner, J. C. Modeling the morphodynamics of coastal responses to extreme events: what shape are we in? Annual Review of Marine Science, 14, (2022): 457–492, https://doi.org/10.1146/annurev-marine-032221-090215.
    Description: This review focuses on recent advances in process-based numerical models of the impact of extreme storms on sandy coasts. Driven by larger-scale models of meteorology and hydrodynamics, these models simulate morphodynamics across the Sallenger storm-impact scale, including swash,collision, overwash, and inundation. Models are becoming both wider (as more processes are added) and deeper (as detailed physics replaces earlier parameterizations). Algorithms for wave-induced flows and sediment transport under shoaling waves are among the recent developments. Community and open-source models have become the norm. Observations of initial conditions (topography, land cover, and sediment characteristics) have become more detailed, and improvements in tropical cyclone and wave models provide forcing (winds, waves, surge, and upland flow) that is better resolved and more accurate, yielding commensurate improvements in model skill. We foresee that future storm-impact models will increasingly resolve individual waves, apply data assimilation, and be used in ensemble modeling modes to predict uncertainties.
    Description: All authors except D.R. were partially supported by the IFMSIP project, funded by US Office of Naval Research grant PE 0601153N under contracts N00014-17-1-2459 (Deltares), N00014-18-1-2785 (University of Delaware), N0001419WX00733 (US Naval Research Laboratory, Monterey), N0001418WX01447 (US Naval Research Laboratory, Stennis Space Center), and N0001418IP00016 (US Geological Survey). C.R.S., C.A.H., T.S.K., and J.C.W. were supported by the US Geological Survey Coastal/Marine Hazards and Resources Program. A.v.D. and M.v.d.L. were supported by the Deltares Strategic Research project Quantifying Flood Hazards and Impacts. M.O. acknowledges support from National Science Foundation project OCE-1554892.
    Keywords: Coastal morphodynamics ; Extreme storms ; Coastal modeling ; Sandy coasts ; Waves ; Sediment transport
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  • 52
    Publication Date: 2022-05-26
    Description: © The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Annual Review of Marine Science 9 (2017): 173-203, doi:10.1146/annurev-marine-010816-060733.
    Description: The events that followed the Tohoku earthquake and tsunami on March 11, 2011, included the loss of power and overheating at the Fukushima Daiichi nuclear power plants, which led to extensive releases of radioactive gases, volatiles, and liquids, particularly to the coastal ocean. The fate of these radionuclides depends in large part on their oceanic geochemistry, physical processes, and biological uptake. Whereas radioactivity on land can be resampled and its distribution mapped, releases to the marine environment are harder to characterize owing to variability in ocean currents and the general challenges of sampling at sea. Five years later, it is appropriate to review what happened in terms of the sources, transport, and fate of these radionuclides in the ocean. In addition to the oceanic behavior of these contaminants, this review considers the potential health effects and societal impacts.
    Description: K.B. was supported in part by the Gordon and Betty Moore Foundation and the Deerbrook Charitable Trust. P.M. was supported in part by the Generalitat de Catalunya through MERS (grant 2014 SGR 1356), the European Commission 7th Framework COMET-FRAME project (grant agreement 604974), and the Ministerio de Economía y Competitividad of Spain (project CTM2011-15152-E). S.C. was supported in part by the French program Investissement d'Avenir run by the National Research Agency (AMORAD project, grant ANR-11-RSNR-0002). D.O. was supported in part by the Center for Environmental Radioactivity (NFR Centers of Excellence grant 223268/F50). J.N.S. was supported in part by the Marine Environmental Observation, Prediction, and Response Network.
    Keywords: Cesium ; Caesium ; North Pacific ; Radioactivity ; Japan
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  • 53
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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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  • 54
    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
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  • 55
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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
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  • 56
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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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  • 57
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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.
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  • 58
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    Public Library of Science (PLoS)
    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.
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  • 59
    Publication Date: 2023-02-28
    Description: © The Author(s), 2023. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Timmermans, M.-L., & Toole, J. The Arctic Ocean’s Beaufort Gyre. Annual Review of Marine Science, 15(1), (2023): 223-248, https://doi.org/10.1146/annurev-marine-032122-012034.
    Description: The Arctic Ocean's Beaufort Gyre is a dominant feature of the Arctic system, a prominent indicator of climate change, and possibly a control factor for high-latitude climate. The state of knowledge of the wind-driven Beaufort Gyre is reviewed here, including its forcing, relationship to sea-ice cover, source waters, circulation, and energetics. Recent decades have seen pronounced change in all elements of the Beaufort Gyre system. Sea-ice losses have accompanied an intensification of the gyre circulation and increasing heat and freshwater content. Present understanding of these changes is evaluated, and time series of heat and freshwater content are updated to include the most recent observations.
    Description: Support was provided by the National Science Foundation Office of Polar Programs and the Office of Naval Research.
    Keywords: Arctic Ocean ; Beaufort Gyre ; Circulation ; Sea ice ; Freshwater ; Ocean heat content
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  • 60
    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.
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  • 61
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    Annual Reviews
    In:  EPIC3Annual Review of Marine Science, Annual Reviews, 16(1), pp. 417-441, ISSN: 1941-1405
    Publication Date: 2024-03-01
    Description: The genus Phaeocystis is globally distributed, with blooms commonly occurring on continental shelves. This unusual phytoplankter has two major morphologies: solitary cells and cells embedded in a gelatinous matrix. Only colonies form blooms. Their large size (commonly 2 mm but up to 3 cm) and mucilaginous envelope allow the colonies to escape predation, but data are inconsistent as to whether colonies are grazed. Cultured Phaeocystis can also inhibit the growth of co-occurring phytoplankton or the feeding of potential grazers. Colonies and solitary cells use nitrate as a nitrogen source, although solitary cells can also grow on ammonium. Phaeocystis colonies might be a major contributor to carbon flux to depth, but in most cases, colonies are rapidly remineralized in the upper 300 m. The occurrence of large Phaeocystis blooms is often associated with environments with low and highly variable light and high nitrate levels, with Phaeocystis antarctica blooms being linked additionally to high iron availability. Emerging results indicate that different clones of Phaeocystis have substantial genetic plasticity, which may explain its appearance in a variety of environments. Given the evidence of Phaeocystis appearing in new systems, this trend will likely continue in the near future.
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  • 62
    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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  • 63
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    Annual Reviews
    In:  EPIC3Annual Review of Marine Science, Annual Reviews, 16(1), pp. 513-536, ISSN: 1941-1405
    Publication Date: 2024-01-31
    Description: 〈jats:p〉 For decades, multiple-driver/stressor research has examined interactions among drivers that will undergo large changes in the future: temperature, pH, nutrients, oxygen, pathogens, and more. However, the most commonly used experimental designs—present-versus-future and ANOVA—fail to contribute to general understanding or predictive power. Linking experimental design to process-based mathematical models would help us predict how ecosystems will behave in novel environmental conditions. We review a range of experimental designs and assess the best experimental path toward a predictive ecology. Full factorial response surface, fractional factorial, quadratic response surface, custom, space-filling, and especially optimal and sequential/adaptive designs can help us achieve more valuable scientific goals. Experiments using these designs are challenging to perform with long-lived organisms or at the community and ecosystem levels. But they remain our most promising path toward linking experiments and theory in multiple-driver research and making accurate, useful predictions. 〈/jats:p〉
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  • 64
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    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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  • 65
    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.
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  • 66
    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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  • 67
    Publication Date: 2007-05-01
    Print ISSN: 0084-6597
    Electronic ISSN: 1545-4495
    Topics: Geosciences , Physics
    Published by Annual Reviews
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  • 68
    Publication Date: 2007-05-01
    Print ISSN: 0084-6597
    Electronic ISSN: 1545-4495
    Topics: Geosciences , Physics
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  • 69
    Publication Date: 2007-05-01
    Print ISSN: 0084-6597
    Electronic ISSN: 1545-4495
    Topics: Geosciences , Physics
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  • 70
    Publication Date: 2007-05-01
    Print ISSN: 0084-6597
    Electronic ISSN: 1545-4495
    Topics: Geosciences , Physics
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  • 71
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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
    Topics: Medicine , Natural Sciences in General
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  • 72
    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.
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  • 73
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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.
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  • 74
    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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  • 75
    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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  • 76
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    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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  • 77
    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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  • 78
    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.
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  • 79
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    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.
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  • 80
    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
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  • 81
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    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.
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  • 82
    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.
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  • 83
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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.
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  • 84
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    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.
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  • 85
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    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.
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  • 86
    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.
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  • 87
    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 .
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  • 88
    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.
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  • 89
    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.
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  • 90
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    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.
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  • 91
    Publication Date: 2015-08-12
    Description: by Lisa Kellman, Amy Myette, Hugo Beltrami Forest harvesting induces a step change in the climatic variables (temperature and moisture), that control carbon dioxide ( CO 2 ) production arising from soil organic matter decomposition within soils. Efforts to examine these vertically complex relationships in situ within soil profiles are lacking. In this study we examined how the climatic controls on CO 2 production change within vertically distinct layers of the soil profile in intact and clearcut forest soils of a humid temperate forest system of Atlantic Canada. We measured mineral soil temperature (0, 5, 10, 20, 50 and 100 cm depth) and moisture (0–15 cm and 30–60 cm depth), along with CO 2 surface efflux and subsurface concentrations (0, 2.5, 5, 10, 20, 35, 50, 75 and 100 cm depth) in 1 m deep soil pits at 4 sites represented by two forest-clearcut pairs over a complete annual cycle. We examined relationships between surface efflux at each site, and soil heat, moisture, and mineral soil CO 2 production. Following clearcut harvesting we observed increases in temperature through depth (1–2°C annually; often in excess of 4°C in summer and spring), alongside increases in soil moisture (30%). We observed a systematic breakdown in the expected exponential relationship between CO 2 production and heat with mineral soil depth, consistent with an increase in the role moisture plays in constraining CO 2 production. These findings should be considered in efforts to model and characterize mineral soil organic matter decomposition in harvested forest soils.
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  • 92
    Publication Date: 2015-08-12
    Description: by Peng Yu, Jing Zhang, Shuchun Yu, Zhenzhong Luo, Fuzhou Hua, Linhui Yuan, Zhidong Zhou, Qin Liu, Xiaohong Du, Sisi Chen, Lieliang Zhang, Guohai Xu Background and Purpose Myocardial infarction leads to heart failure. Autophagy is excessively activated in myocardial ischemia/reperfusion (I/R) in rats. The aim of this study is to investigate whether the protection of sevoflurane postconditioning (SPC) in myocardial I/R is through restored impaired autophagic flux. Methods Except for the sham control (SHAM) group, each rat underwent 30 min occlusion of the left anterior descending coronary (LAD) followed by 2 h reperfusion. Cardiac infarction was determined by 2,3,5-triphenyltetrazolium chloride triazole (TTC) staining. Cardiac function was examined by hemodynamics and echocardiography. The activation of autophagy was evaluated by autophagosome accumulation, LC3 conversion and p62 degradation. Potential molecular mechanisms were investigated by immunoblotting, real-time PCR and immunofluorescence staining. Results SPC improved the hemodynamic parameters, cardiac dysfunction, histopathological and ultrastructural damages, and decreased myocardial infarction size after myocardial I/R injury ( P 〈 0.05 vs. I/R group). Compared with the cases in I/R group, myocardial ATP and NAD + content, mitochondrial function related genes and proteins, and the expressions of SOD2 and HO-1 were increased, while the expressions of ROS and Vimentin were decreased in the SPC group ( P 〈 0.05 vs. I/R group). SPC significantly activated Akt/mTOR signaling, and inhibited the formation of Vps34/Beclin1 complex via increasing expression of Bcl2 protein ( P 〈 0.05 vs. I/R group). SPC suppressed elevated expressions of LC3 II/I ratio, Beclin1, Atg5 and Atg7 in I/R rat, which indicated that SPC inhibited over-activation of autophagy, and promoted autophagosome clearance. Meanwhile, SPC significantly suppressed the decline of Opa1 and increases of Drp1 and Parkin induced by I/R injury ( P 〈 0.05 vs. I/R group). Moreover, SPC maintained the contents of ATP by reducing impaired mitochondria. Conclusion SPC protects rat hearts against I/R injury via ameliorating mitochondrial impairment, oxidative stress and rescuing autophagic clearance.
    Electronic ISSN: 1932-6203
    Topics: Medicine , Natural Sciences in General
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  • 93
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    Public Library of Science (PLoS)
    In: PLoS ONE
    Publication Date: 2015-08-09
    Description: by Lisa Müller, Erich Müller, Carolin Hildebrandt, Elmar Kornexl, Christian Raschner The relative age effect (RAE), which refers to an over-representation of selected athletes born early in the selection year, was proven to be present in alpine ski racing in all age categories at both national and international levels. However, the influential factors on, or the causal mechanisms of, the RAE are still unknown. Therefore, the aim of the present study was to examine three possible influential factors on the relative age effect in alpine skiing: physical performance, anthropometric characteristics and biological maturational status. The study included the investigation of 282 elite Austrian youth ski racers and 413 non-athletes (comparison group) of the same age (10–13 years) and region. Six physical performance tests were performed, body mass and height were assessed, and the age at peak height velocity (APHV) was calculated. A significant RAE was present in the ski racers. No differences were shown in the physical performance characteristics or in the calculated APHV between the relative age quarters. These results suggest that ski racers born in the last quarter can counteract the relative age disadvantages if they already present the same level of physical performance and maturational status as those born at the beginning of the year. The height and weight of ski racers born at the beginning of the year were significantly higher compared to the non-athletes, and ski racers born in relative age quarter 1 were taller and heavier compared to the ski racers of the other quarters. This indicates that the anthropometric characteristics influence the selection process in alpine ski racing, and that relatively older athletes are more likely to be selected if they exhibit advanced anthropometric characteristics.
    Electronic ISSN: 1932-6203
    Topics: Medicine , Natural Sciences in General
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  • 94
    Publication Date: 2015-08-09
    Description: by Andrea Pelletier-Baldelli, Jessica A. Bernard, Vijay A. Mittal Social processes are key to navigating the world, and investigating their underlying mechanisms and cognitive architecture can aid in understanding disease states such as schizophrenia, where social processes are highly impacted. Evidence suggests that social processes are impaired in individuals at ultra high-risk for the development of psychosis (UHR). Understanding these phenomena in UHR youth may clarify disease etiology and social processes in a period that is characterized by significantly fewer confounds than schizophrenia. Furthermore, understanding social processing deficits in this population will help explain these processes in healthy individuals. The current study examined resting state connectivity of the salience (SN) and default mode networks (DMN) in association with facial emotion recognition (FER), an integral aspect of social processes, as well as broader social functioning (SF) in UHR individuals and healthy controls. Consistent with the existing literature, UHR youth were impaired in FER and SF when compared with controls. In the UHR group, we found increased connectivity between the SN and the medial prefrontal cortex, an area of the DMN relative to controls. In UHR youth, the DMN exhibited both positive and negative correlations with the somatosensory cortex/cerebellum and precuneus, respectively, which was linked with better FER performance. For SF, results showed that sensory processing links with the SN might be important in allowing for better SF for both groups, but especially in controls where sensory processing is likely to be unimpaired. These findings clarify how social processing deficits may manifest in psychosis, and underscore the importance of SN and DMN connectivity for social processing more generally.
    Electronic ISSN: 1932-6203
    Topics: Medicine , Natural Sciences in General
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  • 95
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    Public Library of Science (PLoS)
    In: PLoS ONE
    Publication Date: 2015-08-13
    Description: by Marc O. Nadon, Jerald S. Ault, Ivor D. Williams, Steven G. Smith, Gerard T. DiNardo The coral reef fish community of Hawaii is composed of hundreds of species, supports a multimillion dollar fishing and tourism industry, and is of great cultural importance to the local population. However, a major stock assessment of Hawaiian coral reef fish populations has not yet been conducted. Here we used the robust indicator variable “average length in the exploited phase of the population (L¯)”, estimated from size composition data from commercial fisheries trip reports and fishery-independent diver surveys, to evaluate exploitation rates for 19 Hawaiian reef fishes. By and large, the average lengths obtained from diver surveys agreed well with those from commercial data. We used the estimated exploitation rates coupled with life history parameters synthesized from the literature to parameterize a numerical population model and generate stock sustainability metrics such as spawning potential ratios (SPR). We found good agreement between predicted average lengths in an unfished population (from our population model) and those observed from diver surveys in the largely unexploited Northwestern Hawaiian Islands. Of 19 exploited reef fish species assessed in the main Hawaiian Islands, 9 had SPRs close to or below the 30% overfishing threshold. In general, longer-lived species such as surgeonfishes, the redlip parrotfish ( Scarus rubroviolaceus ), and the gray snapper ( Aprion virescens ) had the lowest SPRs, while short-lived species such as goatfishes and jacks, as well as two invasive species ( Lutjanus kasmira and Cephalopholis argus ), had SPRs above the 30% threshold.
    Electronic ISSN: 1932-6203
    Topics: Medicine , Natural Sciences in General
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  • 96
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    Public Library of Science (PLoS)
    In: PLoS ONE
    Publication Date: 2015-08-13
    Description: by Leonie J. P. Steenis, Marjolein Verhoeven, Dave J. Hessen, Anneloes L. van Baar Background The Bayley Scales of Infant and Toddler Development-third edition (Bayley-III) are frequently used to assess early child development worldwide. However, the original standardization only included US children, and it is still unclear whether or not these norms are adequate for use in other populations. Recently, norms for the Dutch version of the Bayley-III (The Bayley-III-NL) were made. Scores based on Dutch and US norms were compared to study the need for population-specific norms. Methods Scaled scores based on Dutch and US norms were compared for 1912 children between 14 days and 42 months 14 days. Next, the proportions of children scoring 〈 1-SD and 〈 -2 SD based on the two norms were compared, to identify over- or under-referral for developmental delay resulting from non-population-based norms. Results Scaled scores based on Dutch norms fluctuated around values based on US norms on all subtests. The extent of the deviations differed across ages and subtests. Differences in means were significant across all five subtests (p 〈 .01) with small to large effect sizes ( η p 2 ) ranging from .03 to .26). Using the US instead of Dutch norms resulted in over-referral regarding gross motor skills, and under-referral regarding cognitive, receptive communication, expressive communication, and fine motor skills. Conclusions The Dutch norms differ from the US norms for all subtests and these differences are clinically relevant. Population specific norms are needed to identify children with low scores for referral and intervention, and to facilitate international comparisons of population data.
    Electronic ISSN: 1932-6203
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  • 97
    Publication Date: 2015-08-13
    Description: by Xiao-Dan Wang, Hui Lu, Zhihong Shi, Li Cai, Shuai Liu, Shuling Liu, Tong Han, Ying Wang, Yuying Zhou, Xinping Wang, Shuo Gao, Yong Ji Posterior cortical atrophy (PCA) is a clinicoradiologic neurodegenerative syndrome characterized by predominant impairment of higher visual functions. Neuroimaging and neuropathological studies show that PCA is probably an atypical presentation of Alzheimer’s disease. However, in China PCA has rarely been studied and remains largely unknown. Our study therefore aimed to analyze the clinical manifestations and patterns of cerebral atrophy, amyloid beta deposition and regional glucose metabolism in Chinese PCA patients, comparing them directly with those of typical Alzheimer’s disease (TAD). Seven PCA patients, 6 TAD patients and 5 controls underwent neuropsychological assessment, MRI scan, 11 C-PIB PET scan and 18 F-FDG PET scan. Cerebral atrophy including ventricular enlargement, posterior atrophy and medial temporal lobe atrophy were evaluated with MRI. The uptake of 11 C-PIB was quantified at the voxel level using the standardized uptake value ratio. Comparisons of regional cerebral glucose metabolism were calculated with statistical parametric mapping. PCA patients showed significant impairment on visuospatial function in neuropsychological assessment. And PCA patients showed more severe posterior atrophy and less severe left medial temporal lobe atrophy compared with TAD patients. The data from 11 C-PIB PET scanning showed that amyloid beta deposition in PCA was comparable to TAD. Moreover, in PCA the results from 18 F-FDG PET scanning revealed significant hypometabolism in the temporoparietooccipital region and identified specific hypometabolism in the right occipital lobe, compared with TAD. Our study thus provides a preliminary view of PCA in Chinese patients. A further study with a larger number of subjects would be recommended to confirm these findings.
    Electronic ISSN: 1932-6203
    Topics: Medicine , Natural Sciences in General
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  • 98
    Publication Date: 2015-08-13
    Description: by Q. Wang, M. Li, Edmond H. M. Lou, M. S. Wong Background Non-ionizing radiation imaging assessment has been advocated for the patients with adolescent idiopathic scoliosis (AIS). As one of the radiation-free methods, ultrasound imaging has gained growing attention in scoliosis assessment over the past decade. The center of laminae (COL) method has been proposed to measure the spinal curvature in the coronal plane of ultrasound image. However, the reliability and validity of this ultrasound method have not been validated in the clinical setting. Objectives To evaluate the reliability and validity of clinical ultrasound imaging on lateral curvature measurements of AIS with their corresponding magnetic resonance imaging (MRI) measurements. Methods Thirty curves (ranged 10.2°–68.2°) from sixteen patients with AIS were eligible for this study. The ultrasound scan was performed using a 3-D ultrasound unit within the same morning of MRI examination. Two researchers were involved in data collection of these two examinations. The COL method was used to measure the coronal curvature in ultrasound image, compared with the Cobb method in MRI. The intra- and inter-rater reliability of the COL method was evaluated by intra-class correlation coefficient (ICC). The validity of this method was analyzed by paired Student’s t -test, Bland–Altman statistics and Pearson correlation coefficient. The level of significance was set as 0.05. Results The COL method showed high intra- and inter-rater reliabilities (both with ICC (2, K) 〉0.9, p
    Electronic ISSN: 1932-6203
    Topics: Medicine , Natural Sciences in General
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  • 99
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    Public Library of Science (PLoS)
    In: PLoS ONE
    Publication Date: 2015-08-13
    Description: by Yongkang Kim, Taesung Park Genome-wide association studies (GWAS) have successfully discovered hundreds of associations between genetic variants and complex traits. Most GWAS have focused on the identification of single variants. It has been shown that most of the variants that were discovered by GWAS could only partially explain disease heritability. The explanation for this missing heritability is generally believed to be gene-gene (GG) or gene-environment (GE) interactions and other structural variants. Generalized multifactor dimensionality reduction (GMDR) has been proven to be reasonably powerful in detecting GG and GE interactions; however, its performance has been found to decline when outlying quantitative traits are present. This paper proposes a robust GMDR estimation method (based on the L-estimator and M-estimator estimation methods) in an attempt to reduce the effects caused by outlying traits. A comparison of robust GMDR with the original MDR based on simulation studies showed the former method to outperform the latter. The performance of robust GMDR is illustrated through a real GWA example consisting of 8,577 samples from the Korean population using the Homeostasis Model Assessment of Insulin Resistance (HOMA-IR) level as a phenotype. Robust GMDR identified the KCNH1 gene to have strong interaction effects with other genes on the function of insulin secretion.
    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: 2015-08-13
    Description: by Min Gao, Renli Tian, Junhao Wen, Qingyu Xiong, Bin Ling, Linda Yang In recent years, recommender systems have become an effective method to process information overload. However, recommendation technology still suffers from many problems. One of the problems is shilling attacks-attackers inject spam user profiles to disturb the list of recommendation items. There are two characteristics of all types of shilling attacks: 1) Item abnormality: The rating of target items is always maximum or minimum; and 2) Attack promptness: It takes only a very short period time to inject attack profiles. Some papers have proposed item anomaly detection methods based on these two characteristics, but their detection rate, false alarm rate, and universality need to be further improved. To solve these problems, this paper proposes an item anomaly detection method based on dynamic partitioning for time series. This method first dynamically partitions item-rating time series based on important points. Then, we use chi square distribution (χ 2 ) to detect abnormal intervals. The experimental results on MovieLens 100K and 1M indicate that this approach has a high detection rate and a low false alarm rate and is stable toward different attack models and filler sizes.
    Electronic ISSN: 1932-6203
    Topics: Medicine , Natural Sciences in General
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