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  • Springer Nature  (98)
  • Wiley  (53)
  • Nature Publishing Group (NPG)  (18)
  • American Physical Society (APS)
  • 2010-2014  (169)
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  • 2010  (169)
  • 1
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    Validation of recombinant Sendai virus in a non-natural host model (2010)
    Springer Nature
    Details
    Publication Date: 2010-10-21
    Print ISSN: 0969-7128
    Electronic ISSN: 1476-5462
    Topics: Biology , Medicine
    Published by Springer Nature
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  • 2
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    Prospective collection of tissue samples at autopsy in children with diffuse intrinsic pontine glioma (2010)
    Wiley
    Details
    Publication Date: 2010-08-19
    Print ISSN: 0008-543X
    Electronic ISSN: 1097-0142
    Topics: Biology , Medicine
    Published by Wiley on behalf of American Cancer Society.
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  • 3
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    The contribution of synchrotron X-ray computed microtomography to understanding volcanic processes (2010)
    Wiley
    Details
    Publication Date: 2017-04-04
    Description: A series of computer microtomography experiments are reported which were performed by using a third-generation synchrotron radiation source on volcanic rocks from various active hazardous volcanoes in Italy and other volcanic areas in the world. The applied technique allowed the internal structure of the investigated material to be accurately imaged at the micrometer scale and three-dimensional views of the investigated samples to be produced as well as three-dimensional quantitative measurements of textural features. Thegeometryof thevesicle (gas-filledvoid) network in volcanic products of both basaltic and trachytic compositions were particularly focused on, as vesicle textures are directly linked to the dynamics of volcano degassing. This investigation provided novel insights into modes of gas exsolution, transport and loss in magmas that were not recognized in previous studies using solely conventional two- dimensional imaging techniques. The results of this study are important to understanding the behaviour of volcanoes and can be combined with other geosciences disciplines to forecast their future activity.
    Description: In press
    Description: 2.3. TTC - Laboratori di chimica e fisica delle rocce
    Description: JCR Journal
    Description: reserved
    Keywords: high-resolution three-dimensional imaging ; X-ray computed microtomography ; volcanic eruptions ; volcanic rock textures ; 04. Solid Earth::04.08. Volcanology::04.08.05. Volcanic rocks ; 04. Solid Earth::04.08. Volcanology::04.08.07. Instruments and techniques
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
    Type: article
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  • 4
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    Water Balance and Nitrate Leaching under Corn in Kura Clover Living Mulch (2010)
    Wiley
    Details
    Publication Date: 2010-07-01
    Print ISSN: 0002-1962
    Electronic ISSN: 1435-0645
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Published by Wiley
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  • 5
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    Numbers War (2010)
    Springer Nature
    Details
    Publication Date: 2010-03-01
    Print ISSN: 0036-8733
    Electronic ISSN: 1946-7087
    Topics: Biology , Natural Sciences in General , Physics
    Published by Springer Nature
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  • 6
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    Polymorphism control of superconductivity and magnetism in Cs(3)C(60) close to the Mott transition (2010)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2010-05-21
    Description: The crystal structure of a solid controls the interactions between the electronically active units and thus its electronic properties. In the high-temperature superconducting copper oxides, only one spatial arrangement of the electronically active Cu(2+) units-a two-dimensional square lattice-is available to study the competition between the cooperative electronic states of magnetic order and superconductivity. Crystals of the spherical molecular C(60)(3-) anion support both superconductivity and magnetism but can consist of fundamentally distinct three-dimensional arrangements of the anions. Superconductivity in the A(3)C(60) (A = alkali metal) fullerides has been exclusively associated with face-centred cubic (f.c.c.) packing of C(60)(3-) (refs 2, 3), but recently the most expanded (and thus having the highest superconducting transition temperature, T(c); ref. 4) composition Cs(3)C(60) has been isolated as a body-centred cubic (b.c.c.) packing, which supports both superconductivity and magnetic order. Here we isolate the f.c.c. polymorph of Cs(3)C(60) to show how the spatial arrangement of the electronically active units controls the competing superconducting and magnetic electronic ground states. Unlike all the other f.c.c. A(3)C(60) fullerides, f.c.c. Cs(3)C(60) is not a superconductor but a magnetic insulator at ambient pressure, and becomes superconducting under pressure. The magnetic ordering occurs at an order of magnitude lower temperature in the geometrically frustrated f.c.c. polymorph (Neel temperature T(N) = 2.2 K) than in the b.c.c.-based packing (T(N) = 46 K). The different lattice packings of C(60)(3-) change T(c) from 38 K in b.c.c. Cs(3)C(60) to 35 K in f.c.c. Cs(3)C(60) (the highest found in the f.c.c. A(3)C(60) family). The existence of two superconducting packings of the same electronically active unit reveals that T(c) scales universally in a structure-independent dome-like relationship with proximity to the Mott metal-insulator transition, which is governed by the role of electron correlations characteristic of high-temperature superconducting materials other than fullerides.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ganin, Alexey Y -- Takabayashi, Yasuhiro -- Jeglic, Peter -- Arcon, Denis -- Potocnik, Anton -- Baker, Peter J -- Ohishi, Yasuo -- McDonald, Martin T -- Tzirakis, Manolis D -- McLennan, Alec -- Darling, George R -- Takata, Masaki -- Rosseinsky, Matthew J -- Prassides, Kosmas -- England -- Nature. 2010 Jul 8;466(7303):221-5. doi: 10.1038/nature09120. Epub 2010 May 19.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, University of Liverpool, Liverpool L69 7ZD, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20485340" target="_blank"〉PubMed〈/a〉
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 7
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    Comparative genomics reveals mobile pathogenicity chromosomes in Fusarium (2010)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2010-03-20
    Description: Fusarium species are among the most important phytopathogenic and toxigenic fungi. To understand the molecular underpinnings of pathogenicity in the genus Fusarium, we compared the genomes of three phenotypically diverse species: Fusarium graminearum, Fusarium verticillioides and Fusarium oxysporum f. sp. lycopersici. Our analysis revealed lineage-specific (LS) genomic regions in F. oxysporum that include four entire chromosomes and account for more than one-quarter of the genome. LS regions are rich in transposons and genes with distinct evolutionary profiles but related to pathogenicity, indicative of horizontal acquisition. Experimentally, we demonstrate the transfer of two LS chromosomes between strains of F. oxysporum, converting a non-pathogenic strain into a pathogen. Transfer of LS chromosomes between otherwise genetically isolated strains explains the polyphyletic origin of host specificity and the emergence of new pathogenic lineages in F. oxysporum. These findings put the evolution of fungal pathogenicity into a new perspective.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3048781/" 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/PMC3048781/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ma, Li-Jun -- van der Does, H Charlotte -- Borkovich, Katherine A -- Coleman, Jeffrey J -- Daboussi, Marie-Josee -- Di Pietro, Antonio -- Dufresne, Marie -- Freitag, Michael -- Grabherr, Manfred -- Henrissat, Bernard -- Houterman, Petra M -- Kang, Seogchan -- Shim, Won-Bo -- Woloshuk, Charles -- Xie, Xiaohui -- Xu, Jin-Rong -- Antoniw, John -- Baker, Scott E -- Bluhm, Burton H -- Breakspear, Andrew -- Brown, Daren W -- Butchko, Robert A E -- Chapman, Sinead -- Coulson, Richard -- Coutinho, Pedro M -- Danchin, Etienne G J -- Diener, Andrew -- Gale, Liane R -- Gardiner, Donald M -- Goff, Stephen -- Hammond-Kosack, Kim E -- Hilburn, Karen -- Hua-Van, Aurelie -- Jonkers, Wilfried -- Kazan, Kemal -- Kodira, Chinnappa D -- Koehrsen, Michael -- Kumar, Lokesh -- Lee, Yong-Hwan -- Li, Liande -- Manners, John M -- Miranda-Saavedra, Diego -- Mukherjee, Mala -- Park, Gyungsoon -- Park, Jongsun -- Park, Sook-Young -- Proctor, Robert H -- Regev, Aviv -- Ruiz-Roldan, M Carmen -- Sain, Divya -- Sakthikumar, Sharadha -- Sykes, Sean -- Schwartz, David C -- Turgeon, B Gillian -- Wapinski, Ilan -- Yoder, Olen -- Young, Sarah -- Zeng, Qiandong -- Zhou, Shiguo -- Galagan, James -- Cuomo, Christina A -- Kistler, H Corby -- Rep, Martijn -- BBS/E/C/00004973/Biotechnology and Biological Sciences Research Council/United Kingdom -- DP1 OD003958/OD/NIH HHS/ -- R01 GM086565/GM/NIGMS NIH HHS/ -- R01 GM086565-03/GM/NIGMS NIH HHS/ -- R01 HG000225/HG/NHGRI NIH HHS/ -- England -- Nature. 2010 Mar 18;464(7287):367-73. doi: 10.1038/nature08850.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉The Broad Institute, Cambridge, Massachusetts 02141, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20237561" target="_blank"〉PubMed〈/a〉
    Keywords: Chromosomes, Fungal/*genetics ; Evolution, Molecular ; Fusarium/classification/*genetics/*pathogenicity ; Genome, Fungal/*genetics ; *Genomics ; Host-Parasite Interactions/genetics ; Multigene Family/genetics ; Phenotype ; Phylogeny ; Proteome/genetics ; Sequence Analysis, DNA ; Synteny/genetics ; Virulence/genetics
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 8
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    Predicting protein structures with a multiplayer online game (2010)
    Nature Publishing Group (NPG)
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    Publication Date: 2010-08-06
    Description: People exert large amounts of problem-solving effort playing computer games. Simple image- and text-recognition tasks have been successfully 'crowd-sourced' through games, but it is not clear if more complex scientific problems can be solved with human-directed computing. Protein structure prediction is one such problem: locating the biologically relevant native conformation of a protein is a formidable computational challenge given the very large size of the search space. Here we describe Foldit, a multiplayer online game that engages non-scientists in solving hard prediction problems. Foldit players interact with protein structures using direct manipulation tools and user-friendly versions of algorithms from the Rosetta structure prediction methodology, while they compete and collaborate to optimize the computed energy. We show that top-ranked Foldit players excel at solving challenging structure refinement problems in which substantial backbone rearrangements are necessary to achieve the burial of hydrophobic residues. Players working collaboratively develop a rich assortment of new strategies and algorithms; unlike computational approaches, they explore not only the conformational space but also the space of possible search strategies. The integration of human visual problem-solving and strategy development capabilities with traditional computational algorithms through interactive multiplayer games is a powerful new approach to solving computationally-limited scientific problems.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2956414/" 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/PMC2956414/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Cooper, Seth -- Khatib, Firas -- Treuille, Adrien -- Barbero, Janos -- Lee, Jeehyung -- Beenen, Michael -- Leaver-Fay, Andrew -- Baker, David -- Popovic, Zoran -- Players, Foldit -- Howard Hughes Medical Institute/ -- England -- Nature. 2010 Aug 5;466(7307):756-60. doi: 10.1038/nature09304.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Computer Science and Engineering, University of Washington, Box 352350, Seattle, Washington 98195, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20686574" target="_blank"〉PubMed〈/a〉
    Keywords: Algorithms ; Computational Biology/*methods ; Computer Graphics ; Computer Simulation ; Cooperative Behavior ; Cues ; *Games, Experimental ; *Group Processes ; Humans ; Hydrogen Bonding ; Hydrophobic and Hydrophilic Interactions ; Imaging, Three-Dimensional ; *Internet ; Leisure Activities ; Models, Molecular ; Nuclear Magnetic Resonance, Biomolecular ; Photic Stimulation ; *Problem Solving ; Protein Conformation ; *Protein Folding ; Proteins/*chemistry/metabolism ; Stochastic Processes ; Thermodynamics
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 9
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    Intense star formation within resolved compact regions in a galaxy at z = 2.3 (2010)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2010-03-23
    Description: Massive galaxies in the early Universe have been shown to be forming stars at surprisingly high rates. Prominent examples are dust-obscured galaxies which are luminous when observed at sub-millimetre wavelengths and which may be forming stars at a rate of 1,000 solar masses (M(middle dot in circle)) per year. These intense bursts of star formation are believed to be driven by mergers between gas-rich galaxies. Probing the properties of individual star-forming regions within these galaxies, however, is beyond the spatial resolution and sensitivity of even the largest telescopes at present. Here we report observations of the sub-millimetre galaxy SMMJ2135-0102 at redshift z = 2.3259, which has been gravitationally magnified by a factor of 32 by a massive foreground galaxy cluster lens. This magnification, when combined with high-resolution sub-millimetre imaging, resolves the star-forming regions at a linear scale of only 100 parsecs. We find that the luminosity densities of these star-forming regions are comparable to the dense cores of giant molecular clouds in the local Universe, but they are about a hundred times larger and 10(7) times more luminous. Although vigorously star-forming, the underlying physics of the star-formation processes at z approximately 2 appears to be similar to that seen in local galaxies, although the energetics are unlike anything found in the present-day Universe.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Swinbank, A M -- Smail, I -- Longmore, S -- Harris, A I -- Baker, A J -- De Breuck, C -- Richard, J -- Edge, A C -- Ivison, R J -- Blundell, R -- Coppin, K E K -- Cox, P -- Gurwell, M -- Hainline, L J -- Krips, M -- Lundgren, A -- Neri, R -- Siana, B -- Siringo, G -- Stark, D P -- Wilner, D -- Younger, J D -- England -- Nature. 2010 Apr 1;464(7289):733-6. doi: 10.1038/nature08880. Epub 2010 Mar 21.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute for Computational Cosmology, Durham University, South Road, Durham DH1 3LE, UK. a.m.swinbank@dur.ac.uk〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20305639" target="_blank"〉PubMed〈/a〉
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 10
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    Mechanism of folding chamber closure in a group II chaperonin (2010)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2010-01-22
    Description: Group II chaperonins are essential mediators of cellular protein folding in eukaryotes and archaea. These oligomeric protein machines, approximately 1 megadalton, consist of two back-to-back rings encompassing a central cavity that accommodates polypeptide substrates. Chaperonin-mediated protein folding is critically dependent on the closure of a built-in lid, which is triggered by ATP hydrolysis. The structural rearrangements and molecular events leading to lid closure are still unknown. Here we report four single particle cryo-electron microscopy (cryo-EM) structures of Mm-cpn, an archaeal group II chaperonin, in the nucleotide-free (open) and nucleotide-induced (closed) states. The 4.3 A resolution of the closed conformation allowed building of the first ever atomic model directly from the single particle cryo-EM density map, in which we were able to visualize the nucleotide and more than 70% of the side chains. The model of the open conformation was obtained by using the deformable elastic network modelling with the 8 A resolution open-state cryo-EM density restraints. Together, the open and closed structures show how local conformational changes triggered by ATP hydrolysis lead to an alteration of intersubunit contacts within and across the rings, ultimately causing a rocking motion that closes the ring. Our analyses show that there is an intricate and unforeseen set of interactions controlling allosteric communication and inter-ring signalling, driving the conformational cycle of group II chaperonins. Beyond this, we anticipate that our methodology of combining single particle cryo-EM and computational modelling will become a powerful tool in the determination of atomic details involved in the dynamic processes of macromolecular machines in solution.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2834796/" 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/PMC2834796/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Zhang, Junjie -- Baker, Matthew L -- Schroder, Gunnar F -- Douglas, Nicholai R -- Reissmann, Stefanie -- Jakana, Joanita -- Dougherty, Matthew -- Fu, Caroline J -- Levitt, Michael -- Ludtke, Steven J -- Frydman, Judith -- Chiu, Wah -- P41 RR002250/RR/NCRR NIH HHS/ -- P41 RR002250-23/RR/NCRR NIH HHS/ -- P41 RR002250-237254/RR/NCRR NIH HHS/ -- P41 RR002250-24/RR/NCRR NIH HHS/ -- P41 RR002250-247897/RR/NCRR NIH HHS/ -- PN2 EY016525/EY/NEI NIH HHS/ -- PN2 EY016525-02S1/EY/NEI NIH HHS/ -- PN2 EY016525-03/EY/NEI NIH HHS/ -- PN2 EY016525-04/EY/NEI NIH HHS/ -- PN2 EY016525-05/EY/NEI NIH HHS/ -- R01 GM063817/GM/NIGMS NIH HHS/ -- R01 GM079429/GM/NIGMS NIH HHS/ -- R01 GM079429-03/GM/NIGMS NIH HHS/ -- R01 GM080139/GM/NIGMS NIH HHS/ -- R01 GM080139-03/GM/NIGMS NIH HHS/ -- R01 GM080139-04/GM/NIGMS NIH HHS/ -- R90 DK071504/DK/NIDDK NIH HHS/ -- R90 DK071504-03/DK/NIDDK NIH HHS/ -- T32 GM007276-30/GM/NIGMS NIH HHS/ -- T32 GM007276-31/GM/NIGMS NIH HHS/ -- England -- Nature. 2010 Jan 21;463(7279):379-83. doi: 10.1038/nature08701.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Graduate Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, Texas 77030, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20090755" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Triphosphate/chemistry/metabolism/pharmacology ; Allosteric Regulation ; Binding Sites ; Cryoelectron Microscopy ; Group II Chaperonins/*chemistry/*metabolism/ultrastructure ; Hydrolysis/drug effects ; Methanococcus/*chemistry ; Models, Molecular ; Protein Binding ; Protein Conformation/drug effects ; *Protein Folding ; Protein Subunits/chemistry/metabolism ; Structure-Activity Relationship
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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