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|  | | 29 January 2013 | | | Featured image: | |  | | | Perry et al. show that current carbonate production rates in 19 Caribbean reefs are ~50% lower than those measured over the last ~8,000 years. | | | | | | |
Advertisement | | | | | | | | Latest Articles | View all Articles | | | | | The evolution and pathogenic mechanisms of the rice sheath blight pathogen OPEN | | | Aiping Zheng, Runmao Lin, Danhua Zhang, Peigang Qin, Lizhi Xu, Peng Ai, Lei Ding, Yanran Wang, Yao Chen, Yao Liu, Zhigang Sun, Haitao Feng, Xiaoxing Liang, Rongtao Fu, Changqing Tang, Qiao Li, Jing Zhang, Zelin Xie, Qiming Deng, Shuangcheng Li, Shiquan Wang, Jun Zhu, Lingxia Wang, Huainian Liu and Ping Li | | | The rice sheath blight pathogen, Rhizoctonia solani, is an important fungal pathogen that can devastate rice and maize crops. Zheng and colleagues sequence and assemble the R. solani AG1 IA genome—the first to be sequenced from the Rhizoctonia genus—using Illumina sequencing technology. | | | 29 Jan | Nat Commun 4:1424 doi:10.1038/ncomms2427 (2013) | | | Biological sciences Bioinformatics | | | Microbiology | | Abstract | Full Text | PDF (753 kB) |
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| FBH1 co-operates with MUS81 in inducing DNA double-strand breaks and cell death following replication stress | | | Kasper Fugger, Wai Kit Chu, Peter Haahr, Arne Nedergaard Kousholt, Halfdan Beck, Miranda J. Payne, Katsuhiro Hanada, Ian D. Hickson and Claus Storgaard Sørensen | | | DNA replication stress promotes genome instability and cell death. Here Fugger et al. describe how FBH1, via its helicase activity, is required to eliminate cells with excessive DNA replication stress, through the generation of MUS81-induced DNA double-strand breaks. | | | 29 Jan | Nat Commun 4:1423 doi:10.1038/ncomms2395 (2013) | | | Biological sciences Cancer | | | Cell biology Molecular biology | | Abstract | Full Text | PDF (787 kB) |
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| The essential role of carefully optimized synthesis for elucidating intrinsic material properties of (Ga,Mn)As | | | P. Nĕmec, V. Novák, N. Tesařová, E. Rozkotová, H. Reichlová, D. Butkovičová, F. Trojánek, K. Olejník, P. Malý, R.P. Campion, B.L. Gallagher, Jairo Sinova and T. Jungwirth | | | The electronic band structure of (Ga,Mn)As has been debated due to contrasting reports of experimental findings from samples differently synthesized. Nĕmec et al. show that a careful optimization of the synthesis protocol is necessary to evaluate the intrinsic semiconducting and magnetic properties of (Ga,Mn)As. | | | 29 Jan | Nat Commun 4:1422 doi:10.1038/ncomms2426 (2013) | | | Physical sciences Condensed matter | | | Materials science | | Abstract | Full Text | PDF (531 kB) |
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| Motional averaging in a superconducting qubit | | | Jian Li, M.P. Silveri, K.S. Kumar, J.-M. Pirkkalainen, A. Vepsäläinen, W.C. Chien, J. Tuorila, M.A. Sillanpää, P.J. Hakonen, E.V. Thuneberg and G.S. Paraoanu | | | One of the advantages that it is hoped quantum computers will have over classical computers is their ability to accurately simulate quantum phenomena. Silveri et al. take a step towards this goal by simulating so-called motional averaging in an artificial atom realized by a superconducting quantum bit. | | | 29 Jan | Nat Commun 4:1420 doi:10.1038/ncomms2383 (2013) | | | Physical sciences Atomic and molecular physics | | | Condensed matter | | Abstract | Full Text | PDF (861 kB) |
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| Composite-pulse magnetometry with a solid-state quantum sensor | | | Clarice D. Aiello, Masashi Hirose and Paola Cappellaro | | | Quantum magnetometry in the solid state is usually affected by short coherence times and control errors that limit the sensitivity. This work demonstrates a continuous-driving scheme based on composite pulses that improves both these shortcomings and can be used in variable sensing environments. | | | 29 Jan | Nat Commun 4:1419 doi:10.1038/ncomms2375 (2013) | | | Physical sciences Applied physics | | | Nanotechnology | | Abstract | Full Text | PDF (412 kB) |
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| Interferon-induced transmembrane protein-3 genetic variant rs12252-C is associated with severe influenza in Chinese individuals OPEN | | | Yong-Hong Zhang, Yan Zhao, Ning Li, Yan-Chun Peng, Eleni Giannoulatou, Rong-Hua Jin, Hui-Ping Yan, Hao Wu, Jin-Hua Liu, Ning Liu, Da-Yan Wang, Yue-Long Shu, Ling-Pei Ho, Paul Kellam, Andrew McMichael and Tao Dong | | | A variant in the IFITM3 gene increases the risk of severe influenza, but homozygosity is rare in Caucasians. The authors show that the variant gene is homozygous in 25% of healthy Chinese people, and 69% of those with severe pandemic influenza, suggesting that this gene influences the epidemiology of influenza in South-East Asia. | | | 29 Jan | Nat Commun 4:1418 doi:10.1038/ncomms2433 (2013) | | | Biological sciences Genetics | | | Immunology Virology | | | Abstract | Full Text | PDF (450 kB) |
| Plant tumour biocontrol agent employs a tRNA-dependent mechanism to inhibit leucyl-tRNA synthetase | | | Shaileja Chopra, Andrés Palencia, Cornelia Virus, Ashutosh Tripathy, Brenda R. Temple, Adrian Velazquez-Campoy, Stephen Cusack and John S. Reader | | | Agrobacterium radiobacter strain K84 generates an antibiotic targeting pathogenic strains of Agrobacterium tumefaciens, enabling its use as a biocontrol to prevent infection of crops. Here the authors show that this antibiotic inhibits leucyl-tRNA synthetases via an unusual mechanism that depends on binding of tRNALeu. | | | 29 Jan | Nat Commun 4:1417 doi:10.1038/ncomms2421 (2013) | | | Biological sciences Biochemistry Microbiology | | | | Abstract | Full Text | PDF (1,258 kB) |
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| Constraining timescales of focused magmatic accretion and extension in the Afar crust using lava geochronology | | | David J. Ferguson, Andrew T. Calvert, David M. Pyle, Jon D. Blundy, Gezahegn Yirgu and Tim J. Wright | | | In mature continental rifts, magma intrusion appears to accommodate significant crustal extension. Here, radiometric ages for lavas suggest that this style of focused magmatic accretion and rifting remained stable in the Ethiopian crust for at least ~200 kyr, prior to the onset of true oceanic spreading. | | | 29 Jan | Nat Commun 4:1416 doi:10.1038/ncomms2410 (2013) | | | Earth sciences Geology and geophysics | | | | Abstract | Full Text | PDF (1,065 kB) |
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| Spatial association with PTEX complexes defines regions for effector export into Plasmodium falciparum-infected erythrocytes OPEN | | | David T. Riglar, Kelly L. Rogers, Eric Hanssen, Lynne Turnbull, Hayley E. Bullen, Sarah C. Charnaud, Jude Przyborski, Paul R. Gilson, Cynthia B. Whitchurch, Brendan S. Crabb, Jake Baum and Alan F. Cowman | | | During red blood cell infection, malaria parasites export hundreds of proteins that remodel the host cell surface. Cowman and colleagues identify a putative protein translocator complex spatially associated with exported proteins, revealing the cellular domains involved in protein export. | | | 29 Jan | Nat Commun 4:1415 doi:10.1038/ncomms2449 (2013) | | | Biological sciences Cell biology | | | Microbiology | | Abstract | Full Text | PDF (5,516 kB) |
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| A platform pathway for production of 3-hydroxyacids provides a biosynthetic route to 3-hydroxy-γ-butyrolactone | | | Collin H. Martin, Himanshu Dhamankar, Hsien-Chung Tseng, Micah J. Sheppard, Christopher R. Reisch and Kristala L.J. Prather | | | 3-hydroxy-γ-butyrolactone (3HBL) is a building block for many valuable drugs and is synthesized via a costly industrial process. Martin et al. engineer a novel biosynthetic pathway for the inexpensive production of 3HBL and other 3-hydroxyacids in E. coli. | | | 29 Jan | Nat Commun 4:1414 doi:10.1038/ncomms2418 (2013) | | | Biological sciences Biotechnology | | | Microbiology | | Abstract | Full Text | PDF (417 kB) |
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| Synthetic RNA devices to expedite the evolution of metabolite-producing microbes | | | Jina Yang, Sang Woo Seo, Sungho Jang, So-I Shin, Chae Hyun Lim, Tae-Young Roh and Gyoo Yeol Jung | | | Genome-wide variation in the directed evolution of metabolite-overproducing microbes requires high-throughput screening platforms. Yang et al. show that synthetic RNA devices can sense target metabolites, enrich pathway optimisation, and expedite the evolution of metabolite-producing microbes. | | | 29 Jan | Nat Commun 4:1413 doi:10.1038/ncomms2404 (2013) | | | Biological sciences Biotechnology | | | Chemical biology | | Abstract | Full Text | PDF (336 kB) |
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| Interplay between myosin IIA-mediated contractility and actin network integrity orchestrates podosome composition and oscillations OPEN | | | K. van den Dries, M.B.M Meddens, S. de Keijzer, S. Shekhar, V. Subramaniam, C.G. Figdor and A. Cambi | | | Dendritic cells use protrusive structures called podosomes to probe the extracellular environment. Here the authors reveal how interplay between actin-mediated core growth and myosin-mediated tension regulates podosome protrusion. | | | 29 Jan | Nat Commun 4:1412 doi:10.1038/ncomms2402 (2013) | | | Biological sciences Biophysics | | | Cell biology | | Abstract | Full Text | PDF (3,815 kB) |
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| Climate change patterns in Amazonia and biodiversity | | | Hai Cheng, Ashish Sinha, Francisco W. Cruz, Xianfeng Wang, R. Lawrence Edwards, Fernando M. d'Horta, Camila C. Ribas, Mathias Vuille, Lowell D. Stott and Augusto S. Auler | | | The long-term hydroclimate variability in Amazonia and its influence on biodiversity remain poorly understood. Here, new speleothem oxygen isotope records characterize spatial–temporal changes in precipitation and provide new insights to understanding the west–east contrasting pattern of biodiversity in Amazonia. | | | 29 Jan | Nat Commun 4:1411 doi:10.1038/ncomms2415 (2013) | | | Earth sciences Atmospheric science | | | Climate science | | Abstract | Full Text | PDF (722 kB) |
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| Selective escape of proteins from the mitochondria during mitophagy | | | Shotaro Saita, Michiko Shirane and Keiichi I. Nakayama | | | Damaged mitochondria are eliminated from the cell by a form of autophagy called mitophagy. Here the authors show that during mitophagy, specific proteins are rescued from degradation by evacuation from the mitochondria to the endoplasmic reticulum. | | | 29 Jan | Nat Commun 4:1410 doi:10.1038/ncomms2400 (2013) | | | Biological sciences Cell biology | | Abstract | Full Text | PDF (7,772 kB) |
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| Modular optimization of multi-gene pathways for fatty acids production in E. coli | | | Peng Xu, Qin Gu, Wenya Wang, Lynn Wong, Adam G.W. Bower, Cynthia H. Collins and Mattheos A.G. Koffas | | | Microbial fatty acid-derived fuels represent promising alternatives to the traditionally used fossil fuels. Koffas and colleagues report that E. coli central metabolism can be modified to produce large quantities of fatty acids through a modular pathway engineering strategy. | | | 29 Jan | Nat Commun 4:1409 doi:10.1038/ncomms2425 (2013) | | | Biological sciences Bioengineering | | | Biotechnology Microbiology | | Abstract | Full Text | PDF (1,342 kB) |
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| Deep proteome profiling of Trichoplax adhaerens reveals remarkable features at the origin of metazoan multicellularity | | | Jeffrey H. Ringrose, Henk W.P. van den Toorn, Michael Eitel, Harm Post, Pieter Neerincx, Bernd Schierwater, A.F. Maarten Altelaar and Albert J.R. Heck | | | Trichoplax is the most primitive multicellular animal on Earth and thus provides insight into the earliest stages of evolution. Delving deep into the proteome, Heck and colleagues observe a burst in tyrosine phosphorylation, confirming the hypothesis that at the onset of this new communication system a surplus of phosphorylation took place. | | | 29 Jan | Nat Commun 4:1408 doi:10.1038/ncomms2424 (2013) | | | Biological sciences Evolution | | Abstract | Full Text | PDF (463 kB) |
Supplementary Information |
| Computational identification of a transiently open L1/S3 pocket for reactivation of mutant p53 OPEN | | | Christopher D. Wassman, Roberta Baronio, Özlem Demir, Brad D. Wallentine, Chiung-Kuang Chen, Linda V. Hall, Faezeh Salehi, Da-Wei Lin, Benjamin P. Chung, G. Wesley Hatfield, A. Richard Chamberlin, Hartmut Luecke, Richard H. Lathrop, Peter Kaiser and Rommie E. Amaro | | | About 40% of human cancers carry missense mutations in the tumour suppressor protein p53. Here the authors identify a transiently open pocket in the protein, and by targeting a small molecule to it, partially restore mutant p53 tumour suppressor activity. | | | 29 Jan | Nat Commun 4:1407 doi:10.1038/ncomms2361 (2013) | | | Biological sciences Cancer | | | | Abstract | Full Text | PDF (1,937 kB) |
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| A point mutation in Semaphorin 4A associates with defective endosomal sorting and causes retinal degeneration OPEN | | | Satoshi Nojima, Toshihiko Toyofuku, Hiroyuki Kamao, Chie Ishigami, Jun Kaneko, Tatsusada Okuno, Hyota Takamatsu, Daisuke Ito, Sujin Kang, Tetsuya Kimura, Yuji Yoshida, Keiko Morimoto, Yohei Maeda, Atsushi Ogata, Masahito Ikawa, Eiichi Morii, Katsuyuki Aozasa, Junichi Takagi, Masayo Takahashi and Atsushi Kumanogoh | | | Semaphorin 4A is implicated in photoreceptor survival. Nojima and colleagues generate transgenic mice with different mutations in the Sema4A gene and find that point mutation of F350 causes severe degeneration in photoreceptor cells, which can be rescued by virus-mediated gene therapy. | | | 29 Jan | Nat Commun 4:1406 doi:10.1038/ncomms2420 (2013) | | | Biological sciences Cell biology | | | Neuroscience | | Abstract | Full Text | PDF (3,075 kB) |
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| Heat shock factor-1 influences pathological lesion distribution of polyglutamine-induced neurodegeneration | | | Naohide Kondo, Masahisa Katsuno, Hiroaki Adachi, Makoto Minamiyama, Hideki Doi, Shinjiro Matsumoto, Yu Miyazaki, Madoka Iida, Genki Tohnai, Hideaki Nakatsuji, Shinsuke Ishigaki, Yusuke Fujioka, Hirohisa Watanabe, Fumiaki Tanaka, Akira Nakai and Gen Sobue | | | Heat shock factor-1 is a transcriptional regulator of heat shock proteins that is implicated in neurodegeneration. Kondo and colleagues study the effects of deleting heat shock factor-1 in a mouse model of muscular dystrophy and find that this augments the condition via the accumulation of androgen receptors. | | | 29 Jan | Nat Commun 4:1405 doi:10.1038/ncomms2417 (2013) | | | Biological sciences Medical research | | | Neuroscience | | Abstract | Full Text | PDF (4,548 kB) |
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| The Tissint Martian meteorite as evidence for the largest impact excavation | | | Ioannis P. Baziotis, Yang Liu, Paul S. DeCarli, H. Jay Melosh, Harry Y. McSween, Robert J. Bodnar and Lawrence A. Taylor | | | High-pressure minerals in meteorites reflect the conditions prevailing when they were excavated and launched from their parent bodies. Tissint—a recent Martian meteorite—contains an unusual number of large high-pressure minerals, suggesting excavation from an impact of larger magnitude than for previous Martian samples. | | | 29 Jan | Nat Commun 4:1404 doi:10.1038/ncomms2414 (2013) | | | Earth sciences Planetary sciences | | Abstract | Full Text | PDF (3,526 kB) |
Supplementary Information |
| Src activation by β-adrenoreceptors is a key switch for tumour metastasis | | | Guillermo N. Armaiz-Pena, Julie K. Allen, Anthony Cruz, Rebecca L. Stone, Alpa M. Nick, Yvonne G. Lin, Liz Y. Han, Lingegowda S. Mangala, Gabriel J. Villares, Pablo Vivas-Mejia, Cristian Rodriguez-Aguayo, Archana S. Nagaraja, Kshipra M. Gharpure, Zheng Wu, Robert D. English, Kizhake V. Soman, Mian M. K. Shazhad, Maya Zigler, Michael T. Deavers, Alexander Zien, Theodoros G. Soldatos, David B. Jackson, John E. Wiktorowicz, Madeline Torres-Lugo, Tom Young, Koen De Geest, Gary E. Gallick, Menashe Bar-Eli, Gabriel Lopez-Berestein, Steve W. Cole, Gustavo E. Lopez, Susan K. Lutgendorf and Anil K. Sood | | | The neurotransmitter noradrenaline can regulate cellular processes that contribute to cancer progression, but the underlying mechanisms remain largely unknown. Here the authors identify Src as a key mediator of noradrenaline signalling networks in tumour metastasis. | | | 29 Jan | Nat Commun 4:1403 doi:10.1038/ncomms2413 (2013) | | | Biological sciences Cancer | | | Cell biology | | Abstract | Full Text | PDF (2,522 kB) |
Supplementary Information |
| Caribbean-wide decline in carbonate production threatens coral reef growth | | | Chris T. Perry, Gary N. Murphy, Paul S. Kench, Scott G. Smithers, Evan N. Edinger, Robert S. Steneck and Peter J. Mumby | | | Coral reef health is declining globally and is projected to lead to net loss of reef structure. This study shows that ecological change across the Caribbean has reduced reef growth rates to levels lower than those measured over the last ~8,000 years, threatening the ability of reefs to keep pace with future sea-level rise. | | | 29 Jan | Nat Commun 4:1402 doi:10.1038/ncomms2409 (2013) | | | Earth sciences Ecology | | | Oceanography | | Abstract | Full Text | PDF (606 kB) |
Supplementary Information |
| Ultrafast universal quantum control of a quantum-dot charge qubit using Landau–Zener–Stückelberg interference OPEN | | | Gang Cao, Hai-Ou Li, Tao Tu, Li Wang, Cheng Zhou, Ming Xiao, Guang-Can Guo, Hong-Wen Jiang and Guo-Ping Guo | | | Universal control of the state of qubits on timescales much shorter than the coherence time is necessary for quantum computation. The authors demonstrate electrical control of a charge qubit in quantum dots on the picosecond scale, which is orders of magnitude faster than previously reported. | | | 29 Jan | Nat Commun 4:1401 doi:10.1038/ncomms2412 (2013) | | | Physical sciences Applied physics | | | Condensed matter Nanotechnology | | Abstract | Full Text | PDF (1,148 kB) |
Supplementary Information |
| Photon-mediated interaction between distant quantum dot circuits | | | M.R. Delbecq, L.E. Bruhat, J.J. Viennot, S. Datta, A. Cottet and T. Kontos | | | Controlling the interaction between distant quantum dots is important if they are to be used in quantum information devices. Delbecq et al. place two quantum dot circuits in a microwave cavity and show that they interact via cavity photons, even though they are separated by 200 times their own size. | | | 29 Jan | Nat Commun 4:1400 doi:10.1038/ncomms2407 (2013) | | | Physical sciences Nanotechnology Optical physics | | | Abstract | Full Text | PDF (1,438 kB) |
| In vitro fabrication of functional three-dimensional tissues with perfusable blood vessels | | | Hidekazu Sekine, Tatsuya Shimizu, Katsuhisa Sakaguchi, Izumi Dobashi, Masanori Wada, Masayuki Yamato, Eiji Kobayashi, Mitsuo Umezu and Teruo Okano | | | Artificially engineered tissues may have many therapeutic applications but complex tissues are hard to create in vitro. Here, Okano and colleagues report the production of functional cardiac tissue sheets with perfusable blood vessels, which increase the thickness and survival of transplanted tissue. | | | 29 Jan | Nat Commun 4:1399 doi:10.1038/ncomms2406 (2013) | | | Biological sciences Biotechnology | | | Medical research | | Abstract | Full Text | PDF (4,112 kB) |
Supplementary Information |
| The phosphatase Dullard negatively regulates BMP signalling and is essential for nephron maintenance after birth | | | Masaji Sakaguchi, Sazia Sharmin, Atsuhiro Taguchi, Tomoko Ohmori, Sayoko Fujimura, Takaya Abe, Hiroshi Kiyonari, Yoshihiro Komatsu, Yuji Mishina, Makoto Asashima, Eiichi Araki and Ryuichi Nishinakamura | | | Kidney maintenance and function are essential for a healthy organism. Here Nishinakamura and colleagues show that the phosphatase Dullard suppresses BMP signalling and apoptosis in the mouse kidney and that Dullard is required for the maintenance of functional nephrons after birth. | | | 29 Jan | Nat Commun 4:1398 doi:10.1038/ncomms2408 (2013) | | | Biological sciences Cell biology | | | Developmental biology | | Abstract | Full Text | PDF (3,867 kB) |
Supplementary Information |
| Human CLPP reverts the longevity phenotype of a fungal ClpP deletion strain OPEN | | | Fabian Fischer, Andrea Weil, Andrea Hamann and Heinz D. Osiewacz | | | The mitochondrial protease CLPP is found in most eukaryotic organisms but its biological role has been unclear. Here Osiewacz and colleagues show that deletion of CLPP extends lifespan of the filamentous fungus Podospora anserina, and that human and fungal CLPP are functionally conserved. | | | 29 Jan | Nat Commun 4:1397 doi:10.1038/ncomms2397 (2013) | | | Biological sciences Cell biology | | | Genetics | | Abstract | Full Text | PDF (370 kB) |
Supplementary Information |
| The impact of free-ranging domestic cats on wildlife of the United States | | | Scott R. Loss, Tom Will and Peter P. Marra | | | Free-ranging domestic cats cause wildlife extinctions on islands, but their impact on wildlife in mainland areas is unclear. This study presents an estimate of mortality caused by cats in the United States, suggesting that 1.4–3.7 billion birds and 6.9–20.7 billion mammals are killed annually. | | | 29 Jan | Nat Commun 4:1396 doi:10.1038/ncomms2380 (2013) | | | Biological sciences Ecology | | | Zoology | | Abstract | Full Text | PDF (297 kB) |
Supplementary Information |
| Quantitative experimental determination of site-specific magnetic structures by transmitted electrons | | | Z.Q. Wang, X.Y. Zhong, R. Yu, Z.Y. Cheng and J. Zhu | | | Understanding magnetic materials at the nanoscale is important for the development of novel applications, but has been hampered by a lack of suitable experimental techniques. Here, the use of transmitted electrons permits the determination of atomic site-specific magnetic information. | | | 29 Jan | Nat Commun 4:1395 doi:10.1038/ncomms2323 (2013) | | | Physical sciences Materials science | | Abstract | Full Text | PDF (778 kB) |
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