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  • 1
    Publication Date: 2009-09-11
    Description: The genome forms extensive and dynamic physical interactions with itself in the form of chromosome loops and bridges, thus exploring the three-dimensional space of the nucleus. It is now possible to examine these interactions at the molecular level, and we have gained glimpses of their functional implications. Chromosomal interactions can contribute to the silencing and activation of genes within the three-dimensional context of the nuclear architecture. Technical advances in detecting these interactions contribute to our understanding of the functional organization of the genome, as well as its adaptive plasticity in response to environmental changes during development and disease.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Gondor, Anita -- Ohlsson, Rolf -- England -- Nature. 2009 Sep 10;461(7261):212-7. doi: 10.1038/nature08453.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Microbiology, Tumor and Cell Biology, Nobels vag 16, Box 280, Karolinska Institute, SE-171 77 Stockholm, Sweden. anita.gondor@ki.se〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19741702" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Cell Nucleus/genetics/metabolism ; *Chromosome Positioning ; Chromosomes/chemistry/*genetics/*metabolism ; *Gene Expression Regulation ; Humans ; Nucleic Acid Conformation ; Transcription, Genetic
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  • 2
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    Nature Publishing Group (NPG)
    Publication Date: 2009-09-19
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Brumfiel, Geoff -- England -- Nature. 2009 Jul 16;460(7253):316. doi: 10.1038/460316a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19606114" target="_blank"〉PubMed〈/a〉
    Keywords: Cooperative Behavior ; History, 20th Century ; History, 21st Century ; *International Cooperation/history ; *Nuclear Weapons/history ; Russia ; *Science/history/trends ; United States
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  • 3
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    Nature Publishing Group (NPG)
    Publication Date: 2009-02-06
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Dalton, Rex -- England -- Nature. 2009 Feb 5;457(7230):645. doi: 10.1038/457645a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19194415" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Chicago ; Congresses as Topic ; Croatia ; Genome/*genetics ; Genome, Human/*genetics ; Germany ; Hominidae/*genetics ; Humans ; Hybridization, Genetic/genetics ; Sequence Analysis, DNA
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  • 4
    Publication Date: 2009-12-25
    Description: Blue straggler stars lie on or near the main sequences of star clusters (all members of which formed around the same time), but typically are more luminous than the turn-off stars and therefore long ago should have evolved off the main sequence to become giants and white dwarfs. They are thought to derive from normal main-sequence stars that have undergone a recent increase in mass. Statistical evidence indicates that in globular star clusters the blue stragglers probably form from binary stars. The specific formation processes, such as mass transfer, mergers or stellar collisions during dynamical encounters of binary stars, remain unresolved. Here we report that 16 of the 21 blue stragglers (76 per cent) in the old (7-Gyr; ref. 2) open cluster NGC 188 are currently in binary systems, a frequency three times that found among normal solar-type main-sequence stars. These blue straggler binaries have a remarkable period-eccentricity distribution, with all but three having orbital periods of approximately 1,000 days. Moreover, these stars are rotating faster than normal main-sequence stars of the same surface temperatures. These data show that most, and possibly all, blue stragglers derive from multiple-star systems, and indicate that the several formation processes operate simultaneously. We suggest that rapid rotation of blue stragglers may place upper limits on their ages.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Mathieu, Robert D -- Geller, Aaron M -- England -- Nature. 2009 Dec 24;462(7276):1032-5. doi: 10.1038/nature08568.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Astronomy, University of Wisconsin-Madison, 475 North Charter Street, Madison, Wisconsin 53706, USA. mathieu@astro.wisc.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20033042" target="_blank"〉PubMed〈/a〉
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  • 5
    Publication Date: 2010-11-12
    Description: The role of different amygdala nuclei (neuroanatomical subdivisions) in processing Pavlovian conditioned fear has been studied extensively, but the function of the heterogeneous neuronal subtypes within these nuclei remains poorly understood. Here we use molecular genetic approaches to map the functional connectivity of a subpopulation of GABA-containing neurons, located in the lateral subdivision of the central amygdala (CEl), which express protein kinase C-delta (PKC-delta). Channelrhodopsin-2-assisted circuit mapping in amygdala slices and cell-specific viral tracing indicate that PKC-delta(+) neurons inhibit output neurons in the medial central amygdala (CEm), and also make reciprocal inhibitory synapses with PKC-delta(-) neurons in CEl. Electrical silencing of PKC-delta(+) neurons in vivo suggests that they correspond to physiologically identified units that are inhibited by the conditioned stimulus, called CEl(off) units. This correspondence, together with behavioural data, defines an inhibitory microcircuit in CEl that gates CEm output to control the level of conditioned freezing.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3597095/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3597095/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Haubensak, Wulf -- Kunwar, Prabhat S -- Cai, Haijiang -- Ciocchi, Stephane -- Wall, Nicholas R -- Ponnusamy, Ravikumar -- Biag, Jonathan -- Dong, Hong-Wei -- Deisseroth, Karl -- Callaway, Edward M -- Fanselow, Michael S -- Luthi, Andreas -- Anderson, David J -- 1 R01 MH085082-01A1/MH/NIMH NIH HHS/ -- R01 MH063912/MH/NIMH NIH HHS/ -- R01 MH063912-09/MH/NIMH NIH HHS/ -- R01 MH063912-09S1/MH/NIMH NIH HHS/ -- R01 MH063912-10/MH/NIMH NIH HHS/ -- R01 MH085082/MH/NIMH NIH HHS/ -- R01 MH085082-01A1/MH/NIMH NIH HHS/ -- RC2 NS069464/NS/NINDS NIH HHS/ -- RC2 NS069464-01/NS/NINDS NIH HHS/ -- RC2 NS069464-02/NS/NINDS NIH HHS/ -- Howard Hughes Medical Institute/ -- England -- Nature. 2010 Nov 11;468(7321):270-6. doi: 10.1038/nature09553.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Biology 216-76, California Institute of Technology, Pasadena, California 91125, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21068836" target="_blank"〉PubMed〈/a〉
    Keywords: Amygdala/anatomy & histology/cytology/enzymology/*physiology ; Animals ; Axonal Transport ; Cells, Cultured ; Conditioning, Classical/*physiology ; Fear/*physiology ; Female ; Freezing Reaction, Cataleptic ; Genetic Techniques ; Humans ; Male ; Mice ; Mice, Transgenic ; Neural Inhibition/*physiology ; Neural Pathways/cytology/enzymology/*physiology ; Neurons/enzymology/metabolism ; Protein Kinase C-delta/deficiency/genetics/metabolism ; Synapses/metabolism ; gamma-Aminobutyric Acid/metabolism
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  • 6
    Publication Date: 2010-01-22
    Description: Robustness seems to be the opposite of evolvability. If phenotypes are robust against mutation, we might expect that a population will have difficulty adapting to an environmental change, as several studies have suggested. However, other studies contend that robust organisms are more adaptable. A quantitative understanding of the relationship between robustness and evolvability will help resolve these conflicting reports and will clarify outstanding problems in molecular and experimental evolution, evolutionary developmental biology and protein engineering. Here we demonstrate, using a general population genetics model, that mutational robustness can either impede or facilitate adaptation, depending on the population size, the mutation rate and the structure of the fitness landscape. In particular, neutral diversity in a robust population can accelerate adaptation as long as the number of phenotypes accessible to an individual by mutation is smaller than the total number of phenotypes in the fitness landscape. These results provide a quantitative resolution to a significant ambiguity in evolutionary theory.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3071712/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3071712/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Draghi, Jeremy A -- Parsons, Todd L -- Wagner, Gunter P -- Plotkin, Joshua B -- 2U54AI057168/AI/NIAID NIH HHS/ -- U54 AI057168/AI/NIAID NIH HHS/ -- U54 AI057168-06S1/AI/NIAID NIH HHS/ -- England -- Nature. 2010 Jan 21;463(7279):353-5. doi: 10.1038/nature08694.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20090752" target="_blank"〉PubMed〈/a〉
    Keywords: Adaptation, Physiological/*genetics ; *Biological Evolution ; Genetic Fitness/genetics ; Genetic Variation/genetics ; Genetics, Population ; Genotype ; Models, Genetic ; Mutagenesis/*genetics ; Mutation/*genetics ; Phenotype ; Population Density ; Time Factors
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  • 7
    Publication Date: 2010-02-19
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Streit, Adrian -- Sommer, Ralf J -- England -- Nature. 2010 Feb 18;463(7283):891-2. doi: 10.1038/463891a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20164917" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Caenorhabditis elegans/embryology/*genetics ; Caenorhabditis elegans Proteins/genetics/metabolism ; Cell Differentiation/genetics ; Cell Lineage/genetics ; DNA-Binding Proteins/genetics/metabolism ; GATA Transcription Factors/genetics/metabolism ; Gene Expression Regulation, Developmental/*genetics ; Gene Regulatory Networks/*genetics ; Intestines/cytology/embryology/metabolism ; *Penetrance ; RNA, Helminth/analysis/genetics ; Stochastic Processes ; Transcription Factors/genetics/metabolism
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  • 8
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    Nature Publishing Group (NPG)
    Publication Date: 2010-12-24
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Duailibe, Allan Kardec -- England -- Nature. 2010 Dec 23;468(7327):1041. doi: 10.1038/4681041b.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21179153" target="_blank"〉PubMed〈/a〉
    Keywords: Brazil ; *Energy-Generating Resources/economics/standards/statistics & numerical data
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  • 9
    Publication Date: 2010-04-20
    Description: Photosynthetic organisms adopt two different strategies for the reduction of the C17 = C18 double bond of protochlorophyllide (Pchlide) to form chlorophyllide a, the direct precursor of chlorophyll a (refs 1-4). The first involves the activity of the light-dependent Pchlide oxidoreductase, and the second involves the light-independent (dark-operative) Pchlide oxidoreductase (DPOR). DPOR is a nitrogenase-like enzyme consisting of two components, L-protein (a BchL dimer) and NB-protein (a BchN-BchB heterotetramer), which are structurally related to nitrogenase Fe protein and MoFe protein, respectively. Here we report the crystal structure of the NB-protein of DPOR from Rhodobacter capsulatus at a resolution of 2.3A. As expected, the overall structure is similar to that of nitrogenase MoFe protein: each catalytic BchN-BchB unit contains one Pchlide and one iron-sulphur cluster (NB-cluster) coordinated uniquely by one aspartate and three cysteines. Unique aspartate ligation is not necessarily needed for the cluster assembly but is essential for the catalytic activity. Specific Pchlide-binding accompanies the partial unwinding of an alpha-helix that belongs to the next catalytic BchN-BchB unit. We propose a unique trans-specific reduction mechanism in which the distorted C17-propionate of Pchlide and an aspartate from BchB serve as proton donors for C18 and C17 of Pchlide, respectively. Intriguingly, the spatial arrangement of the NB-cluster and Pchlide is almost identical to that of the P-cluster and FeMo-cofactor in nitrogenase MoFe-protein, illustrating that a common architecture exists to reduce chemically stable multibonds of porphyrin and dinitrogen.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Muraki, Norifumi -- Nomata, Jiro -- Ebata, Kozue -- Mizoguchi, Tadashi -- Shiba, Tomoo -- Tamiaki, Hitoshi -- Kurisu, Genji -- Fujita, Yuichi -- England -- Nature. 2010 May 6;465(7294):110-4. doi: 10.1038/nature08950.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Life Sciences, University of Tokyo, Komaba, Meguro-ku, Tokyo 153-8902, Japan.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20400946" target="_blank"〉PubMed〈/a〉
    Keywords: Crystallography, X-Ray ; *Models, Molecular ; Oxidoreductases Acting on CH-CH Group Donors/*chemistry/metabolism ; Protein Structure, Tertiary ; Rhodobacter capsulatus/*enzymology
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  • 10
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    Nature Publishing Group (NPG)
    Publication Date: 2010-01-16
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hayden, Erika Check -- England -- Nature. 2010 Jan 14;463(7278):154-6. doi: 10.1038/463154a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20075895" target="_blank"〉PubMed〈/a〉
    Keywords: Brain Diseases/*congenital/prevention & control/therapy ; Cerebral Palsy/congenital/prevention & control ; Female ; Humans ; Hypothermia, Induced ; Infant, Newborn ; Infant, Newborn, Diseases/*prevention & control/*therapy ; Infant, Premature/*physiology ; Intensive Care Units, Neonatal ; Intensive Care, Neonatal ; Neurosciences/trends ; Nurseries, Hospital ; Stroke/congenital/prevention & control
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  • 11
    Publication Date: 2010-01-22
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Law, Kathy -- England -- Nature. 2010 Jan 21;463(7279):307-8. doi: 10.1038/463307a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20090744" target="_blank"〉PubMed〈/a〉
    Keywords: Air Pollutants/analysis/chemistry ; Asia ; Atmosphere/*chemistry ; Europe ; Greenhouse Effect ; Humans ; International Cooperation ; North America ; Ozone/*analysis/chemistry
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  • 12
    Publication Date: 2010-04-03
    Description: Environmental niches in which life first emerged and later evolved on the Earth have undergone dramatic changes in response to evolving tectonic/geochemical cycles and to biologic interventions, as well as increases in the Sun's luminosity of about 25 to 30 per cent over the Earth's history. It has been inferred that the greenhouse effect of atmospheric CO(2) and/or CH(4) compensated for the lower solar luminosity and dictated an Archaean climate in which liquid water was stable in the hydrosphere. Here we demonstrate, however, that the mineralogy of Archaean sediments, particularly the ubiquitous presence of mixed-valence Fe(II-III) oxides (magnetite) in banded iron formations is inconsistent with such high concentrations of greenhouse gases and the metabolic constraints of extant methanogens. Prompted by this, and the absence of geologic evidence for very high greenhouse-gas concentrations, we hypothesize that a lower albedo on the Earth, owing to considerably less continental area and to the lack of biologically induced cloud condensation nuclei, made an important contribution to moderating surface temperature in the Archaean eon. Our model calculations suggest that the lower albedo of the early Earth provided environmental conditions above the freezing point of water, thus alleviating the need for extreme greenhouse-gas concentrations to satisfy the faint early Sun paradox.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Rosing, Minik T -- Bird, Dennis K -- Sleep, Norman H -- Bjerrum, Christian J -- England -- Nature. 2010 Apr 1;464(7289):744-7. doi: 10.1038/nature08955.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Nordic Center for Earth Evolution, Oster Voldgade, Denmark. minik@snm.ku.dk〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20360739" target="_blank"〉PubMed〈/a〉
    Keywords: Atmosphere/chemistry ; Carbon Dioxide/analysis ; *Climate ; *Earth (Planet) ; Ecosystem ; Freezing ; Geologic Sediments/chemistry ; Greenhouse Effect ; History, Ancient ; Hydrogen/analysis ; *Models, Theoretical ; Partial Pressure ; *Sunlight ; Water/*analysis/*chemistry
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  • 13
    Publication Date: 2010-04-03
    Description: The melting Laurentide Ice Sheet discharged thousands of cubic kilometres of fresh water each year into surrounding oceans, at times suppressing the Atlantic meridional overturning circulation and triggering abrupt climate change. Understanding the physical mechanisms leading to events such as the Younger Dryas cold interval requires identification of the paths and timing of the freshwater discharges. Although Broecker et al. hypothesized in 1989 that an outburst from glacial Lake Agassiz triggered the Younger Dryas, specific evidence has so far proved elusive, leading Broecker to conclude in 2006 that "our inability to identify the path taken by the flood is disconcerting". Here we identify the missing flood path-evident from gravels and a regional erosion surface-running through the Mackenzie River system in the Canadian Arctic Coastal Plain. Our modelling of the isostatically adjusted surface in the upstream Fort McMurray region, and a slight revision of the ice margin at this time, allows Lake Agassiz to spill into the Mackenzie drainage basin. From optically stimulated luminescence dating we have determined the approximate age of this Mackenzie River flood into the Arctic Ocean to be shortly after 13,000 years ago, near the start of the Younger Dryas. We attribute to this flood a boulder terrace near Fort McMurray with calibrated radiocarbon dates of over 11,500 years ago. A large flood into the Arctic Ocean at the start of the Younger Dryas leads us to reject the widespread view that Agassiz overflow at this time was solely eastward into the North Atlantic Ocean.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Murton, Julian B -- Bateman, Mark D -- Dallimore, Scott R -- Teller, James T -- Yang, Zhirong -- England -- Nature. 2010 Apr 1;464(7289):740-3. doi: 10.1038/nature08954.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Permafrost Laboratory, Department of Geography, University of Sussex, Brighton BN1 9QJ, UK. .b.murton@sussex.ac.uk〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20360738" target="_blank"〉PubMed〈/a〉
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  • 14
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    Nature Publishing Group (NPG)
    Publication Date: 2010-11-19
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Studer, Lorenz -- England -- Nature. 2010 Nov 18;468(7322):383-4. doi: 10.1038/468383a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21085168" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Brain/cytology/metabolism ; DNA Methylation ; Gene Silencing ; Humans ; Induced Pluripotent Stem Cells/metabolism ; Long Interspersed Nucleotide Elements/*genetics ; Methyl-CpG-Binding Protein 2/deficiency/genetics/*metabolism ; Mice ; Neuroepithelial Cells/metabolism ; Neurons/*metabolism ; Recombination, Genetic/*genetics ; Rett Syndrome/genetics/pathology ; Transcription, Genetic/genetics
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  • 15
    Publication Date: 2010-03-26
    Description: The Lyman-alpha (Lyalpha) emission line is the primary observational signature of star-forming galaxies at the highest redshifts, and has enabled the compilation of large samples of galaxies with which to study cosmic evolution. The resonant nature of the line, however, means that Lyalpha photons scatter in the neutral interstellar medium of their host galaxies, and their sensitivity to absorption by interstellar dust may therefore be greatly enhanced. This implies that the Lyalpha luminosity may be significantly reduced, or even completely suppressed. Hitherto, no unbiased empirical test of the escaping fraction (f(esc)) of Lyalpha photons has been performed at high redshifts. Here we report that the average f(esc) from star-forming galaxies at redshift z = 2.2 is just 5 per cent by performing a blind narrowband survey in Lyalpha and Halpha. This implies that numerous conclusions based on Lyalpha-selected samples will require upwards revision by an order of magnitude and we provide a benchmark for this revision. We demonstrate that almost 90 per cent of star-forming galaxies emit insufficient Lyalpha to be detected by standard selection criteria. Both samples show an anti-correlation of f(esc) with dust content, and we show that Lyalpha- and Halpha-selection recovers populations that differ substantially in dust content and f(esc).〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hayes, Matthew -- Ostlin, Goran -- Schaerer, Daniel -- Mas-Hesse, J Miguel -- Leitherer, Claus -- Atek, Hakim -- Kunth, Daniel -- Verhamme, Anne -- de Barros, Stephane -- Melinder, Jens -- England -- Nature. 2010 Mar 25;464(7288):562-5. doi: 10.1038/nature08881.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Observatoire Astronomique de l'Universite de Geneve, 51 chemin des Maillettes, CH-1290 Sauverny, Switzerland. matthew.hayes@unige.ch〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20336139" target="_blank"〉PubMed〈/a〉
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  • 16
    Publication Date: 2010-03-06
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Rosseinsky, Matthew J -- Prassides, Kosmas -- England -- Nature. 2010 Mar 4;464(7285):39-41. doi: 10.1038/464039a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20203597" target="_blank"〉PubMed〈/a〉
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  • 17
    Publication Date: 2010-11-12
    Description: Photoreceptors for visual perception, phototaxis or light avoidance are typically clustered in eyes or related structures such as the Bolwig organ of Drosophila larvae. Unexpectedly, we found that the class IV dendritic arborization neurons of Drosophila melanogaster larvae respond to ultraviolet, violet and blue light, and are major mediators of light avoidance, particularly at high intensities. These class IV dendritic arborization neurons, which are present in every body segment, have dendrites tiling the larval body wall nearly completely without redundancy. Dendritic illumination activates class IV dendritic arborization neurons. These novel photoreceptors use phototransduction machinery distinct from other photoreceptors in Drosophila and enable larvae to sense light exposure over their entire bodies and move out of danger.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3026603/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3026603/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Xiang, Yang -- Yuan, Quan -- Vogt, Nina -- Looger, Loren L -- Jan, Lily Yeh -- Jan, Yuh Nung -- R01 MH084234/MH/NIMH NIH HHS/ -- R37 NS040929/NS/NINDS NIH HHS/ -- R37 NS040929-11/NS/NINDS NIH HHS/ -- Howard Hughes Medical Institute/ -- England -- Nature. 2010 Dec 16;468(7326):921-6. doi: 10.1038/nature09576. Epub 2010 Nov 10.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute, Departments of Physiology, Biochemistry, and Biophysics, University of California San Francisco, San Francisco, California 94158, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21068723" target="_blank"〉PubMed〈/a〉
    Keywords: Animal Structures/cytology/metabolism/radiation effects ; Animals ; Avoidance Learning/physiology/radiation effects ; Cells, Cultured ; Dermis/metabolism/radiation effects ; Drosophila Proteins/metabolism ; Drosophila melanogaster/*anatomy & histology/cytology/physiology/*radiation ; effects ; Larva/anatomy & histology/cytology/radiation effects ; *Light ; Light Signal Transduction/radiation effects ; Neurons/physiology/radiation effects ; Photoreceptor Cells, Invertebrate/*metabolism/*radiation effects ; Receptors, Cell Surface/metabolism ; TRPC Cation Channels/metabolism
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  • 18
    Publication Date: 2010-07-16
    Description: In the high-transition-temperature (high-T(c)) superconductors the pseudogap phase becomes predominant when the density of doped holes is reduced. Within this phase it has been unclear which electronic symmetries (if any) are broken, what the identity of any associated order parameter might be, and which microscopic electronic degrees of freedom are active. Here we report the determination of a quantitative order parameter representing intra-unit-cell nematicity: the breaking of rotational symmetry by the electronic structure within each CuO(2) unit cell. We analyse spectroscopic-imaging scanning tunnelling microscope images of the intra-unit-cell states in underdoped Bi(2)Sr(2)CaCu(2)O(8 +) (delta) and, using two independent evaluation techniques, find evidence for electronic nematicity of the states close to the pseudogap energy. Moreover, we demonstrate directly that these phenomena arise from electronic differences at the two oxygen sites within each unit cell. If the characteristics of the pseudogap seen here and by other techniques all have the same microscopic origin, this phase involves weak magnetic states at the O sites that break 90 degrees -rotational symmetry within every CuO(2) unit cell.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lawler, M J -- Fujita, K -- Lee, Jhinhwan -- Schmidt, A R -- Kohsaka, Y -- Kim, Chung Koo -- Eisaki, H -- Uchida, S -- Davis, J C -- Sethna, J P -- Kim, Eun-Ah -- England -- Nature. 2010 Jul 15;466(7304):347-51. doi: 10.1038/nature09169.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Physics, Applied Physics and Astronomy, Binghamton University, Binghamton, New York 13902-6000, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20631795" target="_blank"〉PubMed〈/a〉
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  • 19
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    Nature Publishing Group (NPG)
    Publication Date: 2010-06-11
    Description: The characteristics of epigenetic control, including the potential for long-lasting, stable effects on gene expression that outlive an initial transient signal, could be of singular importance for post-mitotic neurons, which are subject to changes with short- to long-lasting influence on their activity and connectivity. Persistent changes in chromatin structure are thought to contribute to mechanisms of epigenetic inheritance. Recent advances in chromatin biology offer new avenues to investigate regulatory mechanisms underlying long-lasting changes in neurons, with direct implications for the study of brain function, behaviour and diseases.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3075582/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3075582/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Dulac, Catherine -- R01 DC003903/DC/NIDCD NIH HHS/ -- R01 DC003903-10/DC/NIDCD NIH HHS/ -- R01 DC009019/DC/NIDCD NIH HHS/ -- R01 DC009019-01A2/DC/NIDCD NIH HHS/ -- Howard Hughes Medical Institute/ -- England -- Nature. 2010 Jun 10;465(7299):728-35. doi: 10.1038/nature09231.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute, Harvard University, 16 Divinity Avenue, Cambridge, Massachusetts 02138, USA. dulac@fas.harvard.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20535202" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Animals, Newborn ; Brain/cytology/metabolism/*physiology ; Chromatin Assembly and Disassembly/genetics/*physiology ; DNA Methylation ; Genomic Imprinting ; Histones/metabolism ; Humans ; Inheritance Patterns ; Neuronal Plasticity/genetics/physiology
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  • 20
    Publication Date: 2010-09-03
    Description: Accumulation of neurotoxic amyloid-beta is a major hallmark of Alzheimer's disease. Formation of amyloid-beta is catalysed by gamma-secretase, a protease with numerous substrates. Little is known about the molecular mechanisms that confer substrate specificity on this potentially promiscuous enzyme. Knowledge of the mechanisms underlying its selectivity is critical for the development of clinically effective gamma-secretase inhibitors that can reduce amyloid-beta formation without impairing cleavage of other gamma-secretase substrates, especially Notch, which is essential for normal biological functions. Here we report the discovery of a novel gamma-secretase activating protein (GSAP) that drastically and selectively increases amyloid-beta production through a mechanism involving its interactions with both gamma-secretase and its substrate, the amyloid precursor protein carboxy-terminal fragment (APP-CTF). GSAP does not interact with Notch, nor does it affect its cleavage. Recombinant GSAP stimulates amyloid-beta production in vitro. Reducing GSAP concentrations in cell lines decreases amyloid-beta concentrations. Knockdown of GSAP in a mouse model of Alzheimer's disease reduces levels of amyloid-beta and plaque development. GSAP represents a type of gamma-secretase regulator that directs enzyme specificity by interacting with a specific substrate. We demonstrate that imatinib, an anticancer drug previously found to inhibit amyloid-beta formation without affecting Notch cleavage, achieves its amyloid-beta-lowering effect by preventing GSAP interaction with the gamma-secretase substrate, APP-CTF. Thus, GSAP can serve as an amyloid-beta-lowering therapeutic target without affecting other key functions of gamma-secretase.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2936959/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2936959/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉He, Gen -- Luo, Wenjie -- Li, Peng -- Remmers, Christine -- Netzer, William J -- Hendrick, Joseph -- Bettayeb, Karima -- Flajolet, Marc -- Gorelick, Fred -- Wennogle, Lawrence P -- Greengard, Paul -- AG09464/AG/NIA NIH HHS/ -- P01 AG009464/AG/NIA NIH HHS/ -- P01 AG009464-16A10010/AG/NIA NIH HHS/ -- T32 DK007017/DK/NIDDK NIH HHS/ -- England -- Nature. 2010 Sep 2;467(7311):95-8. doi: 10.1038/nature09325.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory of Molecular and Cellular Neuroscience, The Rockefeller University, 1230 York Avenue, New York, New York 10065, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20811458" target="_blank"〉PubMed〈/a〉
    Keywords: Alzheimer Disease/*metabolism ; Amyloid Precursor Protein Secretases/chemistry/metabolism ; Amyloid beta-Peptides/metabolism ; Amyloid beta-Protein Precursor/chemistry/metabolism ; Animals ; Benzamides ; Cell Line ; Disease Models, Animal ; Gene Knockdown Techniques ; Humans ; Imatinib Mesylate ; Mice ; Peptide Fragments/metabolism ; Piperazines/pharmacology ; Proteins/*antagonists & inhibitors/genetics/*metabolism ; Pyrimidines/pharmacology ; RNA Interference ; Receptor, Notch1/metabolism
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  • 21
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    Nature Publishing Group (NPG)
    Publication Date: 2010-11-12
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Subhadra, Bobban -- England -- Nature. 2010 Nov 11;468(7321):173. doi: 10.1038/468173c.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21068815" target="_blank"〉PubMed〈/a〉
    Keywords: Agriculture/*trends ; *Biofuels ; India ; Jatropha/growth & development ; Water Supply/*analysis/statistics & numerical data
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  • 22
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    Nature Publishing Group (NPG)
    Publication Date: 2010-03-06
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Butler, Declan -- England -- Nature. 2010 Mar 4;464(7285):16-7. doi: 10.1038/464016a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20203575" target="_blank"〉PubMed〈/a〉
    Keywords: Bibliometrics ; Cultural Characteristics ; Data Collection/*methods ; Databases, Factual ; Europe ; Internationality ; Policy Making ; Universities/*standards
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  • 23
    Publication Date: 2010-08-06
    Description: The recently emerged fields of metamaterials and transformation optics promise a family of exciting applications such as invisibility, optical imaging with deeply subwavelength resolution and nanophotonics with the potential for much faster information processing. The possibility of creating optical negative-index metamaterials (NIMs) using nanostructured metal-dielectric composites has triggered intense basic and applied research over the past several years. However, the performance of all NIM applications is significantly limited by the inherent and strong energy dissipation in metals, especially in the near-infrared and visible wavelength ranges. Generally the losses are orders of magnitude too large for the proposed applications, and the reduction of losses with optimized designs seems to be out of reach. One way of addressing this issue is to incorporate gain media into NIM designs. However, whether NIMs with low loss can be achieved has been the subject of theoretical debate. Here we experimentally demonstrate that the incorporation of gain material in the high-local-field areas of a metamaterial makes it possible to fabricate an extremely low-loss and active optical NIM. The original loss-limited negative refractive index and the figure of merit (FOM) of the device have been drastically improved with loss compensation in the visible wavelength range between 722 and 738 nm. In this range, the NIM becomes active such that the sum of the light intensities in transmission and reflection exceeds the intensity of the incident beam. At a wavelength of 737 nm, the negative refractive index improves from -0.66 to -1.017 and the FOM increases from 1 to 26. At 738 nm, the FOM is expected to become macroscopically large, of the order of 10(6). This study demonstrates the possibility of fabricating an optical negative-index metamaterial that is not limited by the inherent loss in its metal constituent.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Xiao, Shumin -- Drachev, Vladimir P -- Kildishev, Alexander V -- Ni, Xingjie -- Chettiar, Uday K -- Yuan, Hsiao-Kuan -- Shalaev, Vladimir M -- England -- Nature. 2010 Aug 5;466(7307):735-8. doi: 10.1038/nature09278.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Birck Nanotechnology Center and School of Electrical and Computer Engineering, Purdue University, West Lafayette, Indiana 47907, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20686570" target="_blank"〉PubMed〈/a〉
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  • 24
    Publication Date: 2010-10-19
    Description: Piwi-associated RNAs (piRNAs), a specific class of 24- to 30-nucleotide-long RNAs produced by the Piwi-type of Argonaute proteins, have a specific germline function in repressing transposable elements. This repression is thought to involve heterochromatin formation and transcriptional and post-transcriptional silencing. The piRNA pathway has other essential functions in germline stem cell maintenance and in maintaining germline DNA integrity. Here we uncover an unexpected function of the piRNA pathway in the decay of maternal messenger RNAs and in translational repression in the early embryo. A subset of maternal mRNAs is degraded in the embryo at the maternal-to-zygotic transition. In Drosophila, maternal mRNA degradation depends on the RNA-binding protein Smaug and the deadenylase CCR4, as well as the zygotic expression of a microRNA cluster. Using mRNA encoding the embryonic posterior morphogen Nanos (Nos) as a paradigm to study maternal mRNA decay, we found that CCR4-mediated deadenylation of nos depends on components of the piRNA pathway including piRNAs complementary to a specific region in the nos 3' untranslated region. Reduced deadenylation when piRNA-induced regulation is impaired correlates with nos mRNA stabilization and translational derepression in the embryo, resulting in head development defects. Aubergine, one of the Argonaute proteins in the piRNA pathway, is present in a complex with Smaug, CCR4, nos mRNA and piRNAs that target the nos 3' untranslated region, in the bulk of the embryo. We propose that piRNAs and their associated proteins act together with Smaug to recruit the CCR4 deadenylation complex to specific mRNAs, thus promoting their decay. Because the piRNAs involved in this regulation are produced from transposable elements, this identifies a direct developmental function for transposable elements in the regulation of gene expression.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4505748/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4505748/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Rouget, Christel -- Papin, Catherine -- Boureux, Anthony -- Meunier, Anne-Cecile -- Franco, Benedicte -- Robine, Nicolas -- Lai, Eric C -- Pelisson, Alain -- Simonelig, Martine -- R01 GM083300/GM/NIGMS NIH HHS/ -- R01-GM083300/GM/NIGMS NIH HHS/ -- England -- Nature. 2010 Oct 28;467(7319):1128-32. doi: 10.1038/nature09465. Epub 2010 Oct 17.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉mRNA Regulation and Development, Institute of Human Genetics, CNRS UPR1142, 141 rue de la Cardonille, Cedex 5, 34396 Montpellier, France.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20953170" target="_blank"〉PubMed〈/a〉
    Keywords: 3' Untranslated Regions/genetics ; Animals ; Argonaute Proteins ; Cytoplasm/genetics/metabolism ; DNA Transposable Elements/genetics ; Drosophila Proteins/genetics/metabolism ; Drosophila melanogaster/cytology/*embryology/*genetics ; Embryo, Nonmammalian/cytology/embryology/metabolism ; Female ; *Gene Expression Regulation, Developmental ; Mothers ; Peptide Initiation Factors/genetics/metabolism ; Polyadenylation/*genetics ; *RNA Stability ; RNA, Messenger/genetics/*metabolism ; RNA, Small Interfering/*genetics/metabolism ; RNA-Binding Proteins/genetics/metabolism ; Repressor Proteins/genetics/metabolism ; Ribonucleases/genetics/metabolism ; Zygote/metabolism
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  • 25
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    Nature Publishing Group (NPG)
    Publication Date: 2010-08-27
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Mutter, John -- England -- Nature. 2010 Aug 26;466(7310):1042. doi: 10.1038/4661042a.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Earth and Environmental Sciences, Columbia University, New York, New York 10027-6902, USA. jmutter@ei.columbia.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20739992" target="_blank"〉PubMed〈/a〉
    Keywords: Disasters/*economics/statistics & numerical data ; Economics ; Global Warming ; Humans ; Population Growth ; *Poverty ; Socioeconomic Factors
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  • 26
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    Nature Publishing Group (NPG)
    Publication Date: 2010-03-20
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Butler, Declan -- England -- Nature. 2010 Mar 18;464(7287):338. doi: 10.1038/464338a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20237535" target="_blank"〉PubMed〈/a〉
    Keywords: Child ; Developing Countries/economics ; Financing, Government/economics ; Foundations/economics ; Fund Raising/*economics ; *Global Health ; Humans ; Internationality ; Vaccination/*economics/utilization ; Vaccines/*economics/*supply & distribution
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  • 27
    Publication Date: 2010-06-22
    Description: Networks have become a key approach to understanding systems of interacting objects, unifying the study of diverse phenomena including biological organisms and human society. One crucial step when studying the structure and dynamics of networks is to identify communities: groups of related nodes that correspond to functional subunits such as protein complexes or social spheres. Communities in networks often overlap such that nodes simultaneously belong to several groups. Meanwhile, many networks are known to possess hierarchical organization, where communities are recursively grouped into a hierarchical structure. However, the fact that many real networks have communities with pervasive overlap, where each and every node belongs to more than one group, has the consequence that a global hierarchy of nodes cannot capture the relationships between overlapping groups. Here we reinvent communities as groups of links rather than nodes and show that this unorthodox approach successfully reconciles the antagonistic organizing principles of overlapping communities and hierarchy. In contrast to the existing literature, which has entirely focused on grouping nodes, link communities naturally incorporate overlap while revealing hierarchical organization. We find relevant link communities in many networks, including major biological networks such as protein-protein interaction and metabolic networks, and show that a large social network contains hierarchically organized community structures spanning inner-city to regional scales while maintaining pervasive overlap. Our results imply that link communities are fundamental building blocks that reveal overlap and hierarchical organization in networks to be two aspects of the same phenomenon.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ahn, Yong-Yeol -- Bagrow, James P -- Lehmann, Sune -- U01 A1070499-01/PHS HHS/ -- England -- Nature. 2010 Aug 5;466(7307):761-4. doi: 10.1038/nature09182. Epub 2010 Jun 20.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Center for Complex Network Research, Department of Physics, Northeastern University, Boston, Massachusetts 02115, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20562860" target="_blank"〉PubMed〈/a〉
    Keywords: *Cell Phones/utilization ; Cities ; *Community Networks/statistics & numerical data ; Humans ; *Metabolic Networks and Pathways ; Models, Biological ; *Protein Interaction Mapping
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  • 28
    Publication Date: 2010-03-26
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lawry, Theodore -- England -- Nature. 2010 Mar 25;464(7288):486. doi: 10.1038/464486b.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20336110" target="_blank"〉PubMed〈/a〉
    Keywords: Cooperative Behavior ; Ethics, Research ; Industry/*standards/trends ; Public-Private Sector Partnerships/*ethics ; Research/economics/*standards ; Universities/organization & administration/*standards/trends
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  • 29
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    Nature Publishing Group (NPG)
    Publication Date: 2010-01-30
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Butler, Declan -- England -- Nature. 2010 Jan 28;463(7280):415. doi: 10.1038/463415a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20110960" target="_blank"〉PubMed〈/a〉
    Keywords: Acquired Immunodeficiency Syndrome/economics/prevention & control/therapy ; *Budgets ; Foundations/*economics ; Humans ; International Agencies/*economics/statistics & numerical data/trends ; Malaria/economics/prevention & control/therapy ; Tuberculosis/economics/prevention & control/therapy
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  • 30
    Publication Date: 2010-06-19
    Description: Rifting and magmatism are fundamental geological processes that shape the surface of our planet. A relationship between the two is widely acknowledged but its precise nature has eluded geoscientists and remained controversial. Largely on the basis of detailed observations from the North Atlantic Ocean, mantle temperature was identified as the primary factor controlling magmatic production, with most authors seeking to explain observed variations in volcanic activity at rifted margins in terms of the mantle temperature at the time of break-up. However, as more detailed observations have been made at other rifted margins worldwide, the validity of this interpretation and the importance of other factors in controlling break-up style have been much debated. One such observation is from the northwest Indian Ocean, where, despite an unequivocal link between an onshore flood basalt province, continental break-up and a hot-spot track leading to an active ocean island volcano, the associated continental margins show little magmatism. Here we reconcile these observations by applying a numerical model that accounts explicitly for the effects of earlier episodes of extension. Our approach allows us to directly compare break-up magmatism generated at different locations and so isolate the key controlling factors. We show that the volume of rift-related magmatism generated, both in the northwest Indian Ocean and at the better-known North Atlantic margins, depends not only on the mantle temperature but, to a similar degree, on the rift history. The inherited extensional history can either suppress or enhance melt generation, which can explain previously enigmatic observations.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Armitage, John J -- Collier, Jenny S -- Minshull, Tim A -- England -- Nature. 2010 Jun 17;465(7300):913-7. doi: 10.1038/nature09063.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Earth Science & Engineering, Imperial College London, London SW7 2AZ, UK. j.armitage@imperial.ac.uk〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20559385" target="_blank"〉PubMed〈/a〉
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  • 31
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    Nature Publishing Group (NPG)
    Publication Date: 2010-02-25
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉England, John -- England -- Nature. 2010 Jan 14;463(7278):159. doi: 10.1038/463159a.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉NSERC Northern Research Chair at the University of Alberta, Edmonton, Alberta T6G 2E3, Canada. john.england@ualberta.ca〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20075900" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Arctic Regions ; Canada ; Ecology/*economics/instrumentation ; *Ecosystem ; Ice Cover ; Leadership ; Research/*economics/instrumentation ; Research Support as Topic/economics/*organization & administration
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  • 32
    Publication Date: 2010-12-15
    Description: Global systematics in the location of volcanic arcs above subduction zones are widely considered to be a clue to the melting processes that occur at depth, and the locations of the arcs have often been explained in terms of the release of hydrous fluids near the top of the subducting slab (see, for example, refs 3-6). Grove et al. conclude that arc volcano location is controlled by melting in the mantle at temperatures above the water-saturated upper-mantle solidus and below the upper limit of stability of the mineral chlorite and in particular, that the arc fronts lie directly above the shallowest point of such melt regions in the mantle. Here we show that this conclusion is incorrect because the calculated arc locations of Grove et al. are in error owing to the inadequate spatial resolution of their numerical models, and because the agreement that they find between predicted and observed systematics arises from a spurious correlation between calculated arc location and slab dip. A more informative conclusion to draw from their experiments is that the limits of chlorite stability (figure 1b of ref. 7) cannot explain the global systematics in the depth to the slab beneath the sharply localized arc fronts.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉England, Philip C -- Katz, Richard F -- England -- Nature. 2010 Dec 9;468(7325):E6-7; discussion E7-8. doi: 10.1038/nature09154.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Earth Sciences, Parks Road, Oxford OX1 3PR, UK. philip.england@earth.ox.ac.uk〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21150944" target="_blank"〉PubMed〈/a〉
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  • 33
    Publication Date: 2010-12-03
    Description: The multi-subunit DNA-dependent RNA polymerase (RNAP) is the principal enzyme of transcription for gene expression. Transcription is regulated by various transcription factors. Gre factor homologue 1 (Gfh1), found in the Thermus genus, is a close homologue of the well-conserved bacterial transcription factor GreA, and inhibits transcription initiation and elongation by binding directly to RNAP. The structural basis of transcription inhibition by Gfh1 has remained elusive, although the crystal structures of RNAP and Gfh1 have been determined separately. Here we report the crystal structure of Thermus thermophilus RNAP complexed with Gfh1. The amino-terminal coiled-coil domain of Gfh1 fully occludes the channel formed between the two central modules of RNAP; this channel would normally be used for nucleotide triphosphate (NTP) entry into the catalytic site. Furthermore, the tip of the coiled-coil domain occupies the NTP beta-gamma phosphate-binding site. The NTP-entry channel is expanded, because the central modules are 'ratcheted' relative to each other by approximately 7 degrees , as compared with the previously reported elongation complexes. This 'ratcheted state' is an alternative structural state, defined by a newly acquired contact between the central modules. Therefore, the shape of Gfh1 is appropriate to maintain RNAP in the ratcheted state. Simultaneously, the ratcheting expands the nucleic-acid-binding channel, and kinks the bridge helix, which connects the central modules. Taken together, the present results reveal that Gfh1 inhibits transcription by preventing NTP binding and freezing RNAP in the alternative structural state. The ratcheted state might also be associated with other aspects of transcription, such as RNAP translocation and transcription termination.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Tagami, Shunsuke -- Sekine, Shun-Ichi -- Kumarevel, Thirumananseri -- Hino, Nobumasa -- Murayama, Yuko -- Kamegamori, Syunsuke -- Yamamoto, Masaki -- Sakamoto, Kensaku -- Yokoyama, Shigeyuki -- England -- Nature. 2010 Dec 16;468(7326):978-82. doi: 10.1038/nature09573. Epub 2010 Dec 1.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biophysics and Biochemistry, Graduate School of Science, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21124318" target="_blank"〉PubMed〈/a〉
    Keywords: Bacterial Proteins/*chemistry/*metabolism ; Crystallography, X-Ray ; DNA/chemistry/metabolism ; DNA-Directed RNA Polymerases/*chemistry/*metabolism ; Models, Molecular ; Protein Conformation ; Thermus thermophilus/chemistry/*enzymology ; *Transcription, Genetic
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  • 34
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    Nature Publishing Group (NPG)
    Publication Date: 2010-11-05
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hinsen, Konrad -- England -- Nature. 2010 Nov 4;468(7320):37. doi: 10.1038/468037b.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21048747" target="_blank"〉PubMed〈/a〉
    Keywords: *Editorial Policies ; *Motivation ; Periodicals as Topic/standards/*trends ; *Research Personnel/psychology ; *Software/supply & distribution
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  • 35
    Publication Date: 2010-08-27
    Description: The causes of amyotrophic lateral sclerosis (ALS), a devastating human neurodegenerative disease, are poorly understood, although the protein TDP-43 has been suggested to have a critical role in disease pathogenesis. Here we show that ataxin 2 (ATXN2), a polyglutamine (polyQ) protein mutated in spinocerebellar ataxia type 2, is a potent modifier of TDP-43 toxicity in animal and cellular models. ATXN2 and TDP-43 associate in a complex that depends on RNA. In spinal cord neurons of ALS patients, ATXN2 is abnormally localized; likewise, TDP-43 shows mislocalization in spinocerebellar ataxia type 2. To assess the involvement of ATXN2 in ALS, we analysed the length of the polyQ repeat in the ATXN2 gene in 915 ALS patients. We found that intermediate-length polyQ expansions (27-33 glutamines) in ATXN2 were significantly associated with ALS. These data establish ATXN2 as a relatively common ALS susceptibility gene. Furthermore, these findings indicate that the TDP-43-ATXN2 interaction may be a promising target for therapeutic intervention in ALS and other TDP-43 proteinopathies.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2965417/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2965417/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Elden, Andrew C -- Kim, Hyung-Jun -- Hart, Michael P -- Chen-Plotkin, Alice S -- Johnson, Brian S -- Fang, Xiaodong -- Armakola, Maria -- Geser, Felix -- Greene, Robert -- Lu, Min Min -- Padmanabhan, Arun -- Clay-Falcone, Dana -- McCluskey, Leo -- Elman, Lauren -- Juhr, Denise -- Gruber, Peter J -- Rub, Udo -- Auburger, Georg -- Trojanowski, John Q -- Lee, Virginia M-Y -- Van Deerlin, Vivianna M -- Bonini, Nancy M -- Gitler, Aaron D -- 1DP2OD004417-01/OD/NIH HHS/ -- 1R01NS065317-01/NS/NINDS NIH HHS/ -- AG-10124/AG/NIA NIH HHS/ -- AG-17586/AG/NIA NIH HHS/ -- DP2 OD004417/OD/NIH HHS/ -- DP2 OD004417-01/OD/NIH HHS/ -- K08 AG-033101-01/AG/NIA NIH HHS/ -- P01 AG-09215/AG/NIA NIH HHS/ -- R01 NS065317/NS/NINDS NIH HHS/ -- R01 NS065317-01/NS/NINDS NIH HHS/ -- R01 NS065317-02/NS/NINDS NIH HHS/ -- R01 NS065317-03/NS/NINDS NIH HHS/ -- Howard Hughes Medical Institute/ -- England -- Nature. 2010 Aug 26;466(7310):1069-75. doi: 10.1038/nature09320.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20740007" target="_blank"〉PubMed〈/a〉
    Keywords: Adult ; Aged ; Aged, 80 and over ; Amyotrophic Lateral Sclerosis/*genetics ; Animals ; Ataxins ; Cell Line ; DNA-Binding Proteins/metabolism/toxicity ; Drosophila/drug effects/genetics ; Female ; *Genetic Predisposition to Disease ; Humans ; Male ; Middle Aged ; Nerve Tissue Proteins/*genetics/*metabolism ; Neurons/pathology ; Peptides/chemistry/*genetics ; Repetitive Sequences, Amino Acid/*genetics ; Risk Factors ; Saccharomyces cerevisiae/drug effects/genetics/metabolism ; Young Adult
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  • 36
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    Nature Publishing Group (NPG)
    Publication Date: 2010-10-15
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Nesvorny, David -- England -- Nature. 2010 Oct 14;467(7317):792-3. doi: 10.1038/467792a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20944731" target="_blank"〉PubMed〈/a〉
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  • 37
    Publication Date: 2010-03-20
    Description: Cobalamin (Cbl, vitamin B(12)) is a bacterial organic compound and an essential coenzyme in mammals, which take it up from the diet. This occurs by the combined action of the gastric intrinsic factor (IF) and the ileal endocytic cubam receptor formed by the 460-kilodalton (kDa) protein cubilin and the 45-kDa transmembrane protein amnionless. Loss of function of any of these proteins ultimately leads to Cbl deficiency in man. Here we present the crystal structure of the complex between IF-Cbl and the cubilin IF-Cbl-binding-region (CUB(5-8)) determined at 3.3 A resolution. The structure provides insight into how several CUB (for 'complement C1r/C1s, Uegf, Bmp1') domains collectively function as modular ligand-binding regions, and how two distant CUB domains embrace the Cbl molecule by binding the two IF domains in a Ca(2+)-dependent manner. This dual-point model provides a probable explanation of how Cbl indirectly induces ligand-receptor coupling. Finally, the comparison of Ca(2+)-binding CUB domains and the low-density lipoprotein (LDL) receptor-type A modules suggests that the electrostatic pairing of a basic ligand arginine/lysine residue with Ca(2+)-coordinating acidic aspartates/glutamates is a common theme of Ca(2+)-dependent ligand-receptor interactions.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Andersen, Christian Brix Folsted -- Madsen, Mette -- Storm, Tina -- Moestrup, Soren K -- Andersen, Gregers R -- England -- Nature. 2010 Mar 18;464(7287):445-8. doi: 10.1038/nature08874.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Medical Biochemistry, Aarhus University, 8000 Aarhus C, Denmark.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20237569" target="_blank"〉PubMed〈/a〉
    Keywords: Aspartic Acid/metabolism ; Binding Sites ; Calcium/metabolism ; Crystallography, X-Ray ; Glutamic Acid/metabolism ; Humans ; Intrinsic Factor/*chemistry/*metabolism ; Ligands ; Models, Molecular ; Protein Binding ; Protein Structure, Tertiary ; Receptors, Cell Surface/*chemistry/*metabolism ; Static Electricity ; Vitamin B 12/*chemistry/*metabolism
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  • 38
    Publication Date: 2010-07-03
    Description: An era of exploring the interactions of high-intensity, hard X-rays with matter has begun with the start-up of a hard-X-ray free-electron laser, the Linac Coherent Light Source (LCLS). Understanding how electrons in matter respond to ultra-intense X-ray radiation is essential for all applications. Here we reveal the nature of the electronic response in a free atom to unprecedented high-intensity, short-wavelength, high-fluence radiation (respectively 10(18) W cm(-2), 1.5-0.6 nm, approximately 10(5) X-ray photons per A(2)). At this fluence, the neon target inevitably changes during the course of a single femtosecond-duration X-ray pulse-by sequentially ejecting electrons-to produce fully-stripped neon through absorption of six photons. Rapid photoejection of inner-shell electrons produces 'hollow' atoms and an intensity-induced X-ray transparency. Such transparency, due to the presence of inner-shell vacancies, can be induced in all atomic, molecular and condensed matter systems at high intensity. Quantitative comparison with theory allows us to extract LCLS fluence and pulse duration. Our successful modelling of X-ray/atom interactions using a straightforward rate equation approach augurs favourably for extension to complex systems.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Young, L -- Kanter, E P -- Krassig, B -- Li, Y -- March, A M -- Pratt, S T -- Santra, R -- Southworth, S H -- Rohringer, N -- Dimauro, L F -- Doumy, G -- Roedig, C A -- Berrah, N -- Fang, L -- Hoener, M -- Bucksbaum, P H -- Cryan, J P -- Ghimire, S -- Glownia, J M -- Reis, D A -- Bozek, J D -- Bostedt, C -- Messerschmidt, M -- England -- Nature. 2010 Jul 1;466(7302):56-61. doi: 10.1038/nature09177.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Argonne National Laboratory, Argonne, Illinois 60439, USA. young@anl.gov〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20596013" target="_blank"〉PubMed〈/a〉
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  • 39
    Publication Date: 2010-05-28
    Description: The differential formation of excitatory (glutamate-mediated) and inhibitory (GABA-mediated) synapses is a critical step for the proper functioning of the brain. An imbalance in these synapses may lead to various neurological disorders such as autism, schizophrenia, Tourette's syndrome and epilepsy. Synapses are formed through communication between the appropriate synaptic partners. However, the molecular mechanisms that mediate the formation of specific synaptic types are not known. Here we show that two members of the fibroblast growth factor (FGF) family, FGF22 and FGF7, promote the organization of excitatory and inhibitory presynaptic terminals, respectively, as target-derived presynaptic organizers. FGF22 and FGF7 are expressed by CA3 pyramidal neurons in the hippocampus. The differentiation of excitatory or inhibitory nerve terminals on dendrites of CA3 pyramidal neurons is specifically impaired in mutants lacking FGF22 or FGF7. These presynaptic defects are rescued by postsynaptic expression of the appropriate FGF. FGF22-deficient mice are resistant to epileptic seizures, and FGF7-deficient mice are prone to them, as expected from the alterations in excitatory/inhibitory balance. Differential effects of FGF22 and FGF7 involve both their distinct synaptic localizations and their use of different signalling pathways. These results demonstrate that specific FGFs act as target-derived presynaptic organizers and help to organize specific presynaptic terminals in the mammalian brain.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4137042/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4137042/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Terauchi, Akiko -- Johnson-Venkatesh, Erin M -- Toth, Anna B -- Javed, Danish -- Sutton, Michael A -- Umemori, Hisashi -- R01 NS070005/NS/NINDS NIH HHS/ -- England -- Nature. 2010 Jun 10;465(7299):783-7. doi: 10.1038/nature09041. Epub 2010 May 26.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Molecular and Behavioral Neuroscience Institute, University of Michigan Medical School, Ann Arbor, Michigan 48109-2200, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20505669" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Cell Differentiation ; Cells, Cultured ; Dendrites/metabolism ; Disease Susceptibility ; Epilepsy/chemically induced/genetics/physiopathology ; Excitatory Postsynaptic Potentials/*physiology ; Fibroblast Growth Factor 7/deficiency/genetics/*metabolism ; Fibroblast Growth Factors/deficiency/genetics/*metabolism ; Gene Expression Profiling ; Glutamic Acid/metabolism ; Hippocampus/cytology/embryology/metabolism/pathology ; In Situ Hybridization ; Inhibitory Postsynaptic Potentials/*physiology ; Kindling, Neurologic ; Mice ; Mice, Knockout ; Miniature Postsynaptic Potentials/physiology ; Presynaptic Terminals/classification/metabolism/pathology/ultrastructure ; Pyramidal Cells/cytology/metabolism/pathology ; Receptors, Fibroblast Growth Factor/metabolism ; Seizures/chemically induced/genetics/radiotherapy ; Synapses/*classification/*metabolism/pathology/ultrastructure ; Synaptic Transmission ; Synaptic Vesicles/metabolism/pathology/ultrastructure ; gamma-Aminobutyric Acid/metabolism
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  • 40
    Publication Date: 2010-05-28
    Description: The polar layered deposits of Mars contain the planet's largest known reservoir of water ice and the prospect of revealing a detailed Martian palaeoclimate record, but the mechanisms responsible for the formation of the dominant features of the north polar layered deposits (NPLD) are unclear, despite decades of debate. Stratigraphic analyses of the exposed portions of Chasma Boreale-a large canyon 500 km long, up to 100 km wide, and nearly 2 km deep-have led most researchers to favour an erosional process for its formation following initial NPLD accumulation. Candidate mechanisms include the catastrophic outburst of water, protracted basal melting, erosional undercutting, aeolian downcutting and a combination of these processes. Here we use new data from the Mars Reconnaissance Orbiter to show that Chasma Boreale is instead a long-lived, complex feature resulting primarily from non-uniform accumulation of the NPLD. The initial valley that later became Chasma Boreale was matched by a second, equally large valley that was completely filled in by subsequent deposition, leaving no evidence on the surface to indicate its former presence. We further demonstrate that topography existing before the NPLD began accumulating influenced successive episodes of deposition and erosion, resulting in most of the present-day topography. Long-term and large-scale patterns of mass balance achieved through sedimentary processes, rather than catastrophic events, ice flow or highly focused erosion, have produced the largest geomorphic anomaly in the north polar ice of Mars.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Holt, J W -- Fishbaugh, K E -- Byrne, S -- Christian, S -- Tanaka, K -- Russell, P S -- Herkenhoff, K E -- Safaeinili, A -- Putzig, N E -- Phillips, R J -- England -- Nature. 2010 May 27;465(7297):446-9. doi: 10.1038/nature09050.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute for Geophysics, Jackson School of Geosciences, University of Texas at Austin, Austin 78758, Texas, USA. jack@ig.utexas.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20505721" target="_blank"〉PubMed〈/a〉
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  • 41
    Publication Date: 2010-03-12
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Sanderson, Katharine -- England -- Nature. 2010 Mar 11;464(7286):158-9. doi: 10.1038/464158a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20220817" target="_blank"〉PubMed〈/a〉
    Keywords: Bioengineering/methods/*trends ; DNA/*chemistry/metabolism ; Nanostructures/*chemistry ; Nanotechnology/methods/*trends ; Nucleic Acid Conformation
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  • 42
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    Unknown
    Nature Publishing Group (NPG)
    Publication Date: 2010-11-12
    Description: 〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4243609/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4243609/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lee, Chi-Hon -- ZIA HD008776-05/Intramural NIH HHS/ -- England -- Nature. 2010 Nov 11;468(7321):178-9. doi: 10.1038/468178a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21068820" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Calcium Signaling/radiation effects ; Drosophila melanogaster/cytology/metabolism/*physiology/radiation effects ; Gap Junctions/metabolism/radiation effects ; Light ; Models, Neurological ; *Motion ; Motion Perception/*physiology/radiation effects ; Optic Lobe, Nonmammalian/cytology/physiology/radiation effects ; Photoreceptor Cells, Invertebrate/metabolism/radiation effects ; Vision, Ocular/*physiology/radiation effects ; Visual Pathways/cytology/*physiology/radiation effects
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  • 43
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    Nature Publishing Group (NPG)
    Publication Date: 2010-04-03
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Aspelmeyer, Markus -- England -- Nature. 2010 Apr 1;464(7289):685-6. doi: 10.1038/464685a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20360725" target="_blank"〉PubMed〈/a〉
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  • 44
    Publication Date: 2010-01-16
    Description: Rho is the essential RNA helicase that sets the borders between transcription units and adjusts transcriptional yield to translational needs in bacteria. Although Rho was the first termination factor to be discovered, the actual mechanism by which it reaches and disrupts the elongation complex (EC) is unknown. Here we show that the termination-committed Rho molecule associates with RNA polymerase (RNAP) throughout the transcription cycle; that is, it does not require the nascent transcript for initial binding. Moreover, the formation of the RNAP-Rho complex is crucial for termination. We show further that Rho-dependent termination is a two-step process that involves rapid EC inactivation (trap) and a relatively slow dissociation. Inactivation is the critical rate-limiting step that establishes the position of the termination site. The trap mechanism depends on the allosterically induced rearrangement of the RNAP catalytic centre by means of the evolutionarily conserved mobile trigger-loop domain, which is also required for EC dissociation. The key structural and functional similarities, which we found between Rho-dependent and intrinsic (Rho-independent) termination pathways, argue that the allosteric mechanism of termination is general and likely to be preserved for all cellular RNAPs throughout evolution.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2929367/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2929367/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Epshtein, Vitaly -- Dutta, Dipak -- Wade, Joseph -- Nudler, Evgeny -- R01 GM058750/GM/NIGMS NIH HHS/ -- R01 GM058750-12/GM/NIGMS NIH HHS/ -- R01 GM072814/GM/NIGMS NIH HHS/ -- R01GM58750/GM/NIGMS NIH HHS/ -- England -- Nature. 2010 Jan 14;463(7278):245-9. doi: 10.1038/nature08669.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry, New York University School of Medicine, New York, New York 10016, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20075920" target="_blank"〉PubMed〈/a〉
    Keywords: *Allosteric Regulation ; Binding Sites ; Biocatalysis ; Catalytic Domain ; DNA-Directed RNA Polymerases/genetics/*metabolism ; Dicarboxylic Acids/pharmacology ; Escherichia coli/enzymology ; Kinetics ; Mutant Proteins/genetics/metabolism ; Mutation/genetics ; Organophosphorus Compounds/pharmacology ; Protein Binding ; Rho Factor/*metabolism ; Templates, Genetic ; Transcription, Genetic/drug effects/*physiology
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  • 45
    Publication Date: 2010-06-08
    Description: Autophagy is an evolutionarily conserved process by which cytoplasmic proteins and organelles are catabolized. During starvation, the protein TOR (target of rapamycin), a nutrient-responsive kinase, is inhibited, and this induces autophagy. In autophagy, double-membrane autophagosomes envelop and sequester intracellular components and then fuse with lysosomes to form autolysosomes, which degrade their contents to regenerate nutrients. Current models of autophagy terminate with the degradation of the autophagosome cargo in autolysosomes, but the regulation of autophagy in response to nutrients and the subsequent fate of the autolysosome are poorly understood. Here we show that mTOR signalling in rat kidney cells is inhibited during initiation of autophagy, but reactivated by prolonged starvation. Reactivation of mTOR is autophagy-dependent and requires the degradation of autolysosomal products. Increased mTOR activity attenuates autophagy and generates proto-lysosomal tubules and vesicles that extrude from autolysosomes and ultimately mature into functional lysosomes, thereby restoring the full complement of lysosomes in the cell-a process we identify in multiple animal species. Thus, an evolutionarily conserved cycle in autophagy governs nutrient sensing and lysosome homeostasis during starvation.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2920749/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2920749/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Yu, Li -- McPhee, Christina K -- Zheng, Lixin -- Mardones, Gonzalo A -- Rong, Yueguang -- Peng, Junya -- Mi, Na -- Zhao, Ying -- Liu, Zhihua -- Wan, Fengyi -- Hailey, Dale W -- Oorschot, Viola -- Klumperman, Judith -- Baehrecke, Eric H -- Lenardo, Michael J -- 2010CB833704/CB/NCI NIH HHS/ -- GM079431/GM/NIGMS NIH HHS/ -- R01 GM079431/GM/NIGMS NIH HHS/ -- Z01 AI000718-13/Intramural NIH HHS/ -- Z01 AI000718-14/Intramural NIH HHS/ -- ZIA AI000718-15/Intramural NIH HHS/ -- England -- Nature. 2010 Jun 17;465(7300):942-6. doi: 10.1038/nature09076. Epub 2010 Jun 6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory of Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20526321" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Autophagy/*physiology ; Cell Line ; Cercopithecus aethiops ; HeLa Cells ; Homeostasis/physiology ; Humans ; Intracellular Signaling Peptides and Proteins/*metabolism ; Lysosomes/*metabolism/ultrastructure ; *Nutritional Physiological Phenomena ; Protein-Serine-Threonine Kinases/*metabolism ; Rats ; Signal Transduction ; TOR Serine-Threonine Kinases ; Vero Cells
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  • 46
    Publication Date: 2010-04-30
    Description: It has been suggested that Earth's current supply of water was delivered by asteroids, some time after the collision that produced the Moon (which would have vaporized any of the pre-existing water). So far, no measurements of water ice on asteroids have been made, but its presence has been inferred from the comet-like activity of several small asteroids, including two members of the Themis dynamical family. Here we report infrared spectra of the asteroid 24 Themis which show that ice and organic compounds are not only present on its surface but also prevalent. Infrared spectral differences between it and other asteroids make 24 Themis unique so far, and our identification of ice and organics agrees with independent results that rule out other compounds as possible sources of the observed spectral structure. The widespread presence of surface ice on 24 Themis is somewhat unexpected because of the relatively short lifetime of exposed ice at this distance ( approximately 3.2 au) from the Sun. Nevertheless, there are several plausible sources, such as a subsurface reservoir that brings water to the surface through 'impact gardening' and/or sublimation.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Campins, Humberto -- Hargrove, Kelsey -- Pinilla-Alonso, Noemi -- Howell, Ellen S -- Kelley, Michael S -- Licandro, Javier -- Mothe-Diniz, T -- Fernandez, Y -- Ziffer, Julie -- England -- Nature. 2010 Apr 29;464(7293):1320-1. doi: 10.1038/nature09029.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉University of Central Florida, PO Box 162385, Orlando, Florida 32816-2385, USA. campins@physics.ucf.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20428164" target="_blank"〉PubMed〈/a〉
    Keywords: Extraterrestrial Environment/*chemistry ; Ice/*analysis ; *Minor Planets ; Organic Chemicals/*analysis
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  • 47
    Publication Date: 2010-06-04
    Description: An optical quantum computer, powerful enough to solve problems so far intractable using conventional digital logic, requires a large number of entangled photons. At present, entangled-light sources are optically driven with lasers, which are impractical for quantum computing owing to the bulk and complexity of the optics required for large-scale applications. Parametric down-conversion is the most widely used source of entangled light, and has been used to implement non-destructive quantum logic gates. However, these sources are Poissonian and probabilistically emit zero or multiple entangled photon pairs in most cycles, fundamentally limiting the success probability of quantum computational operations. These complications can be overcome by using an electrically driven on-demand source of entangled photon pairs, but so far such a source has not been produced. Here we report the realization of an electrically driven source of entangled photon pairs, consisting of a quantum dot embedded in a semiconductor light-emitting diode (LED) structure. We show that the device emits entangled photon pairs under d.c. and a.c. injection, the latter achieving an entanglement fidelity of up to 0.82. Entangled light with such high fidelity is sufficient for application in quantum relays, in core components of quantum computing such as teleportation, and in entanglement swapping. The a.c. operation of the entangled-light-emitting diode (ELED) indicates its potential function as an on-demand source without the need for a complicated laser driving system; consequently, the ELED is at present the best source on which to base future scalable quantum information applications.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Salter, C L -- Stevenson, R M -- Farrer, I -- Nicoll, C A -- Ritchie, D A -- Shields, A J -- England -- Nature. 2010 Jun 3;465(7298):594-7. doi: 10.1038/nature09078.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Toshiba Research Europe Limited, 208 Cambridge Science Park, Cambridge CB4 0GZ, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20520709" target="_blank"〉PubMed〈/a〉
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  • 48
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    Nature Publishing Group (NPG)
    Publication Date: 2010-02-25
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Cane, Mark A -- England -- Nature. 2010 Jan 14;463(7278):163-4. doi: 10.1038/463163a.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Mark A. Cane is at the Lamont-Doherty Earth Observatory, Columbia University, Palisades, New York 10964-8000, USA. mcane@ldeo.columbia.edu.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20075905" target="_blank"〉PubMed〈/a〉
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  • 49
    Publication Date: 2010-11-19
    Description: Antimatter was first predicted in 1931, by Dirac. Work with high-energy antiparticles is now commonplace, and anti-electrons are used regularly in the medical technique of positron emission tomography scanning. Antihydrogen, the bound state of an antiproton and a positron, has been produced at low energies at CERN (the European Organization for Nuclear Research) since 2002. Antihydrogen is of interest for use in a precision test of nature's fundamental symmetries. The charge conjugation/parity/time reversal (CPT) theorem, a crucial part of the foundation of the standard model of elementary particles and interactions, demands that hydrogen and antihydrogen have the same spectrum. Given the current experimental precision of measurements on the hydrogen atom (about two parts in 10(14) for the frequency of the 1s-to-2s transition), subjecting antihydrogen to rigorous spectroscopic examination would constitute a compelling, model-independent test of CPT. Antihydrogen could also be used to study the gravitational behaviour of antimatter. However, so far experiments have produced antihydrogen that is not confined, precluding detailed study of its structure. Here we demonstrate trapping of antihydrogen atoms. From the interaction of about 10(7) antiprotons and 7 x 10(8) positrons, we observed 38 annihilation events consistent with the controlled release of trapped antihydrogen from our magnetic trap; the measured background is 1.4 +/- 1.4 events. This result opens the door to precision measurements on anti-atoms, which can soon be subjected to the same techniques as developed for hydrogen.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Andresen, G B -- Ashkezari, M D -- Baquero-Ruiz, M -- Bertsche, W -- Bowe, P D -- Butler, E -- Cesar, C L -- Chapman, S -- Charlton, M -- Deller, A -- Eriksson, S -- Fajans, J -- Friesen, T -- Fujiwara, M C -- Gill, D R -- Gutierrez, A -- Hangst, J S -- Hardy, W N -- Hayden, M E -- Humphries, A J -- Hydomako, R -- Jenkins, M J -- Jonsell, S -- Jorgensen, L V -- Kurchaninov, L -- Madsen, N -- Menary, S -- Nolan, P -- Olchanski, K -- Olin, A -- Povilus, A -- Pusa, P -- Robicheaux, F -- Sarid, E -- el Nasr, S Seif -- Silveira, D M -- So, C -- Storey, J W -- Thompson, R I -- van der Werf, D P -- Wurtele, J S -- Yamazaki, Y -- England -- Nature. 2010 Dec 2;468(7324):673-6. doi: 10.1038/nature09610. Epub 2010 Nov 17.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Physics and Astronomy, Aarhus University, DK-8000 Aarhus C, Denmark.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21085118" target="_blank"〉PubMed〈/a〉
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  • 50
    Publication Date: 2010-01-22
    Description: Deformation twinning in crystals is a highly coherent inelastic shearing process that controls the mechanical behaviour of many materials, but its origin and spatio-temporal features are shrouded in mystery. Using micro-compression and in situ nano-compression experiments, here we find that the stress required for deformation twinning increases drastically with decreasing sample size of a titanium alloy single crystal, until the sample size is reduced to one micrometre, below which the deformation twinning is entirely replaced by less correlated, ordinary dislocation plasticity. Accompanying the transition in deformation mechanism, the maximum flow stress of the submicrometre-sized pillars was observed to saturate at a value close to titanium's ideal strength. We develop a 'stimulated slip' model to explain the strong size dependence of deformation twinning. The sample size in transition is relatively large and easily accessible in experiments, making our understanding of size dependence relevant for applications.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Yu, Qian -- Shan, Zhi-Wei -- Li, Ju -- Huang, Xiaoxu -- Xiao, Lin -- Sun, Jun -- Ma, Evan -- England -- Nature. 2010 Jan 21;463(7279):335-8. doi: 10.1038/nature08692.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Center for Advancing Materials Performance from the Nanoscale (CAMP-Nano), State Key Laboratory for Mechanical Behavior of Materials, Xi'an Jiaotong University, Xi'an, 710049, China.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20090749" target="_blank"〉PubMed〈/a〉
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  • 51
    Publication Date: 2010-12-24
    Description: The unusual capability of solid crystalline materials to deform plastically, known as superplasticity, has been found in metals and even in ceramics. Such superplastic behaviour has been speculated for decades to take place in geological materials, ranging from surface ice sheets to the Earth's lower mantle. In materials science, superplasticity is confirmed when the material deforms with large tensile strain without failure; however, no experimental studies have yet shown this characteristic in geomaterials. Here we show that polycrystalline forsterite + periclase (9:1) and forsterite + enstatite + diopside (7:2.5:0.5), which are good analogues for Earth's mantle, undergo homogeneous elongation of up to 500 per cent under subsolidus conditions. Such superplastic deformation is accompanied by strain hardening, which is well explained by the grain size sensitivity of superplasticity and grain growth under grain switching conditions (that is, grain boundary sliding); grain boundary sliding is the main deformation mechanism for superplasticity. We apply the observed strain-grain size-viscosity relationship to portions of the mantle where superplasticity has been presumed to take place, such as localized shear zones in the upper mantle and within subducting slabs penetrating into the transition zone and lower mantle after a phase transformation. Calculations show that superplastic flow in the mantle is inevitably accompanied by significant grain growth that can bring fine grained (〈/=1 mum) rocks to coarse-grained (1-10 mm) aggregates, resulting in increasing mantle viscosity and finally termination of superplastic flow.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hiraga, Takehiko -- Miyazaki, Tomonori -- Tasaka, Miki -- Yoshida, Hidehiro -- England -- Nature. 2010 Dec 23;468(7327):1091-4. doi: 10.1038/nature09685.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Earthquake Research Institute, University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan. hiraga@eri.u-tokyo.ac.jp〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21179165" target="_blank"〉PubMed〈/a〉
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