TY - JOUR A1 - Chipman, Ariel D. A1 - Ferrier, David E. K. A1 - Brena, Carlo A1 - Qu, Jiaxin A1 - Hughes, Daniel S. T. A1 - Schroeder, Reinhard A1 - Torres-Oliva, Montserrat A1 - Znassi, Nadia A1 - Jiang, Huaiyang A1 - Almeida, Francisca C. A1 - Alonso, Claudio R. A1 - Apostolou, Zivkos A1 - Aqrawi, Peshtewani A1 - Arthur, Wallace A1 - Barna, Jennifer C. J. A1 - Blankenburg, Kerstin P. A1 - Brites, Daniela A1 - Capella-Gutierrez, Salvador A1 - Coyle, Marcus A1 - Dearden, Peter K. A1 - Du Pasquier, Louis A1 - Duncan, Elizabeth J. A1 - Ebert, Dieter A1 - Eibner, Cornelius A1 - Erikson, Galina A1 - Evans, Peter D. A1 - Extavour, Cassandra G. A1 - Francisco, Liezl A1 - Gabaldon, Toni A1 - Gillis, William J. A1 - Goodwin-Horn, Elizabeth A. A1 - Green, Jack E. A1 - Griffiths-Jones, Sam A1 - Grimmelikhuijzen, Cornelis J. P. A1 - Gubbala, Sai A1 - Guigo, Roderic A1 - Han, Yi A1 - Hauser, Frank A1 - Havlak, Paul A1 - Hayden, Luke A1 - Helbing, Sophie A1 - Holder, Michael A1 - Hui, Jerome H. L. A1 - Hunn, Julia P. A1 - Hunnekuhl, Vera S. A1 - Jackson, LaRonda A1 - Javaid, Mehwish A1 - Jhangiani, Shalini N. A1 - Jiggins, Francis M. A1 - Jones, Tamsin E. A1 - Kaiser, Tobias S. A1 - Kalra, Divya A1 - Kenny, Nathan J. A1 - Korchina, Viktoriya A1 - Kovar, Christie L. A1 - Kraus, F. Bernhard A1 - Lapraz, Francois A1 - Lee, Sandra L. A1 - Lv, Jie A1 - Mandapat, Christigale A1 - Manning, Gerard A1 - Mariotti, Marco A1 - Mata, Robert A1 - Mathew, Tittu A1 - Neumann, Tobias A1 - Newsham, Irene A1 - Ngo, Dinh N. A1 - Ninova, Maria A1 - Okwuonu, Geoffrey A1 - Ongeri, Fiona A1 - Palmer, William J. A1 - Patil, Shobha A1 - Patraquim, Pedro A1 - Pham, Christopher A1 - Pu, Ling-Ling A1 - Putman, Nicholas H. A1 - Rabouille, Catherine A1 - Ramos, Olivia Mendivil A1 - Rhodes, Adelaide C. A1 - Robertson, Helen E. A1 - Robertson, Hugh M. A1 - Ronshaugen, Matthew A1 - Rozas, Julio A1 - Saada, Nehad A1 - Sanchez-Gracia, Alejandro A1 - Scherer, Steven E. A1 - Schurko, Andrew M. A1 - Siggens, Kenneth W. A1 - Simmons, DeNard A1 - Stief, Anna A1 - Stolle, Eckart A1 - Telford, Maximilian J. A1 - Tessmar-Raible, Kristin A1 - Thornton, Rebecca A1 - van der Zee, Maurijn A1 - von Haeseler, Arndt A1 - Williams, James M. A1 - Willis, Judith H. A1 - Wu, Yuanqing A1 - Zou, Xiaoyan A1 - Lawson, Daniel A1 - Muzny, Donna M. A1 - Worley, Kim C. A1 - Gibbs, Richard A. A1 - Akam, Michael A1 - Richards, Stephen T1 - The first myriapod genome sequence reveals conservative arthropod gene content and genome organisation in the centipede Strigamia maritima JF - PLoS biology N2 - Myriapods (e. g., centipedes and millipedes) display a simple homonomous body plan relative to other arthropods. All members of the class are terrestrial, but they attained terrestriality independently of insects. Myriapoda is the only arthropod class not represented by a sequenced genome. We present an analysis of the genome of the centipede Strigamia maritima. It retains a compact genome that has undergone less gene loss and shuffling than previously sequenced arthropods, and many orthologues of genes conserved from the bilaterian ancestor that have been lost in insects. Our analysis locates many genes in conserved macro-synteny contexts, and many small-scale examples of gene clustering. We describe several examples where S. maritima shows different solutions from insects to similar problems. The insect olfactory receptor gene family is absent from S. maritima, and olfaction in air is likely effected by expansion of other receptor gene families. For some genes S. maritima has evolved paralogues to generate coding sequence diversity, where insects use alternate splicing. This is most striking for the Dscam gene, which in Drosophila generates more than 100,000 alternate splice forms, but in S. maritima is encoded by over 100 paralogues. We see an intriguing linkage between the absence of any known photosensory proteins in a blind organism and the additional absence of canonical circadian clock genes. The phylogenetic position of myriapods allows us to identify where in arthropod phylogeny several particular molecular mechanisms and traits emerged. For example, we conclude that juvenile hormone signalling evolved with the emergence of the exoskeleton in the arthropods and that RR-1 containing cuticle proteins evolved in the lineage leading to Mandibulata. We also identify when various gene expansions and losses occurred. The genome of S. maritima offers us a unique glimpse into the ancestral arthropod genome, while also displaying many adaptations to its specific life history. Y1 - 2014 U6 - https://doi.org/10.1371/journal.pbio.1002005 SN - 1545-7885 VL - 12 IS - 11 PB - PLoS CY - San Fransisco ER - TY - JOUR A1 - Green, Luci M. A1 - Kliem, Bernhard A1 - Wallace, A. J. T1 - Photospheric flux cancellation and associated flux rope formation and eruption JF - Astronomy and astrophysics : an international weekly journal N2 - Aims. We study an evolving bipolar active region that exhibits flux cancellation at the internal polarity inversion line, the formation of a soft X-ray sigmoid along the inversion line and a coronal mass ejection. The aim is to investigate the quantity of flux cancellation that is involved in flux rope formation in the time period leading up to the eruption. Methods. The active region is studied using its extreme ultraviolet and soft X-ray emissions as it evolves from a sheared arcade to flux rope configuration. The evolution of the photospheric magnetic field is described and used to estimate how much flux is reconnected into the flux rope. Results. About one third of the active region flux cancels at the internal polarity inversion line in the 2.5 days leading up to the eruption. In this period, the coronal structure evolves from a weakly to a highly sheared arcade and then to a sigmoid that crosses the inversion line in the inverse direction. These properties suggest that a flux rope has formed prior to the eruption. The amount of cancellation implies that up to 60% of the active region flux could be in the body of the flux rope. We point out that only part of the cancellation contributes to the flux in the rope if the arcade is only weakly sheared, as in the first part of the evolution. This reduces the estimated flux in the rope to similar to 30% or less of the active region flux. We suggest that the remaining discrepancy between our estimate and the limiting value of similar to 10% of the active region flux, obtained previously by the flux rope insertion method, results from the incomplete coherence of the flux rope, due to nonuniform cancellation along the polarity inversion line. A hot linear feature is observed in the active region which rises as part of the eruption and then likely traces out the field lines close to the axis of the flux rope. The flux cancellation and changing magnetic connections at one end of this feature suggest that the flux rope reaches coherence by reconnection immediately before and early in the impulsive phase of the associated flare. The sigmoid is destroyed in the eruption but reforms quickly, with the amount of cancellation involved being much smaller than in the course of its original formation. KW - Sun: activity KW - Sun: coronal mass ejections (CMEs) KW - magnetic fields KW - magnetic reconnection KW - Sun: photosphere KW - Sun: magnetic topology Y1 - 2011 U6 - https://doi.org/10.1051/0004-6361/201015146 SN - 0004-6361 VL - 526 IS - 2 PB - EDP Sciences CY - Les Ulis ER - TY - JOUR A1 - Arhammar, C. A1 - Pietzsch, Annette A1 - Bock, Nicolas A1 - Holmstroem, Erik A1 - Araujo, C. Moyses A1 - Grasjo, Johan A1 - Zhao, Shuxi A1 - Green, Sara A1 - Peery, T. A1 - Hennies, Franz A1 - Amerioun, Shahrad A1 - Föhlisch, Alexander A1 - Schlappa, Justine A1 - Schmitt, Thorsten A1 - Strocov, Vladimir N. A1 - Niklasson, Gunnar A. A1 - Wallace, Duane C. A1 - Rubensson, Jan-Erik A1 - Johansson, Borje A1 - Ahuja, Rajeev C. T1 - Unveiling the complex electronic structure of amorphous metal oxides JF - Proceedings of the National Academy of Sciences of the United States of America N2 - Amorphous materials represent a large and important emerging area of material's science. Amorphous oxides are key technological oxides in applications such as a gate dielectric in Complementary metal-oxide semiconductor devices and in Silicon-Oxide-Nitride-Oxide-Silicon and TANOS (TaN-Al2O3-Si3N4-SiO2-Silicon) flash memories. These technologies are required for the high packing density of today's integrated circuits. Therefore the investigation of defect states in these structures is crucial. In this work we present X-ray synchrotron measurements, with an energy resolution which is about 5-10 times higher than is attainable with standard spectrometers, of amorphous alumina. We demonstrate that our experimental results are in agreement with calculated spectra of amorphous alumina which we have generated by stochastic quenching. This first principles method, which we have recently developed, is found to be superior to molecular dynamics in simulating the rapid gas to solid transition that takes place as this material is deposited for thin film applications. We detect and analyze in detail states in the band gap that originate from oxygen pairs. Similar states were previously found in amorphous alumina by other spectroscopic methods and were assigned to oxygen vacancies claimed to act mutually as electron and hole traps. The oxygen pairs which we probe in this work act as hole traps only and will influence the information retention in electronic devices. In amorphous silica oxygen pairs have already been found, thus they may be a feature which is characteristic also of other amorphous metal oxides. KW - stochastic quench KW - X-ray absorption spectroscopy KW - ab initio KW - coating Y1 - 2011 U6 - https://doi.org/10.1073/pnas.1019698108 SN - 0027-8424 VL - 108 IS - 16 SP - 6355 EP - 6360 PB - National Acad. of Sciences CY - Washington ER - TY - JOUR A1 - Valori, Gherardo A1 - Green, Lucie M. A1 - Demoulin, Pascal A1 - Vargas Dominguez, S. A1 - van Driel-Gesztelyi, L. A1 - Wallace, A. A1 - Baker, Daniel N. A1 - Fuhrmann, Marcel T1 - Nonlinear force-free extrapolation of emerging flux with a global twist and serpentine fine structures JF - Solar physics : a journal for solar and solar-stellar research and the study of solar terrestrial physics N2 - We study the flux emergence process in NOAA active region 11024, between 29 June and 7 July 2009, by means of multi-wavelength observations and nonlinear force-free extrapolation. The main aim is to extend previous investigations by combining, as much as possible, high spatial resolution observations to test our present understanding of small-scale (undulatory) flux emergence, whilst putting these small-scale events in the context of the global evolution of the active region. The combination of these techniques allows us to follow the whole process, from the first appearance of the bipolar axial field on the east limb, until the buoyancy instability could set in and raise the main body of the twisted flux tube through the photosphere, forming magnetic tongues and signatures of serpentine field, until the simplification of the magnetic structure into a main bipole by the time the active region reaches the west limb. At the crucial time of the main emergence phase high spatial resolution spectropolarimetric measurements of the photospheric field are employed to reconstruct the three-dimensional structure of the nonlinear force-free coronal field, which is then used to test the current understanding of flux emergence processes. In particular, knowledge of the coronal connectivity confirms the identity of the magnetic tongues as seen in their photospheric signatures, and it exemplifies how the twisted flux, which is emerging on small scales in the form of a sea-serpent, is subsequently rearranged by reconnection into the large-scale field of the active region. In this way, the multi-wavelength observations combined with a nonlinear force-free extrapolation provide a coherent picture of the emergence process of small-scale magnetic bipoles, which subsequently reconnect to form a large-scale structure in the corona. KW - Active regions, magnetic fields KW - Magnetic field, photosphere, corona Y1 - 2012 U6 - https://doi.org/10.1007/s11207-011-9865-8 SN - 0038-0938 VL - 278 IS - 1 SP - 73 EP - 97 PB - Springer CY - Dordrecht ER -